What changed in this filing

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Item 1. Financial Statements

2025-08-07 compared with 2025-05-08 · 215 added, 117 removed, 540 unchanged (38% of the section changed)

2 unchanged sentences

CONDENSED CONSOLIDATED BALANCE SHEETS

(in thousands, except share and per share amounts) March 31,

(in thousands, except share and per share amounts) June 30,

2025 December 31,

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775,000,000 shares authorized;

131,160,842 and 131,160,842 shares issued and outstanding as of March 31, 2025 and December 31, 2024, respectively

134,494,438 and 131,160,842 shares issued and outstanding as of June 30, 2025 and December 31, 2024, respectively

Additional paid-in capital 852,561 840,358

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Three Months Ended

June 30, Six Months Ended

(in thousands, except share and per share amounts) 2025 2024 2025 2024

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Balance as of March 31, 2025 131,160,842 $ 2 $ 846,039 $ ( 15 ) $ ( 739,102 ) $ 106,924

Exercise of pre-funded warrants 3,199,984 — — — — —

Issuance of common stock under the employee stock purchase plan 133,612 — 197 — — 197

Stock-based compensation expense — — 6,325 — — 6,325

Change in unrealized loss on investments, net of tax — — — 5 — 5

Net loss — — — — ( 52,591 ) ( 52,591 )

Balance as of June 30, 2025 134,494,438 $ 2 $ 852,561 $ ( 10 ) $ ( 791,693 ) $ 60,860

The accompanying notes are an integral part of these unaudited condensed consolidated financial statements.

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— — 18,800 — — 18,800

Issuances of common stock under the employee stock purchase plan 74,488 — 436 — — 436

Issuance of common stock under the employee stock purchase plan 74,488 — 436 — — 436

Issuance of common stock upon exercise of stock options 9,664 — 36 — — 36

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Balance as of March 31, 2024 120,021,274 2 780,950 ( 95 ) ( 537,091 ) 243,766

Issuance of common stock upon exercise of stock options 9,539 — 35 — — 35

Stock-based compensation expense — — 8,091 — — 8,091

Change in unrealized loss on investments, net of tax — — — 24 — 24

Net loss — — — — ( 55,327 ) ( 55,327 )

Balance as of June 30, 2024 120,030,813 $ 2 $ 789,076 $ ( 71 ) $ ( 592,418 ) $ 196,589

The accompanying notes are an integral part of these unaudited condensed consolidated financial statements.

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CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS

Three Months Ended

Six Months Ended

(in thousands) 2025 2024

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CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS

Three Months Ended

Six Months Ended

(in thousands) 2025 2024

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Since its inception, the Company has devoted substantially all of its resources to building its Prime editing platform and advancing development of its portfolio of programs, establishing and protecting its intellectual property, conducting research and development activities, organizing and staffing the company, business planning, raising capital and providing general and administrative support for these operations.

To date, the Company has funded its operations primarily with proceeds from sales of preferred stock and from public offerings of its common stock, and through payments from our collaboration partners.

Since its inception, the Company has incurred substantial losses and, as of March 31, 2025, the Company had an accumulated deficit of $ 739.1 million.

To date, the Company has funded its operations primarily with proceeds from sales of preferred stock, from public offerings, and private placement of its common stock, and through payments from its collaboration partners.

In August 2025, the Company issued and sold 43,700,000 shares of its common stock, including 5,700,000 shares pursuant to the exercise of the underwriters’ option to purchase additional shares, at a price to the public of $ 3.30 per share.

As a result of the offering, the Company received approximately $ 138.2 million in net proceeds, after deducting underwriting discounts, commissions and estimated offering costs of $ 6.0 million.

Since its inception, the Company has incurred substantial losses and, as of June 30, 2025, the Company had an accumulated deficit of $ 791.7 million.

The Company expects to generate operating losses and negative operating cash flows for the foreseeable future.

As of March 31, 2025, the Company maintains cash, cash equivalents, and investments of $ 144.3 million.

Going Concern

In accordance with Accounting Standards Codification (“ASC”) 205-40, Going Concern, (“ASC 205-40”) the Company evaluated whether there are conditions and events, considered in the aggregate, that raise substantial doubt about the Company’s ability to continue as a going concern within one year after the date on which this Quarterly Report on Form 10-Q is filed.

Based on the Company's cash, cash equivalents, short-term investments, and related party short-term investments as of March 31, 2025, the Company's current and forecasted level of operations, and its forecasted cash flows, management has determined that substantial doubt exists about the Company’s ability to continue as a going concern for 12 months from the date these condensed consolidated financial statements are issued.

The Company’s ability to continue as a going concern is dependent upon its ability to obtain the necessary financing to meet its obligations and repay its liabilities arising from normal business operations when they come due, and to generate profitable operations in the future.

Management plans to provide for the Company’s capital requirements through financing or other transactions, and selling shares under the Company's “at the market offering” program.

There can be no assurance that the Company will be able to raise additional capital to fund operations with terms acceptable to the Company, or at all.

Because certain elements of management’s plans to mitigate the conditions that raised substantial doubt about the Company’s ability to continue as a going concern are outside of the Company’s control, including the ability to raise capital through an equity or other financing, those elements cannot be considered probable according to ASC 205-40, and therefore cannot be considered in the evaluation of mitigating factors.

