Denali Therapeutics Inc. 10-Q

ITEM 1. FINANCIAL STATEMENTS Denali Therapeutics Inc. Condensed Consolidated Balance Sheets (Unaudited) (In thousands, except share amounts) June 30, 2020 December 31, 2019 Assets Current assets: Cash and cash equivalents $ 137,184 $ 79,449 Short-term marketable securities 412,397 335,907 Prepaid expenses and other current assets 9,828 14,675 Total current assets 559,409 430,031 Long-term marketable securities 7,229 39,886 Property and equipment, net 43,622 46,732 Operating lease right-of-use asset 33,312 33,923 Other non-current assets 3,765 2,659 Total assets $ 647,337 $ 553,231 Liabilities and stockholders' equity Current liabilities: Accounts payable $ 1,866 $ 2,590 Accrued compensation 5,531 8,739 Accrued clinical costs 4,179 5,042 Other accruals and other current liabilities 8,424 6,569 Operating lease liability, current 4,330 3,665 Contract liabilities 34,134 18,739 Total current liabilities 58,464 45,344 Contract liabilities, less current portion 19,715 43,753 Operating lease liability, less current portion 66,612 68,865 Other non-current liabilities 379 379 Total liabilities 145,170 158,341 Commitments and contingencies (Note 8) Stockholders' equity: Convertible preferred stock, $ 0.01 par value; 40,000,000 shares authorized as of June 30, 2020 and December 31, 2019; 0 shares issued and outstanding as of June 30, 2020 and December 31, 2019 — — Common stock, $ 0.01 par value; 400,000,000 shares authorized as of June 30, 2020 and December 31, 2019; 105,897,872 shares and 96,189,935 shares issued and outstanding as of June 30, 2020 and December 31, 2019, respectively 1,385 1,288 Additional paid-in capital 1,041,303 818,803 Accumulated other comprehensive income 551 350 Accumulated deficit ( 541,072 ) ( 425,551 ) Total stockholders' equity 502,167 394,890 Total liabilities and stockholders’ equity $ 647,337 $ 553,231 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 June 30, Six Months Ended June 30, 2020 2019 2020 2019 Collaboration revenue: Collaboration revenue from customers $ 5,811 $ 4,098 $ 9,363 $ 8,209 Other collaboration revenue 36 99 88 193 Total collaboration revenue 5,847 4,197 9,451 8,402 Operating expenses: Research and development 53,152 51,884 104,168 89,287 General and administrative 13,972 15,076 26,527 24,386 Total operating expenses 67,124 66,960 130,695 113,673 Loss from operations ( 61,277 ) ( 62,763 ) ( 121,244 ) ( 105,271 ) Interest and other income, net 2,598 4,113 5,667 7,629 Loss before income taxes ( 58,679 ) ( 58,650 ) ( 115,577 ) ( 97,642 ) Income tax benefit (provision) ( 79 ) 313 56 313 Net loss ( 58,758 ) ( 58,337 ) ( 115,521 ) ( 97,329 ) Other comprehensive income (loss): Net unrealized gain (loss) on marketable securities, net of tax ( 284 ) 547 201 1,528 Comprehensive loss $ ( 59,042 ) $ ( 57,790 ) $ ( 115,320 ) $ ( 95,801 ) Net loss per share, basic and diluted $ ( 0.56 ) $ ( 0.61 ) $ ( 1.11 ) $ ( 1.02 ) Weighted average number of shares outstanding, basic and diluted 105,717,912 95,495,497 104,068,815 95,241,412 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, 2019 96,189,935 $ 1,288 $ 818,803 $ 350 $ ( 425,551 ) $ 394,890 Issuance of common stock in follow-on offering, net of issuance costs of $ 632 9,000,000 90 193,858 — — 193,948 Issuances under equity incentive plans 589,516 6 5,374 — — 5,380 Vesting of restricted stock units 118,421 1 ( 1 ) — — — Stock-based compensation — — 23,269 — — 23,269 Net loss — — — — ( 115,521 ) ( 115,521 ) Other comprehensive income — — — 201 — 201 Balance at June 30, 2020 105,897,872 $ 1,385 $ 1,041,303 $ 551 $ ( 541,072 ) $ 502,167 Balance at March 31, 2020 105,541,343 $ 1,382 $ 1,025,408 $ 835 $ ( 482,314 ) $ 545,311 Issuances under equity incentive plans 329,947 3 3,411 — — 3,414 Vesting of restricted stock units 26,582 — — — — — Stock-based compensation — — 12,484 — — 12,484 Net loss — — — — ( 58,758 ) ( 58,758 ) Other comprehensive loss — — — ( 284 ) — ( 284 ) Balance at June 30, 2020 105,897,872 $ 1,385 $ 1,041,303 $ 551 $ ( 541,072 ) $ 502,167 Balance at December 31, 2018 94,662,435 $ 1,273 $ 774,158 $ ( 649 ) $ ( 227,937 ) $ 546,845 Issuances under equity incentive plans 547,124 5 3,472 — — 3,477 Vesting of early exercised common stock 93,752 2 62 — — 64 Vesting of restricted stock awards and units 353,585 3 ( 3 ) — — — Stock-based compensation — — 20,588 — — 20,588 Net loss — — — — ( 97,329 ) ( 97,329 ) Other comprehensive income — — — 1,528 — 1,528 Balance at June 30, 2019 95,656,896 $ 1,283 $ 798,277 $ 879 $ ( 325,266 ) $ 475,173 Balance at March 31, 2019 95,257,705 $ 1,279 $ 781,966 $ 332 $ ( 266,929 ) $ 516,648 Issuances under equity incentive plans 347,621 3 2,566 — — 2,569 Vesting of early exercised common stock 46,878 1 31 — — 32 Vesting of restricted stock awards and units 4,692 — — — — — Stock-based compensation — — 13,714 — — 13,714 Net loss — — — — ( 58,337 ) ( 58,337 ) Other comprehensive income — — — 547 — 547 Balance at June 30, 2019 95,656,896 $ 1,283 $ 798,277 $ 879 $ ( 325,266 ) $ 475,173 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) Six Months Ended June 30, 2020 2019 Operating activities Net loss $ ( 115,521 ) $ ( 97,329 ) Adjustments to reconcile net loss to net cash used in operating activities: Depreciation and amortization 4,254 4,046 Stock–based compensation expense 23,269 20,588 Net amortization of discounts on marketable securities ( 1,025 ) ( 2,734 ) Non-cash adjustment to operating lease expense ( 978 ) 1,740 Other non-cash items ( 39 ) ( 313 ) Changes in operating assets and liabilities: Prepaid expenses and other assets 3,794 2,704 Accounts payable ( 744 ) 1,303 Accruals and other current liabilities ( 2,215 ) ( 1,887 ) Contract liabilities ( 8,644 ) ( 1,616 ) Net cash used in operating activities ( 97,849 ) ( 73,498 ) Investing activities Purchases of marketable securities ( 323,607 ) ( 144,029 ) Purchases of property and equipment ( 1,194 ) ( 12,299 ) Maturities and sales of marketable securities 281,057 212,162 Net cash provided by (used in) investing activities ( 43,744 ) 55,834 Financing activities Proceeds from public offering of common stock, net of issuance costs 193,948 — Proceeds from exercise of awards under equity incentive plans 5,380 3,477 Net cash provided by financing activities 199,328 3,477 Net increase (decrease) in cash, cash equivalents and restricted cash 57,735 ( 14,187 ) Cash, cash equivalents and restricted cash at beginning of period 80,949 78,623 Cash, cash equivalents and restricted cash at end of period $ 138,684 $ 64,436 Supplemental disclosures of cash flow information Tenant improvements provided by the landlord $ — $ 11,341 Property and equipment purchases accrued but not yet paid $ 2 $ 2,162 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. 