Xilio Therapeutics, Inc. 10-Q

Item 1. Financial Statements XILIO THERAPEUTICS, INC. Condensed Consolidated Balance Sheets (In thousands, except share and per share data) (Unaudited) ​ ​ ​ ​ ​ ​ ​ ​ March 31, December 31, ​ ​ 2025 ​ 2024 ASSETS ​ ​ Current assets ​ ​ Cash and cash equivalents ​ $ 89,073 ​ $ 55,291 Prepaid expenses and other current assets ​ 4,127 ​ 4,943 Total current assets ​ 93,200 ​ 60,234 Restricted cash ​ 1,788 ​ 1,782 Property and equipment, net ​ 4,289 ​ 4,472 Operating lease right-of-use asset ​ 4,439 ​ 4,587 Total assets ​ $ 103,716 ​ $ 71,075 LIABILITIES AND STOCKHOLDERS’ EQUITY ​ ​ Current liabilities ​ ​ Accounts payable ​ $ 2,275 ​ $ 2,574 Accrued expenses ​ 3,883 ​ 9,981 Deferred revenue, current portion ​ ​ 40,253 ​ ​ 13,518 Operating lease liability, current portion ​ 1,226 ​ 1,188 Total current liabilities ​ 47,637 ​ 27,261 Deferred revenue, net of current portion ​ ​ 38,741 ​ ​ 19,262 Operating lease liability, net of current portion ​ 6,638 ​ 6,954 Total liabilities ​ 93,016 ​ 53,477 Commitments and contingencies (Note 6) ​ ​ Stockholders’ equity ​ ​ Preferred stock, $ 0.0001 par value; 5,000,000 shares authorized, no shares issued or outstanding ​ ​ — ​ ​ — Common stock, $ 0.0001 par value; 200,000,000 shares authorized at March 31, 2025 and December 31, 2024; 51,775,264 shares issued and outstanding at March 31, 2025; 45,756,773 shares issued and outstanding at December 31, 2024 ​ 5 ​ 5 Additional paid-in capital ​ 407,713 ​ 401,346 Accumulated deficit ​ ( 397,018 ) ​ ( 383,753 ) Total stockholders’ equity ​ 10,700 ​ 17,598 Total liabilities and stockholders’ equity ​ $ 103,716 ​ $ 71,075 ​ The accompanying notes are an integral part of these condensed consolidated financial statements. ​ 7 Table of Contents XILIO THERAPEUTICS, INC. Condensed Consolidated Statements of Operations and Comprehensive Loss (In thousands, except share and per share data) (Unaudited) ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended March 31, ​ ​ 2025 2024 Revenue ​ ​ Collaboration and license revenue ​ $ 2,930 ​ $ — Total revenue ​ 2,930 ​ — Operating expenses ​ ​ ​ Research and development ​ $ 8,266 ​ $ 10,400 General and administrative ​ 8,515 ​ 6,139 Restructuring ​ ​ — ​ ​ 948 Total operating expenses ​ 16,781 ​ 17,487 Loss from operations ​ ( 13,851 ) ​ ( 17,487 ) Other income, net ​ ​ Other income, net ​ 586 ​ 284 Total other income, net ​ 586 ​ 284 Net loss and comprehensive loss ​ $ ( 13,265 ) ​ $ ( 17,203 ) Net loss per share, basic and diluted ​ $ ( 0.18 ) ​ $ ( 0.62 ) Weighted average common shares outstanding, basic and diluted ​ 74,700,364 ​ 27,912,584 ​ The accompanying notes are an integral part of these condensed consolidated financial statements. ​ ​ 8 Table of Contents ​ ​ XILIO THERAPEUTICS, INC. Condensed Consolidated Statements of Stockholders’ Equity For the three months ended March 31, 2025 and 2024 (In thousands, except share data) (Unaudited) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Total ​ ​ Common Stock ​ Additional ​ Accumulated ​ Stockholders’ ​ Shares Amount Paid-In Capital Deficit Equity Balance at December 31, 2024 ​ 45,756,773 ​ $ 5 ​ $ 401,346 ​ $ ( 383,753 ) ​ $ 17,598 Issuance of common stock in connection with the AbbVie stock purchase agreement, net of issuance costs ​ 4,347,826 ​ — ​ 2,810 ​ — ​ 2,810 Issuance of common stock in connection with at-the-market offerings, net of issuance costs 1,550,000 ​ — ​ 2,017 ​ — ​ 2,017 Vesting of restricted stock units 111,375 ​ — ​ — ​ — ​ — Exercise of stock options 9,290 ​ — ​ 5 ​ — ​ 5 Stock-based compensation expense — ​ — ​ 1,535 ​ — ​ 1,535 Net loss — ​ — ​ — ​ ( 13,265 ) ​ ( 13,265 ) Balance at March 31, 2025 51,775,264 ​ $ 5 ​ $ 407,713 ​ $ ( 397,018 ) ​ $ 10,700 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Total ​ ​ Common Stock ​ Additional ​ Accumulated ​ Stockholders’ ​ Shares Amount Paid-In Capital Deficit Equity Balance at December 31, 2023 ​ 27,607,646 ​ $ 3 ​ $ 362,336 ​ $ ( 325,512 ) ​ $ 36,827 Issuance of common stock in connection with the Gilead stock purchase agreement, net of issuance costs ​ 6,860,223 ​ — ​ 4,308 ​ — ​ 4,308 Vesting of restricted common stock 4,777 ​ — ​ — ​ — ​ — Stock-based compensation expense — ​ — ​ 1,833 ​ — ​ 1,833 Net loss — ​ — ​ — ​ ( 17,203 ) ​ ( 17,203 ) Balance at March 31, 2024 34,472,646 ​ $ 3 ​ $ 368,477 ​ $ ( 342,715 ) ​ $ 25,765 ​ The accompanying notes are an integral part of these condensed