Protagonist Therapeutics, Inc 10-K

Item 8. Financial Statements and Supplementary Data ​ PROTAGONIST THERAPEUTICS, INC. ​ INDEX TO CONSOLIDATED FINANCIAL STATEMENTS ​ AAW Audited Consolidated Financial Statements Page Report of Independent Registered Public Accounting Firm (PCAOB ID: 42) ​ 78 Consolidated Balance Sheets ​ 80 Consolidated Statements of Operations ​ 81 Consolidated Statements of Comprehensive Income (Loss ) ​ 82 Consolidated Statements of Stockholders’ Equity ​ 83 Consolidated Statements of Cash Flows ​ 84 Notes to the Consolidated Financial Statements ​ 85 ​ ​ ​ ​ 77 Table of Contents Report of Independent Registered Public Accounting Firm ​ To the Stockholders and the Board of Directors of Protagonist Therapeutics, Inc. Opinion on the Financial Statements We have audited the accompanying consolidated balance sheets of Protagonist Therapeutics, Inc. (the Company) as of December 31, 2024 and 2023, the related consolidated statements of operations, comprehensive income (loss), stockholders' equity and cash flows for each of the three years in the period ended December 31, 2024, and the related notes (collectively referred to as the “consolidated financial statements”). In our opinion, the consolidated financial statements present fairly, in all material respects, the financial position of the Company at December 31, 2024 and 2023, and the results of its operations and its cash flows for each of the three years in the period ended December 31, 2024, in conformity with U.S. generally accepted accounting principles. We also have audited, in accordance with the standards of the Public Company Accounting Oversight Board (United States) (PCAOB), the Company's internal control over financial reporting as of December 31, 2024, based on criteria established in Internal Control—Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission (2013 framework), and our report dated February 21, 2025 expressed an unqualified opinion thereon. ​ Basis for Opinion These financial statements are the responsibility of the Company's management. Our responsibility is to express an opinion on the Company’s financial statements based on our audits. We are a public accounting firm registered with the PCAOB and are required to be independent with respect to the Company in accordance with the U.S. federal securities laws and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB. We conducted our audits in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements are free of material misstatement, whether due to error or fraud. Our audits included performing procedures to assess the risks of material misstatement of the financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the financial statements. Our audits also included evaluating the accounting principles used and significant estimates made by management, as well as evaluating the overall presentation of the financial statements. We believe that our audits provide a reasonable basis for our opinion. Critical Audit Matter The critical audit matter communicated below is a matter arising from the current period audit of the financial statements that was communicated or required to be communicated to the audit committee and that: (1) relates to accounts or disclosures that are material to the financial statements and (2) involved our especially challenging, subjective or complex judgments. The communication of the critical audit matter does not alter in any way our opinion on the consolidated financial statements, taken as a whole, and we are not, by communicating the critical audit matter below, providing separate opinion on the critical audit matter or on the accounts or disclosures to which it relates. ​ 78 Table of Contents ​ ​ ​ ​ ​ Takeda Collaboration Agreement ​ ​ Description of the Matter ​ As described in Note 3, the Company entered into a Collaboration and License Agreement with Takeda Pharmaceuticals USA, Inc. (Takeda), pursuant to which the Company and Takeda will collaborate on the development and commercialization of rusfertide (Takeda Agreement). As further described in Note 3, the transaction price was allocated at the inception of the agreement to all identified performance obligations based on the relative standalone selling price. ​ Auditing the Company’s revenue recognition for the Takeda Agreement was complex and required the evaluation of significant judgments made by management, including the determination of the standalone selling price of the license obligation. The estimated standalone selling price for the performance obligation related to the license of intellectual property reflects management’s assumptions, which includes forecasted revenues, development timelines, discount rates and probabilities of technical and regulatory success. Changes to these assumptions can have a material effect on the allocation of the transaction price to the performance obligations as well as the amount and timing of revenue recognized. ​ How We Addressed the Matter in Our Audit ​ We obtained an understanding, evaluated the design and tested the operating effectiveness of controls addressing the risks of material misstatement related to the accounting for the Takeda Agreement. For example, we tested management’s controls over the identification of performance obligations, the determination of the significant assumptions described above with respect to the estimation of the standalone selling price of the performance obligations related to the licensed compounds, and the accuracy and completeness of underlying data used in estimating the standalone selling price and the transaction price. ​ Our audit procedures included, among others, obtaining and reading the Takeda Agreement and evaluating the completeness of the performance obligations identified by management. We also evaluated management’s estimates of the standalone selling price for identified performance obligations. For example, we evaluated the reasonableness and consistency of significant assumptions used in the determination of standalone selling price. We also performed a sensitivity analysis to evaluate the impact that changes in the significant assumptions would have on the estimated standalone selling price of performance obligations and the resulting impact on the allocation of transaction price to each performance obligation, as well as revenue recognized during the period. We involved our valuation professionals to assist in the assessment of certain assumptions used in the determination of the estimated standalone selling price of the license performance obligation. ​ /s/ Ernst & Young LLP We have served as the Company’s auditor since 2020. San Mateo, California February 21, 2025 ​ ​ 79 Table of Contents PR OTAGONIST THERAPEUTICS, INC. Consolidated Balance Sheets (In thousands, except share data) ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ 2024 2023 Assets ​ ​ ​ ​ ​ ​ Current assets: ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 97,249 ​ $ 186,727 Marketable securities ​ ​ 321,664 ​ ​ 154,890 Receivable from collaboration partner ​ ​ 165,000 ​ ​ 10,000 Prepaid expenses and other current assets ​ ​ 7,728 ​ ​ 3,960 Total current assets ​ ​ 591,641 ​ ​ 355,577 Marketable securities - noncurrent ​ ​ 140,252 ​ ​ — Property and equipment, net ​ ​ 3,190 ​ ​ 1,195 Restricted cash - noncurrent ​ ​ 225 ​ ​ 225 Operating lease right-of-use asset ​ ​ 9,417 ​ ​ 954 Total assets ​ $ 744,725 ​ $ 357,951 Liabilities and Stockholders’ Equity ​ ​ ​ ​ ​ ​ Current liabilities: ​ ​ ​ ​ ​ Accounts payable ​ $ 1,615 ​ $ 772 Payable to collaboration partner ​ ​ — ​ ​ 3 Accrued expenses and other payables ​ ​ 23,693 ​ ​ 19,358 Deferred revenue ​ ​ 18,891 ​ ​ — Income taxes payable ​ ​ 2,689 ​ ​ — Operating lease liability ​ ​ 510 ​ ​ 1,141 Total current liabilities ​ ​ 47,398 ​ ​ 21,274 Deferred revenue - noncurrent ​ ​ 11,676 ​ ​ — Operating lease liability - noncurrent ​ ​ 10,356 ​ ​ — Total liabilities ​ ​ 69,430 ​ ​ 21,274 Commitments and contingencies (Note 9) ​ ​ ​ ​ ​ ​ Stockholders’ equity: ​ ​ ​ ​ ​ ​ Preferred stock, $ 0.00001 par value, 10,000,000 shares authorized; no shares issued and outstanding ​ ​ — ​ ​ — Common stock, $ 0.00001 par value, 180,000,000 and 90,000,000 shares authorized as of December 31, 2024 and 2023, respectively; 61,035,139 and 57,708,613 shares issued and outstanding as of December 31, 2024 and 2023, respectively ​ ​ 1 ​ ​ 1 Additional paid-in capital ​ ​ 1,015,898 ​ ​ 952,491 Accumulated other comprehensive loss ​ ​ ( 82 ) ​ ​ ( 105 ) Accumulated deficit ​ ​ ( 340,522 ) ​ ​ ( 615,710 ) Total stockholders’ equity ​ ​ 675,295 ​ ​ 336,677 Total liabilities and stockholders’ equity ​ $ 744,725 ​ $ 357,951 ​ The accompanying notes are an integral part of these consolidated financial statements. ​ 80 Table of Contents PROTAGONIST THERAPEUTICS, INC. Consolidated Statements of Operations (In thousands, except share and per share data) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ 2024 2023 2022 License and collaboration revenue ​ $ 434,433 ​ $ 60,000 ​ $ 26,581 Operating expenses: ​ ​ ​ ​ ​ ​ ​ ​ ​ Research and development ​ ​ 138,128 ​ ​ 120,161 ​ ​ 126,215 General and administrative ​ 43,462 ​ 33,491 ​ 31,739 Total operating expenses ​ 181,590 ​ 153,652 ​ 157,954 Income (loss) from operations ​ 252,843 ​ ( 93,652 ) ​ ( 131,373 ) Interest income ​ 26,315 ​ ​ 14,898 ​ 4,060 Other income (expense), net ​ ​ 250 ​ ​ ( 201 ) ​ ​ ( 80 ) Income (loss) before income tax expense ​ ​ 279,408 ​ ​ ( 78,955 ) ​ ​ ( 127,393 ) Income tax expense ​ ​ 4,220 ​ ​ — ​ ​ — Net income (loss) ​ $ 275,188 ​ $ ( 78,955 ) ​ $ ( 127,393 ) Net income (loss) per share, basic ​ $ 4.47 ​ $ ( 1.39 ) ​ $ ( 2.60 ) Net income (loss) per share, diluted ​ $ 4.23 ​ $ ( 1.39 ) ​ $ ( 2.60 ) Weighted-average shares used to compute net income (loss) per share, basic ​ 61,566,989 56,763,559 49,042,232 Weighted-average shares used to compute net income (loss) per share, diluted ​ 65,077,722 56,763,559 49,042,232 ​ ​ The accompanying notes are an integral part of these consolidated financial statements. ​ 81 Table of Contents PROTAGONIST THERAPEUTICS, INC. Consolidated Statements of Comprehensive Income (Loss ) (In thousands) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ 2024 2023 2022 Net income (loss) ​ $ 275,188 ​ $ ( 78,955 ) ​ $ ( 127,393 ) Other comprehensive income (loss): ​ ​ ​ ​ ​ ​ ​ Unrealized gain on marketable securities ​ ​ 23 ​ ​ 60 ​ ​ 89 Gain (loss) on translation of foreign operations ​ — ​ 194 ​ ( 149 ) Comprehensive income (loss) ​ $ 275,211 ​ $ ( 78,701 ) ​ $ ( 127,453 ) ​ The accompanying notes are an integral part of these consolidated financial statements. ​ ​ 82 Table of Contents PROTAGONIST THERAPEUTICS, INC. Consolidated Statements of Stockholders’ Equity (In thousands, except share data) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Accumulated ​ ​ ​ ​ ​ ​ ​ ​ Additional ​ Other ​ ​ ​ Total ​ ​ Common ​ Paid-In ​ Comprehensive ​ Accumulated ​ Stockholders’ ​ ​ Stock Capital (Loss) Gain Deficit Equity ​ Shares Amount ​ ​ ​ ​ ​ ​ ​ ​ ​ Balance at December 31, 2021 ​ 47,838,330 $ — ​ $ 709,682 $ ( 299 ) ​ $ ( 409,362 ) $ 300,021 Issuance of common stock pursuant to at-the-market offering, net of issuance costs ​ 422,367 ​ ​ — ​ ​ 14,553 ​ ​ — ​ ​ — ​ ​ 14,553 Issuance of common stock under equity incentive and employee stock purchase plans ​ 686,284 — ​ 4,448 — ​ — 4,448 Issuance of common stock upon exercise of Exchange Warrants ​ 399,997 ​ ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ — Shares withheld for net settlement of tax withholding upon vesting of restricted stock units ​ ( 7,726 ) ​ ​ — ​ ​ ( 188 ) ​ ​ — ​ ​ — ​ ​ ( 188 ) Stock-based compensation expense ​ — — ​ 24,202 — ​ — 24,202 Issuance costs related to prior period common stock offering ​ — ​ ​ — ​ ​ 25 ​ ​ — ​ ​ — ​ ​ 25 Other comprehensive income (loss) ​ — — ​ — ( 60 ) ​ — ( 60 ) Net income (loss) ​ — — ​ — — ​ ( 127,393 ) ( 127,393 ) Balance at December 31, 2022 ​ 49,339,252 — ​ 752,722 ( 359 ) ​ ( 536,755 ) 215,608 Issuance of common stock pursuant to public offerings, net of issuance costs ​ 5,750,000 ​ ​ — ​ ​ 107,798 ​ ​ — ​ ​ — ​ ​ 107,798 Issuance of common stock pursuant to at-the-market offering, net of issuance costs ​ 1,749,199 ​ ​ 1 ​ ​ 24,301 ​ ​ — ​ ​ — ​ ​ 24,302 Exercise of Warrants in exchange for issuance of Pre-Funded Warrants ​ — ​ ​ — ​ ​ 33,813 ​ ​ — ​ ​ — ​ ​ 33,813 Issuance of common stock upon exercise of Warrants ​ 44,748 ​ ​ — ​ ​ 559 ​ ​ — ​ ​ — ​ ​ 559 Issuance of common stock under equity incentive and employee stock purchase plans ​ 857,377 — ​ 4,774 — ​ — 4,774 Shares withheld for net settlement of tax withholding upon vesting of restricted stock units ​ ( 31,963 ) ​ ​ — ​ ​ ( 769 ) ​ ​ — ​ ​ — ​ ​ ( 769 ) Stock-based compensation expense ​ — — ​ 29,293 — ​ — 29,293 Other comprehensive income (loss) ​ — — ​ — 254 ​ — 254 Net income (loss) ​ — — ​ — — ​ ( 78,955 ) ( 78,955 ) Balance at December 31, 2023 ​ 57,708,613 1 ​ 952,491 ( 105 ) ​ ( 615,710 ) 336,677 Issuance of common stock under equity incentive and employee stock purchase plans ​ 2,142,094 — ​ 26,453 — ​ — 26,453 Issuance of common stock upon exercise of Pre-Funded Warrants ​ 1,205,225 ​ ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ — Shares withheld for net settlement of tax withholding upon vesting of restricted stock units ​ ( 20,793 ) ​ ​ — ​ ​ ( 600 ) ​ ​ — ​ ​ — ​ ​ ( 600 ) Stock-based compensation expense ​ — — ​ 37,554 — ​ — 37,554 Other comprehensive income (loss) ​ — — ​ — 23 ​ — 23 Net income (loss) ​ — — ​ — — ​ 275,188 275,188 Balance at December 31, 2024 ​ 61,035,139 $ 1 ​ $ 1,015,898 $ ( 82 ) ​ $ ( 340,522 ) $ 675,295 ​ The accompanying notes are an integral part of these consolidated financial statements. ​ ​ 83 Table of Contents PROTAGONIST THERAPEUTICS, INC. Consolidated Statements of Cash Flows (In thousands) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ 2024 2023 2022 Cash Flows from Operating Activities ​ ​ ​ ​ Net income (loss) ​ $ 275,188 ​ $ ( 78,955 ) ​ $ ( 127,393 ) Adjustments to reconcile net income (loss) to net cash provided by (used in) operating activities: ​ ​ ​ ​ ​ ​ ​ ​ ​ Stock-based compensation ​ ​ 37,554 ​ ​ 29,293 ​ ​ 24,202 Operating lease right-of-use asset amortization ​ ​ 2,069 ​ ​ 2,335 ​ ​ 2,335 Depreciation ​ ​ 826 ​ ​ 977 ​ ​ 1,034 Accretion of discount on marketable securities ​ ​ ( 8,875 ) ​ ​ ( 4,569 ) ​ ​ ( 549 ) Other ​ ​ — ​ ​ 194 ​ ​ — Changes in operating assets and liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ Receivable from collaboration partner ​ ​ ( 155,000 ) ​ ​ ( 9,990 ) ​ ​ 1,556 Prepaid expenses and other assets ​ ​ ( 3,768 ) ​ ​ 1,753 ​ ​ 3,754 Research and development tax incentive receivable ​ ​ — ​ ​ — ​ ​ 2,686 Accounts payable ​ ​ 842 ​ ​ ( 2,868 ) ​ ​ 2,045 Payable to collaboration partner ​ ​ ( 3 ) ​ ​ ( 66 ) ​ ​ ( 830 ) Accrued expenses and other payables ​ ​ 4,289 ​ ​ ( 5,597 ) ​ ​ ( 12,715 ) Deferred revenue ​ ​ 30,567 ​ ​ — ​ ​ ( 1,601 ) Income taxes payable ​ ​ 2,689 ​ ​ — ​ ​ — Operating lease liability ​ ​ ( 2,226 ) ​ ​ ( 2,743 ) ​ ​ ( 2,661 ) Net cash provided by (used in) operating activities ​ ​ 184,152 ​ ​ ( 70,236 ) ​ ​ ( 108,137 ) Cash Flows from Investing Activities ​ ​ ​ ​ ​ ​ ​ ​ ​ Purchase of marketable securities ​ ​ ( 621,702 ) ​ ​ ( 191,045 ) ​ ​ ( 214,874 ) Proceeds from maturities of marketable securities ​ ​ 323,574 ​ ​ 152,396 ​ ​ 307,137 Purchases of property and equipment ​ ​ ( 1,355 ) ​ ​ ( 609 ) ​ ​ ( 795 ) Net cash (used in) provided by investing activities ​ ​ ( 299,483 ) ​ ​ ( 39,258 ) ​ ​ 91,468 Cash Flows from Financing Activities ​ ​ ​ ​ ​ ​ ​ ​ ​ Proceeds from issuance of common stock upon exercise of stock options and purchases under employee stock purchase plan ​ ​ 26,453 ​ ​ 4,774 ​ ​ 4,448 Tax withholding payments related to net settlement of restricted stock units ​ ​ ( 600 ) ​ ​ ( 769 ) ​ ​ ( 188 ) Proceeds from public offering of common stock, net of issuance costs ​ ​ — ​ ​ 107,798 ​ ​ — Proceeds from at-the-market offering, net of issuance costs ​ ​ — ​ ​ 24,302 ​ ​ 14,553 Proceeds from exercise of Warrants in exchange for issuance of Pre-Funded Warrants ​ ​ — ​ ​ 33,813 ​ ​ — Proceeds from issuance of common stock upon exercise of Warrants ​ ​ — ​ ​ 559 ​ ​ — Issuance costs related to prior period common stock offering ​ ​ — ​ ​ — ​ ​ 25 Net cash provided by financing activities ​ ​ 25,853 ​ ​ 170,477 ​ ​ 18,838 Effect of exchange rate changes on cash, cash equivalents and restricted cash ​ ​ — ​ ​ — ​ ​ ( 90 ) Net (decrease) increase in cash, cash equivalents and restricted cash ​ ​ ( 89,478 ) ​ ​ 60,983 ​ ​ 2,079 Cash, cash equivalents and restricted cash, beginning of period ​ 186,952 ​ 125,969 ​ 123,890 Cash, cash equivalents and restricted cash, end of period ​ $ 97,474 ​ $ 186,952 ​ $ 125,969 Supplemental Disclosure of Cash Flow Information: ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash paid for taxes ​ $ 1,530 ​ $ — ​ $ — Supplemental Disclosure of Non-Cash Financing and Investing Information: ​ ​ ​ ​ ​ ​ ​ ​ ​ Right-of-use asset obtained in exchange for lease obligation ​ $ 10,511 ​ $ — ​ $ — Leasehold improvements obtained under tenant improvement allowance ​ $ 1,421 ​ $ — ​ $ — Purchases of property and equipment in accounts payable and accrued liabilities ​ $ 46 ​ $ 61 ​ $ 19 ​ The accompanying notes are an integral part of these consolidated financial statements. ​ ​ 84 Table of Contents P ROTAGONIST THERAPEUTICS, INC. Notes to Consolidated Financial Statements Note 1. Organization and Description of Business Protagonist Therapeutics, Inc. (the “Company”) is a discovery through late-stage development biopharmaceutical company focused on peptide therapeutics. The Company’s clinical programs fall into two broad categories of diseases: (i) hematology and blood disorders, and (ii) inflammatory and immunomodulatory (“I&I”) diseases. Two novel peptides derived from the Company’s proprietary discovery technology platform, rusfertide and icotrokinra (formerly known as JNJ-2113), are currently in advanced Phase 3 clinical development. Rusfertide, an injectable mimetic of the natural hormone hepcidin partnered with Takeda Pharmaceuticals, Inc. (“Takeda”), is currently in Phase 3 development for treatment of the rare blood disorder polycythemia vera (“PV”). Icotrokinra is a first-in-class investigational targeted oral peptide that selectively blocks the Interleukin-23 receptor (“IL-23R”), which is licensed to J&J Innovative Medicines (“JNJ”), formerly Janssen Biotech, Inc. Icotrokinra is an orally delivered drug that is designed to block biological pathways currently targeted by marketed injectable antibody drugs. Following Icotrokinra’s joint discovery by the Company and JNJ scientists pursuant to their IL-23R collaboration, the Company was primarily responsible for the development of icotrokinra through Phase 1, with JNJ assuming responsibility for development in Phase 2 and beyond. The Company also has a number of pre-clinical stage oral drug discovery programs to address clinically and commercially validated targets, including IL-17 oral peptide antagonist PN-881, an oral metabolic/obesity peptide program, and an oral hepcidin mimetic/ferroportin blocker program. The Company is headquartered in Newark, California and has one wholly owned subsidiary, Protagonist Pty Limited (“Protagonist Australia”), located in Brisbane, Queensland, Australia. Liquidity As of December 31, 2024, the Company had cash, cash equivalents and marketable securities of $ 559.2 million. The Company has incurred an accumulated deficit from inception through December 31, 2024 of $ 340.5 million. The Company’s ultimate success depends upon the outcome of its research and development and collaboration activities. The Company may incur additional losses in the future as it continues the development of rusfertide through Phase 3 development and a potential NDA filing and invests in its pre-clinical discovery programs and may need to raise additional capital to continue to execute its long-range business plan. Since the Company’s initial public offering in August 2016, it has financed its operations primarily through proceeds from offerings of common stock and payments received under license and collaboration agreements. Note 2. Summary of Significant Accounting Policies Basis of Presentation and Consolidation The accompanying consolidated financial statements include the accounts of the Company and its wholly owned subsidiary, Protagonist Australia, and have been prepared in conformity with accounting principles generally accepted in the United States (“GAAP”) and applicable rules and regulations of the Securities and Exchange Commission (“SEC”). All intercompany balances and transactions have been eliminated upon consolidation. Use of Estimates The preparation of the consolidated financial statements in conformity with GAAP requires management to make estimates, assumptions and judgments that affect the reported amounts of assets and liabilities and disclosure of contingent liabilities as of the date of the consolidated financial statements and the reported amounts of revenues and expenses during the reporting period. On an ongoing basis, management evaluates its estimates, including those related to revenue recognition, accruals for research and development activities, stock-based compensation, income taxes, 85 Table of Contents marketable securities and leases. Estimates related to revenue recognition include assumptions used to determine standalone selling price utilized to allocate the transaction price between distinct performance obligations, assumptions used to recognize revenue over time for certain performance obligations for which a cost-based input method is used as the measure of progress and estimates of whether contingent consideration should be included in the transaction price at each reporting period. Management bases these estimates on historical and anticipated results, trends and various other assumptions that the Company believes are reasonable under the circumstances, including assumptions as to forecasted amounts and future events. There has been uncertainty and disruption in the global economy and financial markets due to a number of factors, including geopolitical instability, inflationary pressures, high interest rates, a recessionary environment, domestic and global monetary and fiscal policy, changes in trade policies, including tariffs or other trade restrictions or the threat of such actions, banking and other financial institution instability and other factors. The Company has taken into consideration any known impacts in its accounting estimates to date and is not aware of any additional specific events or circumstances that would require any additional updates to its estimates or judgments or a revision of the carrying value of its assets or liabilities as of the filing date of this Annual Report on Form 10-K. These estimates may change as new events occur and additional information is obtained. Actual results could differ materially from these estimates under different assumptions or conditions. Concentrations of Credit Risk Financial instruments that potentially subject the Company to a concentration of credit risk consist of cash, cash equivalents and marketable securities. Substantially all of the Company’s cash is held by three financial institutions that management believes are of high credit quality. Such deposits generally exceed federally insured limits. The primary focus of the Company’s investment strategy is to preserve capital and to meet liquidity requirements. The Company’s cash equivalents and marketable securities are managed by external managers within the guidelines of the Company’s investment policy. The Company’s investment policy addresses the level of credit exposure by limiting concentration in any one corporate issuer and establishing a minimum allowable credit rating. To manage its credit risk exposure, the Company maintains its U.S. portfolio of cash equivalents and marketable securities in fixed income securities denominated and payable in U.S. dollars. Permissible investments of fixed income securities include obligations of the U.S. government and its agencies, money market instruments including commercial paper and negotiable certificates of deposit, and highly rated corporate debt obligations and money market funds. Cash Equivalents Cash equivalents that are readily convertible to cash are stated at cost, which approximates fair value. The Company considers all highly liquid investments purchased with an original maturity of three months or less to be cash equivalents. Restricted Cash Restricted cash consists of cash balances held as security in connection with a letter of credit related to the Company’s facility lease entered into in March 2017, as subsequently amended. The Company’s letter of credit balance was $ 0.2 million at December 31, 2024, 2023 and 2022 pursuant to the terms of the facility lease. Cash as Reported in Consolidated Statements of Cash Flows Cash as reported in the consolidated statements of cash flows includes the aggregate amounts of cash and cash equivalents and the restricted cash as presented on the consolidated balance sheets. 86 Table of Contents Cash as reported in the consolidated statements of cash flows consisted of (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ 2024 2023 ​ 2022 Cash and cash equivalents ​ $ 97,249 ​ $ 186,727 ​ $ 125,744 Restricted cash - noncurrent ​ 225 ​ 225 ​ 225 Total cash reported on consolidated statements of cash flows ​ $ 97,474 ​ $ 186,952 ​ $ 125,969 ​ Marketable Securities All marketable securities have been classified as “available-for-sale” and are carried at estimated fair value as determined based upon quoted market prices or pricing models for similar securities. Management determines the appropriate classification of its marketable securities at the time of purchase and reevaluates such designation as of each balance sheet date. Short-term marketable securities have maturities greater than three months but not longer than 365 days as of the balance sheet date. Long-term marketable securities have maturities of 365 days or longer as of the balance sheet date. Unrealized gains and losses are excluded from earnings and are reported as a component of comprehensive income (loss). Realized gains and losses, if any, on available-for-sale securities are included in interest income. The cost of securities sold is based on the specific-identification method. Interest on marketable securities is included in interest income. Fair Value of Financial Instruments Fair value accounting is applied to all financial assets and liabilities that are recognized or disclosed at fair value in the consolidated financial statements on a recurring basis (at least annually). The carrying amount of the Company’s financial instruments, including cash equivalents, receivables from its collaboration partner, accounts payable, payables to its collaboration partner and accrued expenses and other payables approximate fair value due to their short-term maturities. See Note 4 to the Consolidated Financial Statements for additional information regarding the fair value of the Company’s other financial assets and liabilities. Investment Impairment ​ As of each reporting date, the Company assesses each of its investments in available-for-sale debt securities whose fair value is below its cost basis to determine if the investment’s impairment is due to credit-related factors or noncredit-related factors. Factors considered in determining whether an impairment is credit-related include the extent to which the investment’s fair value is less than its cost basis, declines in published credit ratings, issuer default on interest or principal payments, and declines in the financial condition and near-term prospects of the issuer. Credit-related impairments on available-for-sale debt securities are recognized as an allowance for credit losses with a corresponding adjustment to other income (expense), net. The portion of the impairment that is not credit-related is recorded as a reduction of other comprehensive income (loss), net of applicable taxes. ​ Pursuant to Accounting Standard Update 2016-13, Financial Instruments - Credit Losses (Topic 326) , the Company has elected to exclude accrued interest from both the fair value and the amortized cost basis of the available-for-sale debt securities for the purposes of identifying and measuring an impairment. The Company writes off accrued interest as a reduction of interest income when an issuer has defaulted on interest payments due on a security. Property and Equipment Property and equipment are stated at cost, net of accumulated depreciation. Depreciation is computed using the straight-line method over the estimated useful lives of the assets, ranging from three to five years . Leasehold improvements are amortized over the shorter of the lease term or the estimated useful lives of the assets. Maintenance and repairs are charged to expense as incurred. When assets are retired or otherwise disposed of, the cost and accumulated depreciation are removed from the consolidated balance sheet and any resulting gain or loss is reflected in operations in the period realized. 