Amylyx Pharmaceuticals, Inc.

(unaudited)

1. Nature of the Business

Amylyx Pharmaceuticals, Inc., together with its wholly-owned subsidiaries, known as Amylyx or the Company, is a clinical-stage pharmaceutical company with a mission to develop novel therapies for communities with high unmet medical needs. The Company has preclinical and clinical development programs underway in endocrine conditions and neurodegenerative diseases. The Company is currently developing three investigational therapies for potential impact across several diseases: avexitide in PBH, AMX0035 in Wolfram syndrome and AMX0114 in ALS.

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 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. The Company expects that its cash, cash equivalents and marketable securities 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 may 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

Significant Accounting Policies

The Company’s significant accounting policies are disclosed in the audited consolidated financial statements for the year ended December 31, 2024 and the notes thereto, which are included in the Company’s most recent Annual Report on Form 10-K. There have been no material changes to its significant accounting policies since the date of those consolidated financial statements.

Basis of Presentation and Consolidation

The accompanying condensed consolidated financial statements and the related interim disclosures are unaudited and have been prepared in conformity with accounting principles generally accepted in the U.S., or GAAP, and pursuant to the rules and regulations of the SEC for the interim financial information. These unaudited condensed consolidated financial statements include the accounts of the Company and its wholly owned subsidiaries. All intercompany balances and transactions have been eliminated in consolidation. Certain information and footnote disclosures normally included in financial statements prepared in accordance with GAAP have been condensed or omitted as permitted by the SEC’s rules and regulations for interim reporting. Interim period results are not necessarily indicative of results of operations or cash flows for a full year or any subsequent interim period. The accompanying unaudited condensed consolidated financial statements should be read in conjunction with the audited consolidated financial statements and notes included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2024.

In the opinion of the Company’s management, all normal and recurring adjustments necessary for a fair presentation have been reflected. Any reference in these notes to applicable guidance is meant to refer to the authoritative GAAP as found in the ASC, and Accounting Standards Update, or ASU, of the Financial Accounting Standards Board, or FASB.

Use of Estimates

The preparation of the condensed 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 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.

Product Revenue

In 2024, the Company voluntarily discontinued the marketing authorizations for RELYVRIO®/ALBRIOZA™ and removed the product from the market in the U.S. and Canada based on topline results from the Phase 3 PHOENIX trial, or the RELYVRIO®/ALBRIOZA™ Discontinuation. As a result, we do not expect to generate revenue from the sale of RELYVRIO®/ALBRIOZA™ in future periods.

New Accounting Pronouncements Not Yet Adopted

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.

Recent Accounting Pronouncements

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 with its 2025 annual report on a prospective basis. The impact of this ASU on the tax disclosures in the Company’s 2025 annual report is not expected to be material.

3. MARKETABLE SECURITIES

The Company has classified all of its marketable securities at September 30, 2025 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 loss. There wereno realized gains or losses recognized during thethree and nine months ended September 30, 2025 and 2024.

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 condensed consolidated balance sheets, and amounted to less than$0.1 million and$0.1 million at September 30, 2025 and December 31, 2024, respectively.

As of September 30, 2025, there wereno securities in an unrealized loss position for greater than 12 months. The Company does not intend to sell the investments and it is not more likely than not that the Company will be required to sell the investments before recovery of their amortized cost bases. The Company did not record an allowance for credit losses as of September 30, 2025.

Marketable securities, which are classified as available-for-sale, consisted of the following (in thousands):

4. Accrued Expenses

Accrued expenses consisted of the following (in thousands):

5. 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 (in thousands):

The Company classifies its money market funds, including restricted cash equivalents, 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.

6. Stock Option and Grant Plan

Stock Incentive Plan

General Option Information

A summary of option activity for thenine months ended September 30, 2025 is as follows:

The aggregate intrinsic value of options exercised during the nine months ended September 30, 2025 and 2024 was$0.9 million and$0.8 million, respectively.

The total fair value of stock options vested during the nine months ended September 30, 2025 and 2024 was$14.6 million and$28.2 million, respectively.

Restricted Stock Unit Activity

A summary of restricted stock unit, or RSU, activity for thenine months ended September 30, 2025 is as follows:

Performance-Based Restricted Stock Unit Activity

In 2025, the Company granted performance-based restricted stock units, or PSUs, whereby vesting depends upon the occurrence of certain milestone events, or the 2025 PSUs. When achievement of a milestone event becomes probable, compensation cost will be recognized from the grant date over the requisite service period and a cumulative catch-up adjustment will be recorded to reflect the portion of the employees' requisite service that has been provided to date. As of September 30, 2025, none of the milestone events related to the 2025 PSUs had been deemed probable of being achieved.

