AGIOS PHARMACEUTICALS, INC. [AGIO] Filings

10-Q 1 agio-20240930.htm 10-Q agio-20240930

2024Q3FALSE000143922212/31Subsequent Events

[Open until filing]

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Table of Contents

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 10-Q

(Mark One)


☒			QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the quarterly period ended September 30, 2024


☐			TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

Commission File Number: 001-36014

AGIOS PHARMACEUTICALS, INC.

(Exact Name of Registrant as Specified in Its Charter)


Delaware									26-0662915
(State or Other Jurisdiction of Incorporation or Organization)									(I.R.S. Employer Identification No.)

88 Sidney Street, Cambridge, Massachusetts									02139
(Address of Principal Executive Offices)									(Zip Code)

(617) 649-8600

(Registrant’s Telephone Number, Including Area Code)

(Former Name, Former Address and Former Fiscal Year, if Changed Since Last Report)

Securities registered pursuant to Section 12(b) of the Act:


Title of each class	Trading symbol(s)	Name of each exchange on which registered
Common Stock, Par Value $0.001 per share	AGIO	Nasdaq Global Select Market

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. Yes ☒ No ☐

Indicate by check mark whether the registrant has submitted electronically every Interactive Data File required to be submitted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit such files). Yes ☒ No ☐

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, a smaller reporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer,” “smaller reporting company,” and “emerging growth company” in Rule 12b-2 of the Exchange Act.


Large accelerated filer	☒	Accelerated filer	☐
Non-accelerated filer	☐	Smaller reporting company	☐
		Emerging growth company	☐

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. ☐

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act). Yes ☐ No ☒

Number of shares of the registrant’s Common Stock, $0.001 par value, outstanding on October 25, 2024: 57,030,195

Table of Contents

AGIOS PHARMACEUTICALS, INC.

FORM 10-Q

FOR THE THREE AND NINE MONTHS ENDED SEPTEMBER 30, 2024

TABLE OF CONTENTS


		Page No.
PART I. FINANCIAL INFORMATION
Item 1.	Financial Statements (Unaudited)	1
	Condensed Consolidated Balance Sheets as of September 30, 2024 and December 31, 2023	1
	Condensed Consolidated Statements of Operations for the Three and Nine Months Ended September 30, 2024 and 2023	2
	Condensed Consolidated Statements of Comprehensive Inco m e (Loss ) for the Three and Nine Months Ended September 30 , 2024 and 2023	3
	Condensed Consolidated Statements of Stockholders' Equity for the Three and Nine Months Ended September 30 , 2024 and 2023	4
	Condensed Consolidated Statements of Cash Flows for the Nine Months Ended September 30 , 2024 and 2023	6
	Notes to Condensed Consolidated Financial Statements	8
Item 2.	Management’s Discussion and Analysis of Financial Condition and Results of Operations	19
Item 3.	Quantitative and Qualitative Disclosures About Market Risk	30
Item 4.	Controls and Procedures	31
PART II. OTHER INFORMATION		32
Item 1A.	Risk Factors	32
Item 5.	Other Information	63
Item 6.	Exhibits	65
	Signatures	66

Table of Contents

PART I. FINANCIAL INFORMATION

Item 1. Financial Statements (Unaudited)

AGIOS PHARMACEUTICALS, INC.

Condensed Consolidated Balance Sheets

(Unaudited)


(In thousands, except share and per share data)	September 30, 2024		December 31, 2023
Assets
Current assets:
Cash and cash equivalents	$	253,730	$	88,205
Marketable securities	751,027		688,723
Accounts receivable, net	3,118		2,810



Inventory	26,429		19,076
Prepaid expenses and other current assets	39,885		35,021

Total current assets	1,074,189		833,835
Marketable securities	655,889		29,435
Operating lease assets	45,841		54,409
Property and equipment, net	11,819		15,382
Other non-current assets	4,056		4,057

Total assets	$	1,791,794	$	937,118
Liabilities and stockholders’ equity
Current liabilities:

Accounts payable	$	17,143	$	9,780
Accrued expenses	33,307		43,167
Income taxes payable	52,682		—
Operating lease liabilities	16,319		15,008




Total current liabilities	119,451		67,955

Operating lease liabilities, net of current portion	44,515		56,988
Other non-current liabilities	1,156		1,156


Total liabilities	165,122		126,099
Stockholders’ equity:
Preferred stock, $0.001 par value; 25,000,000 shares authorized; no shares issued or outstanding at September 30, 2024 and December 31, 2023	—		—
Common stock, $0.001 par value; 125,000,000 shares authorized; 73,237,954 shares issued and 57,021,543 shares outstanding at September 30, 2024, and 72,161,489 shares issued and 55,945,078 shares outstanding at December 31, 2023	73		72
Additional paid-in capital	2,478,066		2,436,523
Accumulated other comprehensive income (loss)	3,420		(441)
Treasury stock, at cost (16,216,411 shares at September 30, 2024 and December 31, 2023)	(802,486)		(802,486)
Accumulated deficit	(52,401)		(822,649)
Total stockholders’ equity	1,626,672		811,019
Total liabilities and stockholders’ equity	$	1,791,794	$	937,118

See accompanying Notes to Condensed Consolidated Financial Statements.

Table of Contents

AGIOS PHARMACEUTICALS, INC.

Condensed Consolidated Statements of Operations

(Unaudited)


	Three Months Ended September 30,				Nine Months Ended September 30,
(In thousands, except share and per share data)	2024		2023		2024		2023
Revenues:
Product revenue, net	$	8,964	$	7,399	$	25,768	$	19,720


Total revenue	8,964		7,399		25,768		19,720
Operating expenses:
Cost of sales	$	783	$	633	$	2,905	$	2,295
Research and development	72,455		81,841		218,476		218,037
Selling, general and administrative	38,537		25,822		105,087		84,598
Total operating expenses	111,775		108,296		326,468		304,930
Loss from operations	(102,811)		(100,897)		(300,700)		(285,210)
Gain on sale of contingent payments	889,136		—		889,136		—
Milestone payment from gain on sale of oncology business	200,000		—		200,000		—
Interest income, net	13,059		8,375		30,068		24,720
Other income, net	1,651		1,198		4,864		4,342


Net income (loss) before taxes	1,001,035		(91,324)		823,368		(256,148)
Income tax expense	53,120		—		53,120		—

Net income (loss)	$	947,915	$	(91,324)	$	770,248	$	(256,148)


Net income (loss) per share - basic	$	16.65	$	(1.64)	$	13.58	$	(4.61)
Net income (loss) per share - diluted	$	16.22	$	(1.64)	$	13.38	$	(4.61)

Weighted-average number of common shares used in computing net income (loss) per share – basic	56,939,403		55,803,663		56,709,318		55,559,766
Weighted-average number of common shares used in computing net income (loss) per share – diluted	58,432,796		55,803,663		57,581,382		55,559,766

See accompanying Notes to Condensed Consolidated Financial Statements.

Table of Contents

AGIOS PHARMACEUTICALS, INC.

Condensed Consolidated Statements of Comprehensive Income (Loss)

(Unaudited)


	Three Months Ended September 30,				Nine Months Ended September 30,
(In thousands)	2024		2023		2024		2023
Net income (loss)	$	947,915	$	(91,324)	$	770,248	$	(256,148)
Other comprehensive income
Unrealized gain on available-for-sale securities	4,465		2,974		3,861		6,639
Comprehensive income (loss)	$	952,380	$	(88,350)	$	774,109	$	(249,509)

See accompanying Notes to Condensed Consolidated Financial Statements.

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AGIOS PHARMACEUTICALS, INC.

Condensed Consolidated Statements of Stockholders' Equity

(Unaudited)


	Common Stock			Additional Paid-In Capital		Accumulated Other Comprehensive Loss		Accumulated Deficit		Treasury Stock			Total Stockholders’ Equity
(in thousands, except share amounts)	Shares	Amount								Shares	Amount
Balance at December 31, 2023	72,161,489	$	72	$	2,436,523	$	(441)	$	(822,649)	(16,216,411)	$	(802,486)	$	811,019

Unrealized loss on available-for-sale securities	—	—		—		(646)		—		—	—		(646)
Common stock issued under stock incentive plan and ESPP	806,433	1		5,863		—		—		—	—		5,864
Stock-based compensation expense	—	—		9,234		—		—		—	—		9,234

Net loss	—	—		—		—		(81,549)		—	—		(81,549)

Balance at March 31, 2024	72,967,922	$	73	$	2,451,620	$	(1,087)	$	(904,198)	(16,216,411)	$	(802,486)	$	743,922
Unrealized gain on available-for-sale securities	—	—		—		42		—		—	—		42
Common stock issued under stock incentive plan and ESPP	123,568	—		1,099		—		—		—	—		1,099
Stock-based compensation expense	—	—		11,565		—		—		—	—		11,565

Net loss	—	—		—		—		(96,118)		—	—		(96,118)
Balance at June 30, 2024	73,091,490	$	73	$	2,464,284	$	(1,045)	$	(1,000,316)	(16,216,411)	$	(802,486)	$	660,510
Unrealized gain on available-for-sale securities	—	—		—		4,465		—		—	—		4,465
Common stock issued under stock incentive plan and ESPP	146,464	—		2,637		—		—		—	—		2,637
Stock-based compensation expense	—	—		11,145		—		—		—	—		11,145
Net income	—	—		—		—		947,915		—	—		947,915
Balance at September 30, 2024	73,237,954	73		2,478,066		3,420		(52,401)		(16,216,411)	(802,486)		1,626,672

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	Common Stock			Additional Paid-In Capital		Accumulated Other Comprehensive (Loss) Income		Accumulated Deficit		Treasury Stock			Total Stockholders’ Equity
(in thousands, except share amounts)	Shares	Amount								Shares	Amount
Balance at December 31, 2022	71,256,118	$	71	$	2,386,325	$	(12,535)	$	(470,561)	(16,216,411)	$	(802,486)	$	1,100,814
Unrealized gain on available-for-sale securities	—	—		—		4,124		—		—	—		4,124

Common stock issued under stock incentive plan and ESPP	501,660	1		2,466		—		—		—	—		2,467
Stock-based compensation expense	—	—		10,139		—		—		—	—		10,139
Net loss	—	—		—		—		(81,018)		—	—		(81,018)
Balance at March 31, 2023	71,757,778	$	72	$	2,398,930	$	(8,411)	$	(551,579)	(16,216,411)	$	(802,486)	$	1,036,526
Unrealized loss on available-for-sale securities	—	—		—		(459)		—		—	—		(459)

Common stock issued under stock incentive plan and ESPP	193,408	—		238		—		—		—	—		238
Stock-based compensation expense	—	—		11,737		—		—		—	—		11,737

Net loss	—	—		—		—		(83,806)		—	—		(83,806)
Balance at June 30, 2023	71,951,186	$	72	$	2,410,905	$	(8,870)	$	(635,385)	(16,216,411)	$	(802,486)	$	964,236
Unrealized gain on available-for-sale securities	—	—		—		2,974		—		—	—		2,974
Common stock issued under stock incentive plan and ESPP	149,198	—		1,881		—		—		—	—		1,881
Stock-based compensation expense	—	—		9,076		—		—		—	—		9,076
Net loss	—	—		—		—		(91,324)		—	—		(91,324)
Balance at September 30, 2023	72,100,384	$	72	$	2,421,862	$	(5,896)	$	(726,709)	(16,216,411)	$	(802,486)	$	886,843

See accompanying Notes to Condensed Consolidated Financial Statements.

