Akebia Therapeutics, Inc. 10-K

Item 9A. Controls and Procedures Management’s Evaluation of our Disclosure Controls and Procedures “Disclosure controls and procedures”, as defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, as amended, or the Exchange Act , are controls and other procedures that are designed to ensure that information required to be disclosed in our reports filed or submitted under the Exchange Act is recorded, processed, summarized and reported within the time periods specified in the U.S. Securities and Exchange Commission, or the SEC , rules and forms. Disclosure controls and procedures include, without limitation, controls and procedures designed to ensure that information required to be disclosed in company reports filed or submitted under the Exchange Act is accumulated and communicated to our management, including our principal executive and principal financial officers, as appropriate to allow timely decisions regarding required disclosure. As required by Rules 13a-15 and 15d-15 under the Exchange Act, our management, with the participation of our principal executive officer and principal financial officer, carried out an evaluation of our disclosure controls and procedures as of December 31, 2023. Based upon their evaluation, our principal executive officer and principal financial officer concluded that as of December 31, 2023, our disclosure controls and procedures were not effective because of a material weakness in the design of our internal control over financial reporting related to our accounting for inventories and inventory related transactions which is described in more detail below. Management’s Annual Report on Internal Control Over Financial Reporting Our management, with the participation of our principal executive officer and principal financial officer, is responsible for establishing and maintaining adequate internal control over financial reporting. Internal control over financial reporting is defined in Rule 13a-15(f) or 15d-15(f) promulgated under the Exchange Act as a process designed by, or under the supervision of, our principal executive officer and principal financial officer and effected by our board of directors, management and other personnel to provide reasonable assurance regarding the reliability of our financial reporting and the preparation of financial statements for external purposes in accordance with accounting principles generally accepted in the United States of America. Our management conducted the assessment of the effectiveness of our internal control over financial reporting as of December 31, 2023, based on criteria established in Internal Control— Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission in 2013. As a result of this assessment, our management has concluded that, as of December 31, 2023, our internal control over financial reporting was ineffective due to the material weakness described below. Akebia Therapeutics, Inc. | Form 10-K | Page 166 Table of Content s Material Weakness - Inventories As of December 31, 2023, our management concluded that we did not design and maintain effective controls over the completeness and accuracy of accounting for inventory and inventory related transactions, including inventory reconciliations, calculation of overheads, presentation of inventories in our balance sheet between short-term and long-term and our liabilities related to the calculation of firm purchase commitment liability. A material weakness is a deficiency, or combination of deficiencies, in internal control over financial reporting, such that there is a reasonable possibility that a material misstatement of a company’s annual or interim consolidated financial statements will not be prevented or detected on a timely basis. Specifically, we did not maintain effective controls related to (i) the review of inventory reconciliations, (ii) the validation of the inventory costing, (iii) the classification of inventory within the balance sheet and cost of product and other revenue related costs in the statement of operations, (iv) the calculation of estimated excess firm purchase commitment liability and (v) the verification that the existence of all inventories subject to physical inventory counts were accurately counted. Remediation Efforts of the Material Weakness - Inventories The control deficiencies described above resulted in certain accounting errors, including in our internal preliminary consolidated financial statements for the year ended December 31, 2023, that were corrected prior to the issuance of such annual consolidated financial statements. Our management has taken, plans to continue to take, actions to remediate the deficiency in our internal control over financial reporting and has implemented new processes, procedures and controls designed to address the underlying causes associated with the material weakness. For example, we are in the process of: (i) implementing and documenting new processes and controls to help ensure the completeness and accuracy of our inventory reconciliations, (ii) engaging additional third-party subject matter experts and accounting personnel with U.S. GAAP experience specific to inventory accounting, (iii) enhancing the accuracy of key reports used to calculate the firm purchase