The condensed consolidated financial statements as of March 31, 2025 have been prepared under the assumption that the Company will continue as a going concern for the next 12 months and that contemplates the realization of assets and satisfaction of liabilities and commitments in the normal course of business.

The Company’s ability to continue as a going concern is dependent upon its uncertain ability to obtain additional capital, reduce expenditures and/or execute on its business plan.

These condensed consolidated financial statements do not include any adjustments that might result from the outcome of this uncertainty.

The Company further expects that its cash, cash equivalents, and investments as of June 30, 2025 of $ 101.8 million, along with the $ 138.2 million in net proceeds received from the sale of common stock in August 2025 discussed above, will be sufficient to fund its operations for at least the next twelve months from the date of issuance of these financial statements.

Risks and Uncertainties

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The Company will need to raise additional capital to support its continuing operations and to pursue its growth strategy.

Until such time as the Company can generate significant revenue from product sales, if ever, it expects to finance its operations through a combination of equity offerings, debt financings, collaborations, strategic alliances and licensing arrangements.

Until such time as the Company can generate significant revenue from product sales, if ever, it expects to finance its operations through a combination of private and public equity offerings, debt financings, collaborations, strategic alliances, licensing, or other arrangements with third parties, or other similar transactions.

The Company may be unable to raise additional capital or enter into such other agreements when needed on favorable terms or at all.

The inability to raise capital as and when needed would have a negative impact on the Company’s financial condition and its ability to pursue its business strategy.

The inability to raise capital as and when needed would have a negative impact on the Company’s financial

condition and its ability to pursue its business strategy.

The Company will need to generate significant revenue to achieve profitability, and it may never do so.

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are unaudited.

The unaudited interim condensed consolidated financial statements have been prepared on the same basis as the audited annual consolidated financial statements and, in the opinion of management, reflect all adjustments, which include only normal recurring adjustments, necessary for the fair statement of the Company’s financial position as of March 31, 2025, the results of its operations for the three months ended March 31, 2025 and 2024, the condensed consolidated statements of stockholders’ equity for the three months ended March 31, 2025 and 2024, and its cash flows for the three months ended March 31, 2025 and 2024.

The financial data and other information disclosed in these notes related to the three months ended March 31, 2025 and 2024 are also unaudited.

The results for the three months ended March 31, 2025 are not necessarily indicative of results to be expected for the year ending December 31, 2025, any other interim periods, or any future year or period.

The unaudited interim condensed consolidated financial statements have been prepared on the same basis as the audited annual consolidated financial statements and, in the opinion of management, reflect all adjustments, which include only normal recurring adjustments, necessary for the fair statement of the Company’s financial position as of June 30, 2025, the results of its operations for the three and six months ended June 30, 2025 and 2024, the condensed consolidated statements of stockholders’ equity for the three and six months ended June 30, 2025 and 2024, and its cash flows for the six months ended June 30, 2025 and 2024.

The financial data and other information disclosed in these notes related to the three and six months ended June 30, 2025 and 2024 are also unaudited.

The results for the three and six months ended June 30, 2025 are not necessarily indicative of results to be expected for the year ending December 31, 2025, any other interim periods, or any future year or period.

The condensed consolidated balance sheet data as of December 31, 2024 was derived from our audited financial statements, but does not include all disclosures required by U.S.

These interim financial statements should be read in conjunction with the audited financial statements as of and for the year ended December 31, 2024, and notes thereto, which are included in the Company’s Annual Report on Form 10-K that was filed with the Securities and Exchange Commission (the “SEC”) on February 28, 2025.

Change in Presentation

For the three months ended March 31, 2025, “Other income, net” as presented on the condensed consolidated statements of operations and comprehensive loss was disaggregated into “Accretion (amortization) of investments,” “Interest income,” and “Other income, net.” This presentation has been conformed for all previous periods presented and had no impact on previously reported results.

Summary of Significant Accounting Policies

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The following table contains additional information on our consolidated net loss, including significant segment expenses:

Three Months Ended March 31,

Three Months Ended June 30, Six Months Ended June 30,

(in thousands) 2025 2024 2025 2024

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Other segment items (1)

11,081 9,826 20,966 18,914

Total operating expenses 54,492 55,672 108,338 104,604

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The following tables present the Company’s fair value hierarchy for its assets that are measured at fair value on a recurring basis and indicate the level of the fair value hierarchy utilized to determine such fair value:

As of March 31, 2025:

As of June 30, 2025:

(in thousands) Level 1 Level 2 Level 3 Total

1 unchanged sentence

Money market funds $ — $ 40,748 $ — $ 40,748

Treasury and government securities — 20,797 — 20,797

Corporate debt securities — 6,776 — 6,776

Treasury and government securities — 5,216 — 5,216

Short-term investments:

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Unrealized gains and losses of investments in debt securities consisted of the following:

As of March 31, 2025:

As of June 30, 2025:

(in thousands) Amortized Cost Unrealized Gains Unrealized Losses Fair Value

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Total short-term investments in debt securities $ 2,997 $ 1 $ — $ 2,998

The contractual maturities of the Company’s investments in debt securities held were as follows:

(in thousands) March 31,

The contractual maturities of the Company’s investments in debt securities were as follows:

(in thousands) June 30,

2025 December 31,

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Marketable securities in unrealized loss positions consisted of the following:

As of March 31, 2025:

As of June 30, 2025:

(in thousands, except number of securities) Number of Securities Fair Value Gross Unrealized Losses

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Corporate debt securities 9 $ 8,192 $ ( 2 )

Based on factors such as historical experience, market data, issuer-specific factors, and current economic conditions, the Company did not record an allowance for credit losses as of March 31, 2025 related to these investments.

