Voyager Therapeutics(VYGR) - 2025 Q2 - Quarterly Report

PART I. FINANCIAL INFORMATION ITEM 1. CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (UNAUDITED) This section presents the unaudited condensed consolidated financial statements, including balance sheets, statements of operations, stockholders' equity, and cash flows, with detailed notes on business, accounting policies, and agreements CONDENSED CONSOLIDATED BALANCE SHEETS Total assets and stockholders' equity declined, reflecting reduced cash, marketable securities, and an increased accumulated deficit Condensed Consolidated Balance Sheet Highlights (Amounts in thousands) | Item | June 30, 2025 | December 31, 2024 | Change ($) | Change (%) | | :-------------------------------- | :------------ | :---------------- | :--------- | :--------- | | Total Assets | $322,101 | $393,050 | $(70,949) | -18.05% | | Cash and cash equivalents | $43,940 | $71,367 | $(27,427) | -38.43% | | Marketable securities (Current) | $171,653 | $195,317 | $(23,664) | -12.12% | | Marketable securities (Non-current) | $46,446 | $65,704 | $(19,258) | -29.31% | | Total Liabilities | $78,157 | $93,290 | $(15,133) | -16.22% | | Total Stockholders' Equity | $243,944 | $299,760 | $(55,816) | -18.62% | | Accumulated Deficit | $(390,587) | $(326,184) | $(64,403) | 19.74% | - The accumulated deficit increased by $64.403 million from December 31, 2024, to June 30, 2025, reflecting the net loss incurred during the period[17] CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS Net loss significantly increased due to a substantial decrease in collaboration revenue, despite relatively stable operating expenses Condensed Consolidated Statements of Operations and Comprehensive Loss Highlights (Amounts in thousands) | Item | Three Months Ended June 30, 2025 | Three Months Ended June 30, 2024 | Change ($) | Change (%) | | :----------------------------------- | :------------------------------- | :------------------------------- | :--------- | :--------- | | Collaboration revenue | $5,200 | $29,578 | $(24,378) | -82.42% | | Total operating expenses | $41,825 | $44,603 | $(2,778) | -6.23% | | Operating loss | $(36,625) | $(15,025) | $(21,600) | 143.76% | | Net loss | $(33,382) | $(10,141) | $(23,241) | 229.17% | | Net loss per share, basic | $(0.57) | $(0.18) | $(0.39) | 216.67% | | Item | Six Months Ended June 30, 2025 | Six Months Ended June 30, 2024 | Change ($) | Change (%) | | :----------------------------------- | :----------------------------- | :----------------------------- | :--------- | :--------- | | Collaboration revenue | $11,673 | $49,094 | $(37,421) | -76.22% | | Total operating expenses | $82,991 | $80,302 | $2,689 | 3.35% | | Operating loss | $(71,318) | $(31,208) | $(40,110) | 128.53% | | Net loss | $(64,403) | $(21,471) | $(42,932) | 199.95% | | Net loss per share, basic | $(1.10) | $(0.37) | $(0.73) | 197.30% | - The significant decrease in collaboration revenue for both periods was the primary driver of the increased net loss[19] CONDENSED CONSOLIDATED STATEMENTS OF STOCKHOLDERS' EQUITY Stockholders' equity decreased due to net loss, while additional paid-in capital increased from stock option exercises and compensation Stockholders' Equity Changes (Amounts in thousands, except share data) | Item | Balance at Dec 31, 2024 | Balance at Jun 30, 2025 | Change ($) | | :-------------------------- | :---------------------- | :---------------------- | :--------- | | Common Stock (Shares) | 54,731,316 | 55,434,956 | 703,640 | | Common Stock (Amount) | $55 | $56 | $1 | | Additional Paid-In Capital | $626,296 | $634,696 | $8,400 | | Accumulated Other Comp. Loss | $(407) | $(221) | $186 | | Accumulated Deficit | $(326,184) | $(390,587) | $(64,403) | | Total Stockholders' Equity | $299,760 | $243,944 | $(55,816) | - The increase in Additional Paid-In Capital was driven by exercises of stock options ($82k), issuance of common stock under ESPP ($434k), and stock-based compensation expense ($4,133k) during Q2 2025[21] CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS Operating cash flow shifted to net cash used due to lower collaboration payments, while investing provided cash and financing decreased Condensed Consolidated Statements of Cash Flows Highlights (Amounts in thousands) | Cash Flow Activity | Six Months Ended June 30, 2025 | Six Months Ended June 30, 2024 | Change ($) | | :------------------------------------------ | :----------------------------- | :----------------------------- | :--------- | | Net cash (used in) provided by operating activities | $(71,156) | $27,187 | $(98,343) | | Net cash provided by (used in) investing activities | $43,134 | $(132,008) | $175,142 | | Net cash provided by financing activities | $595 | $113,427 | $(112,832) | | Net (decrease) increase in cash, cash equivalents, and restricted cash | $(27,427) | $8,606 | $(36,033) | - The shift in operating cash flow was primarily due to a $78.4 million decrease in accounts receivable during the 2024 period, mainly from the receipt of an $80.0 million upfront payment under the 2023 Novartis Collaboration Agreement in Q1 2024[146] - The increase in cash from investing activities was mainly due to decreased purchases of marketable securities in H1 2025 compared to H1 2024[147] - The significant decrease in financing cash flow was due to the absence of proceeds from the 2024 underwritten public offering ($93.5 million) and the 2023 Novartis Stock Purchase Agreement ($20.0 million) in H1 2025[148] NOTES TO UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS Notes detail business, accounting policies, financial instruments, and agreements, highlighting restructuring, revenue recognition changes, and equity plans - Voyager Therapeutics is a biotechnology company focused on neurological diseases, leveraging its TRACER™ AAV capsid discovery platform and a non-viral therapeutics platform[27][28] - As of June 30, 2025, the company had $262.0 million in cash, cash equivalents, and marketable securities, expected to be sufficient to meet operating and capital expenditure requirements into 2028[30] - No material changes to significant accounting policies were reported during the six months ended June 30, 2025[35] Collaboration Revenue (Amounts in thousands) | Period | 2025 | 2024 | Change ($) | Change (%) | | :-------------------- | :----- | :----- | :--------- | :--------- | | Three Months Ended Jun 30 | $5,200 | $29,578 | $(24,378) | -82.42% | | Six Months Ended Jun 30 | $11,673 | $49,094 | $(37,421) | -76.22% | - The decrease in collaboration revenue was primarily due to the recognition of revenue under the percent complete model for upfront work related to the 2023 Neurocrine Collaboration Agreement during the second quarter of 2024[128] Stock-Based Compensation Expense (Amounts in thousands) | Period | 2025 | 2024 | Change ($) | Change (%) | | :-------------------- | :----- | :----- | :--------- | :--------- | | Three Months Ended Jun 30 | $4,133 | $4,042 | $91 | 2.25% | | Six Months Ended Jun 30 | $7,806 | $7,615 | $191 | 2.51% | - The 2015 Employee Stock Purchase Plan (ESPP) was amended to eliminate the evergreen provision and expand eligibility. The 2025 Stock Incentive Plan was approved, replacing the 2015 Plan for new awards, with 6,258,128 shares available as of June 30, 2025[56][58][60] Note 1. Nature of business - Voyager Therapeutics is a biotechnology company focused on leveraging human genetics to modify and cure neurological diseases, including Alzheimer's, Friedreich's ataxia, and Parkinson's disease[27] - The company's pipeline includes wholly-owned programs and collaborations with Alexion, Novartis, and Neurocrine[27] - Many programs are derived from the TRACER™ AAV capsid discovery platform, which enables high brain penetration with genetic medicines. A second non-viral therapeutics platform is also under development[28] - As of June 30, 2025, the company had an accumulated deficit of $390.6 million and has not generated product revenue, financing operations primarily through equity offerings and collaboration funding[29] - Cash, cash equivalents, and marketable securities totaled $262.0 million as of June 30, 2025, expected to be sufficient for planned operating expenses and capital expenditures for at least twelve months from the issuance of the statements[30] Note 2. Summary of significant accounting policies and basis of presentation - The unaudited condensed consolidated financial statements are prepared in accordance with GAAP for interim financial reporting and include all normal recurring adjustments[32] - The statements include accounts of the company and its wholly-owned subsidiary, with intercompany balances and transactions eliminated[33] - Management's