Exhibit 10.1

CONSULTING AGREEMENT

THIS CONSULTING AGREEMENT (the “Agreement”), made this 8th day of August, 2012 is entered into by LS22, Inc., a Delaware corporation with its principal place of business at One Memorial Drive, 7th Floor, Cambridge, MA 02142 (the “Company”), and Richard A. Young, PhD., (the “Consultant”). The Consultant is a Member of the Whitehead Institute for Biomedical Research (“WIBR”) and faculty member in the Department of Biology of the Massachusetts Institute of Technology (“MIT”).

INTRODUCTION

The Company desires to retain the services of the Consultant and the Consultant desires to perform certain services for the Company. In consideration of the mutual covenants and promises contained herein and other good and valuable consideration, the receipt and sufficiency of which is hereby acknowledged by the parties hereto, the parties agree as follows:

1.Services. The Consultant agrees to perform such consulting, advisory and related services to and for the Company as may be reasonably requested from time to time by the Company. The Consultant agrees to devote up to one (1) day per week to the performance of such services. Without limiting the additional terms and conditions of Section 7 below, during the Consultation Period (as defined below), the Consultant shall not knowingly engage in any activity that has a conflict of interest with the Company, including any competitive employment, business, or other activity, and he shall not knowingly assist any other person or organization that competes, or intends to compete, with the Company, it being further acknowledged and understood by the Company that Consultant is currently involved in those endeavors listed on Annex 1 hereto.

The Whitehead Institute Uniform Consulting Agreement Provisions (“Standard Provisions”) are attached hereto as Exhibit A and are incorporated herein by reference. The parties agree that the Standard Provisions are an integral part of this Agreement and this Agreement shall have no force or effect unless the Standard Provisions are signed by both parties. The parties hereto agree to abide by such Standard Provisions and further agree that in the event of any conflict between this Agreement and the Standard Provisions, the Standard Provisions shall govern and prevail.

2.Term. This Agreement shall commence on the date hereof and shall continue until August 8, 2016 (such period, as it may be extended, being referred to as the “Consultation Period”), unless sooner terminated in accordance with the provisions of Section 4.

3.Compensation.

3.1Equity Compensation. Subject to approval by the Board of Directors of the Company, in consideration for the performance of the services hereunder, the Consultant shall be awarded a grant of 1,600,000 shares of restricted common stock, $0.001 par value per share, of the Company (“Common Stock”), having a purchase price equal to the fair market value of the Common Stock on the date of grant ($0.001 per share) and having such other terms and conditions, including with respect to forfeiture and other transfer restrictions in favor of the Company, as shall be set forth in a Restricted Stock Agreement by and between the Consultant and the Company.

3.2Fees. The Company will not pay the Consultant any consulting fees before the Qualified Financing Date (as defined below). After the Qualified Financing Date and before the Second Qualified Financing Date (as defined below), the Company shall pay to the Consultant consulting fees of $25,000 per year, payable in equal quarterly installments. From and after the Second Qualified Financing Date, the Company shall pay to the Consultant consulting fees of $50,000 per year, payable in equal quarterly installments. Payment for any partial quarter shall be prorated.

For purposes of this Agreement, “Qualified Financing Date” shall mean the first date on which the Company receives aggregate gross proceeds equal to or exceeding $750,000 from the sale to one or more third parties of shares of its capital stock, or notes or other indebtedness that is convertible into or exercisable for shares of its capital stock, in a venture capital transaction. For purposes of this Agreement, “Second Qualified Financing Date” shall mean the first date on which the Company receives aggregate gross proceeds equal to or exceeding $12,500,000 from the sale to one or more third parties of its capital stock, or notes or other indebtedness that is convertible into or exercisable for shares of its capital stock, in a venture capital transaction.

3.3Reimbursement of Expenses. The Company shall reimburse the Consultant for all reasonable and necessary expenses incurred or paid by the Consultant in connection with, or related to, the performance of his services under this Agreement. The Consultant shall submit to the Company itemized monthly statements, in a form satisfactory to the Company, of such expenses incurred in the previous month. The Company shall pay to the Consultant amounts shown on each such statement within 30 days after receipt thereof.

3.4Benefits. The Consultant shall not be entitled to any benefits, coverages or privileges, including, without limitation, social security, unemployment, medical or pension payments, made available to employees of the Company.

