LYRA / Lyra Therapeutics, Inc. - Pengajuan SECLaporan Tahunan, Pernyataan Proksi

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): September 4, 2025 Lyra Therapeuti

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): September 4, 2025 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commissi

Forward Looking Statement This presentation contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. The words “believe,” “may,” “will,” “estimate,” “continue,” “anticipate,” “intend,” “expect,”

EX-99.1 Investor Presentation September 2025 Exhibit 99.1 Forward Looking Statement This presentation contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. The words “believe,” “may,” “will,” “estimate,” “continue,” “anticipate,” “intend,” “expect,” and similar expressions are intended to identify forward-looking statements. All statements

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 20, 2025 Lyra Therapeutics

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 20, 2025 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commission

FORM 8-K Item 2.02 Results of Operations and Financial Condition. Item 9.01 Financial Statements and Exhibits.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 12, 2025 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commission

Lyra Therapeutics Reports Second Quarter 2025 Financial Results and Provides Corporate Update

Exhibit 99.1 Lyra Therapeutics Reports Second Quarter 2025 Financial Results and Provides Corporate Update – Positive ENLIGHTEN 2 Phase 3 results announced in June 2025 propel business activities in manufacturing, regulatory strategy and ENLIGHTEN clinical dataset analysis to advance path forward for LYR-210 for treatment of chronic rhinosinusitis (CRS) – – Financing announced in June 2025 extends

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 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: 001-39273 Lyra Therapeutics, Inc.

Securities Purchase Agreement, dated as of June 26, 2025, by and between Lyra Therapeutics, Inc. and the Purchasers

Exhibit 10.1 SECURITIES PURCHASE AGREEMENT This Securities Purchase Agreement (this “Agreement”) is dated as of June 26, 2025, between Lyra Therapeutics, Inc., a Delaware corporation (the “Company”), and each purchaser identified on the signature pages hereto (each, including its successors and assigns, a “Purchaser” and collectively the “Purchasers”). WHEREAS, subject to the terms and conditions

Second Amendment to the Employment Agreement Between Lyra Therapeutics, Inc. and Maria Palasis, dated March 7, 2025

Exhibit 10.4 SECOND AMENDMENT TO THE EMPLOYMENT AGREEMENT BETWEEN LYRA THERAPEUTICS, INC. AND MARIA PALASIS This Amendment (the “Amendment”) to that certain Employment Agreement between Lyra Therapeutics, Inc., a Delaware corporation (together with any successor thereto, the “Company”), and Maria Palasis (the “Executive”) dated as of April 27, 2020 and as amended as of February 16, 2022 (the “Empl

Investor Presentation August 2025

Investor Presentation August 2025 Forward Looking Statement This presentation contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995.

First Amendment to the Employment Agreement Between Lyra Therapeutics, Inc. and Harlan Waksal, dated March 7, 2025

Exhibit 10.2 FIRST AMENDMENT TO THE EMPLOYMENT AGREEMENT BETWEEN LYRA THERAPEUTICS, INC. AND HARLAN WAKSAL This Amendment (the “Amendment”) to that certain Employment Agreement between Lyra Therapeutics, Inc., a Delaware corporation (together with any successor thereto, the “Company”), and Harlan Waksal (the “Executive”) dated as of February 16, 2022 (the “Employment Agreement”) is made as of this

First Amendment to the Employment Agreement Between Lyra Therapeutics, Inc. and Jason Cavalier, dated March 7, 2025

Exhibit 10.3 FIRST AMENDMENT TO THE EMPLOYMENT AGREEMENT BETWEEN LYRA THERAPEUTICS, INC. AND JASON CAVALIER This Amendment (the “Amendment”) to that certain Employment Agreement between Lyra Therapeutics, Inc., a Delaware corporation (together with any successor thereto, the “Company”), and Jason Cavalier (the “Executive”) dated as of September 13, 2021 (the “Employment Agreement”) is made as of t

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 1, 2025 Lyra Therapeutics,

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 1, 2025 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commission

846,744 Shares Common Stock Offered by the Selling Securityholders

424B3 Table of Contents Filed pursuant to Rule 424B3 Registration No. 333-288872 PROSPECTUS 846,744 Shares Common Stock Offered by the Selling Securityholders The selling securityholders or any of their respective pledgees, donees, transferees, assignees or other successors-in-interest may offer and sell up to 846,744 shares in the aggregate of common stock identified above, which shares are issua

Power of Attorney (included on signature page)

Table of Contents As filed with the Securities and Exchange Commission on July 22, 2025 Registration No.

Form of Private Warrant, together with a schedule of Private Warrants, each dated as of June 27, 2025, issued by Lyra Therapeutics, Inc. to the investors set forth on such schedule

EX-4.6 Exhibit 4.6 Schedule of Holders of Private Warrants to Purchase Common Stock Holder Name Number of Shares Hudson Bay Master Fund Ltd. 254,024 Sabby Volatility Warrant Master Fund, Ltd. 592,720 NEITHER THIS SECURITY NOR THE SECURITIES FOR WHICH THIS SECURITY IS EXERCISABLE HAVE BEEN REGISTERED WITH THE SECURITIES AND EXCHANGE COMMISSION OR THE SECURITIES COMMISSION OF ANY STATE IN RELIANCE U

Pre-Funded Warrant, dated as of June 27, 2025, issued by Lyra Therapeutics, Inc. to Sabby Volatility Warrant Master Fund, Ltd.

EX-4.5 Exhibit 4.5 PRE-FUNDED COMMON STOCK PURCHASE WARRANT LYRA THERAPEUTICS, INC. Warrant Shares: 150,360 Initial Exercise Date: June 27, 2025 Issue Date: June 27, 2025 THIS PRE-FUNDED COMMON STOCK PURCHASE WARRANT (the “Warrant”) certifies that, for value received, Sabby Volatility Warrant Master Fund, Ltd. or its assigns (the “Holder”) is entitled, upon the terms and subject to the limitations

Filing Fee Table

EX-FILING FEES Exhibit 107 Calculation of Filing Fee Table Registration Statement on Form S-1 (Form Type) LYRA THERAPEUTICS, INC.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 26, 2025 Lyra Therapeutics,

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 26, 2025 Lyra Therapeutics, Inc. (Exact name of registrant as specified in its charter) Delaware 001-39273 84-1700838 (State or other jurisdiction of incorporation) (Commission F

Form of Private Warrant

Exhibit 4.2 NEITHER THIS SECURITY NOR THE SECURITIES FOR WHICH THIS SECURITY IS EXERCISABLE HAVE BEEN REGISTERED WITH THE SECURITIES AND EXCHANGE COMMISSION OR THE SECURITIES COMMISSION OF ANY STATE IN RELIANCE UPON AN EXEMPTION FROM REGISTRATION UNDER THE SECURITIES ACT OF 1933, AS AMENDED (THE “SECURITIES ACT”), AND, ACCORDINGLY, MAY NOT BE OFFERED OR SOLD EXCEPT PURSUANT TO AN EFFECTIVE REGISTR

Lyra Therapeutics Announces Up to Approximately $15 Million Registered Direct Offering and Concurrent Private Placement Priced At-The-Market Under Nasdaq Rules Upfront Gross Proceeds of $5.0 Million, with Up to Approximately $9.8 Million of Additiona

EX-99.1 Exhibit 99.1 Lyra Therapeutics Announces Up to Approximately $15 Million Registered Direct Offering and Concurrent Private Placement Priced At-The-Market Under Nasdaq Rules Upfront Gross Proceeds of $5.0 Million, with Up to Approximately $9.8 Million of Additional Gross Proceeds Assuming the Cash Exercise in Full of Private Placement Warrants WATERTOWN, Mass., June 27, 2025 — Lyra Therapeu

Form of Pre-Funded Common Stock Purchase Warrant

EX-4.1 Exhibit 4.1 PRE-FUNDED COMMON STOCK PURCHASE WARRANT LYRA THERAPEUTICS, INC. Warrant Shares: Initial Exercise Date: June 27, 2025 Issue Date: June 27, 2025 THIS PRE-FUNDED COMMON STOCK PURCHASE WARRANT (the “Warrant”) certifies that, for value received, or its assigns (the “Holder”) is entitled, upon the terms and subject to the limitations on exercise and the conditions hereinafter set for

273,012 Shares of Common Stock Pre-Funded Warrants to Purchase up to 150,360 Shares of Common Stock

Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No. 333-278163 PROSPECTUS SUPPLEMENT (To Prospectus dated April 1, 2024) 273,012 Shares of Common Stock Pre-Funded Warrants to Purchase up to 150,360 Shares of Common Stock We are offering to certain accredited and institutional investors 273,012 shares of our common stock and pre-funded warrants to purchase 150,360 shares of our comm

Form of Securities Purchase Agreement, dated as of June 26, 2025, by and between Lyra Therapeutics, Inc. and the Purchasers

EX-10.1 Exhibit 10.1 SECURITIES PURCHASE AGREEMENT This Securities Purchase Agreement (this “Agreement”) is dated as of June 26, 2025, between Lyra Therapeutics, Inc., a Delaware corporation (the “Company”), and each purchaser identified on the signature pages hereto (each, including its successors and assigns, a “Purchaser” and collectively the “Purchasers”). WHEREAS, subject to the terms and con

Common Stock

424B5 As Filed Pursuant to Rule 424(b)(5) Registration No. 333-278163 PROSPECTUS SUPPLEMENT (To Prospectus and Prospectus Supplement dated April 1, 2024) Common Stock This prospectus supplement (the “Prospectus Supplement”) supplements the prospectus dated April 1, 2024 (the “Base Prospectus”) and the prospectus supplement dated April 1, 2024 (together with the Base Prospectus, the “ATM Prospectus

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 13, 2025 Lyra Therapeutics,

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 13, 2025 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commission F

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 9, 2025 Lyra Therapeutics, I

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 9, 2025 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commission Fi

Forward Looking Statement This presentation contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. The words “believe,” “may,” “will,” “would,” “estimate,” “continue,” “anticipate,” “intend,” “

Corporate Presentation June 2025 Exhibit 99.1 Forward Looking Statement This presentation contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. The words “believe,” “may,” “will,” “would,” “estimate,” “continue,” “anticipate,” “intend,” “expect,” and similar expressions are intended to identify forward-looking statements. All statements con

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 27, 2025 Lyra Therapeutics, I

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 27, 2025 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commission Fi

Certificate of Amendment to Restated Certificate of Incorporation of Lyra Therapeutics, Inc., dated May 27, 2025.

