uniQure N.V. 10-Q

Item 1. Financial Statements uniQure N.V. ​ UNAUDITED CONSOLIDATED BALANCE SHEETS ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ March 31, ​ December 31, ​ 2022 2021 ​ ​ (in thousands, except share and per share amounts) Current assets ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 524,886 ​ $ 556,256 Accounts receivable and contract asset ​ ​ 38,644 ​ ​ 58,768 Prepaid expenses ​ ​ 12,422 ​ ​ 10,540 Other current assets and receivables ​ ​ 2,260 ​ ​ 2,675 Total current assets ​ ​ 578,212 ​ ​ 628,239 Non-current assets ​ ​ ​ ​ ​ ​ Property, plant and equipment, net of accumulated depreciation of $ 38.5 million as of March 31, 2022 and $ 36.9 million as of December 31, 2021, respectively. ​ ​ 44,918 ​ ​ 43,505 Operating lease right-of-use assets ​ ​ 24,941 ​ ​ 25,573 Intangible assets, net, including an in-process research and development asset of $ 59.5 million ​ ​ 61,135 ​ ​ 62,686 Goodwill ​ ​ 26,565 ​ ​ 27,633 Deferred tax assets, net ​ ​ 15,442 ​ ​ 15,647 Other non-current assets ​ ​ 5,937 ​ ​ 5,897 Total non-current assets ​ ​ 178,938 ​ ​ 180,941 Total assets ​ $ 757,150 ​ $ 809,180 Current liabilities ​ ​ ​ ​ ​ ​ Accounts payable ​ $ 9,920 ​ $ 2,502 Accrued expenses and other current liabilities ​ ​ 19,945 ​ ​ 28,487 Current portion of contingent consideration ​ ​ 9,081 ​ ​ — Current portion of operating lease liabilities ​ ​ 5,754 ​ ​ 5,774 Total current liabilities ​ ​ 44,700 ​ ​ 36,763 Non-current liabilities ​ ​ ​ ​ ​ ​ Long-term debt ​ ​ 101,421 ​ ​ 100,963 Operating lease liabilities, net of current portion ​ ​ 28,232 ​ ​ 28,987 Contingent consideration, net of current portion ​ ​ 22,059 ​ ​ 29,542 Deferred tax liability, net ​ ​ 11,298 ​ ​ 12,913 Other non-current liabilities ​ ​ 3,439 ​ ​ 4,236 Total non-current liabilities ​ ​ 166,449 ​ ​ 176,641 Total liabilities ​ ​ 211,149 ​ ​ 213,404 Commitments and contingencies ​ ​ ​ ​ ​ ​ Shareholders' equity ​ ​ ​ ​ ​ ​ Ordinary shares, € 0.05 par value: 80,000,000 shares authorized as of March 31, 2022 and December 31, 2021 and 46,641,448 and 46,298,635 ordinary shares issued and outstanding as of March 31, 2022 and December 31, 2021, respectively ​ ​ 2,821 ​ ​ 2,802 Additional paid-in-capital ​ ​ 1,084,306 ​ ​ 1,076,972 Accumulated other comprehensive loss ​ ​ ( 39,306 ) ​ ​ ( 28,856 ) Accumulated deficit ​ ​ ( 501,820 ) ​ ​ ( 455,142 ) Total shareholders' equity ​ ​ 546,001 ​ ​ 595,776 Total liabilities and shareholders' equity ​ $ 757,150 ​ $ 809,180 ​ 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, ​ 2022 2021 ​ ​ (in thousands, except share and per share amounts) Collaboration revenues ​ $ 1,792 ​ $ 454 Total revenues ​ ​ 1,792 ​ ​ 454 Operating expenses: ​ ​ ​ ​ ​ ​ Research and development expenses ​ ​ ( 45,003 ) ​ ​ ( 32,656 ) Selling, general and administrative expenses ​ ​ ( 10,987 ) ​ ​ ( 12,375 ) Total operating expenses ​ ​ ( 55,990 ) ​ ​ ( 45,031 ) Other income ​ ​ 311 ​ ​ 352 Other expense ​ ​ ( 193 ) ​ ​ ( 233 ) Loss from operations ​ ​ ( 54,080 ) ​ ​ ( 44,458 ) Interest income ​ ​ 42 ​ ​ 40 Interest expense ​ ​ ( 2,515 ) ​ ​ ( 1,551 ) Foreign currency gains, net ​ ​ 8,567 ​ ​ 4,626 Other non-operating gains, net ​ ​ 692 ​ ​ — Loss before income tax benefit / (expense) ​ $ ( 47,294 ) ​ $ ( 41,343 ) Income tax benefit / (expense) ​ ​ 616 ​ ​ ( 213 ) Net loss ​ $ ( 46,678 ) ​ $ ( 41,556 ) Other comprehensive loss: ​ ​ ​ ​ ​ ​ Foreign currency translation adjustments ​ ​ ( 10,450 ) ​ ​ ( 7,560 ) Total comprehensive loss ​ $ ( 57,128 ) ​ $ ( 49,116 ) ​ ​ ​ ​ ​ ​ ​ Basic and diluted net loss per ordinary share ​ $ ( 1.00 ) ​ $ ( 0.91 ) Weighted average shares used in computing basic and diluted net loss per ordinary share ​ ​ 46,599,114 ​ ​ 45,468,485 ​ ​ 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-MONTH PERIOD ENDED MARCH 31 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Accumulated ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Additional ​ other ​ ​ ​ ​ Total ​ Ordinary shares ​ paid-in ​ comprehensive ​ Accumulated ​ shareholders’ ​ No. of shares Amount capital income / (loss) deficit equity ​ (in thousands, except share and per share amounts) Balance at December 31, 2020 44,777,799 ​ $ 2,711 ​ $ 1,016,018 ​ $ 9,907 ​ $ ( 784,731 ) ​ $ 243,905 Loss for the period — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 41,556 ) ​ ​ ( 41,556 ) Other comprehensive loss — ​ ​ — ​ ​ — ​ ​ ( 7,560 ) ​ ​ — ​ ​ ( 7,560 ) Issuance of ordinary shares 859,885 ​ ​ 52 ​ ​ 27,647 ​ ​ — ​ ​ — ​ ​ 27,699 Exercise of share options 16,782 ​ ​ 1 ​ ​ 391 ​ ​ — ​ ​ — ​ ​ 392 Restricted share units distributed during the period 269,089 ​ ​ 16 ​ ​ ( 16 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense — ​ ​ — ​ ​ 5,761 ​ ​ — ​ ​ — ​ ​ 5,761 Issuance of ordinary shares relating to employee stock purchase plan 1,174 ​ ​ — ​ ​ 49 ​ ​ — ​ ​ — ​ ​ 49 Balance at March 31, 2021 45,924,729 ​ $ 2,780 ​ $ 1,049,850 ​ $ 2,347 ​ $ ( 826,287 ) ​ $ 228,690 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Balance at December 31, 2021 46,298,635 ​ $ 2,802 ​ $ 1,076,972 ​ $ ( 28,856 ) ​ $ ( 455,142 ) ​ $ 595,776 Loss for the period — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 46,678 ) ​ ​ ( 46,678 ) Other comprehensive loss — ​ ​ — ​ ​ — ​ ​ ( 10,450 ) ​ ​ — ​ ​ ( 10,450 ) Exercise of share options 68,124 ​ ​ 4 ​ ​ 420 ​ ​ — ​ ​ — ​ ​ 424 Restricted share units and performance share units distributed during the period 271,131 ​ ​ 15 ​ ​ ( 15 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense — ​ ​ — ​ ​ 6,868 ​ ​ — ​ ​ — ​ ​ 6,868 Issuance of ordinary shares relating to employee stock purchase plan 3,558 ​ ​ — ​ ​ 61 ​ ​ — ​ ​ — ​ ​ 61 Balance at March 31, 2022 46,641,448 ​ $ 2,821 ​ $ 1,084,306 ​ $ ( 39,306 ) ​ $ ( 501,820 ) ​ $ 546,001 ​ 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, ​ 2022 2021 ​ ​ (in thousands) Cash flows from operating activities ​ ​ ​ ​ ​ ​ Net loss ​ $ ( 46,678 ) ​ $ ( 41,556 ) Adjustments to reconcile net loss to net cash used in operating activities: ​ ​ ​ ​ ​ ​ Depreciation and amortization expense ​ ​ 2,122 ​ ​ 1,862 Share-based compensation expense ​ ​ 6,868 ​ ​ 5,761 Deferred tax (income) / expense ​ ​ ( 616 ) ​ ​ 213 Changes in fair value of contingent consideration and derivative financial instrument, net ​ ​ 1,512 ​ ​ - Unrealized foreign exchange gains, net ​ ​ ( 7,356 ) ​ ​ ( 5,342 ) Changes in operating assets and liabilities: ​ ​ ​ ​ ​ ​ Accounts receivable and contract asset, prepaid expenses, and other current assets and receivables ​ ​ 17,209 ​ ​ ( 8,023 ) Accounts payable ​ ​ 7,306 ​ ​ 2,510 Accrued expenses, other liabilities, and operating leases ​ ​ ( 6,078 ) ​ ​ 3,302 Net cash used in operating activities ​ ​ ( 25,711 ) ​ ​ ( 41,273 ) Cash flows from investing activities ​ ​ ​ ​ ​ ​ Purchases of property, plant, and equipment ​ ​ ( 4,058 ) ​ ​ ( 3,876 ) Acquisition of remaining outstanding ordinary shares related to Corlieve acquisition ​ ​ ( 822 ) ​ ​ - Net cash used in investing activities ​ ​ ( 4,880 ) ​ ​ ( 3,876 ) Cash flows from financing activities ​ ​ ​ ​ ​ ​ Proceeds from issuance of ordinary shares related to employee stock option and purchase plans ​ ​ 485 ​ ​ 442 Proceeds from issuance of ordinary shares ​ ​ - ​ ​ 28,734 Share issuance costs from issuance of ordinary shares ​ ​ - ​ ​ ( 1,161 ) Proceeds from loan increment, net of debt issuance costs ​ ​ - ​ ​ 34,603 Net cash generated from financing activities ​ ​ 485 ​ ​ 62,618 Currency effect on cash, cash equivalents and restricted cash ​ ​ ( 1,168 ) ​ ​ ( 1,620 ) Net (decrease) / increase in cash, cash equivalents and restricted cash ​ ​ ( 31,274 ) ​ ​ 15,849 Cash, cash equivalents and restricted cash at beginning of period ​ ​ 559,353 ​ ​ 247,680 Cash, cash equivalents and restricted cash at the end of period ​ $ 528,079 ​ $ 263,529 Cash and cash equivalents ​ $ 524,886 ​ $ 260,813 Restricted cash related to leasehold and other deposits ​ ​ 3,193 ​ ​ 2,716 Total cash, cash equivalents and restricted cash ​ $ 528,079 ​ $ 263,529 Supplemental cash flow disclosures: ​ ​ ​ ​ ​ ​ Cash paid for interest ​ $ ( 1,906 ) ​ $ ( 1,410 ) Non-cash (decrease) / increase in accounts payables and accrued expenses and other current liabilities related to purchases of property, plant, and equipment ​ $ ( 611 ) ​ $ - ​ The accompanying notes are an integral part of these unaudited consolidated financial statements. ​ ​ 5 Table of Contents 1 General business information ​ uniQure (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 (AMT) 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 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 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 of America (“U.S. GAAP”) and applicable rules and regulations of the SEC regarding interim financial reporting. Any reference in these notes to applicable guidance is meant to refer to authoritative U.S. GAAP as found in the Accounting Standards Codification (“ASC”) and Accounting Standards Update (“ASU”) of the Financial Accounting Standards Board (“FASB”). ​ The unaudited consolidated financial statements are presented in 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, 2022, are not necessarily indicative of the results to be expected for the full year ending December 31, 2022, 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 . ​ 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 periods. Actual results could differ from those estimates. ​ 6 Table of Contents 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, 2021, and the notes thereto, which are included in the Company’s Annual Report . There have been no material changes in the Company’s significant accounting policies during the three months ended March 31, 2022. ​ 2.5 Recent accounting pronouncements ​ There have been no new accounting pronouncements or changes to accounting pronouncements during the three months ended March 31, 2022, as compared to the recent accounting pronouncements described in Note 2.3.23 of the Company’s Annual Report , which could be expected to materially impact the Company’s unaudited consolidated financial statements. ​ ​ ​ ​ 3 Collaboration arrangements and concentration of credit risk ​ CSL Behring collaboration ​ On June 24, 2020 (the “Signing Date”), uniQure biopharma B.V., a wholly-owned subsidiary of uniQure N.V., entered into a commercialization and license agreement (the “CSL Behring Agreement”) with CSL Behring LLC, (“CSL Behring”), pursuant to which CSL Behring received exclusive global rights to etranacogene dezaparvovec, the Company’s investigational gene therapy for patients with hemophilia B, (the “Product”). ​ The transaction became fully effective on May 6, 2021, one day after the waiting period under the Hart-Scott-Rodino Antitrust Improvements Act of 1976 (the “HSR Act”) expired on May 5, 2021 (“Closing”). The Company identified two material performance obligations related to the CSL Behring Agreement: ​ (i) Sale of the exclusive global rights to the Product (“License Sale”); and (ii) Generate information to support the regulatory approval of the current and next generation manufacturing process of Product and to provide any such information generated to CSL Behring (“Manufacturing Development”). The Company determined that the License Sale was completed on May 6, 2021, when it transferred the license and CSL Behring assumed full responsibility for the development and commercialization of the Product. At Closing, the Company evaluated the amounts of potential payments and the likelihood that the payments will be received. The Company utilized the most likely amount method to estimate the variable consideration to be included in the transaction price. Since the Company cannot control the achievement of regulatory and first commercial sales milestones, the Company concluded that the potential payments are constrained as of Closing. The Company determined that it would recognize revenue related to these payments only to the extent that it becomes probable that no significant reversal of recognized cumulative revenue will occur thereafter. Similarly, the Company records expenses related to its existing license and other agreements as well as its financial advisor for a mid-single digit percentage of any such revenue recognized associated to meeting a milestone. The Company includes payments related to sales milestones in the transaction price when their achievement becomes probable, and it will include royalties on the sale of Product once these have been earned. During the three months ended March 31, 2022, the Company did no t recognize any license revenue ( nil for same period in 2021). The Company recognized $ 1.4 million of collaboration revenue in the three months ended March 31, 2022, compared to nil in the same period in 2021. The Company generates such collaboration revenue from services rendered in relation to completing the HOPE-B clinical trial on behalf of CSL Behring as well as additional development services that CSL Behring requested. These collaboration services are reimbursed at the pre-agreed full-time-employee rate (“FTE-rate”). 7 Table of Contents As of December 31, 2021, the Company recorded accounts receivable of $ 2.9 million from CSL Behring related to clinical development services as well as a contract asset of $ 55.0 million associated with milestone payments due upon CSL Behring’s global regulatory submissions for etranacogene dezaparvovec, which were deemed to be probable. In March 2022, CSL Behring submitted the global regulatory submissions, and as of March 31, 2022, the Company collected $ 20.0 million of the total $ 55.0 million owed. As of March 31, 2022, the Company had accounts receivable of $ 38.3 million from CSL Behring, $ 35.0 million of which were related to the uncollected milestone payment associated with the global regulatory submissions. The remaining $ 35.0 million was received in April 2022. Bristol-Myers Squibb collaboration In May 2015, the Company and Bristol-Myers Squibb (“BMS”) entered into a collaboration and license agreement and various related agreements with BMS (“BMS CLA”). On December 1, 2020, the Company and BMS amended the BMS CLA (“amended BMS CLA”) to reduce the scope of the collaboration and license from potentially ten to then four collaboration targets (including a right to replace two of such targets by December 1, 2021). The Company is eligible to receive research, development, and regulatory milestone payments of up to $ 217.0 million for each of the four collaboration targets if defined milestones are achieved. ​ BMS may place purchase orders to provide limited services primarily related to analytical and development efforts in respect of the four collaboration targets. BMS may request such services for a period not to exceed the earlier of (i) the completion of all activities under a Research Plan and (ii) November 30, 2023. BMS reimburses the Company for these services. ​ Collaboration Revenue related to these contracted services is recognized when performance obligations are satisfied. The Company generated $ 0.4 million collaboration revenue for the three months ended March 31, 2022 ($ 0.5 million for the three months ended March 31, 2021). ​ ​ ​ ​ 8 Table of Contents 4 Fair value measurement ​ The Company measures certain financial assets and liabilities at fair value, either upon initial recognition or for subsequent accounting or reporting. U.S. GAAP 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, prepaid expenses, other assets, accounts payable, accrued expenses and other current liabilities reflected in the Consolidated balance sheets approximate their fair values due to their short-term maturities. ​ The following table sets forth the Company’s assets and liabilities that are required to be measured at fair value on a recurring basis as of March 31, 2022, and December 31, 2021: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 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, 2021 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 556,256 ​ $ — ​ $ — ​ $ 556,256 ​ Cash and cash equivalents Restricted cash ​ ​ 3,097 ​ ​ — ​ ​ — ​ ​ 3,097 ​ Other non-current assets Total assets ​ $ 559,353 ​ $ — ​ $ — ​ $ 559,353 ​ ​ Liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Contingent consideration ​ ​ — ​ ​ — ​ ​ 29,542 ​ ​ 29,542 ​ Contingent consideration Derivative financial instrument ​ ​ — ​ ​ — ​ ​ 2,805 ​ ​ 2,805 ​ Other non-current liabilities Consideration for post-acquisition services ​ ​ — ​ ​ — ​ ​ 846 ​ ​ 846 ​ Other non-current liabilities Total liabilities ​ $ — ​ $ — ​ $ 33,193 ​ $ 33,193 ​ ​ At March 31, 2022 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 524,886 ​ $ — ​ $ — ​ $ 524,886 ​ Cash and cash equivalents Restricted cash ​ ​ 3,193 ​ ​ — ​ ​ — ​ ​ 3,193 ​ Other non-current assets Total assets ​ $ 528,079 ​ $ — ​ $ — ​ $ 528,079 ​ ​ Liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Contingent consideration ​ ​ — ​ ​ — ​ ​ 31,140 ​ ​ 31,140 ​ Current portion of contingent consideration; contingent consideration, net of current portion Derivative financial instrument ​ ​ — ​ ​ — ​ ​ 2,116 ​ ​ 2,116 ​ Other non-current liabilities Consideration for post-acquisition services ​ ​ — ​ ​ — ​ ​ 752 ​ ​ 752 ​ Other non-current liabilities Total liabilities ​ $ — ​ $ — ​ $ 34,008 ​ $ 34,008 ​ ​ ​ 9 Table of Contents Derivative financial instrument ​ The Company issued a derivative financial instrument related to its collaboration with BMS. ​ On December 1, 2020, the Company and BMS agreed that upon the consummation of a change of control transaction of uniQure that occurs prior to December 1, 2026 or BMS’ delivery of a target cessation notice for all four collaboration targets, the Company (or its third party acquirer) shall pay to BMS a one-time, non-refundable, non-creditable cash payment of $ 70.0 million, provided that (x) if $ 70.0 million is greater than five percent ( 5.0 %) of the net proceeds (as contractually defined) from such change of control transaction, the payment shall be an amount equal to five percent of such net proceeds, and (y) if $ 70.0 million is less than one percent of such net proceeds, the change of control payment shall be an amount equal to one percent of such net proceeds (“CoC-payment”). The Company has not consummated any change of control transaction as of March 31, 2022 that would obligate it to make a CoC-payment. ​ The Company determined that the CoC-payment should be recorded as a derivative financial liability as of December 1, 2020 and that subsequent changes in the fair market value of this derivative financial liability should be recorded in profit and loss. The fair market value of the derivative financial liability is materially impacted by probability that market participants assign to the likelihood of the occurrence of a change of control transaction that would give rise to a CoC-payment. This probability represents an unobservable input. The Company determines the fair market value of the derivative financial liability by using a present value model based on expected cash flow. The expected cash flows are materially impacted by the probability that market participants assign to the likelihood of the occurrence of a change of control transaction within the biotechnology industry. The Company estimated this unobservable input using the best information available as of March 31, 2022 and December 31, 2021. The Company obtained reasonably available market information that it believed market participants would use in determining the likelihood of the occurrence of a change-of control transaction within the biotechnology industry. Selecting and evaluating market information involves considerable judgement and uncertainty. Based on all such information and its judgment, the Company estimated that the fair market value of the derivative financial liability (presented within “Other non-current liabilities”) as of March 31, 2022 was $ 2.1 million and as of December 31, 2021 was $ 2.8 million. The decrease of the fair value market value of the derivative financial liability of $ 0.7 million for the three months ended March 31, 2022 was recorded as a gain within Other non-operating (losses) / gains ( nil in same period 2021). ​ Contingent consideration ​ The Company is required to pay up to EUR 178.8 million ($ 198.8 million at March 31, 2022) to the former shareholders of Corlieve upon the achievement of contractually defined milestones in connection with the Company’s acquisition of Corlieve. The fair market value of the contingent consideration was determined using unobservable initial inputs with respect to (i) the probability of achieving the relevant milestones, or POS, (ii) the estimated timing of achieving such milestones, and (iii) the interest rate used to discount the payments. The Company determined the fair market value of the contingent consideration by calculating the probability-adjusted payments based on each milestone’s probability of achievement. The probability-adjusted payments were then discounted to present value using a discount rate representing the Company’s credit risk. The discount rate was 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 US bonds with a CCC credit rating. ​ The fair value of the contingent consideration as of March 31, 2022 was $ 31.1 million using discount rates of approximately 10.3 % as well as a 55.0 % likelihood of AMT-260 advancing into clinical development by no later than early 2024. If as of March 31, 2022 the Company had assumed a 100 % likelihood of AMT-260 advancing into clinical development, then the fair value of the contingent consideration would have increased to $ 51.7 million. If as of March 31, 2022 the Company assumed that it would discontinue development of the AMT-260 program, then the contingent consideration would be released to income. Changes in fair value of the contingent consideration are recognized within research and development expenses in the consolidated statements of operations. ​ 10 Table of Contents The following table presents the changes in fair value of contingent consideration between December 31, 2021 and March 31, 2022: ​ ​ ​ ​ ​ ​ Amount of ​ contingent ​ consideration ​ ​ 2022 ​ (in thousands) Balance at December 31, 2021 $ 29,542 Change in fair value (presented within research and development expenses) ​ 2,204 Currency translation effects ​ ( 606 ) Balance at March 31, 2022 $ 31,140 ​ As of March 31, 2022, the Company classified $ 9.1 million of the total contingent consideration of $ 31.1 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. ​ ​ ​ ​ ​ ​ ​ ​ ​ 5 Accrued expenses and other current liabilities ​ Accrued expenses and other current liabilities include the following items: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ March 31, ​ December 31, ​ 2022 2021 ​ ​ (in thousands) Accruals for goods received from and services provided by vendors-not yet billed ​ $ 10,341 ​ $ 13,012 Personnel related accruals and liabilities ​ ​ 9,604 ​ ​ 12,603 Accrued contract fulfillment costs and costs to obtain a contract ​ ​ — ​ ​ 2,872 Total ​ $ 19,945 ​ $ 28,487 ​ ​ ​ ​ 11 Table of Contents 6 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 (“2018 Amended Facility”), January 2021 (“2021 Amended Facility”) and in December 2021 (“2021 Restated Facility”). On January 29, 2021, the Company drew down $ 35.0 million as part of the amendment of the facility at that time. ​ Pursuant to the 2021 Restated Facility, Tranche A and Tranche B of the 2021 Amended Facility with a total outstanding balance of $ 70.0 million were consolidated into one tranche with a total commitment of $ 100.0 million. The Company drew down an additional $ 30.0 million at the time of the December 2021 amendment, resulting in total principal outstanding as of March 31, 2022 of $ 100.0 million. The 2021 Restated Facility extended the loan’s maturity date from June 1, 2023 until December 1, 2025. The interest-only period was extended from January 1, 2023 to December 1, 2024, or December 1, 2025 if, prior to June 30, 2024, either (a) the Biologics License Application (“BLA”) for AMT-061 is approved by the U.S. Food and Drug Administration (“FDA”) or (b) AMT-130 is advanced into a pivotal trial. 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. Under the 2021 Restated Facility, the Company owes a back-end fee of 4.85 % of the outstanding debt. The Company is required to repay the facility in equal monthly installments of principal and interest between the end of the interest-only period and the maturity date. The Company continues to owe a $ 2.5 million back-end fee related to the 2021 Amended Facility which is due on June 1, 2023. The amortized cost (including interest due presented as part of accrued expenses and other current liabilities) of the 2021 Restated Facility was $ 102.1 million as of March 31, 2022, compared to $ 101.6 million as of December 31, 2021, and is recorded net of discount and debt issuance costs. The foreign currency loss on the facility in the three months ended March 31, 2022, was $ 2.1 million compared to a foreign currency loss of $ 3.2 million during the same period in 2021 for the 2018 Amended Facility and 2021 Amended Facility. Interest expense associated with the 2021 Restated Facility during the three months ended March 31, 2022, was $ 2.4 million compared to $ 1.5 million during the same period in 2021 for the 2018 Amended Facility and 2021 Amended Facility. As a covenant in the 2021 Restated Facility the Company has 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. The Company, beginning on April 1, 2023, is also required to keep a minimum of unrestricted cash of at least 50 % of the loan amount outstanding. If, prior to June 30, 2024, either (a) the BLA for AMT-061 is approved by the FDA or (b) AMT-130 is advanced into a pivotal trial, the minimum cash covenant will be lowered to at least 30 % of the loan amount outstanding and its effectiveness will be deferred to April 1, 2024. In combination with other covenants, the 2021 Restated 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 $ 757.2 million, with the exception of $ 101.4 million of cash and cash equivalents and other current assets held by uniQure N.V. ​ The 2021 Restated Facility contains provisions that include the occurrence of a material adverse effect, as defined therein, which would entitle Hercules to declare all principal, interest and other amounts owed by the Company immediately due and payable. As of March 31, 2022, the Company was in material compliance with all covenants and provisions. ​ ​ 12 Table of Contents 7 Share-based compensation ​ The Company’s share-based compensation plans include the 2014 Amended and Restated Share Option Plan (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 2021, the Company’s shareholders approved an increase in the number of ordinary shares authorized for issuance under the 2014 Plan from 8,601,471 to 12,601,471 . ​ a) 2014 Plans ​ Share-based compensation expense recognized by classification included in the Consolidated statements of operations and comprehensive loss in relation to the 2014 Plans for the periods indicated below was as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended March 31, ​ ​ 2022 ​ 2021 ​ ​ (in thousands) Research and development ​ $ 4,050 ​ $ 2,674 Selling, general and administrative ​ ​ 2,813 ​ ​ 3,080 Total ​ $ 6,863 ​ $ 5,754 ​ Share-based compensation expense recognized by award type was as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended March 31, ​ ​ 2022 ​ 2021 ​ ​ (in thousands) Award type ​ ​ ​ ​ ​ ​ Share options ​ $ 3,255 ​ $ 2,840 Restricted share units ​ ​ 3,270 ​ ​ 2,560 Performance share units ​ ​ 338 ​ ​ 354 Total ​ $ 6,863 ​ $ 5,754 ​ As of March 31, 2022, 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 ​ $ 34,041 ​ 2.94 Restricted share units ​ ​ 35,252 ​ 2.40 Performance share units ​ ​ 444 ​ 0.46 Total ​ $ 69,737 ​ 2.65 ​ 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 % 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. 13 Table of Contents The following tables summarize option activity under the Company’s 2014 Plans for the three months ended March 31, 2022: ​ ​ ​ ​ ​ ​ ​ ​ ​ Options ​ ​ Number of ​ Weighted average ​ ordinary shares exercise price ​ ​ ​ ​ ​ ​ Outstanding at December 31, 2021 ​ 3,308,325 ​ $ 31.02 Granted ​ 1,011,876 ​ $ 16.04 Forfeited ​ ( 70,868 ) ​ $ 36.21 Expired ​ ( 55,511 ) ​ $ 37.86 Exercised ​ ( 64,124 ) ​ $ 6.36 Outstanding at March 31, 2022 ​ 4,129,698 ​ $ 27.55 Thereof, fully vested and exercisable on March 31, 2022 ​ 1,925,690 ​ $ 26.44 Thereof, outstanding and expected to vest after March 31, 2022 ​ 2,204,008 ​ $ 28.53 ​ ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of options issued during the period (in $ millions) ​ ​ ​ $ 9.2 Proceeds from option sales during the period (in $ millions) ​ ​ ​ $ 0.4 ​ The fair value of each option issued is estimated at the respective grant date using the Hull & White option pricing model with the following weighted-average assumptions: ​ ​ ​ ​ ​ ​ ​ ​ Three months ended March 31, Assumptions 2022 2021 Expected volatility ​ 70 % ​ 75 % Expected terms ​ 10 