# EDGAR Filing Document

**Accession Number:** 0001782303
**File Stem:** 0000950170-25-102391
**Filing Date:** 2025-8
**Character Count:** 135397
**Document Hash:** e0fb47fe6e548746a435f2920baaa5be
**Contains OCR:** False
**Source Format:** 

## Filing Content

## Filing Summary
**0000950170-25-102391.hdr.sgml**: 20250805

**ACCESSION NUMBER**: 0000950170-25-102391

**CONFORMED SUBMISSION TYPE**: 10-Q

**PUBLIC DOCUMENT COUNT**: 62

**CONFORMED PERIOD OF REPORT**: 20250630

**FILED AS OF DATE**: 20250805

**DATE AS OF CHANGE**: 20250805

**FILER**: 

**COMPANY DATA:**
- **COMPANY CONFORMED NAME:** Boundless Bio, Inc.
- **CENTRAL INDEX KEY:** 0001782303
- **STANDARD INDUSTRIAL CLASSIFICATION:** PHARMACEUTICAL PREPARATIONS [2834]
- **ORGANIZATION NAME:** 03 Life Sciences
- **EIN:** 830751369
- **STATE OF INCORPORATION:** DE
- **FISCAL YEAR END:** 1231

**FILING VALUES:**
- **FORM TYPE:** 10-Q
- **SEC ACT:** 1934 Act
- **SEC FILE NUMBER:** 001-41989
- **FILM NUMBER:** 251182770

**BUSINESS ADDRESS:**
- **STREET 1:** 10955 ALEXANDRIA WAY
- **STREET 2:** SUITE 100
- **CITY:** SAN DIEGO
- **STATE:** CA
- **ZIP:** 92121
- **BUSINESS PHONE:** (858) 766-9912

**MAIL ADDRESS:**
- **STREET 1:** 10955 ALEXANDRIA WAY
- **STREET 2:** SUITE 100
- **CITY:** SAN DIEGO
- **STATE:** CA
- **ZIP:** 92121

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

**UNITED STATES**

**SECURITIES AND EXCHANGE COMMISSION**

**WASHINGTON, DC 20549**

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**FORM** 10-Q

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**(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:** 001-41989

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BOUNDLESS BIO, INC.

**(Exact Name of Registrant as Specified in its Charter)**

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---

| | |
|:---|:---|
| Delaware | 83-0751369 |
| **(State or other jurisdiction of**<br>**incorporation or organization)** | **(I.R.S. Employer<br>Identification No.)** |
| 10955 Alexandria Way**,** Suite 100**,**<br>San Diego**,** CA | 92121 |
| **(Address of principal executive offices)** | **(Zip Code)** |

---

**Registrant's telephone number, including area code:** (858) 766-9912

**Former name, former address and former fiscal year, if changed since last report: N/A**

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

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| | | |
|:---|:---|:---|
| **Title of each class** | **Trading**<br>**Symbol(s)** | **Name of each exchange on which registered** |
| Common stock, par value $0.0001 per share | BOLD | Nasdaq Global Select Market |

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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, 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.

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

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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 July 31, 2025, the registrant had 22,385,611 shares of common stock, $0.0001 par value per share, outstanding.

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**Table of Contents**

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| | | |
|:---|:---|:---|
|  |  | **Page** |
| **PART I.** | [<u>FINANCIAL INFORMATION</u>](#part_i_financial_information) | 1 |
| Item 1. | [<u>Financial Statements (Unaudited)</u>](#item_1_financial_statements) | 1 |
|  | [<u>Condensed Balance Sheets</u>](#condensed_balance_sheets) | 1 |
|  | [<u>Condensed Statements of Operations and Comprehensive Loss</u>](#statements_of_operations) | 2 |
|  | [<u>Condensed Statements of Convertible Preferred Stock and Stockholders' Equity/ (Deficit)</u>](#condensed_cps_and_stockholders_deficit) | 3 |
|  | [<u>Condensed Statements of Cash Flows</u>](#statement_of_cash_flows) | 4 |
|  | [<u>Notes to Condensed Financial Statements</u>](#notes_to_financial_statements) | 5 |
| Item 2. | [<u>Management's Discussion and Analysis of Financial Condition and Results of Operations</u>](#item_2_managements_discussion) | 14 |
| Item 3. | [<u>Quantitative and Qualitative Disclosures About Market Risk</u>](#item_3_quantitative_and_qualitative) | 24 |
| Item 4. | [<u>Controls and Procedures</u>](#item_4_controls_and_procedures) | 24 |
| **PART II.** | [<u>OTHER INFORMATION</u>](#part_ii_other_information) | 25  |
| Item 1. | [<u>Legal Proceedings</u>](#item_1_legal_proceedings) | 25 |
| Item 1A. | [<u>Risk Factors</u>](#item_1a_risk_factors) | 25 |
| Item 2. | [<u>Unregistered Sales of Equity Securities and Use of Proceeds</u>](#item_2_unregistered_sales_of_equity) | 25 |
| Item 3. | [<u>Defaults Upon Senior Securities</u>](#item_3_defaults_upon_senior_securities) | 25 |
| Item 4. | [<u>Mine Safety Disclosures</u>](#item_4_mine_safety_disclosures) | 26 |
| Item 5. | [<u>Other Information</u>](#item_5_other_information) | 26 |
| Item 6. | [<u>Exhibits</u>](#item_6_exhibits) | 26 |
| <u>Signatures</u> | <u>Signatures</u> | 27 |

---

i

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**SPECIAL NOTE REGARDING FORWARD-LOOKING STATEMENTS AND MARKET 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 (the Securities Act), and Section 21E of the Securities Exchange Act of 1934, as amended (the Exchange Act). All statements other than statements of historical facts contained in this Quarterly Report are forward-looking statements, including statements regarding our future results of operations and financial position, our use of the net proceeds from the initial public offering of our common stock, the period over which we estimate our cash position will be sufficient to fund our operations, the sufficiency of our cash position to fund achievement of milestones, including clinical data readouts and regulatory submissions, the expected benefits of the portfolio prioritization we implemented in the second quarter of 2025, the timing and likelihood of success, plans, and objectives of management for future operations, business strategy, research and development plans, the anticipated timing, costs, design, and conduct of our ongoing and planned clinical trials and preclinical studies for our extrachromosomal DNA (ecDNA) directed therapeutic candidates (ecDTx), ecDNA diagnostic, our other discovery programs, the timing of expected data readouts, the potential safety and therapeutic benefits of our ecDTx, the potential addressable patient populations for our ecDTx, the likelihood of development candidate nominations from our discovery-stage programs, the potential to develop future ecDTx, the timing and likelihood of regulatory submissions, filings and approvals for our ecDTx, expected regulatory approval pathways for our ecDTx and any ecDNA diagnostic, our ability to commercialize our ecDTx, if approved, the pricing and reimbursement of our ecDTx, if approved, potential competition for our ecDTx, our intellectual property and other market exclusivity strategies, our intent regarding any strategic collaborations, licenses, or similar arrangements and the potential benefits of any such arrangements.

In some cases, you can identify forward-looking statements by terms such as "anticipate," "believe," "contemplate," "continue," "could," "estimate," "expect," "intend," "may," "plan," "potential," "predict," "project," "should," "would," "target," or "will" or the negative of these terms or other similar expressions. Our forward-looking statements are only predictions. We have based our forward-looking statements largely on our current expectations and projections about future events and financial and other trends that we believe may affect our business, financial condition, and results of operations based upon information available to us as of the date of this report. Such information may be limited or incomplete. These forward-looking statements speak only as of the date of this report and are subject to several risks, uncertainties, and assumptions, including, without limitation:

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•We have a limited operating history, have incurred significant operating losses since our inception and expect to incur significant losses for the foreseeable future. We may never generate any revenue or become profitable or, if we achieve profitability, we may not be able to sustain it;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•We will require substantial additional capital to finance our operations, and a failure to obtain this necessary capital when needed on acceptable terms, or at all, could force us to delay, limit, reduce or terminate our ecDTx development programs, commercialization efforts, or other operations;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•We are early in our development efforts and currently have only one active clinical trial, a combination of BBI-355 and BBI-825. All of our other ecDTx programs are still in the preclinical or discovery stage. If we are unable to successfully develop, obtain regulatory approval, and ultimately commercialize any of our current or future ecDTx, or experience significant delays in doing so, our business will be materially harmed;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•Our approach to treating cancer with oncogene amplifications by developing ecDTx directed against ecDNA is novel and unproven, and we do not know whether we will be able to develop any products of commercial value, or if competing approaches will limit the commercial value of our ecDTx;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•Clinical and preclinical development involves a lengthy and expensive process with uncertain timelines and outcomes, and the results of preclinical studies and early clinical trials are not necessarily predictive of future results. Our ecDTx have not achieved sufficiently favorable clinical results to date and may not achieve favorable results in ongoing or future clinical trials or preclinical studies or receive regulatory approval on a timely basis, if at all;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•Any difficulties or delays in the commencement or completion, or the termination or suspension, of our current or planned clinical trials or preclinical studies could result in increased costs to us, delay or limit our ability to generate revenue, or adversely affect our commercial prospects;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•Use of our ecDTx could be associated with side effects, adverse events, or other properties or safety risks, which could delay or preclude regulatory approval, cause us to suspend or discontinue clinical trials, abandon an ecDTx, limit the commercial profile of an approved label, or result in other significant negative consequences that could severely harm our business, financial condition, results of operations, and prospects;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•If an ecDNA diagnostic is required to enable patient selection for one or more of our ecDTx and we are unable to successfully develop one, or if we experience significant delays in doing so, we may not realize the full commercial potential of our ecDTx;

ii

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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•Interim, topline, and preliminary data from our clinical trials and preclinical studies that we announce or publish from time to time may change as more patient data become available and are subject to audit and verification procedures that could result in material changes in the final data;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•Changes in methods of ecDTx manufacturing or formulation may result in additional costs or delay;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•Changes at the U.S. Food and Drug Administration (FDA), the U.S. Securities and Exchange Commission (SEC), and other government agencies, including due to funding shortages, changes in leadership, changes in policy, significant personnel turnover, or global health concerns, that disrupt their ability to perform routine functions could delay or hinder clinical and preclinical development and potential marketing approval of our ecDTx and our ability to raise capital;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•We rely on third parties to conduct our clinical trials and preclinical studies, to manufacture our ecDTx, and for ecDNA diagnostic development, and these third parties may not perform satisfactorily, which could delay, prevent, or impair our development or commercialization efforts;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•We face significant competition from entities that have developed or may develop product candidates for cancer, including companies developing novel treatments and technology platforms. If our competitors develop and commercialize their product candidates more rapidly than we do, or their technologies or their product candidates are more effective, safer, or less expensive than our ecDTx, our business and our ability to develop and successfully commercialize ecDTx may be adversely affected;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•Current and future healthcare reform legislation or regulation may increase the difficulty and cost for us to obtain coverage for and commercialize our ecDTx and may adversely affect the prices we may set;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•If we are unable to obtain, maintain, defend, and enforce patent or other intellectual property protection for our ecDTx, ecDNA diagnostic, or technology, or if the scope of the patent or other intellectual property protection obtained is not sufficiently broad, our competitors or other third parties could develop and commercialize products similar or identical to ours, and our ability to successfully commercialize our ecDTx may be adversely affected;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•Our information technology systems, or those of any of our service providers, may fail or suffer security incidents and other disruptions, which could result in a material disruption of our ecDTx development programs, compromise sensitive information related to our business, or prevent us from accessing critical information, potentially exposing us to liability or otherwise adversely affecting our business;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•The trading volume and price of our common stock have been and may continue to be highly volatile, and purchasers of our common stock could incur substantial losses;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•If we fail in the future to satisfy the continued listing requirements of Nasdaq, Nasdaq may take steps to delist our common stock; and

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•Unstable market and economic conditions, including as a result of tariff and trade policy changes, inflation, high interest rates, declines in economic growth, geopolitical conflicts and events, or adverse developments with respect to financial institutions and associated liquidity risk, may have serious adverse consequences on our business, financial condition, results of operations, and stock price.

You should carefully read all of the risk factors described 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 SEC on March 27, 2025 (our 2024 10-K) for a detailed description of material risks and uncertainties we face. The events and circumstances reflected in our forward-looking statements may not be achieved or occur and our actual results, performance, or achievements could differ materially from those expressed or implied by our forward-looking statements due to these risks and uncertainties, among other things. We operate in an evolving environment. New risk factors and uncertainties may emerge from time to time, and it is not possible for management to predict all risk factors and uncertainties. Because forward-looking statements are inherently subject to risks and uncertainties, some of which cannot be predicted or quantified and some of which are beyond our control, you should not place undue reliance on any forward-looking statement. Except as required by applicable law, we do not plan to publicly update or revise any forward-looking statements contained herein, whether as a result of any new information, future events, changed circumstances, or otherwise. All forward-looking statements are qualified in their entirety by this cautionary statement, which is made under the safe harbor provisions of the Private Securities Litigation Reform Act of 1995.