consolidated financial statements. ​ ​ ​ ​ ​ 9 Table of Contents XILIO THERAPEUTICS, INC. Condensed Consolidated Statements of Cash Flows (In thousands) (Unaudited) ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended March 31, ​ 2025 2024 Cash flows from operating activities: ​ ​ ​ ​ ​ ​ Net loss $ ( 13,265 ) $ ( 17,203 ) Adjustments to reconcile net loss to net cash provided by (used in) operating activities: ​ ​ Depreciation and amortization ​ 497 ​ 443 Stock-based compensation expense ​ 1,535 ​ 1,833 Changes in operating assets and liabilities: ​ ​ ​ ​ License agreement receivable ​ ​ — ​ ​ ( 30,000 ) Prepaid and other assets ​ 816 ​ ( 1,782 ) Operating lease right-of-use asset ​ 148 ​ 127 Accounts payable ​ ( 590 ) ​ ( 305 ) Accrued expenses and other liabilities ​ ( 6,098 ) ​ ( 2,495 ) Deferred revenue ​ ​ 46,213 ​ ​ 39,124 Operating lease liability ​ ( 278 ) ​ ( 244 ) Net cash provided by (used in) operating activities ​ 28,978 ​ ( 10,502 ) Cash flows from investing activities: ​ ​ Purchases of property and equipment ​ ( 22 ) ​ — Net cash used in investing activities ​ ( 22 ) ​ — Cash flows from financing activities: ​ ​ Repayments of debt principal ​ ​ — ​ ​ ( 3,333 ) Payments of finance lease ​ — ​ ( 21 ) Proceeds from exercise of stock options ​ 5 ​ — Proceeds from issuance of common stock in connection with the Gilead stock purchase agreement, net of issuance costs ​ ​ — ​ 4,308 Proceeds from issuance of common stock in connection with the AbbVie stock purchase agreement, net of issuance costs ​ ​ 2,810 ​ ​ — Proceeds from issuance of common stock in connection with at-the-market offerings, net of issuance costs ​ ​ 2,017 ​ — Net cash provided by financing activities ​ 4,832 ​ 954 Increase (decrease) in cash, cash equivalents and restricted cash ​ 33,788 ​ ( 9,548 ) Cash, cash equivalents and restricted cash, beginning of period ​ 57,073 ​ 46,291 Cash, cash equivalents and restricted cash, end of period $ 90,861 $ 36,743 Supplemental cash flow disclosure: ​ ​ Cash paid for interest $ — $ 62 Supplemental disclosure of non-cash activities: ​ ​ ​ Capital expenditures included in accounts payable or accrued expenses ​ $ 292 ​ $ 21 Reconciliation to amounts within the consolidated balance sheets: ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 89,073 ​ $ 33,980 Restricted cash ​ ​ 1,788 ​ ​ 2,763 Cash, cash equivalents and restricted cash, end of period ​ $ 90,861 ​ $ 36,743 ​ The accompanying notes are an integral part of these condensed consolidated financial statements. ​ 10 Table of Contents XILIO THERAPEUTICS, INC. Notes to Condensed Consolidated Financial Statements (Dollars in thousands, unless otherwise stated) (Unaudited) 1. Description of Business, Liquidity and Going Concern Description of Business 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. The Company was incorporated in Delaware in June 2020, and its headquarters are located in Waltham, Massachusetts. Liquidity and Going Concern Since its inception, the Company has devoted substantially all of its financial resources and efforts to research and development activities. As of March 31, 2025, the Company had an accumulated deficit of $ 397.0 million and has incurred significant operating losses, including net losses of $ 13.3 million and $ 17.2 million for the three months ended March 31, 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 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, 2025, the Company had cash and cash equivalents of $ 89.1 million. Based on its current operating plans, the Company anticipates that its existing cash and cash equivalents as of March 31, 2025 will be sufficient to fund the Company’s operating expenses and capital expenditure requirements into the first quarter of 2026. However, the Company has based this estimate on assumptions that may prove to be wrong, and the Company could exhaust its available capital resources sooner than it anticipates. In addition, since these amounts are not expected to be sufficient to fund its operations for at least twelve months from the date of issuance of the accompanying condensed consolidated financial statements, there is substantial doubt about the Company’s ability to continue as a going concern. To continue to fund the operations of the Company, management has developed plans, which in the near term primarily consist of raising additional capital through one or more of the following: additional equity or debt financings; additional collaborations, partnerships or licensing transactions; or other sources. However, there can be no assurance that the Company will be able to complete any such transaction on acceptable terms or otherwise, and the Company may be unable to obtain sufficient additional capital. If the Company is not able to secure sufficient additional capital in the near term, the Company will 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. 