SC 13D/A

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No. 1)*

Freeline Therapeutics Holdings plc

(Name of Issuer)

American Depositary Shares and Ordinary Shares, nominal value £0.00001 per share

(Title of Class of Securities)

G3664N 103

(CUSIP Number)

Alasdair Moodie, General Counsel

Syncona Investment Management Limited

2nd Floor, 8 Bloomsbury Street

London WC1B 3SR, United Kingdom

020 3981 8888

(Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications)

October 17, 2023

(Date of Event Which Requires Filing of this Statement)

If the filing person has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing this schedule because of §§ 240.13d-1(e), 240.13d-1(f) or 240.13d-1(g), check the following box. ☐

Note: Schedules filed in paper format shall include a signed original and five copies of the schedule, including all exhibits. See Rule 13d-7 for other parties to whom copies are to be sent.

* 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).

SCHEDULE 13D

CUSIP NO. G3664N 103 13D Page 1 of 8

1	NAMES OF REPORTING PERSON  Syncona Portfolio Limited
2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP  (a) ☐  (b) ☒
3	SEC USE ONLY
4	SOURCE OF FUNDS  WC
5	CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEMS 2(d) or 2(e)  ☐
6	CITIZENSHIP OR PLACE OF ORGANIZATION  Guernsey

NUMBER OF SHARES BENEFICIALLY OWNED BY EACH REPORTING PERSON WITH	7	SOLE VOTING POWER  0
	8	SHARED VOTING POWER  37,862,132(1)
	9	SOLE DISPOSITIVE POWER  0
	10	SHARED DISPOSITIVE POWER  37,862,132(1)

11	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON  37,862,132(1)
12	CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES  ☐
13	PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)  57.92%(2)
14	TYPE OF REPORTING PERSON  CO

(1) Consists of 15,864,527 ordinary shares and 1,466,507 American Depositary Shares (“ADSs”) held directly by Syncona Portfolio Limited. Each ADS represents 15 ordinary shares, nominal value £0.00001 per share, of the Issuer. The ordinary shares and the ADSs are collectively referred to as the “Ordinary Shares”.

(2) The percentages used in this Amendment No. 1 to Schedule 13D are calculated based on 65,369,417 Ordinary Shares outstanding as of June 30, 2023, as reported in the Issuer’s Form 6-K filed with the SEC on August 15, 2023.

SCHEDULE 13D

CUSIP NO. G3664N 103 13D Page 2 of 8

1	NAMES OF REPORTING PERSON  Syncona Holdings Limited
2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP  (a) ☐  (b) ☒
3	SEC USE ONLY
4	SOURCE OF FUNDS  WC
5	CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEMS 2(d) or 2(e)  ☐
6	CITIZENSHIP OR PLACE OF ORGANIZATION  Guernsey

NUMBER OF SHARES BENEFICIALLY OWNED BY EACH REPORTING PERSON WITH	7	SOLE VOTING POWER  0
	8	SHARED VOTING POWER  37,862,132(1)
	9	SOLE DISPOSITIVE POWER  0
	10	SHARED DISPOSITIVE POWER  37,862,132(1)

11	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON  37,862,132(1)
12	CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES  ☐
13	PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)  57.92%(2)
14	TYPE OF REPORTING PERSON  CO

(1) Consists of 15,864,527 ordinary shares and 1,466,507 American Depositary Shares (“ADSs”) held directly by Syncona Portfolio Limited. Each ADS represents 15 ordinary shares, nominal value £0.00001 per share, of the Issuer. The ordinary shares and the ADSs are collectively referred to as the “Ordinary Shares”.

(2) The percentages used in this Amendment No. 1 to Schedule 13D are calculated based on 65,369,417 Ordinary Shares outstanding as of June 30, 2023, as reported in the Issuer’s Form 6-K filed with the SEC on August 15, 2023.

