**UNITED STATES**

**SECURITIES AND EXCHANGE COMMISSION**

**Washington, D.C. 20549**

 

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**Form 10-K/A**

**(Amendment No. 1)**

 

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**(Mark One)**

 

**x**      **ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934**

 

**For the fiscal year ended December 31, 2017**

 

**OR**

 

**o**         **TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934**

 

**For the transition period from                     to**

 

**Commission file number 001-37813**

 

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**SYROS PHARMACEUTICALS, INC.**

(Exact Name of Registrant as Specified in Its Charter)

 

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| **Delaware**                                                       |   | **45-3772460**                         |
|--------------------------------------------------------------------|--------|----------------------------------------|
| (State or other   jurisdiction of   incorporation or organization) |   | (I.R.S. Employer   Identification No.) |

 

| **620   Memorial Drive, Suite 300   Cambridge, Massachusetts** |   | **02139**  |
|---------------------------------------------------------------------|--------|------------|
| (Address of principal   executive offices)                          |   | (Zip code) |

 

**(617) 744-1340**

(Registrant’s telephone number, including area code)

 

Securities registered pursuant to Section 12(b) of the Act:

 

| **Title of Class**         | ** ** | **Name of Exchange on Which Registered** |
|--------------------------------------|------------|-------------------------------------------------------------------|
| **Common   Stock, $0.001 par value** |       | **Nasdaq   Global Select Market**                                 |

 

Securities registered pursuant to Section 12(g) of the Act:

**None.**

 

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Indicatebycheckmarkiftheregistrantisawell-knownseasonedissuer,as definedinRule405oftheSecuritiesAct.YesoNox

 

IndicatebycheckmarkiftheregistrantisnotrequiredtofilereportspursuanttoSection13orSection15(d)oftheAct. YesoNox

 

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

 

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files).  Yes  x  No  o

 

Indicate by check mark if disclosure of delinquent filers pursuant to Item 405 of Regulation S-K is not contained herein, and will not be contained, to the best of the registrant’s knowledge, in definitive proxy or information statements incorporated by reference in Part III of this Form 10-K or any amendment to this Form 10-K.  x

 

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

 
| Large accelerated filer               |   | o |   | Accelerated filer              |   | x |
|-------------------------------------------------|--------|---|--------|-------------------------------------|--------|---|
| Non-accelerated filer                           |   | o |   | Smaller reporting company |   | o |
| (Do not check if a   smaller reporting company) |   | o |   | Emerging growth company             |   | x |

 

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

 

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

 

As of June 30, 2017, the last business day of the registrant’s most recently completed second fiscal quarter, the aggregate market value of the registrant’s common stock held by non-affiliates was $289,542,157, based on the last reported sale price of such stock on the Nasdaq Global Select Market as of such date.

 

As of August 20, 2018, the registrant had 33,654,389 shares of Common Stock, $0.001 par value per share, outstanding.

 

 

 

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**EXPLANATORY NOTE**

 

Syros Pharmaceuticals, Inc. (the “Company”) is filing this Amendment No. 1 on Form 10-K/A (the “Amendment”) to its Annual Report on Form 10-K for the fiscal year ended December 31, 2017, as originally filed on March 12, 2018 (the “Original Filing”), to add a report of management’s assessment regarding internal control over financial reporting to Item 9A. In accordance with Rule 12b-15 under the Securities Exchange Act of 1934, as amended, this Amendment No. 1 amends and restates Item 9A of the Original Filing in its entirety, and Item 15 is amended to include new certifications as Exhibits 31.3 and 31.4.

 

This Amendment No. 1 does not update or amend any other items in the Original Filing in any way other than as described in the preceding paragraph, and the Original Filing, as amended by this Amendment No. 1, continues to speak as of the date of the Original Filing.  Accordingly, this Amendment No. 1 should be read in conjunction with the Original Filing and the Company’s other filings with the Securities and Exchange Commission.

 

Unless we specify otherwise, all references in this Amendment to “we,” “our,” “us,” or “the Company” refer to Syros Pharmaceuticals, Inc.

