SEC FORM 4

SEC FORM 4 SEC Form 4

FORM 4

UNITED STATES SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549

STATEMENT OF CHANGES IN BENEFICIAL OWNERSHIP

Filed pursuant to Section 16(a) of the Securities Exchange Act of 1934
or Section 30(h) of the Investment Company Act of 1940

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Check this box if no longer subject to Section 16. Form 4 or Form 5 obligations may continue. See Instruction 1(b).

Check this box to indicate that a transaction was made pursuant to a contract, instruction or written plan for the purchase or sale of equity securities of the issuer that is intended to satisfy the affirmative defense conditions of Rule 10b5-1(c). See Instruction 10.

1. Name and Address of Reporting Person^*

BAKER BROS. ADVISORS LP

(Last)

(First)

(Middle)

860 WASHINGTON STREET, 3RD FLOOR

(Street)

NEW YORK

10014

(City)

(State)

(Zip)

2. Issuer Name and Ticker or Trading Symbol
Denali Therapeutics Inc. [ DNLI ]

5. Relationship of Reporting Person(s) to Issuer
(Check all applicable)

X	Director	10% Owner
	Officer (give title below)	Other (specify below)

3. Date of Earliest Transaction (Month/Day/Year)
12/11/2025

4. If Amendment, Date of Original Filed (Month/Day/Year)

6. Individual or Joint/Group Filing (Check Applicable Line)

	Form filed by One Reporting Person
X	Form filed by More than One Reporting Person

Table I - Non-Derivative Securities Acquired, Disposed of, or Beneficially Owned
1. Title of Security (Instr. 3)	2. Transaction Date (Month/Day/Year)	2A. Deemed Execution Date, if any (Month/Day/Year)	3. Transaction Code (Instr. 8)		4. Securities Acquired (A) or Disposed Of (D) (Instr. 3, 4 and 5)			5. Amount of Securities Beneficially Owned Following Reported Transaction(s) (Instr. 3 and 4)	6. Ownership Form: Direct (D) or Indirect (I) (Instr. 4)	7. Nature of Indirect Beneficial Ownership (Instr. 4)
1. Title of Security (Instr. 3)	2. Transaction Date (Month/Day/Year)	2A. Deemed Execution Date, if any (Month/Day/Year)	Code	V	Amount	(A) or (D)	Price		6. Ownership Form: Direct (D) or Indirect (I) (Instr. 4)	7. Nature of Indirect Beneficial Ownership (Instr. 4)

Table II - Derivative Securities Acquired, Disposed of, or Beneficially Owned (e.g., puts, calls, warrants, options, convertible securities)
1. Title of Derivative Security (Instr. 3)	2. Conversion or Exercise Price of Derivative Security	3. Transaction Date (Month/Day/Year)	3A. Deemed Execution Date, if any (Month/Day/Year)	4. Transaction Code (Instr. 8)		5. Number of Derivative Securities Acquired (A) or Disposed of (D) (Instr. 3, 4 and 5)		6. Date Exercisable and Expiration Date (Month/Day/Year)		7. Title and Amount of Securities Underlying Derivative Security (Instr. 3 and 4)		8. Price of Derivative Security (Instr. 5)	9. Number of derivative Securities Beneficially Owned Following Reported Transaction(s) (Instr. 4)	10. Ownership Form: Direct (D) or Indirect (I) (Instr. 4)	11. Nature of Indirect Beneficial Ownership (Instr. 4)
1. Title of Derivative Security (Instr. 3)	2. Conversion or Exercise Price of Derivative Security	3. Transaction Date (Month/Day/Year)	3A. Deemed Execution Date, if any (Month/Day/Year)	Code	V	(A)	(D)	Date Exercisable	Expiration Date	Title	Amount or Number of Shares	8. Price of Derivative Security (Instr. 5)		10. Ownership Form: Direct (D) or Indirect (I) (Instr. 4)	11. Nature of Indirect Beneficial Ownership (Instr. 4)
$0.01 Prefunded Warrants⁽¹⁾	$0.01	12/11/2025		P		190,523⁽²⁾		⁽²⁾	⁽¹⁾	Common Stock	190,523	$17.49	2,335,469	I	See Footnotes⁽³⁾⁽⁴⁾⁽⁵⁾
$0.01 Prefunded Warrants⁽¹⁾	$0.01	12/11/2025		P		2,095,191⁽²⁾		⁽²⁾	⁽¹⁾	Common Stock	2,095,191	$17.49	25,996,310	I	See Footnotes⁽⁴⁾⁽⁵⁾⁽⁶⁾

