What changed in this filing

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Item 1. Financial Statements

2025-05-08 compared with 2024-11-07 · 372 added, 335 removed, 584 unchanged (55% of the section changed)

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UNAUDITED CONDENSED CONSOLIDATED BALANCE SHEETS

(dollars in thousands, except per share amounts) September 30,

(dollars in thousands, except per share amounts) March 31,

2025 December 31,

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Operating right-of-use assets 7,114 8,218

Intangible asset, net 9,011 36,042

Goodwill 59,044 59,044

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Accrued expenses and other current liabilities 71,337 63,460

Current portion of long-term debt — 17,500

Current portion of deferred revenue 1,241 —

Working Capital Fund liability, current portion 5,991 2,274

Total current liabilities 91,227 80,914

Long-term deferred revenue — 43,296

Long-term operating lease liabilities 2,123 3,547

Long-term debt, net 46,511 38,693

Liability related to settlement royalties 47,731 —

Liability related to settlement royalties, net of current portion 47,440 46,697

Liability related to sale of future royalties, net of current portion 51,549 52,066

Working Capital Fund liability 40,203 40,093

Working Capital Fund liability, net of current portion 34,420 38,013

Warrant liability 7,220 5,176

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Commitments and contingencies (Note 10)

Stockholders' deficit:

Stockholders' equity (deficit):

Preferred stock $ 0.00001 par value, 25,000,000 shares authorized;

no shares issued and

outstanding at September 30, 2024 and December 31, 2023

outstanding at March 31, 2025 and December 31, 2024

Common stock $ 0.00001 par value;

350,000,000 shares authorized at September 30, 2024 and December 31, 2023;

211,542,122 and 194,582,539 shares issued and outstanding at September 30, 2024 and December 31, 2023, respectively

350,000,000 shares authorized at March 31, 2025 and December 31, 2024;

261,644,590 and 224,848,992 shares issued and outstanding at March 31, 2025 and December 31, 2024, respectively

Additional paid-in capital 1,696,821 1,629,167

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Accumulated deficit ( 1,672,248 ) ( 1,678,360 )

Total stockholders' deficit ( 50,402 ) ( 30,584 )

Total liabilities and stockholders' deficit $ 207,142 $ 241,703

Total stockholders' equity (deficit) 24,581 ( 49,185 )

Total liabilities and stockholders' equity (deficit) $ 310,185 $ 220,670

The accompanying notes are an integral part of these unaudited condensed consolidated financial statements.

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Akebia Therapeutics, Inc.

UNAUDITED CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE LOSS

Three Months Ended September 30, Nine Months Ended September 30,

UNAUDITED CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE INCOME (LOSS)

Three Months Ended March 31,

(dollars in thousands, except per share amounts) 2025 2024

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Total operating expenses 36,197 35,938

Loss from operations ( 12,505 ) ( 13,036 ) ( 36,165 ) ( 47,630 )

Income (loss) from operations 13,514 ( 14,936 )

Other income (expense)

Interest expense ( 7,770 ) ( 2,498 )

Other (expense) income ( 17 ) ( 43 ) 39 229

Other income 213 95

Change in fair value of warrant liability 155 ( 129 )

Loss on extinguishment of debt — ( 517 )

Loss on termination of lease — — — ( 524 )

Net loss before income taxes $ ( 20,039 ) $ ( 14,489 ) $ ( 46,606 ) $ ( 52,539 )

Net loss $ ( 20,039 ) $ ( 14,489 ) $ ( 46,606 ) $ ( 52,539 )

Comprehensive loss $ ( 20,039 ) $ ( 14,489 ) $ ( 46,606 ) $ ( 52,539 )

Net loss per share:

Basic and diluted $( 0.10 ) $( 0.08 ) $( 0.22 ) $( 0.28 )

Net income (loss) before income taxes $ 6,112 $ ( 17,985 )

Net income (loss) $ 6,112 $ ( 17,985 )

Comprehensive income (loss) $ 6,112 $ ( 17,985 )

Net income (loss) per share:

Basic $ 0.03 $( 0.09 )

Diluted $ 0.03 $( 0.09 )

Weighted average common shares outstanding:

Basic and diluted 210,348,459 188,306,350 208,343,679 186,643,878

Basic 235,497,720 204,955,151

Diluted 241,602,853 204,955,151

The accompanying notes are an integral part of these unaudited condensed consolidated financial statements.

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Deficit Total Stockholders'

Equity (Deficit)

(dollars in thousands) Shares Amount

Balance at December 31, 2023 194,582,539 $ 2 $ 1,578,358 $ 6 $ ( 1,608,950 ) $ ( 30,584 )

Issuance of common stock, net of

issuance costs 13,261,311 — 18,740 — — 18,740

Proceeds from sale of stock under

employee stock purchase plan 92,321 — 70 — — 70

Exercise of options 280,260 — 141 — — 141

Stock-based compensation expense — — 2,360 — — 2,360

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Balance at March 31, 2024 209,454,149 $ 2 $ 1,599,669 $ 6 $ ( 1,626,935 ) $ ( 27,258 )

Stock-based compensation expense — — 3,490 — — 3,490

Restricted stock unit vesting 2,292,923 — — — — —

Net income — — — — ( 11,172 ) ( 11,172 )

Balance at June 30, 2023 188,128,869 $ 2 $ 1,568,260 $ 6 $ ( 1,595,073 ) $ ( 26,805 )

Proceeds from sale of stock under

employee stock purchase plan 96,694 — 50 — — 50

Stock-based compensation expense

— — 1,824 — — 1,824

Restricted stock unit vesting 88,244 — — — — —

Net loss — — — — ( 14,489 ) ( 14,489 )

Balance at September 30, 2023 188,313,807 $ 2 $ 1,570,134 $ 6 $ ( 1,609,562 ) $ ( 39,420 )

Common Stock Additional Paid-In

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Deficit Total Stockholders'

(Deficit) Equity

(dollars in thousands) Shares Amount

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Restricted stock unit vesting 1,660,547 — — — — —

Net loss — — — — ( 17,985 ) ( 17,985 )

— — — — 6,112 6,112

Balance at March 31, 2025 261,644,590 $ 2 $ 1,696,821 $ 6 $ ( 1,672,248 ) $ 24,581

Exercise of options 23,892 — 14 — — 14

Stock-based compensation expense — — 2,072 — — 2,072

Restricted stock unit vesting 451,104 — — — — —

Net loss — — — — ( 8,582 ) ( 8,582 )

Balance at June 30, 2024 209,929,145 $ 2 $ 1,601,755 $ 6 $ ( 1,635,517 ) $ ( 33,754 )

Issuance of common stock, net of

issuance costs 1,242,662 — 1,662 — — 1,662

Proceeds from sale of stock under

employee stock purchase plan 97,411 — 83 — — 83

Exercise of options 2,312 — — — — —

Stock-based compensation expense — — 1,646 — — 1,646

Restricted stock unit vesting 270,592 — — — — —

Net loss — — — — ( 20,039 ) ( 20,039 )

Balance at September 30, 2024 211,542,122 $ 2 $ 1,605,146 $ 6 $ ( 1,655,556 ) $ ( 50,402 )

The accompanying notes are an integral part of these unaudited condensed consolidated financial statements.

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UNAUDITED CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS

Nine Months Ended September 30,

Three Months Ended March 31,

(dollars in thousands) 2025 2024

Operating Activities:

Net loss $ ( 46,606 ) $ ( 52,539 )

Adjustments to reconcile net loss to net cash used in operating activities:

Net income (loss) $ 6,112 $ ( 17,985 )

Adjustments to reconcile net income (loss) to net cash used in operating activities:

Depreciation 314 364

Amortization of intangible asset — 9,011

Bad debt expense 702 —

Change in fair value of warrant liability ( 155 ) 129

Non-cash royalty revenue related to sale of future royalties ( 369 ) ( 391 )

Non-cash research and development expense — 782

Non-cash interest expense 6,253 326

Non-cash operating lease expense 1,104 1,017

Non-cash write-off from termination of lease — ( 825 )

Non-cash loss on extinguishment of debt — 294

Write-down of inventory 163 590

Change in excess inventory purchase commitments 2,068 —

Gain on the sale of property and equipment ( 172 ) —

Stock-based compensation expense 2,187 2,360

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Purchases of equipment ( 18 ) —

Net cash used in investing activities ( 31 ) —

Proceeds from the sale of property and equipment 172 —

Net cash provided by (used in) investing activities 154 —

Financing Activities:

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Repayment of term debt ( 462 ) ( 36,726 )

Net cash provided by (used in) financing activities 27,338 ( 23,916 )

Decrease in cash, cash equivalents and restricted cash ( 8,886 ) ( 44,992 )

Net cash provided by financing activities 74,942 18,475

Increase (decrease) in cash, cash equivalents and restricted cash 61,509 ( 957 )

Cash, cash equivalents and restricted cash — beginning of period 53,550 44,579

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Issuance of warrants in connection with BlackRock Credit Agreement $ 2,199 $ 4,846

Unpaid issuance costs related to BlackRock Credit Agreement $ — $ 522

The accompanying notes are an integral part of these unaudited condensed consolidated financial statements.

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Akebia Therapeutics, Inc., referred to as Akebia or the Company , was incorporated in the State of Delaware in 2007 and became a public company in 2014.

Akebia is a fully integrated commercial-stage biopharmaceutical company committed to addressing patients' unmet needs.

The Company's purpose is to better the life of each person impacted by kidney disease.

Akebia is a fully integrated commercial-stage biopharmaceutical company focused on developing and commercializing innovative therapeutics.

The Company has two products approved by the Food and Drug Administration, or FDA , in the United States, or U.S.

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Vafseo (vadadustat) Tablets were approved in the U.S.

on March 27, 2024 for the treatment of anemia due to chronic kidney disease, or CKD , in adults who have been receiving dialysis for at least three months.

The Company is launching Vafseo in the U.S.

in March 2024 for the treatment of anemia due to chronic kidney disease, or CKD , in adults who have been receiving dialysis for at least three months.

Vafseo entered the U.S.

market in January 2025.

Auryxia ® (ferric citrate) is marketed for two indications:

(i) the control of serum phosphorus levels in adult patients with dialysis dependent chronic kidney disease, or DD-CKD , and (ii) the treatment of iron deficiency anemia, or IDA, in adult patients with non-dialysis dependent chronic kidney disease, or NDD-CKD .

Auryxia will lose exclusivity in the U.S.

Auryxia lost exclusivity in the U.S.

in March 2025.

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Ferric citrate is also approved in Japan, and is marketed and sold by the Company's collaboration partner, as an oral treatment for the improvement of hyperphosphatemia in patients with CKD, including DD-CKD and NDD-CKD, and for the treatment of adult patients with IDA under the trade name Riona (ferric citrate hydrate).

Since its inception, the Company has devoted most of its resources to research and development, or R&D , including its preclinical and clinical development activities, commercializing Auryxia and providing general and administrative support for these operations.

The Company began recording revenue from the U.S.

sales of Auryxia and revenue from sublicensing rights to Auryxia in Japan from the Company’s Japanese partners, Japan Tobacco, Inc.

and its subsidiary Torii Pharmaceutical Co., Ltd., collectively, JT and Torii , in 2018.

Since its inception, the Company has devoted most of its resources to research and development, or R&D , including its preclinical and clinical development activities, commercializing Auryxia and Vafseo and providing general and administrative support for these operations.