SCHEDULE 13D

CUSIP NO. G3664N 103 13D Page 3 of 8

1	NAMES OF REPORTING PERSON  Syncona Investment Management Limited
2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP  (a) ☐  (b) ☒
3	SEC USE ONLY
4	SOURCE OF FUNDS  WC
5	CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEMS 2(d) or 2(e)  ☐
6	CITIZENSHIP OR PLACE OF ORGANIZATION  United Kingdom

NUMBER OF SHARES BENEFICIALLY OWNED BY EACH REPORTING PERSON WITH	7	SOLE VOTING POWER  0
	8	SHARED VOTING POWER  37,862,132(1)
	9	SOLE DISPOSITIVE POWER  0
	10	SHARED DISPOSITIVE POWER  37,862,132(1)

11	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON  37,862,132(1)
12	CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES  ☐
13	PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)  57.92%(2)
14	TYPE OF REPORTING PERSON  CO

(1) Consists of 15,864,527 ordinary shares and 1,466,507 American Depositary Shares (“ADSs”) held directly by Syncona Portfolio Limited. Each ADS represents 15 ordinary shares, nominal value £0.00001 per share, of the Issuer. The ordinary shares and the ADSs are collectively referred to as the “Ordinary Shares”.

(2) The percentages used in this Amendment No. 1 to Schedule 13D are calculated based on 65,369,417 Ordinary Shares outstanding as of June 30, 2023, as reported in the Issuer’s Form 6-K filed with the SEC on August 15, 2023.

SCHEDULE 13D

CUSIP NO. G3664N 103 13D Page 4 of 8

1	NAMES OF REPORTING PERSON  Syncona Limited
2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP  (a) ☐  (b) ☒
3	SEC USE ONLY
4	SOURCE OF FUNDS  WC
5	CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEMS 2(d) or 2(e)  ☐
6	CITIZENSHIP OR PLACE OF ORGANIZATION  Guernsey

NUMBER OF SHARES BENEFICIALLY OWNED BY EACH REPORTING PERSON WITH	7	SOLE VOTING POWER  0
	8	SHARED VOTING POWER  37,862,132(1)
	9	SOLE DISPOSITIVE POWER  0
	10	SHARED DISPOSITIVE POWER  37,862,132(1)

11	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON  37,862,132(1)
12	CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES  ☐
13	PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)  57.92%(2)
14	TYPE OF REPORTING PERSON  CO

(1) Consists of 15,864,527 ordinary shares and 1,466,507 American Depositary Shares (“ADSs”) held directly by Syncona Portfolio Limited. Each ADS represents 15 ordinary shares, nominal value £0.00001 per share, of the Issuer. The ordinary shares and the ADSs are collectively referred to as the “Ordinary Shares”.

(2) The percentages used in this Amendment No. 1 to Schedule 13D are calculated based on 65,369,417 Ordinary Shares outstanding as of June 30, 2023, as reported in the Issuer’s Form 6-K filed with the SEC on August 15, 2023.

SCHEDULE 13D

CUSIP NO. G3664N 103 13D Page 5 of 8

1	NAMES OF REPORTING PERSON  Martin Murphy
2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP  (a) ☐  (b) ☒
3	SEC USE ONLY
4	SOURCE OF FUNDS  PF
5	CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEMS 2(d) or 2(e)  ☐
6	CITIZENSHIP OR PLACE OF ORGANIZATION  United Kingdom

NUMBER OF SHARES BENEFICIALLY OWNED BY EACH REPORTING PERSON WITH	7	SOLE VOTING POWER  0
	8	SHARED VOTING POWER  37,862,132(1)
	9	SOLE DISPOSITIVE POWER  0
	10	SHARED DISPOSITIVE POWER  37,862,132(1)

11	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON  37,862,132(1)
12	CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES  ☐
13	PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)  57.92%(2)
14	TYPE OF REPORTING PERSON  IN

(1) Consists of 15,864,527 ordinary shares and 1,466,507 American Depositary Shares (“ADSs”) held directly by Syncona Portfolio Limited. Each ADS represents 15 ordinary shares, nominal value £0.00001 per share, of the Issuer. The ordinary shares and the ADSs are collectively referred to as the “Ordinary Shares”.

(2) The percentages used in this Amendment No. 1 to Schedule 13D are calculated based on 65,369,417 Ordinary Shares outstanding as of June 30, 2023, as reported in the Issuer’s Form 6-K filed with the SEC on August 15, 2023.

