NEUROGENE Trademarks this Presentablion may contain racemarks, service mands, trode names and copyights of of ther espropries, which rae the properiy of their espective owner. Sole/ or converie ond copyights pelened to in this Pesentation may be lines without the TM, SM © of @ synbus, but Neurogere will asset, to the ulest esterf uncter applicable owners, il ony t marks, trade names and copyrights. August 2025 Disclaimer Forward Looking Statements this communication contains forward-boking statements within ...

UNITED STATES SECURITIES AND EXCHANGE COMMISSION For the quarterly period ended June 30, 2025 Washington, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 (State or other jurisdiction of incorporation or organization) (I.R.S. Employer Identification No.) 535 W 24th St. 5th Floor New York, NY 10011 (Address of principal executive offices) (Zip Code) (855) 508-3568 OR ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES ...

NGN-401 for Rett Syndrome - NGN-401, a gene therapy leveraging EXACT transgene regulation technology, is being developed for Rett syndrome [15] - Rett syndrome affects an estimated 6,000-9,000 patients in the U S [20] - The worldwide incidence of Rett syndrome is estimated at 1 in 10,000 females [20] - Phase 1/2 data showed durable improvements, including a two-point improvement in CGI-I in all participants [38] - All four participants in the Phase 1/2 trial achieved a CGI-I rating of "Much Improved" [41] - The company expects to announce additional Phase 1/2 clinical data in the second half of 2025 [64] Clinical Trial and Regulatory Updates - The FDA has accepted the conversion of the Phase 1/2 trial to a registrational trial for NGN-401 [28] - The Embolden registrational trial is designed as an open-label, single-arm, baseline-controlled study [27] - The proposed number of participants in the Embolden trial is 18, subject to FDA feedback [28] - The company anticipates providing a regulatory update regarding the registrational trial in the first half of 2025 [64] Manufacturing and Financials - Neurogene has a 42,000 sq ft in-house AAV manufacturing facility in Houston, with 6,000 sq ft of cleanrooms [11] - The company's cash runway is expected to fund operations into early 2028 [6, 64]

Financial Results - Neurogene Inc. reported financial results for Q1 2025, with a focus on operational performance and financial condition[5] - The financial results include key metrics that will be elaborated in the attached press release[5] - The report does not include specific financial figures or performance metrics in the provided content[6] Press Release - The press release detailing these results was issued on May 9, 2025, and is attached as Exhibit 99.1[5] - The report was signed by Christine Mikail, President and Chief Financial Officer, on the date of the press release[11] Company Information - The company is listed on The Nasdaq Global Market under the trading symbol NGNE[3] - Neurogene Inc. is not classified as an emerging growth company under the Securities Act of 1933[4] - The company’s principal executive office is located in New York, NY[2] Compliance and Filing - The filing is intended to comply with the requirements of the Securities Exchange Act of 1934[9] - The report includes an Interactive Data File as part of its exhibits[7]

