What changed in this filing

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Item 1. Financial Statements

2026-05-15 compared with 2025-11-06 · 79 added, 111 removed, 349 unchanged (35% of the section changed)

3 unchanged sentences

(in thousands, except share and per share data)

September 30,

Current assets:

20 unchanged sentences

Preferred stock, $ 0.001 par value per share;

5,000,000 undesignated authorized shares as of September 30, 2025 (unaudited) and December 31, 2024, no shares issued or outstanding as of September 30, 2025 (unaudited) and December 31, 2024

5,000,000 undesignated authorized shares as of March 31, 2026 (unaudited) and December 31, 2025, respectively;

no shares issued or outstanding as of March 31, 2026 (unaudited) and December 31, 2025

Common stock, $ 0.001 par value per share;

170,000,000 authorized shares as of September 30, 2025 (unaudited) and December 31, 2024, issued and outstanding shares – 97,986,634 as of September 30, 2025 (unaudited) and 84,038,922 as of December 31, 2024

170,000,000 authorized shares as of March 31, 2026 (unaudited) and December 31, 2025;

issued and outstanding shares – 98,051,212 as of March 31, 2026 (unaudited) and 98,031,104 as of December 31, 2025

Additional paid-in capital

10 unchanged sentences

(in thousands, except share and per share data)

Three Months Ended September 30,

Nine Months Ended September 30,

License and collaboration agreement revenues

Total revenues

Three Months Ended March 31,

Operating expenses:

5 unchanged sentences

Consolidated net loss

Net loss (gain) attributable to noncontrolling interest in Pangu BioPharma Limited

Net loss attributable to noncontrolling interest in Pangu BioPharma Limited

Net loss attributable to aTyr Pharma, Inc.

5 unchanged sentences

(in thousands)

Three Months Ended September 30,

Nine Months Ended September 30,

Three Months Ended March 31,

Consolidated net loss

Other comprehensive loss:

Change in unrealized gain on available-for-sale investments, net of tax

Change in unrealized loss on available-for-sale investments, net of tax

Comprehensive loss

Comprehensive loss (gain) attributable to noncontrolling interest in Pangu BioPharma Limited

Comprehensive loss attributable to noncontrolling interest in Pangu BioPharma Limited

Comprehensive loss attributable to aTyr Pharma, Inc.

4 unchanged sentences

(in thousands, except share data)

Three and Nine Months Ended September 30, 2025 (unaudited)

Three Months Ended March 31, 2026 (unaudited)

Comprehensive

3 unchanged sentences

Issuance of common stock upon release of restricted stock units

Issuance of common stock upon exercise of stock options

Issuance of common stock from at-the-market offerings, net of offering costs

Stock-based compensation

1 unchanged sentence

Balance as of March 31, 2026

Issuance of common stock upon exercise of stock options

Issuance of common stock pursuant to employee stock purchase plan

Issuance of common stock from at-the-market offerings, net of offering costs

Stock-based compensation

Net unrealized loss on investments, net of tax

Balance as of June 30, 2025

Issuance of common stock from at-the-market offerings, net of offering costs

Stock-based compensation

Net unrealized gain on investments, net of tax

Balance as of September 30, 2025

Three and Nine Months Ended September 30, 2024 (unaudited)

Three Months Ended March 31, 2025 (unaudited)

Comprehensive

3 unchanged sentences

Issuance of common stock upon release of restricted stock units

Issuance of common stock upon exercise of stock options

Issuance of common stock from at-the-market offerings, net of offering costs

1 unchanged sentence

Net unrealized loss on investments, net of tax

Net (loss) gain

Balance as of March 31, 2025

Issuance of common stock pursuant to employee stock purchase plan

Issuance of common stock from at-the-market offerings, net of offering costs

Stock-based compensation

Net unrealized loss on investments, net of tax

Balance as of June 30, 2024

Issuance of common stock from at-the-market offerings, net of offering costs

Stock-based compensation

Net unrealized gain on investments, net of tax

Balance as of September 30, 2024

See accompanying notes.