SCHEDULE 13D

CUSIP NO. G3664N 103 13D Page 6 of 8

1	NAMES OF REPORTING PERSON  Chris Hollowood
2	CHECK THE APPROPRIATE BOX IF A MEMBER OF A GROUP  (a) ☐  (b) ☒
3	SEC USE ONLY
4	SOURCE OF FUNDS  PF
5	CHECK BOX IF DISCLOSURE OF LEGAL PROCEEDINGS IS REQUIRED PURSUANT TO ITEMS 2(d) or 2(e)  ☐
6	CITIZENSHIP OR PLACE OF ORGANIZATION  United Kingdom

NUMBER OF SHARES BENEFICIALLY OWNED BY EACH REPORTING PERSON WITH	7	SOLE VOTING POWER  0
	8	SHARED VOTING POWER  37,862,132(1)
	9	SOLE DISPOSITIVE POWER  0
	10	SHARED DISPOSITIVE POWER  37,862,132(1)

11	AGGREGATE AMOUNT BENEFICIALLY OWNED BY EACH REPORTING PERSON  37,862,132(1)
12	CHECK BOX IF THE AGGREGATE AMOUNT IN ROW (11) EXCLUDES CERTAIN SHARES  ☐
13	PERCENT OF CLASS REPRESENTED BY AMOUNT IN ROW (11)  57.92%(2)
14	TYPE OF REPORTING PERSON  IN

(1) Consists of 15,864,527 ordinary shares and 1,466,507 American Depositary Shares (“ADSs”) held directly by Syncona Portfolio Limited. Each ADS represents 15 ordinary shares, nominal value £0.00001 per share, of the Issuer. The ordinary shares and the ADSs are collectively referred to as the “Ordinary Shares”.

(2) The percentages used in this Amendment No. 1 to Schedule 13D are calculated based on 65,369,417 Ordinary Shares outstanding as of June 30, 2023, as reported in the Issuer’s Form 6-K filed with the SEC on August 15, 2023.

SCHEDULE 13D

CUSIP NO. G3664N 103 13D Page 7 of 8

Explanatory Note

This Amendment No. 1 to Schedule 13D (this “Amendment No. 1”) amends and supplements the statement on Schedule 13D filed with the United States Securities and Exchange Commission (the “SEC”) on March 25, 2022 (the “Original Schedule 13D” and as amended by this Amendment No. 1, the “Schedule 13D”) and is being filed by Syncona Portfolio Limited (“Syncona Portfolio”), Syncona Holdings Limited (“Syncona Holdings”), Syncona Limited (“Syncona Limited”), Syncona Investment Management Limited (“Syncona”), Martin Murphy and Chris Hollowood (collectively, the “Reporting Persons”) to reflect a proposal by Syncona to acquire all of the share capital of Freeline Therapeutics Holdings plc (the “Issuer”) not currently owned by it or its affiliates.

Information and defined terms reported in the Original Schedule 13D remain in effect except to the extent they are amended or superseded by information or defined terms contained in this Amendment No. 1.

Item 1. Security and Issuer.

Item 1 of the Original Schedule 13D is hereby amended and supplemented as follows:

The principal executive office of the Issuer is located at Sycamore House, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2BP, United Kingdom. Each ADS represents 15 ordinary shares, nominal value £0.00001 per share, of the Issuer.

Item 2. Identity and Background.

Item 2(b) of the Original Schedule 13D is hereby amended and supplemented as follows:

The address of the principal business office of Syncona Portfolio, Syncona Holdings and Syncona Limited is Frances House, PO Box 273, Sir William Place, St. Peter Port, Guernsey, GY1 3RD, Channel Islands.

Item 3. Source and Amount of Funds or Other Consideration.

Item 3 of the Original Schedule 13D is hereby amended and supplemented as follows:

The information set forth in Item 4 of this Amendment No. 1 is hereby incorporated by reference into this Item 3.

Item 4. Purpose of Transaction.

Item 4 of the Original Schedule 13D is hereby amended and supplemented as follows:

On October 17, 2023, Syncona submitted to the Issuer a non-binding proposal outlining the principal terms on which an affiliate of Syncona would acquire all of the outstanding Ordinary Shares (including, for the avoidance of doubt, those represented by ADSs) (collectively, the “Issuer Securities”) of the Issuer not currently owned by Syncona and its affiliates (the “Proposal”). A copy of the Proposal is attached to this Amendment No. 1 as Exhibit 99.2. The Proposal was submitted to the special committee of the Board of Directors of the Issuer (the “Board”), which committee is comprised of independent directors of the Issuer and excludes Chris Hollowood, who is Chief Executive Officer of Syncona and a current member of the Board (the “Special Committee”). Syncona stated in the Proposal that it expects the Special Committee advised by independent legal and financial advisors will consider the Proposal and make a recommendation to the shareholders of the Issuer. The Proposal is subject to a number of conditions, including, among other things, the negotiation and execution of definitive agreements; the approval of the transaction by shareholders of the Issuer; and any applicable regulatory and other customary conditions.