Financial Performance - Neurogene reported a net loss of $22.6 million for the three months ended March 31, 2025, compared to a net loss of $16.9 million for the same period in 2024[102]. - The net loss for the three months ended March 31, 2025, was $22.65 million, compared to a net loss of $16.92 million for the same period in 2024, representing an increase of $5.73 million[120]. - The company has not generated any commercial revenue from product sales and does not have any products approved for commercial sale[104]. - As of March 31, 2025, Neurogene had an accumulated deficit of $284.9 million and cash, cash equivalents, and short-term investments totaling $292.6 million[102]. - Interest income for the three months ended March 31, 2025, was $3.21 million, an increase of $0.89 million compared to $2.32 million for the same period in 2024[120]. - General and administrative expenses increased to $8.2 million for the three months ended March 31, 2025, from $5.2 million in the same period of 2024, representing a 56% increase[125]. - The company expects general and administrative expenses to increase in the future to support heightened research and development activities[126]. - Net cash used in operating activities was $20.8 million for the three months ended March 31, 2025, compared to $21.7 million for the same period in 2024, indicating a 4% improvement[136][137]. - The company anticipates needing substantial additional capital to complete the development of product candidates and build necessary infrastructure for commercialization[131]. Research and Development - The Phase 1/2 clinical trial of NGN-401 for Rett syndrome has shown consistent improvements in clinical assessments, with participants achieving meaningful gains in skills and developmental milestones[92]. - The trial for NGN-401 has received FDA clearance for the Investigational New Drug (IND) application, and participants have been dosed in the UK, Australia, and the US[91]. - Neurogene's NGN-401 program is part of the FDA's START Pilot Program, which aims to accelerate the development of therapies for rare diseases[97]. - The RMAT designation for NGN-401 allows for early and frequent communications with the FDA, facilitating a streamlined development process[97]. - The company expects to continue to incur significant research and development expenses as it advances its programs and product candidates through clinical development[124]. - Research and development expenses increased to $17.76 million for the three months ended March 31, 2025, compared to $13.54 million for the same period in 2024, reflecting a change of $4.22 million[120]. - The Rett syndrome program saw an increase in expenses primarily due to a $1.2 million rise in preclinical costs and a $0.6 million increase in clinical trial costs[122]. - The company is currently evaluating options for the NGN-101 program after the RMAT application for CLN5 Batten disease was denied, indicating challenges in advancing this program[99]. - The company’s RMAT application for the NGN-101 CLN5 Batten disease gene therapy program was denied, leading to a reevaluation of the program[104]. Collaborations and Agreements - The collaboration agreement with the University of Edinburgh was amended and extended through December 2026 to support pipeline development and scientific innovation[104]. - The company entered into a collaboration with the University of Edinburgh, extending the initial 40-month term by an additional 33 months, with obligations for semi-annual payments related to project funding[150]. - Under the March 2022 Edinburgh License Agreement, the company obtained an exclusive worldwide license for certain patents, with low single-digit percentage royalties on future commercial net sales of licensed products, and potential milestone payments up to $30.3 million[151]. - The company has a Non-Exclusive License Agreement with Virovek, Inc., which includes development milestone payments of up to $0.2 million and low single-digit percentage royalties on future commercial net sales[152]. - A Non-Exclusive License Agreement with Sigma-Aldrich Co. requires the company to pay up to $2.5 million in development-related milestones and a small annual fee once the first product candidate enters the clinic[153]. - The company entered into a Nonexclusive License Agreement with Stanford University, obligating it to pay up to $0.5 million in licensing fees over a 10-year term[154]. Financial Position and Capital Needs - The company raised approximately $521.9 million from private placements since its inception, primarily funding its operations through outside capital[102]. - Cash, cash equivalents, and short-term investments totaled $292.6 million as of March 31, 2025, with net proceeds from private placements amounting to approximately $521.9 million since inception[130]. - The company may require substantial additional capital to support its operations and product development efforts, which could include income from collaborations or partnerships[104]. - As of December 31, 2024, the company had federal and state net operating loss carryforwards of $319.8 million and $39.6 million, respectively[119]. Regulatory and Compliance - Neurogene discontinued the 3E15 vg dose level in the NGN-401 trial due to safety concerns following a participant's death from a hyperinflammatory syndrome[95]. - Financial statements are prepared in accordance with U.S. GAAP, requiring management to make estimates and judgments that may affect reported amounts[156]. - As a smaller reporting company, the company is not required to provide quantitative and qualitative disclosures about market risk[158]. - The total contingent value rights liability as of March 31, 2025, was $1.1 million, slightly up from $1.09 million as of December 31, 2024[148]. - Other expenses decreased by $0.5 million for the three months ended March 31, 2025, primarily due to the accrual of contingent consideration liabilities related to licensing agreements[128].

Group 1 - The NASDAQ Biotechnology Index increased by 1.56%, closing at 4,260.4, with a gain of 65.2 points [1][3] - Sutro Biopharma saw a significant rise of 20.04%, while Mersana Therapeutics and Neurogene also experienced notable increases of 17.19% and 15.12% respectively [1][3] - Other companies that performed well include Kyverna Therapeutics (+13.24%), Sana Biotechnology (+11.11%), and Larimar Therapeutics (+10.88%) [3] Group 2 - Tempus AI had a decline of 4.83%, ranking fourth from the bottom, followed by Prothena Plc. (-5.06%), Grail (-6.28%), and OmniAb (-8.11%) [2][4] - The overall performance of the biotechnology sector showed mixed results, with several companies experiencing significant losses alongside those that gained [2][4]