commitment liability; and (iv) establishing effective monitoring and oversight controls to help to ensure the completeness and accuracy of inventory included in our financial statements and related disclosures. These control deficiencies did not have any material impact on our current or prior period consolidated annual or interim financial statements, but could have resulted in material misstatements of our annual or interim financial statements that would not have been prevented or detected on a timely basis. Accordingly, our management has concluded that the control deficiencies were a material weakness in the Company’s internal control over financial reporting. As management continues to evaluate and work to improve our internal control over financial reporting, management may determine it is necessary to take additional measures to address the material weakness. Until the controls have been operating for a sufficient period of time and management has concluded, through testing, that these controls are operating effectively, the material weakness described above will continue to exist. Remediation of Previously Identified Material Weakness - Product Return Reserves As disclosed in our 2022 Annual Report on Form 10-K/A, our management identified a material weakness in our internal control over financial reporting relating to product return reserves. Management is committed to maintaining a strong internal control environment. In response to the material weakness previously identified, management, with the oversight of the Audit Committee of the Board of Directors, took comprehensive actions to remediate the material weakness in internal control over financial reporting relating to our product return reserves, including; (i) designed controls to address the completeness and accuracy of key reports utilized in the execution of internal controls related product return reserve calculations, (ii) engaged additional third party subject matter experts with U.S. GAAP experience specific to product returns accounting and (iii) established effective monitoring and oversight controls to help to ensure the completeness and accuracy of our accrued product returns included in our financial statements and related disclosures as well as continued to engage an outside firm to assist management with performing sufficient testing throughout the year to validate the operating effectiveness of certain controls over financial reporting. These remediation efforts also enhanced our overall financial reporting control environment related to product return reserves. As of December 31, 2023, we determined that our previously reported material weakness related to product return reserves has been remediated. Akebia Therapeutics, Inc. | Form 10-K | Page 167 Table of Content s Changes in Internal Control over Financial Reporting Except for the remediation efforts as noted “—Remediation Efforts of the Material Weakness – Inventory” and “—Remediation of Previously Identified Material Weakness – Returns” above, there have been no changes in our internal control over financial reporting during the year ended December 31, 2023, as defined in Rules 13a-15(f) and 15(d)-15(f) promulgated under the Exchange Act, that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting. Limitations of Effectiveness of Controls and Procedures In designing and evaluating our disclosure controls and procedures, management recognizes that any controls and procedures, no matter how well designed and operated, can provide only reasonable assurance of achieving their objectives and management necessarily applies its judgment in evaluating the cost-benefit relationship of possible controls and procedures. Report of Independent Registered Public Accounting Firm To the Stockholders and the Board of Directors of Akebia Therapeutics, Inc. Opinion on Internal Control Over Financial Reporting We have audited Akebia Therapeutics, Inc.’s internal control over financial reporting as of December 31, 2023, based on criteria established in Internal Control—Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission (2013 framework) (the COSO criteria). In our opinion, because of the effect of the material weakness described below on the achievement of the objectives of the control criteria, Akebia Therapeutics, Inc. (the “Company”) has not maintained effective internal control over financial reporting as of December 31, 2023, based on the COSO criteria. A material weakness is a deficiency, or combination of deficiencies, in internal control over financial reporting, such that there is a reasonable possibility that a material misstatement of the company’s annual or interim financial statements will not be prevented or detected on a timely basis. The following material weakness has been identified and included in management’s assessment. Management has identified a material weakness in controls related to the Company’s inventory process. We also have audited, in accordance with the standards of the Public Company Accounting Oversight Board (United States) (PCAOB), the consolidated balance sheets of the Company as of December 31, 2023 and 2022, the related consolidated statements of operations and comprehensive loss, stockholders’ (deficit) equity and cash flows for each of the