Xilio Therapeutics (XLO) 10-Q 7 Nov 24 2024 Q3 Quarterly report Financial data

Document and Entity Information

Document and Entity Information - shares	9 Months Ended
	Sep. 30, 2024	Nov. 01, 2024
Document and Entity Information [Abstract]
Document Type	10-Q
Document Quarterly Report	true
Document Period End Date	Sep. 30, 2024
Document Transition Report	false
Securities Act File Number	001-40925
Entity Registrant Name	Xilio Therapeutics, Inc.
Entity Incorporation, State or Country Code	DE
Entity Tax Identification Number	85-1623397
Entity Address, Address Line One	828 Winter Street
Entity Address, Address Line Two	Suite 300
Entity Address, City or Town	Waltham
Entity Address, State or Province	MA
Entity Address, Postal Zip Code	02451
City Area Code	857
Local Phone Number	524-2466
Title of 12(b) Security	Common stock, par value $0.0001 per share
Trading Symbol	XLO
Security Exchange Name	NASDAQ
Entity Current Reporting Status	Yes
Entity Interactive Data Current	Yes
Entity Filer Category	Non-accelerated Filer
Entity Small Business	true
Entity Emerging Growth Company	true
Entity Ex Transition Period	false
Entity Shell Company	false
Entity Common Stock, Shares Outstanding		43,958,074
Entity Central Index Key	0001840233
Current Fiscal Year End Date	--12-31
Document Fiscal Year Focus	2024
Document Fiscal Period Focus	Q3
Amendment Flag	false

CONDENSED CONSOLIDATED BALANCE

CONDENSED CONSOLIDATED BALANCE SHEETS - USD ($) $ in Thousands	Sep. 30, 2024	Dec. 31, 2023
Current assets
Cash and cash equivalents	$ 61,259	$ 44,704
Prepaid expenses and other current assets	2,050	3,423
Total current assets	63,309	48,127
Restricted cash	1,775	1,587
Property and equipment, net	4,845	5,942
Operating lease right-of-use asset	4,729	5,125
Other non-current assets		145
Total assets	74,658	60,926
Current liabilities
Accounts payable	972	1,050
Accrued expenses	9,793	10,497
Deferred revenue, current portion	26,105
Operating lease liability, current portion	1,152	1,047
Note payable, current portion		3,315
Other current liabilities		48
Total current liabilities	38,022	15,957
Deferred revenue, net of current portion	8,399
Operating lease liability, net of current portion	7,263	8,142
Total liabilities	53,684	24,099
Commitments and contingencies (Note 7)
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 September 30, 2024 and December 31, 2023; 43,958,074 shares issued and outstanding at September 30, 2024; 27,613,263 shares issued and 27,607,646 shares outstanding at December 31, 2023	4	3
Additional paid-in capital	391,630	362,336
Accumulated deficit	(370,660)	(325,512)
Total stockholders' equity	20,974	36,827
Total liabilities and stockholders' equity	$ 74,658	$ 60,926

CONDENSED CONSOLIDATED BALANC_2

CONDENSED CONSOLIDATED BALANCE SHEETS (Parenthetical) - $ / shares	Sep. 30, 2024	Dec. 31, 2023
CONDENSED CONSOLIDATED BALANCE SHEETS
Preferred stock, par value (in dollars per share)	$ 0.0001	$ 0.0001
Preferred stock, shares authorized	5,000,000	5,000,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Common stock, par value (in dollars per share)	$ 0.0001	$ 0.0001
Common stock, shares authorized	200,000,000	200,000,000
Common stock, shares issued	43,958,074	27,613,263
Common stock, shares outstanding	43,958,074	27,607,646

CONDENSED CONSOLIDATED STATEMEN

CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Revenue
Total revenue	$ 2,263		$ 4,620
Revenue from Contract with Customer, Product and Service	us-gaap:LicenseMember		us-gaap:LicenseMember
Operating expenses
Research and development	$ 10,759	$ 11,051	$ 32,375	$ 40,400
General and administrative	6,307	6,310	18,261	20,603
Restructuring	(41)		937
Total operating expenses	17,025	17,361	51,573	61,003
Loss from operations	(14,762)	(17,361)	(46,953)	(61,003)
Other income, net
Other income, net	742	613	1,805	2,254
Total other income, net	742	613	1,805	2,254
Net loss	(14,020)	(16,748)	(45,148)	(58,749)
Comprehensive loss	$ (14,020)	$ (16,748)	$ (45,148)	$ (58,749)
Net loss per share, basic (in dollars per share)	$ (0.22)	$ (0.61)	$ (0.91)	$ (2.14)
Net loss per share, diluted (in dollars per share)	$ (0.22)	$ (0.61)	$ (0.91)	$ (2.14)
Weighted average common shares outstanding, basic (in shares)	63,465,063	27,523,821	49,762,800	27,475,579
Weighted average common shares outstanding, diluted (in shares)	63,465,063	27,523,821	49,762,800	27,475,579

CONDENSED CONSOLIDATED STATEM_2

CONDENSED CONSOLIDATED STATEMENTS OF STOCKHOLDERS' EQUITY - USD ($) $ in Thousands	Common Stock Gilead Stock Purchase Agreement	Common Stock Private Placement	Common Stock At-the-Market Offerings	Common Stock	Additional Paid-in Capital Gilead Stock Purchase Agreement	Additional Paid-in Capital Private Placement	Additional Paid-in Capital At-the-Market Offerings	Additional Paid-in Capital	Accumulated Deficit	Gilead Stock Purchase Agreement	Private Placement	At-the-Market Offerings	Total
Beginning balance at Dec. 31, 2022				$ 3				$ 354,752	$ (249,108)				$ 105,647
Beginning balance (in shares) at Dec. 31, 2022				27,425,447
Stockholders' Deficit
Issuance of common stock under employee stock purchase plan								140					140
Issuance of common stock under employee stock purchase plan (in shares)				68,929
Vesting of restricted common stock (in shares)				31,793
Exercise of stock options								8					8
Exercise of stock options (in shares)				2,757
Stock-based compensation expense								5,452					5,452
Net Income (Loss)									(58,749)				(58,749)
Ending balance at Sep. 30, 2023				$ 3				360,352	(307,857)				52,498
Ending balance (in shares) at Sep. 30, 2023				27,528,926
Beginning balance at Jun. 30, 2023				$ 3				358,483	(291,109)				67,377
Beginning balance (in shares) at Jun. 30, 2023				27,518,895
Stockholders' Deficit
Vesting of restricted common stock (in shares)				7,598
Exercise of stock options								8					8
Exercise of stock options (in shares)				2,433
Stock-based compensation expense								1,861					1,861
Net Income (Loss)									(16,748)				(16,748)
Ending balance at Sep. 30, 2023				$ 3				360,352	(307,857)				52,498
Ending balance (in shares) at Sep. 30, 2023				27,528,926
Beginning balance at Dec. 31, 2023				$ 3				362,336	(325,512)				36,827
Beginning balance (in shares) at Dec. 31, 2023				27,607,646
Stockholders' Deficit
Issuance of common stock and prefunded warrants, net of issuance costs					$ 7,605	$ 9,908				$ 7,605	$ 9,908
Issuance of common stock and prefunded warrants, net of issuance costs (in shares)	7,345,473	1,953,125
Issuance of common stock in connection with at-the-market offerings, net of issuance costs			$ 1				$ 6,824					$ 6,825
Issuance of common stock in connection with at-the-market offerings, net of issuance costs (in shares)			7,000,000									7,000,000
Issuance of common stock under employee stock purchase plan								34					34
Issuance of common stock under employee stock purchase plan (in shares)				38,998
Vesting of restricted common stock (in shares)				5,617
Exercise of stock options								5					$ 5
Exercise of stock options (in shares)				7,215									7,215
Stock-based compensation expense								4,918					$ 4,918
Net Income (Loss)									(45,148)				(45,148)
Ending balance at Sep. 30, 2024				$ 4				391,630	(370,660)				20,974
Ending balance (in shares) at Sep. 30, 2024				43,958,074
Beginning balance at Jun. 30, 2024				$ 4				390,052	(356,640)				33,416
Beginning balance (in shares) at Jun. 30, 2024				43,951,922
Stockholders' Deficit
Issuance of common stock in connection with at-the-market offerings, net of issuance costs (in shares)												0
Exercise of stock options								4					4
Exercise of stock options (in shares)				6,152
Stock-based compensation expense								1,574					1,574
Net Income (Loss)									(14,020)				(14,020)
Ending balance at Sep. 30, 2024				$ 4				$ 391,630	$ (370,660)				$ 20,974
Ending balance (in shares) at Sep. 30, 2024				43,958,074

