[FORM 10-Q Cover Page](index=1&type=section&id=FORM%2010-Q%20Cover%20Page) This section identifies the document as Cyclerion Therapeutics, Inc.'s Quarterly Report on Form 10-Q, detailing its filing status and outstanding common stock - The document is a Quarterly Report on Form 10-Q for Cyclerion Therapeutics, Inc. for the period ended **September 30, 2019**[1](index=1&type=chunk) - The registrant is classified as a Non-accelerated filer, Smaller reporting company, and Emerging growth company[3](index=3&type=chunk) - As of **November 6, 2019**, the registrant had **27,468,904 shares** of common stock outstanding[4](index=4&type=chunk) [Table of Contents](index=3&type=section&id=Table%20of%20Contents) This section outlines the report's structure, dividing it into two main parts: Financial Information and Other Information, with their respective sub-sections - The report is structured into two main parts: **Part I – Financial Information** and **Part II – Other Information**[6](index=6&type=chunk) - Part I includes Financial Statements, Management's Discussion and Analysis, Quantitative and Qualitative Disclosures About Market Risk, and Controls and Procedures[6](index=6&type=chunk) - Part II includes Legal Proceedings, Risk Factors, and Exhibits[6](index=6&type=chunk) [SPECIAL NOTE REGARDING FORWARD-LOOKING STATEMENTS](index=4&type=section&id=SPECIAL%20NOTE%20REGARDING%20FORWARD-LOOKING%20STATEMENTS) This section cautions readers that the report contains forward-looking statements subject to substantial risks and uncertainties, and the company disclaims any obligation to update them - The report contains forward-looking statements that involve substantial risks and uncertainties, based on current expectations and assumptions[8](index=8&type=chunk)[9](index=9&type=chunk) - Key factors that could cause actual results to differ materially include business operations post-separation, financing capabilities, product candidate development (olinciguat, IW-6463, praliciguat), regulatory approvals, intellectual property protection, and market conditions[9](index=9&type=chunk) - The company undertakes no obligation to publicly update any forward-looking statement, except as required by applicable law[11](index=11&type=chunk) [PART I — FINANCIAL INFORMATION](index=6&type=section&id=PART%20I%20%E2%80%94%20FINANCIAL%20INFORMATION) This part presents the company's unaudited financial statements, management's discussion and analysis, market risk disclosures, and controls and procedures [Item 1. Financial Statements (unaudited)](index=6&type=section&id=Item%201.%20Financial%20Statements%20(unaudited)) This section presents Cyclerion Therapeutics, Inc.'s unaudited condensed consolidated and combined financial statements, including balance sheets, statements of operations, stockholders' equity, and cash flows, with explanatory notes [Condensed Consolidated and Combined Balance Sheets](index=6&type=section&id=Condensed%20Consolidated%20and%20Combined%20Balance%20Sheets) This section provides a snapshot of the company's financial position, detailing assets, liabilities, and stockholders' equity at specific reporting dates Condensed Consolidated and Combined Balance Sheets (in thousands) | Metric | Sep 30, 2019 | Dec 31, 2018 | | :----------------------------------- | :----------- | :----------- | | Cash and cash equivalents | $117,034 | $— | | Total current assets | $120,706 | $879 | | Restricted cash | $7,726 | $— | | Property and equipment, net | $12,114 | $6,497 | | Operating lease right-of-use asset | $69,158 | $— | | Total assets | $209,704 | $7,401 | | Accounts payable | $4,818 | $2,781 | | Accrued research and development costs | $3,543 | $5,261 | | Total current liabilities | $19,096 | $17,846 | | Operating lease liabilities, net | $71,411 | $— | | Total stockholders' equity (deficit) | $119,197 | $(10,445) | - Total assets increased significantly from **$7.4 million** at December 31, 2018, to **$209.7 million** at September 30, 2019, primarily driven by cash and cash equivalents and operating lease right-of-use assets following the company's separation and private placement[17](index=17&type=chunk) - Stockholders' equity shifted from a deficit of **$(10.4) million** at December 31, 2018, to a positive **$119.2 million** at September 30, 2019[17](index=17&type=chunk) [Condensed Consolidated and Combined Statements of Operations and Comprehensive Loss](index=7&type=section&id=Condensed%20Consolidated%20and%20Combined%20Statements%20of%20Operations%20and%20Comprehensive%20Loss) This section presents the company's revenues, expenses, and net loss over specific periods, reflecting its operational performance Condensed Consolidated and Combined Statements of Operations and Comprehensive Loss (in thousands, except per share data) | Metric | 3 Months Ended Sep 30, 2019 | 3 Months Ended Sep 30, 2018 | 9 Months Ended Sep 30, 2019 | 9 Months Ended Sep 30, 2018 | | :----------------------------------- | :-------------------------- | :-------------------------- | :-------------------------- | :-------------------------- | | Revenue from related party | $1,398 | $— | $3,026 | $— | | Research and development | $22,295 | $21,499 | $74,458 | $65,264 | | General and administrative | $7,119 | $7,787 | $27,019 | $19,086 | | Total cost and expenses | $29,414 | $29,286 | $101,477 | $84,350 | | Loss from operations | $(28,016) | $(29,286) | $(98,451) | $(84,350) | | Interest and investment income | $699 | $— | $1,498 | $— | | Net loss | $(27,317) | $(29,286) | $(96,953) | $(84,350) | | Basic and diluted net loss per share | $(1.00) | $(1.07) | $(3.54) | $(3.08) | - Revenue from related party