Denali Therapeutics Inc. 10-Q

ITEM 1. FINANCIAL STATEMENTS Denali Therapeutics Inc. Condensed Consolidated Balance Sheets (Unaudited) (In thousands, except share amounts) September 30, 2024 December 31, 2023 Assets Current assets: Cash and cash equivalents $ 90,636 $ 127,106 Short-term marketable securities 745,923 907,405 Prepaid expenses and other current assets 32,280 29,626 Total current assets 868,839 1,064,137 Long-term marketable securities 445,463 — Property and equipment, net 50,822 45,589 Operating lease right-of-use asset 23,717 26,048 Finance lease right-of-use asset 38,685 — Other non-current assets 26,487 18,143 Total assets $ 1,454,013 $ 1,153,917 Liabilities and stockholders' equity Current liabilities: Accounts payable $ 9,594 $ 9,483 Accrued clinical and other research and development costs 23,923 19,035 Accrued manufacturing costs 9,568 15,462 Accrued compensation 14,874 21,590 Operating lease liability, current 8,036 7,260 Deferred research and development funding liability, current 16,269 — Other accrued costs and current liabilities 4,829 5,152 Total current liabilities 87,093 77,982 Operating lease liability, less current portion 38,850 44,981 Finance lease liability, less current portion 5,631 — Deferred research funding and development liability, less current portion 3,944 — Total liabilities 135,518 122,963 Commitments and contingencies (Note 6) Stockholders' equity: Convertible preferred stock, $ 0.01 par value; 40,000,000 shares authorized as of September 30, 2024 and December 31, 2023; 0 shares issued and outstanding as of September 30, 2024 and December 31, 2023 — — Common stock, $ 0.01 par value; 400,000,000 shares authorized as of September 30, 2024 and December 31, 2023; 143,840,029 shares and 138,385,498 shares issued and outstanding as of September 30, 2024 and December 31, 2023, respectively 1,764 1,711 Additional paid-in capital 2,735,433 2,144,811 Accumulated other comprehensive income 5,529 643 Accumulated deficit ( 1,424,231 ) ( 1,116,211 ) Total stockholders' equity 1,318,495 1,030,954 Total liabilities and stockholders’ equity $ 1,454,013 $ 1,153,917 See accompanying notes to unaudited condensed consolidated financial statements. 3 Table of Contents Denali Therapeutics Inc. Condensed Consolidated Statements of Operations and Comprehensive Loss (Unaudited) (In thousands, except share and per share amounts) Three Months Ended September 30, Nine Months Ended September 30, 2024 2023 2024 2023 Collaboration revenue: Collaboration revenue from customers (1) $ — $ 1,267 $ — $ 330,531 Total collaboration revenue — 1,267 — 330,531 Operating expenses: Research and development (2) 98,238 89,737 296,653 316,073 General and administrative 24,949 25,325 75,379 78,585 Total operating expenses 123,187 115,062 372,032 394,658 Gain from divestiture of small molecule programs — — 14,537 — Loss from operations ( 123,187 ) ( 113,795 ) ( 357,495 ) ( 64,127 ) Interest and other income, net 15,995 14,442 49,475 38,376 Net loss ( 107,192 ) ( 99,353 ) ( 308,020 ) ( 25,751 ) Other comprehensive income (loss): Net unrealized gain on marketable securities, net of tax 8,188 790 4,886 6,235 Comprehensive loss $ ( 99,004 ) $ ( 98,563 ) $ ( 303,134 ) $ ( 19,516 ) Net loss per share, basic and diluted $ ( 0.63 ) $ ( 0.72 ) $ ( 1.89 ) $ ( 0.19 ) Weighted average number of shares outstanding, basic and diluted 169,456,988 137,644,534 162,589,325 137,076,199 __________________________________________________ (1) Includes related-party collaboration revenue from customers of $ 1.3 million and $ 295.5 million for the three and nine months ended September 30, 2023, respectively. (2) Includes expenses for cost sharing payments due to a related party of $ 3.4 million and $ 14.5 million for the three and nine months ended September 30, 2023, respectively. See accompanying notes to unaudited condensed consolidated financial statements. 4 Table of Contents Denali Therapeutics Inc. Condensed Consolidated Statements of Stockholders’ Equity (Unaudited) (In thousands, except share amounts) Common Stock Additional Paid-in Capital Accumulated Other Comprehensive Income (Loss) Accumulated Deficit Total Stockholders' Equity Shares Amount Balance at December 31, 2023 138,385,498 $ 1,711 $ 2,144,811 $ 643 $ ( 1,116,211 ) $ 1,030,954 Issuance of common stock and pre-funded warrants, net of issuance costs of $ 480 K 3,244,689 32 499,221 — — 499,253 Issuances under equity incentive plans 948,705 10 13,224 — — 13,234 Vesting of restricted stock units 1,261,137 11 ( 11 ) — — — Stock-based compensation — — 78,188 — — 78,188 Net loss — — — — ( 308,020 ) ( 308,020 ) Other comprehensive income — — — 4,886 — 4,886 Balance at September 30, 2024 143,840,029 $ 1,764 $ 2,735,433 $ 5,529 $ ( 1,424,231 ) $ 1,318,495 Balance at June 30, 2024 143,123,582 $ 1,757 $ 2,704,992 $ ( 2,659 ) $ ( 1,317,039 ) $ 1,387,051 Issuances under equity incentive plans 291,183 3 5,453 — — 5,456 Vesting of restricted stock units 425,264 4 ( 4 ) — — — Stock-based compensation — — 24,992 — — 24,992 Net loss — — — — ( 107,192 ) ( 107,192 ) Other comprehensive income — — — 8,188 — 8,188 Balance at September 30, 2024 143,840,029 $ 1,764 $ 2,735,433 $ 5,529 $ ( 1,424,231 ) $ 1,318,495 Balance at December 31, 2022 135,965,918 $ 1,686 $ 2,018,617 $ ( 6,886 ) $ ( 970,987 ) $ 1,042,430 Issuances under equity incentive plans 953,575 9 13,106 — — 13,115 Vesting of restricted stock units 1,132,305 12 ( 12 ) — — — Stock-based compensation — — 82,302 — — 82,302 Net loss — — — — ( 25,751 ) ( 25,751 ) Other comprehensive income — — — 6,235 — 6,235 Balance at September 30, 2023 138,051,798 $ 1,707 $ 2,114,013 $ ( 651 ) $ ( 996,738 ) $ 1,118,331 Balance at June 30, 2023 137,362,688 $ 1,700 $ 2,083,951 $ ( 1,441 ) $ ( 897,385 ) $ 1,186,825 Issuances under equity incentive plans 222,688 2 2,490 — — 2,492 Vesting of restricted stock units 466,422 5 ( 5 ) — — — Stock-based compensation — — 27,577 — — 27,577 Net loss — — — — ( 99,353 ) ( 99,353 ) Other comprehensive income — — — 790 — 790 Balance at September 30, 2023 138,051,798 $ 1,707 $ 2,114,013 $ ( 651 ) $ ( 996,738 ) $ 1,118,331 See accompanying notes to unaudited condensed consolidated financial statements. 5 Table of Contents Denali Therapeutics Inc. Condensed Consolidated Statements of Cash Flows (Unaudited) (In thousands) Nine Months Ended September 30, 2024 2023 Operating activities Net loss $ ( 308,020 ) $ ( 25,751 ) Adjustments to reconcile net loss to net cash used in operating activities: Depreciation and amortization 5,942 14,549 Stock–based compensation expense 77,800 82,114 Net accretion of discounts on marketable securities ( 28,952 ) ( 31,709 ) Non-cash adjustment to operating lease expense ( 3,025 ) ( 2,762 ) Right-of-use asset amortization for finance lease 431 — Non-cash gain from divestiture of small molecule programs ( 14,537 ) — Changes in operating assets and liabilities: Prepaid expenses and other current assets ( 2,625 ) 1,910 Other non-current assets ( 1,178 ) — Accounts payable 151 4,512 Accruals and other current liabilities 6,090 ( 11,665 ) Related-party contract liability — ( 290,532 ) Deferred research and development funding liability, less current portion 3,944 — Net cash used in operating activities ( 263,979 ) ( 259,334 ) Investing activities Purchases of marketable securities ( 1,056,263 ) ( 1,399,982 ) Maturities and sales of marketable securities 806,120 1,586,947 Purchases of property and equipment ( 10,820 ) ( 10,704 ) Net cash (used in) provided by investing activities ( 260,963 ) 176,261 Financing activities Proceeds from issuance of common stock and pre-funded warrants, net of issuance costs of $ 480 K 499,253 — Proceeds from exercise of awards under equity incentive plans 13,234 13,115 Payments for finance lease right-of-use asset ( 24,015 ) — Net cash provided by financing activities 488,472 13,115 Net decrease in cash, cash equivalents and restricted cash ( 36,470 ) ( 69,958 ) Cash, cash equivalents and restricted cash at beginning of period 128,681 219,544 Cash, cash equivalents and restricted cash at end of period $ 92,211 $ 149,586 Supplemental disclosures of cash flow information Increase in right-of-use asset due to lessor assets $ 7,051 $ — Non-cash recognition of new finance lease $ 5,689 $ — Cash paid for finance lease interest $ 121 $ — Cash paid during the period for income taxes $ — $ 4 Equity consideration received in the divestiture of small molecule programs (Note 10) $ 15,000 $ — Property and equipment purchases accrued but not yet paid $ 263 $ 6,230 See accompanying notes to unaudited condensed consolidated financial statements. 