SecProbe.io

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 aTyr Pharma, Inc . 10240 Sorrento Valley Road, Suite 300 San Diego, California 92121 August 14, 2025 Securities and Exchange Commission Division of Corporation Finance Office of Life Sciences 100 F. Street N.E. Washington, D.C. 20549-3010 Attention: Tyler Howes

 Re:
 aTyr Pharma, Inc.

 Registration Statement on Form S-3

 Filed: August 7, 2025

 File No. 333-289360

   Ladies and Gentlemen: aTyr Pharma, Inc. (the “ Registrant ”) hereby requests that the U.S. Securities and Exchange Commission (the “ Commission ”) take appropriate action to cause the above-referenced Registration Statement on Form S-3 to become effective on August 18, 2025, at 4:00 p.m., Eastern Time, or as soon thereafter as is practicable or at such later time as the Registrant may orally request via telephone call to the staff of the Commission. The Registrant hereby authorizes Charles Bair and Nicholaus Johnson of Cooley LLP, counsel to the Registrant, to make such request on its behalf. Once the Registration Statement has been declared effective, please orally confirm that event with Charles Bair of Cooley LLP at (858) 550-6142 or, in his absence, Nicholaus Johnson of Cooley LLP at (858) 550-6198. [ Signature Page Follows ]

   Very truly yours, ATYR PHARMA, INC.

 By:
 /s/ Jill M. Broadfoot

 Name:
 Jill Broadfoot

 Title:
 Chief Financial Officer

 cc:
 Charles Bair, Cooley LLP

 Nicholaus Johnson, Cooley LLP

 Nancy Denyes, aTyr Pharma, Inc.

 [ Company Signature Page to Acceleration Request ]

<DOCUMENT>
<TYPE>TEXT-EXTRACT
<SEQUENCE>2
<FILENAME>filename2.txt
<TEXT>
 August 13, 2025

Sanjay Shukla
Chief Executive Officer
aTyr Pharma, Inc.
10240 Sorrento Valley Road, Suite 300
San Diego, CA 92121

 Re: aTyr Pharma, Inc.
 Registration Statement on Form S-3
 Filed August 7, 2025
 File No. 333-289360
Dear Sanjay Shukla:

 This is to advise you that we have not reviewed and will not review your
registration
statement.

 Please refer to Rules 460 and 461 regarding requests for acceleration.
We remind you
that the company and its management are responsible for the accuracy and
adequacy of their
disclosures, notwithstanding any review, comments, action or absence of action
by the staff.

 Please contact Tyler Howes at 202-551-3370 with any questions.

 Sincerely,

 Division of
Corporation Finance
 Office of Life
Sciences
cc: Charles Bair, Esq.
</TEXT>
</DOCUMENT>

United States securities and exchange commission logo
June 25, 2024
Jill Broadfoot
Chief Financial Officer
aTYR PHARMA INC
10240 Sorrento Valley Road
Suite 300
San Diego, CA 92014
Re:aTYR PHARMA INC
Form 10-K for Fiscal Year Ended December 31, 2023
File No. 001-37378
Dear Jill Broadfoot:
            We have completed our review of your filings. We remind you that the company and its
management are responsible for the accuracy and adequacy of their disclosures, notwithstanding
any review, comments, action or absence of action by the staff.
Sincerely,
Division of Corporation Finance
Office of Life Sciences

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  CORRESP

  June 18, 2024

  VIA EDGAR

  U.S. Securities and Exchange Commission

  Division of Corporation Finance

  Office of Life Sciences

  100 F Street, N.E.

  Washington, D.C. 20549

    Attn:

    Lynn Dicker

    Kevin Kuhar

    Re:

    aTyr Pharma, Inc.

    Form 10-K for fiscal Year Ended December 31, 2023

    File No. 001-37378

  Dear Lynn Dicker and Kevin Kuhar:

  We are writing in response to the comment received from the staff (the “Staff”) of the Securities and Exchange Commission (the “Commission”) by letter dated June 6, 2024 with respect to the above-referenced filing of aTyr Pharma, Inc. (the “Company”). For your convenience, we have repeated the Staff’s comment before the Company’s response below.

  Form 10-K for Fiscal Year Ended December 31, 2023

  Item 7.  Management’s Discussion and Analysis of Financial Condition and Results of Operations Research and Development Expenses, page 68

  1.We note from the pipeline table on page 6 that you have multiple products in clinical development for several indications. Please revise future filings to disclose the costs incurred during each period presented for each of your key research and development product candidates. If you do not track your research and development costs by project, disclose that fact and explain why you do not maintain and evaluate research and development costs by project. Also, revise to provide other quantitative and qualitative disclosures that give more transparency as to the type of research and development expenses incurred (i.e., by nature or type of expense) which should reconcile to total research and development expenses on your Statements of Operations.

  We acknowledge the Staff’s comment and respectfully advise the Staff that we currently track the majority of our product candidate costs for efzofitimod, our only product candidate in clinical development, which drives the majority of our total research and development (“R&D”) expense. For efzofitimod, we primarily outsource our clinical development efforts, including work with clinical research organizations to administer clinical trials, as well as contracted development and manufacturing organizations to manufacture the drug product needed to conduct the clinical trials and other studies to support the advancement of the product candidate. These external expenses are substantially higher than the expenses we incur on our other product candidates which are all in preclinical development, and we believe tracking R&D expenses for our preclinical product

  1

  candidates would not materially enhance an investor’s understanding of our total R&D expenses. Further, the nature of the internal expenses incurred to advance candidates through preclinical development is primarily personnel expenses and laboratory supply expenses. We do not fully track or allocate these internal expenses between preclinical product candidates because the expenses can often be shared between candidates. Additionally, we incur other shared expenses to support our R&D efforts such as facilities expenses, and these expenses are not allocated to efzofitimod or the preclinical product candidates. Finally, our non-cash R&D expenses such as depreciation and stock-based compensation are not tracked or allocated between product candidates and are shared among all product candidates.

  Given that the majority of our R&D expenses are for efzofitimod, which we track, and that we do not fully track and allocate external and internal R&D expenses for our other preclinical product candidates or for certain shared R&D expenses, we intend to enhance our tabular disclosures of R&D expenses in our future periodic reports as shown below. Additionally, we will continue to provide narrative disclosure about the material drivers affecting period-over-period changes in R&D expenses.

  The following table summarizes our results of operations for the [ ] months ended [ ] and [ ] (in thousands):

    [ ] Months Ended [ ]

    2024

    2023

    Change

    Research and development expenses:

       Efzofitimod expenses

    $

    —

    $

    —

    $

    —

       Preclinical development and other

   shared research and development expenses

—

—

    —

       Non-cash expenses (depreciation and stock-

   based compensation)

—

—

—

    Total research and development expenses

    $

    —

    $

    —

    $

    —

  * * * * *

  The Company respectfully requests the Staff’s assistance in completing the review of the Company’s response as soon as possible. Please advise us if we can provide any further information or assistance to facilitate your review. Please direct any further comments or questions regarding this response letter to me at (858) 731-8389.

  Sincerely,

  aTyr Pharma, Inc.

    By:

    /s/ Jill M. Broadfoot

    Jill M. Broadfoot

    Chief Financial Officer

  2

    cc:

    Sanjay S. Shukla, M.D., M.S.

    Chief Executive Officer

    aTyr Pharma, Inc.

    Nancy E. Denyes

    General Counsel

    aTyr Pharma, Inc.

    Charles J. Bair

    Cooley LLP

    Nicholaus E. Johnson

    Cooley LLP

  3

United States securities and exchange commission logo
June 6, 2024
Jill Broadfoot
Chief Financial Officer
aTYR PHARMA INC
10240 Sorrento Valley Road
Suite 300
San Diego, CA 92014
Re:aTYR PHARMA INC
Form 10-K for Fiscal Year Ended December 31, 2023
File No. 001-37378
Dear Jill Broadfoot:
            We have limited our review of your filings to the financial statements and related
disclosures and have the following comment.
            Please respond to this letter within ten business days by providing the requested
information or advise us as soon as possible when you will respond. If you do not believe a
comment applies to your facts and circumstances, please tell us why in your response.
            After reviewing your response to this letter, we may have additional comments.
Form 10-K for Fiscal Year Ended December 31, 2023
Item 7. Management's Discussion and Analysis of Financial Condition and Results of Operations
Research and development expenses, page 68
1.We note from the pipeline table on page 6 that you have multiple products in clinical
development for several indications. Please revise future filings to disclose the costs
incurred during each period presented for each of your key research and development
product candidates. If you do not track your research and development costs by project,
disclose that fact and explain why you do not maintain and evaluate research and
development costs by project. Also, revise to provide other quantitative and qualitative
disclosures that give more transparency as to the type of research and development
expenses incurred (i.e., by nature or type of expense) which should reconcile to total
research and development expenses on your Statements of Operations.

