What changed in this filing

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Item 1. Financial Statements

2026-05-12 compared with 2025-11-13 · 196 added, 232 removed, 310 unchanged (58% 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

Collaboration and license agreement receivable

Prepaid expenses and other current assets

3 unchanged sentences

Operating lease right-of-use asset

LIABILITIES AND STOCKHOLDERS’ (DEFICIT) EQUITY

LIABILITIES AND STOCKHOLDERS’ EQUITY

Current liabilities

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Common stock warrant liabilities

Liabilities to issue common stock

Total liabilities

Commitments and contingencies (Note 7)

Stockholders’ (deficit) equity

Stockholders’ equity

Preferred stock, $ 0.0001 par value;

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Common stock, $ 0.0001 par value;

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;

600,000,000 shares authorized;

5,782,536 shares issued and outstanding at March 31, 2026;

4,530,641 shares issued and outstanding at December 31, 2025

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Accumulated deficit

Total stockholders’ (deficit) equity

Total liabilities and stockholders’ (deficit) equity

Total stockholders’ equity

Total liabilities and stockholders’ equity

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

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(In thousands, except share and per share data)

Three Months Ended September 30,

Nine Months Ended September 30,

Three Months Ended March 31,

Collaboration and license revenue

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General and administrative

Restructuring

Total operating expenses

Loss from operations

Other income (expense), net

Other income, net

Change in fair value of common stock warrant liabilities

Other income (expense), net

Total other income (expense), net

Other income, net

Total other income, net

Net loss and comprehensive loss

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XILIO THERAPEUTICS, INC.

Condensed Consolidated Statements of Stockholders’ ( Deficit) Equity

For the three months ended September 30, 2025 and 2024

(In thousands, except share data)

Stockholders'

Balance at June 30, 2025

Exercise of stock options

Stock-based compensation expense

Balance at September 30, 2025

Stockholders'

Balance at June 30, 2024

Exercise of stock options

Stock-based compensation expense

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’ (Deficit) Equity

For the nine months ended September 30, 2025 and 2024

Condensed Consolidated Statements of Stockholders’ Equity

For the three months ended March 31, 2026 and 2025

(In thousands, except share data)

1 unchanged sentence

Balance at December 31, 2025

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

Issuance of common stock in connection with the AbbVie stock purchase agreement, 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

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

Issuance of common stock to settle the liabilities to issue common stock

Issuance of common stock in connection with the exercise of prefunded warrants

Vesting of restricted stock units

1 unchanged sentence

Stock-based compensation expense

Balance at September 30, 2025

Balance at March 31, 2026

Stockholders'

Balance at December 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 the AbbVie stock purchase agreement, 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

Vesting of restricted stock units

Exercise of stock options

Stock-based compensation expense

Balance at September 30, 2024

Balance at March 31, 2025

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

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(In thousands)

Nine Months Ended September 30,

Three Months Ended March 31,

Cash flows from operating activities:

Adjustments to reconcile net loss to net cash provided by operating activities:

Adjustments to reconcile net loss to net cash (used in) provided by operating activities:

Depreciation and amortization

1 unchanged sentence

Change in fair value of common stock warrant liabilities

Issuance costs allocated to common stock warrant liabilities

Loss on disposal of property and equipment

Changes in operating assets and liabilities:

License agreement receivable

Collaboration and license agreement receivable

Prepaid and other assets

2 unchanged sentences

Deferred revenue

Net cash used in operating activities

Net cash (used in) provided by operating activities

Cash flows from investing activities:

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Cash flows from financing activities:

Repayments of debt principal

Payments of finance lease

Proceeds from issuance of common stock under employee stock purchase plan

Proceeds from exercise of stock options

Proceeds from issuance of prefunded warrants and common stock warrants in connection with a follow-on public offering, net of issuance costs

Proceeds from issuance of prefunded warrants in connection with a follow-on offering, net of issuance costs

Proceeds from issuance of common stock in connection with the AbbVie stock purchase agreement, net of issuance costs

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

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

Proceeds from exercise of stock options

Payments of issuance costs included in accounts payable or accrued expenses at prior year end

Net cash provided by financing activities

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Cash, cash equivalents and restricted cash, end of period

Supplemental cash flow disclosure:

Cash paid for interest

Supplemental disclosure of non-cash activities:

Transfer of finance lease asset to property and equipment

Capital expenditures included in accounts payable or accrued expenses

Settlement of liabilities to issue common stock by issuing common stock

Reconciliation to amounts within the consolidated balance sheets:

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XILIO THERAPEUTICS, INC.

Notes to Condensed Consolidated Financial Statements

Notes to Condensed Consoli dated Financial Statements

(Dollars in thousands, unless otherwise stated)

Description of Business, Liquidity and Going Concern

Description of Business and Liquidity

Xilio Therapeutics, Inc.

(“Xilio” or the “Company”) is a clinical-stage biotechnology company dedicated to discovering and developing tumor-activated immuno-oncology (“I-O”) therapies with the goal of significantly improving outcomes for people living with cancer without the systemic side effects of current I-O treatments.

