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UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, DC 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 March 31, 2025

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

Commission file number 001-37359

_____________________________

BLUEPRINT MEDICINES CORPORATION

(Exact Name of Registrant as Specified in Its Charter)

_____________________________

Delaware		26-3632015
(State or Other Jurisdiction of Incorporation or Organization)		(I.R.S. Employer Identification No.)

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

(617) 374-7580

(Registrant’s Telephone Number, Including Area Code)

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

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, smaller reporting company, or an emerging growth company. See 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 ☑

Non-accelerated filer ☐

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 ☑

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	BPMC	Nasdaq Global Select Market

Number of shares of the registrant’s common stock, $0.001 par value, outstanding on April 29, 2025: 64,582,163

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TABLE OF CONTENTS


		Page
Part I – FINANCIAL INFORMATION
Item 1. Financial Statements (unaudited)		4
	Condensed Consolidated Balance Sheets as of March 31, 2025 and December 31, 2024	4
	Condensed Consolidated Statements of Operations and Comprehensive Income for the three months ended March 31, 2025 and 2024	5
	Condensed Consolidated Statements of Stockholders’ Equity for the three months ended March 31, 2025 and 2024	6
	Condensed Consolidated Statements of Cash Flows for the three months ended March 31, 2025 and 2024	7
	Notes to Condensed Consolidated Financial Statements	8
Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations		33
Item 3. Quantitative and Qualitative Disclosures About Market Risk		50
Item 4. Controls and Procedures		51

Part II – OTHER INFORMATION
Item 1. Legal Proceedings		52
Item 1A. Risk Factors		52
Item 5. Other Information		105
Item 6. Exhibits		106
Signatures		107

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Unless otherwise stated, all references to “us,” “our,” “Blueprint,” “Blueprint Medicines,” “we,” the “Company” and similar designations in this Quarterly Report on Form 10-Q refer to Blueprint Medicines Corporation and its consolidated subsidiaries. Blueprint Medicines, AYVAKIT^®, AYVAKYT^®, and associated logos are trademarks of Blueprint Medicines Corporation. GAVRETO^®and associated logos are trademarks of Blueprint Medicines Corporation outside of the United States.Other brands, names and trademarks contained in this Quarterly Report on Form 10-Q are the property of their respective owners.

Forward-Looking Statements

This Quarterly Report on Form 10-Q contains forward-looking statements that involve substantial risks and uncertainties. All statements, other than statements of historical facts, contained in this Quarterly Report on Form 10-Q are forward-looking statements. In some cases, you can identify forward-looking statements by words such as “aim,” “anticipate,” “believe,” “contemplate,” “continue,” “could,” “estimate,” “expect,” “intend,” “may,” “plan,” “potential,” “opportunity,” “predict,” “project,” “seek,” “should,” “target,” “will,” “would” or a variation or the negative of these words or other comparable terminology, although not all forward-looking statements contain these identifying words.

The forward-looking statements in this Quarterly Report on Form 10-Q include, but are not limited to, statements about:

●

the timing or likelihood of regulatory actions, filings and approvals for our current and future drug candidates, including our ability to obtain marketing approval for avapritinib in additional geographies;

●

our ability and plans in continuing to build out our commercial infrastructure and successfully launching, marketing and selling AYVAKIT^® (avapritinib) (marketed in Europe under the brand name AYVAKYT^®) and any current and future drug candidates for which we receive marketing approval;

●

our expectations regarding the potential benefits of AYVAKIT/AYVAKYT and any current and future drug candidates in treating patients with indolent systemic mastocytosis (SM) and advanced SM;

●

the rate and degree of market acceptance of AYVAKIT/AYVAKYT and any current and future drug candidates for which we receive marketing approval;

●

the pricing and reimbursement of AYVAKIT/AYVAKYT and any current and future drug candidates for which we receive marketing approval;

●

the initiation, timing, progress and results of our preclinical studies and clinical trials, including our ongoing clinical trials and any planned clinical trials for our current and future drug candidates and research and development programs;

●

our ability to advance drug candidates into, and successfully complete, clinical trials;

●

our ability to successfully develop manufacturing processes for any of our current and future drugs or drug candidates and to secure manufacturing, packaging and labeling arrangements for development activities and commercial production;

●

the implementation of our business model and strategic plans for our business, drugs, drug candidates, platform and technology;

●

the scope and length of protection we are able to establish and maintain for intellectual property rights covering our current and future drugs, drug candidates and technology;

●

the potential benefits of our collaboration with CStone Pharmaceuticals (CStone) to develop and commercialize avapritinib and pralsetinib in Greater China, and our collaboration with Zai Lab to develop and commercialize BLU-525, BLU-945, and any back-up and other forms thereof, as inhibitors of epidermal growth factor receptor (EGFR) in Greater China, as well as our ability to maintain these collaborations and establish additional strategic collaborations;

●

the potential benefits of our exclusive license agreement with Clementia Pharmaceuticals, Inc., a wholly-owned subsidiary of Ipsen S.A. (Clementia), to develop and commercialize BLU-782 for fibrodysplasia ossificans progressiva;

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●

the potential benefit of our strategic financing transaction with Garnich Adjacent Investments S.a.r.l. and Tao Talents, LLC, both affiliates of Sixth Street Partners and the potential acceleration of our commercial products and pipeline resulting from the non-dilutive growth capital;

●

the potential benefits of our license agreement with IDRx, Inc., a subsidiary of GSK plc (IDRx) to develop our development candidate-stage KIT exon 13 inhibitor, IDRX-73, for the treatment of drug-resistant mutations of non-PDGFR-driven gastrointestinal stromal tumor (GIST);

●

our financial performance, estimates of our revenues, expenses and capital requirements and our needs for future financing, including our ability to achieve a self-sustainable financial profile;

●

developments relating to our competitors and our industry;

●

the potential impact of the volatility of capital markets and other adverse macroeconomic factors on our business, financial condition or results of operations, including due to inflation, tariffs, interest rate and currency rate fluctuations, economic slowdown or recession, banking instability, monetary policy changes, geopolitical tensions or the outbreak of hostilities or war;

●

our expectations regarding litigation matters; and

●

the actual or potential benefits of designations granted by the U.S. Food and Drug Administration (FDA), such as orphan drug, fast track and breakthrough therapy designation or priority review.

Any forward-looking statements in this Quarterly Report on Form 10-Q reflect our current views with respect to future events or to our future financial performance and involve known and unknown risks, uncertainties and other important factors that may cause our actual results, performance or achievements to be materially different from any future results, performance or achievements expressed or implied by these forward-looking statements. We have included important factors in the cautionary statements included in this Quarterly Report on Form 10-Q, particularly in the “Risk Factors” section in Part II, Item 1A, that could cause actual results or events to differ materially from the forward-looking statements that we make. Given these uncertainties, you should not place undue reliance on these forward-looking statements. Our forward-looking statements do not reflect the potential impact of any future acquisitions, mergers, dispositions, joint ventures or investments we may make or enter into.

You should read this Quarterly Report on Form 10-Q and the documents that we have filed as exhibits to this Quarterly Report on Form 10-Q completely and with the understanding that our actual future results, performance or achievements may be materially different from what we expect. Except as required by law, we assume no obligation to update or revise these forward-looking statements for any reason, even if new information becomes available in the future.

This Quarterly Report on Form 10-Q also contains estimates, projections and other information concerning our industry, our business and the markets for certain diseases, including data regarding the estimated size of those markets, and the incidence and prevalence of certain medical conditions. Information that is based on estimates, forecasts, projections, market research or similar methodologies is inherently subject to uncertainties and actual events or circumstances may differ materially from events and circumstances reflected in this information. Unless otherwise expressly stated, we obtained this industry, business, market and other data from reports, research surveys, studies and similar data prepared by market research firms and other third parties, industry, medical and general publications, government data and similar sources.

For purposes of this Quarterly Report on Form 10-Q, including the footnotes to our condensed consolidated financial statements, (i) with respect to our terminated collaboration for pralsetinib, Roche means F. Hoffmann-La Roche Ltd and Genentech, Inc., and (ii) with respect to our financing transactions with Sixth Street Partners, Sixth Street Partners means Garnich Adjacent Investments S.a.r.l. and/or Tao Talents, LLC.

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PART I – FINANCIAL INFORMATION

Item 1. Financial Statements

Blueprint Medicines Corporation

Condensed Consolidated Balance Sheets

(in thousands, except share and per share data)

(Unaudited)


	March 31,		December 31,
	2025		2024
Assets
Current assets:
Cash and cash equivalents	$	122,245	$	102,014
Marketable securities		453,992		513,473
Accounts receivable		78,083		75,797
Unbilled accounts receivable		1,718		1,812
Inventory		12,953		13,611
Prepaid expenses and other current assets		33,078		35,971
Total current assets		702,069		742,678
Marketable securities		323,547		248,450
Property and equipment, net		36,050		36,593
Operating lease right-of-use assets, net		61,607		64,181
Restricted cash		11,847		11,625
Equity investment		—		28,699
Other assets		60,484		47,587
Total assets	$	1,195,604	$	1,179,813
Liabilities and stockholders’ equity
Current liabilities:
Accounts payable		800		6,790
Accrued expenses		122,055		133,088
Current portion of operating lease liabilities		13,736		13,346
Current portion of deferred revenue		2,279		2,005
Current portion of liabilities related to the sale of future royalties and revenues		67,917		61,650
Current portion of term loan		43,797		43,917
Total current liabilities		250,584		260,796
Operating lease liabilities, net of current portion		65,216		68,790
Deferred revenue, net of current portion		8,037		8,193
Liabilities related to the sale of future royalties and revenues, net of current portion		178,715		193,524
Term loan, net of current portion		343,949		343,053
Other long-term liabilities		6,972		6,792
Total liabilities		853,473		881,148
Commitments and Contingencies (Note 17)
Stockholders’ equity:
Preferred stock, $0.001 par value; 5,000,000 shares authorized; no shares issued and outstanding		—		—
Common stock, $0.001 par value; 120,000,000 shares authorized; 64,563,911 and 63,712,256 shares issued and outstanding at March 31, 2025 and December 31, 2024, respectively		65		64
Additional paid-in capital		2,751,838		2,709,183
Accumulated other comprehensive loss		(3,237)		(3,551)
Accumulated deficit		(2,406,535)		(2,407,031)
Total stockholders’ equity		342,131		298,665
Total liabilities and stockholders’ equity	$	1,195,604	$	1,179,813

See accompanying notes to the unaudited condensed consolidated financial statements.

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Blueprint Medicines Corporation

Condensed Consolidated Statements of Operations and Comprehensive Income

(in thousands, except per share data)

(Unaudited)


	Three Months Ended
	March 31,
	2025		2024
Revenues:
Product revenue, net	$	149,413	$	92,525
Collaboration, license and other revenue		—		3,591
Total revenues		149,413		96,116
Cost and operating expenses:
Cost of sales		2,802		3,191
Research and development		91,890		88,191
Selling, general and administrative		95,807		83,557
Total cost and operating expenses		190,499		174,939
Other income (expense):
Interest expense, net		(8,129)		(5,895)
Other income, net		461		376
Equity investment gain		50,039		—
Debt extinguishment gain		—		173,658
Total other income, net		42,371		168,139
Income before income taxes		1,285		89,316
Income tax expense		789		180
Net income	$	496	$	89,136
Other comprehensive income (loss):
Unrealized gain (loss) on available-for-sale investments		457		(564)
Currency translation adjustments		(143)		212
Comprehensive income	$	810	$	88,784
Net income per share - basic	$	0.01	$	1.45
Net income per share - diluted	$	0.01	$	1.40
Weighted-average number of common shares used in net income per share - basic		64,096		61,580
Weighted-average number of common shares used in net income per share - diluted		66,526		63,802

See accompanying notes to the unaudited condensed consolidated financial statements.

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Blueprint Medicines Corporation

Condensed Consolidated Statements of Stockholders’ Equity

(in thousands, except share data)

(Unaudited)


							Accumulated
				Additional			Other
	Common Stock			Paid-in		Comprehensive			Accumulated		Stockholders’
	Shares	Amount		Capital			Loss		Deficit		Equity

Balance at December 31, 2024	63,712,256	$	64	$	2,709,183		$	(3,551)	$	(2,407,031)	$	298,665
Issuance of common stock under stock plan	851,655		1		13,356			—		—		13,357
Stock-based compensation expense	—		—		29,299			—		—		29,299
Other comprehensive income	—		—		—			314		—		314
Net income	—		—		—					496		496
Balance at March 31, 2025	64,563,911	$	65	$	2,751,838		$	(3,237)	$	(2,406,535)	$	342,131

Balance at December 31, 2023	61,147,236	$	61	$	2,473,985		$	(3,495)	$	(2,339,942)	$	130,609
Issuance of common stock under stock plan	902,292		1		17,900			—		—		17,901
Stock-based compensation expense	—		—		24,457			—		—		24,457
At-the-market offerings, net of issuance costs	544,719		1		48,935			—		—		48,936
Other comprehensive loss	—		—		—			(352)		—		(352)
Net income	—		—		—			—		89,136		89,136
Balance at March 31, 2024	62,594,247	$	63	$	2,565,277		$	(3,847)	$	(2,250,806)	$	310,687

See accompanying notes to the unaudited condensed consolidated financial statements.

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Blueprint Medicines Corporation

Condensed Consolidated Statements of Cash Flows

(in thousands)

(Unaudited)


	Three Months Ended
	March 31,
	2025		2024
Cash flows from operating activities
Net income	$	496	$	89,136
Adjustments to reconcile net income to net cash used in operating activities:
Depreciation and amortization		4,459		4,810
Non-cash lease expense		2,592		2,404
Stock-based compensation		29,056		24,225
Non-cash interest expense		776		793
Net (accretion of discount) amortization of premium on investments		(3,332)		(5,193)
Non-cash debt extinguishment gain		—		(173,658)
Equity investment gain		(50,039)		—
Other		(141)		(827)
Changes in assets and liabilities:
Accounts receivable		(1,397)		(17,339)
Inventory		187		2,696
Prepaid expenses and other current assets		(961)		1,016
Other assets		(8,876)		(4,332)
Accounts payable		(6,044)		313
Accrued expenses		(13,552)		(25,826)
Deferred revenue and other long-term liabilities		(4,500)		3,158
Operating lease liabilities		(3,203)		(2,889)
Net cash used in operating activities		(54,479)		(101,513)
Cash flows from investing activities
Purchases of property and equipment		(1,831)		(1,104)
Purchases of investments		(283,327)		(200,165)
Maturities of investments		271,500		278,400
Proceeds from sale of equity investment		78,737		—
Net cash provided by investing activities		65,079		77,131
Cash flows from financing activities
Proceeds from at-the-market offerings, net of issuance costs		—		48,936
Net proceeds from stock option exercises and employee stock purchase plan		13,298		18,396
Principal payments for financing arrangements		(4,106)		(369)
Net cash provided by financing activities		9,192		66,963
Net increase in cash, cash equivalents, and restricted cash		19,792		42,581
Cash, cash equivalents and restricted cash at beginning of period		113,639		81,524
Effect of exchange rate changes on cash, cash equivalents and restricted cash		661		(145)
Cash, cash equivalents and restricted cash at end of period	$	134,092	$	123,960
Supplemental cash flow information
Cash paid for interest	$	21,465	$	14,280
Property and equipment purchases unpaid at period end	$	698	$	1,834
Cash paid for taxes, net	$	703	$	520

See accompanying notes to the unaudited condensed consolidated financial statements.

