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 September 30, 2025


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

For the transition period from ____________ to ____________

Commission File Number: 001-40522

Monte Rosa Therapeutics, Inc.

(Exact name of registrant as specified in its charter)


Delaware	84-3766197
(State or other jurisdiction of incorporation or organization)	(I.R.S. Employer Identification No.)

321 Harrison Avenue, Suite 900 Boston, Massachusetts	02118
(Address of principal executive offices)	(Zip Code)

Registrant’s telephone number, including area code: (617) 949-2643

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 $0.0001 per share

GLUE

The Nasdaq Global Select Market

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

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

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


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

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

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

As of October 31, 2025, the registrant had 65,117,761 shares of common stock, $0.0001 per share, outstanding.

Special note regarding forward-looking statements

This Quarterly Report on Form 10-Q, or Quarterly Report, contains forward-looking statements which are made pursuant to the safe harbor provisions of Section 27A of the Securities Act of 1933, as amended, or the or the Securities Act, and Section 21E of the Securities Exchange Act of 1934, as amended, or the Exchange Act. All statements other than statements of historical facts contained in this Quarterly Report are forward-looking statements. In some cases, you can identify forward-looking statements by terminology such as “may”, “will”, “should”, “expects”, “intends”, “plans”, “anticipates”, “believes”, “estimates”, “predicts”, “potential”, “continue” or the negative of these terms or other comparable terminology. These statements are not guarantees of future results or performance and involve substantial risks and uncertainties. Forward-looking statements in this Quarterly Report include, but are not limited to, statements about:

•

the initiation, timing, progress, results, costs, and any expectations and/or predictions of success of our current and future research and development programs and preclinical studies, including our expectations for our molecular glue degraders, or MGDs, molecules, including our GSPT1-directed MGD MRT-2359, VAV1-directed MGD MRT-6160 and NEK7-directed MGDs, including MRT-8102, and our CDK2 and CCNE1 MGDs;

•

the initiation, timing, progress, results, costs, and any expectations and/or predictions of success of our current and any future clinical trials, including our clinical trials for our GSPT1-directed MGD MRT-2359, VAV1-directed MGD MRT-6160 and NEK7 directed MGD MRT-8102, including statements regarding the nature of or the timing for when any results of any clinical trials will become available;

•

our ability to continue to develop our proprietary discovery engine, called QuEENTM, and to expand our proteomics and translational medicine capabilities;

•

the potential advantages of our discovery engine technology and product candidates;

•

the extent to which our scientific approach and discovery engine technology may target proteins that have been considered undruggable or inadequately drugged;

•

our plans to submit Investigational New Drug, or IND applications to the U.S. Food and Drug Administration, or the FDA for current and future product candidates;

•

the potential benefits of strategic collaborations and our ability to enter into strategic collaborations with third parties who have the expertise to enable us to further develop our biological targets, product candidates and discovery engine technologies, including our agreements with Novartis AG, or Novartis, for MRT-6160 and other discovery programs and our agreement with F. Hoffmann-La Roche Ltd., or Roche Basel, and Hoffmann-La Roche Inc., or Roche US, and together with Roche Basel referred herein as Roche;

•

our ability to obtain and maintain regulatory approval of our product candidates;

•

our ability to maintain and expand, including through third-party vendors, our library of MGDs;

•

our ability to manufacture, including through third-party manufacturers, our product candidates for preclinical use, future clinical trials and commercial use, if approved;

•

our ability to commercialize our product candidates, including our ability to establish sales, marketing and distribution capabilities for our product candidates;

•

the rate and degree of market acceptance of our product candidates;

•

the size and growth potential of the markets for our product candidates, and our ability to serve those markets;

•

our ability to establish and maintain intellectual property rights covering our current and future product candidates and technologies;

•

the implementation of our business model and strategic plans for our business, product candidates, and technology;

•

estimates of our future expenses, revenues, capital requirements, and our needs for additional financing;

•

our expected use of proceeds from sales of our common stock in "at-the-market" offerings and other offerings, and the period over which such proceeds, together with existing cash, will be sufficient to meet our operating needs;

•

our ability to obtain funding for our operations necessary to complete further development and commercialization of our product candidates;

•

our financial performance;

•

developments in laws and regulations in the United States, or the U.S., and foreign countries;

•

the success of competing therapies that are or may become available;

•

our ability to attract and retain key scientific or management personnel;

•

the effect of global economic uncertainty and financial market volatility caused by economic effects of rising inflation and interest rates, global health crises, geopolitical events, elections, changes in international trade relationships and military conflicts on any of the foregoing or other aspects of our business or operations;

•

the effect of any geopolitical conflicts or new or increased international tariffs, including mitigation efforts and economic effects, on any of the foregoing or other aspects of our business operations, including but not limited to our preclinical studies, ongoing clinical trials and future clinical trials; and

•

other risks and uncertainties, including those listed under the section entitled “Risk factors" and those included in "Part 1, Item 1A, Risk Factors" in our Annual Report on Form 10-K for the year ended December 31, 2024, or our 2024 Annual Report, filed with the Securities and Exchange Commission, or the SEC, on March 20, 2025.

Any forward-looking statements in this Quarterly Report reflect our current views with respect to future events and with respect to our future financial performance, and involve known and unknown risks, uncertainties and other 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. Factors that may cause actual results to differ materially from current expectations include, among other things, those described under Part II, Item 1A, “Risk Factors” and elsewhere in this Quarterly Report. Given these uncertainties, you should not place undue reliance on these forward-looking statements.

All of our forward-looking statements are as of the date of this Quarterly Report only. In each case, actual results may differ materially from such forward-looking information. We can give no assurance that such expectations or forward-looking statements will prove to be correct. An occurrence of or any material adverse change in one or more of the risk factors or risks and uncertainties referred to in this Quarterly Report or included in our other public disclosures or our other periodic reports or other documents or filings filed with or furnished to the SEC could materially and adversely affect our business, prospects, financial condition and results of operations. Except as required by law, we do not undertake or plan to update or revise any such forward-looking statements to reflect actual results, changes in plans, assumptions, estimates or projections or other circumstances affecting such forward-looking statements occurring after the date of this Quarterly Report, even if new information becomes available in the future or if such results, changes or circumstances make it clear that any forward-looking information will not be realized. Any public statements or disclosures by us following this Quarterly Report that modify or impact any of the forward-looking statements contained in this Quarterly Report will be deemed to modify or supersede such statements in this Quarterly Report.

We may from time to time provide estimates, projections and other information concerning our industry, the general business environment, and the markets for certain diseases, including estimates regarding the potential size of those markets and the estimated 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, circumstances or numbers, including actual disease prevalence rates and market size, may differ materially from the information reflected in this Quarterly Report. Unless otherwise expressly stated, we obtained this industry, business information, market data, prevalence information 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, in some cases applying our own assumptions and analysis that may, in the future, prove not to have been accurate.

TRADEMARKS

Solely for convenience, our trademarks and trade names in this report are sometimes referred to without the ® and ™ symbols, but such references should not be construed as any indicator that we will not assert, to the fullest extent under applicable law, our rights thereto.

Table of Contents


		Page
PART I.	FINANCIAL INFORMATION	1
Item 1.	Financial Statements (Unaudited)	1
	Condensed Consolidated Balance Sheets (Unaudited)	1
	Condensed Consolidated Statements of Operations and Comprehensive (Loss) Income (Unaudited)	2
	Condensed Consolidated Statements of Stockholders’ Equity (Unaudited)	3
	Condensed Consolidated Statements of Cash Flows (Unaudited)	5
	Notes to the Condensed Consolidated Financial Statements (Unaudited)	6
Item 2.	Management’s Discussion and Analysis of Financial Condition and Results of Operations	19
Item 3.	Quantitative and Qualitative Disclosures About Market Risk	30
Item 4.	Controls and Procedures	30

PART II.	OTHER INFORMATION	31
Item 1.	Legal Proceedings	31
Item 1A.	Risk Factors	31
Item 2.	Unregistered Sales of Equity Securities, Use of Proceeds and Issuer Purchases of Equity Securities	34
Item 3.	Defaults Upon Senior Securities	34
Item 4.	Mine Safety Disclosures	34
Item 5	Other Information	34
Item 6.	Exhibits	35
Signatures		36

iii

Part I ─ Financial Information

Item 1. Financial Statements

Monte Rosa Therapeutics, Inc.

Condensed consolidated balance sheets (unaudited)


	September 30,			December 31,
(in thousands, except share and per share amounts)	2025			2024
Assets
Current assets:
Cash and cash equivalents	$	208,343		$	224,254
Marketable securities		182,915			147,895
Other receivables		4,965			173
Prepaid expenses and other current assets		5,594			5,118
Total current assets		401,817			377,440
Property and equipment, net		27,598			29,483
Operating lease right-of-use assets		25,065			26,831
Restricted cash		4,950			4,863
Other long-term assets		411			115
Total assets	$	459,841		$	438,732
Liabilities and stockholders’ equity
Current liabilities:
Accounts payable	$	14,509		$	17,215
Accrued expenses and other current liabilities		17,902			18,785
Current deferred revenue		24,791			117,232
Current portion of operating lease liability		4,241			3,714
Total current liabilities		61,443			156,946
Deferred revenue, net of current		111,894			16,147
Defined benefit plan liability		4,740			3,702
Operating lease liability, net of current		35,927			39,001
Total liabilities		214,004			215,796
Commitments and contingencies (Note 8)
Stockholders’ equity
Preferred stock, $0.0001 par value, 10,000,000 shares authorized		—			—
Common stock, $0.0001 par value; 500,000,000 shares authorized, 61,790,239 and 61,507,446 shares issued and outstanding as of September 30, 2025 and December 31, 2024, respectively		6			6
Additional paid-in capital		680,157			664,874
Accumulated other comprehensive loss		(3,247	)		(3,356	)
Accumulated deficit		(431,079	)		(438,588	)
Total stockholders’ equity		245,837			222,936
Total liabilities and stockholders’ equity	$	459,841		$	438,732

See accompanying notes to the condensed consolidated financial statements.

Monte Rosa Therapeutics, Inc.

Condensed consolidated statements of operations and comprehensive (loss) income (unaudited)


	Three months ended September 30,						Nine months ended September 30,
(in thousands, except share and per share amounts)	2025			2024			2025			2024
Collaboration revenue	$	12,768		$	9,216		$	120,891		$	14,975
Operating expenses:
Research and development		36,678			27,616			99,521			82,697
General and administrative		9,065			8,127			25,863			26,394
Total operating expenses		45,743			35,743			125,384			109,091
Loss from operations		(32,975	)		(26,527	)		(4,493	)		(94,116	)
Other income:
Interest income		2,746			2,892			9,253			7,971
Foreign currency exchange (loss) gain, net		(29	)		(153	)		1,534			414
Gain on disposal of property and equipment		—			—			59			—
Total other income		2,717			2,739			10,846			8,385
Net (loss) income before income taxes		(30,258	)		(23,788	)		6,353			(85,731	)
Income tax benefit (provision)		3,177			(71	)		1,156			(406	)
Net (loss) income	$	(27,081	)	$	(23,859	)	$	7,509		$	(86,137	)
Comprehensive (loss) income:
Provision for pension benefit obligation		53			37			154			107
Unrealized gain (loss) on available-for-sale securities		73			311			(45	)		295
Comprehensive (loss) income	$	(26,955	)	$	(23,511	)	$	7,618		$	(85,735	)
(Loss) earnings per share:
Basic	$	(0.33	)	$	(0.29	)	$	0.09		$	(1.21	)
Diluted	$	(0.33	)	$	(0.29	)	$	0.09		$	(1.21	)
Weighted average number of shares outstanding:
Basic		82,397,753			82,011,670			82,245,324			71,173,647
Diluted		82,397,753			82,011,670			82,942,723			71,173,647

See accompanying notes to the condensed consolidated financial statements.

Monte Rosa Therapeutics, Inc.

Condensed consolidated statements of stockholders’ equity (unaudited)


	Common stock
(in thousands, except share amounts)	Shares		Amount		Additional paid-in capital		Accumulated other comprehensive loss			Accumulated deficit			Total Stockholders’ equity
Balance—January 1, 2025		61,507,446	$	6		664,874	$	(3,356	)	$	(438,588	)	$	222,936
Exercise of common stock options		2,375		—		14		—			—			14
Provision for pension benefit obligation		—		—		—		48			—			48
Stock-based compensation expense		—		—		5,298		—			—			5,298
Unrealized loss on available-for-sale securities		—		—		—		(21	)		—			(21	)
Net income		—		—		—		—			46,885			46,885
Balance—March 31, 2025		61,509,821	$	6	$	670,186	$	(3,329	)	$	(391,703	)	$	275,160
Restricted common stock vesting		112,159		—		—		—			—			—
Provision for pension benefit obligation		—		—		—		53			—			53
Stock-based compensation expense		—		—		4,894		—			—			4,894
Unrealized loss on available-for-sale securities		—		—		—		(97	)		—			(97	)
Issuance of shares under employee stock purchase plan		95,369		—		365		—			—			365
Net loss		—		—		—		—			(12,295	)		(12,295	)
Balance—June 30, 2025		61,717,349	$	6	$	675,445	$	(3,373	)	$	(403,998	)	$	268,080
Exercise of common stock options		72,890		—		348		—			—			348
Provision for pension benefit obligation		—		—		—		53			—			53
Stock-based compensation expense		—		—		4,364		—			—			4,364
Unrealized gain on available-for-sale securities		—		—		—		73			—			73
Net loss		—		—		—		—			(27,081	)		(27,081	)
Balance—September 30, 2025		61,790,239	$	6	$	680,157	$	(3,247	)	$	(431,079	)	$	245,837

See accompanying notes to the condensed consolidated financial statements

Monte Rosa Therapeutics, Inc.

