CUE / Cue Biopharma, Inc. - SEC-Einreichungen, Jahresbericht, Proxy Statement

Security Type

Calculation of Filing Fee Tables S-3 Cue Biopharma, Inc. Table 1: Newly Registered and Carry Forward Securities ☐Not Applicable 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

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, 2026 Cue Biopharma, Inc.

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, 2026 Cue Biopharma, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-38327 47-3324577 (State or Other Jurisdiction of Incorporation) (Commission File N

Table 1: Newly Registered Securities

Calculation of Filing Fee Tables S-8 Cue Biopharma, 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, $0.001 par value per share Other 2,327,826 $ 20.49 $ 47,697,154.74 0.0001381 $ 6,586.98 Total Offer

As filed with the Securities and Exchange Commission on June 3, 2026

S-8 As filed with the Securities and Exchange Commission on June 3, 2026 Registration No.

As filed with the Securities and Exchange Commission on June 3, 2026

S-3 Table of Contents As filed with the Securities and Exchange Commission on June 3, 2026 Registration No.

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 29, 2026 Cue Biopharma, Inc.

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 29, 2026 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission File N

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 (Amendment No.  )

DEF 14A Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.

SEPARATION AND RELEASE OF CLAIMS AGREEMENT ATTACHMENT A

Exhibit 10.3 SEPARATION AND RELEASE OF CLAIMS AGREEMENT This Separation and Release of Claims Agreement (the “Agreement”) is entered into by and between Cue Biopharma, Inc. (the “Company”) and Usman Azam (“Executive”) (together, the “Parties”). WHEREAS, the Company and Executive are parties to that certain Executive Employment Agreement effective as of September 29, 2025 (the “Employment Agreement

CUE BIOPHARMA, INC. LUCINDA WARREN

Exhibit 10.2 CUE BIOPHARMA, INC. AMENDED AND RESTATED EXECUTIVE EMPLOYMENT AGREEMENT This Amended and Restated Executive Employment Agreement (the “Agreement”) is made by and between Cue Biopharma, Inc., a Delaware corporation (“Cue” or the “Company”), and Lucinda Warren (“Executive,” and together with Cue, the “Parties”). WHEREAS, the Company and Executive desire to enter into this Agreement to s

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 14, 2026 Cue Biopharma, Inc.

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 14, 2026 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission File N

Cue Biopharma Reports First Quarter 2026 Financial Results and Recent Strategic Developments Moves designed to strengthen leadership and financial position, advance portfolio, and leverage expertise in precision immunoengineering

Cue Biopharma Reports First Quarter 2026 Financial Results and Recent Strategic Developments Moves designed to strengthen leadership and financial position, advance portfolio, and leverage expertise in precision immunoengineering • Enhanced the company’s portfolio with an exclusive license for, CUE-221, a Phase 2 program targeting allergic disease • Hosted virtual R&D day showcasing CUE-401, a bifunctional IL-2 and TGF-B program targeting autoimmune disease • Strengthened the company’s balance sheet and ability to fund anticipated cash needs with a $30 million private placement and received a $7.

Third Amendment to Rider to License Agreement Vivarium LICENSEE: Exhibit 1-A:

Exhibit 10.1 Third Amendment to Rider to License Agreement Vivarium This Third Amendment to Rider to License Agreement Vivarium (“Amendment”) is dated January 10, 2026 (“Effective Date”) and entered into by and between MIL 40G, LLC (“SmartLabs” or “Licensor”) and Cue Biopharma, Inc., (“Licensee”). WHEREAS, Licensor and Licensee are parties to that certain License Agreement dated March 28, 2022 (as

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

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, 2026 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: 001-38327 Cue Bioph

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 (Amendment No.  )

PRE 14A Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.

Table 1: Newly Registered Securities

Calculation of Filing Fee Tables S-8 Cue Biopharma, 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, $0.001 par value per share Other 3,000,000 $ 14.66 $ 43,980,000.00 0.0001381 $ 6,073.64 Total Offer

FORM OF COMMON STOCK PURCHASE WARRANT CUE BIOPHARMA, INC. Warrant Shares: [ ] Issue Date: [__], 2026

EX-4.3 Exhibit 4.3 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 UNLES

INVESTOR AGREEMENT By and Between ASCENDANT HEALTH SCIENCES LTD. CUE BIOPHARMA, INC. Dated as of [_____], 2026

EX-10.2 Exhibit 10.2 INVESTOR AGREEMENT By and Between ASCENDANT HEALTH SCIENCES LTD. AND CUE BIOPHARMA, INC. Dated as of [], 2026 INVESTOR AGREEMENT THIS INVESTOR AGREEMENT (this “Agreement”) is made as of [], 2026, by and between Ascendant Health Sciences Ltd. (the “Investor”), a corporation organized and existing under the laws of the Cayman Islands, with its principal business office at Palm G

CUE BIOPHARMA, INC. FORM OF PRE-FUNDED WARRANT TO PURCHASE COMMON STOCK

EX-4.2 Exhibit 4.2 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 UNLES

CUE BIOPHARMA, INC. 2026 INDUCEMENT STOCK INCENTIVE PLAN

EX-99.1 Exhibit 99.1 CUE BIOPHARMA, INC. 2026 INDUCEMENT STOCK INCENTIVE PLAN 1. Purpose The purpose of this 2026 Inducement Stock Incentive Plan (the “Plan”) of Cue Biopharma, Inc., a Delaware corporation (the “Company”), is to advance the interests of the Company’s stockholders by enhancing the Company’s ability to attract, retain and motivate persons who are expected to make important contribut

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 27, 2026 Cue Biopharma, Inc

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 27, 2026 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission File

REGISTRATION RIGHTS AGREEMENT

EX-10.4 Exhibit 10.4 REGISTRATION RIGHTS AGREEMENT This REGISTRATION RIGHTS AGREEMENT (this “Agreement”) is made and entered into as of April 30, 2026, by and among Cue Biopharma, Inc., a Delaware corporation (the “Company”), and the “Investors” named in that certain Securities Purchase Agreement, by and among the Company and the Investors, dated as of April 30, 2026 (the “Purchase Agreement”). Ca

SECURITIES PURCHASE AGREEMENT

EX-10.3 Exhibit 10.3 SECURITIES PURCHASE AGREEMENT This SECURITIES PURCHASE AGREEMENT (this “Agreement”) is made and entered into as of April 30, 2026, by and among Cue Biopharma, Inc., a Delaware corporation (the “Company”), and the Investors identified on the signature pages attached hereto (each an “Investor” and collectively, the “Investors”). RECITALS A. The Company and the Investors are exec

CUE BIOPHARMA, INC. WARRANT TO PURCHASE COMMON STOCK

EX-4.1 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 UNLES

As filed with the Securities and Exchange Commission on April 30, 2026

S-8 As filed with the Securities and Exchange Commission on April 30, 2026 Registration No.

SECURITIES PURCHASE AGREEMENT By and Between ASCENDANT HEALTH SCIENCES LTD. CUE BIOPHARMA, INC. Dated as of April 30, 2026

EX-10.1 Exhibit 10.1 SECURITIES PURCHASE AGREEMENT By and Between ASCENDANT HEALTH SCIENCES LTD. AND CUE BIOPHARMA, INC. Dated as of April 30, 2026 SECURITIES PURCHASE AGREEMENT THIS SECURITIES PURCHASE AGREEMENT (this “Agreement”) is dated as of April 30, 2026 (the “Signing Date”), by and between Ascendant Health Sciences Ltd. (the “Investor”), a corporation organized and existing under the laws

CUE BIOPHARMA, INC. 2026 INDUCEMENT STOCK INCENTIVE PLAN

EX-10.5 Exhibit 10.5 CUE BIOPHARMA, INC. 2026 INDUCEMENT STOCK INCENTIVE PLAN 1. Purpose The purpose of this 2026 Inducement Stock Incentive Plan (the “Plan”) of Cue Biopharma, Inc., a Delaware corporation (the “Company”), is to advance the interests of the Company’s stockholders by enhancing the Company’s ability to attract, retain and motivate persons who are expected to make important contribut

Cue Biopharma Announces $30 Million Private Placement

EX-99.2 Exhibit 99.2 Cue Biopharma Announces $30 Million Private Placement BOSTON, April 30, 2026 (GLOBE NEWSWIRE) — Cue Biopharma, Inc. (Nasdaq: CUE), a clinical-stage biopharmaceutical company developing a novel class of therapeutic biologics to selectively engage and modulate disease-specific T cells for the treatment of autoimmune and inflammatory diseases, announced today that it has entered

Novel dual-mechanism anti-IgE antibody designed to improve upon existing and emerging therapies for IgE-mediated diseases Cue Biopharma plans to initiate global Phase 2b trial in food allergy following anticipated results in 2H 2026 from Ascendant He

EX-99.1 Exhibit 99.1 Cue Biopharma Expands Pipeline with Exclusive License from Ascendant Health Sciences Ltd. for Clinical-Stage Dual-Mechanism Anti-IgE Antibody Novel dual-mechanism anti-IgE antibody designed to improve upon existing and emerging therapies for IgE-mediated diseases Cue Biopharma plans to initiate global Phase 2b trial in food allergy following anticipated results in 2H 2026 from

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 22, 2026 Cue Biopharma, Inc

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 22, 2026 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission File

CERTIFICATE OF AMENDMENT AMENDED AND RESTATED CERTIFICATE OF INCORPORATION CUE BIOPHARMA, INC. Pursuant to Section 242 of the General Corporation Law of the State of Delaware

Exhibit 3.1 CERTIFICATE OF AMENDMENT OF AMENDED AND RESTATED CERTIFICATE OF INCORPORATION OF CUE BIOPHARMA, INC. Pursuant to Section 242 of the General Corporation Law of the State of Delaware Cue Biopharma, Inc. (the “Corporation”), a corporation organized and existing under and by virtue of the General Corporation Law of the State of Delaware, does hereby certify: FIRST: That the Board of Direct

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 13, 2026 Cue Biopharma, Inc

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 13, 2026 Cue Biopharma, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-38327 47-3324577 (State or Other Jurisdiction of Incorporation) (Commission File

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 1, 2026 Cue Biopharma, Inc.