 

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**PART II**

 

**ITEM 9A.    CONTROLS AND PROCEDURES**

 

**Management’s Evaluation of Disclosure Controls and Procedures**

 

We maintain “disclosure controls and procedures,” as defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, as amended, or the Exchange Act, that are designed to ensure that information required to be disclosed in the reports that we file or submit under the Exchange Act is (1) recorded, processed, summarized and reported within the time periods specified in the SEC’s rules and forms and (2) accumulated and communicated to our management, including our principal executive and principal financial officer, as appropriate to allow timely decisions regarding required disclosure. Our management recognizes that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving their objectives and our management necessarily applies its judgment in evaluating the cost-benefit relationship of possible controls and procedures. Our disclosure controls and procedures are designed to provide reasonable assurance of achieving their control objectives.

 

Our management, with the participation of our Chief Executive Officer, who serves as our principal executive and principal financial officer, has evaluated the effectiveness of our disclosure controls and procedures as of December 31, 2017. Based upon such evaluation, our Chief Executive Officer and Principal Financial Officer has concluded that our disclosure controls and procedures were effective at the reasonable assurance level as of such date.

 

**Internal Control Over Financial Reporting**

 

***Management’s Report on Internal Control Over Financial Reporting***

 

Our management is responsible for establishing and maintaining adequate internal control over our financial reporting. Internal control over financial reporting is defined in Rules 13a-15(f) and 15d-15(f) promulgated under the Exchange Act as a process designed by, or under the supervision of, our principal executive and principal financial officers and effected by our board of directors, management and other personnel to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with U.S. GAAP. Our internal control over financial reporting includes those policies and procedures that:

 

·                  pertain to the maintenance of records that, in reasonable detail, accurately and fairly reflect our transactions and dispositions of our assets;

 

·                  provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with U.S. GAAP, and that our receipts and expenditures are being made only in accordance with authorizations of our management and directors; and

 

·                  provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use or disposition of our assets that could have a material effect on our financial statements.

 

Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements. Projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate.

 

Our management assessed the effectiveness of our internal control over financial reporting as of December 31, 2017. In making this assessment, management used the criteria set forth by the Committee of Sponsoring Organizations of the Treadway Commission (COSO) in its 2013 Internal Control — Integrated Framework. Based on our assessment, our management has concluded that, as of December 31, 2017, our internal control over financial reporting is effective based on those criteria.

 

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This Annual Report on Form 10-K does not include an attestation report of our independent registered public accounting firm regarding internal control over financial reporting due to an exemption established by the Jumpstart Our Business Startups Act of 2012 for “emerging growth companies.”

 

***Changes in Internal Control Over Financial Reporting***

 

During the year ended December 31, 2017, we implemented an accounting system for purposes of tracking and accounting for stock-based awards, as well as an enterprise resource system for the purposes of maintaining our general ledger and reporting. There were no other changes in our internal control over financial reporting (as defined in Rules 13a-15(f) and 15d-15(f) under the Exchange Act) during the year ended December 31, 2017 that has materially affected, or is reasonably likely to materially affect, our internal control over financial reporting.

 

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**PART IV**

 

**ITEM 15.     EXHIBITS AND FINANCIAL STATEMENT SCHEDULES**

 