1. Name and Address of Reporting Person^*

BAKER BROS. ADVISORS LP

(Last)

(First)

(Middle)

860 WASHINGTON STREET, 3RD FLOOR

(Street)

NEW YORK

10014

(City)

(State)

(Zip)

Relationship of Reporting Person(s) to Issuer

X	Director	10% Owner
	Officer (give title below)	Other (specify below)

1. Name and Address of Reporting Person^*

667, L.P.

(Last)

(First)

(Middle)

860 WASHINGTON STREET, 3RD FLOOR

(Street)

NEW YORK

10014

(City)

(State)

(Zip)

Relationship of Reporting Person(s) to Issuer

X	Director	10% Owner
	Officer (give title below)	Other (specify below)

1. Name and Address of Reporting Person^*

Baker Bros. Advisors (GP) LLC

(Last)

(First)

(Middle)

860 WASHINGTON STREET, 3RD FLOOR

(Street)

NEW YORK

10014

(City)

(State)

(Zip)

Relationship of Reporting Person(s) to Issuer

X	Director	10% Owner
	Officer (give title below)	Other (specify below)

1. Name and Address of Reporting Person^*

Baker Brothers Life Sciences LP

(Last)

(First)

(Middle)

860 WASHINGTON STREET, 3RD FLOOR

(Street)

NEW YORK

10014

(City)

(State)

(Zip)

Relationship of Reporting Person(s) to Issuer

X	Director	10% Owner
	Officer (give title below)	Other (specify below)

1. Name and Address of Reporting Person^*

BAKER FELIX

(Last)

(First)

(Middle)

860 WASHINGTON STREET, 3RD FLOOR

(Street)

NEW YORK

10014

(City)

(State)

(Zip)

Relationship of Reporting Person(s) to Issuer

X	Director	10% Owner
	Officer (give title below)	Other (specify below)

1. Name and Address of Reporting Person^*

BAKER JULIAN

(Last)

(First)

(Middle)

860 WASHINGTON STREET, 3RD FLOOR

(Street)

NEW YORK

10014

(City)

(State)

(Zip)

Relationship of Reporting Person(s) to Issuer

X	Director	10% Owner
	Officer (give title below)	Other (specify below)

Explanation of Responses:

1. 667, L.P. ("667") and Baker Brothers Life Sciences, L.P. ("Life Sciences" and together with 667, the "Funds") purchased, respectively, 190,523 and 2,095,191 warrants to purchase common stock ("Common Stock") of Denali Therapeutics Inc. (the "Issuer") at an exercise price of $0.01 per share with no expiration date ("$0.01 Prefunded Warrants") for $17.49 per share in a public offering that closed on December 11, 2025.

2. The $0.01 Prefunded Warrants are exercisable at any time, at the holder's election, on a 1-for-1 basis into Common Stock to the extent that immediately prior to or after giving effect to such exercise the holders thereof, together with their affiliates and any members of a Section 13(d) group with such holders, would beneficially own, for purposes of Rule 13d-3 under the Securities Act of 1934, as amended, no more thn 4.99% of the outstanding shares of Common Stock (the "Maximum Percentage"). By written notice to the Issuer, the Funds may increase or decrease the Maximum Percentage applicable to that fund to any other percentage not in excess of 19.99%; provided that any such increase will not be effective until the 61st day after such notice is delivered to the Issuer.

