Stoke Therapeutics, Inc.

Previous wording

Following regulatory alignment with the U.S. Food and Drug Administration (“FDA”), European Medicines Agency (“EMA”), and Japan’s Pharmaceuticals and Medical Devices Agency (“PMDA”), a Phase 3 study, EMPEROR, is expected to begin in the second quarter of 2025 to further evaluate efficacy and safety of zorevunersen in children and adolescents ages 2 to up to 18 with Dravet syndrome. We have completed Phase 1/2a clinical trials for zorevunersen in patients with Dravet syndrome. The positive results from the Phase 1/2a and open-label extension (“OLE”) studies showed substantial and durable reductions in convulsive seizure frequency when administered on top of standard of care anti-seizure medicines. In the Ph1/2a studies, 85% of patients were taking at least three and 54% were taking at least four medicines to control seizures. Half the patients in the studies were taking concomitant fenfluramine. Additionally, ongoing treatment has led to continuous improvements in cognition and behavior through two years. Additional improvements were indicated within the first nine months of treatment among patients in the Phase 1/2a ADMIRAL study. These improvements were observed across multiple domains of theVineland-3 (Vineland Adaptive Behavior Scale, Third Edition), a standardized assessment of behavioral outcomes. Zorevunersen has been generally well tolerated across the studies.

Current wording

In addition to these studies, we continue to run open-label extension (“OLE”) studies in patients with Dravet syndrome. The Phase 1/2a ADMIRAL and OLE studies have shown substantial and durable reductions in convulsive seizure frequency when administered on top of standard of care anti-seizure medicines. In the Phase 1/2a studies, 85% of patients were taking at least three and 54% were taking at least four medicines to control seizures. Half the patients in the studies were taking concomitant fenfluramine. Ongoing treatment has led to continuous improvements in cognition and behavior through three years. Additional improvements were indicated within the first nine months of treatment among patients in the Phase 1/2a study. These improvements were observed across multiple domains of the Vineland-3 (Vineland Adaptive Behavior Scale, Third Edition), a standardized assessment of behavioral outcomes that is a key secondary endpoint for the Phase 3 study. Zorevunersen has been generally well tolerated across the studies.

Previous wording

We are also pursuing treatment for a second haploinsufficient disease, autosomal dominant optic atrophy (“ADOA”), the most common inherited optic nerve disorder. STK-002 is our lead clinical candidate for the treatment of ADOA. STK-002 is designed to upregulate OPA1 protein expression by leveraging the non-mutant (wild-type) copy of the OPA1 gene to restore OPA1 protein expression with the aim to stop or slow vision loss in patients with ADOA. There are currently no approved treatments for ADOA. We have received authorization in the UK to proceed with a Phase 1 open-label study (OSPREY) of children and adults ages 6 to 55 who have an established diagnosis of ADOA and have evidence of a genetic mutation in the OPA1 gene. Since then, we have identified additional important pre-clinical activities as we seek to optimize our clinical plans for STK-002 and better understand the potential for targeting OPA1 beyond ADOA. We anticipate that these data, along with research on the commercial landscape, will provide a more complete picture of the opportunity for a potential disease-modifying medicine for ADOA.

Current wording

In addition to our Dravet program, we are also pursuing treatment for a second haploinsufficient disease, autosomal dominant optic atrophy (“ADOA”), the most common inherited optic nerve disorder for which there are currently no approved treatments. STK-002 is our clinical candidate for the treatment of ADOA. STK-002 is designed to upregulate OPA1 protein expression by leveraging the non-mutant (wild-type) copy of the OPA1 gene to restore OPA1 protein expression with the aim to stop or slow vision loss in patients with ADOA. In a non-human primate (NHP) model of ADOA conducted in collaboration with UC Davis, treatment with STK-002 was well tolerated and helped protect, and possibly improve, eye health. The data suggest that STK-002 may help preserve the function of important vision-related nerve cells, which could potentially improve or maintain vision. We have received authorization in the UK to proceed with a Phase 1 open-label study (OSPREY) of children and adults ages 6 to 55 who have an established diagnosis of ADOA and have evidence of a genetic mutation in the OPA1 gene. We plan to enroll our first patient in the Phase 1 study in the second half of 2025.

