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    SEC Form 10-Q filed by Generation Bio Co.

    5/7/25 4:15:25 PM ET
    $GBIO
    Biotechnology: Pharmaceutical Preparations
    Health Care
    Get the next $GBIO alert in real time by email
    GENERATION BIO CO._March 31, 2025
    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    Table of Contents

    ​

    ​

    UNITED STATES

    SECURITIES AND EXCHANGE COMMISSION

    WASHINGTON, D.C. 20549

    FORM 10-Q

    ☒

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

    ​

    For the quarterly period ended March 31, 2025

    OR

    ☐

    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: 001-39319

    GENERATION BIO CO.

    (Exact name of registrant as specified in its charter)

    ​

    Delaware

        

    81-4301284

    (State or other jurisdiction of
    incorporation or organization)

     

    (I.R.S. Employer
    Identification Number)

    301 Binney Street
    Cambridge, Massachusetts

     

    02142

    (Address of principal executive offices)

     

    (Zip Code)

    ​

    (617) 655-7500

    (Registrant’s telephone number, including area code)

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

    ​

    Title of each class

         

    Trading
    Symbol(s)

        

    Name of each exchange
    on which registered

    Common Stock, $0.0001 Par Value

     

    GBIO

     

    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  ☒    No  ☐

    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  ☒    No  ☐

    Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a 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

    ☐

    ​

    Accelerated filer

    ☐

    ​

    ​

    ​

    ​

    ​

    Non-accelerated filer

    ☒

    ​

    Smaller reporting company

    ☒

    ​

    ​

    ​

    ​

    ​

    ​

    Emerging growth company

    ☐

    ​

    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. ☐

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

    As of April 30, 2025 there were 67,035,236 shares of Common Stock, $0.0001 par value per share, outstanding.

    ​

    ​

    ​

    ​

    Table of Contents

    CAUTIONARY NOTE REGARDING FORWARD-LOOKING STATEMENTS

    This Quarterly Report on Form 10-Q, or this Quarterly Report, of Generation Bio Co. contains forward-looking statements within the meaning of the U.S. Private Securities Litigation Reform Act and Section 21E of the Securities Exchange Act of 1934, as amended, or the Exchange Act, that involve substantial risks and uncertainties. All statements, other than statements of historical fact, contained in this Quarterly Report, including statements regarding our strategy, future operations, future financial position, future revenue, projected costs, prospects, plans and objectives of management, are forward-looking statements. The words “anticipate,” “believe,” “contemplate,” “continue,” “could,” “estimate,” “expect,” “intend,” “may,” “might,” “plan,” “potential,” “predict,” “project,” “should,” “target,” “will,” “would,” or the negative of these words or other similar expressions are intended to identify forward-looking statements, although not all forward-looking statements contain these identifying words.

    The forward-looking statements in this Quarterly Report include, among other things, statements about:

    ●our estimates regarding expenses, future revenue, capital requirements, need for additional financing and the period over which we believe that our existing cash, cash equivalents and marketable securities will be sufficient to fund our operating expenses and capital expenditure requirements;
    ●the potential achievement of milestones and receipt of payments under our collaboration with ModernaTX, Inc., or Moderna;
    ●the potential advantages of our technologies;
    ●the initiation, timing, progress and results of our research and development programs and preclinical studies and clinical trials;
    ●the timing of and our ability to submit applications and obtain and maintain regulatory approvals for any product candidates we may develop;
    ●our plans to develop and, if approved, subsequently commercialize any product candidates we may develop;
    ●our commercialization, marketing and manufacturing capabilities and strategy;
    ●our expectations regarding our ability to obtain and maintain intellectual property protection;
    ●our intellectual property position;
    ●our ability to identify additional products, product candidates or technologies with significant commercial potential that are consistent with our commercial objectives;
    ●the impact of government laws and regulations;
    ●our competitive position and expectations regarding developments and projections relating to our competitors and any competing therapies that are or may become available; and
    ●our ability to maintain and establish collaborations or obtain additional funding.

    We may not actually achieve the plans, intentions or expectations disclosed in our forward-looking statements, and stockholders should not place undue reliance on our forward-looking statements. Actual results or events could differ materially from the plans, intentions and expectations disclosed in the forward-looking statements we make. We have included important factors in the cautionary statements included in this Quarterly Report, particularly in the “Risk Factors” section in this Quarterly Report and our most recent Annual Report on Form 10-K, or our 2024 Annual Report, filed with the Securities and Exchange Commission, or SEC, that we believe could cause actual results or events to differ materially

    2

    Table of Contents

    from the forward-looking statements that we make. Moreover, we operate in a competitive and rapidly changing environment. New risk factors and uncertainties may emerge from time to time, and it is not possible for management to predict all risk factors and uncertainties. Our forward-looking statements do not reflect the potential impact of any future acquisitions, mergers, dispositions, collaborations, joint ventures, or investments we may make or enter into.

    Stockholders should read this Quarterly Report and the documents that we file with the SEC with the understanding that our actual future results may be materially different from what we expect. The forward-looking statements contained in this Quarterly Report are made as of the date of this Quarterly Report, and we do not assume any obligation to update any forward-looking statements, whether as a result of new information, future events or otherwise, except as required by applicable law.

    Except where the context otherwise requires or where otherwise indicated, the terms “we,” “us,” “our,” “our company,” “the company,” and “our business” in this Quarterly Report refer to Generation Bio Co. and its consolidated subsidiary.

    ​

    ​

    3

    Table of Contents

    Generation Bio Co.

    INDEX

    ​

    ​

    ​

    ​

    Page(s)

    PART I – FINANCIAL INFORMATION

    Item 1.

    Financial Statements (unaudited)

    ​

    5

    ​

    Condensed Consolidated Balance Sheets

    ​

    5

    ​

    Condensed Consolidated Statements of Operations and Comprehensive Loss

    ​

    6

    ​

    Condensed Consolidated Statements of Stockholders’ Equity

    ​

    7

    ​

    Condensed Consolidated Statements of Cash Flows

    ​

    8

    ​

    Notes to Condensed Consolidated Financial Statements

    ​

    9

    Item 2.

    Management’s Discussion and Analysis of Financial Condition and Results of Operations

    ​

    21

    Item 3.

    Quantitative and Qualitative Disclosures About Market Risk

    ​

    31

    Item 4.

    Controls and Procedures

    ​

    31

    PART II – OTHER INFORMATION

    Item 1.

    Legal Proceedings

    ​

    32

    Item 1A.

    Risk Factors

    ​

    32

    Item 5.

    Other Information

    ​

    32

    Item 6.

    Exhibits

    ​

    33

    ​

    Signatures

    ​

    34

    ​

    ​

    ​

    4

    Table of Contents

    PART I—FINANCIAL INFORMATION

    Item 1. Financial Statements (unaudited)

    Generation Bio Co.

    Condensed Consolidated Balance Sheets

    (In thousands, except share and per share amounts)

    (Unaudited)

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

         

    March 31,

         

    December 31,

    ​

    ​

    2025

    ​

    2024

    Assets

    ​

      

    ​

    ​

      

    ​

    Current assets:

    ​

    ​

    ​

    ​

    ​

    ​

    Cash and cash equivalents

    ​

    $

    50,891

    ​

    $

    76,301

    Marketable securities

    ​

    ​

    106,668

    ​

    ​

    108,922

    Collaboration receivable

    ​

    ​

    1,392

    ​

    ​

    1,224

    Prepaid expenses and other current assets

    ​

    ​

    6,168

    ​

    ​

    6,456

    Total current assets

    ​

    ​

    165,119

    ​

    ​

    192,903

    Property and equipment, net

    ​

    ​

    14,432

    ​

    ​

    15,293

    Operating lease right-of-use assets

    ​

    ​

    19,375

    ​

    ​

    20,310

    Restricted cash

    ​

    ​

    2,152

    ​

    ​

    2,152

    Other long-term assets

    ​

    ​

    270

    ​

    ​

    539

    Total assets

    ​

    $

    201,348

    ​

    $

    231,197

    Liabilities and Stockholders’ Equity

    ​

    ​

    ​

    ​

    ​

    ​

    Current liabilities:

    ​

    ​

    ​

    ​

    ​

    ​

    Accounts payable

    ​

    $

    2,262

    ​

    $

    1,408

    Accrued expenses and other current liabilities

    ​

    ​

    5,765

    ​

    ​

    10,059

    Deferred revenue

    ​

    ​

    2,107

    ​

    ​

    10,582

    Operating lease liabilities

    ​

     

    9,463

    ​

     

    13,006

    Total current liabilities

    ​

    ​

    19,597

    ​

    ​

    35,055

    Deferred revenue, net of current portion

    ​

    ​

    30,305

    ​

    ​

    29,161

    Operating lease liabilities, net of current portion

    ​

    ​

    78,114

    ​

    ​

    80,554

    Other liabilities, net of current portion

    ​

    ​

    —

    ​

    ​

    223

    Total liabilities

    ​

     

    128,016

    ​

     

    144,993

    Commitments and contingencies (Note 9)

    ​

    ​

    ​

    ​

    ​

    ​

    Stockholders’ equity:

    ​

    ​

    ​

    ​

    ​

    ​

    Preferred stock, $0.0001 par value; 5,000,000 shares authorized and no shares
      issued or outstanding at March 31, 2025 and December 31, 2024

    ​

    ​

    —

    ​

    ​

    —

    Common stock, $0.0001 par value; 150,000,000 shares authorized at March 31,
      2025 and December 31, 2024; 67,008,511 and 66,971,977 shares issued and
     outstanding at March 31, 2025 and December 31, 2024, respectively

    ​

    ​

    7

    ​

    ​

    7

    Additional paid-in capital

    ​

    ​

    791,087

    ​

    ​

    789,083

    Accumulated other comprehensive income

    ​

    ​

    85

    ​

    ​

    159

    Accumulated deficit

    ​

    ​

    (717,847)

    ​

    ​

    (703,045)

    Total stockholders’ equity

    ​

     

    73,332

    ​

     

    86,204

    Total liabilities and stockholders’ equity

    ​

    $

    201,348

    ​

    $

    231,197

    ​

    ​

    ​

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

    ​

    5

    Table of Contents

    Generation Bio Co.

    Condensed Consolidated Statements of Operations and Comprehensive Loss

    (In thousands, except share and per share amounts)

    (Unaudited)

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

       

    Three Months Ended March 31,

    ​

    ​

    2025

       

    2024

    Revenues:

    ​

      

    ​

    ​

      

    ​

    Collaboration revenue

    ​

    $

    8,723

    ​

    $

    4,059

    Operating expenses:

    ​

    ​

    ​

    ​

    ​

    ​

    Research and development

    ​

    ​

    15,357

    ​

    ​

    14,335

    General and administrative

    ​

    ​

    8,834

    ​

    ​

    10,428

    Loss on lease termination

    ​

    ​

    1,138

    ​

    ​

    56,930

    Total operating expenses

    ​

    ​

    25,329

    ​

    ​

    81,693

    Loss from operations

    ​

    ​

    (16,606)

    ​

    ​

    (77,634)

    Other income:

    ​

    ​

    ​

    ​

    ​

    ​

    Other income and interest income, net

    ​

    ​

    1,804

    ​

    ​

    3,093

    Net loss

    ​

    $

    (14,802)

    ​

    $

    (74,541)

    Net loss per share, basic and diluted

    ​

    $

    (0.22)

    ​

    $

    (1.12)

    Weighted average common shares outstanding, basic and diluted

    ​

    ​

    67,002,511

    ​

    ​

    66,433,640

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    Comprehensive loss:

    ​

    ​

    ​

    ​

    ​

    ​

    Net loss

    ​

    $

    (14,802)

    ​

    $

    (74,541)

    Other comprehensive loss:

    ​

    ​

    ​

    ​

    ​

    ​

    Unrealized losses on marketable securities

    ​

    ​

    (74)

    ​

    ​

    (471)

    Comprehensive loss

    ​

    $

    (14,876)

    ​

    $

    (75,012)

    ​

    ​

    ​

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

    ​

    6

    Table of Contents

    ​

    ​

    ​

    Generation Bio Co.

