Financial Performance - Total revenues for Q3 2024 were $0, compared to $353,000 in Q3 2023, indicating a decrease in license and collaboration agreement revenues[12] - Consolidated net loss for Q3 2024 was $17.3 million, compared to a net loss of $11.3 million in Q3 2023[12] - General and administrative expenses for Q3 2024 were $3.3 million, compared to $2.6 million in Q3 2023[12] - Research and development expenses for Q3 2024 were $14.8 million, up from $10.3 million in Q3 2023, reflecting increased clinical trial costs[7] Cash and Investments - Cash and investments as of September 30, 2024, were $68.9 million, down from $101.7 million at the end of 2023[13] - Total assets as of September 30, 2024, were $91.6 million, down from $120.7 million at the end of 2023[13] - The company raised approximately $19.4 million in gross proceeds from an at-the-market offering after Q3 2024[7] Clinical Trials - Enrollment completed in the Phase 3 EFZO-FIT™ study with 268 patients, exceeding the target, and topline data expected in Q3 2025[5] - The Phase 2 EFZO-CONNECT™ study is ongoing, aiming to enroll up to 25 patients with interim data expected in Q2 2025[6] - The efzofitimod program showed statistically significant improvement in corticosteroid relapse rates, as published in the European Respiratory Journal[2]

Financial Position - The company has an accumulated deficit of $499.8 million as of June 30, 2024, and expects to continue incurring net losses for the foreseeable future[78]. - As of June 30, 2024, the company had cash, cash equivalents, restricted cash, and available-for-sale investments totaling $81.4 million, sufficient to meet material cash requirements for at least one year[78]. - Net cash used in operating activities for the six months ended June 30, 2024, was $42.8 million, compared to $12.6 million for the same period in 2023, primarily due to increased clinical study costs[83]. - Net cash provided by investing activities for the six months ended June 30, 2024, was $5.4 million, a significant improvement from $(42.3) million in 2023[84]. - Net cash provided by financing activities for the six months ended June 30, 2024, was $21.1 million, down from $57.5 million in 2023, mainly due to reduced proceeds from stock offerings[85]. - As of June 30, 2024, the company has $1.7 million in financing lease liabilities and $2.2 million in cash collateral for the financing lease[91]. Fundraising Activities - The company completed a public offering in February 2023, raising approximately $48.1 million from the sale of 23,125,000 shares at $2.25 per share[80]. - Under the Jefferies ATM Offering Program, the company sold 10,530,795 shares at an average price of $1.82 per share, generating net proceeds of approximately $18.4 million in 2023[81]. - Kyorin triggered a $10.0 million milestone payment for dosing the first patient in Japan in the EFZO-FIT study, recorded as revenue in 2022[82]. - Total milestone payments from the Kyorin Agreement to date amount to $20.0 million, with potential additional payments of up to $155.0 million upon achieving specific milestones[82]. Research and Development - The company initiated a global pivotal Phase 3 clinical trial (EFZO-FIT study) for efzofitimod, enrolling 268 patients, with topline data expected in Q3 2025[69]. - The EFZO-CONNECT study for efzofitimod in patients with systemic sclerosis-associated ILD is designed to enroll up to 25 patients, with interim data expected in Q2 2025[71]. - The company is developing additional tRNA synthetase candidates, including ATYR0101 and ATYR0750, targeting fibrosis and inflammation[75][76]. - The company expects research and development expenses to continue increasing, primarily for the clinical development of efzofitimod and other potential therapeutics[96]. - Research and development expenses increased to $14.0 million for the three months ended June 30, 2024, up from $9.8 million in 2023, representing a $4.1 million increase[100]. - Efzofitimod expenses accounted for $11.3 million in the three months ended June 30, 2024, compared to $6.8 million in 2023, reflecting a $4.5 million increase due to advancements in the EFZO-FIT study[100]. - Total research and development expenses for the six months ended June 30, 2024, were $27.3 million, an increase of $8.1 million from $19.2 million in 2023[103]. - Efzofitimod expenses for the six months ended June 30, 2024, were $22.3 million, up from $13.2 million in 2023, marking a $9.1 million increase[103]. Revenue and Expenses - The company has not generated any revenues from product sales to date and anticipates increased expenses related to ongoing clinical development and potential commercialization efforts[86]. - License and collaboration agreement revenues were $0.2 million for the six months ended June 30, 2024, with no revenues reported in the same period of the prior year[102]. - General and administrative expenses decreased to $3.3 million for the three months ended June 30, 2024, down from $3.7 million in 2023, a reduction of $0.4 million[101]. - General and administrative expenses for the six months ended June 30, 2024, were $6.8 million, a decrease of $0.3 million from $7.1 million in 2023[104]. - Other income, net for the six months ended June 30, 2024, was $2.2 million, compared to $2.1 million in 2023, showing a slight increase[105]. - Non-cash expenses related to research and development increased to $0.6 million for the three months ended June 30, 2024, from $0.5 million in 2023[101]. - Non-cash expenses for general and administrative purposes increased to $1.2 million for the six months ended June 30, 2024, from $1.0 million in 2023[104]. Market and Operational Considerations - The company continues to monitor macroeconomic uncertainties that may impact its operations and financial performance[77]. - The company has no sales or marketing capabilities and will need to expand its organization to support commercialization activities[86]. - The company has a lease agreement for approximately 24,866 rentable square feet with a base rent starting at $5.75 per square foot, subject to annual adjustments[90].

