What changed in this filing

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Item 2. Management’s Discussion and Analysis

2021-10-25 compared with 2021-07-26 · 259 added, 217 removed, 368 unchanged (56% of the section changed)

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Acquisition of Corlieve Therapeutics

On June 21, 2021, we entered into a share and purchase agreement (“SPA”) to acquire all outstanding shares of Corlieve Therapeutics S.A.S (“Corlieve”).

Corlieve’s lead gene therapy program employs miRNA silencing technology to target suppression of aberrantly expressed kainate receptors in the hippocampus of patients with temporal lobe epilepsy (“TLE”).

On June 21, 2021, we entered into a share and purchase agreement (“SPA”) to acquire all of outstanding ordinary shares of Corlieve Therapeutics SAS (“Corlieve”), a privately held French gene therapy company (“Corlieve Transaction”).

Upon the closing of the Corlieve Transaction on July 30, 2021 (“Acquisition Date”), we acquired 97.7% of the outstanding ordinary shares of Corlieve in return for EUR 44.9 million ($53.3 million).

We are contractually required to acquire the remaining outstanding ordinary shares in February 2022 following the expiration of a minimum holding period (“Mandatorily redeemable shares”).

We recorded a liability related to these Mandatorily redeemable shares for an amount of EUR 0.7 million ($0.9 million) as of the Acquisition Date.

We financed the transaction from cash on hand.

Following its formation in November 2019, Corlieve obtained exclusive licenses to certain patents from two French research institutions that continue to collaborate with Corlieve and us.

At the same time, Corlieve also obtained an exclusive license from Regenxbio Inc.

for the use of AAV9 to deliver any sequence that affects the expression of the Glutamate inotropic receptor kainate type subunit 2 (“GRIK 2”) gene sequence in humans.

Corlieve and Regenxbio Inc.

simultaneously entered into a collaboration plan related to agreed joint preclinical research and development activities.

At the Acquisition Date, Corlieve and its Swiss subsidiary, Corlieve Therapeutics AG, employed seven employees.

Corlieve’s gene therapy program, AMT-260, employs miRNA silencing technology to target suppression of aberrantly expressed kainate receptors in the hippocampus of patients with temporal lobe epilepsy (“TLE”).

TLE affects approximately 1.3 million people in the U.S.

and Europe alone, of which approximately 800,000 patients are unable to adequately control acute seizures with currently approved anti-epileptic therapies.

and Europe alone, of which approximately 0.8 million patients are unable to adequately control acute seizures with currently approved anti-epileptic therapies.

Patients with refractory TLE experience increased morbidity, excess mortality, and poor quality of life.

The lead program will be known as AMT-260.

The transaction is subject to customary closing conditions as well as review by the French Ministry of Economy, Finance and Recovery (Ministère de l’Economie, des Finances et de la Relance) pursuant to articles L.151-3 and R.151-1 and seq.

of the French Code Monétaire et Financier.

Currently, the transaction is anticipated to be completed early in the third quarter of 2021.

Upon closing of the Corlieve Transaction we expect to pay EUR 46.3 million in cash to acquire all outstanding ordinary shares of Corlieve.

In accordance with the SPA we owe up to EUR 43.7 million in development milestones through Phase I/II and EUR 160.0 million in milestones associated with Phase III development and the approvals of AMT-260 in the U.S and European Union.

At our election we can pay up to 25% of such milestone payments in our ordinary shares.

The Corlieve transaction is expected to be accounted for as a business combination, which requires that assets acquired and liabilities assumed be recognized at their fair value as of the acquisition date.

Corlieve has an established license and collaboration agreement with REGENXBIO Inc.

that includes an exclusive license to AAV9 for the specific genetic target of AMT-260.

Under the license and collaboration agreement, REGENXBIO Inc.

is eligible to receive milestone payments and royalties on net sales of AMT-260.

In addition, Corlieve’s former and remaining shareholders are eligible to receive up to EUR 35.8 million ($42.5 million) upon the achievement of development milestones through Phase I/II and EUR 143.1 million ($169.9 million) upon the achievement of milestones associated with Phase III development and obtaining approval to commercialize AMT-260 in the United States of America and the European Union.

We may elect to pay up to 25% of such milestone payments through the issuance of our ordinary shares.

We recorded a EUR 20.2 million ($24.0 million) liability related to these contingent consideration payments.

We primarily allocated the total consideration of EUR 65.8 million ($78.1 million) consisting of the cash paid upon the Acquisition Date, the payment we owe in relation to the Mandatorily redeemable shares and the contingent consideration payments to the identifiable intangible assets related to the in-process research and development efforts of AMT-260 (“IPR&D intangible asset”).

The IPR&D intangible asset’s provisional fair value has been determined at EUR 53.3 million ($63.3 million) as of the Acquisition Date.

We recognized a EUR 13.3 million ($15.8 million) deferred tax liability in relation to this IPR&D intangible asset.

We allocated the excess of EUR 23.8 million ($28.2 million) of the total consideration over the net assets acquired to goodwill.

CSL Behring commercialization and license agreement

On June 24, 2020, (“Signing”), uniQure biopharma B.V., a wholly-owned subsidiary of uniQure N.V., entered into a commercialization and license agreement (as amended, the “CSL Behring Agreement”) with CSL Behring LLC (“CSL Behring”) pursuant to which CSL Behring received exclusive global rights to etranacogene dezaparvovec, our investigational gene therapy for patients with hemophilia B (the “Product”).

The effectiveness of the transaction contemplated by the CSL Behring Agreement was contingent on the completion of review under the antitrust laws in the United States, Australia, and the United Kingdom.

The transaction had previously been cleared by the Australian and United Kingdom antitrust authorities and became fully effective on May 6, 2021, after the waiting period under the Hart-Scott-Rodino Antitrust Improvements Act of 1976 expired on May 5, 2021.

As from May 6, 2021, CSL Behring will be responsible for the development and commercialization of the Product.

We agreed to complete the validation of the current manufacturing process as well as to complete the development and validation of a next generation manufacturing process.

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 (as amended, the “CSL Behring Agreement”) with CSL Behring LLC (“CSL Behring”) pursuant to which CSL Behring received exclusive global rights to etranacogene dezaparvovec, our 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 expired on May 5, 2021.

CSL Behring is responsible for the development and commercialization of the Product.

We agreed to complete the validation of the current manufacturing process as well as to the development and validation of a next generation manufacturing process.

We will be entitled to receive a development milestone payment if we complete these activities in accordance with an agreed development plan and timeline.

CSL Behring will also be reimbursing us for our services to facilitate the completion of the HOPE-B clinical trial.

On Signing, we and CSL Behring also entered into a development and commercial supply agreement, pursuant to which, among other things, we will supply the Product to CSL Behring at an agreed-upon price commensurate with the stand-alone selling price (“SSP”).

On the Signing Date, we and CSL Behring also entered into a development and commercial supply agreement, pursuant to which, among other things, we will supply the Product to CSL Behring at an agreed-upon price commensurate with the stand-alone selling price (“SSP”).

We will be responsible to supply the Product until such time that these capabilities may be transferred to CSL Behring or its designated contract manufacturing organization.

We recorded $462.4 million, including a $450.0 million upfront cash payment following the closing of the CSL Behring Agreement as license revenue in the three and six months ended June 30, 2021.

We recorded $462.4 million, including a $450.0 million upfront cash payment, following the closing of the CSL Behring Agreement as license revenue in the nine months ended September 30, 2021 (nil for three months ended September 30, 2021).

We are eligible to receive more than $0.3 billion in regulatory, development, and first commercial sale milestones, $1.3 billion in additional commercial milestones, and tiered double-digit royalties of up to a low-twenties percentage of net product sales arising from the collaboration.

Upon closing, we contractually owed to our licensors $16.7 million of the upfront payment received from CSL Behring.

The payments we received significantly increased our cash and cash equivalents position to $677.3 million as of June 30, 2021.

The payments we received significantly increased our cash and cash equivalents position to $578.5 million as of September 30, 2021.

This is expected to fund our operations into the first half of 2024 (assuming a full repayment of funds borrowed from Hercules Growth Capital, Inc.

under our term loan facilities by 2023, as well as payments we expected to make in relation to our acquisition of Corlieve).

We expect that the achievement of the $0.3 billion regulatory, first commercial sales and development milestones would further extend our runway by 12 to 18 months.

under our term loan facilities by 2023).

We expect that if we were to achieve the $0.3 billion regulatory, first commercial sales and development milestone payments, our runway would be further extended by 12 to 18 months.

Hemophilia B program – Etranacogene dezaparvovec (AMT-061)

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We are currently conducting a pivotal study in patients with severe and moderately-severe hemophilia B.

On June 22, 2021, we presented new data from the HOPE-B pivotal study related to the 52-week period post-infusion.

