10-Q/A

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, DC 20549

____________________________

FORM 10-Q/A

(Amendment No. 1)

____________________________

(Mark One)

x QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the quarterly period ended September 30, 2024

OR

o TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the transition period from                   to                  

Commission File Number: 001-37722

____________________________

SPYRE THERAPEUTICS, INC.

(Exact Name of Registrant as Specified in its Charter)

____________________________

Delaware	46-4312787
(State or other jurisdiction of incorporation or organization)	(I.R.S. Employer Identification No.)
221 Crescent Street Building 23, Suite 105 Waltham, MA 02453
(Address of principal executive offices including zip code)

Registrant’s telephone number, including area code: (617) 651-5940

Former name, former address and former fiscal year, if changed since last report: N/A

____________________________

Securities registered pursuant to Section 12(b) of the Exchange Act:

Title of each class	Trading Symbol(s)	Name of each exchange on which registered
Common Stock, $0.0001 Par Value Per Share	SYRE	The Nasdaq Stock Market LLC (Nasdaq Global Select Market)

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes x No o

Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§ 232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files). Yes x No o

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, smaller reporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company,” and “emerging growth company” in Rule 12b-2 of the Exchange Act.

Large accelerated filer	o	Accelerated filer	o
Non-accelerated filer	x	Smaller reporting company	x
		Emerging growth company	o

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. o

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yes o No x

As of November 1, 2024, the registrant had 51,431,220 shares of common stock, $0.0001 par value per share, outstanding.

EXPLANATORY NOTE

This Amendment No. 1 on Form 10-Q/A (this “Amendment”) amends the Quarterly Report on Form 10-Q of Spyre Therapeutics, Inc. (the “Company”) for the period ended September 30, 2024, as filed with the Securities and Exchange Commission on November 7, 2024 (the “Original Filing”).

Subsequent to the filing of its Form 10-Q for the three and nine months ended September 30, 2024, the Company became aware of a misapplication of Generally Accepted Accounting Principles in the United States ("U.S. GAAP") as it relates to the Company's exclusion of its Series A non-voting convertible preferred stock and Series B non-voting convertible preferred stock in the calculation of basic and diluted net loss per share and a finding of a material weakness in internal control over financial reporting solely related to such matter. This Amendment is being filed for the sole purpose of amending certain disclosures from the Original Filing related to the aforementioned misapplication of U.S. GAAP and related finding of material weakness in internal control over financial reporting.

Specifically, this Amendment amends: (i) Part I, Item 1. “Financial Information (unaudited)” to update the Company's Consolidated Statement of Operations and related footnote disclosures for the three and nine months ended September 30, 2024, (ii) Part I, Item 4. "Controls and Procedures" to address management's re-evaluation of disclosure controls and procedures as of September 30, 2024 and to reflect the identification of a material weakness in our internal control over financial reporting and (iii) Part II, Item 6. "Exhibits" to include, in accordance with Rule 12b-15 under the Securities Exchange Act of 1934, as amended (the “Exchange Act”), updated certifications from our Chief Executive Officer and Chief Financial Officer as required by Sections 302 and 906 of the Sarbanes-Oxley Act of 2002 as Exhibits 31.1, 31.2 and 32.1. In accordance with Rule 12b-15 under the Exchange Act, this Amendment amends and restates in their entirety each item identified in the paragraph above.

Other than as described above, this Amendment does not amend, update or change any other items or disclosures contained in the Original Filing, and accordingly, all other information contained in this Amendment is as of the date of the original filing and does not reflect subsequent information or events beyond the original filing date, November 7, 2024. Accordingly, this Amendment should be read in conjunction with other filings made with the SEC subsequent to the filing of the Original Filing, including any amendments to those filings. Capitalized terms used but not defined herein shall have the meanings ascribed to such terms in the Original Filing.

SPYRE THERAPEUTICS, INC.

QUARTERLY REPORT ON FORM 10-Q

FOR THE QUARTER ENDED SEPTEMBER 30, 2024

TABLE OF CONTENTS

		Page No.
PART I. FINANCIAL INFORMATION		1
Item 1.	Financial Statements (Unaudited)	1
	Condensed Consolidated Balance Sheets as of September 30, 2024 and December 31, 2023	1
	Condensed Consolidated Statements of Operations for the Three and Nine Months Ended September 30, 2024 and 2023	2
	Condensed Consolidated Statements of Comprehensive Loss for the Three and Nine Months Ended September 30, 2024 and 2023	3
	Condensed Consolidated Statements of Changes in Convertible Preferred Stock and Stockholders’ Equity for the Three and Nine Months Ended September 30, 2024 and 2023	4
	Condensed Consolidated Statements of Cash Flows for the Nine Months Ended September 30, 2024 and 2023	7
	Notes to Unaudited Condensed Consolidated Financial Statements	8
Item 4.	Controls and Procedures	28
PART II. OTHER INFORMATION		30
Item 6.	Exhibits	30
	Signatures	31

PART I. – Financial Information

Item 1. Financial Statements (Unaudited).

Spyre Therapeutics, Inc.

Condensed Consolidated Balance Sheets

(Unaudited, in thousands, except share and per share amounts)

	September 30, 2024		December 31, 2023
ASSETS
CURRENT ASSETS
Cash and cash equivalents	$	71,580	$	188,893
Marketable securities	342,647		150,384
Prepaid expenses and other current assets	6,852		2,251
Total current assets	421,079		341,528
Restricted cash	—		322
Other non-current assets	10		9
TOTAL ASSETS	$	421,089	$	341,859
LIABILITIES AND STOCKHOLDERS’ EQUITY
CURRENT LIABILITIES
Accounts payable	$	5,165	$	896
CVR liability	24,740		1,390
Accrued and other current liabilities	13,153		13,108
Related party accounts payable and other current liabilities	14,481		16,584
Total current liabilities	57,539		31,978
Non-current CVR liability	36,160		41,310
TOTAL LIABILITIES	93,699		73,288
Commitments and Contingencies (Note 7 and 8)
Series B non-voting convertible preferred stock, $0.0001 par value; 150,000 shares authorized, issued, and outstanding as of December 31, 2023.	—		84,555
STOCKHOLDERS’ EQUITY
Series A non-voting convertible preferred stock, $0.0001 par value; 1,086,341 shares authorized as of September 30, 2024 and December 31, 2023; 346,045 and 437,037 shares issued and outstanding as of September 30, 2024 and December 31, 2023, respectively.	146,425		184,927
Series B non-voting convertible preferred stock, $0.0001 par value; 271,625 shares authorized and 16,667 shares issued and outstanding as of September 30, 2024.	9,395		—
Preferred stock, $0.0001 par value; 8,642,034 shares and 8,763,659 shares authorized as of September 30, 2024 and December 31, 2023, respectively; no shares issued and outstanding as of September 30, 2024 and December 31, 2023.	—		—
Common stock, $0.0001 par value; 400,000,000 shares authorized as of September 30, 2024 and December 31, 2023; 51,395,608 shares and 36,057,109 shares issued and outstanding as of September 30, 2024 and December 31, 2023, respectively.	12		10
Additional paid-in capital	1,086,237		763,191
Accumulated other comprehensive income	1,457		302
Accumulated deficit	(916,136)		(764,414)
TOTAL STOCKHOLDERS’ EQUITY	327,390		184,016
TOTAL LIABILITIES, CONVERTIBLE PREFERRED STOCK AND STOCKHOLDERS’ EQUITY	$	421,089	$	341,859

The accompanying notes are an integral part of these condensed consolidated financial statements.

1

Spyre Therapeutics, Inc.

Condensed Consolidated Statements of Operations

(Unaudited, in thousands, except share and per share amounts)

	Three Months Ended September 30,				Nine Months Ended September 30,
	2024		2023		2024		2023
Revenue:
Development fee and royalty	$	—	$	—	$	—	$	886
Total revenue	—		—		—		886
Operating expenses:
Research and development (1)	44,744		24,660		112,308		55,822
General and administrative	10,648		8,584		35,005		25,874
Acquired in-process research and development	—		(298)		—		130,188
Gain on sale of in-process research and development asset	—		(14,609)		—		(14,609)
Total operating expenses	55,392		18,337		147,313		197,275
Loss from operations	(55,392)		(18,337)		(147,313)		(196,389)
Other (expense) income:
Interest income	5,184		1,251		15,536		2,021
Change in fair value of forward contract liability	—		(25,360)		—		(83,530)
Other (expense) income, net	(18,802)		2,342		(19,895)		2,262
Total other (expense) income	(13,618)		(21,767)		(4,359)		(79,247)
Loss before income tax expense	(69,010)		(40,104)		(151,672)		(275,636)
Income tax (expense) benefit	(18)		(3)		(50)		26
Net loss	$	(69,028)	$	(40,107)	$	(151,722)	$	(275,610)
Net loss per share, basic and diluted, Series A Preferred Stock (restated)	$	(42.22)	$	(34.28)	$	(95.68)	$	(586.00)
Weighted-average Series A non-voting convertible preferred stock outstanding, basic and diluted (restated)	346,045		1,062,542		383,903		371,286
Net loss per share, basic and diluted, Series B Preferred Stock (restated)	$	(42.24)	$	—	$	(95.68)	$	—
Weighted-average Series B non-voting convertible preferred stock outstanding, basic and diluted (restated)	16,667		—		95,158		—
Net loss per share, basic and diluted, common (restated)	$	(1.06)	$	(0.86)	$	(2.39)	$	(14.65)
Weighted-average common shares outstanding, basic and diluted	50,889,433		4,293,812		44,263,746		3,961,546

(1)Includes $7.7 million and $34.2 million in related party expenses for the three and nine months ended September 30, 2024, respectively, and $19.4 million and $20.8 million related party expenses for the three and nine months ended September 30, 2023, respectively.

The accompanying notes are an integral part of these condensed consolidated financial statements.

2

Spyre Therapeutics, Inc.

Condensed Consolidated Statements of Comprehensive Loss

(Unaudited, in thousands)

	Three Months Ended September 30,				Nine Months Ended September 30,
	2024		2023		2024		2023
Net loss	$	(69,028)	$	(40,107)	$	(151,722)	$	(275,610)
Other comprehensive (loss) income:
Foreign currency translation adjustment	17		(29)		37		(1)
Unrealized gain (loss) on marketable securities	1,993		(114)		1,118		(83)
Total comprehensive loss	$	(67,018)	$	(40,250)	$	(150,567)	$	(275,694)

The accompanying notes are an integral part of these condensed consolidated financial statements.

3

Spyre Therapeutics, Inc.

Condensed Consolidated Statements of Changes in

Convertible Preferred Stock and Stockholders’ Equity

(Unaudited, in thousands)

	Three and Nine Months Ended September 30, 2024
	Series B Non-Voting Convertible Preferred Stock			Series A Non-Voting Convertible Preferred Stock			Series B Non-Voting Convertible Preferred Stock			Common Stock			Additional Paid-In Capital		Accumulated Other Comprehensive Income (Loss)		Accumulated Deficit		Total Stockholders' Equity
	Shares	Amount		Shares	Amount		Shares	Amount		Shares	Amount
Balances - December 31, 2023	150	$	84,555	437	$	184,927	—	$	—	36,057	$	10	$	763,191	$	302	$	(764,414)	$	184,016
Issuance of Series B non-voting convertible preferred stock in connection with private placement, net of financing costs	122	168,850		—	—		—	—		—	—		—		—		—		—
Issuance of common stock in connection with exercise of stock options and employee stock purchase plan	—	—		—	—		—	—		572	—		4,390		—		—		4,390
Stock-based compensation expense	—	—		—	—		—	—		—	—		8,385		—		—		8,385
Foreign currency translation adjustment	—	—		—	—		—	—		—	—		—		16		—		16
Unrealized loss on marketable securities	—	—		—	—		—	—		—	—		—		(681)		—		(681)
Net loss	—	—		—	—		—	—		—	—		—		—		(43,857)		(43,857)
Balances - March 31, 2024	272	$	253,405	437	$	184,927	—	—		36,629	$	10	$	775,966	$	(363)	$	(808,271)	$	152,269
Stockholder approval of the issuance of Common Stock upon conversion of Series B convertible non-voting preferred stock	(272)	(253,405)					272	253,405		—	—		—		—		—		253,405
Exchange of Series A non-voting convertible preferred stock for common stock	—	—		(91)	(38,502)		—	—		3,640	1		38,501		—		—		—
Conversion of Series B non-voting convertible preferred stock into common stock	—	—					(255)	(244,010)		10,198	1		244,009		—		—		—
Issuance of common stock in connection with exercise of pre-funded warrants	—	—		—	—		—	—		250	—		1		—		—		1
Issuance of common stock in connection with exercise of stock options and employee stock purchase plan	—	—		—	—		—	—		66	—		494		—		—		494
Stock-based compensation expense	—	—		—	—		—	—		—	—		7,243		—		—		7,243
Foreign currency translation adjustment	—	—		—	—		—	—		—	—		—		4		—		4
Unrealized loss on marketable securities	—	—		—	—		—	—		—	—		—		(194)		—		(194)
Net loss	—	—		—	—		—	—		—	—		—		—		(38,837)		(38,837)
Balances - June 30, 2024	—	—		346	$	146,425	17	$	9,395	50,783	$	12	$	1,066,214	$	(553)	$	(847,108)	$	374,385

4

Issuance of common stock in connection with at-the-market offerings, net of offering costs	—	—	—	—		—	—		426	—		11,750		—		—		11,750
Vesting of restricted stock units	—	—	—	—		—	—		34	—		—		—		—		—
Issuance of common stock in connection with exercise of stock options and employee stock purchase plan	—	—	—	—		—	—		153	—		1,318		—		—		1,318
Stock-based compensation expense	—	—	—	—		—	—		—	—		6,955		—		—		6,955
Foreign currency translation adjustment	—	—	—	—		—	—		—	—		—		17		—		17
Unrealized gain on marketable securities	—	—	—	—		—	—		—	—		—		1,993		—		1,993
Net loss	—	—	—	—		—	—		—	—		—		—		(69,028)		(69,028)
Balances - September 30, 2024	—	—	346	$	146,425	17	$	9,395	51,396	$	12	$	1,086,237	$	1,457	$	(916,136)	$	327,390

5

	Three and Nine Months Ended September 30, 2023
	Series A Non-Voting Convertible Preferred Stock			Common Stock			Additional Paid-In Capital		Accumulated Other Comprehensive Income (Loss)		Accumulated Deficit		Total Stockholders' Equity
	Shares	Amount		Shares	Amount
Balances - December 31, 2022	—	$	—	2,614	$	6	$	475,971	$	(48)	$	(425,624)	$	50,305
Issuance of common stock in connection with employee stock purchase plan	—	—		2	—		18		—		—		18
Stock-based compensation expense	—	—		—	—		1,709		—		—		1,709
Foreign currency translation adjustment	—	—		—	—		—		10		—		10
Unrealized gain on marketable securities	—	—		—	—		—		32		—		32
Net loss	—	—		—	—		—		—		(18,422)		(18,422)
Balances - March 31, 2023	—	$	—	2,616	$	6	$	477,698	$	(6)	$	(444,046)	$	33,652
Issuance of Series A non-voting convertible preferred stock in connection with private placement, net of financing costs	721	197,323		—	—		—		—		—		—
Issuance of common stock forward in connection with the asset acquisition of Spyre	—	—		—	—		3,768		—		—		3,768
Issuance of common stock in connection with exercise of pre-funded warrants	—	—		624	—		—		—		—		—
CVR distribution to common stockholders	—	—		—	—		(29,500)		—		—		(29,500)
Stock-based compensation expense	—	—		—	—		1,775		—		—		1,775
Foreign currency translation adjustment	—	—		—	—		—		18		—		18
Unrealized loss on marketable securities	—	—		—	—		—		(1)		—		(1)
Net loss				—	—		—		—		(217,081)		(217,081)
Balances - June 30, 2023	721	$	197,323	3,240	$	6	$	453,741	$	11	$	(661,127)	$	(207,369)
Issuance of Series A non-voting convertible preferred stock in connection with the asset acquisition of Spyre and settlement of related forward contract	365	189,741		—	—		—		—		—		—
Settlement of financing costs in connection with private placement of Series A non-voting convertible preferred stock	—	41		—	—		—		—		—		—
Issuance of common stock in connection with the asset acquisition of Spyre and settlement of related forward contract	—	—		518	1		(1)		—		—		—
Issuance of common stock in connection with exercise of pre-funded warrants	—	—		281	—		—		—		—		—
Issuance of common stock in connection with exercise of stock options and employee stock purchase plan	—			10	—		105		—		—		105
CVR distribution to common stockholders	—	—		—	—		—		—		—		—
Stock-based compensation expense	—	—		—	—		2,112		—		—		2,112
Foreign currency translation adjustment	—	—		—	—		—		(29)		—		(29)
Unrealized loss on marketable securities	—	—		—	—		—		(114)		—		(114)
Net loss	—	—		—	—		—		—		(40,107)		(40,107)
Balances - September 30, 2023	1,086	$	387,105	4,049	$	7	$	455,957	$	(132)	$	(701,234)	$	(245,402)

The accompanying notes are an integral part of these condensed consolidated financial statements.

6

Spyre Therapeutics, Inc.

Condensed Consolidated Statements of Cash Flows

(Unaudited, in thousands)

	Nine Months Ended September 30,
	2024		2023
CASH FLOWS FROM OPERATING ACTIVITIES
Net loss	$	(151,722)	$	(275,610)
Adjustments to reconcile net loss to net cash used in operating activities:
Stock-based compensation	35,617		8,405
Acquired in-process research and development	—		130,188
Change in fair value of CVR liability	19,630		(1,300)
Change in fair value of forward contract liability	—		83,530
Gain on sale of in-process research and development asset	—		(14,609)
Lease ROU asset and leasehold improvement impairment loss	—		2,580
Loss on disposal of long-lived assets	—		915
Net accretion of discount on marketable securities	(8,985)		(612)
Interest proceeds from maturities of zero coupon US Treasury Bills	581		—
Depreciation and amortization	—		744
Amortization of operating lease assets	—		220
Other	—		18
Changes in operating assets and liabilities:
Accounts payable	4,268		1,001
Accrued and other liabilities	(257)		(4,000)
Related party accounts payable	(15,138)		(2,115)
Prepaid expenses and other assets	(4,205)		3,310
Deferred revenue	—		575
Development receivables	—		212
Operating lease liabilities	—		(2,326)
Net cash used in operating activities	(120,211)		(68,874)
CASH FLOWS FROM INVESTING ACTIVITIES
Proceeds from maturities and sales of marketable securities	183,419		21,000
Purchases of marketable securities	(366,160)		(112,631)
Cash assumed from asset acquisition of Spyre	—		3,035
Proceeds from sale of in-process research & development asset	—		15,000
Proceeds from sale of property and equipment	—		475
Net cash used in investing activities	(182,741)		(73,121)
CASH FLOWS FROM FINANCING ACTIVITIES
Proceeds from issuance of Series B non-voting convertible preferred stock in connection with private placement, net of placement and other offering costs	168,850		—
Proceeds from issuance of Series A non-voting convertible preferred stock in connection with private placement, net of placement and other offering costs	—		197,364
Proceeds from issuance of common stock in connection with at-the-market offerings, net of issuance costs	11,760		—
Payment of deferred offering costs in connection with shelf registration	(78)
Payments related to contingent value rights liability	(1,430)		—
Proceeds from employee stock option exercises, employee stock plan purchases, and exercise of prefunded warrants	6,203		123
Principal payments on finance lease obligation	—		(16)
Net cash provided by financing activities	185,305		197,471
Effect of exchange rate on cash, cash equivalents, and restricted cash	12		7
NET (DECREASE) INCREASE IN CASH, CASH EQUIVALENTS, AND RESTRICTED CASH	(117,635)		55,483
CASH, CASH EQUIVALENTS, AND RESTRICTED CASH
Beginning of period	189,215		36,416
End of period	$	71,580	$	91,899

(Continued on next page)

	Nine Months Ended September 30,
	2024		2023
Supplemental Disclosure of Non-Cash Investing and Financing Information:
Exchange of Series A non-voting convertible preferred stock for common stock	$	38,502	$	—
Conversion of Series B non-voting convertible preferred stock into common stock	$	244,010	$	—
Unpaid amounts related to issuance of common stock in connection with at-the-market offerings, net of offering costs	$	329	$	—
Allocation of deferred offering costs against proceeds of issuance of common stock	$	10	$	—
Reconciliation of Cash, Cash Equivalents, and Restricted Cash Reported in the Statement of Financial Position
Cash and cash equivalents	$	71,580	$	90,592
Restricted cash	—		1,307
Total cash, cash equivalents, and restricted cash shown in the statement of cash flows	$	71,580	$	91,899

The accompanying notes are an integral part of these condensed consolidated financial statements.

7

Spyre Therapeutics, Inc.

Notes to Unaudited Condensed Consolidated Financial Statements

1. The Company and Basis of Presentation

Spyre Therapeutics, Inc., formerly Aeglea BioTherapeutics, Inc. (“Spyre” or the “Company”), is a clinical stage biotechnology company focused on developing next generation therapeutics for patients living with inflammatory bowel disease. The Company was formed as a Limited Liability Company ("LLC") in Delaware on December 16, 2013 under the name Aeglea BioTherapeutics Holdings, LLC and was converted from a Delaware LLC to a Delaware corporation on March 10, 2015. On November 27, 2023, the Company completed its corporate rebranding, changing the name of the Company to Spyre Therapeutics, Inc. The Company operates in one segment and has its principal offices in Waltham, Massachusetts.

On September 8, 2023, the Company effected a reverse stock split of its Common Stock at a ratio of 1-for-25 (the “Reverse Split”). Except as indicated otherwise, all share numbers related to the Company's Common Stock disclosed in these financial statements have been adjusted on a post-Reverse Split basis.

On April 12, 2023, based on the review of the inconclusive interim results from the Company's Phase 1/2 clinical trial of pegtarviliase for the treatment of Classical Homocystinuria and other business considerations, the Company announced that it had initiated a process to explore strategic alternatives to maximize stockholder value and engaged an independent exclusive financial advisor to support this process. As a result, in April 2023, the Company implemented a restructuring plan resulting in an approximate 83% reduction of the Company’s existing headcount.

On June 22, 2023, the Company acquired, in accordance with the terms of the Agreement and Plan of Merger (the "Acquisition Agreement"), the assets of Spyre Therapeutics, Inc. (“Pre-Merger Spyre”), a privately held biotechnology company advancing a pipeline of antibody therapeutics with the potential to transform the treatment of inflammatory bowel disease through a research and development option agreement ("Paragon Agreement") with Paragon Therapeutics, Inc. ("Paragon"). The asset acquisition was accomplished through a two-step reverse triangular merger whereby a wholly owned subsidiary of the Company merged with and into Pre-Merger Spyre, which existed at the time the Acquisition Agreement was entered into, and became a wholly owned subsidiary of the Company in accordance with the terms of the Acquisition Agreement. Immediately following this merger, Pre-Merger Spyre merged with and into a second wholly owned subsidiary of the Company (“Merger Sub”) in accordance with the terms of the Acquisition Agreement and Pre-Merger Spyre ceased to exist. Subsequently, Aeglea BioTherapeutics, Inc. was renamed Spyre Therapeutics, Inc. and is a different entity than Pre-Merger Spyre, which ceased to exist upon merging with Merger Sub. The transaction was structured as a stock-for-stock transaction pursuant to which all of Pre-Merger Spyre's outstanding equity interests were exchanged based on a fixed exchange ratio of 0.5494488 to 1 for consideration from the Company of 517,809 shares of common stock, par value of $0.0001 per share ("Common Stock"), and 364,887 shares of Series A non-voting convertible preferred stock, par value of $0.0001 per share ("Series A Preferred Stock") (convertible on a 40 to 1 basis), in addition to the assumption of outstanding and unexercised stock options to purchase 2,734 shares of Common Stock from the Amended and Restated Spyre 2023 Equity Incentive Plan (the "Asset Acquisition"). The Common Stock and Series A Preferred Stock related to the Asset Acquisition were issued to the Pre-Merger Spyre stockholders on July 7, 2023.

In connection with the Asset Acquisition, on June 26, 2023, the Company completed a private placement of shares of Series A Preferred Stock (the “June 2023 PIPE”) to a group of investors (the “June 2023 Investors”). The Company sold an aggregate of 721,452 shares of Series A Preferred Stock for an aggregate purchase price of approximately $210.0 million before deducting approximately $12.7 million in placement agent and other offering expenses (together with the Asset Acquisition, the “Transactions”).

In connection with the Asset Acquisition, a non-transferable contingent value right ("CVR") was distributed to stockholders of record of the Company as of the close of business on July 3, 2023 (the "Legacy Stockholders"), but was not distributed to the holders of shares of Common Stock or Series A Preferred Stock issued to the former stockholders of Pre-Merger Spyre or the June 2023 Investors in the Transactions. Holders of the CVRs will be entitled to receive cash payments from proceeds received by the Company for a three-year

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period related to the disposition or monetization of its legacy assets for a period of one-year following the closing of the Asset Acquisition.

On November 21, 2023, the Company's stockholders approved the issuance of Common Stock upon conversion of the Company's Series A Preferred Stock to Common Stock. A total of 649,302 shares of Series A Preferred Stock automatically converted to 25,972,080 shares of Common Stock; 437,037 shares of Series A Preferred Stock did not automatically convert and remained outstanding after the conversion.

On December 11, 2023, the Company completed a private placement of shares of Common Stock and Series B non-voting convertible preferred stock, par value of $0.0001 per share ("Series B Preferred Stock") (convertible on a 40 to 1 basis) (the “December 2023 PIPE”) to a group of investors. The Company sold an aggregate of 6,000,000 shares of Common Stock and 150,000 shares of Series B Preferred Stock for an aggregate purchase price of approximately $180.0 million before deducting approximately $10.9 million of placement agent and other offering expenses.

On March 20, 2024, the Company completed a private placement of Series B Preferred Stock (convertible on a 40 to 1 basis) (the “March 2024 PIPE”) to a group of investors. The Company sold 121,625 shares of Series B Preferred Stock for a purchase price of $180.0 million before deducting approximately $11.2 million of placement agent and other offering costs.

On April 23, 2024, the Company entered into an exchange agreement with Fairmount Healthcare Fund II L.P. (the “Stockholder”), pursuant to which the Stockholder agreed to exchange an aggregate of 90,992 shares of Series A Preferred Stock for an aggregate of 3,639,680 shares of Common Stock (the “April 2024 Exchange”). The Common Stock issued in connection with the April 2024 Exchange was issued without registration under the Securities Act of 1933, as amended (the “Securities Act”) in reliance on the exemption from registration contained in Section 3(a)(9) of the Securities Act. The April 2024 Exchange closed on April 25, 2024, with 346,045 shares of Series A Preferred Stock remaining outstanding following the April 2024 Exchange.

On May 14, 2024, the Company's stockholders approved the issuance of Common Stock upon conversion of the Company's Series B Preferred Stock to Common Stock. A total of 254,958 shares of Series B Preferred Stock automatically converted to 10,198,320 shares of Common Stock; 16,667 shares of Series B Preferred Stock did not automatically convert and remained outstanding as of September 30, 2024.

On September 6, 2024, the Company filed a new shelf registration statement on Form S-3 that was declared effective by the SEC for the potential offering, issuance and sale by the Company of up to $500.0 million of our common stock, preferred stock, debt securities, warrants and/or units consisting of all or some of these securities. Concurrent with the filing of the shelf-registration statement, the Company entered into a sales agreement with TD Securities (USA) LLC (“TD Cowen”), as its sales agent, pursuant to which the Company may issue and sell shares of its common stock for an aggregate offering price of up to $200.0 million under an at-the-market (“ATM’) offering program included in the shelf registration. In September 2024, the Company sold 426,287 shares of common stock under the ATM at a price per share of $28.15, resulting in net proceeds of $11.8 million.

Liquidity

The Company is a clinical stage biotechnology company with a limited operating history, and due to its significant research and development expenditures, the Company has generated operating losses since its inception and has not generated any revenue from the commercial sale of any products. There can be no assurance that profitable operations will ever be achieved, and, if achieved, whether profitability can be sustained on a continuing basis.

Since its inception and through September 30, 2024, the Company has funded its operations by raising an aggregate of approximately $1.1 billion of gross proceeds from the sale and issuance of convertible preferred stock and common stock, pre-funded warrants, the collection of grant proceeds, and the licensing of its product rights for commercialization of pegzilarginase in Europe and certain countries in the Middle East. As of September 30, 2024, Spyre had an accumulated deficit of $916.1 million, and cash, cash equivalents, and marketable securities of $414.2 million.

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Based on current operating plans, the Company has sufficient resources to fund operations for at least one year from the issuance date of these financial statements with existing cash, cash equivalents, and marketable securities. Spyre will need to secure additional financing in the future to fund additional research and development, and before a commercial drug can be produced, marketed and sold. If the Company is unable to obtain additional financing or generate license or product revenue, the lack of liquidity could have a material adverse effect on the Company.

Basis of Presentation

The consolidated financial statements have been prepared in conformity with generally accepted accounting principles in the United States (“U.S. GAAP”) as defined by the Financial Accounting Standards Board and include the accounts of the Company and its wholly owned subsidiaries. All intercompany balances and transactions have been eliminated in consolidation.

Reclassification of Prior Year Presentation

Certain prior year amounts have been reclassified for consistency with the current year presentation. These reclassifications had no effect on the reported results of operations or balance sheets.

Unaudited Interim Financial Information

The interim condensed consolidated financial statements included in this Quarterly Report on Form 10-Q are unaudited. The unaudited interim financial statements have been prepared on the same basis as the annual financial statements and reflect, in the opinion of management, all adjustments of a normal and recurring nature that are necessary for a fair statement of the Company’s financial position as of September 30, 2024, and its results of operations for the three and nine months ended September 30, 2024 and 2023, changes in convertible preferred stock and stockholders’ equity for the three and nine months ended September 30, 2024 and 2023, and cash flows for the nine months ended September 30, 2024 and 2023. The results of operations for the three and nine months ended September 30, 2024, are not necessarily indicative of the results to be expected for the year ending December 31, 2024 or for any other future annual or interim period. The December 31, 2023 balance sheet was derived from audited financial statements, but does not include all disclosures required by U.S. GAAP for complete financial statements. These financial statements should be read in conjunction with the audited financial statements included in the Company’s Form 10-K for the year ended December 31, 2023 (the "Annual Report") as filed with the SEC on February 29, 2024 and amended on March 1, 2024 and November 18, 2024.

