Quarterly Report for Quarter Ending September 30, 2026 (Form 10-Q)

Management's Discussion and Analysis of Financial Condition and Results of Operations

The following discussion and analysis should be read in conjunction with our unaudited condensed consolidated financial statements and accompanying notes included in this Quarterly Report on Form 10-Q (Quarterly Report), our audited consolidated financial statements and accompanying notes thereto for the fiscal year ended December 31, 2025 and the related Management's Discussion and Analysis of Financial Condition and Results of Operations, which are contained in our Annual Report on Form 10-K for the year ended December 31, 2025, filed with the Securities and Exchange Commission (SEC), on March 5, 2026 (2025 Annual Report).

This Quarterly Report contains "forward-looking statements" within the meaning of Section 27A of the Securities Act of 1933, as amended (the Securities Act), and Section 21E of the Securities Exchange Act of 1934, as amended (the Exchange Act). Such forward looking statements, which represent our intent, belief or current expectations, involve risks and uncertainties and other factors that could cause actual results and the timing of certain events to differ materially from future results expressed or implied by such forward-looking statements. In some cases, you can identify forward-looking statements by terms such as "may," "will," "expect," "anticipate," "estimate," "intend," "plan," "predict," "potential," "believe," "should" and similar expressions. Factors that could cause or contribute to differences in results include, but are not limited to those set forth under "Risk Factors" under Part II, Item 1A, and elsewhere in this Quarterly Report. Except as required by law, we undertake no obligation to update these forward-looking statements to reflect events or circumstances after the date of this Quarterly Report or to reflect actual outcomes.

Overview

We are a clinical stage biotechnology company leveraging evolutionary intelligence to translate tRNA synthetase biology into new therapies for fibrosis and inflammation. tRNA synthetases are ancient, essential proteins that have evolved novel domains that regulate diverse pathways extracellularly in humans. Our discovery platform is focused on unlocking hidden therapeutic intervention points by uncovering signaling pathways driven by our proprietary library of domains derived from all 20 tRNA synthetases.

Efzofitimod

Our lead therapeutic candidate is efzofitimod, a novel biologic immunomodulator in clinical development for the treatment of interstitial lung disease (ILD), a group of immune-mediated disorders that can cause inflammation and fibrosis, or scarring, of the lungs. Efzofitimod is a tRNA synthetase derived therapy that selectively modulates activated myeloid cells through neuropilin-2 (NRP2) to resolve aberrant inflammation without immune suppression and potentially prevent the progression of fibrosis. ILDs are predominantly immune-mediated disorders that are characterized by chronic inflammation, which can lead to progressive fibrosis of the lung. There are limited treatment options for ILD and there remains a high unmet medical need. Pulmonary sarcoidosis and systemic sclerosis (SSc, also known as scleroderma)-associated ILD (SSc-ILD) are two major forms of ILD.

