0000950170-24-035912 | 10-K | XBRL Viewer

Net Loss Per Share

12 Months Ended

Dec. 31, 2023

10. Net loss per share

The following table summarizes the computation of basic and diluted net loss per share of the Company:


	Year ended December 31,
	2023			2022
Numerator:
Net loss	$	(104,699	)	$	(101,067	)
Denominator:
Weighted-average number of common shares, basic and diluted		43,994,862			38,897,442
Net loss per share, basic and diluted	$	(2.38	)	$	(2.60	)

The Company’s potential dilutive securities, which include common stock, RSUs, and ESPP purchase rights, have been excluded from the computation of diluted net loss per share as the effect would be anti-dilutive. Therefore, the weighted average number of common shares outstanding used to calculate both basic and diluted net loss per share is the same.

The Company excluded the following potential common shares, presented based on amounts outstanding at period end, from the computation of diluted net loss per share for the periods indicated because including them would have had an anti-dilutive effect:


	As of December 31,
	2023		2022
Outstanding options to purchase common stock		6,478,063		8,274,647
Restricted stock units		1,513,102		—
Total		7,991,165		8,274,647

Nature of the Business and Basis of Presentation - Additional Information (Details) - USD ($)	1 Months Ended	2 Months Ended	12 Months Ended
	May 31, 2022	Mar. 12, 2024	Dec. 31, 2023
Nature Of Business And Basis Of Presentation [Line Items]
Entity incorporation state name			DE
Base Prospectus
Nature Of Business And Basis Of Presentation [Line Items]
Maximum aggregate offering price	$ 400,000,000
Sales Agreement Prospectus
Nature Of Business And Basis Of Presentation [Line Items]
Maximum aggregate offering price	$ 150,000,000
Proceeds from issuance of common stock net of commissions			$ 52,100,000
Issuance of common stock, Shares			6.3
Sales Agreement Prospectus \| Subsequent Event
Nature Of Business And Basis Of Presentation [Line Items]
Issuance of common stock, Shares		200,000
Received deducting commissions related to sales agreement		$ 1,300,000

Consolidated balance sheets - USD ($) $ in Thousands	Dec. 31, 2023	Dec. 31, 2022
Current assets:
Cash and cash equivalents	$ 191,442	$ 113,556
Marketable securities	9,952	116,039
Prepaid expenses	11,320	10,932
Other current assets	2,561	2,955
Interest receivable	64	588
Total current assets	215,339	244,070
Restricted cash	569	569
Operating lease right-of-use assets	6,611	4,753
Property and equipment, net	5,823	6,675
Total assets	228,342	256,067
Current liabilities:
Accounts payable	1,695	766
Accrued and other current liabilities	13,815	15,748
Deferred revenue - current portion	15,309	14,880
Total current liabilities	30,819	31,394
Deferred revenue - net of current portion	33,074	36,856
Other long term liabilities	4,884	2,968
Total long term liabilities	37,958	39,824
Total liabilities	68,777	71,218
Commitments and contingencies (Note 7)
Stockholders’ equity
Common stock, par value of $0.0001 per share; 300,000,000 shares authorized, 45,918,233 and 39,439,575 shares issued and outstanding as of December 31, 2023 and 2022, respectively	5	4
Additional paid-in capital	561,433	483,170
Accumulated other comprehensive loss	(24)	(1,175)
Accumulated deficit	(401,849)	(297,150)
Total stockholders’ equity	159,565	184,849
Total liabilities and stockholders’ equity	$ 228,342	$ 256,067

Consolidated statements of cash flows - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2023	Dec. 31, 2022
Cash flows from operating activities:
Net loss	$ (104,699)	$ (101,067)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation	2,469	1,546
Amortization and accretion of marketable securities	(325)	(211)
Stock-based compensation	25,257	22,854
Loss on disposal of property and equipment	1
Reduction in the carrying amount of right of use assets	2,260	1,989
Changes in assets and liabilities:
Prepaid expenses and other current assets	529	(5,183)
Accounts payable, accrued liabilities, and operating leases	(3,208)	(3,530)
Deferred revenue	(3,351)	51,736
Net cash used in operating activities	(81,067)	(31,866)
Cash flows from investing activities:
Purchases of property and equipment	(1,616)	(3,962)
Purchases of marketable securities	0	(201,320)
Sales of marketable securities	107,562	159,400
Net cash provided by (used in) investing activities	105,946	(45,882)
Cash flows from financing activities:
Proceeds from issuance of common stock upon exercise of stock options	371	494
Proceeds from Employee Stock Purchase Plan	555	570
Proceeds from controlled equity offering sales agreement	52,081	45,344
Other	0	1
Net cash provided by financing activities	53,007	46,409
Net increase (decrease) in cash, cash equivalents and restricted cash	77,886	(31,339)
Cash, cash equivalents and restricted cash—beginning of year	114,125	145,464
Cash, cash equivalents and restricted cash—end of year	192,011	114,125
Supplemental Disclosure of Non-Cash Investing and Financing Activities:
Right-of-use assets recognized in exchange for operating leases	4,118	1,802
Property and equipment included in accrued expense and accounts payable	$ 0	$ 121

Stock-Based Compensation - Additional Information (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended			12 Months Ended
	Dec. 31, 2023	Apr. 30, 2023	Jun. 30, 2019	Dec. 31, 2023	Dec. 31, 2022
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Option granted to purchase shares				1,599,227	3,459,500
Exercise price	$ 14
Options exchanged	2,907,127			2,907,127
Weighted average grant date fair value for stock options granted				$ 6.13	$ 10.32
Aggregate grant date fair value of stock options granted				$ 9,800	$ 35,700
Aggregate intrinsic value of stock options exercised				900	3,500
Stock based compensation expense				25,257	$ 22,854
Unrecognized compensation cost	$ 16,100			$ 16,100
Weighted average period of unrecognized compensation cost expected to be recognized				2 years 7 months 6 days
Restricted Stock Units
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Vesting period				4 years
Restricted stock units granted				1,538,302	0
Restricted stock units vested				0
Options exchanged	730,602			730,602
Stock based compensation expense				$ 2,300
Unrecognized compensation cost	$ 26,500			$ 26,500
Weighted average period of unrecognized compensation cost expected to be recognized				2 years 6 months
Maximum \| Stock Option
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Vesting period				4 years
2019 Plan
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Number of shares of common stock reserved for issuance			2,200,000
Percentage of increase in reserved common shares			4.00%
Number of common shares available for future issuance	2,767,209			2,767,209
2014 Plan
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Number of common shares available for future issuance	0			0
2019 ESPP
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Number of shares of common stock reserved for issuance			315,000
Number of common shares available for future issuance	1,704,168			1,704,168
Weighted average grant date fair value for stock options granted				$ 9.88
Stock based compensation expense				$ 300	$ 300
2019 ESPP \| Maximum
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Number of shares of common stock reserved for issuance			3,150,000
Percentage of increase in reserved common shares			1.00%
2023 Inducement Plan
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Number of common shares available for future issuance	940,300			940,300
2023 Inducement Plan \| Common Stock
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Option granted to purchase shares		1,000,000

Income Taxes

12 Months Ended

Dec. 31, 2023

Income Tax Disclosure [Abstract]

Income taxes

11. Income taxes

A reconciliation of the expected income tax expense (benefit) computed using the federal statutory income tax rate the Company’s effective income tax rate is as follows:


	Year ended December 31,
	2023				2022
Expected income tax benefit at the federal statutory rate		21.0		%		21.0		%
State income taxes, net of federal benefit		7.7				7.4
Non-deductible items		(1.1	)			(0.9	)
Research and development credit, net		3.5				3.9
Other		2.4				0.1
Change in valuation allowance		(33.5	)			(31.5	)
Total		0.0		%		0.0		%

The principal components of the Company’s deferred tax assets and liabilities consist of the following:


	As of December 31,
	2023			2022
Deferred tax assets:
Federal and state net operating loss carryforwards	$	52,643		$	57,746
Research and development tax credits		17,444			12,613
Research and development capitalized expenses		32,290			17,148
Accrued compensation and stock-based compensation		17,912			10,274
Deferred revenue/other		13,017			142
Gross deferred tax assets		133,306			97,923
Less: valuation allowance		(133,306	)		(97,923	)
Net deferred tax assets	$	—		$	—

From inception through December 31, 2022, the Company has incurred net operating losses (“NOL”). During 2023, for income tax purposes, the Company was required to fully recognize any unamortized advanced payments from the Acadia Collaboration Agreement as income, which in addition to capitalizing Section 174 research expenses resulted in taxable income that was fully offset by the use of existing net operating losses and tax credits. The Company does not expect future taxable income and should incur substantial future losses.

In accordance with ASC 740, Accounting for Income Taxes, management of the Company has evaluated the positive and negative evidence bearing upon the realizability of its deferred tax assets and has determined that it is more likely than not that the Company will not recognize the net benefits of federal and state deferred tax assets. A full valuation allowance of $133.3 million and $97.9 million was established at December 31, 2023 and 2022, respectively. The change in the valuation allowance was an increase of $35.4 million and $31.8 million in 2023 and 2022, respectively.

As of December 31, 2023, and 2022, the Company had federal NOL carryforwards of $189.5 million and $210.9 million, respectively, which may be available to reduce future taxable income. Federal NOLs generated prior to December 31, 2018 expire at various dates beginning in 2035 and NOLs generated after December 31, 2018 carryforward indefinitely. As of December 31, 2023, and 2022, the Company had state NOLs of $199.4 million and $212.8 million, respectively, which may be available to reduce future taxable income. The state NOLs expire at various dates beginning in 2035.

As of December 31, 2023 and 2022, the Company had federal research and development tax credit (“R&D Credit”) carryforwards of $12.8 million and $9.2 million, respectively, and state R&D Credit carryforwards of $5.9 million and $4.3 million, respectively. Both federal and state R&D Credit carryforwards may be available to reduce future tax liabilities and expire at various dates beginning in 2034.

The Internal Revenue Code of 1986, as amended (“IRC”), provides for a limitation of the annual use of NOLs, R&D Credits, and other tax attributes following certain ownership changes that could limit our ability to utilize NOL and R&D Credit carryforwards. Under IRC Sections 382 and 383 an ownership change is generally defined as a greater than 50% change (by value) in its equity ownership over a three-year period. The Company has experienced ownership changes in the past and based on the existing Section 382 limitations, $0.9 million and $0.02 million of existing Federal NOLs and R&D credits, respectively, will not be utilizable. The Company may experience additional ownership changes in the future because of subsequent shifts in its stock ownership. As a result, the Company's ability to use its pre-change NOLs to offset taxable income, if any, is subject to limitations, which could potentially result in increased future tax liability. In addition, at the state level, there may be periods during which the use of NOLs is suspended or otherwise limited, which could accelerate or permanently increase state taxes owed.

The Company applies ASC 740 related to accounting for uncertainty in income taxes. The Company’s reserves related to income taxes are based on a determination of whether, and how much of, a tax benefit taken by the Company in its tax filings or positions is more likely than not to be realized following resolution of any potential contingencies present related to the tax benefit. At December 31, 2023, and 2022 the Company had no unrecognized tax benefits. Interest and penalty charges, if any, related to unrecognized tax benefits would be classified as income tax expense in the accompanying consolidated statements of operations and comprehensive loss.

- Definition

The entire disclosure for income taxes. Disclosures may include net deferred tax liability or asset recognized in an enterprise's statement of financial position, net change during the year in the total valuation allowance, approximate tax effect of each type of temporary difference and carryforward that gives rise to a significant portion of deferred tax liabilities and deferred tax assets, utilization of a tax carryback, and tax uncertainties information.

+ References

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+ Details

Nature of the Business and Basis of Presentation

12 Months Ended

Dec. 31, 2023

Accounting Policies [Abstract]

Nature of the business and basis of presentation

1. Nature of the business and basis of presentation

Organization

Stoke Therapeutics, Inc. (the Company) was founded in June 2014 and was incorporated under the laws of the State of Delaware. The Company is an early-stage biopharmaceutical company pioneering a new way to treat the underlying causes of severe genetic diseases by precisely upregulating protein expression.

Shelf Registration

In May 2022, the Company filed a universal Shelf Registration statement on Form S-3 (the “Registration Statement”) with the SEC. The Registration Statement was declared effective by the SEC on May 31, 2022, and contains two prospectuses: a base prospectus, which covers the offering, issuance and sale by the Company of up to a maximum aggregate offering price of $400.0 million of its common stock, preferred stock, debt securities, warrants to purchase common stock, preferred stock or debt securities, subscription rights to purchase common stock, preferred stock or debt securities and/or units consisting of some or all of these securities; and a sales agreement prospectus covering the offering, issuance and sale by the Company of up to a maximum aggregate offering price of $150.0 million of its common stock that may be issued and sold under a Controlled Equity Offering Sales Agreement (“Sales Agreement”). The specific terms of any securities to be offered pursuant to the base prospectus will be specified in a prospectus supplement to the base prospectus. The $150.0 million of common stock that may be offered, issued and sold under the sales agreement prospectus is included in the $400.0 million of securities that may be offered, issued and sold by the Company under the base prospectus. As of December 31, 2023, the Company had issued approximately 6.3 million shares of common stock pursuant to the Sales Agreement for net proceeds of $52.1 million. Since December 31, 2023, through the date of the issuance of these consolidated financial statements, the Company sold approximately 0.2 million shares of common stock and received $1.3 million after deducting commissions related to the Sales Agreement. The Company may terminate this at-the-market program at any time, pursuant to its terms.

