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Table of Contents

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7

​

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 10-Q

​

​

| ​
(Mark one) | ​
☒ | QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
For the quarterly period ended September 30, 2025
OR
☐ | TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

​

For the transition period from to

​

Commission File Number 001-37581

Aclaris Therapeutics, Inc.

(Exact Name of Registrant as Specified in Its Charter)

Delaware (State or Other Jurisdiction of Incorporation or Organization) | 46-0571712 (I.R.S. Employer Identification No.)
701 Lee Road, Suite 103 Wayne, PA (Address of principal executive offices) | 19087 (Zip Code)

​

Registrant’s telephone number, including area code: (484) 324-7933

​

N/A

​

(Former name, former address and former fiscal year, if changed since last report)

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

​

|  | ​ | ​ |
Title of Each Class: |  | Trading Symbol(s) | ​ | Name of Each Exchange on which Registered
Common Stock, $0.00001 par value |  | ACRS | ​ | The Nasdaq Stock Market, LLC

​

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes ☒ No ☐

Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§ 232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files). Yes ☒ No ☐

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller reporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company” and “emerging growth company” in Rule 12b-2 of the Securities Exchange Act of 1934:

​

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

​

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. ☐

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Securities Exchange Act of 1934). Yes ☐ No ☒

The number of outstanding shares of the registrant’s common stock, par value $0.00001 per share, as of the close of business on October 31, 2025 was 108,345,239.

​

​

​

​

Table of Contents

ACLARIS THERAPEUTICS, INC.

​

INDEX TO FORM 10-Q

​

​ |  | PAGE
​ | ​ | ​
PART I. FINANCIAL INFORMATION | ​ | ​
​ | ​ | ​
Item 1. Financial Statements | ​ | 2
​ | ​ | ​
Unaudited Condensed Consolidated Balance Sheets as of September 30, 2025 and December 31, 2024 | ​ | 2
​ | ​ | ​
Unaudited Condensed Consolidated Statements of Operations and Comprehensive Loss for the three and nine months ende d September 30, 2025 and 2024 | ​ | 3
​ | ​ | ​
Unaudited Condensed Consolidated Statements of Stockholders’ Equity for the three and nine months ended September 30, 2025 and 2024 | ​ | 4
​ | ​ | ​
Unaudited Condensed Consolidated Statements of Cash Flows for the nine months ended September 30, 2025 and 2024 | ​ | 5
​ | ​ | ​
Notes to Unaudited Condensed Consolidated Financial Statements | ​ | 6
​ | ​ | ​
Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations | ​ | 22
​ | ​ | ​
Item 3. Quantitative and Qualitative Disclosures about Market Risk | ​ | 36
​ | ​ | ​
Item 4. Controls and Procedures | ​ | 37
​ | ​ | ​
PART II. OTHER INFORMATION | ​ | ​
​ | ​ | ​
Item 1. Legal Proceedings | ​ | 37
​ | ​ | ​
Item 1A. Risk Factors | ​ | 37
​ | ​ | ​
Item 5. Other Information | ​ | 37
​ | ​ | ​
Item 6. Exhibits | ​ | 38
​ | ​ | ​
Signatures | ​ | 39

​

​

Table of Contents

Part I. FINANCIAL INFORMATION

Item 1. Financial Statements

ACLARIS THERAPEUTICS, INC.

CONDENSED CONSOLIDATED BALANCE SHEET S

(Unaudited)

​

(In thousands, except share and per share data)

​

​ | ​ | ​ | ​ | ​ | ​ | ​
​ |  | September 30, | ​ | December 31,
​ |  | 2025 |  | 2024
​ | ​ | ​ | ​ | ​ | ​
Assets | ​ | ​ | ​ | ​ | ​ | ​
Current assets: | ​ | ​ | ​ | ​ | ​ | ​
Cash and cash equivalents | ​ | $ | 25,256 | ​ | $ | 24,570
Short-term marketable securities | ​ |  | 70,656 | ​ |  | 89,024
Accounts receivable, prepaid expenses and other current assets | ​ |  | 4,680 | ​ |  | 12,357
Total current assets | ​ |  | 100,592 | ​ |  | 125,951
Marketable securities | ​ |  | 71,297 | ​ |  | 90,302
Property and equipment, net | ​ |  | 811 | ​ |  | 1,008
Other assets | ​ |  | 2,834 | ​ |  | 3,066
Total assets | ​ | $ | 175,534 | ​ | $ | 220,327
Liabilities and Stockholders’ Equity | ​ | ​ | ​ | ​ | ​ | ​
Current liabilities: | ​ | ​ | ​ | ​ | ​ | ​
Accounts payable | ​ | $ | 9,187 | ​ | $ | 4,690
Accrued expenses | ​ |  | 9,784 | ​ |  | 20,333
Deferred income | ​ | ​ | 3,925 | ​ | ​ | 3,890
Other current liabilities | ​ | ​ | 2,735 | ​ | ​ | 2,683
Total current liabilities | ​ |  | 25,631 | ​ |  | 31,596
Other liabilities | ​ | ​ | 1,711 | ​ |  | 4,439
Deferred income, net of current portion | ​ | ​ | 17,492 | ​ | ​ | 20,038
Contingent consideration | ​ | ​ | 10,600 | ​ | ​ | 8,700
Total liabilities | ​ |  | 55,434 | ​ |  | 64,773
Stockholders’ Equity: | ​ | ​ | ​ | ​ | ​ | ​
Preferred stock, $0.00001 par value; 10,000,000 shares authorized and no shares issued or outstanding at September 30, 2025 and December 31, 2024 | ​ | ​ | — | ​ | ​ | —
Common stock, $0.00001 par value; 400,000,000 and 200,000,000 shares authorized at September 30, 2025 and December 31, 2024, respectively; 108,342,592 and 107,850,124 shares issued and outstanding at September 30, 2025 and December 31, 2024, respectively | ​ |  | 1 | ​ |  | 1
Additional paid‑in capital | ​ |  | 1,067,491 | ​ |  | 1,058,317
Accumulated other comprehensive income | ​ |  | 597 | ​ |  | 97
Accumulated deficit | ​ |  | (947,989) | ​ |  | (902,861)
Total stockholders’ equity | ​ |  | 120,100 | ​ |  | 155,554
Total liabilities and stockholders’ equity | ​ | $ | 175,534 | ​ | $ | 220,327

​

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

​

2

Table of Contents

ACLARIS THERAPEUTICS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS

(Unaudited)

​

(In thousands, except share and per share data)

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended | ​ | Nine Months Ended
​ | ​ | September 30, | ​ | September 30,
​ |  | 2025 |  | 2024 |  | 2025 |  | 2024
Revenues: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Contract research | ​ | $ | 485 | ​ | $ | 645 | ​ | $ | 1,372 | ​ | $ | 1,926
Licensing | ​ | ​ | 2,814 | ​ | ​ | 3,701 | ​ | ​ | 5,159 | ​ | ​ | 7,583
Total revenue | ​ | ​ | 3,299 | ​ | ​ | 4,346 | ​ | ​ | 6,531 | ​ | ​ | 9,509
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Costs and expenses: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Cost of revenue | ​ | ​ | 538 | ​ | ​ | 654 | ​ | ​ | 1,559 | ​ | ​ | 2,087
Research and development |  | ​ | 13,028 | ​ | ​ | 5,956 | ​ |  | 36,061 | ​ |  | 24,560
General and administrative |  | ​ | 4,871 | ​ | ​ | 5,653 | ​ |  | 16,396 | ​ |  | 17,249
Licensing | ​ | ​ | 1,911 | ​ | ​ | 1,754 | ​ | ​ | 4,256 | ​ | ​ | 4,070
Revaluation of contingent consideration | ​ | ​ | 100 | ​ | ​ | 800 | ​ | ​ | 1,900 | ​ | ​ | 3,800
Total costs and expenses |  | ​ | 20,448 | ​ |  | 14,817 | ​ |  | 60,172 | ​ |  | 51,766
Loss from operations |  | ​ | (17,149) | ​ |  | (10,471) | ​ |  | (53,641) | ​ |  | (42,257)
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Other income: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Interest income |  | ​ | 1,819 | ​ |  | 1,991 | ​ |  | 6,003 | ​ |  | 5,850
Non-cash royalty income | ​ | ​ | 716 | ​ | ​ | 894 | ​ | ​ | 2,510 | ​ | ​ | 894
Total other income | ​ | ​ | 2,535 | ​ | ​ | 2,885 | ​ | ​ | 8,513 | ​ | ​ | 6,744
Net loss | ​ | $ | (14,614) | ​ | $ | (7,586) | ​ | $ | (45,128) | ​ | $ | (35,513)
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Net loss per share, basic and diluted | ​ | $ | (0.12) | ​ | $ | (0.11) | ​ | $ | (0.37) | ​ | $ | (0.50)
Weighted average common shares outstanding, basic and diluted | ​ |  | 122,619,311 | ​ |  | 71,381,731 | ​ | ​ | 122,531,032 | ​ |  | 71,249,813
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Other comprehensive income: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Unrealized gain on marketable securities, net of tax of $0 | ​ | $ | 115 | ​ | $ | 890 | ​ | $ | 500 | ​ | $ | 533
Total other comprehensive income | ​ |  | 115 | ​ |  | 890 | ​ |  | 500 | ​ |  | 533
Comprehensive loss | ​ | $ | (14,499) | ​ | $ | (6,696) | ​ | $ | (44,628) | ​ | $ | (34,980)

​

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

​

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ACLARIS THERAPEUTICS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF

STOCKHOLDERS’ EQUITY

(Unaudited)

​

(In thousands, except share data)

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | Accumulated | ​ | ​ | ​ | ​ | ​ | ​ |
​ | Common Stock | ​ | Additional | ​ | Other | ​ | ​ | ​ | Total |
​ | ​ | ​ | Par | ​ | Paid‑in | ​ | Comprehensive | ​ | Accumulated | ​ | Stockholders’ |
​ | Shares |  | Value |  | Capital |  | Income |  | Deficit |  | Equity |
Balance at December 31, 2024 | 107,850,124 | ​ | $ | 1 | ​ | $ | 1,058,317 | ​ | $ | 97 | ​ | $ | (902,861) | ​ | $ | 155,554 | ​
Issuance of common stock in connection with vesting of restricted stock units | 415,405 | ​ | ​ | — | ​ | ​ | (275) | ​ | ​ | — | ​ | ​ | — | ​ |  | (275) | ​
Unrealized gain on marketable securities | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 337 | ​ | ​ | — | ​ |  | 337 | ​
Stock-based compensation expense | — | ​ | ​ | — | ​ | ​ | 3,535 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 3,535 | ​
Net loss | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | (15,085) | ​ |  | (15,085) | ​
Balance at March 31, 2025 | 108,265,529 | ​ | $ | 1 | ​ | $ | 1,061,577 | ​ | $ | 434 | ​ | $ | (917,946) | ​ | $ | 144,066 | ​
Issuance of common stock in connection with vesting of restricted stock units | 63,265 | ​ | ​ | — | ​ | ​ | (9) | ​ | ​ | — | ​ | ​ | — | ​ | ​ | (9) | ​
Unrealized gain on marketable securities | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 48 | ​ | ​ | — | ​ | ​ | 48 | ​
Stock-based compensation expense | — | ​ | ​ | — | ​ | ​ | 3,063 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 3,063 | ​
Net loss | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | (15,429) | ​ | ​ | (15,429) | ​
Balance at June 30, 2025 | 108,328,794 | ​ | $ | 1 | ​ | $ | 1,064,631 | ​ | $ | 482 | ​ | $ | (933,375) | ​ | $ | 131,739 | ​
Issuance of common stock in connection with vesting of restricted stock units | 13,798 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​
Unrealized gain on marketable securities | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 115 | ​ | ​ | — | ​ | ​ | 115 | ​
Stock-based compensation expense | — | ​ | ​ | — | ​ | ​ | 2,860 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 2,860 | ​
Net loss | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | (14,614) | ​ | ​ | (14,614) | ​
Balance at September 30, 2025 | 108,342,592 | ​ | $ | 1 | ​ | $ | 1,067,491 | ​ | $ | 597 | ​ | $ | (947,989) | ​ | $ | 120,100 | ​

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | Accumulated | ​ | ​ | ​ | ​ | ​ | ​
​ | Common Stock | ​ | Additional | ​ | Other | ​ | ​ | ​ | Total
​ | ​ | ​ | Par | ​ | Paid‑in | ​ | Comprehensive | ​ | Accumulated | ​ | Stockholders’
​ | Shares |  | Value |  | Capital |  | Gain (Loss) |  | Deficit |  | Equity
Balance at December 31, 2023 | 70,894,889 | ​ | $ | 1 | ​ | $ | 928,080 | ​ | $ | (106) | ​ | $ | (770,796) | ​ | $ | 157,179
Issuance of common stock in connection with vesting of restricted stock units | 353,128 | ​ | ​ | — | ​ | ​ | (55) | ​ | ​ | — | ​ | ​ | — | ​ | ​ | (55)
Unrealized loss on marketable securities | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | (258) | ​ | ​ | — | ​ | ​ | (258)
Stock-based compensation expense | — | ​ | ​ | — | ​ | ​ | 2,089 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 2,089
Net loss | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | (16,941) | ​ | ​ | (16,941)
Balance at March 31, 2024 | 71,248,017 | ​ | $ | 1 | ​ | $ | 930,114 | ​ | $ | (364) | ​ | $ | (787,737) | ​ | $ | 142,014
Issuance of common stock in connection with vesting of restricted stock units | 84,808 | ​ | ​ | — | ​ | ​ | (10) | ​ | ​ | — | ​ | ​ | — | ​ | ​ | (10)
Unrealized loss on marketable securities | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | (99) | ​ | ​ | — | ​ | ​ | (99)
Stock-based compensation expense | — | ​ | ​ | — | ​ | ​ | 2,903 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 2,903
Net loss | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | (10,986) | ​ | ​ | (10,986)
Balance at June 30, 2024 | 71,332,825 | ​ | $ | 1 | ​ | $ | 933,007 | ​ | $ | (463) | ​ | $ | (798,723) | ​ | $ | 133,822
Issuance of common stock in connection with exercise of stock options and vesting of restricted stock units | 84,688 | ​ | ​ | — | ​ | ​ | 21 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 21
Unrealized gain on marketable securities | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 890 | ​ | ​ | — | ​ | ​ | 890
Stock-based compensation expense | — | ​ | ​ | — | ​ | ​ | 3,004 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 3,004
Net loss | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | — | ​ | ​ | (7,586) | ​ | ​ | (7,586)
Balance at September 30, 2024 | 71,417,513 | ​ | $ | 1 | ​ | $ | 936,032 | ​ | $ | 427 | ​ | $ | (806,309) | ​ | $ | 130,151

​

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

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ACLARIS THERAPEUTICS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS

(Unaudited)

​

(In thousands)

​

​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Nine Months Ended
​ | ​ | September 30,
​ |  | 2025 |  | 2024
Cash flows from operating activities: |  | ​ |  |  | ​ |
Net loss | ​ | $ | (45,128) | ​ | $ | (35,513)
Adjustments to reconcile net loss to net cash used in operating activities: | ​ | ​ | ​ | ​ | ​ | ​
Depreciation and amortization | ​ |  | 352 | ​ |  | 664
Stock-based compensation expense | ​ |  | 9,458 | ​ |  | 7,996
Revaluation of contingent consideration | ​ | ​ | 1,900 | ​ | ​ | 3,800
Changes in operating assets and liabilities: | ​ | ​ | ​ | ​ | ​ | ​
Accounts receivable, prepaid expenses and other assets | ​ |  | 6,810 | ​ |  | 3,699
Accounts payable | ​ |  | 4,484 | ​ |  | (1,216)
Accrued expenses and other liabilities | ​ |  | (9,348) | ​ |  | (15,514)
Deferred income | ​ | ​ | (2,510) | ​ | ​ | 24,947
Net cash used in operating activities | ​ |  | (33,982) | ​ |  | (11,137)
Cash flows from investing activities: | ​ | ​ | ​ | ​ | ​ | ​
Purchases of property and equipment, net | ​ |  | (87) | ​ |  | (121)
Purchases of marketable securities | ​ |  | (35,124) | ​ |  | (49,555)
Proceeds from sales and maturities of marketable securities | ​ |  | 74,040 | ​ |  | 68,630
Payment of deferred transaction consideration for in-licensed assets | ​ | ​ | (833) | ​ | ​ | —
Net cash provided by investing activities | ​ |  | 37,996 | ​ |  | 18,954
Cash flows from financing activities: | ​ | ​ | ​ | ​ | ​ | ​
Payment of deferred transaction consideration for in-licensed assets | ​ | ​ | (3,044) | ​ | ​ | —
Payments of employee withholding taxes related to restricted stock unit award vesting | ​ | ​ | (284) | ​ | ​ | (76)
Proceeds from exercise of employee stock options and the issuance of stock | ​ | ​ | — | ​ | ​ | 32
Net cash used in financing activities | ​ |  | (3,328) | ​ |  | (44)
Net increase in cash and cash equivalents | ​ |  | 686 | ​ |  | 7,773
Cash and cash equivalents at beginning of period | ​ |  | 24,570 | ​ |  | 39,878
Cash and cash equivalents at end of period | ​ | $ | 25,256 | ​ | $ | 47,651
​ | ​ | ​ | ​ | ​ | ​ | ​
Supplemental disclosure of non-cash investing and financing activities: | ​ | ​ | ​ | ​ | ​ | ​
Additions to property and equipment included in accounts payable | ​ | $ | 12 | ​ | $ | —
​ | ​ | ​ | ​ | ​ | ​ | ​

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

​

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Table of Contents

ACLARIS THERAPEUTICS, INC.