 FirstName LastNameJill Broadfoot
 Comapany NameaTYR PHARMA INC
 June 6, 2024 Page 2
 FirstName LastName
Jill Broadfoot
aTYR PHARMA INC
June 6, 2024
Page 2
            In closing, we remind you that the company and its management are responsible for the
accuracy and adequacy of their disclosures, notwithstanding any review, comments, action or
absence of action by the staff.
            Please contact Lynn Dicker at 202-551-3616 or Kevin Kuhar at 202-551-3662 with any
questions.
Sincerely,
Division of Corporation Finance
Office of Life Sciences

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  aTyr Pharma, Inc.

  10240 Sorrento Valley Road, Suite 300

  San Diego, CA, 92121

  November 16, 2023

  VIA EDGAR

  U.S. Securities and Exchange Commission

  Division of Corporation Finance

  100 F Street, N.E.

  Washington, D.C. 20549

  Attn: Daniel Crawford

  Re:	aTyr Pharma, Inc.

   	Registration Statement on Form S-3 (File No. 333-275455)

   	Request for Acceleration of Effective Date

  Ladies and Gentlemen:

  Pursuant to Rule 461 under the Securities Act of 1933, as amended, aTyr Pharma, Inc. (the “Company”) hereby requests that the Securities and Exchange Commission (the “Commission”) accelerate the effective date of the above-referenced Registration Statement on Form S-3 (the “Registration Statement”) and declare the Registration Statement effective as of 4:00 p.m. Eastern time, on November 20, 2023, or as soon thereafter as possible, or at such other time as the Company or its legal counsel, Cooley LLP, may request by telephone to the staff of the Commission. The Company hereby authorizes each of Charles J. Bair and Katherine Denby of Cooley LLP to make such a request on its behalf.

  Once the Registration Statement has been declared effective, please orally confirm that event with Katherine Denby of Cooley LLP at (202) 776-2070 or kdenby@cooley.com.

Sincerely,

    aTyr Pharma, Inc.

    By:

    /s/ Jill Broadfoot

    Jill Broadfoot

    Chief Financial Officer

United States securities and exchange commission logo
November 15, 2023
Sanjay Shukla, M.D., M.S.
President and Chief Executive Officer
aTyr Pharma, Inc.
10240 Sorrento Valley Road, Suite 300
San Diego, CA 92121
Re:aTyr Pharma, Inc.
Registration Statement on Form S-3
Filed November 9, 2023
File No. 333-275455
Dear Sanjay Shukla:
            This is to advise you that we have not reviewed and will not review your registration
statement.
            Please refer to Rules 460 and 461 regarding requests for acceleration. We remind you
that the company and its management are responsible for the accuracy and adequacy of their
disclosures, notwithstanding any review, comments, action or absence of action by the staff.
            Please contact Daniel Crawford at 202-551-7767 with any questions.
Sincerely,
Division of Corporation Finance
Office of Life Sciences
cc:       Charles Bair, Esq.

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aTyr Pharma, Inc.

3545 John Hopkins Court, Suite 250

San Diego, California 92121

April 5, 2022

VIA EDGAR

U.S. Securities and Exchange Commission

Division of Corporation Finance

100 F Street, N.E.

Washington, D.C. 20549

Attn: Dorrie Yale

Re:

aTyr Pharma, Inc.

Registration Statement on Form S-3 (File No. 333-263585)

Request for Acceleration of Effective Date

Ladies and Gentlemen:

Pursuant to Rule 461 under the Securities Act of 1933, as amended, aTyr Pharma, Inc. (the “Company”) hereby requests that the Securities and Exchange Commission (the “Commission”) accelerate the effective date of the above-referenced Registration Statement on Form S-3 (the “Registration Statement”) and declare the Registration Statement effective as of 4:00 p.m. Eastern time, on April 8, 2022, or as soon thereafter as possible, or such , or at such other time as the Company or its legal counsel, Cooley LLP, may request by telephone to the staff of the Commission. The Company hereby authorizes each of Charles J. Bair and Alexa M. Ekman of Cooley LLP to make such a request on its behalf.

Once the Registration Statement has been declared effective, please orally confirm that event with Alexa M. Ekman of Cooley LLP at (858) 550-6183 or aekman@cooley.com.

Sincerely,

aTyr Pharma, Inc.

By:

/s/ Jill M. Broadfoot

Jill M. Broadfoot

Chief Financial Officer

United States securities and exchange commission logo
March 17, 2022
Sanjay Shukla
President and Chief Executive Officer
aTyr Pharma, Inc.
3545 John Hopkins Court, Suite 250
San Diego, CA 92121
Re:aTyr Pharma, Inc.
Registration Statement on Form S-3
Filed March 15, 2022
File No. 333-263585
Dear Mr. Shukla:
            This is to advise you that we have not reviewed and will not review your registration
statement.
            Please refer to Rules 460 and 461 regarding requests for acceleration.  We remind you
that the company and its management are responsible for the accuracy and adequacy of their
disclosures, notwithstanding any review, comments, action or absence of action by the staff.
            Please contact Dorrie Yale at 202-551-8776 with any questions.
Sincerely,
Division of Corporation Finance
Office of Life Sciences
cc:       Alexa Ekman

United States securities and exchange commission logo
August 23, 2021
Sanjay S. Shukla, M.D., M.S.
President and Chief Executive Officer
aTyr Pharma, Inc.
3545 John Hopkins Court, Suite 250
San Diego, CA 92121
Re:aTyr Pharma, Inc.
Registration Statement on Form S-3
Filed August 11, 2021
File No. 333-258725
Dear Dr. Shukla:
            This is to advise you that we have not reviewed and will not review your registration
statement.
            Please refer to Rules 460 and 461 regarding requests for acceleration.  We remind you
that the company and its management are responsible for the accuracy and adequacy of their
disclosures, notwithstanding any review, comments, action or absence of action by the staff.
            Please contact Alan Campbell at 202-551-4224 with any questions.
Sincerely,
Division of Corporation Finance
Office of Life Sciences
cc:       Sean M. Clayton

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aTyr Pharma, Inc.

3545 John Hopkins Court, Suite 250

San Diego, California 92121

August 19, 2021

VIA EDGAR

U.S. Securities and Exchange Commission

Division of Corporation Finance

100 F Street, N.E.

Washington, D.C. 20549

Attn: Alan Campbell

Re:

aTyr Pharma, Inc.

Registration Statement on Form S-3 (File No. 333-258725)

Request for Acceleration of Effective Date

Ladies and Gentlemen:

Pursuant to Rule 461 under the Securities Act of 1933, as amended, aTyr Pharma, Inc. (the “Company”) hereby requests that the Securities and Exchange Commission (the “Commission”) accelerate the effective date of the above-referenced Registration Statement on Form S-3 (the “Registration Statement”) and declare the Registration Statement effective as of 4:00 p.m. Eastern time, on August 23, 2021, or as soon thereafter as possible, or at such other time as the Company or its legal counsel, Cooley LLP, may request by telephone to the staff of the Commission. The Company hereby authorizes each of Sean M. Clayton and Alexa M. Ekman of Cooley LLP to make such a request on its behalf.

Once the Registration Statement has been declared effective, please confirm that event with Sean M. Clayton of Cooley LLP at (858) 550-6034 or sclayton@cooley.com.

Sincerely,

aTyr Pharma, Inc.

By:

/s/ Jill Broadfoot

Jill Broadfoot

Chief Financial Officer

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aTyr Pharma, Inc.

3545 John Hopkins Court, Suite 250

San Diego, California 92121

November 19, 2020

VIA EDGAR

U.S. Securities and Exchange Commission

Division of Corporation Finance

100 F Street, N.E.

Washington, D.C. 20549

Attn: David Gessert

Re:

aTyr Pharma, Inc.

Registration Statement on Form S-3 (File No. 333-250095)

Request of Acceleration of Effective Date

Ladies and Gentlemen:

Pursuant to Rule 461 under the Securities Act of 1933, as amended, aTyr Pharma, Inc. (the “Company”) hereby requests that the Securities and Exchange Commission (the “Commission”) accelerate the effective date of the above-referenced Registration Statement on Form S-3 (the “Registration Statement”) and declare the Registration Statement effective as of 4:00 p.m. Eastern time, on November 23, 2020, or as soon thereafter as possible, or at such other time as the Company or its legal counsel, Cooley LLP, may request by telephone to the staff of the Commission. The Company hereby authorizes each of Sean M. Clayton and Alexa M. Ekman of Cooley LLP to make such a request on its behalf.

Once the Registration Statement has been declared effective, please confirm that event with Sean M. Clayton of Cooley LLP at (858) 550-6034 or sclayton@cooley.com.

Sincerely,

aTyr Pharma, Inc.

