What changed in this filing

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Item 2. Management’s Discussion and Analysis

2025-11-10 compared with 2025-08-07 · 119 added, 118 removed, 357 unchanged (40% of the section changed)

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Our current portfolio includes:

Vafseo was approved by the U.S.

Vafseo is an orally administered medicine that was approved by the U.S.

Food and Drug Administration, or the FDA , in March 2024 for the treatment of anemia due to CKD in adult patients on dialysis for at least three months.

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market opportunity for the treatment of anemia due to CKD in patients with dialysis is approximately $1 billion based on current erythropoiesis stimulating agent, or ESA , pricing and Vafseo is the only oral HIF-based treatment available in the U.S.

We are committed to pursuing a path for label expansion for Vafseo for CKD non-dialysis dependent patients.

We continue to work towards our goal to initiate VALOR, a Phase 3 cardiovascular outcome study of approximately 1,500 U.S.

subjects with late-stage CKD anemia not on dialysis with a comparator to ESA, by the end of 2025 and recently requested a Type-C meeting with the FDA.

The study will be one part of what we believe will be a robust data package that will likely include data from the 1,700 U.S.

patients in the global Phase 3 PRO 2 TECT program, as well as safety data from the commercial use of Vafseo in the U.S.

in dialysis patients, and data on the use of Vafseo in Japan in dialysis and non-dialysis patients where Vafseo has been in the market since 2020.

We recently completed a Type C meeting with the FDA and, while we have not yet received final minutes from the meeting, based on the FDA feedback, we have not come to alignment regarding a path forward for the design of the VALOR clinical trial for the use of vadadustat to treat anemia in patients with late-stage CKD not on dialysis.

As a result, we do not plan to initiate VALOR and therefore do not expect to pursue a broad label for Vafseo for CKD non-dialysis dependent patients.

In the European Union, or EU , the United Kingdom, or UK , Switzerland and Australia, Vafseo is approved for the treatment of symptomatic anemia associated with CKD in adults on chronic maintenance dialysis.

Our partner MEDICE Arzneimittel Pütter GmbH & Co.

KG, or Medice , has an exclusive license to develop and commercialize Vafseo for the treatment of anemia in patients with CKD in defined territories and launched Vafseo in Germany, Austria, Switzerland, the Netherlands and certain other countries in Europe in 2024.

In Japan, Vafseo is approved as a treatment for anemia due to CKD in both dialysis dependent and non-dialysis dependent patients and is marketed and sold by our collaborator Mitsubishi Tanabe Pharma Corporation, or MTPC .

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In March 2025, Auryxia lost exclusivity, or LoE .

We believe the dynamics of

We believe the dynamics of Auryxia reimbursement being included in the ESRD bundle could result in a slower revenue decline after the LoE date

Akebia Therapeutics, Inc.

| Form 10-Q | Page 30

Auryxia reimbursement being included in the ESRD bundle could result in a slower revenue decline after the LoE date than in other LoE situations, but the impact of LoE on future Auryxia revenues will depend on many factors, including our ability to maintain contracts with dialysis organizations, the timing and number of additional generics and the pricing of generics and other products on the market that compete with Auryxia.

than in other LoE situations, but the impact of LoE on future Auryxia revenues will depend on many factors, including our ability to maintain contracts with dialysis organizations, the timing and number of additional generics and the pricing of generics and other products on the market that compete with Auryxia.

Ferric citrate hydrate has also been approved in Japan, and is marketed and sold by our Japanese sublicensee, Japan Tobacco, Inc., and its subsidiary, Torii Pharmaceutical Co., Ltd., collectively, JT and Torii , 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 in Japan.

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The EC granted marketing authorization in June 2025.

In November 2025, the Medicines and Healthcare Products Regulatory Agency, or MHRA , granted Averoa's UK marketing authorization.

However, Averoa has not yet obtained pricing authorization nor commenced sales of ferric citrate in Europe or UK.

Our HIF-based product candidates and other pipeline assets are being evaluated to target areas of unmet needs.

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We cannot determine with certainty the duration and completion costs of our R&D projects, the costs of related clinical development, or if, when, or to what extent we will generate revenue from the commercialization or sale of any of our product candidates.

From inception through June 30, 2025, we have incurred $1.7 billion in R&D expenses.

From inception through September 30, 2025, we have incurred $1.7 billion in R&D expenses.

We expect to incur significant R&D expenditures for the foreseeable future as we continue the development of Auryxia, Vafseo and any other product or product candidate, including those that may be in-licensed or acquired.

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As a result of the Second Amendment, the Prior Tranche C Loan expiry date was extended until February 3, 2025, or the Extended Tranche C Loan .

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

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

Akebia Therapeutics, Inc.

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

See Note 7, Indebtedness, in the accompanying notes to the unaudited condensed consolidated financial statements included in Part I, Item 1 of this Form 10-Q for further information.

