uniQure N.V. 10-Q

Item 1. Financial Statements uniQure N.V. UNAUDITED CONSOLIDATED BALANCE SHEETS ​ ​ ​ ​ ​ ​ ​ ​ ​ March 31, ​ December 31, ​ 2025 2024 ​ ​ (in thousands, except share and per share amounts) Current assets ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 217,229 ​ $ 158,930 Current investment securities ​ ​ 191,782 ​ ​ 208,591 Accounts receivable ​ ​ 2,522 ​ ​ 5,881 Prepaid expenses ​ ​ 13,420 ​ ​ 9,281 Other current assets and receivables ​ ​ 10,468 ​ ​ 7,606 Total current assets ​ ​ 435,421 ​ ​ 390,289 Non-current assets ​ ​ ​ ​ ​ ​ Property, plant and equipment, net of accumulated depreciation of $ 36.1 million as of March 31, 2025 and $ 31.7 million as of December 31, 2024 ​ ​ 18,081 ​ ​ 20,424 Other investments ​ ​ 28,273 ​ ​ 27,464 Operating lease right-of-use assets ​ ​ 13,466 ​ ​ 13,647 Intangible assets, net, including in-process research and development assets of $ 58.0 million as of March 31, 2025 and $ 55.6 million as of December 31, 2024 ​ ​ 71,992 ​ ​ 71,043 Goodwill ​ ​ 23,351 ​ ​ 22,414 Deferred tax assets, net ​ ​ 9,390 ​ ​ 9,856 Other non-current assets ​ ​ 5,429 ​ ​ 1,399 Total non-current assets ​ ​ 169,982 ​ ​ 166,247 Total assets ​ $ 605,403 ​ $ 556,536 Current liabilities ​ ​ ​ ​ ​ ​ Accounts payable ​ $ 5,268 ​ $ 7,227 Accrued expenses and other current liabilities ​ ​ 27,344 ​ ​ 29,225 Current portion of operating lease liabilities ​ ​ 3,698 ​ ​ 3,601 Total current liabilities ​ ​ 36,310 ​ ​ 40,053 Non-current liabilities ​ ​ ​ ​ ​ ​ Long-term debt ​ ​ 51,592 ​ ​ 51,324 Liability from royalty financing agreement ​ ​ 446,660 ​ ​ 434,930 Operating lease liabilities, net of current portion ​ ​ 10,906 ​ ​ 11,136 Contingent consideration ​ ​ 12,560 ​ ​ 10,860 Deferred tax liability, net ​ ​ 7,338 ​ ​ 7,043 Other non-current liabilities, net of current portion ​ ​ 6,351 ​ ​ 7,942 Total non-current liabilities ​ ​ 535,407 ​ ​ 523,235 Total liabilities ​ ​ 571,717 ​ ​ 563,288 Commitments and contingencies ​ ​ ​ ​ ​ ​ Shareholders' equity / (deficit) ​ ​ ​ ​ ​ ​ Ordinary shares, € 0.05 par value: 80,000,000 shares authorized as of March 31, 2025 and December 31, 2024 and 54,698,479 and 48,988,087 ordinary shares issued and outstanding as of March 31, 2025 and December 31, 2024, respectively ​ ​ 3,240 ​ ​ 2,945 Additional paid-in-capital ​ ​ 1,257,853 ​ ​ 1,173,068 Accumulated other comprehensive loss ​ ​ ( 53,805 ) ​ ​ ( 52,800 ) Accumulated deficit ​ ​ ( 1,173,602 ) ​ ​ ( 1,129,965 ) Total shareholders' equity / (deficit) ​ ​ 33,686 ​ ​ ( 6,752 ) Total liabilities and shareholders' equity / (deficit) ​ $ 605,403 ​ $ 556,536 ​ The accompanying notes are an integral part of these unaudited consolidated financial statements. ​ 2 Table of Contents uniQure N.V. ​ UNAUDITED CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended March 31, ​ 2025 2024 ​ ​ (in thousands, except share and per share amounts) License revenues ​ $ 1,567 ​ $ 1,202 Contract manufacturing revenues ​ ​ — ​ ​ 3,990 Collaboration revenues ​ ​ — ​ ​ 3,293 Total revenues ​ ​ 1,567 ​ ​ 8,485 Operating expenses: ​ ​ ​ ​ ​ ​ Cost of license revenues ​ ​ ( 197 ) ​ ​ ( 150 ) Cost of contract manufacturing revenues ​ ​ — ​ ​ ( 9,076 ) Research and development expenses ​ ​ ( 36,140 ) ​ ​ ( 40,692 ) Selling, general and administrative expenses ​ ​ ( 10,908 ) ​ ​ ( 13,937 ) Total operating expenses ​ ​ ( 47,245 ) ​ ​ ( 63,855 ) Other income ​ ​ 8,306 ​ ​ 1,376 Other expense ​ ​ ( 1,959 ) ​ ​ ( 234 ) Loss from operations ​ ​ ( 39,331 ) ​ ​ ( 54,228 ) Interest income ​ ​ 4,127 ​ ​ 6,508 Interest expense ​ ​ ( 15,109 ) ​ ​ ( 16,097 ) Foreign currency gains / (losses), net ​ ​ 7,172 ​ ​ ( 1,145 ) Loss before income tax expense ​ $ ( 43,141 ) ​ $ ( 64,962 ) Income tax expense ​ ​ ( 496 ) ​ ​ ( 656 ) Net loss ​ $ ( 43,637 ) ​ $ ( 65,618 ) Other comprehensive (loss): ​ ​ ​ ​ ​ ​ Foreign currency translation losses, net ​ ​ ( 1,005 ) ​ ​ ( 2,524 ) Defined benefit pension gain, net of taxes ​ ​ — ​ ​ 35 Total comprehensive loss ​ $ ( 44,642 ) ​ $ ( 68,107 ) Earnings per ordinary share - basic and diluted ​ ​ ​ ​ ​ ​ Basic and diluted net loss per ordinary share ​ $ ( 0.82 ) ​ $ ( 1.36 ) Weighted average shares - basic and diluted ​ ​ 53,110,580 ​ ​ 48,384,510 ​ The accompanying notes are an integral part of these unaudited consolidated financial statements. ​ 3 Table of Contents uniQure N.V. ​ UNAUDITED CONSOLIDATED STATEMENTS OF SHAREHOLDERS’ EQUITY FOR THE THREE MONTHS ENDED MARCH 31, 2025 AND 2024 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 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, 2023 ​ 47,833,830 ​ $ 2,883 ​ $ 1,148,749 ​ $ ( 53,553 ) ​ $ ( 890,409 ) ​ $ 207,670 Loss for the period ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 65,618 ) ​ ​ ( 65,618 ) Other comprehensive loss, net ​ — ​ ​ — ​ ​ — ​ ​ ( 2,489 ) ​ ​ — ​ ​ ( 2,489 ) Restricted share units distributed during the period ​ 658,527 ​ ​ 36 ​ ​ ( 36 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense ​ — ​ ​ — ​ ​ 7,191 ​ ​ — ​ ​ — ​ ​ 7,191 Balance at March 31, 2024 ​ 