Exhibit 99.1 IMMEDIATE RELEASE Contact: Ashlee Dunston Director, Investor Relations and Public Affairs adunston@atyrpharma.com aTyr Pharma Announces Second Quarter 2024 Results and Provides Corporate Update Phase 3 EFZO-FIT™ study of efzofitimod in pulmonary sarcoidosis enrollment completed with 268 patients; topline data from this 52-week study expected in the third quarter of 2025. Ended the second quarter 2024 with $81.4 million in cash, cash equivalents, restricted cash and investments. SAN DIEGO – Augu ...

[PART I. FINANCIAL INFORMATION](index=4&type=section&id=PART%20I.%20FINANCIAL%20INFORMATION) [Item 1. Financial Statements](index=4&type=section&id=Item%201.%20Financial%20Statements) Presents unaudited condensed consolidated financial statements for Q1 2024, including balance sheets, statements of operations, and cash flows [Condensed Consolidated Balance Sheets](index=4&type=section&id=Condensed%20Consolidated%20Balance%20Sheets) Balance Sheet Highlights (in thousands) | Balance Sheet Highlights (in thousands) | March 31, 2024 (unaudited) | December 31, 2023 | | :--- | :--- | :--- | | Cash and cash equivalents | $6,808 | $22,544 | | Total current assets | $96,916 | $102,992 | | Total assets | $113,251 | $120,653 | | Total current liabilities | $15,979 | $16,416 | | Total stockholders' equity | $84,282 | $90,470 | - The company's cash and cash equivalents decreased significantly from **$22.5 million** at the end of 2023 to **$6.8 million** at the end of Q1 2024, reflecting cash used in operations[5](index=5&type=chunk) [Condensed Consolidated Statements of Operations](index=5&type=section&id=Condensed%20Consolidated%20Statements%20of%20Operations) Statement of Operations (in thousands) | Statement of Operations (in thousands) | Three Months Ended March 31, 2024 | Three Months Ended March 31, 2023 | | :--- | :--- | :--- | | Total revenues | $235 | $0 | | Research and development | $13,364 | $9,379 | | General and administrative | $3,507 | $3,408 | | Loss from operations | $(16,636) | $(12,787) | | Net loss attributable to aTyr Pharma | $(15,491) | $(11,951) | | Net loss per share, basic and diluted | $(0.23) | $(0.29) | - The net loss for Q1 2024 increased to **$15.5 million** from **$12.0 million** in Q1 2023, primarily driven by a significant rise in research and development expenses[6](index=6&type=chunk) [Condensed Consolidated Statements of Cash Flows](index=8&type=section&id=Condensed%20Consolidated%20Statements%20of%20Cash%20Flows) Cash Flow Summary (in thousands) | Cash Flow Summary (in thousands) | Three Months Ended March 31, 2024 | Three Months Ended March 31, 2023 | | :--- | :--- | :--- | | Net cash used in operating activities | $(22,380) | $(590) | | Net cash used in investing activities | $(1,356) | $(38,172) | | Net cash provided by financing activities | $7,730 | $49,496 | | Net change in cash, cash equivalents and restricted cash | $(16,006) | $10,734 | - Net cash used in operating activities increased substantially to **$22.4 million** in Q1 2024 from **$0.6 million** in Q1 2023. Net cash from financing activities decreased significantly, primarily due to a large follow-on public offering in Q1 2023 that was not repeated in Q1 2024[13](index=13&type=chunk)[14](index=14&type=chunk) [Notes to Condensed Consolidated Financial Statements](index=9&type=section&id=Notes%20to%20Condensed%20Consolidated%20Financial%20Statements) - The company believes its existing cash, cash equivalents, restricted cash, and available-for-sale investments of **$87.7 million** as of March 31, 2024, are sufficient to meet material cash requirements for **at least one year** from the filing date[20](index=20&type=chunk) - In Q1 2024, the company recognized **$0.2 million** in collaboration revenue from Kyorin for drug product material sold for the Japan portion of the EFZO-FIT study. The company is eligible for up to an additional **$155.0 million** in future milestones from this agreement[53](index=53&type=chunk)[51](index=51&type=chunk) - During Q1 2024, the company sold **5,045,518 shares** of common stock through its "at-the-market" (ATM) offering program, generating net proceeds of approximately **$8.6 million**[60](index=60&type=chunk) - Subsequent to the quarter end, from April 1 to April 30, 2024, the company sold an additional **656,907 shares** through its ATM program for net proceeds of **$1.1 million**[66](index=66&type=chunk) [Item 2. Management's Discussion and Analysis of Financial Condition and Results of Operations](index=23&type=section&id=Item%202.%20Management%27s%20Discussion%20and%20Analysis%20of%20Financial%20Condition%20and%20Results%20of%20Operations) Management discusses therapeutic development, focusing on efzofitimod's clinical trials, R&D expenses, liquidity, and capital requirements [Overview](index=23&type=section&id=Overview) - The lead therapeutic candidate, **efzofitimod**, is being evaluated in a global pivotal **Phase 3 trial (EFZO-FIT™ study)** for patients with pulmonary sarcoidosis. Enrollment is expected to be completed in the **second quarter of 2024**[70](index=70&type=chunk)[73](index=73&type=chunk) - A **Phase 2 proof-of-concept clinical trial (EFZO-CONNECT™ study)** is underway to evaluate **efzofitimod** in patients with systemic sclerosis-associated ILD (SSc-ILD)[75](index=75&type=chunk) - The company's discovery pipeline includes **ATYR0101** and **ATYR0750**, which are being investigated for their therapeutic potential in immunology and fibrosis[78](index=78&type=chunk)[79](index=79&type=chunk)[80](index=80&type=chunk) [Liquidity and Capital Resources](index=27&type=section&id=Liquidity%20and%20Capital%20Resources) - As of March 31, 2024, the company had cash, cash equivalents, restricted cash, and available-for-sale investments of **$87.7 million**, which is believed to be sufficient to fund operations for **at least one year**[82](index=82&type=chunk) - Net cash used in operating activities was **$22.4 million** for Q1 2024, a substantial