PTC Therapeutics, Inc.: Form 10-Q for the period ended Sep 30, 2025

The following discussion and analysis is meant to provide material information relevant to an assessment of the financial condition and results of operations of our company, including an evaluation of the amounts and certainty of cash flows from operations and from outside resources, so as to allow investors to better view our company from management’s perspective. The following discussion of our financial condition and results of operations should be read in conjunction with our financial statements and the notes to those financial statements appearing elsewhere in this Quarterly Report on Form 10-Q and the audited consolidated financial statements and notes thereto and management’s discussion and analysis of financial condition and results of operations for the year ended December 31, 2024 included in our Annual Report on Form 10-K filed with the Securities and Exchange Commission on February 27, 2025, or our 2024 Annual Report. This discussion contains forward-looking statements that involve significant risks and uncertainties. As a result of many factors, such as those set forth in Part II, Item 1A. (Risk Factors) of this Quarterly Report on Form 10-Q and Part I, Item 1A. (Risk Factors) of our 2024 Annual Report, our actual results may differ materially from those anticipated in these forward-looking statements.

Our Company

We are a global biopharmaceutical company dedicated to the discovery, development and commercialization of clinically differentiated medicines for children and adults living with rare disorders. We are advancing a robust and diversified pipeline of transformative medicines as part of our mission to provide access to best-in-class treatments for patients with unmet medical needs. Our strategy is to leverage our scientific expertise and global commercial infrastructure to optimize value for our patients and other stakeholders. We have a diversified therapeutic portfolio pipeline that includes several commercial products and product candidates in various stages of development, including clinical, pre-clinical and research and discovery stages, focused on the development of new treatments for multiple therapeutic areas for rare diseases relating to neurology and metabolism.

Corporate Updates

Sephience™ (sepiapterin)

Sephience (sepiapterin) is a product for the treatment of phenylketonuria, or PKU, a rare inherited metabolic disease characterized by the body’s inability to break down an essential amino acid called phenylalanine, and which can result in neurological and other symptoms. On July 28, 2025, Sephience was approved by the U.S. Food and Drug Administration, or the FDA, for the treatment of pediatric and adult patients living with PKU in the United States age one month and above. On June 19, 2025, Sephience was granted marketing authorization by the European Commission, or the EC, for the treatment of children and adults living with PKU within the European Economic Area, or the EEA. We also made regulatory submissions for Sephience for the treatment of PKU in Brazil in the third quarter of 2024, and in Japan in the fourth quarter of 2024, with regulatory decisions expected in the fourth quarter of 2025. During the quarter ended September 30, 2025, we recognized $19.6 million in net sales of Sephience.

Censa Rights Satisfaction Agreement

On August 5, 2025, we, certain of the former securityholders of Censa, and, for the limited purposes set forth in the agreement, Shareholder Representative Services LLC, a Colorado limited liability company, entered into a Rights Satisfaction Agreement, or the Rights Satisfaction Agreement, pursuant to which such former securityholders of Censa, or the Participating Rightsholders, agreed to the cancellation and forfeiture of their rights to receive certain contingent payments from us based on worldwide annual net sales by us of products containing sepiapterin, or Net Sales of Product, under the Agreement and Plan of Merger, dated as of May 5, 2020, or the Censa Merger Agreement, by and among us, Hydro Merger Sub, Inc., our wholly owned, indirect subsidiary, Censa and, solely in its capacity as the representative, agent and attorney-in-fact of the securityholders of Censa, Shareholder Representative Services LLC, in exchange for the consideration set forth in the Rights Satisfaction Agreement and further detailed below.

Pursuant to the terms of the Rights Satisfaction Agreement, the Participating Rightsholders have canceled and forfeited their rights under the Censa Merger Agreement to receive a percentage of annual net sales during the applicable payment term equal to (i) 8% of annual Net Sales of Product for that portion of annual Net Sales of Product less than or equal to $250.0 million, (ii) 10% of annual Net Sales of Product for that portion of annual Net Sales of Product greater than $250.0 million but less than $500.0 million and (iii) 12% of annual Net Sales of Product for that portion of annual Net Sales of Product greater than $500.0 million, which we refer to collectively as the Net Sales Payments.

In consideration of the foregoing, we agreed to pay to the Participating Rightsholders an aggregate amount in cash up to $250.0 million, or the Upfront Consideration, upon the consummation of the transactions contemplated by the Rights Satisfaction Agreement, or the Closing, and potential milestone payments, each, an Additional Milestone Payment, of up to $100.0 million each (or up to $500.0 million in the aggregate) based on the achievement of specified Net Sales Thresholds (as defined in the Censa Merger Agreement). The amount of the Upfront Consideration and the Additional Milestone Payments was subject to adjustment in the Rights Satisfaction Agreement based on the number of Participating Rightsholders.

At the Closing, based on the participation of former Censa securityholders holding approximately 90% of Censa’s equity securities prior to the consummation of the transactions contemplated by the Censa Merger Agreement, we paid an aggregate amount of Upfront Consideration in cash of $225.1 million. Additionally, we are obligated to make Additional Milestone Payments in an amount equal to approximately $90.0 million upon achievement of each of the (i) first occurrence of a three or fewer consecutive calendar year period in which aggregate Net Sales of Product are greater than $3.0 billion, (ii) first occurrence of a five or fewer consecutive calendar year period in which aggregate Net Sales of Product are greater than $5.0 billion, (iii) first occurrence of a seven or fewer consecutive calendar year period in which aggregate Net Sales of Product are greater than $7.0 billion, (iv) first occurrence of a nine or fewer consecutive calendar year period in which aggregate Net Sales of Product are greater than $9.0 billion and (v) first occurrence of an 11 or fewer consecutive calendar year period in which aggregate Net Sales of Product are greater than $11.0 billion. If, after the Closing, any additional former securityholder of Censa executes and delivers a joinder to the Rights Satisfaction Agreement and becomes a party thereto, we will pay such former securityholder an amount in cash equal to such former securityholder’s applicable pro rata share of the Upfront Consideration (less any Net Sale Payments previously received) and any Additional Milestone Payments that become payable to Participating Rightsholders under the Rights Satisfaction Agreement.

In addition to the Additional Milestone Payments, and pursuant to the terms of the Censa Merger Agreement, we will make payments of $30.0 million for the first occurrence of a four consecutive calendar quarter period in which aggregate Net Sales of Product (as defined in the Censa Merger Agreement) exceed $250.0 million, $50.0 million for the first occurrence of a four consecutive calendar quarter period in which aggregate Net Sales of Product exceed $500.0 million, and $80.0 million for the first occurrence of a four consecutive calendar quarter period in which aggregate Net Sales of Product exceed $1.0 billion.

The Rights Satisfaction Agreement has no effect on the Censa Merger Agreement other than to provide for the cancellation and forfeiture of the Participating Rightsholders’ rights to receive the Net Sales Payments described above. As a result, all other rights and obligations under the Censa Merger Agreement remain in effect pursuant to their terms, including, without limitation, our obligation to pay certain contingent payments upon the achievement of certain development and Net Sales of Product milestones.

The Rights Satisfaction Agreement contains customary representations, warranties and covenants of us and the Participating Rightsholders and provided for a simultaneous signing and closing.

Global Commercial Footprint

Global DMD Franchise

We have two products, Translarna™ (ataluren) and Emflaza® (deflazacort), for the treatment of Duchenne muscular dystrophy, or DMD, a rare, life-threatening disorder. Translarna has marketing authorization in Russia for the treatment of nonsense mutation Duchenne muscular dystrophy, or nmDMD, in patients aged two years and older, and in Brazil for the treatment of nmDMD in ambulatory patients two years and older and for continued treatment of patients that become non-ambulatory, as well as in various other countries. During the quarter ended September 30, 2025, we recognized $50.7 million in net sales of Translarna. We hold worldwide commercialization rights to Translarna for all indications in all territories. Emflaza is approved in the United States for the treatment of DMD in patients two years and older. During the quarter ended September 30, 2025, we recognized $35.2 million in net sales of Emflaza.