On July 21, 2025, the Warrant Holder exercised its option to purchase 2,115,384 shares of our common stock under the Initial Warrant on a cashless basis at an exercise price per share of $1.30.

On July 23, 2025, as a result of the cashless exercise, we issued 1,408,588 shares to the Warrant Holder.

See Note 17, Subsequent Events , in the accompanying notes to the unaudited condensed consolidated financial statements included in Part I, Item 1 of this Form 10-Q for further information.

See Note 7, Indebtedness, in the accompanying notes to the unaudited condensed consolidated financial statements included in Part I, Item 1 of this Form 10-Q for further information.

At-the-Market (ATM) Offering

On September 3, 2024, in connection with the filing of a new shelf registration statement on Form S-3, we filed a prospectus related to our amended and restated sales agreement with Jefferies LLC (which amended and restated the prior sales agreement), pursuant to which we are able to offer and sell up to $75.0 million of our common stock at current market prices from time to time.

Since September 12, 2024 (the date our shelf registration statement on Form S-3 went effective) through December 31, 2024, we sold 14,271,631 shares of our common stock under this program with gross proceeds of $24.3 million ($23.8 million, net of offering expenses).

During the six months ended June 30, 2025, we sold 9,437,364 shares of our common stock under this program with gross proceeds of $18.7 million ($18.4 million, net of offering expenses).

From September 12, 2024 (the date our shelf registration statement on Form S-3 went effective) through December 31, 2024, we sold 14,271,631 shares of our common stock under this program with gross proceeds of $24.3 million ($23.8 million, net of offering expenses).

During the nine months ended September 30, 2025, we sold 9,437,364 shares of our common stock under this program with gross proceeds of $18.7 million ($18.4 million, net of offering expenses).

Akebia Therapeutics, Inc.

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Results of Operations

Comparison of the Three Months Ended June 30, 2025 and 2024

Three Months Ended June 30, Change

Comparison of the Three Months Ended September 30, 2025 and 2024

Three Months Ended September 30, Change

(dollars in thousands) 2025 2024 $ %

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Change in fair value of warrant liability 1,464 (856) 2,320 (271) %

Income (loss) before income taxes 1,155 (20,039) 21,194 (106) %

Income tax expense (615) — (615) *

Net income (loss) $ 540 $ (20,039) $ 20,579 (103) %

*Percentage change not meaningful.

Product Revenue, Net— Net product revenue is derived from sales of Auryxia and Vafseo in the U.S.

We distribute Auryxia and Vafseo principally through a limited number of dialysis organizations, wholesale distributors, certain specialty pharmacy providers and our AG Partner.

Net product revenue was $60.5 million for the three months ended June 30, 2025, compared to $41.2 million for the three months ended June 30, 2024.

Net product revenue was $56.8 million for the three months ended September 30, 2025, compared to $35.6 million for the three months ended September 30, 2024.

The increase was primarily due to Vafseo's entry to the market in January 2025 and an increase in sales volumes of Auryxia.

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| Form 10-Q | Page 35

The following table summarizes our product revenue by product for the three months ended June 30, 2025 and 2024 (in thousands):

Three Months Ended June 30,

The following table summarizes our product revenue by product for the three months ended September 30, 2025 and 2024 (in thousands):

Three Months Ended September 30,

42,467 35,592

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market in January 2025.

(2) Includes the authorized generic version of Auryxia sold and distributed by our AG Partner during the three months ended June 30, 2025.

License, Collaboration and Other Revenue— License, collaboration and other revenue was $2.0 million for the three months ended June 30, 2025, compared to $2.4 million for the three months ended June 30, 2024.

The decrease was primarily due to revenue recognized in connection with our supply agreement with MTPC during the three months ended June 30, 2024.

Cost of Goods Sold—Cost of Product and Other Revenue— Cost of product and other revenue was $9.9 million for the three months ended June 30, 2025 compared to $8.0 million for the three months ended June 30, 2024.

The increase was primarily due to a $4.9 million benefit that we recorded during the three months ended June 30, 2024 due to our ability to sell inventory previously written-down as excess inventory and lower Auryxia volume during the three months ended June 30, 2024, which was partially offset by a charge of $2.1 million related to our firm purchase commitment liability during the three months ended June 30, 2024.

(2) Includes the authorized generic version of Auryxia sold and distributed by our AG Partner during the three months ended September 30, 2025.

License, Collaboration and Other Revenue— License, collaboration and other revenue was $2.0 million for the three months ended September 30, 2025, compared to $1.8 million for the three months ended September 30, 2024.

Cost of Goods Sold—Cost of Product and Other Revenue— Cost of product and other revenue was $9.4 million for the three months ended September 30, 2025 compared to $5.2 million for the three months ended September 30, 2024.

The increase was primarily due to higher Auryxia volume during the three months ended September 30, 2025.

In addition, cost of product and other revenue for the three months ended September 30, 2024 was offset by a $3.7 million benefit that we recorded due to our ability to sell inventory previously written-down as excess inventory during the three months ended September 30, 2024.