two years in the period ended December 31, 2023, and the related notes. This material weakness was considered in determining the nature, timing and extent of audit tests applied in our audit of the 2023 consolidated financial statements, and this report does not affect our report dated March 14, 2024, which expressed an unqualified opinion thereon. Basis for Opinion The Company’s management is responsible for maintaining effective internal control over financial reporting and for its assessment of the effectiveness of internal control over financial reporting included in the accompanying Management’s Annual Report on Internal Control over Financial Reporting. Our responsibility is to express an opinion on the Company’s internal control over financial reporting based on our audit. We are a public accounting firm registered with the PCAOB and are required to be independent with respect to the Company in accordance with the U.S. federal securities laws and the applicable rules and regulations of the Securities and Exchange Commission and the PCAOB. We conducted our audit in accordance with the standards of the PCAOB. Those standards require that we plan and perform the audit to obtain reasonable assurance about whether effective internal control over financial reporting was maintained in all material respects. Our audit included obtaining an understanding of internal control over financial reporting, assessing the risk that a material weakness exists, testing and evaluating the design and operating effectiveness of internal control based on the assessed risk, and performing such other procedures as we considered necessary in the circumstances. We believe that our audit provides a reasonable basis for our opinion. Definition and Limitations of Internal Control Over Financial Reporting A company’s internal control over financial reporting is a process designed to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles. A company’s internal control over financial reporting includes those policies and procedures Akebia Therapeutics, Inc. | Form 10-K | Page 168 Table of Content s that (1) pertain to the maintenance of records that, in reasonable detail, accurately and fairly reflect the transactions and dispositions of the assets of the company; (2) provide reasonable assurance that transactions are recorded as necessary to permit preparation of financial statements in accordance with generally accepted accounting principles, and that receipts and expenditures of the company are being made only in accordance with authorizations of management and directors of the company; and (3) provide reasonable assurance regarding prevention or timely detection of unauthorized acquisition, use, or disposition of the company’s assets that could have a material effect on the financial statements. Because of its inherent limitations, internal control over financial reporting may not prevent or detect misstatements. Also, projections of any evaluation of effectiveness to future periods are subject to the risk that controls may become inadequate because of changes in conditions, or that the degree of compliance with the policies or procedures may deteriorate. /s/ Ernst & Young LLP Boston, Massachusetts March 14, 2024 Item 9B. Other Information Rule 10b5-1 - Director and Officer Trading Arrangements From time to time, the Company's directors and officers (as defined in Rule 16a-1(f) under the Securities Exchange Act of 1934, as amended, or the Exchange Act , engage in open-market transactions with respect to Company securities, including to satisfy tax withholding obligations when equity awards vest or are exercised, and for diversification or other personal reasons. Transactions in Company securities by directors and officers are required to be made in accordance with the Company’s insider trading policy, which requires that the transactions be in accordance with applicable U.S. federal securities laws that prohibit trading while in possession of material nonpublic information. Rule 10b5-1 under the Exchange Act provides an affirmative defense that enables directors and officers to prearrange transactions in the Company’s securities in a manner that avoids concerns about initiating transactions while in possession of material nonpublic information. The following table describes, for the fourth quarter of 2023, each trading arrangement for the sale or purchase of Company securities adopted or terminated by our directors and officers that is either (1) a contract, instruction or written plan intended to satisfy the affirmative defense conditions of Rule 10b5-1(c) (a “Rule 10b5-1 trading arrangement”) or (2) a “non-Rule 10b5-1 trading arrangement” (as defined in Item 408(c) of Regulation S-K): Name (Title) Action Taken (Date of Action) Type of Trading Arrangement Nature of Trading Arrangement Duration of Trading Arrangement Aggregate Number of Securities John P. Butler ( President and Chief Executive Officer ) December 1, 2023 Durable Rule 10b5-1 trading arrangement for sell-to-cover transactions relating to all equity awards that have or may be granted Sale Until final settlement of any RSUs Indeterminable (1) Ellen Snow ( Senior Vice President, Chief Financial Officer and Treasurer ) November 20, 2023 Durable Rule 10b5-1 trading