Pulmonary Sarcoidosis

In September 2025, we announced top-line data from a global Phase 3 randomized, double-blind, placebo-controlled clinical trial to evaluate the efficacy and safety of efzofitimod in patients with pulmonary sarcoidosis (the EFZO-FIT study). The EFZO-FIT study was a 52-week study in 268 patients with pulmonary sarcoidosis consisting of three parallel cohorts randomized equally to either 3.0 mg/kg or 5.0 mg/kg of efzofitimod or placebo dosed intravenously once every four weeks for a total of 12 doses, with a 4-week safety follow-up. The study design incorporated a protocol guided steroid taper in the first 12 weeks of the study, followed by continued taper or rescue until week 48. The study did not meet its primary endpoint of change from baseline in mean daily oral corticosteroid (OCS) dose at week 48. The change from baseline in mean daily OCS dose reduced to an average of 2.79 mg for 5.0 mg/kg efzofitimod vs. 3.52 mg for placebo (p=0.3313). The study's statistical analysis plan was designed on a hierarchical assessment basis, as such, since the primary endpoint was not met, all subsequent statistical testing is reported as nominal findings. The study demonstrated a clinically meaningful improvement in the King's Sarcoidosis Questionnaire (KSQ)-Lung score at week 48 for 5.0 mg/kg efzofitimod compared to placebo (p=0.0479), with a responder analysis of patients who achieved complete steroid withdrawal at week 48 with an improved KSQ-Lung score also showing improvement in patients treated with 5.0 mg/kg efzofitimod compared to placebo (p=0.0196). Lung function as measured by forced vital capacity (FVC) at week 48 was maintained in all groups. Efzofitimod was generally well-tolerated at both the 3.0 mg/kg and 5.0 mg/kg doses, consistent with previously observed safety profile in all trials conducted to date. At the European Respiratory Society (ERS) Congress in late September 2025, we announced additional findings from the EFZO-FIT study, including analyses of additional pre-specified outcomes that demonstrated clinical improvements in mean change from baseline in the Fatigue Assessment (FAS) Total Score (p=0.0226) and KSQ-General Health score (p=0.0197) in patients treated with 5.0 mg/kg efzofitimod versus placebo. Treatment with efzofitimod was also associated with a trend toward a greater proportion of patients achieving steroid-free status for at least six months. Based on the trial findings, which we believe indicate drug activity for efzofitimod as evidenced by improvements across multiple clinically relevant efficacy endpoints, we held a Type C meeting with the FDA in mid-April 2026 to review the results of the EFZO-FIT study and determine the path forward for efzofitimod in pulmonary sarcoidosis. In May 2026, we received the official meeting minutes from the FDA.

Based on feedback from the FDA, we planned to continue the development of efzofitimod in pulmonary sarcoidosis in a proposed Phase 3 study in patients with chronic, symptomatic pulmonary sarcoidosis with restrictive lung disease utilizing FVC as the primary endpoint of the study and the KSQ-Lung score as the key secondary endpoint (the Proposed Phase 3 Study). We chose these endpoints based on the FDA's indication that FVC and KSQ-Lung are direct measures of how patients suffering from pulmonary sarcoidosis function and feel, and we concluded FVC to be a more appropriate primary endpoint at this time pending further content validation work for KSQ-Lung as recommended by the FDA. We determined the patient population for the Proposed Phase 3 Study, those with restrictive lung disease, based on data from the EFZO-FIT study which included 44 patients with restrictive lung disease (defined as FVC percent predicted ≤ 80%) and showed a difference of 124 ml in change from baseline in FVC between restrictive patients treated with 5.0 mg/kg efzofitimod and placebo.

In September 2026, we announced that we had reached alignment with the FDA on the Proposed Phase 3 Study protocol, and that we expected to initiate study-related activities in the fourth quarter of 2026. We are prioritizing strategic partnerships to further advance the Proposed Phase 3 Study beyond the completion of these study-related activities.

The Proposed Phase 3 Study would be a global, randomized, double-blind, placebo-controlled study to evaluate the efficacy and safety of efzofitimod in patients with moderate to severe pulmonary sarcoidosis. The Proposed Phase 3 Study would be a 54-week study and would consist of two parallel cohorts randomized equally to either 5.0 mg/kg efzofitimod or placebo dosed intravenously once every 3 weeks for a total of 17 doses. The Proposed Phase 3 Study would be intended to enroll up to approximately 372 patients with symptomatic pulmonary sarcoidosis with restrictive lung disease receiving a stable dose of ≤ 5.0 mg daily oral corticosteroid and/or a background immunosuppressant. All background treatment would remain stable throughout the duration of the Proposed Phase 3 Study. The primary endpoint of the Proposed Phase 3 Study would be changed from baseline in FVC at week 48 and the key secondary endpoint would be changed from baseline in the KSQ-Lung score at week 48. We expect the Proposed Phase 3 Study will include additional risk mitigation strategies, enhanced safety surveillance for potential development of anti-synthetase syndrome and a data safety monitoring committee based on the FDA's acknowledgement of the reasonableness of the increased dosing regimen from a clinical pharmacology perspective, subject to inclusion of adequate safety monitoring and risk mitigation procedures.