    Condensed Consolidated Statements of Stockholders’ Equity

    (In thousands, except share amounts)

    (Unaudited)

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    Accumulated

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

         

    Additional

         

    Other

    ​

    ​

    ​

    ​

    Total

    ​

    ​

    Common Stock

         

    Paid-in

         

    Comprehensive

    ​

    Accumulated

    ​

    Stockholders’

    ​

         

    Shares

         

    Amount

         

    Capital

         

    Income (Loss)

         

    Deficit

         

    Equity

    Balances at December 31, 2024

    ​

    66,971,977

    ​

    $ 

    7

    ​

    $ 

    789,083

    ​

    $ 

    159

    ​

    $ 

    (703,045)

    ​

    $ 

    86,204

    Vesting of restricted common stock

    ​

    36,534

    ​

    ​

    —

    ​

    ​

    (7)

    ​

    ​

    —

    ​

    ​

    —

    ​

    ​

    (7)

    Stock-based compensation expense

    ​

    —

    ​

    ​

    —

    ​

    ​

    2,011

    ​

    ​

    —

    ​

    ​

    —

    ​

    ​

    2,011

    Unrealized losses on marketable securities

    ​

    —

    ​

    ​

    —

    ​

    ​

    —

    ​

    ​

    (74)

    ​

    ​

    —

    ​

    ​

    (74)

    Net loss

    ​

    —

    ​

    ​

    —

    ​

    ​

    —

    ​

    ​

    —

    ​

    ​

    (14,802)

    ​

    ​

    (14,802)

    Balances at March 31, 2025

    ​

    67,008,511

    ​

    $

    7

    ​

    $

    791,087

    ​

    $

    85

    ​

    $

    (717,847)

    ​

    $

    73,332

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    Accumulated

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

         

    Additional

         

    Other

    ​

    ​

    ​

    ​

    Total

    ​

    ​

    Common Stock

         

    Paid-in

         

    Comprehensive

    ​

    Accumulated

    ​

    Stockholders’

    ​

         

    Shares

         

    Amount

         

    Capital

         

    Income (Loss)

         

    Deficit

         

    Equity

    Balances at December 31, 2023

    ​

    66,205,550

    ​

    $ 

    7

    ​

    $ 

    774,224

    ​

    $ 

    274

    ​

    $ 

    (571,377)

    ​

    $ 

    203,128

    Vesting of restricted common stock

    ​

    273,550

    ​

    ​

    —

    ​

    ​

    (125)

    ​

    ​

    —

    ​

    ​

    —

    ​

    ​

    (125)

    Stock-based compensation expense

    ​

    —

    ​

    ​

    —

    ​

    ​

    4,000

    ​

    ​

    —

    ​

    ​

    —

    ​

    ​

    4,000

    Unrealized losses on marketable securities

    ​

    —

    ​

    ​

    —

    ​

    ​

    —

    ​

    ​

    (471)

    ​

    ​

    —

    ​

    ​

    (471)

    Net loss

    ​

    —

    ​

    ​

    —

    ​

    ​

    —

    ​

    ​

    —

    ​

    ​

    (74,541)

    ​

    ​

    (74,541)

    Balances at March 31, 2024

    ​

    66,479,100

    ​

    $

    7

    ​

    $

    778,099

    ​

    $

    (197)

    ​

    $

    (645,918)

    ​

    $

    131,991

    ​

    ​

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

    ​

    ​

    ​

    7

    Table of Contents

    ​

    Generation Bio Co.

    Condensed Consolidated Statements of Cash Flows

    (In thousands)

    (Unaudited)

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

        

    Three Months Ended March 31,

    ​

       

    2025

        

    2024

    Cash flows from operating activities:

    ​

      

    ​

    ​

      

    ​

    Net loss

    ​

    $

    (14,802)

    ​

    $

    (74,541)

    Adjustments to reconcile net loss to net cash used in operating activities:

    ​

    ​

    ​

    ​

    ​

    ​

    Loss on lease termination

    ​

    ​

    1,138

    ​

    ​

    56,930

    Stock-based compensation expense

    ​

    ​

    2,011

    ​

    ​

    4,000

    Depreciation and amortization expense

    ​

    ​

    1,136

    ​

    ​

    1,312

    Accretion of discount on marketable securities, net

    ​

    ​

    (993)

    ​

    ​

    (2,328)

    Other

    ​

    ​

    2

    ​

    ​

    (7)

    Changes in operating assets and liabilities:

    ​

    ​

    ​

    ​

    ​

    ​

    Collaboration receivable

    ​

    ​

    (168)

    ​

    ​

    —

    Prepaid expenses and other current assets

    ​

    ​

    469

    ​

    ​

    (878)

    Operating lease right-of-use assets

    ​

    ​

    935

    ​

    ​

    1,050

    Other noncurrent assets

    ​

    ​

    269

    ​

    ​

    13

    Accounts payable

    ​

    ​

    643

    ​

    ​

    (242)

    Accrued expenses and other current liabilities

    ​

    ​

    (4,319)

    ​

    ​

    (10,032)

    Deferred revenue

    ​

    ​

    (7,331)

    ​

    ​

    (4,059)

    Other noncurrent liabilities

    ​

    ​

    (223)

    ​

    ​

    —

    Operating lease liabilities

    ​

    ​

    (7,127)

    ​

    ​

    (2,915)

    Net cash used in operating activities

    ​

     

    (28,360)

    ​

    ​

    (31,697)

    Cash flows from investing activities:

    ​

    ​

    ​

    ​

    ​

    ​

    Purchases of property and equipment

    ​

    ​

    (246)

    ​

    ​

    (1,918)

    Proceeds from sale of property and equipment

    ​

    ​

    30

    ​

    ​

    —

    Purchases of marketable securities

    ​

    ​

    (41,827)

    ​

    ​

    (86,635)

    Maturities of marketable securities

    ​

    ​

    45,000

    ​

    ​

    88,000

    Net cash provided by (used in) investing activities

    ​

     

    2,957

    ​

    ​

    (553)

    Cash flows from financing activities:

    ​

    ​

    ​

    ​

    ​

    ​

    Tax withholding payments related to net share settlements of restricted stock units

    ​

    ​

    (7)

    ​

    ​

    (125)

    Net cash used in financing activities

    ​

     

    (7)

    ​

    ​

    (125)

    Net decrease in cash, cash equivalents and restricted cash

    ​

    ​

    (25,410)

    ​

    ​

    (32,375)

    Cash, cash equivalents and restricted cash at beginning of period

    ​

    ​

    78,453

    ​

    ​

    72,237

    Cash, cash equivalents and restricted cash at end of period

    ​

    $

    53,043

    ​

    $

    39,862

    Supplemental disclosure of noncash investing and financing information:

    ​

    ​

    ​

    ​

    ​

    ​

    Purchases of property and equipment included in accounts payable and accrued expenses

    ​

    $

    420

    ​

    $

    —

    Unrealized losses on marketable securities

    ​

    $

    (74)

    ​

    $

    (471)

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    Reconciliation of cash, cash equivalents and restricted cash:

    ​

    ​

    ​

    ​

    ​

    ​

    Cash and cash equivalents

    ​

    $

    50,891

    ​

    $

    35,526

    Restricted cash (included in current assets)

    ​

    ​

    —

    ​

    ​

    2,184

    Restricted cash (included in non-current assets)

    ​

    ​

    2,152

    ​

    ​

    2,152

    Total cash, cash equivalents and restricted cash shown in the statement of cash flows

    ​

    $

    53,043

    ​

    $

    39,862

    ​

    ​

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

    ​

    ​

    8

    Table of Contents

    Generation Bio Co.

    Notes to Condensed Consolidated Financial Statements

    (Unaudited)

    ​

    1. Nature of the Business and Basis of Presentation

    Generation Bio Co., or Generation Bio, was incorporated on October 21, 2016 as Torus Therapeutics, Inc. and subsequently changed its name to Generation Bio Co. Generation Bio Co. and its consolidated subsidiary, or the company, we, our or us, are working to change what’s possible for people living with T cell-driven autoimmune diseases. Our strategy is to discover, develop, and commercialize redosable therapeutics that reprogram T cells in vivo to reduce or eliminate the production and persistence of autoreactive T cells, which erroneously recognize and attack the body’s own tissues, causing autoimmune disease. We are leveraging our cell-targeted lipid nanoparticle, or ctLNP, to selectively deliver small interfering RNA, or siRNA, to T cells, and we believe that the combination of selective delivery and an intracellular, genetically precise mechanism of target engagement unlocks a series of high-value historically undruggable disease-driving genes in autoimmunity. We are headquartered in Cambridge, Massachusetts.

    We are subject to risks and uncertainties common to early-stage companies in the biotechnology industry, including, but not limited to, development by competitors of new technological innovations, dependence on key personnel, protection of proprietary technology, compliance with government regulations, the ability to establish clinical- and commercial-scale manufacturing processes and the ability to secure additional capital to fund operations. Programs currently under development will require significant additional research and development efforts, including extensive preclinical and clinical testing and regulatory approval prior to commercialization of a product. These efforts require significant amounts of additional capital, adequate personnel and infrastructure and extensive compliance-reporting capabilities. Even if our development efforts are successful, it is uncertain when, if ever, we will realize significant revenue from product sales.

    The accompanying condensed consolidated financial statements have been prepared on the basis of continuity of operations, realization of assets and the satisfaction of liabilities and commitments in the ordinary course of business. Since inception, we have funded our operations with proceeds from the sale of instruments convertible into convertible preferred stock, sales of convertible preferred stock, and sales of common stock in underwritten public offerings, “at-the-market” offerings, and in a private placement, as well as collaboration revenue under our collaboration with ModernaTX, Inc., or Moderna. We have incurred recurring losses, including net losses of $14.8 million for the three months ended March 31, 2025 and $74.5 million for the three months ended March 31, 2024. As of March 31, 2025 we had an accumulated deficit of $717.8 million. We expect to continue to generate operating losses in the foreseeable future. As of the issuance date of these condensed consolidated financial statements, we expect that our cash, cash equivalents, and marketable securities will be sufficient to fund our operating expenses and capital expenditure requirements for at least 12 months.

    We will need to obtain additional funding through public or private equity offerings, debt financings, collaborations, strategic alliances and/or licensing arrangements. We may not be able to obtain financing on acceptable terms, or at all, and we may not be able to enter into additional collaborative or strategic alliances or licensing arrangements. The terms of any financing may adversely affect the holdings or the rights of our stockholders. Arrangements with collaborators or others may require us to relinquish rights to certain of our technologies or programs. If we are unable to obtain funding, we could be forced to delay, reduce or eliminate some or all of our research and development programs, pipeline expansion or commercialization efforts, which could adversely affect our business prospects. Although management will continue to pursue these plans, there is no assurance that we will be successful in obtaining sufficient funding on terms acceptable to us to fund continuing operations when needed or at all.

    The accompanying condensed consolidated financial statements reflect the operations of Generation Bio and our wholly owned subsidiary, Generation Bio Securities Corporation. Intercompany balances and transactions have been eliminated in consolidation. The accompanying condensed consolidated financial statements have been prepared in conformity with generally accepted accounting principles in the United States of America, or GAAP. Any reference in these notes to applicable guidance is meant to refer to the authoritative GAAP as found in the Accounting Standards Codification, or ASC, and Accounting Standards Update, or ASU, of the Financial Accounting Standards Board, or FASB.