In addition, the Company continues to explore additional development opportunities to expand its pipeline and portfolio of novel therapeutics.

As of September 30, 2024, the Company had cash and cash equivalents of approximately $ 34.0 million.

As of March 31, 2025, the Company had cash and cash equivalents of approximately $ 113.4 million.

Based on its current operating plan, the Company believes that its cash resources and the cash the Company expects to generate from product, royalty, supply and license revenues will be sufficient to fund its current operating plan for at least twelve months from the filing of this Quarterly Report on Form 10-Q, or Form 10-Q .

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In the opinion of management, all adjustments, consisting of normal recurring accruals and revisions of estimates, considered necessary for a fair presentation of the unaudited condensed consolidated financial statements have been included.

Interim results for the three and nine months ended September 30, 2024 are not necessarily indicative of the results that may be expected for the fiscal year ending December 31, 2024 or any other future period.

Interim results for the three months ended March 31, 2025 are not necessarily indicative of the results that may be expected for the fiscal year ending December 31, 2025 or any other future period.

Basis of Presentation and Principles of Consolidation

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Significant estimates and judgments reflected in these unaudited condensed consolidated financial statements include, but are not limited to:

accrued expenses, other long-term liabilities, a liability related to settlement royalties, revenues, including various rebates, returns and reserves related to product sales, inventories, classification of expenses between cost of goods sold, R&D and selling, general and administrative, long-term assets, including the Company's right-of-use assets, intangible asset and goodwill.

Cash, Cash Equivalents and Restricted Cash

In determining its cash, cash equivalents and restricted cash, the Company considers only those highly liquid investments, readily convertible to cash within 90 days from the date of purchase to be cash equivalents.

As of September 30, 2024, cash and cash equivalents primarily included cash on hand.

As of March 31, 2025, cash and cash equivalents primarily included cash on hand.

Restricted cash represents amounts required to secure the outstanding letter of credit in connection with the Company’s office and laboratory space in Cambridge, Massachusetts, or the Cambridge Lease .

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The following table reconciles cash, cash equivalents and restricted cash reported within the Company's consolidated balance sheets to the total amounts showing in the consolidated statements of cash flows:

(in thousands) September 30, 2024 December 31, 2023

(in thousands) March 31, 2025 December 31, 2024

Cash and cash equivalents $ 113,374 $ 51,870

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The Company believes that credit risks associated with its customers and collaboration partners are not significant.

The Company's allowance for credit losses was $ 0.5 million and $ 1.0 million as of September 30, 2024 and December 31, 2023, respectively.

The Company's allowance for credit losses was $ 1.9 million and $ 1.2 million as of March 31, 2025 and December 31, 2024, respectively.

The following table summarizes the activity related to the Company's allowance for credit losses (in thousands):

Akebia Therapeutics, Inc.

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

The following table summarizes the activity related to the Company's allowance for credit losses (in thousands):

Nine Months Ended September 30,

Three Months Ended March 31,

Beginning balance $ 1,212 $ 1,029

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Manufacturing and Distribution Risk

The Company is dependent on third-party manufacturers, logistics companies and distributors to supply products for commercial activities associated with its product and product candidates, as applicable.

In particular, the Company relies and expects to continue to rely on a small number of manufacturers to supply it with its requirements for the active pharmaceutical ingredients and formulated drugs related to the Company's product and product candidate activities.

These activities, including the commercialization of Auryxia and Vafseo, could be adversely affected by a significant interruption in the supply of active pharmaceutical ingredients and formulated drugs or distribution of finished product to the market.

The Company is dependent on third-party manufacturers, logistics companies and distributors to supply products for commercial activities associated with its products and product candidates, as applicable.

In particular, the Company relies and expects to continue to rely on a small number of manufacturers to supply it with its requirements for the active pharmaceutical ingredients, or APIs , and formulated drugs related to the Company's product and product candidate activities.

These activities, including the commercialization of Auryxia and Vafseo, could be adversely affected by a significant interruption in the supply of APIs and formulated drugs or distribution of finished product to the market.

Recent Accounting Pronouncements Not Yet Adopted

In November 2023, the FASB issued ASU 2023-07, Improvements to Reportable Segment Disclosures .

ASU 2023-07 requires disclosure of significant segment expenses that are regularly provided to the chief operating decision maker, or CODM, and included within the segment measure of profit or loss, an amount and description of its composition for other segment items to reconcile to segment profit or loss, and the title and position of the entity’s CODM.

ASU 2023-07 will be applied retrospectively and is effective for annual reporting periods in fiscal years beginning after December 15, 2023, and interim reporting periods in fiscal years beginning after December 31, 2024.

The Company is currently reviewing the impact that the adoption of ASU 2023-07 may have on its consolidated financial statements and disclosure.

In December 2023, the FASB issued ASU 2023-09, Income Taxes (Topic 740):

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The Company is currently evaluating ASU 2023-09 and does not expect it to have a material effect on the Company’s consolidated financial statements.

In November 2024, the FASB issued an accounting standards update, ASU 2024-03, which requires new tabular disclosures in the notes to consolidated financial statements, disaggregating certain cost and expense categories within relevant captions on the consolidated statements of operations and comprehensive income (loss).

The prescribed cost and expense categories requiring disaggregated disclosures include purchases of inventory, employee compensation, depreciation and intangible asset amortization, along with certain other expense disclosures already required by GAAP that would need to be integrated within the new tabular disaggregated expense disclosures.

Additionally, the amendments require the disclosure of total selling expenses and an entity's definition of those expenses.

ASU 2024-03 will be effective for annual reporting periods in fiscal years beginning after December 15, 2026, and interim reporting periods in fiscal years beginning after December 31, 2027.

Early adoption is permitted and the amendments should be applied on a prospective basis.

Retrospective application is permitted.

The Company is currently reviewing the impact that the adoption of ASU 2024-03 may have on its expense disclosures in the notes to the consolidated financial statements.

FAIR VALUE OF FINANCIAL INSTRUMENTS

The tables below present certain assets and liabilities measured at fair value categorized by the level of input used in the valuation of each asset and liability (in thousands):

September 30, 2024

March 31, 2025

Level 1 Level 2 Level 3 Total Fair Value

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Level 1 Level 2 Level 3 Total Fair Value

Cash equivalents:

Money market funds $ 1,504 $ — $ — $ 1,504

Long-term liability:

Warrant liability $ — $ 5,176 $ — $ 5,176

Warrant liability – The warrant liability is classified within Level 2 of the fair value hierarchy because it is valued using inputs which are observable either directly or indirectly.

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volatility, risk-free rate, dividend yield and expected term.

Cash equivalents — Money market funds included within cash and cash equivalents are classified within Level 1 of the fair value hierarchy because they are valued using quoted market prices in active markets.

As of September 30, 2024, the Company did not have any money market funds included in cash equivalents.

Akebia Therapeutics, Inc.

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Inventories consists of the following (in thousands):

September 30, 2024 December 31, 2023

March 31, 2025 December 31, 2024

Inventories, current:

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Work-in-process 35,585 34,572

Finished goods

Inventories, long-term 35,966 34,953

Total inventories $ 55,698 $ 51,196

Inventory written down for Auryxia as a result of excess, obsolescence, scrap or other reasons charged to cost of product and other revenue in the unaudited condensed consolidated statements of operations and comprehensive loss totaled approximately $ 1.3 million and $ 2.4 million during the three and nine months ended September 30, 2024, respectively, and $ 0.7 million and $ 1.3 million during the three and nine months ended September 30, 2023, respectively.

For the three and nine months ended September 30, 2024, the Company realized lower cost of product and other revenue of $ 3.7 million and $ 12.3 million, respectively, due to the Company's ability to commercially sell inventory previously written down to zero, its then net realizable value.

Prior to the FDA’s approval of Vafseo on March 27, 2024, all costs for the manufacture of product to support clinical development and commercial launch, including pre-launch inventory, were expensed as incurred.

Pre-launch inventory manufactured prior to the FDA approval of Vafseo will be used in commercial production until it is depleted.

As of September 30, 2024 and December 31, 2023, the Company had cumulatively expensed $ 28.4 million in pre-launch inventory costs for Vafseo intended for the U.S.

Inventory written down as a result of excess, obsolescence, scrap or other reasons charged to cost of product and other revenue in the unaudited condensed consolidated statements of operations and comprehensive income (loss) totaled approximately $ 0.2 million and $ 0.6 million during the three months ended March 31, 2025 and 2024, respectively.

For the three months ended March 31, 2024, the Company realized lower cost of product and other revenue of $ 3.7 million due to the Company's ability to sell inventory previously written down to zero, its then net realizable value.

INTANGIBLE ASSET AND GOODWILL

Intangible Asset

Intangible asset, net of accumulated amortization, prior impairments and adjustments as of September 30, 2024 and December 31, 2023 consisted of the following (in thousands):

September 30, 2024 December 31, 2023

Intangible asset:

Gross Carrying

Value Accumulated Amortization Net Book Value Net Book Value Estimated Useful Life

Developed product rights for Auryxia $ 214,705 $ ( 205,694 ) $ 9,011 $ 36,042 6 years

The Company recorded $ 9.0 million in amortization expense for each of the three months ended September 30, 2024 and 2023, and $ 27.0 million for each of the nine months ended September 30, 2024 and 2023 related to the developed product rights for Auryxia.

As of September 30, 2024 and December 31, 2023, the Company had goodwill of $ 59.0 million in connection with the December 2018 merger with Keryx.

The Company has not i dentified any goodwill impairment to date.

The Company maintained a definite-lived intangible asset related to developed product rights for Auryxia.

The intangible asset was initially recorded at fair value and was stated net of accumulated amortization.

The Company amortized the intangible asset using the straight-line method over the estimated useful life of six years .

The intangible asset was fully amortized as of December 31, 2024.

The Company recorded $ 9.0 million in amortization expense for the three months ended March 31, 2024 related to the developed product rights for Auryxia.

As of each of March 31, 2025 and December 31, 2024, the Company had goodwill of $ 59.0 million in connection with the December 2018 merger with Keryx.

The Company has not identified any goodwill impairment to date.

ADDITIONAL BALANCE SHEET DETAIL

Prepaid expenses and other current assets are as follows (in thousands):

Akebia Therapeutics, Inc.

| Form 10-Q | Page 9

Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

Description September 30, 2024 December 31, 2023

Description March 31, 2025 December 31, 2024

Prepaid manufacturing $ 1,221 $ 4,029

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Total prepaid expenses and other current assets $ 9,138 $ 11,350

Prepaid manufacturing expenses include advance payments to contract manufacturing organizations, or CMOs , for active pharmaceutical ingredient, or API , or drug substance.

Prepaid manufacturing expenses include advance payments to contract manufacturing organizations, or CMOs , for APIs or drug substance.

Such amounts are reclassified to work-in-process inventory upon the quality release of the batches and transfer of title to the Company from the CMO.

Prior to receiving regulatory approval for Vafseo, such amounts were expensed to R&D upon the quality release of the batches and transfer of title to the Company from the CMO.

See Note 4, Inventories , for further information on inventories, including pre-launch inventory.

Other long-term assets are as follows (in thousands):

Description September 30, 2024 December 31, 2023

Description March 31, 2025 December 31, 2024

Long-term inventories $ 35,966 $ 34,953

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See Note 4, Inventories , for further information on long-term inventories.