By:

/s/ Jill Broadfoot

Jill Broadfoot

Chief Financial Officer

United States securities and exchange commission logo
November 18, 2020
Sanjay S. Shukla, M.D., M.S.
President and Chief Executive Officer
aTyr Pharma, Inc.
3545 John Hopkins Court, Suite 250
San Diego, CA 92121
Re:aTyr Pharma, Inc.
Registration Statement on Form S-3
Filed November 16, 2020
File No. 333-250095
Dear Mr. Shukla:
            This is to advise you that we have not reviewed and will not review your registration
statement.
            Please refer to Rules 460 and 461 regarding requests for acceleration.  We remind you
that the company and its management are responsible for the accuracy and adequacy of their
disclosures, notwithstanding any review, comments, action or absence of action by the staff.
            Please contact David Gessert at 202-551-2326 with any questions.
Sincerely,
Division of Corporation Finance
Office of Life Sciences

United States securities and exchange commission logo
September 24, 2020
Sanjay S. Shukla, M.D., M.S.
President and Chief Executive Officer
aTYR Pharma, Inc.
3545 John Hopkins Court, Suite 250
San Diego, CA 92121
Re:aTYR Pharma, Inc.
Registration Statement on Form S-1
Filed September 18, 2020
File No. 333-248905
Dear Dr. Shukla:
            This is to advise you that we have not reviewed and will not review your registration
statement.
            Please refer to Rules 460 and 461 regarding requests for acceleration.  We remind you
that the company and its management are responsible for the accuracy and adequacy of their
disclosures, notwithstanding any review, comments, action or absence of action by the staff.
            Please contact Alan Campbell at 202-551-4224 with any questions.
Sincerely,
Division of Corporation Finance
Office of Life Sciences
cc:       Sean M. Clayton

CORRESP
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aTyr Pharma, Inc.

3545 John Hopkins Court, Suite 250

San Diego, California 92121

September 24, 2020

VIA EDGAR

U.S. Securities and Exchange Commission

Division of Corporation Finance

100 F Street, N.E.

Washington, D.C. 20549

Attn: Alan Campbell

Re:

aTyr Pharma, Inc.

Registration Statement on Form S-1 (File No. 333-248905)

Request for Acceleration of Effective Date

Ladies and Gentlemen:

Pursuant to Rule 461 under the Securities Act of 1933, as amended, aTyr Pharma, Inc. (the “Company”) hereby requests that the Securities and Exchange Commission (the “Commission”) accelerate the effective date of the above-referenced Registration Statement on Form S-1 (the “Registration Statement”) and declare the Registration Statement effective as of 4:00 p.m. Eastern time, on September 28, 2020, or as soon thereafter as possible, or at such other time as the Company or its legal counsel, Cooley LLP, may request by telephone to the staff of the Commission. The Company hereby authorizes each of Sean M. Clayton and Alexa M. Ekman of Cooley LLP to make such a request on its behalf.

Once the Registration Statement has been declared effective, please orally confirm that event with Sean M. Clayton of Cooley LLP at (858) 550-6034, or in his absence, Alexa M. Ekman of Cooley LLP at (858) 550-6183.

Sincerely,

aTyr Pharma, Inc.

By:

/s/ Jill Broadfoot

Jill Broadfoot

Chief Financial Officer

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OPPENHEIMER & CO. INC.

85 Broad Street

New York, New York 10004

February 3, 2020

VIA EDGAR

United States Securities and Exchange Commission

Division of Corporation Finance

100 F Street, N.E.

Washington, D.C. 20549

Re:

aTyr Pharma, Inc.

Registration Statement on Form S-1, as amended File

No. 333-235951

Ladies and Gentlemen:

In accordance with the above-referenced Registration Statement, and pursuant to Rule 461 of the General Rules and Regulations of the Securities and Exchange Commission under the Securities Act of 1933, as amended (the “Securities Act”), the undersigned, as the representative of the several underwriters (the “Representative”), hereby joins in the request of aTyr Pharma, Inc. that the effective date of the above-referenced Registration Statement be accelerated so that it will be declared effective at 4:30 p.m., Eastern Time, on Tuesday, February 4, 2020, or as soon thereafter as practicable.

Pursuant to Rule 460 under the Securities Act, please be advised that there will be distributed to each underwriter or dealer, who is reasonably anticipated to be invited to participate in the distribution of the security, as many copies of the proposed form of preliminary prospectus as appears to be reasonable to secure adequate distribution of the preliminary prospectus.

The undersigned, as the representative of the several underwriters, represents that the several underwriters have and will comply with the requirements of Rule 15c2-8 under the Securities Exchange Act of 1934, as amended.

Very truly yours,

OPPENHEIMER & CO. INC

As representative of the

Several Underwriters

OPPENHEIMER & CO. INC.

By: /s/ Peter Bennett

Name: Peter Bennett

Title: Managing Director

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aTyr Pharma, Inc.

3545 John Hopkins Court, Suite 250

San Diego, California 92121

February 3, 2020

VIA EDGAR

U.S. Securities and Exchange Commission

Division of Corporation Finance

100 F Street, N.E.

Washington, D.C. 20549

Attn: William Mastrianna

Re: aTyr Pharma, Inc.

Registration Statement on Form S-1 (File No. 333-235951)

Request for Acceleration of Effective Date

Ladies and Gentlemen:

Pursuant to Rule 461 under the Securities Act of 1933, as amended, aTyr Pharma, Inc. (the “Company”) hereby requests that the Securities and Exchange Commission (the “Commission”) accelerate the effective date of the above-referenced Registration Statement on Form S-1 (as amended, the “Registration Statement”) and declare the Registration Statement effective as of 4:30 p.m. Eastern time, on February 4, 2020, or as soon thereafter as possible, or at such other time as the Company or its legal counsel, Cooley LLP, may request by telephone to the staff of the Commission. The Company hereby authorizes each of Sean M. Clayton and Alexa M. Ekman of Cooley LLP to make such a request on its behalf.

Once the Registration Statement has been declared effective, please orally confirm that event with Sean M. Clayton of Cooley LLP at (858) 550-6034, or in his absence, Alexa M. Ekman of Cooley LLP at (858) 550-6183.

Sincerely,

aTyr Pharma, Inc.

By:

/s/ Sanjay S. Shukla, M.D., M.S.

Sanjay S. Shukla, M.D., M.S.

President and Chief Executive Officer

January 23, 2020
Sanjay Shukla
President and Chief Executive Officer
aTyr Pharma, Inc.
3545 John Hopkins Court, Suite 250
San Diego, CA 92121
Re:aTyr Pharma, Inc.
Registration Statement on Form S-1
Filed January 17, 2020
File No. 333-235951
Dear Mr. Shukla:
            This is to advise you that we have not reviewed and will not review your registration
statement.
            Please refer to Rules 460 and 461 regarding requests for acceleration.  We remind you
that the company and its management are responsible for the accuracy and adequacy of their
disclosures, notwithstanding any review, comments, action or absence of action by the staff.
            Please contact William Mastrianna, Attorney-Adviser, at (202) 551-3778 with any
questions.
Sincerely,
Division of Corporation Finance
Office of Life Sciences
cc:       Sean Clayton

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ATYR PHARMA, INC.

3545 John Hopkins Court, Suite 250

San Diego, CA 92121

June 19, 2019

VIA EDGAR

United States Securities and Exchange Commission

Division of Corporation Finance

100 F Street, N.E.

Washington, D.C. 20549

Attention: Dorrie Yale

Re:

aTyr Pharma, Inc.

Acceleration Request for Registration Statement on Form S-3 filed May 22, 2019 (File No. 333-231658), as amended by Amendment No. 1 to Form S-3 filed June 18, 2019 (File No. 333-231658) (collectively, the “Registration Statement”)

Dear Ms. Yale:

Pursuant to Rule 461 under the Securities Act of 1933, as amended (the “Act”), aTyr Pharma, Inc. (the “Company”) hereby requests that the effective date of the Registration Statement be accelerated to June 20, 2019, at 4:00 p.m., Eastern Time, or as soon thereafter as practicable, unless we or our outside counsel, Goodwin Procter LLP, request by telephone that such Registration Statement be declared effective at some other time. In making this acceleration request, the Company acknowledges that it is aware of its responsibilities under the Act.

Once the Registration Statement is effective, please orally confirm the event with our counsel, Goodwin Procter LLP, by calling Mitzi Chang at (415) 733-6017. We also respectfully request that a copy of the written order from the Securities and Exchange Commission (the “Commission”) verifying the effective time and date of the Registration Statement be sent to our counsel, Goodwin Procter LLP, Attention: Mitzi Chang, by facsimile to (415) 384-6006.

In connection with the foregoing, the Company hereby acknowledges the following:

•

should the Commission or the staff of the Commission, acting pursuant to delegated authority, declare the Registration Statement effective, it does not foreclose the Commission from taking any action with respect to the Registration Statement;

•

the action of the Commission or the staff of the Commission, acting pursuant to delegated authority, in declaring the Registration Statement effective, does not relieve the Company from its full responsibility for the adequacy and accuracy of the disclosure in the Registration Statement; and

•

the Company may not assert staff comments and the declaration of effectiveness as a defense in any proceeding initiated by the Commission or any person under the federal securities laws of the United States.

If you have any questions regarding this request, please contact Mitzi Chang of Goodwin Procter LLP at (415) 733-6017.

Very truly yours,

ATYR PHARMA, INC.

By:

/s/ Jill M. Broadfoot

Name:

 Jill M. Broadfoot

Title:

Chief Financial Officer

cc:

Sanjay S. Shukla, M.D., M.S., aTyr Pharma, Inc.

Nancy E. Denyes, aTyr Pharma, Inc.