(“Xilio” or the “Company”) is a clinical-stage biotechnology company dedicated to discovering and developing masked immuno-oncology (“I-O”) therapies with the goal of significantly improving outcomes for people living with cancer without the systemic side effects of current I-O treatments.

The Company was incorporated in Delaware in June 2020, and its headquarters are located in Waltham, Massachusetts.

In June 2025, the Company received initial gross proceeds of $ 50.0 million upon the closing of a follow-on public offering of prefunded warrants and accompanying common stock warrants.

If certain of the common stock warrants are exercised in cash at their initial exercise price of $ 0.75 per warrant, the Company will receive up to $ 100.0 million of additional gross proceeds by the second half of 2026.

See Note 8 for additional information.

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

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 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.

If the Company is not able to secure sufficient additional capital when needed, the Company may need to implement additional cost reduction strategies, which could include delaying, limiting, further reducing or eliminating both internal and external costs related to its operations and research and development programs.

In addition, the Company has based its estimates on assumptions that may prove to be wrong, and the Company could exhaust its available capital resources sooner than it anticipates.

The accompanying condensed consolidated financial statements have been prepared on a going concern basis, which contemplates the realization of assets and satisfaction of liabilities in the ordinary course of business.

The condensed consolidated financial statements do not include any adjustments relating to the recoverability and classification of recorded asset amounts or the amounts and classification of liabilities that might result from the outcome of this uncertainty.

As of March 31, 2026, the Company had an accumulated deficit of $ 428.3 million and has incurred significant operating losses, including net losses of $ 9.5 million and $ 13.3 million for the three months ended March 31, 2026 and 2025, respectively.

The Company expects its operating losses and negative operating cash flows to continue for the foreseeable future as it continues to advance its product candidates through clinical trials, maintains the infrastructure necessary to support these activities and continues to incur costs associated with operating as a public company.

As of March 31, 2026, the Company had cash and cash equivalents of $ 150.3 million.

Based on its current operating plans, the Company anticipates that its existing cash and cash equivalents as of March 31, 2026 will be sufficient to enable it to fund its operating expenses and capital expenditure requirements for at least twelve months from the date of the issuance of these condensed consolidated financial statements.

However, the Company has based its estimates on assumptions that may prove to be wrong.

If actual results differ from the Company’s estimates, the Company could exhaust its available capital resources sooner than it anticipates, in which case, the Company would be required to seek additional capital sooner or curtail planned activities to reduce operating expenses, which may have an adverse impact on the Company’s ability to achieve its business objectives.

Summary of Significant Accounting Policies

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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, 2025 and notes thereto, included in the Company’s Annual Report on Form 10-K filed with the SEC on March 23, 2026.

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 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.

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 March 31, 2026 and the results of its operations for the three months ended March 31, 2026 and 2025 and cash flows for the three months ended March 31, 2026 and 2025.

Such adjustments are of a normal and recurring nature.

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.

The results for the three months ended March 31, 2026 are not necessarily indicative of the results for the year ending December 31, 2026 or for any future period.

On March 13, 2026, the Company effected a reverse stock split of its common stock at a ratio of 1-for-14.

The reverse stock split did not impact the number of authorized shares of common stock or preferred stock or the par value per share of the common stock or preferred stock.

All share and per share amounts in these condensed consolidated financial statements and notes thereto have been adjusted retroactively to reflect the reverse stock split for all periods presented.

Principles of Consolidation

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The significant accounting policies used in preparation of the unaudited condensed consolidated financial statements are described in Note 2, “ Summary of Significant Accounting Policies ” of the audited consolidated financial statements included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2025.

Except as described below, there have been no material changes to the significant accounting policies previously disclosed in the Company’s Annual Report on Form 10-K for the year ended December 31, 2024.

Common Stock Warrants

The Company accounts for warrants to purchase shares of its common stock in accordance with the guidance in ASC 480, Distinguishing Liabilities from Equity (“ASC 480”) and ASC 815, Derivatives and Hedging (“ASC 815”).

The Company classifies warrants issued for the purchase of shares of its common stock as either equity or liability instruments based on an assessment of the specific terms and conditions of each respective contract.

Such assessment includes determining whether the warrants are freestanding financial instruments or embedded in a host instrument, whether the warrants are liabilities within the scope of ASC 480, whether the warrants meet the definition of a derivative in ASC 815 and whether the warrants meet the requirements for equity classification pursuant to the indexation and equity classification criteria in ASC 815.

The Company determines the classification for its warrants at the time of issuance and updates its assessment as necessary.

Warrants that meet all of the criteria for equity classification are recorded as a component of additional paid-in capital and are not subsequently remeasured.

Warrants that are classified as liabilities are recorded at fair value on the issuance date and remeasured to fair value at each reporting period, with the change in fair value recorded as a component of other income (expense), net, on the condensed consolidated statements of operations and comprehensive loss.

There have been no material changes to the significant accounting policies previously disclosed in the Company’s Annual Report on Form 10-K for the year ended December 31, 2025.

Use of Estimates

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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.

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

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.

Actual results could differ from those estimates.

