SCHEDULE 13D/A 0001104659-23-110484 0001699737 XXXXXXXX LIVE 2 Common Stock, $0.001 par value per share 11/18/2024 false 0001556263 87184Q206 Syros Pharmaceuticals, Inc.

35 CambridgePark Drive, 4th Floor Cambridge MA 02140

Abrar Hussain (650) 285-4270 Samsara BioCapital GP, LLC 628 Middlefield Road Palo Alto CA 94301 0001699737 N Samsara BioCapital, L.P. b WC N DE 0.00 707114.00 0.00 707114.00 707114.00 N 2.6 PN 0001888829 N Samsara BioCapital GP, LLC b AF N DE 0.00 707114.00 0.00 707114.00 707114.00 N 2.6 OO 0001253170 N Srinivas Akkaraju b AF N X1 0.00 707114.00 0.00 707114.00 707114.00 N 2.6 IN Common Stock, $0.001 par value per share Syros Pharmaceuticals, Inc. 35 CambridgePark Drive, 4th Floor Cambridge MA 02140 This Amendment No. 2 (this "Amendment No. 2" or this "Schedule 13D/A") amends and supplements the statement on Schedule 13D originally filed with the Securities and Exchange Commission (the "SEC") on October 20, 2023, and amended on December 26, 2023 (as amended, the "Statement") by the Reporting Persons. Unless otherwise defined herein, capitalized terms used in this Amendment No. 2 shall have the meanings ascribed to them in the Statement. Unless amended or supplemented below, the information in the Statement remains unchanged. Rows 11 and 13 of each Reporting Person's cover page to this Schedule 13D/A set forth the aggregate number of shares of common stock and percentages of the shares of common stock beneficially owned by such Reporting Person and are incorporated by reference. The percentage set forth in each row 13 is based upon 26,832,457 shares of the Issuer's common stock outstanding as of October 24, 2024, as reported in the Issuer's Quarterly Report on Form 10-Q filed with the SEC on October 31, 2024. Samsara LP directly holds warrants exercisable for up to 707,114 shares of common stock. Samsara GP is the sole general partner of Samsara LP and Dr. Akkaraju is a managing member of Samsara GP. Each of Samsara GP and Dr. Akkaraju possesses power to direct the voting and disposition of the securities held by Samsara LP. Rows 7 through 10 of each Reporting Person's cover page to this Schedule 13D/A set forth the number of shares of common stock as to which such Reporting Person has the sole or shared power to vote or direct the vote and sole or shared power to dispose or to direct the disposition and are incorporated by reference. Except as set forth below, none of the Reporting Persons has effected any transactions with respect to the securities of the Issuer during the past sixty days. Weighted Low High Reporting No. Average Price Price Transaction Person Date Shares Price ($) ($) ($) Open Market Sale Samsara LP 11/18/2024 958,310 $0.21 $0.18 $0.26 Open Market Sale Samsara LP 11/19/2024 74,128 $0.21 $0.21 $0.21 Open Market Sale Samsara LP 11/20/2024 753,989 $0.26 $0.26 $0.27 Open Market Sale Dr. Akkaraju 12/30/2024 9,333 $0.25 $0.25 $0.25 No other person is known to have the right to receive or the power to direct the receipt of dividends from, or any proceeds from the sale of, the securities beneficially owned by any of the Reporting Persons. The Reporting Persons ceased to be the beneficial owners of more than five percent of the common stock on November 20, 2024. Exhibit 99.1 Joint Filing Agreement Samsara BioCapital, L.P. /s/ Srinivas Akkaraju 03/27/2025 Samsara BioCapital GP, LLC /s/ Srinivas Akkaraju 03/27/2025 Srinivas Akkaraju /s/ Srinivas Akkaraju 03/27/2025