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Blueprint Medicines Corporation

Notes to Condensed Consolidated Financial Statements

(Unaudited)

1. Nature of Business

Blueprint Medicines Corporation (the Company), a Delaware corporation incorporated on October 14, 2008, is a global fully-integrated biopharmaceutical company that invents life-changing medicines in two core focus areas: allergy/inflammation and oncology/hematology. The Company’s approach targets the root causes of disease, using deep scientific knowledge in the Company’s core focus areas and drug discovery expertise across multiple therapeutic modalities.

The Company has a track record of success with two approved medicines, including AYVAKIT®/AYVAKYT® (avapritinib), which the Company is bringing to patients living with systemic mastocytosis (SM) and PDGFRA Exon 18 mutant GIST in the U.S. and Europe. Leveraging the Company’s established research, development, and commercial capability and infrastructure, the Company now aims to significantly scale its impact by advancing a broad pipeline of programs ranging from early science to advanced clinical trials in mast cell diseases including SM and chronic urticaria, breast cancer and other solid tumors.

As of March 31, 2025, the Company had cash, cash equivalents and marketable securities of $899.8 million. Based on the Company’s current operating plans, the Company anticipates that its existing cash, cash equivalents and marketable securities will be sufficient to enable it to fund its current operations for at least the next twelve months from the issuance of the financial statements.

2. Summary of Significant Accounting Policies and Recent Accounting Pronouncements

Basis of Presentation

The unaudited interim condensed consolidated financial statements of the Company included herein have been prepared in accordance with accounting principles generally accepted in the U.S. (GAAP) as found in the Accounting Standards Codification (ASC), Accounting Standards Update (ASU) of the Financial Accounting Standards Board (FASB) and the rules and regulations of the Securities and Exchange Commission (SEC). Certain information and footnote disclosures normally included in financial statements prepared in accordance with GAAP have been condensed or omitted from this report, as is permitted by such rules and regulations. Accordingly, these financial statements should be read in conjunction with the financial statements as of and for the year ended December 31, 2024 and notes thereto included in the Company’s Annual Report on Form 10-K for the year ended December 31, 2024, filed with the SEC on February 13, 2025 (2024 Annual Report on Form 10-K).

The unaudited interim condensed consolidated financial statements have been prepared on the same basis as the audited financial statements, and updated, as necessary, in this report. In the opinion of the Company’s management, the accompanying unaudited interim condensed consolidated financial statements contain all adjustments that are necessary to present fairly the Company’s financial position as of March 31, 2025, the results of its operations for the three months ended March 31, 2025 and 2024, stockholders’ equity for the three months ended March 31, 2025 and 2024 and cash flows for the three months ended March 31, 2025 and 2024. Such adjustments are of a normal and recurring nature. The results for the three months ended March 31, 2025 are not necessarily indicative of the results for the year ending December 31, 2025 or for any other future period.

The accompanying unaudited interim condensed consolidated financial statements include the accounts of the Company and its wholly-owned subsidiaries, Blueprint Medicines Security Corporation, which is a Massachusetts subsidiary created to buy, sell and hold securities, Blueprint Medicines (Switzerland) GmbH, Blueprint Medicines (Netherlands) B.V., Blueprint Medicines (UK) Ltd., Blueprint Medicines (Germany) GmbH, Blueprint Medicines (Spain) S.L., Blueprint Medicines (France) SAS, and Blueprint Medicines (Italy) S.r.L. All intercompany transactions and balances have been eliminated.

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Use of Estimates

The preparation of financial statements in conformity with GAAP requires the Company’s management to make estimates and assumptions that affect the amounts reported in the financial statements and accompanying notes. Actual results could differ from those estimates. Management considers many factors in selecting appropriate financial accounting policies and in developing the estimates and assumptions that are used in the preparation of the financial statements. Management must apply significant judgment in this process. Management’s estimation process often may yield a range of potentially reasonable estimates and management must select an amount that falls within that range of reasonable estimates. Estimates are used in the following areas, among others: revenue recognition, inventory, operating lease right-of-use assets, operating lease liabilities, stock-based compensation expense, accrued expenses, liabilities related to the sale of future royalties and future revenues, equity investment, debt modification, and income taxes.

Significant Accounting Policies

The significant accounting policies used in preparation of these condensed consolidated financial statements for the three months ended March 31, 2025 are consistent with those discussed in Note 2 to the consolidated financial statements in the 2024 Annual Report on Form 10-K.

Recent Accounting Pronouncements

From time to time, new accounting pronouncements are issued by the FASB or other standard setting bodies that the Company adopts as of the specified effective date. Unless otherwise discussed below, the Company does not believe that the adoption of recently issued standards have or may have a material impact on its condensed consolidated financial statements and disclosures.

In December 2023, the FASB issued ASU 2023-09, Improvements to Income Tax Disclosures, which requires entities to disclose disaggregated information about their effective tax rate reconciliation and income taxes paid. The disclosure requirements will be applied on a prospective basis, with the option to apply them retrospectively. The standard is effective for annual reporting periods beginning after December 15, 2024, with early adoption permitted. The Company will adopt the new disclosure requirements in its 2025 Annual Report on Form 10-K.

In November 2024, the FASB issued ASU 2024-03, Disaggregation of Income Statement Expenses, which is intended to improve disclosures by requiring additional information about specific expense categories in the notes to the financial statements on an annual and interim basis. The standard will be effective for annual reporting periods beginning after December 15, 2026, and interim reporting periods beginning after December 15, 2027, with early adoption permitted. The standard updates may be applied on either a prospective or retrospective basis. The Company is currently evaluating the disclosure requirements related to this new standard.

Reclassification

Certain items in the prior year’s condensed consolidated financial statements have been reclassified to conform to the current presentation.

3. Financing Arrangements

Royalty Pharma Purchase and Sale Agreement

On June 30, 2022, the Company entered into a purchase and sale agreement (Royalty Purchase Agreement) with Royalty Pharma Investments 2019 ICAV (Royalty Pharma). Pursuant to the Royalty Purchase Agreement, the Company received an upfront payment of $175.0 million in consideration for the Company’s rights to receive royalty payments on the net sales of GAVRETO worldwide, excluding the CStone Territory (as defined below) and the U.S., under the terms of the Roche pralsetinib collaboration agreement.

Due to the Company's significant involvement in the global co-development of pralsetinib with Roche, which directly contributed to the generation of future GAVRETO royalties, any royalties and development and

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commercialization milestones earned pertaining to the underlying territory under the Roche pralsetinib collaboration agreement were recognized as collaboration revenue on the consolidated statements of operations and comprehensive income (loss) throughout the contract term of the Roche pralsetinib collaboration agreement. The net proceeds received from the transaction were recorded as a liability related to sale of future royalties and revenues on the consolidated balance sheet on June 30, 2022.

The Roche pralsetinib collaboration agreement was terminated in February 2024 and the Company regained commercialization and development rights to GAVRETO from Roche worldwide excluding the CStone Territory. In connection with and effective upon the termination of the Roche pralsetinib collaboration agreement, on February 22, 2024 (the Royalty Pharma Termination Date), Royalty Pharma and the Company agreed to terminate the Royalty Purchase Agreement (Royalty Pharma Termination Agreement). Following the termination of the Royalty Purchase Agreement, the Company has no outstanding obligations under the Royalty Purchase Agreement, other than the remaining royalty payment obligation related to GAVRETO net sales as of the termination effective date. As of March 31, 2025, the Company had no plan to enter into a new arrangement to commercialize GAVRETO outside of the U.S. and the CStone Territory.

The Company has no material outstanding obligations under the Royalty Pharma Termination Agreement. This agreement was accounted for as a debt extinguishment under ASC 470-50 because the terms and conditions of the Royalty Purchase Agreement had undergone a substantial modification, and the modified terms are considered substantially different. As a result, the Company recorded a debt extinguishment gain of $173.7 million as other income in the unaudited condensed consolidated statements of operations and comprehensive income during the three months ended March 31, 2024. As of March 31, 2025, the Company paid off the final royalty amount related to the Royalty Pharma Termination Agreement.

Financing Arrangements with Sixth Street Partners

In July 2022, the Company closed two transactions pursuant to a purchase and sale agreement (Future Revenue Purchase Agreement) and a debt financing transaction for up to $660.0 million (as amended, the Financing Agreement) with Sixth Street Partners. Because two transactions were entered into with the same parties and in contemplation of one another, the Company recorded these transactions based on the relative fair values of each freestanding financial instrument and allocated the proceeds in proportion to those fair value amounts.

Sixth Street Partners Purchase and Sale Agreement

Pursuant to the Future Revenue Purchase Agreement, the Company received gross proceeds of $250.0 million in exchange for future royalty payments at a rate of 9.75% on up to $900 million each year of (i) aggregate worldwide annual net product sales of AYVAKIT/AYVAKYT (avapritinib) and (ii), if it is approved, aggregate worldwide annual net product sales of BLU-263 (elenestinib), but excluding sales in Greater China, subject to a cumulative cap of 1.45 times the upfront invested capital or a total of $362.5 million. In the event that certain revenue targets are not achieved by specified dates, the royalty rate and cumulative cap shall be increased to 15% and 1.85 times the invested capital (or $462.5 million), respectively.

The Company continues to own the research, development, manufacturing and commercialization of AYVAKIT/AYVAKYT and if it is approved, elenestinib, and has significant continuing involvement in the generation of the cash flows under the Future Revenue Purchase Agreement. Therefore, the Company continues to account for any revenue earned from worldwide product sales of AYVAKIT/AYVAKYT and, if it is approved, elenestinib, on its unaudited condensed consolidated statements of operations and comprehensive income. Net proceeds received from the transaction were recorded as a liability related to sale of future royalties and revenues on the consolidated balance sheet. The Company accretes the $250.0 million, net of transaction costs of $5.4 million, to the total of these future payments as interest expense using the effective interest method over the estimated life of the arrangement.

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As payments are made to Sixth Street Partners, the balance of the liability is effectively repaid over the life of the Future Revenue Purchase Agreement. In order to determine the amortization of the liability, the Company estimates the total amount of future revenue payments to be paid to Sixth Street Partners over the life of the arrangement. The exact amount of repayment is likely to change each reporting period. A significant increase or decrease in worldwide product sales of AYVAKIT/AYVAKYT and, if it is approved, elenestinib, will materially impact the liability related to this arrangement, interest expense and the time period for repayment. The Company periodically assesses the expected payments to Sixth Street Partners and prospectively adjusts the amortization of the liability related to this arrangement for material changes in such payments. As of March 31, 2025, the Company’s estimate of this total interest expense resulted in an effective annual interest rate of 10.3%. These estimates contain assumptions that impact the amount recorded and the interest expense that will be recognized in future periods.

As of March 31, 2025, the net carrying value of the liability related to this arrangement was $246.6 million. The following table shows the activity within the liability account during the three months ended March 31, 2025 and 2024 (in thousands):


	Three Months Ended March 31,
	2025		2024
Carrying value as of January 1	$	254,436	$	266,670
Interest expense recognized		6,199		7,096
Payments		(14,003)		(6,875)
Carrying value as of March 31	$	246,632	$	266,891

Sixth Street Partners Term Loan

The Financing Agreement entered into by the parties in connection with the transaction provides for (i) a senior secured term loan facility of up to $150.0 million and (ii) a senior secured delayed draw term loan facility of up to $250.0 million to be funded in two tranches at the Company’s choice subject to certain terms and conditions. The term loans will mature on June 30, 2028 and bear interest at a variable rate equal to either the Secured Overnight Financing Rate (SOFR) plus 6.50% or the base rate plus 5.50%, subject to a floor of 1% and 2% with respect to the SOFR and base rate, respectively.

The following table shows the proceeds the Company has received under the Financing Agreement with Sixth Street Partners (in thousands):


				Debt discount/
Term loan draw	Date	Gross proceeds		Transaction cost		Net proceeds
Senior Secured Term Loan Facility	July 2022	$	150,000	$	12,214	$	137,786
1st Senior Secured Delayed Draw Term Loan Facility	August 2023		100,000		2,067		97,933
2nd Senior Secured Delayed Draw Term Loan Facility	May 2024		150,000		3,027		146,973
		$	400,000	$	17,308	$	382,692

Debt discounts and transaction costs have been recorded as a reduction to the carrying amount of the debt on the Company’s consolidated balance sheet and are amortized as additional interest expenses using the effective interest rate method over the period from issuance through maturity. In addition, the Company may at any time request an incremental term loan in an amount not to exceed $260.0 million on terms to be agreed and subject to the consent of Sixth Street Partners providing such incremental term loan. As of March 31, 2025, the Company’s estimate of the total interest expense resulted in an effective annual interest rate of 12.0%. The carrying amount of the debt as of March 31, 2025 is subject to variable interest rates, which are based on current market rates, and as such, approximates fair value.

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The following table shows the activity within the liability account during the three months ended March 31, 2025 and 2024 (in thousands):


	Three Months Ended March 31,
	2025		2024
Carrying value as of January 1	$	386,970	$	238,813
Interest expense recognized		11,605		7,977
Payments		(10,829)		(7,405)
Carrying value as of March 31	$	387,746	$	239,385

The Company’s obligations under the Financing Agreement are secured, subject to certain exceptions, by security interests in substantially all assets of the Company and certain of its subsidiaries. The Financing Agreement contains customary negative covenants that, among other things and subject to certain exceptions, could restrict the Company’s ability to incur additional liens, incur additional indebtedness, make investments, including acquisitions, engage in fundamental changes, sell or dispose of assets that constitute collateral, including certain intellectual property, pay dividends or make any distribution or payment on or redeem, retire or purchase any equity interests, amend, modify or waive certain material agreements or organizational documents and make payments of certain subordinated indebtedness. The Financing Agreement also requires the Company to maintain a consolidated liquidity of at least $80.0 million. As of March 31, 2025, the Company was in compliance with the applicable terms and conditions of the covenants under the Financing Agreement.