NOTES TO UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

​

​

1. Organization and Nature of Business

​

Overview

​

Aclaris Therapeutics, Inc. was incorporated under the laws of the State of Delaware in 2012. Aclaris Therapeutics, Inc. and its wholly owned subsidiaries are referred to collectively as the “Company.”

​

The Company is a clinical-stage biopharmaceutical company focused on developing novel small and large molecule product candidates for immuno-inflammatory diseases. The Company’s proprietary KINect drug discovery platform combined with its preclinical development capabilities allows the Company to identify and advance potential product candidates that it may develop independently or in collaboration with third parties. In addition to identifying and developing its novel product candidates, the Company is pursuing strategic alternatives, including identifying and consummating transactions with third-party partners, to further develop, obtain marketing approval for and/or commercialize its novel product candidates. The Company also provides contract research services to third parties enabled by its early-stage research and development expertise.

​

Liquidity

​

The Company’s condensed consolidated financial statements have been prepared on the basis of continuity of operations, realization of assets and the satisfaction of liabilities in the ordinary course of business. As of September 30, 2025, the Company had cash, cash equivalents and marketable securities of $167.2 million and an accumulated deficit of $948.0 million. Since inception, the Company has incurred net losses and negative cash flows from its operations. There can be no assurance that profitable operations will ever be achieved, and, if achieved, will be sustained on a continuing basis. In addition, development activities, including clinical and preclinical testing of the Company’s product candidates, will require significant additional financing. The future viability of the Company is dependent on its ability to successfully develop its product candidates and to generate revenue from identifying and consummating transactions with third-party partners to further develop, obtain marketing approval for and/or commercialize its development assets or to raise additional capital to finance its operations. The Company will require additional capital to develop its product candidates and to support its discovery efforts.

​

Additional funds may not be available on a timely basis, on commercially acceptable terms, or at all, and such funds, if raised, may not be sufficient to enable the Company to continue to implement its long-term business strategy. The Company's ability to raise additional capital may be adversely impacted by potentially worsening global economic conditions caused by a variety of factors including geopolitical tensions, inflationary pressures, tariff policies, and the current shutdown of the U.S. federal government. If the Company is unable to raise sufficient additional capital or generate revenue from transactions with potential third-party partners for the development and/or commercialization of its product candidates, it may need to substantially curtail planned operations. The Company’s failure to raise capital as and when needed could have a negative impact on its financial condition and ability to pursue its business strategies.

​

In accordance with Accounting Standards Codification (“ASC”) Subtopic 205-40, Disclosure of Uncertainties about an Entity’s Ability to Continue as a Going Concern, the Company evaluated whether there are conditions and events, considered in the aggregate, that raise substantial doubt about the Company’s ability to continue as a going concern within one year after the date that its condensed consolidated financial statements are issued. As of the report date, the Company does not believe that substantial doubt exists about its ability to continue as a going concern. The Company believes its existing cash, cash equivalents and marketable securities are sufficient to fund its operating and capital expenditure requirements for a period greater than 12 months from the date of issuance of these condensed consolidated financial statements.

6

Table of Contents

​

2. Summary of Significant Accounting Policies

​

Unaudited Interim Financial Information

​

The accompanying condensed consolidated balance sheet as of September 30, 2025, the condensed consolidated statements of operations and comprehensive loss for the three and nine months ended September 30, 2025 and 2024, the condensed consolidated statement of stockholders’ equity for the three and nine months ended September 30, 2025 and 2024, and the condensed consolidated statements of cash flows for the nine months ended September 30, 2025 and 2024 are unaudited. The unaudited interim condensed consolidated financial statements have been prepared on the same basis as the audited annual financial statements contained in the Company’s Annual Report on Form 10-K filed with the Securities and Exchange Commission (“SEC”) on February 27, 2025 (“Annual Report”) and, in the opinion of management, reflect all adjustments, which include only normal recurring adjustments, necessary for the fair statement of the Company’s financial position as of September 30, 2025, the results of its operations and comprehensive loss for the three and nine months ended September 30, 2025 and 2024, its changes in stockholders’ equity for the three and nine months ended September 30, 2025 and 2024 and its cash flows for the nine months ended September 30, 2025 and 2024. The condensed consolidated balance sheet data as of December 31, 2024 was derived from audited financial statements but does not include all disclosures required by generally accepted accounting principles in the United States (“GAAP”). The financial data and other information disclosed in these notes related to the three and nine months ended September 30, 2025 and 2024 are unaudited. The results for the three and nine months ended September 30, 2025 are not necessarily indicative of results to be expected for the year ending December 31, 2025, any other interim periods, or any future year or period. The unaudited interim financial statements of the Company included herein have been prepared pursuant to the rules and regulations of the SEC. Certain information and footnote disclosures normally included in financial statements prepared in accordance with GAAP have been condensed or omitted from this report, as is permitted by such rules and regulations. These unaudited condensed consolidated financial statements should be read in conjunction with the audited consolidated financial statements and the notes thereto for the year ended December 31, 2024 included in the Company’s Annual Report.

​

Basis of Presentation

​

The accompanying condensed consolidated financial statements have been prepared in conformity with GAAP. The condensed consolidated financial statements of the Company include the accounts of the operating parent company, Aclaris Therapeutics, Inc., and its wholly owned subsidiaries. All intercompany transactions have been eliminated. Based upon the nature and size of the Company’s revenue, the Company believes that gross profit does not provide a meaningful measure of profitability and, therefore, has not included a line item for gross profit on the condensed consolidated statement of operations and comprehensive loss.

​

Use of Estimates

​

The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, the disclosure of contingent assets and liabilities at the date of the financial statements and the reported amounts of expenses during the reporting periods. Significant estimates and assumptions reflected in these financial statements include, but are not limited to, contingent consideration and the valuation of stock-based awards. Estimates are periodically reviewed in light of changes in circumstances, facts and experience. Actual results could differ from the Company’s estimates.

​

Reclassifications

​

Certain prior year amounts have been reclassified to conform to the current year’s financial statement presentation.

​

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Table of Contents

Significant Accounting Policies

​

The Company’s significant accounting policies are disclosed in the audited consolidated financial statements for the year ended December 31, 2024 included in the Company’s Annual Report. There have been no changes to the Company’s existing significant accounting policies from those disclosed in the Annual Report.

​

Contingent Consideration

​

The Company records a contingent consideration liability related to future potential payments resulting from the acquisition of Confluence Life Sciences, Inc. (now known as Aclaris Life Sciences, Inc.) (“Confluence”) based upon significant unobservable inputs including the achievement of regulatory and commercial milestones, as well as estimated future sales levels and the discount rates applied to calculate the present value of the potential payments. Significant judgement is involved in determining the appropriateness of these assumptions. These assumptions are considered Level 3 inputs. Revaluation of the contingent consideration liability can result from changes to one or more of these assumptions. The Company evaluates the fair value estimate of the contingent consideration liability on a quarterly basis with changes, if any, recorded as income or expense in the condensed consolidated statement of operations and comprehensive loss.

​

The fair value of contingent consideration is estimated using a probability-weighted expected payment model for regulatory milestone payments and a Monte Carlo simulation model for commercial milestone and royalty payments and then applying a risk-adjusted discount rate to calculate the present value of the potential payments. Significant assumptions used in the Company’s estimates include the probability of achieving regulatory milestones and commencing commercialization (collectively referred to as “probability of success”), which are based on an asset’s current stage of development and a review of existing clinical data. Probability of success assumptions ranged between 21% and 40% at September 30, 2025. Additionally, estimated future sales levels and the risk-adjusted discount rate applied to the potential payments are also significant assumptions used in calculating the fair value. As of September 30, 2025, the discount rate ranged between 6.8% and 8.4% depending on the year of each potential payment.

​

Revenue Recognition

​

The Company accounts for revenue in accordance with ASC Topic 606, Revenue from Contracts with Customers. Under ASC Topic 606, revenue is recognized when a customer obtains control of promised goods or services in an amount that reflects the consideration to which the Company expects to be entitled in exchange for those goods or services.

​

To determine revenue recognition in accordance with ASC Topic 606, the Company performs the following five steps: (i) identify the contract(s) with a customer, (ii) identify the performance obligations in the contract, (iii) determine the transaction price, (iv) allocate the transaction price to the performance obligations in the contract, and (v) recognize revenue when (or as) performance obligations are satisfied. At contract inception, the Company assesses the goods or services promised within a contract with a customer to identify the performance obligations, and to determine if they are distinct. The Company recognizes the revenue that is allocated to each distinct performance obligation when (or as) that performance obligation is satisfied. The Company only recognizes revenue when collection of the consideration it is entitled to under a contract with a customer is probable.

​

Contract Research Revenue

​

The Company earns contract research revenue from the provision of laboratory services. Contract research revenue is generally evidenced by contracts with clients which are on an agreed upon fixed-price, fee-for-service basis and are generally billed on a monthly basis in arrears for services rendered. Revenue related to these contracts is generally recognized as the laboratory services are performed, based upon the rates specified in the contracts. Under ASC Topic 606, the Company elected to apply the “right to invoice” practical expedient when recognizing contract research revenue and as such, recognizes revenue in the amount which it has the right to invoice. ASC Topic 606 also provides an optional exemption, which the Company has elected to apply, from disclosing remaining performance obligations when revenue is recognized from the satisfaction of the performance obligation in accordance with the “right to invoice” practical expedient.

​

8

Table of Contents

Licensing Revenue

​

Licenses of Intellectual Property – The Company recognizes revenue received from non-refundable, upfront fees related to the licensing of intellectual property when the intellectual property is determined to be distinct from the other performance obligations identified in the arrangement, the license has been transferred to the customer, and the customer is able to use and benefit from the license.

Milestone and Royalty Payments – The Company considers any future potential milestones and sales-based royalties to be variable consideration. The Company recognizes revenue from development, regulatory and anniversary milestone payments as they are achieved. The Company recognizes revenue from commercial milestones and royalty payments as the sales occur.

Deferred Income Related to the Sale of Future Royalties

​

The Company amortizes its deferred income liability related to the sale of future OLUMIANT® (baricitinib) royalties under the units-of-revenue method by computing a ratio of the proceeds received to the total expected payments over the term of the royalty purchase agreement and then applying that ratio to the period’s estimated cash payment (see Note 11). The amortization is based on the Company’s current estimate of future royalty payments.

​

Discontinued Operations

​

As of September 30, 2025 and December 31, 2024, the Company had $2.2 million in discontinued operations reported as other current liabilities in the Company’s condensed consolidated balance sheet, related to discontinued commercial products.

​

Recently Issued Accounting Pronouncements

​

In November 2024, the Financial Accounting Standards Board (“FASB”) issued Accounting Standards Update (“ASU”) No. 2024-03, “Income Statement—Reporting Comprehensive Income—Expense Disaggregation Disclosures (Subtopic 220-40): Disaggregation of Income Statement Expenses.” This standard requires disclosure of additional information about specific expense categories in the notes to financial statements on an annual and interim basis. This ASU becomes effective for annual periods beginning after December 15, 2026 and interim periods within annual reporting periods beginning after December 15, 2027. The Company is currently assessing the impact of this ASU.

​

In December 2023, the FASB issued ASU No. 2023-09, “Income Taxes (Topic 740): Improvements to Income Tax Disclosures.” This standard enhances disclosures related to income taxes, including the rate reconciliation and information on income taxes paid. This ASU becomes effective for annual periods beginning after December 15, 2024. The Company is assessing the impact of this ASU and, upon adoption, expects that any impact would be limited to additional income tax disclosures in the footnotes to the Company’s consolidated financial statements.

​

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Table of Contents

3. Fair Value of Financial Assets and Liabilities

​

The following tables present information about the fair value measurements of the Company’s financial assets and liabilities which are measured at fair value on a recurring and non-recurring basis, and indicate the level of the fair value hierarchy utilized to determine such fair values:

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | September 30, 2025
(In thousands) |  | Level 1 |  | Level 2 |  | Level 3 |  | Total
Assets: |  | ​ |  |  | ​ |  |  | ​ |  |  | ​ |
Cash equivalents | ​ | $ | 21,707 | ​ | $ | — | ​ | $ | — | ​ | $ | 21,707
Marketable securities | ​ |  | — | ​ | ​ | 141,953 | ​ | ​ | — | ​ | ​ | 141,953
Total assets | ​ | $ | 21,707 | ​ | $ | 141,953 | ​ | $ | — | ​ | $ | 163,660
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Liabilities: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Contingent consideration | ​ | $ | — | ​ | $ | — | ​ | $ | 10,600 | ​ | $ | 10,600
Total liabilities | ​ | $ | — | ​ | $ | — | ​ | $ | 10,600 | ​ | $ | 10,600

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | December 31, 2024
(In thousands) |  | Level 1 |  | Level 2 |  | Level 3 |  | Total
Assets: |  | ​ |  |  | ​ |  |  | ​ |  |  | ​ |
Cash equivalents | ​ | $ | 22,245 | ​ | $ | — | ​ | $ | — | ​ | $ | 22,245
Marketable securities | ​ |  | — | ​ | ​ | 179,326 | ​ | ​ | — | ​ | ​ | 179,326
Total assets | ​ | $ | 22,245 | ​ | $ | 179,326 | ​ | $ | — | ​ | $ | 201,571
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Liabilities: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Contingent consideration | ​ | $ | — | ​ | $ | — | ​ | $ | 8,700 | ​ | $ | 8,700
Total liabilities | ​ | $ | — | ​ | $ | — | ​ | $ | 8,700 | ​ | $ | 8,700

​

As of September 30, 2025 and December 31, 2024, the Company’s cash equivalents consisted of money market funds, which were valued based upon Level 1 inputs. The Company’s marketable securities as of September 30, 2025 consisted of corporate debt securities and U.S. government debt securities, which were all valued based upon Level 2 inputs. The Company’s marketable securities as of December 31, 2024 consisted of commercial paper, corporate debt securities, foreign government agency debt securities, and U.S. government and government agency debt securities, which were all valued based upon Level 2 inputs.