Cloud Computing Implementation Costs

The Company incurs costs to implement cloud computing arrangements that are hosted by a third-party vendor.

In accordance with ASC 350-40, Goodwill and Other, Internal-Use Software , for cloud computing arrangements that meet the definition of a service contract, the Company capitalizes qualifying implementation costs incurred during the application development stage as a component of other assets.

Capitalization of these costs concludes once the project is substantially complete and the software is ready for the Company's intended use.

Once available for its intended use, the capitalized costs are amortized on a straight-line basis over the term of the associated hosting arrangement including periods covered by an option to extend, and are included in selling, general and administrative expenses in the consolidated statements of operations and comprehensive loss.

Costs related to data conversion, overhead, general and administrative activities, and training are expensed as incurred.

Post-configuration training and maintenance costs will be expensed as incurred.

Prepaid expenses and other current assets and other long-term assets as of September 30, 2024 included approximately $ 0.2 million and $ 0.7 million of capitalized implementation costs, respectively.

There were no implementation costs capitalized as of December 31, 2023.

Amortization expense for the capitalized implementation costs was $ 0.1 million for the three and nine months ended September 30, 2024.

There was no amortization expense for the three and nine months ended September 30, 2023.

Akebia Therapeutics, Inc.

| Form 10-Q | Page 9

Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

Accrued expenses and other current liabilities consists of the following (in thousands):

September 30, 2024 December 31, 2023

March 31, 2025 December 31, 2024

Product revenue allowances $ 27,451 $ 15,727

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Accrued manufacturing costs 1,580 1,468

Restructuring costs, current portion 762 737

Restructuring costs 251 489

BioVectra, Inc.

termination fees, current portion 9,421 7,500

termination fees 4,894 7,204

Liability related to sale of future royalties, current portion 2,048 2,039

Settlement royalties liability, current portion 10,577 5,924

Other 3,088 3,840

Total accrued expenses and other current liabilities $ 71,337 $ 63,460

Akebia Therapeutics, Inc.

| Form 10-Q | Page 10

Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

Entry into BlackRock Loan Facility

On January 29, 2024, or the Closing Date , the Company entered into the Agreement for the Provision of a Loan Facility, or the BlackRock Credit Agreement, with Kreos Capital VII (UK) Limited , or Kreos , which are funds and accounts managed by BlackRock Inc., collectively, BlackRock , and provides for a senior secured term loan facility in the aggregate principal amount of up to $ 55.0 million, or the Term Loan Facility .

The Term Loan Facility is available in three tranches (i) Tranche A — $ 37.0 million was funded on the Closing Date and used to repay the Pharmakon Term Loans;

(ii) Tranche B — $ 8.0 million was funded on April 19, 2024, or the Tranche B Closing Date , and (iii) Tranche C — $ 10.0 million is available in a single draw through December 31, 2024, collectively the Term Loans .

Tranche C is available subject to receipt of a certain amount of cumulative gross cash proceeds after the Closing Date in the form of equity or equity linked securities in one or more series of transactions.

On the Closing Date, the Company drew $ 34.5 million on Tranche A, after deducting debt issuance costs, fees and expenses.

On the Tranche B Closing Date, the Company drew $ 7.5 million, after deducting debt issuance costs, fees and expenses.

The Term Loan Facility was available in three tranches (i) Tranche A — $ 37.0 million was funded on the Closing Date and used to repay the Pharmakon Term Loans;

(ii) Tranche B — $ 8.0 million was funded on April 19, 2024, or the Tranche B Closing Date , and (iii) Tranche C — $ 10.0 million was funded on February 3, 2025, or the Tranche C Closing Date , collectively the Term Loans .

On February 3, 2025, the Company and Kreos entered into a Second Amendment to the BlackRock Credit Agreement , or the Second Amendment , which, among other things, extended the expiry date of Tranche C from December 31, 2024 to the Tranche C Closing Date, or the Extended Tranche C .

Tranche C was available subject to receipt of a certain amount of cumulative gross cash proceeds after the Closing Date in the form of equity or equity linked securities in one or more series of transactions.

The terms of the Extended Tranche C are substantially similar to the terms of the original Tranche C, however, interest will accrue on the Extended Tranche C as if it was advanced on December 31, 2024.

On the Closing Date, the Company received $ 34.5 million on Tranche A, after deducting debt issuance costs, fees and expenses.

On the Tranche B Closing Date, the Company received $ 7.5 million, after deducting debt issuance costs, fees and expenses.

On the Tranche C Closing Date, the Company received $ 9.3 million, after deducting debt issuance costs, interest, fees and expenses.

The BlackRock Term Loan Facility had an initial maturity date of March 31, 2025, which was automatically extended to January 29, 2028, after the Company received FDA approval for Vafseo, or the BlackRock Maturity Date .

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The Term Loan Facility will accrue interest at a floating annual rate equal to the sum of (i) term Secured Overnight Financing Rate , or SOFR , for a tenor of one month (subject to a floor of 4.25 % per annum) plus (ii) a margin of 6.75 % per annum (subject to an overall cap of 15.00 % per annum on the all-in interest rate).

As of September 30, 2024, the Company's interest rate was 11.59 %.

The Company recognized interest expense related to the BlackRock Credit Agreement of $ 1.7 million and $ 5.5 million during the three and nine months ended September 30, 2024, respectively.

As of March 31, 2025, the Company's interest rate was 11.07 %.

The Company recognized interest expense related to the BlackRock Credit Agreement of $ 2.1 million and $ 1.0 million during the three months ended March 31, 2025 and 2024, respectively.

During the continuance of any payment event of default under the BlackRock Credit Agreement, the interest rate on such overdue sum will automatically increase by an additional 3.0 % per annum, and may be subject to an additional late fee of 2.0 % of such overdue sum.

The Term Loan Facility also includes transaction fees ranging from 1.00 % to 1.25 % of the draw down amount as well exit fees of 0.75 % of the amount funded to the relevant tranche.

Akebia Therapeutics, Inc.

| Form 10-Q | Page 10

Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

If the Company prepays the outstanding loan prior to maturity, it will be required to pay a prepayment fee ranging from 1.0 % to 4.0 % of the amount prepaid.

If prepayment is made during the first year, the Company also is required to pay the amount of otherwise due interest payments for the twelve-month period following prepayment.

As of September 30, 2024, future principal payments under the BlackRock Credit Agreement are as follows (in thousands):

As of March 31, 2025, future principal payments under the BlackRock Credit Agreement are as follows (in thousands):

Principal Payments

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If an event of default occurs and is continuing under the BlackRock Credit Agreement, BlackRock is entitled to take enforcement action, including acceleration of amounts due and it could limit the Company's ability to make certain payments under the Vifor Termination Agreement (as defined below).

Akebia Therapeutics, Inc.

| Form 10-Q | Page 11

Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

On July 10, 2024, in connection with the Vifor Termination and Settlement Agreement, or the Vifor Termination Agreement , the Company and Kreos entered into a First Amendment to the BlackRock Credit Agreement, or the BlackRock Credit Amendment , which amended certain provisions of the BlackRock Credit Agreement.

On the Closing Date, Kreos Capital VII Aggregator SCSp, an affiliate of Kreos, or the Warrant Holder , received a warrant to purchase 3,076,923 shares of the Company’s common stock, at an exercise price per share of $ 1.30 , or the Initial Warrant , and upon borrowing of Tranche C, the Company would become obligated to issue to the Warrant Holder additional warrants to purchase 1,153,846 shares of the Company’s common stock at an exercise price per share of $ 1.30 .

See Note 8, Liability Related to Settlement Royalties, Working Capital Fund Liability and Liability Related to Sale of Future Royalties , for further information on the Vifor Termination Agreement.

On the Tranche C Closing Date, the Company issued the Warrant Holder additional warrants to purchase 1,153,846 shares of the Company’s common stock at an exercise price per share of $ 1.30 , or the Tranche C Warrant .

Each warrant shall be exercisable for eight years from the date of issuance.

The Initial Warrant is liability classified under ASC 815, Derivatives and Hedging , as it could potentially require net cash settlement outside of the Company’s control.

The Initial Warrant is measured at fair value each period with changes in fair value presented within the unaudited condensed consolidated statements of operations and comprehensive loss.

The fair value of the warrant liability was $ 3.5 million as of September 30, 2024.

The Initial Warrant and the Tranche C Warrant are liabilities classified under ASC 815, Derivatives and Hedging , as they could potentially require net cash settlement outside of the Company’s control.

The Initial Warrant and the Tranche C Warrant are measured at fair value each period with changes in fair value presented within the unaudited condensed consolidated statements of operations and comprehensive income (loss).

The fair value of the warrant liability was $ 7.2 million and $ 5.2 million as of March 31, 2025 and December 31, 2024, respectively.

See Note 3, Fair Value of Financial Instruments , for information on the fair value determination.

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Pharmakon Term Loans (Extinguished January 29, 2024)

On November 11, 2019, the Company, with Keryx as guarantor, entered into a loan agreement, or Pharmakon Loan Agreement , with BioPharma Credit PLC as collateral agent and a lender, or Collateral Agent, and BioPharma Credit Investments V (Master) LP as a lender, and a Guaranty and Security Agreement with the Collateral Agent.

BioPharma Credit PLC subsequently transferred its interest in the loans, solely in its capacity as a lender, to its affiliate, BPCR Limited Partnership.

The Collateral Agent and the lenders are collectively referred to as Pharmakon .

The Pharmakon Loan Agreement, as amended, consisted of a secured term loan facility in an aggregate amount of up to $ 100.0 million, or Pharmakon Term Loans , which was made available under two tranches:

(i) Pharmakon Tranche A - $ 80.0 million and (ii) Pharmakon Tranche B - $ 20.0 million.

On November 25, 2019, the Company drew $ 77.3 million on Pharmakon Tranche A, net of fees and expenses of $ 2.7 million.

On December 10, 2020, the Company drew $ 20.0 million on Pharmakon Tranche B, net of immaterial lender expenses and issuance costs.

On November 11, 2019, the Company, with Keryx as guarantor, entered into a loan agreement, or Pharmakon Loan Agreement , which consisted of a secured term loan facility in an aggregate amount of up to $ 100.0 million, or Pharmakon Term Loans .

On the Closing Date, using the proceeds from the BlackRock Credit Agreement, the Company paid the then outstanding principal balance on the Pharmakon Term Loans of $ 35.0 million, plus the outstanding interest and a prepayment fee of $ 0.2 million.

During the nine months ended September 30, 2024, the Company recorded a debt extinguishment loss of $ 0.5 million.

The Pharmakon Term Loans, as amended, bore interest through maturity at a variable rate based on the three month SOFR plus a SOFR adjustment of 0.30 % plus 7.50 %.

The SOFR interest rate was capped at 3.35 % through October 31, 2023, the date of the Fourth Amendment to the Pharmakon Loan Agreement, or Fourth Amendment .

Interest expense related to the Pharmakon Loan Agreement was immaterial for the three and nine months ended September 30, 2024.

The Company recognized $ 1.4 million and $ 4.7 million of interest expense related to the Pharmakon Loan Agreement during the three and nine months ended September 30, 2023, respectively.

See Note 7, Indebtedness , of the Notes to the Consolidated Financial Statements in the 2023 Form 10-K for further details.

