uniQure N.V. 10-K

Item 9A. Controls and Procedures . ​ Evaluation of Disclosure Controls and Procedures ​ Our management, with the participation of our chief executive officer (“CEO”, our principal executive officer) and chief financial officer (“CFO”, our principal financial officer), evaluated the effectiveness of our disclosure controls and procedures (as defined in Rules 13a-15(e) and 15d-15(e) under the Exchange Act) as of December 31, 2024. Based on such evaluation, our CEO and CFO have concluded that as of December 31, 2024, our disclosure controls and procedures were effective. 108 ​ Table of Contents ​ Management’s Annual Report on Internal Control Over Financial Reporting ​ Our management is responsible for establishing and maintaining adequate internal control over financial reporting, as defined in Rules 13a-15(f) and 15d-15(f) under the Exchange Act. This rule defines internal control over financial reporting as a process designed by, or under the supervision of, a company’s chief executive officer and chief financial officer and effected by our board of directors, management and other personnel, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles and includes those policies and procedures that (1) pertain to the maintenance of records that, in reasonable detail, accurately and fairly reflect the transactions and dispositions of the assets of the company; (2) provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that receipts and expenditures of the company are being made only in accordance with authorizations of management and directors of the company; and (3) provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use, or disposition of our assets that could have a material effect on the financial statements. ​ We assessed the effectiveness of our internal control over financial reporting as of December 31, 2024. This assessment was performed under the direction and supervision of our CEO and CFO and based on criteria established in Internal Control - Integrated Framework (2013) issued by the Committee of Sponsoring Organizations of the Treadway Commission (“COSO”). Our management’s assessment of the effectiveness of our internal control over financial reporting included testing and evaluating the design and operating effectiveness of our internal controls. In our management’s opinion, we have maintained effective internal control over financial reporting as of December 31, 2024, based on criteria established in the COSO 2013 framework. ​ Our independent registered public accounting firm, which has audited the consolidated financial statements included in this Annual Report on Form 10-K, has also issued an audit report on the effectiveness of our internal control over financial reporting as of December 31, 2024. Their report is filed within this Annual Report on Form 10-K. ​ Inherent Limitations of Internal Controls Our management, including our CEO and CFO, does not expect that our disclosure controls and procedures or our internal controls will prevent all errors and all fraud. A control system, no matter how well conceived and operated, can provide only reasonable, not absolute, assurance that the objectives of the control system are met. Because of the inherent limitations in all control systems, no evaluation of controls can provide absolute assurance that all control issues and instances of fraud, if any, within the Company have been detected. These inherent limitations include the realities that judgments in decision-making can be faulty, and that breakdowns can occur because of a simple error or mistake. Additionally, controls can be circumvented by the individual acts of some persons, by collusion of two or more people, or by management override of the control. The design of any system of controls also is based in part upon certain assumptions about the likelihood of future events, and there can be no assurance that any design will succeed in achieving its stated goals under all potential future conditions. Over time, controls may become inadequate because of changes in conditions, or the degree of compliance with the policies or procedures may deteriorate. Projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate. Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements due to error or fraud. ​ Changes in internal control over financial reporting During the fourth quarter of 2024, there were no changes in our internal control over financial reporting (as defined in Rule 13a-15(f) under the Exchange Act) that materially affected, or are reasonably likely to materially affect, our internal control over financial reporting. ​ Item 9B. Other Information ​ Trading Arrangements ​ During the three months ended December 31, 2024, none of our directors or officers informed us of the adoption , modification or termination of a “ Rule 10b5-1 trading arrangement ” or “ non-Rule 10b5-1 trading arrangement ,” as each term is defined in Item 408(a) of Regulation S-K. 109 ​ Table of Contents ​ Item 9C. Disclosure Regarding Foreign Jurisdictions that Prevent Inspections ​ None. ​ Part III ​ Item 10. Directors, Executive Officers and Corporate Governance ​ We maintain an insider trading policy governing the purchase, sale and/or other dispositions of our securities by our directors, officers, employees, consultants and contractors, as well as the Company itself. We believe that the insider trading policy is reasonably designed to promote compliance with insider trading laws, rules and regulations, as well as the applicable laws and regulations of the Nasdaq listing standards. A copy of our insider trading policy is filed as Exhibit 19.1 to this Annual Report on Form 10-K. ​ The remaining information required by Item 10 is incorporated by reference from our Proxy Statement for our 2025 annual meeting of shareholders, which we will file within 120 days of December 31, 2024, or will be included in an amendment to this Annual Report on Form 10-K. ​ ​ Item 11. Executive Compensation ​ The information required by this item is incorporated by reference from our Proxy Statement for our 2025 annual meeting of shareholders, which we will file within 120 days of December 31, 2024, or will be included in an amendment to this Annual Report on Form 10-K. ​ Item 12. Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters ​ The information required by this item is incorporated by reference from our Proxy Statement for our 2025 annual meeting of shareholders, which we will file within 120 days of December 31, 2024, or will be included in an amendment to this Annual Report on Form 10-K. ​ Item 13. Certain Relationships and Related Transactions, and Director Independence ​ The information required by this item is incorporated by reference from our Proxy Statement for our 2025 annual meeting of shareholders, which we will file within 120 days of December 31, 2024, or will be included in an amendment to this Annual Report on Form 10-K. ​ Item 14. Principal Accounting Fees and Services ​ The information required by this item is incorporated by reference from our Proxy Statement for our 2025 annual meeting of shareholders, which we will file within 120 days of December 31, 2024, or will be included in an amendment to this Annual Report on Form 10-K. ​ ​ 110 ​ Table of Contents Part IV ​ Item 15. Exhibits, Financial Statements Schedules ​ Exhibits, Financial Statements Schedules ​ (a) Financial Statements . The following consolidated financial statements of uniQure N.V. are filed as part of this report: ​ ​ Page Report of Independent Registered Public Accounting Firm – KPMG Accountants N.V. 113 Consolidated Balance Sheets as of December 31, 2024 and 2023 116 Consolidated Statements of Operations and Comprehensive Loss for the Years Ended December 31, 2024, 2023 and 2022 117 Consolidated Statements of Shareholders’ (Deficit) / Equity for the Years Ended December 31, 2024, 2023 and 2022 118 Consolidated Statements of Cash Flows for the Years Ended December 31, 2024, 2023 and 2022 119 Notes to Consolidated Financial Statements for the Years Ended December 31, 2024, 2023 and 2022 120 ​ (b) Financial Statements Schedules . Financial Statement Schedules have been omitted because of the absence of conditions under which they are required or because the required information, where material, is shown in the financial statements or notes. ​ (c) Other Exhibits . The Exhibit Index immediately preceding the signature page of this Annual Report on Form 10-K is incorporated herein by reference. ​ Item 16. Form 10-K Summary ​ Not applicable. ​ ​ 111 ​ Table of Contents ​ ​ INDEX TO CONSOLIDATED FINANCIAL STATEMENTS FOR THE YEARS ENDED DECEMBER 31, 2024, 2023 AND 2022 ​ ​ ​ Page Report of Independent Registered Public Accounting Firm - KPMG Accountants N.V. , Amstelveen, The Netherlands (PCAOB ID 1012 ) 113 Consolidated Balance Sheets as of December 31, 2024 and 2023 116 Consolidated Statements of Operations and Comprehensive Loss for the Years Ended December 31, 2024, 2023 and 2022 117 Consolidated Statements of Shareholders’ (Deficit) / Equity for the Years Ended December 31, 2024, 2023 and 2022 118 Consolidated Statements of Cash Flows for the Years Ended December 31, 2024, 2023 and 2022 119 Notes to Consolidated Financial Statements 120 ​ ​ ​ 112 ​ Table of Contents Report of Independent Registered Public Accounting Firm ​ To the Shareholders and Board of Directors uniQure N.V.: ​ Opinions on the Consolidated Financial Statements and Internal Control Over Financial Reporting We have audited the accompanying consolidated balance sheets of uniQure N.V. and subsidiaries (‘the Company’) as of December 31, 2024 and 2023, the related consolidated statements of operations and comprehensive loss, shareholders’ (deficit) / equity, and cash flows for each of the years in the three-year period ended December 31, 2024, and the related notes (collectively, the consolidated financial statements). We also have audited the Company’s internal control over financial reporting as of December 31, 2024, based on criteria established in Internal Control – Integrated Framework (2013) issued by the Committee of Sponsoring Organizations of the Treadway Commission. In our opinion, the consolidated financial statements referred to above present fairly, in all material respects, the financial position of the Company as of December 31, 2024 and 2023, and the results of its operations and its cash flows for each of the years in the three-year period ended December 31, 2024, in conformity with U.S. generally accepted accounting principles. Also in our opinion, the Company maintained, in all material respects, effective internal control over financial reporting as of December 31, 2024 based on criteria established in Internal Control – Integrated Framework (2013) issued by the Committee of Sponsoring Organizations of the Treadway Commission. Basis for Opinions The Company’s management is responsible for these consolidated financial statements, for maintaining effective internal control over financial reporting, and for its assessment of the effectiveness of internal control over financial reporting, included in the accompanying Management’s Annual Report on Internal Control Over Financial Reporting. Our responsibility is to express an opinion on the Company’s consolidated financial statements and an opinion on the Company’s internal control over financial reporting based on our audits. We are a public accounting firm registered with the Public Company Accounting Oversight Board (United States) (‘PCAOB’) and are required to be independent with respect to the Company in accordance with the U.S. federal securities laws and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB. We conducted our audits in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audits to obtain reasonable assurance about whether the consolidated financial statements are free of material misstatement, whether due to error or fraud, and whether effective internal control over financial reporting was maintained in all material respects. Our audits of the consolidated financial statements included performing procedures to assess the risks of material misstatement of the consolidated financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the consolidated financial statements. Our audits also included evaluating the accounting principles used and significant estimates made by management, as well as evaluating the overall presentation of the consolidated financial statements. Our audit of internal control over financial reporting included obtaining an understanding of internal control over financial reporting, assessing the risk that a material weakness exists, and testing and evaluating the design and operating effectiveness of internal control based on the assessed risk. Our audits also included performing such other procedures as we considered necessary in the circumstances. We believe that our audits provide a reasonable basis for our opinions. ​ 113 ​ Table of Contents Definition and Limitations of Internal Control Over Financial Reporting A company’s internal control over financial reporting is a process designed to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles. A company’s internal control over financial reporting includes those policies and procedures that (1) pertain to the maintenance of records that, in reasonable detail, accurately and fairly reflect the transactions and dispositions of the assets of the company; (2) provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that receipts and expenditures of the company are being made only in accordance with authorizations of management and directors of the company; and (3) provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use, or disposition of the company’s assets that could have a material effect on the financial statements. Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements. Also, projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate. Critical Audit Matters The critical audit matter communicated below is a matter arising from the current period audit of the consolidated financial statements that was communicated to the audit committee and that: (1) relates to accounts or disclosures that are material to the consolidated financial statements and (2) involved our especially challenging, subjective, or complex judgments. The communication of a critical audit matter does not alter in any way our opinion on the consolidated financial statements, taken as a whole, and we are not, by communicating the critical audit matter below, providing a separate opinion on the critical audit matter or on the accounts or disclosures to which it relates. Valuation of intangible asset at initial recognition arising from favorable terms in the Commercial Supply Agreement As described in Notes 3 and 6 to the consolidated financial statements, the Company recorded an intangible asset valued at $16.7 million derived from the consideration received following the sale of the Lexington facility and based on the Commercial Supply Agreement entered into with Genezen. This intangible asset represents the rights to purchase HEMGENIX® at terms considered favorable to market terms. The valuation at initial recognition is based on the difference between the contractually agreed price under the Commercial Supply Agreement and the estimated commercial supply price for purchases to be made under the agreement. We identified the valuation of the intangible asset at initial recognition arising from favorable terms in the Commercial Supply Agreement as a critical audit matter. We performed a sensitivity analysis to identify the significant assumptions used to value the intangible asset, individually and in the aggregate, and determined this assumption to be the commercial supply price. Minor changes in this assumption could have a significant impact on the valuation of the intangible asset at initial recognition A high degree of subjective auditor judgement was required to evaluate the commercial supply price assumption for the goods supplied under the agreement, due to the lack of direct observable commercial supply prices. 