2. Summary of Significant Accounting Policies

These interim condensed consolidated financial statements have been prepared in accordance with U.S. GAAP and SEC instructions for interim financial information, and should be read in conjunction with the Company's Annual Report. Significant accounting policies and other disclosures normally provided have been omitted since such items are disclosed in the Company's Annual Report. The Company uses the same accounting policies in preparing quarterly and annual financial statements.

Other than policies noted below, there have been no significant changes from the significant accounting policies and estimates disclosed in the Notes titled “1. The Company and Basis of Presentation” and "2. Summary of Significant Accounting Policies” of the Company's Annual Report.

License Agreements Contingent Milestone Payments

The Company’s license agreements include specific development, regulatory, and clinical milestone payments that are payable upon the resolution of a contingency, such as upon the selection of a development candidate, first dosing of a human patient in clinical trials or receipt of the Food Drug and Administration’s (“FDA”) approval of a Spyre drug. The achievement of these milestone payments involves many factors outside of the Company’s control and therefore the associated likelihood cannot be considered probable until the

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related contingency is resolved. Based on the preceding, the Company accrues each milestone payment upon the achievement of the applicable milestone event.

Recently Adopted Accounting Pronouncements

There have been no recent accounting pronouncements or changes in accounting pronouncements during the nine months ended September 30, 2024 that are of significance or potential significance to the Company.

Not Yet Adopted Accounting Pronouncements

In November 2024, the Financial Accounting Standards Board issued ASU 2024-03 to require more detailed information about specified categories of expenses (purchases of inventory, employee compensation, depreciation, amortization, and depletion) included in certain expense captions presented on the face of the income statement. This ASU is effective for fiscal years beginning after December 15, 2026, and for interim periods within fiscal years beginning after December 15, 2027. Early adoption is permitted. The amendments may be applied either (1) prospectively to financial statements issued for reporting periods after the effective date of this ASU or (2) retrospectively to all prior periods presented in the financial statements. The Company is currently evaluating the impact this ASU will have on our disclosures.

3. Fair Value Measurements

The Company measures and reports certain financial instruments as assets and liabilities at fair value on a recurring basis. The following tables set forth the fair value of the Company’s financial assets and liabilities at fair value on a recurring basis based on the three-tier fair value hierarchy (in thousands):

	September 30, 2024
	Level 1		Level 2		Level 3		Total
Financial Assets:
Money market funds	$	69,900	$	—	$	—	$	69,900
U.S. government treasury securities	140,072		—		—		140,072
U.S. government agency securities	—		100,328		—		100,328
Commercial paper	—		75,717		—		75,717
Corporate bonds	—		26,530		—		26,530
Total financial assets	$	209,972	$	202,575	$	—	$	412,547
Liabilities:
Parapyre Option Obligation	$	—	$	13,035	$	—	$	13,035
CVR liability	—		—		60,900		60,900
Total liabilities	$	—	$	13,035	$	60,900	$	73,935

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	December 31, 2023
	Level 1		Level 2		Level 3		Total
Financial Assets:
Money market funds	$	150,648	$	—	$	—	$	150,648
U.S. government treasury securities	32,843		—		—		32,843
U.S. government agency securities	—		16,257		—		16,257
Commercial paper	—		104,141		—		104,141
Corporate bonds	—		33,064		—		33,064
Total financial assets	$	183,491	$	153,462	$	—	$	336,953
Liabilities:
CVR liability	$	—	$	—	$	42,700	$	42,700
Total liabilities	$	—	$	—	$	42,700	$	42,700

The Company measures the fair value of money market funds and U.S. government treasury securities on quoted prices in active markets for identical assets or liabilities. The Level 2 assets include U.S. government agency securities, commercial paper and corporate bonds, and are valued based on quoted prices for similar assets in active markets and inputs other than quoted prices that are derived from observable market data. The Company evaluates transfers between levels at the end of each reporting period. There were no transfers between Level 1, Level 2, or Level 3 during the periods presented.

Parapyre Option Obligation

Under the Paragon Agreement, the Company is obligated to issue Parapyre Holding LLC ("Parapyre") an annual equity grant of warrants, on the last business day of each of the years ended December 31, 2023 and December 31, 2024, to purchase 1% of the then outstanding shares of the Company’s Common Stock, on a fully diluted basis, during the term of the Paragon Agreement (the "Parapyre Option Obligation"). The Company determined that the 2023 and 2024 grants are two separate grants, as there would be no obligation for the 2024 grant had the Company exercised or terminated all of the options under the Paragon Agreement prior to December 31, 2023. The service inception period for the grant precedes the grant date, with the full award being vested as of the grant date with no post-grant date service requirement. Accordingly, a liability related to the Parapyre Option Obligation is recorded pursuant to the Paragon Agreement during interim periods. On December 31, 2023, the Company settled its 2023 obligation under the Parapyre Option Obligation by issuing Parapyre 684,407 warrants to purchase the Company's Common Stock, with a $21.52 per share exercise price for each warrant.

The Parapyre Option Obligation is considered a Level 2 liability based on observable market data for substantially the full term of the liability. The Parapyre Option Obligation is measured each period using a Black-Scholes model to estimate the fair value of the option grant. Changes in the fair value of the Parapyre Option Obligation are recorded as stock-based compensation within Research and development expenses for non-employees who provided pre-clinical development services.

CVR Liability

In connection with the Asset Acquisition, a non-transferable CVR was distributed to the Legacy Stockholders, but was not distributed to holders of shares of Common Stock or Series A Preferred Stock issued to the June 2023 Investors or former stockholders of Pre-Merger Spyre in connection with the Transactions. Holders of the CVR will be entitled to receive certain cash payments from proceeds received by the Company for a three-year period, if any, related to the disposition or monetization of the Company’s legacy assets for a period of one year following the closing of the Asset Acquisition.

The fair value of the CVR liability was determined using the probability weighted discounted cash flow method to estimate future cash flows associated with the sale of the legacy assets. Analogous to a dividend being declared/approved in one period and paid out in another, the liability was recorded at the date of approval, June 22, 2023, as a Common Stock dividend, returning capital to the Legacy Stockholders. Changes in fair

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value of the liability will be recognized as a component of Other income (expense) in the consolidated statement of operations and comprehensive loss in each reporting period. The liability value is based on significant inputs not observable in the market such as estimated cash flows, estimated probabilities of regulatory success, and discount rates, which represent a Level 3 measurement within the fair value hierarchy.

The significant inputs used to estimate the fair value of the CVR liability were as follows:

	September 30, 2024
Estimated cash flow dates	05/28/25 - 06/22/26
Estimated probability of success	72% - 100%
Estimated reimbursement rate compared to reimbursement target	81% - 100%
Risk-adjusted discount rates	7.76% - 7.82%

The change in fair value between December 31, 2023 and September 30, 2024 was a $19.6 million increase, primarily driven by changes in the likelihood of achievement of certain milestones and the time value of money, partially offset by an increase in risk-adjusted discount rates.

The following table presents changes in the CVR liability for the periods presented (in thousands):

	CVR Liability
Beginning balance as of December 31, 2023	$	42,700
Changes in the fair value of the CVR liability	19,630
Payments	(1,430)
Ending Balance as of September 30, 2024	$	60,900

Forward Contract Liability

In connection with the Asset Acquisition, the Company entered into a contract for the issuance of 364,887 shares of Series A Preferred Stock as part of the consideration transferred. This forward contract was classified as a liability because the underlying preferred shares were contingently redeemable. The forward contract was carried at fair value on the balance sheet, with changes in fair value between the acquisition date and June 30, 2023 recorded in earnings. The liability was settled with the issuance of the Series A Preferred Stock on July 7, 2023.

The fair value of the forward contract as of the acquisition date, June 22, 2023, was $106.2 million. The liability was settled with the issuance of the Series A Preferred Stock on July 7, 2023 for $189.7 million. For the three and nine months ended September 30, 2023, $25.4 million and $83.5 million, respectively, was recorded as Other (expense) income in the consolidated statements of operations in connection with the change in fair value of the forward contract liability.

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4. Cash Equivalents and Marketable Securities

The following tables summarize the estimated fair value of the Company’s cash equivalents and marketable securities and the gross unrealized gains and losses (in thousands):

	September 30, 2024
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses		Estimated Fair Value
Cash equivalents:
Money market funds	$	69,900	$	—	$	—	$	69,900
Total cash equivalents	$	69,900	$	—	$	—	$	69,900
Marketable securities:
Commercial paper	$	75,503	$	214	$	—	$	75,717
Corporate bonds	26,457		76		(3)		26,530
U.S. government treasury securities	139,313		768		(9)		140,072
U.S. government agency securities	99,973		363		(8)		100,328
Total marketable securities	$	341,246	$	1,421	$	(20)	$	342,647

	December 31, 2023
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses		Estimated Fair Value
Cash equivalents:
Money market funds	$	150,648	$	—	$	—	$	150,648
Commercial paper	24,950		5		—		24,955
U.S. government treasury securities	10,965		1		—		10,966
Total cash equivalents	$	186,563	$	6	$	—	$	186,569
Marketable securities:
Commercial paper	$	79,124	$	62	$	—	$	79,186
Corporate bonds	32,984		81		(1)		33,064
U.S. government treasury securities	21,846		31		—		21,877
U.S. government agency securities	16,147		110		—		16,257
Total marketable securities	$	150,101	$	284	$	(1)	$	150,384

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The following table summarizes the available-for-sale securities in an unrealized loss position for which an allowance for credit losses has not been recorded as of September 30, 2024 and December 31, 2023, aggregated by major security type and length of time in a continuous unrealized loss position:

	September 30, 2024
	Less Than 12 Months				12 Months or Longer				Total
	Fair Value		Unrealized Losses		Fair Value		Unrealized Losses		Fair Value		Unrealized Losses
Corporate bonds	$	1,952	$	(3)	$	—	$	—	$	1,952	$	(3)
U.S. government treasury securities	17,517		(9)		—		—		17,517		(9)
U.S. government agency securities	18,101		(8)		—		—		18,101		(8)
Total marketable securities	$	37,570	$	(20)	$	—	$	—	$	37,570	$	(20)
	December 31, 2023
	Less Than 12 Months				12 Months or Longer				Total
	Fair Value		Unrealized Losses		Fair Value		Unrealized Losses		Fair Value		Unrealized Losses
Corporate bonds	$	9,907	$	(1)	$	—	$	—	$	9,907	$	(1)
U.S. government treasury securities	4,831		—		—		—		4,831		—
Total marketable securities	$	14,738	$	(1)	$	—	$	—	$	14,738	$	(1)

The Company evaluated its securities for credit losses and considered the decline in market value to be primarily attributable to current economic and market conditions and not to a credit loss or other factors. Additionally, the Company does not intend to sell the securities in an unrealized loss position and does not expect it will be required to sell the securities before recovery of the unamortized cost basis. As of September 30, 2024 and December 31, 2023, an allowance for credit losses had not been recognized. Given the Company's intent and ability to hold such securities until recovery, and the lack of significant change in credit risk of these investments, the Company does not consider these marketable securities to be impaired as of September 30, 2024 and December 31, 2023.

The financial instruments that potentially subject the Company to a concentration of credit risk consist principally of cash deposits. Accounts at each of our two U.S. banking institutions are insured by the Federal Deposit Insurance Corporation (“FDIC”) up to $250,000 per depositor. As of September 30, 2024 and December 31, 2023, cash deposits at the Company's U.S. banking institutions exceeded the FDIC limits. Uninsured foreign cash deposits were immaterial for both periods.

There were no realized gains or losses on marketable securities for the three and nine months ended September 30, 2024 and 2023. Interest on marketable securities is included in interest income. Accrued interest receivable on available-for-sale debt securities as of September 30, 2024 and December 31, 2023, was $1.7 million and $0.9 million, respectively, and is reflected in Prepaid expenses and other current assets.

The following table summarizes the contractual maturities of the Company’s marketable securities at estimated fair value (in thousands):

	September 30, 2024		December 31, 2023
Due in one year or less	$	253,613	$	115,784
Due in 1 - 2 years	89,034		34,600
Total marketable securities	$	342,647	$	150,384

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The Company may sell investments at any time for use in current operations even if they have not yet reached maturity. As a result, the Company classifies marketable securities, including securities with maturities beyond twelve months as current assets.

5. Accrued and Other Current Liabilities

Accrued and other current liabilities consist of the following (in thousands):

	September 30, 2024		December 31, 2023
Accrued compensation	$	3,966	$	4,054
Accrued contracted research and development costs	7,527		7,092
Accrued professional and consulting fees	1,134		1,474
Accrued other	526		488
Total accrued and other current liabilities	$	13,153	$	13,108

6. Asset Acquisition

On June 22, 2023, the Company acquired Pre-Merger Spyre pursuant to the Acquisition Agreement, by and among the Company, Aspen Merger Sub I, Inc., a Delaware corporation and a wholly owned subsidiary of the Company (“First Merger Sub”), Sequoia Merger Sub II, LLC, a Delaware limited liability company and wholly owned subsidiary of the Company (“Second Merger Sub”), and Pre-Merger Spyre. Pursuant to the Acquisition Agreement, First Merger Sub merged with and into Pre-Merger Spyre, pursuant to which Pre-Merger Spyre was the surviving corporation and became a wholly owned subsidiary of the Company (the “First Merger”). Immediately following the First Merger, Pre-Merger Spyre merged with and into Second Merger Sub, pursuant to which Second Merger Sub became the surviving entity. Pre-Merger Spyre was a pre-clinical stage biotechnology company that was incorporated on April 28, 2023 under the direction of Peter Harwin, a Managing Member of Fairmount, for the purpose of holding rights to certain intellectual property being developed by Paragon. Fairmount is a founder of Paragon.

The Company completed the Asset Acquisition of Pre-Merger Spyre, in accordance with the terms of the Acquisition Agreement. Under the terms of the Acquisition Agreement, the Company issued 517,809 shares of Common Stock and 364,887 shares of Series A Preferred Stock to former Pre-Merger Spyre security holders. In addition, outstanding and unexercised stock options to purchase 2,734 shares of common stock were assumed from the Amended and Restated Spyre 2023 Equity Incentive Plan.

At the acquisition date, the Company recorded forward contracts to represent the obligation to issue shares of Common Stock and shares of Series A Preferred Stock, respectively. The forward contract related to the Common Stock was recorded as Additional paid-in capital as the instrument is indexed to the Common Stock. The forward contract related to the Series A Preferred Stock was recorded as a liability, as the underlying stock has a cash redemption feature. On July 7, 2023, both the shares of Common Stock and Series A Preferred Stock were issued and the forward contract liability associated with the Series A Preferred Stock was settled accordingly.

The Company concluded that the arrangement met the definition of an asset acquisition rather than a business combination, as substantially all of the fair value of the gross assets acquired was concentrated in a single identifiable asset, Pre-Merger Spyre's option to exclusively license certain intellectual property rights (the "Option"). The Company determined that the Option was a single asset as the Company's strategy relied on developing the entire portfolio of individual treatments to create combination treatments that simultaneously address different mechanisms of inflammatory bowel disease with a single treatment. The Company also determined that the pipeline candidates within the portfolio were similar in nature and risk profile. In addition, the Company did not obtain any substantive processes, assembled workforce, or employees capable of producing outputs in connection with the Asset Acquisition.

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The Company determined that the cost to acquire the asset was $113.2 million which was recorded as acquired in-process research and development ("IPR&D"). The fair value of the consideration issued consisted of the 364,887 shares of Series A Preferred Stock (14,595,480 shares of Common Stock on an as-converted basis) and 517,809 shares of Common Stock, valued at $291.08 per share and $7.277 per share, respectively.

The Asset Acquisition costs are shown on the following table (in millions):

	June 22, 2023
Consideration transferred in Series A Preferred Stock and Common Stock	$	110.0
Transaction costs incurred by Pre-Merger Spyre	3.2
Total cost to acquire asset	$	113.2

The allocation of the purchase price to net assets acquired is as a follows:

	June 22, 2023
Acquired in-process research and development	$	130.2
Cash acquired	3.0
Assumed liabilities	(20.0)
Total cost to acquire asset	$	113.2

7. Licensing Agreements

On July 12, 2023, December 14, 2023, and June 5, 2024, the Company exercised the Option available under the Paragon Agreement with respect to the SPY001, SPY002, and SPY003 research programs, respectively.

On May 14, 2024, the Company and Paragon entered into (i) a license agreement (the “SPY001 License Agreement”), pursuant to which Paragon granted the Company a royalty-bearing, world-wide, exclusive license to develop, manufacture, commercialize or otherwise exploit certain antibodies and products targeting α4ß7 integrin and (ii) a license agreement (the “SPY002 License Agreement”), pursuant to which Paragon granted the Company a royalty-bearing, world-wide, exclusive license to develop, manufacture, commercialize or otherwise exploit certain antibodies and products targeting TL1A, respectively.

On October 11, 2024, the Company and Paragon entered into a license agreement (the "SPY003 License Agreement" and, together with the SPY001 License Agreement and the SPY002 License Agreement, the "License Agreements"), pursuant to which Paragon granted the Company a royalty-bearing, world-wide, exclusive license to develop, manufacture, commercialize or otherwise exploit certain antibodies and products targeting IL-23 in the field of IBD.

Under the terms of each License Agreement, the Company is obligated to pay Paragon up to $22.0 million based on specific development, regulatory and clinical milestones for the first product under each agreement, respectively, that achieves such specified milestones, including a $1.5 million fee for nomination of a development candidate, as applicable, and a further milestone payment of $2.5 million upon the first dosing of a human patient in a Phase 1 trial. In addition, the following summarizes other key terms of each License Agreement:

•Paragon will provide the Company with an exclusive license (such license, with respect to the SPY003 License Agreement only, being limited to the field of IBD) to its patents covering the related antibody, the method of use and its method of manufacture.

•Paragon will not conduct any new campaigns that generate anti-α4ß7 or anti-TL1A monospecific antibodies in any field or anti-IL-23 monospecific antibodies in the field of IBD, in each case for at least 5 years.

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•The Company will pay Paragon a low single-digit percentage royalty for single antibody products and a mid single-digit percentage royalty for products containing more than one antibody from Paragon.

•There is a royalty step-down of 1/3rd if there is no Paragon patent in effect during the royalty term.

•The royalty term ends on the later of (i) the last-to-expire licensed patent or Company patent directed to the manufacture, use or sale of a licensed antibody in the country at issue or (ii) 12 years from the date of first sale of a Company product.

•Agreement may be terminated on 60 days’ notice by the Company; on material breach without cure; and to the extent permitted by law, on a party’s insolvency or bankruptcy.

•With respect to the SPY002 License Agreement only, on a product by product basis, the Company will pay sublicensing fees of up to approximately $20 million upon the achievement of mostly commercial milestones.

The Company recognizes the expense associated with each milestone when the achievement of the milestone is deemed probable. During the three and nine months ended September 30, 2024, the Company recognized expense of nil and $5.5 million related to Paragon license milestone payments recorded within Research and development expenses in the accompanying condensed statement of operations. There was no such expense for the three and nine months ended September 30, 2023.

For the three and nine months ended September 30, 2024, the Company made cash milestone payments to Paragon totaling $2.5 million and $5.5 million, respectively. As of September 30, 2024, there were no Paragon license milestone payments outstanding and payable to Paragon.

Additionally, the Company recognized $0.3 million and $0.4 million related to sublicensing fees and which was recorded as Research and development expenses in the accompanying condensed statement of operations for the three and nine months ended September 30, 2024, respectively. As of September 30, 2024, $0.3 million in sublicensing fees were outstanding and payable to Paragon.

8. Related Party Transactions

Paragon and Parapyre each beneficially own less than 5% of the Company's capital stock through their respective holdings of the Company's Common Stock. Fairmount Funds Management LLC ("Fairmount") beneficially owns more than 5% of the Company's capital stock on an as-converted basis, has two seats on the Company's board of directors (the "Board") and beneficially owns more than 5% of Paragon, which is a joint venture between Fairmount and FairJourney Biologics. Fairmount appointed Paragon's board of directors and has the contractual right to approve the appointment of any executive officers. Parapyre is an entity formed by Paragon as a vehicle to hold equity in Spyre in order to share profits with certain employees of Paragon.

The following is the summary of expenses related to the Paragon Agreement and License Agreements, which are ultimately settled in cash (in millions) and recorded within Research and development in the consolidated statement of operations for the periods presented:

	Three Months Ended September 30,				Nine Months Ended September 30,
	2024		2023		2024		2023
Reimbursable costs under the Paragon Agreement	$	1.3	$	16.7	$	15.3	$	17.9
License Agreements milestone and sublicensing fees	0.3		—		5.9		—
Total related party expense (excludes stock comp)	$	1.6	$	16.7	$	21.2	$	17.9

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The following is the summary of Related party accounts payable and other current liabilities (in millions):

	September 30, 2024		December 31, 2023
Reimbursable costs under the Paragon Agreement	$	1.2	$	16.6
Parapyre warrants liability	13.0		—
License Agreements development milestone liability (see Note 7)	0.3		—
Total related party accounts payable	$	14.5	$	16.6

Paragon Agreement

In connection with the Asset Acquisition, the Company assumed the rights and obligations of Pre-Merger Spyre under the Paragon Agreement. Under the Paragon Agreement, Spyre is obligated to compensate Paragon for its services performed under each research program based on the actual costs incurred with mark-up costs pursuant to the terms of the Paragon Agreement. Spyre is also obligated under the Paragon Agreement to issue Parapyre annual equity grants of warrants in accordance with the Parapyre Option Obligation.

On July 12, 2023, December 14, 2023, and June 5, 2024, the Company exercised the Option available under the Paragon Agreement with respect to the SPY001, SPY002 and SPY003 research programs, respectively. Our Option available under the Paragon Agreement with respect to the SPY004 program remains unexercised. Please refer to Note 7 for additional information on the License Agreements related to the exercised options.

On May 14, 2024, the Company, Paragon and Parapyre entered into a second amended and restated antibody discovery and option agreement that amends and restates that certain amended and restated antibody discovery and option agreement, dated September 29, 2023, by and between Paragon, Parapyre and Spyre Therapeutics, LLC, in order to, among other things, (i) replace the Company’s subsidiary with the Company as a party to the agreement and (ii) amend certain terms related to the SPY003 research program, including without limitation, (a) establishing an SPY003 antibody selection process pursuant to which the Company and Paragon shall alternate in turn to select a project antibody to be included and excluded, respectively, from the Company’s rights under its option to license certain intellectual property rights related to SPY003 from Paragon until all project antibodies under the SPY003 research program have been selected; (b) reducing the development costs invoiced to the Company for the SPY003 research program incurred from and after April 1, 2024 through completion of the SPY003 antibody selection process by 50%; (c) requiring Paragon to reimburse the Company for 50% of the development costs for the SPY003 research program incurred prior to April 1, 2024; provided, that Paragon receives rights to at least one SPY003 project antibody following completion of the SPY003 antibody selection process; (d) obligating the Company to exercise its option to license the intellectual property rights to SPY003 project antibodies and technology following the completion of the SPY003 antibody selection process; and (e) establishing a license agreement term sheet for the SPY003 research program with substantially similar milestone payment terms and royalty payment terms as the SPY001 License Agreement. Please refer to Note 7 for additional disclosures.

For the three and nine months ended September 30, 2024, the Company recognized expenses related to services provided by Paragon totaling $7.4 million and $28.3 million, respectively, which included $6.1 million and $13.0 million, respectively, of stock-based compensation expense, and were recorded as Research and development expenses in the consolidated statements of operations. Included within the expenses recognized for services provided by Paragon for the nine months ended September 30, 2024, is a $5.9 million reduction in Research and development expenses related to the reimbursement of 50% of the development costs for the SPY003 research program by Paragon.

For the three and nine months ended September 30, 2024, the Company made payments totaling $1.2 million and $30.7 million respectively, in connection with the Paragon Agreement.

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Parapyre Option Obligation

Pursuant to the Paragon Agreement, the Company agreed to issue Parapyre an annual equity grant of warrants, on the last business day of each of the years ended December 31, 2023 and December 31, 2024, to purchase 1% of the then outstanding shares of the Company's Common Stock, on a fully diluted basis, during the term of the Paragon Agreement. See Note 10 for disclosures related to the Parapyre Option Obligation.

Paragon License Agreements

See Note 7 for disclosures related to the License Agreements entered into with Paragon.

Mark McKenna Option Grant

On February 1, 2024, the Board appointed Mark McKenna as a Class I director. Mr. McKenna and the Company are parties to a consulting agreement, pursuant to which Mr. McKenna agreed to continue to provide consulting services as an independent contractor to the Company, with an effective date of August 1, 2023 (the “Vesting Commencement Date”). As compensation for Mr. McKenna’s consulting services, on November 22, 2023, he was granted non-qualified stock options to purchase 477,000 shares of the Company’s Common Stock under the 2016 Plan (as defined in Note 8) with an exercise price of $10.39 per share, which vest as to 25% on the one year anniversary of the Vesting Commencement Date and thereafter vest and become exercisable in 36 equal monthly installments, subject to Mr. McKenna’s continued service to the Company through each applicable vesting date. For the three and nine months ended September 30, 2024, the Company recognized $0.3 million and $0.8 million, respectively, in stock-based compensation expense related to Mr. McKenna's consulting agreement. There was no such expense for the three and nine months ended September 30, 2023.

9. Convertible Preferred Stock and Stockholders’ Equity

Pre-Funded Warrants

In February 2019, April 2020 and May 2022, the Company issued pre-funded warrants to purchase the Company’s Common Stock in underwritten public offerings at the offering price of the Common Stock, less the $0.0025 per share exercise price of each warrant. The warrants were recorded as a component of stockholders’ (deficit) equity within additional paid-in capital and have no expiration date. Per the terms of the warrant agreements, the outstanding warrants to purchase shares of Common Stock may not be exercised if the holder’s ownership of the Company’s Common Stock would exceed 4.99% (“Maximum Ownership Percentage”), or 9.99% for certain holders. By written notice to the Company, each holder may increase or decrease the Maximum Ownership Percentage to any other percentage (not in excess of 19.99% for the majority of such warrants). The revised Maximum Ownership Percentage would be effective 61 days after the notice is received by the Company.

As of September 30, 2024, all pre-funded warrants have been exercised and none remain outstanding.

Parapyre Warrants

The Company settled its 2023 obligations under the Parapyre Option Obligation by issuing Parapyre 684,407 warrants to purchase the Company's Common Stock, with a $21.52 per share exercise price for each warrant. Pursuant to the terms of the warrant agreement, the outstanding warrants to purchase shares of Common Stock may not be exercised if the holder’s ownership of the Company’s Common Stock would exceed 4.99%. As of September 30, 2024, none of the warrants issued under the Parapyre Option Obligation have been exercised.

Series A Non-Voting Convertible Preferred Stock

On June 22, 2023, the Company filed a Certificate of Designation of Preferences, Rights and Limitations of the Series A Preferred Stock with the Secretary of State of the State of Delaware (the “Series A Certificate of Designation”) in connection with the Asset Acquisition and the June 2023 PIPE.

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Pursuant to the Series A Certificate of Designation, holders of Series A Preferred Stock are entitled to receive dividends on shares of Series A Preferred Stock equal to, on an as-if-converted-to-Common Stock basis, and in the same form as, dividends actually paid on shares of Common Stock. Except as provided in the Series A Certificate of Designation or as otherwise required by law, the Series A Preferred Stock does not have voting rights. However, as long as any shares of Series A Preferred Stock are outstanding, the Company will not, without the affirmative vote of the holders of a majority of the then outstanding shares of the Series A Preferred Stock: (a) alter or change adversely the powers, preferences or rights given to the Series A Preferred Stock, or alter or amend the Series A Certificate of Designation, amend or repeal any provision of, or add any provision to, the Company’s Certificate of Incorporation or its Bylaws, or file any articles of amendment, certificate of designations, preferences, limitations and relative rights of any series of preferred stock, if such action would adversely alter or change the preferences, rights, privileges or powers of, or restrictions provided for the benefit of the Series A Preferred Stock, regardless of whether any of the foregoing actions will be by means of amendment to the Certificate of Incorporation or by merger, consolidation, recapitalization, reclassification, conversion or otherwise, (b) issue further shares of Series A Preferred Stock or increase or decrease (other than by conversion) the number of authorized shares of Series A Preferred Stock, (c) prior to the stockholder approval of the conversion of the Series A Preferred Stock into shares of Common Stock in accordance with Nasdaq Stock Market Rules (the “Series A Conversion Proposal”) or at any time while at least 30% of the originally issued Series A Preferred Stock remains issued and outstanding, consummate (x) any Fundamental Transaction (as defined in the Series A Certificate of Designation) or (y) any merger or consolidation of the Company with or into another entity or any stock sale to, or other business combination in which our stockholders immediately before such transaction do not hold at least a majority of our capital stock immediately after such transaction or (d) enter into any agreement with respect to any of the foregoing. The Series A Preferred Stock does not have a preference upon any liquidation, dissolution or winding-up of the Company.

On June 26, 2023, the Company completed a private placement of 721,452 shares of Series A Preferred Stock in exchange for gross proceeds of approximately $210.0 million, or net proceeds of $197.3 million, after deducting placement agent and other offering costs.

On July 7, 2023, the Company issued 364,887 shares of Series A Preferred Stock as part of its consideration transferred in connection with the Asset Acquisition that closed on June 22, 2023 which settled the related forward contract liability.

On November 21, 2023, the Company's stockholders approved the Series A Conversion Proposal, among other matters, at a special meeting of stockholders. As a result of the approval of the Series A Conversion Proposal, all conditions that could have required cash redemption of the Series A Preferred Stock were satisfied. Since the Series A Preferred Stock is no longer redeemable, the associated balances of the Series A Preferred Stock were reclassified from mezzanine equity to permanent equity during the fourth quarter of 2023.

Following stockholder approval of the Series A Conversion Proposal, each share of Series A Preferred Stock automatically converted into 40 shares of Common Stock, subject to certain limitations, including that a holder of Series A Preferred Stock is prohibited from converting shares of Series A Preferred Stock into shares of Common Stock if, as a result of such conversion, such holder, together with its affiliates, would beneficially own more than a specified percentage (established by the holder between 0.0% and 19.9%) of the total number of shares of Common Stock issued and outstanding immediately after giving effect to such conversion. 649,302 shares of Series A Preferred Stock automatically converted to 25,972,080 shares of Common Stock; 437,037 shares of Series A Preferred Stock did not automatically convert and remained outstanding following the conversion. This conversion was recorded as a reclassification between Series A Preferred Stock and Common Stock based on the historical per-share contributed capital amount of the Series A Preferred Stock.