increase from **$0.6 million** in Q1 2023. The increase was primarily due to higher costs for ongoing clinical trials and upfront payments for manufacturing efforts[87](index=87&type=chunk) - Financing activities in Q1 2024 provided **$7.7 million**, primarily from the ATM offering program. This is a significant decrease from Q1 2023, which included **$48.1 million** from an underwritten public offering[89](index=89&type=chunk)[84](index=84&type=chunk) [Results of Operations](index=35&type=section&id=Results%20of%20Operations) Operating Results (in thousands) | Operating Results (in thousands) | Three Months Ended March 31, 2024 | Three Months Ended March 31, 2023 | | :--- | :--- | :--- | | License and collaboration revenues | $235 | $0 | | Research and development expenses | $13,364 | $9,379 | | General and administrative expenses | $3,507 | $3,408 | - Research and development expenses increased by **$4.0 million** year-over-year, mainly due to a **$3.7 million** increase in clinical trial costs for the EFZO-FIT and EFZO-CONNECT studies and a **$0.8 million** increase in manufacturing costs in preparation for a possible Biologics License Application (BLA)[105](index=105&type=chunk) [Item 3. Quantitative and Qualitative Disclosures About Market Risk](index=35&type=section&id=Item%203.%20Quantitative%20and%20Qualitative%20Disclosures%20About%20Market%20Risk) This section is not applicable, as permitted for smaller reporting companies - As a smaller reporting company, aTyr Pharma is not required to provide quantitative and qualitative disclosures about market risk[108](index=108&type=chunk) [Item 4. Controls and Procedures](index=35&type=section&id=Item%204.%20Controls%20and%20Procedures) Management concluded disclosure controls and procedures were effective, with no material changes to internal controls over financial reporting - The company's management concluded that its disclosure controls and procedures were **effective** as of the end of the quarter[110](index=110&type=chunk) - **No changes** in internal control over financial reporting occurred during the quarter that have materially affected, or are reasonably likely to materially affect, the company's internal controls[111](index=111&type=chunk) [PART II. OTHER INFORMATION](index=36&type=section&id=PART%20II.%20OTHER%20INFORMATION) [Item 1. Legal Proceedings](index=36&type=section&id=Item%201.%20Legal%20Proceedings) The company is not currently a party to any material legal proceedings - As of the filing date, the company is not involved in any material legal proceedings[112](index=112&type=chunk) [Item 1A. Risk Factors](index=36&type=section&id=Item%201A.%20Risk%20Factors) This section outlines key risks including clinical trial delays, novel therapeutic challenges, capital needs, third-party reliance, and IP protection - The company faces **substantial risk** related to clinical development, including **potential delays** in its EFZO-FIT and EFZO-CONNECT trials and the **lack of an established FDA regulatory pathway** for pulmonary sarcoidosis, which could hinder approval[114](index=114&type=chunk)[117](index=117&type=chunk)[125](index=125&type=chunk) - A **critical financial risk** is the need to **raise additional capital** to fund operations. The company has a history of **significant losses** and anticipates they will continue for the foreseeable future[114](index=114&type=chunk)[169](index=169&type=chunk)[174](index=174&type=chunk) - The company is **heavily reliant on third parties**, including its **collaboration with Kyorin** for development in Japan and its **dependence on Contract Development and Manufacturing Organizations (CDMOs)** for producing its product candidates[114](index=114&type=chunk)[180](index=180&type=chunk)[187](index=187&type=chunk) - The company's product candidates are based on a **novel therapeutic approach (tRNA synthetase biology)**, which presents **unique challenges and uncertainties** in development, regulatory approval, and market acceptance[114](index=114&type=chunk)[136](index=136&type=chunk) [Item 2. Unregistered Sales of Equity Securities and Use of Proceeds](index=105&type=section&id=Item%202.%20Unregistered%20Sales%20of%20Equity%20Securities%20and%20Use%20of%20Proceeds) No unregistered sales of equity securities were reported during the period - There were **no unregistered sales** of equity securities in the reported quarter[312](index=312&type=chunk) [Item 3. Defaults Upon Senior Securities](index=105&type=section&id=Item%203.%20Defaults%20Upon%20Senior%20Securities) No defaults upon senior securities were reported - There were **no defaults** upon senior securities during the period[312](index=312&type=chunk) [Item 4. Mine Safety Disclosures](index=105&type=section&id=Item%204.%20Mine%20Safety%20Disclosures) This section is not applicable to the company's operations - Mine safety disclosures are not applicable to the company's operations[312](index=312&type=chunk) [Item 5. Other Information](index=105&type=section&id=Item%205.%20Other%20Information) No other information required to be disclosed was reported for the period - There was no other information to report for the period[312](index=312&type=chunk) [Item 6. Exhibits](index=105&type=section&id=Item%206.%20Exhibits) This section lists exhibits filed with the Form 10-Q, including corporate governance documents, material contracts, and SOX certifications - The exhibits include **certifications** from the Principal Executive Officer and Principal Financial Officer, as well as **interactive data files (XBRL)**[312](index=312&type=chunk)[313](index=313&type=chunk)