87 Table of Contents Leases The Company determines if an arrangement is a lease at inception. Pursuant to Accounting Standards Codification Topic 842, Leases (“ASC Topic 842”), operating leases are included in operating lease right-of-use (“ROU”) asset, operating lease liability, and noncurrent operating lease liability on the consolidated balance sheets. Operating lease ROU asset and operating lease liability are recognized based on the net present value of the future minimum lease payments over the lease term at commencement date. If the Company’s leases do not provide an implicit rate, the Company uses its incremental borrowing rate based on information available at the commencement date in determining the present value of future payments. The operating lease ROU asset also includes any lease payments made and excludes lease incentives and initial direct costs incurred. Lease terms include options to extend or terminate the lease when it is reasonably certain that the Company will exercise that option. Lease expense for minimum lease payments is recognized on a straight-line basis over the lease term. The Company records tenant improvement allowances as a reduction to the ROU asset with the impact of the decrease recognized prospectively over the remaining lease term. The leasehold improvements are amortized over the shorter of their useful life or the remaining term of the lease. Impairment of Long-Lived Assets The Company reviews long-lived assets, primarily comprised of property, equipment and operating lease ROU assets, for impairment whenever events or changes in circumstances indicate that the carrying amount of an asset may not be recoverable. Recoverability is measured by comparison of the carrying amount to the future net cash flows which the assets are expected to generate. If such assets are considered to be impaired, the impairment to be recognized is measured as the amount by which the carrying amount of the assets exceeds the projected discounted future net cash flows arising from the asset. There have been no such impairments of long-lived assets for any of the periods presented. ​ Comprehensive Income (Loss) Comprehensive income (loss) includes net income (loss) as well as other changes in stockholders’ equity that result from transactions and economic events other than those from stockholders. The Company’s foreign currency translation and unrealized gains and losses on available-for-sale securities represent the only components of other comprehensive income (loss) that are excluded from reported net income (loss) and that are presented in the consolidated statements of comprehensive income (loss). Income Taxes The Company uses the asset and liability method to account for income taxes in accordance with the authoritative guidance for income taxes. Under this method, deferred tax assets and liabilities are determined based on future tax consequences attributable to differences between the financial statement carrying amounts of existing assets and liabilities and their respective tax bases, and tax loss and credit carryforwards. Deferred tax assets and liabilities are measured using enacted tax rates applied to taxable income in the years in which those temporary differences are expected to be recovered or settled. The effect on deferred tax assets and liabilities of a change in tax rates is recognized in the period that includes the enactment date. A valuation allowance is established when necessary to reduce deferred tax assets to the amount expected to be realized. ​ The Company recognizes the effect of income tax positions only if those positions are more likely than not of being sustained. Recognized income tax positions are measured at the largest amount that is greater than a 50% likelihood of being realized. Changes in recognition or measurement are reflected in the period in which the change in judgment occurs. The Company records interest and penalties related to unrecognized tax benefits in income tax expense. To date, there have been no interest or penalties recorded in relation to unrecognized tax benefits. 88 Table of Contents Collaborative Arrangements ​ The Company analyzes its collaborative arrangements to assess whether such arrangements involve joint operating activities performed by parties that are both active participants in the activities and exposed to significant risks and rewards and therefore are within the scope of Accounting Standards Codification Topic 808, Collaborative Arrangements (“ASC Topic 808”). For collaborative arrangements that contain multiple elements, the Company determines which units of account are deemed to be within the scope of ASC Topic 808 and which units of account are more reflective of a vendor-customer relationship and therefore are within the scope of Accounting Standards Codification Topic 606, Revenue from Contracts with Customers (“ASC Topic 606”). For units of account that are accounted for pursuant to ASC Topic 808, an appropriate recognition method is determined and applied consistently, either by analogy to appropriate accounting literature or by applying a reasonable accounting policy election. For collaborative arrangements that are within the scope of ASC Topic 808, the Company evaluates the income statement classification for presentation of amounts due to or owed from other participants associated with multiple units of account in a collaborative arrangement based on the nature of each activity. Payments or reimbursements that are the result of a collaborative relationship instead of a customer relationship, such as co-development and co-commercialization activities, are recorded as increases or decreases to research and development expense or general and administrative expense, as appropriate. ​ Revenue Recognition Under ASC Topic 606, the Company recognizes revenue when its customer obtains control of promised goods or services, in an amount that reflects the consideration which the Company expects to receive in exchange for those goods or services. To determine revenue recognition for arrangements that the Company determines are within the scope of 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) the Company satisfies a performance obligation. The Company applies the five-step model to contracts when it is probable that the Company will collect the consideration it is entitled to in exchange for the goods or services it transfers to the customer. At contract inception, the Company assesses the goods or services promised within each contract, determines those that are performance obligations, and assesses whether each promised good or service is distinct. The Company then recognizes as revenue the amount of the transaction price that is allocated to the respective performance obligations when (or as) the performance obligations are satisfied. The Company constrains its estimate of the transaction price up to the amount (the “variable consideration constraint”) that a significant reversal of recognized revenue is not probable. ​ Licenses of intellectual property: If a license to the Company’s intellectual property is determined to be distinct from the other performance obligations identified in an arrangement, the Company recognizes revenue from non-refundable, upfront fees allocated to the license when the license is transferred to the customer and the customer is able to use and benefit from the license. For licenses that are bundled with other promises, the Company utilizes judgment to assess the nature of the combined performance obligation to determine whether the combined performance obligation is satisfied over time or at a point in time and, if over time, the appropriate method of measuring proportional performance for purposes of recognizing revenue from non-refundable, upfront fees. The Company evaluates the measure of proportional performance each reporting period and, if necessary, adjusts the measure of performance and related revenue recognition. ​ Milestone payments: At the inception of each arrangement or amendment that includes development, regulatory or commercial milestone payments, the Company evaluates whether the milestones are considered probable of being reached and estimates the amount to be included in the transaction price. ASC Topic 606 suggests two alternatives to use when estimating the amount of variable consideration: the expected value method and the most likely amount method. Under the expected value method, an entity considers the sum of probability-weighted amounts in a range of possible consideration amounts. Under the most likely amount method, an entity considers the single most likely amount in a range of possible consideration amounts. Whichever method used should be consistently applied throughout the life of the contract; however, it is not necessary for the Company to use the same approach for all contracts. The Company expects to use the most likely amount method for development and regulatory milestone payments. If it is probable that a significant revenue reversal would not occur, the associated milestone value is included in the transaction price. Milestone payments that are not within the control of the Company or the licensee, such as regulatory approvals, are not considered 89 Table of Contents probable of being achieved until those approvals are received. If there is more than one performance obligation, the transaction price is then allocated to each performance obligation on a relative stand-alone selling price basis. The Company recognizes revenue as or when the performance obligations under the contract are satisfied. At the end of each subsequent reporting period, the Company re-evaluates the probability or achievement of each such milestone and any related constraint, and if necessary, adjusts its estimates of the overall transaction price. Any such adjustments are recorded on a cumulative catch-up basis, which would affect revenues and earnings in the period of adjustment. Any potential milestone payments that the Company determines are not associated with performance obligations as defined under the contract are excluded from the transaction price and are recognized as the triggering event occurs. Royalties: For arrangements that include sales-based royalties, including milestone payments based on the level of sales, where the license is deemed to be the predominant item to which the royalties relate, the Company recognizes revenue at the later of (i) when the related sales occur, or (ii) when the performance obligation to which some or all of the royalty has been allocated has been satisfied (or partially satisfied). Upfront payments and fees are recorded as deferred revenue upon receipt or when due and may require deferral of revenue recognition to a future period until the Company performs its obligations under these arrangements. Amounts payable to the Company are recorded as accounts receivable when the Company’s right to consideration is unconditional. Amounts payable to the Company and not yet billed to the collaboration partner are recorded as contract assets. The Company does not assess whether a contract has a significant financing component if the expectation at contract inception is such that the period between payment by the customer and the transfer of the promised goods or services to the customer will be one year or less. Contractual cost sharing payments made to a customer or collaboration partner are accounted for as a reduction to the transaction price if such payments are not related to distinct goods or services received from the customer or collaboration partner. Contracts may be amended to account for changes in contract specifications and requirements. Contract modifications exist when the amendment either creates new, or changes existing, enforceable rights and obligations. When contract modifications create new performance obligations and the increase in consideration approximates the standalone selling price for goods and services related to such new performance obligations, as adjusted for specific facts and circumstances of the contract, the modification is considered to be a separate contract. If a contract modification is not accounted for as a separate contract, the Company accounts for the promised goods or services not yet transferred at the date of the contract modification (the remaining promised goods or services) prospectively, as if it were a termination of the existing contract and the creation of a new contract, if the remaining goods or services are distinct from the goods or services transferred on or before the date of the contract modification. The Company accounts for a contract modification as if it were a part of the existing contract if the remaining goods or services are not distinct and, therefore, form part of a single performance obligation that is partially satisfied at the date of the contract modification. In such case the effect that the contract modification has on the transaction price, and on the entity’s measure of progress toward complete satisfaction of the performance obligation, is recognized as an adjustment to revenue (either as an increase in or a reduction of revenue) at the date of the contract modification (the adjustment to revenue is made on a cumulative catch-up basis). Research and Development Costs Research and development costs are expensed as incurred, unless there is an alternate future use in other research and development projects or otherwise. Research and development costs include salaries and benefits, stock-based compensation expense, laboratory supplies and facility-related overhead, outside contracted services, including clinical trial costs, manufacturing and process development costs for clinical and pre-clinical materials, research costs, development milestone payments under license and collaboration agreements, and other consulting services. The Company accrues for estimated costs of research and development activities conducted by third-party service providers, which include the conduct of pre-clinical and non-clinical studies, clinical trials and contract manufacturing activities. The Company records the estimated costs of research and development activities based upon the estimated 90 Table of Contents services provided but not yet invoiced and includes these costs in accrued expenses and other payables in the consolidated balance sheets and within research and development expense in the consolidated statements of operations. The Company accrues for these costs based on various factors such as estimates of the work completed and in accordance with agreements established with its third-party service providers. As actual costs become known, the Company adjusts its accrued liabilities. The Company has not experienced any material differences between accrued liabilities and actual costs incurred. However, the status and timing of actual services performed, the number of patients enrolled, the rate