Further, given the lack of significant change in the credit risk, the Company does not consider these investments to be impaired.

1 unchanged sentence

Property and equipment, net consisted of the following:

(in thousands) March 31,

(in thousands) June 30,

2025 December 31,

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Depreciation expense related to property and equipment is as follows:

Three Months Ended March 31,

Three Months Ended June 30, Six Months Ended June 30,

(in thousands) 2025 2024 2025 2024

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Accrued expenses and other current liabilities consisted of the following:

(in thousands) March 31,

(in thousands) June 30,

2025 December 31,

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Research and clinical costs

Facility related 317 2,811

License fee 1,562 1,938

Facility related 1 2,811

Other 1,117 1,272

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Subsequent to the initial non-cancelable term of the lease of ten years , the Company has an option to extend the lease for an additional period of ten years with the rent during the extension term being the then fair market rent.

The Company secured the lease with a $ 13.1 million security deposit, which was recorded as restricted cash on the condensed consolidated balance sheets as of March 31, 2025 and December 31, 2024.

The Company secured the lease with a $ 13.1 million security deposit, which was recorded as restricted cash on the condensed consolidated balance sheets as of June 30, 2025 and December 31, 2024.

Accounting Considerations

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In June 2024, the Company filed a complaint in Massachusetts Superior Court against NW Cambridge Property Owner, LLC (“NWC”), the Company’s landlord at 60 First Street, alleging that NWC had breached the 60 First Street Lease by, among other reasons, refusing to provide the Company with certain rental credits for the late delivery of the leased space.

While this lawsuit is pending, the Company has continued to make the disputed payments under the 60 First Street Lease under protest.

In March 2025, the Court granted NWC’s motion for judgment on the pleadings, dismissing the Company’s claims against NWC.

In April 2025, the Company filed a notice of appeal of the Court’s order granting the motion for judgment on the pleadings and served a motion for leave to amend its complaint on NWC, which is currently pending.

Pending a ruling on the amended complaint, the

disputed payments are recorded within other current assets on the Company’s condensed consolidated balance sheets.

Total payments made under dispute was $ 13.9 million, and $ 10.8 million as of March 31, 2025 and December 31, 2024, respectively.

While this lawsuit is pending, the Company continued to make the disputed payments under the 60 First Street Lease under protest.

The disputed payments are recorded within other current assets on the Company’s condensed consolidated balance sheets.

Total payments made under dispute was $ 13.9 million, and $ 10.8 million as of June 30, 2025 and December 31, 2024, respectively.

Arsenal Street, Watertown, Massachusetts Leases

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The landlords of the spaces at 480 Arsenal Street and 500 Arsenal Street are affiliates.

The 480 Arsenal Amendment provides the Company with an additional 9,400 square feet of combined laboratory and office space (the “Expansion Space”) at no additional cost and also provides an early termination date for the existing space and the Expansion Space as the later of:

1) the date occurring 150 days after the lease commencement of 500 Arsenal Lease, or 2) 30 days after substantial completion, as defined in the 500 Arsenal Lease, of tenant improvements at 500 Arsenal Street.

If the 500 Arsenal Lease is terminated prior to its lease commencement such that the lease commencement never occurs, the Company will begin paying lease payments on the Expansion Space at the current rate for its existing space at 480 Arsenal Street and the early termination provisions of the 480 Arsenal Amendment become null and void.

The lease for space at 480 Arsenal Street, including the Expansion Space, terminated on April 30, 2025.

The 500 Arsenal Lease term commenced in December 2024 with a base term of 11 months.

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Subsequent to the base term, the Company has an option to extend the lease through August 2028, which it exercised in February 2025.

The Company secured the lease with a $ 0.6 million security deposit, which is recorded as restricted cash on the condensed consolidated balance sheets as of March 31, 2025.

The Company secured the lease with a $ 0.6 million security deposit, which is recorded as restricted cash on the condensed consolidated balance sheets as of June 30, 2025.

The 500 Arsenal Lease also provides a tenant improvement allowance of $ 2.4 million and an additional tenant improvement allowance of $ 1.2 million, which the Company would be obligated to repay to the landlord.

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Concurrently, the Company also determined that the termination of its leased space at 480 Arsenal Street was reasonably certain, and the Company recorded a $ 3.1 million reduction to the Company’s operating lease liability and its operating lease right-of-use asset on the condensed consolidated balance sheet.