Syncona intends to engage in discussions with the Issuer and its representatives concerning the Proposal. There can be no certainty as to whether discussions will occur, or if they do, the outcome of such discussions, and no assurances can be given that the transaction contemplated by the Proposal or any other potential transaction involving the Reporting Persons and the Issuer will be consummated, or if a transaction is undertaken, as to its terms or timing.

SCHEDULE 13D

CUSIP NO. G3664N 103 13D Page 8 of 8

The Reporting Persons are not party to any binding agreement with the Issuer concerning the Proposal. The Proposal provides that it is non-binding and, as such, does not constitute a binding contractual commitment or an offer or proposal capable of acceptance, and does not imply or create any obligation on any Reporting Person or any of their respective affiliates to enter into a transaction. Syncona reserves the right to modify or withdraw the Proposal at any time.

In addition to the information disclosed in this Amendment No. 1, the Reporting Persons reserve the right to (i) formulate other plans and proposals, (ii) take any actions with respect to their respective investments in the Issuer and (iii) subject to applicable law and regulation, acquire additional Issuer Securities or dispose of some or all of the Issuer Securities beneficially owned by them, in each case in the open market, through privately negotiated transactions or otherwise. The Reporting Persons may at any time reconsider and/or change their respective plans or proposals relating to the foregoing.

The Proposal may result in one or more of the actions specified in clauses (a) to (j) of Item 4 of Schedule 13D, including, without limitation, the acquisition of additional securities of the Issuer, a merger or other extraordinary transaction involving the Issuer, the delisting of the Issuer Securities from Nasdaq and the Issuer Securities becoming eligible for termination of registration pursuant to Section 12(g)(4) of the Securities Exchange Act of 1934, as amended.

This Amendment No. 1 is not an offer to purchase or a solicitation of an offer to sell any securities. The Reporting Persons do not intend to disclose developments with respect to the foregoing matters, except as may be required by applicable law. The foregoing is not intended to limit the matters previously disclosed in Item 4 of this Amendment No. 1.

Item 5. Interest in Securities of the Issuer.

Item 5 of the Original Schedule 13D is hereby amended and supplemented as follows:

The information set forth in Item 4 of this Amendment No. 1 is hereby incorporated by reference into this Item 5.

See Items 11 and 13 of the cover pages to this Amendment No. 1 for the aggregate number and percentage of ordinary shares and ADSs that are beneficially owned by each Reporting Person as of the date hereof. See Items 7 through 10 of the cover pages to this Amendment No. 1 for the number of ordinary shares and ADSs that are beneficially owned by each Reporting Person as of the date hereof as to whether there is sole or shared power to vote or direct the vote, and sole or shared power to dispose or direct the disposition.

Item 6. Contracts, Arrangements, Understandings or Relationships with Respect to Securities of the Issuer.

Item 6 of the Original Schedule 13D is hereby amended and supplemented as follows:

The information set forth in Item 4 of this Amendment No. 1 is hereby incorporated by reference into this Item 6.

Item 7. Material to be Filed as Exhibits.

Item 7 of the Original Schedule 13D is hereby amended and supplemented as follows:

Exhibit 99.2 Letter from Syncona Investment Management Limited to Freeline Therapeutics Holdings plc, dated October 17, 2023.

SIGNATURE

After reasonable inquiry and to the best of the undersigned’s knowledge and belief, the undersigned hereby certifies that the information set forth in this statement is true, complete and correct.

