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    Amendment: SEC Form SCHEDULE 13D/A filed by Sionna Therapeutics Inc.

    10/20/25 9:40:43 PM ET
    $SION
    Biotechnology: Pharmaceutical Preparations
    Health Care
    Get the next $SION alert in real time by email



    SECURITIES AND EXCHANGE COMMISSION
    Washington, D.C. 20549


    SCHEDULE 13D

    Under the Securities Exchange Act of 1934

    (Amendment No. 1)


    SIONNA THERAPEUTICS, INC.

    (Name of Issuer)


    Common Stock

    (Title of Class of Securities)


    829401108

    (CUSIP Number)


    Ommer Chohan, CFO
    Atlas Venture, 300 Technology Square, 8th Floor
    Cambridge, MA, 02139
    (857) 201-2700

    (Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications)
    10/16/2025

    (Date of Event Which Requires Filing of This Statement)


    If the filing person has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing this schedule because of §§ 240.13d-1(e), 240.13d-1(f) or 240.13d-1(g), check the following box. Checkbox not checked

    The information required on the remainder of this cover page shall not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934 (“Act”) or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes).






    SCHEDULE 13D

    CUSIP No.
    829401108


    1 Name of reporting person

    Atlas Venture Fund XI, L.P.
    2Check the appropriate box if a member of a Group (See Instructions)

    Checkbox not checked  (a)
    Checkbox checked  (b)
    3SEC use only
    4 Source of funds (See Instructions)

    WC
    5 Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)

    Checkbox not checked
    6Citizenship or place of organization

    DELAWARE
    Number of Shares Beneficially Owned by Each Reporting Person With:
    7Sole Voting Power

    0.00
    8Shared Voting Power

    2,382,495.00
    9Sole Dispositive Power

    0.00
    10Shared Dispositive Power

    2,382,495.00
    11Aggregate amount beneficially owned by each reporting person

    2,382,495.00
    12Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)

    Checkbox not checked
    13Percent of class represented by amount in Row (11)

    5.4 %
    14Type of Reporting Person (See Instructions)

    PN



    SCHEDULE 13D

    CUSIP No.
    829401108


    1 Name of reporting person

    Atlas Venture Associates XI, L.P.
    2Check the appropriate box if a member of a Group (See Instructions)

    Checkbox not checked  (a)
    Checkbox checked  (b)
    3SEC use only
    4 Source of funds (See Instructions)

    AF
    5 Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)

    Checkbox not checked
    6Citizenship or place of organization

    DELAWARE
    Number of Shares Beneficially Owned by Each Reporting Person With:
    7Sole Voting Power

    0.00
    8Shared Voting Power

    2,382,495.00
    9Sole Dispositive Power

    0.00
    10Shared Dispositive Power

    2,382,495.00
    11Aggregate amount beneficially owned by each reporting person

    2,382,495.00
    12Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)

    Checkbox not checked
    13Percent of class represented by amount in Row (11)

    5.4 %
    14Type of Reporting Person (See Instructions)

    PN



    SCHEDULE 13D

    CUSIP No.
    829401108


    1 Name of reporting person

    Atlas Venture Associates XI, LLC
    2Check the appropriate box if a member of a Group (See Instructions)

    Checkbox not checked  (a)
    Checkbox checked  (b)
    3SEC use only
    4 Source of funds (See Instructions)

    AF
    5 Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)

    Checkbox not checked
    6Citizenship or place of organization

    DELAWARE
    Number of Shares Beneficially Owned by Each Reporting Person With:
    7Sole Voting Power

    0.00
    8Shared Voting Power

    2,382,495.00
    9Sole Dispositive Power

    0.00
    10Shared Dispositive Power

    2,382,495.00
    11Aggregate amount beneficially owned by each reporting person

    2,382,495.00
    12Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)

    Checkbox not checked
    13Percent of class represented by amount in Row (11)

    5.4 %
    14Type of Reporting Person (See Instructions)

    OO



    SCHEDULE 13D

    CUSIP No.
    829401108


    1 Name of reporting person

    Atlas Venture Opportunity Fund II, L.P.
    2Check the appropriate box if a member of a Group (See Instructions)

    Checkbox not checked  (a)
    Checkbox checked  (b)
    3SEC use only
    4 Source of funds (See Instructions)

    WC
    5 Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)

    Checkbox not checked
    6Citizenship or place of organization

    DELAWARE
    Number of Shares Beneficially Owned by Each Reporting Person With:
    7Sole Voting Power