On April 23, 2024, in connection with the April 2024 Exchange, the Stockholder agreed to exchange an aggregate of 90,992 shares of Series A Preferred Stock for an aggregate of 3,639,680 shares of the Company's Common Stock. This exchange was recorded as a reclassification between Series A Preferred Stock and Common Stock based on the historical per-share contributed capital amount, inclusive of any forward-contract valuation adjustments, of the Series A Preferred Stock. Following the April 2024 Exchange, 346,045 shares of Series A Preferred Stock remained outstanding.

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Series B Non-Voting Convertible Preferred Stock

On December 8, 2023, the Company filed a Certificate of Designation of Preferences, Rights and Limitations of Series B Non-Voting Convertible Preferred Stock with the Secretary of State of the State of Delaware (the “Series B Certificate of Designation”) in connection with the December 2023 PIPE.

Pursuant to the Series B Certificate of Designation, holders of Series B Preferred Stock are entitled to receive dividends on shares of Series B Preferred Stock equal to, on an as-if-converted-to-Common Stock basis, and in the same form as, dividends actually paid on shares of Common Stock. Except as provided in the Series B Certificate of Designation or as otherwise required by law, the Series B Preferred Stock does not have voting rights. However, as long as any shares of Series B Preferred Stock are outstanding, the Company will not, without the affirmative vote of the holders of a majority of the then outstanding shares of the Series B Preferred Stock, alter or change adversely the powers, preferences or rights given to the Series B Preferred Stock, or alter or amend the Series B Certificate of Designation, amend or repeal any provision of, or add any provision to, the Company’s Certificate of Incorporation or its Bylaws, or file any articles of amendment, certificate of designations, preferences, limitations and relative rights of any series of preferred stock, if such action would adversely alter or change the preferences, rights, privileges or powers of, or restrictions provided for the benefit of the Series B Preferred Stock, regardless of whether any of the foregoing actions will be by means of amendment to the Certificate of Incorporation or by merger, consolidation, recapitalization, reclassification, conversion or otherwise. The Series B Preferred Stock does not have a preference upon any liquidation, dissolution or winding-up of the Company.

On December 11, 2023, as part of the December 2023 PIPE, the Company completed a private placement of 150,000 shares of Series B Preferred Stock in exchange for gross proceeds of $90.0 million.

On March 18, 2024, in connection with the March 2024 PIPE, the Company filed a certificate of amendment to its Series B Certificate of Designation to increase the number of authorized shares of Series B Preferred Stock from 150,000 to 271,625.

On March 20, 2024, as part of the March 2024 PIPE, the Company completed a private placement of 121,625 shares of Series B Preferred Stock in exchange for gross proceeds of approximately $180.0 million.

On May 14, 2024, the Company's stockholders approved the issuance of Common Stock upon the conversion of all issued and outstanding Series B Preferred Stock into shares of Common Stock in accordance with the Nasdaq Stock Market Rules (the "Series B Conversion Proposal"), among other matters, at its 2024 annual meeting of stockholders. As a result of the approval of the Series B Conversion Proposal, all conditions that could have required cash redemption of the Series B Preferred Stock were satisfied. Since the Series B Preferred Stock is no longer redeemable, the associated balances of the Series B Preferred Stock were reclassified from mezzanine equity to permanent equity during the second quarter of 2024.

Following stockholder approval of the Series B Conversion Proposal, each share of Series B Preferred Stock automatically converted into 40 shares of the Common Stock, subject to certain limitations, including that a holder of Series B Preferred Stock is prohibited from converting shares of Series B Preferred Stock into shares of Common Stock if, as a result of such conversion, such holder, together with its affiliates, would beneficially own more than a specified percentage (established by the holder between 0.0% and 19.9%) of the total number of shares of Common Stock issued and outstanding immediately after giving effect to such conversion. 254,958 shares of Series B Preferred Stock automatically converted to 10,198,320 shares of Common Stock; 16,667 shares of Series B Preferred Stock did not automatically convert and remain outstanding as of September 30, 2024 due to beneficial ownership limitations. This conversion was recorded as a reclassification between Series B Preferred Stock and Common Stock based on the historical per-share contributed capital amount of the Series B Preferred Stock.

S-3 Shelf & ATM

On September 6, 2024, the Company filed a new shelf registration statement on Form S-3 that was declared effective by the SEC for the potential offering, issuance and sale by the Company of up to $500.0 million of our common stock, preferred stock, debt securities, warrants and/or units consisting of all or some of these securities. Concurrent with the filing of the shelf-registration statement, the Company entered into

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a sales agreement (the "Sales Agreement") with TD Securities (USA) LLC (“TD Cowen”), as its sales agent, pursuant to which the Company may issue and sell shares of its common stock for an aggregate offering price of up to $200.0 million under an at-the-market (“ATM’) offering program included in the shelf registration. In September 2024, the Company sold 426,287 shares of common stock under the ATM at a price per share of $28.15 resulting in net proceeds of $11.8 million. As of November 1, 2024, $188.0 million remained available for sale under the Sales Agreement.

10. Stock-Based Compensation

2015 Equity Incentive Plan

In March 2015, the Company adopted the 2015 Equity Incentive Plan (“2015 Plan”), administered by the board of directors, and provides for the Company to sell or issue share of Common Stock or restricted Common Stock, or to grant incentive stock options or nonqualified stock options for the purchase of Common Stock, to employees, members of the board of directors and consultants of the Company. The Company granted options under the 2015 Plan until April 2016 when it was terminated as to future awards, although it continues to govern the terms of options that remain outstanding under the 2015 Plan.

As of September 30, 2024, a total of 952 shares of Common Stock are subject to options outstanding under the 2015 Plan and will become available under the 2016 Equity Incentive Plan (“2016 Plan”) to the extent the options are forfeited or lapse unexercised.

2016 Equity Incentive Plan

The 2016 Plan became effective in April 2016 and serves as the successor to the 2015 Plan. Under the 2016 Plan, the Company may grant stock options, stock appreciation rights, restricted stock awards, restricted stock units, performance awards, and stock bonuses. The 2016 Plan, as amended, provides for an automatic increase in the number of shares reserved for issuance thereunder on January 1 of each year for the remaining term of the plan equal to (a) 5.0% of the number of issued and outstanding shares of Common Stock (including such shares issuable pursuant to the exercise or conversion, as applicable, of any outstanding pre-funded warrants and nonvoting convertible preferred stock) on December 31 of the immediately preceding year, or (b) a lesser amount as approved by the board each year (the “Evergreen Provision”). As a result of the Evergreen Provision, on January 1, 2024 and 2023, an additional 3,023,650 and 104,561 shares, respectively, became available for issuance under the 2016 Plan.

As of September 30, 2024, the 2016 Plan had 7,228,113 shares available for future issuance, of which 3,247,677 shares were subject to outstanding option awards.

2018 Equity Inducement Plan

The 2018 Equity Inducement Plan (“2018 Plan”) became effective in February 2018.

During the third quarter of 2024, the Company amended the 2018 Plan to increase the number of shares of Common Stock reserved for issuance by 1,000,000. After this amendment and as of September 30, 2024, the 2018 Plan had 6,999,445 shares available for future issuance, of which 5,624,067 shares were subject to outstanding option awards and restricted unit awards.

Service-based awards granted under the 2018 Plan, 2016 Plan, and 2015 Plan generally vest over four years and expire after ten years, although awards have been granted with vesting terms less than four years. Under the 2016 Plan and 2018 Plan, the Company may grant stock-based awards with service conditions (“service-based” awards), performance conditions (“performance-based” awards), and market conditions (“market-based” awards).

Spyre 2023 Equity Incentive Plan

On June 22, 2023, in connection with the Asset Acquisition, the Company assumed the Amended and Restated Spyre 2023 Equity Incentive Plan and its outstanding and unexercised stock options, which were

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converted to options to purchase 2,734 shares of Common Stock. The acquisition-date fair value of these grants will be recognized as an expense on a pro-rata basis over the vesting period.

The following table summarizes the Company’s stock awards granted under all equity incentive and inducement plans for each of the periods indicated:

	Three Months Ended September 30,						Nine Months Ended September 30,
	2024			2023			2024			2023
	Grants	Weighted Average Grant Date Fair Value		Grants	Weighted Average Grant Date Fair Value		Grants	Weighted Average Grant Date Fair Value		Grants	Weighted Average Grant Date Fair Value
Stock options	425,500	$	25.74	1,044,667	$	14.50	1,857,853	$	28.40	3,867,366	$	9.65

Parapyre Option Obligation

As of September 30, 2024, the pro-rated estimated fair value of the options to be granted on December 31, 2024 related to the Parapyre Option Obligation, was approximately $13.0 million. For the three and nine months ended September 30, 2024, $6.1 million and $13.0 million, respectively, was recognized as stock compensation expense related to the Parapyre Option Obligation. For the three and nine months ended September 30, 2023, $2.7 million and $2.9 million, respectively, was recognized as stock compensation expense related to the Parapyre Option Obligation. As of September 30, 2024, the unamortized expense related to the Parapyre Option Obligation was $4.4 million.

2016 Employee Stock Purchase Plan

Under the Company’s 2016 Employee Stock Purchase Plan (“2016 ESPP”), the Company issued and sold 14,053 and 16,383 shares during the three and nine months ended September 30, 2024, respectively, and sold 704 and 2,496 shares during the three and nine months ended September 30, 2023, respectively. The aggregate cash proceeds were not material for all periods.

Stock-based Compensation Expense

Total stock-based compensation expense recognized from the Company’s equity incentive plans, 2018 Plan, 2016 ESPP and Parapyre Option Obligation during the periods presented was as follows (in thousands):

	Three Months Ended September 30,				Nine Months Ended September 30,
	2024		2023		2024		2023
Research and development (1)	$	8,555	$	2,965	$	18,863	$	4,136
General and administrative	4,545		1,820		16,754		4,269
Total stock-based compensation expense (2)	$	13,100	$	4,785	$	35,617	$	8,405
(1) For the three and nine months ended September 30, 2024, $6.1 million and $13.0 million, respectively, was recognized as stock compensation expense related to the Parapyre Option Obligation. For the three and nine months ended September 30, 2023, $2.7 million and $2.9 million, respectively, was recognized as stock compensation expense related to the Parapyre Option Obligation. (2) Of the total $13.1 million and $35.6 million of stock-based compensation expense for the three and nine months ended September 30, 2024, $0.1 million and $3.6 million, respectively, is related to legacy Aeglea employees and directors who had been terminated as of the end of the respective period. Of the total $4.8 million and $8.4 million of stock-based compensation expense for the three and nine months ended September 30, 2023, $0.8 million and $4.2 million, respectively, is related to legacy Aeglea employees and directors who had been terminated as of the end of the period.

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The following table summarizes the weighted-average Black-Scholes option pricing model assumptions used to estimate the fair value of stock options granted under the Company's equity incentive plans, and the shares purchasable under the 2016 ESPP during the periods presented:

	Three Months Ended September 30,		Nine Months Ended September 30,
	2024	2023	2024	2023
Stock Options Granted
Expected term (in years)	6.08	6.08	6.02	6.04
Expected volatility	105%	101%	105%	111%
Risk-free interest	4.13%	4.28%	4.03%	4.07%
Dividend yield	—	—	—	—
2016 ESPP
Expected term (in years)	0.50	0.50	0.50	0.49
Expected volatility	71%	222%	83%	181%
Risk-free interest	5.02%	5.29%	5.15%	4.99%
Dividend yield	—	—	—	—

11. Legacy Strategic License Agreements

On March 21, 2021, the Company entered into an exclusive license and supply agreement with Immedica (the "Immedica Agreement"). On July 27, 2023, the Company announced that it had entered into an agreement to sell the global rights to pegzilarginase, an investigational treatment for the rare metabolic disease Arginase 1 Deficiency, to Immedica for $15.0 million in upfront cash proceeds and up to $100.0 million in contingent milestone payments. The sale of pegzilarginase to Immedica superseded and terminated the Immedica Agreement.

The milestone payments are contingent on formal reimbursement decisions by national authorities in key European markets and pegzilarginase approval by the FDA, among other events. In addition to the payment previously made to holders of the Company's CVRs (as defined in Note 1) related to the upfront cash proceeds, any contingent milestone payments under the Immedica Agreement, if paid within the CVR period, will be distributed to holders of the Company's CVRs net of expenses and adjustments pursuant to the contingent value rights agreement we entered into with Equiniti Trust Company LLC (f/k/a American Stock Transfer & Trust Company LLC) as rights agent in connection with the Asset Acquisition.

The Company did not recognize any revenue under the Immedica Agreement for the three and nine months ended September 30, 2024. For the nine months ended September 30, 2023, the Company recognized $0.9 million of development fee revenue in connection with the Immedica Agreement, which was attributable to the PEACE Phase 3 trial and BLA package for pegzilarginase. There was no such revenue for the three months ended September 30, 2023.

For more details on the Immedica Agreement, which was terminated on July 27, 2023, please refer to the Note under Item 1 of Part I, titled "12. Strategic License Agreements" of the Company's Annual Report.

Contract Balances from Customer Contract

The timing of revenue recognition, billings and cash collections results in contract assets and contract liabilities on the Company's balance sheets. The Company recognizes license and development receivables based on billed services, which are derecognized upon reimbursement. When consideration is received, or such consideration is unconditionally due, from a customer prior to transferring goods or services to the customer under the terms of a contract, a contract liability is recorded. Contract liabilities are recognized as revenue after control of the goods or services is transferred to the customer and all revenue recognition criteria have been met.

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The Company did not have any contract assets or liabilities as of September 30, 2024 and December 31, 2023.

12. Sale of Pegzilarginase to Immedica

On July 27, 2023, the Company announced that it had entered into an agreement to sell the global rights to pegzilarginase, an investigational treatment for the rare metabolic disease Arginase 1 Deficiency, to Immedica for $15.0 million in upfront cash proceeds and up to $100.0 million in contingent milestone payments. The sale of pegzilarginase to Immedica superseded and terminated the previous license agreement between the Company and Immedica. On July 27, 2023, the carrying value of the asset was zero as it was internally developed. Accordingly the Company recognized a $14.6 million gain within operating expenses, which is the full $15.0 million in upfront cash proceeds, net of transaction costs and the derecognition of pegzilarginase related nonfinancial assets and liabilities.

The milestone payments are contingent on formal reimbursement decisions by national authorities in key European markets and pegzilarginase approval by the FDA, among other events. The upfront payment and contingent milestone payments if paid, net of expenses and adjustments, will be distributed to holders of Aeglea’s CVR pursuant to the CVR Agreement resulting from the Asset Acquisition.

13. Net Loss Per Share (as restated)

Restatement

Subsequent to the filing of its Quarterly Report on Form 10-Q for the period ended September 30, 2024, management identified an error related to the calculation and presentation of loss per share. The Company had previously concluded that the Series A Preferred Stock and Series B Preferred Stock had preferences over the Company's Common Stock and were therefore excluded from the calculation of basic and dilutive net loss per share pursuant to the two-class method. The Company has now determined that the Series A Preferred Stock and Series B Preferred Stock do not have preferential rights over the Company’s Common Stock and, accordingly, are considered to be a second and third class of common stock for purposes of calculating net loss per share. Consequently, the Company has now separately calculated and presented net loss per share for its Common Stock, Series A Preferred Stock and Series B Preferred Stock.

For the three months ended September 30, 2024 and 2023, loss per share attributable to common stockholders as previously presented was $1.36 and $9.34, respectively, and as restated was $1.06 and $0.86, respectively. For the nine months ended September 30, 2024 and 2023, loss per share attributable to common stockholders as previously presented was $3.43 and $69.57, respectively, and as restated was $2.39 and $14.65, respectively. Net loss per share attributable to holders of Series A Preferred Stock and Series B Preferred Stock was not previously presented. All related amounts have been updated to reflect the effects of the restatement throughout the financial statements and related footnotes, as applicable.

The Company computes net loss per share of Common Stock, Series A Preferred Stock, and Series B Preferred Stock using the two-class method required for multiple classes of common stock and other participating securities.

The two-class method is an earnings (loss) allocation method under which earnings (loss) per share is calculated for each class of common stock. The Company has determined that the Series A Preferred Stock and Series B Preferred Stock do not have preferential rights when compared to the Company's Common Stock and therefore it must allocate losses to these other classes of common stock, as illustrated in the table below.

Basic and diluted net loss per share is computed by dividing the net loss by the weighted-average number of shares and pre-funded warrants outstanding during the period, without consideration of potential dilutive securities. The pre-funded warrants are included in the computation of basic net loss per share as the exercise price is negligible and they are fully vested and exercisable. For periods in which the Company generated a net loss, the Company does not include potential shares of common stock in diluted net loss per share when the impact of these items is anti-dilutive. The Company has generated a net loss for all periods presented, therefore diluted net loss per share is the same as basic net loss per share since the inclusion of potential shares of common stock would be anti-dilutive.

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The following table sets forth the computation of basic and diluted net loss per share of Common Stock, Series A Preferred Stock, and Series B Preferred Stock (in thousands, except share and per share amounts):

	Three Months Ended September 30,
	2024						2023
	Series A Preferred Stock		Series B Preferred Stock		Common Stock		Series A Preferred Stock		Series B Preferred Stock		Common Stock
Net loss per share, basic and diluted:
Numerator
Allocation of losses	$	(14,610)	$	(704)	$	(53,714)	$	(36,427)	$	—	$	(3,680)
Denominator
Weighted-average shares outstanding	346,045		16,667		50,889,433		1,062,542		—		4,015,661
Weighted-average pre-funded warrants outstanding	—		—		—		—		—		278,151
Number of shares used in per share computation	346,045		16,667		50,889,433		1,062,542		—		4,293,812
Net loss per share, basic and diluted	$	(42.22)	$	(42.24)	$	(1.06)	$	(34.28)	$	—	$	(0.86)
	Nine Months Ended September 30,
	2024						2023
	Series A Preferred Stock		Series B Preferred Stock		Common Stock		Series A Preferred Stock		Series B Preferred Stock		Common Stock
Net loss per share, basic and diluted:
Numerator
Allocation of losses	$	(36,733)	$	(9,105)	$	(105,884)	$	(217,573)	$	—	$	(58,037)
Denominator
Weighted-average shares outstanding	383,903		95,158		44,146,958		371,286		—		3,116,434
Weighted-average pre-funded warrants outstanding	—		—		116,788		—		—		845,112
Number of shares used in per share computation	383,903		95,158		44,263,746		371,286		—		3,961,546
Net loss per share, basic and diluted	$	(95.68)	$	(95.68)	$	(2.39)	$	(586.00)	$	—	$	(14.65)

The following weighted-average equity instruments were excluded from the calculation of diluted net loss per share because their effect would have been anti-dilutive for the periods presented:

	Three Months Ended September 30,		Nine Months Ended September 30,
	2024	2023	2024	2023
Options to purchase common stock	4,733,609	3,135,672	4,583,260	1,426,224
Unvested restricted stock units	65,925	—	69,503	252
Outstanding Parapyre warrants	684,407	—	684,407	—

14. Restructuring Charges

Severance and Stock Compensation

On April 12, 2023, based on the review of the inconclusive interim results from the Company's Phase 1/2 clinical trial of pegtarviliase for the treatment of classical homocystinuria and other business considerations, the Company announced that it had initiated a process to explore strategic alternatives to maximize stockholder value and engaged an independent exclusive financial advisor to support this process.

As a result, the Company implemented a restructuring plan resulting in an approximate 83% reduction of the Company’s existing headcount by June 30, 2023. The Company recognized restructuring expenses consisting of cash severance payments and other employee-related costs of nil and $6.4 million during the three

27

and nine months ended September 30, 2023, respectively. In addition, the Company recognized $1.0 million in non-cash stock-based compensation expense related to the accelerated vesting of stock-based awards for certain employees. The Company recorded these restructuring charges based on each employee’s role to the respective research and development and general and administrative operating expense categories on its condensed consolidated statements of operations and comprehensive loss.

Sale of Assets

During the second quarter of 2023, the Company sold various lab equipment, consumables, and furniture and fixtures for total consideration of $0.5 million. After recording the disposal of all property and equipment net of proceeds, the Company recorded a $0.7 million and $0.2 million loss on disposal of long lived assets within Research and development and General and administrative expenses, respectively.

Lease Right-of-use Asset and Leasehold Improvement Impairment

Effective June 30, 2023, the Company abandoned its leased office space in Austin, Texas. As a result, the Company recognized an impairment loss of $0.9 million related to the operating lease right-of-use asset and $1.7 million related to leasehold improvements. On August 7, 2023, the Company terminated its building lease in Austin, Texas. The negotiated termination agreement obligated the Company to pay the lessor a $2.0 million termination fee in exchange for releasing the Company of all further obligations under the lease.

All charges related to the restructuring activities were recognized during the second quarter of 2023. No further restructuring charges were incurred under the restructuring plan. A summary of the charges related to the restructuring activities is as follows (in thousands):

	Severance Related Expenses		Stock Compensation Expenses		Loss on Disposal of Long Lived Assets		Lease Asset Impairment		Total Restructuring Costs
Research and development	$	3,182	$	123	$	749	$	1,405	$	5,459
General and administrative	3,266		870		182		1,175		5,493
Total	$	6,448	$	993	$	931	$	2,580	$	10,952

As of December 31, 2023, $1.1 million of restructuring costs remained outstanding and unpaid. As of September 30, 2024, there were no remaining liabilities under the restructuring plan described above.

15. Subsequent Events

On October 1, 2024, the Company appointed Sheldon Sloan, M.D., M. Bioethics, to serve as its Chief Medical Officer.

On October 11, 2024, the Company and Paragon entered into the SPY003 License Agreement, pursuant to which Paragon granted the Company a royalty-bearing, world-wide, exclusive license to develop, manufacture, commercialize or otherwise exploit certain antibodies and products targeting IL-23 in the field of IBD.

Item 4. Controls and Procedures.

Disclosure Controls and Procedures

Our management, with the participation of our principal executive officer and principal financial officer, evaluated, as of the end of the period covered by this Quarterly Report on Form 10-Q, the effectiveness of our disclosure controls and procedures. The term “disclosure controls and procedures,” as defined in Rules 13a-15(e) and 15d-15(e) under the Exchange Act, means controls and other procedures of a company that are designed to ensure that information required to be disclosed by a company in the reports that it files or submits under the Exchange Act is recorded, processed, summarized and reported within the time periods specified in the SEC’s rules and forms. Disclosure controls and procedures include, without limitation, controls and procedures designed to ensure that information required to be disclosed by us in the reports we file or submit

28

under the Exchange Act is accumulated and communicated to our management, including our principal executive officer and principal financial officer, as appropriate to allow timely decisions regarding required disclosure. Management recognizes that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving their objectives and our management necessarily applies its judgment in evaluating the cost-benefit relationship of possible controls and procedures.

At the time the Company filed the Original Filing, our principal executive officer and principal financial officer concluded that the Company’s disclosure controls and procedures were effective at the resaonable assurance level as of September 30, 2024. Subsequent to the Original Filing and solely in connection with this Amendment, our principal executive officer and principal financial officer reevaluated the effectiveness of the Company’s disclosure controls and procedures and identified a material weakness in the Company’s internal control over financial reporting as the Company did not design and maintain effective controls related to the earnings per share calculation. A material weakness is a deficiency, or a combination of deficiencies, in internal control over financial reporting, such that there is a reasonable possibility that a material misstatement of a company’s annual or interim financial statements will not be prevented or detected on a timely basis.

Specifically, subsequent to the Original Filing, our principal executive officer and principal financial officer concluded that our disclosure controls and procedures were not effective as of September 30, 2024 as the Company did not design and maintain effective controls related to the earnings per share calculation, as there was not an effectively designed control in place to evaluate the treatment of the Series A Preferred Stock and the Series B Preferred Stock for the purpose of calculating earnings per share under the two-class method. The material weakness resulted in the restatement of the Company’s previously filed consolidated financial statements as of and for the year ended December 31, 2023, as well as the quarterly condensed consolidated financial information for the 2024 interim periods ended March 31, 2024, June 30, 2024, and September 30, 2024 related to earnings per share. Additionally, the material weakness could result in further misstatements of the earnings per share calculation that would result in a material misstatement to the annual or interim financial statements that would not be prevented or detected.

Notwithstanding the material weakness in internal control over financial reporting, our management, including our principal executive officer and the principal financial officer, have concluded that our consolidated financial statements present fairly, in all material respects, our financial position, results of our operations and our cash flows for the periods presented in this Quarterly Report, in conformity with U.S. GAAP.

Remediation Plan

Our remediation process includes, but is not limited to, enhancing the design of the control relevant to the calculation of net earnings (loss) per share calculations and disclosures to ensure that economic substance beyond the legal form of our capital structure is considered when calculating net earnings (loss) per share. We believe that these actions will remediate the material weakness. The material weakness will not be considered remediated, however, until the applicable controls operate, and management has concluded, through testing, that these controls are operating effectively.

Changes in Internal Control Over Financial Reporting

There were no changes in our internal control over financial reporting during the quarter ended September 30, 2024, that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

29

PART II. – Other Information

Item 6. Exhibits.

The exhibits filed or furnished as part of this Quarterly Report on Form 10-Q are set forth below.

Exhibit Number	Description	Form	File No	Date of Filing	Exhibit No.	Filed Herewith
2.1	Agreement and Plan of Merger, dated June 22, 2023, by and among Aeglea BioTherapeutics, Inc. Aspen Merger Sub I, Inc., Sequoia Merger Sub II, LLC and Spyre Therapeutics, Inc.	S-1	333-276251	12/22/2023	2.1
3.1	Second Amended and Restated Certificate of Incorporation of the Company, effective as of May 14, 2024	8-K	001-37722	05/15/2024	3.2
3.2	Amended and Restated Bylaws	S-1/A	333-276251	02/05/2024	3.2
3.3	Certificate of Designation of Series A Non-Voting Convertible Preferred Stock	S-1	333-276251	12/22/2023	3.3
3.4	Certificate of Designation of Series B Non-Voting Convertible Preferred Stock	S-1	333-276251	12/22/2023	3.4
3.5	Certificate of Amendment to Certificate of Designation of Series B Non-Voting Convertible Preferred Stock	8-K	001-37722	03/18/2024	3.2
10.1#	IL-23 (SPY003) License Agreement, dated October 11, 2024, by and between the Company and Paragon Therapeutics, Inc.	8-K	001-37722	10/15/2024	10.1
10.2#	Amended and Restated Biologics Master Services Agreement, dated October 14, 2024, by and between the Company and WuXi Biologics (Hong Kong) Limited.	8-K	001-37722	10/15/2024	10.2
10.3#	Amended and Restated Cell Line License Agreement, dated October 14, 2024, by and between the Company and WuXi Biologics (Hong Kong) Limited.	8-K	001-37722	10/15/2024	10.3
10.4+*	Fifth Amendment to the Spyre Therapeutics, Inc. 2018 Equity Inducement Plan
10.5+*	Offer Letter, dated September 20, 2024, by and between the Company and Sheldon Sloan
10.6	Sales Agreement, dated September 6, 2024, between Spyre Therapeutics, Inc. and TD Securities (USA) LLC	S-3	333-281975	9/6/2024	1.2
31.1	Certification of the Principal Executive Officer pursuant to Rule 13a-14(a) or 15d-14(a) of the Securities Exchange Act of 1934					X
31.2	Certification of the Principal Financial Officer pursuant to Rule 13a-14(a) or 15d-14(a) of the Securities Exchange Act of 1934					X
32.1(1)	Certification of the Principal Executive Officer and Principal Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002					X
101.INS	Inline XBRL Instance Document – the instance document does not appear in the Interactive Data File because its XBRL tags are embedded within the Inline XBRL document.					X
101.SCH	Inline XBRL Taxonomy Extension Schema Document					X
101.CAL	Inline XBRL Taxonomy Extension Calculation Linkbase Document					X
101.DEF	Inline XBRL Taxonomy Extension Definition Linkbase Document					X
101.LAB	Inline XBRL Taxonomy Extension Label Linkbase Document					X
101.PRE	Inline XBRL Taxonomy Extension Presentation Linkbase Document					X
104	The cover page from this Quarterly Report formatted in Inline XBRL and contained in Exhibit 101

+    Indicates management contract or compensatory plan.

* Previously filed with the Original Filing.

#    Portions of this exhibit have been omitted pursuant to Item 601(b)(10)(iv) of Regulation S-K.

(1)The certifications on Exhibit 32 hereto are deemed furnished and not “filed” for purposes of Section 18 of the Exchange Act or otherwise subject to the liability of that Section. Such certifications will not be deemed incorporated by reference into any filing under the Securities Act or the Exchange Act.

30

Signatures

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized.

Date: November 18, 2024

Spyre Therapeutics, Inc.
By:	/s/ Scott Burrows
	Scott Burrows
	Chief Financial Officer
	(Principal Financial Officer and Principal Accounting Officer)

31

EX-31.1

Exhibit 31.1

Certification of Principal Executive Officer Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002

I, Cameron Turtle, certify that:

1.I have reviewed this Quarterly Report on Form 10-Q/A of Spyre Therapeutics, Inc.;

2.Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3.Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4.The registrant’s other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a.Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b.Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c.Evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d.Disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5.The registrant’s other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

a.All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

b.Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.

Date: November 18, 2024

/s/ Cameron Turtle, D.Phil

Cameron Turtle, D.Phil

Chief Executive Officer

(Principal Executive Officer)

EX-31.2

Exhibit 31.2

Certification of Principal Financial Officer Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002

I, Scott Burrows, certify that:

1.I have reviewed this Quarterly Report on Form 10-Q/A of Spyre Therapeutics, Inc.;

2.Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3.Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4.The registrant’s other certifying officer and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a.Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b.Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c.Evaluated the effectiveness of the registrant’s disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d.Disclosed in this report any change in the registrant’s internal control over financial reporting that occurred during the registrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant’s internal control over financial reporting; and

5.The registrant’s other certifying officer and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant’s auditors and the audit committee of the registrant’s board of directors (or persons performing the equivalent functions):

a.All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant’s ability to record, process, summarize and report financial information; and

b.Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant’s internal control over financial reporting.

Date: November 18, 2024

/s/ Scott Burrows

Scott Burrows

Chief Financial Officer

(Principal Financial Officer and Principal Accounting Officer)

EX-32.1

Exhibit 32.1

Certifications of the

Principal Executive Officer and Principal Financial Officer

Pursuant To 18 U.S.C. Section 1350,

As Adopted Pursuant To

Section 906 of The Sarbanes-Oxley Act Of 2002

In connection with the Quarterly Report of Spyre Therapeutics, Inc. (the “Company”) on Form 10-Q/A for the quarterly period ended September 30, 2024, as filed with the Securities and Exchange Commission on the date hereof (the “Report”), each of the undersigned officers of the Company hereby certifies, pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, that to the best of his knowledge:

1)The Report fully complies with the requirements of Section 13(a) or 15(d) of the Securities Exchange Act of 1934; and

2)The information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company.