EX-3.1 Exhibit 3.1 CERTIFICATE OF AMENDMENT TO RESTATED CERTIFICATE OF INCORPORATION OF LYRA THERAPEUTICS, INC. Pursuant to Section 242 of the General Corporation Law of the State of Delaware Lyra Therapeutics, Inc. (the “Corporation”), a corporation organized and existing under and by virtue of the General Corporation Law of the State of Delaware, DOES HEREBY CERTIFY THAT: 1. The Board of Directo

Forward Looking Statement This presentation contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. The words “believe,” “may,” “will,” “estimate,” “continue,” “anticipate,” “intend,” “expect,”

EX-99.2 Corporate Presentation June 2025 Exhibit 99.2 Forward Looking Statement This presentation contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. The words “believe,” “may,” “will,” “estimate,” “continue,” “anticipate,” “intend,” “expect,” and similar expressions are intended to identify forward-looking statements. All statements cont

Lyra Therapeutics Reports Positive Results from the ENLIGHTEN 2 Phase 3 Trial of

EX-99.1 Exhibit 99.1 Lyra Therapeutics Reports Positive Results from the ENLIGHTEN 2 Phase 3 Trial of LYR-210 Achieving Statistically Significant Results for Primary and Key Secondary Endpoints in the Treatment of Chronic Rhinosinusitis (CRS) • ENLIGHTEN 2 trial met primary endpoint with LYR-210 demonstrating statistically significant improvement in the composite of the three cardinal symptoms (3C

Current Report

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 14, 2025 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commission Fi

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A (Rule 14a-101) INFORMATION REQUIRED IN PROXY STATEMENT SCHEDULE 14A INFORMATION Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Ame

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A (Rule 14a-101) INFORMATION REQUIRED IN PROXY STATEMENT SCHEDULE 14A INFORMATION Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No.  ) Filed by the Registrant ☒ Filed by a party other than the Registrant ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confid

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ☒ 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: 001-39273 Lyra Therapeutics, Inc.

Lyra Therapeutics Reports First Quarter 2025 Financial Results and Provides Corporate Update – Phase 3 results from ENLIGHTEN 2 pivotal Phase 3 trial of LYR‑210 in Chronic Rhinosinusitis (CRS) expected in Q2 2025 –

Exhibit 99.1 Lyra Therapeutics Reports First Quarter 2025 Financial Results and Provides Corporate Update – Phase 3 results from ENLIGHTEN 2 pivotal Phase 3 trial of LYR‑210 in Chronic Rhinosinusitis (CRS) expected in Q2 2025 – WATERTOWN, Mass., May 6, 2025 – Lyra Therapeutics, Inc. (Nasdaq: LYRA) (“Lyra” or the “Company”), a clinical-stage biotechnology company developing long-acting, anti-inflam

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 06, 2025 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commission Fi

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A (Rule 14a-101) INFORMATION REQUIRED IN PROXY STATEMENT SCHEDULE 14A INFORMATION Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Ame

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A (Rule 14a-101) INFORMATION REQUIRED IN PROXY STATEMENT SCHEDULE 14A INFORMATION Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No. ) Filed by the Registrant ☒ Filed by a party other than the Registrant ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confide

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A (Rule 14a-101) INFORMATION REQUIRED IN PROXY STATEMENT SCHEDULE 14A INFORMATION Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Ame

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A (Rule 14a-101) INFORMATION REQUIRED IN PROXY STATEMENT SCHEDULE 14A INFORMATION Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No. ) Filed by the Registrant ☒ Filed by a party other than the Registrant ☐ Check the appropriate box: ☐ Preliminary Proxy S

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A (Rule 14a-101) INFORMATION REQUIRED IN PROXY STATEMENT SCHEDULE 14A INFORMATION Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Ame

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A (Rule 14a-101) INFORMATION REQUIRED IN PROXY STATEMENT SCHEDULE 14A INFORMATION Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No. ) Filed by the Registrant ☒ Filed by a party other than the Registrant ☐ Check the appropriate box: ☒ Preliminary Proxy S

Novation Agreement, dated as of November 15, 2024, by and among Lyra Therapeutics, Inc., LianBio, an exempted company organized under the laws of the Cayman Islands, and LianBio Development (HK) Limited (as successor-in-interest to LianBio Inflammatory Limited), a private company limited by shares organized under the laws of Hong Kong

Exhibit 10.28 NOVATION AGREEMENT THIS NOVATION AGREEMENT (this “Novation Agreement”) is made and entered into as of November 15, 2024 (the “Novation Effective Date”) by and among LianBio, an exempted company organized under the laws of the Cayman Islands (“LianBio”), LianBio Development (HK) Limited (as successor-in-interest to LianBio Inflammatory Limited), a private company limited by shares org

Lyra Therapeutics Reports Fourth Quarter and Full Year 2024 Financial Results and Provides Corporate Update

Exhibit 99.1 Lyra Therapeutics Reports Fourth Quarter and Full Year 2024 Financial Results and Provides Corporate Update – Company continues to focus on upcoming results from ENLIGHTEN 2 pivotal Phase 3 trial in CRS patients, expected in 2Q 2025 – – In parallel, the Company continues to analyze data and explore opportunities for LYR‑210 in CRS patient cohort with nasal polyps – WATERTOWN, Mass., M

As filed with the Securities and Exchange Commission on March 13, 2025

As filed with the Securities and Exchange Commission on March 13, 2025 Registration No.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K (Mark One) ☒ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2024 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 001-39273 c Lyra Therapeu

Filing Fee Table.

Exhibit 107.1 CALCULATION OF FILING FEE TABLE FORM S-8 (Form Type) LYRA THERAPEUTICS, INC. (Exact Name of Registrant as Specified in its Charter) Table 1: Newly Registered Securities Plan Security Type Security Class Title Fee Calculation Rule Amount Registered (1) Proposed Maximum Offering Price Per Unit Maximum Aggregate Offering Price Fee Rate Amount of Registration Fee 2020 Incentive Award Pla

Description of Securities

Exhibit 4.8 DESCRIPTION OF THE REGISTRANT’S SECURITIES REGISTERED PURSUANT TO SECTION 12 OF THE SECURITIES EXCHANGE ACT OF 1934, AS AMENDED Lyra Therapeutics, Inc. has one class of securities registered under Section 12 of the Securities Exchange Act of 1934, as amended (the “Exchange Act”). References herein to “we,” “us,” “our” and the “Company” refer to Lyra Therapeutics, Inc. and not to any of

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): March 13, 2025 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commission

Insider Trading Compliance Policy

Exhibit 19.1 Lyra Therapeutics, Inc. Insider Trading Compliance Policy (As of November 8, 2023) This Insider Trading Compliance Policy (this “Policy”) consists of seven sections: • Section I provides an overview; • Section II sets forth the policies of the Company prohibiting insider trading; • Section III explains insider trading; • Section IV consists of procedures that have been put in place by

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): January 10, 2025 Lyra Therapeutic

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): January 10, 2025 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commissio

1) Summary Health Statistics Tables for U.S. Adults: National Health Interview Survey, 2018, Tables A-2b, A-2c; 2) Baguley et al. Int Forum Allergy Rhinol, 2014;4(7):525-3; 3) Subject to additional financing Bioabsorbable sinonasal implant designed t

Corporate Presentation January 2025 Exhibit 99.1 Forward Looking Statement This presentation contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. The words “believe,” “may,” “will,” “estimate,” “continue,” “anticipate,” “intend,” “expect,” and similar expressions are intended to identify forward-looking statements. All statements contained

LYRA / Lyra Therapeutics, Inc. / PERCEPTIVE ADVISORS LLC - SC 13D/A Activist Investment

SC 13D/A SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13D/A Under the Securities Exchange Act of 1934 (Amendment No. 5)* Lyra Therapeutics, Inc. (Name of Issuer) Common Stock, $0.001 par value (Title of Class of Securities) 55234L 105 (CUSIP Number) Alexander Rakitin Perceptive Advisors LLC 51 Astor Place, 10th Floor New York, NY 10003 (646) 205-5340 (Name, Address and Teleph

Current Report

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): December 12, 2024 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commissi

LYRA / Lyra Therapeutics, Inc. / Vestal Point Capital, LP - LYRA THERAPEUTICS, INC. Passive Investment

SC 13G/A 1 p24-3220sc13ga.htm LYRA THERAPEUTICS, INC. SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G/A Under the Securities Exchange Act of 1934 (Amendment No. 1)* Lyra Therapeutics, Inc. (Name of Issuer) Common stock, par value $0.001 per share (Title of Class of Securities) 55234L105 (CUSIP Number) September 30, 2024 (Date of event which requires filing of this statement)

