uniQure N.V. 10-Q

Item 1. Financial Statements uniQure N.V. ​ UNAUDITED CONSOLIDATED BALANCE SHEETS ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ March 31, ​ December 31, ​ 2021 2020 ​ ​ (in thousands, except share and per share amounts) Current assets ​ ​ ​ ​ ​ ​ Cash and cash equivalents ​ $ 260,813 ​ $ 244,932 Accounts receivables ​ ​ 5,445 ​ ​ 6,618 Prepaid expenses ​ ​ 9,186 ​ ​ 4,337 Other current assets ​ ​ 6,886 ​ ​ 3,024 Total current assets ​ ​ 282,330 ​ ​ 258,911 Non-current assets ​ ​ ​ ​ ​ ​ Property, plant and equipment, net of accumulated depreciation of $ 35.9 million as of March 31, 2021 and $ 35.2 million as of December 31, 2020, respectively ​ ​ 33,862 ​ ​ 32,328 Operating lease right-of-use assets ​ ​ 25,313 ​ ​ 26,086 Intangible assets, net ​ ​ 2,908 ​ ​ 3,361 Goodwill ​ ​ 518 ​ ​ 542 Restricted cash ​ ​ 2,716 ​ ​ 2,748 Deferred tax asset ​ ​ 16,206 ​ ​ 16,419 Total non-current assets ​ ​ 81,523 ​ ​ 81,484 Total assets ​ $ 363,853 ​ $ 340,395 Current liabilities ​ ​ ​ ​ ​ ​ Accounts payable ​ $ 5,749 ​ $ 3,772 Accrued expenses and other current liabilities ​ ​ 20,896 ​ ​ 18,038 Current portion of operating lease liabilities ​ ​ 5,457 ​ ​ 5,524 Total current liabilities ​ ​ 32,102 ​ ​ 27,334 Non-current liabilities ​ ​ ​ ​ ​ ​ Long-term debt ​ ​ 70,467 ​ ​ 35,617 Operating lease liabilities, net of current portion ​ ​ 29,487 ​ ​ 30,403 Other non-current liabilities ​ ​ 3,107 ​ ​ 3,136 Total non-current liabilities ​ ​ 103,061 ​ ​ 69,156 Total liabilities ​ ​ 135,163 ​ ​ 96,490 Commitments and contingencies ​ ​ ​ ​ ​ ​ Shareholders' equity ​ ​ ​ ​ ​ ​ Ordinary shares, € 0.05 par value: 60,000,000 shares authorized as of March 31, 2021 and December 31, 2020 and 45,924,729 and 44,777,799 ordinary shares issued and outstanding as of March 31, 2021 and December 31, 2020, respectively ​ ​ 2,780 ​ ​ 2,711 Additional paid-in-capital ​ ​ 1,049,850 ​ ​ 1,016,018 Accumulated other comprehensive income ​ ​ 2,347 ​ ​ 9,907 Accumulated deficit ​ ​ ( 826,287 ) ​ ​ ( 784,731 ) Total shareholders' equity ​ ​ 228,690 ​ ​ 243,905 Total liabilities and shareholders' equity ​ $ 363,853 ​ $ 340,395 ​ 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, ​ 2021 2020 ​ ​ (in thousands, except share and per share amounts) License revenues from related party ​ ​ — ​ ​ 47 Collaboration revenues ​ ​ 454 ​ ​ — Collaboration revenues from related party ​ ​ — ​ ​ 57 Total revenues ​ ​ 454 ​ ​ 104 Operating expenses: ​ ​ ​ ​ ​ ​ Research and development expenses ​ ​ ( 32,656 ) ​ ​ ( 26,013 ) Selling, general and administrative expenses ​ ​ ( 12,375 ) ​ ​ ( 9,072 ) Total operating expenses ​ ​ ( 45,031 ) ​ ​ ( 35,085 ) Other income ​ ​ 352 ​ ​ 857 Other expense ​ ​ ( 233 ) ​ ​ ( 339 ) Loss from operations ​ ​ ( 44,458 ) ​ ​ ( 34,463 ) Interest income ​ ​ 40 ​ ​ 822 Interest expense ​ ​ ( 1,551 ) ​ ​ ( 975 ) Foreign currency gains, net ​ ​ 4,626 ​ ​ 4,602 Other non-operating gains, net ​ ​ — ​ ​ 2,015 Loss before income tax expense ​ $ ( 41,343 ) ​ $ ( 27,999 ) Income tax expense ​ ​ ( 213 ) ​ ​ — Net loss ​ $ ( 41,556 ) ​ $ ( 27,999 ) Other comprehensive loss: ​ ​ ​ ​ ​ ​ Foreign currency translation adjustments ​ ​ ( 7,560 ) ​ ​ ( 5,277 ) Total comprehensive loss ​ $ ( 49,116 ) ​ $ ( 33,276 ) ​ ​ ​ ​ ​ ​ ​ Basic and diluted net loss per ordinary share ​ $ ( 0.91 ) ​ $ ( 0.63 ) Weighted average shares used in computing basic and diluted net loss per ordinary share ​ ​ 45,468,485 ​ ​ 44,279,456 ​ ​ 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 (loss)/income deficit equity ​ (in thousands, except share data) Balance at December 31, 2019 43,711,954 ​ $ 2,651 ​ $ 986,803 ​ $ ( 6,689 ) ​ $ ( 659,707 ) ​ $ 323,058 Loss for the period — ​ ​ — ​ ​ — ​ ​ — ​ ​ ( 27,999 ) ​ ​ ( 27,999 ) Other comprehensive loss — ​ ​ — ​ ​ — ​ ​ ( 5,277 ) ​ ​ — ​ ​ ( 5,277 ) Exercise of share options 64,762 ​ ​ 3 ​ ​ 929 ​ ​ — ​ ​ — ​ ​ 932 Restricted and performance share units distributed during the period 521,079 ​ ​ 29 ​ ​ ( 29 ) ​ ​ — ​ ​ — ​ ​ — Share-based compensation expense — ​ ​ — ​ ​ 4,355 ​ ​ — ​ ​ — ​ ​ 4,355 Issuance of ordinary shares relating to employee stock purchase plan 1,801 ​ ​ — ​ ​ 78 ​ ​ — ​ ​ — ​ ​ 78 Balance at March 31, 2020 44,299,596 ​ $ 2,683 ​ $ 992,136 ​ $ ( 11,966 ) ​ $ ( 687,706 ) ​ $ 295,147 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 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 and performance 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 ​ ​ 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, ​ 2021 2020 ​ ​ ​ (in thousands) Cash flows from operating activities ​ ​ ​ ​ ​ ​ Net loss ​ $ ( 41,556 ) ​ $ ( 27,999 ) Adjustments to reconcile net loss to net cash used in operating activities: ​ ​ ​ ​ ​ ​ Depreciation and amortization ​ ​ 1,862 ​ ​ 1,733 Share-based compensation expense ​ ​ 5,761 ​ ​ 4,355 Change in fair value of derivative financial instruments ​ ​ - ​ ​ ( 2,015 ) Unrealized foreign exchange gains ​ ​ ( 5,342 ) ​ ​ ( 4,824 ) Deferred tax expense ​ ​ 213 ​ ​ - Change in deferred revenue ​ ​ - ​ ​ 270 Changes in operating assets and liabilities: ​ ​ ​ ​ ​ ​ Accounts receivable, prepaid expenses, and other current assets ​ ​ ( 8,023 ) ​ ​ ( 1,282 ) Accounts payable ​ ​ 2,510 ​ ​ ( 546 ) Accrued expenses, other liabilities, and operating leases ​ ​ 3,302 ​ ​ ( 2,645 ) Net cash used in operating activities ​ ​ ( 41,273 ) ​ ​ ( 32,953 ) Cash flows from investing activities ​ ​ ​ ​ ​ ​ Purchases of intangible assets ​ ​ - ​ ​ ( 2,213 ) Purchases of property, plant, and equipment ​ ​ ( 3,876 ) ​ ​ ( 677 ) Net cash used in investing activities ​ ​ ( 3,876 ) ​ ​ ( 2,890 ) Cash flows from financing activities ​ ​ ​ ​ ​ ​ Proceeds from loan increment, net of debt issuance costs ​ ​ 34,603 ​ ​ - Proceeds from issuance of ordinary shares ​ ​ 28,734 ​ ​ - Share issuance costs from issuance of ordinary shares ​ ​ ( 1,161 ) ​ ​ - Proceeds from issuance of shares related to employee stock option and purchase plans ​ ​ 442 ​ ​ 1,010 Net cash generated from financing activities ​ ​ 62,618 ​ ​ 1,010 Currency effect on cash, cash equivalents and restricted cash ​ ​ ( 1,620 ) ​ ​ ( 943 ) Net increase / (decrease) in cash, cash equivalents and restricted cash ​ ​ 15,849 ​ ​ ( 35,776 ) Cash, cash equivalents and restricted cash at beginning of period ​ ​ 247,680 ​ ​ 380,726 Cash, cash equivalents and restricted cash at the end of period ​ $ 263,529 ​ $ 344,950 Cash and cash equivalents ​ $ 260,813 ​ $ 342,029 Restricted cash related to leasehold and other deposits ​ ​ 2,716 ​ ​ 2,921 Total cash, cash equivalents and restricted cash ​ $ 263,529 ​ $ 344,950 Supplemental cash flow disclosures: ​ ​ ​ ​ ​ ​ Cash paid for interest ​ $ ( 1,410 ) ​ $ ( 780 ) ​ 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 Securities and Exchange Commission (“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, 2021, are not necessarily indicative of the results to be expected for the full year ending December 31, 2021 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, 2020, filed with the SEC on March 1, 2021 . ​ 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, 2020, and the notes thereto, which are included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2020, filed with the SEC on March 1, 2021 . There have been no material changes in the Company’s significant accounting policies during the three months ended March 31, 2021. ​ 2.5 Recent accounting pronouncements ​ There have been no new accounting pronouncements or changes to accounting pronouncements during the three months ended March 31, 2021, as compared to the recent accounting pronouncements described in