AGIOS PHARMACEUTICALS, INC. 10-Q

Item 1. Financial Statements (Unaudited) AGIOS PHARMACEUTICALS, INC. Condensed Consolidated Balance Sheets (Unaudited) (In thousands, except share and per share data) March 31, 2025 December 31, 2024 Assets Current assets: Cash and cash equivalents $ 78,964 $ 76,247 Marketable securities 814,411 817,463 Accounts receivable, net 3,344 4,109 Inventory 29,605 27,616 Prepaid expenses and other current assets 42,292 40,165 Total current assets 968,616 965,600 Marketable securities 531,253 638,321 Operating lease assets 39,861 42,879 Property and equipment, net 11,067 11,675 Other non-current assets 4,721 4,724 Total assets $ 1,555,518 $ 1,663,199 Liabilities and stockholders’ equity Current liabilities: Accounts payable $ 13,726 $ 16,643 Accrued expenses 20,761 46,861 Income taxes payable 683 871 Operating lease liabilities 17,196 16,781 Total current liabilities 52,366 81,156 Operating lease liabilities, net of current portion 35,744 40,207 Other non-current liabilities 880 880 Total liabilities 88,990 122,243 Stockholders’ equity: Preferred stock, $ 0.001 par value; 25,000,000 shares authorized; no shares issued or outstanding at March 31, 2025 and December 31, 2024 — — Common stock, $ 0.001 par value; 125,000,000 shares authorized; 74,103,192 shares issued and 57,886,781 shares outstanding at March 31, 2025, and 73,372,696 shares issued and 57,156,285 shares outstanding at December 31, 2024 74 73 Additional paid-in capital 2,506,788 2,493,811 Accumulated other comprehensive income (loss) 365 ( 1,518 ) Treasury stock, at cost ( 16,216,411 shares at March 31, 2025 and December 31, 2024) ( 802,486 ) ( 802,486 ) Accumulated deficit ( 238,213 ) ( 148,924 ) Total stockholders’ equity 1,466,528 1,540,956 Total liabilities and stockholders’ equity $ 1,555,518 $ 1,663,199 See accompanying Notes to Condensed Consolidated Financial Statements. 1 Table of Contents AGIOS PHARMACEUTICALS, INC. Condensed Consolidated Statements of Operations (Unaudited) Three Months Ended March 31, (In thousands, except share and per share data) 2025 2024 Revenues: Product revenue, net $ 8,726 $ 8,189 Total revenue 8,726 8,189 Operating expenses: Cost of sales $ 1,085 $ 627 Research and development 72,743 68,620 Selling, general and administrative 41,527 31,014 Total operating expenses 115,355 100,261 Loss from operations ( 106,629 ) ( 92,072 ) Interest income, net 16,087 8,889 Other income, net 1,253 1,634 Net loss $ ( 89,289 ) $ ( 81,549 ) Net loss per share - basic and diluted $ ( 1.55 ) $ ( 1.45 ) Weighted-average number of common shares used in computing net loss per share – basic and diluted 57,459,195 56,383,475 See accompanying Notes to Condensed Consolidated Financial Statements. 2 Table of Contents AGIOS PHARMACEUTICALS, INC. Condensed Consolidated Statements of Comprehensive Loss (Unaudited) Three Months Ended March 31, (In thousands) 2025 2024 Net loss $ ( 89,289 ) $ ( 81,549 ) Other comprehensive income (loss) Unrealized gain (loss) on available-for-sale securities 1,883 ( 646 ) Comprehensive loss $ ( 87,406 ) $ ( 82,195 ) See accompanying Notes to Condensed Consolidated Financial Statements. 3 Table of Contents AGIOS PHARMACEUTICALS, INC. Condensed Consolidated Statements of Stockholders' Equity (Unaudited) Common Stock Additional Paid-In Capital Accumulated Other Comprehensive Loss Accumulated Deficit Treasury Stock Total Stockholders’ Equity (in thousands, except share amounts) Shares Amount Shares Amount Balance at December 31, 2024 73,372,696 $ 73 $ 2,493,811 $ ( 1,518 ) $ ( 148,924 ) ( 16,216,411 ) $ ( 802,486 ) $ 1,540,956 Unrealized gain on available-for-sale securities — — — 1,883 — — — 1,883 Common stock issued under stock incentive plan and ESPP 730,496 1 1,618 — — — — 1,619 Stock-based compensation expense — — 11,359 — — — — 11,359 Net loss — — — — ( 89,289 ) — — ( 89,289 ) Balance at March 31, 2025 74,103,192 $ 74 $ 2,506,788 $ 365 $ ( 238,213 ) ( 16,216,411 ) $ ( 802,486 ) $ 1,466,528 Common Stock Additional Paid-In Capital Accumulated Other Comprehensive Loss Accumulated Deficit Treasury Stock Total Stockholders’ Equity (in thousands, except share amounts) Shares Amount Shares Amount Balance at December 31, 2023 72,161,489 $ 72 $ 2,436,523 $ ( 441 ) $ ( 822,649 ) ( 16,216,411 ) $ ( 802,486 ) $ 811,019 Unrealized loss on available-for-sale securities — — — ( 646 ) — — — ( 646 ) Common stock issued under stock incentive plan and ESPP 806,433 1 5,863 — — — — 5,864 Stock-based compensation expense — — 9,234 — — — — 9,234 Net loss — — — — ( 81,549 ) — — ( 81,549 ) Balance at March 31, 2024 72,967,922 $ 73 $ 2,451,620 $ ( 1,087 ) $ ( 904,198 ) ( 16,216,411 ) $ ( 802,486 ) $ 743,922 See accompanying Notes to Condensed Consolidated Financial Statements. 