Amylyx Pharmaceuticals, Inc. 10-K

Item 9A. Controls and Procedures. Evaluation of Disclosure Controls and Procedures Our disclosure controls and procedures, as defined in Rules 13a-15(e) and 15d-15(e) under the Exchange Act, are designed to ensure that information we are required to disclose in reports that we file or submit under the Exchange Act is recorded, processed, summarized, and reported within the time periods specified in SEC rules and forms, and that such information is accumulated and communicated to our management, including our co-Chief Executive Officers and Chief Financial Officer, as appropriate, to allow timely decisions regarding required disclosure. Our management, with the participation of our principal executive officers and our principal financial officer, evaluated the effectiveness of our disclosure controls and procedures as of December 31, 2024. Based on the evaluation of our disclosure controls and procedures as of December 31, 2024, our co-Chief Executive Officers and Chief Financial Officer concluded that, as of such date, our disclosure controls and procedures were effective at the reasonable assurance level. Management’s Annual Report on Internal Control Over Financial Reporting Our management is responsible for establishing and maintaining adequate internal control over financial reporting, as defined in Rules 13a-15(f) and 15d‑15(f) under the Exchange Act. Our internal control over financial reporting is a process designed to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles. Our internal control over financial reporting include policies and procedures that: • pertain to the maintenance of records that, in reasonable detail, accurately and fairly reflect transactions relating to our business and dispositions of our assets; • provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with U.S. GAAP, and that receipts and expenditures are being made only in accordance with authorizations of our management and directors; and • provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use, or disposition of our assets that could have a material effect on the financial statements. Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements. Also, projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate. Under the supervision and with the participation of the Company’s Chief Executive Officers and the Company’s Chief Financial Officer, we assessed the effectiveness of our internal control over financial reporting based on the criteria for effective internal control over financial reporting under the 2013 “Internal Control—Integrated Framework”, issued by the 105 Committee of Sponsoring Organizations of the Treadway Commission, or COSO. Based on such assessment, our management concluded that we maintained effective internal control over financial reporting as of December 31, 2024. Changes in Internal Control over Financial Reporting There were no changes in our internal control over financial reporting that occurred during the quarter ended December 31, 2024 that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting. 106 REPORT OF INDEPENDENT REGISTERED PUBLIC ACCOUNTING FIRM To the stockholders and the Board of Directors of Amylyx Pharmaceuticals, Inc. Opinion on Internal Control over Financial Reporting We have audited the internal control over financial reporting of Amylyx Pharmaceuticals, Inc. and subsidiaries (the “Company”) as of December 31, 2024, based on criteria established in Internal Control — Integrated Framework (2013) issued by the Committee of Sponsoring Organizations of the Treadway Commission (COSO). In our opinion, the Company maintained, in all material respects, effective internal control over financial reporting as of December 31, 2024, based on criteria established in Internal Control — Integrated Framework (2013) issued by COSO. We have also audited, in accordance with the standards of the Public Company Accounting Oversight Board (United States) (PCAOB), the consolidated financial statements as of and for the year ended December 31, 2024, of the Company and our report dated March 4, 2025, expressed an unqualified opinion on those financial statements. Basis for Opinion The Company’s management is responsible for maintaining effective internal control over financial reporting and for its assessment of the effectiveness of internal control over financial reporting, included in the accompanying Management’s Annual Report on Internal Control Over Financial Reporting. Our responsibility is to express an opinion on the Company’s internal control over financial reporting based on our audit. We are a public accounting firm registered with the PCAOB and are required to be independent with respect to the Company in accordance with the U.S. federal securities laws and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB. We conducted our audit in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether effective internal control over financial reporting was maintained in all material respects. Our audit included obtaining an understanding of internal control over financial reporting, assessing the risk that a material weakness exists, testing and evaluating the design and operating effectiveness of internal control based on the assessed risk, and performing such other procedures as we considered necessary in the circumstances. We believe that our audit provides a reasonable basis for our opinion. Definition and Limitations of Internal Control over Financial Reporting A company’s internal control over financial reporting is a process designed to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles. A company’s internal control over financial reporting includes those policies and procedures that (1) pertain to the maintenance of records that, in reasonable detail, accurately and fairly reflect the transactions and dispositions of the assets of the company; (2) provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that receipts and expenditures of the company are being made only in accordance with authorizations of management and directors of the company; and (3) provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use, or disposition of the company’s assets that could have a material effect on the financial statements. Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements. Also, projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate. /s/ Deloitte & Touche LLP Boston, Massachusetts March 4, 2025 107 Item 9B. Other Information. (a) None. (b) Rule 10b5-1 Trading Arrangements During the three months ended December 31, 2024 , no officers or directors of the Company (as defined in Rule 16a-1(f)) adopted, modified or terminated a “Rule 10b5-1 trading arrangement” or a “non-Rule 10b5-1 trading arrangement,” as each term is defined in Item 408(c) of Regulation S-K of the Exchange Act, which are intended to satisfy the affirmative defense conditions of Rule 10b5-1(c). Item 9C . Disclosure Regarding Foreign Jurisdictions that Prevent Inspections. Not applicable. 108 PART III Item 10 . Directors, Executive Officers and Corporate Governance. The information required by this Item 10 will be included in the Proposal No. 1, Corporate Governance and Executive Officers section of our definitive proxy statement to be filed with the SEC with respect to our 2025 Annual Meeting of Stockholders and is incorporated herein by reference. Item 11 . Executive Compensation. The information required by this Item 11 will be included in the Executive Compensation and Director Compensation sections (excluding the information under the heading “Pay Versus Performance”) of our definitive proxy statement to be filed with the SEC with respect to our 2025 Annual Meeting of Stockholders and is incorporated herein by reference. Item 12 . Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters. The information required by this Item 12 will be included in the Security Ownership of Certain Beneficial Owners and Management sections of our definitive proxy statement to be filed with the SEC with respect to our 2025 Annual Meeting of Stockholders and is incorporated herein by reference. Item 13 . Certain Relationships and Related Transactions, and Director Independence. The information required by this Item 13 will be included in the Certain Relationships and Related Party Transactions and Corporate Governance sections of our definitive proxy statement to be filed with the SEC with respect to our 2025 Annual Meeting of Stockholders and is incorporated herein by reference. Item 14 . Principal Accountant Fees and Services. Our independent public accounting firm is Deloitte & Touche LLP , Boston, Massachusetts , PCAOB Auditor ID: 34 . The information required by this Item 14 will be included in the Proposal No. 2 section of our definitive proxy statement to be filed with the SEC with respect to our 2025 Annual Meeting of Stockholders and is incorporated herein by reference. 109 PART IV Item 15 . Exhibits, Financial Statement Schedules. a) Financial Statements For a list of the consolidated financial statements included herein, see Index to the Consolidated Financial Statements on page F-1 of this Annual Report, which is incorporated into this Item by reference. b) Exhibits Exhibit Number Description 2.1 † Asset Purchase Agreement by and between the Company and Eiger Biopharmaceuticals, Inc., dated June 21, 2024 (Incorporated by reference to Exhibit 10.1 to the Registrant’s Current Report on Form 8-K filed with the Securities and Exchange Commission on June 21, 2024). 3.1 Fourth Amended and Restated Certificate of Incorporation of Amylyx Pharmaceuticals, Inc. (Incorporated by reference to Exhibit 3.1 to the Registrant’s Current Report on Form 8-K filed with the Securities and Exchange Commission on January 11, 2022). 3.2 Second Amended and Restated Bylaws of Amylyx Pharmaceuticals, Inc. (Incorporated by reference to Exhibit 3.2 to the Registrant’s Current Report on Form 8-K filed with the Securities and Exchange Commission on January 11, 2022). 4.1 Specimen Common Stock Certificate (Incorporated by reference to Exhibit 4.1 to the Registrant’s Registration Statement on Form S-1/A (File No. 333-261703) filed with the Securities and Exchange Commission on January 3, 2022). 4.2 Second Amended and Restated Investors’ Rights Agreement, dated as of July 1, 2021, among the Registrant and the parties thereto (Incorporated by reference to Exhibit 4.2 to the Registrant’s Registration Statement on Form S-1 (File No. 333-261703) filed with the Securities and Exchange Commission on December 16, 2021). 4.3 Description of Securities (Incorporated by reference to Exhibit 4.3 to the Registrant’s Form 10-K filed with the Securities and Exchange Commission on March 31, 2022). 10.1# 2015 Stock Option and Incentive Plan, and form of award agreements thereunder (Incorporated by reference to Exhibit 10.1 to the Registrant’s Registration Statement on Form S-1/A (File No. 333-261703) filed with the Securities and Exchange Commission on January 3, 2022). 10.2# 2022 Stock Option and Incentive Plan, and form of award agreements thereunder (Incorporated by reference to Exhibit 10.2 to the Registrant’s Registration Statement on Form S-1/A (File No. 333-261703) filed with the Securities and Exchange Commission on January 3, 2022). 10.3# Amended and Restated Non-Employee Director Compensation Policy (Incorporated by reference to Exhibit 10.1 to the Registrant’s Quarterly Report on Form 10-Q filed with the Securities and Exchange Commission on May 9, 2024). 10.4# Executive Cash Incentive Bonus Plan (Incorporated by reference to Exhibit 10.4 to the Registrant’s Registration Statement on Form S-1/A (File No. 333-261703) filed with the Securities and Exchange Commission on January 3, 2022). 10.5# 2022 Employee Stock Purchase Plan (Incorporated by reference to Exhibit 10.3 to the Registrant’s Registration Statement on Form S-1/A (File No. 333-261703) filed with the Securities and Exchange Commission on January 3, 2022). 10.6# Lease Agreement, dated as of October 23, 2018, as amended, by and between the Registrant and Bullfinch Square Limited Partnership (Incorporated by reference to Exhibit 10.6 to the Registrant’s Registration Statement on Form S-1 (File No. 333-261703) filed with the Securities and Exchange Commission on December 16, 2021). 10.7# Form of Employment Agreement, between the Registrant and Josh Cohen (Incorporated by reference to Exhibit 10.7 to the Registrant’s Registration Statement on Form S-1/A (File No. 333-261703) filed with the Securities and Exchange Commission on January 3, 2022). 