​

In determining the fair value of its Level 2 investments, the Company relies on quoted prices for identical securities in markets that are not active. These quoted prices are obtained by the Company with the assistance of a third-party pricing service based on available trade, bid and other observable market data for identical securities. During the three and nine months ended September 30, 2025 and 2024, there were no transfers into or out of Level 3.

​

The overall $1.9 million increase in the fair value of the contingent consideration liability during the nine months ended September 30, 2025 was primarily due to changes to the probability of success for certain product candidates and the passage of time.

​

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As of September 30, 2025 and December 31, 2024, the fair value of the Company’s available-for-sale marketable securities by type of security was as follows:

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | September 30, 2025
​ | ​ | ​ | ​ | ​ | Gross | ​ | Gross | ​ | ​ | ​
​ | ​ | Book | ​ | Unrealized | ​ | Unrealized | ​ | Fair
(In thousands) | ​ | Value | ​ | Gain | ​ | Loss | ​ | Value
Marketable securities: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Corporate debt securities(1) | ​ | $ | 90,827 | ​ | $ | 379 | ​ | $ | (4) | ​ | $ | 91,202
U.S. government debt securities(2) | ​ | ​ | 50,529 | ​ | ​ | 222 | ​ | ​ | — | ​ | ​ | 50,751
Total marketable securities | ​ | $ | 141,356 | ​ | $ | 601 | ​ | $ | (4) | ​ | $ | 141,953

| (1) | Included in Corporate debt securities is $45.7 million with maturity dates between one and three years.

| (2) | Included in U.S. government debt securities is $25.6 million with maturity dates between one and three years.

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | December 31, 2024
​ | ​ | ​ | ​ | ​ | Gross | ​ | Gross | ​ | ​ | ​
​ | ​ | Book | ​ | Unrealized | ​ | Unrealized | ​ | Fair
(In thousands) | ​ | Value | ​ | Gain | ​ | Loss | ​ | Value
Marketable securities: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Corporate debt securities(1) | ​ | $ | 105,154 | ​ | $ | 192 | ​ | $ | (156) | ​ | $ | 105,190
Commercial paper | ​ | ​ | 4,720 | ​ | ​ | — | ​ | ​ | (1) | ​ | ​ | 4,719
Foreign government agency debt securities | ​ | ​ | 4,911 | ​ | ​ | 16 | ​ | ​ | — | ​ | ​ | 4,927
U.S. government and government agency debt securities(2) | ​ | ​ | 64,454 | ​ | ​ | 47 | ​ | ​ | (11) | ​ | ​ | 64,490
Total marketable securities | ​ | $ | 179,239 | ​ | $ | 255 | ​ | $ | (168) | ​ | $ | 179,326

​

​

| (1) | Included in Corporate debt securities is $59.8 million with maturity dates between one and three years.

| (2) | Included in U.S. government and government agency debt securities is $30.5 million with maturity dates between one and three years.

​

​

4. Property and Equipment, Net

​

Property and equipment, net consisted of the following:

​

​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | September 30, | ​ | ​ | December 31,
(In thousands) | ​ | 2025 | ​ | 2024
Computer equipment |  | $ | 1,173 |  | $ | 1,198
Lab equipment | ​ | ​ | 3,144 | ​ | ​ | 3,137
Furniture and fixtures | ​ | ​ | 661 | ​ | ​ | 661
Leasehold improvements | ​ | ​ | 817 | ​ | ​ | 817
Property and equipment, gross | ​ |  | 5,795 | ​ |  | 5,813
Accumulated depreciation | ​ |  | (4,984) | ​ |  | (4,805)
Property and equipment, net | ​ | $ | 811 | ​ | $ | 1,008

​

Depreciation expense was $0.1 million and $0.2 million for the three months ended September 30, 2025 and 2024, respectively, and $0.3 million and $0.6 million for the nine months ended September 30, 2025 and 2024, respectively.

​

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5. Accrued Expenses

​

Accrued expenses consisted of the following:

​

​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | September 30, | ​ | December 31,
(In thousands) |  | 2025 |  | 2024
Employee compensation expenses | ​ | $ | 3,756 | ​ | $ | 4,979
Research and development expenses | ​ | ​ | 1,685 | ​ | ​ | 2,173
Deferred transaction consideration | ​ | ​ | 2,372 | ​ | ​ | 3,927
Licensing expenses | ​ | ​ | 1,584 | ​ | ​ | 8,645
Restructuring expenses (Note 13) | ​ | ​ | — | ​ | ​ | 163
Other expenses | ​ |  | 387 | ​ |  | 446
Total accrued expenses | ​ | $ | 9,784 | ​ | $ | 20,333

​

​

6. Stockholders’ Equity

​

Preferred Stock

​

As of September 30, 2025 and December 31, 2024, the Company’s amended and restated certificate of incorporation (the “Charter”) authorized the Company to issue 10,000,000 shares of undesignated preferred stock. There were no shares of preferred stock outstanding as of September 30, 2025 or December 31, 2024.

​

Common Stock

​

On June 5, 2025, at the 2025 Annual Meeting of Stockholders, the Company’s stockholders approved an amendment to the Charter to increase the authorized number of shares of common stock from 200,000,000 shares to 400,000,000 shares. On June 5, 2025, the Company filed a Certificate of Amendment to the Charter with the Secretary of State of the State of Delaware, which became effective upon filing.

​

As of September 30, 2025 and December 31, 2024, the Company’s Charter authorized the Company to issue 400,000,000 and 200,000,000 shares of $0.00001 par value common stock, respectively. There were 108,342,592 and 107,850,124 shares of common stock issued and outstanding as of September 30, 2025 and December 31, 2024, respectively.

​

Each share of common stock entitles the holder to one vote on all matters submitted to a vote of the Company’s stockholders. Common stockholders are entitled to receive dividends, as may be declared by the board of directors, if any, subject to any preferential dividend rights of any series of preferred stock that may be outstanding. No dividends have been declared through September 30, 2025.

​

Warrants

​

In November 2024, the Company issued warrants to Biosion, Inc. (“Biosion”) and Chia Tai Tianqing Pharmaceutical Group, Co., Ltd. (“CTTQ”) to purchase, in the aggregate, 14,281,985 shares of the Company’s common stock (the “Warrants”). The Warrants have an initial exercise price of $0.00001 per share, subject to adjustment as provided in the Warrants. The Warrants are immediately exercisable, subject to any applicable overseas direct investment filing that may be required for the holders. The Warrants will terminate when exercised in full. The Company classified the Warrants within equity because they are indexed to the Company’s own stock. The Company assigned an estimated fair value of $44.8 million to the Warrants, which was based on the fair value of the Company’s common stock on the date of issuance less the nominal exercise price of $0.00001 per share.

​

As of September 30, 2025, all of the Warrants were unexercised.

​

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7. Stock-Based Awards

​

2025 Equity Incentive Plan

​

In April 2025, the Company’s board of directors adopted the 2025 Equity Incentive Plan (the “2025 Plan”) and in June 2025, the Company’s stockholders approved the 2025 Plan. Upon the 2025 Plan becoming effective, no further grants can be made under the Company’s 2015 Equity Incentive Plan (the “2015 Plan”). The 2025 Plan provides for the grant of incentive stock options, nonqualified stock options, stock appreciation rights, restricted stock awards, restricted stock unit (“RSU”) awards, cash-based awards, and other stock-based awards. The number of shares initially reserved for issuance under the 2025 Plan was 25,532,993 shares of common stock, which includes (i) 9,000,000 new shares of common stock, (ii) 3,957,232 shares of common stock that remained available for future grant under the 2015 Plan upon adoption of the 2025 Plan and (iii) up to 12,575,761 shares of common stock underlying outstanding awards under the 2015 Plan and the 2012 Equity Compensation Plan (as amended and restated, the “2012 Plan”), which may become available for issuance under the 2025 Plan if and as such awards expire, are otherwise terminated, settled in cash, or repurchased by the Company. The shares of common stock underlying any awards that expire, or are otherwise terminated, settled in cash or repurchased by the Company under the 2025 Plan will be added back to the shares of common stock available for issuance under the 2025 Plan. As of September 30, 2025, 12,279,431 shares remained available for grant under the 2025 Plan. The Company had 794,760 stock options and 241,840 RSUs outstanding as of September 30, 2025 under the 2025 Plan.

​

2024 Inducement Plan

​

In November 2024, the Company’s board of directors adopted the 2024 Inducement Plan (the “2024 Inducement Plan”). The 2024 Inducement Plan is a non-stockholder approved stock plan adopted pursuant to the “inducement exception” provided under Nasdaq listing rules. The only employees eligible to receive grants of awards under the 2024 Inducement Plan are individuals who satisfy the standards for inducement grants under Nasdaq rules, generally including individuals who were not previously an employee or director of the Company. Under the terms of the 2024 Inducement Plan, the Company may grant up to 2,000,000 shares of common stock pursuant to nonqualified stock options, stock appreciation rights, restricted stock awards, RSU awards, and other stock awards. The shares of common stock underlying any awards that expire, or are otherwise terminated, settled in cash or repurchased by the Company under the 2024 Inducement Plan will be added back to the shares of common stock available for issuance under the 2024 Inducement Plan. As of September 30, 2025, 493,500 shares remained available for grant under the 2024 Inducement Plan. The Company had 1,172,000 stock options and 334,500 RSUs outstanding as of September 30, 2025 under the 2024 Inducement Plan.

​

2017 Inducement Plan

​

In July 2017, the Company’s board of directors adopted the 2017 Inducement Plan (the “2017 Inducement Plan”). The 2017 Inducement Plan is a non-stockholder approved stock plan adopted pursuant to the “inducement exception” provided under Nasdaq listing rules. The Company had 343,500 stock options outstanding as of September 30, 2025 under the 2017 Inducement Plan. All shares of common stock that were eligible for issuance under the 2017 Inducement Plan after October 1, 2018, including any shares underlying any awards that expire or are otherwise terminated, reacquired to satisfy tax withholding obligations, settled in cash or repurchased by the Company in the future that would have been eligible for re-issuance under the 2017 Inducement Plan, were retired.

​

2015 Equity Incentive Plan

​

In September 2015, the Company’s board of directors adopted the 2015 Plan, and the Company’s stockholders approved the 2015 Plan. The 2015 Plan became effective in connection with the Company’s initial public offering in October 2015. Upon the 2015 Plan becoming effective, no further grants can be made under the 2012 Plan. Upon the 2025 Plan becoming effective, no further grants can be made under the 2015 Plan. The Company had 9,144,258 stock options and 3,098,491 RSUs outstanding as of September 30, 2025 under the 2015 Plan.

​

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2012 Equity Compensation Plan

​

In August 2012, the Company’s board of directors adopted the 2012 Plan and the Company’s stockholders approved the 2012 Plan. Upon the 2015 Plan becoming effective, no further grants can be made under the 2012 Plan. The Company had no equity awards outstanding as of September 30, 2025 under the 2012 Plan.

​

Stock Option Valuation

​

The weighted average assumptions the Company used to estimate the fair value of stock options granted during the nine months ended September 30, 2025 and 2024 were as follows:

​

​ | ​ | ​ | ​ | ​ | ​ | ​
​ |  | Nine Months Ended
​ | ​ | September 30,
​ | ​ | 2025 | ​ | ​ | 2024 | ​
Risk-free interest rate |  | 4.28 | % | ​ | 3.85 | %
Expected term (in years) |  | 6.2 | ​ | ​ | 6.0 | ​
Expected volatility |  | 82.77 | % | ​ | 81.95 | %
Expected dividend yield |  | 0 | % | ​ | 0 | %

​

The Company recognizes compensation expense for awards over their vesting period. Compensation expense for awards includes the impact of forfeitures in the period when they occur.

​

Stock Options

​

The following table summarizes stock option activity for the nine months ended September 30, 2025:

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ |  | ​ |  | ​ | ​ |  | Weighted |  | ​ | ​
​ | ​ | ​ | ​ | Weighted | ​ | Average | ​ | ​ | ​
​ | ​ | ​ | ​ | Average | ​ | Remaining | ​ | Aggregate
​ | ​ | Number | ​ | Exercise | ​ | Contractual | ​ | Intrinsic
(In thousands, except share and per share data and years) | ​ | of Shares | ​ | Price | ​ | Term | ​ | Value
​ | ​ | ​ | ​ | ​ | ​ | ​ | (in years) | ​ | ​ | ​
Outstanding as of December 31, 2024 |  | 6,721,967 | ​ | $ | 11.12 | ​ | 6.8 | ​ | $ | 2,968
Granted |  | 5,194,155 | ​ | ​ | 2.16 | ​ | ​ | ​ | ​ | ​
Forfeited and cancelled |  | (461,604) | ​ | ​ | 7.34 | ​ | ​ | ​ | ​ | ​
Outstanding as of September 30, 2025 |  | 11,454,518 | ​ | $ | 7.27 | ​ | 7.8 | ​ | $ | 2,157
Options vested and expected to vest as of September 30, 2025 |  | 11,454,518 | ​ | $ | 7.27 | ​ | 7.8 | ​ | $ | 2,157
Options exercisable as of September 30, 2025 |  | 4,358,272 | ​ | $ | 13.75 | ​ | 5.7 | ​ | $ | 911

​

The weighted average grant date fair value of stock options granted during the nine months ended September 30, 2025 was $1.60 per share.

​

Restricted Stock Units

​

The following table summarizes RSU activity for the nine months ended September 30, 2025:

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | ​ | Weighted | ​ | ​
​ | ​ | ​ | ​ | Average | ​ | ​
​ | ​ | ​ | ​ | Grant Date | ​ | Aggregate
​ | ​ | Number | ​ | Fair Value | ​ | Intrinsic
(In thousands, except share and per share data) | ​ | of Shares | ​ | Per Share | ​ | Value
Outstanding as of December 31, 2024 | ​ | 2,276,151 | ​ | $ | 5.12 | ​ | ​ | ​
Granted | ​ | 2,093,713 | ​ | ​ | 2.23 | ​ | ​ | ​
Vested | ​ | (608,833) | ​ | ​ | 8.32 | ​ | $ | 1,355
Forfeited and cancelled | ​ | (86,200) | ​ | ​ | 4.67 | ​ | ​ | ​
Outstanding as of September 30, 2025 | ​ | 3,674,831 | ​ | $ | 2.96 | ​ | ​ | ​

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​

Stock-Based Compensation

​

Stock-based compensation expense included in total costs and expenses on the condensed consolidated statement of operations and comprehensive loss included the following:

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended | ​ | Nine Months Ended
​ | ​ | September 30, | ​ | September 30,
(In thousands) |  | 2025 |  | 2024 |  | 2025 |  | 2024
Cost of revenue |  | $ | 191 |  | $ | 232 | ​ | $ | 600 |  | $ | 707
Research and development | ​ | ​ | 964 | ​ | ​ | 1,124 | ​ | ​ | 3,255 | ​ | ​ | 2,192
General and administrative | ​ |  | 1,705 | ​ |  | 1,648 | ​ |  | 5,603 | ​ |  | 5,097
Total stock-based compensation expense | ​ | $ | 2,860 | ​ | $ | 3,004 | ​ | $ | 9,458 | ​ | $ | 7,996

​

As of September 30, 2025, the Company had unrecognized stock-based compensation expense for stock options and RSUs of $12.4 million and $7.3 million, respectively, which is expected to be recognized over weighted average periods of 2.6 years and 2.3 years, respectively.

