uniQure N.V. 10-Q

Item 1. Financial Statements uniQure N.V. UNAUDITED CONSOLIDATED BALANCE SHEETS ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, ​ December 31, ​ 2025 2024 ​ ​ (in thousands, except share and per share amounts) Current assets ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 597,056 ​ $ 158,930 Current investment securities ​ ​ 97,189 ​ ​ 208,591 Accounts receivable ​ ​ 3,883 ​ ​ 5,881 Prepaid expenses ​ ​ 10,326 ​ ​ 9,281 Other current assets and receivables ​ ​ 7,739 ​ ​ 7,606 Total current assets ​ ​ 716,193 ​ ​ 390,289 Non-current assets ​ ​ ​ ​ ​ ​ Property, plant and equipment, net of accumulated depreciation of $ 43.5 million as of September 30, 2025 and $ 31.7 million as of December 31, 2024 ​ ​ 15,402 ​ ​ 20,424 Other investments ​ ​ 29,972 ​ ​ 27,464 Operating lease right-of-use assets ​ ​ 13,079 ​ ​ 13,647 Intangible assets, net, including in-process research and development assets of $ 62.9 million as of September 30, 2025 and $ 55.6 million as of December 31, 2024 ​ ​ 74,144 ​ ​ 71,043 Goodwill ​ ​ 25,327 ​ ​ 22,414 Deferred tax assets, net ​ ​ 8,772 ​ ​ 9,856 Other non-current assets ​ ​ 5,493 ​ ​ 1,399 Total non-current assets ​ ​ 172,189 ​ ​ 166,247 Total assets ​ $ 888,382 ​ $ 556,536 Current liabilities ​ ​ ​ ​ ​ ​ Accounts payable ​ $ 6,228 ​ $ 7,227 Accrued expenses and other current liabilities ​ ​ 51,947 ​ ​ 28,932 Liability related to pre-funded warrants ​ ​ 30,722 ​ ​ — Income taxes payable ​ ​ 7,821 ​ ​ 293 Current portion of operating lease liabilities ​ ​ 3,914 ​ ​ 3,601 Total current liabilities ​ ​ 100,632 ​ ​ 40,053 Non-current liabilities ​ ​ ​ ​ ​ ​ Long-term debt ​ ​ 51,880 ​ ​ 51,324 Liability from royalty financing agreement ​ ​ 465,507 ​ ​ 434,930 Operating lease liabilities, net of current portion ​ ​ 10,361 ​ ​ 11,136 Contingent consideration ​ ​ 17,754 ​ ​ 10,860 Deferred tax liability, net ​ ​ 7,958 ​ ​ 7,043 Other non-current liabilities, net of current portion ​ ​ 5,544 ​ ​ 7,942 Total non-current liabilities ​ ​ 559,004 ​ ​ 523,235 Total liabilities ​ ​ 659,636 ​ ​ 563,288 Commitments and contingencies ​ ​ ​ ​ ​ ​ Shareholders' equity / (deficit) ​ ​ ​ ​ ​ ​ Ordinary shares, € 0.05 par value: 80,000,000 shares authorized as of September 30, 2025 and December 31, 2024 and 62,165,900 and 48,988,087 ordinary shares issued and outstanding as of September 30, 2025 and December 31, 2024, respectively ​ ​ 3,678 ​ ​ 2,945 Additional paid-in-capital ​ ​ 1,575,663 ​ ​ 1,173,068 Accumulated other comprehensive loss ​ ​ ( 58,745 ) ​ ​ ( 52,800 ) Accumulated deficit ​ ​ ( 1,291,850 ) ​ ​ ( 1,129,965 ) Total shareholders' equity / (deficit) ​ ​ 228,746 ​ ​ ( 6,752 ) Total liabilities and shareholders' equity / (deficit) ​ $ 888,382 ​ $ 556,536 The accompanying notes are an integral part of these unaudited consolidated financial statements . 2 Table of Contents ​ uniQure N.V. ​ UNAUDITED CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended September 30, ​ Nine months ended September 30, ​ 2025 2024 2025 2024 ​ ​ (in thousands, except share and per share amounts) ​ (in thousands, except share and per share amounts) License revenues ​ $ 3,582 ​ $ 2,111 ​ $ 10,411 ​ $ 5,182 Contract manufacturing revenues ​ ​ — ​ ​ — ​ ​ — ​ ​ 6,114 Collaboration revenues ​ ​ 119 ​ ​ 176 ​ ​ 119 ​ ​ 10,602 Total revenues ​ ​ 3,701 ​ ​ 2,287 ​ ​ 10,530 ​ ​ 21,898 Operating expenses: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cost of license revenues ​ ​ ( 398 ) ​ ​ ( 264 ) ​ ​ ( 1,251 ) ​ ​ ( 648 ) Cost of contract manufacturing revenues ​ ​ — ​ ​ ( 757 ) ​ ​ — ​ ​ ( 17,060 ) Research and development expenses ​ ​ ( 34,366 ) ​ ​ ( 30,595 ) ​ ​ ( 105,889 ) ​ ​ ( 104,942 ) Selling, general and administrative expenses ​ ​ ( 19,438 ) ​ ​ ( 11,575 ) ​ ​ ( 43,846 ) ​ ​ ( 41,279 ) Total operating expenses ​ ​ ( 54,202 ) ​ ​ ( 43,191 ) ​ ​ ( 150,986 ) ​ ​ ( 163,929 ) Other income ​ ​ 1,510 ​ ​ 2,591 ​ ​ 12,413 ​ ​ 5,950 Other expense ​ ​ ( 2,044 ) ​ ​ ( 1,915 ) ​ ​ ( 6,188 ) ​ ​ ( 2,385 ) Loss from operations ​ ​ ( 51,035 ) ​ ​ ( 40,228 ) ​ ​ ( 134,231 ) ​ ​ ( 138,466 ) Interest income ​ ​ 3,503 ​ ​ 4,866 ​ ​ 11,154 ​ ​ 17,179 Interest expense ​ ​ ( 16,721 ) ​ ​ ( 16,611 ) ​ ​ ( 47,421 ) ​ ​ ( 48,865 ) Foreign currency (losses) / gains, net ​ ​ ( 428 ) ​ ​ 7,564 ​ ​ 25,382 ​ ​ 5,430 Other non-operating losses, net ​ ​ ( 7,222 ) ​ ​ — ​ ​ ( 7,222 ) ​ ​ — Loss before income tax expense ​ $ ( 71,903 ) ​ $ ( 44,409 ) ​ $ ( 152,338 ) ​ $ ( 164,722 ) Income tax (expense) / benefit ​ ​ ( 8,626 ) ​ ​ 31 ​ ​ ( 9,547 ) ​ ​ ( 1,573 ) Net loss ​ $ ( 80,529 ) ​ $ ( 44,378 ) ​ $ ( 161,885 ) ​ $ ( 166,295 ) Other comprehensive loss: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Foreign currency translation gains / (losses), net ​ ​ 158 ​ ​ ( 415 ) ​ ​ ( 5,945 ) ​ ​ ( 3,252 ) Defined benefit pension gain, net of taxes ​ ​ — ​ ​ 37 ​ ​ — ​ ​ 107 Total comprehensive loss ​ $ ( 80,371 ) ​ $ ( 44,756 ) ​ $ ( 167,830 ) ​ $ ( 169,440 ) Loss per ordinary share - basic and diluted ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Basic and diluted net loss per ordinary share ​ $ ( 1.38 ) ​ $ ( 0.91 ) ​ $ ( 2.90 ) ​ $ ( 3.42 ) Weighted average shares - basic and diluted ​ ​ 58,516,415 ​ ​ 48,718,533 ​ ​ 55,880,318 ​ ​ 48,576,339 ​ The accompanying notes are an integral part of these unaudited consolidated financial statements. ​ 3 Table of Contents uniQure N.V. ​ UNAUDITED CONSOLIDATED STATEMENTS OF SHAREHOLDERS’ EQUITY / (DEFICIT) FOR THE THREE MONTHS ENDED SEPTEMBER 30, 2025 AND 2024 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Accumulated ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Additional ​ other ​ ​ ​ ​ Total ​ ​ Ordinary shares ​ paid-in ​ comprehensive ​ Accumulated ​ shareholders’ ​ No. of shares Amount capital loss deficit equity / (deficit) ​ ​ (in thousands, except share and per share amounts) Balance at June 30, 2024 ​ 48,694,569 ​ $ 2,930 ​ $ 1,162,823 ​ $ ( 56,320 ) ​ $ ( 1,012,326 ) ​ $ 97,107 Loss for the period ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 44,378 ) ​ ​ ( 44,378 ) Other comprehensive loss, net ​ — ​ ​ — ​ ​ — ​ ​ ( 378 ) ​ ​ — ​ ​ ( 378 ) Exercise of share options ​ 3,900 ​ ​ — ​ ​ 32 ​ ​ — ​ ​ — ​ ​ 32 Restricted share units distributed during the period ​ 40,405 ​ ​ 2 ​ ​ ( 2 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense ​ — ​ ​ — ​ ​ 3,438 ​ ​ — ​ ​ — ​ ​ 3,438 Balance at September 30, 2024 ​ 48,738,874 ​ $ 2,932 ​ $ 1,166,291 ​ $ ( 56,698 ) ​ $ ( 1,056,704 ) ​ $ 55,821 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Balance at June 30, 2025 ​ 54,865,673 ​ $ 3,250 ​ $ 1,262,971 ​ $ ( 58,903 ) ​ $ ( 1,211,321 ) ​ $ ( 4,003 ) Loss for the period ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 80,529 ) ​ ​ ( 80,529 ) Other comprehensive gain, net ​ — ​ ​ — ​ ​ — ​ ​ 158 ​ ​ — ​ ​ 158 Follow-on public offering ​ 6,736,841 ​ ​ 394 ​ ​ 299,832 ​ ​ — ​ ​ — ​ ​ 300,226 Tax benefit related to historical share issuance costs ​ — ​ ​ — ​ ​ 862 ​ ​ ​ ​ ​ ​ ​ ​ 862 Exercises of share options ​ 532,316 ​ ​ 32 ​ ​ 8,478 ​ ​ — ​ ​ — ​ ​ 8,510 Restricted share units distributed during the period ​ 31,070 ​ ​ 2 ​ ​ ( 2 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense ​ — ​ ​ — ​ ​ 3,522 ​ ​ — ​ ​ — ​ ​ 3,522 Balance at September 30, 2025 ​ 62,165,900 ​ $ 3,678 ​ $ 1,575,663 ​ $ ( 58,745 ) ​ $ ( 1,291,850 ) ​ $ 228,746 ​ The accompanying notes are an integral part of these unaudited consolidated financial statements. ​ ​ 4 Table of Contents uniQure N.V. ​ UNAUDITED CONSOLIDATED STATEMENTS OF SHAREHOLDERS’ EQUITY / (DEFICIT) FOR THE NINE MONTHS ENDED