4 Table of Contents AGIOS PHARMACEUTICALS, INC. Condensed Consolidated Statements of Cash Flows (Unaudited) Three Months Ended March 31, (In thousands) 2025 2024 Operating activities Net loss $ ( 89,289 ) $ ( 81,549 ) Adjustments to reconcile net loss from operations to net cash used in operating activities: Depreciation and amortization 1,278 1,348 Stock-based compensation expense 11,359 9,234 Net accretion of discount on marketable securities ( 1,348 ) ( 2,527 ) Gain on disposal of property and equipment — ( 39 ) Non-cash operating lease expense 3,018 2,803 Realized gain on investments ( 2 ) ( 152 ) Changes in operating assets and liabilities: Accounts receivable, net 765 ( 643 ) Inventory ( 1,989 ) ( 3,994 ) Prepaid expenses and other current and non-current assets ( 2,124 ) ( 4,091 ) Accounts payable ( 2,821 ) 1,430 Accrued expenses and other current liabilities ( 26,100 ) ( 18,038 ) Income taxes payable ( 188 ) — Operating lease liabilities ( 4,048 ) ( 3,649 ) Net cash used in operating activities ( 111,489 ) ( 99,867 ) Investing activities Purchases of marketable securities ( 174,903 ) ( 244,059 ) Proceeds from maturities and sales of marketable securities 288,256 368,722 Purchases of property and equipment ( 766 ) ( 141 ) Proceeds from sale of equipment — 40 Net cash provided by investing activities 112,587 124,562 Financing activities Net proceeds from stock option exercises and employee stock purchase plan 1,619 5,864 Net cash provided by financing activities 1,619 5,864 Net change in cash and cash equivalents 2,717 30,559 Cash and cash equivalents at beginning of the period 76,247 88,205 Cash and cash equivalents at end of the period $ 78,964 $ 118,764 Supplemental disclosure of non-cash investing and financing transactions Additions to property and equipment in accounts payable and accrued expenses $ 221 $ — Net cash taxes (returned) paid $ 188 $ ( 525 ) See accompanying Notes to Condensed Consolidated Financial Statements. 5 Table of Contents AGIOS PHARMACEUTICALS, INC. Notes to Condensed Consolidated Financial Statements (Unaudited) 1. Overview and Basis of Presentation References to Agios Throughout this Quarterly Report on Form 10-Q, "Agios," "the company," “we,” “us,” and “our,” and similar expressions, except where the context requires otherwise, refer to Agios Pharmaceuticals, Inc. and its consolidated subsidiaries, and “our Board of Directors” refers to the board of directors of Agios Pharmaceuticals, Inc. Overview We are a biopharmaceutical company committed to transforming patients’ lives through leadership in the field of cellular metabolism, with the goal of creating differentiated medicines for rare diseases, with a focus on classical hematology. With a history of focused study on cellular metabolism, we have a deep and mature understanding of this biology, which is involved in the healthy functioning of nearly every system in the body. Building on this expertise, these learnings can be rapidly applied to our clinical trials with the goal of developing medicines that can have a significant impact for patients. We accelerate the impact of our portfolio by cultivating connections with patient communities, healthcare professionals, partners and colleagues to discover, develop and deliver potential therapies for rare diseases. We are located in Cambridge, Massachusetts. The lead product candidate in our portfolio, PYRUKYND® (mitapivat), is an activator of both wild-type and mutant pyruvate kinase, or PK, enzymes for the potential treatment of hemolytic anemias. PYRUKYND® is approved for use by the U.S. Food and Drug Administration, or FDA, for the treatment of hemolytic anemia in adults with PK deficiency in the United States and by the European Commission for the treatment of PK deficiency in adult patients in the European Union, or EU. Additionally, we received marketing authorization in Great Britain for PYRUKYND® for the treatment of PK deficiency in adult patients under the European Commission Decision Reliance Procedure. In December 2024, we announced that we submitted a supplemental new drug application, or sNDA, to the FDA for PYRUKYND® for the treatment of adult patients with non-transfusion dependent and transfusion-dependent alpha- or beta-thalassemia, which was accepted with standard review by the FDA and granted a Prescription Drug User Fee Act, or PDUFA, goal date of September 7, 2025. Also in December 2024, we announced that we submitted a marketing authorization application, or MAA, to the European Medicines Agency, or EMA, and regulatory applications to the Kingdom of Saudi Arabia and United Arab Emirates health authorities for PYRUKYND® for the treatment of adult patients with non-transfusion dependent and transfusion-dependent alpha- or beta-thalassemia. In addition, we are currently evaluating PYRUKYND® in a phase 3 clinical trial for the treatment of sickle cell disease, or SCD. We are also developing (i) tebapivat, a novel PK activator, for the potential treatment of lower-risk myelodysplastic syndromes, or LR MDS, and SCD; (ii) AG-181, our phenylalanine hydroxylase, or PAH, stabilizer for the potential treatment of phenylketonuria, or PKU; and (iii) AG-236, an siRNA in-licensed from Alnylam Pharmaceuticals, Inc., or Alnylam, targeting the transmembrane serine protease 6, or TMPRSS6 gene for the potential treatment of polycythemia vera, or PV. We are subject to risks common to companies in our industry including, but not limited to, uncertainties relating to conducting preclinical and clinical research and development, the manufacture and supply of products for clinical and commercial use, obtaining and maintaining regulatory approvals and pricing and reimbursement for our products, market acceptance, managing global growth and operating expenses, availability of additional capital, competition, obtaining and enforcing patents, stock price