Kingsley Taft, Goodwin Procter LLP

Mitzi Chang, Goodwin Procter LLP

May 24, 2019
Sanjay Shukla
President and Chief Executive Officer
aTyr Pharma, Inc.
3545 John Hopkins Court, Suite 250
San Diego, CA 92121
Re:aTyr Pharma, Inc.
Registration Statement on Form S-3
Filed May 22, 2019
File No. 333-231658
Dear Dr. Shukla:
            This is to advise you that we have not reviewed and will not review your registration
statement.
            Please refer to Rules 460 and 461 regarding requests for acceleration.  We remind you
that the company and its management are responsible for the accuracy and adequacy of their
disclosures, notwithstanding any review, comments, action or absence of action by the staff.
            Please contact Dorrie Yale at 202-551-8776 with any questions.
Sincerely,
Division of Corporation Finance
Office of Healthcare & Insurance
cc:       Mitzi Chang, Esq. - Goodwin Procter LLP

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 ATYR PHARMA, INC.

3545 John Hopkins Court, Suite #250

San Diego, CA 92121

September 25, 2017

 VIA EDGAR

 United States Securities and Exchange Commission

Division of Corporation Finance

 100 F Street, N.E.

Washington, D.C. 20549

 Attention: Ada Sarmento

Re:
aTyr Pharma, Inc.

Acceleration Request for Registration Statement on Form S-3

File No. 333-220463

 Dear Ms. Sarmento:

Pursuant to Rule 461 under the Securities Act of 1933, as amended (the “Act”), aTyr Pharma, Inc. (the “Company”) hereby
requests that the effective date of the above-referenced registration statement (the “Registration Statement”) be accelerated to September 27, 2017, at 4:00 p.m., Eastern Time, or as soon thereafter as practicable, unless we or
our outside counsel, Goodwin Procter LLP, request by telephone that such Registration Statement be declared effective at some other time. In making this acceleration request, the Company acknowledges that it is aware of its responsibilities under
the Act.

 Once the Registration Statement is effective, please orally confirm the event with our counsel, Goodwin Procter LLP, by calling Mitzi Chang at
(415) 733-6017. We also respectfully request that a copy of the written order from the Securities and Exchange Commission (the “Commission”) verifying the effective time and date of the Registration Statement be sent to our
counsel, Goodwin Procter LLP, Attention: Mitzi Chang, by facsimile to (415) 384-6006.

 In connection with the foregoing, the Company hereby
acknowledges the following:

•

should the Commission or the staff of the Commission, acting pursuant to delegated authority, declare the Registration Statement effective, it does not foreclose the Commission from taking any action with respect to the
Registration Statement;

•

the action of the Commission or the staff of the Commission, acting pursuant to delegated authority, in declaring the Registration Statement effective, does not relieve the Company from its full responsibility for the
adequacy and accuracy of the disclosure in the Registration Statement; and

•

the Company may not assert staff comments and the declaration of effectiveness as a defense in any proceeding initiated by the Commission or any person under the federal securities laws of the United States.

 If you have any questions regarding this request, please contact Mitzi Chang of Goodwin Procter LLP at (415) 733-6017.

 Very truly yours,

ATYR PHARMA, INC.

By:

/s/ John T. Blake

Name:

John T. Blake

Title:

Senior Vice President, Finance

cc:
Nancy D. Krueger, aTyr Pharma, Inc.

Kingsley Taft, Goodwin Procter LLP

Mitzi Chang, Goodwin Procter LLP

June 20, 2016

John D. Mendlein, Ph.D.
Chief Executive Officer
aTyr Pharma, Inc.
3545 John Hopkins Court, Suite 250
San Diego, CA 92121

Re: aTyr Pharma, Inc.
  Registration Statement on Form S-3
Filed  June 13, 2016
  File No.  333-211998

Dear Dr. Mendlein :

This is to advise you that we have not  reviewed and will not review your registration
statement .

We urge all persons who are responsible for the accuracy and adequacy of the disclosure
in the filing to be certain that the filing includes the information the Securities Act of 193 3 and
all applicable Securities  Act rules require.   Since the company and its management are  in
possession of all facts relating to a company’s disclosure, they are responsible for the accuracy
and adequacy of the disclosures they have made.

In the event you request acceleration of the effective date of the pending regist ration
statement , please provide  a written statement from the company acknowledging that:

 should the Commission or the staff, acting pursuant to delegated authority, declare the
filing effective, it does not foreclose the Commission from taking any action wit h respect
to the filing;

 the action of the Commission or the staff, acting pursuant to delegated authority, in
declaring the filing effective, does not relieve the company from its full responsibility for
the adequacy and accuracy of the disclosure in th e filing; and

 the company may not assert staff comments and the declaration of effectiveness as a
defense in any proceeding initiated by the Commission or any person under the federal
securities laws of the United States.

Please refer to Rules 460 and 461 regarding requests for  acceleration .  We will consider a
written request for acceleration of the effective date of the registration statement as confirmation
of the fact that those requesting acceleration are aware of their respective responsibilities under

John D. Mendlein, Ph.D.
aTyr Pharma, Inc.
June 20, 2016
Page 2

 the Securities Act of 1933 and the Securities Exchange Act of 1934 as they relate to the proposed
public offering of the registered securities .

Please  contact Christina Thomas  at (202) 551 -3577  with any questions.

Sincerely,

 /s/ Erin K. Jaskot, for

 Suzanne Hayes
Assistant Director
Office of Healthcare and Insurance

cc: Mitzi Chang, Esq.
 Goodwin Procter LLP

CORRESP
1
filename1.htm

CORRESP

 aTyr Pharma, Inc.

3545 John Hopkins Court, Suite #250

San Diego, CA 92121

 VIA EDGAR

June 20, 2016

 United States Securities and Exchange
Commission

 Division of Corporation Finance

 100 F Street,
N.E.

 Washington, DC 20549

 Attention: Suzanne Hayes,
Assistant Director

                  Christina Thomas

Re:
aTyr Pharma, Inc.

 Acceleration Request for Registration Statement on Form
S-3

 File No. 333-211998

Dear Ms. Hayes:

 Pursuant to Rule 461
under the Securities Act of 1933, as amended (the “Act”), aTyr Pharma, Inc. (the “Company”) hereby requests that the effective date and time of the above-referenced registration statement (the “Registration
Statement”) be accelerated to June 22, 2016, at 4:00 p.m., Eastern Time, or at such later time as the Company or its counsel, Goodwin Procter LLP, may orally request via telephone call to the staff of the Division of Corporation
Finance of the Securities and Exchange Commission (the “Commission”). Once the Registration Statement is effective, please orally confirm the event with our counsel, Goodwin Procter LLP, by calling Mitzi Chang at
(415) 733-6017. We also respectfully request that a copy of the written order from the Commission verifying the effective time and date of the Registration Statement be sent to our counsel, Goodwin Procter LLP, Attention: Mitzi Chang, by
facsimile to (415) 384-6006.

 In connection with the foregoing, the Company hereby acknowledges the following:

•

should the Commission or the staff of the Commission, acting pursuant to delegated authority, declare the Registration Statement effective, it does not foreclose the Commission from taking any action with respect to the
Registration Statement;

•

the action of the Commission or the staff of the Commission, acting pursuant to delegated authority, in declaring the Registration Statement effective, does not relieve the Company from its full responsibility for the
adequacy and accuracy of the disclosure in the Registration Statement; and

•

the Company may not assert staff comments and the declaration of effectiveness as a defense in any proceeding initiated by the Commission or any person under the federal securities laws of the United States.

 If you have any questions regarding this request, please contact Mitzi Chang of Goodwin Procter LLP at (415) 733-6017.

Sincerely,

ATYR PHARMA, INC.

 /s/ John T. Blake

John T. Blake

Vice President, Finance

cc:

John D. Mendlein, Ph.D. (aTyr Pharma, Inc.)

Nancy Krueger (aTyr Pharma, Inc.)

Mitzi Chang (Goodwin Procter LLP)

CORRESP
1
filename1.htm

CORRESP

 Maggie L. Wong

 415.733.6071

mwong@goodwinprocter.com

 Goodwin Procter LLP

 Counselors at Law

Three Embarcadero

 Center

24th Floor

 San Francisco, CA 94111

T: 415.733.6000

 F: 415.677.9041

 May 5, 2015

CONFIDENTIAL

 VIA EDGAR AND FEDEX

 United States Securities and

 Exchange Commission

Washington, D.C. 20459

 Atttention: Jeffrey P. Riedler

Assistant Director

Re:
aTyr Pharma, Inc.

 Amendment No. 1 to Registration Statement on Form S-1

 Filed April 27, 2015

File No. 333-203272

 Ladies and
Gentlemen:

 This letter is submitted on behalf of aTyr Pharma, Inc. (the “Company”) in response to comments contained in the letter dated
May 1, 2015 (the “Letter”) from Jeffrey P. Riedler, Assistant Director of the Staff (the “Staff”) of the Securities and Exchange Commission (the “Commission”) to John D. Mendlein, Ph.D., Chief
Executive Officer and Executive Chairman of the Company, with respect to Amendment No. 1 to Registration Statement on Form S-1 (the “Registration Statement”) that was filed on April 27, 2015. The Company is concurrently
submitting Amendment No. 3 to the Registration Statement (the “Revised Registration Statement”), including changes in response to the Staff’s comments.