Uncertainties

The Company is subject to risks and uncertainties common to early-stage companies in the biotechnology industry including, but not limited to, development by competitors of new technological innovations, dependence on key personnel, protection of proprietary technology, compliance with government regulations and ability to secure additional capital to fund operations. Product candidates currently under development 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 the Company’s product development efforts are successful, it is uncertain when, if ever, the Company will realize significant revenue from product sales.

Liquidity

The Company expects that its operating losses and negative cash flows will continue for the foreseeable future. As of the issuance date of these consolidated financial statements, the Company expects that its cash, cash equivalents, marketable securities and restricted cash will be sufficient to fund its operating expenses and capital expenditure requirements through at least twelve months from the issuance date of these consolidated financial statements.

Stock-Based Compensation - Summary of Stock-based Compensation Expense (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2023	Dec. 31, 2022
Employee Service Share Based Compensation Allocation Of Recognized Period Costs [Line Items]
Stock based compensation expense	$ 25,257	$ 22,854
Research and Development
Employee Service Share Based Compensation Allocation Of Recognized Period Costs [Line Items]
Stock based compensation expense	9,925	8,901
General and Administrative
Employee Service Share Based Compensation Allocation Of Recognized Period Costs [Line Items]
Stock based compensation expense	$ 15,332	$ 13,953

Income Taxes - Reconciliation of Expected Income Tax Expense (Benefit) using Federal Statutory Income Tax Rate to Effective Income Tax Rate (Details)	12 Months Ended
	Dec. 31, 2023	Dec. 31, 2022
Income Tax Disclosure [Abstract]
Expected income tax benefit at the federal statutory rate	21.00%	21.00%
State income taxes, net of federal benefit	7.70%	7.40%
Non-deductible items	(1.10%)	(0.90%)
Research and development credit, net	3.50%	3.90%
Other	2.40%	0.10%
Change in valuation allowance	(33.50%)	(31.50%)
Total	0.00%	0.00%

Fair Value Measurements - Schedule of Financial Assets Measured at Fair Value on Recurring Basis and Level of Fair Value Hierarchy Utilized (Details) - USD ($) $ in Thousands	Dec. 31, 2023	Dec. 31, 2022
Fair Value Assets And Liabilities Measured On Recurring And Nonrecurring Basis [Line Items]
Total Marketable Securities	$ 9,952	$ 116,039
Corporate Bonds
Fair Value Assets And Liabilities Measured On Recurring And Nonrecurring Basis [Line Items]
Total Marketable Securities		34,527
Commercial Paper
Fair Value Assets And Liabilities Measured On Recurring And Nonrecurring Basis [Line Items]
Total Marketable Securities		7,978
US Government Debt Securities
Fair Value Assets And Liabilities Measured On Recurring And Nonrecurring Basis [Line Items]
Total Marketable Securities	9,952	73,534
Fair Value, Recurring
Fair Value Assets And Liabilities Measured On Recurring And Nonrecurring Basis [Line Items]
Total cash equivalents	186,186	111,927
Total Marketable Securities	9,952	116,039
Fair Value, Recurring \| Money Market Funds
Fair Value Assets And Liabilities Measured On Recurring And Nonrecurring Basis [Line Items]
Total cash equivalents	186,186	111,927
Fair Value, Recurring \| Level 1
Fair Value Assets And Liabilities Measured On Recurring And Nonrecurring Basis [Line Items]
Total cash equivalents	186,186	111,927
Fair Value, Recurring \| Level 1 \| Money Market Funds
Fair Value Assets And Liabilities Measured On Recurring And Nonrecurring Basis [Line Items]
Total cash equivalents	186,186	111,927
Fair Value, Recurring \| Level 2
Fair Value Assets And Liabilities Measured On Recurring And Nonrecurring Basis [Line Items]
Total Marketable Securities	9,952	116,039
Fair Value, Recurring \| Corporate Bonds
Fair Value Assets And Liabilities Measured On Recurring And Nonrecurring Basis [Line Items]
Total Marketable Securities		34,527
Fair Value, Recurring \| Corporate Bonds \| Level 2
Fair Value Assets And Liabilities Measured On Recurring And Nonrecurring Basis [Line Items]
Total Marketable Securities		34,527
Fair Value, Recurring \| Commercial Paper
Fair Value Assets And Liabilities Measured On Recurring And Nonrecurring Basis [Line Items]
Total Marketable Securities		7,978
Fair Value, Recurring \| Commercial Paper \| Level 2
Fair Value Assets And Liabilities Measured On Recurring And Nonrecurring Basis [Line Items]
Total Marketable Securities		7,978
Fair Value, Recurring \| US Government Debt Securities
Fair Value Assets And Liabilities Measured On Recurring And Nonrecurring Basis [Line Items]
Total Marketable Securities	9,952	73,534
Fair Value, Recurring \| US Government Debt Securities \| Level 2
Fair Value Assets And Liabilities Measured On Recurring And Nonrecurring Basis [Line Items]
Total Marketable Securities	$ 9,952	$ 73,534

Accrued and Other Current Liabilities (Tables)

12 Months Ended

Dec. 31, 2023

Payables and Accruals [Abstract]

Schedule of Accrued and Other Current Liabilities

Accrued and other current liabilities consisted of the following:


	As of December 31,
	2023		2022
Accrued employee compensation costs	$	5,611	$	5,754
Accrued professional		651		525
Accrued research and development costs		4,634		6,601
Current portion of operating lease liabilities		2,062		2,359
Other current liabilities		857		509
	$	13,815	$	15,748

Commitments and Contingencies - Additional Information (Details)	1 Months Ended					12 Months Ended
	Sep. 30, 2021 ft²	Jun. 30, 2021 ft²	Dec. 31, 2018 USD ($) ft² Option	Aug. 31, 2018 USD ($) ft²	Jul. 31, 2015	Dec. 31, 2023 USD ($) ft²	Dec. 31, 2022 USD ($)	Apr. 01, 2022 USD ($)	Dec. 31, 2021 USD ($)
Commitments And Contingencies [Line Items]
Area of space subject to operating lease \| ft²			2,485	23,000
Operating lease term			3 years	3 years
Operating lease cost per year			$ 200,000	$ 900,000
Annual base rent increase percentage for operating lease			2.50%	3.00%
Operating lease commencement date			May 01, 2019	Dec. 10, 2018
Operating lease right-of-use assets						$ 6,611,000	$ 4,753,000
Operating lease liabilities						6,835,000
Number of options to renewal operating lease term \| Option			1
Operating lease, renewal term			2 years
CSHL Agreement
Commitments And Contingencies [Line Items]
Percentage of maximum required payment of sublicense revenue					20.00%
Annual license maintenance fee						10,000.00
Maximum aggregate potential milestone payments payable						900,000
Expenses related to reimbursable patent costs						$ 0	0
CSHL agreement termination description						After the completion of a 90-day waiting period, in May 2023 the Company terminated the CSHL Agreement.
Southampton Agreement
Commitments And Contingencies [Line Items]
Expenses related to reimbursable patent costs						$ 200,000	20,000.00
Payment for license and collaboration agreement						700,000
Member of Board of Directors
Commitments And Contingencies [Line Items]
Scientific advisory services expenses						0	20,000.00
ASU 2016-02
Commitments And Contingencies [Line Items]
Operating leases expense						$ 2,400,000	$ 2,200,000
Lease Commencement on December 15, 2021
Commitments And Contingencies [Line Items]
Area of space subject to operating lease \| ft²	23,000
Operating lease term	3 years
Operating lease commencement date	Dec. 15, 2021
Operating lease expiration date	Dec. 31, 2024
Operating lease right-of-use assets									$ 3,500,000
Operating lease liabilities									3,500,000
Lease Commencement on January 1, 2025
Commitments And Contingencies [Line Items]
Area of space subject to operating lease \| ft²						38,000
Operating lease term						2 years
Operating lease commencement date						Jan. 01, 2025
Operating lease expiration date						Dec. 31, 2026
Operating lease right-of-use assets						$ 4,100,000
Lease Commencement on April 2022
Commitments And Contingencies [Line Items]
Area of space subject to operating lease \| ft²	15,000
Operating lease commencement date	Apr. 01, 2022
Operating lease expiration date	Dec. 31, 2024
Operating lease right-of-use assets								$ 1,800,000
Operating lease liabilities								$ 1,800,000
Lease Extension End Date April 30, 2025
Commitments And Contingencies [Line Items]
Area of space subject to operating lease \| ft²		2,485
Operating lease term		3 years
Operating lease commencement date		May 01, 2022
Operating lease expiration date		Apr. 30, 2025
Operating lease right-of-use assets									700,000
Operating lease liabilities									700,000
Operating lease, renewal term		2 years
Area of additional space subject to operating lease \| ft²		2,357
Additional operating lease commencement date		Jul. 06, 2021
Additional operating lease expiration date		Apr. 30, 2025
Additional operating lease, right-of-use asset									800,000
Additional operating lease, liabilities									$ 800,000
Operating lease, option to extend		The amended lease provides the Company with the option to extend the term of the lease for an additional two years.
Operating lease, existence of option to extend [true false]		true

Fair Value Measurements (Tables)

12 Months Ended

Dec. 31, 2023

Fair Value Disclosures [Abstract]

Schedule of Financial Assets Measured at Fair Value on Recurring Basis and Level of Fair Value Hierarchy Utilized

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


	Fair value measurements as of December 31, 2023
	Level 1		Level 2		Level 3		Total
Cash equivalents:
Money market funds	$	186,186	$	—	$	—	$	186,186
Total	$	186,186	$	—	$	—	$	186,186

Marketable Securities:
US Government debt securities	$	—	$	9,952	$	—	$	9,952
Total	$	—	$	9,952	$	—	$	9,952


	Fair value measurements as of December 31, 2022
	Level 1		Level 2		Level 3		Total
Cash equivalents:
Money market funds	$	111,927	$	—	$	—	$	111,927
Total	$	111,927	$	—	$	—	$	111,927

Marketable Securities:
Corporate bonds	$	—	$	34,527	$	—	$	34,527
Commercial paper		—		7,978		—		7,978
US Government debt securities		—		73,534		—		73,534
Total	$	—	$	116,039	$	—	$	116,039

Summary of Significant Accounting Policies and Recent Accounting Pronouncements

12 Months Ended

Dec. 31, 2023

Accounting Policies [Abstract]

Summary of significant accounting policies and recent accounting pronouncements

2. Summary of significant accounting policies and recent accounting pronouncements

Basis of presentation and consolidation

The accompanying consolidated financial statements have been prepared in accordance with U.S. generally accepted accounting principles (GAAP), and include the accounts of Stoke Therapeutics, Inc. and its wholly-owned subsidiary. Any reference in these notes to applicable guidance is meant to refer to GAAP as found in the Accounting Standards Codification (“ASC”) and Accounting Standards Update (“ASU”) of the Financial Accounting Standards Board (“FASB”). All intercompany transactions between and among the Company and its consolidated subsidiary have been eliminated.

Use of estimates

The preparation of consolidated financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets, liabilities, equity, expenses and disclosure of contingent assets and liabilities. Estimates are periodically reviewed in light of changes in circumstances, facts and experience. Actual results could differ from those estimates.

Cash and cash equivalents

The Company considers all highly liquid investments with an original maturity of three months or less at the date of purchase to be cash equivalents. The Company deposits its cash in checking, sweep and money market accounts.

Restricted cash

At December 31, 2023, restricted cash consisted of money market accounts collateralizing letters of credit issued as security deposits in connection with the Company’s leases of its corporate facilities.

The following table reconciles cash and cash equivalents and restricted cash per the consolidated balance sheets to the statements of cash flows:


	As of December 31,
	2023		2022
Cash and cash equivalents	$	191,442	$	113,556
Restricted cash		569		569
	$	192,011	$	114,125

Marketable Securities

Marketable securities consist of government securities and obligations, corporate bonds and commercial paper with original maturities of more than 90 days at the purchase date. Investments are classified as available-for-sale and are recorded on the balance sheet at fair value with unrealized gains or losses reported as a separate component of other comprehensive income/(loss). Management determines the appropriate classification of its investments at the time of purchase and reevaluates such determination at each balance sheet date.

Concentration of credit risk

Financial instruments that potentially expose the Company to concentrations of credit risk primarily consist of cash, cash equivalents and marketable securities. The Company maintains its cash, cash equivalents and marketable securities at accredited financial institutions in amounts that exceed federally insured limits. The Company does not believe that it is subject to unusual credit risk beyond the normal credit risk associated with commercial banking relationships.