    0.00
    8Shared Voting Power

    701,985.00
    9Sole Dispositive Power

    0.00
    10Shared Dispositive Power

    701,985.00
    11Aggregate amount beneficially owned by each reporting person

    701,985.00
    12Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)

    Checkbox not checked
    13Percent of class represented by amount in Row (11)

    1.6 %
    14Type of Reporting Person (See Instructions)

    PN



    SCHEDULE 13D

    CUSIP No.
    829401108


    1 Name of reporting person

    Atlas Venture Associates Opportunity II, LP
    2Check the appropriate box if a member of a Group (See Instructions)

    Checkbox not checked  (a)
    Checkbox checked  (b)
    3SEC use only
    4 Source of funds (See Instructions)

    AF
    5 Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)

    Checkbox not checked
    6Citizenship or place of organization

    DELAWARE
    Number of Shares Beneficially Owned by Each Reporting Person With:
    7Sole Voting Power

    0.00
    8Shared Voting Power

    701,985.00
    9Sole Dispositive Power

    0.00
    10Shared Dispositive Power

    701,985.00
    11Aggregate amount beneficially owned by each reporting person

    701,985.00
    12Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)

    Checkbox not checked
    13Percent of class represented by amount in Row (11)

    1.6 %
    14Type of Reporting Person (See Instructions)

    PN



    SCHEDULE 13D

    CUSIP No.
    829401108


    1 Name of reporting person

    Atlas Venture Associates Opportunity II, LLC
    2Check the appropriate box if a member of a Group (See Instructions)

    Checkbox not checked  (a)
    Checkbox checked  (b)
    3SEC use only
    4 Source of funds (See Instructions)

    AF
    5 Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)

    Checkbox not checked
    6Citizenship or place of organization

    DELAWARE
    Number of Shares Beneficially Owned by Each Reporting Person With:
    7Sole Voting Power

    0.00
    8Shared Voting Power

    701,985.00
    9Sole Dispositive Power

    0.00
    10Shared Dispositive Power

    701,985.00
    11Aggregate amount beneficially owned by each reporting person

    701,985.00
    12Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)

    Checkbox not checked
    13Percent of class represented by amount in Row (11)

    1.6 %
    14Type of Reporting Person (See Instructions)

    OO



    SCHEDULE 13D

    Item 1.Security and Issuer
    (a)Title of Class of Securities:

    Common Stock
    (b)Name of Issuer:

    SIONNA THERAPEUTICS, INC.
    (c)Address of Issuer's Principal Executive Offices:

    21 Hickory Drive, Suite 500, Waltham, MASSACHUSETTS , 02451.
    Item 1 Comment:
    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.
    Item 5.Interest in Securities of the Issuer
    (a)
    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.
    (b)
    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)
    (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
    (d)
    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.
    (e)
    Not applicable.
    Item 7.Material to be Filed as Exhibits.
     
    JOINT FILING AGREEMENT

        SIGNATURE 
     
    After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

     
    Atlas Venture Fund XI, L.P.
     
    Signature:/s/ Ommer Chohan
    Name/Title:Atlas Venture Associates XI, L.P., its GP, By Atlas Venture Associates XI, LLC, its GP, By: Ommer Chohan, CFO
    Date:10/20/2025
     
    Atlas Venture Associates XI, L.P.
     
    Signature:/s/ Ommer Chohan
    Name/Title:Atlas Venture Associates XI, LLC, its GP, By: Ommer Chohan, CFO
    Date:10/20/2025
     
    Atlas Venture Associates XI, LLC
     
    Signature:/s/ Ommer Chohan
    Name/Title:Ommer Chohan, CFO
    Date:10/20/2025
     
    Atlas Venture Opportunity Fund II, L.P.
     
    Signature:/s/ Ommer Chohan
    Name/Title:Atlas Venture Associates Opportunity II, L.P., its GP, By: Atlas Venture Associates Opportunity II, LLC, its GP, By: Ommer Chohan, CFO
    Date:10/20/2025
     
    Atlas Venture Associates Opportunity II, LP
     
    Signature:/s/ Ommer Chohan
    Name/Title:Atlas Venture Associates Opportunity II, LLC, its GP, By: Ommer Chohan, CFO
    Date:10/20/2025
     
    Atlas Venture Associates Opportunity II, LLC
     
    Signature:/s/ Ommer Chohan
    Name/Title:By: Ommer Chohan, CFO
    Date:10/20/2025
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