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 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, 2019 , as filed with the Securities and Exchange Commission on February 27, 2020 (the "2019 Annual Report on Form 10-K"). The Condensed Consolidated Balance Sheet as of December 31, 2019 was derived from the audited annual consolidated financial statements as of 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 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 six months ended June 30, 2020, except as discussed below in the sections titled "Marketable Securities" and "Recently Adopted Accounting Pronouncement," there were no material changes to the Company's significant accounting and financial reporting policies from those reflected in the 2019 Annual Report on Form 10-K. For further information with regard to the Company’s Significant Accounting Policies, please refer to Note 1, "Significant Accounting Policies," to the Company’s Consolidated Financial Statements included in the 2019 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 subsidiary. All intercompany balances and transactions have been eliminated in consolidation. For the Company and its subsidiary, 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. Foreign currency transaction 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 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 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, marketable securities and forward foreign currency exchange contracts. 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, its agencies and 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 June 30, 2020 and December 31, 2019, the Company had no off-balance sheet concentrations of credit risk. The Company is exposed to counterparty credit risk on all of its derivative financial instruments. The Company has established and maintains strict counterparty credit guidelines and enters into hedges only with financial institutions that are investment grade or better to minimize the Company’s exposure to potential defaults. The Company does not require collateral to be pledged under these agreements. The Company is subject to a number of risks similar to other early-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. The COVID-19 pandemic has caused increased risk and uncertainty for the Company. Credit risk associated with investments in securities may increase if any institution with which the Company has an investment is significantly impacted by the COVID-19 pandemic. As of June 30, 2020, the Company has not realized any losses on its cash deposits or investments. Further, COVID-19 may impact the timelines and progress of the Company's preclinical activities and clinical trials, and may impact its ability to raise capital in the near term. 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 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. The Company’s restricted cash consists of the letter of credit for the Company’s headquarters building lease, and is included within other non-current assets on the accompanying 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 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. 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 consists 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. 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. Derivatives and Hedging Activities The Company measures its derivative instruments at fair value, and accounts for them as either assets or liabilities included within prepaid assets and other current assets and other accruals and current liabilities, respectively, on the Condensed Consolidated Balance Sheets. Derivatives are adjusted to fair value through interest and other income, net in the Condensed Consolidated Statements of Operations and Comprehensive Loss. 9 Table of Contents Leases The Company adopted Accounting Standards Update ("ASU") No. 2016-02, Leases as of January 1, 2019. A determination is made as to whether an arrangement is a lease at inception. A right-of-use (“ROU”) asset an d operating lease liability is recognized for identified operating leases in the Condensed Consolidated Balance Sheets. The changes in operating lease ROU assets and operating lease liabilities are presented net within non-cash adjustment to operating lease expense in the Condensed Consolidated Statements of Cash Flows. ROU assets represent the Company’s right to use the underlying asset for the lease term and lease liabilities represent the Company’s obligation to make lease payments arising from the lease. Operating lease ROU assets and liabilities are recognized at the lease commencement date based on the present value of lease payments due over the lease term, with the ROU assets adjusted for lease incentives received. 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. Leases with an initial term of 12 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 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. The terms of licensing and collaboration agreements entered into typically include payment of one or more of the following: non-refundable, up-front license 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. 10 Table of Contents 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 performance obligation 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. 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. 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. 11 Table of Contents Comprehensive Income (Loss) Comprehensive income (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. Recently Issued Accounting Pronouncement In December 2019, the Financial Accounting Standards Board ("FASB") issued Accounting Standards Update No. 2019-12 , Income Taxes (Topic 740) Simplifying the Accounting for Income Taxes. ASU No. 2019-12 modifies ASC 740 to simplify several aspects of accounting for income taxes, including eliminating certain exceptions to the guidance in ASC 740 related to the approach for intraperiod tax allocation. The guidance is effective for fiscal years beginning after December 15, 2020 and interim periods within those fiscal years, with early adoption permitted, and is required to be adopted prospectively, with the exception of certain specific amendments. The Company is currently assessing the impact of this ASU on its Condensed Consolidated Financial Statements. Recently Adopted Accounting Pronouncement In June 2016, the FASB issued Accounting Standards Update No. 2016-13, Financial Instruments-Credit Losses: Measurement of Credit Losses on Financial Instruments . ASU 2016-13 requires measurement and recognition of expected credit losses for financial assets. In April 2019, the FASB issued clarification to ASU 2016-13 within ASU 2019-04, Codification Improvements to Topic 326, Financial Instruments-Credit Losses, Topic 815, Derivatives and Hedging , and Topic 825, Financial Instruments . The Company adopted this standard as of January 1, 2020 using a modified retrospective approach. Adoption of the standard did not have a material impact on the Condensed Consolidated Financial Statements. 