Drug Development and Clinical Trials - Efzofitimod is a first-in-class biologic immunomodulator in clinical development for interstitial lung disease (ILD) with orphan drug designations from the FDA for sarcoidosis and systemic sclerosis (SSc) [12] - The EFZO-FIT study, a pivotal Phase 3 trial for efzofitimod in pulmonary sarcoidosis, is currently enrolling up to 264 subjects and aims to complete enrollment by Q2 2024 [14][15] - The Phase 1b/2a clinical trial demonstrated consistent dose response for efzofitimod on key efficacy endpoints, including improvements in lung function and symptom measures compared to placebo [13] - The primary endpoint of the EFZO-FIT study is steroid reduction, with secondary endpoints including forced vital capacity (FVC) and quality of life assessments [14] - The EFZO-CONNECT study for efzofitimod in patients with SSc-ILD was initiated in Q3 2023, with the first patient dosed in October 2023 [17][22] - The ongoing Phase 3 clinical trial, EFZO-FIT, aims to enroll up to 264 patients with symptomatic pulmonary sarcoidosis, evaluating the efficacy and safety of IV efzofitimod at doses of 3.0 mg/kg and 5.0 mg/kg [43] - The Phase 1 clinical trial of efzofitimod in healthy volunteers indicated that the drug was well-tolerated at all dose levels tested, with no significant adverse events [57] - The Phase 1b/2a clinical trial for efzofitimod in pulmonary sarcoidosis demonstrated a 58% overall steroid reduction from baseline and a 22% relative reduction compared to placebo in the 5.0 mg/kg treatment group [51] - The EFZO-CONNECT study, targeting SSc-ILD, is a 28-week trial with a planned enrollment of 25 patients, with the first patient dosed in October 2023 [17] - The Phase 2 clinical trial for efzofitimod in COVID-19 patients showed that a single IV dose was generally safe and well-tolerated, with a signal of activity in the 3.0 mg/kg cohort [56] Financial and Market Considerations - The Kyorin Agreement has generated $20.0 million in upfront and milestone payments, with potential for an additional $155.0 million upon achieving certain milestones [18] - The global market opportunity for pulmonary sarcoidosis and SSc-ILD is estimated to be between $2-3 billion [72] - The company has incurred significant losses since inception and anticipates continued losses for the foreseeable future [10] - The market for ILD treatments remains underserved, presenting a high unmet medical need for effective therapies [12] - The company faces significant uncertainty regarding coverage and reimbursement from third-party payors, which may limit sales of approved products [125][132] - Third-party payors are increasingly scrutinizing pricing and cost-effectiveness, potentially impacting reimbursement rates for approved products [126][129] - The U.S. government and state legislatures are implementing cost containment programs that may reduce the profitability of drug products, including price controls and mandatory discounts [127] Regulatory and Compliance - The FDA requires extensive preclinical and clinical testing before any new biologic can be marketed, which involves significant time and financial resources [96] - A Biologics License Application (BLA) must include all relevant data from preclinical studies and clinical trials, and FDA approval is required before marketing [104] - The FDA may issue a Complete Response Letter (CRL) if the BLA is not ready for approval, outlining deficiencies that need to be addressed [108] - The FDA grants orphan drug designation for drugs treating rare diseases affecting fewer than 200,000 individuals in the U.S., providing financial incentives and exclusivity for seven years if approved first [117][118] - The company is subject to various federal and state healthcare laws, including the Anti-Kickback Statute and the False Claims Act, which could impact operations [136] - The company has implemented safeguards to discourage improper payments under the U.S. Foreign Corrupt Practices Act (FCPA) [135] Research and Development Strategy - The company is focused on advancing efzofitimod toward regulatory approval and exploring its applications in other ILDs [21][22] - The company has advanced two additional tRNA synthetase programs, ATYR0101 and ATYR0750, into preclinical development [23] - The company plans to further elucidate the therapeutic potential of efzofitimod through mechanistic investigations, including in vitro and in vivo preclinical studies [23] - The company plans to invest significant financial and management resources to develop the appropriate commercial infrastructure for its product candidates [75] - The company aims to expand its intellectual property estate by filing patent applications for new methods of treatment and therapeutics [83] Employee and Operational Insights - As of December 31, 2023, the company had 59 employees, with 56 being full-time, including 36 in research and development roles [137] - The company emphasizes the importance of attracting and retaining talented employees to execute its strategy effectively [138] - The company operates in a single accounting segment, indicating a focused business model [141] Drug Mechanism and Efficacy - Efzofitimod targets the NRP2 receptor, which is upregulated during differentiation and activation of myeloid cells, potentially providing a novel therapeutic approach for immune-mediated and fibrotic diseases [32] - Efzofitimod has shown significant reduction in lung inflammation and fibrosis, improving respiratory function parameters in multiple animal models of lung fibrosis [29] - Efzofitimod has been shown to reduce lung and skin fibrosis in an animal model of systemic sclerosis (SSc-ILD), indicating its potential as a therapeutic candidate for this condition [42] - The company has demonstrated that efzofitimod downregulates key inflammatory cytokines such as IL-6, TNF-α, and IFN-γ in both animal models and human clinical trials [29] - Efzofitimod is a novel immunomodulatory Fc fusion protein that selectively modulates NRP2 to downregulate immune responses in inflammatory diseases [24]

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended September 30, 2023 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission File Number: 001-37378 | --- | --- | --- | |-----------------------------------------------------------------------------------------|------ ...