The table below reconciles the undiscounted future annual lease payments to the total operating lease liabilities recorded in the condensed consolidated balance sheet as of March 31, 2025:

The table below reconciles the undiscounted future annual lease payments to the total operating lease liabilities recorded in the condensed consolidated balance sheet as of June 30, 2025:

(in thousands) Undiscounted

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Subject to certain requirements, the pre-funded warrants can be exercised by the holder at any time.

As of March 31, 2025, there have not been any exercises of the pre-funded warrants.

In May 2025, the holder exercised all 3,200,005 of its pre-funded warrants on a cashless basis and received 3,199,984 shares of the Company’s common stock.

Following this exercise, the Company has no pre-funded warrants outstanding.

August 2025 Offering

As a result of the offering, the Company received approximately $ 138.2 million in net proceeds, after deducting underwriting discounts, commissions and offering costs of approximately $ 6.0 million.

At-The-Market Equity Program

In November 2023, the Company entered into Open Market Sale Agreement SM (the “Sales Agreement”) with Jefferies LLC, acting as the Company’s agent and/or principal (the “Sales Agent”), with respect to an “at the market offering” program under which the Company may, from time to time, at its sole discretion, issue and sell shares of its common stock having an aggregate offering price of up to $ 300.0 million through the Sales Agent.

As of March 31, 2025, there have been no sales of common stock pursuant to the Sales Agreement.

Effective July 30 2025, the Company terminated the sales agreement prospectus (the “ATM Prospectus”) filed with the shelf registration statement on Form S-3 (File No.

333-275321) and related to the shares of the Company’s common stock issuable pursuant to the Sales Agreement.

As a result, the Company will not make any sales of its common stock pursuant to the Sales Agreement, unless and until a new prospectus, prospectus supplement or a new

registration statement is filed.

Other than the termination of the ATM Prospectus, the Sales Agreement remains in full force and effect.

As of June 30, 2025 and as of the date these condensed consolidated financial statements are issued, the Company has not sold any shares of common stock under the ATM Prospectus.

Stock-Based Compensation

2019 Equity Incentive Plan

2019 Stock Option and Grant Plan

The Company’s 2019 Stock Option and Grant Plan (the “2019 Plan”) provides for the Company to grant incentive stock options, non-qualified stock options, unrestricted stock awards, restricted stock awards and other stock-based awards to the officers, employees, consultants and other key persons of the Company.

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On January 1, 2025, the annual increase resulted in an additional 6,558,042 shares authorized being added to the 2022 Plan.

As of March 31, 2025, the Company had 28,080,152 shares reserved under the 2022 Plan and the 2019 Plan, and 11,689,462 shares available for issuance under the 2022 Plan.

As of June 30, 2025, the Company had 28,080,152 shares reserved under the 2022 Plan and the 2019 Plan, and 9,478,749 shares available for issuance under the 2022 Plan.

2022 Employee Stock Purchase Plan

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There was no annual increase for the 2022 ESPP on January 1, 2025.

As of March 31, 2025, the Company had 1,753,191 shares available for issuance under the 2022 ESPP.

During the three months ended March 31, 2025, the Company issued no shares of the Company’s common stock under the 2022 ESPP.

As of June 30, 2025, the Company had 1,619,579 shares available for issuance under the 2022 ESPP.

During the six months ended June 30, 2025, the Company issued 133,612 shares of the Company’s common stock under the 2022 ESPP.

Stock Options

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

The following table summarizes the Company’s stock option activity for the six months ended June 30, 2025:

Number of Shares Weighted-Average Exercise Price

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Cancelled or forfeited ( 2,102,462 ) 7.04

Outstanding at March 31, 2025 15,328,960 $ 7.21

Options vested and exercisable at March 31, 2025 6,026,956 $ 8.66

Options vested and expected to vest at March 31, 2025 15,328,960 $ 7.21

As of March 31, 2025, there was $ 40.0 million of total unrecognized compensation cost related to time-based unvested stock options.

Outstanding at June 30, 2025 16,839,673 $ 6.14

Options vested and exercisable at June 30, 2025 7,106,428 $ 8.45

Options vested and expected to vest at June 30, 2025 16,839,673 $ 6.14

As of June 30, 2025, there was $ 30.5 million of total unrecognized compensation cost related to time-based unvested stock options.

The Company expects to recognize such amount over a remaining weighted-average period of 2.9 years.

Performance-Based Stock Options

The following table summarizes the Company’s performance-based stock option activity for the three months ended March 31, 2025:

The following table summarizes the Company’s performance-based stock option activity for the six months ended June 30, 2025:

Number of Shares Weighted-Average

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Outstanding at December 31, 2024 1,061,730 $ 7.31

Granted 700,000 1.34

Exercised — —

Cancelled or forfeited — —

Outstanding at March 31, 2025 1,061,730 $ 7.31

Vested and exercisable at March 31, 2025 590,230 $ 7.07

As of March 31, 2025, there was $ 3.0 million of total unrecognized compensation cost related to performance-based stock options.

Outstanding at June 30, 2025 1,761,730 $ 4.94

Vested and exercisable at June 30, 2025 845,646 $ 6.87

As of June 30, 2025, there was $ 2.1 million of total unrecognized compensation cost related to performance-based stock options.