4.Termination. The Company may, without prejudice to any right or remedy it may have due to any failure of the Consultant to perform his obligations under this Agreement, terminate the Consultation Period upon 30 days’ prior written notice to the Consultant. The Consultant may, without prejudice to any right or remedy it may have due to any failure of the Company to perform its obligations under this Agreement, terminate the Consultation Period upon 90 days’ prior written notice to the Company. In the event of such termination, the Consultant shall be entitled to payment for services performed and expenses paid or incurred prior to the effective date of termination, subject to the limitation on reimbursement of expenses set forth in Section 3.2. Such payments shall constitute full settlement of any and all claims of the Consultant of every description against the Company. Notwithstanding the foregoing, the Company may terminate the Consultation Period, effective immediately upon receipt of written notice, if the Consultant breaches or threatens to breach any provision of Section 6 or Section 7, and the Consultant may terminate the Consultation Period, effective immediately upon receipt of written notice, if the Company breaches any provision of Section 3. The provisions of Sections 4, 6, 7, 8, 10 and 14 shall survive any termination of this Agreement.

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5.Cooperation. The Consultant shall use his best efforts in the performance of his obligations under this Agreement. The Company shall provide such access to its information and property as may be reasonably required in order to permit the Consultant to perform his obligations hereunder. The Consultant shall cooperate with the Company’s personnel, shall not interfere with the conduct of the Company’s business and shall observe all rules, regulations and security requirements of the Company concerning the safety of persons and property.

6.Inventions and Proprietary Information.

6.1Inventions.

(a)All inventions, discoveries, computer programs, data, technology, designs, innovations and improvements (whether or not patentable and whether or not copyrightable) (“Inventions”) which are made, conceived, reduced to practice, created, written, designed or developed by the Consultant, solely or jointly with others and whether during normal business hours or otherwise, (i) during the Consultation Period that result from the performance of Consultant’s services and if related to the business of the Company or (ii) after the Consultation Period if resulting or directly derived from Proprietary Information (as defined below), shall be the sole property of the Company. The Consultant hereby assigns to the Company all Inventions and any and all related patents, copyrights, trademarks, trade names, and other industrial and intellectual property rights and applications therefor, in the United States and elsewhere and appoints any officer of the Company as his duly authorized attorney to execute, file, prosecute and protect the same before any government agency, court or authority. Upon the request of the Company and at the Company’s expense, the Consultant shall execute such further assignments, documents and other instruments as may be necessary or desirable to fully and completely assign all Inventions to the Company and to assist the Company in applying for, obtaining and enforcing patents or copyrights or other rights in the United States and in any foreign country with respect to any Invention. The Consultant also hereby waives all claims to moral rights in any Inventions.

(b)The Consultant shall promptly disclose to the Company all Inventions and will maintain adequate and current written records (in the form of notes, sketches, drawings and as may be specified by the Company) to document the conception and/or first actual reduction to practice of any Invention. Such written records shall be available to and remain the sole property of the Company at all times.

6.2Proprietary Information.

(a)The Consultant acknowledges that his relationship with the Company is one of high trust and confidence and that in the course of his service to the Company he will have access to and contact with Proprietary Information. The Consultant agrees that he will not, during the Consultation Period or at any time thereafter, disclose to others, or use for his benefit or the benefit of others, any Proprietary Information or Invention.

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(b)For purposes of this Agreement, Proprietary Information shall mean, by way of illustration and not limitation, all information (whether or not patentable and whether or not copyrightable) owned, possessed or used by the Company, including, without limitation, any Invention, formula, vendor information, customer information, apparatus, equipment, trade secret, process, research, report, technical data, know-how, computer program, software, software documentation, hardware design, technology, marketing or business plan, forecast, unpublished financial statement, budget, license, price, cost and employee list that is communicated to, learned of, developed or otherwise acquired by the Consultant in the course of his service as a consultant to the Company.