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AGIOS PHARMACEUTICALS, INC.

Condensed Consolidated Statements of Cash Flows
(Unaudited)


	Nine Months Ended September 30,
(In thousands)	2024		2023
Operating activities
Net income (loss)	$	770,248	$	(256,148)


Adjustments to reconcile net income (loss) to net cash used in operating activities:
Depreciation and amortization	4,286		5,220
Stock-based compensation expense	31,944		30,952
Net accretion of discount on marketable securities	(8,870)		(4,658)
(Gain) loss on disposal of property and equipment	(39)		278
Non-cash operating lease expense	8,568		7,967
Expense associated with license agreement	—		17,500
Realized gain on investments	(168)		(28)
Gain on sale of contingent payments	(889,136)		—
Milestone payment from gain on sale of oncology business	(200,000)		—

Changes in operating assets and liabilities:
Accounts receivable, net	(308)		1,030



Inventory	(7,353)		(8,782)


Prepaid expenses and other current and non-current assets	(4,863)		440
Accounts payable	7,357		(5,201)
Accrued expenses and other current liabilities	(9,860)		140

Income taxes payable	52,682		—
Operating lease liabilities	(11,162)		(10,161)

Other non-current liabilities	—		(2,123)


Net cash used in operating activities	(256,674)		(223,574)
Investing activities
Purchases of marketable securities	(1,344,107)		(327,490)
Proceeds from maturities and sales of marketable securities	668,248		488,492
Payments associated with license agreement	—		(17,500)
Proceeds from sale of contingent payments	889,136		—
Proceeds from milestone payment from gain on sale of oncology business	200,000		—
Purchases of property and equipment	(718)		(765)
Proceeds from sale of equipment	40		1,325


Net cash provided by investing activities	412,599		144,062
Financing activities



Net proceeds from stock option exercises and employee stock purchase plan	9,600		4,586


Net cash provided by financing activities	9,600		4,586
Net change in cash and cash equivalents	165,525		(74,926)
Cash and cash equivalents at beginning of the period	88,205		139,259
Cash and cash equivalents at end of the period	$	253,730	$	64,333

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Supplemental disclosure of non-cash investing and financing transactions
Additions to property and equipment in accounts payable and accrued expenses	$	61	$	14




Net cash taxes (returned) paid	$	(637)	$	1,586

See accompanying Notes to Condensed Consolidated Financial Statements.

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AGIOS PHARMACEUTICALS, INC.

Notes to Condensed Consolidated Financial Statements

(Unaudited)

1. Overview and Basis of Presentation

References to Agios

Throughout this Quarterly Report on Form 10-Q, "Agios," "the company," “we,” “us,” and “our,” and similar expressions, except where the context requires otherwise, refer to Agios Pharmaceuticals, Inc. and its consolidated subsidiaries, and “our Board of Directors” refers to the board of directors of Agios Pharmaceuticals, Inc.

Overview

We are a biopharmaceutical company committed to transforming patients’ lives through leadership in the field of cellular metabolism, with the goal of creating differentiated medicines for rare diseases, with a focus on classical hematology. With a history of focused study on cellular metabolism, we have a deep and mature understanding of this biology, which is involved in the healthy functioning of nearly every system in the body. Building on this expertise, these learnings can be rapidly applied to our clinical trials with the goal of developing medicines that can have a significant impact for patients. We accelerate the impact of our portfolio by cultivating connections with patient communities, healthcare professionals, partners and colleagues to discover, develop and deliver potential therapies for rare diseases. We are located in Cambridge, Massachusetts.

The lead product candidate in our portfolio, PYRUKYND® (mitapivat), is an activator of both wild-type and mutant pyruvate kinase, or PK, enzymes for the potential treatment of hemolytic anemias. In February 2022, the U.S. Food and Drug Administration, or FDA, approved PYRUKYND® for the treatment of hemolytic anemia in adults with PK deficiency in the United States. In November 2022, we received marketing authorization from the European Commission for PYRUKYND® for the treatment of PK deficiency in adult patients in the European Union, or EU. In December 2022, we received marketing authorization in Great Britain for PYRUKYND® for the treatment of PK deficiency in adult patients under the European Commission Decision Reliance Procedure. In addition, we are currently evaluating PYRUKYND® in clinical trials for the treatment of thalassemia, sickle cell disease, or SCD, and in pediatric patients with PK deficiency. We are also developing (i) AG-946 (tebapivat), a novel PK activator, for the potential treatment of lower-risk myelodysplastic syndrome, or LR MDS, and hemolytic anemias, and (ii) AG-181, our phenylalanine hydroxylase, or PAH, stabilizer for the potential treatment of phenylketonuria, or PKU. In September 2024, AG-946 (tebapivat) was granted Orphan Drug Designation by the FDA for the treatment of MDS.

In addition to the aforementioned development programs, in July 2023 we entered into a license agreement with Alnylam Pharmaceuticals, Inc., or Alnylam, for the development and commercialization of products containing or comprised of an siRNA preclinical development candidate discovered by Alnylam and targeting the transmembrane serine protease 6, or TMPRSS6, gene, and we have begun preclinical development of a product candidate for the potential disease-modifying treatment of patients with polycythemia vera, or PV, a rare blood disorder.

We are subject to risks common to companies in our industry including, but not limited to, uncertainties relating to conducting preclinical and clinical research and development, the manufacture and supply of products for clinical and commercial use, obtaining and maintaining regulatory approvals and pricing and reimbursement for our products, market acceptance, managing global growth and operating expenses, availability of additional capital, competition, obtaining and enforcing patents, stock price volatility, dependence on collaborative relationships and third-party service providers, dependence on key personnel, potential litigation, potential product liability claims and potential government investigations.

Alnylam License Agreement

On July 28, 2023, we entered into a license agreement with Alnylam under which we acquired the rights to develop and commercialize Alnylam’s novel preclinical siRNA targeting the TMPRSS6 gene, as a potential disease-modifying treatment for patients with PV. Because the acquired assets do not meet the definition of a business in accordance with Accounting Standards Codification, or ASC, 805, Business Combinations, we accounted for the agreement as an asset acquisition.

In accordance with the license agreement, in the three months ended September 30, 2023, we made an up-front payment to Alnylam and recognized in-process research and development of $17.5 million. We will also pay Alnylam for certain expenses associated with the development of the TMPRSS6 program, and these will be recorded in our Consolidated Statements of Operations as incurred. Additionally, we are responsible to pay up to $130.0 million in potential development and regulatory milestones, in addition to sales milestones as well as tiered royalties on annual net sales, if any, of licensed products, which may be subject to specified reductions and offsets.

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Sale of Oncology Business to Servier and Sale of Contingent Payments

On March 31, 2021, we completed the sale of our oncology business to Servier Pharmaceuticals, LLC, or Servier, which represented a discontinued operation. The transaction included the sale of our oncology business, including TIBSOVO®, our clinical-stage product candidates vorasidenib, AG-270 and AG-636, and our oncology research programs for a payment of approximately $1.8 billion in cash at the closing, subject to certain adjustments, and a payment of $200.0 million in cash, if, prior to January 1, 2027, vorasidenib is granted new drug application approval from the FDA with an approved label that permits vorasidenib’s use as a single agent for the adjuvant treatment of patients with Grade 2 glioma that have an isocitrate dehydrogenase, or IDH, 1 or 2 mutation (and, to the extent required by such approval, the vorasidenib companion diagnostic test is granted an FDA premarket approval), or the Vorasidenib Milestone Payment, as well as a royalty of 5% of U.S. net sales of TIBSOVO® from the close of the transaction through loss of exclusivity, and a royalty of 15% of U.S. net sales of vorasidenib from the first commercial sale of vorasidenib through loss of exclusivity, or the Vorasidenib Royalty Rights. The Vorasidenib Milestone Payment, Vorasidenib Royalty Rights and royalty payments related to TIBSOVO® are referred to as contingent payments and recognized as income when realizable. Servier also acquired our co-commercialization rights for Bristol Myers Squibb’s IDHIFA® and the right to receive a $25.0 million potential milestone payment under our prior collaboration agreement with Celgene Corporation, or Celgene, and following the sale Servier has agreed to conduct certain clinical development activities within the IDHIFA® development program.

In October 2022, we sold our rights to future contingent payments associated with the royalty of 5% of U.S. net sales of TIBSOVO® from the close of the transaction through the loss of exclusivity to entities affiliated with Sagard Healthcare Partners, or Sagard, and recognized income of $127.9 million in our consolidated statements of operations for the year ended December 31, 2022.

In August 2024, the FDA approved vorasidenib for adult and pediatric patients 12 years and older with Grade 2 astrocytoma or oligodendroglioma with a susceptible IDH1 or IDH2 mutation, following surgery including biopsy, sub-total resection, or gross total resection. In September 2024, we received the Vorasidenib Milestone Payment from Servier and recognized income of $200.0 million within the milestone payment from gain on sale of oncology business line item in our consolidated statements of operations for the three and nine months ended September 30, 2024.