Repricing of Certain Outstanding Stock Options

On June 22, 2025, the Board of Directors approved, and on August 1, 2025 (the “Repricing Date”), the Company’s stockholders approved, a one-time repricing (the “Option Repricing”) of certain outstanding stock options granted to, and held by, certain of the Company’s current employees, including its executive officers, and members of the Board of Directors through the Repricing Date (collectively, the “Eligible Optionholders”), under the 2019 Plan and 2022 Plan (collectively, the “Plans”).

The Option Repricing impacted up to an aggregate of 8,285,387 shares of common stock (such options, the “Eligible Options”) that have exercise prices in excess of $ 4.04 (the “Repriced Exercise Price”), which was the closing trading price per share of the Company’s common stock on The Nasdaq Global Market on the Repricing Date.

Effective as of the Repricing Date, the per share exercise price of each Eligible Option held by an Eligible Optionholder on the Repricing Date was automatically reduced to the Repriced Exercise Price.

Under the terms of the Option Repricing, a Repriced Option will revert to its original exercise price per share if:

exercised prior to the 18-month anniversary of the Repricing Date for Repriced Options held by members of the Board of Directors or executive officers of the Company, as applicable, or the one-year anniversary of the Repricing Date for Repriced Options held by all other employees of the Company (each, a “Retention Date”);

an Eligible Optionholder’s Service Relationship (as defined in the Plans) is terminated by the Company for Cause (as defined in the applicable award agreement) prior to the applicable Retention Date;

an Eligible Optionholder resigns from the Company (including as a member of the Board of Directors) for any reason prior to the applicable Retention Date, other than described below.

Notwithstanding the foregoing, each Repriced Option shall retain the Repriced Exercise Price, to the extent it has not otherwise reverted to its original exercise price per share in accordance with the foregoing, and the ability to exercise such Repriced Option may be accelerated to earlier than the applicable Retention Date in the event of:

a Sale Event (as defined in the Plans) prior to the applicable Retention Date;

the termination of the Eligible Optionholder’s Service Relationship by the Company without Cause or for “good reason,” or resignation by the Eligible Optionholder for “good reason,” to the extent provided for in the Eligible Optionholder’s employment agreement, offer letter or severance plan (as applicable);

the Eligible Optionholder’s death or disability (as determined in accordance with the Plans, as applicable)..

Except as modified by the Option Repricing, all other terms and conditions of the Repriced Options, including, without limitation, any provisions with respect to vesting and term of the Repriced Options, will remain in full force and effect.

The Company is in the process of evaluating the accounting impact of the Option Repricing.

Performance-Based Restricted Common Stock Awards

The Company awarded restricted common stock to employees and non-employees under its 2019 Plan.

The following table summarizes the Company’s performance-based restricted common stock activity for the three months ended March 31, 2025:

The following table summarizes the Company’s performance-based restricted common stock activity for the six months ended June 30, 2025:

Number of Shares Weighted-Average Grant-Date Fair Value

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Repurchased — —

Outstanding at March 31, 2025 3,472,543 $ 0.06

Outstanding at June 30, 2025 3,472,546 $ 0.06

Stock-Based Compensation

1 unchanged sentence

Three Months Ended

June 30, Six Months Ended

(in thousands) 2025 2024 2025 2024

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The Company’s significant agreements are disclosed in Note 9, License and Collaboration Agreements , in the audited consolidated financial statements for the year ended December 31, 2024, and notes thereto, included in the Company’s Annual Report on Form 10-K that was filed with the SEC on February 28, 2025.

Since the date of those

financial statements, there have been no changes to the Company’s significant agreements except those discussed below.

Since the date of those financial statements, there have been no changes to the Company’s significant agreements except those discussed below.

Bristol-Myers Squibb — Related Party

Supplemental information related to the BMS Collaboration Agreement consisted of the following:

(in thousands) March 31,

(in thousands) June 30,

2025 December 31,

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Deferred revenue, net of current — related party $ 59,562 $ 63,218

Three Months Ended March 31,

Three Months Ended June 30, Six Months Ended June 30,

(in thousands) 2025 2024 2025 2024

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Revenue recognized from performance obligations fully or partially satisfied in previous periods $ 5 $ — $ 3 $ —

As of March 31, 2025, the aggregate amount of the transaction price allocated to performance obligations under the BMS Collaboration Agreement that are partially unsatisfied was $ 70.3 million.

As of June 30, 2025, the aggregate amount of the transaction price allocated to performance obligations under the BMS Collaboration Agreement that are partially unsatisfied was $ 67.9 million.

The Company recognizes the portion of the transaction price as the single performance obligation is satisfied, using an input method, in proportion to costs incurred to date as compared to total costs incurred and expected to be incurred in the future to satisfy the underlying obligation.

Cystic Fibrosis Foundation

In July 2025, the Company entered into an agreement with the Cystic Fibrosis Foundation (“CFF”), under which CFF has agreed to provide up to $ 24 million in additional funding to accelerate the development of Prime Editors designed to permanently correct cystic fibrosis-related lung disease.

The $ 24 million funding will be provided in two equal tranches, subject to certain closing conditions and scientific milestones.