In September 2021, we completed the last patient’s 78-week follow-up visit in the HOPE-B Phase III pivotal study, which enrolled a total of 54 patients.

On June 22, 2021, we presented new data from the HOPE-B study related to the 52-week period post-infusion.

Data showed that participants continued to demonstrate durable, sustained increases in FIX activity at 52-weeks post-infusion with a mean FIX activity of 41.5 percent of normal, as measured by a one-stage APTT-based clotting assay, compared to a mean FIX activity of 39.0 percent of normal at 26-weeks of follow-up.

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The annualized rate of spontaneous bleeding requiring treatment was also significantly reduced by 85 percent from a prospectively collected 1.16 at baseline to 0.18 bleeds per year during the 52-week period (p-value <0.0001).

Usage of FIX replacement therapy (IU/year and infusions/year) in all patients declined 96 percent during the 52-week period, with 52 of 54 patients (96 percent) successfully discontinuing their prophylactic infusions.

As previously announced, of the two non-responders, one patient only received a partial dose (less than 10 percent of the dosage) due to an infusion reaction and a second patient had an unusually high pre-existing NAb titer of 3,212, which is expected in less than 1 percent of the general population.

We expect all patients to complete their 78-week follow-up visits by the end of the third quarter of 2021, and we expect a BLA to be submitted to the FDA and a MAA to be submitted to EMA in the first quarter of 2022.

All patients completed their 78-week follow-up visits by the end of September 2021, and we expect a Biologics License Application (“BLA”) to be submitted to the U.S.

Food and Drug Administration (“FDA”) and a marketing authorization application (“MAA”) to be submitted to EMA in the first half of 2022.

On December 21, 2020, our clinical trials of etranacogene dezaparvovec had been placed on clinical hold by the FDA following a preliminary diagnosis of hepatocellular carcinoma (“HCC”), a form of liver cancer, in one patient in the HOPE-B trial who was treated with etranacogene dezaparvovec.

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AMT-130 has received Orphan Drug and Fast Track designations from the FDA and Orphan Medicinal Product Designation from the EMA.

On April 5, 2021 we announced the completion of enrollment of all ten patients in the first dose cohort of our Phase Ib/II clinical trial of AMT-130.

On April 5, 2021, we announced the completion of enrollment of all 10 patients in the first dose cohort of our Phase I/II clinical trial of AMT-130.

The study is a double-blinded, randomized, and controlled clinical trial being conducted in the United States in a total of 26 patients.

On May 27, 2021, we announced that the study’s independent Data Safety Monitoring Board (“DSMB”) recommended we continue patient dosing after reviewing safety data from all patients in the first dose cohort.

On June 16, 2021, we announced that the first two patient procedures were completed in the second, higher-dose cohort, which will include 16 patients.

The Phase I/II study is a double-blinded, randomized, and controlled clinical trial being conducted in the United States.

To date, seven patients have been treated with AMT-130 across both dose cohorts, and five patients have received an imitation surgical procedure that will serve as a control.

On April 5, 2021 we also announced the initiation of a Phase Ib/II clinical trial in Europe.

The planned Phase Ib/II study is expected to begin enrolling patients in the second half of 2021.

On each of June 16 and August 30, 2021, we completed two patient procedures in the second, higher-dose cohort, which will include a total of 16 patients.

In the study to date, a total of 14 blinded patient procedures have been completed across both dose cohorts, including eight patients treated with AMT-130 and six patients receiving imitation surgery.

Also on April 5, 2021, we announced plans for a Phase Ib/II clinical trial in Europe which, with enrollment beginning before the end of this year.

This open-label study will enroll 15 patients with early manifest Huntington’s disease across two dose cohorts.

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study, the European study is intended to establish safety, proof of concept, and the optimal dose of AMT-130 to take forward into Phase III development or into a confirmatory study should an accelerated registration pathway be feasible.

Research and Development Day

On June 22, 2021, we held a research and development day to outline our vision and strategy of leveraging our AAV engine to deliver gene therapies within our key focus areas.

We provided updates on our Fabry (AMT-191) and SCA3 (AMT-150) programs and announced additional new product candidates, including AMT-210 for Parkinson’s disease, AMT-240 for Alzheimer’s disease, and AMT-161 for Amyotrophic Lateral Sclerosis (“ALS”).

These new programs are key components of our plan to expand our clinical pipeline.

We also announced our plans to construct a second cGMP manufacturing facility located in Amsterdam, The Netherlands.

European Society of Gene and Cell Therapy (“ESGCT”)

In October 2021, the Company presented preclinical data related to four programs at the ESGCT 28 th Annual Meeting:

● AMT-191, a gene-therapy candidate for the treatment of Fabry disease, confirming efficiency and cross correction in a Fabry mouse model, with increased gamma-linolenic acid in the liver, kidney, heart, and brain and normalized lysoglobotriaosylceramide3 levels in main target organs;

● AMT-230, an AAV gene therapy candidate for Parkinson’s Disease, reduces alpha synuclein in dopaminergic neurons and rescues motor phenotypes in a genetic model of Parkinson’s Disease;

● AMT-161, an AAV gene-therapy for the treatment of Amyotrophic lateral sclerosis, reduces the expression of C9ORF72 in human induced pluripotent stem cells derived neurons, reduces C9ORF72-containing ribonucleic acid (“RNA”) foci in a model of the disease and is distributed to relevant regions of the spinal cord and brain when expressed in non-human primates;

● AMT-260, a gene therapy candidate for temporal lobe epilepsy, reduces the expression of GluK2 in cortical neurons, reduces epileptiform activity and hyperlocomotion in a preclinical model of epilepsy and blocks epileptiform discharges in organotypic slices from patients with TLE.

Covid pandemic

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Accordingly, we had mandated a work-from-home policy since March 2020 for all non-essential employees at our Amsterdam and Lexington facilities and had implemented additional protocols for our essential employees.

Effective May 29, 2021, Massachusetts has lifted all industry restrictions, with the exceptions of remaining face-covering requirements for all public and private transportation systems and facilities housing vulnerable populations, and capacity has been increased to 100% for all industries.

Effective May 29, 2021, Massachusetts lifted all industry restrictions, with the exceptions of remaining face-covering requirements for all public and private transportation systems and facilities housing vulnerable populations, and capacity has been increased to 100% for all industries.

Furthermore, the state of emergency was lifted on June 15, 2021.

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We have implemented a mandatory Covid PCR testing protocol in our Lexington facility effective February 2021 that requires employees to have tested negative for Covid prior to entering the facility.

Also in our Lexington facility, allowed occupancy has been increased to 100% in line with the permitted capacity guidelines and all employees are allowed to work at the Lexington facility subject to social distancing protocols, and a daily health screening and compliance with our Covid PCR testing policy for unvaccinated employees.

All employees that are not essential employees, however, remain able to work remotely until December 31, 2021, and we have been operating significantly below 100% capacity.

At least until August 1, 2021, for purposes of monitoring Covid surges due to relaxation of requirements, no employee or contractor may enter the Lexington facility unless they are either:

Effective April 2021, we implemented a policy whereby no employee or contractor may enter the Lexington facility unless they are either:

(i) fully vaccinated;

or (ii) have taken an approved test for Covid and obtained a negative result.

On June 26, 2021, the Dutch government announced updated measures.

Since July 1, we allow for an occupancy rate of 50% at our Amsterdam site as well as the limited presence of visitors.

We continue to operate our laboratories at our Amsterdam site to comply with social distancing rules and to ensure the health and well-being of our employees under the current circumstances.

Employees that can continue to work from home are encouraged to do so through at least August 2021, partly in conjunction with the ongoing expansion of our laboratory space.

or (ii) have taken an approved test for Covid and obtained a negative result, and we expect that policy will remain in effect at least until December 31, 2021.

Also, in our Lexington facility, allowed occupancy has been increased to 100% in line with the permitted capacity guidelines and all employees are allowed to work at the Lexington facility subject to social distancing protocols, and a daily health screening and compliance with our Covid PCR testing policy for unvaccinated employees.

All employees that are not essential employees, however, remain able to work remotely until December 31, 2021, and we have been operating our Lexington facility significantly below 100% capacity.

On September 14, 2021, the Dutch government announced updated Covid-related measures effective as of September 25, 2021.

These updated measures require employees to work from home if possible and grant employers discretion with respect to the division of time spent between working from home or on site.

The mandatory rule to maintain 1.5 meters distance from others is also amended to a strong recommendation to maintain 1.5 meters distance from other people.

From November 1, 2021, employees are expected to be required at our Amsterdam office at least one day a week under our new remote working policy.

The broader implications of Covid, including the implications from the various variants, on our results of operations and overall financial performance remain uncertain.

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However, we may experience more pronounced disruptions in our operations in the future.

As of December 31, 2020, a $35.0 million term loan was outstanding in accordance with the Second Amended and Restated Loan and Security Agreement (the “2018 Amended Facility”) between us and Hercules Capital, Inc.