Fair value of financial instruments

ASC Topic 820, Fair Value Measurement (ASC 820), establishes a fair value hierarchy for instruments measured at fair value that distinguishes between assumptions based on market data (observable inputs) and the Company’s own assumptions (unobservable inputs). Observable inputs are those that market participants would use in pricing the asset or liability based on market data obtained from sources independent of the Company. Unobservable inputs are inputs that reflect the Company’s assumptions about the inputs that market participants would use in pricing the asset or liability and are developed based on the best information available in the circumstances. ASC 820 identifies fair value as the exchange price, or exit price, representing the amount that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants. As a basis for considering market participant assumptions in fair value measurements, ASC 820 establishes a three-tier value hierarchy that distinguishes between the following:

Level 1—Quoted market prices in active markets for identical assets or liabilities.

Level 2—Inputs other than Level 1 inputs that are either directly or indirectly observable, such as quoted market prices, interest rates and yield curves.

Level 3—Unobservable inputs developed using estimates of assumptions developed by the Company, which reflect those that a market participant would use.

To the extent the valuation is based on models or inputs that are less observable or unobservable in the market, the determination of fair values requires more judgment. Accordingly, the degree of judgment exercised by the Company in determining fair value is greatest for instruments categorized as Level 3. A financial instrument’s level within the fair value hierarchy is based on the lowest level of any input that is significant to the fair value measurement.

Revenue recognition

The Company recognizes revenue in accordance with ASC Topic 606, Revenue from Contracts with Customers (“ASC 606”). This standard applies to all contracts with customers, except for contracts that are within the scope of other standards. Under ASC 606, an entity recognizes revenue when its customer obtains control of promised goods or services, in an amount that reflects the consideration which the entity expects to receive in exchange for those goods or services.

In January 2022, the Company entered into a license and collaboration agreement with Acadia Pharmaceuticals, Inc. (“Acadia”) which is within the scope of ASC 606 (see Note 8). In determining the appropriate amount of revenue to be recognized as it fulfills its obligations under this agreement, the Company performs the following steps: (i) identification of the promised goods or services in the contract; (ii) determination of whether the promised goods or services are performance obligations including whether they are distinct in the context of the contract; (iii) measurement of the transaction price, including the constraint on variable consideration; (iv) allocation of the transaction price to the performance obligations; and (v) recognition of revenue when (or as) the Company satisfies each performance obligation. As part of the accounting for this agreement, the Company must use its judgment to determine: (a) the number of performance obligations based on the determination under step (ii) above; (b) the transaction price under step (iii) above; (c) the stand-alone selling price for each performance obligation identified in the contract for the allocation of transaction price in step (iv) above; and (d) the contract term and pattern of satisfaction of the performance obligations under step (v) above. The Company uses judgment to determine whether milestones or other variable consideration, except for royalties, should be included in the transaction price. The transaction price is allocated to each performance obligation on a relative stand-alone selling price basis, for which the Company recognizes revenue as or when the performance obligations under the contract are satisfied.

Amounts due to the Company for satisfying the revenue recognition criteria or that are contractually due based upon the terms of the collaboration agreement are recorded as accounts receivable in the Company’s consolidated balance sheets. Amounts received prior to satisfying the revenue recognition criteria are recorded as deferred revenue in the Company’s consolidated balance sheets. Amounts expected to be recognized as revenue within the 12 months following the balance sheet date are classified as current deferred revenue. Amounts not expected to be recognized as revenue within the 12 months following the balance sheet date are classified as deferred revenue, net of current portion.

Upfront license fees

The licenses of the Company’s intellectual property granted to Acadia was not determined to be distinct from the other promises or performance obligations identified in the agreement. Accordingly, such licenses are therefore combined with other promises in the agreement. The Company exercises judgment to assess the nature of the combined performance obligation to determine whether the combined performance obligation is satisfied over time or at a point in time and, if over time, the appropriate method of measuring progress for purposes of recognizing revenue. The Company evaluates the measure of progress each reporting period and, if necessary, adjusts the measure of performance and related revenue recognition.

Customer options

If an arrangement is determined to contain customer options that allow the customer to acquire additional goods or services, the goods and services underlying the customer options are not considered to be performance obligations at the outset of the arrangement, as they are contingent upon option exercise. The Company evaluates the customer options for material rights or options to acquire additional goods or services for free or at a discount. If the customer options are determined to represent a material right, the material right is recognized as a separate performance obligation at the outset of the arrangement. No such material rights were identified in the arrangement with Acadia. If such material rights were identified, then the Company would allocate the transaction price to material rights based on the relative standalone selling price, which is determined based on the identified discount and the probability that the customer will exercise the option. Amounts allocated to a material right are not recognized or begin to be recognized as revenue until, at the earliest, the option is exercised.

Research and development services

The promises under the Company’s collaboration agreement with Acadia includes research and development services to be performed by the Company for or on behalf of the customer. Payments or reimbursements resulting from the Company’s research and development efforts are recognized as the services are performed and presented on a gross basis because the Company is the principal for such efforts.

Milestone payments

At the inception of the Acadia arrangement that includes development milestone payments, the Company evaluates whether the milestones are considered probable of being achieved and estimates the amount to be included in the transaction price using the most likely amount method. If it is probable that a significant revenue reversal would not occur, the associated milestone value is included in the transaction price. Milestone payments that are not within the control of the Company or the licensee, such as regulatory approvals, are not considered probable of being achieved until those approvals are received. The Company evaluates factors such as the scientific, clinical, regulatory, commercial and other risks that must be overcome to achieve the particular milestone in making this assessment. There is judgment involved in determining whether it is probable that a significant revenue reversal would not occur. At the end of each reporting period, the Company reevaluates the probability of achievement of all milestones subject to constraint and, if necessary, adjusts its estimate of the overall transaction price. Any such adjustments are recorded on a cumulative catch-up basis, which would affect revenues and earnings in the period of adjustment. The development milestones in the Acadia arrangement were not considered probable of achievement at the outset of the arrangement and as of December 31, 2023.

Deferred offering costs

The Company capitalizes certain legal, professional accounting and other third-party fees that are directly associated with in-process equity financings as deferred offering costs until such financings are consummated. After consummation of the equity financing, these costs are recorded in the consolidated statement of stockholders’ equity as a reduction of additional paid-in capital.

Property and equipment

Property and equipment are recorded at cost less accumulated depreciation. Cost includes the acquisition costs and all costs necessary to bring the asset to the location and working condition necessary for its intended use. Depreciation expense is recognized using the straight-line method over the estimated useful life of each asset. Upon retirement or sale, the cost of assets disposed of and the related accumulated depreciation are removed from the accounts and any resulting gain or loss is included in the accompanying consolidated statements of operations and comprehensive loss. Expenditures for normal, recurring or periodic repairs and maintenance related to property and equipment are charged to expense as incurred. The cost for planned major maintenance activities, including the related acquisition or construction of assets, is capitalized if it will result in future economic benefits.

Estimated useful lives for property and equipment are as follows:


Property and equipment		Estimated useful life
Computer and office equipment		3-5 years
Laboratory equipment and Furniture and fixtures		5-7 years
Leasehold improvements		Lesser of estimated useful life or remaining lease term

Impairment of long-lived assets

The Company reviews the recoverability of its long-lived assets when events or changes in circumstances occur that indicate that the carrying value of the assets may not be recoverable. The assessment of possible impairment is based on the ability to recover the carrying value of the assets from the expected future cash flows (undiscounted) of the related operations. If these cash flows are less than the carrying value of such assets, an impairment loss for the difference between the estimated fair value and carrying value is recorded. There were no impairment losses recognized during the years ended December 31, 2023 and 2022.

Research and development costs

Research and development costs are expensed as incurred. Research and development expenses are comprised of costs incurred in performing research and development activities, including salaries and benefits, facilities costs, depreciation, third-party license fees, and costs related to third parties engaged to conduct preclinical research development activities.

The Company has entered into various research and development contracts with research institutions and other companies to conduct research on its behalf. These agreements are generally cancellable. The Company records accruals for estimated ongoing research costs. When evaluating the adequacy of the accrued liabilities, the Company analyzes progress of the studies, including the phase or completion of events, invoices received and contracted costs. Significant judgments and estimates may be required in determining the accrued balances at the end of any reporting period. Actual results could differ from the Company’s estimates. The Company’s historical accrual estimates have not been materially different from the actual costs.

Stock-based compensation

The Company measures its stock-based awards granted based on the estimated fair values of the awards and recognizes the compensation expense for employees and nonemployees over the requisite service period.

Stock options

The Company uses the Black-Scholes option-pricing model to estimate the fair value of its stock options.

The Company has elected the practical expedient to use the midpoint between vesting date and the contractual term as the expected term for certain awards with service or performance conditions. Stock-based compensation is recognized using the straight-line method. Forfeitures of unvested stock-based awards are accounted for when they occur.

Restricted stock units ("RSUs")

For RSUs issued to employees, the Company recognizes the grant date fair value of the RSUs on a straight-line basis over the requisite service period, which is generally the vesting period of the respective awards. RSUs granted typically vest annually over a four-year period but may be granted with different vesting terms.

Patent costs

All patent-related costs incurred in connection with filing and prosecuting patent applications are expensed as incurred due to the uncertainty about the recovery of the expenditure. Amounts incurred are classified as general and administrative expenses in the accompanying consolidated statements of operations and comprehensive loss.

Income taxes

The Company accounts for income taxes using the asset and liability method, which requires the recognition of deferred tax assets and liabilities for the estimated future tax consequences attributable to temporary differences between the consolidated financial statement carrying amounts of existing assets and liabilities and their respective tax base. Deferred tax assets and liabilities are determined on the basis of the differences between the consolidated financial statements and tax basis of assets and liabilities using enacted tax rates in effect for the year in which the temporary differences are expected to be settled or recovered. Changes in deferred tax assets and liabilities are recorded in the provision for income taxes. The Company assesses the likelihood that its deferred tax assets will be recovered from future taxable income and, to the extent it believes, based upon the weight of available evidence that it is more likely than not that all or a portion of the deferred tax assets will not be realized, a valuation allowance is established through a charge to income tax expense. Potential for recovery of deferred tax assets is evaluated by estimating the future taxable profits expected and considering prudent and feasible tax planning strategies. At December 31, 2023 and 2022, the Company has recorded a full valuation allowance.

Reserves are provided for tax benefits for which realization is uncertain. Such benefits are only recognized when the underlying tax position is considered more-likely-than-not to be sustained on examination by a taxing authority, assuming they possess full knowledge of the position and facts. Interest and penalties related to uncertain tax positions are recognized in the provision of income taxes; however, the Company currently has no interest or penalties related to uncertain income tax benefits.

Segment and geographic information

Operating segments are defined as components of an entity about which separate discrete information is available for evaluation by the chief operating decision maker, or decision-making group, in deciding how to allocate resources and in assessing performance. The Company operates in one segment in the United States. The Company’s chief executive officer, as the chief operating decision-maker, manages and allocates resources to the operations of the Company on a total company basis using consolidated financial information.

Emerging growth company and smaller reporting company status

The Company is an emerging growth company, as defined in the Jumpstart Our Business Startups Act of 2012 (the JOBS Act). Under the JOBS Act, emerging growth companies can delay adopting new or revised accounting standards issued subsequent to the enactment of the JOBS Act, until such time as those standards apply to private companies.

The Company has elected to use this extended transition period for complying with new or revised accounting standards that have different effective dates for public and private companies until the earlier of the date that it is (i) no longer an emerging growth company or (ii) affirmatively and irrevocably opt out of the extended transition period provided in the JOBS Act. As a result, the Company’s consolidated financial statements may not be comparable to companies that comply with the new or revised accounting pronouncements as of public company effective dates.

The Company will remain an emerging growth company until the earliest of (i) the last day of the first fiscal year (a) following the fifth anniversary of the completion of our IPO, (b) in which the Company has total annual gross revenue of at least $1.235 billion or (c) in which the Company is deemed to be a large accelerated filer, which means the market value of the Company’s common stock that is held by non-affiliates exceeds $700.0 million as of the prior June 30th, and (ii) the date on which the Company has issued more than $1.0 billion in non-convertible debt securities during the prior three- year period. The Company anticipates ceasing to be an emerging growth company as of December 31, 2024, which is the last day of our fiscal year following the fifth anniversary of the completion of our IPO.

The Company is also a “smaller reporting company,” meaning that in the event of an initial public offering the market value of its stock held by non-affiliates plus the proposed aggregate amount of gross proceeds to the Company as a result of such offering is less than $700.0 million and its annual revenue is less than $100.0 million during the most recently completed fiscal year. The Company may continue to be a smaller reporting company as long as either (i) the market value of its stock held by non-affiliates is less than $250.0 million or (ii) its annual revenue is less than $100.0 million during the most recently completed fiscal year and the market value of its stock held by non-affiliates is less than $700.0 million. If the Company is a smaller reporting company at the time it ceases to be an emerging growth company, the Company may continue to rely on exemptions from certain disclosure requirements that are available to smaller reporting companies. Specifically, as a smaller reporting company, the Company may choose to present only the two most recent fiscal years of audited financial statements in its Annual Report on Form 10-K and, similar to emerging growth companies, smaller reporting companies have reduced disclosure obligations regarding executive compensation.

