Item 9A. Controls and Procedures
ITEM 9A. CONTROLS AND PROCEDURES
Conclusions Regarding the Effectiveness of Disclosure Controls and Procedures
As of December 31, 2025, management, with the participation of our Chief Executive Officer and Chief Financial Officer, performed an evaluation of the effectiveness of the design and operation of our disclosure controls and procedures as defined in Rules 13a-15(e) and 15d-15(e) of the Exchange Act. Our disclosure controls and procedures are designed to ensure that information required to be disclosed in the reports we file or submit under the Exchange Act is recorded, processed, summarized and reported within the time periods specified in the SEC’s rules and forms, and that such information is accumulated and communicated to our management, including the Chief Executive Officer and the Chief Financial Officer, to allow timely decisions regarding required disclosures.
Any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving the desired control objective and management necessarily applies its judgment in evaluating the cost-benefit relationship of possible controls and procedures. Based on this evaluation, our Chief Executive Officer and Chief Financial Officer concluded that, as of December 31, 2025, the design and operation of our disclosure controls and procedures were effective at a reasonable assurance level.
Changes in Internal Control over Financial Reporting
There was no change 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 quarter ended December 31, 2025 that has materially affected, or is reasonably likely to materially affect, our internal control over financial reporting.
Management’s Annual Report on Internal Control Over Financial Reporting
Our management is responsible for establishing and maintaining adequate internal control over financial reporting (as defined in Rule 13a-15(f) under the Exchange Act). Under the supervision of and with the participation of our principal executive officer and principal financial officer, our management assessed the effectiveness of our internal control over financial reporting as of December 31, 2025 based on the criteria set forth by the Committee of Sponsoring Organizations of the Treadway Commission in “Internal Control—Integrated Framework” (2013). Based on this assessment, management concluded that our internal control over financial reporting was effective as of December 31, 2025.
The effectiveness of our internal control over financial reporting as of December 31, 2025 has been audited by Ernst & Young LLP, an independent registered public accounting firm, as stated in their report which is included herein.
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Report of Independent Registered Public Accounting Firm
To the Stockholders and the Board of Directors of Denali Therapeutics Inc.
Opinion on Internal Control Over Financial Reporting
We have audited Denali Therapeutics Inc.’s internal control over financial reporting as of December 31, 2025, based on criteria established in Internal Control—Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission (2013 framework) (the COSO criteria). In our opinion, Denali Therapeutics Inc. (the Company) maintained, in all material respects, effective internal control over financial reporting as of December 31, 2025, based on the COSO criteria.
We also have audited, in accordance with the standards of the Public Company Accounting Oversight Board (United States) (PCAOB), the consolidated balance sheets of the Company as of December 31, 2025 and 2024, the related consolidated statements of operations and comprehensive loss , stockholders' equity and cash flows for each of the three years in the period ended December 31, 2025, and the related notes and our report dated February 26, 2026 expressed an unqualified opinion thereon.
Basis for Opinion
The Company’s management is responsible for maintaining effective internal control over financial reporting and for its assessment of the effectiveness of internal control over financial reporting included in the accompanying Management’s Annual Report on Internal Control Over Financial Reporting. Our responsibility is to express an opinion on the Company’s internal control over financial reporting based on our audit. We are a public accounting firm registered with the PCAOB and are required to be independent with respect to the Company in accordance with the U.S. federal securities laws and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB.
We conducted our audit in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether effective internal control over financial reporting was maintained in all material respects.
Our audit included obtaining an understanding of internal control over financial reporting, assessing the risk that a material weakness exists, testing and evaluating the design and operating effectiveness of internal control based on the assessed risk, and performing such other procedures as we considered necessary in the circumstances. We believe that our audit provides a reasonable basis for our opinion.