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): June 30, 2020 Level 1 Level 2 Level 3 Total Assets: Cash equivalents: Money market funds $ 111,201 $ — $ — $ 111,201 Short-term marketable securities: U.S. government treasuries 333,212 — — 333,212 Corporate debt securities — 49,761 — 49,761 Commercial paper — 29,424 — 29,424 Long-term marketable securities: Corporate debt securities — 7,229 — 7,229 Total $ 444,413 $ 86,414 $ — $ 530,827 Liabilities: Foreign currency derivative contracts $ — $ 108 $ — $ 108 Total $ — $ 108 $ — $ 108 December 31, 2019 Level 1 Level 2 Level 3 Total Assets: Cash equivalents: Money market funds $ 54,163 $ — $ — $ 54,163 U.S. government treasuries 15,989 — — 15,989 Short-term marketable securities: U.S. government treasuries 250,070 — — 250,070 U.S. government agency securities — 2,000 — 2,000 Corporate debt securities — 53,479 — 53,479 Commercial paper — 30,358 — 30,358 Long-term marketable securities: U.S. government treasuries 13,869 — — 13,869 Corporate debt securities — 26,017 — 26,017 Foreign currency derivative contracts — 85 — 85 Total $ 334,091 $ 111,939 $ — $ 446,030 Liabilities: Foreign currency derivative contracts $ — $ 8 $ — $ 8 Total $ — $ 8 $ — $ 8 The carrying amounts of prepaid expenses and other current assets, accounts payable and accrued liabilities approximate their fair values due to their short-term maturities. 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. There were no transfers of assets or liabilities between the fair value measurement levels during the three and six months ended June 30, 2020 or 2019. 13 Table of Contents 3. Cash and Marketable Securities Cash, cash equivalents and restricted cash A reconciliation of cash, cash equivalents, and restricted cash reported within the Condensed Consolidated Balance Sheets to the amount reported within the Condensed Consolidated Statements of Cash Flows is shown in the table below (in thousands): June 30, December 31, June 30, December 31, 2020 2019 2019 2018 Cash and cash equivalents $ 137,184 $ 79,449 $ 62,936 $ 77,123 Restricted cash included within other non-current assets 1,500 1,500 1,500 1,500 Total cash, cash equivalents, and restricted cash $ 138,684 $ 80,949 $ 64,436 $ 78,623 Marketable securities All marketable securities were considered available-for-sale at June 30, 2020 and December 31, 2019. 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): June 30, 2020 Amortized Cost Unrealized Holding Gains Unrealized Holding Losses Aggregate Fair Value Short-term marketable securities: U.S. government treasuries (1) $ 332,659 $ 553 $ — $ 333,212 Corporate debt securities 49,458 303 — 49,761 Commercial paper 29,424 — — 29,424 Total short-term marketable securities 411,541 856 — 412,397 Long-term marketable securities: Corporate debt securities 7,127 102 — 7,229 Total long-term marketable securities 7,127 102 — 7,229 Total $ 418,668 $ 958 $ — $ 419,626 __________________________________________________ (1) Immaterial unrealized holding losses on 4 securities. 14 Table of Contents December 31, 2019 Amortized Cost Unrealized Holding Gains Unrealized Holding Losses Aggregate Fair Value Short-term marketable securities: U.S. government treasuries (1) $ 249,478 $ 594 $ ( 2 ) $ 250,070 U.S. government agency securities 1,999 1 — 2,000 Corporate debt securities (2) 53,396 94 ( 11 ) 53,479 Commercial paper 30,358 — — 30,358 Total short-term marketable securities 335,231 689 ( 13 ) 335,907 Long-term marketable securities: U.S. government treasuries (3) 13,865 6 ( 2 ) 13,869 Corporate debt securities (4) 25,998 34 ( 15 ) 26,017 Total long-term marketable securities 39,863 40 ( 17 ) 39,886 Total $ 375,094 $ 729 $ ( 30 ) $ 375,793 __________________________________________________ (1) Unrealized holding losses on 2 securities with an aggregate fair value of $ 9.3 million. (2) Unrealized holding losses on 4 securities with an aggregate fair value of $ 25.9 million. (3) Unrealized holding losses on 1 security with an aggregate fair value of $ 10.1 million. (4) Unrealized holding losses on 3 securities with an aggregate fair value of $ 17.2 million. As of December 31, 2019, some of the Company’s marketable securities were in an unrealized loss position, and unrealized losses were immaterial as of June 30, 2020. The Company has no t recognized an allowance for credit losses as of June 30, 2020 and there was no other-than-temporary impairment as of December 31, 2019. 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, these marketable securities 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. The Company recorded unrealized gains on marketable securities as other comprehensive income in the six months ended June 30, 2020 and the three and six months ended June 30, 2019. There was no unrealized gain on marketable securities in other comprehensive income for the three months ended June 30, 2020. As a result, the Company recorded a tax benefit of $ 0.1 million for the six months ended June 30, 2020, and a tax benefit of $ 0.3 million for the three and six months ended June 30, 2019 on the Condensed Consolidated Statements of Operations and Comprehensive Loss and a corresponding tax charge in other comprehensive income. All of the Company’s marketable securities have an effective maturity of less than two years . 4. Derivative Financial Instruments Foreign Currency Exchange Rate Exposure The Company uses forward foreign currency exchange contracts to hedge certain operational exposures resulting from potential changes in foreign currency exchange rates. Such exposures result from portions of the Company’s forecasted cash flows being denominated in currencies other than the U.S. dollar, primarily the Euro and British Pound. The derivative instruments the Company uses to hedge this exposure are not designated as cash flow hedges, and as a result, changes in their fair value are recorded in interest and other income, net, on the Company's Condensed Consolidated Statements of Operations and Comprehensive Loss. 15 Table of Contents The fair values of forward foreign currency exchange contracts are estimated using current exchange rates and interest rates and take into consideration the current creditworthiness of the counterparties. Information regarding the specific instruments used by the Company to hedge its exposure to foreign currency exchange rate fluctuations is provided below. The following table summarizes the Company’s forward foreign currency exchange contracts outstanding as of June 30, 2020 and December 31, 2019, respectively (notional amounts in thousands): Foreign Exchange Contracts Number of Contracts Aggregate Notional (1) Amount in Foreign Currency Maturity Euros 26 3,535 July 2020 - May 2021 British Pounds 19 2,868 July 2020 - May 2021 Swiss Francs 2 21 July 2020 - Aug 2020 Total at June 30, 2020 47 Euros 23 1,500 Jan 2020 - Nov 2020 British Pounds 15 2,285 Jan 2020 - Jun 2020 Swiss Francs 10 129 Jan 2020 - Aug 2020 Total at December 31, 2019 48 _________________________________________________ (1) The notional amount represents the net amount of foreign currency that will be received upon maturity of the forward contracts. 