In May 2024, we entered into a purchase and sale agreement to sell the Vorasidenib Royalty Rights to Royalty Pharma Investments 2019 ICAV, or Royalty Pharma, for $905.0 million in cash, or the Upfront Payment. The sale was contingent upon FDA approval of vorasidenib and other customary closing conditions. Upon consummation of the sale in August 2024, Royalty Pharma acquired 100% of the Vorasidenib Royalty Rights payments made by Servier on account of up to $1.0 billion in U.S. net sales for each calendar year. In addition, any such Vorasidenib Royalty Rights payments made by Servier on account of U.S. net sales in each calendar year in excess of $1.0 billion will be split, with Royalty Pharma having the rights to a 12% earn-out on those excess payments and Agios retaining the rights to a 3% earn-out on those excess payments, or the Retained Earn-Out Rights. As a result of the sale, we recognized $889.1 million ($905.0 million net of fees of $15.9 million) within the gain on sale of contingent payments line item in our consolidated statements of operations for the three and nine months ended September 30, 2024. Royalty income related to the Retained Earn-Out Rights will be recognized in the period when realizable.

Basis of Presentation

The condensed consolidated balance sheet as of September 30, 2024, the condensed consolidated statements of operations, comprehensive income (loss) and stockholders' equity for the three and nine months ended September 30, 2024 and 2023, and the condensed consolidated statements of cash flows for the nine months ended September 30, 2024 and 2023 are unaudited. The unaudited condensed consolidated financial statements have been prepared on the same basis as the annual financial statements and, in the opinion of our management, reflect all adjustments, which include only normal recurring adjustments, necessary to fairly state our financial position as of September 30, 2024, our results of operations and stockholders' equity for the three and nine months ended September 30, 2024 and 2023, and cash flows for the nine months ended September 30, 2024 and 2023. The financial data and the other financial information disclosed in these notes to the condensed consolidated financial statements related to the three and nine-month periods are also unaudited. The results of operations for the three and nine months ended September 30, 2024 are not necessarily indicative of the results to be expected for the year ending December 31, 2024 or for any other future annual or interim period. The condensed consolidated balance sheet data as of December 31, 2023 was derived from our audited financial statements, but does not include all disclosures required by U.S. generally accepted accounting principles, or U.S. GAAP. The condensed consolidated interim financial statements should be read in conjunction with the audited consolidated financial statements and notes thereto included in our Annual Report on Form 10-K for the year ended December 31, 2023 that was filed with the Securities and Exchange Commission, or SEC, on February 15, 2024.

Our condensed consolidated financial statements include our accounts and the accounts of our wholly owned subsidiaries. All intercompany transactions have been eliminated in consolidation. The condensed consolidated financial statements have been prepared in conformity with U.S. GAAP.

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Use of Estimates

The preparation of our condensed consolidated financial statements requires us to make estimates, judgments and assumptions that may affect the reported amounts of assets, liabilities, equity, revenues and expenses and related disclosure of contingent assets and liabilities. On an ongoing basis we evaluate our estimates, judgments and methodologies. We base our estimates on historical experience and on various other assumptions that we believe are reasonable, the results of which form the basis for making judgments about the carrying values of assets, liabilities and equity and the amount of revenues and expenses. The full extent to which pandemics or public health emergencies, may in the future directly or indirectly impact our business, results of operations and financial condition, including expenses, reserves and allowances, clinical trials, research and development costs and employee-related amounts, will depend on future developments that are highly uncertain.

Liquidity

As of September 30, 2024, we had cash, cash equivalents and marketable securities of $1.7 billion. Although we have incurred recurring losses and expect to continue to incur losses for the foreseeable future, we expect our cash, cash equivalents and marketable securities to be sufficient to fund current operations for at least the next twelve months from the issuance of the financial statements. If we are unable to raise additional funds through equity or debt financings, we may be required to delay, limit, reduce or terminate product development or future commercialization efforts, or grant rights to develop and market products or product candidates that we would otherwise prefer to develop and market ourselves.

2. Summary of Significant Accounting Policies

There have been no material changes to the significant accounting policies previously disclosed in our Annual Report on Form 10-K for the year ended December 31, 2023.

Recent Accounting Pronouncements

Accounting standards that have been issued by the Financial Accounting Standards Board or other standards-setting bodies that do not require adoption until a future date are not expected to have a material impact on our financial statements upon adoption.

3. Fair Value Measurements

We record cash equivalents and marketable securities at fair value. ASC 820, Fair Value Measurements and Disclosures, establishes a fair value hierarchy for those instruments measured at fair value that distinguishes between assumptions based on market data (observable inputs) and our own assumptions (unobservable inputs). The hierarchy consists of three levels:

Level 1 – Unadjusted quoted prices in active markets for identical assets or liabilities.

Level 2 – Quoted prices for similar assets and liabilities in active markets, quoted prices in markets that are not active, or inputs which are observable, directly or indirectly, for substantially the full term of the asset or liability.

Level 3 – Unobservable inputs that reflect our own assumptions about the assumptions market participants would use in pricing the asset or liability in which there is little, if any, market activity for the asset or liability at the measurement date.

The following table summarizes our cash equivalents and marketable securities measured at fair value and by level on a recurring basis as of September 30, 2024:


(In thousands)	Level 1		Level 2		Level 3		Total
Cash equivalents	$	20,154	$	149,936	$	—	$	170,090
Total cash equivalents	20,154		149,936		—		170,090

Marketable securities:
Certificates of deposit	$	—	$	13,743	$	—	$	13,743
U.S. Treasuries	—		266,598		—		266,598
Government securities	—		297,557		—		297,557
Corporate debt securities	—		829,018		—		829,018
Total marketable securities	—		1,406,916		—		1,406,916
Total cash equivalents and marketable securities	$	20,154	$	1,556,852	$	—	$	1,577,006

Cash equivalents and marketable securities have been initially valued at the transaction price and are subsequently valued, at the end of each reporting period, utilizing third-party pricing services or other observable market data. The pricing services utilize industry standard valuation models, including both income and market-based approaches, and observable market inputs to

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determine value. After completing our validation procedures, we did not adjust or override any fair value measurements provided by the pricing services as of September 30, 2024.

There have been no changes to the valuation methods during the nine months ended September 30, 2024, and we had no financial assets or liabilities that were classified as Level 3 at any point during the nine months ended September 30, 2024.

4. Marketable Securities

Our marketable securities are classified as available-for-sale pursuant to ASC 320, Investments – Debt and Equity Securities, and are recorded at fair value. Unrealized gains and losses are included as a component of accumulated other comprehensive income (loss) in the condensed consolidated balance sheets and statements of stockholders’ equity, and a component of total comprehensive income (loss) in the condensed consolidated statements of comprehensive income (loss), until realized. Unrealized losses are evaluated for impairment under ASC 326, Financial Instruments - Credit Losses, to determine if the impairment is credit-related or noncredit-related. Credit-related impairment is recognized as an allowance on the condensed consolidated balance sheets with a corresponding adjustment to earnings, and noncredit-related impairment is recognized in other comprehensive income, net of taxes. Realized gains and losses are included in investment income on a specific-identification basis. There were no material realized gains or losses on marketable securities for the three and nine months ended September 30, 2024 or 2023.

Marketable securities at September 30, 2024 consisted of the following:


(In thousands)	Amortized Cost		Unrealized Gains		Unrealized Losses		Fair Value
Current:
Certificates of deposit	$	13,724	$	19	$	—	$	13,743
U.S. Treasuries	179,560		299		(10)		179,849
Government securities	160,442		235		(34)		160,643
Corporate debt securities	396,143		718		(69)		396,792
Total Current	749,869		1,271		(113)		751,027

Non-current:

U.S. Treasuries	86,299		477		(27)		86,749
Government securities	136,747		250		(83)		136,914
Corporate debt securities	430,581		1,733		(88)		432,226
Total Non-current	653,627		2,460		(198)		655,889
Total marketable securities	$	1,403,496	$	3,731	$	(311)	$	1,406,916

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Marketable securities at December 31, 2023 consisted of the following:


(In thousands)	Amortized Cost		Unrealized Gains		Unrealized Losses		Fair Value
Current:

U.S. Treasuries	$	30,876	$	—	$	(56)	$	30,820
Government securities	247,460		194		(695)		246,959
Corporate debt securities	411,045		874		(975)		410,944
Total Current	689,381		1,068		(1,726)		688,723

Non-current:

U.S. Treasuries	4,802		30		—		4,832
Government securities	9,986		75		—		10,061
Corporate debt securities	14,430		112		—		14,542
Total Non-current	29,218		217		—		29,435
Total marketable securities	$	718,599	$	1,285	$	(1,726)	$	718,158

As of September 30, 2024 and December 31, 2023, we held both current and non-current investments. Investments classified as current have maturities of less than one year. Investments classified as non-current are those that: (i) have a maturity of greater than one year, and (ii) we do not intend to liquidate within the next twelve months, although these funds are available for use and, therefore, are classified as available-for-sale.

As of September 30, 2024 and December 31, 2023, we held 91 and 151 debt securities, respectively, that were in an unrealized loss position for less than one year. We did not record an allowance for credit losses as of September 30, 2024 and December 31, 2023 related to these securities. The aggregate fair value of debt securities in an unrealized loss position at September 30, 2024 and December 31, 2023 was $336.6 million and $513.5 million, respectively. There were no individual securities that were in a significant unrealized loss position as of September 30, 2024 and December 31, 2023. We regularly review the securities in an unrealized loss position and evaluate the current expected credit loss by considering factors such as historical experience, market data, issuer-specific factors, and current economic conditions. We do not consider these marketable securities to be impaired as of September 30, 2024 and December 31, 2023.

5. Inventory

Inventory, which consists of commercial supply of PYRUKYND®, consisted of the following:


(In thousands)	September 30, 2024		December 31, 2023
Raw materials	$	90	$	51
Work-in-process	24,079		17,568
Finished goods	2,260		1,457
Total inventory	$	26,429	$	19,076

6. Leases

Our building leases are comprised of office and laboratory space under non-cancelable operating leases. These lease agreements have remaining lease terms of approximately three years and contain various clauses for renewal at our option. The renewal options were not included in the calculation of the operating lease assets and the operating lease liabilities as the renewal options are not reasonably certain of being exercised. The lease agreements do not contain residual value guarantees.