Definition and Limitations of Internal Control Over Financial Reporting
A company’s internal control over financial reporting is a process designed to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles. A company’s internal control over financial reporting includes those policies and procedures that (1) pertain to the maintenance of records that, in reasonable detail, accurately and fairly reflect the transactions and dispositions of the assets of the company; (2) provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that receipts and expenditures of the company are being made only in accordance with authorizations of management and directors of the company; and (3) provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use, or disposition of the company’s assets that could have a material effect on the financial statements.
Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements. Also, 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.
/s/ Ernst & Young LLP
San Mateo, California
February 26, 2026
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ITEM 9B. OTHER INFORMATION
Securities Trading Plans of Directors and Executive Officers
No officers or directors, as defined in Rule 16a-1(f), adopted and/or terminated of a “Rule 10b5-1 trading arrangement” or a “non-Rule 10b5-1 trading arrangement,” as defined in Regulation S-K Item 408, during the fourth quarter ended December 31, 2025.
ITEM 9C. DISCLOSURE REGARDING FOREIGN JURISDICTIONS THAT PREVENT INSPECTIONS
Not applicable.
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PART III
ITEM 10. DIRECTORS, EXECUTIVE OFFICERS AND CORPORATE GOVERNANCE
Information required by this item will be contained in our definitive proxy statement to be filed with the SEC on Schedule 14A in connection with our 2026 Annual Meeting of Stockholders (the “Proxy Statement”), which is expected to be filed not later than 120 days after December 31, 2025, and is incorporated herein by reference.
ITEM 11. EXECUTIVE COMPENSATION
Information required by this item will be contained in the Proxy Statement and is incorporated herein by reference.
ITEM 12. SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT AND RELATED STOCKHOLDER MATTERS
Information required by this item will be contained in the Proxy Statement and is incorporated herein by reference.
ITEM 13. CERTAIN RELATIONSHIPS AND RELATED TRANSACTIONS AND DIRECTOR INDEPENDENCE
Information required by this item will be contained in the Proxy Statement and is incorporated herein by reference.
ITEM 14. PRINCIPAL ACCOUNTANT FEES AND SERVICES
Information required by this item will be contained in the Proxy Statement and is incorporated herein by reference.
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PART IV
ITEM 15. EXHIBITS AND FINANCIAL STATEMENT SCHEDULES
(a) The following documents are filed as part of this report:
1. Financial Statements
See Index to Financial Statements in Part II Item 8 of this Annual Report on Form 10-K.
2. Financial Statement Schedules
All schedules are omitted because they are not applicable or the required information is shown in the financial statements or notes thereto.
3. Exhibits
The documents listed in the Exhibit Index are incorporated by reference or are filed with this report, in each case as indicated therein (numbered in accordance with Item 601 of Regulation S-K).
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EXHIBIT INDEX
Incorporated by Reference
Exhibit
Number
Description Form File No. Number Filing Date
3.1 Amended and Restated Certificate of Incorporation of the Registrant.
8-K 001-38311 3.1 12/12/2017
3.2 Amended and Restated Bylaws of the Registrant.
8-K
001-38311 3.1 11/18/2024
4.1 Specimen Common Stock Certificate of the Registrant.
S-1/A 333-221522 4.2 11/27/2017
4.2#
Form of Pre-Funded Warrant (Amended), March 2024.
10-Q
001-38311 4.1 5/7/2024
4.3#
Form of Pre-Funded Warrant to Purchase Common Stock, December 2025.
8-K
001-38311 4.1 12/10/2025
4.4 Description of the Registrant’s Common Stock .
— — — Filed herewith
10.1+ Form of Indemnification Agreement between the Registrant and each of its directors and executive officers.
S-1/A 333-221522 10.1 11/27/2017
10.2+ 2015 Stock Incentive Plan, as amended, and forms of agreement thereunder.
S-1 333-221522 10.2 11/13/2017
10.3+ 2017 Equity Incentive Plan and forms of agreements thereunder.
S-1/A 333-221522 10.3 11/27/2017
10.4+ 2017 Employee Stock Purchase Plan and form of agreement thereunder.