4. Marketable Securities

Marketable securities consisted of the following at March 31, 2025 and December 31, 2024 (in thousands):


	Amortized		Unrealized		Unrealized		Fair
March 31, 2025	Cost		Gain		Losses		Value
Marketable securities, available-for-sale:
U.S. government agency securities	$	190,673	$	91	$	(113)	$	190,651
U.S. treasury obligations		585,897		1,144		(153)		586,888
Total	$	776,570	$	1,235	$	(266)	$	777,539


	Amortized		Unrealized		Unrealized		Fair
December 31, 2024	Cost		Gain		Losses		Value
Marketable securities, available-for-sale:
U.S. government agency securities	$	129,897	$	118	$	(230)	$	129,785
U.S. treasury obligations		631,514		1,025		(401)		632,138
Total	$	761,411	$	1,143	$	(631)	$	761,923

The following table summarizes the amortized cost basis and estimated fair value of the Company’s available-for-sale securities by contractual maturity as of March 31, 2025 and December 31, 2024 (in thousands):


	March 31, 2025				December 31, 2024
	Amortized		Fair		Amortized		Fair
	Cost		value		Cost		value
Within one year	$	453,575	$	453,992	$	512,515	$	513,473
After one through five years		322,995		323,547		248,896		248,450
Total	$	776,570	$	777,539	$	761,411	$	761,923

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As of March 31, 2025 and December 31, 2024, the Company held 33 and 32 debt securities, respectively, that were in an unrealized loss position. The following table summarizes the estimated fair value and the aggregate unrealized loss of the Company’s available-for-sale securities that are in loss position as of March 31, 2025 and December 31, 2024 by the length of time the security has been in loss position (in thousands):


	March 31, 2025				December 31, 2024
	Fair		Unrealized		Fair		Unrealized
	value		losses		value		losses
Debt securities in unrealized loss position for 12 months or less	$	222,844	$	(266)	$	205,910	$	(631)
Debt securities in unrealized loss position for more than 12 months		—		—		—		—
Total debt securities in unrealized loss position	$	222,844	$	(266)	$	205,910	$	(631)

The Company has the intent and ability to hold its debt securities until recovery of amortized cost basis. As a result, the Company did not recognize any differences between the fair value and amortized cost basis as a loss in its condensed consolidated statements of operations and comprehensive income for the three months ended March 31, 2025 and 2024. The Company did not record any credit-related impairments for its available-for-sale securities for the three months ended March 31, 2025 and 2024.

The following table summarizes the proceeds from maturities of debt securities during the three months ended March 31, 2025 and 2024 (in thousands):

The Company did not realize any gains or losses from maturities of debt securities for the three months ended March 31, 2025 and 2024.

5. Fair Value of Financial Instruments

The following table summarizes the Company’s cash equivalents and marketable securities measured at fair value on a recurring basis as of March 31, 2025 (in thousands):


			Active		Observable		Unobservable
	March 31,		Markets		Inputs		Inputs
Description	2025		(Level 1)		(Level 2)		(Level 3)
Cash equivalents:
Money market funds	$	67,898	$	67,898	$	—	$	—
U.S. treasury obligations		22,402		22,402		—		—
Marketable securities, available-for-sale:
U.S. government agency securities		190,651		—		190,651		—
U.S. treasury obligations		586,888		586,888		—		—
Total	$	867,839	$	677,188	$	190,651	$	—

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The following table summarizes the Company’s cash equivalents and marketable securities measured at fair value on a recurring basis as of December 31, 2024 (in thousands):


			Active		Observable		Unobservable
	December 31,		Markets		Inputs		Inputs
Description	2024		(Level 1)		(Level 2)		(Level 3)
Cash equivalents:
Money market funds	$	69,729	$	69,729	$	—	$	—
Marketable securities, available-for-sale:
U.S. government agency securities		129,785		—		129,785		—
U.S. treasury obligations		632,138		632,138		—		—
Total	$	831,652	$	701,867	$	129,785	$	—

6. Product Revenue and Related Reserves

The Company generates product revenue from the sales of AYVAKIT/AYVAKYT. The following table summarizes net revenue recognized from product sales for the three months ended March 31, 2025 and 2024 (in thousands):


	Three Months Ended
	March 31,
	2025		2024
United States	$	129,446	$	83,136
Rest of World		19,967		9,389
Total product revenue	$	149,413	$	92,525

The Company primarily sells AYVAKIT/AYVAKYT through specialty distributors and specialty pharmacies. The following table summarizes the customers that represent 10% or greater of gross product revenue for the three months ended March 31, 2025 and 2024 (in thousands):

* Indicates the customer’s share is under 10%.

The following table summarizes the customers with amounts due that represent 10% or greater of the accounts receivable associated with the Company’s product sales as of March 31, 2025 and December 31, 2024 (in thousands):


	March 31,		December 31,
	2025		2024
Customer 1	28	%	31	%
Customer 2	13	%	11	%
Customer 3	11	%	14	%

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The following table summarizes activity in the product revenue allowance and reserve categories for the three months ended March 31, 2025 and 2024 (in thousands):


	Three Months Ended March 31,
	2025		2024
Beginning balance at January 1	$	33,779	$	19,274
Provision related to sales in the current period		28,964		16,926
Adjustment related to prior periods sales		(2,061)		(309)
Credits and payments made		(17,422)		(12,488)
Ending balance at March 31	$	43,260	$	23,403

The total reserves that are included in the Company’s unaudited condensed consolidated balance sheets as of March 31, 2025 and December 31, 2024, are summarized as follows (in thousands):


	March 31,		December 31,
	2025		2024
Reduction of accounts receivable, net	$	2,912	$	2,963
Component of accrued expenses		40,348		30,816
Total revenue-related reserves	$	43,260	$	33,779

7. Inventory

Capitalized inventory consists of the following at March 31, 2025 and December 31, 2024 (in thousands):


	March 31,		December 31,
	2025		2024
Work in process	$	35,517	$	30,300
Finished goods		10,020		8,975
Total	$	45,537	$	39,275

Balance sheet classification


	March 31,		December 31,
	2025		2024
Inventory	$	12,953	$	13,611
Other assets		32,584		25,664
Total	$	45,537	$	39,275

Inventory amounts written down as a result of excess, obsolescence, unmarketability or other reasons are charged to cost of sales. The Company did not recognize significant write-downs of inventory during the three months ended March 31, 2025 and 2024. Long-term inventory, which consists of work in process and finished goods, is included in other assets in the unaudited condensed consolidated balance sheets.

8. Restricted Cash

The following table provides a reconciliation of cash, cash equivalents, and restricted cash as reported within the Company's condensed consolidated balance sheets to the total of such amounts shown in the condensed consolidated statements of cash flows for the three months ended March 31, 2025 and 2024 (in thousands):


	March 31,		March 31,
	2025		2024
Cash and cash equivalents	$	122,245	$	113,326
Restricted cash		11,847		10,634
Total cash, cash equivalents, and restricted cash shown in condensed consolidated statements of cash flows	$	134,092	$	123,960

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As of March 31, 2025 and December 31, 2024, $11.8 million and $11.6 million, respectively, of the Company’s cash is restricted by a financial institution primarily related to funds held to satisfy the requirements of certain government agreements and the security deposits for the lease agreements for the Company’s office and laboratory spaces. For additional information, see Note 15, Leases.

9. Accrued Expenses

Accrued expenses as of March 31, 2025 and December 31, 2024 consist of the following (in thousands):


	March 31,		December 31,
	2025		2024
Research, development and commercial contract costs	$	32,637	$	33,957
Employee compensation		21,771		48,725
Accrued professional fees		17,999		14,134
Revenue-related reserves		40,348		30,816
Other		9,300		5,456
Total	$	122,055	$	133,088

10. Collaboration, License and Other Agreements

Rigel

On February 22, 2024, the Company entered into an Asset Purchase Agreement with Rigel Pharmaceuticals, Inc. (Rigel) for Rigel to purchase certain assets from the Company comprising the U.S. rights to research, develop, manufacture and commercialize GAVRETO (pralsetinib). Such assets include, among other things, applicable intellectual property related to pralsetinib in the U.S, including patents, copyrights and trademarks, as well as clinical regulatory and commercial data and records. Simultaneously and in connection with entering into the Asset Purchase Agreement, the parties also entered into certain supporting agreements, including a customary transition agreement, (such agreements collectively, the Rigel Agreement), pursuant to which, the Company transitioned certain inventory and regulatory and distribution responsibilities for pralsetinib to Rigel.

Under the terms of the Rigel Agreement, the Company has the right to receive a purchase price of $15.0 million, with $10.0 million paid upon first commercial sale of GAVRETO by Rigel and an additional $5.0 million as a delayed purchase price payable on the later of (i) the first anniversary of the closing date of the transaction, or (ii) the completion of certain transition activities. The Company is also eligible to receive up to $102.5 million in contingent specified regulatory and commercial milestone payments, in addition to tiered percentage royalties ranging from 10 percent to 30 percent on annual net sales of GAVRETO in the U.S. The royalties will be payable until the later of (i) the expiration of the royalty term, as defined in the agreement, which begins on the date of the first commercial sale of GAVRETO in the U.S., (ii) the date of expiration of the last valid patent claim within the Company’s IP that covers GAVRETO in the U.S., and (iii) the expiration of the last regulatory exclusivity for GAVRETO in the U.S.

The Company determined that the Rigel Agreement is a transaction with a customer and therefore accounted for the transaction in accordance with ASC 606. As of the effective date, the Company determined that the agreement includes three performance obligations: the delivery of (1) the U.S. rights to GAVRETO; (2) additional pralsetinib clinical data; and (3) GAVRETO product to be purchased from Genentech.

The transaction price under ASC 606 was fully constrained at the inception of the Rigel Agreement due to the pending completion of key transition activities stipulated in the agreement, including the transfer of the new drug application (NDA). These key transition activities, including the transfer of the NDA, related patents, and GAVRETO product, were completed in the second quarter of 2024. The performance obligations related to the U.S. rights to GAVRETO and the delivery of GAVRETO product were satisfied at a point in time upon the completion of these key transition activities. The transaction price was determined to be $27.7 million, which consisted of $6.5 million consideration for the GAVRETO product, $10.0 million upfront purchase price payment, and $11.2 million in the milestone and royalty payments that were considered probable of achievement and not subject to significant subsequent reversal of revenue. The transaction price was allocated to the three performance obligations on a relative stand-alone

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selling price basis. The transaction price allocated to the U.S. rights to GAVRETO and GAVRETO product was recognized as revenue of $24.3 million in the second quarter of 2024. The additional clinical data performance obligation will be satisfied at a point in time once the transfer of such data to Rigel is completed, and the allocated transaction price of $3.6 million was recorded as deferred revenue on the condensed consolidated financial statements as of March 31, 2025. During the three months ended March 31, 2025, insignificant revenue was recognized under the Rigel agreements.

The Company reevaluates the transaction price at the end of each reporting period and as uncertain events are resolved or other changes in circumstances occur, and if necessary, the Company adjusts its estimate of the transaction price, and any addition to the transaction price would be recognized as revenue when it becomes probable that inclusion would not lead to a significant revenue reversal.

The following table summarizes the assets and liabilities under the Rigel agreements as of March 31, 2025 and December 31, 2024 (in thousands):


	March 31, 2025						December 31, 2024
	Current		Noncurrent		Total		Current		Noncurrent		Total
Contract assets	$	2,915	$	6,602	$	9,517	$	2,939	$	7,380	$	10,319
Contract liabilities	$	—	$	3,562	$	3,562	$	—	$	3,562	$	3,562

IDRx

In August 2022, the Company entered into a license agreement with IDRx, Inc. (IDRx), granting IDRx an exclusive, worldwide, royalty-bearing license to exploit the Company’s internally discovered KIT exon 13 inhibitor IDRX-73 (IDRx License Agreement). IDRx is a clinical-stage biopharmaceutical company and among IDRx’s founders are Alexis Borisy, George Demetri, M.D., and Nicholas Lydon, Ph.D., who were each a member of the Company’s board of directors at the time. Due to these relationships, the transaction with IDRx is a related party transaction.

In connection with the IDRx License Agreement, the Company also entered into a stock purchase agreement with IDRx (IDRx Stock Purchase Agreement), pursuant to which the Company received 4,509,105 shares of IDRx’s Series A preferred stock. In July 2023, the Company received 192,282 additional shares under an anti-dilution provision under the IDRx Stock Purchase Agreement and as of December 31, 2024, the Company owned a total of 4,701,387 shares of IDRx’s Series A preferred stock.

The Company is also eligible to receive up to $217.5 million in contingent cash payments, including specified development, regulatory and sales-based milestone payments. In addition, the Company is eligible to receive royalties on aggregate annual worldwide net sales of licensed products at tiered percentage rates up to low-teens, subject to adjustments in specified circumstances under the IDRx License Agreement.

Unless earlier terminated, the IDRx License Agreement will expire on a country-by-country, licensed product-by-licensed product basis upon the latest of: (a) the expiration of the last valid claim within the licensed patents covering such licensed product in a such country, (b) the expiration of the regulatory exclusivity period for such licensed product in such country, or (c) the 10th anniversary of the first commercial sale of such licensed product in such country. Following the end of the term for any such licensed product and in such region by expiration, the license granted to IDRx will become exclusive, perpetual, irrevocable, fully paid-up and royalty-free. IDRx may terminate the IDRx License Agreement for convenience at any time upon at least twelve months’ prior written notice to the Company. Either party may also terminate the IDRx License Agreement for material breach of the other party or for insolvency, and the Company may terminate the IDRx License Agreement for IDRx’s breach of the anti-dilution provision in the IDRx Stock Purchase Agreement. Upon termination of the license agreement in its entirety, all rights and obligations under the license agreement will terminate and revert back to the Company, and the Company has a license under certain

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intellectual property of IDRx to continue to exploit the compound and terminated product, subject to a royalty that will be negotiated at the time of termination.

The Company combined the IDRx License Agreement and the IDRx Stock Purchase Agreement into a single contract under ASC 606. Therefore, the Company determined that the shares of IDRx’s Series A preferred stock should be attributed to the transaction price of the IDRx License Agreement. The transaction price of the IDRx License Agreement at the contract inception was determined to be $27.5 million, which was based on the fair value derived from IDRx’s then-most recent financing transaction with unrelated investors. The Company identified two material promises in the IDRx License Agreement, which were the exclusive license and the initial know-how transfer, which were combined into one distinct performance obligation. The Company concluded that the license is a functional intellectual property license and that IDRx benefited from the license along with the initial know-how transfer at the time of grant, and therefore the related performance obligation was satisfied at a point in time and the revenue for the transaction price of $27.5 million was recorded in 2022.

All potential milestone payments that the Company is eligible to receive under the IDRx License Agreement have been excluded from the transaction price. The Company reevaluates the transaction price for inclusion of milestone payments and royalties at the end of each reporting period and as uncertain events are resolved or other changes in circumstances occur, and if necessary, the Company adjusts its estimate of the transaction price, and any addition to the transaction price would be recognized as revenue when it becomes probable that inclusion would not lead to a significant revenue reversal. Additionally, revenue from any sales milestones and royalties shall be recognized when the related sales occur.

The Company accounted for the preferred stock investment as an equity investment under the measurement alternative for equity investments without a readily determinable fair value, at cost of $27.8 million including transaction costs of $0.3 million in 2022. Subsequently, in August 2024, IDRx completed a Series B preferred stock financing and accordingly, the Company adjusted the carrying value of its investment in IDRx to $28.7 million.

During the three months ended March 31, 2025, GSK plc (GSK) acquired IDRx for an upfront cash consideration of $1.0 billion with an additional $150.0 million contingent consideration. The Company received $78.7 million in cash from this transaction, which resulted in a net investment gain of $50.0 million. Consequently, the Company derecognized its investment in IDRx on its unaudited condensed consolidated balance sheets. Any additional contingent consideration received related to this acquisition will be recognized as an investment gain once it is realized.