(b)  *Exhibits*

 
| ** **                                                           | ** ** | ** **                                                                                                                                                                                                                        | ** ** | **Incorporation by Reference** | ** ** | ** **              |
|----------------------------------------------------------------------|------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------|------------------------------------------|------------|-------------------------|
| **Exhibit No.**                                                 | ** ** | **Description**                                                                                                                                                                                                                   | ** ** | **Form**                                 | ** ** | **SEC   Filing   Date** | ** ** | **Exhibit   Number** | ** ** | **Filed   with this   10-K** |
|                                                                 |       |                                                                                                                                                                                                                              |       |                                     |       |                    |   |   |   |   |
| **Organizational Documents and Documents Related   to Common Stock** |
| 3.1                                                                  |       | Restated   Certificate of Incorporation of the Registrant                                                                                                                                                                         |       | 8-K                                      |       | 7/6/16                  |   | 3.1 |   |   |
| 3.2                                                                  |       | Amended   and Restated Bylaws of the Registrant                                                                                                                                                                                   |       | 8-K                                      |       | 7/6/16                  |   | 3.2 |   |   |
| 4.1                                                                  |       | Form of   common stock certificate                                                                                                                                                                                           |       | S-1^                                     |       | 6/3/16                  |   | 4.1 |   |   |
| 4.2                                                                  |       | Second   Amended and Restated Investors’ Rights Agreement dated October 9, 2014,   as amended, among the Registrant and the other parties thereto                                                                       |       | S-1^                                     |       | 6/3/16                  |   | 4.2 |   |   |
| 4.3                                                                  |       | Sales   Agreement dated July 20, 2017 by and between the Registrant and Cowen   and Company LLC                                                                                                                              |       | S-3^^                                    |       | 7/20/17                 |   | 1.2 |   |   |
| 4.4                                                                  |       | Stock   Purchase Agreement dated January 8, 2018 by and between the Registrant   and Incyte Corporation, as amended                                                                                                          |       | 10-K                                     |       | 3/12/18                 |   | 4.4 |   |   |
| 4.5                                                                  |       | Underwriting   Agreement dated January 30, 2018 by and among the Registrant, J.P.   Morgan Securities LLC, Cowen and Company, LLC and Piper Jaffray and Co., as representatives   of the several underwriters named thereing |       | 8-K                                      |       | 1/31/18                 |   | 1.1 |   |   |
| 4.6                                                                  |       | Securities   Purchase Agreement dated April 20, 2017 by and among the Registrant and   the persons party thereto                                                                                                             |       | 8-K                                      |       | 4/21/17                 |   | 10.1 |   |   |
| 4.7                                                                  |       | Registration   Rights Agreement, dated April 20, 2017, by and among the Registrant and   the persons party thereto                                                                                                           |       | 8-K                                      |       | 4/21/17                 |   | 10.2 |   |   |
|                                                                 |       |                                                                                                                                                                                                                              |       |                                     |       |                    |   |   |   |   |
| **Equity Plan Documents**                                            |
| 10.1*                                                                |       | 2012   Equity Incentive Plan, as amended                                                                                                                                                                                          |       | S-1^                                     |       | 6/3/16                  |   | 10.1 |   |   |
| 10.2*                                                                |       | Form of   Incentive Stock Option Agreement under 2012 Equity Incentive Plan                                                                                                                                                  |       | S-1^                                     |       | 6/3/16                  |   | 10.2 |   |   |
| 10.3*                                                                |       | Form of   Nonstatutory Stock Option Agreement under 2012 Equity Incentive Plan                                                                                                                                               |       | S-1^                                     |       | 6/3/16                  |   | 10.3 |   |   |
| 10.4*                                                                |       | Form of   Restricted Stock Agreement under 2012 Equity Incentive Plan                                                                                                                                                        |       | S-1^                                     |       | 6/3/16                  |   | 10.4 |   |   |
| 10.5*                                                                |       | 2016   Stock Incentive Plan                                                                                                                                                                                                       |       | S-1^                                     |       | 6/3/16                  |   | 10.5 |   |   |
| 10.6*                                                                |       | Form of   Incentive Stock Option Agreement under 2016 Stock Incentive Plan                                                                                                                                                   |       | S-1^                                     |       | 6/3/16                  |   | 10.6 |   |   |
| 10.7*                                                                |       | Form of   Nonstatutory Stock Option Agreement under 2016 Stock Incentive Plan                                                                                                                                                |       | S-1^                                     |       | 6/3/16                  |   | 10.7 |   |   |
| 10.8*                                                                |       | 2016   Employee Stock Purchase Plan                                                                                                                                                                                               |       | S-1^                                     |       | 6/3/16                  |   | 10.8 |   |   |
|                                                                 |       |                                                                                                                                                                                                                              |       |                                     |       |                    |   |   |   |   |
| **Agreements with Directors and Executive Officers**                 |
| 10.9*                                                                |       | Offer   Letter, dated November 13, 2012 and effective as of July 2, 2012 by   and between the Registrant and Nancy Simonian, M.D., as amended                                                                           |       | S-1^                                     |       | 6/3/16                  |   | 10.9 |   |   |
| 10.10*                                                               |       | Offer   Letter dated August 25, 2015 by and between the Registrant and Kyle D.   Kuvalanka, as amended                                                                                                                       |       | S-1^                                     |       | 6/3/16                  |   | 10.10 |   |   |
| 10.11*                                                               |       | Offer   Letter dated December 2, 2015 by and between the Registrant and David A.   Roth, M.D., as amended                                                                                                                    |       | S-1^                                     |       | 6/3/16                  |   | 10.11 |   |   |
| 10.12*                                                               |       | Offer   Letter dated September 9, 2016 by and between the Registrant and Gerald   E. Quirk, Esq.                                                                                                                        |       | 10-K                                     |       | 3/20/17                 |   | 10.12 |   |   |
| 10.13*                                                               |       | Offer   Letter dated November 6, 2017 by and between the Registrant and Jeremy   Springhorn, Ph.D.                                                                                                                           |       | 10-K                                     |       | 3/12/18                 |   | 10.13 |   |   |
| 10.14*                                                               |       | Consulting   Agreement dated August 8, 2012 by and between the Registrant and Richard   A. Young, Ph.D., as amended                                                                                                          |       | 10-K                                     |       | 3/20/17                 |   | 10.13 |   |   |