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 1, 2026 Cue Biopharma, Inc. (Exact name of Registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission File

CUE BIOPHARMA, INC. 40 Guest Street Boston, Massachusetts 02135

CORRESP CUE BIOPHARMA, INC. 40 Guest Street Boston, Massachusetts 02135 March 27, 2026 VIA EDGAR U.S. Securities and Exchange Commission Division of Corporation Finance, Office of Life Sciences 100 F Street, N.E. Washington, D.C. 20549 Attention: Tim Buchmiller Re: Cue Biopharma, Inc. Registration Statement on Form S-3 Filed March 16, 2026 File No. 333-294366 Request for Acceleration Ladies and Ge

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 23, 2026 Cue Biopharma, Inc

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 23, 2026 Cue Biopharma, Inc. (Exact name of Registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission File

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 (Amendment No. )

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 (Amendment No. ) Filed by the Registrant ☒ 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))

LETTER

March 23, 2026 Lucinda Warren Chief Financial and Business Officer Cue Biopharma, Inc.

Form of Senior Note (FACE OF SECURITY)

EX-4.5 Exhibit 4.5 Form of Senior Note (FACE OF SECURITY) [Each Global Security shall bear substantially the following legend: UNLESS AND UNTIL IT IS EXCHANGED IN WHOLE OR IN PART FOR SECURITIES IN DEFINITIVE REGISTERED FORM, THIS SECURITY MAY NOT BE TRANSFERRED EXCEPT AS A WHOLE BY THE DEPOSITARY TO A NOMINEE OF THE DEPOSITARY OR BY A NOMINEE OF THE DEPOSITARY TO THE DEPOSITARY OR ANOTHER NOMINEE

Cue Biopharma Reports Fourth Quarter and Full Year 2025 Financial Results and Business Highlights

Cue Biopharma Reports Fourth Quarter and Full Year 2025 Financial Results and Business Highlights • Advanced research and development of CUE-401 for IND (Investigational New Drug) readiness – CUE-401 is the Company’s lead asset for the treatment of autoimmune and inflammatory diseases • Appointed industry veteran Lucinda Warren as Chief Financial and Business Officer • Raised net proceeds of $10.

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 16, 2026 Cue Biopharma, Inc

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 16, 2026 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission File

No less frequently than (a) each [**] during the first [**] following the Effective Date, (b) every [**] during the reminder of the Research Period, and (c) [**] of the Term (following expiration of the Research Period), IMSCP shall deliver a written

Certain identified information has been excluded from the exhibit because it is both (i) not material and (ii) is the type of information that the registrant treats as private or confidential.

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 (Amendment No. )

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 (Amendment No. ) Filed by the Registrant ☒ 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 14

ARS

Mobilizing the Patient’s Immune System to Treat Serious Diseases 2025 ANNUAL REPORT 2025 ANNUAL REPORT CUEBIOPHARMA.

SUBSIDIARIES OF CUE BIOPHARMA, INC.

EXHIBIT 21.1 SUBSIDIARIES OF CUE BIOPHARMA, INC. Registrant’s consolidated subsidiaries are shown below, together with the state or jurisdiction of organization of each subsidiary and the percentage of voting securities that Registrant owns in each subsidiary. Name of Subsidiary Jurisdiction of Incorporation or Organization Percent of Outstanding Voting Securities Owned Cue Biopharma Securities Co

SEPARATION AND RELEASE OF CLAIMS AGREEMENT

Execution Version Exhibit 10.28 SEPARATION AND RELEASE OF CLAIMS AGREEMENT This Separation and Release of Claims Agreement (the “Agreement”) is made as of the Agreement Effective Date (as defined below) by and between Cue Biopharma, Inc. (the “Company”) and Matteo Levisetti, M.D. (“Executive”) (together, the “Parties”). WHEREAS, the Company and Executive are parties to an Amended and Restated Exec

CUE BIOPHARMA, INC. EXECUTIVE EMPLOYMENT AGREEMENT Amendment to Employment Agreement Second Amendment to Employment Agreement

Exhibit 10.27 CUE BIOPHARMA, INC. EXECUTIVE EMPLOYMENT AGREEMENT This Executive Employment Agreement (the “Agreement”) is made by and between Cue Biopharma, Inc., a Delaware corporation (“Cue” or the “Company”), and Lucinda Warren (“Executive,” and together with Cue, the “Parties”). WHEREAS, the Company and Executive desire to enter into this Agreement to set forth the conditions under which the E

STOCK OPTION AGREEMENT INCORPORATED TERMS AND CONDITIONS This agreement evidences the grant by the Company, on the grant date (the “Grant Date”) set forth in the Notice of Grant that forms part of this agreement (the “Notice of Grant”), to the Partic

Exhibit 10.14 NOTICE OF GRANT OF INCENTIVE STOCK OPTION CUE BIOPHARMA, INC. 2025 STOCK INCENTIVE PLAN FOR GOOD AND VALUABLE CONSIDERATION, Cue Biopharma, Inc. (the “Company”) hereby grants, pursuant to the provisions of the Cue Biopharma, Inc. 2025 Stock Incentive Plan (the “Plan”), to the Participant designated below, an Incentive Stock Option to purchase the number of Shares specified below (the

Cue Biopharma, Inc. Director Compensation Policy

Exhibit 10.20 Cue Biopharma, Inc. Director Compensation Policy Members of the Board of Directors (the “Board”) of Cue Biopharma, Inc. (the “Company”) who are not employees of the Company or any subsidiary of the Company (“non-employee directors”) shall receive compensation for their services on the Board in accordance with this Director Compensation Policy (this “Policy”). Cash Compensation Each n

As filed with the Securities and Exchange Commission on March 16, 2026

S-3 Table of Contents As filed with the Securities and Exchange Commission on March 16, 2026 Registration No.

DESCRIPTION OF COMMON STOCK OF CUE BIOPHARMA, INC. REGISTERED PURSUANT TO SECTION 12 OF THE SECURITIES EXCHANGE ACT OF 1934

EXHIBIT 4.2 DESCRIPTION OF COMMON STOCK OF CUE BIOPHARMA, INC. REGISTERED PURSUANT TO SECTION 12 OF THE SECURITIES EXCHANGE ACT OF 1934 The following information is a summary of information concerning the common stock, par value $0.001 per share (the “Common Stock”), of Cue Biopharma, Inc. (“we,” “our,” or “us”) and does not purport to be complete. It is subject to and qualified in its entirety by

Security Type

Calculation of Filing Fee Tables S-3 Cue Biopharma, Inc. Table 1: Newly Registered and Carry Forward Securities ☐Not Applicable 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

CUE BIOPHARMA, INC. Dated as of _______________ SUBORDINATED DEBT SECURITIES

EX-4.4 Exhibit 4.4 CUE BIOPHARMA, INC. and Trustee INDENTURE Dated as of SUBORDINATED DEBT SECURITIES CROSS-REFERENCE TABLE 1 Section of Trust Indenture Act of 1939, as amended Section of Indenture 310(a) 6.09 310(b) 6.08 6.10 310(c) Inapplicable 311(a) 6.13 311(b) 6.13 311(c) Inapplicable 312(a) 4.01 4.04 312(b) 4.04(c) 312(c) 4.04(c) 313(a) 4.03 313(b) 4.03 313(c) 4.03 313(d) 4.03 314(a) 4.02 31

STOCK OPTION AGREEMENT INCORPORATED TERMS AND CONDITIONS This agreement evidences the grant by the Company, on the grant date (the “Grant Date”) set forth in the Notice of Grant that forms part of this agreement (the “Notice of Grant”), to the Partic

Exhibit 10.15 NOTICE OF GRANT OF NON-QUALIFIED STOCK OPTION CUE BIOPHARMA, INC. 2025 STOCK INCENTIVE PLAN FOR GOOD AND VALUABLE CONSIDERATION, Cue Biopharma, Inc. (the “Company”) hereby grants, pursuant to the provisions of the Cue Biopharma, Inc. 2025 Stock Incentive Plan (the “Plan”), to the Participant designated below, an Non-Qualified Stock Option to purchase the number of Shares specified be

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

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, 2025 ☐ 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: 001-38327 Cue Biopharma, In

CUE BIOPHARMA, INC. Dated as of _______________ SENIOR DEBT SECURITIES

EX-4.3 Exhibit 4.3 CUE BIOPHARMA, INC. and Trustee INDENTURE Dated as of SENIOR DEBT SECURITIES CROSS-REFERENCE TABLE1 Section of Trust Indenture Act of 1939, as amended Section of Indenture 310(a) 6.09 310(b) 6.08 6.10 310(c) Inapplicable 311(a) 6.13 311(b) 6.13 311(c) Inapplicable 312(a) 4.014.04 312(b) 4.04(c) 312(c) 4.04(c) 313(a) 4.03 313(b) 4.03 313(c) 4.03 313(d) 4.03 314(a) 4.02 314(b) Ina

Form of Subordinated Note (FACE OF SECURITY)

EX-4.6 Exhibit 4.6 Form of Subordinated Note (FACE OF SECURITY) [Each Global Security shall bear substantially the following legend: UNLESS AND UNTIL IT IS EXCHANGED IN WHOLE OR IN PART FOR SECURITIES IN DEFINITIVE REGISTERED FORM, THIS SECURITY MAY NOT BE TRANSFERRED EXCEPT AS A WHOLE BY THE DEPOSITARY TO A NOMINEE OF THE DEPOSITARY OR BY A NOMINEE OF THE DEPOSITARY TO THE DEPOSITARY OR ANOTHER N

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 (Amendment No. )

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 (Amendment No. ) Filed by the Registrant ☒ 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 14

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 18, 2026 Cue Biopharma,

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 18, 2026 Cue Biopharma, Inc. (Exact name of Registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission F

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 9, 2026 Cue Biopharma, 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): February 9, 2026 Cue Biopharma, Inc. (Exact name of Registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission Fi

CUE BIOPHARMA, INC. WARRANT TO PURCHASE COMMON STOCK

EX-4.1 Exhibit 4.1 CUE BIOPHARMA, INC. WARRANT TO PURCHASE COMMON STOCK Number of Shares: [] (subject to adjustment) Warrant No. [] Original Issue Date: December 22, 2025 Cue Biopharma, Inc., a Delaware corporation (the “Company”), hereby certifies that, for good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, [] or its registered assigns (the “Holder”) is