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The Company has not experienced any losses in its cash and cash equivalents and does not believe that it is subject to unusual credit risk beyond the normal credit risk associated with commercial banking relationships.

The Company has one operating and reportable segment, the consolidated Company operations, reflecting the integrated nature of its business focused on discovering and developing tumor-activated I-O therapies.

The Company has one operating and reportable segment, the consolidated Company operations, reflecting the integrated nature of its business focused on discovering and developing masked I-O therapies.

The Company’s chief operating decision maker (“CODM”) is its chief executive officer.

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Recent Accounting Pronouncements Not Yet Adopted

In December 2023, the FASB issued ASU No.

2023-09, Income Taxes (Topic 740):

Improvements to Income Tax Disclosures (“ASU 2023-09”), which modifies the rules on income tax disclosures to require entities to disclose (1) specific categories in the rate reconciliation, (2) the income or loss from continuing operations before income tax expense or benefit (separated between domestic and foreign) and (3) income tax expense or benefit from continuing operations (separated by federal, state and foreign).

ASU 2023-09 also requires entities to disclose their income tax payments to international, federal, state and local jurisdictions, among other changes.

The guidance is effective for annual periods beginning after December 15, 2024.

Early adoption is permitted for annual financial statements that have not yet been issued or made available for issuance.

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

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.

2024-03, Income Statement - Reporting Comprehensive Income - Expense Disaggregation Disclosures (Subtopic 220-40):

Disaggregation of Income Statement Expenses (“ASU 2024-03”), and in January 2025, the FASB issued ASU No.

In November 2024 the FASB issued Accounting Standards Update No.

2024-03, Income Statement—Reporting Comprehensive Income—Expense Disaggregation Disclosures (Subtopic 220-40):

Clarifying the Effective Date (“ASU 2025-01”).

ASU 2024-03 requires additional disclosure of the nature of expenses included in the income statement as well as disclosures about specific types of expenses included in the expense captions presented in the income statement.

ASU 2024-03, as clarified by ASU 2025-01, is effective for public companies for annual periods beginning after December 15, 2026, and interim reporting periods beginning after December 15, 2027.

Disaggregation of Income Statement Expenses (“ASU 2024-03”), which requires disclosure, in the notes to financial statements, of specified information about certain costs and expenses.

The guidance is effective for annual reporting periods beginning after December 15, 2026, and interim reporting periods beginning after December 15, 2027.

Early adoption 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 is currently evaluating the potential impact of adopting this new guidance on its consolidated financial statements and related disclosures.

Fair Value Measurements

The Company measures the following liabilities at fair value on a recurring basis:

Liabilities measured at fair value on a recurring basis consist of the following as of March 31, 2026:

Financial liabilities:

Series A warrant to purchase common stock

Series B warrant to purchase common stock

Series C warrant to purchase common stock

Total financial liabilities

The fair value of the common stock warrant liabilities, which are described in more detail in Note 8, are calculated utilizing a Black-Scholes option pricing model for the Series A warrants and a Monte Carlo simulation model for the Series B warrants and the Series C warrants.

Series A warrants to purchase common stock

Series C warrants to purchase common stock

Total financial liabilities at March 31, 2026

Liabilities measured at fair value on a recurring basis consist of the following as of December 31, 2025:

Financial liabilities:

Series A warrants to purchase common stock

Series C warrants to purchase common stock

Total financial liabilities at December 31, 2025

The Black-Scholes option pricing model and the Monte Carlo simulation model both require the use of assumptions, certain of which are not observable in the market, which represent Level 3 measurements within the fair value hierarchy.

The Black-Scholes pricing model and the Monte Carlo simulation model assumptions include the warrant exercise price, the expected life of the warrant, the current price of the Company’s common stock, expected volatility, the risk-free interest rate for the expected life of the warrant and expected dividend yield.

The Black-Scholes pricing model and the Monte Carlo simulation model assumptions include the warrant exercise price, the expected term of the warrant, the current price of the Company’s common stock, expected volatility, the risk-free interest rate for the expected term of the warrant and expected dividend yield.

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 September 30, 2025 were the following:

September 30,

(issuance date)

The following assumptions were used in determining the fair value of the Company’s common stock warrant liabilities as of March 31, 2026 and December 31, 2025:

Closing price of common stock

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Balance at December 31, 2025

Initial fair value of common stock warrant liabilities

Change in fair value of common stock warrant liabilities

Balance at September 30, 2025

Balance at March 31, 2026

Property and Equipment, Net

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

September 30,

Property and equipment, net consists of the following as of March 31, 2026 and December 31, 2025:

Laboratory equipment

Computers and software

Furniture and fixtures

Leasehold improvements

Construction in process

Total property and equipment

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Property and equipment, net

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 .

The Company recognized depreciation and amortization expense related to property and equipment of $ 0.3 million and $ 0.5 million for the three months ended March 31, 2026 and 2025, respectively .

Accrued Expenses

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

September 30,

Accrued expenses consist of the following as of March 31, 2026 and December 31, 2025:

External research and development

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Total accrued expenses

Collaboration and License Agreements

Collaboration, License and Option Agreements

Collaboration, License and Option Agreement with AbbVie

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 February 2025, Xilio Development entered into a collaboration, license and option agreement (the “Collaboration Agreement”) with AbbVie Group Holdings Limited ("AbbVie") for up to four programs leveraging the Company’s proprietary masking 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”).