 

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| 10.15*                                        |   | Form of   Director and Officer Indemnification Agreement by and between the Registrant   and each of the directors and executive officers of the Registrant                        |   | S-1^   |   | 6/3/16  |   | 10.12   |   |   |
|-----------------------------------------------|--------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|--------|--------|--------|---------|--------|---------|--------|--------|
|                                          |   |                                                                                                                                                                                    |   |   |   |    |   |    |   |   |
| **License and Collaboration Agreements**      |
| 10.16+                                        |   | Exclusive   License Agreement dated February 22, 2013 by and between the Registrant   and the Dana-Farber Cancer Institute, Inc.                                              |   | S-1^   |   | 6/3/16  |   | 10.13   |   |   |
| 10.17+                                        |   | Exclusive   License Agreement dated April 1, 2013 by and among the Registrant, the   Whitehead Institute for Biomedical Research and the Dana-Farber Cancer   Institute, Inc. |   | S-1^   |   | 6/3/16  |   | 10.14   |   |   |
| 10.18+                                        |   | Exclusive   License Agreement dated April 4, 2013 by and between the Registrant and   the Whitehead Institute for Biomedical Research                                              |   | S-1^   |   | 6/3/16  |   | 10.15   |   |   |
| 10.19+                                        |   | Amended   and Restated Cancer License Agreement dated April 28, 2016 by and   between the Registrant and TMRC Co., Ltd.                                                       |   | S-1^   |   | 6/3/16  |   | 10.16   |   |   |
| 10.20+                                        |   | Supply   Management Agreement dated April 28, 2016 by and between the Registrant   and TMRC Co., Ltd.                                                                         |   | S-1^   |   | 6/3/16  |   | 10.18   |   |   |
| 10.21                                         |   | Consent   and Stand-by License Agreement dated April 28, 2016 by and among the   Registrant, Toko Pharmaceutical Ind. Co., Ltd. and TMRC Co., Ltd.                       |   | S-1^   |   | 6/3/16  |   | 10.19   |   |   |
| 10.22+                                        |   | Target   Discovery, Research Collaboration and Option Agreement dated January 8, 2018   by and between the Registrant and Incyte Corporation                                       |   | 10-K   |   | 3/12/18 |   | 10.22   |   |   |
|                                          |   |                                                                                                                                                                                    |   |   |   |    |   |    |   |   |
| **Leases**                                    |
| 10.23                                         |   | Lease   dated March 13, 2015 by and between the Registrant and 620 Memorial   Leasehold LLC                                                                                        |   | S-1^   |   | 6/3/16  |   | 10.17   |   |   |
|                                          |   |                                                                                                                                                                                    |   |   |   |    |   |    |   |   |
| **Subsidiaries, Consents and Certifications** |
| 21.1                                          |   | Subsidiaries   of the Registrant                                                                                                                                                        |   | 10-K   |   | 3/12/18 |   | 21.1    |   |   |
| 23.1                                          |   | Consent   of Ernst & Young LLP, independent public accounting firm                                                                                                             |   | 10-K   |   | 3/12/18 |   | 23.1    |   |   |
| 31.1                                          |   | Certification   of principal executive officer pursuant to   Rule 13a-14(a)/15d-14(a) of the Securities Exchange Act of 1934, as   amended                                    |   | 10-K   |   | 3/12/18 |   | 31.1    |   |   |
| 31.2                                          |   | Certification   of principal financial officer pursuant to   Rule 13a-14(a)/15d-14(a) of the Securities Exchange Act of 1934, as   amended                                    |   | 10-K   |   | 3/12/18 |   | 31.2    |   |   |
