Denali Therapeutics Inc. 10-Q

ITEM 5. OTHER INFORMATION 97 Table of Contents Securities Trading Plans of Directors and Executive Officers Our policy governing transactions in our securities by our directors, officers, and employees permits our officers, directors and employees to enter into trading plans complying with Rule 10b5-1 under the Securities Exchange Act of 1934, as amended. As disclosed in the table below, during the third quarter of 2025, certain directors adopted a “Rule 10b5-1 trading arrangement”. This plan provides for the sale of our common stock and is intended to satisfy the affirmative defense in Rule 10b5-1(c). Name Position Date of Plan Adoption Scheduled End Date of Trading Arrangement (1) Maximum Total Shares of Common Stock to be Sold Under the Plan (2) Steve Krognes Director 9/10/2025 12/10/2026 180,000 __________________________________________________ (1) In each case, the trading arrangement may expire on an earlier date if and when all transactions under the arrangement are completed. (2) This amount represents the maximum total shares that could be sold under the plan, but the amounts may change for executive officers due to the sale of shares to satisfy tax withholding requirements. No other 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 third quarter ended September 30, 2025. Increase in Size of Board; Appointment of New Director On November 4, 2025, the Company's Board of Directors ("Board") increased the size of the Board from eight members to nine members and appointed Tim Van Hauwermeiren to serve as a Class I director, with a term expiring at the Company’s 2027 annual meeting of the stockholders. In accordance with the Company’s amended outside director compensation policy (the “Policy”), Mr. Van Hauwermeiren will receive annual cash compensation of $50,000 for his services as a member of the Board, payable quarterly in arrears on a pro-rata basis, and on November 4, 2025, Mr. Van Hauwermeiren was automatically granted an initial award of a nonstatutory stock option to purchase shares of the Company’s common stock and an initial award RSU, together having an aggregate company-assessed value of approximately $700,000. 60% of the value of the initial awards is in the Initial Option, while the remaining 40% is in the Initial RSU. For purposes of the Policy, the Company values RSUs as 1 RSU for every 2 shares subject to an option. The Initial Option vests as to 25% of the shares on the one-year anniversary of the grant date and as to 1/48th of the shares on each monthly anniversary of the grant date thereafter, provided that he remains a non-employee director through the applicable vesting date. The Initial RSU award vests over a four-year period, with 1/4th of the shares vesting on each anniversary of the grant date (or, for the last tranche that otherwise would vest on the fourth anniversary of the grant date, on such anniversary or, if earlier, on the day prior to the Company’s next annual meeting of stockholders occurring after the third anniversary of the grant date), provided that he remains a non-employee director through the applicable vesting date. Initial awards to Mr. Van Hauwermeiren were granted under and subject to terms of the Company’s 2017 Equity Incentive Plan. Mr. Van Hauwermeiren will be eligible for equity awards on the same terms as other continuing non-employee members of the Board. The Policy provides that on the date of each annual meeting of stockholders, each non-employee director who has been a director for six months or more on the date of the annual meeting will automatically be granted a nonstatutory stock option to purchase shares of the Company’s common stock and a RSU, together having an aggregate company-assessed value of approximately $400,000. 60% of the value of the awards will be in the Annual Option, while the remaining 40% will be in the Annual RSU. Each Annual Option and Annual RSU will vest fully on the earlier of the one year anniversary of the grant date or the day prior to the next annual meeting of stockholders held after the grant date, provided that he remains a non-employee director through the applicable vesting date. 98 Table of Contents Mr. Van Hauwermeiren also executed the Company’s standard form of indemnification agreement, a copy of which has been filed as Exhibit 10.1 to the Company’s Amendment No. 2 to the Registration Statement on Form S-1 (File No. 333-221522) filed with the Securities and Exchange Commission on December 7, 2017. There is no arrangement or understanding between Mr. Van Hauwermeiren and any other persons pursuant to which Mr. Van Hauwermeiren was elected as a director. In addition, Mr. Van Hauwermeiren is not a party to any transaction, or series of transactions, required to be disclosed pursuant to Item 404(a) of Regulation S-K. The Board has determined that Mr. Van Hauwermeiren is independent under the applicable Nasdaq rules. Departure of Chief Medical Officer On November 6, 2025, the Company announced that Carole Ho, M.D., the Company's Chief Medical Officer and Head of Development, will be departing to pursue a new career opportunity. In connection with the announcement of Dr. Ho's departure, the Company also announced that Peter Chin, M.D., is assuming the role of Acting Chief Medical Officer and Head of Development. Dr. Chin joined the Company in 2019 and most recently served as Senior Vice President of the Enzyme TransportVehicle™ Franchise and Late-Stage Clinical Development. Dr. Ho will transition her responsibilities to Dr. Chin through late November 2025. 99 Table of Contents ITEM 6. EXHIBITS EXHIBIT INDEX Incorporated by Reference Exhibit Number Description Form File No. Number Filing Date 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.INS XBRL Instance Document - the instance document does not appear in the Interactive Data File because its XBRL tags are embedded within the Incline XBRL document — — — Furnished herewith 101.SCH Inline XBRL Taxonomy Extension Schema Document. — — — Furnished herewith 101.CAL Inline XBRL Taxonomy Extension Calculation Linkbase Document. — — — Furnished herewith 101.DEF Inline XBRL Taxonomy Extension Definition Linkbase Document. — — — Furnished herewith 101.LAB Inline XBRL Taxonomy Extension Label Linkbase Document. — — — Furnished herewith 101.PRE Inline XBRL Taxonomy Extension Presentation Linkbase Document. — — — Furnished herewith 104 The cover page from the Company's Quarterly Report on Form 10-Q for the three months ended September 30, 2025, formatted in Inline XBRL (contained in Exhibit 101) — — — Furnished herewith * The certifications attached as Exhibits 32.1 and 32.2 that accompany this Quarterly Report on Form 10-Q are not deemed filed with the Securities and Exchange Commission and are not to be incorporated by reference into any filing of Denali Therapeutics Inc. 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 Quarterly Report on Form 10-Q, irrespective of any general incorporation language contained in such filing. 100 Table of Contents SIGNATURES Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized. DENALI THERAPEUTICS INC. Date: November 6, 2025 By: /s/ Ryan J. Watts Ryan J. Watts, Ph.D. President and Chief Executive Officer (Principal Executive Officer) Date: November 6, 2025 By: /s/ Alexander O. Schuth Alexander O. Schuth, M.D. Chief Operating and Financial Officer (Principal Financial and Accounting Officer) 101