Condensed consolidated statements of stockholders’ equity (unaudited) - Continued


	Common stock
(in thousands, except share amounts)	Shares		Amount		Additional paid-in capital		Accumulated other comprehensive loss			Accumulated deficit			Total Stockholders’ equity
Balance—January 1, 2024		50,140,233	$	5		547,857	$	(2,724	)	$	(365,888	)	$	179,250
Restricted common stock vesting		4,691		—		—		—			—			—
Exercise of common stock options		45,108		—		246		—			—			246
Provision for pension benefit obligation		—		—		—		35			—			35
Stock-based compensation expense		—		—		4,873		—			—			4,873
Unrealized loss on available-for-sale securities		—		—		—		(4	)		—			(4	)
Issuance of common stock pursuant to the at-the market sales agreement		10,272		—		87		—			—			87
Net loss		—		—		—		—			(31,968	)		(31,968	)
Balance—March 31, 2024		50,200,304	$	5	$	553,063	$	(2,693	)	$	(397,856	)	$	152,519
Restricted common stock vesting		85,249		—		—		—			—			—
Exercise of common stock options		190,160		—		422		—			—			422
Provision for pension benefit obligation		—		—		—		35			—			35
Stock-based compensation expense		—		—		4,502		—			—			4,502
Unrealized loss on available-for-sale securities		—		—		—		(12	)		—			(12	)
Issuance of shares under employee stock purchase plan		93,859		—		298		—			—			298
Issuance of common stock pursuant to the at-the market sales agreement, net of issuance costs of $89		120,234		—		797		—			—			797
Issuance of common stock pursuant to the Underwritten Public Offering, net of issuance cost of $3,290		10,638,476		1		46,709		—			—			46,710
Issuance of pre-funded warrant, net of issuance costs of $290		—		—		49,710		—			—			49,710
Net loss		—		—		—		—			(30,310	)		(30,310	)
Balance—June 30, 2024		61,328,282	$	6	$	655,501	$	(2,670	)	$	(428,166	)	$	224,671
Restricted common stock vesting		46,166		—		—		—			—			—
Exercise of common stock options		3,036		—		15		—			—			15
Provision for pension benefit obligation		—		—		—		37			—			37
Stock-based compensation expense		—		—		4,282		—			—			4,282
Unrealized gain on available-for-sale securities		—		—		—		311			—			311
Net loss		—		—		—		—			(23,859	)		(23,859	)
Balance—September 30, 2024		61,377,484	$	6	$	659,798	$	(2,322	)	$	(452,025	)	$	205,457

See accompanying notes to the condensed consolidated financial statements

Monte Rosa Therapeutics, Inc.

Condensed consolidated statements of cash flows (unaudited)


	Nine months ended September 30,
(in thousands)	2025			2024
Cash flows from operating activities:
Net income (loss)	$	7,509		$	(86,137	)
Adjustments to reconcile net loss to net cash used in operating activities
Stock-based compensation expense		14,556			13,657
Depreciation		6,268			6,060
Net accretion of discounts/premiums on marketable securities		(2,232	)		(2,252	)
Gain on disposal of property and equipment		(59	)		—
Changes in operating assets and liabilities
Other receivables		(4,792	)		(90	)
Prepaid expenses and other assets		(772	)		(4,940	)
Accounts payable		(3,096	)		(7,056	)
Accrued expenses and other current liabilities		(883	)		487
Defined benefit plan liability		1,192			217
Right-of-use assets and operating lease liabilities		(781	)		(897	)
Deferred revenue		3,306			(5,975	)
Net cash provided by (used in) operating activities	$	20,216		$	(86,926	)
Cash flows from investing activities:
Purchases of property and equipment		(3,933	)		(3,805	)
Purchases of marketable securities		(223,016	)		(162,400	)
Proceeds from maturities of marketable securities		190,182			152,649
Net cash used in investing activities	$	(36,767	)	$	(13,556	)
Cash flows from financing activities:
Proceeds from sale of common stock pursuant to the at-the-market sales agreement, net of underwriter's discount of $29		—			944
Proceeds from underwritten public offering, net of underwriter's discount of $3,000		—			47,001
Proceeds from the issuance of pre-funded warrants		—			50,000
Payment of common stock and pre-funded warrant issuance costs		—			(641	)
Proceeds from exercise of employee stock options		362			682
Proceeds from employee stock purchase plan		365			298
Net cash provided by financing activities	$	727		$	98,284
Net decrease in cash, cash equivalents and restricted cash	$	(15,824	)	$	(2,198	)
Cash, cash equivalents and restricted cash—beginning of period		229,117			132,681
Cash, cash equivalents and restricted cash—end of period	$	213,293		$	130,483
Reconciliation of cash, cash equivalents and restricted cash
Cash and cash equivalents	$	208,343		$	125,575
Restricted cash		4,950			4,908
Total cash, cash equivalents and restricted cash	$	213,293		$	130,483
Supplemental disclosure of noncash items
Purchases of property and equipment in accounts payable and accrued expenses	$	439		$	131

See accompanying notes to the condensed consolidated financial statements.

Monte Rosa Therapeutics, Inc.

Notes to the condensed consolidated financial statements

(unaudited)

1. Description of business and liquidity

Business

Monte Rosa Therapeutics, Inc. is a biotechnology company developing a portfolio of novel small molecule precision medicines that employ the body’s natural mechanisms to selectively degrade therapeutically-relevant proteins. As used in these condensed consolidated financial statements, unless the context otherwise requires, references to the Company or Monte Rosa refer to Monte Rosa Therapeutics, Inc. and its wholly owned subsidiaries Monte Rosa Therapeutics AG and Monte Rosa Therapeutics Securities Corp. Monte Rosa Therapeutics AG, a Swiss operating company, was incorporated under the laws of Switzerland in April 2018. Monte Rosa Therapeutics, Inc. was incorporated in Delaware in November 2019. The Company is headquartered in Boston, Massachusetts with research operations in both Boston and Basel, Switzerland.

Liquidity considerations

Since inception, the Company has devoted substantially all its efforts to business planning, research and development, recruiting management and technical staff, and raising capital and has financed its operations primarily through issuance and sale of convertible promissory notes, convertible preferred stock, public offerings of common stock or warrants to purchase common stock, registered direct offerings, and through its collaborations with F. Hoffman-La Roche Ltd. and Hoffman-La Roche Inc., or Roche, and with Novartis AG, or Novartis.

The Company’s continued discovery and development of its product candidates will require significant additional research and development efforts, including extensive preclinical and clinical testing and regulatory approval prior to commercialization. These efforts require significant amounts of additional capital, adequate personnel and infrastructure and extensive compliance-reporting capabilities. Even if product development efforts are successful, it is uncertain when, if ever, the Company will realize significant revenue from product sales.

As of September 30, 2025, the Company had an accumulated deficit of $431.1 million. The Company has incurred losses and negative cash flows from operations since inception. The Company expects that its operating losses and negative cash flows will continue for the foreseeable future as the Company continues to develop its product candidates. The Company currently expects that its cash, cash equivalents, and marketable securities of $391.3 million as of September 30, 2025 will be sufficient to fund operating expenses and capital requirements for at least 12 months from the date the third quarter interim condensed consolidated financial statements are issued. However, additional funding will be necessary to fund future discovery research, pre-clinical and clinical activities. The Company will seek additional funding through public financings, debt financings, collaboration agreements, strategic alliances and licensing arrangements. Although it has been successful in raising capital in the past, there is no assurance that the Company will be successful in obtaining such additional financing on terms acceptable to it, if at all, and the Company may not be able to enter into collaborations or other arrangements. If the Company is unable to obtain funding, it could be forced to delay, reduce or eliminate its research and development programs, product portfolio expansion or commercialization efforts, which could adversely affect the Company’s business prospects, and even the ability to continue operations.

2. Summary of significant accounting policies

Basis of presentation

The accompanying condensed consolidated financial statements have been prepared in conformity with accounting principles generally accepted in the U.S., or GAAP, and are stated in U.S. dollars. Any reference in these notes to applicable guidance is meant to refer to the authoritative GAAP as found in the Accounting Standards Codification and Accounting Standards Updates, or ASUs, of the Financial Accounting Standards Board, or FASB. All intercompany balances and transactions have been eliminated in consolidation.

Unaudited financial information

The Company’s condensed consolidated financial statements included herein have been prepared in conformity with GAAP and pursuant to the rules and regulations of the Securities and Exchange Commission, or the SEC. In the Company’s opinion, the information furnished reflects all adjustments, all of which are of a normal and recurring nature, necessary for a fair presentation of the financial position and results of operations for the reported interim periods. The Company considers events or transactions that occur after the balance sheet date but before the financial statements are

issued to provide additional evidence relative to certain estimates or to identify matters that require additional disclosure. The results of operations for interim periods are not necessarily indicative of results to be expected for the full year or any other interim period.

Recently issued accounting pronouncements

The Company has elected to use the extended transition period for complying with new or revised accounting standards as available under the Jumpstart Our Business Startups Act, or the JOBS Act.

In December 2023, the FASB issued ASU 2023-09, Income Taxes (Topic 740): Improvements to Income Tax Disclosures, which is intended to provide enhancements to annual income tax disclosures. The standard will require more detailed information in the rate reconciliation table and for income taxes paid, among other enhancements. The standard is effective for years beginning after December 15, 2024 and early adoption is permitted. The Company is currently evaluating the impact the adoption of this standard will have on its consolidated financial statements and related disclosures.

In November 2024, the FASB issued ASU 2024-03, Income Statement Reporting Comprehensive Income—Expense Disaggregation Disclosures (Subtopic 220-40), which requires disaggregated disclosure of income statement expenses for public business entities. ASU 2024-03 requires disclosure of, in a tabular presentation, each relevant expense caption on the face of the income statement that includes any of the following natural expenses: (1) purchases of inventory, (2) employee compensation, (3) depreciation, (4) intangible asset amortization, and (5) depreciation, depletion, and amortization (DD&A) recognized as part of oil- and gas-producing activities or other types of depletion expenses. The tabular disclosure would also include certain other expenses, when applicable. The standard is effective for fiscal years beginning after December 15, 2026, and interim periods within fiscal years beginning after December 15, 2027. The Company is currently evaluating the impact the adoption of this standard will have on its consolidated financial statements and related disclosures.

\\\

3. Fair value measurements

The following tables present information about the Company’s financial assets and liabilities measured at fair value on a recurring basis and indicate the level of the fair value hierarchy utilized to determine such fair values (in thousands):


	As of September 30, 2025
	Level 1		Level 2		Level 3		Total
Current assets
Money market funds	$	207,756	$	—	$	—	$	207,756
Pension plan assets		—		10,956		—		10,956
Corporate debt securities		—		85,550		—		85,550
U.S Treasury securities		—		97,365		—		97,365
Total assets measured at fair value	$	207,756	$	193,871	$	—	$	401,627


	As of December 31, 2024
	Level 1		Level 2		Level 3		Total
Current assets
Money market funds	$	223,657	$	—	$	—	$	223,657
Pension plan assets		—		9,413		—		9,413
Corporate debt securities		—		63,758		—		63,758
U.S Treasury securities		—		84,137		—		84,137
Total assets measured at fair value	$	223,657	$	157,308	$	—	$	380,965

Money market funds are highly liquid investments and are actively traded. The pricing information on the Company’s money market funds is based on quoted prices in active markets for identical securities. This approach results in the classification of these securities as Level 1 of the fair value hierarchy.

The fair value of pension plan assets has been determined as the surrender value of the portfolio of active insured members held within the Columna Collective Foundation Group investment fund and is classified within Level 2 of the fair value hierarchy.

Marketable securities consist of corporate debt securities and U.S. Treasury securities which are classified as available-for-sale pursuant to ASC 320, Investments—Debt and Equity Securities. Marketable securities are classified within Level 2 of the fair value hierarchy because pricing inputs are other than quoted prices in active markets. The fair values of these investments are estimated by taking into consideration valuations obtained from third-party pricing services. The pricing services utilize industry standard valuation models, including both income- and market-based approaches, for which all significant inputs are observable, either directly or indirectly, to estimate fair value. These inputs include reported trades of

and broker/dealer quotes on the same or similar securities, issuer credit spreads, benchmark securities based on historical data and other observable inputs.

There were no transfers among Level 1, Level 2 or Level 3 categories in the nine months ended September 30, 2025 and 2024.

