Cyclerion Therapeutics, Inc. 10-K

Item 9A. Controls and Procedures. Disclosure Controls and Procedures We maintain “disclosure controls and procedures,” as such term is defined in Rules 13a-15(e) and 15d-15(e) under the Exchange Act, that are designed to ensure that information required to be disclosed by us in reports that we file or submit under the Exchange Act is recorded, processed, summarized and reported within the time periods specified in SEC rules and forms, and that such information is accumulated and communicated to our management, including our principal executive and our principal financial officers, as appropriate, to allow timely decisions regarding required disclosure. With respect to the year ended December 31, 2021, under the supervision and with the participation of our management, we conducted an evaluation of the effectiveness of the design and operations of our disclosure controls and procedures. Based upon this evaluation, our Chief Executive Officer and Chief Financial Officer have concluded that our disclosure controls and procedures were effective as of December 31, 2021 to provide reasonable assurance that the information required to be disclosed by us in this Annual Report was (a) reported within the time periods specified by SEC rules and regulations and (b) communicated to our management, including our Chief Executive Officer and Chief Financial Officer, to allow timely decisions regarding any required disclosure. Management's Report on Internal Control Over Financial Reporting Our management is responsible for establishing and maintaining adequate internal control over financial reporting (as defined in Rules 13a-15(f) and 15d-15(f) under the Exchange Act) to provide reasonable assurance regarding the reliability of our financial reporting and the preparation of consolidated financial statements for external purposes in accordance with U.S. generally accepted accounting principles (“GAAP”). Internal control over financial reporting is a process designed by, or under the supervision of, our Chief Executive Officer and Chief Financial Officer, 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 generally accepted accounting principles and includes those policies and procedures that: • Pertain to the maintenance of records that accurately and fairly reflect in reasonable detail the transactions and dispositions of the assets of our company; • Provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that our receipts and expenditures are being made only in accordance with authorizations of our management and directors; and • Provide reasonable assurances regarding prevention or timely detection of unauthorized acquisition, use or disposition of our assets that could have a material adverse effect on our financial statements. Management assessed our internal control over financial reporting as of December 31, 2021, the end of our fiscal year. Management based its assessment on criteria established in Internal Control—Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission (2013 framework). Management’s assessment included evaluation of elements such as the design and operating effectiveness of key financial reporting controls, process documentation, accounting policies, and our overall control environment. Based on this assessment, management has concluded that our internal controls over financial reporting were effective as of December 31, 2021 and provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external reporting purposes in accordance with GAAP. We reviewed the results of management’s assessment with the Audit Committee of our Board of Directors. 58 Internal control over financial reporting has inherent limitations. Internal control over financial reporting is a process that involves human diligence and compliance and is subject to lapses in judgment and breakdowns resulting from human failures. Internal control over financial reporting also can be circumvented by collusion or improper management override. Because of such limitations, there is a risk that material misstatements will not be prevented or detected on a timely basis by internal control over financial reporting. However, these inherent limitations are known features of the financial reporting process. Therefore, it is possible to design into the process safeguards to reduce, though not eliminate, this risk. Attestation Report of the Registered Public Accounting Firm This Annual Report does not include an attestation report of our independent registered public accounting firm regarding internal control over financial reporting. Our report was not subject to attestation by our independent registered public accounting firm pursuant to the rules of the Securities and Exchange Commission for “emerging growth companies” that permit us to provide only management’s report in this report. Changes in Internal Control over Financial Reporting There were no changes in our internal control over financial reporting (as defined in Rules 13a-15(f) and 15d-15(f) under the Exchange Act) that occurred during the fiscal year ended December 31, 2021 which have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting. Inherent Limitations on Effectiveness of Internal Controls In designing and evaluating the disclosure controls and procedures, management does not expect that our internal control over financial reporting will prevent or detect all errors and all fraud. A control system, no matter how well conceived and operated, can provide only reasonable, not absolute, assurance that the objectives of the control systems are met. Further, the design of a control system must reflect the fact that there are resource constraints, and the benefits of controls must be considered relative to their costs. The design of any disclosure controls and procedures also is based in part upon certain assumptions about the likelihood of future events, and there can be no assurance that any design will succeed in achieving its stated goals under all potential future conditions. Our management, including our Chief Executive Officer and Chief Financial Officer, believes that our disclosure controls and procedures and internal control over financial reporting are designed to provide reasonable assurance of achieving their objectives and are effective at the reasonable assurance level. However, our management does not expect that our disclosure controls and procedures or our internal control over financial reporting will prevent all errors and all fraud. Item 9B. Other Information. Not applicable. Item 9C. Disclosure Regarding Foreign Jurisdictions That Prevent Inspections. Not applicable. 59 PART III We will file a definitive Proxy Statement for our 2021 Annual Meeting of Stockholders, or the Proxy Statement, with the SEC, pursuant to Regulation 14A, not later than 120 days after the end of our fiscal year. Accordingly, certain information required by Part III has been omitted under General Instruction G(3) to Form 10-K. Only those sections of the 2021 Proxy Statement that specifically address the items set forth herein are incorporated by reference. Item 10. Directors, Executive Of ficers and Corporate Governance. The information required by this Item 10 will be included in our Proxy Statement under the captions “Information Regarding the Board of Directors and Corporate Governance,” “Election of Directors,” “Executive Officers” and “Section 16(a) Beneficial Ownership Reporting Compliance” and is incorporated herein by reference. Item 11. Executiv e Compensation. The information required by this Item 11 will be included in our Proxy Statement under the captions “Executive Compensation” and “Director Compensation” and is incorporated herein by reference. Item 12. Security Ownership of Certain Beneficial Ow ners and Management and Related Stockholder Matters. The information required by this Item 12 will be included in our Proxy Statement under the captions “Security Ownership of Certain Beneficial Owners and Management” and “Securities Authorized for Issuance under Equity Compensation Plans” and is incorporated herein by reference. Item 13. Certain Relationships and Related Transactions, and Director Independence. The information required by this Item 13 will be included in our Proxy Statement under the captions “Transactions with Related Persons” and “Independence of the Board of Directors” and is incorporated herein by reference. Item 14. Principal Accou nting Fees and Services. The information required by this Item 14 will be included in our Proxy Statement under the caption “Ratification of Selection of Independent Registered Public Accounting Firm” and is incorporated herein by reference. 60 PART IV Item 15. Exhibits, Financ ial Statement Schedules. (a)(1) Financial Statements See the Index to Consolidated Financial Statements in the Financial Statements Section beginning on page F-1 of this Annual Report on Form 10-K. (a)(2) Financial Statement Schedules All financial statement schedules have been omitted as they are not required, not applicable, or the required information is included in the financial statements or notes to the financial statements. (a)(3) Exhibits EXHIBIT INDEX Exhibit No. Description 2.1 Separation Agreement, dated March 30, 2019, by and between Ironwood Pharmaceuticals, Inc. and Cyclerion Therapeutics, Inc. (incorporated by reference to Exhibit 2.1 to Current Report on Form 8-K filed on April 2, 2019 (File No. 001-38787)) 3.1 Restated Articles of Organization of Cyclerion Therapeutics, Inc. (incorporated by reference to Exhibit 4.1 to Registration Statement on Form S-8 filed on March 29, 2019) (File No. 333-230615)) 3.2 Amended and Restated Bylaws of Cyclerion Therapeutics, Inc. (incorporated by reference to Exhibit 4.2 to Registration Statement on Form S-8 filed on March 29, 2019) (File No. 333-230615)) 4.1 Description of Securities Registered pursuant to Section 12 of the Securities Exchange Act of 1934, as amended 10.1 Tax Matters Agreement, dated March 30, 2019, by and between Ironwood Pharmaceuticals, Inc. and Cyclerion Therapeutics, Inc. (incorporated by reference to Exhibit 10.3 to Current Report on Form 8-K filed on April 2, 2019 (File No. 001-38787)) 10.2 Employee Matters Agreement, dated March 30, 2019, by and between Ironwood Pharmaceuticals, Inc. and Cyclerion Therapeutics, Inc. (incorporated by reference to Exhibit 10.4 to Current Report on Form 8-K filed on April 2, 2019 (File No. 001-38787)) 10.3 Development Agreement, dated April 1, 2019, by and between Ironwood Pharmaceuticals, Inc. and Cyclerion Therapeutics, Inc. (incorporated by reference to Exhibit 10.5 to Current Report on Form 8-K filed on April 2, 2019 (File No. 001-38787)) 10.4 Intellectual Property License Agreement, dated April 1, 2019, by and between Ironwood Pharmaceuticals, Inc. and Cyclerion Therapeutics, Inc. (incorporated by reference to Exhibit 10.6 to Current Report on Form 8-K filed on April 2, 2019 (File No. 001-38787)) 10.5 + Form of Indemnification Agreement between Cyclerion Therapeutics, Inc. and individual directors and officers (incorporated by reference to Exhibit 10.7 to Form 10 filed on January 28, 2019 (File No. 001-38787)) 10.6 + Offer Letter, effective April 1, 2019, by and between Cyclerion Therapeutics, Inc. and Peter M. Hecht, Ph.D. (incorporated by reference to Exhibit 10.11 to Current Report on Form 8-K filed on April 2, 2019 (File No. 001-38787)) 10.7 + Cyclerion Therapeutics, Inc. 2019 Employee Stock Purchase Plan (incorporated by reference to Exhibit 4.3 to Registration Statement on Form S-8 filed on March 29, 2019 (File No. 333-230615)) 61 10.8 + Cyclerion Therapeutics, Inc. 2019 Equity Incentive Plan and forms of agreements thereunder (incorporated by reference to Exhibit 4.4 to Registration Statement on Form S-8 filed on March 29, 2019 (File No. 333-230615)) 10.9 + Cyclerion Therapeutics, Inc. Amended and Restated 2010 Employee, Director and Consultant Equity Incentive Plan and forms of agreement thereunder (incorporated by reference to Exhibit 4.5 to Registration Statement on Form S-8 filed on March 29, 2019 (File No. 333-230615)) 10.10 + Cyclerion Therapeutics, Inc. Executive Severance Plan (incorporated by reference to Exhibit 10.1 to Current Report on Form 8-K filed on September 25, 2019 (File No. 001-38787)) 10.11 + Non-Employee Director Compensation Plan (effective June 1, 2019) (incorporated by reference to Exhibit 10.7 on Form 10-Q filed on August 12, 2019 (File No. 001-38737)) 10.12 Open Market Sale Agreement SM , dated September 3, 2020, by and between Cyclerion Therapeutics, Inc. and Jefferies LLC (incorporated by reference to Exhibit 10.1 of the Company’s Form 8-K filed on September 3, 2020). 10.13 * License Agreement, dated as of June 3, 2021, by and between Cyclerion Therapeutics, Inc. and Akebia Therapeutics, Inc (incorporated by reference to Exhibit 10.2 of the Company's Form 10-Q filed on July 30, 2021). 10.14 Common Stock Purchase Agreement, dated as of June 3, 2021, by and between Cyclerion Therapeutics, Inc. and the Investors named therein (incorporated by reference to Exhibit 10.1 to Registration Statement on Form S-3 filed on June 16, 2021 (File No. 333-257145)). 