We previously had a marketing authorization for Translarna in the EEA, which had been subject to annual review and renewal by the EC, following reassessment by the European Medicines Agency, or EMA, of the benefit-risk balance of the authorization. In September 2022, we submitted a Type II variation to the EMA to support conversion of the conditional marketing authorization for Translarna to a standard marketing authorization, which included a report on the placebo-controlled trial of Study 041 and data from the open-label extension as further described below. Study 041 was an 18-month, placebo-controlled trial, followed by an 18-month open-label extension of Translarna in the treatment of ambulatory patients with nmDMD aged five years or older. In February 2023, we also submitted an annual marketing authorization renewal request to the EMA. In September 2023, the Committee for Medicinal Products for Human Use, or CHMP, gave a negative opinion on the conversion of the conditional marketing authorization to full marketing authorization of Translarna for the treatment of nmDMD and a negative opinion on the renewal of the existing conditional marketing authorization of Translarna for the treatment of nmDMD. In January 2024, the CHMP issued a negative opinion for the renewal of the conditional marketing authorization following a re-examination procedure. In May 2024, the EC decided not to adopt the CHMP’s negative opinion for the renewal of the conditional marketing authorization of Translarna and returned such opinion to the CHMP for re-evaluation. In June 2024, following the EC’s request for re-review, the CHMP issued a negative opinion on the renewal of the conditional marketing authorization of Translarna for the treatment of nmDMD. In October 2024, the CHMP maintained its negative opinion for the renewal of the conditional marketing authorization following the requested reexamination procedure. In March 2025, the EC adopted the opinion of the CHMP to not renew the authorization of Translarna for the treatment of nmDMD. However, the EC indicated that individual countries within the European Union, or EU, can leverage Articles 117(3) and 5(1) of the EU Directive 2001/83 to allow continued commercial use of Translarna. There is a substantial risk that as a result of the EC’s adoption of the CHMP’s negative opinion we will lose a significant portion of our ability to generate revenue from sales of Translarna in the EEA.

Translarna is an investigational new drug in the United States. During the first quarter of 2017, we filed a New Drug Application, or NDA, for Translarna for the treatment of nmDMD over protest with the FDA. In October 2017, the Office of Drug Evaluation I of the FDA issued a Complete Response Letter, or CRL, for the NDA, stating that it was unable to approve the application in its current form. In response, we filed a formal dispute resolution request with the Office of New Drugs of the FDA. In February 2018, the Office of New Drugs of the FDA denied our appeal of the CRL. In its response, the Office of New Drugs recommended a possible path forward for the ataluren NDA submission based on the accelerated approval pathway. This would involve a resubmission of an NDA containing the current data on effectiveness of ataluren with new data to be generated on dystrophin production in nmDMD patients’ muscles. We followed the FDA’s recommendation and collected, using newer technologies via procedures and methods that we designed, such dystrophin data in a new study, Study 045, and announced the results of Study 045 in February 2021. Study 045 did not meet its pre-specified primary endpoint. In June 2022, we announced top-line results from the placebo-controlled trial of Study 041. Following this announcement, we submitted a meeting request to the FDA to gain clarity on the regulatory pathway for a potential resubmission of an NDA for Translarna. The FDA provided initial written feedback that Study 041 does not provide substantial evidence of effectiveness to support an NDA resubmission. We held a Type C meeting with the FDA in the fourth quarter of 2023 to discuss the totality of Translarna data. Based on feedback from the FDA, we resubmitted the NDA in July 2024, based on the results from Study 041 and from our international drug registry study for nmDMD patients receiving Translarna. In October 2024, the FDA accepted for review the resubmission of the NDA for Translarna for the treatment of nmDMD. As this was an NDA resubmission following a complete response letter to the NDA which was filed over protest in 2016, the FDA is not obligated to follow the review timelines under Prescription Drug User Fee Act guidelines, and an action date has not been provided.

We have previously relied on Emflaza’s seven-year marketing exclusivity period in the United States for its approved indications under the provisions of the Orphan Drug Act of 1983, or the Orphan Drug Act, when commercializing Emflaza. Emflaza’s seven-year period of orphan drug exclusivity related to the treatment of DMD in patients five years and older expired in February 2024. We expect the expiration of this orphan drug exclusivity to potentially have a significant negative impact on Emflaza net product revenue. Emflaza’s orphan drug exclusivity related to the treatment of DMD in patients two years of age to less than five expires in June 2026.

Upstaza™ (eladocagene exuparvovec) / Kebilidi™ (eladocagene exuparvovec-tneq)

Upstaza/Kebilidi is a gene therapy for the treatment of Aromatic L Amino Acid Decarboxylase, or AADC, deficiency, a rare central nervous system, or CNS, disorder arising from reductions in the enzyme AADC that results from mutations in the dopa decarboxylase gene. In July 2022, the EC approved Upstaza for the treatment of AADC deficiency for patients 18 months and older within the EEA. In November 2022, the Medicines and Healthcare Products Regulatory Agency approved Upstaza for the treatment of AADC deficiency for patients 18 months and older within the United Kingdom. In November 2024, the FDA granted accelerated approval of our gene therapy for the treatment of children and adults with AADC deficiency, which is marketed with the brand name Kebilidi in the United States.

Tegsedi® (inotersen) and Waylivra™ (volanesorsen)

We hold the rights for the commercialization of Tegsedi and Waylivra for the treatment of rare diseases in countries in Latin America and the Caribbean pursuant to a Collaboration and License Agreement, or the Tegsedi-Waylivra Agreement, dated August 1, 2018, by and between us and Akcea Therapeutics, Inc., or Akcea, a subsidiary of Ionis Pharmaceuticals, Inc. Tegsedi has received marketing authorization in the United States, EU, and Brazil for the treatment of stage 1 or stage 2 polyneuropathy in adult patients with hereditary transthyretin amyloidosis, or hATTR amyloidosis. In August 2021, ANVISA, the Brazilian health regulatory authority, approved Waylivra as the first treatment for familial chylomicronemia syndrome, or FCS, in Brazil. In December 2022, ANVISA approved Waylivra for the treatment of familial partial lipodystrophy, or FPL. Waylivra has also received marketing authorization in the EU for the treatment of FCS.

Evrysdi® (risdiplam)

We also have a spinal muscular atrophy, or SMA, collaboration with F. Hoffman-La Roche Ltd. and Hoffman La Roche Inc., which we refer to collectively as Roche, and the Spinal Muscular Atrophy Foundation, or SMA Foundation. The SMA program has one approved product, Evrysdi (risdiplam), which was approved by the FDA in August 2020 for the treatment of SMA in adults and children two months and older and by the EC in March 2021 for the treatment of 5q SMA in patients two months and older with a clinical diagnosis of SMA Type 1, Type 2 or Type 3 or with one to four SMN2 copies. Evrysdi also received marketing authorization for the treatment of SMA in over 100 countries. In May 2022, the FDA approved a label expansion for Evrysdi to include infants under two months old with SMA. In August 2023, the EC approved an extension of the Evrysdi marketing authorization to include infants under two months old in the EU.

Diversified Development Pipeline

Splicing Platform

In addition to our SMA program, our splicing platform also includes votoplam (PTC518), which is being developed for the treatment of Huntington’s disease, or HD. We announced the results from our Phase 1 study of votoplam in healthy volunteers in September 2021 demonstrating dose-dependent lowering of huntingtin messenger ribonucleic acid and protein levels, that votoplam efficiently crosses blood brain barrier at significant levels and that votoplam was well tolerated. We initiated a Phase 2 study of votoplam for the treatment of HD in the first quarter of 2022, which consisted of an initial 12-week placebo-controlled phase focused on safety, pharmacology and pharmacodynamic effects followed by a nine-month placebo-controlled phase focused on votoplam biomarker effect. In June 2024, we announced interim results from the full Phase 2 study of votoplam. At month 12, votoplam treatment demonstrated durable dose-dependent lowering of mHTT protein in the blood and dose-dependent lowering of mHTT protein in the cerebrospinal fluid in the interim cohort of stage 2 patients. In addition, favorable trends were demonstrated on several relevant HD clinical assessments. Furthermore, following 12 months of treatment, votoplam continued to be well tolerated. In September 2024, the FDA granted Fast Track designation to the votoplam program for the treatment of HD. In December 2024, we held a Type C meeting with the FDA to discuss whether huntingtin protein lowering could be considered a surrogate endpoint for accelerated approval of votoplam. The FDA was aligned on the scientific rationale and asked to see additional data supportive of an association between huntingtin protein lowering and changes in clinical outcome scores. In May 2025, we announced that the Phase 2 study of votoplam met its primary endpoints of blood HTT lowering and safety. The results on the full study population are consistent with the previously reported evidence of dose-dependent HTT lowering, favorable safety profile and early signals of dose-dependent clinical effect at 12 months in Stage 2 patients. In addition, at

24 months of treatment, there were continued trends of dose-dependent favorable clinical effect relative to a propensity-matched natural history cohort as well as dose-dependent NfL lowering. In November 2024, we entered into the License and Collaboration Agreement, or the Novartis Agreement, with Novartis Pharmaceuticals Corporation, or Novartis, relating to our votoplam program. This transaction closed in January 2025. Pursuant to the Novartis Agreement, we were responsible for completing the ongoing Phase 2A clinical trial and continuing the ongoing open label extension, or OLE, clinical trial pursuant to its existing development plan, with the goal of transitioning the ongoing OLE clinical trial to Novartis within 12 months after the effective date of the Novartis Agreement. As of September 30, 2025, these were considered substantially complete. Novartis will be responsible for all other development of licensed compounds and licensed products and the manufacture and commercialization of licensed compounds and licensed products worldwide. We continue to collaborate with Novartis on next steps and aim to meet with FDA in the fourth quarter of 2025 to discuss Phase 3 clinical trial design and potential accelerated approval pathway.