4. Marketable securities

Marketable securities as of September 30, 2025 consisted of the following (in thousands):


	Amortized		Unrealized		Unrealized			Fair
	Cost		Gains		Losses			Value
Description
Corporate debt securities	$	85,501	$	51	$	(2	)		85,550
U.S Treasury securities		97,342		25		(2	)		97,365
Total	$	182,843	$	76	$	(4	)	$	182,915

Marketable securities as of December 31, 2024 consisted of the following (in thousands):


	Amortized		Unrealized		Unrealized			Fair
	Cost		Gains		Losses			Value
Description
Corporate debt securities	$	63,710	$	56	$	(8	)		63,758
U.S Treasury securities		84,068		75		(6	)		84,137
Total	$	147,778	$	131	$	(14	)	$	147,895

As of September 30, 2025, unrealized gain and losses on marketable securities are recorded in accumulated other comprehensive loss in equity on the accompanying condensed consolidated balance sheet. There were no realized gains or losses recognized on the sale or maturity of marketable securities for the nine months ended September 30, 2025 and 2024 and, as a result, the Company did not reclassify any amounts out of accumulated other comprehensive loss for the same periods.

The Company holds debt securities of companies with high credit quality and has determined that there was no material change in the credit risk of any of its debt securities. The Company also believes that it will be able to collect both principal and interest amounts due to it at maturity.

5. Property and equipment, net

Property and equipment, net, consist of the following (in thousands):


	September 30, 2025			December 31, 2024
Laboratory equipment	$	26,782		$	25,041
Computer hardware and software		1,376			1,256
Furniture and fixtures		1,310			1,099
Leasehold improvements		23,640			22,387
Construction in process		14			64
Total property and equipment, at cost	$	53,122		$	49,847
Less: accumulated depreciation		(25,524	)		(20,364	)
Property and equipment, net	$	27,598		$	29,483

The following table summarizes depreciation expense incurred (in thousands):


	Three months ended September 30,				Nine months ended September 30,
	2025		2024		2025		2024
Depreciation expense	$	2,095	$	2,103	$	6,268	$	6,060

6. Accrued expenses and other current liabilities

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


	September 30,		December 31,
	2025		2024
Accrued compensation and benefits	$	7,260	$	8,220
Accrued research and development		8,989		7,211
Other		1,653		3,354
Total accrued expenses and other current liabilities	$	17,902	$	18,785

7. Leases

The Company determines if an arrangement is a lease at inception. Operating leases are included in operating lease right-of-use, or ROU, assets and operating lease liabilities in the condensed consolidated balance sheets. The Company has no finance leases as of September 30, 2025.

ROU assets represent the right to use an underlying asset for the lease term and lease liabilities represent the obligation to make lease payments arising from the lease. Operating lease ROU assets and liabilities are recognized at commencement date based on the present value of lease payments over the lease term. As the Company’s leases do not provide an implicit rate, management estimated the incremental borrowing rate based on the rate of interest the Company would have to pay to borrow a similar amount on a collateralized basis over a similar term. The Company uses its incremental borrowing rate based on the information available at commencement date in determining the present value of lease payments.

Klybeckstrasse Lease

In March 2021, the Company entered into an operating lease agreement for office and lab space with Wincasa AG, or the Basel Landlord, that occupies approximately 21,422 square feet located at Klybeckstrasse 191, 4057 Basel, Basel-City, Switzerland. In April 2023, the Company and the Basel Landlord amended the Klybeckstrasse Lease which increased the office and lab space square footage from 21,422 square feet to 44,685 square feet and extended the term of the lease through June 30, 2027.

Harrison Avenue Lease

In December 2021, the Company entered into a non-cancelable lease agreement, or the Harrison Avenue Lease, for 63,327 square feet of office and laboratory space to support its expanding operations. The term of the lease commenced on April 1, 2022 and the Company’s obligation to pay rent began on December 21, 2022. The initial term of the lease is 128 months following the commencement date, at which point the Company has the option to extend the lease an additional 5 years. The Company has determined that it is not reasonably certain to exercise the option to extend the lease and has not included the extension period in the lease term. The annual base rent under the Harrison Avenue Lease is $95 per square foot for the first year, which is subject to scheduled annual increases of 3%, plus certain costs, operating expenses and property management fees.

Pursuant to the terms of the Harrison Avenue Lease, the landlord reimbursed the Company for $13 million of tenant improvements. The Company reduced the related ROU asset by the amounts reimbursed by the landlord and capitalized the leasehold improvements as fixed assets on the consolidated balance sheet.

The components of lease expense for the three and nine months ended September 30, 2025 and 2024 are as follows (in thousands):


	Three months ended September 30,				Nine months ended September 30,
	2025		2024		2025		2024
Operating lease expense	$	1,654	$	1,609	$	4,910	$	4,859
Variable lease expense		745		912		1,877		3,043
Total lease expense	$	2,399	$	2,521	$	6,787	$	7,902

The variable lease expenses generally include common area maintenance and property taxes.

The following table summarizes lease expense incurred (in thousands):


	Three months ended September 30,				Nine months ended September 30,
	2025		2024		2025		2024
Research and development	$	2,028	$	2,099	$	5,714	$	6,596
General and administrative		371		422		1,073		1,306
Total lease expense	$	2,399	$	2,521	$	6,787	$	7,902

Short-term lease costs for the nine months ended September 30, 2025 and 2024 were immaterial.

The weighted average remaining lease term and discount rate related to the Company's leases are as follows:


	September 30, 2025			December 31, 2024
Weighted average remaining lease term (years)		7.0			7.7
Weighted average discount rate		9.8	%		9.8	%

Supplemental cash flow and other information relating to the Company's leases for the three and nine months ended September 30, 2025 and 2024 is as follows (in thousands):


	Three months ended September 30,				Nine months ended September 30,
	2025		2024		2025		2024
Right-of-use assets obtained in exchange for operating lease obligations	$	—	$	—	$	—	$	108
Cash paid for amounts included in the measurement of lease liabilities	$	963	$	953	$	2,818	$	2,325
Amortization of ROU assets	$	637	$	578	$	1,827	$	1,589

Future minimum lease payments under non-cancelable leases as of September 30, 2025 for each of the years ending December 31 are as follows (in thousands):


Undiscounted lease payments
Remainder of 2025	$	1,948
2026		8,005
2027		7,685
2028		7,360
2029		7,581
Thereafter		23,443
Total undiscounted minimum lease payments		56,022
Less: Imputed interest		(15,854	)
Total operating lease liability	$	40,168

8. Commitments and contingencies

Legal Proceedings

From time to time, the Company may be subject to legal proceedings, claims and disputes that arise in the ordinary course of business. The Company accrues a liability for such matters when it is probable that future expenditures will be made and that such expenditures can be reasonably estimated. As of September 30, 2025, the Company is not a party to any litigation and does not have a contingency reserve established for any litigation liabilities.

9. Collaboration and license agreements

Roche Collaboration and License Agreement

Description

In October 2023, Monte Rosa Therapeutics AG, a wholly-owned subsidiary of Monte Rosa Therapeutics, Inc, or the Company, entered into a collaboration and license agreement, or the Roche Agreement, with F. Hoffman-La Roche Ltd. and Hoffman-La Roche Inc., or Roche. Pursuant to the Roche Agreement, the parties will seek to identify and develop molecular glue degraders, or MGDs, against cancer or neurological disease targets using the Company’s proprietary drug discovery engine for an initial set of targets in oncology and neuroscience selected by Roche, wherein a certain number of targets selected by Roche are subject to replacement rights owned by Roche. The Company will lead pre-clinical discovery and research activities with Roche leading late pre-clinical and clinical development activities.

Under the Roche Agreement, Roche will have a worldwide, exclusive license under patents and know-how controlled by the Company to develop and commercialize products directed to applicable targets. The license exclusivity is subject to the Company’s retained rights solely to fulfill its obligations under the arrangement. The research collaboration activities governed by the Roche Agreement will be overseen by a joint research committee.

Unless earlier terminated, the Roche Agreement will remain in effect for each product licensed under the Roche Agreement until expiration of the royalty term for the applicable product. The parties have included termination provisions

in the Roche Agreement, allowing termination of the Roche Agreement in its entirety, on a country-by-country or a target-by-target basis.

Pricing

In November 2023, the Company received a $50.0 million non-refundable upfront payment for the initial set of targets. Pursuant to the terms of the Roche Agreement, the Company expects to be entitled to receive from Roche certain variable consideration including potential pre-clinical milestones up to $172 million, and potential clinical, commercial and sales milestones exceeding $2 billion. The Company is also eligible to receive tiered royalties ranging from high-single-digits to low-teens on any products that are commercialized by Roche as a result of the collaboration.

To date through September 30, 2025, the Company has received $9.0 million related to Roche's decision to pay preclinical milestones and $3.0 million related to Roche's decision to exercise its option rights to replace certain targets for research and development services. The related payments are initially classified as deferred revenue in the accompanying condensed consolidated balance sheet and recognized in revenue as the related research and development services are performed.

Accounting

This agreement represents a transaction with a customer and therefore is accounted for under ASC 606, Revenue From Contracts With Customers.

The Company determined that the development and commercialization licenses for each of the collaboration targets is neither capable of being distinct nor distinct within the context from the promised initial research services. In addition, the Company has determined that each target in the agreement is distinct from other targets because: (i) Roche can benefit from the license and research services for a given target on their own since the results related thereto can be evaluated discretely and (ii) the results of the research and development of each target does not affect either the Company’s ability to perform or Roche’s ability to assess the results for any other target. As such, the Company has identified certain performance obligations within the agreement as follows:

•

Performance obligations for the research and development of initial targets; and

•

Performance obligations for the research and development services related to Roche’s option to replace certain targets.

The total transaction price of the Roche Agreement is allocated to the performance obligations based on their relative standalone selling price. The Company developed the standalone selling price for the performance obligations included in the Roche Agreement by determining the total estimated costs to fulfill each performance obligation identified with the objective of determining the price at which it would sell such an item if it were to be sold regularly on a standalone basis. The allocated transaction price is recognized as revenue from collaboration agreements in one of two ways:

•

Research and development of the initial targets: The Company recognizes the portion of the transaction price allocated to each of the research and development performance obligations as the research and development services are provided, using an input method, in proportion to costs incurred to date for each research development target as compared to total costs incurred and expected to be incurred in the future to satisfy the underlying obligation related to said research and development target. The transfer of control occurs over this period and, in management’s judgment, is the best measure of progress towards satisfying the performance obligation.

•

Option rights to replace targets: The transaction price allocated to the replacement option rights, which are considered material rights, is deferred until the period that Roche elects to exercise or elects to not exercise its option right to license and commercialize the underlying research and development target. Upon Roche's exercise of a replacement option right, the Company will recognize the portion of the transaction price allocated using the input method described above. Any payments made to exercise replacement option rights will be added to the allocated value and recognized as the related services are performed.

To date through September 30, 2025, $44.9 million related to the Roche Agreement has been recognized as collaboration revenue in the condensed consolidated statements of operations and comprehensive loss and the remaining $17.1 million of the upfront payment and subsequent milestone and replacement target payments related to customer options are recorded as deferred revenue in the liabilities section of the condensed consolidated balance sheet.

The following table summarizes the deferred revenue amounts allocated to performance obligations (in thousands):


	September 30,		December 31,
	2025		2024
Roche Agreement performance obligations
Research and development of initial targets	$	8,521	$	19,395
Research and development for replacement targets		8,596		5,622
Total Roche Agreement deferred revenue	$	17,117	$	25,017

The Company expects that the remaining deferred revenue for the initial targets will be recognized within 24 months. The Company expects that deferred revenue related to replacement targets will be recognized within 36 months. Due to the uncertain nature of the research and development being performed by the Company, it may take longer than anticipated to recognize revenue related to the performance obligations for the initial and replacement targets. Any amounts remaining in deferred revenue will be recognized at the conclusion of the Roche Agreement in October 2028.

2024 Novartis License Agreement

Description

In October 2024, Monte Rosa Therapeutics AG, a wholly-owned subsidiary of the Company, entered into a license agreement with Novartis, or the 2024 Novartis Agreement. Pursuant to the 2024 Novartis Agreement, the Company granted to Novartis an exclusive, royalty-bearing, sublicensable and transferable license to develop, manufacture, and commercialize VAV1 MGDs, including MRT-6160, which is currently in Phase 1 clinical development for immune-mediated conditions. The Company was responsible for completing the Phase 1 clinical study and Novartis is responsible for all subsequent development and commercial activities starting at Phase 2.

Pricing

In December 2024, the Company received a $150 million non-refundable upfront payment. Pursuant to the 2024 Novartis Agreement, the Company is entitled to receive from Novartis up to $2.1 billion in development, regulatory, and sales milestones, beginning upon initiation of Phase 2 studies including (a) potential development and regulatory milestone payments, exceeding $1.5 billion if multiple indications achieve regulatory approval in multiple territories, (b) potential sales milestones payments in connection with sales outside of the U.S., and tiered royalties on sales outside of the U.S. Novartis will be responsible for costs associated with Phase 2 clinical studies. The Company and Novartis also agreed to a net profit and loss sharing arrangement, pursuant to which the Company could co-fund any global clinical development from Phase 3 onwards and will share 30% of any profits and losses associated with the manufacturing and commercialization of the licensed products in the U.S. The Company has defined opportunities to opt out of the net profit and loss sharing arrangement prior to the initiation of Phase 3 clinical trials, in such case, sales in the U.S. would be entitled to the potential sales milestones payments and tiered royalties as sales outside of the U.S. Any costs for any co-funded development and commercialization activities are subject to budgets reviewed by the Company and Novartis.

Accounting

The goods and services that the Company was obligated to deliver and perform (the License and Licensor Clinical Trial) were accounted for under ASC 606 as they represented a transaction with a customer.