The components of lease expense and other information related to leases were as follows:


	Three Months Ended September 30,				Nine Months Ended September 30,
(In thousands)	2024		2023		2024		2023
Operating lease costs	$	3,807	$	3,807	$	11,420	$	11,420
Cash paid for amounts included in the measurement of operating lease liabilities	4,684		4,550		14,015		$	13,614

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We have not entered into any material short-term leases or financing leases as of September 30, 2024.

In arriving at the operating lease liabilities as of September 30, 2024 and December 31, 2023, we applied the weighted-average incremental borrowing rate of 5.7% for both periods over a weighted-average remaining lease term of 3.4 and 4.2 years, respectively.

As of September 30, 2024, undiscounted minimum rental commitments under non-cancelable leases were as follows:



(In thousands)
Remaining 2024	$	3,126
2025	19,507
2026	20,151
2027	20,755
2028	3,479


Undiscounted minimum rental commitments	$	67,018
Interest	(6,184)
Operating lease liabilities	$	60,834

We provided our landlord a security deposit of $2.9 million as security for our leases, which is included within other non-current assets on our condensed consolidated balance sheet.

In August 2021, we entered into a long-term sublease agreement for 13,000 square feet of the office space at 38 Sidney Street, Cambridge, Massachusetts, with the term of the lease running through December 2024. In April 2022, we entered into a long-term sublease agreement for 27,000 square feet of the office space at 64 Sidney Street, Cambridge, Massachusetts, with the term of the lease running through April 2025. In May 2023, we entered into a long-term sublease agreement for 7,407 square feet of office space on the first floor of 64 Sidney Street, Cambridge, Massachusetts, with the term of the lease running through April 2025. We recorded operating sublease income of $1.6 million and $1.7 million for the three months ended September 30, 2024 and 2023, respectively, and $4.8 million and $4.5 million for the nine months ended September 30, 2024 and 2023, respectively, in other income, net in the condensed consolidated statements of operations. We hold security deposits from our sublessees of approximately $1.2 million which is recorded within other non-current assets on our condensed consolidated balance sheet.

As of September 30, 2024, the future minimum lease payments to be received under the long-term sublease agreements were as follows:


(In thousands)
Remaining 2024	$	1,284
2025	1,310


Total	$	2,594

7. Accrued Expenses

Accrued expenses consisted of the following:


(In thousands)	September 30, 2024		December 31, 2023
Accrued compensation	$	17,686	$	23,232
Accrued research and development costs	9,731		15,463
Accrued professional fees	3,273		3,115
Accrued other	2,617		1,357
Total accrued expenses	$	33,307	$	43,167

8. Product Revenue

We sell PYRUKYND®, our wholly owned product, to a limited number of specialty distributors and specialty pharmacy providers, or collectively, the Customers. These Customers subsequently resell PYRUKYND® to pharmacies or dispense PYRUKYND® directly to patients. In addition to distribution agreements with Customers, we enter into arrangements with

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healthcare providers and payors that provide for government-mandated and/or privately-negotiated rebates, chargebacks and discounts with respect to the purchase of PYRUKYND®.

The performance obligation related to the sale of PYRUKYND® is satisfied and revenue is recognized when the Customer obtains control of the product, which occurs at a point in time, typically upon delivery to the Customer.

Product revenue, net, were as follows:


	Three Months Ended September 30,				Nine Months Ended September 30,
(In thousands)	2024		2023		2024		2023
Product revenue, net	$	8,964	$	7,399	$	25,768	$	19,720

Reserves for Variable Consideration

Revenues from product sales are recorded at the net sales price, or transaction price, which includes estimates of variable consideration for which reserves are established and result from contractual adjustments, government rebates, returns and other allowances that are offered within the contracts with our Customers, healthcare providers, payors and other indirect customers relating to the sale of our products.

Contractual Adjustments

We generally provide Customers with discounts, including prompt pay discounts, and allowances that are explicitly stated in the contracts and are recorded as a reduction of revenue in the period the related product revenue is recognized. In addition, we receive sales order management, data and distribution services from certain Customers.

Chargebacks and discounts represent the estimated obligations resulting from contractual commitments to sell products to qualified healthcare providers at prices lower than the list prices charged to Customers who directly purchase the product from us. Customers charge us for the difference between what they pay for the product and the ultimate selling price to the qualified healthcare providers. These reserves are estimated using the expected value method, based upon a range of possible outcomes that are probability-weighted for the estimated channel mix and are established in the same period that the related revenue is recognized, resulting in a reduction of product revenue.

Government Rebates

Government rebates include Medicare, TriCare, and Medicaid rebates, which we estimate using the expected value method, based upon a range of possible outcomes that are probability-weighted for the estimated payor mix. These reserves are recorded in the same period the related revenue is recognized, resulting in a reduction of product revenue. For Medicare, we also estimate the number of patients in the prescription drug coverage gap for whom we will owe an additional liability under the Medicare Part D program.

Returns / Replacement

We estimate the amount of product sales that may be returned by Customers or replaced by Agios and record this estimate as a reduction of revenue in the period the related product revenue is recognized. We currently estimate product return and replacement liabilities using the expected value method, based on available industry data, including our visibility into the inventory remaining in the distribution channel.

The following table summarizes balances and activity in each of the product revenue allowance and reserve categories for the nine months ended September 30, 2024:


(In thousands)	Contractual Adjustments		Government Rebates		Returns/ Replacement		Total
Balance at December 31, 2023	$	156	$	1,084	$	232	$	1,472
Current provisions relating to sales in the current year	1,021		1,915		289		3,225
Adjustments relating to prior years	(39)		(49)		40		(48)
Payments/returns relating to sales in the current year	(860)		(731)		—		(1,591)
Payments/returns relating to sales in the prior years	(85)		(373)		(71)		(529)
Balance at September 30, 2024	$	193	$	1,846	$	490	$	2,529

Total revenue-related reserves above, included in our condensed consolidated balance sheets, are summarized as follows:

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(In thousands)	September 30, 2024		December 31, 2023
Reduction of accounts receivable	$	91	$	151
Component of accrued expenses	2,438		1,321
Total revenue-related reserves	$	2,529	$	1,472

The following table presents changes in our contract assets during the nine months ended September 30, 2024:


(In thousands)	December 31, 2023		Additions		Deductions		September 30, 2024
Contract assets(1)
Accounts receivable, net	$	2,810	$	28,921	$	(28,613)	$	3,118

(1) Additions to contract assets relate to amounts billed to Customers for product sales and deductions to contract assets primarily relate to collection of receivables during the reporting period.

9. Share-Based Payments

2023 Stock Incentive Plan and Inducement Grants

In June 2023, our stockholders approved the 2023 Stock Incentive Plan, or the 2023 Plan. The 2023 Plan provides for the grant of incentive stock options, nonstatutory stock options, stock appreciation rights, restricted stock awards, restricted stock units, or RSUs, performance-based share units, or PSUs, and other stock-based awards to employees, advisors, consultants and non-employee directors.

Following the adoption of the 2023 Plan, we ceased granting equity awards under the 2013 Stock Incentive Plan, or the 2013 Plan. Any outstanding equity awards that were previously granted under the 2013 Plan continue to be governed by their terms. Following adoption of the 2013 Plan, we ceased granting equity awards under the 2007 Stock Incentive Plan, or the 2007 Plan. There are no outstanding equity awards under the 2007 Plan.

In connection with the start of employment of our Chief Executive Officer and Chief Financial Officer in 2022, and our Chief Commercial Officer in 2023, our board of directors granted each of them equity awards in the form of stock options, RSUs and PSUs, which awards were made outside our equity incentive plans as inducements material to their respective entry into employment with us in accordance with Nasdaq Listing Rule 5635(c)(4).

As of September 30, 2024, the maximum number of shares reserved under the 2013 Plan, the 2023 Plan and the inducement grants described above was 11,030,891, and we had 2,819,436 shares available for future issuance under the 2023 Plan.

Stock options

The following table presents stock option activity for the nine months ended September 30, 2024:


	Number of Stock Options	Weighted-Average Exercise Price
Outstanding at December 31, 2023	5,263,681	$	44.94
Granted	1,023,433	34.04
Exercised	(223,740)	31.13
Cancelled/Forfeited	(46,427)	42.18
Expired	(24,750)	35.37
Outstanding at September 30, 2024	5,992,197	$	43.65
Exercisable at September 30, 2024	3,840,761	$	50.47
Vested and expected to vest at September 30, 2024	5,992,197	$	43.65

At September 30, 2024, there was approximately $33.5 million of total unrecognized compensation expense related to unvested stock option awards, which we expect to recognize over a weighted-average period of approximately 2.49 years.

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Restricted stock units

The following table presents RSU activity for the nine months ended September 30, 2024:


	Number of Stock Units	Weighted-Average Grant Date Fair Value
Unvested shares at December 31, 2023	1,346,701	$	29.67
Granted	1,117,510	31.95
Vested	(579,370)	32.72
Forfeited	(40,166)	30.41
Unvested shares at September 30, 2024	1,844,675	$	30.08

As of September 30, 2024, there was approximately $39.6 million of total unrecognized compensation expense related to RSUs, which we expect to recognize over a weighted-average period of approximately 2.01 years.

Performance-based stock units

The following table presents PSU activity for the nine months ended September 30, 2024:


	Number of Stock Units	Weighted-Average Grant Date Fair Value
Unvested shares at December 31, 2023	362,133	$	30.66
Granted	183,000	32.27
Vested	(170,550)	35.04

Unvested shares at September 30, 2024	374,583	$	29.45

Stock-based compensation expense associated with these PSUs is recognized if the underlying performance condition is considered probable of achievement using our management’s best estimates.

As of September 30, 2024, there was no unrecognized compensation expense related to PSUs with performance-based vesting criteria that are considered probable of achievement, and $11.0 million of total unrecognized compensation expense related to PSUs with performance-based vesting criteria that are considered not probable of achievement.

Market-based stock units

The following table presents market-based stock unit, or MSU, activity for the nine months ended September 30, 2024:


	Number of Stock Units	Weighted-Average Grant Date Fair Value
Unvested shares at December 31, 2023	42,695	$	41.50


Expired	(42,695)	41.50
Unvested shares at September 30, 2024	—	$	—

The fair value of MSUs are estimated using a Monte Carlo simulation model. Assumptions and estimates utilized in the model include the risk-free interest rate, dividend yield, expected stock volatility and the estimated period to achievement of the market condition. As of September 30, 2024, there was no remaining unrecognized compensation expense related to MSUs.