48,492,357 ​ $ 2,919 ​ $ 1,155,904 ​ $ ( 56,042 ) ​ $ ( 956,027 ) ​ $ 146,754 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Balance at December 31, 2024 ​ 48,988,087 ​ $ 2,945 ​ $ 1,173,068 ​ $ ( 52,800 ) ​ $ ( 1,129,965 ) ​ $ ( 6,752 ) Loss for the period ​ — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 43,637 ) ​ ​ ( 43,637 ) Other comprehensive loss, net ​ — ​ ​ — ​ ​ — ​ ​ ( 1,005 ) ​ ​ — ​ ​ ( 1,005 ) Follow-on public offering ​ 5,073,529 ​ ​ 261 ​ ​ 80,250 ​ ​ — ​ ​ — ​ ​ 80,511 Exercises of share options ​ 15,928 ​ ​ 1 ​ ​ 158 ​ ​ — ​ ​ — ​ ​ 159 Restricted and performance share units distributed during the period ​ 620,935 ​ ​ 33 ​ ​ ( 33 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense ​ — ​ ​ — ​ ​ 4,410 ​ ​ — ​ ​ — ​ ​ 4,410 Balance at March 31, 2025 ​ 54,698,479 ​ $ 3,240 ​ $ 1,257,853 ​ $ ( 53,805 ) ​ $ ( 1,173,602 ) ​ $ 33,686 ​ The accompanying notes are an integral part of these unaudited consolidated financial statements. ​ 4 Table of Contents uniQure N.V. ​ UNAUDITED CONSOLIDATED STATEMENTS OF CASH FLOWS ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended March 31, ​ 2025 2024 ​ ​ (in thousands) Cash flows from operating activities ​ ​ ​ ​ ​ ​ Net loss ​ $ ( 43,637 ) ​ $ ( 65,618 ) Adjustments to reconcile net loss to net cash used in operating activities: ​ ​ ​ ​ ​ ​ Depreciation and amortization ​ ​ 4,527 ​ ​ 2,629 Amortization of discount on investment securities ​ ​ ( 2,117 ) ​ ​ ( 3,695 ) Share-based compensation expense ​ ​ 4,410 ​ ​ 7,191 Royalty financing agreement interest expense, net of interest paid ​ ​ 8,358 ​ ​ 10,925 Deferred tax expense ​ ​ 496 ​ ​ 656 Changes in fair value of contingent consideration ​ ​ 1,216 ​ ​ 165 Unrealized foreign exchange (gains) / losses, net ​ ​ ( 7,105 ) ​ ​ 1,389 Other items, net ​ ​ ( 3,971 ) ​ ​ 2,778 Changes in operating assets and liabilities: ​ ​ ​ ​ ​ ​ Accounts receivable, prepaid expenses, and other current assets and receivables ​ ​ ( 2,979 ) ​ ​ ( 10,417 ) Inventories ​ ​ — ​ ​ 2,236 Accounts payable ​ ​ ( 2,093 ) ​ ​ ( 701 ) Accrued expenses, other liabilities, and operating leases ​ ​ ( 1,205 ) ​ ​ ( 8,113 ) Net cash used in operating activities ​ ​ ( 44,100 ) ​ ​ ( 60,575 ) Cash flows from investing activities ​ ​ ​ ​ ​ ​ Proceeds on maturity of debt securities ​ ​ 85,000 ​ ​ 150,107 Investment in debt securities ​ ​ ( 64,775 ) ​ ​ ( 83,778 ) Purchases of property, plant, and equipment ​ ​ ( 126 ) ​ ​ ( 2,344 ) Net cash generated from investing activities ​ ​ 20,099 ​ ​ 63,985 Cash flows from financing activities ​ ​ ​ ​ ​ ​ Proceeds from public offering of shares in connection with follow on, net of issuance costs ​ ​ 80,511 ​ ​ — Proceeds from issuance of ordinary shares related to employee stock option and purchase plans ​ ​ 159 ​ ​ — Net cash generated from financing activities ​ ​ 80,670 ​ ​ — Currency effect on cash, cash equivalents and restricted cash ​ ​ 1,660 ​ ​ ( 1,725 ) Net increase in cash, cash equivalents and restricted cash ​ ​ 58,329 ​ ​ 1,685 Cash, cash equivalents and restricted cash at beginning of period ​ ​ 160,329 ​ ​ 244,544 Cash, cash equivalents and restricted cash at the end of period ​ $ 218,658 ​ $ 246,229 Cash and cash equivalents ​ $ 217,229 ​ $ 243,062 Restricted cash related to leasehold and other deposits ​ ​ 1,429 ​ ​ 3,167 Total cash, cash equivalents and restricted cash ​ $ 218,658 ​ $ 246,229 Supplemental cash flow disclosures: ​ ​ ​ ​ ​ ​ Cash paid for interest ​ $ ( 6,491 ) ​ $ ( 4,761 ) Non-cash decrease in accounts payables and accrued expenses and other current liabilities related to purchases of property, plant, and equipment ​ $ ( 92 ) ​ $ ( 577 ) ​ The accompanying notes are an integral part of these unaudited consolidated financial statements. ​ ​ 5 Table of Contents uniQure N.V. ​ NOTES TO CONSOLIDATED FINANCIAL STATEMENTS (Unaudited) ​ 1 General business information ​ uniQure N.V. (the “Company”) was incorporated on January 9, 2012, as a private company with limited liability ( besloten vennootschap met beperkte aansprakelijkheid ) under the laws of the Netherlands. The Company is a leader in the field of gene therapy and seeks to deliver to patients suffering from rare and other devastating diseases single treatments with potentially curative results. The Company’s business was founded in 1998 and was initially operated through its predecessor company, Amsterdam Molecular Therapeutics Holding N.V. (“AMT”). In 2012, AMT undertook a corporate reorganization, pursuant to which uniQure B.V. acquired the entire business and assets of AMT and completed a share-for-share exchange with the shareholders of AMT. Effective February 10, 2014, in connection with its initial public offering, the Company converted into a public company with limited liability ( naamloze vennootschap ) and changed its legal name from uniQure B.V. to uniQure N.V. ​ The Company is registered in the trade register of the Dutch Chamber of Commerce ( Kamer van Koophandel ) in Amsterdam, the Netherlands under number 54385229. The Company’s headquarters