5. Acquisition 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. Under the F-star Collaboration Agreement, the Company made payments to F-star totaling $ 11.5 million. In connection with the entry into the F-star Collaboration Agreement, the Company also purchased an option for an upfront option fee of $ 0.5 million (the “buy-out-option”), to acquire all of the outstanding shares of F-star Gamma pursuant to a pre-negotiated buy-out option agreement (the “Option Agreement”). In May 2018, the Company exercised the Option 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”). As a result of the Acquisition, F-star Gamma became a wholly-owned subsidiary of the Company and the Company changed the entity’s name to Denali BBB Holding Limited. In addition, the Company became a direct licensee of certain intellectual property of F-star Ltd by way of the Company’s assumption of F-star Gamma’s license agreement with F-star Ltd, dated August 24, 2016, (the “F-star Gamma License”). The Company made initial exercise payments under the Purchase Agreement and the F-star Gamma License, in the aggregate, of $ 17.8 million. In addition, the Company is required to make future contingent payments, to F-star Ltd and the former shareholders of F-star Gamma, up to a maximum amount of $ 447.0 million in the aggregate upon the achievement of certain defined preclinical, clinical, regulatory and commercial milestones. These include up to $ 27.0 million in preclinical contingent payments, $ 50.0 million in clinical contingent payments, $ 120.0 million in regulatory contingent payments and $ 250.0 million in commercial contingent payments. The amount of the contingent payments will vary based on whether F-star delivers an Fcab (constant Fc-domains with antigen-binding activity) that meets pre-defined criteria and whether the Fcab has been identified solely by the Company or solely by F-star or jointly by the Company and F-star. In June 30, 2019, the Company made a payment of $ 1.5 million to F-star Ltd upon the achievement of a specified preclinical milestone in the Company's ETV:IDS program. 16 Table of Contents The Company concluded that the assets acquired and liabilities assumed upon the exercise of the Option Agreement did not meet the accounting definition of a business, and as such, the acquisition was accounted for as an asset purchase. As the transaction was accounted for as an asset purchase rather than a business combination, the Company did no t recognize any contingent consideration on the acquisition date. To date, the Company has paid consideration of $ 19.8 million in the aggregate, consisting of up-front and contingent consideration, all of which was recorded as research and development expense as incurred. The Company recognized $ 1.5 million of contingent consideration as research and development expense for the three and six months ended June 30, 2019. There has been no contingent consideration recognized for the three and six months ended June 30, 2020. Any future contingent consideration is expected to be recognized as incurred in research and development expense on the Condensed Consolidated Statements of Operations and Comprehensive Loss. Under the F-star Collaboration Agreement, the Company is responsible for certain research costs incurred by F-star Ltd in conducting activities under an agreed development plan for each Fcab, for up to 24 months after the target Fcab is accepted. The Company's responsibility for research costs under the first development plan related to an Fcab that targets the transferrin receptor was completed during the year ended December 31, 2018. The responsibility for costs under the second development plan related to an undisclosed Fcab target commenced in February 2019. The Company recognized $ 0.3 million and $ 0.6 million in research and development expense related to the funding of F-star Ltd activities under this development plan during the three and six months ended June 30, 2020, respectively, and $ 0.3 million and $ 0.5 million for the three and six months ended June 30, 2019, respectively. 6. Collaboration Agreements 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") pursuant to which certain small molecule CNS and peripheral receptor interacting serine/threonine protein kinase 1 (" RIPK1") inhibitors contributed by Sanofi and by Denali will be developed and commercialized. The Sanofi Collaboration Agreement became effective in November 2018 when the Hart-Scott-Rodino ("HSR") requirements were satisfied at which time Sanofi paid the Company an upfront payment of $ 125.0 million. Under the Sanofi Collaboration Agreement, Denali is eligible to receive milestone payments from Sanofi up to approximately $ 1.1 billion upon achievement of certain clinical, regulatory and sales milestone events. Such milestone payments include $ 215.0 million in clinical milestone payments and $ 385.0 million in regulatory milestone payments for CNS Products, as defined, that are developed and approved in the United States, by the European Medicines Agency ("EMA") and in Japan for three indications, including Alzheimer's disease. These milestones also include $ 120.0 million in clinical milestone payments, $ 175.0 million in regulatory milestone payments and $ 200.0 million in commercial milestone payments for Peripheral Products, as defined, that are developed and approved in the United States, by the EMA and Japan for three indications. Denali will share profits and losses equally with Sanofi for CNS Products sold in the United States and China, and receive variable royalties on net sales for CNS Products sold outside of the United States and China and for Peripheral Products sold worldwide. 