Date: November 18, 2024	/s/ Cameron Turtle, D.Phil
	Cameron Turtle, D.Phil
	Chief Executive Officer
	(Principal Executive Officer)
	/s/ Scott Burrows
	Scott Burrows
	Chief Financial Officer
	(Principal Financial Officer and Principal Accounting Officer)

XML

Cover Page - shares	9 Months Ended
	Sep. 30, 2024	Nov. 01, 2024
Cover [Abstract]
Document Type	10-Q/A
Document Quarterly Report	true
Document Period End Date	Sep. 30, 2024
Document Transition Report	false
Entity File Number	001-37722
Entity Registrant Name	SPYRE THERAPEUTICS, INC.
Entity Incorporation, State or Country Code	DE
Entity Tax Identification Number	46-4312787
Entity Address, Address Line One	221 Crescent Street
Entity Address, Address Line Two	Building 23
Entity Address, Address Line Three	Suite 105
Entity Address, City or Town	Waltham
Entity Address, State or Province	MA
Entity Address, Postal Zip Code	02453
City Area Code	617
Local Phone Number	651-5940
Title of 12(b) Security	Common Stock, $0.0001 Par Value Per Share
Trading Symbol	SYRE
Security Exchange Name	NASDAQ
Entity Interactive Data Current	Yes
Entity Current Reporting Status	Yes
Entity Filer Category	Non-accelerated Filer
Entity Small Business	true
Entity Emerging Growth Company	false
Entity Shell Company	false
Entity Common Stock, Shares Outstanding		51,431,220
Amendment Description	This Amendment No. 1 on Form 10-Q/A (this “Amendment”) amends the Quarterly Report on Form 10-Q of Spyre Therapeutics, Inc. (the “Company”) for the period ended September 30, 2024, as filed with the Securities and Exchange Commission on November 7, 2024 (the “Original Filing”).Subsequent to the filing of its Form 10-Q for the three and nine months ended September 30, 2024, the Company became aware of a misapplication of Generally Accepted Accounting Principles in the United States ("U.S. GAAP") as it relates to the Company's exclusion of its Series A non-voting convertible preferred stock and Series B non-voting convertible preferred stock in the calculation of basic and diluted net loss per share and a finding of a material weakness in internal control over financial reporting solely related to such matter. This Amendment is being filed for the sole purpose of amending certain disclosures from the Original Filing related to the aforementioned misapplication of U.S. GAAP and related finding of material weakness in internal control over financial reporting.Specifically, this Amendment amends: (i) Part I, Item 1. “Financial Information (unaudited)” to update the Company's Consolidated Statement of Operations and related footnote disclosures for the three and nine months ended September 30, 2024, (ii) Part I, Item 4. "Controls and Procedures" to address management's re-evaluation of disclosure controls and procedures as of September 30, 2024 and to reflect the identification of a material weakness in our internal control over financial reporting and (iii) Part II, Item 6. "Exhibits" to include, in accordance with Rule 12b-15 under the Securities Exchange Act of 1934, as amended (the “Exchange Act”), updated certifications from our Chief Executive Officer and Chief Financial Officer as required by Sections 302 and 906 of the Sarbanes-Oxley Act of 2002 as Exhibits 31.1, 31.2 and 32.1. In accordance with Rule 12b-15 under the Exchange Act, this Amendment amends and restates in their entirety each item identified in the paragraph above.Other than as described above, this Amendment does not amend, update or change any other items or disclosures contained in the Original Filing, and accordingly, all other information contained in this Amendment is as of the date of the original filing and does not reflect subsequent information or events beyond the original filing date, November 7, 2024. Accordingly, this Amendment should be read in conjunction with other filings made with the SEC subsequent to the filing of the Original Filing, including any amendments to those filings. Capitalized terms used but not defined herein shall have the meanings ascribed to such terms in the Original Filing.
Entity Central Index Key	0001636282
Current Fiscal Year End Date	--12-31
Amendment Flag	true
Document Fiscal Year Focus	2024
Document Fiscal Period Focus	Q3

XML

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Sep. 30, 2024	Dec. 31, 2023
CURRENT ASSETS
Cash and cash equivalents	$ 71,580	$ 188,893
Marketable securities	342,647	150,384
Prepaid expenses and other current assets	6,852	2,251
Total current assets	421,079	341,528
Restricted cash	0	322
Other non-current assets	10	9
TOTAL ASSETS	421,089	341,859
CURRENT LIABILITIES
Accounts payable	5,165	896
CVR liability	24,740	1,390
Accrued and other current liabilities	13,153	13,108
Total current liabilities	57,539	31,978
Non-current CVR liability	36,160	41,310
TOTAL LIABILITIES	93,699	73,288
Commitments and Contingencies (Note 7 and 8)
STOCKHOLDERS’ EQUITY
Common stock, $0.0001 par value; 400,000,000 shares authorized as of September 30, 2024 and December 31, 2023; 51,395,608 shares and 36,057,109 shares issued and outstanding as of September 30, 2024 and December 31, 2023, respectively.	12	10
Additional paid-in capital	1,086,237	763,191
Accumulated other comprehensive income	1,457	302
Accumulated deficit	(916,136)	(764,414)
TOTAL STOCKHOLDERS’ EQUITY	327,390	184,016
TOTAL LIABILITIES, CONVERTIBLE PREFERRED STOCK AND STOCKHOLDERS’ EQUITY	421,089	341,859
Series B Non Voting Convertible Preferred Stock
CURRENT LIABILITIES
Series B non-voting convertible preferred stock, $0.0001 par value; 150,000 shares authorized, issued, and outstanding as of December 31, 2023.	0	84,555
STOCKHOLDERS’ EQUITY
Series A non-voting convertible preferred stock & preferred stock shares authorized, issued, and outstanding, value	$ 9,395	0
Preferred stock, authorized (in shares)	271,625
Preferred stock, issued (in shares)	16,667
Preferred stock, outstanding (in shares)	16,667
Series A Non Voting Convertible Preferred Stock
STOCKHOLDERS’ EQUITY
Series A non-voting convertible preferred stock & preferred stock shares authorized, issued, and outstanding, value	$ 146,425	$ 184,927
Preferred stock, authorized (in shares)	1,086,341	1,086,341
Preferred stock, issued (in shares)	346,045	437,037
Preferred stock, outstanding (in shares)	346,045	437,037
Preferred Stock, Excluding Series A Non Voting Convertible Preferred Stock
STOCKHOLDERS’ EQUITY
Series A non-voting convertible preferred stock & preferred stock shares authorized, issued, and outstanding, value	$ 0	$ 0
Preferred stock, authorized (in shares)	8,642,034	8,763,659
Preferred stock, issued (in shares)	0	0
Preferred stock, outstanding (in shares)	0	0
Related Party
CURRENT LIABILITIES
Related party accounts payable and other current liabilities	$ 14,481	$ 16,584

XML

Condensed Consolidated Balance Sheets (Parenthetical) - $ / shares	Sep. 30, 2024	Dec. 31, 2023
Stockholders' Equity, Number of Shares, Par Value and Other Disclosure [Abstract]
Common stock, par value (in dollars per share)	$ 0.0001	$ 0.0001
Common stock, authorized (in shares)	400,000,000	400,000,000
Common stock, issued (in shares)	51,395,608	36,057,109
Common stock, outstanding (in shares)	51,395,608	36,057,109
Series B Non Voting Convertible Preferred Stock
Temporary Equity [Abstract]
Series B non-voting convertible preferred stock, par value (in dollars per share)		$ 0.0001
Series B non-voting convertible preferred stock, authorized (in shares)		150,000
Series B non-voting convertible preferred stock, issued (in shares)		150,000
Series B non-voting convertible preferred stock, outstanding (in shares)		150,000
Stockholders' Equity, Number of Shares, Par Value and Other Disclosure [Abstract]
Preferred stock, par value (in dollars per share)	$ 0.0001
Preferred stock, authorized (in shares)	271,625
Preferred stock, issued (in shares)	16,667
Preferred stock, outstanding (in shares)	16,667
Series A Non Voting Convertible Preferred Stock
Stockholders' Equity, Number of Shares, Par Value and Other Disclosure [Abstract]
Preferred stock, par value (in dollars per share)	$ 0.0001	$ 0.0001
Preferred stock, authorized (in shares)	1,086,341	1,086,341
Preferred stock, issued (in shares)	346,045	437,037
Preferred stock, outstanding (in shares)	346,045	437,037
Preferred Stock, Excluding Series A Non Voting Convertible Preferred Stock
Stockholders' Equity, Number of Shares, Par Value and Other Disclosure [Abstract]
Preferred stock, par value (in dollars per share)	$ 0.0001	$ 0.0001
Preferred stock, authorized (in shares)	8,642,034	8,763,659
Preferred stock, issued (in shares)	0	0
Preferred stock, outstanding (in shares)	0	0

XML

Condensed Consolidated Statements of Operations - USD ($) $ in Thousands		3 Months Ended		9 Months Ended
		Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Revenue:
Total revenue		$ 0	$ 0	$ 0	$ 886
Operating expenses:
Research and development	[1]	44,744	24,660	112,308	55,822
General and administrative		10,648	8,584	35,005	25,874
Acquired in-process research and development		0	(298)	0	130,188
Gain on sale of in-process research and development asset		0	(14,609)	0	(14,609)
Total operating expenses		55,392	18,337	147,313	197,275
Loss from operations		(55,392)	(18,337)	(147,313)	(196,389)
Other (expense) income:
Interest income		5,184	1,251	15,536	2,021
Other (expense) income, net		(18,802)	2,342	(19,895)	2,262
Total other (expense) income		(13,618)	(21,767)	(4,359)	(79,247)
Loss before income tax expense		(69,010)	(40,104)	(151,672)	(275,636)
Income tax (expense) benefit		(18)	(3)	(50)	26
Net loss		$ (69,028)	$ (40,107)	$ (151,722)	$ (275,610)
Net loss per share, basic (in dollars per share)		$ 1.06	$ 0.86	$ 2.39	$ 14.65
Net loss per share, diluted (in dollars per share)		$ 1.06	$ 0.86	$ 2.39	$ 14.65
Weighted-average common shares outstanding, basic (in shares)		50,889,433	4,293,812	44,263,746	3,961,546
Weighted-average common shares outstanding, diluted (in shares)		50,889,433	4,293,812	44,263,746	3,961,546
Series A Preferred Stock
Other (expense) income:
Net loss		$ (14,610)	$ (36,427)	$ (36,733)	$ (217,573)
Net loss per share, basic (in dollars per share)		$ (42.22)	$ (34.28)	$ (95.68)	$ (586.00)
Net loss per share, diluted (in dollars per share)		$ (42.22)	$ (34.28)	$ (95.68)	$ (586.00)
Weighted-average common shares outstanding, basic (in shares)		346,045	1,062,542	383,903	371,286
Weighted-average common shares outstanding, diluted (in shares)		346,045	1,062,542	383,903	371,286
Series B Preferred Stock
Other (expense) income:
Net loss		$ (704)	$ 0	$ (9,105)	$ 0
Net loss per share, basic (in dollars per share)		$ (42.24)	$ 0	$ (95.68)	$ 0
Net loss per share, diluted (in dollars per share)		$ (42.24)	$ 0	$ (95.68)	$ 0
Weighted-average common shares outstanding, basic (in shares)		16,667	0	95,158	0
Weighted-average common shares outstanding, diluted (in shares)		16,667	0	95,158	0
Common Stock
Other (expense) income:
Net loss		$ (53,714)	$ (3,680)	$ (105,884)	$ (58,037)
Net loss per share, basic (in dollars per share)		$ (1.06)	$ (0.86)	$ (2.39)	$ (14.65)
Net loss per share, diluted (in dollars per share)		$ (1.06)	$ (0.86)	$ (2.39)	$ (14.65)
Weighted-average common shares outstanding, basic (in shares)		50,889,433	4,015,661	44,146,958	3,116,434
Weighted-average common shares outstanding, diluted (in shares)		50,889,433	4,293,812	44,263,746	3,961,546
Forward contract liability
Other (expense) income:
Change in fair value of forward contract liability		$ 0	$ (25,360)	$ 0	$ (83,530)
Development fee and royalty
Revenue:
Total revenue		$ 0	$ 0	$ 0	$ 886

[1] Includes $7.7 million and $34.2 million in related party expenses for the three and nine months ended September 30, 2024, respectively, and $19.4 million and $20.8 million related party expenses for the three and nine months ended September 30, 2023, respectively.

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Condensed Consolidated Statements of Operations (Parenthetical) - USD ($) $ in Thousands		3 Months Ended		9 Months Ended
		Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Research and development	[1]	$ 44,744	$ 24,660	$ 112,308	$ 55,822
Related Party
Research and development		$ 7,700	$ 19,400	$ 34,200	$ 20,800

[1] Includes $7.7 million and $34.2 million in related party expenses for the three and nine months ended September 30, 2024, respectively, and $19.4 million and $20.8 million related party expenses for the three and nine months ended September 30, 2023, respectively.

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Condensed Consolidated Statements of Comprehensive Loss - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Statement of Comprehensive Income [Abstract]
Net loss	$ (69,028)	$ (40,107)	$ (151,722)	$ (275,610)
Other comprehensive income (loss):
Foreign currency translation adjustment	17	(29)	37	(1)
Unrealized gain (loss) on marketable securities	1,993	(114)	1,118	(83)
Total comprehensive loss	$ (67,018)	$ (40,250)	$ (150,567)	$ (275,694)

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Condensed Consolidated Statements of Changes in Convertible Preferred Stock and Stockholders' Equity - USD ($) $ in Thousands	Total	Series A Non Voting Convertible Preferred Stock	Series B Non Voting Convertible Preferred Stock	Preferred Stock Series A Non Voting Convertible Preferred Stock	Preferred Stock Series B Non Voting Convertible Preferred Stock	Common Stock	Additional Paid-In Capital	Accumulated Other Comprehensive Income (Loss)	Accumulated Deficit
Beginning balance (in shares) at Dec. 31, 2022				0
Beginning balance at Dec. 31, 2022				$ 0
Ending balance (in shares) at Mar. 31, 2023				0
Ending balance at Mar. 31, 2023				$ 0
Beginning balance, common stock (in shares) at Dec. 31, 2022						2,614,000
Beginning balance at Dec. 31, 2022	$ 50,305					$ 6	$ 475,971	$ (48)	$ (425,624)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Issuance of common stock in connection with employee stock purchase plan (in shares)						2,000
Issuance of common stock in connection with employee stock purchase plan	18						18
Stock-based compensation expense	1,709						1,709
Foreign currency translation adjustment	10							10
Unrealized gain (loss) on marketable securities	32							32
Net loss	(18,422)								(18,422)
Ending balance, common stock (in shares) at Mar. 31, 2023						2,616,000
Ending balance at Mar. 31, 2023	33,652					$ 6	477,698	(6)	(444,046)
Beginning balance (in shares) at Dec. 31, 2022				0
Beginning balance at Dec. 31, 2022				$ 0
Ending balance (in shares) at Sep. 30, 2023				1,086,000
Ending balance at Sep. 30, 2023				$ 387,105
Beginning balance, common stock (in shares) at Dec. 31, 2022						2,614,000
Beginning balance at Dec. 31, 2022	50,305					$ 6	475,971	(48)	(425,624)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Foreign currency translation adjustment	(1)
Unrealized gain (loss) on marketable securities	(83)
Net loss	(275,610)
Ending balance, common stock (in shares) at Sep. 30, 2023						4,049,000
Ending balance at Sep. 30, 2023	(245,402)					$ 7	455,957	(132)	(701,234)
Beginning balance (in shares) at Mar. 31, 2023				0
Beginning balance at Mar. 31, 2023				$ 0
Increase (Decrease) in Temporary Equity [Roll Forward]
Issuance of Series A/B non-voting convertible preferred stock in connection with private placement, net of financing costs (in shares)				721,000
Issuance of Series A/B non-voting convertible preferred stock in connection with private placement, net of financing costs				$ 197,323
Ending balance (in shares) at Jun. 30, 2023				721,000
Ending balance at Jun. 30, 2023				$ 197,323
Beginning balance, common stock (in shares) at Mar. 31, 2023						2,616,000
Beginning balance at Mar. 31, 2023	33,652					$ 6	477,698	(6)	(444,046)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Issuance of common stock forward in connection with the asset acquisition of Spyre	3,768						3,768
Issuance of common stock in connection with exercise of pre-funded warrants (in shares)						624,000
CVR distribution to common stockholders	(29,500)						(29,500)
Stock-based compensation expense	1,775						1,775
Foreign currency translation adjustment	18							18
Unrealized gain (loss) on marketable securities	(1)							(1)
Net loss	(217,081)								(217,081)
Ending balance, common stock (in shares) at Jun. 30, 2023						3,240,000
Ending balance at Jun. 30, 2023	(207,369)					$ 6	453,741	11	(661,127)
Increase (Decrease) in Temporary Equity [Roll Forward]
Issuance of Series A non-voting convertible preferred stock in connection with the asset acquisition of Spyre and settlement of related forward contract (in shares)				365,000
Issuance of Series A non-voting convertible preferred stock in connection with the asset acquisition of Spyre and settlement of related forward contract				$ 189,741
Settlement of financing costs in connection with private placement of Series A non-voting convertible preferred stock				$ 41
Ending balance (in shares) at Sep. 30, 2023				1,086,000
Ending balance at Sep. 30, 2023				$ 387,105
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Issuance of common stock in connection with exercise of stock options and employee stock purchase plan (in shares)						10,000
Issuance of common stock in connection with exercise of stock options and employee stock purchase plan	105						105
Issuance of common stock in connection with exercise of pre-funded warrants (in shares)						281,000
Issuance of common stock in connection with the asset acquisition of Spyre and settlement of related forward contract (in shares)						518,000
Issuance of common stock in connection with the asset acquisition of Spyre and settlement of related forward contract	0					$ 1	(1)
Stock-based compensation expense	2,112						2,112
Foreign currency translation adjustment	(29)							(29)
Unrealized gain (loss) on marketable securities	(114)							(114)
Net loss	(40,107)								(40,107)
Ending balance, common stock (in shares) at Sep. 30, 2023						4,049,000
Ending balance at Sep. 30, 2023	(245,402)					$ 7	455,957	(132)	(701,234)
Beginning balance (in shares) at Dec. 31, 2023			150,000		150,000
Beginning balance at Dec. 31, 2023			$ 84,555		$ 84,555
Increase (Decrease) in Temporary Equity [Roll Forward]
Issuance of Series A/B non-voting convertible preferred stock in connection with private placement, net of financing costs (in shares)					122,000
Issuance of Series A/B non-voting convertible preferred stock in connection with private placement, net of financing costs					$ 168,850
Ending balance (in shares) at Mar. 31, 2024					272,000
Ending balance at Mar. 31, 2024					$ 253,405
Beginning balance, preferred stock (in shares) at Dec. 31, 2023		437,037		437,000	0
Beginning balance, common stock (in shares) at Dec. 31, 2023						36,057,000
Beginning balance at Dec. 31, 2023	184,016			$ 184,927	$ 0	$ 10	763,191	302	(764,414)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Issuance of common stock in connection with exercise of stock options and employee stock purchase plan (in shares)						572,000
Issuance of common stock in connection with exercise of stock options and employee stock purchase plan	4,390						4,390
Stock-based compensation expense	8,385						8,385
Foreign currency translation adjustment	16							16
Unrealized gain (loss) on marketable securities	(681)							(681)
Net loss	(43,857)								(43,857)
Ending balance, preferred stock (in shares) at Mar. 31, 2024				437,000	0
Ending balance, common stock (in shares) at Mar. 31, 2024						36,629,000
Ending balance at Mar. 31, 2024	152,269			$ 184,927	$ 0	$ 10	775,966	(363)	(808,271)
Beginning balance (in shares) at Dec. 31, 2023			150,000		150,000
Beginning balance at Dec. 31, 2023			$ 84,555		$ 84,555
Ending balance (in shares) at Sep. 30, 2024					0
Ending balance at Sep. 30, 2024			$ 0		$ 0
Beginning balance, preferred stock (in shares) at Dec. 31, 2023		437,037		437,000	0
Beginning balance, common stock (in shares) at Dec. 31, 2023						36,057,000
Beginning balance at Dec. 31, 2023	184,016			$ 184,927	$ 0	$ 10	763,191	302	(764,414)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Foreign currency translation adjustment	37
Unrealized gain (loss) on marketable securities	1,118
Net loss	(151,722)
Ending balance, preferred stock (in shares) at Sep. 30, 2024		346,045	16,667	346,000	17,000
Ending balance, common stock (in shares) at Sep. 30, 2024						51,396,000
Ending balance at Sep. 30, 2024	327,390			$ 146,425	$ 9,395	$ 12	1,086,237	1,457	(916,136)
Beginning balance (in shares) at Mar. 31, 2024					272,000
Beginning balance at Mar. 31, 2024					$ 253,405
Increase (Decrease) in Temporary Equity [Roll Forward]
Stockholder approval of the issuance of Common Stock upon conversion of Series B convertible non-voting preferred stock (in shares)					(272,000)
Stockholder approval of the issuance of Common Stock upon conversion of Series B convertible non-voting preferred stock					$ (253,405)
Ending balance (in shares) at Jun. 30, 2024					0
Ending balance at Jun. 30, 2024					$ 0
Beginning balance, preferred stock (in shares) at Mar. 31, 2024				437,000	0
Beginning balance, common stock (in shares) at Mar. 31, 2024						36,629,000
Beginning balance at Mar. 31, 2024	152,269			$ 184,927	$ 0	$ 10	775,966	(363)	(808,271)
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Shareholder approval of conversion of Series B Convertible Non-Voting Preferred Stock to Common Stock (in shares)					272,000
Stockholder approval of the issuance of Common Stock upon conversion of Series B convertible non-voting preferred stock	253,405				$ 253,405
Issuance of common stock in connection with exercise of stock options and employee stock purchase plan (in shares)						66,000
Issuance of common stock in connection with exercise of stock options and employee stock purchase plan	494						494
Conversion of Series B non-voting convertible preferred stock into common stock (in shares)					(255,000)	10,198,000
Conversion of Series B non-voting convertible preferred stock into common stock	0				$ (244,010)	$ 1	244,009
Exchange of Series A non-voting convertible preferred stock into common stock (in shares)				(91,000)		3,640,000
Exchange of Series A non-voting convertible preferred stock for common stock	0			$ (38,502)		$ 1	38,501
Issuance of common stock in connection with exercise of pre-funded warrants (in shares)						250,000
Issuance of common stock in connection with exercise of pre-funded warrants	1						1
Stock-based compensation expense	7,243						7,243
Foreign currency translation adjustment	4							4
Unrealized gain (loss) on marketable securities	(194)							(194)
Net loss	(38,837)								(38,837)
Ending balance, preferred stock (in shares) at Jun. 30, 2024				346,000	17,000
Ending balance, common stock (in shares) at Jun. 30, 2024						50,783,000
Ending balance at Jun. 30, 2024	374,385			$ 146,425	$ 9,395	$ 12	1,066,214	(553)	(847,108)
Ending balance (in shares) at Sep. 30, 2024					0
Ending balance at Sep. 30, 2024			$ 0		$ 0
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Issuance of common stock in connection with exercise of stock options and employee stock purchase plan (in shares)						153,000
Issuance of common stock in connection with exercise of stock options and employee stock purchase plan	1,318						1,318
Issuance of common stock in connection with at-the-market offerings, net of offering costs (in shares)						426,000
Issuance of common stock in connection with at-the-market offerings, net of offering costs	11,750						11,750
Vesting of restricted stock units (in shares)						34,000
Stock-based compensation expense	6,955						6,955
Foreign currency translation adjustment	17							17
Unrealized gain (loss) on marketable securities	1,993							1,993
Net loss	(69,028)								(69,028)
Ending balance, preferred stock (in shares) at Sep. 30, 2024		346,045	16,667	346,000	17,000
Ending balance, common stock (in shares) at Sep. 30, 2024						51,396,000
Ending balance at Sep. 30, 2024	$ 327,390			$ 146,425	$ 9,395	$ 12	$ 1,086,237	$ 1,457	$ (916,136)

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Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023
CASH FLOWS FROM OPERATING ACTIVITIES
Net loss	$ (151,722)	$ (275,610)
Adjustments to reconcile net loss to net cash used in operating activities:
Stock-based compensation	35,617	8,405
Acquired in-process research and development	0	130,188
Gain on sale of in-process research and development asset	0	(14,609)
Lease ROU asset and leasehold improvement impairment loss	0	2,580
Loss on disposal of long-lived assets	0	915
Net accretion of discount on marketable securities	(8,985)	(612)
Interest proceeds from maturities of zero coupon US Treasury Bills	581	0
Depreciation and amortization	0	744
Amortization of operating lease assets	0	220
Other	0	18
Changes in operating assets and liabilities:
Accounts payable	4,268	1,001
Accrued and other liabilities	(257)	(4,000)
Related party accounts payable	(15,138)	(2,115)
Prepaid expenses and other assets	(4,205)	3,310
Deferred revenue	0	575
Development receivables	0	212
Operating lease liabilities	0	(2,326)
Net cash used in operating activities	(120,211)	(68,874)
CASH FLOWS FROM INVESTING ACTIVITIES
Proceeds from maturities and sales of marketable securities	183,419	21,000
Purchases of marketable securities	(366,160)	(112,631)
Cash assumed from asset acquisition of Spyre	0	3,035
Proceeds from sale of in-process research & development asset	0	15,000
Proceeds from sale of property and equipment	0	475
Net cash used in investing activities	(182,741)	(73,121)
CASH FLOWS FROM FINANCING ACTIVITIES
Proceeds from issuance of common stock in connection with at-the-market offerings, net of issuance costs	11,760	0
Payment of deferred offering costs in connection with shelf registration	(78)
Payments related to contingent value rights liability	(1,430)	0
Proceeds from employee stock option exercises, employee stock plan purchases, and exercise of prefunded warrants	6,203	123
Principal payments on finance lease obligation	0	(16)
Net cash provided by financing activities	185,305	197,471
Effect of exchange rate on cash, cash equivalents, and restricted cash	12	7
NET (DECREASE) INCREASE IN CASH, CASH EQUIVALENTS, AND RESTRICTED CASH	(117,635)	55,483
CASH, CASH EQUIVALENTS, AND RESTRICTED CASH
Beginning of period	189,215	36,416
End of period	71,580	91,899
Supplemental Disclosure of Non-Cash Investing and Financing Information:
Exchange of Series A non-voting convertible preferred stock for common stock	38,502	0
Conversion of Series B non-voting convertible preferred stock into common stock	244,010	0
Allocation of deferred offering costs against proceeds of issuance of common stock	10	0
Reconciliation of Cash, Cash Equivalents, and Restricted Cash Reported in the Statement of Financial Position
Cash and cash equivalents	71,580	90,592
Restricted cash	0	1,307
Total cash, cash equivalents, and restricted cash shown in the statement of cash flows	71,580	91,899
Series B Non Voting Convertible Preferred Stock
CASH FLOWS FROM FINANCING ACTIVITIES
Proceeds from issuance of Series A/B non-voting convertible preferred stock in connection with private placement	168,850	0
Series A Non Voting Convertible Preferred Stock
CASH FLOWS FROM FINANCING ACTIVITIES
Proceeds from issuance of Series A/B non-voting convertible preferred stock in connection with private placement	0	197,364
Supplemental Disclosure of Non-Cash Investing and Financing Information:
Unpaid amounts related to issuance of common stock in connection with at-the-market offerings, net of offering costs	329	0
CVR liability
Adjustments to reconcile net loss to net cash used in operating activities:
Change in fair value of derivative liability	19,630	(1,300)
Forward contract liability
Adjustments to reconcile net loss to net cash used in operating activities:
Change in fair value of derivative liability	$ 0	$ 83,530

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The Company and Basis of Presentation

9 Months Ended

Sep. 30, 2024

Organization, Consolidation and Presentation of Financial Statements [Abstract]

The Company and Basis of Presentation

The Company and Basis of Presentation

Spyre Therapeutics, Inc., formerly Aeglea BioTherapeutics, Inc. (“Spyre” or the “Company”), is a clinical stage biotechnology company focused on developing next generation therapeutics for patients living with inflammatory bowel disease. The Company was formed as a Limited Liability Company ("LLC") in Delaware on December 16, 2013 under the name Aeglea BioTherapeutics Holdings, LLC and was converted from a Delaware LLC to a Delaware corporation on March 10, 2015. On November 27, 2023, the Company completed its corporate rebranding, changing the name of the Company to Spyre Therapeutics, Inc. The Company operates in one segment and has its principal offices in Waltham, Massachusetts.

On September 8, 2023, the Company effected a reverse stock split of its Common Stock at a ratio of 1-for-25 (the “Reverse Split”). Except as indicated otherwise, all share numbers related to the Company's Common Stock disclosed in these financial statements have been adjusted on a post-Reverse Split basis.

On April 12, 2023, based on the review of the inconclusive interim results from the Company's Phase 1/2 clinical trial of pegtarviliase for the treatment of Classical Homocystinuria and other business considerations, the Company announced that it had initiated a process to explore strategic alternatives to maximize stockholder value and engaged an independent exclusive financial advisor to support this process. As a result, in April 2023, the Company implemented a restructuring plan resulting in an approximate 83% reduction of the Company’s existing headcount.

On June 22, 2023, the Company acquired, in accordance with the terms of the Agreement and Plan of Merger (the "Acquisition Agreement"), the assets of Spyre Therapeutics, Inc. (“Pre-Merger Spyre”), a privately held biotechnology company advancing a pipeline of antibody therapeutics with the potential to transform the treatment of inflammatory bowel disease through a research and development option agreement ("Paragon Agreement") with Paragon Therapeutics, Inc. ("Paragon"). The asset acquisition was accomplished through a two-step reverse triangular merger whereby a wholly owned subsidiary of the Company merged with and into Pre-Merger Spyre, which existed at the time the Acquisition Agreement was entered into, and became a wholly owned subsidiary of the Company in accordance with the terms of the Acquisition Agreement. Immediately following this merger, Pre-Merger Spyre merged with and into a second wholly owned subsidiary of the Company (“Merger Sub”) in accordance with the terms of the Acquisition Agreement and Pre-Merger Spyre ceased to exist. Subsequently, Aeglea BioTherapeutics, Inc. was renamed Spyre Therapeutics, Inc. and is a different entity than Pre-Merger Spyre, which ceased to exist upon merging with Merger Sub. The transaction was structured as a stock-for-stock transaction pursuant to which all of Pre-Merger Spyre's outstanding equity interests were exchanged based on a fixed exchange ratio of 0.5494488 to 1 for consideration from the Company of 517,809 shares of common stock, par value of $0.0001 per share ("Common Stock"), and 364,887 shares of Series A non-voting convertible preferred stock, par value of $0.0001 per share ("Series A Preferred Stock") (convertible on a 40 to 1 basis), in addition to the assumption of outstanding and unexercised stock options to purchase 2,734 shares of Common Stock from the Amended and Restated Spyre 2023 Equity Incentive Plan (the "Asset Acquisition"). The Common Stock and Series A Preferred Stock related to the Asset Acquisition were issued to the Pre-Merger Spyre stockholders on July 7, 2023.