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. ​ 11 Table of Contents 2. Summary of Significant Accounting Policies Basis of Presentation The Company’s unaudited interim condensed consolidated financial statements have been prepared in conformity with accounting principles generally accepted in the United States (“U.S. GAAP”), and pursuant to the rules and regulations of the U.S. Securities and Exchange Commission (the “SEC”). 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”). Certain information and footnote disclosures normally included in financial statements prepared in accordance with U.S. GAAP have been condensed or omitted from this report, as is permitted by such rules and regulations. Accordingly, these 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 March 31, 2025 and the results of its operations for the three months ended March 31, 2025 and 2024 and cash flows for the three months ended March 31, 2025 and 2024. Such adjustments are of a normal and recurring nature. The results for the three months ended March 31, 2025 are not necessarily indicative of the results for the year ending December 31, 2025 or for any future period. Principles of Consolidation The accompanying condensed consolidated financial statements include the accounts of the Company and its wholly owned subsidiaries: Xilio Development, Inc. (“Xilio Development”), a Delaware corporation, and Xilio Securities Corporation, a Massachusetts security corporation. All intercompany accounts and transactions have been eliminated in consolidation. Significant Accounting Policies 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, 2024. Use of Estimates The preparation of financial statements in accordance with GAAP requires management to make estimates and judgments that may affect the reported amounts of assets and liabilities and related disclosures of contingent assets and liabilities at the date of the financial statements and the related reporting of revenue and expenses during the reporting period. Management considers many factors in selecting appropriate financial accounting policies and controls and in developing the estimates and assumptions that are used in the preparation of these condensed consolidated financial statements. Factors that may affect estimates include expected business and operational changes, sensitivity and volatility associated with the assumptions used in developing estimates, and whether historical trends are expected to be representative of future trends. 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 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. ​ 12 Table of Contents Concentrations of Credit Risk Financial instruments that potentially expose the Company to concentrations of credit risk consist primarily of cash and cash equivalents. The Company holds all cash and cash equivalents at accredited financial institutions. Bank accounts in the United States are generally insured by the Federal Deposit Insurance Corporation (“FDIC”) up to $250,000. Substantially all of the Company’s cash and cash equivalents are FDIC insured, including funds held through an insured cash sweep program. 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. ​ Segments ​ 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’s chief operating decision maker (“CODM”) is its chief executive officer. The CODM allocates resources and assesses performance on a consolidated basis, focused on the Company’s cash resources and an assessment of the probability of success of its ongoing research and development activities. Resource allocation decisions are informed by forecasted cash expenditures and actual expenses incurred to date. The CODM is not regularly provided with disaggregated actual expense information, other than the actual expense information included in the consolidated statements of operations and comprehensive loss, as the Company’s integrated operating model emphasizes shared resources and centralized decision-making. All of the Company’s collaboration and license revenue is generated in the United States and all of the Company’s long-lived assets are held in the United States. ​ 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 is currently evaluating the potential impact of adopting this new guidance on its condensed consolidated financial statements and related disclosures. 