was **$1.4 million** for the three months and **$3.0 million** for the nine months ended September 30, 2019, with no comparable revenue in 2018, due to services provided under a development agreement with Ironwood[20](index=20&type=chunk)[180](index=180&type=chunk) - Research and development expenses increased by **$0.8 million** (3 months) and **$9.2 million** (9 months) year-over-year, primarily due to clinical advancements in the olinciguat and IW-6463 programs[20](index=20&type=chunk)[181](index=181&type=chunk)[182](index=182&type=chunk) [Condensed Consolidated and Combined Statements of Stockholders' Equity (Deficit)](index=8&type=section&id=Condensed%20Consolidated%20and%20Combined%20Statements%20of%20Stockholders%27%20Equity%20(Deficit)) This section details changes in the company's equity, including common shares, paid-in capital, and accumulated deficit, reflecting ownership structure and retained earnings Condensed Consolidated and Combined Statements of Stockholders' Equity (Deficit) (in thousands) | Metric | Sep 30, 2019 | Dec 31, 2018 | | :---------------------------------------------------------------------------------------------------------------------------- | :----------- | :----------- | | Common Shares Outstanding | 27,468 | — | | Net Parent Company Investment | $— | $(10,445) | | Paid-in capital | $178,768 | $— | | Accumulated deficit | $(59,572) | $— | | Total Stockholders' equity (deficit) | $119,197 | $(10,445) | - The company's net parent investment balance was reclassified to paid-in capital as a result of the Separation[23](index=23&type=chunk)[42](index=42&type=chunk) - The issuance of **11,817,165 shares** of common stock from a private placement contributed **$164.6 million** to paid-in capital[23](index=23&type=chunk) [Condensed Consolidated and Combined Statements of Cash Flows](index=9&type=section&id=Condensed%20Consolidated%20and%20Combined%20Statements%20of%20Cash%20Flows) This section reports the cash inflows and outflows from operating, investing, and financing activities, illustrating the company's liquidity and solvency Condensed Consolidated and Combined Statements of Cash Flows (in thousands) | Metric | 9 Months Ended Sep 30, 2019 | 9 Months Ended Sep 30, 2018 | Change | % Change | | :---------------------------------------------------- | :-------------------------- | :-------------------------- | :----- | :------- | | Net cash used in operating activities | $(80,052) | $(74,351) | $(5,701) | 8% | | Net cash used in investing activities | $(6,615) | $(1,622) | $(4,993) | 308% | | Net cash provided by financing activities | $211,426 | $75,973 | $135,453 | 178% | | Net increase in cash, cash equivalents and restricted cash | $124,760 | $— | $124,760 | — | | Cash, cash equivalents and restricted cash, end of period | $124,760 | $— | $124,760 | — | - Net cash provided by financing activities increased significantly by **$135.5 million** year-over-year, primarily due to **$164.6 million** in net proceeds from a private placement and **$46.4 million** in transfers from Ironwood[27](index=27&type=chunk)[197](index=197&type=chunk) - Net cash used in operating activities increased by **$5.7 million** year-over-year, mainly due to the net loss and changes in working capital[27](index=27&type=chunk)[193](index=193&type=chunk) [Notes to the Condensed Consolidated and Combined Financial Statements](index=10&type=section&id=Notes%20to%20the%20Condensed%20Consolidated%20and%20Combined%20Financial%20Statements) This section provides detailed explanations and additional information supporting the condensed consolidated and combined financial statements, clarifying accounting policies and specific line items [Note 1. Nature of Business](index=10&type=section&id=Note%201.%20Nature%20of%20Business) This note describes Cyclerion Therapeutics, Inc.'s core business as a clinical-stage biopharmaceutical company, its separation from Ironwood, and the basis of its financial statement preparation - Cyclerion Therapeutics, Inc. is a clinical-stage biopharmaceutical company focused on soluble guanylate cyclase (sGC) pharmacology for serious and orphan diseases[29](index=29&type=chunk)[145](index=145&type=chunk) - The company completed its separation from Ironwood Pharmaceuticals, Inc. on **April 1, 2019**, becoming an independent public company trading under 'CYCN' on Nasdaq[31](index=31&type=chunk)[147](index=147&type=chunk) - On **April 2, 2019**, Cyclerion issued **11,817,165 shares** of common stock to accredited investors for gross proceeds of **$175 million** (net proceeds of approximately **$165 million**)[34](index=34&type=chunk)[150](index=150&type=chunk) - The financial statements are prepared on a 'carve out' basis for periods prior to the Separation and consolidated for periods after **April 1, 2019**[35](index=35&type=chunk)[38](index=38&type=chunk) - Management concluded that there is no substantial doubt about the company's ability to continue as a going concern within one year from the financial statement issuance date, considering existing cash and development plans[45](index=45&type=chunk) [Note 2. Summary of Significant Accounting Policies](index=12&type=section&id=Note%202.