​

8. Net Loss per Share

​

Basic and diluted net loss per share is summarized in the following table:

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended | ​ | Nine Months Ended |
​ | ​ | September 30, | ​ | September 30, |
(In thousands, except for share and per share data) | ​ | 2025 | ​ | 2024 |  | 2025 |  | 2024 | ​
Numerator: |  | ​ |  |  | ​ |  | ​ | ​ |  |  | ​ |  | ​
Net loss | ​ | $ | (14,614) | ​ | $ | (7,586) | ​ | $ | (45,128) | ​ | $ | (35,513) | ​
Denominator: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Weighted average shares of common stock outstanding, basic and diluted | ​ |  | 122,619,311 | ​ |  | 71,381,731 | ​ |  | 122,531,032 | ​ |  | 71,249,813 | ​
Net loss per share, basic and diluted | ​ | $ | (0.12) | ​ | $ | (0.11) | ​ | $ | (0.37) | ​ | $ | (0.50) | ​

​

The Company’s potentially dilutive securities, which included stock options and RSUs, have been excluded from the computation of diluted net loss per share since the effect would be to reduce the net loss per share. Therefore, the weighted average number of shares of common stock outstanding used to calculate both basic and diluted net loss per share is the same. For the three and nine months ended September 30, 2025, the basic and diluted weighted-average shares outstanding included the shares of common stock issuable upon exercise of the Warrants, as there were no outstanding contingencies associated with the vesting or exercisability of the Warrants.

​

The following table presents potential shares of common stock excluded from the calculation of diluted net loss per share for the nine months ended September 30, 2025 and 2024. All share amounts presented in the table below represent the total number outstanding as of September 30, 2025 and 2024.

​

​ | ​ | ​ | ​ | ​
​ | ​ | Nine Months Ended
​ | ​ | September 30,
​ | ​ | 2025 | ​ | 2024
Options to purchase common stock | ​ | 11,454,518 | ​ | 6,445,232
Restricted stock units | ​ | 3,674,831 | ​ | 3,071,776
Total potential shares of common stock | ​ | 15,129,349 | ​ | 9,517,008

​

​

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9. Leases

​

Operating Leases

​

Agreements for Office and Laboratory Space

​

In May 2023, the Company entered into a lease agreement pursuant to which it leases 11,564 square feet of office space for its headquarters in Wayne, Pennsylvania. The lease commenced in November 2023 and has a term that runs through February 2029.

​

In February 2019, the Company entered into a sublease agreement for 20,433 square feet of office and laboratory space in St. Louis, Missouri. The lease commenced in June 2019 and has a term that runs through May 2029. In January 2023, the Company amended the sublease agreement to add an additional 6,261 square feet of office and laboratory space effective February 2023. The Company exercised its option to terminate the leasing of the additional space effective as of June 30, 2024.

​

Supplemental balance sheet information related to operating leases is as follows:

​

​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | September 30, | ​ | December 31,
(In thousands) | ​ | 2025 | ​ | 2024
Operating Leases: | ​ | ​ | ​ | ​ | ​ | ​
Gross cost | ​ | $ | 4,530 | ​ | $ | 4,530
Accumulated amortization | ​ | ​ | (2,102) | ​ | ​ | (1,688)
Other assets | ​ | $ | 2,428 | ​ | $ | 2,842
​ | ​ | ​ | ​ | ​ | ​ | ​
Current portion of lease liabilities | ​ | $ | 533 | ​ | $ | 481
Other liabilities | ​ | ​ | 1,711 | ​ | ​ | 2,117
Total operating lease liabilities | ​ | $ | 2,244 | ​ | $ | 2,598

​

Amortization expense related to operating lease right-of-use assets and accretion of operating lease liabilities totaled $0.1 million for each of the three months ended September 30, 2025 and 2024, and $0.4 million for each of the nine months ended September 30, 2025 and 2024.

10. Agreements Related to Intellectual Property

​

Exclusive License Agreement – Biosion, Inc.

​

In November 2024, the Company entered into an exclusive license agreement (the “Biosion Agreement”) with Biosion, pursuant to which it received the exclusive rights to develop, manufacture and commercialize bosakitug (ATI-045) and ATI-052 worldwide, excluding Mainland China, Macau, Hong Kong and Taiwan (“Greater China”). In connection with the Biosion Agreement, the Company also entered into a collaboration agreement (the “CTTQ Agreement”) with Biosion and CTTQ, a licensee of bosakitug in Greater China.

As partial consideration for the rights and licenses under the Biosion Agreement and CTTQ Agreement, the Company, agreed to, in the aggregate, (i) pay $30.0 million in upfront cash consideration, plus $4.5 million for the reimbursement of certain development costs, (ii) issue the Warrants, and (iii) pay $6.2 million for the reimbursement of certain development costs and drug product material as set forth in the Biosion Agreement.

In addition, the Company agreed to pay, in the aggregate, (i) up to $125 million upon the achievement of specified regulatory milestones commencing with product approval, (ii) up to $795 million upon the achievement of specified sales milestones, (iii) a tiered low-to-mid single digit royalty based upon a percentage of annual net sales, subject to specified reductions as set forth in the Biosion Agreement, and (iv) a portion of any sublicense consideration received from the grant of any sublicense or similar rights under any of the rights or licenses granted to the Company under the Biosion Agreement.

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The Company will expense these payments in the period when either they are determined to be probable of occurring or when the payment is triggered.

​

License Agreement – Sun Pharmaceutical Industries, Inc.

​

In December 2023, the Company entered into an exclusive patent license agreement with Sun Pharmaceutical Industries, Inc. (“Sun Pharma”). Under the license agreement, the Company granted Sun Pharma exclusive rights under certain patents that the Company exclusively licenses from a third party. The patents relate to the use of deuruxolitinib, Sun Pharma’s Janus kinase (“JAK”) inhibitor, or other isotopic forms of ruxolitinib, to treat alopecia areata or androgenetic alopecia. Under the license agreement, Sun Pharma has paid the Company upfront, regulatory and commercial milestone payments, and has agreed to pay the Company other regulatory and commercial milestone payments upon the achievement of specified milestones set forth in the agreement, and a mid single-digit tiered royalty calculated as a percentage of Sun Pharma’s net sales. The Company has separate contractual obligations under which the Company has agreed to pay to third parties a portion of the consideration it may receive under the license agreement.

​

The Company recognized $1.5 million of licensing revenue during the three and nine months ended September 30, 2025, a portion of which was payable to third parties.

​

License Agreement – Pediatrix Therapeutics, Inc.

​

In November 2022, the Company entered into a license agreement with Pediatrix Therapeutics, Inc. (“Pediatrix”), under which the Company granted Pediatrix the exclusive rights to develop, manufacture and commercialize lepzacitinib in Greater China. Pediatrix has paid the Company an upfront payment, and has agreed to pay the Company development, regulatory and commercial milestone payments upon the achievement of specified milestones set forth in the agreement, and a tiered royalty ranging from a low-to-high single digit percentage of net sales of lepzacitinib by Pediatrix in Greater China. A portion of the consideration received from Pediatrix is payable to the former Confluence equity holders as described below under the caption “—Agreement and Plan of Merger - Confluence.”

​

License Agreement – Eli Lilly and Company

​

In August 2022, the Company entered into a non-exclusive patent license agreement with Eli Lilly and Company (“Lilly”). Under the license agreement, the Company granted Lilly non-exclusive rights under certain patents and patent applications that the Company exclusively licenses from a third party. The patents and patent applications relate to the use of baricitinib, Lilly’s JAK inhibitor, to treat alopecia areata. Under the license agreement, Lilly has paid the Company upfront, anniversary, regulatory and commercial milestone payments. In addition, Lilly has agreed to pay the Company other commercial milestone payments upon the achievement of specified milestones and additional anniversary payments as set forth in the agreement, as well as a low single-digit royalty calculated as a percentage of Lilly’s net sales of baricitinib for the treatment of alopecia areata. The Company has separate contractual obligations under which the Company has agreed to pay to third parties an amount equal to any regulatory and commercial milestone payments it receives under the Lilly license agreement, as well as a portion of the upfront consideration and a portion of the royalties it may receive under the license agreement. In July 2024, the Company entered into a royalty purchase agreement with OCM IP Healthcare Portfolio LP, an investment vehicle for Ontario Municipal Employees Retirement System (“OMERS”), pursuant to which the Company sold to OMERS a portion of the Company’s future royalty payments and the remaining anniversary payments associated with the license to Lilly (see Note 11).

​

The Company recognized $1.3 million and $3.6 million of licensing revenue during the three and nine months ended September 30, 2025, respectively, all of which was payable to third parties. The Company recognized $0.7 million and $4.6 million of licensing revenue during the three and nine months ended September 30, 2024, respectively, a portion of which was payable to third parties.

​

Asset Purchase Agreement – EPI Health, LLC

​

In October 2019, the Company sold RHOFADE (oxymetazoline hydrochloride) cream, 1% (“RHOFADE”) to EPI Health, LLC (“EPI Health”) pursuant to an asset purchase agreement. In July 2023, EPI Health filed a voluntary

17

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petition for relief under Chapter 11 of the United States Bankruptcy Code. Through the bankruptcy process, EPI Health and its parent company, Novan, Inc., sold the RHOFADE assets to a third party, which excluded the Company’s asset purchase agreement with EPI Health and the outstanding amounts due. The sale was approved by the bankruptcy court in September 2023. As a result of the bankruptcy proceedings, all amounts that were due and outstanding by EPI Health had been fully reserved. During the three months ended September 30, 2025, the Company sold all of its right, title and interest in its bankruptcy claims against EPI Health and wrote off the remaining reserved balance as it was deemed uncollectible.

​

Agreement and Plan of Merger – Confluence

​

In August 2017, the Company entered into an Agreement and Plan of Merger, pursuant to which it acquired Confluence (the “Confluence Agreement”). Under the Confluence Agreement, the Company agreed to pay the former Confluence equity holders aggregate remaining contingent consideration of up to $75.0 million based upon the achievement of specified regulatory and commercial milestones set forth in the Confluence Agreement. In addition, the Company agreed to pay the former Confluence equity holders future royalty payments calculated as a low single-digit percentage of annual net sales, subject to specified reductions, limitations and other adjustments, until the date that all of the patent rights for that product have expired, as determined on a country-by-country and product-by-product basis or, in specified circumstances, ten years from the first commercial sale of such product. In addition to the payments described above, if the Company sells, licenses or transfers any of the intellectual property acquired from Confluence pursuant to the Confluence Agreement to a third party, the Company will be obligated to pay the former Confluence equity holders a portion of any consideration received from such sale, license or transfer in specified circumstances.

​

As of September 30, 2025 and December 31, 2024, the balance of the Company’s contingent consideration liability was $10.6 million and $8.7 million, respectively (see Note 3).

11. Sale of Future Royalties

​

In July 2024, the Company entered into a royalty purchase agreement with OMERS. Under the royalty purchase agreement, the Company sold to OMERS a portion of the Company’s future royalty payments and the remaining anniversary payments associated with the Company’s existing license to Lilly relating to OLUMIANT® (baricitinib) for the treatment of alopecia areata.

​

Under the terms of the royalty purchase agreement, the Company received an upfront payment of $26.5 million. In exchange, OMERS acquired a portion of the royalty payable by Lilly to the Company for worldwide net sales of OLUMIANT for the treatment of alopecia areata from April 1, 2024 through the remainder of the royalty term under the Company’s license agreement with Lilly, and 100% of the remaining anniversary milestone payments payable by Lilly to the Company under the license agreement.

​

The Company evaluated the arrangement and concluded that the proceeds from the sale of future royalties should be recorded as deferred income on the condensed consolidated balance sheet, as the criteria for debt classification were not met in accordance with ASC Topic 470. In particular, the Company does not have significant continuing involvement in the generation of the cash flows due to OMERS and there are no guaranteed rates of return to OMERS. The Company recognizes non-cash royalty income under the “units-of-revenue” method in the condensed consolidated statements of operations and comprehensive loss. For the three and nine months ended September 30, 2025, the Company recognized $0.7 million and $2.5 million of non-cash royalty income, respectively. For each of the three and nine months ended September 30, 2024, the Company recognized $0.9 million of non-cash royalty income. As of September 30, 2025, the current and non-current portions of the remaining deferred income recognized under the units-of revenue method were $3.9 million and $17.5 million, respectively. As of December 31, 2024, the current and non-current portions of the remaining deferred income recognized under the units-of revenue method were $3.9 million and $20.0 million, respectively.

​

12. Income Taxes

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The Company did not record a federal or state income tax benefit for losses incurred during the three and nine months ended September 30, 2025 and 2024. The Company concluded that it is more likely than not that its deferred tax

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assets will not be realized which resulted in recording a full valuation allowance during those periods.

​

On July 4, 2025, the One Big Beautiful Bill (“OBBB”) Act, which includes a broad range of tax reform provisions, was signed into law in the United States and the Company continues to assess its impact. The Company currently does not expect the OBBB Act to have a material impact on the consolidated financial statements.

​

13. Restructuring Charges

​

In December 2023, the Company’s board of directors approved a reduction of the Company’s workforce by approximately 46%, which was completed as of December 31, 2024. During the nine months ended September 30, 2025, the Company made cash severance payments of $0.2 million to impacted employees. During the three and nine months ended September 30, 2024, the Company recognized severance expense of $26 thousand and $2.6 million, respectively, and made cash severance payments of $5.2 million to impacted employees during the nine months ended September 30, 2024.

​

14. Segment Information

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The Company has two reportable segments, therapeutics and contract research. The therapeutics segment is focused on identifying and developing innovative therapies to address significant unmet needs for immuno-inflammatory diseases and earns revenue through licensing of the Company’s intellectual property. The contract research segment earns revenue from the provision of laboratory services.

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All intersegment revenue has been eliminated in the Company’s condensed consolidated statement of operations and comprehensive loss. All customers and revenue pertaining to the Company’s segments are based in the United States and all assets are held in the United States. The Company does not report asset information by segment because it is not regularly provided to the Company’s chief executive officer, who is the Company’s chief operating decision maker (“CODM”).

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Since inception, the Company has incurred net losses and has an accumulated deficit of $948.0 million as of September 30, 2025. As such, the CODM uses segment loss from operations for each segment in assessing segment performance by comparing the results of each segment to forecast. All intercompany activity is eliminated in the intersegment elimination column in the tables below.

