SEC Filing | aTyr Pharma

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10-Q

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

☐ 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 incorporation or organization)	(I.R.S. Employer Identification No.)

10240 Sorrento Valley, Suite 300, San Diego, CA	92121
(Address of principal executive offices)	(Zip Code)

(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	LIFE	The Nasdaq Capital Market

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes ☒ No ☐

Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files). Yes ☒ No ☐

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller reporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company,” and “emerging growth company” in Rule 12b-2 of the Exchange Act.


Large accelerated filer	☐	Accelerated filer	☐

Non-accelerated filer	☒	Smaller reporting company	☒

		Emerging growth company	☐

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. ☐

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yes ☐ No ☒

As of November 3, 2023, there were 58,560,061 shares of the registrant’s common stock, par value $0.001 per share, outstanding.

ATYR PHARMA, INC.

FORM 10-Q

TABLE OF CONTENTS


	Page
PART I. FINANCIAL INFORMATION
Item 1. Financial Statements		3
Condensed Consolidated Balance Sheets as of September 30, 2023 (unaudited) and December 31, 2022		3
Condensed Consolidated Statements of Operations for the three and nine months ended September 30, 2023 and 2022 (unaudited)		4
Condensed Consolidated Statements of Comprehensive Loss for the three and nine months ended September 30, 2023 and 2022 (unaudited)		5
Condensed Consolidated Statements of Stockholders’ Equity for the three and nine months ended September 30, 2023 and 2022 (unaudited)		6
Condensed Consolidated Statements of Cash Flows for the nine months ended September 30, 2023 and 2022 (unaudited)		7
Notes to Condensed Consolidated Financial Statements (unaudited)		8
Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations		16
Item 3. Quantitative and Qualitative Disclosures About Market Risk		23
Item 4. Controls and Procedures		23
PART II. OTHER INFORMATION
Item 1. Legal Proceedings		24
Item 1A. Risk Factors		24
Item 2. Unregistered Sales of Equity Securities and Use of Proceeds		60
Item 3. Defaults Upon Senior Securities		60
Item 4. Mine Safety Disclosures		60
Item 5. Other Information		60
Item 6. Exhibits		60
SIGNATURES		63

PART I. FINANCIAL INFORMATION

Item 1. Financial Statements

aTyr Pharma, Inc.

Condensed Consolidated Balance Sheets

(in thousands, except share and per share data)


	September 30,			December 31,
	2023			2022
	(unaudited)
Assets
Current assets:
Cash and cash equivalents	$	9,787		$	9,981
Available-for-sale investments		92,344			56,165
Other receivables		2,087			11,775
Prepaid expenses		3,080			2,950
Total current assets		107,298			80,871
Restricted cash		3,451			3,165
Property and equipment, net		5,644			3,059
Operating lease, right-of-use assets		6,812			7,250
Financing lease, right-of-use assets		1,791			1,248
Other assets		73			193
Total assets	$	125,069		$	95,786
Liabilities and Stockholders’ Equity
Current liabilities:
Accounts payable	$	2,043		$	3,106
Accrued expenses		9,605			9,862
Current portion of operating lease liability		774			630
Current portion of financing lease liability		459			264
Total current liabilities		12,881			13,862
Long-term operating lease liability, net of current portion		12,548			9,633
Long-term financing lease liability, net of current portion		1,437			1,007
Commitments and contingencies (Note 4)
Stockholders’ equity:
Preferred stock, $0.001 par value per share; 5,000,000 undesignated authorized shares as of September 30, 2023 (unaudited) and December 31, 2022; no shares issued or outstanding as of September 30, 2023 (unaudited) and December 31, 2022		—			—
Common stock, $0.001 par value per share; 170,000,000 and 85,000,000 authorized shares as of September 30, 2023 (unaudited) and December 31, 2022, respectively; issued and outstanding shares – 58,560,061 as of September 30, 2023 (unaudited) and 29,498,488 as of December 31, 2022		59			29
Additional paid-in capital		551,888			489,502
Accumulated other comprehensive loss		(294	)		(433	)
Accumulated deficit		(453,263	)		(417,634	)
Total aTyr Pharma, Inc. stockholders’ equity		98,390			71,464
Noncontrolling interest in Pangu BioPharma Limited		(187	)		(180	)
Total stockholders’ equity		98,203			71,284
Total liabilities and stockholders’ equity	$	125,069		$	95,786

See accompanying notes.

aTyr Pharma, Inc.