Previous wording

In May 2022, we filed a universal Shelf Registration statement on Form S-3 (the “2022 Registration Statement”) with the SEC. The 2022 Registration Statement was declared effective by the SEC on May 31, 2022, and contained two prospectuses: a base prospectus, which covered the offering, issuance and sale by us of up to a maximum aggregate offering price of $400.0 million of our common stock, preferred stock, debt securities, warrants to purchase common stock, preferred stock or debt securities, subscription rights to purchase common stock, preferred stock or debt securities and/or units consisting of some or all of these securities; and a sales agreement prospectus covering the offering, issuance and sale by us of up to a maximum aggregate offering price of $150.0 million of common stock that may be issued and sold under a Controlled Equity Offering Sales Agreement (the “Sales Agreement”).

Current wording

In terms of our liquidity and capital resources, in May 2022, we filed a universal Shelf Registration statement on Form S-3 (the “2022 Registration Statement”) with the SEC. The 2022 Registration Statement was declared effective by the SEC on May 31, 2022, and contained two prospectuses: a base prospectus, which covered the offering, issuance and sale by us of up to a maximum aggregate offering price of $400.0 million of our common stock, preferred stock, debt securities, warrants to purchase common stock, preferred stock or debt securities, subscription rights to purchase common stock, preferred stock or debt securities and/or units consisting of some or all of these securities; and a sales agreement prospectus covering the offering, issuance and sale by us of up to a maximum aggregate offering price of $150.0 million of common stock that may be issued and sold under a Controlled Equity Offering Sales Agreement (the “Sales Agreement”).

Previous wording

As of March 31, 2025 and December 31, 2024 we had $380.3 million and $246.7 million, respectively, in cash, cash equivalents and marketable securities.

Current wording

As of June 30, 2025 and December 31, 2024 we had $355.0 million and $246.7 million, respectively, in cash, cash equivalents and marketable securities.

Previous wording

Since inception, we have primarily had operating losses, the majority of which are attributable to research and development activities. We had a net income of $112.9 million for the three months ended March 31, 2025 and our net loss was $26.4 million for the three months ended March 31, 2024. As of March 31, 2025, we had an accumulated deficit of $378.0 million.

Current wording

Since inception, we have primarily had operating losses, which are attributable to research and development activities. Our net losses were $23.5 million and $25.7 million for the three months ended June 30, 2025 and 2024, respectively. For the six months ended June 30, 2025 we had a net income of $89.4 million and for the six months ended June 30, 2024 we had net losses of $52.1 million. As of June 30, 2025, we had an accumulated deficit of $401.4 million.

Previous wording

Based upon our current operating plan, we believe that our cash, cash equivalents, and marketable securities of approximately $380.3 million as of March 31, 2025, will fund operations to mid-2028. To date, we have not had any products approved for sale and have not generated any product sales. We do not expect to generate any revenues from product sales unless and until we successfully complete development and obtain regulatory approval for one or more of our product candidates, which we expect will take a number of years. If we obtain regulatory approval for any of our product candidates, we expect to incur significant commercialization expenses related to product sales, marketing, manufacturing and distribution. As a result, until such time, if ever, as we can generate substantial product revenue, we expect to finance our cash needs through equity offerings, debt financings or other capital sources, including potentially collaborations, licenses and other similar arrangements. However, we may be unable to raise additional funds or enter into such other arrangements when needed on favorable terms or at all. Any failure to raise capital as and when needed could have a negative impact on our financial condition and on our ability to pursue our business plans and strategies. If we are unable to raise capital, we will need to delay, reduce or terminate planned activities to reduce costs.

Current wording

Based upon our current operating plan, we believe that our cash, cash equivalents, and marketable securities of approximately $355.0 million as of June 30, 2025, will fund operations to mid-2028. To date, we have not had any products approved for sale and have not generated any product sales. We do not expect to generate any revenues from product sales unless and until we successfully complete development and obtain regulatory approval for one or more of our product candidates, which we expect will take a number of years. If we obtain regulatory approval for any of our product candidates, we expect to incur significant commercialization expenses related to product sales, marketing, manufacturing and distribution. As a result, until such time, if ever, as we can generate substantial product revenue, we expect to finance our cash needs through equity offerings, debt financings or other capital sources, including potentially collaborations, licenses and other similar arrangements. However, we may be unable to raise additional funds or enter into such other arrangements when needed on favorable terms or at all. Any failure to raise capital as and when needed could have a negative impact on our financial condition and on our ability to pursue our business plans and strategies. If we are unable to raise capital, we will need to delay, reduce or terminate planned activities to reduce costs.