We began capitalizing our Vafseo costs in March 2024, in connection with the FDA's approval of Vafseo for the treatment of anemia due to CKD in adult patients on dialysis for at least three months.

Prior to the capitalization of Vafseo inventory costs, such costs were recorded as research and development expenses in the period incurred.

Cost of product and other revenue for Vafseo was $0.5 million for the three months ended June 30, 2025, comprised of manufacturing and overhead costs as the associated inventory costs such as raw materials, drug substance and drug product conversion costs were expensed previously.

If Vafseo inventory sold during the three months ended June 30, 2025 was valued at cost, our cost of product and other revenue would have been $1.1 million.

As of June 30, 2025, we had $26.5 million of reduced-cost Vafseo inventory.

Cost of product and other revenue for Vafseo was $0.5 million for the three months ended September 30, 2025, comprised of manufacturing and overhead costs as the associated inventory costs such as raw materials, drug substance and drug product conversion costs were expensed previously.

If Vafseo inventory sold during the three months ended September 30, 2025 was valued at cost, our cost of product and other revenue would have been $1.6 million.

As of September 30, 2025, we had $25.4 million of reduced-cost Vafseo inventory.

We expect our cost of product and other revenue for Vafseo will increase, reflecting the full cost of manufacturing, subsequent to the utilization of our reduced-cost Vafseo inventory.

Cost of Goods Sold—Amortization of Intangible Asset— Amortization of intangible asset related to the acquired developed product rights for Auryxia, and was amortized using a straight-line method over its estimated useful life of approximately six years.

Cost of Goods Sold—Amortization of Intangible Asset— Amortization of intangible asset related to the acquired developed product rights for Auryxia was amortized using a straight-line method over its estimated useful life of approximately six years.

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

We recorded no amortization expense and $9.0 million in amortization expense for the three months ended June 30, 2025 and 2024, respectively, related to the developed product rights for Auryxia.

R&D Expenses— R&D expenses were $11.0 million for the three months ended June 30, 2025, compared to $7.6 million for the three months ended June 30, 2024.

The increase was primarily driven by increased clinical trial activities related to Vafseo as well as our other programs and higher headcount related costs.

The following table summarizes our external research and development expenses by program, as well as costs not allocated to programs, for the three months ended June 30, 2025 and 2024 (in thousands):

Three Months Ended June 30,

We recorded no amortization expense and $9.0 million in amortization expense for the three months ended September 30, 2025 and 2024, respectively, related to the developed product rights for Auryxia.

R&D Expenses— R&D expenses were $14.9 million for the three months ended September 30, 2025, compared to $8.5 million for the three months ended September 30, 2024.

The increase was primarily driven by increased clinical trial activities related to Vafseo and higher headcount related costs.

The following table summarizes our external research and development expenses by program, as well as costs not allocated to programs, for the three months ended September 30, 2025 and 2024 (in thousands):

Three Months Ended September 30,

Vafseo clinical trial and other external costs $ 7,154 $ 3,046

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We expect to incur significant R&D expenses in future periods in support of ongoing or planned studies with respect to the development of our product candidates as well as Vafseo.

Selling, General and Administrative Expenses— Selling, general and administrative expenses were $26.6 million for the three months ended June 30, 2025, compared to $26.9 million for the three months ended June 30, 2024.

The decrease was largely due to lower costs associated with our patient assistance program related to Auryxia and decreased professional fees, partially offset by marketing costs in connection with the Vafseo U.S.

launch during the three months ended June 30, 2025.

License Expenses— License expenses related to royalties due to Panion relating to sales of Riona in Japan were $0.9 million and $0.8 million for the three months ended June 30, 2025 and 2024, respectively.

Other Expense, Net— Other expense, net, was $6.9 million for the three months ended June 30, 2025, compared to $2.2 million for the three months ended June 30, 2024.

The increase was primarily due to non-cash interest expense related to the settlement royalty liability in connection with the Termination and Settlement Agreement entered into on July 10, 2024 between us and CSL Vifor, or the Vifor Termination Agreement , partially offset by interest income related to our money market funds.

See Note 8, Liability Related to Settlement Royalties, Working Capital Fund Liability and Liability Related to Sale of Future Royalties , in the accompanying notes to the unaudited condensed consolidated financial statements included in Part I, Item 1 of this Form 10-Q for further information on our arrangements with CSL Vifor.

Change in Fair Value of Warrant Liability— Change in fair value of warrant liability was $7.0 million and $2.3 million for the three months ended June 30, 2025 and 2024, respectively.

Selling, General and Administrative Expenses— Selling, general and administrative expenses were $29.1 million for the three months ended September 30, 2025, compared to $26.5 million for the three months ended September 30, 2024.

The increase was largely due to higher marketing costs in connection with the Vafseo U.S.

launch and increased headcount related costs during the three months ended September 30, 2025.

