# EDGAR Filing Document

**Accession Number:** 0001645460
**File Stem:** 0000950170-25-107270
**Filing Date:** 2025-8
**Character Count:** 212606
**Document Hash:** fb231ed03ae50b04d00729b4d50aafe2
**Contains OCR:** False
**Source Format:** 

## Filing Content

## Filing Summary
**0000950170-25-107270.hdr.sgml**: 20250812

**ACCESSION NUMBER**: 0000950170-25-107270

**CONFORMED SUBMISSION TYPE**: 10-Q

**PUBLIC DOCUMENT COUNT**: 65

**CONFORMED PERIOD OF REPORT**: 20250630

**FILED AS OF DATE**: 20250812

**DATE AS OF CHANGE**: 20250812

**FILER**: 

**COMPANY DATA:**
- **COMPANY CONFORMED NAME:** Cue Biopharma, Inc.
- **CENTRAL INDEX KEY:** 0001645460
- **STANDARD INDUSTRIAL CLASSIFICATION:** PHARMACEUTICAL PREPARATIONS [2834]
- **ORGANIZATION NAME:** 03 Life Sciences
- **EIN:** 473324577
- **STATE OF INCORPORATION:** DE
- **FISCAL YEAR END:** 1231

**FILING VALUES:**
- **FORM TYPE:** 10-Q
- **SEC ACT:** 1934 Act
- **SEC FILE NUMBER:** 001-38327
- **FILM NUMBER:** 251206471

**BUSINESS ADDRESS:**
- **STREET 1:** 40 GUEST STREET
- **CITY:** BOSTON
- **STATE:** MA
- **ZIP:** 02135
- **BUSINESS PHONE:** 617-949-2680

**MAIL ADDRESS:**
- **STREET 1:** 40 GUEST STREET
- **CITY:** BOSTON
- **STATE:** MA
- **ZIP:** 02135

**FORMER COMPANY:**
- **FORMER CONFORMED NAME:** Imagen Biopharma, Inc.
- **DATE OF NAME CHANGE:** 20150617

?xml version='1.0' encoding='ASCII'? 10-Q

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**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

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Cue Biopharma, Inc.

**(Exact name of registrant as specified in its charter)**

------

---

| | |
|:---|:---|
| Delaware | 47-3324577 |
| **(State or other jurisdiction of**<br>**incorporation or organization)** | **(I.R.S. Employer**<br>**Identification No.)** |
| 40 Guest Street<br>Boston**,** Massachusetts | <br>02135 |
| **(Address of principal executive offices)** | **(Zip Code)** |

---

**(**617**)** 949-2680

**(Registrant's telephone number, including area code)**

------

Securities registered pursuant to Section 12(b) of the Act:

---

| | | |
|:---|:---|:---|
| Title of each class | Trading Symbol(s) | Name of each exchange on which registered |
| Common Stock, par value $0.001 per share | CUE | Nasdaq Capital Market |

---

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes  No 

Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files). Yes  No 

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller reporting company, or an emerging growth company. See the definitions of "large accelerated filer", "accelerated filer", "smaller reporting company," and "emerging growth company" in Rule 12b-2 of the Exchange Act.

---

| | | | |
|:---|:---|:---|:---|
| Large accelerated filer |  | Accelerated filer |  |
| Non-accelerated filer | ☒ | Smaller reporting company | ☒ |
| Emerging growth company |  |  |  |

---

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. ☐

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). ☐ Yes  No

As of August 8, 2025, the registrant had 76,845,904 shares of Common Stock ($0.001 par value per share) outstanding.

------

**CUE BIOPHARMA, INC.**

**TABLE OF CONTENTS**

---

| | |
|:---|:---|
| [**<u>PART I. FINANCIAL INFORMATION</u>**](#part_i_financial_information) |  |
| [<u>Item 1. Financial Statements (Unaudited)</u>](#item_1_financial_statements) | 6 |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[<u>Condensed Consolidated Balance Sheets</u>](#condensed_balance_sheets) | 6 |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[<u>Condensed Consolidated Statements of Operations and Comprehensive Loss</u>](#condensed_consolidated_statements_operat) | 7 |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[<u>Condensed Consolidated Statements of Stockholders' Equity</u>](#consolidated_statements_stockholders_equ) | 8 |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[<u>Condensed Consolidated Statements of Cash Flows</u>](#condensed_consolidated_statements_cash_f) | 9 |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[<u>Notes to the Condensed Consolidated Financial Statements (Unaudited)</u>](#notes_consolidated_financial_statements) | 10 |
| [<u>Item 2. Management's Discussion and Analysis of Financial Condition and Results of Operations</u>](#mda_new) | &nbsp;&nbsp;&nbsp;&nbsp;28 |
| [<u>Item 3. Quantitative and Qualitative Disclosures about Market Risk</u>](#item_3_quantitative_qualitative_disclosu) | 41 |
| [<u>Item 4. Controls and Procedures</u>](#item_4_controls_procedures) | 41 |
| &nbsp;&nbsp;&nbsp;&nbsp;[**<u>PART II. OTHER INFORMATION</u>**](#part_ii_or_information) |  |
| [<u>Item 1. Legal Proceedings</u>](#item_1_legal_proceedings) | 42 |
| [<u>Item 1A. Risk Factors</u>](#item_1a_risk_factors) | 42 |
| [<u>Item 2. Unregistered Sales of Equity Securities and Use of Proceeds</u>](#item_2_unregistered_sales_equity_securit) | 44 |
| [<u>Item 3. Defaults Upon Senior Securities</u>](#item_3_defaults_upon_senior_securities) | 44 |
| [<u>Item 4. Mine Safety Disclosures</u>](#item_4_mine_safety_disclosures) | 44 |
| [<u>Item 5. Other Information</u>](#item_5_or_information) | 44 |
| [<u>Item 6. Exhibits</u>](#item_6_exhibits) | 45 |

---

------

**CAUTIONARY NOTE REGARDING FORWARD-LOOKING STATEMENTS AND INDUSTRY DATA**

This Quarterly Report on Form 10-Q contains "forward-looking statements" within the meaning of Section 27A of the Securities Act of 1933, as amended, and Section 21E of the Securities Exchange Act of 1934, as amended. Forward-looking statements, which are based on certain assumptions and describe our future plans, strategies and expectations, can generally be identified by the use of forward-looking terms such as "believe," "expect," "may," "will," "should," "would," "could," "seek," "intend," "plan," "goal," "project," "estimate," "anticipate," "strategy," "future," "likely" or other comparable terms. All statements, other than statements of historical fact, contained in this Quarterly Report on Form 10-Q, including statements regarding our strategy, future operations, future financial position, future revenue, projected costs, prospects, plans and objectives of management, are forward-looking statements.

The forward-looking statements in this Quarterly Report on Form 10-Q include, among other things, statements about:

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the initiation, timing, progress and results of our ongoing and planned preclinical studies and any future clinical trials and our research and development programs;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•our estimates regarding expenses, future revenue, capital requirements and need for additional financing;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•our expectations regarding our ability to fund our projected operating requirements with our existing cash resources and the period in which we expect that such cash resources will enable us to fund such operating requirements;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•our plans to develop our drug product candidates, including our prioritization of our autoimmune programs, including CUE-401 and the CUE-500 series (excluding CUE-501, which has been licensed to Boehringer Ingelheim International GmbH);

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•our plans to pursue third party support through partnerships and collaborations to further develop the CUE-100 series programs, including CUE-101 and CUE-102;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the timing of and our ability to submit applications for, and to obtain and maintain regulatory approvals for, our drug product candidates;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the potential advantages of our drug product candidates;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the rate and degree of market acceptance and clinical utility of our drug product candidates, if approved;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•our estimates regarding the potential market opportunity for our drug product candidates;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•our commercialization, marketing and manufacturing capabilities and strategy;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•our intellectual property position;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•our ability to identify additional products, drug product candidates or technologies with significant commercial potential that are consistent with our commercial objectives;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the impact of government laws and regulations, general economic and market conditions, inflation, and the imposition of new or revised global trade tariffs;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•our competitive position;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•developments relating to our competitors and our industry;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•our ability to continue as a going concern; and

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•our ability to maintain and establish collaborations or obtain additional funding.

Forward-looking statements are neither historical facts nor assurances of future performance. Instead, they are based only on our current beliefs, expectations and assumptions regarding the future of our business, future plans and strategies, projections, anticipated events and trends, the economy and other future conditions. Because forward-looking statements relate to the future, they are subject to inherent uncertainties, risks and changes in circumstances that are difficult to predict and many of which are outside of our control. Our actual results and financial condition may differ materially from those indicated in the forward-looking statements. Therefore, you should not rely on any of these forward-looking statements. Important factors that could cause our actual results and financial condition to differ materially from those indicated in the forward-looking statements include the factors discussed below under the headings "Risk Factor Summary," and Part II. Item 1A. "Risk Factors," and the risk factors detailed further in Part I. Item 1A., "Risk Factors" of our Annual Report on Form 10-K for the year ended December 31, 2024, filed with the Securities and Exchange Commission on March 31, 2025.

------

This report includes statistical and other industry and market data that we obtained from industry publications and research, surveys, and studies conducted by third parties as well as our own estimates. All of the market data used in this report involve a number of assumptions and limitations, and you are cautioned not to give undue weight to such data. Industry publications and third-party research, surveys, and studies generally indicate that their information has been obtained from sources believed to be reliable, although they do not guarantee the accuracy or completeness of such information. Our estimates of the potential market opportunities for our drug product candidates include several key assumptions based on our industry knowledge, industry publications, third-party research, and other surveys, which may be based on a small sample size and may fail to accurately reflect market opportunities. While we believe that our internal assumptions are reasonable, no independent source has verified such assumptions.

Any forward-looking statement made by us in this Quarterly Report on Form 10-Q is based only on information currently available to us and speaks only as of the date on which it is made. We undertake no obligation to publicly update any forward-looking statement, whether written or oral, that may be made from time to time, whether as a result of new information, future developments or otherwise.

**RISK FACTOR SUMMARY** 

Investment in our securities involves risk. You should carefully consider the following summary of what we believe to be the principal risks facing our business, in addition to the risks described more fully in Part II. Item 1A, "Risk Factors" in this Quarterly Report on Form 10-Q, and Part I. Item 1A, "Risk Factors" of our Annual Report on Form 10-K for the year ended December 31, 2024, filed with the Securities and Exchange Commission on March 31, 2025 and other information included in this report. The risks and uncertainties described below are not the only risks and uncertainties we face. Additional risks and uncertainties not presently known to us or that we presently deem less significant may also impair our business operations.

If any of the following risks occurs, our business, financial condition and results of operations and future growth prospects could be materially and adversely affected, and the actual outcomes of matters as to which forward-looking statements are made in this report could be materially different from those anticipated in such forward-looking statements.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•Our recurring losses from operations raise substantial doubt regarding our ability to continue as a going concern.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•We are a clinical-stage biopharmaceutical company, have no history of generating commercial revenue, have a history of operating losses, and may never achieve or maintain profitability.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•We currently do not have, and may never develop, any FDA-approved or commercialized products.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•We are substantially dependent on the success of our drug product candidates, only two of which are currently being tested in clinical trials, and significant additional research and development and clinical testing will be required before we can potentially seek regulatory approval for or commercialize any of our drug product candidates.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•We have limited experience in conducting clinical trials and no history of commercializing biologic products, which may make it difficult to evaluate the prospects for our future viability.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•Success in preclinical studies or early clinical trials may not be indicative of results obtained in later trials.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•We plan to continue to seek collaborations or strategic alliances. However, we may not be able to establish such relationships, and relationships we have established may not provide the expected benefits.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•We may not be successful in our efforts to identify additional drug product candidates. Due to our limited resources and access to capital, we must prioritize the development of certain drug product candidates; these decisions may prove to be wrong and may adversely affect our business.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•We face significant competition from other biotechnology and pharmaceutical companies, and our operating results will suffer if we fail to compete effectively. Our competitors may be able to develop other compounds or drugs that are able to achieve similar or better results than our drug product candidates.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•We rely on third parties to conduct our clinical trials. If these third parties do not successfully carry out their contractual duties or meet expected deadlines, we may not be able to successfully complete development of, obtain regulatory approval for, or commercialize our drug product candidates and our business could be substantially harmed.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•We rely completely on third parties to manufacture our preclinical and clinical drug supplies for our drug product candidates.

------

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•If we or our licensor(s) are unable to protect our or its intellectual property, then our financial condition, results of operations and the value of our technology and potential products could be adversely affected.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•Even if we, or any collaborators we may have, obtain marketing approvals for any of our drug product candidates, the terms of approvals and ongoing regulation of our products could require the substantial expenditure of resources and may limit how we, or they, manufacture and market our products, which could materially impair our ability to generate revenue.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•We will need substantial additional financing to support our growth and ongoing operations. Additional capital may be difficult to obtain, restrict our operations, require us to relinquish rights to our technologies or drug product candidates, encumber our assets and result in ongoing debt service cost, or result in additional dilution to our stockholders.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•We have a loan agreement that requires us to meet certain operating covenants and place restrictions on our operating and financial flexibility.

------

**PART I. FINANCIAL INFORMATION**

**Item 1. Financial Statements**

**Cue Biopharma, Inc.**

**Condensed Consolidated Balance Sheets**

***(Unaudited)***

***(in thousands, except share and per share amounts)*** 

---

| | | |
|:---|:---|:---|
|  | **June 30,<br>2025** | **December 31,<br>2024** |
| **ASSETS** |  |  |
| Current assets: |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Cash and cash equivalents | $27492 | $22459 |
| &nbsp;&nbsp;&nbsp;&nbsp;Accounts receivable | 532 | 945 |
| &nbsp;&nbsp;&nbsp;&nbsp;Deposits, current portion | 470 | 929 |
| &nbsp;&nbsp;&nbsp;&nbsp;Prepaid expenses and other current assets | 2350 | 805 |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Total current assets | 30844 | 25138 |
| Property and equipment, net | 454 | 471 |
| Operating lease right-of-use asset | 5118 | 4370 |
| Deposits | 1956 | 1955 |
| Restricted cash | 153 | 152 |
| Other long-term assets | 283 | 105 |
| Foreign withholding tax receivable | 1899 |  |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Total assets | $40707 | $32191 |
| **LIABILITIES AND STOCKHOLDERS' EQUITY** |  |  |
| Current liabilities: |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Accounts payable | $3627 | $2823 |
| &nbsp;&nbsp;&nbsp;&nbsp;Accrued expenses | 1518 | 2908 |
| &nbsp;&nbsp;&nbsp;&nbsp;Research and development contract liability, current portion | 9579 | 85 |
| &nbsp;&nbsp;&nbsp;&nbsp;Operating lease liabilities, current | 2114 | 3540 |
| &nbsp;&nbsp;&nbsp;&nbsp;Current portion of long-term debt, net | 2416 | 4333 |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Total current liabilities | 19254 | 13689 |
| &nbsp;&nbsp;&nbsp;&nbsp;Operating lease liabilities, non-current | 3104 | 1003 |
| &nbsp;&nbsp;&nbsp;&nbsp;Other long-term payable | 190 |  |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Total liabilities | $22548 | $14692 |
| Commitments and contingencies (Note 11) |  |  |
| Stockholders' equity: |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Preferred stock, $0.001 par value; 10,000,000 shares authorized and 0 shares issued and outstanding at June 30, 2025 and December 31, 2024 |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Common stock, $0.001 par value; 300,000,000 shares authorized; 76,446,884 and 61,819,101 shares issued and outstanding at June 30, 2025 and December 31, 2024, respectively | 76 | 62 |
| &nbsp;&nbsp;&nbsp;&nbsp;Additional paid in capital | 380686 | 359301 |
| &nbsp;&nbsp;&nbsp;&nbsp;Accumulated deficit | (362603) | (341864) |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Total stockholders' equity | 18159 | 17499 |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Total liabilities and stockholders' equity | $40707 | $32191 |

---

The accompanying notes are an integral part of these condensed consolidated financial statements.

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**Cue Biopharma, Inc.**

**Condensed Consolidated Statements of Operations and Comprehensive Loss**

***(Unaudited)***

***(in thousands, except share and per share amounts)*** 

---

| | | | | |
|:---|:---|:---|:---|:---|
|  | **Three Months Ended<br>June 30,** | **Three Months Ended<br>June 30,** | **Six Months Ended<br>June 30,** | **Six Months Ended<br>June 30,** |
|  | **2025** | **2024** | **2025** | **2024** |
| **Collaboration revenue** | $2954 | $2658 | $3374 | $4375 |
| **Operating expenses:** |  |  |  |  |
| &nbsp;&nbsp;General and administrative | 3679 | 3511 | 7852 | 7697 |
| &nbsp;&nbsp;Research and development | 7910 | 9530 | 16457 | 19729 |
| &nbsp;&nbsp;&nbsp;&nbsp;Total operating expenses | 11589 | 13041 | 24309 | 27426 |
| **Loss from operations** | (8635) | (10383) | (20935) | (23051) |
| **Other income (expense):** |  |  |  |  |
| &nbsp;&nbsp;Interest income | 198 | 427 | 368 | 989 |
| &nbsp;&nbsp;Interest expense | (45) | (215) | (172) | (456) |
| &nbsp;&nbsp;&nbsp;&nbsp;Total other income, net | 153 | 212 | 196 | 533 |
| **Net loss** | $(8482) | $(10171) | $(20739) | $(22518) |
| **Comprehensive loss** | $(8482) | $(10171) | $(20739) | $(22518) |
| Net loss per common share – basic and diluted | $(0.09) | $(0.20) | $(0.24) | $(0.45) |
| Weighted average common shares outstanding – basic and diluted | 95459401 | 50174756 | 84857051 | 49822689 |

---

The accompanying notes are an integral part of these condensed consolidated financial statements.

------

**Cue Biopharma, Inc.**

**Condensed Consolidated Statements of Stockholders' Equity**

***(Unaudited)***

***(in thousands, except share and per share amounts)*** 

---

| | | | | | |
|:---|:---|:---|:---|:---|:---|
| **For the three months ended June 30, 2025 and 2024:** | **For the three months ended June 30, 2025 and 2024:** | **For the three months ended June 30, 2025 and 2024:** | **For the three months ended June 30, 2025 and 2024:** | **For the three months ended June 30, 2025 and 2024:** | **For the three months ended June 30, 2025 and 2024:** |
|  | **Common Stock** | **Common Stock** | **Additional** |  | **Total** |
|  | **Shares** | **Par<br>Value** | **Paid-in<br>Capital** | **Accumulated<br>Deficit** | **Stockholders'<br>Equity** |
| Balance, March 31, 2024 | 48643316 | $48 | $343527 | $(313537) | $30038 |
| Stock-based compensation |  |  | 1755 |  | 1755 |
| Net loss |  |  |  | (10171) | (10171) |
| Balance, June 30, 2024 | 48643316 | $48 | $345282 | $(323708) | $21622 |
| Balance, March 31, 2025 | 61819101 | $62 | $360639 | $(354121) | $6580 |
| Issuance of common stock from ATM offering, net of sales agent commissions and fees | 1097003 | 1 | 751 |  | 752 |
| Issuance of common stock, warrants and pre-funded warrants, net of issuance costs | 13530780 | 13 | 18033 |  | 18046 |
| Stock-based compensation |  |  | 1263 |  | 1263 |
| Net loss |  |  |  | (8482) | (8482) |
| Balance, June 30, 2025 | 76446884 | $76 | $380686 | $(362603) | $18159 |

---

---

| | | | | | |
|:---|:---|:---|:---|:---|:---|
| **For the six months ended June 30, 2025 and 2024:** | **For the six months ended June 30, 2025 and 2024:** | **For the six months ended June 30, 2025 and 2024:** | **For the six months ended June 30, 2025 and 2024:** | **For the six months ended June 30, 2025 and 2024:** | **For the six months ended June 30, 2025 and 2024:** |
|  | **Common Stock** | **Common Stock** | **Additional** |  | **Total** |
|  | **Shares** | **Par<br>Value** | **Paid-in<br>Capital** | **Accumulated<br>Deficit** | **Stockholders'<br>Equity** |
| Balance, December 31, 2023 | 47215116 | $47 | $338228 | $(301190) | $37085 |
| Issuance of common stock from ATM offering, net of sales agent commissions and fees | 1428200 | 1 | 3353 |  | 3354 |
| Stock-based compensation |  |  | 3701 |  | 3701 |
| Net loss |  |  |  | (22518) | (22518) |
| Balance, June 30, 2024 | 48643316 | $48 | $345282 | $(323708) | $21622 |
| Balance, December 31, 2024 | 61819101 | $62 | $359301 | $(341864) | $17499 |
| Issuance of common stock from ATM offering, net of sales agent commissions and fees | 1097003 | 1 | 751 |  | 752 |
| Issuance of common stock, warrants and pre-funded warrants, net of issuance costs | 13530780 | 13 | 18033 |  | 18046 |
| Stock-based compensation |  |  | 2601 |  | 2601 |
| Net loss |  |  |  | (20739) | (20739) |
| Balance, June 30, 2025 | 76446884 | $76 | $380686 | $(362603) | $18159 |

---

The accompanying notes are an integral part of these condensed consolidated financial statements.