Financial Stability and Operations - Neurogene's cash runway extends into the second half of 2027, allowing operations beyond key clinical inflection points[8] - Cash runway is expected to fund operations into the second half of 2027, ensuring continued development and operational stability[71] Clinical Development and Trials - The company is advancing its NGN-401 program for Rett syndrome, with a pivotal trial design evaluating a 1E15 vg dose in female participants aged 4-10 years[32] - The company has discontinued the use of the 3E15 vg dose in favor of the 1E15 vg dose for future participants in the NGN-401 trial, reflecting an adaptive approach to clinical development[37] - The company anticipates providing a regulatory update in the first half of 2025 regarding pivotal trials for NGN-401[71] - The company plans to announce additional Phase 1/2 clinical data in the second half of 2025, indicating ongoing research and development efforts[71] - The company is leveraging the START and RMAT programs to accelerate registration and approval processes with the FDA, enhancing the potential for quicker market access[68] Patient Outcomes and Improvements - Interim clinical data for NGN-401 shows consistent improvements across multiple scales, with all participants achieving a 2-point improvement in the Clinician Global Impression-Improvement (CGI-I) scale[34] - Clinical trial data indicates that participants experienced objective improvements in autonomic function and developmental milestones, surpassing natural history data expectations[35] - Participants experienced significant improvements in various developmental skills post-treatment with NGN-401, including fine motor skills where participant 1 developed a pincer grasp and began self-feeding[55] - Sleep efficiency for participant 1 increased from 83% to 90% and for participant 2 from 90% to over 95% at 6 months post-treatment[47] - Participant 2 showed improvements in communication, now able to say "mama," "dada," and "nana" clearly and in context[58] - Participant 3 improved from requiring spoon-feeding to being able to self-feed solid foods and swallow liquids independently[63] - Participant 4 demonstrated early improvements in hand function, now able to use utensils to self-feed without assistance[67] - Participants demonstrated improvements in self-feeding skills, with some able to take multiple bites and use utensils effectively[78] - Significant gains in gross motor function were observed, with one participant experiencing a 75% reduction in falls[80] - Communication abilities improved, with one participant making food choices 100% of the time, while others showed varying degrees of choice-making capabilities[82] - Breathing dysrhythmias were reduced significantly, with one participant experiencing them less than 5% of the time[87] - Total sleep time increased from 6.6 to 7 hours per night, indicating improved sleep efficiency[89] - Constipation improved over time, as measured by stool consistency, with a transition towards more normal stool types[91] - Participants showed meaningful improvements in hand function, with many achieving higher-level grasping skills[77] - Patient 3 showed significant improvement in swallowing abilities, transitioning from a pureed diet to self-feeding soft foods within 9 months post-NGN-401 treatment[94] - Patient 4 experienced a 100% improvement in constipation by Month 4, as measured by stool consistency and frequency[96] - Sleep quality for both patients was maintained post-treatment, with no baseline deficits reported in the autonomic category of sleep[94][96] Technology and Manufacturing - Neurogene's EXACT technology aims to deliver therapeutic levels of MeCP2 to deficient cells while maintaining non-toxic levels in unaffected cells, addressing the complexities of gene therapy for Rett syndrome[20] - The company operates a 42,000 sq ft GMP manufacturing facility in Houston, which provides flexibility and cost efficiency in producing AAV products[13] - Neurogene's in-house manufacturing capabilities enhance its strategic flexibility and control over product quality and development timelines[12] - NGN-401 program leverages a unique transgene regulation mechanism to optimize gene expression, potentially widening the therapeutic window for treatment[25] - ICV delivery of NGN-401 achieved targeted MeCP2 levels, showing survival rates of 23% in male knockout and 37% in female heterozygous models[98] - EXACT technology delivered consistent levels of MECP2 expression on a cell-by-cell basis, indicating precision in gene therapy[99] - NGN-MECP2 achieved narrow expression of MECP2, suggesting potential for reduced side effects in treatment[100] Disease Context and Market Need - The U.S. prevalence of Rett syndrome is estimated at approximately 6,000-9,000 patients, indicating a significant unmet medical need for effective treatments[17] - The majority of patients with Classic Rett Syndrome have a CGI-S score of 4-6, indicating moderate to severe illness[75] - The data cut-off date for the reported improvements was October 17, 2024, indicating ongoing monitoring of patient progress[79]