Recently issued accounting pronouncements

In November 2023, the FASB issued ASU 2023-07, “Segment Reporting (Topic 280): Improvements to Reportable Segment Disclosures” (“ASU 2023-07”), which expands disclosures about a public entity’s reportable segments and requires more enhanced information about a reportable segment’s expenses, interim segment profit or loss, and how a public entity’s chief operating decision maker uses reported segment profit or loss information in assessing segment performance and allocating resources. The standard is effective for annual reporting periods beginning after December 15, 2023, and interim periods within years beginning after December 15, 2024, with early adoption permitted. The Company is currently assessing the impact that the adoption will have on its consolidated financial statements.

In December 2023, the FASB issued ASU 2023-09, “Income Taxes (Topic 740): Improvements to Income Tax Disclosures” (“ASU 2023-09”). ASU 2023-09 requires that an entity disclose specific categories in the effective tax rate reconciliation as well as provide additional information for reconciling items that meet a quantitative threshold and certain disclosures of state versus federal income tax expenses and taxes paid. ASC 2023-09 is effective for fiscal years beginning after December 15, 2024. The Company does not expect the adoption of ASU 2023-09 to have a material impact on its consolidated financial statements and will adopt the standard effective January 1, 2025.

Property and Equipment, Net - Summary of Property, and Equipment, Net (Details) - USD ($) $ in Thousands	Dec. 31, 2023	Dec. 31, 2022
Property Plant And Equipment [Line Items]
Property, and equipment, gross	$ 12,494	$ 10,882
Less accumulated depreciation	(6,671)	(4,207)
Property, and equipment, net	5,823	6,675
Laboratory Equipment
Property Plant And Equipment [Line Items]
Property, and equipment, gross	9,383	7,903
Furniture and Fixtures
Property Plant And Equipment [Line Items]
Property, and equipment, gross	312	312
Leasehold Improvements
Property Plant And Equipment [Line Items]
Property, and equipment, gross	2,294	1,867
Office Equipment
Property Plant And Equipment [Line Items]
Property, and equipment, gross	440	353
Construction in Progress
Property Plant And Equipment [Line Items]
Property, and equipment, gross	$ 65	$ 447

Net Loss Per Share - Schedule of Antidilutive Securities Excluded from Computation of Diluted Net Loss Per Share (Details) - shares	12 Months Ended
	Dec. 31, 2023	Dec. 31, 2022
Antidilutive Securities Excluded From Computation Of Earnings Per Share [Line Items]
Anti-dilutive securities excluded from computation of earnings per share, amount	7,991,165	8,274,647
Employee Stock Option
Antidilutive Securities Excluded From Computation Of Earnings Per Share [Line Items]
Anti-dilutive securities excluded from computation of earnings per share, amount	6,478,063	8,274,647
Restricted Stock Units
Antidilutive Securities Excluded From Computation Of Earnings Per Share [Line Items]
Anti-dilutive securities excluded from computation of earnings per share, amount	1,513,102

Commitments and Contingencies - Summary of Weighted Average Remaining Lease Term and Weighted Average Discount Rate of Operating Leases (Details)	Dec. 31, 2023
Commitments and Contingencies Disclosure [Abstract]
Weighted average remaining lease term in years	2 years 10 months 24 days
Weighted average discount rate	9.92%

Net Loss Per Share - Schedule of Computation of Basic and Diluted Net Loss Per Share (Details) - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2023	Dec. 31, 2022
Numerator:
Net Income (Loss)	$ (104,699)	$ (101,067)
Denominator:
Weighted-average common shares outstanding, basic	43,994,862	38,897,442
Weighted-average common shares outstanding, diluted	43,994,862	38,897,442
Net loss per share, basic	$ (2.38)	$ (2.60)
Net loss per share, diluted	$ (2.38)	$ (2.60)

- Definition

The amount of net income (loss) for the period per each share of common stock or unit outstanding during the reporting period.

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The amount of net income (loss) for the period available to each share of common stock or common unit outstanding during the reporting period and to each share or unit that would have been outstanding assuming the issuance of common shares or units for all dilutive potential common shares or units outstanding during the reporting period.

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+ Details

- Definition

The portion of profit or loss for the period, net of income taxes, which is attributable to the parent.

+ References

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+ Details

Summary of Significant Accounting Policies and Recent Accounting Pronouncements (Tables)

12 Months Ended

Dec. 31, 2023

Accounting Policies [Abstract]

Schedule of Cash and Cash Equivalents and Restricted Cash

The following table reconciles cash and cash equivalents and restricted cash per the consolidated balance sheets to the statements of cash flows:


	As of December 31,
	2023		2022
Cash and cash equivalents	$	191,442	$	113,556
Restricted cash		569		569
	$	192,011	$	114,125

Schedule of Estimated Useful Lives for Property and Equipment

Estimated useful lives for property and equipment are as follows:


Property and equipment		Estimated useful life
Computer and office equipment		3-5 years
Laboratory equipment and Furniture and fixtures		5-7 years
Leasehold improvements		Lesser of estimated useful life or remaining lease term

Pay vs Performance Disclosure - USD ($) $ in Thousands	12 Months Ended
Pay vs Performance Disclosure - USD ($) $ in Thousands	Dec. 31, 2023	Dec. 31, 2022
Pay vs Performance Disclosure
Net Income (Loss)	$ (104,699)	$ (101,067)

- Definition

The portion of profit or loss for the period, net of income taxes, which is attributable to the parent.

+ References

+ Details

Commitments and Contingencies - Summary of Lease Balances (Details) - USD ($) $ in Thousands	Dec. 31, 2023	Dec. 31, 2022
Commitments and Contingencies Disclosure [Abstract]
Operating lease right-of-use assets	$ 6,611	$ 4,753
Current portion of operating lease liabilities	$ 2,062	$ 2,359
Operating Lease Liability Current Statement Of Financial Position Extensible List	Liabilities, Current	Liabilities, Current
Non-current portion of operating lease liabilities	$ 4,773	$ 2,717
Operating Lease Liability Noncurrent Statement Of Financial Position Extensible List	Other long term liabilities	Other long term liabilities
Total operating lease liabilities	$ 6,835	$ 5,076

Employee Benefits - Additional Information (Details) - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2023	Dec. 31, 2022
Defined Contribution Plan Disclosure [Line Items]
Contributions to 401(k) Plan	$ 0.7	$ 0.6
Maximum
Defined Contribution Plan Disclosure [Line Items]
Maximum matching contribution percentage of employees salary	4.00%

Income Taxes - Schedule of Deferred Tax Assets and Liabilities (Details) - USD ($) $ in Thousands	Dec. 31, 2023	Dec. 31, 2022
Deferred tax assets:
Federal and state net operating loss carryforwards	$ 52,643	$ 57,746
Research and development tax credits	17,444	12,613
Research and development capitalized expenses	32,290	17,148
Accrued compensation and stock-based compensation	17,912	10,274
Deferred revenue/other	13,017	142
Gross deferred tax assets	133,306	97,923
Less: valuation allowance	$ (133,306)	$ (97,923)

Fair Value Measurements

12 Months Ended

Dec. 31, 2023

Fair Value Disclosures [Abstract]

Fair value measurements

3. Fair value measurements


	Fair value measurements as of December 31, 2023
	Level 1		Level 2		Level 3		Total
Cash equivalents:
Money market funds	$	186,186	$	—	$	—	$	186,186
Total	$	186,186	$	—	$	—	$	186,186

Marketable Securities:
US Government debt securities	$	—	$	9,952	$	—	$	9,952
Total	$	—	$	9,952	$	—	$	9,952


	Fair value measurements as of December 31, 2022
	Level 1		Level 2		Level 3		Total
Cash equivalents:
Money market funds	$	111,927	$	—	$	—	$	111,927
Total	$	111,927	$	—	$	—	$	111,927

Marketable Securities:
Corporate bonds	$	—	$	34,527	$	—	$	34,527
Commercial paper		—		7,978		—		7,978
US Government debt securities		—		73,534		—		73,534
Total	$	—	$	116,039	$	—	$	116,039

The Company’s cash equivalents and marketable securities are carried at fair value, determined according to the fair value hierarchy described above and in Note 2. The carrying value of the Company’s accounts payable and accrued expenses approximate their fair values due to the short-term nature of these liabilities.

The Company’s assets with fair value categorized as Level 1 within the fair value hierarchy include money market funds. Money market funds are publicly traded mutual funds and are presented as cash equivalents on the consolidated balance sheets as of December 31, 2023 and 2022.

The Company measures its marketable securities at fair value on a recurring basis and classifies those instruments within Level 2 of the fair value hierarchy. Marketable securities are valued using models or other valuation methodologies that use Level 2 inputs. These models are primarily industry-standard models that consider various assumptions, including time value, yield curve, volatility factors, default rates, current market and contractual prices for the underlying financial instruments, as well as other economic measures. Substantially all of these assumptions are observable in the marketplace, can be derived from observable data or are supported by observable levels at which transactions are executed in the marketplace.

There were no transfers to Level 3 in the periods presented.

- Definition

The entire disclosure for the fair value of financial instruments (as defined), including financial assets and financial liabilities (collectively, as defined), and the measurements of those instruments as well as disclosures related to the fair value of non-financial assets and liabilities. Such disclosures about the financial instruments, assets, and liabilities would include: (1) the fair value of the required items together with their carrying amounts (as appropriate); (2) for items for which it is not practicable to estimate fair value, disclosure would include: (a) information pertinent to estimating fair value (including, carrying amount, effective interest rate, and maturity, and (b) the reasons why it is not practicable to estimate fair value; (3) significant concentrations of credit risk including: (a) information about the activity, region, or economic characteristics identifying a concentration, (b) the maximum amount of loss the entity is exposed to based on the gross fair value of the related item, (c) policy for requiring collateral or other security and information as to accessing such collateral or security, and (d) the nature and brief description of such collateral or security; (4) quantitative information about market risks and how such risks are managed; (5) for items measured on both a recurring and nonrecurring basis information regarding the inputs used to develop the fair value measurement; and (6) for items presented in the financial statement for which fair value measurement is elected: (a) information necessary to understand the reasons for the election, (b) discussion of the effect of fair value changes on earnings, (c) a description of [similar groups] items for which the election is made and the relation thereof to the balance sheet, the aggregate carrying value of items included in the balance sheet that are not eligible for the election; (7) all other required (as defined) and desired information.

+ References + Details

Summary of Significant Accounting Policies and Recent Accounting Pronouncements - Schedule of Estimated Useful Lives for Property and Equipment (Details)	Dec. 31, 2023
Computer and Office Equipment \| Minimum
Property Plant And Equipment [Line Items]
Estimated useful life	3 years
Computer and Office Equipment \| Maximum
Property Plant And Equipment [Line Items]
Estimated useful life	5 years
Laboratory Equipment and Furniture and Fixtures \| Minimum
Property Plant And Equipment [Line Items]
Estimated useful life	5 years
Laboratory Equipment and Furniture and Fixtures \| Maximum
Property Plant And Equipment [Line Items]
Estimated useful life	7 years
Leasehold Improvements
Property Plant And Equipment [Line Items]
Property, Plant, and Equipment, Useful Life, Term, Description [Extensible Enumeration]	us-gaap:UsefulLifeShorterOfTermOfLeaseOrAssetUtilityMember

Income Taxes (Tables)

12 Months Ended

Dec. 31, 2023

Income Tax Disclosure [Abstract]

Reconciliation of Expected Income Tax Expense (Benefit) using Federal Statutory Income Tax Rate to Effective Income Tax Rate

A reconciliation of the expected income tax expense (benefit) computed using the federal statutory income tax rate the Company’s effective income tax rate is as follows:


	Year ended December 31,
	2023				2022
Expected income tax benefit at the federal statutory rate		21.0		%		21.0		%
State income taxes, net of federal benefit		7.7				7.4
Non-deductible items		(1.1	)			(0.9	)
Research and development credit, net		3.5				3.9
Other		2.4				0.1
Change in valuation allowance		(33.5	)			(31.5	)
Total		0.0		%		0.0		%

Schedule of Deferred Tax Assets and Liabilities

The principal components of the Company’s deferred tax assets and liabilities consist of the following:


	As of December 31,
	2023			2022
Deferred tax assets:
Federal and state net operating loss carryforwards	$	52,643		$	57,746
Research and development tax credits		17,444			12,613
Research and development capitalized expenses		32,290			17,148
Accrued compensation and stock-based compensation		17,912			10,274
Deferred revenue/other		13,017			142
Gross deferred tax assets		133,306			97,923
Less: valuation allowance		(133,306	)		(97,923	)
Net deferred tax assets	$	—		$	—

License and Collaboration Agreement with Acadia Pharmaceuticals Inc - Additional Information (Details) - Acadia Pharmaceuticals Inc. - USD ($) $ in Millions	1 Months Ended	12 Months Ended
	Jan. 31, 2022	Dec. 31, 2023
License And Collaboration Agreement [Line Items]
Upfront Payment received	$ 60.0
Potential milestone payments receivable	$ 907.5
Remaining upfront consideration		$ 48.4

Summary of Significant Accounting Policies and Recent Accounting Pronouncements - Schedule of Cash and Cash Equivalents and Restricted Cash (Details) - USD ($) $ in Thousands	Dec. 31, 2023	Dec. 31, 2022	Dec. 31, 2021
Accounting Policies [Abstract]
Cash and cash equivalents	$ 191,442	$ 113,556
Restricted cash	569	569
Total cash, cash equivalents and restricted cash	$ 192,011	$ 114,125	$ 145,464

Stock-Based Compensation

12 Months Ended

Dec. 31, 2023

Share-Based Payment Arrangement [Abstract]

Stock-Based Compensation

9. Stock-Based Compensation

In June 2019, the Company’s board of directors and stockholders approved the 2019 Equity Incentive Plan (the “2019 Plan”) which became effective on June 17, 2019 and replaced the Company’s 2014 Equity Incentive Plan (the “2014 Plan”). In addition to the shares of common stock reserved for future issuance under the 2014 Plan that were added to the 2019 Plan upon its effective date, the Company initially reserved 2,200,000 shares of common stock for issuance under the 2019 Plan. The number of shares reserved for issuance under the Company’s 2019 Plan will increase automatically on January 1 of each of 2020 through 2029 by the number of shares equal to 4% of the aggregate number of outstanding shares of the Company’s common stock as of the immediately preceding December 31, or a lesser number as may be determined by the Company’s board of directors.