[PART I. FINANCIAL INFORMATION](index=3&type=section&id=PART%20I.%20FINANCIAL%20INFORMATION) [Financial Statements](index=3&type=section&id=Item%201.%20Financial%20Statements) Unaudited H1 2023 financial statements show total assets at **$132.7 million**, a **$24.3 million** net loss, and **$57.5 million** from financing activities Condensed Consolidated Balance Sheet Highlights (in thousands) | Account | June 30, 2023 (unaudited) | December 31, 2022 | | :--- | :--- | :--- | | Cash and cash equivalents | $12,313 | $9,981 | | Available-for-sale investments | $96,268 | $56,165 | | **Total Assets** | **$132,747** | **$95,786** | | Total current liabilities | $12,368 | $13,862 | | **Total Liabilities** | **$26,695** | **$24,502** | | **Total Stockholders' Equity** | **$106,052** | **$71,284** | Condensed Consolidated Statements of Operations (in thousands, except per share data) | Metric | Q2 2023 | Q2 2022 | Six Months 2023 | Six Months 2022 | | :--- | :--- | :--- | :--- | :--- | | Research and development | $9,840 | $9,135 | $19,219 | $18,031 | | General and administrative | $3,718 | $3,449 | $7,126 | $6,931 | | **Loss from operations** | **($13,558)** | **($12,584)** | **($26,345)** | **($24,962)** | | **Consolidated net loss** | **($12,342)** | **($12,421)** | **($24,294)** | **($24,575)** | | **Net loss per share** | **($0.22)** | **($0.44)** | **($0.50)** | **($0.88)** | Condensed Consolidated Statements of Cash Flows (in thousands) | Activity | Six Months Ended June 30, 2023 | Six Months Ended June 30, 2022 | | :--- | :--- | :--- | | Net cash used in operating activities | ($12,600) | ($19,236) | | Net cash (used in) provided by investing activities | ($42,328) | $24,597 | | Net cash provided by financing activities | $57,514 | $1,520 | | **Net change in cash, cash equivalents and restricted cash** | **$2,586** | **$6,881** | - In February 2023, the company completed an underwritten follow-on public offering, raising approximately **$48.1 million** in net proceeds[51](index=51&type=chunk) - During the first six months of 2023, the company sold 4,332,210 shares of common stock through its at-the-market (ATM) offering program, generating net proceeds of approximately **$9.5 million**[52](index=52&type=chunk) [Management's Discussion and Analysis of Financial Condition and Results of Operations](index=15&type=section&id=Item%202.%20Management's%20Discussion%20and%20Analysis%20of%20Financial%20Condition%20and%20Results%20of%20Operations) Management discusses efzofitimod's clinical development, including Phase 3 and planned Phase 2 studies, and highlights H1 2023 financing activities that bolstered cash to **$112.0 million** [Overview](index=16&type=section&id=Overview) The company focuses on efzofitimod for ILDs, with a pivotal Phase 3 study underway and a Phase 2 study planned, supported by a **$10.0 million** Kyorin milestone payment - The company's primary focus is on its lead product candidate, efzofitimod, for the treatment of interstitial lung disease (ILD), a group of immune-mediated disorders[62](index=62&type=chunk) - A global pivotal Phase 3 study, EFZO-FIT, is currently enrolling 264 subjects to evaluate efzofitimod in patients with pulmonary sarcoidosis, with the first patient dosed in September 2022[64](index=64&type=chunk) - A Phase 2 proof-of-concept study, EFZO-CONNECT, is planned to evaluate efzofitimod in patients with SSc-ILD and is expected to initiate in Q3 2023[65](index=65&type=chunk) - The collaboration with Kyorin for development in Japan generated a **$10.0 million** milestone payment in February 2023, with eligibility for up to an additional **$155.0 million** in milestones plus royalties[67](index=67&type=chunk)[74](index=74&type=chunk) [Liquidity and Capital Resources](index=18&type=section&id=Liquidity%20and%20Capital%20Resources) As of June 30, 2023, the company held **$112.0 million** in cash and investments, bolstered by **$48.1 million** from a follow-on offering, **$9.5 million** from ATM sales, and a **$10.0 million** Kyorin milestone payment - As of June 30, 2023, the company had cash, cash equivalents, restricted cash, and available-for-sale investments totaling **$112.0 million** and an accumulated deficit of **$441.9 million**[71](index=71&type=chunk) - The company believes its current cash position is sufficient to meet material cash requirements for at least one year from the filing date of the report[71](index=71&type=chunk) Sources of Cash in H1 2023 (in millions) | Source | Net Proceeds | | :--- | :--- | | Underwritten Follow-On Public Offering (Feb 2023) | ~$48.1 | | At-the-Market (ATM) Offering Program | ~$9.5 | | Kyorin Agreement Milestone Payment | $10.0 | Summary of Net Cash Flow (in thousands) | Activity | Six Months 2023 | Six Months 2022 | | :--- | :--- | :--- | | Operating activities | ($12,600) | ($19,236) | | Investing activities | ($42,328) | $24,597 | | Financing activities | $57,514 | $1,520 | [Results of Operations](index=22&type=section&id=Results%20of%20Operations) Q2 2023 R&D expenses increased by **$0.7 million** to **$9.8 million** due to EFZO-FIT study costs, with similar trends for H1 2023 and slight G&A increases Comparison of Operating Expenses - Three Months Ended June 30 (in thousands) | Expense Category | 2023 | 2022 | Change | | :--- | :--- | :--- | :--- | | Research and development | $9,840 | $9,135 | $705 | | General and administrative | $3,718 | $3,449 | $269 | - The **$0.7 million** increase in Q2 2023 R&D expenses was primarily due to a **$2.5 million** increase in clinical trial costs for the EFZO-FIT study, partially offset by a **$1.0 million** reduction in manufacturing costs and a **$0.7 million** decrease in early-stage research costs[96](index=96&type=chunk) Comparison of Operating Expenses - Six Months Ended June 30 (in thousands) | Expense Category | 2023 | 2022 | Change | | :--- | :--- | :--- | :--- | | Research and development | $19,219 | $18,031 | $1,188 | | General and administrative | $7,126 | $6,931 | $195 | - The **$1.2 million** increase in H1 2023 R&D expenses was mainly due to a **$4.4 million** increase in EFZO-FIT clinical trial costs, offset by reductions of **$1.9 million** in manufacturing and **$1.5 million** in early-stage discovery costs[99](index=99&type=chunk) [Quantitative and Qualitative Disclosures About Market Risk](index=22&type=section&id=Item%203.