In addition, statements that "we believe" and similarly qualified statements reflect our beliefs and opinions on the relevant subject. These statements are based upon information available to us as of the date of this report, and while we believe such information forms a reasonable basis for such statements, such information may be limited or incomplete, and our statements should not be read to indicate that we have conducted an exhaustive inquiry into, or review of, all potentially available relevant information. These statements are inherently uncertain, and you are cautioned not to rely unduly upon them.

iii

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This report also contains estimates and other statistical data made by independent parties and by us relating to potential market opportunity and other data about our industry and competitive position. This data involves a number of assumptions and limitations, and you are cautioned not to give undue weight to such estimates. Projections, assumptions and estimates of our future performance and the future performance of the markets in which we operate are necessarily subject to a high degree of uncertainty and risk, and are subject to change based on various factors, including those discussed in Part I, Item 1A, "Risk Factors," of our 2024 10-K. These and other factors could cause results to differ materially from those expressed in the estimates made by the independent parties or by us.

iv

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**PART I—FINANCIAL INFORMATION**

**Item 1. Financial Statements.**

**Boundless Bio, Inc.**

**Condensed Balance Sheets**

*(in thousands, except par value data)*

---

| | | |
|:---|:---|:---|
|  | **June 30,** | **December 31,** |
|  | **2025** | **2024** |
|  | **(unaudited)** |  |
| **Assets** |  |  |
| Current assets |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Cash and cash equivalents | $14697 | $26587 |
| &nbsp;&nbsp;&nbsp;&nbsp;Short-term investments | 112451 | 125527 |
| &nbsp;&nbsp;&nbsp;&nbsp;Prepaid expenses and other current assets | 2542 | 2276 |
| Total current assets | 129690 | 154390 |
| Property and equipment, net | 3794 | 4321 |
| Right-of-use asset, net | 45365 | 47039 |
| Restricted cash | 560 | 560 |
| Other assets | 44 | 99 |
| Total assets | $179453 | $206409 |
| **Liabilities and stockholders' equity** |  |  |
| Current liabilities |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Accounts payable and accrued liabilities | $5855 | $5354 |
| &nbsp;&nbsp;&nbsp;&nbsp;Accrued compensation | 1397 | 2781 |
| &nbsp;&nbsp;&nbsp;&nbsp;Lease liabilities, current portion | 1961 |  |
| Total current liabilities | 9213 | 8135 |
| Lease liabilities, non-current | 47549 | 47632 |
| Total liabilities | 56762 | 55767 |
| Commitments and contingencies (Note 8) |  |  |
| Stockholders' equity |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Preferred stock, $0.0001 par value; 70,000 shares authorized and<br> no shares issued and outstanding as of June 30, 2025 and December 31, 2024 |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Common stock, $0.0001 par value; 700,000 shares authorized at June 30, 2025 and <br> December 31, 2024; 22,386 and 22,300 shares issued and outstanding as of<br> June 30, 2025 and December 31, 2024, respectively | 2 | 2 |
| &nbsp;&nbsp;&nbsp;&nbsp;Additional paid-in-capital | 355598 | 351991 |
| &nbsp;&nbsp;&nbsp;&nbsp;Accumulated other comprehensive income/ (loss) | (4) | 121 |
| &nbsp;&nbsp;&nbsp;&nbsp;Accumulated deficit | (232905) | (201472) |
| Total stockholders' equity | 122691 | 150642 |
| Total liabilities and stockholders' equity | $179453 | $206409 |

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

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**Boundless Bio, Inc.**

**Condensed Statements of Operations and Comprehensive Loss**

(unaudited)

*(in thousands, except per share data)*

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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** |
| Operating expenses: |  |  |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Research and development | $12218 | $14735 | $24355 | $27864 |
| &nbsp;&nbsp;&nbsp;&nbsp;General and administrative | 4843 | 4656 | 10047 | 8410 |
| Total operating expenses | 17061 | 19391 | 34402 | 36274 |
| Loss from operations | (17061) | (19391) | (34402) | (36274) |
| Other income, net: |  |  |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Interest income | 1386 | 2382 | 2971 | 3803 |
| &nbsp;&nbsp;&nbsp;&nbsp;Other income/ (expense), net |  | 33 | (2) | 65 |
| Total other income, net | 1386 | 2415 | 2969 | 3868 |
| Net loss | $(15675) | $(16976) | $(31433) | $(32406) |
| Comprehensive loss: |  |  |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Net loss | $(15675) | $(16976) | $(31433) | $(32406) |
| &nbsp;&nbsp;&nbsp;&nbsp;Unrealized loss on short-term investments | (36) | (43) | (125) | (104) |
| Comprehensive loss | $(15711) | $(17019) | $(31558) | $(32510) |
| Net loss per share, basic and diluted | $(0.70) | $(0.77) | $(1.41) | $(2.78) |
| Shares used in calculation | 22356 | 22023 | 22328 | 11641 |

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

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**Boundless Bio, Inc.**

**Condensed Statements of Convertible Preferred Stock and Stockholders' Equity/ (Deficit)**

(unaudited)

*(in thousands)*

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| | | | | | | | | |
|:---|:---|:---|:---|:---|:---|:---|:---|:---|
|  | **Convertible Preferred Stock** | **Convertible Preferred Stock** | **Common Stock** | **Common Stock** | **Additional<br>paid-in** | **Accumulated<br>other <br>comprehensive** | **Accumulated** | **Total <br>stockholders' <br>equity/** |
|  | **Shares** | **Amount** | **Shares** | **Amount** | **capital** | **income/ (loss)** | **deficit** | **(deficit)** |
| **Balance at December 31, 2024** |  | $— | 22300 | $2 | $351991 | $121 | $(201472) | $150642 |
| Stock-based compensation |  |  |  |  | 1797 |  |  | 1797 |
| Unrealized loss on short-term investments |  |  |  |  |  | (89) |  | (89) |
| Net loss |  |  |  |  |  |  | (15758) | (15758) |
| **Balance at March 31, 2025** |  | $— | 22300 | $2 | $353788 | $32 | $(217230) | $136592 |
| Stock-based compensation |  |  |  |  | 1693 |  |  | 1693 |
| Issuance of common stock under the Employee Stock Purchase Plan |  |  | 86 |  | 117 |  |  | 117 |
| Unrealized loss on short-term investments |  |  |  |  |  | (36) |  | (36) |
| Net loss |  |  |  |  |  |  | (15675) | (15675) |
| **Balance at June 30, 2025** |  | $— | 22386 | $2 | $355598 | $(4) | $(232905) | $122691 |
| **Balance at December 31, 2023** | 287447 | $247617 | 1247 | $— | $8987 | $40 | $(136109) | $(127082) |
| Vesting of early exercised stock options |  |  | 1 |  | 2 |  |  | 2 |
| Exercise of stock options |  |  | 15 |  | 59 |  |  | 59 |
| Stock-based compensation |  |  |  |  | 1328 |  |  | 1328 |
| Unrealized loss on short-term investments |  |  |  |  |  | (61) |  | (61) |
| Net loss |  |  |  |  |  |  | (15430) | (15430) |
| **Balance at March 31, 2024** | 287447 | $247617 | 1263 | $— | $10376 | $(21) | $(151539) | $(141184) |
| Issuance of common stock in initial public offering, net of $12,305 in discounts and offering costs |  |  | 6250 | 1 | 87694 |  |  | 87695 |
| Conversion of convertible preferred stock into common stock upon initial public offering | (287447) | (247617) | 14741 | 1 | 247616 |  |  | 247617 |
| Vesting of early exercised stock options |  |  |  |  | 2 |  |  | 2 |
| Stock-based compensation |  |  |  |  | 2135 |  |  | 2135 |
| Unrealized loss on short-term investments |  |  |  |  |  | (43) |  | (43) |
| Net loss |  |  |  |  |  |  | (16976) | (16976) |
| **Balance at June 30, 2024** |  | $— | 22254 | $2 | $347823 | $(64) | $(168515) | $179246 |

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

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**Boundless Bio, Inc.**

**Condensed Statements of Cash Flows**

(unaudited)

*(in thousands)*

---

| | | |
|:---|:---|:---|
|  | **Six Months Ended<br>June 30,** | **Six Months Ended<br>June 30,** |
|  | **2025** | **2024** |
| **Cash flows from operating activities** |  |  |
| Net loss | $(31433) | $(32406) |
| Adjustments to reconcile net loss to net cash used in operating activities: |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Stock-based compensation | 3490 | 3463 |
| &nbsp;&nbsp;&nbsp;&nbsp;Depreciation and amortization | 634 | 528 |
| &nbsp;&nbsp;&nbsp;&nbsp;Accretion of investments, net | (1508) | (2676) |
| &nbsp;&nbsp;&nbsp;&nbsp;Non-cash lease expense | 1674 | 1249 |
| &nbsp;&nbsp;&nbsp;&nbsp;Changes in operating assets and liabilities: |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Prepaid expenses and other assets | (210) | (1849) |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Accounts payable and accrued liabilities | (884) | 1037 |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Operating lease liabilities | 1878 | (1358) |
| Net cash used in operating activities | (26359) | (32012) |
| **Cash flows from investing activities** |  |  |
| Purchases of investments | (96285) | (124652) |
| Maturities of investments | 110744 | 76185 |
| Purchases of property and equipment | (107) | (1587) |
| Net cash provided by/ (used in) investing activities | 14352 | (50054) |
| **Cash flows from financing activities** |  |  |
| Proceeds from the issuance of common stock from initial public offering, net<br> of discounts |  | 93000 |
| Payments of common stock offering costs |  | (3336) |
| Proceeds from the exercise of stock options |  | 59 |
| Proceeds from issuance of common stock under the Employee Stock Purchase Plan | 117 |  |
| Net cash provided by financing activities | 117 | 89723 |
| Net increase/ (decrease) in cash, cash equivalents, and restricted cash | (11890) | 7657 |
| Cash, cash equivalents, and restricted cash at beginning of period | 27147 | 24266 |
| Cash, cash equivalents, and restricted cash at end of period | $15257 | $31923 |
| **Components of cash, cash equivalents, and restricted cash** |  |  |
| Cash and cash equivalents | $14697 | $31363 |
| Restricted cash | 560 | 560 |
| Cash, cash equivalents, and restricted cash at end of period | $15257 | $31923 |
| **Non-cash investing and financing activities** |  |  |
| Change in unpaid common stock issuance costs | $— | $(183) |
| Vesting of early exercised stock options | $— | $4 |
| Unpaid property and equipment purchases | $— | $107 |

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

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**Boundless Bio, Inc.**

**Notes to Condensed Financial Statements (Unaudited)**

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

***Description of Business***

Boundless Bio, Inc. (the Company) is a clinical-stage precision oncology company dedicated to unlocking a new paradigm in cancer therapeutics that addresses the significant unmet need in patients with oncogene amplified tumors by interrogating extrachromosomal DNA (ecDNA). The Company is focused on identifying targets essential for ecDNA functionality in oncogene amplified cancer cells, then designing and developing small molecule drugs called ecDNA-directed therapeutic candidates (ecDTx) to inhibit those targets, with the aim to prevent cancer cells from using amplified oncogenes to grow, adapt, and become resistant to existing therapies. The Company was incorporated in the state of Delaware on April 10, 2018 and is headquartered in San Diego, California.

***Initial Public Offering***

On April 2, 2024, the Company completed its initial public offering (IPO), pursuant to which it sold 6,250,000 shares of its common stock at a public offering price of $16.00 per share, resulting in net proceeds of approximately $87.7 million, after deducting underwriting discounts, commissions, and other offering expenses. Immediately prior to the closing of the IPO, the Company's outstanding convertible preferred stock automatically converted into 14,740,840 shares of common stock. Following the closing of the IPO, no shares of convertible preferred stock were authorized or outstanding.

In connection with the closing of its IPO, on April 2, 2024, the Company's certificate of incorporation was amended and restated to authorize 700,000,000 shares of common stock, par value $0.0001 per share, and 70,000,000 shares of undesignated preferred stock, par value of $0.0001 per share.

***ATM Offering***

On April 1, 2025, the Company entered into an Open Market Sale Agreement<sup>SM</sup> (the Sales Agreement) with Jefferies LLC (the Agent), under which the Company may, from time to time, sell shares of the Company's common stock in "at the market" (ATM) offerings through or to the Agent, as sales agent or principal. The shares of common stock will be offered and issued pursuant to the Company's shelf registration statement on Form S-3 (File No. 333-286302), including the Sales Agreement prospectus contained therein, filed with the Securities and Exchange Commission (SEC) on April 1, 2025 and declared effective by the SEC on April 10, 2025. Pursuant to the Sales Agreement prospectus, the Company may sell shares of its common stock having an aggregate offering price of up to $14.5 million. Sales of the shares of common stock, if any, will be made at prevailing market prices at the time of sale, or as otherwise agreed with the Agent. The Agent will receive a commission from the Company of up to 3.0% of the gross proceeds of any shares of common stock sold under the Sale Agreement. The Company is not obligated to sell, and the Agent is not obligated to buy or sell, any shares of common stock under the Sales Agreement. No assurance can be given that the Company will sell any shares of common stock under the Sales Agreement, or, if it does, as to the price or amount of shares of common stock that it sells or the dates when such sales will take place. As of June 30, 2025, no shares had been sold under the Sales Agreement.