estimates, including those for revenue recognition, lease incremental borrowing rates, accrued expenses, stock-based compensation, and income taxes, are based on historical experience and market assumptions[34] - There have been no changes in the company's significant accounting policies as described in its Annual Report on Form 10-K for the fiscal year ended December 31, 2024[35] Note 3. Fair value measurements Fair Value Measurements of Assets (Amounts in thousands) | Assets | Total (June 30, 2025) | Level 1 (June 30, 2025) | Level 2 (June 30, 2025) | | :------------------------------------------------ | :-------------------- | :---------------------- | :---------------------- | | Money market funds | $38,063 | $38,063 | $— | | U.S. Treasury notes | $114,854 | $114,854 | $— | | U.S. Government agency securities | $21,871 | $21,871 | $— | | Corporate bonds | $73,222 | $— | $73,222 | | Commercial paper | $8,152 | $— | $8,152 | | Total money market funds and marketable securities | $256,162 | $174,788 | $81,374 | | Assets | Total (Dec 31, 2024) | Level 1 (Dec 31, 2024) | Level 2 (Dec 31, 2024) | | :------------------------------------------------ | :------------------- | :--------------------- | :--------------------- | | Money market funds | $59,658 | $59,658 | $— | | U.S. Treasury notes | $125,783 | $125,783 | $— | | U.S. Government agency securities | $27,518 | $27,518 | $— | | Certificates of deposit | $4,286 | $— | $4,286 | | Corporate bonds | $94,976 | $— | $94,976 | | Commercial paper | $8,458 | $— | $8,458 | | Total money market funds and marketable securities | $320,679 | $212,959 | $107,720 | - Fair values of money market funds, U.S. Treasury notes, and U.S. Government agency securities are based on quoted prices in active markets (Level 1)[37] - Fair values of certificates of deposit, corporate bonds, and commercial paper are based on recent trades in inactive markets or quoted prices of similar instruments (Level 2)[37] Note 4. Cash equivalents and available-for-sale marketable securities Cash Equivalents and Marketable Securities (Amounts in thousands) | Item | Amortized Cost (Jun 30, 2025) | Fair Value (Jun 30, 2025) | Amortized Cost (Dec 31, 2024) | Fair Value (Dec 31, 2024) | | :------------------------------------ | :---------------------------- | :------------------------ | :---------------------------- | :------------------------ | | Money market funds | $38,063 | $38,063 | $59,658 | $59,658 | | U.S. Treasury notes | $114,874 | $114,854 | $125,996 | $125,783 | | U.S. Government agency securities | $21,886 | $21,871 | $27,552 | $27,518 | | Corporate bonds | $73,281 | $73,222 | $95,016 | $94,976 | | Commercial paper | $8,151 | $8,152 | $8,456 | $8,458 | | Total | $256,255 | $256,162 | $320,958 | $320,679 | - All marketable securities as of June 30, 2025, and December 31, 2024, have a contractual maturity of two years or less[39] - As of June 30, 2025, the company held 89 marketable securities in an unrealized loss position ($157.8 million fair value), primarily due to changes in interest rates, not credit losses. The company does not intend to sell these securities before recovery of their amortized cost basis[41] Reconciliation of Cash, Cash Equivalents, and Restricted Cash (Amounts in thousands) | Item | As of June 30, 2025 | As of December 31, 2024 | | :------------------------------------------ | :------------------ | :-------------------- | | Cash and cash equivalents | $43,940 | $71,367 | | Restricted cash | $2,874 | $2,874 | | Total cash, cash equivalents, and restricted cash | $46,814 | $74,241 | Note 5. Accrued expenses Accrued Expenses (Amounts in thousands) | Item | As of June 30, 2025 | As of December 31, 2024 | | :-------------------------- | :------------------ | :-------------------- | | Employee compensation costs | $6,339 | $6,752 | | Research and development costs | $3,603 | $5,246 | | Accrued goods and services | $1,346 | $1,201 | | Professional services | $737 | $972 | | Total | $12,025 | $14,171 | - Total accrued expenses decreased by $2.146 million from December 31, 2024, to June 30, 2025[43] Note 6. Lease obligation - The company leases laboratory and office space in Lexington, Massachusetts (through January 2031) and additional space in Cambridge, Massachusetts (through November 2026)[44] - In August 2023, an amendment for the Lexington Facility added