%20Quantitative%20and%20Qualitative%20Disclosures%20About%20Market%20Risk) This section is not applicable for the current reporting period - The company has indicated that this item is not applicable[104](index=104&type=chunk) [Controls and Procedures](index=22&type=section&id=Item%204.%20Controls%20and%20Procedures) Management concluded that disclosure controls and procedures were effective as of June 30, 2023, with no material changes to internal control over financial reporting - The CEO and CFO concluded that the company's disclosure controls and procedures were effective at the reasonable assurance level as of the end of the quarter[106](index=106&type=chunk) - No changes in internal control over financial reporting were identified during the quarter that have materially affected, or are reasonably likely to materially affect, the company's internal controls[107](index=107&type=chunk) [PART II. OTHER INFORMATION](index=23&type=section&id=PART%20II.%20OTHER%20INFORMATION) [Legal Proceedings](index=23&type=section&id=Item%201.%20Legal%20Proceedings) The company is not currently a party to any material legal proceedings and does not anticipate any material adverse effects from ordinary course claims - As of the reporting date, the company is not a party to any material legal proceedings[108](index=108&type=chunk) [Risk Factors](index=23&type=section&id=Item%201A.%20Risk%20Factors) The company faces significant risks primarily related to clinical development, regulatory pathways, capital needs, historical losses, third-party reliance, and intellectual property protection - The company may face substantial delays in clinical trials and may fail to demonstrate safety and efficacy for its product candidates, including efzofitimod[110](index=110&type=chunk)[113](index=113&type=chunk) - The company will need to raise additional capital to fund operations and has a history of significant losses, which are expected to continue[110](index=110&type=chunk)[170](index=170&type=chunk)[179](index=179&type=chunk) - A significant risk is that the FDA has not approved any product for pulmonary sarcoidosis, meaning there is no established regulatory pathway, and the EFZO-FIT study may not be sufficient for approval[110](index=110&type=chunk)[121](index=121&type=chunk) - The company depends on collaborations, such as with Kyorin, and on third-party manufacturers (CDMOs), and the failure of these partners could materially harm the business[110](index=110&type=chunk)[186](index=186&type=chunk)[191](index=191&type=chunk) - The company's ability to compete depends on obtaining, maintaining, and protecting its intellectual property rights, which is uncertain and costly[111](index=111&type=chunk)[202](index=202&type=chunk) [Unregistered Sales of Equity Securities and Use of Proceeds](index=59&type=section&id=Item%202.%20Unregistered%20Sales%20of%20Equity%20Securities%20and%20Use%20of%20Proceeds) There were no unregistered sales of equity securities during the reporting period - None[316](index=316&type=chunk) [Defaults Upon Senior Securities](index=59&type=section&id=Item%203.%20Defaults%20Upon%20Senior%20Securities) There were no defaults upon senior securities during the reporting period - None[316](index=316&type=chunk) [Mine Safety Disclosures](index=59&type=section&id=Item%204.%20Mine%20Safety%20Disclosures) This section is not applicable to the company - Not applicable[316](index=316&type=chunk) [Other Information](index=59&type=section&id=Item%205.%20Other%20Information) There was no other information to report for the period - None[316](index=316&type=chunk) [Exhibits](index=59&type=section&id=Item%206.%20Exhibits) This section lists exhibits filed with the Quarterly Report on Form 10-Q, including corporate governance documents, material contracts, and certifications - The exhibits include the company's Restated Certificate of Incorporation, Amended and Restated Bylaws, various warrants, and certifications by the Principal Executive Officer and Principal Financial Officer[317](index=317&type=chunk)