(“Hercules”).

On January 29, 2021, we 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, we drew down $35.0 million of the Tranche B.

We 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 us by up to two twelve-month periods.

Advances under the 2021 Amended Facility may not be prepaid until July 29, 2021, following which we may prepay all such advances without charge.

In addition to Tranche B, the 2021 Amended Facility also extends the interest only payment period of the previously funded $35.0 million term loan from January 1, 2022 to June l, 2023.

End of term charges in respect of advances under the 2021 Amended Facility range from 1.65% to 6.85%, depending on the maturity date.

On March 1, 2021, we entered into a Sales Agreement with SVB Leerink LLC (“SVB Leerink”) with respect to an at-the-market (“ATM”) offering program, under which we may, from time to time in our sole discretion, offer and sell through SVB Leerink, acting as agent, our ordinary shares, up to an aggregate offering price of $200.0 million.

We 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 a sales agent under the Sales Agreement.

In March and April of 2021, we issued 921,730 ordinary shares at a weighted average price of $33.52 per share, with net proceeds of $29.6 million, after deducting underwriting discounts and net of offering expenses.

In February 2021, we commenced the expansion of our Amsterdam site to build additional laboratories to support the expansions of our research and development activities as well the construction of a cleanroom designed to be capable of manufacturing cGMP materials at a 500-liter scale.

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The lease expires in October 2028 and includes an option to break the lease on October 31, 2023.

On May 17, 2021, Pierre Caloz was appointed as Chief Operating Officer.

Caloz oversees all manufacturing operations, global CMC development and innovation, supply chain, and facilities.

On June 15, 2021, Christian Klemt was appointed as Chief Financial Officer.

Klemt was our Chief Accounting Officer from August 2017 to June 2021, and he will continue to serve as general manager of our Amsterdam site.

Matthew Kapusta, who has been our Chief Executive Officer since December 2016 and had been our Chief Financial Officer from January 2015 to June 2021, will continue to serve as our Chief Executive Officer.

In connection with his transition to Chief Financial Officer, Mr.

Klemt will also serve as our Principal Financial Officer.

On June 16, 2021, our shareholders voted to approve the reappointment of Mr.

David Meek and Ms.

Paula Soteropoulos as non-executive directors of the Board of Directors.

Meek has been appointed chairman of the Board.

Philip Astley-Sparke did not stand for reappointment and retired from the Board on June 16, 2021.

On October 21, 2021, we held an Extraordinary General Meeting of our shareholders and Ms.

Jacques was appointed to the Board of Directors (the “Board”).

Jacques will also serve as a member of the Audit Committee of the Board effective as of October 21, 2021.

Intellectual Property

On May 11, 2021, Pfizer, Inc.

filed three petitions seeking Inter Partes Review of U.S.

filed three petitions in the United States Patent & Trademark Office (“USPTO”) seeking Inter Partes Review of U.S.

9,982,248 (the “’248 Patent”) and 10,465,180 (the “’180 Patent” and together with the ‘248 Patent, the “Patents”).

The petitions collectively seek to invalidate all claims of the Patents, which relate to the expression of factor IX protein using a modified “Padua” polypeptide having a leucine in position 338.

We are in the process of responding to the petitions.

In August 2021, we filed our responses asking the USPTO to deny institution of the IPR proceedings.

We are awaiting a decision by the USPTO on whether to institute these proceedings.

Financial Overview

Key components of our results of operations include the following:

Three months ended June 30,

Six months ended June 30,

Three months ended September 30,

Nine months ended September 30,

(in thousands)

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Selling, general and administrative expenses

Net income / (loss)

As of June 30, 2021, and December 31, 2020, we had cash and cash equivalents of $677.3 million and $244.9 million, respectively.

We had a net income of $399.5 million and $357.9 million in the three and six months ended June 30, 2021, compared to a net loss of $42.6 million and $70.6 million for the same periods in 2020.

As of June 30, 2021, and December 31, 2020, we had accumulated deficits of $426.8 million and $784.7 million, respectively.

We recorded a net income in the three and six months ended June 30, 2021 as a result of the closing of the CSL Behring transaction on May 6, 2021.

Net (loss) / income

As of September 30, 2021 and December 31, 2020, we had cash and cash equivalents of $578.5 million and $244.9 million, respectively.

We had a net loss of $36.5 million and net income of $321.4 million in the three and nine months ended September 30, 2021, respectively, compared to a net loss of $53.8 million and $124.3 million for the same periods in 2020.

As of September 30, 2021 and December 31, 2020, we had accumulated deficits of $463.4 million and $784.7 million, respectively.

We recorded a net loss in the three months ended September 30, 2021, and we recorded net income in the nine months ended September 30, 2021, as a result of closing the CSL Behring transaction on May 6, 2021.

We anticipate that our expenses will increase substantially as we:

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● maintain, expand, and protect our intellectual property portfolio, including in-licensing additional intellectual property rights from third parties;

● make potential future milestone payments related to the acquisition of Corlieve, if any.

See “Results of Operations” below for a discussion of the detailed components and analysis of the amounts above.

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GAAP and pursuant to the rules and regulations promulgated by the SEC we make assumptions, judgments and estimates that can have a significant impact on our net income/loss and affect the reported amounts of certain assets, liabilities, revenue and expenses, and related disclosures.

On an ongoing basis, we evaluate our estimates and judgments, including those related to the treatment of the CSL Behring Agreement, our arrangements with Bristol-Myers Squibb (“BMS”), including the amended collaboration and license agreement that we entered into with BMS in December 2020 (the “amended BMS CLA”), share-based payments, corporate income taxes related to valuation allowance and accounting for operating leases under ASC 842.

On an ongoing basis, we evaluate our assumptions, estimates and judgments, including those related to what we believe to be our critical accounting policies:

● the treatment of the CSL Behring Agreement,

● our arrangements with Bristol-Myers Squibb (“BMS”), including the amended collaboration and license agreement that we entered into with BMS in December 2020 (the “amended BMS CLA”);

● the treatment of the Corlieve Transaction;

● share-based payments;

● corporate income taxes related to valuation allowance;

● accounting for operating leases under ASC 842.

We base our assumptions, judgments and estimates on historical experience and various other factors that we believe to be reasonable under the circumstances, the results of which form the basis for making judgments about the carrying values of assets and liabilities that are not clear from other sources.

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In making estimates and judgments, management employs critical accounting policies.

During the six months ended June 30, 2021, there were no material changes to our critical accounting policies as reported in our Annual Report on Form 10-K for the year ended December 31, 2020, which was filed with the SEC on March 1, 2021 , with the exception of determining the accounting treatment in accordance with ASC 606 related to the CSL Behring Agreement as discussed below.

We believe that the assumptions, judgments, and estimates related to the treatment of the CSL Behring Agreement, the amended BMS CLA, share-based payments, corporate income taxes related to valuation allowance, and accounting for operating leases under ASC 842 to be our critical accounting policies.

The preparation of our consolidated financial statements for the three- and six- month period ended June 30, 2021, required us to analyze the accounting treatment of the CSL Behring Agreement that we entered into on June 24, 2020 (“Signing”).

During the nine months ended September 30, 2021, there were no material changes to our critical accounting policies as reported in our Annual Report on Form 10-K for the year ended December 31, 2020, which was filed with the SEC on March 1, 2021 , with the exceptions of determining the accounting treatment in accordance with ASC 805 related to the Corlieve Transaction and determining the accounting treatment in accordance with ASC 606 related to the CSL Behring Agreement.

CSL Behring Agreement

The preparation of our consolidated financial statements for the three- and nine- month period ended September 30, 2021, required us to analyze the accounting treatment of the CSL Behring Agreement.

The effectiveness of the transaction had been contingent on completion of review under antitrust laws in the United States, Australia, and the United Kingdom.

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(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”).

We continued to develop the Product between Signing and Closing and performed certain reimbursable activities to fulfill the transfer of the global rights (“Additional Covenants” and together with the License the “License Sale”).

We continued to develop the Product between the Signing Date and Closing and performed certain reimbursable activities to fulfill the transfer of the global rights (“Additional Covenants” and together with the License the “License Sale”).

We determined that the fixed upfront payment of $450.0 million and the $12.4 million that we received in relation to the Additional Covenants should be allocated to the License Sale.

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We determined that the sale of the License was completed on May 6, 2021, when we transferred the License and CSL Behring assumed full responsibility for the development and commercialization of the Product.

At Closing we evaluated the amount of potential payments and the likelihood that the payments will be received.

At Closing we evaluated the amounts of potential payments and the likelihood that the payments will be received.

We utilized the most likely amount method to estimate the variable consideration to be included in the transaction price.

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We will include payments related to sales milestones in the transaction price when their achievement becomes probable, and we will include royalties on the sale of Product once these have been earned.