approximately 61,307 square feet of space, with a contractual obligation of approximately $35.4 million over seven years[45] - A cash deposit or irrevocable letter of credit of $2.9 million is maintained as security for lease obligations[46] - In June 2024, the company vacated the Cambridge Facility and recorded a $2.8 million impairment charge. The facility was subsequently subleased in August 2024, generating operating sublease income[47] Operating Lease Costs and Sublease Income (Amounts in thousands) | Item | Three Months Ended June 30, 2025 | Three Months Ended June 30, 2024 | Six Months Ended June 30, 2025 | Six Months Ended June 30, 2024 | | :------------------------ | :------------------------------- | :------------------------------- | :----------------------------- | :----------------------------- | | Total lease cost | $1,900 | $4,400 | $3,800 | $6,100 | | Operating sublease income | $303 | $— | $606 | $— | Future Minimum Lease Payments (Amounts in thousands) | Year Ending December 31, | Total Minimum Lease Payments | | :----------------------- | :--------------------------- | | Remainder of 2025 | $4,982 | | 2026 | $9,983 | | 2027 | $7,763 | | 2028 | $7,996 | | 2029 | $8,235 | | Thereafter | $8,710 | | Total future minimum lease payments | $47,669 | | Less: imputed interest | $(7,465) | | Total operating lease liabilities | $40,204 | Note 7. Commitments, contingencies and other liabilities - The company has a research and development funding arrangement from 2016 (amended 2022) with a non-profit organization, providing up to $4.0 million upon milestone achievement. A $1.0 million milestone payment was earned in 2017 and is recorded as a non-current liability, as repayment is probable under certain conditions[49] - As of June 30, 2025, and December 31, 2024, the company was not a party to any material legal matters or claims and had no contingency reserves for any litigation liabilities[50] Note 8. Significant agreements - No material changes to collaboration or option and license agreements occurred during the three and six months ended June 30, 2025, and no new agreements were entered into[51] Collaboration Revenue (Amounts in thousands) | Period | 2025 | 2024 | | :-------------------- | :----- | :----- | | Three Months Ended Jun 30 | $5,200 | $29,578 | | Six Months Ended Jun 30 | $11,700 | $49,100 | Related Party Collaboration Receivable and Deferred Revenue (Amounts in thousands) | Item | Balance at Dec 31, 2024 | Additions | Deductions | Balance at Jun 30, 2025 | | :-------------------------------- | :---------------------- | :-------- | :--------- | :---------------------- | | Related party collaboration receivables | $676 | $1,352 | $(1,177) | $851 | | Deferred revenue | $30,397 | $— | $(7,273) | $23,124 | - The change in related party collaboration receivable is due to amounts owed for R&D services provided, offset by collections. Deferred revenue activity includes $7.3 million of collaboration revenue recognized under the 2023 and 2019 Neurocrine Collaboration Agreements[52] Note 9. Stock-based compensation Stock-Based Compensation Expense (Amounts in thousands) | Category | Three Months Ended June 30, 2025 | Three Months Ended June 30, 2024 | Six Months Ended June 30, 2025 | Six Months Ended June 30, 2024 | | :-------------------------------- | :------------------------------- | :------------------------------- | :----------------------------- | :----------------------------- | | Research and development | $1,629 | $1,626 | $3,114 | $2,906 | | General and administrative | $2,504 | $2,416 | $4,692 | $4,709 | | Total stock-based compensation expense | $4,133 | $4,042 | $7,806 | $7,615 | | Award Type | Three Months Ended June 30, 2025 | Three Months Ended June 30, 2024 | Six Months Ended June 30, 2025 | Six Months Ended June 30, 2024 | | :-------------------------------- | :------------------------------- | :------------------------------- | :----------------------------- | :----------------------------- | | Stock options | $2,556 | $2,577 | $4,948 | $4,985 | | Restricted stock awards and units | $1,478 | $1,382 | $2,682 | $2,471 | | Employee stock purchase plan awards | $99 | $83 | $176 | $159 | | Total stock-based compensation expense | $4,133 | $4,042 | $7,806 | $7,615 | - The 2015 Employee Stock Purchase Plan (ESPP) was amended on March 18, 2025, and approved by stockholders