arrangement for sell-to-cover transactions relating to all equity awards that have or may be granted Sale Until final settlement of any RSUs Indeterminable (1) Steven K. Burke, M.D. ( Senior Vice President, Research & Development and Chief Medical Officer ) November 17, 2023 Durable Rule 10b5-1 trading arrangement for sell-to-cover transactions relating to all equity awards that have or may be granted Sale Until final settlement of any RSUs Indeterminable (1) Akebia Therapeutics, Inc. | Form 10-K | Page 169 Table of Content s Michel Dahan ( Senior Vice President, Chief Operating Officer ) December 3, 2023 Durable Rule 10b5-1 trading arrangement for sell-to-cover transactions relating to all equity awards that have or may be granted Sale Until final settlement of any RSUs Indeterminable (1) Nicole R. Hadas ( Senior Vice President, Chief Legal Officer and Corporate Secretary ) November 14, 2023 Durable Rule 10b5-1 trading arrangement for sell-to-cover transactions relating to all equity awards that have or may be granted Sale Until final settlement of any RSUs Indeterminable (1) (1) The number of shares subject to RSUs that will be sold to satisfy applicable tax withholding obligations upon vesting is unknown as the number will vary based on the extent to which vesting conditions are satisfied, the market price of the Company’s common stock at the time of settlement and the potential future grant of additional RSUs subject to this arrangement. This trading arrangement, which applies to RSUs whether vesting is based on the passage of time and/or the achievement of performance goals, provides for the automatic sale of shares that would otherwise be issuable on each settlement date of a RSU in an amount sufficient to satisfy the applicable tax withholding obligation, with the proceeds of the sale delivered to the Company in satisfaction of the applicable tax withholding obligation. Item 9C. Disclosure Regarding Foreign Jurisdictions that Prevent Inspections Not applicable. PART III Item 10. Director, Executive Officers and Corporate Governance The information required by this Item 10 will be included in our Definitive Proxy Statement to be filed with the Securities and Exchange Commission, or SEC, with respect to our 2024 Annual Meeting of Stockholders and is incorporated herein by reference. Item 11. Executive Compensation The information required by this Item 11 will be included in our Definitive Proxy Statement to be filed with the SEC with respect to our 2024 Annual Meeting of Stockholders and, other than the information required by Item 402(v) of Regulation S-K, is incorporated herein by reference. Item 12. Security Ownership of Certain Beneficial Owners and Management and Related Stockholder Matters The information required by this Item 12 will be included in our Definitive Proxy Statement to be filed with the SEC with respect to our 2024 Annual Meeting of Stockholders and is incorporated herein by reference. Item 13. Certain Relationships and Related Transactions, and Director Independence The information required by this Item 13 will be included in our Definitive Proxy Statement to be filed with the SEC with respect to our 2024 Annual Meeting of Stockholders and is incorporated herein by reference. Item 14. Principal Accountant Fees and Services The information required by this Item 14 will be included in our Definitive Proxy Statement to be filed with the SEC with respect to our 2024 Annual Meeting of Stockholders and is incorporated herein by reference. Akebia Therapeutics, Inc. | Form 10-K | Page 170 Table of Content s PART IV Item 15. Exhibits and Financial Statement Schedules (a) Documents filed as part of this Annual Report on Form 10-K. (b) Consolidated Financial Statements Report of Independent Registered Public Accounting Firm Consolidated Balance Sheets Consolidated Statements of Operations and Comprehensive Loss Consolidated Statements of Stockholders’ (Deficit) Equity Consolidated Statements of Cash Flows Notes to Consolidated Financial Statements (2) Schedules Schedules have been omitted as all required information has been disclosed in the consolidated financial statements and related footnotes. (3) Exhibits The Exhibits listed below are filed as part of this Annual Report on Form 10-K. Akebia Therapeutics, Inc. | Form 10-K | Page 171 Table of Content s Incorporated by Reference Exhibit Number Description of Exhibit Schedule/ Form File No. Exhibit Filed Date/ Period End Date 2.1** Agreement and Plan of Merger, dated as of June 28, 2018, by and among Akebia Therapeutics, Inc., Alpha Therapeutics Merger Sub, Inc., and Keryx Biopharmaceuticals, Inc. 8-K 001-36352 2.1 June 28, 2018 2.2 First Amendment to Agreement and Plan of Merger, dated as of October 1, 2018, by and among Akebia Therapeutics, Inc., Alpha Therapeutics Merger Sub, Inc. and Keryx Biopharmaceuticals, Inc. 8-K 001-36352 2.1 October 1, 2018 3.1 Ninth Amended and Restated Certificate of Incorporation 8-K 001-36352 3.1 March 28, 2014 3.2 Certificate of Amendment of Ninth Amended and Restated Certificate of Incorporation of Akebia Therapeutics, Inc. 8-K 001-36352 3.1 June 9, 2020 3.3 Second Amended and Restated Bylaws of Akebia Therape utics, Inc. 8-K 001-36352 3.1 April 28, 2023 4.1 Form of Common Stock Certificate S-1/A 333-193969 