17 Table of Contents Denali and Sanofi will jointly develop CNS Products pursuant to a global development plan. The Company will be responsible, at its own cost, for conducting Phase 1 and Phase 2 trials for CNS Products in Alzheimer’s disease and any activities required to support such clinical trials and specific for Alzheimer’s disease. Denali conducted, at Sanofi’s cost, a Phase 1b trial for the initial lead CNS penetrant RIPK1 inhibitor, DNL747, in ALS. In June 2020, Denali announced that clinical activities on DNL747 would be paused and efforts focused on the development of the backup preclinical candidate, DNL788. Sanofi is responsible, at its cost, for all other Phase 1 and Phase 2 trials for CNS Products, including for multiple sclerosis. Sanofi will lead the conduct of all Phase 3 and later stage development trials for CNS Products, with Sanofi and Denali funding 70 % and 30 % of such costs, respectively. Sanofi will also lead the commercialization activities globally for CNS Products, subject to certain options that Denali has to conduct co-commercialization activities with respect to each CNS Product in the United States and China. Sanofi will be responsible, at its cost, for conducting activities relating to the development and commercialization of all Peripheral Products. Denali will be entitled to receive tiered royalties in the low- to mid- teen percentages on net sales of Peripheral Products. The Company identified the following distinct performance obligations associated with the Sanofi Collaboration Agreement upon inception: the CNS program license, the Peripheral program license, the Phase 1 and Phase 2 trials for CNS Products for Alzheimer’s disease ("Alzheimer's Disease Services"), and the Phase 1b trial for DNL747 for ALS and associated activities ("Retained Activities"). The Company believes that the Sanofi Collaboration Agreement is a collaboration arrangement as defined in ASC 808. The Company also believes that Sanofi meets the definition of a customer as defined in ASC 606, Revenue From Contracts With Customers for three of the performance obligations identified at inception, but does not meet the definition of a customer for the Alzheimer's Disease Services. Further, Sanofi does not meet the definition of a customer for all Phase 3 and later stage development trials for CNS Products led by Sanofi for which Denali will fund 30 % of total costs. Since ASC 808 does not address recognition and measurement, the Company looked to other accounting literature for guidance where the performance obligation does not fall under ASC 606, and determined that for the Alzheimer's Disease Services, the guidance in ASC 606 should be analogized for the recognition, measurement and reporting of this performance obligation, and for the cost sharing provisions, the Company determined that the guidance in ASC 730, Research and Development should be applied. The transaction price at inception included upfront fixed consideration of $ 125.0 million. All potential future milestones and other payments were considered constrained at the inception of the Sanofi Collaboration Agreement since the Company could not conclude it was probable that a significant reversal in the amount recognized would not occur. From inception through June 30, 2020, the transaction price increased by $ 23.5 million, consisting of $ 13.5 million related to costs incurred for Retained Activities that were no longer constrained, and $ 10.0 million related to a milestone triggered in July 2019. The transaction price increased by $ 0.3 million and $ 0.8 million for the three and six months ended June 30, 2020, respectively, and $ 3.4 million and $ 6.8 million for the three and six months ended June 30, 2019, respectively, related entirely to costs incurred for Retained Activities that were determined to no longer be constrained during these periods. The respective standalone value for each of the performance obligations was determined by applying the SSP method and the transaction price allocated based on the relative SSP method with revenue recognition timing to be determined either by delivery or the provision of services. 18 Table of Contents The Company used an adjusted market assessment approach to estimate the selling price for the program licenses, and an expected cost plus margin approach for estimating the Alzheimer’s Disease Services and the Retained Activities. The program licenses and existing know-how were delivered on the effective date of the Sanofi Collaboration Agreement. The Alzheimer’s Disease Services and the Retained Activities are expected to be delivered over time as the services are performed. For the Alzheimer's Disease Services, revenue will be recognized over time using the input method, based on costs incurred to perform the services, since the level of costs incurred over time is thought to best reflect the transfer of services to Sanofi. For the Retained Activities, revenue will be recognized over time using the output method, based on amounts invoiced to Sanofi, since this is believed to directly correlate to the value of the services performed. A contract liability of $ 3.4 million and $ 3.5 million was recorded on the Condensed Consolidated Balance Sheets as of June 30, 2020 and December 31, 2019, respectively. This contract liability relates to the portion of the Alzheimer's Disease Services performance obligation yet to be satisfied, with such amounts to be recognized over the estimated period of the services, which is expected to be several years. There was a receivable of $ 0.3 million and $ 1.2 million at June 30, 2020 and December 31, 2019, respectively, associated with the Sanofi Collaboration Agreement. In assessing the Sanofi Collaboration Agreement, management is required to exercise considerable judgment in estimating revenue to be recognized. Managem ent applies judgment in determining the separate performance obligations, in estimating the selling price, in determining when control was transferred to Sanofi for the licenses, and in estimating total future costs when using the input method. Through June 30, 2020, Denali has received milestone payments of $ 10.0 million and has no t recorded any product sales recorded under the Sanofi Collaboration Agreement. Takeda In January 2018, the Company entered into a Collaboration and Option Agreement ("Takeda Collaboration Agreement") with Takeda Pharmaceutical Company Limited ("Takeda"), pursuant to which the Company granted Takeda an option to develop and commercialize, jointly with the Company, certain biologic products that are enabled by Denali's blood-brain barrier ("BBB") delivery technology and intended for the treatment of neurodegenerative disorders. The programs were Denali’s Antibody Transport Vehicle (“ATV”):BACE1/Tau and ATV:TREM2 and PTV:PGRN programs. The Takeda Collaboration Agreement became effective in February 2018, at which time Takeda paid the Company an upfront payment of $ 40.0 million. Takeda may pay up to an aggregate of $ 25.0 million with respect to each of the three programs directed to a target and based upon the achievement of certain preclinical milestone events, up to $ 75.0 million in total, $ 5.0 million of which was paid upon the Takeda Collaboration Agreement becoming effective. In February 2019, the agreement was amended to replace the ATV:BACE1/Tau program with the ATV:Tau program. The amendment did not have a material impact to the condensed consolidated financial statements. Under the Takeda Collaboration Agreement and unless otherwise agreed jointly between both parties, Denali will be responsible, at its cost, for conducting activities relating to pre-IND development of biologic products directed to the three identified targets and enabled by its BBB delivery technology targeting TfR during the applicable research period. The period through which the option can be exercised continues for each target until the first biologic product directed to the relevant target is IND-ready or approximately five years after selection of the target, whichever is earlier. If Takeda exercises its option with respect to a particular target, then Takeda will have the right to develop and commercialize, jointly with the Company, a specified number of biologic products enabled by its BBB delivery technology that were developed during the research period and which are directed to the relevant target. The Company will grant to Takeda a co-exclusive license under the intellectual property the Company controls related to those biologic products. 