Passage BIO, Inc. 10-K

Item 9A. Controls and Procedures Conclusions Regarding the Effectiveness of Disclosure Controls and Procedures Under the supervision of and with the participation of our management, including our chief executive officer, who is our principal executive officer, and our chief financial officer, who is our principal financial officer, we conducted an evaluation of the effectiveness of our disclosure controls and procedures as of December 31, 2024, the end of the period covered by this Annual Report. The term “disclosure controls and procedures,” as set forth in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, as amended, or the Exchange Act, means controls and other procedures of a company that are designed to provide reasonable assurance that information required to be disclosed by a company in the reports that it files or submits under the Exchange Act is recorded, processed, summarized and reported, within the time periods specified in the rules and forms promulgated by the SEC. Disclosure controls and procedures include, without limitation, controls and procedures designed to ensure that information required to be disclosed by a company in the reports that it files or submits under the Exchange Act is accumulated and communicated to the company’s management, including its principal executive and principal financial officers, as appropriate to allow timely decisions regarding required disclosure. Management recognizes that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving their objectives, and management necessarily applies its judgment in evaluating the cost-benefit relationship of possible controls and procedures. Based on the evaluation of our disclosure controls and procedures as of December 31, 2024, our chief executive officer and chief financial officer concluded that, as of such date, our disclosure controls and procedures were effective at the reasonable assurance level. Management’s Annual Report on Internal Control Over Financial Reporting Our management is responsible for establishing and maintaining adequate internal control over financial reporting. Internal control over financial reporting is defined in Rules 13a-15(f) and 15d-15(f) promulgated under the Exchange Act as a process designed by, or under the supervision of, our chief executive officer and chief financial officer and effected by our board of directors, management and other personnel to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with U.S. GAAP. Our internal control over financial reporting includes those policies and procedures that: ● pertain to the maintenance of records that, in reasonable detail, accurately and fairly reflect our transactions and dispositions of our assets; ● provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with U.S. GAAP, and that our receipts and expenditures are being made only in accordance with authorizations of our management and directors; and ● provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use or disposition of our assets that could have a material effect on our financial statements. ​ Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements. Therefore, even those systems determined to be effective can provide only reasonable assurance with respect to financial statement preparation and presentation. Projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate. Additionally, in designing disclosure controls and procedures, our management necessarily was required to apply its judgment in evaluating the cost-benefit relationship of possible disclosure controls and procedures. The design of any disclosure controls and procedures also is based in part upon certain assumptions about the likelihood of future events, and there can be no assurance that any design will succeed in achieving its stated goals under all potential future conditions. 137 Table of Contents Our management, with the participation of our chief executive officer and chief financial officer, assessed the effectiveness of our internal control over financial reporting as of December 31, 2024. In making this assessment, management used the criteria set forth by the Committee of Sponsoring Organizations of the Treadway Commission (COSO) in its Internal Control – Integrated Framework (2013) . Based on our assessment, our management has concluded that, as of December 31, 2024, our internal control over financial reporting is effective based on those criteria. This Annual Report on Form 10-K does not include an attestation report of our independent registered public accounting firm regarding