S-1/A 333-221522 10.4 12/7/2017
10.5+ Offer Letter between the Registrant and Ryan J. Watts, Ph.D., dated November 10, 2017.
S-1 333-221522 10.5 11/13/2017
10.6+ Offer Letter between the Registrant and Alexander O. Schuth, M.D., dated November 10, 2017.
S-1 333-221522 10.6 11/13/2017
10.8+ Offer Letter between the Registrant and Carole Ho, M.D., dated November 10, 2017.
S-1 333-221522 10.8 11/13/2017
10.9 Lease Agreement between the Registrant and HCP Oyster Point III LLC, dated September 24, 2015.
S-1 333-221522 10.9 11/13/2017
10.10Ü Exclusive License Agreement between the Registrant and Genentech, Inc., dated June 17, 2016.
S-1 333-221522 10.10 11/13/2017
10.11Ü License and Collaboration Agreement between the Registrant, F-star Gamma Limited, F-star Biotechnologische Forschungs-und Entwicklungsges m.b.H. and F-star Biotechnology Limited, dated August 24, 2016.
S-1 333-221522 10.11 11/13/2017
10.12Ü Development and Manufacturing Services Agreement between the Registrant and Lonza Sales AG, dated September 6, 2017.
S-1 333-221522 10.12 11/13/2017
10.12.1# Amendment No. 2 to Development and Manufacturing Services Agreement between the Registrant and Lonza Sales AG, dated January 18, 2018.
10-K 001-38311 10.12.1 3/19/2018
10.12.2# Amendment No. 3 to Development and Manufacturing Services Agreement between the Registrant and Lonza Sales AG, dated July 2, 2018.
10-Q 001-38311 10.1 11/8/2018
10.12.3# Amendment No. 4 to Development and Manufacturing Services Agreement between the Registrant and Lonza Sales AG, dated August 30, 2018.
10-Q 001-38311 10.2 11/8/2018
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10.12.4# Amendment No. 5 to Development and Manufacturing Services Agreement between the Registrant and Lonza Sales AG, dated August 6, 2019.
10-K 001-38311 10.12.4 2/26/2021
10.12.5# Amendment No. 3 to Development and Manufacturing Services Agreement between the Registrant and Lonza Sales AG, dated September 11, 2020.
10-K 001-38311 10.12.5 2/26/2021
10.12.6# Amendment No. 6 to Development and Manufacturing Services Agreement between the Registrant and Lonza Sales AG, dated December 8, 2020.
10-K 001-38311 10.12.6 2/26/2021
10.12.7 Amendment No. 7 to Development and Manufacturing Services Agreement between the Registrant and Lonza Sales AG, dated March 29, 2021.
10-K 001-38311 10.12.7
2/27/2023
10.12.8# Amendment No. 8 to Development and Manufacturing Services Agreement between the Registrant and Lonza Sales AG, dated September 8, 2022.
10-K 001-38311 10.12.8
2/27/2023
10.12.9 Amendment No. 9 to Development and Manufacturing Services Agreement between the Registrant and Lonza Sales AG, dated December 7, 2022.
10-K 001-38311 10.12.9
2/27/2023
10.13+ Amended and Restated Key Executive Change in Control and Severance Plan.
10-Q 001-38311 10.6 11/5/2020
10.14+ Executive Incentive Compensation Plan.
S-1 333-221522 10.14 11/13/2017
10.15+ Amended and Restated Outside Director Compensation Policy.
10-Q
001-38311 10.3 5/06/2025
10.16# Option and Collaboration Agreement between the Registrant and Takeda Pharmaceutical Company Limited, dated January 3, 2018.
10-K/A 001-38311 10.16 7/13/2018
10.17 Common Stock Purchase Agreement between the Registrant and Takeda Pharmaceutical Company Limited, dated January 3, 2018.