    9

    Table of Contents

    2. Summary of Significant Accounting Policies

    Use of estimates

    The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, the disclosure of contingent assets and liabilities at the date of the financial statements and the reported amounts of expenses during the reporting periods. Significant estimates and assumptions reflected in these condensed consolidated financial statements include, but are not limited to, the measurement of proportional performance of the combined license and research services performance obligation of our collaboration agreement and to a lesser extent, our accrual of research and development expenses. We base our estimates on historical experience, known trends and other market-specific or other relevant factors that we believe to be reasonable under the circumstances. On an ongoing basis, management evaluates its estimates, as there are changes in circumstances, facts and experience. Changes in estimates are recorded in the period in which they become known. Actual results may differ from those estimates or assumptions.

    Unaudited interim financial information

    The condensed consolidated balance sheet as of December 31, 2024 was derived from audited financial statements but does not include all disclosures required by GAAP. The accompanying unaudited financial statements as of March 31, 2025 and for the three months ended March 31, 2025 and 2024 have been prepared by us pursuant to the rules and regulations of the Securities and Exchange Commission, or SEC, for interim financial statements. Certain information and footnote disclosures normally included in financial statements prepared in accordance with GAAP have been condensed or omitted pursuant to such rules and regulations. These financial statements should be read in conjunction with our audited financial statements included in our Annual Report on Form 10-K that was most recently filed with the SEC, or our 2024 Annual Report. In the opinion of management, all adjustments, consisting only of normal recurring adjustments necessary for a fair presentation of our financial position as of March 31, 2025, the results of operations for the three months ended March 31, 2025 and 2024, and cash flows for the three months ended March 31, 2025 and 2024 have been made. The results of operations for the three months ended March 31, 2025 are not necessarily indicative of the results of operations that may be expected for the year ending December 31, 2025 or any other period.

    Our significant accounting policies are described in Note 2 of the Notes to Consolidated Financial Statements included in our 2024 Annual Report.

    Recently issued accounting pronouncements

    In December 2023, the FASB issued its final standard to improve income tax disclosures. This standard, issued as ASU 2023-09, requires public business entities to annually disclose specific categories in the rate reconciliation and provide additional information for reconciling items that meet a quantitative threshold. This update is effective for us as of and for the year ended December 31, 2025. We are currently evaluating the impact the guidance will have on our consolidated financial statements.

    In November 2024, the FASB issued its final standard on expense disaggregation disclosures. This standard, issued as ASU 2024-03, requires public business entities to disclose, on an annual and interim basis, disaggregated information about certain income statement line items in a tabular format in the notes to the financial statements. This update is effective for annual periods beginning after December 15, 2026. We are currently evaluating the impact the guidance will have on our consolidated financial statements.

    10

    Table of Contents

    3. Marketable Securities and Fair Value Measurements

    The following tables present our marketable securities by security type:

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

        

    As of March 31, 2025

    ​

       ​

    ​

         

    Gross

         

    Gross

         

    ​

    ​

    ​

    Amortized

    ​

    Unrealized

    ​

    Unrealized

    ​

    Fair

    (in thousands)

    ​

    Cost

    ​

    Gains

    ​

    Losses

    ​

    Value

    U.S. Treasury securities

    ​

    $ 

    106,583

    ​

    $ 

    89

    ​

    $ 

    (4)

    ​

    $ 

    106,668

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

        

    As of December 31, 2024

    ​

       ​

    ​

         

    Gross

         

    Gross

         

    ​

    ​

    ​

    Amortized

    ​

    Unrealized

    ​

    Unrealized

    ​

    Fair

    (in thousands)

    ​

    Cost

    ​

    Gains

    ​

    Losses

    ​

    Value

    U.S. Treasury securities

    ​

    $ 

    108,763

    ​

    $ 

    159

    ​

    $ 

    —

    ​

    $ 

    108,922

    ​

    Our marketable securities as of March 31, 2025 consisted of investments that mature within one year.

    We assess our available-for-sale securities under the available-for-sale security impairment model in ASC 326 Financial Instruments - Credit Losses, as of each reporting date in order to determine if a portion of any decline in fair value below carrying value recognized on our available-for-sale securities is the result of a credit loss. We also evaluate our available-for-sale securities for impairment using a variety of factors including our intent to sell the underlying securities prior to maturity and whether it is more likely than not that we would be required to sell the securities before the recovery of their amortized basis. During the three months ended March 31, 2025 and 2024, we did not recognize any impairment or realized gains or losses on sales of available-for-sale securities, and we did not record an allowance for, or recognize, any expected credit losses.

    The following tables present our assets that are measured at fair value on a recurring basis and indicate the level within the fair value hierarchy of the valuation techniques that we utilized to determine such fair value:

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

        

    Fair Value Measurements at March 31, 2025 Using:

    (in thousands)

    ​

    Level 1

        

    Level 2

        

    Level 3

        

    Total

    Cash equivalents:

    ​

       

    ​

    ​

       

    ​

    ​

       

    ​

    ​

       

    ​

    Money market funds

    ​

    $

    25,616

    ​

    $

    —

    ​

    $

    —

    ​

    $

    25,616

    U.S. Treasury securities

    ​

    ​

    —

    ​

    ​

    14,959

    ​

    ​

    —

    ​

    ​

    14,959

    Marketable securities:

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    U.S. Treasury securities

    ​

    ​

    —

    ​

    ​

    106,668

    ​

    ​

    —

    ​

    ​

    106,668

    Totals

    ​

    $

    25,616

    ​

    $

    121,627

    ​

    $

    —

    ​

    $

    147,243

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

        

    Fair Value Measurements at December 31, 2024 Using:

    (in thousands)

    ​

    Level 1

        

    Level 2

        

    Level 3

        

    Total

    Cash equivalents:

    ​

       

    ​

    ​

       

    ​

       

       

    ​

       

       

    ​

    Money market funds

    ​

    $

    46,802

    ​

    $

    —

    ​

    $

    —

    ​

    $

    46,802

    Marketable securities:

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    U.S. Treasury securities

    ​

    ​

    —

    ​

    ​

    108,922

    ​

    ​

    —

    ​

    ​

    108,922

    Totals

    ​

    $

    46,802

    ​

    $

    108,922

    ​

    $

    —

    ​

    $

    155,724

    ​

    ​

    11

    Table of Contents

    4. Collaboration and License Agreement

    Moderna Collaboration and License Agreement

    In March 2023, we entered into a Collaboration and License Agreement, or the Collaboration Agreement, with Moderna to collaborate on developing treatments for certain diseases by targeting delivery of nucleic acids to liver cells and certain cells outside of the liver.

    Under the Collaboration Agreement, the parties agreed to collaborate on preclinical research programs relating to lipid nanoparticle, or LNP, delivery systems and nucleic acid payloads, with each party obtaining certain rights to intellectual property used in and arising out of such research programs. Each party is solely responsible for its own clinical development and commercialization of products under the Collaboration Agreement. Moderna reimburses us for the internal and external costs incurred by us in conducting the research programs, to the extent consistent with such research plans and budgets.

    Moderna has exclusive options, upon payment of option exercise fees, to obtain worldwide, exclusive, sublicensable licenses under specified company intellectual property to develop, manufacture and commercialize (a) products comprising LNP delivery systems and nucleic acid payloads that are directed to (i) up to two liver targets, (ii) up to two non-liver targets and (iii) a third liver or non-liver target and (b) Exclusive Targets, which are Independent Program Products (as defined below) that include messenger RNA, or mRNA, that are directed to gene and protein targets in any of certain agreed-upon immune cell types, referred to as the Cell Target Types. Subject to the exclusivity obligations described below, each party has granted to the other a worldwide, non-exclusive, sublicensable license under certain LNP-related intellectual property arising out of the non-liver ctLNP program, or the Joint Collaboration ctLNP Intellectual Property, to develop, manufacture and commercialize products comprising LNP delivery systems and nucleic acid payloads directed to gene and protein targets in any of the Cell Target Types, or Independent Program Products.

    Each party is obligated to use commercially reasonable efforts to complete the activities assigned to it under the research plans, and Moderna is further obligated to use commercially reasonable efforts to develop, seek regulatory approval for and commercialize at least one product directed to each target for which Moderna exercises its exclusive license option in at least one indication in the United States and in specified European countries.

    We have agreed not to, directly or indirectly, alone or with, for or through any third party, develop, manufacture, commercialize or exploit (a) products containing mRNA that are directed to any of the Cell Target Types, during an agreed-upon exclusivity period, which may be extended by payment of extension fees, (b) products directed to any liver target or non-liver target during the option periods for those targets, (c) products directed to any liver target or non-liver target for which Moderna has exercised its exclusive license option or (d) products containing mRNA that are directed to any Exclusive Target for which Moderna has exercised its exclusive license option.

    Under the terms of the Collaboration Agreement, in April 2023, Moderna made an upfront payment to us of $40.0 million, and paid us $7.5 million in prepaid research funding. In addition, we are eligible to receive up to $1.8 billion in milestone payments upon the achievement of specified development, regulatory, commercial, and sales milestone events, research term extension fees and exclusivity extension fees. Subject to reductions in specified circumstances, we will also be entitled to receive tiered royalties: (i) ranging from high-single-digits to low-double-digits on sales of licensed products that are directed to any liver target or non-liver target with respect to which Moderna has exercised its exclusive license option, and (ii) in the single digits on sales of Independent Program Products, including the exclusively licensed Independent Program Products directed to the Exclusive Targets. In consideration for the non-exclusive license granted by Moderna to us under the Joint Collaboration ctLNP Intellectual Property, we have agreed to pay Moderna tiered royalties in the single digits on sales of Independent Program Products that include mRNA, subject to reductions in specified circumstances. Royalties will be paid by each party, on a licensed product-by-licensed product and country-by-country basis, until the latest to occur of: (i) expiration of the last-to-expire of specified licensed patent rights; (ii) expiration of regulatory exclusivity; or (iii) ten years after the first commercial sale of the applicable licensed product.

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    Table of Contents

    In addition, in connection with the execution of the Collaboration Agreement, we entered into a Share Purchase Agreement, or the Share Purchase Agreement, with Moderna, pursuant to which we issued and sold 5,859,375 shares of our common stock to Moderna, at a price of $6.14 per share, for an aggregate purchase price of $36.0 million, which closed concurrently with the execution of the Collaboration Agreement, and resulted in Moderna becoming a related party. Under the Share Purchase Agreement, Moderna has the right, subject to certain terms and conditions, to purchase up to 3.06% of the outstanding shares of our common stock (on a post-closing basis) in connection with a future equity financing of at least $25.0 million by us.

    Moderna Agreement Assessment

    ​

    We assessed the promised goods and services under the Collaboration Agreement, in accordance with ASC 606 Revenue from Contracts with Customers, or ASC 606. At inception, the Collaboration Agreement included one combined performance obligation, which includes the license to the ctLNP technology to target indications outside of the liver and the related research services to develop such technology, as the two items are not distinct in context of the contract. The Collaboration Agreement also provides Moderna with options to receive additional research services and options to receive exclusive licenses. The options to receive exclusive licenses allow Moderna to develop and commercialize product candidates that utilize our ctLNP and closed-ended DNA, or ceDNA, technology for targets within the liver, as well as utilizing the ctLNP technology to be developed as part of the Collaboration Agreement and our ceDNA, technology for targets outside the liver. These options are considered to be priced at a discount to its standalone selling price and therefore are considered to be material rights.