10.8# Form of Employment Agreement, between the Registrant and Justin Klee (Incorporated by reference to Exhibit 10.8 to the Registrant’s Registration Statement on Form S-1/A (File No. 333-261703) filed with the Securities and Exchange Commission on January 3, 2022). 110 10.9# Form of Employment Agreement, between the Registrant and James Frates (Incorporated by reference to Exhibit 10.9 to the Registrant’s Registration Statement on Form S-1/A (File No. 333-261703) filed with the Securities and Exchange Commission on January 3, 2022). 10.10# Form of Employment Agreement, between the Registrant and Gina Mazzariello (Incorporated by reference to Exhibit 10.18 to the Registrant’s Annual Report on Form 10-K filed with the Securities and Exchange Commission on March 13, 2023). 10.11#* Form of Employment Agreement, between the Registrant and Camille Bedrosian. 10.12# Form of Officer Indemnification Agreement (Incorporated by reference to Exhibit 10.13 to the Registrant’s Registration Statement on Form S-1 (File No. 333-261703) filed with the Securities and Exchange Commission on December 16, 2021). 10.13† Master Manufacturing Services Agreement, dated as of November 12, 2019, by and between the Registrant and Patheon Inc. (Incorporated by reference to Exhibit 10.14 to the Registrant’s Registration Statement on Form S-1 (File No. 333-261703) filed with the Securities and Exchange Commission on December 16, 2021). 10.14† First Amendment, dated as of January 18, 2021, to Product Agreement, dated as of November 12, 2019, pursuant to the Master Manufacturing Services Agreement, dated as of November 12, 2019, by and between the Registrant and Patheon Inc. (Incorporated by reference to Exhibit 10.2 to the Registrant’s Quarterly Report on Form 10-Q filed with the Securities and Exchange Commission on May 11, 2023). 10.15† Second Amendment, dated as of March 20, 2023, to Product Agreement, dated as of November 12, 2019, as amended by Amendment No. 1, dated as of January 18, 2021, pursuant to the Master Manufacturing Services Agreement, dated as of November 12, 2019, by and between the Registrant and Patheon Inc. (Incorporated by reference to Exhibit 10.3 to the Registrant’s Quarterly Report on Form 10-Q filed with the Securities and Exchange Commission on May 11, 2023). 10.16† Supply Agreement, dated as of October 29, 2019, by and between the Registrant and CU Chemie Uetikon GmbH (Incorporated by reference to Exhibit 10.15 to the Registrant’s Registration Statement on Form S-1 (File No. 333-261703) filed with the Securities and Exchange Commission on December 16, 2021). 10.17† First Amendment, effective as of January 1, 2023, to the Supply Agreement, dated as of October 29, 2019, by and between the Registrant and CU Chemie Uetikon GmbH (Incorporated by reference to Exhibit 10.4 to the Registrant’s Quarterly Report on Form 10-Q filed with the Securities and Exchange Commission on May 11, 2023). 10.18† Research, Development and Supply Agreement, dated as of December 9, 2019, and Deed of Amendment, dated as of July 26, 2021, by and between the Registrant and ICE S.p.A. (formerly Prodotti Chimici e Alimentari S.p.A.), as amended (Incorporated by reference to Exhibit 10.16 to the Registrant’s Registration Statement on Form S-1 (File No. 333-261703) filed with the Securities and Exchange Commission on December 16, 2021). 10.19† Commercial Supply Agreement, dated as of August 8, 2023, by and between the Registrant and ICE S.p.A. (formerly Prodotti Chimici e Alimentari S.p.A.) (Incorporated by reference to Exhibit 10.1 to the Registrant’s Quarterly Report on form 10-Q filed with the Securities and Exchange Commission on August 10, 2023). 19.1* Amylyx Pharmaceuticals, Inc. Insider Trading Policy. 21.1* List of Subsidiaries of Registrant. 23.1* Consent of Deloitte & Touche LLP, independent registered public accounting firm. 31.1* Certification of Co-Principal Executive Officer Pursuant to Rules 13a-14(a) and 15d-14(a) under the Securities Exchange Act of 1934, as Adopted Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002. 31.2* Certification of Co-Principal Executive Officer Pursuant to Rules 13a-14(a) and 15d-14(a) under the Securities Exchange Act of 1934, as Adopted Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002. 31.3* Certification of Principal Financial Officer Pursuant to Rules 13a-14(a) and 15d-14(a) under the Securities Exchange Act of 1934, as Adopted Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002. 32.1 + Certification of Co-Principal Executive Officer Pursuant to 18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002. 32.2 + Certification of Co-Principal Executive Officer Pursuant to 18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002. 32.3 + Certification of Principal Financial Officer Pursuant to 18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002. 97.1* Compensation Recovery Policy. 111 101.INS* Inline XBRL Instance Document – the instance document does not appear in the Interactive Data File because XBRL tags are embedded within the Inline XBRL document. 101.SCH* Inline XBRL Taxonomy Extension Schema With Embedded Linkbase Documents 104 Cover Page Interactive Data File (embedded within the Inline XBRL document) * Filed herewith. + Furnished herewith. This certification will not be deemed “filed” for purposes of Section 18 of the Securities Exchange Act of 1934, as amended, or otherwise subject to the liability of that section. Such certification will not be deemed to be incorporated by reference into any filing under the Securities Act of 1933, as amended, except to the extent specifically incorporated by reference into such filing. # Indicates a management contract or any compensatory plan, contract or arrangement. † Portions of this exhibit (indicated by asterisks) have been omitted in accordance with Item 601(b)(10) of Regulation S-K. c) Financial Statement Schedules No financial statements have been submitted because they are not required or are not applicable or because the information required is included in the consolidated financial statements or the notes thereto. Item 16 . Form 10-K Summary None. 112 SIGNATURES Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, as amended, the Registrant has duly caused this Report to be signed on its behalf by the undersigned, thereunto duly authorized . AMYLYX PHARMACEUTICALS, INC. Date: March 4, 2025 By: /s/ Joshua B. Cohen Joshua B. Cohen Co-Chief Executive Officer Date: March 4, 2025 By: /s/ Justin B. Klee Justin B. Klee Co-Chief Executive Officer Pursuant to the requirements of the Securities Exchange Act of 1934, as amended, this Report has been signed below by the following persons on behalf of the Registrant in the capacities and on the dates indicated. Name Title Date /s/ Joshua B. Cohen Co-Chief Executive Officer and Director (Principal Executive Officer) March 4, 2025 Joshua B. Cohen /s/ Justin B. Klee Co-Chief Executive Officer and Director (Principal Executive Officer) March 4, 2025 Justin B. Klee /s/ James M. Frates Chief Financial Officer (Principal Financial Officer and Principal Accounting Officer) March 4, 2025 James M. Frates /s/ George Mclean Milne Jr. Director March 4, 2025 George Mclean Milne Jr. Ph.D. /s/ Paul Fonteyne Director March 4, 2025 Paul Fonteyne, M.S., M.B.A. /s/ Daphne Quimi Director March 4, 2025 Daphne Quimi /s/ Karen Firestone Director March 4, 2025 Karen Firestone /s/ Bernhardt Zeiher Director March 4, 2025 Bernhardt Zeiher, MD. 113 Amylyx Pharmaceuticals, Inc. INDEX TO CONSOLIDATED FINANCIAL STATEMENTS Report of Independent Registered Public Accounting Firm (PCAOB Auditor ID: 34) F- 2 Consolidated Balance Sheets F- 3 Consolidated Statements of Operations F- 4 Consolidated Statements of Comprehensive Income (Loss ) F- 5 Consolidated Statements of Stockholders’ Equity (Deficit ) F- 6 Consolidated Statements of Cash Flows F- 7 Notes to Consolidated Financial Statements F- 8 F- 1 REPORT of independent registered public accounting firm To the stockholders and the Board of Directors of Amylyx Pharmaceuticals, Inc. Opinion on the Financial Statements We have audited the accompanying consolidated balance sheets of Amylyx Pharmaceuticals, Inc. and subsidiaries (the “Company”) as of December 31, 2024 and 2023, the related consolidated statements of operations, comprehensive income (loss), stockholders’ equity, and cash flows, for each of the years then ended, and the related notes (collectively referred to as the "financial statements"). In our opinion, the financial statements present fairly, in all material respects, the financial position of the Company as of December 31, 2024 and 2023, and the results of its operations and its cash flows for each of the years then ended, in conformity with accounting principles generally accepted in the United States of America. We have also audited, in accordance with the standards of the Public Company Accounting Oversight Board (United States) (PCAOB), the Company's internal control over financial reporting as of December 31, 2024, based on criteria established in Internal Control — Integrated Framework (2013) issued by the Committee of Sponsoring Organizations of the Treadway Commission and our report dated March 4, 2025 , expressed an unqualified opinion on the Company's internal control over financial reporting. Basis for Opinion These financial statements are the responsibility of the Company's management. Our responsibility is to express an opinion on the Company's financial statements based on our audits. We are a public accounting firm registered with the PCAOB and are required to be independent with respect to the Company in accordance with the U.S. federal securities laws and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB. We conducted our audits in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements are free of material misstatement, whether due to error or fraud. Our audits included performing procedures to assess the risks of material misstatement of the financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the financial statements. Our audits also included evaluating the accounting principles used and significant estimates made by management, as well as evaluating the overall presentation of the financial statements. We believe that our audits provide a reasonable basis for our opinion. Critical Audit Matters Critical audit matters are matters arising from the current-period audit of the financial statements that were communicated or required to be communicated to the audit committee and that (1) relate to accounts or disclosures that are material to the financial statements and (2) involved our especially challenging, subjective, or complex judgments. We determined that there are no critical audit matters. /s/ Deloitte & Touche LLP Boston, Massachusetts March 4, 2025 We have served as the Company’s auditor since 2020. F- 2 AMYLYX PHARMACEUTICALS, INC. CONSOLIDATED BALANCE SHEETS (in thousands, except share and per share data) December 31, 2024 2023 Assets Current assets: Cash and cash equivalents $ 77,391 $ 170,201 Marketable securities 99,110 201,161 Accounts receivable, net 447 40,050 Inventories — 38,323 Prepaid expenses and other current assets 12,484 14,931 Total current assets 189,432 464,666 Property and equipment, net 961 2,686 Restricted cash equivalents 1,446 719 Operating lease right-of-use assets 1,771 3,725 Long-term inventories — 44,957 Other assets 24 701 Total assets $ 193,634 $ 517,454 Liabilities and Stockholders’ Equity Current liabilities: Accounts payable $ 2,939 $ 22,061 Accrued expenses 23,949 57,724 Operating lease liabilities, current portion 1,518 2,257 Total current liabilities 28,406 82,042 Operating lease liabilities, net of current portion 463 1,980 Total liabilities 28,869 84,022 Commitments and contingencies (Note 16) Stockholders’ equity: Common stock, $ 0.0001 par value; 300,000,000 shares authorized; 68,629,738 and 67,707,432 shares issued and outstanding as of December 31, 2024 and 2023, respectively 7 7 Additional paid-in capital 771,542 738,177 Accumulated deficit ( 606,692 ) ( 304,949 ) Accumulated other comprehensive (loss) income ( 92 ) 197 Total stockholders’ equity 164,765 433,432 Total liabilities and stockholders' equity $ 193,634 $ 517,454 The accompanying notes are an integral part of these consolidated financial statements. F- 3 AMYLYX PHARMACEUTICALS, INC. CONSOLIDATED STATEMENTS OF OPERATIONS (in thousands, except share and per