DNLI / Denali Therapeutics Inc. - Pengajuan SECLaporan Tahunan, Pernyataan Proksi

Denali Therapeutics Inc.
US ˙ NasdaqGS ˙ US24823R1059

Mga Batayang Estadistika
LEI 549300ZTQ2HO18L3Q830
CIK 1714899
SEC Filings
All companies that sell securities in the United States must register with the Securities and Exchange Commission (SEC) and file reports on a regular basis. These reports include company annual reports (10K, 10Q), news updates (8K), investor presentations (found in 8Ks), insider trades (form 4), ownership reports (13D, and 13G), and reports related to the specific securities sold, such as registration statements and prospectus. This page shows recent SEC filings related to Denali Therapeutics Inc.
SEC Filings (Chronological Order)
Halaman ini menyediakan daftar lengkap dan kronologis dari Pengajuan SEC, tidak termasuk pengajuan kepemilikan yang kami sediakan di tempat lain.
August 11, 2025 10-Q

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

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 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: 00

August 11, 2025 EX-99.1

Denali Therapeutics Reports Second Quarter 2025 Financial Results and Business Highlights

Exhibit 99.1 Denali Therapeutics Reports Second Quarter 2025 Financial Results and Business Highlights •Tividenofusp alfa BLA for Hunter syndrome accepted for priority review and assigned PDUFA target action date of January 5, 2026; company preparing for commercial launch •DNL126 accelerated approval path for Sanfilippo syndrome Type A aligned with FDA; Phase 1/2 study nearing completion of enroll

August 11, 2025 8-K

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 11, 2025 Denali 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): August 11, 2025 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Emplo

July 7, 2025 8-K

Regulation FD Disclosure, 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): July 7, 2025 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Employer

July 7, 2025 EX-99.1

Denali Therapeutics Announces FDA Acceptance and Priority Review of Biologics License Application (BLA) for Tividenofusp Alfa for Hunter Syndrome (MPS II)

Exhibit 99.1 Denali Therapeutics Announces FDA Acceptance and Priority Review of Biologics License Application (BLA) for Tividenofusp Alfa for Hunter Syndrome (MPS II) •FDA assigns PDUFA target action date of January 5, 2026, for decision on accelerated approval •Tividenofusp alfa is designed to deliver missing enzyme to entire body and cross blood-brain barrier into the brain •Tividenofusp alfa l

June 3, 2025 8-K

Entry into a Material Definitive Agreement, Financial Statements and Exhibits, Submission of Matters to a Vote of Security Holders

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 3, 2025 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Employer

June 3, 2025 EX-10.1

Affiliate Registration Rights Agreement, dated June 3, 2025, by and among the Company, Baker Brothers Life Sciences, L.P. and 667, L.P.

Exhibit 10.1 REGISTRATION RIGHTS AGREEMENT This Registration Rights Agreement (this “Agreement”) is made as of June 3, 2025 by and between Denali Therapeutics Inc., a Delaware corporation (the “Company”), and the persons listed on the attached Schedule A who are signatories to this Agreement (collectively, the “Investors”). Unless otherwise defined herein, capitalized terms used in this Agreement

May 6, 2025 EX-99.1

Denali Therapeutics Reports First Quarter 2025 Financial Results and Business Highlights Including Completion of BLA Rolling Submission for Tividenofusp Alfa for Hunter Syndrome

Exhibit 99.1 Denali Therapeutics Reports First Quarter 2025 Financial Results and Business Highlights Including Completion of BLA Rolling Submission for Tividenofusp Alfa for Hunter Syndrome SOUTH SAN FRANCISCO, Calif., – May 6, 2025 – Denali Therapeutics Inc. (Nasdaq: DNLI) today reported financial results for the first quarter ended March 31, 2025, and provided business highlights. “The completi

May 6, 2025 EX-10.3

Amended O

Exhibit. 10.3 DENALI THERAPEUTICS INC. OUTSIDE DIRECTOR COMPENSATION POLICY Initially adopted and approved November 10, 2017; most recently amended and restated January 31, 2025 (the “Restatement Date”) Denali Therapeutics Inc. (the “Company”) believes that granting equity and cash compensation to members of its Board of Directors (the “Board,” and members of the Board, the “Directors”) represents

May 6, 2025 EX-10.1

Notice of Partial Termination from Genzyme Corporation to the Registrant, dated February 24, 2025

Exhibit.10.1 Denali Therapeutics Inc. 151 Oyster Point Blvd South San Francisco, CA 94080 Attention: Alex Schuth, Chief Operating Officer Email: [email protected] with a copy to: Wilson Sonsini Goodrich and Rosati P.C. 12235 El Camino Real, Suite 200 San Diego, California 92130 Attention: Miranda Biven Facsimile: 858-350-2399 Sent by email February 24, 2025 Re: Collaboration and License Agreement –

May 6, 2025 10-Q

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

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 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: 0

May 6, 2025 8-K

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 6, 2025 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Employer

May 6, 2025 EX-10.2

Notice of Partial Termination from Takeda Pharmaceutical Company Limited to the Registrant, dated February 25, 2025

Exhibit 10.2 February 26, 2025 By Overnight Courier and Email / [email protected] Denali Therapeutics, Inc. 151 Oyster Point Boulevard South San Francisco, CA 94080 Attention: Alex Schuth, Chief Operating Officer Re: Option and Collaboration Agreement between Denali Therapeutics Inc. and Takeda Pharmaceutical Company Limited dated January 3, 2018 (the “Agreement”), as supplemented by that certain si

April 17, 2025 DEF 14A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A PROXY STATEMENT PURSUANT TO SECTION 14(a) OF THE SECURITIES EXCHANGE ACT OF 1934

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A PROXY STATEMENT PURSUANT TO SECTION 14(a) OF THE SECURITIES EXCHANGE ACT OF 1934 Filed by the Registrant x Filed by a Party other than the Registrant ¨ Check the appropriate box: ¨ Preliminary Proxy Statement ¨ Confidential, for Use of the Commission Only (as permitted by Rule 14a‑6(e)(2)) x Defi

April 17, 2025 DEFA14A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A PROXY STATEMENT PURSUANT TO SECTION 14(a) OF THE SECURITIES EXCHANGE ACT OF 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A PROXY STATEMENT PURSUANT TO SECTION 14(a) OF THE SECURITIES EXCHANGE ACT OF 1934 Filed by the Registrant x Filed by a Party other than the Registrant ¨ Check the appropriate box: ¨ Preliminary Proxy Statement ¨ Confidential, for Use of the Commission Only (as permitted by Rule 14a‑6(e)(2)) ¨ Definitive Proxy State

April 2, 2025 EX-99.1

Denali Therapeutics Announces Initiation of BLA Filing for Accelerated Approval of Tividenofusp Alfa for the Treatment of Hunter Syndrome (MPS II) and Positive Ongoing Interactions with FDA on DNL126 Through START Program

Exhibit 99.1 Denali Therapeutics Announces Initiation of BLA Filing for Accelerated Approval of Tividenofusp Alfa for the Treatment of Hunter Syndrome (MPS II) and Positive Ongoing Interactions with FDA on DNL126 Through START Program •Rolling submission of BLA initiated for tividenofusp alfa; preparations ongoing for potential U.S. commercial launch in late 2025 or early 2026 •Alignment through r

April 2, 2025 8-K

Regulation FD Disclosure, 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): April 2, 2025 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Employe

March 5, 2025 8-K

Regulation FD Disclosure

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 5, 2025 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Employe

February 27, 2025 8-K

Entry into a Material Definitive Agreement, Termination of a Material Definitive Agreement, 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): February 27, 2025 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Emp

February 27, 2025 10-K

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

Table of Contents 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: 001-38

February 27, 2025 EX-4.4

Description of the Registrant’s Common Stock.

Exhibit 4.4 DESCRIPTION OF THE REGISTRANT’S SECURITIES REGISTERED PURSUANT TO SECTION 12 OF THE SECURITIES EXCHANGE ACT OF 1934 The following summary describes our common stock and preferred stock, as well as certain provisions of our amended and restated certificate of incorporation and amended and restated bylaws. This summary does not purport to be complete and is qualified in its entirety by t

February 27, 2025 EX-FILING FEES

Filing Fee Table.

Calculation of Filing Fee Tables S-3 Denali Therapeutics Inc. Table 1: Newly Registered and Carry Forward Securities Security Type Security Class Title Fee Calculation or Carry Forward Rule Amount Registered Proposed Maximum Offering Price Per Unit Maximum Aggregate Offering Price Fee Rate Amount of Registration Fee Carry Forward Form Type Carry Forward File Number Carry Forward Initial Effective

February 27, 2025 EX-1.1

between the Registrant and Goldman Sachs & Co. LLC and Leerink Partners LLC.

Exhibit 1.2 DENALI THERAPEUTICS INC. Common Stock ($0.01 par value) Having an Aggregate Offering Price of up to $400,000,000 Equity Distribution Agreement February 27, 2025 Goldman, Sachs & Co. LLC 200 West Street New York, New York 10282 Leerink Partners LLC 1301 Avenue of the Americas, 5th Floor New York, New York 10019 Ladies and Gentlemen: Denali Therapeutics Inc., a Delaware corporation (the

February 27, 2025 S-3ASR

As filed with the Securities and Exchange Commission on February 27, 2025

As filed with the Securities and Exchange Commission on February 27, 2025 Registration No.

February 27, 2025 S-8

As filed with the Securities and Exchange Commission on February 27, 2025

As filed with the Securities and Exchange Commission on February 27, 2025 Registration No.

February 27, 2025 EX-FILING FEES

Filing Fee Table

Calculation of Filing Fee Tables S-8 Denali Therapeutics Inc. Table 1: Newly Registered Securities Security Type Security Class Title Fee Calculation Rule Amount Registered Proposed Maximum Offering Price Per Unit Maximum Aggregate Offering Price Fee Rate Amount of Registration Fee 1 Equity Common Stock, $0.01 par value per share, reserved for issuance pursuant to the 2017 Equity Incentive Plan Ot

February 27, 2025 EX-1.2

Equity Distribution Agreement, dated February 27, 2025 between the Registrant and Goldman Sachs & Co. LLC and Leerink Partners LLC.

Exhibit 1.2 DENALI THERAPEUTICS INC. Common Stock ($0.01 par value) Having an Aggregate Offering Price of up to $400,000,000 Equity Distribution Agreement February 27, 2025 Goldman, Sachs & Co. LLC 200 West Street New York, New York 10282 Leerink Partners LLC 1301 Avenue of the Americas, 5th Floor New York, New York 10019 Ladies and Gentlemen: Denali Therapeutics Inc., a Delaware corporation (the

February 27, 2025 EX-21.1

Subsidiaries of the Registrant.