114 ​ Table of Contents The following are the primary procedures we performed to address this critical audit matter: • We evaluated the design and tested the operating effectiveness of certain internal controls related to the valuation of the intangible asset. • We evaluated management’s methodology for determining the commercial supply price in the absence of comparable agreements, by comparing management’s estimate of commercial supply price to contracts in place with other suppliers and to the Company’s historical production costs to assess the reasonableness of management’s commercial supply price assumption. ​ /s/ KPMG Accountants N.V. ​ We have served as the Company’s auditor since 2019. Amstelveen, the Netherlands February 27, 2025 ​ ​ ​ ​ ​ 115 ​ Table of Contents uniQure N.V. ​ CONSOLIDATED BALANCE SHEETS ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ 2024 2023 ​ ​ (in thousands, except share and per share amounts) Current assets ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 158,930 ​ $ 241,360 Current investment securities ​ ​ 208,591 ​ ​ 376,532 Accounts receivable ​ ​ 5,881 ​ ​ 4,193 Inventories, net ​ ​ — ​ ​ 12,024 Prepaid expenses ​ ​ 9,281 ​ ​ 15,089 Other current assets and receivables ​ ​ 7,606 ​ ​ 2,655 Total current assets ​ ​ 390,289 ​ ​ 651,853 Non-current assets ​ ​ ​ ​ ​ ​ Property, plant and equipment, net ​ ​ 20,424 ​ ​ 46,548 Other investments ​ ​ 27,464 ​ ​ 2,179 Operating lease right-of-use assets ​ ​ 13,647 ​ ​ 28,789 Intangible assets, net ​ ​ 71,043 ​ ​ 60,481 Goodwill ​ ​ 22,414 ​ ​ 26,379 Deferred tax assets, net ​ ​ 9,856 ​ ​ 12,276 Other non-current assets ​ ​ 1,399 ​ ​ 3,184 Total non-current assets ​ ​ 166,247 ​ ​ 179,836 Total assets ​ $ 556,536 ​ $ 831,689 Current liabilities ​ ​ ​ ​ ​ ​ Accounts payable ​ $ 7,227 ​ $ 6,586 Accrued expenses and other current liabilities ​ ​ 29,225 ​ ​ 30,534 Current portion of contingent consideration ​ ​ — ​ ​ 28,211 Current portion of operating lease liabilities ​ ​ 3,601 ​ ​ 8,344 Total current liabilities ​ ​ 40,053 ​ ​ 73,675 Non-current liabilities ​ ​ ​ ​ ​ ​ Long-term debt ​ ​ 51,324 ​ ​ 101,749 Liability from royalty financing agreement ​ ​ 434,930 ​ ​ 394,241 Operating lease liabilities, net of current portion ​ ​ 11,136 ​ ​ 28,316 Contingent consideration, net of current portion ​ ​ 10,860 ​ ​ 14,795 Deferred tax liability, net ​ ​ 7,043 ​ ​ 7,543 Other non-current liabilities, net of current portion ​ ​ 7,942 ​ ​ 3,700 Total non-current liabilities ​ ​ 523,235 ​ ​ 550,344 Total liabilities ​ ​ 563,288 ​ ​ 624,019 Commitments and contingencies ​ ​ ​ ​ ​ ​ Shareholders' (deficit) / equity ​ ​ ​ ​ ​ ​ Ordinary shares, € 0.05 par value: 80,000,000 shares authorized as of December 31, 2024 and December 31, 2023 and 48,988,087 and 47,833,830 ordinary shares issued and outstanding as of December 31, 2024 and December 31, 2023, respectively ​ ​ 2,945 ​ ​ 2,883 Additional paid-in-capital ​ ​ 1,173,068 ​ ​ 1,148,749 Accumulated other comprehensive loss ​ ​ ( 52,800 ) ​ ​ ( 53,553 ) Accumulated deficit ​ ​ ( 1,129,965 ) ​ ​ ( 890,409 ) Total shareholders' (deficit) / equity ​ ​ ( 6,752 ) ​ ​ 207,670 Total liabilities and shareholders' (deficit) / equity ​ $ 556,536 ​ $ 831,689 ​ The accompanying notes are an integral part of these consolidated financial statements. ​ 116 ​ Table of Contents uniQure N.V. ​ CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ 2024 2023 ​ 2022 ​ ​ (in thousands, except share and per share amounts) License revenues ​ $ 10,133 ​ $ 2,758 ​ $ 100,000 Contract manufacturing revenues ​ ​ 6,114 ​ ​ 10,835 ​ ​ 1,717 Collaboration revenues ​ ​ 10,872 ​ ​ 2,250 ​ ​ 4,766 Total revenues ​ ​ 27,119 ​ ​ 15,843 ​ ​ 106,483 Operating expenses: ​ ​ ​ ​ ​ ​ ​ ​ ​ Cost of license revenues ​ ​ ( 1,267 ) ​ ​ ( 65 ) ​ ​ ( 1,254 ) Cost of contract manufacturing revenues ​ ​ ( 17,060 ) ​ ​ ( 13,563 ) ​ ​ ( 2,089 ) Research and development expenses ​ ​ ( 143,782 ) ​ ​ ( 214,864 ) ​ ​ ( 197,591 ) Selling, general and administrative expenses ​ ​ ( 52,657 ) ​ ​ ( 74,591 ) ​ ​ ( 55,059 ) Total operating expenses ​ ​ ( 214,766 ) ​ ​ ( 303,083 ) ​ ​ ( 255,993 ) Other income ​ ​ 7,926 ​ ​ 6,059 ​ ​ 7,171 Other expense ​ ​ ( 4,573 ) ​ ​ ( 1,690 ) ​ ​ ( 820 ) Loss from operations ​ ​ ( 184,294 ) ​ ​ ( 282,871 ) ​ ​ ( 143,159 ) Interest income ​ ​ 21,415 ​ ​ 19,562 ​ ​ 609 Interest expense ​ ​ ( 63,741 ) ​ ​ ( 41,557 ) ​ ​ ( 11,704 ) Foreign currency (losses) / gains, net ​ ​ ( 10,507 ) ​ ​ ( 1,691 ) ​ ​ 23,235 Other non-operating gains, net ​ ​ — ​ ​ — ​ ​ 2,760 Loss before income tax (expense) / benefit ​ $ ( 237,127 ) ​ $ ( 306,557 ) ​ $ ( 128,259 ) Income tax (expense) / benefit ​ ​ ( 2,429 ) ​ ​ ( 1,921 ) ​ ​ 1,470 Net loss ​ $ ( 239,556 ) ​ $ ( 308,478 ) ​ $ ( 126,789 ) Other comprehensive income / (loss): ​ ​ ​ ​ ​ ​ ​ ​ ​ Foreign currency translation gain / (losses), net ​ ​ 426 ​ ​ 6,874 ​ ​ ( 29,435 ) Defined benefit pension gain / (loss), net of taxes ​ ​ 327 ​ ​ ( 2,136 ) ​ ​ — Total comprehensive loss ​ $ ( 238,803 ) ​ $ ( 303,740 ) ​ $ ( 156,224 ) Earnings per ordinary share - basic and diluted ​ ​ ​ ​ ​ ​ ​ ​ ​ Basic and diluted net loss per ordinary share ​ $ ( 4.92 ) ​ $ ( 6.47 ) ​ $ ( 2.71 ) Weighted average shares - basic and diluted ​ ​ 48,649,129 ​ ​ 47,670,986 ​ ​ 46,735,045 ​ The accompanying notes are an integral part of these consolidated financial statements. ​ 117 ​ Table of Contents uniQure N.V. ​ CONSOLIDATED STATEMENTS OF SHAREHOLDERS’ (DEFICIT) / EQUITY ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Accumulated ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Additional ​ other ​ ​ ​ ​ Total ​ ​ Ordinary shares ​ paid-in ​ comprehensive ​ Accumulated ​ shareholders’ ​ ​ No. of shares Amount capital loss deficit (deficit) / equity ​ ​ (in thousands, except share and per share amounts) Balance at December 31, 2021 ​ 46,298,635 ​ $ 2,802 ​ $ 1,076,972 ​ $ ( 28,856 ) ​ $ ( 455,142 ) ​ $ 595,776 Loss for the period ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 126,789 ) ​ ​ ( 126,789 ) Other comprehensive loss ​ — ​ ​ — ​ ​ — ​ ​ ( 29,435 ) ​ ​ — ​ ​ ( 29,435 ) Income tax benefit of past share issuance cost ​ — ​ ​ — ​ ​ 808 ​ ​ ​ ​ ​ ​ ​ ​ 808 Exercises of share options ​ 152,356 ​ ​ 8 ​ ​ 1,272 ​ ​ — ​ ​ — ​ ​ 1,280 Restricted and performance share units distributed during the period ​ 505,799 ​ ​ 27 ​ ​ ( 27 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense ​ — ​ ​ — ​ ​ 34,204 ​ ​ — ​ ​ — ​ ​ 34,204 Issuance of ordinary shares relating to employee stock purchase plan ​ 11,242 ​ ​ 1 ​ ​ 164 ​ ​ — ​ ​ — ​ ​ 165 Balance at December 31, 2022 ​ 46,968,032 ​ $ 2,838 ​ $ 1,113,393 ​ $ ( 58,291 ) ​ $ ( 581,931 ) ​ $ 476,009 Loss for the period ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 308,478 ) ​ ​ ( 308,478 ) Other comprehensive income, net ​ — ​ ​ — ​ ​ — ​ ​ 4,738 ​ ​ — ​ ​ 4,738 Exercises of share options ​ 14,070 ​ ​ 1 ​ ​ 129 ​ ​ — ​ ​ — ​ ​ 130 Restricted and performance share units distributed during the period ​ 832,530 ​ ​ 43 ​ ​ ( 43 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense ​ — ​ ​ — ​ ​ 35,093 ​ ​ — ​ ​ — ​ ​ 35,093 Issuance of ordinary shares relating to employee stock purchase plan ​ 19,198 ​ ​ 1 ​ ​ 177 ​ ​ — ​ ​ — ​ ​ 178 Balance at December 31, 2023 ​ 47,833,830 ​ $ 2,883 ​ $ 1,148,749 ​ $ ( 53,553 ) ​ $ ( 890,409 ) ​ $ 207,670 Loss for the period ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 239,556 ) ​ ​ ( 239,556 ) Other comprehensive income, net ​ — ​ ​ — ​ ​ — ​ ​ 753 ​ ​ — ​ ​ 753 Exercises of share options ​ 169,898 ​ ​ 9 ​ ​ 2,065 ​ ​ — ​ ​ — ​ ​ 2,074 Restricted and performance share units distributed during the period ​ 974,209 ​ ​ 52 ​ ​ ( 52 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense ​ — ​ ​ — ​ ​ 22,258 ​ ​ — ​ ​ — ​ ​ 22,258 Issuance of ordinary shares relating to employee stock purchase plan ​ 10,150 ​ ​ 1 ​ ​ 48 ​ ​ — ​ ​ — ​ ​ 49 Balance at December 31, 2024 ​ 48,988,087 ​ $ 2,945 ​ $ 1,173,068 ​ $ ( 52,800 ) ​ $ ( 1,129,965 ) ​ $ ( 6,752 ) ​ The accompanying notes are an integral part of these consolidated financial statements ​ 118 ​ Table of Contents uniQure N.V. ​ CONSOLIDATED STATEMENTS OF CASH FLOWS ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ 2024 2023 2022 ​ ​ (in thousands) Cash flows from operating activities ​ ​ ​ ​ ​ ​ ​ ​ ​ Net loss ​ $ ( 239,556 ) ​ $ ( 308,478 ) ​ $ ( 126,789 ) Adjustments to reconcile net loss to net cash used in operating activities: ​ ​ ​ ​ ​ ​ ​ ​ ​ Depreciation, amortization and impairment ​ ​ 12,641 ​ ​ 11,900 ​ ​ 8,537 Amortization of discount on investment securities ​ ​ ( 10,901 ) ​ ​ ( 10,917 ) ​ ​ — Share-based compensation expense ​ ​ 22,258 ​ ​ 35,093 ​ ​ 34,204 Royalty financing agreement interest expense, net of interest paid ​ ​ 44,203 ​ ​ 25,616 ​ ​ — Deferred tax expense / (income) ​ ​ 2,429 ​ ​ 1,921 ​ ​ ( 1,470 ) Changes in fair value of contingent consideration and derivative financial instrument, net ​ ​ ( 1,817 ) ​ ​ 15,895 ​ ​ 4,320 Unrealized foreign exchange losses / (gains), net ​ ​ 15,415 ​ ​ ( 2,206 ) ​ ​ ( 22,083 ) Other items, net ​ ​ ( 3,848 ) ​ ​ 4,721 ​ ​ 1,605 Changes in operating assets and liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ Accounts receivable, prepaid expenses, and other current assets and receivables ​ ​ ( 2,243 ) ​ ​ ( 1,323 ) ​ ​ ( 4,083 ) Contract asset related to CSL Behring milestone payments ​ ​ - ​ ​ 100,000 ​ ​ ( 45,000 ) Inventories ​ ​ 2,421 ​ ​ ( 6,740 ) ​ ​ ( 6,924 ) Accounts payable ​ ​ 1,520 ​ ​ ( 4,169 ) ​ ​ 9,238 Accrued expenses, other liabilities, and operating leases ​ ​ ( 5,642 ) ​ ​ ( 5,328 ) ​ ​ 3,385 Contingent consideration milestone payment ​ ​ ( 19,608 ) ​ ​ ( 1,914 ) ​ ​ — Net cash used in operating activities ​ ​ ( 182,728 ) ​ ​ ( 145,929 ) ​ ​ ( 145,060 ) Cash flows from investing activities ​ ​ ​ ​ ​ ​ ​ ​ ​ Proceeds on maturity of debt securities ​ ​ 534,498 ​ ​ 167,907 ​ ​ — Investment in debt securities ​ ​ ( 359,841 ) ​ ​ ( 366,439 ) ​ ​ ( 163,146 ) Divestment of commercial manufacturing facility ​ ​ ( 8,321 ) ​ ​ — ​ ​ — Purchases of property, plant, and equipment ​ ​ ( 3,368 ) ​ ​ ( 7,154 ) ​ ​ ( 17,688 ) Acquisition of uniQure France SAS, net of cash acquired ​ ​ — ​ ​ — ​ ​ ( 1,900 ) Net cash generated from / (used in) investing activities ​ ​ 162,968 ​ ​ ( 205,686 ) ​ ​ ( 182,734 ) 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 ​ ​ 2,123 ​ ​ 308 ​ ​ 1,445 Repayment of long-term debt ​ ​ ( 53,050 ) ​ ​ — ​ ​ — Contingent consideration milestone payment ​ ​ ( 8,559 ) ​ ​ ( 7,649 ) ​ ​ — Net cash (used in) / generated from financing activities ​ ​ ( 59,486 ) ​ ​ 362,721 ​ ​ 1,445 Currency effect on cash, cash equivalents and restricted cash ​ ​ ( 4,969 ) ​ ​ 2,265 ​ ​ ( 1,831 ) Net (decrease) / increase in cash, cash equivalents and restricted cash ​ ​ ( 84,215 ) ​ ​ 13,371 ​ ​ ( 328,180 ) Cash, cash equivalents and restricted cash at beginning of period ​ ​ 244,544 ​ ​ 231,173 ​ ​ 559,353 Cash, cash equivalents and restricted cash at the end of period ​ $ 160,329 ​ $ 244,544 ​ $ 231,173 Cash and cash equivalents ​ $ 158,930 ​ $ 241,360 ​ $ 228,012 Restricted cash related to leasehold and other deposits ​ ​ 1,399 ​ ​ 3,184 ​ ​ 3,161 Total cash, cash equivalents and restricted cash ​ $ 160,329 ​ $ 244,544 ​ $ 231,173 Supplemental cash flow disclosures: ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash paid for interest ​ $ ( 20,567 ) ​ $ ( 16,878 ) ​ $ ( 9,247 ) Non-cash decrease in accounts payables and accrued expenses and other current liabilities related to purchases of property, plant, and equipment ​ $ ( 672 ) ​ $ ( 513 ) ​ $ ( 964 ) ​ The accompanying notes are an integral part of these consolidated financial statements. ​ 119 ​ Table of Contents uniQure N.V. ​ NOTES TO CONSOLIDATED FINANCIAL STATEMENTS ​ 1. Corporate information ​ uniQure B.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 25, Amsterdam 1105 BP, the Netherlands and its telephone number is +31 20 240 6000. The Company’s website address is www.uniqure.com. ​ 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 its consolidated financial statements in compliance with generally accepted accounting principles in the United States (“U.S. GAAP”). 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 (“ASU”) of the Financial Accounting Standards Board (“FASB”). ​ The consolidated financial statements have been prepared under the historical cost convention, except for derivative financial instruments and contingent consideration, which are recorded at fair value through profit or loss. ​ The 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. ​ The consolidated financial statements presented have been prepared on a going concern basis based on the Company’s cash and cash equivalents as of December 31, 2024 and the Company’s budgeted cash flows for the twelve months following the issuance date. ​ 2.2 Use of estimates ​ The preparation of consolidated financial statements, in conformity with U.S. GAAP and Securities and Exchange Commission (“SEC”) rules and regulations, 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 consolidated financial statements and reported amounts of revenues and expenses during the reporting period. Estimates and assumptions are primarily made in relation to contingent consideration related to the acquisition of uniQure France SAS, the valuation of the intangible asset with favorable terms recorded as part of the sale the Company’s commercial manufacturing activities located in Lexington, MA (“Lexington Transaction”) in July 2024 and the date at which the Company expects to satisfy its commitment under the Royalty Financing Agreement (refer to definition in Note 2.3.27). If actual results differ from the Company’s estimates, or to the extent these estimates are adjusted in future periods, the Company’s results of operations could either benefit from, or be adversely affected by, any such change in estimate. ​ 120 ​ Table of Contents 2.3 Accounting policies ​ The principal accounting policies applied in the preparation of these consolidated financial statements are set out below. These policies have been consistently applied to all the years presented, unless otherwise stated. ​ 2.3.1 Consolidation ​ The consolidated financial statements comprise the financial statements of the Company and its subsidiaries. Subsidiaries are all entities over which the Company has a controlling financial interest either through variable interest or through voting interest. Currently, the Company is not involved with variable interest entities. ​ Inter-company transactions, balances, income, and expenses on transactions between uniQure entities are eliminated in consolidation. Profits and losses resulting from inter-company transactions that are recognized in assets are also eliminated. Accounting policies of subsidiaries have been changed where necessary to ensure consistency with the policies adopted by the Company. ​ 2.3.2 Current versus non-current classification ​ The Company presents assets and liabilities in the consolidated balance sheets based on current and non-current classification. ​ The term current assets is used to designate cash and other assets, or resources commonly identified as those that are reasonably expected to be realized in cash or sold or consumed during the normal operating cycle of the business. The Company’s normal operating cycle is twelve months . All other assets are classified as non-current. ​ The term current liabilities is used principally to designate obligations whose liquidation is reasonably expected to require the use of existing resources properly classifiable as current assets, or the creation of other current liabilities. Current liabilities are expected to be settled in the normal operating cycle. The Company classifies all other liabilities as non-current. ​ Deferred tax assets and liabilities are classified as non-current assets and liabilities, if any. ​ 2.3.3 Foreign currency translation ​ The functional currency of the Company and each of its entities (except for uniQure Inc. and Corlieve AG) is the euro (€). This represents the currency of the primary economic environment in which the entities operate. The functional currency of uniQure Inc. is the U.S. dollar ($) and the functional currency of Corlieve AG is the Swiss Franc (CHF). The consolidated financial statements are presented in U.S. dollars. ​ Foreign currency transactions are measured and recorded in the functional currency using the exchange rates prevailing at the dates of the transactions. Foreign exchange gains and losses resulting from the settlement of such transactions and from the re-measurement of monetary assets and liabilities denominated in foreign currencies at exchange rates prevailing at balance sheet date are recognized in profit and loss. ​ Upon consolidation, the assets and liabilities of foreign operations are translated into the functional currency of the shareholding entity at the exchange rates prevailing at the balance sheet date; items of income and expense are translated at monthly average exchange rates. The consolidated assets and liabilities are translated from uniQure N.V.’s functional currency, euro, into the reporting currency U.S. dollar at the exchange rates prevailing at the balance sheet date; items of income and expense are translated at monthly average exchange rates. Issued capital and additional paid-in capital are translated at historical rates with differences to the balance sheet date rate recorded as translation adjustments in other comprehensive income / loss. The exchange differences arising on translation for consolidation are recognized in “accumulated other comprehensive income / loss”. On disposal of a foreign operation, the component of other comprehensive income / loss relating to that foreign operation is recognized in profit or loss. ​ 121 ​ Table of Contents 2.3.4 Fair value measurement ​ The Company measures certain 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. ​ Items measured at fair value on a recurring basis include financial instruments and contingent consideration (Note 7, “ 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. ​ 2.3.5 Contingent consideration ​ Each reporting period, the Company revalues the contingent consideration obligations associated with the acquisition of uniQure France SAS in 2021 to their fair value and records changes in the fair value within research and development expenses. Changes in contingent consideration obligations result from changes in assumptions regarding the probabilities of achieving the relevant milestones, the estimated timing of achieving such milestones, and the interest rate to discount the milestone payments. The probability-adjusted payments are discounted to present value using a discount rate representing the Company’s credit risk. This discount rate is determined using the effective interest rate of the Company’s existing debt facility adjusted for difference in maturity dates based on market data on effective yields for U.S. bonds with a CCC credit rating. ​ Payments of portions of contingent consideration initially recorded as of the acquisition date are recorded as cash flows from financing activities, and payments, or the portion of the milestone payments representing changes in the fair value of contingent consideration subsequent to the initial recognition, are recorded as cash flows from operating activities. ​ Refer to Note 7 “ Fair value measurement ” for further information. ​ 2.3.6 Divestiture of commercial manufacturing activities ​ On June 29, 2024, affiliates of the Company entered into an Asset Purchase Agreement (“APA”) with Genezen Holdings Inc. and its affiliate Genezen MA, Inc. (together “Genezen”). Pursuant to the APA, the Company sold its commercial manufacturing activities located in Lexington, MA (the “Lexington Transaction”) to Genezen. The Lexington Transaction closed on July 22, 2024 (the “Closing”). The Lexington Transaction was accounted for as a divestment of the Company’s commercial manufacturing activities in accordance with ASC 805, Business Combinations . ​ 122 ​ Table of Contents 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, (iii) a right to purchase HEMGENIX® at terms considered favorable to market terms and (iv) a firm purchase commitment liability for its customer contract with CSL Behring inherently related to the right to purchase HEMGENIX®. ​ Refer to Note 3 “ Divestiture of commercial manufacturing activities” for further detail. ​ a. Series C preferred stock ​ The Company recorded the Series C preferred stock in Genezen Holdings Inc. issued to the Company at its fair value. 