***Liquidity***

Since the Company commenced operations in 2018, it has devoted substantially all of its efforts and resources to organizing and staffing the Company, business planning, raising capital, building its proprietary Spyglass platform, discovering its ecDTx, developing its ecDNA diagnostic, establishing its intellectual property portfolio, conducting research, preclinical studies, and clinical trials, establishing arrangements with third parties for the manufacture of its ecDTx and related raw materials, and providing other general and administrative support for these operations. The Company does not have any products for sale and has not generated any revenue to date. The Company has funded its operations primarily from the sale and issuance of shares of its convertible preferred stock and common stock.

As of June 30, 2025, the Company had cash, cash equivalents, and short-term investments of $127.1 million. The Company believes that its existing cash, cash equivalents, and short-term investments will be sufficient to fund its operations for at least twelve months from the issuance date of the accompanying unaudited condensed financial statements.

Since inception, the Company has incurred significant operating losses and negative cash flows from its operations and expects that it will continue to do so into the foreseeable future as it continues its development of, seeks regulatory approval for, and potentially commercializes any of its ecDTx and seeks to discover and develop additional ecDTx, utilizes third parties to manufacture its ecDTx and related raw materials, seeks to develop its ecDNA diagnostic, and expands and protects its intellectual property. If the Company obtains regulatory approval for any of its ecDTx, it expects to incur significant commercialization expenses related to product sales,

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**Boundless Bio, Inc.**

**Notes to Condensed Financial Statements (Unaudited)**

marketing, manufacturing, and distribution. The Company does not expect to generate any revenue from product sales until it successfully completes development of and obtains regulatory approval for one or more of its ecDTx, which the Company expects will take several years and may never occur. As of June 30, 2025, the Company had an accumulated deficit of $232.9 million, and, during the six months ended June 30, 2025, the Company incurred a net loss of $31.4 million and had negative cash flows from operations of $26.4 million. As the Company continues to pursue its business plan, it will need to acquire a substantial amount of additional funding until such time as it is able to generate significant revenues to fund its research and development activities and operations. Accordingly, the Company expects to finance its cash requirements through equity offerings, debt financings, or other capital sources, including potential collaborations, licenses, and other similar arrangements. There can be no assurance that the Company will be successful in acquiring additional funding or that any additional funding would be sufficient to continue operations in future periods.

***Basis of Presentation***

The accompanying unaudited condensed financial statements have been prepared in accordance with United States generally accepted accounting principles (U.S. GAAP) and the requirements of the SEC for interim reporting. As permitted under those rules, certain footnote disclosures or other financial information that are normally required by U.S. GAAP have been condensed or omitted. The condensed financial statements are presented in U.S. dollars. Any reference in these notes to applicable guidance is meant to refer to U.S. GAAP as found in the Accounting Standards Codification (ASC) and Accounting Standards Updates (ASU) promulgated by the Financial Accounting Standards Board (FASB).

The condensed balance sheet as of June 30, 2025, the condensed statements of operations and comprehensive loss for the six months ended June 30, 2025 and 2024, the condensed statements of convertible preferred stock and stockholders' equity/ (deficit) for the six months ended June 30, 2025 and 2024, and the condensed statements of cash flows for the six months ended June 30, 2025 and 2024 are unaudited. These unaudited condensed financial statements have been prepared on the same basis as the annual financial statements and, in the opinion of management, reflect all adjustments, which include only normal recurring adjustments, necessary to present fairly the Company's financial position, results of operations, and cash flows for the interim period presented. The financial data and the other financial information contained in these notes to the condensed financial statements are also unaudited. The results of operations for the six months ended June 30, 2025 are not necessarily indicative of the results to be expected for the year ending December 31, 2025 or for any other future annual or interim period. The condensed balance sheet as of December 31, 2024 included herein was derived from the audited financial statements as of that date. The unaudited condensed financial statements and these notes thereto should be read in conjunction with the Company's audited financial statements and the notes thereto included in the Company's Annual Report on Form 10-K (2024 10-K) for the year ended December 31, 2024 filed with the SEC on March 27, 2025.

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

The Company's significant accounting policies are disclosed in Note 2 to the audited financial statements included in the Company's 2024 10-K. There were no material changes to the Company's significant accounting policies during the six months ended June 30, 2025.

The Company qualifies as an "emerging growth company" (EGC) as defined in the Jumpstart Our Business Startups Act of 2012, as amended (JOBS Act). The JOBS Act permits EGCs such as the Company to take advantage of an extended transition period to comply with new or revised financial accounting standards applicable to public companies until those standards would otherwise apply to nonpublic companies. The Company has elected not to "opt out" of such extended transition period, which means that when an accounting standard is issued or revised and it has different application dates for public or nonpublic companies, the Company can adopt the new or revised standard at the time nonpublic companies adopt the new or revised standard and can do so until such time that it either (i) irrevocably elects to "opt out" of such extended transition period or (ii) no longer qualifies as an EGC.

***Segment Reporting***

Operating segments are identified as components of an enterprise about which discrete financial information is available for evaluation by the chief operating decision-maker (CODM) in making decisions regarding resource allocation and assessing performance. The Company operates and manages its business as one reporting and one operating segment, which is the business of designing and developing ecDTx, for which no revenue has been recorded. All of the Company's long-lived assets are located in the United States. The Company's CODM is its Chief Executive Officer. For purposes of assessing the Company's financial performance and making resource allocation decisions, the CODM reviews total expenses, as well as expenses by nature.

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**Boundless Bio, Inc.**

**Notes to Condensed Financial Statements (Unaudited)**

***Recent Accounting Pronouncements Not Yet Adopted***

As of June 30, 2025, several new accounting pronouncements had been issued by the FASB with future adoption dates. All applicable accounting pronouncements will be adopted by the Company by the date required. Management is reviewing the impact of adoption of all pending accounting pronouncements but is not yet in a position to determine the impact on the Company's condensed financial statements and the notes thereto.

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

The following tables summarize the Company's financial assets measured at fair value on a recurring basis and their respective input levels based on the fair value hierarchy described in Note 2 to the audited financial statements included in the Company's 2024 10-K (in thousands):

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| | | | | |
|:---|:---|:---|:---|:---|
|  |  | **Fair Value Measurements Using** | **Fair Value Measurements Using** | **Fair Value Measurements Using** |
| **As of June 30, 2025** | **Amount** | **Level 1** | **Level 2** | **Level 3** |
| **Assets** |  |  |  |  |
| Money market funds (1) | $11797 | $11797 | $— | $— |
| U.S. government obligations (2) | 112451 |  | 112451 |  |
| Total fair value of assets | $124248 | $11797 | $112451 | $— |

---

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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(1)Included in cash and cash equivalents on the balance sheets.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(2)Included in short-term investments on the balance sheets.

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| | | | | |
|:---|:---|:---|:---|:---|
|  |  | **Fair Value Measurements Using** | **Fair Value Measurements Using** | **Fair Value Measurements Using** |
| **As of December 31, 2024** | **Amount** | **Level 1** | **Level 2** | **Level 3** |
| **Assets** |  |  |  |  |
| Money market funds (1) | $24889 | $24889 | $— | $— |
| U.S. government obligations (2) | 118289 |  | 118289 |  |
| Corporate debt securities (2) | 7238 |  | 7238 |  |
| Total fair value of assets | $150416 | $24889 | $125527 | $— |

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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(1)Included in cash and cash equivalents on the balance sheets.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;(2)Included in short-term investments on the balance sheets.

The Company's money market funds are classified as Level 1 because they are valued using quoted market prices. The Company's investments consist of available-for-sale securities and are classified as Level 2 because their value is based on valuations using significant inputs derived from or corroborated by observable market data. No Level 3 assets were held during the periods presented.

There were no transfers of assets between fair value levels for any period presented.

**4.** **Investments**

The following tables summarize investments accounted for as available-for-sale securities (in thousands):

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| | | | | |
|:---|:---|:---|:---|:---|
|  | **As of June 30, 2025** | **As of June 30, 2025** | **As of June 30, 2025** | **As of June 30, 2025** |
|  | **Acquisition<br>Cost** | **Unrealized<br>Gain** | **Unrealized<br>Loss** | **Estimated Fair <br>Value** |
| Money market funds | $11797 | $— | $— | $11797 |
| U.S. government obligations | 112456 | 12 | (17) | 112451 |
| &nbsp;&nbsp;&nbsp;&nbsp;Total cash equivalents and investments | $124253 | $12 | $(17) | $124248 |
| Classified as: |  |  |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Cash equivalents |  |  |  | $11797 |
| &nbsp;&nbsp;&nbsp;&nbsp;Short-term investments |  |  |  | 112451 |
| Total cash equivalents and investments |  |  |  | $124248 |

---

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**Boundless Bio, Inc.**

**Notes to Condensed Financial Statements (Unaudited)**

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| | | | | |
|:---|:---|:---|:---|:---|
|  | **As of December 31, 2024** | **As of December 31, 2024** | **As of December 31, 2024** | **As of December 31, 2024** |
|  | **Acquisition<br>Cost** | **Unrealized<br>Gain** | **Unrealized<br>Loss** | **Estimated Fair <br>Value** |
| Money market funds | $24889 | $— | $— | $24889 |
| U.S. government obligations | 118170 | 121 | (2) | 118289 |
| Corporate debt securities | 7236 | 2 |  | 7238 |
| &nbsp;&nbsp;&nbsp;&nbsp;Total cash equivalents and investments | $150295 | $123 | $(2) | $150416 |
| Classified as: |  |  |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Cash equivalents |  |  |  | $24889 |
| &nbsp;&nbsp;&nbsp;&nbsp;Short-term investments |  |  |  | 125527 |
| Total cash equivalents and investments |  |  |  | $150416 |

---

On June 30, 2025 and December 31, 2024, the remaining contractual maturities of all the Company's available-for-sale investments were less than 12 months. As of June 30, 2025 and December 31, 2024, the Company has not established an allowance for credit losses for any of its available-for-sale securities.

As of June 30, 2025, there were 21 available-for-sale securities, with an estimated fair value of $78.6 million in gross unrealized loss positions. As of December 31, 2024, there was one available-for-sale security, with an estimated fair value of $8.0 million in a gross unrealized loss position. Based on its review of these investments, the Company believes that the unrealized losses reflect the impact of the rising interest rate environment and were not other-than-temporary in nature.

**5.** **Property and Equipment**

Property and equipment, net consisted of the following (in thousands):

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| | | |
|:---|:---|:---|
|  | **As of June 30,** | **As of December 31,** |
|  | **2025** | **2024** |
| Lab equipment | $4374 | $4338 |
| Computers and software | 899 | 895 |
| Leasehold improvements | 1030 | 981 |
| Furniture and fixtures | 1834 | 1816 |
| Total property and equipment | 8137 | 8030 |
| Less accumulated depreciation and amortization | (4343) | (3709) |
| &nbsp;&nbsp;&nbsp;&nbsp; Property and equipment, net | $3794 | $4321 |

---

Depreciation and amortization expense related to property and equipment was $0.3 million and $0.6 million for the three and six months ended June 30, 2025, respectively, and $0.3 million and $0.5 million for the three and six months ended June 30, 2024, respectively.

**6.** **Accounts Payable and Accrued Liabilities**

Accounts payable and accrued liabilities consisted of the following (in thousands):

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| | | |
|:---|:---|:---|
|  | **As of June 30,** | **As of December 31,** |
|  | **2025** | **2024** |
| Accounts payable | $2294 | $1274 |
| Accrued research and development costs | 3058 | 2584 |
| Other accrued liabilities | 503 | 1496 |
| &nbsp;&nbsp;&nbsp;&nbsp;Total accounts payable and accrued liabilities | $5855 | $5354 |

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**7.** **Lease Agreements**

***2024 Lease***

In December 2021, the Company entered into a non-cancelable facility lease for approximately 80,168 square feet of lab and office space in San Diego, California (the 2024 Lease). The 2024 Lease commenced in November 2024 and has a 120-month term from

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**Boundless Bio, Inc.**

**Notes to Condensed Financial Statements (Unaudited)**

the lease commencement date, with base rent payments under the lease commencing in July 2025, after an abatement period of approximately nine months, and continuing through the conclusion of the term. The 2024 Lease includes base rent payments totaling $72.5 million, as well as additional payment obligations for common area maintenance and property taxes. The Company has the right to extend the term of the 2024 Lease for an additional 60 months; however, this option has not been included in the lease term as it is not reasonably assured of exercise. Additionally, as a security deposit under the 2024 Lease, the Company is required to maintain a standby letter-of-credit in the amount of $560,000, which must remain in place until November 2034 and is classified as restricted cash on the balance sheet. The Company has recorded an operating lease liability based on the present value of the lease payments using an estimated incremental borrowing rate of approximately 8.3% as the 2024 Lease does not have a stated rate and the implicit rate was not readily determinable, and a right-of-use (ROU) asset based on the corresponding operating lease liability. The net ROU asset and associated lease liability are reflected in the Company's balance sheet as of June 30, 2025.