%20Summary%20of%20Significant%20Accounting%20Policies) This note outlines the key accounting principles and estimation methods used in preparing the financial statements, including revenue recognition, R&D costs, and lease accounting - The company operates in one reportable business segment: human therapeutics[48](index=48&type=chunk)[146](index=146&type=chunk) - Significant estimates and assumptions include allocations from Ironwood, impairment of long-lived assets, income taxes, R&D expenses, contingencies, and share-based compensation[49](index=49&type=chunk)[174](index=174&type=chunk) - Effective **January 1, 2019**, the company adopted ASC Topic 842, Leases, which had a material impact on the financial statements by requiring recognition of right-of-use assets and lease liabilities[58](index=58&type=chunk)[59](index=59&type=chunk)[75](index=75&type=chunk) - Revenue is generated from a development agreement with Ironwood for research and development services, recognized in accordance with ASC Topic 606[63](index=63&type=chunk)[66](index=66&type=chunk) - Research and development costs are expensed as incurred, while nonrefundable advance payments are deferred and capitalized until related goods are received or services performed[67](index=67&type=chunk)[178](index=178&type=chunk) [Note 3. Related Party - Agreements and Transactions with Ironwood](index=16&type=section&id=Note%203.%20Related%20Party%20-%20Agreements%20and%20Transactions%20with%20Ironwood) This note details the company's agreements and transactions with Ironwood Pharmaceuticals, including corporate cost allocations and post-separation service arrangements - Ironwood became a related party after Cyclerion's President joined Ironwood's board in **April 2019**[83](index=83&type=chunk) - Prior to separation, Ironwood allocated corporate costs (e.g., IT, accounting, HR, legal) to Cyclerion, totaling approximately **$6.8 million** for the three months ended **March 31, 2019**, and **$18.3 million** for the nine months ended **September 30, 2018**[85](index=85&type=chunk)[86](index=86&type=chunk)[87](index=87&type=chunk) - Cyclerion entered into transition services agreements and a development agreement with Ironwood post-separation, providing R&D services to Ironwood for which it recorded **$1.4 million** and **$3.0 million** in revenue for the three and six months ended **September 30, 2019**, respectively[89](index=89&type=chunk)[93](index=93&type=chunk) - As of **September 30, 2019**, approximately **$1.4 million** was due from Ironwood (related party accounts receivable) and **$0.2 million** was due to Ironwood (related party accounts payable)[94](index=94&type=chunk) [Note 4. Fair Value of Financial Instruments](index=17&type=section&id=Note%204.%20Fair%20Value%20of%20Financial%20Instruments) This note describes the fair value measurement of the company's financial instruments, primarily cash equivalents, categorized by the fair value hierarchy Fair Value of Cash Equivalents (in thousands) as of September 30, 2019 | Asset Type | Level 1 | Level 2 | Level 3 | Total | | :----------------- | :------ | :------ | :------ | :------ | | Money market funds | $20,958 | $— | $— | $20,958 | | Repurchase Agreements | $92,506 | $— | $— | $92,506 | | **Total** | **$113,464** | **$—** | **$—** | **$113,464** | - The company's cash equivalents are primarily classified within **Level 1** of the fair value hierarchy, indicating quoted prices in active markets for identical assets[97](index=97&type=chunk)[50](index=50&type=chunk) [Note 5. Property and Equipment](index=18&type=section&id=Note%205.%20Property%20and%20Equipment) This note provides a breakdown of the company's property and equipment, net of accumulated depreciation, and details changes over the reporting periods Property and Equipment, Net (in thousands) | Asset Type | Sep 30, 2019 | Dec 31, 2018 | | :----------------------------------- | :----------- | :----------- | | Laboratory equipment | $16,297 | $17,753 | | Software | $2,232 | $2,593 | | Construction in progress | $33 | $741 | | Computer and office equipment | $1,890 | $901 | | Leasehold improvements | $22,624 | $0 | | Gross property and equipment | $43,076 | $21,988 | | Less: accumulated depreciation and amortization | $(30,962) | $(15,491) | | **Property and equipment, net** | **$12,114** | **$6,497** | - Gross property and equipment increased significantly from **$22.0 million** at December 31, 2018, to **$43.1 million** at September 30, 2019, primarily due to **$22.6 million** in leasehold improvements[98](index=98&type=chunk) - Depreciation and amortization expense for the nine months ended September 30, 2019, was approximately **$2.0 million**, up from **$1.1 million** in the prior year period[99](index=99&type=chunk) [Note 6. Accrued Expenses and Other Current Liabilities](index=18&type=section&id=Note%206.%20Accrued%20Expenses%20and%20Other%20Current%20Liabilities) This note details the composition of the company's accrued expenses and other current liabilities, highlighting changes in key categories Accrued Expenses (in thousands) | Expense Type | Sep 30, 2019 | Dec 31, 2018 | | :----------------------------------- | :----------- | :----------- | | Accrued incentive compensation | $3,419 | $4,889 | | Salaries | $1,687 | $1,513 | | Accrued vacation | $1,271 | $1,048 | | Professional fees | $885 | $1,019 | | Workforce reduction charges | $— | $565 | | Other | $36 | $770 | | **Total** | **$7,298** | **$9,804** | - Total accrued expenses and other current liabilities decreased by **$2.5 million** from December 31, 2018, to September 30, 2019, primarily due to reductions in accrued incentive compensation and the elimination of workforce reduction charges[100](index=100&type=chunk) [Note 7. Commitments and Contingencies](index=18&type=section&id=Note%207.