are in Amsterdam, the Netherlands, and its registered office is located at Paasheuvelweg 25a, Amsterdam 1105 BP, the Netherlands and its telephone number is +31 20 240 6000. ​ The Company’s ordinary shares are listed on the Nasdaq Global Select Market and trade under the symbol “QURE”. ​ 2 Summary of significant accounting policies ​ 2.1 Basis of preparation ​ The Company prepared these unaudited consolidated financial statements in compliance with generally accepted accounting principles in the United States (“U.S. GAAP”) and applicable rules and regulations of the United States Securities and Exchange Commission (the “SEC”) regarding interim financial reporting. Any reference in these notes to applicable guidance is meant to refer to authoritative U.S. GAAP as found in the Accounting Standards Codification (“ASC”) and Accounting Standards Updates of the Financial Accounting Standards Board. ​ The unaudited consolidated financial statements are presented in United States (“U.S.”) dollars, except where otherwise indicated. Transactions denominated in currencies other than U.S. dollars are presented in the transaction currency with the U.S. dollar amount included in parenthesis, converted at the foreign exchange rate as of the transaction date. ​ 2.2 Unaudited interim financial information ​ The interim financial statements and related disclosures are unaudited, have been prepared on the same basis as the annual financial statements and, in the opinion of management, reflect all adjustments, which include only normal recurring adjustments, necessary for a fair statement of the financial position, results of operations and changes in financial position for the period presented. ​ Certain information and footnote disclosures normally included in annual financial statements prepared in accordance with U.S. GAAP have been omitted. The results of operations for the three months ended March 31, 2025, are not necessarily indicative of the results to be expected for the full year ending December 31, 2025, or for any other future year or interim period. The accompanying financial statements should be read in conjunction with the audited financial statements and the related notes thereto included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2024 filed by the Company with the SEC on February 27, 2025 (the “Annual Report”) . ​ 6 Table of Contents 2.3 Use of estimates ​ The preparation of the financial statements in conformity with U.S. GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, disclosure of contingent assets and liabilities at the date of the financial statements and reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates. ​ 2.4 Accounting policies ​ The principal accounting policies applied in the preparation of these unaudited consolidated financial statements are described in the Company’s audited financial statements as of and for the year ended December 31, 2024, and the notes thereto, which are included in the Annual Report . There have been no material changes in the Company’s significant accounting policies during the three months ended March 31, 2025. ​ 2.5 Recent accounting pronouncements ​ There have been no new accounting pronouncements or changes to accounting pronouncements during the three months ended March 31, 2025, as compared to the recent accounting pronouncements described in Note 2.3.29 of the Annual Report , which could be expected to materially impact the Company’s unaudited consolidated financial statements. ​ 3 Other investments ​ Convertible promissory note ​ The Company has an investment in a convertible promissory note with a nominal amount of $ 12.5 million, bearing interest at 8.0 % per annum. The convertible promissory note was issued in July 2024 and matures in October, 2029. The convertible promissory note had a balance of $ 13.9 million as of March 31, 2025 (December 31, 2024: $ 13.7 million), and is presented within “Other investments” on the Company’s unaudited consolidated balance sheets. In the three month period ended March 31, 2025 and March 31, 2024, the Company recognized $ 0.2 million and nil of interest income, respectively. As of March 31, 2025, the Company has not recorded an allowance for credit losses related to the convertible promissory note. ​ Investments valued under measurement alternative ​ The Company has investments in non-publicly traded equity securities without readily determinable fair values. These investments are accounted for at cost, less impairment and adjusted to fair value if there are observable price changes in orderly transactions for identical or similar investments using the measurement alternative in accordance with ASC 321, Investments – Equity Securities . The carrying value of these investments as of March 31, 2025 and December 31, 2024 was $ 14.4 million, and are presented within “Other investments” on the Company’s unaudited consolidated balance sheets. The Company did not recognize any gains, losses, or impairments relating to investments carried under the measurement