FORM OF COMMON STOCK PURCHASE WARRANT CUE BIOPHARMA, INC. Warrant Shares: [ ] Issue Date: December 22, 2025

EX-4.2 Exhibit 4.2 FORM OF COMMON STOCK PURCHASE WARRANT CUE BIOPHARMA, INC. Warrant Shares: [ ] Issue Date: December 22, 2025 Initial Exercise Date: December 22, 2025 THIS COMMON STOCK PURCHASE WARRANT (the “Warrant”) certifies that, for value received, [ ] or its assigns (the “Holder”) is entitled, upon the terms and subject to the limitations on exercise and the conditions hereinafter set forth

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): December 19, 2025 Cue Biopharma,

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): December 19, 2025 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission F

CUE BIOPHARMA, INC. (a Delaware corporation) 12,500,000 Shares of Common Stock Pre-Funded Warrants to Purchase Up to 23,214,286 Shares of Common Stock Common Stock Warrants to Purchase Up to 17,857,143 Shares of Common Stock UNDERWRITING AGREEMENT

EX-1.1 Exhibit 1.1 CUE BIOPHARMA, INC. (a Delaware corporation) 12,500,000 Shares of Common Stock Pre-Funded Warrants to Purchase Up to 23,214,286 Shares of Common Stock Common Stock Warrants to Purchase Up to 17,857,143 Shares of Common Stock UNDERWRITING AGREEMENT Dated: December 19, 2025 CUE BIOPHARMA, INC. (a Delaware corporation) 12,500,000 Shares of Common Stock Pre-Funded Warrants to Purcha

12,500,000 Shares of Common Stock Pre-Funded Warrants to Purchase 23,214,286 Shares of Common Stock Common Stock Warrants to Purchase 17,857,143 Shares of Common Stock

424B5 Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No. 333-271786 PROSPECTUS SUPPLEMENT (To Prospectus dated May 26, 2023) 12,500,000 Shares of Common Stock Pre-Funded Warrants to Purchase 23,214,286 Shares of Common Stock Common Stock Warrants to Purchase 17,857,143 Shares of Common Stock We are offering (i) 12,500,000 shares of our common stock and accompanying common stock wa

Cue Biopharma Announces Pricing of $10 Million Public Offering

EX-99.1 Exhibit 99.1 Cue Biopharma Announces Pricing of $10 Million Public Offering December 19, 2025 BOSTON, December 19, 2025 (GLOBE NEWSWIRE) — Cue Biopharma, Inc. (Nasdaq: CUE), a clinical-stage biopharmaceutical company developing a novel class of therapeutic biologics to selectively engage and modulate disease-specific T cells for the treatment of autoimmune disease, today announced the pric

SUBJECT TO COMPLETION, DATED DECEMBER 18, 2025

424B5 Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No. 333-271786 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

EX-99.1

Exhibit 99.1

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 24, 2025 Cue Biopharma,

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 24, 2025 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission F

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, 2025 Cue Biopharma,

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, 2025 Cue Biopharma, Inc. (Exact name of Registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission F

Advisor Agreement, dated September 27, 2025, between the Registrant and Daniel Passeri

Exhibit 10.3 Certain identified information has been excluded from the exhibit because it is both (i) not material and (ii) is the type of information that the registrant treats as private or confidential. Double asterisks denote omissions. Attachment A Advisor Agreement This Advisor Agreement (the “Agreement”) is entered into as of 9/27/2025 by and between Cue Biopharma, Inc. (the “Company”), and

Press Release dated November 12, 2025

Cue Biopharma Reports Third Quarter 2025 Financial Results and Recent Business Highlights • Announced strategic collaboration and license agreement with ImmunoScape to develop breakthrough cell therapy approach for solid tumors – Company is entitled to receive upfront payments totaling $15M • Announced strategic transition in leadership to further enable next stage of growth with disruptive autoimmune therapeutic candidates most notably, CUE-401, the Company’s lead autoimmune asset BOSTON, Mass.

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

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, 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: 001-38327 Cue B

Separation and Release of Claims Agreement, dated September 27, 2025, between the Registrant and Daniel Passeri

Exhibit 10.2 SEPARATION AND RELEASE OF CLAIMS AGREEMENT This Separation and Release of Claims Agreement (the “Agreement”) is made as of the Agreement Effective Date (as defined below) by and between Cue Biopharma, Inc. (the “Company”) and Daniel Passeri (“Executive”) (together, the “Parties”). WHEREAS, the Company and Executive are parties to a Third Amended and Restated Executive Employment Agree

Executive Employment Agreement, dated September 28, 2025, between the Registrant and Usman Azam

Exhibit 10.1 Certain identified information has been excluded from the exhibit because it is both (i) not material and (ii) is the type of information that the registrant treats as private or confidential. Double asterisks denote omissions. CUE BIOPHARMA, INC. EXECUTIVE EMPLOYMENT AGREEMENT This Executive Employment Agreement (the “Agreement”) is made by and between Cue Biopharma, Inc., a Delaware

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, 2025 Cue Biopharma,

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, 2025 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission F

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, 2025 Cue Biopharma, 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): November 6, 2025 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission Fi

Cue Biopharma and ImmunoScape Announce Strategic Collaboration to Develop Breakthrough Cell Therapy Approach for Solid Tumors

Cue Biopharma and ImmunoScape Announce Strategic Collaboration to Develop Breakthrough Cell Therapy Approach for Solid Tumors  Exclusive collaboration and license agreement focuses on advancing novel, T cell therapy “Seed-and-Boost” approach exploiting the mechanism of the CUE-100 series of Immuno-STATs®  Novel therapeutic approach is designed to enable in vivo expansion and activation of infuse

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): September 26, 2025 Cue Biopharma,

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): September 26, 2025 Cue Biopharma, Inc. (Exact name of Registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission

Cue Biopharma Reports Second Quarter 2025 Financial Results and Recent Business Highlights

Cue Biopharma Reports Second Quarter 2025 Financial Results and Recent Business Highlights ▪ Received FDA feedback on Pre-IND Briefing Document reinforcing Company’s intention to advance investigational new drug (IND) submission for CUE-401 to address unmet need in the treatment of autoimmune disease.

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 12, 2025 Cue Biopharma, In

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 12, 2025 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission Fil

Second Amendment to the License Agreement, dated June 30, 2025, between Cue Biopharma, Inc. and MIL 40G, LLC

Exhibit 10.2 Second Amendment to License Agreement This Second Amendment to License Agreement (“Second Amendment”) is dated June 30, 2025 (“Effective Date”) and entered into by and between Cue Biopharma, Inc. (“Licensee”) and MIL 40G, LLC (“SmartLabs”). Recitals WHEREAS, SmartLabs and Licensee are parties to a certain License Agreement dated March 28, 2022, as amended by a First Amendment dated Ma

Calculation of Filing Fee Tables

Exhibit 107 Calculation of Filing Fee Tables Form S-8 (Form Type) Cue Biopharma, Inc.

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

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: 001-38327 Cue Biopha

As filed with the Securities and Exchange Commission on August 12, 2025

As filed with the Securities and Exchange Commission on August 12, 2025 Registration No.

Amended and Restated Certificate of Incorporation, as amended

Exhibit 3.1 AMENDED AND RESTATED CERTIFICATE OF INCORPORATION OF CUE BIOPHARMA, INC. The present name of the corporation is Cue Biopharma, Inc. The corporation was incorporated under the name “Imagen Biopharma, Inc.” by the filing of its original Certificate of Incorporation with the Secretary of State of the State of Delaware on December 31, 2014. This Amended and Restated Certificate of Incorpor

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 30, 2025 Cue Biopharma, Inc.

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 30, 2025 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission File

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers, Amendments to Articles of Incorporation or Bylaws; Change in Fiscal Year, 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 4, 2025 Cue Biopharma, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-38327 47-3324577 (State or Other Jurisdiction of Incorporation) (Commission File N

Certificate of Amendment to the Company’s Amended and Restated Certificate of Incorporation, as amended

Exhibit 3.1 CERTIFICATE OF AMENDMENT OF AMENDED AND RESTATED CERTIFICATE OF INCORPORATION OF CUE BIOPHARMA, INC. Pursuant to Section 242 of the General Corporation Law of the State of Delaware Cue Biopharma, Inc. (the “Corporation”), a corporation organized and existing under and by virtue of the General Corporation Law of the State of Delaware, does hereby certify: FIRST: That the Board of Direct

For any date that is not a trading day, the Grant Date Fair Market Value of a share of Common Stock for such date will be determined by using the closing sale price or average of the bid and asked prices, as appropriate, for the immediately preceding

Exhibit 99.1 CUE BIOPHARMA, INC. 2025 STOCK INCENTIVE PLAN 1. Purpose The purpose of this 2025 Stock Incentive Plan (the “Plan”) of Cue Biopharma, Inc., a Delaware corporation (the “Company”), is to advance the interests of the Company’s stockholders by enhancing the Company’s ability to attract, retain and motivate persons who are expected to make important contributions to the Company and by pro

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 (Amendment No. )

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 (Amendment No. ) Filed by the Registrant ☒ 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)) ☐ Defin

AMENDED AND RESTATED CERTIFICATE OF INCORPORATION OF CUE BIOPHARMA, INC.

Exhibit 3.1 AMENDED AND RESTATED CERTIFICATE OF INCORPORATION OF CUE BIOPHARMA, INC. The present name of the corporation is Cue Biopharma, Inc. The corporation was incorporated under the name “Imagen Biopharma, Inc.” by the filing of its original Certificate of Incorporation with the Secretary of State of the State of Delaware on December 31, 2014. This Amended and Restated Certificate of Incorpor

Collaboration and License Agreement between the Registrant and Boehringer Ingelheim International GmbH dated April 10, 2025

Exhibit 10.2 Certain identified information has been excluded from the exhibit because it is both (i) not material and (ii) is the type of information that the registrant treats as private or confidential. Double asterisks denote omissions. COLLABORATION AND LICENSE AGREEMENT BY AND BETWEEN BOEHRINGER INGELHEIM INTERNATIONAL GMBH AND Cue Biopharma, Inc. BI Contract No.: 926652 BI PO No.: 43116788

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 12, 2025 Cue Biopharma, Inc.