The responses set forth below have been organized in the same manner in which the Commission’s comments were organized in the Letter. Copies of this
letter and its attachments will also be provided to Matthew Jones, Bryan Pitko and Mark Brunhofer of the Commission.

 United States Securities and

Exchange Commission

 <May 5, 2015>

 Page
 2

 Report of Independent Registered Public Accounting Firm, Page F-2

Exhibit 23.1: Consent of Independent Registered Public Accounting Firm

1.
Please have your auditors remove the restrictive language from their report and consent and sign them in the filing for which you request effectiveness.

RESPONSE: The Company’s auditors have removed the restrictive language from their report and consent and have signed them in the filing of the Revised
Registration Statement.

 If you require additional information, please telephone the undersigned at (415) 733-6071 or Mitzi Chang at
(415) 733-6017.

Sincerely,

/s/ Maggie L. Wong

Maggie L. Wong

cc:
John D. Mendlein (aTyr Pharma, Inc.)

 Frederic Chereau (aTyr Pharma, Inc.)

Nancy D. Krueger (aTyr Pharma, Inc.)

Kingsley L. Taft (Goodwin Procter LLP)

Alan F. Denenberg (Davis Polk & Wardwell LLP)

Mitzi Chang (Goodwin Procter LLP)

CORRESP
1
filename1.htm

CORRESP

 J.P. Morgan Securities LLC

383 Madison Avenue

 New York, NY 10179

Citigroup Global Markets Inc.

 388 Greenwich Street

New York, New York 10013

 May 4, 2015

Securities and Exchange Commission

 Division of Corporation
Finance

 100 F Street, N.E.

 Washington, D.C. 20549-3720

Attention:

  Jeffrey P. Riedler, Assistant Director

  Bryan J. Pitko

  Matthew Jones

Re:
aTyr Pharma, Inc.

 Registration Statement on Form S-1

Filed on April 6, 2015

Registration File No. 333-203272

Ladies and Gentlemen:

 Pursuant to Rule 461
under the Securities Act of 1933, as amended (the “Act”), the undersigned, as representatives of the several underwriters (the “Underwriters”), hereby join in the request of aTyr Pharma, Inc. (the “Company”) for
acceleration of the effective date of the above-referenced registration statement so that it becomes effective at 4:00 p.m., Eastern time, on May 6, 2015, or as soon thereafter as practicable.

Pursuant to Rule 460 under the Act, we, as representatives of the several underwriters, wish to advise you that we have effected the following distribution of
the Company’s Preliminary Prospectus dated April 27, 2015:

(i)
Dates of distribution: April 27, 2015 through the date hereof

(ii)
Number of prospective underwriters to which the preliminary prospectus was furnished: 4

(iii)
Number of prospectuses furnished to investors: approximately 646

(iv)
Number of prospectuses distributed to others, including the Company, the Company’s counsel, independent accountants, and underwriters’ counsel: approximately 40

 The undersigned advise that they have complied and will continue to comply, and each Underwriter
and dealer has advised the undersigned that it has complied and will continue to comply, with Rule 15c2-8 under the Securities Exchange Act of 1934.

[Signature page follows]

Very truly yours,

 J.P. MORGAN SECURITIES LLC

CITIGROUP GLOBAL MARKETS INC.

Acting severally on behalf of themselves and the

 several
Underwriters

By:

J.P. MORGAN SECURITIES LLC

By:

 /s/ Phillip Ross

Name: Phillip Ross

Title: Managing Director

By:

CITIGROUP GLOBAL MARKETS INC.

By:

 /s/ Jennifer Jarrett

Name: Jennifer Jarrett

Title: Managing Director

 [Signature page to
Underwriters’ Acceleration Request]

CORRESP
1
filename1.htm

CORRESP

 aTyr Pharma, Inc.

3545 John Hopkins Court, Suite #250

San Diego, CA 92121

 VIA EDGAR

May 4, 2015

 United States Securities and Exchange Commission

 Division of Corporation Finance

 100 F Street, N.E.

Washington, DC 20549

 Attention: Jeffrey P. Riedler, Assistant
Director

Re:
aTyr Pharma, Inc.

 Acceleration Request for Registration Statement on Form
S-1

 File No. 333-203272

Dear Mr. Riedler:

 Pursuant to Rule 461
under the Securities Act of 1933, as amended (the “Act”), aTyr Pharma, Inc. (the “Company”) hereby requests that the effective date and time of the above-referenced registration statement (the “Registration
Statement”) be accelerated to May 6, 2015, at 4:00 p.m., Eastern Time, or at such later time as the Company or its counsel, Goodwin Procter LLP, may orally request via telephone call to the staff of the Division of Corporation Finance of
the Securities and Exchange Commission (the “Commission”). Once the Registration Statement is effective, please orally confirm the event with our counsel, Goodwin Procter LLP, by calling Maggie Wong at (415) 733-6071 or Mitzi
Chang at (415) 733-6017. We also respectfully request that a copy of the written order from the Commission verifying the effective time and date of the Registration Statement be sent to our counsel, Goodwin Procter LLP, Attention: Mitzi Chang,
by facsimile to (415) 384-6006.

 In connection with the foregoing, the Company hereby acknowledges the following:

•

should the Commission or the staff of the Commission, acting pursuant to delegated authority, declare the Registration Statement effective, it does not foreclose the Commission from taking any action with respect to the
Registration Statement;

•

the action of the Commission or the staff of the Commission, acting pursuant to delegated authority, in declaring the Registration Statement effective, does not relieve the Company from its full responsibility for the
adequacy and accuracy of the disclosure in the Registration Statement; and

•

the Company may not assert staff comments and the declaration of effectiveness as a defense in any proceeding initiated by the Commission or any person under the federal securities laws of the United States.

•

If you have any questions regarding this request, please contact Maggie Wong or Mitzi Chang of Goodwin Procter LLP at (415) 733-6071 or (415) 733-6017.

Sincerely,

ATYR PHARMA, INC.

 /s/ John Mendlein

John Mendlein, Ph.D.

Chief Executive Officer and Executive Chairman

cc:
Nancy Krueger (aTyr Pharma, Inc.)

 Kingsley Taft (Goodwin Procter LLP)

Maggie Wong (Goodwin Procter LLP)

Mitzi Chang (Goodwin Procter LLP)

Alan Denenberg (Davis Polk & Wardwell LLP)

May 1, 2015

Via E -mail
John D. Mendlein, Ph.D.
Chief Executive Officer and Executive Chairman
aTyr Pharma, Inc.
3545 John Hopkins Court, Suite #250
San Diego, CA 92121

Re: aTyr  Pharma, Inc.
Amendment No. 1 to Registration Statement on Form S -1
Filed April 27, 2015
  File No. 333 -203272

Dear Dr. Mendlein :

We have reviewed your  amended  registration statement  and have the following comment.

Please respond to this letter by amending your registration statement and providing the
requested information .  If you do not believe our comment applies  to your facts and
circumstances or do not believe an amendment is appropriate, please tell us why in your
response.

After reviewing any amendment to your registration statement and the information you
provide in response to this comment , we may have  additional comments.

Report of Independent Registered Public Accounting Firm, Page F -2
Exhibit 23.1:  Consent of Indepe ndent Registered Public Accounting Firm

1. Please have your auditors remove the restrictive language from their report and consent
and sign them in the filing for which you request effectiveness.

We urge all persons who are responsible for the accuracy and adequacy of the disclosure
in the filing to be certain that the filing includes the information the Securities Act of 193 3 and
all applicable Securities  Act rules require.   Since the company and its management are in
possession of all facts relating to a c ompany’s disclosure, they are responsible for the accuracy
and adequacy of the disclosures they have made.

Notwithstanding our comments, in the event you request acceleration of the effective date
of the pending regist ration statement , please provide  a written statement from the company
acknowledging that:

John D. Mendlein, Ph.D.
aTyr Pharma, Inc.
May 1, 2015
Page 2

  should the Commission or the staff, acting pursuant to delegated authority, declare the
filing effective, it does not foreclose the Commission from taking any action with respect
to the filing;

 the action of the Commission or the staff, acting pursuant to delegated authority, in
declaring the filing effective, does not relieve the company from its full responsibility for
the adequacy and accuracy of the disclosure in the filing; and

 the company may not assert staff comments and the declaration of effectiveness as a
defense in any proceeding initiated by the Commission or any person under the federal
securities laws of the United States.

Please refer to Rules 460 and 461 regarding reque sts for  acceleration .  We will consider a
written request for acceleration of the effective date of the registration statement as confirmation
of the fact that those requesting acceleration are aware of their respective responsibilities under
the Securitie s Act of 1933 and the Securities Exchange Act of 1934 as they relate to the proposed
public offering of the securities specified in the above registration statement.  Please allow
adequate time  for us to review any amendment prior to the requested effectiv e date of the
registration statement.

