uniQure N.V. 10-Q

Item 1. Financial Statements uniQure N.V. UNAUDITED CONSOLIDATED BALANCE SHEETS ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, ​ December 31, ​ 2024 2023 ​ ​ (in thousands, except share and per share amounts) Current assets ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 251,626 ​ $ 241,360 Current investment securities ​ ​ 183,615 ​ ​ 376,532 Accounts receivable ​ ​ 5,322 ​ ​ 4,193 Inventories, net ​ ​ — ​ ​ 12,024 Prepaid expenses ​ ​ 19,286 ​ ​ 15,089 Other current assets and receivables ​ ​ 4,289 ​ ​ 2,655 Total current assets ​ ​ 464,138 ​ ​ 651,853 Non-current assets ​ ​ ​ ​ ​ ​ Property, plant and equipment, net of accumulated depreciation of $ 30.8 million as of September 30, 2024 and $ 55.7 million as of December 31, 2023 ​ ​ 25,566 ​ ​ 46,548 Other investments ​ ​ 28,260 ​ ​ 2,179 Operating lease right-of-use assets ​ ​ 14,833 ​ ​ 28,789 Intangible assets, net, including in-process research and development asset of $ 59.8 million as of September 30, 2024 and $ 59.1 million as of December 31, 2023 ​ ​ 76,609 ​ ​ 60,481 Goodwill ​ ​ 24,084 ​ ​ 26,379 Deferred tax assets, net ​ ​ 10,863 ​ ​ 12,276 Other non-current assets ​ ​ 1,453 ​ ​ 3,184 Total non-current assets ​ ​ 181,668 ​ ​ 179,836 Total assets ​ $ 645,806 ​ $ 831,689 Current liabilities ​ ​ ​ ​ ​ ​ Accounts payable ​ $ 5,441 ​ $ 6,586 Accrued expenses and other current liabilities ​ ​ 32,301 ​ ​ 30,534 Current portion of contingent consideration ​ ​ 29,233 ​ ​ 28,211 Current portion of operating lease liabilities ​ ​ 4,298 ​ ​ 8,344 Total current liabilities ​ ​ 71,273 ​ ​ 73,675 Non-current liabilities ​ ​ ​ ​ ​ ​ Long-term debt ​ ​ 51,113 ​ ​ 101,749 Liability from royalty financing agreement ​ ​ 426,687 ​ ​ 394,241 Operating lease liabilities, net of current portion ​ ​ 12,185 ​ ​ 28,316 Contingent consideration, net of current portion ​ ​ 12,181 ​ ​ 14,795 Deferred tax liability, net ​ ​ 7,627 ​ ​ 7,543 Other non-current liabilities, net of current portion ​ ​ 8,919 ​ ​ 3,700 Total non-current liabilities ​ ​ 518,712 ​ ​ 550,344 Total liabilities ​ ​ 589,985 ​ ​ 624,019 Commitments and contingencies ​ ​ ​ ​ ​ ​ Shareholders' equity ​ ​ ​ ​ ​ ​ Ordinary shares, € 0.05 par value: 80,000,000 shares authorized as of September 30, 2024 and December 31, 2023 and 48,738,874 and 47,833,830 ordinary shares issued and outstanding as of September 30, 2024 and December 31, 2023, respectively ​ ​ 2,932 ​ ​ 2,883 Additional paid-in-capital ​ ​ 1,166,291 ​ ​ 1,148,749 Accumulated other comprehensive loss ​ ​ ( 56,698 ) ​ ​ ( 53,553 ) Accumulated deficit ​ ​ ( 1,056,704 ) ​ ​ ( 890,409 ) Total shareholders' equity ​ ​ 55,821 ​ ​ 207,670 Total liabilities and shareholders' equity ​ $ 645,806 ​ $ 831,689 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, ​ 2024 2023 2024 2023 ​ ​ (in thousands, except share and per share amounts) ​ (in thousands, except share and per share amounts) License revenues ​ $ 2,111 ​ $ 497 ​ $ 5,182 ​ $ 1,290 Contract manufacturing revenues ​ ​ — ​ ​ 349 ​ ​ 6,114 ​ ​ 6,596 Collaboration revenues ​ ​ 176 ​ ​ 561 ​ ​ 10,602 ​ ​ 1,268 Total revenues ​ ​ 2,287 ​ ​ 1,407 ​ ​ 21,898 ​ ​ 9,154 Operating expenses: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cost of license revenues ​ ​ ( 264 ) ​ ​ — ​ ​ ( 648 ) ​ ​ — Cost of contract manufacturing revenues ​ ​ ( 757 ) ​ ​ ( 1,006 ) ​ ​ ( 17,060 ) ​ ​ ( 4,793 ) Research and development expenses ​ ​ ( 30,595 ) ​ ​ ( 65,400 ) ​ ​ ( 104,942 ) ​ ​ ( 172,245 ) Selling, general and administrative expenses ​ ​ ( 11,575 ) ​ ​ ( 18,074 ) ​ ​ ( 41,279 ) ​ ​ ( 57,103 ) Total operating expenses ​ ​ ( 43,191 ) ​ ​ ( 84,480 ) ​ ​ ( 163,929 ) ​ ​ ( 234,141 ) Other income ​ ​ 2,591 ​ ​ 1,424 ​ ​ 5,950 ​ ​ 4,537 Other expense ​ ​ ( 1,915 ) ​ ​ ( 228 ) ​ ​ ( 2,385 ) ​ ​ ( 673 ) Loss from operations ​ ​ ( 40,228 ) ​ ​ ( 81,877 ) ​ ​ ( 138,466 ) ​ ​ ( 221,123 ) Interest income ​ ​ 4,866 ​ ​ 7,495 ​ ​ 17,179 ​ ​ 12,393 Interest expense ​ ​ ( 16,611 ) ​ ​ ( 15,444 ) ​ ​ ( 48,865 ) ​ ​ ( 25,846 ) Foreign currency gains / (losses), net ​ ​ 7,564 ​ ​ 186 ​ ​ 5,430 ​ ​ ( 1,809 ) Loss before income tax (expense) / benefit ​ $ ( 44,409 ) ​ $ ( 89,640 ) ​ $ ( 164,722 ) ​ $ ( 236,385 ) Income tax benefit / (expense) ​ ​ 31 ​ ​ 69 ​ ​ ( 1,573 ) ​ ​ 1,113 Net loss ​ $ ( 44,378 ) ​ $ ( 89,571 ) ​ $ ( 166,295 ) ​ $ ( 235,272 ) Other comprehensive loss: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Foreign currency translation loss, net ​ ​ ( 415 ) ​ ​ ( 6,118 ) ​ ​ ( 3,252 ) ​ ​ ( 267 ) Defined benefit pension gain, net of taxes ​ ​ 37 ​ ​ — ​ ​ 107 ​ ​ — Total comprehensive loss ​ $ ( 44,756 ) ​ $ ( 95,689 ) ​ $ ( 169,440 ) ​ $ ( 235,539 ) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Basic and diluted net loss per ordinary share ​ ​ ( 0.91 ) ​ ​ ( 1.88 ) ​ ​ ( 3.42 ) ​ ​ ( 4.94 ) Weighted average shares used in computing basic and diluted net loss per ordinary share ​ ​ 48,718,533 ​ ​ 47,770,101 ​ ​ 48,576,339 ​ ​ 47,619,875 ​ 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 FOR THE THREE MONTHS ENDED SEPTEMBER 30, 2024 AND 2023 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Accumulated ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Additional ​ other ​ ​ ​ ​ Total ​ Ordinary shares ​ paid-in ​ comprehensive ​ Accumulated ​ shareholders’ ​ No. of shares Amount capital loss deficit equity ​ (in thousands, except share and per share amounts) Balance at June 30, 2023 47,702,331 ​ $ 2,877 ​ $ 1,130,515 ​ $ ( 52,440 ) ​ $ ( 727,632 ) ​ $ 353,320 Loss for the period — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 89,571 ) ​ ​ ( 89,571 ) Other comprehensive loss, net — ​ ​ — ​ ​ — ​ ​ ( 6,118 ) ​ ​ — ​ ​ ( 6,118 ) Exercises of share options 400 ​ ​ — ​ ​ 2 ​ ​ — ​ ​ — ​ ​ 2 Restricted share units distributed during the period 100,296 ​ ​ 5 ​ ​ ( 5 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense — ​ ​ — ​ ​ 11,097 ​ ​ — ​ ​ — ​ ​ 11,097 Issuance of ordinary shares relating to employee stock purchase plan 7,264 ​ ​ 1 ​ ​ 53 ​ ​ — ​ ​ — ​ ​ 54 Balance at September 30, 2023 47,810,291 ​ $ 2,883 ​ $ 1,141,662 ​ $ ( 58,558 ) ​ $ ( 817,203 ) ​ $ 268,784 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 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 ) Exercises 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 ​ ​ 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 FOR THE NINE MONTHS ENDED SEPTEMBER 30, 2024 AND 2023 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Accumulated ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Additional ​ other ​ ​ ​ ​ Total ​ ​ Ordinary shares ​ paid-in ​ comprehensive ​ Accumulated ​ shareholders’ ​ ​ No. of shares Amount capital loss deficit equity ​ ​ (in thousands, except share and per share amounts) Balance at December 31, 2022 ​ 46,968,032 ​ $ 2,838 ​ $ 1,113,393 ​ $ ( 58,291 ) ​ $ ( 581,931 ) ​ $ 476,009 Loss for the period ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 235,272 ) ​ ​ ( 235,272 ) Other comprehensive loss, net ​ — ​ ​ — ​ ​ — ​ ​ ( 267 ) ​ ​ — ​ ​ ( 267 ) Exercises of share options ​ 12,882 ​ ​ 1 ​ ​ 122 ​ ​ — ​ ​ — ​ ​ 123 Restricted and performance share units distributed during the period ​ 817,107 ​ ​ 43 ​ ​ ( 43 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense ​ — ​ ​ — ​ ​ 28,052 ​ ​ — ​ ​ — ​ ​ 28,052 Issuance of ordinary shares relating to employee stock purchase plan ​ 12,270 ​ ​ 1 ​ ​ 138 ​ ​ — ​ ​ — ​ ​ 139 Balance at September 30, 2023 ​ 47,810,291 ​ $ 2,883 ​ $ 1,141,662 ​ $ ( 58,558 ) ​ $ ( 817,203 ) ​ $ 268,784 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 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 ​ 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, ​ 2024 2023 ​ ​ (in thousands) Cash flows from operating activities ​ ​ ​ ​ ​ ​ Net loss ​ $ ( 166,295 ) ​ $ ( 235,272 ) Adjustments to reconcile net loss to net cash used in operating activities: ​ ​ ​ ​ ​ ​ Depreciation and amortization ​ ​ 8,285 ​ ​ 7,712 Amortization of discount on investment securities ​ ​ ( 8,472 ) ​ ​ ( 6,529 ) Share-based compensation expense ​ ​ 17,509 ​ ​ 28,052 Royalty financing agreement interest expense ​ ​ 37,671 ​ ​ 14,940 Deferred tax expense / (income) ​ ​ 1,573 ​ ​ ( 1,113 ) Changes in fair value of contingent consideration ​ ​ ( 2,032 ) ​ ​ 15,441 Provision for inventory write-downs ​ ​ 6,297 ​ ​ — Unrealized foreign exchange (gains) / losses, net ​ ​ ( 5,726 ) ​ ​ 3,119 Other items, net ​ ​ ( 2,460 ) ​ ​ 2,146 Changes in operating assets and liabilities: ​ ​ ​ ​ ​ ​ Accounts receivable, prepaid expenses, and other current assets and receivables ​ ​ ( 5,764 ) ​ ​ 96,551 Inventories ​ ​ ( 3,876 ) ​ ​ ( 8,730 ) Accounts payable ​ ​ ( 512 ) ​ ​ ( 4,784 ) Accrued expenses, other liabilities, and operating leases ​ ​ ( 6,082 ) ​ ​ ( 6,007 ) Contingent consideration milestone payment ​ ​ — ​ ​ ( 1,914 ) Net cash used in operating activities ​ ​ ( 129,884 ) ​ ​ ( 96,388 ) Cash flows from investing activities ​ ​ ​ ​ ​ ​ Proceeds on maturity of debt securities ​ ​ 480,806 ​ ​ 106,307 Investment in debt securities ​ ​ ( 279,586 ) ​ ​ ( 366,439 ) Divestment of commercial manufacturing facility ​ ​ ( 8,300 ) ​ ​ — Purchases of property, plant, and equipment ​ ​ ( 3,328 ) ​ ​ ( 5,116 ) Net cash generated from / (used in) investing activities ​ ​ 189,592 ​ ​ ( 265,248 ) Cash flows from financing activities ​ ​ ​ ​ ​ ​ Proceeds from royalty financing agreement ​ ​ — ​ ​ 374,350 Payment of debt issuance costs ​ ​ — ​ ​ ( 4,288 ) Proceeds from issuance of ordinary shares related to employee stock option and purchase plans ​ ​ 81 ​ ​ 262 Repayment of long-term debt ​ ​ ( 53,050 ) ​ ​ — Contingent consideration milestone payment ​ ​ — ​ ​ ( 7,649 ) Net cash generated (used in) / generated from financing activities ​ ​ ( 52,969 ) ​ ​ 362,675 Currency effect on cash, cash equivalents and restricted cash ​ ​ 1,796 ​ ​ 424 Net increase in cash, cash equivalents and restricted cash ​ ​ 8,535 ​ ​ 1,463 Cash, cash equivalents and restricted cash at beginning of period ​ ​ 244,544 ​ ​ 231,173 Cash, cash equivalents and restricted cash at the end of period ​ $ 253,079 ​ $ 232,636 Cash and cash equivalents ​ $ 251,626 ​ $ 229,484 Restricted cash related to leasehold and other deposits ​ ​ 1,453 ​ ​ 3,152 Total cash, cash equivalents and restricted cash ​ $ 253,079 ​ $ 232,636 Supplemental cash flow disclosures: ​ ​ ​ ​ ​ ​ Cash paid for interest ​ $ ( 16,892 ) ​ $ ( 12,996 ) Non-cash decrease in accounts payables and accrued expenses and other current liabilities related to purchases of property, plant, and equipment ​ $ ( 673 ) ​ $ ( 995 ) ​ 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, and 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 Update 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. There has been a reclassification of $ 2.2 million from Other non-current assets to Other investments within the comparative consolidated balance sheets at December 31, 2023 to improve the consistency and comparability of the consolidated financial statements. ​ 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, 2024, are not necessarily indicative of the results to be expected for the full year ending December 31, 2024, 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, 2023 filed by the Company with the SEC on February 28, 2024 (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 assets and liabilities at the date of the financial statements