We recognized $462.4 million of revenues related to the License Sale in the three and six months ended June 30, 2021

We recognized nil and $462.4 million of revenues related to the License Sale in the three and nine months ended September 30, 2021, respectively.

We determined that the variable milestone payment related to Manufacturing Development Services should be allocated to the Manufacturing Development performance obligation.

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Since we cannot control the timing or outcome of any regulatory decisions, we concluded that we would recognize revenue related to this payment when it becomes probable that the milestone has been achieved.

We did not recognize any revenue related to Manufacturing Development during the three and six months ended June 30, 2021.

We recognized $0.4 million of collaboration revenue in the three and six months ended June 30, 2021, compared to nil in the same periods in the prior year.

We did not recognize any revenue related to Manufacturing Development during the three and nine months ended September 30, 2021.

We recognized $0.5 million and $0.9 million of collaboration revenue in the three and nine months ended September 30, 2021, respectively, compared to nil in the same periods in the prior year.

We generate such collaboration revenue from services rendered in relation to completing the HOPE-B clinical trial on behalf of CSL Behring.

CSL Behring may request additional development services or to request us to support the transfer of manufacturing to a party designated by CSL Behring.

CSL Behring may request additional development services or to request that we support the transfer of manufacturing to a party designated by CSL Behring.

These collaboration services will be reimbursed at the pre-agreed full-time-employee rate (“FTE-rate”).

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We allocated part of the release to the tax benefit of share issuance cost incurred in 2014, 2015, 2017 and 2018.

This resulted in an increase of additional paid- in capital as well as the recognition of deferred tax expenses of $3.0 million during the three and six months ended June 30, 2021.

This resulted in an increase of additional paid- in capital as well as the recognition of deferred tax expenses of $3.0 million during the nine months ended September 30, 2021 (nil for three months ended September 30, 2021).

Based on changes to Dutch tax law enacted in June 2021 our remaining net operating tax loss related to 2019 can be carried forward indefinitely.

We continue to expect incurring tax losses for the foreseeable future including 2021.

As such, we retain our full valuation allowance related to the remaining net deferred asset as of June 30, 2021.

We continue to expect to incur tax losses for the foreseeable future, including 2021.

As such, we retain our full valuation allowance related to the remaining net deferred asset as of September 30, 2021.

Corlieve Transaction

The preparation of our consolidated financial statements for the three- and nine- month period ended September 30, 2021, required us to analyze the accounting treatment for the Corlieve Transaction.

We evaluated whether or not the Corlieve Transaction should be accounted for as a business combination or asset acquisition by first applying a screen test to determine if substantially all of the fair value of the gross assets acquired is concentrated in a single identifiable asset or group of similar identifiable assets.

Based on the provisional fair values of the gross assets acquired, we determined the screen test was not met.

We further analyzed whether or not the acquired inputs and processes that have the ability to create outputs would meet the definition of a business.

Significant judgment is required in the application of the screen test to determine whether an acquisition is a business combination or an acquisition of assets.

We performed the screen test using provisional fair values.

The finalization of the valuation might result in a different outcome of the screen test.

In this case, we would be required to account for the transaction as an asset acquisition.

In accordance with ASC 805, we in this case, among others, would not record any goodwill and expense all identifiable intangible assets without alternative future use.

Accounting for business combinations requires management to make significant estimates and assumptions as of the Acquisition Date which are inherently uncertain.

We identified various licenses that combined with the results of the research and development activities conducted in relation to AMT-260 since formation of Corlieve in 2019 constitute an IPR&D intangible asset.

The IPR&D intangible asset was measured at its fair value as of the Acquisition Date.

We calculated the fair value of the IPR&D intangible asset using a present value model based on expected cash flows.

Estimating the amounts and timing of cash flows required to complete the development of AMT-260 as well as net sales, cost of goods sold, and sales and marketing costs involved considerable judgment and uncertainty.

The expected cash flows are materially impacted by the probability of successfully completing the various stages of development (i.e., dosing of first patient in clinical trial, advancing into late-stage clinical development and obtaining approval to commercialize a product candidate) as well as the weighted average cost of capital of 10.4% used to discount the expected cash flows.

Based on all of these assumptions, we estimated the fair value of the IPR&D intangible asset at EUR 53.3 million ($63.3 million) as of the Acquisition Date.

Unanticipated events and circumstances may occur that could affect either the accuracy or validity of such assumptions, estimates or actual results.

The IPR&D intangible asset is accounted for as indefinite-lived intangible asset and is measured at the fair value of the incomplete research project acquired as of the Acquisition Date.

The IPR&D intangible asset is considered to be indefinite-lived until the completion or abandonment of the associated research and development efforts and is not amortized.

If and when development is complete, which generally occurs when regulatory approval to market a product is obtained, the associated assets would be deemed finite-lived and would then be amortized based on an estimate of its remaining useful life.

In case of abandonment, the IPR&D intangible asset would be written-off.

In accordance with ASC 350, Intangibles – Goodwill and Other, we test indefinite-lived intangible assets for impairment on an annual basis and between annual tests if we become aware of any events occurring or changes in circumstances that would indicate the fair value of the asset is below its carrying amount.

As of September 30, 2021, no impairment trigger of indefinite-lived intangible assets was identified.

Goodwill represents the excess of the consideration transferred over the fair value of assets acquired and liabilities assumed in a business combination.

Goodwill is not amortized but is evaluated for impairment on an annual basis and between annual tests if we become aware of any events occurring or changes in circumstances that would more likely than not reduce the fair value of the reporting unit below its carrying amount.

As of September 30, 2021, no impairment trigger of goodwill was identified.

We recorded contingent consideration related to amounts potentially payable to Corlieve’s former shareholders.

The amounts payable in accordance with the SPA are contingent upon realization of certain milestones associated with the TLE research program.

Contingent consideration is measured at fair value at the Acquisition Date with changes in fair value recognized in the consolidated statements of operations in research and development expenses.

Changes in contingent consideration can result from changes in the assumed achievement and timing of estimated milestones, the estimated timing in which milestones are achieved and the discount rate used to estimate the fair value of the liability.

In the absence of new information, changes in fair value reflect the passage of time towards achievement of the milestones.

We recognize revenue when the customer obtains control of promised goods or services, in an amount that reflects the consideration which we expect to receive in exchange for those goods or services.

18 unchanged sentences

Following the Closing of the CSL Behring agreement, we recognize license revenue related to the License Sale of the global rights to the Product.

We evaluated that our performance obligation related to the License Sale was satisfied on Closing and recognized $462.4 million in license revenue related to a $450.0 million upfront payment and $12.4 million of payments in relation to Additional Covenants.

We determined that our performance obligation related to the License Sale was satisfied on Closing and recognized $462.4 million in license revenue related to a $450.0 million upfront payment and $12.4 million of payments in relation to Additional Covenants.

We will recognize additional license revenue in relation to the License Sale when it becomes probable that regulatory and sales milestone events will be achieved as well as when royalties on sales of Product have been earned.

19 unchanged sentences

● costs incurred for laboratory research, preclinical and nonclinical studies, clinical trials, statistical analysis and report writing, and regulatory compliance costs incurred with clinical research organizations and other third-party vendors;

● Costs incurred to conduct consistency and comparability studies;

● costs incurred to conduct characterization, consistency and comparability studies;

● costs incurred for the development and improvement of our manufacturing processes and methods;

● Costs associated with our research activities for our next-generation vector and promoter platform;

● Costs associated with the rendering of collaboration services as well as the continued development of Product between Signing and Closing;

● costs associated with research activities for enabling technology platforms, such as next-generation vectors, promoters and re-administration of gene therapies;

● costs associated with the rendering of collaboration services as well as the continued development of Product between the Signing Date and Closing;

● payments related to identifiable intangible assets without an alternative future use;

● facilities, depreciation, and other expenses, which include direct and allocated expenses for rent and maintenance of facilities, insurance, and other supplies;

● changes in the fair value of liabilities recorded in relation to our acquisition of Corlieve.

Our research and development expenses may vary substantially from period to period based on the timing of our research and development activities, including manufacturing campaigns, regulatory submissions and enrollment of patients in clinical trials.

17 unchanged sentences

Results of Operations

Comparison of the three months ended June 30, 2021 and 2020

The following table presents a comparison of our results of operations for the three months ended June 30, 2021 and 2020.

Three months ended June 30,

Comparison of the three months ended September 30, 2021 and 2020

The following table presents a comparison of our results of operations for the three months ended September 30, 2021 and 2020.

Three months ended September 30,

(in thousands)

1 unchanged sentence

Operating expenses:

Cost of contract revenues

Research and development expenses

2 unchanged sentences

Other expense

Income / (loss) from operations

Loss from operations

Other non-operating items, net

Net income / (loss) before income tax expense

Net loss before income tax expense

Income tax expense

Net income / (loss)

Our revenue for the three months ended June 30, 2021 and 2020 was as follows:

Three months ended June 30,

Our revenue for the three months ended September 30, 2021 and 2020 was as follows:

Three months ended September 30,

(in thousands)

2 unchanged sentences

Total revenues

We recognized $462.4 million in license revenue related to the License Sale on Closing of the CSL Behring Agreement in May 2021.