2 unchanged sentences

(in thousands)

Nine Months Ended September 30,

Three Months Ended March 31,

Cash flows from operating activities:

15 unchanged sentences

Maturities of available-for-sale investment securities

Net cash (used in) provided by investing activities

Net cash provided by (used in) investing activities

Cash flows from financing activities:

Proceeds from issuance of common stock through option exercises

Proceeds from issuance of common stock through employee stock purchase plan

Proceeds from issuance of common stock from at-the-market offerings, net of offering costs

Principal paid on finance lease liabilities

Net cash provided by financing activities

Net cash (used in) provided by financing activities

Net change in cash, cash equivalents and restricted cash

30 unchanged sentences

Liquidity and Financial Condition

We have incurred net losses and negative cash flows from operations since our inception in 2005, including a consolidated net loss of $ 25.7 million and $ 60.2 million for the three and nine months ended September 30, 2025.

As of September 30, 2025, we had an accumulated deficit of $ 592.2 million.

We have incurred net losses and negative cash flows from operations since our inception in 2005, including a consolidated net loss of $ 10.8 m illion for the three months ended March 31, 2026.

As of March 31, 2026, we had an accumulated deficit of $ 617.0 million.

We currently have an “at-the-market” offering program (the Jefferies ATM Offering Program) through an Open Market Sale Agreement SM with Jefferies LLC (Jefferies).

During the nine months ended September 30, 2025, we sold an aggregate of 13,887,177 shares of common stock at a weighted-average price of $ 4.94 per share for net proceeds of approximately $ 66.4 million under the Jefferies ATM Offering Program.

We did not utilize the Jefferies ATM Offering Program during the three months ended March 31, 2026.

We do not expect to generate any revenues from product sales unless and until we successfully complete development and obtain regulatory approval for one or more of our product candidates, which we expect will take a number of years at a minimum.

1 unchanged sentence

Accordingly, we will need to raise substantial additional capital to fund our operations.

The amount and timing of our future funding requirements will depend on many factors, including the pace and results of our preclinical, clinical and manufacturing development efforts and the timing and nature of the regulatory approval process for our product candidates, including pre-commercial activities.

The amount and timing of our future funding requirements will depend on many factors, including the pace and results of our preclinical and clinical development efforts and the timing and nature of the regulatory approval process for our product candidates.

We anticipate that we will seek to fund our operations through equity offerings, grant funding, collaborations, strategic partnerships and/or licensing arrangements, and when we are closer to commercialization of our product candidates potentially through debt financings.

1 unchanged sentence

Our failure to raise capital or enter into such arrangements when needed would have a negative impact on our financial condition and ability to develop our product candidates.

We believe that our existing cash, cash equivalents, restricted cash and available-for-sale investments of $ 92.9 million as of September 30, 2025 will be sufficient to meet our material cash requirements from known contractual and other obligations for a period of at least one year from the filing date of this Quarterly Report on Form 10-Q.

We believe that our existing cash, cash equivalents, restricted cash and available-for-sale investments of $ 68.3 million as of March 31, 2026 will be sufficient to meet our material cash requirements from known contractual and other obligations for a period of at least one year from the filing date of this Quarterly Report on Form 10-Q.

Restricted Cash

As of September 30, 2025, restricted cash was approximately $ 2.7 million, of which $ 2.3 million was held as a security deposit in conjunction with our corporate headquarters facility lease and financing leases as discussed further in Note 4 - Commitments and Contingencies and $ 0.4 million was held as security deposit for our corporate credit card program.

Employee Retention Credit

Under the Coronavirus Aid, Relief, and Economic Security Act of 2020, we were eligible to claim the employee retention credit (ERC), which is a refundable tax credit against certain employment taxes.