share data) Year Ended December 31, 2024 2023 Product revenue, net $ 87,371 $ 380,786 Operating expenses: Cost of sales 5,953 25,441 Cost of sales - inventory impairment and loss on firm purchase commitments 118,680 — Acquired in-process research and development 36,203 — Research and development 104,084 128,187 Selling, general and administrative 114,331 188,356 Restructuring expenses 22,851 — Total operating expenses 402,102 341,984 (Loss) income from operations ( 314,731 ) 38,802 Other income, net: Interest income 13,809 16,155 Other expense, net ( 1,214 ) ( 660 ) Total other income, net 12,595 15,495 (Loss) income before income taxes ( 302,136 ) 54,297 (Benefit) provision for income taxes ( 393 ) 5,026 Net (loss) income $ ( 301,743 ) $ 49,271 Net (loss) income per share Basic $ ( 4.43 ) $ 0.73 Diluted $ ( 4.43 ) $ 0.70 Weighted-average shares used in computing net (loss) income per share Basic 68,142,158 67,234,465 Diluted 68,142,158 69,991,340 The accompanying notes are an integral part of these consolidated financial statements. F- 4 AMYLYX PHARMACEUTICALS, INC. CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME (LOSS) (in thousands) Year Ended December 31, 2024 2023 Net (loss) income $ ( 301,743 ) $ 49,271 Other comprehensive (loss) income: Foreign currency translation (loss) gain ( 396 ) 188 Net unrealized gain on marketable securities 107 95 Other comprehensive (loss) income ( 289 ) 283 Comprehensive (loss) income $ ( 302,032 ) $ 49,554 The accompanying notes are an integral part of these consolidated financial statements. F- 5 AMYLYX PHARMACEUTICALS, INC. CONSOLIDATED STATEMENTS OF STOCKHOLDERS’ EQUITY (in thousands, except share data) Common Stock Additional Paid-In Accumulated Other Comprehensive Accumulated Total Stockholders’ Shares Amount Capital Income (Loss) Deficit Equity Balance as of January 1, 2023 66,512,011 $ 7 $ 694,906 $ ( 86 ) $ ( 354,220 ) $ 340,607 Issuance of common stock upon exercise of stock options 1,010,376 — 5,725 — — 5,725 Issuance of common stock upon vesting of RSUs 185,045 — — — — — Stock-based compensation expense — — 37,546 — — 37,546 Other comprehensive income — — — 283 — 283 Net income — — — — 49,271 49,271 Balance as of December 31, 2023 67,707,432 7 738,177 197 ( 304,949 ) 433,432 Issuance of common stock upon exercise of stock options 210,088 — 327 — — 327 Issuance of common stock upon vesting of RSUs 712,218 — — — — — Stock-based compensation expense — — 33,038 — — 33,038 Other comprehensive loss — — — ( 289 ) — ( 289 ) Net loss — — — — ( 301,743 ) ( 301,743 ) Balance as of December 31, 2024 68,629,738 $ 7 $ 771,542 $ ( 92 ) $ ( 606,692 ) $ 164,765 The accompanying notes are an integral part of these consolidated financial statements. F- 6 AMYLYX PHARMACEUTICALS, INC. CONSOLIDATED STATEMENTS OF CASH FLOWS (in thousands) Year Ended December 31, 2024 2023 Cash flows (used in) provided by operating activities: Net (loss) income $ ( 301,743 ) $ 49,271 Adjustments to reconcile net (loss) income to net cash (used in) provided by operating activities: Stock-based compensation expense 33,038 37,161 Depreciation expense 904 1,088 Accretion of investment discounts, net ( 9,856 ) ( 9,940 ) Inventory impairment and loss on firm purchase commitments 118,680 — Property and equipment impairment 958 — Charge for purchase of IPR&D assets 36,203 — Changes in operating assets and liabilities: Accounts receivable, net 39,602 ( 24,744 ) Inventories ( 9,253 ) ( 73,129 ) Prepaid expenses and other assets 4,988 ( 3,226 ) Accounts payable ( 19,102 ) 15,882 Accrued expenses ( 59,810 ) 21,597 Operating lease liabilities ( 2,256 ) ( 2,041 ) Net cash (used in) provided by operating activities ( 167,647 ) 11,919 Cash flows provided by investing activities: Purchases of property and equipment ( 157 ) ( 1,241 ) Purchases of IPR&D assets, including transaction costs ( 36,203 ) — Purchases of investments ( 231,986 ) ( 300,826 ) Proceeds from maturities of marketable securities 344,000 394,120 Net cash provided by investing activities 75,654 92,053 Cash flows provided by financing activities: Follow-on offering costs paid — ( 136 ) Proceeds from exercise of stock options and RSUs vesting 2,132 6,994 Withholding taxes paid on stock-based awards ( 1,784 ) ( 3,315 ) Net cash provided by financing activities 348 3,543 Effect of exchange rate changes on cash, cash equivalents and restricted cash equivalents ( 438 ) 160 Net (decrease) increase in cash, cash equivalents and restricted cash equivalents ( 92,083 ) 107,675 Cash, cash equivalents and restricted cash equivalents, beginning of year 170,920 63,245 Cash, cash equivalents and restricted cash equivalents, end of year $ 78,837 $ 170,920 Reconciliation of cash, cash equivalents and restricted cash equivalents: Cash and cash equivalents $ 77,391 $ 170,201 Restricted cash equivalents 1,446 719 Total cash, cash equivalents and restricted cash equivalents: $ 78,837 $ 170,920 Supplemental disclosure of cash flow information: Taxes withheld on stock-based awards included in accrued expenses $ 2 $ 23 Purchases of property and equipment included in accounts payable $ — $ 20 Income taxes paid $ 708 $ 6,389 The accompanying notes are an integral part of these consolidated financial statements. F- 7 AMYLYX PHARMACEUTICALS, INC. NOTES TO Consolidated FINANCIAL STATEMENTS 1. Nature of Business Amylyx Pharmaceuticals, Inc., together with its wholly-owned subsidiaries, known as Amylyx or the Company, is a biotechnology company that is committed to the discovery and development of new treatment options for communities with high unmet needs, including people living with serious and fatal neurodegenerative diseases and endocrine conditions. Risks and Uncertainties The Company is subject to risks and uncertainties common to companies in the biotechnology industry, including, but not limited to, the outcome of preclinical studies and clinical trials, potential difficulties with or delays in timing with respect to regulatory approval processes, development by competitors of new technological innovations, dependence on key personnel, protection of proprietary technology, compliance with government regulations, ability to secure additional capital to fund operations, and risks associated with the economic challenges caused by economic uncertainty in various global markets caused by geopolitical instability and conflict. The Company and its contractors may experience disruptions in supply of items that are essential for its research and development activities, including, for example, raw materials and bulk drug substances that the Company imports from Europe and Canada used in the manufacturing of avexitide, AMX0035 and any additional or future product candidates. The accompanying consolidated financial statements have been prepared on the basis of continuity of operations, realization of assets and the satisfaction of liabilities and commitments in the ordinary course of business. The Company expects to continue to generate operating losses for the foreseeable future. In January 2025, the Company received gross proceeds of $ 69 million in a public offering of the Company's common stock (see Note 18 Subsequent events ). The Company expects that its cash, cash equivalents, marketable securities and the proceeds from the January 2025 Offering will be sufficient to fund its operating expenses and capital expenditure requirements for at least 12 months from the issuance of these consolidated financial statements. To continue its development efforts, the Company will need to obtain substantial additional funding through public or private equity offerings, debt financings, collaborations, strategic alliances and/or licensing arrangements in order to fund its research and development and ongoing operating expenses. The Company may not be able to obtain financing on acceptable terms, when needed or at all, and the Company may not be able to enter into collaborations, strategic alliances or licensing arrangements. The terms of any financing may adversely affect the holdings or the rights of the Company’s stockholders. Any collaborations, strategic alliances or licensing arrangements may require the Company to relinquish rights to certain of its technologies, future revenue streams, research programs or product candidates or grant licenses on terms that may not be favorable to the Company. If the Company is unable to obtain funding, the Company could be forced to delay, limit, reduce or eliminate some or all of its research and development programs, pipeline expansion or future commercialization efforts or grant rights to develop and market product candidates, which could adversely affect its business prospects. Although management will continue to pursue these plans, there is no assurance that the Company will be successful in obtaining sufficient funding on terms acceptable to the Company to fund continuing operations when needed or at all. 2. Summary of Significant Accounting Policies Basis of Presentation and Consolidation— The accompanying consolidated financial statements have been prepared in conformity with accounting principles generally accepted in the U.S., or GAAP, and include the accounts of the Company and its wholly owned subsidiaries. All intercompany balances and transactions have been eliminated in consolidation. Any reference in these notes to applicable guidance is meant to refer to the authoritative GAAP as found in the Accounting Standards Codification, or ASC, and Accounting Standards Updates, or ASU, of the Financial Accounting Standards Board, or FASB. Use of Estimates— The preparation of the consolidated financial statements in conformity with GAAP requires the Company’s management to make estimates and assumptions that affect the reported amounts of assets and liabilities at the date of the financial statements and the reported amount of expenses during the reporting period. Actual results could differ F- 8 from those estimates. Management considers many factors in selecting appropriate financial accounting policies in developing the estimates and assumptions that are used in the preparation of the financial statements. Management must apply significant judgment in this process. Management’s estimation process often may yield a range of potentially reasonable estimates and management must select an amount that falls within that range of reasonable estimates. Revenue recognition— In June 2022, AMX0035 received marketing authorization with conditions as ALBRIOZA by Health Canada for the treatment of ALS, and the Company launched ALBRIOZA in Canada in July 2022. In September 2022, AMX0035 received approval as RELYVRIO by the FDA for the treatment of ALS in adults, and the Company launched RELYVRIO in the U.S. in October 2022. In April 2024, the Company announced that it had started a process with the FDA and Health Canada to voluntarily discontinue the marketing authorizations for RELYVRIO and ALBRIOZA (AMX0035) for ALS and remove the product from the market based on topline results from the global Phase 3 PHOENIX trial, which did not meet its prespecified primary and secondary endpoints. Amylyx wound down the Open Label Extension as planned. The Company entered into arrangements with wholesalers, specialty pharmacies and specialty distributors, or customers, to distribute ALBRIOZA, RELYVRIO, prior to voluntary discontinuation. In accordance with ASC Topic 606 - Revenue from Contracts with Customers , or Topic 606, revenue is recognized when the customer obtains control of promised goods or services, in an amount that reflects the consideration which the entity expects to be entitled to in exchange for those goods or services. At contract inception, the Company assesses the goods or services promised within each contract and determines those that are performance obligations and assesses whether each promised good or service is distinct. The Company then recognizes as revenue the amount of the transaction price that is allocated to the respective performance obligation when (or as) the performance obligation is satisfied. Product Revenue, Net The Company sold its approved products to its customers. These customers subsequently resold our products to specialty pharmacy providers, specialty distributors, health care providers, certain medical centers or hospitals, and patients. In addition to agreements with the customers, the Company entered into arrangements with specialty pharmacies, health care providers and payors that provide for government mandated and/or privately