The first tranche includes a $ 6 million equity investment in the Company, which was received as part of the August 2025 offering.

CFF’s additional investment builds on initial funding received under the Company’s therapeutic development agreement with CFF in January 2024.

Beam Collaboration Agreement — Related Party

The Company is currently engaged in arbitration proceedings with Beam Therapeutics, Inc.

(“Beam”) regarding the parties’ collaboration and license agreement (the “Agreement”).

A dispute arose between the parties following the Company’s March 18, 2025 announcement that it is developing a Prime Editing-based treatment for alpha-1 antitrypsin deficiency (“AATD”).

On April 16, 2025, Beam filed an arbitration demand with the American Arbitration Association (“AAA”), alleging that the Company has breached the Agreement by developing a product for the treatment of AATD and by allegedly not complying with certain obligations to transfer technical information to Beam pursuant to the Agreement.

Beam also makes related claims for trade secret misappropriation and various business torts based on similar allegations, including allegations made on information and belief.

Beam seeks both declaratory, injunctive, and monetary relief, but has not yet quantified the amount of damages it seeks.

On April 18, 2025, the Company filed an arbitration demand with the AAA seeking a declaration that the Company’s AATD program is within our “Field” as defined by the Agreement.

The arbitrations have been consolidated, and the consolidated proceeding remains in its early stages.

If the final resolution of the matter is adverse to the Company, the arbitration panel may provide Beam with relief including, among other things, monetary damages and/or an order that the Company cease work on its AATD program and transfer such program to Beam.

Net Loss per Share

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Three Months Ended

June 30, Six Months Ended

(in thousands, except share and per share amounts) 2025 2024 2025 2024

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Net loss per share attributable to common stockholders, basic and diluted $ ( 0.41 ) $ ( 0.46 ) $ ( 0.81 ) $ ( 0.90 )

The weighted-average number of common shares outstanding used in the basic and diluted net loss per share calculations includes the weighted-average effect of pre-funded warrants sold by the Company to purchase 3,200,005 shares of the Company's common stock.

The shares of common stock underlying the pre-funded warrants are considered outstanding for the purposes of computing earnings per share, because the shares may be issued for little or no consideration, they are fully vested, and the pre-funded warrants are immediately exercisable upon their issuance date.

Diluted net loss per share available to common stockholders is computed by giving effect to all potentially dilutive common stock equivalents outstanding for the period.

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

As of March 31,

As of June 30,

Anti-dilutive common stock equivalents:

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We are deploying Prime Editing technology, which we believe is a versatile, precise, and efficient gene editing technology.

In March 2025, we announced a preclinical program for the treatment of alpha-1 antitrypsin deficiency, our second program within our liver franchise, which, with our Wilson’s Disease program, we expect to advance into the clinic next year.

Chronic granulomatous disease is our most advanced blood program, and we are advancing PM359 as our candidate in the treatment of this disease.

We believe our Prime Editing programs are well-positioned to leverage the clinical, regulatory, and manufacturing advancements made to date across gene therapy, gene editing, and delivery modalities to accelerate progression to clinical trials and potential approval.

Going forward, we will focus our resources on advancing our in vivo liver franchise, where we are advancing programs to cure two of the largest genetic liver diseases, Wilson’s Disease and Alpha-1 Antitrypsin Deficiency, or AATD.

Both programs are currently in late stages of pre-clinical development and are on track for IND and/or CTA filings in the first half of 2026 for Wilson’s Disease and the middle of 2026 for AATD.

We intend to leverage the modularity of our platform to expeditiously and efficiently develop these programs supported by our universal liver lipid nanoparticle along with potential regulatory, clinical and other synergies from our modular technology.

We will also continue our in vivo Cystic Fibrosis program with support from the Cystic Fibrosis Foundation, and our efforts to develop Prime Edited CAR-T products for hematology, immunology and oncology in partnership with Bristol-Myers Squibb Company.

In addition, we will continue to pursue additional business development opportunities to accelerate innovation, ensure the broadest application of Prime Editing, and further bolster our financial resources.

For example, in July 2025, we announced that the Cystic Fibrosis Foundation has agreed to provide us with up to $24 million in additional funding to accelerate the development of Prime Editors designed to permanently correct cystic fibrosis-related lung disease.

The Cystic Fibrosis Foundation’s additional investment builds on initial funding received under our therapeutic development agreement with the Cystic Fibrosis Foundation in January 2024, and reflects its interest in Prime Editing as a potentially curative approach for cystic fibrosis.

We intend to leverage the technology’s versatility and modularity to address multiple disease-causing mutations, potentially treating the vast majority of people with cystic fibrosis.

We will initially focus on a program targeting G542X, one of the most prevalent cystic fibrosis-causing nonsense mutations and one for which there are no available therapies.

In addition, we will continue to advance hotspot and PASSIGE-based approaches for other mutations with funding received from the Cystic Fibrosis Foundation under its initial commitment in 2024.

We recently announced initial data from the first patient dosed in our Phase 1/2 trial in chronic granulomatous disease, or CGD.

In this patient dosed, a single dose of PM359, our candidate for the treatment of CGD, led to 58% dihydrorhodamine positivity by Day 15, 66% by Day 30 and 71% by Day 60, exceeding levels of dihydrohomadine positivity believed to be potentially curative.