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 series C preferred stock is presented within Other investments on the consolidated balance sheets. ​ b. Convertible promissory note ​ The convertible promissory note was recognized at its fair value. 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 is presented within Other investments on the consolidated balance sheets. ​ c. Right to purchase ​ The Company entered into a Commercial Supply Agreement (“CSA”) with Genezen. The CSA provides the Company with rights to purchase HEMGENIX® at terms considered favorable to market terms. In accordance with ASC 805, Business Combinations, the Company recorded an intangible asset at its fair value with respect to these favorable terms at Closing. The intangible asset is stated at historical cost less accumulated amortization. The Company amortizes the intangible asset on a straight-line basis over a three-year term. The Company presents the amortization expense within Other expense in the Consolidated Statement of Operations and Comprehensive Loss. ​ d. Firm purchase commitment liability ​ The CSA includes a minimum term of three years and minimum purchase commitments of HEMGENIX® over the first three years, unless certain contractual provisions are triggered. The Company expects to resell HEMGENIX® purchased from Genezen via its minimum commitments to CSL Behring at a loss. In accordance with ASC 330, Inventory, the Company recognized a liability related to the net losses expected from the purchase of these minimum commitments. The Company presents the current portion of the firm purchase commitment liability within accrued expenses and other current liabilities and the non-current portion within other non-current liabilities on the consolidated balance sheets. The Company subsequently adjusts the liability for any changes to the losses expected to be incurred. The Company presents changes to the liability within other expenses. ​ 2.3.7 Notes to the consolidated statements of cash flows ​ The consolidated statements of cash flows have been prepared using the indirect method. The cash disclosed in the consolidated statements of cash flows is comprised of cash and cash equivalents and restricted cash. Cash and cash equivalents include bank balances, demand deposits and other short-term highly liquid investments (with maturities of less than three months at the time of purchase) that are readily convertible into a known amount of cash and are subject to an insignificant risk of fluctuation in value. ​ Cash flows denominated in foreign currencies have been translated at the average exchange rates. Exchange differences, if any, affecting cash and cash equivalents are shown separately in the consolidated statements of cash flows. Interest paid and received, and income taxes are included in net cash (used in) / provided by operating activities. 123 ​ Table of Contents 2.3.8 Segment information ​ Operating segments are identified as a component of an enterprise for which separate discrete financial information is available for evaluation by the chief operating decision maker (“CODM”), or decision-making group, in making decisions on how to allocate resources and assess performance. The Company views its operations and manages its business as one operating segment, which comprises the discovery and development of innovative gene therapies. ​ 2.3.9 Net loss per ordinary share ​ The Company follows the provisions of ASC 260 , Earnings Per Share . In accordance with these provisions, net loss per ordinary share is calculated by dividing net (loss) / income by the weighted average number of ordinary shares outstanding during the period. ​ Diluted net loss per ordinary share reflects the dilution that would occur if share options or warrants to issue ordinary shares were exercised, performance or restricted share units were distributed, or shares under the employee share purchase plan were issued. However, potential ordinary shares are excluded if their effect is anti-dilutive. ​ Refer to Note 22 “ Basic and diluted earnings per share ” for further information. ​ 2.3.10 Impairment of long-lived assets ​ Long-lived assets, which include property, plant, and equipment and finite-lived intangible assets, are reviewed for impairment whenever events or changes in circumstances indicate that the carrying value of an asset or asset group may not be recoverable. Right-of-use assets are also reviewed for impairment in accordance with ASC 360 , Property, Plant, and Equipment . The recoverability of the carrying value of an asset or asset group depends on the successful execution of the Company’s business initiatives and its ability to earn sufficient returns on approved products and product candidates. When events or changes in circumstances occur, the Company assesses recoverability by determining whether the carrying value of such assets will be recovered through the undiscounted expected future cash flows. If the future undiscounted cash flows are less than the carrying amount of these assets, the Company recognizes an impairment loss based on the excess of the carrying value over the fair value of the assets. Fair value is determined through various valuation techniques, including discounted cash flow models, quoted market values, and third-party independent appraisals, as considered necessary. ​ 2.3.11 Goodwill and acquired research and development intangible asset ​ a. Goodwill ​ Goodwill represents the excess of the fair value of the consideration transferred over the fair value of the net assets assumed in a business combination. Goodwill is not amortized but is evaluated for impairment on an annual basis and between annual tests if the Company becomes aware of any events occurring or changes in circumstances that would more likely than not reduce the fair value of the reporting unit below its carrying amount. A reporting unit is an operating segment or one level below an operating segment. In the years ended December 31, 2024, 2023 and 2022, the Company has not recognized any impairment charges related to goodwill. ​ b. Acquired research and development ​ As part of the acquisition of uniQure France SAS in 2021 the Company recorded an In-process research and development intangible asset related to the AMT-260 program (“IPR&D Intangible Asset”). The IPR&D Intangible Asset is considered to be indefinite-lived until the completion or abandonment of the associated research and development efforts and is not amortized. If and when development is completed, which would occur when regulatory approval to market a candidate for the treatment of temporal lobe epilepsy is obtained, the associated asset would be deemed finite-lived and would then be amortized based on its respective useful life at that point in time. For the years ended December 31, 2024, 2023 and 2022, the Company has not recognized any impairment charges related to the IPR&D Intangible Asset. ​ 124 ​ Table of Contents In case of abandonment, the IPR&D Intangible Asset will be written-off. In accordance with ASC 350, Intangibles – Goodwill and Other , the Company tests indefinite-lived intangible assets for impairment on an annual basis and between annual tests if the Company becomes aware of any events occurring or changes in circumstances that would indicate the fair value of the IPR&D Intangible Asset is below its carrying amount. ​ 2.3.12 Investment securities ​ Investment securities consist of sovereign debt with residual maturities of less than 12 months (presented as current) and beyond (presented as non-current). The Company classifies these securities as held-to-maturity. Held-to-maturity securities are those securities in which the Company has the ability and intent to hold the security until maturity. Held-to-maturity securities are recorded at amortized cost, adjusted for applicable accrued interest and the amortization or accretion of premiums or discounts. Premiums and discounts are amortized or accreted over the term of the related held-to-maturity security as an adjustment to yield using the effective interest rate method. ​ Investment securities with original maturities of 90 days or less when purchased are presented within cash and cash equivalents (December 31, 2024: $ 15.3 million, December 31, 2023: nil ). ​ A decline in the market value of any investment security below cost that is deemed to be other than temporary results in a reduction in the carrying amount to fair value. The impairment is charged to operations and a new cost base for the security is established. Other-than-temporary impairment charges are included in interest and other income (expense), net. Interest income is recognized when earned. ​ Refer to Note 5 “ Investment securities ” for further information. ​ 2.3.13 Accounts receivable ​ Accounts receivables include amounts due from services provided to CSL Behring as well as unconditional rights to consideration from CSL Behring. ​ 2.3.14 Inventories ​ The Company started producing commercial materials in April 2022 to supply CSL Behring in accordance with a June 2020 Development and Commercial Supply Agreement between the Company and CSL Behring. From this date until the Closing of the Lexington Transaction in July 2024, the Company presented the costs associated with the aforementioned activities as cost of contract manufacturing. ​ Per ASC 330 , Inventory , inventory is stated at the lower of cost or estimated net realizable value, on a first-in, first-out basis. The Company capitalized raw materials to the extent these were used in contract manufacturing for CSL Behring. The Company used standard costs, approximating average costs to determine its cost basis for work in progress and finished goods. The Company’s assessment of recoverability value required the use of estimates regarding the net realizable value of its inventory balances, including an assessment of excess or obsolete inventory. As applicable, write-downs resulting from adjustments to net realizable value were recorded to cost of contract manufacturing. ​ 2.3.15 Prepaid expenses ​ Prepaid expenses are amounts paid in the period, for which the benefit has not been realized, and include payments made for insurance and research and clinical contracts. The related expense will be recognized in the subsequent period as incurred. ​ 2.3.16 Other(non) current assets ​ Deposits paid are either presented as other current assets or as other non-current assets based on duration of the underlying contractual arrangement. Deposits are classified as restricted cash and primarily relate to facility leases. ​ Contract assets are presented in current assets or as non-current assets based on the timing of the right to consideration. ​ 125 ​ Table of Contents 2.3.17 Property, plant, and equipment ​ Property, plant, and equipment is comprised mainly of laboratory equipment, leasehold improvements, construction-in-progress (“CIP”) and office equipment. All property, plant and equipment is stated at cost less accumulated depreciation. CIP consists of capitalized expenses associated with construction of assets not yet placed into service. Depreciation commences on CIP once the asset is placed into service based on its useful life determined at that time. ​ Maintenance and repairs that do not improve or extend the lives of the respective assets are expensed as incurred. Upon disposal, the related cost and accumulated depreciation is removed from the accounts and any resulting gain or loss on the transaction is recognized in the consolidated statements of operations and comprehensive loss. ​ Depreciation is calculated using the straight-line method over the estimated useful lives of the assets (or in the case of leasehold improvements a shorter lease term), which are as follows: ​ ​ ​ ​ ​ ​ ​ · Leasehold improvements Between 10 – 15 years · Laboratory equipment ​ 5 years · Office equipment ​ Between 3 – 5 years ​ 2.3.18 Leases ​ The Company records leases in accordance with ASC 842 , Leases and determines if an arrangement is a lease at inception. Operating lease right-of-use assets and lease liabilities are initially recognized based on the present value of future minimum lease payments over the lease term at commencement date calculated using an incremental borrowing rate applicable to the lease asset unless the implicit rate is readily available. Lease terms may include options to extend or terminate the lease when it is reasonably certain that the Company will exercise that option. Leases with a term of twelve months or less are not recognized on the consolidated balance sheets. ​ The Company recognizes lease cost on a straight-line basis and presents these costs as operating expenses within the Consolidated statements of operations and comprehensive loss. The Company presents lease payments within cash flows from operations within the Consolidated statements of cash flows. ​ 2.3.19 Accounts payable and accrued expenses ​ Accounts payables are invoiced amounts related to obligations to pay for goods or services that have been acquired in the ordinary course of business from suppliers. Accounts payables are recognized at the amounts invoiced by suppliers. ​ Accrued expenses are recognized for goods or services that have been acquired in the ordinary course of business. ​ Contract liabilities, if any, are presented in accrued expenses. ​ 2.3.20 Long-term debt ​ Long-term debt is initially recognized at cost and presented net of original issue discount or premium and debt issuance costs on the consolidated balance sheets. Amortization of debt discount and debt issuance costs is recognized as interest expense in profit and loss over the period of the debt, using the effective interest rate method. ​ 2.3.21 Pensions and other post-retirement benefit plans ​ The Company maintains a defined contribution pension plan for all employees in the Netherlands, which is funded by the Company through payments to an insurance company, with individual accounts for each participants’ assets. The Company has no legal or constructive obligation to pay further contributions if the plan does not hold sufficient assets to pay all employees the benefits relating to services rendered in the current and prior periods. The contributions are expensed as incurred. Prepaid contributions are recognized as an asset to the extent that a cash refund or a reduction in the future payments is available. ​ 126 ​ Table of Contents The Company maintains a qualified 401(k) Plan for all employees located in the United States. The 401(k) Plan offers both a pre-tax and post-tax (Roth) component. Employees may contribute up to the IRS statutory limit each calendar year. The Company matches $ 0.50 for every $ 1.00 contributed to the plan by participants up to 6 % of base compensation. Employer contributions are recognized as they are contributed, as long as the employee is rendering services in that period. If employer contributions are made in periods after an individual retires or terminates, the estimated cost is accrued during the employee’s service period. ​ Expenses under the defined contribution plans were $ 2.7 million, $ 3.6 million and $ 2.7 million for the years ended December 31, 2024, 2023 and 2022, respectively. ​ The Company maintains a defined benefit plan for its Swiss employees, including retirement benefit plans required by applicable local law. The Company accounts for pension assets and liabilities in accordance with ASC 715, Compensation - Retirement Benefits , which requires the recognition of the funded status of pension plans in the Company’s consolidated balance sheet. The liability in respect to defined benefit pension plan is the projected benefit obligation calculated annually by independent actuaries using the projected unit credit method. ​ The projected benefit obligations as of December 31, 2024 and December 31, 2023 represents the actuarial present value of the estimated future payments required to settle the obligation that is attributable to employee services rendered before that date. Service cost is reported in research and development and general and administrative expenses. All other components of net period costs are reported in interest expense in the consolidated statement of operations and comprehensive loss. Plan assets are recorded at their fair value. Gains or losses arising from plan curtailments or settlements are accounted for at the time they occur. Actuarial gains and losses arising from differences between the actual and the expected return on plan assets are recognized in accumulated other comprehensive income (loss). ​ 2.3.22 Share-based compensation ​ The Company accounts for its share-based compensation awards in accordance with ASC 718 , Compensation-Stock Compensation. ​ All the Company’s share-based compensation plans for employees are equity-classified. ASC 718 requires all share-based compensation to employees, including grants of employee options, restricted share units, performance share units and modifications to existing instruments, to be recognized in the consolidated statements of operations and comprehensive loss based on their grant-date fair values, net of an estimated forfeiture rate, over the requisite service period. Forfeitures of employee options are recognized as they occur. Compensation expense related to Performance Share Units is recognized when the Company considers achievement of the milestones to be probable. The requirements of ASC 718 are also applied to nonemployee share-based payment transactions except for specific guidance on certain inputs to an option-pricing