negotiated rebates with respect to the purchase of our products. The Company’s customer identification process considered a number of factors, including contractual and legal factors, and who controls the Company’s product and bears inventory risk. The Company evaluated these factors on a customer-by-customer basis to determine the appropriate customer for revenue recognition purposes. In some cases, the Company used a third-party logistics providers to deliver the Company’s product to its customers, but the Company recognized revenue upon delivery to the customer, as it was determined that the third-party logistics provider was acting as our agent. The Company recognizes revenue on product sales when the customer obtains control of our product, which occurs at a point in time (upon delivery). Product revenues are recorded net of applicable GTN adjustments, which are described below. Taxes collected from customers relating to product sales and remitted to governmental authorities are excluded from revenue. The Company expenses incremental costs of obtaining a contract when incurred, if the expected amortization period of the asset that the Company would have recognized is one year or less. However, no such costs were incurred during the years ended December 31, 2024 and 2023. GTN Adjustments Revenues from product sales are recorded at the net sales price (transaction price), which includes estimates of variable consideration related to certain GTN adjustments. Components of GTN adjustments include trade discounts and allowances, product returns, third-party payor rebates, and other allowances that are offered within contracts between the Company, its customers and payors relating to the sale of our products. These GTN adjustments, as detailed below, are based on the amounts earned, or to be claimed on the related sales, and are classified as reductions of accounts receivable (if the amount is payable to the Customer) or a current liability (if the amount is payable to a party other than a Customer). These estimates take into consideration a range of possible outcomes which are probability-weighted in accordance with the expected value method in Topic 606 for relevant factors such as historical experience, payer channel mix (e.g., Medicare or F- 9 Medicaid), current contract prices under applicable programs, unbilled claims and processing time lags and inventory levels in the distribution channel. In certain circumstances, the Company applies the most likely method in Topic 606. The determination to use the expected value method or the most likely method is based on the type of GTN adjustment and what method better predicts the amount of consideration we expect to be entitled to. Overall, these GTN adjustments reflect in the transaction price the amount of consideration to which the Company expects to be entitled to in exchange for transferring promised goods or services to its customers. The amount of variable consideration which is included in the transaction price may be constrained and is included in the net sales price only to the extent that it is probable that a significant reversal in the amount of the cumulative revenue recognized under the contract will not occur in a future period. Actual amounts of consideration ultimately received may differ from our estimates. If actual results in the future vary from our estimates, the Company will adjust these estimates, which would affect product revenue, net and earnings in the period such variances become known. Trade Discounts and Allowances The Company generally provides customers with prompt payment discounts and pay fees for distribution services and for certain data that distributors provide to us that are explicitly stated in our contracts and are recorded as a reduction of revenue in the period the related product revenue is recognized. Payment from customers is typically due within 30 calendar days of the invoice date, without consideration to the prompt payment discounts. Product Returns Consistent with industry practice, the Company generally offers customers a limited right of return for product that has been purchased from the Company based on the product’s expiration date, which is set to lapse within a specified period stated in the contract. Additionally, our limited right of return policy allows for eligible returns from customers in circumstances where product was shipped in error or was damaged in shipping, or product was returned pursuant to an official drug recall. The Company estimates the amount of product sales that may be returned by our customers and records this estimate as a reduction of revenue in the period the related product revenue is recognized, as well as reductions to accounts receivable, net on the consolidated balance sheets. Provider Chargebacks and Discounts Chargebacks for fees and discounts to providers 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 the Company. Customers charge the Company for the difference between what they pay for the product and the ultimate selling price to the qualified healthcare providers. These GTN adjustments are established in the same period that the related revenue is recognized, resulting in a reduction of product revenue and accounts receivable, net. GTN adjustments for chargebacks consist of credits that customers have not claimed, but for which we expect to issue a credit. Payor Rebates The Company contracts with certain government and private payor organizations, primarily government and commercial health insurance companies, for the payment of rebates with respect to utilization of our products. The Company is subject to discount obligations under state Medicaid programs and Medicare. These GTN adjustments are recorded in the same period the related revenue is recognized, resulting in a reduction of product revenue and the establishment of a current liability which is included in accrued expenses and other current liabilities on the consolidated balance sheets. For Medicare, the Company also estimates the number of patients in the prescription drug coverage gap for whom it will owe an additional liability under the Medicare Part D program. The Company's liability for these rebates consists of invoices received for claims from prior quarters that have not been paid or for which an invoice has not yet been received, estimates of claims for the current quarter, and estimated future claims that will be made for product that has been recognized as revenue, but which remains in the distribution channel inventories at the end of each reporting period. F- 10 Other Incentives Other incentives which the Company offers include voluntary patient assistance programs, such as its co-pay assistance program, which are intended to provide financial assistance to qualified commercially-insured patients with prescription drug co-payments required by payors. The calculation of the accrual for co-pay assistance is based on an estimate of claims and the cost per claim that the Company expects to receive associated with product that has been recognized as revenue for each reporting period. The adjustments are recorded in the same period the related revenue is recognized, resulting in a reduction of product revenue and the establishment of a current liability which is included as a component of accrued expenses and other current liabilities on the consolidated balance sheets. Comprehensive Income (Loss)— Comprehensive income (loss) includes net loss, as well as other changes in stockholders’ equity that result from transactions and economic events other than those with stockholders. Comprehensive income (loss) is composed of net income (loss) and other comprehensive (loss) income. Other comprehensive (loss) income consists of unrealized gains and losses on marketable securities and foreign currency translation. Cash and Cash Equivalents— The Company considers all highly liquid investments with an original maturity of three months or less at the date of purchase to be cash equivalents. Cash equivalents represent funds invested in readily available checking and money market funds. Restricted Cash Equivalents— Restricted cash equivalents consist of cash serving as collateral for a letter of credit issued for the Company’s office spaces and collateral for a corporate credit card program. Accounts receivable, net— The Company’s accounts receivable consists of amounts due from customers related to product sales and have standard payment terms. The Company analyzes accounts that are past due for collectability and provides reserves against accounts receivable for expected credit losses that may result from a customer’s inability to pay. Amounts determined to be uncollectible are written-off against the established reserve. The credit losses were not material in the periods presented. Marketable Securities— Marketable securities are composed of U.S. treasury bills and U.S. agency bonds. The Company classifies all of its marketable securities as available-for-sale. Accordingly, these investments are recorded at fair value, which is determined based on quoted market prices. Unrealized gains and losses on available-for-sale securities are included as a separate component of other accumulated comprehensive loss. The cost of marketable securities is adjusted for amortization of premiums and accretion of discounts. Such amortization and accretion are included in interest income. Realized gains and losses are included in other expense, net. The Company evaluates marketable securities for other-than-temporary impairment at the balance sheet date. Declines in fair value, if any, determined to be other than temporary-than-temporary are also included in other income, net. When assessing marketable securities for other-than-temporary declines in value, the Company considers such factors as, among other things, how significant the decline in value is as a percentage of the original cost, how long the market value of the investment has been less than its original cost, and the Company’s ability and intent to retain the investment for a period of time sufficient to allow for any anticipated recovery in fair value and market conditions in general. There were no impairment charges on marketable securities in the periods presented. Concentrations of Credit Risk— Financial instruments that potentially expose the Company to concentrations of credit risk consist primarily of cash and cash equivalents, marketable securities and accounts receivable, net. The Company maintains its cash in financial institutions that management believes have high credit quality. The Company has not experienced any losses on such accounts, and does not believe it is exposed to any unusual credit risk beyond the normal credit risk associated with commercial banking relationships. The Company’s accounts receivable, net represents amounts due to the Company from customers. Amylyx performs ongoing credit evaluations of its customers and generally does not require collateral. The Company monitors its exposure and records a reserve against uncollectible amounts as necessary. Five and three customers individually accounted for approximately 89 % and 81 % in the aggregate of gross product revenue in 2024 and 2023, respectively. One and three customers individually accounted for approximately 100 % and 81 % of total accounts receivable, net as of December 31, 2024 and 2023 , respectively. Fair Value Measurements— Assets and liabilities recorded at fair value on a recurring basis on the consolidated balance sheet are categorized based upon the level of judgment associated with the inputs used to measure fair values. Fair F- 11 value is defined as the exchange price that would be received for an asset or paid to transfer a liability (an exit price) in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants on the measurement date. Valuation techniques used to measure fair value must maximize the use of observable inputs and minimize the use of unobservable inputs. The authoritative guidance on fair value measurements establishes a three-tier fair value hierarchy for disclosure of fair value measurements as follows: • Level 1 —Quoted prices in active markets for identical assets or liabilities. • Level 2 —Observable inputs (other than Level 1 quoted prices), such as quoted prices in active markets for similar assets or liabilities, quoted prices in markets that are not active for identical or similar assets or liabilities, or other inputs that are observable or can be