SSc-ILD

Our Phase 2 proof-of-concept clinical trial of efzofitimod (the EFZO-CONNECT study) is a randomized, double-blind placebo-controlled proof-of-concept study to evaluate the efficacy, safety and tolerability of efzofitimod in patients with SSc-ILD. This is a 28-week study with three parallel cohorts randomized 2:2:1 to either 270 mg or 450 mg of efzofitimod or placebo dosed intravenously monthly for a total of six doses. The study intended to enroll up to 25 patients at multiple centers in the United States. The objective of the study is to evaluate the efficacy of multiple doses of IV efzofitimod on pulmonary, cutaneous (limited or diffuse) and systemic manifestations in patients with SSc-ILD. The primary endpoint is reduction in FVC. Secondary endpoints include certain measures regarding safety and tolerability. In July 2024, we amended the study to add an open-label extension (OLE) to patients. Patients who complete the study and wish to receive ongoing treatment with efzofitimod are eligible to participate in the 24-week OLE. In June 2025, we announced interim data from the study showing three out of four efzofitimod-treated diffuse SSc-ILD patients showed clinically important improvement based on the modified Rodnan Skin Score (mRSS) assessment at 12 weeks and that efzofitimod was generally well-tolerated at all doses. We have completed enrollment of the study with 23 patients. Full study results are anticipated in the second quarter of 2027.

Discovery Platform

In parallel with our clinical development of efzofitimod, we have been advancing our discovery pipeline of tRNA synthetases and NRP2 antibodies.

tRNA Synthetase Candidates

Using efzofitimod as a model, we have developed a process to advance novel tRNA synthetase domains from a concept to therapeutic candidate. This process leverages our early discovery work as well as current scientific understanding of tRNA synthetase evolution, protein structure, gene splicing and tissue-specific regulation to identify potentially active protein domains. Screening approaches are employed to identify target cells and extracellular receptors for these tRNA synthetase-derived proteins. These cellular systems can then be used in mechanism-of-action studies to elucidate the role these proteins play in cellular responses and their potential therapeutic utility. We are working to identify new tRNA synthetase based drug candidates through our internal discovery efforts and external collaboration efforts. Utilizing our novel approach, we have identified target receptors for domains of certain additional tRNA synthetases, gaining insights into their potential biological activity in immunology and fibrosis. These fragments form the basis of our additional pipeline candidates. We plan to further elucidate the therapeutic potential of these candidates through mechanistic investigations, including nonclinical studies.

ATYR0101

ATYR0101 is a fusion protein derived from a domain of aspartyl-tRNA synthetase (DARS) that is engineered with a human Fc region to extend its serum half-life. The molecule possesses a unique mechanism of action focused on the selective elimination of activated myofibroblasts, which are the primary cellular drivers of pathological extracellular matrix (ECM) deposition in fibrotic diseases. ATYR0101 specifically targets Latent TGF-β Binding Protein-1 (LTBP-1) within the ECM, binding to a region that encompasses the fibrillin-1 binding domain at the C-terminus. LTBP-1 serves a dual role in matrix architecture by organizing structural proteins and modulating the signaling of Transforming Growth Factor-beta (TGF-β) through a complex mechanosensory apparatus. Early data suggest ATYR0101 exerts its antifibrotic effects by inducing apoptosis of myofibroblasts in a TGFβ dependent manner. We believe ATYR0101 may have broad therapeutic applications in multiple fibrotic diseases, such as pulmonary fibrosis, SSc, liver fibrosis and kidney fibrosis. In October 2026, we announced a publication demonstrating the anti-fibrotic effects of ATYR0101 in the Journal of Biological Chemistry. We have initiated IND-enabling activities for ATYR0101 and expect to advance ATYR0101 into a clinical trial in 2027.