Previous wording

On February 14, 2025, we entered into a License and Collaboration Agreement (the “Biogen Agreement”) with Biogen International GmbH (“Biogen”) for the joint development and commercialization of zorevunersen and other compounds targeting the SCN1A gene (the “Licensed Product”). Under the terms of the Biogen Agreement, we granted Biogen an exclusive, royalty-bearing license to develop, manufacture, and export licensed products in all territories outside the U.S., Canada, and Mexico (the “Biogen Territory”). In addition, Biogen has the option to exercise an exclusive, royalty-bearing, sublicensable and transferable license for certain future follow-on ASOs directed to SCN1A controlled by us.

Current wording

On February 14, 2025, we entered into a License and Collaboration Agreement (the “Biogen Agreement”) with Biogen International GmbH (“Biogen”) for the joint development and commercialization of zorevunersen and other compounds targeting the SCN1A gene (the “Licensed Product”). Under the terms of the Biogen Agreement, we granted Biogen an exclusive, royalty-bearing license to develop, manufacture, and export licensed products in all territories outside the U.S., Canada, and Mexico (the “Biogen Territory”). In addition, Biogen has the option to exercise an exclusive, royalty-bearing, sublicensable and transferable license for certain future follow-on ASOs directed to SCN1A controlled by us. Under the Biogen Agreement, the parties are jointly developing zorevunersen, and we are leading global development. Together with Biogen, we share global development costs based on an agreed budget. We are responsible for 70.0% of these development costs and Biogen is responsible for the remaining 30.0% of these development costs.

Previous wording

For the three months ended, March 31, 2025, we recognized revenue related to the Biogen collaboration of $152.4 million.

Current wording

For the six months ended, June 30, 2025, we recognized revenue related to the Biogen collaboration of $155.6 million.

Previous wording

For the three months ended, March 31, 2025, we recognized revenue related to the Acadia collaboration of $6.1 million.

Current wording

For the six months ended, June 30, 2025, we recognized revenue related to the Acadia collaboration of $16.8 million.

Previous wording

Revenue for the three months ended March 31, 2025 was $158.6 million compared to $4.2 million for the three months ended March 31, 2024, an increase of $154.4 million. Revenue is generated from satisfying contractual obligations of the collaboration and licensing agreements with Acadia and Biogen. The increase of $154.4 million is primarily driven by $150.8 million related to the IP license performance obligation as part of the Biogen agreement.

Current wording

Revenue for the three months ended June 30, 2025 was $13.8 million compared to $4.8 million for the three months ended June 30, 2024, an increase of $9.0 million. Revenue is generated from satisfying contractual obligations of the collaboration and licensing agreements with Acadia and Biogen. The increase of $9.0 million is driven by $3.2 million for global development activities as part of the Biogen Agreement and $5.8 million related to the Acadia Agreement.

Previous wording

Research and development expenses were $32.7 million for the three months ended March 31, 2025 as compared to $22.4 million for the three months ended March 31, 2024, an increase of $10.3 million. The table below summarizes our research and development expenses (in thousands):

Current wording

Research and development expenses were $25.9 million for the three months ended June 30, 2025 as compared to $21.1 million for the three months ended June 30, 2024, an increase of $4.8 million. The table below summarizes our research and development expenses (in thousands):

Previous wording

The increase in research and development expenses was primarily attributable to an increase of $3.1 million in personnel-related expenses, $8.4 million in expenses related to our zorevunersen program, which is comprised of third-party services and scientific consulting fees, an increase of $0.4 million in external third-party expenses related to SYNGAP1 and MECP2, offset by a decrease of $0.3 million in expenses related to our ADOA program, which is comprised of third-party services and scientific consulting fees, and a decrease of $0.3 million in facilities and other non-program related costs.