corroborated by observable market data. • Level 3 —Unobservable inputs that are supported by little or no market activity that are significant to determining the fair value of the assets or liabilities, including pricing models, discounted cash flow methodologies and similar techniques. To the extent that the valuation is based on models or inputs that are less observable or unobservable in the market, the determination of fair value requires more judgment. Accordingly, the degree of judgment exercised by the Company in determining fair value is greatest for instruments categorized in Level 3. A financial instrument’s level within the fair value hierarchy is based on the lowest level of any input that is significant to the fair value measurement. The Company’s financial instruments consist of cash, cash equivalents, restricted cash, marketable securities, accounts receivable, net, accounts payable and accrued expenses. The Company’s marketable securities are carried at fair value, determined according to Level 1 and Level 2 inputs to the fair value hierarchy described above. The remaining financial instruments are stated at their respective carrying amounts, which approximate fair value due to the short-term nature of these assets and liabilities. Inventories— The Company values its inventories at the lower of cost or estimated net realizable value. The Company determines the cost of its inventories, which includes amounts related to materials and manufacturing overhead, on a first-in, first-out basis. The Company classifies inventory as long-term when consumption or sale of the inventory is expected beyond its normal operating cycle of twelve months. The Company performs an assessment of the recoverability of capitalized inventory during each reporting period, and it writes down any excess and obsolete inventories to their estimated realizable value in the period in which the impairment is first identified. Such impairment charges are recorded within cost of sales. The Company capitalizes inventory costs associated with the Company’s products after regulatory approval when, based on management’s judgment, future commercialization is considered probable and the future economic benefit is expected to be realized. Inventory acquired prior to receipt of regulatory approval of a product candidate is expensed as research and development expense as incurred. Inventory that can be used in either the production of clinical or commercial product is initially capitalized and subsequently expensed as research and development expense when identified for use in the manufacture of drugs still in development. Property and Equipment, net— Property and equipment are stated at cost, net of accumulated depreciation. Depreciation of property and equipment is calculated using the straight-line method over the estimated useful lives of the respective assets. Maintenance and repairs that do not improve or extend the life of the assets are expensed when incurred. Upon sale or retirement of assets, the cost and accumulated depreciation are removed from the consolidated balance sheets and any resulting gain or loss is reflected in the consolidated statements of operations in the period realized. The range of useful lives of property and equipment is as follows: Estimated Useful Life Leasehold improvements Lesser of the estimated life or remaining lease term Furniture and fixtures 4 years Computer hardware and software 3 years Construction in progress Not depreciated Impairment of Long-Lived Assets— The Company evaluates assets for potential impairment when events or changes in circumstances indicate the carrying value of the assets may not be recoverable. Recoverability is measured by comparing the book values of the assets to the expected future net undiscounted cash flows that the assets are expected to F- 12 generate. If such assets are considered to be impaired, the impairment to be recognized is measured by the amount by which the book values of the assets exceed fair value. Business Combinations and Asset Acquisitions— The Company evaluates acquisitions of assets and other similar transactions to assess whether or not the transaction should be accounted for as a business combination or asset acquisition by first applying a screen test to determine if substantially all of the fair value of the gross assets acquired is concentrated in a single identifiable asset or group of similar identifiable assets. If the screen test is met, the transaction is accounted for as an asset acquisition. If the screen test is not met, further determination is required as to whether or not the Company has acquired inputs and processes that have the ability to create outputs which would meet the requirements of a business. If determined to be an asset acquisition, the Company accounts for the transaction under ASC 805-50, which requires the acquiring entity in an asset acquisition to recognize assets acquired and liabilities assumed based on the cost to the acquiring entity on a relative fair value basis, which includes transaction costs in addition to consideration given. Goodwill is not recognized in an asset acquisition and any excess consideration transferred over the fair value of the net assets acquired is allocated to the identifiable assets based on relative fair values. In-process research and development, or IPR&D, projects with no alternative future use are recorded in R&D expense upon acquisition, and contingent consideration obligations incurred in connection with an asset acquisition are recorded when it is probable that they will occur and they can be reasonably estimated. Research and Development— Research and development expenses include costs directly attributable to the conduct of research and development activities. Expenditures relating to research and development are expensed in the period incurred. Nonrefundable advance payments for goods and services that will be used in future research and development activities are expensed when the activity has been performed or when the goods have been received rather than when the payment is made. In addition, research and development-related salaries and benefits, facility, and overhead costs, supplies and other related costs are included in research and development expense. License and Collaboration Agreements — The Company analyzes license and collaboration arrangements pursuant to ASC Topic 808 - Collaborative Arrangement Guidance and Considerations , or ASC 808, to assess whether such arrangements, or transactions between arrangement participants, involve joint operating activities performed by parties that are both active participants in the activities and exposed to significant risks and rewards dependent on the commercial success of such activities. Collaboration arrangements often require upfront payments and may include additional milestone, research and development cost sharing, royalty or profit share payments, contingent upon the occurrence of certain future events linked to the success of the asset in development and commercialization. Upfront payments associated with collaborative arrangements and subsequent payments made to the partner for the achievement of development milestones prior to regulatory approval are expensed to acquired IPR&D expense as incurred. Contingent consideration obligations are recorded when it is probable that they will occur and they can be reasonably estimated. Sales and Marketing Costs— Sales and marketing expenses consist primarily of wages and benefits for sales and marketing personnel, professional and consulting fees, administrative travel expenses, and marketing and advertising costs such as marketing literature, promotional activities, conferences and seminars and branding. Sales and marketing, and advertising costs are expensed as incurred and included in selling, general and administrative expenses in the accompanying consolidated statements of operations. The Company considers advertising costs as expenses related to the promotion of the Company's commercial products. For the years ended December 31, 2024 and 2023, advertising costs were $ 2.7 million and $ 9.5 million , respectively. Patent-Related Costs— Patent-related costs incurred in connection with filing and prosecuting patent applications are expensed as incurred due to the uncertainty about the recovery of the expenditure. Amounts incurred are classified as selling, general and administrative expenses in the accompanying consolidated statements of operations. Stock-Based Compensation Expense— Stock-based compensation is recognized in the consolidated statements of operations based on the fair value on the date of grant over the requisite service period, which is generally equal to the vesting period of the respective award. Forfeitures are accounted for as incurred. Generally, the Company issues stock awards with only service-based vesting conditions and records the expense for these awards using the straight-line method. The Company classifies stock-based compensation expense in the same manner in which the award recipient’s payroll costs are classified. F- 13 The fair value of each restricted common stock award is measured based on the fair value of the Company’s common stock on the grant date. The fair value of each option grant is estimated on the date of grant using the Black-Scholes option pricing model, which requires inputs based on certain subjective assumptions, including the expected stock price volatility, the expected term of the award, the risk-free interest rate, and expected dividends. The Company estimates its expected stock price volatility based on the historical volatility of publicly traded peer companies. The expected term of the Company’s stock options has been determined utilizing the “simplified” method for awards that qualify as “plain vanilla” options. The risk-free interest rate is determined by reference to the U.S. Treasury yield curve in effect at the time of grant of the award for time periods approximately equal to the expected term of the award. There is no expected dividend yield since the Company has never paid cash dividends on common stock and does not expect to pay any cash dividends in the foreseeable future. The stock price of the Company is based on the closing price on the date of grant. Contingencies— From time to time, the Company may have certain contingent liabilities that arise in the ordinary course of business activities. The Company accrues for loss contingencies when losses become probable and are reasonably estimable. If the reasonable estimate of the loss is a range and no amount within the range is a better estimate, the minimum amount of the range is recorded as a liability on the Company’s consolidated balance sheets. The Company does not accrue for contingent losses that, in its judgment, are considered to be reasonably possible, but not probable; however, it discloses the range of reasonably possible losses. Leases— The Company leases its offices, and may from time to time, enter into other lease agreements in conducting its business. The Company determines if an arrangement includes a lease at the inception of the agreement. For each of the Company’s lease arrangements, the Company records a right-of-use asset representing the Company’s right to use an underlying asset for the lease term and a lease liability representing the Company’s obligation to make lease payments. Operating lease right-of-use assets and operating lease liabilities are recognized at the lease commencement date based on the net present value of the remaining future minimum lease payments over the lease term. If the interest rate implicit in the Company’s leases is not readily determinable, in determining the weighted-average discount rate used to calculate the net present value of lease payments, the Company utilizes an estimate of its incremental borrowing rate based on market sources including interest rates for companies with similar credit quality for agreements of similar duration to discount the lease payments. Lease expense for the Company’s operating leases is recognized on a straight-line basis over the lease term and variable lease costs are expensed as incurred. The Company did not have financing leases as of December 31, 2024 and 2023. The Company elected the practical expedient not to apply the recognition and measurement requirements to short-term leases, which is any lease with a term of one year or less as of the lease commencement date. The lease may