License Expenses— License expenses related to royalties due to Panion relating to sales of Riona in Japan were $0.9 million and $0.8 million for the three months ended September 30, 2025 and 2024, respectively.

Other Expense, Net— Other expense, net, was $4.8 million for the three months ended September 30, 2025, compared to $6.7 million for the three months ended September 30, 2024.

The decrease was primarily due to increased interest income related to our money market funds which offset interest expense during the three months ended September 30, 2025.

Change in Fair Value of Warrant Liability— Change in fair value of warrant liability was $1.5 million and $0.9 million for the three months ended September 30, 2025 and 2024, respectively.

Income Tax Expense— Income tax expense was $0.6 million for the three months ended September 30, 2025.

There was no income tax expense for the three months ended September 30, 2024.

Akebia Therapeutics, Inc.

| Form 10-Q | Page 37

Comparison of the Six Months Ended June 30, 2025 and 2024

Six Months Ended June 30, Change

Comparison of the Nine Months Ended September 30, 2025 and 2024

Nine Months Ended September 30, Change

(dollars in thousands) 2025 2024 $ %

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Loss on extinguishment of debt — (517) 517 (100) %

Income (loss) before income taxes 7,514 (46,606) 54,120 (116) %

Income tax expense (615) — (615) *

Net income (loss) $ 6,899 $ (46,606) $ 53,505 (115) %

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We distribute Auryxia and Vafseo principally through a limited number of dialysis organizations, wholesale distributors, certain specialty pharmacy providers and our AG Partner.

Net product revenue was $116.3 million for the six months ended June 30, 2025, compared to $72.2 million for the six months ended June 30, 2024.

Net product revenue was $173.0 million for the nine months ended September 30, 2025, compared to $107.8 million for the nine months ended September 30, 2024.

The increase was primarily due to Vafseo's entry to the market in January 2025 and an increase in sales volumes of Auryxia.

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| Form 10-Q | Page 38

The following table summarizes our product revenue by product for the six months ended June 30, 2025 and 2024 (in thousands):

Six Months Ended June 30,

The following table summarizes our product revenue by product for the nine months ended September 30, 2025 and 2024 (in thousands):

Nine Months Ended September 30,

133,406 107,810

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market in January 2025.

(2) Includes the authorized generic version of Auryxia sold and distributed by our AG Partner during the six months ended June 30, 2025.

License, Collaboration and Other Revenue— License, collaboration and other revenue was $3.6 million for the six months ended June 30, 2025, compared to $4.0 million for the six months ended June 30, 2024.

The decrease was primarily due to revenue recognized in connection with our supply agreement with MTPC during the six months ended June 30, 2024.

Cost of Goods Sold—Cost of Product and Other Revenue— Cost of product and other revenue was $17.5 million for the six months ended June 30, 2025 compared to $10.6 million for the six months ended June 30, 2024.

The increase was primarily due to a $8.6 million benefit that we recorded during the six months ended June 30, 2024 due to our ability to sell inventory previously written-down as excess inventory and lower Auryxia volume during the six months ended June 30, 2024, which was partially offset by a charge of $2.1 million related to our firm purchase commitment liability during the six months ended June 30, 2024.

(2) Includes the authorized generic version of Auryxia sold and distributed by our AG Partner during the nine months ended September 30, 2025.

License, Collaboration and Other Revenue— License, collaboration and other revenue was $5.5 million for the nine months ended September 30, 2025, compared to $5.9 million for the nine months ended September 30, 2024.

The decrease was primarily due to revenue recognized in connection with our supply agreement with MTPC during the nine months ended September 30, 2024.

Cost of Goods Sold—Cost of Product and Other Revenue— Cost of product and other revenue was $26.9 million for the nine months ended September 30, 2025 compared to $15.8 million for the nine months ended September 30, 2024.

The increase was primarily due to higher Auryxia volume during the nine months ended September 30, 2025.

In addition, cost of product and other revenue for the nine months ended September 30, 2024 was offset by a $12.3 million benefit that we recorded due to our ability to sell inventory previously written-down as excess inventory during the nine months ended September 30, 2024.

We also recorded a charge of $2.1 million related to our firm purchase commitment liability during the nine months ended September 30, 2024.

We began capitalizing our Vafseo costs in March 2024, in connection with the FDA's approval of Vafseo for the treatment of anemia due to CKD in adult patients on dialysis for at least three months.

Prior to the capitalization of Vafseo inventory costs, such costs were recorded as research and development expenses in the period incurred.

Cost of product and other revenue for Vafseo was $1.9 million for the six months ended June 30, 2025, comprised of manufacturing and overhead costs as the associated inventory costs such as raw materials, drug substance and drug product conversion costs were expensed previously.

If Vafseo inventory sold during the six months ended June 30, 2025 was valued at cost, our cost of product and other revenue would have been $3.0 million.

As of June 30, 2025, we had $26.5 million of reduced-cost Vafseo inventory.