10-K 001-38311 10.17 3/19/2018
10.18 Standstill and Stock Restriction Agreement between the Registrant and Takeda Pharmaceutical Company Limited, dated February 23, 2018.
10-K 001-38311 10.18 3/19/2018
10.19 First Amendment to Lease Agreement between the Registrant and HCP Oyster Point III LLC, dated May 2, 2018.
10-Q 001-38311 10.1 8/9/2018
10.20Ü Amended and Restated Gamma IP License Agreement between the Registrant and F-star Gamma Limited, dated August 24, 2016.
10-Q/A 001-38311 10.2 12/6/2018
10.21Ü Side Letter between the Registrant and F-star Gamma Limited, dated May 21, 2018.
10-Q 001-38311 10.3 8/9/2018
10.22Ü Share Purchase Agreement between the Registrant and F-star Gamma Limited, dated May 30, 2018.
10-Q/A 001-38311 10.4 12/6/2018
10.23# Collaboration and License Agreement between registrant and Genzyme Corporation ("Sanofi"), dated October 29, 2018.
10-K 001-38311 10.25 3/12/2019
10.24 Common Stock Purchase Agreement between the Registrant and Biogen Inc., dated August 5, 2020.
10-Q 001-38311 10.1 11/5/2020
10.25# Provisional LRRK2 Collaboration and License Agreement between the Registrant and Biogen Inc., dated August 5, 2020.
10-Q 001-38311 10.2 11/5/2020
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10.26 Standstill and Stock Restriction Agreement between the Registrant and Biogen Inc., dated September 22, 2020.
10-Q 001-38311 10.3 11/5/2020
10.27# Definitive LRRK2 Collaboration and License Agreement between the Registrant and Biogen Inc., dated October 4, 2020.
10-Q 001-38311 10.4 11/5/2020
10.28# Definitive Right of First Negotiation, Option and License Agreement between the Registrant and Biogen Inc., dated October 6, 2020.
10-Q 001-38311 10.5 11/5/2020
10.29# Side Letter between the Registrant and F-star Gamma Limited, dated June 30, 2021.
10-Q 001-38311 10.1 8/4/2021
10.30#
Amendment to Definitive LRRK2 Agreement and Waiver of and Amendment to Right of First Negotiation, Option, and License Agreement.
10-Q 001-38311 10.1 11/7/2023
10.31 Securities Purchase Agreement, dated February 27, 2024, by and among the Company and the Purchasers named therein
8-K
001-38311 10.1 2/27/2024
10.32 Nominating Agreement by and among the Company and Investor
8-K
001-38311 10.2
2/27/2024
10.33 Compensation Recovery Policy (“Clawback Policy”)
10-K 001-38311 10.34 2/28/2024
10.34#
Denali - Biogen Side Letter
10-Q 001-38311 10.10 8/1/2024
10.35#
Notice of Partial Termination from Genzyme Corporation to the Registrant, dated February 24, 2025
10-Q
001-38311 10.1 5/06/2025
10.36#
Notice of Partial Termination from Takeda Pharmaceutical Company Limited to the Registrant, dated February 25, 2025
10-Q
001-38311 10.2 5/06/2025
10.37 Affiliate Registration Rights Agreement, dated June 3, 2025, by and among the Company, Baker Brothers Life Sciences, L.P. and 667, L.P.
8-K
001-38311 10.1 6/03/2025
19.1 Denali Insider Trading Policy and Guidelines with Respect to Certain Transactions in Securities as amended through May 20, 2025 .
— — — Filed herewith
21.1 Subsidiaries of the Registrant.
— — — Filed herewith
23.1 Consent of Independent Registered Public Accounting Firm.
— — — Filed herewith
24.1 Powers of Attorney (incorporated by reference to the signature page hereto)
31.1 Certification of Chief Executive Officer pursuant to Section 302 of the Sarbanes-Oxley Act.
— — — Filed herewith
31.2 Certification of Chief Financial Officer pursuant to Section 302 of the Sarbanes-Oxley Act.
— — — Filed herewith
32.1* Certification of Chief Executive Officer pursuant to Section 906 of the Sarbanes-Oxley Act.