Note 2.3.22 of the Company’s Annual Report on Form 10-K for the year ended December 31, 2020 , 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, 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 will receive exclusive global rights to etranacogene dezaparvovec, the Company’s investigational gene therapy for patients with hemophilia B, (the “Product”). ​ Under the terms of the CSL Behring Agreement, the Company is entitled to receive a $ 450.0 million upfront cash payment upon the closing of the transaction contemplated by the CSL Behring Agreement and will be eligible to receive up to $ 1.6 billion in additional payments based on regulatory and commercial milestones. The CSL Behring Agreement also provides that the Company will be eligible to receive tiered double-digit royalties in a range of up to a low-twenties percent of net sales of the Product based on sales thresholds. Pursuant to the CSL Behring Agreement, the Company will be responsible for the completion of the HOPE-B clinical trial, manufacturing process validation, and the manufacturing supply of the Product until such time that these capabilities may be transferred to CSL Behring or its designated contract manufacturing organization. Concurrently with the execution of the CSL Behring Agreement, the Company and CSL Behring entered into a development and commercial supply agreement, pursuant to which, among other things, the Company will supply the Product to CSL Behring at an agreed-upon price. Clinical development and regulatory activities performed by the Company pursuant to the CSL Behring Agreement will be reimbursed by CSL Behring. CSL Behring will be responsible for global regulatory submissions and commercialization requirements for the Product. The effectiveness of the transaction contemplated by the CSL Behring Agreement was contingent on completion of review under antitrust laws in the United States, Australia, and the United Kingdom. As of March 31, 2021, such regulatory approvals had not been received in the United States. On May 5, 2021 the waiting period under the Hart-Scott-Rodino Antitrust Improvements Act of 1976 (the “HSR Act”) expired, and as such the CSL Behring Agreement became fully effective on May 6, 2021. As of March 31, 2021, the Company concluded it has no enforceable right to the upfront payment, the regulatory and sale milestone payments, or the royalties (together “CSL Behring License Revenue”) that the Company will receive in accordance with the CSL Behring Agreement, as all payments were contingent upon the successful completion of reviews, or the expiration of the waiting period, under the HSR Act, which had not occurred as of March 31, 2021. Therefore, the Company determined to not recognize any revenue in relation to the CSL Behring License Revenue, in accordance with ASC 606 during the three-month period ended March 31, 2021. In accordance with its existing license and other agreements, the Company is contractually required to pay in total a low to high single digit percentage of any upfront payment to its licensors and financial advisor (“License Fees”) following the closing of the transaction. The Company did no t record any License Fees for the three-month period ended March 31, 2021, as the Company had no t recognized the upfront payment as of this date. 7 Table of Contents The Company incurred $ 5.0 million of expenses related to the obligations related to the CSL Behring Agreement that had not been satisfied as of March 31, 2021. The Company capitalized these expenses as contract fulfillment costs (presented within Other current assets). As of March 31, 2021, the Company also recognized a $ 5.0 million receivable (presented within Accounts receivable) from CSL Behring for expenses for which the Company has a right of reimbursement. A contract liability was also recognized for the entire amount of expenses for which the Company has a right to reimbursement (presented within Accrued expenses and other current liabilities). In accordance with ASC 606 it cannot recognize any CSL Behring License Revenue as of this date. 