------

**Cue Biopharma, Inc.**

**Condensed Consolidated Statements of Cash Flows**

***(Unaudited)***

***(in thousands)***

---

| | | |
|:---|:---|:---|
|  | **Six Months Ended June 30,** | **Six Months Ended June 30,** |
|  | **2025** | **2024** |
| **Cash flows from operating activities** |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Net loss | $(20739) | $(22518) |
| &nbsp;&nbsp;&nbsp;&nbsp;Adjustments to reconcile net loss to cash used in operating activities: |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Depreciation and amortization | 200 | 198 |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Stock-based compensation | 2601 | 3701 |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Decrease in the carrying amount of right-of-use-assets | 1478 | 1513 |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Gain on sale of property and equipment |  | 1 |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Amortization of debt issuance costs | 18 | 18 |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Accretion of final payment on term loans | 65 | 65 |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Changes in operating assets and liabilities: |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Accounts receivable | 413 | (149) |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Prepaid expenses and other current assets | (1545) | (782) |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Deposits | 458 |  |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Foreign withholding tax receivable | (1899) |  |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Other payable | 189 |  |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Accounts payable | 804 | 405 |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Accrued expenses | (1390) | 426 |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Research and development contract liability | 9494 | (1136) |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Operating lease liability | (1550) | (1516) |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Other assets | (184) |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Net cash used in operating activities | (11587) | (19774) |
| **Cash flows from investing activities** |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Purchases of property and equipment | (177) | (65) |
| &nbsp;&nbsp;&nbsp;&nbsp;Net cash used in investing activities | (177) | (65) |
| **Cash flows from financing activities** |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Proceeds from ATM offering, net of sales agent commissions and fees | 752 | 3354 |
| &nbsp;&nbsp;&nbsp;&nbsp;Proceeds from issuance of common stock, warrants and pre-funded warrants, net of transaction costs | 18046 |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Repayment of term loans | (2000) | (2000) |
| &nbsp;&nbsp;&nbsp;&nbsp;Net cash provided by financing activities | 16798 | 1354 |
| **Net increase (decrease) in cash, cash equivalents, and restricted cash** | 5034 | (18485) |
| Cash, cash equivalents, and restricted cash at beginning of period | 22611 | 48665 |
| Cash, cash equivalents, and restricted cash at end of period | $27645 | $30180 |
| **Supplemental disclosures of non-cash investing and financing activities:** |  |  |
| Cash paid for interest | $157 | $392 |
| Lease liabilities arising from obtaining right-of-use assets | $2226 | $— |

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The accompanying notes are an integral part of these condensed consolidated financial statements.

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**Cue Biopharma, Inc.**

**Notes to Condensed Consolidated Financial Statements** 

***(Unaudited)***

**1.** **Organization and Basis of Presentation** 

Cue Biopharma, Inc. (the "Company") is a clinical-stage biopharmaceutical company developing a novel class of injectable therapeutics engineered to selectively engage and modulate disease-specific T cells for the treatment of autoimmune disease and cancer. Unlike conventional approaches that broadly activate the immune system, the Company's Immuno-STAT® platform is designed to selectively modulate disease-relevant T cells, enhancing efficacy while minimizing off-target effects. The Company believes its Immuno-STAT platform holds the promise of producing drug product candidates with the potential of establishing new standards of care in the treatment of autoimmune disease and cancer.

The accompanying financial statements have been prepared on a going concern basis, which contemplates the realization of assets and satisfaction of liabilities and commitments in the normal course of business. The Company is in the clinical development and preclinical research and development stages and has incurred recurring losses and negative cash flows from operations since inception. As of June 30, 2025, the Company had cash and cash equivalents of $27.5 million. The future viability of the Company is dependent on its ability to raise additional capital to finance its operations and fund research and development costs in order to seek approval for commercialization of its drug product candidates.

The Company continues to explore raising additional capital through a combination of equity offerings, collaborations, and other strategic alliances, and, depending on the availability and level of additional financings, potential cash expenditure reduction, there is no guarantee that the Company will be successful in these mitigation efforts. The Company's failure to access additional capital as and when needed would have a negative impact on its financial condition and its ability to pursue its business strategies as this capital is necessary for the Company to perform the research and development activities required to develop and commercialize the Company's drug product candidates in order to generate future revenue streams. The Company's accumulated deficit, history of losses, negative cash flows from operations and future expected losses raises substantial doubt about the Company's ability to continue as a going concern within one year of the issuance date of these financial statements.

**2.** **Summary of Significant Accounting Policies**

**Basis of Presentation** 

The accompanying unaudited condensed consolidated financial statements as of June 30, 2025, and for the three and six months ended June 30, 2025 and 2024, have been prepared in accordance with the rules and regulations of the Securities and Exchange Commission (the "SEC") and generally accepted accounting principles in the United States ("U.S. GAAP") for financial information, which prescribes elimination of all significant intercompany accounts and transactions in the accounts of the Company and its wholly owned subsidiary, Cue Biopharma Securities Corp., which was incorporated in the Commonwealth of Massachusetts in December 2018. In the opinion of management, these financial statements reflect all adjustments which are necessary for a fair statement of the Company's financial position and results of its operations, as of and for the periods presented. Certain information and footnote disclosures normally included in financial statements prepared in accordance with U.S. GAAP have been condensed or omitted from this report, as is permitted by such rules and regulations. Accordingly, these financial statements should be read in conjunction with the financial statements and notes thereto contained in the Company's Annual Report on Form 10-K for the year ended December 31, 2024, filed with the Securities and Exchange Commission on March 31, 2025.

Interim results for the three and six months ended June 30, 2025 are not necessarily indicative of the results that may be expected for the fiscal year ending December 31, 2025, or any future periods.

***Public Offerings***

In October 2021, the Company entered into an open market sale agreement (the "ATM Sales Agreement") with Jefferies LLC ("Jefferies"), as agent, to sell shares of the Company's common stock for aggregate gross proceeds of up to $80 million, from time to time, through an at-the-market equity offering program. The ATM Sales Agreement will terminate upon the earliest of (a) the sale of $80 million of shares of the Company's common stock pursuant to the ATM Sales Agreement or (b) the termination of the ATM Sales Agreement by the Company or Jefferies.

During the three and six months ended June 30, 2025, the Company sold 1,097,003 shares of common stock under the ATM Sales Agreement for proceeds of $0.8 million, net of commissions paid, but excluding transaction expenses. During the three months ended June 30, 2024, there were no sales under the ATM Sales Agreement. During the six months ended June 30, 2024, the Company sold 1,428,200 shares of common stock under the ATM Sales Agreement for proceeds of $3.4 million, net of commissions paid, but excluding transaction expenses. As of June 30, 2025, the Company had sold an aggregate of 10,169,234 shares of common stock

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under the ATM Sales Agreement for proceeds of $41.2 million, net of commissions paid, but excluding transaction expenses, since its inception.

On September 26, 2024, the Company entered into an underwriting agreement (the "2024 Underwriting Agreement") with Oppenheimer & Co. Inc., as representative of the several underwriters named therein (collectively, the "2024 Underwriters"), relating to an underwritten public offering of (i) 11,564,401 shares (the "2024 Shares") of the Company's common stock, $0.001 par value per share, and accompanying common stock warrants (the "2024 Common Stock Warrants") to purchase 2,891,100 shares of the Company's common stock, and (ii) to certain investors in lieu of common stock, pre-funded warrants (the "2024 Pre-Funded Warrants," and together with the 2024 Common Stock Warrants, the "2024 Warrants") to purchase 12,435,599 shares of the Company's common stock and accompanying 2024 Common Stock Warrants to purchase 3,108,900 shares of the Company's common stock. All of the 2024 Shares and the 2024 Warrants were sold by the Company. Each 2024 Share was offered and sold together with an accompanying 2024 Common Stock Warrant at a combined offering price of $0.50, and each 2024 Pre-Funded Warrant was offered and sold together with an accompanying 2024 Common Stock Warrant at a combined offering price of $0.499, which is equal to the combined offering price per share of common stock and accompanying 2024 Common Stock Warrant less the $0.001 exercise price of each 2024 Pre-Funded Warrant. The Company received net proceeds from the offering of $10.8 million, after deducting underwriting discounts and commissions and offering expenses of $1.2 million, excluding any proceeds that may be received from exercise of the 2024 Warrants. At June 30, 2025, the weighted average exercise price of the 2024 Warrants was $0.50 and the weighted average contractual life was 4.25 years.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;On April 14, 2025, the Company entered into an underwriting agreement (the "2025 Underwriting Agreement") with Oppenheimer & Co. Inc., as representative of the several underwriters named therein (collectively, the "2025 Underwriters"), relating to an underwritten public offering of (i) 13,530,780 shares (the "2025 Shares") of the Company's common stock, $0.001 par value per share, and accompanying common stock warrants ("2025 Common Stock Warrants") to purchase 3,382,695 shares of the Company's common stock, and (ii) to certain investors in lieu of common stock, pre-funded warrants (the "2025 Pre-Funded Warrants," and together with the 2025 Common Stock Warrants, the "2025 Warrants") to purchase 11,469,216 shares of the Company's common stock and accompanying 2025 Common Stock Warrants to purchase 2,867,304 shares of common stock. All of the 2025 Shares and 2025 Warrants were sold by the Company. Each 2025 Share was offered and sold together with an accompanying 2025 Common Stock Warrant at a combined offering price of $0.79, and each 2025 Pre-Funded Warrant was offered and sold together with an accompanying 2025 Common Stock Warrant at a combined offering price of $0.789, which is equal to the combined offering price per share of common stock and accompanying 2025 Common Stock Warrant less the $0.001 exercise price of each 2025 Pre-Funded Warrant. The 2025 Underwriters purchased (i) each 2025 Share and accompanying 2025 Common Stock Warrant from the Company pursuant to the 2025 Underwriting Agreement at a combined price of $0.7426 and (ii) each 2025 Pre-Funded Warrant and accompanying 2025 Common Stock Warrant from the Company pursuant to the 2025 Underwriting Agreement at a combined price of $0.74166. The Company received net proceeds from the offering of $18.0 million, after deducting underwriting discounts and commissions and offering expenses of $0.5 million, excluding any proceeds that may be received from exercise of the 2025 Warrants. At June 30, 2025, the weighted average exercise price of the 2025 Warrants was $0.79 and the weighted average contractual life was 4.80 years.

***Consolidation***

The accompanying condensed consolidated financial statements include the Company and its wholly owned subsidiary, Cue Biopharma Securities Corp. The Company has eliminated all intercompany transactions.

***Use of Estimates*** 

The preparation of financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities at the date of the financial statements and the reported amounts of expenses during the reporting period. Significant estimates include estimates related to collaboration revenue, the accounting for potential liabilities and accrued expenses, the assumptions utilized in valuing stock-based compensation issued for services, the realization of deferred tax assets, and the useful life with respect to long-lived assets and intangibles. Actual results could differ from those estimates.

***Cash Concentrations*** 

The Company maintains its cash balances with financial institutions in federally insured accounts and may periodically have cash balances in excess of insurance limits. The Company maintains its accounts with financial institutions with a high credit rating. The Company has not experienced any losses to date from the Company's deposits with these financial institutions and believes that it is not exposed to any significant credit risk on cash.

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***Cash and Cash Equivalents***

The Company considers all highly liquid investments with a maturity of three months or less at the date of purchase to be cash equivalents. The Company invests available cash in money market funds.

***Marketable Securities***

Marketable securities consist of investments with original maturities greater than ninety days and less than one year from the date of the Company's condensed consolidated balance sheets. The Company classifies all of its investments as available-for-sale securities. Accordingly, these investments are recorded at fair value, which is based on quoted market prices. Unrealized gains and losses are recognized and determined on a specific identification basis and are included in comprehensive loss. Realized gains and losses are determined on a specific identification basis and are included in other income on the condensed consolidated statements of operations and comprehensive loss. Amortization and accretion of discounts and premiums is recorded in interest income.

***Restricted Cash***

The Company had $0.2 million in restricted cash deposited with a separate commercial bank to collateralize Company credit cards as of June 30, 2025 and December 31, 2024.

***Property and Equipment*** 

Property and equipment is recorded at cost. Major improvements are capitalized, while maintenance and repairs are charged to expense as incurred. Gains and losses from dispositions of property and equipment are included in income and expense when realized. Amortization of leasehold improvements is provided using the straight-line method over the shorter of the lease term or the useful life of the underlying assets. Depreciation of property and equipment is provided using the straight-line method over the following estimated useful lives:

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| | |
|:---|:---|
| Laboratory equipment | 5 years |
| Computer equipment | 3 years |
| Furniture and fixtures | 3-8 years |

---

The Company recognizes depreciation and amortization expense in general and administrative expenses and in research and development expenses in the Company's condensed consolidated statements of operations and comprehensive loss, depending on how each category of property and equipment is utilized in the Company's business activities.

***Trademark***

Trademark consists of the Company's right, title and interest to the CUE BIOLOGICS Mark, and any derivative mark incorporating CUE, throughout the world, together with all associated goodwill and common law rights appurtenant thereto, including, but not limited to, any right, title and interest in any corporate name, company name, business, name, trade name, dba, domain name, or other source identifier incorporating CUE.

The Company has classified the trademark as a component of other long-term assets, having a useful life of 15 years. The Company evaluates the status of this intangible asset for amortization and impairment at each quarter end and year end reporting date. For each of the three and six months ended June 30, 2025 and 2024, the Company recorded approximately $3,000 and $6,000, respectively, in amortization expense on a straight-line basis.

***Debt Issuance Costs***

Debt issuance costs are deferred and presented as a reduction to long-term debt. Debt issuance costs are amortized using the effective interest rate method over the term of the loan. Amortization of deferred debt issuance costs are included in interest expense in the condensed consolidated statements of operations and comprehensive loss.

***Revenue Recognition***

The Company recognizes collaboration revenue under certain of the Company's license and collaboration agreements that are within the scope of Accounting Standards Codification ("ASC"), Topic 606, *Revenue from Contracts with Customers* ("ASC 606"). The Company's contracts with customers typically include promises related to licenses to intellectual property and research and development services. If the license to the Company's intellectual property is determined to be distinct from the other performance obligations identified in the arrangement, the Company recognizes revenue from non-refundable, up-front fees allocated to the license

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when the license is transferred to the licensee and the licensee is able to use and benefit from the license. For licenses that are bundled with other promises, the Company utilizes judgment to assess the nature of the combined performance obligation to determine whether the combined performance obligation is satisfied over time or at a point in time and, if over time, the appropriate method of measuring progress for purposes of recognizing revenue from non-refundable, up-front fees. Accordingly, the transaction price is generally comprised of a fixed fee due at contract inception and variable consideration in the form of milestone payments due upon the achievement of specified events and tiered royalties earned when customers recognize net sales of licensed products. The Company measures the transaction price based on the amount of consideration to which it expects to be entitled in exchange for transferring the promised goods and/or services to the customer. The Company utilizes the "expected value method" method to estimate the amount of variable consideration, to predict the amount of consideration to which it will be entitled for its one open contract. Amounts of variable consideration are included in the transaction price to the extent that it is probable that a significant reversal in the amount of cumulative revenue recognized will not occur when the uncertainty associated with the variable consideration is subsequently resolved. At the inception of each arrangement that includes development and regulatory milestone payments, the Company evaluates whether the associated event is considered probable of achievement and estimates the amount to be included in the transaction price using the expected value method.

***Research and Development Expenses*** 

Research and development expenses consist primarily of compensation costs, fees paid to consultants, outside service providers and organizations (including research institutes at universities), facility costs, and development and clinical trial costs with respect to the Company's drug product candidates.

Research and development expenses incurred under contracts are expensed ratably over the life of the underlying contracts, unless the achievement of milestones, the completion of contracted work, or other information indicates that a different pattern of performance is more appropriate. Other research and development expenses are charged to operations as incurred.

Nonrefundable advance payments are recognized as an expense as the related services are performed. The Company evaluates whether it expects the services to be rendered at each quarter end and year end reporting date. If the Company does not expect the services to be rendered, the advance payment is charged to expense. Nonrefundable advance payments for research and development services are included in prepaid and other current assets on the Company's condensed consolidated balance sheets. To the extent that a nonrefundable advance payment is for contracted services to be performed within 12 months from the reporting date, such advance is included in current assets; otherwise, such advance is included in non-current assets.

The Company evaluates the status of its research and development agreements and contracts, and the carrying amount of the related assets and liabilities, at each quarter end and year end reporting date, and adjusts the carrying amounts and their classification on the Company's condensed consolidated balance sheets as appropriate.

***Patent Expenses*** 

The Company is the exclusive worldwide licensee of, and has patent applications pending for, numerous domestic and foreign patents. Due to the significant uncertainty associated with the successful development of one or more commercially viable drug product candidates based on the Company's research efforts and any related patent applications, all patent costs, including patent-related legal fees, filing fees and other costs are charged to general and administrative expense as incurred.

***Licensing Fees and Costs*** 

Licensing fees and costs consist primarily of costs relating to the acquisition of the Company's license agreement with the Albert Einstein College of Medicine, including related royalties, maintenance fees, milestone payments and product development costs. Licensing fees and costs are charged to research and development expense as incurred.

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***Long-Lived Assets*** 

The Company reviews long-lived assets, consisting of property and equipment, for impairment when events or changes in circumstances indicate the carrying value of these assets may exceed their current fair values. Recoverability of assets to be held and used is measured by a comparison of the carrying amount of an asset to the estimated undiscounted future cash flows expected to be generated by the asset. If the carrying amount of an asset exceeds its estimated future cash flows, an impairment charge is recognized for the amount by which the carrying amount of the asset exceeds the fair value of the assets. Assets to be disposed of are separately presented in the Company's condensed consolidated balance sheets and reported at the lower of the carrying amount or fair value less costs to sell and are no longer depreciated. The Company has not historically recorded any impairment to its long-lived assets. In the future, if events or market conditions affect the estimated fair value to the extent that a long-lived asset is impaired, the Company will adjust the carrying value of these long-lived assets in the period in which the impairment occurs.

***Leases*** 

The Company accounts for leases under ASC 842, *Leases*, which requires a lessee to record a right-of-use asset and a corresponding lease liability for most lease arrangements on the Company's condensed consolidated balance sheets. Under the standard, disclosure of key information about leasing arrangements to assist users of the financial statements with assessing the amount, timing and uncertainty of cash flows arising from leases are required.

***Stock-Based Compensation*** 

The Company periodically issues stock-based awards to officers, directors, employees, scientific and clinical advisory board members and consultants for services rendered. Such awards vest and expire according to terms established at the issuance date.

Stock-based compensation to officers, directors, employees, scientific and clinical advisory board members and consultants, including grants of employee stock options, is recognized in the financial statements based on their grant date fair values. Stock option grants, which are generally time-vested, are measured at the grant date fair value and charged to operations on a straight-line basis over the service period, which generally approximates the vesting term. The Company also grants performance-based awards periodically to officers of the Company. The Company recognizes compensation costs related to performance awards over the requisite service period if and when the Company concludes that it is probable that the performance condition will be achieved.

The fair value of stock options and restricted stock units is determined utilizing the Black-Scholes valuation model. This valuation model takes into account the exercise price of the award, as well as a variety of significant assumptions. The assumptions used to estimate the fair value of stock options include the expected term, the expected volatility of the Company's stock over the expected term, the risk-free interest rate over the expected term, and the Company's expected annual dividend yield. The risk-free interest rate is based on the U.S. Treasury yield curve in effect at the time of grant. The expected dividend yield is based on the current yield at the grant date; the Company has never declared or paid dividends and has no plans to do so for the foreseeable future. As permitted by Staff Accounting Bulletin No. 107, due to the Company's limited trading history and option activity, management utilizes the simplified method to estimate the expected term of options at the date of grant. The exercise price is determined based on the fair value of the Company's common stock at the date of grant. The Company accounts for forfeitures as they occur.