In connection with the Asset Acquisition, on June 26, 2023, the Company completed a private placement of shares of Series A Preferred Stock (the “June 2023 PIPE”) to a group of investors (the “June 2023 Investors”). The Company sold an aggregate of 721,452 shares of Series A Preferred Stock for an aggregate purchase price of approximately $210.0 million before deducting approximately $12.7 million in placement agent and other offering expenses (together with the Asset Acquisition, the “Transactions”).

In connection with the Asset Acquisition, a non-transferable contingent value right ("CVR") was distributed to stockholders of record of the Company as of the close of business on July 3, 2023 (the "Legacy Stockholders"), but was not distributed to the holders of shares of Common Stock or Series A Preferred Stock issued to the former stockholders of Pre-Merger Spyre or the June 2023 Investors in the Transactions. Holders of the CVRs will be entitled to receive cash payments from proceeds received by the Company for a three-year

period related to the disposition or monetization of its legacy assets for a period of one-year following the closing of the Asset Acquisition.

On November 21, 2023, the Company's stockholders approved the issuance of Common Stock upon conversion of the Company's Series A Preferred Stock to Common Stock. A total of 649,302 shares of Series A Preferred Stock automatically converted to 25,972,080 shares of Common Stock; 437,037 shares of Series A Preferred Stock did not automatically convert and remained outstanding after the conversion.

On December 11, 2023, the Company completed a private placement of shares of Common Stock and Series B non-voting convertible preferred stock, par value of $0.0001 per share ("Series B Preferred Stock") (convertible on a 40 to 1 basis) (the “December 2023 PIPE”) to a group of investors. The Company sold an aggregate of 6,000,000 shares of Common Stock and 150,000 shares of Series B Preferred Stock for an aggregate purchase price of approximately $180.0 million before deducting approximately $10.9 million of placement agent and other offering expenses.

On March 20, 2024, the Company completed a private placement of Series B Preferred Stock (convertible on a 40 to 1 basis) (the “March 2024 PIPE”) to a group of investors. The Company sold 121,625 shares of Series B Preferred Stock for a purchase price of $180.0 million before deducting approximately $11.2 million of placement agent and other offering costs.

On April 23, 2024, the Company entered into an exchange agreement with Fairmount Healthcare Fund II L.P. (the “Stockholder”), pursuant to which the Stockholder agreed to exchange an aggregate of 90,992 shares of Series A Preferred Stock for an aggregate of 3,639,680 shares of Common Stock (the “April 2024 Exchange”). The Common Stock issued in connection with the April 2024 Exchange was issued without registration under the Securities Act of 1933, as amended (the “Securities Act”) in reliance on the exemption from registration contained in Section 3(a)(9) of the Securities Act. The April 2024 Exchange closed on April 25, 2024, with 346,045 shares of Series A Preferred Stock remaining outstanding following the April 2024 Exchange.

On May 14, 2024, the Company's stockholders approved the issuance of Common Stock upon conversion of the Company's Series B Preferred Stock to Common Stock. A total of 254,958 shares of Series B Preferred Stock automatically converted to 10,198,320 shares of Common Stock; 16,667 shares of Series B Preferred Stock did not automatically convert and remained outstanding as of September 30, 2024.

On September 6, 2024, the Company filed a new shelf registration statement on Form S-3 that was declared effective by the SEC for the potential offering, issuance and sale by the Company of up to $500.0 million of our common stock, preferred stock, debt securities, warrants and/or units consisting of all or some of these securities. Concurrent with the filing of the shelf-registration statement, the Company entered into a sales agreement with TD Securities (USA) LLC (“TD Cowen”), as its sales agent, pursuant to which the Company may issue and sell shares of its common stock for an aggregate offering price of up to $200.0 million under an at-the-market (“ATM’) offering program included in the shelf registration. In September 2024, the Company sold 426,287 shares of common stock under the ATM at a price per share of $28.15, resulting in net proceeds of $11.8 million.

Liquidity

The Company is a clinical stage biotechnology company with a limited operating history, and due to its significant research and development expenditures, the Company has generated operating losses since its inception and has not generated any revenue from the commercial sale of any products. There can be no assurance that profitable operations will ever be achieved, and, if achieved, whether profitability can be sustained on a continuing basis.

Since its inception and through September 30, 2024, the Company has funded its operations by raising an aggregate of approximately $1.1 billion of gross proceeds from the sale and issuance of convertible preferred stock and common stock, pre-funded warrants, the collection of grant proceeds, and the licensing of its product rights for commercialization of pegzilarginase in Europe and certain countries in the Middle East. As of September 30, 2024, Spyre had an accumulated deficit of $916.1 million, and cash, cash equivalents, and marketable securities of $414.2 million.

Based on current operating plans, the Company has sufficient resources to fund operations for at least one year from the issuance date of these financial statements with existing cash, cash equivalents, and marketable securities. Spyre will need to secure additional financing in the future to fund additional research and development, and before a commercial drug can be produced, marketed and sold. If the Company is unable to obtain additional financing or generate license or product revenue, the lack of liquidity could have a material adverse effect on the Company.

Basis of Presentation

The consolidated financial statements have been prepared in conformity with generally accepted accounting principles in the United States (“U.S. GAAP”) as defined by the Financial Accounting Standards Board and include the accounts of the Company and its wholly owned subsidiaries. All intercompany balances and transactions have been eliminated in consolidation.

Reclassification of Prior Year Presentation

Certain prior year amounts have been reclassified for consistency with the current year presentation. These reclassifications had no effect on the reported results of operations or balance sheets.

Unaudited Interim Financial Information

The interim condensed consolidated financial statements included in this Quarterly Report on Form 10-Q are unaudited. The unaudited interim financial statements have been prepared on the same basis as the annual financial statements and reflect, in the opinion of management, all adjustments of a normal and recurring nature that are necessary for a fair statement of the Company’s financial position as of September 30, 2024, and its results of operations for the three and nine months ended September 30, 2024 and 2023, changes in convertible preferred stock and stockholders’ equity for the three and nine months ended September 30, 2024 and 2023, and cash flows for the nine months ended September 30, 2024 and 2023. The results of operations for the three and nine months ended September 30, 2024, are not necessarily indicative of the results to be expected for the year ending December 31, 2024 or for any other future annual or interim period. The December 31, 2023 balance sheet was derived from audited financial statements, but does not include all disclosures required by U.S. GAAP for complete financial statements. These financial statements should be read in conjunction with the audited financial statements included in the Company’s Form 10-K for the year ended December 31, 2023 (the "Annual Report") as filed with the SEC on February 29, 2024 and amended on March 1, 2024 and November 18, 2024.

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Summary of Significant Accounting Policies

9 Months Ended

Sep. 30, 2024

Accounting Policies [Abstract]

Summary of Significant Accounting Policies

Summary of Significant Accounting Policies

These interim condensed consolidated financial statements have been prepared in accordance with U.S. GAAP and SEC instructions for interim financial information, and should be read in conjunction with the Company's Annual Report. Significant accounting policies and other disclosures normally provided have been omitted since such items are disclosed in the Company's Annual Report. The Company uses the same accounting policies in preparing quarterly and annual financial statements.

Other than policies noted below, there have been no significant changes from the significant accounting policies and estimates disclosed in the Notes titled “1. The Company and Basis of Presentation” and "2. Summary of Significant Accounting Policies” of the Company's Annual Report.

License Agreements Contingent Milestone Payments

The Company’s license agreements include specific development, regulatory, and clinical milestone payments that are payable upon the resolution of a contingency, such as upon the selection of a development candidate, first dosing of a human patient in clinical trials or receipt of the Food Drug and Administration’s (“FDA”) approval of a Spyre drug. The achievement of these milestone payments involves many factors outside of the Company’s control and therefore the associated likelihood cannot be considered probable until the

related contingency is resolved. Based on the preceding, the Company accrues each milestone payment upon the achievement of the applicable milestone event.

Recently Adopted Accounting Pronouncements

There have been no recent accounting pronouncements or changes in accounting pronouncements during the nine months ended September 30, 2024 that are of significance or potential significance to the Company.

Not Yet Adopted Accounting Pronouncements

In November 2024, the Financial Accounting Standards Board issued ASU 2024-03 to require more detailed information about specified categories of expenses (purchases of inventory, employee compensation, depreciation, amortization, and depletion) included in certain expense captions presented on the face of the income statement. This ASU is effective for fiscal years beginning after December 15, 2026, and for interim periods within fiscal years beginning after December 15, 2027. Early adoption is permitted. The amendments may be applied either (1) prospectively to financial statements issued for reporting periods after the effective date of this ASU or (2) retrospectively to all prior periods presented in the financial statements. The Company is currently evaluating the impact this ASU will have on our disclosures.

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Fair Value Measurements

9 Months Ended

Sep. 30, 2024

Fair Value Disclosures [Abstract]

Fair Value Measurements

Fair Value Measurements

The Company measures and reports certain financial instruments as assets and liabilities at fair value on a recurring basis. The following tables set forth the fair value of the Company’s financial assets and liabilities at fair value on a recurring basis based on the three-tier fair value hierarchy (in thousands):

	September 30, 2024
	Level 1		Level 2		Level 3		Total
Financial Assets:
Money market funds	$	69,900	$	—	$	—	$	69,900
U.S. government treasury securities	140,072		—		—		140,072
U.S. government agency securities	—		100,328		—		100,328
Commercial paper	—		75,717		—		75,717
Corporate bonds	—		26,530		—		26,530
Total financial assets	$	209,972	$	202,575	$	—	$	412,547
Liabilities:
Parapyre Option Obligation	$	—	$	13,035	$	—	$	13,035
CVR liability	—		—		60,900		60,900
Total liabilities	$	—	$	13,035	$	60,900	$	73,935

	December 31, 2023
	Level 1		Level 2		Level 3		Total
Financial Assets:
Money market funds	$	150,648	$	—	$	—	$	150,648
U.S. government treasury securities	32,843		—		—		32,843
U.S. government agency securities	—		16,257		—		16,257
Commercial paper	—		104,141		—		104,141
Corporate bonds	—		33,064		—		33,064
Total financial assets	$	183,491	$	153,462	$	—	$	336,953
Liabilities:
CVR liability	$	—	$	—	$	42,700	$	42,700
Total liabilities	$	—	$	—	$	42,700	$	42,700

The Company measures the fair value of money market funds and U.S. government treasury securities on quoted prices in active markets for identical assets or liabilities. The Level 2 assets include U.S. government agency securities, commercial paper and corporate bonds, and are valued based on quoted prices for similar assets in active markets and inputs other than quoted prices that are derived from observable market data. The Company evaluates transfers between levels at the end of each reporting period. There were no transfers between Level 1, Level 2, or Level 3 during the periods presented.

Parapyre Option Obligation

Under the Paragon Agreement, the Company is obligated to issue Parapyre Holding LLC ("Parapyre") an annual equity grant of warrants, on the last business day of each of the years ended December 31, 2023 and December 31, 2024, to purchase 1% of the then outstanding shares of the Company’s Common Stock, on a fully diluted basis, during the term of the Paragon Agreement (the "Parapyre Option Obligation"). The Company determined that the 2023 and 2024 grants are two separate grants, as there would be no obligation for the 2024 grant had the Company exercised or terminated all of the options under the Paragon Agreement prior to December 31, 2023. The service inception period for the grant precedes the grant date, with the full award being vested as of the grant date with no post-grant date service requirement. Accordingly, a liability related to the Parapyre Option Obligation is recorded pursuant to the Paragon Agreement during interim periods. On December 31, 2023, the Company settled its 2023 obligation under the Parapyre Option Obligation by issuing Parapyre 684,407 warrants to purchase the Company's Common Stock, with a $21.52 per share exercise price for each warrant.

The Parapyre Option Obligation is considered a Level 2 liability based on observable market data for substantially the full term of the liability. The Parapyre Option Obligation is measured each period using a Black-Scholes model to estimate the fair value of the option grant. Changes in the fair value of the Parapyre Option Obligation are recorded as stock-based compensation within Research and development expenses for non-employees who provided pre-clinical development services.

CVR Liability

In connection with the Asset Acquisition, a non-transferable CVR was distributed to the Legacy Stockholders, but was not distributed to holders of shares of Common Stock or Series A Preferred Stock issued to the June 2023 Investors or former stockholders of Pre-Merger Spyre in connection with the Transactions. Holders of the CVR will be entitled to receive certain cash payments from proceeds received by the Company for a three-year period, if any, related to the disposition or monetization of the Company’s legacy assets for a period of one year following the closing of the Asset Acquisition.

The fair value of the CVR liability was determined using the probability weighted discounted cash flow method to estimate future cash flows associated with the sale of the legacy assets. Analogous to a dividend being declared/approved in one period and paid out in another, the liability was recorded at the date of approval, June 22, 2023, as a Common Stock dividend, returning capital to the Legacy Stockholders. Changes in fair

value of the liability will be recognized as a component of Other income (expense) in the consolidated statement of operations and comprehensive loss in each reporting period. The liability value is based on significant inputs not observable in the market such as estimated cash flows, estimated probabilities of regulatory success, and discount rates, which represent a Level 3 measurement within the fair value hierarchy.

The significant inputs used to estimate the fair value of the CVR liability were as follows:

	September 30, 2024
Estimated cash flow dates	05/28/25 - 06/22/26
Estimated probability of success	72% - 100%
Estimated reimbursement rate compared to reimbursement target	81% - 100%
Risk-adjusted discount rates	7.76% - 7.82%

The change in fair value between December 31, 2023 and September 30, 2024 was a $19.6 million increase, primarily driven by changes in the likelihood of achievement of certain milestones and the time value of money, partially offset by an increase in risk-adjusted discount rates.

The following table presents changes in the CVR liability for the periods presented (in thousands):

	CVR Liability
Beginning balance as of December 31, 2023	$	42,700
Changes in the fair value of the CVR liability	19,630
Payments	(1,430)
Ending Balance as of September 30, 2024	$	60,900

Forward Contract Liability

In connection with the Asset Acquisition, the Company entered into a contract for the issuance of 364,887 shares of Series A Preferred Stock as part of the consideration transferred. This forward contract was classified as a liability because the underlying preferred shares were contingently redeemable. The forward contract was carried at fair value on the balance sheet, with changes in fair value between the acquisition date and June 30, 2023 recorded in earnings. The liability was settled with the issuance of the Series A Preferred Stock on July 7, 2023.

The fair value of the forward contract as of the acquisition date, June 22, 2023, was $106.2 million. The liability was settled with the issuance of the Series A Preferred Stock on July 7, 2023 for $189.7 million. For the three and nine months ended September 30, 2023, $25.4 million and $83.5 million, respectively, was recorded as Other (expense) income in the consolidated statements of operations in connection with the change in fair value of the forward contract liability.

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Cash Equivalents and Marketable Securities

9 Months Ended

Sep. 30, 2024

Cash and Cash Equivalents [Abstract]

Cash Equivalents and Marketable Securities

Cash Equivalents and Marketable Securities

The following tables summarize the estimated fair value of the Company’s cash equivalents and marketable securities and the gross unrealized gains and losses (in thousands):

	September 30, 2024
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses		Estimated Fair Value
Cash equivalents:
Money market funds	$	69,900	$	—	$	—	$	69,900
Total cash equivalents	$	69,900	$	—	$	—	$	69,900
Marketable securities:
Commercial paper	$	75,503	$	214	$	—	$	75,717
Corporate bonds	26,457		76		(3)		26,530
U.S. government treasury securities	139,313		768		(9)		140,072
U.S. government agency securities	99,973		363		(8)		100,328
Total marketable securities	$	341,246	$	1,421	$	(20)	$	342,647

	December 31, 2023
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses		Estimated Fair Value
Cash equivalents:
Money market funds	$	150,648	$	—	$	—	$	150,648
Commercial paper	24,950		5		—		24,955
U.S. government treasury securities	10,965		1		—		10,966
Total cash equivalents	$	186,563	$	6	$	—	$	186,569
Marketable securities:
Commercial paper	$	79,124	$	62	$	—	$	79,186
Corporate bonds	32,984		81		(1)		33,064
U.S. government treasury securities	21,846		31		—		21,877
U.S. government agency securities	16,147		110		—		16,257
Total marketable securities	$	150,101	$	284	$	(1)	$	150,384

The following table summarizes the available-for-sale securities in an unrealized loss position for which an allowance for credit losses has not been recorded as of September 30, 2024 and December 31, 2023, aggregated by major security type and length of time in a continuous unrealized loss position:

	September 30, 2024
	Less Than 12 Months				12 Months or Longer				Total
	Fair Value		Unrealized Losses		Fair Value		Unrealized Losses		Fair Value		Unrealized Losses
Corporate bonds	$	1,952	$	(3)	$	—	$	—	$	1,952	$	(3)
U.S. government treasury securities	17,517		(9)		—		—		17,517		(9)
U.S. government agency securities	18,101		(8)		—		—		18,101		(8)
Total marketable securities	$	37,570	$	(20)	$	—	$	—	$	37,570	$	(20)
	December 31, 2023
	Less Than 12 Months				12 Months or Longer				Total
	Fair Value		Unrealized Losses		Fair Value		Unrealized Losses		Fair Value		Unrealized Losses
Corporate bonds	$	9,907	$	(1)	$	—	$	—	$	9,907	$	(1)
U.S. government treasury securities	4,831		—		—		—		4,831		—
Total marketable securities	$	14,738	$	(1)	$	—	$	—	$	14,738	$	(1)

The Company evaluated its securities for credit losses and considered the decline in market value to be primarily attributable to current economic and market conditions and not to a credit loss or other factors. Additionally, the Company does not intend to sell the securities in an unrealized loss position and does not expect it will be required to sell the securities before recovery of the unamortized cost basis. As of September 30, 2024 and December 31, 2023, an allowance for credit losses had not been recognized. Given the Company's intent and ability to hold such securities until recovery, and the lack of significant change in credit risk of these investments, the Company does not consider these marketable securities to be impaired as of September 30, 2024 and December 31, 2023.

The financial instruments that potentially subject the Company to a concentration of credit risk consist principally of cash deposits. Accounts at each of our two U.S. banking institutions are insured by the Federal Deposit Insurance Corporation (“FDIC”) up to $250,000 per depositor. As of September 30, 2024 and December 31, 2023, cash deposits at the Company's U.S. banking institutions exceeded the FDIC limits. Uninsured foreign cash deposits were immaterial for both periods.

There were no realized gains or losses on marketable securities for the three and nine months ended September 30, 2024 and 2023. Interest on marketable securities is included in interest income. Accrued interest receivable on available-for-sale debt securities as of September 30, 2024 and December 31, 2023, was $1.7 million and $0.9 million, respectively, and is reflected in Prepaid expenses and other current assets.

The following table summarizes the contractual maturities of the Company’s marketable securities at estimated fair value (in thousands):

	September 30, 2024		December 31, 2023
Due in one year or less	$	253,613	$	115,784
Due in 1 - 2 years	89,034		34,600
Total marketable securities	$	342,647	$	150,384

The Company may sell investments at any time for use in current operations even if they have not yet reached maturity. As a result, the Company classifies marketable securities, including securities with maturities beyond twelve months as current assets.

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Accrued and Other Current Liabilities

9 Months Ended

Sep. 30, 2024

Payables and Accruals [Abstract]

Accrued and Other Current Liabilities

Accrued and Other Current Liabilities

Accrued and other current liabilities consist of the following (in thousands):

	September 30, 2024		December 31, 2023
Accrued compensation	$	3,966	$	4,054
Accrued contracted research and development costs	7,527		7,092
Accrued professional and consulting fees	1,134		1,474
Accrued other	526		488
Total accrued and other current liabilities	$	13,153	$	13,108

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Asset Acquisition

9 Months Ended

Sep. 30, 2024

Business Combination, Asset Acquisition, and Joint Venture Formation [Abstract]

Asset Acquisition

Asset Acquisition

On June 22, 2023, the Company acquired Pre-Merger Spyre pursuant to the Acquisition Agreement, by and among the Company, Aspen Merger Sub I, Inc., a Delaware corporation and a wholly owned subsidiary of the Company (“First Merger Sub”), Sequoia Merger Sub II, LLC, a Delaware limited liability company and wholly owned subsidiary of the Company (“Second Merger Sub”), and Pre-Merger Spyre. Pursuant to the Acquisition Agreement, First Merger Sub merged with and into Pre-Merger Spyre, pursuant to which Pre-Merger Spyre was the surviving corporation and became a wholly owned subsidiary of the Company (the “First Merger”). Immediately following the First Merger, Pre-Merger Spyre merged with and into Second Merger Sub, pursuant to which Second Merger Sub became the surviving entity. Pre-Merger Spyre was a pre-clinical stage biotechnology company that was incorporated on April 28, 2023 under the direction of Peter Harwin, a Managing Member of Fairmount, for the purpose of holding rights to certain intellectual property being developed by Paragon. Fairmount is a founder of Paragon.

The Company completed the Asset Acquisition of Pre-Merger Spyre, in accordance with the terms of the Acquisition Agreement. Under the terms of the Acquisition Agreement, the Company issued 517,809 shares of Common Stock and 364,887 shares of Series A Preferred Stock to former Pre-Merger Spyre security holders. In addition, outstanding and unexercised stock options to purchase 2,734 shares of common stock were assumed from the Amended and Restated Spyre 2023 Equity Incentive Plan.

At the acquisition date, the Company recorded forward contracts to represent the obligation to issue shares of Common Stock and shares of Series A Preferred Stock, respectively. The forward contract related to the Common Stock was recorded as Additional paid-in capital as the instrument is indexed to the Common Stock. The forward contract related to the Series A Preferred Stock was recorded as a liability, as the underlying stock has a cash redemption feature. On July 7, 2023, both the shares of Common Stock and Series A Preferred Stock were issued and the forward contract liability associated with the Series A Preferred Stock was settled accordingly.

The Company concluded that the arrangement met the definition of an asset acquisition rather than a business combination, as substantially all of the fair value of the gross assets acquired was concentrated in a single identifiable asset, Pre-Merger Spyre's option to exclusively license certain intellectual property rights (the "Option"). The Company determined that the Option was a single asset as the Company's strategy relied on developing the entire portfolio of individual treatments to create combination treatments that simultaneously address different mechanisms of inflammatory bowel disease with a single treatment. The Company also determined that the pipeline candidates within the portfolio were similar in nature and risk profile. In addition, the Company did not obtain any substantive processes, assembled workforce, or employees capable of producing outputs in connection with the Asset Acquisition.

The Company determined that the cost to acquire the asset was $113.2 million which was recorded as acquired in-process research and development ("IPR&D"). The fair value of the consideration issued consisted of the 364,887 shares of Series A Preferred Stock (14,595,480 shares of Common Stock on an as-converted basis) and 517,809 shares of Common Stock, valued at $291.08 per share and $7.277 per share, respectively.

The Asset Acquisition costs are shown on the following table (in millions):

	June 22, 2023
Consideration transferred in Series A Preferred Stock and Common Stock	$	110.0
Transaction costs incurred by Pre-Merger Spyre	3.2
Total cost to acquire asset	$	113.2

The allocation of the purchase price to net assets acquired is as a follows:

	June 22, 2023
Acquired in-process research and development	$	130.2
Cash acquired	3.0
Assumed liabilities	(20.0)
Total cost to acquire asset	$	113.2

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Licensing Agreements

9 Months Ended

Sep. 30, 2024

Licensing Agreements [Abstract]

Licensing Agreements

Licensing Agreements

On July 12, 2023, December 14, 2023, and June 5, 2024, the Company exercised the Option available under the Paragon Agreement with respect to the SPY001, SPY002, and SPY003 research programs, respectively.

On May 14, 2024, the Company and Paragon entered into (i) a license agreement (the “SPY001 License Agreement”), pursuant to which Paragon granted the Company a royalty-bearing, world-wide, exclusive license to develop, manufacture, commercialize or otherwise exploit certain antibodies and products targeting α4ß7 integrin and (ii) a license agreement (the “SPY002 License Agreement”), pursuant to which Paragon granted the Company a royalty-bearing, world-wide, exclusive license to develop, manufacture, commercialize or otherwise exploit certain antibodies and products targeting TL1A, respectively.

On October 11, 2024, the Company and Paragon entered into a license agreement (the "SPY003 License Agreement" and, together with the SPY001 License Agreement and the SPY002 License Agreement, the "License Agreements"), pursuant to which Paragon granted the Company a royalty-bearing, world-wide, exclusive license to develop, manufacture, commercialize or otherwise exploit certain antibodies and products targeting IL-23 in the field of IBD.

Under the terms of each License Agreement, the Company is obligated to pay Paragon up to $22.0 million based on specific development, regulatory and clinical milestones for the first product under each agreement, respectively, that achieves such specified milestones, including a $1.5 million fee for nomination of a development candidate, as applicable, and a further milestone payment of $2.5 million upon the first dosing of a human patient in a Phase 1 trial. In addition, the following summarizes other key terms of each License Agreement:

•Paragon will provide the Company with an exclusive license (such license, with respect to the SPY003 License Agreement only, being limited to the field of IBD) to its patents covering the related antibody, the method of use and its method of manufacture.

•Paragon will not conduct any new campaigns that generate anti-α4ß7 or anti-TL1A monospecific antibodies in any field or anti-IL-23 monospecific antibodies in the field of IBD, in each case for at least 5 years.

•The Company will pay Paragon a low single-digit percentage royalty for single antibody products and a mid single-digit percentage royalty for products containing more than one antibody from Paragon.

•There is a royalty step-down of 1/3rd if there is no Paragon patent in effect during the royalty term.

•The royalty term ends on the later of (i) the last-to-expire licensed patent or Company patent directed to the manufacture, use or sale of a licensed antibody in the country at issue or (ii) 12 years from the date of first sale of a Company product.

•Agreement may be terminated on 60 days’ notice by the Company; on material breach without cure; and to the extent permitted by law, on a party’s insolvency or bankruptcy.

•With respect to the SPY002 License Agreement only, on a product by product basis, the Company will pay sublicensing fees of up to approximately $20 million upon the achievement of mostly commercial milestones.

The Company recognizes the expense associated with each milestone when the achievement of the milestone is deemed probable. During the three and nine months ended September 30, 2024, the Company recognized expense of nil and $5.5 million related to Paragon license milestone payments recorded within Research and development expenses in the accompanying condensed statement of operations. There was no such expense for the three and nine months ended September 30, 2023.

For the three and nine months ended September 30, 2024, the Company made cash milestone payments to Paragon totaling $2.5 million and $5.5 million, respectively. As of September 30, 2024, there were no Paragon license milestone payments outstanding and payable to Paragon.

Additionally, the Company recognized $0.3 million and $0.4 million related to sublicensing fees and which was recorded as Research and development expenses in the accompanying condensed statement of operations for the three and nine months ended September 30, 2024, respectively. As of September 30, 2024, $0.3 million in sublicensing fees were outstanding and payable to Paragon.

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Related Party Transactions

9 Months Ended

Sep. 30, 2024

Related Party Transactions [Abstract]

Related Party Transactions

Related Party Transactions

Paragon and Parapyre each beneficially own less than 5% of the Company's capital stock through their respective holdings of the Company's Common Stock. Fairmount Funds Management LLC ("Fairmount") beneficially owns more than 5% of the Company's capital stock on an as-converted basis, has two seats on the Company's board of directors (the "Board") and beneficially owns more than 5% of Paragon, which is a joint venture between Fairmount and FairJourney Biologics. Fairmount appointed Paragon's board of directors and has the contractual right to approve the appointment of any executive officers. Parapyre is an entity formed by Paragon as a vehicle to hold equity in Spyre in order to share profits with certain employees of Paragon.

The following is the summary of expenses related to the Paragon Agreement and License Agreements, which are ultimately settled in cash (in millions) and recorded within Research and development in the consolidated statement of operations for the periods presented:

	Three Months Ended September 30,				Nine Months Ended September 30,
	2024		2023		2024		2023
Reimbursable costs under the Paragon Agreement	$	1.3	$	16.7	$	15.3	$	17.9
License Agreements milestone and sublicensing fees	0.3		—		5.9		—
Total related party expense (excludes stock comp)	$	1.6	$	16.7	$	21.2	$	17.9

The following is the summary of Related party accounts payable and other current liabilities (in millions):

	September 30, 2024		December 31, 2023
Reimbursable costs under the Paragon Agreement	$	1.2	$	16.6
Parapyre warrants liability	13.0		—
License Agreements development milestone liability (see Note 7)	0.3		—
Total related party accounts payable	$	14.5	$	16.6

Paragon Agreement

In connection with the Asset Acquisition, the Company assumed the rights and obligations of Pre-Merger Spyre under the Paragon Agreement. Under the Paragon Agreement, Spyre is obligated to compensate Paragon for its services performed under each research program based on the actual costs incurred with mark-up costs pursuant to the terms of the Paragon Agreement. Spyre is also obligated under the Paragon Agreement to issue Parapyre annual equity grants of warrants in accordance with the Parapyre Option Obligation.

On July 12, 2023, December 14, 2023, and June 5, 2024, the Company exercised the Option available under the Paragon Agreement with respect to the SPY001, SPY002 and SPY003 research programs, respectively. Our Option available under the Paragon Agreement with respect to the SPY004 program remains unexercised. Please refer to Note 7 for additional information on the License Agreements related to the exercised options.