LIABILITY RELATED TO SETTLEMENT ROYALTIES, WORKING CAPITAL FUND LIABILITY AND LIABILITY RELATED TO SALE OF FUTURE ROYALTIES

Vifor License Agreement

Summary of Agreement

O n February 18, 2022, the Company entered into a Second Amended and Restated License Agreement, or the Vifor License Agreement , with CSL Vifor, which amended and restated the License Agreement dated May 12, 2017, or the Original License Agreement .

The Vifor License Agreement granted CSL Vifor an exclusive license to sell Vafseo to Fresenius Medical Care North America, or FMCNA , and its affiliates, including Fresenius Kidney Care Group LLC, to certain third-party dialysis organizations

During the three months ended March 31, 2024, the Company recorded a debt extinguishment loss of $ 0.5 million.

Akebia Therapeutics, Inc.

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

approved by the Company, to independent dialysis organizations that are members of certain group purchasing organizations and certain non-retail specialty pharmacies, collectively, the Supply Group , in the U.S.

The Company recognized no interest expense and immaterial interest expense related to the Pharmakon Loan Agreement during the three months ended March 31, 2025 and 2024, respectively.

See Note 7, Indebtedness , of the Notes to the Consolidated Financial Statements in the 2024 Form 10-K for further details.

LIABILITY RELATED TO SETTLEMENT ROYALTIES, WORKING CAPITAL FUND LIABILITY AND LIABILITY RELATED TO SALE OF FUTURE ROYALTIES

Vifor License Agreement

Summary of Agreement

The Vifor License Agreement granted CSL Vifor an exclusive license to sell Vafseo to Fresenius Medical Care North America and its affiliates, including Fresenius Kidney Care Group LLC, to certain third-party dialysis organizations approved by the Company, to independent dialysis organizations that are members of certain group purchasing organizations and certain non-retail specialty pharmacies, collectively, the Supply Group , in the U.S.

The Vifor License Agreement was structured as a profit share arrangement between the Company and CSL Vifor in which the Company would receive approximately 66 % of the profits, net of certain pre-specified costs.

In addition, CSL Vifor made an upfront payment to the Company of $ 25.0 million in February 2022 in connection with the amendment and restatement of the Vifor License Agreement, which was previously recorded as long-term deferred revenue in the consolidated balance sheets.

See Note 8, Deferred Revenue, Refund Liability and Liability Related to Sale of Future Royalties , of the Notes to the Consolidated Financial Statements in the 2023 Form 10-K for a more detailed description of the Vifor License Agreement.

See Note 8, Liability Related to Settlement Royalties, Working Capital Fund Liability and Liability Related to Sale of Future Royalties , of the Notes to the Consolidated Financial Statements in the 2024 Form 10-K for a more detailed description of the Vifor License Agreement.

Investment Agreements

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In February 2022, in connection with the Vifor License Agreement, the Company sold an aggregate of 4,000,000 shares of its common stock, or 2022 Shares , to CSL Vifor at a price per share of $ 5.00 for a total of $ 20.0 million.

The $ 18.3 million representing the premium over the closing stock price, or $ 4.7 million for the 2017 Shares and $ 13.6 million for the 2022 Shares, was previously recorded as long-term deferred revenue in the consolidated balance sheets as it represented consideration related to the Vifor License Agreement.

The $ 18.3 million, which represented the premium over the closing stock price, or $ 4.7 million for the 2017 Shares and $ 13.6 million for the 2022 Shares, was previously recorded as long-term deferred revenue in the consolidated balance sheets as it represented consideration related to the Vifor License Agreement.

The 2017 Shares and 2022 Shares are subject to standstill agreement and are subject to voting agreements.

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during a calendar year, or the Settlement Royalty Payments .

The Settlement Royalty Payments will commence upon the first sale of Vafseo by the Company, its affiliates or third-party licensees to a third party for use in the U.S., and will continue until the later of the (i) expiration of the last-to-expire valid claim listed in the FDA Orange Book that would be infringed by the making, using, selling or importing of Vafseo in the U.S.

The Settlement Royalty Payments commenced upon the first sale of Vafseo by the Company, its affiliates or third-party licensees to a third party for use in the U.S., and will continue until the later of the (i) expiration of the last-to-expire valid claim listed in the FDA Orange Book, or OB , that would be infringed by the making, using, selling or importing of Vafseo in the U.S.

or (ii) the expiration of marketing or regulatory exclusivity for Vafseo in the U.S., or the Settlement Royalty Term .

1 unchanged sentence

during a calendar year in lieu of the above Settlement Royalty Payments.

If the Company exercises the Royalty Buy-Down Option, the WCF Royalty Payments, as described below, will continue as described above.

If the Company exercises the Royalty Buy-Down Option, the WCF Royalty Payments, as described below, will continue as described below.

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| Form 10-Q | Page 12

Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

The WCF Royalty Payments, as described below, the Settlement Royalty Payments and the Royalty Buy-Down Option are in consideration for the termination of the Vifor License Agreement and all obligations thereunder, and the covenants and agreements set forth in the Vifor Termination Agreement, including the settlement and release of all disputes and claims arising from the Vifor License Agreement.

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The liability related to settlement royalties and the amortization are based on the Company’s current estimates of future royalties expected to be paid over the life of the arrangement.

To the extent the Company’s estimates of future

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Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

royalty payments are greater or less than previous estimates or the estimated timing of such payments is materially different than previous estimates, the Company will adjust the effective interest rate and recognize related non-cash interest expense on a prospective basis.

To the extent the Company’s estimates of future royalty payments are greater or less than previous estimates or the estimated timing of such payments is materially different than previous estimates, the Company will adjust the effective interest rate and recognize related non-cash interest expense on a prospective basis.

On a quarterly basis, the Company reassesses the expected royalty payments.

The annual effective interest rate as of September 30, 2024 was 41.0 % which is reflected as interest expense in the unaudited condensed consolidated statements of operations and comprehensive loss.

The Company recognized interest expense of $ 4.4 million for the three and nine months ended September 30, 2024.

As of September 30, 2024, the $ 47.7 million liability related to settlement royalties is classified as a long-term liability based on the timing of payments.

The annual effective interest rate as of March 31, 2025 was 41.0 % which is reflected as interest expense in the unaudited condensed consolidated statements of operations and comprehensive income (loss).

The Company recognized interest expense of $ 5.4 million for the three months ended March 31, 2025.

The Company did not recognize interest expense related to the settlement royalties liability during the three months ended March 31, 2024.

As of March 31, 2025 and December 31, 2024, the balances related to the settlement royalties liability were as follows (in thousands):

March 31, 2025 December 31, 2024

Current portion (included in accrued expenses and other current liabilities)

$ 10,577 $ 5,924

Long-term portion

47,440 46,697

Total settlement royalties liability

$ 58,017 $ 52,621

Working Capital Fund Liability (Previously Referred to as Refund Liability to Customer)

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The deferred gain is amortized to interest income on a straight-line basis over the WCF Royalty Term.

The amortization of the discount was $ 1.1 million and $ 2.7 million for the three and nine months ended September 30, 2024, respectively, and $ 0.7 million and $ 2.4 million for the three and nine months ended September 30, 2023, respectively.

The amortization of the deferred gain was $ 0.9 million and $ 2.6 million for the three and nine months ended September 30, 2024, respectively, and $ 1.0 million and $ 3.0 million for the three and nine months ended September 30, 2023, respectively.

As of September 30, 2024, the $ 40.2 million Working Capital Fund liability is classified as a long-term liability based on management's estimated timing of the repayment of the Working Capital Fund liability to CSL Vifor exceeding one-year.

The amortization of the discount was $ 1.1 million and $ 0.7 million for the three months ended March 31, 2025 and 2024,

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Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

respectively.

The amortization of the deferred gain was $ 1.0 million and $ 0.9 million for the three months ended March 31, 2025 and 2024, respectively.

As of March 31, 2025 and December 31, 2024, the balances related to the Working Capital Fund liability were as follows (in thousands):

March 31, 2025 December 31, 2024

Current portion

$ 5,991 $ 2,274

Long-term portion

34,420 38,013

Total Working Capital Fund liability

$ 40,411 $ 40,287

Liability Related to Sale of Future Royalties

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The liability related to sale of future royalties and the debt amortization are based on the Company’s current estimates of future royalties expected to be paid over the life of the arrangement.

Akebia Therapeutics, Inc.

| Form 10-Q | Page 14

Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

prospective basis.

In the event the Company's estimates of future royalties are less than the proceeds from the sale of future royalties, the Company will not recognize related non-cash interest expense.

On a quarterly basis, the Company reassesses the effective interest rate and adjusts the rate prospectively as needed.

The annual effective interest rate as of September 30, 2024 was 0 % and, therefore the Company did not recognize any non-cash interest expense in the unaudited condensed consolidated statements of operations and comprehensive loss.

As a result of its ongoing involvement in the cash flows related to the royalties and sales milestones in the MTPC Territory, the Company will continue to account for these royalties as non-cash royalty revenue which is reflected in license, collaboration and other revenue in the unaudited condensed consolidated statements of operations and comprehensive loss.

The Company paid $ 0.5 million and $ 1.4 million of royalties to HCR during the three and nine months ended September 30, 2024, respectively, and $ 0.5 million and $ 1.5 million during the three and nine months ended September 30, 2023, respectively.

As of September 30, 2024 and December 31, 2023 the balances were as follows (in thousands):

Liability related to sale of future royalties September 30, 2024 December 31, 2023

The annual effective interest rate as of March 31, 2025 was 0 % and, therefore the Company did not recognize any non-cash interest expense in the unaudited condensed consolidated statements of operations and comprehensive income (loss).

The Company paid $ 0.5 million and $ 0.4 million of royalties to HCR during the three months ended March 31, 2025 and 2024, respectively.

As of March 31, 2025 and December 31, 2024 the balances were as follows (in thousands):

Liability related to sale of future royalties March 31, 2025 December 31, 2024

Current portion (included in accrued expenses and other current liabilities) $ 2,048 $ 2,039

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The Cambridge Lease does not contain residual value guarantees.

In arriving at the operating lease liabilities, the Company applied incremental borrowing rates ranging from 6.65 % to 6.94 %, which were based on the remaining lease term at either the date of adoption of ASC 842 or the effective date of any subsequent lease term extensions.

As of September 30, 2024, the remaining lease term for the Cambridge Lease was 1.95 years.

Operating lease costs were $ 1.2 million and $ 3.7 million for the three and nine months ended September 30, 2024, respectively, and $ 1.2 million and $ 4.4 million for the three and nine months ended September 30, 2023, respectively.

Cash paid for amounts included in the measurement of operating lease liabilities was $ 1.4 million and $ 4.3 million for the three and nine months ended September 30, 2024, respectively, and $ 1.4 million and $ 4.5 million for the three and nine months ended September 30, 2023, respectively.

The security deposit in connection with the Cambridge Lease is $ 1.7 million in the form of a letter of credit, which is included as restricted cash in other long-term assets in the accompanying unaudited condensed consolidated balance sheets as of September 30, 2024 and December 31, 2023.

Sublease and Former Boston Lease

Previously, the Company leased 27,924 square feet of office space in Boston, Massachusetts, or Boston Lease , under a non-cancelable operating lease that was set to expire in July 2031.

The Company subleased the entire Boston Lease, effective October 2019 through February 2023.