***Operating leases***

Lease expense under the 2024 Lease and a leasing arrangement for the Company's prior corporate headquarters (lab and office space) that ended in November 2024 were approximately $2.4 million and $0.7 million, which includes operating lease costs of $1.8 million and $0.7 million, and variable lease costs of $0.6 million and $0, for the three months ended June 30, 2025 and 2024, respectively. Lease expense under the 2024 Lease and the leasing arrangement for the Company's prior corporate headquarters were approximately $4.7 million and $1.3 million, which includes operating lease costs of $3.7 million and $1.3 million, and variable lease costs of $1.0 million and $0, for the six months ended June 30, 2025 and 2024, respectively.

The Company paid $0.1 million and $1.4 million for operating lease liabilities, which was included in the operating activities section of the condensed statements of cash flows for the six months ended June 30, 2025 and 2024, respectively. The remaining lease term and the discount rate of the Company's operating lease was 9.3 years and 8.3% at June 30, 2025. The remaining lease term and the discount rate of the Company's operating lease was 9.8 years and 8.3% at December 31, 2024. The remaining lease term does not include the renewal option. The 2024 Lease does not contain any material residual value guarantees or material restrictive covenants.

Future minimum lease payments under the 2024 Lease as of June 30, 2025, exclusive of future variable lease payments, are as follows (in thousands):

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| | |
|:---|:---|
| **Year ending December 31,** |  |
| 2025 (remaining six months) | $2484 |
| 2026 | 7056 |
| 2027 | 7259 |
| 2028 | 7469 |
| 2029 | 7684 |
| Thereafter | 40387 |
| &nbsp;&nbsp;Total minimum lease payments | $72339 |
| Less: Amount representing interest | (22829) |
| &nbsp;&nbsp;Operating lease liabilities | $49510 |

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**8.** **Commitments and Contingencies**

***Contracts***

The Company enters into contracts in the normal course of business with various third parties for preclinical research studies, clinical trials, testing, manufacturing, and other services. These contracts generally provide for termination upon notice and are cancellable without significant penalty or payment and do not contain any minimum purchase commitments.

***Indemnification Agreements***

In the ordinary course of business, the Company may provide indemnification of varying scope and terms to vendors, lessors, business partners, and other parties with respect to certain matters including, but not limited to, losses arising out of breach of such agreements or from intellectual property infringement claims made by third parties. In addition, the Company has entered into indemnification agreements with its officers and members of its board of directors that require the Company, among other things, to indemnify them against certain liabilities that may arise by reason of their status or service as officers or directors. The maximum

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**Boundless Bio, Inc.**

**Notes to Condensed Financial Statements (Unaudited)**

potential future payments the Company could be required to make under these indemnification agreements is, in many cases, unlimited. To date, the Company has not incurred any material costs because of these indemnifications. The Company has not accrued any liabilities related to such indemnification arrangements in its financial statements as of June 30, 2025 or December 31, 2024 because it determined the likelihood of incurring a payment obligation pursuant to such arrangements was not probable.

***Litigation***

Liabilities for loss contingencies arising from claims, assessments, litigation, fines, penalties, and other sources are recorded when it is probable that a liability has been incurred and the amount can be reasonably estimated. There are no matters currently outstanding for which any liabilities have been accrued. The Company was not a defendant in any lawsuit for the six months ended June 30, 2025 or the year ended December 31, 2024.

**9.** **Common Stock**

***Common Stock Reserved for Future Issuance***

Common stock reserved for future issuance consisted of the following (in thousands):

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| | | |
|:---|:---|:---|
|  | **As of June 30,** | **As of December 31,** |
|  | **2025** | **2024** |
| Common stock options issued and outstanding | 4647 | 3818 |
| Equity awards available for future issuance | 2934 | 2648 |
| Shares available for purchase under employee stock purchase plan | 325 | 187 |
| &nbsp;&nbsp;&nbsp;&nbsp;Total | 7906 | 6653 |

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**10.** **Stock-Based Compensation**

***Equity Incentive Plan***

In March 2024, the Company's board of directors adopted, and the Company's stockholders approved, the 2024 Incentive Award Plan (the Plan), which became effective in connection with the IPO and has a term of ten years. As of June 30, 2025, a total of 3,765,892 shares of common stock were authorized for issuance under the Plan, which includes a January 1, 2025 increase of 1,115,002 shares, pursuant to the evergreen provision of the Plan. See Note 11 to the audited financial statements included in the Company's 2024 10-K for a description of the evergreen provision of the Plan. On June 30, 2025, 2,934,333 of these shares were available for grant under the Plan.

Prior to the adoption of the Plan, the Company had awarded common stock options under the 2018 Equity Incentive Plan (as amended, the Predecessor Plan). Under the provisions of the Plan, the shares subject to awards issued under the Predecessor Plan that were outstanding as of March 27, 2024, the effective date of the Plan, and that are subsequently cancelled or forfeited, will become available for issuance under, and will increase the number of shares that may be issued under, the Plan.

In August 2024, the compensation committee of the Company's board of directors, as administrator of the Plan and the Predecessor Plan, approved an option repricing (2024 Repricing), which was effective on August 19, 2024 (the Repricing Effective Date). The repricing applied to options to purchase up to an aggregate of 3,484,346 shares of the Company's common stock with an exercise price per share in excess of the closing price per share of the Company's common stock on the Repricing Effective Date, held by eligible employees of the Company that were granted under the Plan or the Predecessor Plan and were outstanding as of the Repricing Effective Date (the Repriced Options). See Note 11 to the audited financial statements included in the Company's 2024 10-K for a description of the 2024 Repricing.

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**Boundless Bio, Inc.**

**Notes to Condensed Financial Statements (Unaudited)**

***Stock Options*** 

Stock option activity under the Plan and the Predecessor Plan and certain other related information is as follows (in thousands except weighted-average exercise price and remaining term):

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| | | | | |
|:---|:---|:---|:---|:---|
|  | **Number** | **Weighted-<br>Average<br>Exercise<br>Price** | **Weighted-<br>Average<br>Remaining<br>Term (years)** | **Aggregate-<br>Intrinsic<br>Value** |
| Balance as of December 31, 2024 | 3818 | $6.37 | 7.2 | $— |
| &nbsp;&nbsp;&nbsp;&nbsp;Granted | 1508 | $2.29 |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Exercised |  | $— |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Forfeited and expired | (679) | $5.24 |  |  |
| Balance as of June 30, 2025 | 4647 | $5.10 | 8.0 | $— |
| Vested and expected to vest at June 30, 2025 | 4647 | $5.10 | 8.0 | $— |
| Exercisable as of June 30, 2025 | 2048 | $5.26 | 6.8 | $— |

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Aggregate intrinsic value in the above table is the difference between the estimated fair value of the Company's common stock as of either June 30, 2025 or December 31, 2024, and the exercise price of stock options that had exercise prices below that value.

For the Repriced Options, the weighted-average prices and intrinsic value information in the table above is calculated based on the exercise price per share that applied immediately prior to the Repricing Effective Date pending satisfaction of the requisite service requirement or other service conditions.

The options exercised during the six months ended June 30, 2024 had an insignificant intrinsic value at exercise. No options were exercised during the six months ended June 30, 2025.

***Employee Stock Purchase Plan***

In March 2024, the Company's board of directors adopted, and the Company's stockholders approved, the Company's 2024 Employee Stock Purchase Plan (ESPP), which became effective in connection with the IPO. On January 1, 2025, pursuant to the evergreen provision of the ESPP, the aggregate number of shares that may be issued under the ESPP was automatically increased by 223,000 shares to 454,919. See Note 11 to the audited financial statements included in the Company's 2024 10-K for a description of the evergreen provision of the ESPP.

The Company recognized stock-based compensation expense related to the ESPP of $0.2 million and $0.3 million for the three months ended June 30, 2025 and 2024, respectively, and $0.3 million and $0.3 million for the six months ended June 30, 2025 and 2024, respectively.

The Company issued and sold 85,568 and 0 shares under the ESPP during the six months ended June 30, 2025 and 2024, respectively.

***Stock-Based Compensation Expense***

Stock-based compensation expense, including the expense related to the ESPP, as recorded in the accompanying condensed statements of operations and comprehensive loss was as follows (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** |
| Research and development | $642 | $888 | $1357 | $1412 |
| General and administrative | 1051 | 1247 | 2133 | 2051 |
| Total stock-based compensation | $1693 | $2135 | $3490 | $3463 |

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**Boundless Bio, Inc.**

**Notes to Condensed Financial Statements (Unaudited)**

As of June 30, 2025, unrecognized compensation cost related to outstanding stock options (all of which have time-based vesting) was $11.8 million, which is expected to be recognized over a weighted-average period of 2.5 years.

As of June 30, 2025, unrecognized compensation cost related to the ESPP was $0.7 million, which is expected to be recognized as expense over approximately 1.8 years.

Excluding any effect of the Repriced Options, except for Repriced Options held by employees who experienced a Qualifying Termination (as defined in Note 11 to the audited financial statements included in the Company's 2024 10-K), the weighted-average assumptions used in the Black-Scholes option pricing model to determine the fair value of the stock options granted during the periods indicated in the table were 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,** |
|  | **2025** | **2024** | **2025** | **2024** |
| Expected option life (in years) | 5.9 | 6.0 | 5.9 | 6.0 |
| Assumed volatility | 105.0% | 91.3% | 105.0% | 94.9% |
| Assumed risk-free interest rate | 4.0% | 4.3% | 4.4% | 4.2% |
| Expected dividend yield |  |  |  |  |

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Excluding any effect due to the Repriced Options, except for Repriced Options held by employees who experienced a Qualifying Termination, the weighted-average grant date per share fair value of options granted during the three months ended June 30, 2025 and 2024 were $0.89 and $4.55, respectively, and the weighted-average grant date per share fair value of options granted during the six months ended June 30, 2025 and 2024 were $1.89 and $11.59, respectively.

**11.** **Net Loss Per Common Share**

The following table summarizes the calculation of basic and diluted net loss per common share attributable to common stockholders (in thousands, except per share data):

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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** |
| Net loss | $(15675) | $(16976) | $(31433) | $(32406) |
| Weighted-average shares of common stock used in<br> computing net loss per share, basic and diluted | 22356 | 22023 | 22328 | 11641 |
| Net loss per share, basic and diluted | $(0.70) | $(0.77) | $(1.41) | $(2.78) |

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The Company excluded the following potential shares of its common stock, presented based on amounts outstanding at each period end, from the calculation of diluted net loss per share for the periods indicated because including them would have had an anti-dilutive effect (in thousands):

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| | | |
|:---|:---|:---|
|  | **As of June 30,** | **As of June 30,** |
|  | **2025** | **2024** |
| Options to purchase common stock | 4647 | 4188 |
| Options early exercised subject to future vesting |  | 1 |
| Total | 4647 | 4189 |

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**Boundless Bio, Inc.**

**Notes to Condensed Financial Statements (Unaudited)**

**12.** **Segment Information**

The CODM reviews the budget versus actual expense by nature of expense. The following table sets forth our segment loss disclosure for the three and six months ended June 30, 2025 and 2024 (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** |
| R&D – Compensation and benefits (1) | $3217 | $3679 | $6512 | $7165 |
| R&D – Clinical trial costs | 2448 | 2935 | 5298 | 5532 |
| R&D – Outsourced services & consulting | 3132 | 5363 | 5514 | 10042 |
| R&D – Lab and pharmacology supplies | 256 | 695 | 546 | 1399 |
| R&D – Other costs (2) | 440 | 465 | 1036 | 898 |
| G&A – Compensation and benefits (1) | 1528 | 1645 | 3102 | 3192 |
| G&A – Professional service fees | 810 | 748 | 1807 | 1541 |
| G&A – Insurance | 202 | 213 | 420 | 243 |
| G&A – Other costs (3) | 618 | 595 | 1344 | 967 |
| Facilities related | 2400 | 652 | 4699 | 1304 |
| Stock-based compensation and depreciation | 2010 | 2401 | 4124 | 3991 |
| Total operating expense | 17061 | 19391 | 34402 | 36274 |
| Loss from operations | (17061) | (19391) | (34402) | (36274) |
| Interest and other income, net | 1386 | 2415 | 2969 | 3868 |
| Segment net loss | $(15675) | $(16976) | $(31433) | $(32406) |

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(1)Excludes stock-based compensation expense.

(2)Includes software expense, database subscriptions expense, lab service contract expense, travel expense, and other miscellaneous expenses.

(3)Includes travel expense, public & investor relations expense, software expense, employee training & development expense, and other miscellaneous expenses.

