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(Mark One) ☒ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934For the fiscal year endedDecember 31,2024or ☐TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF1934 For the transition period fromto Commission File Number001-39527 PRELUDE THERAPEUTICS INCORPORATED (Exact name of registrant as specified in its charter) Delaware(State or other jurisdiction ofincorporation or organization)175 Innovation BoulevardWilmington,Delaware(Address of principal executive offices) Registrant’s telephone number, including area code: (302)467-1280 Securities registered pursuant to Section 12(b) of the Act: Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or 15(d) of the Act.YES☐NO☒ 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 thepreceding 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 thepast 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 RegulationS-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 emerginggrowth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company” and “emerging growth company” in Rule 12b-2 ofthe Exchange Act. Accelerated filer☐Smaller reporting company☒Emerging growth company☒ Large accelerated filer☐Non-accelerated filer☒ 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 revisedfinancial accounting standards provided pursuant to Section 13(a) of the Exchange Act.☐ Indicate by check mark whether the registrant has filed a report on and attestation to its management’s assessment of the effectiveness of its internal control overfinancial reporting under Section 404(b) of the Sarbanes-Oxley Act (15 U.S.C. 7262(b)) by the registered public accounting firm that prepared or issued its auditreport.☐ If securities are registered pursuant to Section 12(b) of the Act, indicate by check mark whether the financial statements of the registrant included in the filing reflectthe correction of an error to previously issued financial statements.☐Indicate by check mark whether any of those error corrections are restatements that required a recovery analysis of incentive-based compensation received by any of the registrant’s executive officers during the relevant recovery period pursuant to § 240.10D-1(b).☐ Indicate by check mark whether the Registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act).YES☐NO☒ The aggregate market value of the voting and non-voting common equity held by non-affiliates of the registrant was approximately $66.1million as of the lastbusiness day of the registrant’s most recently completed second fiscal quarter, based upon the closing sale price on The Nasdaq Global Select Market reported forsuch date.The number of shares of registrant’s Common Stock outstanding as of March 6, 2025 was55,154,634. Table of Contents PART I Item 1.BusinessItem 1A.Risk FactorsItem 1B.Unresolved Staff CommentsItem 1C.CybersecurityItem 2.PropertiesItem 3.Legal ProceedingsItem 4.Mine Safety Disclosures PART IIItem 5. Market for Registrant’s Common Equity, Related Stockholder Matters and Issuer Purchases of EquitySecurities80Item 6.[Reserved]80Item 7.Management’s Discussion and Analysis of Financial Condition and Results of Operations81Item 7A.Quantitative and Qualitative Disclosures About Market Risk90Item 8.Financial Statements and Supplementary Data90Item 9.Changes in and Disagreements With Accountants on Accounting and Financial Disclosure114Item 9A.Controls and Procedures114Item 9B.Other Information114Item 9C.Disclosure Regarding Foreign Jurisdictions that Prevent Inspections114 PART IIIItem 10. Directors, Executive Officers and Corporate Governance115Item 11.Executive Compensation115Item 12.Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters115Item 13.Certain Relationships and Related Transactions, and Director Independence115Item 14.Principal Accounting Fees and Services115 PART IVItem 15. Exhibits and Financial Statement Schedules116Item 16Form 10-K Summary118Signatures119 PART I This Annual Report on Form 10-K contains forward-looking statements within the meaning of Section 27A of the Securities Actof 1933, as amended, and Section 21E of the Securities Exchange A