LYRA / Lyra Therapeutics, Inc. / Venrock Healthcare Capital Partners II, L.P. - SC 13G/A Passive Investment

SC 13G/A 1 tm2428137d11sc13ga.htm SC 13G/A UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 13G/A UNDER THE SECURITIES EXCHANGE ACT OF 1934 (Amendment No. 3)* Lyra Therapeutics, Inc. (Name of Issuer) Common Stock, $0.001 par value (Title of Class of Securities) 55234L105 (CUSIP Number) September 30, 2024 (Date of Event Which Requires Filing of This Statement) Check

LYRA / Lyra Therapeutics, Inc. / Point72 Asset Management, L.P. - LYRA THERAPEUTICS, INC. Passive Investment

SC 13G/A 1 p24-3155sc13ga.htm LYRA THERAPEUTICS, INC. SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G/A Under the Securities Exchange Act of 1934 (Amendment No. 2)* Lyra Therapeutics, Inc. (Name of Issuer) Common Stock, par value $0.001 per share (Title of Class of Securities) 55234L105 (CUSIP Number) September 30, 2024 (Date of Event Which Requires Filing of this Statement)

LYRA / Lyra Therapeutics, Inc. / Samsara BioCapital, L.P. - SC 13G/A Passive Investment

SC 13G/A 1 tm2427620d24sc13ga.htm SC 13G/A UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 1)* Lyra Therapeutics, Inc. (Name of Issuer) Common Stock, par value $0.001 (Title of Class of Securities) 55234L105 (CUSIP Number) September 30, 2024 (Date of Event Which Requires Filing of this Statement) Check th

Lyra Therapeutics Reports Third Quarter 2024 Financial Results and Provides Corporate Update

Lyra Therapeutics Reports Third Quarter 2024 Financial Results and Provides Corporate Update – Company continues to focus on upcoming results from ENLIGHTEN 2 pivotal Phase 3 trial in CRS patients expected in 2Q 2025 – – Company reports topline safety results from ENLIGHTEN 1 Phase 3 extension study indicating no product-related serious adverse events and general consistency with the primary treatment phase – WATERTOWN, Mass.

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 12, 2024 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commissi

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended September 30, 2024 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: 001-39273 Lyra Therapeutics, Inc.

LYRA / Lyra Therapeutics, Inc. / PERCEPTIVE ADVISORS LLC - SC 13D/A Activist Investment

SC 13D/A SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13D/A Under the Securities Exchange Act of 1934 (Amendment No. 4)* Lyra Therapeutics, Inc. (Name of Issuer) Common Stock, $0.001 par value (Title of Class of Securities) 55234L 105 (CUSIP Number) Alexander Rakitin Perceptive Advisors LLC 51 Astor Place, 10th Floor New York, NY 10003 (646) 205-5340 (Name, Address and Teleph

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2024 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: 001-39273 Lyra Therapeutics, Inc.

Regulation FD Disclosure, Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 14, 2024 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commission

LYRA THERAPEUTICS, INC. Condensed Consolidated Balance Sheets (in thousands, except share data)

Lyra Therapeutics Reports Second Quarter 2024 Financial Results and Provides Corporate Update – Primary focus continues to be on upcoming results from ENLIGHTEN 1 Phase 3 extension study in 4Q 2024 and ENLIGHTEN 2 pivotal Phase 3 trial in CRS patients in 1H 2025, as planned – – In parallel, the company continues to analyze data from ENLIGHTEN 1; further analysis of the ENLIGHTEN 1 data has revealed that LYR-210 demonstrated improvement over control in symptomatic endpoints in the CRS patient cohort with nasal polyps – WATERTOWN, Mass.

Corporate Presentation August 2024

Corporate Presentation August 2024 Forward Looking Statement This presentation contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): July 19, 2024 Lyra Therapeutics,

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): July 19, 2024 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commission F

Restated Certificate of Incorporation of Lyra Therapeutics, Inc., dated May 5, 2020 and the Certificate of Amendment to the Restated Certificate of Incorporation of Lyra Therapeutics, Inc., dated June 13, 2024

EX-3.1 Exhibit 3.1 RESTATED CERTIFICATE OF INCORPORATION OF LYRA THERAPEUTICS, INC. The name of the corporation is Lyra Therapeutics, Inc. The corporation was originally incorporated by the filing of its original Certificate of Incorporation with the Secretary of State of the State of Delaware on November 21, 2005 under the corporate name WMR Biomedical, Inc. This Restated Certificate of Incorpora

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 13, 2024 Lyra Therapeutics,

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 13, 2024 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commission F

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K/A (Amendment No. 1) CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 16, 2024

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K/A (Amendment No. 1) CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 16, 2024 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorpora

Costs Associated with Exit or Disposal Activities

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 16, 2024 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commission Fi

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended March 31, 2024 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: 001-39273 Lyra Therapeutics, Inc.

Lyra Therapeutics Reports First Quarter 2024 Financial Results and Provides Corporate Update -- Phase 3 Results from ENLIGHTEN 1 Trial of LYR-210 in Chronic Rhinosinusitis (CRS) Expected in May --

Lyra Therapeutics Reports First Quarter 2024 Financial Results and Provides Corporate Update - Phase 3 Results from ENLIGHTEN 1 Trial of LYR-210 in Chronic Rhinosinusitis (CRS) Expected in May - WATERTOWN, Mass.

Lyra Therapeutics, Inc. 2020 Incentive Award Plan Performance Stock Option Grant Notice and Performance Stock Option Agreement issued to Maria Palasis, Ph.D. on March 21, 2024

LYRA THERAPEUTICS, INC. 2020 INCENTIVE AWARD PLAN PERFORMANCE STOCK OPTION GRANT NOTICE Capitalized terms not specifically defined in this Performance Stock Option Grant Notice (the “Grant Notice”) have the meanings given to them in the 2020 Incentive Award Plan (as amended from time to time, the “Plan”) of Lyra Therapeutics, Inc. (the “Company”). The Company has granted to the participant listed

Resolutions adopted by the Board of Directors of the Registrant setting forth the information with respect to the Ratification required under Section 204 of the Delaware General Corporation Law

EXHIBIT 99.1 LYRA THERAPEUTICS, INC. Written Consent of the Board of Directors The undersigned, constituting all of the members of the Board of Directors (the “Board”) of Lyra Therapeutics, Inc., a Delaware corporation (the “Corporation”), and acting in accordance with Section 141(f) of the General Corporation Law of the State of Delaware (the “DGCL”) and the Amended and Restated Bylaws of the Cor

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): April 30, 2024 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commission

Lyra Therapeutics, Inc. 2020 Incentive Award Plan Performance Based Restricted Stock Unit Grant Notice and Performance Based Restricted Stock Unit Agreement issued to Harlan Waksal, M.D. on March 21, 2024

LYRA THERAPEUTICS, INC. 2020 INCENTIVE AWARD PLAN PERFORMANCE based RESTRICTED STOCK Unit Grant Notice Capitalized terms not specifically defined in this Performance Based Restricted Stock Unit Grant Notice (the “Grant Notice”) have the meanings given to them in the 2020 Incentive Award Plan (as amended from time to time, the “Plan”) of Lyra Therapeutics, Inc. (the “Company”). The Company has gran

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A (Rule 14a-101) INFORMATION REQUIRED IN PROXY STATEMENT SCHEDULE 14A INFORMATION Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Ame

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A (Rule 14a-101) INFORMATION REQUIRED IN PROXY STATEMENT SCHEDULE 14A INFORMATION Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No. ) Filed by the Registrant ☒ Filed by a party other than the Registrant ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confide

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A (Rule 14a-101) INFORMATION REQUIRED IN PROXY STATEMENT SCHEDULE 14A INFORMATION Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Ame

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A (Rule 14a-101) INFORMATION REQUIRED IN PROXY STATEMENT SCHEDULE 14A INFORMATION Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No. ) Filed by the Registrant ☒ Filed by a party other than the Registrant ☐ Check the appropriate box: ☐ Preliminary Proxy S

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A (Rule 14a-101) INFORMATION REQUIRED IN PROXY STATEMENT SCHEDULE 14A INFORMATION Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Ame

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A (Rule 14a-101) INFORMATION REQUIRED IN PROXY STATEMENT SCHEDULE 14A INFORMATION Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No. ) Filed by the Registrant ☒ Filed by a party other than the Registrant ☐ Check the appropriate box: ☒ Preliminary Proxy S

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): April 15, 2024 Lyra Therapeutics,

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): April 15, 2024 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commission

LYRA THERAPEUTICS, INC. 480 Arsenal Way Watertown, Massachusetts 02472

LYRA THERAPEUTICS, INC. 480 Arsenal Way Watertown, Massachusetts 02472 March 28, 2024 VIA EDGAR TRANSMISSION Securities and Exchange Commission Division of Corporation Finance 100 F Street, N.E. Washington, D.C. 20549 Attention: Benjamin Richie Re: LYRA THERAPEUTICS, INC. Registration Statement on Form S-3 (Registration No. 333-278163) To the addressee set forth above: In accordance with Rule 461

Amended and Restated Controlled Equity OfferingSM Sales Agreement, dated March 22, 2024, between Lyra Therapeutics, Inc. and Cantor Fitzgerald & Co.

Exhibit 1.2 LYRA THERAPEUTICS, INC. Shares of Common Stock (par value $0.001 per share) Amended and Restated Controlled Equity OfferingSM Sales Agreement March 22, 2024 Cantor Fitzgerald & Co. 110 East 59th Street New York, NY 10022 Ladies and Gentlemen: Lyra Therapeutics, Inc., a Delaware corporation (the “Company”), and Cantor Fitzgerald & Co. (the “Agent”), are parties to that certain Sales Agr

As filed with the Securities and Exchange Commission on March 22, 2024

S-3 Table of Contents As filed with the Securities and Exchange Commission on March 22, 2024 Registration No.