2013 Employee Stock Purchase Plan

In June 2013, our Board of Directors adopted, and in July 2013 our stockholders approved, the 2013 Employee Stock Purchase Plan, or the 2013 ESPP. We issued and sold 102,805 and 112,832 shares of common stock during the nine months ended September 30, 2024 and 2023, respectively, under the 2013 ESPP. The 2013 ESPP provides participating employees with the opportunity to purchase up to an aggregate of 2,363,636 shares of our common stock. As of September 30, 2024, we had 1,583,234 shares of common stock available for future issuance under the 2013 ESPP.

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Stock-based compensation expense

Stock-based compensation expense by award type included within the condensed consolidated statements of operations is as follows:


	Three Months Ended September 30,				Nine Months Ended September 30,
(In thousands)	2024		2023		2024		2023
Stock options	$	4,579	$	4,171	$	13,011	$	13,065
Restricted stock units	6,314		4,735		17,491		14,436
Performance-based stock units	—		—		750		2,784
Employee stock purchase plan	252		170		692		667

Total stock-based compensation expense	$	11,145	$	9,076	$	31,944	$	30,952

Expenses related to stock options and stock-based awards were allocated as follows in the condensed consolidated statements of operations:


	Three Months Ended September 30,				Nine Months Ended September 30,
(In thousands)	2024		2023		2024		2023
Research and development expense	$	4,391	$	3,635	$	12,626	$	12,530
Selling, general and administrative expense	6,754		5,441		19,318		18,422
Total stock-based compensation expense	$	11,145	$	9,076	$	31,944	$	30,952

10. Income (Loss) per Share

Basic net income (loss) per share is calculated by dividing net income (loss) by the weighted-average shares outstanding during the period, without consideration for common stock equivalents. Diluted net income (loss) per share is calculated by adjusting the weighted-average shares outstanding for the dilutive effect of common stock equivalents outstanding for the period, determined using the treasury stock method. For purposes of the dilutive net income (loss) per share calculation, stock options, RSUs and PSUs for which the performance and market vesting conditions, respectively, have been deemed probable, and 2013 ESPP shares are considered to be common stock equivalents, while PSUs with performance and market vesting conditions, respectively, that were not deemed probable as of September 30, 2024 are not considered to be common stock equivalents.

We utilize the control number concept in the computation of diluted earnings per share to determine whether potential common stock equivalents are dilutive. The control number used is net income (loss) from continuing operations. The control number concept requires that the same number of potentially dilutive securities applied in computing diluted earnings per share from continuing operations be applied to all other categories of income or loss, regardless of their anti-dilutive effect on such categories. Since we had a net loss for the three and nine months ended September 30, 2023, no dilutive effect was recognized in the calculation of loss per share and basic and diluted net loss per share was the same for those periods.

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The following is a reconciliation of basic weighted-average number of common shares used in computing net income (loss) per share to diluted weighted-average number of common shares used in computing net income (loss) per share for the periods indicated:


	Three Months Ended September 30,		Nine Months Ended September 30,
	2024	2023	2024	2023
Basic shares	56,939,403	55,803,663	56,709,318	55,559,766
Effect of dilutive securities
Stock options	557,300	—	231,082	—
Restricted stock units	927,149	—	626,208	—
Performance-based stock units	—	—	11,793	—
Employee stock purchase plan shares	8,944	—	2,981	—
Diluted shares	58,432,796	55,803,663	57,581,382	55,559,766

The following common stock equivalents were excluded from the calculation of diluted net income (loss) per share applicable to common stockholders for the periods indicated because including them would have had an anti-dilutive effect:


	Three Months Ended September 30,		Nine Months Ended September 30,
	2024	2023	2024	2023
Stock options	3,463,344	5,542,418	5,176,610	5,542,418
Restricted stock units	—	1,355,987	90,480	1,355,987

Employee stock purchase plan shares	3,139	11,383	4,393	11,383
Total common stock equivalents	3,466,483	6,909,788	5,271,483	6,909,788

11. Income Taxes

We are subject to taxation in numerous U.S. states and territories. As a result, our effective tax rate is derived from a combination of applicable tax rates in the various places that we operate. In preparing our financial statements, we estimate the amount of tax that will become payable in each of such places. Nevertheless, our effective tax rate may be different from previous periods or our current expectations due to numerous factors, including as a result of changes in the mix of our profitability from state to state, the results of examinations and audits of our tax filings, our inability to secure or sustain acceptable agreements with tax authorities, changes in accounting for income taxes and changes in tax laws. Any of these factors may result in tax obligations in excess of amounts accrued in our financial statements.

We recorded income tax expense of $53.1 million for the three and nine months ended September 30, 2024 compared to no income tax expense for the three and nine months ended September 30, 2023. The income tax expense in the three and nine months ended September 30, 2024 was predominantly due to the current tax impact of the sale of the Vorasidenib Royalty Rights and the Vorasidenib Milestone Payment received in the three months ended September 30, 2024 as discussed above in Note 1, Overview and Basis of Presentation. While we released a portion of our valuation allowance when we utilized certain net operating loss carryforwards, or NOLs, and research and development tax credits as a result of the income associated with the sale of Vorasidenib Royalty Rights and the Vorasidenib Milestone Payment in the three months ended September 30, 2024, we continue to maintain a full valuation allowance against all of our net deferred tax assets.

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Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations

Forward-looking Information

The following discussion of our financial condition and results of operations should be read in conjunction with our unaudited condensed consolidated financial statements as of September 30, 2024 and for the three and nine months ended September 30, 2024 and 2023, and related notes included in Part I, Item 1 of this Quarterly Report on Form 10-Q, as well as the audited consolidated financial statements and notes and Management’s Discussion and Analysis of Financial Condition and Results of Operations, included in our Annual Report on Form 10-K for the year ended December 31, 2023 filed with the SEC on February 15, 2024. This Management’s Discussion and Analysis of Financial Condition and Results of Operations contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. These forward-looking statements are based on current expectations, estimates, forecasts and projections, and the beliefs and assumptions of our management, and include, without limitation, statements with respect to our expectations regarding our research, development and commercialization plans and prospects, results of operations, selling, general and administrative expenses, research and development expenses, and the sufficiency of our cash for future operations. Words such as “aim,” “anticipate,” “believe,” “continue,” “could,” “estimate,” “expect,” “goal,” “intend,” “may,” “might,” “plan,” “potential,” “predict,” “project,” “should,” “strategy,” “target,” “vision,” “will,” “would” or the negatives of these words and similar expressions are intended to identify these forward-looking statements, although not all forward-looking statements contain these identifying words. Readers are cautioned that these forward-looking statements are predictions and are subject to risks, uncertainties and assumptions that are difficult to predict. Therefore, actual results may differ materially and adversely from those expressed in any forward-looking statements. Among the important factors that could cause actual results to differ materially from those indicated by our forward-looking statements are those discussed under the heading “Risk Factors” in Part II, Item 1A and elsewhere in this report, and in our Annual Report on Form 10-K for the year ended December 31, 2023. We undertake no obligation to revise the forward-looking statements contained herein to reflect events or circumstances after the date hereof or to reflect the occurrence of unanticipated events, except as required by law.

Overview

Alnylam License Agreement

In accordance with the license agreement with Alnylam, in the three months ended September 30, 2023, we made an up-front payment to Alnylam and recognized in-process research and development of $17.5 million. We will also pay Alnylam for certain expenses associated with the development of the TMPRSS6 program, and these will be recorded in our Consolidated Statements of Operations as incurred. Additionally, we are responsible to pay up to $130.0 million in potential development and regulatory milestones, in addition to sales milestones as well as tiered royalties on annual net sales, if any, of licensed products,

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which may be subject to specified reductions and offsets. Because the acquired assets under the license agreement with Alnylam do not meet the definition of a business in accordance with ASC 805, Business Combinations, we accounted for the agreement as an asset acquisition.

Sale of Oncology Business to Servier and Sale of Contingent Payments

On March 31, 2021, we completed the sale of our oncology business to Servier Pharmaceuticals, LLC, or Servier, which represented a discontinued operation. The transaction included the sale of our oncology business, including TIBSOVO®, our clinical-stage product candidates vorasidenib, AG-270 and AG-636, and our oncology research programs for a payment of approximately $1.8 billion in cash at the closing, subject to certain adjustments, and a payment of $200.0 million in cash, if, prior to January 1, 2027, vorasidenib is granted new drug application, or NDA, approval from the FDA with an approved label that permits vorasidenib’s use as a single agent for the adjuvant treatment of patients with Grade 2 glioma that have an isocitrate dehydrogenase, or IDH, 1 or 2 mutation (and, to the extent required by such approval, the vorasidenib companion diagnostic test is granted an FDA premarket approval), or the Vorasidenib Milestone Payment, as well as a royalty of 5% of U.S. net sales of TIBSOVO® from the close of the transaction through loss of exclusivity, and a royalty of 15% of U.S. net sales of vorasidenib from the first commercial sale of vorasidenib through loss of exclusivity, or the Vorasidenib Royalty Rights. The Vorasidenib Milestone Payment, Vorasidenib Royalty Rights and royalty payments related to TIBSOVO® are referred to as contingent payments and recognized as income when realizable. Servier also acquired our co-commercialization rights for Bristol Myers Squibb’s IDHIFA® and the right to receive a $25.0 million potential milestone payment under our prior collaboration agreement with Celgene Corporation, or Celgene, and following the sale Servier agreed to conduct certain clinical development activities within the IDHIFA® development program.

Financial Operations Overview

General

Since inception, our operations have primarily focused on organizing and staffing our company, business planning, raising capital, assembling our core capabilities in cellular metabolism and classical hematology, identifying potential product candidates, undertaking preclinical studies, conducting clinical trials, establishing a commercial infrastructure, preparing for and executing on the commercial launch of PYRUKYND® and, prior to the sale of our oncology business to Servier on March 31, 2021, marketing TIBSOVO® and IDHIFA®. Through March 31, 2021, we financed our operations primarily through proceeds from the sale of our royalty rights, commercial sales of TIBSOVO®, funding received from our collaboration agreements, private placements of our preferred stock, our initial public offering of our common stock and concurrent private placement of common stock to an affiliate of Celgene, and our follow-on public offerings. Following the sale of our oncology business to Servier on March 31, 2021, we have financed and expect to continue to finance our operations primarily through cash on hand, potential royalty payments with respect to the Retained Earn-Out Rights, the actual and potential future sales of PYRUKYND® and, potentially, collaborations, strategic alliances, licensing arrangements and other nondilutive strategic transactions. In addition, we may pursue opportunistic debt offerings, and equity or equity-linked offerings.