4.1 March 4, 2014 4.2 Fourth Amended and Restated Investors’ Rights Agreement, dated March 5, 2014 10-K 001-36352 4.4 March 4, 2015 4.3# Amendment No. 1 to Fourth Amended and Restated Investors’ Rights Agreement, dated June 28, 2017 10-K 001-36352 4.5 March 12, 2018 4.4# Investment Agreement between Akebia Therapeutics, Inc. and Vifor (International) Ltd., dated May 12, 2017 10-Q 001-36352 4.1 August 8, 2017 4.5! Investment Agreement between Akebia Therapeutics, Inc. and Vifor (International) Ltd., dated February 18, 2022 10-K 001-36352 4.5 March 1, 2022 4.6 Description of Registrant’s Securities 10-K 001-36352 4.6 February 25, 2021 4.7* Form of Warrant 10.1† Form of Director and Officer Indemnification Agreement 10-K 001-36352 10.1 March 12, 2018 10.2 Office Lease Agreement Between MA-Riverview/245 First Street, L.L.C. and Akebia Therapeutics, Inc., dated December 3, 2013 S-1 333-193969 10.2 February 14, 2014 10.3 First Amendment to Office Lease Agreement Between Jamestown Premier 245 First, LLC and Akebia Therapeutics, Inc., dated December 15, 2014 10-K 001-36352 10.3 March 4, 2015 10.4 Second Amendment to Office Lease Agreement Between Jamestown Premier 245 First, LLC and Akebia Therapeutics, Inc., dated November 23, 2015 10-K 001-36352 10.4 March 14, 2016 Akebia Therapeutics, Inc. | Form 10-K | Page 172 Table of Content s Incorporated by Reference Exhibit Number Description of Exhibit Schedule/ Form File No. Exhibit Filed Date/ Period End Date 10.5 Third Amendment to Office Lease Agreement Between Jamestown Premier 245 First, LLC and Akebia Therapeutics, Inc., dated July 25, 2016 10-Q 001-36352 10.1 November 9, 2016 10.6 Fourth Amendment to Office Lease Agreement Between CLPF-Cambridge Science Center, LLC and Akebia Therapeutics, Inc., dated May 1, 2017 10-K 001-36352 10.6 March 12, 2018 10.7 Fifth Amendment to Office Lease Agreement Between CLPF-Cambridge Science Center, LLC and Akebia Therapeutics, Inc. dated April 9, 2018 10-Q 001-36352 10.1 August 8, 2018 10.8 Sixth Amendment to Office Lease Agreement Between CLPF-Cambridge Science Center, LLC and Akebia Therapeutics, Inc. dated November 30, 2020 10-K 001-36352 10.8 February 25, 2021 10.9 One Marina Park Drive Office Lease dated April 29, 2015, by and between Keryx Biopharmaceuticals, Inc. and Fallon Cornerstone One MPD LLC 10-K 000-30929 10.29 March 1, 2017 10.10 First Amendment to One Marina Park Drive Office Lease, dated February 24, 2022, by and between Keryx Biopharmaceuticals, Inc. and CLPF One Marina Park Drive LLC (successor-in-interest to Fallon Cornerstone One MPD LLC) 10-K 001-36352 10.10 March 1, 2022 10.11 Assignment and Assumption Agreement, dated February 24, 2022, by and between Keryx Biopharmaceuticals, Inc. and Akebia Therapeutics, Inc. 10-K 001-36352 10.11 March 1, 2022 10.12 Sublease, dated as of September 9, 2019, by and between Keryx Biopharmaceuticals, Inc. and Foundation Medicine, Inc. 10-Q 001-36352 10.1 November 12, 2019 10.13† Amended and Restated 2008 Equity Incentive Plan S-1 333-193969 10.5 February 14, 2014 10.14† Amendment No. 1 to Amended and Restated 2008 Equity Incentive Plan S-1 333-193969 10.6 February 14, 2014 10.15† Executive Employment Agreement with John P. Butler, dated September 16, 2013 S-1 333-193969 10.7 February 14, 2014 10.16† Offer Letter to David Spellman, dated as of June 13, 2020 10-Q 001-36352 10.1 August 10, 2020 10.17† Form of Non-Statutory Stock Option Agreement for O fficers S-1/A 333-193969 10.24 March 4, 2014 10.18† Form of Non-Statutory Stock Option Agreement for Non-Employee Directors S-1/A 333-193969 10.25 March 4, 2014 10.19† A mended and Restated Non-Employee Director Compensation Program, effective April 27, 2 023 10-Q 001-36352 10.1 May 8, 2023 10.20† S econd A mended and Restated Non-Employee Director Compensation Program, effec tive June 6, 2023 10-Q 001-36352 10.8 August 28, 2023 Akebia Therapeutics, Inc. | Form 10-K | Page 173 Table of Content s Incorporated by Reference Exhibit Number Description of Exhibit Schedule/ Form File No. Exhibit Filed Date/ Period End Date 10.21†* Third Amended and Res tated Non-Employee Director Compensation Program, effective January 1 , 202 4 10.22† Form of Executive Severance Agreement for O fficers S-1/A 333-193969 10.27 March 4, 2014 10.23† 2014 Incentive Plan S-1 333-193969 10.29 March 4, 2014 10.24† Amendment No. 1 to the Akebia Therapeutics, Inc. 2014 Incentive Plan S-8 333-229366 4.4 January 25, 2019 10.25† Amended and Restated 2014 Employee Stock Purchase Plan DEF 14A 001-36352 Appendix A April 26, 2019 10.26† Amended and Restated Cash Incentive Plan, effective January 19, 2022 10-K 001-36352 10.28 March 1, 2022 10.27† Form of Officer Restricted Stock Unit Award Agreement under 2014 Incentive Plan 10-K 001-36352 10.18 March 12, 2018 10.28† Form of Officer Restricted Stock Unit Award Agreement under 2014 Incentive Plan 10-K 001-36352 10.29 March 26, 2019 10.29† Form of Officer Inducement Award Non-Statutory Stock Option Agreement S-8 333-222728 4.4 January 26, 2018 10.30† Form of Inducement Award Non-Statutory Stock Option Agreement for N on- O fficers S-8 333-222728 4.5 January 26, 2018 10.31† Form of Officer Performance-Based Stock Option Award, under the Company's 2014 Incentive Plan, as amended 10-Q 001-36352 10.1 November 4, 2021 10.32† Form