21.1 List of Subsidiaries 23.1 Consent of Ernst & Young LLP, Independent Registered Public Accounting Firm 31.1 Certificate of Chief Executive Officer (Principal Executive Officer) pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 31.2 Certificate of Chief Financial Officer (Principal Financial Officer) pursuant to Section 302 of the Sarbanes-Oxley Act of 2002 32.1 Certificate of Chief Executive Officer (Principal Executive Officer) pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002 32.2 Certificate of Chief Financial Officer (Principal Executive Officer) pursuant to 18 U.S.C. Section 1350, as adopted pursuant to Section 906 of the Sarbanes-Oxley Act of 2002 101.INS Inline XBRL Instance Document 101.SCH Inline XBRL Taxonomy Extension Schema Document 101.CAL Inline XBRL Taxonomy Extension Calculation Linkbase Document 101.DEF Inline XBRL Taxonomy Extension Definition Linkbase Document 101.LAB Inline XBRL Taxonomy Extension Label Linkbase Document 101.PRE Inline XBRL Taxonomy Extension Presentation Linkbase Document 104 Cover Page Interactive Data File + Indicates a management contract or compensatory plan. * Certain portions of this exhibit (indicated by asterisks) have been omitted because they are not material and are the type that the Registrant treats as private or confidential. Item 16. Form 10-K Summary. Not applicable. 62 SIGNAT URES Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrants have duly caused this report to be signed on their behalf by the undersigned, thereunto duly authorized, on February 24, 2022. CYCLERION THERAPEUTICS, INC. By: /s/ Peter Hecht Peter M. Hecht Chief Executive Officer Pursuant to the requirements of the Securities Exchange Act of 1934, this report has been signed below by the following persons on behalf of the registrant and in the capacities indicated on February 24, 2022. Signature Title /s/ Peter Hecht Peter M. Hecht Chief Executive Officer (Principal Executive Officer) /s/ Anjeza Gjino Anjeza Gjino Chief Financial Officer (Principal Financial Officer and Principal Accounting Officer) /s/ Errol De Souza Errol De Souza Director /s/ George Conrades George Conrades Director /s/ Marsha Fanucci Marsha Fanucci Director /s/ Ole Isacson Ole Isacson Director /s/ Stephanie Lovell Stephanie Lovell Director /s/ Terrance McGuire Terrance McGuire Director /s/ Michael Mendelsohn Michael Mendelsohn Director 63 Index to Consolidated Financial Statements of Cyclerion Therapeutics, Inc. Page Report of Independent Registered Public Accounting Firm - PCAOB ID: 42 F- 2 Consolidated Balance Sheets as of December 31, 2021 and 2020 F - 3 Consolidated Statements of Operations and Comprehensive Loss for the Years Ended December 31, 2021 and 2020 F- 4 Consolidated Statement of Stockholders’ Equity for the Years Ended December 31, 2021 and 2020 F- 5 Consolidated Statements of Cash Flows for the Years Ended December 31, 2021 and 2020 F- 6 Notes to the Consolidated Financial Statements F- 7 F- 1 Report of Independent Registered Public Accounting Firm To the Shareholders and the Board of Directors of Cyclerion Therapeutics, Inc Opinion on the Financial Statements We have audited the accompanying consolidated balance sheets of Cyclerion Therapeutics, Inc (the Company) as of December 31, 2021 and 2020, the related consolidated statements of operations and comprehensive loss , shareholders' equity and cash flows for each of the two years in the period ended December 31, 2021, and the related notes (collectively referred to as the “consolidated financial statements”). In our opinion, the consolidated financial statements present fairly, in all material respects, the financial position of the Company at December 31, 2021 and 2020, and the results of its operations and its cash flows for each of the two years in the period ended December 31, 2021, in conformity with U.S. generally accepted accounting principles. Basis for Opinion These financial statements are the responsibility of the Company's management. Our responsibility is to express an opinion on the Company’s financial statements based on our audits. We are a public accounting firm registered with the Public Company Accounting Oversight Board (United States) (PCAOB) and are required to be independent with respect to the Company in accordance with the U.S. federal securities laws and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB. We conducted our audits in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether the financial statements are free of material misstatement, whether due to error or fraud. The Company is not required to have, nor were we engaged to perform, an audit of its internal control over financial reporting. As part of our audits we are required to obtain an understanding of internal control over financial reporting but not for the purpose of expressing an opinion on the effectiveness of the Company's internal control over financial reporting. Accordingly, we express no such opinion. Our audits included performing procedures to assess the risks of material misstatement of the financial statements, whether due to error or fraud, and performing procedures that respond to those risks. Such procedures included examining, on a test basis, evidence regarding the amounts and disclosures in the financial statements. Our audits also included evaluating the accounting principles used and significant estimates made by management, as well as evaluating the overall presentation of the financial statements. We believe that our audits provide a reasonable basis for our opinion. /s/ Ernst & Young LLP We have served as the Company’s auditor since 2018. Boston, Massachusetts February 24, 2022 F- 2 Cyclerion Therapeutics, Inc. Consolidated Balance Sheets (In thousands except share and per share data) December 31, 2021 December 31, 2020 ASSETS Current assets: Cash and cash equivalents $ 53,961 $ 54,395 Accounts receivable 100 — Related party accounts receivable — 127 Prepaid expenses 928 816 Other current assets 468 3,163 Total current assets 55,457 58,501 Restricted cash, net of current portion — 3,837 Property and equipment, net 65 6,865 Operating lease right-of-use asset 1,402 43,402 Other assets 2,407 2,773 Total assets $ 59,331 $ 115,378 LIABILITIES AND STOCKHOLDERS’ EQUITY Current liabilities: Accounts payable $ 1,828 $ 1,149 Related party accounts payable — 286 Accrued research and development costs 6,353 1,421 Accrued expenses and other current liabilities 2,904 7,294 Short-term note payable — 3,509 Current portion of operating lease liabilities — 3,293 Total current liabilities 11,085 16,952 Operating lease liabilities, net of current portion — 38,933 Commitments and contingencies (Note 7) — — Stockholders' equity Common stock, no par value, 400,000,000 shares authorized and 43,410,185 issued and outstanding at December 31, 2021 and 400,000,000 shares authorized and 34,047,300 issued and outstanding at December 31, 2020 — — Accumulated deficit ( 215,076 ) ( 163,429 ) Paid-in capital 263,345 222,949 Accumulated other comprehensive loss ( 23 ) ( 27 ) Total stockholders' equity 48,246 59,493 Total liabilities and stockholders' equity $ 59,331 $ 115,378 The accompanying notes are an integral part of these consolidated financial statements. F- 3 Cyclerion Therapeutics, Inc. Consolidated Statements of Operations and Comprehensive Loss (In thousands except per share data) Year Ended December 31, 2021 2020 Revenues: Revenue from license agreement $ 3,000 $ — Revenue from development agreement 320 — Revenue from grants 622 — Revenue from related party — 2,296 Total revenues 3,942 2,296 Cost and expenses: Research and development 37,636 56,414 General and administrative 20,620 28,816 Loss/ (Gain) on lease modification and termination 881 ( 1,669 ) Total cost and expenses 59,137 83,561 Loss from operations ( 55,195 ) ( 81,265 ) Sublease termination income, net — 2,875 Gain on extinguishment of debt 3,564 — Interest and other (expenses) income, net ( 16 ) 588 Net loss $ ( 51,647 ) $ ( 77,802 ) Net loss per share: Basic and diluted net loss per share $ ( 1.32 ) $ ( 2.56 ) Weighted average shares used in calculating: Basic and diluted net loss per share 39,144 30,403 Other comprehensive loss: Net loss $ ( 51,647 ) $ ( 77,802 ) Other comprehensive loss: Foreign currency translation adjustment (loss) gain 4 ( 7 ) Comprehensive loss $ ( 51,643 ) $ ( 77,809 ) The accompanying notes are an integral part of these consolidated financial statements. F- 4 Cyclerion Therapeutics, Inc. Consolidated Statement s of Stockholders’ Equity (In thousands except share data) Common Stock Paid-in Accumulated Accumulated other comprehensive Total Stockholders’ Shares Amount capital deficit loss equity Balance at December 31, 2019 27,598,133 $ — $ 183,376 $ ( 85,627 ) $ ( 20 ) $ 97,729 Net loss — — — ( 77,802 ) — ( 77,802 ) Issuance of common stock - 2020 private placement 6,062,500 24,250 24,250 Issuance of common stock upon exercise of stock options, RSUs and employee stock purchase plan 386,667 — 331 — — 331 Share-based compensation expense related to issuance of stock options and RSUs to employees and employee stock purchase plan — — 14,992 — — 14,992 Foreign currency translation adjustment — — — — ( 7 ) ( 7 ) Balance at December 31, 2020 34,047,300 $ — $ 222,949 $ ( 163,429 ) $ ( 27 ) $ 59,493 Net loss — $ — $ — $ ( 51,647 ) $ — ( 51,647 ) Issuance of common stock - 2021 equity private placement 5,735,988 — 18,028 — — 18,028 Issuance of common stock - ATM 3,353,059 — 12,475 — — 12,475 Issuance of common stock upon exercise of stock options, RSUs and employee stock purchase plan 273,838 — 282 — — 282 Share-based compensation expense related to issuance of stock options and RSUs to employees and employee stock purchase plan — — 7,915 — — 7,915 Share‑based compensation expense related to issuance of stock options and RSUs to non-employees — — 1,696 — — 1,696 Foreign currency translation adjustment — — — — 4 4 Balance at December 31, 2021 43,410,185 $ — $ 263,345 $ ( 215,076 ) $ ( 23 ) $ 48,246 The accompanying notes are an integral part of these consolidated financial statements. F- 5 Cyclerion Therapeutics, Inc. Consolidated Statements of Cash Flows (In thousands) Year Ended December 31, 2021 2020 CASH FLOWS FROM OPERATING ACTIVITIES: Net loss $ ( 51,647 ) $ ( 77,802 ) Adjustments to reconcile net loss to net cash (used in) operating activities: Depreciation and amortization 472 2,297 Net loss on disposal of property and equipment 6,322 159 (Gain) / loss on lease modification and termination 881 ( 1,669 ) Sublease termination income, net — ( 2,875 ) Gain on extinguishment of debt ( 3,564 ) — Share-based compensation expense 9,611 14,992 Changes in operating assets and liabilities: Accounts receivable ( 100 ) — Related party accounts receivable 127 1,346 Prepaid expenses ( 112 ) 1,150 Other current assets 1,244 ( 55 ) Operating lease assets ( 59 ) ( 2,598 ) Other assets 366 ( 888 ) Accounts payable 679 ( 1,301 ) Related party accounts payable ( 286 ) 205 Accrued research and development costs 4,932 ( 776 ) Accrued expenses and other current liabilities ( 4,335 ) ( 1,983 ) Operating lease liabilities ( 1,048 ) ( 2,692 ) Net cash (used in) operating activities ( 36,517 ) ( 72,490 ) CASH FLOWS FROM INVESTING ACTIVITIES: Purchases of property and equipment ( 7 ) ( 1,524 ) Proceeds from sale of property and equipment 1,464 1,542 Net cash provided by investing activities 1,457 18 CASH FLOWS FROM FINANCING ACTIVITIES: Proceeds from equity private placement and ATM 30,503 24,250 Proceeds from exercises of stock options and ESPP 282 331 Proceeds from short-term note payable — 3,509 Net cash provided by financing activities 30,785 28,090 Effect of exchange rate changes on cash, cash equivalents and restricted cash 4 ( 7 ) Net decrease in cash, cash equivalents and restricted cash ( 4,271 ) ( 44,389 ) Cash, cash equivalents and restricted cash, beginning of period 58,232 102,621 Cash, cash equivalents and restricted cash, end of period $ 53,961 $ 58,232 Supplemental cash flow disclosure: Cash paid for initial direct costs of lease modification $ — $ 6,507 Reconciliation of cash, cash equivalents and restricted cash to the consolidated balance sheets Cash and cash equivalents $ 53,961 $ 54,395 Restricted cash — 3,837 Total cash, cash equivalents and restricted cash $ 53,961 $ 58,232 The accompanying notes are an integral part of these consolidated financial statements. F- 6 Cyclerion Therapeutics, Inc. Notes to the Consolidated Financial Statements 1. Nature of Business Nature of Operations Cyclerion Therapeutics, Inc. (“Cyclerion”, the “Company” or “we”) is a clinical-stage biopharmaceutical company on a mission to develop treatments that restore cognitive function. Our lead asset, CY6463, is a pioneering, central nervous system (CNS) penetrant, soluble guanylate cyclase (sGC) stimulator that is currently in clinical development for Alzheimer's disease with vascular pathology (ADv), cognitive impairment associated with schizophrenia (CIAS), and Mitochondrial Encephalomyopathy, Lactic Acidosis and Stroke-like episodes (MELAS). sGC stimulators are small molecules that act synergistically with nitric oxide (NO) as positive allosteric modulators of sGC to boost production of cyclic guanosine monophosphate (cGMP). cGMP is a key second messenger that, when produced by sGC, regulates diverse and critical biological functions in the CNS including neuronal function, neuroinflammation, cellular bioenergetics, and vascular function. Cyclerion GmbH, a wholly owned subsidiary, was incorporated in Zug, Switzerland on May 3, 2019. Cyclerion GmbH is an operational entity with one employee who is the Company’s Chief Scientific Officer. The functional currency is the Swiss franc. Cyclerion Securities Corporation, a wholly owned subsidiary, was incorporated in Massachusetts on November 15, 2019 and was granted securities corporation status in Massachusetts for the 2019 tax year. Cyclerion Securities Corporation has no employees. Company Overview The Company’s mission is to develop treatments that restore cognitive function. Its priorities are advancing its ongoing CY6463 clinical programs and next generation compound, CY3018. CNS assets. CY6463 is an orally administered CNS-penetrant sGC stimulator that is being developed as a symptomatic and