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. 2025-01, 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. 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. ​ 13 Table of Contents 3. Property and Equipment, Net Property and equipment, net consists of the following as of March 31, 2025 and December 31, 2024: ​ ​ ​ ​ ​ ​ ​ ​ ​ March 31, December 31, ​ ​ 2025 ​ 2024 Laboratory equipment ​ $ 6,225 ​ $ 5,911 Computers and software ​ — ​ 183 Furniture and fixtures ​ 681 ​ 681 Leasehold improvements ​ 5,124 ​ 5,124 Total property and equipment ​ ​ 12,030 ​ ​ 11,899 Less: accumulated depreciation ​ ( 7,741 ) ​ ( 7,427 ) Property and equipment, net ​ $ 4,289 ​ $ 4,472 ​ The Company recognized depreciation and amortization expense related to property and equipment of $ 0.5 million and $ 0.4 million for the three months ended March 31, 2025 and 2024, respectively. 4. Accrued Expenses Accrued expenses consist of the following as of March 31, 2025 and December 31, 2024: ​ ​ ​ ​ ​ ​ ​ ​ ​ March 31, December 31, ​ ​ 2025 ​ 2024 External research and development ​ $ 1,025 ​ $ 4,899 Personnel-related ​ 1,425 ​ 4,208 Professional and consulting fees ​ 1,265 ​ 743 Other ​ ​ 168 ​ ​ 131 Total accrued expenses ​ $ 3,883 ​ $ 9,981 ​ ​ 5. Collaboration and License 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 Group Holdings (“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”). 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. During the three-year period following the effective date of the Collaboration Agreement, AbbVie has the right to initiate up to two Additional Option Programs by (a) selecting an initial target and backup target for each such Additional Option Program (excluding the target known as prostate-specific membrane antigen and any other target for which Xilio Development has completed specified activities prior to lead selection) and (b) paying Xilio Development an additional program nomination fee for each Additional Option Program. 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”). 14 Table of Contents 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. In addition, on an Option Program-by-Option Program basis, prior to the initiation of specified activities related to lead optimization and selection for the initial target for such Option Program, AbbVie has a one-time right to substitute the initial target with the backup target agreed upon by the parties at the time of Option Program initiation, subject to the payment by AbbVie of a one-time substitution fee with respect to such substituted target and the other terms of the Collaboration Agreement. In connection with the execution of the Collaboration Agreement, in February 2025, the Company also entered into a stock purchase agreement with AbbVie Inc. pursuant to which the Company issued and sold 4,347,826 shares of its common stock to AbbVie Inc. in a private placement at a purchase price of $ 2.30 per share for an aggregate purchase price of $ 10.0 million. As of March 31, 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 March 31, 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. The Company considered the criteria of ASC 606, Revenue from Contracts with Customers (“ASC 606”) for combining contracts and determined the Collaboration Agreement and the stock purchase agreement should be combined into a single contract because they were negotiated and entered into in contemplation of one another. The Company accounted for the common stock issued to AbbVie Inc. 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. 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. The Company determined that the premium paid by AbbVie Inc. for the common stock purchased should be attributed to the transaction price of the Collaboration Agreement. The Company determined that the Collaboration Agreement represents a contract with a customer within the scope of ASC 606 and identified the following promises under the Collaboration Agreement: (i) the exclusive license granted to AbbVie related to the Collaboration Program, (ii) the Collaboration Program Services and (iii) the Option Program Services for the Initial Option Program. 