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 ...

UNITED STATES SECURITIES AND EXCHANGE COMMISSION WASHINGTON, DC 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, 2018 ☐ 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 Delaware 20- ...