The Company did not record any rental income for the three and nine months ended September 30, 2024 and recorded no rental income and $ 0.3 million in rental income as other income in the unaudited condensed consolidated statements of operations and comprehensive loss during the three and nine months ended September 30, 2023, respectively.

In May 2023, pursuant to an Assignment and Assumption of Lease Agreement, or Lease Assignment Agreement, the Company assigned all of its rights, title and interest in, to, and under the Boston Lease to LG Chem Life Sciences Innovation Center, Inc., or LG Chem , and made a payment to LG Chem of $ 1.3 million.

As of May 2023, LG Chem assumed all of the rights and obligations of the Company under the Boston Lease and the Company has no further obligations for rent or other payments under the Boston Lease.

In accordance with ASC 842, Leases , the Company wrote off the right-of-use asset and lease liability associated with the Boston Lease, and recognized the difference between the right-of-use asset and the lease liability offset

In arriving at the operating lease liabilities, the Company applied incremental borrowing rates ranging from 6.65 % to 6.94 %,

Akebia Therapeutics, Inc.

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

by the $ 1.3 million payment as a loss on lease termination in the unaudited condensed consolidated statements of operations and comprehensive loss of $ 0.5 million during the nine months ended September 30, 2023.

which were based on the remaining lease term at either the date of adoption of ASC 842 or the effective date of any subsequent lease term extensions.

As of March 31, 2025, the remaining lease term for the Cambridge Lease was 1.45 years.

Operating lease costs were $ 1.2 million for each of the three months ended March 31, 2025 and 2024.

Cash paid for amounts included in the measurement of operating lease liabilities was $ 1.5 million and $ 1.4 million for the three months ended March 31, 2025 and 2024, respectively.

Future Lease Commitments

1 unchanged sentence

Lease Commitments

Remainder of 2024 $ 1,440

Total lease commitments $ 7,980

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The Company and Siegfried entered into a Master Manufacturing Services and Supply Agreement, most recently amended in February 2023, or the Siegfried Agreement , under which the Company has agreed to purchase a minimum quantity of drug substance of Auryxia at a predetermined price.

As of September 30, 2024, the Company is required to purchase a minimum quantity of drug substance for Auryxia annually at a total cost of approximately $ 22.3 million through the end of 2026.

As of March 31, 2025, the Company is required to purchase a minimum quantity of drug substance for Auryxia annually at a total cost of approximately $ 15.6 million through the end of 2026.

The term of the Siegfried Agreement expires on December 31, 2026.

The Siegfried Agreement provides the Company and Siegfried with certain early termination rights.

The excess firm commitment liability recorded in other long-term liabilities related to the Company's contractual purchase commitments with Siegfried was $ 3.6 million and $ 1.5 million as of September 30, 2024 and December 31, 2023, respectively.

The Company regularly reviews its estimate of the excess firm purchase commitment liability which relates to the amount of minimum purchase commitments under the Siegfried Agreement that exceed the current forecast, including review of assumptions of expected future demand and expiry of inventory.

The excess firm commitment liability recorded in other long-term liabilities was $ 3.6 million as of March 31, 2025 and December 31, 2024.

Patheon Manufacturing

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Under the Patheon Agreement, the Company agreed to purchase from Patheon a certain percentage of the estimated global demand for Vafseo drug product based on certain quarterly and annual forecasts provided by the Company.

As of September 30, 2024, the Company had no minimum commitments with Patheon, however, as estimated global demand fluctuates, the Company may have future obligations under the Patheon Agreement.

As of March 31, 2025, the Company has committed to purchase $ 1.1 million of Vafseo drug product from Patheon through the end of 2026, however, as estimated global demand fluctuates, the Company may have additional future obligations under the Patheon Agreement.

WuXi STA Manufacturing

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Pursuant to the WuXi STA DS Agreement, the Company has agreed to purchase a certain percentage of the global demand for Vafseo drug substance from WuXi STA.

As of September 30, 2024, the Company has committed to purchase $ 6.9 million of Vafseo drug substance from WuXi STA through the first half of 2025.

On February 10, 2021, the Company entered into a Supply Agreement with WuXi STA, which was amended on October 15, 2024, or the WuXi STA DP Agreement , under which WuXi STA will manufacture and supply Vafseo drug product for commercial purposes under a volume-based pricing structure through January 1, 2032.

As of March 31, 2025, the Company has committed to purchase $ 6.1 million of Vafseo drug substance from WuXi STA through the first half of 2025, however, as estimated global demand fluctuates, the Company may have additional future obligations under the WuXi STA DS Agreement.

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Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

Additionally, on February 10, 2021, the Company entered into a Supply Agreement with WuXi STA, which was amended on October 15, 2024, or the WuXi STA DP Agreement , under which WuXi STA will manufacture and supply Vafseo drug product for commercial purposes under a volume-based pricing structure through January 1, 2032.

The Vafseo drug product price is reviewed annually by the Company and WuXi STA.

The Company will also reimburse WuXi STA for certain reasonable expenses.

The Company also reimburses WuXi STA for certain reasonable expenses.

Pursuant to the WuXi STA DP Agreement, the Company has agreed to purchase a certain percentage of global demand for Vafseo drug product from WuXi STA.

2 unchanged sentences

In addition, each party has the ability to terminate the WuXi STA DP Agreement upon the occurrence of certain conditions.

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Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

September 30, 2024, the Company has committed to purchase $ 1.2 million of Vafseo drug product from WuXi STA through the end of 2025.

As of March 31, 2025, the Company has committed to purchase $ 0.9 million of Vafseo drug product from WuXi STA through the end of 2025, however, as estimated global demand fluctuates, the Company may have additional future obligations under the WuXi STA DP Agreement.

Esteve - Assigned Supply Agreement

On April 9, 2019, the Company entered into a Supply Agreement with Esteve Química, S.A., or Esteve , or the Esteve Agreement , under which Esteve would manufacture Vafseo drug substance for commercial use under a volume-based pricing structure.

On December 16, 2022, the Company, Mitsubishi Tanabe Pharma Corporation, or MTPC , and Esteve executed the Esteve Assignment Agreement, pursuant to which the Esteve Agreement was assigned to MTPC.

The Esteve Assignment Agreement transferred the rights and obligations of the Esteve Agreement to MTPC, specifically including the obligations under certain purchase orders issued by the Company and accepted by Esteve.

Although the Esteve Agreement was assigned to MTPC in December 2022, the Company and Esteve have agreed to negotiate the terms of a new commercial supply relationship.

As of March 31, 2025, the Company has committed to purchase $ 7.6 million of Vafseo drug substance from Esteve through the end of 2025.

BioVectra - Former Manufacturing and Unconditional Purchase Commitments

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The discount on the liability balance is being amortized to interest expense using the effective interest rate method over the term of the liability.

The amortization of the discount was $ 0.4 million and $ 1.3 million for the three and nine months ended September 30, 2024, respectively, and $ 0.5 million and $ 1.4 million for the three and nine months ended September 30, 2023, respectively.

In-Licensing - Panion License Agreement

The amortization of the discount was $ 0.2 million and $ 0.5 million for the three months ended March 31, 2025 and 2024, respectively.

License Agreements

Panion License Agreement

On April 17, 2019, the Company and Panion & BF Biotech, Inc., or Panion , entered into a second amended and restated license agreement, or Panion Amended License Agreement , which amended and restated in full the license agreement between the Company and Panion.

The Panion Amended License Agreement provides the Company with an exclusive license under Panion-owned know-how and patents with the right to sublicense, develop, make, use, sell, offer for sale, import and export ferric citrate worldwide, excluding certain Asian-Pacific countries, or the Licensor Territory .

The Panion Amended License Agreement also provides Panion with an exclusive license under the Company-owned patents, with the right to sublicense (with the Company’s written consent), develop, make, use, sell, offer for sale, import and export ferric citrate in certain countries in the Licensor Territory.

The Panion Amended License Agreement also provides Panion with an exclusive license under the Company-owned patents, with the right to

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

sublicense (with the Company’s written consent), develop, make, use, sell, offer for sale, import and export ferric citrate in certain countries in the Licensor Territory.

Under the Panion Amended License Agreement, Panion is eligible to receive from the Company or any sublicensee royalty payments based on a mid-single digit percentage of sales of ferric citrate in the Company’s licensed territories.

1 unchanged sentence

See Note 10, Commitments and Contingencies , of the Notes to the Consolidated Financial Statements in the 2024 Form 10-K for a more detailed description of this license agreement.

The Company incurred royalty payments due to Panion of approximately $ 2.1 million and $ 6.4 million during the three and nine months ended September 30, 2024, respectively, and $ 3.1 million and $ 9.3 million during the three and nine months ended September 30, 2023, respectively, relating to the Company’s sales of Auryxia in the U.S.

and JT and Torii’s net sales of Riona in Japan.

The Company incurred royalty payments due to Panion of approximately $ 2.6 million and $ 1.9 million during the three months ended March 31, 2025 and 2024, respectively, relating to the Company’s sales of Auryxia in the U.S.

and Japan Tobacco, Inc.

and its subsidiary Torii Pharmaceutical Co., Ltd., collectively, JT and Torii’s , net sales of Riona in Japan.

Cyclerion Agreement

In June 2021, the Company entered into a license agreement, or Cyclerion Agreement , with Cyclerion Therapeutics Inc., or Cyclerion , under which the Company obtained an exclusive global license under certain intellectual property rights to research, develop and commercialize praliciguat, an investigational oral soluble guanylate cyclase stimulator.

Under the terms of the Cyclerion Agreement, the Company made an upfront payment of $ 3.0 million to Cyclerion, which was paid during the second quarter of 2021.

Substantially all of the fair value of the assets acquired in conjunction with the Cyclerion Agreement was concentrated in the acquired license.

As a result, the Company accounted for this transaction as an asset acquisition under ASU No.

2017-01, Business Combinations (Topic 805):

Clarifying the Definition of a Business .

The $ 3.0 million upfront payment was charged to research and development expense at acquisition in June of 2021, as it relates to a development stage compound with no alternative future use.

In December 2024, the Company and Cyclerion entered into Amendment #1 to the License Agreement, or the Cyclerion Amendment , pursuant to which the Company agreed to pay Cyclerion (i) $ 1.25 million, which was paid in December 2024, and (ii) $ 0.5 million on or before September 30, 2025.

In addition, the parties agreed to the reduction of certain development milestones and the increase of certain royalty rates on net sales and sublicense income.

During the year ended December 31, 2024, the Company recorded the $ 1.25 million payment and $ 0.5 million future payment to research and development expense in accordance with ASC 730, Research and Development, as praliciguat remains a development stage compound with no alternative future use.

Furthermore, the only contingency as it relates to the $ 0.5 million payment due on or before September 30, 2025 is the passage of time.

Under the Cyclerion Agreement, as amended, Cyclerion is eligible to receive up to an aggregate of $ 198.5 million from the Company in specified development and regulatory milestone payments on a product-by-product basis.

Cyclerion will also be eligible to receive specified commercial milestones as well as tiered royalties ranging from a mid-single-digit percentage to twenty percent of net sales, on a product-by-product basis, and subject to reduction upon expiration of patent rights or the launch of a generic product in the territory.

Unless earlier terminated, the Cyclerion Agreement will expire on a product-by-product and country-by-country basis upon the expiration of the last royalty term, which ends upon the longest of (i) the expiration of the patents licensed under the Cyclerion Agreement, (ii) the expiration of regulatory exclusivity for such product and (iii) ten years from first commercial sale of such product.