Condensed Consolidated Statements of Operations

(in thousands, except share and per share data)


	Three Months Ended September 30,						Nine Months Ended September 30,
	2023			2022			2023			2022
	(unaudited)
Revenues:
License and collaboration agreement revenues	$	353		$	—		$	353		$	—
Total revenues		353			—			353			—
Operating expenses:
Research and development		10,319			9,867			29,538			27,898
General and administrative		2,649			3,625			9,775			10,556
Total operating expenses		12,968			13,492			39,313			38,454
Loss from operations		(12,615	)		(13,492	)		(38,960	)		(38,454	)
Total other income (expense), net		1,273			247			3,324			634
Consolidated net loss		(11,342	)		(13,245	)		(35,636	)		(37,820	)
Net loss attributable to noncontrolling interest in Pangu BioPharma Limited		2			1			7			3
Net loss attributable to aTyr Pharma, Inc.	$	(11,340	)	$	(13,244	)	$	(35,629	)	$	(37,817	)
Net loss per share, basic and diluted	$	(0.20	)	$	(0.46	)	$	(0.69	)	$	(1.34	)
Shares used in computing net loss per share, basic and diluted		57,885,393			28,663,047			51,700,864			28,184,698

See accompanying notes.

aTyr Pharma, Inc.

Condensed Consolidated Statements of Comprehensive Loss

(in thousands)


	Three Months Ended September 30,						Nine Months Ended September 30,
	2023			2022			2023			2022
	(unaudited)
Consolidated net loss	$	(11,342	)	$	(13,245	)	$	(35,636	)	$	(37,820	)
Other comprehensive loss:
Change in unrealized (loss) gain on available-for-sale investments, net of tax		39			141			139			(406	)
Comprehensive loss		(11,303	)		(13,104	)	$	(35,497	)	$	(38,226	)
Comprehensive loss attributable to noncontrolling interest in Pangu BioPharma Limited		2			1			7			3
Comprehensive loss attributable to aTyr Pharma, Inc. common stockholders	$	(11,301	)	$	(13,103	)	$	(35,490	)	$	(38,223	)

See accompanying notes.

aTyr Pharma, Inc.

Condensed Consolidated Statements of Stockholders’ Equity

(in thousands, except share data)


	Three and Nine Months Ended September 30, 2023 (unaudited)
	Common Stock				Additional Paid-In		Other Comprehensive			Accumulated			Noncontrolling			Total Stockholders’
	Shares		Amount		Capital		Gain/(Loss)			Deficit			Interest			Equity
Balance as of December 31, 2022		29,498,488	$	29	$	489,502	$	(433	)	$	(417,634	)	$	(180	)	$	71,284
Issuance of common stock upon release of restricted stock units		22,111		—		—		—			—			—			—
Issuance of common stock from at-the-market offerings, net of offering costs		694,012		1		1,488		—			—			—			1,489
Issuance of common stock from underwritten follow-on public offering, net of offering costs		23,125,000		23		48,050		—			—			—			48,073
Stock-based compensation		—		—		619		—			—			—			619
Net unrealized gain on investments, net of tax		—		—		—		185			—			—			185
Net loss		—		—		—		—			(11,951	)		(1	)		(11,952	)
Balance as of March 31, 2023		53,339,611		53		539,659		(248	)		(429,585	)		(181	)		109,698
Issuance of common stock pursuant to employee stock purchase plan		32,363		—		65		—			—			—			65
Issuance of common stock upon release of restricted stock units		36,000		—		—		—			—			—			—
Issuance of common stock from at-the-market offerings, net of offering costs		3,638,198		4		8,054		—			—			—			8,058
Stock-based compensation		—		—		658		—			—			—			658
Net unrealized loss on investments, net of tax		—		—		—		(85	)		—			—			(85	)
Net loss		—		—		—		—			(12,338	)		(4	)		(12,342	)
Balance as of June 30, 2023		57,046,172		57		548,436		(333	)		(441,923	)		(185	)		106,052
Issuance of common stock from at-the-market offerings, net of offering costs		1,513,889		2		2,788		—			—			—			2,790
Stock-based compensation		—		—		664		—			—			—			664
Net unrealized gain on investments, net of tax		—		—		—		39			—			—			39
Net loss		—		—		—		—			(11,340	)		(2	)		(11,342	)
Balance as of September 30, 2023		58,560,061	$	59	$	551,888	$	(294	)	$	(453,263	)	$	(187	)	$	98,203