of patient enrollment and the number and location of sites activated may vary from the Company’s estimate and may result in adjustments to research and development expenses in future periods. Changes in these estimates that result in material changes to the Company’s accruals could materially affect the Company’s results of operations. Research and Development Tax Incentive The Company is eligible under the AusIndustry research and development tax incentive program to obtain either a refundable tax offset or a nonrefundable tax offset from the Australian Taxation Office. The refundable cash offset is available to the Company on the basis of specific criteria with which the Company must comply. Specifically, the Company must have aggregated annual turnover of less than AUD 20.0 million and cannot be controlled by income tax exempt entities. The refundable tax offset is recognized as a reduction to research and development expense when the right to receive has been attained and funds are considered to be collectible. The Company may alternatively be eligible for a nonrefundable tax offset in years when the aggregated annual turnover exceeds AUD 20.0 million. The Company evaluates its eligibility under tax incentive programs as of each balance sheet date and makes accrual and related adjustments based on the most current and relevant data available. Unused nonrefundable tax offsets may be carried forward to future years, subject to satisfying specific criteria. Stock-based Compensation The Company has granted stock options, restricted stock units (“RSUs”) and performance share units (“PSUs”). ​ Stock-based compensation expense associated with stock options is based on the estimated grant date fair value using the Black-Scholes valuation model, which requires the use of subjective assumptions related to expected stock price volatility, option term, risk-free interest rate and dividend yield. The Company recognizes compensation expense over the vesting period of the awards that are ultimately expected to vest. ​ Stock-based compensation expense associated with RSUs is based on the fair value of the Company’s common stock on the grant date, which equals the closing market price of the Company’s common stock on the grant date. For RSUs, the Company recognizes compensation expense over the vesting period of the awards that are ultimately expected to vest. PSUs allow the recipients of such awards to earn fully vested shares of the Company’s common stock upon the achievement of pre-established performance objectives. Stock-based compensation expense associated with PSUs is based on the fair value of the Company’s common stock on the grant date, which equals the closing market price of the Company’s common stock on the grant date and is recognized when the performance objective is expected to be achieved. The Company evaluates the probability of achieving the performance criteria on a quarterly basis. The cumulative effect on current and prior periods of a change in the estimated number of PSUs expected to be earned is recognized as compensation expense or as reduction of previously recognized compensation expense in the period of the revised estimate. ​ The Company recognizes forfeitures of stock-based awards as they occur. ​ If stock-based awards are granted in contemplation of or shortly before a planned release of material nonpublic information, and such information is expected to result in a material increase in the Company’s share price, the Company considers whether an adjustment to the observable market price is required when estimating fair values. Net Income (Loss) per Share The computation of basic net income (loss) per share of common stock is based on the weighted-average number of shares of common stock outstanding during each period. The computation of diluted net income (loss) per share of 91 Table of Contents common stock is based on the weighted-average number of shares of common stock outstanding during the period plus, when their effect is dilutive, incremental shares consisting of shares subject to stock options, RSUs, PSUs, the Company’s employee stock purchase plan (“ESPP”), and warrants. In accordance with Accounting Standards Codification Topic 260, Earnings Per Share (“ASC Topic 260”), outstanding Exchange and Pre-Funded Warrants (as defined in Note 10. Stockholders’ Equity) are included in the computation of weighted-average shares of common stock, basic because the exercise price was negligible, and they were fully vested and exercisable after the original issuance date. In periods when the Company has net income, the dilutive effect of all potentially outstanding shares is computed using the treasury stock method. In periods in which the Company reports a net loss, all common stock equivalents are deemed anti-dilutive such that basic net loss per share of common stock and diluted net loss per share of common stock are equal. ​ Recently Adopted Accounting Pronouncements In August 2020, the Financial Accounting Standards Board (“FASB”) issued Accounting Standards Update No. 2020-06, Debt - Debt with Conversion and Other Options (Subtopic 470-20) and Derivatives and Hedging - Contracts in Entity’s Own Equity (Subtopic 815-40): Accounting for Convertible Instruments and Contracts in an Entity’s Own Equity (“ASU 2020-06”), which simplified accounting for convertible instruments by removing major separation models required under current GAAP. ASU 2020-06 also removed certain settlement conditions that were required for equity-linked contracts to qualify for the derivative scope exception, and it simplified the diluted earnings per share calculation in certain areas. ASU 2020-06 is effective for the Company beginning January 1, 2024. The adoption of this guidance did not have a material impact on the Company’s consolidated financial statements or related disclosures. In November 2023, the FASB issued Accounting Standards Update No. 2023-07 Segment Reporting (Topic 280) – Improvements to Reportable Segment Disclosures (“ASU 2023-07”), which requires public entities to disclose incremental segment information on an annual and interim basis. ASU 2023-07 requires all public entities, including public entities with a single reportable segment, to provide one or more measures of segment profit or loss used by the chief operating decision maker to allocate resources and assess performance. Additionally, the guidance requires disclosures of significant segment expenses and other segment items as well as incremental qualitative disclosures. ASU 2023-07 is effective for the Company for fiscal years beginning on January 1, 2024, and interim periods within fiscal years beginning on January 1, 2025. The Company currently operates as one reportable segment and the impact of the adoption of this standard was limited to certain enhanced disclosures in the consolidated financial statements. See Note 15 to these consolidated financial statements for disclosures related to the adoption of this guidance. ​ Recently Issued Accounting Pronouncements Not Yet Adopted as of December 31, 2024 In December 2023, the FASB issued Accounting Standards Update No. 2023-09 Income Taxes (Topic 740) – Improvements to Income Tax Disclosures (“ASU 2023-09”), which requires public business entities to disclose specific categories in the income tax rate reconciliation annually and provide additional information for reconciling items that meet a qualitative threshold. ASU 2023-09 also requires that entities disclose annually additional information about income taxes paid and disaggregated information for certain items. The standard can be applied prospectively or retrospectively. ASU 2023-09 is effective for the Company beginning on January 1, 2025. The Company will adopt this guidance in its 2025 Annual Report on Form 10-K but does not expect the adoption of this guidance to have a material impact on its financial position, results of operations or cashflows. ​ In November 2024, the FASB issued Accounting Standards Update No. 2024-03 Income Statement – Reporting Comprehensive Income – Expense Disaggregation Disclosures (Subtopic 220-40): Disaggregation of Income Statement Expenses (“ASU 2024-03”), which requires detailed disclosures about specified categories of expenses (including employee compensation, depreciation, and amortization) included in certain expense captions presented on the face of the income statement. ASU 2024-03 is effective for the Company or fiscal years beginning on January 1, 2027, and for interim periods within fiscal years beginning on January 1, 2028. Early adoption is permitted. The guidance may be applied either (1) prospectively to financial statements issued for reporting periods after the effective date of ASU 2024-03 or (2) retrospectively to all prior periods presented in the financial statements. The Company does not expect the adoption of this guidance to have a material effect on its consolidated financial statements and continues to evaluate disclosure presentation alternatives. 92 Table of Contents ​ Note 3. License and Collaboration Agreements Takeda Collaboration Agreement In January 2024, the Company entered into the Takeda Collaboration Agreement, which became effective in March 2024. Pursuant to the Takeda Collaboration Agreement, the Company and Takeda are jointly developing and commercializing rusfertide and potentially other specified second-generation injectable hepcidin mimetic compounds (the “Licensed Products”) in the United States (the “Profit-Share Territory”). Takeda is solely and exclusively responsible for the development and commercialization of the Licensed Products in all other countries (the “Takeda Territory”). The Company and Takeda share the costs of the development, manufacture and commercialization activities for the Licensed Products in the Profit-Share Territory, provided that (i) the Company leads, and is solely responsible for its costs associated with, completion of the ongoing Phase 3 VERIFY program evaluating rusfertide for the treatment of PV as well as associated U.S. regulatory activities; (ii) Takeda leads, and is solely responsible for its costs associated with, pre-commercialization activities related to rusfertide in the Profit-Share Territory; and (iii) Takeda leads commercialization of rusfertide in the Profit-Share Territory, with the Company holding an option to co-detail. Takeda is solely responsible for all costs for the development, manufacture and commercialization of the Licensed Products in the Takeda Territory. The Company granted Takeda a non-transferable, sublicensable and, except for certain specified exceptions, exclusive license to certain intellectual property of the Company to exercise its rights and perform its obligations under the Takeda Collaboration Agreement. ​ The Company received a one-time, non-refundable upfront payment of $ 300.0 million in April 2024. In addition, the Company is eligible to receive additional worldwide development, regulatory and commercial milestone payments for rusfertide of up to $ 330.0 million, and tiered royalties from 10 % to 17 % on net sales of the Licensed Products in the Takeda Territory. The Company and Takeda also share equally in profits and losses ( 50 % to the Company and 50 % to Takeda) for Licensed Products in the Profit-Share Territory. Takeda will book sales of the Licensed Products globally. ​ The Company has the right to opt-out entirely of profit- and loss-sharing in the Profit-Share Territory for rusfertide and all other Licensed Products (the “Full Opt-out Right”) (i) during the 90-day period beginning 120 days after the filing of an NDA with the FDA for rusfertide for PV (the “Initial Opt-out Period”); and (ii) for convenience without receipt of the Opt-out Payment (as defined below) (generally following the Initial Opt-out Period). In addition, if the Company does not exercise the Full Opt-out Right, the Company may opt-out of any Licensed Product other than rusfertide on a Licensed Product-by-Licensed Product basis (each, a “Partial Opt-out Right” and either the Full Opt-out Right or a Partial Opt-out right being an “Opt-out Right”). Following the Company’s exercise of an Opt-out Right, the Company has agreed to transition applicable development and commercial activities to Takeda, and Takeda has agreed to assume sole operational and financial responsibility for such activities in the United States. The Takeda Collaboration Agreement provides for aggregate development, regulatory and commercial milestone payments from Takeda to the Company for rusfertide of up to $ 975 million if the Company exercises the Full Opt-out Right. In addition to these milestone payments, in the event the Company exercises the Full Opt-out Right during the Initial Opt-out Period, the Company will receive: (i) a $ 200 million payment following its exercise of the Full Opt-out Right; and (ii) an additional $ 200 million payment following FDA approval of the NDA for rusfertide for PV (together, the “Opt-out Payment”). If the Company exercises an Opt-out Right, Takeda has agreed to pay the Company royalties of 14 % to 29 % on worldwide net sales of the Licensed Products with respect to which the Company has exercised an Opt-out Right. Upcoming potential development and regulatory milestones under the Takeda Collaboration Agreement include: ● $ 25.0 million upon successful achievement of the primary endpoint in the Phase 3 VERIFY clinical trial for rusfertide in PV; and ● $ 50.0 million upon FDA approval of an NDA for rusfertide in PV (or $ 75.0 million if the Company exercises the Full Opt-out Right). 