Current wording

The increase in research and development expenses was attributable to an increase of $2.7 million in personnel-related expenses, $2.9 million in expenses related to our zorevunersen program, which is comprised of third-party services and scientific consulting fees, an increase of $0.1 million in external third-party expenses related to SYNGAP1 and MECP2, offset by a decrease of $0.6 million in expenses related to our ADOA program, which is comprised of third-party services and scientific consulting fees, and a decrease of $0.3 million in facilities and other non-program related costs.

Previous wording

General and administrative expenses were $14.7 million for the three months ended March 31, 2025 as compared to $10.2 million for the three months ended March 31, 2024. The increase of $4.5 million in general and administrative expenses was primarily attributable to an increase of $1.9 million in personnel expenses, $2.3 million in professional fees, and an increase $0.3 million in facilities and other general and administrative costs.

Current wording

General and administrative expenses were $15.3 million for the three months ended June 30, 2025 as compared to $13.0 million for the three months ended June 30, 2024. The increase of $2.3 million in general and administrative expenses was attributable to an increase of $1.9 million in professional fees, $0.3 million in personnel expenses and an increase $0.1 million in facilities and other general and administrative costs.

Previous wording

Since our inception through March 31, 2025, our operations have been financed by net proceeds of $836.6 million from the sale of convertible notes payable and our convertible preferred stock, our initial public offering, public offerings of common stock and pre-funded warrants, proceeds from the Sales Agreement and the upfront payments from Acadia and Biogen. As of March 31, 2025, we had $380.3 million in cash, cash equivalents and marketable securities. Cash in excess of immediate requirements is invested in accordance with our investment policy, primarily with a view to liquidity and capital preservation. On April 2, 2024, we completed an underwritten public offering of our common stock and issued and sold 5,555,557 shares of common stock at a public offering price of $13.50 per share and issued pre-funded warrants to purchase 3,703,730 shares of common stock at a public offering price of $13.499 per share subject to an exercise price equal to $0.0001. The common stock and warrants sold resulted in net proceeds of $119.9 million after deducting underwriting discounts, commissions and offering costs. No pre-funded warrants have been exercised.

Current wording

Since our inception through June 30, 2025, our operations have been financed by net proceeds of $836.6 million from the sale of convertible notes payable and our convertible preferred stock, our initial public offering, public offerings of common stock and pre-funded warrants, proceeds from the Sales Agreement and the upfront payments from Acadia and Biogen. As of June 30, 2025, we had $355.0 million in cash, cash equivalents and marketable securities. Cash in excess of immediate requirements is invested in accordance with our investment policy, primarily with a view to liquidity and capital preservation. On April 2, 2024, we completed an underwritten public offering of our common stock and issued and sold 5,555,557 shares of common stock at a public offering price of $13.50 per share and issued pre-funded warrants to purchase 3,703,730 shares of common stock at a public offering price of $13.499 per share subject to an exercise price equal to $0.0001. The common stock and warrants sold resulted in net proceeds of $119.9 million after deducting underwriting discounts, commissions and offering costs. No pre-funded warrants have been exercised.

Previous wording

We have primarily incurred losses since our inception in June 2014 and, as of March 31, 2025, we had an accumulated deficit of $378.0 million. Our primary use of cash is to fund operating expenses, which consist primarily of research and development expenditures, and to a lesser extent, general and administrative expenditures. Cash used to fund operating expenses is impacted by the timing of when we pay these expenses, as reflected in the change in our outstanding accounts payable and accrued expenses.

Current wording

We have primarily incurred losses since our inception in June 2014 and, as of June 30, 2025, we had an accumulated deficit of $401.4 million. Our primary use of cash is to fund operating expenses, which consist primarily of research and development expenditures, and to a lesser extent, general and administrative expenditures. Cash used to fund operating expenses is impacted by the timing of when we pay these expenses, as reflected in the change in our outstanding accounts payable and accrued expenses.