You may contact Mark Brunhofer at (202) 551 -3638 if you have questions regarding
comments on the financial statements and related matters.  Please contact Matthew Jones at
(202) 551 -3786, Bryan Pitko at (202) 551 -3203 or me at (202) 551 -3715 with any other
questions.

Sincerely,

 /s/ Jeffrey P. Riedler

Jeffrey P. Riedler
Assistant Director

cc:  Kingsley L. Taft
Maggie L. Wong
Mitzi Chang
Goodwin Procter LLP
3 Embarcadero Center, 24th Floor
San Francisco, CA 94111

CORRESP
1
filename1.htm

CORRESP

 Goodwin Procter LLP

Counselors at Law

Three Embarcadero Center

24th Floor

San Francisco, CA 94111

T: 415.733.6000

F: 415.677.9041

 April 17, 2015

 FOIA
Confidential Treatment Request

 The entity requesting confidential treatment is

aTyr Pharma, Inc.

 3545 John Hopkins Court, Suite #250

San Diego, CA 92121

 Attn: John D. Mendlein, Ph.D., Chief
Executive Officer and Executive Chairman

 Telephone: (858) 731-8389

CERTAIN PORTIONS OF THIS LETTER HAVE BEEN OMITTED FROM THE VERSION FILED VIA EDGAR. CONFIDENTIAL TREATMENT HAS BEEN
REQUESTED WITH RESPECT TO THE OMITTED PORTIONS. INFORMATION THAT WAS OMITTED IN THE EDGAR VERSION HAS BEEN NOTED IN THIS LETTER WITH A PLACEHOLDER IDENTIFIED BY THE MARK “[***].”

VIA EDGAR AND FEDERAL EXPRESS

 United States
Securities and Exchange Commission

 Division of Corporation Finance

Mail Stop 4720

 100 F Street, N.E.

Washington, D.C. 20549

 Attention: Matt Jones

Re:

aTyr Pharma, Inc.

Registration Statement on Form S-1

File No. 333-203272

 Dear Mr. Jones:

Rule 83 Confidential Treatment Request by aTyr Pharma, Inc.

This letter is being provided on behalf of aTyr Pharma, Inc., a Delaware corporation (the “Company”), with respect to the
Company’s Registration Statement on Form S-1 (File No. 333-203272) (the “Registration Statement”) that was filed with the Securities and Exchange Commission (the “Commission”) on April 6, 2015. To assist the staff
of the Division of

Mr. Matt Jones

United States Securities and Exchange Commission

CONFIDENTIAL TREATMENT REQUESTED

April 17, 2015

BY ATYR PHARMA, INC.

 Page
 2

Corporation Finance (the “Staff”) in its evaluation of stock compensation disclosures and certain other matters, the Company advises the Staff that, considering information currently
available and current market conditions based in part on input received from its underwriters, the Company currently estimates a price range of $[***] to $[***] per share for the initial public offering (“IPO”) of the Company’s Common
Stock, $0.001 par value per share (which is referred to in the Registration Statement as the Company’s “common stock”). This per share price range does not reflect or give effect to a reverse split of the Company’s common stock
that is expected to be effected prior to the offering and which the Company expects to reflect in the preliminary prospectus prior to the commencement of the roadshow. For clarity, the Company advises the Staff that, given the volatility of the
public trading market and the uncertainty of the timing of the offering, the Company and the underwriters have not yet agreed to a final price range for the offering and the Company has not yet conclusively determined the size or ratio of the split
of the common stock referred to above. Accordingly, the information in this letter provided to the Staff is for illustrative purposes only and may differ in the actual preliminary prospectus for the offering. We confirm on behalf of the Company
that, prior to circulating copies of the preliminary prospectus in connection with the offering, the Company will file a pre-effective amendment to the Registration Statement that will include the information set forth in this letter and the actual
price range that complies with the Staff’s interpretation regarding the parameters of a bona fide price range.

 aTyr Pharma, Inc.
respectfully requests that the bracketed information contained in this letter be treated as confidential information and that the Commission provide timely notice to Nancy Krueger, Vice President, Legal Affairs, aTyr Pharma, Inc., 3545 John Hopkins
Court, Suite #250, San Diego, CA 92121, before it permits any disclosure of the bracketed information in this letter.

 Stock
Option Grants in the Last 12 Months and Related Common Stock Valuations

 As described in detail in the Registration Statement
beginning on page 69, historically, the fair value of the common stock underlying the Company’s stock-based awards has been determined on each grant date by the Company’s board of directors (the “Board”), with input from
management. All options to purchase shares of the Company’s common stock were intended to be granted with an exercise price per share no less than the fair value per share of the Company’s common stock underlying those options on the
date of grant, determined in good faith and based on the information known to the Board on the date of grant. In the absence of a public trading market for the Company’s common stock, on each grant date, the Board considered various
objective and subjective factors described in detail in the Registration Statement, along with input from management, to determine the fair value of the Company’s common stock. In addition to these factors, as part of its assessment of the
fair value of the Company’s common stock for purposes of making stock option grants, the Board also considered and relied upon appraisals of the fair value of the Company’s common stock from independent third-party valuation specialists
using methodologies, approaches and assumptions consistent with the American Institute of Certified Public Accountants Audit and Accounting Practice Aid

 2

Mr. Matt Jones

United States Securities and Exchange Commission

CONFIDENTIAL TREATMENT REQUESTED

April 17, 2015

BY ATYR PHARMA, INC.

 Page
 3

Series: Valuation of Privately Held Company Equity Securities Issued as Compensation (the “Practice Aid”). Furthermore, as described in the Registration Statement and below, the
Company engaged in a retrospective reassessment of the fair value of its common stock for financial reporting purposes for each stock option granted between October 1, 2013 and September 30, 2014.

During the last 12 months, the Company granted options to purchase (i) 2,061,736 shares of common stock on July 10, 2014 (the
“July 2014 Grants”); (ii) an aggregate of 1,381,517 shares of common stock on October 10, 2014 and October 24, 2014 (the “October 2014 Grants”); (iii) 2,288,777 shares of common stock on
March 31, 2015 (the “March 2015 Grants”); and (iv) an aggregate of 2,350,000 shares of common stock on April 2, 2015 and April 17, 2015 (the “April 2015 Grants”). The Company has not granted any
other equity awards since April 17, 2015.

 July 2014 Grants

As described in detail in the Registration Statement beginning on page 72, as part of the preparation of the financial statements
necessary for inclusion in the Registration Statement, the Company reassessed the fair value of its common stock for the period including the July 2014 Grants and certain other prior period option grants on a retrospective basis for financial
reporting purposes. For purposes of this reassessment, the Company relied in part on appraisals of the value of its common stock as of May 31, 2014 and September 30, 2014 that were prepared by an independent third-party valuation
specialist using methodologies, approaches and assumptions consistent with the Practice Aid. Since the reassessed fair value of $1.65 per share of common stock for the July 2014 Grants is within the price range noted above, no further discussion is
included herein.

 October 2014 Grants

As described in detail in the Registration Statement beginning on page 72, the common stock valuation effective September 30, 2014
was used to determine the exercise price for the October 2014 Grants and utilized both the income and market approaches to determine the Company’s enterprise value, and the enterprise value was allocated based on the PWERM. The Company
transitioned to the PWERM once it had initiated its IPO process because it then had greater clarity as to its potential future liquidity events. At the time of the preparation of the September 30, 2014 valuation, and prior to the filing of its
Draft Registration Statement on December 22, 2014, the Company had indications that its enterprise value was at or near the levels indicated by its Series D preferred stock financing, pursuant to which shares were issued at $2.662 per share.
The Company’s increased probability of consummating an IPO and related change from an OPM model to a PWERM contributed significantly to the increased common stock valuation as of September 30, 2014. Since the fair value of $2.23 per share
of common stock for the October 2014 Grants is above the price range noted above, no further discussion is included herein.

 3

Mr. Matt Jones

United States Securities and Exchange Commission

CONFIDENTIAL TREATMENT REQUESTED

April 17, 2015

BY ATYR PHARMA, INC.

 Page
 4

 Common Stock Valuation as of December 31, 2014

As described in detail in the Registration Statement beginning on page 72, the Company determined the fair value of its common stock as of
December 31, 2014 on substantially the same basis as the September 30, 2014 valuation, with the exception of updated assumptions regarding the increased probability that an IPO would be completed in the near term and certain other
assumptions regarding the timing, value and probability of other scenarios in the event a near-term IPO did not occur. In addition, the model was updated to consider the estimated pre-money valuation expected in its Series E preferred stock
financing, which was the primary driver of the decrease in the fair value of the common stock from $2.23 per share as of September 30, 2014 to $1.48 per share as of December 31, 2014.