potentially disease-modifying therapy for serious CNS diseases. NO-sGC-cGMP is a fundamental CNS signaling network, but it has not yet been leveraged for its full therapeutic potential. CY6463 enhances the brain’s natural ability to produce cGMP, an important second messenger in the CNS, by stimulating sGC, a key node in the NO-sGC-cGMP pathway. This pathway is critical to basic CNS functions and deficient NO-sGC-cGMP signaling is believed to play an important role in the pathogenesis of neurodegenerative diseases. Agents that stimulate sGC to produce cGMP may compensate for deficient NO signaling. On January 13, 2020, we announced positive results from our Phase 1 first-in-human study that provided the foundation for continued development of CY6463. The Phase 1 healthy participant study results indicate that CY6463 was well tolerated. Pharmacokinetic (PK) data, obtained from both blood and cerebral spinal fluid (CSF), support once-daily dosing, with or without food, and demonstrated CY6463 penetration of the blood-brain-barrier with CSF concentrations expected to be pharmacologically active. On October 14, 2020, we announced positive topline results from our CY6463 Phase 1 translational pharmacology study in healthy elderly participants. Treatment with CY6463 for 15 days in this 24-subject study confirmed and extended results seen in the earlier first-in-human Phase 1 study: once daily oral treatment demonstrated blood-brain-barrier penetration with expected CNS exposure and target engagement. Results also showed significant improvements in neurophysiological and objective performance measures as well as in inflammatory biomarkers associated with aging and neurodegenerative diseases. CY6463 was shown to be safe and generally well tolerated. Significant effects on cerebral blood flow and markers of bioenergetics were not observed in this study of healthy elderly participants. We believe that these results, together with nonclinical data, support continued development of CY6463 as a potential new medicine for serious CNS diseases. We have initiated exploratory clinical trials with CY6463 ADv, CIAS, and MELAS. The ADv study will be supported in part by a grant from the Alzheimer’s Association’s Part the Cloud-Gates Partnership Grant Program, which provides Cyclerion with $2 million of funding over two years. F- 7 Our next generation CNS asset, CY3018, is a differentiated CNS-penetrant sGC stimulator with greater CSF-to-plasma exposure relative to CY6463. CY3018 is intended to expand the potential of sGC stimulation for the treatment of disorders of the CNS. Non-CNS assets. We have other assets that are outside of our current strategic focus. These non-core assets are not being internally developed at this time. Praliciguat is an orally administered, once-daily systemic sGC stimulator. On June 3, 2021, we entered into a License Agreement with Akebia relating to the exclusive worldwide license to Akebia of our rights to the development, manufacture, medical affairs and commercialization of pharmaceutical products containing the pharmaceutical compound praliciguat and other related products and forms thereof enumerated in such agreement. Olinciguat is an orally administered, once-daily, vascular sGC stimulator that was evaluated in a Phase 2 study of participants with sickle cell disease. We released topline results from this study in October 2020. Olinciguat is available for licensing to a third party partner. The Separation On April 1, 2019, Ironwood completed the separation of its sGC business, and certain other assets and liabilities, into a separate, independent publicly traded company by way of a pro-rata distribution of all of the outstanding shares of common stock of Cyclerion Therapeutics, Inc. through a dividend distribution of one share of the Company’s common stock, with no par value per share, for every 10 shares of Ironwood common stock held by Ironwood stockholders as of the close of business on March 19, 2019, the record date for the Distribution (the entire transaction being the “Separation”). As a result of the Separation, the Company became an independent public company and commenced trading under the symbol “CYCN” on the Nasdaq Global Select Market on April 2, 2019. 2020 Equity Private Placement On July 29, 2020, the Company entered into a Common Stock Purchase Agreement (the “2020 Equity Private Placement”) for the private placement of 6,062,500 shares of the Company’s common stock, for total gross proceeds of approximately $ 24.3 million. The closing of the 2020 Equity Private Placement occurred on July 29, 2020. The Company did not utilize the services of a placement agent or broker and accordingly incurred no material related transaction fees, or commissions. 2021 Equity Private Placement On June 3, 2021, the Company entered into a Common Stock Purchase Agreement (the “June 2021 Equity Private Placement”) for the private placement of 5,735,988 shares of the Company’s common stock, for total gross proceeds of approximately $ 18 million. The closing of the June 2021 Equity Private Placement occurred on June 7, 2021. The Company did not utilize the services of a placement agent or broker and accordingly incurred no material related transaction fees or commissions. At-the-Market Offering On July 24, 2020, the Company filed a Registration Statement on Form S-3 with the Securities and Exchange Commission (the “SEC”) in relation to the registration of common stock, preferred stock, debt securities, warrants and units of any combination thereof for an aggregate initial offering price not to exceed $ 150.0 million. The Shelf was declared effective as of July 31, 2020. On September 3, 2020, the Company entered into a Sales Agreement (the “Sales Agreement”) with Jefferies LLC (“Jefferies”) with respect to an at-the-market offering (the “ATM Offering”) under the Shelf. Under the ATM Offering, the Company may offer and sell, from time to time at its sole discretion, shares of its common stock, having an aggregate offering price of up to $ 50.0 million through Jefferies as its sales agent. The Company will pay to Jefferies cash commissions of 3.0 percent of the gross proceeds of sales of common stock under the Sales Agreement. During the year ended December 31, 2021 , the Company sold 3,353,059 shares of its common stock for net proceeds of $ 12.5 million under the ATM Offering, after deducting commissions paid to Jefferies of approximately $ 0.4 million. F- 8 Basis of Presentation The consolidated financial statements and the related disclosures have been prepared in accordance with U.S. generally accepted accounting principles . In the opinion of management, the consolidated financial statements reflect all normal recurring adjustments considered necessary for a fair presentation of the Company’s financial position and the results of its operations for the fiscal years presented. The consolidated financial statements include the financial statements of the Company and its wholly owned subsidiaries, Cyclerion GmbH, and Cyclerion Securities Corporation. All significant intercompany accounts and transactions have been eliminated in the preparation of the accompanying consolidated financial statements. Going Concern At each reporting period, the Company evaluates whether there are conditions or events that raise substantial doubt about the Company’s ability to continue as a going concern within one year after the date that the financial statements are issued. The Company’s evaluation entails analyzing prospective operating budgets and forecasts for expectations of the Company’s cash needs and comparing those needs to the current cash and cash equivalent balances. The Company is required to make certain additional disclosures if it concludes substantial doubt exists and it is not alleviated by the Company’s plans or when its plans alleviate substantial doubt about the Company’s ability to continue as a going concern. The Company has experienced negative operating cash flows for all historical periods presented and the Company expects these losses to continue into the foreseeable future as the Company continues the development and clinical testing of its product candidates CY6463, CY3018 and its discovery research programs. Through December 31, 2021, the Company had raised an aggregate of $ 219.8 million (in net proceeds) from equity private placements and the ATM Offering. After considering the Company’s current research and development plans and the timing expectations related to the progress of its programs, and after considering its existing cash and cash equivalents of $ 54.0 million as of December 31, 2021 , the Company did not identify conditions or events that would raise substantial doubt about the Company’s ability to continue as a going concern within one year from the date these financial statements were issued. 2. Summary of Significant Accounting Policies Principles of Consolidation The accompanying consolidated financial statements include the accounts of Cyclerion Therapeutics, Inc. and its wholly owned subsidiaries, Cyclerion GmbH and Cyclerion Securities Corporation. All intercompany transactions and balances are eliminated in consolidation. Segment Information Operating segments are components of an enterprise for which separate financial information is available and is evaluated regularly by the Company's chief operating decision maker in deciding how to allocate resources and in assessing performance. The Company currently operates in one reportable business segment - human therapeutics. Use of Estimates The preparation of consolidated financial statements in accordance with U.S. GAAP requires the Company’s management to make estimates and judgments that may affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the consolidated financial statements, and the amounts of expenses during the reported periods. On an ongoing basis, the Company’s management evaluates its estimates, judgments and methodologies. Significant estimates and assumptions in the consolidated financial statements include those related to revenue, impairment of long-lived assets, valuation procedures for right-of-use F- 9 ("ROU") assets and operating lease liabilities, income taxes, including the valuation allowance for deferred tax assets, research and development expenses, contingencies, share-based compensation, and going concern. The Company bases its estimates on historical experience and on various other assumptions that are believed to be reasonable, the results of which form the basis for making judgments about the carrying values of assets and liabilities. Actual results may differ materially from these estimates under different assumptions or conditions. Changes in estimates are reflected in reported results in the period in which they become known. Cash and Cash Equivalents including Restricted Cash The Company considers all highly liquid investment instruments with a remaining maturity when purchased of three months or less to be cash equivalents. Investments qualifying as cash equivalents may consist of money market funds and overnight repurchase agreements. The carrying amount of cash equivalents approximates fair value. As of December 31, 2021, T he Company did not have any restricted cash balances. As of December 31, 2020, the Company was contingently liable under an unused letter of credit with a bank, related to the Company's facility lease, in the amount of approximately $ 3.8 million. The Company recorded the collateral used to secure the letter of credit as restricted cash. The full amount of restricted cash was recorded as a component of non-current assets at December 31, 2020 . Property and Equipment Property and equipment, including leasehold improvements, are recorded at cost, and are depreciated when placed into service using the straight-line method based on their estimated useful lives as follows: Asset Description Estimated Useful Life (In Years) Laboratory equipment 5 Computer and office equipment 3 Furniture and fixtures 7 Software 3 Included in property and equipment are certain costs of software obtained for internal use. Costs incurred during the preliminary project stage are expensed as incurred, while costs incurred during the application development stage are capitalized and amortized over the estimated useful life of the software. The Company also capitalizes costs related to specific upgrades and enhancements when it is probable the expenditures will result in additional functionality. Maintenance and training costs related to software obtained for internal use are expensed as incurred. Costs for capital assets not yet placed into service have been capitalized as construction in progress and are depreciated in accordance with the above guidelines once placed into service. Maintenance and repair costs are expensed as incurred. Leasehold improvements are amortized over the shorter of the estimated useful life of the asset or the lease term. The Company has no capital leases. Property and equipment that is no longer required for the business is considered disposed of when it ceases to be used. Disposals are either sold or retired and the net book value is removed from the consolidated balance sheet and a corresponding gain or loss on the sale or disposal is recognized as a component of operating expenses in the consolidated statements of operations and comprehensive loss. Fair Value of Investment Instruments Fair value is defined as the exchange price that would be received for an asset or paid to transfer a liability (an exit price) in the principal or most advantageous market for the asset or liability in an orderly transaction between market participants on the measurement date. Valuation techniques used