Inflammation and Ferroptosis Platform

Our inflammation and ferroptosis platform consists of small molecule compounds that target key enzymes that regulate oxidative stress and inflammatory pathways central to the pathology of a number of CNS and non-CNS diseases. The most advanced molecule in our inflammation and ferroptosis platform is vatiquinone. We announced topline results from a registration-directed Phase 3 trial of vatiquinone in children and young adults with Friedreich’s Ataxia, called MOVE-FA, in May 2023. While the study did not meet its primary endpoint of statistically significant change in modified Friedreich Ataxia Rating Scale, or mFARS, score at 72 weeks in the primary analysis population, vatiquinone treatment did demonstrate significant benefit on key disease subscales and secondary endpoints. In addition, in the population of subjects that completed the study protocol, significance was reached in the mFARS endpoint and several secondary endpoints, including the upright stability subscale. Furthermore, vatiquinone was well tolerated. In October 2024, we announced that the pre-specified endpoint for two different FA long-term extension studies was met, with statistically significant evidence of durable treatment benefit on disease progression. In December 2024, we submitted an NDA to the FDA for vatiquinone for the treatment of children and adults living with FA. In August 2025, the FDA issued a complete response letter related to the NDA stating that substantial evidence of efficacy was not demonstrated for vatiquinone and that an additional adequate and well-controlled study would be needed to support NDA resubmission. We plan to meet with the FDA in the fourth quarter to discuss the vatiquinone development program.

Multi-Platform Discovery

In addition, we have a pipeline of product candidates and discovery programs that are in early clinical, pre-clinical and research and development stages focused on the development of new treatments for multiple therapeutic areas for rare diseases.

Funding

The success of our products and any other product candidates we may develop depends largely on obtaining and maintaining reimbursement from governments and third-party insurers. Our revenues are primarily generated from sales of Translarna in countries where we were able to obtain acceptable commercial pricing and reimbursement terms and in select countries where we are permitted to distribute Translarna under our early access programs, or EAP, programs or through similar styled programs, and from sales of Emflaza for the treatment of DMD in the United States. Beginning in the three months ended September 30, 2025, our revenues are also generated from sales of Sephience for the treatment of PKU in the United States and in territories outside of the United States. We also generate revenue from sales of Upstaza/Kebilidi for the treatment of AADC deficiency based on regulatory approvals in the EEA and the United States, we have recognized revenue associated with milestone and royalty payments from Roche pursuant to a License and Collaboration Agreement, or the SMA License Agreement, by and among us, Roche and, for the limited purposes set forth therein, the SMA Foundation, under our SMA program and we have recognized license revenues related to performance obligations already completed pursuant to the Novartis Agreement.

We have financed our operations to date primarily through the private offerings of convertible senior notes, public and “at the market offerings” of common stock, proceeds from royalty purchase agreements, private placements of our convertible preferred stock and common stock, collaborations, bank and institutional lender debt, other convertible debt, grant funding and clinical trial support from governmental and philanthropic organizations and patient advocacy groups in the disease area addressed by our product candidates. We have relied on revenue generated from net sales of our products. We have also relied on revenue associated with milestone and royalty payments from Roche pursuant to the SMA License Agreement under our SMA program, revenue generated from net sales of Tegsedi and Waylivra in Latin America and the Caribbean, and license revenues related to performance obligations already completed pursuant to the Novartis Agreement.

In June 2024, we entered into an amendment with Royalty Pharma Investments 2019 ICAV, or Royalty Pharma, and Royalty Pharma plc, to the Amended and Restated Royalty Purchase Agreement, dated October 18, 2023, or the A&R Royalty Purchase Agreement, which amends and restated in its entirety the Royalty Purchase Agreement by and among us, RPI Intermediate Finance Trust, and for the limited purposes set forth in the agreement, Royalty Pharma plc, dated as of July 17, 2020, or the Original Royalty Purchase Agreement, and we exercised our first put option in exchange for $241.8 million in cash consideration. To date, Royalty Pharma has paid to us cash consideration of $1.9 billion (less payments on our right to receive sales-based royalty payments, or the Royalty, on worldwide net sales of Evrysdi and any other product in development pursuant to the SMA License Agreement received by us with respect to assigned Royalties, or the Assigned Royalty Rights) in exchange for 90.49% of the Royalty, which will be reduced to 83.33% after Royalty Pharma receives $1.3 billion in aggregate payments, or the Assigned Royalty Cap, from the Royalty assigned under the Original Royalty Purchase Agreement. We currently retain 9.51% of the Royalty, which increases to 16.67% after the Assigned Royalty Cap has been met. We have the option to sell our retained portions of the Royalty to Royalty Pharma in up to three tranches for the following payments: (1) $100.0 million in exchange for 3.81% of the Royalty, which increases to 6.67% after the Assigned Royalty Cap has been met, (2) $100.0 million in exchange for 3.81% of the Royalty, which increases to 6.67% after the Assigned Royalty Cap has been met, and (3) $50.0 million in exchange for 1.90% of the Royalty, which increases to 3.33% after the Assigned Royalty Cap has been met, in each case less Royalty payments received by us with respect to the Assigned Royalty Rights.

In November 2024, we entered into the Novartis Agreement relating to our votoplam HD program which includes related molecules. Pursuant to the Novartis Agreement, we were responsible for completing the ongoing Phase 2A clinical trial and continuing the ongoing OLE clinical trial pursuant to its existing development plan, with the goal of transitioning the ongoing OLE clinical trial to Novartis within 12 months after the effective date. As of September 30, 2025, these were considered substantially complete. Novartis will be responsible for all other development of licensed compounds and licensed products and the manufacture and commercialization of licensed compounds and licensed products worldwide. Under the Novartis Agreement, and upon the closing of the transaction contemplated by the Novartis Agreement in January 2025, we received an upfront payment of $1.0 billion on the effective date and can receive up to $1.9 billion in development, regulatory and sales milestones, a 40% share of U.S. profits and losses, and tiered double-digit royalties on ex-U.S. sales.

In August 2019, we entered into an At the Market Offering Sales Agreement, or the Sales Agreement, with Cantor Fitzgerald and RBC Capital Markets, LLC, or together, the Sales Agents, pursuant to which, we may offer and sell shares of our common stock, having an aggregate offering price of up to $125.0 million from time to time through the Sales Agents by any method that is deemed to be an “at the market offering” as defined in Rule 415(a)(4) promulgated under the Securities Act of 1933, as amended, or the Securities Act. During the three and nine months ended September 30, 2025, we did not issue or sell any shares of common stock pursuant to the Sales Agreement. The remaining shares of our common stock available to be issued and sold, under the Sales Agreement, have an aggregate offering price of up to $93.0 million as of September 30, 2025.

As of September 30, 2025, we had an accumulated deficit of $2,829.3 million. We had a net income of $817.6 million and a net loss of $297.4 million for the nine months ended September 30, 2025 and 2024, respectively.

We anticipate that we will continue to incur significant expenses in connection with our commercialization efforts in the United States, the EEA, Latin America and other territories, including expenses related to our commercial infrastructure and corresponding sales and marketing, legal and regulatory, and distribution and manufacturing undertakings as well as administrative and employee-based expenses. In addition to the foregoing, we expect to continue to incur significant costs in connection with ongoing, planned and potential future clinical trials and studies for our splicing and inflammation and ferroptosis programs as well as studies in our products for maintaining authorizations, label extensions and additional indications. We continue to seek marketing authorization for Translarna for the treatment of nmDMD and Sephience for the treatment of pediatric and adult patients living with PKU in territories in which we do not currently have marketing authorization. These efforts may significantly impact the timing and extent of our commercialization and manufacturing expenses.

We may seek to expand and diversify our product pipeline through opportunistically in-licensing or acquiring the rights to products, product candidates or technologies and we may incur expenses, including with respect to transaction costs, subsequent development costs or any upfront, milestone or other payments or other financial obligations associated with any such transaction, which would increase our future capital requirements.

With respect to our outstanding 1.50% convertible senior notes due September 15, 2026, or the 2026 Convertible Notes,

cash interest payments are payable on a semi-annual basis in arrears, which will require total funding of $4.3 million

annually.