require the Company to pay additional amounts for maintenance and other expenses, which are generally referred to as non-lease components. Non-lease components (e.g., common area maintenance) are paid separately from rent based on actual costs incurred and therefore are not included in the operating lease right-of-use assets and lease liabilities and are reflected as an expense in the period incurred. If a lease includes options to extend the lease term, the Company does not assume the option will be exercised in its initial lease term assessment unless there is reasonable certainty that the Company will renew based on an assessment of economic factors present as of the lease commencement date. Income Taxes— The Company accounts for income taxes using the asset and liability approach. Deferred tax assets and liabilities represent future tax consequences of temporary differences between the financial statement carrying amounts and the tax basis of assets and liabilities and for loss carryforwards using enacted tax rates expected to be in effect in the years in which the differences reverse. A valuation allowance is established to reduce deferred tax assets to the amounts expected to be realized. The Company also recognizes a tax benefit from uncertain tax positions only if it is “more likely than not” that the position is sustainable based on its technical merits. The Company accounts for interest and penalties related to uncertain tax positions as part of its provision for income taxes. To date, the Company has not incurred material interest and penalties related to income tax positions. Valuation allowances are provided, if, based upon the weight of available evidence, it is more likely than not that some or all of the deferred tax assets will not be realized. As of December 31, 2024 , we continued to maintain a full valuation allowance against all of our deferred tax assets based on management’s evaluation of all available evidence, including our history of incurring significant losses from operations. F- 14 Recent Accounting Pronouncements New Accounting Pronouncements Not Yet Adopted In December 2023, the FASB issued ASU No. 2023-09, Income Taxes (Topic 740): Improvement to Income Tax Disclosures , or ASU 2023-09, to enhance the transparency and decision usefulness of income tax disclosures. ASU 2023-09 is effective for the Company beginning January 1, 2025 on a prospective basis. The impact of this ASU on the tax disclosures is not expected to be material. In November 2024, the FASB issued ASU No. 2024-03, Income Statement – Reporting Comprehensive Income – Expense Disaggregation Disclosures (Subtopic 220-40): Disaggregation of Income Statement Expenses, which requires new financial statement disclosures in tabular format, in the notes to financial statements, of specified information about certain costs and expenses. The amendments in this update do not change or remove current expense disclosure requirements. The amendments in this update are effective for the Company's annual financial statement disclosure beginning December 31, 2027, and interim periods within the years beginning January 1, 2028. Early adoption is permitted. The Company is currently evaluating the impact of this ASU on its consolidated financial statements and related disclosures. 3. PRODUCT REVENUE, NET To date, the Company’s only source of product revenue had been from the sales of RELYVRIO, known as ALBRIOZA in Canada. In April 2024, the Company announced it had started a process with the FDA and Health Canada to voluntarily discontinue the marketing authorizations for RELYVRIO®/ALBRIOZA™ and remove the product from the market in the U.S. and Canada based on topline results from the Phase 3 PHOENIX trial. The following table reconciles gross product revenue to net product revenue: Year Ended December 31, 2024 2023 (in thousands) Product revenue, gross $ 114,265 $ 431,433 GTN adjustments ( 26,894 ) ( 50,647 ) Product revenue, net $ 87,371 $ 380,786 The activity and ending reserve balance for GTN adjustments were as follows for the periods indicated: Chargebacks and Cash Discounts Medicaid and Medicare Rebates Other Rebates, Returns, Discounts and Adjustments Total (in thousands) Balance at January 1, 2022 $ 648 $ 1,992 $ 1,664 $ 4,304 Provision related to sales in the current year 17,898 10,887 22,378 51,163 Adjustments related to prior period sales ( 280 ) ( 236 ) — ( 516 ) Credits and payments made ( 15,123 ) ( 7,697 ) ( 12,969 ) ( 35,789 ) Balance at December 31, 2023 $ 3,143 $ 4,946 $ 11,073 $ 19,162 Provision related to sales in the current year 4,983 3,402 21,333 29,718 Adjustments related to prior period sales ( 1,696 ) ( 191 ) ( 961 ) ( 2,848 ) Credits and payments made ( 6,430 ) ( 8,157 ) ( 25,665 ) ( 40,252 ) Balance at December 31, 2024 $ — $ — $ 5,780 $ 5,780 Included in the ending reserve balance for GTN adjustments are chargebacks 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 the Company, rebates and estimates for product returns. Chargebacks, discounts and returns are recorded as reductions of accounts receivable, net on the condensed consolidated balance sheets to the extent there are receivable balances to reduce. If there are net balances owed to customers, they are recorded as a component of accrued expenses on the consolidated balance sheets. F- 15 4. MARKETABLE SECURITIES The Company has classified all of its marketable securities as “available-for-sale”. The Company records available-for-sale securities at fair value, with the unrealized gains and losses included as a separate component of other accumulated comprehensive income (loss). There were no realized gains or losses recognized in the periods presented. The Company adjusts the cost of available-for-sale debt securities for amortization of premiums and accretion of discounts to maturity. Such amortization and accretion are included in interest income. The cost of securities sold is based on the specific identification method. The Company includes interest and dividends on securities classified as available-for-sale in interest income. Accrued interest receivable relating to the Company's available-for-sale securities is presented within prepaid expenses and other current assets in the accompanying consolidated balance sheets, and amounted to $ 0.1 million and $ 0.5 million at December 31, 2024 and 2023, respectively. Marketable securities, which are classified as available-for-sale, consisted of the following (in thousands): December 31, 2024 Amortized Cost Basis Unrealized Gain Unrealized Loss Fair Values (in thousands) Treasury bills $ 98,939 $ 171 $ — $ 99,110 Total marketable securities $ 98,939 $ 171 $ — $ 99,110 December 31, 2023 Amortized Cost Basis Unrealized Gain Unrealized Loss Fair Values (in thousands) Treasury bills $ 196,098 $ 67 $ — $ 196,165 U.S. agency bonds 4,999 — ( 3 ) 4,996 Total marketable securities $ 201,097 $ 67 $ ( 3 ) $ 201,161 5. INVENTORIES Inventories consisted of the following: December 31, 2024 2023 (in thousands) Raw materials $ — $ 53,144 Work in process — 18,945 Finished goods — 11,191 Total inventories $ — $ 83,280 In April 2024, the Company announced it had started a process with the FDA and Health Canada to voluntarily discontinue the marketing authorizations for RELYVRIO ® /ALBRIOZA™ and remove the product from the market in the U.S. and Canada based on topline results from the global Phase 3 PHOENIX trial. As a result, the Company recorded approximately $ 92.5 million of charges associated with the write-down of inventory for the year ended December 31, 2024. For the year ended December 31, 2023, the Company recognized inventory write-downs of $ 3.3 million . Inventory amounts written down as a result of obsolescence or other reasons are charged to cost of sales. F- 16 6. Property and equipment, net Property and equipment, net consisted of the following: December 31, 2024 2023 (in thousands) Furniture and fixtures $ 382 $ 382 Computer hardware and software 1,541 3,167 Leasehold improvements 176 176 Construction in progress 221 589 Total property and equipment 2,320 4,314 Less: accumulated depreciation ( 1,359 ) ( 1,628 ) Total property and equipment, net $ 961 $ 2,686 7. Accrued Expenses Accrued expenses consisted of the following: December 31, 2024 2023 (in thousands) Accrued external research and development $ 4,353 $ 12,625 Accrued benefits and incentive compensation 9,992 16,790 Accrued manufacturing 500 1,652 Accrued consulting and other professional fees 1,974 6,506 Accrued returns, rebates and co-pay assistance 5,334 16,063 Accrued royalties — 3,111 Accrued loss on future purchase commitments 1,538 — Other accrued expenses 258 977 Total accrued expenses $ 23,949 $ 57,724 8. FAIR VALUE MEASUREMENTS The following tables present information about the Company’s financial assets and liabilities measured at fair value on a recurring basis and indicates the level of the fair value hierarchy utilized to determine such fair values: December 31, 2024 Level 1 Level 2 Level 3 Total (in thousands) Assets: Cash equivalents $ 37,550 $ — $ — $ 37,550 Restricted cash equivalents 1,446 — — 1,446 Treasury bills 99,110 — — 99,110 Total financial assets $ 138,106 $ — $ — $ 138,106 F- 17 December 31, 2023 Level 1 Level 2 Level 3 Total (in thousands) Assets: Cash equivalents $ 76,710 $ — $ — $ 76,710 Marketable securities: Treasury bills 196,165 — — 196,165 U.S. agency bonds — 4,996 — 4,996 Total marketable securities 196,165 4,996 — 201,161 Restricted cash equivalents 719 — — 719 Total financial assets $ 273,594 $ 4,996 $ — $ 278,590 The Company classifies its money market funds and treasury bills as Level 1 assets under the fair value hierarchy, as these assets have been valued using quoted market prices for identical assets in active markets without any valuation adjustment. The Company classifies its U.S. agency bonds as Level 2 assets under the fair value hierarchy, as these assets have been valued using information obtained through a third-party pricing service at each balance sheet date, using observable market inputs that may include trade information, broker or dealer quotes, bids, offers, or a combination of these data sources. 9. LEASES The Company leases its office facilities under non-cancelable operating leases that expire at various dates through October 2026. On September 12, 2024, the Company entered into a new office lease in Cambridge, Massachusetts for office space for its headquarters facility. The lease commencement date is expected to be June 1, 2025 when the premises are expected to be available for occupancy and, therefore, as the office lease has not commenced, the related operating lease right-of-use assets and liabilities are not recorded in the Company's consolidated balance sheet as of December 31, 2024. Components of lease expense required by ASC 842 are presented below for the years ended December 31, 2024 and 2023: Year Ended December 31, 2024 2023 (in thousands) Lease cost Operating lease cost $ 2,175 $ 2,175 Total lease cost $ 2,175 $ 2,175 Lease liabilities are measured by calculating the present value of remaining lease payments under the lease arrangement. Since the rates implicit in our leases are not readily determinable, the Company uses estimated incremental borrowing rates in determining the discount rate used to calculate the present value of remaining lease payments. The incremental borrowing rate is the rate of interest that the Company would have to pay to borrow, on a collateralized basis, an amount equal to the lease payments over a similar term equal to the lease term in a similar economic environment. The incremental borrowing rate is based on the information available at commencement date. As the Company has no recent external borrowings, the incremental borrowing is a hypothetical rate based on our understanding of what our credit rating would be and adjusted to reflect a collateralized borrowing. The Company’s leases contain renewal options that can extend the lease for additional years. Because the Company is not reasonably certain to exercise these renewal options, they are not considered in determining the lease terms, and associated potential additional payments are excluded from lease payments. The Company has existing net leases in which the non-lease components (e.g., common area maintenance) are paid separately from rent based on actual costs incurred and therefore are not included in the operating lease right-of-use assets and lease liabilities and are reflected as an expense in the period incurred. Variable lease payments during the years ended December 31, 2024 and 2023 were not material. F- 18 The following table summarizes the presentation in the Company’s consolidated balance sheet of its operating leases: December 31, 2024 2023 (in thousands) Assets Operating lease right-of-use assets $ 1,771 $ 3,725 Liabilities Operating lease right-of-use liabilities, current $ 1,518 $ 2,257 Operating lease right-of-use liabilities, net of current portion 463 1,980 Total operating lease liabilities $ 1,981 $ 4,237 During the years ended December 31, 2024 and 2023, the Company made cash payments for operating leases of $ 2.5 million and $ 2.4 million , respectively. Future minimum lease payments under non-cancelable leases as of December 31, 2024, were as detailed below (in thousands): As of December 31, 2024 2025 $ 1,587 2026 476 2027 — 2028 — 2029 — Total undiscounted lease payments 2,063 Less: imputed interest ( 82 ) Total operating lease liabilities $ 1,981 As of December 31, 2024 and 2023, the weighted average remaining lease term was 1.2 years and 2 years , respectively. As of December 31, 2024 and 2023, the weighted average incremental borrowing rate used to determine the operating lease right-of-use assets was 7.4 % and 7.3 % , respectively . 