Cost of product and other revenue for Vafseo was $2.4 million for the nine months ended September 30, 2025, comprised of manufacturing and overhead costs as the associated inventory costs such as raw materials, drug substance and drug product conversion costs were expensed previously.

If Vafseo inventory sold during the nine months ended September 30, 2025 was valued at cost, our cost of product and other revenue would have been $4.6 million.

As of September 30, 2025, we had $25.4 million of reduced-cost Vafseo inventory.

We expect our cost of product and other revenue for Vafseo will increase, reflecting the full cost of manufacturing, subsequent to the utilization of our reduced-cost Vafseo inventory.

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

We recorded no amortization expense and $18.0 million in amortization expense for the six months ended June 30, 2025 and 2024, respectively, related to the developed product rights for Auryxia.

R&D Expenses— R&D expenses were $20.8 million for the six months ended June 30, 2025, compared to $17.4 million for the six months ended June 30, 2024.

The increase was primarily due to clinical trial activities related to Vafseo as well as our other programs.

The following table summarizes our external research and development expenses by program, as well as costs not allocated to programs, for the six months ended June 30, 2025 and 2024 (in thousands):

Six Months Ended June 30,

We recorded no amortization expense and $27.0 million in amortization expense for the nine months ended September 30, 2025 and 2024, respectively, related to the developed product rights for Auryxia.

R&D Expenses— R&D expenses were $35.7 million for the nine months ended September 30, 2025, compared to $25.9 million for the nine months ended September 30, 2024.

The increase was primarily due to clinical trial activities related to Vafseo and higher headcount related costs.

The following table summarizes our external research and development expenses by program, as well as costs not allocated to programs, for the nine months ended September 30, 2025 and 2024 (in thousands):

Nine Months Ended September 30,

Vafseo clinical trial and other external costs $ 14,914 $ 6,337

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We expect to incur significant R&D expenses in future periods in support of ongoing or planned studies with respect to the development of our product candidates as well as Vafseo.

Selling, General and Administrative Expenses— Selling, general and administrative expenses were $52.3 million for the six months ended June 30, 2025, compared to $52.4 million for the six months ended June 30, 2024.

launch during the six months ended June 30, 2025.

License Expenses— License expenses related to royalties due to Panion relating to sales of Riona in Japan were $1.6 million and $1.5 million for the six months ended June 30, 2025 and 2024, respectively.

Restructuring Expenses— There were no restructuring expenses and $0.1 million of restructuring expenses for the six months ended June 30, 2025 and 2024, respectively.

Other Expense, Net— Other expense, net, was $14.4 million for the six months ended June 30, 2025, compared to $4.6 million for the six months ended June 30, 2024.

The increase was primarily due to non-cash interest expense related to the settlement royalty liability in connection with the Vifor Termination Agreement, partially offset by interest income related to our money market funds.

Selling, General and Administrative Expenses— Selling, general and administrative expenses were $81.4 million for the nine months ended September 30, 2025, compared to $78.9 million for the nine months ended September 30, 2024.

The increase was largely due to higher marketing costs in connection with the Vafseo U.S.

launch and increased headcount related costs during the nine months ended September 30, 2025.

License Expenses— License expenses related to royalties due to Panion relating to sales of Riona in Japan were $2.5 million and $2.2 million for the nine months ended September 30, 2025 and 2024, respectively.

Restructuring Expenses— There were no restructuring expenses and $0.1 million of restructuring expenses for the nine months ended September 30, 2025 and 2024, respectively.

Other Expense, Net— Other expense, net, was $19.2 million for the nine months ended September 30, 2025, compared to $11.3 million for the nine months ended September 30, 2024.

The increase was primarily due to non-cash interest expense related to the settlement royalty liability in connection with the Vifor Termination Agreement which we entered into in July 2024, partially offset by interest income related to our money market funds.

Change in Fair Value of Warrant Liability— Change in fair value of warrant liability was $6.8 million and $2.2 million for the six months ended June 30, 2025 and 2024, respectively.

Loss on Extinguishment of Debt.

During the six months ended June 30, 2024, we recorded a $0.5 million loss on the extinguishment of debt in connection with the repayment of the Pharmakon Term Loans.

We did not record any loss on the extinguishment of debt during the six months ended June 30, 2025.

Change in Fair Value of Warrant Liability— Change in fair value of warrant liability was $5.4 million and $1.3 million for the nine months ended September 30, 2025 and 2024, respectively.

Loss on Extinguishment of Debt— During the nine months ended September 30, 2024, we recorded a $0.5 million loss on the extinguishment of debt in connection with the repayment of the Pharmakon Term Loans.

We did not record any loss on the extinguishment of debt during the nine months ended September 30, 2025.

Income Tax Expense— Income tax expense was $0.6 million for the nine months ended September 30, 2025.

There was no income tax expense for the nine months ended September 30, 2024.

Liquidity and Capital Resources

As of June 30, 2025, we had cash and cash equivalents of $137.3 million and restricted cash of $1.7 million.