The acquisition does not affect the Company's rights related to the license agreement. The Company will continue to be eligible to receive contingent cash payments under the IDRx License Agreement as outlined above. No revenue was recorded under the IDRx License Agreement during the three months ended March 31, 2025 and 2024.

VantAI

In February 2022, the Company entered into an exclusive collaboration agreement with Oncopia Therapeutics, Inc. d/b/a Proteovant Therapeutics, Inc. (Proteovant) (the 2022 Agreement) to jointly research and advance certain protein degrader therapies into development candidates, with VantAI, Inc. (VantAI) performing computational chemistry services on behalf of Proteovant under the agreement. In December 2023, the Company entered into an Amended and Restated Collaboration and License Agreement (the A&R Agreement) with VantAI and Proteovant, which amended and restated and replaced in its entirety the 2022 Agreement. Under the A&R Agreement, Proteovant ceased its role under the 2022 Agreement and VantAI provides expanded computational support directly to the Company, including computational biology and expanded computational chemistry to advance three novel protein degrader programs, and the Company has the option, at its sole discretion, to expand the collaboration to include a fourth target program.

Under the A&R Agreement, VantAI is eligible to receive up to a total of $1.67 billion in contingent payments including specified research, development, regulatory and commercialization milestones for all the target programs. As of March 31, 2025, VantAI has achieved $8.5 million of such contingent payments. The Company will be obligated to pay VantAI tiered percentage royalties on a licensed product-by-licensed product basis ranging from the mid-single digits on annual net sales of each licensed product in the applicable territory, subject to adjustment in specified circumstances.

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Under the 2022 Agreement, the Company paid Proteovant an upfront payment of $20.0 million in connection with the execution of the 2022 Agreement. This upfront payment was recorded as a prepaid asset on the Company’s consolidated balance sheet and was amortized as research and development expense over the expected research period because the Company concluded that Proteovant was providing the Company with research services throughout such period. The Company determined to continue to amortize the remaining prepaid asset balance as research and development expense over the expected research period of the A&R Agreement as VantAI continued to provide such research and development services. During the three months ended March 31, 2025 and 2024, the Company recorded research and development expense of $1.8 million and $2.1 million, respectively, under the A&R Agreement.

The following table summarizes the assets associated with the A&R Agreement as of March 31, 2025 and December 31, 2024 (in thousands):


	March 31, 2025						December 31, 2024
	Current		Noncurrent		Total		Current		Noncurrent		Total
Prepaid and other assets	$	5,030	$	5,816	$	10,846	$	4,971	$	2,666	$	7,637

The Company reevaluates the expected research period at the end of each reporting period and prospectively adjusts the amortization of the asset for changes in the expected research period. Each research and development milestone payment is accrued and expensed when probable.

Zai Lab

In November 2021, the Company entered into a collaboration (the Zai Lab agreement) with Zai Lab (Shanghai) Co., Ltd., (Zai Lab) to develop and commercialize certain licensed products for the treatment of EGFR-driven non-small cell lung cancer in Greater China, including Mainland China, Hong Kong, Macau and Taiwan (collectively, the Zai Lab Territory), which currently include BLU-945 and BLU-525. In January 2024, the Company decided to discontinue further investment in the early clinical-stage therapies for EGFR-mutant NSCLC globally. Zai Lab retains its rights to BLU-945 and BLU-525 under the agreement. The Company retains exclusive rights to the licensed products outside the Zai Lab Territory. The decision to deprioritize the licensed products does not have an impact on the Company’s accounting treatment related to the Zai Lab agreement.

Under the Zai Lab agreement, the Company received an upfront cash payment of $25.0 million and, in addition to the upfront payment received, the Company is eligible to receive up to $590.0 million in contingent payments, including specified development, regulatory and sales-based milestones and tiered percentage royalties on a licensed product-by-licensed product basis ranging from the low-teens to mid-teens on annual net sales of each licensed product in the Zai Lab Territory, subject to adjustment in specified circumstances. Zai Lab is responsible for costs related to clinical trials in the Zai Lab Territory, other than the specified shared services costs as defined in the Zai Lab agreement which are shared by the Company and Zai Lab. Zai Lab is responsible for conducting all development and commercialization activities in the Zai Lab Territory related to the licensed drug candidates.

The Zai Lab agreement will continue on a licensed product-by-product and region-by-region basis until the later of (i) the 12^th anniversary of the date of the first commercial sale of a licensed product in the Zai Lab Territory, (ii) the date of expiration of the last valid patent claim related to the Company’s patent rights of the product in the Zai Lab Territory, and (iii) the expiration of the last regulatory exclusivity for that product in a region in the Zai Lab Territory. Zai Lab may terminate the agreement for convenience by giving a written notice (a) at least 12 months after the date of notice, in the event such notice is given after the first commercial sale of a licensed product in the Zai Lab Territory or (b) at least nine months after the date of such notice, in the event such notice is given prior to the first commercial sale of the first licensed product in the Zai Lab Territory. Either party may terminate the Zai Lab agreement for the other party’s uncured material breach or insolvency. Upon termination, all licenses and all other rights granted by the Company to Zai Lab will terminate. Each party will retain its joint ownership interests in any joint collaboration technology.

The Company concluded that the Zai Lab agreement is a collaborative agreement under ASC 808. The Company determined that the Zai Lab agreement contained two material components: (i) licenses granted to Zai Lab to exploit and develop each licensed product in the Zai Lab Territory and related activities in the Zai Lab Territory, including manufacturing, and (ii) global development of the licensed products. The Company concluded that Zai Lab is

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the Company’s customer for the licenses and related activities in the Zai Lab Territory under ASC 606, whereas payments received by the Company for global development activities, including manufacturing, are accounted for as a reduction of related expenses. No reduction of expenses was recorded under the Zai Lab agreement during the three months ended March 31, 2025 and 2024.

The Company evaluated the Zai Lab Territory specific licenses and related activities under ASC 606 and identified one performance obligation, which consists of the licenses and their initial know-how transfer at the outset of the arrangement. The manufacturing activities were excluded as performance obligation at the outset of the arrangement because it represented a customer option that was not a material right.

The Company determined that the license is a functional intellectual property license as Zai Lab benefited from the license along with the initial know-how transfer at the time of grant, and therefore the related performance obligation is satisfied at a point in time. The transaction price of the Zai Lab agreement at the outset of the arrangement was determined to be $25.0 million and the Company satisfied the performance obligation upon delivery of the licenses and initial know-how transfer and accordingly, the upfront payment of $25.0 million was recognized as revenue in 2021. All milestone and royalty payments that the Company is eligible to receive were excluded from the transaction price, as all milestone amounts were fully constrained based on the probability of achievement. The Company reevaluates the transaction price at the end of each reporting period and as uncertain events are resolved or other changes in circumstances occur. Costs that are incurred associated with Zai Lab Territory specific activities are reimbursable from Zai Lab and are recognized as revenue. No revenue was recorded under the Zai Lab agreement during the three months ended March 31, 2025 and 2024.

Roche – Pralsetinib Collaboration

In July 2020, the Company entered into a collaboration agreement (the Roche pralsetinib collaboration agreement) with F. Hoffmann-La Roche Ltd and Genentech, Inc., a member of the Roche Group (collectively, Roche), granting Roche exclusive rights to develop and commercialize the Company’s drug candidate pralsetinib worldwide, excluding the CStone Territory (as defined below), and a co-exclusive license in the U.S. to develop and commercialize pralsetinib. The Roche pralsetinib collaboration agreement was terminated on February 22, 2024 (the collaboration termination effective date), at which time the Company regained worldwide commercialization and development rights to GAVRETO excluding the CStone Territory. The Company and Roche continued to perform their respective obligations under the Roche pralsetinib collaboration agreement through the collaboration termination effective date, when the Company and Roche entered into a transition agreement (the Roche transition agreement).

Under the Roche pralsetinib collaboration agreement, the Company received an upfront cash payment of $675.0 million and Roche Holdings, Inc. (Roche Holdings) purchased shares of the Company’s common stock at a purchase price of $100.0 million, with a premium of $20.7 million attributed to the transaction price of the Roche pralsetinib collaboration agreement.

In the U.S., the Company and Roche co-commercialized pralsetinib and shared profits and losses equally. In addition, the Company received tiered royalties on annual net sales of pralsetinib outside the U.S., excluding the CStone Territory (the Roche Territory). The Company and Roche shared global development costs for pralsetinib at a rate of 45 percent for the Company and 55 percent for Roche.

The Company concluded that the Roche pralsetinib collaboration agreement contained two material promises within the scope of ASC 606, pralsetinib license and the Roche Territory activities. The pralsetinib license was deemed a functional intellectual property license and a distinct performance obligation, satisfied at the time of grant. The initial transaction price of the Roche pralsetinib collaboration agreement at the outset of the arrangement was determined to be $695.7 million, including the $675.0 million upfront cash payment and the $20.7 million premium on the sale of common stock to Roche Holdings, which was allocated to the performance obligation related to the pralsetinib licenses. Through the collaboration termination effective date, the Company achieved an aggregate of $105.0 million in specified regulatory and commercialization milestones which were added to the estimated transaction price of the Roche pralsetinib collaboration agreement and recorded as revenue in the respective periods when they were achieved.

For the parties’ participation in global development for pralsetinib and the U.S. commercialization activities for GAVRETO, the Company concluded that those activities and cost-sharing payments related to such activities were

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within the scope of ASC 808, as both parties were active participants in the development, manufacturing and commercialization activities and are exposed to significant risks and rewards of those activities under the Roche pralsetinib collaboration agreement. Payments to or reimbursements from Roche related to the global development activities were accounted for either as an increase or reduction of research and development expenses.

No operating expenses have been recorded under the Roche pralsetinib collaboration since June 30, 2024. During the three months ended March 31, 2024, the Company recorded a $1.0 million reduction to selling, general and administrative expenses in connection with the commercialization of GAVRETO in the U.S and a $1.4 million increase in research and development expenses related to global development activities for pralsetinib under the Roche pralsetinib collaboration.

Roche was the principal for recording product sales to customers in the U.S., and the Company recognized a portion of the profit as revenue and losses as collaboration loss sharing in its consolidated statements of operations and comprehensive income. No collaboration revenue has been recorded under the Roche pralsetinib collaboration since June 30, 2024. During the three months ended March 31, 2024, the Company recorded revenue of $1.4 million derived from profit sharing on Roche sales of GAVRETO in the U.S. and $0.5 million revenue related to Roche Territory specific activities and royalties earned during the three months ended March 31, 2024.

Upon termination of the Roche pralsetinib collaboration agreement, the Company chose not to assume responsibility for any ongoing pralsetinib clinical trials, and under the terms of the Roche pralsetinib collaboration agreement, Roche bears sole responsibility for all costs associated with the wind-down of these trials.

Pursuant to the Roche transition agreement, the Company is obligated to reimburse Roche for wind-down costs associated with the marketing and commercialization activities occurred for Roche Territory until December 31, 2026. Additionally, the Company is obligated to reimburse Roche for any U.S. transition related costs that exceeds GAVRETO’s net sales in the U.S., and any remaining net profit are shared equally between the Company and Roche until December 31, 2025. The Company has concluded that such activities and associated payments to Roche are not within the scope of ASC 808 as only the Company is exposed to significant risks and awards associated with those activities. The Company records those wind-down costs and the net amount of U.S. transition costs reimbursable to Roche as selling, general, and administrative expenses when they are incurred. During the three months ended March 31, 2025, the Company recorded $0.4 million in such costs. Such costs were insignificant during the three months ended March 31, 2024.

The following table summarizes the Company’s liabilities associated with the Roche transition agreement as of March 31, 2025 and December 31, 2024 (in thousands):


	March 31,		December 31,
	2025		2024
Accrued expenses	$	365	$	1,712

Clementia

In October 2019, the Company entered into a license agreement (the Clementia agreement) with Clementia Pharmaceuticals, Inc. (Clementia), a wholly-owned subsidiary of Ipsen S.A. Under the Clementia agreement, the Company granted an exclusive, worldwide, royalty-bearing license to Clementia to develop and commercialize BLU-782, the Company’s oral, highly selective investigational ALK2 inhibitor in clinical development for the treatment of fibrodysplasia ossificans progressiva (FOP), now referred to as fidrisertib, as well as specified other compounds related to the BLU-782 program.

Under the Clementia agreement, the Company received an upfront cash payment of $25.0 million and through March 31, 2025, the Company has received an aggregate of $50.0 million in cash milestone payments. Subject to the terms of the Clementia agreement, in addition to the upfront and milestone payments received through March 31, 2025, the Company is eligible to receive up to $460.0 million in contingent payments, including specified development, regulatory and sales-based milestones for licensed products. In addition, Clementia is obligated to pay to the Company royalties on aggregate annual worldwide net sales of licensed products at tiered percentage rates ranging from the low-

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to mid-teens, subject to adjustment in specified circumstances under the Clementia agreement, and Clementia purchased specified manufacturing inventory from the Company for a total of $1.5 million.

Unless earlier terminated in accordance with the terms of the Clementia agreement, the agreement will expire on a country-by-country, licensed product-by-licensed product basis on the date when no royalty payments are or will become due. Clementia may terminate the agreement at any time upon at least 12 months’ prior written notice to the Company. Either party may terminate the agreement for the other party’s uncured material breach or insolvency and in certain other circumstances agreed to by the parties. In certain termination circumstances, the Company is entitled to retain specified licenses to be able to continue to exploit the Clementia licensed products.

The Company evaluated the Clementia agreement under ASC 606, as the agreement represented a transaction with a customer. The Company identified the following material promises under the agreement: (1) the exclusive license to develop, manufacture and commercialize BLU-782; (2) the technology transfer of BLU-782 program; (3) the transfer of existing manufacturing inventory; and (4) the transfer of in-process manufacturing inventory. In addition, the Company determined that the exclusive license and technology transfer were not distinct from each other, as the exclusive license has limited value without the corresponding technology transfer. As such, for the purposes of ASC 606, the Company determined that these four material promises, described above, should be combined into three performance obligations: (1) the exclusive license and the technology transfer; (2) the transfer of existing manufacturing inventory; and (3) the transfer of in-process manufacturing inventory.

The Company determined that the transaction price at the outset of the arrangement was $46.5 million, which was allocated to the three performance obligations on a relative stand-alone selling price basis, and was recognized as revenue in prior years.

No revenue was recorded under the Clementia Agreement during the three months ended March 31, 2025 and 2024. All potential milestone payments that the Company is eligible to receive were excluded from the transaction price, as the amounts were fully constrained based on the probability of achievement. The Company reevaluates the transaction price at the end of each reporting period and as uncertain events are resolved or other changes in circumstances occur, and if necessary, the Company adjusts its estimate of the transaction price, and any addition to the transaction price would be recognized as revenue when it becomes probable that inclusion would not lead to a significant revenue reversal.

CStone Pharmaceuticals

In June 2018, the Company entered into a collaboration and license agreement (the CStone agreement) with CStone Pharmaceuticals (CStone) pursuant to which the Company granted CStone exclusive rights to develop and commercialize the Company’s drug candidates avapritinib, pralsetinib and fisogatinib, including back-up and other forms thereof, in Mainland China, Hong Kong, Macau and Taiwan (each, a CStone region and collectively, the CStone Territory), either as a monotherapy or as part of a combination therapy.