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 12, 2025 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission File N

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

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: 001-38327 Cue Bioph

Third Amendment to the Amended and Restated License Agreement with Albert Einstein College of Medicine dated April 10, 2025

Exhibit 10.3 Certain identified information has been excluded from the exhibit because it is both (i) not material and (ii) is the type of information that the registrant treats as private or confidential. Double asterisks denote omissions. BOEHRINGER INGELHEIM AMENDMENT TO THE AMENDED AND RESTATED LICENSE AGREEMENT This Boehringer Ingelheim Amendment to the Amended and Restated License Agreement

Cue Biopharma Reports First Quarter 2025 Financial Results and Recent Business Highlights Announced Boehringer Ingelheim strategic collaboration and license agreement for CUE-501, including an upfront payment of $12 million and ~$345 million in poten

Cue Biopharma Reports First Quarter 2025 Financial Results and Recent Business Highlights Announced Boehringer Ingelheim strategic collaboration and license agreement for CUE-501, including an upfront payment of $12 million and ~$345 million in potential milestone payments Raised gross proceeds of ~$20 million in follow-on capital raise Successfully regained worldwide rights for lead autoimmune program, CUE-401, with potential to become a new standard of care for autoimmune and inflammatory diseases Virtual Event planned for May 15, 2025 at 11 AM ET, featuring two prominent Key Opinion Leaders in the field of Immunology BOSTON, MA, May 12, 2025 - Cue Biopharma, Inc.

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 (Amendment No. )

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 (Amendment No. ) Filed by the Registrant ☒ 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)) ☐ Defin

For any date that is not a trading day, the Grant Date Fair Market Value of a share of Common Stock for such date will be determined by using the closing sale price or average of the bid and asked prices, as appropriate, for the immediately preceding

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 (Amendment No. ) Filed by the Registrant ☒ 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 14

Cue Biopharma Announces Pricing of Approximately $20 Million Public Offering

Exhibit 99.1 Cue Biopharma Announces Pricing of Approximately $20 Million Public Offering April 14, 2025 BOSTON, Apr. 14, 2025 (GLOBE NEWSWIRE) — Cue Biopharma, Inc. (Nasdaq: CUE), a clinical-stage biopharmaceutical company developing a novel class of therapeutic biologics to selectively engage and modulate disease-specific T cells for the treatment of cancer and autoimmune disease, today announce

Form of Common Stock Warrant

EX-4.2 Exhibit 4.2 FORM OF COMMON STOCK PURCHASE WARRANT CUE BIOPHARMA, INC. Warrant Shares: [ ] Issue Date: April 16, 2025 Initial Exercise Date: April 16, 2025 THIS COMMON STOCK PURCHASE WARRANT (the “Warrant”) certifies that, for value received, [ ] or its assigns (the “Holder”) is entitled, upon the terms and subject to the limitations on exercise and the conditions hereinafter set forth, at a

Form of Pre-Funded Warrant

EX-4.1 Exhibit 4.1 CUE BIOPHARMA, INC. WARRANT TO PURCHASE COMMON STOCK Number of Shares: [     ] (subject to adjustment) Warrant No. [  ] Original Issue Date: April 16, 2025 Cue Biopharma, Inc., a Delaware corporation (the “Company”), hereby certifies that, for good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, [     ] or its registered assigns (the “Ho

Underwriting Agreement, dated April 14, 2025, by and between Cue Biopharma, Inc. and Oppenheimer & Co. Inc., as representative of the underwriters named therein

EX-1.1 Exhibit 1.1 CUE BIOPHARMA, INC. (a Delaware corporation) 13,530,780 Shares of Common Stock Pre-Funded Warrants to Purchase Up to 11,469,216 Shares of Common Stock Warrants to Purchase Up to 6,249,999 Shares of Common Stock UNDERWRITING AGREEMENT Dated: April 14, 2025 CUE BIOPHARMA, INC. (a Delaware corporation) 13,530,780 Shares of Common Stock Pre-Funded Warrants to Purchase Up to 11,469,2

13,530,780 Shares of Common Stock Pre-Funded Warrants to Purchase 11,469,216 Shares of Common Stock Common Stock Warrants to Purchase 6,249,999 Shares of Common Stock

Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No. 333-271786 PROSPECTUS SUPPLEMENT (To Prospectus dated May 26, 2023) 13,530,780 Shares of Common Stock Pre-Funded Warrants to Purchase 11,469,216 Shares of Common Stock Common Stock Warrants to Purchase 6,249,999 Shares of Common Stock We are offering (i) 13,530,780 shares of our common stock and accompanying common stock warrants

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 14, 2025 Cue Biopharma, Inc

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 14, 2025 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission File

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 10, 2025 Cue Biopharma, Inc

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 10, 2025 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission File

For any date that is not a trading day, the Grant Date Fair Market Value of a share of Common Stock for such date will be determined by using the closing sale price or average of the bid and asked prices, as appropriate, for the immediately preceding

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 (Amendment No. ) Filed by the Registrant ☒ 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 14

SUBJECT TO COMPLETION, DATED APRIL 14, 2025

Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No. 333-271786 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

First Amendment to Rider to License Agreement, dated May 3, 2024, between Cue Biopharma, Inc. and MIL 40G, LLC

Exhibit 10.31 First Amendment to Rider to License Agreement Vivarium This First Amendment to Rider to License Agreement Vivarium (“Amendment”) is dated May 3, 2024 (“Effective Date”) and entered into by and between Cue Biopharma, Inc., (“Licensee”) and MIL 40G, LLC (“Licensor”). WHEREAS, Licensor and Licensee are parties to a certain Rider to License Agreement Vivarium dated July 7, 2022 (“Rider”)

Form of Indemnification Agreement between the Registrant and its directors and officers

Exhibit 10.12 INDEMNIFICATION AGREEMENT THIS INDEMNIFICATION AGREEMENT (the “Agreement”) is made and entered into as of between Cue Biopharma, Inc., a Delaware corporation (the “Company”), and (“Indemnitee”). WITNESSETH THAT: WHEREAS, highly competent persons have become more reluctant to serve corporations as directors or officers or in other capacities unless they are provided with adequate prot

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): March 31, 2025 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission File

Form of inducement stock option award

Exhibit 10.43 NOTICE OF GRANT OF NON-QUALIFIED STOCK OPTION CUE BIOPHARMA, INC. INDUCEMENT GRANT FOR GOOD AND VALUABLE CONSIDERATION, Cue Biopharma, Inc. (the “Company”) hereby grants to the Grantee designated below a Non-qualified Stock Option to purchase the number of shares of common stock of the Company (“Shares”) specified below (the “Option”). The Option shall be subject to this Notice of Gr

Amended and Restated Insider Trading Policy effective March 21, 2025

Exhibit 19.1 CUE BIOPHARMA, INC. Insider Trading Policy 1. Background and purpose 1.1 Why Have We Adopted This Policy? The federal securities laws prohibit any member of the Board of Directors (a “Director”), officer (as defined in Rule 16a-1(f) under the Securities Exchange Act of 1934 (the “Exchange Act”), an “executive officer”) or employee of Cue Biopharma, Inc. (together with its subsidiaries

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

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 ☐ 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: 001-38327 Cue Biopharma, In

Description of Common Stock of the Registrant Registered Pursuant to Section 12 of the Securities Exchange Act of 1934

EXHIBIT 4.2 DESCRIPTION OF COMMON STOCK OF CUE BIOPHARMA, INC. REGISTERED PURSUANT TO SECTION 12 OF THE SECURITIES EXCHANGE ACT OF 1934 The following information is a summary of information concerning the common stock, par value $0.001 per share (the “Common Stock”), of Cue Biopharma, Inc. (“we,” “our,” or “us”) and does not purport to be complete. It is subject to and qualified in its entirety by

Calculation of Filing Fee Tables

Exhibit 107 Calculation of Filing Fee Tables Form S-8 (Form Type) Cue Biopharma, Inc.

Cue Biopharma Reports Fourth Quarter and Full Year 2024 Financial Results and Business Highlights

Cue Biopharma Reports Fourth Quarter and Full Year 2024 Financial Results and Business Highlights BOSTON, Mass.

Ninth Amendment to Collaboration, License and Option Agreement, dated March 6, 2025, between the Registrant and LG CHEM LTD.

Exhibit 10.11 Certain identified information has been excluded from the exhibit because it is both (i) not material and (ii) is the type of information that the registrant treats as private or confidential. Double asterisks denote omissions. Ninth Amendment TO Collaboration, LICENSE and Option Agreement This Ninth Amendment to the Collaboration, License and Option Agreement (the “Ninth Amendment”)

Second Amendment to Rider to License Agreement, dated November 20, 2024, between Cue Biopharma, Inc. and MIL 40G, LLC

Exhibit 10.32 Second Amendment to Rider to License Agreement Vivarium This Second Amendment to Rider to License Agreement Vivarium (“Amendment”) is dated November 18, 2024 (“Effective Date”) and entered into by and between Cue Biopharma, Inc., (“Licensee”) and MIL 40G, LLC (“Licensor”). WHEREAS, Licensor and Licensee are parties to a certain Rider to License Agreement Vivarium dated July 7, 2022,

List of Subsidiaries

EXHIBIT 21.1 SUBSIDIARIES OF CUE BIOPHARMA, INC. Registrant’s consolidated subsidiaries are shown below, together with the state or jurisdiction of organization of each subsidiary and the percentage of voting securities that Registrant owns in each subsidiary. Name of Subsidiary Jurisdiction of Incorporation or Organization Percent of Outstanding Voting Securities Owned Cue Biopharma Securities Co

As filed with the Securities and Exchange Commission on March 31, 2025

As filed with the Securities and Exchange Commission on March 31, 2025 Registration No.

