Spyre Therapeutics, Inc.

1. The Company and Basis of Presentation

Spyre Therapeutics, Inc. (“Spyre” or the “Company”) is a clinical stage biotechnology company committed to developing next-generation therapies that elevate the standard in immunology by delivering more complete disease control, greater durability, and a simpler treatment experience for patients. The Company was formed as a Limited Liability Company in Delaware on December 16, 2013 under the name Aeglea BioTherapeutics Holdings, LLC and was converted from a Delaware LLC to a Delaware corporation on March 10, 2015. On June 22, 2023, the Company acquired the assets of Spyre Therapeutics, Inc., a privately held biotechnology company (the “Asset Acquisition”), and on November 27, 2023, the Company completed its corporate rebranding, changing the name of the Company to Spyre Therapeutics, Inc. The Company operates inone segment and has its principal offices in Waltham, Massachusetts.

In connection with the Asset Acquisition, a non-transferable contingent value right (“CVR”) was distributed to stockholders of record of the Company as of the close of business on July 3, 2023 (the “Legacy Stockholders”). Holders of the CVRs are entitled to receive certain cash payments from proceeds received by the Company prior to July 3, 2026, the third anniversary of the contingent value rights agreement (the “CVR Agreement”) we entered into with Equiniti Trust Company LLC (f/k/a American Stock Transfer & Trust Company LLC) as rights agent in connection with the Asset Acquisition, if any, related to the disposition or monetization of its legacy assets during theone-year period following the closing of the Asset Acquisition.

On September 6, 2024, the Company entered into a sales agreement (the “2024 Sales Agreement”) with TD Securities (USA) LLC as its agent, pursuant to which the Company may issue and sell up to $200.0 million of shares of common stock under an at-the-market (“ATM”) offering program. During the three and nine months ended September 30, 2026, the Company sold an aggregate ofnil and 296,396 shares of common stock, respectively, under the ATM offering program pursuant to the 2024 Sales Agreement resulting in net proceeds ofnil and $9.7 million, respectively. The 2024 Sales Agreement was terminated on June 26, 2026 and the Company concurrently entered into a new sales agreement (the “2026 Sales Agreement”) with TD Securities (USA) LLC as its agent, pursuant to which the Company may issue and sell up to $500.0 million of shares of common stock under an ATM offering program. During the three and nine months ended September 30, 2026, the Company sold 327,391 shares under the ATM offering program pursuant to the 2026 Sales Agreement, resulting in net proceeds of $29.5 million. As of September 30, 2026, $469.9 million remained available for sale under the 2026 Sales Agreement. Subsequent to September 30, 2026, and through November 3, 2026, the Company sold 200,111 shares under the ATM offering program pursuant to the 2026 Sales Agreement, resulting in net proceeds of $18.0 million and $451.6 million remaining available for sale under the 2026 Sales Agreement as of November 3, 2026.

On October 13, 2025, the Company entered into an underwriting agreement (the “October 2025 Underwriting Agreement”), pursuant to which the Company sold an aggregate of 17,094,594 shares of its common stock, inclusive of 2,229,729 shares pursuant to the full exercise of the underwriters' over-allotment option, at a public offering price per share of $18.50, resulting in net proceeds of approximately $296.4 million after deducting approximately $19.9 million of underwriting discounts and other offering costs. The over-allotment option was exercised in full on October 14, 2025 and the transaction closed on October 15, 2025.

On April 13, 2026, the Company entered into an underwriting agreement (the “April 2026 Underwriting Agreement”), pursuant to which the Company sold an aggregate of 7,475,000 shares of its common stock, inclusive of 975,000 shares pursuant to the full exercise of the underwriters' over-allotment option, at a public offering price per share of $62.00, resulting in net proceeds of approximately $435.2 million after deducting approximately $28.2 million of underwriting discounts and other offering costs (the “April 2026 Offering”). The over-allotment option was exercised in full on April 15, 2026 and the transaction closed on April 16, 2026.

On October 5, 2026, the Company entered into an underwriting agreement (the “October 2026 Underwriting Agreement”) for the sale of 4,117,648 shares of its common stock (the “Firm Shares”) at a public offering price of $85.00 per share. The Company also granted the underwriters an option to purchase up to 617,647 additional shares (the “Option Shares”) at the same price. The sale of the Firm Shares closed on

October 7, 2026. The underwriters exercised their option in full on October 12, 2026, and the sale of the Option Shares closed on October 13, 2026. In total, the Company sold an aggregate of 4,735,295 shares of its common stock in the offering, resulting in net proceeds of approximately $378.0 million after deducting approximately $24.5 million of underwriting discounts and other offering costs (the “October 2026 Offering”).