The Company received an upfront cash payment of $40.0 million, and through March 31, 2025, the Company has achieved an aggregate of $38.5 million in milestones under this collaboration. Subject to the terms of the CStone agreement, in addition to the upfront payments received and milestones achieved through March 31, 2025, the Company will be eligible to receive up to $307.5 million in contingent payments, including specified development, regulatory and sales-based milestones for licensed products. In addition, CStone is obligated to pay the Company tiered percentage royalties on a licensed product-by-licensed product basis ranging from the mid-teens to low twenties on annual net sales of each licensed product in the CStone Territory, subject to adjustment in specified circumstances. CStone is responsible for costs related to the development of the licensed products in the CStone Territory, other than specified costs related to the development of fisogatinib as a combination therapy in the CStone Territory that are shared by the Company and CStone.

Pursuant to the terms of the CStone agreement, CStone is responsible for conducting all development and commercialization activities in the CStone Territory related to the licensed products. Subject to specified exceptions, during the term of the CStone agreement, each party has agreed that neither it nor its affiliates will conduct specified development and commercialization activities in the CStone Territory related to selective inhibitors of FGFR4, KIT, PDGFRA and RET. In addition, under the CStone agreement, each party has granted the other party specified

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intellectual property licenses to enable the other party to perform its obligations and exercise its rights under the CStone agreement, including license grants to enable each party to conduct research, development and commercialization activities pursuant to the terms of the CStone agreement.

The CStone agreement will continue on a licensed product-by-licensed product and CStone region-by-CStone region basis until the later of (i) 12 years after the first commercial sale of a licensed product in a CStone region in the CStone Territory and (ii) the date of expiration of the last valid patent claim related to the Company’s patent rights or any joint collaboration patent rights for the licensed product that covers the composition of matter, method of use or method of manufacturing such licensed product in such region. Subject to the terms of the CStone agreement, CStone may terminate the CStone agreement in its entirety or with respect to one or more licensed products for convenience by providing written notice to the Company, and CStone may terminate the CStone agreement with respect to a licensed product for convenience at any time by providing written notice to the Company following the occurrence of specified events. In addition, the Company may terminate the CStone agreement under specified circumstances if CStone or certain other parties challenges the Company’s patent rights or any joint collaboration patent rights or if CStone or its affiliates do not conduct any material development or commercialization activities with respect to one or more licensed products for a specified period of time, subject to specified exceptions. Either party may terminate the CStone agreement for the other party’s uncured material breach or insolvency. In certain termination circumstances, the parties are entitled to retain specified licenses to be able to continue to exploit the licensed products, and in the event of termination by CStone for the Company’s uncured material breach, the Company will be obligated to pay CStone a low single digit percentage royalty on a licensed product-by-licensed product basis on annual net sales of such licensed product in the CStone Territory, subject to a cap and other specified exceptions.

The Company evaluated the CStone agreement to determine whether it is a collaborative arrangement for purposes of ASC 808. The Company determined that there were two material components of the CStone agreement: (i) the CStone Territory-specific license and related activities in the CStone Territory, and (ii) the parties’ participation in global development of the licensed products. The Company concluded that the CStone Territory-specific license and related activities in the CStone Territory are not within the scope of ASC 808 because the Company is not exposed to significant risks and rewards. The Company concluded that CStone is a customer with regard to the component that includes the CStone Territory-specific license and related activities in CStone Territory, which include manufacturing. For the parties’ participation in global development of the licensed products, the Company concluded that the research and development activities and cost-sharing payments related to such activities are within the scope of ASC 808 as both parties are active participants exposed to the risk of the activities under the CStone agreement. The Company concluded that CStone is not a customer with regard to the global development component in the context of the CStone agreement. Therefore, net payments received by the Company for global development activities under the CStone agreement, including manufacturing, are accounted for as a reduction of related expenses.

The Company did not have significant manufacturing and research and development services related to the global development activities during the three months ended March 31, 2025 and 2024.

The Company evaluated the CStone Territory-specific license and related activities in the CStone Territory under ASC 606, as these transactions are considered transactions with a customer. The Company identified the following material promises under the arrangement: (1) the three exclusive licenses granted in the CStone Territory to develop, manufacture and commercialize the three licensed products; (2) the initial know-how transfer for each licensed product; (3) manufacturing activities related to development and commercial supply of the licensed products; (4) participation in the joint steering committee (JSC) and joint project teams (JPT); (5) regulatory responsibilities; and (6) manufacturing technology and continuing know-how transfers. The Company determined that each licensed product is distinct from the other licensed products. In addition, the Company determined that the exclusive licenses and initial know-how transfers for each licensed product were not distinct from each other, as each exclusive license has limited value without the corresponding initial know-how transfer. For purposes of ASC 606, the Company determined that participation on the JSC and JPTs, the regulatory responsibilities and the manufacturing technology and continuing know-how transfers are qualitatively and quantitatively immaterial in the context of the CStone agreement and therefore are excluded from performance obligations. As such, the Company determined that these six material promises, described above, should be combined into one performance obligation for each of the three candidates.

The Company evaluated the provision of manufacturing activities related to development and commercial supply of the licensed products as an option for purposes of ASC 606 to determine whether these manufacturing

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activities provide CStone with any material rights. The Company concluded that the manufacturing activities were not issued at a significant and incremental discount, and therefore do not provide CStone with any material rights. As such, the manufacturing activities are excluded as performance obligations at the outset of the arrangement.

Based on these assessments, the Company identified three distinct performance obligations at the outset of the CStone agreement, which consists of the following for each licensed product: (1) the exclusive license and (2) the initial know-how transfer.

Under the CStone agreement, in order to evaluate the transaction price for purposes of ASC 606, the Company determined that the upfront amount of $40.0 million constituted the entirety of the consideration to be included in the transaction price at the outset of the arrangement, which was allocated to the three performance obligations. The potential milestone payments that the Company is eligible to receive were excluded from the transaction price, as all milestone amounts were fully constrained based on the probability of achievement. The Company satisfied the performance obligations upon delivery of the licenses, initial know-how transfers and product trademark and recognized the upfront payment of $40.0 million as revenue in 2018.

The Company did not achieve any milestones under the CStone agreement during the three months ended March 31, 2025 and 2024. The Company reevaluates the transaction price at the end of each reporting period and as uncertain events are resolved or other changes in circumstances occur, and if necessary, the Company adjusts its estimate of the transaction price, and any addition to the transaction price would be recognized as revenue when it becomes probable that inclusion would not lead to a significant revenue reversal.

Subsequent to the CStone agreement, the Company entered into various commercial supply and manufacturing technology transfer agreements for avapritinib and pralsetinib related to supply of active pharmaceutical ingredient (API), drug substance and commercialization activities conducted specifically for the CStone Territory. The manufacturing activities in these agreements were considered as distinct performance obligations from the CStone collaboration agreement and collaboration revenue is recognized upon delivery of the supply to CStone. Considerations payable to CStone related to the Company’s obligations in connection with commercial supply of pralsetinib for the CStone Territory was recognized as a reduction of collaboration revenue.

A summary of revenue recognized under the CStone agreement during the three months ended March 31, 2025 and 2024 is as follows (in thousands):

The following table presents the contract liabilities associated with the CStone collaboration as of March 31, 2025 and December 31, 2024 (in thousands):


	March 31,		December 31,
	2025		2024
Accrued expenses	$	548	$	2,027

The Company’s liabilities associated with the CStone collaboration as of March 31, 2025 primarily related to payment associated with the Company’s manufacturing services and royalty revenue related to the CStone territory-specific activities. The Company’s liabilities as of December 31, 2024 resulted from the Company’s obligations in connection with commercial supply of pralsetinib for the CStone Territory.

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11. Stockholders’ Equity

In February 2022, the Company entered into an at-the-market (ATM) facility (ATM Facility) with Cowen and Company, LLC (Cowen), pursuant to which the Company may offer and sell, from time to time at its sole discretion, shares of its common stock having an aggregate offering price of up to $300.0 million through Cowen as sales agent. The Company did not issue any shares under the ATM Facility during the three months ended March 31, 2025. During the three months ended March 31, 2024, the Company issued and sold 544,719 shares of its common stock under the ATM Facility and received net proceeds of $48.9 million.

12. Stock-based Compensation

Stock Plans

In 2015, the Company’s board of directors and stockholders approved the 2015 Stock Option and Incentive Plan (the 2015 Plan), which replaced the Company’s 2011 Stock Option and Grant Plan, as amended (the 2011 Plan). The 2015 Plan includes incentive stock options, nonstatutory stock options, stock appreciation rights, restricted stock, restricted stock units, performance-based restricted stock units, unrestricted stock, performance-based awards and cash-based awards. The Company initially reserved a total of 1,460,084 shares of common stock for the issuance of awards under the 2015 Plan. The 2015 Plan provided that the number of shares reserved and available for issuance under the 2015 Plan would be cumulatively increased on January 1 of each calendar year by 4% of the number of shares of common stock issued and outstanding on the immediately preceding December 31 or such lesser amount as specified by the compensation committee of the board of directors.

In March 2020, the Company’s board of directors adopted the 2020 Inducement Plan (the Inducement Plan), pursuant to which the Company may grant, subject to the terms of the Inducement Plan and Nasdaq rules, nonstatutory stock options, stock appreciation rights, restricted stock awards, restricted stock units, and other stock-based awards. The Company initially reserved a total of 1,000,000 shares of common stock for the issuance of awards under the Inducement Plan and in June 2022, the Company’s board of directors approved the reservation of an additional 1,500,000 shares of common stock for the issuance of awards under the Inducement Plan.

At the Company’s annual meeting of stockholders held on June 12, 2024, the Company’s stockholders approved the 2024 Stock Incentive Plan (the 2024 Plan), which replaced the Company’s 2015 Plan and the Inducement Plan. As of March 31, 2025, there were 6,983,233 and 668,819 shares underlying awards outstanding under the 2015 Plan and the Inducement Plan, respectively. No further shares will be granted under the 2015 Plan and the Inducement Plan after the effective date of the 2024 Plan. The 2024 Plan provides for the granting of incentive stock options, nonstatutory stock options, stock appreciation rights, restricted stock, restricted stock units, performance-based restricted stock units, unrestricted stock and cash-based awards. The 2024 Plan provides for the issuance of up to 9,200,000 shares. Any shares of common stock underlying any awards that are forfeited, canceled, held back upon exercise or settlement of an award to satisfy the exercise price or tax withholding, repurchased, expire or are otherwise terminated by the Company under the 2024 Plan and the 2015 Plan will be added back to the shares of common stock available for issuance under the 2024 Plan. As of March 31, 2025, there were 7,281,467 shares available for future grant under the 2024 Plan.

2015 Employee Stock Purchase Plan

In 2015, the Company’s board of directors and stockholders approved the 2015 Employee Stock Purchase Plan (the 2015 ESPP), which became effective upon the closing of the Company’s initial public offering in May 2015. The Company initially reserved a total of 243,347 shares of common stock for issuance under the 2015 ESPP. The 2015 ESPP provides that the number of shares reserved and available for issuance under the 2015 ESPP will be cumulatively increased on January 1 of each calendar year by 1% of the number of shares of common stock issued and outstanding on the immediately preceding December 31 or such lesser amount as specified by the compensation committee of the board of directors. For the calendar year beginning January 1, 2025, the number of shares reserved for issuance under the 2015 ESPP was increased by 637,122 shares.

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Stock options

The following table summarizes the stock option activity for the three months ended March 31, 2025:


		Weighted-Average
	Shares	Exercise Price
Outstanding at December 31, 2024	6,369,724	$	72.09
Granted	795,360		97.50
Exercised	(213,210)		62.65
Canceled	(26,578)		74.98
Outstanding at March 31, 2025	6,925,296	$	75.28
Exercisable at March 31, 2025	4,538,663	$	72.02

As of March 31, 2025, the total unrecognized compensation expense related to unvested stock option awards was $102.6 million, which is expected to be recognized over a weighted-average period of approximately 2.8 years.

Restricted stock units

The following table summarizes the restricted stock units activity for the three months ended March 31, 2025:


		Weighted-Average
	Shares	Grant Date Fair Value
Unvested shares at December 31, 2024	2,290,931	$	75.36
Granted	932,355		97.06
Vested	(638,445)		75.03
Forfeited	(34,936)		75.91
Unvested shares at March 31, 2025	2,549,905	$	83.37

As of March 31, 2025, the total unrecognized compensation expense related to unvested restricted stock units was $197.4 million, which is expected to be recognized over a weighted-average period of approximately 2.9 years.

Performance-based restricted stock units

In 2023, the Company began granting performance-based restricted stock units (PSUs) that will settle in stock. PSUs awarded to employees have a three-year performance period and vest on the third anniversary of the grant date. The vesting of these awards is subject to the respective employee’s continued employment. The number of PSUs granted represents the target number of units that are eligible to be earned based on the achievement of cumulative three-year performance measures established at the beginning of the performance period, which ends on December 31 of the third year of the performance period.

Participants may ultimately earn between zero and 200.0% of the target number of PSUs granted based on the degree of achievement of the performance metric which is measured on a three-year cumulative relative total shareholder return metric. Accordingly, additional PSUs may be issued or currently issued PSUs may be cancelled upon final determination of the number of units earned.

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The following table summarizes the PSU activity for the three months ended March 31, 2025:


		Weighted-Average
		Grant Date
	Shares	Grant Date Fair Value
Unvested shares at December 31, 2024	142,500	$	107.65
Granted	152,825		136.93
Vested	—		—
Forfeited	—		—
Unvested shares at March 31, 2025	295,325	$	122.80

As of March 31, 2025, the total unrecognized compensation expense related to unvested PSUs was $29.1 million, which is expected to be recognized over a weighted-average period of approximately 2.26 years.

The Company values PSUs on the grant date using a lattice model with a Monte Carlo simulation. This valuation methodology utilizes several key assumptions, including defined consecutive trading day average closing stock price on the grant date, valuation date stock price, expected volatilities using historical volatilities, correlation coefficients based on the volatility data, risk-free rates of return and expected dividend yield. The probability of actual shares expected to be earned is considered in the grant date valuation and the expense is not adjusted to reflect the actual units earned.

Stock-based compensation expense

The Company recognized stock-based compensation expense of $29.1 million and $24.2 million for the three months ended March 31, 2025 and 2024, respectively. Stock-based compensation expense by award type included within the unaudited condensed consolidated statements of operations and comprehensive income was as follows (in thousands):


	Three Months Ended
		March 31,
		2025		2024
Stock options	$	10,268	$	9,573
Restricted stock units		16,827		13,836
Performance-based restricted stock units		1,844		594
Employee stock purchase plan		360		454
Subtotal		29,299		24,457
Capitalized stock-based compensation costs		(243)		(232)
Stock-based compensation expense included in total cost and operating expenses	$	29,056	$	24,225

Stock-based compensation expense, that is included in operating expenses, by classification within the unaudited condensed consolidated statements of operations and comprehensive income was as follows (in thousands):


	Three Months Ended
	March 31,
	2025		2024
Research and development	$	12,127	$	10,875
Selling, general and administrative		16,929		13,350
Total	$	29,056	$	24,225

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13. Net Earnings per Share

Basic earnings per share (EPS) is calculated by dividing net income by the weighted average number of shares of common stock outstanding during the period, without consideration of common stock equivalents. Diluted EPS is calculated by adjusting weighted average shares outstanding for the dilutive effect of common stock equivalents outstanding for the period. For purposes of the diluted EPS calculation, the effect of stock options, unvested restricted stock units, PSUs and ESPP shares on the weighted average number of shares is calculated using the treasury stock method. In periods with reported net operating losses, all common stock equivalents are deemed anti-dilutive such that basic net loss per share and diluted net loss per share are equal.