Exhibit 21.1 SUBSIDIARIES Subsidiary Name Jurisdiction of Incorporation or Organization Denali BBB Holding Limited United Kingdom Denali Therapeutics CH GmbH Switzerland

February 27, 2025 EX-4.2

Statement of Eligibility on Form T-1 under the Trust Indenture Act of 1939, as amended, of the trustee under the indenture filed as Exhibit 4.2 above

Exhibit 4.2 DENALI THERAPEUTICS INC. INDENTURE Dated as of , 20 [] Trustee TABLE OF CONTENTS Page ARTICLE I DEFINITIONS AND INCORPORATION BY REFERENCE 1 Section 1.1 Definitions 4 Section 1.2 Other Definitions 4 Section 1.3 Incorporation by Reference of Trust Indenture Act 4 Section 1.4 Rules of Construction 4 ARTICLE II THE SECURITIES 5 Section 2.1 Issuable in Series 5 Section 2.2 Establishment of

February 27, 2025 EX-99.1

Denali Therapeutics Reports Fourth Quarter and Full Year 2024 Financial Results and Business Highlights

Exhibit 99.1 Denali Therapeutics Reports Fourth Quarter and Full Year 2024 Financial Results and Business Highlights SOUTH SAN FRANCISCO, Calif., – February 27, 2025 – Denali Therapeutics Inc. (Nasdaq: DNLI) today reported financial results for the fourth quarter and year ended December 31, 2024, and provided business highlights. “In 2024, we made significant strides across our portfolio, particul

January 13, 2025 8-K

Regulation FD Disclosure, 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): January 13, 2025 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Empl

January 13, 2025 EX-99.1

Denali Therapeutics Announces Key Anticipated 2025 Milestones and Priorities to Further Advance Its Therapeutics Portfolio for Neurodegeneration and Lysosomal Storage Diseases

Exhibit 99.1 Denali Therapeutics Announces Key Anticipated 2025 Milestones and Priorities to Further Advance Its Therapeutics Portfolio for Neurodegeneration and Lysosomal Storage Diseases •FDA Breakthrough Therapy Designation received for tividenofusp alfa for Hunter syndrome (MPS II); on track to submit biologics license application (BLA) in early 2025 •Preparing for commercial launch of tividen

January 7, 2025 EX-99.1

Denali Therapeutics Announces Topline Results for Regimen G Evaluating eIF2B Agonist DNL343 in the Phase 2/3 HEALEY ALS Platform Trial

Exhibit 99.1 Denali Therapeutics Announces Topline Results for Regimen G Evaluating eIF2B Agonist DNL343 in the Phase 2/3 HEALEY ALS Platform Trial •Primary endpoint of overall function (ALSFRS-R) and survival, and key secondary endpoints of muscle strength and respiratory function, were not met at 24 weeks •Overall, DNL343 was found to be safe and well tolerated •Additional analyses, including ne

January 7, 2025 8-K

Regulation FD Disclosure, 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): January 6, 2025 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Emplo

November 18, 2024 8-K

Amendments to Articles of Incorporation or Bylaws; Change in Fiscal Year, 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): November 12, 2024 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Emp

November 18, 2024 EX-3.1

Amended and Restated Bylaws of Denali Therapeutics Inc., effective November 12, 2024

Exhibit 3.1 DENALI THERAPEUTICS INC. AMENDED AND RESTATED BYLAWS (as amended on November 12, 2024) TABLE OF CONTENTS Page ARTICLE I — CORPORATE OFFICES 1 1.1 REGISTERED OFFICE 1 1.2 OTHER OFFICES 1 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 2 2.5 NOTICE OF STOCKHOLDERS’ MEETINGS 10 2.6 QUORUM 11 2.7 ADJOU

November 12, 2024 SC 13G

DNLI / Denali Therapeutics Inc. / Capital Research Global Investors - SEC SCHEDULE 13G Passive Investment

SC 13G 1 SEC13GFiling.htm SEC SCHEDULE 13G UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. )* Denali Therapeutics Inc. (Name of Issuer) Common Stock (Title of Class of Securities) 24823R105 (CUSIP Number) September 30, 2024 (Date of Event Which Requires Filing of this Statement) Check the appropriate box

November 8, 2024 EX-99

JOINT FILING AGREEMENT

JOINT FILING AGREEMENT The undersigned hereby agree that this Schedule 13G (the “Schedule 13G”) with respect to the common stock of Denali Therapeutics Inc.

November 8, 2024 SC 13G/A

DNLI / Denali Therapeutics Inc. / WELLINGTON MANAGEMENT GROUP LLP - SEC SCHEDULE 13G Passive Investment

SC 13G/A 1 SEC13GFiling.htm SEC SCHEDULE 13G UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 1 )* Denali Therapeutics Inc. (Name of Issuer) Common Stock (Title of Class of Securities) 24823R105 (CUSIP Number) September 30, 2024 (Date of Event Which Requires Filing of this Statement) Check the appropriate

November 7, 2024 SC 13G/A

DNLI / Denali Therapeutics Inc. / BIOGEN INC. - SC 13G/A Passive Investment

SC 13G/A 1 d883964dsc13ga.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. 2)* DENALI THERAPEUTICS INC. (Name of Issuer) Common Stock, $0.01 par value (Title of Class of Securities) 24823R105 (CUSIP Number) October 30, 2024 (Date of Event Which Requires Filing of this Statement) Check the appr

November 6, 2024 8-K

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 6, 2024 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Empl

November 6, 2024 10-Q

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

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 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 Numbe

November 6, 2024 EX-99.1

Denali Therapeutics Reports Third Quarter 2024 Financial Results and Business Highlights

Exhibit 99.1 Denali Therapeutics Reports Third Quarter 2024 Financial Results and Business Highlights SOUTH SAN FRANCISCO, Calif., – November 6, 2024 – Denali Therapeutics Inc. (Nasdaq: DNLI) today reported financial results for the third quarter ended September 30, 2024, and provided business highlights. "As leaders in pioneering a new class of therapeutics that cross the blood-brain barrier, we

October 10, 2024 8-K

Regulation FD Disclosure

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 10, 2024 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Empl

August 1, 2024 8-K

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 1, 2024 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Employ

August 1, 2024 EX-10.1

Denali - Biogen Side Letter.

Exhibit 10.1 July 26, 2024 From: Denali Therapeutics Inc. 161 Oyster Point Blvd. South San Francisco, CA 94080 To: Biogen MA, Inc. 225 Binney Street Cambridge, MA 02142 [***] RE: Side Letter to Right of First Negotiation, Option and License Agreement regarding termination of the ATV:Abeta Program As you know, Denali Therapeutics Inc. (“Denali”), Biogen MA, Inc. (“BIMA”) and Biogen International Gm

August 1, 2024 10-Q

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

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 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: 00

August 1, 2024 EX-99.1

Denali Therapeutics Reports Second Quarter 2024 Financial Results and Business Highlights

Exhibit 99.1 Denali Therapeutics Reports Second Quarter 2024 Financial Results and Business Highlights SOUTH SAN FRANCISCO, Calif., – August 1, 2024 – Denali Therapeutics Inc. (Nasdaq: DNLI), a biopharmaceutical company developing a broad portfolio of product candidates engineered to cross the blood-brain barrier (BBB) for the treatment of neurodegenerative diseases and lysosomal storage diseases,

May 31, 2024 8-K

Financial Statements and Exhibits, Submission of Matters to a Vote of Security Holders

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 31, 2024 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Employer

May 7, 2024 10-Q

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

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 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: 0

May 7, 2024 EX-4.1

Form of

Exhibit 4.1 THESE SECURITIES REPRESENTED HEREBY AND THE SECURITIES ISSUABLE UPON EXERCISE OF THESE SECURITIES HAVE NOT BEEN REGISTERED WITH THE SECURITIES AND EXCHANGE COMMISSION OR THE SECURITIES COMMISSION OF ANY STATE BUT HAVE BEEN OR WILL BE ISSUED IN RELIANCE UPON AN EXEMPTION FROM REGISTRATION UNDER THE SECURITIES ACT OF 1933, AS AMENDED, AND, ACCORDINGLY, MAY NOT BE TRANSFERRED UNLESS (i) S

May 7, 2024 EX-99.1

Denali Therapeutics Reports First Quarter 2024 Financial Results and Business Highlights

Exhibit 99.1 Denali Therapeutics Reports First Quarter 2024 Financial Results and Business Highlights SOUTH SAN FRANCISCO, Calif., – May 7, 2024 – Denali Therapeutics Inc. (Nasdaq: DNLI), a biopharmaceutical company developing a broad portfolio of product candidates engineered to cross the blood-brain barrier (BBB) for the treatment of neurodegenerative diseases and lysosomal storage diseases, tod

May 7, 2024 8-K

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 7, 2024 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Employer

April 18, 2024 DEFA14A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A PROXY STATEMENT PURSUANT TO SECTION 14(a) OF THE SECURITIES EXCHANGE ACT OF 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A PROXY STATEMENT PURSUANT TO SECTION 14(a) OF THE SECURITIES EXCHANGE ACT OF 1934 Filed by the Registrant x Filed by a Party other than the Registrant ¨ Check the appropriate box: ¨ Preliminary Proxy Statement ¨ Confidential, for Use of the Commission Only (as permitted by Rule 14a‑6(e)(2)) ¨ Definitive Proxy State

April 18, 2024 DEF 14A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A PROXY STATEMENT PURSUANT TO SECTION 14(a) OF THE SECURITIES EXCHANGE ACT OF 1934

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A PROXY STATEMENT PURSUANT TO SECTION 14(a) OF THE SECURITIES EXCHANGE ACT OF 1934 Filed by the Registrant x Filed by a Party other than the Registrant ¨ Check the appropriate box: ¨ Preliminary Proxy Statement ¨ Confidential, for Use of the Commission Only (as permitted by Rule 14a‑6(e)(2)) x Defi

March 22, 2024 S-3ASR

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.

March 22, 2024 EX-FILING FEES

Filing Fee Table.

Exhibit 107.1 Calculation of Filing Fee Table Form S-3 (Form Type) Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Table 1 – Newly Registered Securities Security Type Security Class Title Fee Calculation Rule Amount Registered(1) (2) Proposed Maximum Offering Price Per Unit(3) Maximum Aggregate Offering Price Fee Rate Amount of Registration Fee Equity Common Stock,

February 28, 2024 EX-FILING FEES

Filing Fee Table

Exhibit 107.1 Calculation of Filing Fee Tables Form S-8 (Form Type) Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Table 1 – Newly Registered Securities 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 Equity Common Stock, $0.01

February 28, 2024 EX-10.34

Compensation Recovery Policy (“Clawback Policy”)

Ex 10.34 DENALI THERAPEUTICS INC. COMPENSATION RECOVERY POLICY As adopted on November 13, 2023 Denali Therapeutics Inc. (the “Company”) is committed to strong corporate governance. As part of this commitment, the Compensation Committee (the “Committee”) of the Company’s Board of Directors (the “Board”) has adopted this clawback policy called the Compensation Recovery Policy (the “Policy”). The Pol

February 28, 2024 EX-10.35

Denali Insider Trading Policy and Guidelines with Respect to Certain Transactions in Securities as amended through March 31, 2023

Ex 10.35 DENALI THERAPEUTICS INC. INSIDER TRADING POLICY and Guidelines with Respect to Certain Transactions in Securities (As amended through March 31, 2023) TABLE OF CONTENTS Page INTRODUCTION................................................................................................................................ 1 Legal prohibitions on insider trading......................................

February 28, 2024 EX-4.4

Description of the Registrant’s Common Stock.