During the year ended December 31, 2023, we amended certain payroll tax filings and applied for a refund of $ 1.2 million of ERC benefits.

The refund was recorded within the other receivables in our audited consolidated balance sheets, and as a $ 0.8 million reduction of research and development expenses and a $ 0.4 million reduction of general and administrative expenses in our audited consolidated statements of operations for the year ended December 31, 2023.

As of September 30, 2025, we have fully received the ERC benefits refund.

As of March 31, 2026, restricted cash was approximate ly $ 1.8 mil lion, which was held as a security deposit in conjunction with our corporate headquarters facility lease and financing leases as discussed further in Note 4 - Commitments and Contingencies.

Allowance of Credit Losses

55 unchanged sentences

Potentially dilutive securities not considered for the calculation of diluted net loss per share are as follows (in common stock equivalents):

Nine Months Ended September 30,

Common stock warrants

Common stock options and restricted stock units

4 unchanged sentences

Our CODM is our Chief Executive Officer , who reviews and evaluates consolidated research and development expenses, general and administrative expenses, net loss, net cash used in operating activities and our consolidated cash and cash equivalents for purposes of making operating decisions, allocating resources and planning and forecasting future periods.

The table below summarizes the significant expense categories regularly reviewed by our CODM for the three and nine months ended September 30, 2025 and 2024.

Three Months Ended September 30,

Nine Months Ended September 30,

License and collaboration agreement revenues

The table below summarizes the significant expense categories regularly reviewed by our CODM for the three months ended March 31, 2026 and 2025.

Three Months Ended March 31,

Research and development expenses:

9 unchanged sentences

Consolidated net loss

(1) Other segment items included interest income and interest expense.

(1) Other segment items includes interest income and interest expense.

Recent Accounting Pronouncements

In December 2023, the Financial Accounting Standards Board (FASB) issued Accounting Standard Update (ASU) 2023-09, Improvements to Income Tax Disclosures, which requires entities to disclose disaggregated information about their effective tax rate reconciliation as well as expanded information on income taxes paid by jurisdiction.

The disclosure requirements will be applied on a prospective basis, with the option to apply them retrospectively.

We adopted the standard on January 1, 2025 .

The adoption did not have a material effect on our consolidated financial statements disclosures.

In November 2024, the FASB issued ASU 2024-03, which requires entities to disclose, on an annual and interim basis, disaggregated information about certain income statement expense line items on the face of the income statement.

The guidance addresses investors’ requests for more detailed expense information, which they said is critical to understanding an entity’s performance, assessing its prospects for future cash flows, and comparing its performance both over time and with that of other entities.

The standard is effective for fiscal years beginning after December 15, 2026 and interim periods within fiscal years beginning after December 15, 2027 with early adoption permitted .

We are currently evaluating the disclosure requirements related to the new standard.

In November 2024, the Financial Accounting Standards Board (FASB) issued Accounting Standard Update (ASU) 2024-03, Income Statement - Reporting Comprehensive Income - Expense Disaggregation Disclosures (Subtopic 220-40), which requires entities to disclose, on an annual and interim basis, disaggregated information about certain income statement expense line items on the face of the income statement.

The standard is effective for annual reporting periods beginning after December 15, 2026 and interim periods within annual reporting periods beginning after December 15, 2027, with early adoption permitted.

We are currently evaluating the impact of the standard on our consolidated financial statements and related disclosure.

Fair Value Measurements

20 unchanged sentences

for Identical

As of September 30, 2025

As of March 31, 2026

Cash equivalents

14 unchanged sentences

Corporate debt securities

government agencies

Municipal bonds

Total available-for-sale investments

Total assets measured at fair value

As of September 30, 2025 and December 31, 2024, available-for-sale investments are detailed as follows (in thousands):

September 30, 2025

As of March 31, 2026 and December 31, 2025, available-for-sale investments are detailed as follows (in thousands):

March 31, 2026

Contractual Maturity

5 unchanged sentences

Municipal bonds

Within 2 years

Within 1 year

December 31, 2025

4 unchanged sentences

Corporate debt securities

Within 1 years

government agencies

Within 1 year

Municipal bonds

Within 1 year

We evaluate our available-for-sale debt securities for credit losses when the amortized cost basis exceeds fair value.