6 Table of Contents Denali Therapeutics Inc. Notes to Condensed Consolidated Financial Statements (Unaudited) 1. Significant Accounting Policies Organization and Description of Business Denali Therapeutics Inc. ("Denali" or the “Company”) is a biopharmaceutical company, incorporated in Delaware, that discovers and develops therapeutics to defeat neurodegenerative diseases and lysosomal storage diseases. The Company is headquartered in South San Francisco, California. Basis of Presentation The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with accounting principles generally accepted in the United States of America (“U.S. GAAP”) for interim financial information and the instructions to Form 10-Q and Article 10 of the Securities and Exchange Commission ("SEC") Regulation S-X for interim financial information. These unaudited condensed consolidated financial statements and notes should be read in conjunction with the audited consolidated financial statements and notes thereto contained in the Annual Report on Form 10-K for the year ended December 31, 2023, as filed with the SEC on February 28, 2024 (the "2023 Annual Report on Form 10-K"). The Condensed Consolidated Balance Sheet as of December 31, 2023 was derived from the audited annual consolidated financial statements as of and for the period then ended. Certain information and footnote disclosures typically included in the Company's annual consolidated financial statements have been condensed or omitted. The accompanying unaudited condensed consolidated financial statements reflect all adjustments that, in the opinion of management, are necessary for a fair statement of the results of the interim periods presented. All such adjustments are of a normal recurring nature except for the impacts of adopting new accounting standards, if any, discussed below. These interim financial results are not necessarily indicative of results expected for the full fiscal year or for any subsequent interim period. During the nine months ended September 30, 2024 the only material change to the Company's significant accounting and financial reporting policies from those reflected in the 2023 Annual Report on Form 10-K was the addition of accounting policies related to the finance lease included herein. For further information with regard to the remainder of the Company’s Significant Accounting Policies, please refer to Note 1, "Significant Accounting Policies," to the Company’s Consolidated Financial Statements included in the 2023 Annual Report on Form 10-K. Principles of Consolidation These unaudited condensed consolidated financial statements include the accounts of the Company and its wholly-owned subsidiaries. All intercompany balances and transactions have been eliminated in consolidation. For the Company and its subsidiaries, the functional currency has been determined to be U.S. dollars. Monetary assets and liabilities denominated in foreign currency are remeasured at period-end exchange rates, non-monetary assets and liabilities denominated in foreign currencies are remeasured at historical rates, and transactions in foreign currencies are remeasured at average exchange rates. Foreign currency gains and losses resulting from remeasurement are recognized in interest and other income, net in the Condensed Consolidated Statements of Operations and Comprehensive Loss. 7 Table of Contents Use of Estimates The preparation of financial statements in conformity with U.S. GAAP requires the Company to make certain estimates, judgments and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the condensed consolidated financial statements, as well as the reported amounts of expenses during the reporting period. Actual results could differ from those estimates, and such differences could be material to the Condensed Consolidated Balance Sheets and Condensed Consolidated Statements of Operations and Comprehensive Loss. Concentration of Credit Risk and Other Risks and Uncertainties Financial instruments that potentially subject the Company to significant concentrations of credit risk consist primarily of cash, cash equivalents, and marketable securities. Substantially all of the Company’s cash and cash equivalents are deposited in accounts with financial institutions that management believes are of high credit quality. Such deposits have and will continue to exceed federally insured limits. The Company maintains its cash with accredited financial institutions and accordingly, such funds are subject to minimal credit risk. The Company’s investment policy limits investments to certain types of securities issued by the U.S. government and its agencies, as well as institutions with investment-grade credit ratings and places restrictions on maturities and concentration by type and issuer. The Company is exposed to credit risk in the event of a default by the financial institutions holding its cash, cash equivalents and marketable securities and issuers of marketable securities to the extent recorded on the Condensed Consolidated Balance Sheets. As of September 30, 2024 and December 31, 2023, the Company had no off-balance sheet concentrations of credit risk. The Company is subject to a number of risks similar to other clinical-stage biopharmaceutical companies, including, but not limited to, the need to obtain adequate additional funding, possible failure of current or future preclinical testing or clinical trials, its reliance on third parties to conduct its clinical trials, the need to obtain regulatory and marketing approvals for its product candidates, competitors developing new technological innovations, the need to successfully commercialize and gain market acceptance of the Company’s product candidates, its right to develop and commercialize its product candidates pursuant to the terms and conditions of the licenses granted to the Company, protection of proprietary technology, the ability to make milestone, royalty or other payments due under any license or collaboration agreements, and the need to secure and maintain adequate manufacturing arrangements with third parties. If the Company does not successfully commercialize or partner any of its product candidates, it will be unable to generate product revenue or achieve profitability. Further, the company is also subject to broad market risks and uncertainties resulting from recent events, such as bank failures or instability in the financial services sector, global pandemics, war and armed conflicts, inflation, rising interest rates, and recession risks as well as supply chain and labor shortages. Segments The Company has one operating segment. The Company’s chief operating decision maker, its Chief Executive Officer, manages the Company’s operations on a consolidated basis for the purposes of allocating resources. 