volatility, dependence on collaborative relationships and third-party service providers, dependence on key personnel, potential litigation, potential product liability claims and potential government investigations. Sale of Oncology Business to Servier and Sale of Contingent Payments On March 31, 2021, we completed the sale of our oncology business to Servier Pharmaceuticals, LLC, or Servier, which represented a discontinued operation. The transaction included the sale of our oncology business, including TIBSOVO®, our clinical-stage product candidates vorasidenib, AG-270 and AG-636, and our oncology research programs, for a payment of approximately $ 1.8 billion in cash at the closing, subject to certain adjustments, and a payment of $ 200.0 million in cash, if, prior to January 1, 2027, vorasidenib is granted new drug application approval from the FDA with an approved label that permits vorasidenib’s use as a single agent for the adjuvant treatment of patients with Grade 2 glioma that have an isocitrate dehydrogenase, or IDH, 1 or 2 mutation (and, to the extent required by such approval, the vorasidenib companion diagnostic test is granted an FDA premarket approval), or the Vorasidenib Milestone Payment, as well as a royalty of 5 % of U.S. net sales of TIBSOVO® from the close of the transaction through loss of exclusivity, and a royalty of 15 % of U.S. net sales of vorasidenib from the first commercial sale of vorasidenib through loss of exclusivity, or the Vorasidenib Royalty Rights. The Vorasidenib Milestone Payment, Vorasidenib Royalty Rights and royalty payments related to TIBSOVO® are referred to as contingent payments and recognized as income when realizable. Servier also acquired our co-commercialization rights for 6 Table of Contents Bristol Myers Squibb’s IDHIFA® and the right to receive a $ 25.0 million potential milestone payment under our prior collaboration agreement with Celgene Corporation, or Celgene, and following the sale Servier has agreed to conduct certain clinical development activities within the IDHIFA® development program. In October 2022, we sold our rights to future contingent payments associated with the royalty of 5 % of U.S. net sales of TIBSOVO® from the close of the transaction through the loss of exclusivity to entities affiliated with Sagard Healthcare Partners, or Sagard, and recognized income of $ 127.9 million in our consolidated statements of operations for the year ended December 31, 2022. In August 2024, the FDA approved vorasidenib for adult and pediatric patients 12 years and older with Grade 2 astrocytoma or oligodendroglioma with a susceptible IDH1 or IDH2 mutation, following surgery including biopsy, sub-total resection, or gross total resection. In September 2024, we received the Vorasidenib Milestone Payment from Servier and recognized income of $ 200.0 million within the milestone payment from gain on sale of oncology business line item in our consolidated statements of operations for the three months ended September 30, 2024. In May 2024, we entered into a purchase and sale agreement to sell the Vorasidenib Royalty Rights to Royalty Pharma Investments 2019 ICAV, or Royalty Pharma, for $ 905.0 million in cash, or the Upfront Payment. The sale was contingent upon FDA approval of vorasidenib and other customary closing conditions. Upon consummation of the sale in August 2024, Royalty Pharma acquired 100 % of the Vorasidenib Royalty Rights payments made by Servier on account of up to $ 1.0 billion in U.S. net sales for each calendar year. In addition, any such Vorasidenib Royalty Rights payments made by Servier on account of U.S. net sales in each calendar year in excess of $ 1.0 billion will be split, with Royalty Pharma having the rights to a 12 % earn-out on those excess payments and Agios retaining the rights to a 3 % earn-out on those excess payments, or the Retained Earn-Out Rights. As a result of the sale, we recognized income of $ 889.1 million ($ 905.0 million net of fees of $ 15.9 million) within the gain on sale of contingent payments line item in our consolidated statements of operations for the three months ended September 30, 2024. Royalty income related to the Retained Earn-Out Rights, if any, will be recognized in the period when realizable. Basis of Presentation The condensed consolidated balance sheet as of March 31, 2025, the condensed consolidated statements of operations, comprehensive income (loss) and stockholders' equity for the three months ended March 31, 2025 and 2024, and the condensed consolidated statements of cash flows for the three months ended March 31, 2025 and 2024 are unaudited. The unaudited condensed consolidated financial statements have been prepared on the same basis as the annual financial statements and, in the opinion of our management, reflect all adjustments, which include only normal recurring adjustments, necessary to fairly state our financial position as of March 31, 2025, our results of operations and stockholders' equity for the three months ended March 31, 2025 and 2024, and cash flows for the three months ended March 31, 2025 and 2024. The financial data and the other financial information disclosed in these notes to the condensed consolidated financial statements related to the three-month periods are also unaudited. The results of operations