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 10, 2025 Cue Biopharma, Inc

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 10, 2025 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission File

LETTER

December 16, 2024 Kerri-Ann Millar Chief Financial Officer Cue Biopharma, Inc. 40 Guest Street Boston, MA 02135 Re: Cue Biopharma, Inc. Form 10-K for Fiscal Year Ended December 31, 2023 File No. 001-38327 Dear Kerri-Ann Millar: We have completed our review of your filings. We remind you that the company and its management are responsible for the accuracy and adequacy of their disclosures, notwiths

December 11, 2024

CORRESP December 11, 2024 By Electronic Submission Securities and Exchange Commission Division of Corporation Finance Office of Life Sciences 100 F Street, N.

LETTER

December 5, 2024 Kerri-Ann Millar Chief Financial Officer Cue Biopharma, Inc. 40 Guest Street Boston, MA 02135 Re: Cue Biopharma, Inc. Form 10-K for Fiscal Year Ended December 31, 2023 File No. 001-38327 Dear Kerri-Ann Millar: We have limited our review of your filings to the financial statements and related disclosures and have the following comment. Please respond to this letter within ten busin

Cue Biopharma Reports Third Quarter 2024 Financial Results and Recent Business Highlights

Cue Biopharma Reports Third Quarter 2024 Financial Results and Recent Business Highlights BOSTON, Mass.

Director Compensation Policy effective June 5, 2024

Exhibit 10.2 Cue Biopharma, Inc. Director Compensation Policy Members of the Board of Directors (the “Board”) of Cue Biopharma, Inc. (the “Company”) who are not employees of the Company or any subsidiary of the Company (“non-employee directors”) shall receive compensation for their services on the Board in accordance with this Director Compensation Policy (this “Policy”). Cash Compensation Each no

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

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 number: 001-38327 Cue B

Amended and Restated Certificate of Incorporation, as amended

Exhibit 3.1 AMENDED AND RESTATED CERTIFICATE OF INCORPORATION OF CUE BIOPHARMA, INC. The present name of the corporation is Cue Biopharma, Inc. The corporation was incorporated under the name “Imagen Biopharma, Inc.” by the filing of its original Certificate of Incorporation with the Secretary of State of the State of Delaware on December 31, 2014. This Amended and Restated Certificate of Incorpor

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 14, 2024 Cue Biopharma,

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 14, 2024 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission F

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 8, 2024 Cue Biopharma, In

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 8, 2024 Cue Biopharma, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-38327 47-3324577 (State or Other Jurisdiction of Incorporation) (Commission Fil

Certificate of Amendment to the Company’s Amended and Restated Certificate of Incorporation

Exhibit 3.1 CERTIFICATE OF AMENDMENT OF AMENDED AND RESTATED CERTIFICATE OF INCORPORATION OF CUE BIOPHARMA, INC. Pursuant to Section 242 of the General Corporation Law of the State of Delaware Cue Biopharma, Inc. (the “Corporation”), a corporation organized and existing under and by virtue of the General Corporation Law of the State of Delaware, does hereby certify: FIRST: That the Board of Direct

Exhibit 99.1

Exhibit 99.1 The identity and the Item 3 classification of the relevant subsidiary is: Bleichroeder LP, which is an Investment Adviser in accordance with Rule 13d-1(b)(1)(ii)(E).

Second Amendment to Loan and Security Agreement, dated October 2, 2024, by and between Silicon Valley Bank, a division of First-Citizens Bank & Trust Company, and Cue Biopharma, Inc.

SECOND AMENDMENT TO LOAN AND SECURITY AGREEMENT This Second Amendment to Loan and Security Agreement (this “Amendment”) is entered into this 2nd day of October, 2024 by and between Silicon Valley Bank, a division of First-Citizens Bank & Trust Company (“Bank”) and Cue Biopharma, Inc.

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 2, 2024 Cue Biopharma, In

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 2, 2024 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission Fil

Underwriting Agreement, dated September 26, 2024, by and between Cue Biopharma, Inc. and Oppenheimer & Co. Inc., as representative of the underwriters named therein

EX-1.1 Exhibit 1.1 CUE BIOPHARMA, INC. (a Delaware corporation) 11,564,401 Shares of Common Stock Pre-Funded Warrants to Purchase Up to 12,435,599 Shares of Common Stock Warrants to Purchase Up to 6,000,000 Shares of Common Stock UNDERWRITING AGREEMENT Dated: September 26, 2024 CUE BIOPHARMA, INC. (a Delaware corporation) 11,564,401 Shares of Common Stock Pre-Funded Warrants to Purchase Up to 12,4

11,564,401 Shares of Common Stock Pre-Funded Warrants to Purchase 12,435,599 Shares of Common Stock Common Stock Warrants to Purchase 6,000,000 Shares of Common Stock

Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No. 333-271786 PROSPECTUS SUPPLEMENT (To Prospectus dated May 26, 2023) 11,564,401 Shares of Common Stock Pre-Funded Warrants to Purchase 12,435,599 Shares of Common Stock Common Stock Warrants to Purchase 6,000,000 Shares of Common Stock We are offering (i) 11,564,401 shares of our common stock and accompanying common stock warrants

Cue Biopharma Announces Pricing of $12.0 Million Public Offering

EX-99.1 Exhibit 99.1 Cue Biopharma Announces Pricing of $12.0 Million Public Offering BOSTON, Mass., September 26, 2024— Cue Biopharma, Inc. (Nasdaq: CUE), a clinical-stage biopharmaceutical company developing a novel class of therapeutic biologics to selectively engage and modulate disease-specific T cells, today announced the pricing of an underwritten public offering of (i) 11,564,401 shares of

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): September 26, 2024 Cue Biopharma,

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): September 26, 2024 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission

Form of Common Stock Warrant

EX-4.2 Exhibit 4.2 FORM OF COMMON STOCK PURCHASE WARRANT CUE BIOPHARMA, INC. Warrant Shares: [ ] Issue Date: September 30, 2024 Initial Exercise Date: September 30, 2024 THIS COMMON STOCK PURCHASE WARRANT (the “Warrant”) certifies that, for value received, [ ] or its assigns (the “Holder”) is entitled, upon the terms and subject to the limitations on exercise and the conditions hereinafter set for

Form of Pre-Funded Warrant

EX-4.1 Exhibit 4.1 CUE BIOPHARMA, INC. WARRANT TO PURCHASE COMMON STOCK Number of Shares: [] (subject to adjustment) Warrant No. [] Original Issue Date: September 30, 2024 Cue Biopharma, Inc., a Delaware corporation (the “Company”), hereby certifies that, for good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, [] or its registered assigns (the “Holder”) i

SUBJECT TO COMPLETION, DATED SEPTEMBER 26, 2024

424B5 Table of Contents Filed Pursuant to Rule 424(b)(5) Registration No. 333-271786 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

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 (Amendment No. )

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 (Amendment No. ) Filed by the Registrant ☒ 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)) ☒ Defin

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 28, 2024 Cue Biopharma, In

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 28, 2024 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission Fil

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 (Amendment No. )

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 (Amendment No. ) Filed by the Registrant ☒ 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)) ☐ Defin

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 15, 2024 Cue Biopharma, In

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 15, 2024 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission Fil

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

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: 001-38327 Cue Biopha

Form of stock option award under 2016 Non-Employee Equity Incentive Plan

EXHIBIT 10.2 NOTICE OF GRANT OF NON-QUALIFIED STOCK OPTION CUE BIOPHARMA, INC. 2016 OMNIBUS INCENTIVE PLAN FOR GOOD AND VALUABLE CONSIDERATION, Cue Biopharma, Inc. (the “Company”) hereby grants, pursuant to the provisions of the Cue Biopharma, Inc. 2016 Omnibus Incentive Plan (the “Plan”), to the Grantee designated below a Non-qualified Stock Option to purchase the number of Shares specified below

Form of stock option award under 2016 Omnibus Incentive Plan

EXHIBIT 10.1 NOTICE OF GRANT OF INCENTIVE STOCK OPTION CUE BIOPHARMA, INC. 2016 OMNIBUS INCENTIVE PLAN FOR GOOD AND VALUABLE CONSIDERATION, Cue Biopharma, Inc. (the “Company”) hereby grants, pursuant to the provisions of the Cue Biopharma, Inc. 2016 Omnibus Incentive Plan (the “Plan”), to the Grantee designated in below an Incentive Stock Option to purchase the number of Shares specified below (th

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers, 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 24, 2024 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission File

Cue Biopharma Announces Strategic Prioritization of Autoimmune Programs Enabling Optimization of Workforce and Reduction of Capital Requirements Prioritizing autoimmune programs aims to focus upon near-term and intermediate value creation potential,

Cue Biopharma Announces Strategic Prioritization of Autoimmune Programs Enabling Optimization of Workforce and Reduction of Capital Requirements Prioritizing autoimmune programs aims to focus upon near-term and intermediate value creation potential, while retaining oncology programs as promising clinical data continues to mature  Company anticipates annualized capital and workforce requirements to be reduced by approximately 25 percent BOSTON, Mass.

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers, 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 5, 2024 Cue Biopharma, Inc. (Exact name of Registrant as Specified in Its Charter) Delaware 001-38327 47-3324577 (State or Other Jurisdiction of Incorporation) (Commission File N

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 (Amendment No. )

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 (Amendment No. ) Filed by the Registrant ☒ 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)) ☐ Defin

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

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: 001-38327 Cue Bioph

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 9, 2024 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission File Nu

Cue Biopharma Reports First Quarter 2024 Financial Results and Recent Business Highlights

Cue Biopharma Reports First Quarter 2024 Financial Results and Recent Business Highlights BOSTON, Mass.

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 (Amendment No. )

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 (Amendment No. ) Filed by the Registrant ☒ 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 14

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 (Amendment No. )

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 (Amendment No. ) Filed by the Registrant ☒ 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)) ☐ Defin

ARS

ABOUTTHECOVER Cue Biopharma aims to restore immune balance to address major areas of disease, cancer and autoimmune disease, through its therapeutic Immuno-STAT™ (Selective Targeting and Alteration of T Cells) platform.

SUBSIDIARIES OF CUE BIOPHARMA, INC.