In July 2025, Sephience™ (sepiapterin) was granted FDA approval for the treatment of children and adults living with PKU. Pursuant to the Censa Merger Agreement, the approval triggered a $32.5 million milestone to the former Censa securityholders, which was recorded in accounts payable and accrued expenses on our consolidated balance sheet as of September 30, 2025.

We also have certain significant contractual obligations and commercial commitments that require funding and we have disclosed these items under the heading “Management’s Discussion and Analysis of Financial Condition and Results of Operations-Funding Obligations” in our 2024 Annual Report. There were no material changes to these obligations and commitments during the period ended September 30, 2025. Furthermore, since we are a public company, we have incurred and expect to continue to incur additional costs associated with operating as such including significant legal, accounting, investor relations and other expenses.

We will need to generate significant revenues to sustain profitability, and we may never do so. Accordingly, we may need to obtain substantial additional funding in connection with our continuing operations. Adequate additional financing may not be available to us on acceptable terms, or at all. If we are unable to raise capital when needed or on attractive terms, we could be forced to delay, reduce or eliminate our research and development programs or our commercialization efforts.

Financial operations overview

Revenues

Net product revenues. To date, our net product revenues have consisted primarily of sales of Translarna for the treatment of nmDMD in territories outside of the United States, sales of Emflaza for the treatment of DMD in the United States. Beginning in the three months ended September 30, 2025, net product revenues also includes Sephience for the treatment of PKU. We recognize revenue when performance obligations with customers have been satisfied and if it is probable that a significant revenue reversal will not occur. Our performance obligations are to provide products based on customer orders from distributors, hospitals, specialty pharmacies or retail pharmacies. The performance obligations are satisfied at a point in time when our customer obtains control of the product, which is typically upon delivery. We invoice customers after the products have been delivered and invoice payments are generally due within 30 to 90 days of invoice date. We determine the transaction price based on fixed consideration in its contractual agreements. Contract liabilities arise in certain circumstances when consideration is due for goods not yet provided. As we have identified only one distinct performance obligation, the transaction price is allocated entirely to the product sale. In determining the transaction price, a significant financing component does not exist since the timing from when we deliver product to when the customers pay for the product is typically less than one year. Customers in certain countries pay in advance of product delivery. In those instances, payment and delivery typically occur in the same month.

We record product sales net of any variable consideration, which includes discounts, allowances, rebates related to Medicaid and other government pricing programs, and distribution fees. We use the expected value or most likely amount method when estimating variable consideration, unless discount or rebate terms are specified within contracts. The identified variable consideration is recorded as a reduction of revenue at the time revenues from product sales are recognized. These estimates for variable consideration are adjusted to reflect known changes in factors and may impact such estimates in the quarter those changes are known. Revenue recognized does not include amounts of variable consideration that are constrained.

During the three and nine months ended September 30, 2025 and 2024, net product revenues consisted of the following:

Disaggregated net product revenues by country for the three and nine months ended September 30, 2025 and 2024, are as follows:

For the three months ended September 30, 2025, four of our distributors each accounted for over 10% of our net product sales. For the three months ended September 30, 2024, two of our distributors each accounted for over 10% of our net product sales. For the nine months ended September 30, 2025, three of our distributors each accounted for over 10% of our net product sales. For the nine months ended September 30, 2024, two of our distributors each accounted for over 10% of our net product sales.

In relation to customer contracts, we incur costs to fulfill a contract but do not incur costs to obtain a contract. These costs to fulfill a contract do not meet the criteria for capitalization and are expensed as incurred. We consider any shipping and handling costs that are incurred after the customer has obtained control of the product as a cost to fulfill a promise. Shipping and handling costs associated with finished goods delivered to customers are recorded as a selling expense.

Roche and the SMA Foundation Collaboration. In November 2011, we entered into the SMA License Agreement pursuant to which we are collaborating with Roche and the SMA Foundation to further develop and commercialize compounds identified under our SMA program with the SMA Foundation. The research component of this agreement terminated effective December 31, 2014. We are eligible to receive additional payments from Roche if specified events are achieved with respect to each licensed product, including up to $135.0 million in research and development event milestones, up to $325.0 million in sales milestones upon achievement of specified sales events, and up to double digit royalties on worldwide annual net sales of a commercial product. As of September 30, 2025, we had recognized a total of $310.0 million in milestone payments and $710.4 million royalties on net sales pursuant to the SMA License Agreement. As of September 30, 2025, there are no remaining research and development event milestones that we can receive. The remaining potential sales milestones as of September 30, 2025 are $150.0 million upon achievement of certain sales events.

For the three and nine months ended September 30, 2025, collaboration revenue related to the SMA License Agreement with Roche was immaterial. For the three and nine months ended September 30, 2024, we did not recognize collaboration revenue related to the SMA License Agreement with Roche.

For the three and nine months ended September 30, 2025, we recognized $70.8 million and $164.8 million of royalty revenue, respectively, related to Evrysdi. For the three and nine months ended September 30, 2024, we recognized $61.4 million and $145.7 million of royalty revenue, respectively, related to Evrysdi.

Novartis Collaboration for votoplam HD. In November 2024, we entered into the Novartis Agreement with Novartis related to our votoplam HD program. Upon the closing of the transaction contemplated by the Novartis Agreement in January 2025, we received an upfront payment of $1.0 billion on the effective date and can receive up to $1.9 billion in development, regulatory and sales milestones, a 40% share of U.S. profits and losses, and tiered double-digit royalties on ex-U.S. sales.

During the three and nine months ended September 30, 2025, we recognized $9.3 million and $1.0 billion in license revenues, respectively, related to Novartis. As all performance obligations are considered to be substantially complete, there is no remaining deferred revenue on the consolidated balance sheet as of September 30, 2025. Collaboration and license revenue during the nine months ended September 30, 2025 was partially offset by $3.5 million related to a refund for a prior collaboration arrangement in relation to votoplam.

Research and development expense

Research and development expenses consist of the costs associated with our research activities, as well as the costs associated with our drug discovery efforts, conducting preclinical studies and clinical trials, manufacturing development efforts and activities related to regulatory filings. Our research and development expenses consist of:

• external research and development expenses incurred under agreements with third-party contract research organizations and investigative sites, third-party manufacturing organizations and consultants;
• employee-related expenses, which include salaries and benefits, including share-based compensation, for the personnel involved in our drug discovery and development activities; and
• facilities, depreciation and other allocated expenses, which include direct and allocated expenses for rent and maintenance of facilities, IT, human resources and other support functions, depreciation of leasehold improvements and equipment, and laboratory and other supplies.

We use our employee and infrastructure resources across multiple research projects, including our drug development programs. We track expenses related to our clinical programs and certain preclinical programs on a per project basis.

We expect our research and development expenses to fluctuate in connection with our ongoing activities, particularly in connection with our activities under our splicing and inflammation and ferroptosis programs and performance of our post-marketing requirements imposed by regulatory agencies with respect to our products. The timing and amount of these expenses will depend upon the outcome of our ongoing clinical trials and the costs associated with our planned clinical trials. The timing and amount of these expenses will also depend on the costs associated with potential future clinical trials of our products or product candidates and the related expansion of our research and development organization, regulatory requirements, advancement of our preclinical programs, and product candidate manufacturing costs.

The following tables provides research and development expense for our most advanced principal product development programs, for the three and nine months ended September 30, 2025 and 2024.

(in thousands)

(in thousands)

Development. Consists of costs incurred for product candidates following initiation of a clinical trial.

For the three and nine months ended September 30, 2025, compared to the three and nine months ended September 30, 2024, the changes reflect progressing through different phases of studies as we continue to focus our resources on our differentiated, high potential research and development programs. The decrease is primarily due to a decrease relating to Global DMD, Gene Therapy, and Splicing platform, offset by an increase in Sephience related development.

Research. Consists of costs incurred for product candidates before initiation of a clinical trial.

For the three and nine months ended September 30, 2025, compared to the three and nine months ended September 30, 2024, the decrease in research expenses primarily reflected our continued focus of our resources on product candidates approaching approval during the current year periods.

Milestones. Consists of development and regulatory milestone expenses incurred in connection with our collaborative arrangements.

For the three and nine months ended September 30, 2025, compared to the three and nine months ended September 30, 2024, the decrease in milestone expenses related to the achievement of a total of $65.0 million regulatory success-based milestones paid to the former Censa securityholders for the nine months ended September 30, 2024.

Payroll, benefits, and share-based stock compensation. Consists of costs incurred for salaries and wages, bonus, payroll taxes, benefits and share-based stock compensation associated with employees involved in research and development activities. Share-based stock compensation may fluctuate from period to period based on factors that are not within our control, such as our stock price on the dates share-based grants are issued.