In the second patient dosed in the trial, a single dose of PM359 led to a 70% dihydrorhodamine positivity by day 15 and 80% by day 30.

In both patients, we also observed successful manufacturing from a single mobilization, no serious adverse events related to PM359 and rapid neutrophil and platelet engraftment when compared to other commercially available autologous genetic therapy benchmarks.

We continue to believe PM359 has the potential to transform the care of p47phox CGD.

We are planning to have regulatory interactions based on the current data set.

Components of Our Results of Operations

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General and administrative expenses consist of salaries and personnel-related costs, including stock-based compensation, for our personnel in executive, legal, finance and accounting, human resources and other administrative functions.

General and administrative expenses also include legal fees relating to patents and corporate matters;

General and administrative expenses also include legal fees relating to patents and

corporate matters;

professional fees paid for accounting, auditing, consulting and tax service;

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Results of Operations

Comparison of the Three Months Ended March 31, 2025 and 2024

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

Operating Expenses

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Personnel expenses $ 14,448 $ 16,198 $ (1,750)

Research costs 11,036 11,619 (583)

Facility related 13,765 11,302 2,463

Research costs 8,116 11,390 (3,274)

License, intellectual property fees, and other 2,812 1,250 1,562

Clinical expense 1,173 547 626

Professional and consultant fees 1,660 1,281 379

Clinical expense 574 1,650 (1,076)

Total research and development expenses $ 41,375 $ 43,071 $ (1,696)

The $2.8 million increase in research and development expense for the three months ended March 31, 2025 as compared to the three months ended March 31, 2024 was primarily driven by a $3.6 million increase in facility-related expense primarily due to the expansion and build out of our laboratory space at 60 First Street and 500 Arsenal Street.

The $1.7 million decrease in research and development expense for the three months ended June 30, 2025 as compared to the three months ended June 30, 2024 was primarily driven by:

• $3.3 million decrease in research costs due to the deprioritization of our CGD programs as we strategically focus our internal efforts on advancing our in vivo liver franchise;

• $1.8 million decrease in personnel expenses, driven primarily by a decrease of $1.0 million in stock-based compensation expense and fewer R&D personnel resulting from workforce reduction;

• $1.1 million decrease in clinical expenses due to the deprioritization of our CGD programs and discontinuation of our efforts to independently advance our PM359 program to focus on our liver franchise and programs funded through external partnerships.

These were offset by:

• $2.5 million increase in facility-related expense primarily due to the expansion and build out of our laboratory space at 60 First Street and 500 Arsenal Street;

• $1.6 million increase in license and IP costs as we advance our in vivo liver franchise and pipeline.

General and Administrative Expenses

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Total general and administrative expenses $ 13,117 $ 12,601 $ 516

The $2.1 million increase in general and administrative expense for the three months ended March 31, 2025 as compared to the three months ended March 31, 2024 is primarily driven by a $1.3 million increase in personnel expenses.

The $0.5 million increase in general and administrative expense for the three months ended June 30, 2025 as compared to the three months ended June 30, 2024 is primarily driven by a $1.1 million increase in professional and consultant fees due to an increase in corporate legal expenses.

Other Income (Expense)

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The change in fair value of related party short-term investment for each of the periods presented is a result of Beam’s stock price movement.

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

Operating Expenses

Research and Development Expenses

Six Months Ended

(in thousands) 2025 2024 Change

Research and development expenses:

Personnel expenses $ 29,248 $ 31,205 $ (1,957)

Facility related 24,734 18,636 6,098

Research costs 19,152 23,009 (3,857)

License, intellectual property fees, and other 4,237 2,925 1,312

Professional and consultant fees 2,819 2,873 (54)

Clinical expense 1,747 2,197 (450)

Total research and development expenses $ 81,937 $ 80,845 $ 1,092

The $1.1 million increase in research and development expense for the six months ended June 30, 2025 as compared to the six months ended June 30, 2024 was primarily driven by:

• $6.1 million increase in facility-related expense primarily due to the expansion and build out of our laboratory space at 60 First Street and 500 Arsenal Street;

• $1.3 million increase in license and IP costs as we advance our in vivo liver franchise and pipeline.

This is offset by:

• $3.9 million decrease in research costs due to the deprioritization of our CGD programs as we strategically focus our internal efforts on advancing our in vivo liver franchise;

• $2.0 million decrease in personnel expenses, driven primarily by a decrease of $0.9 million in stock-based compensation expense and fewer R&D personnel resulting from the workforce reduction.

General and Administrative Expenses

Six Months Ended

(in thousands) 2025 2024 Change

General and administrative expenses:

Personnel expenses $ 14,238 $ 12,840 $ 1,398

Professional and consultant fees 7,228 5,931 1,297

Facility related and other 4,935 4,988 (53)

Total general and administrative expenses $ 26,401 $ 23,759 $ 2,642

The $2.6 million increase in general and administrative expense for the six months ended June 30, 2025 as compared to the six months ended June 30, 2024 is primarily driven by:

• $1.4 million increase in personnel expenses in connection with the reduction in force, primarily consisting of one-time severance payments and other employee termination-related expenses;

• $1.3 million increase in professional and consultant fees due an increase in corporate legal expenses.