NRP2 antibodies

ATYR2810

ATYR2810 is a fully humanized monoclonal antibody that is designed to specifically and functionally block the interaction between NRP2 and one of its primary ligands, vascular endothelial growth factor (VEGF). NRP2 is a pleiotropic cell surface receptor that is highly expressed on certain tumors and increased NRP2 expression is associated with worse outcomes in many cancers, such as overall survival, metastasis and resistance to targeted therapies. The role of NRP2 and VEGF signaling in the tumor microenvironment and its importance in the progression of certain aggressive cancers is becoming increasingly validated. In October 2026, we announced that we entered into a research collaboration with Albert Einstein College of Medicine to further the development and testing of ATYR2810. The collaboration will be led by Bang H. Hoang, M.D., Arnold and Madaleine Penner, Professor and Co-Director of Orthopaedic Oncology in the Department of Orthopaedic Surgery at Montefiore Einstein. Dr. Hoang's research focuses on the pathophysiology and molecular mechanisms of bone and soft tissue cancer, including evaluating the role of NRP2 in pediatric bone cancers such as osteosarcoma. ATYR2810 has demonstrated anti-tumor effects in multiple nonclinical models, including non-small cell lung cancer, triple-negative breast cancer, renal cell carcinoma and glioblastoma. These findings have been presented at scientific conferences, including the American Academy of Cancer Research, and published in a landmark publication in Science Translational Medicine.

Corporate Restructuring and Program Prioritization

In August 2026, our board of directors approved the implementation of a corporate restructuring and program prioritization plan (the Restructuring Plan) to streamline our operations and conserve capital. In connection with the Restructuring Plan, we reduced our total workforce by approximately 60% to 20 full-time employees. We recorded charges of approximately $4.6 million for employee severance, employee health benefit obligations and other related termination benefits. As of September 30, 2026, approximately $2.9 million of these amounts remain to be paid through September 2027. In addition, we recorded approximately $1.8 million in non-cash stock-based compensation charges related to the acceleration of vesting of outstanding equity awards in accordance with our Executive Severance and Change in Control Policy as well as for modifications to certain stock option awards to extend the post-termination exercise periods, and we recorded approximately $1.5 million in non-cash impairment charges of certain of our long-lived assets, including approximately $0.9 million in non-cash impairment of our operating lease ROU and approximately $0.6 million related to our property and equipment.

Liquidity and Capital Resources

We have incurred losses and negative cash flows from operations since our inception. As of September 30, 2026, we had an accumulated deficit of $645.5 million, and we expect to continue to incur net losses for the foreseeable future. As of September 30, 2026, we had cash, cash equivalents, restricted cash and available-for-sale investments of $50.3 million. We believe that our current cash, cash equivalents, restricted cash and available-for-sale investments, will be sufficient to meet our material cash requirements from known contractual and other obligations for a period of at least one year from the date of this Quarterly Report. In addition to the factors discussed under "Material Cash Requirements," our ability to fund our longer-term operating needs will depend on our ability to raise additional funding through equity or debt offerings, grant funding, collaborations, strategic partnerships and/or licensing arrangements, and other factors, including those discussed in Part II, Item 1A. "Risk Factors-Risks related to our financial condition and need for additional capital-We will need to raise additional capital or enter into strategic partnering relationships to fund our operations."

Sources of Cash

From our inception through September 30, 2026, we have financed our operations primarily through the sale of equity securities and convertible debt, venture debt, term loans and through license and collaboration agreement revenues. In recent years, we have relied primarily on our "at-the-market" offering program (the Jefferies ATM Offering Program) implemented through our Open Market Sale

AgreementSM with Jefferies LLC (Jefferies) for financing our activities. Given ongoing volatility in capital markets generally, the price of our common stock has fluctuated materially since the start of 2025 and, since the announcement of top-line data from the EFZO-FIT study particularly, we have experienced a material decline in our stock price. If markets remain volatile or our stock price continues to remain depressed, this may negatively affect our ability to generate cash from financing activities in future periods, including negatively affecting our ability to generate sufficient funds through our Jefferies ATM Offering Program.