on June 3, 2025, to eliminate the evergreen provision and expand eligibility. As of June 30, 2025, 1,912,387 shares were available for future purchase under the ESPP[56][57] - The 2025 Stock Incentive Plan was adopted on March 18, 2025, and approved by stockholders on June 3, 2025, replacing the 2015 Plan for new equity awards. As of June 30, 2025, 6,258,128 shares were available under the 2025 Plan[58][59][60] Restricted Stock Unit (RSU) and Performance Restricted Stock Unit (PRSU) Activity (Six Months Ended June 30, 2025) | Item | Units | Weighted Average Grant Date Fair Value Per Unit | | :-------------------------------- | :------ | :------------------------------------ | | Unvested as of December 31, 2024 | 1,649,943 | $7.44 | | Granted | 1,770,961 | $4.23 | | Vested | (550,084) | $7.00 | | Forfeited | (144,522) | $6.69 | | Outstanding as of June 30, 2025 | 2,726,298 | $5.50 | - As of June 30, 2025, unrecognized stock-based compensation expense for unvested RSUs was $12.5 million (average vesting 3.2 years) and for unvested PRSUs was $3.3 million (recognized upon milestone achievement)[62][64] Stock Option Activity (Six Months Ended June 30, 2025) | Item | Shares | Weighted Average Exercise Price | | :-------------------------------- | :------- | :------------------------------ | | Outstanding as of December 31, 2024 | 8,800,464 | $8.10 | | Granted | 2,206,170 | $4.13 | | Exercised | (55,046) | $2.91 | | Cancelled or forfeited | (606,421) | $7.01 | | Outstanding as of June 30, 2025 | 10,345,167 | $7.29 | | Exercisable as of June 30, 2025 | 5,725,046 | $8.23 | - As of June 30, 2025, unrecognized stock-based compensation expense for unvested stock options was $17.9 million (average vesting 2.5 years)[66] Note 10. Net loss per share - Unvested restricted common stock awards, RSUs, PRSUs, and outstanding stock options were excluded from diluted net loss per share calculations for the three and six months ended June 30, 2025 and 2024, as their effect would be anti-dilutive[67] Potentially Dilutive Securities Excluded from Diluted EPS | Item | As of June 30, 2025 | As of June 30, 2024 | | :------------------------------ | :------------------ | :------------------ | | Unvested restricted common stock awards | — | 22,500 | | Unvested RSUs and PRSUs | 2,726,298 | 1,803,540 | | Outstanding stock options | 10,345,167 | 8,866,118 | | Total | 13,071,465 | 10,692,158 | Note 11. Underwritten public offering - On January 9, 2024, the company issued 7,777,778 shares of common stock and 3,333,333 pre-funded warrants through an underwritten public offering, generating net proceeds of approximately $93.5 million[70] - The pre-funded warrants are classified as stockholders' equity and are included in basic and diluted weighted average shares outstanding[70][71] Note 12. Related-party transactions Fees Paid to Former CSO (Amounts in thousands) | Period | 2025 | 2024 | | :-------------------- | :----- | :----- | | Three Months Ended Jun 30 | $129.3 | $150.0 | | Six Months Ended Jun 30 | $279.3 | $300.0 | - Collaboration revenue from the 2023 and 2019 Neurocrine Collaboration Agreements decreased from $28.7 million in Q2 2024 to $3.7 million in Q2 2025, and from $46.7 million in H1 2024 to $8.6 million in H1 2025[74] - Amounts due from Neurocrine are reflected as related party collaboration receivable, and amounts received but not yet recognized as revenue are deferred revenue[73] Note 13. Segment Information - The company operates as a single operating segment focused on developing and commercializing neurogenetic medicines[75] - The Chief Operating Decision Maker (CEO) reviews the segment's profit or loss based on net loss and assesses performance by reviewing forecast-to-actual variances for significant expenses[76] - All long-lived assets are held in the United States[76] ITEM 2. MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS Management discusses financial condition, operations, strategic focus on neurological diseases, pipeline, collaborations, and restructuring, emphasizing net losses and funding needs Overview Voyager Therapeutics focuses on neurological diseases with its TRACER™ platform, advancing AD programs and collaborations, with a 2025 restructuring extending cash runway into 2028 - Voyager Therapeutics is a biotechnology company focused on leveraging human genetics to modify and cure