%20Commitments%20and%20Contingencies) This note describes the company's contractual commitments, particularly with CROs, and potential contingent liabilities such as indemnification obligations - The company's most significant clinical trial expenditures are with contract research organizations (CROs), and these contracts are generally cancellable with notice and no significant penalties[101](index=101&type=chunk)[207](index=207&type=chunk) - The company indemnifies its officers and directors, as well as business partners, contractors, clinical sites, and customers; while the maximum potential amount is unlimited, no material costs have been incurred to date, and the estimated fair value of these obligations is minimal[102](index=102&type=chunk)[104](index=104&type=chunk) [Note 8. Leases](index=19&type=section&id=Note%208.%20Leases) This note details the company's lease arrangements, including its headquarters lease, the recognition of right-of-use assets and lease liabilities, and future minimum lease payments - On **April 1, 2019**, Cyclerion entered into a direct operating lease (HQ Lease) for its **114,000 square feet** headquarters in Cambridge, MA, for a term of **123 months**[106](index=106&type=chunk) - The HQ Lease includes a **$7.7 million** letter of credit as a security deposit, collateralized by restricted cash[106](index=106&type=chunk) - The company recorded a lease liability of **$71.3 million** and a right-of-use asset of **$71.3 million** on **April 1, 2019**, using an estimated incremental borrowing rate of **10.9%**[108](index=108&type=chunk)[110](index=110&type=chunk) Future Minimum Lease Payments (in thousands) as of September 30, 2019 | Year | Operating lease payments | | :----------------------------------- | :----------------------- | | 2019 (remaining three months) | $2,743 | | 2020 | $11,212 | | 2021 | $11,537 | | 2022 | $11,872 | | 2023 | $12,217 | | 2024 and hereafter | $73,847 | | **Total future minimum lease payments** | **$123,428** | | Less: present value adjustment | $48,767 | | **Operating lease liabilities at September 30, 2019** | **$74,661** | | Less: current portion of operating lease liabilities | $3,250 | | **Operating lease liabilities, net of current portion** | **$71,411** | [Note 9. Share-based Compensation Plans](index=20&type=section&id=Note%209.%20Share-based%20Compensation%20Plans) This note describes the company's share-based compensation plans, including the impact of the separation from Ironwood on equity awards and the associated compensation expense - Cyclerion adopted its own share-based compensation plans (2019 ESPP and 2019 Equity Plan) and mirrored Ironwood's plans (2005 Equity Plan and 2010 Equity Plan) in connection with the Separation[116](index=116&type=chunk)[117](index=117&type=chunk) - The conversion of Ironwood equity awards to Cyclerion awards upon separation resulted in a one-time incremental expense of approximately **$0.3 million** for vested stock options and an expected **$7.5 million** for unvested stock options[120](index=120&type=chunk) Share-based Compensation Expense (in thousands) | Category | 3 Months Ended Sep 30, 2019 | 3 Months Ended Sep 30, 2018 | 9 Months Ended Sep 30, 2019 | 9 Months Ended Sep 30, 2018 | | :----------------------------------- | :-------------------------- | :-------------------------- | :-------------------------- | :-------------------------- | | Research and development | $2,192 | $1,796 | $6,774 | $5,350 | | General and administrative | $2,756 | $1,515 | $8,386 | $3,474 | | **Total** | **$4,948** | **$3,311** | **$15,160** | **$8,824** | - As of **September 30, 2019**, unrecognized share-based compensation expense for unvested stock options was **$29.4 million** (over **2.79 years**) and for unvested restricted stock units was **$8.4 million** (over **2.8 years**)[124](index=124&type=chunk)[127](index=127&type=chunk) [Note 10. Loss per share](index=23&type=section&id=Note%2010.%20Loss%20per%20share) This note presents the calculation of basic and diluted net loss per share, detailing the net loss and weighted average common shares outstanding Loss Per Share (in thousands, except per share data) | Metric | 3 Months Ended Sep 30, 2019 | 3 Months Ended Sep 30, 2018 | 9 Months Ended Sep 30, 2019 | 9 Months Ended Sep 30, 2018 | | :---------------------------------------------------------------- | :-------------------------- | :-------------------------- | :-------------------------- | :-------------------------- | | Net loss | $(27,317) | $(29,286) | $(96,953) | $(84,350) | | Weighted average number of common shares outstanding | 27,434 | 27,380 | 27,380 | 27,380 | | Basic and diluted net loss per share | $(1.00) | $(1.07) | $(3.54) | $(3.08) | - Common stock equivalents (**6.9 million** stock options and **0.9 million** restricted stock units) were excluded from the calculation of diluted loss per share because their inclusion would have been anti-dilutive[132](index=132&type=chunk) [Note 11. Defined Contribution Plan](index=24&type=section&id=Note%2011.%20Defined%20Contribution%20Plan) This note describes the company's 401(k) Savings Plan, including its matching contribution policy and the associated compensation expense - Subsequent to the Separation, Cyclerion adopted a defined contribution 401(k) Savings Plan, providing a matching contribution of **75%** of employee contributions, up to **$6,000** annually[134](index=134&type=chunk) - Compensation expense for the 401(k) match was approximately **$0.1 million** for the three months and **$0.5 million** for the nine months ended September 30, 2019[135](index=135&type=chunk) [Note 12. Ironwood Workforce Reduction](index=24&type=section&id=Note%2012.