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, 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 Common Stock, par value $0.001 per share LIFE The Nasdaq Capital Market Indicate by check mark whether the registrant (1) ...

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 March 31, 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 (Exact name of registrant as specified in its charter) Delaware 20-3435077 (State or other jurisdiction of incorporation ...

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 ...

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 March 31, 2022 or (858) 731-8389 (Registrant's telephone number, including area code) Securities registered pursuant to Section 12(b) of the Act: | Title of each class | Trading Symbol(s) | Name of each exchange on which registered | | --- | --- | --- | | Common Stock, par value $0.001 per share | ...

Clinical Development - The lead therapeutic candidate, efzofitimod, demonstrated positive results in a Phase 1b/2a clinical trial involving 37 patients with pulmonary sarcoidosis, showing consistent dose response on key efficacy endpoints and improvements compared to placebo[20]. - The company plans to initiate a registrational trial for efzofitimod in the third quarter of 2022, targeting pulmonary sarcoidosis and other interstitial lung diseases (ILDs) such as chronic hypersensitivity pneumonitis (CHP) and connective tissue disease-related ILD (CTD-ILD)[30]. - The Phase 1b/2a clinical trial for efzofitimod included 37 patients with pulmonary sarcoidosis, demonstrating safety and tolerability across all doses[55][59]. - Efzofitimod demonstrated a well-tolerated safety profile in a Phase 1 clinical trial with 36 healthy volunteers, with no significant adverse events reported[62]. - The ongoing COVID-19 pandemic has caused delays in clinical trial enrollment and other research activities, impacting the company's operations[28]. - The company has faced delays in clinical trials, particularly with the Phase 1b/2a trial of efzofitimod due to operational issues related to the COVID-19 pandemic, impacting data evaluation[185]. - The company acknowledges that interim and preliminary data from clinical trials may change as more patient data become available, which could affect business prospects[192]. - The company has not yet commenced or completed any human clinical trials designed to demonstrate efficacy to the satisfaction of the FDA, which is critical for obtaining marketing approval[195]. - The company has not extensively studied efzofitimod's activity in patients with interstitial lung disease (ILD), raising concerns about its therapeutic relevance[208]. Product Candidates - Efzofitimod is designed to selectively modulate NRP2 to downregulate immune responses in inflammatory disease states, with preclinical models demonstrating its therapeutic potential[34]. - ATYR2810, a fully humanized monoclonal antibody targeting NRP2, is in preclinical development for aggressive cancers, with plans to initiate a Phase 1 clinical trial in the second half of 2022[23]. - Efzofitimod is a potential first-in-class immunomodulator targeting immune-mediated disorders, specifically pulmonary sarcoidosis[44]. - The primary target population for efzofitimod is interstitial lung disease (ILD), with a focus on progressive, immune-mediated forms[51]. - The company aims to expand applications of efzofitimod to additional immune-mediated diseases and advance ATYR2810 for cancer indications[217]. Financials and Funding - As of December 31, 2021, the company had cash, cash equivalents, and available-for-sale investments of approximately $107.9 million, expected to meet material cash requirements for at least one year[172]. - The company incurred consolidated net losses of $33.8 million, $16.2 million, and $23.8 million for the years ended December 31, 2021, 2020, and 2019, respectively, with an accumulated deficit of $372.3 million as of December 31, 2021[178]. - The company has not yet generated any revenues from product sales and does not anticipate doing so for the foreseeable future[182]. - The company may seek additional capital through equity or debt offerings, collaborations, or licensing arrangements to fund its operations[172]. - The company anticipates incurring significant costs associated with the commercialization of any approved product candidates, which may exceed expectations due to potential additional clinical trials required by regulatory agencies[184]. Regulatory and Compliance - Efzofitimod received orphan drug designation from the FDA in January 2022 for the treatment of sarcoidosis[22]. - The FDA regulates biologics under the Federal Food, Drug, and Cosmetic Act, requiring approval before marketing any new biologic or dosage form[119]. - The process for obtaining FDA approval involves substantial time and financial resources, with no guarantee of timely approval for product candidates[121]. - A Biologics License Application (BLA) must include all relevant data from preclinical studies and clinical trials, and must demonstrate the safety and effectiveness of the product[129]. - The FDA may condition BLA approval on the sponsor's agreement to conduct