In April 2023, the Company’s board of directors adopted the Stoke Therapeutics, Inc. 2023 Inducement Plan (the “2023 Plan”). As permitted by Nasdaq stock market rules, the Company’s stockholders were not required to approve the Inducement Plan. The Inducement Plan provides for up to 1,000,000 shares of the Company’s common stock under awards granted to newly hired employees. An “award” is any right to receive common stock of the Company through nonstatutory stock options or restricted stock units.

As of December 31, 2023 there were no shares available for future issuance under the 2014 Plan, 2,767,209 shares were available for future issuance under the 2019 Plan and 940,300 shares were available under the 2023 Plan.

During the years ended December 31, 2023 and 2022, the Company granted options to purchase 1,599,227 and 3,459,500 shares of common stock to certain of its employees, and directors, respectively. The options vest over a period of up to four years. During the year ended December 31, 2023, the Company granted 1,538,302 restricted stock units to its employees. The restricted stock units vest over a period of up to four years.

In December 2023, the Company offered employees with outstanding option grants that had an exercise price of greater than $14.00 per share the opportunity to exchange those options for a number of restricted stock units with a fair value equal to the then fair value of the options surrendered. As a result, there was no material incremental compensation expense associated with those RSUs issued in exchange for options. The RSUs vest annually over a period of one to two years. In the aggregate, 2,907,127 options were exchanged for 730,602 RSUs.

A summary of stock option activity for awards is presented below:


	Number of shares			Weighted average exercise price		Weighted average remaining contractual life (years)		Aggregate intrinsic value(1)
Outstanding as of December 31, 2022		8,274,647		$	18.28		7.6	$	20,598
Granted		1,599,227			9.32
Exercised		(145,877	)		2.55
Forfeitures(2)		(1,449,164	)		28.00
Expired(2)		(1,800,770	)		34.88
Outstanding as of December 31, 2023		6,478,063		$	9.64		6.9	$	8,435
Exercisable as of December 31, 2023		4,034,517		$	8.88		5.7	$	8,439

(1)

The aggregate intrinsic value is calculated as the difference between the exercise price of the underlying options and the fair value of the common stock for the options that were in the money at December 31, 2023 and 2022.

(2)

Options exchanged are classified as either forfeitures or expired based on vesting status at the time of Exchange Offer.

The weighted average grant date fair value for stock options granted during the years ended December 31, 2023 and 2022 was $6.13 and $10.32, respectively. The aggregate grant date fair value of stock options granted during the years ended

December 31, 2023 and 2022 was $9.8 million and $35.7 million, respectively. The aggregate intrinsic value of stock options exercised during the year ended December 31, 2023 and 2022 was $0.9 million and $3.5 million, respectively.

A summary of restricted stock unit activity is presented below:


	Number of shares			Aggregate intrinsic value		Weighted average grant date fair value
Outstanding as of December 31, 2022		—		$	—	$	—
Awarded		807,700					9.04
RSUs in exchange for options as part of option exchange		730,602					3.95
Vested		—					—
Forfeitures		(25,200	)				9.15
Outstanding as of December 31, 2023		1,513,102		$	7,959	$	6.58
Vested or expected to vest as of December 31, 2023		1,513,102		$	7,959	$	6.58

For the year ended December 31, 2023, there were no vested RSUs.

Stock-based compensation

The Company recorded stock-based compensation expense of $25.3 million and $22.9 million during the years ended December 31, 2023 and 2022, respectively. Of the total stock-based compensation recorded during the year ending December 31, 2023, $2.3 million is related to restricted stock units. There were no grants of restricted stock units prior to 2023.

As of December 31, 2023, there was $16.1 million of unrecognized compensation cost related to unvested stock options granted under the 2019 and the 2023 Plans. Compensation expense is expected to be recognized over a weighted average period of 2.6 years as of December 31, 2023. As of December 31, 2023, there was $26.5 million of unrecognized stock-based compensation related to restricted stock units and it is expected to be recognized over a weighted average period of 2.5 years.

Stock-based compensation expense recorded as research and development and general and administrative expenses in the accompanying consolidated statements of operations and comprehensive loss is as follows:


	Year ended December 31,
	2023		2022
Research and development	$	9,925	$	8,901
General and administrative		15,332		13,953
	$	25,257	$	22,854

The Company uses the Black-Scholes option pricing model to calculate the grant-date fair value of stock options. The fair values of the options granted to employees and directors were calculated using the following assumptions for the years ended December 31, 2023 and 2022:


	Year ended December 31,
	2023	2022
Risk-free interest rate	3.57-3.94%	1.82-4.15%
Expected dividend yield	0%	0%
Expected life	5.5-6.25 years	5.5-6.25 years
Expected volatility	70-73%	70-71%

2019 Employee stock purchase plan

In June 2019, the Company adopted the 2019 Employee Stock Purchase Plan (“ESPP”), which became effective on June 18, 2019. The Company initially reserved 315,000 shares of common stock for sale under the ESPP. At December 31, 2023, the Company had 1,704,168 shares available for issuance under the plan. The average grant date fair value per share under the plan was $9.88 for 2023. The total ESPP stock-based compensation expense for the year ended December 31, 2023 was $0.3 million and for the year ended December 31, 2022 was $0.3 million. The number of shares reserved for issuance under the ESPP will increase automatically on January 1st of each of the first ten calendar years following the first offering

date by the number of shares equal to the lesser of 1% of the total outstanding shares of the Company’s common stock as of the immediately preceding December 31 or a lower amount determined by the Company’s board of directors. The aggregate number of shares issued over the term of the ESPP will not exceed 3,150,000 shares of the Company’s common stock.

Consolidated statements of stockholders' equity - USD ($) $ in Thousands	Total	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive Gain (Loss)	Accumulated Deficit
Balance at Dec. 31, 2021	$ 217,777	$ 4	$ 414,024	$ (168)	$ (196,083)
Balance, Shares at Dec. 31, 2021		36,902,499
Unrealized gain (loss) on marketable securities	(1,007)			(1,007)
Stock-based compensation	22,854		22,854
Issuance of common stock upon exercise of stock options	494		494
Issuance of common stock upon exercise of stock options, Shares		269,288
Issuance of common stock related to employee stock purchase plan	570		570
Issuance of common stock related to employee stock purchase plan, Shares		44,002
Shares sold as part of controlled equity offering sales agreement	45,228		45,228
Shares sold as part of controlled equity offering sales agreement, Shares		2,223,786
Net Income (Loss)	(101,067)				(101,067)
Balance at Dec. 31, 2022	184,849	$ 4	483,170	(1,175)	(297,150)
Balance, Shares at Dec. 31, 2022		39,439,575
Unrealized gain (loss) on marketable securities	1,151			1,151
Stock-based compensation	25,257		25,257
Issuance of common stock upon exercise of stock options	$ 371		371
Issuance of common stock upon exercise of stock options, Shares	145,877	148,211
Issuance of common stock related to employee stock purchase plan	$ 555		555
Issuance of common stock related to employee stock purchase plan, Shares		71,471
Shares sold as part of controlled equity offering sales agreement	52,081	$ 1	52,080
Shares sold as part of controlled equity offering sales agreement, Shares		6,258,976
Net Income (Loss)	(104,699)				(104,699)
Balance at Dec. 31, 2023	$ 159,565	$ 5	$ 561,433	$ (24)	$ (401,849)
Balance, Shares at Dec. 31, 2023		45,918,233

Subsequent Events - Additional Information (Details) - Sales Agreement Prospectus - USD ($) $ in Millions	2 Months Ended	12 Months Ended
	Mar. 12, 2024	Dec. 31, 2023
Subsequent Event [Line Items]
Issuance of common stock, Shares		6.3
Subsequent Event
Subsequent Event [Line Items]
Issuance of common stock, Shares	200,000
Received deducting commissions related to sales agreement	$ 1.3

Accrued and Other Current Liabilities - Schedule of Accrued and Other Current Liabilities (Details) - USD ($) $ in Thousands	Dec. 31, 2023	Dec. 31, 2022
Payables and Accruals [Abstract]
Accrued employee compensation costs	$ 5,611	$ 5,754
Accrued professional	651	525
Accrued research and development costs	4,634	6,601
Current portion of operating lease liabilities	2,062	2,359
Other current liabilities	857	509
Total accrued and other current liabilities	$ 13,815	$ 15,748

Net Loss Per Share (Tables)

12 Months Ended

Dec. 31, 2023

Earnings Per Share [Abstract]

Schedule of Computation of Basic and Diluted Net Loss Per Share

The following table summarizes the computation of basic and diluted net loss per share of the Company:


	Year ended December 31,
	2023			2022
Numerator:
Net loss	$	(104,699	)	$	(101,067	)
Denominator:
Weighted-average number of common shares, basic and diluted		43,994,862			38,897,442
Net loss per share, basic and diluted	$	(2.38	)	$	(2.60	)

Schedule of Antidilutive Securities Excluded from Computation of Diluted Net Loss Per Share


	As of December 31,
	2023		2022
Outstanding options to purchase common stock		6,478,063		8,274,647
Restricted stock units		1,513,102		—
Total		7,991,165		8,274,647

Commitments and Contingencies (Tables)

12 Months Ended

Dec. 31, 2023

Commitments and Contingencies Disclosure [Abstract]

Schedule of Future Minimum Lease Payments Under Non-Cancellable Leases

Future minimum lease payments under non-cancellable leases as of December 31, 2023, are as follows (in thousands):


2024	$	2,608
2025		2,661
2026		2,564
Total lease payments		7,833
Less imputed interest		(998	)
Present value of lease liabilities	$	6,835

Summary of Lease Balances

Lease balances as of December 31, 2023 and December 31, 2022 are as follows (in thousands):


	As of December 31,
	2023		2022
Operating right-of-use assets	$	6,611	$	4,753
Current portion of operating lease liabilities	$	2,062	$	2,359
Non-current portion of operating lease liabilities		4,773		2,717
Total operating lease liabilities	$	6,835	$	5,076

Summary of Weighted Average Remaining Lease Term and Weighted Average Discount Rate of Operating Leases

The weighted average remaining lease term and weighted average discount rate of our operating leases as of December 31, 2023 are as follows:


Weighted average remaining lease term in years	2.9
Weighted average discount rate	9.92	%

Insider Trading Arrangements

3 Months Ended

Dec. 31, 2023

Trading Arrangements, by Individual

Material Terms of Trading Arrangement

Trading Arrangements

During the three months ended December 31, 2023, none of our directors or officers, as defined in Rule 16a-1(f), informed us of the adoption, modification or termination of a “Rule 10b5-1 trading arrangement” or “non-Rule 10b5-1 trading arrangement,” as those terms are defined in Regulation S-K, Item 408, except as described in the table below:

      Name

      Title

      Action

      Date

      Rule 10b5-1*

      Non Rule 10b5-1**

      Total Shares to be Sold

      Expiration Date(1)

 Jonathan Allan

 General Counsel and Corporate Secretary

 Termination(2)

12/6/2023

X

43,896

3/20/2024

 Jonathan Allan

 General Counsel and Corporate Secretary

 Adoption

12/15/2023

X

16,065

12/15/2024

 Edward Kaye

 Chief Executive Officer

 Adoption

12/26/2023

X

45,000

3/20/2025

 Huw Nash

 Chief Operating Officer & Chief Business Officer

 Termination(3)

12/29/2023

X

631,450

6/1/2024

 Huw Nash

 Chief Operating Officer & Chief Business Officer

 Adoption

12/29/2023

X

670,338

4/1/2025

* Intended to satisfy the affirmative defense of Rule 10b5-1(c) Act.