%20Ironwood%20Workforce%20Reduction) This note details the workforce reductions initiated by Ironwood, the allocation of associated charges to Cyclerion prior to separation, and the subsequent transfer of liabilities - Ironwood initiated workforce reductions in **June 2018** and **February 2019**; certain associated charges were allocated to Cyclerion prior to the separation[136](index=136&type=chunk)[137](index=137&type=chunk) - Pursuant to the Separation Agreement, the accrued liability related to these workforce reductions remained with Ironwood[138](index=138&type=chunk) Accrued Liabilities Activity for Workforce Reduction (in thousands) | Reduction | Accrued at Dec 31, 2018 | Charges | Amount Paid | Assumed by Ironwood | Accrued at Sep 30, 2019 | | :-------------------- | :---------------------- | :------ | :---------- | :------------------ | :---------------------- | | June 2018 Reduction | $565 | $— | $(268) | $(297) | $— | | February 2019 Reduction | $— | $580 | $(90) | $(490) | $— | | **Total** | **$565** | **$580** | **$(358)** | **$(787)** | **$—** | [Note 13. Subsequent Events](index=24&type=section&id=Note%2013.%20Subsequent%20Events) This note discloses significant events occurring after the reporting period, including a sublease agreement and a company-initiated workforce reduction - On **October 18, 2019**, the company entered into an agreement to sublease approximately **16,000 square feet** of lab space to a third party, with annual base rent of approximately **$1.5 million**[139](index=139&type=chunk) - On **October 30, 2019**, the company began a workforce reduction of approximately **30 full-time employees**, expecting to incur charges of approximately **$3.0 million** for severance and benefit costs, primarily in **Q4 2019**[140](index=140&type=chunk) [Item 2. Management's Discussion and Analysis of Financial Condition and Results of Operations](index=25&type=section&id=Item%202.%20Management%27s%20Discussion%20and%20Analysis%20of%20Financial%20Condition%20and%20Results%20of%20Operations) This section provides management's perspective on Cyclerion's financial condition and operational results, covering its business overview, separation from Ironwood, key financial items, liquidity, and funding requirements [Overview](index=25&type=section&id=Overview) This section provides a high-level summary of Cyclerion's business as a clinical-stage biopharmaceutical company focused on sGC pharmacology for serious and orphan diseases - Cyclerion is a clinical-stage biopharmaceutical company focused on sGC pharmacology to develop treatments for serious and orphan diseases[145](index=145&type=chunk) - The company operates in one reportable business segment: human therapeutics[146](index=146&type=chunk) [Separation from Ironwood Pharmaceuticals](index=25&type=section&id=Separation%20from%20Ironwood%20Pharmaceuticals) This section discusses the company's separation from Ironwood, its transition to an independent public entity, and the impact on historical financial reporting - The separation from Ironwood was completed on **April 1, 2019**, making Cyclerion an independent public company[147](index=147&type=chunk) - A private placement on **April 2, 2019**, resulted in gross proceeds of **$175 million** (net **$165 million**) from the issuance of **11,817,165 shares** of common stock[150](index=150&type=chunk) - Historical combined financial statements, derived from Ironwood's records, may not be indicative of Cyclerion's future standalone performance[152](index=152&type=chunk) [Financial Overview](index=26&type=section&id=Financial%20Overview) This section outlines the company's R&D strategy, provides updates on its product candidates (olinciguat, praliciguat, IW-6463), and summarizes research and development expenses - The core R&D strategy is to develop sGC pharmacology therapies for serious and orphan diseases[155](index=155&type=chunk) - Olinciguat, for sickle cell disease (SCD), is in a **Phase 2** study (STRONG-SCD) with topline data expected in **mid-2020**; it received Orphan Drug Designation in **June 2018**[155](index=155&type=chunk)[156](index=156&type=chunk) - Praliciguat's **Phase 2** studies in diabetic nephropathy and HFpEF did not meet statistical significance on primary endpoints; development in HFpEF is discontinued, and the company intends to out-license praliciguat for diabetic nephropathy[158](index=158&type=chunk)[159](index=159&type=chunk)[160](index=160&type=chunk) - IW-6463, a CNS-penetrant sGC stimulator for neurodegenerative diseases, initiated its first-in-human study in **January 2019**, with topline data expected in **Q4 2019**[161](index=161&type=chunk) Research and Development Expenses (in thousands) | Category | 3 Months Ended Sep 30, 2019 | 3 Months Ended Sep 30, 2018 | 9 Months Ended Sep 30, 2019 | 9 Months Ended Sep 30, 2018 | | :----------------------------------- | :-------------------------- | :-------------------------- | :-------------------------- | :-------------------------- | | Praliciguat | $2,575 | $4,396 | $12,102 | $12,391 | | Olinciguat | $2,891 | $1,651 | $10,794 | $4,887 | | IW-6463 | $1,559 | $740 | $3,797 | $2,157 | | Discovery research | $364 | $693 | $999 | $1,652 | | Total product pipeline external costs | $7,389 | $7,480 | $27,692 | $21,087 | | Personnel and related internal costs | $9,517 | $8,818 | $29,540 | $27,936 | | Facilities and other | $5,389 | $5,201 | $17,226 | $16,241 | | **Total R&D expenses** | **$22,295** | **$21,499** | **$74,458** | **$65,264** | [Critical Accounting Policies and Estimates](index=27&type=section&id=Critical%20Accounting%20Policies%20and%20Estimates) This section highlights the significant judgments and estimates involved in the company's financial reporting, including those for long-lived assets, income taxes, and R&D expenses - Significant judgments and estimates are required for impairment of long-lived