8 Table of Contents Investments Investments in equity securities may be accounted for using (i) the fair value option, if elected, (ii) fair value through earnings if fair value is readily determinable or (iii) for equity investments without readily determinable fair values, the measurement alternative to measure at cost adjusted for any impairment and observable price changes, as applicable. The election to use the measurement alternative is made for each eligible investment. Cash, Cash Equivalents and Restricted Cash The Company considers all highly liquid investments with original maturities of 90 days or less at the date of purchase to be cash and cash equivalents. Cash equivalents are reported at fair value. Cash, cash equivalents, and restricted cash reported within the Condensed Consolidated Statements of Cash Flows is composed of cash and cash equivalents reported in the Condensed Consolidated Balance Sheets and $ 1.6 million of restricted cash for the letter of credit for the Company’s headquarters building lease which is included within other non-current assets in the Condensed Consolidated Balance Sheets. Marketable Securities The Company generally invests its excess cash in money market funds and investment grade short to intermediate-term fixed income securities. Such investments are included in cash and cash equivalents, short-term marketable securities or long-term marketable securities on the Condensed Consolidated Balance Sheets, are considered available-for-sale, and are reported at fair value with net unrealized gains and losses included as a component of stockholders’ equity. The Company classifies investments in securities with remaining maturities of less than one year, or where its intent is to use the investments to fund current operations or to make them available for current operations, as short-term investments. The Company classifies investments in securities with remaining maturities of over one year as long-term investments, unless intended to fund current operations. The amortized cost of debt securities is adjusted for amortization of premiums and accretion of discounts to maturity, which is included in interest and other income, net in the Condensed Consolidated Statements of Operations and Comprehensive Loss. Realized gains and losses and declines in value determined to be due to credit losses on marketable securities, if any, are included in interest and other income, net. The Company periodically evaluates the need for an allowance for credit losses. This evaluation includes consideration of several qualitative and quantitative factors, including whether it has plans to sell the security, whether it is more likely than not it will be required to sell any marketable securities before recovery of its amortized cost basis, and if the entity has the ability and intent to hold the security to maturity, and the portion of any unrealized loss that is the result of a credit loss. Factors considered in making these evaluations include quoted market prices, recent financial results and operating trends, implied values from any recent transactions or offers of investee securities, credit quality of debt instrument issuers, expected cash flows from securities, other publicly available information that may affect the value of the marketable security, duration and severity of the decline in value, and the Company's strategy and intentions for holding the marketable security. 9 Table of Contents Accounts Receivable Accounts receivable are included within prepaid expenses and other current assets on the Condensed Consolidated Balance Sheets. The accounts receivable balance represents amounts receivable from the Company's collaboration partners net of an allowance for credit losses, if required. Leases The Company leases real estate and certain equipment for use in its operations. A determination is made as to whether an arrangement is a lease at inception. The Company recognizes finance and operating lease right-of-use (ROU) assets, and finance and operating lease liabilities based on the present value of the future minimum lease payments at the commencement date. The Company adjusts ROU assets as needed for any lease incentives it receives and for assets it purchases that are regarded as landlord-owned. When determining the present value of lease payments, the Company uses its incremental borrowing rate on the date of lease commencement, or the rate implicit in the lease, if known. The Company does not assume renewals in its determination of the lease term unless the renewals are deemed by management to be reasonably certain at lease inception. The Company recognizes amortization of the ROU assets and interest on the lease liabilities for its finance lease. Finance lease ROU assets are amortized on a straight-line basis from the commencement date to the earlier of the end of the useful life of the ROU asset or the end of the lease term. Operating lease expense is recognized on a straight-line basis over the lease term. Leases with an initial term of twelve months or less are not recorded on the balance sheet, unless they include an option to purchase the underlying asset that the Company is reasonably certain to exercise. The Company recognizes lease expenses on a straight-line basis over the lease term. The Company has leases with lease and non-lease components, which the Company has elected to account for as a single lease component. Revenue Recognition License, Option and Collaboration Revenue The Company analyzes its collaboration arrangements to assess whether they are within the scope of ASC 808, Collaborative Arrangements (“ASC 808”) to determine whether such arrangements involve joint operating activities performed by parties that are both active participants in the activities and exposed to significant risks and rewards dependent on the commercial success of such activities. This assessment is performed throughout the life of the arrangement based on changes in the responsibilities of all parties in the arrangement. For collaboration arrangements within the scope of ASC 808 that contain multiple elements, the Company first determines which elements of the collaboration are deemed to be within the scope of ASC 808 and those that are more reflective of a vendor-customer relationship and, therefore, within the scope of Topic 606. For elements of collaboration arrangements that are accounted for pursuant to ASC 808, an appropriate recognition method is determined and applied consistently, generally by analogy to Topic 606. The accounting treatment pursuant to Topic 606 is outlined below. 10 Table of Contents The terms of license, option and collaboration agreements entered into typically include payment of one or more of the following: non-refundable, up-front license fees; option exercise fees; development, regulatory and commercial milestone payments; payments for manufacturing supply and research and development services and royalties on net sales of licensed products. Each of these payments results in license, collaboration and other revenue, except for revenues from royalties on net sales of licensed products, which are classified as royalty revenue. The core principle of Topic 606 is to recognize revenue when promised goods or services are transferred to customers in an amount that reflects the consideration that is expected to be received in exchange for those goods or services. The Company may also receive reimbursement or make payments to a collaboration partner to satisfy cost sharing requirements. These payments are accounted for pursuant to ASC 808 and are recorded as an offset or increase to research and development expenses, respectively. In determining the appropriate amount of revenue to be recognized as the Company fulfills its obligations under each of its agreements, the Company performs the following steps: (i) identification of the promised goods or