The calculation of net income and the number of shares used to compute basic and diluted EPS are as follows (in thousands, except for per share data):


	Three Months Ended
	March 31,
	2025		2024
Net income	$	496	$	89,136
Weighted average shares outstanding - basic		64,096		61,580
Effect of dilutive securities:
Stock options		1,381		1,165
Restricted stock units		942		985
Performance-based restricted stock units		107		72
Weighted average shares outstanding - diluted		66,526		63,802
Net income per share - basic	$	0.01	$	1.45
Net income per share - diluted	$	0.01	$	1.40

The following table sets forth the potential shares excluded from the calculation of EPS for the three months ended March 31, 2025 and 2024 because their inclusion would be anti-dilutive (in thousands):


	March 31,
	2025	2024
Stock options	2,026	2,126
Restricted stock units	18	372
Performance-based restricted stock units	53	31
ESPP shares	28	39
Total	2,125	2,568

14. Income Taxes

The Company utilizes the asset and liability method of accounting for income taxes. Under this method, deferred tax assets and liabilities are determined based on the difference between the financial statement carrying amounts and tax basis of assets and liabilities using enacted tax rates in effect for years in which the temporary differences are expected to reverse. The Company provides a valuation allowance when it is more likely than not that deferred tax assets will not be realized.

The realization of deferred income tax assets is dependent on the generation of sufficient taxable income during future periods in which temporary differences are expected to reverse. Where the realization of such assets does not meet the more likely than not criterion, the Company applies a valuation allowance against the deferred income tax asset under consideration. The valuation allowance is reviewed periodically and if the assessment of the more likely than not criterion changes, the valuation allowance is adjusted accordingly. As of March 31, 2025, the Company has a full valuation allowance applied against its U.S. and foreign deferred tax assets.

During the three months ended March 31, 2025, GSK acquired IDRx for an upfront consideration of $1.0 billion and an additional $150.0 million in regulatory approval-based milestone payments. The Company received consideration in the amount of $78.7 million and the Company recorded a gain on sale of investment in the amount of

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$50.0 million during the three months ended March 31, 2025. For tax purposes, the gain will also be included in the taxable income calculation for the year ended December 31, 2025.

As of March 31, 2025, the Company expects to be in a taxable income position for the calendar year ended December 31, 2025, and has recorded an income tax expense of $0.8 million for the three months ended March 31, 2025.

The Company recognizes interest and penalties related to unrecognized tax benefits in the provision for income taxes. As of March 31, 2025, the Company did not have any gross unrecognized tax benefit.

15. Leases

The Company’s building leases are comprised of office and laboratory spaces under non-cancelable operating leases. The lease agreements contain various clauses for renewal at the Company’s option and only certain exercised renewal options were included in the calculation of the operating lease assets and the operating lease liabilities, as other renewal options were not reasonably certain of being exercised as of March 31, 2025. The lease agreements do not contain residual value guarantees.

Lease costs for the three months ended March 31, 2025 and 2024 were as follows (in thousands):

The Company has not entered into any material short-term leases or financing leases as of March 31, 2025.

Supplemental cash flow information related to leases for the three months ended March 31, 2025 and 2024 was as follows (in thousands):


	Three Months Ended
	March 31,
	2025		2024
Cash paid for amounts included in the measurement of lease liabilities:	$	4,663	$	4,546
Lease liabilities arising from obtaining right-of-use assets:
Operating leases	$	—	$	—

The weighted average remaining lease term and weighted average discount rate of the operating leases are as follows:

16. Segment Information

The Company operates as one operating segment, focused on discovering, developing and delivering therapies for allergy/immunology and oncology/hematology. The determination of a single business segment is consistent with the consolidated financial information regularly provided to the Company’s chief operating decision maker (CODM). The Company’s CEO, as the CODM, uses consolidated, single-segment financial information for purposes of evaluating performance, making operating decisions, allocating resources, and planning and forecasting for future periods.

The CODM assesses performance and decides how to allocate resources based on consolidated net income (loss). This measure is used to monitor budget versus actual results to evaluate the performance of the segment.

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The CODM reviews cash, cash equivalents and marketable securities as a measure of segment assets. As of March 31, 2025 and December 31, 2024, the Company’s cash, cash equivalents and marketable securities were $899.8 million and $863.9 million, respectively.

The following tables illustrates information about segment revenue, significant segment expenses and segment operating loss for the three months ended March 31, 2025 and 2024 (in thousands):


	Three Months Ended
	March 31,
	2025		2024
Revenue	$	149,413	$	96,116
Less¹:
Cost of sales		2,802		3,191
Research and development expense²:
Compensation and related expenses		31,790		29,592
Early drug discovery and platform⁵		18,170		14,565
Facilities and IT⁵		12,977		10,580
Clinical and manufacturing related activities⁵		8,251		17,857
Consulting and professional services		7,446		4,294
Other		1,129		428
Total research and development expense²		79,763		77,316
Selling, general and administrative expense³:
Compensation and related expenses		33,852		33,116
Commercial and related expenses⁵		27,053		17,552
Consulting and professional services		9,869		14,500
Facilities and IT		4,834		2,779
Other⁵		3,270		2,260
Total selling, general and administrative expense³		78,878		70,207
Stock-based compensation		29,056		24,225
Other segment items⁴		41,582		167,959
Net income	$	496	$	89,136

The significant expense categories and amounts align with the segment-level information that is regularly provided to the chief operating decision maker.

Research and development expense for the three months ended March 31, 2025 and 2024 exclude $12.1 million and $10.9 million of stock-based compensation expense, respectively.

Selling, general and administrative expense for the three months ended March 31, 2025 and 2024 exclude $16.9 million and $13.4 million of stock-based compensation expense, respectively.

Other segment items include interest expense, net, other income, net, equity investment gain, debt extinguishment gain, and income tax expense.

Certain prior period items are recast to conform to the current period presentation.

The Company operates in the U.S. and Europe. All material long-lived assets of the Company reside in the U.S. For geographic information about the Company’s product revenues, see Note 6, Product Revenue and Related Reserves.

17. Commitments and Contingencies

Purchase Commitments Associated with Clinical and Commercial Supply Agreements

In connection with the commercialization of AYVAKIT/AYVAKYT, the Company has negotiated manufacturing agreements with certain vendors that require the Company to meet minimum purchase obligations on an annual basis. The aggregate amount of future unconditional purchase obligations under these manufacturing agreements over the period of next five years is approximately $2.0 million as of March 31, 2025.

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Legal Proceedings

In the normal course of business, the Company from time to time is named as a party to various legal claims, actions and complaints, which have included and may include matters involving securities, employment, intellectual property, arising from the use of therapeutics utilizing its technology, or others. The Company records a loss contingency reserve for a legal proceeding when it considers the potential loss probable and it can reasonably estimate the amount of the loss or determine a probable range of loss. The Company provides disclosure when it considers a loss reasonably possible or when it determines that a loss in excess of a reserve is reasonably possible. The Company provides an estimate of such reasonably possible losses or an aggregate range of such reasonably possible losses, unless the Company believes that such an estimate cannot be made. The Company expenses the costs related to its legal proceedings as they are incurred. As of March 31, 2025, the Company has not recorded any significant accruals for loss contingencies.

On June 7, 2024, a purported stockholder filed a putative class action lawsuit against the Company in the Court of Chancery of the State of Delaware, with the caption Johnson v. Blueprint Medicines Corporation, Case No. 2024-0625. Plaintiff claims in the complaint that a “Proxy Access” provision in the Company’s Amended and Restated Bylaws, effective November 30, 2022, is invalid under Delaware law because it allegedly usurps the right of stockholders to select the members of the board of directors, and plaintiff seeks declaratory relief invalidating that provision, as well as attorneys’ fees and costs. On October 7, 2024, the lawsuit was consolidated with twelve other lawsuits against companies with similar bylaw provisions, and a fourteenth lawsuit was consolidated on April 7, 2025, all under the caption In re Irrevocable Resignation Bylaw Litigation, Consolidated C.A. No. 2024-0538-JTL. On October 11, 2024, the Company, together with the other companies in the consolidated action, filed an opening brief in support of a motion to dismiss the complaint. Plaintiff filed an answering brief on November 25, 2024, and the Company filed a reply brief on December 20, 2024. The Company does not believe the outcome of this matter will have a material effect on its financial position, results of operations, or liquidity.

On November 22, 2024, a purported stockholder filed a putative class action lawsuit against the Company, the members of the board of directors and certain executive officers of the Company, as well as a derivative action against the members of the board of directors and certain executive officers of the Company, in the Court of Chancery of the State of Delaware in an action captioned Taylor v. Haviland, et al., C.A. No. 2024-1203-JTL (the Taylor Action). Plaintiff in the Taylor Action claimed that the record date for the Company’s 2024 annual meeting of stockholders, which was the close of business on Friday, April 12, 2024, did not comply with the 60-day maximum under Section 213(a) of the DGCL, because it was 61 days before the date of the 2024 annual meeting. Plaintiff brought direct claims for violation of Section 213(a) of the DGCL and breach of fiduciary duty, and derivative claims for breach of fiduciary duty and unjust enrichment, and sought a declaration that certain actions taken in connection with the Company’s annual meeting of stockholders were void, as well as attorneys’ fees and costs.

On December 2, 2024, the Company filed a petition pursuant to Section 205 of the DGCL seeking the validation of certain actions taken in connection with the Company’s 2024 annual meeting of stockholders, retroactive to the date of the 2024 annual meeting, in the Court of Chancery of the State of Delaware in an action captioned In re Blueprint Medicines Corporation, C.A. No. 2024-1234-JTL (the Section 205 Action). On December 4, 2024, plaintiff in the Taylor Action agreed to hold the defendants’ answer in abeyance pending resolution of the Section 205 Action. Following the Company’s brief in support of its petition in the Section 205 Action on December 20, 2024, and the lack of any objection, the Court granted the petition on January 23, 2025, such that the stockholder proposals that were presented to and approved by the Company’s stockholders at the 2024 annual meeting, and all actions taken in reliance on the stockholder votes at the annual meeting, were declared valid and effective as of the date of the 2024 annual meeting. As a result, on March 17, 2025, the Taylor Action was dismissed as moot, with the court retaining jurisdiction to determine plaintiff’s counsel’s application for an award of attorneys’ fees and reimbursement of expenses.

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Indemnification Agreements

In the ordinary course of business, the Company may provide indemnification of varying scope and terms to vendors, lessors, business partners, and other parties with respect to certain matters including, but not limited to, losses arising out of breach of such agreements or from intellectual property infringement claims made by third parties. In addition, the Company has entered into indemnification agreements with members of its board of directors and senior management that will require the Company, among other things, to indemnify them against certain liabilities that may arise by reason of their status or service as directors or officers of the Company. The maximum potential amount of future payments the Company could be required to make under these indemnification agreements is, in many cases, unlimited. To date, the Company has not incurred any material costs as a result of such indemnifications. The Company is not aware of any material claims under indemnification arrangements, and it has not accrued any liabilities related to such obligations in its condensed consolidated financial statements as of March 31, 2025 or December 31, 2024.

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

The following discussion and analysis of our financial condition and results of operations should be read in conjunction with our unaudited condensed consolidated financial statements and related notes appearing elsewhere in this Quarterly Report on Form 10-Q and the audited consolidated financial statements and related notes thereto 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, 2024, filed with the Securities and Exchange Commission (the SEC) on February 13, 2025. Some of the information contained in this discussion and analysis or set forth elsewhere in this Quarterly Report on Form 10-Q, including information with respect to our plans and strategy for our business, includes forward-looking statements that involve risks and uncertainties. As a result of many factors, including those factors set forth in the “Risk Factors” section of this Quarterly Report on Form 10-Q, our actual results or timing of certain events could differ materially from the results or timing described in, or implied by, these forward-looking statements.

Overview

We are a global, fully integrated biopharmaceutical company that invents life-changing medicines.  We seek to alleviate  human suffering by solving important medical problems in two core focus areas: allergy/inflammation and oncology/hematology. Our approach begins by targeting the root causes of disease, using deep scientific knowledge in our core focus areas and drug discovery expertise across multiple therapeutic modalities. We have a track record of success with two approved medicines, including AYVAKIT®/AYVAKYT® (avapritinib) which we are bringing to patients with systemic mastocytosis (SM) in the U.S. and Europe. Leveraging our established research, development, and commercial capability and infrastructure, we now aim to significantly scale our impact by advancing a broad pipeline of programs ranging from early science to advanced clinical trials in mast cell diseases including SM and chronic urticaria, breast cancer and other solid tumors.

Since 2011, we have advanced a drug discovery approach that combines evolving biological insights with our proprietary research platform and drug design capabilities, with a focus on small molecule inhibitors and target protein degraders. We aim to rapidly and reproducibly translate science into a potentially life-changing clinical benefit for broad populations of patients with significant medical needs. Our focused business model integrates our research engine with robust clinical development and commercial capabilities in allergy/inflammation and solid tumors to create a sustainable cycle of innovation.

Mast Cell-Mediated Diseases — AYVAKIT®/AYVAKYT® (avapritinib), Elenestinib (BLU-263), and BLU-808

Mast cells are core drivers of biology in a range of inflammatory diseases. KIT is a clinically validated mast cell target. The KIT receptor regulates growth, proliferation, and activation of mast cells – characterized by the release of inflammatory molecules like cytokines, histamine, tryptase, and heparin in a process called degranulation. KIT-mediated signaling plays a central role in survival, proliferation, and activation of mast cells. Under normal conditions, these molecules mediate the normal physiological response to an inflammatory stimulus – leading to symptoms like sneezing, swelling, itching, and gastrointestinal effects.

There are many disease states caused by increased activation of mast cells. In addition to diseases caused by a KIT receptor mutation, there are also diseases that may be treated by dialing down mast cell activation. For instance, in nearly all cases, SM is a disorder of mast cells driven by the KIT D816V mutation. Other mast cell disorders, including chronic urticaria, asthma and other skin, respiratory, and gastrointestinal disorders are characterized by generalized mast cell dysregulation, which has been shown to be modifiable with inhibition of wild-type KIT.