The Company may terminate the Cyclerion Agreement in its entirety or only with respect to a particular licensed compound or product upon 180 days' prior written notice to Cyclerion.

The parties also have customary termination rights, subject to a cure period, in the event of the other party’s material breach of the Cyclerion Agreement or in the event of certain additional circumstances.

Other Third-Party Contracts

The Company contracts with various organizations to conduct R&D activities with remaining contract costs to the Company of approximately $ 47.0 million at September 30, 2024.

The Company contracts with various organizations to conduct R&D activities with remaining contract costs to the Company of approximately $ 42.2 million at March 31, 2025.

The scope of the services under these R&D contracts can be modified and the contracts cancelled by the Company upon written notice.

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The Company provides disclosure when a loss in excess of any reserve is reasonably possible, and if estimable, the Company discloses the potential loss or range of possible loss.

Significant judgment is required to assess the likelihood of various

Significant judgment is required to assess the likelihood of various potential outcomes and the quantification of loss in those scenarios.

Changes in the Company’s estimates could have a material impact and are recorded as litigation progresses and new information comes to light.

Although the outcomes of

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

potential outcomes and the quantification of loss in those scenarios.

Changes in the Company’s estimates could have a material impact and are recorded as litigation progresses and new information comes to light.

Although the outcomes of potential legal proceedings are inherently difficult to predict, the Company does not expect the resolution of current legal proceedings to have a material adverse effect on its financial position, results of operations or cash flows of the Company.

potential legal proceedings are inherently difficult to predict, the Company does not expect the resolution of current legal proceedings to have a material adverse effect on its financial position, results of operations or cash flows of the Company.

Guarantees and Indemnifications

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Further, the Company is a party to a variety of agreements in the ordinary course of business under which it may be obligated to indemnify third parties with respect to certain matters.

For the three and nine months ended September 30, 2024 and 2023, the Company did not experience any losses related to these indemnification obligations, and no claims were outstanding as of September 30, 2024.

For the three months ended March 31, 2025 and 2024, the Company did not experience any losses related to these indemnification obligations, and no claims were outstanding as of March 31, 2025.

The Company does not have any claims related to these indemnification obligations and consequently concluded that the fair value of these obligations is negligible and no related accruals were recorded.

PRODUCT REVENUE AND RESERVES FOR VARIABLE CONSIDERATION

To date, the Company’s only source of product revenue has been from the U.S.

Until Vafseo's market entry in January 2025, the Company’s only source of product revenue was from the U.S.

sales of Auryxia.

Total net product revenue was $ 35.6 million and $ 107.8 million for the three and nine months ended September 30, 2024, respectively, and $ 40.1 million and $ 117.1 million for the three and nine months ended September 30, 2023, respectively.

The Company recognized the following revenue from Vafseo and Auryxia (in thousands):

Three Months Ended March 31,

43,757 31,009

Total product revenues

$ 55,791 $ 31,009

(1) Includes the authorized generic version of Auryxia sold and distributed by the Company's authorized generic distribution partner, Mylan Therapeutics, Inc., or AG Partner , during the three months ended March 31, 2025.

The following table presents changes in the Company’s contract assets and liabilities related to the Company's sales to its AG Partner (in thousands):

Three Months Ended March 31, 2025

Period Additions Deductions Balance

Contract assets:

Accounts receivable

$ — $ 1,241 $ — $ 1,241

Contract liabilities:

Deferred revenue

$ — $ 1,241 $ — $ 1,241

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

Product revenue allowance and reserve categories were as follows:

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Credits/payments made ( 1,389 ) ( 8,822 ) ( 145 ) ( 10,356 )

Balance at September 30, 2024 $ 1,343 $ 15,316 $ 4,507 $ 21,166

Balance at March 31, 2025 $ 496 $ 27,451 $ 6,520 $ 34,467

(in thousands) Chargebacks

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Credits/payments made ( 2,216 ) ( 18,282 ) ( 1,974 ) ( 22,472 )

Balance at September 30, 2023 $ 843 $ 23,834 $ 4,644 $ 29,321

Chargebacks, discounts and estimated product returns are recorded as a reduction of revenue in the period the related product revenue is recognized in the unaudited condensed consolidated statements of operations and comprehensive loss.

Balance at March 31, 2024 $ 1,208 $ 13,564 $ 5,798 $ 20,570

Chargebacks are recorded as a reduction to accounts receivable while discounts, rebates, fees and other deductions are recorded with a corresponding increase to accrued expenses and other current liabilities or accounts payable on the condensed consolidated balance sheets.

Estimated product returns on product sales that are not expected to be returned within one year are recorded as other long-term liabilities in the unaudited condensed consolidated balance sheets.

Accounts receivable, net related to product sales, was approximately $ 30.3 million and $ 35.9 million as of September 30, 2024 and December 31, 2023, respectively.

Accounts receivable, net related to product sales, was approximately $ 60.0 million and $ 32.4 million as of March 31, 2025 and December 31, 2024, respectively.

LICENSE, COLLABORATION AND OTHER REVENUE

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

The Company recognized the following revenue from its license, collaboration and other revenue agreements (in thousands):

Three Months Ended September 30, Nine Months Ended September 30,

Three Months Ended March 31,

Entity Description 2025 2024

Medice License and royalties related to the sale of Vafseo in the EU

$ 29 $ — $ 29 $ 10,000

MTPC License and Product Supply of Vafseo in Japan 369 412

JT and Torii License and royalties related to the sale of Riona in Japan 1,169 1,186

Otsuka Terminated U.S.

and International Agreements — — — 2,225

Total license and other revenue $ 1,545 $ 1,598

The following tables present changes in the Company’s contract assets and liabilities related to license and other revenue (in thousands):

Nine Months Ended September 30, 2024

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

Three Months Ended March 31, 2025

Period Additions Deductions Balance

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$ 2,010 $ 1,545 $ ( 1,989 ) $ 1,566

Contract liability:

Deferred revenue (2)

$ 43,296 $ — $ ( 43,296 ) $ —

Nine Months Ended September 30, 2023

Three Months Ended March 31, 2024

Period Additions Deductions Balance

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$ 3,333 $ 2,327 $ ( 2,968 ) $ 2,692

Prepaid expenses and other current assets $ 781 $ — $ ( 781 ) $ —

Contract liabilities:

Deferred revenue (2)

(1) Excludes accounts receivable related to amounts due to the Company from product sales of Auryxia which are included in the accompanying unaudited condensed consolidated balance sheets as of September 30, 2024 and 2023.

$ 43,296 $ 695 $ — $ 43,991

(1) Excludes accounts receivable related to amounts due to the Company from product sales of Auryxia and Vafseo which are included in the accompanying unaudited condensed consolidated balance sheets as of March 31, 2025 and 2024.

(2) See Note 8, Liability Related to Settlement Royalties, Working Capital Fund Liability and Liability Related to Sale of Future Royalties , for further information.

The Company recognized the following revenues as a result of changes in the contract asset and contract liability balances in the respective periods (in thousands):

Three Months Ended September 30, Nine Months Ended September 30,

Three Months Ended March 31,

Revenue Recognized in the Period:

2024 2023 2024 2023

Deferred revenue — beginning of the period $ — $ —

During each of the three and nine months ended September 30, 2024 and 2023, the Company recognized no revenue from performance obligations satisfied in previous periods.

During each of the three months ended March 31, 2025 and 2024, the Company recognized no revenue from performance obligations satisfied in previous periods.

Medice License Agreement

On May 24, 2023, or Medice Effective Date , the Company and MEDICE Arzneimittel Pütter GmbH & Co.

KG, or Medice , entered into a License Agreement, or the Medice License Agreement , pursuant to which the Company granted to Medice an exclusive license to market and sell Vafseo for the treatment of anemia in adult patients with CKD in the Medice Territory.

KG, or Medice , entered into a License Agreement, or the Medice License Agreement , pursuant to which the Company granted to Medice an exclusive license to develop and commercialize Vafseo for the treatment of anemia in adult patients with CKD in the European Economic Area, the United Kingdom, Switzerland and Australia, or collectively the Medice Territory .

Under the Medice License Agreement, the Company received an up-front payment of $ 10.0 million and is eligible to receive the following payments:

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(i) commercial milestone payments up to an aggregate of $ 100.0 million, and

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Accordingly, if the Company develops Vafseo for non-dialysis patients, the Company will account for the joint activities in accordance with ASC No.

808, Collaborative Arrangements , or ASC 808 .

808, Collaborative

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

Arrangements , or ASC 808 .

Additionally, the Company has determined that in the context of the development of Vafseo for non-dialysis patients, Medice does not represent a customer as contemplated by ASC 606.

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The transaction price at inception was comprised of the up-front payment of $ 10.0 million, of which the Company received $ 8.6 million during the quarter ended June 30, 2023.

The remaining $ 1.4 million was withheld by the German Federal Tax Office and is included in prepaid expenses and other current assets as of September 30, 2024 and other long-term assets as of December 31, 2023 on the unaudited condensed consolidated balance sheets.

The remaining $ 1.4 million was withheld by the German Federal Tax Office and was included in prepaid expenses and other current assets as of December 31, 2024 on the audited consolidated balance sheets.

The $ 1.4 million was received during the three months ended March 31, 2025.

Pursuant to the terms of the Medice License Agreement, the up-front payment of $ 10.0 million is non-refundable and non-creditable against any other amount due to the Company and was allocated to the License Performance Obligation, which was satisfied as of the Medice Effective Date.

As such, the Company recognized the $ 10.0 million up-front payment as license, collaboration and other revenue in the unaudited condensed consolidated statements of operations and comprehensive loss during the nine months ended September 30, 2023.

In accordance with ASC 606, the Company will recognize sales-based royalties and milestone payments at the later of when the performance obligation is satisfied or the related sales occur.

During the three and nine months ended September 30, 2024, the Company recognized immaterial revenue from Medice royalties.

The Company did not recognize any revenue from Medice royalties during the three and nine months ended September 30, 2023.

As of September 30, 2024, there were immaterial contract assets, and no accounts receivable, payables or deferred revenue in connection with the Medice License Agreement.

Medice Letter Agreement

On December 6, 2023, the Company and Medice entered into a letter agreement, or the Medice Letter Agreement , pursuant to which the Company agreed to sell to Medice a partial batch of Vafseo in order to achieve packaging validation for the Medice Territory.

The Company previously recognized revenue under this arrangement when risk of loss passed to Medice and delivery occurred.

As of September 30, 2024, there were no accounts receivable, contract assets, payables or deferred revenue recorded in connection with the Medice Letter Agreement.

During the three months ended March 31, 2025, the Company recognized immaterial revenue from Medice royalties.

The Company did not recognize any revenue from Medice royalties during the three months ended March 31, 2024.

As of March 31, 2025, there were immaterial contract assets, and no accounts receivable, payables or deferred revenue in connection with the Medice License Agreement.

Supply of Drug Product to Medice

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

On September 13, 2024, the Company and Medice entered into a supply agreement, or the Medice Supply Agreement , under which the Company will supply Vafseo drug product to Medice for commercial and developmental use in the Medice Territory.

The Company recognizes revenue under this arrangement when risk of loss passes to Medice, delivery has occurred, and Medice has accepted the product.