PART I. FINANCIAL INFORMATION [Item 1. Financial Statements](index=3&type=section&id=Item%201.%20Financial%20Statements) Presents aTyr Pharma's unaudited condensed consolidated financial statements for Q1 2023 and 2022, covering Balance Sheets, Operations, and Cash Flows [Condensed Consolidated Balance Sheets](index=3&type=section&id=Condensed%20Consolidated%20Balance%20Sheets) Total assets increased from **$95.8 million** (2022) to **$136.8 million** (Q1 2023), driven by cash and investments from a public offering Condensed Consolidated Balance Sheets (in thousands) | Balance Sheet Highlights | March 31, 2023 (unaudited) | December 31, 2022 | | :--- | :--- | :--- | | **Assets** | | | | Cash and cash equivalents | $20,690 | $9,981 | | Available-for-sale investments | $93,695 | $56,165 | | Total current assets | $119,447 | $80,871 | | **Total assets** | **$136,838** | **$95,786** | | **Liabilities & Stockholders' Equity** | | | | Total current liabilities | $13,654 | $13,862 | | Total liabilities | $27,140 | $24,502 | | **Total stockholders' equity** | **$109,698** | **$71,284** | | **Total liabilities and stockholders' equity** | **$136,838** | **$95,786** | [Condensed Consolidated Statements of Operations](index=4&type=section&id=Condensed%20Consolidated%20Statements%20of%20Operations) Net loss for Q1 2023 was **$12.0 million** (($0.29) per share), a slight decrease from **$12.2 million** (Q1 2022) due to higher other income Condensed Consolidated Statements of Operations (in thousands, except per share data) | Income Statement Highlights | Three Months Ended March 31, 2023 (unaudited) | Three Months Ended March 31, 2022 (unaudited) | | :--- | :--- | :--- | | Research and development | $9,379 | $8,896 | | General and administrative | $3,408 | $3,482 | | **Total operating expenses** | **$12,787** | **$12,378** | | Loss from operations | ($12,787) | ($12,378) | | Total other income (expense), net | $835 | $224 | | **Consolidated net loss** | **($11,952)** | **($12,154)** | | Net loss per share, basic and diluted | ($0.29) | ($0.44) | [Condensed Consolidated Statements of Cash Flows](index=7&type=section&id=Condensed%20Consolidated%20Statements%20of%20Cash%20Flows) Net cash used in operations decreased to **$0.6 million** (Q1 2023) from **$10.1 million** (Q1 2022) due to a **$10.0 million** milestone payment and **$49.5 million** from financing Condensed Consolidated Statements of Cash Flows (in thousands) | Cash Flow Highlights | Three Months Ended March 31, 2023 (unaudited) | Three Months Ended March 31, 2022 (unaudited) | | :--- | :--- | :--- | | Net cash used in operating activities | ($590) | ($10,119) | | Net cash (used in) provided by investing activities | ($38,172) | $14,626 | | Net cash provided by financing activities | $49,496 | $1,481 | | **Net change in cash, cash equivalents and restricted cash** | **$10,734** | **$5,988** | | Cash, cash equivalents and restricted cash at end of period | $23,880 | $8,324 | [Notes to Condensed Consolidated Financial Statements](index=8&type=section&id=Notes%20to%20Condensed%20Consolidated%20Financial%20Statements) Notes detail accounting policies, financial instruments, and collaborations, highlighting liquidity, a **$10.0 million** Kyorin milestone, and a significant public offering - The company believes its existing cash, cash equivalents, restricted cash, and available-for-sale investments of **$117.6 million** as of **March 31, 2023**, are sufficient to meet material cash requirements for at least one year from the filing date[22](index=22&type=chunk) - In **February 2023**, a **$10.0 million** milestone payment was triggered from the Kyorin Agreement after the first patient was dosed in Japan in the EFZO-FIT study. The company is eligible for up to an additional **$155.0 million** in future milestones[46](index=46&type=chunk)[48](index=48&type=chunk) - In **February 2023**, the company completed an underwritten follow-on public offering, raising net proceeds of approximately **$48.1 million**[55](index=55&type=chunk) - Subsequent to the quarter end, from **April 1, 2023**, through **May 5, 2023**, the company sold an additional **916,143 shares** of common stock through its ATM program for net proceeds of **$1.8 million**[63](index=63&type=chunk) [Item 2. Management's Discussion and Analysis of Financial Condition and Results of Operations](index=15&type=section&id=Item%202.%20Management's%20Discussion%20and%20Analysis%20of%20Financial%20Condition%20and%20Results%20of%20Operations) Management discusses efzofitimod development for ILD, including ongoing Phase 3 EFZO-FIT and planned Phase 2 SSc-ILD studies, noting improved liquidity from a public offering and Kyorin milestone [Overview](index=16&type=section&id=Overview) aTyr Pharma develops biotherapeutics from its tRNA synthetase platform, focusing on **efzofitimod** for interstitial lung diseases (ILD) by targeting NRP2, and advancing its discovery pipeline - The company's primary focus is on **efzofitimod**, a clinical-stage product candidate targeting **neuropilin-2 (NRP2)** to treat interstitial lung disease (ILD)[67](index=67&type=chunk) - The global pivotal **Phase 3 EFZO-FIT study** for efzofitimod in patients with pulmonary sarcoidosis is currently enrolling subjects in the United States, Europe, and Japan[69](index=69&type=chunk) - The company plans to initiate a **Phase 2 proof-of-concept study** of efzofitimod in patients with SSc-ILD in the **third quarter of 2023**[70](index=70&type=chunk) [Liquidity and Capital Resources](index=17&type=section&id=Liquidity%20and%20Capital%20Resources) As of **March 31, 2023**, the company held **$117.6 million** in cash and investments, bolstered by a **$48.1 million** public offering and a **$10.0 million** Kyorin milestone, ensuring liquidity for at least one year - As of **March 31, 2023**, the company had cash, cash equivalents, restricted cash and available-for-sale investments of **$117.6 million** and an accumulated deficit of **$429.6 million**[77](index=77&type=chunk) - In **February 2023**, the company raised approximately **$48.1 million** in net proceeds from an underwritten follow-on public offering[78](index=78&type=chunk) - During **Q1 2023**, the company received a **$10.0 million** milestone payment from its partner Kyorin[80](index=80&type=chunk) [Results