for the three months ended March 31, 2025 are not necessarily indicative of the results to be expected for the year ending December 31, 2025 or for any other future annual or interim period. The condensed consolidated balance sheet data as of December 31, 2024 was derived from our audited financial statements, but does not include all disclosures required by U.S. generally accepted accounting principles, or U.S. GAAP. The condensed consolidated interim financial statements should be read in conjunction with the audited consolidated financial statements and notes thereto included in our Annual Report on Form 10-K for the year ended December 31, 2024 that was filed with the Securities and Exchange Commission, or SEC, on February 13, 2025. Our condensed consolidated financial statements include our accounts and the accounts of our wholly owned subsidiaries. All intercompany transactions have been eliminated in consolidation. The condensed consolidated financial statements have been prepared in conformity with U.S. GAAP. Use of Estimates The preparation of our condensed consolidated financial statements requires us to make estimates, judgments and assumptions that may affect the reported amounts of assets, liabilities, equity, revenues and expenses and related disclosure of contingent assets and liabilities. On an ongoing basis we evaluate our estimates, judgments and methodologies. We base our estimates on historical experience and on various other assumptions that we believe are reasonable, the results of which form the basis for making judgments about the carrying values of assets, liabilities and equity and the amount of revenues and expenses. 7 Table of Contents Liquidity As of March 31, 2025, we had cash, cash equivalents and marketable securities of $ 1.4 billion. Although we have incurred recurring losses and expect to continue to incur losses for the foreseeable future, we expect our cash, cash equivalents and marketable securities to be sufficient to fund current operations for at least the next twelve months from the issuance of the financial statements. If we are unable to raise additional funds through equity or debt financings, we may be required to delay, limit, reduce or terminate product development or future commercialization efforts, or grant rights to develop and market products or product candidates that we would otherwise prefer to develop and market ourselves. 2. Summary of Significant Accounting Policies There have been no material changes to the significant accounting policies previously disclosed in our Annual Report on Form 10-K for the year ended December 31, 2024. Recent Accounting Pronouncements Accounting standards that have been issued by the Financial Accounting Standards Board or other standards-setting bodies that do not require adoption until a future date are not expected to have a material impact on our financial statements upon adoption. 3. Fair Value Measurements We record cash equivalents and marketable securities at fair value. ASC 820, Fair Value Measurements and Disclosures , establishes a fair value hierarchy for those instruments measured at fair value that distinguishes between assumptions based on market data (observable inputs) and our own assumptions (unobservable inputs). The hierarchy consists of three levels: Level 1 – Unadjusted quoted prices in active markets for identical assets or liabilities. Level 2 – Quoted prices for similar assets and liabilities in active markets, quoted prices in markets that are not active, or inputs which are observable, directly or indirectly, for substantially the full term of the asset or liability. Level 3 – Unobservable inputs that reflect our own assumptions about the assumptions market participants would use in pricing the asset or liability in which there is little, if any, market activity for the asset or liability at the measurement date. The following table summarizes our cash equivalents and marketable securities measured at fair value and by level on a recurring basis as of March 31, 2025: (In thousands) Level 1 Level 2 Level 3 Total Cash equivalents $ 49,604 $ 11,666 $ — $ 61,270 Total cash equivalents 49,604 11,666 — 61,270 Marketable securities: Certificates of deposit $ — $ 6,763 $ — $ 6,763 U.S. Treasuries — 234,111 — 234,111 Government securities — 271,964 — 271,964 Corporate debt securities — 832,826 — 832,826 Total marketable securities — 1,345,664 — 1,345,664 Total cash equivalents and marketable securities $ 49,604 $ 1,357,330 $ — $ 1,406,934 Cash equivalents and marketable securities have been initially valued at the transaction price and are subsequently valued, at the end of each reporting period, utilizing third-party pricing services or other observable market data. The pricing services utilize industry standard valuation models, including both income and market-based approaches, and observable market inputs to determine value. After completing our validation procedures, we did not adjust or override any fair value measurements provided by the pricing services as of March 31, 2025. There have been no changes to the valuation methods during the three months ended March 31, 2025, and we had no financial assets or liabilities that were classified as Level 3 at any point during the three months ended March 31, 2025. 