    ​

    The initial transaction price included a $40.0 million upfront fee, premium paid over the fair value of the common stock of $13.3 million in connection with shares issued and sold to Moderna under the Share Purchase Agreement, and estimated revenue associated with the payment for research services, including $7.5 million in prepaid research services. We utilized the expected amount method to determine the amount of reimbursement for these activities. We utilized the most likely amount method to determine the amount of consideration to include in the transaction price related to any variable consideration related to exclusivity fees, and milestones, and the royalty payments are constrained based on the royalty constraint. No amounts are included in the transaction price related to these elements.

    We initially allocated the transaction price to each unit of account as follows:

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    Performance Obligations (in thousands)

     

    Standalone Selling Price

     

    Transaction Price Allocated

    ctLNP technology and research
      license

    ​

    $ 

    52,500

    ​

    $ 

    42,576

    First liver program
      commercialization option license

    ​

    ​

    7,000

    ​

    ​

    5,677

    Second liver program
      commercialization option license

    ​

     

    7,000

    ​

     

    5,677

    First non-liver program
      commercialization option license

    ​

     

    11,700

    ​

     

    9,488

    Second non-liver program
      commercialization option license

    ​

     

    11,700

    ​

     

    9,488

    Third liver or non-liver program
      commercialization option license

    ​

    ​

    6,150

    ​

    ​

    4,987

    Total

    ​

    $

    96,050

    ​

    $

    77,893

    ​

    The transaction price was allocated to each unit of account based on the relative estimated standalone selling prices, over which management has applied significant judgment, of each element. We developed the estimated standalone selling price for combined performance obligation and each of the options to receive licenses primarily based on the probability-weighted present value of expected future cash flows associated with each license related to each specific program and an estimate of the costs to provide services including a reasonable return. In developing such estimate, we also considered applicable market conditions and relevant entity-specific factors, including those factors contemplated in negotiating the agreement, the probability of success and the time needed to commercialize a product candidate pursuant to the associated license.

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    Table of Contents

    ​

    On a quarterly basis, we measure proportional performance of the combined performance obligation over time using an input method based on cost incurred relative to the total estimated costs by determining the proportion of effort incurred as a percentage of total effort we expect to expend. This ratio is then applied to the transaction price allocated to the combined performance obligation and each of the options to receive licenses. Any changes to these estimates are recognized in the period in which they change as a cumulative catch up. All allocated consideration for the material rights is deferred until such time that Moderna exercises its options or the right to exercise the options expires.

    During the three months ended March 31, 2025, we recorded additional revenue related to a change in estimate due to revisions in the research plan. The change in estimate resulted in a $3.5 million decrease in the allocated transaction price, a $5.3 million increase in collaboration revenue, a $5.3 million decrease in deferred revenue and a $0.08 decrease in net loss per share, basic and diluted, for the three months ended March 31, 2025.

    The following table provides a summary of the transaction price allocated to each unit of account, in addition to revenue activity during the period:

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

        

    Transaction Price Allocated

        

    Revenue Recognized During

        

    ​

    ​

    ​

    as of

    ​

    Three Months Ended

    ​

    Deferred Revenue as of

    Performance Obligations (in thousands)

    ​

    March 31, 2025

    ​

    March 31, 2025

    ​

    March 31, 2025

    ctLNP technology and research
      license

    ​

    $ 

    37,112

    ​

    $ 

    8,629

    ​

    $ 

    2,109

    First liver program
      commercialization option license

    ​

    ​

    4,948

    ​

    ​

    —

    ​

    ​

    4,871

    Second liver program
      commercialization option license

    ​

    ​

    4,948

    ​

    ​

    —

    ​

    ​

    4,871

    First non-liver program
      commercialization option license

    ​

    ​

    8,271

    ​

    ​

    —

    ​

    ​

    8,141

    Second non-liver program
      commercialization option license

    ​

    ​

    8,271

    ​

    ​

    —

    ​

    ​

    8,141

    Third liver or non-liver program
      commercialization option license

    ​

    ​

    4,347

    ​

    ​

    —

    ​

    ​

    4,279

    Total

    ​

    $

    67,897

    ​

    $

    8,629

    ​

    $

    32,412

    ​

    The following table presents the balance of our collaboration receivable and contract liabilities related to the Collaboration Agreement:

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    Balance at

    ​

    ​

    ​

    ​

    ​

    Balance at

    (in thousands)

    ​

    December 31, 2024

    ​

    Additions

    ​

    Deductions

    ​

    March 31, 2025

    Collaboration receivable

    ​

    $

    1,224

    ​

    $

    1,298

    ​

    $

    (1,224)

    ​

    $

    1,298

    Contract liabilities:

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    Deferred revenue

    ​

    $

    39,743

    ​

    $

    1,298

    ​

    $

    (8,629)

    ​

    $

    32,412

    ​

    On January 21, 2025, Moderna exercised an option to receive additional services under the Agreement on a time and materials basis. The Company accounts for these services as a separate contract under ASC 606 and recognizes revenue as services are performed. During the three months ended March 31, 2025, the Company recognized revenue of $0.1 million, which amount is included in collaboration receivable as of March 31, 2025.

    ​

    ​

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    Table of Contents

    5. Accrued Expenses

    Accrued expenses and other current liabilities consisted of the following:

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

        

    March 31,

        

    December 31,

    (in thousands)

      

    2025

    ​

    2024

    Accrued employee compensation and benefits

    ​

    $ 

    2,345

    ​

    $ 

    5,975

    Accrued external research and development expenses

      

    ​

    848

    ​

    ​

    720

    Accrued professional fees

    ​

    ​

    950

    ​

    ​

    597

    Property and equipment

    ​

    ​

    140

    ​

    ​

    109

    Other

      

      

    1,482

    ​

    ​

    2,658

    Total

    ​

    $

    5,765

    ​

    $

    10,059

    ​

    Accrued employee compensation and benefits as of each of March 31, 2025 and December 31, 2024 includes salary continuation and severance costs of $0.4 million related to our strategic reorganization. For additional information, refer to Note 11, Reduction in Force.

    6. Leases

    Office and Lab Lease

    We lease our office and laboratory space under a noncancelable operating lease that expires in 2029, or the Office and Lab Lease. There have been no material changes to our Office and Lab Lease during the three months ended March 31, 2025. For additional information, refer to Note 7, Leases, to the consolidated financial statements in our 2024 Annual Report.

    Seyon Lease

    In July 2021, we entered into a lease agreement for a manufacturing facility in Waltham, Massachusetts, or the Seyon Lease. The Seyon Lease commenced in December 2021, when we were granted access to the facility and monthly rent payments began in September 2022, and the total rent payment was expected to be approximately $104.3 million for the 12-year lease term. We had an option to extend the Seyon Lease term for two additional terms of five years each at the greater of the then-current base rent or the then-current fair market value. Exercise of this option was not determined to be reasonably certain and thus was not considered in determining the operating lease liability. In connection with the Seyon Lease, we provided a security deposit of $3.6 million in the form of a letter of credit. We paid an initial monthly base rent of approximately $0.4 million that increased annually, up to a monthly base rent of $0.6 million. We were obligated to pay operating costs, taxes and utilities applicable to the facility. We were responsible for costs of constructing interior improvements within the facility that exceed a construction allowance of $26.0 million provided by Waltham CenterPoint I Investment Group, LLC, or the Landlord. On January 31, 2024, we notified the Landlord of termination of the Seyon Lease due to the Landlord’s breach of its obligations to us under the Seyon Lease and returned possession of the premises to the Landlord, effective January 31, 2024. On February 20, 2024, the Landlord served us with a complaint, filed in Massachusetts Superior Court, or the Court, with respect to the Seyon Lease. The complaint seeks declaratory judgment that we unlawfully terminated the Seyon Lease and also asserts a claim for breach of contract damages. As of December 31, 2024, the Landlord had collected $3.6 million from our security deposit in lieu of monthly payments and has fully utilized such deposit.

    In connection with the termination of the Seyon Lease, during the three months ended March 31, 2024, we recorded a material impairment loss of non-cash charges of $45.8 million in an impairment of the Seyon Lease right-of-use asset, $6.2 million in an impairment of construction in progress, and the write-off of $3.9 million in tenant improvement allowance receivable from the Landlord. In addition, during the three months ended March 31, 2024, we recognized $1.0 million in accretion and other related expenses, which resulted in a $56.9 million loss on termination of lease in our condensed consolidated statements of operations and comprehensive loss for the three months ended March 31, 2024.

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    Table of Contents

    During the three months ended March 31, 2025, we recognized $1.1 million in accretion and other related expenses. Accretion and other related expenses will continue to be recognized in loss on lease termination in our condensed consolidated statements of operations and comprehensive loss. After the Court’s preliminary injunction ruling in January 2025, we began making monthly payments to the Landlord. During the three months ended March 31, 2025, we paid $7.1 million to the Landlord, which included $4.9 million due from July through December 2024.

    As of March 31, 2025 and December 31, 2024, we have not met the criteria to extinguish the lease liability pursuant to ASC 405 Liabilities. Accordingly, we had a total operating lease liability related to the Seyon Lease of $58.5 million and $63.1 million as of March 31, 2025 and December 31, 2024, respectively, of which $3.4 million and $7.1 million were included in current liabilities on our consolidated balance sheets as of March 31, 2025 and December 31, 2024, respectively. Additionally, in accordance with ASC 450 Contingencies, we have assessed the probability of realizing a material loss contingency for the potential losses, including obligations to pay any future variable lease costs, under the Seyon Lease. Based on this assessment, we have determined that it is not probable that we will be obligated to pay any such material amounts.

    For additional information, refer to Note 9 Commitments and Contingencies.

    ​

    7. Equity

    As of March 31, 2025, our amended and restated certificate of incorporation authorizes us to issue 150,000,000 shares of common stock, par value $0.0001 per share, and 5,000,000 shares of preferred stock, par value $0.0001 per share, all of which preferred stock is undesignated.

    In August 2024, we entered into an “at-the-market” sales agreement pursuant to which we may, from time to time, sell shares of our common stock having an aggregate offering price of up to $237.0 million. As of the issuance date of these condensed consolidated financial statements, we have not issued and sold any shares of our common stock pursuant to the August 2024 sales agreement.

    Each share of common stock entitles the holder to one vote on all matters submitted to a vote of our stockholders. Holders of common stock are not entitled to receive dividends, unless declared by the board of directors.

    8. Stock-Based Compensation

    Stock incentive plans

    Our 2017 Stock Incentive Plan, or the 2017 Plan, provided for us to grant incentive or nonstatutory stock options, restricted stock, restricted stock units and other equity awards to employees, non-employees, and directors.

    In May 2020, our board of directors adopted, and in June 2020, our stockholders approved, the 2020 Stock Incentive Plan, or the 2020 Plan, and, together with the 2017 Plan, the Plans, which became effective on June 11, 2020. The 2020 Plan provides for the grant of incentive stock options, nonstatutory stock options, stock appreciation rights, restricted stock awards, restricted stock units and other stock-based awards. The number of shares of common stock reserved for issuance under the 2020 Plan is the sum of (1) 2,547,698 shares; plus (2) the number of shares (up to a maximum of 7,173,014 shares) as was equal to the sum of (x) the number of shares of common stock reserved for issuance under the 2017 Plan that remained available for grant under the 2017 Plan on June 11, 2020 and (y) the number of shares of common stock subject to outstanding awards granted under the 2017 Plan that expire, terminate or are otherwise surrendered, cancelled, forfeited or repurchased by us at their original issuance price pursuant to a contractual repurchase right; plus (3) an annual increase, to be added on the first day of each fiscal year, beginning with the fiscal year ending December 31, 2021 and continuing until, and including, the fiscal year ending December 31, 2030, equal to the lesser of (i) 4% of the number of shares of common stock outstanding on such date, and (ii) an amount determined by the board of directors. In January 2025, the number of shares of common stock authorized for issuance under the 2020 Plan was increased from 19,462,688 shares to 22,141,904 shares. Upon the effectiveness of the 2020 Plan, we ceased granting additional awards under the 2017 Plan.