SEPTEMBER 30, 2025 AND 2024 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Accumulated ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Additional ​ other ​ ​ ​ ​ Total ​ ​ Ordinary shares ​ paid-in ​ comprehensive ​ Accumulated ​ shareholders’ ​ No. of shares Amount capital loss deficit equity / (deficit) ​ ​ (in thousands, except share and per share amounts) Balance at December 31, 2023 ​ 47,833,830 ​ $ 2,883 ​ $ 1,148,749 ​ $ ( 53,553 ) ​ $ ( 890,409 ) ​ $ 207,670 Loss for the period ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 166,295 ) ​ ​ ( 166,295 ) Other comprehensive loss, net ​ — ​ ​ — ​ ​ — ​ ​ ( 3,145 ) ​ ​ — ​ ​ ( 3,145 ) Exercises of share options ​ 3,900 ​ ​ — ​ ​ 32 ​ ​ — ​ ​ — ​ ​ 32 Restricted share units distributed during the period ​ 890,994 ​ ​ 48 ​ ​ ( 48 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense ​ — ​ ​ — ​ ​ 17,509 ​ ​ — ​ ​ — ​ ​ 17,509 Issuance of ordinary shares relating to employee stock purchase plan ​ 10,150 ​ ​ 1 ​ ​ 49 ​ ​ — ​ ​ — ​ ​ 50 Balance at September 30, 2024 ​ 48,738,874 ​ $ 2,932 ​ $ 1,166,291 ​ $ ( 56,698 ) ​ $ ( 1,056,704 ) ​ $ 55,821 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Balance at December 31, 2024 ​ 48,988,087 ​ $ 2,945 ​ $ 1,173,068 ​ $ ( 52,800 ) ​ $ ( 1,129,965 ) ​ $ ( 6,752 ) Loss for the period ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 161,885 ) ​ ​ ( 161,885 ) Other comprehensive loss, net ​ — ​ ​ — ​ ​ — ​ ​ ( 5,945 ) ​ ​ — ​ ​ ( 5,945 ) Follow-on public offerings ​ 11,810,370 ​ ​ 655 ​ ​ 380,082 ​ ​ — ​ ​ — ​ ​ 380,737 Tax benefit related to historical share issuance costs ​ — ​ ​ — ​ ​ 862 ​ ​ ​ ​ ​ ​ ​ ​ 862 Exercises of share options ​ 553,556 ​ ​ 33 ​ ​ 8,680 ​ ​ — ​ ​ — ​ ​ 8,713 Restricted and performance share units distributed during the period ​ 813,887 ​ ​ 45 ​ ​ ( 45 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense ​ — ​ ​ — ​ ​ 13,016 ​ ​ — ​ ​ — ​ ​ 13,016 Balance at September 30, 2025 ​ 62,165,900 ​ $ 3,678 ​ $ 1,575,663 ​ $ ( 58,745 ) ​ $ ( 1,291,850 ) ​ $ 228,746 ​ The accompanying notes are an integral part of these unaudited consolidated financial statements. ​ 5 Table of Contents uniQure N.V. ​ UNAUDITED CONSOLIDATED STATEMENTS OF CASH FLOWS ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Nine months ended September 30, ​ 2025 2024 ​ ​ (in thousands) Cash flows from operating activities ​ ​ ​ ​ ​ ​ Net loss ​ $ ( 161,885 ) ​ $ ( 166,295 ) Adjustments to reconcile net loss to net cash used in operating activities: ​ ​ ​ ​ ​ ​ Depreciation and amortization ​ ​ 11,789 ​ ​ 8,285 Amortization of discount on investment securities ​ ​ ( 6,091 ) ​ ​ ( 8,472 ) Share-based compensation expense ​ ​ 13,016 ​ ​ 17,509 Royalty financing agreement interest expense, net of interest paid ​ ​ 29,209 ​ ​ 33,107 Deferred tax expense ​ ​ 1,979 ​ ​ 1,573 Changes in fair value of contingent consideration ​ ​ 5,293 ​ ​ ( 2,032 ) Changes in fair value of liability related to pre-funded warrants ​ ​ 5,722 ​ ​ — Unrealized foreign exchange gains, net ​ ​ ( 24,534 ) ​ ​ ( 5,726 ) Allowance for inventory write-downs ​ ​ — ​ ​ 6,297 Other items, net ​ ​ ( 3,013 ) ​ ​ ( 2,460 ) Changes in operating assets and liabilities: ​ ​ ​ ​ ​ ​ Accounts receivable, prepaid expenses, and other current assets and receivables ​ ​ 2,880 ​ ​ ( 5,764 ) Inventories ​ ​ — ​ ​ ( 3,876 ) Accounts payable ​ ​ ( 1,648 ) ​ ​ ( 512 ) Income tax payable ​ ​ 7,568 ​ ​ 167 Accrued expenses, other liabilities, and operating leases ​ ​ 19,321 ​ ​ ( 1,685 ) Net cash used in operating activities ​ ​ ( 100,394 ) ​ ​ ( 129,884 ) Cash flows from investing activities ​ ​ ​ ​ ​ ​ Proceeds on maturity of debt securities ​ ​ 337,195 ​ ​ 480,806 Investment in debt securities ​ ​ ( 217,124 ) ​ ​ ( 279,586 ) Divestment of commercial manufacturing facility ​ ​ — ​ ​ ( 8,300 ) Purchases of property, plant, and equipment ​ ​ ( 320 ) ​ ​ ( 3,328 ) Net cash generated from investing activities ​ ​ 119,751 ​ ​ 189,592 Cash flows generated from / (used in) financing activities ​ ​ ​ ​ ​ ​ Proceeds from follow-on public offerings of ordinary shares, net of issuance costs ​ ​ 380,737 ​ ​ — Proceeds from issuance of pre-funded warrants, net of issuance costs ​ ​ 23,499 ​ ​ — Proceeds from issuance of ordinary shares related to employee stock options and purchase plans ​ ​ 8,713 ​ ​ 81 Repayment of long-term debt ​ ​ — ​ ​ ( 53,050 ) Net cash generated from / (used in) financing activities ​ ​ 412,949 ​ ​ ( 52,969 ) Currency effect on cash, cash equivalents and restricted cash ​ ​ 5,914 ​ ​ 1,796 Net increase in cash, cash equivalents and restricted cash ​ ​ 438,220 ​ ​ 8,535 Cash, cash equivalents and restricted cash at beginning of period ​ ​ 160,329 ​ ​ 244,544 Cash, cash equivalents and restricted cash at the end of period ​ $ 598,549 ​ $ 253,079 Cash and cash equivalents ​ $ 597,056 ​ $ 251,626 Restricted cash related to leasehold and other deposits ​ ​ 1,493 ​ ​ 1,453 Total cash, cash equivalents and restricted cash ​ $ 598,549 ​ $ 253,079 Supplemental cash flow disclosures: ​ ​ ​ ​ ​ ​ Cash paid for interest ​ $ ( 16,659 ) ​ $ ( 16,892 ) Non-cash decrease in accounts payables and accrued expenses and other current liabilities related to purchases of property, plant, and equipment ​ $ ( 54 ) ​ $ ( 673 ) ​ The accompanying notes are an integral part of these unaudited consolidated financial statements. ​ ​ 6 Table of Contents uniQure N.V. ​ NOTES TO CONSOLIDATED FINANCIAL STATEMENTS (Unaudited) ​ 1 General business information ​ uniQure N.V. (the “Company”) was incorporated on January 9, 2012, as a private company with limited liability ( besloten vennootschap met beperkte aansprakelijkheid ) under the laws of the Netherlands. The Company is a leader in the field of gene therapy and seeks to deliver to patients suffering from rare and other devastating diseases single treatments with potentially curative results. The Company’s business was founded in 1998 and was initially operated through its predecessor company, Amsterdam Molecular Therapeutics Holding N.V. (“AMT”). In 2012, AMT undertook a corporate reorganization, pursuant to which uniQure B.V. acquired the entire business and assets of AMT and completed a share-for-share exchange with the shareholders of AMT. Effective February 10, 2014, in connection with its initial public offering, the Company converted into a public company with limited liability ( naamloze vennootschap ) and changed its legal name from uniQure B.V. to uniQure N.V. ​ The Company is registered in the trade register of the Dutch Chamber of Commerce ( Kamer van Koophandel ) in Amsterdam, the Netherlands under number 54385229. The Company’s headquarters are in Amsterdam, the Netherlands, its registered office is located at Paasheuvelweg 25a, Amsterdam 1105 BP, the Netherlands and its telephone number is +31 20 240 6000. ​ The Company’s ordinary shares are listed on the Nasdaq Global Select Market and trade under the symbol “QURE”. ​ 2 Summary of significant accounting policies ​ 2.1 Basis of preparation ​ The Company prepared these unaudited consolidated financial statements in compliance with generally accepted accounting principles in the United States (“U.S. GAAP”) and applicable rules and regulations of the United States Securities and Exchange Commission (the “SEC”) regarding interim financial reporting. Any reference in these notes to applicable guidance is meant to refer to authoritative U.S. GAAP as found in the Accounting Standards Codification (“ASC”) and Accounting Standards Updates of the Financial Accounting Standards Board. ​ The unaudited consolidated