services in the contract; (ii) determination of whether the promised goods or services are performance obligations including whether they are distinct in the context of the contract; (iii) measurement of the transaction price, including the constraint on variable consideration; (iv) allocation of the transaction price to the performance obligations based on estimated selling prices; and (v) recognition of revenue when (or as) the Company satisfies each performance obligation. Amounts received prior to satisfying the revenue recognition criteria are recorded as contract liabilities in the Company’s Condensed Consolidated Balance Sheets. If the related performance obligation is expected to be satisfied within the next twelve months this will be classified in current liabilities. Amounts recognized as revenue prior to the Company having an unconditional right (other than a right that is conditioned only on the passage of time) to receipt are recorded as contract assets in the Company's Condensed Consolidated Balance Sheets. If the Company expects to have an unconditional right to receive the consideration in the next twelve months, this will be classified in current assets. A net contract asset or liability is presented for each contract with a customer. At contract inception, the Company assesses the goods or services promised in a contract with a customer and identifies those distinct goods and services that represent a performance obligation. A promised good or service may not be identified as a performance obligation if it is immaterial in the context of the contract with the customer, if it is not separately identifiable from other promises in the contract (either because it is not capable of being separated or because it is not separable in the context of the contract), or if the promised good or service does not provide the customer with a material right. The Company considers the terms of the contract to determine the transaction price. The transaction price is the amount of consideration to which the Company expects to be entitled in exchange for transferring promised goods or services to a customer. The consideration promised in a contract with a customer may include fixed amounts, variable amounts, or both. Variable consideration will only be included in the transaction price when it is not considered constrained, which is when it is probable that a significant reversal in the amount of cumulative revenue recognized will not occur. If it is determined that multiple performance obligations exist, the transaction price is allocated at the inception of the agreement to all identified performance obligations based on the relative standalone selling prices ("SSP"). The relative SSP for each deliverable is estimated using external sourced evidence if it is available. If external sourced evidence is not available, the Company uses its best estimate of the SSP for the deliverable. Revenue is recognized when, or as, the Company satisfies a performance obligation by transferring a promised good or service to a customer. An asset is transferred when, or as, the customer obtains control of that asset, which for a service is considered to be as the services are received and used. The Company recognizes revenue over time by measuring the progress toward complete satisfaction of the relevant performance obligation using an appropriate input or output method based on the nature of the service promised to the customer. 11 Table of Contents After contract inception, the transaction price is reassessed at every period end and updated for changes such as resolution of uncertain events. Any change in the transaction price is allocated to the performance obligations on the same basis as at contract inception, or to a single performance obligation as applicable. The Company accounts for the exercise of a material right as either a contract modification or as a continuation of the existing contract, as is most appropriate based on the facts and circumstances. Management may be required to exercise considerable judgment in estimating revenue to be recognized. Judgment is required in identifying performance obligations, estimating the transaction price, estimating the SSP of identified performance obligations, which may include forecasted revenue, development timelines, reimbursement rates for personnel costs, discount rates and probabilities of technical and regulatory success, and estimating the progress towards satisfaction of performance obligations. Comprehensive Loss Comprehensive loss is composed of net loss and certain changes in stockholders’ equity that are excluded from net loss, primarily unrealized gains or losses on the Company’s marketable securities. Net Loss Per Share Basic net loss per share is calculated by dividing the net loss by the weighted-average number of shares of common stock outstanding during the period, without consideration for common stock equivalents. Diluted net loss per share is the same as basic net loss per share, since the effects of potentially dilutive securities are antidilutive given the net loss for each period presented. The weighted-average common shares outstanding as of September 30, 2024 includes pre-funded warrants to purchase shares of common stock that were issued in connection with the February 2024 private placement, as discussed further in Note 7 - " Common Stock ". Recently Issued Accounting Pronouncements In November 2023, the Financial Accounting Standards Board ("FASB") issued Accounting Standards Update No. 2023-07, Segment Reporting (Topic 280): Improvements to Reportable Segment Disclosures , which is intended to improve reportable segment disclosure requirements primarily through enhanced disclosures about significant segment expenses. The amendments in this Update are effective for all public entities for fiscal years beginning after December 15, 2023, and interim periods within fiscal years beginning after December 15, 2024, with early adoption permitted. The guidance is to be applied retrospectively to all prior periods presented in the financial statements. The Company has not early adopted this update, and is currently evaluating the impact of the new standard on its consolidated financial statements and related disclosures. In December 2023, the FASB issued Accounting Standards Update No. 2023-09, Income Taxes (Topic 740): Improvements to Income Tax Disclosures , which requires that an entity, on an annual basis, disclose additional income tax information, primarily related to the rate reconciliation and income taxes paid. The amendments in this Update are effective to be applied prospectively for annual periods beginning after December 15, 2024, with early adoption permitted. The Company has not early adopted this update, and is currently evaluating the impact of the new standard on its income tax disclosures. In November 2024, the FASB issued Accounting Standards Update No. 2024-03, Income Statement - Reporting Comprehensive Income - Expense Disaggregation Disclosures (Subtopic 220-40): D isaggregation of Income Statement Expenses , which is intended to improve the disclosures of expenses by providing more detailed information about the types of expenses in commonly presented expense captions. The amendments in this update are effective for annual reporting periods beginning after December 15, 2026, and interim reporting periods beginning after December 15, 2027. Early adoption is permitted. The amendments can be applied either prospectively or retrospectively. The Company has not early adopted this update, and is currently evaluating the impact of this new standard on its consolidated financial statements and related disclosures. 