alternative in the three month period ended March 31, 2025 and March 31, 2024. ​ ​ ​ 7 Table of Contents 4 Investment securities The following tables summarize the Company’s investments in government debt securities as of March 31, 2025 and December 31, 2024: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ At March 31, 2025 ​ Amortized cost Gross unrealized holding gains Gross unrealized holding losses Estimated fair value ​ ​ (in thousands) Current investments: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Government debt securities (held-to-maturity) ​ $ 191,782 ​ $ 9 ​ $ — ​ $ 191,791 Total ​ $ 191,782 ​ $ 9 ​ $ — ​ $ 191,791 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ At December 31, 2024 ​ Amortized cost Gross unrealized holding gains Gross unrealized holding losses Estimated fair value ​ ​ (in thousands) Current investments: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Government debt securities (held-to-maturity) ​ $ 208,591 ​ $ 164 ​ $ — ​ $ 208,755 Total ​ $ 208,591 ​ $ 164 ​ $ — ​ $ 208,755 ​ The Company invests in short-term U.S. and European government debt securities with 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 (March 31, 2025: $ 43.4 million, December 31, 2024: $ 15.3 million). ​ Inputs to the fair value of the investments are considered Level 2 inputs. ​ 5 Fair value measurement ​ The Company measures certain financial assets and liabilities at fair value, either upon initial recognition or for subsequent accounting or reporting. ASC 820, Fair Value Measurements and Disclosures requires disclosure of methodologies used in determining the reported fair values and establishes a hierarchy of inputs used when available. The three levels of the fair value hierarchy are described below: ​ Level 1 – Valuations based on unadjusted quoted prices in active markets for identical assets or liabilities that the Company can access at the measurement date. ​ Level 2 – Valuations based on quoted prices for similar assets or liabilities in markets that are not active or models for which the inputs are observable, either directly or indirectly. ​ Level 3 – Valuations that require inputs that reflect the Company’s own assumptions that are both significant to the fair value measurement and are unobservable. ​ To the extent that valuation is based on models or inputs that are less observable or unobservable in the market, the determination of fair value requires more judgment. Accordingly, the degree of judgment exercised by the Company in determining fair value is greatest for instruments categorized as Level 3. A financial instrument’s level within the fair value hierarchy is based on the lowest level of any input that is significant to the fair value measurement. ​ The carrying amount of cash and cash equivalents, accounts receivable from licensing and collaboration partners, other assets, accounts payable, accrued expenses and other current liabilities reflected in the consolidated balance sheets approximate their fair values due to their short-term maturities. ​ 8 Table of Contents The following table sets forth the Company’s assets and liabilities that are required to be measured at fair value on a recurring basis as of March 31, 2025 and December 31, 2024 : ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Quoted prices in active markets (Level 1) Significant other observable inputs (Level 2) Significant unobservable inputs (Level 3) Total Classification in Consolidated balance sheets ​ ​ ​ (in thousands) ​ ​ At December 31, 2024 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 158,930 ​ $ — ​ $ — ​ $ 158,930 ​ Cash and cash equivalents Restricted cash ​ ​ 1,399 ​ ​ — ​ ​ — ​ ​ 1,399 ​ Other non-current assets Total assets ​ $ 160,329 ​ $ — ​ $ — ​ $ 160,329 ​ ​ Liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Contingent consideration ​ ​ — ​ ​ — ​ ​ 10,860 ​ ​ 10,860 ​ Contingent consideration Consideration for post-acquisition services ​ ​ — ​ ​ — ​ ​ 370 ​ ​ 370 ​ Other non-current liabilities Total liabilities ​ $ — ​ $ — ​ $ 11,230 ​ $ 11,230 ​ ​ At March 31, 2025 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 217,229 ​ $ — ​ $ — ​ $ 217,229 ​ Cash and cash equivalents Restricted cash ​ ​ 1,429 ​ ​ — ​ ​ — ​ ​ 1,429 ​ Other non-current assets Total assets ​ $ 218,658 ​ $ — ​ $ — ​ $ 218,658 ​ ​ Liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Contingent consideration ​ ​ — ​ ​ — ​ ​ 12,560 ​ ​ 12,560 ​ Contingent consideration Consideration for post-acquisition services ​ ​ — ​ ​ — ​ ​ 428 ​ ​ 428 ​ Other non-current liabilities Total liabilities ​ $ — ​ $ — ​ $ 12,988 ​ $ 12,988 ​ ​ ​ Contingent consideration ​ The Company is required to pay up to EUR 143.1 million (or $ 154.8 million based on the foreign exchange rate on March 31, 2025) 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 SAS. ​ The fair value of the contingent consideration as of March 31, 2025 was $ 12.6 million (December 31, 2024: $ 10.9 million) using discount rates of approximately 14.8 % to 15.5 % (December 31, 