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. As such, the Company identified the following performance obligations at contract inception: (i) the performance obligation consisting of the exclusive license and the Collaboration Program Services (the “Collaboration Program Performance Obligation”); (ii) the Option Program Services for the Initial Option Program (the “Initial Option Program Performance Obligation”); (iii) a material right to receive an exclusive license to the Initial Option Program; (iv) a material right to receive additional services related to the Initial Option Program; and (v) a material right related to AbbVie’s one-time right to substitute the initial target with the backup target 15 Table of Contents for the Initial Option Program. For purposes of ASC 606, the transaction price at the outset of the arrangement was determined to be $ 49.1 million, which consisted of the upfront cash payment of $ 42.0 million under the Collaboration Agreement and the $ 7.1 million premium on the sale of common stock to AbbVie Inc. The Company used the most likely amount method to estimate variable consideration. All contingent payments are fully constrained as of March 31, 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. 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. Sales-based royalties, including milestone payments based on the level of sales, were also excluded from the transaction price, as the license is deemed to be the predominant item to which the royalties relate. 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: (i) $ 32.4 million related to the Collaboration Program Performance Obligation; (ii) $ 6.9 million related to the Initial Option Program Performance Obligation; (iii) $ 8.2 million related to the material right to receive an exclusive license to the Initial Option Program; (iv) $ 1.1 million related to the material right to receive additional services related to the Initial Option Program; and (v) $ 0.5 million related to the material right for AbbVie’s one-time right to substitute the initial target with the backup target for the Initial Option Program. The Company determined the estimated standalone selling price for the licenses using an adjusted market assessment approach, whereby the Company adjusted a comparable transaction previously entered into by the Company and comparable third-party transactions to reflect the stage of development of the Company’s assets under the Collaboration Agreement. The Company determined the estimated standalone selling price for services based on estimated costs to be incurred plus a reasonable margin. The Company determined the estimated standalone selling price for material rights by estimating the standalone selling price of the underlying performance obligations included in the material right and estimating the probability that AbbVie will exercise such material right. Revenue associated with the Collaboration Program Performance Obligation and the Initial Option Program Performance Obligation are recognized as the underlying services are provided as control is transferred over time. The Company measures progress based on the amount of costs incurred relative to the total costs expected to fulfill the combined performance obligation. 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. 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 months ended March 31, 2025, the Company recognized collaboration revenue of $ 0.7 million under the Collaboration Agreement and the stock purchase agreement. As of March 31, 2025, the Company recorded deferred revenue of $ 48.4 million, of which $ 25.6 million was recorded as a current liability on the Company’s condensed consolidated balance sheet. The deferred revenue is expected to be recognized as 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. 