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”). ​ The initial four-year research term under the collaboration terminated on May 21, 2019. On December 1, 2020, the Company and BMS amended the BMS CLA (“amended BMS CLA”). Under the amended BMS CLA, BMS is limited to four Collaboration Targets. BMS may until November 30, 2021 replace up to two of these four Collaboration Targets with up to two new targets in the field of cardiovascular disease. The Company continues to be eligible to receive research, development, and regulatory milestone payments of up to $ 217.0 million for each Collaboration Target, if defined milestones are achieved. ​ For as long as any of the four Collaboration Targets are being advanced, BMS may place a purchase order to be supplied with research, clinical and commercial supplies. Subject to the terms of the amended BMS CLA, BMS has the right to terminate the research, clinical and commercial supply relationships, and has certain remedies for failures of supply, up to and including technology transfer for any such failure that otherwise cannot be reasonably resolved. Both BMS and the Company may agree to a technology transfer of manufacturing capabilities pursuant to the terms of the amended BMS CLA. ​ The amended BMS CLA does not extend the initial four-year research term. 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) either (A) three years after the last replacement target has been designated by BMS during the one-year replacement period ending on November 30, 2021, or (B) November 30, 2023 if no replacement targets are designated. BMS continues to reimburse the Company for these services. ​ The Company evaluated the impact of the amended BMS CLA in relation to its performance obligation to provide access to BMS to its technology and know-how in the field of gene therapy and to participate in joint steering committee and other governing bodies (“License Revenue”). ​ The Company determined that its remaining performance obligation under the amended BMS CLA was immaterial and recognized the remaining balance of unrecognized License Revenue as of November 30, 2020. The Company includes variable consideration related to any research, development, and regulatory milestone payments, in the transaction price once it is considered probable that including these payments in the transaction price would not result in the reversal of cumulative revenue recognized. Due to the significant uncertainty surrounding the development of gene-therapy product candidates and the dependence on BMS’s performance and decisions, the Company does no t generally consider this probable and did not record any License Revenue during 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, 2021, and December 31, 2020: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 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, 2020 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash, cash equivalents and restricted cash ​ $ 247,680 ​ $ — ​ $ — ​ $ 247,680 ​ Cash and cash equivalents; restricted cash Total assets ​ $ 247,680 ​ $ — ​ $ — ​ $ 247,680 ​ ​ Liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Derivative financial instruments ​ ​ — ​ ​ — ​ ​ 2,645 ​ ​ 2,645 ​ Other non-current liabilities Total liabilities ​ $ — ​ $ — ​ $ 2,645 ​ $ 2,645 ​ ​ At March 31, 2021 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Assets: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Cash, cash equivalents and restricted cash ​ $ 263,529 ​ $ — ​ $ — ​ $ 263,529 ​ Cash