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A reconciliation of operating loss to total consolidated loss before income taxes for the three and nine months ended September 30, 2025 and 2024 is as follows:

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
(In thousands) | ​ | ​ | Contract | ​ | Intersegment | ​ | ​
Three Months Ended September 30, 2025 | Therapeutics | ​ | Research | ​ | Elimination | ​ | Total
Revenue from external customers | $ | 2,814 | ​ | $ | 485 | ​ | $ | — | ​ | $ | 3,299
Intercompany revenue | ​ | — | ​ | ​ | 4,130 | ​ | ​ | (4,130) | ​ | ​ | —
Cost of revenue | ​ | — | ​ | ​ | 4,454 | ​ | ​ | (3,916) | ​ | ​ | 538
Research and development: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Bosakitug | ​ | 3,062 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 3,062
ATI-2138 | ​ | 1,469 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 1,469
ATI-052 | ​ | 1,837 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 1,837
Discovery | ​ | 2,340 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 2,340
Total Research and development project expenses | ​ | 8,708 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 8,708
Personnel | ​ | 2,993 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 2,993
Other research and development expense(1) | ​ | 1,541 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 1,541
Total research and development | ​ | 13,242 | ​ | ​ | — | ​ | ​ | (214) | ​ | ​ | 13,028
General and administrative | ​ | — | ​ | ​ | 467 | ​ | ​ | — | ​ | ​ | 467
Licensing | ​ | 1,911 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 1,911
Revaluation of contingent consideration | ​ | 100 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 100
Segment operating loss | $ | (12,439) | ​ | $ | (306) | ​ | $ | — | ​ | $ | (12,745)
Non-segment general and administrative | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | 4,404
Other income | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | 2,535
Loss before income taxes | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | $ | (14,614)
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
(In thousands) | ​ | ​ | Contract | ​ | Intersegment | ​ | ​
Three Months Ended September 30, 2024 | Therapeutics | ​ | Research | ​ | Elimination | ​ | Total
Revenue from external customers | $ | 3,701 | ​ | $ | 645 | ​ | $ | — | ​ | $ | 4,346
Intercompany revenue | ​ | — | ​ | ​ | 3,035 | ​ | ​ | (3,035) | ​ | ​ | —
Cost of revenue | ​ | — | ​ | ​ | 3,485 | ​ | ​ | (2,831) | ​ | ​ | 654
Research and development: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
ATI-2138 | ​ | 745 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 745
Discovery | ​ | 1,263 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 1,263
Total Research and development project expenses | ​ | 2,008 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 2,008
Personnel | ​ | 1,970 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 1,970
Other research and development expense(1) | ​ | 2,182 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 2,182
Total research and development | ​ | 6,160 | ​ | ​ | — | ​ | ​ | (204) | ​ | ​ | 5,956
General and administrative | ​ | — | ​ | ​ | 905 | ​ | ​ | — | ​ | ​ | 905
Licensing | ​ | 1,754 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 1,754
Revaluation of contingent consideration | ​ | 800 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 800
Segment operating loss | $ | (5,013) | ​ | $ | (710) | ​ | $ | — | ​ | $ | (5,723)
Non-segment general and administrative | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | 4,748
Other income | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | 2,885
Loss before income taxes | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | $ | (7,586)

| (1) | Other segment items for the Therapeutics segment consist primarily of the following research and development expenses: former development assets, stock-based compensation, depreciation and amortization, and regulatory.

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​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
(In thousands) | ​ | ​ | Contract | ​ | Intersegment | ​ | ​
Nine Months Ended September 30, 2025 | Therapeutics | ​ | Research | ​ | Elimination | ​ | Total
Revenue from external customers | $ | 5,159 | ​ | $ | 1,372 | ​ | $ | — | ​ | $ | 6,531
Intercompany revenue | ​ | — | ​ | ​ | 11,085 | ​ | ​ | (11,085) | ​ | ​ | —
Cost of revenue | ​ | — | ​ | ​ | 11,983 | ​ | ​ | (10,424) | ​ | ​ | 1,559
Research and development: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Bosakitug | ​ | 9,293 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 9,293
ATI-2138 | ​ | 4,395 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 4,395
ATI-052 | ​ | 3,874 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 3,874
Discovery | ​ | 5,306 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 5,306
Total Research and development project expenses | ​ | 22,868 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 22,868
Personnel | ​ | 8,904 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 8,904
Other research and development expense(1) | ​ | 4,950 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 4,950
Total research and development | ​ | 36,722 | ​ | ​ | — | ​ | ​ | (661) | ​ | ​ | 36,061
General and administrative | ​ | — | ​ | ​ | 1,989 | ​ | ​ | — | ​ | ​ | 1,989
Licensing | ​ | 4,256 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 4,256
Revaluation of contingent consideration | ​ | 1,900 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 1,900
Segment operating loss | $ | (37,719) | ​ | $ | (1,515) | ​ | $ | — | ​ | $ | (39,234)
Non-segment general and administrative | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | 14,407
Other income | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | 8,513
Loss before income taxes | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | $ | (45,128)
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
(In thousands) | ​ | ​ | Contract | ​ | Intersegment | ​ | ​
Nine Months Ended September 30, 2024 | Therapeutics | ​ | Research | ​ | Elimination | ​ | Total
Revenue from external customers | $ | 7,583 | ​ | $ | 1,926 | ​ | $ | — | ​ | $ | 9,509
Intercompany revenue | ​ | — | ​ | ​ | 10,122 | ​ | ​ | (10,122) | ​ | ​ | —
Cost of revenue | ​ | — | ​ | ​ | 11,558 | ​ | ​ | (9,471) | ​ | ​ | 2,087
Research and development: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
ATI-2138 | ​ | 1,560 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 1,560
Discovery | ​ | 4,408 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 4,408
Total Research and development project expenses | ​ | 5,968 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 5,968
Personnel | ​ | 9,002 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 9,002
Other research and development expense(1) | ​ | 10,241 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 10,241
Total research and development | ​ | 25,211 | ​ | ​ | — | ​ | ​ | (651) | ​ | ​ | 24,560
General and administrative | ​ | — | ​ | ​ | 3,033 | ​ | ​ | — | ​ | ​ | 3,033
Licensing | ​ | 4,070 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 4,070
Revaluation of contingent consideration | ​ | 3,800 | ​ | ​ | — | ​ | ​ | — | ​ | ​ | 3,800
Segment operating loss | $ | (25,498) | ​ | $ | (2,543) | ​ | $ | — | ​ | $ | (28,041)
Non-segment general and administrative | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | 14,216
Other income | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | 6,744
Loss before income taxes | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | $ | (35,513)

| (1) | Other segment items for the Therapeutics segment consist primarily of the following research and development expenses: former development assets, stock-based compensation, depreciation and amortization, and regulatory.

​

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

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Certain statements contained in this Quarterly Report on Form 10-Q may constitute forward-looking statements within the meaning of Section 27A of the Securities Act of 1933, as amended, and Section 21E of the Securities Exchange Act of 1934, as amended (the “Exchange Act”). The words “may,” “might,” “can,” “will,” “to be,” “could,” “would,” “should,” “expect,” “intend,” “plan,” “objective,” “anticipate,” “believe,” “estimate,” “predict,” “project,” “potential,” “likely,” “continue,” “ongoing” or similar expressions, or the negative of such words, are intended to identify “forward-looking statements.” We have based these forward-looking statements on our current expectations and projections about future events. Because such statements include risks and uncertainties, actual results may differ materially from those expressed or implied by such forward-looking statements. Factors that could cause or contribute to these differences include those under the caption “Risk Factors” in this Quarterly Report on Form 10-Q, our Annual Report on Form 10-K filed with the SEC on February 27, 2025 (“Annual Report”), and in our other filings with the Securities and Exchange Commission (“SEC”). Statements made herein are as of the date of the filing of this Form 10-Q with the SEC and should not be relied upon as of any subsequent date. Unless otherwise required by applicable law, we do not undertake, and we specifically disclaim, any obligation to update any forward-looking statements to reflect occurrences, developments, unanticipated events or circumstances after the date of such statement.

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The following discussion and analysis of our financial condition and results of operations should be read in conjunction with our unaudited condensed consolidated financial statements and related notes that appear in Item 1 of this Quarterly Report on Form 10-Q and with our audited consolidated financial statements and related notes for the year ended December 31, 2024, which are included in our Annual Report.

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Overview

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We are a clinical-stage biopharmaceutical company focused on developing novel small and large molecule product candidates for immuno-inflammatory diseases. Our proprietary KINect drug discovery platform combined with our preclinical development capabilities allows us to identify and advance potential product candidates that we may develop independently or in collaboration with third parties. In addition to identifying and developing our novel product candidates, we are pursuing strategic alternatives, including identifying and consummating transactions with third-party partners, to further develop, obtain marketing approval for and/or commercialize our novel product candidates. We also provide contract research services to third parties enabled by our early-stage research and development expertise.

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Our Key Product Candidates

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Bosakitug, an Investigational, Novel Anti-TSLP Monoclonal Antibody

​

Bosakitug (ATI-045) is an investigational, novel, humanized anti-thymic stromal lymphopoietin (“TSLP”) monoclonal antibody that specifically binds to human TSLP, blocking its interaction with the receptor complex and disrupting signal transduction. This mechanism prevents immune cells targeted by TSLP from releasing proinflammatory cytokines. Bosakitug has potential best-in-class properties, including a very high affinity to TSLP, very high potency, an extremely low dissociation rate from TSLP leading to long residence time and enhanced neutralization activity, and a half-life that can potentially support an extended dosing interval. Bosakitug has the potential to treat a variety of atopic, immunologic and respiratory diseases. We exclusively license global rights (excluding Mainland China, Macau, Hong Kong and Taiwan (“Greater China”)) to bosakitug from Biosion, Inc. (“Biosion”).

​

In a Phase 2a, single-arm, proof-of-concept trial in 22 U.S. patients with moderate to severe atopic dermatitis conducted by Biosion, bosakitug demonstrated a positive pharmacodynamic, safety and efficacy profile, with 94% of patients achieving a 75% improvement in the Eczema Area and Severity Index (“EASI”), 65% of patients achieving EASI-90, and 88% of patients achieving an Investigator’s Global Assessment (“IGA”) score of 0 or 1 (clear or almost clear skin), at week 26 (n=17). Bosakitug was generally well-tolerated with no serious adverse events reported. The most common treatment-emergent adverse event was headache (22.7% of patients). Grade 1 injection site reactions, primarily tenderness, occurred in 47.6% of patients.

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In June 2025, we initiated a Phase 2 trial to investigate the efficacy, safety, tolerability, pharmacokinetics (“PK”) and pharmacodynamics (“PD”) of bosakitug compared to placebo in approximately 90 patients with moderate to severe atopic dermatitis. The primary endpoint is percent change from baseline in EASI at week 24. Secondary endpoints at week 24 include EASI response (EASI-50, EASI-75, EASI-90), validated IGA response, body surface area (“BSA”) response, and Peak Pruritus Numerical Rating Scale (“PP-NRS”) score, relative to baseline. We expect to announce top-line data in the second half of 2026.

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Bosakitug is also currently being studied in severe asthma, chronic rhinosinusitis with nasal polyps and moderate to severe chronic obstructive pulmonary disease in China by Chia Tai Tianqing Pharmaceutical Group, Co., Ltd. (“CTTQ”). CTTQ licenses bosakitug from Biosion in Greater China. Our clinical focus for bosakitug will remain on dermatological immuno-inflammatory indications and further global (excluding Greater China) development in respiratory indications will be dependent on entering into potential partnerships.

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ATI-2138, an Investigational Oral Covalent ITK/JAK3 Inhibitor

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ATI-2138 is a highly potent and selective novel investigational dual inhibitor of interleukin-2-inducible T cell kinase (“ITK”) and Janus kinase 3 (“JAK3”) for the potential treatment of T cell-mediated autoimmune diseases. The ITK/JAK3 compound interrupts T cell signaling through the combined inhibition of ITK/JAK3 pathways in lymphocytes.

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In July 2025, we announced positive top-line results from our open-label, single-arm Phase 2a trial of ATI-2138 in patients with moderate to severe atopic dermatitis. The trial met the primary and key secondary endpoints. The trial was designed to investigate the safety, tolerability, PK, efficacy, and PD of 10 mg of ATI-2138 administered twice daily (“BID”) for 12 weeks. The trial enrolled 14 patients in the United States, with 12 patients completing treatment and up to 10 patients available for the per protocol analysis. The primary endpoints were safety related parameters and the secondary endpoints included PD and efficacy related measures. No meaningful safety findings were observed, and ATI-2138 was very well tolerated. We observed consistent and rapid improvement across the efficacy assessments, with a mean and median improvement in EASI score at week 12 of 61% and 77%, respectively. Excluding one patient determined to be a statistical molecular outlier by more than four standard deviations who demonstrated systemic findings inconsistent with atopic dermatitis alone including significant non-lesional inflammation and who was not fully compliant with study drug administration, the mean and median improvement in EASI score at week 12 was 77% and 82%, respectively. At week 12, 63% of patients experienced a greater than or equal to 4-point improvement (which is considered a clinically meaningful response) in PP-NRS. ATI-2138 demonstrated near complete and sustained inhibition and occupancy of ITK ranging from approximately 90% at peak to 60% to 70% at trough, and a high level of inhibition of JAK3. Proteome and transcriptome lesional skin tap strip analyses showed significant ATI-2138-dependent reduction of multiple inflammatory pathways associated with ITK, including strong downregulation of Th2, Th17, and T cell receptor (“TCR”) pathways, along with the Th1 pathway and fibrosis-related markers.

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We are exploring the potential of ATI-2138 in additional indications that are relevant to the mechanism of action, including lichen planus, scarring alopecias, and alopecia areata. We plan to initiate a Phase 2 trial in the additional indication in the first half of 2026.

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ATI-052, an Investigational, Novel Anti-TSLP and Anti-IL-4R Bispecific Antibody

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ATI-052 is an investigational, novel, humanized anti-TSLP and anti-interleukin-4 receptor (“IL-4R”) bispecific antibody that exhibits high binding affinity to and dual blockade of both the upstream TSLP receptor signal transduction and downstream IL-4R activation thereby inhibiting this central proinflammatory pathway. ATI-052 targets TSLP, which sits at the top of the inflammatory cascade; by targeting IL-4R, it blocks both downstream IL-4 and IL-13, which are key cytokines involved in Th2-mediated inflammation and allergic diseases. ATI-052 utilizes the same TSLP antigen-binding fragment (“Fab”) as bosakitug but is engineered to bind more tightly to the neonatal Fc receptor (“FcRn”), potentially extending its half-life. In addition, the AQQ mutation in the Fc limits effector functionality, reducing off-target binding and potential toxicity. ATI-052 has the potential to treat a variety of atopic, immunologic and respiratory diseases. We exclusively license global rights (excluding Greater China) to ATI-052 from Biosion.

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Our Investigational New Drug (“IND”) application for ATI-052 was cleared by the U.S. Food and Drug Administration (“FDA”) in April 2025, and in June 2025, we initiated a Phase 1a/1b program. The randomized, blinded, placebo-controlled Phase 1a portion is designed to evaluate the safety, tolerability, PK and PD of ATI-052 in healthy volunteers receiving single ascending doses (“SAD”) and multiple ascending doses (“MAD”). We expect to announce top-line results from the Phase 1a SAD/MAD portion in early 2026. We plan to initiate Phase 1b proof-of-concept trials in asthma (subject to IND submission and clearance) and atopic dermatitis in the first half of 2026, with top-line results from both trials expected in the second half of 2026.

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Next-Generation ITK Inhibitors

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We are developing next-generation covalent ITK selective inhibitors with differentiated pharmacological properties and selectivity profiles. These JAK3-sparing inhibitors have the potential to differentially modulate T cell biology across a broad range of disease indications with extended half-lives and best-in-class potential potency, ITK occupancy, and ITK activation. We are progressing to lead candidate selection and expect to file an IND application for a next-generation ITK inhibitor in the second half of 2026.

