uniQure N.V. 10-Q

Item 1. Financial Statements uniQure N.V. UNAUDITED CONSOLIDATED BALANCE SHEETS ​ ​ ​ ​ ​ ​ ​ ​ ​ June 30, ​ December 31, ​ 2024 2023 ​ ​ (in thousands, except share and per share amounts) Current assets ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 287,877 ​ $ 241,360 Current investment securities ​ ​ 236,553 ​ ​ 376,532 Accounts receivable ​ ​ 7,850 ​ ​ 4,193 Inventories, net ​ ​ — ​ ​ 12,024 Prepaid expenses ​ ​ 18,278 ​ ​ 15,089 Assets held for sale ​ ​ 37,964 ​ ​ — Other current assets and receivables ​ ​ 3,446 ​ ​ 2,655 Total current assets ​ ​ 591,968 ​ ​ 651,853 Non-current assets ​ ​ ​ ​ ​ ​ Property, plant and equipment, net of accumulated depreciation of $ 27.9 million as of June 30, 2024 and $ 55.7 million as of December 31, 2023 ​ ​ 26,186 ​ ​ 46,548 Operating lease right-of-use assets ​ ​ 14,925 ​ ​ 28,789 Intangible assets, net, including in-process research and development asset of $ 57.4 million as of June 30, 2024 and $ 59.1 million as of December 31, 2023 ​ ​ 58,659 ​ ​ 60,481 Goodwill ​ ​ 23,112 ​ ​ 26,379 Deferred tax assets, net ​ ​ 10,718 ​ ​ 12,276 Other non-current assets ​ ​ 5,278 ​ ​ 5,363 Total non-current assets ​ ​ 138,878 ​ ​ 179,836 Total assets ​ $ 730,846 ​ $ 831,689 Current liabilities ​ ​ ​ ​ ​ ​ Accounts payable ​ $ 4,407 ​ $ 6,586 Accrued expenses and other current liabilities ​ ​ 26,491 ​ ​ 30,534 Current portion of contingent consideration ​ ​ 28,060 ​ ​ 28,211 Current portion of operating lease liabilities ​ ​ 3,625 ​ ​ 8,344 Liabilities held for sale ​ ​ 17,885 ​ ​ — Total current liabilities ​ ​ 80,468 ​ ​ 73,675 Non-current liabilities ​ ​ ​ ​ ​ ​ Long-term debt ​ ​ 102,507 ​ ​ 101,749 Liability from royalty financing agreement ​ ​ 415,940 ​ ​ 394,241 Operating lease liabilities, net of current portion ​ ​ 12,369 ​ ​ 28,316 Contingent consideration, net of current portion ​ ​ 12,078 ​ ​ 14,795 Deferred tax liability, net ​ ​ 7,323 ​ ​ 7,543 Other non-current liabilities ​ ​ 3,054 ​ ​ 3,700 Total non-current liabilities ​ ​ 553,271 ​ ​ 550,344 Total liabilities ​ ​ 633,739 ​ ​ 624,019 Commitments and contingencies ​ ​ ​ ​ ​ ​ Shareholders' equity ​ ​ ​ ​ ​ ​ Ordinary shares, € 0.05 par value: 80,000,000 shares authorized as of June 30, 2024 and December 31, 2023 and 48,694,569 and 47,833,830 ordinary shares issued and outstanding as of June 30, 2024 and December 31, 2023, respectively ​ ​ 2,930 ​ ​ 2,883 Additional paid-in-capital ​ ​ 1,162,823 ​ ​ 1,148,749 Accumulated other comprehensive loss ​ ​ ( 56,320 ) ​ ​ ( 53,553 ) Accumulated deficit ​ ​ ( 1,012,326 ) ​ ​ ( 890,409 ) Total shareholders' equity ​ ​ 97,107 ​ ​ 207,670 Total liabilities and shareholders' equity ​ $ 730,846 ​ $ 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 June 30, ​ Six months ended June 30, ​ 2024 2023 2024 2023 ​ ​ (in thousands, except share and per share amounts) ​ (in thousands, except share and per share amounts) License revenues ​ $ 1,869 ​ $ 793 ​ $ 3,071 ​ $ 793 Contract manufacturing revenues ​ ​ 2,124 ​ ​ 1,310 ​ ​ 6,114 ​ ​ 6,247 Collaboration revenues ​ ​ 7,133 ​ ​ 319 ​ ​ 10,426 ​ ​ 707 Total revenues ​ ​ 11,126 ​ ​ 2,422 ​ ​ 19,611 ​ ​ 7,747 Operating expenses: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cost of license revenues ​ ​ ( 234 ) ​ ​ — ​ ​ ( 384 ) ​ ​ — Cost of contract manufacturing revenues ​ ​ ( 7,227 ) ​ ​ ( 1,352 ) ​ ​ ( 16,303 ) ​ ​ ( 3,787 ) Research and development expenses ​ ​ ( 33,655 ) ​ ​ ( 46,036 ) ​ ​ ( 74,347 ) ​ ​ ( 106,845 ) Selling, general and administrative expenses ​ ​ ( 15,767 ) ​ ​ ( 21,181 ) ​ ​ ( 29,704 ) ​ ​ ( 39,029 ) Total operating expenses ​ ​ ( 56,883 ) ​ ​ ( 68,569 ) ​ ​ ( 120,738 ) ​ ​ ( 149,661 ) Other income ​ ​ 1,983 ​ ​ 1,302 ​ ​ 3,359 ​ ​ 3,113 Other expense ​ ​ ( 236 ) ​ ​ ( 229 ) ​ ​ ( 470 ) ​ ​ ( 445 ) Loss from operations ​ ​ ( 44,010 ) ​ ​ ( 65,074 ) ​ ​ ( 98,238 ) ​ ​ ( 139,246 ) Interest income ​ ​ 5,805 ​ ​ 3,229 ​ ​ 12,313 ​ ​ 4,898 Interest expense ​ ​ ( 16,157 ) ​ ​ ( 6,840 ) ​ ​ ( 32,254 ) ​ ​ ( 10,402 ) Foreign currency losses, net ​ ​ ( 989 ) ​ ​ 374 ​ ​ ( 2,134 ) ​ ​ ( 1,995 ) Loss before income tax (expense) / benefit ​ $ ( 55,351 ) ​ $ ( 68,311 ) ​ $ ( 120,313 ) ​ $ ( 146,745 ) Income tax (expense) / benefit ​ ​ ( 948 ) ​ ​ ( 163 ) ​ ​ ( 1,604 ) ​ ​ 1,044 Net loss ​ $ ( 56,299 ) ​ $ ( 68,474 ) ​ $ ( 121,917 ) ​ $ ( 145,701 ) Other comprehensive (loss) / income: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Foreign currency translation (loss) / gains, net ​ ​ ( 313 ) ​ ​ 54 ​ ​ ( 2,837 ) ​ ​ 5,851 Defined benefit pension gain, net of taxes ​ ​ 35 ​ ​ — ​ ​ 70 ​ ​ — Total comprehensive loss ​ $ ( 56,577 ) ​ $ ( 68,420 ) ​ $ ( 124,684 ) ​ $ ( 139,850 ) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Basic and diluted net loss per ordinary share ​ ​ ( 1.16 ) ​ ​ ( 1.44 ) ​ ​ ( 2.51 ) ​ ​ ( 3.06 ) Weighted average shares used in computing basic and diluted net loss per ordinary share ​ ​ 48,622,440 ​ ​ 47,649,520 ​ ​ 48,503,475 ​ ​ 47,543,516 ​ 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 JUNE 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 March 31, 2023 47,546,673 ​ $ 2,869 ​ $ 1,121,554 ​ $ ( 52,494 ) ​ $ ( 659,158 ) ​ $ 412,771 Loss for the period — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 68,474 ) ​ ​ ( 68,474 ) Other comprehensive income — ​ ​ — ​ ​ — ​ ​ 54 ​ ​ — ​ ​ 54 Exercises of share options 2,427 ​ ​ — ​ ​ 34 ​ ​ — ​ ​ — ​ ​ 34 Restricted share units distributed during the period 150,720 ​ ​ 8 ​ ​ ( 8 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense — ​ ​ — ​ ​ 8,894 ​ ​ — ​ ​ — ​ ​ 8,894 Issuance of ordinary shares relating to employee stock purchase plan 2,511 ​ ​ — ​ ​ 41 ​ ​ — ​ ​ — ​ ​ 41 Balance at June 30, 2023 47,702,331 ​ $ 2,877 ​ $ 1,130,515 ​ $ ( 52,440 ) ​ $ ( 727,632 ) ​ $ 353,320 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Balance at March 31, 2024 48,492,357 ​ $ 2,919 ​ $ 1,155,904 ​ $ ( 56,042 ) ​ $ ( 956,027 ) ​ $ 146,754 Loss for the period — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 56,299 ) ​ ​ ( 56,299 ) Other comprehensive loss, net — ​ ​ — ​ ​ — ​ ​ ( 278 ) ​ ​ — ​ ​ ( 278 ) Restricted share units distributed during the period 192,062 ​ ​ 10 ​ ​ ( 10 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense — ​ ​ — ​ ​ 6,880 ​ ​ — ​ ​ — ​ ​ 6,880 Issuance of ordinary shares relating to employee stock purchase plan 10,150 ​ ​ 1 ​ ​ 49 ​ ​ — ​ ​ — ​ ​ 50 Balance at June 30, 2024 48,694,569 ​ $ 2,930 ​ $ 1,162,823 ​ $ ( 56,320 ) ​ $ ( 1,012,326 ) ​ $ 97,107 ​ ​ 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 SIX MONTHS ENDED JUNE 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 ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 145,701 ) ​ ​ ( 145,701 ) Other comprehensive income ​ — ​ ​ — ​ ​ — ​ ​ 5,851 ​ ​ — ​ ​ 5,851 Exercises of share options ​ 12,482 ​ ​ 1 ​ ​ 120 ​ ​ — ​ ​ — ​ ​ 121 Restricted and performance share units distributed during the period ​ 716,811 ​ ​ 38 ​ ​ ( 38 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense ​ — ​ ​ — ​ ​ 16,955 ​ ​ — ​ ​ — ​ ​ 16,955 Issuance of ordinary shares relating to employee stock purchase plan ​ 5,006 ​ ​ — ​ ​ 85 ​ ​ — ​ ​ — ​ ​ 85 Balance at June 30, 2023 ​ 47,702,331 ​ $ 2,877 ​ $ 1,130,515 ​ $ ( 52,440 ) ​ $ ( 727,632 ) ​ $ 353,320 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Balance at December 31, 2023 ​ 47,833,830 ​ $ 2,883 ​ $ 1,148,749 ​ $ ( 53,553 ) ​ $ ( 890,409 ) ​ $ 207,670 Loss for the period ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 121,917 ) ​ ​ ( 121,917 ) Other comprehensive loss, net ​ — ​ ​ — ​ ​ — ​ ​ ( 2,767 ) ​ ​ — ​ ​ ( 2,767 ) Restricted share units distributed during the period ​ 850,589 ​ ​ 46 ​ ​ ( 46 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense ​ — ​ ​ — ​ ​ 14,071 ​ ​ — ​ ​ — ​ ​ 14,071 Issuance of ordinary shares relating to employee stock purchase plan ​ 10,150 ​ ​ 1 ​ ​ 49 ​ ​ — ​ ​ — ​ ​ 50 Balance at June 30, 2024 ​ 48,694,569 ​ $ 2,930 ​ $ 1,162,823 ​ $ ( 56,320 ) ​ $ ( 1,012,326 ) ​ $ 97,107 ​ 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 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Six months ended June 30, ​ 2024 2023 ​ ​ (in thousands) Cash flows from operating activities ​ ​ ​ ​ ​ ​ Net loss ​ $ ( 121,917 ) ​ $ ( 145,701 ) Adjustments to reconcile net loss to net cash used in operating activities: ​ ​ ​ ​ ​ ​ Depreciation and amortization ​ ​ 5,299 ​ ​ 5,115 Amortization of discount on investment securities ​ ​ ( 6,672 ) ​ ​ ( 1,837 ) Share-based compensation expense ​ ​ 14,071 ​ ​ 16,955 Royalty financing agreement interest expense ​ ​ 24,840 ​ ​ 3,154 Deferred tax expense / (income) ​ ​ 1,604 ​ ​ ( 1,044 ) Changes in fair value of contingent consideration ​ ​ ( 1,621 ) ​ ​ 1,212 Provision for inventory write-downs ​ ​ 5,839 ​ ​ - Unrealized foreign exchange losses, net ​ ​ 2,940 ​ ​ 944 Other items, net ​ ​ 1,681 ​ ​ 1,006 Changes in operating assets and liabilities: ​ ​ ​ ​ ​ ​ Accounts receivable, prepaid expenses, and other current assets and receivables ​ ​ ( 7,227 ) ​ ​ 813 Inventories ​ ​ ( 2,606 ) ​ ​ ( 3,288 ) Accounts payable ​ ​ ( 1,619 ) ​ ​ ( 1,212 ) Accrued expenses, other liabilities, and operating leases ​ ​ ( 7,898 ) ​ ​ ( 11,416 ) Net cash used in operating activities ​ ​ ( 93,286 ) ​ ​ ( 135,299 ) Cash flows from investing activities ​ ​ ​ ​ ​ ​ Proceeds on maturity of debt securities ​ ​ 297,806 ​ ​ 52,234 Investment in debt securities ​ ​ ( 152,936 ) ​ ​ - Purchases of property, plant, and equipment ​ ​ ( 2,948 ) ​ ​ ( 3,416 ) Net cash generated from investing activities ​ ​ 141,922 ​ ​ 48,818 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 ​ ​ 50 ​ ​ 206 Net cash generated from financing activities ​ ​ 50 ​ ​ 370,268 Currency effect on cash, cash equivalents and restricted cash ​ ​ ( 2,191 ) ​ ​ 1,812 Net increase in cash, cash equivalents and restricted cash ​ ​ 46,495 ​ ​ 285,599 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 ​ $ 291,039 ​ $ 516,772 Cash and cash equivalents ​ $ 287,877 ​ $ 513,598 Restricted cash related to leasehold and other deposits ​ ​ 3,162 ​ ​ 3,174 Total cash, cash equivalents and restricted cash ​ $ 291,039 ​ $ 516,772 Supplemental cash flow disclosures: ​ ​ ​ ​ ​ ​ Cash paid for interest ​ $ ( 9,261 ) ​ $ ( 8,882 ) Non-cash decrease in accounts payables and accrued expenses and other current liabilities related to purchases of property, plant, and equipment ​ $ ( 458 ) ​ $ ( 651 ) ​ 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. ​ 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 six months ended June 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 six months ended June 30, 2024 except as described within Note 3 “ Assets held for sale and divestiture of commercial manufacturing facilities ”. ​ 2.5 Recent accounting pronouncements ​ There have been no new accounting pronouncements or changes to accounting pronouncements during the six months ended June 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 Assets held for sale and divestiture of commercial manufacturing activities ​ Description of transaction ​ On June 29, 2024, the Company and its affiliates entered into various agreements with Genezen Holdings Inc. and its affiliate Genezen MA, Inc. (together “Genezen”) to sell its commercial manufacturing activities located in Lexington, MA (the “Lexington Facility”) (the “Lexington Transaction”). The transaction closed on July 22, 2024 (the “Closing”). As consideration, the Company received (i) shares of newly issued Series C preferred stock of Genezen Holdings Inc. valued at $ 12.5 million, which are convertible into common stock and will accrue an 8.0 % per annum cumulative dividend, and (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. ​ uniQure Inc. and uniQure biopharma B.V. (the “Sellers”), both wholly owned subsidiaries of the Company (together “Company”) entered into an asset purchase agreement (“APA”) with Genezen. Pursuant to the APA, Genezen agreed to acquire the manufacturing equipment and related manufacturing operations along with certain other assets associated with the Lexington Facility. ​ 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. uniQure N.V. 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. ​ Genezen extended offers of employment to a significant majority of the Company’s employees located at the Lexington Facility, with the remaining employees terminated effective August 30, 2024. ​ Concurrent with entering into the APA, uniQure Inc. entered into a commercial supply agreement (“CSA”) with Genezen. Pursuant to the terms of the CSA, the Company subcontracted 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 Company will continue to sell these HEMGENIX® commercial supplies to CSL Behring in accordance with the Development and Commercial Supply Agreement between uniQure biopharma B.V. and CSL Behring Inc. ​ 8 Table of Contents Additionally, uniQure biopharma B.V. entered into a development and other manufacturing services agreement (“DMSA”) with Genezen. Pursuant to the terms of the DMSA, the Company has preferred customer status to receive manufacturing and development services to support the Company’s investigational gene therapy programs and other services related to the manufacture of HEMGENIX® 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. ​ The CSA and DMSA became effective at Closing. ​ On July 19, 2024, in connection with the closing of the Lexington Transaction, the Company prepaid $ 50.0 million of the $ 100.0 million of principal outstanding under its amended and restated loan facility with Hercules Capital, Inc. ​ Accounting as of June 30, 2024 ​ The Company classified the following assets and liabilities as held for sale as of June 30, 2024: ​ ​ ​ ​ ​ ​ ​ ​ (in thousands) ​ ​ $ ​ Inventories, net ​ ​ 8.0 Prepaid expenses ​ ​ 0.3 Property, plant and equipment, net of accumulated depreciation ​ ​ 15.3 Operating lease right-of-use asset ​ ​ 11.9 Goodwill ​ ​ 2.5 Total assets held for sale ​ $ 38.0 ​ ​ ​ ​ Operating lease liability ​ ​ 17.9 Total liabilities held for sale ​ $ 17.9 ​ The Company recorded the assets at the lower of cost or fair market value. ​ The Company accrued $ 1.4 million of other postemployment benefits, presented within both research and development expenses as well as general and administrative expenses, related to the Lexington Facility employees who were terminated effective August 30, 2024. ​ Subsequent accounting at Closing ​ As of the Closing, the Company will record the sale of the net assets associated with the Lexington Facility as of Closing. The Company expects the fair market value of the consideration received less costs to sell to approximate the carrying amount of the net assets held for sale. ​ 4 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 $ 1.9 million and $ 3.1 million of royalty revenue in the three and six months ended June 30, 2024, respectively, compared to $ 0.8 million of royalty revenue in each of the three and six months ended June 30, 2023. Royalties on the sale of HEMGENIX® are recorded once earned and are presented as license revenue. ​ ​ 9 Table of Contents Collaboration revenue The Company recognized $ 7.1 million and $ 10.4 million of collaboration revenue in the three and six months ended June 30, 2024, respectively, compared to $ 0.3 million and $ 0.7 million of collaboration revenue in each of the three and six months ended June 30, 2023. In accordance with the CSL Behring Agreement, certain development and other services rendered by the Company are reimbursed by CSL. Accounts receivable and contract asset ​ 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. ​ As of June 30, 2024 , the Company had accounts receivable of $ 7.8 million from CSL Behring related to collaboration services, contract manufacturing revenue and royalty revenue. ​ 5 Investment securities The following tables summarize the Company’s investments in sovereign debt as of June 30, 2024 and December 31, 2023: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ At June 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) ​ $ 236,553 ​ $ 15 ​ $ — ​ $ 236,568 Total ​ $ 236,553 ​ $ 15 ​ $ — ​ $ 236,568 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 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 ​ 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 less than 90 days when purchased are presented within cash and cash equivalents and measured at amortized cost (June 30, 2024: $ 26.9 million, December 31, 2023: nil ). ​ Inputs to the fair value of the investments are considered Level 2 inputs. ​ ​ 6 Inventories, net ​ The following table summarizes the inventories, net balances as of June 30, 2024 and December 31, 2023: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ June 30, ​ December 31, ​ 2024 2023 ​ ​ (in thousands) Raw materials ​ $ — ​ $ 7,157 Work in progress ​ ​ — ​ ​ 4,109 Finished goods ​ ​ — ​ ​ 758 Inventories ​ $ — ​ $ 12,024 ​ 10 Table of Contents The Company recorded write downs to net realizable value of $ 4.1 million and $ 5.8 million in the three and six months ended June 30, 2024, respectively, compared to nil in the same periods in 2023. The costs are recognized as Cost of Contract Manufacturing Revenues. At June 30, 2024, and December 31, 2023, the Company recorded an allowance for inventory of $ 5.3 million and $ 1.6 million, respectively. ​ As of June 30, 2024, $ 8.0 million of inventory is presented as assets held for sale on the consolidated balance sheet (refer to Note 3 “ Assets held for sale and divestiture of commercial manufacturing activities ”). ​ 7 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. ​ 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 June 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 June 30, 2024 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 287,877 ​ $ — ​ $ — ​ $ 287,877 ​ Cash and cash equivalents Restricted cash ​ ​ 3,162 ​ ​ — ​ ​ — ​ ​ 3,162 ​ Other non-current assets Total assets ​ $ 291,039 ​ $ — ​ $ — ​ $ 291,039 ​ ​ Liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Contingent consideration ​ ​ — ​ ​ — ​ ​ 40,138 ​ ​ 40,138 ​ Contingent consideration Consideration for post-acquisition services ​ ​ — ​ ​ — ​ ​ 412 ​ ​ 412 ​ Other non-current liabilities Total liabilities ​ $ — ​ $ — ​ $ 40,550 ​ $ 40,550 ​ ​ ​ 11 Table of Contents Contingent consideration ​ The Company is required to pay up to EUR 178.8 million (or $ 191.6 million based on the foreign exchange rate on June 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 June 30, 2024 was $ 40.1 million (December 31, 2023: $ 43.0 million) using discount rates of approximately 13.4 % to 15.6 % (December 31, 2023: 15.3 % to 15.6 %). The Company assumes the probability of achieving a EUR 30.0 million (or $ 32.1 million based on the foreign exchange rate on June 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 June 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 $ 67.0 million. If as of June 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 June 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) ​ ( 1,621 ) Currency translation effects ​ ( 1,247 ) Balance at June 30, 2024 $ 40,138 ​ As of June 30, 2024, the Company classified $ 28.1 million (December 31, 2023: $ 28.2 million) of the total contingent consideration of $ 40.1 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 5 “ Investment securities ” for the fair value of the investment securities as of June 30, 2024 and December 31, 2023. ​ 8 Accrued expenses and other current liabilities ​ Accrued expenses and other current liabilities include the following items: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ June 30, ​ December 31, ​ 2024 2023 ​ ​ (in thousands) Personnel related accruals and liabilities ​ $ 11,019 ​ $ 16,263 Accruals for goods received from and services provided by vendors-not yet billed ​ ​ 13,576 ​ ​ 12,834 Liability owed to the Purchaser pursuant to the Royalty Financing Agreement ​ ​ 1,896 ​ ​ 1,437 Total ​ $ 26,491 ​ $ 30,534 ​ ​ 9 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”), May 12, 2023 (the “2023 Amended Facility”) and June 28, 2024 (the “2024 Amended Facility”). ​ 12 Table of Contents 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 June 30, 2024 under the 2023 Amended Facility was $ 100.0 million. On July 19, 2024, in connection with the closing of the Lexington Transaction and pursuant to the 2024 Amended Facility, the Company prepaid $ 50.0 million of the $ 100.0 million of principal outstanding under the 2024 Amended Facility as well as $ 3.1 million in end-of-term fees. ​ 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) of the 2023 Amended Facility was $ 103.6 million as of June 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 loss on the facility in the three and six months ended June 30, 2024 was $ 0.7 million and $ 3.0 million, respectively, compared to a foreign currency gain $ 0.8 million and $ 1.6 million, respectively, during the same period in 2023. Interest expense associated with the 2023 Amended Facility during the three and six months ended June 30, 2024 was $ 3.7 million and $ 7.4 million, respectively, compared to $ 3.7 million and $ 7.3 million during the same period in 2023. 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 $ 730.8 million, less $ 3.3 million of cash and cash equivalents and other current assets held by the Company, and $ 87.5 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 June 30, 2024, the Company was in material compliance with all covenants and provisions. ​ 10 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. 13 Table of Contents 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. The Company would have recorded between $ 24.5 million and $ 27.7 million of interest expense through the six months ended June 30, 2024 ($ 12.4 million and $ 14.0 million, respectively, for the three months ended June 30, 2024) if it had used 12.0 % or 13.5 %, instead of the $ 24.8 million recorded in the six months ended June 30, 2024 ($ 12.4 million for the three months ended June 30, 2024). 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. ​ The following table presents the movement in the liability related to the Royalty Financing Agreement between the December 31, 2023 and June 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 ​ ​ ( 2,682 ) Liability owed to the Purchaser (presented as "Accrued expense and other current liabilities") ​ ​ ( 1,896 ) Interest expense for the period ​ ​ 24,840 Liability related to the royalty financing agreement ​ $ 415,940 ​ ​ ​ 11 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. ​ 14 Table of Contents 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 June 30, ​ Six months ended June 30, ​ 2024 2023 ​ 2024 ​ 2023 ​ ​ (in thousands) ​ (in thousands) Cost of manufacturing services revenue ​ $ 690 ​ $ 138 ​ $ 1,035 ​ $ 162 Research and development ​ ​ 2,856 ​ ​ 4,732 ​ ​ 6,281 ​ ​ 9,037 Selling, general and administrative ​ ​ 3,334 ​ ​ 4,024 ​ ​ 6,755 ​ ​ 7,756 Total ​ $ 6,880 ​ $ 8,894 ​ $ 14,071 ​ $ 16,955 ​ Share-based compensation expense recognized by award type for the 2014 Plans as well as the ESPP was as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended June 30, ​ Six months ended June 30, ​ 2024 2023 ​ 2024 ​ 2023 ​ ​ (in thousands) ​ (in thousands) Award type/ESPP ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Share options ​ $ 2,660 ​ $ 3,485 ​ $ 5,573 ​ $ 6,759 Restricted share units ​ ​ 4,214 ​ ​ 5,388 ​ ​ 8,584 ​ ​ 10,018 Performance share units ​ ​ 3 ​ ​ 12 ​ ​ ( 96 ) ​ ​ 162 Employee share purchase plan ​ ​ 3 ​ ​ 9 ​ ​ 10 ​ ​ 16 Total ​ $ 6,880 ​ $ 8,894 ​ $ 14,071 ​ $ 16,955 ​ As of June 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 ​ $ 18,140 ​ 2.39 Restricted share units ​ ​ 23,471 ​ 1.82 Performance share units ​ ​ 52 ​ 0.36 Total ​ $ 41,663 ​ 2.07 ​ 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 divestment of the Lexington Facility as of the date employment with the Company ends, which are expected to occur in the third quarter of 2024. The Company expects this to reduce the unrecognized share-based compensation expense by approximately $ 4.7 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. 15 Table of Contents The following tables summarize option activity under the 2014 Plans for the six months ended June 30, 2024: ​ ​ ​ ​ ​ ​ ​ ​ ​ Options ​ ​ Number of ​ Weighted average ​ ordinary shares exercise price ​ ​ ​ ​ ​ ​ Outstanding at December 31, 2023 ​ 4,974,030 ​ ​ 23.25 Granted ​ 1,041,780 ​ $ 5.48 Forfeited ​ ( 95,379 ) ​ $ 20.17 Expired ​ ( 213,446 ) ​ $ 29.34 Outstanding at June 30, 2024 ​ 5,706,985 ​ $ 19.83 Thereof, fully vested, and exercisable on June 30, 2024 ​ 3,206,653 ​ $ 24.96 Thereof, outstanding and expected to vest after June 30, 2024 ​ 2,500,332 ​ $ 13.25 ​ ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of options issued during the period (in $ millions) ​ ​ ​ $ 3.3 ​ As a result of the Lexington Transaction (refer to Note 3 “ Assets held for sale and divestiture of commercial manufacturing activities” ) 87,281 options are expected to be forfeited during the third quarter of 2024. ​ 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 June 30, Six months ended June 30, Assumptions 2024 2023 2024 2023 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 six months ended June 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 ​ 1,277,560 ​ $ 5.50 Vested ​ ( 850,589 ) ​ $ 20.09 Forfeited ​ ( 129,787 ) ​ $ 13.96 Non-vested at June 30, 2024 ​ 2,561,553 ​ $ 11.32 ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of RSUs granted during the period (in $ millions) ​ ​ ​ $ 7.0 ​ 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 Lexington Transaction (refer to Note 3 “ Assets held for sale and divestiture of commercial manufacturing activities” ) 391,038 RSUs are expected to be forfeited during the third quarter of 2024. ​ 16 Table of Contents PSUs ​ The following table summarizes the PSU activity for the six months ended June 30, 2024: ​ ​ ​ ​ ​ ​ ​ ​ ​ PSUs ​ ​ Weighted average ​ ​ Number of ​ grant-date fair ​ ​ ordinary shares ​ value Non-vested at December 31, 2023 ​ 222,550 ​ $ 28.09 Forfeited ​ ( 21,580 ) ​ $ 26.18 Non-vested at June 30, 2024 ​ 200,970 ​ $ 28.11 ​ 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 June 30, 2024, two milestones had been achieved and vested in either 2022 or 2023. Additionally, another two milestones are considered probable as of December 31, 2023 and June 30, 2024. ​ ESPP ​ During the six months ended June 30, 2024, 10,150 ordinary shares were issued under the ESPP compared to 5,006 during the same period in 2023. As of June 30, 2024, 86,712 ordinary shares remain available for issuance under the ESPP compared to a total of 111,054 as of June 30, 2023. ​ 12 Income taxes ​ The Company recorded $ 0.9 million and $ 1.6 million deferred tax expense in relation to its operations in the U.S. during the three and six months ended June 30, 2024, respectively. The Company recorded $ 0.2 million deferred tax expense and $ 1.0 million deferred tax benefit in relation to its operations in the U.S. and France during the three and six months ended June 30, 2023, respectively. ​ The effective income tax rate of 1.7 % and 1.3 % during the three and six months ended June 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 six months ended June 30, 2023 was 0.2 % and ( 0.7 %), respectively, as the Company had recorded a valuation allowance against its net deferred tax assets in the Netherlands. ​ ​ 13 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 six months ended June 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 six months ended June 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 June 30, 2024 and June 30, 2023, respectively. ​ 17 Table of Contents ​ The potentially dilutive ordinary shares are summarized below: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended June 30, ​ Six months ended June 30, ​ 2024 2023 ​ 2024 ​ 2023 Anti-dilutive ordinary share equivalents ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Stock options under 2014 Plans and previous plan ​ ​ 5,706,985 ​ ​ 5,297,277 ​ ​ 5,706,985 ​ ​ 5,297,277 Non-vested RSUs and PSUs ​ ​ 2,762,523 ​ ​ 2,730,672 ​ ​ 2,762,523 ​ ​ 2,730,672 ESPP ​ ​ — ​ ​ 2,455 ​ ​ — ​ ​ 2,455 Total anti-dilutive ordinary share equivalents ​ ​ 8,469,508 ​ ​ 8,030,404 ​ ​ 8,469,508 ​ ​ 8,030,404 ​ ​ 14 Subsequent events ​ On June 29, 2024 the Company entered into a transaction with Genezen (refer to Note 3 “ Assets held for sale and divestiture of commercial manufacturing activities” ). ​ On July 23, 2024 the Company announced the closing of the sale of its Lexington Facility to Genezen and on August 1, 2024, the Company announced an organizational restructuring. These actions were the outcome of a recently completed, comprehensive review of the Company’s operations with the goals of conserving capital and streamlining the organization. As part of these changes, the Company expects to eliminate approximately 300 positions or 65 % of its workforce. The Company estimates that it will incur costs in the range of $ 6.5 million to $ 7.5 million in connection with the restructuring, consisting primarily of cash expenditures related to employee severance costs. These costs are subject to assumptions, including local law requirements, and actual expenses may differ materially from the estimates disclosed above. The restructuring is subject to the review by the Company’s Amsterdam-based works council, which is expected to be completed in the third quarter of 2024. The Company expects the restructuring to be substantially completed by the end of 2024. ​ ​ 18 Table of Contents