2024: 15.3 % to 16.2 %). ​ If, as of March 31, 2025, the Company had assumed a 100 % likelihood of AMT-260 advancing into a Phase III clinical study, then the fair value of the contingent consideration would have increased to $ 40.5 million. If, as of March 31, 2025, the Company had assumed that it would discontinue development of the AMT-260 program, then the contingent consideration would have been released to income. ​ The following table presents the changes in fair value of the contingent consideration between December 31, 2024 and March 31, 2025: ​ ​ ​ ​ ​ ​ ​ ​ Amount of ​ ​ contingent ​ ​ consideration ​ 2025 ​ ​ (in thousands) Balance at December 31, 2024 ​ $ 10,860 Change in fair value (presented within research and development expenses) ​ ​ 1,216 Currency translation effects ​ ​ 484 Balance at March 31, 2025 ​ $ 12,560 ​ As of March 31, 2025, the Company classified nil (December 31, 2024: nil ) of the total contingent consideration of $ 12.6 million (December 31, 2024: $ 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. ​ 9 Table of Contents Investment securities ​ Refer to Note 4 “ Investment securities ” for the fair value of the investment securities as of March 31, 2025 and December 31, 2024. ​ 6 Accrued expenses and other current liabilities ​ Accrued expenses and other current liabilities include the following items: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ March 31, ​ December 31, ​ 2025 2024 ​ ​ (in thousands) Personnel related accruals and liabilities ​ $ 10,921 ​ $ 12,583 Accruals for goods received from and services provided by vendors-not yet billed ​ ​ 11,594 ​ ​ 10,109 Current portion of firm purchase commitment liability ​ ​ 3,249 ​ ​ 1,582 Liability owed to the Purchaser pursuant to the Royalty Financing Agreement (refer to Note 8 "Royalty Financing Agreement") ​ ​ 1,580 ​ ​ 4,951 Total ​ $ 27,344 ​ $ 29,225 ​ ​ 7 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, 2021 and on May 12, 2023 (the “2023 Amended Facility”) and July 22, 2024 (the “2024 Amended Facility”). ​ In July 2024, in connection with the divestment of the Company’s commercial manufacturing activities located in Lexington, MA 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 March 31, 2025 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) was $ 52.1 million as of March 31, 2025, compared to $ 51.9 million as of December 31, 2024, and is recorded net of discount and debt issuance costs. The foreign currency gain on the facility in the three months ended March 31, 2025 was $ 2.1 million compared to a foreign currency loss of $ 2.3 million during the same period in 2024. ​ Interest expense during the three months ended March 31, 2025 was $ 1.8 million, compared to $ 3.7 million during the same period in 2024. ​ 10 Table of Contents Under the 2024 Amended Facility, the Company must remain current in its periodic reporting requirements and is required to keep a minimum cash balance deposited in bank accounts in the U.S. equivalent to the lesser of (i) 65 % of the outstanding balance of principal due or (ii) 100 % of worldwide cash and cash equivalents. This restriction on cash and cash equivalents only relates to the location of the cash and cash equivalents, and such cash and cash equivalents can be used at the discretion of the Company. Beginning on April 1, 2024, the Company is required to keep a minimum of unrestricted cash equal to at least 30 % of the loan amount outstanding. In combination with other covenants, the 2024 Amended Facility restricts the Company’s ability to, among other things, incur future indebtedness and obtain additional debt financing, to make investments in securities or in other companies, to transfer assets, to perform certain corporate changes, to make loans to employees, officers, and directors, and to make dividend payments and other distributions to its shareholders. The Company secured the facilities by directly or indirectly pledging its total assets of $ 605.4 million, less $ 78.4 million of cash and cash equivalents and other current assets held by the Company, and $ 82.4 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 March 31, 2025, the Company was in material compliance with all covenants and provisions of the Amended Facility. ​ 8 Royalty Financing Agreement ​ On May 12, 2023, the Company entered into a royalty purchase agreement (the “Royalty Financing Agreement”) with HemB SPV, L.P. (the “Purchaser”). Under the terms of the Royalty Financing Agreement, the Company received an upfront payment of $ 375.0 million in exchange for its rights to the lowest royalty tier on CSL Behring LLC’s (“CSL Behring”) 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 through December 31, 2038 (“Second Hard Cap Date”). If, on or prior to the defined dates for each cap amount, the total amount of royalty payments received by the Purchaser equals or exceeds the cap amount applicable to such date, the Royalty Financing Agreement will automatically terminate and all rights to the HEMGENIX® royalty payments will revert