CONDENSED CONSOLIDATED STATEM_3

CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023
Cash flows from operating activities:
Net loss	$ (45,148)	$ (58,749)
Adjustments to reconcile net loss to net cash provided by (used in) operating activities:
Depreciation and amortization	1,269	1,451
Non-cash interest (income) expense	(1)	141
Stock-based compensation expense	4,918	5,452
Loss on disposal of property and equipment	2	3
Changes in operating assets and liabilities:
Prepaid and other assets	1,373	(597)
Operating lease right-of-use asset	396	338
Accounts payable	(76)	(1,625)
Accrued expenses and other liabilities	(684)	(928)
Deferred revenue	34,504
Operating lease liability	(774)	(679)
Net cash provided by (used in) operating activities	(4,221)	(55,193)
Cash flows from investing activities:
Purchases of property and equipment	(30)	(486)
Net cash used in investing activities	(30)	(486)
Cash flows from financing activities:
Repayments of debt principal	(3,333)	(5,000)
Payments of finance lease	(49)	(64)
Proceeds from issuance of common stock under employee stock purchase plan	34	140
Proceeds from exercise of stock options	5	8
Net cash provided by (used in) financing activities	20,994	(4,916)
Increase (decrease) in cash, cash equivalents and restricted cash	16,743	(60,595)
Cash, cash equivalents and restricted cash, beginning of period	46,291	121,947
Cash, cash equivalents and restricted cash, end of period	63,034	61,352
Supplemental cash flow disclosure:
Cash paid for interest	62	474
Supplemental disclosure of non-cash activities:
Transfer of finance lease asset to property and equipment	85
Reconciliation to amounts within the consolidated balance sheets:
Cash and cash equivalents	61,259	59,772
Restricted cash	1,775	1,580
Cash, cash equivalents and restricted cash, end of period	63,034	$ 61,352
Gilead Stock Purchase Agreement
Cash flows from financing activities:
Proceeds from issuance of common stock and prefunded warrants in connection with the stock purchase agreement/private placement, net of issuance costs	7,605
Private Placement
Cash flows from financing activities:
Proceeds from issuance of common stock and prefunded warrants in connection with the stock purchase agreement/private placement, net of issuance costs	9,908
At-the-Market Offerings
Cash flows from financing activities:
Proceeds from issuance of common stock in connection with at-the-market offering	$ 6,824

Description of Business and Liq

Description of Business and Liquidity and Going Concern	9 Months Ended
	Sep. 30, 2024
Description of Business, Liquidity and Going Concern
Description of Business, Liquidity and Going Concern	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 September 30, 2024, the Company had an accumulated deficit of $370.7 million and has incurred significant operating losses, including net losses of $45.1 million and $58.7 million for the nine months ended September 30, 2024 and 2023, 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 September 30, 2024, the Company had cash and cash equivalents of $61.3 million. Based on its current operating plans, the Company anticipates that its existing cash and cash equivalents as of September 30, 2024 will be sufficient to fund the Company’s operating expenses and capital expenditure requirements through the end of the second quarter of 2025. 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 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. In addition, if the Company’s efforts to secure sufficient additional capital in the near term are unsuccessful, the Company may in the future need to seek to engage in one or more other strategic alternatives, including without limitation, the sale or divestiture of some or all of its assets or proprietary technologies. 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.

Summary of Significant Accounti

Summary of Significant Accounting Policies	9 Months Ended
	Sep. 30, 2024
Summary of Significant Accounting Policies
Summary of Significant Accounting Policies	2. Summary of Significant Accounting Policies Basis of Presentation The Company’s unaudited interim condensed consolidated financial statements have been prepared in accordance with accounting principles generally accepted in the United States (“U.S. GAAP”). 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, 2023 and notes thereto, included in the Company’s Annual Report on Form 10-K filed with the U.S. Securities and Exchange Commission (“SEC”) on April 1, 2024. 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, 2024 and the results of its operations for the three and nine months ended September 30, 2024 and 2023 and cash flows for the nine months ended September 30, 2024 and 2023. Such adjustments are of a normal and recurring nature. The results for the three and nine months ended September 30, 2024 are not necessarily indicative of the results for the year ending December 31, 2024 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., 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, 2023. 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, 2023. 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 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. Revenue Recognition The Company recognizes revenue in accordance with ASC Topic 606, Revenue from Contracts with Customers Under ASC 606, the Company recognizes revenue when its customer obtains control of promised goods or services, in an amount that reflects the consideration which the entity expects to receive in exchange for those goods or services. To determine the appropriate amount of revenue to be recognized for arrangements that the Company determines are within the scope of ASC 606, the Company performs the following five steps: (i) identification of the contract with the customer; (ii) determination of whether the promised goods or services are performance obligations, including whether they are distinct in the context of the contract; (iii) measurement of the transaction price, including the constraint on variable consideration; (iv) allocation of the transaction price to the performance obligations; and (v) recognition of revenue when (or as) the Company satisfies each performance obligation. ● Performance Obligations . The promised goods or services in the Company’s arrangements typically consist of a license, or option to license, rights to the Company’s intellectual property or research and development services. The Company may provide options to additional items in such arrangements, which are accounted for as separate contracts when the customer elects to exercise such options, unless the option provides a material right to the customer. Performance obligations are promised goods or services in a contract to transfer a distinct good or service to the customer and are considered distinct when (i) the customer can benefit from the good or service on its own or together with other readily available resources and (ii) the promised good or service is separately identifiable from other promises in the contract. In assessing whether promised goods or services are distinct, the Company considers factors such as the stage of development of the underlying intellectual property, the capabilities of the customer to develop the intellectual property on its own or whether the required expertise is readily available and whether the goods or services are integral or dependent to other goods or services in the contract. ● Customer Options. If an arrangement is determined to contain customer options that allow the customer to acquire additional goods or services, the goods and services underlying the customer options that are not determined to be material rights are not considered to be performance obligations at the outset of the arrangement, as they are contingent upon option exercise. The Company evaluates the customer options for material rights, or options to acquire additional goods or services for free or at a discount. If the customer options are determined to represent a material right, the material right is recognized as a separate performance obligation at the outset of the arrangement. The Company allocates the transaction price to material rights based on the relative standalone selling price, which is determined based on the identified discount and the probability that the customer will exercise the option. Amounts allocated to a material right are not recognized as revenue until, at the earliest, the option is exercised or the option expires. ● Transaction Price . The Company estimates the transaction price based on the amount expected to be received for transferring the promised goods or services in the contract. The consideration may include fixed consideration or variable consideration. At the inception of each arrangement that includes variable consideration, the Company evaluates the amount of potential payments and the likelihood that the payments will be received. The Company utilizes either the most likely amount method or expected value method to estimate the amount expected to be received based on which method best predicts the amount expected to be received. The amount of variable consideration that is included in the transaction price may be constrained and is included in the transaction price only to the extent that it is probable that a significant reversal in the amount of the cumulative revenue recognized will not occur in a future period. At the end of each subsequent reporting period, the Company reevaluates the probability of achievement of all variable consideration subject to constraint, and if necessary, adjusts its estimate of the overall transaction price. Any such adjustments are recorded on a cumulative catch-up basis, which would affect revenues in the period of adjustment. The Company allocates the transaction price to the identified performance obligations based on the estimated standalone selling price. The Company must develop assumptions that require judgment to determine the standalone selling price for each performance obligation identified in the contract. The Company utilizes key assumptions to determine the standalone selling price, which may include other comparable transactions, pricing considered in negotiating the transaction and the estimated costs. Variable consideration is allocated specifically to one or more performance obligations in a contract when the terms of the variable consideration relate to the satisfaction of the performance obligation and the resulting amounts allocated are consistent with the amounts the Company would expect to receive for the satisfaction of each performance obligation. ● Milestone Payments. At the inception of each arrangement that includes development or regulatory milestone payments, the Company evaluates whether the milestones are considered probable of being achieved and estimates the amount to be included in the transaction price using the most likely amount method. If it is probable that a significant revenue reversal would not occur, the associated milestone value is included in the transaction price. Milestone payments that are not within the Company’s control or the licensee’s control, such as regulatory approvals, are not considered probable of being achieved until those approvals are received. The Company evaluates factors such as the scientific, clinical, regulatory, commercial, and other risks that must be overcome to achieve the particular milestone in making this assessment. There is considerable judgment involved in determining whether it is probable that a significant revenue reversal would not occur. ● Royalties. For arrangements that include sales-based royalties, including milestone payments based on the level of sales, and the license is deemed to be the predominant item to which the royalties relate, the Company recognizes 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). To date, the Company has not recognized any royalty revenue resulting from any of the Company’s collaboration or licensing arrangements. ● Recognition. The consideration allocated to each performance obligation is recognized as revenue when control is transferred for the related goods or services. For performance obligations that consist of licenses and other promises, the Company utilizes judgment to assess the nature of the combined performance obligation to determine whether the combined performance obligation is satisfied over time or at a point in time and, if over time, the appropriate method of measuring progress. The Company evaluates the measure of progress each reporting period and, if necessary, adjusts the measure of performance and related revenue recognition. The Company receives payments from its customers based on billing schedules established in each contract. Non-refundable upfront payments are included in the estimation of the transaction price, allocated to the performance obligation(s) based upon relative standalone selling price and recognized for each performance obligation based upon the measure of progress (point in time or over time) for each performance obligation. Payments received for goods and services not yet provided are recorded as deferred revenue. Amounts are recorded as accounts receivable when the Company’s right to consideration is unconditional. For a discussion of accounting for collaboration and license revenues, see Note 6, Collaboration and License Agreements 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. ​ Recent Accounting Pronouncements Not Yet Adopted In November 2023, the FASB issued ASU No. 2023-07, Segment Reporting (Topic 280): Improvements to Reportable Segment Disclosures (“ASU 2023-07”), which is intended to improve reportable segment disclosure requirements, primarily through enhanced disclosures about significant segment expenses that are regularly provided to the chief operating decision maker. The guidance is effective for fiscal years beginning after December 15, 2023 and interim periods within fiscal years beginning after December 15, 2024. Early adoption is permitted. The guidance is to be applied retrospectively to all prior periods presented in the financial statements. Upon transition, the segment expense categories and amounts disclosed in the prior periods should be based on the significant segment expense categories identified and disclosed in the period of adoption. The Company is currently evaluating the potential impact of adopting this new guidance on its condensed consolidated financial statements and related disclosures. 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. This Company is currently evaluating the potential impact of adopting this new guidance on its condensed consolidated financial statements and related disclosures.