As of September 30, 2025, we had cash and cash equivalents of $166.4 million and restricted cash of $1.7 million.

To date, we have funded our operations principally through sales of our common stock, including through our employee stock purchase plan, product sales, payments received from our collaboration and licensing partners, borrowings under term loans, a working capital payment from CSL Vifor also referred to as a Working Capital Fund liability and a royalty transaction.

From inception through June 30, 2025, we raised approximately $929.2 million of net proceeds from the sale of equity, including $567.9 million from various underwritten public offerings, $291.3 million from at-the-market offerings pursuant to our sales agreement with Jefferies LLC and prior sales agreements with Cantor Fitzgerald & Co., and $70.0 million from the sale of 7,571,429 shares of common stock to CSL Vifor.

We generated net income of $0.2 million and $6.4 million during the three and six months ended June 30, 2025, respectively, and incurred net loss of $8.6 million and $26.6 million during the three and six months ended June 30, 2024, respectively.

As of June 30, 2025 and December 31, 2024, we had an accumulated deficit of $1.7 billion.

From inception through September 30, 2025, we raised approximately $929.2 million of net proceeds from the sale of equity, including $567.9 million from various underwritten public offerings, $291.3 million from at-the-market offerings pursuant to our sales agreement with Jefferies LLC and prior sales agreements with Cantor Fitzgerald & Co., and $70.0 million from the sale of 7,571,429 shares of common stock to CSL Vifor.

We generated net income of $0.5 million and $6.9 million during the three and nine months ended September 30, 2025, respectively, and incurred net loss of $20.0 million and $46.6 million during the three and nine months ended September 30, 2024, respectively.

As of September 30, 2025 and December 31, 2024, we had an accumulated deficit of $1.7 billion.

We had exclusive rights under a series of patents and patent applications to commercialize Auryxia in the U.S.

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Additionally, since March 2025, our AG Partner has been selling an authorized generic version of Auryxia in the U.S., which may slightly offset the revenue decline following the LoE.

We believe our existing cash resources and the cash we expect to generate from product, royalty, supply and license revenues are sufficient to fund our current operating plan for the foreseeable future, including to commercialize Vafseo and Auryxia, pursue label expansion for Vafseo, and advance our other existing programs.

However, if our operating performance deteriorates significantly from the levels expected in our long-term operating plan, it would have an adverse effect on our liquidity and capital resources and could affect our ability to achieve and maintain profitability or continue as a going concern in the future.

However, if our operating performance deteriorates significantly from the levels expected in our long-term operating plan, including if we do not achieve our future anticipated Vafseo revenue projections, it would have an adverse effect on our liquidity and capital resources and could affect our ability to achieve and maintain profitability or continue as a going concern in the future.

In addition, we may also seek to sell additional private or public equity, enter into new debt transactions, explore potential strategic transactions or a combination of these approaches or other strategic alternatives.

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Any debt financing or additional equity that we raise may contain terms that are not favorable to us or our stockholders.

Additional financing may not be available to us in amounts or on terms acceptable to us, if at all.

Akebia Therapeutics, Inc.

| Form 10-Q | Page 40

any additional products and product candidates, including those that may be in-licensed or acquired.

financing may not be available to us in amounts or on terms acceptable to us, if at all.

If we are unable to raise additional capital in sufficient amounts when needed or on attractive terms, we may not be able to pursue development and commercial activities related to Auryxia and Vafseo, or any additional products and product candidates, including those that may be in-licensed or acquired.

Any of these events could significantly harm our business, financial condition and prospects.

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If we prepay the Term Loans prior to the BlackRock Maturity Date, we 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, we are required to pay the amount of otherwise due interest payments for the twelve-month period following pre-payment.

On the Closing Date, the Warrant Holder received a warrant to purchase 3,076,923 shares of our common stock, at an exercise price per share of $1.30, and upon the borrowing of Tranche C in February 2025, we issued additional warrants to purchase 1,153,846 shares of our common stock at an exercise price per share of $1.30.

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

See Note 7, Indebtedness, in the accompanying notes to the unaudited condensed consolidated financial statements included in Part I, Item 1 of this Form 10-Q for further information.

On July 21, 2025, the Warrant Holder exercised its option to purchase 2,115,384 shares of our common stock under the Initial Warrant on a cashless basis at an exercise price per share of $1.30.

On July 23, 2025, as a result of the cashless exercise, we issued 1,408,588 shares to the Warrant Holder.

See Note 17, Subsequent Events , in the accompanying notes to the unaudited condensed consolidated financial statements included in Part I, Item 1 of this Form 10-Q for further information.

See Note 7, Indebtedness, in the accompanying notes to the unaudited condensed consolidated financial statements included in Part I, Item 1 of this Form 10-Q for further information.

Liability Related to Settlement Royalties

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On July 10, 2024, we and CSL Vifor entered into the Vifor Termination Agreement.

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during a calendar year, or the Settlement Royalty Payments .