2 unchanged sentences

When evaluating an investment for impairment, we review factors such as the severity of the impairment, changes in underlying credit ratings, our intent to sell or the likelihood that we would be required to sell the investment before its anticipated recovery in market value and the probability that the scheduled cash payments will continue to be made.

We recorded no allowance for credit losses in the unaudited condensed consolidated statements of operations and comprehensive loss during the three and six months ended September 30, 2025.

As of September 30, 2025, all available-for-sale investments had a variety of effective maturity dates of less than two years .

As of September 30, 2025, $ 79.0 million of our short-term investments had maturities less than one year and $ 5.1 million had maturities greater than one year.

As of September 30, 2025, 7 out of 28 available-for-sale investments were in a gross unrealized loss position, no ne of which were at such position for greater than 12 months .

As of September 30, 2025 and December 31, 2024, accrued interest receivable on available-for-sale investments was $ 0.5 million and $ 0.3 million, respectively.

We recorded no allowance for credit losses in the unaudited condensed consolidated statements of operations and comprehensive loss during the three months ended March 31, 2026.

As of March 31, 2026, all available-for-sale investments had a variety of effective maturity dates of less than one year .

As of March 31, 2026, 11 out of 18 available-for-sale investments were in a gross unrealized loss position, all of which have held this status for less than one year.

As of March 31, 2026 and December 31, 2025, accrued interest receivable on available-for-sale investments was $ 0.4 million for each period.

License, Collaboration and Other Agreements

8 unchanged sentences

In February 2023, Kyorin dosed the first patient in Japan in the EFZO-FIT study which triggered a $ 10.0 million milestone payment to us.

To date, the Kyorin Agreement has generated $ 20.0 million in upfront and milestone payments to us and we are eligible to receive up to an additional $ 155.0 million in the aggregate upon achievement of certain development, regulatory and sales milestones, as well as tiered royalties on any net sales in Japan.

Either party may terminate the Kyorin Agreement in the event that the other party breaches the agreement and fails to cure the breach, becomes insolvent or challenges certain of the intellectual property rights licensed under the agreement.

To date, the Kyorin Agreement has generated $ 20.0 million in upfront and milestone payments to us.

We assessed our license and collaboration with Kyorin in accordance with Topic 606 which applies to delivered goods or services to a customer and concluded that Kyorin is a customer.

For each of the nine months ended September 30, 2025 and 2024, we recognized $ 0.2 million in collaboration revenue from Kyorin for drug product material sold to Kyorin.

The remaining milestones and royalty payments under the Kyorin Agreement are variable consideration.

Since milestone payments are binary in nature, we will use the “most-likely” method to evaluate whether the milestones should be included as revenue.

We will constrain these amounts until the milestone is probable of being achieved.

The royalties are dependent on future sales by Kyorin which are at the full discretion of Kyorin.

Accordingly, we constrain these amounts until the future sales have occurred.

For the three months ended March 31, 2026 and 2025, t here were no activities that triggered additional license and collaboration agreement revenue under the Kyorin Agreement.

On May 12, 2026 we received notice of termination of the Kyorin Agreement with Kyorin.

Refer to our discussion of the termination in Note 6 – Subsequent Events.

Commitments and Contingencies

6 unchanged sentences

The amendment increased the total rentable square feet from 23,696 rentable square feet to 24,866 rentable square feet.

We provided a $ 0.7 million security deposit in the form of a letter of credit which is included in restricted cash as of September 30, 2025.