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

*The following discussion and analysis of our financial condition and results of operations should be read in conjunction with our unaudited condensed financial statements and notes thereto included elsewhere in this Quarterly Report on Form 10-Q and with our audited financial statements and notes thereto and management's discussion and analysis of financial condition and results of operations for the year ended December 31, 2024, included in our 2024 10-K. Unless the context requires otherwise, references in this report to "Boundless," the "Company," "we," "us," and "our" refer to Boundless Bio, Inc. In addition, in this report we refer to our extrachromosomal DNA directed therapeutic candidates as "ecDTx," which are under clinical or preclinical investigation and which have not yet been approved for marketing by the FDA or any other regulatory authority.*

**Overview** 

We are a clinical-stage precision oncology company dedicated to unlocking a new paradigm in cancer therapeutics that addresses the significant unmet need in patients with oncogene amplified tumors by interrogating extrachromosomal DNA (ecDNA), a root cause of oncogene amplification observed in 14% to 17% of cancer patients. ecDNA are large circular units of nuclear DNA that are a primary mechanism of gene amplification and are detected only in cancer cells, not in healthy cells. Despite tremendous advancements in treating cancer broadly, patients with oncogene amplified cancers generally derive little benefit from existing therapies, such as molecular targeted therapies or immunotherapies, and have worse survival rates than patients without oncogene amplification.

Using our proprietary Spyglass platform, we identify targets essential for ecDNA functionality in oncogene amplified cancer cells, then design and develop small molecule drugs called ecDNA-directed therapeutic candidates (ecDTx) to inhibit those targets, with the aim to prevent cancer cells from using amplified oncogenes to grow, adapt, and become resistant to existing therapies. Instead of directly targeting the proteins produced by amplified oncogenes, which is the approach of traditional targeted therapies, our ecDTx are intended to be synthetic lethal in tumor cells reliant on amplification biology. In the context of drug development, synthetic lethality is a therapeutic approach wherein using a drug to inhibit one target is lethal to cancer cells harboring a specific genetic alteration to a second target, but not lethal to healthy cells that lack the genetic alteration to the second target. Accordingly, our ecDTx are designed to preferentially kill amplification-dependent cancer cells, but not healthy cells. They are engineered to disrupt the underlying cellular machinery that enables functional amplification. To our knowledge, Spyglass is the only platform in the biopharma industry using ecDNA biology to identify specific druggable targets in oncogene amplified cancers. All of our ecDTx have been discovered internally and we retain global rights for all of our programs.

On May 23, 2025, we announced a portfolio prioritization focused on the following: evaluating our clinical stage ecDTx, BBI-355 and BBI-825, in combination, advancing our Kinesin program with the announcement of a development candidate, BBI-940, and extending our expected cash runway into the first half of 2028, through expected proof-of-concept readouts for each of these programs as further described below.

We have been investigating BBI-355, a novel, oral, selective inhibitor of checkpoint kinase 1 (CHK1) designed to target replication stress in oncogene-amplified cancers, in a first-in-human, Phase 1/2 clinical trial in patients with oncogene amplified cancers. We refer to this trial as POTENTIATE (Precision Oncology Trial Evaluating Novel Therapeutic Interrupting Amplifications Tied to ecDNA). On May 23, 2025, we announced that, with continuous every other day dosing (Q2D), BBI-355 demonstrated a narrow therapeutic index resulting in hematological toxicity at or near doses associated with clinical activity. The combinations of BBI-355 with the EGFR inhibitor erlotinib, and with the FGFR inhibitor futibatinib, were also not well-tolerated with Q2D dosing at exposure levels believed to be required for robust, sustained anti-tumor activity. Based on these findings and market considerations, we discontinued further clinical development in these arms of the POTENTIATE clinical trial.

We also investigated BBI-825, a novel, oral, selective ribonucleotide reductase (RNR) inhibitor, in a first-in-human, Phase 1/2 clinical trial in patients with solid tumors. This trial was called STARMAP (Study Treating Acquired Resistance: MAPK Amplifications). In the STARMAP trial, with a continuous twice daily dosing schedule, we observed a lack of dose proportional pharmacokinetic exposure at steady-state due to BBI-825 inducing its own metabolism in trial subjects. In December 2024, we announced that we would not continue dose escalation of Part 1 or proceed into the Part 2 portion of the STARMAP trial.

Recently, we have observed results in preclinical studies that we believe provide a strong mechanistic rationale to combine BBI-825 with BBI-355 for synergistic anti-tumor activity as a combination regimen that does not require continuous dosing, nor involve overlapping toxicity. The BBI-355/BBI-825 combination demonstrated preclinical evidence of synergistic cytotoxicity in cancer cell lines and tumor regression in mouse xenograft models using weekly dosing at exposures not associated with hematological toxicity. We have now opened the BBI-355/BBI-825 combination arm of the POTENTIATE trial for enrollment. We expect to deliver initial proof-of-concept clinical data within our existing cash runway timeline.

Our next program targets a kinesin involved in DNA segregation, including ecDNA segregation, during mitosis, and, to our knowledge, there have been no prior drug efforts directed against it. We have discovered orally bioavailable, highly selective kinesin

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degraders that have demonstrated potent anti-tumor activity in a range of cancer cell lines, as well as single agent tumor regressions in mouse xenograft cancer models. We selected BBI-940 as the development candidate for our novel Kinesin program and we expect to submit an investigational new drug application (IND) to the FDA in the first half of 2026. We also expect to deliver initial proof-of-concept clinical data on BBI-940 within our existing cash runway timeline.

To assist in identifying patients that may benefit from our ecDTx, we have developed an ecDNA diagnostic, which we internally call ECHO (ecDNA Harboring Oncogenes), to detect ecDNA in patient tumor samples. This test analyzes the genomic data obtained from routine next-generation sequencing (NGS) of patient tumor samples. ECHO is currently being used as a clinical trial assay to determine ecDNA status of patients enrolled in the POTENTIATE trial.

Since we commenced operations in 2018, we have devoted substantially all of our efforts and resources to organizing and staffing our company, business planning, raising capital, building our proprietary Spyglass platform, discovering our ecDTx, developing our ecDNA diagnostic, establishing our intellectual property portfolio, conducting research, preclinical studies, and clinical trials, establishing arrangements with third parties for the manufacture of our ecDTx and related raw materials, and providing general and administrative support for these operations. During this time, we have incurred significant operating losses and, as of June 30, 2025, we had an accumulated deficit of $232.9 million. We expect to continue to incur losses for the foreseeable future, and anticipate these losses will increase substantially as we continue our development of, seek regulatory approval for, and potentially commercialize any of our ecDTx, seek to discover and develop additional ecDTx, develop our ecDNA diagnostic, conduct our ongoing and planned clinical trials and preclinical studies, continue our research and development activities, utilize third parties to manufacture our ecDTx and related raw materials, seek to expand and protect our intellectual property, as well as incur additional costs associated with being a public company. If we obtain regulatory approval for any of our ecDTx, we expect to incur significant commercialization expenses related to product sales, marketing, manufacturing, and distribution. Our net losses may fluctuate significantly from quarter-to-quarter and year-to-year, depending on the timing of our clinical trials, preclinical studies, and our other research and development activities and capital expenditures.

Through June 30, 2025, we have raised a total of $353.8 million to fund our operations primarily from the gross proceeds from the sale and issuance of our convertible preferred and common stock. In April 2024, we completed our initial public offering, or IPO, in which we sold and issued 6,250,000 shares of our common stock for gross proceeds of $100.0 million. In April 2025, we commenced an "at the market" (ATM) offering as defined in Rule 415(a)(4) under the Securities Act, under which we may offer and sell shares of our common stock having an aggregate offering price of up to $14.5 million from time to time through or to our sales agent, as described further under "Liquidity and Capital Resources" below. As of June 30, 2025, we had cash, cash equivalents, and short-term investments of $127.1 million.

On May 23, 2025, in connection with the portfolio prioritization described above, we took steps to streamline our operations, which included a workforce reduction of approximately one-third of our workforce. The workforce reduction was substantially completed as of June 30, 2025, and approximately $1.0 million in related charges, primarily related to one-time severance payments, was recognized in our results of operations for the quarter ended June 30, 2025. Based on our current operating plans, we believe that our existing cash, cash equivalents, and short-term investments will be sufficient to fund our operations into the first half of 2028. We have based this estimate on assumptions that may prove to be wrong, and we could deplete our capital resources sooner than we expect. See "Liquidity and Capital Resources" below for more information.

We do not have any products approved for sale and have not generated any revenue to date. We do not expect to generate any revenue from product sales until we successfully complete development and obtain regulatory approval for one or more of our ecDTx, which we expect will take several years and may never occur. We will need substantial additional funding to support our continuing operations and pursue our long-term business plan, including to complete the development and commercialization of our ecDTx, if approved. Accordingly, until such time as we can generate significant revenue from sales of our ecDTx, if ever, we expect to finance our cash needs through equity offerings, debt financings, or other capital sources, including potential collaborations, licenses, and other similar arrangements. However, we may be unable to raise additional funds or enter such other arrangements when needed on favorable terms or at all. Our failure to raise capital or enter such other arrangements when needed would have a negative impact on our financial condition and could force us to delay, limit, reduce, or terminate our research and development programs or other operations, or grant rights to develop and market ecDTx that we would otherwise prefer to develop and market ourselves.

We do not own or operate, and currently have no plans to establish, any manufacturing facilities. We rely, and expect to continue to rely, on third parties for the manufacture of our ecDTx for preclinical and clinical testing, as well as for commercial manufacture if any of our ecDTx obtain marketing approval. We are working with our current manufacturers to ensure that we will be able to scale up our manufacturing capabilities to support our clinical plans. In addition, we rely on third parties to package, label, store, and distribute our ecDTx, and we intend to rely on third parties for our commercial products if marketing approval is obtained. We believe that this strategy allows us to maintain a more efficient infrastructure by eliminating the need for us to invest in our own manufacturing facilities, equipment, and personnel while also enabling us to focus our expertise and resources on the discovery and development of our ecDTx.

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**Macroeconomic, Political, and Regulatory Environment Considerations**

Uncertainty in the United States and global macroeconomic, political, and regulatory environments present significant risks to our business. Our operating costs, ability to raise additional capital, and stock price could be materially and adversely affected by macroeconomic and geopolitical events and conditions outside of our control, including market volatility, high interest rates, inflation, tariffs and other trade barriers, retaliatory measures taken by foreign countries, slowed economic growth or recession, uncertainty with respect to the federal budget and debt ceiling and potential government shutdowns related thereto, liquidity concerns at financial institutions, supply chain disruptions, military conflicts, and other geopolitical events and instability. Further, one or more of our current service providers, manufacturers, clinical investigative sites, financial institutions, and other partners may be adversely affected by the foregoing risks, which could directly affect our ability to attain our operating goals on schedule and on budget.

In addition, FDA-regulated industries, such as ours, face uncertainty with regard to the regulatory environment we will face as we proceed with research and development and possibly in the future commercialization. Recent initiatives of the current U.S. presidential administration have resulted in significant voluntary and involuntary FDA staff departures and could impact the FDA's ability to retain key personnel and hire additional personnel, which may result in delays or limitations on our ability to obtain guidance from agency staff and slow review times for applications we submit to obtain the requisite regulatory approvals in the future. Moreover, the new presidential administration has taken and may take additional future actions to freeze or reduce federal funding for medical research, which could decrease the ability of facilities that rely on such funding to conduct clinical trials or increase the costs to us of conducting clinical trials at those facilities. There remains general uncertainty regarding future activities. New executive orders, regulations, policies, or guidance could be issued or promulgated that adversely affect us or create a more challenging or costly environment to pursue the development and commercialization of our ecDTx, including in areas relating to regulatory framework and oversight, research and development funding, drug pricing reform, intellectual property rights, global trade policy, and tariffs.

Although, to date, our business has not been materially impacted, the ultimate impact of global economic and market conditions and changes in government agencies, regulations and policies remains highly uncertain and will depend on future developments and factors that continue to evolve. We closely monitor these ongoing developments and the potential impact of these factors on our business, operating expenses, and cash position and, if circumstances warrant, we may make adjustments to our operating plan. For more information regarding these risks and uncertainties, see Item 1A, "Risk Factors," in Part I of our 2024 10-K.

**Components of Our Results of Operations**

***Revenue***

To date, we have not generated any revenue from the sale of products. We do not expect to generate any such revenue unless and until such time that our ecDTx have advanced through clinical development and regulatory approval, if ever. If we fail to complete preclinical and clinical development of ecDTx or obtain regulatory approval for them, our ability to generate future revenues, and our results of operations and financial position would be adversely affected.

***Operating Expenses***

Our operating expenses consist of research and development expenses and general and administrative expenses.

*Research and Development*

Our research and development (R&D) expenses have related primarily to building our Spyglass platform, our ecDTx discovery efforts, our preclinical and clinical development activities, and the development of an ecDNA diagnostic test. R&D expenses are recognized as incurred, and payments made prior to the receipt of goods or services to be used in R&D are capitalized until the goods or services are received. We use internal resources primarily to conduct our research and discovery activities, as well as for managing our preclinical development, process development, manufacturing, and clinical development activities. We track direct costs on a development program specific basis. Indirect costs are not included in program costs, as these costs are general in nature and benefit all our discovery efforts and development programs.

Our direct, or development program specific, R&D costs consist of:

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•costs incurred under agreements with our contract research organizations (CROs), investigative sites, and consultants to conduct our clinical trials and preclinical studies, as well as third party costs related to the development of an ecDNA diagnostic test; and

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•expenses related to manufacturing our ecDTx for clinical trials and preclinical studies, including fees paid to third-party manufacturers.