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Additionally, since inception, we have historically incurred significant operating losses. Our net income for the nine months ended September 30, 2024 was $770.2 million and our net loss for the nine months ended September 30, 2023 was $256.1 million. As of September 30, 2024, we had an accumulated deficit of $52.4 million. The net income we generated in the nine months ended September 30, 2024 was primarily due to the sale of the Vorasidenib Royalty Rights to Royalty Pharma and our receipt of the Vorasidenib Milestone Payment discussed above in Overview. We expect to incur significant expenses and net losses until such time we are able to report profitable results. Our net losses may fluctuate significantly from year to year. We expect that we will continue to incur significant expenses as we continue to advance and expand clinical development and commercialization activities for PYRUKYND®, including with respect to our anticipated regulatory submissions for the treatment of thalassemia; continue to advance and expand clinical development of AG-946 (tebapivat), our novel PK activator; continue to advance AG-181, our PAH stabilizer; continue preclinical development of a licensed siRNA development candidate pursuant to our license agreement with Alnylam; expand and protect our intellectual property portfolio, including by in-licensing or acquiring assets for pipeline growth; and hire additional commercial and development personnel.

Revenues

Our wholly owned product, PYRUKYND®, received approval from the FDA on February 17, 2022, for the treatment of hemolytic anemia in adults with PK deficiency in the United States. Upon FDA approval of PYRUKYND® in the United States, we began generating product revenue from sales of PYRUKYND®. We sell PYRUKYND® to a limited number of specialty distributors and specialty pharmacy providers, or collectively, the Customers. These Customers subsequently resell PYRUKYND® to pharmacies or dispense PYRUKYND® directly to patients. In addition to distribution agreements with Customers, we enter into arrangements with healthcare providers and payors that provide for government-mandated and/or privately-negotiated rebates, chargebacks and discounts with respect to the purchase of PYRUKYND®. In July 2024, we entered into a distribution agreement with NewBridge Pharmaceuticals FZ-LLC, or the NewBridge Agreement, pursuant to which we granted NewBridge the right to commercialize PYRUKYND® in Bahrain, Kuwait, Oman, Qatar, Saudi Arabia, and the United Arab Emirates, or the GCC region. For further discussion of our revenue recognition policy, see Note 8, Product Revenue, to the condensed consolidated financial statements in this Quarterly Report on Form 10-Q.

In the future, we expect to continue to generate revenue from product sales, and we may potentially generate revenue from the Retained Earn-Out Rights. We may also generate revenue from milestone payments, upfront payments or royalties on product sales from collaborations or licensing agreements that we may enter into in the future.

Cost of Sales

Cost of sales consists primarily of manufacturing costs for sales of PYRUKYND®. Based on our policy to expense costs associated with the manufacturing of our products prior to regulatory approval, certain of the manufacturing costs associated with product shipments of PYRUKYND® recorded during the three and nine months ended September 30, 2024 and 2023 were expensed prior to February 17, 2022, and, therefore, are not included in costs of sales during the three and nine months ended September 30, 2024 and 2023. The amounts excluded from cost of sales were not significant during the three and nine months ended September 30, 2024 and 2023.

Inventories are reviewed periodically to identify excess or obsolete inventory based on projected sales activity as well as product shelf-life. Expired inventory is disposed of, and the related costs are recognized as cost of sales in our consolidated statements of operations, when, based on the expiry date, we do not believe we are able to sell the inventory. We have not reserved for excess or obsolete inventory during the three and nine months ended September 30, 2024 and 2023.

Research and Development Expenses

Research and development activities are central to our business model. Product candidates in later stages of clinical development generally have higher development costs than those in earlier stages of clinical development, primarily due to the increased size and duration of later-stage clinical trials. We expect research and development costs related to our portfolio to increase as our product candidate development programs progress. However, the successful development of our product candidates is highly uncertain. As such, at this time, we cannot reasonably estimate or know the nature, timing and estimated costs of the efforts that will be necessary to complete the development of and to commercialize these product candidates. We are unable to predict the amount of net cash inflows from PYRUKYND® or any of our product candidates. This is due to the numerous risks and uncertainties associated with developing medicines, including the uncertainty of:

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•establishing an appropriate safety profile with an investigational new drug application, or IND, and/or NDA-enabling toxicology and clinical trials;

•successfully enrolling in, and completion of, clinical trials;

•receiving marketing approvals from applicable regulatory authorities;

•establishing compliant commercial manufacturing capabilities or making arrangements with third-party manufacturers;

•obtaining and maintaining patent and trade secret protection and regulatory exclusivity for our product candidates;

•launching commercial sales of the products, if and when approved, in the United States or in other jurisdictions, whether alone or in collaboration with others, including pursuant to the NewBridge Agreement; and

•maintaining an acceptable safety profile of the products following approval.

A change in the outcome of any of these variables with respect to the development of any of our product candidates would significantly change the costs and timing associated with the development of that product candidate.

Research and development expenses consist primarily of costs incurred for our research activities, including our drug discovery efforts, and the development of our product candidates, which include:

•employee-related expenses, including salaries, benefits and stock-based compensation expense;

•expenses incurred under agreements with third parties, including contract research organizations, or CROs, that conduct research and development and both preclinical and clinical activities on our behalf, and the cost of consultants;

•the cost of lab supplies and acquiring, developing and manufacturing preclinical and clinical study materials; and

•facilities, depreciation, and other expenses, which include direct and allocated expenses for rent and the maintenance of facilities, insurance and other operating costs.

The following summarizes our most advanced programs:

PYRUKYND® (mitapivat): First-in-Class PK Activator

We are developing PYRUKYND® for the treatment of PK deficiency and other hemolytic anemias such as thalassemia and SCD. PYRUKYND® is an orally available small molecule and a potent activator of the wild-type and mutated PK enzymes.

In February 2022, the FDA approved PYRUKYND® for the treatment of hemolytic anemia in adults with PK deficiency in the United States. In November 2022, we received marketing authorization from the European Commission for PYRUKYND® for the treatment of PK deficiency in adult patients in the EU. In December 2022, we received marketing authorization in Great Britain for PYRUKYND® for the treatment of PK deficiency in adult patients under the European Commission Decision Reliance Procedure. In addition, we are currently evaluating PYRUKYND® in clinical trials for the treatment of thalassemia, SCD, and in pediatric patients with PK deficiency. We have worldwide development and commercial rights to PYRUKYND®, subject to the commercialization rights granted to Newbridge in the GCC region pursuant to the Newbridge Agreement, and expect to fund the future development and commercialization costs related to this program. PYRUKYND® has been granted orphan drug designation for the treatment of PK deficiency by the FDA and the EMA. Additionally, PYRUKYND® has received orphan drug designation from the FDA for the treatment of thalassemia and SCD, and breakthrough medicine designation by the Saudi Food and Drug Authority for the treatment of thalassemia.

We have built our commercial infrastructure to support the commercialization of PYRUKYND® in adult PK deficiency in the United States. In connection with our regulatory approvals in the EU and Great Britain, we are currently providing access to PYRUKYND® on a free of charge basis for eligible patients in those jurisdictions through a global managed access program. We provide access to PYRUKYND® for adult patients with PK deficiency in other jurisdictions upon request through the global managed access program, on either a free of charge or for charge basis. Our global managed access program has not had a significant impact on our business, financial condition or results of operations. Beyond the global managed access program, we continue to evaluate options for the commercialization of PYRUKYND® outside of the United States, including through exploring potential partnership opportunities, such as the NewBridge Agreement which we entered into in July 2024.

We are evaluating PYRUKYND® in numerous clinical trials, including the following:

•An extension study evaluating the long-term safety, tolerability and efficacy of treatment with PYRUKYND® in patients from ENERGIZE, our completed phase 3, double-blind, randomized, placebo-controlled multicenter study pivotal trial of PYRUKYND® in adults with non-transfusion-dependent alpha- or beta-thalassemia. We announced topline data for

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ENERGIZE in January 2024 and a more detailed analysis of the data in June 2024. A total of 194 patients were enrolled in the study, with 130 randomized to PYRUKYND® 100 mg twice-daily, or BID, and 64 randomized to matched placebo. 122 patients (93.8%) in the PYRUKYND® arm and 62 patients (96.9%) in the placebo arm completed the 24-week double-blind period of the study. The study met the primary endpoint of hemoglobin response, where treatment with PYRUKYND® demonstrated a statistically significant increase in hemoglobin response compared to placebo, as 42.3% of patients in the PYRUKYND® arm achieved a hemoglobin response, compared to 1.6% of patients in the placebo arm (2-sided p<0.0001). Treatment with PYRUKYND® also demonstrated statistically significant improvements compared to placebo for both key secondary endpoints: (i) change from baseline in average Functional Assessment of Chronic Illness Therapy-Fatigue, or FACIT-Fatigue, subscale score from week 12 to week 24 and (ii) change from baseline in average hemoglobin concentration from week 12 to week 24. During the 24-week double-blind period, four (3.1%) subjects in the PYRUKYND® arm experienced adverse events, or AEs, leading to discontinuation, and there were no AEs in the placebo arm leading to discontinuation. AEs that led to discontinutation in the PYRUKIND® arm were thrombocytopenia, arthralgia, abdominal distension, and 5 concurrent laboratory adverse events (alanine aminotransferase increase, aspartate aminotransferase increase, blood bilirubin increase, blood LDH increase, and international normalized ratio increase), all in one patient each. We aim to submit an sNDA for PYRUKYND® in thalassemia to the FDA by the end of 2024.