The Company has concluded that the License and the completion of the Licensor Clinical Trial promises are treated as a single, combined performance obligation. The Company has determined the total transaction price to be $150 million, which consists solely of the upfront payment. All milestone payments were constrained as the achievement of the milestones are contingent upon the success of the underlying research and development activities and are generally outside the control of the Company. The Company’s options to share in further development and commercialization efforts via its opt-in/opt-out rights will be assessed and accounted for as separate units of accounting under the relevant guidance if, and when, such options are exercised by the Company.

The revenue the Company recognized associated with the combined performance obligation was recognized over time using a cost-based input methodology. The transfer of control occurred over the course of the Licensor Clinical Trial promise and, in management’s judgment, was the best measure of progress towards satisfying the combined performance obligation.

As of September 30, 2025, the total transaction price of $150.0 million plus $1.2 million of incremental cost reimbursements related to the Novartis Agreement, of which the Company has concluded represents a contract modification, has been recognized as collaboration revenue in the condensed consolidated statements of operations and comprehensive (loss) income.

2025 Novartis License Agreement

Description

In September 2025, Monte Rosa Therapeutics AG, a wholly-owned subsidiary of the Company, entered into a collaboration, option, and license agreement with Novartis, or the 2025 Novartis Agreement. Pursuant to the 2025 Novartis Agreement, the Company granted to Novartis an exclusive, royalty-bearing, sublicensable and transferable license to degraders for one immunology and inflammation, or I&I program, or the First Licensed Program, and the exclusive option to obtain exclusive, royalty-bearing, sublicensable and transferable licenses with respect to two programs from the Company’s growing preclinical immunology portfolio, or the Options, and the programs, or the Optioned I&I Programs. Such Options are individually exercisable at Novartis’ discretion until a program meets criteria for investigational new drug application-filing-readiness. On a program-by-program basis, if Novartis does not exercise an Option, all rights with respect to such program are retained by the Company; if Novartis does exercise its Option, such program becomes a Licensed Program, or together, with the First Licensed Program, the Licensed Programs. Under the 2025 Novartis Agreement, the Company will apply its proprietary AI/ML-enabled QuEEN™ product engine for the discovery and development of degraders for the First Licensed Program and the Optioned I&I Programs. The Licensed Programs will be further developed and commercialized by Novartis, unless otherwise agreed to by the parties in accordance with the 2025 Novartis Agreement. Research activities for the Licensed Programs governed by the Agreement will be overseen by a Joint Research Committee.

Pricing

In September 2025, the Company received a $120.0 million non-refundable upfront payment from Novartis. Pursuant to the 2025 Novartis Agreement, the Company is entitled to receive from Novartis payments to maintain the Options totaling up to $60.0 million, and is eligible to receive from Novartis (1) preclinical milestone payments relating to the First Licensed Program and option exercise payments related to the Options of up to $180.0 million, (2) up to $5.4 billion in clinical development, regulatory, and sales milestones relating to the First Licensed Program and the two Optioned I&I Programs, beginning upon initiation of Phase 1 studies, including (a) potential development and regulatory milestone payments up to $2.2 billion if regulatory approval is achieved for multiple indications in multiple territories and (b) potential sales milestones payments up to $3.2 billion, allocated across licensed products, and (3) tiered royalties on global net sales in the high-single to low double-digit range for the First Licensed Program and in the low double-digit range for the two Optioned I&I Programs. The Company will be responsible for costs related to research activities, while Novartis will be responsible for costs related to development and commercialization activities.

Accounting

The goods and services that the Company is obligated to deliver and perform under the 2025 Novartis Agreement will be accounted for under ASC 606 as they represent a transaction with a customer.

The Company has concluded that the transaction price at inception is $180 million, which consists of the $120 million upfront payment and $60 million of option maintenance payments due over the course of the contract term. The Company has identified the following performance obligations in the contract:

•

License and research services for an immunology target

•

Research services for certain immunology targets to support the Immunology License Options

•

Material Right First Immunology License Option

•

Material Right Second Immunology License Option

The total transaction price of the 2025 Novartis Agreement is allocated to the performance obligations based on their relative standalone selling prices. The Company developed the standalone selling price for each performance obligation identified in the Novartis Agreement by determining the total estimated costs to fulfill each performance obligation with the objective of determining the price at which it would sell such an item if it were to be sold regularly on a standalone basis. The standalone selling price of performance obligations related to license and research services were determined using a cost-plus margin approach. The standalone selling price related to material rights for immunology license options were determined by benchmarking to comparable transactions, probability adjusted for the likelihood of exercise.

The allocated transaction price is recognized as revenue from collaboration agreements in one of two ways:

•

License and research services for immunology targets: The Company recognizes the portion of the transaction price allocated to each of the research performance obligations as the research services are provided, using an input method, in proportion to costs incurred to date for each research development target as compared to total costs incurred and expected to be incurred in the future to satisfy the underlying obligation related to said research services. The transfer of control occurs over this period and, in management’s judgment, is the best measure of progress towards satisfying the performance obligation.

•

Material option rights: The transaction price allocated to the options rights, which are considered material rights, is deferred until the period that Novartis elects to exercise its option right to license and commercialize the underlying immunology program. The Company will recognize the portion of the transaction price allocated to the option rights upon exercise.

To date through September 30, 2025, $0.4 million of revenue related to the 2025 Novartis Agreement has been recognized as collaboration revenue in the condensed consolidated statements of operations and comprehensive (loss) income. The remaining $119.6 million has been recorded as deferred revenue on the condensed consolidated balance sheets, with $18.4 million included in current liabilities related to performance obligations expected to be completed within 12 months from September 30, 2025 and $101.2 million included in non-current liabilities related to performance obligations expected to be completed later than 12 months from September 30, 2025.

The following table summarizes the transaction price allocated to performance obligations (in thousands):


	September 30,
	2025
2025 Novartis Agreement performance obligations
License and research services for named immunology target	$	7,077
Research services to support immunology license options		86,962
Material right - first immunology license option		49,091
Material right - second immunology license option		36,439
Total unearned amount of transaction price	$	179,569

The Company expects that that the remaining deferred revenue for the license and research services for a named immunology target and research services for two additional immunology targets to be recognized within 60 months. The deferred revenue related to material right license options will be recognized when Novartis exercises such options rights or at the expiration of the option rights. Due to the uncertain nature of the research and development being performed by the Company, it may take longer than anticipated to recognize revenue related to the performance obligations related to research services.

10. Equity

Undesignated preferred stock

The Company had 10,000,000 shares authorized of undesignated preferred stock, par value of $0.0001, of which no shares were issued and outstanding as of September 30, 2025.

Common stock

The Company had 500,000,000 shares of common stock authorized, of which 61,790,239 shares were issued and outstanding as of September 30, 2025.

Additionally, the Company has issued pre-funded warrants to purchase 20,638,924 shares of the Company's common stock to accredited investors. The pre-funded warrants are immediately exercisable at an exercise price of $0.0001 per share. The pre-funded warrants are exercisable at any time after the date of issuance. A holder of a pre-funded warrant may not exercise such pre-funded warrant if the holder, together with its affiliates, would beneficially own more than 4.99% (or, at the election of the holder, up to 19.99%) of the number of shares of the Company’s common stock outstanding immediately after giving effect to such exercise. No pre-funded warrants have been exercised as of September 30, 2025.

The holders of common stock are entitled to dividends when and if declared by the Company's board of directors, subject to the preferences applicable to any outstanding shares of preferred stock. The Company's board of directors has not declared any dividends and the Company has not paid any dividends.

The holders of common stock are entitled to one vote per share on all matters to be voted upon by the stockholders.

As of September 30, 2025 and December 31, 2024, the Company has reserved the following shares of common stock for the exercise of stock options, vesting of restricted stock and pre-funded warrants:


	September 30, 2025		December 31, 2024
Options to purchase common stock		14,943,250		11,589,269
Unvested restricted common stock units		774,675		112,159
Pre-funded warrants		20,638,924		20,638,924
		36,356,849		32,340,352

Underwritten public offering

In May 2024, the Company entered into an underwriting agreement with TD Securities (USA) LLC, as representative of the several underwriters, related to an underwritten public offering, or the Offering, of 10,638,476 shares of common stock at a price of $4.70 per share, and, in lieu of common stock to certain investors, pre-funded warrants to purchase 10,638,524 shares of common stock at a price of $4.6999 per pre-funded warrant, which represents the price per share at which shares of common stock were sold in this Offering, minus $0.0001, which is the exercise price of each pre-funded warrant. The pre-funded warrants are immediately exercisable and may be exercised at any time until the pre-funded warrants are exercised in full. Aggregate gross proceeds from the Offering were $100 million, or aggregate net proceeds of $96.4 million after deducting the underwriter discounts, commissions, and other offering costs.

At-the-market offering

In July 2022, the Company entered into a sales agreement, or the Sales Agreement, with Jefferies LLC, or Jefferies, as amended on March 20, 2025, pursuant to which the Company may offer and sell shares of its common stock pursuant to the then-effective prospectus from time to time in “at-the-market” offerings through Jefferies, as the Company’s sales agent. The Company had a prospectus for $100 million pursuant to which it could sell shares through July 2025, and has a prospectus for $150 million, pursuant to which it may sell shares through March 2028. The Company agreed to pay Jefferies a commission of up to 3.0% of the gross proceeds of any shares sold by Jefferies under the Sales Agreement. During the nine months ended September 30, 2025, the Company did not sell shares under the Sales Agreement. During the nine months ended September 30, 2024, the Company sold 130,506 shares of common stock under the Sales Agreement for aggregate gross proceeds of $1.0 million, respectively, or aggregate net proceeds of $0.9 million, after deducting sales agent discounts, commissions, and other offering costs. See Note 16, Subsequent Events, for information regarding shares sold under the Sales Agreement subsequent to September 30, 2025.

11. Stock-based compensation

2020 Stock incentive plan

The Company’s 2020 Stock Option and Grant Plan, or the 2020 Plan, provided for the Company to grant stock options, restricted stock and other stock awards, to employees, non-employee directors, and consultants. Upon the effectiveness of the 2021 Plan (as defined below), no further issuances were made under the 2020 Plan.

2021 Stock incentive plan

The Company’s 2021 Stock Option and Incentive Plan, or the 2021 Plan, was approved by the Company’s board of directors on May 28, 2021 and the Company’s stockholders on June 17, 2021 and became effective on the date immediately prior to the date on which the registration statement for the Company’s initial public offering, or IPO, was declared effective. The 2021 Plan provides for the grant of incentive stock options; non-qualified stock options; stock appreciation rights; restricted stock units, or RSUs; restricted stock awards; unrestricted stock awards; cash-based awards and dividend equivalent rights to the Company’s officers, employees, directors and consultants. The number of shares initially reserved for issuance under the 2021 Plan was 4,903,145. Under the evergreen provision of the 2021 Plan, the shares available for issuance under the 2021 Plan will be automatically increased each January 1st by 5% of the outstanding number of shares of the Company’s common stock on the immediately preceding December 31st or such lesser number of shares as may be determined by the Company’s compensation, nomination and corporate governance committee. Effective January 1, 2025 the number of shares available under the 2021 Plan automatically increased by 3,075,372 shares pursuant to the evergreen provision of the 2021 Plan. As of September 30, 2025, 2,097,616 shares were available for issuance under the 2021 Plan.

2021 Employee stock purchase plan

The Company’s 2021 Employee Stock Purchase Plan, or the 2021 ESPP, was approved by the Company’s board of directors on May 28, 2021 and the Company’s stockholders on June 17, 2021 and became effective on the date

immediately prior to the date on which the registration statement for the Company’s IPO was declared effective. A total of 439,849 shares of the Company’s common stock were initially reserved for issuance under the 2021 ESPP. The shares available for issuance under the 2021 ESPP will be automatically increased on each January 1st, through January 1, 2031, by the least of (i) 439,849 shares of the Company’s common stock, (ii) 1% of the outstanding number of shares of the Company’s common stock on the immediately preceding December 31st or (iii) such lesser number of shares of the Company’s common stock as determined by the plan administrator of the 2021 ESPP. Effective January 1, 2025 the number of shares available under the 2021 ESPP automatically increased by 439,849 shares pursuant to the evergreen provision of the 2021 ESPP. As of September 30, 2025, 1,780,308 shares were available for issuance under the 2021 ESPP.

Stock option activity

The following summarizes stock option activity:


	Number of options			Weighted average exercise price		Weighted average remaining contractual term (years)		Aggregate intrinsic value (in thousands)
Outstanding—December 31, 2024		11,589,269		$	8.10		7.6	$	11,419
Granted		3,839,450			6.90
Exercised		(75,265	)		4.81
Forfeited		(410,204	)		7.96
Outstanding—September 30, 2025		14,943,250		$	7.81		7.2	$	15,762
Vested or expected to vest—September 30, 2025		14,943,250		$	7.81		7.2	$	15,762
Exercisable—September 30, 2025		8,475,663		$	8.57		6.0	$	10,616

The aggregate intrinsic value of options granted is calculated as the difference between the exercise price of the options and the estimated fair value of the Company’s common stock.