Property and Equipment, Net

Property and Equipment, Net	9 Months Ended
	Sep. 30, 2024
Property and Equipment, Net
Property and Equipment, Net	3. Property and Equipment, Net Property and equipment, net consists of the following as of September 30, 2024 and December 31, 2023: ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, December 31, ​ ​ 2024 ​ 2023 Laboratory equipment ​ $ 5,917 ​ $ 5,815 Computers and software ​ 183 ​ 183 Furniture and fixtures ​ 681 ​ 681 Leasehold improvements ​ 5,124 ​ 5,124 Total property and equipment ​ ​ 11,905 ​ ​ 11,803 Less: accumulated depreciation ​ (7,060) ​ (5,861) Property and equipment, net ​ $ 4,845 ​ $ 5,942 ​ The Company recognized depreciation and amortization expense related to property and equipment of $1.2 million and $1.4 million for the nine months ended September 30, 2024 and 2023, respectively.

Accrued Expenses

Accrued Expenses	9 Months Ended
	Sep. 30, 2024
Accrued Expenses
Accrued Expenses	4. Accrued Expenses and Restructuring Accrued expenses consist of the following as of September 30, 2024 and December 31, 2023: ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, December 31, ​ ​ 2024 ​ 2023 External research and development ​ $ 5,143 ​ $ 4,867 Personnel-related ​ 3,360 ​ 4,690 Restructuring ​ ​ 15 ​ ​ — Professional and consulting fees ​ 1,137 ​ 845 Other ​ ​ 138 ​ ​ 95 Total accrued expenses ​ $ 9,793 ​ $ 10,497 ​ In March 2024, the Company’s board of directors approved a strategic portfolio reprioritization and workforce reduction. As part of the workforce reduction, the Company recognized restructuring charges of $0.9 million during the nine months ended September 30, 2024, primarily related to employee severance, benefits continuation and outplacement service costs. The workforce reduction was completed in April 2024. The Company made payments of $0.9 million related to the restructuring during the nine months ended September 30, 2024. All remaining employee severance, benefits continuation and outplacement service cost payments were completed in October 2024. ​ The following table summarizes the accrued restructuring liability activity for the Company’s workforce reduction for the nine months ended September 30, 2024: ​ ​ ​ ​ ​ ​ Severance and ​ ​ Related Benefits Accrued restructuring liability as of December 31, 2023 ​ $ — Restructuring charges ​ 937 Restructuring payments ​ ​ (922) Accrued restructuring liability as of September 30, 2024 ​ $ 15 ​

Loan and Security Agreement

Loan and Security Agreement	9 Months Ended
	Sep. 30, 2024
Loan and Security Agreement
Loan and Security Agreement	5. Loan and Security Agreement ​ In November 2019, the Company’s wholly owned subsidiary, Xilio Development, Inc. (“Xilio Development”), entered into a loan and security agreement (as amended and restated in May 2023, the “Loan Agreement”) with Pacific Western Bank (“PacWest”), with the Company as a guarantor, and borrowed $10.0 million under a term loan. Interest on amounts outstanding under the Loan Agreement accrued at a variable annual rate equal to the greater of (i) the prime rate ​ The Company recognized $0.1 million and $0.6 million of interest expense related to the Loan Agreement for the nine months ended September 30, 2024 and 2023, respectively, which is reflected in other income, net on the condensed consolidated statements of operations and comprehensive loss.