19 Table of Contents Takeda is obligated to pay Denali a $ 5.0 million option fee for each target for which Takeda exercises its option, up to $ 15.0 million in total. In addition, if Takeda exercises its option for all three collaboration programs, Takeda may be obligated to pay Denali up to an aggregate of $ 407.5 million upon achievement of certain clinical milestone events and up to an aggregate of $ 300.0 million in regulatory milestone events relating to receipt of regulatory approval in the United States, certain European countries and Japan. Takeda may also be obligated to pay Denali up to $ 75.0 million per biologic product upon achievement of a certain sales-based milestone, or an aggregate of $ 225.0 million if one biologic product from each program achieves this milestone. If Takeda exercises its option for a particular target, Denali and Takeda will share equally the development and commercialization costs, and, if applicable, the profits, for each collaboration program. Pursuant to the terms of the Takeda Collaboration Agreement, the Company entered into a common stock purchase agreement (the "Stock Purchase Agreement") with Takeda on January 3, 2018, pursuant to which Takeda purchased 4,214,559 shares of Denali’s common stock (the "Shares") for an aggregate purchase price of $ 110.0 million. The sale of the Shares closed on February 23, 2018. The fair market value of the common stock sold to Takeda was $ 94.4 million, based on the closing stock price of $ 22.40 on the date of issuance, resulting in a $ 15.6 million premium paid to the Company above the fair value of the Company's common stock which was credited to contract liability in the Company's Condensed Consolidated Balance Sheets. The Company believes that the Takeda Collaboration Agreement is a collaboration arrangement as defined in ASC 808. Further, during the research period, the Company believes that the arrangement is a contract with a customer as defined in ASC 606, Revenue From Contracts With Customers . The Takeda Collaboration Agreement and the Stock Purchase Agreement are being accounted for as one arrangement because they were entered into at the same time with interrelated financial terms. The Company identified performance obligations during the research period consisting of the license, the development options, and joint steering committee ("JSC") participation together with the research services for each collaboration program. The license rights, JSC involvement, option and research services are considered to be a single performance obligation for each program since the research services are highly interrelated with the option and JSC involvement and will significantly modify the license. The performance obligations under each of the three programs are separate since the activities and risks under the programs are distinct. The Company determined that all other goods or services which are contingent upon Takeda exercising its option for each program were not considered performance obligations at the inception of the Takeda Collaboration Agreement. The transaction price at inception included fixed consideration consisting of the upfront fee of $ 40.0 million, the $ 15.6 million premium on the sale of common stock, and the first preclinical milestone payment of $ 5.0 million. It also included variable consideration of $ 26.0 million relating to future milestones that were not constrained. The amount of variable consideration was estimated using the most likely amount method. The remaining $ 44.0 million of preclinical milestones were considered constrained at the inception of the Takeda Collaboration Agreement since the Company could not conclude it is probable that a significant reversal in the amount recognized will not occur. Additionally, cost and profit sharing income, and the development and commercial milestones as outlined above, have not been considered given Takeda has not exercised its options for the development and commercial phases for any program. No change in the transaction price has been recorded since inception. This will be reassessed at each reporting period. The transaction price has been ascribed in its entirety to the three performance obligations identified in the research term of the Takeda Collaboration Agreement. 20 Table of Contents Revenue is recognized when, or as, the Company satisfies its performance obligations by transferring the promised services to Takeda. Revenue is being recognized over time using the input method, based on costs incurred to perform the research services, since the level of costs incurred over time is thought to best reflect the transfer of services to Takeda. There were no material changes in estimates during the three and six months ended June 30, 2020 or June 30, 2019. A contract liability of $ 50.4 million and $ 59.0 million is recorded on the Condensed Consolidated Balance Sheets as of June 30, 2020 and December 31, 2019, respectively. This contract liability relates to the three performance obligations identified, with such amounts to be recognized over the estimated period of the pre-IND research services, which is expected to be several years. There was no receivable as of June 30, 2020 or December 31, 2019, related to the Takeda Collaboration Agreement. Revenue recognized relating to future milestone payments of $ 4.9 million and $ 2.4 million, which the Company concluded is probable that a significant reversal in the amount recognized will not occur, is presented net in the contract liability on the Condensed Consolidated Balance Sheets as of June 30, 2020 and December 31, 2019, respectively. In assessing the Takeda Collaboration Agreement, management is required to exercise considerable judgment in estimating revenue to be recognized. Management applies judgment in determining the separate performance obligations in the research period, estimating variable consideration, and estimating total future costs when using the input method. There is some increase in the judgment required in estimating the timing of future costs due to the