Future minimum payments under the facility lease and a reconciliation to the operating lease liability as of September 30, 2025 were as follows (in thousands):

We provided a $ 0.7 million security deposit in the form of a letter of credit which is included in restricted cash as of March 31, 2026.

Future minimum payments under the facility lease and a reconciliation to the operating lease liability as of March 31, 2026 were as follows (in thousands):

Operating Leases

4 unchanged sentences

Long-term operating lease liability, net of current portion

For each of the three months ended September 30, 2025 and 2024, we recorded an operating lease expense of $ 0.4 million.

For the nine months ended September 30, 2025 and 2024, we recorded an operating lease expense of $ 1.2 million and $ 1.1 million, respectively.

As of September 30, 2025, the weighted-average remaining lease term was 7.8 years and the weighted average discount rate was 8.8 %.

For each of the three months ended March 31, 2026 and 2025, we recorded an operating lease expense of $ 0.4 million.

As of March 31, 2026, the weighted-average remaining lease term was 7.3 years and the weighted average discount rate was 8.8 %.

Financing Leases

In April 2022, we entered into a master financing lease agreement to lease various research and development and information technology equipment over a 48-month term.

Future minimum payments under the financing lease and reconciliation to the financing lease liability as of September 30, 2025 were as follows (in thousands):

Future minimum payments under the financing lease and reconciliation to the financing lease liability as of March 31, 2026 were as follows (in thousands):

Financing Leases

3 unchanged sentences

Long-term financing lease liability, net of current portion

As of September 30, 2025, the weighted-average remaining lease term was 1.3 years and the weighted-average discount rate was 8.4 %.

As of September 30, 2025, we have a $ 1.5 million deposit held as collateral for the leased equipment, and this deposit is included in restricted cash.

As of March 31, 2026, the weighted-average remaining lease term was 1.0 years and the weighted-average discount rate was 8.4 %.

As of March 31, 2026, we have a $ 1.1 million deposit held as collateral for the leased equipment, and this deposit is included in restricted cash.

On October 9, 2025 and October 22, 2025 , two substantially similar putative securities class action complaints were filed in the U.S.

1 unchanged sentence

and our Chief Executive Officer, Sanjay Shukla.

The complaints allege certain violations of the U.S.

federal securities laws and seek unspecific damages.

The complaints assert that we and Mr.

Shukla violated Section 10(b) of the Exchange Act of 1934, as amended (the Exchange Act), and SEC Rule 10b-5, by making materially false or misleading statements related to efzofitimod.

The complaints also assert that Mr.

Shukla violated Section 20(a) of the Exchange Act.

Plaintiffs seek class certification, an award of unspecified damages, and award of reasonable costs and expenses, including attorneys’ fees and expert fees, and further relief as the court may deem just and proper.

On February 9, 2026, the court consolidated the two cases and appointed co-lead plaintiffs to oversee the litigation.

On May 1, 2026, co-lead plaintiffs filed an Amended Consolidated Complaint.

The Amended Consolidated Complaint is based on the same underlying allegations as the original complaints, asserts the same claims and seeks the same relief, and adds our Chief Financial Officer, Jill M.

Broadfoot, as a defendant.

Under the current schedule, the deadline to respond to the Amended Consolidated Complaint, including by filing a motion to dismiss, is July 17, 2026.

Any opposition to a motion to dismiss is due August 28, 2026 , with any reply due September 28, 2026 .

We make provisions for liabilities when they are both probable that a liability has been incurred and the amount can be reasonably estimated.

5 unchanged sentences

In December 2024, we amended the Jefferies ATM Offering Program.

Under the Jefferies ATM Offering Program we may offer and sell, from time to time and at our option, up to an aggregate of $ 215.0 million of shares of our common stock (inclusive of $ 65.0 million of sales made prior to the amendment) through Jefferies, acting as sales agent.

Under the Jefferies ATM Offering Program we may

offer and sell, from time to time and at our option, up to an aggregate of $ 215.0 million of shares of our common stock (inclusive of $ 65.0 million of sales made prior to the amendment) through Jefferies, acting as sales agent.