Restricted stock unit activity

Starting in 2022, the Company granted RSUs to employees under the 2021 Plan. Each of the RSUs represents the right to receive one share of the Company’s common stock upon vesting. The RSUs will typically vest over two or four years provided the individual remains in continuous service of the Company. Accordingly, stock-based compensation expense for each RSU is recognized on a straight-line basis over the vesting term. The fair value of each RSU is based on the closing price of the Company’s common stock on the date of grant.

The following summarizes RSU activity:


	Number of shares			Weighted average grant date fair value
Unvested restricted stock units as of December 31, 2024		112,159		$	7.55
Granted		795,325		$	7.02
Vested		(112,159	)	$	7.55
Forfeited		(20,650	)	$	7.11
Unvested restricted stock units as of September 30, 2025		774,675		$	7.02

The aggregate fair value of restricted stock units that vested during each of the nine months ended September 30, 2025 and 2024 was $0.5 million. The weighted average grant date fair value RSUs that vested during each of the nine months ended September 30, 2025 and 2024 was $7.55 and $8.42, respectively.

Stock-based compensation expense

Stock-based compensation expense is classified as follows (in thousands):


	Three months ended September 30,				Nine months ended September 30,
	2025		2024		2025		2024
Research and development	$	2,460	$	2,613	$	8,500	$	7,928
General and administrative		1,904		1,669		6,056		5,729
Total stock-based compensation expense	$	4,364	$	4,282	$	14,556	$	13,657

As of September 30, 2025 total unrecognized stock-based compensation cost related to unvested stock options and restricted stock units was $28.3 million and $4.4 million, respectively. The Company expects to recognize this remaining cost over a weighted average period of 2.5 years and 3.3 years, respectively.

12. Income taxes

The following table summarizes the income tax benefit (provision) recorded (in thousands):


	Three months ended September 30,					Nine months ended September 30,
	2025		2024			2025		2024
Income tax benefit (provision)	$	3,177	$	(71	)	$	1,156	$	(406	)

For the three months ended September 30, 2025, the income tax benefit is primarily related to the enactment of the “One Big Beautiful Bill Act”, or OBBBA. On July 4, 2025, H.R. 1, the OBBBA, was signed into law. The modification to IRC Sec. 174 included in OBBBA allows the deduction of domestic based research and development expenses in the period in which they are incurred which reduced the taxable income which was being generated from the $150 million upfront payment for the 2024 Novartis Agreement. In accordance with U.S. GAAP, the Company has accounted for the tax effects of changes in tax law in the period of enactment. As a result of these factors, in the third quarter of 2025, the Company has reduced its provision for income taxes by $3.2 million. For the nine months ended September 30, 2025 the tax benefit of $1.2 million is primarily related to the requirement of carrying back the Research and Development credit generated in tax year 2025 to the tax liability of 2024.

For the three and nine months ended September 30, 2024, the income tax provision was primarily related to interest income on marketable securities in Massachusetts and the U.S. taxable income generated from the capitalization of research and development expenses.

The Company continues to maintain a full valuation allowance against all of its deferred tax assets. The Company has evaluated the positive and negative evidence involving its ability to realize its deferred tax assets. The Company has considered its history of cumulative net losses incurred since inception and its lack of any commercial products. The Company has concluded that it is more likely than not that it will not realize the benefits of its deferred tax assets. The Company reevaluates the positive and negative evidence at each reporting period.

13. Net (loss) earnings per common share

Basic and diluted net (loss) earnings per share is calculated based upon the weighted-average number of shares of common stock outstanding during the period. Shares of the Company's common stock underlying pre-funded warrants are included in the calculation of the basic and diluted earnings per share. Basic and diluted net (loss) earnings per share are as follows (in thousands except share and per share amounts):


	Three months ended September 30,						Nine months ended September 30,
	2025			2024			2025		2024
Net (loss) income	$	(27,081	)	$	(23,859	)	$	7,509	$	(86,137	)
Basic weighted average shares outstanding		82,397,753			82,011,670			82,245,324		71,173,647
Effect of potentially dilutive securities:
Stock options to purchase common stock		—			—			649,847		—
Restricted stock units		—			—			47,552		—
Diluted weighted average shares outstanding		82,397,753			82,011,670			82,942,723		71,173,647

Basic net (loss) earnings per share	$	(0.33	)	$	(0.29	)	$	0.09	$	(1.21	)
Diluted net (loss) earnings per share	$	(0.33	)	$	(0.29	)	$	0.09	$	(1.21	)

The following outstanding potentially dilutive securities have been excluded from the calculation of diluted net (loss) earnings per common share, as their effect is anti-dilutive:


	Three months ended September 30,				Nine months ended September 30,
	2025		2024		2025		2024
Stock options to purchase common stock		14,943,250		11,591,425		14,293,403		11,591,425
Restricted stock awards		—		624		—		624
Restricted stock units		774,675		112,159		727,123		112,159

14. Employee retirement plans

The Company, in compliance with Swiss Law, is contracted with the AXA Leben AG, or AXA, for the provision of pension benefits in a defined benefit plan. All benefits are organized in a semi-autonomous collective foundation within the framework of the contract with AXA. Insurance benefits due are paid directly to the entitled persons by AXA in the name of and for the account of the collective foundation. The pension plan is financed by contributions of both employees and the Company. The contract between the Company and the collective foundation can be terminated by either side. In the event of a termination, the Company would have an obligation to find alternative pension arrangements for its employees. Because there is no guarantee that the employee pension arrangements would be continued under the same conditions, there is a risk, albeit remote, that a pension obligation may fall on the Company. The pension assets are pooled for all affiliated companies; the investment of assets is done by the governing bodies of the collective foundation.

The following table summarizes pension expense incurred (in thousands):


	Three months ended September 30,				Nine months ended September 30,
	2025		2024		2025		2024
Pension expense	$	463	$	279	$	1,306	$	822

In February 2021, the Company adopted a defined contribution plan intended to qualify under Section 401(k) of the Internal Revenue Code covering all eligible U.S. based employees of the Company. All employees are eligible to become participants of the plan immediately upon hire. Each active employee may elect, voluntarily, to contribute a percentage of their compensation to the plan each year, subject to certain limitations. The Company reserves the right, but is not obligated, to make additional contributions to this plan. The Company makes safe-harbor match contributions of 100% of the first 4% of each participant’s eligible compensation. In January 2024, the Company adopted a defined contribution supplemental pension plan for eligible Swiss based employees defined by Swiss Law Art.1e BVV 2, or the 1e Plan. Employees earning above a defined threshold are eligible and automatically enrolled in the 1e Plan and required contributions are determined by age and salary under Swiss Law. The Company and the employee share the costs of the 1e Plan.

The following table summarizes defined contribution expenses incurred (in thousands):


	Three months ended September 30,				Nine months ended September 30,
	2025		2024		2025		2024
Defined contribution expense	$	201	$	164	$	830	$	701

15. Segment data

The Company defines its segments based on the way in which internally reported financial information is regularly reviewed by the chief operating decision maker, or CODM, to analyze financial performance, make decisions, and allocate resources. The Company manages its operations as a single operating and reportable segment committed to developing a portfolio of novel and proprietary MGDs. MGDs are small molecule drugs that employ the body’s natural protein destruction mechanisms to selectively degrade therapeutically-relevant proteins. As the internal reporting is based on the consolidated results, the Company has identified one operating and reportable segment. The CODM uses net (loss) income in the budget and forecasting process and considers budget-to-actual variances on a quarterly basis when making decisions about the allocation of operating and capital resources. The measure of the operating segment assets is reported on the consolidated balance sheet as total assets.

The accounting policies used in the segment reporting are the same as those described in the summary significant

accounting policies. (See Note 2 in our annual report on Form 10-K for the year ended December 31, 2024.) The Company’s CODM is the Chief Executive Officer.

The Company's reportable segment net revenues and loss (income) for the three and nine months ended September 30, 2025 and 2024 consisted of the following (in thousands):


	Three months ended September 30,						Nine months ended September 30,
	2025			2024			2025		2024
Revenue:
Collaboration revenue	$	12,768		$	9,216		$	120,891	$	14,975
Operating expense:
Research and development:
External research and development expenses:
MRT-2359		2,176			2,434			6,363		9,357
MRT-6160		1,444			1,914			6,902		6,468
MRT-8102		7,307			2,053			10,388		4,849
Other development and discovery programs		6,288			3,898			17,216		10,553
Personnel expense		10,889			9,862			33,999		29,585
Overhead and administrative expense		8,574			7,455			24,653		21,885
General and administrative expenses:
Personnel expense		5,696			5,702			16,854		16,443
Professional services		1,619			572			4,147		3,850
Facility costs and other expense		1,750			1,853			4,862		6,101
Interest and other income, net		2,717			2,739			10,846		8,385
Income tax benefit (provision)		3,177			(71	)		1,156		(406	)
Net (loss) income	$	(27,081	)	$	(23,859	)	$	7,509	$	(86,137	)

Other development and discovery expenses are related to the development of our QuEENTM discovery engine and our disclosed and undisclosed programs, including CDK2 and CCNE1. The Company's tangible assets are held in the U.S. and Switzerland with 29% of the assets held in Switzerland. All of the Company's revenue has been generated in Switzerland.

16. Subsequent Events

During October 2025, the Company sold 2,955,082 shares of common stock under the Sales Agreement for aggregate gross proceeds of $25.0 million, or aggregate net proceeds of $23.9 million, after deducting sales agent discounts, commissions, and other offering costs.

Item 2. Management’s discussion and analysis of financial condition and results of operations

The following discussion and analysis should be read in conjunction with the unaudited condensed consolidated financial statements and related notes included elsewhere in this Quarterly Report. This discussion and analysis and other parts of this Quarterly Report contain forward-looking statements based upon current beliefs, plans and expectations that involve risks, uncertainties and assumptions, such as statements regarding our plans, objectives, expectations, intentions and projections. Our actual results and the timing of selected events could differ materially from those anticipated in these forward-looking statements as a result of several factors, including those set forth in “Part I, Item 1A, Risk Factors” in our 2024 Annual Report and under Part II, Item 1A, “Risk Factors” and elsewhere in this Quarterly Report. You should carefully read the “Risk Factors” section of this Quarterly Report to gain an understanding of the important factors that could cause actual results to differ materially from our forward-looking statements. Please also see the section entitled “Special note regarding forward-looking statements.”

Overview

We are a biotechnology company developing a portfolio of novel and proprietary MGDs. MGDs are small molecule drugs that employ the body’s natural protein destruction mechanisms to selectively degrade therapeutically-relevant proteins. MGDs work by inducing the engagement of defined surfaces identified on target proteins by an E3 ligase, such as cereblon. We have developed a proprietary and industry-leading protein degradation discovery engine, called QuEENTM to enable our unique, target-centric, MGD discovery and development and our rational design of MGD products. We believe

our small molecule MGDs may give us significant advantages over existing therapeutic modalities, including other protein degradation approaches. We prioritize our product development on therapeutic targets backed by strong biological and genetic rationale with the goal of discovering and developing novel medicines.

Monte Rosa Therapeutics AG, a Swiss operating company, was incorporated under the laws of Switzerland in April 2018. Monte Rosa Therapeutics, Inc. was incorporated in Delaware in November 2019. In 2020, through a common control reorganization, Monte Rosa Therapeutics, Inc. acquired the net assets and shareholding of Monte Rosa Therapeutics AG. Monte Rosa Therapeutics, Inc. includes wholly owned subsidiaries Monte Rosa Therapeutics AG and Monte Rosa Securities Corporation. We are headquartered in Boston, Massachusetts with research operations in both Boston and Basel, Switzerland.

Recent Developments

In June 2025, the United States Food and Drug Administration cleared the investigational new drug application for MRT-8102, a NEK7-directed MGD being developed for the treatment of inflammatory diseases driven by the NLRP3 inflammasome and IL-1β. In July 2025, we initiated a Phase 1 study evaluating MRT-8102, with the first patients being dosed. The MRT-8102 Phase 1 study is a randomized, double-blind, placebo-controlled trial in healthy volunteers that includes both single ascending dose (SAD) and multiple ascending dose (MAD) cohorts. The study is designed to evaluate safety and tolerability, pharmacokinetics (PK), and pharmacodynamics (PD), including NEK7 degradation and ex vivo responses to inflammasome stimulation. Part 3 of the Phase 1 study is a randomized, placebo-controlled trial that will enroll subjects with increased CVD risk due to obesity and elevated CRP, designed to evaluate safety and tolerability, change in CRP levels, pharmacokinetics, and changes in other inflammatory markers. Initial results from the Phase 1 study are anticipated in the first half of 2026.

In September 2025, our wholly-owned subsidiary Monte Rosa Therapeutics AG entered into a collaboration, option, and license agreement with Novartis, or the 2025 Novartis Agreement. Pursuant to the 2025 Novartis Agreement, we granted to Novartis an exclusive, royalty-bearing, sublicensable and transferable license to degraders for one I&I program, or the First Licensed Program, and the exclusive option to obtain exclusive, royalty-bearing, sublicensable and transferable licenses with respect to two programs from our growing preclinical immunology portfolio, or the Options, and together with the programs, the Optioned I&I Programs. Such Options are individually exercisable at Novartis’ discretion until a program meets criteria for investigational new drug application-filing-readiness. On a program-by-program basis, if Novartis does not exercise an Option, all rights with respect to such program are retained by us; if Novartis does exercise its Option, such program becomes a Licensed Program, and together, with the First Licensed Program, the Licensed Programs. Under the 2025 Novartis Agreement, we will apply our proprietary AI/ML-enabled QuEEN™ product engine for the discovery and development of degraders for the First Licensed Program and the Optioned I&I Programs. The Licensed Programs will be further developed and commercialized by Novartis, unless otherwise agreed to by the parties in accordance with the 2025 Novartis Agreement.