EXHIBIT 21.1 SUBSIDIARIES OF CUE BIOPHARMA, INC. Registrant’s consolidated subsidiaries are shown below, together with the state or jurisdiction of organization of each subsidiary and the percentage of voting securities that Registrant owns in each subsidiary. Name of Subsidiary Jurisdiction of Incorporation or Organization Percent of Outstanding Voting Securities Owned Cue Biopharma Securities Co

As filed with the Securities and Exchange Commission on March 28, 2024

As filed with the Securities and Exchange Commission on March 28, 2024 Registration No.

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

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 ☐ 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: 001-38327 Cue Biopharma, In

Exhibit 4.2

EXHIBIT 4.2 DESCRIPTION OF COMMON STOCK OF CUE BIOPHARMA, INC. REGISTERED PURSUANT TO SECTION 12 OF THE SECURITIES EXCHANGE ACT OF 1934 The following information is a summary of information concerning the common stock, par value $0.001 per share (the “Common Stock”), of Cue Biopharma, Inc. (“we,” “our,” or “us”) and does not purport to be complete. It is subject to and qualified in its entirety by

Director Compensation Policy effective December 7, 2023

EXHIBIT 10.17 DIRECTOR COMPENSATION POLICY Members of the Board of Directors (the “Board”) of Cue Biopharma, Inc. (the “Company”) who are not employees of the Company or any subsidiary of the Company (“non-employee directors”) shall receive compensation for their services on the Board in accordance with this Director Compensation Policy (this “Policy”). Cash Compensation Each non-employee director

Calculation of Filing Fee Tables

Exhibit 107 Calculation of Filing Fee Tables Form S-8 (Form Type) Cue Biopharma, Inc.

Compensation Recovery Policy

EXHIBIT 97.1 DODD-FRANK COMPENSATION RECOVERY POLICY This Compensation Recovery Policy (this “Policy”) is adopted by Cue Biopharma, Inc. (the “Company”) in accordance with Nasdaq Listing Rule 5608 (“Rule 5608”), which implements Rule 10D-1 under the Securities Exchange Act of 1934, as amended (the “Exchange Act”) (as promulgated pursuant to Section 954 of the Dodd-Frank Wall Street Reform and Cons

Second Amendment to the Amended and Restated License Agreement with Albert Einstein College of Medicine dated January 13, 2024

EXHIBIT 10.38 Certain identified information has been excluded from the exhibit because it is both (i) not material and (ii) is the type of information that the registrant treats as private or confidential. Double asterisks denote omissions. SECOND AMENDMENT TO THE AMENDED AND RESTATED LICENSE AGREEMENT This Second Amendment to the Amended and Restated License Agreement (“Second Amendment”) is by

CUE / Cue Biopharma, Inc. / Bleichroeder LP - CUEBIOPHARMA13G Passive Investment

SC 13G 1 cuebiopharma13g.htm CUEBIOPHARMA13G UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 Schedule 13G Under the Securities Exchange Act of 1934 (Amendment No. 1) Cue Biopharma, Inc. (Name of Issuer) Common Shares (Title of Class of Securities) 22978P106 (CUSIP Number) February 27, 2024 (Date of Event which Requires Filing of this Statement) Check the appropriate box to

CUE / Cue Biopharma, Inc. / BlackRock Inc. Passive Investment

SC 13G 1 us22978p1066020724.txt us22978p1066020724.txt SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No: ) CUE BIOPHARMA INC - (Name of Issuer) Common Stock - (Title of Class of Securities) 22978P106 - (CUSIP Number) January 31, 2024 - (Date of Event Which Requires Filing of this Statement) Check the appropriate box to d

CUE / Cue Biopharma, Inc. / BlackRock Inc. Passive Investment

SC 13G 1 us22978p1066013124.txt us22978p1066013124.txt SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No: ) CUE BIOPHARMA INC - (Name of Issuer) Common Stock - (Title of Class of Securities) 22978P106 - (CUSIP Number) December 31, 2023 - (Date of Event Which Requires Filing of this Statement) Check the appropriate box to

Amendment No. 1 to Consulting Agreement between Cue Biopharma, Inc. and Peter A. Kiener, dated September 1, 2023

EXHIBIT 10.1 AMENDMENT NO. 1 TO CONSULTING AGREEMENT THIS AMENDMENT NO. 1 TO CONSULTING AGREEMENT (this “Amendment No. 1”) effective September 1, 2023 is entered into between Cue Biopharma, Inc., a Delaware corporation having an address of 40 Guest Street, Boston MA 02135 (the “Company”), and Peter Kiener D.Phil, (“Consultant”) whose address is [**}. Company and Consultant may be referred to herei

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

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 number: 001-38327 Cue B

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): September 12, 2023 Cue Biopharma,

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): September 12, 2023 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission

Consulting Agreement effective June 7, 2023 entered into between Cue Biopharma, Inc. and Peter A Kiener, D.Phil

Exhibit 10.3 CONSULTING AGREEMENT THIS CONSULTING AGREEMENT (the “Agreement”), effective June 7, 2023 (the “Effective Date”), is entered into between Cue Biopharma, Inc., a Delaware corporation having an address of 40 Guest Street, Boston, Massachusetts 02135 (the “Company”), and Peter A Kiener, D.Phil, having an address of [**]. INTRODUCTION The Company desires to contract with Consultant to prov

Amendment No. 1 to Cue Biopharma, Inc. 2016 Non-Employee Equity Incentive Plan

Exhibit 10.2 Amendment No. 1 to the Cue Biopharma, Inc. 2016 Non-Employee Equity Incentive Plan This Amendment No. 1 (“Amendment”) of the 2016 Non-Employee Equity Incentive Plan (the “Existing Plan”; as amended hereby, the “Plan”), of Cue Biopharma, Inc., a Delaware corporation (the “Company”), is made and adopted by the Company. NOW, THEREFORE, the Existing Plan is hereby amended as follows: 1. C

Amendment No. 2 to Cue Biopharma, Inc. 2016 Omnibus Incentive Plan

Exhibit 10.1 Amendment No. 2 to the Cue Biopharma, Inc. 2016 Omnibus Equity Incentive Plan This Amendment No. 2 (“Amendment”) of the 2016 Omnibus Equity Incentive Plan, as amended (the “Existing Plan”; as amended hereby, the “Plan”), of Cue Biopharma, Inc., a Delaware corporation (the “Company”), is made and adopted by the Company. NOW, THEREFORE, the Existing Plan is hereby amended as follows: 1.

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

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: 001-38327 Cue Biopha

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 7, 2023 Cue Biopharma, Inc.

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 7, 2023 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission File N

CUE BIOPHARMA, INC. 40 Guest Street Boston, Massachusetts 02135

CORRESP CUE BIOPHARMA, INC. 40 Guest Street Boston, Massachusetts 02135 May 24, 2023 VIA EDGAR U.S. Securities and Exchange Commission Division of Corporation Finance, Office of Life Sciences 100 F Street, N.E. Washington, D.C. 20549 Attention: Tyler Howes Re: Cue Biopharma, Inc. Registration Statement on Form S-3 Filed May 9, 2023 File No. 333-271786 Request for Acceleration Ladies and Gentlemen:

LETTER

United States securities and exchange commission logo May 16, 2023 Daniel R. Passeri Chief Executive Officer Cue Biopharma, Inc. 40 Guest Street Boston, MA 02135 Re: Cue Biopharma, Inc. Registration Statement on Form S-3 Filed May 9, 2023 File No. 333-271786 Dear Daniel R. Passeri: This is to advise you that we have not reviewed and will not review your registration statement. Please refer to Rule

As filed with the Securities and Exchange Commission on May 9, 2023

S-3 Table of Contents As filed with the Securities and Exchange Commission on May 9, 2023 Registration No.

Form of Subordinated Indenture

Exhibit 4.4 CUE BIOPHARMA, INC. and Trustee INDENTURE Dated as of SUBORDINATED DEBT SECURITIES CROSS-REFERENCE TABLE 1 Section of Trust Indenture Act of 1939, as amended Section of Indenture 310(a) 6.09 310(b) 6.08 6.10 310(c) Inapplicable 311(a) 6.13 311(b) 6.13 311(c) Inapplicable 312(a) 4.01 4.04 312(b) 4.04(c) 312(c) 4.04(c) 313(a) 4.03 313(b) 4.03 313(c) 4.03 313(d) 4.03 314(a) 4.02 314(b) In

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

stifelSti 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: 001-38327

Form of Senior Indenture

EX-4.3 Exhibit 4.3 CUE BIOPHARMA, INC. and Trustee INDENTURE Dated as of SENIOR DEBT SECURITIES CROSS-REFERENCE TABLE1 Section of Trust Indenture Act of 1939, as amended Section of Indenture 310(a) 6.09 310(b) 6.08 6.10 310(c) Inapplicable 311(a) 6.13 311(b) 6.13 311(c) Inapplicable 312(a) 4.014.04 312(b) 4.04(c) 312(c) 4.04(c) 313(a) 4.03 313(b) 4.03 313(c) 4.03 313(d) 4.03 314(a) 4.02 314(b) Ina

Waiver and First Amendment to Loan and Security Agreement, dated April 10, 2023, by and between Cue Biopharma, Inc. and Silicon Valley Bridge Bank, N.A., as successor in interest to Silicon Valley Bank

Exhibit 10.2 WAIVER AND FIRST AMENDMENT TO LOAN AND SECURITY AGREEMENT This First Amendment to Loan and Security Agreement (this “Amendment”) is entered into this 10th day of April, 2023 by and between Silicon Valley Bank, a division of First-Citizens Bank & Trust Company (successor by purchase to the Federal Deposit Insurance Corporation as Receiver for Silicon Valley Bridge Bank, N.A. (as succes

Director Compensation Policy dated March 31, 2023

EXHIBIT 10.1 Cue Biopharma, Inc. Director Compensation Policy Members of the Board of Directors (the “Board”) of Cue Biopharma, Inc. (the “Company”) who are not employees of the Company or any subsidiary of the Company (“non-employee directors”) shall receive compensation for their services on the Board in accordance with this Director Compensation Policy (this “Policy”). Cash Compensation Each no

Form of Senior Note

EX-4.5 Exhibit 4.5 Form of Senior Note (FACE OF SECURITY) [Each Global Security shall bear substantially the following legend: UNLESS AND UNTIL IT IS EXCHANGED IN WHOLE OR IN PART FOR SECURITIES IN DEFINITIVE REGISTERED FORM, THIS SECURITY MAY NOT BE TRANSFERRED EXCEPT AS A WHOLE BY THE DEPOSITARY TO A NOMINEE OF THE DEPOSITARY OR BY A NOMINEE OF THE DEPOSITARY TO THE DEPOSITARY OR ANOTHER NOMINEE

Filing Fee Table

EX-FILING FEES Exhibit 107 Calculation of Filing Fee Tables Form S-3 (Form Type) Cue Biopharma, Inc.