(c)The Consultant’s obligations under this Section 6.2 shall not apply to any information (none of which shall be deemed Proprietary Information) that (i) was known to Consultant prior to it being furnished to the Consultant by or on behalf of the Company provided that such information was or is not known to Consultant to be subject to another confidentiality agreement with, or other contractual, legal or fiduciary obligation of confidentiality to the Company, (ii) is developed by Consultant independently of the Proprietary Information disclosed to Consultant by the Company as demonstrated by the Consultant through third party written records, (iii) is acquired by Consultant on a non-confidential basis from any person entitled to make disclosure to Consultant unless such person is under an obligation of confidentiality to Company which is known to Consultant, (iv) is or becomes known to the general public under circumstances involving no breach by the Consultant or others of the terms of this Section 6.2, (v) is generally disclosed to third parties by the Company without restriction on such third parties, (vi) is approved for release by written authorization of the Board of Directors of the Company, or (vii) Consultant is obligated to produce pursuant to an order of a court of competent jurisdiction or a valid administrative or Congressional subpoena, provided that the Consultant promptly notify Company and cooperate reasonably with Company’s efforts to contest or limit the scope of such order.

(d)Upon termination of this Agreement or at any other time upon request by the Company, the Consultant shall promptly deliver to the Company all records, files, memoranda, notes, designs, data, reports, price lists, customer lists, drawings, plans, computer programs, software, software documentation, sketches, laboratory and research notebooks and other documents (and all copies or reproductions of such materials) relating to the business of the Company.

(e)The Consultant represents that his retention as a consultant with the Company and his performance under this Agreement does not, and shall not, breach any agreement that obligates him to keep in confidence any trade secrets or confidential or proprietary information of his or of any other party or to refrain from competing, directly or indirectly, with the business of any other party. The Consultant shall not disclose to the Company any trade secrets or confidential or proprietary information of any other party.

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(f)The Consultant acknowledges that the Company from time to time may have agreements with other persons or with the United States Government, or agencies thereof, that impose obligations or restrictions on the Company regarding inventions made during the course of work under such agreements or regarding the confidential nature of such work. The Consultant agrees to be bound by all such obligations and restrictions that are known to him and to take all action necessary to discharge the obligations of the Company under such agreements.

7.Non-Competition and Non-Solicitation.

7.1Restrictions. During the term of this Agreement and for a period of one (1) year after termination of the Agreement, the Consultant will not directly or indirectly:

(a)Engage or assist others in engaging in any business or enterprise (whether as owner, partner, officer, director, employee, consultant, investor, lender or otherwise, except as the holder of not more than 1% of the outstanding stock of a publicly-held company) that is competitive with the Company’s business, including but not limited to any business or enterprise that develops, manufactures, markets, licenses, sells or provides any product or service that competes with any product or service developed, manufactured, marketed, licensed, sold or provided, or planned to be developed, manufactured, marketed, licensed, sold or provided, by the Company while the Consultant was employed by the Company; or

(b)Either alone or in association with others, divert or take away, or attempt to divert or take away, the business or patronage of any of the clients, customers, or business partners of the Company which were contacted, solicited, or served by the Company during the 12-month period prior to the termination or cessation of the Consultant’s services with the Company; or

(c)Either alone or in association with others (i) solicit, induce or attempt to induce, any employee or independent contractor of the Company to terminate his or her employment or other engagement with the Company, or (ii) hire, or recruit or attempt to hire, or engage or attempt to engage as an independent contractor, any person who was employed or otherwise engaged by the Company at any time during the term of the Consultant’s services with the Company; provided, that this clause (ii) shall not apply to the recruitment or hiring or other engagement of any individual whose employment or other engagement with the Company has been terminated for a period of six months or longer.

7.2Extension. If the Consultant violates the provisions of Section 7.1, the Consultant shall continue to be bound by the restrictions set forth in such paragraph until a period of one (1) year has expired without any violation of such provisions.

7.3Company’s Business. For purposes of this Agreement, the “Company’s business” shall mean the discovery and development of therapeutic, diagnostic, and/or research products related to mechanisms by which gene transcription is regulated, provided, however, that the “Company’s business” shall exclude the discovery and development of therapeutic, diagnostic, and/or research products that target BET bromodomains and histone deacetylases 1, 2 and 6.

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8.Remedies. The Consultant acknowledges that any breach of the provisions of Section 6 or 7 could result in serious and irreparable injury to the Company for which the Company cannot be adequately compensated by monetary damages alone. The Consultant agrees, therefore, that in the event of such breach, in addition to any other remedy it may have, the Company shall be entitled to enforce the specific performance of this Agreement by the Consultant and to seek both temporary and permanent injunctive relief (to the extent permitted by law) without the necessity of proving actual damages.

