enGene (ENGN) SC 13G/A enGene / Omega Fund VII ownership change

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

(Amendment No. 1)

enGene Holdings, Inc.

(Name of Issuer)

Common Shares, no par value per share

(Title of Class of Securities)

29286M105

(CUSIP Number)

September 30, 2024

(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)

* The remainder of this cover page shall be filled out for a reporting person’s initial filing on this form with respect to the subject class of securities, and for any subsequent amendment containing information which would alter disclosures provided in a prior cover page.

The information required on the remainder of this cover page shall not be deemed to be “filed” for the purpose of Section 18 of the Securities Exchange Act of 1934 (“Act”) or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes).

CUSIP NO. 29286M105 13G Page 2 of 10 Pages

1	NAMES OF REPORTING PERSONS  Omega Fund VII, L.P.
2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (SEE INSTRUCTIONS)  (a) ☐ (b) ☒ (1)
3	SEC USE ONLY
4	CITIZENSHIP OR PLACE OF ORGANIZATION  Cayman Islands

NUMBER OF SHARES  BENEFICIALLY  OWNED BY EACH REPORTING PERSON WITH	5	SOLE VOTING POWER  0
	6	SHARED VOTING POWER  1,397,859
	7	SOLE DISPOSITIVE POWER  0
	8	SHARED DISPOSITIVE POWER  1,397,859

9	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON  1,397,859
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  3.1% (2)
12	TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)  PN

(1) This Schedule 13G is filed by Omega Fund VII, L.P. (“Omega Fund”), Omega Fund VII GP, L.P. (“Omega GP”), Omega Fund VII GP Manager, Ltd. (“Omega Ltd”), Claudio Nessi (“Nessi”), Otello Stampacchia (“Stampacchia”) and Francesco Draetta (“Draetta”) (together, the “Reporting Persons”). Omega Ltd serves as the general partner of Omega GP, which serves as the general partner of Omega Fund; and each of Omega Ltd and Omega GP may be deemed to own beneficially the shares held by Omega Fund. Nessi, Stampacchia and Draetta are the directors of Omega Ltd and may be deemed to beneficially own the shares held by Omega Fund. The Reporting Persons may be deemed a “group” for purposes of Section 13 of the Exchange Act and expressly disclaim status as a “group” for purposes of this Schedule 13G.

(2) The following percentages are based on (i) 44,215,577 Common Shares outstanding as of September 6, 2024, as set forth in the Issuer’s Quarterly Report on 10-Q for the period ended July 31, 2024, filed with the Securities and Exchange Commission on September 10, 2024 and (ii) immediately exercisable warrants to purchase 321,502 Common Shares held by Omega Fund.

CUSIP NO. 29286M105 13G Page 3 of 10 Pages

1	NAMES OF REPORTING PERSONS  Omega Fund VII GP, L.P.
2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (SEE INSTRUCTIONS)  (a) ☐ (b) ☒ (1)
3	SEC USE ONLY
4	CITIZENSHIP OR PLACE OF ORGANIZATION  Cayman Islands

NUMBER OF SHARES  BENEFICIALLY  OWNED BY EACH REPORTING PERSON WITH	5	SOLE VOTING POWER  0
	6	SHARED VOTING POWER  1,397,859
	7	SOLE DISPOSITIVE POWER  0
	8	SHARED DISPOSITIVE POWER  1,397,859

9	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON  1,397,859
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  3.1% (2)
12	TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)  PN

(1) This Schedule 13G is filed by Omega Fund VII, L.P. (“Omega Fund”), Omega Fund VII GP, L.P. (“Omega GP”), Omega Fund VII GP Manager, Ltd. (“Omega Ltd”), Claudio Nessi (“Nessi”), Otello Stampacchia (“Stampacchia”) and Francesco Draetta (“Draetta”) (together, the “Reporting Persons”). Omega Ltd serves as the general partner of Omega GP, which serves as the general partner of Omega Fund; and each of Omega Ltd and Omega GP may be deemed to own beneficially the shares held by Omega Fund. Nessi, Stampacchia and Draetta are the directors of Omega Ltd and may be deemed to beneficially own the shares held by Omega Fund. The Reporting Persons may be deemed a “group” for purposes of Section 13 of the Exchange Act and expressly disclaim status as a “group” for purposes of this Schedule 13G.