internal control over financial reporting. For as long as we remain an “emerging growth company” as defined in Section 2(a) of the Securities Act of 1933, or the Securities Act, as modified by the Jumpstart Our Business Startups Act of 2012, or a non-accelerated filer as defined in the Exchange Act, we intend to take advantage of the exemption permitting us not to comply with the requirement that our independent registered public accounting firm provide an attestation on the effectiveness of our internal control over financial reporting. Changes in Internal Control over Financial Reporting There were no changes in our internal control over financial reporting identified in connection with the evaluation required by Rule 13a-15(d) and 15d-15(d) of the Exchange Act that occurred during the three months ended December 31, 2024, that have materially affected, or are reasonably likely to materially affect, our internal controls over financial reporting. Item 9B. Other Information During the three months ended December 31, 2024, none of our directors or officers, as defined in Rule 16a-1(f), informed us of the adoption, modification or termination of a “ Rule 10b5-1 trading agreement” or “ non-Rule 10b-51 trading agreement,” as those terms are defined in Regulations S-K, Item 408. Item 9C. Disclosure Regarding Foreign Jurisdictions that Prevent Inspections None. ​ ​ 138 Table of Contents PART III Item 10. Directors, Executive Officers and Corporate Governance The information required by this item is incorporated herein by reference to our Proxy Statement with respect to our 2025 Annual Meeting of Stockholders to be filed with the SEC within 120 days of the end of the fiscal year covered by this Annual Report on Form 10-K. ​ 139 Table of Contents Item 11. Executive Compensation The information required by this item is incorporated herein by reference to our Proxy Statement with respect to our 2025 Annual Meeting of Stockholders to be filed with the SEC within 120 days of the end of the fiscal year covered by this Annual Report on Form 10-K. ​ 140 Table of Contents Item 12. Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters The information required by this item is incorporated herein by reference to our Proxy Statement with respect to our 2025 Annual Meeting of Stockholders to be filed with the SEC within 120 days of the end of the fiscal year covered by this Annual Report on Form 10-K. ​ 141 Table of Contents Item 13. Certain Relationships and Related Transactions and Director Independence The information required by this item is incorporated herein by reference to our Proxy Statement with respect to our 2025 Annual Meeting of Stockholders to be filed with the SEC within 120 days of the end of the fiscal year covered by this Annual Report on Form 10-K. ​ 142 Table of Contents Item 14. Principal Accountant Fees and Services The information required by this item is incorporated herein by reference to our Proxy Statement with respect to our 2025 Annual Meeting of Stockholders to be filed with the SEC within 120 days of the end of the fiscal year covered by this Annual Report on Form 10-K. ​ 143 Table of Contents PART IV Item 15. Exhibits and Financial Statement Schedules (1) Financial Statements The financial statements required by Item 15(a) are filed as part of this Annual Report on Form 10-K under Item 8 “Financial Statements and Supplementary Data.” (2) Financial Statement Schedules The financial statement schedules required by Item 15(a) are omitted because they are not applicable, not required or the required information is included in the financial statements or notes thereto as filed in Item 8 of this Annual Report on Form 10-K. (3) Exhibits Exhibit Number Description Form File No. Exhibit Filing Date Filed/ Furnished Herewith 3.1 Restated Certificate of Incorporation, dated May 30, 2023. 10-Q 001-39231 August 7, 2023 ​ 3.2 Amended and Restated Bylaws, dated December 1, 2022. 