Collaboration and License Agree

Collaboration and License Agreements	9 Months Ended
	Sep. 30, 2024
Collaboration and License Agreements
Collaboration and License Agreements	6. Collaboration and License Agreements 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 agreed to purchase up to an aggregate of $25.0 million of the Company’s common stock (or at Gilead’s election, prefunded warrants in lieu of shares of common stock) in an initial private placement in connection with the execution of the license agreement and in up to three additional private placements through March 2025 at a predetermined mechanism for the purchase price per share, at all times subject to Gilead not being deemed the beneficial owner of greater than 19.9% of the Company’s common stock upon the closing of the applicable private placement. In March 2024, the Company initially issued and sold 6,860,223 shares of common stock to Gilead at a purchase price of $1.97 per share and received approximately $13.5 million in aggregate gross proceeds. In April 2024, the Company exercised its right to a first additional private placement with Gilead and received approximately $3.3 million in aggregate gross proceeds from the issuance and sale of an additional 485,250 shares of its common stock at a purchase price of $0.76 per share and prefunded warrants to purchase up to an aggregate of 3,882,450 shares of its common stock at a purchase price of $0.7599 per prefunded warrant. 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 September 30, 2024, the Company has received approximately $46.8 million in payments under the Gilead agreements, consisting of the $30.0 million upfront cash payment under the license agreement and approximately $16.8 million in gross proceeds from private placements under the stock purchase agreement. As of September 30, 2024, the Company is eligible to receive up to $600.7 million in additional contingent payments, which consist of (i) approximately $8.2 million in proceeds from up to two additional private placements, (ii) the $75.0 million transition fee and (iii) up to $517.5 million in specified development, regulatory and sales-based milestones. Prior to the potential transition fee, up to $25.7 million of the total additional contingent payments are related to the potential additional private placements and 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 September 30, 2024, 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 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 and nine months ended September 30, 2024, the Company recognized license revenue of $2.3 million and $4.6 million, respectively, under the license agreement and the stock purchase agreement. As of September 30, 2024, the Company recorded deferred revenue of $34.5 million, of which $26.1 million was recorded as a current liability on the Company’s condensed consolidated balance sheet. ​ Summary of Contract Assets and Liabilities ​ The following table presents changes in the balances of the Company's contract liabilities: ​ ​ ​ ​ ​ ​ Deferred ​ ​ Revenue Deferred revenue as of December 31, 2023 ​ $ — Additions ​ 39.1 License revenue recognized ​ ​ (4.6) Deferred revenue as of September 30, 2024 ​ $ 34.5 ​ 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 (the “Roche Clinical Collaboration”) pursuant to a clinical supply agreement to evaluate vilastobart (XTX101) 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 sponsoring and conducting the Phase 1/2 clinical trial and retains global development and commercialization rights to vilastobart. The Company concluded that the cost-sharing payments from the Roche Clinical Collaboration 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 from the Roche Clinical Collaboration 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. During the three months ended September 30, 2024, the Company did not recognize a reduction of research and development expenses under the Roche Clinical Collaboration. During the three months ended September 30, 2023, the Company recognized a reduction of research and development expenses of $2.0 million under the Roche Clinical Collaboration. During each of the nine months ended September 30, 2024 and 2023, the Company recognized a reduction of research and development expenses of $2.0 million under the Roche Clinical Collaboration.

Commitments and Contingencies

Commitments and Contingencies	9 Months Ended
	Sep. 30, 2024
Commitments and Contingencies
Commitments and Contingencies	7. 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 September 30, 2024 and December 31, 2023, the Company had a letter of credit for the benefit of its landlord in the amount of $1.6 million, collateralized by a money market account, which is recorded as restricted cash on the condensed consolidated balance sheets.

Preferred Stock and Common Stoc

Preferred Stock and Common Stock	9 Months Ended
	Sep. 30, 2024
Preferred Stock and Common Stock
Preferred Stock and Common Stock	8. Preferred Stock and Common Stock Undesignated Preferred Stock As of September 30, 2024 and December 31, 2023, the Company’s certificate of incorporation, as amended, authorized 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, 2024 and December 31, 2023, there were no shares of preferred stock issued or outstanding. Common Stock As of September 30, 2024 and December 31, 2023, 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. ​ Sales Agreement ​ In November 2022, the Company filed a universal shelf registration statement on Form S-3 with the SEC to register for sale up to $250,000,000 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 November 18, 2022 (333-268264). In November 2022, the Company also entered into a sales agreement (the “Sales Agreement”) with Cowen and Company LLC, under which the Company may issue and sell shares of its common stock at prevailing market prices from time to time, having an aggregate offering price of up to $75.0 million, subject to the terms and conditions of the Sales Agreement. Issuances or sales of common stock pursuant to the Sales Agreement are made under the Form S-3 and the corresponding prospectus related to the Sales Agreement, as supplemented by a prospectus supplement filed on April 15, 2024. During the nine months ended September 30, 2024, the Company issued and sold 7,000,000 shares of its common stock pursuant to the Sales Agreement at a weighted average price of $1.00 per share for aggregate gross proceeds of $7.0 million, before deducting commissions. The Company did not sell any shares of its common stock pursuant to the Sales Agreement during the three months ended September 30, 2024. ​ Shares Reserved for Future Issuance The Company has reserved for future issuances the following shares of common stock as of September 30, 2024 and December 31, 2023: ​ ​ ​ ​ ​ ​ ​ ​ September 30, ​ December 31, ​ ​ 2024 ​ 2023 Stock options and unvested restricted stock units 10,829,685 9,456,237 Employee stock purchase plan 938,378 701,244 Prefunded warrants ​ 19,509,891 ​ — Warrants 2,631 2,631 Total shares reserved for future issuance 31,280,585 10,160,112 ​

Stock-Based Compensation

Stock-Based Compensation	9 Months Ended
	Sep. 30, 2024
Stock-Based Compensation
Stock-Based Compensation	9. 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, 2024, the number of shares reserved for issuance under the 2021 Plan automatically increased by 1,380,663 shares. As of September 30, 2024, there were 2,157,814 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. An aggregate of 275,000 shares of the Company’s common stock has been reserved for issuance under the 2022 Inducement Plan. As of September 30, 2024, there were 220,000 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, 2024, the number of shares reserved for issuance under the 2021 ESPP was increased by 276,132 shares. During the nine months ended September 30, 2024 and 2023, the Company issued 38,998 shares of common stock and 68,929 shares of common stock under the 2021 ESPP, respectively. As of September 30, 2024, there were 938,378 shares of common stock available for future issuance under the 2021 ESPP. Stock-Based Compensation Expense During the three and nine months ended September 30, 2024 and 2023, 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, ​ 2024 2023 2024 2023 Research and development expense ​ $ 384 ​ $ 548 ​ $ 1,275 ​ $ 1,670 General and administrative expense ​ 1,190 ​ ​ 1,313 ​ 3,643 ​ 3,782 Total stock-based compensation expense ​ $ 1,574 ​ $ 1,861 ​ $ 4,918 ​ $ 5,452 ​ 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, 2023 7,455,795 ​ $ 5.52 8.0 ​ $ — Granted 2,085,853 ​ $ 0.89 ​ Exercised (7,215) ​ $ 0.55 ​ Cancelled/forfeited (1,528,062) ​ $ 5.36 ​ ​ Outstanding as of September 30, 2024 8,006,371 ​ $ 4.35 8.0 ​ $ 99 Exercisable as of September 30, 2024 3,964,796 ​ $ 5.92 7.0 ​ $ 17 ​ (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, 2024 and 2023 was $0.68 and $2.02, respectively. The following assumptions were used in determining the fair value of options granted during the nine months ended September 30, 2024 and 2023: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Nine Months Ended September 30, ​ ​ ​ 2024 ​ 2023 ​ Risk-free interest rate ​ ​ 3.7 - 4.6 % ​ 3.6 - 4.4 % Expected dividend yield ​ ​ 0 % ​ 0 % Expected term (in years) ​ ​ 5.5 - 6.1 ​ ​ 5.5 - 6.1 ​ Expected volatility ​ ​ 87.7 - 91.4 % ​ 81.7 - 87.3 % ​ As of September 30, 2024, the Company had unrecognized stock-based compensation expense of $7.0 million related to stock options issued to employees and directors, which is expected to be recognized over a weighted-average period of 2.1 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, 2023 ​ — $ — Granted ​ 481,500 ​ $ 0.55 Forfeited ​ (36,000) ​ $ 0.55 Unvested as of September 30, 2024 445,500 $ 0.55 ​ For the nine months ended September 30, 2024, the Company recognized less than $0.1 million of stock-based compensation expense related to these awards. As of September 30, 2024, 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 3.3 years. Restricted Common Stock A summary of the Company’s restricted common stock activity and related information is as follows: ​ ​ ​ ​ ​ ​ ​ ​ Number Weighted ​ ​ of Shares ​ Average ​ ​ of Restricted ​ Grant Date ​ Common Stock Fair Value Unvested as of December 31, 2023 ​ 5,617 $ 5.51 Vested ​ (5,617) ​ $ 5.51 Unvested as of September 30, 2024 — $ — ​ In June 2020, the Company granted 552,546 shares of common stock underlying restricted stock awards, and the Company has not subsequently granted any additional restricted stock awards. The aggregate fair value of the restricted stock awards that vested during the nine months ended September 30, 2024 and 2023 was less than $0.1 million.