Our indirect R&D costs include:

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&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•personnel-related costs, including salaries, severance, bonuses, benefits, travel, and stock-based compensation expenses for employees engaged in R&D functions,

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the costs of outside services from third parties, including consultants,

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the costs of lab and pharmacology supplies,

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•facilities-related costs, including rent and maintenance costs, and other costs including insurance, depreciation, supplies, and miscellaneous expenses, and

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•other costs, including costs related to travel, repairs and maintenance, service contracts, computer supplies, software, and publications and subscription services.

Although R&D activities are central to our business model, the successful development of our ecDTx is highly uncertain. There are numerous factors associated with the successful development of any ecDTx, including future trial design and various regulatory requirements, many of which cannot be determined with accuracy at this time based on our stage of development. In addition, future regulatory factors beyond our control may impact our clinical development programs. Product candidates in later stages of development generally have higher development costs than those in earlier stages of development. As a result, we expect that our R&D expenses will increase substantially for the foreseeable future as we continue to conduct our ongoing R&D activities, advance preclinical research programs toward clinical development, conduct clinical trials, and maintain, expand, protect, and enforce our intellectual property portfolio.

Our future R&D expenses may vary significantly based on a wide variety of factors such as:

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the number, scope, rate of progress, expense, and results of our discovery and preclinical activities and clinical trials;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•per patient trial costs;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the number of trials required for approval;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the number of sites included in the trials;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the countries in which the trials are conducted;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the length of time required to enroll eligible patients;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the cost of developing an ecDNA diagnostic test;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the number of patients that participate in the trials;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the number of doses that patients receive;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the drop-out or discontinuation rates of patients;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the potential additional safety monitoring requested by regulatory agencies;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the duration of patient participation in the trials and follow-up;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the cost and timing of manufacturing our ecDTx;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the phase of development of our ecDTx;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•a decision not to advance the clinical development of an ecDTx;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the costs of laboratory supplies and equipment and pharmacology supplies for our preclinical activities and clinical trials;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the extent of changes in government regulation and regulatory guidance;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•disruptions at the FDA that hinder its ability to perform routine activities or function in the normal course;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the efficacy and safety profile of our ecDTx;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the timing, receipt, and terms of any approvals from applicable regulatory authorities; and

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the extent to which we establish collaboration, license, or other arrangements.

A change in the outcome of any of these variables with respect to development of any of our ecDTx could significantly change the costs and timing associated with the development of that ecDTx. While we made a strategic decision in late 2024 not to advance the STARMAP clinical trial of BBI-825, we expect to incur significant R&D expenses in 2025 in connection with winding down that trial. In addition, while, in connection with the portfolio prioritization discussed above, we decided to discontinue further clinical development in the current arms of the POTENTIATE clinical trial, we expect to incur significant R&D expenses relating to winding down those arms of the trial and initiating clinical development of the BBI-355/BBI-825 combination within the POTENTIATE trial in 2025.

The process of conducting the necessary preclinical and clinical research to obtain regulatory approval is costly and time-consuming. The actual probability of success for our current ecDTx or any future ecDTx may be affected by a variety of factors. We may never succeed in achieving regulatory approval for any of our ecDTx. Preclinical and clinical development timelines, the probability of success, and total development costs can differ materially from expectations. As we have done in recent months, we anticipate that we will continue to make determinations as to which ecDTx to pursue and how much funding to direct to each ecDTx on an ongoing basis in response to the results of ongoing and future preclinical studies and clinical trials, regulatory developments, and our ongoing assessments as to each ecDTx's commercial potential. We will need to raise substantial additional capital in the future. In addition, we cannot forecast which ecDTx may be subject to future collaborations, when such arrangements will be secured, if at all, and to what degree such arrangements would affect our development plans and capital requirements.

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*General and Administrative*

General and administrative (G&A) expenses consist primarily of personnel-related costs, including salaries, bonuses, benefits, travel, and stock-based compensation expenses for employees in executive, accounting and finance, business development, legal, and other administrative functions. Other significant costs include allocated facility-related costs, legal fees relating to intellectual property and corporate matters, professional fees for accounting and consulting services, insurance costs, and business development expenses.

We expect that our G&A expenses will increase substantially in the future as we grow our business and, if any ecDTx receive marketing approval, when we commence commercialization activities. We also expect to continue to incur increased facilities-related costs related to our current headquarters facilities, as well as increased expenses related to audit, legal, regulatory, and tax-related services associated with maintaining compliance with securities exchange listing and SEC requirements, director and officer insurance premiums, and investor relations costs associated with operating as a public company.

***Other Income, Net***

Other income, net consists primarily of interest income earned on our cash, cash equivalents, and investments.

**Results of Operations**

***Comparison of the Three Months Ended June 30, 2025 and 2024***

The following table summarizes our results of operations for each of the periods indicated (in thousands):

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| | | | |
|:---|:---|:---|:---|
|  | **Three Months Ended<br>June 30,** | **Three Months Ended<br>June 30,** |  |
|  | **2025** | **2024** | **Change** |
| Operating expenses: |  |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Research and development | $12218 | $14735 | $(2517) |
| &nbsp;&nbsp;&nbsp;&nbsp;General and administrative | 4843 | 4656 | 187 |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Total operating expenses | 17061 | 19391 | (2330) |
| Loss from operations | (17061) | (19391) | 2330 |
| Other income, net: |  |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Interest income | 1386 | 2382 | (996) |
| &nbsp;&nbsp;&nbsp;&nbsp;Other income/ (expense), net | - | 33 | (33) |
| Total other income, net | 1386 | 2415 | (1029) |
| Net loss | $(15675) | $(16976) | $1301 |

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*Research and Development Expenses* 

The following table summarizes our R&D expenses for each of the periods indicated (in thousands):

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| | | | |
|:---|:---|:---|:---|
|  | **Three Months Ended<br>June 30,** | **Three Months Ended<br>June 30,** |  |
|  | **2025** | **2024** | **Change** |
| **Direct program costs:** |  |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;BBI-355 | $2808 | $2761 | $47 |
| &nbsp;&nbsp;&nbsp;&nbsp;BBI-825 | 839 | 3325 | (2486) |
| &nbsp;&nbsp;&nbsp;&nbsp;Other development programs | 1582 | 1068 | 514 |
| Total direct program costs | 5229 | 7154 | (1925) |
| **Indirect program costs:** |  |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Personnel-related (including stock compensation) | 3862 | 4573 | (711) |
| &nbsp;&nbsp;&nbsp;&nbsp;Outside services and consulting | 426 | 1196 | (770) |
| &nbsp;&nbsp;&nbsp;&nbsp;Lab and pharmacology supplies | 192 | 642 | (450) |
| &nbsp;&nbsp;&nbsp;&nbsp;Facilities-related (including depreciation) | 2082 | 710 | 1372 |
| &nbsp;&nbsp;&nbsp;&nbsp;Other indirect program costs | 427 | 460 | (33) |
| Total indirect program costs | 6989 | 7581 | (592) |
| Total R&D expenses | $12218 | $14735 | $(2517) |

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R&D expenses were $12.2 million and $14.7 million for the three months ended June 30, 2025 and 2024, respectively. The $2.5 million decrease was primarily attributable to (i) a $1.9 million decrease in direct program costs, driven by reduced spending on our Phase 1/2 STARMAP clinical trial of BBI-825, partially offset by increased investment in our ongoing Phase 1/2 POTENTIATE clinical trial of BBI-355 and other development programs, (ii) a $0.7 million decrease in personnel-related costs primarily due to the use of federal research tax credit carryforwards to reduce payroll taxes, (iii) a $0.8 million decrease in outside services and consulting costs, and (iv) a $0.5 million decrease in laboratory and pharmacology supply costs due to lower material needs in certain early-stage development programs. These decreases were partially offset by a $1.4 million increase in facilities-related expenses, primarily due to commencement of the lease related to our corporate headquarters in the fourth quarter of 2024.

*General and Administrative Expenses*

G&A expenses were $4.8 million and $4.6 million for the three months ended June 30, 2025 and 2024, respectively. The $0.2 million increase in G&A expenses was primarily attributable to a $0.5 million increase in facilities-related costs primarily due to commencement of the lease related to our corporate headquarters in the fourth quarter of 2024, partially offset by (i) a $0.2 million decrease in stock-based compensation, and (ii) a $0.1 million decrease in other personnel-related costs.

*Other Income, Net* 

Other income, net was $1.4 million and $2.4 million for the three months ended June 30, 2025 and 2024, respectively. The $1.0 million decrease resulted from a reduction in the interest income generated by our available-for-sale investment securities portfolio due to the decrease in the amount of cash equivalents available for investing purposes as well as the decline in the market yields available for such investment securities compared to the prior year period.

***Comparison of the Six Months Ended June 30, 2025 and 2024***

The following table summarizes our results of operations for each of the periods indicated (in thousands):

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| | | | |
|:---|:---|:---|:---|
|  | **Six Months Ended<br>June 30,** | **Six Months Ended<br>June 30,** |  |
|  | **2025** | **2024** | **Change** |
| Operating expenses: |  |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Research and development | $24355 | $27864 | $(3509) |
| &nbsp;&nbsp;&nbsp;&nbsp;General and administrative | 10047 | 8410 | 1637 |
| &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Total operating expenses | 34402 | 36274 | (1872) |
| Loss from operations | (34402) | (36274) | 1872 |
| Other income, net: |  |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Interest income | 2971 | 3803 | (832) |
| &nbsp;&nbsp;&nbsp;&nbsp;Other income/ (expense), net | (2) | 65 | (67) |
| Total other income, net | 2969 | 3868 | (899) |
| Net loss | $(31433) | $(32406) | $973 |

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*Research and Development Expenses* 

The following table summarizes our R&D expenses for each of the periods indicated (in thousands):

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| | | | |
|:---|:---|:---|:---|
|  | **Six Months Ended<br>June 30,** | **Six Months Ended<br>June 30,** |  |
|  | **2025** | **2024** | **Change** |
| **Direct program costs:** |  |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;BBI-355 | $5776 | $4993 | $783 |
| &nbsp;&nbsp;&nbsp;&nbsp;BBI-825 | 1989 | 5461 | (3472) |
| &nbsp;&nbsp;&nbsp;&nbsp;Other development programs | 2397 | 2288 | 109 |
| Total direct program costs | 10162 | 12742 | (2580) |
| **Indirect program costs** |  |  |  |
| &nbsp;&nbsp;&nbsp;&nbsp;Personnel-related (including stock compensation) | 7871 | 8586 | (715) |
| &nbsp;&nbsp;&nbsp;&nbsp;Outside services and consulting | 795 | 2981 | (2186) |
| &nbsp;&nbsp;&nbsp;&nbsp;Lab and pharmacology supplies | 425 | 1249 | (824) |
| &nbsp;&nbsp;&nbsp;&nbsp;Facilities-related (including depreciation) | 4092 | 1417 | 2675 |
| &nbsp;&nbsp;&nbsp;&nbsp;Other indirect program costs | 1010 | 889 | 121 |
| Total indirect program costs | 14193 | 15122 | (929) |
| Total R&D expenses | $24355 | $27864 | $(3509) |

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R&D expenses were $24.4 million and $27.9 million for the six months ended June 30, 2025 and 2024, respectively. The $3.5 million decrease was primarily attributable to (i) a $2.6 million decrease in direct program costs, driven by reduced spending on our Phase 1/2 STARMAP clinical trial of BBI-825, partially offset by increased investment in our ongoing Phase 1/2 POTENTIATE clinical trial of BBI-355 and other development programs, (ii) a $0.7 million decrease in personnel-related costs primarily due to the use of federal research tax credit carryforwards to reduce payroll taxes, (iii) a $2.2 million decrease in outside services and consulting costs, and (iv) a $0.8 million decrease in laboratory and pharmacology supply costs due to lower material needs in certain early-stage development programs. These decreases were partially offset by a $2.7 million increase in facilities-related expenses, primarily due to commencement of the lease related to our corporate headquarters in the fourth quarter of 2024.

*General and Administrative Expenses*

G&A expenses were $10.0 million and $8.4 million for the six months ended June 30, 2025 and 2024, respectively. The $1.6 million increase in G&A expenses was primarily attributable to (i) a $1.0 million increase in facilities-related costs primarily due to commencement of the lease related to our corporate headquarters in the fourth quarter of 2024, and (ii) a $0.5 million increase in professional service fees primarily for legal and accounting services related to our shelf registration statement on Form S-3 and ATM offering.

*Other Income, Net*

Other income, net was $3.0 million and $3.9 million for the six months ended June 30, 2025 and 2024, respectively. The $0.9 million decrease resulted from a reduction in the interest income generated by our available-for-sale investment securities portfolio due to the decrease in the amount of cash equivalents available for investing purposes as well as the decline in the market yields available for such investment securities compared to the prior year period.