On May 14, 2024, the Company, Paragon and Parapyre entered into a second amended and restated antibody discovery and option agreement that amends and restates that certain amended and restated antibody discovery and option agreement, dated September 29, 2023, by and between Paragon, Parapyre and Spyre Therapeutics, LLC, in order to, among other things, (i) replace the Company’s subsidiary with the Company as a party to the agreement and (ii) amend certain terms related to the SPY003 research program, including without limitation, (a) establishing an SPY003 antibody selection process pursuant to which the Company and Paragon shall alternate in turn to select a project antibody to be included and excluded, respectively, from the Company’s rights under its option to license certain intellectual property rights related to SPY003 from Paragon until all project antibodies under the SPY003 research program have been selected; (b) reducing the development costs invoiced to the Company for the SPY003 research program incurred from and after April 1, 2024 through completion of the SPY003 antibody selection process by 50%; (c) requiring Paragon to reimburse the Company for 50% of the development costs for the SPY003 research program incurred prior to April 1, 2024; provided, that Paragon receives rights to at least one SPY003 project antibody following completion of the SPY003 antibody selection process; (d) obligating the Company to exercise its option to license the intellectual property rights to SPY003 project antibodies and technology following the completion of the SPY003 antibody selection process; and (e) establishing a license agreement term sheet for the SPY003 research program with substantially similar milestone payment terms and royalty payment terms as the SPY001 License Agreement. Please refer to Note 7 for additional disclosures.

For the three and nine months ended September 30, 2024, the Company recognized expenses related to services provided by Paragon totaling $7.4 million and $28.3 million, respectively, which included $6.1 million and $13.0 million, respectively, of stock-based compensation expense, and were recorded as Research and development expenses in the consolidated statements of operations. Included within the expenses recognized for services provided by Paragon for the nine months ended September 30, 2024, is a $5.9 million reduction in Research and development expenses related to the reimbursement of 50% of the development costs for the SPY003 research program by Paragon.

For the three and nine months ended September 30, 2024, the Company made payments totaling $1.2 million and $30.7 million respectively, in connection with the Paragon Agreement.

Parapyre Option Obligation

Pursuant to the Paragon Agreement, the Company agreed to issue Parapyre an annual equity grant of warrants, on the last business day of each of the years ended December 31, 2023 and December 31, 2024, to purchase 1% of the then outstanding shares of the Company's Common Stock, on a fully diluted basis, during the term of the Paragon Agreement. See Note 10 for disclosures related to the Parapyre Option Obligation.

Paragon License Agreements

See Note 7 for disclosures related to the License Agreements entered into with Paragon.

Mark McKenna Option Grant

On February 1, 2024, the Board appointed Mark McKenna as a Class I director. Mr. McKenna and the Company are parties to a consulting agreement, pursuant to which Mr. McKenna agreed to continue to provide consulting services as an independent contractor to the Company, with an effective date of August 1, 2023 (the “Vesting Commencement Date”). As compensation for Mr. McKenna’s consulting services, on November 22, 2023, he was granted non-qualified stock options to purchase 477,000 shares of the Company’s Common Stock under the 2016 Plan (as defined in Note 8) with an exercise price of $10.39 per share, which vest as to 25% on the one year anniversary of the Vesting Commencement Date and thereafter vest and become exercisable in 36 equal monthly installments, subject to Mr. McKenna’s continued service to the Company through each applicable vesting date. For the three and nine months ended September 30, 2024, the Company recognized $0.3 million and $0.8 million, respectively, in stock-based compensation expense related to Mr. McKenna's consulting agreement. There was no such expense for the three and nine months ended September 30, 2023.

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Convertible Preferred Stock and Stockholders' Equity

9 Months Ended

Sep. 30, 2024

Equity [Abstract]

Convertible Preferred Stock and Stockholders' Equity

Convertible Preferred Stock and Stockholders’ Equity

Pre-Funded Warrants

In February 2019, April 2020 and May 2022, the Company issued pre-funded warrants to purchase the Company’s Common Stock in underwritten public offerings at the offering price of the Common Stock, less the $0.0025 per share exercise price of each warrant. The warrants were recorded as a component of stockholders’ (deficit) equity within additional paid-in capital and have no expiration date. Per the terms of the warrant agreements, the outstanding warrants to purchase shares of Common Stock may not be exercised if the holder’s ownership of the Company’s Common Stock would exceed 4.99% (“Maximum Ownership Percentage”), or 9.99% for certain holders. By written notice to the Company, each holder may increase or decrease the Maximum Ownership Percentage to any other percentage (not in excess of 19.99% for the majority of such warrants). The revised Maximum Ownership Percentage would be effective 61 days after the notice is received by the Company.

As of September 30, 2024, all pre-funded warrants have been exercised and none remain outstanding.

Parapyre Warrants

The Company settled its 2023 obligations under the Parapyre Option Obligation by issuing Parapyre 684,407 warrants to purchase the Company's Common Stock, with a $21.52 per share exercise price for each warrant. Pursuant to the terms of the warrant agreement, the outstanding warrants to purchase shares of Common Stock may not be exercised if the holder’s ownership of the Company’s Common Stock would exceed 4.99%. As of September 30, 2024, none of the warrants issued under the Parapyre Option Obligation have been exercised.

Series A Non-Voting Convertible Preferred Stock

On June 22, 2023, the Company filed a Certificate of Designation of Preferences, Rights and Limitations of the Series A Preferred Stock with the Secretary of State of the State of Delaware (the “Series A Certificate of Designation”) in connection with the Asset Acquisition and the June 2023 PIPE.

Pursuant to the Series A Certificate of Designation, holders of Series A Preferred Stock are entitled to receive dividends on shares of Series A Preferred Stock equal to, on an as-if-converted-to-Common Stock basis, and in the same form as, dividends actually paid on shares of Common Stock. Except as provided in the Series A Certificate of Designation or as otherwise required by law, the Series A Preferred Stock does not have voting rights. However, as long as any shares of Series A Preferred Stock are outstanding, the Company will not, without the affirmative vote of the holders of a majority of the then outstanding shares of the Series A Preferred Stock: (a) alter or change adversely the powers, preferences or rights given to the Series A Preferred Stock, or alter or amend the Series A Certificate of Designation, amend or repeal any provision of, or add any provision to, the Company’s Certificate of Incorporation or its Bylaws, or file any articles of amendment, certificate of designations, preferences, limitations and relative rights of any series of preferred stock, if such action would adversely alter or change the preferences, rights, privileges or powers of, or restrictions provided for the benefit of the Series A Preferred Stock, regardless of whether any of the foregoing actions will be by means of amendment to the Certificate of Incorporation or by merger, consolidation, recapitalization, reclassification, conversion or otherwise, (b) issue further shares of Series A Preferred Stock or increase or decrease (other than by conversion) the number of authorized shares of Series A Preferred Stock, (c) prior to the stockholder approval of the conversion of the Series A Preferred Stock into shares of Common Stock in accordance with Nasdaq Stock Market Rules (the “Series A Conversion Proposal”) or at any time while at least 30% of the originally issued Series A Preferred Stock remains issued and outstanding, consummate (x) any Fundamental Transaction (as defined in the Series A Certificate of Designation) or (y) any merger or consolidation of the Company with or into another entity or any stock sale to, or other business combination in which our stockholders immediately before such transaction do not hold at least a majority of our capital stock immediately after such transaction or (d) enter into any agreement with respect to any of the foregoing. The Series A Preferred Stock does not have a preference upon any liquidation, dissolution or winding-up of the Company.

On June 26, 2023, the Company completed a private placement of 721,452 shares of Series A Preferred Stock in exchange for gross proceeds of approximately $210.0 million, or net proceeds of $197.3 million, after deducting placement agent and other offering costs.

On July 7, 2023, the Company issued 364,887 shares of Series A Preferred Stock as part of its consideration transferred in connection with the Asset Acquisition that closed on June 22, 2023 which settled the related forward contract liability.

On November 21, 2023, the Company's stockholders approved the Series A Conversion Proposal, among other matters, at a special meeting of stockholders. As a result of the approval of the Series A Conversion Proposal, all conditions that could have required cash redemption of the Series A Preferred Stock were satisfied. Since the Series A Preferred Stock is no longer redeemable, the associated balances of the Series A Preferred Stock were reclassified from mezzanine equity to permanent equity during the fourth quarter of 2023.

Following stockholder approval of the Series A Conversion Proposal, each share of Series A Preferred Stock automatically converted into 40 shares of Common Stock, subject to certain limitations, including that a holder of Series A Preferred Stock is prohibited from converting shares of Series A Preferred Stock into shares of Common Stock if, as a result of such conversion, such holder, together with its affiliates, would beneficially own more than a specified percentage (established by the holder between 0.0% and 19.9%) of the total number of shares of Common Stock issued and outstanding immediately after giving effect to such conversion. 649,302 shares of Series A Preferred Stock automatically converted to 25,972,080 shares of Common Stock; 437,037 shares of Series A Preferred Stock did not automatically convert and remained outstanding following the conversion. This conversion was recorded as a reclassification between Series A Preferred Stock and Common Stock based on the historical per-share contributed capital amount of the Series A Preferred Stock.

On April 23, 2024, in connection with the April 2024 Exchange, the Stockholder agreed to exchange an aggregate of 90,992 shares of Series A Preferred Stock for an aggregate of 3,639,680 shares of the Company's Common Stock. This exchange was recorded as a reclassification between Series A Preferred Stock and Common Stock based on the historical per-share contributed capital amount, inclusive of any forward-contract valuation adjustments, of the Series A Preferred Stock. Following the April 2024 Exchange, 346,045 shares of Series A Preferred Stock remained outstanding.

Series B Non-Voting Convertible Preferred Stock

On December 8, 2023, the Company filed a Certificate of Designation of Preferences, Rights and Limitations of Series B Non-Voting Convertible Preferred Stock with the Secretary of State of the State of Delaware (the “Series B Certificate of Designation”) in connection with the December 2023 PIPE.

Pursuant to the Series B Certificate of Designation, holders of Series B Preferred Stock are entitled to receive dividends on shares of Series B Preferred Stock equal to, on an as-if-converted-to-Common Stock basis, and in the same form as, dividends actually paid on shares of Common Stock. Except as provided in the Series B Certificate of Designation or as otherwise required by law, the Series B Preferred Stock does not have voting rights. However, as long as any shares of Series B Preferred Stock are outstanding, the Company will not, without the affirmative vote of the holders of a majority of the then outstanding shares of the Series B Preferred Stock, alter or change adversely the powers, preferences or rights given to the Series B Preferred Stock, or alter or amend the Series B Certificate of Designation, amend or repeal any provision of, or add any provision to, the Company’s Certificate of Incorporation or its Bylaws, or file any articles of amendment, certificate of designations, preferences, limitations and relative rights of any series of preferred stock, if such action would adversely alter or change the preferences, rights, privileges or powers of, or restrictions provided for the benefit of the Series B Preferred Stock, regardless of whether any of the foregoing actions will be by means of amendment to the Certificate of Incorporation or by merger, consolidation, recapitalization, reclassification, conversion or otherwise. The Series B Preferred Stock does not have a preference upon any liquidation, dissolution or winding-up of the Company.

On December 11, 2023, as part of the December 2023 PIPE, the Company completed a private placement of 150,000 shares of Series B Preferred Stock in exchange for gross proceeds of $90.0 million.

On March 18, 2024, in connection with the March 2024 PIPE, the Company filed a certificate of amendment to its Series B Certificate of Designation to increase the number of authorized shares of Series B Preferred Stock from 150,000 to 271,625.

On March 20, 2024, as part of the March 2024 PIPE, the Company completed a private placement of 121,625 shares of Series B Preferred Stock in exchange for gross proceeds of approximately $180.0 million.

On May 14, 2024, the Company's stockholders approved the issuance of Common Stock upon the conversion of all issued and outstanding Series B Preferred Stock into shares of Common Stock in accordance with the Nasdaq Stock Market Rules (the "Series B Conversion Proposal"), among other matters, at its 2024 annual meeting of stockholders. As a result of the approval of the Series B Conversion Proposal, all conditions that could have required cash redemption of the Series B Preferred Stock were satisfied. Since the Series B Preferred Stock is no longer redeemable, the associated balances of the Series B Preferred Stock were reclassified from mezzanine equity to permanent equity during the second quarter of 2024.

Following stockholder approval of the Series B Conversion Proposal, each share of Series B Preferred Stock automatically converted into 40 shares of the Common Stock, subject to certain limitations, including that a holder of Series B Preferred Stock is prohibited from converting shares of Series B Preferred Stock into shares of Common Stock if, as a result of such conversion, such holder, together with its affiliates, would beneficially own more than a specified percentage (established by the holder between 0.0% and 19.9%) of the total number of shares of Common Stock issued and outstanding immediately after giving effect to such conversion. 254,958 shares of Series B Preferred Stock automatically converted to 10,198,320 shares of Common Stock; 16,667 shares of Series B Preferred Stock did not automatically convert and remain outstanding as of September 30, 2024 due to beneficial ownership limitations. This conversion was recorded as a reclassification between Series B Preferred Stock and Common Stock based on the historical per-share contributed capital amount of the Series B Preferred Stock.

S-3 Shelf & ATM

On September 6, 2024, the Company filed a new shelf registration statement on Form S-3 that was declared effective by the SEC for the potential offering, issuance and sale by the Company of up to $500.0 million of our common stock, preferred stock, debt securities, warrants and/or units consisting of all or some of these securities. Concurrent with the filing of the shelf-registration statement, the Company entered into

a sales agreement (the "Sales Agreement") with TD Securities (USA) LLC (“TD Cowen”), as its sales agent, pursuant to which the Company may issue and sell shares of its common stock for an aggregate offering price of up to $200.0 million under an at-the-market (“ATM’) offering program included in the shelf registration. In September 2024, the Company sold 426,287 shares of common stock under the ATM at a price per share of $28.15 resulting in net proceeds of $11.8 million. As of November 1, 2024, $188.0 million remained available for sale under the Sales Agreement.

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Stock-Based Compensation

9 Months Ended

Sep. 30, 2024

Share-Based Payment Arrangement [Abstract]

Stock-Based Compensation

Stock-Based Compensation

2015 Equity Incentive Plan

In March 2015, the Company adopted the 2015 Equity Incentive Plan (“2015 Plan”), administered by the board of directors, and provides for the Company to sell or issue share of Common Stock or restricted Common Stock, or to grant incentive stock options or nonqualified stock options for the purchase of Common Stock, to employees, members of the board of directors and consultants of the Company. The Company granted options under the 2015 Plan until April 2016 when it was terminated as to future awards, although it continues to govern the terms of options that remain outstanding under the 2015 Plan.

As of September 30, 2024, a total of 952 shares of Common Stock are subject to options outstanding under the 2015 Plan and will become available under the 2016 Equity Incentive Plan (“2016 Plan”) to the extent the options are forfeited or lapse unexercised.

2016 Equity Incentive Plan

The 2016 Plan became effective in April 2016 and serves as the successor to the 2015 Plan. Under the 2016 Plan, the Company may grant stock options, stock appreciation rights, restricted stock awards, restricted stock units, performance awards, and stock bonuses. The 2016 Plan, as amended, provides for an automatic increase in the number of shares reserved for issuance thereunder on January 1 of each year for the remaining term of the plan equal to (a) 5.0% of the number of issued and outstanding shares of Common Stock (including such shares issuable pursuant to the exercise or conversion, as applicable, of any outstanding pre-funded warrants and nonvoting convertible preferred stock) on December 31 of the immediately preceding year, or (b) a lesser amount as approved by the board each year (the “Evergreen Provision”). As a result of the Evergreen Provision, on January 1, 2024 and 2023, an additional 3,023,650 and 104,561 shares, respectively, became available for issuance under the 2016 Plan.

As of September 30, 2024, the 2016 Plan had 7,228,113 shares available for future issuance, of which 3,247,677 shares were subject to outstanding option awards.

2018 Equity Inducement Plan

The 2018 Equity Inducement Plan (“2018 Plan”) became effective in February 2018.

During the third quarter of 2024, the Company amended the 2018 Plan to increase the number of shares of Common Stock reserved for issuance by 1,000,000. After this amendment and as of September 30, 2024, the 2018 Plan had 6,999,445 shares available for future issuance, of which 5,624,067 shares were subject to outstanding option awards and restricted unit awards.

Service-based awards granted under the 2018 Plan, 2016 Plan, and 2015 Plan generally vest over four years and expire after ten years, although awards have been granted with vesting terms less than four years. Under the 2016 Plan and 2018 Plan, the Company may grant stock-based awards with service conditions (“service-based” awards), performance conditions (“performance-based” awards), and market conditions (“market-based” awards).

Spyre 2023 Equity Incentive Plan

On June 22, 2023, in connection with the Asset Acquisition, the Company assumed the Amended and Restated Spyre 2023 Equity Incentive Plan and its outstanding and unexercised stock options, which were

converted to options to purchase 2,734 shares of Common Stock. The acquisition-date fair value of these grants will be recognized as an expense on a pro-rata basis over the vesting period.

The following table summarizes the Company’s stock awards granted under all equity incentive and inducement plans for each of the periods indicated:

	Three Months Ended September 30,						Nine Months Ended September 30,
	2024			2023			2024			2023
	Grants	Weighted Average Grant Date Fair Value		Grants	Weighted Average Grant Date Fair Value		Grants	Weighted Average Grant Date Fair Value		Grants	Weighted Average Grant Date Fair Value
Stock options	425,500	$	25.74	1,044,667	$	14.50	1,857,853	$	28.40	3,867,366	$	9.65

Parapyre Option Obligation

As of September 30, 2024, the pro-rated estimated fair value of the options to be granted on December 31, 2024 related to the Parapyre Option Obligation, was approximately $13.0 million. For the three and nine months ended September 30, 2024, $6.1 million and $13.0 million, respectively, was recognized as stock compensation expense related to the Parapyre Option Obligation. For the three and nine months ended September 30, 2023, $2.7 million and $2.9 million, respectively, was recognized as stock compensation expense related to the Parapyre Option Obligation. As of September 30, 2024, the unamortized expense related to the Parapyre Option Obligation was $4.4 million.

2016 Employee Stock Purchase Plan

Under the Company’s 2016 Employee Stock Purchase Plan (“2016 ESPP”), the Company issued and sold 14,053 and 16,383 shares during the three and nine months ended September 30, 2024, respectively, and sold 704 and 2,496 shares during the three and nine months ended September 30, 2023, respectively. The aggregate cash proceeds were not material for all periods.

Stock-based Compensation Expense

Total stock-based compensation expense recognized from the Company’s equity incentive plans, 2018 Plan, 2016 ESPP and Parapyre Option Obligation during the periods presented was as follows (in thousands):

	Three Months Ended September 30,				Nine Months Ended September 30,
	2024		2023		2024		2023
Research and development (1)	$	8,555	$	2,965	$	18,863	$	4,136
General and administrative	4,545		1,820		16,754		4,269
Total stock-based compensation expense (2)	$	13,100	$	4,785	$	35,617	$	8,405
(1) For the three and nine months ended September 30, 2024, $6.1 million and $13.0 million, respectively, was recognized as stock compensation expense related to the Parapyre Option Obligation. For the three and nine months ended September 30, 2023, $2.7 million and $2.9 million, respectively, was recognized as stock compensation expense related to the Parapyre Option Obligation. (2) Of the total $13.1 million and $35.6 million of stock-based compensation expense for the three and nine months ended September 30, 2024, $0.1 million and $3.6 million, respectively, is related to legacy Aeglea employees and directors who had been terminated as of the end of the respective period. Of the total $4.8 million and $8.4 million of stock-based compensation expense for the three and nine months ended September 30, 2023, $0.8 million and $4.2 million, respectively, is related to legacy Aeglea employees and directors who had been terminated as of the end of the period.

The following table summarizes the weighted-average Black-Scholes option pricing model assumptions used to estimate the fair value of stock options granted under the Company's equity incentive plans, and the shares purchasable under the 2016 ESPP during the periods presented:

	Three Months Ended September 30,		Nine Months Ended September 30,
	2024	2023	2024	2023
Stock Options Granted
Expected term (in years)	6.08	6.08	6.02	6.04
Expected volatility	105%	101%	105%	111%
Risk-free interest	4.13%	4.28%	4.03%	4.07%
Dividend yield	—	—	—	—
2016 ESPP
Expected term (in years)	0.50	0.50	0.50	0.49
Expected volatility	71%	222%	83%	181%
Risk-free interest	5.02%	5.29%	5.15%	4.99%
Dividend yield	—	—	—	—

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Legacy Strategic License Agreements

9 Months Ended

Sep. 30, 2024

License And Collaboration Agreement [Abstract]

Legacy Strategic License Agreements

Legacy Strategic License Agreements

On March 21, 2021, the Company entered into an exclusive license and supply agreement with Immedica (the "Immedica Agreement"). On July 27, 2023, the Company announced that it had entered into an agreement to sell the global rights to pegzilarginase, an investigational treatment for the rare metabolic disease Arginase 1 Deficiency, to Immedica for $15.0 million in upfront cash proceeds and up to $100.0 million in contingent milestone payments. The sale of pegzilarginase to Immedica superseded and terminated the Immedica Agreement.

The milestone payments are contingent on formal reimbursement decisions by national authorities in key European markets and pegzilarginase approval by the FDA, among other events. In addition to the payment previously made to holders of the Company's CVRs (as defined in Note 1) related to the upfront cash proceeds, any contingent milestone payments under the Immedica Agreement, if paid within the CVR period, will be distributed to holders of the Company's CVRs net of expenses and adjustments pursuant to the contingent value rights agreement we entered into with Equiniti Trust Company LLC (f/k/a American Stock Transfer & Trust Company LLC) as rights agent in connection with the Asset Acquisition.

The Company did not recognize any revenue under the Immedica Agreement for the three and nine months ended September 30, 2024. For the nine months ended September 30, 2023, the Company recognized $0.9 million of development fee revenue in connection with the Immedica Agreement, which was attributable to the PEACE Phase 3 trial and BLA package for pegzilarginase. There was no such revenue for the three months ended September 30, 2023.

For more details on the Immedica Agreement, which was terminated on July 27, 2023, please refer to the Note under Item 1 of Part I, titled "12. Strategic License Agreements" of the Company's Annual Report.

Contract Balances from Customer Contract

The timing of revenue recognition, billings and cash collections results in contract assets and contract liabilities on the Company's balance sheets. The Company recognizes license and development receivables based on billed services, which are derecognized upon reimbursement. When consideration is received, or such consideration is unconditionally due, from a customer prior to transferring goods or services to the customer under the terms of a contract, a contract liability is recorded. Contract liabilities are recognized as revenue after control of the goods or services is transferred to the customer and all revenue recognition criteria have been met.

The Company did not have any contract assets or liabilities as of September 30, 2024 and December 31, 2023.

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Sale of Pegzilarginase to Immedica

9 Months Ended

Sep. 30, 2024

Discontinued Operations and Disposal Groups [Abstract]

Sale of Pegzilarginase to Immedica

Sale of Pegzilarginase to Immedica

On July 27, 2023, the Company announced that it had entered into an agreement to sell the global rights to pegzilarginase, an investigational treatment for the rare metabolic disease Arginase 1 Deficiency, to Immedica for $15.0 million in upfront cash proceeds and up to $100.0 million in contingent milestone payments. The sale of pegzilarginase to Immedica superseded and terminated the previous license agreement between the Company and Immedica. On July 27, 2023, the carrying value of the asset was zero as it was internally developed. Accordingly the Company recognized a $14.6 million gain within operating expenses, which is the full $15.0 million in upfront cash proceeds, net of transaction costs and the derecognition of pegzilarginase related nonfinancial assets and liabilities.

The milestone payments are contingent on formal reimbursement decisions by national authorities in key European markets and pegzilarginase approval by the FDA, among other events. The upfront payment and contingent milestone payments if paid, net of expenses and adjustments, will be distributed to holders of Aeglea’s CVR pursuant to the CVR Agreement resulting from the Asset Acquisition.

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Net Loss Per Share (as restated)

9 Months Ended

Sep. 30, 2024

Earnings Per Share [Abstract]

Net Loss Per Share (as restated)

Net Loss Per Share (as restated)

Restatement

Subsequent to the filing of its Quarterly Report on Form 10-Q for the period ended September 30, 2024, management identified an error related to the calculation and presentation of loss per share. The Company had previously concluded that the Series A Preferred Stock and Series B Preferred Stock had preferences over the Company's Common Stock and were therefore excluded from the calculation of basic and dilutive net loss per share pursuant to the two-class method. The Company has now determined that the Series A Preferred Stock and Series B Preferred Stock do not have preferential rights over the Company’s Common Stock and, accordingly, are considered to be a second and third class of common stock for purposes of calculating net loss per share. Consequently, the Company has now separately calculated and presented net loss per share for its Common Stock, Series A Preferred Stock and Series B Preferred Stock.

For the three months ended September 30, 2024 and 2023, loss per share attributable to common stockholders as previously presented was $1.36 and $9.34, respectively, and as restated was $1.06 and $0.86, respectively. For the nine months ended September 30, 2024 and 2023, loss per share attributable to common stockholders as previously presented was $3.43 and $69.57, respectively, and as restated was $2.39 and $14.65, respectively. Net loss per share attributable to holders of Series A Preferred Stock and Series B Preferred Stock was not previously presented. All related amounts have been updated to reflect the effects of the restatement throughout the financial statements and related footnotes, as applicable.

The Company computes net loss per share of Common Stock, Series A Preferred Stock, and Series B Preferred Stock using the two-class method required for multiple classes of common stock and other participating securities.

The two-class method is an earnings (loss) allocation method under which earnings (loss) per share is calculated for each class of common stock. The Company has determined that the Series A Preferred Stock and Series B Preferred Stock do not have preferential rights when compared to the Company's Common Stock and therefore it must allocate losses to these other classes of common stock, as illustrated in the table below.

Basic and diluted net loss per share is computed by dividing the net loss by the weighted-average number of shares and pre-funded warrants outstanding during the period, without consideration of potential dilutive securities. The pre-funded warrants are included in the computation of basic net loss per share as the exercise price is negligible and they are fully vested and exercisable. For periods in which the Company generated a net loss, the Company does not include potential shares of common stock in diluted net loss per share when the impact of these items is anti-dilutive. The Company has generated a net loss for all periods presented, therefore diluted net loss per share is the same as basic net loss per share since the inclusion of potential shares of common stock would be anti-dilutive.

The following table sets forth the computation of basic and diluted net loss per share of Common Stock, Series A Preferred Stock, and Series B Preferred Stock (in thousands, except share and per share amounts):

	Three Months Ended September 30,
	2024						2023
	Series A Preferred Stock		Series B Preferred Stock		Common Stock		Series A Preferred Stock		Series B Preferred Stock		Common Stock
Net loss per share, basic and diluted:
Numerator
Allocation of losses	$	(14,610)	$	(704)	$	(53,714)	$	(36,427)	$	—	$	(3,680)
Denominator
Weighted-average shares outstanding	346,045		16,667		50,889,433		1,062,542		—		4,015,661
Weighted-average pre-funded warrants outstanding	—		—		—		—		—		278,151
Number of shares used in per share computation	346,045		16,667		50,889,433		1,062,542		—		4,293,812
Net loss per share, basic and diluted	$	(42.22)	$	(42.24)	$	(1.06)	$	(34.28)	$	—	$	(0.86)
	Nine Months Ended September 30,
	2024						2023
	Series A Preferred Stock		Series B Preferred Stock		Common Stock		Series A Preferred Stock		Series B Preferred Stock		Common Stock
Net loss per share, basic and diluted:
Numerator
Allocation of losses	$	(36,733)	$	(9,105)	$	(105,884)	$	(217,573)	$	—	$	(58,037)
Denominator
Weighted-average shares outstanding	383,903		95,158		44,146,958		371,286		—		3,116,434
Weighted-average pre-funded warrants outstanding	—		—		116,788		—		—		845,112
Number of shares used in per share computation	383,903		95,158		44,263,746		371,286		—		3,961,546
Net loss per share, basic and diluted	$	(95.68)	$	(95.68)	$	(2.39)	$	(586.00)	$	—	$	(14.65)

The following weighted-average equity instruments were excluded from the calculation of diluted net loss per share because their effect would have been anti-dilutive for the periods presented:

	Three Months Ended September 30,		Nine Months Ended September 30,
	2024	2023	2024	2023
Options to purchase common stock	4,733,609	3,135,672	4,583,260	1,426,224
Unvested restricted stock units	65,925	—	69,503	252
Outstanding Parapyre warrants	684,407	—	684,407	—

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Restructuring Charges

9 Months Ended

Sep. 30, 2024

Restructuring and Related Activities [Abstract]

Restructuring Charges

Restructuring Charges

Severance and Stock Compensation

On April 12, 2023, based on the review of the inconclusive interim results from the Company's Phase 1/2 clinical trial of pegtarviliase for the treatment of classical homocystinuria and other business considerations, the Company announced that it had initiated a process to explore strategic alternatives to maximize stockholder value and engaged an independent exclusive financial advisor to support this process.

As a result, the Company implemented a restructuring plan resulting in an approximate 83% reduction of the Company’s existing headcount by June 30, 2023. The Company recognized restructuring expenses consisting of cash severance payments and other employee-related costs of nil and $6.4 million during the three

and nine months ended September 30, 2023, respectively. In addition, the Company recognized $1.0 million in non-cash stock-based compensation expense related to the accelerated vesting of stock-based awards for certain employees. The Company recorded these restructuring charges based on each employee’s role to the respective research and development and general and administrative operating expense categories on its condensed consolidated statements of operations and comprehensive loss.

Sale of Assets

During the second quarter of 2023, the Company sold various lab equipment, consumables, and furniture and fixtures for total consideration of $0.5 million. After recording the disposal of all property and equipment net of proceeds, the Company recorded a $0.7 million and $0.2 million loss on disposal of long lived assets within Research and development and General and administrative expenses, respectively.

Lease Right-of-use Asset and Leasehold Improvement Impairment

Effective June 30, 2023, the Company abandoned its leased office space in Austin, Texas. As a result, the Company recognized an impairment loss of $0.9 million related to the operating lease right-of-use asset and $1.7 million related to leasehold improvements. On August 7, 2023, the Company terminated its building lease in Austin, Texas. The negotiated termination agreement obligated the Company to pay the lessor a $2.0 million termination fee in exchange for releasing the Company of all further obligations under the lease.

All charges related to the restructuring activities were recognized during the second quarter of 2023. No further restructuring charges were incurred under the restructuring plan. A summary of the charges related to the restructuring activities is as follows (in thousands):

	Severance Related Expenses		Stock Compensation Expenses		Loss on Disposal of Long Lived Assets		Lease Asset Impairment		Total Restructuring Costs
Research and development	$	3,182	$	123	$	749	$	1,405	$	5,459
General and administrative	3,266		870		182		1,175		5,493
Total	$	6,448	$	993	$	931	$	2,580	$	10,952

As of December 31, 2023, $1.1 million of restructuring costs remained outstanding and unpaid. As of September 30, 2024, there were no remaining liabilities under the restructuring plan described above.

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Subsequent Events

9 Months Ended

Sep. 30, 2024

Subsequent Events [Abstract]

Subsequent Events

Subsequent Events

On October 1, 2024, the Company appointed Sheldon Sloan, M.D., M. Bioethics, to serve as its Chief Medical Officer.