Net Loss Per Share

Net Loss Per Share	9 Months Ended
	Sep. 30, 2024
Net Loss Per Share
Net Loss Per Share	10. 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 September 30, 2024, no prefunded warrants have been exercised and 19,509,891 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 attributable to common stockholders during each period because including them would have been anti-dilutive: ​ ​ ​ ​ ​ ​ ​ Nine Months Ended ​ ​ September 30, ​ ​ 2024 ​ 2023 Unvested restricted common stock — 13,074 Unvested restricted stock units 445,500 — Outstanding stock options 8,006,371 7,823,478 Warrants 2,631 2,631 Unvested employee stock purchase plan shares ​ 37,097 ​ 60,488 Total common stock equivalents 8,491,599 7,899,671 ​

Pay vs Performance Disclosure

Pay vs Performance Disclosure - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Pay vs Performance Disclosure
Net Income (Loss)	$ (14,020)	$ (16,748)	$ (45,148)	$ (58,749)

Insider Trading Arrangements

Insider Trading Arrangements	3 Months Ended
	Sep. 30, 2024
Trading Arrangements, by Individual
Rule 10b5-1 Arrangement Adopted	false
Non-Rule 10b5-1 Arrangement Adopted	false
Rule 10b5-1 Arrangement Terminated	false
Non-Rule 10b5-1 Arrangement Terminated	false

Summary of Significant Accoun_2

Summary of Significant Accounting Policies (Policies)	9 Months Ended
	Sep. 30, 2024
Summary of Significant Accounting Policies
Basis of Presentation	Basis of Presentation The Company’s unaudited interim condensed consolidated financial statements have been prepared in accordance with accounting principles generally accepted in the United States (“U.S. GAAP”). 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, 2023 and notes thereto, included in the Company’s Annual Report on Form 10-K filed with the U.S. Securities and Exchange Commission (“SEC”) on April 1, 2024. 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, 2024 and the results of its operations for the three and nine months ended September 30, 2024 and 2023 and cash flows for the nine months ended September 30, 2024 and 2023. Such adjustments are of a normal and recurring nature. The results for the three and nine months ended September 30, 2024 are not necessarily indicative of the results for the year ending December 31, 2024 or for any future period.
Principles of Consolidation	Principles of Consolidation The accompanying condensed consolidated financial statements include the accounts of the Company and its wholly owned subsidiaries: Xilio Development, Inc., a Delaware corporation and Xilio Securities Corporation, a Massachusetts security corporation. All intercompany accounts and transactions have been eliminated in consolidation.
Use of Estimates	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 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.
Revenue Recognition	Revenue Recognition The Company recognizes revenue in accordance with ASC Topic 606, Revenue from Contracts with Customers Under ASC 606, the Company recognizes revenue when its customer obtains control of promised goods or services, in an amount that reflects the consideration which the entity expects to receive in exchange for those goods or services. To determine the appropriate amount of revenue to be recognized for arrangements that the Company determines are within the scope of ASC 606, the Company performs the following five steps: (i) identification of the contract with the customer; (ii) determination of whether the promised goods or services are performance obligations, including whether they are distinct in the context of the contract; (iii) measurement of the transaction price, including the constraint on variable consideration; (iv) allocation of the transaction price to the performance obligations; and (v) recognition of revenue when (or as) the Company satisfies each performance obligation. ● Performance Obligations . The promised goods or services in the Company’s arrangements typically consist of a license, or option to license, rights to the Company’s intellectual property or research and development services. The Company may provide options to additional items in such arrangements, which are accounted for as separate contracts when the customer elects to exercise such options, unless the option provides a material right to the customer. Performance obligations are promised goods or services in a contract to transfer a distinct good or service to the customer and are considered distinct when (i) the customer can benefit from the good or service on its own or together with other readily available resources and (ii) the promised good or service is separately identifiable from other promises in the contract. In assessing whether promised goods or services are distinct, the Company considers factors such as the stage of development of the underlying intellectual property, the capabilities of the customer to develop the intellectual property on its own or whether the required expertise is readily available and whether the goods or services are integral or dependent to other goods or services in the contract. ● Customer Options. If an arrangement is determined to contain customer options that allow the customer to acquire additional goods or services, the goods and services underlying the customer options that are not determined to be material rights are not considered to be performance obligations at the outset of the arrangement, as they are contingent upon option exercise. The Company evaluates the customer options for material rights, or options to acquire additional goods or services for free or at a discount. If the customer options are determined to represent a material right, the material right is recognized as a separate performance obligation at the outset of the arrangement. The Company allocates the transaction price to material rights based on the relative standalone selling price, which is determined based on the identified discount and the probability that the customer will exercise the option. Amounts allocated to a material right are not recognized as revenue until, at the earliest, the option is exercised or the option expires. ● Transaction Price . The Company estimates the transaction price based on the amount expected to be received for transferring the promised goods or services in the contract. The consideration may include fixed consideration or variable consideration. At the inception of each arrangement that includes variable consideration, the Company evaluates the amount of potential payments and the likelihood that the payments will be received. The Company utilizes either the most likely amount method or expected value method to estimate the amount expected to be received based on which method best predicts the amount expected to be received. The amount of variable consideration that is included in the transaction price may be constrained and is included in the transaction price only to the extent that it is probable that a significant reversal in the amount of the cumulative revenue recognized will not occur in a future period. At the end of each subsequent reporting period, the Company reevaluates the probability of achievement of all variable consideration subject to constraint, and if necessary, adjusts its estimate of the overall transaction price. Any such adjustments are recorded on a cumulative catch-up basis, which would affect revenues in the period of adjustment. The Company allocates the transaction price to the identified performance obligations based on the estimated standalone selling price. The Company must develop assumptions that require judgment to determine the standalone selling price for each performance obligation identified in the contract. The Company utilizes key assumptions to determine the standalone selling price, which may include other comparable transactions, pricing considered in negotiating the transaction and the estimated costs. Variable consideration is allocated specifically to one or more performance obligations in a contract when the terms of the variable consideration relate to the satisfaction of the performance obligation and the resulting amounts allocated are consistent with the amounts the Company would expect to receive for the satisfaction of each performance obligation. ● Milestone Payments. At the inception of each arrangement that includes development or regulatory milestone payments, the Company evaluates whether the milestones are considered probable of being achieved and estimates the amount to be included in the transaction price using the most likely amount method. If it is probable that a significant revenue reversal would not occur, the associated milestone value is included in the transaction price. Milestone payments that are not within the Company’s control or the licensee’s control, such as regulatory approvals, are not considered probable of being achieved until those approvals are received. The Company evaluates factors such as the scientific, clinical, regulatory, commercial, and other risks that must be overcome to achieve the particular milestone in making this assessment. There is considerable judgment involved in determining whether it is probable that a significant revenue reversal would not occur. ● Royalties. For arrangements that include sales-based royalties, including milestone payments based on the level of sales, and the license is deemed to be the predominant item to which the royalties relate, the Company recognizes 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). To date, the Company has not recognized any royalty revenue resulting from any of the Company’s collaboration or licensing arrangements. ● Recognition. The consideration allocated to each performance obligation is recognized as revenue when control is transferred for the related goods or services. For performance obligations that consist of licenses and other promises, the Company utilizes judgment to assess the nature of the combined performance obligation to determine whether the combined performance obligation is satisfied over time or at a point in time and, if over time, the appropriate method of measuring progress. The Company evaluates the measure of progress each reporting period and, if necessary, adjusts the measure of performance and related revenue recognition. The Company receives payments from its customers based on billing schedules established in each contract. Non-refundable upfront payments are included in the estimation of the transaction price, allocated to the performance obligation(s) based upon relative standalone selling price and recognized for each performance obligation based upon the measure of progress (point in time or over time) for each performance obligation. Payments received for goods and services not yet provided are recorded as deferred revenue. Amounts are recorded as accounts receivable when the Company’s right to consideration is unconditional.
Concentrations of Credit Risk	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.
Recent Accounting Pronouncements Not Yet Adopted	Recent Accounting Pronouncements Not Yet Adopted In November 2023, the FASB issued ASU No. 2023-07, Segment Reporting (Topic 280): Improvements to Reportable Segment Disclosures (“ASU 2023-07”), which is intended to improve reportable segment disclosure requirements, primarily through enhanced disclosures about significant segment expenses that are regularly provided to the chief operating decision maker. The guidance is effective for fiscal years beginning after December 15, 2023 and interim periods within fiscal years beginning after December 15, 2024. Early adoption is permitted. The guidance is to be applied retrospectively to all prior periods presented in the financial statements. Upon transition, the segment expense categories and amounts disclosed in the prior periods should be based on the significant segment expense categories identified and disclosed in the period of adoption. The Company is currently evaluating the potential impact of adopting this new guidance on its condensed consolidated financial statements and related disclosures. 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. This Company is currently evaluating the potential impact of adopting this new guidance on its condensed consolidated financial statements and related disclosures.