of Officer Performance-Based Stock Restricted Stock Unit Award, under the Company's 2014 Incentive Plan, as amended 10-Q 001-36352 10.2 November 4, 2021 10.33† Form of Officer Restricted Stock Unit Award Agreement under 2014 Incentive Plan (Retention Awards) 10-Q 001-36352 10.6 August 4, 2022 10.34† Form of Officer Non-Statutory Stock Option Agreement under 2014 Incentive Plan (Retention Awards) 10-Q 001-36352 10.7 August 4, 2022 10.35†! Form of Officer Cash Bonus Letter Agreement 10-Q 001-36352 10.3 November 4, 2021 10.36† Form of Officer Stock Appreciation Rights Award Agreement un der 2014 Incentive Plan 10-Q 001-36352 10.3 May 8, 2023 10.37† Akebia Therapeutics, Inc. 2023 Stock Incentive Plan S-8 333-272453 99.1 June 6, 2023 10.38† Form of Non-Employee Director Stock Option Agreement under 2023 Stock Incentive Plan 10-Q 001-36352 10.10 August 28, 2023 Akebia Therapeutics, Inc. | Form 10-K | Page 174 Table of Content s Incorporated by Reference Exhibit Number Description of Exhibit Schedule/ Form File No. Exhibit Filed Date/ Period End Date 10.39† Form of Non-Employee Director Restricted Stock Unit Agreement under 2023 Stock Incentive Plan 10-Q 001-36352 10.12 August 28, 2023 10.40† Form of Officer Stock Option Agreement under 2023 Stock Incentive Plan 10-Q 001-36352 10.11 August 28, 2023 10.41† Form of Officer Restricted Stock Unit Agreement under 2023 Stock Incentive Plan 10-Q 001-36352 10.13 August 28, 2023 10.42† Form of Officer Inducement Award Stock Option Agreement under 2023 Stock Incentive Plan 10-Q 001-36352 10.14 August 28, 2023 10.43*† Form of Officer Executive Severance Agreement ( Refle cting Clawback Policy) 10.44*† Form of Officer Cash Bonus Agreement ( Reflecting Clawback Policy) 10.45*† Form of Officer Stock Option Agreement under 2023 Stock Incentive Plan ( Reflecting Clawback Policy) 10.46*† Form of Officer Restricted Stock Unit Agreement under 2023 Stock Incentive Plan ( Reflecting Clawback Policy) 10.47*† Form of Officer Inducement Award Stock Option Agreement under 2023 Stock Incentive Plan (Reflecting Clawback Polic y) 10.48† Keryx Biopharmaceuticals, Inc. 1999 Stock Option Plan 10-Q 001-30929 10.2 March 21, 2003 10.49† Keryx Biopharmaceuticals, Inc. 2004 Long-Term Incentive Plan DEF 14A 000-30929 Annex C April 29, 2004 10.50† Amendment to the Keryx Biopharmaceuticals, Inc. 2004 Long-Term Incentive Plan dated April 11, 2006 10-Q 000-30929 10.1 August 9, 2006 10.51† Keryx Biopharmaceuticals, Inc. 2007 Incentive Plan DEF 14A 000-30929 Annex D April 30, 2007 10.52† Keryx Biopharmaceuticals, Inc. Amended and Restated 2013 Incentive Plan 8-K 000-30929 10.1 May 27, 2016 10.53† Keryx Biopharmaceuticals, Inc. 2018 Equity Incentive Plan S-8 333-226005 99.1 June 29, 2018 10.54† Form of Indemnification Agreement between Keryx Biopharmaceuticals, Inc. and its D irectors and O fficers 10-Q 000-30929 10.1 November 9, 2016 10.55† Form of Employee Agreement (Confidentiality, Non-Competition, Non-Solicitation and Development Agreement) applicable to O fficers 10-K 001-36352 10.56 March 26, 2019 Akebia Therapeutics, Inc. | Form 10-K | Page 175 Table of Content s Incorporated by Reference Exhibit Number Description of Exhibit Schedule/ Form File No. Exhibit Filed Date/ Period End Date 10.56† Keryx Biopharmaceuticals, Inc. Fourth Amended and Restated Directors Equity Compensation Plan 8-K 000-30929 10.2 May 27, 2016 10.57† Keryx Biopharmaceuticals, Inc. Third Amended and Restated Directors Equity Compensation Plan 10-Q 000-30929 10.1 August 7, 2014 10.58† Keryx Biopharmaceuticals, Inc. Director Non-Statutory Stock Option Award Terms and Conditions under the Third Amended and Restated Directors Equity Compensation Plan 10-K 001-36352 10.59 March 26, 2019 10.59† Form of Officer Retention Letter Agreement 10-Q 001-36352 10.6 May 9, 2022 10.60†! Form of Retention and Separation Agreement for Michel Dahan and Nicole R. Hadas 10-Q 001-36352 10.7 May 9, 2022 10.61†! Form of Amendment to Retention and Separation Agreement for Michel Dahan and Nicole R. Hadas 10-Q 001-36352 10.2 November 3, 2022 10.62†! Form of May 2023 Amendment to Retention and Separation Agreement for Michel Dahan and Nicole R. Hadas 10-Q 001-36352 10.4 August 28, 2023 10.63†! July 2023 Amendment to Retention and Separation Agreement for Michel Dahan 10-Q 001-36352 10.5 August 28, 2023 10.64†! July 2023 Amendment to Retention and Separation Agreement for Nicole R. Hadas 10-Q 001-36352 10.6 August 28, 2023 10.65†! October 2023 Amendment to Retention and Separation Agreement for Nicole R. Hadas 10-Q 001-36352 10.3 November 8, 2023 10.66*†! February 2024 Amendment to Retention and Separation Agreement for Nicole R. Hadas 10.67*†! February 2024 Amendment to Retention and Separation Agreement for Michel Dahan 10.68† Retention Agreement with David Spellman, dated June 22, 2022 10-Q 001-36352 10.5 August 4, 2022 10.69† Separation Agreement with David Spellman, dated June 9, 2023 and Amendment to Separation Agreement dated July 6, 2023 10-Q 001-36352 10.7 August 28, 2023 10.70 ! Collaboration Agreement between Akebia Therapeutics, Inc. and Mitsubishi Tanabe Pharma Corporation, dated December 11, 2015 10-K 001-36352 10.49 March 1, 2022 10.71# Letter Agreement between Akebia Therapeutics, Inc. and Mitsubishi Tanabe Pharma Corporation, dated