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Discovery and Preclinical Programs

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We conduct small molecule drug discovery through KINect, our proprietary drug discovery platform. We also engage in discovery efforts for novel, injectable, multi-specific antibodies. Through our integrated discovery approach, we can progress product candidates from concept through lead optimization, employing robust screening cascades and protein characterization techniques to identify molecules with desired therapeutic properties.

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Our KINect platform allows us to address challenges associated with difficult to drug kinases including selectivity and biochemical efficiency, through a unique combination of our proprietary chemical library of kinase inhibitors, our novel approaches to inhibitor modalities, our expertise in structure-based drug design, and our custom kinase assays. Our approach involves the following mechanisms: (1) reversible and irreversible covalent inhibitors, (2) molecular glue/complex targeted inhibitors, (3) tissue specific inhibitors, and (4) targeted protein degraders. These novel approaches are currently being utilized to prosecute additional validated, difficult to drug kinase targets with the goal of demonstrating broad target utility. Our small molecule discovery efforts center on targeting kinases that play pivotal roles in various inflammatory and autoimmune pathways.

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Our discovery efforts to develop multi-specific antibodies are focused on generating antibodies with superior target affinity, specificity, and potency utilizing combinations of (a) two or more clinically validated targets with non-overlapping biology, (b) clinically validated targets with novel biology, and/or (c) synergistic target combinations in an effort to address shortcomings of multi-drug administration. This complementary approach to our small molecule programs enables us to pursue optimal therapeutic modalities for each target and indication of interest. For example, we are progressing several bispecific antibodies utilizing the bosakitug anti-TSLP binding region paired with binding fragments targeting other undisclosed cytokine signaling pathways.

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We intend to evaluate both internal and external development options, including strategic partnerships, for these assets.

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Other Investigational Product Candidates

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Lepzacitinib, an Investigational Topical “Soft” JAK 1/3 Inhibitor

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Lepzacitinib (ATI-1777) is an investigational topical “soft” JAK 1/3 inhibitor for the potential treatment of atopic dermatitis and potentially other dermatologic conditions. “Soft” JAK inhibitors are designed to be topically applied and active in the skin, but rapidly metabolized and inactivated when they enter the bloodstream, which may result in low systemic exposure. We are currently seeking a global development and commercialization partner for this program (excluding Greater China). In 2022, we granted Pediatrix Therapeutics, Inc. (“Pediatrix”) exclusive rights to develop and commercialize lepzacitinib in Greater China.

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Financial Overview

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Since our inception, we have incurred significant net losses. Our net loss was $45.1 million for the nine months ended September 30, 2025 and $132.1 million for the year ended December 31, 2024. As of September 30, 2025, we had an accumulated deficit of $948.0 million. We expect to incur significant expenses and operating losses for the foreseeable future as we advance our product candidates from discovery through preclinical and clinical development. In addition, our product candidates, even if they are approved by regulatory agencies for marketing, may not achieve commercial success. We may also not be successful in pursuing strategic alternatives, including identifying and consummating transactions with third-party partners, to further develop, obtain marketing approval for and/or commercialize our product candidates. Furthermore, we have incurred and expect to continue to incur significant costs associated with operating as a public company, including legal, accounting, investor relations and other expenses. As a result, we will need substantial additional funding to support our continuing operations.

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We have historically financed our operations primarily with sales of equity securities and non-dilutive financing. In the near term, we expect to finance our operations through these and other capital sources, including potential partnerships with other companies or other strategic transactions. We may be unable to raise additional funds or enter into such other agreements or arrangements when needed on commercially acceptable terms, or at all. If we fail to raise capital or enter into such agreements as, and when needed, we may have to significantly delay, scale back or discontinue the development of one or more of our product candidates.

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Impact of Macroeconomic Conditions on Our Business

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Unfavorable conditions in the economy both in the United States and abroad may negatively affect the growth of our business and our results of operations. For example, macroeconomic events, including inflationary pressure, tariff policies, geopolitical conflicts, and the current shutdown of the U.S. federal government, have led to economic uncertainty globally. The effect of macroeconomic conditions may not be fully reflected in our results of operations until future periods. If, however, economic uncertainty increases or the global economy worsens, our business, financial condition and results of operations may be harmed.

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Acquisition and License Agreements

Exclusive License Agreement with Biosion

In November 2024, we entered into an exclusive license agreement (the “Biosion Agreement”) with Biosion pursuant to which we received the exclusive rights to develop, manufacture and commercialize bosakitug and ATI-052 worldwide, excluding Greater China. In connection with the Biosion Agreement, we also entered into a collaboration agreement (the “CTTQ Agreement”) with Biosion and CTTQ, a licensee of bosakitug in Greater China.

As partial consideration for the rights and licenses under the Biosion Agreement and CTTQ Agreement, we agreed to, in the aggregate, (i) pay $30.0 million in upfront cash consideration, plus $4.5 million for the reimbursement of certain development costs, (ii) issue warrants (the “Warrants”) to purchase 14,281,985 shares of our common stock and (iii) pay $6.2 million for the reimbursement of certain development costs and drug product material as set forth in the Biosion Agreement.

In addition, we agreed to pay, in the aggregate, (i) up to $125 million upon the achievement of specified regulatory milestones commencing with product approval, (ii) up to $795 million upon the achievement of specified sales milestones, (iii) a tiered low-to-mid single digit royalty based upon a percentage of annual net sales, subject to specified reductions as set forth in the Biosion Agreement, and (iv) a portion of any sublicense consideration received from the grant of any sublicense or similar rights under any of the rights or licenses granted to us under the Biosion Agreement. We will expense these payments in the period when either they are determined to be probable of occurring or when the payment is triggered.

Royalty Purchase Agreement with OCM IP Healthcare Portfolio LP

In July 2024, we entered into a royalty purchase agreement with OCM IP Healthcare Portfolio LP, an investment vehicle for Ontario Municipal Employees Retirement System (“OMERS”). Under the royalty purchase agreement, we

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sold to OMERS a portion of the future royalty payments and the remaining anniversary payments associated with our existing license to Eli Lilly and Company (“Lilly”), relating to OLUMIANT® (baricitinib) for the treatment of alopecia areata (see “—License Agreement with Eli Lilly and Company”). Under the terms of the royalty purchase agreement, we received an upfront payment of $26.5 million. In exchange, OMERS acquired a portion of the royalty payable by Lilly to us for worldwide net sales of OLUMIANT for the treatment of alopecia areata from April 1, 2024 through the remainder of the royalty term under our license agreement with Lilly, and 100% of the remaining anniversary milestone payments payable by Lilly to us under the license agreement. The royalty payments and milestones we sold to OMERS represent our entire financial interest in the Lilly license agreement after taking into account our other contractual third-party obligations.

We recognized $0.7 million and $2.5 million of non-cash royalty income during the three and nine months ended September 30, 2025, respectively. We recognized $0.9 million of non-cash royalty income during each of the three and nine months ended September 30, 2024.

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License Agreement with Sun Pharmaceutical Industries, Inc.

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In December 2023, we entered into an exclusive patent license agreement with Sun Pharmaceutical Industries, Inc. (“Sun Pharma”). Under the license agreement, we granted Sun Pharma exclusive rights under certain patents that we exclusively license from a third party. The patents relate to the use of deuruxolitinib, Sun Pharma’s JAK inhibitor, or other isotopic forms of ruxolitinib, to treat alopecia areata or androgenetic alopecia. Under the license agreement, Sun Pharma has paid us upfront, regulatory and commercial milestone payments, and has agreed to pay us other regulatory and commercial milestone payments upon the achievement of specified milestones set forth in the agreement, and a mid single-digit tiered royalty calculated as a percentage of Sun Pharma’s net sales. We have separate contractual obligations under which we have agreed to pay to third parties a portion of the consideration we may receive under the license agreement. We may seek to monetize this asset.

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We recognized $1.5 million of licensing revenue during the three and nine months ended September 30, 2025, a portion of which was payable to third parties.

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License Agreement with Pediatrix Therapeutics, Inc.

​

In November 2022, we entered into a license agreement with Pediatrix under which we granted Pediatrix the exclusive rights to develop, manufacture and commercialize lepzacitinib in Greater China. Pediatrix has paid us an upfront payment, and has agreed to pay us development, regulatory and commercial milestone payments upon the achievement of specified milestones set forth in the agreement, and a tiered royalty ranging from a low-to-high single digit percentage of net sales of lepzacitinib by Pediatrix in Greater China. A portion of the consideration received from Pediatrix is payable to the former Confluence (as defined below) equity holders as described below under the caption “—Agreement and Plan of Merger with Confluence.”

​

License Agreement with Eli Lilly and Company

​

In August 2022, we entered into a non-exclusive patent license agreement with Lilly. Under the license agreement, we granted Lilly non-exclusive rights under certain patents and patent applications that we exclusively license from a third party. The patents and patent applications relate to the use of baricitinib, Lilly’s JAK inhibitor, to treat alopecia areata. Under the license agreement, Lilly has paid us upfront, anniversary, regulatory and commercial milestone payments. In addition, Lilly has agreed to pay us other commercial milestone payments upon the achievement of specified milestones and additional anniversary payments as set forth in the agreement, as well as a low single-digit royalty calculated as a percentage of Lilly’s net sales of baricitinib for the treatment of alopecia areata. We have separate contractual obligations under which we have agreed to pay to third parties an amount equal to any regulatory and commercial milestone payments we receive under the Lilly license agreement, as well as a portion of the upfront consideration and a portion of the royalties we may receive under the license agreement. In July 2024, we entered into a royalty purchase agreement with OMERS pursuant to which we sold to OMERS a portion of our future royalty payments and the remaining anniversary payments associated with the license to Lilly (see “—Royalty Purchase Agreement with OCM IP Healthcare Portfolio LP” above).

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​

We recognized $1.3 million and $3.6 million of licensing revenue during the three and nine months ended September 30, 2025, respectively, all of which was payable to third parties. We recognized $0.7 million and $4.6 million of licensing revenue during the three and nine months ended September 30, 2024, respectively, a portion of which was payable to third parties.

​

Asset Purchase Agreement with EPI Health

​

In October 2019, we sold RHOFADE (oxymetazoline hydrochloride) cream, 1% (“RHOFADE”), to EPI Health, LLC (“EPI Health”) pursuant to an asset purchase agreement. In July 2023, EPI Health filed a voluntary petition for relief under Chapter 11 of the United States Bankruptcy Code. Through the bankruptcy process, EPI Health and its parent company, Novan, Inc., sold the RHOFADE assets to a third party, which excluded our asset purchase agreement with EPI Health and the outstanding amounts due. The sale was approved by the bankruptcy court in September 2023. As a result of the bankruptcy proceedings, all amounts that were due and outstanding by EPI Health had been fully reserved. During the three months ended September 30, 2025, we sold all of our right, title and interest in our bankruptcy claims against EPI Health and wrote off the remaining reserved balance as it was deemed uncollectible.

​

Agreement and Plan of Merger with Confluence

​

In 2017, we entered into an Agreement and Plan of Merger (the “Confluence Agreement”), with Confluence Life Sciences, Inc. (now known as Aclaris Life Sciences, Inc.) (“Confluence”), Aclaris Life Sciences, Inc., our wholly owned subsidiary (“Merger Sub”), and Fortis Advisors LLC, as representative of the equity holders of Confluence. Pursuant to the terms of the Confluence Agreement, Merger Sub merged with and into Confluence, with Confluence surviving as our wholly owned subsidiary.

​

Under the Confluence Agreement, we agreed to pay the former Confluence equity holders aggregate remaining contingent consideration of up to $75.0 million based upon the achievement of specified regulatory and commercial milestones set forth in the Confluence Agreement. In addition, we agreed to pay the former Confluence equity holders future royalty payments calculated as a low single-digit percentage of annual net sales, subject to specified reductions, limitations and other adjustments, until the date that all of the patent rights for that product have expired, as determined on a country-by-country and product-by-product basis or, in specified circumstances, ten years from the first commercial sale of such product. In addition to the payments described above, if we sell, license or transfer any of the intellectual property acquired from Confluence pursuant to the Confluence Agreement to a third party, we will be obligated to pay the former Confluence equity holders a portion of any consideration received from such sale, license, or transfer in specified circumstances.

​

Restructuring

​

In December 2023, our board of directors approved a reduction of our workforce by approximately 46%, which was completed as of December 31, 2024. During the nine months ended September 30, 2025, we made cash severance payments of $0.2 million to impacted employees. During the three and nine months ended September 30, 2024, we recognized severance expense of $26 thousand and $2.6 million, respectively, and made cash severance payments of $5.2 million to impacted employees during the nine months ended September 30, 2024.

​

Components of Our Results of Operations

​

Revenue

​

Contract Research

​

We earn revenue from the provision of laboratory services. Contract research revenue is generally evidenced by contracts with clients which are on an agreed upon fixed-price, fee-for-service basis and are generally billed on a monthly basis in arrears for services rendered.

​

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Licensing

​

Licensing revenue primarily consists of upfront consideration, royalties and milestone payments earned pursuant to license and acquisition agreements with third parties, as described above.

​

Cost and Expenses

​

Cost of Revenue

​

Cost of revenue consists of the costs incurred in connection with the provision of contract research services. Cost of revenue primarily includes:

​

| ● | employee-related expenses, which include salaries, benefits, and stock-based compensation;

| ● | outsourced professional scientific services;

| ● | depreciation of laboratory equipment;

| ● | facility-related costs; and

| ● | laboratory materials and supplies used to support the services provided.

​

Research and Development

​

Research and development expenses consist of expenses incurred in connection with the discovery and development of our product candidates. These expenses primarily include:

​

| ● | expenses incurred under agreements with contract research organizations (“CROs”), as well as clinical trial sites and consultants that conduct our clinical trials and preclinical studies, and investigator-initiated trials;

| ● | manufacturing scale-up expenses and the cost of acquiring and manufacturing active pharmaceutical ingredients and preclinical and clinical trial materials, including domestic technology transfer expenses;

| ● | quality assurance and quality control costs;

| ● | outsourced professional scientific development services;

| ● | medical affairs expenses related to our product candidates;

| ● | employee-related expenses, which include salaries, benefits, and stock-based compensation;

| ● | expenses relating to regulatory activities, including filing fees paid to regulatory agencies; and

| ● | laboratory materials and supplies used to support our research activities.

​

Research and development activities are central to our business model. Product candidates in later stages of clinical development generally have higher development costs than those in earlier stages of clinical development, primarily due to the increased size and duration of later-stage clinical trials. We expect to continue to incur research and development expenses in the near term as we continue the development of our product candidates and pursue our discovery programs. We expense research and development costs as incurred. Our direct research and development expenses primarily consist of external costs including fees paid to CROs, consultants, clinical trial sites, regulatory agencies and third parties that manufacture our preclinical and clinical trial materials and are tracked on a program-by-program basis. We do not allocate personnel costs or other indirect expenses to specific research and development programs.

​

The successful development of our product candidates is highly uncertain. We cannot reasonably estimate or know the nature, timing and costs of the efforts that will be necessary to complete the remainder of the development of, or when, if ever, material net cash inflows may commence from any of our product candidates. This uncertainty is due to the numerous risks and uncertainties associated with the duration and cost of discovery, as well as clinical trials, which vary significantly over the life of a project as a result of many factors, including:

​

| ● | the number of clinical sites included in the trials;

| ● | the length of time required to enroll suitable subjects;

| ● | the number of subjects that ultimately participate in the trials;

| ● | the number of doses subjects receive;

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| ● | the duration of subject follow-up; and

| ● | the results of our clinical trials.