On October 11, 2024, the Company and Paragon entered into the SPY003 License Agreement, pursuant to which Paragon granted the Company a royalty-bearing, world-wide, exclusive license to develop, manufacture, commercialize or otherwise exploit certain antibodies and products targeting IL-23 in the field of IBD.

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Summary of Significant Accounting Policies (Policies)

9 Months Ended

Sep. 30, 2024

Accounting Policies [Abstract]

Basis of Presentation

Basis of Presentation

The consolidated financial statements have been prepared in conformity with generally accepted accounting principles in the United States (“U.S. GAAP”) as defined by the Financial Accounting Standards Board and include the accounts of the Company and its wholly owned subsidiaries. All intercompany balances and transactions have been eliminated in consolidation.

Reclassification of Prior Year Presentation

Reclassification of Prior Year Presentation

Certain prior year amounts have been reclassified for consistency with the current year presentation. These reclassifications had no effect on the reported results of operations or balance sheets.

License Agreements Contingent Milestone Payments

License Agreements Contingent Milestone Payments

The Company’s license agreements include specific development, regulatory, and clinical milestone payments that are payable upon the resolution of a contingency, such as upon the selection of a development candidate, first dosing of a human patient in clinical trials or receipt of the Food Drug and Administration’s (“FDA”) approval of a Spyre drug. The achievement of these milestone payments involves many factors outside of the Company’s control and therefore the associated likelihood cannot be considered probable until the

related contingency is resolved. Based on the preceding, the Company accrues each milestone payment upon the achievement of the applicable milestone event.

Recently Adopted and Not Yet Adopted Accounting Pronouncements

Recently Adopted Accounting Pronouncements

There have been no recent accounting pronouncements or changes in accounting pronouncements during the nine months ended September 30, 2024 that are of significance or potential significance to the Company.

Not Yet Adopted Accounting Pronouncements

In November 2024, the Financial Accounting Standards Board issued ASU 2024-03 to require more detailed information about specified categories of expenses (purchases of inventory, employee compensation, depreciation, amortization, and depletion) included in certain expense captions presented on the face of the income statement. This ASU is effective for fiscal years beginning after December 15, 2026, and for interim periods within fiscal years beginning after December 15, 2027. Early adoption is permitted. The amendments may be applied either (1) prospectively to financial statements issued for reporting periods after the effective date of this ASU or (2) retrospectively to all prior periods presented in the financial statements. The Company is currently evaluating the impact this ASU will have on our disclosures.

Net Loss Per Share

The Company computes net loss per share of Common Stock, Series A Preferred Stock, and Series B Preferred Stock using the two-class method required for multiple classes of common stock and other participating securities.

The two-class method is an earnings (loss) allocation method under which earnings (loss) per share is calculated for each class of common stock. The Company has determined that the Series A Preferred Stock and Series B Preferred Stock do not have preferential rights when compared to the Company's Common Stock and therefore it must allocate losses to these other classes of common stock, as illustrated in the table below.

Basic and diluted net loss per share is computed by dividing the net loss by the weighted-average number of shares and pre-funded warrants outstanding during the period, without consideration of potential dilutive securities. The pre-funded warrants are included in the computation of basic net loss per share as the exercise price is negligible and they are fully vested and exercisable. For periods in which the Company generated a net loss, the Company does not include potential shares of common stock in diluted net loss per share when the impact of these items is anti-dilutive. The Company has generated a net loss for all periods presented, therefore diluted net loss per share is the same as basic net loss per share since the inclusion of potential shares of common stock would be anti-dilutive.

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Fair Value Measurement (Tables)

9 Months Ended

Sep. 30, 2024

Fair Value Disclosures [Abstract]

Financial Assets and Liabilities Measured at Fair Value on Recurring Basis

The following tables set forth the fair value of the Company’s financial assets and liabilities at fair value on a recurring basis based on the three-tier fair value hierarchy (in thousands):

	September 30, 2024
	Level 1		Level 2		Level 3		Total
Financial Assets:
Money market funds	$	69,900	$	—	$	—	$	69,900
U.S. government treasury securities	140,072		—		—		140,072
U.S. government agency securities	—		100,328		—		100,328
Commercial paper	—		75,717		—		75,717
Corporate bonds	—		26,530		—		26,530
Total financial assets	$	209,972	$	202,575	$	—	$	412,547
Liabilities:
Parapyre Option Obligation	$	—	$	13,035	$	—	$	13,035
CVR liability	—		—		60,900		60,900
Total liabilities	$	—	$	13,035	$	60,900	$	73,935

	December 31, 2023
	Level 1		Level 2		Level 3		Total
Financial Assets:
Money market funds	$	150,648	$	—	$	—	$	150,648
U.S. government treasury securities	32,843		—		—		32,843
U.S. government agency securities	—		16,257		—		16,257
Commercial paper	—		104,141		—		104,141
Corporate bonds	—		33,064		—		33,064
Total financial assets	$	183,491	$	153,462	$	—	$	336,953
Liabilities:
CVR liability	$	—	$	—	$	42,700	$	42,700
Total liabilities	$	—	$	—	$	42,700	$	42,700

Significant Inputs used to Estimate the Fair Value of Derivative Liabilities

The significant inputs used to estimate the fair value of the CVR liability were as follows:

	September 30, 2024
Estimated cash flow dates	05/28/25 - 06/22/26
Estimated probability of success	72% - 100%
Estimated reimbursement rate compared to reimbursement target	81% - 100%
Risk-adjusted discount rates	7.76% - 7.82%

Changes in Derivative Liabilities

The following table presents changes in the CVR liability for the periods presented (in thousands):

	CVR Liability
Beginning balance as of December 31, 2023	$	42,700
Changes in the fair value of the CVR liability	19,630
Payments	(1,430)
Ending Balance as of September 30, 2024	$	60,900

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Cash Equivalents and Marketable Securities (Tables)

9 Months Ended

Sep. 30, 2024

Cash and Cash Equivalents [Abstract]

Estimated Fair Value of Cash Equivalents and Marketable Securities and the Gross Unrealized Gains and Losses

The following tables summarize the estimated fair value of the Company’s cash equivalents and marketable securities and the gross unrealized gains and losses (in thousands):

	September 30, 2024
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses		Estimated Fair Value
Cash equivalents:
Money market funds	$	69,900	$	—	$	—	$	69,900
Total cash equivalents	$	69,900	$	—	$	—	$	69,900
Marketable securities:
Commercial paper	$	75,503	$	214	$	—	$	75,717
Corporate bonds	26,457		76		(3)		26,530
U.S. government treasury securities	139,313		768		(9)		140,072
U.S. government agency securities	99,973		363		(8)		100,328
Total marketable securities	$	341,246	$	1,421	$	(20)	$	342,647

	December 31, 2023
	Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses		Estimated Fair Value
Cash equivalents:
Money market funds	$	150,648	$	—	$	—	$	150,648
Commercial paper	24,950		5		—		24,955
U.S. government treasury securities	10,965		1		—		10,966
Total cash equivalents	$	186,563	$	6	$	—	$	186,569
Marketable securities:
Commercial paper	$	79,124	$	62	$	—	$	79,186
Corporate bonds	32,984		81		(1)		33,064
U.S. government treasury securities	21,846		31		—		21,877
U.S. government agency securities	16,147		110		—		16,257
Total marketable securities	$	150,101	$	284	$	(1)	$	150,384

Available-for-Sale Securities in an Unrealized Loss Position

The following table summarizes the available-for-sale securities in an unrealized loss position for which an allowance for credit losses has not been recorded as of September 30, 2024 and December 31, 2023, aggregated by major security type and length of time in a continuous unrealized loss position:

	September 30, 2024
	Less Than 12 Months				12 Months or Longer				Total
	Fair Value		Unrealized Losses		Fair Value		Unrealized Losses		Fair Value		Unrealized Losses
Corporate bonds	$	1,952	$	(3)	$	—	$	—	$	1,952	$	(3)
U.S. government treasury securities	17,517		(9)		—		—		17,517		(9)
U.S. government agency securities	18,101		(8)		—		—		18,101		(8)
Total marketable securities	$	37,570	$	(20)	$	—	$	—	$	37,570	$	(20)
	December 31, 2023
	Less Than 12 Months				12 Months or Longer				Total
	Fair Value		Unrealized Losses		Fair Value		Unrealized Losses		Fair Value		Unrealized Losses
Corporate bonds	$	9,907	$	(1)	$	—	$	—	$	9,907	$	(1)
U.S. government treasury securities	4,831		—		—		—		4,831		—
Total marketable securities	$	14,738	$	(1)	$	—	$	—	$	14,738	$	(1)

Contractual Maturities of Marketable Securities at Estimated Fair Value

The following table summarizes the contractual maturities of the Company’s marketable securities at estimated fair value (in thousands):

	September 30, 2024		December 31, 2023
Due in one year or less	$	253,613	$	115,784
Due in 1 - 2 years	89,034		34,600
Total marketable securities	$	342,647	$	150,384

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Accrued and Other Current Liabilities (Tables)

9 Months Ended

Sep. 30, 2024

Payables and Accruals [Abstract]

Accrued and Other Current Liabilities

Accrued and other current liabilities consist of the following (in thousands):

	September 30, 2024		December 31, 2023
Accrued compensation	$	3,966	$	4,054
Accrued contracted research and development costs	7,527		7,092
Accrued professional and consulting fees	1,134		1,474
Accrued other	526		488
Total accrued and other current liabilities	$	13,153	$	13,108

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Asset Acquisition (Tables)

9 Months Ended

Sep. 30, 2024

Business Combination, Asset Acquisition, and Joint Venture Formation [Abstract]

Asset Acquisition Cost

The Asset Acquisition costs are shown on the following table (in millions):

	June 22, 2023
Consideration transferred in Series A Preferred Stock and Common Stock	$	110.0
Transaction costs incurred by Pre-Merger Spyre	3.2
Total cost to acquire asset	$	113.2

The allocation of the purchase price to net assets acquired is as a follows:

	June 22, 2023
Acquired in-process research and development	$	130.2
Cash acquired	3.0
Assumed liabilities	(20.0)
Total cost to acquire asset	$	113.2

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Related Party Transactions (Tables)

9 Months Ended

Sep. 30, 2024

Related Party Transactions [Abstract]

Expenses related to Related Party which were Settled in Cash

The following is the summary of expenses related to the Paragon Agreement and License Agreements, which are ultimately settled in cash (in millions) and recorded within Research and development in the consolidated statement of operations for the periods presented:

	Three Months Ended September 30,				Nine Months Ended September 30,
	2024		2023		2024		2023
Reimbursable costs under the Paragon Agreement	$	1.3	$	16.7	$	15.3	$	17.9
License Agreements milestone and sublicensing fees	0.3		—		5.9		—
Total related party expense (excludes stock comp)	$	1.6	$	16.7	$	21.2	$	17.9

Related Party Accounts Payable

The following is the summary of Related party accounts payable and other current liabilities (in millions):

	September 30, 2024		December 31, 2023
Reimbursable costs under the Paragon Agreement	$	1.2	$	16.6
Parapyre warrants liability	13.0		—
License Agreements development milestone liability (see Note 7)	0.3		—
Total related party accounts payable	$	14.5	$	16.6

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Stock-Based Compensation (Tables)

9 Months Ended

Sep. 30, 2024

Share-Based Payment Arrangement [Abstract]

Stock Awards Granted

The following table summarizes the Company’s stock awards granted under all equity incentive and inducement plans for each of the periods indicated:

	Three Months Ended September 30,						Nine Months Ended September 30,
	2024			2023			2024			2023
	Grants	Weighted Average Grant Date Fair Value		Grants	Weighted Average Grant Date Fair Value		Grants	Weighted Average Grant Date Fair Value		Grants	Weighted Average Grant Date Fair Value
Stock options	425,500	$	25.74	1,044,667	$	14.50	1,857,853	$	28.40	3,867,366	$	9.65

Stock-Based Compensation Expense

Total stock-based compensation expense recognized from the Company’s equity incentive plans, 2018 Plan, 2016 ESPP and Parapyre Option Obligation during the periods presented was as follows (in thousands):

	Three Months Ended September 30,				Nine Months Ended September 30,
	2024		2023		2024		2023
Research and development (1)	$	8,555	$	2,965	$	18,863	$	4,136
General and administrative	4,545		1,820		16,754		4,269
Total stock-based compensation expense (2)	$	13,100	$	4,785	$	35,617	$	8,405
(1) For the three and nine months ended September 30, 2024, $6.1 million and $13.0 million, respectively, was recognized as stock compensation expense related to the Parapyre Option Obligation. For the three and nine months ended September 30, 2023, $2.7 million and $2.9 million, respectively, was recognized as stock compensation expense related to the Parapyre Option Obligation. (2) Of the total $13.1 million and $35.6 million of stock-based compensation expense for the three and nine months ended September 30, 2024, $0.1 million and $3.6 million, respectively, is related to legacy Aeglea employees and directors who had been terminated as of the end of the respective period. Of the total $4.8 million and $8.4 million of stock-based compensation expense for the three and nine months ended September 30, 2023, $0.8 million and $4.2 million, respectively, is related to legacy Aeglea employees and directors who had been terminated as of the end of the period.

Assumptions used to Estimate the Fair Value of Stock Options Granted

The following table summarizes the weighted-average Black-Scholes option pricing model assumptions used to estimate the fair value of stock options granted under the Company's equity incentive plans, and the shares purchasable under the 2016 ESPP during the periods presented:

	Three Months Ended September 30,		Nine Months Ended September 30,
	2024	2023	2024	2023
Stock Options Granted
Expected term (in years)	6.08	6.08	6.02	6.04
Expected volatility	105%	101%	105%	111%
Risk-free interest	4.13%	4.28%	4.03%	4.07%
Dividend yield	—	—	—	—
2016 ESPP
Expected term (in years)	0.50	0.50	0.50	0.49
Expected volatility	71%	222%	83%	181%
Risk-free interest	5.02%	5.29%	5.15%	4.99%
Dividend yield	—	—	—	—

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Net Loss Per Share (as restated) (Tables)

9 Months Ended

Sep. 30, 2024

Earnings Per Share [Abstract]

Reconciliation of Basic and Diluted Net Loss Per Share

The following table sets forth the computation of basic and diluted net loss per share of Common Stock, Series A Preferred Stock, and Series B Preferred Stock (in thousands, except share and per share amounts):

	Three Months Ended September 30,
	2024						2023
	Series A Preferred Stock		Series B Preferred Stock		Common Stock		Series A Preferred Stock		Series B Preferred Stock		Common Stock
Net loss per share, basic and diluted:
Numerator
Allocation of losses	$	(14,610)	$	(704)	$	(53,714)	$	(36,427)	$	—	$	(3,680)
Denominator
Weighted-average shares outstanding	346,045		16,667		50,889,433		1,062,542		—		4,015,661
Weighted-average pre-funded warrants outstanding	—		—		—		—		—		278,151
Number of shares used in per share computation	346,045		16,667		50,889,433		1,062,542		—		4,293,812
Net loss per share, basic and diluted	$	(42.22)	$	(42.24)	$	(1.06)	$	(34.28)	$	—	$	(0.86)
	Nine Months Ended September 30,
	2024						2023
	Series A Preferred Stock		Series B Preferred Stock		Common Stock		Series A Preferred Stock		Series B Preferred Stock		Common Stock
Net loss per share, basic and diluted:
Numerator
Allocation of losses	$	(36,733)	$	(9,105)	$	(105,884)	$	(217,573)	$	—	$	(58,037)
Denominator
Weighted-average shares outstanding	383,903		95,158		44,146,958		371,286		—		3,116,434
Weighted-average pre-funded warrants outstanding	—		—		116,788		—		—		845,112
Number of shares used in per share computation	383,903		95,158		44,263,746		371,286		—		3,961,546
Net loss per share, basic and diluted	$	(95.68)	$	(95.68)	$	(2.39)	$	(586.00)	$	—	$	(14.65)

Weighted-Average Equity Instruments Excluded from Calculation of Diluted Net Loss Per Share

The following weighted-average equity instruments were excluded from the calculation of diluted net loss per share because their effect would have been anti-dilutive for the periods presented:

	Three Months Ended September 30,		Nine Months Ended September 30,
	2024	2023	2024	2023
Options to purchase common stock	4,733,609	3,135,672	4,583,260	1,426,224
Unvested restricted stock units	65,925	—	69,503	252
Outstanding Parapyre warrants	684,407	—	684,407	—

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Restructuring Charges (Tables)

9 Months Ended

Sep. 30, 2024

Restructuring and Related Activities [Abstract]

Charges Related to the Restructuring Activities

A summary of the charges related to the restructuring activities is as follows (in thousands):

	Severance Related Expenses		Stock Compensation Expenses		Loss on Disposal of Long Lived Assets		Lease Asset Impairment		Total Restructuring Costs
Research and development	$	3,182	$	123	$	749	$	1,405	$	5,459
General and administrative	3,266		870		182		1,175		5,493
Total	$	6,448	$	993	$	931	$	2,580	$	10,952

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The Company and Basis of Presentation (Details) $ / shares in Units, $ in Thousands										1 Months Ended		3 Months Ended			9 Months Ended	115 Months Ended
	May 14, 2024 shares	Apr. 23, 2024 shares	Mar. 20, 2024 USD ($) shares	Mar. 18, 2024 shares	Dec. 11, 2023 USD ($) $ / shares shares	Nov. 21, 2023 shares	Sep. 08, 2023	Jun. 26, 2023 USD ($) shares	Jun. 22, 2023 $ / shares shares	Sep. 30, 2024 USD ($) $ / shares shares	Apr. 30, 2023	Jun. 30, 2024 shares	Mar. 31, 2024 shares	Jun. 30, 2023 shares	Sep. 30, 2024 USD ($) segment $ / shares shares	Sep. 30, 2024 USD ($) $ / shares shares	Sep. 06, 2024 USD ($)	Apr. 25, 2024 shares	Apr. 24, 2024 shares	Dec. 31, 2023 USD ($) $ / shares shares	Nov. 22, 2023 shares
Company and Basis of Presentation [Line Items]
Number of operating segments | segment															1
Employee workforce, termination percentage											83.00%			83.00%
Common stock, par value (in dollars per share) | $ / shares										$ 0.0001					$ 0.0001	$ 0.0001				$ 0.0001
Series B non-voting convertible preferred stock, par value (in dollars per share) | $ / shares					$ 0.0001
Proceeds from raising capital | $																$ 1,100,000
Accumulated deficit | $										$ 916,136					$ 916,136	916,136				$ 764,414
Marketable securities | $										$ 414,200					$ 414,200	$ 414,200
Asset Acquisition
Company and Basis of Presentation [Line Items]
Fixed exchange ratio									54.94488%
Spyre Therapeutics, Inc.
Company and Basis of Presentation [Line Items]
Asset acquisition, stockholder payment period									3 years
Asset acquisition, cash payment, threshold period									1 year
Spyre 2023 Equity Incentive Plan | Asset Acquisition
Company and Basis of Presentation [Line Items]
Number of outstanding and unexercised stock options to purchase (in shares)									2,734
Spyre 2023 Equity Incentive Plan | Spyre Therapeutics, Inc.
Company and Basis of Presentation [Line Items]
Number of outstanding and unexercised stock options to purchase (in shares)									2,734
Series A Non Voting Convertible Preferred Stock
Company and Basis of Presentation [Line Items]
Preferred stock, par value (in dollars per share) | $ / shares										$ 0.0001					$ 0.0001	$ 0.0001				$ 0.0001
Conversion basis									40
Preferred stock, not automatically converted, outstanding (in shares)																					437,037
Issuance of non-voting convertible preferred stock (in shares)								721,452
Exchange of Series A non-voting convertible preferred stock into common stock (in shares)		90,992
Preferred stock, outstanding (in shares)										346,045					346,045	346,045		346,045	346,045	437,037
Series A Non Voting Convertible Preferred Stock | Asset Acquisition
Company and Basis of Presentation [Line Items]
Number of shares transferred as equity interest in asset acquisition (in shares)									364,887
Preferred stock, par value (in dollars per share) | $ / shares									$ 0.0001
Conversion basis									40
Series A Non Voting Convertible Preferred Stock | Spyre Therapeutics, Inc.
Company and Basis of Presentation [Line Items]
Number of shares transferred as equity interest in asset acquisition (in shares)									364,887
Series B Non Voting Convertible Preferred Stock
Company and Basis of Presentation [Line Items]
Preferred stock, par value (in dollars per share) | $ / shares										$ 0.0001					$ 0.0001	$ 0.0001
Conversion basis			40
Preferred stock, not automatically converted, outstanding (in shares)										16,667					16,667	16,667
Series B non-voting convertible preferred stock, par value (in dollars per share) | $ / shares																				$ 0.0001
Issuance of non-voting convertible preferred stock (in shares)			121,625	271,625	150,000
Preferred stock, outstanding (in shares)										16,667					16,667	16,667
Common Stock
Company and Basis of Presentation [Line Items]
Exchange of Series A non-voting convertible preferred stock into common stock (in shares)		3,639,680
Private Placement
Company and Basis of Presentation [Line Items]
Gross proceeds received in private placement | $					$ 180,000
Placement agent and other offering costs | $			$ 11,200		10,900
Private Placement | Series A Non Voting Convertible Preferred Stock
Company and Basis of Presentation [Line Items]
Number of shares sold in private placement (in shares)								721,452
Gross proceeds received in private placement | $								$ 210,000
Placement agent and other offering expenses in private placement | $								$ 12,700
Private Placement | Series B Non Voting Convertible Preferred Stock
Company and Basis of Presentation [Line Items]
Gross proceeds received in private placement | $			$ 180,000		$ 90,000
At-The-Market Offering
Company and Basis of Presentation [Line Items]
Sale of stock, authorized amount | $																	$ 500,000
At-The-Market Offering | Common Stock
Company and Basis of Presentation [Line Items]
Number of shares of common stock sold (in shares)										426,287
Sale of stock, aggregate offering price | $																	$ 200,000
Sale of stock, price per share (in dollars per share) | $ / shares										$ 28.15					$ 28.15	$ 28.15
Sale of stock, proceeds received | $										$ 11,800
Common Stock
Company and Basis of Presentation [Line Items]
Reverse stock split, conversion ratio							0.04
Shares converted (in shares)												10,198,000
Exchange of Series A non-voting convertible preferred stock into common stock (in shares)												3,640,000
Common Stock | Conversion Of Series A Non-Voting Convertible Preferred Stock
Company and Basis of Presentation [Line Items]
Shares converted (in shares)						25,972,080
Common Stock | Conversion Of Series B Non-Voting Convertible Preferred Stock
Company and Basis of Presentation [Line Items]
Shares converted (in shares)	10,198,320														10,198,320
Common Stock | Asset Acquisition
Company and Basis of Presentation [Line Items]
Number of shares transferred as equity interest in asset acquisition (in shares)									517,809
Common stock, par value (in dollars per share) | $ / shares									$ 0.0001
Common Stock | Private Placement
Company and Basis of Presentation [Line Items]
Number of shares of common stock sold (in shares)					6,000,000
Preferred Stock | Series A Non Voting Convertible Preferred Stock
Company and Basis of Presentation [Line Items]
Issuance of non-voting convertible preferred stock (in shares)														721,000
Exchange of Series A non-voting convertible preferred stock into common stock (in shares)												(91,000)
Preferred stock, outstanding (in shares)										346,000		346,000	437,000		346,000	346,000				437,000
Preferred Stock | Series A Non Voting Convertible Preferred Stock | Conversion Of Series A Non-Voting Convertible Preferred Stock
Company and Basis of Presentation [Line Items]
Shares converted (in shares)						649,302
Preferred Stock | Series B Non Voting Convertible Preferred Stock
Company and Basis of Presentation [Line Items]
Shares converted (in shares)												(255,000)
Issuance of non-voting convertible preferred stock (in shares)													122,000
Preferred stock, outstanding (in shares)										17,000		17,000	0		17,000	17,000				0
Preferred Stock | Series B Non Voting Convertible Preferred Stock | Conversion Of Series B Non-Voting Convertible Preferred Stock
Company and Basis of Presentation [Line Items]
Shares converted (in shares)	254,958														254,958

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Fair Value Measurements - Financial Assets and Liabilities Measured at Fair Value on Recurring Basis (Details) - Fair Value, Measurements, Recurring - USD ($) $ in Thousands	Sep. 30, 2024	Dec. 31, 2023
Financial Assets:
Total financial assets	$ 412,547	$ 336,953
Liabilities:
Total liabilities	73,935	42,700
U.S. government treasury securities
Financial Assets:
Total financial assets	140,072	32,843
U.S. government agency securities
Financial Assets:
Total financial assets	100,328	16,257
Commercial paper
Financial Assets:
Total financial assets	75,717	104,141
Corporate bonds
Financial Assets:
Total financial assets	26,530	33,064
Parapyre Option Obligation
Liabilities:
Total liabilities	13,035
CVR liability
Liabilities:
Total liabilities	60,900	42,700
Level 1
Financial Assets:
Total financial assets	209,972	183,491
Liabilities:
Total liabilities	0	0
Level 1 | U.S. government treasury securities
Financial Assets:
Total financial assets	140,072	32,843
Level 1 | U.S. government agency securities
Financial Assets:
Total financial assets	0	0
Level 1 | Commercial paper
Financial Assets:
Total financial assets	0	0
Level 1 | Corporate bonds
Financial Assets:
Total financial assets	0	0
Level 1 | Parapyre Option Obligation
Liabilities:
Total liabilities	0
Level 1 | CVR liability
Liabilities:
Total liabilities	0	0
Level 2
Financial Assets:
Total financial assets	202,575	153,462
Liabilities:
Total liabilities	13,035	0
Level 2 | U.S. government treasury securities
Financial Assets:
Total financial assets	0	0
Level 2 | U.S. government agency securities
Financial Assets:
Total financial assets	100,328	16,257
Level 2 | Commercial paper
Financial Assets:
Total financial assets	75,717	104,141
Level 2 | Corporate bonds
Financial Assets:
Total financial assets	26,530	33,064
Level 2 | Parapyre Option Obligation
Liabilities:
Total liabilities	13,035
Level 2 | CVR liability
Liabilities:
Total liabilities	0	0
Level 3
Financial Assets:
Total financial assets	0	0
Liabilities:
Total liabilities	60,900	42,700
Level 3 | U.S. government treasury securities
Financial Assets:
Total financial assets	0	0
Level 3 | U.S. government agency securities
Financial Assets:
Total financial assets	0	0
Level 3 | Commercial paper
Financial Assets:
Total financial assets	0	0
Level 3 | Corporate bonds
Financial Assets:
Total financial assets	0	0
Level 3 | Parapyre Option Obligation
Liabilities:
Total liabilities	0
Level 3 | CVR liability
Liabilities:
Total liabilities	60,900	42,700
Money market funds
Financial Assets:
Total financial assets	69,900	150,648
Money market funds | Level 1
Financial Assets:
Total financial assets	69,900	150,648
Money market funds | Level 2
Financial Assets:
Total financial assets	0	0
Money market funds | Level 3
Financial Assets:
Total financial assets	$ 0	$ 0

XML

Fair Value Measurements - Narrative (Details) - USD ($) $ / shares in Units, $ in Thousands			3 Months Ended		9 Months Ended
	Jul. 07, 2023	Jun. 22, 2023	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023	Dec. 31, 2023
Series A Non Voting Convertible Preferred Stock
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Proceeds from issuance of stock, settled liability	$ 189,700				$ 0	$ 197,364
Parapyre Option Obligation
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Percentage of annual equity grant of options			1.00%		1.00%
CVR liability
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Changes in the fair value of the CVR liability					$ 19,630
Change in fair value of forward contract liability					19,630	(1,300)
Forward contract liability
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Fair value of forward contract liability		$ 106,200
Change in fair value of forward contract liability			$ 0	$ 25,360	$ 0	$ 83,530
Spyre Therapeutics, Inc.
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Asset acquisition, stockholder payment period		3 years
Asset acquisition, cash payment, threshold period		1 year
Spyre Therapeutics, Inc. | Series A Non Voting Convertible Preferred Stock
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Number of shares transferred as equity interest in asset acquisition (in shares)		364,887
Outstanding Parapyre warrants
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Warrants to purchase shares (in shares)							684,407
Exercise price per warrant (in dollars per share)							$ 21.52

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Fair Value Measurements - Significant Inputs used to Estimate the Fair Value of Derivative Liability (Details) - Level 3	Sep. 30, 2024
Minimum | Estimated reimbursement rate compared to reimbursement target | CVR liability
Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation [Line Items]
Derivative liability, measurement input	0.81
Minimum | Risk-adjusted discount rates | CVR liability
Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation [Line Items]
Derivative liability, measurement input	0.0776
Minimum | CVR liability | Estimated probability of success
Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation [Line Items]
Derivative liability, measurement input	0.72
Maximum | Estimated reimbursement rate compared to reimbursement target | CVR liability
Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation [Line Items]
Derivative liability, measurement input	1
Maximum | Risk-adjusted discount rates | CVR liability
Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation [Line Items]
Derivative liability, measurement input	0.0782
Maximum | CVR liability | Estimated probability of success
Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation [Line Items]
Derivative liability, measurement input	1

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Fair Value Measurements - Changes in Derivative Liabilities (Details) - CVR liability $ in Thousands	9 Months Ended
	Sep. 30, 2024 USD ($)
Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]
Beginning balance	$ 42,700
Changes in the fair value of the CVR liability	19,630
Payments	(1,430)
Ending balance	$ 60,900