assets, income taxes (including valuation allowance), research and development expenses, contingencies, and share-based compensation[174](index=174&type=chunk) - Research and development expenses are expensed as incurred, with nonrefundable advance payments deferred and capitalized until related goods or services are received[178](index=178&type=chunk) [Results of Operations](index=28&type=section&id=Results%20of%20Operations) This section analyzes the company's financial performance, detailing changes in revenue, research and development expenses, general and administrative expenses, and net loss over the reporting periods Summary of Operations (in thousands) | Metric | 3 Months Ended Sep 30, 2019 | 3 Months Ended Sep 30, 2018 | 9 Months Ended Sep 30, 2019 | 9 Months Ended Sep 30, 2018 | | :----------------------------------- | :-------------------------- | :-------------------------- | :-------------------------- | :-------------------------- | | Revenue from related party | $1,398 | $— | $3,026 | $— | | Research and development | $22,295 | $21,499 | $74,458 | $65,264 | | General and administrative | $7,119 | $7,787 | $27,019 | $19,086 | | Total cost and expenses | $29,414 | $29,286 | $101,477 | $84,350 | | Loss from operations | $(28,016) | $(29,286) | $(98,451) | $(84,350) | | Interest and investment income | $699 | $— | $1,498 | $— | | Net Loss | $(27,317) | $(29,286) | $(96,953) | $(84,350) | - Revenue from related party increased due to services performed under the development agreement with Ironwood[180](index=180&type=chunk) - Research and development expense increased by **$0.8 million** for the three months and **$9.2 million** for the nine months ended September 30, 2019, primarily due to increased employee-related expenses and external research costs for olinciguat and IW-6463[181](index=181&type=chunk)[182](index=182&type=chunk) - General and administrative expenses decreased by **$0.7 million** for the three months but increased by **$7.9 million** for the nine months ended September 30, 2019, influenced by non-recurring separation costs and higher stock-based compensation[185](index=185&type=chunk)[186](index=186&type=chunk) [Liquidity and Capital Resources](index=29&type=section&id=Liquidity%20and%20Capital%20Resources) This section discusses the company's cash position, sources of funding, and cash flow activities, highlighting the impact of the private placement and separation from Ironwood - Post-separation, the company raised approximately **$165 million** net from a private placement on **April 2, 2019**[188](index=188&type=chunk) - As of **September 30, 2019**, the company had approximately **$117.0 million** in unrestricted cash and cash equivalents[189](index=189&type=chunk) Cash Flow Summary (in thousands) | Metric | 9 Months Ended Sep 30, 2019 | 9 Months Ended Sep 30, 2018 | Change | % Change | | :---------------------------------------------------- | :-------------------------- | :-------------------------- | :----- | :------- | | Net cash used in operating activities | $(80,052) | $(74,351) | $(5,701) | 8% | | Net cash used in investing activities | $(6,615) | $(1,622) | $(4,993) | 308% | | Net cash provided by financing activities | $211,426 | $75,973 | $135,453 | 178% | - Net cash provided by financing activities increased by **$135.5 million** year-over-year, primarily from the private placement proceeds and transfers from Ironwood[197](index=197&type=chunk) [Funding Requirements](index=30&type=section&id=Funding%20Requirements) This section outlines the company's projected funding needs, expected cash runway, and potential future financing sources, acknowledging the inherent uncertainties in pharmaceutical development - Existing cash, cash equivalents, and restricted cash are expected to fund operating expenses and capital expenditures through at least the **first quarter of 2021**[191](index=191&type=chunk)[200](index=200&type=chunk) - Future expenses are expected to increase due to advancing preclinical/clinical trials, seeking regulatory approvals, potential hiring, enhancing systems, and maintaining intellectual property[198](index=198&type=chunk) - Future funding requirements are uncertain due to the inherent risks and complexities of pharmaceutical product development, regulatory review, and commercialization[201](index=201&type=chunk) - Potential future funding sources include equity offerings, debt financings, collaborations, strategic alliances, or licensing arrangements, with potential dilution or restrictive covenants[203](index=203&type=chunk)[204](index=204&type=chunk) [Contractual Commitments and Obligations](index=31&type=section&id=Contractual%20Commitments%20and%20Obligations) This section addresses the company's contractual obligations, including clinical trial expenditures with CROs and the treatment of uncertain tax positions - The company excludes uncertain tax positions from contractual commitments as reliable estimates of cash settlement periods cannot be made; no uncertain tax positions existed as of **September 30, 2019**[206](index=206&type=chunk) - Ongoing clinical trial studies involve commitments with CROs, but these contracts are generally cancellable with notice and do not have significant cancellation penalties[207](index=207&type=chunk) [Transition from Ironwood and Costs to Operate as an Independent Company](index=33&type=section&id=Transition%20from%20Ironwood%20and%20Costs%20to%20Operate%20as%20an%20Independent%20Company) This section discusses the additional operating expenses and capital expenditures incurred as Cyclerion transitions to an independent public company, including reliance