to measure fair value must F- 10 maximize the use of observable inputs and minimize the use of unobservable inputs. Financial assets and liabilities carried at fair value are to be classified and disclosed in one of the following three levels of the fair value hierarchy, of which the first two are considered observable and the last is considered unobservable: • Level 1 — Quoted prices in active markets for identical assets or liabilities. • Level 2 — Observable inputs (other than Level 1 quoted prices), such as quoted prices in active markets for similar assets or liabilities, quoted prices in markets that are not active for identical or similar assets or liabilities, or other inputs that are observable or can be corroborated by observable market data. • Level 3 — Unobservable inputs that are supported by little or no market activity and that are significant to determining the fair value of the assets or liabilities, including pricing models, discounted cash flow methodologies and similar techniques. Foreign Currency Translation Adjustment The functional currency of the Company’s foreign subsidiary is its local currency, the Swiss franc. The assets and liabilities of the Company’s foreign subsidiary are translated into U.S. dollars at exchange rates in effect at the balance sheet date. Income and expense items are translated at the average exchange rates prevailing during the period. The cumulative translation effect for the Company’s foreign subsidiary is included as a foreign currency translation adjustment in the consolidated statements of stockholders’ equity and as a component of comprehensive loss in the consolidated statements of operations and comprehensive loss. The Company’s intercompany accounts are typically denominated in the functional currency of the foreign subsidiary. Gains and losses resulting from the re-measurement of intercompany balances are recorded in the consolidated statements of operations. Accounts Receivable The Company makes judgments as to its ability to collect outstanding receivables and provides an allowance for receivables when collection becomes doubtful. Provisions are made based upon a specific review of all significant outstanding invoices. The Company’s receivables primarily relate to amounts earned under a development agreement with Ironwood, licensing agreement, and supply agreement. The Company believes that credit risks associated with these agreements are not significant. To date, the Company has not had significant write-offs of bad debt and the Company did not have an allowance for doubtful accounts as of December 31, 2021 or 2020 . Impairment of Long-Lived Assets The Company regularly reviews the carrying amount of its long-lived assets to determine whether indicators of impairment may exist, which warrant adjustments to carrying values or estimated useful lives. If indications of impairment exist, projected future undiscounted cash flows associated with the asset are compared to the carrying amount to determine whether the asset’s value is recoverable. If the carrying value of the asset exceeds such projected undiscounted cash flows, the asset will be written down to its estimated fair value. There were no significant impairments of long-lived assets for the years ended December 31, 2021 or 2020 . Leases Effective January 1, 2019, the Company adopted Accounting Standards Codification (“ASC”) Topic 842, Leases (“ASC 842”) using the optional transition method. The adoption of ASC 842 represents a change in accounting principle that aims to increase transparency and comparability among organizations by requiring the recognition of right-of-use assets and lease liabilities on the balance sheet for both operating and finance leases. In addition, the standard requires enhanced disclosures that meet the objective of enabling financial statement users to assess the amount, timing, and uncertainty of cash flows arising from leases. The reported results for the years ended December 31, 2021 and 2020 reflect the application of ASC 842 guidance. F- 11 The recognition of right-of-use assets and lease liabilities related to the Company’s operating leases under ASC 842 has had a material impact on the Company’s consolidated financial statements. As part of the ASC 842 adoption, the Company has used certain practical expedients outlined in the guidance. These practical expedients include: • Account policy election to use the short-term lease exception by asset class; • Election of the practical expedient package during transition, which includes: • An entity need not reassess whether any expired or existing contracts are or contain leases. • An entity need not reassess the classification for any expired or existing leases. As a result, all leases that were classified as operating leases in accordance with ASC 840 are classified as operating leases under ASC 842, and all leases that were classified as capital leases in accordance with ASC 840 are classified as finance leases under ASC 842. • An entity need not reassess initial direct costs for any existing leases. The Company had a property lease for its headquarters location at 301 Binney Street, Cambridge, MA (the “Head Lease”). The Company determined if the arrangement was a lease at the inception of the contract. The asset component of the Company’s operating leases was recorded as operating lease right-of-use assets, and the liability component was recorded as current portion of operating lease liabilities and operating lease liabilities, net of current portion, in the Company’s consolidated balance sheets. ROU assets and operating lease liabilities are recognized based on the present value of lease payments over the lease term at the commencement date. The Company uses an incremental borrowing rate based on the information available at commencement date in determining the present value of lease payments if an implicit rate of return is not provided with the lease contract. Operating lease right-of-use assets are adjusted for incentives received. Lease cost was recognized on a straight-line basis over the lease term, and included amounts related to short-term leases. Variable lease costs that do not depend on an index or rate were recognized as incurred. ROU assets and operating lease liabilities were remeasured upon certain modifications to leases using the present value of remaining lease payments and estimated incremental borrowing rate upon lease modification. The difference between the remeasured ROU assets and the operating lease liabilities were recognized as a gain or loss in operating expenses. The Company reviewed any changes to its lease agreements for potential modifications and/or indicators of impairment of the respective ROU asset. On October 18, 2019, the Company entered into an agreement to sublease 15,700 rentable square feet of its Head Lease to a subtenant (the “Sublease Agreement”). Sublease income was recognized on straight-line basis over the term of the sublease agreement and was recorded net of the related rent expense from the Head Lease within interest and other income, net in the consolidated statements of operations and comprehensive loss. In sublease agreements that contain non-monetary consideration, the Company estimated the fair market value of the non-monetary consideration received using market data and recognized it on a straight-line basis over the sublease term. Variable lease consideration that did not depend on an index or rate was allocated to a non-lease component and was recognized over time in accordance with the pattern of transfer. No modification or impairment was deemed to have occurred by entering into the sublease agreement because the Company was not released, either fully or in part, from its obligations under the Head Lease. See Note 8, Leases . On February 28, 2020 the Company entered into an amendment to its Head Lease (the “Lease Amendment”). The Lease Amendment provided for the partial termination of the Company's rights and obligations with respect to a portion of the leased premises of approximately 40,000 rentable square feet. The Company continued to lease approximately 74,000 rentable square feet under terms of the amended lease. The Lease Amendment was determined to be a lease modification that qualified as a change of accounting on the existing lease F- 12 and not a separate contract. As such, the ROU assets and operating lease liabilities were remeasured using an incremental borrowing rate at the date of modification and the Company recorded a gain of approximately $ 2.1 million as a component of operating expenses for the year ended December 31, 2020. No impairment of the ROU asset was deemed to have occurred. See Note 8, Leases . On September 15, 2020, the Company entered into an amendment to its Head Lease (the “Second Lease Amendment”). The Second Lease Amendment provided for the partial termination of the Company's rights and obligations with respect to a portion of the leased premises of approximately 17,000 rentable square feet (the “Surrender Space”). The Surrender Space included the 15,700 rentable square feet being subleased by the Company to a subtenant. The Company continued to lease approximately 57,000 rentable square feet under terms of the amended lease. The Second Lease Amendment was determined to be a lease modification that qualified as a change of accounting on the existing lease and not a separate contract. As such, the ROU assets and operating lease liabilities were remeasured using an incremental borrowing rate at the date of modification and the Company recorded a loss of approximately $ 0.4 million as a component of operating expenses for the year ended December 31, 2020. No impairment of the ROU asset was deemed to have occurred. See Note 8, Leases . On September 15, 2020, concurrent with the execution of the Second Lease Amendment, the Company entered into an agreement with its subtenant to terminate the Sublease Agreement of approximately 15,700 rentable square feet (“the Sublease Termination Agreement”). Under the terms of the Sublease Termination Agreement, the former subtenant is obligated to provide licensed rooms and services to the Company free of charge through the original sublease term. Upon termination of the sublease, the Company recognized sublease termination income of approximately $ 3.1 million related to the prepaid rooms and services, and wrote off the remaining indirect costs from the sublease of approximately $ 0.2 million, in the consolidated statements of operations and comprehensive loss for the year ended December 31, 2020. See Note 8, Leases . On April 30, 2021, the Company entered into a Termination Agreement (the "Termination Agreement") for its Head Lease as initially amended on February 28, 2020, and further amended on September 15, 2020. Pursuant to the Termination Agreement, the Company surrendered the leased space of approximately 57,000 square feet to the building’s landlord. The Company did not pay any termination fees with the Termination Agreement. As a result of the termination of the Head Lease, the related right-of-use asset was written off, the lease liability was derecognized, and the $ 3.8 million security deposit was returned to the Company and recorded as part of our cash balance. In total, the Company recognized a loss on the termination of the Head Lease of $ 0.9 million for the year ended December 31, 2021. The loss is included in “General and administrative” expenses on our consolidated statement of operations and comprehensive loss. Paycheck Protection Program Loan On April 21, 2020, the Company received loan proceeds in the amount of approximately $ 3.5 million pursuant to a promissory note agreement with a bank under the Paycheck Protection Program. The Paycheck Protection Program, established as part of the Coronavirus Aid, Relief and Economic Security Act (“CARES Act”), provides for loans to qualifying businesses for amounts up to 2.5 times of the average monthly payroll expenses of the qualifying business. The Promissory Note had an original loan maturity of April 20, 2022, a stated interest rate of 1.0% per annum, and had payments of principal and interest that were due monthly after an initial six-month deferral period where interest accrued, but no payments were due. The Promissory Note provided for customary events of default, including, among others, those relating to failure to make payment when due and breaches of representations. The loan was subject to all the terms and conditions applicable under the PPP and was subject to review by the SBA for compliance with program requirements, including the Company’s certification that the economic uncertainty, at the time, made the PPP loan request necessary to support ongoing operations. On October 2, 2020, the SBA issued procedural guidance with respect to PPP loans and changes in ownership and the Company believes that it is compliant with respect to the 2020 Equity Private Placement and the ATM Offering. In June 2020, the Payroll Protection Program Flexibility Act was signed into law adjusting certain key terms of loans issued under the PPP. In accordance with the PPPFA, the initial deferral period may be extended from six to up to ten months and the loan maturity may be extended from two to five years. The PPPFA also provided for certain other changes, including the extent to which the loan may be forgiven. The loan’s principal and accrued interest were forgivable to the extent that the proceeds were used for eligible purposes, subject to certain limitations, and that the Company maintained its payroll levels over a twenty-four-week period following the loan date. The loan forgiveness amount may have been reduced if the Company F- 13 terminated