At-the-Market Offering Program

In April 2022, we entered into an Open Market Sale AgreementSM with Jefferies implementing the Jefferies ATM Offering Program. In December 2024, we amended the Jefferies ATM Offering Program. Under the Jefferies ATM Offering Program, we may offer and sell, from time to time and at our option, up to an aggregate of $215.0 million of shares of our common stock (inclusive of $65.0 million of sales made prior to the amendment) through Jefferies, acting as sales agent. Jefferies is entitled to a fixed commission rate of up to 3.0% of the gross sales proceeds of shares sold under the Jefferies ATM Offering Program. During the year ended December 31, 2025, we sold an aggregate of 347,181 shares of common stock at a weighted-average price of $197.52 per share for net proceeds of approximately $66.4 million under the Jefferies ATM Offering Program. During the nine months ended September 30, 2026, we sold an aggregate of 59,513 shares of common stock at a weighted-average price of $16.80 per share for net proceeds of approximately $0.9 million under the Jefferies ATM Offering Program.

Cash Flows

The following table sets forth a summary of the net cash flow activity for each of the periods indicated (in thousands):

Operating activities. Net cash used in operating activities for the nine months ended September 30, 2026 and 2025 was $31.4 million and $49.8 million, respectively. The net cash used during the nine months ended September 30, 2026 was primarily attributable to discovery costs for our nonclinical product candidates and for efzofitimod development, which includes certain close-out costs relating to the EFZO-FIT study as well as ongoing costs for the EFZO-CONNECT study. The net cash used during the nine months ended September 30, 2025 was primarily for efzofitimod development and pre-commercialization activities. We expect cash used in operating activities will decrease in the near term in conjunction with the implementation of our Restructuring Plan as well as our prioritization of strategic partnerships to further advance the Proposed Phase 3 Study beyond the initial study-related activities.

Investing activities. Net cash provided by (used in) investing activities for the nine months ended September 30, 2026 and 2025 was $32.5 million and $(21.5) million, respectively. The fluctuation in net cash provided by or used in investing activities resulted primarily from the timing differences in investment purchases, sales and maturities, and the fluctuation of our portfolio mix between cash equivalents and investment holdings. The average term to maturity in our investment portfolio is less than one year.

Financing activities. Net cash provided by financing activities for the nine months ended September 30, 2026 and 2025 was $0.5 million and $66.1 million, respectively. Net cash provided by financing activities for the nine months ended September 30, 2026 primarily consisted of $0.9 million in proceeds from the issuance of common stock through the Jefferies ATM Offering Program, net of offering costs, offset by $0.4 million principal payments on our financing lease agreement. Net cash provided by financing activities for the nine months ended September 30, 2025 primarily consisted of $66.4 million in proceeds from the issuance of common stock through the Jefferies ATM Offering Program, net of offering costs.

Material Cash Requirements

To date, we have not generated any revenues from product sales. Our expenses may increase in connection with the potential advancement of our product candidates in clinical development, manufacturing, and regulatory activities. In addition, if we obtain marketing approval for any of our product candidates, we expect to incur significant commercialization expenses related to product sales, marketing, manufacturing and distribution. We currently have minimal sales and marketing capabilities and would need to expand our organization to support these activities. Accordingly, we will need to obtain substantial additional funding in connection with our continuing operations. Our forecast of the period of time through which our financial resources will be adequate to support our operations is a forward-looking statement that involves risks and uncertainties, and actual results could vary materially.

Our future capital requirements are difficult to forecast and will depend on many factors. Refer to Part II, Item 1A, "Risk Factors - Risks related to our financial condition and need for additional capital-We will need to raise additional capital or enter into strategic partnering relationships to fund our operations." for a discussion of these factors.