and reported amounts of revenues and expenses 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, 2023, 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, 2024 except as described within Note 3 “ Divestiture of commercial manufacturing activities ” and Note 5 “ CSL Behring collaboration .” ​ 2.5 Recent accounting pronouncements ​ There have been no new accounting pronouncements or changes to accounting pronouncements during the nine months ended September 30, 2024, as compared to the recent accounting pronouncements described in Note 2.3.27 of the Annual Report , which could be expected to materially impact the Company’s unaudited consolidated financial statements. ​ 3 Divestiture of commercial manufacturing activities ​ Description of transaction ​ On June 29, 2024, affiliates of the Company agreed with Genezen Holdings Inc. and its affiliate Genezen MA, Inc. (together “Genezen”) to sell the Company’s commercial manufacturing activities located in Lexington, MA (the “Lexington Transaction”). The Lexington Transaction closed on July 22, 2024 (the “Closing”). ​ Genezen extended offers of employment to a significant majority of the Company’s employees located at the Lexington facility (the “Lexington Facility”), with the remaining employees terminated effective August 30, 2024. ​ uniQure Inc. and uniQure biopharma B.V., both wholly owned subsidiaries of the Company, entered into an Asset Purchase Agreement (“APA”) with Genezen on June 29, 2024. Pursuant to the APA, Genezen agreed to acquire the manufacturing equipment with a carrying value of $ 5.7 million and related manufacturing operations, inventory with a carrying value of $ 8.8 million and certain other assets with a carrying value of $ 12.3 million associated with the Lexington Facility on Closing. ​ As consideration, the Company received (i) shares of newly issued Series C preferred stock of Genezen Holdings Inc. which are convertible into Genezen common stock and will accrue an 8.0 % per annum cumulative dividend, (ii) a convertible promissory note with a nominal amount of $ 12.5 million, bearing interest at 8.0 % per annum and maturing 63 months following the date of issuance and (iii) a right to purchase HEMGENIX® at terms considered favorable to market terms. ​ The Company recorded the Series C preferred stock in Genezen Holdings Inc. issued to the Company at Closing at its fair market value of $ 12.5 million. The Company subsequently measures these non-marketable equity securities at cost less any impairment, adjusted to fair value if there are observable price changes in orderly transactions for an identical or similar investment of the Genezen Holdings Inc., in accordance with topic ASC 321, Investments – Equity Securities. The value of the Series C preferred stock was $ 12.5 million as of September 30, 2024. ​ 8 Table of Contents The convertible promissory note was recognized at its fair value of $ 13.3 million at Closing. The convertible promissory note is classified as not held for sale and subsequently measured at amortized cost, net of allowance for credit losses in accordance with topic ASC 310, Receivables as it did not meet the definition of a debt security under topic ASC 320, Investments – Debt Securities. The Company accrues interest income on its convertible promissory note using the effective interest method over the convertible promissory note’s contractual term. The convertible promissory note had a balance of $ 13.4 million and nil as of September 30, 2024 and December 31, 2023, respectively. During the three and nine months ended September 30, 2024, the Company recognized $ 0.1 million and $ 0.1 million, respectively, of interest income. As of September 30, 2024, the Company has not recorded an allowance for credit losses related to the convertible promissory note. ​ uniQure Inc., Genezen and the landlord of the Lexington Facility entered into an agreement for uniQure to assign and Genezen to assume the existing lease agreement between uniQure and the landlord at Closing. The Company also amended its original July 2013 guarantee to continue guaranteeing rental payments owed by Genezen until the end of the current term on May 31, 2029. In the event of Genezen’s default related to rental payments owed to the landlord, uniQure is entitled to terminate the assignment agreement and step into the original lease agreement. On Closing, the Company de-recognized its right of use asset with a carrying amount of $ 11.8 million and related lease liability for the facility, of $ 17.9 million, which were classified as held-for-sale as at June 30, 2024. Following the Closing, $ 1.7 million of deposits were released and reclassified from restricted cash into cash. ​ At Closing, uniQure Inc. entered into a Commercial Supply Agreement (“CSA”) with Genezen. Pursuant to the terms of the CSA, the parties agreed to subcontract the manufacturing of HEMGENIX® to Genezen. The CSA includes a minimum term of three years and minimum purchase commitments of HEMGENIX® commercial supplies of $ 43.3 million over the first three years , unless certain contractual provisions are triggered. The CSA provides the Company with rights to purchase HEMGENIX® at terms considered favorable to arms-length market terms. In accordance with ASC 805 Business Combinations, the Company recorded an intangible asset valued at $ 16.7 million with respect to these favorable terms. The intangible asset will be amortized on a straight-line basis over a three-year term, commencing at Closing. Amortization expense of $ 1.2 million (presented within Other expense in the Consolidated Statement of Operations and Comprehensive Loss) was recorded during the three and nine-month