employees or reduced salaries during the twenty-four-week period. PPP loans are subject to audit and the SBA has indicated that companies that received over $2 million in proceeds should expect an audit. The Company believes that it has used the proceeds for eligible purposes consistent with the provisions of the PPPFA. As the legal form of the Promissory Note is a debt obligation, the Company accounted for it as debt under Accounting Standards Codification (ASC) 470, Debt and recorded a short-term liability of $ 3.5 million in the consolidated balance sheets upon receipt of the loan proceeds. The Company accrued interest over the term of the loan and did not record additional interest at a market rate because the guidance on imputing interest in ASC 835-30, Interest excludes transactions where interest rates are prescribed by a government agency. Approximately $ 0.1 million of interest expense has been recognized within interest and other income, net in the consolidated statements of operations and comprehensive loss for the year ended December 31, 2021. In August 2021, the Company applied with the SBA for forgiveness of the PPP loan and was notified on November 4, 2021 that the SBA has approved our application to forgive the entire amount of the loan and accrued interest. The Company recorded a gain on extinguishment of debt of $ 3.6 million representing the principal and accrued interest for the PPP Loan. Revenue Upon executing a revenue generating arrangement, the Company assesses whether it is probable the Company will collect consideration in exchange for the good or service it transfers to the customer. To determine revenue recognition for arrangements that the Company determines are within the scope of ASC Topic 606, Revenue from Contracts with Customers (“ASC 606”), it performs the following five steps: (i) identify the contract(s) with a customer; (ii) identify the performance obligations in the contract; (iii) determine the transaction price; (iv) allocate the transaction price to the performance obligations in the contract; and (v) recognize revenue when (or as) the Company satisfies the performance obligations. The Company must develop assumptions that require significant judgment to determine the stand-alone selling price for each performance obligation identified in the contract. The assumptions that are used to determine the stand-alone selling price may include forecasted revenues, development timelines, reimbursement rates for personnel costs, discount rates and probabilities of technical and regulatory success. The Company derives revenue from (1) license agreement and (2) supply agreement which are fully described in Note 14, License Agreement . The Company generated revenue from a Development Agreement with Ironwood, pursuant to which the Company provided certain research and development services with respect to certain of Ironwood’s products and product candidates. Such research and development activities were governed by a joint steering committee composed of representatives of both companies. Services performed were invoiced at a mutually agreed upon rate and the initial term of the agreement was two years from the date of Separation and automatically renewed for one year unless either party notified the other at least six months prior to the expiration. Ironwood and the Company agreed that the Development Agreement would not be renewed beyond its initial term which ended on March 31, 2021. The Company generates revenue from research and development grants under contracts with third parties that do not create customer-vendor relationships. The Company’s research and development grants are non-exchange transactions and are not within the scope of ASC Topic 606, Revenue from Contracts with Customers (“ASC 606”). Contribution revenue earned from activities performed pursuant to research and development grants is reported as grant revenue in the Company’s consolidated statements of operations. Revenue from these grants is recognized as the Company incurs qualifying expenses as stipulated by the terms of the respective grant. Cash received from grants in advance of incurring qualifying expenses is recorded as deferred revenue. The Company records revenue and a corresponding receivable when qualifying costs are incurred before receiving payment from the grants. Research and Development Costs The Company expenses research and development costs to operations as incurred. The Company defers and capitalizes nonrefundable advance payments made by the Company for research and development activities until the related goods are received or the related services are performed. The Company estimates the period over which such services will be performed and the level of effort to be expended in each period. If actual timing of performance or the level of effort varies from the estimate, the Company will adjust the amounts recorded accordingly. The F- 14 Company has not experienced any material differences between accrued or prepaid costs and actual costs since inception. Research and development expenses are comprised of costs incurred in performing research and development activities, which may include salary, benefits and other employee-related expenses; share-based compensation expense; laboratory supplies and other direct expenses; facilities expenses; overhead expenses; third-party contractual costs relating to nonclinical studies and clinical trial activities and related contract manufacturing expenses, development of manufacturing processes and regulatory registration of third-party manufacturing facilities; and other outside expenses. General and Administrative Expenses The Company expenses general and administrative costs to operations as incurred. General and administrative expense consists of compensation, share-based compensation, benefits and other employee-related expenses for personnel in the Company’s administrative, finance, legal, information technology, business development and human resource functions. Other costs include the legal costs of pursuing patent protection of the Company’s intellectual property, general and administrative related facility costs, insurance costs and professional fees for accounting and legal services. Income taxes The Company is primarily subject to U.S. federal and Massachusetts state income taxes. For federal and state income taxes, deferred tax assets and liabilities are recognized based upon temporary differences between the financial statement and the tax basis of assets and liabilities. Deferred income taxes are based upon prescribed rates and enacted laws applicable to periods in which differences are expected to reverse. A valuation allowance is recorded when it is more likely than not that some portion or all of the deferred tax assets will not be realized. Accordingly, the Company provides a valuation allowance, if necessary, to reduce deferred tax assets to amounts that are realizable. The tax positions taken or expected to be taken in the course of preparing the Company tax returns are required to be evaluated to determine whether the tax positions are “more-likely-than-not” of being sustained by the applicable tax authority. Tax positions not deemed to meet a more-likely-than-not threshold would be recorded as a tax expense in the current year. The determination as to whether the tax benefit will more likely than not be realized is based upon the technical merits of the tax position as well as consideration of the available facts and circumstances. It does not consider the likelihood of whether or not the IRS will review the position. Cyclerion evaluates uncertain tax positions on a quarterly basis and adjusts the level of the liability to reflect any subsequent changes in the relevant facts surrounding the uncertain positions. Any changes to these estimates, based on the actual results obtained and/or a change in assumptions, could affect Cyclerion's income tax provision in future periods. There were no uncertain tax positions that require accrual or disclosure in the consolidated financial statements as of December 31, 2021, and 2020. The Company’s policy is to recognize interest and penalties related to income tax, if any, in income tax expense. As of December 31, 2021, and 2020 , the Company has no accruals for interest or penalties related to income tax matters. Patent Costs Patent fees and patent related costs in connection with filing and prosecuting patent applications are expensed as incurred and are classified as general and administrative expenses in the accompanying consolidated financial statements. The Company incurred and recorded as operating expense legal and other fees related to patents of approximately $1.4 million and $1.7 million for the years ended December 31, 2021 and 2020, respectively. Interest and Other Income, Net For the year ended December 31, 2021, interest and other income, net consisted of a de minimis amount of interest income related to interest generated from our cash and cash equivalents balances and a de minimis amount F- 15 of interest expense related to the PPP loan. For the year ended December 31, 2020 , interest and other income, net consisted of $ 0.3 million of interest income related to interest generated from our cash and cash equivalents balances and $ 0.3 million of net sublease income. Subsequent Events The Company considers events or transactions that have occurred after the balance sheet date of December 31, 2021, but prior to the filing of the financial statements with the Securities and Exchange Commission, to provide additional evidence relative to certain estimates or to identify matters that require additional recognition or disclosure. Subsequent events have been evaluated through the filing of the financial statements accompanying this Annual Report on Form 10-K. See Note 14, Subsequent Events . New Accounting Pronouncements From time to time, new accounting pronouncements are issued by the Financial Accounting Standards Board (“FASB”) or other standard setting bodies that are adopted by the Company as of the specified effective date. Except as discussed elsewhere in the notes to the consolidated financial statements, the Company did not adopt any new accounting pronouncements during the years ended December 31, 2021 and 2020, that had a material effect on its consolidated financial statements. In June 2016 the FASB issued ASU 2016-13, Financial Instruments-Credit Losses. This standard requires entities to measure all expected credit losses for financial assets held at the reporting date based on historical experience, current conditions, and reasonable and supportable forecasts. As a smaller reporting company, ASU 2016-13 will become effective for the Company for fiscal years beginning after December 15, 2022, and early adoption is permitted. The Company is currently evaluating the impact that ASU 2016-13 will have on its financial statements and related disclosures. In May 2021 the FASB issued Accounting Standards Update No. 2021-04, Earnings Per Share (Topic 260), Debt-Modifications and Extinguishments (Subtopic 470-50), Compensation-Stock Compensation (Topic 718), and Derivatives and Hedging-Contracts in Entity’s Own Equity (Subtopic 815-40): Issuer’s Accounting for Certain Modifications or Exchanges of Freestanding Equity-Classified Written Call Options, a consensus of the Emerging Issues Task Force (EITF) , which amends the FASB Accounting Standards Codification (ASC or the “Codification”) to provide explicit guidance, and, thus, reduce diversity in practice, on accounting by issuers for modifications or exchanges of freestanding equity-classified written call options that remain equity classified after the modification or exchange. This amendment provides that for an entity that presents earnings per share (EPS) in accordance with Topic 260, the effects of a modification or an exchange of a freestanding equity-classified written call option that is recognized as a dividend should be an adjustment to net income (or net loss) in the basic EPS calculation. The amended guidance becomes mandatorily effective for all entities for fiscal years beginning after December 15, 2021, including interim periods within those fiscal years, and should be applied prospectively to modifications or exchanges occurring on or after the effective date. The Company is currently evaluating the impact that ASU 2021-04 will have on its financial statements and related disclosures. No other accounting standards known by the Company to be applicable to it that have been issued by the FASB or other standard-setting bodies and that do not require adoption until a future date are expected to have a material impact on the Company’s consolidated financial statements upon adoption. 