For the three and nine months ended September 30, 2025, compared to the three and nine months ended September 30, 2024, the change in payroll, benefits, and share-based stock compensation expenses was relatively flat.

Facilities and other. Consists of indirect costs incurred for the benefit of multiple programs, including information technology, and other facility-based expenses, such as rent expense.

For the three months ended September 30, 2025, compared to the three months ended September 30, 2024, the change in facilities and other expenses was relatively flat. For the nine months ended September 30, 2025 compared to the nine months ended September 30, 2024, the decrease in facilities and other expenses primarily related to decreases in facility-based expenses at our facility in Hopewell Township, New Jersey as a result of an amendment and restatement of our lease for such facility in June 2024 and at our facility in Warren, New Jersey as a result of an amendment to our lease for such facility in December 2024.

The successful development of our products and product candidates is highly uncertain. This is due to the numerous risks and uncertainties associated with developing drugs, including the uncertainty of:

• the scope, rate of progress and expense of our clinical trials and other research and development activities;
• the potential benefits of our products and product candidates over other therapies;
• our ability to market, commercialize and achieve market acceptance for any of our products or product candidates that we are developing or may develop in the future, including our ability to negotiate pricing and reimbursement terms acceptable to us;
• clinical trial results;
• the terms and timing of regulatory approvals; and
• the expense of filing, prosecuting, defending and enforcing patent claims and other intellectual property rights.

A change in the outcome of any of these variables with respect to the development of our products or product candidates could mean a significant change in the costs and timing associated with the development of those products or product candidates. For example, if the EMA or FDA or other regulatory authority were to require us to conduct clinical trials beyond those which we currently anticipate will be required for the completion of clinical development of any of our products or product candidates or if we experience significant delays in enrollment in any of our clinical trials, we could be required to expend significant additional financial resources and time on the completion of clinical development.

Selling, general and administrative expense

Selling, general and administrative expenses consist primarily of salaries and other related costs for personnel, including share-based compensation expenses, in our executive, legal, business development, commercial, finance, accounting, information technology and human resource functions. Other selling, general and administrative expenses include facility-related costs not otherwise included in research and development expense; advertising and promotional expenses; costs associated with industry and trade shows; and professional fees for legal services, including patent-related expenses, accounting services and miscellaneous selling costs.

We expect that selling, general and administrative expenses will increase in future periods in connection with our continued efforts to commercialize our products, including increased payroll, expanded infrastructure, commercial operations, increased consulting, legal, accounting and investor relations expenses.

Interest expense, net

Interest expense, net consists of interest expense from the liability for the sale of future royalties related to the A&R Royalty Purchase Agreement and the 2026 Convertible Notes outstanding, offset by interest income earned on investments.

Critical accounting policies and significant judgments and estimates

Our management’s discussion and analysis of our financial condition and results of operations is based on our financial statements, which we have prepared in accordance with generally accepted accounting principles in the United States. The preparation of these financial statements requires us to make estimates and assumptions that affect the reported amounts of assets and liabilities and the disclosure of contingent assets and liabilities at the date of the financial statements, as well as the reported revenues and expenses during the reporting periods. Actual results may differ from these estimates under different assumptions or conditions.

During the three and nine months ended September 30, 2025, there were no material changes to our critical accounting policies as reported in our 2024 Annual Report.

Results of operations

Three months ended September 30, 2025 compared to the three months ended September 30, 2024

The following table summarizes revenues and selected expense and other income data for the three months ended September 30, 2025 and 2024.

(in thousands)

Net product revenue. Net product revenue was $131.0 million for the three months ended September 30, 2025, a decrease of $4.5 million, or 3%, from $135.4 million for the three months ended September 30, 2024. The decrease in net product revenue was primarily due to a decrease in net product sales of Emflaza and Translarna, partially offset by an increase in net product sales of Kebilidi/Upstaza and Sephience due to the timing of approvals for those products. The decrease in Emflaza sales is primarily driven by additional generic competition. The decrease in Translarna sales is primarily due to the EC’s adoption of the CHMP’s negative opinion.

Collaboration and license revenue. Collaboration and license revenue was $9.3 million for the three months ended September 30, 2025, an increase of $9.3 million, or 100%, from $0.0 million for the three months ended

September 30, 2024. For the three months ended September 30, 2025, we recognized $9.3 million related to license revenue from the Novartis Agreement for performance obligations completed during the period. For the three months ended September 30, 2024, we did not recognize any collaboration or license revenue.

Royalty revenue. Royalty revenue was $70.8 million for the three months ended September 30, 2025, an increase of $9.4 million, or 15%, from $61.4 million for the three months ended September 30, 2024. The increase in royalty revenue was due to higher Evrysdi sales in the three months ended September 30, 2025 as compared to the three months ended September 30, 2024. In accordance with the SMA License Agreement, we are entitled to royalties on worldwide annual net sales of the product.

Cost of product, collaboration and license sales, excluding amortization of acquired intangible assets. Cost of product, collaboration and license sales, excluding amortization of acquired intangible assets was $15.8 million for the three months ended September 30, 2025, an increase of $4.9 million, or 45%, from $10.8 million for the three months ended September 30, 2024. Cost of product, collaboration and license sales, excluding amortization of acquired intangible assets during the period consisted primarily of costs associated with the Novartis agreement, as well as production costs, royalty payments, and costs associated with sales of Emflaza, Translarna, Sephience, and Upstaza/Kebilidi. The increase was primarily due to costs associated with the Novartis agreement, inventory costs associated with the Sephience launch, Upstaza/Kebilidi royalty payments, and costs associated with new product sales, which was partially offset by a decrease in Emflaza royalties as a result of the completion of the royalty agreement with Marathon Pharmaceuticals, LLC (now known as Complete Pharma Holdings, LLC).

Amortization of acquired intangible assets. Amortization of acquired intangible assets was $7.5 million for the three months ended September 30, 2025, an increase of $4.5 million, or over 100%, from $3.0 million for the three months ended September 30, 2024. These amounts are related to the Waylivra, Tegsedi, Upstaza/Kebilidi, and Sephience intangible assets, which are all being amortized on a straight-line basis over their estimated useful lives. The amortization increase was driven by a string of approvals received, beginning with PTC-AADC in October 2024. In October 2024, we received regulatory approval for Upstaza in Brazil, and in November 2024, the BLA for our gene therapy treatments of AADC deficiency was approved by the FDA, marketed under the brand name Kebilidi. With these approvals, $10.7 million and $17.4 million for Kebilidi and Upstaza, respectively, was reclassed from the PTC-AADC indefinite lived intangible asset to definite lived intangible assets. We will amortize these allocated balances of $10.7 million and $17.4 million over their expected useful lives of 12 years on a straight-line basis. In June 2025, the EC granted marketing authorization to Sephience for the treatment of children and adults living with PKU in the EEA, which triggered a $25.0 million milestone to the former Censa securityholders. The milestone was recorded as an intangible asset and is being amortized to cost of product sales over its expected useful life on a straight-line basis. Pursuant to the Censa Merger Agreement, in July 2025, a $32.5 million milestone from the Company to the former Censa securityholders was triggered when the FDA approved Sephience for the treatment of children and adults living with PKU. The milestone was recorded as an intangible asset and is being amortized to cost of product sales over its expected useful life on a straight-line basis. Pursuant to the Censa Rights Satisfaction Agreement, in August 2025, an upfront cash consideration of $225.1 million was paid to the former Censa securityholders. The upfront consideration was recorded as an intangible asset and is being amortized to cost of product sales over its expected useful life on a straight-line basis.

Research and development expense. Research and development expense was $100.2 million for the three months ended September 30, 2025, a decrease of $61.3 million, or 38%, from $161.4 million for the three months ended September 30, 2024. The decrease in research and development expenses primarily related to a $50.0 million regulatory success-based milestone payable to the former Censa securityholders for the three months ended September 30, 2024.

Selling, general and administrative expense. Selling, general and administrative expense was $84.0 million for the three months ended September 30, 2025, an increase of $10.6 million, or 14%, from $73.5 million for the three months ended September 30, 2024. The increase reflected our continued investment to support our commercial activities including our expanding commercial portfolio.

Change in the fair value of contingent consideration. The change in the fair value of contingent consideration was $0.0 million for the three months ended September 30, 2025, a change of $0.7 million, or 100%, from a loss of $0.7 million for the three months ended September 30, 2024. During the first quarter of 2025, the probability of triggering the remaining contingent consideration was determined to be remote, and therefore the balance was written down to zero.