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    Table of Contents

    The Plans are administered by the board of directors or, at the discretion of the board of directors, by a committee of the board of directors. The exercise prices, vesting and other restrictions on any award under the Plans are determined at the discretion of the board of directors, or its committee if so delegated. Stock options granted under the Plans with service-based vesting conditions generally vest over four years and expire after ten years. The exercise price for stock options granted is not less than the fair value of common stock as of the date of grant.

    As of March 31, 2025, 700,090 shares remained available for future issuance under the 2020 Plan. Shares subject to outstanding awards granted under the Plans that expire, terminate or are otherwise surrendered, cancelled, forfeited or repurchased by us at their original issuance price pursuant to a contractual repurchase right will be available for future awards under the 2020 Plan.

    Grant of stock options

    During the three months ended March 31, 2025, we granted time-based options to certain employees for the purchase of an aggregate of 3,681,752 shares of common stock with a weighted average grant date fair value of $0.77 per share that vest over a weighted average period of approximately four years.

    Employee stock purchase plan

    In May 2020, our board of directors adopted, and in June 2020, our stockholders approved, the 2020 Employee Stock Purchase Plan, or the 2020 ESPP, which became effective June 11, 2020. The 2020 ESPP is administered by our board of directors or by a committee appointed by the board of directors. The number of shares of common stock authorized for issuance under the 2020 ESPP automatically increases on the first day of each fiscal year, beginning with the fiscal year that commenced on January 1, 2021 and continuing for each fiscal year until, and including the fiscal year commencing on, January 1, 2030, in an amount equal to the lowest of (1) 1,302,157 shares of common stock, (2) 1% of the number of shares of common stock outstanding on such date, and (3) an amount determined by the board of directors. In January 2025, the number of shares of common stock authorized for issuance under the 2020 ESPP was increased from 2,777,974 shares to 3,447,778 shares. As of March 31, 2025, 2,698,529 shares remained available for issuance under the 2020 ESPP.

    Stock-based compensation

    Stock-based compensation expense was classified in the condensed consolidated statements of operations and comprehensive loss as follows:

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

       

    Three Months Ended March 31,

    (in thousands)

    ​

    2025

       

    2024

    Research and development expenses

    ​

    $ 

    714

    ​

    $ 

    1,521

    General and administrative expenses

    ​

     

    1,297

    ​

     

    2,479

    Total

    ​

    $

    2,011

    ​

    $

    4,000

    ​

    As of March 31, 2025, total unrecognized compensation cost related to unvested time-based stock options and restricted stock units was $10.3 million, with $9.4 million expected to be recognized over a weighted average period of 2.5 years and $0.9 million expected to be recognized over a weighted average period of 1.8 years.

    17

    Table of Contents

    9. Commitments and Contingencies

    401(k) Plan

    We have a defined-contribution plan under Section 401(k) of the Internal Revenue Code of 1986, as amended, or the 401(k) Plan. The 401(k) Plan covers all employees who meet defined minimum age and service requirements and allows participants to contribute a portion of their annual compensation on a pre-tax and/or after-tax basis. In September 2020, we adopted a match program, beginning on January 1, 2021, for employee contributions to the 401(k) Plan up to a maximum of four percent of the employee’s salary, subject to the maximums established under the U.S. Internal Revenue Code of 1986, as amended.

    Indemnification agreements

    In the ordinary course of business, we may provide indemnification of varying scope and terms to vendors, lessors, contract research organizations, business partners and other parties with respect to certain matters including, but not limited to, losses arising out of breach of such agreements or from intellectual property infringement claims made by third parties. In addition, we have entered into indemnification agreements with members of our board of directors and our officers that will require us, among other things, to indemnify them against certain liabilities that may arise by reason of their status or service as directors or officers. The maximum potential amount of future payments we could be required to make under these indemnification agreements is, in many cases, unlimited. We have not incurred any material costs as a result of such indemnifications and are not currently aware of any indemnification claims.

    Legal proceedings

    We, from time to time, may be party to litigation arising in the ordinary course of business. On February 20, 2024, the Landlord served us with a complaint, filed in the Court with respect to the Seyon Lease. The complaint sought declaratory judgment that we unlawfully terminated the Seyon Lease and also asserted a claim for breach of contract damages. Following receipt of the complaint, we filed a counterclaim against the Landlord asserting breach of contract and violation of Massachusetts General Law Chapter 93A. On October 29, 2024, the Court determined that although we did not have the right to terminate the Seyon Lease, the Landlord’s subsequent termination was effective, and that we had alleged sufficient facts to state a claim for breach of contract and violation of Massachusetts General Law Chapter 93A by the Landlord. On January 21, 2025, the Court granted the Landlord’s motion for preliminary injunction and ordered us to pay, until further notice, monthly amounts equal to the rent and other charges that would have been due to the Landlord under the Seyon Lease had it not been terminated. On February 14, 2025, we filed a notice of appeal of the Court’s preliminary injunction ruling and our appeal is pending before the Massachusetts Appeals Court. On March 28, 2025, we filed a petition for direct appellate review with the Massachusetts Supreme Judicial Court. We are continuing to make monthly payments under the Seyon Lease during the pendency of the appeal. We will continue to vigorously defend the action and prosecute our counterclaims against the Landlord with respect to this matter. As a result, we may continue to incur costs and expenses relating to this facility, and we may remain responsible for payments under the Seyon Lease, which may have a material adverse effect on our business, results of operations or financial condition.

    10. Net Loss per Share

    We have generated a net loss in all periods presented, therefore the basic and diluted net loss per share attributable to common stockholders are the same as the inclusion of the potentially dilutive securities would be anti-dilutive. We excluded the following potential common shares, presented based on amounts outstanding at each period end, from the computation of diluted net loss per share attributable to common stockholders for the periods indicated:

    ​

    ​

    ​

    ​

    ​

    ​

    ​

        

    March 31,

    ​

    ​

    2025

      

    2024

    Unvested restricted stock units

    ​

    225,341

    ​

    497,121

    Stock options to purchase common stock

    ​

    16,041,622

    ​

    12,514,950

    Total

    ​

    16,266,963

    ​

    13,012,071

    ​

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    Table of Contents

    ​

    11. Reduction in Force

    In January 2025, our management and board of directors approved a reduction in force, or the January 2025 RIF, to support our new focus on applying our ctLNP delivery technology to develop siRNA therapeutics to silence disease-driving targets in T cells. In connection with the January 2025 RIF, affected employees are eligible to receive one-time severance benefits, including cash severance, temporary healthcare coverage, to the extent they are eligible for and elect such coverage, and transition support services, subject to each such employee entering into an effective separation agreement, which will include a general release of claims against us. We also offered a retention bonus to certain affected employees if such employees remain in continuous employment with us through their respective separation dates and execute a general release of claims against us. Retention amounts are expensed as services are performed.

    During the three months ended March 31, 2025, we recorded $0.6 million of restructuring expenses related to the January 2025 RIF in our condensed consolidated statements of operation and comprehensive loss, of which $0.4 million was classified as research and development expense and $0.2 million was classified as general and administrative expense. During the three months ended March 31, 2024, we recorded $0.3 million of restructuring expenses in our condensed consolidated statements of operation and comprehensive loss, all of which was classified as general and administrative expense, and related to our prior strategic reorganization that commenced in November 2023 and was completed during the second quarter of 2024, or the November 2023 RIF.

    Below is a summary of accrued restructuring costs recorded and included in accrued expenses and other current liabilities on our condensed consolidated balance sheets:

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    (in thousands)

        

    Payroll-Related Costs

    ​

    Stock-Based Compensation

    ​

    Total

    Balance at December 31, 2024

    ​

    $ 

    446

    ​

    $ 

    —

    ​

    $ 

    446

    Restructuring expenses

      

    ​

    618

    ​

    ​

    13

    ​

    ​

    631

    Cash payments

    ​

    ​

    (690)

    ​

    ​

    —

    ​

    ​

    (690)

    Non-cash expenses

    ​

    ​

    —

    ​

    ​

    (13)

    ​

    ​

    (13)

    Adjustments

    ​

    ​

    (5)

    ​

    ​

    —

    ​

    ​

    (5)

    Balance at March 31, 2025

    ​

    $

    369

    ​

    $

    —

    ​

    $

    369

    ​

    ​

    ​

    ​

    12. Reportable Segments

    Our Chief Executive Officer is our chief operating decision maker, or CODM and we operate as one reportable segment related to the research and development of therapeutics that can deliver siRNA, leveraging our ctLNP delivery system, to T cells. The measure of segment profit or loss is the Company’s consolidated net loss.

    Resource allocation decisions are based on the best use of our resources to advance our ctLNP delivery system with the goal of selecting and advancing a drug candidate into clinical development. These decisions are informed by our cash resources, reflected in the balance of cash, cash equivalents and marketable securities on our consolidated balance sheets, forecasted financial results, the actual results included in our consolidated balance sheets, consolidated statements of operations and comprehensive loss, and significant segment expenses included in the table below.

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    Table of Contents

    Significant segment revenues and expenses include the following:

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

     

    Three Months Ended March 31,

    (in thousands)

    ​

    2025

      

    2024

    Revenue:

    ​

      

    ​

    ​

      

    ​

    Collaboration revenue

    ​

    $

    8,723

    ​

    $

    4,059

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    Operating expenses:

    ​

    ​

    ​

    ​

    ​

    ​

    Personnel-related

    ​

    ​

    8,947

    ​

    ​

    6,735

    Preclinical and manufacturing

    ​

    ​

    3,489

    ​

    ​

    3,296

    Facilities-related

    ​

    ​

    4,753

    ​

    ​

    5,757

    Stock-based compensation

    ​

    ​

    2,011

    ​

    ​

    4,000

    Lab supplies

    ​

    ​

    803

    ​

    ​

    915

    Consulting and professional services

    ​

    ​

    3,234

    ​

    ​

    2,598

    Loss on lease termination

    ​

    ​

    1,138

    ​

    ​

    56,930

    Other (1)

    ​

    ​

    954

    ​

    ​

    1,462

    Total operating expenses

    ​

    ​

    25,329

    ​

    ​

    81,693

    Loss from operations

    ​

    ​

    (16,606)

    ​

    ​

    (77,634)

    Other income:

    ​

    ​

    ​

    ​

    ​

    ​

    Other income and interest income, net

    ​

    ​

    1,804

    ​

    ​

    3,093

    Net Loss

    ​

    $

    (14,802)

    ​

    $

    (74,541)

    (1)Other segment items include depreciation, amortization, license fees and other costs. Depreciation and amortization expense for the three months ended March 31, 2025 and 2024 were $1.1 million and $1.3 million, respectively, and are included in facilities-related and other segment operating expenses.

    ​

    All collaboration revenue recognized to date which has been entirely in connection to our License and Collaboration Agreement with Moderna and long-lived assets are attributable solely to our operations in the United States.

    ​

    20

    Table of Contents

    Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations.

    The following discussion and analysis of our financial condition and results of operations is meant to provide material information relevant to an assessment of the financial condition and results of operations of our company, including an evaluation of the amounts and uncertainties of cash flows from operations and from outside resources, so as to allow investors to better view our company from management’s perspective. It should be read in conjunction with our condensed consolidated financial statements and related notes appearing elsewhere in this Quarterly Report and our consolidated financial statements and related notes appearing in our 2024 Annual Report. Some of the information contained in this discussion and analysis or set forth elsewhere in this Quarterly Report, including information with respect to our plans and strategy for our business, includes forward-looking statements that involve risks and uncertainties. As a result of many factors, including those factors set forth in the “Risk Factors” section of this Quarterly Report, in our 2024 Annual Report and in the other documents filed with the SEC, our actual results could differ materially from the results described in, or implied by, the forward-looking statements contained in the following discussion and analysis.