3. Related Party Transactions Development Agreement with Ironwood As part of the Separation from Ironwood, the Company entered into a Development Agreement with Ironwood. Under the Development Agreement, the Company provided certain research and development services to Ironwood at mutually agreed upon rates and the amounts earned are recorded as revenue from related party for the year ended December 31, 2020. Such research and development activities were governed by a joint steering F- 16 committee composed of representatives of both Ironwood and the Company. Ironwood and the Company have agreed not to renew the Development Agreement beyond the end of its initial term on March 31, 2021. These transactions under the Development Agreement were considered related party transactions due to Mark Currie’s role as President of the Company through December 31, 2020, and board member of Ironwood. In January 2021, Mark Currie’s role transitioned from President of the Company to a senior advisor on a consulting basis. Therefore, effective January 2021, transactions under the Development Agreement are no longer accounted for as related party transactions. The Company recorded approximately $ 2.3 million for the year ended December 31, 2020. Other Related Party Transactions During the year ended December 31, 2020, the Company recorded approximately $ 1.5 million of research and development costs to a related party which it engaged to provide research and development transaction support services. The entity became a related party when Mark Currie, the Company’s President through December 31, 2020, joined its board in January 2020. There was approximately $ 0.3 million due to the related party for the year ended December 31, 2020. In January 2021, Mark Currie’s role transitioned from President of the Company to a senior advisor on a consulting basis. Therefore, effective January 2021, transactions under this agreement are no longer accounted for as related party transactions. 4. Fair Value of Financial Instruments The Company’s cash equivalents are generally classified within Level 1 of the fair value hierarchy. The following tables present information about the Company’s financial assets measured at fair value on a recurring basis and indicate the level of the fair value hierarchy used to determine such fair values as of December 31, 2021 and December 31, 2020 (in thousands): Fair Value Measurements as of December 31, 2021: Level 1 Level 2 Level 3 Total Cash equivalents: Money market funds $ 52,917 $ — $ — $ 52,917 Cash equivalents $ 52,917 $ — $ — $ 52,917 Fair Value Measurements as of December 31, 2020: Level 1 Level 2 Level 3 Total Cash equivalents: Money market funds $ 53,240 $ — $ — $ 53,240 Cash equivalents $ 53,240 $ — $ — $ 53,240 During the year ended December 31, 2021 and 2020, there were no transfers between levels. The fair value of the Company's cash equivalents, consisting of money market funds, is based on quoted market prices in active markets with no valuation adjustment. The Company believes the carrying amounts of its prepaid expenses and other current assets, restricted cash, accounts payable, and accrued expenses approximate their fair value due to the short-term nature of these amounts. F- 17 5. Property and Equipment Property and equipment, net consisted of the following (in thousands): December 31, December 31, 2021 2020 Software $ 2,214 $ 2,214 Computer and office equipment 51 44 Leasehold improvements — 14,894 Property and equipment, gross 2,265 17,152 Less: accumulated depreciation and amortization ( 2,200 ) ( 10,287 ) Property and equipment, net $ 65 $ 6,865 As of December 31, 2021, and 2020, the Company’s property and equipment was primarily located in Cambridge, Massachusetts. Depreciation and amortization expense of the Company’s property and equipment was approximately $ 0.5 million and $ 2.3 million for the years ended December 31, 2021 and 2020, respectively. During the year ended December 31, 2021, the Company recorded a non-cash loss of $ 6.3 million, on the disposal of leasehold improvements as a result of its Head Lease (as defined below) termination (see Note 8 to the Consolidated Financial Statements). The non-cash loss on the disposal of leasehold improvements was recognized as a component of operating expenses in the consolidated statements of operations and comprehensive loss for the year ended December 31, 2021 . 6. Accrued Expenses and Other Current Liabilities Accrued expenses and other current liabilities consisted of the following (in thousands): December 31, December 31, 2021 2020 Accrued incentive compensation $ 1,369 $ 1,720 Salaries 266 514 Accrued vacation 345 555 Professional fees 398 689 Accrued severance and benefit costs 28 3,640 Other 498 176 Accrued expenses and other current liabilities $ 2,904 $ 7,294 7. Commitments and Contingencies Other Funding Commitments In the normal course of business, the Company enters into contracts with clinical research organizations and other third parties for clinical and preclinical research studies and other services and products for operating purposes. These contracts are generally cancellable, with notice, at the Company’s option and do not have any significant cancellation penalties. Guarantees On September 6, 2018, Cyclerion was incorporated in Massachusetts and its officers and directors are indemnified for certain events or occurrences while they are serving in such capacity. The Company enters into certain agreements with other parties in the ordinary course of business that contain indemnification provisions. These typically include agreements with directors and officers, business F- 18 partners, contractors, clinical sites and customers. Under these provisions, the Company generally indemnifies and holds harmless the indemnified party for losses suffered or incurred by the indemnified party as a result of the Company’s activities. These indemnification provisions generally survive termination of the underlying agreements. The maximum potential amount of future payments the Company could be required to make under these indemnification provisions is unlimited. However, to date the Company has not incurred material costs to defend lawsuits or settle claims related to these indemnification provisions. As a result, the estimated fair value of these obligations is minimal. Accordingly, the Company did not have any liabilities recorded for these obligations as of December 31, 2021 or December 31, 2020 . 8. Leases The FASB issued ASU 2016-02, or the leasing standard or ASC 842, in February 2016. ASU 2016-02 requires lessees to recognize assets and liabilities on the balance sheet for the rights and obligations created by all leases with terms of more than 12 months. ASU 2016-02 also requires certain qualitative and quantitative disclosures designed to give financial statement users information on the amount, timing, and uncertainty of cash flows arising from leases. On April 1, 2019, the Company entered into the Head Lease ("the Head Lease"), a direct operating lease for its former headquarters located at 301 Binney Street, Cambridge, MA consisting of approximately 114,000 rentable square feet of office and laboratory space on the first and second floors. The Head Lease had a term of 123 months with two five-year extension options and certain expansion rights. The Head Lease also included a letter of credit of $ 7.7 million, posted with the landlord as a security deposit, which was collateralized by a money market account recorded as restricted cash on the Company’s consolidated balance sheets. The Company had also entered into customary non-disturbance arrangements with the building landlord’s mortgagee and with the property ground lessor recognizing Company's leasehold interest in this property. On February 28, 2020 the Company entered into an amendment to its Head Lease. The Lease Amendment partially terminated the Company’s rights and obligations with respect to an approximately 40,000 rentable square feet. The Company continued to lease the remaining space of approximately 74,000 square feet including the area covered by the subleased premise, discussed below. In connection with this Lease Amendment, the Company reduced its remaining lease payments through June 2029 by approximately $ 41.9 million and paid a $ 6.3 million termination fee and $ 0.2 million related to other initial direct costs, which were deferred and recognized over the remaining lease term. The Company’s security deposit was also reduced by approximately $ 2.7 million to approximately $ 5.0 million. The Lease Amendment was determined to be a lease modification that qualified as a change of accounting on the existing lease and not a separate contract. As such, the ROU assets and operating lease liabilities were remeasured using an incremental borrowing rate at the date of modification of 9.7 %, which resulted in a reduction of the ROU asset of $ 21.4 million and a reduction in the operating lease liabilities of $ 23.5 million. The Company recorded the resulting gain of approximately $ 2.1 million as a component of operating expenses in the consolidated statement of operations and comprehensive loss for the year ended December 31, 2020. On September 15, 2020 the Company entered into the Second Lease Amendment to its Head Lease. The Second Lease Amendment provided for the partial termination of the Company’s rights and obligations with respect to a portion of the leased premises of approximately 17,000 rentable square feet. The Surrender Space included 15,700 rentable square feet being subleased by the Company to a subtenant. The Company continued to lease approximately 57,000 square feet of space. The Company reduced its remaining lease payments through June 2029 by approximately $ 16.9 million. The Company paid no termination or other initial direct costs related to the execution of the Second Lease Amendment. The Company’s security deposit was reduced by approximately $ 1.2 million to approximately $ 3.8 million, which is classified as restricted cash on the Company’s consolidated balance sheet as of December 31, 2020. The Second Lease Amendment was determined to be a lease modification that qualified as a change of accounting on the existing lease and not a separate contract. As such, the ROU assets and operating lease liabilities were remeasured using an incremental borrowing rate at the date of modification of 6.1 %, which resulted in a reduction of the ROU asset of $ 5.9 million and a reduction in the operating lease liabilities of $ 5.5 million. The F- 19 Company recorded the resulting loss of approximately $ 0.4 million as a component of operating expenses in the consolidated statement of operations and comprehensive loss for the year ended December 31, 2020. On April 30, 2021, the Company entered into a Termination Agreement (the "Termination Agreement") for its Head Lease as initially amended on February 28, 2020, and further amended on September 15, 2020. Pursuant to the Termination Agreement, the Company surrendered the leased space of approximately 57,000 square feet to the building’s landlord. The Company did not pay any termination fees in connection with the Termination Agreement. As a result of the termination of the Head Lease, the related right-of-use asset was written off, the lease liability was derecognized, and the $ 3.8 million security deposit was returned to the Company and recorded as part of our cash balance. In total, the Company recognized a loss on the termination of the Head Lease of $ 0.9 million for the year ended December 31, 2021. The loss is included in “General and administrative” expenses on our consolidated statement of operations and comprehensive loss. The Company had an operating lease ROU asset of approximately $ 43.4 million related to the amended Head Lease recorded in its consolidated balance sheets as of December 31, 2020. The Company had current and non-current operating lease liabilities of approximately $ 3.3 million, and $ 38.9 million, respectively, related to the amended Head Lease recorded in its consolidated balance sheets as of December 31, 2020. Lease cost was recognized on a straight-line basis over the lease term. For the years ended December 31, 2021 and 2020, the Company recognized a total of approximately $ 2.4 million and $ 8.6 million, respectively, of total lease costs. Variable lease costs not subject to an index or rate were recognized as incurred. For the years ended December 31, 2021 and 2020, the Company recognized a total of approximately $ 0.7 million and $ 2.2 million, respectively, of variable lease costs related to the Head Lease, as amended. In May 2021, the Company signed a membership agreement to lease space with WeWork at 501 Boylston Street, Boston, Massachusetts. The lease commenced on August 1, 2021 and was accounted for as a short term lease. The Company recorded $ 0.1 million in lease expense associated with the membership agreement during the year ended December 31, 2021. Supplemental cash flow information related to leases for the periods reported is as follows: December 31, December 31, 2021 2020 Decrease in right-of-use assets related to lease modifications and termination (in thousands) $ 42,058 $ 27,333 Decrease in operating lease liabilities due to lease modifications and termination (in thousands) $ 41,177 $ 29,002 Cash paid for amounts included in the measurement of lease liabilities (in thousands) $ 1,887 $ 7,411 Weighted-average remaining lease term of operating leases (in years) — 8.5 Weighted-average discount rate of operating leases — 6.1 % On October 18, 2019, the Company entered into an agreement with a third party to sublease 15,700 rentable square feet of its lease premises under the Head Lease. The sublease was scheduled to expire on June 30, 2029, unless earlier terminated in accordance with the sublease agreement, and has no extension options. The sublease provides for annual base rent of approximately $ 1.5 million in the first year, which increases on a yearly basis by 3.0 % (subject to an abatement of base rent of approximately $ 0.7 million for the first six months of the sublease). As part of the consideration for the sublease, the sublessee agreed to provide licensed rooms and services within the sublease premises to the Company over the sublease term free of charge. In addition, the sublessee is responsible for its pro rata share of certain costs, taxes and operating expenses related to the subleased space, the consideration for which is variable and is based on the actual operating costs of the lessor. The Company allocated the total consideration in the sublease agreement between the lease and non-lease components in the