XML

Cash Equivalents and Marketable Securities - Estimated Fair Value of Cash Equivalents and Marketable Securities and the Gross Unrealized Gains and Losses (Details) - USD ($) $ in Thousands	Sep. 30, 2024	Dec. 31, 2023
Debt Securities, Available-for-Sale [Line Items]
Cash equivalents, amortized cost	$ 69,900	$ 186,563
Cash equivalents, gross unrealized gains	0	6
Cash equivalents, gross unrealized losses	0	0
Cash equivalents, estimated fair value	69,900	186,569
Marketable securities, amortized cost	341,246	150,101
Marketable securities, gross unrealized gains	1,421	284
Marketable securities, gross unrealized losses	(20)	(1)
Marketable securities, estimated fair value	342,647	150,384
Money market funds
Debt Securities, Available-for-Sale [Line Items]
Cash equivalents, amortized cost	69,900	150,648
Cash equivalents, gross unrealized gains	0	0
Cash equivalents, gross unrealized losses	0	0
Cash equivalents, estimated fair value	69,900	150,648
Commercial paper
Debt Securities, Available-for-Sale [Line Items]
Cash equivalents, amortized cost		24,950
Cash equivalents, gross unrealized gains		5
Cash equivalents, gross unrealized losses		0
Cash equivalents, estimated fair value		24,955
Marketable securities, amortized cost	75,503	79,124
Marketable securities, gross unrealized gains	214	62
Marketable securities, gross unrealized losses	0	0
Marketable securities, estimated fair value	75,717	79,186
Corporate bonds
Debt Securities, Available-for-Sale [Line Items]
Marketable securities, amortized cost	26,457	32,984
Marketable securities, gross unrealized gains	76	81
Marketable securities, gross unrealized losses	(3)	(1)
Marketable securities, estimated fair value	26,530	33,064
U.S. government treasury securities
Debt Securities, Available-for-Sale [Line Items]
Cash equivalents, amortized cost		10,965
Cash equivalents, gross unrealized gains		1
Cash equivalents, gross unrealized losses		0
Cash equivalents, estimated fair value		10,966
Marketable securities, amortized cost	139,313	21,846
Marketable securities, gross unrealized gains	768	31
Marketable securities, gross unrealized losses	(9)	0
Marketable securities, estimated fair value	140,072	21,877
U.S. government agency securities
Debt Securities, Available-for-Sale [Line Items]
Marketable securities, amortized cost	99,973	16,147
Marketable securities, gross unrealized gains	363	110
Marketable securities, gross unrealized losses	(8)	0
Marketable securities, estimated fair value	$ 100,328	$ 16,257

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Cash Equivalents and Marketable Securities - Available-for-Sale Securities in an Unrealized Loss Position (Details) - USD ($) $ in Thousands	Sep. 30, 2024	Dec. 31, 2023
Fair Value
Less Than 12 Months	$ 37,570	$ 14,738
12 Months or Longer	0	0
Total, fair value	37,570	14,738
Unrealized Losses
Less Than 12 Months	(20)	(1)
12 Months or Longer	0	0
Total, unrealized losses	(20)	(1)
Corporate bonds
Fair Value
Less Than 12 Months	1,952	9,907
12 Months or Longer	0	0
Total, fair value	1,952	9,907
Unrealized Losses
Less Than 12 Months	(3)	(1)
12 Months or Longer	0	0
Total, unrealized losses	(3)	(1)
U.S. government treasury securities
Fair Value
Less Than 12 Months	17,517	4,831
12 Months or Longer	0	0
Total, fair value	17,517	4,831
Unrealized Losses
Less Than 12 Months	(9)	0
12 Months or Longer	0	0
Total, unrealized losses	(9)	$ 0
U.S. government agency securities
Fair Value
Less Than 12 Months	18,101
12 Months or Longer	0
Total, fair value	18,101
Unrealized Losses
Less Than 12 Months	(8)
12 Months or Longer	0
Total, unrealized losses	$ (8)

XML

Cash Equivalents and Marketable Securities - Narrative (Details)	3 Months Ended		9 Months Ended		12 Months Ended
	Sep. 30, 2024 USD ($) bank	Sep. 30, 2023 USD ($)	Sep. 30, 2024 USD ($) bank	Sep. 30, 2023 USD ($)	Dec. 31, 2023 USD ($)
Cash Equivalents And Marketable Securities [Line Items]
Number of domestic banking institutions (in banks) | bank	2		2
US Government Agencies Debt Securities
Cash Equivalents And Marketable Securities [Line Items]
Debt securities, available-for-sale, allowance for credit loss	$ 0		$ 0		$ 0
Impairment of marketable securities			0		0
Realized gains or losses on marketable securities	0	$ 0	0	$ 0
Accrued interest receivable on available-for-sale debt securities	1,700,000		1,700,000		$ 900,000
U.S. Banking Institution | Maximum
Cash Equivalents And Marketable Securities [Line Items]
Cash, FDIC insured amount	$ 250,000		$ 250,000

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Cash Equivalents and Marketable Securities - Contractual Maturities of Marketable Securities at Estimated Fair Value (Details) - USD ($) $ in Thousands	Sep. 30, 2024	Dec. 31, 2023
Cash and Cash Equivalents [Abstract]
Due in one year or less	$ 253,613	$ 115,784
Due in 1 - 2 years	89,034	34,600
Total marketable securities	$ 342,647	$ 150,384

XML

Accrued and Other Current Liabilities (Details) - USD ($) $ in Thousands	Sep. 30, 2024	Dec. 31, 2023
Payables and Accruals [Abstract]
Accrued compensation	$ 3,966	$ 4,054
Accrued contracted research and development costs	7,527	7,092
Accrued professional and consulting fees	1,134	1,474
Accrued other	526	488
Total accrued and other current liabilities	$ 13,153	$ 13,108

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Asset Acquisition - Narrative (Details) - Spyre Therapeutics, Inc. $ / shares in Units, $ in Millions	Jun. 22, 2023 USD ($) $ / shares shares
Asset Acquisition [Line Items]
Cost to acquire asset | $	$ 113.2
Asset acquisition consideration transferred issuable shares of common stock on an as-converted basis	14,595,480
Spyre 2023 Equity Incentive Plan
Asset Acquisition [Line Items]
Number of outstanding and unexercised stock options to purchase (in shares)	2,734
Series A Non Voting Convertible Preferred Stock
Asset Acquisition [Line Items]
Number of shares transferred as equity interest in asset acquisition (in shares)	364,887
Shares issued, price per share (in dollars per share) | $ / shares	$ 291.08
Common Stock
Asset Acquisition [Line Items]
Number of shares transferred as equity interest in asset acquisition (in shares)	517,809
Shares issued, price per share (in dollars per share) | $ / shares	$ 7.277

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Asset Acquisition - Asset Acquisition Cost (Details) - USD ($) $ in Thousands		3 Months Ended		9 Months Ended
	Jun. 22, 2023	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Asset Acquisition [Line Items]
Acquired in-process research and development		$ 0	$ (298)	$ 0	$ 130,188
Cash acquired				$ 0	$ 3,035
Spyre Therapeutics, Inc.
Asset Acquisition [Line Items]
Consideration transferred in Series A Preferred Stock and Common Stock	$ 110,000
Transaction costs incurred by Pre-Merger Spyre	3,200
Acquired in-process research and development	130,200
Cash acquired	3,000
Assumed liabilities	(20,000)
Total cost to acquire asset	$ 113,200

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Licensing Agreements (Details) - Related Party - USD ($) $ in Millions			3 Months Ended		9 Months Ended
	Dec. 14, 2023	Jul. 12, 2023	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Paragon Agreement
Related Party Transaction [Line Items]
Campaign timeline, minimum term					5 years
Royalty step-down percentage			33.00%		33.00%
Royalty term expiration period					12 years
Termination notice period					60 days
Sublicensing fee			$ 0.3		$ 0.4
Milestone expense recognized			0.0	$ 0.0	5.5	$ 0.0
Milestone payments			2.5		5.5
Milestone payments, outstanding and payable			$ 0.0		0.0
SPY001 License Agreement
Related Party Transaction [Line Items]
Nomination fee		$ 1.5
First milestone payment		2.5
SPY001 License Agreement | Maximum
Related Party Transaction [Line Items]
Contingent obligation based on milestones		$ 22.0
SPY002 License Agreement
Related Party Transaction [Line Items]
Nomination fee	$ 1.5
First milestone payment	2.5
SPY002 License Agreement | Maximum
Related Party Transaction [Line Items]
Contingent obligation based on milestones	$ 22.0
Sublicensing fee					$ 20.0

XML

Related Party Transactions - Narrative (Details)		3 Months Ended		9 Months Ended
	Nov. 22, 2023 $ / shares shares	Sep. 30, 2024 USD ($) seat shares	Sep. 30, 2023 USD ($) shares	Sep. 30, 2024 USD ($) seat shares	Sep. 30, 2023 USD ($) shares	Apr. 01, 2024	Mar. 31, 2024
Related Party Transaction [Line Items]
Stock-based compensation		$ 13,100,000	$ 4,800,000	$ 35,617,000	$ 8,405,000
Options granted (in shares) | shares		425,500	1,044,667	1,857,853	3,867,366
Stock-based compensation expense		$ 13,100,000	$ 4,785,000	$ 35,617,000	$ 8,405,000
Related Party
Related Party Transaction [Line Items]
Development cost reduction, percent						50.00%
Development cost reimbursement, percent							50.00%
Related Party | Paragon Agreement
Related Party Transaction [Line Items]
Number of board seats held by related party | seat		2		2
Amount of related party transaction		$ 1,200,000		$ 30,700,000
Stock-based compensation		6,100,000		13,000,000.0
Reduction in research and development expense		$ 5,900,000		$ 5,900,000
Common stock, shares outstanding, percentage available to purchase on a diluted basis		1.00%		1.00%
Related Party | Subsequent to Asset Acquisition
Related Party Transaction [Line Items]
Amount of related party transaction		$ 7,400,000		$ 28,300,000
Related Party | Consulting Agreement
Related Party Transaction [Line Items]
Options granted (in shares) | shares	477,000
Exercise price (in dollars per share) | $ / shares	$ 10.39
Vesting period	36 months
Stock-based compensation expense		$ 300,000	$ 0	$ 800,000	$ 0
Related Party | Consulting Agreement | Share-Based Payment Arrangement, Tranche One
Related Party Transaction [Line Items]
Vesting percentage	25.00%
Vesting period	1 year
Paragon Therapeutics Inc | Maximum | Related Party | Paragon Agreement
Related Party Transaction [Line Items]
Percentage of ownership by noncontrolling owner		5.00%		5.00%
Fairmount Funds Management LLC | Minimum | Related Party | Paragon Agreement
Related Party Transaction [Line Items]
Percentage of ownership by noncontrolling owner		5.00%		5.00%
Percentage of ownership held in third party		5.00%		5.00%

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Related Party Transactions - Expenses related to Related Party which were Settled in Cash (Details) - USD ($) $ in Thousands		3 Months Ended		9 Months Ended
		Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Related Party Transaction [Line Items]
Research and development	[1]	$ 44,744	$ 24,660	$ 112,308	$ 55,822
Related Party
Related Party Transaction [Line Items]
Research and development		7,700	19,400	34,200	20,800
Paragon and License Agreement | Related Party
Related Party Transaction [Line Items]
Research and development		1,600	16,700	21,200	17,900
Paragon Agreement | Related Party
Related Party Transaction [Line Items]
Research and development		1,300	16,700	15,300	17,900
License Agreement | Related Party
Related Party Transaction [Line Items]
Research and development		$ 300	$ 0	$ 5,900	$ 0

[1] Includes $7.7 million and $34.2 million in related party expenses for the three and nine months ended September 30, 2024, respectively, and $19.4 million and $20.8 million related party expenses for the three and nine months ended September 30, 2023, respectively.

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Related Party Transactions - Related Party Accounts Payable (Details) - Related Party - USD ($) $ in Millions	Sep. 30, 2024	Dec. 31, 2023
Related Party Transaction [Line Items]
Total related party accounts payable	$ 14.5	$ 16.6
Paragon Agreement
Related Party Transaction [Line Items]
Total related party accounts payable	1.2	16.6
Parapyre warrants liability
Related Party Transaction [Line Items]
Total related party accounts payable	13.0	0.0
License Agreements development milestone liability (see Note 7)
Related Party Transaction [Line Items]
Total related party accounts payable	$ 0.3	$ 0.0

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Convertible Preferred Stock and Stockholders' Equity - Narrative (Details) $ / shares in Units, $ in Thousands										1 Months Ended	3 Months Ended			9 Months Ended	40 Months Ended
	May 14, 2024 shares	Apr. 23, 2024 shares	Mar. 20, 2024 USD ($) shares	Mar. 18, 2024 shares	Dec. 11, 2023 USD ($) shares	Nov. 21, 2023 shares	Jul. 07, 2023 shares	Jun. 26, 2023 USD ($) shares	Jun. 22, 2023	Sep. 30, 2024 USD ($) $ / shares shares	Jun. 30, 2024 shares	Mar. 31, 2024 USD ($) shares	Jun. 30, 2023 USD ($) shares	Sep. 30, 2024 $ / shares shares	May 31, 2022 $ / shares	Nov. 01, 2024 USD ($)	Sep. 06, 2024 USD ($)	Apr. 25, 2024 shares	Apr. 24, 2024 shares	Dec. 31, 2023 $ / shares shares	Nov. 22, 2023 shares
Common Stock
Class of Stock [Line Items]
Shares converted (in shares)											10,198,000
Exchange of Series A non-voting convertible preferred stock into common stock (in shares)											3,640,000
Conversion Of Series A Non-Voting Convertible Preferred Stock | Common Stock
Class of Stock [Line Items]
Shares converted (in shares)						25,972,080
Conversion Of Series B Non-Voting Convertible Preferred Stock | Common Stock
Class of Stock [Line Items]
Shares converted (in shares)	10,198,320													10,198,320
Private Placement
Class of Stock [Line Items]
Gross proceeds received in private placement | $					$ 180,000
Private Placement | Common Stock
Class of Stock [Line Items]
Number of shares of common stock sold (in shares)					6,000,000
At-The-Market Offering
Class of Stock [Line Items]
Sale of stock, authorized amount | $																	$ 500,000
Series A Non Voting Convertible Preferred Stock
Class of Stock [Line Items]
Preferred stock issued and outstanding percentage									30.00%
Issuance of non-voting convertible preferred stock (in shares)								721,452
Issuance of Series A/B non-voting convertible preferred stock in connection with private placement, net of financing costs | $								$ 197,300
Conversion basis									40
Preferred stock, not automatically converted, outstanding (in shares)																					437,037
Exchange of Series A non-voting convertible preferred stock into common stock (in shares)		90,992
Preferred stock, outstanding (in shares)										346,045				346,045				346,045	346,045	437,037
Series A Non Voting Convertible Preferred Stock | Preferred Stock
Class of Stock [Line Items]
Issuance of non-voting convertible preferred stock (in shares)													721,000
Issuance of Series A/B non-voting convertible preferred stock in connection with private placement, net of financing costs | $													$ 197,323
Exchange of Series A non-voting convertible preferred stock into common stock (in shares)											(91,000)
Preferred stock, outstanding (in shares)										346,000	346,000	437,000		346,000						437,000
Series A Non Voting Convertible Preferred Stock | Conversion Of Series A Non-Voting Convertible Preferred Stock | Preferred Stock
Class of Stock [Line Items]
Shares converted (in shares)						649,302
Series A Non Voting Convertible Preferred Stock | Asset Acquisition
Class of Stock [Line Items]
Number of shares transferred as equity interest in asset acquisition (in shares)							364,887
Series A Non Voting Convertible Preferred Stock | Private Placement
Class of Stock [Line Items]
Number of shares sold in private placement (in shares)								721,452
Gross proceeds received in private placement | $								$ 210,000
Common Stock
Class of Stock [Line Items]
Exchange of Series A non-voting convertible preferred stock into common stock (in shares)		3,639,680
Common Stock | At-The-Market Offering
Class of Stock [Line Items]
Sale of stock, aggregate offering price | $																	$ 200,000
Number of shares of common stock sold (in shares)										426,287
Sale of stock, price per share (in dollars per share) | $ / shares										$ 28.15				$ 28.15
Sale of stock, proceeds received | $										$ 11,800
Common Stock | At-The-Market Offering | Subsequent Events
Class of Stock [Line Items]
Sale of stock, remaining authorized amount | $																$ 188,000
Series B Non Voting Convertible Preferred Stock
Class of Stock [Line Items]
Issuance of non-voting convertible preferred stock (in shares)			121,625	271,625	150,000
Conversion basis			40
Preferred stock, not automatically converted, outstanding (in shares)										16,667				16,667
Preferred stock, outstanding (in shares)										16,667				16,667
Series B Non Voting Convertible Preferred Stock | Preferred Stock
Class of Stock [Line Items]
Issuance of non-voting convertible preferred stock (in shares)												122,000
Issuance of Series A/B non-voting convertible preferred stock in connection with private placement, net of financing costs | $												$ 168,850
Shares converted (in shares)											(255,000)
Preferred stock, outstanding (in shares)										17,000	17,000	0		17,000						0
Series B Non Voting Convertible Preferred Stock | Conversion Of Series B Non-Voting Convertible Preferred Stock | Preferred Stock
Class of Stock [Line Items]
Shares converted (in shares)	254,958													254,958
Series B Non Voting Convertible Preferred Stock | Private Placement
Class of Stock [Line Items]
Gross proceeds received in private placement | $			$ 180,000		$ 90,000
Maximum | Series A Non Voting Convertible Preferred Stock
Class of Stock [Line Items]
Beneficially holders owned percentage									19.90%
Maximum | Series B Non Voting Convertible Preferred Stock
Class of Stock [Line Items]
Beneficial holders owned percentage														19.90%
Minimum | Series A Non Voting Convertible Preferred Stock
Class of Stock [Line Items]
Beneficially holders owned percentage									0.00%
Minimum | Series B Non Voting Convertible Preferred Stock
Class of Stock [Line Items]
Beneficial holders owned percentage														0.00%
Pre-Funded Warrants
Class of Stock [Line Items]
Exercise price per warrant (in dollars per share) | $ / shares															$ 0.0025
Maximum ownership percentage of common stock shares for outstanding warrants to be exercised															4.99%
Ownership percentage for outstanding warrants to purchase shares of common stock to be exercised to certain holders															9.99%
Revised ownership percentage, period to take effect after notice															61 days
Number of shares sold in private placement (in shares)										0				0
Pre-Funded Warrants | Maximum
Class of Stock [Line Items]
Maximum ownership percentage of common stock shares for outstanding warrants to be exercised															19.99%
Outstanding Parapyre warrants
Class of Stock [Line Items]
Exercise price per warrant (in dollars per share) | $ / shares																				$ 21.52
Maximum ownership percentage of common stock shares for outstanding warrants to be exercised														4.99%
Warrants to purchase shares (in shares)																				684,407
Number of warrants exercised (in shares)										0				0

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Stock-Based Compensation - Narrative (Details) - USD ($) $ in Thousands		3 Months Ended		9 Months Ended		12 Months Ended
	Jun. 22, 2023	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023	Dec. 31, 2016	Jan. 01, 2024	Jan. 01, 2023
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Stock-based compensation		$ 13,100	$ 4,800	$ 35,617	$ 8,405
2015 and 2016 and 2018 Equity Inducement Plan | Service Based Awards
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Vest period grant date				4 years
Share-based payment award, term				10 years
2015 Equity Incentive Plan
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Shares subject to options outstanding (in shares)				952
2016 Equity Incentive Plan
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Annual percentage of additional shares						5.00%
Additional number of shares available for issuance (in shares)							3,023,650	104,561
Common stock available for future issuance (in shares)		7,228,113		7,228,113
Outstanding option awards (in shares)		3,247,677		3,247,677
2018 Equity Inducement Plan
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Common stock available for future issuance (in shares)		6,999,445		6,999,445
Outstanding option awards (in shares)		5,624,067		5,624,067
2018 Equity Inducement Plan, Amended
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Common stock available for future issuance, additional amount authorized (in shares)		1,000,000		1,000,000
Spyre 2023 Equity Incentive Plan | Asset Acquisition
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Number of outstanding and unexercised stock options to purchase (in shares)	2,734
Parapyre Option Obligation
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Pro-rated estimated fair value of options				$ 13,000
Stock-based compensation		$ 6,100	$ 2,700	13,000	$ 2,900
Unamortized expense		$ 4,400		$ 4,400
2016 Employee Stock Purchase Plan | Employee Stock
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Number of shares issued (in shares)		14,053		16,383
2016 Employee Stock Purchase Plan | 2016 ESPP | Employee Stock
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Number of shares sold (in shares)		14,053	704	16,383	2,496

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Stock-Based Compensation - Stock Awards Granted (Details) - $ / shares	3 Months Ended		9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Share-Based Payment Arrangement [Abstract]
Grants (in shares)	425,500	1,044,667	1,857,853	3,867,366
Weighted Average Grant Date Fair Value (in dollars per share)	$ 25.74	$ 14.50	$ 28.40	$ 9.65

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Stock-Based Compensation - Stock-Based Compensation Expense (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Employee Service Share Based Compensation Allocation of Recognized Period Costs [Line Items]
Total stock-based compensation expense	$ 13,100	$ 4,785	$ 35,617	$ 8,405
Stock-based compensation	13,100	4,800	35,617	8,405
Aeglea Employees and Directors
Employee Service Share Based Compensation Allocation of Recognized Period Costs [Line Items]
Stock-based compensation	100	800	3,600	4,200
Parapyre Option Obligation
Employee Service Share Based Compensation Allocation of Recognized Period Costs [Line Items]
Stock-based compensation	6,100	2,700	13,000	2,900
Research and Development Expense
Employee Service Share Based Compensation Allocation of Recognized Period Costs [Line Items]
Total stock-based compensation expense	8,555	2,965	18,863	4,136
General and administrative
Employee Service Share Based Compensation Allocation of Recognized Period Costs [Line Items]
Total stock-based compensation expense	$ 4,545	$ 1,820	$ 16,754	$ 4,269

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Stock-Based Compensation - Assumptions used to Estimate the Fair Value of Stock Options Granted (Details)	3 Months Ended		9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Stock Options Granted
Employee Service Share Based Compensation Allocation of Recognized Period Costs [Line Items]
Expected term (in years)	6 years 29 days	6 years 29 days	6 years 7 days	6 years 14 days
Expected volatility	105.00%	101.00%	105.00%	111.00%
Risk-free interest	4.13%	4.28%	4.03%	4.07%
Dividend yield	0.00%	0.00%	0.00%	0.00%
2016 ESPP
Employee Service Share Based Compensation Allocation of Recognized Period Costs [Line Items]
Expected term (in years)	6 months	6 months	6 months	5 months 26 days
Expected volatility	71.00%	222.00%	83.00%	181.00%
Risk-free interest	5.02%	5.29%	5.15%	4.99%
Dividend yield	0.00%	0.00%	0.00%	0.00%

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Legacy Strategic License Agreements - Narrative (Details) - USD ($)		3 Months Ended		9 Months Ended
	Jul. 27, 2023	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023	Dec. 31, 2023
Research And Development Arrangement Contract To Perform For Others [Line Items]
Proceeds from sale of in-process research & development asset				$ 0	$ 15,000,000
Total revenue		$ 0	$ 0	0	886,000
Contract assets		0		0		$ 0
Contract liabilities		0		0		$ 0
Immedica Pharma AB
Research And Development Arrangement Contract To Perform For Others [Line Items]
Total revenue		$ 0		$ 0
Immedica Pharma AB | Peace Phase 3 Trial and Drug Supply
Research And Development Arrangement Contract To Perform For Others [Line Items]
Total revenue			$ 0		$ 900,000
Disposal Group, Disposed of by Sale, Not Discontinued Operations | Global Rights To Pegzilarginase
Research And Development Arrangement Contract To Perform For Others [Line Items]
Proceeds from sale of in-process research & development asset	$ 15,000,000.0
Contingent consideration	$ 100,000,000.0

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Sale of Pegzilarginase to Immedica (Details) - USD ($)		3 Months Ended		9 Months Ended
	Jul. 27, 2023	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Proceeds from sale of in-process research & development asset				$ 0	$ 15,000,000
Gain recognized within operating expenses		$ 0	$ 14,609,000	$ 0	$ 14,609,000
Disposal Group, Disposed of by Sale, Not Discontinued Operations | Global Rights To Pegzilarginase
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]
Proceeds from sale of in-process research & development asset	$ 15,000,000.0
Contingent consideration	100,000,000.0
Carrying value of assets	0
Gain recognized within operating expenses	$ 14,600,000

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Net Loss Per Share (as restated) - Narrative (Details) - $ / shares	3 Months Ended		9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Error Corrections and Prior Period Adjustments Restatement [Line Items]
Net loss per share, basic (in dollars per share)	$ 1.06	$ 0.86	$ 2.39	$ 14.65
Net loss per share, diluted (in dollars per share)	1.06	0.86	2.39	14.65
Previously Reported
Error Corrections and Prior Period Adjustments Restatement [Line Items]
Net loss per share, basic (in dollars per share)	1.36	9.34	3.43	69.57
Net loss per share, diluted (in dollars per share)	$ 1.36	$ 9.34	$ 3.43	$ 69.57

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Net Loss Per Share (as restated) - Reconciliation of Basic and Diluted Net Loss Per Share (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended						9 Months Ended
	Sep. 30, 2024	Jun. 30, 2024	Mar. 31, 2024	Sep. 30, 2023	Jun. 30, 2023	Mar. 31, 2023	Sep. 30, 2024	Sep. 30, 2023
Earnings Per Share, Basic, by Common Class, Including Two Class Method [Line Items]
Allocation of losses	$ (69,028)	$ (38,837)	$ (43,857)	$ (40,107)	$ (217,081)	$ (18,422)	$ (151,722)	$ (275,610)
Weighted-average shares outstanding (in shares)	50,889,433			4,293,812			44,263,746	3,961,546
Total diluted weighed average shares (in shares)	50,889,433			4,293,812			44,263,746	3,961,546
Net loss per share, basic (in dollars per share)	$ 1.06			$ 0.86			$ 2.39	$ 14.65
Net loss per share, diluted (in dollars per share)	$ 1.06			$ 0.86			$ 2.39	$ 14.65
Series A Preferred Stock
Earnings Per Share, Basic, by Common Class, Including Two Class Method [Line Items]
Allocation of losses	$ (14,610)			$ (36,427)			$ (36,733)	$ (217,573)
Weighted-average shares outstanding (in shares)	346,045			1,062,542			383,903	371,286
Weighted average pre-funded warrants (in shares)	0			0			0	0
Total diluted weighed average shares (in shares)	346,045			1,062,542			383,903	371,286
Net loss per share, basic (in dollars per share)	$ (42.22)			$ (34.28)			$ (95.68)	$ (586.00)
Net loss per share, diluted (in dollars per share)	$ (42.22)			$ (34.28)			$ (95.68)	$ (586.00)
Series B Preferred Stock
Earnings Per Share, Basic, by Common Class, Including Two Class Method [Line Items]
Allocation of losses	$ (704)			$ 0			$ (9,105)	$ 0
Weighted-average shares outstanding (in shares)	16,667			0			95,158	0
Weighted average pre-funded warrants (in shares)	0			0			0	0
Total diluted weighed average shares (in shares)	16,667			0			95,158	0
Net loss per share, basic (in dollars per share)	$ (42.24)			$ 0			$ (95.68)	$ 0
Net loss per share, diluted (in dollars per share)	$ (42.24)			$ 0			$ (95.68)	$ 0
Common Stock
Earnings Per Share, Basic, by Common Class, Including Two Class Method [Line Items]
Allocation of losses	$ (53,714)			$ (3,680)			$ (105,884)	$ (58,037)
Weighted-average shares outstanding (in shares)	50,889,433			4,015,661			44,146,958	3,116,434
Weighted average pre-funded warrants (in shares)	0			278,151			116,788	845,112
Total diluted weighed average shares (in shares)	50,889,433			4,293,812			44,263,746	3,961,546
Net loss per share, basic (in dollars per share)	$ (1.06)			$ (0.86)			$ (2.39)	$ (14.65)
Net loss per share, diluted (in dollars per share)	$ (1.06)			$ (0.86)			$ (2.39)	$ (14.65)

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Net Loss Per Share (as restated) - Weighted-Average Equity Instruments Excluded from Calculation of Diluted Net Loss Per Share (Details) - shares	3 Months Ended		9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Options to purchase common stock
Antidilutive Securities Excluded From Computation Of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share (in shares)	4,733,609	3,135,672	4,583,260	1,426,224
Unvested restricted stock units
Antidilutive Securities Excluded From Computation Of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share (in shares)	65,925	0	69,503	252
Outstanding Parapyre warrants
Antidilutive Securities Excluded From Computation Of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share (in shares)	684,407	0	684,407	0

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Restructuring Charges - Narrative (Details) - USD ($)		1 Months Ended	3 Months Ended		9 Months Ended
	Jun. 30, 2023	Apr. 30, 2023	Sep. 30, 2023	Jun. 30, 2023	Sep. 30, 2024	Sep. 30, 2023	Dec. 31, 2023	Aug. 07, 2023
Restructuring Cost and Reserve [Line Items]
Employee workforce, termination percentage		83.00%		83.00%
Cash severance payments and other employee-related costs			$ 0			$ 6,400,000
Non-cash stock-based compensation expense related to accelerated vesting of stock-based awards						1,000,000.0
Total consideration from disposal of long lived assets	$ 500,000			$ 500,000
Loss on disposal of long-lived assets					$ 0	$ 915,000
Lease asset impairment	900,000
Impairment on leasehold improvements	$ 1,700,000
Termination fee amount								$ 2,000,000.0
Restructuring costs outstanding and unpaid					$ 0		$ 1,100,000
Research and Development Expense
Restructuring Cost and Reserve [Line Items]
Loss on disposal of long-lived assets				700,000
General and administrative
Restructuring Cost and Reserve [Line Items]
Loss on disposal of long-lived assets				$ 200,000

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Restructuring Charges - Charges Related to the Restructuring Activities (Details) - USD ($) $ in Thousands		3 Months Ended			9 Months Ended
	Jun. 30, 2023	Sep. 30, 2024	Sep. 30, 2023	Jun. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Restructuring Cost and Reserve [Line Items]
Severance Related Expenses			$ 0			$ 6,400
Stock-based compensation expense		$ 13,100	4,785		$ 35,617	8,405
Loss on Disposal of Long Lived Assets					0	915
Lease Asset Impairment	$ 900
Research and Development Expense
Restructuring Cost and Reserve [Line Items]
Stock-based compensation expense		8,555	2,965		18,863	4,136
Loss on Disposal of Long Lived Assets				$ 700
General and administrative
Restructuring Cost and Reserve [Line Items]
Stock-based compensation expense		$ 4,545	$ 1,820		$ 16,754	$ 4,269
Loss on Disposal of Long Lived Assets				200
Restructuring Activities
Restructuring Cost and Reserve [Line Items]
Severance Related Expenses				6,448
Stock-based compensation expense				993
Loss on Disposal of Long Lived Assets				931
Lease Asset Impairment				2,580
Total Restructuring Costs				10,952
Restructuring Activities | Research and Development Expense
Restructuring Cost and Reserve [Line Items]
Severance Related Expenses				3,182
Stock-based compensation expense				123
Loss on Disposal of Long Lived Assets				749
Lease Asset Impairment				1,405
Total Restructuring Costs				5,459
Restructuring Activities | General and administrative
Restructuring Cost and Reserve [Line Items]
Severance Related Expenses				3,266
Stock-based compensation expense				870
Loss on Disposal of Long Lived Assets				182
Lease Asset Impairment				1,175
Total Restructuring Costs				$ 5,493