The Settlement Royalty

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Payments commenced upon the first sale of Vafseo by us, our 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 us, our 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.

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

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

The annual effective interest rate as of June 30, 2025 was 37.0% which is reflected as interest expense in the unaudited condensed consolidated statements of operations and comprehensive income (loss).

The Company recognized interest expense related to the settlement royalties liability of $5.4 million and $10.8 million for the three and six months ended June 30, 2025, respectively.

As of June 30, 2025, $14.7 million and $48.7 million of the settlement royalties liability is classified as a current and non-current liability, respectively.

The annual effective interest rate as of September 30, 2025 was 24.6% which is reflected as interest expense in the unaudited condensed consolidated statements of operations and comprehensive income (loss).

The Company recognized interest expense related to the settlement royalties liability of $3.9 million and $14.7 million for the three and nine months ended September 30, 2025, respectively.

As of September 30, 2025, $14.3 million and $53.0 million of the settlement royalties liability is classified as a current and non-current liability, respectively.

See Note 8, Liability Related to Settlement Royalties, Working Capital Fund Liability and Liability Related to Sale of Future Royalties , in the accompanying notes to the unaudited condensed consolidated financial statements in Part I, Item 1 of this Form 10-Q for further information.

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The Working Capital Fund is considered a debt arrangement with zero coupon interest and we impute interest on the Working Capital Fund liability at a rate of 15.0% per annum.

As of June 30, 2025, $10.0 million and $30.6 million of the Working Capital Fund liability is classified as a current and non-current liability, respectively, based on management’s estimated timing of the repayment of the Working Capital Fund liability to CSL Vifor.

As of September 30, 2025, $13.0 million and $27.7 million of the Working Capital Fund liability is classified as a current and non-current liability, respectively, based on management’s estimated timing of the repayment of the Working Capital Fund liability to CSL Vifor.

See Note 8, Liability Related to Settlement Royalties, Working Capital Fund Liability and Liability Related to Sale of Future Royalties , in the accompanying notes to the unaudited condensed consolidated financial statements in Part I, Item 1 of this Form 10-Q for further information.

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The Royalty Interest Payments are subject to an annual maximum “cap” of $13.0 million, after which we will receive 85% of the Royalty Interest Payments for the remainder of that year.

The Royalty Interest Payments are also subject to an aggregate maximum “cap” of $150.0 million, after which the Royalty Interest Payments will revert back to us.

We received $44.8 million from HCR, net of certain transaction expenses, which we recorded as a liability at the transaction date.

We amortize the liability related to the sale of future royalties using the effective interest method over the life of the arrangement.

The annual effective interest rate as of June 30, 2025 was 0%.

We retain the right to receive all potential future

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regulatory milestones for Vafseo under the MTPC Agreement.

We recorded non-cash royalty revenue of $0.5 million during each of the three months ended June 30, 2025 and 2024, and $0.9 million during each of the six months ended June 30, 2025 and 2024.

As of June 30, 2025, $2.2 million and $51.1 million of the liability related to the sale of future royalties is classified as a current and non-current liability, respectively.

Interest Payments are also subject to an aggregate maximum “cap” of $150.0 million, after which the Royalty Interest Payments will revert back to us.

We received $44.8 million from HCR, net of certain transaction expenses, which we recorded as a liability at the transaction date.

We amortize the liability related to the sale of future royalties using the effective interest method over the life of the arrangement.

The annual effective interest rate as of September 30, 2025 was 0%.

We retain the right to receive all potential future regulatory milestones for Vafseo under the MTPC Agreement.

We recorded non-cash royalty revenue of $0.5 million during each of the three months ended September 30, 2025 and 2024, and $1.3 million and $1.4 million during the nine months ended September 30, 2025 and 2024, respectively.

As of September 30, 2025, $2.1 million and $50.6 million of the liability related to the sale of future royalties is classified as a current and non-current liability, respectively.

See Note 8, Liability Related to Settlement Royalties, Working Capital Fund Liability and Liability Related to Sale of Future Royalties , in the accompanying notes to the unaudited condensed consolidated financial statements in Part I, Item 1 of this Form 10-Q for further information.

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Letter of Credit

As of June 30, 2025, in connection with the Cambridge Lease (as defined below), we had $1.7 million in a letter of credit outstanding.

As of September 30, 2025, in connection with the Cambridge Lease (as defined below), we had $1.7 million in a letter of credit outstanding.

Director and Officer Indemnification

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We are party to contractual obligations involving commitments to make payments to third parties in the future.

Certain contractual obligations are reflected on our condensed consolidated balance sheet as of June 30, 2025, while others are considered future obligations.

Our material cash requirements as of June 30, 2025, include contractual obligations and commitments arising in the normal course of business, including leases, license agreements, manufacturing agreements and unconditional purchase commitments which are described in more detail below.

Certain contractual obligations are reflected on our condensed consolidated balance sheet as of September 30, 2025, while others are considered future obligations.