Jefferies is entitled to a fixed commission rate of up to 3.0 % of the gross sales proceeds of shares sold under the Jefferies ATM Offering Program.

We did not utilize the Jefferies ATM Offering Program during the three months ended March 31, 2026.

During the year ended December 31, 2025, we sold an aggregate of 13,887,177 shares of common stock at a weighted-average price of $ 4.94 per share for net proceeds of approximately $ 66.4 million under the Jefferies ATM Offering Program.

Common Stock Reserved for Future Issuance

Common stock reserved for future issuance was as follows:

September 30, 2025

March 31, 2026

Common stock options and restricted stock units

2 unchanged sentences

Shares available under the employee stock purchase plan

The following table summarizes our stock option activity under all equity incentive plans for the nine months ended September 30, 2025:

The following table summarizes our stock option activity under all equity incentive plans for the three months ended March 31, 2026:

Stock Options

2 unchanged sentences

Canceled/forfeited/expired

Outstanding as of September 30, 2025

Outstanding as of March 31, 2026

The assumptions used in the Black-Scholes option pricing model to determine the fair value of the employee stock option grants were as follows:

Three Months Ended September 30,

Nine Months Ended September 30,

Three Months Ended March 31,

Expected term (in years)

2 unchanged sentences

4.1 % – 4.5 %

3.8 % – 4.5 %

3.6 % – 4.5 %

Expected volatility

1 unchanged sentence

75.9 % – 77.2 %

75.9 % – 77.9 %

76.6 % – 80.5 %

Expected dividend yield

The following table summarizes our restricted stock unit activity under all equity incentive plans for the nine months ended September 30, 2025:

The following table summarizes our restricted stock unit activity under all equity incentive plans for the three months ended March 31, 2026:

Number of Outstanding

2 unchanged sentences

Balance as of December 31, 2025

Balance as of September 30, 2025

Balance as of March 31, 2026

Stock-based Compensation

The allocation of stock-based compensation for all options and restricted stock units and stock issued pursuant to our employee stock purchase plan is as follows (in thousands):

Three Months Ended September 30,

Nine Months Ended September 30,

Three Months Ended March 31,

Research and development

1 unchanged sentence

Total stock-based compensation expense

Subsequent Events

On May 12, 2026, we received notice of termination of the Kyorin Agreement with Kyorin.

Kyorin elected to terminate the Kyorin Agreement without cause in accordance with the terms of the Kyorin Agreement, and the termination will become effective 90 days after the date of receipt of the notice of termination (the Termination Date).

Under the terms of the Kyorin Agreement, Kyorin received exclusive rights to develop and commercialize efzofitimod in Japan for all forms of interstitial lung disease and is obligated to fund all research, development, regulatory, marketing and commercialization activities in Japan until the Termination Date.

We are responsible for supplying all drug product for Japan, as well as supporting development activities for efzofitimod, until the Termination Date.

As a result of the termination of the Kyorin Agreement, we will not be entitled to receive any further milestone or other payments, including $ 155.0 million in the aggregate that would have been due upon achievement of certain development, regulatory and sales milestones, as well as tiered royalties on any net sales in Japan.

Both parties will also cease to have any development or commercialization obligations after the Termination Date and the licenses we granted to Kyorin pursuant to the Kyorin Agreement will cease to be in effect after the Termination Date.

Following the Termination Date, the rights to develop and commercialize efzofitimod in Japan for all forms of ILD will revert to us.

Consequently, we will hold the rights to develop and commercialize efzofitimod globally.

Compared sentence by sentence after normalising whitespace, quotation marks, case and digits, so re-formatting and restated figures do not read as changed language. Wording changes appear as one removal and one addition. The current filing and the prior one are authoritative.

What changed 10-Q

Item 1. Financial Statements