Tangible asset impairment and losses (gains) on transactions, net. Tangible asset impairment and losses (gains) on transactions, net was $0.5 million for the three months ended September 30, 2025, a decrease of $1.4 million, or 74%, from $1.8 million for the three months ended September 30, 2024. This decrease was primarily related to a $1.3 million loss for fixed asset impairments related to the South Plainfield, New Jersey office closure in August 2024, as well as a $0.5 million loss on sales of fixed assets during the three months ended September 30, 2024. During the three months ended September 30, 2025, we recorded fixed asset impairments of $0.4 million, as well as a $0.1 million loss related to sales of fixed assets.

Interest expense, net. Interest expense, net was $32.6 million for the three months ended September 30, 2025, a decrease of $9.0 million, or 22%, from $41.6 million for the three months ended September 30, 2024. Interest income was $19.1 million for the three months ended September 30, 2025, an increase of $6.3 million, from $12.8 million for the three months ended September 30, 2024, which primarily related to an increase in interest from marketable securities-available for sale. Interest expense was $51.7 million for the three months ended September 30, 2025, a decrease of $2.7 million, from $54.4 million for the three months ended September 30, 2024, which primarily related to a decrease in interest related to RPI.

Other income (expense), net. Other income, net was $6.5 million for the three months ended September 30, 2025, a change of $8.4 million, or over 100%, from other expense, net of $1.9 million for the three months ended September 30, 2024. Other income, net primarily related to net unrealized gains of $8.8 million on our ClearPoint Neuro. Inc. equity investments, partially offset by net realized and unrealized foreign exchange losses of $2.4 million for the three months ended September 30, 2025. Other expense, net for the three months ended September 30, 2024 was primarily related to net unrealized and realized gains of $4.6 million on our ClearPoint Neuro. Inc. equity investments and convertible debt security, offset by net realized and unrealized foreign exchange losses of $6.0 million for the three months ended September 30, 2024.

Income tax benefit (expense). Income tax benefit was $39.0 million for the three months ended September 30, 2025, a change of $47.6 million, or over 100%, compared to income tax expense of $8.7 million for the three months ended September 30, 2024. The change in income tax benefit (expense) was driven by the projected utilization of additional tax attributes in 2025 as a result of the provisions within the One Big Beautiful Bill Act.

Nine months ended September 30, 2025 compared to the nine months ended September 30, 2024

The following table summarizes revenues and selected expense and other income data for the nine months ended September 30, 2025 and 2024.

(in thousands)

Net product revenue. Net product revenue was $402.7 million for the nine months ended September 30, 2025, a decrease of $43.5 million, or 10%, from $446.2 million for the nine months ended September 30, 2024. The decrease in net product revenue was primarily due to a decrease in net product sales of Emflaza and Translarna, partially offset by an increase in net product sales of Kebilidi/Upstaza and Sephience due to the timing of approvals for those products. The decrease in Emflaza sales is primarily driven by additional generic competition. The decrease in Translarna sales is primarily due to the EC’s adoption of the CHMP’s negative opinion.

Collaboration and license revenue. Collaboration and license revenue was $998.4 million for the nine months ended September 30, 2025, an increase of $998.4 million, or 100%, from $0.0 million for the nine months ended September 30, 2024. The increase in collaboration and license revenue was due to the receipt of the $1.0 billion upfront payment upon the effective date of the license and collaboration agreement with Novartis related to our votoplam HD program. For the nine months ended September 30, 2025, we recognized $1.0 billion related to license revenue from the Novartis Agreement which was partially offset by $3.5 million related to a refund for a prior collaboration arrangement in relation to votoplam. For the nine months ended September 30, 2024, we did not recognize any collaboration or license revenue.

Royalty revenue. Royalty revenue was $164.8 million for the nine months ended September 30, 2025, an increase of $19.1 million, or 13%, from $145.7 million for the nine months ended September 30, 2024. The increase in royalty revenue was due to higher Evrysdi sales in the nine months ended September 30, 2025 as compared to the nine months ended September 30, 2024. In accordance with the SMA License Agreement, we are entitled to royalties on worldwide annual net sales of the product.

Manufacturing revenue. Manufacturing revenue was $0.0 million for the nine months ended September 30, 2025, a decrease of $1.7 million, or 100%, from $1.7 million for the nine months ended September 30, 2024. The decrease was due to the prior completion of all manufacturing services related to the production of plasmid DNA and AAV vectors for gene therapy applications for external customers. In June 2024, we sold our gene therapy manufacturing business in Hopewell Township, New Jersey. Accordingly, we do not expect to have manufacturing revenue going forward.

Cost of product, collaboration and license sales, excluding amortization of acquired intangible assets. Cost of product, collaboration and license sales, excluding amortization of acquired intangible assets was $40.1 million for the nine months ended September 30, 2025, a decrease of $1.1 million, or 3%, from $41.1 million for the nine months ended September 30, 2024. Cost of product, collaboration and license sales, excluding amortization of acquired intangible assets during the period consisted primarily of costs associated with the Novartis agreement, as well as production costs, royalty payments, inventory reserves, and costs associated with sales of Emflaza, Translarna, Sephience, and Upstaza/Kebilidi. The decrease was primarily due to decreases in royalty costs driven by Emflaza as a result of the completion of the royalty agreement with Marathon Pharmaceuticals, LLC (now known as Complete Pharma Holdings, LLC), which was partially offset by costs associated with the Novartis Agreement, inventory costs associated with the Sephience launch, Upstaza/Kebilidi royalty payments, an increase in inventory reserves, and costs associated with new product sales.

Amortization of acquired intangible assets. Amortization of acquired intangible assets was $15.4 million for the nine months ended September 30, 2025, a decrease of $42.0 million, or 73%, from $57.4 million for the nine months ended September 30, 2024. These amounts are related to the Waylivra, Tegsedi, Upstaza/Kebilidi, Sephience, and Emflaza intangible assets, which are all being amortized on a straight-line basis over their estimated useful lives. The amortization decrease was primarily driven by the Emflaza intangible asset being fully amortized as of February 2024. As a result, there is no further amortization for Emflaza as of February 2024.

Research and development expense. Research and development expense was $322.1 million for the nine months ended September 30, 2025, a decrease of $87.6 million, or 21%, from $409.7 million for the nine months ended September 30, 2024. The decrease in research and development expenses related to decreases in program spend as we continued to focus our resources on our differentiated, high potential research and development programs. For the nine months ended September 30, 2024, research and development expense also includes $65.0 million regulatory success-based milestones paid to the former Censa securityholders.

Selling, general and administrative expense. Selling, general and administrative expense was $250.3 million for the nine months ended September 30, 2025, an increase of $34.0 million, or 16%, from $216.2 million for the nine months ended

September 30, 2024. The increase reflected our continued investment to support our commercial activities including our expanding commercial portfolio.

Change in the fair value of contingent consideration. The change in the fair value of contingent consideration was a gain of $0.8 million for the nine months ended September 30, 2025, a change of $6.5 million, or over 100%, from a loss of $5.7 million for the nine months ended September 30, 2024. During the first quarter of 2025, the probability of triggering the remaining contingent consideration was determined to be remote, and therefore the balance was written down to zero.

Tangible asset impairment and losses (gains) on transactions, net. Tangible asset impairment and losses (gains) on transactions, net was $0.6 million for the nine months ended September 30, 2025, a decrease of $3.0 million, or 82%, from $3.6 million for the nine months ended September 30, 2024. This decrease was primarily related to a $4.4 million loss primarily related to the sale of certain assets for gene therapy manufacturing, and a $1.5 million loss primarily related to fixed asset impairments in connection with the South Plainfield, New Jersey office closure in August 2024. These amounts were partially offset by a gain of $2.2 million on lease terminations and a $0.1 million gain on sales of fixed assets. During the nine months ended September 30, 2025, we recorded fixed asset impairments of $0.5 million, as well as a $0.1 million loss related to sales of fixed assets.

Interest expense, net. Interest expense, net was $97.0 million for the nine months ended September 30, 2025, a decrease of $28.9 million, or 23%, from $125.9 million for the nine months ended September 30, 2024. Interest income was $57.3 million for the nine months ended September 30, 2025, an increase of $23.0 million, from $34.3 million for the nine months ended September 30, 2024, which primarily related to an increase in interest from marketable securities-available for sale. Interest expense was $154.4 million for the nine months ended September 30, 2025, a decrease of $5.8 million, from $160.2 million for the nine months ended September 30, 2024, which primarily related to a decrease in interest related to RPI.