The Company recognizes the fair value of stock-based compensation in general and administrative expenses and in research and development expenses in the Company's condensed consolidated statements of operations and comprehensive loss, depending on the type of services provided by the recipient of the equity award.

***Comprehensive Income (Loss)***

Components of comprehensive income or loss, including net income or loss, are reported in the financial statements in the period in which they are recognized. Other comprehensive income or loss is defined as the change in equity during a period from transactions and other events and circumstances from non-owner sources. Net income (loss) and other comprehensive income (loss) are reported net of any related tax effect to arrive at comprehensive income (loss). Comprehensive income (loss) includes net income (loss) as well as changes in stockholders' equity that result from transactions and economic events other than those with stockholders. There were no elements of other comprehensive income (loss) in the periods presented.

***Earnings (Loss) Per Share*** 

The Company's computation of earnings (loss) per share ("EPS") for the respective periods includes basic and diluted EPS. Basic EPS is measured as the income (loss) attributable to common stockholders divided by the weighted average number of common shares outstanding for the period. Diluted EPS is similar to basic EPS but presents the dilutive effect on a per share basis of potential common shares that would result from the exercise of outstanding stock options and warrants as if they had been exercised at the

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beginning of the periods presented, or issuance date, if later. Potential common shares that have an anti-dilutive effect (i.e., those that increase income per share or decrease loss per share) are excluded from the calculation of diluted EPS. Basic and diluted loss per common share is the same for all periods presented because all outstanding stock options and warrants are anti-dilutive.

The Company computes EPS in accordance with the Financial Accounting Standards Board ("FASB") Accounting Standards Codification ("ASC") 260, "Earnings per Share". Per ASC 260-10-45-13, shares issuable for little to no consideration should be included in the number of outstanding shares used for basic EPS. The FASB proposed that warrants or options exercisable for little to no cost (sometimes referred to as "penny warrants") be included in the denominator of basic EPS (and therefore diluted EPS) once there were no further vesting conditions or contingencies associated with them. The Company included 23,904,815 and 1,531,440 pre-funded warrants in the denominator of basic EPS at June 30, 2025 and June 30, 2024, respectively.

At June 30, 2025 and 2024, the Company excluded the securities summarized below, which entitled the holders thereof to acquire shares of common stock, from its calculation of EPS, as their effect would have been anti-dilutive.

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| | | |
|:---|:---|:---|
|  | **June 30,** | **June 30,** |
|  | **2025** | **2024** |
| Common stock warrants | 21401905 | 9188406 |
| Common stock options | 23819212 | 9462908 |
| Total | 45221117 | 18651314 |

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***Fair Value of Financial Instruments*** 

The authoritative guidance with respect to fair value established a fair value hierarchy that prioritizes the inputs to valuation techniques used to measure fair value into three levels and requires that assets and liabilities carried at fair value be classified and disclosed in one of three categories, as presented below.

Level 1. Observable inputs such as quoted prices in active markets for an identical asset or liability that the Company has the ability to access as of the measurement date. Financial assets and liabilities utilizing Level 1 inputs include active exchange-traded securities and exchange-based derivatives.

Level 2. Inputs, other than quoted prices included within Level 1, which are directly observable for the asset or liability or indirectly observable through corroboration with observable market data. Financial assets and liabilities utilizing Level 2 inputs include fixed income securities, non-exchange-based derivatives, mutual funds, and fair-value hedges.

Level 3. Unobservable inputs in which there is little or no market data for the asset or liability which requires the reporting entity to develop its own assumptions. Financial assets and liabilities utilizing Level 3 inputs include infrequently traded non-exchange-based derivatives and commingled investment funds and are measured using present value pricing models.

The Company determines the level in the fair value hierarchy within which each fair value measurement falls in its entirety, based on the lowest level input that is significant to the fair value measurement in its entirety. In determining the appropriate levels, the Company performs an analysis of the assets and liabilities at each reporting period end.

The carrying value of financial instruments (consisting of cash, a certificate of deposit, debt, accounts payable, accrued compensation and accrued expenses) is considered to be representative of their respective fair values due to the short-term nature of those instruments.

***Recent Accounting Pronouncements*** 

*ASU 2023-07 - Segment Reporting*

In November 2023, the FASB issued ASU 2023-07, Segment Reporting (Topic 280): Improvements to Reportable Segment Disclosures ("ASU 2023-07"). ASU 2023-07 requires disclosure of incremental segment information on an annual and interim basis. The amendments also require companies with a single reportable segment to provide all disclosures required by these amendments and all existing segment disclosures in ASC 280, Segment Reporting. The amendments are effective for fiscal years beginning after December 15, 2023, and interim periods beginning after December 15, 2024. The Company adopted ASU 2023-07 effective December 31, 2024.

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Operating segments are defined as components of an entity for which separate financial information is available and that is regularly reviewed by the Chief Operating Decision Maker (the "CODM") in deciding how to allocate resources to an individual segment and in assessing performance. The Company's CODM is the chief executive officer.

The Company is in the development stage, has not yet earned revenue from product sales, and has incurred recurring losses and negative cash flows from operations since inception. The Company operates as a single reporting segment, focused on developing a novel class of therapeutic biologics to selectively modulate disease-specific T cells directly within the patient's body. The CODM manages and allocates resources to the operations of the Company on a total company basis and therefore does not measure separate segment profit or loss. Managing and allocating resources on a total company basis enables the CODM to assess the overall level of resources available and how to best deploy these resources across functions and research and development programs that are in line with the Company's long-term strategic corporate goals. Consistent with this decision-making process, the CODM uses consolidated financial information for purposes of evaluating performance, forecasting future period financial results, allocating resources and setting incentive targets. Operating expenses are used to monitor budget versus actual results. All the Company's long-lived assets are held in the United States and all the Company's revenues since inception have been earned from collaboration agreements as none of the Company's drug product candidates have yet been approved for commercial sale. The resources utilized for any specific purpose may vary significantly and will depend on a number of factors, including, but not limited to, the Company's research and development activities and programs, clinical testing, regulatory approval, market conditions, and changes in or revisions to the Company's business strategy and technology development plans.

*ASU 2023-09 - Income Taxes*

In December 2023, the FASB issued ASU No. 2023-09, *Income Taxes* (Topic 740): *Improvements to Income Tax Disclosures* ("ASU 2023-09"). The guidance in ASU 2023-09 improves the transparency of income tax disclosures by greater disaggregation of information in the rate reconciliation and income taxes paid disaggregated by jurisdiction. The standard is effective for public companies for fiscal years beginning after December 15, 2024, with early adoption permitted. The Company is currently evaluating the impact that the adoption of ASU 2023-09 may have on its consolidated financial statements.

Management does not believe that any other recently issued, but not yet effective, authoritative guidance, if currently adopted, would have a material impact on the Company's financial statement presentation or disclosures.

**3.** **Fair Value** 

The Company accounts for its financial assets and liabilities using fair value measurements. The authoritative accounting guidance defines fair value, establishes a framework for measuring fair value under U.S. GAAP and enhances disclosures about fair value measurements. Fair value is defined as the exchange price that would be received for an asset or paid to transfer a liability (an exit price) in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants on the measurement date.

The following table presents information about the Company's assets that are measured at fair value on a recurring basis as of June 30, 2025 and December 31, 2024, and indicates the level of the fair value hierarchy utilized to determine such fair value:

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| | | | | |
|:---|:---|:---|:---|:---|
|  | **Fair Value Measurements as of June 30, 2025** | **Fair Value Measurements as of June 30, 2025** | **Fair Value Measurements as of June 30, 2025** | **Fair Value Measurements as of June 30, 2025** |
|  | **(in thousands)** | **(in thousands)** | **(in thousands)** | **(in thousands)** |
|  | **Level 1** | **Level 2** | **Level 3** | **Fair Value** |
| Cash equivalents | $26984 | $— | $— | $26984 |
| Total | $26984 | $— | $— | $26984 |
|  | **Fair Value Measurements as of December 31, 2024** | **Fair Value Measurements as of December 31, 2024** | **Fair Value Measurements as of December 31, 2024** | **Fair Value Measurements as of December 31, 2024** |
|  | **(in thousands)** | **(in thousands)** | **(in thousands)** | **(in thousands)** |
|  | **Level 1** | **Level 2** | **Level 3** | **Fair Value** |
| Cash equivalents | $21813 | $— | $— | $21813 |
| Total | $21813 | $— | $— | $21813 |

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As of June 30, 2025, the Company had $27.0 million in cash equivalents, and did not hold any marketable securities. The Company measures the cash equivalents that are invested in money market funds using Level 1 inputs for identical securities. As of December 31, 2024, the Company had $21.8 million in cash equivalents, and did not hold any marketable securities. For each of the three and six months ended June 30, 2025 and 2024 there were no transfers between Levels 1, 2 or 3.

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**4.** **Property and Equipment, Net**

Property and equipment, net as of June 30, 2025 and December 31, 2024 consisted of the following:

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| | | |
|:---|:---|:---|
|  | **June 30,<br>2025** | **December 31,<br>2024** |
|  | **(in thousands)** | **(in thousands)** |
| Laboratory equipment | $3935 | $3785 |
| Furniture and fixtures | 68 | 68 |
| Computer equipment | 207 | 180 |
| Leasehold improvements | 118 | 118 |
| &nbsp;&nbsp;&nbsp;&nbsp;Total property and equipment | 4328 | 4151 |
| Less: accumulated depreciation | (3874) | (3680) |
| &nbsp;&nbsp;&nbsp;&nbsp;Property and equipment, net | $454 | $471 |

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Depreciation expense for the three and six months ended June 30, 2025 and 2024 was included in the condensed consolidated statements of operations and comprehensive loss as follows, and excludes trademark amortization of $3,000 and $6,000 for the three and six months ended June 30, 2025 and 2024, respectively:

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| | | | | |
|:---|:---|:---|:---|:---|
|  | **Three Months Ended<br>June 30,** | **Three Months Ended<br>June 30,** | **Six Months Ended<br>June 30,** | **Six Months Ended<br>June 30,** |
|  | **2025** | **2024** | **2025** | **2024** |
|  | **(in thousands)** | **(in thousands)** | **(in thousands)** | **(in thousands)** |
| General and administrative | $4 | $5 | $8 | $10 |
| Research and development | 93 | 95 | 186 | 188 |
| Depreciation total | $97 | $100 | $194 | $198 |

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**5.** **Loan with First Citizens Bank (formerly with Silicon Valley Bank)**

On February 15, 2022 (the "Closing Date"), the Company entered into a Loan and Security Agreement (the "Loan Agreement"), with Silicon Valley Bank, as lender ("SVB"). The Company drew $10,000,000 in term loans under the Loan Agreement (the "Term Loans") on the Closing Date. The Loan Agreement was amended in April 2023 and October 2024.

The Term Loans bear interest at a floating rate per annum equal to the greater of (A) the prime rate (as published in the money rates section of The Wall Street Journal) plus 2.25% and (B) 5.50%. The Term Loans were interest only from the Closing Date through June 30, 2023, after which the Company is required to pay 30 equal monthly installments of principal. At June 30, 2025, the interest rate was 9.75% which is based on the prime rate plus 2.25%.

The Term Loans may be prepaid in full with payment of a 1.00% prepayment premium. Upon prepayment or repayment in full of the Term Loans, the Company will be required to pay a one-time final payment fee equal to 5.00% of the original principal amount of any funded Term Loans being repaid. This one-time final payment fee is recorded to interest expense using the effective interest method over the period of the Term Loans in the condensed consolidated statements of operations and comprehensive loss.

The Term Loans and related obligations under the Loan Agreement are secured by substantially all of the Company's properties, rights and assets, except for its intellectual property which is subject to a negative pledge under the Loan Agreement.

The Loan Agreement, as amended, contains customary representations, warranties, events of default and covenants. In addition to the foregoing, the Company is required to have at all times on deposit in accounts of the Company maintained with SVB, unrestricted and unencumbered cash in an amount equal to the lesser of (i) 100% of the dollar value of the Company's consolidated cash, in the aggregate, at all financial institutions and (ii) $20,000,000. On March 10, 2023, SVB was closed and the Federal Deposit Insurance Corporation (the "FDIC") was appointed receiver for the bank. The FDIC created a successor bridge bank, and all deposits and loans of SVB were transferred to the bridge bank under a systemic risk exception approved by the United States Department of the Treasury, the Federal Reserve and the FDIC. On March 27, 2023, First Citizens Bank & Trust Company ("First Citizens Bank"), assumed all of SVB's deposits and certain other liabilities and acquired substantially all of SVB's loans and certain other assets from the FDIC. First Citizens Bank continues to hold the Company's Term Loans under the same existing terms and covenants which were in place with SVB.

During the three and six months ended June 30, 2025, the Company recognized interest expense related to the Term Loans of $0.05 million and $0.1 million, respectively, and interest expense related to accretion of the final payment of $33,000 and $65,000, respectively. During the three and six months ended June 30, 2024, the Company recognized interest expense related to the Term Loans of $0.2 million and $0.4 million, respectively, and interest expense related to accretion of the final payment of $33,000 and $65,000, respectively. All outstanding principal and accrued and unpaid interest under the Term Loans and all other outstanding obligations with respect to the Term Loans are due and payable in full on December 1, 2025.

***Debt Issuance Costs***

Debt issuance costs are deferred and presented as a reduction to long-term debt. Debt issuance costs are amortized using the effective interest rate method over the term of the loan. Amortization of deferred debt issuance costs are included in interest expense in the condensed consolidated statements of operations and comprehensive loss.

The Company incurred $142,000 in debt issuance costs related to the Loan Agreement at its onset. For each of the three months ended June 30, 2025 and 2024, the Company recorded $9,000 in amortization of debt issuance costs to interest expense in the condensed consolidated statements of operations and comprehensive loss. For each of the six months ended June 30, 2025 and 2024, the Company recorded $18,000 in amortization of debt issuance costs to interest expense in the condensed consolidated statements of operations and comprehensive loss. The Company recorded less than $0.1 million to short- and long-term debt issuance costs contra-liabilities as of June 30, 2025.

**6.** **Accrued Expenses**

Accrued expenses consist of the following:

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| | | |
|:---|:---|:---|
|  | **June 30,** | **December 31,** |
| *(In thousands)* | **2025** | **2024** |
| Employee and board compensation | $202 | $1812 |
| Contract research services | 357 | 773 |
| Contract manufacturing services | 649 | 9 |
| Professional services | 310 | 314 |
| Total | $1518 | $2908 |

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**7.** **Einstein License Agreement**

On January 14, 2015, the Company entered into a license agreement, as amended and restated on July 31, 2017 and as further amended on October 30, 2018, January 13, 2024, and April 10, 2025 (the "Einstein License"), with Albert Einstein College of Medicine ("Einstein") for certain patent rights relating to the Company's core technology platform for the engineering of biologics to control T cell activity, precision, immune-modulatory drug product candidates, and two supporting technologies that enable the discovery of costimulatory signaling molecules (ligands) and T cell targeting peptides.

Pursuant to the April 2025 amendment, Einstein consented to the Company's entry into the Collaboration and License Agreement (the "BI Collaboration and License Agreement") with Boehringer Ingelheim International GmbH ("BI") and granted the Company the right to sublicense to BI. In addition, Einstein and the Company agreed to amend specified upstream payment obligations that may be owed to Einstein by the Company, solely in connection with the sublicense to BI.

Under the Einstein License, the Company holds an exclusive worldwide license, with the right to sublicense, import, make, have made, use, provide, offer to sell, and sell all products, processes and services that use the patents covered by the Einstein License, including certain technology received from Einstein relating thereto (the "Einstein Licensed Products"). Under the Einstein License, the Company is required to:

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•Pay royalties and amounts based on a certain percentage of proceeds, as defined in the Einstein License, from sales of Einstein Licensed Products and sublicense agreements.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•Pay escalating annual maintenance fees, which are nonrefundable, but are creditable against the amount due to Einstein for royalties.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•Make significant payments based upon the achievement of certain milestones, as defined in the Einstein License. Payments made upon achievement of milestones are nonrefundable and are not creditable against any other payment due to Einstein. At June 30, 2025, the Company had made aggregate payments totaling $2.14 million since inception with respect to achievement of these milestones.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•Incur minimum product development costs until the first commercial sale of the first Einstein Licensed Product.

The Company was in compliance with its obligations under the Einstein License at June 30, 2025 and 2024.

The Einstein License expires upon the expiration of the Company's last obligation to make royalty payments to Einstein which may be due with respect to certain Einstein Licensed Products, unless terminated earlier under the provisions thereof. The Einstein License includes certain termination provisions if the Company fails to meet its obligations thereunder.

Pursuant to the Einstein License, the Company issued to Einstein 671,572 shares of the Company's common stock in connection with the consummation of the initial public offering of its common stock on December 27, 2017.

The Company accounts for license fees incurred in connection with the Einstein License in accordance with ASC 730, Research and Development. Please refer to Note 10 Collaboration Revenue.

**8.** **Stock-Based Compensation**

***Stock Option Valuation*** 

For stock options requiring an assessment of value during the six months ended June 30, 2025 and 2024, the fair value of each stock option award was estimated using the Black-Scholes option-pricing model utilizing the following assumptions:

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| | |
|:---|:---|
|  | **June 30, 2025** |
| Risk-free interest rate | 4.05% - 4.46% |
| Expected dividend yield | 0% |
| Expected volatility | 86.46% - 88.15% |
| Expected life | 5.50 to 6.25 years |
|  | **June 30, 2024** |
| Risk-free interest rate | 3.83% - 4.43% |
| Expected dividend yield | 0% |
| Expected volatility | 50.1% - 109.86% |
| Expected life | 5.50 to 8.91 years |

---

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A summary of stock option activity for the six months ended June 30, 2025 is as follows:

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| | | | |
|:---|:---|:---|:---|
|  | **Number of<br>Shares** | **Weighted<br>Average<br>Exercise<br>Price** | **Weighted <br>Average<br>Remaining <br>Contractual <br>Life <br>(in Years)** |
| Stock options outstanding at December 31, 2024 | 10471724 | $5.61 | 7.27 |
| Granted | 1938100 | 0.99 |  |
| Exercised |  |  |  |
| Cancelled | (1527640) | 5.33 |  |
| Stock options outstanding at June 30, 2025 | 10882184 | 4.83 | 7.06 |
| Stock options exercisable at June 30, 2025 | 6315208 | $7.12 | 5.67 |

---

The aggregate intrinsic value of exercisable but unexercised in-the-money stock options at June 30, 2025 was less than $0.1 million based on a weighted average exercise price of $7.12 per share. The aggregate intrinsic value of options is calculated as the difference of the market close price of $0.68 on June 30, 2025, and the weighted average exercise price of $7.12, with a weighted average remaining contractual term of 5.67 years.

***Stock-based Compensation*** 

Stock-based compensation for the three and six months ended June 30, 2025 and 2024 was included in the Company's condensed consolidated statements of operations and comprehensive loss as follows:

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| | | | | |
|:---|:---|:---|:---|:---|
|  | **Three Months Ended<br>June 30,** | **Three Months Ended<br>June 30,** | **Six Months ended <br>June 30,** | **Six Months ended <br>June 30,** |
| **(in thousands)** | **2025** | **2024** | **2025** | **2024** |
| General and administrative | $580 | $859 | $1275 | $1814 |
| Research and development | 683 | 896 | 1326 | 1887 |
| &nbsp;&nbsp;Total stock-based compensation | $1263 | $1755 | $2601 | $3701 |

---

As of June 30, 2025, total unrecognized stock-based compensation expense was $4.2 million, which is expected to be recognized as an operating expense in the Company's condensed consolidated statements of operations and comprehensive loss over the weighted average remaining period of 2.24 years.

As of June 30, 2024, total unrecognized stock-based compensation expense was $9.2 million, which is expected to be recognized as an operating expense in the Company's condensed consolidated statements of operations and comprehensive loss over the weighted average remaining period of 2.52 years.

During the three and six months ended June 30, 2025, the Company granted stock options to purchase 48,800 shares of common stock with a weighted average grant date fair value of $0.62 per share and stock options to purchase 1,938,100 shares of common stock with a weighted average grant date fair value of $0.99 per share, respectively.

During the three and six months ended June 30, 2024, the Company granted stock options to purchase 593,800 shares of common stock with a weighted average grant date fair value of $1.65 per share and stock options to purchase 2,463,300 shares of common stock with a weighted average grant date fair value of $1.93 per share, respectively.