years ​ 10 years Risk free interest rate ​ 2.12 % ​ 1.21 - 1.71 % Expected dividend yield ​ 0 % ​ 0 % ​ Restricted share units (“RSUs”) ​ The following table summarizes the RSUs activity for the three months ended March 31, 2022: ​ ​ ​ ​ ​ ​ ​ ​ ​ RSU ​ ​ Weighted average ​ ​ Number of ​ grant-date fair ​ ​ ordinary shares ​ value Non-vested at December 31, 2021 ​ 710,617 ​ $ 38.89 Granted ​ 1,273,763 ​ $ 16.04 Vested ​ ( 195,261 ) ​ $ 39.90 Forfeited ​ ( 45,050 ) ​ $ 27.93 Non-vested at March 31, 2022 ​ 1,744,069 ​ $ 22.37 ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of RSUs granted during the period (in $ millions) ​ ​ ​ $ 20.4 ​ RSUs vest over one to three years . RSUs granted to non-executive directors vest one year from the date of grant. ​ 14 Table of Contents Performance share units (“PSUs”) ​ The following table summarizes the PSUs activity for the three months ended March 31, 2022: ​ ​ ​ ​ ​ ​ ​ ​ ​ PSU ​ ​ Weighted average ​ ​ Number of ​ grant-date fair ​ ​ ordinary shares ​ value Non-vested at December 31, 2021 ​ 632,930 ​ $ 33.54 Granted ​ 8,100 ​ $ 16.04 Vested ​ ( 77,330 ) ​ $ 57.56 Forfeited ​ ( 19,800 ) ​ $ 29.35 Non-vested at March 31, 2022 ​ 543,900 ​ $ 30.01 ​ ​ ​ ​ ​ ​ ​ PSUs granted in 2019 vested on the third anniversary of the grant, subject to the grantee’s continued employment. ​ The Company granted shares to certain employees in September and December 2021 that will be earned upon achievement of defined milestones. Earned shares will vest upon the later of a minimum service period of one year or three years , or the achievement of defined milestones, subject to the grantee’s continued employment. In addition, portions of the December 2021 shares granted to executives and other members of senior management are subject to achieving a minimum total shareholder return relative to the Nasdaq biotechnology index. The Company recognizes the compensation cost related to these grants to the extent it considers achievement of the milestones to be probable. ​ b) 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 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. During the three months ended March 31, 2022, 3,558 ordinary shares were issued under the ESPP compared to 1,174 during the same period in 2021. As of March 31, 2022, a total of 123,744 ordinary shares remain available for issuance under the ESPP plan compared to a total of 130,852 as of March 31, 2021. ​ ​ 8 Income taxes ​ The Company recorded $ 0.6 million deferred tax benefit in relation to its operations in the United States, France and Switzerland during the three-month period ended March 31, 2022. The Company recorded $ 0.2 million net deferred tax expense in the prior year in the United States as of March 31, 2021. ​ The effective income tax rate of ( 1.3 )% during the three months ended March 31, 2022 is substantially lower than the enacted rated of 25.8 % in the Netherlands as the Company recorded a valuation allowance against its net deferred tax assets in the Netherlands. The effective income tax rate during the three months ended March 31, 2021 was 0.5 % as the Company had recorded a valuation allowance against all its net deferred tax assets in the Netherlands. ​ ​ ​ 15 Table of Contents 9 Basic and diluted earnings per share ​ Diluted earnings per share are calculated by adjusting the weighted average number of ordinary shares outstanding, assuming conversion of all potentially dilutive ordinary shares. As the Company has incurred a loss, all potentially dilutive ordinary shares would have an antidilutive effect, if converted, and thus have been excluded from the computation of loss per share. The 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, 2022 and March 31, 2021, respectively. ​ The potentially dilutive ordinary shares are summarized below: ​ ​ ​ ​ ​ ​ ​ ​ March 31, ​ 2022 2021 ​ ​ (ordinary shares) Stock options under 2014 Plans and previous plan ​ 4,139,698 ​ 3,345,646 Non-vested RSUs and PSUs ​ 2,287,969 ​ 796,982 Employee share purchase plan ​ 745 ​ 729 Total potential dilutive ordinary shares ​ 6,428,412 ​ 4,143,357 ​ ​ ​ ​ ​ ​ ​ 10 Subsequent events ​ None. ​ ​ ​ 16 Table of Contents