**Liquidity and Capital Resources**

***Sources of Liquidity***

Through June 30, 2025, we have raised a total of $353.8 million to fund our operations primarily from the gross proceeds from the sale and issuance of shares of our convertible preferred stock prior to our IPO and the sale and issuance of 6,250,000 shares of our common stock in our IPO, which closed in April 2024. Our IPO generated gross proceeds of $100.0 million, which resulted in net proceeds to us of approximately $87.7 million, after deducting underwriting discounts and commissions and other offering expenses.

In April 2025, we entered into an Open Market Sale Agreement<sup>SM</sup> (the Sales Agreement) with Jefferies LLC (the Agent) under which we may, from time to time, sell shares of our common stock in ATM offerings through or to the Agent, as sales agent or principal. The shares of common stock will be offered and issued pursuant to our shelf registration statement on Form S-3 (File No. 333-286302), including the Sales Agreement prospectus contained therein, filed with the SEC on April 1, 2025 and declared effective by the SEC on April 10, 2025. Pursuant to the Sales Agreement prospectus, we may sell shares of our common stock having an aggregate offering price

------

of up to $14.5 million. Sales of the shares of common stock, if any, will be made at prevailing market prices at the time of sale, or as otherwise agreed with the Agent. The Agent will receive a commission from us of up to 3.0% of the gross proceeds of any shares of common stock sold under the Sales Agreement. We are not obligated to sell, and the Agent is not obligated to buy or sell, any shares of our common stock under the Sales Agreement. No assurance can be given that we will sell any shares of our common stock under the Sales Agreement, or, if we do, as to the price or amount of shares of common stock that are sold or the dates when such sales will take place. As of the date of this report, no shares have been sold under the Sales Agreement.

***Future Funding Requirements***

As of June 30, 2025, we had cash, cash equivalents, and short-term investments of $127.1 million. Based upon our current operating plans, we believe that our existing cash, cash equivalents, and short-term investments will be sufficient to fund our operations into the first half of 2028. However, our forecast of the period of time through which our financial resources will be adequate to support our operations is a forward-looking statement that involves risks and uncertainties, and actual results could vary materially. We have based this estimate on assumptions that may prove to be wrong, and we could deplete our capital resources sooner than we expect. Additionally, the process of conducting preclinical studies, manufacturing ecDTx, developing our ecDNA diagnostic, and testing ecDTx in clinical trials is costly, and the timing of progress and expenses in these studies and trials is uncertain.

We have incurred significant operating losses since our inception and, as of June 30, 2025, we had an accumulated deficit of $232.9 million. We expect to continue to incur losses for the foreseeable future, and we anticipate these losses will increase substantially as we continue our development of, seek regulatory approval for, and potentially commercialize any of our ecDTx, seek to discover and develop additional ecDTx, develop our ecDNA diagnostic, conduct our ongoing and planned clinical trials and preclinical studies, continue our research and development activities, utilize third parties to manufacture our ecDTx and related raw materials, seek to expand and protect our intellectual property, as well as incur additional costs associated with being a public company. If we obtain regulatory approval for any of our ecDTx, we expect to incur significant commercialization expenses related to product sales, marketing, manufacturing, and distribution. Our net losses may fluctuate significantly from quarter-to-quarter and year-to-year, depending on the timing of our clinical trials, preclinical studies, and our other research and development activities and capital expenditures.

Our future capital requirements are difficult to predict and depend on many factors, including but not limited to:

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the initiation, type, number, scope, progress, expansions, results, costs, and timing of clinical trials and preclinical studies of our ecDTx that we are pursuing or may choose to pursue in the future, including the costs of any third-party products used as combination agents in any future combination clinical trials;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the costs and timing of manufacturing for our ecDTx, including commercial manufacture at sufficient scale, if any ecDTx is approved;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the costs and timing of developing ecDNA diagnostics, if required, and the outcome of their regulatory review;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the costs, timing, and outcome of regulatory meetings and reviews of our ecDTx;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•changes in regulatory policies or approval pathways;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•disruptions at the FDA that hinder its ability to perform routine activities or function in the normal course;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the costs of obtaining, maintaining, enforcing, and protecting our patents and other intellectual property and proprietary rights;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the costs and timing of purchasing laboratory supplies and equipment and pharmacology supplies for our preclinical activities and clinical trials;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•potential additional costs not currently contemplated due to events that may occur as a result of, or that are associated with, streamlining our operations in connection with the portfolio prioritization discussed above, including the workforce reduction;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the costs associated with hiring additional personnel and consultants, as needed, to support our clinical and preclinical development efforts;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the costs and timing of establishing or securing sales and marketing capabilities if any ecDTx is approved;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•our ability to achieve sufficient market acceptance, coverage, and adequate reimbursement from third-party payors and adequate market share and revenue for any approved products;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•patients' willingness to pay out-of-pocket for any approved products in the absence of coverage and/or adequate reimbursement from third-party payors;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the terms and timing of establishing and maintaining collaborations, licenses, and other similar arrangements;

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•costs associated with any products or technologies that we may in-license or acquire; and

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;•the effects of competing technological and market developments as well as disruptions to and volatility in the credit and financial markets.

------

We have no committed sources of capital. Until we can generate sufficient product revenue to finance our cash requirements, if ever, we expect to finance our future cash needs primarily through equity offerings (including through the Sales Agreement), debt financings, or other capital sources, including potential collaborations, licenses, and other similar arrangements. However, we may be unable to raise additional funds or enter such other arrangements when needed on favorable terms or at all. To the extent that we raise additional capital through the sale of equity or convertible debt securities, the ownership interest of our stockholders will be or could be diluted, and the terms of these securities may include liquidation or other preferences that adversely affect the rights of our common stockholders. Debt financing, if available, may involve agreements that include covenants limiting or restricting our ability to take specific actions, such as incurring additional debt, making capital expenditures, or declaring dividends. If we raise additional funds through other collaborations or licensing arrangements with third parties, we may have to relinquish valuable rights to our future revenue streams, ecDTx, research programs, intellectual property or proprietary technology, or grant licenses on terms that may not be favorable to us. Our ability to raise additional funds may be adversely impacted by global economic conditions, disruptions to, and volatility in, the credit and financial markets in the United States, inflation, diminished liquidity and credit availability, declines in consumer confidence, declines in economic growth, increases in unemployment rates, and uncertainty about economic stability. If we are unable to raise additional funds through equity or debt financings or other arrangements when needed, we may be required to delay, limit, reduce, or terminate our R&D programs or other operations, or grant rights to develop and market ecDTx to third parties that we would otherwise prefer to develop and market ourselves, or on less favorable terms than we would otherwise choose.

**Cash Flows** 

The following table summarizes our cash flows for each of the periods indicated (in thousands):

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| | | | |
|:---|:---|:---|:---|
|  | **Six Months Ended<br>June 30,** | **Six Months Ended<br>June 30,** |  |
|  | **2025** | **2024** | **Change** |
| Net cash used in operating activities | $(26359) | $(32012) | $5653 |
| Net cash provided by/ (used in) investing activities | 14352 | (50054) | 64406 |
| Net cash provided by financing activities | 117 | 89723 | (89606) |
| &nbsp;&nbsp;&nbsp;&nbsp;Net increase/ (decrease) in cash, cash equivalents, and restricted cash | $(11890) | $7657 | $(19547) |

---

*Operating Activities*

Net cash used in operating activities was $26.4 million and $32.0 million for the six months ended June 30, 2025 and 2024, respectively. The net cash used in operating activities during the six months ended June 30, 2025 was primarily due to our reported net loss of $31.4 million, net of noncash charges (including stock-based compensation expense, depreciation, and right-of-use asset amortization) totaling $4.3 million and a $0.8 million decrease of our net operating assets. The net cash used in operating activities during the six months ended June 30, 2024 was primarily due to our reported net loss of $32.4 million, net of noncash charges (including stock-based compensation expense, depreciation, and right-of-use asset amortization) totaling $2.6 million and a $2.2 million increase of our net operating assets. The decrease in cash used in operations during the six months ended June 30, 2025 in comparison to the six months ended June 30, 2024 was primarily attributable a decrease in third-party spending associated with our discovery, development, and clinical activities.

*Investing Activities* 

Investing activities consist primarily of the cash flows of purchases and maturities of investment securities and the cash outflow associated with purchases of property and equipment. Such activities resulted in a net inflow of funds of approximately $14.4 million during the six months ended June 30, 2025, primarily from the net maturities of our available-for-sale securities portfolio, and a net outflow of funds of approximately $50.1 million during the six months ended June 30, 2024, primarily from the net purchases of our available-for-sale securities portfolio.

*Financing Activities*

Our financing activities relate to the offering and sale of shares of our common stock in our IPO and under our 2024 Employee Stock Purchase Plan (ESPP), and the exercise of common stock options by our employees and consultants. Net cash provided by financing activities was $0.1 million during the six months ended June 30, 2025, primarily due to the net proceeds from the sale of shares of our common stock under our ESPP. Net cash provided by financing activities was $89.7 million during the six months ended June 30, 2024, primarily due to the net proceeds from our IPO.

------

**Contractual Obligations and Other Commitments**

We lease office and lab space under a non-cancellable lease agreement that expires in October 2034. As of June 30, 2025, total future aggregate operating lease commitments was $72.3 million, which is exclusive of variable lease payments for common area maintenance and property taxes. Of this amount, approximately $2.5 million will be due over the remaining six months of 2025 and approximately $7.1 million will be due in 2026, with the remainder due in periods from 2027 through 2034. See Note 7 to our unaudited condensed financial statements included elsewhere in this Quarterly Report on Form 10-Q for further information.

We enter into contracts in the normal course of our business for clinical trial and preclinical research services, contract manufacturing services, professional services and other services and products for research and operating purposes. These contracts generally provide for termination after a notice period, and, therefore, are cancelable contracts and not separately presented.

**Off-Balance Sheet Arrangements**

Since our inception, we have not had, and we do not currently have, any off-balance sheet arrangements as defined under rules and regulations of the SEC.

**Critical Accounting Policies and Significant Estimates and Judgments**

Our management's discussion and analysis of our financial condition and results of operations are based on our unaudited condensed financial statements, which have been prepared in accordance with U.S. generally accepted accounting principles. The preparation of these financial statements requires us to make estimates and judgments that affect the reported amounts of assets, liabilities, and expenses and the disclosure of contingent assets and liabilities in our financial statements. On an ongoing basis, we evaluate our estimates and judgments, including those related to accrued R&D expenses and stock-based compensation expense. We base our estimates on historical experience, known trends and events, 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 values of assets and liabilities that are not readily apparent from other sources. Actual results may differ from these estimates under different assumptions or conditions.

There have been no material changes to our critical accounting policies and estimates from those described in "Management's Discussion and Analysis of Financial Condition and Results of Operations – Critical Accounting Policies and Significant Estimates and Judgments" included in our 2024 10-K.

**Emerging Growth Company and Smaller Reporting Company Status**

As an emerging growth company under the Jumpstart Our Business Startups Act of 2012 (the JOBS Act), we can take advantage of an extended transition period for complying with new or revised accounting standards. This period allows an emerging growth company to delay the adoption of certain accounting standards until those standards would otherwise apply to private companies. We have elected to avail ourselves of this exemption from new or revised accounting standards and, therefore, our financial statements may not be comparable to companies that comply with new or revised accounting pronouncements as of public company effective dates. We also intend to rely on other exemptions provided by the JOBS Act, including without limitation, not being required to comply with the auditor attestation requirements of Section 404(b) of Sarbanes-Oxley for so long as we are exempt from doing so.

We will remain an emerging growth company until the earliest of (i) December 31, 2029, which is the last day of the fiscal year following the fifth anniversary of the consummation of our IPO; (ii) the last day of the fiscal year in which we have total annual gross revenue of at least $1.235 billion; (iii) the last day of the fiscal year in which we are deemed to be a "large accelerated filer" as defined in Rule 12b-2 under the Exchange Act, which would occur if the market value of our common stock held by non-affiliates exceeded $700.0 million as of the last business day of the second fiscal quarter of such year; or (iv) the date on which we have issued more than $1.0 billion in nonconvertible debt securities during the prior three-year period.

We are also a smaller reporting company as defined in Rule 12b-2 under the Exchange Act. We may continue to be a smaller reporting company even after we are no longer an emerging growth company. We may take advantage of certain of the scaled disclosures available to smaller reporting companies and will be able to take advantage of these scaled disclosures for so long as our voting and non-voting common stock held by non-affiliates is less than $250.0 million measured on the last business day of our second fiscal quarter, or our annual revenue is less than $100.0 million during the most recently completed fiscal year and our voting and non-voting common stock held by non-affiliates is less than $700.0 million measured on the last business day of our second fiscal quarter.

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**Item 3. Quantitative and Qualitative Disclosures About Market Risk.**

We are a smaller reporting company, as defined in Rule 12b-2 under the Exchange Act and Item 10(f)(1) of Regulation S-K, and are not required to provide the information under this item.