A summary of PSU activity for thenine months ended September 30, 2025, is as follows:

Summary of Stock-Based Compensation Expense

Stock-based compensation expense for thethree and nine months ended September 30, 2025 and 2024, is as follows (in thousands):

The following table summarizes unrecognized stock-based compensation expense as of September 30, 2025, by type of awards (in thousands), and the weighted-average period over which that expense is expected to be recognized (in years). The total unrecognized stock-based compensation expense will be adjusted for actual forfeitures as they occur.

7. STOCKHOLDERS’ EQUITY

Common Stock

Under the Company’s Fourth Amended and Restated Certificate of Incorporation, or the certificate of incorporation, each share of common stock entitles the holder to one vote on all matters submitted to the stockholders for a vote provided, however, that, except as otherwise required by law, holders of common stock shall not be entitled to vote on any amendment to the Company’s certificate of incorporation that relates solely to the terms of one or more outstanding series of preferred stock if the holders of such affected series are entitled, either separately or together with the holders of one or more other such series, to vote thereon pursuant to the certificate of incorporation or pursuant to the Delaware General Corporation Law. Holders of common stock are entitled to receive dividends, as may be declared by the Company’s Board of Directors, if any, subject to the preferential dividend rights of the preferred stock. No dividends were declared or paid during thenine months ended September 30, 2025 and 2024.

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.

On September 10, 2025, the Company closed an underwritten public offering of 20,125,000 shares of its common stock at a public offering price of $10.00 per share. The net proceeds from this offering were approximately$190.7 million, after deducting underwriting discounts and commissions and offering expenses.

8. NET LOSS PER SHARE

Net Loss per Share

Basic earnings per share is computed by dividing net loss 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, unvested RSUs and unvested PSUs. In computing diluted earnings per share, the Company utilizes the treasury stock method.

Because the Company reports a net loss attributable to common stockholders, basic and diluted net loss per share attributable to common stockholders are the same for both periods presented. All stock options, RSUs and PSUs units were excluded from the computation of diluted weighted-average shares outstanding because such securities would have an antidilutive impact for the three and nine months ended September 30, 2025. The following stock options, RSUs and PSUs outstanding at each period end have been excluded from the calculation of diluted net loss per share because their inclusion would have been antidilutive:

9. Commitments and Contingencies

Letter of Credit

Restricted cash equivalents consist of$0.9 million of cash serving as collateral for a letter of credit issued for the Company’s office spaces, and$0.1 million as collateral for a corporate credit card program. As of September 30, 2025 and December 31, 2024, the Company’s restricted cash equivalents balance was$1.0 million and $1.4 million on its condensed consolidated balance sheets, respectively.

Legal Proceedings

On February 9, 2024, a putative class action lawsuit was filed in the U.S. District Court for the Southern District of New York against us and certain of our current and former officers (Shih v. Amylyx Pharmaceuticals, Inc., et al., Case Number 1:24-CV-00988, or the Shih Complaint). Plaintiff filed an amended complaint on June 24, 2024. The Shih Complaint asserts a claim against all defendants for alleged violations of Section 10(b) of the Exchange Act and Rule 10b-5 promulgated thereunder and a claim under Section 20(a) against certain current and former officers as alleged controlling persons. The Shih Complaint alleges that defendants made materially false and misleading statements related to the commercial results and prospects for RELYVRIO. The Shih Complaint seeks unspecified damages, interest, costs and attorneys’ fees, and other unspecified relief that the court deems appropriate.

On August 12, 2024, the case was transferred from the U.S. District Court for the Southern District of New York to the U.S. District Court for the District of Massachusetts, or the Court, and assigned docket number 1:24-CV-12068. Following the transfer, on September 6, 2024, defendants moved to dismiss the Shih Complaint. On September 30, 2025, the Court issued an order finding that the majority of the alleged misstatements are inactionable, but ultimately denied the motion to dismiss. The Company filed an answer on October 30, 2025.

In addition to the Shih Complaint, on October 2, 2024, a derivative complaint was filed in the U.S. District Court for the District of Massachusetts against certain current and former director and officer defendants, or the Individual Defendants, naming the Company as a nominal defendant (Jones v. Cohen, et al., 1:24-CV-12527, or the Jones Derivative Complaint). The substantive allegations mirror those of the Shih Complaint but also include claims for alleged violations of Section 14(a) of the Exchange Act, breach of fiduciary duty, insider trading, and unjust enrichment against the Individual Defendants. The Jones Derivative Complaint seeks unspecified damages to be awarded to the Company along with interest, restitution, unspecified corporate governance and internal procedural reforms and improvements, and plaintiff's attorneys' fees and costs. On October 31, 2024, the Court entered an order staying the action until the earlier of the dismissal of the Shih Complaint with prejudice, including the exhaustion of all appeals, or defendants file an answer to the Shih Complaint.