** Not intended to satisfy the affirmative defense of Rule 10b5-1(c) Act.

(1) Except as indicated by footnote, each trading arrangement permitted or permits transactions through and including the earlier to occur of (a) the completion of all purchases or sales or (b) the date listed in the table.

(2) On December 6, 2023, Jonathan Allan, General Counsel and Corporate Secretary, terminated a trading arrangement that was intended to satisfy the affirmative defense of Rule 10b5-1 (the “Allan 10b5-1 Plan”). The Allan 10b5-1 Plan was entered into on March 22, 2023, with an expiration date of March 20, 2024.

(3) On December 29, 2023, Huw Nash, COO and CBO, terminated a trading arrangement that was intended to satisfy the affirmative defense of Rule 10b5-1 (the “Nash 10b5-1 Plan”). The Nash 10b5-1 Plan was entered into on March 28, 2022, with an expiration date of June 1, 2024.

Each new Rule 10b5-1 Plan that was adopted in the above table includes a representation from Messrs. Allan, Kaye and Nash, respectively, to the broker administering the plan that he was not in possession of any material nonpublic information regarding the Company or the securities subject to the Rule 10b5-1 Plan at the time the Rule 10b5-1 Plan was entered into. A similar representation was made to us in connection with the adoption of the Rule 10b5-1 Plan under our insider trading policy. Those representations were made as of the Adoption Date set forth above, and speak only as of that date. In making those representations, there is no assurance with respect to any material nonpublic information of which the

directors and officers was unaware, or with respect to any material nonpublic information acquired by the above directors and officers or passage after the date of the representation.

Once executed, transactions under a Rule 10b5-1 Plan adopted during the period described above will be disclosed publicly through Form 4 and/or Form 144 filings with the SEC in accordance with applicable securities laws, rules, and regulations. Except as may be required by law, we do not undertake any obligation to update or report any modification, termination, or other activity under current or future Rule 10b5-1 plans that may be adopted by Messrs. Allan, Kaye or Nash, respectively, or other officers or directors of the Company.

Directors or Officers Except Corporate Secretary, CEO, COO And CBO

Trading Arrangements, by Individual

Rule 10b5-1 Arrangement Adopted

false

Non-Rule 10b5-1 Arrangement Adopted

false

Rule 10b5-1 Arrangement Terminated

false

Non-Rule 10b5-1 Arrangement Terminated

false

Rule 10b5-1 Arr Modified Flag

false

Non Rule 10b5-1 Arr Modified Flag

false

Edward Kaye

Trading Arrangements, by Individual

Name

Edward Kaye

Title

Chief Executive Officer

Rule 10b5-1 Arrangement Adopted

true

Adoption Date

12/26/2023

Aggregate Available

45,000

Expiration Date

3/20/2025

Rule 10b5-1 Trading Plan One | Jonathan Allan

Trading Arrangements, by Individual

Name

Jonathan Allan

Title

General Counsel and Corporate Secretary

Adoption Date

March 22, 2023

Rule 10b5-1 Arrangement Terminated

true

Termination Date

12/6/2023

Aggregate Available

43,896

Expiration Date

3/20/2024

Rule 10b5-1 Trading Plan One | Huw Nash

Trading Arrangements, by Individual

Name

Huw Nash

Title

Chief Operating Officer & Chief Business Officer

Adoption Date

March 28, 2022

Rule 10b5-1 Arrangement Terminated

true

Termination Date

12/29/2023

Aggregate Available

631,450

Expiration Date

6/1/2024

Rule 10b5-1 Trading Plan Two | Jonathan Allan

Trading Arrangements, by Individual

Name

Jonathan Allan

Title

General Counsel and Corporate Secretary

Rule 10b5-1 Arrangement Adopted

true

Adoption Date

12/15/2023

Aggregate Available

16,065

Expiration Date

12/15/2024

Rule 10b5-1 Trading Plan Two | Huw Nash

Trading Arrangements, by Individual

Name

Huw Nash

Title

Chief Operating Officer & Chief Business Officer

Rule 10b5-1 Arrangement Adopted

true

Adoption Date

12/29/2023

Aggregate Available

670,338

Expiration Date

4/1/2025

Stock-Based Compensation (Tables)

12 Months Ended

Dec. 31, 2023

Share-Based Payment Arrangement [Abstract]

Summary of Stock Option Activity for Awards

A summary of stock option activity for awards is presented below:


	Number of shares			Weighted average exercise price		Weighted average remaining contractual life (years)		Aggregate intrinsic value(1)
Outstanding as of December 31, 2022		8,274,647		$	18.28		7.6	$	20,598
Granted		1,599,227			9.32
Exercised		(145,877	)		2.55
Forfeitures(2)		(1,449,164	)		28.00
Expired(2)		(1,800,770	)		34.88
Outstanding as of December 31, 2023		6,478,063		$	9.64		6.9	$	8,435
Exercisable as of December 31, 2023		4,034,517		$	8.88		5.7	$	8,439

(1)

(2)

Options exchanged are classified as either forfeitures or expired based on vesting status at the time of Exchange Offer.

Summary of Restricted Stock Unit Activity

A summary of restricted stock unit activity is presented below:


	Number of shares			Aggregate intrinsic value		Weighted average grant date fair value
Outstanding as of December 31, 2022		—		$	—	$	—
Awarded		807,700					9.04
RSUs in exchange for options as part of option exchange		730,602					3.95
Vested		—					—
Forfeitures		(25,200	)				9.15
Outstanding as of December 31, 2023		1,513,102		$	7,959	$	6.58
Vested or expected to vest as of December 31, 2023		1,513,102		$	7,959	$	6.58

Summary of Stock-based Compensation Expense


	Year ended December 31,
	2023		2022
Research and development	$	9,925	$	8,901
General and administrative		15,332		13,953
	$	25,257	$	22,854

Summary of Fair Values of Options Granted to Employees and Directors


	Year ended December 31,
	2023	2022
Risk-free interest rate	3.57-3.94%	1.82-4.15%
Expected dividend yield	0%	0%
Expected life	5.5-6.25 years	5.5-6.25 years
Expected volatility	70-73%	70-71%

Subsequent Events

12 Months Ended

Dec. 31, 2023

Subsequent Events [Abstract]

Subsequent events

13. Subsequent events

Since December 31, 2023, through the date of the issuance of these consolidated financial statements, the Company sold 0.2 million shares of our common stock and received $1.3 million after deducting commissions related to the Sales Agreement.

Employee Benefits

12 Months Ended

Dec. 31, 2023

Retirement Benefits [Abstract]

Employee benefits

12. Employee benefits

In 2016, the Company established a defined-contribution savings plan under Section 401(k) of the Internal Revenue Code (the “401(k) Plan”). The 401(k) Plan covers all employees who meet defined minimum age and service requirements and allows participants to defer a portion of their annual compensation on a pretax basis. The Company matches contributions up to 4% of annual salary for those employees who are participating in the 401(k) Plan. For the year ended December 31, 2023, the Company made matching contributions of $0.7 million and for the year ended December 31, 2022, the Company made matching contributions of $0.6 million.

Document and Entity Information - USD ($) $ in Millions	12 Months Ended
Document and Entity Information - USD ($) $ in Millions	Dec. 31, 2023	Mar. 15, 2024	Jun. 30, 2023
Cover [Abstract]
Document Type	10-K
Amendment Flag	false
Document Period End Date	Dec. 31, 2023
Document Fiscal Year Focus	2023
Document Fiscal Period Focus	FY
Entity Registrant Name	Stoke Therapeutics, Inc.
Entity Central Index Key	0001623526
Entity Current Reporting Status	Yes
Entity Voluntary Filers	No
Entity Interactive Data Current	Yes
Current Fiscal Year End Date	--12-31
Entity Filer Category	Non-accelerated Filer
Entity Well Known Seasoned Issuer	No
Entity Public Float			$ 290
Entity Common Stock, Shares Outstanding		46,303,743
Entity Shell Company	false
Entity Small Business	true
Entity Emerging Growth Company	true
Entity Ex Transition Period	false
Entity File Number	001-38938
Entity Incorporation State Country Code	DE
Entity Tax Identification Number	47-1144582
Entity Address, Address Line One	45 Wiggins Ave
Entity Address City Or Town	Bedford
Entity Address State Or Province	MA
Entity Address Postal Zip Code	01730
City Area Code	781
Local Phone Number	430-8200
Document Annual Report	true
Document Transition Report	false
ICFR Auditor Attestation Flag	false
Auditor Firm ID	185
Auditor Name	KPMG LLP
Auditor Location	Boston, MA USA
Title of 12(b) Security	Common Stock, $0.0001 par value per share
Trading Symbol	STOK
Security Exchange Name	NASDAQ
Document Financial Statement Error Correction [Flag]	false
Documents Incorporated by Reference	Portions of the registrant’s Definitive Proxy Statement relating to the 2024 Annual Meeting of Stockholders are incorporated by reference into Part III of this Annual Report on Form 10-K to the extent stated herein. The Definitive Proxy Statement will be filed within 120 days of the Registrant’s fiscal year ended December 31, 2023. Except with respect to information specifically incorporated by reference in this Form 10-K, the Definitive Proxy Statement is not deemed to be filed as part of this Form 10-K. Auditor Firm Id: 185 Auditor Name: KPMG LLP Auditor Location: Boston, MA USA

Marketable Securities - Additional Information (Details) $ in Thousands	12 Months Ended
	Dec. 31, 2023 USD ($)
Marketable Securities [Line Items]
Allowance for credit losses	$ 0
Minimum
Marketable Securities [Line Items]
Weighted average maturity marketable securities period	1 month 2 days
Maximum
Marketable Securities [Line Items]
Weighted average maturity marketable securities period	1 month 28 days

Consolidated balance sheets (Parenthetical) - $ / shares	Dec. 31, 2023	Dec. 31, 2022
Statement of Financial Position [Abstract]
Common stock, par value	$ 0.0001	$ 0.0001
Common stock, shares authorized	300,000,000	300,000,000
Common stock, shares issued	45,918,233	39,439,575
Common stock, shares outstanding	45,918,233	39,439,575

Commitments and Contingencies - Schedule of Future Minimum Lease Payments Under Non-Cancellable Leases (Details) $ in Thousands	Dec. 31, 2023 USD ($)
Future minimum lease payments under non-cancellable leases
2024	$ 2,608
2025	2,661
2026	2,564
Total lease payments	7,833
Less imputed interest	(998)
Present value of lease liabilities	$ 6,835

Consolidated statements of operations and comprehensive loss - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2023	Dec. 31, 2022
Income Statement [Abstract]
Revenue	$ 8,780	$ 12,405
Operating expenses:
Research and development	82,231	77,837
General and administrative	41,322	38,924
Total operating expenses	123,553	116,761
Loss from operations	(114,773)	(104,356)
Other income (expense):
Interest income (expense), net	9,908	3,122
Other income (expense), net	166	167
Total other income (expense)	10,074	3,289
Net loss	$ (104,699)	$ (101,067)
Net loss per share, basic	$ (2.38)	$ (2.60)
Net loss per share, diluted	$ (2.38)	$ (2.60)
Weighted-average common shares outstanding, basic	43,994,862	38,897,442
Weighted-average common shares outstanding, diluted	43,994,862	38,897,442
Comprehensive loss:
Net Income (Loss)	$ (104,699)	$ (101,067)
Other comprehensive loss:
Unrealized gain (loss) on marketable securities	1,151	(1,007)
Total other comprehensive gain (loss)	1,151	(1,007)
Comprehensive loss	$ (103,548)	$ (102,074)

Stock-Based Compensation - Summary of Restricted Stock Unit Activity (Details) - Restricted Stock Units $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2023 USD ($) $ / shares shares
Share-Based Compensation Arrangement by Share-Based Payment Award [Line Items]
Number of shares, Awarded \| shares	807,700
RSUs in exchange for options as part of option exchange \| shares	730,602
Number of shares, Forfeitures \| shares	(25,200)
Number of shares, Outstanding balance \| shares	1,513,102
Number of shares, Vested and expected to vest as of December 31, 2023 \| shares	1,513,102
Aggregate intrinsic value, Outstanding value \| $	$ 7,959
Aggregate intrinsic value, Vested and expected to vest as of December 31, 2023 \| $	$ 7,959
Weighted average grant date fair value, Awarded \| $ / shares	$ 9.04
Weighted average grant date fair value, In exchange for options as part of UWOE \| $ / shares	3.95
Weighted average grant date fair value, Forfeitures \| $ / shares	9.15
Weighted average grant date fair value, Outstanding balance \| $ / shares	6.58
Weighted average grant date fair value, Vested and expected to vest as of December 31, 2023 \| $ / shares	$ 6.58

Marketable Securities

12 Months Ended

Dec. 31, 2023

Investments, Debt and Equity Securities [Abstract]

Marketable Securities

4. Marketable Securities

The following table summarizes the Company’s marketable securities as of December 31, 2023 (in thousands):


	As of December 31, 2023
	Amortized Cost		Unrealized Gains		Unrealized Loss			Fair Value
Marketable securities:
US Government debt securities	$	9,976	$	—	$	(24	)		9,952
Total	$	9,976	$	—	$	(24	)	$	9,952

The following table summarizes the Company’s marketable securities as of December 31, 2022 (in thousands):


	As of December 31, 2022
	Amortized Cost		Unrealized Gains		Unrealized Loss			Fair Value
Marketable securities:
Corporate bonds	$	34,662	$	—	$	(135	)	$	34,527
Commercial paper		8,019		—		(41	)		7,978
US Government debt securities		74,533		—		(999	)		73,534
Total	$	117,214	$	—	$	(1,175	)	$	116,039

The weighted average maturity of the Company’s marketable securities as of December 31, 2023 ranges from approximately 0.09 years to 0.16 years.