We continue to build a mast cell disease franchise, based on our deep understanding of mast cell biology and the KIT pathway. We are commercializing our first KIT D816V inhibitor, AYVAKIT/AYVAKYT globally for the treatment of advanced SM and indolent SM. We are developing elenestinib, or BLU-263, an investigational, orally available, potent and highly selective KIT D816V inhibitor, for the treatment of indolent SM. Additionally, we are advancing BLU-808, a potent and selective wild-type KIT inhibitor, for mast cell diseases, including chronic urticaria allergic rhinitis/allergic conjunctivitis, allergic asthma, and mast cell activation syndrome (MCAS). With AYVAKIT, we were able to demonstrate that successful inhibition of mutated KIT with a highly potent and specific molecule can result in the first and only approved disease modifying therapy for SM. Through AYVAKIT development, we have amassed considerable data on mast cell biology and a strong clinical understanding of disease areas connected to mast cell

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activation, which is helping to drive our efforts to extend our position in SM and expand into other mast cell disorders. We are doing this by leveraging our deep understanding of mast cell biology to drive scientific innovation, bringing that innovation to patients with our clinical and regulatory know-how, and driving compelling top-line revenue growth through commercial execution.

AYVAKIT/AYVAKYT (avapritinib)

We are commercializing avapritinib for the treatment of advanced SM and indolent SM. The FDA approved avapritinib under the brand name AYVAKIT for the treatment of adult patients with advanced SM, including ASM, SM-AHN, and MCL in June 2021, and for adult patients with indolent SM in May 2023. In March 2022, the European Commission approved the marketing authorization for AYVAKYT for the treatment of adult patients with ASM, SM-AHN, or MCL, after at least one systemic therapy. In December 2023, the European Commission approved AYVAKYT for the treatment of adult patients with indolent SM with moderate to severe symptoms inadequately controlled on symptomatic treatment. These approvals in advanced SM were supported by our Phase 1 clinical trial in advanced SM, which we refer to as our EXPLORER trial, and our ongoing registrational clinical trial in advanced SM, which we refer to as our PATHFINDER trial. The approvals of AYVAKIT for the treatment of patients with indolent SM were supported by data from our ongoing Phase 2/3 clinical trial in indolent SM, which we refer to as the PIONEER trial. At the European Academy of Allergy and Clinical Immunology (EAACI) Congress 2024, we presented long-term data from PIONEER, demonstrating that with a median follow-up of more than two years, AYVAKIT showed durable efficacy and a favorable safety profile in patients with indolent SM, and that safety data were consistent for the small number of patients whose doses escalated to 50 mg once daily.

The FDA has granted breakthrough therapy designation to avapritinib for (i) the treatment of advanced SM, including the subtypes of ASM, SM-AHN and MCL and (ii) the treatment of moderate to severe indolent SM. In addition, the FDA has granted orphan drug designation to avapritinib for the treatment of mastocytosis, and the European Commission has granted orphan medicinal product designation to avapritinib for the treatment of mastocytosis.

Avapritinib is also approved in the U.S. under the brand name AYVAKIT for the treatment of adults with unresectable or metastatic GIST harboring a PDGFRA exon 18 mutation, including PDGFRA D842V mutations, and is approved in the EU, the UK and Switzerland with conditional marketing authorization under the brand name AYVAKYT as a monotherapy for the treatment of adult patients with unresectable or metastatic GIST harboring a PDGFRA D842V mutation. Currently, AYVAKIT is the only FDA-approved treatment for patients with D842V mutant PDGFRA-driven GIST. Through our collaboration with CStone, China’s National Medicinal Products Administration approved AYVAKIT for the treatment of adults with unresectable or metastatic GIST harboring a PDGFRA exon 18 mutation, including PDGFRA D842V mutations. AYVAKIT also received accelerated approval from the Taiwan Food and Drug Administration and approval in Hong Kong, both for adults with unresectable or metastatic GIST harboring PDGFRA D842V mutations. We also have distributor arrangements to commercialize AYVAKIT in global jurisdictions, including Israel and Canada, where approvals have been received. To date, AYVAKIT/AYVAKYT is approved and reimbursed for one or more indications in 16 countries, where we or our distribution partners are commercializing it. The FDA has granted breakthrough therapy designation for avapritinib for the treatment of unresectable or metastatic GIST harboring the PDGFRA D842V mutation. In addition, the FDA has granted orphan drug designation to avapritinib for the treatment of GIST, and the European Commission has granted orphan medicinal product designation to avapritinib for the treatment of GIST.

Elenestinib (BLU-263)

We are developing elenestinib an investigational, orally available, potent and highly selective KIT inhibitor, for the treatment of indolent SM and other mast cell disorders. Elenestinib is designed to have equivalent potency as avapritinib, with low off-target activity and minimal penetration of the central nervous system relative to avapritinib based on preclinical data.

We are evaluating elenestinib in an ongoing Phase 2/3 clinical trial in indolent SM, which we refer to as our HARBOR trial. In December 2022, we announced top-line, 12-week data from the dose-finding Part 1 of the HARBOR trial. In December 2023, we presented HARBOR Part 1 trial data for elenestinib in indolent SM at the 65th American

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Society of Hematology (ASH) Annual Meeting and Exposition. We initiated the registration-enabling Phase 3 HARBOR trial of elenestinib in indolent SM in the fourth quarter of 2024.

BLU-808

In the first half of 2023, we nominated the development candidate BLU-808 from our discovery programs, an oral, highly potent and selective wild-type KIT inhibitor. We are developing BLU-808 as a potential first- and best-in-class treatment for mast cell disorders, including chronic urticaria, a debilitating inflammatory skin disorder characterized by wheals (hives), and sleep disruption, stress and anxiety due to severe itching are major contributors to disease burden. Wild-type KIT inhibition has an established proof-of-concept in chronic urticaria, and BLU-808 represents a small molecule approach with the opportunity to drive market expansion with an oral regimen. Beyond chronic urticaria, we plan to initiate proof of concept studies in other related allergic-inflammatory indications, including but not limited to allergic rhinitis/allergic conjunctivitis, allergic asthma, and MCAS.

In February 2024, at the AAAAI Annual Meeting, we presented the preclinical attributes of BLU-808 that demonstrate its potency, selectivity, low potential for drug-drug interactions, and peripheral restriction. BLU-808 treatment led to dose-dependent inhibition and depletion of mast cells in multiple in vivo studies, and also improved lung function in an ovalbumin-induced asthma model. In June 2024, we submitted an Investigational New Drug (IND) application to FDA for BLU-808. We received FDA clearance to proceed with a Phase 1 study in healthy volunteers and initiated that study in the third quarter of 2024. In January 2025, we reported results from this study, showing a differentiated profile that enables the evaluation of tunable dosing strategies. BLU-808 was well-tolerated at all doses tested, showed consistent pharmacokinetics supporting once daily oral dosing, and achieved dose-dependent reductions in tryptase exceeding 80 percent. In the second quarter of 2025, we initiated the Phase 2a proof of concept study in allergic rhinoconjunctivitis. This is a randomized, double blind placebo-controlled challenge study designed to measure the safety, pharmacokinetic (PK), and clinical efficacy of multiple doses of BLU-808. We also initiated the Phase 2a proof of concept study in chronic urticaria. This study comprises an open-label portion in chronic inducible urticaria and a randomized, double blind portion in chronic spontaneous urticaria. Both portions will evaluate the safety, PK and clinical efficacy of multiple doses of BLU-808.

Oncology/Hematology

Our oncology research program has delivered a number of innovative therapies and continues to be an active area of discovery. Based on early clinical success, we plan to further advance discovery research in oncology in 2025.

Cell Cycle Inhibition Programs

We are advancing multiple therapeutic candidates and research programs targeting the cell cycle as potential treatments for patients with hormone-receptor-positive/human epidermal growth receptor 2 negative (HR+/HER2-) breast cancer and other solid tumors. These include CDK2 and CDK4 targeted protein degraders, which have progressed rapidly in preclinical development toward potentially best-in-class development candidate profiles supporting our prioritization of these programs. We are completing the Phase 1 dose escalation study of our CDK2 inhibitor BLU-222 and are de-prioritizing any further investment in this program. We continue to engage strategic partners on potential opportunities to broadly advance our franchise of CDK programs.

Discovery Platform

We continue to drive organic growth with our innovative and highly productive research platform, which has nominated 17 development candidates to date. With drug design capabilities spanning small molecule inhibitors and targeted protein degraders, our approach begins by choosing the best modality for the targets we are pursuing and designing highly potent and selective therapeutic candidates. Within our focus areas of allergy/inflammation and oncology/hematology, we pursue targets where the biology is clear and there is opportunity to impact large patient populations. We consistently aim to achieve first- or best-in-class profiles with the potential to disrupt the current standard of care and dramatically improve patient outcomes. In addition, we prioritize opportunities where early data can de-risk future investment and we deeply integrate the insights and capabilities of our R&D and commercial functions to create significant and sustainable growth opportunities.

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Collaborations, Licenses and Other Agreements Summary

Roche—Pralsetinib Collaboration. In July 2020, we entered into a collaboration agreement with Roche, which we refer to as the Roche pralsetinib collaboration, to develop and commercialize pralsetinib for the treatment of RET-altered cancers. Under the Roche pralsetinib collaboration, we and Genentech co-commercialized GAVRETO in the U.S., and Roche was granted exclusive commercialization rights for pralsetinib outside of the U.S., excluding Mainland China, Hong Kong, Macau and Taiwan (each a CStone region and, collectively, the CStone Territory). In February 2023, we received written notice from Roche of their election to terminate for convenience the Roche pralsetinib collaboration agreement. The termination became effective on February 22, 2024, at which time we entered into a transition agreement with Roche (the Roche transition agreement) and sold the U.S. rights to research, develop, manufacture and commercialize pralsetinib to Rigel Pharmaceuticals (Rigel). In January 2024, we decided to discontinue global development and marketing of GAVRETO in territories excluding the U.S. and CStone Territory, due to a lack of an alternate partner in these regions. We continue to work with Roche on the transition and wind-down activities contemplated in the Roche transition agreement.

CStone. In June 2018, we entered into a collaboration with CStone to develop and commercialize avapritinib, pralsetinib and fisogatinib, as well as any back-up and other forms thereof, in the CStone Territory either as a monotherapy or as part of a combination therapy.

Clementia. In October 2019, we entered into a license agreement with Clementia, which we refer to as the Clementia license agreement. Pursuant to the Clementia license agreement, we granted Clementia an exclusive, worldwide, royalty-bearing license to develop and commercialize BLU-782, as well as specified other compounds related to the BLU-782 program. BLU-782 is an investigational, orally available, potent and highly selective inhibitor that targets mutant activin-like kinase 2 (ALK2) in development for the treatment of fibrodysplasia ossificans progressiva (FOP). The FDA has granted a rare pediatric disease designation, orphan drug designation and fast track designation to BLU-782, each for the treatment of FOP. Clementia has an ongoing Phase 2 clinical trial of BLU-782, now referred to as fidrisertib.

Zai Lab. In November 2021, we entered into a license and collaboration agreement with Zai Lab, which we refer to as the Zai Lab agreement, to develop and commercialize certain licensed products for the treatment of EGFR-driven NSCLC in Greater China, including Mainland China, Hong Kong, Macau and Taiwan, which currently includes BLU-945 and BLU-525. In January 2024 at the J.P. Morgan Healthcare Conference, we announced that we are discontinuing further investment in early clinical-stage therapies for EGFR-mutant NSCLC globally; however, Zai Lab retains its rights to BLU-945 and BLU-525 under the Zai Lab agreement.

IDRx. In August 2022, we entered into a license agreement with IDRx, Inc. (IDRx), which we refer to as the IDRx License Agreement. Pursuant to the IDRx License Agreement, we granted IDRx an exclusive, worldwide, royalty-bearing license to exploit our internally discovered development candidate-stage KIT exon 13 inhibitor, IDRX-73.

In connection with the IDRx License Agreement, we also entered into a stock purchase agreement with IDRx, which we refer to as the IDRx Stock Purchase Agreement, pursuant to which we received 4,509,105 shares of IDRx’s Series A preferred stock. In July 2023, we received an additional 192,282 shares of Series A preferred stock pursuant to the anti-dilution provision in the IDRx Stock Purchase Agreement and as of December 31, 2024, we owned a total of 4,701,387 shares of IDRx’s Series A preferred stock. In the first quarter of 2025, IDRx was acquired by GSK plc (GSK) for an upfront cash consideration of $1.0 billion with an additional $150.0 million contingent consideration, and we received $78.7 million for our shares in IDRx. We continue to be eligible to receive cash payments under the license agreement with IDRx.

For additional information, see Note 10, Collaborations, License and Other Agreements, to our unaudited condensed consolidated financial statements.

Financing Arrangements Summary

Royalty Purchase Agreement. In June 2022, we entered into a purchase and sale agreement with Royalty Pharma, which we refer to as the Royalty Purchase Agreement. Pursuant to the Royalty Purchase Agreement, we received an upfront cash payment of $175.0 million in exchange for all of our existing rights to receive royalty payments

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on the net sales of GAVRETO worldwide, excluding the CStone Territory and U.S. territory under the terms of the Roche pralsetinib collaboration agreement. However, in February 2023, we received written notice from Roche of their election to terminate for convenience the Roche pralsetinib collaboration agreement. The termination became effective in February 2024. In connection with and effective upon the termination of the Roche pralsetinib collaboration agreement, on February 22, 2024, we and Royalty Pharma agreed to terminate the Royalty Purchase Agreement, which we refer to as the Royalty Pharma Termination Agreement. Following the termination of the Royalty Purchase Agreement, we have no outstanding obligations under the Royalty Purchase Agreement, other than the remaining royalty payment obligation related to GAVRETO net sales as of the termination effective date, which has since been paid. As of March 31, 2025, we have no plans to enter into a new arrangement to commercialize GAVRETO outside of the U.S. and the CStone Territory. As of March 31, 2025, we had paid off the final royalty amount related to the Royalty Pharma Termination Agreement.

Synthetic Royalty Facility. In June 2022, we entered into a purchase and sale agreement with Sixth Street Partners, which we refer to as the Future Revenue Purchase Agreement. In July 2022, upon the closing of the transaction pursuant to the Future Revenue Purchase Agreement, we received gross proceeds of $250.0 million in exchange for future royalty payments at a rate of 9.75% on up to $900 million each year of (i) aggregate worldwide annual net product sales of AYVAKIT/AYVAKYT and (ii) if it is approved, aggregate worldwide annual net product sales of elenestinib, excluding sales in Greater China, subject to a cumulative cap of 1.45 times the upfront invested capital or a total of $362.5 million. In the event that certain revenue targets are not achieved by specified dates, the royalty rate and cumulative cap shall be increased to 15% and 1.85 times the invested capital (or $462.5 million), respectively.

Debt Facility. In June 2022, we entered into a financing agreement for up to $660.0 million with Sixth Street Partners, which we refer to as the Financing Agreement. The Financing Agreement, as amended, provides for (i) a senior secured term loan facility of up to $150.0 million and (ii) a senior secured delayed draw term loan facility of up to $250.0 million to be funded in two tranches at our choice, subject to certain terms and conditions. The loans will mature on June 30, 2028 and bear interest at a variable rate equal to either the Secured Overnight Financing Rate (SOFR) plus 6.50% or the base rate plus 5.50%, subject to a floor of 1% and 2% with respect to the SOFR and base rate, respectively. The initial gross proceeds of $150.0 million was funded in July 2022. In August 2023, we received the first tranche of the senior secured delayed draw term loan facility in the amount of $100.0 million in gross proceeds and in May 2024, we received the second tranche in the amount of $150.0 million in gross proceeds. In addition, we may at any time request an incremental term loan in an amount not to exceed $260.0 million on terms to be agreed and subject to the consent of the lenders providing such incremental term loan.