Exhibit 4.4 DESCRIPTION OF THE REGISTRANT’S SECURITIES REGISTERED PURSUANT TO SECTION 12 OF THE SECURITIES EXCHANGE ACT OF 1934 The following summary describes our common stock and preferred stock, as well as certain provisions of our amended and restated certificate of incorporation and amended and restated bylaws. This summary does not purport to be complete and is qualified in its entirety by t

February 28, 2024 EX-21.1

Subsidiaries of the Registrant.

Exhibit 21.1 SUBSIDIARIES Subsidiary Name Jurisdiction of Incorporation or Organization Denali BBB Holding Limited United Kingdom Denali Therapeutics CH GmbH Switzerland

February 28, 2024 S-8

As filed with the Securities and Exchange Commission on February 27, 2024

As filed with the Securities and Exchange Commission on February 27, 2024 Registration No.

February 28, 2024 10-K

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

Table of Contents 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: 001-38

February 27, 2024 EX-99.1

Denali Therapeutics Announces $500 million Private Placement Equity Financing

Exhibit 99.1 Denali Therapeutics Announces $500 million Private Placement Equity Financing SOUTH SAN FRANCISCO, Calif., February 27, 2024 – Denali Therapeutics Inc. (Nasdaq: DNLI), a biopharmaceutical company developing a broad portfolio of product candidates engineered to cross the blood-brain barrier (BBB) for the treatment of neurodegenerative diseases and lysosomal storage diseases, today anno

February 27, 2024 EX-10.1

Securities Purchase Agreement, dated February 27, 2024, by and among the Company and the Purchasers named therein

Exhibit 10.1 DENALI THERAPEUTICS INC. SECURITIES PURCHASE AGREEMENT This Securities Purchase Agreement (the “Agreement”) is made as of February 27, 2024 (the “Effective Date”), by and among Denali Therapeutics Inc., a Delaware corporation (the “Company”), and each of the purchasers whose names and addresses are set forth on the signature pages hereof (each, a “Purchaser” and, collectively, the “Pu

February 27, 2024 8-K

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): February 27, 2024 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Emp

February 27, 2024 8-K

Regulation FD Disclosure, Entry into a Material Definitive Agreement, Unregistered Sales of Equity Securities, 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): February 27, 2024 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Emp

February 27, 2024 EX-4.1

Form of Pre-Funded Warrant

Exhibit 4.1 THESE SECURITIES REPRESENTED HEREBY AND THE SECURITIES ISSUABLE UPON EXERCISE OF THESE SECURITIES HAVE NOT BEEN REGISTERED WITH THE SECURITIES AND EXCHANGE COMMISSION OR THE SECURITIES COMMISSION OF ANY STATE BUT HAVE BEEN OR WILL BE ISSUED IN RELIANCE UPON AN EXEMPTION FROM REGISTRATION UNDER THE SECURITIES ACT OF 1933, AS AMENDED, AND, ACCORDINGLY, MAY NOT BE TRANSFERRED UNLESS (i) S

February 27, 2024 EX-99.1

Denali Therapeutics Reports Fourth Quarter and Full Year 2023 Financial Results and Business Highlights

Exhibit 99.1 Denali Therapeutics Reports Fourth Quarter and Full Year 2023 Financial Results and Business Highlights SOUTH SAN FRANCISCO, Calif., – February 27, 2024 – Denali Therapeutics Inc. (Nasdaq: DNLI), a biopharmaceutical company developing a broad portfolio of product candidates engineered to cross the blood-brain barrier (BBB) for the treatment of neurodegenerative diseases and lysosomal

February 27, 2024 EX-10.2

Nominating Agreement by and among the Company and Investor

Exhibit 10.2 NOMINATING AGREEMENT THIS NOMINATING AGREEMENT (this “Agreement”), dated as of February [29], 2024, is by and between Denali Therapeutics Inc., a Delaware corporation (the “Company”) and Baker Brothers Life Sciences, L.P. and 667, L.P. (collectively, the “Investor”). WHEREAS, the Company and the Investor are parties to that certain Securities Purchase Agreement dated February 27, 2024

February 16, 2024 8-K

Regulation FD Disclosure

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 16, 2024 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Emp

February 13, 2024 SC 13G/A

DNLI / Denali Therapeutics Inc. / BRATTON DOUGLAS K Passive Investment

SC 13G/A 1 formsc13ga-denali.htm UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 5)* DENALI THERAPEUTICS INC. (Name of Issuer) Common Stock, Par Value $0.01 Per Share (Title of Class of Securities) 24823R105 (CUSIP Number) December 31, 2023 (Date of Event which Requires Filing of this Statement) Check the

February 13, 2024 SC 13G/A

DNLI / Denali Therapeutics Inc. / VANGUARD GROUP INC - SCHEDULE 13G/A Passive Investment

SC 13G/A 1 tv0744-denalitherapeuticsinc.htm SCHEDULE 13G/A SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 Schedule 13G Under the Securities Exchange Act of 1934 (Amendment No.: 5)* Name of issuer: Denali Therapeutics Inc Title of Class of Securities: Common Stock CUSIP Number: 24823R105 Date of Event Which Requires Filing of this Statement: December 29, 2023 Check the appropriate box to

February 12, 2024 SC 13G/A

DNLI / Denali Therapeutics Inc. / BIOGEN INC. - SC 13G/A Passive Investment

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)* DENALI THERAPEUTICS INC. (Name of Issuer) Common Stock, $0.01 par value (Title of Class of Securities) 24823R105 (CUSIP Number) December 31, 2023 (Date of Event Which Requires Filing of this Statement) Check the appropriate box to designate the

February 8, 2024 SC 13G

DNLI / Denali Therapeutics Inc. / WELLINGTON MANAGEMENT GROUP LLP - SEC SCHEDULE 13G Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. )* Denali Therapeutics Inc. (Name of Issuer) Common Stock (Title of Class of Securities) 24823R105 (CUSIP Number) December 29, 2023 (Date of Event Which Requires Filing of this Statement) Check the appropriate box to designate the rule pursuant to which this

January 30, 2024 SC 13G/A

DNLI / Denali Therapeutics Inc. / Temasek Holdings (Private) Ltd - 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 § 240.13d-1(b), (c) AND (d) AND AMENDMENTS THERETO FILED PURSUANT TO § 240.13d-2 UNDER THE SECURITIES EXCHANGE ACT OF 1934 (Amendment No. 1 )* Denali Therapeutics Inc. (Name of Issuer) Common Stock, par value $0.01 per share (Title of Class of Se

January 8, 2024 8-K

Regulation FD Disclosure, 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): January 8, 2024 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Emplo

January 8, 2024 EX-99.1

Denali Therapeutics Announces Key Anticipated 2024 Milestones and Priorities to Further Advance Its Therapeutics Portfolio for Neurodegeneration and Lysosomal Storage Diseases

Exhibit 99.1 Denali Therapeutics Announces Key Anticipated 2024 Milestones and Priorities to Further Advance Its Therapeutics Portfolio for Neurodegeneration and Lysosomal Storage Diseases •Complete enrollment in Denali-led, late-stage programs for MPS II and ALS, and establish commercial readiness •Advance broad clinical-stage portfolio of seven therapeutic product candidates across neurodegenera

November 7, 2023 EX-99.1

Denali Therapeutics Reports Third Quarter 2023 Financial Results and Business Highlights

Exhibit 99.1 Denali Therapeutics Reports Third Quarter 2023 Financial Results and Business Highlights SOUTH SAN FRANCISCO, Calif., – November 7, 2023 – Denali Therapeutics Inc. (Nasdaq: DNLI), a biopharmaceutical company developing a broad portfolio of product candidates engineered to cross the blood-brain barrier (BBB) for the treatment of neurodegenerative diseases and lysosomal storage diseases

November 7, 2023 8-K

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 7, 2023 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Empl

November 7, 2023 10-Q

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

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 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 Numbe

November 7, 2023 EX-10.1

Amendment to Definitive LRRK2 Agreement and Waiver of and Amendment to Right of First Negotiation, Option, and License Agreement.

Exhibit 10.1 Amendment to Definitive LRRK2 Agreement and Waiver of and Amendment to Right of First Negotiation, Option, and License Agreement Reference is hereby made to the Definitive LRRK2 Collaboration and License Agreement, entered into as of October 4, 2020 (the “LRRK2 Agreement”), by and between Denali Therapeutics Inc., a Delaware corporation with its principal place of business located at

August 21, 2023 8-K

Entry into a Material Definitive Agreement

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 17, 2023 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Emplo

August 8, 2023 EX-99.1

Denali Therapeutics Reports Second Quarter 2023 Financial Results and Business Highlights

Exhibit 99.1 Denali Therapeutics Reports Second Quarter 2023 Financial Results and Business Highlights SOUTH SAN FRANCISCO, Calif., – August 8, 2023 – Denali Therapeutics Inc. (Nasdaq: DNLI), a biopharmaceutical company developing a broad portfolio of product candidates engineered to cross the blood-brain barrier (BBB) for the treatment of neurodegenerative diseases and lysosomal storage diseases,

August 8, 2023 10-Q

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

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 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: 00

August 8, 2023 8-K

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 8, 2023 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Employ

June 20, 2023 EX-99.1

Denali Therapeutics Announces Robust Reduction in Neurofilament Light (NfL) with DNL310 (ETV:IDS) Treatment in MPS II (Hunter Syndrome)

Exhibit 99.1 Denali Therapeutics Announces Robust Reduction in Neurofilament Light (NfL) with DNL310 (ETV:IDS) Treatment in MPS II (Hunter Syndrome) •Interim results demonstrate average reduction of 64% (p <0.001) from baseline in serum NfL after 2 years of dosing with DNL310 in Phase 1/2 study •FDA has recommended assessment of NfL, a marker of neuroaxonal damage, as a possible biomarker in MPS I

June 20, 2023 8-K

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 20, 2023 Denali 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 20, 2023 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Employe

June 5, 2023 8-K

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 5, 2023 Denali 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 5, 2023 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of incorporation) (Commission F

June 2, 2023 8-K

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 1, 2023 Denali 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 1, 2023 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Employer

May 8, 2023 10-Q

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

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 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: 0

May 8, 2023 8-K

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 8, 2023 Denali 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 8, 2023 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Employer

May 8, 2023 EX-99.1

Denali Therapeutics Reports First Quarter 2023 Financial Results and Business Highlights

Exhibit 99.1 Denali Therapeutics Reports First Quarter 2023 Financial Results and Business Highlights SOUTH SAN FRANCISCO – May 8, 2023 – Denali Therapeutics Inc. (Nasdaq: DNLI), a biopharmaceutical company developing a broad portfolio of product candidates engineered to cross the blood-brain barrier (BBB) for the treatment of neurodegenerative diseases and lysosomal storage diseases, today report

April 18, 2023 DEF 14A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A PROXY STATEMENT PURSUANT TO SECTION 14(a) OF THE SECURITIES EXCHANGE ACT OF 1934

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A PROXY STATEMENT PURSUANT TO SECTION 14(a) OF THE SECURITIES EXCHANGE ACT OF 1934 Filed by the Registrant x Filed by a Party other than the Registrant ¨ Check the appropriate box: ¨ Preliminary Proxy Statement ¨ Confidential, for Use of the Commission Only (as permitted by Rule 14a‑6(e)(2)) x Defi

April 18, 2023 DEFA14A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A PROXY STATEMENT PURSUANT TO SECTION 14(a) OF THE SECURITIES EXCHANGE ACT OF 1934

DEFA14A 1 a2023fy22defa14aproxy-defi.htm DEFA14A UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A PROXY STATEMENT PURSUANT TO SECTION 14(a) OF THE SECURITIES EXCHANGE ACT OF 1934 Filed by the Registrant x Filed by a Party other than the Registrant ¨ Check the appropriate box: ¨ Preliminary Proxy Statement ¨ Confidential, for Use of the Commission Only (as permit

March 30, 2023 SC 13G

DNLI / Denali Therapeutics Inc / Temasek Holdings (Private) Ltd - SC 13G Passive Investment

SC 13G 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 UNDER THE SECURITIES EXCHANGE ACT OF 1934 (Amendment No. )* Denali Therapeutics Inc. (Name of Issuer) Common Stock, par value $0.01 per share (Title of Class of Securi

February 27, 2023 10-K

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

Table of Contents 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, 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: 001-38

February 27, 2023 EX-4.4

Description of the Registrant’s Common Stock.