model and the attribution of cost. ​ The Company uses a Hull & White option model to determine the fair value of option awards. The model captures early exercises by assuming that the likelihood of exercises will increase when the share-price reaches defined multiples of the strike price. This analysis is performed over the full contractual term. ​ ​ 127 ​ Table of Contents 2.3.23 Revenue recognition ​ The Company primarily generates revenue from its commercialization and license agreement with CSL Behring. The Company generated revenue from services provided to Bristol-Myers Squibb (“BMS”) until February 21, 2023. ​ License revenue ​ In June 2020 the Company entered into a commercialization and license agreement pursuant to which CSL Behring received exclusive global rights to HEMGENIX® which became fully effective in May 2021. The Company concluded that CSL Behring is a customer in accordance with ASC 606 , Revenue from Contracts with Customers. The Company recognized the revenue related to its performance obligation to sell the exclusive global rights to HEMGENIX® in May 2021. The Company also allocated the following consideration to this performance obligation: ​ i) Variable milestone payments; and ii) Sales milestone payments and royalties ​ The Company recognizes license revenue in relation to the regulatory and sales milestone payments when it becomes probable that these be achieved as well as when royalties on sales of HEMGENIX® have been earned. ​ Refer to Note 18 “ Collaboration arrangements and concentration of credit risk ” for further detail. ​ Contract manufacturing revenue ​ The Company between April 2022 and July 2024 contract manufactured HEMGENIX® for CSL Behring in accordance with a June 2020 Development and Commercial Supply Agreement between the Company and CSL Behring. Following the Closing of the Lexington Transaction in July 2024, title to HEMGENIX® drug product 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 with related accounts receivable presented in other receivables in the consolidated balance sheets. ​ The Company recognized contract manufacturing revenue when ownership transferred to CSL Behring. ​ Collaboration revenue ​ Collaboration revenue related to contracted services is recognized when performance obligations are satisfied. ​ 2.3.24 Other income, other expense ​ The Company receives certain government and regional grants, which support its research efforts in defined projects, and include contributions towards the cost of research and development. These grants generally provide for reimbursement of approved costs incurred as defined in the respective grants and are deferred and recognized in the statements of operations and comprehensive loss over the period necessary to match them with the costs they are intended to compensate, when it is probable that the Company has complied with any conditions attached to the grant and will receive the reimbursement. 128 ​ Table of Contents 2.3.25 Research and development expenses ​ Research and development costs are expensed as incurred. Research and development expenses generally consist of laboratory research, clinical trials, statistical analysis, and report writing, regulatory compliance costs incurred with clinical research organizations and other third-party vendors (including post-approval commitments to conduct consistency and comparability studies). In addition, research and development expenses consisted of start-up and validation costs related to the Company’s Lexington facility and the development and improvement of the Company’s manufacturing processes and methods. Furthermore, research and development costs include costs of materials and costs of intangible assets purchased from others for use in research and development activities. The costs of intangibles that are purchased from others for a particular research and development project and that have no alternative future uses (in other research and development projects or otherwise) are expensed as research and development costs at the time the costs are incurred or at the time when no alternative future use is identified. ​ 2.3.26 Income taxes ​ Income taxes are recorded in accordance with ASC 740 , Income Taxes , which provides for deferred taxes using an asset and liability approach. The Company recognizes deferred tax assets and liabilities for the expected future tax consequences of events that have been included in the financial statements or tax returns. Deferred tax assets and liabilities are determined based on the difference between the financial statement carrying amount and the tax bases of assets and liabilities using enacted tax rates in effect for the year in which the differences are expected to reverse. Valuation allowances are provided, if based upon the weight of available evidence, it is more-likely-than-not that some or all the deferred tax assets will not be realized. ​ The benefits of tax positions are recognized only if those positions are more likely than not, based on the technical merits, to be sustained upon examination. Recognized tax positions are measured at the largest amount of tax benefit that is greater than 50 percent likely of being realized upon settlement. The determination as to whether the tax benefit will more-likely-than-not be realized is based upon the technical merits of the tax position as well as consideration of the available facts and circumstances. As of December 31, 2024, and 2023, the Company did not have any significant unrecognized tax benefits. ​ 2.3.27 Royalty Financing Agreement ​ In May 2023, uniQure biopharma B.V. (“uniQure biopharma”), a wholly-owned subsidiary of the Company entered into an agreement (the “Royalty Financing Agreement”) with the HemB SPV, L.P. (the “Purchaser”) to sell certain current and future royalties due to uniQure biopharma from CSL Behring under the CSL Behring Agreement by and between uniQure biopharma and CSL Behring from the net sales of HEMGENIX®. Refer to Note 13 “Royalty Financing Agreement” for further details of the Royalty Financing Agreement. The Company determined that the Royalty Financing Agreement should be accounted for as debt in accordance with topic ASC 470, Debt . The Company initially recognized the debt at fair value. The Company subsequently records the debt at amortized cost and determines the effective interest rate based on its projection of contractual cash flows. Interest expense (presented as “Interest Expense” in the consolidated statements of operations and comprehensive (loss) / income) is recorded over the projected repayment period using the effective interest method. The Company periodically assesses and adjusts the effective interest rate to reflect changes in projected cash flows. The Company prospectively applies the adjusted effective interest rate following the date of change. ​ In accordance with topic ASC 835, Interest , debt issuance costs incurred in relation to the Royalty Financing Agreement are presented as a reduction of carrying amount of the debt. Debt issuance cost is amortized together with the interest expense recorded. ​ Interest expense, net of interest paid is presented as an adjustment to reconcile net loss to net cash used in operating activities in the consolidated statement of cash flows. ​ 2.3.28 Restructuring expenses ​ Restructuring charges consist of one-time termination benefits. The Company records one-time termination benefits in accordance with ASC 420, Exit or Disposal Cost Obligations . One-time termination benefits are expensed at the date the Company notifies the employee, unless the employee must provide future service, in which case the benefits are expensed ratably over the future service period. 129 ​ Table of Contents ​ ​ The Company recorded restructuring charges in accordance with ASC 712, Compensation—Nonretirement Postemployment Benefits when the terms offered were substantially similar to the terms recently offered. Under this standard, the Company recognizes a liability when the obligation is probable and can be estimated. The Company estimates the cost of these benefits and records a liability for the expected future payments. The liability is adjusted periodically to reflect changes in estimates, and related costs are recognized in the period incurred. ​ Other costs relate to the impairment of the Company’s research and development laboratory in Lexington that was closed as a result of an October 2023 reorganization. The Company recognized an impairment loss of the right-of-use asset and corresponding leasehold improvements in accordance with ASC 360 , Property, Plant and Equipment . ​ 2.3.29 Recently Adopted Accounting Pronouncements ​ In the year ended December 31, 2024, the Company adopted Accounting Standards Update (ASU) 2023-07, Segment Reporting (Topic 280): Improvements to Reportable Segment Disclosures (“ASU 2023-07”). This update requires the Company to disclose segment expenses that are significant and regularly provided to the Company’s chief operating decision maker (“CODM”). In addition, ASU 2023-07 requires the Company to disclose the title and position of its CODM and how the CODM uses segment profit or loss information in assessing segment performance and deciding how to allocate resources. The adoption of this update did not have a material impact on the Company’s financial position or results of operations but resulted in expanded disclosures in the segment reporting section of the consolidated financial statements. The Company adopted ASU 2023-07 using a retrospective transition method. ​ There are no other recently issued accounting pronouncements pending adoption that are applicable or expected to have a material impact on the Company. ​ ​ 130 ​ Table of Contents 3. Divestiture of commercial manufacturing activities ​ Description of transaction ​ On June 29, 2024, affiliates of the Company agreed with Genezen to sell the Company’s commercial manufacturing activities located in Lexington, MA. The Lexington Transaction closed on July 22, 2024. ​ 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 B.V., both wholly owned subsidiaries of the Company, entered into an APA with Genezen on June 29, 2024. Pursuant to the APA, Genezen agreed to acquire the manufacturing facility including equipment and related manufacturing operations with a carrying value of $ 15.2 million, inventory with a carrying value of $ 8.8 million and certain other assets (including allocated goodwill) with a carrying value of $ 2.8 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 also included a firm purchase commitment liability for its customer contract with CSL Behring inherently related to the right to purchase HEMGENIX® in the consideration received. ​ 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 Series C preferred stock had a carrying value of $ 11.8 million as of December 31, 2024. ​ The convertible promissory note was recognized at its fair value of $ 13.3 million at Closing. The convertible promissory note had a balance of $ 13.7 million as of December 31, 2024. During the year ended December 31, 2024, the Company recognized $ 0.4 million of interest income. As of December 31, 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 $ 17.7 million. Following the Closing, $ 1.7 million of deposits were released and reclassified from restricted cash into cash. ​ At Closing, uniQure Inc. entered into a 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 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 $ 2.5 million (presented within Other expense in the Consolidated Statement of Operations and Comprehensive Loss) was recorded during the year ended December 31, 2024. ​ 131 ​ Table of Contents 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 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 was accounted for as a reduction of the consideration received. As of December 31, 2024, the Company classified $ 1.6 million of the liability as Accrued expenses and other current liabilities and $ 4.8 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 total net 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 in the Consolidated Statement of Operations and Comprehensive Loss. ​ At Closing, the Company paid a total of $ 8.3 million to Genezen and CSL related to adjustments of working capital and to obtain consent to proceed with the divestiture. ​ Additionally, uniQure biopharma 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. ​ 4. Restructuring ​ In 2024, 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 year ended December 31, 2024. ​ On August 1, 2024, the Company announced a global organizational restructuring. As a result, the Company recorded $ 3.8 million of severance and other personnel-related expenses during the year ended December 31, 2024. ​ On October 5, 2023, the Company announced a reorganization plan. As a result, the Company recorded $ 2.5 million of severance and other personnel related expenses for the impacted employees. ​ A summary of the restructuring charges for the years ended December 31, 2024 and December 31, 2023 are as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ Year ended December 31, ​ ​ 2024 ​ 2023 Severance and other personnel costs ​ (in thousands) Research and development ​ $ 3,967 ​ $ 2,188 Selling, general and administrative ​ ​ 1,223 ​ ​ 361 Total ​ $ 5,190 ​ $ 2,549 ​ ​ ​ 132 ​ Table of Contents A summary of the changes in the severance and other personnel liabilities, included within accrued expenses and other current liabilities on the consolidated balance sheets, related to the workforce reduction is as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ ​ 2024 ​ ​ 2023 ​ (in thousands) ​ (in thousands) Amount of liability at beginning of period $ 1,027 ​ $ — Severance and other personnel costs ​ 5,190 ​ ​ 2,549 Cash payments during the period ​ ( 4,740 ) ​ ​ ( 1,522 ) Amount of liability at end of period $ 1,477 ​ $ 1,027 ​ ​ 5. Investment securities ​ The following table summarizes the Company’s investments into government debt securities as of December 31, 2024 and 2023: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ At December 31, 2024 ​ ​ Amortized cost ​ Gross unrealized holding gains ​ Gross unrealized holding losses ​ Estimated fair value ​ ​ (in thousands) Current investments: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Government debt securities (held-to-maturity) ​ $ 208,591 ​ $ 164 ​ $ — ​ $ 208,755 Total ​ $ 208,591 ​ $ 164 ​ $ — ​ $ 208,755 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 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 debt securities 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 (December 31, 2024: $ 15.3 million, December 31, 2023: nil ). Inputs to the fair value of the investments are considered Level 2 inputs. 133 ​ Table of Contents ​ 6. Inventories ​ The following table summarizes the inventories, net balances as of December 31, 2024 and December 31, 2023: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ 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 $ 6.3 million and $ 1.6 million for the years ended December 31, 2024 and December 31, 2023. The costs were recognized as Cost of Contract Manufacturing Revenues. At December 31, 2023, the Company recorded an allowance for inventory of $ 1.6 million. The Company sold its inventories as part of the Lexington Transaction (refer to Note 3 “Divestiture of commercial manufacturing activities” and Note 4 “Restructuring” ). ​ ​ ​ 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. ​ 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 Company’s material financial assets include cash and cash equivalents, restricted cash and investment securities. Cash and cash equivalents and restricted cash are measured at fair value using Level 1 inputs. Restricted cash is included within “Other non-current assets” within the consolidated balance sheets. Investment securities are measured at amortized cost. ​ The following table sets forth the balances and changes in fair values of liabilities that are measured at fair value using Level 3 inputs: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Derivative ​ ​ ​ ​ ​ Contingent ​ financial ​ ​ ​ ​ consideration instruments Total ​ ​ (in thousands) Balance at December 31, 2021 ​ $ 29,542 ​ $ 2,805 ​ $ 32,347 Net losses / (gains) recognized in profit or loss ​ ​ 7,080 ​ ​ ( 2,760 ) ​ ​ 4,320 Currency translation effects ​ ​ ( 1,306 ) ​ ​ ( 45 ) ​ ​ ( 1,351 ) Balance at December 31, 2022 ​ $ 35,316 ​ $ — ​ $ 35,316 Net losses recognized in profit or loss ​ ​ 15,895 ​ ​ — ​ ​ 15,895 Contingent consideration milestone payment ​ ​ ( 9,563 ) ​ ​ — ​ ​ ( 9,563 ) Currency translation effects ​ ​ 1,358 ​ ​ — ​ ​ 1,358 Balance at December 31, 2023 ​ $ 43,006 ​ $ — ​ $ 43,006 Net (gain) recognized in profit or loss ​ ​ ( 1,817 ) ​ ​ — ​ ​ ( 1,817 ) Contingent consideration milestone payment ​ ​ ( 28,167 ) ​ ​ — ​ ​ ( 28,167 ) Currency translation effects ​ ​ ( 2,162 ) ​ ​ — ​ ​ ( 2,162 ) Balance at December 31, 2024 ​ $ 10,860 ​ $ — ​ $ 10,860 ​ ​ 134 ​ Table of Contents Contingent consideration ​ The Company is required to pay up to EUR 143.1 million ($ 148.6 million at the December 31, 2024 foreign exchange rate) to the former shareholders of uniQure France SAS (formerly Corlieve Therapeutics SAS) upon the achievement of the remaining contractually defined milestones in connection with the Company’s acquisition of uniQure France in 2021 . ​ The fair value of the contingent consideration liability related to this acquisition as of December 31, 2024 was $ 10.9 million (December 31, 2023: $ 43.0 million) using discount rates of approximately 15.3 % to 16.2 % (December 31, 2023: 15.3 % to 15.6 %). ​ Following the clearance of an Investigational New Drug (“IND”) application for AMT-260 in August 2023, the Company had increased the probability of achieving a EUR 30.0 million ($ 33.1 million) milestone payment following the dosing of the first patient in Phase I/II clinical trial from 66.0 % to 100.0 %. This also resulted in an increase of the probability that AMT-260 may advance to late-stage development and commercialization. ​ In December 2024, a milestone payment of EUR 30.0 million ($ 31.5 million) was paid, of which EUR 26.8 million ($ 28.2 million) related to contingent consideration. In September 2023, a milestone payment of EUR 10.0 million ($ 10.6 million) was paid, of which EUR 8.9 million ($ 9.6 million) related to contingent consideration. ​ If as of December 31, 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 EUR 33.7 million ($ 35.0 million). If as of December 31, 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. ​ As of December 31, 2024, the Company classified no ne of the total contingent consideration of $ 10.9 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. ​ Derivative financial instruments ​ Derivative financial instruments BMS ​ In December 2020, as part of the amended BMS CLA, the Company and BMS had agreed that upon the consummation of a change of control transaction of uniQure occurring prior to December 2026 or BMS’ delivery of a cessation notice (as contractually defined) the Company (or its third party acquirer) should have paid to BMS a one-time, non-refundable, non-creditable contractually defined payment (“CoC-payment”). The amended BMS CLA was terminated on February 21, 2023. ​ The Company had previously determined that the CoC-payment should be recorded as a derivative financial liability upon initial recognition and that subsequent changes in the fair market value of this derivative financial liability should be recorded in profit and loss. As a result of the derecognition of the derivative financial liability in the year ended December 31, 2022, the Company recorded a $ 2.8 million gain within “Other non-operating (losses) / gains”. ​ Other ​ As of December 31, 2024, the Company recorded $ 0.4 million liabilities related to consideration for post-acquisition services, presented within Other non-current liabilities in connection with the Company’s acquisition of uniQure France SAS (December 31, 2023: $ 0.5 million). ​ Investment securities ​ Refer to Note 5 “ Investment securities ” for the fair value of the investment securities as of December 31, 2024. ​ Pension plan assets ​ Refer to Note 14 “ Retirement benefits ” for the fair value of the plan assets as of December 31, 2024. 