93 Table of Contents The Company evaluated the Takeda Collaboration Agreement and concluded that it has elements that are within the scope of ASC Topic 606 and ASC Topic 808. As of the effective date of the Takeda Collaboration Agreement, the Company identified two distinct performance obligations: (i) the rusfertide license delivered upon the effectiveness of the Takeda Collaboration Agreement and (ii) certain development services to be provided prior to the Initial Opt-out Period, including the Company’s responsibilities to complete the VERIFY Phase 3 clinical trial in PV and to file an NDA with the FDA upon successful completion of the VERIFY trial and associated manufacturing services. The Company determined that the initial transaction price totaled $ 300.0 million, comprised of the upfront payment. The Company has excluded any future estimated milestones or royalties from this transaction price to date, all of which are either currently constrained or subject to the sales-and usage-based royalty exception. As part of the Company’s evaluation of this variable consideration constraint, it determined that the potential payments are contingent upon developmental and regulatory milestones that are uncertain and are highly susceptible to factors outside of its control. The Company allocated $ 254.1 million of the initial transaction price to the license and $ 45.9 million to the development services based upon the relative standalone selling price of each performance obligation. The estimate of standalone selling price for the license was determined based on discounted cash flows for the expected development and commercialization of rusfertide and includes assumptions for forecasted revenues, development timelines and expenses, discount rates, and probabilities of technical and regulatory success. The estimate of standalone selling price for the development services was determined based on forecasted costs and expenses over the expected development period. For the license of rusfertide, the Company determined that Takeda could benefit from the license at the time the license was granted and therefore, the related performance obligation was satisfied at a point in time. ​ The amount allocated to the license, which represents functional intellectual property that was transferred at a point in time, was satisfied upon transfer of the license to Takeda. The amount allocated to development services will be recognized over time based on a measure of the Company’s efforts toward satisfying the performance obligation relative to the total expected efforts or inputs to satisfy the performance obligation (e.g., costs incurred compared to total budget). The Company recognized $ 15.3 million of revenue allocated to development services with respect to the period from the effective date of the contract through December 31, 2024. ​ The Company determined that the Takeda Collaboration Agreement met the definition of a collaborative arrangement under ASC Topic 808. Both parties are active participants in directing and carrying out the development of the Licensed Products and both are exposed to the significant risk and rewards related to the commercial success of the Products. If the Company does not exercise an Opt-out Right (“Company Opt-in”), the Company and Takeda would co-detail the Licensed Products in the U.S. and share in the economic results through a profit-sharing structure. The Company determined that development costs subsequent to the Company Opt-in date are within the scope of ASC Topic 808, which does not provide recognition and measurement guidance. As such, the Company determined that Accounting Standards Codification Topic 730, “ Research and Development” was appropriate to analogize to based on the cost-sharing provisions of the agreement. The Company concluded that payments to or reimbursements from Takeda related to these services will be accounted for as an increase to or reduction of research and development expense, respectively. ​ JNJ License and Collaboration Agreement ​ On July 27, 2021, the Company entered into an Amended and Restated License and Collaboration Agreement with JNJ, formerly Janssen Biotech, Inc., which amended and restated the License and Collaboration Agreement, effective July 13, 2017, by and between the Company and JNJ, as amended effective May 7, 2019 and November 14, 2024 (together, the “JNJ License and Collaboration Agreement”). Prior to January 1, 2023, JNJ was a related party to us as Johnson & Johnson Innovation - JJDC, Inc. was a significant (greater than 5%) stockholder of the Company, and both companies are subsidiaries of Johnson & Johnson. The JNJ License and Collaboration Agreement relates to the development, manufacture and commercialization of oral IL-23 receptor antagonist drug candidates and enables JNJ to develop collaboration compounds for multiple indications. Under the JNJ License and Collaboration Agreement, JNJ is required to use commercially reasonable efforts to develop at least one collaboration compound for at least two indications. ​ During the fourth quarter of 2023, the Company earned a $ 50.0 million milestone payment in connection with the dosing of the third patient in the ICONIC-TOTAL Phase 3 clinical trial of icotrokinra (formerly JNJ-2113) in patients with moderate-to-severe psoriasis and a $ 10.0 million milestone payment upon the dosing of the third patient in the 94 Table of Contents ANTHEM Phase 2b trial moderately-to-severely active UC. The JNJ License and Collaboration Agreement was further amended in November 2024 to: ● increase the milestone payment for a Phase 3 clinical trial of any licensed product for any indication meeting its primary endpoint by $ 50.0 million, from $ 115.0 million to $ 165.0 million; ● eliminate the $ 35.0 million milestone payment previously due for the acceptance of an NDA filing by the FDA for use of a licensed product for any indication; and ● eliminate the $ 15.0 million milestone payment previously due for the dosing of the third patient in the first Phase 3 clinical trial of a licensed product for a second indication. The Company earned the $ 165.0 million milestone payment described above during the fourth quarter of 2024. The Company has earned a total of $ 337.5 million in non-refundable payments from JNJ from inception in 2017 through December 31, 2024. Upcoming potential development and regulatory milestones include: ● $ 50.0 million upon FDA approval of an NDA in any indication; ● $ 25.0 million upon the acceptance of an NDA filing by the FDA for a second indication; and ● $ 45.0 million upon FDA approval of an NDA for a second indication. Pursuant to the agreement, the Company is eligible to receive future sales milestone payments and tiered royalties on net product sales at percentages ranging from 6 % to 10 %. Revenue Recognition For the year ended December 31, 2024, the Company recognized $ 434.4 million of license and collaboration revenue. This was comprised of $ 269.4 million related to the Takeda Collaboration Agreement, including (i) $ 254.1 million allocated to the rusfertide license delivered to Takeda upon the effectiveness of the agreement in March 2024 and (ii) $ 15.3 million for development services provided by the Company during the period based on the cost-based input method, and $ 165.0 million related to the JNJ License and Collaboration Agreement, as described above. For the year ended December 31, 2023, the Company recognized $ 60.0 million of collaboration revenue related to the JNJ License and Collaboration Agreement , which included a $ 50.0 million milestone payment earned in October 2023 in connection with the dosing of the third patient in the ICONIC-TOTAL Phase 3 trial of icotrokinra in patients with moderate-to-severe psoriasis, and a $ 10.0 million milestone payment earned in December 2023 upon the dosing of the third patient in the ANTHEM Phase 2b trial for patients with UC. For the year ended December 31, 2022, the Company recognized $ 26.6 million of collaboration revenue related to the JNJ License and Collaboration Agreement, which was primarily related to the transaction price under the Restated Agreement recognized based on proportional performance. The Company completed its performance obligation under the collaboration as of June 30, 2022. During the years ended December 31, 2024 and 2023, no revenue was recognized from amounts included in the deferred revenue balance at the beginning of the year. During the year ended December 31, 2022, the Company recognized revenue of $ 0.9 million from amounts included in the deferred revenue balance at the beginning of the year. None of the costs to obtain or fulfill the contracts were capitalized. The remaining unrecognized transaction price amount of $ 30.6 million related to the Takeda Collaboration Agreement was recorded as deferred revenue on the Company’s consolidated balance sheet as of December 31, 2024 and will be recognized over time based on a measure of the Company’s efforts toward satisfying the performance obligation relative to the total expected efforts or inputs to satisfy the performance obligation (e.g. costs incurred compared to total budget). 95 Table of Contents Note 4. Fair Value Measurements Financial assets and liabilities are recorded at fair value. The accounting guidance for fair value provides a framework for measuring fair value, clarifies the definition of fair value and expands disclosures regarding fair value measurements. Fair value is defined as the price that would be received to sell an asset or paid to transfer a liability (an exit price) in an orderly transaction between market participants at the reporting date. The accounting guidance establishes a three-tiered hierarchy, which prioritizes the inputs used in the valuation methodologies in measuring fair value as follows: Level 1 —Inputs are unadjusted quoted prices in active markets for identical assets or liabilities at the measurement date. Level 2— Inputs (other than quoted market prices included in Level 1) are either directly or indirectly observable for the asset or liability through correlation with market data at the measurement date and for the duration of the instrument’s anticipated life. Level 3 —Inputs reflect management’s best estimate of what market participants would use in pricing the asset or liability at the measurement date. Consideration is given to the risk inherent in the valuation technique and the risk inherent in the inputs to the model. In determining fair value, the Company utilizes quoted market prices, broker or dealer quotations, or valuation techniques that maximize the use of observable inputs and minimize the use of unobservable inputs to the extent possible and considers counterparty credit risk in its assessment of fair value. The following tables present the fair value of the Company’s financial assets determined using the inputs defined above (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, 2024 ​ Level 1 Level 2 Level 3 Total Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Money market funds ​ $ 19,563 ​ $ — ​ $ — $ 19,563 Certificates of deposit ​ — ​ ​ 15,835 ​ — 15,835 U.S. Treasury and agency securities ​ ​ — ​ ​ 299,217 ​ ​ — ​ ​ 299,217 Commercial paper ​ — ​ ​ 110,832 ​ — 110,832 Corporate debt securities ​ ​ — ​ ​ 102,705 ​ ​ — ​ ​ 102,705 Total financial assets ​ $ 19,563 ​ $ 528,589 $ — $ 548,152 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, 2023 ​ Level 1 Level 2 Level 3 Total Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Money market funds ​ $ 19,212 ​ $ — ​ $ — $ 19,212 Certificates of deposit ​ — ​ ​ 13,004 ​ — 13,004 U.S. Treasury and agency securities ​ ​ — ​ ​ 145,085 ​ ​ — ​ ​ 145,085 Commercial paper ​ — ​ 130,296 ​ — 130,296 Corporate debt securities ​ — ​ 7,672 — 7,672 Total financial assets ​ $ 19,212 ​ $ 296,057 $ — $ 315,269 ​ The Company’s certificates of deposit, U.S. Treasury and agency securities, including U.S. Treasury bills, commercial paper, and corporate debt securities are classified as Level 2 as they were valued based upon quoted market prices for similar instruments in active markets, quoted prices for identical or similar instruments in markets that are not active and model-based valuation techniques, for which all significant inputs are observable in the market or can be corroborated by observable market data for substantially the full term of the assets. 96 Table of Contents The carrying amount of the Company’s remaining financial assets and liabilities, including cash, receivables and payables, approximates their fair value due to their short-term nature. Note 5. Cash Equivalents and Marketable Securities Cash equivalents and marketable securities consisted of the following (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, 2024 ​ ​ Amortized ​ Gross Unrealized ​ ​ Cost Gains Losses Fair Value Money market funds ​ $ 19,563 ​ $ — ​ $ — ​ $ 19,563 Certificates of deposit ​ ​ 15,820 ​ ​ 22 ​ ( 7 ) ​ 15,835 U.S. Treasury and agency securities ​ ​ 299,211 ​ ​ 429 ​ ​ ( 423 ) ​ ​ 299,217 Commercial paper ​ 110,815 ​ ​ 28 ​ ​ ( 11 ) ​ 110,832 Corporate debt securities ​ ​ 102,714 ​ ​ 103 ​ ​ ( 112 ) ​ ​ 102,705 Total cash equivalents and marketable securities ​ $ 548,123 ​ $ 582 $ ( 553 ) ​ $ 548,152 Classified as: ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash equivalents ​ ​ ​ ​ ​ ​ ​ $ 86,236 Marketable securities - current ​ ​ ​ ​ ​ ​ ​ 321,664 Marketable securities - noncurrent ​ ​ ​ ​ ​ ​ ​ 140,252 Total cash equivalents and marketable securities ​ ​ ​ ​ ​ ​ ​ $ 548,152 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, 2023 ​ ​ Amortized ​ Gross Unrealized ​ ​ Cost Gains Losses Fair Value Money market funds ​ $ 19,212 ​ $ — $ — ​ $ 19,212 Certificates of deposit ​ ​ 12,998 ​ ​ 6 ​ ​ — ​ 13,004 U.S. Treasury and agency securities ​ ​ 145,024 ​ ​ 63 ​ ​ ( 2 ) ​ ​ 145,085 Commercial paper ​ 130,351 ​ 5 ( 60 ) ​ 130,296 Corporate debt securities ​ ​ 7,678 ​ — ( 6 ) ​ 7,672 Total cash equivalents and marketable securities ​ $ 315,263 ​ $ 74 $ ( 68 ) ​ $ 315,269 Classified as: ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash equivalents ​ ​ ​ ​ ​ ​ ​ $ 160,379 Marketable securities - current ​ ​ ​ ​ ​ ​ ​ 154,890 Total cash equivalents and marketable securities ​ ​ ​ ​ ​ ​ ​ $ 315,269 ​ All of the Company’s marketable securities are classified as available-for-sale. Current marketable securities of $ 321.7 million and $ 154.9 million held as of December 31, 2024 and 2023, respectively, had contractual maturities of less than one year. Noncurrent marketable securities of $ 140.3 million held as of December 31, 2024 had contractual maturities of at least one year but no more than two years . The Company does not intend to sell its securities that are in an unrealized loss position, and it is not more likely than not that the Company will be required to sell its securities before recovery of their amortized cost basis, which may be at maturity. There were no material realized gains or realized losses on marketable securities for the periods presented. The Company evaluated securities with unrealized losses to determine whether such losses, if any, were due to credit-related factors and determined that there were no credit-related losses to be recognized as of December 31, 2024 and 2023. ​ 97 Table of Contents Note 6. Balance Sheet Components Prepaid Expenses and Other Current Assets Prepaid expenses and other current assets consisted of the following (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ ​ 2024 ​ 2023 Accrued interest receivable ​ $ 3,242 ​ $ 256 Prepaid clinical and research related expenses ​ ​ 1,830 ​ ​ 649 Prepaid insurance ​ ​ 1,159 ​ ​ 1,410 Prepaid licenses ​ ​ 600 ​ ​ 529 Other prepaid expenses ​ 649 ​ 1,040 Other receivable ​ ​ 248 ​ ​ 76 Prepaid expenses and other current assets ​ $ 7,728 ​ $ 3,960 ​ Property and Equipment, Net Property and equipment, net consisted of the following (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ ​ 2024 ​ 2023 Laboratory equipment ​ $ 6,354 ​ $ 5,323 Furniture and computer equipment ​ 1,447 ​ 1,143 Leasehold improvements ​ 2,424 ​ 963 Total property and equipment ​ 10,225 ​ 7,429 Accumulated depreciation ​ ( 7,035 ) ​ ( 6,234 ) Property and equipment, net ​ $ 3,190 ​ $ 1,195 ​ Depreciation expense for the years ended December 31, 2024, 2023 and 2022, was $ 894,000 , $ 977,000 and $ 1,032,000 , respectively. As of December 31, 2024, 2023 and 2022, $ 47,000 , $ 56,000 and $ 156,000 , respectively, of the Company’s property and equipment, net, was located in Australia. The remainder of the Company’s property and equipment, net was located in the United States. Accrued Expenses and Other Payables Accrued expenses and other payables consisted of the following (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ 2024 ​ 2023 Accrued clinical and research related expenses ​ $ 11,923 ​ $ 11,841 Accrued employee related expenses ​ 11,078 ​ 6,786 Accrued professional service fees ​ ​ 618 ​ ​ 632 Other ​ 74 ​ 99 Total accrued expenses and other payables ​ $ 23,693 ​ $ 19,358 ​ ​ ​ Note 7. Research Collaboration and License Agreement Pursuant to a collaboration agreement between the Company and Zealand Pharma A/S (“Zealand”) entered into in June 2012 and a related arbitration resolution agreement entered into in August 2021, the Company is obligated to pay Zealand certain milestone and royalty payments for rusfertide. The potential future payments include: (i) up to $ 2.75 million in future development milestone payments; (ii) a low single digit royalty on worldwide net sales; and (iii) sales milestones for achievement of annual net sales amounts in specified geographies. 