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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.

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in a private placement at a purchase price of $ 32.20 per share for an aggregate purchase price of $ 10.0 million.

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.

As of March 31, 2026 , the Company has received $ 57.0 million in payments under the AbbVie agreements, consisting of a $ 42.0 million upfront cash payment under the Collaboration Agreement, $ 10.0 million in gross proceeds from the private placement under the stock purchase agreement and a $ 5.0 million development milestone related to the Collaboration Program, which was recorded as a receivable on the condensed consolidated balance sheet as of December 31, 2025 and was received in the first quarter of 2026.

In the second quarter of 2026, the Company achieved an additional $ 6.0 million development milestone.

T he 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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based on the fair market value of the common stock on the date of issuance.

The fair market value of the common stock issued to AbbVie Inc.

The fair market value of the common stock issued to AbbVie

was $ 2.9 million, based on the closing price of the Company’s common stock on the date of issuance, resulting in a $ 7.1 million premium.

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In addition, the Company identified several customer options that were evaluated to determine if such options represented material rights, each of which would be considered a performance obligation at contract inception only if the option provides a material right to AbbVie that it would not receive without entering into that contract.

The Company determined that the exclusive license and development services related to the Collaboration Program Services were not capable of being distinct on the basis that the services to be provided by Xilio Development are specialized in nature, specifically with respect to its specialized expertise in developing masked antibody-based immunotherapies and the Company’s proprietary platform for tumor-activated biologics.

Accordingly, the Company concluded that these promises should be a combined performance obligation consisting of the exclusive license and the development services for the Collaboration Program Services.

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

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.

During the year ended December 31, 2025, the overall transaction price was adjusted to include the achievement of the $ 5.0 million development milestone related to the Collaboration Program in the fourth quarter of 2025.

All additional contingent payments are fully constrained as of March 31, 2026, 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.

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.

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The Company plans to recognize such revenue at the later of (i) when the related sales occur or (ii) when the performance obligation to which some or all of the royalty has been allocated has been satisfied (or partially satisfied).

The Company allocated the transaction price to the performance obligations on a relative selling price basis as follows:

The Company allocated the transaction price at the outset of the arrangements to the performance obligations on a relative selling price basis as follows:

(i) $ 32.4 million related to the Collaboration Program Performance Obligation;

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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.

Revenue associated with the material rights will be recognized upon expiry if the option is not exercised.

Revenue associated with the material rights will be recognized upon expiry if the option is not

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 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.

During the three months ended March 31, 2026 and 2025 , the Company recognized collaboration and license revenue of $ 8.0 million and $ 0.7 million, respectively, under the Collaboration Agreement and the stock purchase agreement.

As of March 31, 2026 , the Company recorded deferred revenue of $ 26.0 million, of which $ 16.1 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 efarindodekin alfa (XTX301), the Company’s tumor-activated IL-12 product candidate, and specified other molecules directed to IL-12.

In March 2024, Xilio Development entered into a license agreement (the "License Agreement") with Gilead Sciences, Inc.

("Gilead"), pursuant to which it granted Gilead an exclusive global license to develop and commercialize efarindodekin alfa, the Company’s masked 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.

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The prefunded warrants are exercisable any time at an exercise price of $ 0.0014 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 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.

The Company has received $ 72.5 million in payments under the Gilead agreements, consisting of the $ 30.0 million upfront cash payment under the License Agreement, $ 25.0 million in gross proceeds from private placements under the stock purchase agreement and a $ 17.5 million development milestone.

As of March 31, 2026 , the Company is eligible to receive up to $ 575.0 million in additional contingent payments, which consist of 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.

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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(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 e farindodekin alfa 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 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.

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

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.

During the year ended December 31, 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 March 31, 2026, 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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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.

During the three months ended March 31, 2026 and 2025 , the Company recognized collaboration and license revenue of $ 4.7 million and $ 2.2 million, respectively, under the License Agreement and the stock purchase agreement with Gilead.

As of March 31, 2026 , the Company recorded deferred revenue under the License Agreement and the stock purchase agreement of $ 22.0 million, of which $ 15.5 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.

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Collaboration and license revenue recognized

Deferred revenue as of September 30, 2025

Deferred revenue as of March 31, 2026

Clinical Trial Collaboration with F.

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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 metastatic 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.

Under the clinical supply agreement, the Company is eligible to receive specified cost-sharing payments from Roche.

As of March 31, 2026, 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.

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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 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 .

During the three months ended March 31, 2026, the Company did no t recognize a reduction of research and development expense and during the three months ended March 31, 2025, t he Company recognized a reduction of research and development expense of $ 2.0 million .

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 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.

As of March 31, 2026 and December 31, 2025 , 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 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.

Follow-On Public Offering

In June 2025, the Company closed a follow-on public offering of prefunded warrants and accompanying common stock warrants and received initial gross proceeds of $ 50.0 million before deducting underwriting discounts and commissions and offering expenses payable by the Company.