Liquidity

The Company is a clinical stage biotechnology company with a limited operating history, and due to its significant research and development expenditures, the Company has generated operating losses since its inception and has not generated any revenue from the commercial sale of any products. There can be no assurance that profitable operations will ever be achieved, and, if achieved, whether profitability can be sustained on a continuing basis.

Since its inception and through September 30, 2026, the Company has funded its operations by raising an aggregate of approximately $2.2 billion of gross proceeds from the sale and issuance of convertible preferred stock and common stock, pre-funded warrants, the collection of grant proceeds, and the licensing of its product rights for commercialization of pegzilarginase in Europe and certain countries in the Middle East. As of September 30, 2026, Spyre had an accumulated deficit of $1.3 billion, and cash, cash equivalents, and marketable securities of $1.1 billion.

Based on its current operating plans, the Company has sufficient resources to fund operations for at least one year from the issuance date of these financial statements with existing cash, cash equivalents, and marketable securities. The Company will need to secure additional financing in the future to fund additional research and development, and before a commercial drug can be produced, marketed and sold. If the Company is unable to obtain additional financing or generate license or product revenue, the lack of liquidity could have a material adverse effect on the Company.

Basis of Presentation

The condensed consolidated financial statements have been prepared in conformity with generally accepted accounting principles in the United States (“U.S. GAAP”) as defined by the Financial Accounting Standards Board (“FASB”) and include the accounts of the Company and its wholly owned subsidiaries. All intercompany balances and transactions have been eliminated in consolidation.

Unaudited Interim Financial Information

The interim condensed consolidated financial statements included in this Quarterly Report on Form 10-Q are unaudited. The unaudited interim financial statements have been prepared on the same basis as the annual financial statements and reflect, in the opinion of management, all adjustments of a normal and recurring nature that are necessary for a fair statement of the Company’s financial position as of September 30, 2026, and its results of operations for the three and nine months ended September 30, 2026 and 2025, changes in convertible preferred stock and stockholders’ equity for the three and nine months ended September 30, 2026 and 2025, and cash flows for the nine months ended September 30, 2026 and 2025. The results of operations for the three and nine months ended September 30, 2026 are not necessarily indicative of the results to be expected for the year ending December 31, 2026 or for any other future annual or interim period. The December 31, 2025 balance sheet was derived from audited financial statements, but does not include all disclosures required by U.S. GAAP for complete financial statements. These financial statements should be read in conjunction with the audited financial statements included in the Company’s Form 10-K for the year ended December 31, 2025 (the “Annual Report”) as filed with the U.S. Securities and Exchange Commission (“SEC”) on February 19, 2026.

2. Summary of Significant Accounting Policies

These interim condensed consolidated financial statements have been prepared in accordance with U.S. GAAP and SEC instructions for interim financial information, and should be read in conjunction with the Annual Report. Significant accounting policies and other disclosures normally provided have been omitted since such items are disclosed in the Annual Report. The Company uses the same accounting policies in preparing quarterly and annual financial statements.

There have been no significant changes from the significant accounting policies and estimates disclosed in the Notes titled “1. The Company and Basis of Presentation” and “2. Summary of Significant Accounting Policies” of the Annual Report, except as disclosed below:

Contingent Value Rights

As of June 30, 2026, CVRs are no longer a significant accounting policy. The Company determined that remaining significant contingencies regarding its future payment obligations under the CVR Agreement have been resolved. Accordingly, the Company has measured the fair value of its CVR liability by discounting the estimated future payments to be made under the CVR Agreement using the Company’s weighted average cost of capital. This fair value measurement is based on inputs observable in the market and thus represents a Level 2 measurement as defined in ASC 820, Fair Value Measurement. The estimated value of the CVR consideration is based upon available information and certain assumptions which the Company's management believes are reasonable under the circumstances. The ultimate payout under the CVRs may differ materially from the assumptions used in determining the fair value of the CVR consideration.

Recently Adopted Accounting Pronouncements

There have been no recent accounting pronouncements or changes in accounting pronouncements adopted during the three months ended September 30, 2026 that are of significance or potential significance to the Company.

Not Yet Adopted Accounting Pronouncements

In November 2024, the FASB issued Accounting Standards Update 2024-03 (“ASU 2024-03”) Income Statement - Reporting Comprehensive Income - Expense Disaggregation Disclosures (Subtopic 220-40): Disaggregation of Income Statement Expenses to require more detailed information about specified categories of expenses (purchases of inventory, employee compensation, depreciation, amortization, and depletion) included in certain expense captions presented on the face of the income statement. ASU 2024-03 is effective for fiscal years beginning after December 15, 2026, and for interim periods within fiscal years beginning after December 15, 2027. Early adoption is permitted. The amendments may be applied either (1) prospectively to financial statements issued for reporting periods after the effective date of this ASU 2024-03 or (2) retrospectively to all prior periods presented in the financial statements. The Company is currently evaluating the impact ASU 2024-03 will have on its disclosures.