98 Table of Contents See Note 9. Commitments and Contingencies – Legal Proceedings for additional information on the results of arbitration proceedings related to this research and collaboration agreement. Milestone payments to collaboration partners are recorded as research and development expense in the period that the expense is incurred. No expense was recorded under this agreement for the years ended December 31, 2024, 2023 or 2022. Note 8. Lease The Company applies ASC Topic 842 to recognize assets and liabilities for leases with lease terms of more than 12 months on the balance sheet. The Company has elected to account for each separate lease component and non-lease component as one single component for all lease assets. Leases with terms of 12 months or less are not recorded on the balance sheet, and the related lease expenses are recognized on a straight-line basis over the lease term. ​ The Company has one operating lease agreement originally entered into in March 2017 for approximately 42,900 square feet for laboratory and office space located in Newark, California. In July 2021, the Company entered into a second amendment to its original facility lease agreement, as amended, for 15,000 square feet of additional office space in Newark, California. ​ On May 6, 2024, the Company amended its facility lease agreement (the “Amended Lease”) to extend the lease term for its existing office and laboratory space from one to 66 months and lease approximately 17,700 rentable square feet of additional office space, all located in Newark, California. The Company began occupying the additional space under the Amended Lease on July 1, 2024. The Amended Lease, which expires in November 2029, provides for an agreed-upon period of rent abatement and a tenant improvement allowance of $ 1.8 million. As a result of this amendment, the Company recorded an additional right-of-use-asset and the related liability of $ 10.5 million. ​ The Company provided the landlord with a $ 225,000 letter of credit collateralized by restricted cash as security deposit for the operating lease agreement. No additional security deposit was required pursuant to the Amended Lease, and the Company is responsible for its proportional share of operating expenses and tax obligations. Balance sheet information related to the Company’s operating lease is as follows for the periods presented (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, Operating Lease: ​ 2024 ​ 2023 Operating lease right-of-use asset ​ $ 9,417 ​ $ 954 ​ ​ ​ ​ ​ ​ ​ Operating lease liability - current ​ $ 510 ​ $ 1,141 Operating lease liability - noncurrent ​ ​ 10,356 ​ ​ — Total operating lease liabilities ​ $ 10,866 ​ $ 1,141 ​ ​ ​ ​ ​ ​ ​ Weighted-average remaining lease term (years) ​ ​ 4.9 ​ ​ 0.4 Weighted-average discount rate ​ ​ 5.7 % ​ ​ 10.4 % ​ Other information related to the Company’s operating lease is as follows for the periods presented (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ 2024 ​ 2023 ​ 2022 Operating lease cost ​ $ 2,459 ​ $ 2,335 ​ $ 2,335 Short-term rent expense ​ ​ 51 ​ ​ — ​ ​ — Less: Sublease income ​ ​ ( 34 ) ​ ​ ( 137 ) ​ ​ ( 123 ) Total lease expense ​ $ 2,476 ​ $ 2,198 ​ $ 2,212 ​ 99 Table of Contents Supplemental cash flow information is as follows for the periods presented (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ 2024 ​ 2023 ​ 2022 Operating cash flow used by operating leases ​ $ 2,226 ​ $ 2,743 ​ $ 2,661 New operating lease asset obtained in exchange for operating lease liability ​ $ 10,511 ​ $ — ​ $ — ​ Future lease payments required under lease obligations as of December 31, 2024 are as follows (in thousands): ​ ​ ​ ​ Year Ending December 31: Amount 2025 ​ $ 1,159 2026 ​ ​ 2,786 2027 ​ ​ 2,882 2028 ​ ​ 2,983 Thereafter ​ 2,825 Total future minimum lease payments ​ ​ 12,635 Less: Imputed interest ​ ​ ( 1,769 ) Present value of lease liabilities ​ $ 10,866 ​ ​ Note 9. Commitments and Contingencies Contract Service Providers In the normal course of business, the Company enters into agreements with contract service providers to assist in the performance of its research and development activities and clinical and commercial manufacturing activities. Subject to the required notice periods and the Company’s obligations under binding purchase orders, the Company can elect to discontinue the work under these agreements at any time. However, the financial terms of some of these agreements may include non-refundable upfront payments, payments by the Company for options to acquire certain rights, contingent obligations by the Company for potential development and regulatory milestone payments and/or sales-based milestone payments and royalty payments. These obligations are recorded in the Company’s consolidated statements of operations as incurred, which is generally when the corresponding events become probable. Certain payments are contingent upon the occurrence of various future events that have a high degree of uncertainty. The Company expects to enter into additional clinical development, contract research, clinical and commercial manufacturing, supplier and collaborative research agreements in the future, which may require upfront payments and long-term commitments of capital resources. Indemnification Agreements In the ordinary course of business, the Company enters into agreements that may include indemnification provisions. Pursuant to such agreements, the Company may indemnify, hold harmless and defend an indemnified party for losses suffered or incurred by the indemnified party. Some of the provisions will limit losses to those arising from third-party actions. In some cases, the indemnification will continue after the termination of the agreement. The maximum potential amount of future payments the Company could be required to make under these provisions is not determinable. The Company has also entered into indemnification agreements with its directors and officers that may require the Company to indemnify its directors and officers against liabilities that may arise by reason of their status or service as directors or officers to the fullest extent permitted by law. The Company carries a directors’ and officers’ insurance policy. To date, the Company has not incurred material costs to defend lawsuits or settle claims related to the indemnification agreements. The Company believes that the fair value of these indemnification agreements is minimal and has not accrued any amounts for the obligations. Legal Proceedings The Company recognizes accruals for legal actions to the extent that it concludes that a loss is both probable and reasonably estimable. The Company accrues for the best estimate of a loss within a range; however, if no estimate in the 100 Table of Contents range is better than any other, it accrues the minimum amount in the range. If the Company determines that a loss is reasonably possible and the loss or range of loss can be estimated, it discloses the possible loss. In January 2020, the Company initiated arbitration proceedings with the International Court of Arbitration of the International Chamber of Commerce against Zealand related to a collaboration agreement the Company and Zealand entered into in 2012 and terminated in 2014. The agreement provides for certain post-termination payment obligations to Zealand with respect to compounds related to the collaboration that the Company elects to further develop and meet specified conditions. In August 2021, the Company and Zealand agreed to resolve the dispute and reached an Arbitration Resolution Agreement. Under the Arbitration Resolution Agreement, the Company recognized $ 4.0 million in development milestone payments to Zealand in the third quarter of 2021 and is obligated to pay Zealand certain milestone and royalty payments for rusfertide. The potential future payments include (i) up to $ 2.75 million in future development milestone payments, (ii) a low single digit royalty on worldwide net sales, and (iii) sales milestones for achievement of annual net sales amounts in specific geographies. The Company considered the outcome of these arbitration proceedings as being related to its research and development projects; therefore, payments or milestone payments were recorded as research and development expenses. Note 10. Stockholders’ Equity Shares of Common Stock Authorized for Issuance At the Company’s 2024 Annual Meeting of Stockholders held on June 20, 2024, the Company’s stockholders approved an amendment to the Company’s Amended and Restated Certificate of Incorporation (the “Certificate of Incorporation”) to increase the number of authorized shares of the Company’s common stock from 90,000,000 to 180,000,000 , which also has the effect of increasing the total number of authorized shares from 100,000,000 to 190,000,000 (the “Amendment”). On June 21, 2024, the Company filed a Certificate of Amendment to the Certificate of Incorporation with the Secretary of State of the State of Delaware to effect the Amendment, which became effective immediately upon such filing. Public Offering In April 2023, the Company completed an underwritten public offering of 5,000,000 shares of its common stock at a public offering price of $ 20.00 per share and issued an additional 750,000 shares of common stock at a price of $ 20.00 per share following the underwriters’ exercise of their option to purchase additional shares. Net proceeds, after deducting underwriting commissions and offering costs paid by the Company, were $ 107.8 million. ​ ATM Offering In August 2022, the Company entered into an Open Market Sale Agreement SM , pursuant to which the Company may offer and sell up to $ 100.0 million shares of its common stock from time to time in “at-the-market” offerings (the “2022 ATM Facility”). During the year ended December 31, 2023, the Company sold 1,749,199 shares of its common stock under the 2022 ATM Facility for net proceeds of $ 24.3 million, after deducting issuance costs. There were no sales of the Company’s common stock under the 2022 ATM Facility during the years ended December 31, 2024 and 2022. ​ Exchange Warrants In December 2018, the Company entered into an exchange agreement (the “Exchange Agreement”) with an investor and its affiliates (the “Exchanging Stockholders”), pursuant to which the Company exchanged an aggregate of 1,000,000 shares of the Company’s common stock, par value $ 0.00001 per share, owned by the Exchanging Stockholders for pre-funded warrants (the “Exchange Warrants”) to purchase an aggregate of 1,000,000 shares of common stock (subject to adjustment in the event of any stock dividends and splits, reverse stock split, recapitalization, reorganization or similar transaction, as described in the Exchange Warrants), with an exercise price of $ 0.00001 per share. The Exchange Warrants expired ten years from the date of issuance. The Exchange Warrants were exercisable at any time prior to expiration except that the Exchange Warrants could not be exercised by the Exchanging Stockholders if, after giving 101 Table of Contents effect thereto, the Exchanging Stockholders would beneficially own more than 9.99 % of the Company’s common stock, subject to certain exceptions. In accordance with Accounting Standards Codification Topic 505, Equity , the Company recorded the retirement of the common stock exchanged as a reduction of common stock shares outstanding and a corresponding debit to additional paid-in-capital at the fair value of the Exchange Warrants on the issuance date. The Exchange Warrants met the criteria for equity classification and the fair value of the Exchange Warrants was recorded as a credit to additional paid-in capital and was not subject to remeasurement. The Company determined that the fair value of the Exchange Warrants was substantially similar to the fair value of the retired shares on the issuance date due to the negligible exercise price for the Exchange Warrants. During the year ended December 31, 2022, the remaining Exchange Warrants to purchase 400,000 shares of the Company’s common stock were net exercised, resulting in the issuance of 399,997 shares of common stock. As of December 31, 2024, there were no outstanding Exchange Warrants. Pre-Funded Warrants In August 2018, the Company entered into a Securities Purchase Agreement with certain accredited investors (each, an “Investor” and, collectively, the “Investors”), pursuant to which the Company sold an aggregate of 2,750,000 shares of its common stock at a price of $ 8.00 per share for aggregate net proceeds of $ 21.7 million, after deducting offering expenses payable by the Company. In a concurrent private placement, the Company issued the Investors warrants to purchase an aggregate of 2,750,000 shares of its common stock (each, a “Warrant” and, collectively, the “Warrants”). Each Warrant was exercisable from August 8, 2018 through August 8, 2023 . Warrants to purchase 1,375,000 shares of the Company’s common stock had an exercise price of $ 10.00 per share and Warrants to purchase 1,375,000 shares of the Company’s common stock had an exercise price of $ 15.00 per share. In August 2023, prior to the expiration of the Warrants, the Company entered into certain agreements with the Investors and their affiliates under which the Company agreed to allow the Warrants to be exercised in exchange for pre-funded warrants representing the same number of Warrant Shares underlying the Warrants with an exercise price of $ 0.001 per share (the “Pre-Funded Warrants”). Subsequent to the execution of the agreements and prior to the expiration of the Warrants, all outstanding Warrants were exercised for gross proceeds of $ 34.4 million in exchange for 44,748 shares of the Company’s common stock and Pre-Funded Warrants to purchase 2,705,252 shares of common stock (subject to adjustment in the event of any stock dividends and splits, reverse stock split, recapitalization, reorganization or similar transaction, as described in the Pre-Funded Warrants) with an exercise price of $ 0.001 per share. The Pre-Funded Warrants will expire upon the day they are exercised in full. The Pre-Funded Warrants are exercisable at any time prior to expiration except that the Pre-Funded Warrants cannot be exercised by the Investors if, after giving effect thereto, the Investors would beneficially own more than 9.99 % of the Company’s common stock, subject to certain exceptions. The common stock and Pre-Funded Warrants met the criteria for equity classification and the net proceeds from the transaction were recorded as a credit to additional paid-in capital. In accordance with ASC Topic 260, outstanding Pre-Funded Warrants are included in the computation of basic net loss per share because the exercise price is negligible, and they are fully vested and exercisable after the original issuance date. During the year ended December 31, 2024, Pre-Funded Warrants to purchase 1,205,252 shares were net exercised, resulting in the issuance of 1,205,225 shares of common stock. As of December 31, 2024, Pre-Funded Warrants to purchase 1,500,000 shares of common stock remained outstanding. 