9.Independent Contractor Status. The Consultant shall perform all services under this Agreement as an “independent contractor” and not as an employee or agent of the Company. The Consultant is not authorized to assume or create any obligation or responsibility, express or implied, on behalf of, or in the name of, the Company or to bind the Company in any manner.

10.Notices. All notices required or permitted under this Agreement shall be in writing and shall be deemed effective upon personal delivery or upon deposit in the United States Post Office, by registered or certified mail, postage prepaid, addressed to the other party at the address shown above, or at such other address or addresses as either party shall designate to the other in accordance with this Section 10.

11.Pronouns. Whenever the context may require, any pronouns used in this Agreement shall include the corresponding masculine, feminine or neuter forms, and the singular forms of nouns and pronouns shall include the plural, and vice versa.

12.Entire Agreement. This Agreement constitutes the entire agreement between the parties and supersedes all prior agreements and understandings, whether written or oral, relating to the subject matter of this Agreement.

13.Amendment. This Agreement may be amended or modified only by a written instrument executed by both the Company and the Consultant.

14.Governing Law. This Agreement shall be construed, interpreted and enforced in accordance with the laws of the Commonwealth of Massachusetts.

15.Successors and Assigns. This Agreement shall be binding upon, and inure to the benefit of, both parties and their respective successors and assigns, including any corporation with which, or into which, the Company may be merged or which may succeed to its assets or business, provided, however, that the obligations of the Consultant are personal and shall not be assigned by him.

16.Miscellaneous.

16.1No delay or omission by the Company in exercising any right under this Agreement shall operate as a waiver of that or any other right. A waiver or consent given by the Company on any one occasion shall be effective only in that instance and shall not be construed as a bar or waiver of any right on any other occasion.

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16.2The captions of the sections of this Agreement are for convenience of reference only and in no way define, limit or affect the scope or substance of any section of this Agreement. In the event that any provision of this Agreement shall be invalid, illegal or otherwise unenforceable, the validity, legality and enforceability of the remaining provisions shall in no way be affected or impaired thereby.

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IN WITNESS WHEREOF, the parties hereto have executed this Agreement as of the day and . year set forth above.

Signature Page to Consulting Agreement

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WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH

UNIFORM CONSULTING AGREEMENT PROVISIONS

STANDARD CONSULTING AGREEMENT PROVISIONS

Page 1 (Revised December 7, 2006)

STANDARD CONSULTING AGREEMENT PROVISIONS

Page 2 (Revised December 7, 2006)

STANDARD CONSULTING AGREEMENT PROVISIONS

Page 3 (Revised December 7, 2006)

ANNEX 1

Existing Endeavors

STANDARD CONSULTING AGREEMENT PROVISIONS

Page 4 (Revised December 7, 2006)

CONSULTING AGREEMENT-FIRST AMENDMENT

This First Amendment to the CONSULTING AGREEMENT (the “First Amendment”), made this 3rd day of December, 2012 is entered into by Syros Pharmaceuticals, Inc. (f/k/a LS22, Inc.), a Delaware corporation with its principal place of business at One Memorial Drive, 7th Floor, Cambridge, MA 02142 (the “Company”), and Richard A. Young, Ph.D. (the “Consultant”).

WHEREAS, Company and Consultant entered into a Consulting Agreement dated August 8, 2012 (the “Agreement”); and

WHEREAS, Company and Consultant desire to amend the Term of the Agreement under Section 2 and the Compensation under Section 3.

NOW THEREFORE, in consideration of the mutual covenants, conditions and agreements set forth herein, and for such other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereto agree as follows:

1. Defined Terms. Unless otherwise defined herein, the meaning of the terms used herein shall have the same meanings set forth in the Agreement.

2A. Term. Section 2 of the Agreement is deleted and replaced in its entirety with the following:

“2. Term. This Agreement shall commence July 3, 2012 and shall continue until July 3, 2016 (such period, as it may be extended, being referred to as the “Consultation Period”), unless sooner terminated in accordance with the provisions of Section 4.”

2B. Fees. Section 3.2 of the Agreement is deleted and replaced in its entirety with the following:

“3.2 Fees. The Company shall pay to the Consultant consulting fees of $75,000 per year, payable in equal quarterly installments. Payment for any partial quarter shall be prorated.