In connection with the offering, the Company issued prefunded warrants to purchase 66,676,000 shares of common stock, accompanied by Series A warrants to purchase 66,676,000 shares of common stock (or, in certain circumstances, prefunded warrants) (the “Series A warrants”), Series B warrants to purchase 66,676,000 shares of common stock (or, in certain circumstances, prefunded warrants) (the “Series B warrants”), and Series C warrants to purchase 66,676,000 shares of common stock (or, in certain circumstances, prefunded warrants) (the “Series C warrants”).

As of March 31, 2026 and December 31, 2025 , 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 March 31, 2026 and December 31, 2025 , there were no shares of preferred stock issued or outstanding.

As of March 31, 2026 and December 31, 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.

February 2026 Follow-On Offering

In February 2026, the Company closed a follow-on offering of prefunded warrants and received net proceeds of $ 37.3 million.

In connection with the offering, the Company issued prefunded warrants to purchase 5,341,404 shares of its common stock.

Each prefunded warrant is exercisable for one share of the Company's common stock.

The purchase price of each prefunded warrant was $ 7.4886 .

Each prefunded warrant has an exercise price of $ 0.0014 per share and will be exercisable from the date of issuance until fully exercised, subject to beneficial ownership limitations for each holder.

June 2025 Follow-On Offering

In June 2025, the Company closed a follow-on offering of prefunded warrants and accompanying common stock warrants and received net proceeds of $ 47.0 million.

In connection with the offering, the Company issued prefunded warrants to purchase 4,762,533 shares of common stock, accompanied by Series A warrants to purchase 4,762,533 shares of common stock (or prefunded warrants in lieu of common stock) (the “Series A warrants”), Series B warrants to purchase 4,762,533 shares of common stock (or prefunded warrants in lieu of common stock) (the “Series B warrants”), and Series C warrants to purchase 4,762,533 shares of common stock (or prefunded warrants in lieu of common stock) (the “Series C warrants”).

The combined public offering price of one prefunded warrant, one Series A warrant, one Series B warrant and one Series C warrant, which were sold together but are immediately separable, was $ 10.4986 , which was equal to the combined offering price of the prefunded warrants, Series A warrants, Series B warrants and Series C warrants, less the $ 0.0014 per share exercise price of the prefunded warrants.

The exercisability of the prefunded warrants and common stock warrants is subject to limitations on exercise.

Specifically, a holder will be prohibited from exercising any portion of any warrant if immediately prior to or following such exercise such holder (together with its affiliates) would beneficially own more than 4.99 % (or up to 19.99 % at the election of the holder) of the Company’s issued and outstanding common stock immediately after giving effect to the exercise, as such percentage ownership is determined in accordance with the terms of the warrant.

However, any holder of any warrant may increase or decrease such percentage to any other percentage not in excess of 19.99 %, provided that any such increase will not be effective until the 61 st day after notice from the holder is delivered to the Company.

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;

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 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.

In addition, if the closing sale price of the Company’s common stock is below the exercise price on December 2, 2026, the exercise price will reset to the closing sale price on December 1, 2026 and the expiration time will be extended to December 31, 2026.

The prefunded warrants and Series A warrants may be exercised for cash or on a net exercise or “cashless” basis, and the Series B warrants and Series C warrants may be exercised for cash or on a net exercise or “cashless” basis in the event there is no effective registration statement or prospectus available which covers the Series B warrants and Series C warrants and shares of common stock issuable upon exercise of the Series B warrants and Series C warrants.

There can be no assurance that any of the warrants will be exercised for cash or at all, and it is possible that the common stock warrants may expire without being exercised.

If all of the Series B warrants and the Series C warrants sold in the offering are exercised in cash at their initial exercise price, the Company will receive additional gross proceeds of approximately $ 100.0 million by the end of 2026.

In the event of certain fundamental transactions, each holder of the prefunded warrants and the common stock warrants has the right to receive, upon exercise of such warrant, the same amount and kind of securities, cash or property as such holder would have been entitled to receive upon the occurrence of such fundamental transaction if it had been, immediately prior to such fundamental transaction, the holder of the number of shares of common stock underlying such holder’s warrant without regard to any limitations on exercise contained in such holder’s warrant.

The holders of Series A warrants are alternatively entitled to elect to receive consideration in an amount equal to the Black Scholes value of the unexercised portion of such holder’s Series A warrants and if the fundamental transaction is within the Company’s control, the Series A warrant holders can require the Black Scholes value to be paid in cash.

In addition, for each dollar of non-dilutive capital received by the Company prior to the exercise or expiration of the Series B warrants and Series C warrants, the Company may elect to cancel a number of warrant shares equal to $1.00 divided by the $0.75 warrant exercise price (or one and one-third warrants ) without any compensation paid by the Company to the warrant holders.

For example, if the Company received $30.0 million in non-dilutive capital, it could elect to cancel 40.0 million of warrant shares.