102 Table of Contents Note 11. Equity Plans Equity Incentive Plan In May 2007, the Company established the 2007 Stock Option and Incentive Plan (“2007 Plan”) which provided for the granting of stock options to employees and consultants of the Company. Options granted under the 2007 Plan were either incentive stock options (“ISOs”) or nonqualified stock options (“NSOs”). ISOs were granted only to Company employees. NSOs were granted to Company employees, non-employee members of the Company’s Board of Directors (“Board”) and consultants. Options under the 2007 Plan have a term of ten years and generally vested over a four-year period. In July 2016, the Company’s Board and stockholders approved the 2016 Equity Incentive Plan (“2016 Plan”) to replace the 2007 Plan. Under the 2016 Plan, 1,200,000 shares of the Company’s common stock were initially reserved for the issuance of stock options, restricted stock units and other awards to employees, directors and consultants. Pursuant to the “evergreen” provision contained in the 2016 Plan, the number of shares reserved for issuance under the 2016 Plan automatically increases on January 1 of each year, starting on January 1, 2017 and continuing through (and including) January 1, 2026, by 4 % of the total number of shares of the Company’s capital stock outstanding on December 31 of the preceding fiscal year, or a lesser number of shares determined by the Company’s Board. Upon adoption of the 2016 Plan, no additional stock awards were issued under the 2007 Plan. Options granted under the 2007 Plan that were outstanding on the date the 2016 Plan became effective remain subject to the terms of the 2007 Plan. The number of options available for grant under the 2007 Plan was ceased and the number was added to the common stock reserved for issuance under the 2016 Plan. As of December 31, 2024, approximately 1,109,629 shares of common stock were available for issuance under the 2016 Plan. The 2016 Plan is administered by the Board, or a committee appointed by the Board, which determines the types of awards to be granted, including the number of shares subject to the awards, the exercise price and the vesting schedule. Options granted under the 2016 Plan expire no later than ten years from the date of grant. The exercise price of each option may not be less than 100 % of the fair market value of the common stock at the date of grant. Options may be granted to stockholders possessing more than 10 % of the total combined voting power of all classes of stocks of the Company at an exercise price at least 110 % of the fair value of the common stock at the date of grant and the options are not exercisable after the expiration of 10 years from the date of grant. Employee stock options generally vest over a period of approximately four years . Employee RSUs generally vest over a period of approximately three or four years . Non-employee Board director initial stock options generally vest monthly over a period of approximately three years . Non-employee Board director annual refresher options and RSUs generally vest over a period of approximately one year . Inducement Plan In May 2018, the Company’s Board approved the 2018 Inducement Plan, as subsequently amended. The 2018 Inducement Plan is a non-stockholder approved stock plan, under which awards options and restricted stock unit awards to persons that were not previously employees or directors of the Company, or following a bona fide period of non-employment, as an inducement material to such persons entering into employment with the Company, within the meaning of Rule 5635(c)(4) of the Nasdaq Listing Rules. The 2018 Inducement Plan is administered by the Board or the Compensation Committee of the Board, which determines the types of awards to be granted, including the number of shares subject to the awards, the exercise price and the vesting schedule. Awards granted under the 2018 Inducement Plan expire no later than ten years from the date of grant. Employee stock options granted under the 2018 Inducement Plan generally vest over a period of approximately four years . As of December 31, 2024, approximately 645,858 shares of common stock were available for issuance under the 2018 Inducement Plan, as amended. 103 Table of Contents Stock Options Stock option activity under the Company’s equity incentive and inducement plans is set forth below: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted- ​ Weighted- ​ ​ ​ ​ ​ ​ Average ​ Average ​ ​ ​ ​ ​ ​ Exercise ​ Remaining ​ Aggregate ​ ​ Options ​ Price Per ​ Contractual ​ Intrinsic ​ Outstanding Share Life (years) Value (1) ​ ​ ​ ​ ​ ​ ​ ​ (in millions) Balances at December 31, 2023 7,922,043 $ 17.21 ​ ​ ​ Options granted 2,068,570 ​ ​ 24.39 ​ ​ Options exercised ( 1,766,092 ) ​ ​ 14.33 ​ ​ ​ Options forfeited ​ ( 407,365 ) ​ ​ 27.57 ​ ​ ​ ​ ​ Balances at December 31, 2024 7,817,156 $ 19.22 ​ 6.89 ​ $ 152.9 Options exercisable – December 31, 2024 ​ 4,877,064 $ 18.60 ​ 5.96 ​ ​ 98.5 Options vested and expected to vest – December 31, 2024 ​ 7,817,156 ​ $ 19.22 6.89 ​ $ 152.9 ____________________ (1) The aggregate intrinsic values were calculated as the difference between the exercise price of the options and the closing price of the Company’s common stock on December 31, 2024. The calculation excludes options with an exercise price higher than the closing price of the Company’s common stock on December 31, 2024. The aggregate intrinsic value of options exercised was $ 40.7 million, $ 3.3 million and $ 5.4 million for the years ended December 31, 2024, 2023 and 2022, respectively. During the years ended December 31, 2024, 2023 and 2022, the estimated weighted-average grant-date fair value of common stock underlying options granted was $ 20.07 , $ 10.81 and $ 17.52 per share, respectively. For the years ended December 31, 2024, 2023 and 2022, the aggregate fair value of stock options that vested during the year was $ 30.3 million, $ 25.9 million and $ 23.3 million, respectively. Stock Options Valuation Assumptions The fair value of stock option awards was estimated at the date of grant using a Black-Scholes option-pricing model with the following assumptions: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ ​ 2024 ​ 2023 ​ 2022 Expected term (in years) 5.27 - 6.08 5.27 - 6.08 5.27 - 6.08 Expected volatility 96.6 % - 106.2 % ​ 105.7 % - 110.1 % ​ 96.3 % - 101.7 % Risk-free interest rate 3.46 % - 4.71 % ​ 3.57 % - 4.86 % ​ 1.64 % - 4.23 % Dividend yield — — — ​ In determining the fair value of the options granted, the Company uses the Black-Scholes option-pricing model and assumptions discussed below. Each of these inputs is subjective, and generally requires judgment to determine. Expected Term —The Company’s expected term represents the period that the Company’s options granted are expected to be outstanding and is determined using the simplified method (based on the mid-point between the vesting date and the end of the contractual term). The Company has limited historical exercise information to develop reasonable expectations about future exercise patterns and post-vesting employment termination behavior for its stock option grants. Expected Volatility — Beginning January 1, 2023, the Company’s expected volatility is estimated based upon the volatility of the Company’s stock price over a period equal to the expected term of the stock option grants. For the year ended December 31, 2022, the Company’s expected volatility was estimated based upon a mix of 25 % of the average 104 Table of Contents volatility for comparable publicly traded biopharmaceutical companies over a period equal to the expected term of the stock option grants and 75 % of the volatility of the Company’s stock price since its initial public offering in August 2016. Risk-Free Interest Rate —The risk-free interest rate is based on the U.S. Treasury zero coupon issues in effect at the time of grant for periods corresponding with the expected term of the option. Expected Dividend —The Company has never paid dividends on its common stock and has no plans to pay dividends on its common stock. Therefore, the Company used an expected dividend yield of zero. RSUs An RSU is an agreement to issue shares of the Company’s common stock at the time of vesting. RSUs generally vest annually in equal installments over three or four years on approximately the anniversary of the grant date. RSUs granted to certain non-executive employees in 2022 vested 100 % on approximately the first anniversary of the grant date. RSU activity under the Company’s equity incentive plans is set forth below: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted ​ ​ ​ ​ Average ​ ​ Number of ​ Grant Date ​ Shares Fair Value Unvested RSUs at December 31, 2023 ​ 664,491 ​ $ 18.40 Granted ​ 564,465 ​ ​ 23.56 Vested ​ ( 316,748 ) ​ ​ 18.93 Forfeited ​ ( 67,500 ) ​ ​ 23.31 Unvested RSUs at December 31, 2024 ​ 844,708 ​ $ 21.03 ​ Stock-based compensation expense associated with RSUs is based on the fair value of the Company’s common stock on the grant date, which equals the closing market price of the Company’s common stock on the grant date. For RSUs, the Company recognizes compensation expense over the vesting period of the awards that are ultimately expected to vest. For the years ended December 31, 2024, 2023 and 2022, the aggregate fair value of RSUs that vested during the year was $ 6.0 million, $ 5.9 million and $ 1.7 million, respectively. PSUs ​ PSU activity under the Company’s equity incentive plans is set forth below: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted ​ ​ ​ ​ Average ​ ​ Number of ​ Grant Date ​ Shares Fair Value Unvested PSUs at December 31, 2023 ​ 75,500 ​ $ 23.57 Granted — ​ ​ — Vested ​ — ​ ​ — Forfeited ​ — ​ ​ — Unvested PSUs at December 31, 2024 ​ 75,500 ​ $ 23.57 ​ The terms of the PSUs provide for 100 % of shares to be earned based on the achievement of certain pre-determined performance objectives, subject to the participant’s continued employment. The PSUs will vest, if at all, upon certification by the Compensation Committee of the Board of the actual achievement of the performance objectives, subject to specified change of control exceptions. ​ 105 Table of Contents Stock-based compensation expense associated with PSUs is based on the fair value of the Company’s common stock on the grant date, which equals the closing market price of the Company’s common stock on the grant date. The Company recognizes compensation expense over the vesting period of the awards that are ultimately expected to vest when the achievement of the related performance objective becomes probable. During the year ended December 31, 2023, the Compensation Committee of the Board certified the actual achievement of performance objectives related to certain PSUs. As a result, recipients earned a total of 114,000 shares of common stock. The total fair market value of the PSUs at vest date during the year ended December 31, 2023 was $ 3.0 million. No PSUs vested during the years ended December 31, 2024 and 2022. The total fair value of grant date fair value of unvested PSUs outstanding as of December 31, 2024 was $ 1.8 million. As of December 31, 2024, the achievement of the related performance objectives was deemed not probable and, accordingly, no stock-based compensation expense for unvested PSUs has been recognized as of December 31, 2024. Employee Stock Purchase Plan In July 2016, the Company’s Board and stockholders approved the 2016 Employee Stock Purchase Plan (“2016 ESPP”). The 2016 ESPP is intended to qualify as an employee stock purchase plan under Section 423 of the Internal Revenue Code of 1986, as amended, and is administered by the Company’s Board and the Compensation Committee of the Board. Under the 2016 ESPP, 150,000 shares of the Company’s common stock were initially reserved for employee purchases of the Company’s common stock. Pursuant to the “evergreen” provision contained in the 2016 ESPP, the number of shares reserved for issuance automatically increases on January 1 of each year, starting on January 1, 2017 and continuing through (and including) January 1, 2026 by the lesser of (i) 1 % of the total number of shares of common stock outstanding on December 31 of the preceding fiscal year (ii) 300,000 shares, or (iii) such other number of shares determined by the Board. The 2016 ESPP allows eligible employees to purchase shares of the Company’s common stock at a discount through payroll deductions of up to 15 % of their eligible compensation. At the end of each offering period, eligible employees are able to purchase shares at 85 % of the lower of the fair market value of the Company’s common stock at the beginning of the offering period or at the end of each applicable purchase period. During the year ended December 31, 2024, a total of 59,254 shares of common stock were issued under the 2016 ESPP, and approximately 1,700,648 shares of common stock were available for issuance as of December 31, 2024. The fair value of the rights granted under the 2016 ESPP was calculated using the Black-Scholes option-pricing model with the following assumptions: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ ​ 2024 2023 2022 Expected term (in years) ​ 0.50 ​ 0.50 ​ 0.50 Expected volatility ​ 48.2 % - 52.6 % ​ 82.6 % - 128.2 % ​ 117.5 % - 128.2 % Risk-free interest rate ​ 4.65 % - 5.35 % ​ 3.56 % - 5.17 % ​ 0.75 % - 3.56 % Dividend yield ​ — — — ​ Stock-Based Compensation Total stock-based compensation expense was as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ 2024 2023 2022 Research and development ​ $ 20,919 ​ $ 17,061 ​ $ 14,719 General and administrative ​ 16,635 ​ 12,232 ​ 9,483 Total stock-based compensation expense ​ $ 37,554 ​ $ 29,293 ​ $ 24,202 ​ 106 Table of Contents As of December 31, 2024, total unrecognized stock-based compensation expense was approximately $ 56.9 million, which the Company expects to recognize over a weighted-average period of approximately 2.3 years. Note 12. 