additional clinical trials post-approval, known as Phase 4 clinical trials[126]. - The company must comply with Good Clinical Practice (GCP) requirements during clinical trials, which include obtaining informed consent from all research subjects[123]. - The FDA's approval process includes inspections of manufacturing facilities to ensure compliance with current Good Manufacturing Practices (cGMP)[130]. - The company is subject to various regulatory compliance risks, including the U.S. Foreign Corrupt Practices Act and federal civil and criminal false claims laws[161][164]. Market and Competition - The biotechnology and pharmaceutical industries are highly competitive, with potential competition from companies with greater resources[89]. - The oncology market is highly competitive, with over 70 new drug approvals by the FDA since 2015 and more than 100 new treatments projected to be approved in the next five years[96]. - The U.S. government and third-party payors are increasingly scrutinizing pharmaceutical pricing, affecting reimbursement rates[151]. - The marketability of approved products may suffer if adequate coverage and reimbursement are not provided by payors[157]. Intellectual Property - The company has a patent portfolio for efzofitimod that includes over 220 issued patents and allowed patent applications, with expiration dates ranging from 2026 to 2034[102]. - The efzofitimod patent portfolio includes families directed to specific product forms and splice variants, with expected expiration between 2030 and 2038[111]. - The company is expanding its intellectual property estate by filing new patent applications for novel therapeutic compositions and methods[106]. - The company relies on trade secrets and careful monitoring to protect proprietary information that is not suitable for patent protection[103]. Challenges and Risks - The ongoing COVID-19 pandemic has broadly impacted clinical trials, leading to delays in patient enrollment and data availability, particularly for the efzofitimod trial[191]. - The company faces challenges in recruiting suitable patients for clinical trials due to the rarity of certain diseases, which could delay or halt development[198]. - The company faces risks associated with undesirable side effects that could delay or prevent regulatory approval of its product candidates[212]. - The company is developing efzofitimod and ATYR2810, facing challenges related to public perception of safety and adoption of new therapeutics[205].

Financial Position - As of September 30, 2021, the company had an accumulated deficit of $363.7 million and cash, cash equivalents, and available-for-sale investments of $116.4 million, expected to meet cash requirements for at least one year[76]. - The company has incurred losses and negative cash flows from operations since inception, with expectations to continue this trend for the foreseeable future[76]. - The company expects to finance cash needs through equity offerings, collaborations, and strategic partnerships until substantial product revenues are generated[89]. - The company faces risks related to funding requirements and may need to delay or limit product development if additional funds cannot be raised[90]. Cash Flow - The company reported net cash used in operating activities of $24.99 million for the nine months ended September 30, 2021, compared to $9.9 million for the same period in 2020[84]. - The company reported net cash used in investing activities of $(42.2) million for the nine months ended September 30, 2021, compared to $3.7 million for the same period in 2020[86]. - Net cash provided by financing activities for the nine months ended September 30, 2021 was $80.6 million from common stock issuance, compared to $18.8 million for the same period in 2020[87]. Clinical Development - The Phase 1b/2a clinical trial of ATYR1923 in patients with pulmonary sarcoidosis showed positive results in 37 patients, demonstrating safety and a consistent dose response on key efficacy endpoints[68]. - The company plans to initiate a registrational trial for ATYR1923 for pulmonary sarcoidosis next year based on positive clinical trial results[68]. - The company is advancing its discovery pipeline, including the lead IND candidate ATYR2810 for oncology, with plans to submit an IND application and initiate a Phase 1 clinical trial in 2022[72]. - The company anticipates increased research and development expenses in the current and future years, primarily for ATYR1923 and ATYR2810[97]. Revenue and Expenses - License and collaboration agreement revenues were $0 for the nine months ended September 30, 2021, a decrease of $8.4 million compared to $8.4 million in 2020[108]. - The company has not generated any revenues from product sales to date and expects significant commercialization expenses if marketing approval is obtained for product candidates[88]. - Research and development expenses increased to $17.3 million for the nine months ended September 30, 2021, up from $12.6 million in 2020, reflecting a $4.7 million rise in product development and manufacturing costs[109]. - General and administrative expenses rose to $8.1 million for the nine months ended September 