financial statements are presented in United States (“U.S.”) dollars, except where otherwise indicated. Transactions denominated in currencies other than U.S. dollars are presented in the transaction currency with the U.S. dollar amount included in parenthesis, converted at the foreign exchange rate as of the transaction date. ​ 2.2 Unaudited interim financial information ​ The interim financial statements and related disclosures are unaudited, have been prepared on the same basis as the annual financial statements and, in the opinion of management, reflect all adjustments, which include only normal recurring adjustments, necessary for a fair statement of the financial position, results of operations and changes in financial position for the period presented. ​ Certain information and footnote disclosures normally included in annual financial statements prepared in accordance with U.S. GAAP have been omitted. The results of operations for the three and nine months ended September 30, 2025, are not necessarily indicative of the results to be expected for the full year ending December 31, 2025, or for any other future year or interim period. The accompanying financial statements should be read in conjunction with the audited financial statements and the related notes thereto included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2024 filed by the Company with the SEC on February 27, 2025 (the “Annual Report”) . ​ 7 Table of Contents 2.3 Use of estimates ​ The preparation of the financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, disclosure of contingent liabilities at the date of the financial statements and reported amounts of revenues, expenses and tax related items during the reporting period. Actual results could differ from those estimates. ​ 2.4 Accounting policies ​ The principal accounting policies applied in the preparation of these unaudited consolidated financial statements are described in the Company’s audited financial statements as of and for the year ended December 31, 2024, and the notes thereto, which are included in the Annual Report . There have been no material changes in the Company’s significant accounting policies during the nine months ended September 30, 2025, except as noted below: ​ Liability related to pre-funded warrants ​ As part of the Company’s September 2025 follow-on public offering, the Company issued pre-funded warrants (the “Pre-Funded Warrants”), denominated in U.S. dollars. As the Pre-Funded Warrants are not denominated in the Company’s functional currency, they are not indexed to the Company’s ordinary shares in accordance with ASC 815-40, Derivatives and Hedging, Contracts in Entity’s Own Equity . The obligation to issue ordinary shares at an offering price of $ 47.50 per ordinary share, less a $ 0.0001 per ordinary share exercise price, is classified as a liability. The liability related to pre-funded warrants is accounted for at fair value in accordance with ASC 820, Fair Value Measurement . Changes in the fair value of the liability related to pre-funded warrants are recognized within Other non-operating items, net in the Company’s Consolidated Statements of Operations and Comprehensive Loss. The liability related to pre-funded warrants is classified as current due to the Pre-Funded Warrant holder’s right to exercise at any time. The Company made an accounting policy election to exclude the Pre-Funded Warrants from the denominator in the computation of basic net loss per ordinary share, as such instruments are not considered outstanding ordinary shares. ​ 2.5 Recent accounting pronouncements ​ There have been no new accounting pronouncements or changes to accounting pronouncements during the nine months ended September 30, 2025, as compared to the recent accounting pronouncements described in Note 2.3.29 of the Annual Report , which could be expected to materially impact the Company’s unaudited consolidated financial statements. ​ 3 Other investments ​ Convertible promissory note ​ The Company has an investment in a convertible promissory note with a nominal amount of $ 12.5 million, bearing interest at 8.0 % per annum. The convertible promissory note was issued in July 2024 and matures in October, 2029. The convertible promissory note had a balance of $ 14.4 million as of September 30, 2025 (December 31, 2024: $ 13.7 million) and is presented within Other investments on the Company’s Consolidated Balance Sheets. In the three and nine months ended September 30, 2025, the Company recognized $ 0.2 million and $ 0.7 million of interest income, respectively, compared to nil during the same periods in 2024. As of September 30, 2025, the Company has not recorded an allowance for credit losses related to the convertible promissory note. ​ Investments valued under measurement alternative ​ The Company has investments in non-publicly traded equity securities without readily determinable fair values. These investments are accounted for at cost, less impairment and adjusted to fair value if there are observable price changes in orderly transactions for identical or similar investments using the measurement alternative in accordance with ASC 321, Investments – Equity Securities . The carrying value of these investments as of September 30, 2025 and December 31, 2024 was $ 15.6 million and $ 13.8 million, respectively, as presented within Other Investments on the Company’s Consolidated Balance Sheets. The Company did not recognize any gains, losses, or impairments relating to investments carried under the measurement alternative in the three and nine month periods ended September 30, 2025 and September 30, 2024. ​ ​ 8 Table of Contents 4 Investment securities The following tables summarize the Company’s investments in government debt securities as of September 30, 2025 and December 31, 2024: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ At September 30, 2025 ​ Amortized cost Gross unrealized holding gains Gross unrealized holding losses Estimated fair value ​ ​ (in thousands) Current investments: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Government debt securities (held-to-maturity) ​ $ 97,189 ​ $ 51 ​ $ — ​ $ 97,240 Total ​ $ 97,189 ​ $ 51 ​ $ — ​ $ 97,240 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ At December 31, 2024 ​ Amortized cost Gross unrealized holding gains Gross unrealized holding losses Estimated fair value ​ ​ (in thousands) Current investments: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Government debt securities (held-to-maturity) ​ $ 208,591 ​ $ 164 ​ $ — ​ $ 208,755 Total ​ $ 208,591 ​ $ 164 ​ $ — ​ $ 208,755 ​ The Company invests in short-term U.S. and European government debt securities with high investment credit ratings. The U.S. and European government bonds are U.S. dollar and euro denominated, respectively. ​ Investment securities with original maturities of 90 days or less when purchased are presented within cash and cash equivalents and measured at amortized cost (September 30, 2025: $ 119.3 million, December 31, 2024: $ 15.3 million). ​ Inputs to the fair value of the investments are considered Level 2 inputs. ​ 5 Fair value measurement ​ The Company measures certain financial assets and liabilities at fair value, either upon initial recognition or for subsequent accounting or reporting. ASC 820 , Fair Value Measurement requires disclosure of the methodologies used in determining the reported fair values and establishes a hierarchy of inputs used when available. The three levels of the fair value hierarchy are described below: ​ Level 1 – Valuations