Exhibit 4.4 DESCRIPTION OF THE REGISTRANT’S SECURITIES REGISTERED PURSUANT TO SECTION 12 OF THE SECURITIES EXCHANGE ACT OF 1934 The following summary describes our common stock and preferred stock, as well as certain provisions of our amended and restated certificate of incorporation and amended and restated bylaws. This summary does not purport to be complete and is qualified in its entirety by t

February 27, 2023 EX-10.127

Amendment No. 7 to Development and Manufacturing Services Agreement between the Registrant and Lonza Sales AG, dated March 29, 2021.

Exhibit 10.12.7 AMENDMENT NO. 7 to the DEVELOPMENT AND MANUFACTURING SERVICES AGREEMENT dated 6th September 2017 between LONZA SALES AG and LONZA AG and DENALI THERAPEUTICS INC. 24Mar21/TS/DC/825148 1 THIS AMENDMENT is made on the Mar 29, 2021 BETWEEN LONZA SALES AG incorporated and registered in Switzerland whose registered office is at Muenchensteinerstrasse 38, CH-4002, Basel, Switzerland (here

February 27, 2023 EX-99.1

Denali Therapeutics Reports Fourth Quarter and Full Year 2022 Financial Results and Business Highlights

Exhibit 99.1 Denali Therapeutics Reports Fourth Quarter and Full Year 2022 Financial Results and Business Highlights SOUTH SAN FRANCISCO – February 27, 2023 – Denali Therapeutics Inc. (Nasdaq: DNLI), a biopharmaceutical company developing a broad portfolio of product candidates engineered to cross the blood-brain barrier (BBB) for the treatment of neurodegenerative diseases and lysosomal storage d

February 27, 2023 EX-10.128

Amendment No. 8 to Development and Manufacturing Services Agreement between the Registrant and Lonza Sales AG, dated September 8, 2022.

Exhibit 10.12.8 *** Certain information has been excluded from this agreement because it is both (i) not material and (ii) would be competitively harmful if publicly disclosed. AMENDMENT NO. 8 to the Agreement dated 6th September 2017 between Lonza Sales AG And Lonza AG and Denali Therapeutics Inc. With respect to: Quality Agreement 19Jul22/MM/EP(FA)/B26647 Page 1 of 7 THIS AMENDMENT is made the 8

February 27, 2023 8-K

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 27, 2023 Denali Therapeu

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 27, 2023 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Emp

February 27, 2023 EX-21.1

Subsidiaries of the Registrant.

Exhibit 21.1 SUBSIDIARIES Subsidiary Name Jurisdiction of Incorporation or Organization Denali BBB Holding Limited United Kingdom Denali Therapeutics CH GmbH Switzerland

February 27, 2023 S-8

As filed with the Securities and Exchange Commission on February 27, 2023

As filed with the Securities and Exchange Commission on February 27, 2023 Registration No.

February 27, 2023 EX-10.129

Amendment No. 9 to Development and Manufacturing Services Agreement between the Registrant and Lonza Sales AG, dated December 7, 2022.

Exhibit 10.12.9 AMENDMENT NO. 9 to the DEVELOPMENT AND MANUFACTURING SERVICES AGREEMENT dated 6th September 2017 between LONZA SALES AG and LONZA AG and DENALI THERAPEUTICS INC. B27002/MM/RC/18Nov22 THIS AMENDMENT is made on the 07-Dec-2022 I 12:56:23 GET BETWEEN LONZA SALES AG incorporated and registered in Switzerland whose registered office is at Muenchensteinerstrasse 38, CH-4002, Basel, Switz

February 27, 2023 EX-FILING FEES

Filing Fee Table

Exhibit 107.1 Calculation of Filing Fee Tables Form S-8 (Form Type) Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Table 1 – Newly Registered Securities 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 Equity Common Stock, $0.01

February 13, 2023 SC 13G/A

DNLI / Denali Therapeutics Inc / BRATTON DOUGLAS K Passive Investment

SC 13G/A 1 formsc13ga-denali.htm UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 4)* DENALI THERAPEUTICS INC. (Name of Issuer) Common Stock, Par Value $0.01 Per Share (Title of Class of Securities) 24823R105 (CUSIP Number) December 31, 2022 (Date of Event which Requires Filing of this Statement) Check the

February 9, 2023 SC 13G/A

DNLI / Denali Therapeutics Inc / VANGUARD GROUP INC - SCHEDULE 13G/A Passive Investment

SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 Schedule 13G Under the Securities Exchange Act of 1934 (Amendment No.: 4)* Name of issuer: Denali Therapeutics Inc. Title of Class of Securities: Common Stock CUSIP Number: 24823R105 Date of Event Which Requires Filing of this Statement: December 30, 2022 Check the appropriate box to designate the rule pursuant to which this Schedule is fil

January 9, 2023 EX-99.1

Denali Therapeutics Announces Key Anticipated 2023 Milestones for Its Therapeutic Portfolio for Neurodegeneration and Lysosomal Storage Diseases

Exhibit 99.1 Denali Therapeutics Announces Key Anticipated 2023 Milestones for Its Therapeutic Portfolio for Neurodegeneration and Lysosomal Storage Diseases •Four programs expected to progress in late-stage clinical studies for MPS II (Hunter syndrome), ALS, and Parkinson’s disease •Further validation and expansion of Transport Vehicle (TV) technology, including multiple interim clinical data rea

January 9, 2023 8-K

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 9, 2023 Denali 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): January 9, 2023 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Emplo

November 3, 2022 8-K

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 3, 2022 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Empl

November 3, 2022 EX-99.1

Denali Therapeutics Reports Third Quarter 2022 Financial Results and Business Highlights

Exhibit 99.1 Denali Therapeutics Reports Third Quarter 2022 Financial Results and Business Highlights SOUTH SAN FRANCISCO ? November 3, 2022 ? Denali Therapeutics Inc. (Nasdaq: DNLI), a biopharmaceutical company developing a broad portfolio of product candidates engineered to cross the blood-brain barrier (BBB) for neurodegenerative diseases, today reported financial results for the third quarter

November 3, 2022 10-Q

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

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 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 Numbe

October 20, 2022 EX-99.1

Denali Therapeutics Announces Pricing of $275 Million Public Offering of Common Stock

Exhibit 99.1 Denali Therapeutics Announces Pricing of $275 Million Public Offering of Common Stock SOUTH SAN FRANCISCO, CA ? Oct. 19, 2022 - Denali Therapeutics Inc. (NASDAQ: DNLI) today announced the pricing of its underwritten public offering of 10,377,359 shares of its common stock at a price to the public of $26.50 per share. All of the shares are to be sold by Denali Therapeutics. In addition

October 20, 2022 424B5

10,377,359 shares Common Stock

Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No. 333-263107 PROSPECTUS SUPPLEMENT (To prospectus dated February 28, 2022) 10,377,359 shares Common Stock We are offering 10,377,359 shares of our common stock in this offering. Our common stock is quoted on the Nasdaq Global Select Market under the symbol ?DNLI". On October 19, 2022, the last reported sale price of our common stock

October 20, 2022 EX-1.1

as representatives of the several underwriters named therein

Exhibit 1.1 Denali Therapeutics Inc. Common Stock, par value $0.01 per share Underwriting Agreement October 19, 2022 Goldman Sachs & Co. LLC J.P. Morgan Securities LLC As representatives (the ?Representatives?) of the several Underwriters named in Schedule I hereto, c/o Goldman Sachs & Co. LLC 200 West Street, New York, New York 10282-2198 c/o J.P. Morgan Securities LLC 383 Madison Avenue New York

October 20, 2022 EX-FILING FEES

Calculation of Filing Fee Tables (Form Type) Denali Therapeutics Inc. (Exact Name of Registrant as Specified in its Charter) Table 1 – Newly Registered and Carry Forward Securities

Exhibit 107 Calculation of Filing Fee Tables 424(b)(5) (Form Type) Denali Therapeutics Inc.

October 20, 2022 8-K

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 19, 2022 Denali 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): October 19, 2022 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Empl

October 18, 2022 424B5

Subject to Completion Preliminary Prospectus Supplement dated October 18, 2022

Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No. 333-263107 The information in this preliminary prospectus supplement is not complete and may be changed. A registration statement relating to these securities has been filed with the Securities and Exchange Commission and is effective. This preliminary prospectus supplement and the accompanying prospectus are not an offer to sell

October 18, 2022 EX-99.2

Updated Financial Disclosure

Exhibit 99.2 Updated Financial Disclosure As of September 30, 2022, we estimate we had approximately $1.11 billion in cash, cash equivalents and marketable securities. This financial data as of September 30, 2022 is preliminary and is based on information available to management as of the date of this prospectus supplement and is subject to completion by management of our unaudited condensed conso

October 18, 2022 EX-99.1

Denali Therapeutics Announces Proposed Offering of Common Stock

Exhibit 99.1 Denali Therapeutics Announces Proposed Offering of Common Stock SOUTH SAN FRANCISCO, Calif. - Oct. 18, 2022 - Denali Therapeutics Inc. (NASDAQ: DNLI) today announced that it intends to offer and sell $250 million of shares of its common stock in an underwritten public offering. In addition, Denali Therapeutics intends to grant the underwriters a 30-day option to purchase up to an addi

October 18, 2022 8-K

Financial Statements and Exhibits, Results of Operations and Financial Condition, 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): October 18, 2022 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Empl

October 18, 2022 EX-99.3

RISK FACTORS

Exhibit 99.3 RISK FACTORS Investing in our securities involves a high degree of risk. You should carefully consider the risks discussed below, before making a decision about investing in our securities. The risks and uncertainties discussed below are not the only ones facing us. Additional risks and uncertainties not presently known to us, or that we currently see as immaterial, may also harm our

August 8, 2022 EX-99.1

Denali Therapeutics Reports Second Quarter 2022 Financial Results and Business Highlights

Exhibit 99.1 Denali Therapeutics Reports Second Quarter 2022 Financial Results and Business Highlights SOUTH SAN FRANCISCO ? August 8, 2022 ? Denali Therapeutics Inc. (Nasdaq: DNLI), a biopharmaceutical company developing a broad portfolio of product candidates engineered to cross the blood-brain barrier (BBB) for neurodegenerative diseases, today reported financial results for the second quarter

August 8, 2022 8-K

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 8, 2022 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Employ

August 8, 2022 10-Q

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

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 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: 00

July 5, 2022 8-K

Regulation FD Disclosure

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 4, 2022 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Employer

June 3, 2022 8-K

Financial Statements and Exhibits, Submission of Matters to a Vote of Security Holders

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 2, 2022 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Employer

May 5, 2022 EX-99.1

Denali Therapeutics Reports First Quarter 2022 Financial Results and Business Highlights

Exhibit 99.1 Denali Therapeutics Reports First Quarter 2022 Financial Results and Business Highlights SOUTH SAN FRANCISCO ? May 5, 2022 ? Denali Therapeutics Inc. (Nasdaq: DNLI), a biopharmaceutical company developing a broad portfolio of product candidates engineered to cross the blood-brain barrier (BBB) for neurodegenerative diseases, today reported financial results for the first quarter ended

May 5, 2022 10-Q

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

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 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, 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: 0

May 5, 2022 8-K

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 5, 2022 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Employer

April 19, 2022 DEFA14A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A PROXY STATEMENT PURSUANT TO SECTION 14(a) OF THE SECURITIES EXCHANGE ACT OF 1934

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A PROXY STATEMENT PURSUANT TO SECTION 14(a) OF THE SECURITIES EXCHANGE ACT OF 1934 Filed by the Registrant x Filed by a Party other than the Registrant ? Check the appropriate box: ? Preliminary Proxy Statement ? Confidential, for Use of the Commission Only (as permitted by Rule 14a?6(e)(2)) ? Definitive Proxy State

April 19, 2022 DEF 14A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A PROXY STATEMENT PURSUANT TO SECTION 14(a) OF THE SECURITIES EXCHANGE ACT OF 1934

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A PROXY STATEMENT PURSUANT TO SECTION 14(a) OF THE SECURITIES EXCHANGE ACT OF 1934 Filed by the Registrant x Filed by a Party other than the Registrant ? Check the appropriate box: ? Preliminary Proxy Statement ? Confidential, for Use of the Commission Only (as permitted by Rule 14a?6(e)(2)) x Defi

March 16, 2022 8-K

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers, 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): March 14, 2022 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of incorporation) (Commission

March 16, 2022 EX-99.1

Denali Therapeutics Appoints Alexander Schuth as Chief Operating and Financial Officer as Steve Krognes Transitions to Denali Board of Directors

Exhibit 99.1 Denali Therapeutics Appoints Alexander Schuth as Chief Operating and Financial Officer as Steve Krognes Transitions to Denali Board of Directors SOUTH SAN FRANCISCO, Calif., March 15, 2022 ? Denali Therapeutics Inc. (NASDAQ: DNLI), a biopharmaceutical company developing a broad portfolio of product candidates engineered to cross the blood-brain barrier (BBB) for neurodegenerative dise

February 28, 2022 10-K

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

Table of Contents 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, 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: 001-38

February 28, 2022 S-8

As filed with the Securities and Exchange Commission on February 28, 2022

As filed with the Securities and Exchange Commission on February 28, 2022 Registration No.

February 28, 2022 EX-FILING FEES

Calculation of Filing Fee Tables Form S-8 (Form Type) Denali Therapeutics Inc. (Exact name of registrant as specified in its charter)

Exhibit 107.1 Calculation of Filing Fee Tables Form S-8 (Form Type) Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Table 1 ? Newly Registered Securities 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 Equity Common Stock, $0.01

February 28, 2022 S-3ASR

As filed with the Securities and Exchange Commission on February 28, 2022

As filed with the Securities and Exchange Commission on February 28, 2022 Registration No.

February 28, 2022 EX-FILING FEES

Filing Fee Table.

EX-FILING FEES 2 s-3ex1071filingfeetable.htm EX-FILING FEES Exhibit 107.1 Calculation of Filing Fee Table Form S-3 (Form Type) Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Table 1 – Newly Registered and Carry Forward Securities Security Type Security Class Title Fee Calculation or Carry Forward Rule Amount Registered Proposed Maximum Offering Price Per Unit Maxim

February 28, 2022 EX-99.1

Denali Therapeutics Reports Fourth Quarter and Full Year 2021 Financial Results and Business Highlights

Exhibit 99.1 Denali Therapeutics Reports Fourth Quarter and Full Year 2021 Financial Results and Business Highlights SOUTH SAN FRANCISCO ? February 28, 2022 ? Denali Therapeutics Inc. (NASDAQ: DNLI), a biopharmaceutical company developing a broad portfolio of product candidates engineered to cross the blood-brain barrier (BBB) for neurodegenerative diseases, today reported financial results for th

February 28, 2022 8-K

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): February 28, 2022 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Emp

February 28, 2022 EX-10.15

Amended and Restated Outside Director Compensation Policy.

Exhibit 10.15 DENALI THERAPEUTICS INC. OUTSIDE DIRECTOR COMPENSATION POLICY Initially adopted and approved November 10, 2017; most recently amended and restated February 3, 2022 (the ?Restatement Date?) Denali Therapeutics Inc. (the ?Company?) believes that granting equity and cash compensation to members of its Board of Directors (the ?Board,? and members of the Board, the ?Directors?) represents

February 28, 2022 EX-21.1

Subsidiaries of the Registrant

Exhibit 21.1 SUBSIDIARIES Subsidiary Name Jurisdiction of Incorporation or Organization Denali BBB Holding Limited United Kingdom Denali Therapeutics CH GmbH Switzerland

February 28, 2022 EX-1.2

Equity Distribution Agreement, dated February 28, 2022 between the Registrant and Goldman Sachs & Co. LLC, SVB Securities LLC and Cantor Fitzgerald & Co.

Exhibit 1.2 DENALI THERAPEUTICS INC. Common Stock ($0.01 par value) Having an Aggregate Offering Price of up to $400,000,000 Equity Distribution Agreement February 28, 2022 Goldman, Sachs & Co. LLC 200 West Street New York, New York 10282 SVB Securities LLC 255 California Street San Francisco, CA 94111 Cantor Fitzgerald & Co. 499 Park Avenue New York, NY 10022 Ladies and Gentlemen: Denali Therapeu

February 28, 2022 EX-4.3

Form of Indenture.

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

February 28, 2022 EX-4.3

Description of the Registrant’s Common Stock.

Exhibit 4.3 DESCRIPTION OF THE REGISTRANT?S SECURITIES REGISTERED PURSUANT TO SECTION 12 OF THE SECURITIES EXCHANGE ACT OF 1934 The following summary describes our common stock and preferred stock, as well as certain provisions of our amended and restated certificate of incorporation and amended and restated bylaws. This summary does not purport to be complete and is qualified in its entirety by t

February 28, 2022 EX-1.1

Equity Distribution Agreement between the Company and Goldman Sachs & Co. LLC, SVB Securities LLC and Cantor Fitzgerald & Co., dated as of February 28, 2022

Exhibit 1.1 DENALI THERAPEUTICS INC. Common Stock ($0.01 par value) Having an Aggregate Offering Price of up to $400,000,000 Equity Distribution Agreement February 28, 2022 Goldman, Sachs & Co. LLC 200 West Street New York, New York 10282 SVB Securities LLC 255 California Street San Francisco, CA 94111 Cantor Fitzgerald & Co. 499 Park Avenue New York, NY 10022 Ladies and Gentlemen: Denali Therapeu

February 28, 2022 8-K

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): February 28, 2022 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Emp

February 14, 2022 8-K

Regulation FD Disclosure

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 14, 2022 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of incorporation) (Commiss

February 14, 2022 SC 13G/A

DNLI / Denali Therapeutics Inc / BRATTON DOUGLAS K Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 3)* DENALI THERAPEUTICS INC. (Name of Issuer) Common Stock, Par Value $0.01 Per Share (Title of Class of Securities) 24823R105 (CUSIP Number) December 31, 2021 (Date of Event Which Requires Filing of this Statement) Check the appropriate box to designate the

February 10, 2022 EX-99.1

Denali Therapeutics Announces Continued Progress in DNL310 (ETV:IDS) Program for MPS II (Hunter Syndrome) Supporting Planned Initiation of Phase 2/3 Clinical Trial

Exhibit 99.1 Denali Therapeutics Announces Continued Progress in DNL310 (ETV:IDS) Program for MPS II (Hunter Syndrome) Supporting Planned Initiation of Phase 2/3 Clinical Trial ?Longer-term data in 20 patients show sustained normalization to healthy levels of CSF heparan sulfate and improvements in markers of lysosomal function consistent with durable CNS activity, now with up to one year of intra

February 10, 2022 8-K

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): February 10, 2022 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Emp

February 9, 2022 SC 13G/A

DNLI / Denali Therapeutics Inc / VANGUARD GROUP INC - SCHEDULE 13G/A Passive Investment

SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 Schedule 13G Under the Securities Exchange Act of 1934 (Amendment No.: 3)* Name of issuer: Denali Therapeutics Inc. Title of Class of Securities: Common Stock CUSIP Number: 24823R105 Date of Event Which Requires Filing of this Statement: December 31, 2021 Check the appropriate box to designate the rule pursuant to which this Schedule is fil

February 8, 2022 SC 13G/A

DNLI / Denali Therapeutics Inc / ARCH Venture Fund VIII, L.P. - ARCH VENTURE FUND VIII, L.P. - DENALI THERAPEUTICS INC. -- SCH 13G/A (#3E) Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 3 - Exit Filing)* Denali Therapeutics Inc. (Name of Issuer) Common Stock par value $0.01 per share (Title of Class of Securities) 24823R105 (CUSIP Number) December 31, 2021 (Date of Event Which Requires Filing of This Statement) Check the appropriate box to

February 7, 2022 EX-99.1

Denali Therapeutics Announces Appointment of Erik Harris to Board of Directors

Exhibit 99.1 Denali Therapeutics Announces Appointment of Erik Harris to Board of Directors SOUTH SAN FRANCISCO, Calif., February 7, 2022 - Denali Therapeutics Inc. (NASDAQ: DNLI), a biopharmaceutical company developing a broad portfolio of product candidates engineered to cross the blood-brain barrier (BBB) for neurodegenerative diseases, today announced that Erik Harris has joined the Board of D

February 7, 2022 8-K

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers, 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): February 7, 2022 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Empl

January 10, 2022 8-K

Regulation FD Disclosure, 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): January 10, 2022 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Empl

January 10, 2022 EX-99.1

Denali Therapeutics Announces Progression and Expansion of Broad Therapeutic Portfolio for Neurodegeneration and Expected Key Milestones in 2022

Exhibit 99.1 Denali Therapeutics Announces Progression and Expansion of Broad Therapeutic Portfolio for Neurodegeneration and Expected Key Milestones in 2022 ?Key data readouts to include additional Phase 1/2 data on DNL310 (ETV:IDS) in MPS II (Hunter syndrome) and the first clinical data on DNL919 (ATV:TREM2), both potentially further validating Denali?s Transport Vehicle (TV) platform; in additi

November 17, 2021 EX-99.1

Denali Therapeutics Announces Strategic Partner Takeda Exercises Option to Co-Develop and Co-Commercialize DNL593 (PTV:PGRN) — Companies to advance clinical development of DNL593 as a brain-penetrant progranulin replacement therapy for frontotemporal