Description of Securities

Exhibit 4.8 DESCRIPTION OF THE REGISTRANT’S SECURITIES REGISTERED PURSUANT TO SECTION 12 OF THE SECURITIES EXCHANGE ACT OF 1934, AS AMENDED Lyra Therapeutics, Inc. has one class of securities registered under Section 12 of the Securities Exchange Act of 1934, as amended (the “Exchange Act”). References herein to “we,” “us,” “our” and the “Company” refer to Lyra Therapeutics, Inc. and not to any of

Sublease dated as of December 21, 2023, by and between RVAC Medicines (US), Inc. and Lyra Therapeutics, Inc.

SUBLEASE THIS SUBLEASE (this “Sublease”) is dated for reference purposes as of December 21, 2023 and is made by and between RVAC MEDICINES (US), INC.

As filed with the Securities and Exchange Commission on March 22, 2024

As filed with the Securities and Exchange Commission on March 22, 2024 Registration No.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K (Mark One) ☒ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2023 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 001-39273 c Lyra Therapeu

Form of Indenture.

Exhibit 4.3 LYRA THERAPEUTICS, INC. INDENTURE Dated as of , 20 [] Trustee TABLE OF CONTENTS Page ARTICLE I. DEFINITIONS AND INCORPORATION BY REFERENCE 1 Section 1.1. Definitions 1 Section 1.2. Other Definitions 4 Section 1.3. Incorporation by Reference of Trust Indenture Act 4 Section 1.4. Rules of Construction 5 ARTICLE II. THE SECURITIES 6 Section 2.1. Issuable in Series 6 Section 2.2. Establish

Policy for Recovery of Erroneously Awarded Compensation

LYRA THERAPEUTICS, INC. POLICY FOR RECOVERY OF ERRONEOUSLY AWARDED COMPENSATION Lyra Therapeutics, Inc. (the “Company”) has adopted this Policy for Recovery of Erroneously Awarded Compensation (the “Policy”), effective as of October 2, 2023 (the “Effective Date”). Capitalized terms used in this Policy but not otherwise defined herein are defined in Section 11. 1. Persons Subject to Policy This Pol

Filing Fee Table.

Exhibit 107 CALCULATION OF FILING FEE TABLE Registration Statement on Form S-3 (Form Type) Lyra Therapeutics, Inc.

Filing Fee Table.

Exhibit 107.1 CALCULATION OF FILING FEE TABLE FORM S-8 (Form Type) LYRA THERAPEUTICS, INC. (Exact Name of Registrant as Specified in its Charter) Table 1: Newly Registered Securities Plan Security Type Security Class Title Fee Calculation Rule Amount Registered (1) Proposed Maximum Offering Price Per Unit Maximum Aggregate Offering Price Fee Rate Amount of Registration Fee 2022 Employment Induceme

Lyra Therapeutics Reports Fourth Quarter and Full Year 2023 Financial Results and Provides Corporate Update -- Data from ENLIGHTEN I Pivotal Phase 3 Trial of LYR-210 in Chronic Rhinosinusitis (CRS) Anticipated Q2 2024 --

Lyra Therapeutics Reports Fourth Quarter and Full Year 2023 Financial Results and Provides Corporate Update - Data from ENLIGHTEN I Pivotal Phase 3 Trial of LYR-210 in Chronic Rhinosinusitis (CRS) Anticipated Q2 2024 - WATERTOWN, Mass.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): March 21, 2024 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commission

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): February 26, 2024 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commissi

LYRA / Lyra Therapeutics, Inc. / PERCEPTIVE ADVISORS LLC - SC 13D/A Activist Investment

SC 13D/A SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13D/A Under the Securities Exchange Act of 1934 (Amendment No. 3)* Lyra Therapeutics, Inc. (Name of Issuer) Common Stock, $0.001 par value (Title of Class of Securities) 55234L 105 (CUSIP Number) Alexander Rakitin Perceptive Advisors LLC 51 Astor Place, 10th Floor New York, NY 10003 (646) 205-5340 (Name, Address and Teleph

LYRA / Lyra Therapeutics, Inc. / Nantahala Capital Management, LLC - SC 13G/A Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 1)* Lyra Therapeutics, Inc. (Name of Issuer) Common Stock, $0.001 par value per share (Title of Class of Securities) 55234L105 (CUSIP Number) December 31, 2023 (Date of Event which Requires Filing of this Statement) Check the appropriate box to designate the

LYRA / Lyra Therapeutics, Inc. / Point72 Asset Management, L.P. - LYRA THERAPEUTICS, INC. Passive Investment

SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G/A Under the Securities Exchange Act of 1934 (Amendment No. 1)* Lyra Therapeutics, Inc. (Name of Issuer) Common Stock, par value $0.001 per share (Title of Class of Securities) 55234L105 (CUSIP Number) December 31, 2023 (Date of Event Which Requires Filing of this Statement) Check the appropriate box to designate the rule pursua

JOINT FILING AGREEMENT PURSUANT TO RULE 13d-1(k)

EX-99 2 p24-0669exhitbit99.htm JOINT FILING AGREEMENT EXHIBIT 99.1 JOINT FILING AGREEMENT PURSUANT TO RULE 13d-1(k) The undersigned acknowledge and agree that the foregoing statement on Schedule 13G is filed on behalf of each of the undersigned and that all subsequent amendments to this statement on Schedule 13G shall be filed on behalf of each of the undersigned without the necessity of filing ad

LYRA / Lyra Therapeutics, Inc. / Venrock Healthcare Capital Partners II, L.P. - SC 13G/A Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 13G/A UNDER THE SECURITIES EXCHANGE ACT OF 1934 (Amendment No. 2)* Lyra Therapeutics, Inc. (Name of Issuer) Common Stock, $0.001 par value (Title of Class of Securities) 55234L105 (CUSIP Number) December 31, 2023 (Date of Event Which Requires Filing of This Statement) Check the appropriate box to designate the rule pu

LYRA / Lyra Therapeutics, Inc. / CITADEL ADVISORS LLC - SC 13G/A Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G* (Rule 13d-102) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO § 240.13d-1(b), (c), AND (d) AND AMENDMENTS THERETO FILED PURSUANT TO § 240.13d-2 (Amendment No. 1)* Lyra Therapeutics, Inc. (Name of Issuer) Common Stock, $0.001 par value per share (the “Shares”) (Title of Class of Securities) 55234L105 (

LYRA / Lyra Therapeutics, Inc. / Vestal Point Capital, LP - LYRA THERAPEUTICS, INC. Passive Investment

SC 13G 1 p24-0812sc13g.htm LYRA THERAPEUTICS, INC. SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. )* Lyra Therapeutics, Inc. (Name of Issuer) Common stock, par value $0.001 per share (Title of Class of Securities) 55234L105 (CUSIP Number) December 31, 2023 (Date of event which requires filing of this statement) Check

JOINT ACQUISITION STATEMENT PURSUANT TO RULE 13d-1(k)

EX-99.1 2 exhibit99.htm JOINT ACQUISITION STATEMENT EXHIBIT 99.1 JOINT ACQUISITION STATEMENT PURSUANT TO RULE 13d-1(k) The undersigned acknowledge and agree that the foregoing statement on Schedule 13G is filed on behalf of each of the undersigned and that all subsequent amendments to this statement on Schedule 13G shall be filed on behalf of each of the undersigned without the necessity of filing

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): January 08, 2024 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commissio

Forward Looking Statement This presentation contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. The words “believe,” “may,” “will,” “estimate,” “continue,” “anticipate,” “intend,” “expect,”

Corporate Presentation January 2024 Exhibit 99.1 Forward Looking Statement This presentation contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. The words “believe,” “may,” “will,” “estimate,” “continue,” “anticipate,” “intend,” “expect,” and similar expressions are intended to identify forward-looking statements. All statements contained

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): December 21, 2023 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commissi

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): December 14, 2023 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commissi

Amended and Restated Bylaws of the Registrant

AMENDED AND RESTATED BYLAWS OF LYRA THERAPEUTICS, INC. (a Delaware corporation) TABLE OF CONTENTS Page Article I - CORPORATE OFFICES 1 1.1 REGISTERED OFFICE 1 1.2 OTHER OFFICES 1 Article II ARTICLE II - MEETINGS OF STOCKHOLDERS 1 2.1 PLACE OF MEETINGS 1 2.2 ANNUAL MEETING 1 2.3 SPECIAL MEETING 1 2.4 ADVANCE NOTICE PROCEDURES FOR BUSINESS BROUGHT BEFORE A MEETING 2 2.5 ADVANCE NOTICE PROCEDURES FOR

JOINT FILING AGREEMENT PURSUANT TO RULE 13d-1(k)

EX-99 2 p23-2843exhibit99.htm JOINT FILING AGREEMENT EXHIBIT 99.1 JOINT FILING AGREEMENT PURSUANT TO RULE 13d-1(k) The undersigned acknowledge and agree that the foregoing statement on Schedule 13G is filed on behalf of each of the undersigned and that all subsequent amendments to this statement on Schedule 13G shall be filed on behalf of each of the undersigned without the necessity of filing add

LYRA / Lyra Therapeutics Inc / Point72 Asset Management, L.P. - LYRA THERAPEUTICS, INC. Passive Investment

SC 13G 1 p23-2843sc13g.htm LYRA THERAPEUTICS, INC. SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. )* Lyra Therapeutics, Inc. (Name of Issuer) Common Stock, par value $0.001 per share (Title of Class of Securities) 55234L105 (CUSIP Number) November 15, 2023 (Date of Event Which Requires Filing of this Statement) Check

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended September 30, 2023 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: 001-39273 Lyra Therapeutics, Inc.