3. Fair Value Measurements

The Company measures and reports certain financial instruments as assets and liabilities at fair value on a recurring basis. The following tables set forth the fair value of the Company’s financial assets and liabilities at fair value on a recurring basis based on the three-tier fair value hierarchy (in thousands):

The Company measures the fair value of money market funds and U.S. government treasury securities on quoted prices in active markets for identical assets or liabilities. The Level 2 assets include U.S. government agency securities, commercial paper and corporate bonds, and are valued based on quoted prices for similar assets in active markets and inputs other than quoted prices that are derived from observable market data. The Company evaluates transfers between levels at the end of each reporting period. There were no financial asset transfers between Level 1, Level 2, or Level 3 during the periods presented.

CVR Liability

In connection with the Asset Acquisition, a non-transferable CVR was distributed to the Legacy Stockholders. Holders of the CVR are entitled to receive certain cash payments from proceeds received by the Company for athree-year period ending July 3, 2026, related to the disposition or monetization of the Company’s legacy assets for a period ofone year following the closing of the Asset Acquisition.

As of December 31, 2025, the fair value of the CVR liability was determined using the probability weighted discounted cash flow method to estimate future cash flows associated with the sale of the legacy assets. Analogous to a dividend being declared/approved in one period and paid out in another, the liability was recorded at the date of approval, June 22, 2023, as a common stock dividend, returning capital to the Legacy

Stockholders. Changes in fair value of the liability were recognized as a component of Other income (expense), net in the consolidated statement of operations and comprehensive loss in each reporting period. The liability value was based on significant inputs not observable in the market such as estimated cash flows, estimated probabilities of regulatory success, and discount rates, which represent a Level 3 measurement within the fair value hierarchy.

As of June 30, 2026, all contingencies related to the disposition or monetization of the Company’s legacy assets are resolved and the fair value of the CVR liability was determined by discounting future payments to holders of the CVR. Changes in fair value of the liability will be recognized as a component of Other income (expense), net in the consolidated statement of operations and comprehensive loss in each reporting period. The liability is based on inputs observable in the market such as estimated discount rates which represent a Level 2 measurement within the fair value hierarchy.

The significant inputs used to estimate the fair value of the CVR liability were as follows:

The CVR liability decreased by $19.9 million between December 31, 2025 and September 30, 2026, reflecting payments totaling $55.7 million to CVR holders, partially offset by a $35.8 million increase in fair value. The fair value increase was primarily driven by the achievement status of certain milestones, the receipt of certain cash consideration within the CVR term and time value of money adjustments.

The following table presents changes in the CVR liability for the periods presented (in thousands):

4. Cash Equivalents and Marketable Securities

The following tables summarize the estimated fair value of the Company’s cash equivalents and marketable securities and the gross unrealized gains and losses (in thousands):

The following table summarizes the available-for-sale securities in an unrealized loss position for which an allowance for credit losses has not been recorded as of September 30, 2026 and December 31, 2025, aggregated by major security type and length of time in a continuous unrealized loss position (in thousands):

The Company evaluated its securities for credit losses and considered the decline in market value to be primarily attributable to current economic and market conditions and not to a credit loss or other factors. Additionally, the Company does not intend to sell the securities in an unrealized loss position and does not expect it will be required to sell the securities before recovery of the unamortized cost basis. As of September 30, 2026 and December 31, 2025, an allowance for credit losses hadnot been recognized. Given the Company's intent and ability to hold such securities until recovery, and the lack of significant change in credit risk of these investments, the Company doesnot consider these marketable securities to be impaired as of September 30, 2026 and December 31, 2025.

The financial instruments that potentially subject the Company to a concentration of credit risk consist principally of cash deposits. Accounts at each of the Company'stwo U.S. banking institutions are insured by the Federal Deposit Insurance Corporation (“FDIC”) up to $250,000 per depositor. As of September 30, 2026 and December 31, 2025, cash deposits at the Company's U.S. banking institutions exceeded the FDIC limits.

There wereno realized gains or losses on marketable securities for both the three and nine months ended September 30, 2026 and 2025. Interest on marketable securities is included in interest income. Accrued interest receivable on available-for-sale debt securities as of September 30, 2026 and December 31, 2025, was $5.8 million and $4.5 million, respectively, and is reflected in Prepaid expenses and other current assets.