Liquidity

To date, we have financed our operations primarily through the issuance and sale of convertible promissory notes, convertible preferred stock, public offerings of our common stock or warrants to purchase common stock, registered direct offerings, and through our collaboration agreements. From our inception through the date hereof, there have been aggregate inflows of $836.0 million of gross proceeds from such transactions. Since inception, we have had significant operating losses. Our primary use of cash is to fund operating expenses, which consist primarily of research and development expenditures and, to a lesser extent, general and administrative expenditures. For the nine months ended September 30, 2025, we reported net income of $7.5 million. For the years ended December 31, 2024 and 2023, we reported net losses of $72.7 million and $135.4 million, respectively. As of September 30, 2025, we had an accumulated deficit of $431.1 million and $396.2 million in cash, cash equivalents, restricted cash and marketable securities, which includes a $120.0 million non-refundable upfront payment we received from Novartis in September 2025 pursuant to the 2025 Novartis Agreement. We also received $9.7 million from Novartis for value added taxes related to the transaction, which is included in our accounts payable balance as of September 30, 2025 and is expected to be remitted to the Swiss government in the fourth quarter of 2025. Subsequent to September 30, 2025, we sold 2,955,082 shares of common stock under the Sales Agreement for aggregate gross proceeds of $25.0 million, respectively, or aggregate net proceeds of $23.9 million, after deducting sales agent discounts, commissions, and other offering costs. We anticipate that our proceeds from sales of our common stock in “at-the-market” offerings, other offerings and collaboration agreements, together with existing cash, cash equivalents, restricted cash and marketable securities, supports our cash runway through 2028.

Impact of global economic and political developments

The development of our product candidates could be disrupted and materially adversely affected in the future by global economic or political developments. In addition, economic uncertainty in global markets caused by political instability and conflict, and economic challenges caused by global pandemics or other public health events, may lead to market disruptions, including significant volatility in commodity prices, credit and capital market instability and supply chain interruptions. Our business, financial condition and results of operations could be materially and adversely affected by negative impacts on the global economy and capital markets resulting from these global economic conditions, particularly if such conditions are prolonged or worsen.

Components of operating results

Collaboration revenue

Collaboration revenue represents amounts earned from our collaboration and license agreements with Roche and Novartis. We expect that our revenue for the next several years will be derived primarily through our current collaboration and license agreements and any additional collaborations that we may enter into in the future.

Research and development expenses

Our research and development expenses include:

•

expenses incurred under agreements with consultants, third-party service providers that conduct research and development activities on our behalf;

•

personnel costs, which include salaries, benefits, pension and stock-based compensation;

•

laboratory and vendor expenses related to the execution of preclinical and clinical studies;

•

laboratory supplies and materials used for internal research and development activities; and

•

facilities and equipment costs.

Most of our research and development expenses have been related to the development of our QuEENTM discovery engine and advancement of our GSPT1 and VAV1 programs, advancement of our disclosed and undisclosed programs including for NEK7, CDK2, and CCNE1.

We expense all research and development costs in the periods in which they are incurred. Costs for certain research and development activities are recognized based on an evaluation of the progress to completion of specific tasks using information and data provided to us by our vendors and third-party service providers.

The process of conducting the necessary clinical research to obtain regulatory approval is costly and time-consuming, and the successful development of our product candidates is highly uncertain. As a result, we are unable to determine the duration and completion costs of our research and development projects, the costs of related clinical development costs or when and to what extent we will generate revenue from the commercialization and sale of any of our product candidates.

We expect our research and development expenses to increase substantially for the foreseeable future as we continue to invest in research and development activities related to developing our product candidates, including investments in manufacturing, as we advance our programs and conduct clinical trials. The process of conducting the necessary clinical research to obtain regulatory approval is costly and time-consuming, and the successful development of our product candidates is highly uncertain. As a result, we are unable to determine the duration and completion costs of our research and development projects, the costs of related clinical development costs or when and to what extent we will generate revenue from the commercialization and sale of any of our product candidates.

General and administrative expenses

Our general and administrative expenses consist primarily of personnel costs and other expenses for outside professional services, including legal fees relating to patent and corporate matters, professional fees for accounting, auditing, tax and administrative consulting services, insurance costs and other operating costs. We expect our general and administrative expenses to increase over the next several years to support our continued research and development activities, manufacturing activities, and the potential commercialization of our product candidates and development of commercial infrastructure. We also anticipate our general and administrative costs will increase with respect to the hiring of additional personnel, fees to outside consultants, lawyers and accountants, and increased costs associated with being a public company, such as expenses related to services associated with maintaining compliance with Nasdaq listing rules and SEC reporting requirements, insurance and investor relations costs.

Non-operating income and (expense)

Our non-operating income and (expense) includes (i) interest earned on our investments, including principally U.S. government-backed money-market funds and marketable securities; (ii) gains and losses on transactions of our Swiss subsidiary denominated in currencies other than the U.S. Dollar; and (iii) proceeds from the sale of fixed assets.

Results of operations for the three months ended September 30, 2025 and 2024

The following sets forth our results of operations (in thousands):


	Three months ended September 30,
	2025			2024			Dollar change
Collaboration revenue	$	12,768		$	9,216		$	3,552
Operating expenses:
Research and development	$	36,678		$	27,616		$	9,062
General and administrative		9,065			8,127			938
Total operating expenses		45,743			35,743			10,000
Loss from operations		(32,975	)		(26,527	)		(6,448	)
Other income		2,717			2,739			(22	)
Net loss before income taxes		(30,258	)		(23,788	)		(6,470	)
Income tax benefit (provision)		3,177			(71	)		3,248
Net loss	$	(27,081	)	$	(23,859	)	$	(3,222	)

Collaboration revenue

Collaboration revenue of $12.8 million and $9.2 million for the three months ended September 30, 2025 and 2024, respectively, represents revenue recorded under our collaboration and license agreements with Roche and Novartis. As of September 30, 2025, $24.8 million was classified as current deferred revenue on the condensed consolidated balance sheet.

Research and development expenses

Research and development expenses were comprised of (in thousands):


	Three months ended September 30,
	2025		2024		Dollar change
External research and development expense:
MRT-2359	$	2,176	$	2,434	$	(258	)
MRT-6160		1,444		1,914		(470	)
MRT-8102		7,307		2,053		5,254
Other development and discovery programs		6,288		3,898		2,390
Personnel expense		10,889		9,862		1,027
Overhead and administrative expense		8,574		7,455		1,119
Total research and development expense	$	36,678	$	27,616	$	9,062

As of September 30, 2025, we had 116 employees engaged in research and development activities in our facilities in the U.S. and Switzerland. As of September 30, 2024, we had 105 research and development employees in our facilities in the U.S. and Switzerland.

Most of our research and development expenses were driven by the successful achievement of key research milestones in our research and development organization, including the the advancement of MRT-8102 into the clinic, continuation of the MRT-2359 clinical study, continued program activities for MRT-6160 in preparation for Phase 2 studies, the progression of our preclinical pipeline including research performed for our collaboration with Roche, and the continued development of our QuEEN™ discovery engine, and reflect increased personnel expense and external R&D costs to achieve these milestones. Research and development expenses for the three months ended September 30, 2025 and 2024 included non-cash stock-based compensation expense of $2.5 million and $2.6 million, respectively.

General and administrative expenses

General and administrative expenses to support our business activities were comprised of (in thousands):


	Three months ended September 30,
	2025		2024		Dollar change
Personnel costs	$	5,696	$	5,702	$	(6	)
Professional services		1,619		572		1,047
Facility costs and other expense		1,750		1,853		(103	)
Total general and administrative expense	$	9,065	$	8,127	$	938

As of September 30, 2025 and 2024, we had 31 and 28 employees engaged in general and administrative activities, respectively.

General and administrative expenses for the three months ended September 30, 2025 and 2024 included non-cash stock-based compensation expense of $1.9 million and $1.7 million, respectively.

Other income

Other income was comprised of (in thousands):


	Three months ended September 30,
	2025			2024			Dollar change
Interest income	$	2,746		$	2,892		$	(146	)
Foreign currency exchange loss		(29	)		(153	)		124
Other income	$	2,717		$	2,739		$	(22	)

Other income for the three months ended September 30, 2025,was primarily attributable to interest earned on marketable securities and remained consistent with the three months ended September 30, 2024.

Income tax benefit (provision)

For the three months ended September 30, 2025, the income tax benefit is primarily related to the enactment of the the “One Big Beautiful Bill Act”, or OBBBA. On July 4, 2025, H.R. 1, the OBBBA, was signed into law. The modification to IRC Sec. 174 included in this act allows the deduction of domestic based research and development expenses in the period in which they are incurred which reduced the taxable income which was being generated from the $150 million upfront payment for the 2024 Novartis Agreement. In accordance with U.S. GAAP, we have accounted for the tax effects of changes in tax law in the period of enactment. As a result of these factors, in the third quarter of 2025, we have reduced our provision for income taxes by $3.2 million.

For the three months ended September 30, 2024, the income tax provision was primarily related to interest income on marketable securities in Massachusetts and the U.S. taxable income generated from the capitalization of research and development expenses.

Results of operations for the nine months ended September 30, 2025 and 2024

The following sets forth our results of operations (in thousands):


	Nine months ended September 30,
	2025			2024			Dollar change
Collaboration revenue	$	120,891		$	14,975		$	105,916
Operating expenses:
Research and development		99,521			82,697			16,824
General and administrative		25,863			26,394			(531	)
Total operating expenses		125,384			109,091			16,293
Loss from operations		(4,493	)		(94,116	)		89,623
Other income		10,846			8,385			2,461
Net income (loss) before income taxes	$	6,353		$	(85,731	)	$	92,084
Income tax benefit (provision)		1,156			(406	)		1,562
Net income (loss)	$	7,509		$	(86,137	)	$	93,646

Collaboration revenue

Collaboration revenue of $120.9 million and $15.0 million for the nine months ended September 30, 2025 and 2024, respectively, represents revenue recorded under our collaboration and license agreements with Roche and Novartis. As of September 30, 2025, $24.8 million was classified as current deferred revenue on the condensed consolidated balance sheet.

Research and development expenses

Research and development expenses were comprised of (in thousands):


	Nine months ended September 30,
	2025	2024	Dollar change
External research and development expense:
MRT-2359	$6,363	$9,357	$(2,994)
MRT-6160	6,902	6,468	434
MRT-8102	10,388	4,849	5,539
Other development and discovery programs	17,216	10,553	6,663
Personnel expense	33,999	29,585	4,414
Overhead and administrative expense	24,653	21,885	2,768
Total research and development expense	$99,521	$82,697	$16,824

Most of our research and development expenses were driven by the successful achievement of key research milestones in our research and development organization, including the advancement of MRT-8102 into the clinic, the continuation of the MRT-2359 clinical study, continued program activities for MRT-6160 in preparation for Phase 2 studies, the progression of our preclinical pipeline including research performed for our collaboration with Roche, and the continued development of our QuEEN™ discovery engine, and reflect increased personnel expense and external R&D costs to achieve these milestones. Research and development expenses for the nine months ended September 30, 2025 and 2024 included non-cash stock-based compensation expense of $8.5 million and $7.9 million, respectively.

General and administrative expenses

General and administrative expenses to support our business activities were comprised of (in thousands):


	Nine months ended September 30,
	2025		2024		Dollar change
Personnel costs	$	16,854	$	16,443	$	411
Professional services		4,147		3,850		297
Facility costs and other expenses		4,862		6,101		(1,239	)
Total general and administrative expenses	$	25,863	$	26,394	$	(531	)

As of September 30, 2025 and 2024, we had 31 and 28 employees engaged in general and administrative activities, respectively. General and administrative expenses for the nine months ended September 30, 2025 and 2024 included non-cash stock-based compensation expense of $6.1 million and $5.7 million, respectively.

Other income

Other income was comprised of (in thousands):


	Nine months ended September 30,
	2025		2024		Dollar change
Interest income	$	9,253	$	7,971	$	1,282
Foreign currency exchange gain		1,534		414		1,120
Gain on disposal of property and equipment		59		—		59
Other income	$	10,846	$	8,385	$	2,461

The increase in other income for the nine months ended September 30, 2025, as compared to the nine months ended September 30, 2024, is principally attributable to higher marketable securities balances during the nine months ended September 30, 2025 and to fluctuations in currency exchange rates, principally between the U.S. Dollar and Swiss Franc.

Income tax provision (benefit)

For the nine months ended September 30, 2025 the tax benefit of $1.2 million is primarily related to the requirement of carrying back the Research and Development credit generated in tax year 2025 to the tax liability of 2024.

For the nine months ended September 30, 2024, the income tax provision was primarily related to interest income on marketable securities in Massachusetts and the U.S. taxable income generated from the capitalization of research and development expenses.