The Company did not recognize any revenue under the Medice Supply Agreement during the three and nine months ended September 30, 2024 or 2023.

The Company did not recognize any revenue under the Medice Supply Agreement during the three months ended March 31, 2025 or 2024.

MTPC Collaboration Agreement

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In February 2021, the Company entered into the Royalty Agreement with HCR, whereby the Company sold its right to receive royalties and sales milestones under the MTPC Agreement, subject to certain caps and other terms and conditions.

See Note 8, Deferred Revenue, Refund Liability and Liability Related to Sale of Future Royalties , for additional information and Note 12, License, Collaboration and Other Revenue , of the Notes to the Consolidated Financial Statements in the 2023 Form 10-K for a more detailed description of the MTPC Agreement.

See Note 8, Liability Related to Settlement Royalties, Working Capital Fund Liability and Liability Related to Sale of Future Royalties , for additional information and Note 12, License, Collaboration and Other Revenue , of the Notes to the Consolidated Financial Statements in the 2024 Form 10-K for a more detailed description of the MTPC Agreement.

The Company evaluated the elements of the MTPC Agreement in accordance with the provisions of ASC 606 and concluded that the contract counterparty, MTPC, is a customer.

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The Company re-evaluates the transaction price in each reporting period and as uncertain events are resolved or other changes in circumstances occur.

As of September 30, 2024, all development milestones and $ 25.0 million in regulatory milestones have been achieved.

As of March 31, 2025, all development milestones and $ 25.0 million in regulatory milestones have been achieved.

No other regulatory milestones have been assessed as probable of being achieved and as a result have been fully constrained.

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

The Company allocates the transaction price to each performance obligation based on the Company’s best estimate of the relative standalone selling price.

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The Company recognizes any revenue from MTPC royalties in the period in which the sales occur.

The Company recognized revenue from MTPC royalties of $ 0.5 million during each of the three months ended September 30, 2024 and 2023 and $ 1.4 million during each of the nine months ended September 30, 2024 and 2023.

The Company recognized revenue from MTPC royalties of $ 0.4 million during each of the three months ended March 31, 2025 and 2024.

As noted above, in February 2021, the Company entered into the Royalty Agreement, whereby the Company sold its right to receive these royalties and sales milestones under the MTPC Agreement, subject to certain caps and other terms and conditions.

See Note 8, Liability Related to Settlement Royalties, Working Capital Fund Liability and Liability Related to Sale of Future Royalties , for additional information.

The revenue is classified as license and other revenue in the accompanying unaudited condensed consolidated statements of operations and comprehensive loss.

As of September 30, 2024, there were no accounts receivable, payables or deferred revenue and $ 0.5 million in contract assets recorded in connection with the MTPC Agreement.

Supply of Drug Product to MTPC

On July 15, 2020, the Company and MTPC entered into a supply agreement, or MTPC Supply Agreement , under which the Company supplies Vafseo drug product to MTPC for commercial use in Japan and certain other Asian countries, as contemplated by the MTPC Agreement.

See Note 12, License, Collaboration and Other Revenue , of the Notes to the Consolidated Financial Statements in the 2023 Form 10-K for a more detailed description of this supply agreement.

On December 16, 2022, the Company, MTPC and Esteve Química, S.A., or Esteve, executed an Assignment of Supply Agreement, or Esteve Assignment Agreement , pursuant to which the Supply Agreement between the Company and Esteve, or Esteve Agreement was assigned to MTPC.

The Esteve Assignment Agreement transferred the rights and obligations of the Company under the Esteve Agreement to MTPC.

The Company has no further obligation to take delivery of, or pay for, product delivered by Esteve.

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

The Company does not recognize revenue under this arrangement until risk of loss on the drug product passes to MTPC and delivery has occurred and MTPC has accepted the product.

The Company recognized no revenue and $ 0.7 million in revenue under the MTPC Supply Agreement during the three and nine months ended September 30, 2024, respectively, and no revenue and $ 3.7 million in revenue under the MTPC Supply Agreement during the three and nine months ended September 30, 2023, respectively.

As of September 30, 2024, there were no accounts receivable, deferred revenue or other current liabilities relating to the MTPC Supply Agreement.

The revenue is classified as license and other revenue in the accompanying unaudited condensed consolidated statements of operations and comprehensive income (loss).

As of March 31, 2025, there were no accounts receivable, payables or deferred revenue and $ 0.4 million in contract assets recorded in connection with the MTPC Agreement.

JT and Torii Sublicense Agreement

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As such, the Company allocated the entire transaction price to the License and Supply Performance Obligation.

The Company recognized license revenue of $ 1.3 million and $ 3.7 million during the three and nine months ended September 30, 2024, respectively, and $ 1.4 million and $ 4.0 million during the three and nine months ended September 30, 2023, respectively, related to royalties earned on net sales of ferric citrate hydrate in Japan under the trade name Riona.

The Company recognized license revenue of $ 1.2 million during each of the three months ended March 31, 2025 and 2024 related to royalties earned on net sales of ferric citrate hydrate in Japan under the trade name Riona.

The Company records the associated mid-single digit percentage of net sales royalty expense due to Panion, the licensor of Riona, in the same period as the royalty revenue from JT and Torii is recorded.

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Authorized and Outstanding Capital Stock

As of September 30, 2024, the authorized capital stock of the Company included 350,000,000 shares of common stock, $ 0.00001 par value per share, of which 211,542,122 and 194,582,539 shares were issued and outstanding as of September 30, 2024 and December 31, 2023, respectively;

and 25,000,000 shares of undesignated preferred stock, $ 0.00001 par value per share, of which no shares were issued and outstanding as of September 30, 2024 and December 31, 2023.

As of March 31, 2025, the authorized capital stock of the Company included 350,000,000 shares of common stock, $ 0.00001 par value per share, of which 261,644,590 and 224,848,992 shares were issued and outstanding as of March 31, 2025 and December 31, 2024, respectively;

and 25,000,000 shares of undesignated preferred stock, $ 0.00001 par value per share, of which no shares were issued and outstanding as of March 31, 2025 and December 31, 2024.

At-the-Market Facility

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During the year ended December 31, 2023, the Company sold 6,189,974 shares of common stock under this program with gross proceeds of $ 6.8 million ($ 6.7 million, net of offering expenses).

During the nine months ended September 30, 2024, the Company sold 13,261,311 shares of its common stock under this program with gross proceeds of $ 19.2 million ($ 18.7 million, net of offering expenses).

During the three months ended March 31, 2024, the Company sold 13,261,311 shares of its common stock under this program with gross proceeds of $ 19.2 million ($ 18.7 million, net of offering expenses).

On September 3, 2024, in connection with the filing of a new shelf registration statement on Form S-3, the Company filed a prospectus related to the Company's amended and restated sales agreement (which amended and restated the Original Sales Agreement), with Jefferies, as the Company’s sales agent, pursuant to which the Company is able to offer and sell up to $ 75.0 million of its common stock at current market prices from time to time.

During the three and nine months ended September 30, 2024, the Company sold 1,242,662 shares of its common stock under this program with gross proceeds of $ 1.7 million ($ 1.7 million, net of offering expenses).

STOCK-BASED COMPENSATION AND BENEFIT PLAN

Stock-Based Compensation and Benefit Plans

The Company incurred stock-based compensation expenses of $ 1.6 million and $ 6.1 million for the three and nine months ended September 30, 2024, respectively, and $ 1.8 million and $ 7.8 million for the three and nine months ended September 30, 2023, respectively.

Since September 12, 2024 (the date the Company’s shelf registration statement on Form S-3 went effective) through December 31, 2024, the Company sold

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

14,271,631 shares of its common stock under this program with gross proceeds of $ 24.3 million ($ 23.8 million, net of offering expenses).

During the three months ended March 31, 2025, the Company sold 9,437,364 shares of its common stock under this program with gross proceeds of $ 18.7 million ($ 18.4 million, net of offering expenses).

Public Offering

On March 19, 2025, the Company entered into an underwriting agreement, or the Underwriting Agreement , with Leerink Partners LLC and Piper Sandler & Co., as representatives of the several underwriters named therein, collectively, the Underwriters , relating to an underwritten public offering, or the Offering , of 25,000,000 shares, or the Shares , of the Company's common stock.

The offering price was $ 2.00 per share, and the Underwriters agreed to purchase the Shares from the Company pursuant to the Underwriting Agreement at a price of $ 1.88 per share.

Under the terms of the Underwriting Agreement, the Company granted the Underwriters a 30-day option to purchase up to 3,750,000 additional shares of common stock, or the Additional Shares , at the public offering price per share and the Underwriters partially exercised their option and purchased 850,000 Additional Shares on April 22, 2025.

Net proceeds from the Offering of the Shares were $ 46.5 million, after deducting underwriting discounts and commissions and estimated offering expenses and net proceeds from the Offering of the Additional Shares were $ 1.6 million, after deducting underwriting discounts and commissions and estimated offering expenses.

Unregistered Common Stock

In connection with the Vifor License Agreement, CSL Vifor owns 7,571,429 shares of common stock that are unregistered under the Securities Act.

See Note 8, Liability Related to Settlement Royalties, Working Capital Fund Liability and Liability Related to Sale of Future Royalties , for more information.

Warrants to Purchase Common Stock

In connection with the BlackRock Credit Agreement, described in more detail in Note 7, Indebtedness , the Company issued a warrant to purchase 3,076,923 shares of the Company’s common stock, at an exercise price per share of $ 1.30 , and upon the borrowing of Tranche C in February 2025, the Company issued additional warrants to purchase 1,153,846 shares of the Company’s common stock at an exercise price per share of $ 1.30 .

Each warrant is exercisable for eight years from the date of issuance.

The warrants and the common stock issuable upon the exercise of such warrants were not registered under the Securities Act and, accordingly, the holder thereof may only sell common stock issued upon exercise of such warrants pursuant to an effective registration statement under the Securities Act covering the resale of those shares, an exemption under Rule 144 under the Securities Act or another applicable exemption under the Securities Act.

STOCK-BASED COMPENSATION AND BENEFIT PLAN

Stock-Based Compensation and Benefit Plans

The Company incurred stock-based compensation expenses of $ 2.2 million and $ 2.4 million for the three months ended March 31, 2025 and 2024, respectively.

Equity Incentive Plans

The following table contains information about the Company's equity plans:

September 30, 2024 December 31, 2023

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

March 31, 2025 December 31, 2024

Title of Plan Group Eligible Type of Award Granted (or to be Granted) Awards Outstanding Additional Awards Authorized for Grant Awards Outstanding Additional Awards Authorized for Grant

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(3) This table includes inducement awards that are subject to the terms and conditions of the applicable plan but were granted as inducement awards consistent with Nasdaq Listing Rule 5635(c)(4) and not under the applicable plan:

1,195,250 options included as outstanding under the 2014 Plan in the table and 2,528,550 options included as outstanding under the 2023 Plan in the table as of September 30, 2024 and 1,616,019 options included as outstanding under the 2014 Plan and 794,000 options included as outstanding under the 2023 Plan in the table as of December 31, 2023.

1,120,196 options included as outstanding under the 2014 Plan in the table and 2,274,138 options included as outstanding under the 2023 Plan in the table as of March 31, 2025 and 1,151,127 options included as outstanding under the 2014 Plan and 2,534,775 options included as outstanding under the 2023 Plan in the table as of December 31, 2024.