periods ended September 30, 2024. ​ The Company’s obligations with respect to the supply of HEMGENIX® to CSL Behring pursuant to the Development and Commercial Supply Agreement between uniQure biopharma B.V. and CSL Behring Inc (the “DCSA”) remain in effect notwithstanding the subcontracting to Genezen. The Company expects to resell HEMGENIX® material purchased from Genezen via its minimum commitments to CSL Behring at a loss. In accordance with ASC 330 Inventory, the Company, at Closing, recognized a liability of $ 8.8 million related to the net losses expected from the purchase of these minimum commitments. The liability is accounted for as a reduction of the consideration received. The Company will subsequently adjust the liability for any changes to the losses expected to be incurred. Changes to the liability are recorded as Other expense within the Company’s Consolidated Statements of Operations and Comprehensive Loss. As of September 30, 2024, the Company classified $ 2.4 million of the liability as accrued expenses and other current liabilities and $ 5.5 million within Other non-current liabilities in the Consolidated Balance Sheets. ​ The Lexington Transaction was accounted for as a divestment of the Company’s commercial manufacturing activities. The net fair value of consideration received of $ 25.4 million, less costs associated with the sale of $ 3.3 million, exceeded the $ 20.9 million fair market value of the net assets transferred (including allocated goodwill) by $ 1.2 million. The excess over the fair market value was recognized as a net gain in Other income on the Company’s Consolidated Statement of Operations and Comprehensive Loss. ​ At Closing, the Company paid a total of $ 8.3 million to Genezen and a third party related to adjustments of working capital and to obtain consent to proceed with the divestment. ​ Additionally, uniQure biopharma B.V. entered into a development and other manufacturing services agreement (“DMSA”) with Genezen at Closing. Pursuant to the DMSA, the Company is entitled to receive, as a preferred customer, manufacturing and development services to support the Company’s investigational gene therapy programs and other services related to HEMGENIX® (other than its manufacturing and supply obligations under the CSA). The DMSA has a minimum term of three years and requires the Company to purchase services for a total minimum of $ 14.0 million. ​ 9 Table of Contents 4 Restructuring ​ As part of the Lexington Transaction, the Company terminated certain employees that did not transfer to Genezen. The Company incurred $ 1.4 million of expenses related to termination benefits offered to these employees, which were recorded as Research and Development Expense and Selling, General and Administrative Expense during the nine-month period ended September 30, 2024. ​ On August 1, 2024, the Company announced an organizational restructuring (the “Restructuring”). As a result, the Company recorded $ 4.1 million of severance and other personnel-related expenses during the three-month period ended September 30, 2024. ​ A summary of the charges for the three and nine months ended September 30, 2024 by major activity type is as follows ( nil in prior periods) : ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended September 30, ​ Nine months ended September 30, ​ ​ 2024 ​ 2024 Severance and other personnel costs ​ (in thousands) Research and development ​ $ 3,378 ​ $ 4,475 General and administrative ​ ​ 706 ​ ​ 1,040 Total ​ $ 4,084 ​ $ 5,515 ​ In October 2023, the Company announced a reorganization and recorded a $ 1.0 million liability as of December 31, 2023 related to the termination of certain employees. A summary of the changes in the severance and other personnel liabilities related to the workforce reduction, which are included within Accrued Expenses and Other Current Liabilities on the Consolidated Balance Sheets, are as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Amount of liability ​ ​ (in thousands) Balance as of December 31, 2023 ​ $ 1,027 Severance and other personnel costs ​ ​ 5,515 Cash payments during the period ​ ​ ( 2,444 ) Balance as of September 30, 2024 ​ $ 4,098 ​ ​ ​ 5 CSL Behring collaboration ​ On June 24, 2020, uniQure biopharma B.V. entered into a commercialization and license agreement with CSL Behring (the “CSL Behring Agreement”), pursuant to which CSL Behring received exclusive global rights to HEMGENIX® . ​ The transaction became fully effective on May 6, 2021. ​ License revenue The Company recognized $ 2.1 million and $ 5.2 million of royalty revenue in the three and nine months ended September 30, 2024, respectively, compared to $ 0.5 million and $ 1.3 million of royalty revenue in the three and nine months ended September 30, 2023, respectively. Royalties on the sale of HEMGENIX® are recorded once earned and are presented as license revenue. ​ ​ ​ 10 Table of Contents Manufacturing revenue The Company recognized nil and $ 6.1 million of manufacturing revenue in the three and nine months ended September 30, 2024, respectively, compared to $ 0.3 million and $ 6.6 million of manufacturing revenue recorded in the three and nine months ended September 30, 2023, respectively. The Company recognized contract manufacturing revenue when ownership transferred to CSL Behring. Following the Closing of the Lexington Transaction, title to HEMGENIX® supply directly passes from the contract manufacturer, Genezen, to CSL Behring. The Company does not control HEMGENIX® before it is transferred to CSL Behring. The Company arranges for HEMGENIX® to be provided by Genezen to CSL Behring. The Company determined that it is an agent in the sale of HEMGENIX® to