Transaction Bonus. If, within eighteen (18) months from the date hereof, the Company signs an agreement with a Partner (as defined below) encompassing a Qualifying Transaction (as defined below), the Company shall pay to the Consultant a cash bonus of $125,000 within fifteen (15) days of the signing of such agreement. For purposes of this Agreement, “Partner” means any third party for-profit entity. For purposes of this Agreement, “Qualifying Transaction” means a transaction pursuant to which the consideration received by the Company will, in the reasonable judgment of the Board of Directors of the Company, exceed $50 million within two (2) years from the date of the agreement with the Partner.”

3. Full Force and Effect. Except as expressly provided  in this First Amendment,  all other terms, conditions and provisions of the Agreement  shall  continue  in full force and effect as provided therein.

4. Entire Agreement. This First Amendment together with the Agreement constitute the full and complete agreement and understanding between Company and Consultant concerning the subject matter hereof.

IN WITNESS WHEREOF, Company and Consultant have caused this First Amendment to be executed by their duly authorized officer as ofthe Effective Date.

CONSULTING AGREEMENT- SECOND AMENDMENT

This Second Amendment to the CONSULTING AGREEMENT (the “Second Amendment”), dated as of September 29, 2016 (the “Agreement Date”) and effective as of July 3, 2016, is entered into by Syros Pharmaceuticals, Inc. (f/k/a LS22, Inc.), a Delaware corporation with its principal place of business at 620 Memorial Drive, Suite 300, Cambridge, MA 02139 (the “Company”), and Richard A. Young, Ph.D. (the “Consultant”).

WHEREAS, the Company and the Consultant entered into a Consulting Agreement dated August 8, 2012 (the “Original Agreement”);

WHEREAS, the parties entered into that certain First Amendment dated December 3, 2012 (the “First Amendment”; and the Original Agreement, as amended by the First Amendment, the “Agreement”), to amend the term of the Original Agreement and the compensation to the Consultant set forth therein; and

WHEREAS, the Company and the Consultant desire to further amend the term of the Agreement under Section 2 and the compensation set forth under Section 3 as described herein.

NOW THEREFORE, in consideration of the mutual covenants, conditions and agreements set forth herein, and for such other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereto agree as follows:

“3.1 Equity Compensation. In consideration for the performance of the services hereunder, the Consultant has been awarded (a) a grant of 1,600,000 shares of restricted common stock, $0.001 par value per share, of the Company (“Common Stock”), having a purchase price of $0.001, pursuant to that certain Restricted Stock Agreement dated as of August 8, 2012 and (b) an option to purchase 75,000 shares of Common Stock, with an exercise price equal to the fair market value of such options on the date of grant, vesting upon certain performance-based milestones approved by the Board of Directors of the Company and having such other terms and conditions as shall be set forth in an option grant agreement between the Consultant and the Company.”

“3.2 Fees. The Company shall pay to the Consultant consulting fees of $125,000 per year, payable in equal quarterly installments. Payment for any partial quarter shall be prorated.”

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IN WITNESS WHEREOF, the Company and the Consultant have caused this Second Amendment to be executed by their duly authorized officer as of the Agreement Date.

AMENDMENT NO.3

TO CONSULTING AGREEMENT

This Amendment No. 3 to Consulting Agreement (this “Amendment”) is made effective July 3, 2019 (the “Amendment Effective Date”) by and between Syros Pharmaceuticals, Inc., having offices located at 620 Memorial Drive, Suite 300, Cambridge, Massachusetts 02139 (“Syros”), and Richard A. Young, Ph.D. (“Consultant”). Syros and Consultant may be referred to herein individually as a “Party” or together as the “Parties”.

WHEREAS, the Parties entered a Consulting Agreement dated August 8, 2012, as amended effective December 3, 2012 and July 3, 2016 (as so amended, the “Agreement”);

WHEREAS, the Parties wish to amend the Agreement as described more fully below; and WHEREAS, pursuant to Section 13 of the Agreement, the Agreement may be amended by a written instrument executed by the Parties.

NOW THEREFORE, for good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the Parties hereby agree as follows:

1.Amendments to Agreement. The Parties agree to amend the Agreement as follows :

1.1Term. The reference to “July 3, 2019” in Section 2 of the Agreement shall be replaced with “July 3, 2022”.

1.2Fees. The reference to “$125,000 per year” in Section 3.2 of the Agreement shall be replaced with “$115,000 per year”.

IN WITNESS HEREOF, the Parties hereto have executed this Amendment as of the date set forth above.