back to the Company. The Company has no obligation to repay any amounts received from the Purchaser in the event that the applicable cap amount is not reached during the term of the Royalty Financing Agreement. The Company has retained the rights to all other royalties, as well as contractual milestones totaling up to $ 1.3 billion, under the terms of the commercialization and license agreement with CSL Behring (the “CSL Behring Agreement”). Net proceeds from the Royalty Financing Agreement were $ 370.1 million. The Company initially recorded these net proceeds as “Liability from royalty financing agreement” at their fair market value on its consolidated balance sheet as of closing of the transaction on June 5, 2023. Following the initial recognition, the Company records the debt at amortized cost. As of March 31, 2025 the Company expects to satisfy its commitment to the Purchaser prior to the Second Hard Cap Date. The Company recorded 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. The Company would have recorded the following amounts of interest expense if it had used the effective interest rate at the lower and upper end of this range: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended March 31, ​ 2025 2024 ​ ​ ​ (in millions) Interest expenses at effective interest rate of 12.0 % per annum ​ $ 13.2 ​ $ 12.1 Interest recorded in the statement of operations and comprehensive loss and income ​ ​ 13.3 ​ ​ 12.4 Interest expenses at effective interest rate of 13.5 % per annum ​ ​ 14.9 ​ ​ 13.7 ​ 11 Table of Contents The Company prospectively updates the effective interest rate at each reporting date based on updated cash flow projections. ​ The following table presents the movement in the liability related to the Royalty Financing Agreement between December 31, 2024 and March 31, 2025: ​ ​ ​ ​ ​ ​ Amount of liability ​ ​ (in thousands) Balance as of December 31, 2024 (includes $ 5.0 million presented as "Accrued expenses and other current liabilities) ​ $ 439,881 Royalty payments to the Purchaser ​ ​ ( 4,951 ) Interest expense for the period ​ ​ 13,309 Balance as of March 31, 2025 (includes $ 1.6 million presented as "Accrued expenses and other current liabilities) ​ $ 448,239 ​ ​ 9 Shareholders’ Equity ​ 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. ​ ​ 10 Share-based compensation ​ The Company’s share-based compensation plans include the amended and restated 2014 Share Incentive Plan (as amended, the “2014 Plan”) and inducement grants under Rule 5653(c)(4) of the Nasdaq Global Select Market with terms similar to the 2014 Plan (together the “2014 Plans”). At the annual general meeting of shareholders in June 2024, the Company’s shareholders authorized an additional 1,500,000 shares for issuance. As of March 31, 2025, a total of 3,912,283 ordinary shares remain available for issuance under the 2014 Plan. ​ In June 2018, the Company’s shareholders adopted and approved an employee share purchase plan (the “ESPP”) allowing the Company to issue up to 150,000 ordinary shares. The ESPP is intended to qualify under Section 423 of the Internal Revenue Code of 1986, as amended. Under the ESPP, employees are eligible to purchase ordinary shares through payroll deductions, subject to any plan limitations. The purchase price of the ordinary shares on each purchase date is equal to 85 % of the lower of the closing market price on the offering date and the closing market price on the purchase date of each three-month offering period. ​ 2014 Plans and ESPP ​ Share-based compensation expense recognized by classification included in the Consolidated Statements of Operations and Comprehensive Loss in relation to the 2014 Plans and the ESPP for the periods indicated below was as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended March 31, ​ ​ 2025 ​ 2024 ​ ​ (in thousands) Cost of manufacturing services revenue ​ $ — ​ $ 345 Research and development ​ ​ 2,463 ​ ​ 3,425 Selling, general and administrative ​ ​ 1,947 ​ ​ 3,421 Total ​ $ 4,410 ​ $ 7,191 ​ 12 Table of Contents Share-based compensation expense / (income) recognized by award type for the 2014 Plans as well as the ESPP was as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended March 31, ​ ​ 2025 ​ 2024 ​ ​ (in thousands) Award type/ESPP ​ ​ ​ ​ ​ ​ Share options ​ $ 1,637 ​ $ 2,913 Restricted share units ​ ​ 2,213 ​ ​ 4,370 Performance share units ​ ​ 560 ​ ​ ( 99 ) Employee share purchase plan ​ ​ — ​ ​ 7 Total ​ $ 4,410 ​ $ 7,191 ​ As of March 31, 2025, the unrecognized share-based compensation expense related to unvested awards under the 2014 Plans were: ​ ​ ​ ​ ​ ​ ​ ​ Unrecognized Weighted average ​ share-based remaining ​ ​ compensation ​ period for ​ ​ expense ​ recognition ​ ​ (in thousands) ​ (in years) Award type ​ ​ ​ ​ ​ Share options ​ $ 13,399 ​ 2.77 Restricted share units ​ ​ 17,583 ​ 2.27 Performance share units ​ ​ 2,321 ​ 0.75 Total ​ $ 33,303 ​ 2.36 ​ The Company satisfies the exercise of share options and vesting of Restricted Share Units (“RSUs”) and Performance Share