March 2015 and April 2015 Grants

Subsequent to the closing of the Company’s Series E preferred stock financing, the Board elected to grant certain stock options, the
fair value of which was based in part on an appraisal of the value of the Company’s common stock as of March 31, 2015 that was prepared by an independent third-party valuation specialist using methodologies, approaches and assumptions
consistent with the Practice Aid. The valuation was prepared on substantially the same basis as the September 30, 2014 and December 31, 2014 valuations described in the Registration Statement beginning on page 72, with the exception
of updated assumptions regarding the increased probability that an IPO would be completed in the near-term and certain other assumptions regarding the timing, value and probability of other scenarios in the event a near-term IPO did not occur. In
addition, the model was updated to use a backsolve method for the price paid by investors in the Series E preferred stock financing, in which approximately 82% of the aggregate number of shares sold were purchased by new investors in the Company.
The March 31, 2015 valuation resulted in the $1.15 per share fair value of the Company’s common stock that was utilized for the April 2015 Grants as the Board concluded that no significant internal or external value-generating events had
taken place between March 31, 2015 and each of the April 2, 2015 and April 17, 2015 grant dates. The Company’s Series E redeemable convertible preferred stock was issued in March 31, 2015 for a price of
approximately $1.119 per share as a result of arm’s length negotiations with third-party investors. If the Company completes a qualified IPO as defined in its certificate of incorporation, each share of Series E preferred stock would convert
into 0.8216 shares of common stock. The Company’s common stock fair value of $1.15 per share is in excess of the Series E price of $1.119 due to the Company’s consideration, in its valuation models, of the Series E conversion rate
adjustment that would take place upon a qualified IPO in which the Company receives at least $50 million in gross proceeds at a price of at least $1.6344 per share of common stock. In such conversion rate adjustment, each share of Series E preferred
stock would convert into 0.8216 shares of common stock instead of converting to common stock on a 1-for-1 basis. After the conversion rate adjustment, the effective Series E purchase price would be $1.362 per share and the common stock fair value of
$1.15 per share for the April 2015 Grants would represent an approximately 15% discount to the effective price paid by the Series E investors. The Company respectfully

 4

Mr. Matt Jones

United States Securities and Exchange Commission

CONFIDENTIAL TREATMENT REQUESTED

April 17, 2015

BY ATYR PHARMA, INC.

 Page
 5

submits to the Staff that the 15% discount is reasonable given superior rights and preferences of the preferred stock, and this, in addition to the Practice Aid compliant valuation methodology
employed, indicates that the Board valuation was appropriate.

 Bridge from Exercise Price of April 2015 Grants to Mid-Point of
Estimated Price Range

 The Company respectfully advises the Staff the following factors contributed to the $[***] per share
difference between the mid-point of estimated price range of $[***] per share and the $1.15 per share used for the Company’s April 2015 Grants:

•

The estimated price range necessarily assumes the IPO has occurred and a public market for the Company’s common stock has been created, and therefore excludes any marketability or illiquidity discount for the
Company’s common stock, which was appropriately taken into account in the Board’s determinations of fair value in connection with April 2015 Grants. As is typical for initial public offerings, the estimated price range was not derived
using a formal determination of fair value, but was determined as a result of discussions among representatives of the Company’s management and its underwriters. The impact of the application of a discount for lack of marketability represents
approximately $[***] per share.

•

The differences in the valuation methodologies, assumptions and inputs used by the underwriters in their valuation analysis discussed with the Company, which do not take into account the current lack of liquidity for
the Company’s common stock and assume a successful IPO as of today’s date with no weighting attributed to any other outcome for the Company’s business, such as remaining a privately held company, compared to the valuation
methodologies, assumptions and inputs used in the valuations considered by the Board. The impact of the consideration of non-IPO scenarios in its valuation models was approximately $[***] per share.

•

The remaining $[***] per share difference primarily results from variations in the underlying enterprise values in the Company’s Series E backsolve model and the implied pre-money valuations utilized by the
underwriters in the proposed IPO. Although it is difficult to precisely identify the specific differences between concluded enterprise values determined by the investors in the Company’s Series E preferred stock financing and the proposed price
range for the IPO, the Company believes the following factors contributed to the difference: (i) continuing robust capital markets activity in the biotechnology sector, including a significant number of successful initial public offerings by a
wide range of companies, (ii) the preliminary price range was in part informed by discussions with potential investors during “testing the waters” meetings conducted pursuant to the Jumpstart Our Business Startups Act of 2012 and is
more reflective of the current state of the public equity markets than what may have been considered during the Series E pricing negotiations, and (iii) the Series E purchase price was negotiated with an inherent uncertainty of completing a
successful IPO.

 5

Mr. Matt Jones

United States Securities and Exchange Commission

CONFIDENTIAL TREATMENT REQUESTED

April 17, 2015

BY ATYR PHARMA, INC.

 Page
 6

 To further assist the Staff in its evaluation of stock compensation and certain other
matters, the Company advises the Staff that it intends to include the disclosure set forth in Appendix A to this letter in a subsequent amendment to the Registration Statement. Such disclosure would be inserted on pages 72-73 of the
Registration Statement, following the disclosure regarding the Company’s December 31, 2014 common stock

CORRESP
1
filename1.htm

CORRESP

 April 6, 2015

CONFIDENTIAL

 VIA FEDEX

United States Securities and

 Exchange Commission

Washington, D.C. 20459

 Attention: Jeffrey P. Riedler

Assistant Director

Re:
aTyr Pharma, Inc.

Amendment No. 1 to Draft Registration Statement on Form S-1

Submitted February 2, 2015

CIK No. 0001339970

 Ladies and Gentlemen:

This letter is submitted on behalf of aTyr Pharma, Inc. (the “Company”) in response to comments contained in the letter dated
February 18, 2015 (the “Letter”) from Jeffrey P. Riedler, Assistant Director of the Staff (the “Staff”) of the Securities and Exchange Commission (the “Commission”) to John D. Mendlein, Ph.D.,
Chief Executive Officer and Executive Chairman of the Company, with respect to the Company’s confidential submission of Amendment No. 1 to Draft Registration Statement on Form S-1 (the “Draft Registration Statement”)
that was submitted on February 2, 2015. The Company is concurrently submitting a revised version of the Registration Statement (the “Revised Registration Statement”), including changes in response to the Staff’s
comments.

 The responses set forth below have been organized in the same manner in which the Commission’s comments were organized and all page
references in the Company’s response are to the Revised Registration Statement as marked. Copies of this letter and its attachments will also be provided to Matthew Jones, Bryan Pitko and Mark Brunhofer of the Commission.

Prospectus Summary, page 1

1.
 We note on page 95 that you believe data from your Fc fusion experiments may produce data that will provide iModFc molecules for you to
explore. We also note on page 96 that

 United States Securities and

Exchange Commission

 <April 6, 2015>

 Page
 2

you are continuing to investigate potential therapeutic Physiocrines that may have the potential to inhibit inflammation in both the lung and the liver. As you do not have a drug candidate for
your programs identified by the arrows labeled “iModFc non-RMIC,” “Liver,” or “Lung.” Please eliminate these programs from the pipeline table on pages 2 and 80.

RESPONSE: The Company acknowledges the Staff’s comment and has removed the programs with respect to “Liver” and “Lung” from the
pipeline table on pages 2 and 83 of the Revised Registration Statement. While the Company has not yet selected a drug candidate for its iMod.Fc program, the Company has included additional disclosure on pages 5 and 100 of the Revised
Registration Statement describing the results of preclinical studies with respect to one iMod.Fc molecule. Additionally, the Company has revised the pipeline table to provide additional detail with respect to the expected timing of the anticipated
next milestones for certain of the programs and has added a separate diagram immediately below relating to the discovery engine process.

If you require additional information, please telephone the undersigned at (415) 733-6071 or Mitzi Chang at (415) 733-6017.

Very truly yours,

 /s/ Maggie Wong

Maggie Wong

cc:
John D. Mendlein (aTyr Pharma, Inc.)

Frederic Chereau (aTyr Pharma, Inc.)

Nancy D. Krueger (aTyr Pharma, Inc.)

Kingsley L. Taft (Goodwin Procter LLP)

Alan F. Denenberg (Davis Polk & Wardwell LLP)

February 18, 2015

Via E -mail
John D. Mendlein, Ph.D.
Chief Executive Officer and Executive Chairman
aTyr Pharma, Inc.
3545 John Hopkins Court, Suite #250
San Diego, CA 92121

Re: aTyr Pharma, Inc.
Amendment No. 1 to Draft Registration Statement on Form  S-1
Submitted February 2, 2015
  CIK No. 0001339970

Dear Dr. Mendlein :

We have reviewed your amended draft registration statement  and have the following
comment.

Please respond to this letter by providing the requested information and either submitting
an amended draft registration statement or  publicly  filing your registration statement on
EDGAR.  If  you do not believe our comment applies  to your facts and circumstances or do not
believe an amendment is appropriate, please tell us why in your response.

After reviewing the information you provide in response to this comment  and your
amended draft registration statement or filed registration statement,  we may have  additional
comments.

Prospectus Summary, page 1

1. We note on page 95 that you believe data from your Fc fusion experiments may produce
data that will provide iModFc molecules for you to explore.  We also note on page 96
that you are continuing to investigate potential therapeutic Physiocrines that may hav e the
potential to inhibit inflammation in both the lung and the liver. As you do not have a drug
candidate for your programs identified by the arrows labeled “iModFc non -RMIC,”
“Liver,” or “Lung.” Please eliminate these programs from the pipeline table on  pages 2
and 80.