Common Stock Options and Stock Appreciation Rights

During the nine months ended September 30, 2024, the Company issued 3,432,500 options to employees under the 2023 Plan.

During the three months ended March 31, 2025, the Company issued 3,634,400 options to employees under the 2023 Plan.

Options and SARs granted by the Company generally vest over periods of between 12 and 48 months, subject, in each case, to the individual’s continued service through the applicable vesting date.

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The Company also maintains an inducement award program with a share pool that is separate from the Company's equity plans under which inducement awards may be granted consistent with Nasdaq Listing Rule 5635(c)(4).

During the nine months ended September 30, 2024, the Company granted 1,767,550 options to purchase shares of the Company’s common stock to new hires as inducements to such employees entering into employment with the Company, of which 1,763,550 options remained outstanding as of September 30, 2024.

During the three months ended March 31, 2025, the Company granted 217,613 options to purchase shares of the Company’s common stock to new hires as inducements to such employees entering into employment with the Company, of which 211,088 options remained outstanding as of March 31, 2025.

The Company grants annual service-based stock options to employees and directors and SARs to certain executives under the 2023 and 2014 Plans.

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

The combined stock option activity for the nine months ended September 30, 2024, is as follows:

The combined stock option activity for the three months ended March 31, 2025, is as follows:

Options Weighted Average Exercise Price Weighted-Average Contractual Life (years) Aggregate Intrinsic Value (in thousands)

Outstanding at December 31, 2023 13,312,835 $ 4.20 7.27 years —

Outstanding at December 31, 2024

16,684,325 $ 3.19 7.17 years $ 6,797

Granted 3,852,013 $ 2.23 — —

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Canceled and forfeited ( 580,529 ) $ 1.65 — —

Outstanding at September 30, 2024 16,755,825 $ 3.22 7.41 years $ 2,878

Exercisable at September 30, 2024 8,415,196 $ 4.97 5.89 years

As of September 30, 2024, there was approximately $ 8.5 million of unrecognized compensation costs related to stock options, which is expected to be recognized over a weighted average period of 2.79 years.

Outstanding at March 31, 2025

19,102,010 $ 3.01 7.54 years $ 6,152

Exercisable at March 31, 2025

9,208,835 $ 4.40 5.92 years —

As of March 31, 2025, there was approximately $ 13.2 million of unrecognized compensation costs related to stock options, which is expected to be recognized over a weighted average period of 3.17 years.

Restricted Stock Units

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The expense recognized for these awards is based on the grant date fair value of the Company’s common stock multiplied by the number of units granted and recognized over time based on the probability of meeting such commercial, regulatory and corporate milestones.

In addition, the Company has granted PSUs to certain employees under the 2023 Plan with a market condition.

The PSUs also generally feature a time-based vesting component.

The Company uses a Monte Carlo simulation to determine fair value of the award at the grant date.

The expense recognized for these awards is based on the calculated fair value multiplied by the number of the target units granted and is amortized over the service period.

RSU and PSU activity is as follows:

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Number of Shares Weighted Average Fair Value Number of Shares Weighted Average Fair Value

Outstanding as of December 31, 2023 3,339,869 $ 1.30 603,400 $ 1.48

Unvested as of December 31, 2024

1,321,423 $ 0.95 4,108,367 $ 1.59

Granted — $ — 4,126,200 $ 2.19

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Forfeited and canceled ( 13,133 ) $ 0.63 ( 423,635 ) $ 1.74

Outstanding as of September 30, 2024 1,474,517 $ 1.05 4,142,067 $ 1.59

As of September 30, 2024, there was $ 6.2 million of unrecognized compensation costs related to time-based RSUs and PSUs, which is expected to be recognized over a weighted-average period of 2.07 years.

Unvested as of March 31, 2025

741,969 $ 0.76 6,716,706 $ 1.94

As of March 31, 2025, there was $ 12.2 million of unrecognized compensation costs related to time-based RSUs and PSUs, which is expected to be recognized over a weighted-average period of 2.38 years.

Employee Stock Purchase Plan

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Under the ESPP substantially all employees may voluntarily enroll to purchase shares of the Company’s common stock through payroll deductions at a price equal to 85 % of the lower of the fair market values of the stock as of the beginning or the end of the six-month offering period.

An employee's payroll deductions under the ESPP are limited to 15 % of the employee's compensation, and an employee may not purchase more than $ 25,000 worth of stock during any calendar year.

In addition, an employee may not purchase more than 1,500 shares in any offering period.

As of September 30, 2024 and December 31, 2023, a total of 4,448,069 and 4,637,801 shares of the Company’s common stock were available for future issuance under the ESPP, respectively.

The Company issued 189,732 shares under the ESPP during the nine months ended September 30, 2024.

An employee's payroll deductions under the ESPP are limited to 15 % of the

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NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

employee's compensation, and an employee may not purchase more than $ 25,000 worth of stock during any calendar year.

In addition, an employee may not purchase more than 1,500 shares in any offering period.

As of March 31, 2025 and December 31, 2024, a total of 4,354,707 and 4,448,069 shares of the Company’s common stock were available for future issuance under the ESPP, respectively.

The Company issued 93,362 shares under the ESPP during the three months ended March 31, 2025.

Stock-Based Compensation Expense

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The weighted-average assumptions used in calculating the fair values of the rights to acquire stock under the 2023 Plan, the 2014 Plan and inducement awards were as follows:

Three Months Ended September 30, Nine Months Ended September 30,

Three Months Ended March 31,

Stock Options 2025

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Expected volatility 111.97 % - 117.83 % 111.33 % - 114.25 %

Expected term (years) 6.25 years - 6.25 years 6.25 years - 6.25 years 5.51 years - 6.25 years 5.51 years - 6.25 years

Expected term (years) 6.25 years - 6.25 years 6.25 years - 6.25 years

Expected dividend yield — % — %

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$ 1.92 $ 1.46

The Company has classified stock-based compensation in its unaudited condensed consolidated statements of operations and comprehensive loss as follows (in thousands):

Three Months Ended September 30, Nine Months Ended September 30,

2024 2023 2024 2023

The Company has classified stock-based compensation in its unaudited condensed consolidated statements of operations and comprehensive income (loss) as follows (in thousands):

Three Months Ended March 31,

Cost of goods sold $ 139 $ 87

3 unchanged sentences

Total stock-based compensation $ 2,187 $ 2,360

NET LOSS PER SHARE

Potentially dilutive securities, warrants, common stock options, RSUs and SARs have been excluded from the calculation of diluted net loss per share as their effects would be anti-dilutive.

For periods in which the Company reports a net loss, the weighted average number of shares outstanding used to calculate both basic and diluted net loss per share were the same.

The shares in the table below were excluded from the calculation of diluted net loss per share, prior to the use of the treasury stock method, due to their anti-dilutive effect:

Three Months Ended September 30, Nine Months Ended September 30,

2024 2023 2024 2023

3,076,923 — 3,076,923 —

NET INCOME (LOSS) PER SHARE

Potentially dilutive securities, warrants, common stock options, RSUs and SARs have been excluded from the calculation of diluted net income (loss) per share as their effects would be anti-dilutive.

For periods in which the Company reports a net loss, the weighted average number of shares outstanding used to calculate both basic and diluted net loss per share were the same except for the three months ended March 31, 2025, as the Company had net income for that period.

The shares in the table below were excluded from the calculation of diluted net income (loss) per share, prior to the use of the treasury stock method, due to their anti-dilutive effect:

Three Months Ended March 31,

Warrants 2,848,259 3,076,923

Outstanding common stock options 16,338,423 16,242,463

Unvested RSUs 4,877,428 6,067,233

Unvested PSUs 350,500 —

Stock appreciation rights 273,077 635,313

Total 24,687,687 26,021,932

(1) In the event of a drawdown of Tranche C, the Company would become obligated to issue to the Warrant Holder additional warrants to purchase 1,153,846 shares of the common stock which are excluded from this table.

(1) The Company granted the Underwriters a 30-day option to purchase up to 3,750,000 additional shares of common stock at the public offering price per share.

These shares are excluded from this table.

See Note 13, Capital Stock , for more information.

Segment Information

The Company operates as one operating segment focused on developing and commercializing innovative therapeutics primarily in the U.S.

The accounting policies of the segment are the same as those described in the summary of significant accounting policies.

Akebia Therapeutics, Inc.

| Form 10-Q | Page 26

Akebia Therapeutics, Inc.

NOTES TO THE UNAUDITED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

The determination of a single business segment is consistent with the consolidated financial information regularly reviewed by the chief executive officer, who is the Company's chief operating decision maker, or CODM , in assessing segment performance and deciding how to allocate resources on a consolidated basis.

The CODM makes decisions on resource allocation, assesses performance of the business, and monitors budget versus actual results using income from operations.

Net income is also a measure that is considered in monitoring budget versus actual results.

The measure of segment assets is reported on the consolidated balance sheets as total consolidated assets.

The following table presents information about reported segment revenues, segment profit and significant segment expenses for the three months ended March 31, 2025 and 2024:

Three Months Ended March 31,

Revenues $ 57,336 $ 32,607

Direct cost of product and other revenue 5,059 741

Panion royalty 2,566 1,853

Amortization of intangible asset — 9,011

Research and development 9,754 9,731

Selling, general and administrative 25,742 25,438

License 701 711

Restructuring — 58

Income (loss) from operations 13,514 ( 14,936 )

Other income (expense)

Interest expense ( 7,770 ) ( 2,498 )

Other (expense) income 213 95

Change in fair value of warrant liability 155 ( 129 )

Loss on extinguishment of debt — ( 517 )

Net income (loss) before income taxes $ 6,112 $ ( 17,985 )

Net income (loss) $ 6,112 $ ( 17,985 )

SUBSEQUENT EVENTS

The Company has evaluated events and transactions occurring after the balance sheet date through the filing date of this Form 10-Q with the Securities and Exchange Commission, to ensure that the unaudited condensed consolidated financial statements include appropriate disclose of events both recognized in the accompanying unaudited condensed consolidated financial statements as of September 30, 2024, and events which occurred subsequently but were not recognized in the consolidated financial statements.

The Company has concluded that no subsequent events have occurred that require disclosure other than the following:

Amendment to WuXi STA DP Agreement

On October 15, 2024, the Company and WuXi STA entered into Amendment #1 to the WuXi STA DP Agreement pursuant to which the parties agreed to extend the term of the WuXi STA DP Agreement until January 1, 2032.

In addition, the volume-based pricing structure under the WuXi STA DP Agreement was amended.

See Note 10, Commitments and Contingencies , for further information on the WuXi STA DP Agreement.

The Company has evaluated events and transactions occurring after the balance sheet date through the filing date of this Form 10-Q with the Securities and Exchange Commission, to ensure that the unaudited condensed consolidated financial statements include appropriate disclose of events both recognized in the accompanying unaudited condensed consolidated financial statements as of March 31, 2025, and events which occurred subsequently but were not recognized in the consolidated financial statements.

The Company has concluded that no subsequent events have occurred that require disclosure.

Akebia Therapeutics, Inc.

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Compared sentence by sentence after normalising whitespace, quotation marks, case and digits, so re-formatting and restated figures do not read as changed language. Wording changes appear as one removal and one addition. The current filing and the prior one are authoritative.

What changed 10-Q

Item 1. Financial Statements