What changed in this filing

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Item 1. Financial Statements

2025-11-13 compared with 2025-08-14 · 123 added, 118 removed, 419 unchanged (37% of the section changed)

3 unchanged sentences

(In thousands, except share and per share data)

September 30,

Current assets

Cash and cash equivalents

License agreement receivable

Prepaid expenses and other current assets

3 unchanged sentences

Operating lease right-of-use asset

LIABILITIES AND STOCKHOLDERS’ EQUITY

LIABILITIES AND STOCKHOLDERS’ (DEFICIT) EQUITY

Current liabilities

9 unchanged sentences

Commitments and contingencies (Note 7)

Stockholders’ equity

Stockholders’ (deficit) equity

Preferred stock, $ 0.0001 par value;

1 unchanged sentence

Common stock, $ 0.0001 par value;

600,000,000 shares authorized at June 30, 2025 and 200,000,000 shares authorized at December 31, 2024;

51,827,910 shares issued and outstanding at June 30, 2025;

600,000,000 shares authorized at September 30, 2025 and 200,000,000 shares authorized at December 31, 2024;

51,829,013 shares issued and outstanding at September 30, 2025;

45,756,773 shares issued and outstanding at December 31, 2024

1 unchanged sentence

Accumulated deficit

Total stockholders’ equity

Total liabilities and stockholders’ equity

Total stockholders’ (deficit) equity

Total liabilities and stockholders’ (deficit) equity

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

2 unchanged sentences

(In thousands, except share and per share data)

Three Months Ended June 30,

Six Months Ended June 30,

Three Months Ended September 30,

Nine Months Ended September 30,

Collaboration and license revenue

15 unchanged sentences

XILIO THERAPEUTICS, INC.

Condensed Consolidated Statements of Stockholders’ Equity

For the three months ended June 30, 2025 and 2024

Condensed Consolidated Statements of Stockholders’ ( Deficit) Equity

For the three months ended September 30, 2025 and 2024

(In thousands, except share data)

Stockholders'

Paid-In Capital

Balance at March 31, 2025

Issuance of prefunded warrants in connection with a follow-on public offering, net of issuance costs

Issuance of common stock under employee stock purchase plan

Balance at June 30, 2025

Exercise of stock options

Stock-based compensation expense

Balance at June 30, 2025

Balance at September 30, 2025

Stockholders'

Paid-In Capital

Balance at March 31, 2024

Issuance of common stock and prefunded warrants to Gilead and certain accredited investors in private placements, net of issuance costs

Issuance of common stock in connection with at-the-market offerings, net of issuance costs

Issuance of common stock under employee stock purchase plan

Vesting of restricted common stock

Balance at June 30, 2024

Exercise of stock options

Stock-based compensation expense

Balance at June 30, 2024

Balance at September 30, 2024

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

XILIO THERAPEUTICS, INC.

Condensed Consolidated Statements of Stockholders’ Equity

For the six months ended June 30, 2025 and 2024

Condensed Consolidated Statements of Stockholders’ (Deficit) Equity

For the nine months ended September 30, 2025 and 2024

(In thousands, except share data)

Stockholders'

Paid-In Capital

Balance at December 31, 2024

6 unchanged sentences

Stock-based compensation expense

Balance at June 30, 2025

Balance at September 30, 2025

Stockholders'

Paid-In Capital

Balance at December 31, 2023

5 unchanged sentences

Stock-based compensation expense

Balance at June 30, 2024

Balance at September 30, 2024

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

2 unchanged sentences

(In thousands)

Six Months Ended June 30,

Nine Months Ended September 30,

Cash flows from operating activities:

4 unchanged sentences

Issuance costs allocated to common stock warrant liabilities

Loss on disposal of property and equipment

Changes in operating assets and liabilities:

License agreement receivable

Prepaid and other assets

2 unchanged sentences

Deferred revenue

Net cash provided by operating activities

Net cash used in operating activities

Cash flows from investing activities:

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Supplemental disclosure of non-cash activities:

Capital expenditures included in accounts payable or accrued expenses

Issuance costs included in accounts payable or accrued expenses

Transfer of finance lease asset to property and equipment

Reconciliation to amounts within the consolidated balance sheets:

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Since its inception, the Company has devoted substantially all of its financial resources and efforts to research and development activities.

As of June 30, 2025, the Company had an accumulated deficit of $ 412.9 million and has incurred significant operating losses, including net losses of $ 29.1 million and $ 31.1 million for the six months ended June 30, 2025 and 2024, respectively.

As of September 30, 2025, the Company had an accumulated deficit of $ 429.1 million and has incurred significant operating losses, including net losses of $ 45.4 million and $ 45.1 million for the nine months ended September 30, 2025 and 2024, respectively.

The Company expects its operating losses and negative operating cash flows to continue for the foreseeable future as it continues to advance its pipeline of novel, tumor-activated I-O molecules through preclinical and clinical development, maintains the infrastructure necessary to support these activities and continues to incur costs associated with operating as a public company.

These conditions raise substantial doubt about the Company’s ability to continue as a going concern within twelve months from the date of the issuance of these condensed consolidated financial statements.

In order to fund its operations, the Company will need to raise additional capital, which could be obtained through the cash exercise, if any, of common stock warrants issued in connection with the June 2025 follow-on public offering, the receipt of milestone payments, option-related fees or other contingent payments under the Company’s existing agreements with Gilead Sciences, Inc.

In order to fund its operations, the Company will need to raise additional capital, which could be obtained through the cash exercise of common stock warrants issued in connection with the June 2025 follow-on public offering, the receipt of milestone payments, option-related fees or other contingent payments under the Company’s existing agreements with Gilead Sciences, Inc.

(“Gilead”) and AbbVie Group Holdings Limited (“AbbVie”), additional public or private equity offerings, debt financings, additional collaborations, partnerships or licensing arrangements or other sources.

In the fourth quarter of 2025, the Company received a $ 17.5 million development milestone payment from Gilead.

However, there can be no assurance that the Company will receive additional proceeds from the exercise of the common stock warrants or from contingent payments under its existing agreements with Gilead or AbbVie or that the Company will be able to complete any additional transactions on acceptable terms or otherwise.

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Securities and Exchange Commission (the “SEC”).

Any reference in these notes to applicable guidance is meant

to refer to the authoritative U.S.

Any reference in these notes to applicable guidance is meant to refer to the authoritative U.S.

GAAP as found in the Accounting Standards Codification (“ASC”) and Accounting Standards Updates (“ASUs”) of the Financial Accounting Standards Board (“FASB”).

1 unchanged sentence

GAAP have been condensed or omitted from this report, as is permitted by such rules and regulations.

Accordingly, these unaudited interim condensed consolidated financial statements should be read in conjunction with the audited financial statements as of and for the year ended December 31, 2024 and notes thereto, included in the Company’s Annual Report on Form 10-K filed with the SEC on March 11, 2025.

Accordingly, these unaudited interim condensed consolidated financial statements should be read in conjunction with the audited

financial statements as of and for the year ended December 31, 2024 and notes thereto, included in the Company’s Annual Report on Form 10-K filed with the SEC on March 11, 2025.

The unaudited interim condensed consolidated financial statements have been prepared on the same basis as the audited financial statements.

In the opinion of the Company’s management, the unaudited interim condensed consolidated financial statements contain all adjustments which are necessary to present fairly the Company’s financial position as of June 30, 2025 and the results of its operations for the three and six months ended June 30, 2025 and 2024 and cash flows for the six months ended June 30, 2025 and 2024.

In the opinion of the Company’s management, the unaudited interim condensed consolidated financial statements contain all adjustments which are necessary to present fairly the Company’s financial position as of September 30, 2025 and the results of its operations for the three and nine months ended September 30, 2025 and 2024 and cash flows for the nine months ended September 30, 2025 and 2024.

Such adjustments are of a normal and recurring nature.

The results for the three and six months ended June 30, 2025 are not necessarily indicative of the results for the year ending December 31, 2025 or for any future period.

The results for the three and nine months ended September 30, 2025 are not necessarily indicative of the results for the year ending December 31, 2025 or for any future period.

Principles of Consolidation

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The estimation process often may yield a range of potentially reasonable estimates of the ultimate future outcomes and management must select an amount that falls within that range of reasonable estimates.

Significant estimates of accounting reflected in these condensed consolidated financial statements include, but are not limited to, estimates related to revenue recognition, accrued expenses, the valuation of the common stock warrant liabilities, the valuation of stock-based compensation, including stock options and restricted stock units, useful life of long-lived assets and income taxes.

stock-based compensation, including stock options and restricted stock units, useful life of long-lived assets and income taxes.

Actual results could differ from those estimates.

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ASU 2023-09 should be applied on a prospective basis, but retrospective application is permitted.

The Company is currently evaluating the potential impact of adopting this new guidance on its condensed consolidated

financial statements and related disclosures.

The Company anticipates that the adoption of ASU 2023-09 will expand its income tax footnote disclosures, including a more detailed effective tax rate reconciliation.

In November 2024, the FASB issued ASU No.

18 unchanged sentences

The Monte Carlo simulation assumptions also include the potential impacts of the warrant strike price reset features.

The inputs used in the fair market value of the Company’s common stock warrants liabilities as of the issuance date and June 30, 2025 were the following:

The inputs used in the fair market value of the Company’s common stock warrants liabilities as of the issuance date and September 30, 2025 were the following:

September 30,

(issuance date)

June 30, 2025

Closing price of common stock

5 unchanged sentences

The following table summarizes the changes in the fair market value of the Company’s common stock warrant liabilities, which are classified within the Level 3 fair value hierarchy:

warrant liability

Total level 3

Balance at December 31, 2024

Initial fair value of common stock warrant liability

Change in fair value of common stock warrant liability

Balance at June 30, 2025

Initial fair value of common stock warrant liabilities

Change in fair value of common stock warrant liabilities

Balance at September 30, 2025

Property and Equipment, Net

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

Property and equipment, net consists of the following as of September 30, 2025 and December 31, 2024:

September 30,

Laboratory equipment

5 unchanged sentences

Property and equipment, net

The Company recognized depreciation and amortization expense related to property and equipment of $ 0.9 million and $ 0.8 million for the six months ended June 30, 2025 and 2024, respectively.

The Company recognized depreciation and amortization expense related to property and equipment of $ 0.3 million and $ 0.4 million for the three months ended September 30, 2025 and 2024, respectively.

The Company recognized depreciation and amortization expense related to property and equipment of $ 1.2 million for each of the nine months ended September 30, 2025 and 2024 .

Accrued Expenses

Accrued expenses consist of the following as of June 30, 2025 and December 31, 2024:

Accrued expenses consist of the following as of September 30, 2025 and December 31, 2024:

September 30,

External research and development

5 unchanged sentences

In February 2025, Xilio Development entered into a collaboration, license and option agreement (the “Collaboration Agreement”) with AbbVie for up to four programs leveraging the Company’s proprietary tumor-activation technology and platform, consisting of (i) an exclusive license for a program to develop and commercialize a masked antibody-based immunotherapy (the “Collaboration Program”) and (ii) an exclusive option for (a) an initial program to discover, develop and commercialize masked T cell engager molecules for an agreed upon initial target and backup target (“Initial Option Program”), and (b) subject to the terms of the Collaboration Agreement, up to two additional programs (each, an “Additional Option Program” and together with the Initial Option Program, the “Option Programs”).

In connection with the Collaboration Program, Xilio Development is responsible for conducting all preclinical

development through lead generation (“Collaboration Program Services”).

In connection with the Collaboration Program, Xilio Development is responsible for conducting all preclinical development through lead generation (“Collaboration Program Services”).

For the Initial Option Program, AbbVie’s option right is exercisable beginning on the effective date of the Collaboration Agreement, and for each Additional Option Program, AbbVie’s option right is exercisable following delivery of written notice of nomination of such Additional Option Program.

1 unchanged sentence

For each Option Program, prior to option exercise, Xilio Development is responsible for conducting preclinical discovery and development up to the completion of investigational new drug application (“IND”) enabling studies, subject to AbbVie paying Xilio Development option extension fees upon completion of specified stages of preclinical discovery and development (“Option Program Services”).

Unless AbbVie elects to extend preclinical development through the next stage and pays the applicable option extension fee, AbbVie’s option right terminates within a specified time period following completion of each stage of preclinical development.

Unless AbbVie elects to extend preclinical development through the next stage and pays the applicable option extension fee, AbbVie’s option right terminates within a specified

time period following completion of each stage of preclinical development.

Upon exercising its option for an Option Program, AbbVie will be responsible for any remaining preclinical development, if applicable, and all clinical development, regulatory and commercialization activities with respect to licensed products under the applicable Option Program.

3 unchanged sentences

in a private placement at a purchase price of $ 2.30 per share for an aggregate purchase price of $ 10.0 million.

As of June 30, 2025, the Company has received $ 52.0 million in payments under the AbbVie agreements, consisting of a $ 42.0 million upfront cash payment under the Collaboration Agreement and $ 10.0 million in gross proceeds from the private placement under the stock purchase agreement.

In addition, as of June 30, 2025, the Company is eligible to receive up to approximately $ 2.1 billion in additional contingent payments under the Collaboration Agreement, consisting of (i) up to $ 305.0 million in aggregate program nomination fees, preclinical development option extension fees and option fees for the Option Programs and (ii) up to $ 1.8 billion in aggregate development, regulatory and sales-based milestones for all Option Programs and the Collaboration Program.

As of September 30, 2025 , the Company has received $ 52.0 million in payments under the AbbVie agreements, consisting of a $ 42.0 million upfront cash payment under the Collaboration Agreement and $ 10.0 million in gross proceeds from the private placement under the stock purchase agreement.

In addition, as of September 30, 2025 , the Company is eligible to receive up to approximately $ 2.1 billion in additional contingent payments under the Collaboration Agreement, consisting of (i) up to $ 305.0 million in aggregate program nomination fees, preclinical development option extension fees and option fees for the Option Programs and (ii) up to $ 1.8 billion in aggregate development, regulatory and sales-based milestones for all Option Programs and the Collaboration Program.

In addition, the Company is eligible to receive tiered royalties ranging in the high single digits on annual global net product sales for the Option Program and is eligible to receive tiered royalties ranging in the mid-single digits on annual global net product sales for the Collaboration Program.

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The Company used the most likely amount method to estimate variable consideration.

All contingent payments are fully constrained as of June 30, 2025, as the achievement of the milestones underlying such contingent payments is based on either the Company or AbbVie’s ability to execute under the development plan which is not certain at contact inception.

Accordingly, all such contingent payments are excluded from the transaction price.

All contingent payments are fully constrained as of September 30, 2025, as the achievement of the milestones underlying such contingent payments is based on either the Company or AbbVie’s ability to execute under the development plan which is not certain at contact inception.

all such contingent payments are excluded from the transaction price.

The Company reevaluates the transaction price at the end of each reporting period and as uncertain events are resolved or other changes in circumstances occur and may adjust the transaction price as necessary.

15 unchanged sentences

If the material right is exercised, the Company will evaluate the performance obligations underlying the option exercised and recognize the amount allocated to the material right and any additional consideration over the appropriate recognition period associated with the underlying performance obligations.

During the three and six months ended June 30, 2025, the Company recognized collaboration and license revenue of $ 4.8 million and $ 5.6 million, respectively, under the Collaboration Agreement and the stock purchase agreement.

As of June 30, 2025, the Company recorded deferred revenue of $ 43.6 million, of which $ 26.7 million was recorded as a current liability on the Company’s condensed consolidated balance sheet.

The deferred revenue is expected to be recognized as revenue through at least 2026 depending on (i) the timing of services being provided for the Collaboration Program and

the Initial Option Program and (ii) the timing of AbbVie’s exercise or expiration of the material rights.

During the three and nine months ended September 30, 2025 , the Company recognized collaboration and license revenue of $ 8.3 million and $ 13.9 million, respectively, under the Collaboration Agreement and the stock purchase agreement.

As of September 30, 2025 , the Company recorded deferred revenue of $ 35.3 million, of which $ 24.3 million was recorded as a current liability on the Company’s condensed consolidated balance sheet.

The deferred revenue is expected to be recognized as collaboration and license revenue through at least 2026 depending on (i) the timing of services being provided for the Collaboration Program and the Initial Option Program and (ii) the timing of AbbVie’s exercise or expiration of the material rights.

License Agreement with Gilead Sciences, Inc.

In March 2024, Xilio Development entered into a license agreement with Gilead, pursuant to which it granted Gilead an exclusive global license to develop and commercialize XTX301, the Company’s tumor-activated IL-12 product candidate, and specified other molecules directed to IL-12.

Xilio Development is responsible for conducting clinical development for XTX301 through an initial Phase 2 clinical trial.

Following the delivery by Xilio Development of a specified clinical data package for XTX301 related to the Phase 1 clinical trial and an initial Phase 2 clinical trial, Gilead can elect to transition responsibilities for the development and commercialization of XTX301 to Gilead, subject to the terms of the license agreement and payment by Gilead of a $ 75.0 million transition fee.

In March 2024, Xilio Development entered into a license agreement with Gilead, pursuant to which it granted Gilead an exclusive global license to develop and commercialize efarindodekin alfa (XTX301), the Company’s tumor-activated IL-12 product candidate, and specified other molecules directed to IL-12.

Xilio Development is responsible for conducting clinical development for efarindodekin alfa through an initial Phase 2 clinical trial.

Following the delivery by Xilio Development of a specified clinical data package for efarindodekin alfa related to the Phase 1 clinical trial and the initial Phase 2 clinical trial, Gilead can elect to transition responsibilities for the development and commercialization of efarindodekin alfa to Gilead, subject to the terms of the license agreement and payment by Gilead of a $ 75.0 million transition fee.

In connection with the execution of the license agreement, in March 2024, the Company also entered into a stock purchase agreement with Gilead.

1 unchanged sentence

The prefunded warrants are exercisable any time at an exercise price of $ 0.0001 per share, subject to Gilead not being deemed a beneficial owner of greater than 19.9 % of the Company’s common stock upon the exercise of the prefunded warrants.

As of June 30, 2025, the Company has received $ 55.0 million in payments under the Gilead agreements, consisting of the $ 30.0 million upfront cash payment under the license agreement and $ 25.0 million in gross proceeds from private placements under the stock purchase agreement.

As of June 30, 2025, the Company is eligible to receive up to $ 592.5 million in additional contingent payments, which consist of the $ 75.0 million transition fee and up to $ 517.5 million in specified development, regulatory and sales-based milestones.

Prior to the potential transition fee, up to $ 17.5 million of the total additional contingent payments are related to a near-term development milestone.

As of September 30, 2025 , the Company has received $ 55.0 million in payments under the Gilead agreements, consisting of the $ 30.0 million upfront cash payment under the license agreement and $ 25.0 million in gross proceeds from private placements under the stock purchase agreement.

As of September 30, 2025 , the Company is eligible to receive up to $ 592.5 million in additional contingent payments, which consist of a $17.5 million development milestone prior to opt-in, a $ 75.0 million transition fee if Gilead exercises its option for the IL-12 program and up to $ 500.0 million in specified development, regulatory and sales-based milestones after opt-in.

The Company achieved the $ 17.5 million development milestone in the third quarter of 2025 in connection with the initiation of the Phase 2 trial and recorded the milestone as a receivable on the condensed consolidated balance sheet as of September 30, 2025.

The Company received payment of the milestone from Gilead during the fourth quarter of 2025.

In addition, the Company is eligible to receive tiered royalties ranging from high single digits to mid-teens on annual global net product sales.

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The Company determined that the license agreement represents a contract with a customer within the scope of ASC 606 and identified two promises under the license agreement:

(i) the exclusive licenses granted to Gilead related to the Company’s IL-12 program and (ii) the provision by Xilio Development and its affiliates of development services related to ongoing and planned clinical trials for XTX301 through an initial Phase 2 clinical trial.

The Company determined that the exclusive license and development services were not capable of being distinct on the basis that the development services to be provided by Xilio Development are specialized in nature, specifically with respect to its specialized expertise related to XTX301, the IL-12 program and the Company’s proprietary platform for tumor-activated biologics.

The Company determined that the exclusive license and development services were not capable of being distinct on the basis that the development services to be provided by Xilio Development are specialized in nature, specifically with respect to its specialized expertise related to efarindodekin alfa, the IL-12 program and the Company’s proprietary platform for tumor-activated biologics.

Accordingly, the Company concluded that there is a single identified combined performance obligation consisting of the exclusive license and the development services.

1 unchanged sentence

The Company used the most likely amount method to estimate variable consideration.

All contingent payments are fully constrained as of June 30, 2025, as the achievement of the milestones underlying such contingent payments is uncertain and highly susceptible to factors outside of the Company’s control.

Accordingly, all such contingent payments are excluded from the transaction price.

During the three and nine months ended September 30, 2025, the overall transaction price was adjusted to include the achievement of the $ 17.5 million development milestone in the third quarter of 2025.

All additional contingent payments are fully constrained as of September 30, 2025, as the achievement of the milestones underlying such contingent payments are uncertain and highly susceptible to factors outside of the Company’s control.

Accordingly, all such additional contingent payments are excluded from the transaction price.

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In management’s judgment, this input method is the best measure of progress towards satisfying the combined performance obligation and reflects a faithful depiction of the transfer of goods and services.

During the three and six months ended June 30, 2025, the Company recognized collaboration and license revenue of $ 3.3 million and $ 5.5 million, respectively, under the license agreement and the stock purchase agreement with Gilead.

During each of the three and six months ended June 30, 2024, the Company recognized $ 2.4 million of collaboration and license revenue under the license agreement and the stock purchase agreement with Gilead.

As of June 30, 2025, the Company recorded deferred revenue under the license agreement and the stock purchase agreement of $ 27.3 million, of which $ 15.6 million was recorded as a current liability on the Company’s condensed consolidated balance sheet.

During the three and nine months ended September 30, 2025 , the Company recognized collaboration and license revenue of $ 10.7 million and $ 16.2 million, respectively, under the license agreement and the stock purchase agreement with Gilead.

Each of the three and nine months ended September 30, 2025 included a cumulative catch-up of revenue of $ 7.0 million related to the adjustment of the overall transaction price due to the achievement of the $ 17.5 million development milestone during the third quarter of 2025.

During the three and nine months ended September 30, 2024 , the Company recognized collaboration and license revenue of $ 2.3 million and $ 4.6 million, respectively, under the license agreement and the stock purchase agreement with Gilead.

As of September 30, 2025 , the

Company recorded deferred revenue under the license agreement and the stock purchase agreement of $ 34.1 million, of which $ 19.6 million was recorded as a current liability on the Company’s condensed consolidated balance sheet.

The deferred revenue is expected to be recognized as collaboration and license revenue through at least 2027 depending on the timing of certain clinical development activities.

3 unchanged sentences

Collaboration and license revenue recognized

Deferred revenue as of June 30, 2025

Deferred revenue as of September 30, 2025

Clinical Trial Collaboration with F.

1 unchanged sentence

In July 2023, the Company and F.

Hoffmann-La Roche Ltd (“Roche”) entered into a clinical trial collaboration pursuant to a clinical supply agreement to evaluate vilastobart in combination with atezolizumab (Tecentriq®) in a Phase 1/2 clinical trial consisting of Phase 1 dose escalation assessing the combination in patients with advanced solid tumors and Phase 2 assessing the combination in patients with microsatellite stable colorectal cancer.

Under the clinical supply agreement, the Company is eligible to receive specified cost-sharing payments from Roche, and each company will supply its respective anti-cancer agent to support the Phase 1/2 clinical trial.

As of September 30, 2025, the Company has received $8.0 million in total cost-sharing payments from Roche.

The Company is responsible for conducting the Phase 1/2 clinical trial and retains global development and commercialization rights to vilastobart.

1 unchanged sentence

Therefore, the Company applied a reasonable, rational, and consistently applied accounting policy election to record the cost-sharing payments under the clinical supply agreement as a reduction of research and development expenses in the condensed consolidated statements of operations and comprehensive loss for the period in which a study development event is achieved.

The Company did no t recognize a reduction of research and development expense during each of the three months ended June 30, 2025 and 2024.

The Company recognized a reduction of research and development expense of $ 2.0 million during each of the six months ended June 30, 2025 and 2024.

The Company did no t recognize a reduction of research and development expense during each of the three months ended September 30, 2025 and 2024 .

The Company recognized a reduction of research and development expense of $ 2.0 million during each of the nine months ended September 30, 2025 and 2024 .

Commitments and Contingencies

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The Company is obligated to pay its portion of real estate taxes and costs related to the premises, including costs of operations, maintenance, repair, replacement, and management of the leased premises, which it began paying simultaneous with the rent commencement date in March 2020.

As of June 30, 2025 and December 31, 2024, the Company had a letter of credit for the benefit of its landlord in the amount of $ 1.8 million, collateralized by a money market account, which is recorded as restricted cash on the condensed consolidated balance sheets.

As of September 30, 2025 and December 31, 2024 , the Company had a letter of credit for the benefit of its landlord in the amount of $ 1.8 million, collateralized by a money market account, which is recorded as restricted cash on the condensed consolidated balance sheets.

Preferred Stock and Common Stock

Undesignated Preferred Stock

As of June 30, 2025 and December 31, 2024, the Company’s restated certificate of incorporation, as amended, authorizes the Company to issue up to 5,000,000 shares of undesignated preferred stock at $ 0.0001 par value per share.

As of June 30, 2025 and December 31, 2024, there were no shares of preferred stock issued or outstanding.

As of June 30, 2025, the Company’s restated certificate of incorporation, as amended, authorized the Company to issue up to 600,000,000 shares of common stock, $ 0.0001 par value per share.

As of September 30, 2025 and December 31, 2024 , the Company’s restated certificate of incorporation, as amended, authorizes the Company to issue up to 5,000,000 shares of undesignated preferred stock at $ 0.0001 par value per share.

As of September 30, 2025 and December 31, 2024 , there were no shares of preferred stock issued or outstanding.

As of September 30, 2025 , the Company’s restated certificate of incorporation, as amended, authorized the Company to issue up to 600,000,000 shares of common stock, $ 0.0001 par value per share.

As of December 31, 2024 , the Company’s restated certificate of incorporation, as amended, authorized the Company to issue up to 200,000,000 shares of common stock, $ 0.0001 par value per share.

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Each Series A warrant will be exercisable on the earlier of (i) December 1, 2025 and (ii) the trading day immediately following a period of five consecutive trading days on which the closing sale price of the Company’s common stock is a minimum of $ 1.50 per share for one share of common stock and will have an exercise price of $ 0.75 per share of common stock.

In addition, each Series A warrant will expire upon the earlier of (i) June 5, 2030 or (ii) immediately upon the

exercise of the corresponding prefunded warrant held by a holder in proportion to the extent that such corresponding prefunded warrant is exercised prior to December 1, 2025;

In addition, each Series A warrant will expire upon the earlier of (i) June 5, 2030 or (ii) immediately upon the exercise of the corresponding prefunded warrant held by a holder in proportion to the extent that such corresponding prefunded warrant is exercised prior to December 1, 2025;

provided that this term (ii) will no longer apply to the Series A warrants beginning on the first trading day immediately following a period of five consecutive trading days on which the closing sale price of the Company’s common stock is a minimum of $ 1.50 per share for one share of common stock.

Each Series B warrant will be exercisable on or after November 1, 2025, with an exercise price of $ 0.75 per share of common stock, and will expire on December 2, 2025, provided that if the closing sale price of the Company’s common stock is below the exercise price on such date, the exercise price will reset to the closing sale price on December 1, 2025 and the expiration time will be extended to December 31, 2025.

Each Series B warrant is exercisable beginning on November 1, 2025, with an exercise price of $ 0.75 per share of common stock, and will expire on December 2, 2025, provided that if the closing sale price of the Company’s common stock is below the exercise price on such date, the exercise price will reset to the closing sale price on December 1, 2025 and the expiration time will be extended to December 31, 2025.

Each Series C warrant will be exercisable on or after June 1, 2026, with an exercise price of $ 0.75 per share of common stock, and will expire on the earlier of (i) December 2, 2026 and (ii) the expiration time of the Series B warrant held by a holder in proportion to the extent that the corresponding Series B warrant expires without being exercised.

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The Company concluded the Series A warrants, the Series B warrants and the Series C warrants are required to be initially classified as liabilities as a result of their settlement provisions.

The Series A warrants, the Series B warrants and the Series

C warrants will continue to be classified as liabilities until such time as the applicable warrant is exercised, expires, or qualifies for equity classification.

The Series A warrants, the Series B warrants and the Series C warrants will continue to be classified as liabilities until such time as the applicable warrant is exercised, expires, or qualifies for equity classification.

The Company received initial gross proceeds from the offering of $ 50.0 million, before deducting approximately $ 3.0 million in aggregate issuance costs related to the offering, which consisted of underwriting discounts and commissions and offering expenses payable by the Company.

The Company allocated the gross proceeds as follows:

The Company allocated the initial gross proceeds as follows:

$ 26.8 million to the Series A warrants, $ 6.6 million to the Series B warrants and $ 5.1 million to the Series C warrants, in each case, based on the fair value of each instrument on the date of issuance with the remaining $ 11.5 million allocated to the prefunded warrants.

The Company allocated the issuance costs to the financial instruments in a manner consistent with the allocation of the proceeds.

The Company allocated approximately $ 2.3 million in issuance costs to the common stock warrants that are classified as liabilities, which was recorded as a component of other income (expense), net, on the condensed consolidated statements of operations and comprehensive loss during the three and six months ended June 30, 2025.

The Company allocated approximately $ 0.7 million in issuance costs to the prefunded warrants that are classified in equity, which was recorded as a reduction to additional paid in capital on the condensed consolidated balance sheets as of June 30, 2025.

During the three and six months ended June 30, 2025, the Company recognized a loss of less than $ 0.1 million related to the change in fair value of the common stock warrants, which is recorded as a component of the change in fair value of common stock warrant liabilities on the condensed consolidated statements of operations and comprehensive loss.

During each of the three and nine months ended September 30, 2025 , the Company recognized a loss of $ 15.4 million, related to the change in fair value of the common stock warrants, which is recorded as a component of the change in fair value of common stock warrant liabilities on the condensed consolidated statements of operations and comprehensive loss.

Private Placement

In March 2024, the Company entered into a securities purchase agreement with certain existing accredited investors pursuant to which the Company issued and sold an aggregate of 1,953,125 shares of its common stock at a purchase price of $ 0.64 per share and, in lieu of shares of the Company’s common stock, prefunded warrants to purchase up to an aggregate of 15,627,441 shares of its common stock at a purchase price of $ 0.6399 per prefunded warrant, through a private placement.

of shares of the Company’s common stock, prefunded warrants to purchase up to an aggregate of 15,627,441 shares of its common stock at a purchase price of $ 0.6399 per prefunded warrant, through a private placement.

The prefunded warrants are exercisable any time at an exercise price of $ 0.0001 per share.

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During the year ended December 31, 2024 , the Company issued and sold 7,000,000 shares of its common stock pursuant to the Cowen Sales Agreement at a price of $ 1.00 per share for aggregate gross proceeds of $ 7.0 million.

During the six months ended June 30, 2025, the Company issued and sold an additional 1,550,000 shares of its common stock pursuant to the Cowen Sales Agreement at a weighted average price of $ 1.3348 per share for aggregate gross proceeds of approximately $ 2.1 million.

During the nine months ended September 30, 2025 , the Company issued and sold an additional 1,550,000 shares of its common stock pursuant to the Cowen Sales Agreement at a weighted average price of $ 1.3348 per share for aggregate gross proceeds of approximately $ 2.1 million.

In March 2025, the Company filed a universal shelf registration statement on Form S-3 with the SEC to register for sale up to $ 250.0 million of its common stock, preferred stock, debt securities, units and warrants, which the Company may issue and sell from time to time in one or more offerings, which became effective on May 8, 2025 (333-285703) (the “New S-3 Shelf”).

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Shares Reserved for Future Issuance

The Company has reserved for future issuances the following shares of common stock underlying the securities issued below as of June 30, 2025 and December 31, 2024:

The Company has reserved for future issuances the following shares of common stock underlying the securities issued below as of September 30, 2025 and December 31, 2024:

September 30,

Stock options and unvested restricted stock units

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Upon effectiveness of the 2021 Plan, the Company ceased granting awards under the 2020 Plan.

The 2021 Plan provides for the grant of incentive stock options, nonstatutory stock options, stock appreciation rights, restricted stock awards, restricted stock units and other stock-based awards.

The 2021 Plan provides for the grant of

incentive stock options, nonstatutory stock options, stock appreciation rights, restricted stock awards, restricted stock units and other stock-based awards.

The Company initially reserved 6,579,016 shares of common stock under the 2021 Plan.

1 unchanged sentence

On January 1, 2025, the number of shares reserved for issuance under the 2021 Plan automatically increased by 2,293,405 shares.

As of June 30, 2025, there were 1,822,188 shares of common stock available for future issuance under the 2021 Plan.

As of September 30, 2025 , there were 1,907,013 shares of common stock available for future issuance under the 2021 Plan.

2022 Inducement Plan

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In March 2025, the number of shares reserved for issuance under the 2022 Inducement Plan increased by an additional 500,000 shares.

As of June 30, 2025, there were 383,000 shares of common stock available for future issuance under the 2022 Inducement Plan.

As of September 30, 2025 , there were 238,300 shares of common stock available for future issuance under the 2022 Inducement Plan.

2021 Employee Stock Purchase Plan

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The Company initially reserved 292,031 shares of common stock for issuance under the 2021 ESPP.

The 2021 ESPP provides that the number of shares of common

stock reserved for issuance under the 2021 ESPP will be cumulatively increased on January 1 of each calendar year by 1 % of the number of shares of the Company’s common stock outstanding on such date or such lesser amount determined by the Company’s board of directors (up to a maximum increase of 584,062 shares of common stock per year).

The 2021 ESPP provides that the number of shares of common stock reserved for issuance under the 2021 ESPP will be cumulatively increased on January 1 of each calendar year by 1 % of the number of shares of the Company’s common stock outstanding on such date or such lesser amount determined by the Company’s board of directors (up to a maximum increase of 584,062 shares of common stock per year).

On January 1, 2025, the number of shares reserved for issuance under the 2021 ESPP was increased by 458,681 shares.

During the six months ended June 30, 2025 and 2024, the Company issued 45,505 shares of common stock and 38,998 shares of common stock under the 2021 ESPP, respectively.

As of June 30, 2025, there were 1,314,384 shares available for future issuance under the 2021 ESPP.

During the nine months ended September 30, 2025 and 2024 , the Company issued 45,505 shares of common stock and 38,998 shares of common stock under the 2021 ESPP, respectively.

As of September 30, 2025 , there were 1,314,384 shares available for future issuance under the 2021 ESPP.

Stock-Based Compensation Expense

During the three and six months ended June 30, 2025 and 2024, the Company recorded compensation expense related to stock options, restricted stock units and restricted common stock for employees and non-employees and share purchases under the 2021 ESPP for employees, which was allocated as follows in the condensed consolidated statements of operations and comprehensive loss:

Three Months Ended June 30,

Six Months Ended June 30,

During the three and nine months ended September 30, 2025 and 2024, the Company recorded compensation expense related to stock options, restricted stock units and restricted common stock for employees and non-employees and share purchases under the 2021 ESPP for employees, which was allocated as follows in the condensed consolidated statements of operations and comprehensive loss:

Three Months Ended September 30,

Nine Months Ended September 30,

Research and development expense

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Outstanding as of December 31, 2024

Outstanding as of June 30, 2025

Exercisable as of June 30, 2025

Outstanding as of September 30, 2025

Exercisable as of September 30, 2025

(1) The aggregate intrinsic value of stock options is calculated as the difference between the exercise price of the stock options and the fair value of the Company’s common stock for those stock options that had exercise prices lower than the fair value of the Company’s common stock as of the end of the period.

Using the Black-Scholes option pricing model, the weighted average fair value of options granted to employees and directors during the six months ended June 30, 2025 and 2024 was $ 0.72 per share and $ 0.68 per share, respectively.

The following assumptions were used in determining the fair value of options granted during the six months ended June 30, 2025 and 2024:

Six Months Ended June 30,

Using the Black-Scholes option pricing model, the weighted average fair value of options granted to employees and directors during the nine months ended September 30, 2025 and 2024 was $ 0.71 per share and $ 0.68 per share, respectively.

The following assumptions were used in determining the fair value of options granted during the nine months ended September 30, 2025 and 2024:

Nine Months Ended September 30,

Risk-free interest rate

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Expected volatility

As of June 30, 2025, the Company had unrecognized stock-based compensation expense of $ 5.2 million related to stock options issued to employees and directors, which is expected to be recognized over a weighted-average period of 2.3 years.

As of September 30, 2025 , the Company had unrecognized stock-based compensation expense of $ 4.1 million related to stock options issued to employees and directors, which is expected to be recognized over a weighted-average period of 2.8 years.

Restricted Stock Units

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Unvested as of December 31, 2024

Unvested as of June 30, 2025

For each of the six months ended June 30, 2025 and 2024, the Company recognized less than $ 0.1 million of stock-based compensation expense related to these awards.

As of June 30, 2025, the Company had unrecognized stock-based compensation expense of $ 0.2 million related to these restricted stock units, which is expected to be recognized over 2.5 years.

Unvested as of September 30, 2025

For each of the nine months ended September 30, 2025 and 2024 , the Company recognized less than $ 0.1 million of stock-based compensation expense related to these awards.

As of September 30, 2025 , the Company had unrecognized stock-based compensation expense of $ 0.2 million related to these restricted stock units, which is expected to be recognized over 2.3 years.

Net Loss Per Share

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The weighted average number of shares of common stock used in the basic and diluted net loss per share calculation includes the prefunded warrants to purchase common stock issued in connection with the Company’s private placements with certain existing investors and Gilead and the Company’s follow-on public offering, as the prefunded warrants are exercisable at any time for nominal cash consideration.

As of June 30, 2025, no prefunded warrants have been exercised and 92,278,707 prefunded warrants are outstanding.

As of September 30, 2025 , no prefunded warrants have been exercised and 92,278,707 prefunded warrants are outstanding.

The following table sets forth the outstanding shares of common stock equivalents, presented based on amounts outstanding at each period end, that were excluded from the calculation of diluted net loss per share for the periods indicated because including them would have been anti-dilutive:

Six Months Ended

Nine Months Ended

September 30,

Unvested restricted stock units

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Total common stock equivalents

Subsequent Events

On October 20, 2025, the Company filed a proxy statement seeking stockholder approval of the following:

(i) a one-time repricing of certain outstanding employee stock options and (ii) the Xilio Therapeutics, Inc.

2025 Stock Incentive Plan, with an aggregate of 32.0 million shares of common stock reserved for issuing stock options to employees .

The stockholder meeting to vote on the proposals stated within the proxy statement is scheduled to be held on November 21, 2025.

Compared sentence by sentence after normalising whitespace, quotation marks, case and digits, so re-formatting and restated figures do not read as changed language. Wording changes appear as one removal and one addition. The current filing and the prior one are authoritative.

What changed 10-Q

Item 1. Financial Statements