(2) The following percentages are based on (i) 44,215,577 Common Shares outstanding as of September 6, 2024, as set forth in the Issuer’s Quarterly Report on 10-Q for the period ended July 31, 2024, filed with the Securities and Exchange Commission on September 10, 2024 and (ii) immediately exercisable warrants to purchase 321,502 Common Shares held by Omega Fund.

CUSIP NO. 29286M105 13G Page 4 of 10 Pages

1	NAMES OF REPORTING PERSONS  Omega Fund VII GP Manager, Ltd.
2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (SEE INSTRUCTIONS)  (a) ☐ (b) ☒ (1)
3	SEC USE ONLY
4	CITIZENSHIP OR PLACE OF ORGANIZATION  Cayman Islands

NUMBER OF SHARES  BENEFICIALLY  OWNED BY EACH REPORTING PERSON WITH	5	SOLE VOTING POWER  0
	6	SHARED VOTING POWER  1,397,859
	7	SOLE DISPOSITIVE POWER  0
	8	SHARED DISPOSITIVE POWER  1,397,859

9	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON  1,397,859
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  3.1% (2)
12	TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)  OO

(1) This Schedule 13G is filed by Omega Fund VII, L.P. (“Omega Fund”), Omega Fund VII GP, L.P. (“Omega GP”), Omega Fund VII GP Manager, Ltd. (“Omega Ltd”), Claudio Nessi (“Nessi”), Otello Stampacchia (“Stampacchia”) and Francesco Draetta (“Draetta”) (together, the “Reporting Persons”). Omega Ltd serves as the general partner of Omega GP, which serves as the general partner of Omega Fund; and each of Omega Ltd and Omega GP may be deemed to own beneficially the shares held by Omega Fund. Nessi, Stampacchia and Draetta are the directors of Omega Ltd and may be deemed to beneficially own the shares held by Omega Fund. The Reporting Persons may be deemed a “group” for purposes of Section 13 of the Exchange Act and expressly disclaim status as a “group” for purposes of this Schedule 13G.

(2) The following percentages are based on (i) 44,215,577 Common Shares outstanding as of September 6, 2024, as set forth in the Issuer’s Quarterly Report on 10-Q for the period ended July 31, 2024, filed with the Securities and Exchange Commission on September 10, 2024 and (ii) immediately exercisable warrants to purchase 321,502 Common Shares held by Omega Fund.

CUSIP NO. 29286M105 13G Page 5 of 10 Pages

1	NAMES OF REPORTING PERSONS  Claudio Nessi
2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (SEE INSTRUCTIONS)  (a) ☐ (b) ☒ (1)
3	SEC USE ONLY
4	CITIZENSHIP OR PLACE OF ORGANIZATION  Switzerland

NUMBER OF SHARES  BENEFICIALLY  OWNED BY EACH REPORTING PERSON WITH	5	SOLE VOTING POWER  0
	6	SHARED VOTING POWER  1,397,859
	7	SOLE DISPOSITIVE POWER  0
	8	SHARED DISPOSITIVE POWER  1,397,859

9	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON  1,397,859
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  3.1% (2)
12	TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)  IN

(1) This Schedule 13G is filed by Omega Fund VII, L.P. (“Omega Fund”), Omega Fund VII GP, L.P. (“Omega GP”), Omega Fund VII GP Manager, Ltd. (“Omega Ltd”), Claudio Nessi (“Nessi”), Otello Stampacchia (“Stampacchia”) and Francesco Draetta (“Draetta”) (together, the “Reporting Persons”). Omega Ltd serves as the general partner of Omega GP, which serves as the general partner of Omega Fund; and each of Omega Ltd and Omega GP may be deemed to own beneficially the shares held by Omega Fund. Nessi, Stampacchia and Draetta are the directors of Omega Ltd and may be deemed to beneficially own the shares held by Omega Fund. The Reporting Persons may be deemed a “group” for purposes of Section 13 of the Exchange Act and expressly disclaim status as a “group” for purposes of this Schedule 13G.

(2) The following percentages are based on (i) 44,215,577 Common Shares outstanding as of September 6, 2024, as set forth in the Issuer’s Quarterly Report on 10-Q for the period ended July 31, 2024, filed with the Securities and Exchange Commission on September 10, 2024 and (ii) immediately exercisable warrants to purchase 321,502 Common Shares held by Omega Fund.