Amendment No. 1 to Lyra Therapeutics, Inc. 2022 Employment Inducement Award Plan, as Amended and Restated Effective December 12, 2022

Exhibit 10.1 AMENDMENT NO. 1 TO LYRA THERAPEUTICS, INC. 2022 EMPLOYMENT INDUCEMENT AWARD PLAN, AS AMENDED AND RESTATED EFFECTIVE DECEMBER 12, 2022 THIS AMENDMENT NO. 1 TO THE LYRA THERAPEUTICS, INC. 2022 EMPLOYMENT INDUCEMENT AWARD PLAN, AS AMENDED AND RESTATED EFFECTIVE DECEMBER 12, 2022 (this “Amendment”) is made and adopted by Lyra Therapeutics, Inc., a Delaware corporation (the “Company”). Cap

Lyra Therapeutics Reports Third Quarter 2023 Financial Results and Provides Corporate Update – Additional Phase 2 BEACON trial CT scan data demonstrated statistically significant improvement in sinus opacification with LYR-220 and provided radiologic

Lyra Therapeutics Reports Third Quarter 2023 Financial Results and Provides Corporate Update – Additional Phase 2 BEACON trial CT scan data demonstrated statistically significant improvement in sinus opacification with LYR-220 and provided radiological evidence of improvement in chronic rhinosinusitis (CRS) patients who have had prior ethmoid sinus surgery – – Emerging data further support the previously reported positive BEACON topline results demonstrating CRS symptom improvement – – ENLIGHTEN I pivotal Phase 3 trial of LYR-210 in CRS patients who have not had ethmoid sinus surgery is fully enrolled; topline results expected in 1H 2024 – WATERTOWN, Mass.

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 07, 2023 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commissi

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): September 12, 2023 Lyra Therapeut

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): September 12, 2023 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commiss

Disclaimer This presentation contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. All statements contained in this presentation that do not relate to matters of historical fact should be cons

EX-99.1 BEACON Study Topline Results LYR-220-2021-001 A Phase II, Patient-blinded, Two-part, Randomized, Parallel-group Trial to Evaluate the Safety, Tolerability, Pharmacokinetics, and Efficacy of LYR-220 in Chronic Rhinosinusitis (CRS) Patients Who Have Had a Prior Ethmoidectomy https://clinicaltrials.gov/study/NCT05035654 September 12, 2023 Exhibit 99.1 Disclaimer This presentation contains for

Up to $50,000,000 Common Stock

424B5 Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No. 333-256020 PROSPECTUS SUPPLEMENT (to Prospectus dated May 20, 2021) Up to $50,000,000 Common Stock We have entered into a Controlled Equity OfferingSM Sales Agreement, or the Sales Agreement, with Cantor Fitzgerald & Co., or Cantor, dated September 1, 2023, relating to the sale of shares of our common stock offered by this p

Entry into a Material Definitive Agreement, Financial Statements and Exhibits

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): September 1, 2023 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commissi

Controlled Equity OfferingSM Sales Agreement, dated September 1, 2023, between Lyra Therapeutics, Inc. and Cantor Fitzgerald & Co.

Exhibit 1.1 LYRA THERAPEUTICS, INC. Shares of Common Stock (par value $0.001 per share) Controlled Equity OfferingSM Sales Agreement September 1, 2023 Cantor Fitzgerald & Co. 499 Park Avenue New York, NY 10022 Ladies and Gentlemen: Lyra Therapeutics, Inc., a Delaware corporation (the “Company”), confirms its agreement (this “Agreement”) with Cantor Fitzgerald & Co. (the “Agent”), as follows: 1. Is

LYRA / Lyra Therapeutics Inc / Samsara BioCapital, L.P. - SC 13G Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. )* Lyra Therapeutics, Inc. (Name of Issuer) Common Stock, par value $0.001 (Title of Class of Securities) 55234L105 (CUSIP Number) April 12, 2022 (Date of Event Which Requires Filing of this Statement) Check the appropriate box to designate the rule pursuant

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): August 08, 2023 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commission

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2023 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: 001-39273 Lyra Therapeutics, Inc.

Lyra Therapeutics Reports Second Quarter 2023 Financial Results and Provides Corporate Update -- ENLIGHTEN I Pivotal Phase 3 Trial of LYR-210 in Pre-Surgical Chronic Rhinosinusitis (CRS) on Track to Complete Enrollment in the Coming Weeks, with Data

Lyra Therapeutics Reports Second Quarter 2023 Financial Results and Provides Corporate Update - ENLIGHTEN I Pivotal Phase 3 Trial of LYR-210 in Pre-Surgical Chronic Rhinosinusitis (CRS) on Track to Complete Enrollment in the Coming Weeks, with Data Expected in 1H 2024 - - Initial Topline Results from BEACON Phase 2 Trial of LYR-220 in Post-Surgical CRS Now Anticipated Earlier Than Expected, in September 2023 - WATERTOWN, Mass.

Seventh Amendment to Lease, dated July 12, 2023, by and between Lyra Therapeutics, Inc. and ARE-480 Arsenal Street, LLC

DocuSign Envelope ID: EB0D6AB9-C161-41D6-8BF2-6B0C1890AE0D SEVENTH AMENDMENT TO LEASE This Seventh Amendment to Lease (the “Seventh Amendment”) is made as of July 12, 2023, by and between ARE-480 ARSENAL STREET, LLC, a Delaware limited liability company (“Landlord”), and LYRA THERAPEUTICS, INC.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): July 12, 2023 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commission F

LYRA THERAPEUTICS, INC. 21,967,353 Shares Common Stock Offered by the Selling Securityholders

424B3 Table of Contents As filed Pursuant to Rule 424(b)(3) Registration No. 333-272981 PROSPECTUS LYRA THERAPEUTICS, INC. 21,967,353 Shares Common Stock Offered by the Selling Securityholders The selling securityholders may offer and sell up to 21,967,353 shares in the aggregate of common stock identified above, of which 12,236,714 shares are presently issued and outstanding and 9,730,639 shares

Lyra Therapeutics, Inc. 480 Arsenal Way Watertown, MA 02472

Lyra Therapeutics, Inc. 480 Arsenal Way Watertown, MA 02472 July 6, 2023 Via EDGAR Securities and Exchange Commission Division of Corporation Finance Office of Finance 100 F Street, N.E. Washington, D.C. 20549 Attention: Ben Richie Re: Lyra Therapeutics, Inc. Registration Statement on Form S-3 Filed June 28, 2023 File No. 333-272981 To whom it may concern: Pursuant to Rule 461(a) under the Securit

As filed with the Securities and Exchange Commission on June 28, 2023

Table of Contents As filed with the Securities and Exchange Commission on June 28, 2023 File No.

Filing Fee Table.

EX-FILING FEES Exhibit 107 Calculation of Filing Fee Table Registration Statement on Form S-3 (Form Type) LYRA THERAPEUTICS, INC.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): June 13, 2023 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commission F

JOINT FILING AGREEMENT

EXHIBIT 99.1 JOINT FILING AGREEMENT The undersigned hereby agree that the Statement on Schedule 13G filed herewith (and any amendments thereto), relating to the Shares of Lyra Therapeutics, Inc., a Delaware corporation, is being filed jointly with the Securities and Exchange Commission pursuant to Rule 13d-1(c) under the Securities Exchange Act of 1934, as amended, on behalf of each of the undersi

LYRA / Lyra Therapeutics Inc / CITADEL ADVISORS LLC - SC 13G Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G* (Rule 13d-102) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO § 240.13d-1(b), (c), AND (d) AND AMENDMENTS THERETO FILED PURSUANT TO § 240.13d-2 (Amendment No. )* Lyra Therapeutics, Inc. (Name of Issuer) Common Stock, par value $0.001 per share (the “Shares”) (Title of Class of Securities) 55234L105 (C

LYRA / Lyra Therapeutics Inc / NBVM GP, LLC - SC 13D/A Activist Investment

SC 13D/A SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13D Under the Securities Exchange Act of 1934 (Amendment No. 2) LYRA THERAPEUTICS, INC. (Name of Issuer) Common Stock, $0.001 par value per share (Title of Class of Securities) 55234L105 (CUSIP Number) Edward T. Anderson Managing Member North Bridge Venture Partners 150 A Street, Suite 102 Needham, MA 02494 (781) 290-0004

LYRA / Lyra Therapeutics Inc / PERCEPTIVE ADVISORS LLC - SC 13D/A Activist Investment

SC 13D/A Table of Contents SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13D/A Under the Securities Exchange Act of 1934 (Amendment No. 2)* Lyra Therapeutics, Inc. (Name of Issuer) Common Stock, $0.001 par value (Title of Class of Securities) 55234L 105 (CUSIP Number) Alexander Rakitin Perceptive Advisors LLC 51 Astor Place, 10th Floor New York, NY 10003 (646) 205-5340 (Name,

Form of Purchase Warrant, together with a schedule of Purchase Warrants, each dated as of May 31, 2023, issued by Lyra Therapeutics, Inc. to the investors set forth on such schedule

EX-4.3 Exhibit 4.3 LYRA THERAPEUTICS, INC. Schedule of Holders of Warrants to Purchase Common Stock Holder Warrant No. Number of Shares Maximum Percentage Beneficial Ownership Blocker Armistice Capital Master Fund Ltd., or its registered assigns CS-01 2,006,018 4.99 % Perceptive Life Sciences Master Fund, Ltd., or its registered assigns CS-02 1,805,416 9.99 % Citadel CEMF Investments Ltd., or its