    Overview

    We are a biotechnology company working to change what’s possible for people living with T cell-driven autoimmune diseases. Our strategy is to discover, develop, and commercialize redosable therapeutics that reprogram T cells in vivo to reduce or eliminate the production and persistence of autoreactive T cells, which erroneously recognize and attack the body’s own tissues, causing autoimmune disease. We are leveraging our cell-targeted lipid nanoparticle, or ctLNP, to selectively deliver small interfering RNA, or siRNA, to T cells, and we believe that the combination of selective delivery and an intracellular, genetically precise mechanism of target engagement unlocks a series of high-value historically undruggable disease-driving genes in autoimmunity.

    T cells are central to the normal function of the immune system, but when inactivated or naïve T cells are inappropriately activated against proteins or molecules naturally present in the body, known as autoantigens, they expand, differentiate, and drive tissue inflammation that results in the development of autoimmune disease. Modulating T cell activity has historically been limited by a lack of selectivity along two dimensions – selective delivery to T cells while sparing other immune cell types, and precisely inhibiting or silencing the intended genetic sequence to block disease causing pathways.

    We believe that the advantage of our approach to combatting T cell-driven autoimmune disease is in the combination of highly selective delivery and precise gene silencing in T cells to drive potency while sparing broader immune cells, thus potentially expanding the therapeutic margin of safety, or index. We achieve selective delivery using our modular, redosable ctLNP delivery system, which is designed to reach cell type targets of interest selectively through active ligand-mediated uptake. We are leveraging our T cell-selective LNP to deliver siRNA, a cargo that can potently and precisely regulate protein expression in T cells without off-target effects. The intracellular mechanism of action of siRNA means that our T cell-selective LNP-siRNA has the potential to reach targets inaccessible by other modalities, creating a large and new target space for autoimmune disease.

    Selective and potent siRNA delivery to T cells opens a broad landscape of protein targets to address T cell-driven autoimmune disease indications, including targets that are undruggable or poorly drugged by conventional modalities. We intend to build a portfolio of therapeutic candidates for T cell-driven autoimmune indications, selecting those with a strong link to protein target biology, high unmet need, a clear clinical/regulatory pathway, and path to demonstrate clinical superiority. We are prioritizing protein target selection for these indications based on the following:

    -targets in T cells that are undruggable or poorly drugged with conventional modalities;

    -well-characterized biology;

    -superiority of mechanism of action (selective delivery and intracellular knockdown); and

    -clear target engagement in early clinical development.

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    Table of Contents

    We expect to announce the target and indication of our lead T cell-selective LNP-siRNA program for autoimmune disease by mid-year 2025. We expect to submit our investigational new drug, or IND, application for our lead program in the second half of 2026.

    We are collaborating with Moderna under a Collaboration and License Agreement, or the Collaboration Agreement, entered into in March 2023 to develop treatments for certain diseases by targeting delivery of nucleic acids to liver cells and certain cells outside of the liver. Under the Collaboration Agreement, we and Moderna have agreed to collaborate on preclinical research programs relating to lipid nanoparticle, or LNP, delivery systems and nucleic acid payloads, with each party obtaining certain rights to intellectual property used in and arising out of such research programs.

    Since our inception in October 2016, we have focused substantially all of our resources on building our technologies, establishing and protecting our intellectual property portfolio, conducting research and development activities, developing our manufacturing process, organizing and staffing our company, business planning, raising capital and providing general and administrative support for these operations. We do not have any products approved for sale and have not generated any revenue from product sales. We expect that any revenue recognized for the next several years will be derived primarily from our current collaboration with Moderna and any additional collaborations that we may enter into in the future. Historically, we have funded our operations with proceeds from the sale of instruments convertible into convertible preferred stock, sales of convertible preferred stock, and sales of common stock in underwritten public offerings, “at-the-market” offerings, and in a private placement, as well as collaboration revenue under our collaboration with Moderna.

    Historically, we have incurred significant operating losses. Our ability to generate any product revenue or product revenue sufficient to achieve profitability will depend on the successful development and eventual commercialization of one or more product candidates we may develop. For the three months ended March 31, 2025 and 2024, we reported net losses of $14.8 million and $74.5 million, respectively. As of March 31, 2025, we had an accumulated deficit of $717.8 million. We expect to continue to incur significant expenses and increasing operating losses for at least the next several years. We expect that our expenses and capital requirements will increase substantially in connection with our ongoing activities, particularly if and as we:

    ●continue our current research programs and conduct additional research programs, including pursuant to our collaboration with Moderna;
    ●expand the capabilities of our proprietary technologies;
    ●advance any product candidates we identify into preclinical and clinical development;
    ●obtain, expand, maintain, defend and enforce our intellectual property portfolio;
    ●seek marketing approvals for any product candidates that successfully complete clinical trials;
    ●hire additional clinical, regulatory and scientific personnel;
    ●establish additional manufacturing sources and secure supply chain capacity sufficient to provide necessary quantities of any product candidates we may develop for clinical or commercial use;
    ●ultimately establish a sales, marketing and distribution infrastructure to commercialize any products for which we may obtain marketing approval; and
    ●add operational, legal, compliance, financial and management information systems and personnel to support our research, product development, and future commercialization efforts.

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    Table of Contents

    We will not generate revenue from product sales unless and until we successfully complete clinical development and obtain regulatory approval for any product candidates we may develop. If we obtain regulatory approval for any product candidates we may develop, we expect to incur significant expenses related to developing our commercial capability to support product sales, marketing and distribution.

    As a result, we will need substantial additional funding to support our continuing operations and pursue our growth strategy. Until such time as we can generate significant revenue from product sales, if ever, we expect to finance our operations through a combination of equity offerings, debt financings, collaborations, strategic alliances and/or licensing arrangements, including our collaboration with Moderna. We may be unable to raise additional funds or enter into such other agreements or arrangements when needed on favorable terms, or at all. If we fail to raise capital or enter into such agreements when needed or on terms acceptable to us, we would be required to delay, limit, reduce or terminate our product development or future commercialization of one or more of our product candidates.

    Because of the numerous risks and uncertainties associated with pharmaceutical product development, we are unable to accurately predict the timing or amount of increased expenses or when, or if, we will be able to achieve or maintain profitability. Even if we are able to generate product sales, we may not become profitable. If we fail to become profitable or are unable to sustain profitability on a continuing basis, then we may be unable to continue our operations at planned levels and be forced to reduce or terminate our operations.

    We believe that our existing cash, cash equivalents, and marketable securities will enable us to fund our operating expenses and capital expenditures into the second half of 2027. We have based our estimates as to how long we expect we will be able to fund our operations on assumptions that may prove to be wrong, and we could use our available capital resources sooner than we currently expect, in which case we would be required to obtain additional financing, which may not be available to us on acceptable terms, or at all. See “—Liquidity and Capital Resources”.

    Components of Our Results of Operations

    Collaboration revenue

    Our revenue consists of collaboration revenue, including amounts recognized as payments for licenses, research funding and milestone payments earned under our collaboration and license agreements.

    In March 2023, we entered into the Collaboration Agreement, with Moderna, to collaborate on developing treatments for certain diseases by targeting delivery of nucleic acids to liver cells and certain cells outside of the liver. Under the Collaboration Agreement, the parties have agreed to collaborate on preclinical research programs relating to lipid nanoparticle, or LNP, delivery systems and nucleic acid payloads, with each party obtaining certain rights to intellectual property used in and arising out of such research programs.

    The research programs will be conducted pursuant to research plans and associated research budgets established by governance committees formed by the parties. Moderna will reimburse us for the internal and external costs we incur in conducting the research programs, to the extent consistent with such research plans and budgets. Each party will be solely responsible for its own clinical development and commercialization of products under the Collaboration Agreement.

    In addition, Moderna has exclusive options, upon payment of option exercise fees, to obtain worldwide, exclusive, sublicensable licenses under certain of our specified intellectual property to develop, manufacture and commercialize (a) products comprising LNP delivery systems and nucleic acid payloads that are directed to (i) up to two liver targets, (ii) up to two agreed-upon non-liver targets and (iii) a third liver or non-liver target and (b) Independent Program Products, which are products comprising LNP delivery systems that include mRNA that are directed to gene and protein targets in any of the agreed-upon immune cell types, or Cell Targets Types.

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    Table of Contents

    Under the terms of the Collaboration Agreement, in April 2023, Moderna made an upfront payment to us of $40.0 million, and paid us $7.5 million in prepaid research funding. In addition, we are eligible to receive up to $1.8 billion in milestone payments upon the achievement of specified development, regulatory, commercial, and sales milestone events, research term extension fees and exclusivity extension fees. Subject to reduction in specified circumstances, we will also be entitled to receive tiered royalties: (i) ranging from high-single-digits to low-double-digits on sales of licensed products that are directed to the liver targets and non-liver targets with respect to which Moderna has exercised its exclusive license options, and (ii) in the single digits on sales of Independent Program Products, including the exclusively licensed Independent Program Products. In consideration for the non-exclusive license granted by Moderna to us under the LNP-related intellectual property arising out of the research program focused on the discovery and development of ctLNPs directed to agreed-upon immune cell types, we have agreed to pay Moderna tiered royalties ranging from low-single-digits to mid-single-digits on sales of Independent Program Products that include mRNA, subject to reductions in specified circumstances.

    In connection with the Collaboration Agreement, we entered into a Share Purchase Agreement with Moderna, pursuant to which we issued and sold 5,859,375 shares of our common stock to Moderna, at a price of $6.14 per share, for an aggregate purchase price of $36.0 million. In addition, under the Share Purchase Agreement, Moderna has the right, subject to certain terms and conditions, to purchase up to 3.06% of the outstanding shares of our common stock (on a post-closing basis) in connection with a future equity financing of at least $25.0 million by us. For additional information on our collaboration with Moderna and the accounting thereunder, refer to Note 4, Collaboration and License Agreement.

    Operating expenses

    Research and development expenses

    Research and development expenses consist primarily of costs incurred for our research activities, including our discovery efforts, and the development of our programs, which include:

    ●personnel-related costs, including salaries, benefits, stock-based compensation and severance expense, for employees engaged in research and development functions;
    ●expenses incurred in connection with our research programs, including under agreements with third parties, such as consultants, contractors and contract research organizations, or CROs, and regulatory agency fees;
    ●the cost of developing and scaling our manufacturing process and capabilities and manufacturing drug substance and drug product for use in our research and preclinical studies, including under agreements with third parties, such as consultants, contractors and contract development organizations, or CDOs;
    ●laboratory supplies and research materials;
    ●facilities, depreciation and amortization and other expenses, which include direct and allocated expenses for rent and maintenance of facilities and insurance; and
    ●payments made under third-party licensing agreements.

    We expense research and development costs as incurred. Advance payments that we make for goods or services to be received in the future for use in research and development activities are recorded as prepaid expenses. The prepaid amounts are expensed as the related goods are delivered or the services are performed.