CSL Behring. In accordance with ASC 330 Inventory , at Closing, the Company recognized a liability of $ 8.8 million related to the expected net losses from the resale of HEMGENIX® to be purchased pursuant to its contractual minimum commitments . As a result of the Company being an agent, the Company recognizes corresponding costs related to the purchase of HEMGENIX® from Genezen net of income from the sales of HEMGENIX® to CSL Behring and 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. Collaboration revenue The Company recognized $ 0.2 million and $ 10.6 million of collaboration revenue in the three and nine months ended September 30, 2024, respectively, compared to $ 0.6 million and $ 1.3 million of collaboration revenue in each of the three and nine months ended September 30, 2023. In accordance with the DCSA, certain development and other services rendered by the Company are reimbursed by CSL Behring. Accounts receivable ​ As of September 30, 2024 , the Company had accounts receivable of $ 5.0 million from CSL Behring related to collaboration services and royalty revenue. ​ As of December 31, 2023, the Company recorded accounts receivable of $ 4.0 million from CSL Behring related to collaboration services, contract manufacturing revenue and royalty revenue. ​ ​ ​ 6 Investment securities The following tables summarize the Company’s investments in sovereign debt as of September 30, 2024 and December 31, 2023: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ At September 30, 2024 ​ ​ Amortized cost ​ Gross unrealized holding gains ​ Gross unrealized holding losses ​ Estimated fair value ​ ​ (in thousands) Current investments: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Government debt securities (held-to-maturity) ​ $ 183,615 ​ $ 250 ​ $ — ​ $ 183,865 Total ​ $ 183,615 ​ $ 250 ​ $ — ​ $ 183,865 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ At December 31, 2023 ​ ​ Amortized cost ​ Gross unrealized holding gains ​ Gross unrealized holding losses ​ Estimated fair value ​ ​ (in thousands) Current investments: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Government debt securities (held-to-maturity) ​ $ 376,532 ​ $ 139 ​ $ — ​ $ 376,671 Total ​ $ 376,532 ​ $ 139 ​ $ — ​ $ 376,671 ​ 11 Table of Contents The Company invests in short-term U.S. and European government bonds with the highest investment credit rating. 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, 2024: $ 44.6 million, December 31, 2023: nil ). ​ Inputs to the fair value of the investments are considered Level 2 inputs. ​ ​ 7 Inventories, net ​ The following table summarizes the inventories, net balances as of September 30, 2024 and December 31, 2023: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, ​ December 31, ​ 2024 2023 ​ ​ (in thousands) Raw materials ​ $ — ​ $ 7,157 Work in progress ​ ​ — ​ ​ 4,109 Finished goods ​ ​ — ​ ​ 758 Inventories ​ $ — ​ $ 12,024 ​ The Company recorded write downs to net realizable value of $ 0.5 million and $ 6.3 million in the three and nine months ended September 30, 2024, respectively, compared to nil in the same periods in 2023. The costs are recognized as Cost of Contract Manufacturing Revenues. At September 30, 2024, and December 31, 2023, the Company recorded an allowance for inventory of nil and $ 1.6 million, respectively. The Company sold its inventories as part of the divestment of its commercial manufacturing activities (refer to Note 3 “ Divestiture of commercial manufacturing activities ” and Note 4 “Restructuring ”). ​ ​ 8 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 Measurements and Disclosures requires disclosure of 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 consolidated balance sheets approximate their fair values due to their short-term maturities. ​ ​ ​ 12 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, 2024 and December 31, 2023 : ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 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) ​ ​ At December 31, 2023 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 241,360 ​ $ — ​ $ — ​ $ 241,360 ​ Cash and cash equivalents Restricted cash ​ ​ 3,184 ​ ​ — ​ ​ — ​ ​ 3,184 ​ Other non-current assets Total assets ​ $ 244,544 ​ $ — ​ $ — ​ $ 244,544 ​ ​ Liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Contingent consideration ​ ​ — ​ ​ — ​ ​ 43,006 ​ ​ 43,006 ​ Contingent consideration Consideration for post-acquisition services ​ ​ — ​ ​ — ​ ​ 457 ​ ​ 457 ​ Other non-current liabilities Total liabilities ​ $ — ​ $ — ​ $ 43,463 ​ $ 43,463 ​ ​ At September 30, 2024 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 251,626 ​ $ — ​ $ — ​ $ 251,626 ​ Cash and cash equivalents Restricted cash ​ ​ 1,453 ​ ​ — ​ ​ — ​ ​ 1,453 ​ Other non-current assets Total assets ​ $ 253,079 ​ $ — ​ $ — ​ $ 253,079 ​ ​ Liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Contingent consideration ​ ​ — ​ ​ — ​ ​ 41,414 ​ ​ 41,414 ​ Contingent consideration Consideration for post-acquisition services ​ ​ — ​ ​ — ​ ​ 415 ​ ​ 415 ​ Other non-current liabilities Total liabilities ​ $ — ​ $ — ​ $ 41,829 ​ $ 41,829 ​ ​ ​ Contingent consideration ​ The Company is required to pay up to EUR 178.8 million (or $ 199.6 million based on the foreign exchange rate on September 30, 2024) to the former shareholders of uniQure France SAS (formerly Corlieve Therapeutics SAS) upon the achievement of contractually defined milestones in connection with the Company’s July 2021 acquisition of uniQure France SAS. ​ The fair value of the contingent consideration as of September 30, 2024 was $ 41.4 million (December 31, 2023: $ 43.0 million) using discount rates of approximately 14.4 % to 15.4 % (December 31, 2023: 