September 26, 2017 10-Q 001-36352 10.1 November 8, 2017 Akebia Therapeutics, Inc. | Form 10-K | Page 176 Table of Content s Incorporated by Reference Exhibit Number Description of Exhibit Schedule/ Form File No. Exhibit Filed Date/ Period End Date 10.72! Amendment No. 1 to Collaboration Agreement, dated December 2, 2022, by and between Akebia Therapeutics, Inc. and Mitsubishi Tanabe Pharma Corporation 10-K 001-36352 10.53 March 10, 2022 10.73! Termination and Sett lement Agreement , dated June 30, 2022, by and between the Company and Otsuka P harmaceutical Co. Ltd. 10-Q 001-36352 10.8 August 4, 2022 10.74! Packaging Validation Transfer Agreement, dated April 20, 2023, by and between the Company and Otsuka Pharmaceutical Co. Ltd. 10-Q 001-36352 10.3 August 28, 2023 10.75! Second Amended and Restated License Agreement, dated February 18, 2022, by and between Akebia Therapeutics, Inc. and Vifor (International) Ltd. 10-K 001-36352 10.54 March 1, 2022 10.76 Open Market Sale Agreement SM , dated April 7, 2022, by and between Akebia Therapeutics, Inc. and Jefferies LLC 8-K 001-36352 1.1 April 7, 2022 10.77! Second Amended and Restated License Agreement dated April 17, 2019, by and between Akebia Therapeutics, Inc. and Panion & BF Biotech, Inc. 10-Q 001-36352 10.1 August 8, 2019 10.78# Amended and Restated Sub-License Agreement, dated June 8, 2009, as amended by the First Amendment thereto, dated June 12, 2013, by and between Keryx Biopharmaceuticals, Inc., Japan Tobacco, Inc. and Torii Pharmaceutical Co., Ltd 10-Q 000-30929 10.1 November 7, 2017 10.79! Master Manufacturing Services Agreement by and between Keryx Biopharmaceuticals, Inc. and Patheon Manufacturing Services LLC and certain of its affiliates, dated September 27, 2016, and related Product Agreement dated September 27, 2016, and related Product Agreement dated October 12, 2016 10-K 001-36352 10.58 March 1, 2022 10.80# Product Agreement, dated August 29, 2017, by and between Keryx Biopharmaceuticals, Inc. and Patheon Inc. (an affiliate of Patheon Manufacturing Services LLC) related to the Master Manufacturing Services Agreement by and between Keryx Biopharmaceuticals, Inc. and Patheon Manufacturing Services LLC and certain of its affiliates dated November 12, 2016 10-Q 000-30929 10.2 November 7, 2017 10.81# Master Manufacturing Services and Supply Agreement, dated December 20, 2017, by and between Keryx Biopharmaceuticals, Inc. and Siegfried Evionnaz SA 10-K 000-30929 10.13 February 21, 2018 10.82 Amendment No. 1 to Master Manufacturing Services and Supply Agreement, dated as of December 21, 2020, by and between Siegfried Evionnaz SA and Keryx Biopharmaceuticals, Inc. 10-K 001-36352 10.57 February 25, 2021 10.83 Amendment No. 2 to Master Manufacturing Services and Supply Agreement, dated as of January 29, 2021, by and between Siegfried Evionnaz SA and Keryx Biopharmaceuticals, Inc. 10-K 001-36352 10.58 February 25, 2021 Akebia Therapeutics, Inc. | Form 10-K | Page 177 Table of Content s Incorporated by Reference Exhibit Number Description of Exhibit Schedule/ Form File No. Exhibit Filed Date/ Period End Date 10.84! Amendment No. 3 to Master Manufacturing Services and Supply Agreement, dated as of February 11, 2021, by and between Siegfried Evionnaz SA and Keryx Biopharmaceuticals, Inc. 10-K 001-36352 10.59 February 25, 2021 10.85 Amendment No. 4 to Master Manufacturing Services and Supply Agreement, dated as of December 17, 2021, by and between Siegfried Evionnaz SA and Keryx Biopharmaceuticals, Inc. 10-K 001-36352 10.64 March 1, 2022 10.86! Amendment No. 5 to Master Manufacturing Services and Supply Agreement, dated February 28, 2023, by and between Keryx Biopharmaceuticals, Inc. and Siegfried Evionnaz SA 10-Q 001-36352 10.2 May 8, 2023 10.87# Exclusive Distribution Agreement between Keryx Biopharmaceuticals, Inc. and Cardinal Health 105, Inc., dated October 16, 2014 and First Amendment to Exclusive Distribution Agreement between Keryx Biopharmaceuticals, Inc. and Cardinal Health 105, Inc., dated April 14, 2015 10-K 001-36352 10.60 March 26, 2019 10.88! Termination and Settlement Agreement, dated December 22, 2022, b y and between Keryx Biopharmaceuticals, Inc. and BioVectra Inc. 10-K 001-36352 10.70 March 10, 2023 10.89! Loan Agreement, dated November 11, 2019, by and among the Company, Keryx Biopharmaceuticals, Inc., Biopharma Credit plc and Biopharma Credit Investments V (Master) LP 10-K 001-36352 10.62 March 12, 2020 10.90! First Amendment and Waiver, dated February 18, 2022, by and among the Company, Biopharma Credit plc, B P C R Limited Partnership and Biopharma Credit Investments V (Master) LP 10-K 001-36352 10.69 March 1, 2022 10.91! Second Amendment and Waiver, dated July 15, 2022, by and among the Company, Biopharma Credit plc, B P C R Limited Partnership and Biopharma Credit Investments V (Master) LP 10-Q 001-36352 10.9 August 4, 2022 10.92! Third Amendment to Loan Agreement, dated as of June 30, 2023, by and among the Company, Biopharma Credit plc, BPCR Limited Partnership and Biopharma Credit Investments V (Master) LP 10-Q 001-36352 10.2 August 28, 2023 10.93*! Fourth Amendment to Loan Agreement dated as of October 31, 2023, by and among the Company, BioPharma Credit PLC, BPCR Limted Partnership, and BioPharma Credit Investments V (Master) LP 