12 Table of Contents 2. Fair Value Measurements Assets and liabilities measured at fair value at each balance sheet date are as follows (in thousands): September 30, 2024 Level 1 Level 2 Level 3 Total Assets: Cash equivalents: Money market funds $ 75,600 $ — $ — $ 75,600 Short-term marketable securities: U.S. government treasuries 703,259 — — 703,259 Corporate debt securities — 16,386 — 16,386 Commercial paper — 26,278 — 26,278 Long-term marketable securities: U.S. government treasuries 415,891 — — 415,891 Corporate debt securities — 29,572 — 29,572 Total $ 1,194,750 $ 72,236 $ — $ 1,266,986 December 31, 2023 Level 1 Level 2 Level 3 Total Assets: Cash equivalents: Money market funds $ 121,034 $ — $ — $ 121,034 Short-term marketable securities: U.S. government treasuries 869,172 — — 869,172 U.S. government agency securities — 7,086 — 7,086 Commercial paper — 31,147 — 31,147 Total $ 990,206 $ 38,233 $ — $ 1,028,439 The Company’s Level 2 securities are valued using third-party pricing sources. The pricing services utilize industry standard valuation models, including both income and market-based approaches, for which all significant inputs are observable, either directly or indirectly. The Company has not transferred any assets or liabilities between the fair value measurement levels for the nine months ended September 30, 2024 or for the year ended December 31, 2023. 13 Table of Contents 3. Marketable Securities All marketable securities were considered available-for-sale at September 30, 2024 and December 31, 2023. On a recurring basis, the Company records its marketable securities at fair value using Level 1 or Level 2 inputs as discussed in Note 2, "Fair Value Measurements". The amortized cost, gross unrealized holding gains or losses, and fair value of the Company’s marketable securities by major security type at each balance sheet date are summarized in the tables below (in thousands): September 30, 2024 Amortized Cost Unrealized Holding Gains Unrealized Holding Losses Aggregate Fair Value Short-term marketable securities: U.S. government treasuries (1) $ 701,700 $ 1,565 $ ( 6 ) $ 703,259 Corporate debt securities 16,279 107 — 16,386 Commercial paper 26,278 — — 26,278 Total short-term marketable securities 744,257 1,672 ( 6 ) 745,923 Long-term marketable securities: U.S. government treasuries (2) 412,031 3,861 ( 1 ) 415,891 Corporate debt securities 29,217 355 — 29,572 Total long-term marketable securities 441,248 4,216 ( 1 ) 445,463 Total $ 1,185,505 $ 5,888 $ ( 7 ) $ 1,191,386 __________________________________________________ (1) Unrealized holding losses on 1 security with an aggregate fair value of $ 59.9 million. (2) Unrealized holding losses on 1 security with an aggregate fair value of $ 5.0 million. December 31, 2023 Amortized Cost Unrealized Holding Gains Unrealized Holding Losses Aggregate Fair Value Short-term marketable securities: U.S. government treasuries $ 868,174 $ 998 $ — $ 869,172 U.S. government agency securities (1) 7,089 — ( 3 ) 7,086 Commercial paper 31,147 — — 31,147 Total $ 906,410 $ 998 $ ( 3 ) $ 907,405 __________________________________________________ (1) Unrealized holding losses on 2 securities with an aggregate fair value of $ 7.1 million. As of September 30, 2024 and December 31, 2023, some of the Company's marketable securities were in an unrealized loss position. The Company has no t recognized an allowance for credit losses as of September 30, 2024 or December 31, 2023. The Company determined that it had the ability and intent to hold all marketable securities that have been in a continuous loss position until maturity or recovery. Further, a majority of these marketable securities are held in U.S. government securities, and the remainder were initially, and continue to be, held with investment grade, high credit quality institutions. All marketable securities with unrealized losses as of each balance sheet date have been in a loss position for less than twelve months or the loss is not material. As of September 30, 2024, all of the Company’s marketable securities have an effective maturity of less than two years . 14 Table of Contents 4. Acquisition and Research and Development Funding Collaboration Agreement Acquisition of F-star Gamma In August 2016, the Company entered into a License and Collaboration Agreement (“F-star Collaboration Agreement”) with F-star Gamma Limited (“F-star Gamma”), F-star Biotechnologische Forschungs-und Entwicklungsges M.B.H ("F-star GmbH") and F-star Biotechnology Limited ("F-star Ltd") (collectively, “F-star”) to leverage F-star’s modular antibody technology and the Company’s expertise in the development of therapies for neurodegenerative diseases. In May 2018, the Company exercised the pre-negotiated option agreement (the "Option Agreement") under the F-star Collaboration Agreement and entered into a Share Purchase Agreement (the “Purchase Agreement”) with the shareholders of F-star Gamma and Shareholder Representative Services LLC, pursuant to which the Company acquired all of the outstanding shares of F-star Gamma (the “Acquisition”). The details of the Acquisition are further described in Note 4, "Acquisition", to the consolidated financial statements in the Company's 2023 Annual Report on Form 10-K. As of September 30, 2024, the Company had paid consideration of $ 49.8 million in the aggregate consisting of up-front, preclinical, and clinical contingent consideration, all of which was recorded as research and development expense as incurred. This amount includes a $ 30.0 million contingent consideration payment which was triggered and recorded as research and development expense in March 2023 upon the achievement of a specified clinical milestone in the ETV:IDS program. This contingent consideration payment fully satisfies the Company's clinical contingent consideration obligations under the Purchase Agreement. There was no contingent consideration expense recognized for the three and nine months ended September 30, 2024 or the three months ended September 30, 2023. Collaboration and Development Funding Agreement On January 29, 2024, the Company entered into a Collaboration and Development Funding Agreement with an unrelated third party, pursuant to which this third party will provide up to $ 75.0 million of funding and collaborate with the Company to conduct a global Phase 2a study of BIIB122/DNL151 in patients with Parkinson’s disease and confirmed pathogenic variants of LRRK2. Pursuant to this agreement, an upfront payment of $ 12.5 million was received in January 2024, and a further payment of $ 12.5 million was received in July 2024, with the remainder to be paid upon achievement of operational milestones in the study. After the full $ 75.0 million in consideration has been paid, the third party will be eligible to receive low single-digit royalties from the Company on annual worldwide net sales of LRRK2 inhibitors for the treatment of Parkinson’s disease. The Company determined that this arrangement is an R&D funding arrangement under ASC 730. As the third party is sharing in the risk associated with research and development activities with the Company, the development funding is recognized as an obligation to perform contractual services. Accordingly, payments received will be recorded as a liability, and recognized by the Company as a reduction to research and development expenses over the estimated Phase 2a study period as the underlying research and development costs are incurred. R&D funding under this arrangement of $ 2.5 million and $ 4.8 million offset research and development expenses in the Condensed Consolidated Statements of Operations and Comprehensive Loss for the three and nine months ended September 30, 2024, respectively. As of September 30, 2024, $ 16.3 million and $ 3.9 million of current and non-current deferred research and development funding liability were recorded on the Condensed Consolidated Balance Sheet, respectively. 