On July 2, 2025, a second derivative complaint was filed in the Court against certain current and former directors and officer defendants, naming the Company as nominal defendant (Hassine v. Cohen, et al., 1:25-CV-11879, or the Hassine Derivative Complaint and, together with the Jones Derivative Complaint, the Derivative Complaints”). The substantive allegations mirror those of the Shih Complaint but also include claims for alleged violations of Sections 14(a), 10(b), and 21D of the Exchange Act, breach of fiduciary duty, and certain other common law claims. The Hassine Derivative Complaint seeks unspecified damages to be awarded to the Company along with interest, costs, and attorneys’ fees, restitution, and certain corporate governance and internal procedural reforms and improvements. On July 16, 2025, the parties to both derivative cases moved the Court to consolidate the Hassine Derivative Complaint with the Jones Derivative Complaint and stay the action according to the terms of the previously entered stay of the Jones Derivative Complaint. The Court approved the motion on July 22, 2025. Now that the motion to dismiss the Shih Complaint has been resolved, the parties will meet and confer to either extend the stay or propose a schedule for the consolidated derivative action, as provided in the order staying the action.

We intend to defend against the Shih Complaint and Derivative Complaints vigorously. At this time, an estimate of the impact, if any, of the claims made in the Shih Complaint and Derivative Complaints cannot be made.

Royalty Payments

The Company has entered into a limited number of grant and royalty agreements that include payment obligations contingent upon future events, such as commercialization or the receipt of proceeds from revenue-generating transactions related to the underlying technologies. As the conditions that would trigger royalty payments have not been met, 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, or CMOs, for raw material purchases and manufacturing services. As of September 30, 2025, there are no amounts committed under these agreements.

Facility Leases

In September 2024, the Company entered into a lease agreement for the lease of approximately 15,000 square feet of office space in Cambridge, Massachusetts, which serves as the Company's corporate headquarters facility. The lease commenced on June 1, 2025, at which time the Company recognized a right-of-use, or ROU, asset and corresponding lease liability of $5.1 million. The initial lease term is approximately 67 months with rental payments beginning seven months after the lease commencement. In addition to base rent, the Company will reimburse the landlord for certain operating expenses under the terms of the lease. The Company has theoption to extend the lease one time for an additional five-year period, subject to the terms therein; however, the exercise of the option to extend the lease term was not determined to be reasonably certain, and the Company will therefore recognize lease expense through the expiration of the initial lease term ending in December 2030.

10. aCQUISITIONS

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 acquired in-process research and development, or 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 IPR&D expense on the condensed consolidated statements of operations during the three and nine months ended September 30, 2024, andno IPR&D expense was recorded during the three and nine months ended September 30, 2025.

As part of the transaction, the Company assumed 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. There wereno other contingent obligations or assumed liabilities from the acquisition as of September 30, 2024 or September 30, 2025.

11. Segments

The Company views its operations and manages its business asone operating segment and reporting unit. Our operating segments are determined based on how our Co-Chief Executive Officers, who collectively serve as our chief operating decision makers, or CODM, manage our business, regularly access discrete financial information, and evaluate 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 CODM assess segment performance and decide how to allocate resources based on consolidated net loss. The CODM use net loss to monitor budget and forecast versus actual results in assessing segment performance and to determine how to allocate resources. The measure of segment assets used in determining how to manage and allocate resources is reported on the consolidated balance sheets as total assets. All of the Company's long-lived assets were held within the U.S.

The following table reconciles segment revenue and expenses to consolidated net loss for thethree and nine months ended September 30, 2025 and 2024 (in thousands):

1. The significant expense categories and amounts align with the segment-level information that is regularly provided to the CODM. As the Company hasone reportable segment, there wereno intersegment eliminations for thethree and nine months ended September 30, 2025 and 2024.

2. Includes inventory impairment and loss on firm purchase commitm ents of$0.8 million and$118.7 million during the three and nine months ended September 30, 2024, 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 expenseof$0.1 million and$0.4 million during the three and nine months ended September 30, 2025, respectively, and$0.2 million and$0.7 million during the three and nine months ended September 30, 2024, respectively, are allocated across the significant expense captions.