401(k) Plan The Company has a retirement and savings plan under Section of 401(k) of Internal Revenue Code (the “401(k) Plan”) covering all U.S. employees. The 401(k) Plan allows employees to make pre- and post-tax contributions up to the maximum allowable amount set by the Internal Revenue Service. The Company may make contributions to this plan at its discretion. The Company matched 50 % of each employee’s contribution up to a maximum of $ 4,000 for the years ended December 31, 2024, 2023 and 2022, resulting in recognized expense of approximately $ 0.4 million, $ 0.4 million and $ 0.3 million for the years ended December 31, 2024, 2023 and 2022, respectively. Note 13. Income Taxes The following table presents domestic and foreign components of net loss before income taxes (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ 2024 2023 2022 Domestic ​ $ 279,379 ​ $ ( 76,779 ) ​ $ ( 124,208 ) Foreign ​ 29 ​ ( 2,176 ) ​ ( 3,185 ) Total net income (loss) before taxes ​ $ 279,408 ​ $ ( 78,955 ) ​ $ ( 127,393 ) ​ The federal, state and foreign components of the income tax expense are summarized as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ ​ 2024 ​ 2023 ​ 2022 Current: ​ ​ ​ ​ ​ ​ ​ ​ ​ Federal ​ $ 4,078 ​ $ — ​ $ — State ​ ​ 142 ​ ​ — ​ ​ — Other ​ ​ — ​ ​ — ​ ​ — Total current tax expense ​ ​ 4,220 ​ ​ — ​ ​ — Deferred: ​ ​ ​ ​ ​ ​ ​ ​ ​ Federal ​ ​ — ​ ​ — ​ ​ — State ​ ​ — ​ ​ — ​ ​ — Other ​ ​ — ​ ​ — ​ ​ — Total deferred tax expense ​ ​ — ​ ​ — ​ ​ — Total income tax expense ​ $ 4,220 ​ $ — ​ $ — ​ The effective tax rate of the provision for income taxes differs from the federal statutory rate as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ 2024 2023 2022 Federal statutory income tax rate 21.0 % 21.0 % 21.0 % State taxes, net of federal benefit 2.1 8.1 1.4 Tax credits ​ ( 2.9 ) ​ 8.5 ​ 5.9 ​ Foreign tax rate difference — 0.2 0.2 Change in valuation allowance ( 18.2 ) ( 34.4 ) ( 25.8 ) Other ( 0.5 ) ( 3.4 ) ( 2.7 ) Provision for income taxes 1.5 % — % — % ​ 107 Table of Contents The components of the deferred tax assets are as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ 2024 2023 Deferred tax assets: ​ ​ ​ ​ ​ Net operating loss carryforwards ​ $ 8,876 ​ $ 70,469 Depreciation ​ 2,717 ​ 950 Accruals and other ​ 2,246 ​ 1,430 Operating lease liability ​ ​ 2,430 ​ ​ 265 Research and development and foreign credits ​ ​ 30,852 ​ ​ 38,759 Section 174 capitalized research and development expenditures ​ 58,630 ​ 43,841 Stock-based compensation ​ 11,759 ​ 10,772 Total deferred tax assets ​ 117,510 ​ 166,486 Deferred tax liabilities: ​ ​ ​ ​ ​ ​ Operating right-of-use asset ​ ​ ( 2,105 ) ​ ​ ( 221 ) Total deferred tax liabilities ​ ​ ( 2,105 ) ​ ​ ( 221 ) Valuation allowance ​ ( 115,405 ) ​ ( 166,265 ) Net deferred tax assets ​ $ — ​ $ — ​ Accounting Standards Codification Topic 740, Income Taxes , requires that the tax benefit of net operating losses, temporary differences and credit carryforwards be recorded as an asset to the extent that management assesses that realization is “more likely than not.” Realization of the future tax benefits is dependent on the Company’s ability to generate sufficient taxable income within the carryforward period. Because of the Company’s recent history of operating losses, management believes that recognition of the deferred tax assets arising from the above-mentioned future tax benefits is currently not likely to be realized and, accordingly, has provided a valuation allowance. The valuation allowance decreased by approximately $ 50.9 million during the year ended December 31, 2024, and increased by $ 28.1 million and $ 34.2 million during the years ended December 31, 2023 and 2022, respectively. Federal and state laws impose substantial restrictions on the utilization of net operating loss and tax credit carryforwards in the event of an ownership change for tax purposes, as defined in Section 382 of the Internal Revenue Code. As a result of such ownership changes, the annual limitation may result in the expiration of net operating losses and credits before utilization. The Company performed a Section 382 analysis through December 31, 2024. The Company has experienced ownership changes in the past. The ownership changes will not result in a limitation that will materially reduce the total amount of net operating loss carryforwards and credits that can be utilized. Subsequent ownership changes may affect the limitation in future years. As of December 31, 2024, the Company had $ 29.2 million of federal net operating loss carryforwards and $ 215.8 million of state net operating loss carryforwards. $ 5.9 million of the federal net operating loss carryforwards will begin to expire in 2037, if not utilized, and the remaining $ 23.3 million have no expiration date. The state net operating loss carryforwards will begin to expire in 2035, if not utilized. As of December 31, 2024, the Company had $ 35.6 million of federal and $ 7.7 million of state research and development tax credit carryforwards available to reduce future income taxes. The federal research and development tax credits will begin to expire in 2035, if not utilized. The state research and development tax credits have no expiration date. As of December 31, 2024, the Company had AUD 5.7 million ($ 3.5 million) of Australian research and development tax credit carryforwards available to reduce future income taxes. The Australian research and development tax credits have no expiration date. 108 Table of Contents A reconciliation of the beginning and ending amount of unrecognized tax benefits is as follows (in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ 2024 2023 2022 Balance at beginning of year ​ $ 28,025 ​ $ 25,295 ​ $ 33,159 Decreases based on tax positions related to prior years ​ ( 902 ) ​ — ​ ( 10,779 ) Increases based on tax positions related to current year ​ 3,450 ​ 2,730 ​ 2,915 Balance at end of year ​ $ 30,573 ​ $ 28,025 ​ $ 25,295 ​ At December 31, 2024, the Company had unrecognized tax benefits of $ 30.6 million, which are subject to a valuation allowance and would not affect the effective tax rate if recognized. The Company does not anticipate that the total amount of unrecognized tax benefits will significantly increase or decrease in the next 12 months. The Company’s policy is to include interest and penalties related to unrecognized tax benefits within the provision for income taxes, as necessary. Management determined that no accrual for interest or penalties was required as of December 31, 2024, 2023 and 2022. The Company files income tax returns in the United States federal jurisdiction, the State of California, the State of Florida, and Australia. The Company is not currently under examination by income tax authorities in federal, state or other jurisdictions. The Company’s tax returns remain open for examination for all years. Protagonist Australia had an accumulated deficit at December 31, 2024 and, accordingly, no provision has been provided thereon for any unremitted earnings. The Company has received orphan drug designation from the FDA for its clinical asset rusfertide (PTG-300) for the treatment of polycythemia vera and beta-thalassemia and may qualify for a related 25 % U.S. Federal income tax credit on qualifying clinical trial expenditures. Note 14. Net Income (Loss) per Share The following table sets forth the computation of basic and diluted net income (loss) per share (in thousands, except share and per share data): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ 2024 2023 2022 Numerator: ​ ​ ​ ​ ​ ​ ​ ​ ​ Net income (loss) ​ $ 275,188 ​ $ ( 78,955 ) ​ $ ( 127,393 ) Denominator: ​ ​ ​ ​ ​ ​ ​ Weighted-average shares of common stock, basic ​ 61,566,989 56,763,559 49,042,232 Dilutive effect of common stock equivalents ​ 3,510,733 — — Weighted-average shares of common stock, dilutive ​ ​ 65,077,722 ​ ​ 56,763,559 ​ ​ 49,042,232 Net income (loss) per share of common stock ​ ​ ​ ​ ​ ​ ​ ​ ​ Basic net income (loss) per share of common stock ​ $ 4.47 $ ( 1.39 ) $ ( 2.60 ) Diluted net income (loss) per share of common stock ​ $ 4.23 ​ $ ( 1.39 ) ​ $ ( 2.60 ) ​ Approximately 2.9 million potentially dilutive shares of common stock (consisting of shares subject to outstanding stock options, RSUs, and under the ESPP) were excluded from the diluted net income per share of common stock computations for the year ended December 31, 2024 because their effect was anti-dilutive. Approximately 8.7 million and 9.9 million potentially dilutive shares of common stock (consisting of shares subject to outstanding stock options, RSUs, PSUs, warrants and under the ESPP, as applicable) were excluded from the diluted net loss per share of common stock computations for the years ended December 31, 2023 and 2022, respectively, due to the Company’s net losses for these periods. ​ ​ 109 Table of Contents ​ Note 15. Segment Reporting Operating segments are components of an enterprise for which separate financial information is available and which are evaluated by a company’s chief operating decision maker (“CODM”), in deciding how to allocate resources and to assess performance. The Company operates and manages its business as one operating segment, which primarily focuses on the discovery and development of innovative medicines in areas of unmet medical need. The Company’s Chief Executive Officer serves as the Company’s CODM and manages and allocates resources to the operations of the Company on an entity-wide basis. Managing and allocating resources on an entity-wide basis enables the CODM to assess the overall level of resources available and how to best deploy these resources across functions and research and development projects based on unmet medical need, scientific data, probability of technical and regulatory successful development, market potential and other considerations, and, as necessary, reallocate resources among our internal research and development portfolio and external opportunities to best support the long-term growth of our business. The Company’s CODM reviews financial information on an aggregate basis for the purposes of allocating resources and evaluating financial performance, including segment net income (loss), which is also reported on the consolidated statement of operations as consolidated net income (loss). The Company derives revenues from its collaboration partners, consisting of nonrefundable upfront and milestone payments and cost sharing payments under its license and collaboration agreements. The Company’s customers are comprised of its two collaboration partners, Takeda and JNJ, formerly Janssen Biotech. Takeda and JNJ accounted for 62 % and 38 % of the Company’s revenues for the year ended December 31, 2024, respectively. JNJ accounted for 100 % of the Company’s revenues for the years ended December 31, 2023 and 2022. All of the Company’s revenues for the years ended December 31, 2024, 2023 and 2022 were generated in the United States. See Note 3 to the consolidated financial statements for additional information. 110 Table of Contents Segment information was as follows for the years presented (dollars in thousands): ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year Ended December 31, ​ 2024 2023 2022 ​ ​ ​ ​ ​ ​ ​ Revenue ​ $ 434,433 ​ $ 60,000 ​ $ 26,581 Discovery department expenses (1) ​ ​ ( 13,411 ) ​ ​ ( 5,471 ) ​ ​ ( 11,608 ) Development department expenses (1) ​ ​ ( 62,262 ) ​ ​ ( 65,574 ) ​ ​ ( 66,941 ) General and administrative department expenses (1) ​ ​ ( 24,249 ) ​ ​ ( 19,620 ) ​ ​ ( 21,702 ) Employee wages and benefits - discovery ​ ​ ( 6,601 ) ​ ​ ( 4,531 ) ​ ​ ( 6,162 ) Employee wages and benefits - development ​ ​ ( 23,365 ) ​ ​ ( 19,301 ) ​ ​ ( 19,279 ) Employee wages and benefits - general and administrative ​ ​ ( 14,148 ) ​ ​ ( 9,862 ) ​ ​ ( 8,060 ) Stock-based compensation ​ ​ ( 37,554 ) ​ ​ ( 29,293 ) ​ ​ ( 24,202 ) Other segment items (2) ​ ​ 250 ​ ​ ( 201 ) ​ ​ ( 80 ) Interest income ​ ​ 26,315 ​ ​ 14,898 ​ ​ 4,060 Income tax expense ​ ​ ( 4,220 ) ​ ​ — ​ ​ — Segment profit (loss) ​ $ 275,188 ​ $ ( 78,955 ) ​ $ ( 127,393 ) Reconciliation of profit (loss) ​ ​ ​ ​ ​ ​ ​ ​ ​ Adjustments and reconciling items ​ $ — ​ $ — ​ $ — Consolidated net income (loss) ​ $ 275,188 ​ $ ( 78,955 ) ​ $ ( 127,393 ) Other segment information ​ ​ ​ ​ ​ ​ ​ ​ ​ Segment assets (3) ​ $ 744,725 ​ $ 357,951 ​ $ 247,928 Long-lived assets (4) ​ $ 12,607 ​ $ 2,149 ​ $ 4,626 Expenditures for long-lived assets ​ $ 1,355 ​ $ 609 ​ $ 795 (1) Amounts exclude employee wages and benefits, stock-based compensation and expense allocations. (2) Other segment items include foreign currency related income (expense) and other miscellaneous income (expense). (3) The measure of segment assets is reported on the consolidated balance sheet as total assets. (4) Long-lived assets include property and equipment, net and operating lease right-of-use asset. ​ The accounting policies of the Company’s operating segment are the same as those described in the summary of significant accounting policies. Substantially all of the Company’s long-lived assets are in the United States. See Note 6 to the consolidated financial statements for depreciation expense for the periods presented. ​ ​ 111 Table of Contents Item 9. Changes in and Disagreements with Accountants on Accounting and Financial Disclosure ​ None.