Dated: October 18, 2023

SYNCONA PORTFOLIO LIMITED
By:	/s/ Rob Hutchinson
Name:	Rob Hutchinson
Title:	Director
SYNCONA HOLDINGS LIMITED
By:	/s/ Rob Hutchinson
Name:	Rob Hutchinson
Title:	Director
SYNCONA INVESTMENT MANAGEMENT LIMITED
By:	/s/ Chris Hollowood
Name:	Chris Hollowood
Title:	CEO
SYNCONA LIMITED
By:	/s/ Rob Hutchinson
Name:	Rob Hutchinson
Title:	Director
/s/ Martin Murphy
Martin Murphy
/s/ Chris Hollowood
Chris Hollowood

EX-99.2

Exhibit 99.2

17 October 2023   Special Committee of the Board of Directors Freeline Therapeutics Holdings plc Sycamore House Gunnels Wood Road Stevenage Hertfordshire SG1 2BP Syncona Investment Management Limited 8 Bloomsbury Street, 2^nd Floor London WC1B 3SR contact@synconaltd.com

Non-binding indication of interest in acquiring Freeline

Dear Special Committee,

We write to you to express our interest in an acquisition of the entire share capital of Freeline Therapeutics Holdings plc (“Freeline”) not currently owned by us or our affiliates, by a newco (“Newco”) established by affiliates of Syncona Investment Management Limited (“Syncona”).

Strategic rationale

Syncona is already well-known to Freeline but, briefly, we seek to create, build and scale substantial global businesses that deliver novel products to patients in areas of high unmet medical need to extend and enhance human life. Syncona’s business model is to set our portfolio companies up to compete on a world stage, through significant funding, a long-term commercial strategy and the recruitment of leading management teams. We have substantial experience in gene therapy and consider ourselves a differentiated owner of AAV assets, with expertise extending along the entire lifecycle of such products.

We have been a long-term shareholder in Freeline, and supported the company to IPO on NASDAQ in 2020 and subsequently invested in its follow-on equity fundraising in March 2022. However, given that the company is only funded to Q2 2024, we see significant challenges to the company in its current form. We therefore think it is the right time to consider whether being publicly listed remains in the best interests of Freeline, its shareholders, its employees or the patients who its products are being developed for.

We believe that the FLT201 programme has the potential to deliver a drug with transformational impact for patients, and that Freeline has a team that can execute effectively on that opportunity, if it can raise the relevant funding. We see an opportunity to now change Freeline’s capital structure, with Syncona’s support, to allow it to take FLT201 through to BLA approval.

Our proposal

Our proposal is for Newco to acquire the entire share capital of Freeline not currently owned by Syncona or its affiliates for an upfront cash payment of $5.00 per American Depositary Share, representing a premium of 20% over the volume weighted average price of $4.16 over the period since the release of the Galileo data on 4 October 2023 until close on 16 October 2023.

We believe this to be an attractive proposal for shareholders, which on closing removes the risk to them of an insolvent outcome in which they receive no value from the company, and delivers a path forward for the company and the FLT201 programme.

We anticipate the acquisition would be structured as a scheme of arrangement, requiring approval by the company’s shareholders and the English courts, and that Newco would enter into an implementation agreement setting out the terms of the transaction with Freeline.

We are prepared to sign an implementation agreement as soon as the documentation can be agreed. Given our familiarity with the company, we do not anticipate requiring any further due diligence. This proposal is subject to any applicable regulatory and other customary conditions, but is not subject to any financing condition and has received all required Syncona approvals.

Next steps

We recognise the importance of timing to you. It is our intention to move quickly as indicated above.

In line with legal requirements, Syncona will disclose this letter through an update to its Schedule 13D filing.

We expect that the Special Committee (comprised of independent directors appointed by Freeline’s Board, which committee excludes Chris Hollowood, who is Chief Executive Officer of Syncona and a current member of the Board) advised by independent legal and financial advisors will consider this proposal and make a recommendation to Freeline’s shareholders.

Costs

Each party will bear their own costs in connection with the proposed transaction.

Other Matters

This letter is governed by English law. The paragraph headed “Costs” is intended to be immediately binding; all other sections of this letter are non-binding and, as such, do not constitute a binding contractual commitment or an offer or proposal capable of acceptance, and do not imply or create any obligation on Syncona or any of its affiliates to enter into a transaction.

We look forward to hearing from you and are available at any time to discuss and to answer any questions you may have regarding our proposal or intentions. Please contact Andrew Cossar or Alex Hamilton with any questions.

Yours sincerely,

/s/ Andrew Cossar

Andrew Cossar

Executive Partner

For Syncona Investment Management Limited