[SCHEDULE 13G/A] Amylyx Pharmaceuticals, Inc. SEC Filing

Rhea-AI Filing Summary

Adage Capital Management, L.P., together with Robert Atchinson and Phillip Gross, reports shared beneficial ownership of 8,800,000 shares of Amylyx Pharmaceuticals, Inc. ("AMLX"). Those shares represent 9.87% of the company's common stock, based on an aggregate of 89,141,087 shares outstanding as of April 28, 2025. The holding is reported as shared voting and shared dispositive power of 8,800,000 shares, with 0 shares of sole voting or sole dispositive power.

The filing is submitted on Schedule 13G/A and includes a certification that the securities were acquired and are held in the ordinary course of business and not to influence control of the issuer.

Positive

• Adage Capital Management and affiliated reporting persons beneficially own 8,800,000 shares, representing 9.87% of AMLX.

Negative

• None.

Insights

Financial Analyst

TL;DR: Adage and affiliated persons report a passive 9.87% stake (8.8M shares) in AMLX with shared voting and dispositive power.

The disclosure shows a material passive position just below the 10% threshold, disclosed on a Schedule 13G/A. Key metrics are explicit: 8,800,000 shares beneficially owned, representing 9.87% of 89,141,087 outstanding shares as of April 28, 2025. The report indicates shared voting and dispositive power and no sole power. This is a straightforward, transparent ownership disclosure without statements of control intent.

Corporate Governance Expert

TL;DR: A near-10% passive holding by Adage is reported, with certification that the position is held in the ordinary course and not to influence control.

The filing names Adage Capital Management, L.P., Robert Atchinson and Phillip Gross as Reporting Persons and ties the shares to Adage Capital Partners, L.P. It documents shared voting and dispositive authority for 8,800,000 shares and explicitly records 0 sole powers. The certification language confirms the position is presented as passive under Schedule 13G/A rather than an active control filing.

SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549

SCHEDULE 13G

UNDER THE SECURITIES EXCHANGE ACT OF 1934

(Amendment No. 1)

Amylyx Pharmaceuticals, Inc.

(Name of Issuer)

Common Stock, $0.0001 par value per share

(Title of Class of Securities)

03237H101

(CUSIP Number)

06/30/2025

(Date of Event Which Requires Filing of this Statement)

Check the appropriate box to designate the rule pursuant to which this Schedule is filed:

Rule 13d-1(b)

Rule 13d-1(c)

Rule 13d-1(d)

SCHEDULE 13G

CUSIP No. 03237H101

1

Names of Reporting Persons

Adage Capital Management, L.P.

2

Check the appropriate box if a member of a Group (see instructions)

(a)
(b)

3

Sec Use Only

4

Citizenship or Place of Organization

DELAWARE

Number of Shares Beneficially Owned by Each Reporting Person With:

5	Sole Voting Power 0.00
6	Shared Voting Power 8,800,000.00
7	Sole Dispositive Power 0.00
8	Shared Dispositive Power 8,800,000.00

9

Aggregate Amount Beneficially Owned by Each Reporting Person

8,800,000.00

10

Check box if the aggregate amount in row (9) excludes certain shares (See Instructions)

11

Percent of class represented by amount in row (9)

9.87 %

12

Type of Reporting Person (See Instructions)

IA, PN

SCHEDULE 13G

CUSIP No. 03237H101

1

Names of Reporting Persons

Robert Atchinson

2

Check the appropriate box if a member of a Group (see instructions)

(a)
(b)

3

Sec Use Only

4

Citizenship or Place of Organization

UNITED STATES

Number of Shares Beneficially Owned by Each Reporting Person With:

5	Sole Voting Power 0.00
6	Shared Voting Power 8,800,000.00
7	Sole Dispositive Power 0.00
8	Shared Dispositive Power 8,800,000.00

9

Aggregate Amount Beneficially Owned by Each Reporting Person

8,800,000.00

10

Check box if the aggregate amount in row (9) excludes certain shares (See Instructions)

11

Percent of class represented by amount in row (9)

9.87 %

12

Type of Reporting Person (See Instructions)

HC, IN

SCHEDULE 13G

CUSIP No. 03237H101

1

Names of Reporting Persons

Phillip Gross

2

Check the appropriate box if a member of a Group (see instructions)

(a)
(b)

3

Sec Use Only

4

Citizenship or Place of Organization

UNITED STATES

Number of Shares Beneficially Owned by Each Reporting Person With:

5	Sole Voting Power 0.00
6	Shared Voting Power 8,800,000.00
7	Sole Dispositive Power 0.00
8	Shared Dispositive Power 8,800,000.00

9

Aggregate Amount Beneficially Owned by Each Reporting Person

8,800,000.00

10

Check box if the aggregate amount in row (9) excludes certain shares (See Instructions)

11

Percent of class represented by amount in row (9)

9.87 %

12

Type of Reporting Person (See Instructions)

HC, IN

SCHEDULE 13G

Item 1.
(a)	Name of issuer: Amylyx Pharmaceuticals, Inc.
(b)	Address of issuer's principal executive offices: 43 Thorndike Street Cambridge, MA 02141
Item 2.
(a)	Name of person filing: This statement is filed by: (i) Adage Capital Management, L.P., a Delaware limited partnership ("ACM"), as the investment manager of Adage Capital Partners, L.P., a Delaware limited partnership ("ACP"), with respect to the shares of common stock, par value $0.0001 per share ("Common Stock") of Amylyx Pharmaceuticals, Inc., a Delaware corporation (the "Company") directly held by ACP; (ii) Robert Atchinson ("Mr. Atchinson"), as (1) managing member of Adage Capital Advisors, L.L.C., a limited liability company organized under the laws of the State of Delaware ("ACA"), managing member of Adage Capital Partners GP, L.L.C., a limited liability company organized under the laws of the State of Delaware ("ACPGP"), general partner of ACP and (2) managing member of Adage Capital Partners LLC, a Delaware limited liability company ("ACPLLC"), general partner of ACM, with respect to the shares of Common Stock directly held by ACP; and (iii) Phillip Gross ("Mr. Gross"), as (1) managing member of ACA, managing member of ACPGP and (2) managing member of ACPLLC, general partner of ACM, with respect to the shares of Common Stock directly held by ACP. The foregoing persons are hereinafter sometimes collectively referred to as the "Reporting Persons." Any disclosures herein with respect to persons other than the Reporting Persons are made on information and belief after making inquiry to the appropriate party. The filing of this statement should not be construed in and of itself as an admission by any Reporting Person as to beneficial ownership of the securities reported herein.
(b)	Address or principal business office or, if none, residence: The address of the business office of each of the Reporting Persons is 200 Clarendon Street, 52nd Floor, Boston, Massachusetts 02116.
(c)	Citizenship: ACM is a limited partnership organized under the laws of the State of Delaware. Messrs. Gross and Atchinson are citizens of the United States.
(d)	Title of class of securities: Common Stock, $0.0001 par value per share
(e)	CUSIP No.: 03237H101
Item 3.	If this statement is filed pursuant to §§ 240.13d-1(b) or 240.13d-2(b) or (c), check whether the person filing is a:
(a)	Broker or dealer registered under section 15 of the Act (15 U.S.C. 78o);
(b)	Bank as defined in section 3(a)(6) of the Act (15 U.S.C. 78c);
(c)	Insurance company as defined in section 3(a)(19) of the Act (15 U.S.C. 78c);
(d)	Investment company registered under section 8 of the Investment Company Act of 1940 (15 U.S.C. 80a-8);
(e)	An investment adviser in accordance with § 240.13d-1(b)(1)(ii)(E);
(f)	An employee benefit plan or endowment fund in accordance with § 240.13d-1(b)(1)(ii)(F);
(g)	A parent holding company or control person in accordance with § 240.13d-1(b)(1)(ii)(G);
(h)	A savings associations as defined in Section 3(b) of the Federal Deposit Insurance Act (12 U.S.C. 1813);
(i)	A church plan that is excluded from the definition of an investment company under section 3(c)(14) of the Investment Company Act of 1940 (15 U.S.C. 80a-3);
(j)	A non-U.S. institution in accordance with § 240.13d-1(b)(1)(ii)(J). If filing as a non-U.S. institution in accordance with § 240.13d-1(b)(1)(ii)(J), please specify the type of institution:
(k)	Group, in accordance with Rule 240.13d-1(b)(1)(ii)(K).
Item 4.	Ownership
(a)	Amount beneficially owned: The information required by Item 4(a) is set forth in Row 9 of the cover page for each of the Reporting Persons and is incorporated herein by reference. The percentage set forth in this Schedule 13G is calculated based upon an aggregate of 89,141,087 shares of Common Stock outstanding as of April 28, 2025, as reported in the Company's Quarterly Report on Form 10-Q for the quarterly period ended March 31, 2025, filed with the Securities and Exchange Commission on May 8, 2025.
(b)	Percent of class: 9.87%
(c)	Number of shares as to which the person has:
	(i) Sole power to vote or to direct the vote: The information required by Item 4(c)(i) is set forth in Row 5 of the cover page for each of the Reporting Persons and is incorporated herein by reference.
	(ii) Shared power to vote or to direct the vote: The information required by Item 4(c)(ii) is set forth in Row 6 of the cover page for each of the Reporting Persons and is incorporated herein by reference.
	(iii) Sole power to dispose or to direct the disposition of: The information required by Item 4(c)(iii) is set forth in Row 7 of the cover page for each of the Reporting Persons and is incorporated herein by reference.
	(iv) Shared power to dispose or to direct the disposition of: The information required by Item 4(c)(iv) is set forth in Row 8 of the cover page for each of the Reporting Persons and is incorporated herein by reference.
Item 5.	Ownership of 5 Percent or Less of a Class.
Item 6.	Ownership of more than 5 Percent on Behalf of Another Person.
	If any other person is known to have the right to receive or the power to direct the receipt of dividends from, or the proceeds from the sale of, such securities, a statement to that effect should be included in response to this item and, if such interest relates to more than 5 percent of the class, such person should be identified. A listing of the shareholders of an investment company registered under the Investment Company Act of 1940 or the beneficiaries of employee benefit plan, pension fund or endowment fund is not required. See Item 2(a).
Item 7.	Identification and Classification of the Subsidiary Which Acquired the Security Being Reported on by the Parent Holding Company or Control Person.
	Not Applicable
Item 8.	Identification and Classification of Members of the Group.
	Not Applicable
Item 9.	Notice of Dissolution of Group.
	Not Applicable

Item 10.

Certifications:

By signing below I certify that, to the best of my knowledge and belief, the securities referred to above were acquired and are held in the ordinary course of business and were not acquired and are not held for the purpose of or with the effect of changing or influencing the control of the issuer of the securities and were not acquired and are not held in connection with or as a participant in any transaction having that purpose or effect, other than activities solely in connection with a nomination under ?? 240.14a-11.

SIGNATURE

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

Adage Capital Management, L.P.

Signature:	/s/ Robert Atchinson
Name/Title:	By: Adage Capital Partners LLC, its General Partner, By: Robert Atchinson, its Managing Member
Date:	08/12/2025

Robert Atchinson

Signature:	/s/ Robert Atchinson
Name/Title:	Robert Atchinson, individually
Date:	08/12/2025

Phillip Gross

Signature:	/s/ Phillip Gross
Name/Title:	Phillip Gross, individually
Date:	08/12/2025

FAQ

How many AMLX shares does Adage Capital report owning?

The filing reports beneficial ownership of 8,800,000 shares of Amylyx (AMLX).

What percentage of AMLX does the 8.8M share position represent?

The reported position represents 9.87% of the outstanding common stock based on 89,141,087 shares outstanding as of April 28, 2025.

Do the reporting persons have sole voting or dispositive power over these AMLX shares?

No. The filing shows 0 shares with sole voting or sole dispositive power and 8,800,000 shares with shared voting and shared dispositive power.

Who are the reporting persons named in the Schedule 13G/A for AMLX?

The reporting persons are Adage Capital Management, L.P., and individuals Robert Atchinson and Phillip Gross.

Does the filing state the stake is intended to influence control of Amylyx?

The certification in the filing states the securities were acquired and are held in the ordinary course of business and were not acquired and are not held for the purpose of changing or influencing control of the issuer.