16 Table of Contents License Agreement with Gilead Sciences, Inc. In March 2024, Xilio Development entered into a license agreement with Gilead Sciences, Inc. (“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 in the ongoing Phase 1 clinical trial through an initial planned Phase 2 dose expansion clinical trial. Following the delivery by Xilio Development of a specified clinical data package for XTX301 related to the Phase 1 clinical trial and planned 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 connection with the execution of the license agreement, in March 2024, the Company also entered into a stock purchase agreement with Gilead. Under the stock purchase agreement, Gilead purchased $ 25.0 million of the Company’s common stock and prefunded warrants in three private placements, consisting of an aggregate of 9,105,451 shares of common stock and prefunded warrants to purchase up to an aggregate of 9,975,266 shares of its common stock. 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 March 31, 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 March 31, 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. In addition, the Company is eligible to receive tiered royalties ranging from high single digits to mid-teens on annual global net product sales. The Company considered the ASC 606 criteria for combining contracts and determined the license agreement and the stock purchase agreement should be combined into a single contract because they were negotiated and entered into in contemplation of one another. The Company concluded the initial private placement and the additional private placements do not represent freestanding financial instruments as such instruments are not legally detachable due to contractual transfer restrictions. The Company accounted for the common stock issued to Gilead in the initial private placement 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 Gilead in the initial private placement was $ 4.4 million, based on the closing price of the Company’s common stock on the date of issuance, resulting in a $ 9.1 million premium. The Company determined that the premium paid by Gilead for the common stock purchased in the initial private placement should be attributed to the transaction price of the license agreement. 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 planned 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. Accordingly, the Company concluded that there is a single identified combined performance obligation consisting of the exclusive license and the development services. For purposes of ASC 606, the transaction price of the license agreement at the outset of the arrangement was determined to be $ 39.1 million, which consisted of the upfront cash payment of $ 30.0 million under the license agreement and the $ 9.1 million premium on the sale of common stock to Gilead in the initial private placement, which was allocated to the single combined performance obligation. The Company used the most likely amount method to estimate variable consideration. All contingent payments are fully constrained as of March 31, 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. The Company reevaluates the 17 Table of Contents 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. Sales-based royalties, including milestone payments based on the level of sales, were also excluded from the transaction price, as the license is deemed to be the predominant item to which the royalties relate. 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). Revenue associated with the combined performance obligation is recognized as services are provided as control is transferred over time. The Company measures progress based on the amount of costs incurred relative to the total costs expected to fulfill the combined performance obligation. 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 months ended March 31, 2025, the Company recognized collaboration and license revenue of $ 2.2 million under the license agreement and the stock purchase agreement with Gilead. During the three months ended March 31, 2024, the Company did not recognize any collaboration and license revenue under the license agreement and the stock purchase agreement with Gilead As of March 31, 2025, the Company recorded deferred revenue under the license agreement and the stock purchase agreement of $30.6 million, of which $ 14.7 million was recorded as a current liability on the Company’s condensed consolidated balance sheet. The deferred revenue is expected to be recognized as collaboration and license revenue through at least 2027 depending on the timing of certain clinical development activities. ​ Summary of Contract Assets and Liabilities ​ The following table presents changes in the balances of the Company's contract liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Gilead ​ AbbVie ​ Total Deferred revenue as of December 31, 2024 ​ $ 32,780 ​ $ — ​ $ 32,780 Additions ​ — ​ ​ 49,144 ​ ​ 49,144 Collaboration and license revenue recognized ​ ​ ( 2,190 ) ​ ​ ( 740 ) ​ ​ ( 2,930 ) Deferred revenue as of March 31, 2025 ​ $ 30,590 ​ $ 48,404 ​ $ 78,994 ​ Clinical Trial Collaboration with F. Hoffmann-La Roche Ltd 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. The Company is responsible for conducting the Phase 1/2 clinical trial and retains global development and commercialization rights to vilastobart. The Company concluded that the cost-sharing payments under the clinical supply agreement are not in the scope of ASC 606 because the Company does not consider performing research and development services for reimbursement to be part of its ongoing major or central operations. 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 recognized a reduction of research and development expense of $ 2.0 million during each of the three months ended March 31, 2025 and 2024. As of each of March 31, 2025 and 2024, $ 2.0 million of earned but unpaid cost-sharing payments were included in prepaid expenses and other current assets of the Company’s condensed consolidated balance sheets. 18 Table of Contents 6. Commitments and Contingencies The Company has an operating lease for its headquarters and a finance lease for certain lab equipment. In August 2019, the Company entered into a facility lease agreement with a landlord providing funding for tenant improvements and occupancy of approximately 27,830 square feet of office and laboratory space (the “premises”) at 828 Winter Street, Waltham, Massachusetts. The initial term of the lease expires in March 2030, unless terminated earlier in accordance with the terms of the lease. The Company has an option to extend the lease for an additional term of five years at then-market rates. 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 March 31, 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. 7. Preferred Stock and Common Stock Undesignated Preferred Stock As of March 31, 2025 and December 31, 2024, the Company’s 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, 2025 and December 31, 2024, there were no shares of preferred stock issued or outstanding. Common Stock As of March 31, 2025 and December 31, 2024, the Company is authorized to issue up to 200,000,000 shares of common stock, $ 0.0001 par value per share under its certificate of incorporation, as amended. 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 three months ended March 31, 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 19 Table of Contents 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. 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 March 31, 2025 and December 31, 2024: ​ ​ ​ ​ ​ ​ ​ ​ March 31, ​ December 31, ​ ​ 2025 ​ 2024 Stock options and unvested restricted stock units 14,000,874 11,328,134 Employee stock purchase plan 1,359,889 901,208 Prefunded warrants ​ 25,602,707 ​ 25,602,707 Warrants 2,631 2,631 Total shares reserved for future issuance 40,966,101 37,834,680 ​ ​ 8. Stock-Based Compensation Equity Incentive Plans 2020 Stock Incentive Plan Under the 2020 Stock Incentive Plan (as amended, the “2020 Plan”), the Company was authorized to issue shares of common stock to the Company’s employees, officers, directors, consultants and advisors in the form of options, restricted stock awards or other stock-based awards. 2021 Stock Incentive Plan In September 2021, the Company’s board of directors and stockholders adopted the 2021 Stock Incentive Plan (the “2021 Plan”), which became effective immediately prior to the Company’s initial public offering of common stock (“IPO”) in October 2021. 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 Company initially reserved 6,579,016 shares of common stock under the 2021 Plan. The 2021 Plan provides that the number of shares reserved and available for issuance under the 2021 Plan will be cumulatively increased on January 1 of each calendar year by 5 % of the number of shares of common stock outstanding on such date or such lesser amount determined by the Company’s board of directors. On January 1, 2025, the number of shares reserved for issuance under the 2021 Plan automatically increased by 2,293,405 shares. As of March 31, 2025, there were 2,217,457 shares of common stock available for future issuance under the 2021 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. The Company initially reserved 275,000 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 20 Table of Contents 500,000 shares. As of March 31, 2025, there were 592,200 shares of common stock available for future issuance under the 2022 Inducement Plan. 2021 Employee Stock Purchase Plan In 2021, the Company’s board of directors and stockholders adopted the 2021 Employee Stock Purchase Plan (the “2021 ESPP”), which became effective immediately prior to the IPO in October 2021. 