10.94! Guaranty and Security Agreement, dated November 25, 2019, by and between the Company, Keryx Biopharmaceuticals, Inc. and Biopharma Credit plc 10-K 001-36352 10.63 March 12, 2022 10.95! Supply Agreement, dated as of March 11, 2020, by and between Akebia Therapeutics, Inc. and Patheon, Inc. 10-Q 001-36352 10.1 May 5, 2020 Akebia Therapeutics, Inc. | Form 10-K | Page 178 Table of Content s Incorporated by Reference Exhibit Number Description of Exhibit Schedule/ Form File No. Exhibit Filed Date/ Period End Date 10.96! Supply Agreement, dated as of April 2, 2020, by and between Akebia Therapeutics, Inc. and STA Pharmaceutical Hong Kong Limited 10-Q 001-36352 10.2 August 10, 2020 10.97! Amendment No. 1 to the Supply Agreement, dated as of April 15, 2021, by and between Akebia Therapeutics, Inc, and STA Pharmaceutical Hong Kong Limited 10-Q 001-36352 10.1 August 5, 2021 10.98! Supply Agreement, dated February 10, 2021, by and between the Company and STA Pharmaceutical Hong Kong Limited 10-Q 001-36352 10.4 May 10, 2021 10.99! Royalty Interest Acquisition Agreement, dated February 25, 2021, by and between the Company and HealthCare Royalty Partners IV, L.P. 10-Q 001-36352 10.5 May 10, 2021 10.100! License Agreement, dated December 22, 2022, by and among Akebia Therapeutics, Inc., Keryx Biopharmaceuticals, Inc. and Averoa SAS 10-K 001-36352 10.81 March 10, 2023 10.101! License Agreement, dated May 24, 2023, by and between the Company and MEDICE Arzneimittel Pütter GmbH & Co. KG 10-Q 001-36352 10.1 August 28, 2023 10.102*! A greement for the Provi sion of a Loan Facility dated January 2 9 , 202 4 between the Company and Kreos Capital VII (UK) Limited 10.103* Warra nt Agreement dated January 29, 2024 by and between the Compa ny and Kreos Capital VII Aggregator SCSp 21.1 List of Subsidiaries 10-K 001-36352 21.1 February 25, 2021 23.1* Consent of Ernst & Young LLP 31.1* Certification of Principal Executive Officer Required Under Rule 13a-14(a) of the Securities Exchange Act of 1934, as amended 31.2* Certification of Principal Financial Officer Required Under Rule 13a-14(a) of the Securities Exchange Act of 1934, as amended 32.1* Certification of Principal Executive Officer and Principal Financial Officer Required Under Rule 13a-14(b) of the Securities Exchange Act of 1934, as amended, and 18 U.S.C. 1350 97.1†* Akebia Therapeutics, Inc. Dodd-Frank Compensation Recovery Policy 101.INS* Inline XBRL Instance Document (the instance document does not appear in the Interactive Data File because XBRL tags are embedded within the Inline XBRL document) Akebia Therapeutics, Inc. | Form 10-K | Page 179 Table of Content s Incorporated by Reference Exhibit Number Description of Exhibit Schedule/ Form File No. Exhibit Filed Date/ Period End Date 101.SCH* Inline XBRL Taxonomy Extension Schema Document 101.CAL* Inline XBRL Taxonomy Extension Calculation Linkbase Document 101.DEF* Inline XBRL Taxonomy Extension Definition Linkbase Document 101.LAB* Inline XBRL Taxonomy Extension Labels Linkbase Document 101.PRE* Inline XBRL Taxonomy Extension Presentation Linkbase Document 104 Cover Page Interactive Data File (formatted as Inline XBRL and contained in Exhibit 101) * Filed, or submitted electronically, herewith † Indicates management contract or compensatory plan # Indicates portions of the exhibit (indicated by asterisks) have been omitted pursuant to a request for confidential treatment ! Indicates portions of the exhibit (indicated by asterisks) have been omitted pursuant to Item 601(b)(10)(iv) of Regulation S-K ** The schedules to the Agreement and Plan of Merger have been omitted pursuant to Item 601(b)(2) of Regulation S-K. The Company will furnish copies of such schedules to the Securities and Exchange Commission upon request by the Commission Item 16. Form 10-K Summary None. Akebia Therapeutics, Inc. | Form 10-K | Page 180 Table of Content s SIGNATURES Pursuant to the requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized. AKEBIA THERAPEUTICS, INC. Date: March 14, 2024 By: /s/ John P. Butler John P. Butler President and Chief Executive Officer Pursuant to the requirements of the Securities Exchange Act of 1934, this report was signed by the following persons on behalf of the registrant and in the capacities and on the date indicated. Akebia Therapeutics, Inc. | Form 10-K | Page 181 Table of Content s Date: March 14, 2024 By: /s/ John P. Butler John P. Butler Director, President and Chief Executive Officer (Principal Executive Officer) Date: March 14, 2024 By: /s/ Ellen E. Snow Ellen E. Snow Senior Vice President, Chief Financial Officer and Treasurer (Principal Financial Officer) Date: March 14, 2024 /s/ Richard C. Malabre Richard C. Malabre Chief Accounting Officer (Principal Accounting Officer) Date: March 14, 2024 By: /s/ Adrian Adams Adrian Adams Chairperson and Director Date: March 14, 2024 By: /s/ Ron Frieson Ron Frieson Director Date: March 14, 2024 By: /s/ Steven C. Gilman Steven C. Gilman Director Date: March 14, 2024 By: /s/ Michael Rogers Michael Rogers Director Date: March 14, 2024 By: /s/ Cynthia Smith Cynthia Smith Director Date: March 14, 2024 By: /s/ Myles Wolf Myles Wolf Director Date: March 14, 2024 By: /s/ LeAnne M. Zumwalt LeAnne M. Zumwalt Director Akebia Therapeutics, Inc. | Form 10-K | Page 182