CUSIP NO. 29286M105 13G Page 6 of 10 Pages

1	NAMES OF REPORTING PERSONS  Otello Stampacchia
2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (SEE INSTRUCTIONS)  (a) ☐ (b) ☒ (1)
3	SEC USE ONLY
4	CITIZENSHIP OR PLACE OF ORGANIZATION  Italy

NUMBER OF SHARES  BENEFICIALLY  OWNED BY EACH REPORTING PERSON WITH	5	SOLE VOTING POWER  0
	6	SHARED VOTING POWER  1,397,859
	7	SOLE DISPOSITIVE POWER  0
	8	SHARED DISPOSITIVE POWER  1,397,859

9	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON  1,397,859
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  3.1% (2)
12	TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)  IN

(1) This Schedule 13G is filed by Omega Fund VII, L.P. (“Omega Fund”), Omega Fund VII GP, L.P. (“Omega GP”), Omega Fund VII GP Manager, Ltd. (“Omega Ltd”), Claudio Nessi (“Nessi”), Otello Stampacchia (“Stampacchia”) and Francesco Draetta (“Draetta”) (together, the “Reporting Persons”). Omega Ltd serves as the general partner of Omega GP, which serves as the general partner of Omega Fund; and each of Omega Ltd and Omega GP may be deemed to own beneficially the shares held by Omega Fund. Nessi, Stampacchia and Draetta are the directors of Omega Ltd and may be deemed to beneficially own the shares held by Omega Fund. The Reporting Persons may be deemed a “group” for purposes of Section 13 of the Exchange Act and expressly disclaim status as a “group” for purposes of this Schedule 13G.

(2) The following percentages are based on (i) 44,215,577 Common Shares outstanding as of September 6, 2024, as set forth in the Issuer’s Quarterly Report on 10-Q for the period ended July 31, 2024, filed with the Securities and Exchange Commission on September 10, 2024 and (ii) immediately exercisable warrants to purchase 321,502 Common Shares held by Omega Fund.

CUSIP NO. 29286M105 13G Page 7 of 10 Pages

1	NAMES OF REPORTING PERSONS  Francesco Draetta
2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP (SEE INSTRUCTIONS)  (a) ☐ (b) ☒ (1)
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
	6	SHARED VOTING POWER  1,397,859
	7	SOLE DISPOSITIVE POWER  0
	8	SHARED DISPOSITIVE POWER  1,397,859

9	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON  1,397,859
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  3.1% (2)
12	TYPE OF REPORTING PERSON (SEE INSTRUCTIONS)  IN

(1) This Schedule 13G is filed by Omega Fund VII, L.P. (“Omega Fund”), Omega Fund VII GP, L.P. (“Omega GP”), Omega Fund VII GP Manager, Ltd. (“Omega Ltd”), Claudio Nessi (“Nessi”), Otello Stampacchia (“Stampacchia”) and Francesco Draetta (“Draetta”) (together, the “Reporting Persons”). Omega Ltd serves as the general partner of Omega GP, which serves as the general partner of Omega Fund; and each of Omega Ltd and Omega GP may be deemed to own beneficially the shares held by Omega Fund. Nessi, Stampacchia and Draetta are the directors of Omega Ltd and may be deemed to beneficially own the shares held by Omega Fund. The Reporting Persons may be deemed a “group” for purposes of Section 13 of the Exchange Act and expressly disclaim status as a “group” for purposes of this Schedule 13G.

(2) The following percentages are based on (i) 44,215,577 Common Shares outstanding as of September 6, 2024, as set forth in the Issuer’s Quarterly Report on 10-Q for the period ended July 31, 2024, filed with the Securities and Exchange Commission on September 10, 2024 and (ii) immediately exercisable warrants to purchase 321,502 Common Shares held by Omega Fund.

CUSIP NO. 29286M105 13G Page 8 of 10 Pages

Introductory Note: This statement on Schedule 13G is filed on behalf of the Reporting Persons, in respect of Common Shares, no par value per share (the “Common Shares”), of enGene Holdings, Inc. (the “Issuer”).

Item 1(a) Name of Issuer:

enGene Holdings, Inc. (the “Issuer”)

Item 1(b) Address of Issuer’s principal executive offices:

enGene Holdings, Inc.