For additional information, see Note 3, Financing Arrangements, to our unaudited condensed consolidated financial statements.

Financial Operations Overview

To date, we have financed our operations primarily through public offerings of our common stock, private placements of our convertible preferred and common stock, collaboration, license and other agreements, future royalty and revenue monetization, and a term loan. Through March 31, 2025, we have received an aggregate of $4.0 billion from such transactions, including $1.9 billion in aggregate gross proceeds from the sale of common stock in our initial public offering (IPO), follow-on public offerings, through our “at the market” stock offering program and the equity investment by Roche, $115.1 million in gross proceeds from the issuance of convertible preferred stock, $175.0 million in gross proceeds from our Royalty Purchase Agreement with Royalty Pharma, $250.0 million in gross proceeds from our Future Revenue Purchase Agreement with Sixth Street Partners, $1.1 billion in upfront and milestone payments under our collaborations with CStone and Zai Lab, our now terminated collaborations with Roche, our license agreement with Clementia, our agreement with Rigel and our former collaboration with Alexion Pharma Holding (Alexion), $400.0 million in gross proceeds from a term loan from Sixth Street Partners, and $78.7 million in net proceeds received related to the sale of our equity investment in IDRx. In addition, since January 2020, we have also generated meaningful revenue through the sales of our approved drug products.

Since inception, we have incurred significant operating losses. Our net income was $0.5 million for the three months ended March 31, 2025 primarily due to the $50.0 million equity investment gain recognized upon sale of our equity investment in IDRx. Our net losses were $67.1 million and $507.0 million for the years ended December 31, 2024 and 2023, respectively. As of March 31, 2025, we had an accumulated deficit of $2,406.5 million. We expect to continue

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to incur significant expenses over the next few years, with anticipated variability in these expenses due to our ongoing activities, particularly as we:

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maintain and expand our sales, marketing and distribution infrastructure to continue to commercialize avapritinib and any current or future drug candidates for which we may obtain marketing approval;

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seek marketing approval for avapritinib in additional geographies;

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initiate or advance clinical development activities for other current or future drug candidates as monotherapies or in combination with other agents;

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continue to discover, validate and develop additional drug candidates or development candidates, including elenestinib (BLU-263) and BLU-808;

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continue to manufacture increasing quantities of drug substance and drug product material for use in preclinical studies, clinical trials and commercialization; and to purchase quantities of other agents for use in our clinical trials as we develop our drugs and drug candidates either as potential combination therapies or for use as comparator agents;

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conduct research and development activities under current or future collaborations;

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maintain, expand and protect our intellectual property portfolio;

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acquire or in-license additional businesses, technologies, drugs or drug candidates, form strategic alliances or create joint ventures with third parties; and

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hire additional research, clinical, quality, manufacturing, regulatory, commercial and general and administrative personnel.

In addition, the U.S. and other countries have recently imposed, and may continue to impose, new tariffs. While pharmaceuticals are largely exempt from the recently imposed U.S. tariffs, such exemptions may be terminated or may not apply to any future tariffs. Additionally, pharmaceuticals are not exempt from certain tariffs recently imposed outside of the U.S. We continue to evaluate the impacts of tariffs on our business and results of operations. Based on current information, we do not believe the impact of tariffs on our business, financial condition or results of operations will be material.

Revenue

In January 2020, the FDA granted approval of avapritinib under the brand name AYVAKIT for the treatment of adults with unresectable or metastatic GIST harboring a PDGFRA exon 18 mutation, including PDGFRA D842V mutations. In September 2020, the European Commission granted conditional marketing authorization for avapritinib under the brand name AYVAKYT as a monotherapy for the treatment of adult patients with unresectable or metastatic GIST harboring the PDGFRA D842V mutation. In June 2021, the FDA granted a subsequent approval for AYVAKIT, expanding the labeled indications to include adult patients with advanced SM. In March 2022, the European Commission expanded the marketing authorization for AYVAKYT to include the treatment of adult patients with ASM, SM-AHN, or MCL, after at least one systemic therapy. In May 2023, the FDA approved AYVAKIT for the treatment of adult patients with indolent SM and in December 2023, the European Commission approved AYVAKYT for the treatment of adult patients with indolent SM with moderate to severe symptoms inadequately controlled on symptomatic treatment.

For the three months ended March 31, 2025, our revenue primarily consisted of product sales of AYVAKIT/AYVAKYT. In the future, we expect to generate revenue from a combination of sources, including sales of our current drug product and any current or future drug candidates for which we receive marketing approval, royalties on drug sales, upfront, milestone, profit sharing and other payments, if any, under any current or future collaboration, license and other agreements, including revenues related to the supply of our drug candidates or approved drugs to our

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various collaboration partners. We anticipate variability in revenue in the future as a result of the timing and amount of product sales, license fees, manufacturing services, and achievement of milestones or other payments under our collaboration, license or other agreements, if any.

In 2025, we anticipate a robust increase in net product revenues compared to 2024, as we continue to add new patients onto AYVAKIT/AYVAKYT, including those with indolent SM and advanced SM.

Cost of Sales

Our cost of sales includes the cost of producing and distributing inventories that are related to product revenue as well as the sales of drug substance and drug product to our collaboration partners during the respective period, including salary related expenses and stock-based compensation expense for employees involved with production, distribution, freight, and indirect overhead costs as well as amounts written down as a result of excess, obsolescence, unmarketability or other reasons. In addition, shipping and handling costs for product shipments are recorded in cost of sales as incurred.

We estimate our costs of goods sold related to product sales to be within the low to mid-single digit percentage range. Cost of goods sold related to sales of drug products to our collaboration partners are at lower margins.

Expenses

Research and Development Expenses

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

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

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expenses incurred under agreements with third parties that conduct research and development, preclinical activities, clinical activities and manufacturing on our behalf;

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expenses incurred in connection with research and development activities under our collaboration with VantAI and development activities under our now terminated collaboration for pralsetinib with Roche;

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the cost of consultants in connection with our research and development activities;

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the cost associated with regulatory quality assurance and quality control operations;

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the cost of lab supplies and acquiring, developing and manufacturing preclinical study materials, clinical trial materials and pre-validated commercial supply materials; and

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facilities, depreciation, and other expenses, which include direct and allocated lease, information technology and maintenance of facilities expenses, insurance, and other operating costs in support of research and development activities.

Research and development costs are expensed as incurred. Costs for certain activities are recognized based on an evaluation of the progress to completion of specific tasks. Nonrefundable advance payments for goods or services to be received in the future for use in research and development activities are capitalized. The capitalized amounts are expensed as the related goods are delivered or the services are performed.

The successful development of our drug 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 remainder of the development of these drug candidates. We are also unable to predict when material net cash inflows

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will commence from the sale of our current or future drug candidates for which we received marketing approval. This is due to the numerous risks and uncertainties associated with developing drugs, including the uncertainty of:

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establishing an appropriate safety profile with IND-enabling toxicology studies;

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successful initiation, enrollment in, and completion of clinical trials;

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receipt of marketing approvals from applicable regulatory authorities;

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establishing manufacturing capabilities or making arrangements with third-party manufacturers to ensure adequate clinical and commercial supply;

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

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commercializing our drug candidates, if and when approved, whether alone or in collaboration with others;

●

market acceptance of AYVAKIT/AYVAKYT and any future drug we may commercialize; and

●

continued acceptable safety profile of the drugs following approval.

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

Research and development activities are central to our business model. Drug 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.

A significant portion of our research and development expenses have been external expenses, which we track on a program-by-program basis following nomination as a development candidate. Our internal research and development expenses are primarily personnel-related expenses, including stock-based compensation expense. Except for internal research and development expenses related to collaboration agreements, we do not allocate our internal research and development expenses to specific drug candidate programs as they are deployed across multiple projects under development.

The following table summarizes our research and development expenses by principal program for the three months ended March 31, 2025 and 2024 (in thousands). Other development and pre-development candidate expenses, unallocated expenses and internal research and development expenses have been classified separately.


	Three Months Ended March 31,
	2025		2024		Dollar change		% Change
Avapritinib external expenses	$	952	$	4,487	$	(3,535)	(79)	%
Elenestinib external expenses		7,303		3,544		3,759	106
BLU-222 external expenses		1,914		6,479		(4,565)	(70)
BLU-808 external expenses		11,333		3,179		8,154	256
Other development and pre-development candidate expenses and unallocated expenses*		27,567		30,838		(3,271)	(11)
Internal research and development expenses		42,821		39,664		3,157	8
Total research and development expenses	$	91,890	$	88,191	$	3,699	4	%

Certain prior period items have been reclassified to conform to the current presentation.

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We expect increases in our research and development expenses in future periods as our drug candidate development programs progress. The costs related to the implementation and expansion of clinical trial sites and related patient enrollment, monitoring, program management and manufacturing expenses for active pharmaceutical ingredient (API), drug product and drug substance for current and future clinical trials will vary depending on clinical data results and our resource allocation priorities. In addition, our research and development expenses may increase with potential new collaborations and future acquisitions. We do not believe that it is possible at this time to accurately project total program-specific expenses through commercialization. There are numerous factors associated with the successful commercialization of any of our approved drugs or drug candidates for which we may receive marketing approval, including future trial design and various regulatory requirements, many of which cannot be determined with accuracy at this time based on our stage of development. In addition, future commercial and regulatory factors beyond our control will impact our clinical development programs and plans.

In 2025, we anticipate a modest increase in our research and development expenses compared to 2024. This is due to increased investment in our priority programs to advance the associated clinical trials, in contrast to our focused approach towards optimizing operational efficiency across our portfolio in 2024.

Selling, General and Administrative Expenses

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

We expect that our selling, general and administrative expenses will continue to increase in the future to support additional research and development activities and commercialization activities, including expanding our sales, marketing and distribution infrastructure to commercialize any drugs for which we may obtain marketing approval for additional indications or in additional geographies and expanding our operations globally. These increases will likely include increased costs related to the hiring of additional personnel, legal, auditing and filing fees and general compliance and consulting expenses, among other expenses. We have incurred and will continue to incur additional expenses associated with operating as a public company and expanding the scope of our operations.

In 2025, we anticipate a modest increase in selling, general, and administrative expenses compared to 2024. This increase is driven by our enhanced efforts to expand our global commercial and compliance infrastructure to support the commercialization of AYVAKIT/AYVAKYT.

Interest Expense, net

Interest expense, net consists primarily of interest expense related to our financing arrangements with Sixth Street Partners. Interest expense on liabilities related to the sale of future revenues consists of the periodic interest calculated using the effective interest rate method over the future estimated royalty payments due to Sixth Street Partners over the life of the Future Revenue Purchase Agreement. Interest expense on the term loan with Sixth Street Partners results from the amortization of the debt liability using the effective interest method over the maturity of the term loan. We anticipate variability in interest expense from period to period as a result of the timing and amount of the sales of the underlying products and the changes in interest rates. For additional information, see Note 3, Financing Arrangements, to our unaudited condensed consolidated financial statements.

Interest expense, net also includes income earned on cash equivalents and marketable securities. Our interest income may fluctuate depending on the movement of interest rates and our total amount of cash equivalents and marketable securities.

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Other Income, net

Other income, net, consists of miscellaneous income and expenses unrelated to our core operations, including the impacts of foreign currency exchange differences.

Equity Investment Gain

Equity investment gain consists of the net gain recognized upon the sale of our equity investment in IDRx following its acquisition by GSK. For additional information, see Note 10, Collaboration, License and Other Agreements, to our unaudited condensed consolidated financial statements.

Debt Extinguishment Gain

Debt extinguishment gain consists of the gain recognized as a result of the Royalty Pharma Termination Agreement entered into on February 22, 2024. For additional information, see Note 3, Financing Arrangements, to our unaudited condensed consolidated financial statements.

Income Tax Expense

Income tax expense consists of U.S. federal, state and foreign income taxes incurred.

Critical Accounting Policies and Estimates

For a description of our critical accounting policies and estimates, please see “Management’s Discussion and Analysis of Financial Condition and Results of Operations—Financial Operations Overview—Critical Accounting Policies and Estimates” in our Annual Report on Form 10-K for the year ended December 31, 2024. There have been no significant changes to our critical accounting policies and estimates since December 31, 2024.

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Results of Operations

Comparison of Three Months Ended March 31, 2025 and 2024

The following table summarizes our results of operations for the three months ended March 31, 2025 and 2024, together with the changes in those items in dollars and as a percentage (in thousands):


	Three Months Ended March 31,
	2025		2024		Dollar Change		% Change
Total revenues	$	149,413	$	96,116	$	53,297	55	%
Total cost and operating expenses		190,499		174,939		15,560	9
Total other income, net		42,371		168,139		(125,768)	(75)
Income before income taxes		1,285		89,316		(88,031)	(99)
Income tax expense		789		180		609	338
Net income	$	496	$	89,136	$	(88,640)	(99)	%

Total Revenues

Total revenues consist of the following during the three months ended March 31, 2025 and 2024 (in thousands):


	Three Months Ended March 31,
	2025		2024		Dollar Change		% Change
Product revenue, net	$	149,413	$	92,525	$	56,888	61	%
Collaboration, license and other revenue		—		3,591		(3,591)	(100)
Total revenues	$	149,413	$	96,116	$	53,297	55	%

Product Revenue, Net

The following table summarizes revenue recognized from sales of AYVAKIT/AYVAKYT during the three months ended March 31, 2025 and 2024 (in thousands):


	Three Months Ended March 31,
	2025		2024		Dollar Change		% Change
United States	$	129,446	$	83,136	$	46,310	56	%
Rest of World		19,967		9,389		10,578	113
Total	$	149,413	$	92,525	$	56,888	61	%

Product revenue, net increased during the three months ended March 31, 2025 as compared to the three months ended March 31, 2024, primarily driven by growth in the number of indolent SM and advanced SM patients on therapy.

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Collaboration, License and Other Revenue

The following table summarizes the revenue recognized from our collaboration, license and other agreements during the three months ended March 31, 2025 and 2024 (in thousands):


	Three Months Ended March 31,
	2025		2024		Dollar change		% Change
Collaboration, license and other revenue	$	—	$	3,591	$	(3,591)	(100)	%

Revenue recognized from our collaboration, license and other agreements decreased during the three months ended March 31, 2025 as compared to the three months ended March 31, 2024. The decrease was primarily due to a decrease in manufacturing services and royalty revenue related to CStone Territory-specific activities, as well as a decrease in profit sharing on Roche sales of GAVRETO in the U.S. following the termination of Roche pralsetinib collaboration agreement which became effective in February 2024.

Cost of Sales

The following table summarizes the cost of sales during the three months ended March 31, 2025 and 2024 (in thousands):

Three Months Ended March 31,

2025

2024

Dollar change

% Change

Cost of product sales

2,747

Three Months Ended March 31,

Proceeds from maturities of debt securities

Blueprint Medicines Corp 10-Q