Securities Purchase Agreement, dated as of May 25, 2023, by and among Lyra Therapeutics, Inc. and the Investors named therein

EX-10.1 Exhibit 10.1 Execution Version SECURITIES PURCHASE AGREEMENT This SECURITIES PURCHASE AGREEMENT (this “Agreement”) is made and entered into as of May 25, 2023 by and among Lyra Therapeutics, Inc., a Delaware corporation (the “Company”), and the Investors identified on Exhibit A attached hereto (each an “Investor” and collectively the “Investors”). RECITALS A. The Company and each Investor

Lyra Therapeutics Announces $50.0 Million Private Placement

EX-99.1 Exhibit 99.1 Lyra Therapeutics Announces $50.0 Million Private Placement May 26, 2023 WATERTOWN, Mass., May 26, 2023 (GLOBE NEWSWIRE) — Lyra Therapeutics, Inc. (Nasdaq: LYRA) (“Lyra” or the “Company”), a clinical-stage biotechnology company developing innovative therapies for the localized treatment of chronic rhinosinusitis, today announced that it has entered into a securities purchase a

Registration Rights Agreement, dated as of May 25, 2023, by and among Lyra Therapeutics, Inc. and the Investors named therein

EX-10.2 Exhibit 10.2 Execution Version REGISTRATION RIGHTS AGREEMENT This REGISTRATION RIGHTS AGREEMENT (this “Agreement”) is made and entered into as of May 25, 2023 by and among Lyra Therapeutics, Inc., a Delaware corporation (the “Company”), and the “Investors” named in the Securities Purchase Agreement, dated as of the date hereof, by and among the Company and the Investors identified on Exhib

Amendment No. 1 to Ninth Amended and Restated Investor Rights Agreement, dated as of May 25, 2023, by and among Lyra Therapeutics, Inc. and the Investors named therein

EX-4.1 Exhibit 4.1 Execution Version LYRA THERAPEUTICS, INC. AMENDMENT NO. 1 TO NINTH AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT This Amendment No. 1 to Ninth Amended and Restated Investor Rights Agreement, dated as of May 25, 2023 (this “Amendment”) is entered into by and among Lyra Therapeutics, Inc., a Delaware corporation (the “Company”), and the undersigned Investors party to the Ninth Am

Form of Pre-Funded Warrant, together with a schedule of Pre-Funded Warrants, each dated as of May 31, 2023, issued by Lyra Therapeutics, Inc. to the Investors set forth on such schedule

EX-4.2 Exhibit 4.2 LYRA THERAPEUTICS, INC. Schedule of Holders of Pre-Funded Warrants to Purchase Common Stock Holder Warrant No. Number of Shares Venrock Healthcare Capital Partners EG, L.P., or its registered assigns PFCS-6 1,711,738 Venrock Healthcare Capital Partners III, L.P., or its registered assigns PFCS-7 633,114 VHCP Co-Investment Holdings III, LLC, or its registered assigns PFCS-8 63,33

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 25, 2023 LYRA THERAPEUTICS, I

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 25, 2023 LYRA THERAPEUTICS, INC. (Exact name of Registrant as Specified in its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commission Fi

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): May 12, 2023 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commission Fi

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended March 31, 2023 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: 001-39273 Lyra Therapeutics, Inc.

Lyra Therapeutics Reports First Quarter 2023 Financial Results and Provides Corporate Update -- ENLIGHTEN I Pivotal Phase 3 Trial of LYR-210 in Pre-Surgical Chronic Rhinosinusitis (CRS) on Track to Complete Enrollment, with Data Expected in 1H 2024 -

Exhibit 99.1 Lyra Therapeutics Reports First Quarter 2023 Financial Results and Provides Corporate Update - ENLIGHTEN I Pivotal Phase 3 Trial of LYR-210 in Pre-Surgical Chronic Rhinosinusitis (CRS) on Track to Complete Enrollment, with Data Expected in 1H 2024 - - Data from BEACON Phase 2 Trial of LYR-220 in Post-Surgical CRS Anticipated Q4 2023 - WATERTOWN, Mass., May 12, 2023 - Lyra Therapeutics

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A (Rule 14a-101) INFORMATION REQUIRED IN PROXY STATEMENT SCHEDULE 14A INFORMATION Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Ame

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A (Rule 14a-101) INFORMATION REQUIRED IN PROXY STATEMENT SCHEDULE 14A INFORMATION Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No. ) Filed by the Registrant ☒ Filed by a party other than the Registrant ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confide

Definitive Proxy Statement

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A (Rule 14a-101) INFORMATION REQUIRED IN PROXY STATEMENT SCHEDULE 14A INFORMATION Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No. ) Filed by the Registrant ☒ Filed by a party other than the Registrant ☐ Check the appropriate box: ☐Preliminary Proxy Statement ☐Confident

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): March 29, 2023 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commission

Form 10-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K o (Mark One) ☒ ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2022 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 001-39273 c Lyra Therap

Second Amendment to Lease Agreement (Notice and Acknowledgement thereof), dated March 3, 2023, between Registrant, as the tenant, and BXP Waltham woods LLC, as the landlord

bxP Boston Properties Prudential Center 800 Boylston Street Boston, MA 02199-8103 www.

Employment Agreement between the Registrant and John Bishop dated as of February 2, 2023

Exhibit 10.15 Employment Agreement This Employment Agreement (this “Agreement”), dated as of February 2, 2023, is made by and between Lyra Therapeutics, Inc., a Delaware corporation (together with any successor thereto, the “Company”), and John Bishop (“Executive”) (collectively referred to herein as the “Parties” or individually referred to as a “Party”). RECITALS A. It is the desire of the Compa

Power of Attorney (included on signature page below).

S-8 As filed with the Securities and Exchange Commission on March 29, 2023 Registration No.

Investor Presentation March 2023

Investor Presentation March 2023 Disclaimer This presentation contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995.

Filing Fee Table.

Exhibit 107.1 CALCULATION OF FILING FEE TABLE FORM S-8 (Form Type) LYRA THERAPEUTICS, INC. (Exact Name of Registrant as Specified in its Charter) Table 1: Newly Registered Securities Plan Security Type Security Class Title Fee Calculation Rule Amount Registered (1) Proposed Maximum Offering Price Per Unit Maximum Aggregate Offering Price Fee Rate Amount of Registration Fee 2022 Employment Induceme

Lyra Therapeutics, Inc. 2022 Employment Inducement Award Plan as Amended and Restated, Effective December 9, 2022

Exhibit 10.4.6 LYRA THERAPEUTICS, INC. 2022 EMPLOYMENT INDUCEMENT AWARD PLAN AS AMENDED AND RESTATED EFFECTIVE DECEMBER 12, 2022 ARTICLE I. Purpose The Plan’s purpose is to enhance the Company’s ability to attract, retain and motivate persons who are expected to make important contributions to the Company by providing these individuals with equity ownership opportunities. Capitalized terms used in

Lyra Therapeutics Reports Fourth Quarter and Full Year 2022 Financial Results and Provides Corporate Update -- ENLIGHTEN I Pivotal Phase 3 Trial of LYR-210 in Pre-Surgical Chronic Rhinosinusitis (CRS) on Track to Complete Enrollment in mid-2023 -- --

Exhibit 99.1 Lyra Therapeutics Reports Fourth Quarter and Full Year 2022 Financial Results and Provides Corporate Update - ENLIGHTEN I Pivotal Phase 3 Trial of LYR-210 in Pre-Surgical Chronic Rhinosinusitis (CRS) on Track to Complete Enrollment in mid-2023 - - Data from BEACON Phase 2 Trial of LYR-220 in Post-Surgical CRS Anticipated Q4 2023 - - Advancing In-House Manufacturing Capabilities to Pre

Exhibit 4.5

Exhibit 4.5 DESCRIPTION OF THE REGISTRANT’S SECURITIES REGISTERED PURSUANT TO SECTION 12 OF THE SECURITIES EXCHANGE ACT OF 1934, AS AMENDED Lyra Therapeutics, Inc. has one class of securities registered under Section 12 of the Securities Exchange Act of 1934, as amended (the “Exchange Act”). References herein to “we,” “us,” “our” and the “Company” refer to Lyra Therapeutics, Inc. and not to any of

LYRA / Lyra Therapeutics Inc / Venrock Healthcare Capital Partners II, L.P. - SC 13G/A Passive Investment

SC 13G/A 1 tm236635d1sc13ga.htm SC 13G/A UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 13G/A UNDER THE SECURITIES EXCHANGE ACT OF 1934 (Amendment No. 1)* Lyra Therapeutics, Inc. (Name of Issuer) Common Stock, $0.001 par value (Title of Class of Securities) 55234L105 (CUSIP Number) December 31, 2022 (Date of Event Which Requires Filing of This Statement) Check the

LYRA / Lyra Therapeutics Inc / Nantahala Capital Management, LLC - SC 13G Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. )* Lyra Therapeutics, Inc. (Name of Issuer) Common Stock, $0.001 par value per share (Title of Class of Securities) 55234L105 (CUSIP Number) December 31, 2022 (Date of Event which Requires Filing of this Statement) Check the appropriate box to designate the

LYRA / Lyra Therapeutics Inc / INTERSOUTH PARTNERS VII L P - SC 13G/A Passive Investment

SC 13G/A 1 d466318dsc13ga.htm SC 13G/A UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 1)* Lyra Therapeutics, Inc. (Name of Issuer) Common Stock, $0.001 par value per share (Title of Class of Securities) 55234L105 (CUSIP Number) December 31, 2022 (Date of Event Which Requires Filing of this Statement) Che

LYRA / Lyra Therapeutics Inc / Polaris Venture Partners V, L.P. - SC 13G/A Passive Investment

SC 13G/A SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 Schedule 13G (Rule 13d-102) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULES 13d-1 (b), (c) AND (d) AND AMENDMENTS THERETO FILED PURSUANT TO 13d-2 (b) (Amendment No. 1) Lyra Therapeutics, Inc. (Name of Issuer) Common Stock, par value $0.001 per share (Title of Class of Securities) 55234L105 (CUSIP Number) December 3

Sixth Amendment to Lease, dated November 14, 2022, by and between Lyra Therapeutics, Inc. and ARE-480 Arsenal Street, LLC

SIXTH AMENDMENT TO LEASE This Sixth Amendment to Lease (the “Sixth Amendment”) is made as of November 14, 2022, by and between ARE-480 ARSENAL STREET, LLC, a Delaware limited liability company (“Landlord”), and LYRA THERAPEUTICS, INC.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 14, 2022 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commissi

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): November 08, 2022 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commissi

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ? QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended September 30, 2022 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: 001-39273 Lyra Therapeutics, Inc.