Property and Equipment, Net (Ta

Property and Equipment, Net (Tables)	9 Months Ended
	Sep. 30, 2024
Property and Equipment, Net
Summary of property and equipment, net	​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, December 31, ​ ​ 2024 ​ 2023 Laboratory equipment ​ $ 5,917 ​ $ 5,815 Computers and software ​ 183 ​ 183 Furniture and fixtures ​ 681 ​ 681 Leasehold improvements ​ 5,124 ​ 5,124 Total property and equipment ​ ​ 11,905 ​ ​ 11,803 Less: accumulated depreciation ​ (7,060) ​ (5,861) Property and equipment, net ​ $ 4,845 ​ $ 5,942

Accrued Expenses (Tables)

Accrued Expenses (Tables)	9 Months Ended
	Sep. 30, 2024
Accrued Expenses
Summary of accrued expenses	​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, December 31, ​ ​ 2024 ​ 2023 External research and development ​ $ 5,143 ​ $ 4,867 Personnel-related ​ 3,360 ​ 4,690 Restructuring ​ ​ 15 ​ ​ — Professional and consulting fees ​ 1,137 ​ 845 Other ​ ​ 138 ​ ​ 95 Total accrued expenses ​ $ 9,793 ​ $ 10,497
Summary of accrued restructuring liability activity	​ ​ ​ ​ ​ ​ Severance and ​ ​ Related Benefits Accrued restructuring liability as of December 31, 2023 ​ $ — Restructuring charges ​ 937 Restructuring payments ​ ​ (922) Accrued restructuring liability as of September 30, 2024 ​ $ 15 ​

Collaboration and License Agr_2

Collaboration and License Agreements (Tables)	9 Months Ended
	Sep. 30, 2024
Collaboration and License Agreements
Schedule of changes in the balances of contract liabilities	​ ​ ​ ​ ​ ​ Deferred ​ ​ Revenue Deferred revenue as of December 31, 2023 ​ $ — Additions ​ 39.1 License revenue recognized ​ ​ (4.6) Deferred revenue as of September 30, 2024 ​ $ 34.5

Preferred Stock and Common St_2

Preferred Stock and Common Stock (Tables)	9 Months Ended
	Sep. 30, 2024
Preferred Stock and Common Stock
Schedule of Shares Reserved for Future Issuance	​ ​ ​ ​ ​ ​ ​ ​ September 30, ​ December 31, ​ ​ 2024 ​ 2023 Stock options and unvested restricted stock units 10,829,685 9,456,237 Employee stock purchase plan 938,378 701,244 Prefunded warrants ​ 19,509,891 ​ — Warrants 2,631 2,631 Total shares reserved for future issuance 31,280,585 10,160,112 ​

Stock-Based Compensation (Table

Stock-Based Compensation (Tables)	9 Months Ended
	Sep. 30, 2024
Stock-Based Compensation
Schedule of stock-based compensation expense	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three Months Ended September 30, ​ Nine Months Ended September 30, ​ 2024 2023 2024 2023 Research and development expense ​ $ 384 ​ $ 548 ​ $ 1,275 ​ $ 1,670 General and administrative expense ​ 1,190 ​ ​ 1,313 ​ 3,643 ​ 3,782 Total stock-based compensation expense ​ $ 1,574 ​ $ 1,861 ​ $ 4,918 ​ $ 5,452
Summary of stock option activity	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 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, 2023 7,455,795 ​ $ 5.52 8.0 ​ $ — Granted 2,085,853 ​ $ 0.89 ​ Exercised (7,215) ​ $ 0.55 ​ Cancelled/forfeited (1,528,062) ​ $ 5.36 ​ ​ Outstanding as of September 30, 2024 8,006,371 ​ $ 4.35 8.0 ​ $ 99 Exercisable as of September 30, 2024 3,964,796 ​ $ 5.92 7.0 ​ $ 17 ​ (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.
Schedule of assumptions used in determining fair value of options granted	​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Nine Months Ended September 30, ​ ​ ​ 2024 ​ 2023 ​ Risk-free interest rate ​ ​ 3.7 - 4.6 % ​ 3.6 - 4.4 % Expected dividend yield ​ ​ 0 % ​ 0 % Expected term (in years) ​ ​ 5.5 - 6.1 ​ ​ 5.5 - 6.1 ​ Expected volatility ​ ​ 87.7 - 91.4 % ​ 81.7 - 87.3 %
Summary of restricted stock unit activity	​ ​ ​ ​ ​ ​ ​ ​ Number Weighted ​ ​ of Shares ​ Average ​ ​ of Restricted ​ Grant Date ​ Stock Units Fair Value Unvested as of December 31, 2023 ​ — $ — Granted ​ 481,500 ​ $ 0.55 Forfeited ​ (36,000) ​ $ 0.55 Unvested as of September 30, 2024 445,500 $ 0.55
Summary of restricted stock activity	​ ​ ​ ​ ​ ​ ​ ​ Number Weighted ​ ​ of Shares ​ Average ​ ​ of Restricted ​ Grant Date ​ Common Stock Fair Value Unvested as of December 31, 2023 ​ 5,617 $ 5.51 Vested ​ (5,617) ​ $ 5.51 Unvested as of September 30, 2024 — $ —

Net Loss Per Share (Tables)

Net Loss Per Share (Tables)	9 Months Ended
	Sep. 30, 2024
Net Loss Per Share
Schedule of antidilutive securities excluded from computation of diluted net loss per share	​ ​ ​ ​ ​ ​ ​ Nine Months Ended ​ ​ September 30, ​ ​ 2024 ​ 2023 Unvested restricted common stock — 13,074 Unvested restricted stock units 445,500 — Outstanding stock options 8,006,371 7,823,478 Warrants 2,631 2,631 Unvested employee stock purchase plan shares ​ 37,097 ​ 60,488 Total common stock equivalents 8,491,599 7,899,671 ​

Description of Business and L_2

Description of Business and Liquidity and Going Concern - Liquidity and Going Concern (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023	Dec. 31, 2023
Description of Business, Liquidity and Going Concern
Accumulated deficit	$ 370,660		$ 370,660		$ 325,512
Net loss	14,020	$ 16,748	45,148	$ 58,749
Cash and cash equivalents	$ 61,259	$ 59,772	$ 61,259	$ 59,772	$ 44,704
Substantial doubt about going concern within one year			true

Property and Equipment, Net (De

Property and Equipment, Net (Details) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Dec. 31, 2023
Property and Equipment
Property and equipment	$ 11,905		$ 11,803
Less accumulated depreciation	(7,060)		(5,861)
Property and equipment, net	4,845		5,942
Depreciation	1,200	$ 1,400
Laboratory equipment
Property and Equipment
Property and equipment	5,917		5,815
Computers and software
Property and Equipment
Property and equipment	183		183
Furniture & fixtures
Property and Equipment
Property and equipment	681		681
Leasehold improvements
Property and Equipment
Property and equipment	$ 5,124		$ 5,124

Accrued Expenses and Restructur

Accrued Expenses and Restructuring - Accrued Expenses (Details) - USD ($) $ in Thousands	Sep. 30, 2024	Dec. 31, 2023
Accrued Expenses
External research and development	$ 5,143	$ 4,867
Personnel-related	3,360	4,690
Restructuring	15
Professional and consulting fees	1,137	845
Other	138	95
Total accrued expenses	$ 9,793	$ 10,497