Form of Subordinated Note

EX-4.6 Exhibit 4.6 Form of Subordinated Note (FACE OF SECURITY) [Each Global Security shall bear substantially the following legend: UNLESS AND UNTIL IT IS EXCHANGED IN WHOLE OR IN PART FOR SECURITIES IN DEFINITIVE REGISTERED FORM, THIS SECURITY MAY NOT BE TRANSFERRED EXCEPT AS A WHOLE BY THE DEPOSITARY TO A NOMINEE OF THE DEPOSITARY OR BY A NOMINEE OF THE DEPOSITARY TO THE DEPOSITARY OR ANOTHER N

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 (Amendment No. )

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 (Amendment No. ) Filed by the RegistrantFiled by the Registrant ☒ Filed by a Party other than the Registrant ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confidential, for Use of the Commission Only (as permitt

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 (Amendment No. )

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 (Amendment No. ) Filed by the Registrant ☒ 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 14

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 19, 2023 Cue Biopharma, Inc

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 19, 2023 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission File

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 11, 2023 Cue Biopharma, Inc

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 11, 2023 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission File

Cue Biopharma, Inc. Director Compensation Policy

Exhibit 10.1 Cue Biopharma, Inc. Director Compensation Policy Members of the Board of Directors (the “Board”) of Cue Biopharma, Inc. (the “Company”) who are not employees of the Company or any subsidiary of the Company (“non-employee directors”) shall receive compensation for their services on the Board in accordance with this Director Compensation Policy (this “Policy”). Cash Compensation Each no

Form of Indemnification Agreement between the Registrant and its directors and officers

EXHIBIT 10.11 INDEMNIFICATION AGREEMENT THIS INDEMNIFICATION AGREEMENT (the “Agreement”) is made and entered into as of between Cue Biopharma, Inc., a Delaware corporation (the “Company”), and (“Indemnitee”). WITNESSETH THAT: WHEREAS, highly competent persons have become more reluctant to serve corporations as directors or officers or in other capacities unless they are provided with adequate prot

SUBSIDIARIES OF CUE BIOPHARMA, INC.

EXHIBIT 21.1 SUBSIDIARIES OF CUE BIOPHARMA, INC. Registrant’s consolidated subsidiaries are shown below, together with the state or jurisdiction of organization of each subsidiary and the percentage of voting securities that Registrant owns in each subsidiary. Name of Subsidiary Jurisdiction of Incorporation or Organization Percent of Outstanding Voting Securities Owned Cue Biopharma Securities Co

Calculation of Filing Fee Tables

Exhibit 107 Calculation of Filing Fee Tables Form S-8 (Form Type) Cue Biopharma, Inc.

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

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 ☐ 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: 001-38327 Cue Biopharma, In

As filed with the Securities and Exchange Commission on March 21, 2023

As filed with the Securities and Exchange Commission on March 21, 2023 Registration No.

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers

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 7, 2023 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission File

CUE / Cue Biopharma Inc / Slate Path Capital LP - CUE BIOPHARMA, INC. Passive Investment

SC 13G 1 p23-0869sc13g.htm CUE BIOPHARMA, INC. SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. )* Cue Biopharma, Inc. (Name of Issuer) Common Stock, par value $0.001 (Title of Class of Securities) 22978P106 (CUSIP Number) December 31, 2022 (Date of event which requires filing of this statement) Check the appropriate bo

CUE / Cue Biopharma Inc / STATE STREET CORP Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 13G UNDER THE SECURITIES EXCHANGE ACT OF 1934 EXIT FILING CUE BIOPHARMA INC (NAME OF ISSUER) COMMON STOCK (TITLE OF CLASS OF SECURITIES) 22978P106 (CUSIP NUMBER) 12/31/2022 (DATE OF EVENT WHICH REQUIRES FILING OF THIS STATEMENT) CHECK THE APPROPRIATE BOX TO DESIGNATE THE RULE PURSUANT TO WHICH THIS SCHEDULE IS FILED:

Common Stock

Filed Pursuant to Rule 424(b)(7) Registration No. 333-268687 Prospectus Supplement dated December 30, 2022 (To Prospectus dated December 14, 2022) Common Stock This prospectus supplement supplements the prospectus dated December 14, 2022 (as supplemented, the ?prospectus?), which forms a part of our registration statement on Form S-3 (No. 333-268687). This prospectus supplement is being filed to u

18,376,812 Shares Common Stock

Table of Contents Filed Pursuant to Rule 424(b)(3) Registration No. 333-268687 PROSPECTUS 18,376,812 Shares Common Stock This prospectus relates to the resale from time to time of up to 18,376,812 shares of common stock of Cue Biopharma, Inc. by the selling stockholders listed on page 8, including their donees, pledgees, assignees, transferees or other successors-in-interest, which consist of 7,65

December 12, 2022

CORRESP 1 filename1.htm December 12, 2022 VIA EDGAR SUBMISSION Securities and Exchange Commission Division of Corporation Finance 100 F Street, NE Washington, DC 20549 Attention: Doris Stacey Gama Re: Cue Biopharma, Inc. Registration Statement on Form S-3 File No. 333-268687 Request for Acceleration Ladies and Gentlemen: Pursuant to Rule 461 under the Securities Act of 1933, as amended, Cue Biopha

LETTER

United States securities and exchange commission logo December 9, 2022 Kerri-Ann Millar Chief Financial Officer Cue Biopharma, Inc.

As filed with the Securities and Exchange Commission on December 6, 2022

Table of Contents As filed with the Securities and Exchange Commission on December 6, 2022 Registration No.

Filing Fee Table.

EX-FILING FEES 4 d376752dexfilingfees.htm EX-FILING FEES Exhibit 107 Calculation of Filing Fee Tables Form S-3 (Form Type) Cue Biopharma, 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 Maximum Aggrega

CUE / Cue Biopharma Inc / Nantahala Capital Management, LLC - SC 13G/A Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 3)* Cue Biopharma, Inc. (Name of Issuer) Common Stock, par value $0.001 per share (Title of Class of Securities) 22978P106 (CUSIP Number) December 1, 2022 (Date of Event which Requires Filing of this Statement) Check the appropriate box to designate the rule

Joint Filing Agreement

Exhibit 99.1 Joint Filing Agreement The undersigned hereby agree that the Statement on Schedule 13G dated November 18, 2022 with respect to the Common Stock, par value $0.001 per share, of Cue Biopharma, Inc., a Delaware corporation, and any further amendments thereto executed by each and any of the undersigned shall be filed on behalf of each of the undersigned pursuant to and in accordance with

CUE / Cue Biopharma Inc / Slate Path Capital LP Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G (Rule 13d-102) INFORMATION TO BE INCLUDED IN STATEMENTS FILED PURSUANT TO RULES 13d-1(b), (c), AND (d) AND AMENDMENTS THERETO FILED PURSUANT TO RULE 13d-2(b) (Amendment No. )1 Cue Biopharma, Inc. (Name of Issuer) Common Stock, par value $0.001 per share (Title of Class of Securities) 22978P106 (CUSIP Number) Novem

Cue Biopharma Announces $30 Million Private Investment in Public Equity (PIPE) Financing

EX-99.1 Exhibit 99.1 Cue Biopharma Announces $30 Million Private Investment in Public Equity (PIPE) Financing BOSTON, Nov. 14, 2022 (GLOBE NEWSWIRE) — Cue Biopharma, Inc. (Nasdaq: CUE), a clinical-stage biopharmaceutical company developing a novel class of injectable biologics to selectively engage and modulate tumor-specific T cells directly within the patient’s body, announced today that it has

Form of Warrant to Purchase Common Stock or Pre-Funded Warrant

EX-4.2 Exhibit 4.2 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 UNLES

Form of Securities Purchase Agreement, dated November 14, 2022, by and among the Company and the other parties thereto

EX-10.1 Exhibit 10.1 SECURITIES PURCHASE AGREEMENT This SECURITIES PURCHASE AGREEMENT (this “Agreement”) is made and entered into as of November 14, 2022, by and among Cue Biopharma, Inc., a Delaware corporation (the “Company”), and the Investors identified on Exhibit A attached hereto (each an “Investor” and collectively the “Investors”). RECITALS A. The Company and the Investors are executing an

Registration Rights Agreement, dated November 14, 2022, by and among the Company and the other parties thereto

EX-10.2 Exhibit 10.2 REGISTRATION RIGHTS AGREEMENT This REGISTRATION RIGHTS AGREEMENT (this “Agreement”) is made and entered into as of November 14, 2022, by and among Cue Biopharma, Inc., a Delaware corporation (the “Company”), and the “Investors” named in those certain Securities Purchase Agreements, by and among the Company and the Investors named therein, dated as of November 14, 2022 (collect

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 14, 2022 Cue Biopharma,

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 14, 2022 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission F

Form of Pre-Funded Warrant to Purchase Common Stock

EX-4.1 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 UNLES

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

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 number: 001-38327 Cue B

Termination of License Agreement, dated September 9, 2022, between Cue Biopharma, Inc. and MIL 21E, LLC

EXHIBIT 101 Termination of License Agreement This Early Termination of Vivarium Agreement (?Termination Agreement?) is dated September 9, 2022 (?Execution Date?) and is entered into by and between Cue Biopharma, Inc.