​

Our expenditures are subject to additional uncertainties, including the preparation of regulatory filings for our product candidates. We may obtain unexpected results from our clinical trials or other development activities. We may elect to discontinue, delay or modify the development, including clinical trials, of some product candidates or focus on others. A change in the outcome of any of these variables with respect to the development of a product candidate could mean a significant change in the costs and timing associated with the development of that product candidate. For example, if the FDA or other regulatory authorities were to require us to conduct clinical trials beyond those that we currently anticipate, or if we experience significant delays in enrollment in any of our clinical trials, we could be required to expend significant additional financial resources and time on the completion of clinical development.

​

General and Administrative

​

General and administrative expenses consist principally of salaries and related costs, including stock-based compensation, for personnel in executive, administrative, finance and legal functions. General and administrative expenses also include facility-related costs, patent filing and prosecution costs, professional fees for legal, auditing and tax services, investor relations costs, business development costs, insurance costs, and travel expenses.

​

Licensing

​

Licensing expenses consist of third-party contractual obligations incurred under license and acquisition agreements with third parties, as described above.

​

Revaluation of Contingent Consideration

​

Revaluation of contingent consideration consists of changes in the fair value of our contingent consideration liability between reporting dates, as described below.

​

Other Income

​

Interest Income

​

Interest income primarily consists of interest earned on our cash, cash equivalents and marketable securities.

​

Non-cash Royalty Income

​

Non-cash royalty income includes income related to the proceeds from the sale of future royalties to OMERS, recognized under the “units-of-revenue” method.

​

Critical Accounting Estimates

​

This discussion and analysis of our financial condition and results of operations is based on our condensed consolidated financial statements, which have been prepared in accordance with generally accepted accounting principles in the United States. The preparation of our condensed consolidated financial statements requires us to make estimates and judgments that affect the reported amounts of assets, liabilities, revenues and expenses and the disclosure of contingent assets and liabilities in our condensed consolidated financial statements. We base our estimates on historical experience, known trends and events and various other factors that we believe to be reasonable under the circumstances, the results of which form the basis for making judgments about the carrying values of assets and liabilities that are not readily apparent from other sources. We evaluate our estimates and judgments on an ongoing basis. Our actual results may differ from these estimates under different assumptions or conditions. There have been no material changes to our significant accounting policies and use of estimates as disclosed in the footnotes to our audited consolidated financial statements for the year ended December 31, 2024 included in our Annual Report.

​

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Contingent Consideration

​

We record a contingent consideration liability related to future potential payments resulting from the acquisition of Confluence based upon significant unobservable inputs including the achievement of regulatory and commercial milestones, as well as estimated future sales levels and the discount rates applied to calculate the present value of the potential payments. Significant judgement is involved in determining the appropriateness of these assumptions. These assumptions are considered Level 3 inputs. Revaluation of our contingent consideration liability can result from changes to one or more of these assumptions. These assumptions are highly dependent on the outcome and timing of the development of certain of our product candidates. We evaluate the fair value estimate of our contingent consideration liability on a quarterly basis with changes, if any, recorded as income or expense in our condensed consolidated statement of operations and comprehensive loss. Any such changes could have a material impact on our financial results.

​

The fair value of contingent consideration is estimated using a probability-weighted expected payment model for regulatory milestone payments and a Monte Carlo simulation model for commercial milestone and royalty payments and then applying a risk-adjusted discount rate to calculate the present value of the potential payments. Significant assumptions used in our estimates include the probability of achieving regulatory milestones and commencing commercialization (collectively referred to as “probability of success”), which are based on an asset’s current stage of development and a review of existing clinical data. Probability of success assumptions ranged between 21% and 40% at September 30, 2025. Additionally, estimated future sales levels and the risk-adjusted discount rate applied to the potential payments are also significant assumptions used in calculating the fair value. As of September 30, 2025, the discount rate ranged between 6.8% and 8.4% depending on the year of each potential payment.

​

During the nine months ended September 30, 2025, we recorded a charge to the contingent consideration liability of $1.9 million, which was primarily due to changes to the probability of success for certain product candidates and the passage of time.

​

Results of Operations

​

Comparison of Three and Nine Months Ended September 30, 2025 and 2024

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended September 30, | ​ | Nine Months Ended September 30, |
(In thousands) |  | 2025 |  | 2024 |  | Change |  | 2025 |  | 2024 |  | Change |
Revenues: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Contract research | ​ | $ | 485 | ​ | $ | 645 | ​ | $ | (160) | ​ | $ | 1,372 | ​ | $ | 1,926 | ​ | $ | (554) | ​
Licensing | ​ | ​ | 2,814 | ​ | ​ | 3,701 | ​ | ​ | (887) | ​ | ​ | 5,159 | ​ | ​ | 7,583 | ​ | ​ | (2,424) | ​
Total revenue | ​ | ​ | 3,299 | ​ | ​ | 4,346 | ​ | ​ | (1,047) | ​ | ​ | 6,531 | ​ | ​ | 9,509 | ​ | ​ | (2,978) | ​
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Costs and expenses: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Cost of revenue | ​ | ​ | 538 | ​ | ​ | 654 | ​ | ​ | (116) | ​ | ​ | 1,559 | ​ | ​ | 2,087 | ​ | ​ | (528) | ​
Research and development | ​ |  | 13,028 | ​ |  | 5,956 | ​ |  | 7,072 | ​ |  | 36,061 | ​ |  | 24,560 | ​ |  | 11,501 | ​
General and administrative | ​ |  | 4,871 | ​ |  | 5,653 | ​ |  | (782) | ​ |  | 16,396 | ​ |  | 17,249 | ​ |  | (853) | ​
Licensing | ​ | ​ | 1,911 | ​ | ​ | 1,754 | ​ | ​ | 157 | ​ | ​ | 4,256 | ​ | ​ | 4,070 | ​ | ​ | 186 | ​
Revaluation of contingent consideration | ​ | ​ | 100 | ​ | ​ | 800 | ​ | ​ | (700) | ​ | ​ | 1,900 | ​ | ​ | 3,800 | ​ | ​ | (1,900) | ​
Total costs and expenses | ​ |  | 20,448 | ​ |  | 14,817 | ​ |  | 5,631 | ​ |  | 60,172 | ​ |  | 51,766 | ​ |  | 8,406 | ​
Loss from operations | ​ |  | (17,149) | ​ |  | (10,471) | ​ |  | (6,678) | ​ |  | (53,641) | ​ |  | (42,257) | ​ |  | (11,384) | ​
​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Other income: | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
Interest income | ​ |  | 1,819 | ​ |  | 1,991 | ​ |  | (172) | ​ |  | 6,003 | ​ |  | 5,850 | ​ |  | 153 | ​
Non-cash royalty income | ​ | ​ | 716 | ​ |  | 894 | ​ |  | (178) | ​ |  | 2,510 | ​ |  | 894 | ​ |  | 1,616 | ​
Total other income | ​ | ​ | 2,535 | ​ | ​ | 2,885 | ​ | ​ | (350) | ​ | ​ | 8,513 | ​ | ​ | 6,744 | ​ | ​ | 1,769 | ​
Net loss | ​ | $ | (14,614) | ​ | $ | (7,586) | ​ | $ | (7,028) | ​ | $ | (45,128) | ​ | $ | (35,513) | ​ | $ | (9,615) | ​

​

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Revenue

​

Contract research

​

The decrease in contract research revenue for the three and nine months ended September 30, 2025 compared to the three and nine months ended September 30, 2024, respectively, was driven by lower overall hours billed for laboratory services. The decrease during the nine-month period was partially offset by a higher average billing rate.

​

Licensing

​

The decrease in licensing revenue during the three months ended September 30, 2025 compared to the three months ended September 30, 2024 was primarily due to a larger milestone achieved under the Sun Pharma license agreement during the three months ended September 30, 2024.

​

The decrease in licensing revenue during the nine months ended September 30, 2025 compared to the nine months ended September 30, 2024 was primarily due to a larger milestone achieved under the Sun Pharma license agreement and higher licensing revenue earned under the Lilly license agreement during the nine months ended September 30, 2024. We sold a portion of the royalties we may receive under the Lilly license agreement to OMERS in July 2024.

​

Costs and Expenses

​

Cost of Revenue

​

The decrease in cost of revenue for the three and nine months ended September 30, 2025 compared to the three and nine months ended September 30, 2024 was driven by lower overall hours billed for laboratory services.

​

Research and Development

​

The following table summarizes our research and development expenses by product candidate or, for unallocated expenses, by type:

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended | ​ | Nine Months Ended
​ | ​ | September 30, | ​ | September 30,
(In thousands) | ​ | 2025 |  | 2024 | ​ | Change | ​ | 2025 |  | 2024 | ​ | Change
Bosakitug |  | $ | 3,062 | ​ | $ | — |  | $ | 3,062 |  | $ | 9,293 | ​ | $ | — |  | $ | 9,293
ATI-2138 | ​ | ​ | 1,469 | ​ | ​ | 745 | ​ | ​ | 724 | ​ | ​ | 4,395 | ​ | ​ | 1,560 | ​ | ​ | 2,835
ATI-052 | ​ | ​ | 1,837 | ​ | ​ | — | ​ | ​ | 1,837 | ​ | ​ | 3,874 | ​ | ​ | — | ​ | ​ | 3,874
Discovery | ​ | ​ | 2,340 | ​ | ​ | 1,263 | ​ | ​ | 1,077 | ​ | ​ | 5,306 | ​ | ​ | 4,408 | ​ | ​ | 898
Other research and development | ​ | ​ | 363 | ​ | ​ | 854 | ​ | ​ | (491) | ​ | ​ | 1,034 | ​ | ​ | 7,398 | ​ | ​ | (6,364)
Personnel | ​ | ​ | 2,993 | ​ | ​ | 1,970 | ​ | ​ | 1,023 | ​ | ​ | 8,904 | ​ | ​ | 9,002 | ​ | ​ | (98)
Stock-based compensation | ​ | ​ | 964 | ​ | ​ | 1,124 | ​ | ​ | (160) | ​ | ​ | 3,255 | ​ | ​ | 2,192 | ​ | ​ | 1,063
Total research and development expenses | ​ | $ | 13,028 | ​ | $ | 5,956 | ​ | $ | 7,072 | ​ | $ | 36,061 | ​ | $ | 24,560 | ​ | $ | 11,501

​

Bosakitug

​

The expenses incurred for bosakitug during the three and nine months ended September 30, 2025 consisted primarily of product candidate manufacturing costs and clinical development expenses associated with a Phase 2 trial in atopic dermatitis.

​

ATI-2138

​

The increase in expenses for ATI-2138 during the three months ended September 30, 2025 compared to the three months ended September 30, 2024 was primarily due to preclinical development expenses associated with toxicity studies, which was partially offset by a decrease in clinical development expenses associated with a Phase 2a trial in atopic dermatitis.

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​

The increase in expenses for ATI-2138 during the nine months ended September 30, 2025 compared to the nine months ended September 30, 2024 was primarily due to an increase in preclinical development expenses and clinical development expenses associated with a Phase 2a trial in atopic dermatitis.

​

ATI-052

​

Research and development expenses related to ATI-052 for the three and nine months ended September 30, 2025 primarily consisted of product candidate manufacturing costs, preclinical development activities, and clinical development expenses associated with a Phase 1a/1b program.

​

Discovery

​

Discovery expenses increased during the three and nine months ended September 30, 2025 compared to the three and nine months ended September 30, 2024 primarily due to increased investment in our discovery-stage programs as we progressed our next generation ITK selective inhibitors toward candidate selection.

​

Other research and development

​

The decrease in other research and development expenses during the three and nine months ended September 30, 2025 compared to the three and nine months ended September 30, 2024 was primarily due to clinical development expenses associated with former development assets.

​

Personnel and stock-based compensation

​

The increase in personnel expenses during the three months ended September 30, 2025 compared to the three months ended September 30, 2024 was primarily due to higher headcount. The increase in stock-based compensation expense during the nine months ended September 30, 2025 compared to the nine months ended September 30, 2024 was due to higher forfeiture credits during the nine months ended September 30, 2024.

​

General and Administrative

​

The following table summarizes our general and administrative expenses:

​

​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Three Months Ended | ​ | Nine Months Ended
​ | ​ | September 30, | ​ | September 30,
(In thousands) | ​ | 2025 |  | 2024 | ​ | Change | ​ | 2025 |  | 2024 | ​ | Change
Personnel |  | $ | 1,930 |  | $ | 1,189 |  | $ | 741 |  | $ | 5,667 |  | $ | 5,041 |  | $ | 626
Professional and legal fees | ​ | ​ | 771 | ​ | ​ | 1,854 | ​ | ​ | (1,083) | ​ | ​ | 2,688 | ​ | ​ | 3,881 | ​ | ​ | (1,193)
Facility and support services | ​ |  | 707 | ​ |  | 480 | ​ |  | 227 | ​ |  | 1,931 | ​ |  | 1,676 | ​ |  | 255
Other general and administrative | ​ | ​ | (242) | ​ | ​ | 482 | ​ | ​ | (724) | ​ | ​ | 507 | ​ | ​ | 1,554 | ​ | ​ | (1,047)
Stock-based compensation | ​ | ​ | 1,705 | ​ | ​ | 1,648 | ​ | ​ | 57 | ​ | ​ | 5,603 | ​ | ​ | 5,097 | ​ | ​ | 506
Total general and administrative expenses | ​ | $ | 4,871 | ​ | $ | 5,653 | ​ | $ | (782) | ​ | $ | 16,396 | ​ | $ | 17,249 | ​ | $ | (853)

​

Personnel and stock-based compensation

​

The increase in personnel expenses during the three and nine months ended September 30, 2025 compared to the three and nine months ended September 30, 2024 was primarily due to higher headcount. The increase in stock-based compensation expense during the nine months ended September 30, 2025 compared to the nine months ended September 30, 2024 was due to higher forfeiture credits during the nine months ended September 30, 2024.

​

​

​

​

​

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Professional and legal fees

​

The decrease in professional and legal fees during the three and nine months ended September 30, 2025 compared to the three and nine months ended September 30, 2024 was primarily due to business development expenses incurred in the prior year in connection with the royalty purchase agreement with OMERS.

​

Other general and administrative

​

The decrease in other general and administrative expenses during the three and nine months ended September 30, 2025 compared to the three and nine months ended September 30, 2024 was primarily due to the sale of our bankruptcy claims against EPI Health.

​

Revaluation of Contingent Consideration

​

The revaluation of contingent consideration loss decreased during the three months ended September 30, 2025 compared to the three months ended September 30, 2024 mainly due to higher discount rates resulting from changes in credit spreads being applied to potential payments during the three months ended September 30, 2025.

​

The revaluation of contingent consideration loss decreased during the nine months ended September 30, 2025 compared to the nine months ended September 30, 2024 mainly due to changes in estimated sales levels and changes to the probability of success for certain product candidates during the nine months ended September 30, 2024.

​

Other Income

​

Non-cash Royalty Income

​

Non-cash royalty income includes income related to the proceeds from the sale of a portion of our OLUMIANT® royalty payments to OMERS in July 2024.

