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FORM10-K(Mark One)xANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF1934For the fiscal year endedDecember 31,2024oroTRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACTOF 1934For the transition period fromtoCommission file number:001-37378ATYR PHARMA, INC.(Exact name of registrant as specified in its charter)Delaware20-3435077(State or other jurisdiction ofincorporation or organization)(I.R.S. EmployerIdentification No.)10240 Sorrento Valley Road,Suite 300,San Diego,CA92121(Address of principal executive offices)(Zip Code)Registrant’s telephone number, including area code:(858)731-8389Securities registered pursuant to Section 12(b) of the Act:Title of each classTrading SymbolName of each exchange on which registeredCommon Stock, par value $0.001 per shareATYRTheNasdaqCapital MarketSecurities registered pursuant to Section 12(g) of the Act: None Indicate by check mark if the registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Act.Yeso No x Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or Section 15(d) of the Securities ExchangeAct 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 tosuch filing requirements for the past 90 days.Yes x Noo Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule405 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 suchfiles). xYes o 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 growthcompany” in Rule 12b-2 of the Exchange Act. Large accelerated fileroAccelerated filer oNon-accelerated filer x Smaller reporting companyx Emerging growth companyo If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying withany new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act.o Indicate by check mark whether the registrant has filed a report on and attestation to its management’s assessment of the effectiveness of itsinternal control over financial reporting under Section 404(b) of the Sarbanes-Oxley Act (15 U.S.C. 7262(b)) by the registered public accounting firm thatprepared or issued its audit report.o Indicate by check mark whether any of those error corrections are restatements that required a recovery analysis of incentive-based compensationreceived 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 Act). YesoNo x The aggregate market value of the registrant’s voting and non-voting common equity held by non-affiliates of the registrant was approximately$116,242,729based on the closing price of the registrant’s common stock on the Nasdaq Capital Market of $1.56 per share on June 30, 2024, the lastbusiness day of the registrant’s most recently completed second fiscal quarter. Shares of common stock held by each executive officer and director havebeen excluded from this calculation. This determination of affiliate status may not be conclusive for other purposes. The number of outstanding shares of the registrant’s common stock, par value $0.001 per share, as of March 7, 2025 was88,858,612. DOCUMENTS INCORPORATED BY REFERENCEPortions of the registrant’s definitive proxy statement to be filed with the Securities and Exchange Commission (SEC), pursuant to Regulation 14A in connection with the registrant’s 2025 Annual Meeting of Stockholders, which will be filed subsequent to the date hereof, are incorporated by referenceinto Part III of this Annual Report on Form 10-K. Such proxy statement will be filed with the SEC not later than 120 days following the end of theregistrant’s fiscal year ended December 31, 2024. ATYR PHARMA, INC. ANNUAL REPORT ON FORM 10-K Table of Contents PageForward-Looking Statements3Summary of Risks Associated with Our Business3 PART IItem 1 BusinessItem 1ARisk FactorsItem 1BUnresolved Staff CommentsItem 1CCybersecurityItem 2PropertiesItem 3Legal ProceedingsItem 4Mine Safety Disclosures PART IIItem 5 Market for Registrant's Common Equity, Related Stockholder Matters and Issuer Purchases of EquitySecurities61Item 6[Reserved]61Item 7Management’s Discussion and Analysis of Financial Condition and Results of Operations61Item 7AQuantitative and Qualitative Disclosures About Market Risk68Item 8F