neurological diseases, including Alzheimer's disease (AD), Friedreich's ataxia (FA), and Parkinson's disease[81] - The company's proprietary pipeline includes VY7523 (anti-tau antibody for AD), which initiated a Phase 1 MAD clinical trial in early AD patients in February 2025, with initial data expected in the second half of 2026[82][90] - VY1706 (tau silencing gene therapy for AD) is anticipated to have an IND submission and clinical trial initiation in 2026, following preclinical studies showing 50-73% tau mRNA reduction in non-human primates[82][90] - Collaborations with Neurocrine include five gene therapy programs, with IND filings expected in 2025 for GBA1 and FA programs, and clinical trials in 2026. These programs have the potential for $35 million in regulatory and clinical milestones in 2025-2026[84][85] - Partnerships have delivered over $500.0 million in non-dilutive funding to date, with potential for up to $7.4 billion in future milestone payments and royalties[86] - A restructuring in the first half of 2025, involving reductions in force and streamlined clinical trial designs, is expected to extend the company's cash runway into 2028[88] Overview of Our Pipeline This section overviews the company's wholly-owned and partnered drug candidate pipeline for neurological diseases, leveraging the TRACER capsid platform Collaboration and License Agreements Key collaboration agreements with Novartis, Neurocrine, and Alexion provide funding and advance the gene therapy pipeline through upfront, milestone, and royalty payments - The company is eligible to receive up to $7.4 billion in milestone payments across its partnered portfolio, including $2.6 billion in potential development milestone payments, as well as royalties[86] - Under the 2023 Novartis Collaboration Agreement, Novartis paid an $80.0 million upfront payment, with potential for up to $200.0 million for the SMA Program and $225.0 million for the HD Program in development, regulatory, and commercialization milestones, plus sales milestones and tiered royalties[95] - Novartis exercised options for two gene therapy programs under the 2022 Novartis Option and License Agreement and paid a $15.0 million one-time fee in October 2024 for a direct license to a TRACER Capsid. Potential milestones include up to $125.0 million per Initial Licensed Product and $130.0 million for the Direct Licensed Product, plus sales milestones and tiered royalties[97][98][99] - Under the 2023 Neurocrine Collaboration Agreement, a $3.0 million milestone payment was received in October 2024 for a development candidate selection. Potential milestones include up to $985.0 million for the GBA1 Program and $175.0 million for each of three 2023 Discovery Programs, plus commercial milestones and tiered royalties[101][102] - Under the 2019 Neurocrine Collaboration Agreement, a $5.0 million milestone payment was received in March 2024 for the FA Program. However, Neurocrine deprioritized and discontinued both 2019 Discovery Programs in April 2025, resulting in the loss of associated milestones and royalties[104][106] - The Alexion Option and License Agreement (successor to Pfizer) involves an exclusive license for a TRACER Capsid for a rare neurological disease, with the research term extended to October 1, 2025[108][109][110] Accumulated Deficit; Expenses The company has a $390.6 million accumulated deficit from net operating losses and anticipates continued substantial expenses for R&D and clinical trials - As of June 30, 2025, the company had an accumulated deficit of $390.6 million and reported a net loss of $64.4 million for the six months ended June 30, 2025[111] - Significant expenses are expected to continue due to ongoing clinical trials for VY7523, investments in proprietary platforms and R&D initiatives, joint research and development under collaborations, and costs associated with operating as a public company[111][115] Regulatory Developments The "One Big Beautiful Bill Act" introduced tax changes, including immediate expensing for domestic research, with the company evaluating its financial impacts - The One Big Beautiful Bill Act, signed July 4, 2025, includes tax changes such as making certain Tax Cuts and Jobs Act provisions permanent, updating international tax rules, and reinstating immediate expensing for domestic research expenditures[112](index=1