The following table summarizes the contractual maturities of the Company’s marketable securities at estimated fair value (in thousands):

The Company may sell investments at any time for use in current operations even if they have not yet reached maturity. As a result, the Company classifies marketable securities, including securities with maturities beyond twelve months as current assets.

5. Accrued and Other Current Liabilities

Accrued and other current liabilities consist of the following (in thousands):

6. Licensing Agreements

On July 12, 2023, December 14, 2023, and June 5, 2024, the Company exercised the Option (as defined below) available under the antibody discovery and option agreement, dated May 25, 2023, and subsequently amended and restated on September 29, 2023 and May 14, 2024, by and among the Company, Paragon Therapeutics, Inc. (“Paragon”) and Parapyre Holding LLC (“Parapyre”) (as amended, the “Paragon Agreement”) with respect to the SPY001, SPY002 and SPY072, and SPY003 research programs, respectively.

On May 14, 2024, the Company and Paragon entered into (i) a license agreement (the “SPY001 License Agreement”), pursuant to which Paragon granted the Company a royalty-bearing, world-wide, exclusive license to develop, manufacture, commercialize or otherwise exploit certain antibodies and products targeting α4β7 integrin and (ii) a license agreement (the “SPY002 and SPY072 License Agreement”), pursuant to which Paragon granted the Company a royalty-bearing, world-wide, exclusive license to develop, manufacture, commercialize or otherwise exploit certain antibodies and products targeting TL1A, respectively, which includes the Company's SPY002 and SPY072 product candidates.

On October 11, 2024, the Company and Paragon entered into a license agreement (as amended, the “SPY003 License Agreement”, and together with the SPY001 License Agreement and the SPY002 and SPY072 License Agreement, the “License Agreements”), pursuant to which Paragon granted the Company a royalty- bearing, world-wide, exclusive license to develop, manufacture, commercialize or otherwise exploit certain antibodies and products targeting IL-23 in the field of IBD.

On February 24, 2025, the SPY003 License Agreement was amended and restated to, among other things, clarify each party's rights and obligations with respect to license exclusivity and patent prosecution. On May 29, 2026, the SPY003 License Agreement was further amended to expand the definition of “Field” to encompass all therapeutic, prophylactic, palliative and diagnostic uses of SPY003, subject to certain restrictions (as summarized below).

Under the terms of each License Agreement, the Company is obligated to pay Paragon up to $22.0 million based on specific development, regulatory and clinical milestones for the first product under each agreement, respectively, that achieves such specified milestones, including a milestone payment of $5.0 million upon the first dosing of a human patient in a Phase 3 trial. In addition, the following summarizes other key terms of each License Agreement:

•Paragon will provide the Company with an exclusive license to its patents covering the related antibody, the method of use and its method of manufacture.

•Paragon will not conduct any new campaigns that generate anti-α4β7 or anti-TL1A monospecific antibodies in any field or anti-IL-23 monospecific antibodies in the field of IBD, in each case for at least 5 years.

•The Company will pay Paragon a low single-digit percentage royalty for single antibody products and a mid single-digit percentage royalty for products containing more than one antibody from Paragon.

•There is a royalty step-down of 1/3rd if there is no Paragon patent in effect during the royalty term.

•The royalty term ends on the later of (i) the last-to-expire licensed patent or Company patent directed to the manufacture, use or sale of a licensed antibody in the country at issue or (ii)12 years from the date of first sale of a Company product.

•Each License Agreement may be terminated on 60 days’ notice by the Company; on material breach without cure; and to the extent permitted by law, on a party’s insolvency or bankruptcy.

•With respect to the SPY002 and SPY072 License Agreement only, on a product by product basis, the Company will pay sublicensing fees of up to approximately $20 million upon the achievement of mostly commercial milestones.

•With respect to the SPY003 License Agreement only, the Company will not dose a human patient in a clinical trial of SPY003 for an indication outside of inflammatory bowel disease as part of a combination until June 1, 2028 or as a monotherapy until June 1, 2030 (the “Monotherapy Dosing Restriction”). In the event the Company or a licensee of Paragon's retained rights under the SPY003 License Agreement consummates a material transaction, including a change of control of the Company or such licensee, then any remaining restrictions outside of the initial definition of “Field” set forth in the Monotherapy Dosing Restriction shall remain in effect only until June 1, 2028 and thereafter terminate and be of no further force or effect.

The Company recognizes the expense associated with each milestone when the achievement of the milestone is deemed probable.

The Company recognized expense related to Paragon license milestone payments, recorded within Research and development expenses in the accompanying condensed statement of operations, ofnil and $6.0 million for the three months ended September 30, 2026 and 2025, respectively. The Company recognized expense related to Paragon license milestone payments, recorded within Research and development expenses in the accompanying condensed statement of operations, of $3.0 million and $8.5 million for the nine months ended September 30, 2026 and 2025, respectively.