John D. Mendlein, Ph.D.
aTyr Pharma, Inc.
February 18, 2015
Page 2

 You may contact Mark Brunhofer at (202) 551 -3638 if you have questions regarding
comments on the financial statements and related matters.  Please contact Matthew Jones at
(202) 551 -3786, Bryan Pitko at (202) 551 -3203 or me at (202) 551 -3715 with any other
questions.

Sincerely,

 /s/ Bryan J. Pitko for

Jeffrey P. Riedler
Assistant Director

cc:  Kingsley L. Taft
Maggie L. Wong
Mitzi Chang
Goodwin Procter LLP
3 Embarcadero Center, 24th Floor
San Francisco, CA 94111

January 20, 2015

Via E -mail
John D. Mendlein, Ph.D.
Chief Executive Officer and Executive Chairman
aTyr Pharma, Inc.
3545 John Hopkins Court, Suite #250
San Diego, CA 92121

Re: aTyr Pharma, Inc.
Draft Registration Statement on Form S -1
Submitted December 22, 2014
  CIK No. 0001339970

Dear Dr. Mendlein :

We have reviewed your draft registration statement  and have the following comments.  In
some of our comments, we may ask you to provide us with information so we may better
understand your disclosure.

Please respond to this letter by providing the requested information and either submitting
an amended draft registration statement or  publicly  filing your registration statement on
EDGAR.  If you do not believe our comments apply to your facts  and circumstances or do not
believe an amendment is appropriate, please tell us why in your response.

After reviewing the information you provide in response to these  comments  and your
amended draft registration statement or filed registration statemen t, we may have  additional
comments.

Prospectus Summary, page 1

1. Please revise the table on pages pages  2 and 80 to reflect only the current stage of
development for each product candidate and indication. Accordingly, please eliminate
columns for anticipated next milestone due to the uncertainty of such events.  Anticipated
milestone and other future events  are properly discussed in the text where they can be
placed in an appropriate context.

2. Please revise your pipeline table under the column labeled “Pathway” and in the text
included within the arrows to identify the applicable pathway, drug candidate, and
indication.  Alternatively, if you have not yet identified an indication for the arrow
labeled “Resolaris 4th Indication” or a drug candidate for the arrow labeled “iModFc non -
RMIC” or “Liver,” or a pathway for the arrow labeled “Lung,” please eliminate t hese
programs from the pipeline table on pages 2 and 80.

John D. Mendlein, Ph.D.
aTyr Pharma, Inc.
January 20, 2015
Page 2

Risks Associated with Our Business, page 4

3. We note your risk factor disclosure that the FDA has placed a full clinical hold on your
IND to evaluate Resolaris for adult patients with FSHD and that t his hold prohibits you
from continuing clinical trials of Resolaris in the United States.    In the sections of your
prospectus summary and business section where you discuss the expected timing of your
receipt of initial results for your Phase 1b/2 trial o f Resolaris, please expand your
disclosure to discuss the clinical hold, the specific issues highlighted by the FDA, any
material actions that you have taken or plan to take in response to the FDA’s
communications, any updates from the FDA with respect you r response to the clinical
hold, and how the clinical hold impacts your planned development of Resolaris for adult
patients with FSHD.

Risk Factors
We face potential product liability, and, if succe ssful claims are brought …, page 43

4. Please quantify the amount of product liability insurance you carry and whether the
amount of your coverage is typical for a company in your industry.

Use of Proceeds, page 53

5. Please disclose how far in the clinical development of Resolaris you expect the proceeds
from this  offering will enable you to proceed  by indication .  In this regard, we note that
your development of Resolaris in Adults with FSHD is your most advanced product
candidate.  You should disclose whether you expect the applicable proceeds will be
sufficient to fully fund each planned clinical trial or state what aspects of such trials you
will be able to accomplish using the applicable proceeds.

Management’s Discussion and Analysis of Financial Condition and Results of Operations
Stock -Based Compensation, pa ge 66

6. We may have additional comments on your accounting for equity issuances including
stock compensation and beneficial conversion features. Once you have an estimated
offering price, please provide us an analysis explaining the reasons for the differences
between recent valuations of your common stock leading up to the IPO and the estimated
offering price.

Business, page 77

7. Please provide a brief summary for each drug candidate included on your pipeline table
on pages 2 and 80.  For example, w e note that you have not provided a discussion of the
“discoveries” labeled Resolaris 4th Indication, Liver, or Lung.

John D. Mendlein, Ph.D.
aTyr Pharma, Inc.
January 20, 2015
Page 3

 8. Please discuss your plans to apply for orphan designation for Resolaris for any applicable
indications in the U.S. or European Union.

9. Please discuss the terms of Pangu BioPharma’s joint research agreement with HKUST R
and D Corporation Limited.  Please include all of the material terms agreed to by the
parties. This includes, but is not limited to:
 the material services provided;
 paymen t terms;
 the duration of the agreement; and
 the material termination provisions.

Phase 1b/2 Clinical Trial, page 93

10. We note on page 12 that your Phase 1b/2 trial of Resolaris is designed to show efficacy.
Please expand your disclosure to include the tr ials primary and secondary endpoints for
the trial in adult patients with FSHD.

Our Advisors , page 1 14

11. Please briefly discuss the function of your scientific advisory board and therapeutic
advisory board as well as the specific responsibilities of the advisory board members  and
the frequency of advisory board meetings.

Executive and Director Compensation, page 124

12. Please update your executive and director compensation disclosure to reflect
compensation information as of the registrant’s last completed fiscal year ended
December 31, 2014.  You should also continue to include 2013 executive compensation
information in your Summary Compensation Table.  Please refer to Instruction 1 to Item
402(n) of Regulation S -K.

Principal Stockholders, page 134

13. Please  update your table on page 134 as of the most recent practicable date.

Description of Capital Stock
Warrants, page 139

14. We note that you entered into a loan and security agreement with Comerica Bank in
September 2007.  Please expand your disclosure to cla rify whether this agreement has
terminated.  If this agreement is outstanding, please expand your disclosure to discuss the
material terms of this loan and security agreement.  Additionally, please file this
agreement as an exhibit pursuant to Item 601(b)( 10) of Regulation S -K. Alternatively,

John D. Mendlein, Ph.D.
aTyr Pharma, Inc.
January 20, 2015
Page 4

 please provide us with an analysis supporting your determination that this agreement is
not material to the company.

Shares Eligible for Future Sale, page 143

15. Please state the number of shares of common stock, upon c ompletion of this offering that
will be restricted securities under Rule 144.

16. Please state the number of shares that are subject to a lock -up.

Notes to Consolidated Financial Statements
Preferred Stock Warrant Liabilities, page F -10

17. You disclose that y ou will carry the warrants to purchase various shares of redeemable
convertible preferred stock as liabilities until such time as the warrant are no longer
outstanding or the underlying securities are no longer redeemable outside your control,
including th e completion of your IPO.  On page 139 you disclose that the various
warrants contain provisions for the adjustment of the warrant exercise price and number
of shares issuable for certain dilutive issuances.  Please explain to us how the exercise
terms of these warrants can be adjusted after the completion of your IPO and why these
provisions do not also trigger liability accounting.  In your response, please tell us
specifically whether the provision in Article IV Section B.4(c) of your existing
Certificat e of Incorporation will carry over in your post -IPO Certificate and, if so, how
this provision complies with the guidance in ASC 815 -40-55-42 and 55 -43.  In this
regard, it appears that the formula provided in this section adjusts for any issuance below
the previous exercise price of the warrants and is not limited to the dilutive effect of
future issuances below the then -current fair value.

Exhibit

18. Please file the join research agreement between Pangu BioPharma and HKUST R and D
Corporation Limited  as exhibit s pursuant to Item 601(b)(10) of Regulation S -K.
Alternatively, please provide us with an analysis supporting your determination that the
agreement is not material to the company.

Other Comments

19. Please file all exhibits as soon as practicable.  We may have further comments  upon
examination of these exhibits.

20. Prior to its use please provide us proofs of all graphic, visual or photographic  information
you will provide in the printed prospectus. Please note that we may  have comments
regarding this  material.

John D. Mendlein, Ph.D.
aTyr Pharma, Inc.
January 20, 2015
Page 5

 21. Please supplementally provide us with copies of all written communications, as defined
in Rule 405 under the Securities Act, that you, or anyone authorized to do so on your
behalf, present to potential investors in reliance on Section 5(d) of t he Securities Act,
whether or not they retain  copies of the communications.

You may contact Mark Brunhofer at (202) 551 -3638 if you have questions regarding
comments on the financial statements and related matters.  Please contact Matthew Jones at
(202) 5 51-3786, Bryan Pitko at (202) 551 -3203 or me at (202) 551 -3715 with any other
questions.

Sincerely,

 /s/ Bryan J. Pitko  for

Jeffrey P. Riedler
Assistant Director

cc:  Kingsley L. Taft
Maggie L. Wong
Mitzi Chang
Goodwin Procter LLP
3 Embarcadero Center, 24th Floor
San Francisco, CA 94111