**Item 4. Controls and Procedures.**

***Evaluation of Disclosure Controls and Procedures***

Our management, with the participation and supervision of our principal executive officer and our principal financial and accounting officer, have evaluated our disclosure controls and procedures as defined in Rules 13a-15(e) and 15d-15(e) under the Exchange Act. Based on that evaluation, our principal executive officer and our principal financial and accounting officer have concluded that, as of the end of the period covered by this Quarterly Report on Form 10-Q, our disclosure controls and procedures were effective to provide reasonable assurance that information we are required to disclose in reports that we file or submit under the Exchange Act is recorded, processed, summarized, and reported within the time periods specified in SEC rules and forms, and that such information is accumulated and communicated to our management, including our principal executive officer and principal financial and accounting officer, as appropriate, to allow timely decisions regarding required disclosure.

***Changes in Internal Control over Financial Reporting***

Due to a transition period established by SEC rules applicable to newly public companies, our management is not required to evaluate the effectiveness of our internal control over financial reporting until after the filing of our Annual Report on Form 10-K for the year ending December 31, 2025. As a result, this Quarterly Report on Form 10-Q does not address whether there have been any changes in our internal control over financial reporting.

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**PART II—OTHER INFORMATION**

**Item 1. Legal Proceedings.**

There currently is no material pending legal proceeding to which we are a party or to which any of our property is subject, and our management is not aware of any contemplated proceeding by any governmental authority against us. From time to time, we may become involved in legal proceedings or subject to claims incident to the ordinary course of business. Regardless of outcome, such proceedings or claims can have an adverse impact on us because of defense and settlement costs, diversion of resources, negative publicity, reputational harm, and other factors and there can be no assurances that favorable outcomes will be obtained.

**Item 1A. Risk Factors.**

Investing in our common stock involves a high degree of risk. You should carefully consider the risks and uncertainties described in Part I, Item 1A,"Risk Factors," of our 2024 10-K, together with all of the information in this Quarterly Report, before making an investment decision to purchase or sell shares of our common stock. If any of those risks are realized, our business, financial condition, results of operations, and prospects could be materially and adversely affected. In that event, the trading price of our common stock could decline, and you could lose part or all of your investment. There have been no material changes to the risk factors set forth in Part I, Item 1A of our 2024 10-K.

**Item 2. Unregistered Sales of Equity Securities and Use of Proceeds.** 

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;**(a)** **Recent Sales of Unregistered Securities.**

None.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;**(b)** **Use of Proceeds.**

On March 27, 2024, our registration statement on Form S-1 (File No. 333-277696), as amended, was declared effective by the SEC for our IPO. At the closing of the IPO on April 2, 2024, we sold 6,250,000 shares of common stock at a public offering price of $16.00 per share and received gross proceeds of $100.0 million, which resulted in net proceeds to us of approximately $87.7 million, after deducting underwriting discounts and commissions and other offering expenses.

Pending the uses described below, the net proceeds from our IPO have been held in cash, cash equivalents, and short-term investments. There has been no material change in our planned use of net proceeds from our IPO from that described in the prospectus for our IPO, except that, due to our decisions with regard to the POTENTIATE and STARMAP clinical trials discussed above, net proceeds that may have been used to fund the development of BBI-355 and BBI-825 as a single agent or in combination with targeted therapies in those clinical trials, respectively, and are not used to wind down the STARMAP trial or the initial arms of the POTENTIATE trial, are now expected to be directed to support the development of the BBI-355/BBI-825 combination and BBI-940, including through initial proof-of-concept clinical data for each of these programs, research and development of our other ecDTx development programs, and to be used for working capital and other general corporate purposes, including our ecDNA diagnostic and Spyglass platform. We may also use a portion of the net proceeds and our existing cash, cash equivalents, and short-term investments to in-license, acquire, or invest in complementary businesses, technologies, products, or assets. However, we have no current commitments or obligations to do so. We cannot predict with certainty all of the particular uses for the net proceeds from our IPO. Our expected use of the net proceeds from our IPO represents our intentions based upon our current plans and business conditions, which could change in the future as our plans and business conditions evolve. The amounts and timing of our actual expenditures may vary significantly depending on numerous factors, including the progress and costs of our development activities, the status of and results from clinical trials and preclinical studies, as well as any collaborations that we may enter into with third parties for our ecDTx, and the amount of cash used in our operations and any unforeseen cash needs, as well as other factors described in Item 1A, "Risk Factors," in Part I of our 2024 10-K. Our management has broad discretion in the application of the net proceeds from our IPO, and investors will be relying on their judgment regarding the application of the net proceeds.

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;**(c)** **Issuer Purchases of Equity Securities.**

None.

**Item 3. Defaults Upon Senior Securities.**

None.

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**Item 4. Mine Safety Disclosures.**

Not applicable.

**Item 5. Other Information.**

***Rule 10b5-1 Trading Arrangements***

From time to time, our officers (as defined in Rule 16a-1(f) of the Exchange Act) and directors may enter into or terminate Rule 10b5-1 trading arrangements or non-Rule 10b5-1 trading arrangements (as each such term is defined in Item 408 of Regulation S-K). During the three months ended June 30, 2025, our officers or directors adopted, modified, or terminated such trading arrangements as set forth below.

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| | | | | | | |
|:---|:---|:---|:---|:---|:---|:---|
|  | &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;**<u><br>Action</u>** | &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<br>**<u>Date</u>** | &nbsp;&nbsp;**<u>Trading Arrangement</u>** | &nbsp;&nbsp;**<u>Trading Arrangement</u>** |  |  |
|  | &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;**<u><br>Action</u>** | &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<br>**<u>Date</u>** | &nbsp;&nbsp;**<u>Rule 10b5-1\*</u>** | &nbsp;&nbsp;**<u>Non-Rule 10b5-1\*\*</u>** | **<u>Total Shares Subject to Plan</u>** | **<u>Expiration Date</u>** |
| &nbsp;&nbsp;Robert Doebele, MD, Ph.D. Chief Medical Officer | &nbsp;&nbsp;Adopted | &nbsp;&nbsp;April 3, 2025 | &nbsp;&nbsp;X |  | &nbsp;&nbsp;45000 | &nbsp;&nbsp;August 3, 2026 |
| &nbsp;&nbsp;____________________<br>\* Intended to satisfy the affirmative defense of Rule 10b5-1(c)<br>\*\* Not intended to satisfy the affirmative defense of Rule 10b5-1(c) | &nbsp;&nbsp;____________________<br>\* Intended to satisfy the affirmative defense of Rule 10b5-1(c)<br>\*\* Not intended to satisfy the affirmative defense of Rule 10b5-1(c) | &nbsp;&nbsp;____________________<br>\* Intended to satisfy the affirmative defense of Rule 10b5-1(c)<br>\*\* Not intended to satisfy the affirmative defense of Rule 10b5-1(c) | &nbsp;&nbsp;____________________<br>\* Intended to satisfy the affirmative defense of Rule 10b5-1(c)<br>\*\* Not intended to satisfy the affirmative defense of Rule 10b5-1(c) | &nbsp;&nbsp;____________________<br>\* Intended to satisfy the affirmative defense of Rule 10b5-1(c)<br>\*\* Not intended to satisfy the affirmative defense of Rule 10b5-1(c) | &nbsp;&nbsp;____________________<br>\* Intended to satisfy the affirmative defense of Rule 10b5-1(c)<br>\*\* Not intended to satisfy the affirmative defense of Rule 10b5-1(c) | &nbsp;&nbsp;____________________<br>\* Intended to satisfy the affirmative defense of Rule 10b5-1(c)<br>\*\* Not intended to satisfy the affirmative defense of Rule 10b5-1(c) |

---

------

**Item 6. Exhibits.**

---

| | | | | | |
|:---|:---|:---|:---|:---|:---|
| **Exhibit** |  | **Incorporated by Reference** | **Incorporated by Reference** | **Incorporated by Reference** | **Filed** |
| **Number** | **Description** | **Form** | **Date** | **Number** | **Herewith** |
| 3.1 | [<u>Amended and Restated Certificate of Incorporation</u>](https://www.sec.gov/Archives/edgar/data/1782303/000119312524084736/d796750dex31.htm) | 8-K | 4/2/2024 | 3.1 |  |
| 3.2 | [<u>Amended and Restated Bylaws</u>](https://www.sec.gov/Archives/edgar/data/1782303/000119312524084736/d796750dex32.htm) | 8-K | 4/2/2024 | 3.2 |  |
| 31.1 | [<u>Certification of Principal Executive Officer Pursuant to Rules 13a-14(a) and 15d-14(a) under the Securities Exchange Act of 1934, as Adopted Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.</u>](bold-ex31_1.htm) |  |  |  | X |
| 31.2 | [<u>Certification of Principal Financial Officer Pursuant to Rules 13a-14(a) and 15d-14(a) under the Securities Exchange Act of 1934, as Adopted Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.</u>](bold-ex31_2.htm) |  |  |  | X |
| 32.1\* | [<u>Certifications of Principal Executive Officer and Principal Financial Officer Pursuant to 18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.</u>](bold-ex32_1.htm) |  |  |  | X |
| 101.INS | Inline XBRL Instance Document – the instance document does not appear in the Interactive Data File because XBRL tags are embedded within the Inline XBRL document. |  |  |  | X |
| 101.SCH | Inline XBRL Taxonomy Extension Schema With Embedded Linkbase Documents |  |  |  | X |
| 104 | Cover Page Interactive Data File (embedded within the Inline XBRL document) |  |  |  | X |

---

------

\* These certifications are deemed not filed for purposes of Section 18 of the Exchange Act or otherwise subject to the liability of that section, nor shall they be deemed incorporated by reference into any filing under the Securities Act or the Exchange Act.

------

**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.

---

| | | |
|:---|:---|:---|
|  | **Boundless Bio, Inc.** | **Boundless Bio, Inc.** |
| Date: August 5, 2025 | By: | /s/ Zachary D. Hornby |
|  |  | Zachary D. Hornby |
|  |  | President and Chief Executive Officer |
|  |  | (Principal Executive Officer) |
| Date: August 5, 2025 | By: | /s/ David Hinkle |
|  |  | David Hinkle |
|  |  | Senior Vice President, Finance, Controller and Treasurer |
|  |  | (Principal Financial and Accounting Officer) |

---

------

## Exhibit 31.1

**Exhibit 31.1**

**Certification of Principal Executive Officer<br>Pursuant to Rules 13a-14(a) and 15d-14(a) under the Securities Exchange Act of 1934, as Adopted**

**Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002**

I, Zachary D. Hornby, certify that:

1. I have reviewed this Quarterly Report on Form 10-Q of Boundless Bio, 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 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)) for the registrant and have:

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&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;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;b.(Paragraph intentionally omitted);

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&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;&nbsp;&nbsp;&nbsp;&nbsp;&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 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;&nbsp;&nbsp;&nbsp;&nbsp;&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;&nbsp;&nbsp;&nbsp;&nbsp;&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 5, 2025 | /s/ Zachary D. Hornby |
|  | Zachary D. Hornby |
|  | President and Chief Executive Officer |
|  | **(Principal Executive Officer)** |

---

------

## Exhibit 31.2

**Exhibit 31.2**

**Certification of Principal Financial Officer**

**Pursuant to Rules 13a-14(a) and 15d-14(a) under the Securities Exchange Act of 1934, as Adopted**

**Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002**

I, David Hinkle, certify that:

1. I have reviewed this Quarterly Report on Form 10-Q of Boundless Bio, 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 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)) for the registrant and have:

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&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;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;b.(Paragraph intentionally omitted);

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&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;&nbsp;&nbsp;&nbsp;&nbsp;&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 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;&nbsp;&nbsp;&nbsp;&nbsp;&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;&nbsp;&nbsp;&nbsp;&nbsp;&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.

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| | |
|:---|:---|
| Date: August 5, 2025 | /s/ David Hinkle |
|  | David Hinkle |
|  | Senior Vice President, Finance, Controller and Treasurer |
|  | **(Principal Financial and Accounting Officer)** |

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## Exhibit 32.1

**Exhibit 32.1**

**CERTIFICATIONS PURSUANT TO**

**18 U.S.C. SECTION 1350, AS ADOPTED PURSUANT TO**

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

In connection with the Quarterly Report on Form 10-Q of Boundless Bio, Inc. (the Company) for the quarter ended June 30, 2025 as filed with the Securities and Exchange Commission on the date hereof (the Report), Zachary D. Hornby, President and Chief Executive Officer of the Company, and David Hinkle, Senior Vice President, Finance, Controller, and Treasurer of the Company, each hereby certifies, pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002, to his knowledge, that:

&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1.The Report fully complies with the requirements of Section 13(a) or Section 15(d) of the Securities Exchange Act of 1934, as amended; 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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| | | |
|:---|:---|:---|
| Date: August 5, 2025 | By: | /s/ Zachary D. Hornby |
|  |  | Zachary D. Hornby |
|  |  | President and Chief Executive Officer |
|  |  | **(Principal Executive Officer)** |
| Date: August 5, 2025 | By: | /s/ David Hinkle |
|  |  | David Hinkle |
|  |  | Senior Vice President, Finance, Controller and Treasurer |
|  |  | **(Principal Financial and Accounting Officer)** |

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The foregoing certifications are being furnished solely pursuant to 18 U.S.C. Section 1350 and are not being filed as part of the Report or as a separate disclosure document.

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