15 Table of Contents 5. Collaboration Agreements Biogen In October 2020, the Company entered into a Definitive Collaboration and License Agreement (“LRRK2 Agreement”), pursuant to which it granted Biogen a license to co-develop and co-commercialize its small molecule LRRK2 inhibitor program (the “LRRK2 Program”), and a Right of First Negotiation, Option and License Agreement (the “ROFN and Option Agreement”), pursuant to which it granted an option and right of first negotiation to certain of the Company's programs utilizing our TV technology platform, including its amyloid beta program (collectively the "Biogen Collaboration Agreement"), with Biogen Inc.’s subsidiaries, Biogen MA Inc. (“BIMA”) and Biogen International GmbH (“BIG”) (BIMA and BIG, collectively, “Biogen”). The details of the Biogen Collaboration Agreement, the August 2023 amendment to the ROFN and Option Agreement, and the payments the Company has received, and is entitled to receive, are further described in Note 5, "Collaboration Agreements", to the consolidated financial statements in the 2023 Annual Report on Form 10-K. In April 2023, Biogen exercised its option to license Denali’s ATV:Abeta program which was previously concluded to be a material right, triggering payment of a $ 5.0 million option fee which was received in May 2023 and allocated to the material right in its entirety. On July 26, 2024, Denali and Biogen executed a Side Letter to the ROFN and Option Agreement, pursuant to which, effective as of the date of the Side Letter, Biogen terminated its license to the ATV:Abeta program enabled by Denali’s TfR-targeting technology against amyloid beta for the potential treatment of Alzheimer's disease, and granted Denali rights to data generated during the collaboration. The side letter also effected the immediate termination of the ROFN and Option Agreement; as such, the Company expects to receive no future milestone or royalty payments from Biogen related to the ATV:Abeta program. There were no changes to the terms of the LRRK2 Agreement during the three and nine months ended September 30, 2024 or 2023. The Company has no remaining performance obligations under the Biogen Collaboration Agreement, and therefore no contract liability remained on the Condensed Consolidated Balance Sheets as of September 30, 2024 or December 31, 2023 . As of December 31, 2023, Biogen was no longer considered a related party as defined in ASC 850. As of September 30, 2024, the Company has no t recorded milestone revenue or product sales under the Biogen Collaboration Agreement. Sanofi In October 2018, the Company entered into a Collaboration and License Agreement ("Sanofi Collaboration Agreement") with Genzyme Corporation, a wholly owned subsidiary of Sanofi S.A. ("Sanofi"). The details of the Sanofi Collaboration Agreement and the payments the Company has received, and is entitled to receive, are further described in Note 5, "Collaboration Agreements", to the consolidated financial statements in the Company's 2023 Annual Report on Form 10-K. The Company has no remaining performance obligations under the Sanofi Collaboration Agreement, and therefore no contract liability remains on the Condensed Consolidated Balance Sheets as of September 30, 2024 or December 31, 2023 . As of September 30, 2024, the Company had earned milestone payments of $ 100.0 million and had no t recorded any product sales under the Sanofi Collaboration Agreement. 16 Table of Contents Takeda In January 2018, the Company entered into a Collaboration and Option Agreement ("Takeda Collaboration Agreement") with Takeda Pharmaceutical Company Limited ("Takeda"). The details of the Takeda Collaboration Agreement are further described in Note 5, "Collaboration Agreements", to the consolidated financial statements in the Company's 2023 Annual Report on Form 10-K. There are no remaining performance obligations or potential payments remaining under the initial Takeda Collaboration Agreement. The opt-in by Takeda on the PTV:PGRN and ATV:TREM2 programs represented two new contracts with a customer for accounting purposes (the "PTV:PGRN Collaboration Agreement" and the "ATV:TREM2 Collaboration Agreement"), both of which became effective in December 2021. The details of the PTV:PGRN Collaboration Agreement and the ATV:TREM2 Collaboration Agreement are further described in Note 5, "Collaboration Agreements", to the consolidated financial statements in the Company's 2023 Annual Report on Form 10-K. As of September 30, 2024, the Company had earned an aggregate of $ 10.0 million in option fee payments and $ 10.0 million in milestone payments from Takeda under the PTV:PGRN and ATV:TREM2 Collaboration Agreements, and had no t recorded any product sales under either agreement. Collaboration Revenue Revenue disaggregated by collaboration agreement and performance obligation is as follows (in thousands): Three Months Ended September 30, Nine Months Ended September 30, 2024 2023 2024 2023 Takeda Collaboration Agreement: PTV:PGRN Collaboration Agreement (1) $ — $ — — 10,000 Total Takeda Collaboration Revenue — — — 10,000 Sanofi Collaboration Agreement CNS Program License (2) — — — 25,000 Total Sanofi Collaboration Revenue — — — 25,000 Biogen Collaboration Agreement ATV:Abeta Program License (3) — — — 293,912 Option Research Services (4) — 1,267 — 1,619 Total Biogen Collaboration Revenue — 1,267 — 295,531 Total Collaboration Revenue $ — $ 1,267 $ — $ 330,531 _________________________________________________ (1) Revenue for the nine months ended September 30, 2023 from a specified clinical milestone in the Phase 1/2 study of DNL593 in patients with frontotemporal dementia-granulin (FTD-GRN). (2) Revenue for the nine months ended September 30, 2023 from a milestone payment triggered and received in January 2023 upon the commencement of dosing in a Phase 2 study of SAR443820/DNL788 in individuals with multiple sclerosis. (3) Revenue for the nine months ended September 30, 2023 was associated with Biogen exercising its option to license Denali’s ATV:Abeta program which was previously concluded to be a material right, $ 288.9 million of which was included in the contract liability balance at the beginning of the period and $ 5.0 million of which was an option exercise fee received in April 2023. (4) Revenue for the three and nine months ended September 30, 2023 was included in the contract liability balance at the beginning of the period. 17 Table of Contents Cost Sharing Payments and Reimbursements Cost sharing payments to collaboration partners recorded as expenses in research and development expenses in the Condensed Consolidated Statements of Operations and Comprehensive Loss, and cost sharing reimbursements from collaboration partners recorded as an offset to expense in research and development expenses in the Condensed Consolidated Statements of Operations and Comprehensive Loss are as follows (in thousands): Three Months Ended September 30, Nine Months Ended September 30, 2024 2023 2024 2023 Takeda Collaboration Agreement: PTV:PGRN cost sharing (reimbursements) $ ( 1,211 ) $ ( 1,777 ) $ ( 3,549 ) $ ( 5,120 ) ATV:TREM2 cost sharing (reimbursements) ( 208 ) ( 1,018 ) ( 936 ) ( 4,279 ) Total Takeda cost sharing (reimbursements) (1) ( 1,419 ) ( 2,795 ) ( 4,485 ) ( 9,399 ) Biogen Collaboration Agreement: LRRK2 cost sharing payments (2) 4,965 3,378 14,194 14,504 Net cost sharing payments (reimbursements) $ 3,546 $ 583 $ 9,709 $ 5,105 _________________________________ (1) Cost sharing reimbursements of $ 1.4 million and $ 2.7 million were recorded as a receivable within prepaid expenses and other current assets on the Condensed Consolidated Balance Sheets as of September 30, 2024 and December 31, 2023, respectively. (2) Cost sharing payments due to Biogen of $ 5.0 million and $ 3.2 million were recorded within accounts payable on the Condensed Consolidated Balance Sheets as of September 30, 2024 and December 31, 2023, respectively. 