Financial Performance - As of December 31, 2024, total assets increased to $335.73 million from $222.57 million as of December 31, 2023, representing a 50.9% growth[678] - The company reported an accumulated deficit of $262.30 million as of December 31, 2024, compared to $187.15 million in the previous year, indicating a 40.1% increase in losses[678] - Total stockholders' equity rose to $310.38 million from $186.02 million, reflecting a 66.8% increase[678] - Revenue under licensing agreements for 2024 is $925 million, with total operating expenses of $83.53 million, resulting in a net loss of $75.14 million[681] - The company reported a net loss per share of $(4.28) for 2024, compared to $(117.28) for the pre-merger period in 2023[681] - The Company reported net losses of $75.1 million and $36.3 million for the years ended December 31, 2024 and 2023, respectively[699] - The Company expects to incur substantial and increasing losses in future periods as it advances its products through clinical and regulatory processes[699] Cash Flow and Liquidity - Cash and cash equivalents decreased to $136.59 million from $148.20 million, a decline of 7.3% year-over-year[678] - Cash, cash equivalents, and restricted cash at the end of 2024 totaled $136.93 million, down from $148.72 million at the beginning of the period[690] - Net cash used in operating activities for 2024 was $(70.60) million, compared to $(51.42) million in 2023[690] - Total cash used in investing activities for 2024 was $(125.26) million, primarily due to purchases of held-to-maturity investments[690] - Cash used in operations was $70.6 million and $51.4 million for the years ended December 31, 2024 and 2023, respectively[699] Research and Development - Research and development expenses increased to $60.92 million in 2024 from $44.39 million in 2023, while general and administrative expenses rose to $22.61 million from $11.18 million[681] - The company is focused on gene therapy and is currently conducting a Phase 1/2 clinical trial for its first program, NGN-401, targeting Rett syndrome[692] - Research and development costs are expensed as incurred, including employee-related expenses and external costs, with no alternative future use of rights in other projects leading to immediate expensing of IPR&D[732][735] Regulatory and Market Risks - The company has not generated any product revenue and may never achieve profitability, as stated in the risk factors[22] - The company is substantially dependent on the success of its advanced product candidate, NGN-401, which is still in early development stages[22] - Significant additional capital will be required to finance future operations, with potential delays in clinical trials if capital is not raised[22] - The regulatory approval processes for product candidates are lengthy and unpredictable, which may delay commercialization efforts[22] - The market price of the company's common stock may continue to be volatile, influenced by various factors including future sales by existing stockholders[22] Stock and Equity - The reverse merger was completed on December 18, 2023, merging Neurogene OpCo with a wholly owned subsidiary of Neoleukin Therapeutics, Inc.[681] - The company raised approximately $95 million through pre-closing financing, issuing 2,792,206 shares and 1,811,739 pre-funded warrants[694] - Neurogene OpCo stockholders owned approximately 84% of the voting rights in the Company, influencing management and board composition[701] - The company issued an aggregate of 10,472,635 shares of common stock to Neurogene OpCo stockholders upon the effective time of the reverse merger[806] - The company is authorized to issue 450,000,000 shares of common stock with a par value of $0.000001 per share as of December 31, 2024[804] Expenses and Liabilities - The Company recorded stock-based compensation expense of $8.32 million for the year ended December 31, 2024, compared to $1.42 million in 2023, reflecting a significant increase[819] - General and administrative expenses primarily consist of personnel expenses, including salaries and stock-based compensation, along with corporate facility costs and legal fees[736] - The Company recorded impairment losses on idle equipment of $0.1 million for the year ended December 31, 2024, while no impairments were recognized in 2023[722] - The Company accrued trial wind-down costs of $1.962 million for the Phase 1 NL-201 Trial, with $1.203 million paid and a remaining balance of $0.209 million as of December 31, 2024[731] Tax and Valuation - The effective income tax rate for the Company was impacted by a full valuation allowance against its net deferred tax assets, maintaining no provision for federal or state income taxes for the years ended December 31, 2024 and 2023[828] - The Company had a federal net operating loss carryforward of $319.8 million as of December 31, 2024, up from $277.9 million in 2023[830] - The valuation allowance at the end of 2024 was $114.972 million, compared to $98.926 million at the end of 2023[835] - Liabilities for uncertain tax positions were $3.4 million in 2024, up from $2.6 million in 2023, which could impact the effective income tax rate[837] Future Commitments and Agreements - The company is obligated to pay up to $5.3 million in regulatory-related milestones and up to $25 million in sales-related milestones based on annual net sales of licensed products[788] - In November 2023, the company amended its Master Collaboration Agreement with the University of Edinburgh to continue funding projects through December 2026[790] - The company entered into a Nonexclusive License Agreement with Stanford University, obligating it to pay up to $0.5 million in licensing fees over a ten-year term[794]

Core Viewpoint - Pomerantz LLP is investigating claims of potential securities fraud or unlawful business practices by Neurogene Inc. and its officers or directors [1] Group 1: Clinical Trial and Stock Performance - On November 11, 2024, Neurogene reported interim clinical data from its Phase 1/2 trial for NGN-401 gene therapy, which was characterized as "positive," but one patient experienced a serious adverse event [2] - Following the adverse event news, Neurogene's stock price dropped by $31.53, or 44.08%, closing at $40.00 per share on November 12, 2024 [2] - On November 18, 2024, Neurogene updated that the patient was in critical condition and would not complete enrollment in the low-dose cohort as anticipated [3] - This update led to a sharp decline in Neurogene's stock price during intraday trading on November 18, 2024 [3] Group 2: Pomerantz LLP Background - Pomerantz LLP is recognized as a leading firm in corporate, securities, and antitrust class litigation, with a history of fighting for victims of securities fraud and corporate misconduct [4] - The firm has a track record of recovering multimillion-dollar damages for class members over its 80-year history [4]

UNITED STATES __________________________________________________ __________________________________________________ __________________________________________________ __________________________________ SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended September 30, 2024 OR ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES ACT OF 1934 For th ...