on transition services from Ironwood - As an independent public company, Cyclerion has incurred additional ongoing operating expenses for corporate functions, IT, accounting, legal, HR, and other administrative functions[209](index=209&type=chunk) - The company entered into a transition services agreement with Ironwood to provide certain corporate services for up to **two years**, aiding in establishing standalone infrastructure[211](index=211&type=chunk) - Non-recurring expenses and capital expenditures are being incurred to establish independent information technology systems and expand infrastructure[210](index=210&type=chunk)[211](index=211&type=chunk) [Transactions with Related and Certain Other Parties](index=33&type=section&id=Transactions%20with%20Related%20and%20Certain%20Other%20Parties) This section lists the various agreements Cyclerion entered into with Ironwood concurrently with the Separation, governing ongoing relationships and responsibilities - Concurrently with the Separation, Cyclerion entered into various agreements with Ironwood, including a separation agreement, two transition services agreements, a development agreement, a tax matters agreement, an intellectual property license agreement, and an employee matters agreement[213](index=213&type=chunk) [Off-Balance Sheet Arrangements](index=33&type=section&id=Off-Balance%20Sheet%20Arrangements) This section confirms that the company does not have significant off-balance sheet arrangements with unconsolidated entities or financial partnerships - The company does not have relationships with unconsolidated entities or financial partnerships for off-balance sheet arrangements[214](index=214&type=chunk) - Guarantees are entered into in the ordinary course of business related to the company's own performance[214](index=214&type=chunk) [New Accounting Pronouncements](index=33&type=section&id=New%20Accounting%20Pronouncements) This section directs readers to Note 2 for a detailed discussion of new accounting pronouncements and their impact on the financial statements - For a discussion of new accounting pronouncements, refer to **Note 2, Summary of Significant Accounting Policies**, in the condensed consolidated and combined financial statements[215](index=215&type=chunk) [Item 3. Quantitative and Qualitative Disclosures About Market Risk](index=33&type=section&id=Item%203.%20Quantitative%20and%20Qualitative%20Disclosures%20About%20Market%20Risk) This section assesses the company's exposure to market risks, primarily interest rate risk and foreign currency risk. It concludes that due to the short-term nature and low-risk profile of its investments, interest rate changes would not materially affect its financial position, and foreign currency exposure is not material [Interest Rate Risk](index=33&type=section&id=Interest%20Rate%20Risk) This section evaluates the company's exposure to interest rate fluctuations, primarily through its short-term investments, and assesses the potential impact on its financial position - The company is exposed to market risk related to changes in interest rates, primarily through its investments in money market instruments and overnight repurchase agreements[216](index=216&type=chunk) - Due to the short-term duration and low-risk profile of its investment portfolio, an immediate **1%** change in interest rates would not have a material effect on the fair market value of the portfolio[217](index=217&type=chunk) - The company maintains significant cash and cash equivalents at financial institutions in excess of federally insured limits, which presents a risk of loss[219](index=219&type=chunk) [Foreign Currency Risk](index=34&type=section&id=Foreign%20Currency%20Risk) This section assesses the company's exposure to foreign currency exchange rate fluctuations from its international operations, concluding that the risk is not material - The company has operations in Switzerland and conducts other business that may be subject to foreign currency exchange rate fluctuations[220](index=220&type=chunk) - Management does not believe the company is materially exposed to market risk related to changes in foreign currency exchange rates[220](index=220&type=chunk) [Effects of Inflation](index=34&type=section&id=Effects%20of%20Inflation) This section concludes that inflation and changing prices did not significantly impact the company's results of operations during the reported periods - The company does not believe that inflation and changing prices had a significant impact on its results of operations during the three and nine months ended **September 30, 2019**[221](index=221&type=chunk) [Item 4. Controls and Procedures](index=34&type=section&id=Item%204.%20Controls%20and%20Procedures) This section details management's evaluation of disclosure controls and procedures, concluding their effectiveness. It also outlines the company's status as an emerging growth company (EGC) and smaller reporting company (SRC) and its compliance roadmap for Section 404 of the Sarbanes-Oxley Act [Evaluation of Disclosure Controls and Procedures](index=34&type=section&id=Evaluation%20of%20Disclosure%20Controls%20and%20Procedures) This section confirms management's conclusion that the company's disclosure controls and procedures were effective at a reasonable assurance level as of the reporting date - Management, including the principal executive officer and principal financial officer, concluded that the company's disclosure controls and procedures were effective at the reasonable assurance level as of **September 30, 2019**[222](index=222&type=chunk) [Changes in Internal