8-K 001-39231 December 2, 2022 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 4.1 ​ Form of Common Stock Certificate ​ S-1/A ​ 333-236214 ​ February 18, 2020 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 4.2 ​ Description of Registrant’s Securities ​ 10-K ​ 001-39231 ​ March 3, 2021 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 10.1 ​ Lease, dated April 10, 2020, by and between the Registrant and Commerce Square Partners - Philadelphia Plaza, L.P. ​ 10-Q ​ 001-39231 ​ May 11, 2020 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 10.2 First Amendment to Lease, dated April 10, 2020, by and between the Registrant and Philadelphia Plaza – Phase II LP 10-Q 001-39231 May 11, 2020 ​ 10.3 Form of Indemnification Agreement between the Registrant and its directors and officers S-1 333-236214 February 3, 2020 ​ 10.4 ​ Amended and Restated 2018 Equity Incentive Plan, as amended, and forms of award agreements. ​ S-1 ​ 333-236214 ​ February 3, 2020 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 10.5 2020 Equity Incentive Plan of the Registrant, and forms of award agreements. S-1/A 333-236214 February 18, 2020 ​ 10.6 2020 Employee Stock Purchase Plan of the registrant S-1/A 333-236214 February 18, 2020 ​ 144 Table of Contents 10.7˄ ​ Lease, dated December 15, 2020 by and between the Registrant and Hopewell Campus Owner, LLC ​ 8-K ​ 001-39231 ​ December 18, 2020 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 10.8 ​ 2021 Equity Inducement Plan ​ S-8 ​ 333-258000 ​ July 19, 2021 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 10.9+† ​ Employment Agreement, dated October 10, 2022 by and between the Registrant and William Chou. ​ ​ 10-Q ​ 001-39231 ​ November 10, 2022 ​ ​ 10.10+† ​ Employment Agreement dated September 10, 2019, as amended on February 26, 2020, by and between the Registrant and Edgar B. (Chip) Cale. ​ 10-K ​ 001-39231 ​ March 6, 2023 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 10.11†˄ ​ Amended and Restated Development Services and Clinical Supply Agreement, dated November 9, 2023, by and between the Registrant and Catalent Maryland, Inc. ​ 10-K ​ 001-39231 ​ March 4, 2024 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 10.12+† ​ Employment Agreement, dated March 30, 2022, by and between the Registrant and Mark Forman. ​ 10-K ​ 001-39231 ​ March 4, 2024 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 10.13+† ​ Employment Agreement, dated March 1, 2024, by and between the Registrant and Kathleen Borthwick. ​ 10-K ​ 001-39231 ​ March 4, 2024 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 10.14+ ​ Non-Employee Director Compensation Policy effective as of April 4, 2024 ​ 10-Q ​ 001-39231 ​ May 14, 2024 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 10.15†˄ ​ Exclusive License Agreement (PBGM01), dated July 31, 2024, by and between the Registrant and Gemma Biotherapeutics, Inc. ​ 10-Q ​ 001-39231 ​ November 13, 2024 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 10.16†˄ ​ Exclusive License Agreement (PBKR03), dated July 31, 2024, by and between the Registrant and Gemma Biotherapeutics, Inc. ​ 10-Q ​ 001-39231 ​ November 13, 2024 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 10.17†˄ ​ Exclusive License Agreement (PBML04), dated July 31, 2024, by and between the Registrant and Gemma Biotherapeutics, Inc. ​ 10-Q ​ 001-39231 ​ November 13, 2024 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 10.18†˄ ​ Transition Services Agreement, dated July 31, 2024, by and between the Registrant and Gemma Biotherapeutics, Inc. ​ 10-Q ​ 001-39231 ​ November 13, 2024 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 10.19†˄ ​ Research, Collaboration & License Agreement, dated July 31, 2024, by and between the Registrant and Gemma Biotherapeutics, Inc. ​ 10-Q ​ 001-39231 ​ November 13, 2024 ​ ​ 145 Table of Contents ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 10.20†˄ ​ Second Amended and Restated Research, Collaboration & License Agreement, dated July 31, 2024, by and between the Registrant and the Trustees of the University of Pennsylvania ​ 10-Q ​ 001-39231 ​ November 13, 2024 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 19.1˄ ​ Insider Trading Policy ​ ​ ​ ​ ​ ​ ​ X ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 23.1 ​ Consent of KPMG LLP, an independent registered public accounting firm. ​ ​ ​ ​ ​ ​ ​ X ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 24.1 ​ Power of Attorney. Reference is made to the signature page hereto. ​ ​ ​ ​ ​ ​ ​ X ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 31.1 ​ Certification of Principal Executive Officer Pursuant to Rules 13a-14(a) and 15d-14(a) under the Securities Exchange Act of 1934, as Adopted Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002. ​ ​ ​ ​ ​ ​ ​ X ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 31.2 Certification of Principal Financial Officer Pursuant to Rules 13a-14(a) and 15d-14(a) under the Securities Exchange Act of 1934, as Adopted Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002. X ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 32.1* ​ Certification of Principal Executive Officer Pursuant to 18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002. ​ ​ ​ ​ ​ ​ ​ X ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 32.2* ​ Certification of Principal Financial Officer Pursuant to 18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002. ​ ​ ​ ​ ​ ​ ​ X ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 97 ​ Policy Relating to Recovery of Erroneously Awarded Compensation ​ 10-K ​ 001-39231 ​ March 4, 2024 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 101.INS ​ Inline XBRL Instance Document ​ ​ ​ ​ ​ ​ ​ X ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 101.SCH ​ XBRL Taxonomy Extension Schema Document ​ ​ ​ ​ ​ ​ ​ X ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 101.CAL ​ XBRL Taxonomy Extension Calculation Linkbase Document. ​ ​ ​ ​ ​ ​ ​ X ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 101.DEF ​ XBRL Taxonomy Extension Definition Linkbase Document. ​ ​ ​ ​ ​ ​ ​ X ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 146 Table of Contents 101.LAB ​ XBRL Taxonomy Extension Label Linkbase Document. ​ ​ ​ ​ ​ ​ ​ X ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 101.PRE ​ XBRL Taxonomy Extension Presentation Linkbase Document. ​ ​ ​ ​ ​ ​ ​ ​ X 104 ​ Cover Page Interactive Data File (formatted as Inline XBRL). ​ ​ ​ ​ ​ ​ ​ X ​ + Indicates management contract or compensatory plan, contract or agreement. † Registrant has omitted portions of the exhibit as permitted under Item 601(b)(10) of Regulation S-K. ˄ Registrant has omitted schedules and exhibits pursuant to Item 601(a)(5) of Regulation S-K. The Registrant agrees to furnish supplementally a copy of the omitted schedules and exhibits to the SEC upon request. * This certification is deemed not filed for purposes of section 18 of the Exchange Act or otherwise subject to the liability of that section, nor shall it be deemed incorporated by reference into any filing under the Securities Act or the Exchange Act. ​ 147 Table of Contents Item 16. Form 10-K Summary. Registrants may voluntarily include a summary of information required by Form 10-K under Item 16. We have elected not to include such summary. ​ 148 Table of Contents SIGNATURES Pursuant to the requirements of Section 13 or 15(d) the Securities Exchange Act of 1934, the registrant has duly caused this Registration Statement to be signed on its behalf by the undersigned, thereunto duly authorized. ​ ​ ​ ​ PASSAGE BIO, INC. ​ ​ ​ Date: March 4, 2025 By: /s/ William Chou, M.D. ​ Name: William Chou, M.D. ​ Title: Chief Executive Officer and Director ​ ​ ​ Date: March 4, 2025 By: /s/ Kathleen Borthwick ​ Name: Kathleen Borthwick ​ Title: Chief Financial Officer ​ ​ ​ 149 Table of Contents POWER OF ATTORNEY Each person whose individual signature appears below hereby authorizes and appoints William Chou, M.D., Kathleen Borthwick and Edgar B. Cale, and each of them, with full power of substitution and resubstitution, as his or her true and lawful attorney-in-fact and agent to act in his or her name, place and stead and to execute in the name and on behalf of each person, individually and in each capacity stated below, and to file any and all amendments to this Annual Report on Form 10-K and to file the same, with all exhibits thereto, and other documents in connection therewith, with the Securities and Exchange Commission, granting unto said attorney-in-fact and agents full power and authority to do and perform each and every act and thing, ratifying and confirming all that said attorney-in-fact and agents or his substitute or substitutes may lawfully do or cause to be done by virtue thereof. Pursuant to the requirements of the Securities Exchange Act of 1934, this report has been signed below by the following persons on behalf of the registrant and in the capacities and on the dates indicated. ​ ​ ​ ​ ​ ​ Signature ​ Title ​ Date ​ /s/ William Chou, M.D. ​ President, Chief Executive Officer and Director ​ March 4, 2025 William Chou, M.D. ​ (Principal Executive Officer) ​ ​ /s/ Kathleen Borthwick ​ Chief Financial Officer ​ March 4, 2025 Kathleen Borthwick ​ (Principal Financial and Accounting Officer) ​ ​ /s/ Maxine Gowen, Ph.D. ​ Director ​ March 4, 2025 Maxine Gowen, Ph.D. ​ ​ ​ ​ /s/ Athena Countouriotis, M.D. ​ Director ​ March 4, 2025 Athena Countouriotis, M.D. ​ ​ ​ ​ /s/ Saqib Islam ​ Director ​ March 4, 2025 Saqib Islam ​ ​ ​ ​ /s/ Sandip Kapadia ​ Director ​ March 4, 2025 Sandip Kapadia ​ ​ ​ ​ /s/ Thomas Kassberg ​ Director ​ March 4, 2025 Thomas Kassberg ​ ​ ​ ​ /s/ Derrell Porter, M.D. ​ Director ​ March 4, 2025 Derrell Porter, M.D. ​ ​ ​ ​ /s/ Dolan Sondhi, Ph.D. ​ Director ​ March 4, 2025 Dolan Sondhi, Ph.D. ​ ​ ​ ​ ​ ​ ​ 150