Until such time, if ever, as we can generate substantial product revenues, we expect to finance our cash needs through a combination of equity or debt offerings, grant funding, collaborations, strategic partnerships and/or licensing arrangements. To the extent we raise additional capital through the sale of equity, the ownership interest of our stockholders will be diluted, and the terms of these securities may include liquidation or other preferences that adversely affect the rights of our common stockholders. If we raise additional funds through collaborations, strategic partnerships or licensing arrangements with third parties, we may have to relinquish valuable rights to our product candidates, our other technologies, future revenue streams or research programs or grant licenses on terms that may not be favorable to us. The incurrence of additional indebtedness would increase our fixed payment obligations and may require us to agree to certain restrictive covenants, such as limitations on our ability to incur additional debt, limitations on our ability to acquire, sell or license intellectual property rights and other operating restrictions that could adversely impact our ability to conduct our business. We may be unable to raise additional funds on acceptable terms or at all. If the equity and credit markets deteriorate, it may make any necessary debt or equity financing more difficult, more costly and more dilutive. If we are unable to raise additional funds, we may be required to delay, limit, reduce or terminate our product development or future commercialization efforts or grant rights to develop and market our product candidates even if we would otherwise prefer to develop and market such product candidates ourselves.

As of September 30, 2026, our material cash requirements from known contractual and other obligations consisted primarily of (i) an operating lease for our corporate headquarters and laboratory space, and (ii) our master financing lease agreement for various research and development and informational technology equipment.

Corporate Headquarters Facility Lease

In May 2022, we entered into a non-cancelable facility lease that is subject to base lease payments that started at $5.75 per square foot of rentable area per month for the first 12 months of the lease and which escalate 3.0% annually over the term of the lease, and additional charges for common area maintenance and other costs. The term of the lease (the Lease Term) commenced on March 20, 2023 (the Lease Commencement Date) and will continue for 124 months from the Lease Commencement Date. We also have one option to extend the Lease Term for five years. In April 2024, we entered into a lease amendment for additional common area amenities, effective as of June 2023. The amendment increased the total rentable square feet from 23,696 rentable square feet to 24,866 rentable square feet. We provided a $0.7 million security deposit in the form of a letter of credit which is included in restricted cash as of September 30, 2026.

Financing Lease

In April 2022, we entered into a master financing lease agreement. Under this master agreement, we entered into various financing lease agreements from July 2022 through November 2023 to lease various research and development and information technology equipment over a 48-month term. Financing lease liabilities total $0.4 million as of September 30, 2026. Additionally, as of September 30, 2026, we have $0.8 million in cash collateral for the financing lease, and this amount is included in restricted cash.

We did not have any off-balance sheet arrangements as of September 30, 2026.

Financial Operations Overview

Organization and Business; Principles of Consolidation

We conduct substantially all of our activities through aTyr Pharma, Inc., a Delaware corporation, at our facility in San Diego, California. aTyr Pharma, Inc. was incorporated in the State of Delaware in September 2005. The unaudited condensed consolidated financial statements in this Quarterly Report include our accounts and our 98% majority-owned subsidiary in Hong Kong, Pangu BioPharma, as of September 30, 2026. All intercompany transactions and balances are eliminated in consolidation.

In August 2026, our board of directors approved the implementation of the Restructuring Plan to streamline our operations and conserve capital. In connection with the Restructuring Plan, we reduced our total workforce by approximately 60% to 20 full-time employees. We recorded charges of approximately $4.6 million for employee severance, employee health benefit obligations and other related termination benefits. As of September 30, 2026, approximately $2.9 million of these amounts remain to be paid through September 2027. In addition, we recorded approximately $1.8 million in non-cash stock-based compensation charges related to the acceleration of vesting of outstanding equity awards in accordance with our Executive Severance and Change in Control Policy as well as for modifications to certain stock option awards to extend the post-termination exercise periods, and we recorded approximately $1.5 million in non-cash impairment charges of certain of our long-lived assets, including approximately $0.9 million in non-cash impairment of our operating lease ROU and approximately $0.6 million related to our property and equipment.