•An extension study evaluating the long-term safety, tolerability and efficacy of treatment with PYRUKYND® in patients from ENERGIZE-T, our completed phase 3, double-blind, randomized, placebo-controlled multicenter study evaluating the efficacy and safety of PYRUKYND® as a potential treatment for adults with transfusion-dependent alpha- or beta-thalassemia, defined as 6 to 20 red blood cell, or RBC, units transfused and ≤ six-week transfusion-free period during the 24-week period before randomization. The primary endpoint of the trial is percentage of patients with transfusion reduction response, defined as a ≥50% reduction in transfused RBC units with a reduction of ≥2 units of transfused RBCs in any consecutive 12-week period through week 48 compared with baseline. Secondary endpoints include additional transfusion reduction measures and percentage of participants with transfusion-independence. We announced topline data for ENERGIZE-T in June 2024. A total of 258 patients were enrolled in the study, with 171 randomized to PYRUKYND® 100 mg twice-daily and 87 randomized to matched placebo. 155 patients (90.6%) in the PYRUKYND® arm and 83 patients (95.4%) in the placebo arm completed the 48-week double-blind period of the study. The study met the primary endpoint of transfusion reduction response, where treatment with PYRUKYND® demonstrated a statistically significant reduction in transfusion burden compared to placebo, as 30.4% of patients achieved a transfusion reduction response, compared to 12.6% of patients in the placebo arm (2-sided p=0.0003). Treatment with PYRUKYND® also demonstrated a statistically significant reduction in additional measures of transfusion reduction response compared to placebo as assessed by the three key secondary endpoints: (i) ≥50% reduction in transfused RBC units in any consecutive 24-week period through week 48 compared with baseline, (ii) ≥33% reduction in transfused RBC units from week 13 through week 48 compared with baseline, and (iii) ≥50% reduction in transfused RBC units from week 13 through week 48 compared with baseline. In addition, a higher proportion of patients in the PYRUKYND® arm (9.9%) compared to the placebo arm (1.1%) achieved the secondary endpoint of transfusion independence (transfusion-free for ≥8 consecutive weeks through week 48). During the 48-week double-blind period, 5.8% of the patients in the PYRUKYND® arm experienced an AE leading to discontinuation compared to 1.2% of patients in the placebo arm. As mentioned above, we aim to submit an sNDA for PYRUKYND® in thalassemia to the FDA by the end of 2024.

•RISE UP, a phase 2/3 study evaluating the efficacy and safety of PYRUKYND® in SCD patients who are 16 years of age or older, have had between two and 10 sickle cell pain crises in the past 12 months, and have hemoglobin within the range of 5.5 to 10.5 g/dL during screening. We enrolled 79 patients in the phase 2 portion of the trial, with 26 patients in the 50 mg twice daily mitapivat arm, 26 patients in the 100 mg twice daily mitapivat arm and 27 patients in the placebo arm. The primary endpoints of the phase 2 portion of the trial were hemoglobin response, defined as ≥ 1 g/dL increase in average hemoglobin concentration from week 10 to week 12 compared to baseline, and safety. In June 2023, we announced the phase 2 portion of this trial had achieved its primary endpoint of hemoglobin response in patients in both the 50 mg and 100 mg twice daily mitapivat arms. 46.2% of patients (n=12) in the 50 mg twice daily mitapivat arm and 50.0% of patients (n=13) in the 100 mg twice daily mitapivat arm achieved a hemoglobin response, compared to 3.7% of patients (n=1) in the placebo arm (2-sided p=0.0003 and 0.0001, respectively). In December 2023, we announced the following additional results of the phase 2 portion of the trial: (i) the least-squares mean (95% confidence interval) for average change from baseline in hemoglobin levels, from week 10 through week 12, for patients in the 50 mg twice daily mitapivat, 100 mg twice daily mitapivat, and placebo arms, respectively, was 1.11 (0.77, 1.45) g/dL, 1.13 (0.79, 1.47) g/dL, and 0.05 (−0.28, 0.39) g/dL; (ii) we observed improvements in annualized rates of sickle cell pain crises as the annualized rate of sickle cell pain crises (95% confidence interval) for patients in the 50 mg twice daily and 100 mg twice daily mitapivat arms, respectively, was 0.83 (0.34, 1.99) and 0.51 (0.16, 1.59), compared to 1.71 (0.95, 3.08) for patients in the placebo arm; (iii) we observed improvement in patient-reported fatigue scores in the 50 mg twice daily mitapivat arm compared to the placebo arm, and the least-squares mean (95% confidence interval) for average changes

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from baseline in patient-reported fatigue score, from week 10 through week 12, for patients in the 50 mg twice daily mitapivat, 100 mg twice daily mitapivat, and placebo arms, respectively, was −3.80 (−7.16, −0.45), −0.10 (−3.27, 3.08), and −0.17 (−3.40, 3.07). The safety profile for mitapivat observed in the phase 2 portion of the trial was generally consistent with previously reported data in other studies of SCD and other hemolytic anemias. The most common treatment-emergent adverse events, or TEAEs, in the 50 mg BID, 100 mg BID, and placebo arms, respectively, were: headache (n=6, 6, 7), arthralgia (n=3, 5, 9), dysmenorrhea (n=0, 3, 0), pain (n=3, 3, 2), pain in extremity (n=1, 3, 6), back pain (n=4, 2, 3), nausea (n=1, 2, 4), fatigue (n=4, 1, 5), and influenza-like illness (n=1, 1, 3). There were no serious TEAEs attributed to mitapivat and there were no AEs leading to drug reduction, discontinuation, interruption or death in either the mitapivat or the placebo arms. Of the 79 patients enrolled in the study, 73 continued into the Phase 2 open-label extension period. In October 2023, we enrolled the first patient in the phase 3 portion of this trial. The phase 3 portion includes a 52-week randomized, placebo-controlled period in which participants will be randomized in a 2:1 ratio to receive the recommended (100 mg twice daily) PYRUKYND® dose level or the placebo. The primary endpoints are hemoglobin response, defined as ≥1 g/dL increase in average hemoglobin from baseline to week 52, and annualized rate of sickle cell pain crises. Participants who complete either the phase 2 or phase 3 portion will have the option to move into a 216-week open-label extension period to continue to receive PYRUKYND®. We have completed enrollment and expect to announce topline data for this trial in late 2025.

•ACTIVATE-kids and ACTIVATE-kidsT, double-blind phase 3 studies evaluating the efficacy and safety of PYRUKYND® as a potential treatment for PK deficiency in not regularly transfused and regularly transfused patients between one and 18 years old, respectively.

A total of 49 patients were enrolled in the study, with 32 randomized to mitapivat twice-daily and 17 randomized to matched placebo. 30 patients (93.8%) in the mitapivat arm and 16 (94.1%) in the placebo arm completed the 32-week double-blind period of the study. The primary endpoint of ACTIVATE-kidsT is transfusion reduction response, defined as ≥33% reduction in total RBC transfusion volume from week 9 through week 32 of the double-blind period. We announced topline data for ACTIVATE-kidsT in August 2024. Using Bayesian methodology, the prespecified statistical criterion for the primary endpoint in ACTIVATE-kidsT was not met using low or moderate borrowing of data from the ACTIVATE-T study in adults. In the study, 28.1% of patients in the mitapivat arm achieved the primary endpoint of transfusion reduction response, compared to 11.8% of patients in the placebo arm. Transfusion-free response and normal hemoglobin response were secondary endpoints in this study and only observed in patients in the mitapivat arm. In the 32-week double-blind treatment period, mitapivat was generally safe and well-tolerated, with safety results consistent with the safety profile for mitapivat previously observed in adults with PK deficiency who are regularly transfused.

The primary endpoint of ACTIVATE-kids is percentage of patients with hemoglobin response, defined as ≥1.5 g/dL increase in hemoglobin concentration from baseline that is sustained at two or more scheduled assessments at weeks 12, 16, and 20 during the double-blind period. ACTIVATE-kids has completed enrollment and we anticipate announcing topline data for this trial in 2025.

•An extension study evaluating the long-term safety, tolerability and efficacy of treatment with PYRUKYND® in patients from ACTIVATE and ACTIVATE-T, our completed pivotal trials of PYRUKYND® in not regularly transfused and regularly transfused adult patients with PK deficiency.

•An extension study evaluating the long-term safety, tolerability and efficacy of treatment with PYRUKYND® in patients from DRIVE PK, our completed global phase 2, first-in-patient, open-label safety and efficacy clinical trial of PYRUKYND® in adult, not regularly transfused patients with PK deficiency.

AG-946 (tebapivat): Novel PK Activator

We are developing AG-946 (tebapivat), a novel PK activator for the potential treatment of LR MDS and hemolytic anemias. AG-946 (tebapivat) has been granted orphan drug designation for the treatment of MDS by the FDA.

We are evaluating AG-946 (tebapivat) in a phase 1 clinical trial of AG-946 (tebapivat) in healthy volunteers and in patients with SCD. We have presented data from the healthy volunteer cohorts, and we have completed the SCD patient cohort of this phase 1 trial.

We also initiated a phase 2a clinical trial of AG-946 (tebapivat) in adults with LR MDS in the third quarter of 2022, and the trial has completed enrollment with 22 patients, including 12 patients classified as non-transfused and 10 patients classified as low transfusion burden. Patients received 5 mg of AG-946 (tebapivat) once daily for up to 16 weeks. The two primary endpoints of the trial were transfusion independence (for patients classified as low transfusion burden), defined as transfusion-

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free for ≥ eight consecutive weeks during the 16-week treatment period, and hemoglobin response, defined as a ≥ 1.5 g/dL increase from baseline in the average hemoglobin concentration measured from week 8 through week 16.

In November 2023, we announced that we achieved clinical proof-of-concept in the phase 2a portion of the trial. We observed that four of the 10 patients with low transfusion burden achieved the transfusion independence endpoint, and one of the 22 patients achieved the hemoglobin response endpoint in the 16-week treatment period. The safety profile observed was consistent with data reported in the healthy volunteer study of AG-946 (tebapivat). 19 patients elected to enroll in the extension period for up to 156 weeks. We evaluated the phase 2a trial results and assessed the impact of those results on the phase 2b portion of the protocol, and based on the data generated in the Phase 2a trial, we plan to increase the dosage levels evaluated in the upcoming Phase 2b trial, which we initiated in the third quarter of 2024.

Other Programs

In addition to the aforementioned development programs, we are developing AG-181, a PAH stabilizer for the potential treatment of PKU, for which we filed an IND in December 2023. We initiated a phase 1 clinical trial of AG-181 in healthy volunteers in the first quarter of 2024. Also, in July 2023, we entered into a license agreement with Alnylam for the development and commercialization of products containing or comprised of an siRNA preclinical development candidate discovered by Alnylam and targeting the TMPRSS6 gene, and we have begun preclinical development of a product candidate for the potential treatment of patients with PV.