Accrued Expenses and Restruct_2

Accrued Expenses and Restructuring - Restructuring (Details) - USD ($) $ in Thousands	3 Months Ended	9 Months Ended
	Sep. 30, 2024	Sep. 30, 2024
Summary of accrued restructuring liability activity
Accrued restructuring liability as of beginning of period
Restructuring charges	$ (41)	937
Restructuring payments		(922)
Accrued restructuring liability as of end of period	$ 15	$ 15

Loan and Security Agreement - D

Loan and Security Agreement - Description (Details) - Loan Agreement $ in Millions	1 Months Ended
	Nov. 30, 2019 USD ($)
Loan and security agreement
Borrowed amount	$ 10
Basis spread (as percent)	0.25%
Debt Instrument, Variable Interest Rate, Type	us-gaap:PrimeRateMember
Minimum
Loan and security agreement
Stated interest rate	4.75%

Loan and Security Agreement - I

Loan and Security Agreement - Interest expense (Details) - USD ($) $ in Millions	9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023
Loan Agreement
Minimum aggregate future loan payments
Interest expense	$ 0.1	$ 0.6

Collaboration and License Agr_3

Collaboration and License Agreements - Gilead Sciences, Inc. (Details) $ / shares in Units, $ in Thousands	1 Months Ended		3 Months Ended	9 Months Ended
	Apr. 30, 2024 USD ($) $ / shares shares	Mar. 31, 2024 USD ($) item $ / shares shares	Sep. 30, 2024 USD ($) item	Sep. 30, 2024 USD ($) item
Agreements
Revenue			$ 2,263	$ 4,620
Revenue from Contract with Customer, Product and Service			us-gaap:LicenseMember	us-gaap:LicenseMember
Deferred revenue, current portion			$ 26,105	$ 26,105
License and Stock Purchase Agreement | Gilead Sciences, Inc.
Agreements
Maximum additional contingent payments receivable, Transition fee		$ 75,000		$ 75,000
Value of shares counterparty agreed to purchase		$ 25,000
Number of additional private placements | item		3	2	2
Maximum beneficial ownership (as a percent)	19.90%	19.90%
Common stock issued and sold (in shares) | shares	485,250	6,860,223
Purchase price (in dollars per share) | $ / shares	$ 0.76	$ 1.97
Gross proceeds from private placement	$ 3,300	$ 13,500		$ 16,800
Upfront payment				46,800
Upfront payment, cash				30,000
Maximum additional contingent payments receivable				600,700
Contingent payments Company is eligible to receive, Private placements				8,200
Additional contingent payments receivable, Maximum milestones				517,500
Additional contingent payments receivable, Maximum additional private placements and near-term development milestones				25,700
Fair market value of common stock issued (in dollars)		4,400
Premium of common stock issued (in dollars)		$ 9,100
Number of promises | item		2
Transaction price		$ 39,100
Transaction price, Cash payment		30,000
Transaction price, Premium on sale of stock		$ 9,100
Revenue			$ 2,300	$ 4,600
Revenue from Contract with Customer, Product and Service			us-gaap:LicenseMember	us-gaap:LicenseMember
Deferred revenue			$ 34,500	$ 34,500
Deferred revenue, current portion			26,100	26,100
Current liability			$ 26,100	$ 26,100
License and Stock Purchase Agreement | Gilead Sciences, Inc. | Prefunded warrants
Agreements
Warrants issued (in shares) | shares	3,882,450
Purchase price, warrant (in dollars per share) | $ / shares	$ 0.7599
Exercise price, warrants (in dollars per share) | $ / shares	$ 0.0001

Collaboration and License Agr_4

Collaboration and License Agreements - Summary of Contract Assets and Liabilities (Details) - License and Stock Purchase Agreement - Gilead Sciences, Inc. $ in Millions	9 Months Ended
	Sep. 30, 2024 USD ($)
Deferred revenue
Additions	$ 39.1
Deductions	(4.6)
Deferred revenue as of end of period	$ 34.5

Collaboration and License Agr_5

Collaboration and License Agreements - Collaboration Agreement (Details) - USD ($) $ in Millions	3 Months Ended	9 Months Ended
	Sep. 30, 2023	Sep. 30, 2024
Clinical Supply Agreement | F. Hoffmann-La Roche Ltd. | Research and development
Agreements
Reduction in research and development expenses	$ 2	$ 2

Commitments and Contingencies (

Commitments and Contingencies (Details) $ in Millions	1 Months Ended
	Aug. 31, 2019 ft²	Sep. 30, 2024 USD ($)	Dec. 31, 2023 USD ($)
Leases
Area leased (in square feet) | ft²	27,830
Option to extend	true
Term of option to extend	5 years
Landlord
Leases
Letter of credit | $		$ 1.6	$ 1.6

Preferred Stock and Common St_3

Preferred Stock and Common Stock - Authorized (Details) - $ / shares	Sep. 30, 2024	Dec. 31, 2023
Preferred stock and Common stock
Preferred stock, shares authorized	5,000,000	5,000,000
Preferred stock, par value (in dollars per share)	$ 0.0001	$ 0.0001
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Common stock, shares authorized	200,000,000	200,000,000
Common stock, par value (in dollars per share)	$ 0.0001	$ 0.0001

Preferred Stock and Common St_4

Preferred Stock and Common Stock - Private Placement and Sales Agreement (Details) $ / shares in Units, $ in Thousands	1 Months Ended			3 Months Ended	9 Months Ended
	Apr. 30, 2024 USD ($) $ / shares shares	Mar. 31, 2024 USD ($) $ / shares shares	Nov. 30, 2022 USD ($) Offering	Sep. 30, 2024 $ / shares shares	Sep. 30, 2024 USD ($) $ / shares shares
Private Placement
Preferred stock and Common stock
Common stock issued and sold (in shares) | shares	1,953,125
Purchase price (in dollars per share)	$ 0.64
Gross proceeds from private placement | $	$ 11,300
Private Placement | Prefunded warrants
Preferred stock and Common stock
Warrants issued (in shares) | shares	15,627,441
Purchase price, warrant (in dollars per share)	$ 0.6399
Exercise price, warrants (in dollars per share)	$ 0.0001
2022 Shelf Registration Statement, Private Placement
Preferred stock and Common stock
Maximum amount of securities available | $			$ 250,000
2022 Shelf Registration Statement, Private Placement | Minimum
Preferred stock and Common stock
Number of potential offerings | Offering			1
At-the-Market Offerings
Preferred stock and Common stock
Common stock issued and sold (in shares) | shares				0	7,000,000
Purchase price (in dollars per share)				$ 1	$ 1
Gross proceeds from private placement | $					$ 7,000
Maximum amount of shares available | $			$ 75,000
License and Stock Purchase Agreement | Gilead Sciences, Inc.
Preferred stock and Common stock
Common stock issued and sold (in shares) | shares	485,250	6,860,223
Purchase price (in dollars per share)	$ 0.76	$ 1.97
Gross proceeds from private placement | $	$ 3,300	$ 13,500			$ 16,800
License and Stock Purchase Agreement | Gilead Sciences, Inc. | Prefunded warrants
Preferred stock and Common stock
Warrants issued (in shares) | shares	3,882,450
Purchase price, warrant (in dollars per share)	$ 0.7599
Exercise price, warrants (in dollars per share)	$ 0.0001

Preferred Stock and Common St_5

Preferred Stock and Common Stock - Shares Reserved for Future Issuance (Details) - shares	Sep. 30, 2024	Dec. 31, 2023	Dec. 31, 2021
Shares for future issuance
Shares reserved for future issuance (in shares)	31,280,585	10,160,112
Prefunded warrants
Shares for future issuance
Shares reserved for future issuance (in shares)	19,509,891
Warrants, Excluding prefunded warrants
Shares for future issuance
Shares reserved for future issuance (in shares)	2,631	2,631
2021 ESPP
Shares for future issuance
Shares reserved for future issuance (in shares)	938,378	701,244	292,031
Stock options and unvested restricted stock units
Shares for future issuance
Shares reserved for future issuance (in shares)	10,829,685	9,456,237

