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(Mark One)☒QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF1934 For the quarterly period endedJune 30,2025OR ☐TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF1934 For the transition period from ___________________ to ___________________Commission File Number:001-39273 Lyra Therapeutics, Inc.(Exact Name of Registrant as Specified in its Charter) 84-1700838(I.R.S. EmployerIdentification No.) 480 Arsenal WayWatertown,MA(Address of principal executive offices) Registrant’s telephone number, including area code: (617)393-4600 N/A (Former name, former address and former fiscal year, if changed since last report) Securities registered pursuant to Section 12(b) of the Act: Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the SecuritiesExchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) hasbeen 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 toRule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was requiredto 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 reportingcompany, 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☐Non-accelerated filer☒ 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 forcomplying 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 August 8, 2025, the registrant had1,644,454shares of common stock, $0.001 par value per share, outstanding. SPECIAL NOTE REGARDING FORWARD-LOOKING STATEMENTS This Quarterly Report on Form 10-Q contains forward-looking statements within the meaning of the Private SecuritiesLitigation Reform Act of 1995. We intend such forward-looking statements to be covered by the safe harbor provisions forforward-looking statements contained in Section 27A of the Securities Act of 1933, as amended, and Section 21E of the SecuritiesExchange Act of 1934, as amended. All statements other than statements of historical fact contained in this Quarterly Report onForm 10-Q are forward-looking statements, including but not limited to statements regarding: •our restructuring initiatives and our ability to continue as a going concern;•our evaluation of strategic transactions, if any, to maximize shareholder value;•our estimates and statements regarding our future revenue, future results of operations, and financial position;•the sufficiency of our cash and cash equivalents to fund our operations;•plans to develop, manufacture, and commercialize LYR-210;•the timing of and our ability to obtain and maintain regulatory approvals for LYR-210, and any future productcandidates;•the clinical utility of LYR-210;•our commercialization, marketing, and manufacturing capabilities and strategy;•our expectations about the willingness of healthcare professionals to use LYR-210, and any future productcandidates;•our expectations regarding the development and commercialization of LYR-210 pursuant to the terms of theLianBio License Agreement (as defined below);•our intellectual property position;•our competitive position and developments and projections relating to our competitors or our industry;•the impact of laws and regulations;•risks associated with the COVID-19 pandemic and related macroeconomic factors, which may adversely impactour business and clinical trials;•our expectations regarding the time during which we will be an emerging growth company under the JumpstartOur Business Startups Act, or the JOBS Act;•our business strategy;•our projected research and development costs; and•the plans and objectives of management for future operations. These statements are neither promises nor guarantees, but involve known and unknown risks, uncertainties and otherimportant factors that may cause our actual results, performance or achievements to be materially different from any future results,performance or achievements expressed or implied by the forward-looking statements. In some cases, you can identify forward-looking statements by terms such as “may,” “will,” “should,” “expect,” “plan,”“anticipate,” “could,” “intend,” “target,