The Company did not record an allowance for credit losses as of December 31, 2023 related to our marketable securities. Further, given the lack of significant change in the credit risk of these investments, the Company did not recognize any other-than-temporary impairment losses.

Stock-Based Compensation - Summary of Fair Values of Options Granted to Employees and Directors (Details)	12 Months Ended
	Dec. 31, 2023	Dec. 31, 2022
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Risk-free interest rate, minimum	3.57%	1.82%
Risk-free interest rate, maximum	3.94%	4.15%
Expected dividend yield	0.00%	0.00%
Expected volatility, minimum	70.00%	70.00%
Expected volatility, maximum	73.00%	71.00%
Minimum
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Expected life	5 years 6 months	5 years 6 months
Maximum
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Expected life	6 years 3 months	6 years 3 months

- Definition

Line items represent financial concepts included in a table. These concepts are used to disclose reportable information associated with domain members defined in one or many axes to the table.

+ References

Reference 1: http://www.xbrl.org/2003/role/disclosureRef
-Topic 718
-SubTopic 10
-Name Accounting Standards Codification
-Section 35
-Paragraph 1D
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147480483/718-10-35-1D

Reference 2: http://www.xbrl.org/2003/role/disclosureRef
-Topic 718
-SubTopic 10
-Name Accounting Standards Codification
-Section 35
-Paragraph 3
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147480483/718-10-35-3

Reference 3: http://www.xbrl.org/2003/role/disclosureRef
-Topic 718
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 2
-Subparagraph (a)(1)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147480429/718-10-50-2

Reference 4: http://www.xbrl.org/2003/role/disclosureRef
-Topic 718
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 2
-Subparagraph (a)(2)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147480429/718-10-50-2

Reference 5: http://www.xbrl.org/2003/role/disclosureRef
-Topic 718
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 2
-Subparagraph (a)(3)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147480429/718-10-50-2

Reference 6: http://www.xbrl.org/2003/role/disclosureRef
-Topic 718
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 2
-Subparagraph (c)(1)(i)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147480429/718-10-50-2

Reference 7: http://www.xbrl.org/2003/role/disclosureRef
-Topic 718
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 2
-Subparagraph (c)(1)(ii)
-Publisher FASB
-URI https://asc.fasb.org//1943274/2147480429/718-10-50-2

Reference 8: http://www.xbrl.org/2003/role/disclosureRef
-Topic 718
-SubTopic 10
-Name Accounting Standards Codification
-Section 50
-Paragraph 2
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+ Details

License and Collaboration Agreement with Acadia Pharmaceuticals Inc

12 Months Ended

Dec. 31, 2023

License And Collaboration Agreement [Abstract]

License and collaboration agreement with Acadia Pharmaceuticals Inc

8. License and Collaboration Agreement with Acadia Pharmaceuticals Inc.

In January 2022, the Company entered into a license and collaboration agreement with Acadia Pharmaceuticals Inc. for the discovery, development and commercialization of novel RNA-based medicines for the treatment of severe and rare genetic neurodevelopmental diseases of the central nervous system. The agreement focuses on the targets SYNGAP1, MECP2 (Rett syndrome), and an undisclosed neurodevelopmental target of mutual interest. In connection with each target, the Company will collaborate with Acadia to identify potential treatments for further development and commercialization as licensed products. With respect to SYNGAP1, the Company has agreed with Acadia to co-develop and co-commercialize licensed products for such target globally, and in connection therewith the Company granted to Acadia worldwide, co-exclusive (with Stoke) licenses for such licensed products. With respect to MECP2 and the neurodevelopmental target, the Company granted to Acadia worldwide, exclusive licenses to develop and commercialize licensed products for such targets.

Pursuant to the terms of the agreement, the Company received an upfront payment of $60.0 million from Acadia. Acadia agreed to fund the research to identify potential licensed products for MECP2 and the neurodevelopmental target, and the Company will equally fund with Acadia the research to identify potential licensed products for SYNGAP1. The Company is eligible to receive up to $907.5 million in potential total milestone payments based upon the achievement of certain development, regulatory, first commercial sales and sales milestone events across the programs for the three targets, assuming each milestone were achieved at least once. With respect to licensed products for MECP2 and the neurodevelopmental target, the Company is also eligible to receive tiered royalties at percentages ranging from the mid-single digits to the mid-teens on future net sales by Acadia of licensed products worldwide. Royalties payable under the agreement are subject to standard royalty reductions. For SYNGAP1 licensed products that the Company is co-developing and co-commercializing, the Company will be responsible for 50% of the development and commercialization costs and will receive 50% of the profits from global commercialization. The Company is provided with a co-development and co-commercialization opt out option relating to the SYNGAP1 target indication at the Company’s discretion. Such opt-out would reduce development and commercialization milestones but would provide the Company with royalties on an escalating basis attributable to net sales milestones.

Acadia Agreement Accounting

At the commencement of the Acadia agreement the Company identified three performance obligations consisting of pre-clinical research activities for each of the three targets, SYNGAP1, MECP2, and the undisclosed neurodevelopmental target. The exclusive or co-exclusive licenses granted to Acadia to conduct pre-clinical research activities on each of the three targets, and participation on each of the respective joint research committees were identified as promised services. However, the licenses granted to Acadia and the research activities were determined to be not distinct from each other, and therefore are considered a combined performance obligation for each of the three targets. Participation on each of the joint research committees was determined to be quantitatively and qualitatively immaterial in the context of the arrangement with Acadia.

The Company is recognizing the transaction price for the pre-clinical research activities for each of the three targets over time as the research services are provided. The transfer of control to Acadia occurs over this time period, and in management’s judgment, is the best measure of progress towards satisfying the performance obligation. An input method is used that measures the cost incurred to date in satisfying each of the three research activities in relation to the estimated total projected cost of each of the research activities to fulfill the respective obligations. The cumulative effect of revisions to estimated costs and/or the transaction price to complete the research performance obligations will be recorded in the period in which changes are identified and amounts can be reasonably estimated. Payments or reimbursements resulting from the Company’s research and development efforts were recognized as the services are performed.

Milestone payments that are not within the control of the Company, such as regulatory approvals, are not considered probable of being achieved until those approvals are received. For other milestones, the Company evaluated factors such as the scientific, clinical, regulatory, commercial, and other risks that must be overcome to achieve the particular milestone in making this assessment. Milestones that are outside of the Company’s or Acadia’s control will not be recognized until such milestones are achieved. As to the other milestones, to date, no milestone payments have been included in the transaction price due the uncertainty as to whether these milestones will be achieved. The Company will at the end of each reporting period reevaluate the probability of achievement of all milestones subject to constraint and, if necessary, adjust its estimate of

the overall transaction price for each of the research activities on the three targets. Any such adjustments will be recorded on a cumulative catch-up basis.

As of December 31, 2023, the Company had $48.4 million in upfront consideration associated with the Acadia agreement relating to performance obligations that are unsatisfied or partially unsatisfied.

Income Taxes - Additional Information (Details) - USD ($)	12 Months Ended
	Dec. 31, 2023	Dec. 31, 2022
Income Taxes [Line Items]
Valuation allowance	$ 133,306,000	$ 97,923,000
Change in valuation allowance	35,400,000	31,800,000
Unrecognized tax benefits	0	0
Unrecognized income tax benefits, interest or penalties	0	0
Federal
Income Taxes [Line Items]
Operating loss carryforwards	$ 189,500,000	$ 210,900,000
Operating loss carryforwards, expiration beginning year	2035	2035
Federal \| Research and Development Tax Credit
Income Taxes [Line Items]
Tax credit carryforwards	$ 12,800,000	$ 9,200,000
Tax credit carryforwards, expiration beginning year	2034	2034
Federal \| Internal Revenue Code
Income Taxes [Line Items]
Operating loss carryforwards	$ 900,000
Federal \| Internal Revenue Code \| Research and Development Tax Credit
Income Taxes [Line Items]
Tax credit carryforwards	20,000.00
State
Income Taxes [Line Items]
Operating loss carryforwards	$ 199,400,000	$ 212,800,000
Operating loss carryforwards, expiration beginning year	2035	2035
State \| Research and Development Tax Credit
Income Taxes [Line Items]
Tax credit carryforwards	$ 5,900,000	$ 4,300,000
Tax credit carryforwards, expiration beginning year	2034	2034

Property and Equipment, Net (Tables)

12 Months Ended

Dec. 31, 2023

Property, Plant and Equipment [Abstract]

Summary of Property, and Equipment, Net

Property and equipment, net consisted of the following:


	As of December 31,
	2023			2022
Laboratory equipment	$	9,383		$	7,903
Furniture and fixtures		312			312
Leasehold improvements		2,294			1,867
Office equipment		440			353
Construction in progress		65			447
		12,494			10,882
Less accumulated depreciation		(6,671	)		(4,207	)
	$	5,823		$	6,675

Fair Value Measurements - Additional Information (Details) - USD ($)	12 Months Ended
	Dec. 31, 2023	Dec. 31, 2022
Fair Value Disclosures [Abstract]
Fair value assets, transfers to level 3, amount	$ 0	$ 0

Property and Equipment, Net

12 Months Ended

Dec. 31, 2023

Property, Plant and Equipment [Abstract]

Property and equipment, net

5. Property and equipment, net

Property and equipment, net consisted of the following:


	As of December 31,
	2023			2022
Laboratory equipment	$	9,383		$	7,903
Furniture and fixtures		312			312
Leasehold improvements		2,294			1,867
Office equipment		440			353
Construction in progress		65			447
		12,494			10,882
Less accumulated depreciation		(6,671	)		(4,207	)
	$	5,823		$	6,675

Depreciation expense was $2.5 million and $1.5 million for the years ended December 31, 2023 and 2022, respectively.

Accrued and Other Current Liabilities

12 Months Ended

Dec. 31, 2023

Payables and Accruals [Abstract]

Accrued and other current liabilities

6. Accrued and other current liabilities

Accrued and other current liabilities consisted of the following:


	As of December 31,
	2023		2022
Accrued employee compensation costs	$	5,611	$	5,754
Accrued professional		651		525
Accrued research and development costs		4,634		6,601
Current portion of operating lease liabilities		2,062		2,359
Other current liabilities		857		509
	$	13,815	$	15,748

Summary of Significant Accounting Policies and Recent Accounting Pronouncements (Policies)

12 Months Ended

Dec. 31, 2023

Accounting Policies [Abstract]

Basis of Presentation and Consolidation

Basis of presentation and consolidation

Use of Estimates

Use of estimates

Cash and Cash Equivalents

Cash and cash equivalents

Restricted Cash

Restricted cash

The following table reconciles cash and cash equivalents and restricted cash per the consolidated balance sheets to the statements of cash flows:


	As of December 31,
	2023		2022
Cash and cash equivalents	$	191,442	$	113,556
Restricted cash		569		569
	$	192,011	$	114,125

Marketable Securities

Concentration of Credit Risk

Concentration of credit risk

Fair Value of Financial Instruments

Fair value of financial instruments

Level 1—Quoted market prices in active markets for identical assets or liabilities.

Level 2—Inputs other than Level 1 inputs that are either directly or indirectly observable, such as quoted market prices, interest rates and yield curves.

Level 3—Unobservable inputs developed using estimates of assumptions developed by the Company, which reflect those that a market participant would use.

Revenue Recognition

Revenue recognition

Upfront license fees

Customer options

Research and development services

Milestone payments

Deferred Offering Costs

Deferred offering costs

Property and Equipment

Property and equipment

Estimated useful lives for property and equipment are as follows:


Property and equipment		Estimated useful life
Computer and office equipment		3-5 years
Laboratory equipment and Furniture and fixtures		5-7 years
Leasehold improvements		Lesser of estimated useful life or remaining lease term

Impairment of Long-Lived Assets

Impairment of long-lived assets

Research and Development Costs

Research and development costs

Stock-based Compensation

Stock-based compensation

Stock options

The Company uses the Black-Scholes option-pricing model to estimate the fair value of its stock options.