Other expense, net. Other expense, net was $5.5 million for the nine months ended September 30, 2025, an increase of $3.2 million, or over 100%, from other expense, net of $2.3 million for the nine months ended September 30, 2024. Other expense, net, for the nine months ended September 30, 2025, was primarily related to net realized and unrealized losses from foreign currency of $17.4 million, partially offset by unrealized gains on our ClearPoint Neuro, Inc. equity investments of $5.7 million and $6.0 million related to other income items. Other expense, net for the nine months ended September 30, 2024, was primarily related to net realized and unrealized losses from foreign currency of $3.8 million for the nine months ended September 30, 2024, partially offset by net unrealized and realized gains on our ClearPoint Neuro, Inc. convertible debt security and equity investments of $1.4 million.

Income tax expense. Income tax expense was $18.1 million for the nine months ended September 30, 2025, a decrease of $10.9 million, or 38%, compared to income tax expense of $29.0 million for the nine months ended September 30, 2024. The decrease in income tax expense was driven by the projected utilization of additional tax attributes in 2025 as a result of the provisions within the One Big Beautiful Bill Act. Additionally, we incur income tax expenses in various foreign jurisdictions, and our foreign tax liabilities are largely dependent upon the distribution of pre-tax earnings among these different jurisdictions.

Liquidity and capital resources

Sources of liquidity

While we have generated net income in the three and nine months ended September 30, 2025, we have historically incurred significant operating losses.

As a growing commercial-stage biopharmaceutical company, we are engaging in significant commercialization efforts for our products while also devoting a substantial portion of our efforts on research and development related to our products, product candidates and other programs. To date, our product revenue has primarily consisted of sales of Translarna for the treatment of nmDMD in territories outside of the United States and from Emflaza for the treatment of DMD in the United States. Beginning in the three months ended September 30, 2025, net product revenues also includes sales of Sephience for the treatment of PKU in the United States and in territories outside of the United States. Our ongoing ability to generate revenue from sales of Translarna for the treatment of nmDMD is dependent upon our ability to maintain our marketing authorizations in Brazil and Russia and secure market access through commercial programs following the conclusion of pricing and reimbursement terms at sustainable levels in the member states of the EEA or through EAP programs or similar styled programs in the EEA and other territories. In March 2025, the EC adopted the opinion of the CHMP to not renew the authorization of Translarna for the treatment of nmDMD. However, the EC indicated that individual countries within the EU can leverage Articles 117(3) and 5(1) of the EU Directive 2001/83 to allow continued use of Translarna. Our ability to generate product revenue from Sephience and Emflaza will largely depend on the coverage and reimbursement levels set by governmental authorities, private health insurers and other third-party payors. Additionally, Emflaza’s seven-year period of orphan drug exclusivity related to the treatment of DMD in patients five years and older expired in February 2024. We have previously relied on this exclusivity period to commercialize Emflaza in the United States. We expect the expiration of this orphan drug exclusivity to potentially have a significant negative impact on Emflaza net product revenue. Emflaza’s orphan drug exclusivity related to the treatment of DMD in patients two years of age to less than five expires in June 2026.

We have financed our operations to date primarily through the private offerings of convertible senior notes, public offerings and “at the market offerings” of common stock, proceeds from royalty purchase agreements, private placements of our preferred stock and common stock, collaborations, bank and institutional lender debt, other convertible debt, grant funding and clinical trial support from governmental and philanthropic organizations and patient advocacy groups in the disease areas addressed by our product candidates. We expect to continue to incur significant expenses and operating losses for at least the next fiscal year. The net income and losses we incur may fluctuate significantly from quarter to quarter.

In August 2019, we entered into the Sales Agreement, pursuant to which, we may offer and sell shares of our common stock, having an aggregate offering price of up to $125.0 million from time to time through the Sales Agents by any method that is deemed to be an “at the market offering” as defined in Rule 415(a)(4) promulgated under the Securities Act. See “Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations—Corporate Updates—Funding” for additional information.

In September 2019, we closed a private offering of $287.5 million aggregate principal amount of 2026 Convertible Notes, which included an option to purchase up to an additional $37.5 million in aggregate principal amount of the 2026 Convertible Notes, which was fully exercised by the initial purchasers. The 2026 Convertible Notes bear cash interest at a rate of 1.50% per year, payable semi-annually on March 15 and September 15 of each year, beginning on March 15, 2020. The 2026 Convertible Notes will mature on September 15, 2026, unless earlier repurchased or converted. We received net proceeds of $279.3 million after deducting the initial purchasers’ discounts and commissions and the offering expenses payable by us.

We have received fundings from Royalty Pharma under the A&R Royalty Purchase Agreement in July 2020, October 2023 and June 2024 totaling $1.9 billion (less Royalty payments received by us with respect to the Assigned Royalty Rights). In exchange for these fundings, we sold Royalty Pharma 90.49% of the Royalty, which will be reduced to 83.33% after Royalty Pharma receives the Assigned Royalty Cap from the Royalty assigned under the Original Royalty Purchase Agreement. We currently retain 9.51% of the Royalty, which increases to 16.67% after the Assigned Royalty Cap has been met. We have the option to sell our retained portions of the Royalty to Royalty Pharma in up to three tranches for the following payments: (1) $100.0 million in exchange for 3.81% of the Royalty, which increases to 6.67% after the Assigned Royalty Cap has been met, (2) $100.0 million in exchange for 3.81% of the Royalty, which increases to 6.67% after the Assigned Royalty Cap has been met, and (3) $50.0 million in exchange for 1.90% of the Royalty, which increases to 3.33% after the Assigned Royalty Cap has been met, in each case less Royalty payments received by us with respect to the Assigned Royalty Rights.

In November 2024, we and Novartis entered into the Novartis Agreement relating to our votoplam HD program which includes related molecules. Pursuant to the Novartis Agreement, we were responsible for completing the ongoing Phase 2A clinical trial and continuing the ongoing OLE clinical trial pursuant to its existing development plan, with the goal of transitioning the ongoing OLE clinical trial to Novartis within 12 months after the effective date. As of September 30, 2025, these were considered substantially complete. Novartis will be responsible for all other development of licensed compounds and licensed products and the manufacture and commercialization of licensed compounds and licensed products worldwide. Under the Novartis Agreement, and upon the closing of the transaction contemplated by the Novartis Agreement in January 2025, we received an upfront payment of $1.0 billion on the effective date and can receive up to $1.9 billion in development, regulatory and sales milestones, a 40% share of U.S. profits and losses, and tiered double-digit royalties on ex-U.S. sales.

Cash flows

As of September 30, 2025, we had cash, cash equivalents and marketable securities of $1.69 billion.

The following table provides information regarding our cash flows and our capital expenditures for the periods indicated.

(in thousands)

Net cash provided by operating activities was $745.5 million for the nine months ended September 30, 2025, compared to net cash used in operating activities of $77.7 million for the nine months ended September 30, 2024. The net cash provided by operating activities for the nine months ended September 30, 2025, was primarily related to the upfront payment of $1.0 billion in cash received upon the closing of the Novartis Agreement in January 2025, partially offset by spend supporting clinical development and commercial activities. The net cash used in operating activities for the nine months ended September 30, 2024, was primarily related to spend supporting clinical development and commercial activities, partially offset by the cash received from the sales milestone of $100.0 million for the achievement of $1.5 billion in worldwide net sales from Evrysdi.

Net cash used in investing activities was $896.0 million for the nine months ended September 30, 2025, compared to $223.5 million for the nine months ended September 30, 2024. Cash used in investing activities for the nine months ended September 30, 2025 and 2024, were primarily related to the acquisition of product rights, purchases of marketable securities, and purchases of fixed assets, partially offset by net sales and redemption of marketable securities and proceeds from sale of fixed assets.

Net cash provided by financing activities was $28.6 million for the nine months ended September 30, 2025, compared to $229.4 million for the nine months ended September 30, 2024. Cash provided by financing activities for the nine months ended September 30, 2025 was primarily attributable to proceeds from our employee stock purchase plan and proceeds from the exercise of options, partially offset by payments on contingent consideration obligation and payments on our finance lease principal. Cash provided by financing activities for the nine months ended September 30, 2024 was primarily attributable to proceeds from sales of future royalties, proceeds from our employee stock purchase plan, and proceeds from the exercise of options, partially offset by payments on contingent consideration obligation and payments on our finance lease principal.

Funding requirements

We anticipate that we will continue to incur significant expenses in connection with our commercialization efforts in the United States, the EEA, Latin America and other territories, including expenses related to our commercial infrastructure and corresponding sales and marketing, legal and regulatory, and distribution and manufacturing undertakings as well as administrative and employee-based expenses. In addition to the foregoing, we expect to continue to incur significant costs in connection with ongoing, planned and potential future clinical trials and studies for our splicing and inflammation and ferroptosis programs as well as studies in our products for maintaining authorizations, label extensions and additional indications. We continue to seek marketing authorization for Translarna for the treatment of nmDMD in territories that we do not currently have marketing authorization in. We submitted an NDA to the FDA for vatiquinone for the treatment of FA in December 2024. In August 2025, the FDA issued a complete response letter related to the NDA stating that substantial evidence of efficacy was not demonstrated for vatiquinone and that an additional adequate and well-controlled study would be needed to support NDA resubmission. We plan to meet with the FDA in the fourth quarter to discuss the vatiquinone development program. These efforts may significantly impact the timing and extent of our commercialization and manufacturing expenses.