10. aSSET aCQUISITIONS AND COLLABORATION AGREEMENTS Eiger Asset Acquisition On July 9, 2024, the Company completed the acquisition of substantially all the assets and interests in the development, manufacture and commercialization of avexitide from Eiger BioPharmaceuticals, Inc., or Eiger, for $ 35.1 million, or the Eiger Acquisition. The Eiger Acquisition includes the acquisition of all of Eiger’s owned and co-owned patents and applications directed to avexitide, as well as the assumption of Eiger’s licenses to patents and applications directed to avexitide and owned and co-owned by other entities, and the samples, retains, raw materials and active pharmaceutical ingredients in Eiger’s possession and control. The transaction was accounted for as an asset acquisition as the acquired assets did not meet the definition of a business. The Company did not acquire any outputs and there was not an acquired substantive process in place to create outputs. The total purchase consideration of $ 36.2 million was composed of cash paid at closing of $ 35.1 million and direct transaction costs of $ 1.1 million. The fair value was allocated to in-process research and development (IPR&D) assets with no alternative future use for these assets at the closing of the acquisition. As a result, the Company recorded a charge of $ 36.2 million related to acquired in-process research and development expense on the consolidated statements of operations in 2024. As part of the transaction, the Company assumed certain contractual obligations from Eiger, including royalty obligations between 4 % and 7 % on future sales owed to certain academic institutions and individuals. The Company will recognize these royalty payments related to avexitide in the period in which the achievement of the underlying milestones becomes probable. F- 19 Gubra A/S Collaboration and License Agreement On December 23, 2024, the Company entered into a collaboration and license agreement, or the Gubra Agreement, with Gubra pursuant to which the parties will perform research and discovery activities for the development of a potential novel long-acting GLP-1 receptor antagonist, under the oversight of a joint research committee. The collaboration provides the Company an exclusive license to develop, manufacture, commercialize and otherwise exploit any development candidate and product(s) arising in the performance of activities under the agreement. The Company made an immaterial upfront payment in January 2025, which became due upon the effective date of the Gubra Agreement. Since the payment was made for the use of Gubra’s intellectual property and research and development services and there is no alternative use, the Company recorded the upfront payment to research and development expense on the consolidated statements of operations in 2024. Gubra is eligible to receive an additional $ 53.5 million upon the achievement of certain development, regulatory and commercial milestones, as well as tiered royalties on future sales from any products that result from the agreement. None of these payments are deemed probable at December 31, 2024 and have not been recognized. The Company has agreed to make quarterly payments to fund Gubra's ongoing research activities, which are not expected to be material. 11. Stock Option and Grant PlanS Stock Incentive Plan— In January 2022, the Company’s board of directors adopted, and its stockholders approved the 2022 Stock Option and Incentive Plan, or 2022 Plan. Under the 2022 Plan, the Company may grant incentive stock options, or ISOs, non-statutory stock options, stock appreciation rights, restricted stock units, restricted stock awards and other stock-based awards. As of December 31, 2024 , there were 7,080,463 shares available for future issuance under the 2022 Plan. The options issued under the 2022 Plan expire 10 years following the date of grant. Stock options and restricted stock units typically vest over 4 years. We recognize the compensation cost of awards subject to service-based vesting conditions over the requisite service period, which is generally equal to the vesting period of the respective award. Initially, subject to adjustment as provided in the 2022 Plan, the aggregate number of shares of the Company’s common stock available for issuance under the 2022 Plan is 7,650,000 . The number of shares of the Company’s common stock reserved for issuance under the 2022 Plan will automatically increase on January 1 of each year commencing January 1, 2023, by 5 % of the total number of shares of the Company’s common stock outstanding on December 31 of the preceding calendar year, or a lesser number of shares as may be determined by the Company’s board of directors. Inducement Plan— In July 2023, the Company’s board of directors adopted the Amylyx Pharmaceuticals, Inc. 2023 Inducement Plan, or the Inducement Plan, to grant equity awards to induce highly-qualified prospective officers and employees who are not currently employed by the Company to accept employment and provide them with a proprietary interest in the Company. The Company has reserved 750,000 shares of its common stock that may be issued under the Inducement Plan. As of December 31, 2024, there were 360,167 shares available for future issuance under the Inducement Plan. Employee Stock Purchase Plan— In January 2022, the Company’s board of directors adopted the 2022 Employee Stock Purchase Plan, or ESPP, which was subsequently approved by the Company's stockholders. The ESPP initially reserves and authorizes the issuance of up to a total of 605,000 shares of common stock to participating employees. The ESPP provides that the number of shares reserved and available for issuance will automatically increase each January 1, beginning on January 1, 2023 and each January 1 thereafter through January 1, 2032, by the least of (i) 1 % of the outstanding number of shares of our common stock on the immediately preceding December 31, (ii) 1,210,000 shares or (iii) such number of shares of common stock as determined by the ESPP administrator. The initial purchase period under the ESPP has not yet commenced. As of December 31, 2024, there were 1,947,194 shares available for future issuance under the ESPP. F- 20 The Company estimates the fair value of stock option awards on the grant date using the Black-Scholes option pricing model with the following weighted-average assumptions: Year Ended December 31, 2024 2023 Risk-free interest rate 4.44 % 3.77 % Expected term (in years) 6.08 6.05 Expected volatility 69.17 % 70.35 % Dividend yield 0.00 % 0.00 % The weighted average grant date fair value of stock options granted during the year ended December 31, 2024 and 2023 was $ 5.61 per share and $ 19.56 per share, respectively. A summary of option activity for the year ended December 31, 2024, is as follows: Number of Options Weighted- Average Exercise Price Weighted- Average Remaining Contractual Term (in years) Aggregate Intrinsic Value (in thousands) Outstanding at January 1, 2024 9,823,248 $ 18.39 7.9 $ 27,639 Granted 3,072,661 $ 8.54 Exercised ( 210,088 ) $ 1.55 Cancelled or forfeited ( 4,957,114 ) $ 19.30 Outstanding at December 31, 2024 7,728,707 $ 14.34 7.5 $ 3,584 Exercisable at December 31, 2024 3,671,292 $ 15.79 6.2 $ 587 Unvested at December 31, 2024 4,057,415 $ 13.03 8.7 $ 2,998 The aggregate intrinsic value of options exercised during the years ended December 31, 2024 and 2023 was $ 1.0 million and $ 20.6 million , respectively. The total fair value of stock options vested during the years ended December 31, 2024 and 2023 was $ 32.5 million and $ 31.2 million , respectively. Restricted Stock Unit Activity A summary of restricted stock unit activity for the year ended December 31, 2024, is as follows: Number of shares Weighted Average Grant Date Fair Value Nonvested as of January 1, 2024 1,112,542 $ 24.80 Granted 2,865,128 $ 8.74 Vested ( 712,218 ) $ 10.88 Forfeited ( 1,052,547 ) $ 19.61 Nonvested as of December 31, 2024 2,212,905 $ 10.96 Stock-Based Compensation Expense— The Company recorded stock-based compensation expense in the following expense categories of its statements of operations: Year Ended December 31, 2024 2023 (in thousands) Research and development expenses $ 8,758 $ 9,843 Selling, general and administrative expenses 24,280 27,318 Total stock-based compensation $ 33,038 $ 37,161 F- 21 The following table summarizes unrecognized stock-based compensation expense as of December 31, 2024, by type of awards, and the weighted-average period over which that expense is expected to be recognized. The total unrecognized stock-based compensation expense will be adjusted for actual forfeitures as they occur. As of December 31, 2024 Unrecognized Expense Weighted-average Recognition Period (in thousands) (in years) Stock options $ 31,627 2.14 Restricted stock units $ 17,892 2.50 12. Income Taxes The components of net (loss) income before the provision for income taxes are as follows: Year Ended December 31, 2024 2023 (in thousands) U.S. $ ( 301,757 ) $ 52,263 Non-U.S. ( 379 ) 2,034 (Loss) income before income taxes $ ( 302,136 ) $ 54,297 The (benefit) provision for income taxes is as follows: Year Ended December 31, 2024 2023 (in thousands) Current income tax provision U.S. - Federal $ 130 $ 1,219 U.S. - State 23 2,839 Non-U.S. ( 770 ) 1,192 $ ( 617 ) $ 5,250 Deferred income tax provision Non-U.S. $ 224 $ ( 224 ) Provision for income taxes $ ( 393 ) $ 5,026 A reconciliation of the Company’s effective income tax rate to the U.S. statutory federal income tax rate of 21 % for the years ended December 31, 2024 and 2023 is as follows: Year Ended December 31, 2024 2023 Tax at U.S. statutory tax rate 21.0 % 21.0 % State income tax benefit 4.0 % 3.3 % Research and development tax credits 2.7 % ( 12.6 )% Executive Compensation ( 0.8 )% 6.2 % Uncertain Tax Positions ( 0.5 )% 2.1 % Valuation allowances ( 24.7 )% ( 12.2 )% Stock Based Compensation ( 1.2 )% ( 0.5 )% Other ( 0.4 )% 2.0 % Effective income tax rate 0.1 % 9.3 % F- 22 Deferred tax assets and liabilities were as follows: Year Ended December 31, 2024 2023 (in thousands) Deferred tax assets: Federal net operating loss carryforwards $ 55,174 $ 14,667 State net operating loss carryforwards 7,881 8,164 Capitalized research and development costs 61,280 39,297 Inventory — 1,090 Tax credits 16,005 8,039 Stock Based Compensation 3,396 3,792 Intangibles 7,507 — Accruals and other 7,906 10,425 Total deferred tax assets $ 159,149 $ 85,474 Valuation allowance ( 158,542 ) ( 83,922 ) Net total deferred tax assets $ 607 $ 1,552 Deferred tax liabilities: Other ( 607 ) ( 1,328 ) Total deferred tax liabilities $ ( 607 ) $ ( 1,328 ) Net deferred tax assets $ — $ 224 On a periodic basis the Company reassess the valuation allowance that has been established, weighing all positive and negative evidence. As of December 31, 2024, the Company maintained a full valuation against net deferred tax assets. As of December 31, 2024 and 2023, the Company had federal NOL loss carryforwards of approximately $ 262.7 million and $ 69.8 million , respectively, and state NOL loss carryforwards of approximately $ 126.9 million and $ 124.6 million , respectively, which are available to reduce future taxable