Restricted stock units ("RSUs")

Patent Costs

Patent costs

Income Taxes

Income taxes

Segment and Geographic Information

Segment and geographic information

Emerging Growth Company and Smaller Reporting Company Status

Emerging growth company and smaller reporting company status

Recently Issued Accounting Pronouncements

Recently issued accounting pronouncements

Stock-Based Compensation - Summary of Stock Option Activity for Awards (Details) - USD ($)
$ / shares in Units, $ in Thousands

12 Months Ended

Dec. 31, 2023

Dec. 31, 2022

Share-Based Payment Arrangement [Abstract]

Number of shares, Outstanding balance

8,274,647

Number of shares, Granted

1,599,227

3,459,500

Number of shares, Exercised

(145,877)

Number of shares, Forfeitures

^[1]

(1,449,164)

Number of shares, Expired

^[1]

(1,800,770)

Number of shares, Outstanding balance

6,478,063

8,274,647

Number of shares, Exercisable as of December 31, 2023

4,034,517

Weighted average exercise price, Outstanding balance

$ 18.28

Weighted average exercise price, Granted

9.32

Weighted average exercise price, Exercised

2.55

Weighted average exercise price, Forfeitures

^[1]

28.00

Weighted average exercise price, Expired

^[1]

34.88

Weighted average exercise price, Outstanding balance

9.64

$ 18.28

Weighted average exercise price, Exercisable as of December 31, 2023

$ 8.88

Weighted average remaining contractual life, Outstanding

6 years 10 months 24 days

7 years 7 months 6 days

Weighted average remaining contractual life, Exercisable

5 years 8 months 12 days

Aggregate intrinsic value, Outstanding value

^[2]

$ 8,435

$ 20,598

Aggregate intrinsic value, Exercisable as of December 31, 2023

^[2]

$ 8,439

[1]	Options exchanged are classified as either forfeitures or expired based on vesting status at the time of Exchange Offer.
[2]	The aggregate intrinsic value is calculated as the difference between the exercise price of the underlying options and the fair value of the common stock for the options that were in the money at December 31, 2023 and 2022.

Marketable Securities (Tables)

12 Months Ended

Dec. 31, 2023

Investments, Debt and Equity Securities [Abstract]

Summary of Marketable Securities

The following table summarizes the Company’s marketable securities as of December 31, 2023 (in thousands):


	As of December 31, 2023
	Amortized Cost		Unrealized Gains		Unrealized Loss			Fair Value
Marketable securities:
US Government debt securities	$	9,976	$	—	$	(24	)		9,952
Total	$	9,976	$	—	$	(24	)	$	9,952

The following table summarizes the Company’s marketable securities as of December 31, 2022 (in thousands):


	As of December 31, 2022
	Amortized Cost		Unrealized Gains		Unrealized Loss			Fair Value
Marketable securities:
Corporate bonds	$	34,662	$	—	$	(135	)	$	34,527
Commercial paper		8,019		—		(41	)		7,978
US Government debt securities		74,533		—		(999	)		73,534
Total	$	117,214	$	—	$	(1,175	)	$	116,039

Property and Equipment, Net - Additional Information (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2023	Dec. 31, 2022
Property, Plant and Equipment [Abstract]
Depreciation	$ 2,469	$ 1,546

Summary of Significant Accounting Policies and Recent Accounting Pronouncements - Additional Information (Details)	12 Months Ended
	Dec. 31, 2023 USD ($) Segment	Dec. 31, 2022 USD ($)
Accounting Policies [Line Items]
Impairment losses recognized	$ 0	$ 0
Unrecognized income tax benefits, interest or penalties	$ 0	$ 0
Number of operating segments \| Segment	1
Restricted Stock Units
Accounting Policies [Line Items]
Vesting period	4 years

Marketable Securities - Summary of Marketable Securities (Details) - USD ($) $ in Thousands	Dec. 31, 2023	Dec. 31, 2022
Marketable Securities [Line Items]
Marketable Securities, Amortized Cost	$ 9,976	$ 117,214
Marketable Securities, Unrealized Loss	(24)	(1,175)
Marketable Securities, Fair Value	9,952	116,039
Corporate Bonds
Marketable Securities [Line Items]
Marketable Securities, Amortized Cost		34,662
Marketable Securities, Unrealized Loss		(135)
Marketable Securities, Fair Value		34,527
Commercial Paper
Marketable Securities [Line Items]
Marketable Securities, Amortized Cost		8,019
Marketable Securities, Unrealized Loss		(41)
Marketable Securities, Fair Value		7,978
US Government Debt Securities
Marketable Securities [Line Items]
Marketable Securities, Amortized Cost	9,976	74,533
Marketable Securities, Unrealized Loss	(24)	(999)
Marketable Securities, Fair Value	$ 9,952	$ 73,534

Commitments and Contingencies

12 Months Ended

Dec. 31, 2023

Commitments and Contingencies Disclosure [Abstract]

Commitments and contingencies

7. Commitments and contingencies

Operating leases

The Company determines whether an arrangement is a lease at inception. The Company accounts for a lease when it has the right to control the leased asset for a period of time while obtaining substantially all of the assets’ economic benefits. Operating lease right-of-use assets and operating lease liabilities are recognized based on the present value of the future minimum lease payments over the lease term at the lease commencement date. The discount rate used to determine the present value of the lease payments is the Company’s incremental borrowing rate based on the information available at lease inception, as the Company did not have information to determine the rate implicit in the leases. Lease expense for operating

leases is recognized on a straight-line basis over the reasonably assured lease term based on the total lease payments (which include initial direct costs and lease incentives). Lease expense is included in operating expenses in the consolidated statements of operations and comprehensive loss. The Company’s lease agreements also contain variable payments, primarily maintenance-related costs, which are expensed as incurred and not included in the measurement of the right-of-use assets and lease liabilities.

In August 2018, the Company entered into an agreement to lease approximately 23,000 square feet of space for a term of three years. Lease terms are triple net lease commencing at $0.9 million per year, then with 3% annual base rent increases plus operating expenses, real estate taxes, utilities and janitorial fees. The lease commencement date was December 10, 2018.

In September 2021, the Company entered into an agreement to extend the initial term of the 23,000 square foot lease for a period of three years commencing on December 15, 2021 and ending December 31, 2024. In addition, this lease provides for the lease of an additional 15,000 square feet of rentable space beginning on April 1, 2022 and ending on December 31, 2024. In December 2021, the Company recognized a right-of-use asset and operating lease liability of $3.5 million for the 23,000 square feet. On April 1, 2022, the Company recognized a right-of-use asset and operating lease liability of $1.8 million for the 15,000 square feet.

In December 2023, the Company entered into an agreement to extend the term of the 38,000 square foot lease for a period of two years commencing on January 1, 2025 and ending on December 31, 2026. In December 2023, the Company recognized a right-of-use asset and operating lease liability of $4.1 million.

In December 2018, the Company entered into an agreement to lease 2,485 square feet of space for an initial term of three years. The lease includes one renewal option for an additional two years, however, any time after the initial term the landlord may relocate the Company from the premises to a space reasonably comparable in size and utility. As the Company does not have the right to control the use of the identified asset after the initial term, the renewal option was excluded from the lease liability calculation. Lease terms commence at $0.2 million per annum, with 2.5% annual base rent increases plus operating expenses, real estate taxes, utilities and janitorial fees. The lease commencement date was May 1, 2019.

In June 2021, the Company amended the agreement to extend the initial term of the 2,485 square foot lease for a period of three years commencing May 1, 2022 and ending April 30, 2025. In addition, the amendment provided for the lease of an additional 2,357 square feet of rentable space beginning on July 6, 2021 and ending on April 30, 2025. The amended lease provides the Company with the option to extend the term of the lease for an additional two years. In 2021, the Company recognized a right-of-use asset and operating lease liabilities of $0.7 million for the extension of the lease to April 30, 2025 and a right-of-use asset and operating lease liabilities of $0.8 million for the additional 2,357 square feet of rentable space.

Future minimum lease payments under non-cancellable leases as of December 31, 2023, are as follows (in thousands):


2024	$	2,608
2025		2,661
2026		2,564
Total lease payments		7,833
Less imputed interest		(998	)
Present value of lease liabilities	$	6,835

Lease balances as of December 31, 2023 and December 31, 2022 are as follows (in thousands):


	As of December 31,
	2023		2022
Operating right-of-use assets	$	6,611	$	4,753
Current portion of operating lease liabilities	$	2,062	$	2,359
Non-current portion of operating lease liabilities		4,773		2,717
Total operating lease liabilities	$	6,835	$	5,076

The weighted average remaining lease term and weighted average discount rate of our operating leases as of December 31, 2023 are as follows:


Weighted average remaining lease term in years	2.9
Weighted average discount rate	9.92	%

In accordance with Topic 842, lease expense incurred under operating leases was $2.4 million for the year ended December 31, 2023, and $2.2 million for the year ended December 31, 2022.

Scientific Advisory Board Agreement

In June 2020, the Company entered into a scientific advisory board agreement with a member of the Company’s board of directors, who is also an employee of Cold Spring Harbor Laboratory (“CSHL”), to provide scientific advisory services related to the Company’s Targeted Augmentation of Nuclear Gene Output (“TANGO”) antisense oligonucleotide technology and other antisense oligonucleotide technologies, as well as current and future therapeutic targets and programs. Following the expiration of the initial scientific agreement in June 2021 and a renewal agreement in June 2022, the parties entered into subsequent scientific board agreements on substantially the same terms. The Company did not recognize any expense in the year ending December 31, 2023 compared to expense of $0.02 million for the year ended December 31, 2022. The agreement has expired with no renewal put in place.

License and research agreements

In July 2015, the Company entered into a worldwide license agreement with CSHL (the “CSHL Agreement”), with respect to TANGO patents. Under the CSHL Agreement, the Company received an exclusive (except with respect to certain government rights and non-exclusive licenses), worldwide license under certain patents and applications relating to TANGO. The CSHL Agreement obligated the Company to make payments that are contingent upon certain milestones being achieved. The Company was also required to pay royalties, tiered based on the scope of patent coverage for each licensed product, ranging from a low-single digit percentage to a mid-single digit percentage on annual net sales. These royalty obligations applied on a licensed product-by-licensed product and country-by-country basis until the latest of (i) the expiration of the last valid claim of a CSHL patent covering the applicable licensed product or (ii) the expiration of any regulatory exclusivity for the applicable licensed product. In addition, if the Company sublicensed the rights under the CSHL Agreement, it was required to pay a maximum of twenty percent of the sublicense revenue to CSHL, which may have been reduced to a mid-teens or a mid-single digit percentage upon achievement of certain clinical milestones for the applicable licensed product. Finally, the Company was required to pay an annual license maintenance fee of $0.01 million, which amount is creditable against any owed royalty or milestone payments. The maximum aggregate potential milestone payments payable totaled approximately $0.90 million. Additionally, certain licenses under the CSHL Agreement required the Company to reimburse CSHL for certain past and ongoing patent related expenses, however there were no expenses related to these reimbursable patent costs during the years ended December 31, 2023 and 2022. After the completion of a 90-day waiting period, in May 2023 the Company terminated the CSHL Agreement. The Company does not expect the termination of the CSHL Agreement to have a significant impact on the intellectual property underlying any of its current product candidates, including STK-001 and STK-002, or its continued development of the TANGO platform.

In April 2016, the Company entered into an exclusive, worldwide license agreement with the University of Southampton (the “Southampton Agreement”), whereby the Company acquired rights to foundational technologies related to the Company’s TANGO technology. Under the Southampton Agreement, the Company receives an exclusive, worldwide license under certain licensed patents and applications relating to TANGO. Under the Southampton Agreement, the Company may be obligated to make additional payments that are contingent upon certain milestones being achieved, as well as royalties on future product sales. These royalty obligations survive until the latest of (i) the expiration of the last valid claim of a licensed patent covering a subject product or (ii) the expiration of any regulatory exclusivity for the subject product in a country. In addition, if the Company sublicenses its rights under the Southampton Agreement, the Company is required to pay a mid-single digit percentage of the sublicense revenue to the University of Southampton. As of December 31, 2023, the Company had paid $0.7 million under the Southampton Agreement as a result of entering into the Acadia Pharmaceuticals Inc. license and collaboration agreement in January 2022 (see Note 8). Additionally, certain licenses under the Southampton Agreement require the Company to reimburse the University of Southampton for certain past and ongoing patent related expenses. For the year ended December 31, 2023 these expenses were $0.2 million compared to $0.02 million for the year ended December 31, 2022.

Litigation

The Company may periodically become subject to legal proceedings and claims arising in connection with ongoing business activities, including claims or disputes related to patents that have been issued or that are pending in the field of research on which it is focused. As of December 31, 2023, the Company had no legal proceedings to which it was a party or to which its property was subject that, in the opinion of management, would have a material adverse effect on its business.