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FORM 10-K ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the fiscal year ended December 31, 2025 TRANSITIONREPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 For the transition period from ___________ to ___________ Commission file number 000-19125 Ionis Pharmaceuticals, Inc.(Exact name of Registrant as specified in its charter) Delaware33-0336973(State or other jurisdiction of incorporation or organization)(IRS Employer Identification No.) 2855 Gazelle Court, Carlsbad, CA92010(Address of Principal Executive Offices)(Zip Code) 760-931-9200(Registrant’s telephone number, including area code) Securities registered pursuant to Section 12(b) of the Act: Title of each classTrading symbolName of each exchange on which registeredCommon Stock, $.001 Par Value“IONS”The Nasdaq Stock Market LLC Securities registered pursuant to Section 12(g) of the Act:None Indicate by check mark if the Registrant is a well-known seasoned issuer, as defined in Rule 405 of the Securities Act. Yes☒No☐ Indicate by check if the Registrant is not required to file reports pursuant to Section 13 or Section 15(d) of the Act. Yes☐No☒ Indicate by check mark whether the Registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the SecuritiesExchange Act of 1934 during the preceding 12 months (or for such shorter period that the Registrant was required to file such reports),and (2) has been subject to such filing requirements for the past 90 days. Yes☒No☐ Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submittedpursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that theregistrant was required to submit such files). Yes☒No☐ Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smallerreporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smallerreporting company,” and “emerging growth company” in Rule 12b-2 of the Exchange Act. Large Accelerated Filer☒ Accelerated Filer☐ Smaller Reporting Company☐Emerging Growth Company☐ Non-accelerated Filer☐ If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period forcomplying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act.☐ Indicate by check mark whether the registrant has filed a report on and attestation to its management assessment of the effectiveness ofits internal controls over financial reporting under Section 404(b) of the Sarbanes-Oxley Act (15 U.S.C. 7262(b)) by the registeredpublic accounting firm that prepared or issued its audit report☒ If securities are registered pursuant to Section 12(b) of the Act, indicate by check mark whether the financial statements of theregistrant included in the filing reflect the correction of an error to previously issued financial statements.☐ Indicate by check mark whether any of those error corrections are restatements that required a recovery analysis of incentive-basedcompensation received by any of the registrant’s executive officers during the relevant recovery period pursuant to §240.10D-1(b).☐ Indicate by check mark whether the Registrant is a shell company (as defined in Rule 12b-2 of the Act). Yes☐No☒ The approximate aggregate market value of the voting common stock held by non-affiliates of the Registrant, based upon the last saleprice of the common stock reported on The Nasdaq Global Select Market was $5,275,488,712 as of June 30, 2025.* The number of shares of voting common stock outstanding as of February 19, 2026 was 165,192,011. DOCUMENTS INCORPORATED BY REFERENCE Portions of the Registrant’s definitive Proxy Statement to be filed on or about April 23, 2026 with the Securities and ExchangeCommission in connection with the Registrant’s annual meeting of stockholders to be held on June 4, 2026 are incorporated byreference into Part III of this Report. *Excludes 25,673,909shares of common stock held by directors and officers and by stockholders whose beneficial ownership isknown by the Registrant to exceed 10 percent of the common stock outstanding at June 30, 2025. Exclusion of shares held by anyperson should not be construed to indicate that such person possesses the power, direct or indirect, to direct or cause the directionof the management or policies of the Registrant, or that such person is controlled by or under common control with the Registrant. FORWARD-LOOKING STATEMENTS This report on Form 10-K and the information incorporated herein by reference includes forward-looking statementsregarding our business and the therapeutic and commercial potential of our commercial medicines, additional medicines indevelopment,