In addition, for each dollar of non-dilutive capital received by the Company prior to the exercise or expiration of the remaining outstanding Series C warrants, the Company may elect to cancel a number of warrant shares equal to $ 14.00 divided by the $ 10.50 warrant exercise price (or one and one-third warrants ) without any compensation paid by the Company to the warrant holders.

Subject to certain specified exceptions, non-dilutive capital includes:

upfront payments under any future collaboration, license or similar agreement;

upfront payments under any future collaboration, license or similar

milestone payments and option fees under any current or future collaboration, license or similar agreement;

and net proceeds pursuant to any equity issuance where the purchase price per share is above $ 21.00 .

The Company concluded that the prefunded warrants, the Series A warrants, the Series B warrants and the Series C warrants are freestanding financial instruments because each of these instruments can be transferred or assigned by the holder subject to compliance with the applicable securities laws and are legally detachable and separately exercisable.

At the June 2025 issuance date, the Company concluded that the prefunded warrants, the Series A warrants, the Series B warrants and the Series C warrants are freestanding financial instruments because each of these instruments can be transferred or assigned by the holder subject to compliance with the applicable securities laws and are legally detachable and separately exercisable.

The Company determined the classification of each warrant based on the guidance in ASC 480 and ASC 815.

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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 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 Series B warrants that were exercised for common stock and prefunded warrants in lieu of shares of common stock were reclassified to equity on the later of the date of each exercise, or December 2, 2025, the date the remaining outstanding Series B warrants qualified for equity classification due to the settlement of the exercise price reset feature.

The Series A warrants and the remaining outstanding 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 underwriting discounts and commissions and offering expenses payable by the Company.

The Company allocated the initial gross proceeds as follows:

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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 nine months ended September 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 September 30, 2025.

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.

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

The private placement closed in April 2024.

The Company received aggregate gross proceeds of $ 11.3 million from the private placement, before deducting placement agent fees and expenses payable by the Company.

The shares of common stock issued and sold in the private placement were registered for resale pursuant to the Company’s registration statement on Form S-3 filed with the SEC on April 30, 2024, which became effective on May 6, 2024.

“At-The-Market” Offering Program

In November 2022, 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 could issue and sell from time to time in one or more offerings, which became effective on November 18, 2022 (333-268264) (the “Prior S-3 Shelf”).

In November 2022, the Company entered into a sales agreement (the “Cowen Sales Agreement”) with Cowen and Company LLC under which the Company could issue and sell shares of its common stock, from time to time, having an aggregate offering price of up to $ 75.0 million under a sales agreement prospectus filed as part of the Prior S-3 Shelf.

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 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”).

In March 2025, the Company terminated the Cowen Sales Agreement, and the Company entered into a new sales agreement with Leerink Partners, LLC (the “Leerink Sales Agreement”), under which the Company may issue and sell shares of its common stock from time to time at an aggregate offering price of up to $ 50.0 million.

Prior to the effectiveness of the New S-3 Shelf, the offering of shares under the Leerink Sales Agreement was registered under the Prior S-3 Shelf.

In connection with the effectiveness of the New S-3 Shelf, the registration of such offering under the Prior S-3 Shelf was terminated and such offering was registered under the New S-3 Shelf.

During the three months ended March 31, 2026 , the Company recognized a gain of $ 3.3 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.

The exercisability of the prefunded warrants and common stock warrants is subject to limitations on exercise.

During the year ended December 31, 2025, 524,033 prefunded warrants were exercised and 4,238,500 prefunded warrants remain outstanding as of December 31, 2025.

No prefunded warrants were exercised during the three months ended March 31, 2026.

Each Series A warrant became exercisable on December 1, 2025 , with an exercise price of $ 10.50 per share of common stock, and will expire on June 5, 2030.

Through March 31, 2026 , no Series A warrants have been exercised and 4,762,533 Series A warrants remain outstanding.

Each Series B warrant became exercisable on November 1, 2025 and was exercisable through December 31, 2025.

During the year ended December 31, 2025, 3,443,388 of the Series B warrants were exercised for 1,008,415 shares of common stock and 2,434,973 prefunded warrants in lieu of shares of common stock.

The Company received net proceeds of $ 34.3 million from the exercise of the Series B warrants, after deducting underwriting discounts and commissions and offering expenses payable by the Company.

The remaining 1,319,145 Series B warrants were not exercised and expired on December 31, 2025.

In addition, 1,319,145 Series C warrants expired according to their terms on December 31, 2025 in connection with the expiration of unexercised Series B warrants, and 3,443,388 of the Series C warrants remained outstanding as of December 31, 2025.

Through March 31, 2026 , no ne of the Series B warrants that were exercised for prefunded warrants in lieu of shares of common stock have been exercised for shares of common stock.

Each remaining Series C warrant will be exercisable on or after June 1, 2026, with an exercise price of $ 10.50 per share of common stock, and will expire on December 2, 2026.

In addition, if the closing sale price of the Company's common stock is below the exercise

price on December 2, 2026, the exercise price will reset to the closing sale price on December 1, 2026 and the expiration time will be extended to December 31, 2026.

