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].

FORM 10-Q (Mark One) UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 Commission File Number: 001-37378 ATYR PHARMA, INC. (Exact name of registrant as specified in its charter) (State or other jurisdiction of incorporation or organization) 3545 John Hopkins Court, Suite #250, San Diego, CA 92121 (Address of principal executive offices) (Zip Code) For the transition period from to ☒ QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterl ...

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, 2020 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 ...

Revenue and Financial Performance - The company recognized $7.9 million in license revenue under the Kyorin Agreement for the three months ended March 31, 2020[96]. - Revenues for the three months ended March 31, 2020, were $8.1 million, a significant increase from $0 in the same period of 2019[111]. - The company reported a net income of $2.1 million for the three months ended March 31, 2020, compared to a net loss of $6.1 million in the same period of 2019[121]. - As of March 31, 2020, the company had an accumulated deficit of $320.6 million and expected to continue incurring net losses for the foreseeable future[114]. - The company had cash, cash equivalents, and available-for-sale investments totaling $49.8 million as of March 31, 2020, which is expected to meet cash requirements for at least one year[114]. - Net cash provided by operating activities for the three months ended March 31, 2020, was $2.1 million, compared to net cash used of $6.0 million in the same period of 2019[121]. - The company completed a follow-on public offering in February 2020, raising approximately $20.7 million in gross proceeds[120]. Research and Development - The company is currently enrolling a proof-of-concept Phase 1b/2a clinical trial for ATYR1923 in patients with pulmonary sarcoidosis[85]. - The company anticipates increased research and development expenses primarily related to the ATYR1923 clinical trials and other potential therapeutics[103]. - Research and development expenses increased to $3.6 million for the three months ended March 31, 2020, up from $3.3 million in 2019, primarily due to the progression of the Phase 1b/2a clinical trial for ATYR1923[112]. - The company is investigating ATYR1923's potential as a treatment for COVID-19 patients with severe respiratory complications, with a Phase 2 clinical trial expected to provide data this year[86]. - The company has received a grant of approximately $750,000 to develop a high-throughput platform for bi-specific antibodies, funded by the Hong Kong government's Innovation and Technology Commission[89]. Agreements and Collaborations - The company has entered into a research collaboration with CSL Behring, which includes potential payments of up to $4.25 million per tRNA synthetase program, totaling $17.0 million if all four programs advance[98]. - The company has entered into a license agreement with Kyorin for the development and commercialization of ATYR1923 in Japan, with Kyorin funding all related activities[87]. - The company is eligible to receive an additional $167.0 million in aggregate upon achieving certain development, regulatory, and sales milestones under the Kyorin Agreement[87]. Operational Challenges - The company has experienced delays in clinical trial enrollment and operations due to the COVID-19 pandemic, impacting the timeline for top-line results[104]. Financial Risks and Exposures - The company has financed operations primarily through equity securities and convertible debt, with no revenues generated from product sales to date[115][126]. - The company is exposed to interest rate risk, with Term Loans bearing interest at variable rates, which could increase expenses by approximately $0.1 million annually with a 1% rate increase[133]. - The company incurs expenses in foreign currencies, including Pounds Sterling, Euro, Hong Kong dollar, and Australian dollar, which may affect its financial position due to exchange rate fluctuations[134]. - The company does not engage in foreign currency hedging transactions, leaving it exposed to foreign currency exchange risks[134]. - A 10% movement in the U.S. dollar to Pounds Sterling or Euro exchange rates would not have a material effect on the company's results of operations or financial condition[134]. - Inflation has increased costs related to labor, manufacturing, clinical trials, and research and development, but has not materially affected the company's financial results[135]. Future Projections - The company anticipates significant commercialization expenses if marketing approval is obtained for any product candidates, necessitating substantial additional funding[125].

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, 2019 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 orga ...

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, 2019 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 incorporatio ...

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, 2019 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 ATYR PHARMA, INC. (Exact name of registrant as specified in its charter) 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, 2019 or ☐ TRANSITION REPORT UNDER SECTION 13 OF 15(d) OR THE EXCHANGE ACT OF 1934 From the transition period from to Commission File Number 001-37378 Indicate by check mark whether the registrant is a large accelera ...