30, 2021, compared to $6.8 million in 2020, an increase of $1.3 million[108]. - General and administrative expenses increased to $8.1 million for the nine months ended September 30, 2021, up from $6.8 million in 2020, representing a $1.3 million increase[110]. - Other income improved to $0.2 million for the nine months ended September 30, 2021, compared to a loss of $(0.3) million in 2020, primarily due to the repayment of term loans[111]. Collaborations and Agreements - In January 2020, the company entered into a collaboration agreement with Kyorin Pharmaceutical for the development of ATYR1923 in Japan, receiving an upfront payment of $8.0 million and a milestone payment of $2.0 million[71]. - The company received an $8.0 million upfront payment and a $2.0 million milestone payment from Kyorin under a collaboration agreement for ATYR1923[93]. Stock and Share Issuance - The company completed a follow-on public offering in September 2021, raising approximately $80.6 million from the sale of 10,781,250 shares at $8.00 per share[79]. - The company sold an aggregate of 3,000,000 shares at an average price of $5.09 per share for net proceeds of $15.2 million under a common stock purchase agreement with Aspire Capital[83]. Subsidiaries and Arrangements - The company has a 98% majority-owned subsidiary in Hong Kong, Pangu BioPharma, included in its consolidated financial statements[92]. - The company currently has no off-balance sheet arrangements during the periods presented[113]. - There are no applicable quantitative and qualitative disclosures about market risk[114].

Financial Position - The company reported an accumulated deficit of $356.1 million as of June 30, 2021, and expects to continue incurring net losses for the foreseeable future[72]. - As of June 30, 2021, the company had cash, cash equivalents, and available-for-sale investments totaling $44.1 million, sufficient to meet anticipated cash requirements for at least one year[72]. - The company reported net cash provided by financing activities of $26.1 million for the six months ended June 30, 2021, primarily from stock issuances[79]. Operating Activities - For the six months ended June 30, 2021, net cash used in operating activities was $(13.5) million, compared to $(4.3) million for the same period in 2020[79]. - The company has not generated any revenues from product sales to date and expects expenses to increase as it advances clinical development of ATYR1923 and other therapies[82]. Clinical Development - The company completed enrollment in a Phase 1b/2a clinical trial for ATYR1923, targeting pulmonary sarcoidosis, and expects to report data in mid-September 2021[65]. - A Phase 2 study of ATYR1923 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[66]. - The company is advancing its discovery pipeline, including the lead IND candidate ATYR2810 for oncology, which is in preclinical development[68]. - The company has faced delays in clinical trials due to the COVID-19 pandemic, impacting the timelines and costs of ongoing studies[92]. Revenue and Expenses - For the three months ended June 30, 2021, license and collaboration agreement revenues were $0, a decrease of $189,000 compared to $189,000 in the same period of 2020[97]. - For the six months ended June 30, 2021, license and collaboration agreement revenues were $0, a decrease of $8.3 million compared to $8.3 million in the same period of 2020[102]. - Research and development expenses increased to $7.7 million for the three months ended June 30, 2021, up from $4.4 million in 2020, primarily due to a $3.5 million increase in manufacturing costs for ATYR1923[99]. - Research and development expenses for the six months ended June 30, 2021, were $12.2 million, an increase of $4.2 million from $8.0 million in 2020, driven by a $3.8 million increase in manufacturing costs for ATYR1923[103]. - General and administrative expenses rose to $2.7 million for the three months ended June 30, 2021, compared to $2.1 million in 2020, mainly due to a $0.4 million increase in payroll-related expenses[100]. - General and administrative expenses for the six months ended June 30, 2021, were $5.5 million, up from $4.7 million in 2020, primarily due to a $0.5 million increase in payroll-related expenses[104]. - The company anticipates an increase in research and development expenses in the current and future years, primarily related to the clinical development of ATYR1923 and ATYR2810[91]. Collaborations and Agreements - The company received an $8.0 million upfront payment and a $2.0 million milestone payment from Kyorin Pharmaceutical for the development of ATYR1923 in Japan, with potential additional payments of up to $165.0 million[67]. - The company received an $8.0 million upfront payment and a $2.0 million milestone payment from Kyorin, with potential additional payments of up to $165.0 million upon achieving certain milestones[86]. - The company has entered into a Capital on Demand Sales Agreement with JonesTrading for an ATM Offering Program with an aggregate offering price of up to $25.0 million[78]. Off-Balance Sheet Arrangements - The company has no off-balance sheet arrangements as defined by SEC regulations[107].