18 Table of Contents 6. Commitments and Contingencies Lease Obligations In May 2018, the Company entered into an operating lease for its corporate headquarters in South San Francisco (the "Headquarters Lease"), as further described in Note 8, "Commitments and Contingencies," to the consolidated financial statements in the Company's 2023 Annual Report on Form 10-K. In August 2021, the Company entered into a lease for laboratory, office and warehouse premises in Salt Lake City, Utah . In March 2023, the Company terminated this lease, which resulted in the recognition of $ 7.9 million of accelerated depreciation on leasehold improvements in the nine months ended September 30, 2023 . In April 2023, the Company entered into a lease in Salt Lake City (the “SLC Lease”) for a 59,336 square foot laboratory, office and warehouse premises with a contractual term of approximately 15 years upon commencement, and undiscounted lease payments of approximately $ 13.4 million, which was subsequently amended in October 2023. The accounting lease commencement date was determined to be August 1, 2024, the date the Company was deemed to have obtained control over the property, at which time the lease was determined to be a finance lease and the lease liability and ROU asset were recorded on the Condensed Consolidated Balance Sheet. Included in the ROU asset as of September 30, 2024 are $ 33.1 million of assets purchased by the Company, which are considered to be owned by the landlord. Management exercised judgment in applying the requirements of ASC 842, including the determination as to whether certain contracts contain a lease, lease classification, the lease consideration, the commencement date of the leases, and for leases identified under the standard, the discount rate used to determine the measurement of the lease liability. The discount rates of the Company's operating and finance leases are an approximation of the Company's incremental borrowing rate and are dependent upon the term and economics of the agreement. To estimate the incremental borrowing rate, management considers observable debt yields of comparable market instruments, as well as benchmarks within the lease agreement that may be indicative of the rate implicit in the lease. There were no changes to the terms of the leases recognized under ASC 842 during the three and nine months ended September 30, 2024. Operating lease costs were $ 1.9 million and $ 5.8 million for the three and nine months ended September 30, 2024, respectively, and $ 1.9 million and $ 6.1 million for the three and nine months ended September 30, 2023, respectively. Variable lease costs were $ 1.6 million and $ 3.9 million for the three and nine months ended September 30, 2024, respectively, and $ 1.3 million and $ 3.3 million for the three and nine months ended September 30, 2023, respectively. Finance lease costs representing amortization of ROU assets and interest on lease liability were $ 0.4 million and $ 0.1 million, respectively, for both the three and nine months ended September 30, 2024. There was no finance lease cost for the three and nine months ended September 30, 2023. The following tables contain a summary of other information pertaining to the Company’s leases for the periods presented (in thousands): Three Months Ended September 30, Nine Months Ended September 30, 2024 2023 2024 2023 Operating cash flows from operating lease $ 2,885 $ 2,793 $ 8,532 $ 8,552 19 Table of Contents As of September 30, 2024 2023 Weighted-average remaining lease term (in years): Operating lease 4.6 years 5.6 years Finance lease 14.5 years — Weighted-average discount rate applied (%): Operating lease 9.0 % 9.0 % Finance lease 13.7 % — % The following table reconciles the undiscounted cash flows for the next five years and total of the remaining years to the operating and finance lease liabilities recorded in the Condensed Consolidated Balance Sheet as of September 30, 2024 (in thousands): Year Ended December 31: Operating Lease Finance Lease 2024 (three months) $ 2,885 $ 191 2025 11,793 777 2026 12,182 794 2027 12,584 811 2028 13,001 829 Thereafter 4,381 9,661 Total undiscounted lease payments 56,826 13,063 Less: present value adjustment ( 9,940 ) — Less: imputed interest — ( 7,381 ) Total future minimum lease payments $ 46,886 $ 5,682 Indemnification In the ordinary course of business, the Company may provide indemnifications of varying scope and terms to vendors, lessors, business partners, board members, officers, and other parties with respect to certain matters, including, but not limited to, losses arising out of breach of such agreements, services to be provided by the Company, negligence or willful misconduct of the Company, violations of law by the Company, or from intellectual property infringement claims made by third parties. In addition, the Company has entered into indemnification agreements with directors and certain officers and employees that will require the Company, among other things, to indemnify them against certain liabilities that may arise by reason of their status or service as directors, officers or employees. No demands have been made upon the Company to provide indemnification under such agreements, and thus, there are no claims that the Company is aware of that could have a material effect on the Company’s Condensed Consolidated Balance Sheets , Condensed Consolidated Statements of Operations and Comprehensive Loss , or Condensed Consolidated Statements of Cash Flows . 20 Table of Contents Commitments In September 2017, the Company entered into a Development and Manufacturing Services Agreement as amended (“DMSA”) with Lonza Sales AG (“Lonza”) for the development and manufacture of biologic products. Under the DMSA, the Company will execute purchase orders based on project plans authorizing Lonza to provide development and manufacturing services with respect to certain of the Company's antibody and enzyme products, and will pay for the services provided and batches delivered in accordance with the DMSA and project plan. Unless earlier terminated, the DMSA will expire when all development and manufacturing services are completed, which is not expected to be before January 2028. As of September 30, 2024 and December 31, 2023, the Company had total non-cancellable purchase commitments under the DMSA of $ 23.4 million and $ 37.6 million, respectively. During the three months ended September 30, 2024 and 2023, the Company incurred costs of $ 6.0 million and $ 10.4 million, respectively, and made payments of $ 1.9 million and $ 12.8 million, respectively, for the development and manufacturing services rendered under the DMSA. During the nine months ended September 30, 2024 and 2023, the Company incurred costs of $ 28.6 million and $ 26.5 million, respectively, and made payments of $ 32.2 million and $ 24.9 million, respectively, for the development and manufacturing services rendered under the DMSA. In the normal course of business, the Company enters into other firm purchase commitments primarily related to research and development activities. The Company had contractual obligations under certain clinical and manufacturing agreements other than the DMSA of $ 25.6 million and $ 34.8 million, as of September 30, 2024 and December 31, 2023, respectively, with certain amounts subject to cost sharing with Takeda. Contingencies From time to time, the Company may be involved in lawsuits, arbitration, claims, investigations and proceedings consisting of intellectual property, employment and other matters which arise in the ordinary course of business. The Company records accruals for loss contingencies to the extent that the Company concludes that it is probable that a liability has been incurred and the amount of the related loss can be reasonably estimated. 