contract based on their relative standalone prices. The Company determined that the variable consideration relates exclusively to non-lease components and will be recognized as incurred. The sublease included an initial security deposit of $ 0.5 million, which was provided by the sublessee in the form of a letter of credit, and an additional security deposit of $ 0.4 million within nine months of the sublease commencement. F- 20 On September 15, 2020, concurrent with execution of the Second Lease Amendment, the Company entered into the Sublease Termination Agreement to terminate its sublease of 15,700 rentable square feet. Under the terms of the Sublease Termination Agreement, the subtenant is relieved of its obligation to provide future cash rental payments to the Company. The agreements requiring the former subtenant to provide licensed rooms and services to the Company free of charge through the original sublease term survived the sublease termination. The Company gained access to the licensed rooms and services beginning in the third quarter of 2021. The letter of credit security deposit related to the sublease was released. The Company determined that the Sublease Termination Agreement constituted a non-monetary exchange under ASC 845 Nonmonetary Transactions (“ASC 845”) where, in return for the free rooms and the services, the Company agreed to terminate its rights and obligations under the sublease agreement. In accordance with ASC 845, the Company determined that the accounting for the transaction should be based on the fair value of assets or services involved. The Company estimated the fair value of the rooms and services to be approximately $ 1.5 million and $ 2.9 million, respectively. Accordingly, prepaid rooms and services of $ 4.4 million were recorded upon the sublease termination, of which $ 1.6 million was recorded in other current assets and $ 2.8 million was recorded in other assets in the consolidated balance sheets as of December 31, 2020. Termination fee income of $ 3.1 million was recognized related to the rooms and services, after considering the rent receivable balance of $ 1.3 million outstanding from the subtenant. The remaining unamortized direct costs of $ 0.2 million were written off. The effects of the Sublease Termination Agreement were recorded within sublease termination income, net in the consolidated statements of operations and comprehensive loss. Total gross sublease income of approximately $ 1.5 million, and net sublease income of approximately $ 0.3 million was recorded in interest and other income, net in the consolidated statements of operations and comprehensive loss for year ended December 31, 2020. The Company determined that the licensed rooms represent a lease under ASC 842. The Company obtained control of the rooms in the third quarter of 2021 and the prepaid rooms balance of approximately $ 1.4 million was reclassified from other assets to a ROU asset. The related lease expense is recognized on a straight-line basis over the lease term of 8.88 years. The Company recorded $ 0.1 million of lease expense during the year ended December 31, 2021. The Company determined that the licensed services represent a non-lease component, which is recognized separately from the lease component for this asset class. The expense related to the licensed services is recognized on a straight-line basis over the period the services are received. The Company recorded $ 0.2 million for the year ended December 31, 2021. Both the lease expense and services expense are recognized as a component of research and development costs in the consolidated statements of operations and comprehensive loss. 9. Share-based Compensation Plans In 2019, Cyclerion adopted share-based compensation plans. Specifically, Cyclerion adopted the 2019 Employee Stock Purchase Plan (“2019 ESPP”) and the 2019 Equity Incentive Plan (“2019 Equity Plan”). Under the 2019 ESPP, eligible employees may use payroll deductions to purchase shares of stock in offerings under the plan, and thereby acquire an interest in the future of the Company. The 2019 Equity Plan provides for stock options and restricted stock units (“RSUs”). Cyclerion also mirrored two of Ironwood’s existing plans, the Amended and Restated 2005 Stock Incentive Plan (“2005 Equity Plan”) and the Amended and Restated 2010 Employee, Director and Consultant Equity Incentive Plan (“2010 Equity Plan). These mirror plans were adopted to facilitate the exchange of Ironwood equity awards for Cyclerion equity awards upon the Separation as part of the equity conversion. As a result of the Separation and in accordance with the EMA, employees of both companies retained their existing Ironwood vested options and received a pro-rata share of Cyclerion options, regardless of which company employed them post-Separation. For employees that were ultimately employed by Cyclerion, unvested Ironwood options and RSUs were converted to unvested Cyclerion options and RSUs. F- 21 The following table provides share-based compensation reflected in the Company’s consolidated statements of operations and comprehensive loss for the years ended December 31, 2021 and 2020 (in thousands): Year Ended December 31, 2021 2020 Research and development $ 3,945 $ 6,799 General and administrative 5,666 8,193 $ 9,611 $ 14,992 Stock Options Stock options granted under the Company’s equity plans generally have a ten-year term and vest over a period of four years, provided the individual continues to serve at the Company through the vesting dates. Options granted under all equity plans are exercisable at a price per share not less than the fair market value of the underlying common stock on the date of grant. The estimated fair value of options, including the effect of estimated forfeitures, is recognized over the requisite service period, which is typically the vesting period of each option. A summary of stock option activity for the year ended December 31, 2021 is as follows: Weighted Weighted Average Average Average Remaining Intrinsic Number Exercise Contractual Value (in of Options Price Term (Years) thousands) Outstanding as of December 31, 2020 7,426,356 $ 11.87 7.0 $ 1,178 Granted 1,176,250 2.98 Exercised ( 72,419 ) 2.17 Cancelled or forfeited ( 1,449,761 ) 10.69 Outstanding as of December 31, 2021 7,080,426 $ 10.73 6.9 — Exercisable at December 31, 2021 4,518,213 $ 13.46 5.9 $ — During the years ended December 31, 2021 and 2020, the Company granted stock options to purchase an aggregate of 1,176,250 shares and 1,382,846 shares, respectively, at weighted average grant fair values per option share of $ 2.17 and $ 1.97 , respectively. The total grant fair value of options granted during the years ended December 31, 2021 and 2020 was $ 2.6 million and $ 2.7 million, respectively. The total intrinsic value of options exercised for the years ended December 31, 2021 and 2020 was $ 0.1 million and $ 0.1 million, respectively. As of December 31, 2021, the unrecognized share-based compensation expense, net of estimated forfeitures, related to all unvested time-based stock options held by the Company’s employees is $ 8.1 million and the weighted average period over which that expense is expected to be recognized is 3.29 years. The weighted-average Black-Scholes assumptions used in estimating the fair value of the stock options granted by Cyclerion following the Separation during the years ended December 31, 2021 and 2020 were as follows: Year ended December 31, 2021 2020 Weighted average risk-free interest rate 1.09 % 0.43 % Expected dividend yield — — Expected option term (in years) 5.9 6.3 Expected stock price volatility 85.45 % 91.73 % For the years ended December 31, 2021 and 2020, expected volatility was estimated using an average of the historical volatility of the common stock of a group of similar companies that were publicly traded. The F- 22 Company will continue to apply this process until a sufficient amount of historical information regarding the volatility of its own stock price becomes available. The Company has granted to certain employees performance based options to purchase shares of common stock. These options are subject to performance based milestone vesting. During the year ended December 31, 2021 , 50,000 shares vested as a result of performance milestone achievements and no shares vested during the year ended December 31, 2020. The Company recorded a de minimis and no share-based compensation expense related to these performance-based options for the years ended December 31, 2021, and 2020, respectively. Market-based Stock Options The Company also has granted to certain employees stock options containing market conditions that vest upon the achievement of specified price targets of the Company’s share price for a period through December 31, 2024. Vesting is measured based upon the average closing price of the Company’s share price for any thirty consecutive trading days, subject to certain service requirements. Stock compensation cost is expensed on a straight-line basis over the derived service period for each stock price target within the award, ranging from approximately 4.0 to 4.6 years. The Company accelerates expense when a stock price target is achieved prior to the derived service period. The Company does not reverse expense recognized if the share price target(s) are ultimately not achieved but expense is reversed when a stock award recipient has a break in service prior to the completion of the derived service period. As of December 31, 2021, there was $ 0.2 million of unrecognized compensation costs related to stock options containing market conditions, which is expected to be recognized over a weighted-average period of 2.17 years. A summary of stock awards containing market conditions activity for the years ended December 31, 2021 and 2020 is as follows: Weighted Weighted Average Aggregate Average Remaining Intrinsic Number of Exercise Contractual Value (in Options Price Term (years) thousands) Outstanding as of December 31, 2020 600,000 $ 2.01 $ 8.9 $ 630 Granted — — — — Exercised — — — — Cancelled or forfeited ( 150,000 ) $ — $ — $ — Outstanding as of December 31, 2021 450,000 $ 2.01 7.9 $ — Exercisable at December 31, 2021 — $ — — $ — The fair value of stock options containing market conditions is estimated using Monte Carlo simulations. No stock options containing market conditions were granted during the years ended December 31, 2021 and 2020. Restricted Stock Units The RSUs generally vest 25 % per year on the approximate anniversary of the date of grant until fully vested, provided the employee remains continuously employed with the Company through each vesting date. Shares of the Company’s common stock are delivered to the employee upon vesting, subject to payment of applicable withholding taxes. The fair value of all RSUs is based on the market value of the Company’s common stock on the date of grant. Compensation expense, including the effect of estimated forfeitures, is recognized over the applicable service period. F- 23 A summary of RSU activity for the years ended December 31, 2021 is as follows: Weighted Average Number Grant Date of Shares Fair Value Unvested as of December 31, 2020 294,913 $ 14.52 Granted 39,369 3.17 Vested ( 143,774 ) 12.01 Forfeited ( 97,704 ) 14.41 Unvested as of December 31, 2021 92,804 $ 13.70 As of December 31, 2021, the unrecognized share-based compensation expense, net of estimated forfeitures, related to all unvested restricted stock units by the Company’s employees is $ 0.7 million and the weighted-average period over which that expense is expected to be recognized is 1.13 years. 10. Loss per share Basic and diluted net loss per common share is computed by dividing net loss by the weighted average number of common shares outstanding during the period as follows: Year Ended December 31, 2021 2020 Numerator: Net loss (in thousands) $ ( 51,647 ) $ ( 77,802 ) Denominator: Weighted average shares used in calculating net loss per share — basic and diluted (in thousands) 39,144 30,403 Net loss per share — basic and diluted $ ( 1.32 ) $ ( 2.56 ) We exclude shares of common stock related to stock options and RSUs from the calculation of diluted net loss per share since the inclusion of such shares would be anti-dilutive. The following table sets forth potential shares that were considered anti-dilutive for the years ended December 31, 2021 and 2020: Year Ended December 31, 2021 2020 Stock Options $ 7,530,426 $ 294,913 RSUs 92,804 8,026,356 $ 7,623,230 $ 8,321,269 11. Income Taxes There was no provision for income taxes for the years ended December 31, 2021, and 2020, due to the Company’s operating losses and a full valuation allowance on deferred tax assets. Deferred income taxes reflect the net tax effects of temporary differences between the carrying amounts of assets and liabilities for financial reporting purposes and the amounts used for income tax purposes. A reconciliation of income taxes computed using the U.S. federal statutory rate to that reflected in operations follows (in thousands): F- 24 Year Ended December 31, 2021 2020 U.S. $ ( 51,686 ) $ ( 77,884 ) International 39 82 Loss before benefit from income taxes $ ( 51,647 ) $ ( 122,406 ) Income tax benefit using U.S. federal statutory rate $ ( 10,846 ) $ ( 16,338 ) State income taxes, net of federal benefit ( 3,631 ) ( 5,619 ) Non-deductible share-based compensation ( 911 ) 16 Share-based compensation - shortfalls/(windfalls) 946 1,047 Permanent differences ( 420 ) ( 94 ) PPP loan forgiveness ( 748 ) — Tax credits ( 805 ) ( 2,469 ) Other ( 9 ) ( 16 ) Change in valuation allowance 16,424 23,473 $ — $ — The effective income tax rate is based upon the income for the year, the composition of the