​

Liquidity and Capital Resources

​

Overview

​

Since our inception, we have incurred net losses and negative cash flows from our operations. We have financed our operations over the last several years primarily through sales of our equity securities and non-dilutive financing. We may engage in additional equity and other financing transactions in order to raise funds. We may receive royalties and milestone payments under third-party licensing and acquisition agreements. In addition, to the extent we are able to consummate transactions with potential third-party partners to further develop, obtain marketing approval for and/or commercialize our product candidates, we may receive upfront payments, milestone payments or royalties from such arrangements that would increase our liquidity.

​

As of September 30, 2025, we had cash, cash equivalents and marketable securities of $167.2 million. Cash in excess of immediate requirements is invested in accordance with our investment policy, primarily with a view towards liquidity and capital preservation.

​

We currently have no ongoing material financing commitments, such as lines of credit or guarantees, that are expected to affect our liquidity, other than our contingent obligations under the Confluence Agreement, Biosion Agreement and CTTQ Agreement, which are summarized above under “Overview—Acquisition and License Agreements,” and our lease obligations.

​

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Cash Flows

​

Cash and cash equivalents were $25.3 million as of September 30, 2025 compared to $24.6 million as of December 31, 2024. We also had $142.0 million in short- and long-term marketable securities as of September 30, 2025 compared to $179.3 million as of December 31, 2024.

​

The sources and uses of cash that contributed to the change in cash and cash equivalents were:

​

​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Nine Months Ended
​ | ​ | September 30,
(In thousands) |  | 2025 |  | 2024
Cash and cash equivalents beginning balance | ​ | $ | 24,570 | ​ | $ | 39,878
Net cash used in operating activities | ​ |  | (33,982) | ​ |  | (11,137)
Net cash provided by investing activities | ​ |  | 37,996 | ​ |  | 18,954
Net cash used in financing activities | ​ | ​ | (3,328) | ​ | ​ | (44)
Cash and cash equivalents ending balance | ​ | $ | 25,256 | ​ | $ | 47,651

​

Operating Activities

​

Cash flow related to operating activities was the result of:

​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Nine Months Ended
​ | ​ | September 30,
(In thousands) |  | 2025 |  | 2024
Net loss | ​ | $ | (45,128) | ​ | $ | (35,513)
Non-cash adjustments to reconcile net loss to net cash used in operating activities | ​ |  | 11,710 | ​ |  | 12,460
Change in accounts receivable, prepaid expenses and other assets | ​ |  | 6,810 | ​ |  | 3,699
Change in accounts payable and accrued expenses | ​ | ​ | (4,864) | ​ | ​ | (16,730)
Change in deferred income | ​ | ​ | (2,510) | ​ | ​ | 24,947
Net cash used in operating activities | ​ | $ | (33,982) | ​ | $ | (11,137)

​

Net cash used in operating activities increased for the nine months ended September 30, 2025 compared to the nine months ended September 30, 2024 primarily as a result of proceeds from the royalty sale to OMERS and lower net losses after adjusting for non-cash items during the nine months ended September 30, 2024. This increase was partially offset by a decrease in cash used for accounts payable and accrued expenses, which was due to the timing of payments to vendors and severance payments in connection with the reduction in our workforce.

​

Investing Activities

​

Cash flow related to investing activities was the result of:

​

​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Nine Months Ended
​ | ​ | September 30,
(In thousands) |  | 2025 |  | 2024
Purchases of property and equipment, net | ​ | $ | (87) | ​ | $ | (121)
Purchases of marketable securities | ​ |  | (35,124) | ​ |  | (49,555)
Proceeds from sales and maturities of marketable securities | ​ | ​ | 74,040 | ​ | ​ | 68,630
Payment of deferred transaction consideration for in-licensed assets | ​ | ​ | (833) | ​ | ​ | —
Net cash provided by investing activities | ​ | $ | 37,996 | ​ | $ | 18,954

​

The increase in net cash provided by investing activities for the nine months ended September 30, 2025 compared to the nine months ended September 30, 2024 resulted primarily from lower purchases of marketable securities and higher proceeds from sales and maturities of marketable securities during the nine months ended September 30, 2025.

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Financing Activities

​

Cash flow related to financing activities was the result of:

​

​ | ​ | ​ | ​ | ​ | ​ | ​
​ | ​ | Nine Months Ended
​ | ​ | September 30,
(In thousands) |  | 2025 |  | 2024
Payment of deferred transaction consideration for in-licensed assets | ​ | $ | (3,044) | ​ | $ | —
Payments of employee withholding taxes related to restricted stock unit award vesting | ​ | ​ | (284) | ​ | ​ | (76)
Proceeds from exercise of employee stock options and the issuance of stock | ​ |  | — | ​ |  | 32
Net cash used in financing activities | ​ | $ | (3,328) | ​ | $ | (44)

​

Net cash used in financing activities increased for the nine months ended September 30, 2025 compared to the nine months ended September 30, 2024 due to the payment of deferred transaction consideration in connection with the Biosion Agreement during the nine months ended September 30, 2025.

​

Funding Requirements

​

We anticipate we will incur net losses in the near term as we continue the development of our product candidates and continue to discover and develop additional product candidates. We may not be able to generate revenue from these programs if, among other things, our clinical trials are not successful, the FDA does not approve our product candidates currently in clinical trials when we expect, or at all, or we are not able to identify and consummate transactions with third-party partners to further develop, obtain marketing approval for and/or commercialize our product candidates.

​

Our primary uses of capital are, and we expect will continue to be, research and development expenses, compensation and related expenses, laboratory and related supplies, professional and legal expenses, and administrative and overhead costs. Our future funding requirements will be heavily determined by the resources needed to support the development of our product candidates, without taking into account any potential business development activities.

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As a publicly traded company, we incur and will continue to incur significant legal, accounting, and other similar expenses. In addition, the Sarbanes-Oxley Act of 2002, as well as rules adopted by the SEC and the Nasdaq Stock Market LLC, requires public companies to implement specified corporate governance practices that could increase our compliance costs.

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We believe our existing cash, cash equivalents and marketable securities are sufficient to fund our operating and capital expenditure requirements for a period greater than 12 months from the date of issuance of our condensed consolidated financial statements that appear in Item 1 of this Quarterly Report on Form 10-Q based on our current operating assumptions. We will require additional capital to develop our product candidates and to support our discovery efforts. Additional funds may not be available on a timely basis, on commercially acceptable terms, or at all, and such funds, if raised, may not be sufficient to enable us to continue to implement our long-term business strategy. Our ability to raise additional capital may be adversely impacted by potentially worsening global economic conditions caused by a variety of factors including geopolitical tensions, tariff policies, inflationary pressures, and the current shutdown of the U.S. federal government. If we are unable to raise sufficient additional capital or generate revenue from transactions with potential third-party partners for the development and/or commercialization of our product candidates, we may need to substantially curtail our planned operations.

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We may raise additional capital through the sale of equity or debt securities. In such an event, our stockholders’ ownership will be diluted, and the terms of these securities may include liquidation or other preferences that adversely affect the rights of a holder of our common stock.

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Because of the numerous risks and uncertainties associated with research and development of pharmaceutical product candidates, we are unable to estimate the exact amount of our working capital requirements. Our funding requirements in the near term will depend on many factors, including:

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| ● | the number and development requirements of the product candidates that we may pursue;

| ● | the scope, progress, results and costs of preclinical development, laboratory testing and conducting preclinical and clinical trials for our product candidates;

| ● | the costs, timing, and outcome of regulatory review of our product candidates;

| ● | the extent to which we in-license or acquire additional product candidates and technologies;

| ● | the costs and timing of preparing, filing and prosecuting patent applications, maintaining and enforcing our intellectual property rights and defending any intellectual property-related claims;

| ● | our ability to identify and consummate transactions with third-party partners to further develop, obtain marketing approval for and/or commercialize our product candidates; and

| ● | our ability to earn revenue as a result of licenses to, or partnerships or other arrangements with, third parties.

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Leases

​

We occupy space for our headquarters in Wayne, Pennsylvania under a lease agreement which has a term through February 2029. We also occupy office and laboratory space in St. Louis, Missouri under a sublease agreement which has a term through May 2029.

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Our aggregate remaining lease payment obligation for these two spaces was $2.7 million as of September 30, 2025.

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Agreement and Plan of Merger with Confluence

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We have agreed to certain payment obligations in accordance with and subject to the terms of the Confluence Agreement (see “Overview—Acquisition and License Agreements—Agreement and Plan of Merger with Confluence”). As of September 30, 2025, the balance of our contingent consideration liability was $10.6 million.

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Exclusive License Agreement with Biosion; Collaboration Agreement with Biosion and CTTQ

​

We have agreed to certain payment obligations in accordance with and subject to the terms of the Biosion and CTTQ Agreements (see “Overview—Acquisition and License Agreements—Exclusive License Agreement with Biosion”).

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R&D Obligations

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We enter into contracts in the normal course of business with CROs, contract manufacturing organizations and other service providers for clinical trials, preclinical studies and testing, manufacturing and other services and products for operating purposes. These contracts generally provide for termination upon notice, and therefore we believe that our non-cancelable obligations under these agreements are not material.

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Segment Information

We have two reportable segments, therapeutics and contract research. The therapeutics segment is focused on identifying and developing innovative therapies to address significant unmet needs for immuno-inflammatory diseases. The contract research segment earns revenue from the provision of laboratory services.

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Item 3. Quantitative and Qualitative Disclosures about Market Risk

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We are a smaller reporting company as defined by Rule 12b-2 of the Exchange Act and are not required to provide the information under this item.

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Item 4. Controls and Procedures

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(a) Evaluation of Disclosure Controls and Procedures

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Under the supervision of and with the participation of our management, including our principal executive officer and our principal financial officer, we conducted an evaluation of the effectiveness of our disclosure controls and procedures as of September 30, 2025, the end of the period covered by this Quarterly Report on Form 10-Q. The term “disclosure controls and procedures,” as set forth in Rules 13a-15(e) and 15d-15(e) under the Exchange Act means controls and other procedures of a company that are designed to ensure that information required to be disclosed by a company in the reports that it files or submits under the Exchange Act is recorded, processed, summarized and reported, within the time periods specified in the rules and forms promulgated by the SEC. Disclosure controls and procedures include, without limitation, controls and procedures designed to ensure that information required to be disclosed by a company in the reports that it files or submits under the Exchange Act is accumulated and communicated to the company’s management, including its principal executive and principal financial officers, or persons performing similar functions, as appropriate to allow timely decisions regarding required disclosure. Management recognizes that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving their objectives, and management necessarily applies its judgment in evaluating the cost-benefit relationship of possible controls and procedures. Based on the evaluation of our disclosure controls and procedures as of September 30, 2025, our principal executive officer and principal financial officer concluded that, as of such date, our disclosure controls and procedures were effective at the reasonable assurance level.

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(b) Changes in Internal Control Over Financial Reporting

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There were no changes in our internal control over financial reporting identified in connection with the evaluation required by Rules 13a-15(d) and 15d-15(d) of the Exchange Act that occurred during the quarter ended September 30, 2025 that has materially affected, or is reasonably likely to materially affect, our internal control over financial reporting.

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PART II. OTHER INFORMATION

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Item 1. Legal Proceedings

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From time to time, we are subject to litigation and claims arising in the ordinary course of business. We are not currently a party to any material legal proceedings, and we are not aware of any other pending or threatened legal proceeding against us that we believe could have a material adverse effect on our business, operating results, cash flows or financial condition.

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Item 1A. Risk Factors

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Our business is subject to risks and events that, if they occur, could adversely affect our financial condition and results of operations and the trading price of our securities. Our risk factors have not changed materially from those described in “Part I, Item 1A. Risk Factors” of our Annual Report.

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Item 5. Other Information

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Adoption, Modification and Termination of Rule 10b5-1 Plans and Certain Other Trading Arrangements.

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During the quarter ended September 30, 2025, n o n e of our directors or officers (as defined in Rule 16a-1(f) under the Exchange Act) adopted, modified or terminated a “Rule 10b5-1 trading arrangement” or a “non-Rule 10b5-1 trading arrangement” (as each term is defined in Item 408 of Regulation S-K).

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​

Item 6. Exhibits

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| ​ |
Exhibit No. |  | Document
3.1 | ​ | Amended and Restated Certificate of Incorporation of the Registrant (incorporated herein by reference to Exhibit 3.1 to the Registrant’s Current Report on Form 8-K (File No. 001-37581), filed with the SEC on October 13, 2015).
​ | ​ | ​
3.2 | ​ | Certificate of Amendment to the Amended and Restated Certificate of Incorporation of the Registrant (incorporated herein by reference to Exhibit 3.2 to the Registrant’s Quarterly Report on Form 10-Q (File No. 001-37581), filed with the SEC on August 7, 2023).
​ | ​ | ​
3.3 | ​ | Certificate of Amendment to the Amended and Restated Certificate of Incorporation of the Registrant (incorporated herein by reference to Exhibit 3.1 to the Registrant’s Current Report on Form 8-K (File No. 001-37581), filed with the SEC on June 5, 2025).
​ | ​ | ​
3.4 | ​ | Amended and Restated Bylaws of the Registrant (incorporated herein by reference to Exhibit 3.1 to the Registrant’s Current Report on Form 8-K (File No. 001-37581), filed with the SEC on June 24, 2020).
​ | ​ | ​
10.1+* | ​ | Employment Agreement, effective as of July 28, 2025, by and between the Registrant and Roland Kolbeck.
​ | ​ | ​
31.1* | ​ | Certification of Principal Executive Officer under Section 302 of the Sarbanes-Oxley Act.
| ​ |
31.2* | ​ | Certification of Principal Financial Officer under Section 302 of the Sarbanes-Oxley Act.
| ​ |
32.1** | ​ | Certifications of Principal Executive Officer and Principal Financial Officer under Section 906 of the Sarbanes-Oxley Act.
| ​ |
101.INS | ​ | XBRL Instance Document (the instance document does not appear in the Interactive Data File because its XBRL tags are embedded within the Inline XBRL document)
| ​ |
101.SCH | ​ | Inline XBRL Taxonomy Extension Schema Document
| ​ |
101.CAL | ​ | Inline XBRL Taxonomy Extension Calculation Linkbase Document
| ​ |
101.DEF | ​ | Inline XBRL Taxonomy Extension Definition Linkbase Document
| ​ |
101.LAB | ​ | Inline XBRL Taxonomy Extension Label Linkbase Document
| ​ |
101.PRE | ​ | Inline XBRL Taxonomy Extension Presentation Linkbase Document
| ​ |
104 | ​ | Cover Page Interactive Data File (formatted as Inline XBRL and contained in Exhibit 101)

​

* | Filed herewith.

** | These certifications are being furnished solely to accompany this quarterly report pursuant to 18 U.S.C. Section 1350, and are not being filed for purposes of Section 18 of the Exchange Act and are not to be incorporated by reference into any filing of the registrant, whether made before or after the date hereof, regardless of any general incorporation language in such filing.

+ | Indicates management contract or compensatory plan.

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SIGNATURES

​

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.

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​ | ​ | ​
​ | ACLARIS THERAPEUTICS, INC.
​ | ​ | ​
Date: November 6, 2025 | By: | /s/ Neal Walker
​ | ​ | Neal Walker
​ | ​ | Chief Executive Officer
​ | ​ | (On behalf of the Registrant)
​ | ​ | ​
​ | ​ | ​
Date: November 6, 2025 | By: | /s/ Kevin Balthaser
​ | ​ | Kevin Balthaser
​ | ​ | Chief Financial Officer
​ | ​ | (Principal Financial Officer)

​

​

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