income. All U.S. federal NOL carryforwards as of December 31, 2024 carry forward indefinitely. Of the $ 126.9 million state NOL carryforwards, $ 119.9 million relate to Massachusetts and begin to expire in 2040 . As of December 31, 2024 and 2023, the Company also had federal tax credits of $ 13.4 million and $ 6.8 million , respectively, and state tax credits of $ 3.3 million and $ 1.6 million , respectively. The tax credit carryforwards will expire at various dates beginning in 2035. The utilization of NOL and research and development tax credit carryforwards may be subject to a substantial annual limitation under Sections 382 and 383 of the IRC. Ownership changes occurred in the years ended December 31, 2016 and 2023. These ownership changes do not impact the Company’s overall ability to utilize NOL carryforwards and research and development tax credit carryforwards but may limit the amount that can be utilized annually to offset future taxable income. The following table reflects the roll-forward of the Company’s valuation allowance for the years ended December 31, 2024 and 2023: Year Ended December 31, 2024 2023 (in thousands) Valuation allowance at beginning of year $ 83,922 $ 90,587 Increases (decreases) recorded to income tax provision 74,620 ( 6,665 ) Valuation allowance at end of year $ 158,542 $ 83,922 The increase in the valuation allowance recorded during the year was primarily due to the increase in net operating loss generated by the Company in 2024 and required capitalization of research and development costs. The Company accounts for uncertainty in income taxes under the provisions of ASC 740 which defines the thresholds for recognizing the benefits of tax return positions in the consolidated financial statements as “more likely than not” to be sustained by the taxing authority. The tax benefit is measured based on the largest benefit that has a greater than 50% F- 23 likelihood of being realized upon ultimate settlemen t. A reconciliation of the beginning and ending amount of gross unrecognized tax benefits is as follows: Year Ended December 31, 2024 2023 (in thousands) Balance at beginning of the period $ 2,209 $ 1,013 Increases related to tax positions taken during prior years 55 271 Increases related to tax positions taken during the current year 1,498 925 Balance at end of the period $ 3,762 $ 2,209 The Company has reviewed the tax positions taken, or to be taken, in its tax returns for all tax years currently open to examination by a taxing authority. All uncertain tax benefits, if recognized, would impact the effective tax rate if recognized, offset by changes to the Company’s valuation allowance which also would impact the effective tax rate. The Company does not expect the amount of unrecognized tax benefits to materially change over next 12 months. The Company accrues interest and penalties related to unrecognized tax benefits as a component of its provision for income taxes. The Company did no t recognize any material interest or penalties related to uncertain tax positions during the years ended December 31, 2024 and 2023. The Company files U.S. federal, foreign and state income tax returns in various jurisdictions. The status of limitations varies by jurisdiction. There are currently no federal or state audits or examinations in process. 13. EMPLOYEE BENEFIT PLANS The Company maintains a tax-qualified retirement plan that provides eligible U.S. employees with an opportunity to save for retirement on a tax-advantaged basis. Plan participants are able to defer eligible compensation subject to applicable annual IRC limits. The Company made $ 2.8 million and $ 2.3 million of contributions for the years ended December 31, 2024 and 2023, respectively. F- 24 14. NET (LOSS) INCOME PER SHARE Net (Loss) Income per Share Basic earnings per share is computed by dividing net (loss) income by the weighted average number of common shares outstanding during the period. Diluted earnings per share is calculated based on the combined weighted average number of common shares and potentially dilutive shares, which include the assumed exercise of employee stock options and unvested restricted stock units. In computing diluted earnings per share, the Company utilizes the treasury stock method. A summary of the numerator and denominators used in the computation of earnings per share follows (in thousands, except share and per share data: December 31, 2024 2023 Numerator: Net (loss) income $ ( 301,743 ) $ 49,271 Denominator: Weighted-average shares used to compute basic net (loss) income per share 68,142,158 67,234,465 Dilutive effect of employee stock options and restricted stock units — 2,756,875 Weighted-average shares used to compute diluted net (loss) income per share 68,142,158 69,991,340 Net (loss) income per share Basic $ ( 4.43 ) $ 0.73 Diluted $ ( 4.43 ) $ 0.70 All stock options and restricted stock units were excluded from the computation of diluted weighted-average shares outstanding because such securities would have an antidilutive impact for the year ended December 31, 2024 . The following stock options and restricted stock units outstanding at each period end have been excluded from the calculation of diluted net (loss) income per share because their inclusion would have been antidilutive: December 31, 2024 2023 Options to purchase common stock 7,728,707 5,775,303 Restricted stock units 2,212,905 543,233 Total excluded common stock equivalents 9,941,612 6,318,536 15. Segments The Company has one operating segment which is the business of researching and developing therapeutics for neurodegenerative diseases and endocrine conditions. Our operating segments are determined based on how our Co-Chief Executive Officers , Justin Klee and Joshua Cohen, who collectively serve as our chief operating decision makers ("CODM") manages our business, regularly accesses discrete financial information, and evaluates performance for operating decision-making purposes, including allocation of resources or capital to specific compounds or projects in line with the Company’s overall strategies and goals. The Company's entire business is managed by a single management team, which reports to the CODM. The accounting policies of the Company's segment are the same as those described in Note 2 Significant Accounting Policies . The CODM assesses segment performance and decides how to allocate resources based on consolidated net (loss) income that also is reported on the consolidated statement of operations. The CODM uses net income to monitor budget and forecast versus actual results in assessing segment performance and to evaluate income generated from segment assets in deciding how to allocate resources. The measure of segment assets is reported on the consolidated balance sheets as total consolidated assets. For the years ended December 31, 2024 and 2023, all of the Company's long-lived assets were held within the U.S. F- 25 The following table reconciles segment revenue and expenses to consolidated net loss (income) for the year ended December 31, 2024 and 2023 (in thousands): Year Ended December 31, 2024 2023 Product revenue, net $ 87,371 $ 380,786 Less 1,5 : Cost of sales 2 124,633 25,441 Direct research and development expenses by program: AMX0035 - ALS 36,727 60,843 AMX0035 - PSP 16,917 6,404 Avexitide 2,766 — Other programs 8,698 13,870 Acquired in-process research and development 36,203 — Personnel-related research and development 3 38,976 47,070 Selling, general and administrative 114,331 188,356 Restructuring expenses 22,851 — (Benefit) provision for income taxes ( 393 ) 5,026 Interest income ( 13,809 ) ( 16,155 ) Other segment items 4 1,214 660 Net (loss) income $ ( 301,743 ) $ 49,271 1. The significant expense categories and amounts align with the segment-level information that is regularly provided to the CODM. As the Company has one reportable segment, there were no intersegment eliminations for the year ended December 31, 2024 and 2023. 2. Includes inventory impairment and loss on firm purchase commitments of $ 118.7 million and zero during year ended December 31, 2024 and 2023, respectively. 3. The Company does not allocate personnel and other similar costs to specific programs because these costs are deployed across multiple programs. 4. Other segment items primarily consists of net realized and unrealized losses on foreign exchange transactions 5. Depreciation and amortization expense of $ 0.9 million and $ 1.1 million durin g the years ended December 31, 2024 and 2023, respectively, are allocated across the significant expense captions. 16. Commitments and Contingencies Legal Proceedings— As of December 31, 2024, the Company is not a party to any legal proceedings that are expected to have a material impact on the Company's consolidated financial statements. The Company recognizes expenses for its costs related to its legal proceedings, as incurred. Royalty Payments— Between August 2016 and February 2019, the Company entered into grant agreements with the ALS Association, ALS Finding a Cure Foundation, Alzheimer’s Drug Discovery Foundation, Alzheimer’s Association and Cure Alzheimer’s Fund, or Grantors. Pursuant to the terms of the grant agreements, the Company has certain payment obligations that are contingent upon future events such as the achievement of commercialization or the receipt of proceeds from a revenue generating transaction resulting from the projects for which the grants are used for. The Company does not expect to incur any costs under the agreements given the discontinuation of sales of RELYVRIO®/ALBRIOZA. As disclosed in Note 10 Asset Acquisitions and Collaboration Agreements, the Company assumed royalty obligations from Eiger related to the acquisition of avexitide and Gubra A/S related to a collaboration arrangement. As the conditions that would trigger royalty payments under the agreements have not occurred, no amounts have been recorded in the consolidated financial statements. Purchase Commitments— The Company enters into agreements in the normal course of business with contract manufacturing organizations for raw material purchases and manufacturing services. As of December 31, 2024, the amounts committed under these agreements are not material. Following the discontinuation of the sales of RELYVRIO®/ALBRIOZA in 2024, the Company recognized a loss on purchase commitments of $ 26.1 million , which was recorded to cost of sales on the condensed consolidated statement of operations. F- 26 17. Restructuring In April 2024, the Company announced a restructuring plan designed to focus the Company’s resources on key clinical and preclinical programs, or the Restructuring Plan. The Restructuring Plan included a reduction in force which reduced the Company’s workforce by approximately 70 % and decreased external financial commitments outside of its priority areas. The Company completed the Restructuring Plan in 2024. Restructuring expenses consists primarily of employee severance and termination benefits, contract termination costs, impairment of long-lived assets and other costs. Liabilities for costs associated with a restructuring activity are recognized when the liability is incurred and are measured at fair value. One-time employee severance and termination benefits are expensed at the date the entity notifies the employee of the plan. One-time termination benefits primarily include severance, continuation of health insurance coverage, and other benefits such as outplacement support services for a specified period of time. In connection with the Restructuring Plan, the Company performed an impairment evaluation of its long-lived assets resulting in an impairment charge of $ 0.9 million during the year ended December 31, 2024 related to the impairment of capitalized internal-use software. Restructuring expenses for the year ended December 31, 2024 included $ 21.8 million of severance and employee benefit costs and $ 1.0 million of other contract termination costs and impairment charges. All costs related to this restructuring activity were paid as of December 31, 2024 , and the Company does not expect to incur costs in future periods for the Restructuring Plan. 18 . Subsequent Events On January 13, 2025, the Company closed an underwritten public offering of 19,714,285 shares of its common stock at a public offering price of $ 3.50 per share. The net proceeds from this offering were approximately $ 65.5 million, after deducting underwriting discounts and commissions and offering expenses. F- 27