135 ​ Table of Contents ​ ​ ​ 8. Property, plant, and equipment, net ​ The following table presents the Company’s property, plant, and equipment as of December 31: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ 2024 2023 ​ ​ (in thousands) Leasehold improvements ​ $ 24,808 ​ $ 46,512 Laboratory equipment ​ ​ 23,359 ​ ​ 43,657 Office equipment ​ ​ 3,913 ​ ​ 6,383 Construction-in-progress ​ ​ — ​ ​ 5,668 Total property, plant, and equipment ​ ​ 52,080 ​ ​ 102,220 Less accumulated depreciation ​ ​ ( 31,656 ) ​ ​ ( 55,672 ) Property, plant and equipment, net ​ $ 20,424 ​ $ 46,548 ​ Total depreciation expense was $ 10.1 million for the year ended December 31, 2024 (December 31, 2023: $ 10.3 million, December 31, 2022: $ 8.2 million). Depreciation expense is allocated to research and development expenses and cost of contract manufacturing to the extent it related to the Company’s commercial manufacturing facility and equipment and laboratory equipment. All other depreciation expenses are allocated to selling, general and administrative expense. ​ The Company sold property, plant and equipment with a carrying value of $ 15.2 million, including leasehold improvements with a carrying value of $ 6.4 million, laboratory and office equipment with a carrying value of $ 6.0 million as well as assets under construction with a carrying value of $ 2.8 million as part of the Lexington Transaction (refer to Note 3 “ Divestment of commercial manufacturing activities” ). ​ The following table summarizes property, plant, and equipment by geographic region. ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, December 31, ​ ​ 2024 ​ 2023 ​ ​ (in thousands) Dutch sites ​ $ 19,463 ​ $ 27,095 Lexington, Massachusetts (United States of America) ​ 730 ​ 19,437 Other ​ ​ 231 ​ ​ 16 Total ​ $ 20,424 ​ $ 46,548 ​ ​ 9. Right-of-use asset and lease liabilities ​ The Company’s most significant leases relate to office and laboratory space under the following operating lease agreements: ​ Lexington, Massachusetts / United States ​ In July 2013, the Company entered into a lease for a facility in Lexington, Massachusetts, United States. In November 2018, the term was expanded by five years to June 2029 and include an additional 30,655 square feet within the same facility and for the same term. The Company in July 2024 assigned the leases to Genezen as part of its divestment of its commercial manufacturing activities and as a result de-recognized its right of use asset and related lease liability. Refer to Note 3 “ Divestment of commercial manufacturing activities”. In December 2021, the Company entered into a lease for an research and development facility in Lexington, Massachusetts, United States of approximately 13,501 square feet of space. The lease commenced in May 2022 and is set for a non-cancellable period ending March 2029. Following the Company’s announcement of a reorganization in 2023, the Company incurred costs amounting to $ 1.4 million for the year ended December 31, 2023, associated with the impairment of the right-of-use asset and its associated leasehold improvements’ carrying value that was determined not be recoverable as of the cease-use date in late 2023. Commencing August 2024 the Company subleased this facility for the residual term. 136 ​ Table of Contents The fixed lease payments to be received during the remaining term under the agreement to sub-lease amount to $ 3.2 million as of December 31, 2024. In February 2022, the Company entered into a new lease for an additional facility in Lexington, Massachusetts, United States of approximately 12,716 square feet. The lease commenced in November 2022 and is set for a non-cancellable period ending March 2030. The lease is renewable for one five-year term. Amsterdam / The Netherlands ​ In March 2016, the Company entered into a 16-year lease for a facility in Amsterdam, the Netherlands and amended this agreement in June 2016. The lease for the facility terminates in February 2032, with an option to extend in increments of five-year periods. The lease contract includes variable lease payments related to annual increases in payments based on a consumer price index. In May 2021 the Company leased an additional approximately 1,080 square meters of office space. The lease expires in October 2028. ​ As of December 31, 2024 the Company is sub-leasing two of the seven floors of its Amsterdam facility for a ten-year term ending on December 31, 2027 with an option for the sub-lessee to extend until December 31, 2031. The sublessee has informed the Company during 2024 of its intention to terminate the sub-lease. ​ The fixed lease payments to be received during the remaining term under the agreement to sub-lease amount to EUR 2.7 million ($ 2.8 million) as of December 31, 2024. ​ Operating lease liabilities ​ The components of lease cost were as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ 2024 2023 2022 ​ ​ (in thousands) ​ ​ ​ Operating lease cost ​ $ 6,486 ​ $ 7,018 ​ $ 5,932 Variable lease cost ​ ​ 1,137 ​ ​ 1,238 ​ ​ 785 Sublease income ​ ​ ( 1,162 ) ​ ​ ( 957 ) ​ ​ ( 849 ) Total lease cost ​ $ 6,461 ​ $ 7,299 ​ $ 5,868 ​ The table below presents the lease-related assets and liabilities recorded on the Consolidated balance sheets. ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ ​ 2024 ​ 2023 ​ ​ (in thousands) Assets ​ ​ ​ ​ ​ ​ Operating lease right-of-use assets ​ $ 13,647 ​ ​ 28,789 Liabilities ​ ​ ​ ​ ​ ​ Current ​ ​ ​ ​ ​ ​ Current operating lease liabilities ​ ​ 3,601 ​ ​ 8,344 Non-current ​ ​ ​ ​ ​ ​ Non-current operating lease liabilities ​ ​ 11,136 ​ ​ 28,316 Total lease liabilities ​ $ 14,737 ​ ​ 36,660 ​ Other information The weighted-average remaining lease term as of December 31, 2024, is 5.9 years, compared to 6.1 years as of December 31, 2023, and the weighted-average discount rate as of December 31, 2024 is 11.3 % , compared to 11.2 % as of December 31, 2023. The Company uses an incremental borrowing rate applicable to the lease asset. ​ 137 ​ Table of Contents The table below presents supplemental cash flow and non-cash information related to leases. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ 2024 2023 2022 ​ ​ (in thousands) Cash paid for amounts included in the measurement of lease liabilities ​ ​ ​ ​ ​ ​ ​ ​ ​ Operating cash flows for operating leases ​ $ 6,113 ​ $ 7,921 ​ $ 7,532 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Right-of-use asset obtained in exchange for lease obligation ​ ​ ​ ​ ​ ​ ​ ​ ​ Operating lease ​ $ — ​ $ 561 ​ $ 9,824 ​ Undiscounted cash flows The table below reconciles the undiscounted cash flows as of December 31, 2024, for each of the first five following years and the total of the remaining years to the operating lease liabilities recorded on the Consolidated balance sheet as of December 31, 2024. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Lexington ​ Amsterdam (1) ​ Other (2) ​ Total ​ (in thousands) 2025 $ 1,394 ​ $ 1,934 ​ $ 274 ​ $ 3,602 2026 ​ 1,431 ​ ​ 1,934 ​ ​ 228 ​ ​ 3,593 2027 ​ 1,469 ​ ​ 1,938 ​ ​ 0 ​ ​ 3,407 2028 ​ 1,508 ​ ​ 1,867 ​ ​ — ​ ​ 3,375 2029 ​ 763 ​ ​ 1,752 ​ ​ — ​ ​ 2,515 Thereafter ​ 130 ​ ​ 3,358 ​ ​ — ​ ​ 3,488 Total lease payments $ 6,695 ​ $ 12,783 ​ $ 502 ​ $ 19,980 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Less: amount of lease payments representing interest payments ​ ( 1,344 ) ​ ​ ( 3,842 ) ​ ​ ( 57 ) ​ ​ ( 5,243 ) Present value of lease payments ​ 5,351 ​ ​ 8,941 ​ ​ 445 ​ ​ 14,737 Less: current operating lease liabilities ​ ( 1,394 ) ​ ​ ( 1,934 ) ​ ​ ( 273 ) ​ ​ ( 3,601 ) Non-current operating lease liabilities $ 3,957 ​ $ 7,007 ​ $ 172 ​ $ 11,136 (1) Payments are due in EUR and have been translated at the foreign exchange rate as of December 31, 2024, of $ 1.04 / €1.00 (2) Payments are due in CHF and have been translated at the foreign exchange rate as of December 31, 2024, of $ 1.10 / CHF1.00 ​ 10. Intangible assets, net and Goodwill ​ The following table presents the Company’s acquired licenses, intangible asset related to the favorable supply terms under the CSA and acquired IPR&D as of December 31: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ At December 31, 2024 ​ ​ Gross Carrying Amount ​ Accumulated Amortization ​ Net ​ ​ (in thousands) Acquired licenses ​ $ 2,276 ​ $ ( 1,117 ) ​ $ 1,159 Favorable supply terms under CSA ​ ​ 16,700 ​ ​ ( 2,454 ) ​ ​ 14,246 Total amortizable intangible assets ​ ​ 18,976 ​ ​ ( 3,571 ) ​ ​ 15,405 Acquired IPR&D intangible asset ​ ​ 55,638 ​ ​ — ​ ​ 55,638 Total intangible assets ​ $ 74,614 ​ $ ( 3,571 ) ​ $ 71,043 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ At December 31, 2023 ​ ​ Gross Carrying Amount ​ Accumulated Amortization ​ Net ​ ​ (in thousands) Acquired licenses ​ $ 2,419 ​ $ ( 1,057 ) ​ $ 1,362 Total amortizable intangible assets ​ ​ 2,419 ​ ​ ( 1,057 ) ​ ​ 1,362 Acquired IPR&D intangible asset ​ ​ 59,119 ​ ​ — ​ ​ 59,119 Total intangible assets ​ $ 61,538 ​ $ ( 1,057 ) ​ $ 60,481 ​ 138 ​ Table of Contents As of December 31, 2024, the estimated future amortization expense for each of the five succeeding years and the period thereafter is as follows: ​ ​ ​ ​ ​ Years Amount ​ ​ (in thousands) 2025 ​ $ 5,689 2026 ​ 5,689 2027 ​ 3,234 2028 ​ 122 2029 ​ 122 Thereafter ​ 549 Total ​ $ 15,405 ​ a. Acquired licenses ​ All acquired licenses are owned by uniQure biopharma B.V, a subsidiary of the Company. The remaining weighted average life is 9.5 years as of December 31, 2024 (December 31, 2023 10.5 years). ​ The amortization expense related to acquired licenses for the year ended December 31, 2024 was $ 0.1 million (December 31, 2023: $ 0.1 million; December 31, 2022: $ 0.4 million). ​ b. Favorable supply terms under CSA ​ As part of the Lexington Transaction, the Company recognized an intangible asset related to its rights to purchase HEMGENIX® at terms considered favorable to market terms. Refer to Note 3 “ Divestment of commercial manufacturing activities”. The intangible asset is amortized on a straight line basis over a three year period that commenced in July 2024. ​ The amortization expense related to the intangible asset for the year ended December 31, 2024 was $ 2.5 million (December 31, 2023 and 2022: nil ). ​ c. Acquired in-process research and development ​ The IPR&D Intangible Asset was recorded as part of the Company’s July 2021 acquisition of uniQure France SAS. Refer to Note 2.3.11. ​ d. Goodwill ​ The goodwill was recorded as part of the Company’s July 2021 acquisition of uniQure France SAS. Refer to Note 2.3.11. ​ ​ 11. Accrued expenses and other current liabilities ​ Accrued expenses and other current liabilities include the following items: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ 2024 2023 ​ ​ (in thousands) Personnel related accruals and liabilities ​ $ 12,583 ​ $ 16,263 Accruals for goods received from and services provided by vendors-not yet billed ​ ​ 10,109 ​ ​ 12,834 Current portion of firm purchase commitment liability (refer to Note 3 "Divestiture of commercial manufacturing activities") ​ ​ 1,582 ​ ​ - Liability owed to the Purchaser pursuant to the Royalty Financing Agreement ​ ​ 4,951 ​ ​ 1,437 Total ​ $ 29,225 ​ $ 30,534 ​ ​ ​ ​ 139 ​ Table of Contents ​ ​ 12. 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 December 31, 2024 under the 2024 Amended Facility was $ 50.0 million. ​ The Company is required to repay the residual principal balance 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 2024 Amended Facility was $ 51.9 million as of December 31, 2024, compared to an amortized cost of $ 102.9 million as of December 31, 2023, and is recorded net of discount and debt issuance costs. The foreign currency loss on the loan was $ 4.1 million in 2024 (2023: gain of $ 3.0 million; 2022: loss of $ 5.8 million). The fair value of the loan approximates its carrying amount. Inputs to the fair value of the loan are considered Level 3 inputs. ​ Interest expense recorded during the years ended December 31 was as follows: ​ ​ ​ ​ ​ Years Amount ​ ​ (in millions) 2024 ​ $ 12.9 2023 ​ 14.6 2022 ​ ​ 11.5 ​ 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 United States, 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 of 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 $ 556.5 million, less $ 4.1 million of cash and cash equivalents and other current assets held by the Company and $ 80.5 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 December 31, 2024, the Company was in material compliance with all covenants and provisions. ​ 140 ​ Table of Contents The aggregate maturities of the loans, including $ 16.0 million of coupon interest payments and financing fees, for each of the 25 months after December 31, 2024, are as follows: ​ ​ ​ ​ ​ Years Amount ​ ​ (in thousands) 2025 ​ $ 8,616 2026 ​ ​ 6,185 2027 ​ ​ 51,218 Total ​ $ 66,019 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 13. Royalty Financing Agreement ​ On May 12, 2023, the Company entered into the Royalty Financing Agreement with 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 will be obligated to pay $ 25.0 million of the first worldwide sales milestone payment from CSL Behring, if received, to the Purchaser. ​ The Purchaser will receive 1.85 times the upfront payment (or $ 693.8 million) until June 30, 2032 (“First Hard Cap Date”) if such thresholds are met or, if such cap is not met by June 30, 2032, up to 2.25 times of the upfront payment through December 31, 2038 (“Second Hard Cap Date”). If, on or prior to the defined dates for each cap amount, the total amount of royalty payments received by the Purchaser equals or exceeds the cap amount applicable to such date, the Royalty Financing Agreement will automatically terminate and all rights to the HEMGENIX® royalty payments will revert back to the Company. The Company has no obligation to repay any amounts received from the Purchaser in the event that the applicable cap amount is not reached during the term of the Royalty Financing Agreement. ​ The Company has retained the rights to all other royalties, as well as commercial 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 balance sheet as of closing of the transaction on June 5, 2023. Following the initial recognition, the Company records the debt at amortized cost. ​ As of December 31, 2024 the Company expects to satisfy its commitment to the Purchaser prior to the Second Hard Cap Date. The Company until December 2024 assumed that it would satisfy the commitments to the Purchaser prior to the First Hard Cap Date. This change in assumption did not have a material impact on the amount of debt or interest expense recorded for the year ended December 31, 2024. The Company will record the difference of $ 473.7 million between the total expected payments of $ 843.8 million to the Purchaser and the $ 370.1 million net proceeds as interest expense using the effective interest rate method. The Company determined the effective interest rate based on the projected cash flows up to the Second Hard Cap Date. Based on the Company’s projections the effective interest rate is expected to be within a range of 12.0 % to 13.5 % per annum, which is consistent with the range that was used prior to the change in assumption in December 2024. The Company would have recorded the following amounts: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ ​ 2024 2023 ​ 2022 ​ ​ (in millions) Interest expenses at effective interest rate of 12.0 % per annum $ 50.7 ​ $ 26.5 ​ $ — Interest recorded in the statement of operations and comprehensive loss and income ​ 50.9 ​ ​ 26.9 ​ ​ — Interest expenses at effective interest rate of 13.5 % per annum ​ 57.8 ​ ​ 29.9 ​ ​ — ​ The Company prospectively updates the effective interest rate at each reporting date based on updated cash flow projections. ​ The liability was initially recognized at fair value and inputs were considered Level 3 inputs. ​ 141 ​ Table