The Company paid milestone payments to Paragon totalingnil and $3.0 million for the three months ended September 30, 2026 and 2025, respectively. The Company paid milestone payments to Paragon totaling $3.0 million and $5.5 million for the nine months ended September 30, 2026 and 2025, respectively. As of

September 30, 2026 and December 31, 2025, there wereno milestone payments outstanding and payable to Paragon.

Additionally, the Company recognized $0.1 million in sublicensing fees expense for the three and nine months ended September 30, 2026, and $1.0 million in sublicensing fees expense for the three and nine months ended September 30, 2025, which were recorded as Research and development expenses in the accompanying condensed statement of operations.

There wereno payments related to sublicensing fees for the three and nine months ended September 30, 2026. The Company paid sublicensing fees to Paragon totalingnil and $0.5 million for the three and nine months ended September 30, 2025, respectively.

As of September 30, 2026 and December 31, 2025, there were $0.1 million andnil sublicensing fees outstanding and payable to Paragon, respectively.

7. Related Party Transactions

Paragon and Parapyre each beneficially own less than 5% of a class of the Company's voting securities through their respective holdings of the Company's common stock. Fairmount Funds Management LLC (“Fairmount”) beneficially owns more than 5% of a class of the Company's voting securities, hasone seat on the Board (held by Tomas Kiselak) and beneficially owns more than 5% of Paragon. Fairmount appointed Paragon's board of directors and has the contractual right to approve the appointment of any executive officers of Paragon.

The following is the summary of expenses related to the License Agreements and other Paragon reimbursable expenses, which are ultimately settled in cash (in millions) and recorded within Research and development in the consolidated statement of operations for the periods presented:

For the three months ended September 30, 2026 and 2025, the Company recognized de minimis expenses related to services provided by Paragon, which were recorded as Research and development expenses in the consolidated statements of operations. For the nine months ended September 30, 2026 and 2025, the Company recognized $0.1 million of Paragon reimbursable expenses.

Related party accounts payable were $0.1 million and de minimis as of September 30, 2026 and December 31, 2025.

For the three months ended September 30, 2026 and 2025, the Company made de minimis payments in connection with Paragon reimbursable expenses. For the nine months ended September 30, 2026 and 2025, the Company made payments totaling $0.1 million and $0.2 million, respectively, in connection with Paragon reimbursable expenses.

Paragon License Agreements

See Note 6 for disclosures related to the License Agreements entered into with Paragon.

Mark McKenna Option Grant

On February 1, 2024, the Board appointed Mark McKenna as a Class I director. Mr. McKenna and the Company are parties to a consulting agreement, pursuant to which Mr. McKenna agreed to continue to provide consulting services as an independent contractor to the Company, with an effective date of August 1, 2023 (the “Vesting Commencement Date”). As compensation for Mr. McKenna’s consulting services, on November 22, 2023, he was granted non-qualified stock options to purchase 477,000 shares of the Company’s common stock under the 2016 Plan (as defined in Note 9) with an exercise price of $10.39 per share, which vest as to 25% on theone year anniversary of the Vesting Commencement Date and thereafter vest and become exercisable in 36 equal monthly installments, subject to Mr. McKenna’s continued service to the Company through each applicable vesting date. The Company recognized stock-based compensation expense related to Mr. McKenna's consulting agreement of $0.3 million for the three months ended September 30, 2026 and 2025, and $0.8 million for the nine months ended September 30, 2026 and 2025.

8. Convertible Preferred Stock and Stockholders’ Equity

Warrants

As of September 30, 2026, all 1,532,591 warrants previously issued to Parapyre pursuant to the Paragon Agreement, with a weighted-average exercise price of $22.49, have been exercised, andno warrants remain outstanding.