7. Common Stock On February 27, 2024, the Company entered into a securities purchase agreement (the "Purchase Agreement") with certain investors for the private placement of (i) 3,244,689 shares of Denali's common stock at a price of $ 17.07 per share and (ii) pre-funded warrants to purchase an aggregate of 26,046,065 shares of Denali's common stock (the "Pre-Funded Warrants") at a purchase price of $ 17.06 per Pre-Funded Warrant, which represents the per share price for the common stock less the $ 0.01 exercise price. The private placement closed on February 29, 2024, at which time the Company received aggregate net proceeds of approximately $ 499.3 million, after deducting issuance costs of approximately $ 0.5 million. The Pre-Funded Warrants were classified as a component of permanent equity in the Company’s consolidated balance sheet as they are freestanding financial instruments that are immediately exercisable, do not embody an obligation for the Company to repurchase its shares and permit the holders to receive a fixed number of shares of common stock upon exercise. All of the Pre-Funded Warrants issued in the private placement were outstanding as of September 30, 2024. 8. Stock-Based Awards The Company has issued stock-based awards from various equity incentive and stock purchase plans, as more fully described in Note 9, "Stock-Based Awards" to the consolidated financial statements in the Company's 2023 Annual Report on Form 10-K. 21 Table of Contents Stock Option Activity The following table summarizes stock option activity for the nine months ended September 30, 2024: Number of Options Weighted-Average Exercise Price Balance at December 31, 2023 16,490,551 $ 27.34 Granted 4,498,161 20.30 Exercised ( 744,389 ) 13.47 Forfeited ( 1,663,311 ) 31.29 Balance at September 30, 2024 18,581,012 $ 25.84 Vested and expected to vest at September 30, 2024 17,771,141 $ 26.98 Exercisable at September 30, 2024 11,543,850 $ 27.89 The estimated fair value of stock options granted to employees were calculated using the Black-Scholes option-pricing model using the following assumptions: Nine Months Ended September 30, 2024 2023 Expected term (in years) 5.50 - 6.08 5.50 - 6.08 Volatility 64.5 % - 66.0 % 67.9 % - 69.6 % Risk-free interest rate 3.7 % - 4.5 % 3.4 % - 4.3 % Dividend yield — — Restricted Stock Activity The following table summarizes restricted stock unit ("RSU") activity for the nine months ended September 30, 2024: Number of RSU shares Weighted-Average Fair Value at Date of Grant per Share Unvested at December 31, 2023 3,635,157 $ 35.60 Granted 2,347,721 20.49 Vested and released ( 1,261,137 ) 37.07 Forfeited ( 727,400 ) 28.85 Unvested and expected to vest at September 30, 2024 3,994,341 $ 27.48 Stock-Based Compensation Expense The Company’s results of operations include expenses relating to stock-based compensation as follows (in thousands): Three Months Ended September 30, Nine Months Ended September 30, 2024 2023 2024 2023 Research and development $ 14,141 $ 15,821 $ 44,847 $ 47,795 General and administrative 10,719 11,638 32,953 34,319 Total $ 24,860 $ 27,459 $ 77,800 $ 82,114 22 Table of Contents 9. Net Loss Per Share Since the Company was in a loss position for all periods presented, basic net loss per share is the same as diluted net loss per share for all periods as the inclusion of all potential shares of common stock outstanding would have been anti-dilutive. The following table sets forth the computation of basic and diluted net loss per share (in thousands, except share and per share amounts): Three Months Ended September 30, Nine Months Ended September 30, 2024 2023 2024 2023 Numerator: Net loss $ ( 107,192 ) $ ( 99,353 ) $ ( 308,020 ) $ ( 25,751 ) Denominator: Weighted average number of: Common stock shares outstanding 143,410,923 137,644,534 142,151,719 137,076,199 Private placement pre-funded warrants 26,046,065 — 20,437,606 — Total 169,456,988 137,644,534 162,589,325 137,076,199 Net loss per share $ ( 0.63 ) $ ( 0.72 ) $ ( 1.89 ) $ ( 0.19 ) Potentially dilutive securities, including options issued and outstanding, Employee Stock Purchase Plan (“ESPP”) shares issuable, and restricted shares subject to future vesting that were not included in the diluted per share calculations for the periods presented because they would be anti-dilutive totaled approximately 22.7 million and 20.7 million shares as of September 30, 2024 and September 30, 2023, respectively. 10. Divestiture of Preclinical Small Molecule Programs On March 1, 2024, the Company divested certain assets, including specified intellectual property, tangible assets, and equipment used to conduct early stage small molecule drug discovery ("Divested Assets") through an Asset Purchase and License Agreement (the "Asset Purchase Agreement") executed with a venture-backed private company ("VBPC"). Additionally, certain of the Company’s employees terminated their employment with the Company and became employees of VBPC. In exchange for the Divested Assets, the Company received equity consideration in the form of a simple agreement for future equity (“SAFE”), equal to $ 15.0 million of equity in VBPC’s next financing round or, if VBPC’s next equity financing does not occur prior to December 31, 2024, a number of shares of preferred stock issued in VBPC’s previous round of equity financing prior to this agreement equal to $ 15.0 million divided by the price per share paid by investors in that previous equity financing. The Company may also be eligible to receive certain market valuation, development and sales based milestone payments up to approximately $ 1.2 billion in the form of either cash or equity at the election of VBPC. The Company will also be entitled to receive future royalties on aggregate net sales of any products that bind to certain identified targets, on a product-by-product and country-by-country basis during the periods of time commencing at the time of the first commercial sale of such product in such country, until the later of (i) the expiration of certain related patents, (ii) the expiration of Regulatory Exclusivity, or (iii) ten years after such first commercial sale. Concurrently, VBPC and the Company also entered into a sublease for 12,985 square feet of office and lab space within the Company's corporate headquarters, and transition and research services agreement ("Service Agreements"). The sublease commenced in May 2024 and continues for a period of approximately ten months , with two optional six month extension periods. The Service Agreements allow Denali to provide access to equipment and provision of certain specified administrative and research services to VBPC for a period up to the end of the sublease term. 23 Table of Contents This divestiture did not meet the criteria for reporting discontinued operations as the sale does not represent a strategic shift in the Company’s business. The Company recognized a gain on divestiture of approximately $ 14.5 million in the Condensed Consolidated Statements of Operations and Comprehensive Loss during the nine months ended September 30, 2024, representing the difference between the fair value of the consideration received and the carrying amount of the Divested Assets. The Company recorded the SAFE at $ 15.0 million based on the expected value of the equity to be received within other non-current assets in the Condensed Consolidated Balance Sheet. The SAFE remains outstanding as of September 30, 2024. 24 Table of Contents