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

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: 001-38327 Cue Biopha

First Amendment to the License Agreement, dated May 3, 2022, between Cue Biopharma, Inc. and MIL 40G, LLC

Exhibit 10.1 First Amendment to License Agreement This First Amendment to License Agreement (?First Amendment?) is dated May 3, 2022 (?Effective Date?) and entered into by and between Cue Biopharma, Inc. (?Licensee?) and MIL 40G, LLC (?Licensor?). WHEREAS, Licensor and Licensee are parties to a certain License Agreement dated March 28, 2022 (?License Agreement?); WHEREAS, Licensee warrants and rep

Rider to License Agreement, dated as of July 7, 2022, between Cue Biopharma, Inc. and MIL 40G, LLC

Exhibit 102 Rider to License Agreement Vivarium This Rider to License Agreement (?Rider?), is made as of July 7, 2022, by and between MIL 40G, LLC (?SmartLabs?), and Cue Biopharma, Inc.

CUE / Cue Biopharma Inc / BlackRock Inc. Passive Investment

us22978p1066070822.txt SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No: ) CUE BIOPHARMA INC - (Name of Issuer) Common Stock - (Title of Class of Securities) 22978P106 - (CUSIP Number) June 30, 2022 - (Date of Event Which Requires Filing of this Statement) Check the appropriate box to designate the rule pursuant to which

Departure of Directors or Certain Officers; Election of Directors; Appointment of Certain Officers; Compensatory Arrangements of Certain Officers

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 16, 2022 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission File

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 9, 2022 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission File N

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

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: 001-38327 Cue Bioph

Director Compensation Policy dated January 1, 2021

Exhibit 10.3 1. Cue Biopharma, Inc. 2. Director Compensation Policy Members of the Board of Directors (the ?Board?) of Cue Biopharma, Inc. (the ?Company?) who are not employees of the Company or any subsidiary of the Company (?non-employee directors?) shall receive compensation for their services on the Board in accordance with this Director Compensation Policy (this ?Policy?). a. Cash Compensatio

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 (Amendment No. )

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 (Amendment No. ) Filed by the Registrant ? 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 14

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 (Amendment No. )

DEFA14A 1 d274629ddefa14a.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 (Amendment No. ) Filed by the RegistrantFiled by the Registrant ☒ Filed by a Party other than the Registrant ☐ Check the appropriate box: ☐ Preliminary Proxy Statement ☐ Confidential, for Use of t

Entry into a Material Definitive Agreement, Financial Statements and Exhibits, Creation of a Direct Financial Obligation or an Obligation under an Off-Balance Sheet Arrangement of a Registrant

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 28, 2022 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission File

License Agreement, dated March 28, 2022, between Cue Biopharma, Inc. and MIL 40G, LLC

EX-10.1 2 d339157dex101.htm EX-10.1 Exhibit 10.1 License Agreement This License Agreement, made and entered into as of March 28, 2022 (“Agreement”), by and between Cue Biopharma, Inc., a Delaware corporation, having a place of business located at 40 Guest Street, Boston, MA 02135 (“Licensee”) and MIL 40 G, LLC, a Delaware limited liability company, having a place of business located at 40 Guest St

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

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 ? 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: 001-38327 Cue Biopharma, In

SUBSIDIARIES OF CUE BIOPHARMA, INC.

EXHIBIT 21.1 SUBSIDIARIES OF CUE BIOPHARMA, INC. Registrant?s consolidated subsidiaries are shown below, together with the state or jurisdiction of organization of each subsidiary and the percentage of voting securities that Registrant owns in each subsidiary. Name of Subsidiary Jurisdiction of Incorporation or Organization Percent of Outstanding Voting Securities Owned Cue Biopharma Securities Co

Consulting Agreement, dated January 1, 2017, between the Registrant and Ken Pienta, as amended by Amendment No. 1 to Consulting Agreement dated December 15, 2021

EXHIBIT 10.28 AMENDMENT NO. 1 TO CONSULTING AGREEMENT THIS AMENDMENT NO. 1 TO CONSULTING AGREEMENT (this ?Amendment?), dated as of December 15, 2021, is entered into by and between Cue Biopharma, Inc., a Delaware corporation (the ?Company?), and Kenneth J. Pienta (the ?Consultant?). Reference is made to that certain Consulting Agreement, dated as of January 1, 2017, by and between the Company and

Loan and Security Agreement, dated February 15, 2022, by and between Cue Biopharma, Inc. and Silicon Valley Bank

Exhibit 10.34 Certain identified information has been excluded from the exhibit because it is both (i) not material and (ii) is the type of information that the registrant treats as private or confidential. Double asterisks denote omissions. LOAN AND SECURITY AGREEMENT THIS LOAN AND SECURITY AGREEMENT (this ?Agreement?) is dated as of the Effective Date between SILICON VALLEY BANK, a California co

As filed with the Securities and Exchange Commission on March 16, 2022

As filed with the Securities and Exchange Commission on March 16, 2022 Registration No.

Calculation of Filing Fee Tables

Exhibit 107 Calculation of Filing Fee Tables Form S-8 (Form Type) Cue Biopharma, Inc.

Entry into a Material Definitive Agreement, Creation of a Direct Financial Obligation or an Obligation under an Off-Balance Sheet Arrangement of a Registrant

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 15, 2022 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission F

CUE / Cue Biopharma Inc / Corriente Advisors, LLC - SC 13G/A Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 1)* Cue Biopharma, Inc. (Name of Issuer) Common Stock, par value $0.001 per share (Title of Class of Securities) 22978P106 (CUSIP Number) December 31, 2021 (Date of Event which Requires Filing of this Statement) Check the appropriate box to designate the rul

A. Joint Filing Agreement

EXHBIIT A JOINT FILING AGREEMENT The undersigned hereby agree that the statement on Schedule 13G with respect to the shares of common stock, par value $0.

CUE / Cue Biopharma Inc / Nantahala Capital Management, LLC - SC 13G/A Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No. 2)* Cue Biopharma, Inc. (Name of Issuer) Common Stock, par value $0.001 per share (Title of Class of Securities) 22978P106 (CUSIP Number) December 31, 2021 (Date of Event which Requires Filing of this Statement) Check the appropriate box to designate the rul

CUE / Cue Biopharma Inc / STATE STREET CORP Passive Investment

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 SCHEDULE 13G UNDER THE SECURITIES EXCHANGE ACT OF 1934 INITIAL FILING CUE BIOPHARMA INC (NAME OF ISSUER) COMMON STOCK (TITLE OF CLASS OF SECURITIES) 22978P106 (CUSIP NUMBER) 12/31/2021 (DATE OF EVENT WHICH REQUIRES FILING OF THIS STATEMENT) CHECK THE APPROPRIATE BOX TO DESIGNATE THE RULE PURSUANT TO WHICH THIS SCHEDULE IS FILE

CUE / Cue Biopharma Inc / BlackRock Inc. Passive Investment

us22978p1066020322.txt SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 SCHEDULE 13G Under the Securities Exchange Act of 1934 (Amendment No: 2) CUE BIOPHARMA INC - (Name of Issuer) Common Stock - (Title of Class of Securities) 22978P106 - (CUSIP Number) December 31, 2021 - (Date of Event Which Requires Filing of this Statement) Check the appropriate box to designate the rule pursuant to

© 2021 CUE BIOPHARMA Forward-Looking Statements Disclosure This presentation has been prepared by Cue Biopharma, Inc. (“we,” “us,” “our,” “Cue” or the “Company”) and is made for informational purposes only and does not constitute an offer to sell or

Corporate Presentation Immune Responses, On Cue? Nasdaq: CUE November 2021 Exhibit 99.

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 15, 2021 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission F

Third Amendment to License Agreement, dated October 22, 2021, by and between Cue Biopharma, Inc. and MIL 21E, LLC

Exhibit 10.2 Third Amendment to License Agreement This Third Amendment to License Agreement (?Third Amendment?) is made as of October 1, 2021, by and between Cue Biopharma, Inc. (?Licensee?) and MIL 21E, LLC (?Licensor?). WHEREAS, Licensor and Licensee are parties to a certain License Agreement dated January 19, 2018, as amended by that certain First Amendment to License Agreement dated June 18, 2

Open Market Sale AgreementSM, dated October 1, 2021, by and between Cue Biopharma, Inc. and Jefferies LLC

Exhibit 10.1 Execution Version OPEN MARKET SALE AGREEMENTSM October 1, 2021 JEFFERIES LLC 520 Madison Avenue New York, New York 10022 Ladies and Gentlemen: Cue Biopharma, Inc., a Delaware corporation (the ?Company?), proposes, subject to the terms and conditions stated herein, to issue and sell from time to time through Jefferies LLC, as sales agent and/or principal (the ?Agent?), shares of the Co

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

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 number: 001-38327 Cue B

Entry into a Material Definitive Agreement, 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): October 1, 2021 Cue Biopharma, Inc. (Exact name of registrant as specified in its charter) Delaware 001-38327 47-3324577 (State or other jurisdiction of incorporation) (Commission Fil

Common Stock

Filed Pursuant to Rule 424(b)(5) Registration No. 333-239357 PROSPECTUS SUPPLEMENT (To Prospectus Dated May 21, 2021) Common Stock This prospectus supplement supplements the sales agreement prospectus dated May 21, 2021 related to the offer and sale of shares of our common stock, $0.001 par value per share, pursuant to an At-the-Market Equity Offering Sales Agreement, or the Sales Agreement, dated

Open Market Sale AgreementSM, dated as of October 1, 2021, by and between Cue Biopharma, Inc. and Jefferies LLC (incorporated by reference to Exhibit 1.1 to the Registrant’s Current Report on Form 8-K (File No. 001-38327) filed on October 1, 2021)

EX-1.1 2 d197369dex11.htm EX-1.1 Exhibit 1.1 Execution Version OPEN MARKET SALE AGREEMENTSM October 1, 2021 JEFFERIES LLC 520 Madison Avenue New York, New York 10022 Ladies and Gentlemen: Cue Biopharma, Inc., a Delaware corporation (the “Company”), proposes, subject to the terms and conditions stated herein, to issue and sell from time to time through Jefferies LLC, as sales agent and/or principal

Up to $80,000,000 Common Stock

Table of Contents As Filed Pursuant to Rule 424(b)(5) Registration No. 333-239357 PROSPECTUS SUPPLEMENT (To Prospectus Dated May 21, 2021) Up to $80,000,000 Common Stock We have entered into an Open Market Sale AgreementSM, or sales agreement, with Jefferies LLC, or Jefferies, dated October 1, 2021, relating to the sale of shares of our common stock offered by this prospectus supplement. In accord