Units (“PSUs”) through newly issued ordinary shares. ​ Share options Share options are priced on the date of grant and, except for certain grants made to non-executive directors, vest over a period of four years . The first 25 % of each grant vests after one year from the initial grant date and the remainder vests in equal quarterly installments over years two, three and four. Certain grants to non-executive directors vest in full after one year . Any options that vest must be exercised by the tenth anniversary of the initial grant date. The following table summarizes option activity under the 2014 Plans for the three months ended March 31, 2025: ​ ​ ​ ​ ​ ​ ​ ​ ​ Options ​ ​ Number of ​ Weighted average ​ ordinary shares exercise price ​ ​ ​ ​ ​ ​ Outstanding at December 31, 2024 ​ 4,967,160 ​ ​ 19.87 Granted ​ 791,000 ​ $ 10.90 Forfeited ​ ( 72,965 ) ​ $ 13.39 Expired ​ ( 385,871 ) ​ $ 31.06 Exercised ​ ( 15,928 ) ​ $ 9.96 Outstanding at March 31, 2025 ​ 5,283,396 ​ $ 17.83 Thereof, fully vested, and exercisable on March 31, 2025 ​ 3,053,176 ​ $ 15.91 Thereof, outstanding and expected to vest after March 31, 2025 ​ 2,230,220 ​ $ 11.15 Outstanding and expected to vest after December 31, 2024 ​ 1,838,603 ​ $ 11.46 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of options issued during the period (in $ millions) ​ ​ ​ $ 5.3 ​ 13 Table of Contents The fair value of each option issued is estimated at the respective grant date using the Hull & White option pricing model with the following weighted-average assumptions: ​ ​ ​ ​ ​ ​ ​ ​ Three months ended March 31, ​ 2025 2024 Assumptions ​ ​ ​ ​ Expected volatility ​ 80 % ​ 70 % Expected terms ​ 10 years ​ 10 years Risk free interest rate ​ 4.4 % ​ 4.3 % Expected dividend yield ​ 0.0 % ​ 0.0 % ​ RSUs ​ The following table summarizes the RSU activity for the three months ended March 31, 2025: ​ ​ ​ ​ ​ ​ ​ ​ ​ RSUs ​ ​ Weighted average ​ ​ Number of ​ grant-date fair ​ ​ ordinary shares ​ value Non-vested at December 31, 2024 ​ 1,659,898 ​ $ 10.71 Granted ​ 949,600 ​ $ 10.90 Vested ​ ( 565,613 ) ​ $ 12.80 Forfeited ​ ( 87,137 ) ​ $ 9.99 Non-vested at March 31, 2025 ​ 1,956,748 ​ $ 10.23 ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of RSUs granted during the period (in $ millions) ​ ​ ​ $ 10.4 ​ RSUs generally vest over one to three years . RSUs granted to non-executive directors vest one year from the date of grant. ​ PSUs ​ Awards of PSUs are subject to the achievement of specified performance objectives. The fair value of PSUs granted in 2022 and 2024 is determined at the grant date by reference to share-price. The fair value of PSUs awarded in 2024 and for which the service period precedes the grant date, is being determined by reference to the price of the Company’s ordinary shares as of March 31, 2025. ​ The following table summarizes the PSU activity for the three months ended March 31, 2025: ​ ​ ​ ​ ​ ​ ​ ​ ​ PSUs ​ ​ Weighted average ​ ​ Number of ​ grant-date fair ​ ​ ordinary shares ​ value Non-vested at December 31, 2024 ​ 150,120 ​ $ 21.65 Vested ​ ( 55,322 ) ​ $ 29.10 Forfeited ​ ( 38,620 ) ​ $ 19.25 Non-vested at March 31, 2025 ​ 56,178 ​ $ 5.02 PSUs awarded but not yet earned ​ 230,000 ​ $ 10.60 Total non-vested and discretionary PSUs ​ 286,178 ​ $ 9.50 ​ In the three months ended March 31, 2025, there was an increase in the number of ordinary shares awarded, of 115,000 shares, related to the PSUs awarded but not yet earned, as a result of the increase of the expected payout from 100 % to 200 %. ​ 14 Table of Contents ESPP ​ During the three months ended March 31, 2025 and 2024, nil ordinary shares were issued under the ESPP. As of March 31, 2025, 86,712 ordinary shares remain available for issuance under the ESPP compared to a total of 96,862 as of March 31, 2024. ​ 11 Segment Reporting ​ The Company is advancing a pipeline of innovative gene therapies seeking to deliver to patients suffering from rare and other devastating diseases single treatments with potentially curative results. The Company manages the operations related to these research and development activities within one operating segment because they rely on a common set of infrastructure, resources and technology of the products and production processes, types of customers, distribution methods and regulatory environment. ​ The leadership team is identified as the Chief Operating Decision Maker (“CODM”). ​ The CODM allocates resources to research projects and clinical candidates based on scientific data as well as quantitative and qualitative expected risk adjusted returns on investment. The CODM uses segment operating loss to monitor that cash operating losses remain within the approved budget. ​ The accounting policies of the operating segment are the same as those described in the summary of significant accounting policies. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended March 31, ​ 2025 2024 ​ ​ (in thousands) Revenue ​ $ 1,567 ​ $ 8,485 Less: ​ ​ ​ ​ ​ Employee related expenses ​ ( 14,216 ) ​ ( 24,383 ) Laboratory and development expenses ​ ​ ( 15,967 ) ​ ​ ( 9,076 ) Professional fees ​ ​ ( 2,057 ) ​ ​ ( 2,263 ) Facility expenses ​ ​ ( 1,667 ) ​ ​ ( 5,139 ) Consumables ​ ​ ( 936 ) ​ ​ ( 3,212 ) Other segment items (1) ​ ​ ( 1,034 ) ​ ​ ( 7,432 ) Segment operating loss ​ ​ ( 34,310 ) ​ ​ ( 43,020 ) Reconciliation ​ ​ ​ ​ ​ ​ Depreciation and amortization expense ​ ​ ( 4,527 ) ​ ​ ( 2,629 ) Share-based compensation expense ​ ​ ( 4,410 ) ​ ​ ( 7,191 ) Fair value loss - contingent consideration ​ ​ ( 1,216 ) ​ ​ ( 165 ) Foreign currency gains / (losses), net ​ ​ 7,172 ​ ​ ( 1,145 ) Interest income ​ ​ 4,127 ​ ​ 6,508 Interest expense - Royalty Financing Agreement ​ ​ ( 13,309 ) ​ ( 12,401 ) Interest expense - Hercules debt facility ​ ​ ( 1,800 ) ​ ​ ( 3,696 ) Other reconciling items ​ ​ 5,132 ​ ​ ( 1,223 ) Consolidated loss before income tax expense ​ $ ( 43,141 ) ​ $ ( 64,962 ) ​ (1) Other segment items included in segment operating loss include costs related to intellectual property, information technology and insurance offset by income related to payments received from European authorities to subsidize the Company’s research and development in the Netherlands and France. ​ 15 Table of Contents ​ 12 CSL Behring collaboration ​ In June 2020, uniQure biopharma B.V. entered into the CSL Behring Agreement, pursuant to which CSL Behring received exclusive global rights to HEMGENIX®. Following the divestiture of the Company’s commercial manufacturing activities located in Lexington, MA (“Lexington Transaction”), the Company determined that it is an agent in the sale of HEMGENIX® to CSL Behring. As a result of the Company being an agent, the Company recognizes corresponding costs related to the purchase of HEMGENIX® from Genezen Holdings Inc. and its affiliate Genezen MA, Inc. (together “Genezen”) net of income from the sales of HEMGENIX® to CSL Behring as well as income related to the release of liabilities associated with expected net losses in Other expense within the Company’s Consolidated Statements of Operations and Comprehensive Loss. Accounts receivable related to collaboration services and royalty revenue were as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ March 31, ​ December 31, ​ 2025 2024 ​ ​ (in thousands) Accounts receivable ​ $ 2,522 ​ $ 5,657 Total ​ $ 2,522 ​ $ 5,657 ​ ​ ​ 13 Other income ​ Other income for the three months ended March 31, 2025 and 2024: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended March 31, ​ 2025 2024 ​ ​ (in thousands) Sale of critical reagents to Genezen ​ $ 6,000 ​ $ — Research and development grants from Dutch authorities ​ 1,719 ​ 1,224 Sublease income ​ 458 ​ 152 Other ​ 129 ​ — Total ​ $ 8,306 ​ $ 1,376 ​ In the three months ended March 31, 2025 the Company recognized $ 6.0 million in income related to a one-time sale of critical reagents to Genezen. There were no sales of critical reagents in the comparative prior period. ​ 14 Income taxes ​ The Company recorded $ 0.5 million deferred tax expense in relation to its operations in the U.S. during the three months ended March 31, 2025. The Company recorded $ 0.7 million deferred tax expense in relation to its operations in the U.S. during the three months ended March 31, 2024. ​ The effective income tax rate of 1.1 % during the three months ended March 31, 2025 is substantially lower than the enacted rate of 25.8 % in the Netherlands as the Company records a valuation allowance against its net deferred tax assets in the Netherlands and a partial valuation allowance against its net deferred tax assets in France. The effective income tax rate during the three months ended March 31, 2024 was 1.0 % as the Company had recorded a valuation allowance against its net deferred tax assets in the Netherlands and a partial valuation allowance against its net deferred tax asset in France. ​ 16 Table of Contents ​ 15 Basic and diluted earnings per share ​ Diluted earnings per share is calculated by adjusting the weighted average number of ordinary shares outstanding, assuming conversion of all potentially dilutive ordinary shares. As the Company has incurred a loss in the three months ended March 31, 2025, all potentially dilutive ordinary shares would have an antidilutive effect, if converted, and thus have been excluded from the computation of loss per share for the three months ended March 31, 2025. The ordinary shares are presented without giving effect to the application of the treasury method or exercise prices that would be above the share price as of March 31, 2025 and March 31, 2024, respectively. ​ The potentially dilutive ordinary shares are summarized below: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended March 31, ​ 2025 2024 Anti-dilutive ordinary share equivalents ​ ​ ​ ​ ​ ​ Stock options under 2014 Plans and previous plan ​ ​ 5,283,396 ​ ​ 5,821,909 Non-vested RSUs and PSUs ​ ​ 2,242,926 ​ ​ 2,913,048 ESPP ​ ​ — ​ ​ 3,140 Total anti-dilutive ordinary share equivalents ​ ​ 7,526,322 ​ ​ 8,738,097 ​ ​ 16 Subsequent events ​ None. ​ 17 Table of Contents