SCHEDULE 13D/A 0001415889-25-004453 0001708269 XXXXXXXX LIVE 1 Common Stock 10/16/2025 false 0002036042 829401108 SIONNA THERAPEUTICS, INC.

21 Hickory Drive, Suite 500 Waltham MA 02451

Ommer Chohan, CFO (857) 201-2700 Atlas Venture 300 Technology Square, 8th Floor Cambridge MA 02139 0001708269 N Atlas Venture Fund XI, L.P. b WC N DE 0.00 2382495.00 0.00 2382495.00 2382495.00 N 5.4 PN 0001780068 N Atlas Venture Associates XI, L.P. b AF N DE 0.00 2382495.00 0.00 2382495.00 2382495.00 N 5.4 PN 0001780067 N Atlas Venture Associates XI, LLC b AF N DE 0.00 2382495.00 0.00 2382495.00 2382495.00 N 5.4 OO 0001885327 N Atlas Venture Opportunity Fund II, L.P. b WC N DE 0.00 701985.00 0.00 701985.00 701985.00 N 1.6 PN 0001935814 N Atlas Venture Associates Opportunity II, LP b AF N DE 0.00 701985.00 0.00 701985.00 701985.00 N 1.6 PN 0001935810 N Atlas Venture Associates Opportunity II, LLC b AF N DE 0.00 701985.00 0.00 701985.00 701985.00 N 1.6 OO Common Stock SIONNA THERAPEUTICS, INC. 21 Hickory Drive, Suite 500 Waltham MA 02451 This Amendment No. 1 (this "Amendment No. 1" or this "Schedule 13D/A") amends and supplements the statement on Schedule 13D originally filed with the Securities and Exchange Commission (the "SEC") on February 18, 2025, (the "Statement") by the Reporting Persons. Unless otherwise defined herein, capitalized terms used in this Amendment No. 1 shall have the meanings ascribed to them in the Statement. Unless amended or supplemented below, the information in the Statement remains unchanged. As of the date hereof, Atlas XI is the record owner of 2,382,495 shares of Common Stock. AVA XI LP is the general partner of Atlas XI and AVA XI LLC is the general partner of AVA XI LP. Each of Atlas XI, AVA XI LP and AVA XI LLC has shared voting and dispositive power over the shares held by Atlas XI. As such, each of Atlas XI, AVA XI LP and AVA XI LLC may be deemed to beneficially own the shares held by Atlas XI. As of the date hereof, AVOF II is the record owner of 701,985 shares of Common Stock. AVAO II LP is the general partner of AVOF II and AVAO II LLC is the general partner of AVAO II LP. Each of AVOF II, AVAO II LP and AVAO II LLC has shared voting and dispositive power over the shares held by AVOF II. As such, each of AVOF II, AVAO II LP and AVAO II LLC may be deemed to beneficially own the shares held by AVOF II. Each of the Fund XI Reporting Persons and Opportunity Fund II Reporting Persons may be deemed to beneficially own 5.4% and 1.6%, respectively, of the Issuer's outstanding Common Stock, which percentages are calculated based upon 44,139,823 outstanding shares of Common Stock of the Issuer, as reported in the Issuer's Quarterly Report on Form 10-Q, filed with the Securities and Exchange Commission on August 11, 2025. Collectively, the Reporting Persons beneficially own an aggregate of 3,084,480 shares of Common Stock, which represents 7.0% of the Issuer's outstanding Common Stock. The Fund XI Reporting Persons and the Opportunity Fund II Reporting Persons are under common control and as a result, the Reporting