3. After giving effect to the transactions reported herein and as a result of their ownership interest in (i) Baker Biotech Capital, L.P. and (ii) 667, Julian C. Baker and Felix J. Baker each may be deemed to have an indirect pecuniary interest in the securities reported in column 9 of Table II held directly by 667, a limited partnership of which the sole general partner is Baker Biotech Capital, L.P., a limited partnership of which the sole general partner is Baker Biotech Capital (GP), LLC, due to their interest in 667 and Baker Biotech Capital, L.P.'s right to receive an allocation of a portion of the profits from 667.

4. Baker Bros. Advisors LP (the "Adviser") serves as the investment adviser to the Funds. In connection with the services provided by the Adviser, the Adviser receives an asset-based management fee that does not confer any pecuniary interest in the securities held directly by the Funds. The Adviser GP is the Adviser's sole general partner. Julian C. Baker and Felix J. Baker are managing members of the Adviser GP. The Adviser has complete and unlimited discretion and authority with respect to the investment and voting power of the securities held directly by the Funds. The general partners of the Funds relinquished to the Adviser all discretion and authority with respect to the investment and voting power of the securities held directly by the Funds.

5. Julian C. Baker, Felix J. Baker, the Adviser GP and the Adviser disclaim beneficial ownership of the securities held directly by the Funds except to the extent of their pecuniary interest therein, and this report shall not be deemed an admission that any of Julian C. Baker, Felix J. Baker, the Adviser GP or the Adviser is a beneficial owner of such securities for purposes of Section 16 or any other purpose.

6. After giving effect to the transactions reported herein and as a result of their ownership interest in (i) Baker Brothers Life Sciences Capital, L.P. and (ii) Life Sciences, Julian C. Baker and Felix J. Baker each may be deemed to have an indirect pecuniary interest in the securities reported in column 9 of Table II held directly by Life Sciences, a limited partnership of which the sole general partner is Baker Brothers Life Sciences Capital, L.P., a limited partnership of which the sole general partner is Baker Brothers Life Sciences Capital (GP), LLC, due to their interest in Life Sciences and Baker Brothers Life Sciences Capital, L.P.'s right to receive an allocation of a portion of the profits from Life Sciences.

Remarks:

Julian C. Baker, a managing member of Baker Bros. Advisors (GP) LLC is a director of Denali Therapeutics Inc. (the "Issuer"). By virtue of their representation on the board of directors of the Issuer, for purposes of Section 16 of the Securities Exchange Act of 1934, as amended, the reporting persons other than Julian C. Baker are deemed directors by deputization of the Issuer.

	By: Baker Bros. Advisors LP, Name: Scott L. Lessing, Title: President /s/ Scott L. Lessing	12/15/2025
	Baker Bros. Advisors LP, Mgmt. Co. and Inv. Adviser to 667, L.P., pursuant to authority granted by Baker Biotech Capital, L.P., GP to 667, L.P. Name: Scott L. Lessing, Title: President /s/ Scott L. Lessing	12/15/2025
	By: Baker Bros. Advisors (GP) LLC, Name: Scott L. Lessing, Title: President /s/ Scott L. Lessing	12/15/2025
	Baker Bros. Advisors LP, Mgmt. Co. and Inv. Adviser to BAKER BROTHERS LIFE SCIENCES, L.P., pursuant to authority granted by Baker Brothers Life Sciences Capital, L.P., GP to Baker Brothers Life Sciences, L.P., /s/ Name: Scott L. Lessing, Title: President	12/15/2025
	/s/ Felix J. Baker	12/15/2025
	/s/ Julian C. Baker	12/15/2025
	** Signature of Reporting Person	Date
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SEC Form 4 filed by Director Baker Bros. Advisors Lp