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 March 31, 2021 or ☐ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE 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 incorpo ...

Clinical Development of ATYR1923 - The lead clinical product candidate, ATYR1923, is being developed for severe inflammatory lung diseases, with a focus on interstitial lung diseases (ILD) and COVID-19 related respiratory complications[19]. - ATYR1923 has completed enrollment in a Phase 1b/2a clinical trial, designed to evaluate safety, tolerability, and preliminary clinical activity, with results expected to guide future development[19]. - A Phase 2 study of ATYR1923 for COVID-19 patients showed positive data, meeting its primary endpoint of safety, with no drug-related serious adverse events reported[19]. - The Phase 1b/2a clinical trial of ATYR1923 for pulmonary sarcoidosis completed enrollment with 37 patients, exceeding the target of 36 patients[33]. - The primary endpoint of the Phase 2 clinical trial in hospitalized COVID-19 patients was met, demonstrating safety and tolerability with no drug-related serious adverse events[34]. - ATYR1923 showed a statistically significant reduction in serum amyloid A (SAA) levels, a marker of inflammation and fibrosis, in treated patients[34]. - The clinical trial for ATYR1923 is designed to evaluate multiple ascending doses of 1.0 mg/kg, 3.0 mg/kg, and 5.0 mg/kg[51]. - The study aims to assess the potential steroid-sparing effects of ATYR1923 while evaluating its pharmacokinetics and immunogenicity[52]. - ATYR1923 was generally well tolerated in a Phase 1b/2a clinical trial with no drug-related serious adverse events reported among 15 pulmonary sarcoidosis patients[56]. - The Phase 2 clinical trial for ATYR1923 in hospitalized COVID-19 patients enrolled 32 patients, exceeding the target of 30[63]. - Patients receiving the 3.0 mg/kg dose of ATYR1923 had a median time to recovery of 5.5 days compared to 6 days in the placebo group, with 83% achieving recovery by Day 6[64]. - ATYR1923 demonstrated a trend of overall improvement in 82% of analyzed biomarkers compared to placebo, indicating its potential as a therapeutic for severe inflammatory lung disease[65]. - The company aims to expedite the development of ATYR1923 for pulmonary sarcoidosis towards regulatory approval, leveraging data from ongoing clinical trials[27]. - The company aims to develop ATYR1923 for other interstitial lung diseases (ILD) based on insights gained from the pulmonary sarcoidosis trial[27]. - The therapeutic candidate pipeline includes new discovery programs for tRNA synthetases, focusing on immunology, fibrosis, and cancer[23]. - The company is also investigating ATYR1923's potential as a treatment for COVID-19 patients with severe respiratory complications due to its mechanism of action overlapping with inflammatory lung injury[62]. Financial Agreements and Collaborations - The company received an $8.0 million upfront payment and a $2.0 million milestone payment from Kyorin Pharmaceutical for the development and commercialization of ATYR1923 in Japan, with potential total payments of up to $165.0 million[20]. - Kyorin received exclusive rights to develop and commercialize ATYR1923 in Japan, with an upfront payment of $8.0 million and potential additional payments of up to $165.0 million upon achieving certain milestones[58]. - The Kyorin Agreement allows for termination by either party after the first anniversary with 90 days' notice, highlighting the agreement's flexibility[59]. - The Kyorin Agreement grants exclusive rights to develop and commercialize ATYR1923 for ILD in Japan, with an upfront payment of $8.0 million and potential additional payments of up to $165.0 million upon achieving certain milestones[58]. Research and Development Pipeline - The company is advancing its discovery pipeline, including ATYR2810, a monoclonal antibody targeting NRP2 for aggressive cancers, currently in preclinical development[21]. - New discovery programs from the tRNA synthetase platform are investigating the functionality of Alanyl-tRNA synthetase and Aspartyl-tRNA synthetase in immunology, fibrosis, and cancer[23]. - ATYR2810 is currently in preclinical development targeting the NRP2 receptor, which is associated with negative outcomes in various cancers[67][68]. - Preclinical data