15.3 % to 15.6 %). The Company assumes the probability of achieving a EUR 30.0 million (or $ 33.5 million based on the foreign exchange rate on September 30, 2024) milestone payment following the dosing of the first patient in Phase I/II clinical trial of AMT-260 to be 100 %. ​ If, as of September 30, 2024, 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 $ 68.5 million. If as of September 30, 2024 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 contingent consideration between December 31, 2023 and September 30, 2024: ​ ​ ​ ​ ​ ​ Amount of ​ contingent ​ consideration ​ ​ 2024 ​ (in thousands) Balance at December 31, 2023 $ 43,006 Change in fair value (presented within research and development expenses) ​ ( 2,031 ) Currency translation effects ​ 439 Balance at September 30, 2024 $ 41,414 ​ ​ ​ 13 Table of Contents As of September 30, 2024, the Company classified $ 29.2 million (December 31, 2023: $ 28.2 million) of the total contingent consideration of $ 41.4 million (December 31, 2023: $ 43.0 million) as current liabilities. The balance sheet classification 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 6 “ Investment securities ” for the fair value of the investment securities as of September 30, 2024 and December 31, 2023. ​ 9 Accrued expenses and other current liabilities ​ Accrued expenses and other current liabilities include the following items: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ September 30, ​ December 31, ​ 2024 2023 ​ ​ (in thousands) Personnel related accruals and liabilities ​ $ 15,438 ​ $ 16,263 Accruals for goods received from and services provided by vendors-not yet billed ​ ​ 12,350 ​ ​ 12,834 Current portion of firm purchase commitment liability ​ ​ 2,428 ​ ​ - Liability owed to the Purchaser pursuant to the Royalty Financing Agreement ​ ​ 2,085 ​ ​ 1,437 Total ​ $ 32,301 ​ $ 30,534 ​ ​ 10 Long-term debt ​ On June 14, 2013, the Company entered into a venture debt loan facility with Hercules Capital, Inc. (formerly known as Hercules Technology Growth Capital, Inc.) (“Hercules”). The facility was amended and restated in 2014, 2016, 2018, January 2021, December 2021 (the “2021 Restated Facility”), and on May 12, 2023 (the “2023 Amended Facility”) and July 22, 2024 (the “2024 Amended Facility”). ​ On July 19, 2024, in connection with the Closing of the Lexington Transaction and the amendment of the 2023 Amended Facility, the Company prepaid $ 50.0 million of the $ 100.0 million of principal outstanding as well as $ 3.1 million in end-of-term fees. ​ The 2023 Amended Facility extended the maturity date and interest-only period from December 1, 2025 to January 5, 2027 (the “Maturity Date”). ​ The total principal outstanding as of September 30, 2024 under the 2024 Amended Facility was $ 50.0 million. ​ The Company is required to repay the residual principal balance of $ 50.0 million on the Maturity Date. The interest rate is adjustable and is the greater of (i) 7.95 % and (ii) 7.95 % plus the prime rate less 3.25 % per annum. Pursuant to the terms of the 2024 Amended Facility, the Company owes a back-end fee of $ 2.4 million on December 1, 2025 and a back-end fee of $ 0.6 million on the Maturity Date. The amortized cost (including interest due presented as part of accrued expenses and other current liabilities) was $ 51.7 million as of September 30, 2024, compared to $ 102.9 million as of December 31, 2023, and is recorded net of discount and debt issuance costs. The foreign currency gain on the facility in the three months ended September 30, 2024 was $ 2.6 million and the foreign currency loss on the facility in the nine months ended September 30, 2024 was $ 0.4 million compared to a foreign currency loss of $ 3.0 million and $ 1.4 million, respectively, during the same periods in 2023. Interest expense during the three and nine months ended September 30, 2024 was $ 3.7 million and $ 11.1 million, respectively, compared to $ 3.7 million and $ 10.9 million during the same periods in 2023. ​ ​ ​ ​ 14 Table of Contents Under the 2024 Amended Facility, the Company must remain current in its periodic reporting requirements and is required to keep a minimum cash balance deposited in bank accounts in the U.S. equivalent to the lesser of (i) 65 % of the outstanding balance of principal due or (ii) 100 % of worldwide cash and cash equivalents. This restriction on cash and cash equivalents only relates to the location of the cash and cash equivalents, and such cash and cash equivalents can be used at the discretion of the Company. Beginning on April 1, 2024, the Company is required to keep a minimum of unrestricted cash equal to at least 30 % of the loan amount outstanding. In combination with other covenants, the 2024 Amended Facility restricts the Company’s ability to, among other things, incur future indebtedness and obtain additional debt financing, to make investments in securities or in other companies, to transfer assets, to perform certain corporate changes, to make loans to employees, officers, and directors, and to make dividend payments and other distributions to its shareholders. The Company secured the facilities by directly or indirectly pledging its total assets of $ 645.8 million, less $ 1.2 million of cash and cash equivalents and other current assets held by the Company, and $ 89.7 million of other current assets and investment held by uniQure France SAS as well as receivables sold to the Purchaser. Under the 2024 Amended Facility, the occurrence of a material adverse effect, as defined therein, would entitle Hercules to declare all principal, interest and other amounts owed by the Company immediately due and payable. As of September 30, 2024, the Company was in material compliance with all covenants and provisions. ​ 11 Royalty Financing Agreement ​ On May 12, 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’s worldwide net sales of HEMGENIX® for certain current and future royalties due to the Company. The Company is also eligible to receive an additional $ 25.0 million milestone payment under the Royalty Financing Agreement if 2024 net sales of HEMGENIX® exceed a pre-specified threshold, as set forth in the Royalty Financing Agreement. The Purchaser will receive 1.85 times the upfront payment (or $ 693.8 million) and 1.85 times the $ 25.0 million milestone payment (if paid) 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 of the upfront and milestone payment (if paid) through December 31, 2038. If 2024 net sales do not exceed a pre-specified threshold, the Company will be obligated to pay $ 25.0 million to the Purchaser but only to the extent that the Company achieves a future sales milestone under the CSL Behring Agreement. If such milestone payment is not due from CSL Behring, the Company is not obligated to pay any amounts to the Purchaser. 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 CSL Behring Agreement. Net proceeds from the Royalty Financing Agreement, after deducting professional and financial advisory fees related to the transaction of $ 4.9 million, 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 closing of the transaction on June 5, 2023. Following the initial recognition, the Company records the debt at amortized cost. The Company expects to satisfy its commitment to the Purchaser prior to the First Hard Cap Date. The Company will record the difference of $ 323.7 million between the total expected payments of $ 693.8 million to the Purchaser and the $ 370.1 million net proceeds as interest expense using the effective interest rate method. The Company determined the effective interest rate based on the projected cash flows up to the First Hard Cap Date. Based on the Company’s projections the effective interest rate is expected to be within a range of 12.0 % per annum to 13.5 % per annum. Interest expense during the three and nine months ended September 30, 2024 was $ 12.8 and $ 37.7 million, respectively, compared to $ 11.8 million and $ 14.9 million, during the same period in 2023. The Company would have recorded between $ 37.4 million and $ 42.3 million of interest expense through the nine months ended September 30, 2024 ( $ 12.9 million and $ 14.6 million, respectively, for the three months ended September 30, 2024) if it had used 12.0 % or 13.5 % instead. The Company will prospectively update the effective interest rate at each reporting date based on updated projections. ​ The liability was initially recognized at fair value and inputs were considered Level 3 inputs. ​ ​ 15 Table of Contents The following table presents the movement in the liability related to the Royalty Financing Agreement between the December 31, 2023 and September 30, 2024: ​ ​ ​ ​ ​ ​ ​ Amount of liability ​ ​ (in thousands) Balance as of December 31, 2023 (includes $ 1.4 million presented as "Accrued expenses and other current liabilities) ​ $ 395,678 Royalty payments to Purchaser ​ ​ ( 4,577 ) Liability owed to the Purchaser (presented as "Accrued expense and other current liabilities") ​ ​ ( 2,085 ) Interest expense for the period ​ ​ 37,671 Liability related to the royalty financing agreement ​ $ 426,687 ​ ​ ​ 12 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 2024, the Company’s shareholders approved an increase in the number of ordinary shares authorized for issuance under the 2014 Plan from 14,351,471 to 15,851,471 . ​ In June 2018, the Company’s shareholders adopted and approved an employee share purchase plan (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 85 % of the lower of the closing market price on the offering date and the closing market price on the purchase date of each three-month offering period. ​ 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, ​ 2024 2023 ​ 2024 ​ 2023 ​ ​ (in thousands) ​ (in thousands) Cost of manufacturing services revenue ​ $ — ​ $ 315 ​ $ 1,035 ​ $ 477 Research and development ​ ​ 1,413 ​ ​ 5,638 ​ ​ 7,694 ​ ​ 14,675 Selling, general and administrative ​ ​ 2,025 ​ ​ 5,144 ​ ​ 8,780 ​ ​ 12,900 Total ​ $ 3,438 ​ $ 11,097 ​ $ 17,509 ​ $ 28,052 ​ Share-based compensation expense / (income) 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, ​ 2024 2023 ​ 2024 ​ 2023 ​ ​ (in thousands) ​ (in thousands) Award type/ESPP ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Share options ​ $ 2,003 ​ $ 3,497 ​ $ 7,576 ​ $ 10,256 Restricted share units ​ ​ 1,615 ​ ​ 5,293 ​ ​ 10,199 ​ ​ 15,311 Performance share units ​ ​ ( 180 ) ​ ​ 2,299 ​ ​ ( 276 ) ​ ​ 2,461 Employee share purchase plan ​ ​ — ​ ​ 8 ​ ​ 10 ​ ​ 24 Total ​ $ 3,438 ​ $ 11,097 ​ $ 17,509 ​ $ 28,052 ​ 16 Table of Contents As of September 30, 2024, 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 ​ $ 13,083 ​ 2.21 Restricted share units ​ ​ 15,113 ​ 1.67 Performance share units ​ ​ 20 ​ 0.04 Total ​ $ 28,216 ​ 1.92 ​ 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. ​ The Company will account for the forfeitures of awards to employees impacted by the August 2024 restructuring as of the date employment with the Company ends, which is expected to occur between November 2024 and June 2025. The Company expects this to reduce the unrecognized share-based compensation expense by approximately $ 3.2 million. ​ 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 tables summarize option activity under the 2014 Plans for the nine months ended September 30, 2024: ​ ​ ​ ​ ​ ​ ​ ​ ​ Options ​ ​ Number of ​ Weighted average ​ ordinary shares exercise price ​ ​ ​ ​ ​ ​ Outstanding at December 31, 2023 ​ 4,974,030 ​ ​ 23.25 Granted ​ 1,093,080 ​ $ 5.47 Forfeited ​ ( 285,065 ) ​ $ 16.05 Expired ​ ( 352,570 ) ​ $ 29.90 Exercised ​ ( 3,900 ) ​ $ 8.22 Outstanding at September 30, 2024 ​ 5,425,575 ​ $ 19.63 Thereof, fully vested, and exercisable on September 30, 2024 ​ 3,233,831 ​ $ 24.50 Thereof, outstanding and expected to vest after September 30, 2024 ​ 2,191,744 ​ $ 12.43 ​ ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of options issued during the period (in $ millions) ​ ​ ​ $ 3.5 ​ 17 Table of Contents As a result of the August 2024 restructuring, 67,755 options are expected to be forfeited between November 2024 and June 2025. ​ 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, ​ 2024 2023 2024 2023 Assumptions ​ ​ ​ ​ ​ ​ ​ ​ Expected volatility ​ 70 % ​ 70 % ​ 70 % ​ 70 % Expected terms ​ 10 years ​ 10 years ​ 10 years ​ 10 years Risk free interest rate ​ 4.32 % ​ 3.71 % - 4.00 % ​ 4.32 % ​ 3.71 % - 4.10 % Expected dividend yield ​ 0 % ​ 0 % ​ 0 % ​ 0 % ​ RSUs ​ The following table summarizes the RSU activity for the nine months ended September 30, 2024: ​ ​ ​ ​ ​ ​ ​ ​ ​ RSUs ​ ​ Weighted average ​ ​ Number of ​ grant-date fair ​ ​ ordinary shares ​ value Non-vested at December 31, 2023 ​ 2,264,369 ​ $ 18.07 Granted ​ 1,311,360 ​ $ 5.49 Vested ​ ( 890,994 ) ​ $ 19.98 Forfeited ​ ( 703,206 ) ​ $ 12.49 Non-vested at September 30, 2024 ​ 1,981,529 ​ $ 10.85 ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of RSUs granted during the period (in $ millions) ​ ​ ​ $ 7.2 ​ RSUs generally vest over one to three years . RSUs granted to non-executive directors vest one year from the date of grant. ​ As a result of the August 2024 restructuring, 229,113 RSUs are expected to be forfeited between November 2024 and June 2025. ​ PSUs ​ The following table summarizes the PSU activity for the nine months ended September 30, 2024: ​ ​ ​ ​ ​ ​ ​ ​ ​ PSUs ​ ​ Weighted average ​ ​ Number of ​ grant-date fair ​ ​ ordinary shares ​ value Non-vested at December 31, 2023 ​ 222,550 ​ $ 28.09 Forfeited ​ ( 52,270 ) ​ $ 28.04 Non-vested at September 30, 2024 ​ 170,280 ​ $ 27.88 ​ The Company granted ordinary shares to certain employees in December 2021 and at various dates during the year ended December 31, 2022 that will be earned upon achievement of defined milestones. Earned ordinary shares will vest upon the later of a minimum service period of one year or three years , or the achievement of defined milestones, subject to the grantee’s continued employment. In addition, portions of the ordinary shares granted in December 2021 to executives and other members of senior management are subject to achieving a minimum total shareholder return relative to the NASDAQ Biotechnology Index. The Company recognizes the compensation cost related to these grants to the extent it considers achievement of the milestones to be probable. As of September 30, 2024, three milestones had been achieved. Additionally, another milestone was achieved in October 2024. ​ 18 Table of Contents ESPP ​ During the nine months ended September 30, 2024, 10,150 ordinary shares were issued under the ESPP compared to 12,270 during the same period in 2023. As of September 30, 2024, 86,712 ordinary shares remain available for issuance under the ESPP compared to a total of 103,790 as of September 30, 2023. ​ 13 Income taxes ​ The Company recorded $ 0.0 million deferred tax benefit and $ 1.6 million deferred tax expense in relation to its operations in the U.S. during the three and nine months ended September 30, 2024, respectively. The Company recorded $ 0.1 million and $ 1.1 million deferred tax benefit in relation to its operations in the U.S. and France during the three and nine months ended September 30, 2023, respectively. ​ The effective income tax rate of ( 0.1 %) and 1.0 % during the three and nine months ended September 30, 2024 is substantially lower than the enacted rate of 25.8 % in the Netherlands as the Company records a valuation allowance against its net deferred tax assets in the Netherlands and a partial a valuation allowance against its net deferred tax assets in France. The effective income tax rate during the three and nine months ended September 30, 2023 was ( 0.1 %) and ( 0.5 %), respectively, as the Company had recorded a valuation allowance against its net deferred tax assets in the Netherlands. ​ ​ 14 Basic and diluted earnings per share ​ Diluted earnings per share are calculated by adjusting the weighted average number of ordinary shares outstanding, assuming conversion of all potentially dilutive ordinary shares. As the Company has incurred a loss in the three and nine months ended September 30, 2024, all potentially dilutive ordinary shares would have an antidilutive effect, if converted, and thus have been excluded from the computation of loss per share for the three and nine months ended 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, 2024 and September 30, 2023, respectively. ​ The potentially dilutive ordinary shares are summarized below: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended September 30, ​ Nine months ended September 30, ​ 2024 2023 ​ 2024 ​ 2023 Anti-dilutive ordinary share equivalents ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Stock options under 2014 Plans and previous plan ​ ​ 5,425,575 ​ ​ 5,411,599 ​ ​ 5,425,575 ​ ​ 5,411,599 Non-vested RSUs and PSUs ​ ​ 2,151,809 ​ ​ 2,749,755 ​ ​ 2,151,809 ​ ​ 2,749,755 ESPP ​ ​ — ​ ​ 2,857 ​ ​ — ​ ​ 2,857 Total anti-dilutive ordinary share equivalents ​ ​ 7,577,384 ​ ​ 8,164,211 ​ ​ 7,577,384 ​ ​ 8,164,211 ​ ​ 15 Subsequent events ​ None. ​ 19 Table of Contents