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TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934For the transition period from _________________ to _________________Commission File Number:001-42366 Upstream Bio, Inc. (Exact name of Registrant as specified in its charter) Registrant’s telephone number, including area code: (781)208-2466 Securities registered pursuant to Section 12(b) of the Act: Title of each classTradingsymbol(s)Name of each exchange on which registeredCommon Stock, par value $0.001 per shareUPBThe Nasdaq Global Select Market 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-2of the 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 ofthe 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 number of shares of Registrant’s common stock outstanding as of March 5, 2025 was53,640,895. Portions of the Registrant’s definitive proxy statement for its 2025 Annual Meeting of Stockholders to be filed pursuant to Regulation 14A within 120 days of theend of the Registrant’s fiscal year ended December 31, 2024 are incorporated by reference in Part III of this Annual Report on Form 10-K to the extent stated herein. 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 II Item 5.Market for Registrant’s Common Equity, Related Stockholder Matters and Issuer Purchases of EquitySecurities105Item 6.[Reserved]105Item 7.Management’s Discussion and Analysis of Financial Condition and Results of Operations106Item 7A.Quantitative and Qualitative Disclosures About Market Risk119Item 8.Financial Statements and Supplementary Data119Item 9.Changes in and Disagreements With Accountants on Accounting and Financial Disclosure119Item 9A.Controls and Procedures119Item 9B.Other Information119Item 9C.Disclosure Regarding Foreign Jurisdictions that Prevent Inspections120 PART III Item 10.Directors, Executive Officers and Corporate Governance121Item 11.Executive Compensation121Item 12.Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters121Item 13.Certain Relationships and Related Transactions, and Director Independence121Item 14.Principal Accounting Fees and Services121 PART IV Item 15.Exhibits and Financial Statement Schedules122Item 16.Form 10-K Summary123 124 Signatures SPECIAL NOTE REGARDING FORWARD-LOOKING STATEMENTS This Annual Report on Form 10-K (this “Annual Report”) contains express or implied forward-looking statements that are basedon our management’s belief and assumptions and on information currently available to our management. We intend such forward-looking s