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). On January 1, 2025, the number of shares reserved for issuance under the 2021 ESPP was increased by 458,681 shares. As of March 31, 2025, there were 1,359,889 shares available for future issuance under the 2021 ESPP. Stock-Based Compensation Expense During the three months ended March 31, 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 March 31, ​ ​ 2025 2024 Research and development expense ​ $ 389 ​ $ 506 ​ General and administrative expense ​ 1,146 ​ ​ 1,327 ​ Total stock-based compensation expense ​ $ 1,535 ​ $ 1,833 ​ ​ Stock Options A summary of stock option activity under the Company’s 2020 Plan, 2021 Plan and 2022 Inducement Plan is as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted ​ ​ ​ ​ ​ ​ ​ ​ ​ Average ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Remaining ​ Aggregate ​ ​ ​ ​ Weighted ​ Contractual ​ Intrinsic ​ ​ Number of ​ Average ​ Term ​ Value (1) ​ Stock Options Exercise Price (In years) (In thousands) Outstanding as of December 31, 2024 8,333,932 ​ $ 4.15 8.0 ​ $ 282 Granted 2,852,630 ​ $ 0.95 ​ Exercised ( 9,290 ) ​ $ 0.61 ​ Forfeited ( 320,180 ) ​ $ 1.88 ​ ​ Outstanding as of March 31, 2025 10,857,092 ​ $ 3.38 8.1 ​ $ 59 Exercisable as of March 31, 2025 4,529,651 ​ $ 5.75 6.6 ​ $ 19 ​ (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 three months ended March 31, 2025 and 2024 was $ 0.74 per share and $ 0.41 per share, respectively. The following assumptions were used in determining the fair value of options granted during the three months ended March 31, 2025 and 2024: ​ ​ ​ 21 Table of Contents ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended March 31, ​ ​ ​ 2025 ​ 2024 ​ Risk-free interest rate ​ ​ 4.4 % ​ 3.9 % Expected dividend yield ​ ​ 0 % ​ 0 % Expected term (in years) ​ ​ 6.0 - 6.1 ​ ​ 6.0 ​ Expected volatility ​ ​ 94.5 - 95.6 % ​ 87.7 % ​ As of March 31, 2025, the Company had unrecognized stock-based compensation expense of $ 6.0 million related to stock options issued to employees and directors, which is expected to be recognized over a weighted-average period of 2.4 years. Restricted Stock Units In January 2024, the Company awarded 481,500 restricted stock units to certain employees of the Company. The restricted stock units vest in four equal annual installments beginning on the first anniversary of the grant date. The restricted stock units are generally forfeited if the individual’s service relationship with the Company or any subsidiary terminates prior to vesting. A summary of the Company’s restricted stock unit activity and related information is as follows: ​ ​ ​ ​ ​ ​ ​ ​ Number Weighted ​ ​ of Shares ​ Average ​ ​ of Restricted ​ Grant Date ​ Stock Units Fair Value Unvested as of December 31, 2024 ​ 445,500 $ 0.55 Granted ​ — ​ $ — Vested ​ ( 111,375 ) ​ $ 0.55 Forfeited ​ — ​ $ — Unvested as of March 31, 2025 334,125 $ 0.55 ​ For each of the three months ended March 31, 2025 and 2024, the Company recognized less than $ 0.1 million of stock-based compensation expense related to these awards. As of March 31, 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 2.8 years. 9. 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 issued in connection with the Company’s private placements with certain existing investors and Gilead, as the prefunded warrants are exercisable at any time for nominal cash consideration. As of March 31, 2025, no prefunded warrants have been exercised and 25,602,707 prefunded warrants are outstanding. 22 Table of Contents 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: ​ ​ ​ ​ ​ ​ ​ Three Months Ended ​ ​ March 31, ​ ​ 2025 ​ 2024 Unvested restricted common stock — 840 Unvested restricted stock units 334,125 481,500 Outstanding stock options 10,857,092 7,584,651 Warrants 2,631 2,631 Unvested employee stock purchase plan shares ​ 45,504 ​ 48,201 Total common stock equivalents 11,239,352 8,117,823 ​ ​ ​ ​ ​ 23 Table of Contents