4. Marketable Securities Our marketable securities are classified as available-for-sale pursuant to ASC 320, Investments – Debt and Equity Securities , and are recorded at fair value. Unrealized gains and losses are included as a component of accumulated other comprehensive income (loss) in the condensed consolidated balance sheets and statements of stockholders’ equity, and a component of total 8 Table of Contents comprehensive income (loss) in the condensed consolidated statements of comprehensive loss, until realized. Unrealized losses are evaluated for impairment under ASC 326, Financial Instruments - Credit Losses , to determine if the impairment is credit-related or noncredit-related. Credit-related impairment is recognized as an allowance on the condensed consolidated balance sheets with a corresponding adjustment to earnings, and noncredit-related impairment is recognized in other comprehensive income, net of taxes. Realized gains and losses are included in investment income on a specific-identification basis. There were no material realized gains or losses on marketable securities for the three months ended March 31, 2025 or 2024. Marketable securities at March 31, 2025 consisted of the following: (In thousands) Amortized Cost Unrealized Gains Unrealized Losses Fair Value Current: Certificates of deposit $ 6,758 $ 5 $ — $ 6,763 U.S. Treasuries 127,826 95 ( 102 ) 127,819 Government securities 157,990 27 ( 88 ) 157,929 Corporate debt securities 521,864 278 ( 242 ) 521,900 Total Current 814,438 405 ( 432 ) 814,411 Non-current: U.S. Treasuries 105,858 476 ( 42 ) 106,292 Government securities 114,181 27 ( 173 ) 114,035 Corporate debt securities 310,822 390 ( 286 ) 310,926 Total Non-current 530,861 893 ( 501 ) 531,253 Total marketable securities $ 1,345,299 $ 1,298 $ ( 933 ) $ 1,345,664 Marketable securities at December 31, 2024 consisted of the following: (In thousands) Amortized Cost Unrealized Gains Unrealized Losses Fair Value Current: Certificates of deposit $ 10,374 $ 11 $ — $ 10,385 U.S. Treasuries 173,465 153 ( 27 ) 173,591 Government securities 167,970 103 ( 75 ) 167,998 Corporate debt securities 465,427 321 ( 259 ) 465,489 Total Current 817,236 588 ( 361 ) 817,463 Non-current: U.S. Treasuries 107,725 106 ( 303 ) 107,528 Government securities 112,175 3 ( 469 ) 111,709 Corporate debt securities 420,166 181 ( 1,263 ) 419,084 Total Non-current 640,066 290 ( 2,035 ) 638,321 Total marketable securities $ 1,457,302 $ 878 $ ( 2,396 ) $ 1,455,784 As of March 31, 2025 and December 31, 2024, we held both current and non-current investments. Investments classified as current have maturities of less than one year. Investments classified as non-current are those that: (i) have a maturity of greater than one year, and (ii) we do not intend to liquidate within the next twelve months, although these funds are available for use and, therefore, are classified as available-for-sale. As of March 31, 2025 and December 31, 2024, we held 156 and 213 debt securities, respectively, that were in an unrealized loss position for less than one year. We did no t record an allowance for credit losses as of March 31, 2025 and December 31, 2024 related to these securities. The aggregate fair value of debt securities in an unrealized loss position at March 31, 2025 and December 31, 2024 was $ 586.9 million and $ 768.1 million, respectively. There were no individual securities that were in a significant unrealized loss position as of March 31, 2025 and December 31, 2024. We regularly review the securities in an unrealized loss position and evaluate the current expected credit loss by considering factors such as historical experience, 9 Table of Contents market data, issuer-specific factors, and current economic conditions. We do not consider these marketable securities to be impaired as of March 31, 2025 and December 31, 2024. 5. Inventory Inventory, which consists of commercial supply of PYRUKYND®, consisted of the following: (In thousands) March 31, 2025 December 31, 2024 Raw materials $ 89 $ 89 Work-in-process 25,498 24,509 Finished goods 4,018 3,018 Total inventory $ 29,605 $ 27,616 6. Leases Our building leases are comprised of office and laboratory space under non-cancelable operating leases. These lease agreements have remaining lease terms of approximately three years and contain various clauses for renewal at our option. The renewal options were not included in the calculation of the operating lease assets and the operating lease liabilities as the renewal options are not reasonably certain of being exercised. The lease agreements do not contain residual value guarantees. The components of lease expense and other information related to leases were as follows: Three Months Ended March 31, (In thousands) 2025 2024 Operating lease costs $ 3,807 $ 3,807 Cash paid for amounts included in the measurement of operating lease liabilities 4,837 4,653 We have not entered into any material short-term leases or financing leases as of March 31, 2025. In arriving at the operating lease liabilities as of March 31, 2025 and December 31, 2024, we applied the weighted-average incremental borrowing rate of 5.7 % for both periods over a weighted-average remaining lease term of 2.9 and 3.2 years, respectively. As of March 31, 2025, undiscounted minimum rental commitments under