COVID-19 pandemic. This is because it is challenging to predict the duration and extent of the impact of the COVID-19 pandemic on the third-party service providers assisting with the Company's ATV:Tau, ATV:TREM2 and PTV:PGRN programs. This may impact the split between current and non-current contract liability on the Condensed Consolidated Balance Sheet in the future. Through June 30, 2020, Denali has received $ 15.0 million in preclinical milestone payments from Takeda and has no t recorded any product sales under the Takeda Collaboration Agreement. Collaboration Revenue Revenue disaggregated by collaboration agreement and performance obligation is as follows (in thousands): Three Months Ended June 30, Six Months Ended June 30, 2020 2019 2020 2019 Takeda Collaboration Agreement (1) $ 5,537 $ 740 $ 8,555 $ 1,422 Sanofi Collaboration Agreement Alzheimer's Disease Services (1) 36 99 88 193 Retained Activities 274 3,358 808 6,787 Total Sanofi Collaboration Revenue 310 3,457 896 6,980 Total Collaboration Revenue $ 5,847 $ 4,197 $ 9,451 $ 8,402 _________________________________________________ (1) Amounts represent revenue recognized during the period that was included in the contract liability balance at the beginning of the period. 21 Table of Contents 7. License Agreements Genentech In June 2016, the Company entered into an Exclusive License Agreement with Genentech, Inc. (“Genentech”). The agreement gives the Company access to Genentech’s leucine-rich repeat kinase 2 (“LRRK2”) inhibitor small molecule program for Parkinson’s disease. Under the agreement, Genentech granted the Company (i) an exclusive, worldwide, sublicensable license under Genentech’s rights to certain patents and patent applications directed to small molecule compounds which bind to and inhibit LRRK2 and (ii) a non-exclusive, worldwide, sublicensable license to certain related know-how, in each case, to develop and commercialize certain compounds and licensed products incorporating any such compound. The Company may owe Genentech milestone payments upon the achievement of certain development, regulatory, and commercial milestones, up to a maximum of $ 315.0 million in the aggregate. These milestones include up to $ 37.5 million in clinical milestone payments, $ 102.5 million in regulatory milestone payments and $ 175.0 million in commercial milestone payments. In addition, the Company may owe royalties on net sales of licensed products ranging from low to high single-digit percentages. To date, the Company has paid Genentech $ 12.5 million in the aggregate, including an upfront fee, a technology transfer fee and a clinical milestone payment, all of which was recorded as research and development expense as incurred. No amounts were recorded in the three and six months ended June 30, 2020 or 2019. 8. Commitments and Contingencies Lease Obligations In May 2018, the Company entered into an amendment to its operating lease for its former corporate headquarters in South San Francisco (the "Headquarters Lease Amendment") to relocate and expand its headquarters to 148,020 rentable square feet in a building in South San Francisco, California (the "New Premises"). The Headquarters Lease Amendment has a contractual term of ten years from the legal commencement date, which was April 1, 2019, when the building was ready for occupancy. For accounting purposes, the lease commencement date was determined to be August 1, 2018, which was the date at which the Company was deemed to have obtained control over the property. The Company has an option to extend the lease term for a period of ten years by giving the landlord written notice of the election to exercise the option at least nine months , but not more than twelve months , prior to the expiration of the Headquarters Lease Amendment lease term. The Company determined that this renewal was not reasonably certain at lease inception. The Headquarters Lease Amendment provides for monthly base rent amounts escalating over the term of the lease. In addition, the Headquarters Lease Amendment provided a tenant improvement allowance ("TIA") of up to $ 25.9 million, which was fully utilized, of which $ 4.4 million will be repaid to the landlord in the form of additional monthly rent. This is recorded as leasehold improvement assets and an offset to the lease ROU asset on the Condensed Consolidated Balance Sheets as of June 30, 2020 and December 31, 2019. The Company is also required to pay the operating expenses for the New Premises, such as taxes and insurance, which are treated as variable lease payments. 22 Table of Contents Management exercised judgment in applying the requirements of ASC 842, including the determination as to whether certain contracts contain a lease and for the Headquarters Lease Amendment, the discount rate used to determine the measurement of the lease liability. As the implicit rate of the Headquarters Lease Amendment was not known, the Company estimated a 9.0 % discount rate, which was management’s estimate of the Company’s incremental borrowing rate. To estimate the incremental borrowing rate, management considered observable debt yields of comparable market instruments, as well as benchmarks within the Headquarters Lease Amendment that may be indicative of the rate implicit in the lease. Total operating lease costs, including variable and short-term lease costs, were $ 2.9 million and $ 5.5 million for the three and six months ended June 30, 2020, respectively, and $ 2.5 million and $ 4.8 million for the three and six months ended June 30, 2019, respectively. Operating lease liabilities are calculated as the net present value of the remaining lease payments over the remaining lease term. In determining the present value of lease payments, the Company uses its incremental borrowing rate based on the information available at the lease commencement date. As of June 30, 2020, the weighted average remaining lease term was 8.8 years and the weighted average discount rate used to determine the operating lease liability was 9.0 %. Cash paid for amounts included in the measurement of lease liabilities for the six months ended June 30, 2020 and June 30, 2019 of $ 4.7 million and $ 1.9 million, respectively, was included in net cash used in operating activities in the Company's Condensed Consolidated Statements of Cash Flows. The following table reconciles the undiscounted cash flows for the next five years and total of the remaining years to the operating lease liabilities recorded in the Condensed Consolidated Balance Sheet as of June 30, 2020 (in thousands): Year Ended December 31: 2020 (six months) $ 5,071 2021 10,391 2022 10,731 2023 11,083 2024 11,447 Thereafter 54,074 Total undiscounted lease payments 102,797 Present value adjustment ( 31,855 ) Net operating lease liabilities $ 70,942 In October 2018, the Company entered into a sublease agreement ("Sublease Agreement") to sublease approximately 36,835 rentable square feet of space in its New Premises. The Sublease Agreement has a term of five years from the commencement date of April 12, 2019 and provides for the Company to receive monthly base rent amounts escalating over the term of the lease. The Company also passes through a portion of the operating expenses, such as taxes and insurance for the New Premises to the sublessee, which are treated as variable sublease income. Total sublease income, including rent and variable sublease cost reimbursements, was $ 1.0 million and $ 1.9 million for the three and six months ended June 30, 2020, respectively, and $ 0.8 million for the three and six months ended June 30, 2019, respectively. 