— — — Furnished herewith
32.2* Certification of Chief Financial Officer pursuant to Section 906 of the Sarbanes-Oxley Act.
— — — Furnished herewith
101 The following materials from the Company’s Annual Report on Form 10-K for the year ended December 31, 2025, formatted in Inline XBRL: (i) Consolidated Balance Sheets, (ii) Consolidated Statements of Operations and Comprehensive Loss, (iii) Consolidated Statements of Cash Flows (iv) Consolidated Statements of Stockholders’ Equity and (v) Notes to Consolidated Financial Statements.
— — — Filed herewith
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104 The cover page from the Company's Annual Report on Form 10-K for the year ended December 31, 2025, formatted in Inline XBRL (contained in Exhibit 101)
— — — Filed herewith
* The certifications attached as Exhibits 32.1 and 32.2 that accompany this Annual Report on Form 10-K are deemed furnished and not filed with the Securities and Exchange Commission and are not to be incorporated by reference into any filing of the Registrant under the Securities Act of 1933, as amended, or the Securities Exchange Act of 1934, as amended, whether made before or after the date of this Annual Report on Form 10-K, irrespective of any general incorporation language contained in such filing.
Ü Portions of the exhibit have been omitted pursuant to an order granted by the Securities and Exchange Commission for confidential treatment.
# Certain confidential information contained in this exhibit has been omitted because it is both (i) not material and (ii) is the type that the Registrant treats as private or confidential.
+ Indicates management contract or compensatory plan.
ITEM 16. FORM 10-K SUMMARY
None.
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SIGNATURES
Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this Annual Report on Form 10-K to be signed on its behalf by the undersigned, thereunto duly authorized.
DENALI THERAPEUTICS INC.
Date: February 26, 2026 By: /s/ Ryan J. Watts
Ryan J. Watts, Ph.D.
President and Chief Executive Officer
POWER OF ATTORNEY
Each person whose signature appears below constitutes and appoints Ryan J. Watts, Ph.D. and Alexander O. Schuth, M.D., and each of them acting individually, as his or her true and lawful attorney-in-fact and agent, with full power of substitution and resubstitution, for him or her and in his or her name, place and stead, in any and all capacities, to sign 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 attorneys-in-fact and agents, and each of them, full power and authority to do and perform each and every act and thing requisite and necessary to be done in connection therewith, as fully to all intents and purposes as he or she might or could do in person, hereby ratifying and confirming all that said attorneys-in-fact and agents, or any of them, or their or his substitutes, may lawfully do or cause to be done by virtue thereof.
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Pursuant to the requirements of the Securities Exchange Act of 1934, this report has been signed by the following persons on behalf of the registrant and in the capacities and on the dates indicated:
Signature Title Date
/s/ Ryan J. Watts
President, Chief Executive Officer and Director
(Principal Executive Officer)
February 26, 2026
Ryan J. Watts, Ph.D.
/s/ Alexander O. Schuth
Chief Operating and Financial Officer
(Principal Financial and Accounting Officer)
February 26, 2026
Alexander O. Schuth, M.D.
/s/ Julian C. Baker
Chairperson of our Board of Directors February 26, 2026
Julian C. Baker
/s/ Jennifer Cook Director February 26, 2026
Jennifer Cook
/s/ Jay Flatley
Director February 26, 2026
Jay Flatley
/s/ Peter Klein Director February 26, 2026
Peter Klein
/s/ Steve E. Krognes
Director February 26, 2026
Steve E. Krognes
/s/ David Schenkein
Director February 26, 2026
David Schenkein, M.D.
/s/ Nancy A. Thornberry
Director February 26, 2026
Nancy A. Thornberry
/s/ Tim Van Hauwermeiren
Director February 26, 2026
Tim Van Hauwermeiren
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