Persons may be deemed to be members of a group. However, the Reporting Persons disclaim such group membership, and this Schedule 13D shall not be deemed an admission that the Reporting Persons are members of a group for purposes of Section 13 or for any other purposes. (c) Except as set forth below, none of the Reporting Persons has effected any transactions with respect to the securities of the Issuer in the past sixty days: Date Seller No. Shares Price Range Weighted Average Price Per Share 9/29/2025 Atlas XI 54,637 $29.95 to $30.41 $30.09 9/29/2025 AVOF II 11,468 $29.95 to $30.41 $30.09 9/30/2025 Fund XI 10,239 $29.95 to $30.20 $30.06 9/30/2025 AVOF II 2,149 $29.95 to $30.20 $30.06 10/1/2025 Atlas XI 165 $29.95 $29.95 10/1/2025 AVOF II 35 $29.95 $29.95 10/3/2025 Atlas XI 31,198 $29.95 to $30.11 $30.00 10/3/2025 AVOF II 6,548 $29.95 to $30.11 $30.00 10/6/2025 Atlas XI 9,753 $29.95 to $30.00 $29.95 10/6/2025 AVOF II 2,047 $29.95 to $30.00 $29.95 10/10/2025 Atlas XI 16,727 $29.95 to $30.11 $29.98 10/10/2025 AVOF II 3,511 $29.95 to $30.11 $29.98 10/13/2025 Atlas XI 44,048 $29.95 to $30.93 $30.32 10/13/2025 Atlas XI 4,082 $31.03 $31.03 10/13/2025 AVOF II 9,245 $29.95 to $30.93 $30.32 10/13/2025 AVOF II 857 $31.03 $31.03 10/14/2025 Atlas XI 501 $29.95 $29.95 10/14/2025 AVOF II 105 $29.95 $29.95 10/15/2025 Atlas XI 65,726 $29.95 to $30.94 $30.37 10/15/2025 Atlas XI 30,032 $30.95 to $31.30 $31.12 10/15/2025 AVOF II 13,795 $29.95 to $30.94 $30.37 10/15/2025 AVOF II 6,303 $30.95 to $31.30 $31.12 10/16/2025 Atlas XI 8,596 $30.14 to $30.74 $30.15 10/16/2025 Atlas XI 45,117 $31.21 to $32.205 $31.69 10/16/2025 Atlas XI 73,296 $32.21 to $33.205 $32.84 10/16/2025 Atlas XI 12,888 $33.21 to $33.86 $33.38 10/16/2025 AVOF II 1,804 $30.14 to $30.74 $30.15 10/16/2025 AVOF II 9,470 $31.21 to $32.205 $31.69 10/16/2025 AVOF II 15,384 $32.21 to $33.205 $32.84 10/16/2025 AVOF II 2,705 $33.21 to $33.86 $33.38 10/17/2025 Atlas XI 28,821 $31.325 to $32.32 $32.10 10/17/2025 Atlas XI 21,451 $32.335 to $33.25 $32.71 10/17/2025 Atlas XI 248 $33.47 to $33.475 $33.47 10/17/2025 AVOF II 6,049 $31.325 to $32.32 $32.10 10/17/2025 AVOF II 4,503 $32.335 to $33.25 $32.71 10/17/2025 AVOF II 52 $33.47 to $33.475 $33.47 10/20/2025 Atlas XI 20,485 $31.06 to $32.05 $31.79 10/20/2025 Atlas XI 25,788 $32.06 to $32.59 $32.33 10/20/2025 AVOF II 4,300 $31.06 to $32.05 $31.79 10/20/2025 AVOF II 5,412 $32.06 to $32.59 $32.33 No other person is known by the Reporting Persons to have the right to receive or the power to direct the receipt of dividends from, or the proceeds from the sale of, the shares of Common Stock beneficially owned by the Reporting Persons. Not applicable. JOINT FILING AGREEMENT Atlas Venture Fund XI, L.P. /s/ Ommer Chohan 10/20/2025 Atlas Venture Associates XI, L.P. /s/ Ommer Chohan 10/20/2025 Atlas Venture Associates XI, LLC /s/ Ommer Chohan 10/20/2025 Atlas Venture Opportunity Fund II, L.P. /s/ Ommer Chohan 10/20/2025 Atlas Venture Associates Opportunity II, LP /s/ Ommer Chohan 10/20/2025 Atlas Venture Associates Opportunity II, LLC /s/ Ommer Chohan 10/20/2025