non-cancelable leases were as follows: (In thousands) Remaining 2025 $ 13,106 2026 20,151 2027 20,755 2028 3,479 Undiscounted minimum rental commitments $ 57,491 Interest ( 4,551 ) Operating lease liabilities $ 52,940 We provided our landlord a security deposit of $ 2.9 million as security for our leases, which is included within other non-current assets on our condensed consolidated balance sheet. In August 2021, we entered into a long-term sublease agreement for 13,000 square feet of the office space at 38 Sidney Street, Cambridge, Massachusetts, which expired on December 31, 2024. In April 2022, we entered into a long-term sublease agreement for 27,000 square feet of the office space at 64 Sidney Street, Cambridge, Massachusetts, with the term of the lease running through April 2025. In May 2023, we entered into a long-term sublease agreement for 7,407 square feet of office space on the first floor of 64 Sidney Street, Cambridge, Massachusetts, with the term of the lease running through April 2025. 10 Table of Contents We recorded operating sublease income of $ 1.3 million and $ 1.6 million for the three months ended March 31, 2025 and 2024, respectively, in other income, net in the condensed consolidated statements of operations. We hold security deposits from our sublessees of approximately $ 0.9 million which is recorded within other non-current assets on our condensed consolidated balance sheet. As of March 31, 2025, the future minimum lease payments to be received under the long-term sublease agreements were as follows: (In thousands) 2025 $ 327 Total $ 327 7. Accrued Expenses Accrued expenses consisted of the following: (In thousands) March 31, 2025 December 31, 2024 Accrued compensation $ 7,802 $ 29,935 Accrued research and development costs 9,063 10,548 Accrued professional fees 1,681 4,316 Accrued other 2,215 2,062 Total accrued expenses $ 20,761 $ 46,861 8. Product Revenue We generate product revenue from sales of PYRUKYND® to a limited number of specialty distributors and specialty pharmacy providers, or collectively, the Customers. These Customers subsequently resell PYRUKYND® to pharmacies or dispense PYRUKYND® directly to patients. In addition to distribution agreements with Customers, we enter into arrangements with healthcare providers and payors that provide for government-mandated and/or privately-negotiated rebates, chargebacks and discounts with respect to the purchase of PYRUKYND®. The performance obligation related to the sale of PYRUKYND® is satisfied and revenue is recognized when the Customer obtains control of the product, which occurs at a point in time, typically upon delivery to the Customer. Product revenue, net, were as follows: Three Months Ended March 31, (In thousands) 2025 2024 Product revenue, net $ 8,726 $ 8,189 Reserves for Variable Consideration Revenues from product sales are recorded at the net sales price, or transaction price, which includes estimates of variable consideration for which reserves are established and result from contractual adjustments, government rebates, returns and other allowances that are offered within the contracts with our Customers, healthcare providers, payors and other indirect customers relating to the sale of our products. Contractual Adjustments We generally provide Customers with discounts, including prompt pay discounts, and allowances that are explicitly stated in the contracts and are recorded as a reduction of revenue in the period the related product revenue is recognized. In addition, we receive sales order management, data and distribution services from certain Customers. Chargebacks and discounts represent the estimated obligations resulting from contractual commitments to sell products to qualified healthcare providers at prices lower than the list prices charged to Customers who directly purchase the product from us. Customers charge us for the difference between what they pay for the product and the ultimate selling price to the qualified healthcare providers. These reserves are estimated using the expected value method, based upon a range of possible outcomes that are probability-weighted for the estimated channel mix and are established in the same period that the related revenue is recognized, resulting in a reduction of product revenue. 11 Table of Contents Government Rebates Government rebates include Medicare, TriCare, and Medicaid rebates, which we estimate using the expected value method, based upon a range of possible outcomes that are probability-weighted for the estimated payor mix. These reserves are recorded in the same period the related revenue is recognized, resulting in a reduction of product revenue. For Medicare, we also estimate the number of patients for whom we will owe an additional liability under the Medicare Part D Manufacturer Discount Program. Returns / Replacement We estimate the amount of product sales that may be returned by Customers or replaced by Agios and record this estimate as a reduction of revenue in the period the related product revenue is recognized. We currently estimate product return and replacement liabilities using the expected value method, based on available industry data, including our visibility into the inventory remaining in the distribution channel. The following table summarizes balances and