Series A Non-Voting Convertible Preferred Stock

Pursuant to the Company's Certificate of Designation of Preferences, Rights and Limitations of the Series A Non-Voting Convertible Preferred Stock (the “Series A Preferred Stock”) (the “Series A Certificate of Designation”), holders of Series A Preferred Stock are entitled to receive dividends on shares of Series A Preferred Stock equal to, on an as-if-converted-to-common stock basis, and in the same form as, dividends actually paid on shares of common stock. Except as provided in the Series A Certificate of Designation or as otherwise required by law, the Series A Preferred Stock does not have voting rights. However, as long as any shares of Series A Preferred Stock are outstanding, the Company will not, without the affirmative vote of the holders of a majority of the then outstanding shares of the Series A Preferred Stock: (a) alter or change adversely the powers, preferences or rights given to the Series A Preferred Stock, or alter or amend the Series A Certificate of Designation, amend or repeal any provision of, or add any provision to, the Company’s Certificate of Incorporation or its Bylaws, or file any articles of amendment, certificate of designations, preferences, limitations and relative rights of any series of preferred stock, if such action would adversely alter or change the preferences, rights, privileges or powers of, or restrictions provided for the benefit of the Series A Preferred Stock, regardless of whether any of the foregoing actions will be by means of amendment to the Certificate of Incorporation or by merger, consolidation, recapitalization, reclassification, conversion or otherwise, (b) issue further shares of Series A Preferred Stock or increase or decrease (other than by conversion) the number of authorized shares of Series A Preferred Stock, (c) prior to the stockholder approval of the conversion of the Series A Preferred Stock into shares of common stock in accordance with Nasdaq Stock Market Rules or at any time while at least 30% of the originally issued Series A Preferred Stock remains issued and outstanding, consummate (x) any Fundamental Transaction (as defined in the Series A Certificate of Designation) or (y) any merger or consolidation of the Company with or into another entity or any stock sale to, or other business combination in which the Company's stockholders immediately before such transaction do not hold at least a majority of the Company's capital stock immediately after such transaction or (d) enter into any agreement with respect to any of the foregoing. The Series A Preferred Stock does not have a preference upon any liquidation, dissolution or winding-up of the Company.

As of September 30, 2026,346,045 shares of Series A Preferred Stock remained outstanding and are convertible into 13,841,800 common shares.

Series B Non-Voting Convertible Preferred Stock

Prior to the retirement of the Company’s Series B Non-Voting Convertible Preferred Stock (the “Series B Preferred Stock”) described below, pursuant to the Company's Certificate of Designation of Preferences, Rights and Limitations of Series B Non-Voting Convertible Preferred Stock (as amended, the “Series B Certificate of Designation”), holders of Series B Preferred Stock were entitled to receive dividends on shares of Series B Preferred Stock equal to, on an as-if-converted-to-common stock basis, and in the same form as, dividends actually paid on shares of common stock. Except as provided in the Series B Certificate of

Designation or as otherwise required by law, the Series B Preferred Stock did not have voting rights. However, as long as any shares of Series B Preferred Stock were outstanding, the Company would not, without the affirmative vote of the holders of a majority of the then outstanding shares of the Series B Preferred Stock, alter or change adversely the powers, preferences or rights given to the Series B Preferred Stock, or alter or amend the Series B Certificate of Designation, amend or repeal any provision of, or add any provision to, the Company’s Certificate of Incorporation or its Bylaws, or file any articles of amendment, certificate of designations, preferences, limitations and relative rights of any series of preferred stock, if such action would adversely alter or change the preferences, rights, privileges or powers of, or restrictions provided for the benefit of the Series B Preferred Stock, regardless of whether any of the foregoing actions were by means of amendment to the Certificate of Incorporation or by merger, consolidation, recapitalization, reclassification, conversion or otherwise. The Series B Preferred Stock did not have a preference upon any liquidation, dissolution or winding-up of the Company.

On June 23, 2026, all 16,667 shares of Series B Preferred Stock outstanding were converted at the option of the holder into 666,680 shares of common stock. As of September 30, 2026, no shares of Series B Preferred Stock remained outstanding.

On October 29, 2026, the Company filed with the Secretary of State of the State of Delaware (i) a Corrected Second Amended and Restated Certificate of Incorporation to correct the inadvertent omission from its Second Amended and Restated Certificate of Incorporation of the Series A Certificate of Designation and the Series B Certificate of Designation and (ii) a Certificate of Elimination of Series B Non-Voting Convertible Preferred Stock to effect the retirement of its Series B Preferred Stock, which resulted in the previously authorized shares of the retired Series B Preferred Stock being returned to authorized, unissued and undesignated preferred stock.

ATM Facility

On September 6, 2024, the Company entered into the 2024 Sales Agreement, pursuant to which the Company may issue and sell up to $200.0 million of shares of common stock under an ATM offering program.

During the year ended December 31, 2025, the Company sold an aggregate of 445,668 shares of common stock under its ATM offering program pursuant to the 2024 Sales Agreement resulting in net proceeds of $14.8 million.

During the nine months ended September 30, 2026, the Company sold an aggregate of 296,396 shares of common stock under the ATM offering program pursuant to the 2024 Sales Agreement resulting in net proceeds of $9.7 million.

The 2024 Sales Agreement was terminated on June 26, 2026 and the Company concurrently entered into a new sales agreement (the “2026 Sales Agreement”) with TD Securities (USA) LLC as its agent, pursuant to which the Company may issue and sell up to $500.0 million of shares of common stock under an ATM offering program.