| 31.3                                          |   | Certification   of principal executive officer pursuant to   Rule 13a-14(a)/15d-14(a) of the Securities Exchange Act of 1934, as   amended                                    |   |   |   |    |   |    |   | X      |
| 31.4                                          |   | Certification   of principal financial officer pursuant to   Rule 13a-14(a)/15d-14(a) of the Securities Exchange Act of 1934, as   amended                                    |   |   |   |    |   |    |   | X      |
| 32.1#                                         |   | Statement   of principal executive officer pursuant to 18 U.S.C. §1350, as adopted   pursuant to Section 906 of the Sarbanes-Oxley Act of 2002                                |   | 10-K   |   | 3/12/18 |   | 32.1    |   |   |
| 32.2#                                         |   | Statement   of principal financial officer pursuant to 18 U.S.C. §1350, as adopted pursuant   to Section 906 of the Sarbanes-Oxley Act of 2002                                |   | 10-K   |   | 3/12/18 |   | 32.2    |   |   |
| ** **                                    |
| **XBRL Documents**                            |
| 101.INS                                       |   | XBRL Instance Document                                                                                                                                                                  |   | 10-K   |   | 3/12/18 |   | 101.INS |   |   |
| 101.SCH                                       |   | XBRL Taxonomy Extension Schema Document                                                                                                                                                 |   | 10-K   |   | 3/12/18 |   | 101.SCH |   |   |
| 101.CAL                                       |   | XBRL Calculation Linkbase Document                                                                                                                                                      |   | 10-K   |   | 3/12/18 |   | 101.CAL |   |   |
| 101.DEF                                       |   | XBRL Taxonomy Extension Definition Linkbase Document                                                                                                                                    |   | 10-K   |   | 3/12/18 |   | 101.DEF |   |   |
| 101.LAB                                       |   | XBRL Label Linkbase Document                                                                                                                                                            |   | 10-K   |   | 3/12/18 |   | 101.LAB |   |   |
| 101.PRE                                       |   | XBRL Taxonomy Presentation Linkbase Document                                                                                                                                            |   | 10-K   |   | 3/12/18 |   | 101.PRE |   |   |

 

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*      Indicates management contract or compensatory plan.

 

+                 Confidential treatment has been requested and/or granted as to certain portions, which portions have been omitted and filed separately with the U.S. Securities and Exchange Commission

 

^                  SEC File No. 333-211818

 

^^            SEC File No. 333-219369

 

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#                 This certification will not be deemed “filed” for purposes of Section 18 of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), or otherwise subject to the liability of that section. Such certification will not be deemed to be incorporated by reference into any filing under the Securities Act of 1933, as amended, or the Exchange Act, except to the extent specifically incorporated by reference into such filing.

 

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**SIGNATURES**

 

Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned, thereunto duly authorized.

 
|                              | **SYROS   PHARMACEUTICALS, INC.** |
|-----------------------------------|----------------------------------------|
| ** **                        | ** **                             | ** ** |
| ** **                        | ** **                             | ** ** |
| Date: August 24,   2018 | By:                                    | /s/ Nancy Simonian,   M.D. |
|                              |                                   | Nancy Simonian, M.D. |
|                              | * *                               | *President   and Chief Executive Officer* |

 

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