What changed in this filing

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Item 1. Financial Statements

2025-11-06 compared with 2025-08-07 · 70 added, 54 removed, 390 unchanged (24% 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 June 30, 2025 (unaudited) and December 31, 2024, no shares issued or outstanding as of June 30, 2025 (unaudited) and December 31, 2024

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

Common stock, $ 0.001 par value per share;

170,000,000 authorized shares as of June 30, 2025 (unaudited) and December 31, 2024, issued and outstanding shares – 92,871,182 as of June 30, 2025 (unaudited) and 84,038,922 as of December 31, 2024

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

Additional paid-in capital

10 unchanged sentences

(in thousands, except share and per share data)

Three Months Ended June 30,

Six Months Ended June 30,

Three Months Ended September 30,

Nine Months Ended September 30,

License and collaboration agreement revenues

15 unchanged sentences

(in thousands)

Three Months Ended June 30,

Six Months Ended June 30,

Three Months Ended September 30,

Nine Months Ended September 30,

Consolidated net loss

Other comprehensive loss:

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

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

Comprehensive loss

6 unchanged sentences

(in thousands, except share data)

Three and Six Months Ended June 30, 2025 (unaudited)

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

Comprehensive

14 unchanged sentences

Balance as of June 30, 2025

Three and Six Months Ended June 30, 2024 (unaudited)

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)

Comprehensive

13 unchanged sentences

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)

Six Months Ended June 30,

Nine Months Ended September 30,

Cash flows from operating activities:

54 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 $ 19.5 million and $ 34.4 million for the three and six months ended June 30, 2025.

As of June 30, 2025, we had an accumulated deficit of $ 566.5 million.

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 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 six months ended June 30, 2025, we sold an aggregate of 8,771,725 shares of common stock at a weighted-average price of $ 4.32 per share for net proceeds of approximately $ 36.7 million under the Jefferies ATM Offering Program.

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 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.

5 unchanged sentences

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 $ 83.2 million as of June 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 $ 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.

Restricted Cash

As of June 30, 2025, restricted cash was approximately $ 2.9 million, of which $ 2.4 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 $ 0.5 million was held as security deposit for our corporate credit card program.

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 (CARES Act), we were eligible to claim the employee retention credit (ERC), which is a refundable tax credit against certain employment taxes.

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 June 30, 2025, we have fully received the ERC benefits refund.

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

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):

Six Months Ended June 30,

Nine Months Ended September 30,

Common stock warrants

5 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 six months ended June 30, 2025 and 2024.

Three Months Ended June 30,

Six Months Ended June 30,

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

42 unchanged sentences

for Identical

As of June 30, 2025

As of September 30, 2025

Cash equivalents

2 unchanged sentences

Corporate debt securities

government agencies

Municipal bonds

Total available-for-sale investments

12 unchanged sentences

Total assets measured at fair value

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

June 30, 2025

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

September 30, 2025

Contractual Maturity

4 unchanged sentences

Within 1 year

government agencies

Within 1 year

Municipal bonds

Within 2 years

December 31, 2024

11 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 June 30, 2025.

As of June 30, 2025, all available-for-sale investments had a variety of effective maturity dates of less than one year .

As of June 30, 2025, 21 out of 23 available-for-sale investments were in a gross unrealized loss position.

As of June 30, 2025 and December 31, 2024, accrued interest receivable on available-for-sale investments was $ 0.3 million and $ 0.2 million, respectively.

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.

License, Collaboration and Other Agreements

6 unchanged sentences

Efzofitimod was observed to be generally well-tolerated with no drug-related serious adverse events, and PK findings were consistent with previous studies of efzofitimod.

Kyorin is also participating in the EFZO-FIT study as the local sponsor in Japan.

Kyorin has also participated in the EFZO-FIT study as the local sponsor in Japan.

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.

2 unchanged sentences

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 the six months ended June 30, 2025 and 2024, we recognized $ 0 and $ 0.2 million, respectively, in collaboration revenue from Kyorin for drug product material sold to Kyorin for the Japan portion of the EFZO-FIT study.

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.

11 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 June 30, 2025.

Future minimum payments under the facility lease and a reconciliation to the operating lease liability as of June 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 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):

Operating Leases

4 unchanged sentences

Long-term operating lease liability, net of current portion

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

For the six months ended June 30, 2025 and 2024, we recorded an operating lease expense of $ 0.8 million and $ 0.7 million, respectively.

As of June 30, 2025, the weighted-average remaining lease term was 8.1 years and the weighted average discount rate was 8.8 %.

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 %.

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 June 30, 2025 were as follows (in thousands):

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

Financing Leases

3 unchanged sentences

Long-term financing lease liability, net of current portion

As of June 30, 2025, the weighted-average remaining lease term was 1.6 years and the weighted-average discount rate was 8.3 %.

As of June 30, 2025, we have a $ 1.7 million deposit held as collateral for the leased equipment, and this deposit is included in restricted cash.

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.

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

District Court for the Southern District of California, naming aTyr Pharma, Inc.

and our Chief Executive Officer, Sanjay Shukla .

The complaints allege certain violations of the U.S.

federal securities laws and seek unspecific damages.

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

No such liability has been recorded related to this matter.

With regard to legal fees, such as attorney fees related to this matter or any other legal matters, we recognize such costs as incurred.

Stockholders’ Equity

5 unchanged sentences

During the year ended December 31, 2024, we sold an aggregate of 20,653,450 shares of common stock at a weighted-average price of $ 2.02 per share for net proceeds of approximately $ 40.3 million under the Jefferies ATM Offering Program.

Common Stock Reserved for Future Issuance

Common stock reserved for future issuance was as follows:

June 30, 2025

September 30, 2025

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 six months ended June 30, 2025:

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

Stock Options

2 unchanged sentences

Canceled/forfeited/expired

Outstanding as of June 30, 2025

Outstanding as of September 30, 2025

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 June 30,

Six Months Ended June 30,

Three Months Ended September 30,

Nine Months Ended September 30,

Expected term (in years)

3 unchanged sentences

3.8 % – 4.5 %

3.6 % – 4.5 %

Expected volatility

4 unchanged sentences

Expected dividend yield

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

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

Number of Outstanding

2 unchanged sentences

Balance as of December 31, 2024

Balance as of June 30, 2025

Balance as of September 30, 2025

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 June 30,

Six Months Ended June 30,

Three Months Ended September 30,

Nine Months Ended September 30,

Research and development

1 unchanged sentence

Total stock-based compensation expense

Subsequent Events

Sales of Common Stock through the Jefferies ATM Offering Program

From July 1, 2025 through August 6, 2025, we sold an aggregate of 5,115,452 shares of common stock at a weighted-average price of $ 6.00 per share through the Jefferies ATM Offering Program for net proceeds of $ 29.8 million.

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