Previous wording

Based upon our current operating plan, we believe that our cash, cash equivalents, and marketable securities of approximately $380.3 million as of March 31, 2025, will fund operations to mid-2028. We have based this estimate on assumptions that may prove to be wrong, and we could utilize our available capital resources sooner than we currently expect. We will continue to require additional financing to advance our current product candidates through clinical development, to develop, acquire or in-license other potential product candidates and to fund operations for the foreseeable future. We will continue to seek funds through equity offerings, debt financings or other capital sources, including potentially collaborations, licenses and other similar arrangements. However, we may be unable to raise additional funds or enter into such other arrangements when needed on favorable terms or at all. Our ability to raise additional funds may be adversely impacted by potential worsening global macroeconomic conditions, including inflation, changing interest rates and instability in the global banking system, tariffs, and disruptions to and volatility in the credit and financial markets in the United States and worldwide. If we do raise additional capital through public or private equity offerings, the ownership interest of our existing stockholders will be diluted, and the terms of these securities may include liquidation or other preferences that adversely affect our stockholders’ rights. If we raise additional capital through debt financing, we may be subject to covenants limiting or restricting our ability to take specific actions, such as incurring additional debt, making capital expenditures or declaring dividends. Any failure to raise capital as and when needed could have a negative impact on our financial condition and on our ability to pursue our business plans and strategies. If we are unable to raise capital, we will need to delay, reduce or terminate planned activities to reduce costs.

Current wording

Based upon our current operating plan, we believe that our cash, cash equivalents, and marketable securities of approximately $355.0 million as of June 30, 2025, will fund operations to mid-2028. We have based this estimate on assumptions that may prove to be wrong, and we could utilize our available capital resources sooner than we currently expect. We will continue to require additional financing to advance our current product candidates through clinical development, to develop, acquire or in-license other potential product candidates and to fund operations for the foreseeable future. We will continue to seek funds through equity offerings, debt financings or other capital sources, including potentially collaborations, licenses and other similar arrangements. However, we may be unable to raise additional funds or enter into such other arrangements when needed on favorable terms or at all. Our ability to raise additional funds may be adversely impacted by potential worsening global macroeconomic conditions, including inflation, changing interest rates and instability in the global banking system, tariffs, and disruptions to and volatility in the credit and financial markets in the United States and worldwide. If we do raise additional capital through public or private equity offerings, the ownership interest of our existing stockholders will be diluted, and the terms of these securities may include liquidation or other preferences that adversely affect our stockholders’ rights. If we raise additional capital through debt financing, we may be subject to covenants limiting or restricting our ability to take specific actions, such as incurring additional debt, making capital expenditures or declaring dividends. Any failure to raise capital as and when needed could have a negative impact on our financial condition and on our ability to pursue our business plans and strategies. If we are unable to raise capital, we will need to delay, reduce or terminate planned activities to reduce costs.

Previous wording

During the three months ended March 31, 2025, cash provided by operating activities was $131.8 million. This was primarily attributable to a net income of $112.9 million, a net change of $11.5 million in our net operating assets and liabilities to non-cash charges of $7.3 million for stock-based compensation, depreciation, amortization and accretion of marketable securities, and a reduction in the carrying amount of right of use assets.

Current wording

During the six months ended June 30, 2025, cash provided by operating activities was $106.4 million. This was attributable to a net income of $89.4 million, a net change of $0.5 million in our net operating assets and liabilities and non-cash charges of $16.5 million for stock-based compensation, depreciation, amortization and accretion of marketable securities, and a reduction in the carrying amount of right of use assets.

Previous wording

During the three months ended March 31, 2024, cash used in operating activities was $24.6 million. This was primarily attributable to a net loss of $26.4 million, a net change of $4.7 million in our net operating assets and liabilities, offset by non-cash charges of $6.5 million for stock-based compensation, depreciation, amortization and accretion of marketable securities, and a reduction in the carrying amount of right of use assets.

Current wording

During the six months ended June 30, 2024, cash used in operating activities was $42.0 million. This was primarily attributable to a net loss of $52.1 million, a net change of $4.6 million in our net operating assets and liabilities, offset by non-cash charges of $14.7 million for stock-based compensation, depreciation, amortization and accretion of marketable securities, and a reduction in the carrying amount of right of use assets.

Previous wording

Our investing activities during the three months ended March 31, 2024 consisted of $10.0 million from the sales of marketable securities partially offset by purchases of property and equipment.