Liquidity and capital resources

Overview

Due to our significant research and development expenditures, we have generated operating losses since our inception. We have funded our operations primarily through the issuance and sale of convertible promissory notes, convertible preferred stock, public offerings of our common stock or warrants to purchase common stock, registered direct offerings, and through our collaboration agreements. As of September 30, 2025, we had $396.2 million in cash, cash equivalents, restricted cash and marketable securities, which includes a $120.0 million non-refundable upfront payment we received from Novartis in September 2025. We also received from Novartis $9.7 million for value added taxes related to the transaction, which is included in our accounts payable balance as of September 30, 2025 and is expected to be remitted to the Swiss government in the fourth quarter of 2025. We have incurred losses since our inception and, as of September 30, 2025, we had an accumulated deficit of $431.1 million. Our primary use of cash is to fund operating expenses, which consist primarily of research and development expenditures, and to a lesser extent, general and administrative expenditures. Cash used to fund operating expenses is impacted by the timing of when we pay these expenses, as reflected in the change in our outstanding accounts payable and accrued expenses.

Underwritten public offering

In May 2024, we entered into an underwriting agreement with TD Securities (USA) LLC, as representative of the several underwriters, related to an underwritten public offering, or the Offering, of 10,638,476 shares of common stock at a price of $4.70 per share, and, in lieu of common stock to certain investors, pre-funded warrants to purchase 10,638,524 shares of common stock at a price of $4.6999 per pre-funded warrant, which represents the price per share at which shares of common stock were sold in this Offering, minus $0.0001, which is the exercise price of each pre-funded warrant. The pre-funded warrants are immediately exercisable and may be exercised at any time until the pre-funded warrants are exercised in full. Aggregate gross proceeds from the Offering were $100 million, or aggregate net proceeds of $96.4 million after deducting the underwriter discounts, commissions, and other offering costs.

At-the-market offering

On July 1, 2022, we filed a registration statement on Form S-3 (File No. 333-266003) with the SEC, which was declared effective on July 13, 2022, or the 2022 Shelf Registration Statement, in relation to the registration of common stock, preferred stock, debt securities, warrants and/or units of any combination thereof for the purposes of selling, from time to time, our common stock, debt securities or other equity securities in one or more offerings. We also simultaneously entered into the Open Market Sale AgreementSM, or the Sales Agreement, with Jefferies LLC, or Jefferies, to provide for the offering, issuance and sale of up to an aggregate amount of $100.0 million of our common stock from time to time in “at-the-market” offerings, or the ATM Program, under the 2022 Shelf Registration Statement and subject to the limitations thereof.

On March 20, 2025, we filed a registration statement on Form S-3 (File No. 333-285942) with the SEC, which was declared effective on March 31, 2025, or the 2025 Shelf Registration Statement, in relation to the registration of common stock, preferred stock, debt securities, warrants and/or units of any combination thereof for the purposes of selling, from time to time, our common stock, debt securities or other equity securities in one or more offerings. We also simultaneously entered into the Amendment No. 1 to the Sales Agreement, or the Amendment, with Jefferies, to provide for the offering, issuance and sale of up to an aggregate amount of $150.0 million of our common stock from time to time under the ATM Program, pursuant to the 2025 Shelf Registration Statement and subject to the limitations thereof.

We will pay to the Jefferies cash commissions of up to 3.0% of the aggregate gross proceeds of sales of common stock under the Sales Agreement. To date through September 30, 2025, 2,612,514 shares have been sold pursuant to the ATM Program. During October 2025, we sold 2,955,082 shares of common stock under the Sales Agreement for aggregate gross proceeds of $25.0 million, or aggregate net proceeds of $23.9 million, after deducting sales agent discounts, commissions, and other offering costs.

Cash flows

The following table summarizes our cash flows for the periods indicated (in thousands):


	Nine months ended September 30,
	2025			2024
Net cash provided by (used in):
Operating activities	$	20,216		$	(86,926	)
Investing activities		(36,767	)		(13,556	)
Financing activities		727			98,284
Net decrease in cash, cash equivalents and restricted cash	$	(15,824	)	$	(2,198	)

Operating activities

Net cash provided by operating activities of $20.2 million during the nine months ended September 30, 2025, was attributable to our net income of $7.5 million; non-cash charges of $18.5 million, principally with respect to depreciation expense and stock-based compensation; and an increase in deferred revenue of $3.3 million. This was partially offset by decreases in our working capital of $9.1 million.

Net cash used in operating activities of $86.9 million during the nine months ended September 30, 2024 was attributable to our net loss of $86.1 million and decreases in our working capital of $18.3 million, partially off-set by non-cash charges of $17.5 million, principally with respect to depreciation expense and stock-based compensation.

Investing activities

Cash used in investing activities of $36.8 million during the nine months ended September 30, 2025 was primarily attributable to purchases of marketable securities of $223.0 million and purchases of property and equipment of $3.9 million, partially offset by proceeds from the maturity of marketable securities of $190.2 million.

Cash used in investing activities of $13.6 million during the nine months ended September 30, 2024 was primarily attributable to proceeds from the maturity of marketable securities of $152.6 million, offset by purchases of marketable securities of $162.4 million and purchases of property and equipment of $3.8 million.

Financing activities

Cash provided by financing activities of $0.7 million for the nine months ended September 30, 2025 was primarily due to the proceeds from purchases from the 2021 ESPP and to the exercise of employee stock options.

Net cash provided by financing activities of $98.3 million for the nine months ended September 30, 2024 was primarily due to the net proceeds from our Offering of $96.4 million.

Funding requirements

Any product candidates we may develop may never achieve commercialization and we anticipate that we will continue to incur losses for the foreseeable future. We expect that our research and development expenses, general and administrative expenses and capital expenditures will continue to increase. As a result, until such time, if ever, as we can generate substantial product revenue, we expect to finance our cash needs through a combination of equity offerings, debt financings or other capital sources, including potential collaborations, licenses and other similar arrangements. Our primary uses of capital are, and we expect will continue to be, compensation and related expenses, third-party clinical research, manufacturing and development services, costs relating to the build-out of our headquarters, laboratories and manufacturing facility, license payments or milestone obligations that may arise, laboratory and related supplies, clinical costs, manufacturing costs, legal and other regulatory expenses and general overhead costs.

Based upon our current operating plan, we believe that our existing cash, cash equivalents and marketable securities will enable us to fund our operating expenses and capital expenditure requirements for at least the next twelve months. We base this estimate on assumptions that may prove to be wrong, and we could utilize our available capital resources sooner than we currently expect.

We will continue to require additional financing to advance our current product candidates through clinical development, to develop, acquire or in-license other potential product candidates and to fund operations for the foreseeable future. We will continue to seek funds through equity offerings, debt financings or other capital sources, including potential collaborations, licenses and other similar arrangements. However, we may be unable to raise additional funds or enter into such other arrangements when needed on favorable terms or at all. If we do raise additional capital through public or private equity offerings, the ownership interest of our existing stockholders will be diluted, and the terms of these securities may include liquidation or other preferences that adversely affect our stockholders’ rights. If we raise additional capital through debt

financing, we may be subject to covenants limiting or restricting our ability to take specific actions, such as incurring additional debt, making capital expenditures or declaring dividends. Any failure to raise capital as and when needed could have a negative impact on our financial condition and on our ability to pursue our business plans and strategies. If we are unable to raise capital, we will need to delay, reduce or terminate planned activities to reduce costs.

Because of the numerous risks and uncertainties associated with research, development and commercialization of pharmaceutical products, we are unable to estimate the exact amount of our operating capital requirements. Our future funding requirements will depend on many factors, including, but not limited to:

•

the scope, progress, results and costs of researching, developing and manufacturing our current product candidates or any future product candidates, and conducting preclinical studies and clinical trials;

•

the timing of, and the costs involved in, obtaining regulatory approvals or clearances for our lead product candidates or any future product candidates;

•

the number and characteristics of any additional product candidates we develop or acquire;

•

the cost of manufacturing our lead product candidate or any future product candidates and any products we successfully commercialize, including costs associated with building-out our manufacturing capabilities;

•

our ability to establish and maintain strategic collaborations, licensing or other arrangements and the financial terms of any such agreements that we may enter into;

•

the expenses needed to attract and retain skilled personnel;

•

the costs associated with being a public company;

•

the timing, receipt and amount of sales of any future approved or cleared products, if any; and

•

the impact of global economic and political developments, future public health events and the corresponding responses of businesses and governments.

Further, our operating plans may change, and we may need additional funds to meet operational needs and capital requirements for clinical trials and other research and development activities. We currently have no credit facility or committed sources of capital. Because of the numerous risks and uncertainties associated with the development and commercialization of our product candidates, we are unable to estimate the amounts of increased capital outlays and operating expenditures associated with our current and anticipated product development programs.

Critical accounting policies and significant judgments and estimates

Our unaudited interim condensed consolidated financial statements are prepared in accordance with generally accepted accounting principles in the U.S. The preparation of our unaudited interim condensed consolidated financial statements and related disclosures requires us to make estimates and judgments that affect the reported amounts of assets, liabilities, costs and expenses, and the disclosure of contingent assets and liabilities in our condensed financial statements. We base our estimates on historical experience, known trends and events and various other factors that we believe are reasonable under the circumstances, the results of which form the basis for making judgments about the carrying values of assets and liabilities that are not readily apparent from other sources. We evaluate our estimates and assumptions on an ongoing basis. However, even though we believe we have used reasonable estimates and assumptions in preparing our interim condensed consolidated financial statements, the future effects of global economic and political developments and any future public health events on our results of operations, cash flows, and financial position are unclear. Our actual results may differ from these estimates under different assumptions or conditions.

There have been no significant changes to our critical accounting policies from those described in “Part II, Item 7, Management’s Discussion and Analysis of Financial Condition and Results of Operations” included in our 2024 Annual Report, and our revenues related to the 2025 Novartis Agreement are accounted for consistent with the revenue recognition policy described therein.

For a complete discussion of our significant accounting policies and recent accounting pronouncements, see Note 2 to our condensed consolidated financial statements appearing elsewhere in this Quarterly Report and Note 2 to our 2024 Annual Report.

Recently issued and adopted accounting pronouncements

Refer to Note 2, “Summary of Significant Accounting Policies,” in the accompanying notes to our and consolidated financial statements appearing elsewhere in this Quarterly Report on Form 10-Q for a discussion of recent accounting pronouncements.

Contractual obligations and commitments

In September 2025, we entered into the 2025 Novartis Agreement. Pursuant to the 2025 Novartis Agreement, we granted to Novartis an exclusive, royalty-bearing, sublicensable and transferable license to degraders for the First Licensed Program and the exclusive option to obtain exclusive, royalty-bearing, sublicensable and transferable licenses with respect to the Optioned I&I Programs. Such Options are individually exercisable at Novartis’ discretion until a program meets criteria for investigational new drug application-filing-readiness. On a program-by-program basis, if Novartis does not exercise an Option, all rights with respect to such program are retained by us; if Novartis does exercise its Option, such program becomes a Licensed Program. Under the Agreement, we will apply our proprietary AI/ML-enabled QuEEN™ product engine for the discovery and development of degraders for the First Licensed Program and the Optioned I&I Programs. The Licensed Programs will be further developed and commercialized by Novartis, unless otherwise agreed to by the parties in accordance with the 2025 Novartis Agreement.

In September 2025, we received a $120.0 million non-refundable upfront payment from Novartis. Pursuant to the 2025 Novartis Agreement, we are entitled to receive from Novartis payments to maintain the Options totaling up to $60.0 million, and are eligible to receive from Novartis (1) preclinical milestone payments relating to the First Licensed Program and option exercise payments related to the Options of up to $180.0 million, (2) up to $5.4 billion in clinical development, regulatory, and sales milestones relating to the First Licensed Program and the two Optioned I&I Programs, beginning upon initiation of Phase 1 studies, including (a) potential development and regulatory milestone payments up to $2.2 billion if regulatory approval is achieved for multiple indications in multiple territories and (b) potential sales milestones payments up to $3.2 billion, allocated across licensed products, and (3) tiered royalties on global net sales in the high-single to low double-digit range for the First Licensed Program and in the low double-digit range for the two Optioned I&I Programs. We will be responsible for costs related to research activities, while Novartis will be responsible for costs related to development and commercialization activities.

During the three months ended September 30, 2025, there have been no other material changes to our contractual obligations and commitments from those described under “Part II, Item 7, 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 on March 20, 2025.

Emerging growth and smaller reporting company status

In April 2012, the Jumpstart Our Business Startups Act of 2012, or the JOBS Act, was enacted. Section 107 of the JOBS Act provides that an “emerging growth company” may take advantage of the extended transition period provided in Section 7(a)(2)(B) of the Securities Act for complying with new or revised accounting standards. Therefore, an emerging growth company can delay the adoption of certain accounting standards until those standards would otherwise apply to private companies. We have elected to avail ourselves of this extended transition period and, as a result, we may adopt new or revised accounting standards on the relevant dates on which adoption of such standards is required for non-public companies instead of the dates required for other public companies. However, we may early adopt these standards.

We will cease to be an emerging growth company on the date that is the earliest of (i) the last day of the fiscal year in which we have total annual gross revenues of $1.235 billion or more, (ii) the last day of our fiscal year following the fifth anniversary of the date of the closing of our initial public offering, or our IPO, (iii) the date on which we have issued more than $1.0 billion in nonconvertible debt during the previous three years or (iv) the date on which we are deemed to be a large, accelerated filer under the rules of the SEC.