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    Table of Contents

    Our external research and development expenses consist of costs that include fees and other costs paid to consultants, contractors, CDOs and CROs in connection with our research, preclinical and manufacturing activities. We do not allocate our research and development costs to specific programs because costs are deployed across multiple programs and our technologies and, as such, are not separately classified. We expect that our research and development expenses will increase substantially as we advance our programs into clinical development and expand our discovery, research and preclinical activities in the near term and in the future. At this time, we cannot accurately estimate or know the nature, timing and costs of the efforts that will be necessary to complete the preclinical and clinical development of any product candidates we may develop. The successful development of any of our product candidates is highly uncertain. This is due to the numerous risks and uncertainties associated with product development, including the following:

    ●the timing and progress of preclinical studies, including IND-enabling studies;
    ●the number and scope of preclinical and clinical programs we decide to pursue;
    ●our ability to raise additional funds necessary to complete preclinical and clinical development of any product candidates we may develop;
    ●the timing of the submission and acceptance of IND applications or comparable foreign applications that allow commencement of future clinical trials for any product candidates we may develop;
    ●the successful initiation, enrollment and completion of clinical trials, including under Good Clinical Practices;
    ●our ability to achieve positive results from our future clinical programs that support a finding of safety and effectiveness and an acceptable risk-benefit profile in the intended patient populations of any product candidates we may develop;
    ●our ability to establish arrangements with third-party manufacturers for preclinical, clinical and initial commercial supply;
    ●the availability of specialty raw materials for use in production of any product candidates we may develop;
    ●our ability to establish new licensing or collaboration arrangements;
    ●the receipt and related terms of regulatory approvals from the U.S. Food and Drug Administration and other applicable regulatory authorities;
    ●our ability to establish, obtain, maintain, enforce and defend patent, trademark, trade secret protection and other intellectual property rights or regulatory exclusivity for any product candidates we may develop and our technology;
    ●our ability to maintain a continued acceptable safety, tolerability and efficacy profile of our product candidates following approval; and
    ●the terms and timing of any existing or future collaboration, license or other arrangement, including the terms and timing of any achievement of milestones and the receipt of payments thereunder.

    A change in the outcome of any of these variables with respect to any product candidates we may develop could significantly change the costs and timing associated with the development of that product candidate. We may never succeed in obtaining regulatory approval for any product candidates we may develop.

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    Table of Contents

    General and administrative expenses

    General and administrative expenses consist primarily of personnel-related costs, including salaries, benefits, stock-based compensation and severance expense, for employees engaged in executive, legal, finance and accounting and other administrative functions. General and administrative expenses also include professional fees for legal, patent, consulting, investor and public relations and accounting and audit services as well as direct and allocated facility-related costs.

    We anticipate that our general and administrative expenses will increase in the future as our research progresses towards clinical studies and will increase our headcount to support our operational growth. We also anticipate that we will continue to incur substantial accounting, audit, legal, regulatory, compliance, director and officer insurance costs and investor and public relations expenses associated with operating as a public company.

    Loss on lease termination

    Loss on lease termination consists of expenses recognized for the impairment of the right-of-use asset and construction in progress, the write-off of the related tenant improvement allowance receivable, accretion and other related expenses in connection with the termination of our lease for a manufacturing facility in Waltham, Massachusetts, or the Seyon Lease.

    Other income and interest income, net

    Other income and interest income, net consists of interest income earned on our invested cash balances and miscellaneous income and expenses unrelated to our core operations.

    Results of Operations

    Comparison of the three months ended March 31, 2025 and 2024

    The following table summarizes our results of operations for the three months ended March 31, 2025 and 2024:

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

       

    Three Months Ended March 31,

      

    Change

    (in thousands)

    ​

    2025

      

    2024

    ​

    2025 vs. 2024

    Revenues:

    ​

      

    ​

    ​

      

    ​

    ​

      

    ​

    Collaboration revenue

    ​

    $

    8,723

    ​

    $

    4,059

    ​

    $

    4,664

    Operating expenses:

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    Research and development

    ​

    ​

    15,357

    ​

    ​

    14,335

    ​

    ​

    1,022

    General and administrative

    ​

    ​

    8,834

    ​

    ​

    10,428

    ​

    ​

    (1,594)

    Loss on lease termination

    ​

    ​

    1,138

    ​

    ​

    56,930

    ​

    ​

    (55,792)

    Total operating expenses

    ​

    ​

    25,329

    ​

    ​

    81,693

    ​

    ​

    (56,364)

    Loss from operations

    ​

    ​

    (16,606)

    ​

    ​

    (77,634)

    ​

    ​

    61,028

    Other income:

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    Other income and interest income, net

    ​

    ​

    1,804

    ​

    ​

    3,093

    ​

    ​

    (1,289)

    Net loss

    ​

    $

    (14,802)

    ​

    $

    (74,541)

    ​

    $

    59,739

    ​

    Collaboration revenue

    During the three months ended March 31, 2025, we recognized $8.7 million in collaboration revenue, compared to $4.1 million for the three months ended March 31, 2024. The increase in collaboration revenue of $4.7 million during the three months ended March 31, 2025 was primarily due to $5.3 million of additional revenue related to a change in the total estimated research services due to revisions in the research plan, partially offset by decreased reimbursable activity. For additional information on our collaboration with Moderna and the accounting thereunder, refer to Note 4, Collaboration and License Agreement.

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    Table of Contents

    Research and development expenses

    The following table summarizes our research and development expenses for the three months ended March 31, 2025 and 2024:

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    Three Months Ended March 31,

    ​

    Change

    (in thousands)

    ​

    2025

    ​

    2024

    ​

    2025 vs. 2024

    Personnel-related

    ​

    $

    5,637

    ​

    $

    3,722

    ​

    $

    1,915

    Facilities-related

    ​

    ​

    3,611

    ​

    ​

    3,531

    ​

    ​

    80

    Preclinical and manufacturing

    ​

    ​

    3,489

    ​

    ​

    3,296

    ​

    ​

    193

    Stock-based compensation

    ​

    ​

    714

    ​

    ​

    1,521

    ​

    ​

    (807)

    Lab supplies

    ​

    ​

    803

    ​

    ​

    915

    ​

    ​

    (112)

    Consulting and professional services

    ​

    ​

    363

    ​

    ​

    387

    ​

    ​

    (24)

    License fees

    ​

    ​

    17

    ​

    ​

    89

    ​

    ​

    (72)

    Other

    ​

    ​

    723

    ​

    ​

    874

    ​

    ​

    (151)

    Total research and development expenses

    ​

    $

    15,357

    ​

    $

    14,335

    ​

    $

    1,022

    Research and development expenses were $15.4 million for the three months ended March 31, 2025, compared to $14.3 million for the three months ended March 31, 2024. The increase in personnel-related costs of $1.9 million was driven primarily by an employee tax credit in the first quarter of 2024 that did not recur in the first quarter of 2025 as well as severance expenses, partially offset by a decrease in headcount. The decrease in stock-based compensation costs of $0.8 million was driven primarily by decreased headcount.

    General and administrative expenses

    The following table summarizes our general and administrative expenses for the three months ended March 31, 2025 and 2024:

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    Three Months Ended March 31,

    ​

    Change

    (in thousands)

    ​

    2025

    ​

    2024

    ​

    2025 vs. 2024

    Personnel-related

    ​

    $

    3,310

    ​

    $

    3,013

    ​

    $

    297

    Stock-based compensation

    ​

    ​

    1,297

    ​

    ​

    2,479

    ​

    ​

    (1,182)

    Facilities-related

    ​

    ​

    1,142

    ​

    ​

    2,226

    ​

    ​

    (1,084)

    Consulting and professional services

    ​

    ​

    2,871

    ​

    ​

    2,211

    ​

    ​

    660

    Other

    ​

    ​

    214

    ​

    ​

    499

    ​

    ​

    (285)

    Total general and administrative expenses

    ​

    $

    8,834

    ​

    $

    10,428

    ​

    $

    (1,594)

    ​

    General and administrative expenses were $8.8 million for the three months ended March 31, 2025, compared to $10.4 million for the three months ended March 31, 2024. The decrease in stock-based compensation costs of $1.2 million was driven primarily by decreased headcount. The decrease in facilities-related costs of $1.1 million was driven primarily by the termination of the Seyon Lease in in the first quarter of 2024. The increase in consulting and professional services of $0.7 million was driven primarily by higher legal fees and recruiting expenses.

    Loss on lease termination

    During the three months ended March 31, 2025, we recognized a non-cash charge of $1.1 million in accretion and other related expenses in connection with the termination of the Seyon Lease. During the three months ended March 31, 2024, we recognized a non-cash charge of $56.9 million in connection with the termination of the Seyon Lease which included impairments of $45.8 million on the right-of-use asset and $6.2 million on construction in progress, a write-off of $3.9 million in tenant improvement allowance receivable from the landlord and $1.0 million in accretion and other related expenses.

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    Table of Contents

    Other income and interest income, net

    Other income and interest income, net for the three months ended March 31, 2025 was $1.8 million as compared to $3.1 million for the three months ended March 31, 2024. The decrease in other income and interest income, net during the three months ended March 31, 2025 was primarily due to decreases in interest yields and invested cash balances.

    Liquidity and Capital Resources

    Sources of Liquidity

    Since our inception, we have incurred significant operating losses. We expect to incur significant expenses and operating losses for the foreseeable future as we support our continued research activities and development of our programs and technologies. We have not yet commercialized any product candidates and we do not expect to generate revenue from sales of any product candidates for several years, if at all. We expect that any revenue recognized for the next several years will be derived primarily from our current collaboration with Moderna and any additional collaborations that we may enter into in the future.

    Historically, we have funded our operations with proceeds from the sale of instruments convertible into convertible preferred stock, sales of convertible preferred stock and sales of common stock in underwritten public offerings, “at-the-market” offerings and in a private placement, as well as collaboration revenue under our collaboration with Moderna. In August 2024, we entered into an “at-the-market” sales agreement pursuant to which we may, from time to time, sell shares of our common stock having an aggregate offering price of up to $237.0 million. As of the date of this Quarterly Report, we have not issued and sold any shares of our common stock pursuant to the August 2024 sales agreement. As of March 31, 2025, we had cash, cash equivalents, and marketable securities of $157.6 million.

    Cash flows

    The following table summarizes our sources and uses of cash for each of the periods presented:

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    Three Months Ended March 31,

    (in thousands)

    ​

    2025

    ​

    2024

    Net cash used in operating activities

    ​

    $

    (28,360)

    ​

    $

    (31,697)

    Net cash provided by (used in) investing activities

    ​

    ​

    2,957

    ​

    ​

    (553)

    Net cash used in financing activities

    ​

    ​

    (7)

    ​

    ​

    (125)

    Net decrease in cash, cash equivalents and restricted cash

    ​

    $

    (25,410)

    ​

    $

    (32,375)

    ​

    ​

    Operating activities

    During the three months ended March 31, 2025, operating activities used $28.4 million of cash, primarily resulting from our net loss of $14.8 million and the net changes in our operating assets and liabilities of $16.9 million, partially offset by net non-cash charges of $3.3 million. Net changes in our operating assets and liabilities for the three months ended March 31, 2025 consisted of a $7.3 million decrease in deferred revenue, a $7.1 million decrease of operating lease liabilities due primarily to payments for the Seyon Lease, a $3.7 million decrease of accrued expense and other current liabilities and accounts payable, due primarily to payments of accrued employee bonus, partially offset by a $0.9 million decrease in operating lease right-of-use assets and a $0.5 million decrease in prepaid expenses and other current assets.

    During the three months ended March 31, 2024, operating activities used $31.7 million of cash, primarily resulting from our net loss of $74.5 million and the net changes in our operating assets and liabilities of $17.1 million and offset by the net of non-cash charges of $59.9 million. Net changes in our operating assets and liabilities for the three months ended March 31, 2024 consisted of a $4.1 million decrease of deferred revenue, a $1.1 million decrease in operating lease right of-use assets, a $0.9 million increase in prepaid expenses and other current assets, a $10.3 million decrease of accrued expense and other current liabilities and accounts payable and a $2.9 million decrease in operating lease liability.