activity in each of the product revenue allowance and reserve categories for the three months ended March 31, 2025: (In thousands) Contractual Adjustments Government Rebates Returns/ Replacement Total Balance at December 31, 2024 $ 253 $ 1,354 $ 489 $ 2,096 Current provisions relating to sales in the current year 422 555 124 1,101 Adjustments relating to prior years ( 38 ) — — ( 38 ) Payments/returns relating to sales in the current year ( 334 ) — — ( 334 ) Payments/returns relating to sales in the prior years ( 201 ) ( 415 ) — ( 616 ) Balance at March 31, 2025 $ 102 $ 1,494 $ 613 $ 2,209 Total revenue-related reserves above, included in our condensed consolidated balance sheets, are summarized as follows: (In thousands) March 31, 2025 December 31, 2024 Reduction of accounts receivable $ 78 $ 124 Component of accrued expenses 2,131 1,972 Total revenue-related reserves $ 2,209 $ 2,096 The following table presents changes in our contract assets during the three months ended March 31, 2025: (In thousands) December 31, 2024 Additions Deductions March 31, 2025 Contract assets (1) Accounts receivable, net $ 4,109 $ 9,789 $ ( 10,554 ) $ 3,344 (1) Additions to contract assets relate to amounts billed to Customers for product sales and deductions to contract assets primarily relate to collection of receivables during the reporting period. 9. Share-Based Payments 2023 Stock Incentive Plan and Inducement Grants In June 2023, our stockholders approved the 2023 Stock Incentive Plan, or the 2023 Plan. The 2023 Plan provides for the grant of incentive stock options, nonstatutory stock options, stock appreciation rights, restricted stock awards, restricted stock units, or RSUs, performance-based share units, or PSUs, and other stock-based awards to employees, advisors, consultants and non-employee directors. Following the adoption of the 2023 Plan, we ceased granting equity awards under the 2013 Stock Incentive Plan, or the 2013 Plan. Any outstanding equity awards that were previously granted under the 2013 Plan continue to be governed by their terms. Following adoption of the 2013 Plan, we ceased granting equity awards under the 2007 Stock Incentive Plan, or the 2007 Plan. There are no outstanding equity awards under the 2007 Plan. In connection with the start of employment of our Chief Executive Officer and Chief Financial Officer in 2022, our Chief Commercial Officer in 2023, and our Chief Corporate Development and Strategy Officer in March 2025, our Board of Directors granted each of them equity awards in the form of stock options, RSUs and PSUs, which awards were made outside 12 Table of Contents our equity incentive plans as inducements material to their respective entry into employment with us in accordance with Nasdaq Listing Rule 5635(c)(4). As of March 31, 2025, the maximum number of shares reserved under the 2013 Plan, the 2023 Plan and the inducement grants described above was 10,325,619 , and we had 1,215,876 shares available for future issuance under the 2023 Plan. Stock options The following table presents stock option activity for the three months ended March 31, 2025: Number of Stock Options Weighted-Average Exercise Price Outstanding at December 31, 2024 5,834,256 $ 43.48 Granted 723,313 33.18 Exercised ( 1,513 ) 29.64 Cancelled/Forfeited ( 27,373 ) 58.81 Expired ( 150,500 ) 107.89 Outstanding at March 31, 2025 6,378,183 $ 40.73 Exercisable at March 31, 2025 4,021,549 $ 45.85 Vested and expected to vest at March 31, 2025 6,378,183 $ 40.73 At March 31, 2025, there was approximately $ 38.1 million of total unrecognized compensation expense related to unvested stock option awards, which we expect to recognize over a weighted-average period of approximately 2.81 years. Restricted stock units The following table presents RSU activity for the three months ended March 31, 2025: Number of Stock Units Weighted-Average Grant Date Fair Value Unvested shares at December 31, 2024 1,818,563 $ 30.31 Granted 1,056,231 33.20 Vested ( 676,891 ) 29.77 Forfeited ( 26,376 ) 29.82 Unvested shares at March 31, 2025 2,171,527 $ 31.89 As of March 31, 2025, there was approximately $ 61.2 million of total unrecognized compensation expense related to RSUs, which we expect to recognize over a weighted-average period of approximately 2.30 years. Performance-based stock units The following table presents PSU activity for the three months ended March 31, 2025: Number of Stock Units Weighted-Average Grant Date Fair Value Unvested shares at December 31, 2024 374,583 $ 29.45 Granted 185,450 33.12 Unvested shares at March 31, 2025 560,033 $ 30.67 Stock-based compensation expense associated with these PSUs is recognized if the underlying performance condition is considered probable of achievement using our management’s best estimates. As of March 31, 2025, there was no unrecognized compensation expense related to PSUs with performance-based vesting criteria that are considered probable of achievement, and $ 17.2 million of total unrecognized compensation expense related to PSUs with performance-based vesting criteria that are considered not probable of achievement. 