	Three and Nine Months Ended September 30, 2022 (unaudited)
	Common Stock				Additional Paid-In		Other Comprehensive			Accumulated			Noncontrolling			Total Stockholders’
	Shares		Amount		Capital		Gain/(Loss)			Deficit			Interest			Equity
Balance as of December 31, 2021		27,793,035	$	28	$	481,832	$	(263	)	$	(372,296	)	$	(175	)	$	109,126
Issuance of common stock upon release of restricted stock units		2,500		—		—		—			—			—			—
Issuance of common stock upon exercise of stock options		259		—		1		—			—			—			1
Issuance of common stock from at-the-market offerings, net of offering costs		260,455		—		1,480		—			—			—			1,480
Stock-based compensation		—		—		417		—			—			—			417
Net unrealized loss on investments, net of tax		—		—		—		(496	)		—			—			(496	)
Net loss		—		—		—		—			(12,153	)		(1	)		(12,154	)
Balance as of March 31, 2022		28,056,249		28		483,730		(759	)		(384,449	)		(176	)		98,374
Issuance of common stock pursuant to employee stock purchase plan		1,958		—		5		—			—			—			5
Issuance of common stock from at-the-market offerings, net of offering costs		69,251		—		34		—			—			—			34
Stock-based compensation		—		—		517		—			—			—			517
Net unrealized loss on investments, net of tax		—		—		—		(51	)		—			—			(51	)
Net loss		—		—		—		—			(12,420	)		(1	)		(12,421	)
Balance as of June 30, 2022		28,127,458		28		484,286		(810	)		(396,869	)		(177	)		86,458
Issuance of common stock from at-the-market offerings, net of offering costs		881,924		1		3,036		—			—			—			3,037
Stock-based compensation		—		—		615		—			—			—			615
Net unrealized gain on investments, net of tax		—		—		—		141			—			—			141
Net loss		—		—		—		—			(13,244	)		(1	)		(13,245	)
Balance as of September 30, 2022		29,009,382	$	29	$	487,937	$	(669	)	$	(410,113	)	$	(178	)	$	77,006

See accompanying notes.

aTyr Pharma, Inc.

Condensed Consolidated Statements of Cash Flows

(in thousands)


	Nine Months Ended September 30,
	2023			2022
	(unaudited)
Cash flows from operating activities:
Consolidated net loss	$	(35,636	)	$	(37,820	)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization		417			193
Stock-based compensation		1,941			1,549
(Accretion) amortization of (discount) premium of available-for-sale investment securities		(2,278	)		565
Amortization of right-of-use assets		1,917			805
Gain on disposal of property and equipment		(13	)		(95	)
Changes in operating assets and liabilities:
Other receivables		9,512			70
Prepaid expenses and other assets		(10	)		(1,174	)
Accounts payable and accrued expenses		(126	)		4,878
Operating lease liability		2,117			(488	)
Net cash used in operating activities		(22,159	)		(31,517	)
Cash flows from investing activities:
Purchases of property and equipment		(4,198	)		(522	)
Purchases of available-for-sale investment securities		(97,312	)		(17,124	)
Maturities of available-for-sale investment securities		63,550			62,713
Proceeds from sale of property and equipment		15			179
Net cash (used in) provided by investing activities		(37,945	)		45,246
Cash flows from financing activities:
Proceeds from issuance of common stock through option exercises		—			1
Proceeds from issuance of common stock through employee stock purchase plan		65			5
Proceeds from issuance of common stock from at-the-market offerings, net of offering costs		12,337			4,551
Proceeds from issuance of common stock from underwritten follow-on public offering, net of offering costs		48,073			(24	)
Principal paid on finance lease liabilities		(279	)		—
Net cash provided by financing activities		60,196			4,533
Net change in cash, cash equivalents and restricted cash		92			18,262
Cash, cash equivalents and restricted cash at beginning of period		13,146			2,336
Cash, cash equivalents and restricted cash at the end of period	$	13,238		$	20,598

Cash and cash equivalents at the end of period	$	9,787		$	18,359
Restricted cash at the end of period		3,451			2,239
Cash, cash equivalents and restricted cash at the end of period	$	13,238		$	20,598

Supplemental disclosure of cash flow information:
Interest paid	$	133		$	—