and cash equivalents; restricted cash Total assets ​ $ 263,529 ​ $ — ​ $ — ​ $ 263,529 ​ ​ Liabilities: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Derivative financial instruments ​ $ — ​ $ — ​ $ 2,645 ​ $ 2,645 ​ Other non-current liabilities Total liabilities ​ $ — ​ $ — ​ $ 2,645 ​ $ 2,645 ​ ​ ​ Changes in Level 3 items during the three months ended March 31, 2021, are as follows: ​ ​ ​ ​ ​ ​ ​ Derivative ​ ​ financial ​ instruments ​ ​ (in thousands) Balance at December 31, 2020 ​ $ 2,645 Net (gains) / losses recognized in profit or loss ​ ​ — Balance at March 31, 2021 ​ $ 2,645 ​ ​ ​ ​ ​ 9 Table of Contents Derivative financial instruments ​ The Company issued derivative financial instruments related to its collaboration with BMS. ​ In 2015, the Company granted BMS two warrants that were subsequently terminated in connection with the amendment to the BMS CLA on December 1, 2020. ​ 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, 2021 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 determined 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, 2021 and December 31, 2020. 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, 2021 and December 31, 2020 was $ 2.6 million. ​ ​ ​ 5 Accrued expenses and other current liabilities ​ Accrued expenses and other current liabilities include the following items: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ March 31, ​ December 31, ​ 2021 2020 ​ ​ (in thousands) Accruals for services provided by vendors-not yet billed ​ $ 11,180 ​ $ 8,269 Personnel related accruals and liabilities ​ ​ 4,716 ​ ​ 7,687 Contract liability (see Note 3. "Collaboration arrangements") ​ ​ 5,000 ​ ​ 2,082 Total ​ $ 20,896 ​ $ 18,038 ​ ​ ​ ​ 10 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”), which was amended and restated on June 26, 2014, and again on May 6, 2016 (“2016 Amended Facility”). On December 6, 2018, the Company signed an amendment that both refinanced the then-existing $ 20.0 million 2016 Amended Facility and allowed the Company to draw down an additional $ 15.0 million (“2018 Amended Facility”). The 2018 Amended Facility extended the loan’s maturity date from May 1, 2020 until June 1, 2023. The interest-only period was initially extended from November 2018 to January 1, 2021 and was further extended to January 1, 2022 as a result of raising more than $ 90.0 million in equity financing in September 2019. The interest only period was again further extended to June 1, 2023 as a result of the January 2021 amendment (see below). The interest rate is adjustable and is the greater of (i) 8.85 % and (ii) 8.85 % plus the prime rate less 5.50 % per annum. Under the 2018 Amended Facility, the Company owes a back-end fee of 4.95 % of the outstanding debt. In addition, in May 2020 the Company paid a back-end fee of $ 1.0 million in relation to the 2016 Amended Facility. On January 29, 2021, the Company and Hercules amended the 2018 Amended Facility (“2021 Amended Facility”). Pursuant to the 2021 Amended Facility, Hercules agreed to an additional Facility of $ 100.0 million (“Tranche B”), increasing the aggregate principal amount of the term loan facilities from $ 35.0 million to up to $ 135.0 million. On January 29, 2021, the Company drew down $ 35.0 million of the Tranche B. The Company may draw down the remaining $ 65.0 million under the Tranche B in a series of one or more advances of not less than $ 20.0 million each until December 15, 2021. Advances under Tranche B bear interest at a rate equal to the greater of (i) 8.25 % or (ii) 8.25 % plus the prime rate, less 3.25 % per annum. The principal balance and all accrued but unpaid interest on advances under Tranche B is due on June 1, 2023, which date may be extended by the Company by up to two twelve-month periods. Advances under Tranche B may not be prepaid prior to July 29, 2021, following which the Company may prepay all such advances without charge. The Company owes a back-end fee of 4.85 % of amounts outstanding under Tranche B. The back-end fee is reduced if prepayment occurs at an earlier date. The amortized cost (including interest due presented as part of accrued expenses and other current liabilities) of the 2018 Amended Facility and 2021 Amended Facility was $ 71.0 million as of March 31, 2021, compared to $ 35.9 million amortized cost for the 2018 Amended Facility as of December 31, 2020, and is recorded net of discount and debt issuance costs. The foreign currency loss on the facilities in the three months ended March 31, 2021, was $ 3.2 million compared to a foreign currency loss of $ 0.7 million during the same period in 2020 for the 2018 Amended Facility. Interest expense associated with the 2018 Amended Facility and 2021 Amended Facility during the three months ended March 31, 2021 was $ 1.5 million, compared to $ 0.9 million during the same periods in 2020 for the 2018 Amended Facility. As a covenant in the 2018 Amended Facility and 2021 Amended 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. In combination with other covenants, the 2018 Amended Facility and 2021 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 $ 363.9 million with the exception of $ 97.6 million of cash and cash equivalents and other current assets held by uniQure N.V. The 2018 Amended Facility and 2021 Amended Facility contain 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, 2021, the Company was in material compliance with all covenants and provisions. ​ 11 Table of Contents 7 Shareholders’ Equity ​ On March 1, 2021, the Company entered into a Sales Agreement with SVB Leerink LLC (“SVB Leerink”) with respect to an at-the-market (“ATM”) offering program, under which the Company may, from time to time in its sole discretion, offer and sell through SVB Leerink, acting as agent, its ordinary shares, up to an aggregate offering price of $ 200.0 million. The Company will pay SVB Leerink a commission equal to 3 % of the gross proceeds of the sales price of all ordinary shares sold through it as sales agent under the Sales Agreement. Through March 31, 2021 the Company issued 859,885 ordinary shares at a weighted average price of $ 33.42 per share, with net proceeds of $ 27.6 million, after deducting underwriting discounts and net of offering expenses. The Company defers direct, incremental costs associated to this offering, except for the commission costs to SVB Leerink, which are a reduction to additional paid-in capital, and will deduct these costs from additional paid-in capital in the consolidated balance sheets proportionately to the amount of proceeds raised. As of March 31, 2021, $ 1.0 million of direct, incremental costs were deducted from additional paid-in capital. ​ 8 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 2018, the Company’s shareholders approved amendments of the 2014 Plan, increasing the shares authorized for issuance by 3,000,000 to a total of 8,601,471 . ​ 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, ​ ​ 2021 ​ 2020 ​ ​ (in thousands) Research and development ​ $ 2,674 ​ $ 2,382 Selling, general and administrative ​ ​ 3,080 ​ ​ 1,958 Total ​ $ 5,754 ​ $ 4,340 ​ Share-based compensation expense recognized by award type was as follows: ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Three months ended March 31, ​ ​ 2021 ​ 2020 ​ ​ (in thousands) Award type ​ ​ ​ ​ ​ ​ Share options ​ $ 2,840 ​ $ 2,208 Restricted share units ​ ​ 2,560 ​ ​ 1,444 Performance share units ​ ​ 354 ​ ​ 688 Total ​ $ 5,754 ​ $ 4,340 ​ As of March 31, 2021, 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 ​ $ 35,517 ​ 3.09 Restricted share units ​ ​ 26,227 ​ 2.40 Performance share units ​ ​ 1,241 ​ 0.83 Total ​ $ 62,985 ​ 2.76 ​ 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. 12 Table of Contents 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. The following tables summarize option activity under the Company’s 2014 Plans for the three months ended March 31, 2021: ​ ​ ​ ​ ​ ​ ​ ​ ​ Options ​ ​ Number of ​ Weighted average ​ ordinary shares exercise price ​ ​ ​ ​ ​ ​ Outstanding at December 31, 2020 ​ 2,659,279 ​ $ 28.13 Granted ​ 734,683 ​ $ 36.95 Forfeited ​ ( 40,440 ) ​ $ 43.85 Expired ​ ( 5,094 ) ​ $ 37.85 Exercised ​ ( 16,782 ) ​ $ 23.34 Outstanding at March 31, 2021 ​ 3,331,646 ​ $ 29.90 Thereof, fully vested and exercisable at March 31, 2021 ​ 1,718,923 ​ $ 20.19 Thereof, outstanding and expected to vest after March 31, 2021 ​ 1,612,723 ​ $ 40.24 ​ ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of options issued during the period (in $ millions) ​ ​ ​ $ 15.8 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 2021 2020 Expected volatility ​ 75 % ​ 70 % Expected terms ​ 10 years ​ 10 years Risk free interest rate ​ 1.21 % - 1.71 % ​ 1.44 % Expected dividend yield ​ 0 % ​ 0 % ​ Restricted share units (“RSUs”) ​ The following table summarizes the RSUs activity for the three months ended March 31, 2021: ​ ​ ​ ​ ​ ​ ​ ​ ​ RSU ​ ​ Weighted average ​ ​ Number of ​ grant-date fair ​ ​ ordinary shares ​ value Non-vested at December 31, 2020 ​ 467,344 ​ $ 43.56 Granted ​ 404,967 ​ $ 36.96 Vested ​ ( 136,721 ) ​ $ 38.63 Forfeited ​ ( 15,938 ) ​ $ 43.46 Non-vested at March 31, 2021 ​ 719,652 ​ $ 40.79 ​ ​ ​ ​ ​ ​ Total weighted average grant date fair value of RSUs granted during the period (in $ millions) ​ ​ ​ $ 15.0 ​ RSUs vest over one to three years . RSUs granted to non-executive directors vest one year from the date of grant. 13 Table of Contents Performance share units (“PSUs”) ​ The following table summarizes the PSUs activity for the three months ended March 31, 2021: ​ ​ ​ ​ ​ ​ ​ ​ ​ PSU ​ ​ Weighted average ​ ​ Number of ​ grant-date fair ​ ​ ordinary shares ​ value Non-vested at December 31, 2020 ​ 212,614 ​ $ 42.32 Vested ​ ( 132,368 ) ​ $ 33.09 Forfeited ​ ( 2,916 ) ​ $ 57.56 Non-vested at March 31, 2021 ​ 77,330 ​ $ 57.56 ​ The PSUs will vest on the third anniversary of the grant, subject to the grantee’s continued employment. ​ 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, 2021, 1,174 ordinary shares were issued under the ESPP compared to 1,801 during the same period in 2020. As of March 31, 2021, a total of 130,852 ordinary shares remain available for issuance under the ESPP plan compared to a total of 136,406 as of March 31, 2020. ​ 9 Income taxes ​ The Company released its valuation allowance against the Company’s deferred tax assets in the United States as of December 31, 2020. The Company recorded $ 0.2 million deferred tax expense in relation to its operations in the United States during the three month period ended March 31, 2021. The Company recorded a nil net deferred tax expense in the prior year as it had recorded a valuation allowance against its net deferred tax assets in the United States as of March 31, 2020. ​ The effective income tax rate of 0.5 % during the three months ended March 31, 2021 is substantially lower than the enacted rated of 25 % in the Netherlands as the Company recorded a valuation allowance against its net deferred tax assets in the Netherlands. Refer to Note 3 “Collaboration arrangements and concentration of credit risk” for discussion on the effectiveness of the CSL Behring Agreement. The effective income tax rate during the three months ended March 31, 2020 was 0 % as the Company had recorded a valuation allowance against all its net deferred tax assets. ​ The closing of the transaction contemplated by the CSL Behring agreement on May 6, 2021 is expected to materially impact the Company’s operating result as well as the taxable income for the year ended December 31, 2021 as well as in future periods. The Company expects to utilize a material portion of its net operating loss carryforwards in the Netherlands during 2021 as a result of closing the transaction. As of March 31, 2021 the Company expects to continue incurring tax losses in the years thereafter and expects to record a valuation allowance against all its Dutch net deferred tax assets as of December 31, 2021. The Company determined the impact which recognition of CSL Behring License Revenue is estimated to have, with regards to the expected effective tax rate of 0 % that was applied with respect to the Company’s Dutch operations as of March 31, 2021, is immaterial. ​ ​ ​ ​ ​ 14 Table of Contents 10 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, 2021 and March 31, 2020, respectively. In addition, the BMS warrants were not exercisable as of March 31, 2020 since this would have required the prior designation of Collaboration Targets by BMS. This would generally result in a lower number of potentially dilutive ordinary shares as some stock option grants as well as the BMS warrants would have been excluded. ​ The potentially dilutive ordinary shares are summarized below: ​ ​ ​ ​ ​ ​ ​ ​ March 31, ​ 2021 2020 ​ ​ (ordinary shares) BMS warrants (derecognized as of December 1, 2020 - see Note 4, "Fair value measurement") ​ — ​ 10,262,500 Stock options under 2014 Plans ​ 3,331,646 ​ 3,003,430 Non-vested RSUs and earned PSUs ​ 796,982 ​ 635,390 Stock options under previous option plan ​ 14,000 ​ 14,000 Employee share purchase plan ​ 729 ​ 681 Total potential dilutive ordinary shares ​ 4,143,357 ​ 13,916,001 ​ ​ ​ ​ 11 Subsequent events ​ Appointment of Chief Operating Officer ​ Effective May 17, 2021, Pierre Caloz will be appointed as Chief Operating Officer and will be based out of the Amsterdam facility. Mr. Caloz will be responsible for all Manufacturing Operations, Global Chemistry, Manufacturing and Controls development and innovation, and Supply Chain and Facilities. As a result, Alex Kuta, Ph.D., will transition from Executive Vice President, Operations to Executive Vice President, Quality and Regulatory. ​ Closing of Collaboration and Licensing transaction with CSL Behring (see also note 3) ​ On May 5, 2021, the waiting period under the HSR Act expired, and on May 6, 2021 the CSL Behring Agreement became fully effective. Under the CSL Behring Agreement, the upfront payment of $ 450.0 million was paid to the Company on May 7, 2021. Additionally, the Company is eligible to receive more than $ 300 million in regulatory and first commercial sale milestones, up to an additional $ 1.3 billion in commercial milestones, and tiered double-digit royalties of up to a low-twenties percentage of net sales of the Product arising from the collaboration. The Company contractually owes a single-digit percentage of revenue from the collaboration to its licensors. The Company expects to utilize a material portion of its net operating loss carryforwards in the Netherlands during 2021 as a result of closing the transaction contemplated by the CSL Behring Agreement. ​ The Company will be responsible for the completion of the HOPE-B clinical trial, manufacturing process validation, and the manufacturing supply of the Product until such time that these capabilities may be transferred to CSL Behring or its designated contract manufacturing organization. Clinical development and regulatory activities performed by the Company pursuant to the CSL Behring Agreement will be reimbursed by CSL Behring. CSL Behring will be responsible for global regulatory submissions and commercialization requirements for the Product. ​ ​ ​ ​ 15 Table of Contents