Research and Development Expenses

To date, our research and development expenses have been related primarily to the development of, and clinical trials for, our product candidates, and to research efforts targeting the potential therapeutic application of other tRNA synthetase-based immunomodulators and efforts related to NRP2 biology. These expenses consist primarily of:

Product candidates in later stages of clinical development, such as efzofitimod, generally have higher development costs than those in earlier stages of clinical development, primarily due to the increased size and duration of later-stage clinical trials. We primarily outsource our clinical trial administration to CROs, and we outsource our manufacturing of clinical trial materials to CDMOs. These outsourced expenses are typically substantially higher than the expenses we incur on candidates in earlier stages of development. As such, we separately track and report on the majority of our research and development expenses associated with the advancement of efzofitimod. For our candidates in nonclinical development, the nature of the research and development expenses incurred to advance these candidates is primarily internal personnel, laboratory supply expenses and IND-enabling activities. We do not fully track or allocate these internal expenses between nonclinical product candidates because the expenses can often be shared between candidates. We also incur other shared expenses to support our research and development efforts such as facilities expenses, and these expenses are not allocated to efzofitimod or our nonclinical product candidates. Additionally, non-cash research and development expenses such as depreciation and stock-based compensation are not tracked or allocated between product candidates and are shared among all product candidates.

We anticipate that our research and development expenses will decrease in the near term in conjunction with the implementation of our Restructuring Plan as well as our prioritization of strategic partnerships to further advance the Proposed Phase 3 Study beyond the initial study-related activities. At this time, due to the inherently unpredictable nature of nonclinical and clinical development and given the early stage of our programs, we are unable to estimate with any certainty the costs we will incur or the timelines we will require in the continued development of our product candidates. Clinical and nonclinical development timelines, the probability of success and development costs can differ materially from expectations. We anticipate that we will make determinations as to which product candidates to pursue and how much funding to direct to each product candidate on an ongoing basis in response to the results of ongoing and future nonclinical studies and clinical trials, regulatory developments and our ongoing assessments as to each product candidate's commercial potential. In addition, we cannot forecast which programs or product candidates may be subject to future collaborations, when such arrangements will be secured, if at all, and to what degree such arrangements would affect our development plans and capital requirements.

General and Administrative Expenses

General and administrative expenses consist primarily of salaries and related costs for employees in executive, finance and administration, pre-commercialization, corporate development and administrative support functions, including stock-based compensation expenses and benefits. Other significant general and administrative expenses include accounting, legal services, expenses associated with applying for and maintaining patents, cost of insurance, cost of various consultants, occupancy costs, information systems costs and depreciation.

Critical Accounting Policies and Significant Judgments and Estimates

Our management's discussion and analysis of financial condition and results of operations is based on our unaudited condensed consolidated financial statements, which have been prepared in accordance with accounting principles generally accepted in the United States. The preparation of these unaudited condensed consolidated financial statements requires us to make estimates and assumptions that affect the reported amounts of assets and liabilities and the disclosure of contingent assets and liabilities as of the date of the unaudited condensed consolidated financial statements, as well as the reported expenses during the reporting periods. We monitor and analyze these items for changes in facts and circumstances, and material changes in these estimates could occur in the future. We base our estimates on our historical experience and on various other factors we believe to be reasonable under the circumstances, the results

of which form the basis for making judgments about the carrying value of assets and liabilities that are not readily apparent from other sources. Changes in estimates are reflected in reported results for the period in which they become known. Actual results may differ materially from these estimates under different assumptions or conditions.

We discuss our accounting policies and assumptions that involve a higher degree of judgment and complexity within Note 2 to our audited consolidated financial statements in our 2025 Annual Report. There have been no material changes to our critical accounting policies and estimates as disclosed in our 2025 Annual Report.

Results of Operations

Comparison of the Three Months Ended September 30, 2026 and 2025

The following table summarizes our results of operations for the three months ended September 30, 2026 and 2025 (in thousands):

License and collaboration agreement revenues. Revenues for the three months ended September 30, 2025 consisted of drug product material sold to Kyorin Pharmaceutical Co. Ltd. (Kyorin) to support analytical method validation in Japan.