based on unadjusted quoted prices in active markets for identical assets or liabilities that the Company can access at the measurement date. ​ Level 2 – Valuations based on quoted prices for similar assets or liabilities in markets that are not active or models for which the inputs are observable, either directly or indirectly. ​ Level 3 – Valuations that require inputs that reflect the Company’s own assumptions that are both significant to the fair value measurement and are unobservable. ​ To the extent that valuation is based on models or inputs that are less observable or unobservable in the market, the determination of fair value requires more judgment. Accordingly, the degree of judgment exercised by the Company in determining fair value is greatest for instruments categorized as Level 3. A financial instrument’s level within the fair value hierarchy is based on the lowest level of any input that is significant to the fair value measurement. ​ The carrying amount of cash and cash equivalents, accounts receivable from licensing and collaboration partners, other assets, accounts payable, accrued expenses and other current liabilities reflected in the Company’s Consolidated Balance Sheets approximate their fair values due to their short-term maturities. ​ 9 Table of Contents The following table sets forth the Company’s assets and liabilities that are required to be measured at fair value on a recurring basis as of September 30, 2025 and December 31, 2024 : ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Quoted prices in active markets (Level 1) Significant other observable inputs (Level 2) Significant unobservable inputs (Level 3) Total Classification in Consolidated balance sheets ​ ​ ​ (in thousands) ​ ​ Balance at December 31, 2024 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 158,930 ​ $ — ​ $ — ​ $ 158,930 ​ Cash and cash equivalents Restricted cash ​ ​ 1,399 ​ ​ — ​ ​ — ​ ​ 1,399 ​ Other non-current assets Total assets ​ $ 160,329 ​ $ — ​ $ — ​ $ 160,329 ​ ​ Liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Contingent consideration ​ ​ — ​ ​ — ​ ​ 10,860 ​ ​ 10,860 ​ Contingent consideration Consideration for post-acquisition services ​ ​ — ​ ​ — ​ ​ 370 ​ ​ 370 ​ Other non-current liabilities Total liabilities ​ $ — ​ $ — ​ $ 11,230 ​ $ 11,230 ​ ​ Balance at September 30, 2025 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 597,056 ​ $ — ​ $ — ​ $ 597,056 ​ Cash and cash equivalents Restricted cash ​ ​ 1,493 ​ ​ — ​ ​ — ​ ​ 1,493 ​ Other non-current assets Total assets ​ $ 598,549 ​ $ — ​ $ — ​ $ 598,549 ​ ​ Liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Liability related to pre-funded warrants ​ ​ — ​ ​ 30,722 ​ ​ — ​ ​ 30,722 ​ Liability related to pre-funded warrants Contingent consideration ​ ​ — ​ ​ — ​ ​ 17,754 ​ ​ 17,754 ​ Contingent consideration Consideration for post-acquisition services ​ ​ — ​ ​ — ​ ​ 605 ​ ​ 605 ​ Other non-current liabilities Total liabilities ​ $ — ​ $ 30,722 ​ $ 18,359 ​ $ 49,081 ​ ​ ​ Contingent consideration ​ The Company is required to pay up to EUR 143.1 million (or $ 167.9 million based on the foreign exchange rate on September 30, 2025) to the former shareholders of uniQure France SAS (formerly Corlieve Therapeutics SAS) upon the achievement of the remaining contractually defined milestones related to the development of AMT-260 in connection with the Company’s acquisition of uniQure France SAS. ​ The fair value of the contingent consideration as of September 30, 2025 was $ 17.8 million (December 31, 2024: $ 10.9 million) using discount rates of approximately 12.1 % to 12.5 % (December 31, 2024: 15.3 % to 16.2 %). ​ If, as of September 30, 2025, the Company had assumed a 100 % likelihood of AMT-260 advancing into a Phase III clinical study, then the fair value of the contingent consideration would have increased to $ 57.2 million. If, as of September 30, 2025, the Company had assumed that it would discontinue development of the AMT-260 program, then the contingent consideration would have been released to income. ​ The following table presents the changes in fair value of the contingent consideration between December 31, 2024 and September 30, 2025: ​ ​ ​ ​ ​ ​ ​ ​ Amount of ​ ​ contingent ​ ​ consideration ​ 2025 ​ ​ (in thousands) Balance at December 31, 2024 ​ $ 10,860 Unrealized change in fair value (presented within research and development expenses) ​ ​ 5,293 Currency translation effects ​ ​ 1,601 Balance at September 30, 2025 ​ $ 17,754 ​ 10 Table of Contents The Company classified the total contingent consideration liability as non-current as of September 30, 2025 and December 31, 2024. The classification of the contingent consideration within the Company’s Consolidated Balance Sheets between current and non-current liabilities is based upon the Company’s best estimate of the timing of settlement of the remaining relevant milestones. ​ Investment securities ​ Refer to Note 4 “ Investment securities ” for the fair value of the investment securities as of September 30, 2025 and December 31, 2024. ​ Liability related to pre-funded warrants ​ In September 2025, the Company completed a follow-on public offering which included the issuance of Pre-Funded Warrants to purchase 526,316 of the Company’s ordinary shares at the public offering price of $ 47.50 per ordinary share, less a $ 0.0001 per ordinary share exercise price for each Pre-Funded Warrant. The obligation to issue ordinary shares upon the exercise of the Pre-Funded Warrants is classified as a liability related to pre-funded warrants. The liability related to pre-funded warrants is accounted for at fair value in accordance with ASC 820, Fair Value Measurement , with the total gross proceeds received with respect to the Pre-Funded Warrants determined as reflective of the fair value of the obligation on the date of issuance. Changes in fair value of the liability related to pre-funded warrants are recognized within Other non-operating losses, net in the Company’s Consolidated Statements of Operations and Comprehensive Loss. ​ The Pre-Funded Warrants are not exchange-quoted and are measured using a valuation technique whose significant inputs are observable; therefore the fair value measurement is classified within Level 2 of the fair value hierarchy. ​ ​ ​ ​ ​ Liability related ​ to pre-funded ​ warrants ​ 2025 ​ (in thousands) Balance at December 31, 2024 $ — Issuance of pre-funded warrants in connection with follow-on public offering ​ 25,000 Unrealized change in fair value ​ 5,722 Balance at September 30, 2025 $ 30,722 ​ The fair value of the liability related to pre-funded warrants as of September 30, 2025 was $ 30.7 million (December 31, 2024: nil ), classified as current. Classification is based upon the Pre-Funded Warrant holder’s right to exercise at any time. During the three and nine months ended September 30, 2025, the Company recorded a $ 5.7 million remeasurement in the fair value of the liability related to pre-funded warrants, respectively. ​ ​ ​ 6 Accrued expenses and other current liabilities ​ Accrued expenses and other current liabilities include the following items: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, ​ December 31, ​ 2025 2024 ​ ​ (in thousands) Personnel-related accruals and liabilities (As of September 30, 2025, $ 15.7 million (December 31, 2024: $ 0.1 million) related to cash proceeds from employees stock option exercises) ​ $ 26,526 ​ $ 12,290 Accruals for goods received from and services provided by vendors-not yet billed ​ ​ 16,941 ​ ​ 10,109 Current portion of firm purchase commitment liability ​ ​ 3,773 ​ ​ 1,582 Liability owed to the Purchaser pursuant to the Royalty Financing Agreement (refer to Note 8 " Royalty Financing Agreement") ​ ​ 3,583 ​ ​ 4,951 Other current liabilities ​ ​ 1,124 ​ ​ — Total ​ $ 51,947 ​ $ 28,932 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 11 Table of Contents 7 Long-term debt ​ On June 14, 2013, the Company entered into a venture debt loan facility with Hercules Capital, Inc. (“Hercules”). The facility has been amended at various times, including on July 22, 2024 (the “2024 Amended Facility”) and most recently on September 22, 2025 (the “2025 Amended Facility), upon which date the amendment closed (the “Amendment Closing Date”). ​ On the Amendment Closing Date, the Company drew down $ 50.0 million (the “Tranche 1 Advance”) of the 2025 Amended Facility to repay the $ 50.0 million then outstanding under the 2024 Amended Facility. A facility charge of $ 0.2 million was incurred on the Amendment Closing Date. The 2024 Amended Facility was due on January 7, 2027 and bore interest at a rate equal to the greater of (i) 7.95 % and (ii) 7.95 % plus the prime rate less 3.25 % per annum, reflecting a floating rate of 11.95 % at the Amendment Closing Date. ​ Pursuant to the 2025 Amended Facility, additional term loans of $ 125.0 million were made available. The Company may draw down (i) an additional $ 100.0 million in two increments of at least $ 25.0 million (the “Tranche 2 Advances”), following the approval of a Biologics License Application (“BLA”) for AMT-130 prior to June 15, 2027, provided that confirmatory trials to the extent and in the manner required to support full approval (if applicable) remain ongoing or are being planned, and (ii) an additional $ 25.0 million in a single advance (the “Tranche 3 Advance”), subject to approval by Hercules. Advances under the 2025 Amended Facility bear interest at a rate equal to the greater of (i) 9.45 % and (ii) the sum of the prime rate and 2.45 %, reflecting a current floating rate of 9.70 %. ​ The 2025 Amended Facility matures on October 1, 2030, upon which date the Company is required to repay the principal balance and any unpaid interest on advances received. The interest-only period of the 2025 Amended Facility is effective through October 1, 2028. The interest-only period will be extended to October 1, 2029 if the BLA for AMT-130 is approved prior to June 15, 2027. The 2025 Amended Facility will be interest-only if certain commercial milestones are met prior to December 31, 2028. ​ The Company may prepay all or part of the outstanding principal together with a prepayment charge of 1.50 % if repayment occurs within the first 30 months following the Amendment Closing Date, and thereafter, with a prepayment charge of 0.75 %. Pursuant to the terms of the 2025 Amended Facility, the Company owes a back-end fee on December 1, 2025. Absent a default or prepayment of the loan, a back-end fee of $ 0.6 million is due on January 5, 2027. An end-of-term charge of 2.75 % of the aggregate principal outstanding is due if repaid within 18 months of the Amendment Closing Date, otherwise 5.50 % if repaid thereafter. ​ The total principal outstanding as of September 30, 2025 under the 2025 Amended Facility was $ 50.0 million. The amortized cost, including interest due presented as part of Accrued expenses and other current liabilities, was $ 52.4 million as of September 30, 2025, compared to $ 51.9 million as of December 31, 2024, and is recorded net of discount and debt issuance costs. The foreign currency gain on the loan facilities in the three and nine months ended September 30, 2025 was $ 2.8 million and $ 9.2 million, respectively, compared to a foreign currency gain of $ 2.6 million and a foreign currency loss of $ 0.4 million, respectively, during the same periods in 2024. ​ Interest expense during the three and nine months ended September 30, 2025 was $ 1.8 million and $ 5.4 million, respectively, compared to $ 3.7 million and $ 11.1 million, respectively, during the same periods in 2024. The Company repaid $ 50.0 million of the outstanding principal amount of the 2024 Amended Facility on July 19, 2024. ​ 12 Table of Contents Under the 2025 Amended Facility, the Company must remain current in its periodic reporting requirements. Unless the Company maintains a minimum market capitalization threshold of at least $ 1,200.0 million, the Company, beginning January 1, 2027 (the “Test Date”), is required at all times to keep a minimum cash balance deposited in bank accounts in the U.S. of at least the lesser of (i) 65 % of the outstanding balance of aggregate principal due, provided that such percentage will be reduced to 50 % upon the occurrence of the approval of a BLA for AMT-130 prior to June 15, 2027, and further reduced to 35 % upon the occurrence of the contractually defined commercial milestones or (ii) 100 % of worldwide cash and cash equivalents. The 2025 Amended Facility also provides for a certain performance covenant related to AMT-130 net product revenue which would apply nine months past a potential BLA approval of AMT-130, unless the Company maintains a minimum market capitalization threshold of at least $ 1,200.0 million. The 2025 Amended Facility restricts the Company’s ability, among other things, to incur future indebtedness and obtain additional debt financing, make investments in securities or in other companies, transfer assets, perform certain corporate changes, own or hold certain digital assets, make loans to employees, officers, and directors, and make dividend payments and other distributions to its shareholders. The 2025 Amended Facility is secured by a direct or indirect pledge of the Company’s total assets of $ 888.4 million, less $ 80.6 million of cash and cash equivalents and other current assets held by the Company, and $ 88.7 million of other current assets and investments held by uniQure France SAS as well as receivables sold to HemB SPV, L.P. as described in Note 8 “ Royalty Financing Agreement” . In accordance with the 2025 Amended Facility, the Company was in compliance with all applicable covenants as of September 30, 2025. ​ ​ 8 Royalty Financing Agreement ​ In May 2023, the Company entered into a royalty purchase agreement (the “Royalty Financing Agreement”) with HemB SPV, L.P. (the “Purchaser”). Under the terms of the Royalty Financing Agreement, the Company received an upfront payment of $ 375.0 million in exchange for its rights to the lowest royalty tier on CSL Behring LLC’s (“CSL Behring”) worldwide net sales of etranacogene dezaparvovec-drlb (HEMGENIX®) for certain current and future royalties due to the Company. The Company will be obligated to pay $ 25.0 million of the first worldwide sales milestone payment from CSL Behring, if received, to the Purchaser. The Purchaser will receive 1.85 times the upfront payment (or $ 693.8 million) until June 30, 2032 (“First Hard Cap Date”) if such thresholds are met or, if such cap is not met by June 30, 2032, up to 2.25 times the upfront payment through December 31, 2038 (“Second Hard Cap Date”). If, on or prior to the defined dates for each cap amount, the total amount of royalty payments received by the Purchaser equals or exceeds the cap amount applicable to such date, the Royalty Financing Agreement will automatically terminate and all rights to the HEMGENIX® royalty payments will revert back to the Company. The Company has no obligation to repay any amounts received from the Purchaser in the event that the applicable cap amount is not reached during the term of the Royalty Financing Agreement. The Company has retained the rights to all other royalties, as well as contractual milestones totaling up to $ 1.3 billion, under the terms of the commercialization and license agreement with CSL Behring (the “CSL Behring Agreement”). Net proceeds from the Royalty Financing Agreement were $ 370.1 million. The Company initially recorded these net proceeds as Liability from royalty financing agreement at their fair market value on its Consolidated Balance Sheet as of the date the transaction closed on June 5, 2023. Following the initial recognition, the Company records the debt at amortized cost. 13 Table of Contents As of September 30, 2025 the Company expects to satisfy its commitment to the Purchaser prior to the Second Hard Cap Date. The Company records the difference of $ 473.7 million between the total expected payments of $ 843.8 million to the Purchaser and the $ 370.1 million net proceeds as interest expense over the term using the effective interest rate method. The Company determined the effective interest rate based on the projected cash flows up to the Second Hard Cap Date. As of September 30, 2025 the effective interest rate is expected to be within a range of 10.5 % to 12.0 % per annum, compared to a range of 12.0 % to 13.5 % per annum as of September 30, 2024. The Company would have recorded the following amounts of interest expense if it had used the effective interest rate at the lower and upper end of this range: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended September 30, ​ Nine months ended September 30, ​ 2025 2024 ​ 2025 2024 ​ ​ ​ (in millions) ​ ​ (in millions) Interest expense at effective interest rate of 10.5 % per annum for the three months and nine months ended September 30, 2025, and 12.0 % per annum for the three and nine months ended September 30, 2024, respectively ​ $ 12.3 ​ $ 12.9 ​ $ 35.8 ​ $ 37.4 Interest recorded in the Consolidated Statements of Operations and Comprehensive Loss ​ ​ 13.8 ​ ​ 12.8 ​ ​ 40.9 ​ ​ 37.7 Interest expense at effective interest rate of 12.0 % per annum for the three months and nine months ended September 30, 2025, and 13.5 % per annum for the three and nine months ended September 30, 2024, respectively ​ ​ 14.2 ​ ​ 14.6 ​ ​ 41.1 ​ ​ 42.3 ​ The Company prospectively updates the effective interest rate at each reporting date based on updated cash flow projections. ​ The following table presents the movement in the liability related to the Royalty Financing Agreement between December 31, 2024 and September 30, 2025: ​ ​ ​ ​ ​ ​ Amount of liability ​ ​ (in thousands) Balance as of December 31, 2024 (includes $ 5.0 million presented as "Accrued expenses and other current liabilities") ​ $ 439,881 Royalty payments to the Purchaser ​ ​ ( 11,675 ) Interest expense for the period ​ ​ 40,884 Balance as of September 30, 2025 (includes $ 3.6 million presented as "Accrued expenses and other current liabilities") ​ $ 469,090 ​ ​ ​ ​ 9 Shareholders' equity / (deficit) ​ In January 2025, the Company received net proceeds of $ 70.1 million, after deducting underwriting discounts and commissions and other offering expenses payable by the Company, through a follow-on public offering of 4.4 million ordinary shares at a public offering price of $ 17.00 per ordinary share. ​ In February 2025, the Company received an additional $ 10.4 million in net proceeds after related offering expenses upon the underwriters’ exercise of their option to purchase an additional 0.7 million ordinary shares at the public offering price. ​ In July 2025, the Company entered into a Sales Agreement with Leerink Partners LLC (“Leerink Partners”) with respect to an at-the-market (“ATM”) offering program, under which the Company may, from time to time and at the Company’s sole discretion, offer and sell through Leerink Partners, acting as agent, the Company’s ordinary shares, up to an aggregate offering of $ 200.0 million. As of September 30, 2025, no sales have been made under the ATM offering program. ​ 14 Table of Contents In September 2025, the Company received net proceeds of $ 323.7 million, after deducting underwriting discounts and commissions and other offering expenses payable by the Company, through a follow-on public offering of 6.7 million ordinary shares, at a public offering price of $ 47.50 per ordinary share, and, in lieu of ordinary shares to certain investors, Pre-Funded Warrants to purchase 0.5 million of the Company’s ordinary shares at the public offering price less a $ 0.0001 per ordinary share exercise price. The Company has authorized and reserved a sufficient number of ordinary shares to permit the full exercise of all outstanding Pre-Funded Warrants. The Pre-Funded Warrants are classified as a liability. ​ In connection with the recognition as taxable income of the $ 375.0 million upfront payment received in relation to the Royalty Financing Agreement, and the consumption of $ 30.3 million of losses carried forward, as well as the release of the valuation allowance related to these losses carried forward (refer to Note 14, “I ncome Taxes” ), the Company allocated the tax benefit from the release of the valuation allowance related to net operating loss carryforwards generated by share issuance costs incurred in 2019 to additional paid-in capital. This resulted in an increase in additional paid-in capital of $ 0.9 million in the three and nine months ended September 30, 2025. ​ ​ 10 Share-based compensation ​ The Company’s share-based compensation plans include the amended and restated 2014 Share Incentive Plan (as amended, the “2014 Plan”) and inducement grants under Rule 5653(c)(4) of the Nasdaq Global Select Market with terms similar to the 2014 Plan (together the “2014 Plans”). At the annual general meeting of shareholders in June 2025, the Company’s shareholders authorized an additional 2,400,000 shares for issuance under the 2014 Plan. As of September 30, 2025, a total of 4,414,685 ordinary shares remain available for issuance under the 2014 Plan. ​ In June 2018, the Company’s shareholders adopted and approved the uniQure N.V. Employee Stock Purchase Plan (as amended, the “ESPP”) allowing the Company to issue up to 150,000 ordinary shares. The ESPP is intended to qualify under Section 423 of the Internal Revenue Code of 1986, as amended. Under the ESPP, employees are eligible to purchase ordinary shares through payroll deductions, subject to any plan limitations. The purchase price of the ordinary shares on each purchase date is equal to the lower of: (i) 85 % of the closing market price on the offering date or (ii) 85 % of the closing market price on the purchase date. ​ 2014 Plans and ESPP ​ Share-based compensation expense recognized by classification included in the Consolidated Statements of Operations and Comprehensive Loss in relation to the 2014 Plans and the ESPP for the periods indicated below was as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended September 30, ​ Nine months ended September 30, ​ 2025 2024 2025 2024 ​ ​ (in thousands) ​ (in thousands) Cost of contract manufacturing revenues ​ $ — ​ $ — ​ $ — ​ $ 1,035 Research and development expenses ​ ​ 695 ​ ​ 1,413 ​ ​ 5,916 ​ ​ 7,694 Selling, general and administrative expenses ​ ​ 2,827 ​ ​ 2,025 ​ ​ 7,100 ​ ​ 8,780 Total ​ $ 3,522 ​ $ 3,438 ​ $ 13,016 ​ $ 17,509 ​ Share-based compensation expense recognized by award type for the 2014 Plans as well as the ESPP was as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended September 30, ​ Nine months ended September 30, ​ 2025 2024 2025 2024 ​ ​ (in thousands) ​ (in thousands) Award type/ESPP ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Share options ​ $ 1,829 ​ $ 2,003 ​ $ 5,128 ​ $ 7,576 Restricted share units ​ ​ 2,837 ​ ​ 1,615 ​ ​ 7,597 ​ ​ 10,199 Performance share units ​ ​ ( 1,159 ) ​ ​ ( 180 ) ​ ​ 276 ​ ​ ( 276 ) ESPP ​ ​ 15 ​ ​ — ​ ​ 15 ​ ​ 10 Total ​ $ 3,522 ​ $ 3,438 ​ $ 13,016 ​ $ 17,509 ​ 15 Table of Contents As of September 30, 2025, the unrecognized share-based compensation expense related to unvested awards under the 2014 Plans were: ​ ​ ​ ​ ​ ​ ​ ​ Unrecognized Weighted average ​ share-based remaining ​ ​ compensation ​ period for ​ ​ expense ​ recognition ​ ​ (in thousands) ​ (in years) Award type ​ ​ ​ ​ ​ Share options ​ $ 13,621 ​ 2.63 Restricted share units ​ ​ 20,501 ​ 2.23 Performance share units ​ ​ 166 ​ 0.25 Total ​ $ 34,288 ​ 2.38 ​ The Company satisfies the exercise of share options and vesting of Restricted Share Units (“RSUs”) and Performance Share Units (“PSUs”) through newly issued ordinary shares. ​ Share options Share options are priced on the date of grant and, except for certain grants made to non-executive directors, vest over a period of four years . The first 25 % of each grant vests after one year from the initial grant date and the remainder vests in equal quarterly installments over years two, three and four. Certain grants to non-executive directors vest in full after one year . Any options that vest must be exercised by the tenth anniversary of the initial grant date. The following table summarizes option activity under the 2014 Plans for the nine months ended September 30, 2025: ​ ​ ​ ​ ​ ​ ​ ​ ​ Options ​ ​ Number of ​ Weighted average ​ ordinary shares exercise price ​ ​ ​ ​ ​ ​ Outstanding at December 31, 2024 ​ 4,967,160 ​ ​ 19.87 Granted ​ 1,220,410 ​ $ 12.63 Forfeited ​ ( 118,432 ) ​ $ 13.17 Expired ​ ( 833,550 ) ​ $ 29.86 Exercised ​ ( 553,556 ) ​ $ 15.74 Outstanding at September 30, 2025 ​ 4,682,032 ​ $ 17.04 Thereof, fully vested, and exercisable on September 30, 2025 ​ 2,534,300 ​ $ 21.41 Thereof, outstanding and expected to vest after September 30, 2025 ​ 2,147,732 ​ $ 11.88 Outstanding and expected to vest after December 31, 2024 ​ 1,838,603 ​ $ 11.46 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of options issued during the period (in $ millions) ​ ​ ​ $ 9.4 ​ The fair value of each option issued is estimated at the respective grant date using the Hull & White option pricing model with the following weighted-average assumptions: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended September 30, Nine months ended September 30, ​ 2025 2024 2025 2024 Assumptions ​ ​ ​ ​ ​ ​ ​ ​ Expected volatility ​ 80 % ​ 70 % ​ 70 % - 80 % ​ 70 % Expected terms ​ 10 years ​ 10 years ​ 10 years ​ 10 years Risk-free interest rate ​ 4,38 % ​ 4,32 % ​ 4.36 % - 4.64 % ​ 4,32 % Expected dividend yield ​ 0,0 % ​ 0,0 % ​ 0,0 % ​ 0,0 % ​ 16 Table of Contents RSUs ​ The following table summarizes the RSU activity for the nine months ended September 30, 2025: ​ ​ ​ ​ ​ ​ ​ ​ ​ RSUs ​ ​ Weighted average ​ ​ Number of ​ grant-date fair ​ ​ ordinary shares ​ value Non-vested at December 31, 2024 ​ 1,659,898 ​ $ 10.71 Granted ​ 1,587,990 ​ $ 12.46 Vested ​ ( 747,388 ) ​ $ 12.14 Forfeited ​ ( 213,147 ) ​ $ 10.11 Non-vested at September 30, 2025 ​ 2,287,353 ​ $ 11.51 ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of RSUs granted during the period (in $ millions) ​ ​ ​ $ 19.8 ​ RSUs generally vest over one to three years . RSUs granted to non-executive directors vest one year from the date of grant. ​ PSUs ​ Awards of PSUs are subject to the achievement of specified performance objectives. The fair value of PSUs granted in 2022 and 2024 was determined on the grant date by reference to the market price of the Company’s ordinary shares. ​ The following table summarizes the PSU activity for the nine months ended September 30, 2025: ​ ​ ​ ​ ​ ​ ​ ​ ​ PSUs ​ ​ Weighted average ​ ​ Number of ​ grant-date fair ​ ​ ordinary shares ​ value Non-vested at December 31, 2024 ​ 150,120 ​ $ 21.65 Vested ​ ( 66,500 ) ​ $ 26.70 Forfeited ​ ( 38,620 ) ​ $ 20.24 Non-vested at September 30, 2025 ​ 45,000 ​ $ 15.40 ​ ESPP ​ During the nine months ended September 30, 2025, nil ordinary shares were issued under the ESPP compared to 10,150 ordinary shares issued during the same period in 2024. As of September 30, 2025, 86,712 ordinary shares remain available for issuance under the ESPP compared to a total of 86,712 ordinary shares as of September 30, 2024. ​ 17 Table of Contents ​ 11 Segment Reporting ​ The Company is advancing a pipeline of innovative gene therapies seeking to deliver to patients suffering from rare and other devastating diseases single treatments with potentially curative results. The Company manages the operations related to these research and development activities within one operating segment because they rely on a common set of infrastructure, resources and technology of the products and production processes, types of customers, distribution methods and regulatory environment. ​ The leadership team is identified as the Chief Operating Decision Maker (“CODM”). ​ The CODM allocates resources to research projects and clinical candidates based on scientific data as well as quantitative and qualitative expected risk-adjusted returns on investment. The CODM uses segment operating loss to monitor that cash operating losses remain within the approved budget. ​ The accounting policies of the operating segment are the same as those described in the summary of significant accounting policies. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended September 30, ​ Nine months ended September 30, ​ 2025 2024 ​ 2025 2024 ​ ​ (in thousands) ​ (in thousands) Revenue ​ $ 3,701 ​ $ 2,287 ​ $ 10,530 ​ $ 21,898 Less: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Employee related expenses ​ ( 14,666 ) ​ ( 14,712 ) ​ ( 43,407 ) ​ ( 61,760 ) Laboratory and development expenses ​ ​ ( 18,675 ) ​ ​ ( 9,028 ) ​ ​ ( 50,235 ) ​ ​ ( 27,508 ) Professional fees ​ ​ ( 4,814 ) ​ ​ ( 1,792 ) ​ ​ ( 9,995 ) ​ ​ ( 6,751 ) Facility expenses ​ ​ ( 1,677 ) ​ ​ ( 2,572 ) ​ ​ ( 5,048 ) ​ ​ ( 12,335 ) Consumables ​ ​ ( 750 ) ​ ​ ( 1,439 ) ​ ​ ( 2,383 ) ​ ​ ( 8,123 ) Other segment items (1) ​ ​ ( 2,418 ) ​ ​ ( 2,185 ) ​ ​ ( 5,397 ) ​ ​ ( 10,248 ) Segment operating loss ​ ​ ( 39,299 ) ​ ​ ( 29,441 ) ​ ​ ( 105,935 ) ​ ​ ( 104,827 ) Reconciliation ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Depreciation and amortization expense ​ ​ ( 3,632 ) ​ ​ ( 2,986 ) ​ ​ ( 11,789 ) ​ ​ ( 8,285 ) Share-based compensation expense ​ ​ ( 3,522 ) ​ ​ ( 3,438 ) ​ ​ ( 13,016 ) ​ ​ ( 17,509 ) Fair value loss - contingent consideration ​ ​ ( 1,823 ) ​ ​ 411 ​ ​ ( 5,293 ) ​ ​ 2,032 Fair value loss - liability related to pre-funded warrants ​ ​ ( 5,722 ) ​ ​ — ​ ​ ( 5,722 ) ​ ​ — Foreign currency gains, net ​ ​ ( 428 ) ​ ​ 7,564 ​ ​ 25,382 ​ ​ 5,430 Interest income ​ ​ 3,503 ​ ​ 4,866 ​ ​ 11,154 ​ ​ 17,179 Interest expense - Royalty Financing Agreement ​ ​ ( 13,806 ) ​ ( 12,832 ) ​ ​ ( 40,885 ) ​ ( 37,671 ) Interest expense - Hercules debt facility ​ ​ ( 1,794 ) ​ ​ ( 3,779 ) ​ ​ ( 5,415 ) ​ ​ ( 11,194 ) Other reconciling items ​ ​ ( 5,379 ) ​ ​ ( 4,774 ) ​ ​ ( 818 ) ​ ​ ( 9,877 ) Consolidated loss before income tax expense ​ $ ( 71,903 ) ​ $ ( 44,409 ) ​ $ ( 152,338 ) ​ $ ( 164,722 ) ​ (1) Other segment items included in segment operating loss include costs related to intellectual property, information technology and insurance offset by income related to payments received from European authorities to subsidize the Company’s research and development in the Netherlands. ​ 18 Table of Contents 12 CSL Behring collaboration ​ In June 2020, uniQure biopharma B.V. entered into the CSL Behring Agreement, pursuant to which CSL Behring received the exclusive global rights to HEMGENIX®. Following the divestiture of the Company’s commercial manufacturing activities located in Lexington, MA in July 2024 (the “Lexington Transaction”), the Company determined that it is an agent in the sale of HEMGENIX® to CSL Behring. As a result of the Company being an agent, the Company recognizes corresponding costs related to the purchase of HEMGENIX® from Genezen Holdings Inc. and its affiliate Genezen MA, Inc. (together “Genezen”) net of income from the sales of HEMGENIX® to CSL Behring as well as income related to the release of liabilities associated with expected net losses in Other expense within the Company’s Consolidated Statements of Operations and Comprehensive Loss. Accounts receivable related to collaboration services and royalty revenue were as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, ​ December 31, ​ 2025 2024 ​ ​ (in thousands) Accounts receivable ​ $ 3,883 ​ $ 5,881 Total ​ $ 3,883 ​ $ 5,881 ​ ​ 13 Other income ​ Other income for the three and nine months ended September 30, 2025 and 2024: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended September 30, ​ Nine months ended September 30, ​ 2025 2024 ​ 2025 2024 ​ ​ (in thousands) ​ (in thousands) Sale of critical reagents to Genezen ​ $ — ​ $ — ​ $ 6,000 ​ $ — Research and development grants from Dutch authorities ​ 1,013 ​ 1,071 ​ 4,124 ​ 3,957 Sublease income ​ 488 ​ 333 ​ 1,747 ​ 658 Gain on sale of commercial manufacturing activities ​ ​ — ​ ​ 1,171 ​ ​ — ​ ​ 1,171 Other ​ 9 ​ 16 ​ 542 ​ 164 Total ​ $ 1,510 ​ $ 2,591 ​ $ 12,413 ​ $ 5,950 ​ In the three and nine months ended September 30, 2025 the Company recognized nil and $ 6.0 million in income, respectively, related to a one-time sale of critical reagents to Genezen. There were no sales of critical reagents in the comparative period in 2024. ​ 14 Income taxes ​ The effective income tax rate of 12.0 % and 6.3 % during the three and nine months ended September 30, 2025 (during the three and nine months ended September 30, 2024, ( 0.1 %) and 1.0 %, respectively) was substantially lower than the enacted rate of 25.8 % in the Netherlands as the Company recorded a valuation allowance against its net deferred tax assets in the Netherlands and a partial valuation allowance against its net deferred tax assets in France. ​ Since 2023, the Company has been engaged with the Dutch tax authorities regarding the tax treatment of the $ 375.0 million upfront payment received in exchange for the rights to the lowest royalty tier on CSL Behring’s worldwide net sales of HEMGENIX®. Refer to Note 8, “ Royalty Financing Agreement” . In September 2025, the Dutch tax authorities communicated their position that, for Dutch corporate income tax purposes, the upfront payment would be treated as taxable income in 2023. This would result in a taxable profit instead of a net operating loss for that year. ​ 19 Table of Contents On a provisional basis, the recognition of the $ 375.0 million upfront payment as taxable income resulted in the consumption of $ 30.3 million of losses carried forward, as well as the release of the associated valuation allowance. During the three and nine months ended September 30, 2025, the Company recorded, on a discrete basis, an estimate of $ 7.5 million of current tax expense related to the Dutch operations and $ 1.1 million of related interest expense, in accordance with ASC 740, Income Taxes . These estimates remain subject to change upon finalization of the 2023 filing position. ​ In connection with the estimate and associated release of the valuation allowance, the Company allocated part of such release to the tax benefit of share issuance costs incurred in 2019. This resulted in an increase in additional paid-in capital as well as deferred tax expenses of $ 0.9 million. ​ The following table summarizes the income tax (expense) / benefit for the three and nine months ended September 30, 2025 and 2024, respectively: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended September 30, ​ Nine months ended September 30, ​ 2025 2024 2025 2024 ​ ​ (in thousands) ​ (in thousands) Current tax expense ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Dutch operations ​ $ ( 7,479 ) ​ $ — ​ $ ( 7,479 ) ​ $ — Other ​ ​ ( 42 ) ​ ​ ( 89 ) ​ ​ ( 89 ) ​ ​ ( 160 ) Total current income tax expense ​ $ ( 7,521 ) ​ $ ( 89 ) ​ $ ( 7,568 ) ​ $ ( 160 ) Deferred tax (expense) / benefit ​ ​ ​ ​ ​ ​ ​ ​ Dutch operations ​ $ ( 860 ) ​ $ — ​ $ ( 860 ) ​ $ — Other ​ ​ ( 245 ) ​ ​ 120 ​ ​ ( 1,119 ) ​ ​ ( 1,413 ) Total deferred tax (expense) / benefit ​ ​ ( 1,105 ) ​ ​ 120 ​ ​ ( 1,979 ) ​ ​ ( 1,413 ) Total income tax (expense) / benefit ​ $ ( 8,626 ) ​ $ 31 ​ $ ( 9,547 ) ​ $ ( 1,573 ) ​ ​ 15 Basic and diluted loss per share ​ Diluted loss per share is calculated by adjusting the weighted average number of ordinary shares outstanding, assuming conversion of all potentially dilutive ordinary shares. As the Company incurred a loss in the three and nine months ended September 30, 2025 and September 30, 2024, all potentially dilutive ordinary shares would have an antidilutive effect, if converted, and thus have been excluded from the computation of diluted loss per share for the three and nine months ended September 30, 2025 and September 30, 2024. The ordinary shares are presented without giving effect to the application of the treasury method or exercise prices that would be above the share price as of September 30, 2025 and September 30, 2024, respectively. ​ The potentially dilutive ordinary shares are summarized below: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended September 30, ​ Nine months ended September 30, ​ 2025 2024 2025 2024 Anti-dilutive ordinary share equivalents ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Stock options under 2014 Plans ​ $ 4,682,032 ​ $ 5,425,575 ​ $ 4,682,032 ​ $ 5,425,575 Non-vested RSUs and PSUs ​ ​ 2,332,353 ​ ​ 2,151,809 ​ ​ 2,332,353 ​ ​ 2,151,809 Pre-Funded Warrants ​ ​ 526,316 ​ ​ — ​ ​ 526,316 ​ ​ — ESPP ​ ​ 7,239 ​ ​ — ​ ​ 7,239 ​ ​ — Total anti-dilutive ordinary share equivalents ​ ​ 7,547,940 ​ ​ 7,577,384 ​ ​ 7,547,940 ​ ​ 7,577,384 ​ ​ 20 Table of Contents 16 Subsequent events ​ As of September 30, 2025, the Company recorded its liability related to pre-funded warrants (refer to Note 5, “ Fair value Measurement ”) at a fair value of $ 30.7 million. The Company determined the fair value of the liability using the closing market price of its ordinary shares of $ 58.37 per ordinary share as of September 30, 2025. On November 3, 2025 the Company announced preliminary feedback from the FDA based on discussions at the Company’s pre-BLA meeting. Following such announcement, there was a decrease of the market price of the Company’s ordinary shares to $ 34.29 per ordinary share as of the close of the market on November 3, 2025. This reduced the fair value of the liability related to pre-funded warrants by $ 12.7 million to $ 18.0 million. The Company will determine the fair value of its liability related to pre-funded warrants based on the price of its ordinary shares at the close of the market on December 31, 2025. The Company will record the difference between the fair value as of September 30, 2025 and December 31, 2025 in income during the twelve month period ended December 31, 2025. ​ ​ 21 Table of Contents