Control](index=34&type=section&id=Changes%20in%20Internal%20Control) This section addresses the company's new obligations under Section 404 of the Sarbanes-Oxley Act post-separation and its exemptions as an Emerging Growth Company and Smaller Reporting Company - The company is now subject to **Section 404** of the Sarbanes-Oxley Act post-separation[223](index=223&type=chunk) - As an Emerging Growth Company (EGC) and Smaller Reporting Company (SRC), Cyclerion is exempt from **Section 404(b)** (auditor attestation) but is subject to **Section 404(a)** (management assessment) starting **December 31, 2020**[223](index=223&type=chunk) [PART II — OTHER INFORMATION](index=34&type=section&id=PART%20II%20%E2%80%94%20OTHER%20INFORMATION) This part covers legal proceedings, risk factors, and exhibits, providing additional context beyond the financial statements [Item 1. Legal Proceedings](index=34&type=section&id=Item%201.%20Legal%20Proceedings) This section states that the company is not currently involved in any pending or threatened legal proceedings that are expected to have a material adverse effect on its business or financial results - The company is not currently subject to any pending or threatened litigation that is reasonably expected to have a material adverse effect on its business or financial results[224](index=224&type=chunk) [Item 1A. Risk Factors](index=34&type=section&id=Item%201A.%20Risk%20Factors) This section highlights updated risk factors, emphasizing the challenges in out-licensing praliciguat for diabetic nephropathy, the volatility of the company's stock price following recent clinical trial results, and the inherent risks of biopharmaceutical product development and collaborations - There is no certainty that Cyclerion will find a commercial or financial partner to fund and undertake further development and commercialization of praliciguat for diabetic nephropathy; failure to do so could materially adversely affect financial condition[226](index=226&type=chunk)[227](index=227&type=chunk)[229](index=229&type=chunk) - The market price for Cyclerion's common stock is particularly volatile, influenced by its short operating history, lack of revenues, and the uncertain success of its product candidates[230](index=230&type=chunk) - Topline results from **Phase 2** trials of praliciguat in diabetic nephropathy and HFpEF did not meet statistical significance on primary endpoints, leading to a substantial decrease in stock price[230](index=230&type=chunk) - Topline data are preliminary and subject to change after comprehensive review; third parties, including regulatory agencies and potential licensees, may interpret data differently, potentially harming approval or out-licensing efforts[231](index=231&type=chunk)[232](index=232&type=chunk) - Biopharmaceutical product development is inherently risky, with potential for substantial delays, failure to achieve statistical significance, or inability to demonstrate safety and efficacy to regulatory authorities[233](index=233&type=chunk)[235](index=235&type=chunk) - Future collaboration or license arrangements may not be successful, depending heavily on partner efforts, resource commitment, intellectual property protection, and potential termination, which could impede development and commercialization[237](index=237&type=chunk)[238](index=238&type=chunk)[239](index=239&type=chunk) [Item 6. Exhibits](index=37&type=section&id=Item%206.%20Exhibits) This section provides an index of exhibits filed with the Form 10-Q, including executive severance plans, certifications from principal officers, and XBRL documents - The Exhibit Index lists various documents, including the Cyclerion Therapeutics, Inc. Executive Severance Plan (**Exhibit 10.1+**), Certifications of Principal Executive Officer and Principal Financial Officer (**Exhibits 31.1***, **31.2***, **32.1***, **32.2***), and XBRL Instance, Schema, Calculation, Definition, Label, and Presentation Linkbase Documents (**Exhibits 101.INS** to **101.PRE**)[243](index=243&type=chunk) - Certifications furnished in **Exhibit 32.1** and **Exhibit 32.2** are deemed to accompany the report but are not considered 'filed' for purposes of **Section 18** of the Securities Exchange Act of 1934, unless specifically incorporated by reference[243](index=243&type=chunk) [Signatures](index=39&type=section&id=Signatures) This section contains the required signatures for the Form 10-Q, confirming that the report has been duly authorized and signed on behalf of Cyclerion Therapeutics, Inc. by its Chief Executive Officer and Chief Financial Officer - The report was signed by **Peter M. Hecht**, Chief Executive Officer (Principal Executive Officer), and **William Huyett**, Chief Financial Officer (Principal Financial and Accounting Officer)[248](index=248&type=chunk) - The signing date for the report was **November 12, 2019**[248](index=248&type=chunk)

Table of Contents Title of each class Trading Symbol(s) Name of each exchange on which registered Common Stock, no par value CYCN The Nasdaq Stock Market LLC (Nasdaq Global Select Market) UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) x QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended June 30, 2019 or o TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 Fo ...

Table of Contents UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 FORM 10-Q (Mark One) x QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended March 31, 2019 or o TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from to Commission File Number 001-38787 CYCLERION THERAPEUTICS, INC. (Exact Name of Registrant as Specified in its Charter) Massachusetts (State ...