of Operations](index=21&type=section&id=Results%20of%20Operations) Q1 2023 R&D expenses increased by **$0.5 million** to **$9.4 million** due to EFZO-FIT study costs, while other income rose to **$0.8 million** from **$0.2 million** Comparison of Operating Results (in thousands) | Expense/Income Category | Q1 2023 | Q1 2022 | Change | | :--- | :--- | :--- | :--- | | Research and development expenses | $9,379 | $8,896 | $483 | | General and administrative expenses | $3,408 | $3,482 | ($74) | | Other income (expense), net | $835 | $224 | $611 | - The increase in R&D expenses was primarily due to a **$1.9 million** rise in clinical trial costs for the **EFZO-FIT study**, partially offset by reductions in manufacturing and other R&D costs[100](index=100&type=chunk) [Item 3. Quantitative and Qualitative Disclosures About Market Risk](index=22&type=section&id=Item%203.%20Quantitative%20and%20Qualitative%20Disclosures%20About%20Market%20Risk) This item is **not applicable**, as the company, a smaller reporting company, is not required to provide this information - The company has indicated that this section is **not applicable**[103](index=103&type=chunk) [Item 4. Controls and Procedures](index=22&type=section&id=Item%204.%20Controls%20and%20Procedures) Management concluded disclosure controls and procedures were **effective** as of **March 31, 2023**, with no material changes to internal control over financial reporting - The Chief Executive Officer and Chief Financial Officer concluded that the company's disclosure controls and procedures were **effective** at a reasonable assurance level as of **March 31, 2023**[105](index=105&type=chunk) - No changes in internal control over financial reporting occurred during the quarter that have materially affected, or are reasonably likely to materially affect, the company's internal control over financial reporting[106](index=106&type=chunk) PART II. OTHER INFORMATION [Item 1. Legal Proceedings](index=22&type=section&id=Item%201.%20Legal%20Proceedings) The company is **not currently a party to any material legal proceedings** and does not expect current claims to have a material adverse effect - As of the filing date, aTyr Pharma is **not a party to any material legal proceedings**[107](index=107&type=chunk) [Item 1A. Risk Factors](index=22&type=page&id=Item%201A.%20Risk%20Factors) Details significant business risks, including clinical trial delays for efzofitimod, lack of FDA pathway, financial losses, need for capital, reliance on third parties, and CRO transition - The company may face substantial delays in clinical trials and there is **no established FDA regulatory pathway** for pulmonary sarcoidosis, meaning the **EFZO-FIT study** may not be sufficient for approval[109](index=109&type=chunk)[112](index=112&type=chunk)[121](index=121&type=chunk) - The company has a history of significant losses (**$429.6 million accumulated deficit** as of **March 31, 2023**) and will need to raise additional capital to fund operations, which may be challenging due to macroeconomic conditions[110](index=110&type=chunk)[165](index=165&type=chunk)[174](index=174&type=chunk) - The company is in the process of transitioning its Clinical Research Organization (CRO) for the ongoing **EFZO-FIT study**, which could lead to delays, increased costs, and divert management attention[192](index=192&type=chunk) - The company's business could be adversely affected by macroeconomic conditions, including the effects of the **COVID-19 pandemic**, the **Ukraine-Russia conflict**, and recent **bank failures**[110](index=110&type=chunk)[247](index=247&type=chunk)[248](index=248&type=chunk) [Item 2. Unregistered Sales of Equity Securities and Use of Proceeds](index=59&type=section&id=Item%202.%20Unregistered%20Sales%20of%20Equity%20Securities%20and%20Use%20of%20Proceeds) The company reported no unregistered sales of equity securities during the period covered by this report - **None**[314](index=314&type=chunk) [Item 3. Defaults Upon Senior Securities](index=59&type=section&id=Item%203.%20Defaults%20Upon%20Senior%20Securities) The company reported no defaults upon senior securities during the period - **None**[314](index=314&type=chunk) [Item 4. Mine Safety Disclosures](index=59&type=section&id=Item%204.%20Mine%20Safety%20Disclosures) This item is **not applicable** to the company - **Not applicable**[314](index=314&type=chunk) [Item 5. Other Information](index=59&type=section&id=Item%205.%20Other%20Information) The company reported no other information required to be disclosed in this item - **None**[314](index=314&type=chunk) [Item 6. Exhibits](index=59&type=section&id=Item%206.%20Exhibits) Lists exhibits filed with Form 10-Q, including corporate governance documents, warrants, and officer certifications - The exhibits include various corporate governance documents, warrants, and required SEC certifications (**31.1, 31.2, 32.1, 32.2**)[315](index=315&type=chunk)

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, D.C. 20549 FORM 10-K (Mark One) ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2022 or TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission file number: 001-37378 ATYR PHARMA, INC. (Exact name of registrant as specified in its charter) Delaware 20-3435077 (State or other jurisdiction of incor ...

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2022 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission File Number: 001-37378 ATYR PHARMA, INC. (Exact name of registrant as specified in its charter) (State or other jurisdiction of incorporation or ...