4868 Rue Levy, Suite 220

Saint-Laurent, QC, Canada

Items 2(a) Name of Reporting Persons filing:

Omega Fund VII, L.P. (“Omega Fund”)

Omega Fund VII GP, L.P. (“Omega GP”)

Omega Fund VII GP Manager, Ltd. (“Omega Ltd”)

Claudio Nessi (“Nessi”)

Otello Stampacchia (“Stampacchia”)

Francesco Draetta (“Draetta”)

Item 2(b) Address or principal business office or, if none, residence:

The address of the principal business office of Omega Fund, Omega GP, Omega Ltd, Nessi, Stampacchia and Draetta, is c/o Omega Fund Management, LLC, 888 Boylston Street, Suite 1111, Boston, MA 02199.

Item 2(c) Citizenship:

Name	Citizenship or Place of Organization
Omega Fund	Cayman Islands
Omega GP	Cayman Islands
Omega Ltd	Cayman Islands
Nessi	Switzerland
Stampacchia	Italy
Draetta	United States

Item 2(d) Title of class of securities:

Common Shares

Item 2(e) CUSIP No.:

29286M105

Item 3 If this statement is filed pursuant to §§ 240.13d-1(b), or 240.13d-2(b) or (c), check whether the person filings is a:

Not applicable.

CUSIP NO. 29286M105 13G Page 5 of 10 Pages

Item 4 Ownership

The following information with respect to the ownership of Common Shares of the Issuer by the Reporting Persons filing this statement on Schedule 13G is provided as of September 30, 2024.

Reporting Persons	Shares of Common Stock Held Directly		Sole Voting Power		Shared Voting Power		Sole Dispositive Power		Shared Dispositive Power		Beneficial Ownership		Percentage of Class (1)
Omega Fund(2)(3)		1,397,859		0		1,397,859		0		1,397,859		1,397,859		3.1	%
Omega GP(2)(3)		0		0		1,397,859		0		1,397,859		1,397,859		3.1	%
Omega Ltd(2)(3)		0		0		1,397,859		0		1,397,859		1,397,859		3.1	%
Nessi(2)(3)		0		0		1,397,859		0		1,397,859		1,397,859		3.1	%
Stampacchia(2)(3)		0		0		1,397,859		0		1,397,859		1,397,859		3.1	%
Draetta(2)(3)		0		0		1,397,859		0		1,397,859		1,397,859		3.1	%

(1) The following percentages are based on (i) 44,215,577 Common Shares outstanding as of September 6, 2024, as set forth in the Issuer’s Quarterly Report on 10-Q for the period ended July 31, 2024, filed with the Securities and Exchange Commission on September 10, 2024 and (ii) immediately exercisable warrants to purchase 321,502 Common Shares held by Omega Fund.

(2) Omega Fund owns 1,076,357 Common Shares and warrants to purchase 321,502 Common Shares. Omega Ltd serves as the general partner of Omega GP, which serves as the general partner of Omega Fund, and each of Omega GP and Omega Ltd may be deemed to own beneficially the shares held by Omega Fund. Nessi, Stampacchia and Draetta are the directors of Omega Ltd and may be deemed to beneficially own the shares held by Omega Fund.

(3) The Reporting Persons may be deemed a “group” for purposes of Section 13 of the Exchange Act and expressly disclaim status as a “group” for purposes of this Schedule 13G.

Item 5 Ownership of Five Percent or Less of a Class

If this statement is being filed to report the fact that as of the date hereof the reporting person has ceased to be the beneficial owner of more than five percent of the class of securities, check the following: ☒

Item 6 Ownership of More than Five Percent on Behalf of Another Person

Not applicable.

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 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 Rule 14a-11.

CUSIP NO. 29286M105 13G Page 10 of 10 Pages

SIGNATURES

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.

Dated:	November 14, 2024
OMEGA FUND VII, L.P.
BY:	Omega Fund VII GP, L.P.
ITS:	GENERAL PARTNER
BY:	Omega Fund VII GP Manager, Ltd.
ITS:	GENERAL PARTNER
By:	/s/ Otello Stampacchia
	Director
OMEGA FUND VII GP, L.P.
BY:	Omega Fund VII GP Manager, Ltd.
ITS:	GENERAL PARTNER
By:	/s/ Otello Stampacchia
	Director
OMEGA FUND VII GP MANAGER, LTD.
By:	/s/ Otello Stampacchia
	Director
/s/ * Otello Stampacchia, as Attorney-in-Fact
Claudio Nessi
/s/ Otello Stampacchia
Otello Stampacchia
/s/ Francesco Draetta
Francesco Draetta