Selling, General and Administrative Expenses

Selling, general and administrative expenses consist primarily of salaries and other related costs, including stock-based compensation, for personnel in executive, finance, business development, commercial, legal, information technology and human resources functions. Other significant costs include facility-related costs not otherwise included in research and development expenses, legal fees relating to patent and corporate matters, and fees for accounting and consulting services.

We anticipate that our selling, general and administrative expenses will increase in the future to support continued research and development activities, and ongoing and future commercialization activities related to our portfolio, including the ongoing commercialization of PYRUKYND® and any of our other product candidates, which may include the hiring of additional personnel.

Critical Accounting Estimates

Our critical accounting estimates are those which require the most significant judgments and estimates in the preparation of our condensed consolidated financial statements. We have determined that our most critical accounting estimates are those relating to revenue recognition, accrued research and development expenses and stock-based compensation. As of September 30, 2024, there have been no material changes to our existing critical accounting estimates discussed in Part II, Item 7 of our Annual Report on Form 10-K for the year ended December 31, 2023.

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Results of Operations

Comparison of the three and nine months ended September 30, 2024 and 2023

Revenues


	Three Months Ended September 30,				Nine Months Ended September 30,
(In thousands)	2024		2023		2024		2023
Revenues:
Product revenue, net	$	8,964	$	7,399	$	25,768	$	19,720



Total revenue	$	8,964	$	7,399	$	25,768	$	19,720

Total Revenue - Three Months Ended September 30, 2024 vs. Three Months Ended September 30, 2023 – The increase in total revenue of $1.6 million for the three months ended September 30, 2024 compared to the three months ended September 30, 2023 was due to increased volume associated with PYRUKYND®.

Total Revenue - Nine Months Ended September 30, 2024 vs. Nine Months Ended September 30, 2023 – The increase in total revenue of $6.0 million for the nine months ended September 30, 2024 compared to the nine months ended September 30, 2023 was due to increased volume associated with PYRUKYND®.

Total Operating Expenses


	Three Months Ended September 30,				Nine Months Ended September 30,
(In thousands)	2024		2023		2024		2023
Operating expenses:
Cost of sales	$	783	$	633	$	2,905	$	2,295
Research and development	72,455		81,841		218,476		218,037
Selling, general and administrative	38,537		25,822		105,087		84,598
Total operating expenses	$	111,775	$	108,296	$	326,468	$	304,930

Total Operating Expenses - Three Months Ended September 30, 2024 vs. Three Months Ended September 30, 2023 – The increase in total operating expenses of $3.5 million for the three months ended September 30, 2024 compared to the three months ended September 30, 2023 was primarily due to an increase in selling, general and administrative expenses of $12.7 million, driven by an increase in commercial-related activities as we prepare for the potential approval of PYRUKYND® in thalassemia, partially offset by a decrease in research and development expenses of $9.4 million which is described below under Research and Development Expenses.

Total Operating Expenses - Nine Months Ended September 30, 2024 vs. Nine Months Ended September 30, 2023 – The increase in total operating expenses of $21.5 million for the nine months ended September 30, 2024 compared to the nine months ended September 30, 2023 was primarily due to an increase in selling, general and administrative expenses of $20.5 million, driven by an increase in commercial-related activities as we prepare for the potential approval of PYRUKYND® in thalassemia.

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Research and Development Expenses

Our research and development expenses, by major program, are outlined in the table below:


	Three Months Ended September 30,				Nine Months Ended September 30,
(In thousands)	2024		2023		2024		2023



PK activator (PYRUKYND®)	$	26,829	$	24,000	$	80,833	$	71,491


Novel PK activator (AG-946) (tebapivat)	3,768		4,220		10,151		11,817
In-process research and development	—		17,500		—		17,500
Other research and platform programs	4,316		1,250		15,271		6,775
Total direct research and development expenses	34,913		46,970		106,255		107,583
Compensation and related expenses	28,115		25,529		83,225		81,483
Facilities and IT related expenses & other	9,427		9,342		28,996		28,971

Total indirect research and development expenses	37,542		34,871		112,221		110,454
Total research and development expense	$	72,455	$	81,841	$	218,476	$	218,037

Total Research and Development Expenses - Three Months Ended September 30, 2024 vs. Three Months Ended September 30, 2023 – The decrease in total research and development expenses of $9.4 million for the three months ended September 30, 2024 compared to the three months ended September 30, 2023 was primarily due to a $12.1 million decrease in our direct expenses, partially offset by a $2.7 million increase in our indirect expenses. The decrease in direct expenses was primarily due to in-process research and development in the three months ended September 30, 2023 as a result of the $17.5 million up-front payment associated with the agreement with Alnylam discussed above under Overview, partially offset by an increase in other research and platform programs as a result of costs associated with the in-licensed siRNA TMPRSS6 program for PV and an increase in PYRUKYND® costs due to increased costs associated with clinical trials for patients with SCD. The increase in our indirect expenses was primarily due to an increase in compensation and related expenses, driven principally by workforce- related expenses.

Total Research and Development Expenses - Nine Months Ended September 30, 2024 vs. Nine Months Ended September 30, 2023 – Total research and development expenses for the nine months ended September 30, 2024 were relatively consistent with the total research and development expenses for the nine months ended September 30, 2023. Included in the decrease in direct expenses in the nine months ended September 30, 2024 compared to the nine months ended September 30, 2023 was the $17.5 million up-front payment in the nine months ended September 30, 2023 associated with the agreement with Alnylam discussed above under Overview, an increase in PYRUKYND® costs due to increased process development expenses and increased costs associated with clinical trials for patients with SCD, partially offset by lower costs associated with the phase 3 clinical trials of PYRUKYND® in patients with thalassemia, ENERGIZE and ENERGIZE-T, and an increase in other research and platform programs as a result of costs associated with the in-licensed siRNA TMPRSS6 program for PV.

Other Income and Expense


	Three Months Ended September 30,				Nine Months Ended September 30,
(In thousands)	2024		2023		2024		2023
Gain on sale of contingent payments	$	889,136	$	—	$	889,136	$	—
Milestone payment from gain on sale of oncology business	200,000		—		200,000		—
Interest income, net	13,059		8,375		30,068		24,720
Other income, net	1,651		1,198		4,864		4,342

Other Income and Expense - Three Months Ended September 30, 2024 vs. Three Months Ended September 30, 2023 – The increase in gain on sale of contingent payments was due to the sale of the Vorasidenib Royalty Rights in the three months ended September 30, 2024 discussed above in Overview. The increase in milestone payment from gain on sale of oncology business was due to the receipt of the Vorasidenib Milestone Payment in the three months ended September 30, 2024 discussed above in O verview. The increase in interest income, net in the three months ended September 30, 2024 compared to the three months ended September 30, 2023 was primarily attributable to increased return on our investments.

Other Income and Expense - Nine Months Ended September 30, 2024 vs. Nine Months Ended September 30, 2023 – The increase in gain on sale of contingent payments was due to the sale of the Vorasidenib Royalty Rights in the nine months ended September 30, 2024 discussed above in Overview. The increase in milestone payment from gain on sale of oncology business was due to the receipt of the Vorasidenib Milestone Payment in the nine months ended September 30, 2024 discussed above in Overview. The increase in interest income, net was primarily attributable to increased return on our investments.

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Net Income (Loss)


	Three Months Ended September 30,				Nine Months Ended September 30,
(In thousands)	2024		2023		2024		2023


Net income (loss)	$	947,915	$	(91,324)	$	770,248	$	(256,148)

Net Income (Loss) - Three Months Ended September 30, 2024 vs. Three Months Ended September 30, 2023 – The increase in net income for the three months ended September 30, 2024 compared to the three months ended September 30, 2023 was primarily driven by the sale of the Vorasidenib Royalty Rights in the three months ended September 30, 2024 discussed above in Overview and the receipt of the Vorasidenib Milestone Payment in the three months ended September 30, 2024 discussed above in Overview, partially offset by the increase in income tax expense as a result of the income related to the Vorasidenib Royalty Rights and Vorasidenib Milestone Payment.

Net Income (Loss) - Nine Months Ended September 30, 2024 vs. Nine Months Ended September 30, 2023 – The increase in net income for the nine months ended September 30, 2024 compared to the nine months ended September 30, 2023 was primarily driven by the sale of the Vorasidenib Royalty Rights in the nine months ended September 30, 2024 discussed above in Overview and the receipt of the Vorasidenib Milestone Payment in the nine months ended September 30, 2024 discussed above in Overview, partially offset by the increase in income tax expense as a result of the income related to the Vorasidenib Royalty Rights and Vorasidenib Milestone Payment.

Liquidity and Capital Resources

Sources of Liquidity

Since our inception, and through March 31, 2021, we financed our operations primarily through proceeds from the sale of our royalty rights, commercial sales of TIBSOVO®, funding received from our collaboration agreements, private placements of our preferred stock, our initial public offering of our common stock and concurrent private placement of common stock to an affiliate of Celgene, and our follow-on public offerings. Following the sale of our oncology business to Servier on March 31, 2021, we have financed and expect to continue to finance our operations primarily through cash on hand, potential royalty payments with respect to the Retained Earn-Out Rights, the actual and potential future sales of PYRUKYND® and, potentially, collaborations, strategic alliances, licensing arrangements and other nondilutive strategic transactions. In addition, we may pursue opportunistic debt offerings, and equity or equity-linked offerings.

On March 31, 2021, we completed the sale of our oncology business to Servier. The transaction included the sale of our oncology business, including TIBSOVO®, our clinical-stage product candidates vorasidenib, AG-270 and AG-636, and our oncology research programs for a payment of approximately $1.8 billion in cash at the closing, subject to certain adjustments, and the right to the Vorasidenib Milestone Payment, as well as a royalty of 5% of U.S. net sales of TIBSOVO® from the close of the transaction through loss of exclusivity, and the Vorasidenib Royalty Rights. The Vorasidenib Milestone Payment, Vorasidenib Royalty Rights and royalty payments related to TIBSOVO® are referred to as contingent payments and recognized as income when realizable. Servier also acquired our co-commercialization rights for Bristol Myers Squibb's IDHIFA® and the right to receive a $25.0 million potential milestone payment under our prior collaboration agreement with Celgene, and following the sale Servier has agreed to conduct certain clinical development activities

AGIOS PHARMACEUTICALS, INC. [AGIO] Filings
10-Q	[2024-10-31]
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