We did not recognize any such license revenue related to the CSL Behring Agreement in the three months ended June 30, 2020.

We recognized $1.5 million in license revenue related to upfront payments and target designation fees received from BMS in 2015 under the BMS CLA for the three months ended June 30, 2020.

We did not recognize any license revenue under the amended BMS CLA during the three months ended June 30, 2021.

We recognized $1.5 million collaboration revenue in the three months ended June 30, 2021, compared to $0.0 million for the same period in 2020.

The CSL Behring transaction closed on May 6, 2021.

We did not recognize any license revenue related to the CSL Behring Agreement for the three months ended September 30, 2021.

Additionally, we did not recognize any license revenue related to the CSL Behring Agreement in the three months ended September 30, 2020.

We recognized $1.8 million of license revenue related to upfront payments and target designation fees received from BMS in 2015 under the BMS CLA for the three months ended September 30, 2020.

We did not recognize any license revenue under the amended BMS CLA during the three months ended September 30, 2021.

We recognized $2.0 million of collaboration revenue in the three months ended September 30, 2021, compared to $0.0 million for the same period in 2020.

Since May 6, 2021, we recognize collaboration revenue related to services we provide in accordance with the CSL Behring Agreement.

Our collaboration revenue increased further as a result of increased services provided to BMS following our December 2020 amendment of the BMS CLA.

Cost of contract revenues

We recognized $23.2 million in cost of contract revenues for the three months ended June 30, 2021, compared to nil the same period in 2020.

We recorded $16.7 million of expenses related to payments owed to our licensors on Closing as well as $6.5 million of other external expenses incurred to fulfill the License Sale to CSL Behring.

Research and development expenses

Research and development expenses for the three months ended June 30, 2021 were $32.7 million, compared to $28.4 million for the same period in 2020.

Research and development expenses for the three months ended September 30, 2021 were $36.4 million, compared to $36.3 million for the same period in 2020.

Other research and development expenses are separately classified in the table below.

These are not allocated as they are deployed across multiple projects under development.

Three months ended June 30,

These other expenses are not allocated as they are deployed across multiple projects under development.

Three months ended September 30,

(in thousands)

7 unchanged sentences

Other expenses

Fair value changes related to contingent consideration

Total other research and development expenses

2 unchanged sentences

Etranacogene dezaparvovec (AMT-060/061)

In the three months ended June 30, 2021 and 2020, the external costs for our hemophilia B program were primarily related to the execution of our Phase III clinical trial.

We enrolled patients into a six-month lead in phase between January 2018 and September 2019 and dosed a total of 54 patients between January 2019 and March 2020.

We also incur costs related to the long-term follow-up of patients in our Phase I/II clinical trial of AMT-060 and our Phase IIb clinical trial of etranacogene dezaparvovec.

During 2020 and up to the Closing of the CSL Behring Agreement we also incurred costs related to the preparation of a Biologics License Application (“BLA”) and marketing authorization application (“MAA”) and for commercialization of the Product.

After the Closing, CSL Behring will be responsible for the clinical and regulatory development and commercialization of the Product.

Direct research and development expenses related to clinical development incurred between Closing and June 30, 2021 are presented net of reimbursements due from CSL Behring.

In the three months ended September 30, 2020, the external costs for our hemophilia B program were primarily related to the execution of our Phase III clinical trial.

We dosed a total of 54 patients between January 2019 and March 2020.

In the same period, we also incurred costs related to the long-term follow-up of patients in our Phase I/II clinical trial of AMT-060 and our Phase IIb clinical trial of etranacogene dezaparvovec.

During 2020 and up to the Closing of the CSL Behring Agreement we also incurred costs related to the preparation of a BLA and MAA and for commercialization of the Product.

We also incurred costs for manufacturing development.

After the Closing, CSL Behring is responsible for the clinical and regulatory development and commercialization of the Product.

Direct research and development expenses related to clinical development incurred in the three months ended September 30, 2021 are presented net of reimbursements due from CSL Behring.

Huntington disease (AMT-130)

In the three months ended June 30, 2021, and June 30, 2020, our external costs for the development of Huntington’s disease were primarily related to the execution of our Phase I/II clinical trial in the United States.

In addition, our external costs in the three months ended June 30, 2021, included expenses related to the preparation of our Phase I/II clinical trial in Europe that we announced in April 2021.

In the three months ended September 30, 2021, and September 30, 2020, our external costs for the development of AMT-130 were primarily related to the execution of our Phase I/II clinical trial in the United States.

In addition, our external costs in the three months ended September 30, 2021 included expenses related to the preparation of a second Phase I/II clinical trial that will be conducted in Europe.

Preclinical programs & platform development

In the three months ended June 30, 2021, we incurred $2.4 million of costs primarily related to our preclinical activities primarily associated with product candidates, SCA3 (AMT-150) and Fabry disease (AMT-190 and AMT-191), as well as various other research programs and technology innovation projects, compared to costs of $1.8 million in the same period in 2020, which also included costs related to our product candidate for Hemophilia A (AMT-180) that was deprioritized in June 2020.

In the three months ended September 30, 2021, we incurred $2.5 million of costs primarily related to our preclinical activities associated with product candidates for the treatment of SCA3 (AMT-150), Fabry disease (AMT-191) and temporal lobe epilepsy (AMT-260), as well as various other research programs and technology innovation projects, compared to costs of $1.9 million in the same period in 2020.

Other research & development expenses

● We incurred $13.1 million in personnel and contractor related expenses in the three months ended June 30, 2021, compared to $10.0 million for the same period in 2020.

Our costs during the three months ended June 30, 2021 increased by $3.1 million as a result of the recruitment of personnel to support the development of our product candidates;

● We incurred $4.4 million in operating expenses and depreciation expenses related to our rented facilities in the three months ended June 30, 2021, compared to $4.2 million in the same period in 2020;

● We incurred $3.3 million in share-based compensation expenses in the three months ended June 30, 2021, compared to $2.9 million for the same period in 2020 primarily driven by increase in awards granted, including those to newly recruited personnel.

● We incurred $14.6 million in personnel and contractor related expenses in the three months ended September 30, 2021, compared to $11.8 million for the same period in 2020.

The increase was primarily as a result of the recruitment of personnel to support the development of our product candidates;

● We incurred $4.8 million in operating expenses and depreciation expenses related to our rented facilities in the three months ended September 30, 2021, compared to $4.4 million in the same period in 2020;

● We incurred $3.3 million in share-based compensation expenses in the three months ended September 30, 2021, compared to $3.9 million for the same period in 2020.

The decrease was primarily a result of compensation expense recorded during the three months ended September 30, 2020 related to the termination of one of our executives;

● We incurred $1.3 million of other expenses for the three months ended September 30, 2021, compared to $3.7 million for the same period in 2020.

The decrease was primarily due to $3.0 million of expense recorded for the three months ended September 30, 2020 related to license payments that have no alternative future use;

● We incurred $0.4 million of expenses in the three months ended September 30, 2021 related to an increase in the fair value of contingent consideration associated with the Corlieve Transaction, compared to nil for the same period in 2020.

Selling, general and administrative expenses

Selling, general and administrative expenses for the three months ended June 30, 2021 were $17.3 million, compared to $11.5 million for the same period in 2020.

● We incurred $4.5 million in financial advisory fees in relation to our licensing transaction with CSL Behring in the three months ended June 30, 2021, compared to nil in the same period in 2020;

● We incurred $4.2 million in personnel and contractor related expenses in the three months ended June 30, 2021, compared to $2.9 million in the same period in 2020.

The increase in the three months ended June 30, 2021, relates to the recruitment of personnel;

● We incurred $3.7 million in share-based compensation expenses in the three months ended June 30, 2021, compared to $2.8 million in the same period in 2020 primarily driven by increase in awards granted, including those to newly recruited personnel;

● We incurred $2.0 million in professional fees in the three months ended June 30, 2021, compared to $3.0 million in the same period in 2020.

Selling, general and administrative expenses for the three months ended September 30, 2021 were $12.0 million, compared to $10.8 million for the same period in 2020.

● We incurred $3.8 million in personnel and contractor related expenses in the three months ended September 30, 2021, compared to $3.6 million in the same period in 2020;

● We incurred $2.7 million in share-based compensation expenses in the three months ended September 30, 2021, compared to $2.5 million in the same period in 2020;

● We incurred $1.5 million in professional fees in the three months ended September 30, 2021, compared to $2.0 million in the same period in 2020.

We regularly incur accounting, audit and legal fees associated with operating as a public company.