Research and development expenses. Research and development expenses were $10.4 million and $22.1 million for the three months ended September 30, 2026 and 2025, respectively. The decrease of $11.7 million was primarily driven by a reduction in efzofitimod expenses for the EFZO-FIT study since it was completed in September 2025 as well as decreased manufacturing costs due to the timing of certain manufacturing activities being completed. Nonclinical development and other shared research and development expenses increased by $4.1 million, and this increase was primarily attributable to increased discovery costs for our nonclinical product candidates, including IND-enabling activities for our ATYR0101 nonclinical candidate, as well as $1.7 million of employee severance and other termination benefits related to the Restructuring Plan. Non-cash expenses increased by $1.4 million, and this increase was primarily attributable to impairment charges recorded associated with our long-lived assets during the three months ended September 30, 2026 as well as $0.3 million of non-cash stock-based compensation related to the Restructuring Plan. We anticipate that our research and development expenses will decrease in the near term in conjunction with the implementation of our Restructuring Plan as well as our prioritization of strategic partnerships to further advance the Proposed Phase 3 Study beyond the initial study-related activities.

General and administrative expenses. General and administrative expenses were $8.3 million and $4.8 million for the three months ended September 30, 2026 and 2025, respectively. The increase of $3.5 million was attributable to $2.9 million of employee severance and other termination benefits and $1.5 million of non-cash stock-based compensation related to the Restructuring Plan. The increase was offset by a decrease of $0.6 million pre-commercialization expenses incurred during the same period in the prior year ahead of the announcement of top-line data from the EFZO-FIT study. We anticipate that our general and administrative expenses will decrease in the near term in conjunction with the implementation of our Restructuring Plan.

Other income (expense), net. Other income (expense), net was $0.5 million and $1.0 million for the three months ended September 30, 2026 and 2025, respectively. The change was primarily a result of lower interest rates and lower interest earned on lower cash balances as compared to the same period in the prior year.

Comparison of the Nine Months Ended September 30, 2026 and 2025

The following table summarizes our results of operations for the nine months ended September 30, 2026 and 2025 (in thousands):

License and collaboration agreement revenues. Revenues for the nine months ended September 30, 2025 consisted of drug product material sold to Kyorin to support analytical method validation in Japan.

Research and development expenses. Research and development expenses were $24.5 million and $49.3 million for the nine months ended September 30, 2026 and 2025, respectively. The decrease of $24.8 million was primarily driven by a reduction in efzofitimod expenses for the EFZO-FIT study since it was completed in September 2025 as well as decreased manufacturing costs due to the timing of certain manufacturing activities being completed. Nonclinical development and other shared research and development expenses increased by $6.5 million, and this increase was primarily attributable to increased discovery costs for our nonclinical product candidates, including IND-enabling activities for our ATYR0101 nonclinical candidate, as well as $1.7 million of employee severance and other termination benefits related to the Restructuring Plan. Non-cash expenses increased by $1.3 million, and this increase was primarily attributable to impairment charges recorded associated with our long-lived assets during the nine months ended September 30, 2026, and $0.3 million of non-cash stock-based compensation related to the Restructuring Plan. We anticipate that our research and development expenses will decrease in the near term in conjunction with the implementation of our Restructuring Plan as well as our prioritization of strategic partnerships to further advance the Proposed Phase 3 Study beyond the initial study-related activities.

General and administrative expenses. General and administrative expenses were $16.6 million and $13.7 million for the nine months ended September 30, 2026 and 2025, respectively. The increase of $2.9 million was attributable to $2.9 million of employee severance and other termination benefits and $1.5 million of non-cash stock-based compensation related to the Restructuring Plan. The increase was offset by a decrease of $1.0 million pre-commercialization expenses incurred during the same period in the prior year ahead of the announcement of top-line data from the EFZO-FIT study. We anticipate that our general and administrative expenses will decrease in the near term in conjunction with the implementation of our Restructuring Plan.

Other income (expense), net. Other income (expense), net was $1.8 million and $2.7 million for the nine months ended September 30, 2026 and 2025, respectively. The change was primarily a result of lower interest rates and lower interest earned on lower cash balances as compared to the same period in the prior year.

Recent Accounting Pronouncements

For discussion of recently issued accounting pronouncements, refer to Part I, Item 1, Notes to Condensed Consolidated Financial Statements (Unaudited) - Note 1 - Recent Accounting Pronouncements of this Quarterly Report.