In addition, our expenses will increase if and as we:

• seek to satisfy contractual and regulatory obligations that we assumed through our acquisitions and collaborations;
• execute our commercialization strategy for our products, including initial commercialization launches of our products, label extensions or entering new markets;
• are required to complete any additional clinical trials, non-clinical studies or Chemistry, Manufacturing and Controls, or CMC, assessments or analyses in order to advance our products or product candidates in the United States or elsewhere;
• are required to take other steps to maintain our current marketing authorization in Brazil and Russia for Translarna for the treatment of nmDMD or to obtain further marketing authorizations for Translarna for the treatment of nmDMD or other indications;
• initiate or continue the research and development of Sephience and our splicing and inflammation and ferroptosis programs as well as studies in our products for maintaining authorizations, label extensions and additional indications;
• seek to discover and develop additional product candidates;
• seek to expand and diversify our product pipeline through strategic transactions;
• maintain, expand and protect our intellectual property portfolio; and
• add operational, financial and management information systems and personnel, including personnel to support our product development and commercialization efforts.

We believe that our cash flows from product sales, together with existing cash and cash equivalents, and marketable securities, will be sufficient to fund our operating expenses and capital expenditure requirements for at least the next twelve months. We have based this estimate on assumptions that may prove to be wrong, and we could use our capital resources sooner than we currently expect.

Our future capital requirements will depend on many factors, including:

• our ability to commercialize and market our products and product candidates that may receive marketing authorization;
• our ability to negotiate, secure and maintain adequate pricing, coverage and reimbursement terms, on a timely basis, with third-party payors for our products and products candidates;
• our ability to successfully launch and commercialize Sephience in markets where we receive regulatory approval;
• our ability to maintain the marketing authorization for Translarna and our other products in territories outside of the EEA;
• the amount of generic drug competition that we face for Emflaza for the treatment of DMD in patients five years and older;
• our ability to obtain marketing authorization for Translarna for the treatment of nmDMD in the United States;
• our plans for vatiquinone including with respect to the expected timing of clinical trials and studies, availability of data, regulatory submissions and responses, meetings with regulatory agencies, and other matters;
• our ability to successfully complete all post-marketing requirements imposed by regulatory agencies with respect to our products;
• the progress and results of activities for Sephience and our splicing and inflammation and ferroptosis programs as well as studies in our products for maintaining authorizations, label extensions and additional indications;
• the scope, costs and timing of our commercialization activities, including product sales, marketing, legal, regulatory, distribution and manufacturing, for any of our products and for any of our other product candidates that may receive marketing authorization or any additional territories in which we receive authorization to market Sephience or Translarna;
• the costs, timing and outcome of regulatory review of our splicing and inflammation and ferroptosis programs and Sephience, Translarna and Upstaza/Kebilidi in other territories;
• our ability to satisfy our obligations under the indenture governing the 2026 Convertible Notes;
• the timing and scope of any potential future growth in our employee base;
• the scope, progress, results and costs of preclinical development, laboratory testing and clinical trials for our other product candidates, including those in our splicing and inflammation and ferroptosis programs;
• revenue received from commercial sales of our products or any of our product candidates;
• our ability to obtain additional and maintain existing reimbursed named patient and cohort EAP programs for Translarna for the treatment of nmDMD on adequate terms, or at all;
• the ability and willingness of patients and healthcare professionals to access Translarna through alternative means if pricing and reimbursement negotiations in the applicable territory do not have a positive outcome;
• the costs of preparing, filing and prosecuting patent applications, maintaining, and protecting our intellectual property rights and defending against intellectual property-related claims;
• the extent to which we acquire or invest in other businesses, products, product candidates, and technologies, including the success of any acquisition, in-licensing or other strategic transaction we may pursue, and the costs of subsequent development requirements and commercialization efforts, including with respect to our acquisitions of Emflaza, Agilis, our inflammation and ferroptosis platform and Censa and our licensing of Tegsedi and Waylivra;
• our ability to establish and maintain collaborations, including our collaborations with Roche and the SMA Foundation, and our ability to obtain research funding and achieve milestones under these agreements.
• the progress and results of activities for our votoplam program, including our right to receive any development, regulatory and sales milestones, profit sharing and royalty payments from Novartis; and
• unexpected decreases in revenue or increase in expenses resulting from potential widespread outbreaks of contagious disease.

With respect to our outstanding 2026 Convertible Notes, cash interest payments are payable on a semi-annual basis in arrears, which will require total funding of $4.3 million annually.

In July 2025, Sephience™ (sepiapterin) was granted FDA approval for the treatment of children and adults living with PKU. Pursuant to the Censa Merger Agreement, the approval triggered a $32.5 million milestone to the former Censa securityholders, which was recorded in accounts payable and accrued expenses on our consolidated balance sheet as of September 30, 2025.

We also have certain significant contractual obligations and commercial commitments that require funding and we have disclosed these items under the heading “Management’s Discussion and Analysis of Financial Condition and Results of Operations-Funding Obligations” in our 2024 Annual Report. There were no material changes to these obligations and commitments during the period ended September 30, 2025.

We will need to generate significant revenues to achieve and sustain profitability, and we may never do so. We may need to obtain substantial additional funding in connection with our continuing operations. Until such time, if ever, as we can generate substantial product revenues, we expect to finance our cash needs primarily through a combination of equity offerings, debt financings, collaborations, strategic alliances, grants and clinical trial support from governmental and philanthropic organizations and patient advocacy groups in the disease areas addressed by our product and product candidates and marketing, distribution or licensing arrangements. Adequate additional financing may not be available to us on acceptable terms, or at all. To the extent that we raise additional capital through the sale of equity or convertible debt securities, our shareholders ownership interests will be diluted, and the terms of these securities may include liquidation or other preferences that adversely affect the rights of our common stockholders. Debt financing, if available, may involve agreements that include covenants limiting or restricting our ability to take specific actions, such as incurring additional debt, making capital expenditures or declaring dividends. 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, research programs or product candidates or to grant licenses on terms that may not be favorable to us.

If we are unable to raise additional funds through equity, debt or other financings when needed or on attractive terms, we may be required to delay, limit, reduce or terminate our product development or commercialization efforts or grant rights to develop and market product candidates that we would otherwise prefer to develop and market ourselves.

During the period ended September 30, 2025, there were no material changes in our market risk or how our market risk is managed, compared to those disclosed under the heading “Quantitative and Qualitative Disclosures about Market Risk” in our 2024 Annual Report.

Evaluation of Disclosure Controls and Procedures

Our management, with the participation of our Chief Executive Officer and our Chief Financial Officer, evaluated the effectiveness of our disclosure controls and procedures as of September 30, 2025. The term “disclosure controls and procedures”, as defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, as amended, or the Exchange Act, means controls and other procedures of a company that are designed to ensure that information required to be disclosed by a company in the reports that it files or submits under the Exchange Act is recorded, processed, summarized and reported, within the time periods specified in the Securities and Exchange Commission’s rules and forms. Disclosure controls and procedures include, without limitation, controls and procedures designed to ensure that information required to be disclosed by a company in the reports that it files or submits under the Exchange Act is accumulated and communicated to the company’s management, including its principal executive and principal financial officers, as appropriate to allow timely decisions regarding required disclosure. Management recognizes that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving their objectives and management necessarily applies its judgment in evaluating the cost-benefit relationship of possible controls and procedures. Based on the evaluation of our disclosure controls and procedures as of September 30, 2025, our Chief Executive Officer and Chief Financial Officer concluded that, as of such date, our disclosure controls and procedures were effective at the reasonable assurance level.

Changes in Internal Control over Financial Reporting

No change in our internal control over financial reporting occurred during the quarter ended September 30, 2025 that has materially affected, or is reasonably likely to materially affect, our internal control over financial reporting.

We have set forth in Item 1A to our Annual Report on Form 10-K for the year ended December 31, 2024, risk factors relating to our business, our industry, our structure and our common stock. Readers of this Quarterly Report on Form 10-Q are referred to such Item 1A for a more complete understanding of risks concerning us. There have been no material changes in our risk factors since those published in such Form 10-K for the year ended December 31, 2024, other than as reported in Item 1A to our Quarterly Form 10-Q for the period ended June 30, 2025.