Our material cash requirements as of September 30, 2025, include contractual obligations and commitments arising in the normal course of business, including leases, license agreements, manufacturing agreements and unconditional purchase commitments which are described in more detail below.

Cambridge Lease

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Cyclerion will also be eligible to receive specified commercial milestones as well as tiered royalties ranging from 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.

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See Note 10, Commitments and Contingencies , in the accompanying notes to the unaudited condensed consolidated financial statements included in Part I, Item 1 of this Form 10-Q for further information.

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We have various supply arrangements to which we are a party, and we are obligated to pay for drug substance and drug product for commercial use.

Under one of our agreements, we are required to purchase a minimum quantity of Auryxia drug

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substance at a predetermined price.

Under one of our agreements, we are required to purchase a minimum quantity of Auryxia drug substance at a predetermined price.

We are also obligated to purchase a certain percentage of the global demand for Vafseo drug substance and drug product based on certain quarterly and annual forecasts we provide to certain suppliers.

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Payments due upon cancellation consist only of payments for services provided or expenses incurred, including non-cancellable obligations of service providers, up to the date of cancellation.

In addition, we contract with various organizations to conduct R&D activities with remaining contract costs to us of approximately $57.7 million as of June 30, 2025.

In addition, we contract with various organizations to conduct R&D activities with remaining contract costs to us of approximately $86.8 million as of September 30, 2025.

The scope of the services under these R&D contracts can be modified upon mutual agreement of the parties, and the contracts or scope of services can be cancelled by us upon written notice.

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The following table provides a summary of cash flow data for each applicable period:

Six Months Ended June 30,

Nine Months Ended September 30,

NET CASH PROVIDED BY/(USED IN) ( in thousands ):

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Operating Activities

Net cash provided by operating activities was $8.8 million for the six months ended June 30, 2025.

Net cash provided by operating activities for the six months ended June 30, 2025 consisted of net income of $6.4 million as well as net non-cash adjustments of $27.0 million, including a change in fair value of the warrant liability of $6.8 million, offset by a reduction of $24.6 million in working capital.

Net cash used in operating activities was $29.5 million for the six months ended June 30, 2024.

Net cash provided by operating activities was $36.9 million for the nine months ended September 30, 2025.

Net cash provided by operating activities for the nine months ended September 30, 2025 consisted of net income of $6.9 million as well as net non-cash adjustments of $35.4 million, including a change in fair value of the warrant liability of $5.4 million, offset by a reduction of $5.4 million in working capital.

Net cash used in operating activities was $36.2 million for the nine months ended September 30, 2024.

Net cash used in operating activities consisted of a net loss of $46.6 million and net non-cash adjustments of $46.9 million, including amortization of our intangible asset of $27.0 million, and a reduction of $36.4 million in working capital.

Investing Activities

Immaterial net cash was provided by investing activities for the six months ended June 30, 2025.

Immaterial net cash was used in investing activities for the six months ended June 30, 2024.

Financing Activities

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Net cash provided by financing activities was $76.7 million for the six months ended June 30, 2025, which primarily consisted of proceeds of $10.0 million from the issuance of debt under the BlackRock Credit Agreement and net proceeds of $66.4 million from the sale of common stock from our March 2025 underwritten public offering and under our ATM facility.

Net cash provided by financing activities was $26.1 million for the six months ended June 30, 2024, which primarily consisted of proceeds of $45.0 million from the issuance of debt under the BlackRock Credit Agreement and net proceeds of $18.7 million from the sale of common stock under our ATM Facility, partially offset by principal payments of debt of $37.1 million primarily related to the Pharmakon Term Loans which were repaid in January 2024.

Immaterial net cash was used in investing activities for each of the nine months ended September 30, 2025 and 2024.

Financing Activities

Net cash provided by financing activities was $77.8 million for the nine months ended September 30, 2025, which primarily consisted of proceeds of $10.0 million from the issuance of debt under the BlackRock Credit Agreement and net proceeds of $66.4 million from the sale of common stock from our March 2025 underwritten public offering and under our ATM facility.

Net cash provided by financing activities was $27.3 million for the nine months ended September 30, 2024, which primarily consisted of proceeds of $45.0 million from the issuance of debt under the BlackRock Credit Agreement and net proceeds of $20.4 million from the sale of common stock under our ATM Facility, partially offset by principal payments of debt of $37.1 million primarily related to the Pharmakon Term Loans which were repaid in January 2024.

Recent Accounting Pronouncements

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In making estimates and judgments, management employs critical accounting policies.

During the six months ended June 30, 2025, there were no material changes to our methodologies used for our critical accounting estimates as reported in our 2024 Form 10-K.

During the nine months ended September 30, 2025, there were no material changes to our methodologies used for our critical accounting estimates as reported in our 2024 Form 10-K.

Quantitative and Qualitative Disclosures about Market Risk.

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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 2. Management’s Discussion and Analysis