**9.** **Warrants**

On April 14, 2025, the Company entered into the 2025 Underwriting Agreement with Oppenheimer & Co. Inc., as representative of the 2025 Underwriters, relating to an underwritten public offering of (i) 13,530,780 shares of the Company's common stock, $0.001 par value per share, and accompanying common stock warrants to purchase 3,382,695 shares of the Company's common stock, and (ii) to certain investors in lieu of common stock, pre-funded warrants to purchase 11,469,216 shares of the Company's common stock and accompanying common stock warrants to purchase 2,867,304 shares of common stock. All of the 2025 Shares and 2025 Warrants were sold by the Company. Each 2025 Share was offered and sold together with an accompanying 2025 Common Stock Warrant at a combined offering price of $0.79, and each 2025 Pre-Funded Warrant was offered and sold together with an accompanying 2025 Common Stock Warrant at a combined offering price of $0.789, which is equal to the combined offering

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price per share of common stock and accompanying 2025 Common Stock Warrant less the $0.001 exercise price of each 2025 Pre-Funded Warrant. The Company received net proceeds from the offering of $18.0 million, after deducting underwriting discounts and commissions and offering expenses of $0.5 million, excluding any proceeds that may be received from exercise of the 2025 Warrants. At June 30, 2025, all of the 2025 Warrants remained outstanding.

On September 26, 2024, the Company entered into the 2024 Underwriting Agreement with Oppenheimer & Co. Inc., as representative of the 2024 Underwriters, relating to an underwritten public offering of (i) 11,564,401 shares of the Company's common stock, $0.001 par value per share, and accompanying common stock warrants to purchase 2,891,100 shares of common stock, and (ii) to certain investors in lieu of common stock, pre-funded warrants to purchase 12,435,599 shares of common stock and accompanying common stock warrants to purchase 3,108,900 shares of common stock. All of the 2024 Shares and the 2024 Warrants were sold by the Company. Each 2024 Share was offered and sold together with an accompanying 2024 Common Stock Warrant at a combined offering price of $0.50, and each 2024 Pre-Funded Warrant was offered and sold together with an accompanying 2024 Common Stock Warrant at a combined offering price of $0.499, which is equal to the combined offering price per share of common stock and accompanying 2024 Common Stock Warrant less the $0.001 exercise price of each 2024 Pre-Funded Warrant. The Company received net proceeds from the offering of $10.8 million, after deducting underwriting discounts and commissions and offering expenses of $1.2 million, excluding any proceeds that may be received from exercise of the 2024 Warrants. At June 30, 2025, 5,963,500 of the 2024 Common Stock Warrants and 12,435,599 of the 2024 Pre-Funded Warrants remained outstanding.

On November 16, 2022, the Company issued 9,188,406 warrants with an exercise price of $3.93 and a 5-year term (the "2022 Common Stock Warrants"), and 1,531,440 pre-funded warrants at a nominal exercise price of $0.0001 per share (the "2022 Pre-Funded Warrants"). The Company recorded cash received from 7,656,966 shares of common stock, 9,188,406 2022 Common Stock Warrants and 1,531,440 2022 Pre-Funded Warrants to additional paid in capital in the amount of $27.4 million, net of placement fees of $2.6 million during the year ended December 31, 2022. At June 30, 2025, 9,188,406 of the 2022 Common Stock Warrants and zero of the 2022 Pre-Funded Warrants remained outstanding.

Each tranche of warrants was evaluated under ASC 480, Distinguishing Liabilities from Equity, and ASC 815, Derivatives and Hedging, and the Company determined that equity classification was appropriate. The Company determined equity classification for both warrants and pre-funded warrants as they do not embody an obligation for the Company to repurchase its shares and permit the holders to receive a fixed number of shares of common stock upon exercise. Per ASC 815-40-25, the Company accounts for the warrants and pre-funded warrants as equity, as the Company does not provide the holder a fixed or guaranteed return.

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**10.** **Collaboration Revenue** 

The Company recognizes collaboration revenue under certain of the Company's license or collaboration agreements that are within the scope of ASC 606. The Company's contracts with customers typically include promises related to licenses to intellectual property and research and development services. If the license to the Company's intellectual property is determined to be distinct from the other performance obligations identified in the arrangement, the Company recognizes revenue from non-refundable, up-front fees allocated to the license when the license is transferred to the licensee and the licensee is able to use and benefit from the license. For licenses that are bundled with other promises, the Company utilizes judgment to assess the nature of the combined performance obligation to determine whether the combined performance obligation is satisfied over time or at a point in time and if, over time, the appropriate method of measuring progress for purposes of recognizing revenue from non-refundable, up-front fees. The Company's contracts may include options to acquire additional goods and/or services.

The terms of the Company's arrangements with customers typically include the payment of one or more of the following: (i) non-refundable, up-front payment, and pass through costs related to research activities, (ii) development, regulatory and commercial milestone payments, (iii) future options and (iv) royalties on net sales of licensed products. Accordingly, the transaction price is generally comprised of a fixed fee due at contract inception and variable consideration in the form of pass through costs and milestone payments due upon the achievement of specified events and tiered royalties earned when customers recognize net sales of licensed products. The Company measures the transaction price based on the amount of consideration to which it expects to be entitled in exchange for transferring the promised goods and/or services to the customer. The Company utilizes the "expected value method" method to estimate the amount of variable consideration, to predict the amount of consideration to which it will be entitled for its one open contract. Amounts of variable consideration are included in the transaction price to the extent that it is probable that a significant reversal in the amount of cumulative revenue recognized will not occur when the uncertainty associated with the variable consideration is subsequently resolved. Milestone payments that are not within the control of the Company or the licensee, such as those dependent upon receipt of regulatory approval, are not considered to be probable of achievement until the triggering event occurs. At the end of each reporting period, the Company reevaluates the probability of achievement of each milestone and any related constraint, and, if necessary, adjusts its estimate of the overall transaction price. Any such adjustments are recorded on a cumulative catch-up basis, which would affect revenue and net loss in the period of adjustment.

For arrangements that include sales-based royalties, including milestone payments based upon the achievement of a certain level of product sales, the Company recognizes revenue upon the later of: (i) when the related sales occur or (ii) when the performance obligation to which some or all of the payment has been allocated has been satisfied (or partially satisfied). To date, the Company has not recognized any development, regulatory or commercial milestones or royalty revenue resulting from any of its collaboration arrangements. Consideration that would be received for optional goods and/or services is excluded from the transaction price at contract inception.

The Company allocates the transaction price to each performance obligation identified in the contract on a relative standalone selling price basis, when applicable. However, certain components of variable consideration are allocated specifically to one or more particular performance obligations in a contract to the extent both of the following criteria are met: (i) the terms of the payment relate specifically to the efforts to satisfy the performance obligation or transfer the distinct good or service and (ii) allocating the variable amount of consideration entirely to the performance obligation or the distinct good or service is consistent with the allocation objective of the standard whereby the amount allocated depicts the amount of consideration to which the entity expects to be entitled in exchange for transferring the promised goods or services. The Company develops assumptions that require judgment to determine the standalone selling price for each performance obligation identified in each contract. The key assumptions utilized in determining the standalone selling price for each performance obligation may include forecasted revenues, development timelines, estimated research and development costs, discount rates, likelihood of exercise and probabilities of technical and regulatory success.

Revenue is recognized based on the amount of the transaction price that is allocated to each respective performance obligation when or as the performance obligation is satisfied by transferring a promised good and/or service to the customer. For performance obligations that are satisfied over time, the Company recognizes revenue by measuring the progress toward complete satisfaction of the performance obligation using a single method of measuring progress which depicts the performance in transferring control of the associated goods and/or services to the customer. The Company uses input methods to measure progress toward the complete satisfaction of performance obligations satisfied over time. The Company evaluates the measure of progress each reporting period and, if necessary, adjusts the measure of performance and related revenue recognition. Any such adjustments are recorded on a cumulative catch-up basis, which would affect revenue and net loss in the period of adjustment. The Company measures progress toward satisfaction of the performance obligation over time as effort is expended.

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***Collaboration Agreement with LG Chem***

On November 6, 2018, the Company entered into a Collaboration, License and Option Agreement (as amended from time to time, the "LG Chem Collaboration Agreement"), with LG Chem Ltd. ("LG Chem") related to the development of the Company's CUE-101 and CUE-102 Immuno-STATs focused in the field of oncology. Pursuant to the LG Chem Collaboration Agreement, the Company granted LG Chem an exclusive license to develop, manufacture and commercialize CUE-101, as well as CUE-102 Immuno-STATs that target T cells against two additional cancer antigens, in certain Asian countries (collectively, the "LG Chem Territory").

Aside from the $6.8 million in milestone payments earned to date, the Company does not believe that any variable consideration should be included in the transaction price as of June 30, 2025. Such assessment considered the application of the constraint to ensure that estimates of variable consideration would be included in the transaction price only to the extent the Company had a high degree of confidence that revenue would not be reversed in a subsequent reporting period. The Company will re-evaluate the transaction price, including the estimated variable consideration included in the transaction price and all constrained amounts, in each reporting period and as other changes in circumstances occur. For the three and six months ended June 30, 2025, the Company did not recognize any revenue related to the LG Chem Collaboration Agreement. For each of the three and six months ended June 30, 2024, the Company recognized revenue of less than $0.1 million related to the LG Chem Collaboration Agreement. The Company did not record short or long-term research and development liabilities on its condensed consolidated balance sheets dated June 30, 2025 and 2024, as the performance obligations have been met and completed. Research and development cost sharing provisions under the agreement expired on March 31, 2022, and thereafter, the Company recognized revenue on intellectual patent filing passthrough costs in the LG Chem Territory.

On March 11, 2025, the Company and LG Chem entered into the Ninth Amendment to the LG Chem Collaboration Agreement. As of the date of the amendment, the Company regained its rights to the LG Chem Territory for the CUE-101 program which had been licensed to LG Chem, and LG Chem terminated all of its rights to the same program. Pursuant to the Ninth Amendment, the Company agreed to make future payments to LG Chem, if and when, one or more potential scenarios related to the CUE-101 program occur up to a predetermined aggregate amount. LG Chem continues to maintain its interest and rights in the CUE-102 program, targeting Wilms' tumor 1 protein expressing cancers, pursuant to the LG Chem Collaboration Agreement.

***Collaboration and Option Agreement with Ono***

In February 2023, the Company entered into a strategic collaboration agreement (the "Ono Collaboration and Option Agreement") with Ono Pharmaceutical Co., Ltd. ("Ono") to further develop CUE-401. In March 2025, the Company and Ono agreed to terminate the Ono Collaboration and Option Agreement effective as of March 6, 2025. At such time, the Ono Collaboration and Option Agreement had no further force or effect with the exception of certain customary provisions which are intended to survive termination and expiration of the Ono Collaboration and Option Agreement. The Company retained all rights to CUE-401.

Under the terms of the Ono Collaboration and Option Agreement, Ono paid the Company an upfront payment and agreed to fully fund all research and development activities related to CUE-401 through a specified option period of 24 months (the "Ono Research Term"). Per the agreement, as consideration for the research and development activities performed by the Company, Ono (i) made a one-time, non-refundable, non-creditable upfront payment of $3.0 million to the Company in March 2023 and (ii) agreed to reimburse the Company for all costs incurred in conducting research, including (a) pass through costs from third party contractors and (b) full-time employee salaries capped at $2.1 million in the first 18 months of the Ono Research Term. Subsequently, the Company and Ono agreed to increase this cap for full-time employee salaries to $3.1 million.

As of the date of this report, both Ono and the Company have satisfied all of their performance obligations and made all outstanding payments required under the agreement. For each of the three and six months ended June 30, 2025, the Company recognized revenue of $0.4 million related to the Ono Collaboration and Option Agreement. For the three and six months ended June 30, 2024, the Company recognized revenue of $2.6 million and $4.3 million, respectively, related to the Ono Collaboration and Option Agreement. The Company did not record short or long-term research and development liabilities on its condensed consolidated balance sheet dated June 30, 2025, as the performance obligation has been met and completed. For the year ended December 31, 2024, the Company recorded short-term research and development liabilities on its consolidated balance sheets of $0.1 million.

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***BI Collaboration and License Agreement***

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;On April 10, 2025, the Company entered into the BI Collaboration and License Agreement to research, develop and commercialize differentiated B cell depletion molecules, including CUE-501.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Under the terms of the BI Collaboration and License Agreement, the Company and BI will conduct collaborative research focused on CUE-501 during the BI Research Term. In addition to, or instead of, CUE-501, BI may elect, at its sole discretion, to include additional or alternative compounds targeted at B cell depletion. BI will have an exclusive, royalty-bearing, worldwide, sublicensable license, under the Company's applicable patents and know-how, to develop, manufacture and commercialize the BI Licensed Products, for all uses, and BI shall be responsible for all further research, preclinical and clinical development, manufacturing, regulatory approvals, and commercialization of BI Licensed Products at its expense. During the BI Research Term, the Company is prohibited from developing or commercializing any molecule for applications in B cell depletion.

Pursuant to the terms of the BI Collaboration and License Agreement, the Company received an upfront payment of $10.1 million in cash in the second quarter of 2025, which is net of $1.9 million of German withholding taxes that the Company is seeking to get refunded. The withholding has been recorded as a foreign withholding tax receivable at June 30, 2025 on the Company's condensed consolidated balance sheet. The Company will also be eligible to receive up to an aggregate of approximately $345.0 million in success-based research, development and commercial milestone payments, beginning with two preclinical development milestones, as well as royalty payments on net sales. The royalty payments will be subject to reduction due to patent expiration, payments made under certain licenses for third-party intellectual property and generic competition. BI has agreed to reimburse the Company for agreed upon costs incurred in conducting research during the BI Research Term, including certain pass through costs from third party contractors and full-time employee salaries.

The BI Collaboration and License Agreement will continue, on a product-by-product and country-by-country basis, until the expiration of the applicable royalty term, unless earlier terminated. BI has the right to terminate the BI Collaboration and License Agreement for any reason after a specified notice period. Each party has the right to terminate the BI Collaboration and License Agreement on account of the other party's bankruptcy or material, uncured breach. In connection with the Company's entry into the BI Collaboration and License Agreement, the Company entered into an amendment to the Company's Einstein License whereby Einstein consented to the Company's entry into the BI Collaboration and License Agreement and granted the Company the right to sublicense to BI. In addition, the Company and Einstein agreed to amend specified upstream payment obligations that may be owed to Einstein by the Company, solely in connection with the sublicense to BI.

For the three and six months ended June 30, 2025, the Company recognized revenue of $2.9 million related to the BI Collaboration and License Agreement. The Company recorded short or long-term research and development liabilities of $9.6 million on its condensed consolidated balance sheet as of June 30, 2025.

The Company considered the capitalization of contract costs under the guidance in ASC 340-40, Other Assets and Deferred Costs: Contracts with Customers, as it relates to the BI Collaboration and License Agreement. The Company capitalized license expenses of approximately $1.1 million as of June 30, 2025, paid to Einstein pursuant to the Einstein License Agreement which requires the Company to pay a percentage of sublicenses related to the Company's patent rights for components of its core technology that is licensed from Einstein. This amount is comprised of approximately $1.1 million of capitalized license expenses related to the up-front payment received from BI in May 2025, net of accumulated amortization of approximately $0.2 million. As of June 30, 2025, $0.7 million was included in prepaid expenses and other short-term assets and $0.2 million was included in other long-term assets related to the BI Collaboration and License Agreement.

**11.** **Commitments and Contingencies** 

***Einstein License Agreement*** 

In 2015, the Company entered into the Einstein License with Einstein for certain patent rights relating to the Company's core technology platform for the engineering of biologics to control T cell activity, precision, immune-modulatory drug product candidates, and two supporting technologies that enable the discovery of costimulatory signaling molecules (ligands) and T cell targeting peptides. The Company entered into an amended and restated license agreement on July 31, 2017, as amended on October 2018, which modified certain obligations of the parties under the Einstein License. The Einstein License was further amended on January 13, 2024 and April 10, 2025.

The Company pays $0.1 million in annual maintenance license fees to Einstein, which are amortized equally throughout the year. The Company incurred less than $0.1 million in annual maintenance fees for each of the three and six months ended June 30, 2025 and 2024.

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In the second quarter of 2025, the Company paid Einstein $0.9 million in fees under the amendment to the Einstein License in relation to the BI Collaboration and License Agreement.

The Company's remaining commitments with respect to the Einstein License are based on the attainment of future milestones. The aggregate amount of milestone payments made under the Einstein License may equal up to $1.85 million for each Einstein Licensed Product, and up to $1.85 million for each new indication of an Einstein Licensed Product. Additionally, the aggregate amount of one-time milestone payments based on cumulative sales of all Einstein Licensed Products may equal up to $5.75 million. The Company is also party to a service agreement with Einstein to support the Company's ongoing research and development activities.

***Collaboration Agreement with LG Chem***

See discussion of the LG Chem Collaboration Agreement in Note 10.

***Collaboration and Option Agreement with Ono***

See discussion of the Ono Collaboration and Option Agreement in Note 10.

***Collaboration and License Agreement with BI***

See discussion of the BI Collaboration and License Agreement in Note 10.

***Contingencies*** 

The Company accrues contingent liabilities to the extent that the liability is probable and estimable. There are no accruals for contingent liabilities in the Company's condensed consolidated financial statements.

The Company may be subject to various legal proceedings from time to time as part of its business. As of June 30, 2025, the Company was not a party to any legal proceedings or threatened legal proceedings, the adverse outcome of which, individually or in the aggregate, would have a material adverse effect on its business, financial condition or results of operations.

**12.** **Leases**

On March 28, 2022, the Company entered into a License Agreement (the "License") with MIL 40G, LLC (the "Licensor"), pursuant to which the Company leases approximately 13,000 square feet of office, research and development and laboratory space located at 40 Guest Street, Boston, Massachusetts 02135 (the "Office and Laboratory Space"). The Company recognized a right of use asset of $9.1 million and an operating lease liability of $9.1 million which were recorded as of the Term Commencement Date (as defined below) related to the License. The term of the License commenced on April 15, 2022 (the "Term Commencement Date").

On May 3, 2022, the Company entered into the First Amendment to the License with the Licensor, pursuant to which the License was expanded to include an additional room effective July 15, 2022. On July 7, 2022, the Company entered into an operating lease for additional laboratory space (the "Additional Laboratory Space") at 40 Guest Street for the period from December 1, 2022 through December 1, 2024 (the "40G Additional Laboratory Lease").

On November 20, 2024, the Company extended the term of the 40G Additional Laboratory Lease through July 14, 2026. The monthly rental rate for the Additional Laboratory Space is $61,519 through November 30, 2025 and $63,979 for the remainder of the term until July 14, 2026. During the year ended December 31, 2024, the Company recognized a right of use asset of $1.1 million and short-term and long-term operating lease liabilities of $0.7 million and $0.4 million, respectively, using a discount rate of 10%, which were recorded as of the term commencement date of the 40G Additional Laboratory Lease.

On June 30, 2025, the Company entered into the Second Amendment to the License with the Licensor. Pursuant to the Second Amendment, effective June 30, 2025, the monthly rental rate for the Office and Laboratory Space decreased from $235,884 to $147,546, subject to a 4% increase on April 15, 2027, and the term of the License was extended from April 14,

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2026 to April 14, 2028. In addition, the Licensor agreed to provide the Company a partial credit of $44,169 for rent the Company had paid at the new monthly rental rate for the month of June 2025.

For each of the three and six months ended June 30, 2025, the Company recorded $0.1 million in interest expense to the lease liability.

At June 30, 2025, operating lease right-of-use assets totaled $5.1 million. Corresponding operating lease liabilities totaled $5.2 million, of which $2.1 million were recorded in current liabilities, and $3.1 million were recorded in long-term liabilities on the Company's condensed consolidated balance sheets.

As of both June 30, 2025 and December 31, 2024, security deposits of $0.6 million related to the 40G Additional Laboratory Lease were included in deposits on the Company's consolidated balance sheets.

Future minimum lease payments under these leases at June 30, 2025 are as follows:

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| | |
|:---|:---|
|  | *(in thousands)* |
| 2025 (remaining 6 months) | $1257 |
| 2026 | 2228 |
| 2027 | 1884 |
| 2028 | 558 |
| Total lease payments | 5927 |
| &nbsp;&nbsp;&nbsp;&nbsp;Less: imputed interest | (709) |
| Present value of lease payments | $5218 |

---

Rent expense of $0.8 million and $1.6 million was included in the condensed consolidated statements of operations and comprehensive loss for the three and six months ended June 30, 2025, respectively. Rent expense of $0.9 million and $1.7 million was included in the condensed consolidated statements of operations and comprehensive loss for the three and six months ended June 30, 2024, respectively.

The weighted average remaining lease term and discount rate related to the Company's leases were as follows:

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| | | |
|:---|:---|:---|
|  | **June 30,<br>2025** | **December 31,<br>2024** |
| Weighted average remaining lease term (years) | 2.54 | 1.35 |
| Weighted average discount rate | 9.78% | 6.85% |

---

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**Item 2. Management's Discussion and Analysis of Financial Condition and Results of Operations**

*The following Management's Discussion and Analysis of Financial Condition and Results of Operations of Cue Biopharma, Inc. and its subsidiary ("Cue Biopharma", "we", "us", "our" or the "Company") should be read in conjunction with our financial statements and accompanying notes included in this Quarterly Report on Form 10-Q and the financial statements and accompanying notes thereto for the fiscal year ended December 31, 2024 and the related Management's Discussion and Analysis of Financial Condition and Results of Operations included in our Annual Report on Form 10-K filed with the Securities and Exchange Commission, or SEC, on March 31, 2025, or the 2024 Annual Report.*

**Overview**

We are a clinical-stage biopharmaceutical company developing a novel class of injectable therapeutics engineered to selectively engage and modulate disease-specific T cells for the treatment of autoimmune disease and cancer. Unlike conventional approaches that broadly activate the immune system, our Immuno-STAT® platform is designed to selectively modulate disease-relevant T cells, enhancing efficacy while minimizing off-target effects. We believe our Immuno-STAT platform holds the promise of producing drug product candidates with the potential of establishing new standards of care in the treatment of autoimmune disease and cancer. Our programs include, but are not limited to, drug product candidates designed to:

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•CUE-400 series (Autoimmune Diseases): Exploit transforming growth factor beta (TGF-β) signaling to induce an anti-inflammatory process, with a novel and unique mechanism to not only foster proliferation of regulatory T cells (Tregs) but also induce Tregs from T effector cells with the potential of restoring immune balance and functional immune tolerance (e.g., CUE-401 for autoimmune conditions).

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•CUE-500 series (Targeted Cell Depletion): Redirect anti-viral killer T cells to target and eliminate defined pathogenic cells (e.g., CUE-501 for autoimmune B cell depletion, which has been licensed to Boehringer Ingelheim International GmbH).

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•CUE-100 series (Oncology): Selectively activate and expand tumor-specific T cells (e.g., CUE-101 for HPV+ cancers and CUE-102 for Wilms' tumor 1 protein (WT1), expressing cancers).

We aim to leverage our differentiated platform to establish new standards of care, forge strategic partnerships, and accelerate clinical development.

As represented in the following image, the Immuno-STAT framework is engineered to be highly flexible and modular, potentially enabling us to deploy the same or similar core functional elements to restore immune balance across diverse therapeutic approaches.

<u>Immuno-STAT Platform Pipeline of Assets for Restoration of Immune Balance</u>

![img78870974_0.jpg](img78870974_0.jpg)

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<u>CUE-401</u>

In autoimmune disease, Tregs are the master regulators of maintaining immune homeostasis, or balance, and health. Autoreactive T cells, referred to as T effector cells (Teff cells), are reactive against "self" proteins and foster inflammation and induce chronic tissue damage. Tregs are important to maintaining immune balance in that they possess the ability to dampen and control the Teff cells.

CUE-401 is a preclinical, bispecific fusion protein designed to promote immune tolerance by modulating key components of the immune system, including the induction of newly formed Tregs (iTregs) from Teff cells, as well as expansion of existing or natural regulatory T cells (nTregs). Through the co-activity of engineered variants of TGF-β and interleukin 2 (IL-2), CUE-401 has the therapeutic potential to re-establish immune balance and induce tolerance across a range of T cell mediated autoimmune and inflammatory diseases.

CUE-401 has been engineered to harness the capacity of TGF-β to re-establish immune balance combined with the complementary signaling of IL-2, to provide an anti-inflammatory environment, as well as Treg induction and expansion for what we believe will provide long-lasting tolerance, which is considered to be the ultimate goal of treating autoimmune disease.

CUE-401, our first-in-class, bispecific molecule integrating a masked TGF-ß with our clinically validated, attenuated IL-2 variant, is designed to address multiple hurdles to fully exploiting the therapeutic potential of an immunology master switch. This novel design provides for "conditional binding" to avoid off target activity and has generated highly differentiated data in multiple preclinical autoimmune animal disease models.

In these preclinical animal models, CUE-401 behaves as a master switch to ameliorate inflammation as well as convert autoreactive effector T cells into stable iTregs. These findings suggest that CUE-401 acts by establishing a "tolerance positive feedback loop" that not only increases nonspecific Treg populations, but also reduces and converts specific autoreactive T cells into transdifferentiated iTregs that are specific for the disease-causing autoantigens.

We believe these results, along with advances in the manufacturing of CUE-401, have substantially reduced the risk profile for the development of this program and we have selected a lead candidate molecule. Scale-up manufacturing and other IND-enabling studies for CUE-401 are presently ongoing. We are preparing to file an investigational new drug (IND) application in the second quarter of 2026, with human proof-of-mechanism data anticipated in the first half of 2027. These early clinical trial results are anticipated to provide mechanistic evidence and validation further supporting the underlying premise of establishing immune balance and inducing durable immune tolerance which could represent a potential breakthrough as a new standard of care in multiple high-value autoimmune disease indications.

<u>CUE-500 Series</u>

The CUE-500 series has been developed to enable targeted anti-viral T cell-mediated depletion of pathogenic cell types, including autoreactive B cells. We believe these biologics have the potential to achieve immune balance in autoimmune patients and are significantly differentiated from other competing approaches such as bispecific antibody drug conjugates, pan-T cell engagers, IL-2 muteins, TNFR2 agonists, and CAR-T therapies.

The CUE-500 series represents a novel approach to selectively target disease-causing cells by redirecting existing anti-viral memory T cells to target and deplete such disease-causing cells. CUE-501, for which we recently established a collaboration and license agreement with Boehringer Ingelheim International GmbH (BI), is being developed to target and deplete autoimmune disease-causing B cells, in patients with autoimmune disease caused by autoreactive, pathogenic B cells. Targeted B cell depletion is widely recognized in the industry as a clinically validated and important approach for the treatment of B cell mediated autoimmune and inflammatory diseases, and we believe the selective mechanism of action exploiting the anti-viral memory T cell repertoire will provide highly effective killing of the targeted cells while preventing or substantially reducing the side effect profile often experienced with competing approaches.

Due to its modularity, we believe that the CUE-500 series has therapeutic potential across multiple disease areas. The mode of redirecting a defined population of already existing anti-viral T cells may apply to many pathogenic cell types readily addressed by swapping different cell-targeting antibody domains into the CUE-500 series framework.

We believe the preclinical data generated to date for CUE-401 and the CUE-500 series demonstrates the intended mechanistic effect of these novel approaches for the potential treatment of autoimmune disease, and each represent potential

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breakthrough therapeutic opportunities for significant patient populations and potential near-term value creation opportunities for our shareholders.

<u>CUE-100 Series</u>

Historically, we have primarily focused our resources on the development of our CUE-100 series for oncology, namely the CUE-101 and CUE-102 drug product candidates, which are representative of our approach to selectively activate targeted CD8+ T cells against cancer.

Although we are prioritizing CUE-401 and the CUE-500 series, we are currently continuing to treat and monitor patients in a Phase 1b open-label expansion study investigating CUE-101 in the treatment of HPV+ recurrent metastatic, or R/M, head and neck squamous cell carcinoma (HNSCC), in second line and beyond patients as a monotherapy, and as a first line therapy in combination with pembrolizumab (KEYTRUDA®). We are also continuing to monitor patients in a Phase 1b clinical trial of CUE-102 as a monotherapy in late line R/M WT1+ colorectal, gastric, ovarian, and pancreatic cancer and are enabling an investigator sponsored trial to evaluate CUE-102 in recurrent glioblastoma (rGBM).

Key data highlights (data cutoff date of July 14, 2025) from the ongoing open-label Phase 1b study of CUE-101 in HPV+ R/M HNSCC include:

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•Overall response rate (ORR) of 50% (2 complete responses and 10 partial responses) in treatment-naïve patients treated with CUE-101 and KEYTRUDA with combined positive score (CPS) ≥1, compared to an ORR of 19% observed with KEYTRUDA alone.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•12-month overall survival (OS) of 88% compared to 57% with KEYTRUDA alone in the historical KEYNOTE-048 trial, representing an unprecedented reduction in the risk of death (hazard ratio of 0.23) compared to historical data.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•Median OS of 32 months compared to 12.3 months in the historical KEYNOTE-048 trial.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•ORR of 50% in patients, including 50% with low PD-L1 expression (CPS 1-19).

**Plan of Operation**

Our approach to developing precision immunotherapies has yielded a growing portfolio of novel proteins with the potential to address multiple unmet needs across autoimmune disease and cancer. We believe that our science is derisked with clinical tolerability and activity from our Phase 1 clinical trials of CUE-101 and CUE-102, with the potential for significant market opportunities. As a result of our insights and learnings from our growing body of supportive data, we believe our corresponding strategic plans position us well to optimize shareholder value.

We intend to maximize this value by focusing on the development of CUE-401, for which we are preparing to file an IND application in the second quarter of 2026, while also establishing collaborations across our pipeline, such as our strategic collaboration and license agreement with BI for the development of CUE-501.

As a development-stage company, the majority of our business activities to date have been, and our planned future activities will be, devoted to furthering research and development of our drug product candidates.

As a fundamental element of our corporate development strategy, we are actively seeking collaborations for our oncology assets CUE-101 and CUE-102. This will allow us to more fully exploit the potential of our technology platform in the area of autoimmune disease and accelerate and expand our pipeline.

**Events that Raise Substantial Doubt About Our Ability to Continue as a Going Concern**

We will need to raise additional capital to fund our future operations and remain as a going concern. We expect to finance our future cash needs through a combination of equity offerings, collaborations, and other strategic alliances. Volatility in capital markets and general economic conditions in the U.S. may be a significant obstacle to raising the required funds and, as a result, we may be unable to secure the necessary funding on acceptable terms. This raises substantial doubt about our ability to continue as a going concern. For a further discussion of factors that raise substantial doubt about our ability to continue as a going concern, please see "– Liquidity and Capital Resources – Funding Requirements" and Part II. Item 1A, "Risk Factors" herein.

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**Critical Accounting Estimates and Significant Judgments**

Our management's discussion and analysis of our financial condition and results of operations is based on our financial statements, which have been prepared in accordance with generally accepted accounting principles in the United States, or U.S. GAAP. The preparation of our financial statements requires us to make estimates and assumptions that affect the reported amounts of assets and liabilities and the disclosure of contingent assets and liabilities at the date of our financial statements, and the reported revenue and expenses during the reported periods. We evaluate these estimates and judgments, including those described below, on an ongoing basis. We base our estimates on historical experience, known trends and events, contractual milestones and various other factors that we believe are reasonable under the circumstances, the results of which form the basis for making judgments about the carrying value of assets and liabilities that are not readily apparent from other sources. Actual results may differ from these estimates under different assumptions or conditions.

While our significant accounting policies are more fully described in Note 2 to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q, we believe that the estimates, assumptions and judgments involved in the accounting policies described in Management's Discussion and Analysis of Financial Condition and Results of Operations in Item 7 of our 2024 Annual Report have the greatest potential impact on our financial statements, so we consider those estimates, assumptions and judgments to be our critical accounting policies and estimates. There were no material changes to our critical accounting policies and estimates during the six months ended June 30, 2025.

**Recent Accounting Pronouncements and Adopted Standards**

A discussion of recent accounting pronouncements is included in Note 2 to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q.

**Significant Contracts and Agreements Related to Research and Development Activities**

***Einstein License Agreement***

On January 14, 2015, we entered into a license agreement, as amended and restated on July 31, 2017, and as further amended on October 30, 2018, January 13, 2024 and April 10, 2025, or the Einstein License, with Albert Einstein College of Medicine, or Einstein, for certain patent rights, or the Patents, relating to our core technology platform for the engineering of biologics to control T cell activity, precision, immune-modulatory drug product candidates, and two supporting technologies that enable the discovery of costimulatory signaling molecules (ligands) and T cell targeting peptides.

We hold an exclusive worldwide license, with the right to sublicense, import, make, have made, use, provide, offer to sell, and sell all products, processes and services that use the Patents, including certain technology received from Einstein related thereto, which we refer to as the Einstein Licensed Products. Under the Einstein License, we are required to:

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•Pay royalties and amounts based on a certain percentage of proceeds, as defined in the Einstein License, from sales of Einstein Licensed Products and sublicense agreements.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•Pay escalating annual maintenance fees, which are non-refundable, but are creditable against the amount due to Einstein for royalties.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•Make significant payments based upon the achievement of certain milestones, as defined in the Einstein License. As of June 30, 2025, two of these milestones had been achieved, as we had filed an IND application in 2019, and initiated the investigator sponsored Phase 1b neoadjuvant clinical trial for CUE-101 in 2021.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•Incur minimum product development costs per year and meet certain diligence obligations until the first commercial sale of the first Einstein Licensed Product.

On April 10, 2025, we entered into an amendment to the Einstein License. Pursuant to the amendment, Einstein consented to our entry into the BI Collaboration and License Agreement and granted us the right to sublicense to BI. In addition, we and Einstein agreed to amend specified upstream payment obligations that may be owed to Einstein by us, solely in connection with the sublicense to BI. In the second quarter of 2025, we paid Einstein $0.9 million in fees in relation to the amendment to this license with Einstein.

As of June 30, 2025, we were in compliance with our obligations under the Einstein License.

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We account for the costs incurred in connection with the Einstein License in accordance with Accounting Standards Codification 730, *Research and Development*.

We pay $0.1 million in annual maintenance license fees to Einstein, which are amortized equally throughout the year. We incurred less than $0.1 million in annual maintenance fees for each of the three and six months ended June 30, 2025 and 2024. Such costs are included in research and development costs in our condensed consolidated statements of operations and comprehensive loss.

***Collaboration Agreement with LG Chem***

On November 6, 2018, we entered into a Collaboration, License and Option Agreement, and as amended from time to time, or the LG Chem Collaboration Agreement, with LG Chem Ltd., or LG Chem, pertaining to the development of CUE-101 and CUE-102 Immuno-STATs focused in the field of oncology.

Pursuant to the LG Chem Collaboration Agreement, we granted LG Chem an exclusive license to develop, manufacture and commercialize CUE-101, as well as CUE-102 Immuno-STATs that target T cells against two additional cancer antigens in certain Asian countries, which we refer to collectively as the LG Chem Territory.

On March 11, 2025, we and LG Chem entered into the Ninth Amendment to the LG Chem Collaboration Agreement, or the Ninth Amendment. As of the date of the Ninth Amendment, we regained our rights to the LG Chem Territory for the CUE-101 program, which had been licensed to LG Chem, and LG Chem terminated all of its rights to the same program. Pursuant to the Ninth Amendment, we agreed to make future payments to LG Chem, if and when one or more potential scenarios related to the CUE-101 program occur, up to a predetermined aggregate amount. LG Chem continues to maintain its interest and rights in the CUE-102 program, targeting WT1 expressing cancers, pursuant to the LG Chem Collaboration Agreement.

We did not recognize any revenue related to the LG Chem Collaboration Agreement for the three and six months ended June 30, 2025. For each of the three and six months ended June 30, 2024 we recognized revenue of less than $0.1 million related to the LG Chem Collaboration Agreement. As of June 30, 2025, we had recorded $20.0 million in collaboration revenue related to this agreement since the agreement was entered into. The majority of the research phase of the LG Chem Collaboration Agreement was completed by March 31, 2022.

***Collaboration and Option Agreement with Ono*** 

In February 2023, we entered into a strategic collaboration agreement, or the Ono Collaboration and Option Agreement, with Ono Pharmaceutical Co., Ltd., or Ono, to further develop CUE-401. In March 2025, we and Ono agreed to terminate the Ono Collaboration and Option Agreement, effective as of March 6, 2025. At such time, the Ono Collaboration and Option Agreement had no further force or effect with the exception of certain customary provisions which are intended to survive termination and expiration of the Ono Collaboration and Option Agreement. We retained all rights to CUE-401.

Under the terms of the Ono Collaboration and Option Agreement, Ono paid us an upfront payment and agreed to fully fund all research and development activities related to CUE-401 through a specified option period of 24 months, or the Ono Research Term. Per the agreement, as consideration for the research and development activities performed by us, Ono (i) made a one-time, non-refundable, non-creditable upfront payment of $3.0 million to us in March 2023, and (ii) agreed to reimburse us for all costs incurred in conducting research, including (a) pass through costs from third party contractors and (b) full time employee salaries capped at $2.1 million in the first 18 months of the Ono Research Term. Subsequently, we and Ono agreed to increase this cap for full-time employee salaries to $3.1 million.

As of the date of this report, both we and Ono have satisfied all of our respective performance obligations and made all outstanding payments required under the agreement. For each of the three and six months ended June 30, 2025, we recognized revenue of $0.4 million related to the Ono Collaboration and Option Agreement. For each of the three and six months ended June 30, 2024, we recognized revenue of $2.6 million and $4.3 million, respectively, related to the Ono Collaboration and Option Agreement. We did not record short or long-term research and development liabilities on our condensed consolidated balance sheet as of June 30, 2025, as the performance obligation has been met and completed. For the year ended December 31, 2024, we recorded short-term research and development liabilities on our consolidated balance sheets of $0.1 million.

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***BI Collaboration and License Agreement***

On April 10, 2025, we entered into a Collaboration and License Agreement with BI, or the BI Collaboration and License Agreement, to research, develop and commercialize differentiated B cell depletion molecules, including CUE-501.

Under the terms of the BI Collaboration and License Agreement, we and BI will conduct collaborative research focused on CUE-501 during a four-year period or, if earlier, the completion of activities under the research plans, or the BI Research Term. In addition to, or instead of, CUE-501, BI may elect, at its sole discretion, to include additional or alternative compounds targeted at B cell depletion. BI will have an exclusive, royalty-bearing, worldwide, sublicensable license, under our applicable patents and know-how, to develop, manufacture and commercialize such compounds and their derivatives, or BI Licensed Products, for all uses, and BI shall be responsible for all further research, preclinical and clinical development, manufacturing, regulatory approvals, and commercialization of BI Licensed Products at its expense. During the BI Research Term, we are prohibited from developing or commercializing any molecule for applications in B cell depletion.

Pursuant to the terms of the BI Collaboration and License Agreement, we received an upfront payment of $10.1 million in cash in the second quarter of 2025, which is net of $1.9 million of German withholding taxes that we are seeking to get refunded. We will also be eligible to receive up to an aggregate of approximately $345.0 million in success-based research, development and commercial milestone payments, beginning with two preclinical development milestones, as well as royalty payments on net sales. The royalty payments will be subject to reduction due to patent expiration, payments made under certain licenses for third-party intellectual property and generic competition. BI has agreed to reimburse us for agreed upon costs incurred in conducting research during the BI Research term, including certain pass through costs from third party contractors and full time employee salaries.

The BI Collaboration and License Agreement will continue, on a product-by-product and country-by-country basis, until the expiration of the applicable royalty term, unless earlier terminated. BI has the right to terminate the BI Collaboration and License Agreement for any reason after a specified notice period. Each party has the right to terminate the BI Collaboration and License Agreement on account of the other party's bankruptcy or material, uncured breach. In connection with our entry into the BI Collaboration and License Agreement, we entered into an amendment to our Einstein License whereby Einstein consented to our entry into the BI Collaboration and License Agreement and granted us the right to sublicense to BI. In addition, we and Einstein agreed to amend specified upstream payment obligations that may be owed to Einstein by us, solely in connection with the sublicense to BI.

For the three and six months ended June 30, 2025, we recognized revenue of $2.9 million related to the BI Collaboration and License Agreement. We recorded short or long-term research and development liabilities of $9.6 million on our condensed consolidated balance sheet dated June 30, 2025.

**Components of Results of Operations**

***Collaboration Revenue***

We have not yet generated commercial revenue from product sales. To date, we have generated revenue from collaboration agreements with BI, LG Chem, Ono (which terminated in March 2025), and Merck Sharp & Dohme Corp. (which terminated in December 2022). Our collaboration revenue may vary from period to period depending on the progress of our work in connection with our collaboration agreements.

***Research and Development Expenses***

Research and development expenses consist primarily of compensation costs, fees paid to consultants, outside service providers and organizations (including research institutes at universities), facility costs, and development and clinical trial costs with respect to our drug product candidates. We utilize our employee and infrastructure resources across multiple research and development programs, and do not track these costs by project. We believe the attempted allocation of these costs by project would be arbitrary and not meaningful.

Research and development expenses incurred under contracts are expensed ratably over the life of the underlying contracts, unless the achievement of milestones, the completion of contracted work, or other information indicates that a different pattern of performance is more appropriate. Other research and development expenses are charged to operations as incurred.

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Nonrefundable advance payments are recognized as an expense as the related services are performed. We evaluate whether we expect the services to be rendered at each quarter end and year end reporting date. If we do not expect the services to be rendered, the advance payment is recorded as expense. Nonrefundable advance payments for research and development services are included in prepaid and other current assets on the balance sheet. To the extent that a nonrefundable advance payment is for contracted services to be performed within 12 months from the reporting date, such advance is included in current assets; otherwise, such advance is included in non-current assets.

We evaluate the status of our research and development agreements and contracts, and the carrying amount of the related assets and liabilities, at each quarter end and year end reporting date, and adjust the carrying amounts and their classification on the balance sheet as appropriate.

The following table summarizes our research and development expenses by category for the six months ended June 30, 2025 and 2024 (in millions):

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| | | |
|:---|:---|:---|
|  | **June 30,** | **June 30,** |
|  | **2025** | **2024** |
| Employee compensation | $5.5 | $7.0 |
| Clinical trial costs | 2.7 | 4.5 |
| Facilities and overhead | 2.6 | 2.6 |
| Contract manufacturing costs | 3.7 | 3.5 |
| Lab costs | 0.5 | 0.5 |
| Professional fees | 1.5 | 1.6 |
| Total | $16.5 | $19.7 |

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The following table summarizes our research and development expenses by category for the three months ended June 30, 2025 and 2024 (in millions):

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| | | |
|:---|:---|:---|
|  | **June 30,** | **June 30,** |
|  | **2025** | **2024** |
| Employee compensation | $2.4 | $3.1 |
| Clinical trial costs | 0.9 | 1.9 |
| Facilities and overhead | 1.3 | 1.3 |
| Contract manufacturing costs | 1.8 | 1.9 |
| Lab costs | 0.3 | 0.3 |
| Professional fees | 1.2 | 1.0 |
| Total | $7.9 | $9.5 |

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***General and Administrative Expenses***

General and administrative expenses consist of salaries and related expenses for executive, legal, finance, human resources, information technology and administrative personnel, as well as professional fees, insurance costs, and other general corporate expenses. We expect general and administrative expenses to remain consistent in future periods as we continue to incur expenses related to our operation as a public company, which requires our ongoing compliance with certain laws and regulations.

***Interest Income***

We earn interest income from cash invested in money market funds.

***Interest Expense***

We incur interest expense from borrowings under our Loan and Security Agreement, as amended, or the Loan Agreement, with Silicon Valley Bank, a division of First Citizens Bank & Trust Company, or SVB.

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**Results of Operations**

***Three and Six Months Ended June 30, 2025 and 2024***

Our condensed consolidated statements of operations and comprehensive loss for the three and six months ended June 30, 2025 and 2024, as discussed herein, are presented below in thousands.

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| | | | | |
|:---|:---|:---|:---|:---|
|  | **Three Months Ended<br>June 30,** | **Three Months Ended<br>June 30,** | **Six Months Ended<br>June 30,** | **Six Months Ended<br>June 30,** |
|  | **2025** | **2024** | **2025** | **2024** |
| **Collaboration revenue** | $2954 | $2658 | $3374 | $4375 |
| **Operating expenses:** |  |  |  |  |
| &nbsp;&nbsp;General and administrative | 3679 | 3511 | 7852 | 7697 |
| &nbsp;&nbsp;Research and development | 7910 | 9530 | 16457 | 19729 |
| &nbsp;&nbsp;&nbsp;&nbsp;Total operating expenses | 11589 | 13041 | 24309 | 27426 |
| **Loss from operations** | (8635) | (10383) | (20935) | (23051) |
| **Other income (expense):** |  |  |  |  |
| &nbsp;&nbsp;Interest income | 198 | 427 | 368 | 989 |
| &nbsp;&nbsp;Interest expense | (45) | (215) | (172) | (456) |
| &nbsp;&nbsp;&nbsp;&nbsp;Total other income, net | 153 | 212 | 196 | 533 |
| **Net loss** | $(8482) | $(10171) | $(20739) | $(22518) |

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***Collaboration Revenue***

Collaboration revenue increased by $0.3 million for the three months ended June 30, 2025 compared to the three months ended June 30, 2024. The increase was due to more revenue earned during the three months ended June 30, 2025 from our BI Collaboration and License Agreement compared to revenue earned during the three months ended June 30, 2024 from our Ono Collaboration and Option Agreement due to the timing of activities pursuant to the respective agreements.

Collaboration revenue decreased by $1.0 million for the six months ended June 30, 2025 compared to the six months ended June 30, 2024. The decrease was due to more revenue earned during the six months ended June 30, 2024 from our Ono Collaboration and Option Agreement compared to revenue earned during the six months ended June 30, 2025 from our BI Collaboration and License Agreement due to the timing of activities pursuant to the respective agreements.

***General and Administrative Expenses***

General and administrative expenses increased by $0.2 million for the three months ended June 30, 2025 compared to the three months ended June 30, 2024. The increase was primarily due to an increase in professional fees.

General and administrative expenses increased by $0.2 million for the six months ended June 30, 2025 compared to the six months ended June 30, 2024. The increase was primarily due to an increase in professional fees, partially offset by a decrease in employee compensation, which includes stock-based compensation.

***Research and Development Expenses***

Research and development expenses decreased by $1.6 million for the three months ended June 30, 2025 compared to the three months ended June 30, 2024. The decrease was primarily due to decreases in clinical trial costs for our CUE-100 series Phase 1 trials, as activities shifted to patient survival monitoring, as well as decreases in employee compensation, which includes stock-based compensation.

Research and development expenses decreased by $3.3 million for the six months ended June 30, 2025 compared to the six months ended June 30, 2024. The decrease was primarily due to decreases in clinical trial costs for our CUE-100 series Phase 1 trials, as activities shifted to patient survival monitoring, as well as decreases in employee compensation, which includes stock-based compensation.

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***Interest Income***

Interest income decreased by $0.2 million for the three months ended June 30, 2025 compared to the three months ended June 30, 2024. The decrease was due to lower interest earned on cash and cash equivalents.

Interest income decreased by $0.6 million for the six months ended June 30, 2025 compared to the six months ended June 30, 2024. The decrease was due to lower interest earned on cash and cash equivalents.

***Interest Expense***

Interest expense decreased by $0.2 million for the three months ended June 30, 2025 compared to the three months ended June 30, 2024. This was due to a decrease in interest owed from borrowings under our Loan Agreement with SVB.

Interest expense decreased by $0.3 million for the six months ended June 30, 2025 compared to the six months ended June 30, 2024. This was due to a decrease in interest owed from borrowings under our Loan Agreement with SVB.

**Liquidity and Capital Resources**

We have financed our working capital requirements primarily through private and public offerings of equity securities, cash received from BI, LG Chem, Ono, and Merck Sharp & Dohme Corp. under the respective collaboration agreements we have with them, and borrowings under the Loan Agreement.

The amounts that we actually spend for any specific purpose may vary significantly and will depend on a number of factors, including, but not limited to, our research and development activities and programs, clinical testing, regulatory approval, market conditions, and changes in or revisions to our business strategy and technology development plans.

On May 9, 2023, we filed a registration statement on Form S-3, which was declared effective on May 26, 2023 (File No. 333-271786), to register for sale from time to time up to $300 million of our common stock, preferred stock, debt securities, warrants, subscription rights and/or units in one or more offerings.

In October 2021, we entered into an open market sale agreement, or the ATM Sales Agreement, with Jefferies LLC, or Jefferies, as agent, to sell shares of our common stock for aggregate gross proceeds of up to $80 million, from time to time, through an at-the-market equity offering program. The ATM Sales Agreement will terminate upon the earliest of (a) the sale of $80 million of shares of our common stock pursuant to the ATM Sales Agreement or (b) the termination of the ATM Sales Agreement by us or Jefferies. During the three and six months ended June 30, 2025, we sold 1,097,003 shares of common stock under the ATM Sales Agreement for proceeds of $0.8 million, net of commissions paid, but excluding transaction expenses. During the three months ended June 30, 2024, there were no sales under the ATM Sales Agreement. During the six months ended June 30, 2024, we sold 1,428,200 shares of common stock under the ATM Sales Agreement for proceeds of $3.4 million, net of commissions paid, but excluding transaction expenses. As of June 30, 2025, we had sold an aggregate of 10,169,234 shares of common stock under the ATM Sales Agreement for proceeds of $41.2 million, net of commissions paid, but excluding transaction expenses, since its inception.

On February 15, 2022, we entered into the Loan Agreement, pursuant to which we have borrowed $10.0 million. The Loan Agreement was amended in April 2023 and October 2024. The term loans under the Loan Agreement, or the Term Loans, bear interest at a floating rate per annum equal to the greater of (A) the prime rate (as published in the money rates section of The Wall Street Journal) plus 2.25% and (B) 5.50%. On the first calendar day of each month, we will be required to make monthly interest payments and commencing on June 30, 2023, we began repayment of the Term Loans in (i) 30 consecutive installments of principal plus monthly payments of accrued interest if the additional term loans are not advanced and (ii) 24 months if the additional term loans are advanced. All outstanding principal and accrued and unpaid interest under the Term Loans and all other outstanding obligations with respect to the Term Loans are due and payable in full on December 1, 2025.

The Loan Agreement permits voluntary prepayment of all, but not less than all, of the Term Loans, subject to a prepayment premium except if the facility is refinanced with another First Citizens Bank facility. Such prepayment premium would be 1.00% of the principal amount of the Term Loans. Upon prepayment or repayment in full of the Term Loans, we will be required to pay a one-time final payment fee equal to 5.00% of the original principal amount of any funded Term Loans being repaid. The Loan Agreement, as amended, also requires us to have at all times on deposit in our accounts maintained with SVB, unrestricted and unencumbered cash in an amount equal to the lesser of (i) 100% of the dollar value of our consolidated cash, in the aggregate, at all financial institutions, and (ii) $20,000,000.

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On March 10, 2023, SVB was closed and the Federal Deposit Insurance Company, or FDIC, was appointed receiver for the bank. The FDIC created a successor bridge bank, and all deposits of SVB were transferred to the bridge bank under a systemic risk exception approved by the U.S. Department of the Treasury, the Federal Reserve and the FDIC. On March 27, 2023, First Citizens Bank assumed all of SVB's deposits and certain other liabilities and acquired substantially all of SVB's loans and certain other assets from the FDIC. First Citizens Bank continues to hold our Term Loans under the same existing terms and covenants which were in place with SVB.

On September 26, 2024, we entered into an underwriting agreement, or the 2024 Underwriting Agreement, with Oppenheimer & Co. Inc., as representative of the several underwriters named therein, or, collectively, the 2024 Underwriters, relating to an underwritten public offering of (i) 11,564,401 shares, or the 2024 Shares, of our common stock, $0.001 par value per share, and accompanying common stock warrants, or the2024 Common Stock Warrants, to purchase 2,891,100 shares of our common stock, and (ii) to certain investors in lieu of common stock, pre-funded warrants, or the 2024 Pre-Funded Warrants, to purchase 12,435,599 shares of our common stock and accompanying 2024 Common Stock Warrants to purchase 3,108,900 shares of common stock. All of the 2024 Shares, the 2024 Pre-Funded Warrants and the 2024 Common Stock Warrants were sold by us. Each 2024 Share was offered and sold together with an accompanying 2024 Common Stock Warrant at a combined offering price of $0.50, and each 2024 Pre-Funded Warrant was offered and sold together with an accompanying 2024 Common Stock Warrant at a combined offering price of $0.499, which is equal to the combined offering price per share of common stock and accompanying 2024 Common Stock Warrant less the $0.001 exercise price of each 2024 Pre-Funded Warrant. The 2024 Underwriters purchased (i) each 2024 Share and accompanying 2024 Common Stock Warrant from us pursuant to the 2024 Underwriting Agreement at a combined price of $0.47 and (ii) each 2024 Pre-Funded Warrant and accompanying 2024 Common Stock Warrant from us pursuant to the 2024 Underwriting Agreement at a combined price of $0.46906. We recorded net proceeds from the offering of $10.8 million, after deducting underwriting discounts and commissions and offering expenses of $1.1 million, excluding any proceeds that may be received from exercise of the 2024 Common Stock Warrants and the 2024 Pre-Funded Warrants.

On April 14, 2025, we entered into an underwriting agreement, or the 2025 Underwriting Agreement, with Oppenheimer & Co. Inc., as representative of the several underwriters named therein, or, collectively, the 2025 Underwriters, relating to an underwritten public offering of (i) 13,530,780 shares, or the 2025 Shares, of our common stock, $0.001 par value per share, and accompanying common stock warrants, or the 2025 Common Stock Warrants to purchase 3,382,695 shares of our common stock, and (ii) to certain investors in lieu of common stock, pre-funded warrants, or the 2025 Pre-Funded Warrants, to purchase 11,469,216 shares of our common stock and accompanying 2025 Common Stock Warrants to purchase 2,867,304 shares of common stock. All of the 2025 Shares, the 2025 Pre-Funded Warrants and the 2025 Common Stock Warrants were sold by us. Each 2025 Share was offered and sold together with an accompanying 2025 Common Stock Warrant at a combined offering price of $0.79, and each 2025 Pre-Funded Warrant was offered and sold together with an accompanying 2025 Common Stock Warrant at a combined offering price of $0.789, which is equal to the combined offering price per share of common stock and accompanying 2025 Common Stock Warrant less the $0.001 exercise price of each 2025 Pre-Funded Warrant. The 2025 Underwriters purchased (i) each 2025 Share and accompanying 2025 Common Stock Warrant from us pursuant to the 2025 Underwriting Agreement at a combined price of $0.7426 and (ii) each 2025 Pre-Funded Warrant and accompanying 2025 Common Stock Warrant from us pursuant to the 2025 Underwriting Agreement at a combined price of $0.74166. We received net proceeds from the offering of approximately $18.0 million, after deducting underwriting discounts and commissions and offering expenses of $0.5 million excluding any proceeds that may be received from exercise of the 2025 Common Stock Warrants and the 2025 Pre-Funded Warrants.

***Cash Flows***

Based on our current plans and forecasted expenses, we believe our existing cash and cash equivalents as of June 30, 2025 will enable us to fund our operations into the second quarter of 2026. However, we will need to raise substantial additional capital to fund our future operations and remain as a going concern. We expect to finance our future cash needs through a combination of equity offerings, collaborations, and other strategic alliances. Volatility in capital markets and general economic conditions in the United States may be a significant obstacle to raising the required funds and, as a result, we may be unable to secure the necessary funding on acceptable terms. This raises substantial doubt about our ability to continue as a going concern.

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The following table summarizes our changes in cash, cash equivalents, and restricted cash for the six months ended June 30, 2025 and 2024 in thousands:

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| | | |
|:---|:---|:---|
|  | **Six Months Ended** | **Six Months Ended** |
|  | **June 30,** | **June 30,** |
|  | **2025** | **2024** |
| &nbsp;&nbsp;Net cash provided by (used in): |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Operating activities | $(11587) | $(19774) |
| &nbsp;&nbsp;&nbsp;&nbsp;Investing activities | (177) | (65) |
| &nbsp;&nbsp;&nbsp;&nbsp;Financing activities | 16798 | 1354 |
| &nbsp;&nbsp;Net change in cash, cash equivalents, and restricted cash | $5034 | $(18485) |

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***Operating Activities*** 

Net cash used in operating activities totaled $11.6 million for the six months ended June 30, 2025 compared to $19.8 million for the six months ended June 30, 2024. The decrease of $8.2 million was primarily due to decreases in cash outflows from changes in stock-based compensation and changes in right-of-use assets, partially offset by increases from changes in research and development contract liabilities.

***Investing Activities*** 

Net cash used in investing activities totaled $0.2 million for the six months ended June 30, 2025 compared to $0.1 million during the six months ended June 30, 2024. The increase of $0.1 million in cash used was due to an increase in purchases of property and equipment during the six months ended June 30, 2025.

***Financing Activities*** 

Net cash provided by financing activities totaled $16.8 million for the six months ended June 30, 2025 compared to $1.4 million for the six months ended June 30, 2024. The increase of $15.4 million was due to proceeds received from our underwriting agreement entered into in April 2025, as well as sales under our ATM Sales Agreement during the six months ended June 30, 2025.

***Funding Requirements***

We expect our expenses to increase in connection with our ongoing activities, particularly as we continue the research and development of our Immuno-STAT platform and continue ongoing and initiate new clinical trials of and seek marketing approval for our drug product candidates. In addition, we expect to incur additional costs associated with operating as a public company. Our expenses will also increase if, and as, we:

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•continue the preclinical development of CUE-401 and the CUE-500 series (excluding CUE-501, which has been licensed to BI);

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•continue to assess maturing clinical data of our CUE-100 series, including CUE-101 and CUE-102, which we have deprioritized;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•leverage our programs, including our autoimmune programs, to advance our other drug product candidates into preclinical and clinical development;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•seek regulatory approvals for any drug product candidates for which we successfully complete clinical trials;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•seek to discover and develop additional drug product candidates;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•establish a sales, marketing, medical affairs and distribution infrastructure to commercialize any drug product candidates for which we may obtain marketing approval and intend to commercialize on our own or jointly;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•expand our manufacturing, quality, operational, financial and management systems, including personnel to support these functions;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•maintain, expand and protect our intellectual property portfolio;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•acquire or in-license other drug product candidates and technologies; and

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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•incur additional legal, accounting and other expenses in operating as a public company.

Under Accounting Standards Update, or ASU, 2014-15, Presentation of Financial Statements—Going Concern (Subtopic 205-40), or, ASC 205-40, we have the responsibility to evaluate whether conditions or events raise substantial doubt about our ability to meet our future financial obligations as they become due within one year after the date the financial statements are issued. Under ASC 205-40, this evaluation initially cannot take into consideration the potential mitigating effects of plans that have not been fully implemented as of the date the financial statements are issued. Since we currently believe that our existing cash and cash equivalents, as of June 30, 2025, and our current operating plans will enable us to fund our operations into the second quarter of 2026, we have determined that this cash runway of less than 12 months from the date of issuance of our financial statements included in this Quarterly Report on Form 10-Q, along with our accumulated deficit, history of losses, and future expected losses meet the ASC 205-40 standard for raising substantial doubt about our ability to continue as a going concern within one year of the issuance date of our financial statements included in this Quarterly Report on Form 10-Q. While we have plans in place to mitigate this risk, which primarily consist of raising additional capital through a combination of equity offerings, collaborations, and other strategic alliances, and, depending on the availability and level of additional financings, and cash expenditure reduction, there is no guarantee that we will be successful in these mitigation efforts.

We will need to raise additional capital or incur additional indebtedness to continue to fund our operations in the near term. Our ability to raise additional funds will depend on financial, economic and market conditions, many of which are outside of our control, and we may be unable to raise financing when needed, or on terms favorable to us. If we are unable to raise additional funds when needed, we may be required to delay, reduce or eliminate our product development or future commercialization efforts, or grant rights to develop and market drug product candidates that we would otherwise prefer to develop and market ourselves, which could adversely affect our business prospects, and we may be unable to continue our operations. Because of numerous risks and uncertainties associated with the research, development and commercialization of our drug product candidates, we are unable to estimate the exact amount of our working capital requirements. Factors that may affect our planned future capital requirements and accelerate our need for additional working capital include the following:

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the progress, timing, scope and costs of our clinical trials, including the ability to timely enroll patients in our ongoing, planned and any future clinical trials;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•our ability to secure third party support through partnerships and collaborations to further develop the CUE-100 series programs, including CUE-101 and CUE-102, as we have done for CUE-501;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the outcome, timing and cost of regulatory approvals by the FDA and other comparable regulatory authorities, including the potential that the FDA or other comparable regulatory authorities may require that we perform more studies than those that we currently expect;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the number and characteristics of drug product candidates that we may in-license and develop;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•our ability to successfully commercialize our drug product candidates, if approved;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the amount of sales and other revenues from drug product candidates that we may commercialize, if any, including the selling prices for such potential products and the availability of adequate third-party reimbursement;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•selling and marketing costs associated with our potential products, including the cost and timing of expanding our marketing and sales capabilities;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the terms and timing of any potential future collaborations, licensing or other arrangements that we may establish;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•cash requirements of any future acquisitions and/or the development of other drug product candidates;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the costs of operating as a public company;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the cost and timing of completion of commercial-scale, outsourced manufacturing activities;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the time and cost necessary to respond to technological and market developments;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the impact of government laws and regulations, general economic and market conditions, inflation, and the imposition of new or revised global trade tariffs;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•any disputes which may occur between us and our employees, collaborators, including Einstein, LG Chem and BI, or other prospective business partners; and

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the costs of filing, prosecuting, defending and enforcing any patent claims and other intellectual property rights.

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A change in the outcome of any of these or other variables with respect to the development of any of our drug product candidates could significantly change the costs and timing associated with the development of that drug product candidate. Further, our operating plans may change in the future, and we may need additional funds to meet operational needs and capital requirements associated with such operating plans.

Until such time, if ever, as we can generate substantial product revenue, we expect to finance our cash needs through a combination of public or private equity offerings, debt financings, collaborations, strategic partnerships or marketing, distribution or licensing arrangements with third parties and grants from organizations and foundations. If we raise additional funds by selling shares of our common stock or other equity-linked securities, the ownership interest of our current stockholders will be diluted. New investors may demand rights, preferences or privileges senior to those of existing holders of our common stock. If we issue debt securities, we may be required to grant security interests in our assets, could have substantial debt service obligations, and lenders may have a senior position (compared to stockholders) in any potential future bankruptcy or liquidation. We may seek to access the public or private capital markets whenever conditions are favorable, even if we do not have an immediate need for additional capital at that time. If we raise additional funds through collaborations, strategic alliances or marketing, distribution or licensing arrangements with third parties, we may have to relinquish valuable rights to our technologies, future revenue streams or drug product candidates or to grant licenses on terms that may not be acceptable to us. Additionally, corporate collaboration and licensing arrangements may require us to incur non-recurring and other charges, give up certain rights relating to our intellectual property and research and development activities, increase our near and long-term expenditures, issue securities that dilute our existing stockholders, issue debt which may require liens on our assets and which will increase our monthly expense obligations, or disrupt our management and business.

If we are unable to raise additional capital when needed, we may be required to curtail the development of our technology or materially curtail or reduce our operations. We could be forced to sell or dispose of our rights or assets. Any inability to raise adequate funds on commercially reasonable terms could have a material adverse effect on our business, results of operation and financial condition, including the possibility that a lack of funds could cause our business to fail, dissolve and liquidate with little or no return to investors.

***Principal Commitments*** 

There have been no material changes to our contractual obligations and commitments as described in Management's Discussion and Analysis of Financial Condition and Results of Operations in Item 7 of our 2024 Annual Report. Additional information regarding the BI Collaboration and License Agreement, the amendment to our Einstein License, and the second amendment to our License Agreement with MIL 40G, LLC, may be found in Notes 10 and 12 to our condensed consolidated financial statements in this Quarterly Report on Form 10-Q.

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**ITEM 3. QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK**

As a smaller reporting company, we are not required to provide the information required by this Item 3.

**ITEM 4. CONTROLS AND PROCEDURES**

**Disclosure Controls and Procedures**

We are responsible for maintaining disclosure controls and procedures, as defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, or the Exchange Act. Disclosure controls and procedures are controls and other procedures designed to ensure that the information required to be disclosed by us in the reports that we file or submit under the Exchange Act is recorded, processed, summarized, and reported within the time periods specified in the SEC's rules and forms. Disclosure controls and procedures include, without limitation, controls and procedures designed to ensure that information required to be disclosed by us in the reports that we file or submit under the Exchange Act is accumulated and communicated to our management, including our principal executive officer and our principal financial officer, as appropriate to allow timely decisions regarding required disclosure.

Based on our management's evaluation (with the participation of our principal executive officer and our principal financial officer) of our disclosure controls and procedures as required by Rule 13a-15 under the Exchange Act, our principal executive officer and our principal financial officer have concluded that our disclosure controls and procedures were effective as of June 30, 2025, the end of the period covered by this report.

**Inherent Limitations on Effectiveness of Controls**

Our management, including our principal executive officer and our principal financial officer, do not expect that our disclosure controls or our internal control over financial reporting will prevent or detect all errors and all fraud. A control system, no matter how well designed and operated, can provide only reasonable, not absolute, assurance that the control system's objectives will be met. The design of a control system must reflect the fact that there are resource constraints, and the benefits of controls must be considered relative to their costs. Further, because of the inherent limitations in all control systems, no evaluation of controls can provide absolute assurance that misstatements due to error or fraud will not occur or that all control issues and instances of fraud, if any, have been detected. These inherent limitations include the realities that judgments in decision-making can be faulty and that breakdowns can occur because of a simple error or mistake. Controls can also be circumvented by the individual acts of some persons, by collusion of two or more people, or by management override of the controls. The design of any system of controls is based in part on certain assumptions about the likelihood of future events, and there can be no assurance that any design will succeed in achieving its stated goals under all potential future conditions. Projections of any evaluation of control effectiveness to future periods are subject to risks. Over time, controls may become inadequate because of changes in conditions or deterioration in the degree of compliance with policies or procedures.

**Changes in Internal Control over Financial Reporting**

There were no changes in our internal control over financial reporting during the three months ended June 30, 2025 that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.

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**PART II. OTHER INFORMATION**

**ITEM 1. LEGAL PROCEEDINGS**

We are not currently a party to any material legal proceedings.

**ITEM 1A. RISK FACTORS**

We operate in a rapidly changing environment that involves a number of risks that could materially affect our business, financial condition or future results, some of which are beyond our control. The occurrence of any of these risks could harm our business, financial condition, results of operations and/or growth prospects or cause our actual results to differ materially from those contained in forward-looking statements we have made in this report and those we may make from time to time. In evaluating us and our business, you should carefully consider the following risks, the information included in this Quarterly Report on Form 10-Q and in other documents we file with the SEC and the risk factors previously disclosed in Part I. Item 1A, "Risk Factors" of our 2024 Annual Report.

***Our recurring losses from operations raise substantial doubt regarding our ability to continue as a going concern.*** 

We have incurred significant losses since our inception and have never generated revenue or profit from product sales, and it is possible we will never generate revenue or profit from product sales. As of June 30, 2025, we had cash and cash equivalents of $27.5 million. Based on our current operating plans, we believe we will have sufficient funds to meet our obligations into the second quarter of 2026. However, we will need to raise substantial additional capital to fund our future operations. There can be no assurance that we will be able to obtain additional funding, including through a combination of equity offerings, collaborations, and other strategic alliances, or other sources on acceptable terms, if at all. To the extent that we raise additional capital through future equity offerings, the ownership interest of common stockholders will be diluted, which dilution may be significant. We cannot guarantee that we will be able to obtain any or sufficient additional funding or that such funding, if available, will be obtainable on terms satisfactory to us. In the event that we are unable to obtain any or sufficient additional funding, there can be no assurance that we will be able to continue as a going concern, and we will be forced to delay, reduce or discontinue our product development programs or consider other various strategic alternatives.

Moreover, these factors raise substantial doubt about our ability to continue as a going concern. Substantial doubt about our ability to continue as a going concern may materially and adversely affect the price per share of our common stock, and it may be more difficult for us to obtain financing. If existing or potential collaborators decline to do business with us or potential investors decline to participate in any future financings due to such concerns, our ability to increase our cash position may be limited. The perception that we may not be able to continue as a going concern may cause others to choose not to deal with us due to concerns about our ability to meet our contractual obligations.

***Changes in and uncertainty surrounding U.S. trade policy could have a material adverse impact on our business, financial condition and results of operations.***

This past spring, the Trump Administration initiated a series of tariff-related actions against U.S. trading partners. On April 2, 2025, the President issued an Executive Order announcing a "baseline" reciprocal tariff of 10% on all U.S. trading partners effective April 5, 2025, and higher individualized reciprocal tariffs on 57 countries (with certain product exemptions for pharmaceutical-related products, among others). Previously, the administration had imposed a 25% tariff on Canada and Mexico for goods not covered by the United States-Mexico-Canada Agreement, or USMCA, and tariffs equaling 20% on China. In response, several countries threatened retaliatory measures, including Canada and China, which then imposed retaliatory tariffs. Prior to when the country-specific reciprocal tariffs were scheduled to take effect, the administration delayed the effective date of such tariffs for all countries except China. Later, the U.S. and China reached a framework agreement that resulted in the suspension of the higher reciprocal tariffs on China until August 12, 2025. Several countries including, among others, the European Union, Japan and the United Kingdom, have reached deals with the U.S. that include reduced tariff rates to varying levels and other measures. The administration has not definitively indicated the effective date for these deals. As of July 31, 2025, the 10% baseline reciprocal tariff announced in April on all countries remains in effect, in addition to the other tariffs on China (which were a minimum of an additional 20% as of July 15, 2025) and Canada and Mexico (which were 25% as of July 15, 2025 for goods that are not covered by the USMCA).

Separately, on April 16, 2025, the U.S. Department of Commerce announced an investigation under Section 232 of the Trade Expansion Act of 1962 into imports of pharmaceuticals and pharmaceutical ingredients, including finished drug products, medical countermeasures, critical inputs such as active pharmaceutical ingredients, and key starting materials, and derivative products of those items. The investigation will examine the impact of these imports on U.S. national security

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culminating in a decision by the President whether to take action to remedy any identified threats, including by imposing additional tariffs. The statute provides that the Commerce Department report must be completed within 270 days of initiation of the investigation and that the President must decide whether to act within 90 days of receiving the report.

As a result of changes in tariffs that have been announced and/or implemented, and the underlying uncertainty currently surrounding international trade, we could experience a negative impact to our costs of materials and production processes, and supply chain disruptions and delays as a result of any new tariff policies or trade restrictions. If we are unable to obtain necessary raw materials or product components in sufficient quantity and in a timely manner due to disruptions in the global supply chain caused by macroeconomic events and conditions, the development, testing and clinical trials of our product candidates may be delayed or infeasible, and regulatory approval or commercial launch of any resulting product may be delayed or not obtained, which could significantly harm our business. We cannot yet predict the effect of the recently imposed U.S. tariffs on imports, or the extent to which other countries will impose quotas, duties, tariffs, taxes or other similar restrictions upon imports or exports in the future, nor can we predict future trade policy or the terms of any renegotiated trade agreements and their impact on our business.

***Changes in tax laws or in their implementation or interpretation could adversely affect our business and financial condition.***

Income, sales, use or other tax laws, statutes, rules, or regulations could be enacted or amended at any time, which could affect our business or financial condition, including causing potentially adverse impacts to our effective tax rate, tax liabilities, and cash tax obligations. For example, the Inflation Reduction Act, or IRA, was signed into law in August 2022, and the One Big Beautiful Bill Act, or OBBBA, was signed into law in July 2025. The IRA introduced new tax provisions, including a one percent excise tax imposed on certain stock repurchases by publicly traded companies. The one percent excise tax generally applies to any acquisition of stock by the publicly traded company (or certain of its affiliates) from a stockholder of the company in exchange for money or other property (other than stock of the company itself), subject to a de minimis exception. Thus, the excise tax could apply to certain transactions that are not traditional stock repurchases. The OBBBA contains numerous tax provisions that we are currently in the process of evaluating, and which may significantly affect our business or financial condition. The recent changes under the OBBBA include tax rate extensions and changes to the business interest deduction limitation, the expensing of domestic research and development expenditures (in contrast to the continued capitalization and amortization of foreign research and development expenditures), the bonus depreciation deduction rules, and the international tax framework. Regulatory guidance under the IRA, the OBBBA, and other tax-related legislation is and continues to be forthcoming, and such guidance could ultimately increase or lessen the impact of these laws on our business and financial condition. In addition, it is uncertain if and to what extent various states will conform to changes to federal tax legislation.

***If we fail to comply with the continued listing requirements of Nasdaq, our common stock may be delisted and the price of our common stock and our ability to access the capital markets could be negatively impacted.***

We are required to comply with the continued listing requirements of the Nasdaq Stock Market LLC, or Nasdaq, including, among other things, maintaining a minimum closing bid price of at least $1.00 per share, or the Minimum Bid Requirement, or shares of our common stock may be subject to delisting, which would have a material adverse effect on our business.

On May 12, 2025, we received a deficiency letter, or the Notice, from the Listing Qualifications Department, or the Staff, of Nasdaq indicating that we failed to comply with the Minimum Bid Requirement.

The Notice has no immediate effect on the listing of our common stock. In accordance with Nasdaq Listing Rule 5810(c)(3)(A), we have an initial period of 180 calendar days (which expires on November 10, 2025) to regain compliance with the Minimum Bid Requirement. To regain compliance, the closing bid price of our common stock must be at least $1.00 per share for a minimum of 10 consecutive business days during this 180 calendar day period, at which time the Staff will provide written notification to us that we comply with the Minimum Bid Requirement, unless the Staff exercises its discretion to extend this ten-day period pursuant to Nasdaq Listing Rule 5810(c)(3)(H).

If we do not regain compliance with the Minimum Bid Requirement during the initial 180 calendar day period, we may be eligible for an additional 180 calendar day compliance period. To qualify, we will be required to meet the continued listing requirement for market value of publicly held shares and all other initial listing standards for The Nasdaq Capital Market, with the exception of the Minimum Bid Requirement, and will need to provide written notice to the Staff of our intention to cure the deficiency during the additional compliance period by effecting a reverse stock split, if necessary.

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However, if we do not regain compliance with the Minimum Bid Requirement by November 10, 2025 and it appears to the Staff that we will not be able to regain compliance with the Minimum Bid Requirement during the additional compliance period, or that we are otherwise not eligible for an additional compliance period at that time, the Staff will provide notice that our common stock will become subject to delisting. Upon receipt of such notice, under Nasdaq rules, we may appeal the Staff's delisting determination to a Hearings Panel, or the Panel. However, if we do appeal the delisting determination by the Staff to the Panel, there can be no assurance that such appeal would be successful, or that we will be able to regain compliance with the Minimum Bid Requirement or maintain compliance with the other listing requirements.

We intend to actively monitor the closing bid price of our common stock and will evaluate available options to regain compliance with the Minimum Bid Requirement. However, there can be no assurance that we will be able to regain compliance with the Minimum Bid Requirement. This potential delisting, and any other potential delisting, of our common stock could have a material adverse effect on the market for, and liquidity and price of, our common stock and would adversely affect our ability to raise capital on terms acceptable to us, or at all. Delisting from Nasdaq could also have other negative results, including, without limitation, the potential loss of confidence by investors, customers and employees and fewer business development opportunities. Any delisting of our common stock from Nasdaq would also make it more difficult for our stockholders to sell their shares of our common stock in the public market.

**ITEM 2. UNREGISTERED SALES OF EQUITY SECURITIES AND USE OF PROCEEDS**

None.

**ITEM 3. DEFAULTS UPON SENIOR SECURITIES**

None.

**ITEM 4. MINE SAFETY DISCLOSURES**

Not applicable.

**ITEM 5. OTHER INFORMATION** 

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(c) Director and Officer Trading Arrangements

None of our directors or officers adopted or terminated a Rule 10b5-1 trading arrangement or a non-Rule 10b5-1 trading arrangement (as defined in Item 408(c) of Regulation S-K) during the quarterly period covered by this report.

------

**ITEM 6. EXHIBITS**

---

| | | | | | | |
|:---|:---|:---|:---|:---|:---|:---|
|  |  | **Incorporated by Reference** | **Incorporated by Reference** | **Incorporated by Reference** | **Incorporated by Reference** | **Incorporated by Reference** |
| **Exhibit**<br>**Number** | **Exhibit Description** | **Filed**<br>**Herewith** | **Form** | **Exhibit** | **Filing Date** | **Registration/File No.** |
| 3.1 | [<u>Amended and Restated Certificate of Incorporation, as amended</u>](cue-ex3_1.htm) | X<br>|  |  |  |  |
| 4.1 | [<u>Form of Pre-Funded Warrant</u>](https://www.sec.gov/Archives/edgar/data/0001645460/000119312525081592/d923668dex41.htm) |  | 8-K | 4.1 | 4/15/2025 | 001-38327 |
| 4.2 | [<u>Form of Common Stock Warrant</u>](https://www.sec.gov/Archives/edgar/data/0001645460/000119312525081592/d923668dex42.htm) |  | 8-K | 4.2 | 4/15/2025 | 001-38327 |
| 10.1 | [<u>Cue Biopharma, Inc. 2025 Stock Incentive Plan</u>](https://www.sec.gov/Archives/edgar/data/0001645460/000095017025084279/cue-ex99_1.htm) |  | 8-K | 99.1 | 6/10/2025 | 001-38327 |
| 10.2 | [<u>Second Amendment to the License Agreement, dated June 30, 2025, between Cue Biopharma, Inc. and MIL 40G, LLC</u>](cue-ex10_2.htm) | X |  |  |  |  |
| 10.3# | [<u>Collaboration and License Agreement between the Registrant and Boehringer Ingelheim International GmbH dated April 10, 2025</u>](https://www.sec.gov/Archives/edgar/data/0001645460/000095017025069125/cue-ex10_2.htm) |  | 10-Q | 10.2 | 5/12/2025 | 001-38327<br>|
| 10.4# | [<u>Third Amendment to the Amended and Restated License Agreement with Albert Einstein College of Medicine dated April 10, 2025</u>](https://www.sec.gov/Archives/edgar/data/0001645460/000095017025069125/cue-ex10_3.htm) |  | 10-Q<br>| 10.3 | 5/12/2025<br>| 001-38327<br>|
| 31.1 | [<u>Certification Pursuant to Rule 13a-14(a) or Rule 15d-14(a) of the Securities Exchange Act of 1934</u>](cue-ex31_1.htm) | X |  |  |  |  |
| 32.1 | [<u>Certification Pursuant to 18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002</u>](cue-ex32_1.htm) | X |  |  |  |  |
| 101.INS | Inline XBRL Instance Document – the instance document does not appear in the Interactive Data File because its XBRL tags are embedded within the Inline XBRL document. | X |  |  |  |  |
| 101.SCH | Inline XBRL Taxonomy Extension Schema With Embedded Linkbase Documents | X |  |  |  |  |
| 104 | The cover page from the Company's Quarterly Report on Form 10-Q for the quarter ended June 30, 2025, has been formatted in Inline XBRL. | X |  |  |  |  |

---

------

# Portions of this exhibit have been omitted pursuant to Item 601(b)(10)(iv) of Regulation S-K.

------

**SIGNATURES** 

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized.

---

| | | |
|:---|:---|:---|
|  | Cue Biopharma, Inc. | Cue Biopharma, Inc. |
| Dated: August 12, 2025 | By: | /s/ Daniel R. Passeri |
|  |  | Daniel R. Passeri<br>Chief Executive Officer <br>(Principal Executive Officer, Principal Financial Officer, and Principal Accounting Officer) |

---

------

## Exhibit 3.1

**Exhibit 3.1**

**AMENDED AND RESTATED**

**CERTIFICATE OF INCORPORATION<br>OF<br>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 Incorporation of the corporation, which restates and integrates and also further amends the provisions of the corporation's Certificate of Incorporation was duly adopted in accordance with the provisions of Sections 242 and 245 of the Delaware General Corporation Law and by the written (or electronic) consent of its stockholders in accordance with Section 228 of the Delaware General Corporation Law. The Certificate of Incorporation of the corporation is hereby amended, integrated and restated to read in its entirety as follows:

**ARTICLE I**

***Identification***

SECTION 1.01. <u>Name</u>. The name of the Corporation is "Cue Biopharma, Inc." (the "Corporation").

**ARTICLE II**

***Purpose***

SECTION 2.01. <u>Purpose</u>. The purpose for which the Corporation is organized is to engage in any lawful act or activity for which corporations may be organized under the Delaware General Corporation Law ("DGCL").

**ARTICLE III**

***Capital Stock***

SECTION 3.01. <u>Amount</u>. The total number of shares which the Corporation has authority to issue is 60,000,000 shares, consisting of: 10,000,000 shares designated as Preferred Stock, par value of $0.001 per share ("Preferred Stock"), and 50,000,000 shares designated as Common Stock, par value of $0.001 per share ("Common Stock").

SECTION 3.02. <u>Preferred Stock</u>. Shares of Preferred Stock may be issued from time to time in one or more series. The Board of Directors (or any committee to which it may duly delegate the authority granted in this Article III) is hereby empowered to authorize the issuance from time to time of shares of Preferred Stock in one or more series, for such consideration and for such corporate purposes as the Board of Directors (or such committee thereof) may from time to time determine, and by filing a certificate (a "Preferred Stock Designation") pursuant to applicable law of the State of Delaware, as it presently exists or may hereafter be amended, to establish from time to time for each such series the number of shares to be included in each such series and to fix the designations, powers, rights, and preferences of the shares of each such series, and the qualifications, limitations, and restrictions thereof to the fullest extent now or hereafter permitted by this Amended and Restated Certificate of Incorporation and the laws of the State of Delaware, including, without limitation, voting rights (if any), dividend rights, dissolution rights, conversion rights, exchange rights, and redemption rights thereof, as shall be stated and expressed in a resolution or resolutions adopted by the Board of Directors (or such committee thereof) providing for the issuance of such series of Preferred Stock. Each series of Preferred Stock shall be distinctly designated.

------

SECTION 3.03. <u>Common Stock</u>.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(A) The holders of shares of Common Stock shall be entitled to one vote for each such share on each matter submitted to the stockholders on which the holders of shares of Common Stock are entitled to vote. Except as otherwise required by law or this Amended and Restated Certificate of Incorporation, and subject to the rights of the holders of Preferred Stock, at any annual or special meeting of the stockholders the holders of shares of Common Stock shall have the right to vote for the election of directors and on all other matters submitted to a vote of the stockholders; provided, however, that, except as otherwise required by law, holders of Common Stock shall not be entitled to vote on any amendment to this Amended and Restated Certificate of Incorporation that relates solely to the terms, number of shares, powers, designations, preferences, or relative participating, optional, or other special rights (including, without limitation, voting rights), or to qualifications, limitations, or restrictions thereon, of one or more outstanding series of Preferred Stock if the holders of such affected series are entitled, either separately or together with the holders of one more other such series, to vote thereon pursuant to this Amended and Restated Certificate of Incorporation (including, without limitation, by any Preferred Stock Designation or pursuant to the DGCL.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(B) Subject to the rights of the holders of Preferred Stock, the holders of shares of Common Stock shall be entitled to receive such dividends and other distributions (payable in cash, property, or capital stock of the Corporation) when, as and if declared thereon by the Board of Directors from time to time out of any assets or funds of the Corporation legally available therefor, and shall share equally on a per share basis in such dividends and distributions.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(C) In the event of any voluntary or involuntary liquidation, dissolution, or winding-up of the Corporation, after payment or provision for payment of the debts and other liabilities of the Corporation, and subject to the rights of the holders of Preferred Stock in respect thereof, the holders of shares of Common Stock shall be entitled to receive all the remaining assets of the Corporation available for distribution to its stockholders, ratably in proportion to the number of shares of Common Stock held by them.

**ARTICLE IV**

***Directors***

SECTION 4.01. <u>Management of the Corporation.</u> The business and affairs of the Corporation shall be managed by or under the direction of the Board of Directors of the Corporation.

SECTION 4.02. <u>Number</u>. The number of directors of the Corporation shall be determined exclusively by resolution adopted by a majority of the Whole Board. For purposes of this Amended and Restated Certificate of Incorporation, the term "Whole Board" means the total number of authorized directors whether or not there exist any vacancies in previously authorized directorships.

SECTION 4.03. <u>Election of Directors.</u> The directors shall be elected at the annual meeting of stockholders by such stockholders as have the right to vote on such election. Directors need not be stockholders of the Corporation. Unless required by the Bylaws, the election of the Board of Directors need not be by written ballot.

SECTION 4.04. <u>Vacancies</u>. Any vacancy in the Board of Directors, however occurring, including a vacancy resulting from an enlargement of the Board of Directors, may be filled only by vote of a majority of the directors then in office, even if less than a quorum, or by a sole remaining director.

SECTION 4.05. <u>Amendment of the Bylaws by the Board.</u> The Board of Directors of the Corporation is expressly authorized to adopt, amend or repeal the Bylaws of the Corporation.

------

**ARTICLE V**

***Indemnification***

SECTION 5.01. <u>Right to Indemnification and Advancement</u>. The Corporation shall indemnify (and advance expenses to) its officers and directors to the fullest extent permitted by the DGCL, as amended from time to time.

**ARTICLE VI**

***Director Liability***

SECTION 6.01. <u>Waiver of Liability</u>. A director of the Corporation shall not be personally liable either to the Corporation or to any of its stockholders for monetary damages for breach of fiduciary duty as a director, except to the extent such exemption from liability or limitation thereof is not permitted under the DGCL. Any amendment or modification or repeal of the foregoing sentence or of the DGCL shall not adversely affect any right or protection of a director of the Corporation hereunder in respect of any act or omission occurring prior to the time of such amendment, modification, or repeal. If the DGCL hereafter is amended to further eliminate or limit the liability of a director, then a director of the Corporation, in addition to the circumstances in which a director is not personally liable as set forth in the preceding sentence, shall not be liable to the fullest extent permitted by the amended DGCL.

**ARTICLE VII**

***Registered Agent and Registered Office***

SECTION 7.01. <u>Registered Agent and Office</u>. The name and street address of the registered agent at the Corporation's registered office are:

National Registered Agents, Inc.

160 Greentree Drive, Suite 101

Dover, DE 19904

County of Kent

**ARTICLE VIII**

***Quorum Requirement***

SECTION 8.01. <u>Quorum</u>. The holders representing a majority of the combined voting power of the capital stock issued and outstanding and entitled to vote at a meeting, present in person or represented by proxy, shall constitute a quorum.

**ARTICLE IX**

***Cumulative Voting***

SECTION 9.01. <u>No Cumulative Voting</u>. No holder of any shares of any class of stock of the Corporation shall be entitled to cumulative voting rights in any circumstances.

**ARTICLE X**

***Preemptive Rights***

SECTION 10.01. <u>No Preemptive Rights</u>. No stockholder shall have any preemptive rights to acquire unissued shares of the Corporation or securities of the Corporation convertible into or carrying a right to subscribe to or acquire shares.

------

**ARTICLE XI**

***Internal Corporate Claims***

SECTION 11.01. <u>Venue for Internal Corporate Claims.</u> Unless the Corporation consents in writing to the selection of an alternative forum, the Court of Chancery in the State of Delaware shall be the sole and exclusive forum for all "internal corporate claims." "Internal corporate claims" mean claims, including claims in the right of the Corporation, (i) that are based upon a violation of a duty by a current or former director or officer or stockholder in such capacity or (ii) as to which Title 8 of the Delaware Code confers jurisdiction upon the Court of Chancery, except for, as to each of (i) through (ii) above, any claim as to which the Court of Chancery determines that there is an indispensable party not subject to the jurisdiction of the Court of Chancery (and the indispensable party does not consent to the personal jurisdiction of the Court of Chancery within ten days following such determination), which is vested in the exclusive jurisdiction of a court or forum other than the Court of Chancery, or for which the Court of Chancery does not have subject matter jurisdiction. If any provision or provisions of this Article XI shall be held to be invalid, illegal or unenforceable as applied to any person or entity or circumstance for any reason whatsoever, then, to the fullest extent permitted by law, the validity, legality and enforceability of such provisions in any other circumstance and of the remaining provisions of this Article XI (including, without limitation, each portion of any sentence of this Article XI containing any such provision held to be invalid, illegal or unenforceable that is not itself held to be invalid, illegal or unenforceable) and the application of such provision to other persons or entities and circumstances shall not in any way be affected or impaired thereby.

**ARTICLE XII**

***Supermajority Provisions***

SECTION 12.01. <u>Amendment of the Certificate of Incorporation by Stockholders.</u> The Corporation reserves the right to amend, alter, change or repeal any provision contained in this Amended and Restated Certificate of Incorporation, in the manner now or hereafter prescribed by statute, and all rights conferred upon stockholders herein are granted subject to this reservation; provided, however, that, notwithstanding any other provision of the Amended and Restated Certificate of Incorporation or any provision of law that might otherwise permit a lesser vote or no vote, but in addition to any vote of the holders of any class or series of the stock of the Corporation required by law or by this Amended and Restated Certificate of Incorporation, the affirmative vote of the holders of at least sixty-six and two-thirds percent (66 2/3%) of the voting power of the outstanding shares of stock of the Corporation entitled to vote generally in the election of directors, voting together as a single class, shall be required to amend or repeal, or adopt any provision of this Amended and Restated Certificate of Incorporation inconsistent with Articles IV, V, XI and XII.

SECTION 12.02. <u>Amendments to Bylaws by Stockholders</u>. The stockholders shall also have the power to adopt, amend or repeal the Bylaws of the Corporation; provided, however, that, in addition to any vote of the holders of any class or series of stock of the Corporation required by law or by this Amended and Restated Certificate of Incorporation, the amendment of the Bylaws by the Corporation's stockholders shall require the affirmative vote of the holders of at least sixty-six and two-thirds percent (66 2/3%) of the voting power of all of the then outstanding shares of the capital stock of the Corporation entitled to vote generally in the election of directors, voting together as a single class.

------

**IN WITNESS WHEREOF**, this Amended and Restated Certificate of Incorporation has been executed by a duly authorized officer of this corporation on this 21<sup>st</sup> day of December, 2017.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;**CUE BIOPHARMA, INC.**

---

| | |
|:---|:---|
|  | /s/ Daniel R. Passeri |
| &nbsp;&nbsp;By:<br>Title:  | &nbsp;&nbsp;Daniel R. Passeri <br>Chief Executive Officer |

---

------

**STATE OF DELAWARE**

**CERTIFICATE OF AMENDMENT**

**OF AMENDED AND RESTATED**

**CERTIFICATE OF INCORPORATION**

**CUE BIOPHARMA, INC.**, a corporation duly organized and existing under the General Corporation Law of the State of Delaware (the "**Corporation**"), does hereby certify that:

**FIRST:** Pursuant to Section 242 of the General Corporation Law of the State of Delaware, this Certificate of Amendment of Amended and Restated Certificate of Incorporation amends and restates Section 3.01 of this corporation's Amended and Restated Certificate of Incorporation to read in its entirety as follows:

SECTION 3.01. <u>Amount</u>: The total number of shares which the Corporation has authority to issue is 110,000,000 shares, consisting of: 10,000,000 shares designated as Preferred Stock, par value of $0.001 per share ("Preferred Stock"), and 100,000,000 shares designated as Common Stock, par value of $0.001 per share ("Common Stock").

**SECOND**: The foregoing amendment was duly adopted in accordance with the provisions of Section 242 of the General Corporation Law of the State of Delaware.

**IN WITNESS WHEREOF,** said corporation has caused this certificate to be signed this 15th day of July, 2020.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;**CUE BIOPHARMA, INC.**

---

| | |
|:---|:---|
|  | /s/ Daniel R. Passeri |
| &nbsp;&nbsp;By:<br>Title:  | &nbsp;&nbsp;Daniel R. Passeri <br>Chief Executive Officer |

---

------

**CERTIFICATE OF AMENDMENT**

**OF**

**AMENDED AND RESTATED CERTIFICATE OF INCORPORATION**

**OF**

**CUE BIOPHARMA, INC.**

Pursuant to Section 242 of the

<u>General Corporation Law of the State of Delaware</u>

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 Directors of the Corporation has duly adopted resolutions in accordance with the provisions of Section 242 of the General Corporation Law of the State of Delaware authorizing, declaring advisable and approving an amendment to the Amended and Restated Certificate of Incorporation of the Corporation to (i) increase the number of authorized shares of capital stock of the Corporation and (ii) increase the number of authorized shares of Common Stock of the Corporation. Thereafter, the stockholders of the Corporation duly adopted such amendment in accordance with the provisions of Section 242 of the General Corporation Law of the State of Delaware.

SECOND: That the amendment to the Amended and Restated Certificate of Incorporation of the Corporation set forth in this Certificate of Amendment was duly adopted in accordance with the provisions of Section 242 of the General Corporation Law of the State of Delaware by the Board of Directors and stockholders of the Corporation.

THIRD: That, upon the effectiveness of this Certificate of Amendment, Section 3.01 of Article III of the Amended and Restated Certificate of Incorporation, as heretofore amended, is hereby amended and restated in its entirety as follows:

"SECTION 3.01. <u>Amount</u>: The total number of shares which the Corporation has authority to issue is 210,000,000 shares, consisting of: 10,000,000 shares designated as Preferred Stock, par value of $0.001 per share ("Preferred Stock"), and 200,000,000 shares designated as Common Stock, par value of $0.001 per share ("Common Stock")."

------

IN WITNESS WHEREOF, this Certificate of Amendment of Amended and Restated Certificate of Incorporation has been executed by a duly authorized officer of the Corporation on this 8th day of October, 2024.

**CUE BIOPHARMA, INC.**

---

| | |
|:---|:---|
|  | /s/ Daniel R. Passeri |
| &nbsp;&nbsp;By:<br>Title:  | &nbsp;&nbsp;Daniel R. Passeri <br>Chief Executive Officer |

---

------

**CERTIFICATE OF AMENDMENT**

**OF**

**AMENDED AND RESTATED CERTIFICATE OF INCORPORATION**

**OF**

**CUE BIOPHARMA, INC.**

Pursuant to Section 242 of the

<u>General Corporation Law of the State of Delaware</u>

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 Directors of the Corporation has duly adopted resolutions in accordance with the provisions of Section 242 of the General Corporation Law of the State of Delaware authorizing, declaring advisable and approving an amendment to the Amended and Restated Certificate of Incorporation of the Corporation to (i) increase the number of authorized shares of capital stock of the Corporation and (ii) increase the number of authorized shares of Common Stock of the Corporation. Thereafter, the stockholders of the Corporation duly adopted such amendment in accordance with the provisions of Section 242 of the General Corporation Law of the State of Delaware.

SECOND: That the amendment to the Amended and Restated Certificate of Incorporation of the Corporation set forth in this Certificate of Amendment was duly adopted in accordance with the provisions of Section 242 of the General Corporation Law of the State of Delaware by the Board of Directors and stockholders of the Corporation.

THIRD: That, upon the effectiveness of this Certificate of Amendment, Section 3.01 of Article III of the Amended and Restated Certificate of Incorporation, as heretofore amended, is hereby amended and restated in its entirety as follows:

"SECTION 3.01. <u>Amount</u>: The total number of shares which the Corporation has authority to issue is 310,000,000 shares, consisting of: 10,000,000 shares designated as Preferred Stock, par value of $0.001 per share ("Preferred Stock"), and 300,000,000 shares designated as Common Stock, par value of $0.001 per share ("Common Stock")."

------

IN WITNESS WHEREOF, this Certificate of Amendment of Amended and Restated Certificate of Incorporation has been executed by a duly authorized officer of the Corporation on this 5th day of June, 2025.

**CUE BIOPHARMA, INC.**

---

| | |
|:---|:---|
|  | /s/ Daniel R. Passeri |
| &nbsp;&nbsp;By:<br>Title:  | &nbsp;&nbsp;Daniel R. Passeri <br>Chief Executive Officer |

---

------

## Exhibit 10.2

# **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 May 3, 2022 (together, the "**License Agreement**");

WHEREAS, Licensee warrants and represents that, to the best of its knowledge, SmartLabs has fulfilled its obligations under the License Agreement and is not in default of any covenants or obligations contained in the License Agreement;

WHEREAS, Licensee currently pays a monthly License Fee equal to $235,883.98 ("**Current License Fee**"; excluding monthly parking fees and equipment rental fee); which is comprised of (i) a monthly License Fee equal to $225,760.20 for use of the Licensed Premises, and (ii) a monthly License Fee equal to $10,123.78 for use of the Expanded Premises (the Expanded Premises and the Licensed Premises are referred to collectively herein as the **"Premises")**

WHEREAS, the Expiration Date of the License Agreement is currently April 14, 2026;

WHEREAS, SmartLabs has agreed to reduce the current License Fee to $147,545.69 effective on the Effective Date ("**New License Fee**"; excluding monthly parking fees and equipment rental fee), in exchange for extending the Expiration Date until April 14, 2028;

WHEREAS, Licensee has already paid the Current License Fee to SmartLabs for the month of June

2025;

WHEREAS, SmartLabs agrees to provide a credit to Licensee equal to the difference in daily rate of the Current License Fee and the New License Fee for each day from June 16, 2025 to and including June 30, 2025, which is equal to $44,169.14 ("**Credit**");

WHEREAS, SmartLabs and Licensee desire to amend the License Agreement in certain respects as set forth herein; and,

WHEREAS, all capitalized terms contained herein shall, unless otherwise defined in this Second Amendment, have the same meaning as set forth in the License Agreement.

NOW THEREFORE, for good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties agree that the License Agreement is hereby amended as follows:

*Agreement*

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1.<u>Term</u>. The Expiration Date, which is currently defined as April 14, 2026 in Section 2(a) of the License Agreement, is hereby modified to, and now shall be defined as, April 14, 2028.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;2.<u>License Fee</u>. Effective on the Effective Date and notwithstanding anything in the License Agreement to the contrary, Licensee shall pay in lieu of the **Current License Fee**, the **New License Fee** for use of the Premises, which Licensee shall pay in advance on or before the first day of each

------

and every month during the Term by electronic payment to SmartLabs. The New License Fee shall be subject to a four percent (4%) increase upon each anniversary of the Term Commencement Date.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;3.<u>Credit</u>. As set forth in the Recitals, SmartLabs acknowledges that Licensee has paid the Current License Fee for June 2025 and SmartLabs is therefore agreeing to provide the Credit to Licensee. The Credit shall be applied against any sums owed under the License Agreement on April 1, 2026.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;4.<u>Broker</u>. Licensee warrants and represents that Licensee has dealt with no broker in connection with the consummation of this Second Amendment, and, in the event of any brokerage claims asserted against SmartLabs predicated upon prior dealings with Licensee, Licensee agrees to defend the same and indemnify SmartLabs against any such claim.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;5.<u>Ratification</u>. Except as amended herein, all terms and conditions of the License Agreement shall remain unchanged and in full force and effect.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;6.<u>Counterparts</u>. This Second Amendment to License Agreement may be executed in any number of counterparts, each of which shall be an original and all of which together shall constitute one and the same document.

**IN WITNESS WHEREOF**, SmartLabs and Licensee have duly executed this Second Amendment as of the date first written above.

 **SMARTLABS:** 

---

| |
|:---|
| /s/ Brian Taylor |
| By: Brian Taylor |
| Title: CEO |

---

**LICENSEE:** 

---

| |
|:---|
| /s/ Lucinda Warren |
| By: Lucinda Warren |
| Title: Chief Business Officer |

---

------

## Exhibit 31.1

**EXHIBIT 31.1**

**CERTIFICATION OF THE PRINCIPAL EXECUTIVE OFFICER AND PRINCIPAL FINANCIAL OFFICER**

**PURSUANT TO SECTION 302 OF THE SARBANES-OXLEY ACT OF 2002**

I, Daniel R. Passeri, certify that:

1. I have reviewed this Quarterly Report on Form 10-Q of Cue Biopharma, Inc.;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrant's other certifying officer(s) and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(a)Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(b)Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(c)Evaluated the effectiveness of the registrant's disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(d)Disclosed in this report any change in the registrant's internal control over financial reporting that occurred during the registrant's most recent fiscal quarter (the registrant's fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant's internal control over financial reporting; and

5. The registrant's other certifying officer(s) and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant's auditors and the audit committee of the registrant's board of directors (or persons performing the equivalent functions):

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(a)All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant's ability to record, process, summarize and report financial information; and

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(b)Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant's internal control over financial reporting.

Date: August 12, 2025

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| |
|:---|
| /s/ Daniel R. Passeri |
| Name: Daniel R. Passeri |
| Title: Chief Executive Officer |
| (Principal Executive Officer, Principal Financial Officer, and Principal Accounting Officer) |

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## Exhibit 32.1

**EXHIBIT 32.1**

**CERTIFICATION PURSUANT TO** 

**18 U.S.C. SECTION 1350,** 

**AS ADOPTED PURSUANT TO**

**SECTION 906 OF THE SARBANES-OXLEY ACT OF 2002**

In connection with this Quarterly Report on Form 10-Q of Cue Biopharma, Inc. (the "Company") for the period ended June 30, 2025 as filed with the Securities and Exchange Commission on the date hereof (the "Report"), I Daniel R. Passeri, Chief Executive Officer of the Company certify, pursuant to 18 U.S.C. § 1350, as adopted pursuant to § 906 of the Sarbanes-Oxley Act of 2002, to my knowledge that:

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1.The Report fully complies with the requirements of Section 13(a) or 15(d) of the Securities Exchange Act of 1934; and

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;2.The information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company.

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| |
|:---|
| /s/ Daniel R. Passeri |
| Name: Daniel R. Passeri |
| Title: Chief Executive Officer  |
| (Principal Executive Officer, Principal Financial Officer, and Principal Accounting Officer) |
| Date: August 12, 2025 |

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