We are also a “smaller reporting company,” meaning that the market value of our stock held by non-affiliates plus the aggregate amount of gross proceeds to us as a result of our IPO is less than $700 million and our annual revenue was less than $100 million during the most recently completed fiscal year. We may continue to be a smaller reporting company after our IPO if either (i) the market value of our stock held by non-affiliates is less than $250 million or (ii) our annual revenue was less than $100 million during the most recently completed fiscal year and the market value of our stock held by non-affiliates is less than $700 million. If we are a smaller reporting company at the time we cease to be an emerging growth company, we may continue to rely on exemptions from certain disclosure requirements that are available to smaller reporting companies. Specifically, as a smaller reporting company we may choose to present only the two most

recent fiscal years of audited financial statements in our annual reports on Form 10-K and, similar to emerging growth companies, smaller reporting companies have reduced disclosure obligations regarding executive compensation.

Item 3. Quantitative and qualitative disclosures about market risk

We are a smaller reporting company as defined by Rule 12b-2 of the Exchange Act and are not required to provide the information required under this Item 3.

Item 4. Controls and procedures

Evaluation of Disclosure Controls and Procedures

Our management, with the participation of our principal executive officer and our principal financial officer, has evaluated the effectiveness of our disclosure controls and procedures as defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, as amended, or the Exchange Act, as of September 30, 2025. The term “disclosure controls and procedures,” as defined in the Exchange Act, means controls and other procedures of a company that are designed to ensure that information required to be disclosed by a company in the reports that it files or submits under the Exchange Act is recorded, processed, summarized and reported, within the time periods specified in the SEC’s rules and forms. Disclosure controls and procedures include, without limitation, controls and procedures designed to ensure that information required to be disclosed by a company in the reports that it files or submits under the Exchange Act is accumulated and communicated to the company’s management, including its principal executive and principal financial officers, or persons performing similar functions, as appropriate to allow timely decisions regarding required disclosure.

Based on the evaluation of our disclosure controls and procedures as of September 30, 2025, our principal executive officer and principal financial officer concluded that our disclosure controls and procedures as of such date are effective at the reasonable assurance level.

Changes in Internal Control over Financial Reporting

There were no changes in our internal control over financial reporting (as defined in Rules 13a-15(f) and 15d-15(f) under the Exchange Act) during three months ended September 30, 2025 that materially affected, or were reasonably likely to materially affect, our internal control over financial reporting.

Inherent Limitations on Effectiveness of Controls

Our disclosure controls and procedures and internal control over financial reporting are designed to provide reasonable assurance of achieving the desired control objectives. Our management recognizes that any control system, no matter how well designed and operated, is based upon certain judgments and assumptions and cannot provide absolute assurance that its objectives will be met. Similarly, an evaluation of controls cannot provide absolute assurance that misstatements due to error or fraud will not occur or that all control issues and instances of fraud, if any, have been detected.

Part II ─ Other Information

Item 1. Legal proceedings

From time to time, we may become subject to various legal proceedings and claims that arise in the ordinary course of our business activities. Although the results of litigation and claims cannot be predicted with certainty, as of September 30, 2025, we do not believe we are party to any claim or litigation the outcome of which, if determined adversely to us, would individually or in the aggregate be reasonably expected to have a material adverse effect on our business. Regardless of the outcome, litigation can have an adverse impact on us because of defense and settlement costs, diversion of management resources and other factors.

Item 1A. Risk factors

Investing in our common stock involves a high degree of risk. You should carefully consider the following risks and uncertainties, those risks and uncertainties discussed in “Part I, Item 1A, Risk Factors” in our 2024 Annual Report, as amended and supplemented by the information in our subsequent Quarterly Reports on Form 10-Q, together with all of the other information contained in this Quarterly Report, including our unaudited condensed consolidated financial statements and the related notes appearing elsewhere in this Quarterly Report. The risk factor disclosure in our 2024 Annual Report and subsequent Quarterly Reports on Form 10-Q is qualified by the information that is described in this Quarterly Report. If any of the risks described below or in our 2024 Annual Report actually occur, our business, prospects, operating results and financial condition could suffer materially. In such event, the trading price of our common stock could decline and you might lose all or part of your investment.

Other than as set forth below, there have been no material changes to the risk factors set forth in our 2024 Annual Report.

We have incurred significant operating losses since our inception and anticipate that we will incur continued losses for the foreseeable future.

Since our inception, we have focused substantially all of our efforts and financial resources on developing our proprietary QuEENTM discovery engine, our proprietary MGD library and our initial pipeline of product candidates. To date, we have financed our operations primarily through the issuance and sale of convertible promissory notes, convertible preferred stock, public offerings of our common stock or warrants to purchase common stock, registered direct offerings, and our collaboration agreements with Roche and Novartis. From our inception through the date hereof, we raised an aggregate of $836.0 million of gross proceeds from such transactions. As of September 30, 2025, our cash, cash equivalents, restricted cash and marketable securities were $396.2 million. We have incurred significant operating losses since our inception, and we had an accumulated deficit of $431.1 million as of September 30, 2025. For the nine months ended September 30, 2025, we reported net income of $7.5 million. For the years ended December 31, 2024 and 2023, we reported net losses of $72.7 million and $135.4 million, respectively. Substantially all of our operating losses have resulted from costs incurred in connection with our research and initial pipeline programs and from general and administrative costs associated with our operations. We expect to continue to incur significant expenses and increasing operating losses over the next several years and for the foreseeable future. Our prior losses, combined with expected future losses, have had and will continue to have an adverse effect on our stockholders’ deficit and working capital. We expect our expenses to significantly increase in connection with our ongoing activities, as we:

•

conduct our clinical trial for MRT-2359, our MGD product candidate targeting GSPT1;

•

finalize our Phase 1 clinical trial for MRT-6160, our MGD candidate targeting VAV1 for immune-mediated conditions and, if applicable, co-fund any global clinical development of Phase 3 onward;

•

finalize our Phase 1 clinical trial for MRT-8102, our NEK7-directed MGD being developed for the treatment of inflammatory conditions driven by the NLRP3 inflammasome, IL-1β, and IL-6;

•

continue preclinical activities for our NEK7, CDK2, CCNE1, and other currently undisclosed programs;

•

prepare and submit IND applications with the FDA for other current and future product candidates;

•

complete preclinical studies for current or future product candidates;

•

progress MGD molecules from our initial programs through lead optimization to development candidates and multiple areas of interest and indication;

•

initiate and complete clinical trials for current or future product candidates;

•

expand and improve the capabilities of our QuEENTM discovery engine;

•

continue to build our proprietary library of MGDs;

•

contract to manufacture our product candidates;

•

advance research and development related activities to expand our product pipeline;

•

seek regulatory approval for our product candidates that successfully complete clinical development;

•

develop and scale up our capabilities to support our ongoing preclinical activities and future clinical trials for our product candidates and commercialization of any of our product candidates for which we may obtain marketing approval;

•

maintain, expand, and protect our intellectual property portfolio;

•

hire additional staff, including clinical, scientific and management personnel; and

•

secure facilities to support continued growth in our research, development and commercialization efforts.

In addition, if we obtain marketing approval for our current or future product candidates, we will incur significant expenses relating to our commercialization of such product candidates via our sales, marketing, product manufacturing and distribution efforts. Because of the numerous risks and uncertainties associated with developing pharmaceutical drugs, including in light of economic fluctuations, we are unable to predict the extent of any future losses or when we will become profitable, if at all.

Even if we achieve profitability, we may not be able to sustain or increase our profitability on a quarterly or annual basis. Our failure to become and remain profitable would depress the value of our company and could impair our ability to raise capital, expand our business, maintain our development efforts, obtain product approvals, diversify our offerings or continue our operations. A decline in the value of our company could also cause you to lose all or part of your investment.

Changes in funding or disruptions at the FDA, the SEC and other government agencies caused by funding shortages or global health concerns, or changes in policy could hinder their ability to hire and retain key leadership and other personnel, or otherwise prevent new or modified products from being developed, approved or commercialized in a timely manner or at all, or otherwise prevent those agencies from performing normal business functions on which the operation of our business may rely, which could negatively impact our business.

The ability of the FDA to review and approve new products can be affected by a variety of factors, including government budget and funding levels, ability to hire and retain key personnel and accept the payment of user fees, and statutory, regulatory and policy changes and other events that may otherwise affect the FDA’s ability to perform routine functions. Average review times at the FDA have fluctuated in recent years as a result. In addition, government funding of the SEC and other government agencies on which our operations may rely, including those that fund research and development activities is subject to the political process, which is inherently fluid and unpredictable.

Disruptions at the FDA and other agencies may also slow the time necessary for new drugs to be reviewed and/or approved by necessary government agencies, which would adversely affect our business. For example, over the past decade, the U.S. government shut down several times, including beginning on October 1, 2025, and certain regulatory agencies, such as the FDA and the SEC, had to furlough critical employees and stop critical activities. The duration of the current government shutdown is unknown.

If a prolonged government shutdown occurs, or a widespread freeze on federal funding [continues or] occurs in the future, or if global health concerns prevent the FDA or other regulatory authorities from conducting their regular inspections, reviews or other regulatory activities, it could significantly impact the ability of the FDA to timely review and process our regulatory submissions, which could have a material adverse effect on our business. Further, in our operations as a public company, future government shutdowns or delays could impact our ability to access the public markets and obtain necessary capital in order to properly capitalize and continue our operations.

Significant economic, trade, regulatory, or geopolitical developments, and other circumstances beyond our control, could have a material effect on our financial condition or results of operations.

Significant economic, trade, regulatory, or geopolitical developments are difficult to predict and may have a material effect on us. The U.S. recently imposed tariffs on virtually all imports to the U.S. and significantly higher reciprocal tariffs applicable to imports from many countries, certain of which reciprocal tariffs were subsequently temporarily paused. If tariffs are broadly imposed it could lead to additional corresponding punitive actions by the countries with which the U.S. trades. Historically, tariffs have led to increased trade and political tensions, between not only the U.S. and China, but also

between the U.S. and other countries in the international community. Political tensions could reduce trade volume, investment, technological exchange and other economic activities between major international economies, resulting in a material adverse effect on global economic conditions and the stability of global financial markets. Any changes in political, trade, regulatory, and economic conditions, or new legislative and/or regulatory developments, could have a material adverse effect on our financial condition or results of operations. Until we know how such changes may impact our business and the business of our competitors, suppliers and other parties we work with over the long term, we will not know if, overall, we will benefit from them or be negatively affected by them.

Item 2. Unregistered sales of equity securities, use of proceeds and issuer purchases of equity securities

Recent sales of unregistered equity securities

None.

Issuer purchases of equity securities

None.

Item 3. Defaults upon senior securities

None.

Item 4. Mine safety disclosures

Not Applicable.

Item 5. Other information

Rule 10b5-1 Trading Plans

During the fiscal quarter ended on September 30, 2025, none of our directors and officers (as defined in Rule 16a-1(f) under the Exchange Act) adopted, modified or terminated a “Rule 10b5-1 trading arrangement” or “non-Rule 10b5-1 trading arrangement,” as those terms are defined in Item 408(a) of Regulation S-K.

Item 6. Exhibits


Exhibit Number		Description

3.1		Fourth Amended and Restated Certificate of Incorporation of Registrant, as currently in effect (incorporated by reference to Exhibit 3.1 of the Registrant's Current Report on Form 8-K (File No. 001-40522) filed on June 28, 2021).
3.2		Certificate of Amendment to the Fourth Amended and Restated Certificate of Incorporation of Registrant (incorporated by reference to Exhibit 3.1 of the Registrant’s Current Report on Form 8-K (File No. 001-40522) filed on June 14, 2023).
3.3		Second Amended and Restated By-laws of the Registrant, as currently in effect (incorporated by reference to Exhibit 3.3 of the Registrant's Quarterly Report on Form 10-Q (File No. 001-40522) filed on May 9, 2024)
10.1†*		Collaboration, Option, and License Agreement between Monte Rosa Therapeutics AG and Novartis Pharma AG, dates as of September 13, 2025.
31.1*		Certification of Principal Executive Officer and Principal Financial Officer Pursuant to Rules 13a-14(a) and 15d-14(a) under the Securities Exchange Act of 1934, as Adopted Pursuant to Section 302 of the Sarbanes-Oxley Act of 2002.
32.1**		Certification of Principal Executive Officer and Principal Financial Officer Pursuant to 18 U.S.C. Section 1350, as Adopted Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002.

101.INS*		Inline XBRL Instance Document – the instance document does not appear in the Interactive Data File because XBRL tags are embedded within the Inline XBRL document.
101.SCH*		Inline XBRL Taxonomy Extension Schema Document
104*		Cover Page Interactive Data File (embedded within the Inline XBRL document)

* Filed herewith.

** Deemed to be furnished with this Quarterly Report on Form 10-Q and will not be deemed to be “filed” for purposes of Section 18 of the Securities Exchange Act of 1934, as amended, except to the extent that the registrant specifically incorporates it by reference.

† Portions of this exhibit (indicated by asterisks) will be omitted in accordance with the rules of the SEC.

SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.


	Monte Rosa Therapeutics, Inc.

Date: November 6, 2025	By:	/s/ Markus Warmuth
		Markus Warmuth
		Chief Executive Officer
		(Principal Executive Officer and Principal Financial Officer)