Current wording

Our investing activities during the six months ended June 30, 2025 consisted primarily of $200.6 million of purchases of marketable securities and $0.3 million of purchases of property plant and equipment offset by $66.0 million from the sales of marketable securities.

Previous wording

Our investing activities during the three months ended March 31, 2025 consisted primarily of $32.8 million from the sales of marketable securities offset by $19.0 million of purchases of marketable securities.

Current wording

Our investing activities during the six months ended June 30, 2024 consisted of $88.2 million of purchases of marketable securities offset by $10.0 million from the sales of marketable securities.

Previous wording

Our financing activities during the three months ended March 31, 2025 consisted of $1.0 million from the exercise of stock options and $0.4 million in proceeds from our Employee Stock Purchase Plan (the “ESPP”).

Current wording

Our financing activities during the three months ended June 30, 2025 consisted of $1.6 million from the exercise of stock options and $0.4 million in proceeds from our Employee Stock Purchase Plan (the “ESPP”).

Previous wording

Our financing activities during the three months ended March 31, 2024 consisted of $1.3 million of net proceeds from the controlled equity offering sales agreement, $0.2 million from the exercise of stock options and $0.2 million in proceeds from our Employee Stock Purchase Plan (the "ESPP").

Current wording

Our financing activities during the six months ended June 30, 2024 consisted of $119.9 million of net proceeds from a follow-on offering, $1.3 million of net proceeds from the controlled equity offering sales agreement, $1.0 million from the exercise of stock options and $0.2 million in proceeds from our ESPP.

Previous wording

In June 2021, we amended the agreement to extend the initial term of the 2,485 square foot lease for a period of three years ending April 30, 2025. In addition, the amendment provided for the lease of an additional 2,357 square feet of rentable space beginning on July 6, 2021 and ending on April 30, 2025. The amended lease provides us with the option to extend the term of the lease for an additional two years with a base annual rent increase of 3%. In March 2025, we further amended this lease to extend the term from April 30, 2025 to June 30, 2025. In 2021, we recognized a right-of-use asset and operating lease liabilities of $0.7 million for the extension of the lease to April 30, 2025 and a right-of-use asset and operating lease liabilities of $0.8 million for the additional 2,357 square feet of rentable space.

Current wording

In June 2021, we amended the agreement to extend the initial term of the 2,485 square foot lease for a period of three years ending April 30, 2025. In addition, the amendment provided for the lease of an additional 2,357 square feet of rentable space beginning on July 6, 2021 and ending on April 30, 2025. The amended lease provides us with the option to extend the term of the lease for an additional two years with a base annual rent increase of 3%. In March 2025, we further amended this lease to extend the term from April 30, 2025 to June 30, 2025. In 2021, we recognized a right-of-use asset and operating lease liabilities of $0.7 million for the extension of the lease to April 30, 2025 and a right-of-use asset and operating lease liabilities of $0.8 million for the additional 2,357 square feet of rentable space. This lease expired June 30, 2025.

Previous wording

In January 2025, we entered into an agreement to lease 7,581 square feet of space for an initial term of three years and three months. The lease includes two renewal options for an additional three years each. Lease terms commence at $0.7 million per annum, with 2.0% annual base rent increases plus operating expenses, real estate taxes, and utilities. The lease commencement date is expected to be July 1, 2025.

Current wording

In January 2025, we entered into an agreement to lease 7,581 square feet of space for an initial term of three years and three months. The lease includes two renewal options for an additional three years each. Lease terms commence at $0.7 million per annum, with 2.0% annual base rent increases plus operating expenses, real estate taxes, and utilities. The lease commencement date was July 8, 2025. As we did not have access to the space, a right-of-use asset was not recognized as of June 30, 2025.

Previous wording

There have been no significant changes in our critical accounting policies and estimates as compared to the critical accounting policies and estimates disclosed in the section titled “Management’s Discussion and Analysis of Financial Condition and Operations” included in our Annual Report on Form 10-K filed with the SEC on March 18, 2025, other than revenue recognition discussed below.

Current wording

There have been no significant changes in our critical accounting policies and estimates as compared to the critical accounting policies and estimates disclosed in the section titled “Management’s Discussion and Analysis of Financial Condition and Operations” included in our Annual Report on Form 10-K filed with the SEC on March 18, 2025.