Stock-Based Compensation - Stoc

Stock-Based Compensation - Stock Incentive Plan (Details) - shares		1 Months Ended
	Jan. 01, 2024	Sep. 30, 2021	Sep. 30, 2024	Dec. 31, 2023
Stock-Based Compensation
Common stock reserved for issuance (in shares)			31,280,585	10,160,112
2021 Plan
Stock-Based Compensation
Common stock reserved for issuance (in shares)		6,579,016
Annual increase in number of shares reserved for issuance (as a percent)		5%
Additional common stock reserved under the plan (in shares)	1,380,663
Shares available for future issuance (in shares)			2,157,814

Stock-Based Compensation - 2022

Stock-Based Compensation - 2022 Inducement Plan (Details) - shares	Sep. 30, 2024	Dec. 31, 2023	Dec. 31, 2022
Stock-Based Compensation
Common stock reserved for issuance (in shares)	31,280,585	10,160,112
2022 Inducement Plan
Stock-Based Compensation
Common stock reserved for issuance (in shares)			275,000
Shares available for future issuance (in shares)	220,000

Stock-Based Compensation - Empl

Stock-Based Compensation - Employee Stock Purchase Plan (Details) - shares		9 Months Ended		12 Months Ended
	Jan. 01, 2024	Sep. 30, 2024	Sep. 30, 2023	Dec. 31, 2021	Dec. 31, 2023
Stock-Based Compensation
Common stock reserved for issuance (in shares)		31,280,585			10,160,112
2021 ESPP
Stock-Based Compensation
Common stock reserved for issuance (in shares)		938,378		292,031	701,244
Annual increase in number of shares reserved for issuance (as a percent)				1%
Additional common stock reserved under the plan (in shares)	276,132
Shares issued under plan (in shares)		38,998	68,929
Shares available for future issuance (in shares)		938,378
2021 ESPP | Maximum
Stock-Based Compensation
Annual increase in number of shares reserved and available for issuance (in shares)				584,062

Stock-Based Compensation - St_2

Stock-Based Compensation - Stock-based compensation expense (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Stock-Based Compensation
Total stock-based compensation expense	$ 1,574	$ 1,861	$ 4,918	$ 5,452
Research and development expense
Stock-Based Compensation
Total stock-based compensation expense	384	548	1,275	1,670
General and administrative expense
Stock-Based Compensation
Total stock-based compensation expense	$ 1,190	$ 1,313	$ 3,643	$ 3,782

Stock-Based Compensation - St_3

Stock-Based Compensation - Stock option activity (Details) $ / shares in Units, $ in Thousands	9 Months Ended	12 Months Ended
	Sep. 30, 2024 USD ($) $ / shares shares	Dec. 31, 2023 $ / shares shares
Options Outstanding
Outstanding at beginning of period (in shares)	7,455,795
Granted (in shares)	2,085,853
Exercised (in shares)	(7,215)
Cancelled/forfeited (in shares)	(1,528,062)
Outstanding at end of period (in shares)	8,006,371	7,455,795
Exercisable at end of period (in shares)	3,964,796
Weighted Average Exercise Price
Outstanding (in dollars per share) | $ / shares	$ 4.35	$ 5.52
Granted (in dollars per share) | $ / shares	0.89
Exercised (in dollars per share) | $ / shares	0.55
Cancelled/forfeited (in dollars per share) | $ / shares	5.36
Exercisable at end of period (in dollars per share) | $ / shares	$ 5.92
Weighted Average Remaining Contractual Term (In years)
Outstanding (in years)	8 years	8 years
Exercisable at end of period (in years)	7 years
Aggregate Intrinsic Value
Outstanding (in dollars) | $	$ 99
Exercisable (in dollars) | $	$ 17

Stock-Based Compensation - St_4

Stock-Based Compensation - Stock options, fair value assumptions (Details) - USD ($) $ / shares in Units, $ in Millions	9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023
Stock-Based Compensation
Fair value of options granted (in dollars per share)	$ 0.68	$ 2.02
Employee Stock Option
Stock-Based Compensation
Risk-free interest rate, minimum (as a percent)	3.70%	3.60%
Risk-free interest rate, maximum (as a percent)	4.60%	4.40%
Expected dividend yield (as a percent)	0%	0%
Expected volatility, minimum (as percentage)	87.70%	81.70%
Expected volatility, maximum (as percentage)	91.40%	87.30%
Unrecognized stock-based compensation expense	$ 7
Weighted-average period for unrecognized compensation expense to be recognized	2 years 1 month 6 days
Employee Stock Option | Minimum
Stock-Based Compensation
Expected term (in years)	5 years 6 months	5 years 6 months
Employee Stock Option | Maximum
Stock-Based Compensation
Expected term (in years)	6 years 1 month 6 days	6 years 1 month 6 days

Stock-Based Compensation - Rest

Stock-Based Compensation - Restricted Stock Units (Details) $ / shares in Units, $ in Thousands	1 Months Ended	3 Months Ended		9 Months Ended
	Jan. 31, 2024 item shares	Sep. 30, 2024 USD ($) $ / shares shares	Sep. 30, 2023 USD ($)	Sep. 30, 2024 USD ($) $ / shares shares	Sep. 30, 2023 USD ($)
Weighted Average Grant Date Fair Value
Stock-based compensation expense | $		$ 1,574	$ 1,861	$ 4,918	$ 5,452
Restricted stock units
Stock-Based Compensation
Number of equal annual installments in which units vest | item	4
Equity Based Compensation
Granted (in shares) | shares	481,500			481,500
Forfeited (in shares) | shares				(36,000)
Unvested awards at end of period (in shares) | shares		445,500		445,500
Weighted Average Grant Date Fair Value
Granted (in dollars per share) | $ / shares				$ 0.55
Forfeited (in dollars per share) | $ / shares				0.55
Unvested awards at end of period (in dollars per share) | $ / shares		$ 0.55		$ 0.55
Unrecognized stock-based compensation expense | $		$ 200		$ 200
Weighted-average period for unrecognized compensation expense to be recognized				3 years 3 months 18 days
Restricted stock units | Maximum
Weighted Average Grant Date Fair Value
Stock-based compensation expense | $				$ 100

Stock-Based Compensation - Re_2

Stock-Based Compensation - Restricted Stock (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended	3 Months Ended		9 Months Ended
	Jun. 30, 2020	Sep. 30, 2024	Sep. 30, 2023	Sep. 30, 2024	Sep. 30, 2023
Weighted Average Grant Date Fair Value
Stock-based compensation expense		$ 1,574	$ 1,861	$ 4,918	$ 5,452
Restricted stock
Equity Based Compensation
Unvested awards at beginning of period (in shares)				5,617
Granted (in shares)	552,546
Vested (in shares)				(5,617)
Weighted Average Grant Date Fair Value
Unvested awards at beginning of period (in dollars per share)				$ 5.51
Vested (in dollars per share)				$ 5.51
Restricted stock | Maximum
Weighted Average Grant Date Fair Value
Aggregate fair value of restricted stock awards that vested				$ 100	$ 100

Net Loss Per Share (Details)

Net Loss Per Share (Details) - shares	9 Months Ended
	Sep. 30, 2024	Sep. 30, 2023
Net Loss Per Share
Total common stock equivalents	8,491,599	7,899,671
Restricted stock
Net Loss Per Share
Total common stock equivalents		13,074
Restricted stock units
Net Loss Per Share
Total common stock equivalents	445,500
Employee Stock Option
Net Loss Per Share
Total common stock equivalents	8,006,371	7,823,478
Warrants
Net Loss Per Share
Total common stock equivalents	2,631	2,631
Employee stock purchase plan
Net Loss Per Share
Total common stock equivalents	37,097	60,488
Prefunded warrants
Net Loss Per Share
Warrants exercised (in shares)	0
Warrants outstanding (in shares)	19,509,891