suggest that ATYR2810 could be effective against aggressive tumors, including triple-negative breast cancer, by blocking the NRP2/VEGF signaling pathway[69]. - The company is committed to advancing ATYR2810 through IND enabling studies to address unmet medical needs in aggressive cancers[28]. - The ATYR2810 program includes US patent applications for anti-neuropilin 2 antibodies, forming part of a broader IP strategy[107]. Regulatory and Compliance Challenges - The impact of the COVID-19 pandemic has caused delays in clinical trials and operations, affecting the company's ability to conduct business development activities[25]. - The company is subject to various federal and state laws targeting fraud and abuse in the healthcare industry, which may impact its operations[152]. - The company may face substantial risks related to regulatory compliance, including potential penalties and exclusion from government healthcare programs[155]. - The FDA requires substantial time and financial resources for obtaining regulatory approvals, which includes compliance with various federal, state, and local regulations[112]. - The FDA's approval process for biologics involves multiple phases, including preclinical testing, IND submission, and clinical trials, which require significant resources and time[115]. - The company must submit a Biologics License Application (BLA) to the FDA, which includes all relevant data from preclinical studies and clinical trials to establish safety and effectiveness[121]. - The FDA may condition BLA approval on the completion of additional clinical trials or post-market studies, which could impact the product's market entry[119]. - The FDA may issue a Complete Response Letter (CRL) if the BLA is not ready for approval, outlining deficiencies that need to be addressed before reconsideration[126]. - The FDA may grant accelerated approval for drugs based on surrogate endpoints that predict clinical benefit, requiring post-marketing trials to verify clinical benefits[129]. - Orphan drug designation can be granted for drugs treating rare diseases affecting fewer than 200,000 individuals in the U.S., providing financial incentives and potential exclusivity for seven years[135][136]. - Pediatric exclusivity can extend marketing protection by an additional six months if pediatric data is submitted in response to FDA requests[138]. - The approval process for drugs varies significantly across countries, with potential delays in obtaining regulatory approval outside the U.S.[140][141]. Intellectual Property and Manufacturing - The ATYR1923 patent portfolio includes over 220 issued patents or allowed applications, with expiration dates ranging from 2026 to 2034[97]. - The company is expanding its intellectual property estate by filing new patent applications for therapeutics and treatment methods[100]. - The pipeline of extracellular tRNA synthetase proteins is covered by multiple patent families, with expected expiration dates between 2026 and 2031[108]. - The company is eligible for patent term extensions of up to five years under the Hatch-Waxman Act for drugs approved by the FDA, but extensions cannot exceed a total of 14 years from the date of product approval[110]. - The company relies on trade secret protection for proprietary information, but there is a risk that third parties may independently develop equivalent information[111]. - The company relies on contract manufacturing organizations (CMOs) for the production of its product candidates, with no plans to build its own facilities[94]. - Current CDMOs and CROs are meeting manufacturing requirements, but delays in raw material delivery due to COVID-19 may impact production[96]. Market and Competitive Landscape - The biotechnology and pharmaceutical industries are highly competitive, with competitors potentially having greater resources and capabilities[85]. - Third-party payors are increasingly scrutinizing drug pricing and may not provide adequate reimbursement, impacting the profitability of approved products[143][144]. - The U.S. government has shown interest in implementing cost containment programs, which may affect drug pricing and reimbursement policies[145]. - In the European Community, governments influence pharmaceutical pricing through reimbursement rules, creating high barriers for new product entry[150].