The prefunded warrants and Series A warrants may be exercised for cash or on a net exercise or “cashless” basis, and the Series C warrants may be exercised for cash or on a net exercise or “cashless” basis in the event there is no effective registration statement or prospectus available which covers the Series C warrants and shares of common stock issuable upon exercise of the Series C warrants.

There can be no assurance that any of the warrants that remain outstanding as of March 31, 2026 will be exercised for cash or at all, and it is possible that the common stock warrants may expire without being exercised.

If all of the outstanding Series C warrants are exercised in cash at their current exercise price of $ 10.50 per warrant, the Company will receive up to $ 36.2 million in additional total gross proceeds by the end of 2026 , before deducting underwriting discounts and commissions and any offering expenses.

Sales Agreement and “At-The-Market” Facility

In March 2025, the Company entered into an “at-the-market” (“ATM”) facility with Leerink Partners, LLC (“Leerink”) pursuant to which the Company could initially issue and sell shares of its common stock from time to time at an aggregate offering price of up to $ 50.0 million through Leerink as sales agent.

In February 2026, the Company filed a prospectus supplement to reduce the amount of common stock it may offer and sell under the ATM facility to an aggregate offering price of up to $ 9.5 million.

The Company did no t issue any shares under the ATM facility during the three months ended March 31, 2026.

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 September 30, 2025 and December 31, 2024:

September 30,

Shares of common stock reserved for future issuance consists of the following as of March 31, 2026 and December 31, 2025:

Stock options and unvested restricted stock units

Employee stock purchase plan

Common stock in process of settlement at period end

Prefunded warrants

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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 469,929 shares of common stock under the 2021 Plan.

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On January 1, 2026, the number of shares reserved for issuance under the 2021 Plan automatically increased by 226,931 shares.

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

As of March 31, 2026 , there were 356,869 shares of common stock available for future issuance under the 2021 Plan.

2025 Stock Incentive Plan

In November 2025, the Company’s stockholders adopted the 2025 Stock Incentive Plan (the “2025 Plan”), which had previously been adopted by the Company’s board of directors subject to stockholder approval.

The 2025 Plan provides for the grant of stock options to employees for 2,285,592 shares of common stock, divided into four equal tranches of 571,398 total shares per tranche, with the vesting of each tranche of stock options tied to a tranche of the June 2025 warrants, which are further described in Note 8.

The stock options granted under the 2025 Plan vest as follows:

• The first tranche of stock options vests in equal monthly installments over a period of three years , subject to the employee continuing to provide services to the Company on each vesting date.

• The second tranche of stock options ("Tranche 2 Stock Options") will become eligible to vest based on the portion of such stock options that equals the percentage of the Series A warrants that are exercised by December 31 of each of 2025, 2026, 2027, 2028, and 2029 and on June 30, 2030 (each, a “measurement date”).

Any Tranche 2 Stock Options will vest in three equal installments with one-third vesting on the applicable measurement date and the remaining two-thirds vesting in equal annual installments on each of the subsequent two anniversaries thereafter.

• The third tranche of stock options ("Tranche 3 Stock Options") became eligible to vest based on the portion of such stock options that equaled the percentage of Series B warrants that were exercised by December 31, 2025.

The Tranche 3 Stock Options vest in three equal installments with one-third vesting on December 31, 2025 and the remaining two-thirds vesting in equal annual installments on each of the subsequent two anniversaries thereafter.

• The fourth tranche of stock options ("Tranche 4 Stock Options") will become eligible to vest based on the portion of such stock options that equal the percentage of the Series C warrants that are exercised or are cancelled due to the Company’s receipt of non-dilutive capital by December 31, 2026.

Any Tranche 4 Stock Options that become eligible for vesting will vest in three equal installments with one-third vesting on December 31, 2026 and the remaining two-thirds vesting in equal annual installments on each of the subsequent two anniversaries thereafter.

As of March 31, 2026, there were 21,805 shares of common stock available for future issuance under the 2025 Plan.

2022 Inducement Plan

In 2022, the Company’s board of directors adopted the 2022 Inducement Stock Incentive Plan pursuant to Nasdaq Rule 5635(c)(4) (the “2022 Inducement Plan”).

In accordance with Rule 5635(c)(4), stock-based incentive awards under the 2022 Inducement Plan may only be made to a newly hired employee who has not previously been a member of the Company’s board of directors, or an employee who is being rehired following a bona fide period of non-employment by the Company as a material inducement to the employee’s entering into employment with the Company.

In accordance with Nasdaq Rule 5635(c)(4), stock-based incentive awards under the 2022 Inducement Plan may only be made to a newly hired employee who has not previously been a member of the Company’s board of directors, or an employee who is being rehired following a bona fide period of non-employment by the Company as a material inducement to the employee’s entering into employment with the Company.

The Company initially reserved 19,642 shares of the Company’s common stock for issuance under the 2022 Inducement Plan.

In November 2024, the number of shares reserved for issuance under the 2022 Inducement Plan increased by 500,000 shares.

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

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

T he number of shares reserved for issuance under the 2022 Inducement Plan was increased by 35,714 in both November 2024 and March 2025.

I n January 2026, the number of shares reserved for issuance under the 2022 Inducement Plan increased by an additional 32,485 shares.

As of March 31, 2026 , there were 52,812 shares of common stock available for future issuance under the 2022 Inducement Plan.

2021 Employee Stock Purchase Plan

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On January 1, 2026, the number of shares reserved for issuance under the 2021 ESPP was increased by 41,718 shares.

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.

During each of the three months ended March 31, 2026 and 2025 , the Company did no t issue any shares of common stock under the 2021 ESPP.

As of March 31, 2026 , there were 131,321 shares available for future issuance under the 2021 ESPP.

Stock-Based Compensation Expense

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,

During the three months ended March 31, 2026 and 2025, 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 March 31,

Research and development expense

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Stock Options

A summary of stock option activity under the Company’s 2020 Plan, 2021 Plan and 2022 Inducement Plan is as follows:

A summary of stock option activity under the Company’s 2020 Plan, 2021 Plan, 2025 Plan and 2022 Inducement Plan is as follows:

Stock Options

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Outstanding as of December 31, 2025

Outstanding as of September 30, 2025

Exercisable as of September 30, 2025

Outstanding as of March 31, 2026 (2)

Exercisable as of March 31, 2026 (2)

(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 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,

(2) The weighted-average exercise price per share of the options outstanding and exercisable as of March 31, 2026 includes the impact of the stock option repricing described below.

As of March 31, 2026 , the Company had unrecognized stock-based compensation expense of $ 16.7 million related to stock options issued to employees and directors, i ncluding $ 9.8 million of unrecognized stock-based compensation expense related to awards with performance conditions for which the likelihood of satisfying such performance conditions are considered probable, which is expected to be recognized over a weighted-average period of 3.0 years.

Using the Black-Scholes option pricing model, the weighted average fair value of options granted to employees and directors during the three months ended March 31, 2026 and 2025 was $ 6.82 per share and $1 0.36 per share, respectively.

The following assumptions were used in determining the fair value of options granted during the three months ended March 31, 2026 and 2025:

Three Months Ended March 31,

Risk-free interest rate

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Expected volatility

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.

102.3 - 103.3

Stock Option Repricing

In October 2025, the Company's board of directors approved a stock option repricing (the “Option Repricing”), which was effective upon stockholder approval on November 21, 2025 (the “Repricing Date”).

The Option Repricing applied to all outstanding options to purchase shares of common stock of the Company granted to employees under the Company’s 2020 Plan, 2021 Plan and 2022 Inducement Plan with an exercise price greater than $ 21.00 for members of the Company's executive team and $ 14.00 for all other employees (the “underwater options”) with grant dates prior to January 1, 2025 (the “Eligible Options”).

The total number of shares of common stock underlying all Eligible Options was 354,200 .

Non-employee members of the Company’s board of directors were not eligible to participate in the Option Repricing.

If such Eligible Options are exercised prior to the one-year anniversary of the Repricing Date (the "Retention Period"), the original exercise price must be paid.

The repricing of the Eligible Options was accounted for as a modification under ASC 718.

Accordingly, the Company calculated incremental compensation cost on the modification date in an amount equal to the difference between the fair value of the awards before and after modification.

The total amount of the incremental compensation expense to be recognized was determined to be $ 0.6 million, which is being recognized over the Retention Period.

Stock Options with Performance Conditions

The Company determined that the Tranche 2, Tranche 3 and Tranche 4 Stock Options contain performance conditions for which the likelihood of satisfying each of the performance conditions is considered probable as of March 31, 2026.

As of March 31, 2026 and December 31, 2025 , no Tranche 2 Stock Options were eligible to vest as there have been no exercises of Series A warrants to date.

Based on the Series B warrants exercised during the year ended December 31, 2025, 412,043 Tranche 3 Stock Options became eligible to vest and will vest in three equal annual installments beginning on December 31, 2025.

On December 31, 2025, 157,875 Tranche 3 Stock Options were cancelled in proportion to the respective amount of unexercised Series B warrants.

The Series C warrants are cancellable to the extent Series B warrants are not exercised or cancelled due to the Company’s receipt of non-dilutive capital.

Therefore, on December 31, 2025, 157,875 Tranche 4 Stock Options were cancelled in proportion to the respective amount of unexercised Series B warrants.

Restricted Stock Units

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Unvested as of December 31, 2025

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.

Unvested as of March 31, 2026

For each of the three months ended March 31, 2026 and 2025 , the Company recognized less than $ 0.1 million of stock-based compensation expense related to these awards.

As of March 31, 2026 , the Company had unrecognized stock-based compensation expense of $ 0.1 million related to these restricted stock units, which is expected to be recognized over 1.7 years.

Net Loss Per Share

The Company calculates basic net loss per share by dividing net loss by the weighted average number of shares of common stock outstanding.

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

The weighted average number of shares of common stock used in the basic and diluted net loss per share calculation includes prefunded warrants to purchase common stock, as the prefunded warrants are exercisable at any time for nominal cash consideration.

As of March 31, 2026 , 1,059,743 prefunded warrants have been exercised for common stock and 13,307,918 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:

Nine Months Ended

September 30,

Three Months Ended

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