Lyra Therapeutics Reports Third Quarter 2022 Financial Results and Provides Corporate Update -- Company Prioritizing ENLIGHTEN I Pivotal Phase 3 Trial of LYR-210 in Chronic Rhinosinusitis (CRS); Study Remains on Track, with Full Enrollment Anticipate

Exhibit 99.1 Lyra Therapeutics Reports Third Quarter 2022 Financial Results and Provides Corporate Update - Company Prioritizing ENLIGHTEN I Pivotal Phase 3 Trial of LYR-210 in Chronic Rhinosinusitis (CRS); Study Remains on Track, with Full Enrollment Anticipated mid-2023 - - Company to Manufacture All Clinical Trial Supply to Leverage its In-House Expertise and Capabilities; Temporarily Pausing E

First Amendment to License and Collaboration Agreement, dated September 26, 2022, between Registrant and LianBio Inflammatory Limited and LianBio

Exhibit 10.1 EXECUTION VERSION CERTAIN CONFIDENTIAL INFORMATION CONTAINED IN THIS DOCUMENT, MARKED BY [***], HAS BEEN OMITTED BECAUSE IT IS NOT MATERIAL AND IS THE TYPE THAT THE REGISTRANT TREATS AS PRIVATE OR CONFIDENTIAL FIRST AMENDMENT TO THE LICENSE AND COLLABORATION AGREEMENT This FIRST AMENDMENT TO THE LICENSE AND COLLABORATION AGREEMENT (this ?Amendment?), entered into as of September 26, 2

Amendment No. 3 to Lyra Therapeutics, Inc. 2022 Inducement Award Plan

Exhibit 10.2 AMENDMENT NO. 3 TO LYRA THERAPEUTICS, INC. 2022 EMPLOYMENT INDUCEMENT AWARD PLAN THIS AMENDMENT NO. 3 TO THE LYRA THERAPEUTICS, INC. 2022 EMPLOYMENT INDUCEMENT AWARD PLAN (this ?Amendment?) is made and adopted by Lyra Therapeutics, Inc., a Delaware corporation (the ?Company?). Capitalized terms used but not otherwise defined herein shall have the meanings ascribed to them in the Plan

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q/A (Amendment No. 1)

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q/A (Amendment No.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q/A (Amendment No. 1)

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q/A (Amendment No.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of Report (Date of earliest event reported): October 26, 2022 Lyra Therapeutics, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-39273 84-1700838 (State or Other Jurisdiction of Incorporation) (Commissio

Long-acting corticosteroid matrices improve CRS cardinal symptoms Brent A. Senior, MD1*, Anders Cervin, MD, PhD2, Joanne Rimmer, MD3, Agnieszka Wrobel, MD, PhD4, Lindsay Brayton, BA5, James Shao, MS5, Vineeta Belanger, PhD5, Robert C. Kern, MD6 1Depa

Long-acting corticosteroid matrices improve CRS cardinal symptoms Brent A. Senior, MD1*, Anders Cervin, MD, PhD2, Joanne Rimmer, MD3, Agnieszka Wrobel, MD, PhD4, Lindsay Brayton, BA5, James Shao, MS5, Vineeta Belanger, PhD5, Robert C. Kern, MD6 1Department of Otolaryngology - Head & Neck Surgery, University of North Carolina, Chapel Hill, NC, USA; 2University of Queensland Centre for Clinical Rese

Financial Statements and Exhibits, Other Events

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of report (Date of earliest event reported): September 10, 2022 LYRA THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 001-39273 84-1700838 (State or other jurisdiction of incorporation) (Commiss

Amendment No. 1 to Lyra Therapeutics, Inc. 2022 Inducement Award Plan

Exhibit 10.1 AMENDMENT NO. 1 TO LYRA THERAPEUTICS, INC. 2022 EMPLOYMENT INDUCEMENT AWARD PLAN THIS AMENDMENT NO. 1 TO THE LYRA THERAPEUTICS, INC. 2022 EMPLOYMENT INDUCEMENT AWARD PLAN (this ?Amendment?) is made and adopted by Lyra Therapeutics, Inc., a Delaware corporation (the ?Company?). Capitalized terms used but not otherwise defined herein shall have the meanings ascribed to them in the Plan

Amendment No. 2 to Lyra Therapeutics, Inc. 2022 Inducement Award Plan

Exhibit 10.2 AMENDMENT NO. 2 TO LYRA THERAPEUTICS, INC. 2022 EMPLOYMENT INDUCEMENT AWARD PLAN THIS AMENDMENT NO. 2 TO THE LYRA THERAPEUTICS, INC. 2022 EMPLOYMENT INDUCEMENT AWARD PLAN (this ?Amendment?) is made and adopted by Lyra Therapeutics, Inc., a Delaware corporation (the ?Company?). Capitalized terms used but not otherwise defined herein shall have the meanings ascribed to them in the Plan

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ? QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2022 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: 001-39273 Lyra Therapeutics, Inc.

Lease Agreement, dated May 31, 2022, between the Registrant, as the tenant, and BXP Waltham Woods LLC, as the landlord

Exhibit 4.2 WALTHAM WOODS CORPORATE CENTER 880 WINTER STREET WALTHAM, MASSACHUSETTS Lease Dated May 31, 2022 (the ?Execution Date?) THIS INSTRUMENT IS AN INDENTURE OF LEASE in which the Landlord and the Tenant are the parties hereinafter named, and which relates to space in a certain building (the ?Building?) known as, and with an address at, 880 Winter Street, Waltham, Massachusetts 02451. The pa

Lyra Therapeutics Reports Second Quarter 2022 Financial Results and Provides Corporate Update

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First Amendment to Lease Agreement, dated July 20, 2022, between Registrant, as the tenant, and BXP Waltham Woods LLC, as the landlord

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Employment Agreement by and between the Registrant and Richard Nieman, M.D. dated as of June 30, 2022

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As filed with the Securities and Exchange Commission on May 11, 2022

Table of Contents As filed with the Securities and Exchange Commission on May 11, 2022 Registration No.

Filing Fee Table.

Exhibit 107 Calculation of Filing Fee Table Registration Statement on Form S-3 (Form Type) LYRA THERAPEUTICS, INC.

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Schedule 14A

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SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13D Under the Securities Exchange Act of 1934 (Amendment No. 1) LYRA THERAPEUTICS, INC. (Name of Issuer) Common Stock, $0.001 par value per share (Title of Class of Securities) 55234L105 (CUSIP Number) Edward T. Anderson Managing Member North Bridge Venture Partners 60 William St. #350 Wellesley, MA 02481 (781) 290-0004 (Name, Addr

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Form of Common Stock Purchase Warrant, together with a schedule of Warrants, each dated April 12, 2022, issued by Lyra Therapeutics, Inc. to the Investors set forth on such schedule

Exhibit 4.2 LYRA THERAPEUTICS, INC. Schedule of Holders of Warrants to Purchase Common Stock Holder Warrant No. Number of Shares Venrock Healthcare Capital Partners EG, L.P. PFCS-1 1,956,500 Venrock Healthcare Capital Partners III, L.P. PFCS-2 1,739,000 VHCP Co-Investment Holdings III, LLC PFCS-3 174,000 Venrock Healthcare Capital Partners II, L.P. PFCS-4 804,500 VHCP Co-Investment Holdings II, LL

Securities Purchase Agreement, dated as of April 7, 2022, by and among Lyra Therapeutics, Inc. and the Investors named therein

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Registration Rights Agreement, dated as of April 7, 2022, by and among Lyra Therapeutics, Inc. and the Investors named therein

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Filing Fee Table.

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Employment Agreement between the Registrant and Robert Richard dated as of June 20, 2020

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As filed with the Securities and Exchange Commission on March 9, 2022

As filed with the Securities and Exchange Commission on March 9, 2022 Registration No.