23 Table of Contents The following table details the future undiscounted cash inflows relating to the Sublease Agreement as of June 30, 2020 (in thousands): Year Ended December 31: 2020 (six months) $ 1,431 2021 2,925 2022 3,009 2023 3,096 2024 876 Thereafter — Total undiscounted sublease receipts $ 11,337 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. Commitments Effective 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 on September 6, 2022. As of June 30, 2020 and December 31, 2019, the Company had open non-cancellable purchase orders for biological product development and manufacturing costs totaling $ 18.0 million and $ 21.2 million, respectively. The activities under these purchase orders are expected to be completed by May 2027. As of June 30, 2020 and December 31, 2019, the Company had total non-cancellable purchase commitments under the DMSA of $ 12.1 million and $ 11.2 million, respectively. During the three months ended June 30, 2020 and 2019, the Company incurred costs of $ 3.8 million and $ 3.1 million, respectively, and made payments of $ 2.0 million and $ 3.9 million, respectively, for the development and manufacturing services rendered under the DMSA. During the six months ended June 30, 2020 and 2019, the Company incurred costs of $ 4.8 million and $ 6.7 million, respectively, and made payments of $ 5.2 million and $ 6.5 million, respectively, for the development and manufacturing services rendered under the DMSA. 24 Table of Contents 9. Stock-Based Awards The Company has issued stock-based awards from various equity incentive and stock purchase plans, as more fully described in Note 11, Stock-Based Awards to the consolidated financial statements in the Company's 2019 Annual Report on Form 10-K. Stock Option Activity The following table summarizes option award activity under the Company's 2017 Equity Incentive Plan and the 2015 Stock Incentive Plan: Number of Options Weighted- Average Exercise Price Balance at December 31, 2019 11,640,734 $ 12.96 Granted 3,244,298 24.78 Exercised ( 461,968 ) 7.67 Forfeited ( 232,093 ) 19.08 Balance at June 30, 2020 14,190,971 $ 15.74 Vested and expected to vest at June 30, 2020 12,446,239 $ 17.85 Exercisable at June 30, 2020 5,318,846 $ 13.52 The estimated fair value of stock options granted to employees were calculated using the Black-Scholes option-pricing model using the following assumptions: Six Months Ended June 30, 2020 2019 Expected term (in years) 5.50 - 6.08 5.50 - 6.08 Volatility 65.2 % - 67.1 % 66.9 % - 77.8 % Risk-free interest rate 0.4 % - 1.7 % 2.0 % - 2.6 % Dividend yield — — Restricted Stock Activity Aggregated information regarding restricted stock for the six months ended June 30, 2020 is summarized below: Share Awards & Units Weighted-Average Fair Value at Date of Grant per Share Unvested at December 31, 2019 882,636 $ 18.67 Granted 957,249 24.62 Vested and released ( 118,421 ) 19.13 Forfeited ( 48,412 ) 21.52 Unvested at June 30, 2020 1,673,052 $ 21.98 Expected to vest at June 30, 2020 1,673,052 $ 21.98 25 Table of Contents Stock-Based Compensation Expense The Company’s results of operations include expenses relating to stock-based compensation as follows (in thousands): Three Months Ended June 30, Six Months Ended June 30, 2020 2019 2020 2019 Research and development $ 7,146 $ 5,295 $ 13,200 $ 9,277 General and administrative 5,338 8,419 10,069 11,311 Total $ 12,484 $ 13,714 $ 23,269 $ 20,588 10. 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. Potentially dilutive securities that were not included in the diluted per share calculations because they would be anti-dilutive were as follows: Three and Six Months Ended June 30, 2020 2019 Options issued and outstanding and ESPP shares issuable 14,351,795 12,214,029 Restricted shares subject to future vesting 1,673,052 610,003 Early exercised common stock subject to future vesting — 41,672 Total 16,024,847 12,865,704 11. Subsequent Event On August 5, 2020, the Company entered into a binding Provisional Collaboration and License Agreement (“Provisional Collaboration Agreement”) with Biogen Inc.’s subsidiaries Biogen MA, Inc. and Biogen International GmbH (collectively “Biogen”), to co-develop and co-commercialize Denali’s small molecule inhibitors of LRRK2 for Parkinson’s disease. In addition to the LRRK2 program, Biogen will also receive an exclusive option to license two preclinical programs from our TV platform, which aims to improve brain uptake of biotherapeutics, including our Antibody Transport Vehicle (“ATV”): Abeta program (ATV enabled anti-amyloid beta program) and a second program utilizing our TV technology. Further, Biogen will have right of first negotiation on two additional TV-enabled therapeutics, currently at a preclinical stage, should we decide to seek a collaboration for such programs. Under the terms of the agreement, Biogen will make an upfront payment to Denali of $ 560 million. Should the LRRK2 program achieve certain development and commercial milestones, Denali will be eligible to receive milestone payments exceeding $ 1.1 billion as well as profit sharing and royalties. Biogen and Denali will share responsibility and costs for global development ( 60 percent Biogen; 40 percent Denali), and will share responsibility and costs as well as profits and losses for commercialization in the U.S. ( 50 percent Biogen; 50 percent Denali) and China ( 60 percent Biogen and 40 percent Denali). Outside the U.S. and China, Biogen will be responsible for commercialization and pay Denali tiered royalties. Further, under an associated common stock purchase agreement, Denali will receive proceeds of $ 465 million for the sale of approximately 13.3 million newly issued shares of Denali common stock at $ 34.94 per share, representing approximately 11.2 percent of Denali’s outstanding stock. 26 Table of Contents Closing of the transaction is contingent on satisfaction of requirements under applicable antitrust laws, including the HSR Antitrust Improvements Act of 1976, as amended, in the U.S., and other customary closing conditions, and with respect to the collaboration, execution of a definitive collaboration agreement. 27 Table of Contents