Other items, net

We recognized $3.0 million in other income in relation to the equity stake received in VectorY B.V.

in conjunction with the Settlement Agreement in the three months ended June 30, 2021, compared to no such income for the same period in 2020.

We recognized $1.3 million in other income of employee retention credit under the U.S.

CARES Act in the three months ended June 30, 2021, compared to no such income for the same period in 2020.

We recognized $3.0 million in other income from payments received from European authorities to subsidize our research and development efforts in the Netherlands in the three months ended June 30, 2021, compared to $0.3 million for the same period in 2020.

CARES Act in the three months ended September 30, 2021, compared to no such income for the same period in 2020.

We recognized $0.0 million in other income from payments received from European authorities to subsidize our research and development efforts in the Netherlands in the three months ended September 30, 2021, compared to $0.5 million for the same period in 2020.

Other non-operating items, net

3 unchanged sentences

We issued warrants to BMS in 2015.

We recognize changes in the fair value of these warrants within other non-operating income / (expense).

We recognized changes in the fair value of these warrants within other non-operating income / (expense).

Following the termination of the BMS warrants on December 1, 2020, we no longer recognize changes in the fair value of these warrants within other non-operating (expense) / income.

As of the same date, we recognized a derivative financial liability related to a contingent payment due to BMS upon the consummation of a change of control transaction (“CoC-payment”) as described elsewhere in the Quarterly Report on Form 10-Q .

Our other non-operating items, net, for the three months ended June 30, 2021 and 2020 were as follows:

Three months ended June 30,

Our other non-operating items, net, for the three months ended September 30, 2021 and 2020 were as follows:

Three months ended September 30,

(in thousands)

4 unchanged sentences

Total other non-operating income / (loss), net

We recognized a net foreign currency gain, related to our borrowings from Hercules and our cash and cash equivalents as well as loans between entities within the uniQure group, of $6.6 million during the three months ended June 30, 2021, compared to a net loss of $3.6 million during the same period in 2020.

In the three months ended June 30, 2021, we recognized income of nil within other non-operating gains as there was no change in the fair value of the BMS derivative financial liability for the CoC-payment, compared to income of $0.2 million during the same period in 2020 related to changes in the fair value of the BMS warrants from the BMS CLA.

We recognized a net foreign currency gain, related to our borrowings from Hercules and our cash and cash equivalents as well as loans between entities within the uniQure group, of $10.4 million during the three months ended September 30, 2021, compared to a net loss of $8.7 million during the same period in 2020.

In the three months ended September 30, 2021, we recognized income of nil within other non-operating gains as there was no change in the fair value of the BMS derivative financial liability for the CoC-payment, compared to income of $0.3 million during the same period in 2020 related to changes in the fair value of the BMS warrants from the BMS CLA.

Income tax expense

We recognized $3.3 million of deferred tax expense in the three months ended June 30, 2021, and nil in the same period ended 2020.

Comparison of the six months ended June 30, 2021 and 2020

The following table presents a comparison of the six months ended June 30, 2021 and 2020.

Six months ended June 30,

We recognized $0.1 million of deferred tax expense in the three months ended September 30, 2021, and nil in the same period ended 2020.

Comparison of the nine months ended September 30, 2021 and 2020

The following table presents a comparison of the nine months ended September 30, 2021 and 2020.

Nine months ended September 30,

(in thousands)

11 unchanged sentences

Net income / (loss)

Our revenue for the six months ended June 30, 2021 and 2020 was as follows:

Six months ended June 30,

Our revenue for the nine months ended September 30, 2021 and 2020 was as follows:

Nine months ended September 30,

(in thousands)

2 unchanged sentences

Total revenues

We recognized $462.4 million license revenue related to the License Sale on Closing of the CSL Behring Agreement in May 2021.

We did not recognize any such license revenue related to the CSL Behring Agreement in the six months ended June 30, 2020.

We recognized $1.6 million license revenue related to upfront payments and target designation fees received from BMS in 2015 under the BMS CLA for the six months ended June 30, 2020.

We did not recognize any license revenue under the amended BMS CLA during the six months ended June 30, 2021.

We recognized $1.9 million collaboration revenue in the six months ended June 30, 2021, compared to $0.1 million for the same period in 2020.

We recognized $462.4 million of license revenue related to the License Sale on Closing of the CSL Behring Agreement in May 2021.

We did not recognize any such license revenue related to the CSL Behring Agreement in the nine months ended September 30, 2020.

We recognized $3.4 million of license revenue related to upfront payments and target designation fees received from BMS in 2015 under the BMS CLA for the nine months ended September 30, 2020.

We did not recognize any license revenue under the amended BMS CLA during the nine months ended September 30, 2021.

We recognized $3.9 million of collaboration revenue in the nine months ended September 30, 2021, compared to $0.1 million for the same period in 2020.

The increase in collaboration revenue primarily relates to the increased activities under the amended BMS CLA and the CSL Behring Agreement.

Cost of contract revenues

We recognized $23.2 million in cost of contract revenues for the six months ended June 30, 2021 compared to nil the same period in 2020.

We recognized $23.2 million in cost of contract revenues for the nine months ended September 30, 2021, compared to nil during the same period in 2020.

We recorded $16.7 million of expenses related to payments owed to our licensors on Closing as well as $6.5 million of other external expenses incurred to fulfill the License Sale to CSL Behring.

Research and development

Research and development expenses for the six months ended June 30, 2021 were $64.8 million, compared to $54.4 million for the same period in 2020.

Research and development expenses for the nine months ended September 30, 2021 were $101.2 million, compared to $90.7 million for the same period in 2020.

Other research and development expenses are separately classified in the table below.

These are not allocated as they are deployed across multiple projects under development.

Six months ended June 30,

These other expenses are not allocated as they are deployed across multiple projects under development.

Nine months ended September 30,

(in thousands)

7 unchanged sentences

Other expenses

Fair value changes related to contingent consideration

Total other research and development expenses

2 unchanged sentences

Etranacogene dezaparvovec (AMT-060/061)

In the six months ended June 30, 2021 and 2020, the external costs for our hemophilia B program were primarily related to the execution of our Phase III clinical trial.

We enrolled patients into a six-month lead in phase between January 2018 and September 2019 and dosed a total of 54 patients between January 2019 and March 2020.

In the nine months ended September 30, 2021 and 2020, the external costs for our hemophilia B program were primarily related to the execution of our Phase III clinical trial.

We dosed a total of 54 patients between January 2019 and March 2020.

We also incur costs related to the long-term follow-up of patients in our Phase I/II clinical trial of AMT-060 and our Phase IIb clinical trial of etranacogene dezaparvovec.

During 2020 and up to the Closing of the CSL Behring Agreement, we also incurred costs related to the preparation of a BLA and MAA and for commercialization of the Product.

After the Closing, CSL Behring will be responsible for the clinical and regulatory development and commercialization of the Product.

Direct research and development expenses related to clinical development incurred between Closing and June 30, 2021, are presented net of reimbursements due from CSL Behring.

We also incurred costs for manufacturing development.

After the Closing, CSL Behring is responsible for the clinical and regulatory development and commercialization of the Product.

Direct research and development expenses related to clinical development incurred between Closing and September 30, 2021, are presented net of reimbursements due from CSL Behring.

Huntington disease (AMT-130)

In the six months ended June 30, 2021 and June 30, 2020, our external costs for the development of Huntington’s disease were primarily related to the execution of our Phase I/II clinical trial in the United States.

In addition, our external costs in the six months ended June 30, 2021, included expenses related to the preparation of our Phase I/II clinical trial in Europe that we announced in April 2021.

In the nine months ended September 30, 2021 and September 30, 2020, our external costs for the development of Huntington’s disease were primarily related to the execution of our Phase I/II clinical trial in the United States.

In addition, our external costs in the nine months ended September 30, 2021 included expenses related to the preparation of a second Phase I/II clinical trial that will be conducted in Europe.

Preclinical programs & platform development

In the six months ended June 30, 2021, we incurred $4.7 million of costs primarily related to our preclinical activities primarily associated with product candidates, SCA3 (AMT-150) and Fabry disease (AMT-190 and AMT-191), as well as various other research programs and technology innovation projects, compared to costs of $3.2 million in the same period in 2020, which also included costs related to our product candidate for Hemophilia A (AMT-180) that was deprioritized in June 2020.

In the nine months ended September 30, 2021, we incurred $6.5 million of costs primarily related to our preclinical activities primarily associated with product candidates for the treatment of SCA3 (AMT-150), Fabry disease (AMT-191) and temporal lobe epilepsy (AMT-260), as well as various other research programs and technology innovation projects, compared to costs of $4.7 million in the same period in 2020.

These expenses exclude costs related to our product candidate for Hemophilia A (AMT-180), which was deprioritized in June 2020.

Other research & development expenses

● We incurred $24.7 million in personnel and contractor related expenses in the six months ended June 30, 2021, compared to $19.3 million for the same period in 2020.

Our costs during the six months ended June 30, 2021 increased by $5.4 million as a result of the recruitment of personnel to support the development of our product candidates;

● We incurred $9.0 million in operating expenses and depreciation expenses related to our rented facilities in the six months ended June 30, 2021, compared to $8.2 million in the same period in 2020 as a result of expanding our organization;

● We incurred $6.0 million in share-based compensation expenses in the six months ended June 30, 2021, compared to $5.3 million for the same period in 2020 primarily driven by increase in awards granted, including those to newly recruited personnel.

● We incurred $39.3 million in personnel and contractor related expenses in the nine months ended September 30, 2021, compared to $31.1 million for the same period in 2020.

The increase was primarily a result of the recruitment of personnel to support the development of our product candidates;

● We incurred $13.8 million in operating expenses and depreciation expenses related to our rented facilities in the nine months ended September 30, 2021, compared to $12.6 million in the same period in 2020.

The increase is related to the expansion of our organization;

● We incurred $9.2 million in share-based compensation expenses in the nine months ended September 30, 2021, compared to $9.2 million for the same period in 2020;

● We incurred $4.5 million of other expenses for the nine months ended September 30, 2021, compared to $4.8 million for the same period in 2020.

The decrease was primarily due to $3.0 million of expense recorded in the nine months ended September 30, 2020 related to license payments that have no alternative future, offset by an increase in various other expenses as a result of expanding our organization;

● We incurred $0.4 million of expenses in the nine months ended September 30, 2021 related to an increase in the fair value of contingent consideration associated with the Corlieve Transaction, compared to nil for the same period in 2020.

Selling, general and administrative expenses

Selling, general and administrative expenses for the six months ended June 30, 2021 were $30.3 million, compared to $20.6 million for the same period in 2020.

● We incurred $8.1 million in personnel and contractor related expenses in the six months ended June 30, 2021, compared to $6.1 million in the same period in 2020.

The increase in the six months ended June 30, 2021, relates to the recruitment of personnel;

● We incurred $6.8 million in share-based compensation expenses in the six months ended June 30, 2021, compared to $4.8 million in the same period in 2020 primarily driven by increase in awards granted, including those to newly recruited personnel;

● We incurred $5.0 million in professional fees in the six months ended June 30, 2021, compared to $4.2 million in the same period in 2020.

Selling, general and administrative expenses for the nine months ended September 30, 2021 were $42.3 million, compared to $31.4 million for the same period in 2020.

● We incurred $11.8 million in personnel and contractor related expenses in the nine months ended September 30, 2021, compared to $9.7 million in the same period in 2020.

The increase was primarily related to the recruitment of personnel;

● We incurred $9.5 million in share-based compensation expenses in the nine months ended September 30, 2021, compared to $7.2 million in the same period in 2020.

The increase was primarily related to the increase in awards granted, including those to newly recruited personnel;

● We incurred $6.5 million in professional fees in the nine months ended September 30, 2021, compared to $6.2 million in the same period in 2020.

We regularly incur accounting, audit and legal fees associated with operating as a public company;

● We incurred $4.5 million in financial advisory fees in relation to our licensing transaction with CSL Behring in the six months ended June 30, 2021, compared to nil in the same period in 2020.

● We incurred $4.5 million in financial advisory fees in relation to our licensing transaction with CSL Behring in the nine months ended September 30, 2021, compared to nil in the same period in 2020.

Other items, net

We recognized $3.0 million in other income in relation to the equity stake received in VectorY B.V.

in conjunction with the Settlement Agreement in the six months ended June 30, 2021, compared to no such income for the same period in 2020.

in conjunction with the Settlement Agreement in the nine months ended September 30, 2021, compared to no such income for the same period in 2020.

We recognized $2.6 million in other income of employee retention credit under the U.S.

CARES Act in the six months ended June 30, 2021, compared to no such income for the same period in 2020.

We recognized $3.0 million in income from payments received from European authorities to subsidize our research and development efforts in the Netherlands in the six months ended June 30, 2021, compared $0.5 million for the same period in 2020.

CARES Act in the nine months ended September 30, 2021, compared to no such income for the same period in 2020.

We recognized $3.0 million in income from payments received from European authorities to subsidize our research and development efforts in the Netherlands in the nine months ended September 30, 2021, compared $1.0 million for the same period in 2020.

Other non-operating items, net

3 unchanged sentences

We issued warrants to BMS in 2015.

We recognize changes in the fair value of these warrants within other non-operating income / (expense).

We recognized changes in the fair value of these warrants within other non-operating income / (expense).

Following the termination of the BMS warrants on December 1, 2020, we no longer recognize changes in the fair value of these warrants within other non-operating (expense) / income.

As of the same date, we recognized a derivative financial liability related to a contingent payment due to BMS upon the consummation of a CoC-payment as described elsewhere in the Quarterly Report on Form 10-Q .

Six months ended June 30,

As of the same date, we recognized a derivative financial liability related to a contingent payment due to BMS upon the consummation of a CoC-payment as described elsewhere in this Quarterly Report on Form 10-Q .

Nine months ended September 30,

(in thousands)

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Interest expense

Foreign currency gains, net

Foreign currency gains / (losses), net

Other non-operating gains, net

Total non-operating income, net

We recognized a net foreign currency gain, related to our borrowings from Hercules and our cash and cash equivalents as well as loans between entities within the uniQure group, of $11.2 million during the six months ended June 30, 2021, compared to a net gain of $1.0 million during the same period in 2020.

In the six months ended June 30, 2021, we recognized income of nil within other non-operating items as there was no change in the fair value of the BMS derivative financial liability for the CoC-payment, compared to income of $2.2 million during the same period in 2020 related to changes in the fair value of the BMS warrants from the BMS CLA.

Total non-operating income / (loss), net

We recognized a net foreign currency gain related to our borrowings from Hercules and our cash and cash equivalents as well as loans between entities within the uniQure group, of $21.6 million during the nine months ended September 30, 2021, compared to a net loss of $7.7 million during the same period in 2020.

In the nine months ended September 30, 2021, we recognized income of nil within other non-operating items as there was no change in the fair value of the BMS derivative financial liability for the CoC-payment, compared to income of $2.5 million during the same period in 2020 related to changes in the fair value of the BMS warrants from the BMS CLA.

Income tax expense

We recognized $3.5 million of deferred tax expense for the six months ended June 30, 2021 and nil in the same period ended 2020.

We recognized $3.6 million of deferred tax expense for the nine months ended September 30, 2021, and nil in the same period ended 2020.

Financial Position, Liquidity and Capital Resources

As of June 30, 2021, we had cash, cash equivalents and restricted cash of $680.2 million which include payments received from CSL Behring following the Closing.

This is expected to fund our operations into the first half of 2024 (assuming a full repayment of funds borrowed from Hercules under our term loan facility by 2023, as well as payments we expected to make in relation to our acquisition of Corlieve).

We expect that the achievement of $0.3 billion of regulatory, first commercial sale, and development milestones would further extend our runway by 12 to 18 months.

Six months ended June 30,

As of September 30, 2021, we had cash, cash equivalents and restricted cash of $581.3 million which include payments received from CSL Behring following the Closing.

This is expected to fund our operations into the first half of 2024 (assuming a full repayment of funds borrowed from Hercules under our term loan facility by 2023).

We expect that if we were to achieve the $0.3 billion in regulatory, first commercial sales, and development milestone payments, our runway would be further extended by 12 to 18 months.

Nine months ended September 30,

(in thousands)

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We had previously incurred losses and cumulative negative cash flows from operations since our business was founded by our predecessor entity AMT Therapeutics (“AMT”) Holding N.V.

As a result of receiving the upfront payment upon Closing of the CSL Behring Agreement, we generated $375.2 million cash flows from operations during the six months ended June 30, 2021.

We recorded net income of $399.5 million and $357.9 during the three and six months ended June 30, 2021, compared to a net loss of $42.6 million and $70.6 million during the same period in 2020.

As of June 30, 2021, we had an accumulated deficit of $426.8 million.

As a result of receiving the upfront payment upon Closing of the CSL Behring Agreement, we generated $335.0 million cash flows from operations during the nine months ended September 30, 2021.

We recorded net loss of $36.5 million in the three months ended September 30, 2021 and net income of $321.4 during the nine months ended September 30, 2021, compared to a net loss of $53.8 million and $124.3 million during the same periods in 2020.

As of September 30, 2021, we had an accumulated deficit of $463.4 million.

Sources of liquidity

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We 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 a sales agent under the Sales Agreement.

In the six months ended June 30, 2021, we issued 921,730 million ordinary shares for net proceeds of $29.6 million.

In the nine months ended September 30, 2021, we received net proceeds of $29.6 million from the issuance of 921,730 million ordinary shares that took place during March and April of this year.

On December 6, 2018, we signed the 2018 Amended Facility with Hercules that both refinanced our then-existing $20.0 million credit facility and provided us with an additional unconditional commitment of $15.0 million as well as a conditional commitment of $15 million that expired on June 30, 2020.

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The principal balance and all accrued but unpaid interest on advances under the Tranche B is due on June 1, 2023, which date may be extended by us by up to two twelve-month periods.

Advances under the Tranche B may not be prepaid until six-months after the Closing Date, following which we may prepay all such advances without charge.

As of June 30, 2021, $70.0 million was outstanding under the 2018 Amended Facility and the 2021 Amended Facility (December 31, 2020:

Advances under the Tranche B may now be prepaid without charge as six-months have passed from the Closing Date.

As of September 30, 2021, $70.0 million was outstanding under the 2018 Amended Facility and the 2021 Amended Facility (December 31, 2020:

$35.0 million under the 2018 Amended Facility).

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Net Cash generated from / used in operating activities

Net cash generated from operating activities was $375.2 million for the six months ended June 30, 2021 and consisted of net income of $357.9 million adjusted for non-cash items, including depreciation and amortization expense of $3.7 million, share-based compensation expense of $12.8 million, unrealized foreign exchange gains of $12.3 million and other non-cash items, net, of $0.5 million.

Net cash generated from operating activities was $335.0 million for the nine months ended September 30, 2021 and consisted of net income of $321.4 million adjusted for non-cash items, including depreciation and amortization expense of $5.4 million, share-based compensation expense of $18.7 million, a change in fair value of contingent consideration of $0.4 million, unrealized foreign exchange gains of $23.2 million, a change in deferred taxes of $3.6 million and other non-cash items, net, of $2.9 million.

Net cash generated from operating activities also included favorable changes in operating assets and liabilities of $11.6 million.

These changes primarily related to a net increase in accounts receivable, prepaid expenses, and other current assets and receivables of $3.4 million primarily related to an increase in various prepayments and a net increase in accounts payable, accrued expenses, other liabilities, and operating leases of $15.9 million primarily related to an increase in amounts to be paid to licensors upon the CSL Behring Closing.

These changes primarily related to a net increase in accounts receivable, prepaid expenses, and other current assets and receivables of $2.0 million primarily related to an increase in various prepayments and a net increase in accounts payable, accrued expenses, other liabilities, and operating leases of $13.6 million primarily related to an increase in amount to be paid to licensors upon the CSL Behring Closing and an increase in various other accruals for services provided by vendors and personnel accruals.

Net income primarily consisted of $462.4 million license revenue recognized on Closing.

Net cash used in operating activities was $62.9 million for the six months ended June 30, 2020 and consisted of a net loss of $70.6 million adjusted for non-cash items, including depreciation and amortization expense of $3.5 million, share-based compensation expense of $10.1 million, fair value gains on derivative financial instruments of $2.2 million, unrealized foreign exchange gain of $0.9 million, and a decrease in other non-cash items, net of $1.6 million.

Net cash used in operating activities was $97.7 million for the nine months ended September 30, 2020 and consisted of a net loss of $124.3 million adjusted for non-cash items, including depreciation and amortization expense of $8.4 million, share-based compensation expense of $16.5 million, fair value gains on derivative financial instruments of $2.5 million, unrealized foreign exchange losses of $7.8 million, and a decrease in other non-cash items, of $2.1 million.

Net cash used in operating activities also included unfavorable changes in operating assets and liabilities of $1.3 million.

These changes primarily related to a net decrease in accounts receivable and accrued income, prepaid expenses, and other current assets of $1.1 million and a net decrease in accounts payable, accrued expenses and other liabilities of $2.3 million.

These changes primarily related to a net increase in accounts receivable and accrued income, prepaid expenses, and other current assets of $1.2 million and a net decrease in accounts payable, accrued expenses and other liabilities of $0.1 million.

Net cash used in investing activities

In the six months ended June 30, 2021, we used $6.2 million in our investing activities compared to $4.6 million for the same period in 2020.

Six months ended June 30,

In the nine months ended September 30, 2021, we used $63.8 million in our investing activities compared to $6.8 million for the same period in 2020.

Nine months ended September 30,

(in thousands)

Acquisition of Corlieve, net of cash acquired

Build out of Amsterdam site

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Total investments

The build out of the Amsterdam site consumed $4.5 million cash during the six months ended June 30, 2021, compared to $1.8 million for the same period in 2020.

We paid EUR 42.1 million ($49.9 million), net of EUR 2.8 million ($3.4 million) of cash acquired, during the nine months ended September 30, 2021 to acquire 97.7% of the outstanding shares of Corlieve on July 30, 2021.

The build out of the Amsterdam site consumed $9.9 million cash during the nine months ended September 30, 2021, compared to $3.4 million for the same period in 2020.

The increase is a result of the construction of additional laboratories to support the expansions of our research and development activities as well as the construction of a cleanroom designed to be capable of manufacturing cGMP materials at a 500-liter scale.

Net cash generated from financing activities

In the six months ended June 30, 2021, we generated $65.1 million in our financing activities compared to $3.5 million for the same period in 2020.

Six months ended June 30,

In the nine months ended September 30, 2021, we generated $65.0 million in our financing activities compared to $3.7 million for the same period in 2020.

Nine months ended September 30,

(in thousands)

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Proceeds from issuance of shares related to employee stock option and purchase plans

Repayment of debt assumed through Corlieve Transaction

Net cash generated from financing activities

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We received net proceeds of $29.6 million associated with our ATM offering in March and April 2021.

During the six months ended June 30, 2021, we received $1.0 million from the exercise of options to purchase ordinary shares in relation to our share incentive plans compared to $3.5 million for the same period in 2020.

Upon the acquisition of Corlieve, Corlieve held a loan with an outstanding amount equal to EUR 1.0 million ($1.2 million).

During the nine months ended September 30, 2021, the loan was repaid in its entirety.

Funding requirements

We believe our cash and cash equivalents as of June 30, 2021, will fund our operations into the first half of 2024 (assuming a full repayment of funds borrowed from Hercules under our term loan facilities by 2023, as well as payments we expected to make in relation to our acquisition of Corlieve).

We expect that the achievement of the $0.3 billion in regulatory, first commercial sales and development milestones would further extend our runway by 12 to 18 months.

We believe our cash and cash equivalents as of September 30, 2021 will fund our operations into the first half of 2024 (assuming a full repayment of funds borrowed from Hercules under our term loan facilities by 2023).

We expect that if we were to achieve the $0.3 billion in regulatory, first commercial sales and development milestone payments, our runway would further be extended by 12 to 18 months.

Our future capital requirements will depend on many factors, including but not limited to:

● achieving the milestones and royalties as defined within the CSL Behring Agreement;

● payments we will make in relation to the contemplated acquisition of Corlieve;

● the payment of milestone payments that we might owe to former shareholders of Corlieve;

● the scope, timing, results, and costs of our current and planned clinical trials, including those for AMT-130 in Huntington’s disease;

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Contractual obligations and commitments

The table below sets forth our contractual obligations and commercial commitments as of June 30, 2021, that are expected to have an impact on liquidity and cash flows in future periods.

The table below sets forth our contractual obligations and commercial commitments as of September 30, 2021, that are expected to have an impact on liquidity and cash flows in future periods.

(in thousands)

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Operating lease obligations

Commitments related to Corlieve acquisition (nominal amounts)

In relation to the Corlieve Transaction, we entered into commitments to make payments to the former shareholders upon the achievement of certain contractual milestones.

The commitments include payments related to post-acquisition services that we agreed to as part of the SPA.

The timing of achieving these milestones and consequently the timing of payments is generally uncertain with the exception of a payment we owe upon acquiring the remaining outstanding shares as well as certain payments for post-acquisition services in 2022.

These payments are owed in Euro and have been translated at the foreign exchange rate as of September 30, 2021, of $1.16/€1.00.

As of September 30, 2021, we expect these obligations will become payable between 2022 and 2031.

When due, up to 25% of the milestone payments can be settled with our ordinary shares.

We also have obligations to make future payments to third parties that become due and payable on the achievement of certain development, regulatory and commercial milestones (such as the start of a clinical trial, filing of a BLA, approval by the FDA or product launch).

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Off-Balance Sheet Arrangements

As of June 30, 2021, we did not have any off-balance sheet arrangements as defined in Item 303(a)(4) of Regulation S-K.

As of September 30, 2021, we did not have any off-balance sheet arrangements as defined in Item 303(a)(4) of Regulation S-K.

Compared sentence by sentence after normalising whitespace, quotation marks, case and digits, so re-formatting and restated figures do not read as changed language. Wording changes appear as one removal and one addition. The current filing and the prior one are authoritative.

What changed 10-Q

Item 2. Management’s Discussion and Analysis