of Contents The following table presents the movement in the liability related to the Royalty Financing Agreement between the year ended December 31, 2024 and December 31, 2023: ​ ​ ​ ​ ​ Amount of liability ​ (in thousands) Gross proceeds from royalty financing agreement on June 5, 2023 ​ 375,000 Debt issuance costs paid ​ ( 4,938 ) Royalty payments to Purchaser ​ ( 1,317 ) Interest expense for the period ​ 26,933 Balance as of December 31, 2023 (includes $ 1.4 million presented as "Accrued expenses and other current liabilities) $ 395,678 Royalty payments to Purchaser ​ ( 6,662 ) Interest expense for the period ​ 50,865 Balance as of December 31, 2024 (includes $ 5.0 million presented as "Accrued expenses and other current liabilities) $ 439,881 ​ ​ ​ 14. Retirement benefits ​ Defined benefit pension plan ​ The Company operates a defined benefit pension plan for its Swiss employees (the “Swiss Plan”) in accordance with local regulations and practices. The normal retirement age under the Swiss Plan is 65 years. All benefits are immediately vested. Under the Swiss Plan, a percentage of pensionable salary is contributed as a retirement credit with additional contributions being made for death and disability benefits. Under Swiss pension law, participants who are covered by the pension plan of another employer are required to transfer the termination benefit of that pension plan into the plan of the Company. When employment at the Company ends before reaching retirement, the termination benefit is transferred out of the defined benefit pension plan. At time of retirement the accumulated retirement credit can be converted into a life-long annuity or be paid-out as a lump-sum. Participants are also permitted to withdraw a part of the accumulated termination benefit in special circumstances before reaching retirement age for example for payments related to obtain home ownership. ​ The Company initially recognized its net projected benefit obligation as of December 31, 2023 at a carrying amount of CHF 2.1 million ($ 2.6 million), presented within other non-current liabilities in the consolidated balance sheets. ​ A summary of the changes in the projected benefit obligation (“PBO”) and plan assets is presented below: ​ ​ ​ ​ ​ ​ ​ December 31, ​ ​ 2024 ​ ​ (in thousands) Beginning projected benefit obligation ​ $ 11,499 Service cost ​ ​ 551 Interest cost ​ ​ 167 Liabilities assumed from participants joining the plan ​ ​ 643 Actuarial losses ​ ​ 509 Liabilities extinguished through participants leaving the plan ​ ​ ( 984 ) Foreign currency exchange rate changes ​ ​ ( 890 ) Ending projected benefit obligation ​ $ 11,495 ​ ​ 142 ​ Table of Contents ​ ​ ​ ​ ​ ​ ​ December 31, ​ ​ 2024 ​ ​ (in thousands) Beginning fair value of plan assets ​ $ 8,946 Return on plan assets ​ ​ 690 Interest income ​ ​ 226 Contributions by the employer ​ ​ 643 Assets contributed to the plan from participants joining the plan ​ ​ 643 Assets distributed to participants leaving the plan ​ ​ ( 984 ) Foreign currency exchange rate changes ​ ​ ( 664 ) Ending fair value of plan assets ​ $ 9,500 ​ Amounts recognized on the consolidated balance sheet, presented within other non-current liabilities, were as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ ​ 2024 2023 ​ ​ (in thousands) Fair value of plan assets ​ $ 9,500 ​ $ 8,946 Present value of projected benefit obligation ​ ​ ( 11,495 ) ​ ​ ( 11,499 ) Funded status: (net liability) ​ $ ( 1,995 ) ​ $ ( 2,553 ) ​ ​ ​ ​ ​ ​ ​ Accumulated benefit obligation as of December 31 ​ $ 11,075 ​ $ 10,739 ​ Amounts recorded in accumulated other comprehensive (income) / loss: ​ ​ ​ ​ ​ ​ ​ December 31, ​ ​ 2024 ​ ​ (in thousands) Actuarial loss - beginning of year ​ $ 2,540 Actuarial (gain) of current year ​ ​ ( 241 ) Amortization of prior service costs ​ ​ ( 142 ) Total ​ $ 2,157 ​ Net pension expense related to the defined benefit plans included the following components: ​ ​ ​ ​ ​ ​ ​ December 31, ​ ​ 2024 ​ ​ (in thousands) Service cost ​ $ 551 Interest cost ​ ​ 167 Interest income ​ ​ ( 226 ) Amortization of net loss ​ ​ 142 Net pension expense ​ $ 634 ​ 143 ​ Table of Contents The assumptions related to the Swiss Plan are as follows: ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, Actuarial assumptions (% p.a.) 2024 ​ 2023 Discount rate ​ 0.90 % ​ 1.50 % Expected return on plan assets ​ 1.80 % ​ 2.60 % Expected inflation rate ​ 0.70 % ​ 1.60 % Interest credit rate ​ 1.25 % ​ 1.25 % Long-term expected rate of salary increases ​ 0.70 % ​ 1.60 % Pension increase ​ 0.00 % ​ 0.00 % ​ Future benefits expected to be paid are as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ 2024 2023 ​ ​ (in thousands) Year 1 ​ $ 490 ​ $ 533 Year 2 ​ ​ 409 ​ ​ 610 Year 3 ​ ​ 417 ​ ​ 528 Year 4 ​ ​ 440 ​ ​ 529 Year 5 ​ ​ 480 ​ ​ 540 Next 5 years ​ ​ 4,747 ​ ​ 4,992 ​ ​ ​ ​ ​ ​ ​ Other disclosure items: ​ ​ ​ ​ ​ ​ Next year's expected employer contribution ​ $ 575 ​ $ 552 ​ ​ ​ ​ ​ ​ ​ ​ The Company's investment strategy for its pension plan is to optimize the long-term investment return on plan assets in relation to the liability structure to maintain an acceptable level of risk while minimizing the cost of providing pension benefits and maintaining adequate funding levels in accordance with the applicable rules in each jurisdiction. The Company does not manage any assets internally. The plan assets relate to assets being held by the Swiss pension foundations in which the Company's pension plan is set-up. ​ The allocation of plan assets is presented below: ​ ​ ​ ​ ​ ​ ​ ​ December 31, ​ December 31, ​ 2024 2023 Bonds ​ 61 % ​ 61 % Equities ​ 25 % ​ 25 % Real estate ​ 10 % ​ 10 % Others ​ 4 % ​ 4 % ​ The fair value of the plan assets is determined based on Level 2 inputs. ​ ​ ​ 144 ​ Table of Contents 15. Shareholders’ (deficit) / equity ​ As of December 31, 2024, the Company’s authorized share capital is € 4.0 million (or $ 4.2 million when translated at an exchange rate as of December 31, 2024, of $ 1.04 / €1.00), divided into 80,000,000 ordinary shares, each with a nominal value of € 0.05 . ​ All ordinary shares issued by the Company were fully paid. The minimum amount of share capital to be held under Dutch law is EUR 0.0 million. Under the Company’s Articles of Association, the Company is required to maintain a minimum amount of share capital in reserve. In addition, the Company is only permitted to make distributions on its ordinary shares to the extent that its shareholders’ (deficit) / equity exceeds the sum of the paid-up and called-up capital and the reserves it is required to maintain under Dutch law. There are no other distribution restrictions applicable to the Company’s shares. As the Company’s equity is negative as of December 31, 2024 the Company cannot distribute any equity. ​ As of December 31, 2024, and 2023 and 2022 the Company’s other comprehensive result was restricted for payment of dividends for an accumulated other comprehensive loss of $ 52.8 million in 2024, an accumulated other comprehensive loss of $ 53.6 million in 2023, and an accumulated other comprehensive loss of $ 58.3 million in 2022. ​ The Company recorded a $ 0.8 million increase of additional paid-in capital in the year ended December 31, 2022 resulting from the release of valuation allowance for the tax benefit of share issuance costs incurred in 2018, 2019 and 2021 within the Netherlands. ​ 16. Share-based compensation ​ Share-based compensation expense recognized by classification included in the consolidated statements of operations and comprehensive loss was as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ ​ 2024 ​ 2023 ​ 2022 ​ ​ (in thousands) Cost of manufacturing services revenue ​ $ 1,035 ​ $ 826 ​ $ 323 Research and development ​ ​ 9,295 ​ ​ 16,881 ​ ​ 18,402 Selling, general and administrative ​ ​ 11,928 ​ ​ 17,386 ​ ​ 15,479 Total ​ $ 22,258 ​ $ 35,093 ​ $ 34,204 ​ Share-based compensation expense recognized by award type was as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ ​ 2024 ​ 2023 ​ 2022 ​ ​ (in thousands) Award type/ESPP ​ ​ ​ ​ ​ ​ ​ ​ ​ Share options ​ $ 9,178 ​ $ 13,302 ​ $ 13,425 Restricted share units ​ ​ 11,490 ​ ​ 18,524 ​ ​ 15,486 Performance share units ​ ​ 1,580 ​ ​ 3,234 ​ ​ 5,267 Employee share purchase plan ​ ​ 10 ​ ​ 33 ​ ​ 26 Total ​ $ 22,258 ​ $ 35,093 ​ $ 34,204 ​ As of December 31, 2024, the unrecognized compensation cost related to unvested awards under the various share-based compensation plans were: ​ ​ ​ ​ ​ ​ ​ ​ Unrecognized Weighted average ​ share-based remaining ​ ​ compensation ​ period for ​ ​ expense ​ recognition ​ ​ (in thousands) ​ (in years) Award type ​ ​ ​ ​ ​ Share options ​ $ 9,439 ​ 2.09 Restricted share units ​ ​ 9,873 ​ 1.54 Performance share units ​ ​ 3,013 ​ 0.97 Total ​ $ 22,324 ​ 1.80 ​ 145 ​ Table of Contents 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’s share-based compensation plans include the 2014 Amended and Restated Share Option Plan as approved by the shareholders in 2014, (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”). ​ The shareholders have approved amendment to the 2014 Plan from time to time to increase the shares authorized for issuance. At an extraordinary general meeting of shareholders in November 2023, an additional 1,750,000 shares were authorized for issuance. At the annual general meeting of shareholders in June 2024, the Company’s shareholders authorized an additional 1,500,000 shares for issuance. As of December 31, 2024, a total of 3,912,283 ordinary shares remain available for issuance under the 2014 Plan. ​ 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 % 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. 2014 Plans The following tables summarize option activity under the Company’s 2014 Plans for the year ended December 31, 2024: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Options ​ ​ Number of ​ Weighted average ​ Weighted average ​ Aggregate intrinsic ​ ordinary shares exercise price remaining contractual life value ​ ​ ​ ​ ​ ​ ​ in years ​ ​ (in thousands) Outstanding at December 31, 2023 ​ 4,974,030 ​ ​ 23.25 ​ 6.71 ​ $ 182 Granted ​ 1,093,080 ​ $ 5.47 ​ ​ ​ ​ ​ Forfeited ​ ( 316,056 ) ​ $ 16.69 ​ ​ ​ ​ ​ Expired ​ ( 613,996 ) ​ $ 25.04 ​ ​ ​ ​ ​ Exercised ​ ( 169,898 ) ​ $ 13.39 ​ ​ ​ ​ ​ Outstanding at December 31, 2024 ​ 4,967,160 ​ $ 19.87 ​ 5.91 ​ ​ 19,196 Thereof, fully vested, and exercisable on December 31, 2024 ​ 3,128,557 ​ $ 24.82 ​ 4.48 ​ ​ 5,923 Thereof, outstanding and expected to vest after December 31, 2024 ​ 1,838,603 ​ $ 11.46 ​ 8.34 ​ ​ 13,273 Outstanding and expected to vest after December 31, 2023 ​ 2,235,435 ​ $ 19.78 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of options issued during the period (in $ millions) ​ ​ ​ $ 3.5 ​ ​ ​ ​ ​ Granted to directors and officers during the period (options, grant date fair value $ in millions) ​ 626,880 ​ $ 2.0 ​ ​ ​ ​ ​ Proceeds from option sales during the period (in $ millions) ​ ​ ​ $ 2.1 ​ ​ ​ ​ ​ 146 ​ Table of Contents ​ The following table summarizes information about the weighted average grant-date fair value of options during the years ended December 31: ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted average ​ ​ Options ​ grant ‑ date fair value Granted, 2024 1,093,080 ​ $ 3.19 Granted, 2023 1,650,030 ​ ​ 10.57 Granted, 2022 1,426,966 ​ ​ 9.04 Vested, 2024 ​ 992,777 ​ ​ 12.21 Forfeited, 2024 ​ ( 316,056 ) ​ ​ 9.74 ​ The following table summarizes information about the weighted average grant-date fair value of options at December 31: ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted average ​ ​ Options ​ grant ‑ date fair value Outstanding and expected to vest, 2024 1,838,603 ​ $ 6.66 Outstanding and expected to vest, 2023 2,235,435 ​ ​ 11.50 ​ ​ 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: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ 2024 2023 ​ 2022 Assumptions ​ ​ ​ ​ ​ ​ Expected volatility ​ 70 % ​ 70 % ​ 70 % Expected terms ​ 10 years ​ 10 years ​ 10 years Risk free interest rate ​ 3.7 % - 4.3 % ​ 3.7 % - 4.8 % ​ 2.1 % - 4.2 % Expected dividend yield ​ 0 % ​ 0 % ​ 0 % ​ The Hull & White option model captures early exercises by assuming that the likelihood of exercises will increase when the share price reaches defined multiples of the strike price. This analysis is performed over the full contractual term. ​ The following table summarizes information about options exercised during the years ended December 31: ​ ​ ​ ​ ​ ​ ​ ​ Exercised ​ ​ ​ ​ during the year ​ Intrinsic value ​ ​ ​ ​ (in thousands) 2024 169,898 ​ $ 248 2023 14,070 ​ 154 2022 138,356 ​ 1,848 147 ​ Table of Contents ​ Restricted Share Units ​ The following table summarizes the RSU activity for the year ended December 31, 2024: ​ ​ ​ ​ ​ ​ ​ ​ ​ RSUs ​ ​ Weighted average ​ ​ Number of ​ grant-date fair ​ ​ ordinary shares ​ value Non-vested at December 31, 2023 ​ 2,264,369 ​ $ 18.07 Granted ​ 1,321,360 ​ $ 5.57 Vested ​ ( 931,450 ) ​ $ 19.49 Forfeited ​ ( 994,381 ) ​ $ 12.44 Non-vested at December 31, 2024 ​ 1,659,898 ​ $ 10.71 ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of RSUs granted during the period (in $ millions) ​ ​ ​ $ 7.4 Granted to directors and officers during the period (shares, $ in millions) ​ 355,060 ​ $ 1.9 ​ The following table summarizes information about the weighted average grant-date fair value of RSUs granted during the years ended December 31: ​ ​ ​ ​ ​ ​ ​ ​ Granted Weighted average ​ ​ during the year ​ grant ‑ date fair value 2024 1,321,360 ​ $ 5.57 2023 1,770,025 ​ ​ 17.88 2022 1,604,533 ​ ​ 16.10 ​ The following table summarizes information about the total fair value of RSUs that vested during the years ended December 31: ​ ​ ​ ​ ​ Total fair value ​ (in thousands) 2024 $ 5,603 2023 13,729 2022 5,104 ​ RSUs generally vest over one to three years . RSUs granted to non-executive directors will vest one year from the date of grant. ​ 148 ​ Table of Contents Performance Share Units ​ The following table summarizes the PSU activity for the year ended December 31, 2024: ​ ​ ​ ​ ​ ​ ​ ​ ​ PSUs ​ ​ Weighted average ​ ​ Number of ​ grant-date fair ​ ​ ordinary shares ​ value Non-vested at December 31, 2023 ​ 222,550 ​ $ 28.09 Granted ​ 65,000 ​ $ 15.40 Vested ​ ( 42,759 ) ​ $ 29.35 Forfeited ​ ( 94,671 ) ​ $ 28.63 Non-vested at December 31, 2024 ​ 150,120 ​ $ 21.65 PSUs awarded but not yet earned ​ 115,000 ​ $ 17.66 Total non-vested and discretionary PSUs ​ 265,120 ​ $ 19.92 ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of PSUs granted during the period (in $ millions) ​ ​ ​ $ 1.0 ​ The Company granted shares to certain employees in September and December 2021 and various dates during the year ended December 31, 2022 and December 31, 2024 that will be earned upon achievement of defined milestones. Earned shares vested upon the later of a minimum service period of three years , or the achievement of defined milestones, subject to the grantee’s continued employment. In addition, portions of the December 2021 granted to executives and other members of senior management were subject to achieving a minimum total shareholder return relative to the Nasdaq biotechnology index. As of December 31, 2024, four milestones had been achieved and vested in either 2022, 2023 or 2024. As of December 31, 2024, two milestones were considered probable. The Company recognizes the compensation cost related to these grants to the extent it considers achievement of the milestones to be probable. ​ The Company awarded PSUs to certain employees in December 2024 that will be earned upon the Board of Directors’ (the “Board”) assessment of the level of achievement of agreed upon performance targets through December January 2, 2026 ​ The following table summarizes information about the weighted average grant-date fair value of the PSUs determined as of the grant date for the years ended December 31: ​ ​ ​ ​ ​ ​ ​ ​ Granted Weighted average ​ ​ during the year ​ grant ‑ date fair value 2024 65,000 ​ $ 15.40 2023 — ​ $ — 2022 34,700 ​ $ 15.11 ​ The following table summarizes information about the total fair value of PSUs that vested during the years ended December 31: ​ ​ ​ ​ ​ Total fair value ​ (in thousands) 2024 $ 319 2023 1,474 2022 4,450 ​ 149 ​ Table of Contents Employee Share Purchase Plan (“ESPP”) ​ In June 2018, the Company’s shareholders adopted and approved an 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. Under the ESPP, employees are eligible to purchase ordinary shares through payroll deductions, subject to any plan limitations. The purchase price of the shares on each purchase date is equal to 85 % of the lower of the closing market price on the offering date or the closing market price on the purchase date of each three-month offering period. During the year ended December 31, 2024, 10,150 ordinary shares have been issued (December 31, 2023: 19,198 and December 31, 2022: 11,242 ). As of December 31, 2024, a total of 86,712 ordinary shares remain available for issuance under the ESPP plan. ​ ​ ​ ​ ​ 17. Segment reporting ​ The Company is advancing a pipeline of innovative gene therapies seeking to deliver to patients suffering from rare and other devastating diseases single treatments with potentially curative results. The Company manages the operations related to these research and development activities within one operating segment because they rely on a common set of infrastructure, resources and technology of the products and production processes, types of customers, distribution methods and regulatory environment. ​ The leadership team is identified as the CODM. ​ The CODM allocates resources to research projects and clinical candidates based on scientific data as well as quantitative and qualitative expected risk adjusted returns on investment. The CODM uses segment operating loss to monitor that cash operating losses remain within the approved budget. ​ The Company does not evaluate performance or allocate resources based on segment asset data and therefore such information is not presented. Refer to Note 8 “ Property, plant and equipment, net ” and Note 9 “ Right-of-use asset and lease liabilities ” for geographic information related to long-lived assets. ​ The accounting policies of the operating segment are the same as those described in the summary of significant accounting policies. ​ 150 ​ Table of Contents ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ 2024 2023 2022 ​ ​ (in thousands) Revenue ​ $ 27,119 ​ $ 15,843 ​ $ 106,483 Less: ​ ​ ​ ​ ​ ​ ​ ​ Employee related expenses ​ ( 75,184 ) ​ ( 98,903 ) ​ ( 85,292 ) Laboratory and development expenses ​ ​ ( 47,848 ) ​ ​ ( 44,346 ) ​ ​ ( 52,231 ) Professional fees ​ ​ ( 8,503 ) ​ ​ ( 16,918 ) ​ ​ ( 10,884 ) Facility expenses ​ ​ ( 14,247 ) ​ ​ ( 21,550 ) ​ ​ ( 16,066 ) Consumables ​ ​ ( 9,172 ) ​ ​ ( 19,029 ) ​ ​ ( 19,896 ) Other segment items (a) (b) ​ ​ ( 12,482 ) ​ ​ ( 28,299 ) ​ ​ ( 14,099 ) Segment operating loss ​ ​ ( 140,317 ) ​ ​ ( 213,202 ) ​ ​ ( 91,985 ) Reconciliation ​ ​ ​ ​ ​ ​ ​ ​ ​ Depreciation, amortization and impairment expense ​ ​ ( 12,641 ) ​ ​ ( 11,900 ) ​ ​ ( 8,537 ) Share-based compensation expense ​ ​ ( 22,258 ) ​ ​ ( 35,093 ) ​ ​ ( 34,204 ) Fair value gain / (loss) - contingent consideration and derivative financial instrument ​ ​ 1,817 ​ ​ ( 15,895 ) ​ ​ ( 4,320 ) Foreign currency (losses) / gains, net ​ ​ ( 10,507 ) ​ ​ ( 1,691 ) ​ ​ 23,235 Interest income ​ ​ 21,415 ​ ​ 19,562 ​ ​ 609 Interest expense - Royalty Financing Agreement ​ ​ ( 50,865 ) ​ ( 26,934 ) ​ — Interest expense - Hercules debt facility ​ ​ ( 12,876 ) ​ ​ ( 14,623 ) ​ ​ ( 11,704 ) Other reconciling items (c) (d) ​ ​ ( 10,895 ) ​ ​ ( 6,781 ) ​ ​ ( 1,353 ) Consolidated loss before income tax (expense) / benefit ​ $ ( 237,127 ) ​ $ ( 306,557 ) ​ $ ( 128,259 ) (a) Other segments items included in segment operating loss include costs related to intellectual property, information technology and insurance offset by income related to payments received from European authorities to subsidize the Company’s research and development in the Netherlands and France. (b) For the year ended December 31, 2023, other segment items include $ 10.0 million related to the upfront consideration paid to Apic Bio for the global licensing agreement for AMT-162. (c) For the year ended December 31, 2024, other reconciling items include costs related to the divestment of the Company’s commercial manufacturing activities and the August 2024 reorganization. (d) For the year ended December 31, 2023, other reconciling items include costs related to the October 2023 reorganization and professional fees related to the Apic Bio transaction. ​ ​ 18. Collaboration arrangements and concentration of credit risk ​ Revenues recorded for the years ended December 31, are as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ 2024 2023 2022 ​ ​ (in thousands) License revenue (royalty payments) from CSL Behring ​ $ 10,133 ​ $ 2,758 ​ $ — License revenue (milestone payments) from CSL Behring ​ ​ — ​ — ​ ​ 100,000 Contract manufacturing revenue from CSL Behring ​ ​ 6,114 ​ 10,835 ​ 1,717 Collaboration revenue from CSL Behring ​ ​ 10,872 ​ 2,250 ​ ​ 3,014 Collaboration revenue from BMS ​ ​ — ​ ​ — ​ ​ 1,752 Total ​ $ 27,119 ​ $ 15,843 ​ $ 106,483 ​ License revenue (milestone payments) from CSL Behring ​ The Company recorded $ 100.0 million in variable milestone revenue related to a first sale of HEMGENIX ® in the U.S. during the year ended December 31, 2022 as the Company considered the occurrence of this event to be probable following the November 2022 BLA approval of HEMGENIX ® . The Company collected the $ 100.0 million payment from CSL Behring in July 2023 following the first sale of the Product in the U.S in June 2023. 151 ​ Table of Contents Contract manufacturing revenue from CSL Behring ​ The Company provided contract manufacturing services to CSL Behring from April 2022 until the July 2024 divestment of the commercial manufacturing activities to Genezen. 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. ​ The Company’s development and commercial supply agreement requires the Company to supply HEMGENIX ® to CSL Behring until such time that these capabilities are transferred to CSL Behring or a contract manufacturing organization designated by CSL Behring. On September 6, 2022, CSL Behring notified the Company of its intent to transfer manufacturing technology related to HEMGENIX ® in the coming years to a third-party contract manufacturer designated by CSL Behring. The Company generated $ 6.1 million, $ 10.8 million and $ 1.7 million contract manufacturing revenue from sales to CSL Behring during the years ended December 31, 2024, 2023 and 2022. The Company incurred $ 17.1 million, $ 13.6 million and $ 2.1 million of costs in relation to its contract manufacturing activities during the years ended December 2024, 2023 and 2022. 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 as well as income related to the release of liabilities associated with expected net losses in Other expense within the Company’s Consolidated Statements of Operations and Comprehensive Loss. Collaboration revenue from CSL Behring ​ The Company provides on-demand development services and other services to CSL Behring. These activities are reimbursed at an agreed full-time-employee rate and CSL Behring also reimbursed agreed third-party expenses incurred in relation to performing these activities. The Company recognized $ 10.9 million of collaboration revenue in the year ended December 31, 2024, compared to $ 2.3 million and $ 3.0 million in the same periods in 2023 and 2022. Accounts r eceivable As of December 31, 2024, the Company had accounts receivable of $ 5.7 million 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. ​ ​ 19. Other income ​ Other income during the year ended December 31, 2024 was $ 7.9 million compared to $ 6.1 million and $ 7.2 million during the same periods in 2023 and 2022. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ 2024 2023 2022 ​ ​ (in thousands) Research and development grants from Dutch and French authorities ​ $ 5,602 ​ $ 5,293 ​ $ 6,084 Gain on sale of commercial manufacturing facility ​ 1,150 ​ — ​ — Sublease income ​ 1,073 ​ 609 ​ 763 Other ​ 101 ​ 157 ​ 324 Total ​ $ 7,926 ​ $ 6,059 ​ $ 7,171 ​ ​ 152 ​ Table of Contents ​ 20. Other expense ​ Other expense during the year ended December 31, 2024 was $ 4.6 million compared to $ 1.7 million and $ 0.8 million during the same periods in 2023 and 2022, respectively. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ 2024 2023 2022 ​ ​ (in thousands) Supply of HEMGENIX® to CSL Behring ​ $ 3,215 ​ $ — ​ $ — Sublease expense ​ 1,358 ​ 900 ​ 820 Fair value loss related to equity stake in VectorY B.V. ​ ​ — ​ ​ 790 ​ ​ — Total ​ $ 4,573 ​ $ 1,690 ​ $ 820 ​ In the year ended December 31, 2024, the Company recognized $ 3.2 million net ( nil in periods ended December 31, 2023 and 2022) in other expense related to the purchase of HEMGENIX® from Genezen net of income from the sales of HEMGENIX® to CSL Behring, amortization of the intangible asset for the favorable supply terms under the CSA and credits from the release of liabilities related to expected net losses associated with the minimum purchase commitments under the CSA. ​ ​ 21. Income taxes ​ a. Income tax (benefit) / expense ​ Due to the uncertainty surrounding the realization of favorable tax attributes in future tax returns, the Company has recorded a valuation allowance against the Company’s net deferred tax assets in the Netherlands and a partial valuation allowance against the Company’s net deferred tax assets in France. ​ There are no significant unrecognized tax benefits as of December 31, 2024 and 2023. ​ For the years ended December 31, 2024, 2023 and 2022, (loss) / income before income tax benefit / (expense) consists of the following: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ 2024 2023 2022 ​ ​ (in thousands) Dutch operations ​ $ ( 215,251 ) ​ $ ( 282,530 ) ​ $ ( 96,872 ) U.S. operations ​ ( 1,133 ) ​ ( 6,903 ) ​ ( 14,934 ) Other ​ ​ ( 20,743 ) ​ ​ ( 17,124 ) ​ ​ ( 16,453 ) Total ​ $ ( 237,127 ) ​ $ ( 306,557 ) ​ $ ( 128,259 ) ​ The income tax (expense) / benefit for the years ended December 31, 2024, 2023 and 2022, consists of the following: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ 2024 2023 2022 ​ ​ (in thousands) Current tax expense ​ ​ ​ ​ ​ ​ ​ ​ ​ Other ​ $ ( 145 ) ​ $ ( 110 ) ​ $ ( 24 ) Total current income tax expense ​ $ ( 145 ) ​ $ ( 110 ) ​ $ ( 24 ) Deferred tax (expense) / benefit ​ ​ ​ ​ ​ ​ Dutch operations ​ $ — ​ $ — ​ $ ( 808 ) U.S. operations ​ ( 2,275 ) ​ ( 2,708 ) ​ ( 1,075 ) Other ​ ​ ( 9 ) ​ ​ 897 ​ ​ 3,377 Total deferred tax (expense) / benefit ​ $ ( 2,284 ) ​ $ ( 1,811 ) ​ $ 1,494 Total income tax (expense) / benefit ​ $ ( 2,429 ) ​ $ ( 1,921 ) ​ $ 1,470 ​ 153 ​ Table of Contents b. Tax benefit recognized in other comprehensive income ​ The reconciliation of the amount of income tax (loss) / benefit recognized in Other comprehensive income / (loss) for the years ended December 31, 2024 and December 31, 2023 is as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, 2024 ​ Year ended December 31, 2023 ​ Before tax Tax Net of tax ​ Before tax Tax Net of tax ​ (in thousands) ​ (in thousands) Unrecognized (loss) / gain related to defined benefit pension plan liability $ 384 ​ $ ( 57 ) ​ $ 327 ​ $ ( 2,553 ) ​ $ 417 ​ $ ( 2,136 ) Total $ 384 ​ $ ( 57 ) ​ $ 327 ​ $ ( 2,553 ) ​ $ 417 ​ $ ( 2,136 ) ​ No income tax benefit or expense has been recognized in Other Comprehensive Loss for the year ended December 31, 2022. ​ c. Tax rate reconciliation ​ The reconciliation of the amount of income tax (expense) / benefit that would result from applying the Dutch statutory income tax rate to the Company’s reported amount of loss before income tax (expense) / benefit for the years ended December 31, 2024, 2023 and 2022, is as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ ​ 2024 ​ 2023 ​ 2022 ​ ​ (in thousands) Loss before income tax (expense) / benefit for the period ​ $ ( 237,127 ) ​ $ ( 306,557 ) ​ $ ( 128,259 ) Expected income tax benefit at the 25.8 % tax rate enacted in the Netherlands ​ 61,179 ​ 79,092 ​ 33,091 Difference in tax rates between the Netherlands and other foreign countries ​ ( 149 ) ​ ( 124 ) ​ 99 Other net change in valuation allowance ​ ( 57,550 ) ​ ( 67,004 ) ​ ( 20,591 ) Non-deductible expenses ​ ( 5,909 ) ​ ( 13,885 ) ​ ( 11,129 ) Income tax (expense) / benefit ​ $ ( 2,429 ) ​ $ ( 1,921 ) ​ $ 1,470 ​ Non-deductible expenses predominantly relate to share-based compensation expenses. These expenses affected the effective tax rate by an amount of $ 5.6 million in 2024 (2023: $ 9.0 million; 2022: $ 8.5 million). The fair value gain on contingent consideration affected the effective tax rate by an amount of $ 0.5 million in 2024 ($ 4.1 million and $ 1.9 million in 2023 and 2022, respectively). ​ 154 ​ Table of Contents d. Significant components of deferred taxes ​ The tax effects of temporary differences and carryforwards that give rise to significant portions of deferred tax assets and deferred tax liabilities as of December 31, 2024 and 2023 are as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ ​ 2024 ​ 2023 ​ ​ (in thousands) Deferred tax assets: ​ ​ Net operating loss carryforwards ​ $ 178,421 ​ $ 145,826 Liability from Royalty Financing agreement ​ ​ 19,476 ​ ​ 6,155 Intangibles ​ ​ 4,702 ​ ​ 6,417 Operating lease liabilities ​ ​ 3,846 ​ ​ 9,790 Accrued expenses and other current liabilities ​ ​ 3,069 ​ ​ 1,435 Interest carryforwards ​ ​ 2,956 ​ ​ 3,711 Property, plant and equipment ​ 365 ​ — Defined benefit pension plan liability ​ ​ 260 ​ ​ 406 Inventory ​ ​ — ​ ​ 497 Total deferred tax assets ​ $ 213,095 ​ $ 174,237 Less valuation allowance ​ ( 191,864 ) ​ ( 145,191 ) Deferred tax assets, net of valuation allowance ​ $ 21,231 ​ $ 29,046 Acquired IPR&D intangible asset ​ ​ ( 14,341 ) ​ ​ ( 15,242 ) Operating lease right-of-use assets ​ ​ ( 3,864 ) ​ ​ ( 8,159 ) Property, plant and equipment ​ ​ ( 165 ) ​ ​ ( 719 ) Other current assets and receivables ​ ​ ( 48 ) ​ ​ ( 193 ) Deferred tax liability ​ $ ( 18,418 ) ​ $ ( 24,313 ) Net deferred tax asset ​ $ 2,813 ​ $ 4,733 ​ Changes in the valuation allowance were as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Years ended December 31, ​ 2024 2023 2022 ​ ​ (in thousands) January 1, ​ $ 145,191 ​ $ 74,547 ​ $ 60,289 Changes recorded in the statement of operations ​ ​ 57,550 ​ ​ 67,004 ​ ​ 20,593 Changes recorded in equity ​ ​ — ​ ​ — ​ ​ ( 972 ) Other changes including currency translation adjustments ​ ( 10,877 ) ​ 3,640 ​ ​ ( 5,363 ) December 31, ​ $ 191,864 ​ $ 145,191 ​ $ 74,547 ​ The valuation allowance of $ 191.9 million as of December 31, 2024 is primarily related to EUR 178.7 million ($ 185.6 million) deferred tax assets in the Netherlands resulting from net operating loss carryforwards of EUR 153.1 million ($ 159.1 million), liability from Royalty Financing Agreement of EUR 18.8 million ( $ 19.5 million), intangible assets of EUR 3.6 million ($ 3.8 million), interest carryforwards of EUR 2.8 million ($ 3.0 million) and property, plant and equipment of EUR 0.4 million ($ 0.4 million). ​ Netherlands ​ As of December 31, 2024, the total amount of net operating losses carried forward under the Dutch tax regime was EUR 593.6 million ($ 616.5 million) (December 31, 2023: EUR 446.4 million ($ 492.7 million)). The Company has historically recorded a full valuation allowance. The Company evaluates all positive and negative evidence in assessing the need for a full valuation allowance. Management considers reversing taxable temporary differences, projected future taxable income and tax-planning strategies in making this assessment. The Company concluded that as of December 31, 2024, and December 31, 2023 it is more likely than not that the remaining deferred tax assets will not be realized. The Company’s Dutch net operating tax losses carried forward relate to 2019, 2022, 2023 and 2024. ​ 155 ​ Table of Contents As of December 31, 2024, the tax treatment of the Royalty Agreement has not been agreed with the Dutch tax authorities. A different tax treatment could result in a different categorization of temporary differences and an offsetting deferred tax asset. ​ A portion of the valuation allowance for deferred tax assets recorded as of December 31, 2024 continues to relate to follow-on offering costs incurred in 2019. Any subsequently recognized tax benefits will be credited directly to contributed capital. As of December 31, 2024, that amount was EUR 3.0 million ($ 3.2 million) and EUR 3.0 million ($ 3.4 million) as of December 31, 2023. ​ The Dutch corporate tax rate is 25.8 % from 2022 onwards. ​ Net operating loss carryforwards subject to a limit of offsetting taxable profit in excess of EUR 1.0 million to 50% of the taxable profit can be carried forward indefinitely. ​ The fiscal periods from 2022 onwards are still open for inspection by the Dutch tax authorities. ​ United States of America ​ The federal corporate tax rate in the U.S. is 21.0 %. In addition, the Company is subject to state income taxes resulting in a combined tax rate of 27.3 % for its U.S. operation. As of December 31, 2024, an estimated $ 22.9 million of net operating losses remain to be carried forward. These net operating losses carried forward will expire in 2036 and 2037 except for $ 0.7 million which can be carried forward indefinitely with a deduction limited to 80% of taxable income in a given year. ​ The Company’s U.S. operations have been generating taxable income since 2018 with the exception of 2022. The Company expects to continue to generate taxable income in the U.S. during the foreseeable future. ​ Under the provision of the Internal Revenue Code, the U.S. net operating losses carried forward may become subject to an annual limitation in the event of certain cumulative exchange in the ownership interest of significant shareholders over a three-year period in excess of 50 percent, as defined under Section 382 and 383 of the Internal Revenue Code. This could limit the amount of tax attributes that can be utilized annually to offset future taxable income or tax liabilities. The amount of the annual limitation is determined based on the value of the Company immediately prior to the ownership change. Subsequent ownership changes may further affect the limitation. ​ The fiscal periods from 2021 are still open for inspection by the Internal Revenue Service (“IRS”). To the extent the Company has tax attribute carryforwards, the tax years in which the attribute was generated may still be adjusted upon examination by the IRS or Massachusetts Department of Revenue to the extent utilized in a future period. The Company is currently not under examination by the IRS for any tax years. ​ France ​ The French corporate tax rate for fiscal year 2024 was 25.0 %. In addition, the Company is subject to a surcharge of 3.3 % of the 25.0 % standard corporate tax rate resulting in a combined rate of 25.8 %. ​ The Company’s French operations have incurred losses since incorporation and are expected to continue incurring tax losses for the foreseeable future. The French operations as of December 31, 2024 have an estimated EUR 48.9 million ($ 50.8 million) (December 31, 2023: EUR 35.9 million ($ 39.6 million)) of net operating losses that are available for carry forward indefinitely. The Company recorded a partial valuation allowance during the years ended December 31, 2024 and 2023. No such valuation allowance was recorded in the years ended December 31, 2022 or 2021. The Company evaluates all positive and negative evidence including future income from reversing taxable temporary differences (particularly from reversing the deferred tax liability related to the acquired IPR&D intangible asset), projected future taxable income subject to the loss limitation rules applicable in France and tax-planning strategies in making this assessment. ​ ​ 156 ​ Table of Contents 22. Basic and diluted earnings per ordinary share ​ Basic net loss per ordinary share is computed by dividing net loss for the period by the weighted average number of ordinary shares outstanding during the period. Diluted earnings per ordinary 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 years presented, all potentially dilutive ordinary shares for these years would have an antidilutive effect, if converted, and thus have been excluded from the computation of loss per share. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ ​ 2024 ​ 2023 ​ 2022 ​ ​ (in thousands, except share amounts) Numerator: ​ ​ ​ ​ ​ ​ ​ ​ ​ Net loss attributable to ordinary shares ​ $ ( 239,556 ) ​ $ ( 308,478 ) ​ $ ( 126,789 ) Denominator: ​ ​ ​ ​ ​ ​ ​ ​ ​ Weighted-average number of ordinary shares outstanding - basic and diluted ​ ​ 48,649,129 ​ ​ 47,670,986 ​ ​ 46,735,045 ​ The following table presents ordinary share equivalents that were excluded from the calculation of diluted net loss per ordinary share for the years presented as the effect of their inclusion would have been anti-dilutive: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Year ended December 31, ​ ​ 2024 ​ 2023 ​ 2022 Anti-dilutive ordinary share equivalents ​ ​ ​ ​ ​ ​ ​ ​ ​ Stock options under 2014 Plans and previous plan ​ ​ 4,967,160 ​ ​ 4,974,030 ​ ​ 4,237,917 Non-vested RSUs and PSUs ​ ​ 1,810,018 ​ ​ 2,486,919 ​ ​ 2,219,464 ESPP ​ ​ — ​ ​ 3,640 ​ ​ 1,048 Total anti-dilutive ordinary share equivalents ​ ​ 6,777,178 ​ ​ 7,464,589 ​ ​ 6,458,429 ​ The anti-dilutive ordinary shares are presented without giving effect to the application of the treasury method or exercise prices that exceeded the price of the Company’s ordinary shares as of December 31, 2024, December 31, 2023 and December 31, 2022. ​ ​ ​ 23. Commitments and contingencies ​ In the course of its business, the Company enters as a licensee into contracts with other parties regarding the development and marketing of its pipeline products. Among other payment obligations, the Company is obligated to pay royalties to the licensors based on future sales levels and milestone payments whenever specified development, regulatory and commercial milestones are met. As both future sales levels and the timing and achievement of milestones are uncertain, the financial effect of these agreements cannot be estimated reliably. The Company also has obligations to make future payments that become due and payable upon the collection of milestone payments from CSL Behring. The achievement and timing of these milestones is not fixed and determinable. Relevant commitments and contingencies are further discussed in other sections of this form 10-K, such as, Note 3 “ Divestiture of manufacturing facility ” and Note 18 “ Collaboration arrangements and concentration of credit risk ”, amongst others. ​ 24. Related party transaction ​ None. ​ 25. Subsequent events ​ In January 2025, the Company received net proceeds of $ 70.1 million, after deducting underwriting discounts and commissions and other offering expenses payable by the Company, through a follow-on public offering of 4.4 million ordinary shares at a public offering price of $ 17.00 per ordinary share. ​ In February 2025, the Company received an additional $ 10.6 million in net proceeds upon the underwriters’ exercise of their option to purchase an additional 0.7 million ordinary shares at the public offering price. ​ 157 ​ Table of Contents EXHIBIT INDEX ​ Exhibit No. Description 2.1† ​ Sale and Purchase Agreement, executed June 21, 2021, by and between uniQure N.V. and Corlieve Therapeutics SAS (incorporated by reference to Exhibit 2.1 of the Company’s Quarterly Report on Form 10-Q (file no. 001-36294) for the period ended June 30, 2021 filed with the SEC on July 26, 2021). 3.1 ​ Amended Articles of Association of the Company (incorporated by reference to Exhibit 3.1 of the Company’s Quarterly Report on Form 10-Q (file no. 001-36294) for the period ended June 30, 2021 filed with the SEC on July 26, 2021). 4.1 * Description of the Registrant’s Securities Registered Pursuant to Section 12 of the Securities Exchange Act of 1934. 10.1 t ​ 2014 Share Incentive Plan (incorporated by reference to Exhibit 4.3 of the Company’s Registration Statement on Form S-8 (file no. 333-225629) filed with the SEC on June 14, 2018). 10.2t ​ Amended and Restated 2014 Share Incentive Plan (incorporated by reference to Exhibit 10.1 of the Company’s Current Report on Form 8-K (file no. 001-36294) filed with the SEC on November 17, 2023). 10.3t ​ Amended and Restated 2014 Share Incentive Plan (incorporated by reference to Exhibit 10.1 of the Company’s Current Report on Form 8-K (file no. 001-36294) filed with the SEC on June 20, 2024). 10.4t ​ Form of Share Option Agreement, effective December 8, 2021, under the 2014 Share Incentive Plan (incorporated by reference to Exhibit 10.65 of the Company’s Annual Report on Form 10-K for the year ended December 31, 2021 (file no. 001-36294) filed with the SEC on February 25, 2022). 10.5t ​ Form of Restricted Stock Unit Award, effective December 8, 2021, under the 2014 Share Incentive Plan (incorporated by reference to Exhibit 10.66 of the Company’s Annual Report on Form 10-K for the year ended December 31, 2021 (file no. 001-36294) filed with the SEC on February 25, 2022). 10.6†t ​ Form of Performance Stock Unit Award, effective December 8, 2021 under the 2014 Share Incentive Plan (incorporated by reference to Exhibit 10.67 of the Company’s Annual Report on Form 10-K for the year ended December 31, 2021 (file no. 001-36294) filed with the SEC on February 25, 2022). 10.7t ​ Employee Share Purchase Plan (incorporated by reference to Exhibit 4.2 of the Company’s Registration Statement on Form S-8 (file no. 333-225629) filed with the SEC on June 14, 2018). 10.8t ​ Employment Agreement between uniQure, Inc. and Matthew Kapusta, dated December 9, 2014 (incorporated by reference to Exhibit 10.6 of the Company's Annual Report on Form 10-K (file no. 001-36294) for the year ended December 31, 2016 filed with the SEC on March 15, 2017). 10.9 t ​ Amendment to the Employment Agreement between uniQure, Inc. and Matthew Kapusta, dated March 14, 2017 (incorporated by reference to Exhibit 10.7 of the Company’s Annual Report on Form 10-K (file no. 001-36294) for the year ended December 31, 2016 filed with the SEC on March 15, 2017). 10.10 t ​ Amendment to the Employment Agreement between uniQure, Inc. and Matthew Kapusta, dated October 26, 2017 (incorporated by reference to Exhibit 10.1 of the Company’s Quarterly Report on Form 10-Q (file no. 001-36294) for the period ended September 30, 2017 filed with the SEC on November 1, 2017). 10.11t ​ Amended and Restated Employment Agreement, effective June 15, 2021, by and between uniQure biopharma B.V. and Christian Klemt (incorporated by reference to Exhibit 10.3 of the Company’s Quarterly Report on Form 10-Q (file no. 001-36294) for the period ended June 30, 2021 filed with the SEC on July 26, 2021). 10.12t ​ Employment Agreement, effective May 17, 2021, by and between uniQure biopharma B.V. and Pierre Caloz (incorporated by reference to Exhibit 10.1 of the Company’s Quarterly Report on Form 10-Q (file no. 001-36294) for the period ended June 30, 2021 filed with the SEC on July 26, 2021). 158 ​ Table of Contents 10.13t ​ Equity Side Letter, effective May 17, 2021, by and between uniQure N.V. and Pierre Caloz (incorporated by reference to Exhibit 10.2 of the Company’s Quarterly Report on Form 10-Q (file no. 001-36294) for the period ended June 30, 2021 filed with the SEC on July 26, 2021). 10.14t ​ Termination Agreement, dated July 22, 2024, by and between uniQure biopharma B.V. and Pierre Caloz (incorporated by reference to Exhibit 10.5 of the Company’s Quarterly Report on Form 10-Q for the period ended June 30, 2024 (file no. 001-36294) filed with the SEC on August 1, 2024). 10.15t ​ Employment Agreement dated June 13, 2023 between uniQure, Inc. and Jeannette Potts (incorporated by reference to Exhibit 10.77 of the Company’s Annual Report on Form 10-K for the year ended December 31, 2023 (file no. 001-36294) filed with the SEC on February 28, 2024). 10.16t * Employment Agreement dated June 26, 2023 between Corlieve Therapeutics AG and Walid Abi-Saab. 10.17 ​ Lease relating to 113 Hartwell Avenue, Lexington, Massachusetts, dated as of July 24, 2013, by and between uniQure Inc. and King 113 Hartwell LLC (incorporated by reference to Exhibit 10.28 of the Company’s Registration Statement on Form F-1 (file no. 333-193158) filed with the SEC on January 2, 2014). 10.18 ​ First Amendment Lease relating to 113 Hartwell Avenue, Lexington, Massachusetts, dated as of July 24, 2013, by and between the Company and King113 Hartwell LLC (incorporated by reference to Exhibit 10.1 of the Company’s Current Report on Form 8-K (file no. 001-36294) filed with the SEC on November 15, 2018). 10.19 ​ Second Amendment Lease relating to 113 Hartwell Avenue, Lexington Massachusetts, dated as of June 17, 2019, by and between the Company and King 113 Hartwell LLC (incorporated by reference to Exhibit 10.42 of the Company’s Quarterly Report on Form 10-Q (file no. 001-36294) for the period ended June 30, 2019 filed with the SEC on July 29, 2019). 10.20 ​ Landlord Consent to Assignment and Assumption of Lease and Third Amendment to Lease, dated June 28, 2024, by and among Hartwell Innovation Campus, LLC, uniQure, Inc. and Genezen MA, Inc. (incorporated by reference to Exhibit 10.3 of the Company’s Quarterly Report on Form 10-Q (file no. 001-36294) for the period ending June 30, 2024 filed with the SEC on August 1, 2024). 10.21 ​ Assignment and Assumption of Lease, dated July 22, 2024, by and between uniQure, Inc. and Genezen MA, Inc. (incorporated by reference to Exhibit 10.4 of the Company’s Quarterly Report on Form 10-Q (file no. 001-36294) for the period ending June 30, 2024 filed with the SEC on August 1, 2024). 10.22 ​ Lease relating to Paasheuvelweg 25, dated as of March 7, 2016, by and between 52 IFH GmbH & Co. KG and uniQure biopharma B.V. (incorporated by reference to Exhibit 10.36 of the Company’s Annual Report on Form 10-K (file no. 001-36294) for the year ended December 31, 2016 filed with the SEC on March 15, 2017). 10.23 ​ Lease Agreement relating to 91 Hartwell Avenue, Lexington, Massachusetts, dated as of February 1, 2022, by and between uniQure Inc. and NRL 91 Hartwell LLC (incorporated by reference to Exhibit 10.70 of the Company’s Annual Report on Form 10-K for the year ended December 31, 2021 (file no. 001-36294) filed with the SEC on February 25, 2022). 10.24 ​ Lease Agreement relating to Peter Merian-Weg 4, 4052 Basel, Switzerland, dated as of November 1, 2023, by and between Corlieve Therapeutics AG and Stiftung Sympany. 10.25 ​ Business Acquisition Agreement, dated as of February 16, 2012, by and among Amsterdam Molecular Therapeutics (AMT) Holding N.V., the Company and the other Parties listed therein (incorporated by reference to Exhibit 10.29 of the Company’s Registration Statement on Form F-1 (file no. 333-193158) filed with the SEC on January 2, 2014). 10.26 ​ Deed of Assignment of Certain Assets and Liabilities of Amsterdam Molecular Therapeutics (AMT) Holding N.V., dated as of April 5, 2012, by and among Amsterdam Molecular Therapeutics (AMT) Holding B.V., Amsterdam Molecular Therapeutics (AMT) Holding IP B.V. and Amsterdam Molecular Therapeutics (AMT) Holding N.V. (incorporated by reference to Exhibit 10.30 of the Company's Registration Statement on Form F-1 (file no. 333-193158) filed with the SEC on January 2, 2014). 159 ​ Table of Contents 10.27 ​ Agreement for Transfer of Certain Assets and Liabilities of Amsterdam Molecular Therapeutics (AMT) Holding N.V., dated as of February 16, 2012, by and among Amsterdam Molecular Therapeutics (AMT) Holding B.V., Amsterdam Molecular Therapeutics (AMT) Holding IP B.V. and Amsterdam Molecular Therapeutics (AMT) Holding N.V. (incorporated by reference to Exhibit 10.31 of the Company’s Registration Statement on Form F-1 (file no. 333-193158) filed with the SEC on January 2, 2014). 10.28† ​ Assignment and License Agreement dated April 17, 2017 between Professor Paolo Simioni and uniQure biopharma B.V. (incorporated by reference to Exhibit 10.1 of the Company’s Current Report on Form 8-K (file no. 001-36294) filed with the SEC on October 19, 2017). 10.29† ​ Commercialization and License Agreement by and between uniQure biopharma B.V. and CSL Behring LLC dated June 24, 2020 (incorporated by reference to Exhibit 10.1 of the Company’s Quarterly Report on Form 10-Q (file no. 001-36294) for the period ended June 30, 2020 filed with the SEC on July 30, 2020). 10.30† ​ Third Amended and Restated Loan and Security Agreement as of December 15, 2021, by and among uniQure biopharma B.V., uniQure Inc., uniQure IP B.V., the Company and Hercules Capital Inc (incorporated by reference to Exhibit 10.68 of the Company’s Annual Report on Form 10-K for the year ended December 31, 2021 (file no. 001-36294) filed with the SEC on February 25, 2022). 10.31† ​ Amendment No. 1 to Third Amended and Restated Loan and Security Agreement, dated of May 12, 2023, by and among uniQure biopharma, B.V., uniQure, Inc., uniQure IP B.V., the Company and Hercules Capital, Inc. (incorporated by reference to Exhibit 10.1 of the Company’s Quarterly Report on Form 10-Q for the period ended June 30, 2023 (file no. 001-36294) filed with the SEC on August 1, 2023). 10.32† ​ Consent and Amendment No. 2 to Third Amended and Restated Loan and Security Agreement, dated June 28, 2024, by and among uniQure biopharma B.V., uniQure, Inc., uniQure IP B.V., the Company and Hercules Capital, Inc. (incorporated by reference to Exhibit 10.2 of the Company’s Quarterly Report on Form 10-Q for the period ended June 30, 2024 (file no. 001-36294) filed with the SEC on August 1, 2024). 10.33† ​ Royalty Purchase Agreement, dated May 12, 2023, by and between uniQure biopharma B.V. and HemB SPV, L.P. (incorporated by reference to Exhibit 10.2 of the Company’s Quarterly Report on Form 10-Q for the period ended June 30, 2023 (file no. 001-36294) filed with the SEC on August 1, 2023). 10.34† ​ Asset Purchase Agreement, by and among uniQure, Inc., uniQure biopharma B.V., Genezen Holdings Inc. and Genezen MA, Inc., dated as of June 29, 2024 (incorporated by reference to Exhibit 10.1 of the Company’s Quarterly Report on Form 10-Q for the period ended June 30, 2024 (file no. 001-36294) filed with the SEC on August 1, 2024). 14.1* ​ Code of Ethics. 19.1* ​ Insider Trading Policy. 21.1* ​ Subsidiaries of the Company. 23.1* ​ Consent of Independent Registered Public Accounting Firm – KPMG Accountants N.V. 24.1* ​ Power of Attorney (incorporated by reference to the signature page of this Annual Report on Form 10-K). 31.1* ​ Rule 13a-14(a)/15d-14(a) Certification of Chief Executive Officer. 31.2* ​ Rule 13a-14(a)/15d-14(a) Certification of Chief Financial Officer. 32.1** ​ Certification of Principal Executive Officer and Principal Financial Officer pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002. 97.1 ​ Compensation Clawback Policy (incorporated by reference to Exhibit 97.1 of the Company’s Annual Report on Form 10-K for the year ended December 31, 2023 (file no. 001-36294) filed with the SEC on February 28, 2024). 160 ​ Table of Contents 101* ​ The following materials from the Company’s Annual Report on Form 10-K for the year ended December 31, 2024, formatted in Inline XBRL (eXtensible Business Reporting Language): (i) Consolidated Balance Sheets, (ii) Consolidated Statements of Operations and Comprehensive Income (Loss), (iii) Consolidated Statements of Shareholders’ (Deficit) / Equity, (iv) Consolidated Statements of Cash Flows and (v) Notes to Consolidated Financial Statements. 104* ​ The cover page from the Company’s Annual Report on Form 10-K for the year ended December 31, 2024 has been formatted in Inline XBRL. ​ ​ † Confidential treatment requested as to certain portions, which portions have been omitted and filed separately with the Securities and Exchange Commission ​ * Filed herewith. ​ ** Furnished herewith. ​ t Indicates a management contract or compensatory plan or arrangement. ​ ​ 161 ​ Table of Contents SIGNATURES ​ Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized. ​ ​ ​ ​ ​ UNIQURE N.V. ​ ​ ​ Date: February 27, 2025 By: /s/ MATTHEW KAPUSTA ​ ​ Matthew Kapusta ​ ​ Chief Executive Officer (Principal Executive Officer) ​ ​ ​ Date: February 27, 2025 By: /s/ CHRISTIAN KLEMT ​ ​ Christian Klemt ​ ​ Chief Financial Officer (Principal Financial Officer and Principal Accounting Officer) ​ POWER OF ATTORNEY ​ KNOW ALL PERSONS BY THESE PRESENTS, that each person whose signature appears below constitutes and appoints Matthew Kapusta and Christian Klemt, jointly and severally, his or her attorney-in-fact, with the power of substitution, for him or her in any and all capacities, to sign any amendments to this Annual Report on Form 10-K and to file the same, with exhibits thereto and other documents in connection therewith, with the Securities and Exchange Commission, hereby ratifying and confirming all that each of said attorneys-in-fact, or his or her substitute or substitutes, may do or cause to be done by virtue hereof. ​ Pursuant to the requirements of the Securities Exchange Act of 1934, this Annual Report on Form 10-K has been signed below by the following persons on behalf of the Registrant and in the capacities and on the dates indicated. ​ Signatures Title Date ​ ​ ​ ​ ​ /s/ MATTHEW KAPUSTA ​ Chief Executive Officer and Director (Principal Executive Officer) ​ February 27, 2025 Matthew Kapusta ​ ​ ​ ​ ​ ​ ​ /s/ CHRISTIAN KLEMT ​ Chief Financial Officer (Principal Financial Officer and Principal Accounting Officer) ​ February 27, 2025 Christian Klemt ​ ​ ​ ​ ​ ​ ​ /s/ MADHAVAN BALACHANDRAN ​ Director ​ February 27, 2025 Madhavan Balachandran ​ ​ ​ ​ ​ ​ ​ /s/ ROBERT GUT ​ Director ​ February 27, 2025 Robert Gut ​ ​ ​ ​ ​ ​ ​ /s/ RACHELLE JACQUES ​ Director ​ February 27, 2025 Rachelle Jacques ​ ​ ​ ​ ​ ​ ​ /s/ JACK KAYE ​ Director ​ February 27, 2025 Jack Kaye ​ ​ ​ ​ ​ ​ ​ /s/ DAVID MEEK ​ Director ​ February 27, 2025 David Meek ​ ​ ​ ​ ​ ​ ​ /s/ LEONARD POST ​ Director ​ February 27, 2025 Leonard Post ​ ​ ​ ​ ​ ​ ​ /s/ JEREMY P. SPRINGHORN ​ Director ​ February 27, 2025 Jeremy P. Springhorn ​ ​ ​ ​ ​ ​ 162 ​