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    Table of Contents

    Changes in deferred revenue relate to the recognition of revenue for consideration allocated to research activities performed under our Collaboration Agreement with Moderna. Changes in prepaid expenses and other current assets and accrued expenses and other current liabilities and accounts payable are generally due to the timing of employee compensation and vendor invoicing and payments.

    Investing activities

    During the three months ended March 31, 2025, net cash provided by investing activities was $3.0 million, primarily due to $45.0 million in maturities of marketable securities, partially offset by purchases of marketable securities of $41.8 million. During the three months ended March 31, 2024, net cash used in investing activities was $0.6 million, due to purchases of marketable securities of $86.6 million and property and equipment of $1.9 million during the period, partially offset by $88.0 million in maturities of marketable securities.

    Financing activities

    During the three months ended March 31, 2025, net cash used in financing activities was less than $0.1 million, consisting of payments for repurchases of common stock for employee tax withholdings. During the three months ended March 31, 2024, net cash used in financing activities was $0.1 million, consisting of payments for repurchase of common stock for employee tax withholdings.

    Funding requirements

    We expect our expenses to increase substantially in connection with our ongoing activities, particularly as we advance preclinical activities and initiate clinical trials for our product candidates in development. The timing and amount of our operating expenditures will depend largely on:

    ●the costs and scope of the continued development of our technologies;
    ●the identification of additional research programs and product candidates;
    ●the costs and timing of preparing, filing and prosecuting applications for patents; obtaining, maintaining, defending and enforcing our intellectual property rights and defending against any intellectual property-related claims, including claims of infringement, misappropriation or other violation of third-party intellectual property;
    ●the scope, progress, costs and results of preclinical and clinical development for any product candidates we may develop;
    ●our research and development costs and the receipt of milestone payments under our collaboration with Moderna;
    ●the costs, timing and outcome of regulatory review of any product candidates we may develop;
    ●the cost and timing of completion of commercial-scale manufacturing activities;
    ●the costs and timing of future commercialization activities, including product manufacturing, marketing, sales and distribution, for any product candidates we may develop for which we receive marketing approval;
    ●the costs of satisfying any post-marketing requirements;
    ●the revenue, if any, received from commercial sales of product candidates we may develop for which we receive marketing approval;
    ●the costs of operational, financial and management information systems and associated personnel;

    29

    Table of Contents

    ●the associated costs in connection with any acquisition of in-licensed products, intellectual property and technologies; and
    ●the costs of operating as a public company.

    In July 2021, we entered into the Seyon Lease for a manufacturing facility in Waltham, Massachusetts. On January 31, 2024, we notified the Landlord of termination of the Seyon Lease due to the Landlord’s breach of its obligations to us under the Seyon Lease and returned possession of the premises to the Landlord, effective January 31, 2024. On February 20, 2024, the Landlord served us with a complaint, filed in Massachusetts Superior Court, or the Court, with respect to the Seyon Lease. The complaint seeks declaratory judgment that we unlawfully terminated the Seyon Lease and also asserts a claim for breach of contract damages. Following receipt of the complaint, we filed a counterclaim against the Landlord asserting breach of contract and violation of Massachusetts General Law Chapter 93A. On October 29, 2024, the Court determined that although we did not have the right to terminate the Seyon Lease, the Landlord’s subsequent termination was effective, and that we had alleged sufficient facts to state a claim for breach of contract and violation of Massachusetts General Law Chapter 93A by the Landlord. On January 21, 2025, the Court granted the Landlord’s motion for preliminary injunction and ordered us to pay, until further notice, monthly amounts equal to the rent and other charges that would have been due to the Landlord under the Seyon Lease had it not been terminated. On February 14, 2025, we filed a notice of appeal of the Court’s preliminary injunction ruling and our appeal is pending before the Massachusetts Appeals Court. On March 28, 2025, we filed a petition for direct appellate review with the Massachusetts Supreme Judicial Court. We are continuing to make monthly payments under the Seyon Lease during the pendency of the appeal. We will continue to vigorously defend the action and prosecute our counterclaims against the Landlord with respect to this matter.

    We believe that our existing cash, cash equivalents, and marketable securities will enable us to fund our operating expenses and capital expenditures into the second half of 2027. We have based our estimates as to how long we expect we will be able to fund our operations on assumptions that may prove to be wrong. We could use our available capital resources sooner than we currently expect, in which case we would be required to obtain additional financing, which may not be available to us on acceptable terms, or at all. Our failure to raise capital as and when needed would have a negative impact on our financial condition and our ability to pursue our business strategy. Although we may receive potential future payments under our collaboration with Moderna, we do not have any committed external source of funds. Accordingly, we will be required to obtain further funding through public or private equity offerings, debt financings, collaborations and licensing arrangements or other sources. If we raise additional funds by issuing equity securities, our stockholders may experience dilution. Any future debt financing into which we enter would result in fixed payment obligations and may involve agreements that include grants of security interests on our assets and restrictive covenants that limit our ability to take specific actions, such as incurring additional debt, making capital expenditures, granting liens over our assets, redeeming stock or declaring dividends, that could adversely impact our ability to conduct our business. Any debt financing or additional equity that we raise may contain terms that could adversely affect the holdings or the rights of our common stockholders.

    If we are unable to raise sufficient capital as and when needed, we may be required to significantly curtail, delay or discontinue one or more of our research or development programs or the commercialization of any product candidate we may develop, or be unable to expand our operations or otherwise capitalize on our business opportunities. If we raise additional funds through collaborations or licensing arrangements with third parties, we may have to relinquish valuable rights to future revenue streams or product candidates or grant licenses on terms that may not be favorable to us.

    See the “Risk Factors” section of this Quarterly Report and in our 2024 Annual Report for additional risks associated with our substantial capital requirements.

    30

    Table of Contents

    Critical Accounting Policies and Significant Judgments and Estimates

    Our condensed consolidated financial statements are prepared in accordance with generally accepted accounting principles in the United States of America, or GAAP. The preparation of our condensed consolidated financial statements and related disclosures requires us to make estimates and judgments that affect the reported amounts of assets, liabilities, costs and expenses and the disclosure of contingent assets and liabilities in our condensed consolidated financial statements. We base our estimates on historical experience, known trends and events and various other factors that we believe are reasonable under the circumstances, the results of which form the basis for making judgments about the carrying values of assets and liabilities that are not readily apparent from other sources. We evaluate our estimates and assumptions on an ongoing basis. Our actual results may differ from these estimates under different assumptions or conditions. There have been no material changes to our critical accounting policies and estimates from those disclosed in our 2024 Annual Report.

    Item 3. Quantitative and Qualitative Disclosures about Market Risks.

    Interest Rate Market Risk

    We are exposed to market risk related to changes in interest rates. We had marketable securities of $106.7 million as of March 31, 2025. We did not record any impairment charges to our marketable securities during the three months ended March 31, 2025. Our primary exposure to market risk is interest rate sensitivity, which is affected by changes in the general level of U.S. interest rates, particularly because a majority of our investments are generally invested in short-term securities. Interest rate changes would result in a change in the net fair value of these financial instruments due to the difference between the current market interest rate and the market interest rate at the date of purchase of the financial instrument. As of March 31, 2025, a hypothetical increase in interest rates of 100 basis points across the entire yield curve on our holdings would have resulted in a $0.4 million decrease to the fair value of our holdings. We currently do not seek to hedge this exposure to fluctuations in interest rates. We have not been exposed to, nor do we anticipate being exposed to, material risks due to changes in interest rates.

    ​

    Item 4. Controls and Procedures.

    Evaluation of Disclosure Controls and Procedures

    Our management, under the supervision and with the participation of our President and Chief Executive Officer and our Chief Financial Officer, our principal executive officer and principal financial and accounting officer, respectively, evaluated the effectiveness of our disclosure controls and procedures  as of March 31, 2025. The term “disclosure controls and procedures,” as defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, as amended, or 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 a company in the reports that it files or submits under the Exchange Act is accumulated and communicated to the company’s management, including its principal executive and principal financial officers, as appropriate to allow timely decisions regarding required disclosure. Management recognizes that any disclosure controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving their objectives, and management necessarily applies its judgment in evaluating the cost-benefit relationship of possible controls and procedures. Based on the evaluation of our disclosure controls and procedures as of March 31, 2025, our President and Chief Executive Officer and our Chief Financial Officer concluded that, as of such date, our disclosure controls and procedures were effective at the reasonable assurance level.

    Changes in Internal Control over Financial Reporting

    There were no other changes in our internal control over financial reporting (as defined in Rules 13a–15(f) and 15d–15(f) under the Exchange Act) during the three months ended March 31, 2025 that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

    31

    Table of Contents

    PART II—OTHER INFORMATION

    Item 1. Legal Proceedings.

    For a discussion of material legal proceedings, see Note 9. Commitments and Contingencies—Legal Proceedings in Part I, Item 1, Financial Statements of this Quarterly Report.

    ​

    Item 1A. Risk Factors.

    In addition to the other information set forth in this Quarterly Report, you should carefully consider the factors discussed in Part I, Item 1A Risk Factors in our 2024 Annual Report, which could materially affect our business, financial condition, or future results.

    Item 5. Other Information.

    Director and Officer Trading Arrangements

    The following table describes, for the period covered by this Quarterly Report, each trading arrangement for the sale or purchase of Company securities adopted or terminated by our directors and officers that is a contract, instruction or written plan intended to satisfy the affirmative defense conditions of Rule 10b5-1(c) (a “Rule 10b5-1 trading arrangement”):

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    Name

    ​

    Title

    ​

    Action taken

    ​

    Date

    ​

    Shares to be sold

    ​

    Expiration Date

    Kevin Conway

    ​

    Chief Financial Officer

    ​

    Adopted

    ​

    January 28, 2025

    ​

    111,397

    ​

    May 29, 2026

    ​

    ​

    ​

    ​

    ​

    ​

    ​

    32

    Table of Contents

    Item 6. Exhibits.

    Exhibit
    Number

        

    Description of Exhibit

        31.1*

      

    Certification of Principal Executive Officer pursuant to Rule 13a-14(a) of the Securities Exchange Act, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002

        31.2*

      

    Certification of Principal Financial Officer pursuant to Rule 13a-14(a) of the Securities Exchange Act, as adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002

        32.1**

      

    Certification of Principal Executive Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002

        32.2**

      

    Certification of Principal Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002

    101.SCH

      

    Inline XBRL Taxonomy Extension Schema Document

    101.CAL

      

    Inline XBRL Taxonomy Extension Calculation Linkbase Document

    101.DEF

      

    Inline XBRL Taxonomy Extension Definition Linkbase Document

    101.LAB

      

    Inline XBRL Taxonomy Extension Label Linkbase Document

    101.PRE

      

    Inline XBRL Taxonomy Extension Presentation Linkbase Document

    ​

    ​

    ​

    104

    ​

    Cover Page Interactive Data File (formatted as inline XBRL and contained in Exhibit 101)

    ​

    *

    Filed herewith.

    **

    Furnished herewith.

    ​

    ​

    ​

    ​

    33

    Table of Contents

    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.

    GENERATION BIO CO.

    Date: May 7, 2025

    By:

      /s/ Geoff McDonough

    ​

    Geoff McDonough, M.D.

    ​

    President and Chief Executive Officer

    ​

    (Principal Executive Officer)

    Date: May 7, 2025

    By:

      /s/ Kevin Conway

    ​

    Kevin Conway

    ​

    Chief Financial Officer

    ​

    (Principal Financial and Accounting Officer)

    ​

    ​

    ​

    ​

    ​

    34

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