During the three and nine months ended September 30, 2026, the Company sold 327,391 shares under the ATM offering program pursuant to the 2026 Sales Agreement, resulting in net proceeds of $29.5 million. As of September 30, 2026, $469.9 million remained available for sale under the 2026 Sales Agreement.

Subsequent to September 30, 2026, and through November 3, 2026, the Company sold 200,111 shares under the ATM offering program pursuant to the 2026 Sales Agreement, resulting in net proceeds of $18.0 million and $451.6 million remaining available for sale under the 2026 Sales Agreement as of November 3, 2026.

October 2025 Underwritten Offering

On October 13, 2025, the Company entered into the October 2025 Underwriting Agreement, pursuant to which the Company sold an aggregate of 17,094,594 shares of common stock, inclusive of 2,229,729 shares pursuant to the full exercise of the underwriters’ over-allotment option, at a public offering price per share of $18.50, resulting in net proceeds of approximately $296.4 million after deducting approximately $19.9 million of underwriting discounts and other offering costs. The over-allotment option was exercised in full on October 14, 2025 and the transaction closed on October 15, 2025.

April 2026 Underwritten Offering

On April 13, 2026, the Company entered into the April 2026 Underwriting Agreement, pursuant to which the Company sold an aggregate of 7,475,000 shares of its common stock, inclusive of 975,000 shares pursuant to the full exercise of the underwriters' over-allotment option, at a public offering price per share of $62.00, resulting in net proceeds of approximately $435.2 million after deducting approximately $28.2 million of underwriting discounts and other offering costs. The over-allotment option was exercised in full on April 15, 2026 and the transaction closed on April 16, 2026.

October 2026 Underwritten Offering

On October 5, 2026, the Company entered into the October 2026 Underwriting Agreement for the sale of 4,117,648 Firm Shares at a public offering price of $85.00 per share. The Company also granted the underwriters an option to purchase up to 617,647 Option Shares at the same price. The sale of the Firm Shares closed on October 7, 2026. The underwriters exercised their option in full on October 12, 2026, and the sale of the Option Shares closed on October 13, 2026. In total, the Company sold an aggregate of 4,735,295 shares of its common stock in the offering, resulting in net proceeds of approximately $378.0 million after deducting approximately $24.5 million of underwriting discounts and other offering costs.

9. Stock-based Compensation

2016 Equity Incentive Plan

The Company's 2016 Equity Incentive Plan (the “2016 Plan”) became effective in April 2016 and serves as the successor to the Company’s 2015 Equity Incentive Plan. Under the 2016 Plan, the Company may grant stock options, stock appreciation rights, restricted stock awards, restricted stock units, performance awards, and stock bonuses. The 2016 Plan, as amended, provides for an automatic increase in the number of shares reserved for issuance thereunder on January 1 of each year for the remaining term of the plan equal to (a)5.0% of the number of issued and outstanding shares of common stock (including such shares issuable pursuant to the exercise or conversion, as applicable, of any outstanding pre-funded warrants and nonvoting convertible preferred stock) on December 31 of the immediately preceding year, or (b) a lesser amount as approved by the board each year (the “Evergreen Provision”). As a result of the Evergreen Provision, on January 1, 2026 and 2025, an additional 4,711,544 and 3,814,905 shares, respectively, became available for issuance under the 2016 Plan.

As of September 30, 2026, the 2016 Plan had 14,999,732 shares available for future issuance, of which 6,822,482 shares were subject to outstanding option awards and restricted unit awards.

2018 Equity Inducement Plan

The 2018 Equity Inducement Plan (“2018 Plan”) became effective in February 2018.

During the second quarter of 2025, the Company amended the 2018 Plan to increase the number of shares of common stock reserved for issuance by 750,000. After this amendment and as of September 30, 2026, the 2018 Plan had 6,164,834 shares available for future issuance, of which 5,735,274 shares were subject to outstanding option awards and restricted unit awards.

Service-based awards granted under the 2018 Plan and 2016 Plan generally vest over four years and expire afterten years, although awards have been granted with vesting terms less than four years. Under the

2016 Plan and 2018 Plan, the Company may grant stock-based awards with service conditions, performance conditions, and market conditions.

The following table summarizes the Company’s stock awards granted under all equity incentive and inducement plans for each of the periods indicated:

2016 Employee Stock Purchase Plan

Under the Company’s Amended and Restated 2016 Employee Stock Purchase Plan (“2016 ESPP”), the Company issued and sold 19,967 shares of the Company’s common stock during the nine months ended September 30, 2026, resulting in aggregate cash proceeds of $0.5 million. There were no shares issued or sold under the ESPP during the three months ended September 30, 2026.