Exhibit 99.1 Denali Therapeutics Announces Strategic Partner Takeda Exercises Option to Co-Develop and Co-Commercialize DNL593 (PTV:PGRN) ? Companies to advance clinical development of DNL593 as a brain-penetrant progranulin replacement therapy for frontotemporal dementia-granulin (FTD-GRN) ? SOUTH SAN FRANCISCO, Calif., November 17, 2021 - Denali Therapeutics Inc. (NASDAQ: DNLI), a biopharmaceuti

November 17, 2021 8-K

Regulation FD Disclosure, 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): November 17, 2021 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Emp

November 4, 2021 8-K

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 4, 2021 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Empl

November 4, 2021 10-Q

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

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 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, 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 Numbe

November 4, 2021 EX-99.1

Denali Therapeutics Reports Third Quarter 2021 Financial Results and Business Highlights

Exhibit 99.1 Denali Therapeutics Reports Third Quarter 2021 Financial Results and Business Highlights SOUTH SAN FRANCISCO ? November 4, 2021 ? Denali Therapeutics Inc. (NASDAQ: DNLI), a biopharmaceutical company developing a broad portfolio of product candidates engineered to cross the blood-brain barrier (BBB) for neurodegenerative diseases, today reported financial results for the third quarter

August 4, 2021 10-Q

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

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 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: 00

August 4, 2021 8-K

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 4, 2021 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Employ

August 4, 2021 EX-99.1

Denali Therapeutics Reports Second Quarter 2021 Financial Results and Business Highlights

Exhibit 99.1 Denali Therapeutics Reports Second Quarter 2021 Financial Results and Business Highlights SOUTH SAN FRANCISCO ? August 4, 2021 ? Denali Therapeutics Inc. (NASDAQ: DNLI), a biopharmaceutical company developing a broad portfolio of product candidates engineered to cross the blood-brain barrier (BBB) for neurodegenerative diseases, today reported financial results for the second quarter

August 4, 2021 EX-10.1

Side Letter between the Registrant and F-star Gamma Limited, dated June 30, 2021.

Exhibit 10.1 From: Denali Therapeutics Inc. 161 Oyster Point Blvd. South San Francisco CA 94080 U.S.A. BBB Holding Ltd Hill House 1 Little New Street London, United Kingdom EC4A 3TR To: F-star Biotechnology Limited Eddeva B920 Babraham Research Campus Cambridge, United Kingdom CB22 3AT Attn: Chief Executive Officer F-star Biotechnologische Forschungs- und Entwicklungsges.m.b.h. C/O - F-star Biotec

July 26, 2021 8-K

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): July 25, 2021 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Employe

July 26, 2021 EX-99.1

Denali Therapeutics Announces Positive Interim Data from Phase 1/2 Study with ETV:IDS (DNL310) in Patients with the Lysosomal Storage Disease Hunter Syndrome (MPS II)

Exhibit 99.1 Denali Therapeutics Announces Positive Interim Data from Phase 1/2 Study with ETV:IDS (DNL310) in Patients with the Lysosomal Storage Disease Hunter Syndrome (MPS II) ?Rapid reduction and sustained normalization of heparan sulfate in CSF demonstrated robust and durable CNS activity with intravenous administration, and enhanced peripheral activity with reductions in urine and serum hep

June 4, 2021 8-K

Financial Statements and Exhibits, Submission of Matters to a Vote of Security Holders

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 2, 2021 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Employer

May 5, 2021 10-Q

Quarterly Report - 10-Q

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 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: 0

May 5, 2021 EX-10.1

Amended and Restated Outside Director Compensation Policy

Exhibit 10.1 DENALI THERAPEUTICS INC. OUTSIDE DIRECTOR COMPENSATION POLICY Initially adopted and approved November 10, 2017; most recently amended and restated April 16, 2021 (the ?Restatement Date?) Denali Therapeutics Inc. (the ?Company?) believes that granting equity and cash compensation to members of its Board of Directors (the ?Board,? and members of the Board, the ?Directors?) represents an

May 3, 2021 EX-99.1

Denali Therapeutics Reports First Quarter 2021 Financial Results and Business Highlights

Exhibit 99.1 Denali Therapeutics Reports First Quarter 2021 Financial Results and Business Highlights SOUTH SAN FRANCISCO ? May 3, 2021 ? Denali Therapeutics Inc. (NASDAQ: DNLI), a biopharmaceutical company developing a broad portfolio of product candidates engineered to cross the blood-brain barrier (BBB) for neurodegenerative diseases, today reported financial results for the first quarter ended

May 3, 2021 8-K

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 3, 2021 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Employer

April 22, 2021 DEF 14A

- DEF 14A

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A PROXY STATEMENT PURSUANT TO SECTION 14(a) OF THE SECURITIES EXCHANGE ACT OF 1934 Filed by the Registrant x Filed by a Party other than the Registrant ? Check the appropriate box: ? Preliminary Proxy Statement ? Confidential, for Use of the Commission Only (as permitted by Rule 14a?6(e)(2)) x Defi

April 22, 2021 DEFA14A

- DEFA14A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A PROXY STATEMENT PURSUANT TO SECTION 14(a) OF THE SECURITIES EXCHANGE ACT OF 1934 Filed by the Registrant x Filed by a Party other than the Registrant ? Check the appropriate box: ? Preliminary Proxy Statement ? Confidential, for Use of the Commission Only (as permitted by Rule 14a?6(e)(2)) ? Definitive Proxy State

February 26, 2021 EX-10.12.6

Amendment No. 6 to Development and Manufacturing Services Agreement between the Registrant and Lonza Sales AG, dated December 8, 2020.

Exhibit 10.12.6 Amendment No. 6 to the DEVELOPMENT AND MANUFACTURING SERVICES AGREEMENT Dated 6th September 2017 Between LONZA SALES AG and DENALI THERAPEUTICS lNC. THIS Amendment is made the 8th day of December, 2020 BETWEEN LONZA SALES AG, of Muenchensteinerstrasse 38, Ch-4002 Basel, Switzerland ("Lonza"); LONZA AG of Muenchensteinerstrasse 38, Ch-4002 Basel, Switzerland; and DENALI THERAPEUTICS

February 26, 2021 EX-10.12.5

Amendment No. 3 to Development and Manufacturing Services Agreement between the Registrant and Lonza Sales AG, dated September 11, 2020.

Exhibit 10.12.5 AMENDMENT num, 3 to the Development and Manufacturing Services Agreement of 6 September 2017 BETWEEN 1. LONZA SALES AG of Muenchensteinerstrasse 38, CH-4002 Basel, Switzerland (?Lonza?), and 2. DENALI THERAPEUTICS INC. of 151 Oyster Point Blvd, 2nd Floor, South San Francisco, CA 94080 U.S.A. (?Customer?). Recitals WHEREAS, Lonza and Customer have entered into a Development and Manu

February 26, 2021 10-K

Annual Report - 10-K

Table of Contents 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: 001-38

February 26, 2021 EX-4.3

Description of the registrant’s common stock.

Exhibit 4.3 DESCRIPTION OF THE REGISTRANT?S SECURITIES REGISTERED PURSUANT TO SECTION 12 OF THE SECURITIES EXCHANGE ACT OF 1934 The following summary describes our common stock and preferred stock, as well as certain provisions of our amended and restated certificate of incorporation and amended and restated bylaws. This summary does not purport to be complete and is qualified in its entirety by t

February 26, 2021 S-8

- S-8

As filed with the Securities and Exchange Commission on February 26, 2021 Registration No.

February 26, 2021 EX-10.12.4

Amendment No. 5 to Development and Manufacturing Services Agreement between the Registrant and Lonza Sales AG, dated August 6, 2019.

Exhibit 10.12.4 Amendment No. 5 to the DEVELOPMENT AND MANUFACTURING SERVICES AGREEMENT Dated 6th September 2017 Between LONZA SALES AG and DENALI THERAPEUTICS INC. THIS Amendment is made the 6th day of August 2019 BETWEEN LONZA SALES AG, of Muenchensteinerstrasse 38, Ch-4002 Basel, Switzerland ("Lonza") and DENALI THERAPEUTICS INC., of 151 Oyster Point Blvd, 2nd Floor, South San Francisco, CA 940

February 26, 2021 EX-21.1

Subsidiaries of the Registrant

EX-21.1 7 exhibit211q42020subsidiari.htm EX-21.1 Exhibit 21.1 SUBSIDIARIES Subsidiary Name Jurisdiction of Incorporation or Organization Denali BBB Holding Limited United Kingdom

February 26, 2021 EX-10.15

Amended and Restated Outside Director Compensation Policy.

Exhibit 10.15 DENALI THERAPEUTICS INC. OUTSIDE DIRECTOR COMPENSATION POLICY Initially adopted and approved November 10, 2017; most recently amended and restated February 5, 2021 (the ?Restatement Date?) Denali Therapeutics Inc. (the ?Company?) believes that granting equity and cash compensation to members of its Board of Directors (the ?Board,? and members of the Board, the ?Directors?) represents

February 25, 2021 EX-99.1

Denali Therapeutics Reports Full Year 2020 Financial Results and Business Highlights

Exhibit 99.1 Denali Therapeutics Reports Full Year 2020 Financial Results and Business Highlights SOUTH SAN FRANCISCO ? February 25, 2021 ? Denali Therapeutics Inc. (NASDAQ: DNLI), a biopharmaceutical company developing a broad portfolio of product candidates engineered to cross the blood-brain barrier (BBB) for neurodegenerative diseases, today reported financial results for the full year ended D

February 25, 2021 8-K

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): February 25, 2021 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Emp

February 16, 2021 SC 13G/A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 2)* Denali Therapeutics Inc. (Name of Issuer) Common Stock, $0.01 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. 2)* Denali Therapeutics Inc. (Name of Issuer) Common Stock, $0.01 par value per share (Title of Class of Securities) 24823R 10 5 (CUSIP Number) DECEMBER 31, 2020 (Date of Event Which Requires Filing of this Statement) Check the appropriate box to de

February 12, 2021 8-K

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): February 12, 2021 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Emp

February 12, 2021 SC 13G/A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 2)* DENALI THERAPEUTICS INC. (Name of Issuer) Common Stock, Par Value $0.01 Per Share (Title of Class of Sec

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 2)* DENALI THERAPEUTICS INC. (Name of Issuer) Common Stock, Par Value $0.01 Per Share (Title of Class of Securities) 24823R105 (CUSIP Number) December 31, 2020 (Date of Event which Requires Filing of this Statement) Check the appropriate box to designate the

February 12, 2021 EX-99.1

Denali Therapeutics Reports Positive Three-Month Data from Phase 1/2 Study with ETV:IDS (DNL310) in Patients with Hunter Syndrome (MPS II)

Exhibit 99.1 Denali Therapeutics Reports Positive Three-Month Data from Phase 1/2 Study with ETV:IDS (DNL310) in Patients with Hunter Syndrome (MPS II) ?Sustained normalization and further decreased levels of CSF glycosaminoglycan heparan sulfate, a key CNS disease biomarker, observed after three months of intravenous dosing ?Reductions in exploratory CSF biomarkers consistent with improved lysoso

February 10, 2021 8-K/A

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers, Financial Statements and Exhibits

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K/A 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 8, 2021 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Emp

February 10, 2021 SC 13G/A

SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 Schedule 13G Under the Securities Exchange Act of 1934 (Amendment No.: 2)*

SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 Schedule 13G Under the Securities Exchange Act of 1934 (Amendment No.: 2)* Name of issuer: Denali Therapeutics Inc. Title of Class of Securities: Common Stock CUSIP Number: 24823R105 Date of Event Which Requires Filing of this Statement: December 31, 2020 Check the appropriate box to designate the rule pursuant to which this Schedule is fil

February 5, 2021 8-K

Financial Statements and Exhibits, Other Events - 8-K

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 4, 2021 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of incorporation) (Commissi

February 5, 2021 EX-99.1

IN THE COURT OF CHANCERY OF THE STATE OF DELAWARE JOHN SOLAK, derivatively on behalf of DENALI THERAPEUTICS, INC., Plaintiff, v. VICKI L. SATO, Ph.D., RYAN J. WATTS, Ph.D., DOUGLAS G. COLE, M.D., JENNIFER COOK, JAY FLATLEY, PETER KLEIN, ROBERT T. NEL

EX-99.1 Exhibit 99.1 IN THE COURT OF CHANCERY OF THE STATE OF DELAWARE JOHN SOLAK, derivatively on behalf of DENALI THERAPEUTICS, INC., Plaintiff, v. VICKI L. SATO, Ph.D., RYAN J. WATTS, Ph.D., DOUGLAS G. COLE, M.D., JENNIFER COOK, JAY FLATLEY, PETER KLEIN, ROBERT T. NELSEN, DAVID P. SCHENKEIN, M.D. and MARC TESSIER-LAVIGNE, Ph.D., Defendants, and DENALI THERAPEUTICS, INC., a Delaware corporation,

February 2, 2021 SC 13G/A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 2)* Denali Therapeutics Inc. (Name of Issuer) Common Stock par value $0.01 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. 2)* Denali Therapeutics Inc. (Name of Issuer) Common Stock par value $0.01 per share (Title of Class of Securities) 24823R105 (CUSIP Number) December 31, 2020 (Date of Event Which Requires Filing of This Statement) Check the appropriate box to designate the

January 11, 2021 8-K

Regulation FD Disclosure, Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers, Financial Statements and Exhibits - 8-K

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 8, 2021 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Emplo

January 11, 2021 EX-99.2

Denali Therapeutics Announces Significant Program Progress and Expected Key Milestones in 2021 for Its Broad Therapeutic Portfolio in Neurodegeneration

Exhibit 99.2 Denali Therapeutics Announces Significant Program Progress and Expected Key Milestones in 2021 for Its Broad Therapeutic Portfolio in Neurodegeneration •Late-breaker presentation on 12-week data from Cohort A in Phase 1/2 study of DNL310 (ETV:IDS) in Hunter syndrome (MPS II) to be held at WORLD Symposium on February 12th •Following previously announced data on CSF GAG reduction with D

January 11, 2021 EX-99.1

Denali Therapeutics Announces Appointment of Nancy Thornberry to Board of Directors

Exhibit 99.1 Denali Therapeutics Announces Appointment of Nancy Thornberry to Board of Directors SOUTH SAN FRANCISCO, Calif., January 11, 2021 - Denali Therapeutics Inc. (NASDAQ: DNLI), a biopharmaceutical company developing a broad portfolio of product candidates engineered to cross the blood-brain barrier (BBB) for neurodegenerative diseases, today announced that Nancy Thornberry has joined the

November 10, 2020 EX-99.1

Denali Therapeutics Announces First Human Biomarker Proof of Concept for Its Transport Vehicle (TV) Technology Achieved in Phase 1/2 Study of ETV:IDS (DNL310) in Hunter Syndrome (MPS II)

Exhibit 99.1 Denali Therapeutics Announces First Human Biomarker Proof of Concept for Its Transport Vehicle (TV) Technology Achieved in Phase 1/2 Study of ETV:IDS (DNL310) in Hunter Syndrome (MPS II) •After four weekly intravenous doses of DNL310, a 76% mean reduction in CSF GAG levels (heparan sulfate) from baseline was observed, with normal healthy levels being achieved in four of five patients

November 10, 2020 8-K

Financial Statements and Exhibits, Other Events - 8-K

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 10, 2020 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Emp

November 5, 2020 8-K

Financial Statements and Exhibits, Results of Operations and Financial Condition - 8-K

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 5, 2020 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Empl

November 5, 2020 EX-99.1

Denali Therapeutics Reports Third Quarter 2020 Financial Results and Business Highlights

Exhibit 99.1 Denali Therapeutics Reports Third Quarter 2020 Financial Results and Business Highlights SOUTH SAN FRANCISCO – November 5, 2020 – Denali Therapeutics Inc. (NASDAQ: DNLI), a biopharmaceutical company developing a broad portfolio of product candidates engineered to cross the blood-brain barrier (BBB) for neurodegenerative diseases, today reported financial results for the third quarter

November 5, 2020 EX-10.4

Definitive LRRK2 Collaboration and License Agreement between the Registrant and Biogen Inc., dated October 4, 2020.

Exhibit 10.4 Definitive LRRK2 Collaboration and License Agreement Between Denali Therapeutics Inc., Biogen MA, Inc. and Biogen International GmbH Dated October 4, 2020 DEFINITIVE LRRK2 COLLABORATION AND LICENSE AGREEMENT This Definitive LRRK2 Collaboration and License Agreement (“Definitive LRRK2 Agreement”) is entered into as of October 4, 2020 (the “Effective Date”) by and between Denali Therape

November 5, 2020 EX-10.5

Definitive Right of First Negotiation, Option and License Agreement between the Registrant and Biogen Inc., dated October 6, 2020.

Exhibit 10.5 Right of First Negotiation, Option and License Agreement Between Denali Therapeutics Inc., Biogen MA, Inc. and Biogen International GmbH Dated October 6, 2020 [***] Right of First Negotiation, Option and License Agreement This Right of First Negotiation, Option and License Agreement (this “Agreement”) is entered into as of October 6, 2020 (the “Effective Date”) by and among Denali The

November 5, 2020 EX-10.2

Provisional LRRK2 Collaboration and License Agreement between the Registrant and Biogen Inc., dated August 5, 2020.

Exhibit 10.2 Provisional Collaboration and License Agreement Between Denali Therapeutics, Inc., Biogen MA, Inc. and Biogen International GmbH Dated August 5, 2020 PROVISIONAL COLLABORATION AND LICENSE AGREEMENT This Provisional Collaboration and License Agreement (“Provisional Collaboration and License Agreement”) is entered into as of August 5, 2020 (the “Execution Date”) by and between Denali Th

November 5, 2020 10-Q

Quarterly Report - 10-Q

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 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, 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 Numbe

November 5, 2020 EX-10.3

Standstill and Stock Restriction Agreement between the Registrant and Biogen Inc., dated September 22, 2020.

Exhibit 10.3 Final Form DENALI THERAPEUTICS INC. STANDSTILL AND STOCK RESTRICTION AGREEMENT This Standstill and Stock Restriction Agreement (this “Agreement”) is made as of September 22, 2020 (“Effective Date”) by and among Denali Therapeutics Inc., a Delaware corporation (the “Company”) and Biogen MA Inc., a Massachusetts corporation (the “Investor”). WHEREAS, the Investor has agreed to purchase

November 5, 2020 EX-10.1

Common Stock Purchase Agreement between the Registrant and Biogen Inc., dated August 5, 2020.

Exhibit 10.1 Execution Version COMMON STOCK PURCHASE AGREEMENT TABLE OF CONTENTS Page 1. Defined Terms Used in this Agreement 1 2. Purchase and Sale of Common Stock. 4 2.1 Sale and Issuance of Common Stock 4 2.2 Closing; Delivery; Adjustments 4 3. Representations and Warranties of the Company 4 3.1 Organization, Good Standing, Corporate Power and Qualification 5 3.2 Company Capitalization and Voti

November 5, 2020 EX-10.6

Amended and Restated Key Executive Change in Control and Severance Plan.

Exhibit 10.6 DENALI THERAPEUTICS INC. KEY EXECUTIVE CHANGE IN CONTROL AND SEVERANCE PLAN (Effective November 10, 2017) 1. Introduction. This Denali Therapeutics Inc. Key Executive Change in Control and Severance Plan (the “Plan”) has been established by Denali Therapeutics Inc., a Delaware corporation, for the benefit of a select group of management or highly compensated employees of the Employer,

October 7, 2020 EX-99.1

Denali Therapeutics Announces Closing of Collaboration and Share Purchase Agreements with Biogen

Exhibit 99.1 Denali Therapeutics Announces Closing of Collaboration and Share Purchase Agreements with Biogen SOUTH SAN FRANCISCO, Calif., Oct 7, 2020 — Denali Therapeutics Inc. (NASDAQ: DNLI), a biopharmaceutical company developing a broad portfolio of product candidates engineered to cross the blood-brain barrier (BBB) for neurodegenerative diseases, today announced the signing of a Definitive L

October 7, 2020 8-K

Regulation FD Disclosure, Entry into a Material Definitive Agreement, Financial Statements and Exhibits, Other Events - 8-K

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 4, 2020 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Emplo

September 28, 2020 SC 13G

DNLI / Denali Therapeutics Inc. / BIOGEN INC. - SC 13G Passive Investment

SC 13G UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 13G UNDER THE SECURITIES EXCHANGE ACT OF 1934 (Amendment No.) Denali Therapeutics Inc. (Name of Issuer) Common Stock (Title of Class of Securities) 24823R105 (CUSIP Number) September 22, 2020 (Date of Event Which Requires Filing of this Statement) Check the appropriate box to designate the rule pursuant to whic

August 20, 2020 8-K

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers, 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 17, 2020 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Emplo

August 20, 2020 8-K/A

Financial Statements and Exhibits, Submission of Matters to a Vote of Security Holders

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 8-K/A 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 3, 2020 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Employ

August 7, 2020 8-K

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 7, 2020 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Employ

August 7, 2020 10-Q

Quarterly Report - 10-Q

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 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, 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: 00

August 7, 2020 EX-99.1

Denali Therapeutics Reports Second Quarter 2020 Financial Results and Business Highlights

Exhibit 99.1 Denali Therapeutics Reports Second Quarter 2020 Financial Results and Business Highlights SOUTH SAN FRANCISCO – August 7, 2020 – Denali Therapeutics Inc. (NASDAQ: DNLI), a biopharmaceutical company developing a broad portfolio of product candidates engineered to cross the blood-brain barrier ("BBB") for neurodegenerative diseases, today reported financial results for the second quarte

August 6, 2020 8-K

Regulation FD Disclosure, Entry into a Material Definitive Agreement, Unregistered Sales of Equity Securities, 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 5, 2020 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Employ

August 6, 2020 EX-99.2

DENALI THERAPEUTICS ANNOUNCES DECISION TO ADVANCE DNL151 INTO LATE STAGE CLINICAL STUDIES IN PARKINSON’S PATIENTS

Exhibit 99.2 DENALI THERAPEUTICS ANNOUNCES DECISION TO ADVANCE DNL151 INTO LATE STAGE CLINICAL STUDIES IN PARKINSON’S PATIENTS •DNL151 selected to advance into two late stage studies in Parkinson’s disease in patients with a kinase activating mutation in LRRK2 and in patients with sporadic disease •Denali and collaboration partner Biogen are finalizing DNL151 clinical development plans and intend

August 6, 2020 EX-99.1

# # #

Exhibit 99.1 BIOGEN AND DENALI TO COLLABORATE ON LRRK2 PROGRAM FOR PARKINSON’S DISEASE AND CERTAIN TV PLATFORM-ENABLED PROGRAMS FOR NEURODEGENERATIVE DISEASES •Biogen to receive license to co-develop and co-commercialize Denali’s small molecule LRRK2 inhibitor program, expanding pipeline of potential therapies in Parkinson’s disease and other movement disorders •Biogen to receive exclusive option

June 8, 2020 8-K

Financial Statements and Exhibits, Submission of Matters to a Vote of Security Holders

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 3, 2020 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Employer

May 7, 2020 EX-99.1

Denali Therapeutics Reports First Quarter 2020 Financial Results and Provides COVID-19 Response Update

Exhibit 99.1 Denali Therapeutics Reports First Quarter 2020 Financial Results and Provides COVID-19 Response Update SOUTH SAN FRANCISCO – May 7, 2020 – Denali Therapeutics Inc. (NASDAQ: DNLI), a biopharmaceutical company developing a broad portfolio of product candidates engineered to cross the blood-brain barrier ("BBB") for neurodegenerative diseases, today reported financial results for the fir

May 7, 2020 EX-10.1

Amended and Restated Outside Director Compensation Policy

Exhibit 10.1 DENALI THERAPEUTICS INC. OUTSIDE DIRECTOR COMPENSATION POLICY Initially adopted and approved November 10, 2017; amended and restated March 24, 2020 (the “Restatement Date”) Denali Therapeutics Inc. (the “Company”) believes that granting equity and cash compensation to members of its Board of Directors (the “Board,” and members of the Board, the “Directors”) represents an effective too

May 7, 2020 8-K

Financial Statements and Exhibits, Results of Operations and Financial Condition, 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): May 7, 2020 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Employer

May 7, 2020 10-Q

Quarterly Report - 10-Q

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 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, 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: 0

April 22, 2020 DEF 14A

DNLI / Denali Therapeutics Inc. DEF 14A - - DEF 14A

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A PROXY STATEMENT PURSUANT TO SECTION 14(a) OF THE SECURITIES EXCHANGE ACT OF 1934 Filed by the Registrant x Filed by a Party other than the Registrant ¨ Check the appropriate box: ¨ Preliminary Proxy Statement ¨ Confidential, for Use of the Commission Only (as permitted by Rule 14a‑6(e)(2)) x Defi

April 22, 2020 DEFA14A

DNLI / Denali Therapeutics Inc. DEFA14A - - DEFA14A

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 14A PROXY STATEMENT PURSUANT TO SECTION 14(a) OF THE 
SECURITIES EXCHANGE ACT OF 1934 Filed by the Registrant x Filed by a Party other than the Registrant ¨ Check the appropriate box: ¨ Preliminary Proxy Statement ¨ Confidential, for Use of the Commission Only (as permitted by Rule 14a‑6(e)(2)) ¨ Definitive Proxy Stat

April 2, 2020 8-K

Financial Statements and Exhibits, Results of Operations and Financial Condition, 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 2, 2020 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Employe

April 2, 2020 EX-99.1

DENALI THERAPEUTICS PROVIDES PIPELINE AND BUSINESS UPDATE IN RESPONSE TO THE COVID-19 PANDEMIC

Exhibit 99.1 DENALI THERAPEUTICS PROVIDES PIPELINE AND BUSINESS UPDATE IN RESPONSE TO THE COVID-19 PANDEMIC SOUTH SAN FRANCISCO –- April 2, 2020 –- Denali Therapeutics Inc. (NASDAQ: DNLI), a biopharmaceutical company developing a broad portfolio of product candidates engineered to cross the blood-brain barrier (“BBB”) for neurodegenerative diseases, today provided an update on the expected pipelin

February 28, 2020 S-8

As filed with the Securities and Exchange Commission on February 27, 2020

As filed with the Securities and Exchange Commission on February 27, 2020 Registration No.

February 27, 2020 EX-4.3

Description of the registrant’s common stock.

Exhibit 4.3 DESCRIPTION OF THE REGISTRANT’S SECURITIES REGISTERED PURSUANT TO SECTION 12 OF THE SECURITIES EXCHANGE ACT OF 1934 The following summary describes our common stock and preferred stock, as well as certain provisions of our amended and restated certificate of incorporation and amended and restated bylaws. This summary does not purport to be complete and is qualified in its entirety by t

February 27, 2020 8-K

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): February 27, 2020 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Emp

February 27, 2020 EX-99.1

Denali Therapeutics Reports Full Year 2019 Financial Results and Business Highlights

Exhibit 99.1 Denali Therapeutics Reports Full Year 2019 Financial Results and Business Highlights SOUTH SAN FRANCISCO – February 27, 2020 – Denali Therapeutics Inc. (NASDAQ: DNLI), a biopharmaceutical company developing a broad portfolio of product candidates engineered to cross the blood-brain barrier ("BBB") for neurodegenerative diseases, today reported financial results for the fourth quarter

February 27, 2020 10-K

Annual Report - 10-K

Table of Contents 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, 2019 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: 001-38

February 27, 2020 EX-21.1

Subsidiaries of the Registrant

Exhibit 21.1 SUBSIDIARIES Subsidiary Name Jurisdiction of Incorporation or Organization Denali BBB Holding Limited United Kingdom

February 13, 2020 SC 13G/A

DNLI / Denali Therapeutics Inc. / ARCH Venture Fund VIII, L.P. - ARCH VENTURE FUND VIII, L.P. - DENALI THERAPEUTICS INC. -- SCHEDULE 13G/A(#1) Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 1)* Denali Therapeutics Inc. (Name of Issuer) Common Stock par value $0.01 per share (Title of Class of Securities) 24823R105 (CUSIP Number) December 31, 2019 (Date of Event Which Requires Filing of this Statement) Check the appropriate box to designate the

February 13, 2020 SC 13G/A

DNLI / Denali Therapeutics Inc. / Flagship Ventures Fund V, L.p. - SC 13G/A Passive Investment

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)* Denali Therapeutics Inc. (Name of Issuer) Common Stock, $0.01 par value per share (Title of Class of Securities) 24823R 10 5 (CUSIP Number) DECEMBER 31, 2019 (Date of Event Which Requires Filing of this Statement) Check the appropriate box to de

February 12, 2020 SC 13G/A

DNLI / Denali Therapeutics Inc. / VANGUARD GROUP INC - SCHEDULE 13G/A Passive Investment

SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 Schedule 13G Under the Securities Exchange Act of 1934 (Amendment No.: 1)* Name of issuer: Denali Therapeutics Inc Title of Class of Securities: Common Stock CUSIP Number: 24823R105 Date of Event Which Requires Filing of this Statement: December 31, 2019 Check the appropriate box to designate the rule pursuant to which this Schedule is file

February 11, 2020 SC 13G/A

DNLI / Denali Therapeutics Inc. / BRATTON DOUGLAS K Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 1)* DENALI THERAPEUTICS INC. (Name of Issuer) Common Stock, Par Value $0.01 Per Share (Title of Class of Securities) 24823R105 (CUSIP Number) December 31, 2019 (Date of Event which Requires Filing of this Statement) Check the appropriate box to designate the

January 29, 2020 8-K

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): January 28, 2020 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Empl

January 29, 2020 EX-99.1

Denali Therapeutics Announces Pricing of Public Offering of Common Stock

Exhibit 99.1 Denali Therapeutics Announces Pricing of Public Offering of Common Stock SOUTH SAN FRANCISCO, CA — Jan. 28, 2020 — Denali Therapeutics Inc. (NASDAQ: DNLI) today announced the pricing of its underwritten public offering of 7,826,087 shares of its common stock at a price to the public of $23.00 per share. All of the shares are to be sold by Denali Therapeutics. In addition, Denali Thera

January 29, 2020 424B5

CALCULATION OF REGISTRATION FEE Title of Each Class of Securities to be Registered Amount to be Registered(1) Proposed Maximum Offering Price Per Unit Proposed Maximum Aggregate Offering Price Amount of Registration Fee(2) Common Stock, par value $0.

Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No. 333-230232 CALCULATION OF REGISTRATION FEE Title of Each Class of Securities to be Registered Amount to be Registered(1) Proposed Maximum Offering Price Per Unit Proposed Maximum Aggregate Offering Price Amount of Registration Fee(2) Common Stock, par value $0.01 per share 9,000,000 $ 23.00 $ 207,000,000 $ 26,868.60 (1)Includes 1,

January 29, 2020 EX-1.1

Underwriting Agreement, dated as of January 28, 2020, among Denali Therapeutics Inc. and Goldman Sachs & Co. LLC, J.P. Morgan Securities LLC, and Jefferies LLC, as representatives of the several underwriters named therein

Exhibit 1.1 Denali Therapeutics Inc. Common Stock, par value $0.01 per share Underwriting Agreement January 28, 2020 Goldman Sachs & Co. LLC, J.P. Morgan Securities LLC and Jefferies LLC As representatives (the “Representatives”) of the several Underwriters named in Schedule I hereto, c/o Goldman Sachs & Co. LLC 200 West Street, New York, New York 10282-2198 c/o J.P. Morgan Securities LLC 383 Madi

January 27, 2020 8-K

Financial Statements and Exhibits, Results of Operations and Financial Condition, 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): January 27, 2020 Denali Therapeutics Inc. (Exact name of registrant as specified in its charter) Delaware 001-38311 46-3872213 (State or other jurisdiction of (Commission (I.R.S. Empl

January 27, 2020 424B5

Subject to Completion Preliminary Prospectus Supplement dated January 27, 2020

Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No. 333-230232 The information in this preliminary prospectus supplement is not complete and may be changed. A registration statement relating to these securities has been filed with the Securities and Exchange Commission and is effective. This preliminary prospectus supplement and the accompanying prospectus are not an offer to sell

January 27, 2020 EX-99.3

Risk Factors

Exhibit 99.3 Risk Factors Investing in our securities involves a high degree of risk. You should carefully consider the risks discussed below and under the heading "Risk Factors" in our Annual Report on Form 10-K for the fiscal year ended December 31, 2018, filed with the SEC on March 12, 2019 and our Quarterly Report on Form 10-Q for the quarter ended September 30, 2019, filed with the SEC on Nov

January 27, 2020 EX-99.1

Denali Therapeutics Announces Proposed Offering of Common Stock

Exhibit 99.1 Denali Therapeutics Announces Proposed Offering of Common Stock SOUTH SAN FRANCISCO, Calif. — Jan. 27, 2020 — Denali Therapeutics Inc. (NASDAQ: DNLI) today announced that it intends to offer and sell shares of its common stock in an underwritten public offering of $150 million of shares of its common stock. In addition, Denali Therapeutics intends to grant the underwriters a 30-day op

January 27, 2020 EX-99.2

Updated Financial Disclosure

Exhibit 99.2 Updated Financial Disclosure As of December 31, 2019, we estimate we had cash, cash equivalents and marketable securities of approximately $455 million, as compared to $502.9 million at September 30, 2019. This financial data as of December 31, 2019 is preliminary and is based on information available to management as of the date of this prospectus supplement and is subject to complet

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