income in different countries, and adjustments, if any, for the potential tax consequences, benefits or resolutions of audits or other tax contingencies. Our income tax rate in foreign jurisdictions is lower than our income tax rate in the United States. Deferred tax assets (liabilities) consist of the following as of December 31, 2021 and 2020 (in thousands): Year Ended December 31, 2021 2020 Deferred tax assets: Net operating loss carryforwards $ 43,700 $ 27,007 Tax credit carryforwards 8,044 7,185 Share-based compensation 7,702 5,890 Operating lease - liability — 11,536 Property and equipment ( 1 ) 1,362 Capitalized research and development 11,147 12,684 Accruals and reserves 91 518 Other 4 — Total deferred tax assets $ 70,687 $ 66,182 Deferred tax liabilities: Operating lease - right of use asset $ ( 383 ) $ ( 11,857 ) Prepaid sublease termination ( 758 ) ( 1,203 ) Total deferred tax liabilities ( 1,141 ) ( 13,060 ) Net deferred tax assets 69,546 53,122 Valuation allowance ( 69,546 ) ( 53,122 ) Net deferred tax assets $ — $ — Management of Cyclerion has evaluated the positive and negative evidence bearing upon the possible realization of its deferred tax assets. Management has considered the Company's history of operating losses, in addition to the expected timing of the reversal of existing temporary differences and concluded, in accordance with the applicable accounting standards, that it is more likely than not that the Company will not realize the benefit of its deferred tax assets. Accordingly, the net deferred tax assets have been fully reserved at December 31, 2021 and December 31, 2020. Management reevaluates the positive and negative evidence on a quarterly basis. F- 25 The valuation allowance increased by approximately $ 16.4 million during the year ended December 31, 2021 primarily due to increases in capitalized research and development expenses, net operating losses, tax credit carryforwards and deferred tax assets related to share-based compensation. Cyclerion did not generate net operating loss carryforwards or tax credit carryforwards available for its use until its inception and operation as a standalone legal entity. At December 31, 2021 and 2020 , Cyclerion has federal net operating loss carryforwards of approximately $ 160 million and $ 98.8 million, respectively, to offset future federal taxable income that will be carried forward indefinitely until utilized. As of December 31, 2021, and 2020 , Cyclerion had state net operating loss carryforwards of approximately $ 159.6 million and $ 98.9 million, respectively, to offset future state taxable income, which will begin to expire in 2039 and will continue to expire through 2040 . Cyclerion also had tax credit carryforwards of approximately $ 8.4 million and $ 7.5 million as of December 31, 2021 and 2020 , respectively, to offset future federal and state income taxes. Federal credits begin to expire in 2039 and will continue to expire through 2040. State credits begin to expire in 2022 and continue through 2034 . The Company’s ability to use its operating loss carryforwards and tax credits to offset future taxable income could be subject to restrictions under Section 382 of the U.S. Internal Revenue Code of 1986, as amended (the “Internal Revenue Code”). These potential restrictions may limit the future use of the operating loss carryforwards and tax credits if certain ownership changes described in the Internal Revenue Code occur. Changes in stock ownership may occur that would create these limitations on the Company’s use of the operating loss carryforwards and tax credits. In such a situation, the Company may be required to pay income taxes, even though significant operating loss carryforwards and tax credits exist. The Company has not as yet conducted a study of its research and development credit carry forwards. This study may result in an adjustment to the Company’s research and development credit carryforwards; however, until a study is completed and any adjustment is known, no amounts are being presented as an uncertain tax position. A full valuation allowance has been provided against the Company’s research and development credits, and if an adjustment is required, this adjustment would be offset by an adjustment to the valuation allowance. Thus, there would be no impact to the consolidated balance sheets or statements of operations if an adjustment were required. Upon audit, taxing authorities may challenge all or part of an uncertain income tax position. While Cyclerion has no history of tax audits since its inception on a standalone basis, it may be subject to tax audits by federal and state taxing authorities in the future. Accordingly, Cyclerion regularly assesses the outcome of potential examinations in each of the taxing jurisdictions when determining the adequacy of the amount of unrecognized tax benefit recorded. Cyclerion had no unrecognized tax benefits as of December 31, 2021 and 2020. Cyclerion will recognize interest and penalties, if any, related to uncertain tax positions in income tax expense. As of December 31, 2021 and 2020 , no interest or penalties have been accrued. There are no current federal or state income tax audits in progress. On March 27, 2020, the Coronavirus Aid, Relief and Economic Security (“CARES”) Act was enacted and signed into law. The CARES Act is an emergency economic stimulus package in response to the COVID-19 pandemic, which among other things contains numerous income tax provisions, some of which are effective retroactively for fiscal years ended before the date of enactment. The CARES Act includes certain tax relief provisions, including modifications to the NOL rules, including a provision to carryback losses from 2018 – 2021 tax years, temporary changes to business interest expense disallowance rules (IRC §163(j)), qualified improvement property, payroll tax delays/ credits, and several other tax and non-tax benefits. These tax provisions should have no significant income tax ramifications for Cyclerion, but the Company will continue to monitor any changes and guidance in order to consider potential opportunities. The CARES Act also created a program called the Paycheck Protection Program to be administered by the SBA. Cyclerion received $ 3.5 million of loan proceeds on April 21, 2020 under the PPP, as fully described in Note 2, Summary of Significant Accounting Policies . 12. Defined Contribution Plan In 2019, Cyclerion adopted a defined contribution 401(k) Savings Plan similar to the plan in place at Ironwood. The plan assets under the Ironwood defined contribution 401(k) Savings Plan were transferred to the Cyclerion plan. Subject to certain IRS limits, eligible employees may elect to contribute from 1 % to 100 % of their F- 26 compensation. Cyclerion contributions to the plan are at the sole discretion of the board of directors. Currently, Cyclerion provides a matching contribution of 75 % of the employee’s contributions, up to $ 6,000 annually. Included in compensation expense is approximately $ 0.3 million and $ 0.5 million related to the defined contribution 401(k) Savings Plan for the years ended December 31, 2021 and 2020 , respectively. 13. Workforce Reduction 2020 Workforce Reduction On November 5, 2020, the Company began a reduction of its current workforce by forty-eight (48) full-time employees to align its resources with its current priorities of focusing on the MELAS study, the planned ADv study and further characterization of CY6463 novel pharmacology. The Company recorded total costs related to the 2020 Workforce Reduction were approximately $ 5.0 million including approximately $ 0.1 million in stock-based compensation from the modification of certain share-based equity awards. The Company reduced its workforce by thirty-one (31) employees in the fourth quarter of 2020 and recorded approximately $ 4.1 million of severance and benefits costs in accordance with ASC Topic 420, Exit or Disposal Cost Obligations, or ASC 420, including a de minimis amount of stock-based compensation expense, for the year ended December 31, 2020. The workforce reduction was completed by the end of the first quarter of 2021. The following table summarizes the accrued liabilities activity recorded in connection with the reduction in workforce for the year ended December 31, 2021 (in thousands): Amounts accrued at December 31, 2020 Charges Amount paid Adjustments Amounts accrued at December 31, 2021 2020 workforce reduction $ ( 3,640 ) $ ( 878 ) $ 4,490 $ — $ ( 28 ) Total $ ( 3,640 ) $ ( 878 ) $ 4,490 $ — $ ( 28 ) 14. License Agreement Akebia License Agreement On June 3, 2021, the Company and Akebia entered into a License Agreement (the “License Agreement”) relating to the exclusive worldwide license by the Company to Akebia of our rights to the development, manufacture, medical affairs and commercialization of pharmaceutical products containing the pharmaceutical compound known as praliciguat and other related products and forms thereof enumerated in the License Agreement (collectively, the “Products”). Pursuant to the License Agreement, Akebia will be responsible for all future research, development, regulatory, and commercialization activities for the Products. Akebia paid a $ 3.0 million up-front payment to the Company upon signing of the License Agreement and the Company is eligible to receive additional milestone cash payments of up to $ 12.0 million in the next 18 months. Further milestone cash payments by Akebia are scheduled in the License Agreement based on the initiation of phase 3 clinical trials in the U.S. for Products for first and second indication, for FDA approvals, for approvals in certain other major markets, and for certain sales milestones. In addition to these cash milestone payments, Akebia will pay the Company tiered royalty payments on net sales in certain major markets at percentages ranging from the mid-single digits to the high-teens, subject to certain reductions and offsets. Pursuant to the License Agreement, the Company determined the License Agreement represents a service arrangement under the scope of ASC 606. Given the reversion of the rights under the License Agreement represents a penalty in substance for a termination by Akebia, the contract term would be the stated term of the License Agreement. F- 27 The Company determined that the grant of license to our patents and trademarks, know how transfer, the assignment of regulatory submissions and trademarks and additional knowledge transfer assistance obligations represent a single promise and performance obligation to be transferred to Akebia over time due to the nature of the promises in the contract. The provision of development materials on hand was identified as a separate performance obligation. However, it is immaterial in the context of the contract as the development materials are low value and do not have an alternative use to the Company. The consideration related to sales-based milestone payments, including royalties, will be recognized when the related sales occur as these amounts have been determined to relate predominantly to the license. The Company will re-evaluate the probability of achievement of the milestones and any related constraints each reporting period. Akebia Supply Agreement On August 3, 2021, the Company and Akebia entered into a Supply Agreement (the “Supply Agreement”) relating to the manufacturing by the Company of the Initial Supply of the Drug Product and placebo ("Initial Supply") for Akebia's use pursuant to the License Agreement. Akebia will pay the Company for the manufacturing costs at mutually agreed upon rates. The Company determined the Supply Agreement has stand-alone value under the scope of ASC 606 and should not be combined with the License Agreement. Given that the Supply Agreement can be terminated at any time without cause with 30 days notice, the Company deemed the Supply Agreement to be a month-to-month contract. The manufacturing of the Initial Supply by the Company represents a single performance obligation and consideration related to the manufacturing costs will be recognized over time as costs are incurred based on an input method. The Company recorded $ 0.3 million amount as revenue from the Supply Agreement for the year ended December 31, 2021. 15. Grant Revenue In August 2021, the Company was approved to receive funding from the PTC Grant for the Phase 2 study of CNS sGC stimulation in AD with vascular features. The granting period is July 1, 2021, to December 31, 2022, and the Company will receive an award of up to $ 2 million. The Company determined that this transaction is non-reciprocal as there is not considered to be a commensurate value exchanged with the Alzheimer's Association as the funding provider. Where commensurate value is not exchanged for goods and services provided, a recipient assesses whether the grant is conditional or unconditional. The Company considered all conditions and barriers associated with this grant and determined the grant is conditional and revenue will be recognized upon achieving certain milestones and incurring internal costs specifically covered by this grant. Under ASC 958-605, revenues will be recognized as the Company incurs expenses related to the PTC Grant. The Company incurred approximately $ 0.6 million of allowable expenses and recognized a corresponding amount of grant revenue for the year ended December 31, 2021. 16. Subsequent Events The Company has evaluated all events and transactions that occurred after the balance sheet date through the date the consolidated financial statements were issued and determined that there were no such events requiring recognition or disclosure in the consolidated financial statements. F- 28