The Company issued and sold 17,298 and 34,175 shares during the three and nine months ended September 30, 2025, respectively, resulting in aggregate cash proceeds of $0.2 million and $0.6 million, respectively.

Stock-based Compensation Expense

Total stock-based compensation expense recognized from the Company’s equity incentive plans, 2018 Plan and 2016 ESPP during the periods presented was as follows (in thousands):

The following table summarizes the weighted-average Black-Scholes option pricing model assumptions used to estimate the fair value of stock options granted under the Company's equity incentive plans, and the shares purchased under the 2016 ESPP during the periods presented:

10. Sale of Pegzilarginase to Immedica

On July 27, 2023, the Company announced that it had entered into an agreement to sell the global rights to pegzilarginase to Immedica Pharma AB (“Immedica”) for $15.0 million in upfront cash proceeds and up to $100.0 million in contingent milestone payments.

The milestone payments are contingent on formal reimbursement decisions by national authorities in key European markets and pegzilarginase approval by the U.S. Food and Drug Administration (“FDA”), among other events. In the three and nine months ended September 30, 2026, the Company recognized a gain ofnil and $70.0 million, respectively, within Gain on Sale of in-process research and development, for achieving certain milestones. As of September 30, 2026 and December 31, 2025, $3.0 million remains outstanding and due to the Company from a previously achieved milestone, which is reflected in Prepaid expenses and other current assets.

Milestone payments received by the Company by July 3, 2026, net of allowable expenses and adjustments, will be distributed to CVR holders pursuant to the CVR agreement resulting from the Asset Acquisition and will reduce the CVR liability.

11. Segment Reporting

The Company operates under a single operating and reportable segment, which is the development of biopharmaceutical products for the treatment of patients with immune-mediated diseases. The Company's Chief Operating Decision Maker (“CODM”) is the Company's Chief Executive Officer. The CODM uses consolidated Net loss as the measure of segment profit or loss and uses consolidated Total Assets as reported on the balance sheet as the measure of segment assets. The CODM compares Net loss against budgeted and/or forecasted amounts to track the Company's financial performance against expectations and to inform, along with development timelines and scientific and commercial considerations, their decisions regarding resource allocations to fund the Company's development of its pipeline.

The following table sets forth the significant expenses provided to the CODM on a regular basis (in thousands):

(1)Includes related party expenses of $0.3 million for the three months ended September 30, 2026 and 2025, and $0.8 million for thenine months ended September 30, 2026 and 2025.

(2) Includes non-clinical study, clinical trial, and manufacturing expenses.

(3) Includes related party expenses of $0.1 million and $7.0 million for the three months ended September 30, 2026 and 2025, respectively. Includes related party expenses of $3.2 million and $9.6 million for the nine months ended September 30, 2026 and 2025, respectively.

(4) Includes general and administrative expenses — such as audit, legal, and other professional fees — interest income, and other expense, net.

(5)Includes gains of $70.0 million and $10.0 million for the nine months ended September 30, 2026 and 2025, respectively, related to milestone payments earned in connection with the 2023 sale of the global rights to the legacy assets, pegzilarginase, to Immedica. There wereno related gains for the three months ended September 30, 2026 and 2025.

(6)Includes a $0.9 million increase and a $40.4 million decrease in the fair value of the CVR liability for the three months ended September 30, 2026 and 2025, respectively. Includes a $35.8 million increase and a $42.2 million decrease in the fair value of the CVR liability for the nine months ended September 30, 2026 and 2025, respectively.

12. Net Loss Per Share

The Company computes net loss per share of common stock, Series A Preferred Stock, and Series B Preferred Stock using the two-class method required for multiple classes of common stock and other participating securities.

The two-class method is an earnings (loss) allocation method under which earnings (loss) per share is calculated for each class of common stock. The Company has determined that the Series A Preferred Stock and Series B Preferred Stock do not have preferential rights when compared to the Company's common stock and therefore it must allocate losses to these other classes of common stock, as illustrated in the table below.

Basic and diluted net loss per share is computed by dividing the net loss by the weighted-average number of shares outstanding during the period, without consideration of potential dilutive securities. For periods in which the Company generated a net loss, the Company does not include potential shares of common stock in diluted net loss per share when the impact of these items is anti-dilutive. The Company has generated a net loss for all periods presented, therefore diluted net loss per share is the same as basic net loss per share since the inclusion of potential shares of common stock would be anti-dilutive.

The following table sets forth the computation of basic and diluted net loss per share of common stock, Series A Preferred Stock, and Series B Preferred Stock (in thousands, except share and per share amounts):

The following weighted-average equity instruments were excluded from the calculation of diluted net loss per share because their effect would have been anti-dilutive for the periods presented: