What changed in this filing

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Item 2. Management’s Discussion and Analysis

2025-05-09 compared with 2024-11-05 · 191 added, 372 removed, 164 unchanged (77% of the section changed)

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Business Developments

Huntington’s disease program (AMT-130) u pdated interim clinical data

AMT-130 is our novel gene therapy candidate for the treatment of Huntington’s disease, which utilizes our proprietary, gene-silencing miQURE platform and incorporates an AAV vector carrying a micro ribonucleic acid (“miRNA”) specifically designed to silence the huntingtin gene and the potentially highly toxic exon 1 protein fragment.

We are currently conducting a multi-center randomized, controlled Phase I/II clinical trial for AMT-130 in the U.S.

(“US study”) as well as an open-label Phase Ib/II study in Europe with the same early-manifest criteria for Huntington’s disease as the U.S.

study (“European study”).

We completed the enrollment of all 26 patients in the first two cohorts of our US study in March 2022 and the enrollment of 13 patients in the two cohorts of our European study in June 2023.

In November 2023, we initiated patient dosing in a third cohort of up to 12 patients across both U.S.

sites to further investigate both doses of AMT-130 in combination with perioperative immunosuppression.

Patient enrollment is ongoing in this cohort with a focus on evaluating near-term safety and tolerability.

In June 2024, we announced that the U.S.

Food and Drug Administration (“FDA”) granted Regenerative Medicine Advanced Therapy (“RMAT”) designation for AMT-130 based on the potential of AMT-130 to address the major unmet medical need among patients with Huntington’s disease.

The designation follows the FDA’s review of interim Phase I/II clinical data for AMT-130 announced in December 2023 and is based on an analysis comparing these 24-month clinical data to a non-concurrent criteria-matched natural history cohort.

In July 2024, we announced updated interim clinical data including up to 24 months of follow-up data from 29 treated patients enrolled in the ongoing U.S.

and European Phase I/II clinical trials of AMT-130 for the treatment of Huntington’s disease.

In conjunction with the July 2024 update, we conducted a post-hoc statistical analysis of clinical outcomes for the 21 treated patients at 24 months compared to an expanded, propensity-weighted external control developed in collaboration with the Cure Huntington’s Disease Initiative (CHDI) using data from the TRACK-HD, TRACK-ON and PREDICT-HD natural history studies.

The external control includes 154 patients that met the Phase I/II clinical trial eligibility criteria, and whose data contributions were statistically weighted using propensity scoring to closely match the baseline characteristics of patients treated with AMT-130.

Disease-related outcomes for these well-balanced cohorts were then compared after 24 months follow-up and are summarized below.

Measures of statistical significance in this analysis were based on nominal p values and are unadjusted.

● A statistically significant, dose-dependent, slowing in disease progression measured by the composite Unified Huntington’s Disease Rating Scale (cUHDRS) was observed through 24 months in patients receiving the high dose of AMT-130.

o At 24 months, the mean change in cUHDRS for patients receiving the high-dose of AMT-130 was -0.2 compared to -1.0 for patients in the propensity score-weighted external control, representing an 80% slowing of disease progression (p=0.007).

o At 24 months, the mean change in cUDHRS for patients receiving the low-dose of AMT-130 was -0.7 compared to -1.0 for patients in the propensity score-weighted external control, representing a 30% slowing of disease progression (p=0.21).

o cUHDRS has been demonstrated to be the most sensitive measurement of clinical progression in Huntington’s disease patients.

● Trends in measurements of motor and cognitive function showed near-baseline stability throughout the 24 months of follow-up in patients receiving the high dose of AMT-130.

● A statistically significant reduction of neurofilament light chain (NfL) in cerebrospinal fluid (CSF) was observed in patients treated with AMT-130.

o Patients treated with AMT-130 had a mean reduction in CSF NfL of 11% compared to baseline (p=0.02) at 24 months.

o Mean CSF NfL levels for both high and low doses were below baseline at 24 months.

o CSF NfL is a biomarker of neurodegeneration that has been shown to be associated with the clinical severity of Huntington’s disease.

An independent natural history study demonstrated a 26% increase in CSF NfL at 24 months in patients with early manifest Huntington’s disease (n=19).

Based on data observed as of the July 2024 interim update, AMT-130 remains generally well-tolerated, with a manageable safety profile at both doses.

There were no new AMT-130-related serious adverse events reported.

Based on the granting of the RMAT designation, we have scheduled a Type B, multi-disciplinary meeting with the U.S.

Food and Drug Administration (FDA) in late November 2024 at which we plan to present the most recent clinical data and initiate discussions regarding the potential for an expedited development pathway for AMT-130.

We will also discuss with the FDA a future communication plan that is expected to include additional sub-disciplinary meetings to take place in the first half of 2025.

Sale of commercial manufacturing activities

On June 29, 2024, our affiliates, uniQure Inc.

and uniQure biopharma B.V., entered into an asset purchase agreement (the “APA”) with Genezen Holdings Inc.

and its subsidiary, Genezen MA, Inc.

(together “Genezen”) to sell certain assets and assume certain liabilities related to uniQure’s manufacturing facility (the “Lexington Facility”) and operations in Lexington, Massachusetts (the “Lexington Transaction”).

The Lexington Transaction closed on July 22, 2024 (the “Closing”).

Our Chief Executive Officer, Matthew Kapusta, joined the board of directors of Genezen in connection with the Closing.

In conjunction with the Lexington Transaction, Genezen extended offers of employment to a significant majority of our employees located at the Lexington Facility, with the remaining employees terminated effective August 30, 2024.

As consideration for the Lexington Transaction, we received (i) shares of newly issued Series C preferred stock of Genezen Holdings Inc.

valued at $12.5 million, which are convertible into common stock and will accrue an 8.0% per annum cumulative dividend, (ii) a convertible promissory note with a nominal amount of $12.5 million, bearing interest at 8.0% per annum and maturing 63 months following the date of issuance and (iii) a right to purchase HEMGENIX® at terms considered favorable to market terms (the “Consideration”).

In connection with the Closing, we, Genezen and the landlord of the Lexington Facility entered into an agreement for us to assign and Genezen to assume the existing lease agreement between us and the landlord.

We also amended our original July 2013 guarantee to continue guaranteeing rental payments owed by Genezen until the end of the current term on May 31, 2029.

In the event of Genezen’s default related to rental payments owed to the landlord, we are entitled to terminate the assignment agreement and step into the original lease agreement.

At the Closing, we entered into a commercial supply agreement (“CSA”) with Genezen.

Pursuant to the terms of the CSA, the parties agreed to subcontract the manufacturing of HEMGENIX® to Genezen.

The CSA includes a minimum term of three years and minimum purchase commitments of HEMGENIX® commercial supplies of $43.3 million over the first three years, unless certain contractual provisions are triggered.

Our obligations with respect to the supply of HEMGENIX® to CSL Behring remain in effect notwithstanding the subcontracting to Genezen.

We recorded a $1.2 million gain from the divestment.

We paid a total of $8.3 million to Genezen and a third party related to adjustments of working capital and to obtain consent to proceed with the divestment.

Additionally, we entered into a development and other manufacturing services agreement (“DMSA”) with Genezen at Closing.

Pursuant to the DMSA, we are entitled to preferred customer status to receive manufacturing and development services to support our investigational gene therapy programs and other services related to HEMGENIX® (other than our manufacturing and supply obligations under the CSA).

The DMSA has a minimum term of three years and requires us to purchase services for a total minimum of $14.0 million.

Hercules Loan Repayment and Amendment

In connection with the Closing on July 22, 2024, we and Hercules amended the 2023 Amended Facility (“2024 Amended Facility”).

As a condition to Hercule’s consent to the Lexington Transaction, on July 19, 2024 we prepaid $50.0 million of the total $100.0 million principal outstanding.

The remaining $50.0 million principal outstanding will need to be repaid on January 5, 2027 (the “Maturity Date”).

Results of the business review

On July 23, 2024, we announced the Closing and on August 1, 2024, we announced an organizational restructuring (the “Restructuring”).

These actions were the outcome of a recently completed, comprehensive review of our operations with the goals of conserving capital and streamlining the organization.

As part of these changes, we eliminated approximately 300 positions or 65% of our workforce.

We estimate that we will incur costs in the range of $6.5 million to $7.5 million related to employee severance costs depending on whether or not employees continue to provide services through the residual service periods.

The Restructuring was subject to the review by our Amsterdam-based works council, which was completed in the third quarter of 2024.

We expect the Restructuring to be substantially completed by the end of 2024 with some employees continuing through second quarter 2025.

In January 2025, we received net proceeds of $70.1 million, after deducting underwriting discounts and commissions and other offering expenses payable by us, through a follow-on public offering of 4.4 million ordinary shares at a public offering price of $17.00 per ordinary share.

In February 2025, we received an additional $10.6 million in net proceeds upon the underwriters’ exercise of their option to purchase an additional 0.7 million ordinary shares at the public offering price.

Huntington’s disease program (AMT-130)

RMAT and Breakthrough Therapy Designations

On April 17, 2025, we announced that the U.S.

Food and Drug Administration (“FDA”) granted Breakthrough Therapy designation to AMT-130 for the treatment of Huntington’s disease.

The Breakthrough Therapy designation is supported by clinical data from the ongoing Phase I/II trials of AMT-130 for the treatment of Huntington’s disease showing the potential for meaningful slowing of disease progression.

Breakthrough Therapy designation is intended to expedite the development and review of investigational therapeutic candidates that are intended to treat a serious condition and preliminary clinical evidence indicates that the drug may demonstrate substantial improvement over available therapy on a clinically significant endpoint(s).

In general, the preliminary clinical evidence should show a clear advantage over available therapy.

In June 2024, we announced that the FDA granted us Regenerative Medicine Advanced Therapy (“RMAT”) designation for AMT-130 based on the potential of AMT-130 to address the major unmet medical need among patients with Huntington’s disease.

In addition to the RMAT and Breakthrough Therapy designations, the FDA previously granted Orphan Drug designation and Fast Track designation to AMT-130.

Regulatory Alignment

In March 2025, we held a Type B meeting with the FDA to discuss chemistry, manufacturing and controls (“CMC”) requirements for AMT-130, in support of a planned Biologics License Application, (“BLA”) submission.

An additional Type B meeting focused on the pivotal statistical analysis plan was held in the second quarter of 2025.

In December 2024, following our initial Type B meeting, we announced that we had reached agreement with FDA on key elements of an Accelerated Approval pathway for AMT-130.

In correspondence leading up to and following the Type B meeting, FDA agreed that data from the ongoing Phase I/II studies of AMT-130, compared to a natural history external control, may serve as the primary basis for a BLA, submission under FDA’s accelerated approval pathway.

The FDA also agreed that composite Unified Huntington’s Disease Rating Scale (“cUHDRS”) may be used as an intermediate clinical endpoint and that reductions in neurofilament light chain (“NfL”) measured in cerebrospinal fluid (“CSF”) may serve as supportive evidence of therapeutic benefit in the application for such accelerated approval.

Recent Developments of other Product Candidates

Temporal lobe epilepsy program (AMT-260)

In August 2023, the FDA cleared the IND application for AMT-260, our investigational gene therapy candidate for refractory MTLE.

AMT-260 is comprised of an AAV9 vector that locally delivers two engineered miRNAs designed to degrade the GRIK2 gene and suppress the aberrant expression of glutamate receptor subtype GLUK2 that is believed to trigger seizures in patients with refractory MTLE.

We are initiating a Phase I/IIa clinical trial that will be conducted in the United States and consist of two parts.

We are conducting a Phase I/IIa clinical trial (GenTLE) AMT-260 for the treatment of MTLE in the United States.

GenTLE consists of two parts.

The first part is a multicenter, open-label trial with two dosing cohorts of six patients each to assess safety, tolerability, and first signs for efficacy of AMT-260 in patients with refractory mTLE.

The second part is expected to be a randomized, controlled trial to generate proof of concept (“POC”) data.

The first patient has been enrolled into the observational phase of the Phase I/II clinical trial of AMT-260 for the treatment of mTLE.

The second part is expected to be a randomized, controlled trial to generate proof of concept data.

The FDA-approved study protocol provides that the first three patients to be enrolled in the study are required to have MRI-confirmed unilateral, hippocampal sclerosis.

Due to the more restrictive inclusion criteria for these sentinel patients, enrollment has taken longer than expected.

We are rapidly activating recruitment sites with 10 centers currently open and an additional two sites expected to be activated by the end of 2024.

In November 2024 we announced that the first patient had been dosed in GenTLE.

In addition, the FDA in February 2025 approved a protocol amendment expanding the inclusion criteria for certain patients in the first cohort to include patients with non-lesional mesial temporal lobe epilepsy in the non-dominant hemisphere.

Fabry disease program (AMT-191)

AMT-191 is our investigational gene therapy candidate for the treatment of Fabry disease.

AMT-191 is comprised of an AAV5 capsid that incorporates the α-galactosidase A (“GLA”) transgene and a proprietary, highly potent, liver-specific promoter.

In November 2023 we announced that the FDA had cleared the IND application for AMT-191.

In August 2024, we announced that the first patient has been dosed in a Phase I/IIa clinical trial of AMT-191 for the treatment of Fabry disease.

We are conducting a Phase I/IIa clinical trial of AMT-191 for the treatment of Fabry disease.

The multicenter, open-label clinical trial consists of two dose-escalating cohorts of up to six adult male patients each to assess safety, tolerability, and early signs of efficacy of AMT-191 in patients with Fabry disease.

In September 2024, we announced the FDA has granted Orphan Drug Designation to AMT-191 and in October 2024, the FDA granted Fast Track Designation to AMT-191.

In February 2025, we announced a favorable recommendation from the independent data monitoring committee (“IDMC”) following a review of safety data from the first two patients treated in the Phase I/IIa study.

The IDMC’s review did not identify any significant safety concerns and recommended proceeding with enrollment in the second cohort.

In August 2024, we announced that the first patient has been dosed.

In September 2024, we announced the FDA granted Orphan Drug Designation to AMT-191 and in October 2024, the FDA granted Fast Track Designation to AMT-191.

Amyotrophic Lateral Sclerosis (AMT-162)

AMT-162 is our investigational gene therapy candidate for a one-time, intrathecally administered investigational gene therapy for SOD1-ALS.

AMT-162 is comprised of a recombinant AAVrh10 vector that expresses a miRNA designed to knock down the expression of SOD1 with the goal of slowing down or potentially reversing the progression of ALS in patients with SOD1 mutations.

The FDA has cleared the IND application for AMT-162 and has granted Orphan Drug and Fast Track Designation.

In October 2024, we announced the first patient has been dosed in a Phase I/IIa clinical trial of AMT-162 for the treatment of SOD1-ALS.

The first-in-human Phase I/II clinical trial is a U.S.-based, multi-center, open-label trial consisting of three cohorts with up to four patients each receiving a one-time intrathecal infusion with immunosuppression.

Safety, tolerability and early signs of efficacy will be evaluated in the study.

EPISOD1 is a Phase I/II multi-center, open-label trial of AMT-162 for the treatment of SOD1-ALS being conducted in the United States consisting of three dose-escalating cohorts with up to four patients each receiving a short course of immunosuppression prior to and after an intrathecal infusion of AMT-162.

The trial will explore the safety and tolerability of AMT-162 and will assess exploratory signs of efficacy by measuring neurofilament light chain, a biomarker of neuronal damage, and SOD1 protein.

In October 2024, we announced the first patient had been dosed in EPISOD1.

In January 2025, we announced that the IDMC had recommended proceeding with enrollment of the second cohort after a review of the 28-day safety data from the first cohort.

We completed enrollment in the second dose cohort and we expect to initiate enrollment in the third dose cohort in the third quarter of 2025.

Financial Overview

Key components of our results of operations include the following:

Three months ended September 30,

Nine months ended September 30,

(in thousands)

Three months ended March 31,

(in thousands)

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Selling, general and administrative expenses

As of September 30, 2024 and December 31, 2023, we had cash and cash equivalents and investment securities of $435.2 million and $617.9 million, respectively.

We had a net loss of $44.4 million and $166.3 million in the three and nine months ended September 30, 2024, respectively, compared to a net loss of $89.6 million and $235.3 million for the same periods in 2023.

As of September 30, 2024 and December 31, 2023, we had accumulated deficits of $1,056.7 million and $890.4 million, respectively.

As of March 31, 2025 and December 31, 2024, we had cash and cash equivalents and investment securities of $409.0 million and $367.5 million, respectively.

We had a net loss of $43.6 million in the three months ended March 31, 2025, compared to a net loss of $65.6 million for the same period in 2024.

As of March 31, 2025 and December 31, 2024, we had accumulated deficits of $1,173.6 million and $1,130.0 million, respectively.

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

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A summary of our critical accounting policies as well as a discussion of our critical accounting estimates are presented in our Annual Report .

There were no material changes to our critical accounting policies during the nine months ended September 30, 2024 with the exception of determining the valuation of the intangible asset with favorable terms recorded as part of the Lexington Transaction.

Intangible asset

We entered into the APA with Genezen on June 29, 2024 to divest our commercial manufacturing activities in return for the Consideration.

The Lexington Transaction closed on July 22, 2024.

Part of the Consideration received was a right, with an estimated fair market value of $16.7 million, to purchase HEMGENIX® from Genezen up to the termination of our supply agreement with CSL Behring at terms considered favorable to market terms.

The determination of the fair market value required us to estimate the current and future commercial supply prices of HEMGENIX® to compare these to the contractually agreed terms.

Prices for the commercial supply of HEMGENIX® are not readily observable in the market.

Therefore, our estimate of the commercial supply price was based on what a market participant would be willing to pay in a comparable transaction, using industry benchmarks and relevant market data as reference points.

If the estimated commercial supply price used in the valuation had increased by 5% per drug product batch, then the fair market value of the intangible asset and the consideration received as well as the gain recorded on the divestment would have been increased by $3.0 million.

If the estimated commercial supply price used in the valuation had been decreased by 5% per drug product batch, then the fair market value of the intangible asset and the consideration received on the divestment would have been decreased by $2.9 million.

This would have resulted in a loss on divestment of $1.7 million instead of the $1.2 million gain presented.

Cost of contract manufacturing

We entered into a development and commercial supply agreement with CSL Behring in June 2020.

Prior to Closing, we recognized the cost to manufacture HEMGENIX® under such agreement as cost of contract manufacturing.

There were no material changes to our critical accounting policies during the three months ended March 31, 2025.

Contract manufacturing

We entered into a development and commercial supply agreement with CSL Behring LLC (“CSL Behring”) in June 2020 for the commercial supply of HEMGENIX®.

In July 2024, we divested our commercial manufacturing activities located in Lexington, MA (“Lexington Transaction”).

Prior to the Lexington Transaction, we recognized contract manufacturing revenues related to contract manufacturing HEMGENIX® for CSL Behring and the cost to manufacture HEMGENIX® under such an agreement as cost of contract manufacturing.

Research and development expenses

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Other items, net

Our other income primarily consists of the net gain resulting from the sale of the commercial manufacturing activities located in Lexington, MA in July 2024, payments received to subsidize our research and development efforts, and income from the subleasing of our Amsterdam facility and our Lexington, MA research and development facility which, commenced in September 2024.

Our other expense primarily consists of costs incurred under our commercial supply agreement with Genezen.

Our other income generally consists of payments received to subsidize our research and development efforts, income from the subleasing of our Amsterdam facility and our Lexington, MA research and development facility, and for the three months ended March 31, 2025, income from a one-time sale of critical reagents.

Following the Lexington Transaction, our other expense primarily consists of costs incurred under our commercial supply agreement (“CSA”) with Genezen Holdings Inc.

and its affiliate Genezen MA, Inc.

(together “Genezen”).

These include costs related to the purchase of HEMGENIX® from Genezen net of income from the sales of HEMGENIX® to CSL Behring, amortization of the intangible asset for our favorable supply terms under the CSA and credits from the release of liabilities related to expected net losses associated with minimum purchase commitments under the CSA .

Additionally, other expense also consists of expenses we incur in relation to our subleasing income.

Additionally, other expenses also consist of expenses we incur in relation to our subleasing income.

Results of Operations

Comparison of the three months ended September 30, 2024 and 2023

The following table presents a comparison of our results of operations for the three months ended September 30, 2024 and 2023.

Three months ended September 30,

Comparison of the three months ended March 31, 2025 and 2024

The following table presents a comparison of our results of operations for the three months ended March 31, 2025 and 2024:

Three months ended March 31,

(in thousands)

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Loss from operations

Other non-operating items, net

Net loss before income tax expense

Income tax benefit

Our revenues for the three months ended September 30, 2024 and 2023 were as follows:

Three months ended September 30,

Non-operating expense, net

Loss before income tax benefit

Income tax expense

Our revenue for the three months ended March 31, 2025 and 2024 was as follows:

Three months ended March 31,

(in thousands)

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We recognize license revenues from CSL Behring related to royalty payments owed on HEMGENIX® sales, when earned.

For the three months ended September 30, 2024, we recognized $2.1 million of license revenues, compared to $0.5 million for the same period in 2023.

Contract manufacturing revenues

We recognized contract manufacturing revenues related to contract manufacturing HEMGENIX® for CSL Behring prior to the Closing of the Lexington Transaction.

Contract manufacturing revenues were realized when earned upon sales of HEMGENIX® drug product to CSL Behring.

We recognized nil contract manufacturing revenues in the three months ended September 30, 2024 , compared to $0.3 million for the same period in 2023.

For the three months ended March 31, 2025 and March 31, 2024, we recognized $1.6 million and $1.2 million of license revenues, respectively.

Collaboration revenues

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Collaboration revenue related to these contracted services is recognized when the performance obligations are satisfied.

For the three months ended September 30, 2024 and 2023 we recognized $0.2 million and $0.6 million of collaboration revenue for CSL Behring, respectively.

For the three months ended March 31, 2025 and 2024 we recognized nil and $3.3 million of collaboration revenue for CSL Behring, respectively.

The decrease in collaboration revenue of $3.3 million in the three months ended March 31, 2025 compared to the same period in 2024 resulted from us not providing any development and other services to CSL Behring in relation to the CSL Behring Agreement in 2025.

Contract manufacturing revenues

We recognized contract manufacturing revenues related to the manufacturing of HEMGENIX® for CSL Behring prior to the Lexington Transaction.

Contract manufacturing revenues were realized when earned upon sales of HEMGENIX® drug product to CSL Behring.

We recognized nil contract manufacturing revenues in the three months ended March 31, 2025 , compared to $4.0 million for the same period in 2024.

Cost of contract manufacturing

We incurred $0.8 million of cost of contract manufacturing related to the manufacture of HEMGENIX® prior to the Closing of the Lexington Transaction in the three months ended September 30, 2024, compared to $1.0 million cost of contract manufacturing in the three months ended September 30, 2023.

R&D expenses for the three months ended September 30, 2024 were $30.6 million, compared to $65.4 million for the same period in 2023.

We incurred nil costs of contract manufacturing in the three months ended March 31, 2025.

In the three months ended March 31, 2024 we incurred $9.1 million costs of contract manufacturing related to the manufacture of HEMGENIX® prior to the Lexington Transaction in July 2024.

R&D expenses for the three months ended March 31, 2025 were $36.1 million, compared to $40.7 million for the same period in 2024.

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

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

Three months ended September 30,

Three months ended March 31,

(in thousands)

Huntington's disease (AMT-130)

Fabry disease (AMT-191)

Temporal lobe epilepsy (AMT-260)

Programs in preclinical development and platform related expenses

Amyotrophic lateral sclerosis (AMT-162)

Fabry disease (AMT-191)

Programs in preclinical development and platform related expenses

Total direct research and development expenses

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Facility expenses

Severance costs

Share-based compensation expense

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Direct research and development expenses

Prior to the Lexington Transaction, we supplied Good Manufacturing Processes (“GMP”) material utilized in our clinical programs for Huntington’s disease and Fabry disease as well as GMP material needed for our preclinical programs using our in-house manufacturing facility.

The related expenses were part of “other research and development expenses”.

Following the closing of the Lexington Transaction we rely on third party suppliers and present associated expenses for these activities within “direct research and development expenses”.

Huntington’s disease (AMT-130)

In the three months ended September 30, 2024 and September 30, 2023, we incurred costs of $4.5 million and $3.1 million respectively.

Our external costs for the development of AMT-130 were primarily related to the execution of our Phase I/II clinical trials in the U.S.

and in Europe.

We completed enrollment of the first two cohorts in the U.S.

in March 2022 and in Europe in June 2023.

Temporal lobe epilepsy (AMT-260)

In the three months ended September 30, 2024 and September 30, 2023, we incurred costs of $1.6 million and $4.7 million respectively, for the development of AMT-260.

In August 2023, the FDA cleared our IND application, and we continue to incur costs for the preparation of a Phase I clinical trial.

Preclinical programs and platform development

In the three months ended September 30, 2024 and September 30, 2023, we incurred $1.0 million and $3.1 million of costs, respectively, primarily related to our preclinical activities associated with product candidates for various other research programs and technology innovation projects.

Amyotrophic Lateral Sclerosis caused by mutations in SOD1 (AMT-162)

On January 31, 2023, we entered into a global licensing agreement with Apic Bio for AMT-162.

In the three months ended September 30, 2024 and September 30, 2023, we incurred costs of $0.9 million and $2.4 million, respectively, to initiate a Phase I/II clinical trial.

In three months ended March 31, 2025 and March 31, 2024, we incurred costs of $8.2 million and $2.4 million respectively.

Our external costs for the development of AMT-130 were primarily related to the execution of our U.S.

and European studies.

The increase of $5.8 million in external cost in 2025 compared to 2024 was primarily driven by activities related to the preparation of the BLA submission for AMT-130 in the United States.

Fabry disease (AMT-191)

In the three months ended September 30, 2024 and September 30, 2023, we incurred costs of $0.8 million and $0.4 million, respectively, related to our development of AMT-191.

In the three months ended March 31, 2025 and March 31, 2024, we incurred costs of $2.2 million and $1.4 million, respectively, related to our development of AMT-19.

We incurred $2.1 million and $0.1 million related to clinical trials and CMC development, respectively, compared to $1.3 million and $0.0 million in the comparative period.

In November 2023, the FDA cleared the IND application, and we started incurring additional costs for the Phase I/II clinical trial preparation.

Temporal lobe epilepsy (AMT-260)

In three months ended March 31, 2025 and March 31, 2024, we incurred costs of $2.1 million and $2.3 million respectively, for the development of AMT-260.

We incurred $1.6 million and $0.4 million related to clinical trials and CMC development, respectively, compared to $0.5 million and $1.7 million in the comparative period.

Amyotrophic Lateral Sclerosis caused by mutations in SOD1 (AMT-162)

In the three months ended March 31, 2025 and March 31, 2024, we incurred $1.8 million and $2.0 million of expenses, respectively, to initiate a Phase I/II clinical trial which enrolled the first patient in October 2024.

We incurred $1.7 million and $0.1 million related to clinical trials and CMC development, respectively, compared to $0.9 million and $1.1 million in the comparative period.

Preclinical programs & platform development

In the three months ended March 31, 2025 and March 31, 2024 , we incurred $1.3 million and $0.4 million of costs, respectively, related primarily to our preclinical activities associated with product candidates for various other research programs and technology innovation projects.

Other research & development expenses

● We incurred $10.0 million in personnel and contractor-related expenses in the three months ended September 30, 2024 , compared to $19.4 million for the same period in 2023.

The decrease was primarily related to the divestment of our commercial manufacturing activities as well as a reduction in expense from the restructuring that occurred in October 2023;

● We incurred $3.8 million in operating expenses and depreciation expenses related to our rented facilities in Amsterdam and Lexington, Massachusetts in the three months ended September 30, 2024 , compared to $6.7 million in the same period in 2023.

The decrease was primarily related to the divestment of our commercial manufacturing activities as well as the subleasing of our 20 Maguire facility;

● We incurred $2.7 million of other expenses for the three months ended September 30, 2024 , compared to $1.1 million for the same period in 2023;

● We incurred $1.4 million in share-based compensation expenses in the three months ended September 30, 2024 , compared to $5.6 million for the same period in 2023.

The decrease was primarily related to the divestment of our commercial manufacturing activities, a reduction in expense from the restructuring that occurred in October 2023 and a decrease in the fair value of the awards granted;

● We incurred $1.0 million in disposable costs in the three months ended September 30, 2024 , compared to $4.7 million for the same period in 2023.

The decrease was primarily related to the divestment of our commercial manufacturing activities as well as a reduction in expense from the restructuring that occurred in October 2023;

● We included $3.4 million of severance costs related to the divestment of our commercial manufacturing activities and the organizational restructuring in the three months ended September 30, 2024 with no such cost in the same period in 2023;

● We recognized a $0.4 million gain in the three months ended September 30, 2024 related to a decrease in the fair value of contingent consideration associated with the acquisition of uniQure France SAS, compared to a loss of $14.2 million related to the increase in fair value for the same period in 2023.

Selling, general and administrative expenses

Selling, general and administrative expenses for the three months ended September 30, 2024 were $11.6 million, compared to $18.1 million for the same period in 2023.

● We incurred $5.5 million in personnel and contractor-related expenses in the three months ended September 30, 2024 , compared to $6.4 million in the same period in 2023;

● We incurred $2.0 million in share-based compensation expenses in the three months ended September 30, 2024 , compared to $5.1 million in the same period in 2023.

The decrease was primarily related to the divestment of our Lexington Facility, a reduction in expense from the restructuring that occurred in October 2023 and a decrease in the fair value of the awards granted;

● We incurred $1.5 million in professional fees in the three months ended September 30, 2024 , compared to $2.8 million in the same period in 2023.

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

● We incurred $0.9 million in other expenses in the three months ended September 30 , 2024, compared to $2.8 million in the same period in 2023;

● We incurred $0.7 million of severance costs related to the organizational restructuring in the three months ended September 30, 2024 with no such cost in the same period in 2023.

Other items, net

We recognized $1.2 million net gain resulting from the sale of the commercial manufacturing activities located in Lexington, MA in July 2024 in other income.

We recognized $1.5 million net in other expenses during the three months ended September 30, 2024 (nil in three months ended September 30, 2023) related to the purchase of HEMGENIX® from Genezen net of income from the sales of HEMGENIX® to CSL Behring, amortization of the intangible asset for our favorable supply terms under the CSA and credits from the release of liabilities related to expected net losses associated with minimum purchase commitments under the CSA .

We recognized $1.1 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, 2024, compared to $1.4 million for the same period in 2023.

Other items, net for the periods presented primarily related to income from the subleasing of our Amsterdam facility and Lexington research and development facility and expenses we incur in relation to the subleasing facility.

Other non-operating items, net

Our other non-operating items, net, for the three months ended September 30, 2024 and 2023 were as follows:

Three months ended September 30,

(in thousands)

Interest income

Interest expense

Foreign currency gains, net

Total non-operating expense, net

We recognize interest income associated with our cash and cash equivalents, investment securities and convertible promissory note.

We recognized $4.9 million in interest income in the three months ended September 30, 2024, compared to $7.5 million in the same period in the prior year.

Our interest income decreased by $2.6 million due to less interest income earned on investment securities during the three months ended September 30, 2024.

We recognized $16.6 million in interest expense for the three months ended September 30, 2024 and $15.4 million for the three months ended September 30, 2023.

Our interest expense in 2024 increased due to an increase of $1.0 million in non-cash interest expense related to the Royalty Financing Agreement that we entered into in May 2023.

We hold monetary items and enter into transactions in foreign currencies, predominantly in euros and U.S.

We recognize foreign exchange results related to changes in these foreign currencies.

We recognized a net foreign currency gain, related to our borrowings from Hercules, the Royalty Financing Agreement and our cash and cash equivalents and investment securities as well as loans between entities within the uniQure group, of $7.6 million during the three months ended September 30, 2024, compared to a net gain of $0.2 million during the same period in 2023.

Income tax benefit

We recognized $0.0 million of deferred tax benefit in the three months ended September 30, 2024 , and $0.1 million of deferred tax benefit for the same period in 2023.

Comparison of the nine months ended September 30, 2024 and 2023

The following table presents a comparison of our results of operations for the nine months ended September 30, 2024 and 2023:

Nine months ended September 30,

(in thousands)

Total revenues

Operating expenses:

Cost of license revenues

Cost of contract manufacturing

Research and development expenses

● We incurred $10.2 million in personnel and contractor-related expenses in the three months ended March 31, 2025 , compared to $16.9 million for the same period in 2024.

The decrease was primarily related to the divestment of our commercial manufacturing activities in July 2024 as well as a reduction in expense from the restructuring that occurred in August 2024;

● We incurred $4.6 million in operating expenses and depreciation expenses related to our rented facilities in Amsterdam and Lexington, Massachusetts in the three months ended March 31, 2025 , compared to $7.1 million in the same period in 2024.

The decrease was primarily related to the divestment of our commercial manufacturing activities in July 2024;

● We incurred $2.5 million in share-based compensation expenses in the three months ended March 31, 2025 , compared to $3.4 million for the same period in 2024.

The decrease was primarily related to the divestment of our commercial manufacturing activities and a reduction in expense from the restructuring that occurred in August 2024;

● We recognized a $1.2 million loss in the three months ended March 31, 2025, related to an increase in the fair value of contingent consideration associated with the acquisition of uniQure France SAS, compared to $0.2 million loss for the same period in 2024;

● We incurred $0.8 million in disposable costs in the three months ended March 31, 2025 , compared to $1.9 million for the same period in 2024;

● We incurred $1.3 million of other expenses for the three months ended March 31, 2025 , compared to $2.7 million for the same period in 2024.

Selling, general and administrative expenses

Total operating expenses

Other expense

Loss from operations

Non-operating expense, net

Loss before income tax benefit

Income tax (expense) / benefit

Our revenue for the nine months ended September 30, 2024 and 2023 was as follows:

Nine months ended September 30,

(in thousands)

License revenues

Contract manufacturing revenues

Collaboration revenues

Total revenues

License revenues

We recognize license revenues from CSL Behring, related to royalty payments owed on HEMGENIX® sales, when earned.

For the nine months ended September 30, 2024, we recognized $5.2 million of license revenues, compared to $1.3 million for the same period in 2023.

Contract manufacturing revenues

We recognized contract manufacturing revenues related to contract manufacturing HEMGENIX® for CSL Behring prior to the Closing of the Lexington Transaction.

Contract manufacturing revenues were realized when earned upon sales of HEMGENIX® drug product to CSL Behring.

We recognized $6.1 million contract manufacturing revenues in the nine months ended September 30, 2024 , compared to $6.6 million for the same period in 2023.

Collaboration revenues

We provide services to CSL Behring in accordance with the CSL Behring Agreement.

Collaboration revenue related to these contracted services is recognized when the performance obligations are satisfied.

For the nine months ended September 30, 2024 and 2023 we recognized $10.6 million and $1.3 million of collaboration revenue for CSL Behring, respectively.

The increase in collaboration revenue of $9.3 million in the nine months ended September 30, 2024 compared to the same period in 2023 was primarily related to additional development and other services provided to CSL Behring in relation to the CSL Behring Agreement.

Cost of contract manufacturing

We incurred $17.1 million of cost of contract manufacturing related to the manufacture of HEMGENIX® prior to the Closing of the Lexington Transaction in the nine months ended September 30, 2024, compared to $4.8 million cost of contract manufacturing in the nine months ended September 30, 2023.

The increase in cost of $12.3 million in 2024 is primarily related to expensing costs that could not be recovered from selling HEMGENIX® under the terms of our development and commercial supply agreement with CSL Behring.

R&D expenses for the nine months ended September 30, 2024 were $104.9 million, compared to $172.2 million for the same period in 2023.

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

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

Nine months ended September 30,

Selling, general and administrative expenses for the three months ended March 31, 2025 were $10.9 million, compared to $13.9 million for the same period in 2024.

Three months ended March 31,

(in thousands)

Huntington's disease (AMT-130)

Temporal lobe epilepsy (AMT-260)

Amyotrophic lateral sclerosis (AMT-162)

Fabry disease (AMT-191)

Programs in preclinical development and platform related expenses

Etranacogene dezaparvovec (AMT-060/061)

Total direct research and development expenses

Employee and contractor-related expenses

Facility expenses

Share-based compensation expense

Professional fees

Depreciation and facility costs

Intellectual property fees

Information technology costs

Other expenses

Severance costs

Fair value changes related to contingent consideration

Total other research and development expenses

Total research and development expenses

Direct research and development expenses

Huntington’s disease (AMT-130)

In the nine months ended September 30, 2024 and September 30, 2023, we incurred costs of $9.8 million and $11.1 million respectively.

Our external costs for the development of AMT-130 were primarily related to the execution of our Phase I/II clinical trials in the U.S.

and in Europe.

We completed enrollment of the first two cohorts in the U.S.

in March 2022 and in Europe in June 2023.

This resulted in a $1.3 million reduction of cost in 2024 compared to the prior year as we typically incur higher costs per patient during the first six months of enrollment compared to the follow-up period thereafter.

Temporal lobe epilepsy (AMT-260)

In the nine months ended September 30, 2024 and September 30, 2023, we incurred costs of $5.9 million and $12.0 million respectively, for the development of AMT-260.

In August 2023, the FDA cleared our IND application, and we continue to incur costs for the preparation of a Phase I clinical trial.

Amyotrophic Lateral Sclerosis caused by mutations in SOD1 (AMT-162)

On January 31, 2023, we entered into a global licensing agreement with Apic Bio for AMT-162.

In the nine months ended September 30, 2024, we incurred $4.5 million of costs to initiate a Phase I/II clinical trial in 2024.

In the nine months ended September 30, 2023 we incurred $3.1 million of costs to initiate the Phase I/II clinical trial as well as $10.0 million related to the upfront consideration paid to Apic Bio for the global licensing rights to AMT-162.

Fabry disease (AMT-191)

In the nine months ended September 30, 2024 and September 30, 2023, we incurred costs of $3.6 million and $1.8 million, respectively, related to our development of AMT-191.

In November 2023, the FDA cleared the IND application, and we started incurring additional costs for the Phase I/II clinical trial preparation.

Preclinical programs & platform development

In the nine months ended September 30, 2024 and September 30, 2023, 2023, we incurred $2.3 million and $7.2 million of costs, respectively, primarily related to our preclinical activities associated with product candidates for various other research programs and technology innovation projects.

Etranacogene dezaparvovec (AMT-060/061)

We transitioned activities related to the clinical trial and long-term follow-up of patients to CSL Behring in December 2022.

Direct research and development expenses related to clinical development and other regulatory activities and commercialization expenses incurred in the nine months ended September 30, 2024 and September 30, 2023 are presented net of reimbursements due from CSL Behring and include settlement amounts from the transition.

Other research & development expenses

● We incurred $39.9 million in personnel and contractor-related expenses in the nine months ended September 30, 2024 , compared to $55.9 million for the same period in 2023.

The decrease was primarily related to the divestment of our commercial manufacturing activities as well as a reduction in expense from the restructuring that occurred in October 2023;

● We incurred $16.9 million in operating expenses and depreciation expenses related to our rented facilities in Amsterdam and Lexington, Massachusetts in the nine months ended September 30, 2024 , compared to $21.1 million in the same period in 2023.

The decrease was primarily related to the divestment of our commercial manufacturing activities;

● We incurred $7.7 million in share-based compensation expenses in the nine months ended September 30, 2024 , compared to $14.7 million for the same period in 2023.

● We incurred $7.5 million of other expenses for the nine months ended September 30, 2024 , compared to $6.8 million for the same period in 2023;

● We incurred $4.5 million of severance costs related to the divestment of our commercial manufacturing activities and the organizational restructuring in the nine months ended September 30, 2024 with no such cost in the same period in 2023;

● We incurred $4.4 million in disposable costs in the nine months ended September 30, 2024 , compared to $14.5 million for the same period in 2023.

The decrease was primarily related to the divestment of our commercial manufacturing activities as well as a reduction in expense from the restructuring that occurred in October 2023;

● We recognized a $2.0 million gain in the nine months ended September 30, 2024 related to a decrease in the fair value of contingent consideration associated with the acquisition of uniQure France SAS, compared to $15.4 million loss related to an increase in fair value for the same period in 2023.

Selling, general and administrative expenses

Selling, general and administrative expenses for the nine months ended September 30, 2024 were $41.3 million, compared to $57.1 million for the same period in 2023.

● We incurred $17.4 million in personnel and contractor-related expenses in the nine months ended September 30, 2024 , compared to $18.8 million in the same period in 2023.

The decrease was primarily related to the reduction in personnel and contractors as a result of the Lexington Transaction and the October 2023 and August 2024 reorganizations;

● We incurred $8.8 million in share-based compensation expenses in the nine months ended September 30, 2024 , compared to $12.9 million in the same period in 2023.

The decrease was primarily related to the Lexington Transaction, the October 2023 and August 2024 organizational restructurings, and a decrease in the fair value of the awards granted;

● We incurred $5.7 million in professional fees in the nine months ended September 30, 2024 , compared to $8.5 million in the same period in 2023.

Total selling, general and administrative expenses

● We incurred $5.5 million in personnel and contractor-related expenses in the three months ended March 31, 2025, compared to $6.2 million in the same period in 2024.

The decrease was primarily related to the reduction in personnel and contractors as a result of the divestment of our commercial manufacturing activities and the organizational restructuring in August 2024;

● We incurred $1.9 million in share-based compensation expenses in the three months ended March 31, 2025 , compared to $3.4 million in the same period in 2024.

The decrease was primarily related to the divestment of our commercial manufacturing activities and a reduction in expense from the restructuring that occurred in August 2024;

● We incurred $1.9 million in professional fees in the three months ended March 31, 2025 , compared to $2.0 million in the same period in 2024.

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

In 2024, we incurred professional fees related to the Lexington Transaction.

There was a partial offset as in the prior period we incurred professional fees related to our global licensing agreement with Apic Bio;

● We incurred $5.7 million in other expenses in the nine months ended September 30 , 2024, compared to $9.0 million in the same period in 2023.

The $3.3 million decrease was primarily related to a reduction of expenses for information technology;

● We incurred $1.4 million in intellectual property fees including registration and professional fees in the nine months ended September 30, 2024 compared to $3.3 million in the same period in 2023.

The decrease mainly related to an decrease in professional fees;

● We incurred $1.0 million of severance costs related to the Lexington Transaction and August 2024 organizational restructuring in the nine months ended September 30, 2024 with no such cost in the same period in 2023;

● We incurred nil in financial advisory fees in relation to our licensing transaction with CSL Behring in the nine months ended September 30, 2024, compared to $3.8 million in 2023.

● We incurred $0.3 million in intellectual property fees including registration and professional fees in the three months ended March 31, 2025 compared to $0.6 million in the same period in 2024.

The decrease mainly related to a decrease in professional fees;

● We incurred $0.6 million in other expenses in the three months ended March 31 , 2025, compared to $1.0 million in the same period in 2024.

Other items, net

We recognized $1.2 million net gain resulting from the sale of the commercial manufacturing activities located in Lexington, MA in July 2024.

We recognized $1.5 million in net other expenses during the nine months ended September 30, 2024 (nil in same period in 2023) related to the purchase of HEMGENIX® from Genezen net of income from the sales of HEMGENIX® to CSL Behring, amortization of the intangible asset for our favorable supply terms under the CSA and credits from the release of liabilities related to expected net losses associated with minimum purchase commitments under the CSA .

We recognized $4.0 million in other income from payments received from European authorities to subsidize our research and development efforts in the Netherlands in the nine months ended September 30, 2024, compared to $3.9 million for the same period in 2023.

Our other items, net, for the three months ended March 31, 2025 and March 31, 2024 were as follows:

Three months ended March 31,

(in thousands)

Sale of critical reagents to Genezen

Research and development grants from Dutch authorities

Sublease income

Supply of HEMGENIX® to CSL Behring

Sublease expense

Other income, net

Total other income, net

In the three months ended March 31, 2025 we recognized $6.0 million in income related to a one-time sale of critical reagents to Genezen (nil in the prior period).

We recognized $1.5 million in net other expenses during the three months ended March 31, 2025, related to the purchase of HEMGENIX® from Genezen, net of income from the sales of HEMGENIX® to CSL Behring, amortization of the intangible asset for our favorable supply terms under the CSA and credits from the release of liabilities related to expected net losses associated with minimum purchase commitments under the CSA.

Other non-operating items, net

Our other non-operating items, net, for the nine months ended September 30, 2024 and 2023 were as follows:

Nine months ended September 30,

Our other non-operating items, net, for the three months ended March 31, 2025 and March 31, 2024 were as follows:

Three months ended March 31,

(in thousands)

Interest income

Interest expense

Interest expense - Royalty Financing Agreement

Interest expense - Hercules debt facility

Foreign currency gains / (losses), net

Total non-operating expense, net

We recognize interest income associated with our cash and cash equivalents, investment securities and convertible note.

We recognized $17.2 million in interest income in the nine months ended September 30, 2024, compared to $12.4 million in the same period in the prior year.

Our interest income increased by $4.8 million due to the interest income earned on investment securities as well as cash on hand during the nine months ended September 30, 2024.

We recognized $48.9 million in interest expense for the nine months ended September 30, 2024 and $25.8 million for the nine months ended September 30, 2023.

Our interest expense in 2024 mainly increased due to an increase of $22.7 million in non-cash interest expense related to the Royalty Financing Agreement that we entered into in May 2023.

We recognize interest income associated with our cash and cash equivalents and investment securities.

We recognized $4.1 million in interest income in the three months ended March 31, 2025, compared to $6.5 million in the same period in the prior year.

Our interest income decreased by $2.4 million due to the interest income earned on investment securities as well as cash on hand during the three months ended March 31, 2025.

We recognized interest expense of $1.8 million and $3.7 million in the three months ended March 31, 2025 , and March, 31, 2024, respectively, related to the Hercules Capital, Inc.

(“Hercules”) debt facility.

Interest expense decreased by $1.9 million in 2025, compared to 2024, primarily due to the $50.0 million repayment of Hercules debt in July 2024, as well as a decrease in market interest rates.

We hold monetary items and enter into transactions in foreign currencies, predominantly in euros and U.S.

We recognize foreign exchange results related to changes in these foreign currencies.

We recognized a net foreign currency gain, related to our borrowings from Hercules, the Royalty Financing Agreement and our cash and cash equivalents and investment securities as well as loans between entities within the uniQure group, of $5.4 million during the nine months ended September 30, 2024, compared to a net loss of $1.8 million during the same period in 2023.

Income tax benefit

We recognized $1.6 million of deferred tax expense in the nine months ended September 30, 2024 , and $1.1 million of deferred tax benefit for the same period in 2023 .

We recognized a net foreign currency gain, related to our borrowings from Hercules, the Royalty Financing Agreement and our cash and cash equivalents and investment securities as well as loans between entities within the uniQure group, of $7.2 million during the three months ended March 31, 2025, compared to a net loss of $1.1 million during the same period in 2024 .

Income tax expense

We recognized $0.5 million of deferred tax expense in the three months ended March 31, 2025 , and $0.7 million of deferred tax expense for the same period in 2024 .

Financial Position, Liquidity and Capital Resources

As of September 30, 2024, we had cash and cash equivalents, restricted cash and investment securities of $436.7 million.

As of March 31, 2025, we had cash and cash equivalents, restricted cash and investment securities of $410.4 million.

Until such time, if ever, as we can generate substantial cash flows from successfully commercializing our proprietary product candidates, we expect to finance our cash needs through a combination of equity offerings, debt financings, collaborations, strategic alliances and marketing, distribution, and licensing arrangements.

Based on our current operating plan, research and development plans and our timing expectations related to the progress of our programs, we believe that our cash and cash equivalents and investment securities will fund our operations through the end of 2027.

We have based this estimate on assumptions that may prove to be wrong, and we could exhaust our available capital resources sooner than we expect.

We expect that we will require additional funding if we decide to advance AMT-130 for our Huntington’s disease gene therapy program or any of our other product candidates into late-stage clinical development.

The amount and timing of our actual expenditures may vary significantly depending on numerous factors, including the timing of a potential BLA submission, the progress of regulatory interactions, approval (if any) and commercialization efforts with respect to AMT-130.

We expect that we will require additional funding if we decide to advance any of our other clinical product candidates into late-stage clinical development.

Our material cash requirements include the following contractual and other obligations:

As of September 30, 2024, we had an outstanding loan amount owed to Hercules Capital, Inc.

(“Hercules”) for an aggregate principal amount of $50.0 million.

On July 19, 2024, in connection with the closing of the Lexington Transaction, we repaid $50.0 million of the $100.0 million of principal outstanding as well as $3.1 million in end-of-term fees.

As of March 31, 2025, we had an outstanding loan amount owed to Hercules for an aggregate principal amount of $50.0 million.

Future interest payments and financing fees associated with the loan total $14.5 million, with $8.6 million payable within 12 months.

We are contractually required to repay the $50.0 million in full in January 2027.

We entered into lease arrangements for facilities, including corporate, manufacturing and office space.

As of September 30, 2024, we had fixed lease payment obligations of $25.3 million, with $4.3 million payable within 12 months.

Following the closing of the Lexington Transaction on July 22, 2024 we assigned our lease for the Lexington Facility to Genezen.

This reduced our fixed lease payment obligations by $21.8 million, including $4.4 million payable within 12 months.

We continue to guarantee such payments until the end of the lease term in May 2029.

We have entered into lease arrangements for facilities, including corporate, laboratories and office space.

As of March 31, 2025, we had fixed lease payment obligations of $22.8 million, with $4.2 million payable within 12 months.

Following the Lexington Transaction, we assigned our lease for the Lexington Facility to Genezen.

As of March 31, 2025, we continue to guarantee $19.6 million of fixed lease payments under the lease for the Lexington Facility until the end of the lease term in May 2029.

Commitments related to uniQure France SAS acquisition (nominal amounts)

In relation to our acquisition of uniQure France SAS in 2021, we entered into commitments to make payments to the former shareholders upon the achievement of certain contractual milestones.

In relation to our acquisition of uniQure France SAS, 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 transaction.

In September 2023, we made a payment of EUR 10.0 million ($10.6 million) to the former shareholders of uniQure France SAS following the FDA’s clearance of the IND application for AMT-260.

As of September 30, 2024, our remaining commitment amounts include a EUR 30.0 million ($33.5 million) milestone payment due upon treating the first patient in a Phase I/II clinical trial for AMT-260 and EUR 160.0 million ($178.6 million) in potential milestone payments associated with Phase III development and the approvals of AMT-260 in the U.S.

In December 2024, we made a payment of EUR 30.0 million ($31.5 million) to the former shareholders of uniQure France SAS following the dosing of the first patient in Phase I/II clinical trial for AMT-260.

As of March 31, 2025, our remaining commitment amounts include EUR 160.0 million ($166.2 million) in potential milestone payments associated with Phase III development and the approval of AMT-260 in the U.S.

and European Union.

The timing of achieving these milestones and consequently the timing of payments, as well as whether the milestones will be achieved at all, is generally uncertain.

These payments are owed in euro and have been translated at the foreign exchange rate as of September 30, 2024, of $1.12/€1.00.

As of September 30, 2024, we expect these obligations will become payable between 2024 and 2033.

The timing of achieving these milestones and consequently the timing of payments, as well as whether the milestone will be achieved at all, is generally uncertain.

These payments are owed in euro and have been translated at the foreign exchange rate as of March 31, 2025, of $1.08/€1.00.

As of March 31, 2025, we expect these obligations will become payable between 2029 and 2033.

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

2 unchanged sentences

We also owe payments to a financial advisor related to certain payments we will collect under the CSL Behring Agreement.

Commitments related to the CSA and DMSA with Genezen

Commitments related to the CSA and the DMSA with Genezen

Our CSA with Genezen requires us to take or pay contract manufacturing services for HEMGENIX® during a three-year period ending July 2027.

As of September 30, 2024, our remaining minimum purchase commitments to Genezen amount to $39.9 million, with $14.7 million to be paid within the next 12 months.

As of March 31, 2025, our remaining minimum purchase commitments to Genezen amount to $33.1 million, with $17.0 million to be paid within the next 12 months.

CSL Behring’s minimum purchase commitments to us over the next 12 months are $16.2 million.

Our DMSA with Genezen requires us to take or pay contract development services during a three-year period ending July 22, 2027.

As of September 30, 2024 our remaining minimum purchase commitments amount to $13.3 million with $3.5 million to be paid within the next 12 months.

The table below summarizes our consolidated cash flow data for the nine months ended September 30, 2024 and 2023:

Nine months ended September 30,

Our development and other manufacturing services agreement (“DMSA”) with Genezen requires us to take or pay contract development services during a three-year period ending July 2027.

As of March 31, 2025 our remaining minimum purchase commitments amount to $11.6 million with $4.5 million to be paid within the next 12 months.

The table below summarizes our consolidated cash flow data for the three months ended March 31, 2025 and 2024:

Three months ended March 31,

(in thousands)

1 unchanged sentence

Net cash used in operating activities

Net cash generated from / (used in) investing activities

Net cash (used in) / generated from financing activities

Net cash generated from investing activities

Net cash generated from financing activities

Foreign exchange impact

3 unchanged sentences

We continue to incur losses in the current period.

We recorded a net loss of $44.4 million and $166.3 million in the three and nine months ended September 30, 2024, respectively, compared to a net loss of $89.6 million and $235.3 million during the same periods in 2023.

As of September 30, 2024, we had an accumulated deficit of $1,056.7 million.

We recorded a net loss of $43.6 million in the three months ended March 31, 2025, respectively, compared to a net loss of $65.6 million during the same period in 2024.

As of March 31, 2025, we had an accumulated deficit of $1,173.6 million.

Sources of liquidity

From our first institutional venture capital financing in 2006 through the current period, we funded our operations primarily through private and public placements of equity securities, debt securities, payments from our collaboration partners as well as from selling a portion of royalties due from our collaboration partner CSL Behring.

We collected $100.0 million in July 2023 related to the first sale milestone of HEMGENIX® in the U.S., and are eligible to receive additional milestone payments, as well as royalties (to the extent not owed to settle the liability from royalty financing) on net sales of HEMGENIX®.

On May 12, 2023 we and Hercules amended the 2021 Restated Facility.

The 2023 Amended Facility extended the maturity date and interest-only period from December 1, 2025 to January 5, 2027.

In connection with the closing of the Lexington Transaction on July 22, 2024 we amended the 2023 Amended Facility and repaid $50.0 million of the principal.

From our first institutional venture capital financing in 2006 through the current period, we funded our operations primarily through private and public placements of equity securities, debt securities, payments from our collaboration partners as well as $370.1 million from selling a portion of royalties due from our collaboration partner CSL Behring in 2023.

Between July 2021 and July 2023, we collected $617.4 million from CSL Behring as a result of the sale of HEMGENIX® to CSL and other milestones collected from CSL, and we are eligible to receive additional milestone payments, as well as royalties (to the extent not owed to settle the liability from the Royalty Financing Transaction) on net sales of HEMGENIX®.

In January 2025, we raised net proceeds of $70.1 million, after deducting underwriting discounts and commissions and other offering expenses payable by us, through a follow-on public offering of 4.4 million ordinary shares at a price to the public of $17.00 per ordinary share.

In February 2025, we raised an additional $10.6 million in net proceeds upon the underwriters’ exercise of their option to purchase an additional 0.7 million ordinary shares at the public offering price.

On May 12, 2023, we and Hercules amended our debt facility.

The amendment extends the Maturity Date and interest-only period from December 2025 to January 2027.

In connection with the Lexington Transaction in July 2024 we amended the debt facility again and repaid $50.0 million of the principal balance outstanding.

We are required to repay the remaining principal balance of $50.0 million on the Maturity Date.

The interest rate is adjustable and is the greater of (i) 7.95% and (ii) 7.95% plus the prime rate less 3.25% per annum.

Under the 2024 Amended Facility, we owe a back-end fee of $2.4 million on December 1, 2025 and a back-end fee of $0.6 million on the maturity date.

We are subject to certain covenants under the 2024 Amended Facility and may become subject to covenants under any future indebtedness that could limit our ability to take specific actions, such as incurring additional debt, making capital expenditures, or declaring dividends, which could adversely impact our ability to conduct our business.

We owe a back-end fee of $2.4 million on December 1, 2025 and a back-end fee of $0.6 million on the Maturity Date.

We are subject to certain covenants under the debt facility and may become subject to covenants under any future indebtedness that could limit our ability to take specific actions, such as incurring additional debt, making capital expenditures, or declaring dividends, which could adversely impact our ability to conduct our business.

In addition, our pledge of assets as collateral to secure our obligations under the 2024 Amended Facility may limit our ability to obtain debt financing.

The 2024 Amended Facility permits us to issue up to $500.0 million of convertible debt.

The debt facility permits us to issue up to $500.0 million of convertible debt.

To the extent we need to finance our cash needs through equity offerings or debt financings, such financing may be subject to unfavorable terms including without limitation, the negotiation and execution of definitive documentation, as well as credit and debt market conditions, and we may not be able to obtain such financing on terms acceptable to us or at all.

If financing is not available when needed, including through debt or equity financing, or is available only on unfavorable terms, we may be unable to meet our cash needs.

If financing is not available when needed, including through debt or equity financings, or is available only on unfavorable terms, we may be unable to meet our cash needs.

If we raise additional funds through collaborations, strategic alliances or marketing, distribution, or licensing arrangements with third parties, we may have to relinquish valuable rights to our technologies, future revenue streams or product candidates or grant licenses on terms that may not be favorable to us.

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Net cash used in operating activities

Net cash used in operating activities was $129.9 million for the nine months ended September 30, 2024 and consisted of net loss of $166.3 million adjusted for non-cash items, including depreciation and amortization expense of $8.3 million, amortization of the discount on investment securities of $8.5 million, share-based compensation expense of $17.5 million, $37.7 million of interest expense related to the Royalty Financing Agreement, a change in deferred taxes of $1.6 million, changes in the fair value of contingent consideration of $2.0 million, a provision for inventory write-downs of $6.3 million and unrealized foreign exchange gains of $5.7 million.

Net cash used in operating activities was $44.1 million for the three months ended March 31, 2025 and consisted of net loss of $43.6 million adjusted for non-cash items, including depreciation and amortization expense of $4.5 million, amortization of the discount on investment securities of $2.1 million, share-based compensation expense of $4.4 million, $8.4 million of interest expense net of interest paid related to May 2023 Royalty Financing Agreement, a change in deferred taxes of $0.5 million, changes in the fair value of contingent consideration of $1.2 million, and unrealized foreign exchange gains of $7.1 million.

Net cash used in operating activities also included unfavorable changes in operating assets and liabilities of $6.3 million.

There was a net increase in accounts receivable, prepaid expenses, and other current assets and receivables of $3.0 million.

There was an increase in inventory balances of $3.9 million.

There was a net decrease in accounts payable, accrued expenses, other liabilities, and operating leases of $3.3 million.

Net cash used in operating activities was $96.4 million for the nine months ended September 30, 2023 and consisted of net loss of $235.3 million adjusted for non-cash items, including depreciation and amortization expense of $7.7 million, amortization of the premium/discount on investment securities of $6.5 million, share-based compensation expense of $28.1 million, changes in the fair value of contingent consideration of $15.4 million, unrealized foreign exchange losses of $3.1 million, $14.9 million of interest expense related to the Royalty Financing Agreement and a change in deferred taxes of $1.1 million.

Net cash used in operating activities also included favorable changes in operating assets and liabilities of $77.0 million.

There was a net decrease in accounts receivable, prepaid expenses, and other current assets and receivables of $96.6 million, primarily related to the collection of the $100.0 million milestone due from CSL Behring in July 2023.

There was an increase in inventory balances of $8.7 million.

There was a net decrease in accounts payable, accrued expenses, other liabilities, and operating leases of $10.8 million, primarily related to a decrease of $4.8 million in accounts payable and a decrease of $6.0 million related to various accruals.

Net cash used in operating activities also includes a payment for a contingent consideration milestone of $1.9 million.

Net cash generated from / (used in) investing activities

In the nine months ended September 30, 2024, we generated $189.6 million in our investing activities compared to using $265.2 million for the same period in 2023.

Nine months ended September 30,

Net cash used in operating activities was $60.6 million for the three months ended March 31, 2024 and consisted of net loss of $65.6 million adjusted for non-cash items, including depreciation and amortization expense of $2.6 million, amortization of the discount on investment securities of $3.7 million, share-based compensation expense of $7.2 million, $10.9 million of interest expense net of interest paid related to May 2023 Royalty Financing Agreement, a change in deferred taxes of $0.7 million, changes in the fair value of contingent consideration of $0.2 million and unrealized foreign exchange losses of $1.4 million.

Net cash used in operating activities also included unfavorable changes in operating assets and liabilities of $17.0 million.

There was a net increase in accounts receivable, prepaid expenses, and other current assets and receivables of $10.4 million.

There was a decrease in inventory balances of $2.2 million.

There was a net decrease in accounts payable, accrued expenses, other liabilities, and operating leases of $8.8 million, primarily related to a decrease of $6.7 million from personnel-related accruals.

Net cash generated from investing activities

In the three months ended March 31, 2025, we generated $20.1 million in our investing activities compared to generating $64.0 million for the same period in 2024.

Three months ended March 31,

(in thousands)

Cash flows from investing activities

Proceeds from maturity of debt securities

Investment in debt securities

Divestment of commercial manufacturing facility

Capital expenditures - Amsterdam site

Capital expenditures - European sites

Capital expenditures - Lexington site

Net cash generated from / (used in) investing activities

During the nine months ended September 30, 2024, we received $480.8 million from the repayment of previous investments into euro and U.S.

dollar denominated government bonds ($106.3 million for nine months ended September 30, 2023).

During the nine months ended September 30, 2024, we invested $279.6 million of our cash on hand into euro and dollar denominated government bonds ($366.4 for the nine months ended September 30, 2023).

During the nine months ended September 30, 2024 we incurred a cash outflow of $8.3 million related to the divestment of our commercial manufacturing facility.

We invested $1.7 million and $1.6 million, respectively, into our Amsterdam, Netherlands and Lexington, Massachusetts sites during the nine months ended September 30, 2024, compared to $2.2 million and $3.0 million for the same period in 2023.

Net cash generated from / (used in) financing activities

In the nine months ended September 30, 2024, we used $53.0 million in financing activities compared to generating $362.7 million for the same period in 2023.

Nine months ended September 30,

Net cash generated from investing activities

Net cash generated from financing activities

In the three months ended March 31, 2025, we generated $80.6 million in financing activities compared to generating nil for the same period in 2024.

Three months ended March 31,

(in thousands)

Cash flows from financing activities

Proceeds from royalty financing agreement, net of debt issuance costs

Proceeds from public offering of shares in connection with follow on, net of issuance costs

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

Contingent consideration payment

Repayment of long-term debt

Net cash (used in) / generated from financing activities

In June 2023, we received $370.1 million net proceeds from the Royalty Financing Agreement.

During the nine months ended September 30, 2024, we received $0.1 million from the exercise of options to purchase ordinary shares in relation to our 2014 Plans, compared to $0.3 million for the same period in 2023.

In September 2023, following the FDA’s clearance of the IND application for AMT-260, we made a contingent consideration payment of $9.5 million to the former shareholders of uniQure France SAS related to a contractually defined milestone, of which $7.6 million was classified as cash flows from financing activities and $1.9 million was classified as a net cash flow used in operating activities.

We made nil payments for the period ended September 30, 2024.

During the nine months ended September 30, 2024 we repaid $50.0 million of the $100.0 million of principal outstanding of the Hercules debt as well as $3.1 million in end-of-term fees.

Net cash generated from financing activities

Funding requirements

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

● contractual milestone payments and royalties we might be owed in accordance with the CSL Behring Agreement;

● activities related to submission of a BLA for AMT-130 in Huntington’s disease;

● activities to prepare for the commercialization of AMT-130 in Huntington’s disease in the United States;

● investments to launch AMT-130 in Huntington’s disease in the United States including the amounts of revenue we generate following the launch;

● earnout payments we might owe the former shareholders of uniQure France SAS, which are subject to the achievement of specific development and regulatory milestones;

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

● contractual milestone payments and royalties we might be owed in accordance with the CSL Behring Agreement;

● the scope, timing, results, and costs of our current and planned clinical trials;

● the scope, obligations and restrictions on our business related to our existing equity, debt or royalty monetization financings and underlying agreements;

● the extent to which we acquire or in-license other businesses, products, product candidates or technologies;

● the amount and timing of revenue, if any, we receive from manufacturing products for CSL Behring;

● the scope, timing, results and costs of preclinical development and laboratory testing of our additional product candidates;

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What changed 10-Q

Item 2. Management’s Discussion and Analysis