2013 Employee Stock Purchase Plan In June 2013, our Board of Directors adopted, and in July 2013 our stockholders approved, the 2013 Employee Stock Purchase Plan, or the 2013 ESPP. We issued and sold 52,092 and 52,514 shares of common stock during the three months ended March 31, 2025 and 2024, respectively, under the 2013 ESPP. The 2013 ESPP provides participating employees with the opportunity 13 Table of Contents to purchase up to an aggregate of 2,363,636 shares of our common stock. As of March 31, 2025, we had 1,531,142 shares of common stock available for future issuance under the 2013 ESPP. Stock-based compensation expense Stock-based compensation expense by award type included within the condensed consolidated statements of operations is as follows: Three Months Ended March 31, (In thousands) 2025 2024 Stock options $ 4,400 $ 4,071 Restricted stock units 6,684 4,966 Employee stock purchase plan 275 197 Total stock-based compensation expense $ 11,359 $ 9,234 Expenses related to stock options and stock-based awards were allocated as follows in the condensed consolidated statements of operations: Three Months Ended March 31, (In thousands) 2025 2024 Research and development expense $ 4,604 $ 3,775 Selling, general and administrative expense 6,755 5,459 Total stock-based compensation expense $ 11,359 $ 9,234 10. Loss per Share Basic net income (loss) per share is calculated by dividing net income (loss) by the weighted-average shares outstanding during the period, without consideration for common stock equivalents. Diluted net income (loss) per share is calculated by adjusting the weighted-average shares outstanding for the dilutive effect of common stock equivalents outstanding for the period, determined using the treasury stock method. For purposes of the dilutive net income (loss) per share calculation, stock options, RSUs and PSUs for which the performance and market vesting conditions, respectively, have been deemed probable, and 2013 ESPP shares are considered to be common stock equivalents, while PSUs with performance and market vesting conditions, respectively, that were not deemed probable as of March 31, 2025 are not considered to be common stock equivalents. We utilize the control number concept in the computation of diluted earnings per share to determine whether potential common stock equivalents are dilutive. The control number used is net loss from continuing operations. The control number concept requires that the same number of potentially dilutive securities applied in computing diluted earnings per share from continuing operations be applied to all other categories of income or loss, regardless of their anti-dilutive effect on such categories. Since we had a net loss for all periods presented, no dilutive effect has been recognized in the calculation of loss per share. Basic and diluted net loss per share was the same for all periods presented. The following common stock equivalents were excluded from the calculation of diluted net income (loss) per share applicable to common stockholders for the periods indicated because including them would have had an anti-dilutive effect: Three Months Ended March 31, 2025 2024 Stock options 6,378,183 5,908,863 Restricted stock units 2,171,527 1,865,185 Employee stock purchase plan shares — 11,016 Total common stock equivalents 8,549,710 7,785,064 14 Table of Contents 11. Segment Information Operating segments are identified as components of an enterprise about which separate discrete financial information is available for evaluation by the chief operating decision maker, or CODM, or decision-making group in making decisions on how to allocate resources and assess performance. Our CODM is our CEO. Our CEO views our operations and manages our business as one operating segment, which derives its revenues from the development and commercialization of therapies for patients with rare diseases. Our CEO manages and allocates resources to the operations of our company on a total company basis by assessing the overall level of resources available and how to best deploy these resources across functions and research and development projects that are in line with our long-term company-wide strategic goals. In making these decisions, our CEO uses consolidated financial information for purposes of evaluating performance, forecasting future period financial results, allocating resources and setting incentive targets. The CODM performs this assessment based on the Company’s consolidated net income (loss). Through this analysis, the CODM assesses performance by comparing actual consolidated net income (loss) versus the budget, and then decides how to allocate resources to invest in the Company’s research and development programs. The measure of segment assets is reported on the consolidated balance sheets as total assets. The following table contains additional information on our consolidated revenue and net loss, including significant segment expenses: Three Months Ended March 31, (In thousands) 2025 2024 Product revenue, net $ 8,726 $ 8,189 PK activator (PYRUKYND®) direct expenses - research and development ( 21,321 ) ( 26,036 ) Compensation and related expenses - research and development ( 32,990 ) ( 27,634 ) Total selling, general and administrative expenses ( 41,527 ) ( 31,014 ) Other segment items* ( 2,177 ) ( 5,054 ) Net loss $ ( 89,289 ) $ ( 81,549 ) *Other segment items primarily include cost of sales, other research and development expenses and interest income. 15 Table of Contents