Employment Agreement between the Registrant and Corinne Noyes dated as of April 27, 2020

Exhibit 10.14 Employment Agreement This Employment Agreement (this ?Agreement?), dated as of April 27, 2020, is made by and between Lyra Therapeutics, Inc., a Delaware corporation (together with any successor thereto, the ?Company?), and Corinne Noyes (?Executive?) (collectively referred to herein as the ?Parties? or individually referred to as a ?Party?). RECITALS A. It is the desire of the Compa

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Employment Agreement between the Registrant and Pamela Nelson dated as of July 17, 2020

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Lyra Therapeutics, Inc. 2020 Incentive Award Plan Performance Stock Option Grant Notice and Performance Stock Option Agreement issued to Maria Palasis, Ph.D. on February 16, 2022

Exhibit 10.3 LYRA THERAPEUTICS, INC. 2020 INCENTIVE AWARD PLAN PERFORMANCE STOCK OPTION GRANT NOTICE Capitalized terms not specifically defined in this Performance Stock Option Grant Notice (the ?Grant Notice?) have the meanings given to them in the 2020 Incentive Award Plan (as amended from time to time, the ?Plan?) of Lyra Therapeutics, Inc. (the ?Company?). The Company has granted to the partic

Lyra Therapeutics, Inc. 2022 Inducement Award Plan Performance Stock Option Grant Notice and Performance Stock Option Agreement issued to Harlan Waksal, M.D. on February 16, 2022

Exhibit 10.4 LYRA THERAPEUTICS, INC. 2022 INDUCEMENT INCENTIVE AWARD PLAN PERFORMANCE STOCK OPTION GRANT NOTICE Capitalized terms not specifically defined in this Performance Stock Option Grant Notice (the ?Grant Notice?) have the meanings given to them in the 2022 Inducement Incentive Award Plan (as amended from time to time, the ?Plan?) of Lyra Therapeutics, Inc. (the ?Company?). The Company has

Employment Agreement between the Registrant and Harlan Waksal, M.D. dated as of February 16, 2022

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First Amendment to the Employment Agreement between the Registrant and Maria Palasis, Ph.D. dated as of February 16, 2022

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Employment Agreement between the Registrant and Jason Cavalier dated as of September 13, 2021

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UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ? QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2021 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: 001-39273 Lyra Therapeutics, Inc.

Lyra Therapeutics Reports Second Quarter 2021 Financial Results and Highlights Recent Accomplishments

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License and Collaboration Agreement dated May 31, 2021, by and between the Registrant and LianBio Inflammatory Limited and LianBio.

Exhibit 10.1 Certain information marked as [***] has been excluded from this exhibit because it is both (i) not material and (ii) the type that the Registrant treats as private or confidential. LICENSE AND COLLABORATION AGREEMENT THIS LICENSE AND COLLABORATION AGREEMENT (this ?Agreement?), entered into as of May 31, 2021 (the ?Effective Date?), is entered into by and among LianBio Inflammatory Lim

Other Events

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Entry into a Material Definitive Agreement

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$50,000,000 Common Stock

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LYRA THERAPEUTICS, INC. 480 Arsenal Way Watertown, Massachusetts 02472

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Quarterly Report - 10-Q

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 20549 FORM 10-Q (Mark One) ? QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended March 31, 2021 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: 001-39273 Lyra Therapeutics, Inc.

Financial Statements and Exhibits, Results of Operations and Financial Condition

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Open Market Sale AgreementSM, dated as of May 11, 2021, by and among Lyra Therapeutics, Inc. and Jefferies LLC

Exhibit 1.2 OPEN MARKET SALE AGREEMENTSM May 11, 2021 JEFFERIES LLC 520 Madison Avenue New York, New York 10022 Ladies and Gentlemen: Lyra Therapeutics, Inc., a Delaware corporation (the ?Company?), proposes, subject to the terms and conditions stated herein, to issue and sell from time to time through Jefferies LLC, as sales agent and/or principal (the ?Agent?), shares of the Company?s common sto

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Exhibit 4.3 LYRA THERAPEUTICS, INC. INDENTURE Dated as of , 20 [ ] Trustee TABLE OF CONTENTS Page ARTICLE I. DEFINITIONS AND INCORPORATION BY REFERENCE 1 Section 1.1. Definitions. 1 Section 1.2. Other Definitions. 4 Section 1.3. Incorporation by Reference of Trust Indenture Act. 4 Section 1.4. Rules of Construction. 5 ARTICLE II. THE SECURITIES 5 Section 2.1. Issuable in Series. 5 Section 2.2. Est

Lyra Therapeutics Reports First Quarter 2021 Financial Results and Provides Corporate Update - Presented positive full data from LANTERN Phase 2 study of LYR-210 at COSM – - Appointed Robert Kern, MD, as Chief Medical Officer - - Conference call and

Exhibit 99.1 Lyra Therapeutics Reports First Quarter 2021 Financial Results and Provides Corporate Update - Presented positive full data from LANTERN Phase 2 study of LYR-210 at COSM ? - Appointed Robert Kern, MD, as Chief Medical Officer - - Conference call and webcast today at 4:30 p.m. ET - WATERTOWN, MA ? May 11, 2021 - Lyra Therapeutics, Inc. (Nasdaq: LYRA), a clinical-stage therapeutics comp

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Table of Contents As filed with the Securities and Exchange Commission on May 11, 2021 Registration No.

Schedule 14A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, DC 20549 SCHEDULE 14A (Rule 14a-101) INFORMATION REQUIRED IN PROXY STATEMENT SCHEDULE 14A INFORMATION Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No.

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UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, DC 20549 SCHEDULE 14A (Rule 14a-101) INFORMATION REQUIRED IN PROXY STATEMENT SCHEDULE 14A INFORMATION Proxy Statement Pursuant to Section 14(a) of the Securities Exchange Act of 1934 (Amendment No.

Financial Statements and Exhibits, Other Events

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of report (Date of earliest event reported): April 11, 2021 LYRA THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 001-39273 84-1700838 (State or other jurisdiction of incorporation) (Commission

DISCLAIMER This presentation contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. All statements contained in this presentation that do not relate to matters of historical fact should be cons

Anders Cervin1, Joanne Rimmer2, Agnieszka Wrobel3, Yogen Abelak4, Lindsay Brayton5, Yina Kuang5 1University of Queensland Centre for Clinical Research, Royal Brisbane & Women?s Hospital Campus, Herston, QLD, Australia; 2Monash Health and Department of Surgery, Monash University, Melbourne, Australia; 3Centrum Medyczne ALL-MED, Krakow, Poland; 4Vistamed Sp.

Lyra Therapeutics Reports Fourth Quarter and Full Year 2020 Financial Results, Provides Corporate Update - Positive Topline Results for LANTERN Phase 2 Study of LYR-210- - Robert Kern, MD, appointed Chief Medical Officer - - Conference call and webca

Exhibit 99.1 Lyra Therapeutics Reports Fourth Quarter and Full Year 2020 Financial Results, Provides Corporate Update - Positive Topline Results for LANTERN Phase 2 Study of LYR-210- - Robert Kern, MD, appointed Chief Medical Officer - - Conference call and webcast today at 4:30 p.m. ET - WATERTOWN, MA ? March 9, 2021 - Lyra Therapeutics, Inc. (Nasdaq: LYRA), a clinical-stage therapeutics company

Annual Report - 10-K

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-K (Mark One) ? ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2020 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 001-39273 Lyra Therapeuti

Description of Securities

Exhibit 4.4 DESCRIPTION OF THE REGISTRANT?S SECURITIES REGISTERED PURSUANT TO SECTION 12 OF THE SECURITIES EXCHANGE ACT OF 1934, AS AMENDED As of December 31, 2020, Lyra Therapeutics, Inc. had one class of securities registered under Section 12 of the Securities Exchange Act of 1934, as amended (the ?Exchange Act?). References herein to ?we,? ?us,? ?our? and the ?Company? refer to Lyra Therapeutic

Financial Statements and Exhibits, Results of Operations and Financial Condition

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 8-K CURRENT REPORT Pursuant to Section 13 or 15(d) of the Securities Exchange Act of 1934 Date of report (Date of earliest event reported): March 9, 2021 LYRA THERAPEUTICS, INC. (Exact name of registrant as specified in its charter) Delaware 001-39273 84-1700838 (State or other jurisdiction of incorporation) (Commission F

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, DC 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. )* Lyra Therapeutics, Inc.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, DC 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No.

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. )* LYRA THERAPEUTICS, INC. (Name of Issuer) Common Stock, par value $0.001 per share (Title of Class of Secu

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. )* LYRA THERAPEUTICS, INC. (Name of Issuer) Common Stock, par value $0.001 per share (Title of Class of Securities) 55234L105 (CUSIP Number) December 31, 2020 (Date of Event Which Requires Filing of this Statement) Check the appropriate box to designate the

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 1)* Lyra Therapeutics, Inc. (Name of Issuer) Common Stock, $0.001 par value per share (Title of Class of Sec

SC 13G/A UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 1)* Lyra Therapeutics, Inc. (Name of Issuer) Common Stock, $0.001 par value per share (Title of Class of Securities) 55234L105 (CUSIP Number) December 31, 2020 (Date of Event which Requires Filing of this Statement) Check the appropriate box to desi

AGREEMENT REGARDING THE JOINT FILING OF SCHEDULE 13G

EX-99.A Exhibit A AGREEMENT REGARDING THE JOINT FILING OF SCHEDULE 13G The undersigned, being duly authorized thereunto, hereby execute this agreement as an exhibit to this Schedule 13G to evidence the agreement of the below-named parties, in accordance with the rules promulgated pursuant to the Securities Exchange Act of 1934, to file this Schedule jointly on behalf of each such party. Date: Febr

AGREEMENT REGARDING THE JOINT FILING OF SCHEDULE 13G

EX-99.A Exhibit A AGREEMENT REGARDING THE JOINT FILING OF SCHEDULE 13G The undersigned, being duly authorized thereunto, hereby execute this agreement as an exhibit to this Schedule 13G to evidence the agreement of the below-named parties, in accordance with the rules promulgated pursuant to the Securities Exchange Act of 1934, to file this Schedule and all amendments thereto jointly on behalf of