Other Income (Expense)

Six Months Ended

(in thousands) 2025 2024 Change

Other income:

Interest income $ 1,925 $ 1,287 $ 638

Accretion (amortization) of investments 869 2,316 (1,447)

Change in fair value of short-term investment — related party (1,561) (759) (802)

Other income, net 55 81 (26)

Total other income, net $ 1,288 $ 2,925 $ (1,637)

Accretion (amortization of investments

Accretion (amortization) of investments for each of the periods presented is a result of increase (decrease) in the value of the our marketable securities purchased at a discount (premium) to their face value.

Liquidity and Capital Resources

Since our inception, we have incurred significant operating losses.

We expect to incur significant expenses and operating losses for the foreseeable future as we commence the clinical development of our programs and continue our platform development and early-stage research activities.

We expect to incur significant expenses and operating losses for the foreseeable future as we advance the preclinical development of our current research programs, commence the clinical development of any product candidates we may identify, and continue our platform development and early-stage research activities.

We have not yet commercialized any products and we do not expect to generate revenue from sales of products for several years, if at all.

To date, we have funded our operations primarily with proceeds from sales of preferred stock and from our public offerings and through payments from our collaboration partners.

As of March 31, 2025, we had cash, cash equivalents, and investments of $144.3 million, excluding our restricted cash, or $158.3 million, including restricted cash.

Going Concern

Since our inception, we have incurred substantial losses.

As of March 31, 2025, we had an accumulated deficit of $739.1 million and we expect to generate operating losses and negative operating cash flows for the foreseeable future.

As stated above, as of March 31, 2025, we maintained cash, cash equivalents, short-term investments, and related party short-term investments of $144.3 million.

In accordance with Accounting Standards Codification, or ASC, 205-40, Going Concern, or ASC 205-40, we evaluated whether there are conditions and events, considered in the aggregate, that raise substantial doubt about our ability to continue as a going concern within one year after the date on which this Quarterly Report on Form 10-Q is filed.

Based on the our cash, cash equivalents, short-term investments, and related party short-term investments as of March 31, 2025, our current and forecasted level of operations and forecasted cash flows we determined that substantial doubt exists about our ability to continue as a going concern for 12 months from the date these condensed consolidated financial statements are issued.

Our ability to continue as a going concern is dependent upon our ability to obtain the necessary financing to meet our obligations and repay our liabilities arising from normal business operations when they come due.

Management plans to provide for capital requirements through financing or other transactions, and selling shares under our “at the market offering” program.

There can be no assurance that we will be able to raise additional capital to fund operations with terms acceptable to us, or at all.

Because certain elements of our plans to mitigate the conditions that raised substantial doubt about our ability to continue as a going concern are outside of our control, including the ability to raise capital through an equity or other financing, those elements cannot be considered probable according to ASC 205-40, and therefore cannot be considered in the evaluation of mitigating factors.

The condensed consolidated financial statements as of March 31, 2025 have been prepared under the assumption that we will continue as a going concern for the next 12 months and that contemplates the realization of assets and satisfaction of liabilities and commitments in the normal course of business.

Our ability to continue as a going concern is dependent upon our uncertain ability to obtain additional capital, reduce expenditures and/or execute on its business plan.

These condensed consolidated financial statements do not include any adjustments that might result from the outcome of this uncertainty.

As of June 30, 2025, we had cash, cash equivalents, and investments of $101.8 million, excluding our restricted cash, or $115.4 million, including restricted cash.

In November 2023, we entered into an Open Market Sale Agreement SM (the “Sales Agreement”) with Jefferies LLC (“Jefferies”) under which we may, from time to time, issue and sell shares of our common stock having aggregate sales proceeds of up to $300.0 million, in a series of one or more at-the-market equity offerings (the “ATM Program”).

Effective July 30, 2025, we terminated the sales agreement prospectus (the “ATM Prospectus”) filed with the shelf registration statement on Form S-3 (File No.

333-275321) and related to the shares of our common stock issuable pursuant to the Sales Agreement.

As a result, we will not make any sales of our common stock pursuant to the Sales Agreement, unless and until a new prospectus, prospectus supplement or a new registration statement is filed.

Other than the termination of the ATM Prospectus, the Sales Agreement remains in full force and effect.

As of the date of this Quarterly Report on Form 10-Q, we have not sold any shares of common stock under the 2023 ATM program.

In August 2025, we issued and sold 43,700,000 shares of our common stock, including 5,700,000 shares pursuant to the exercise of the underwriters’ option to purchase additional shares, at a price to the public of $3.30 per share.

As a result of the offering, we received approximately $138.2 million in net proceeds, after deducting underwriting discounts, commissions and offering costs of approximately $6.0 million.

The following table summarizes our sources and uses of cash for each of the periods presented:

Three Months Ended

Six Months Ended

(in thousands) 2025 2024

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Operating Activities

Net cash used in operating activities for the three months ended March 31, 2025 was driven primarily by the following uses of cash:

Net cash used in operating activities for the six months ended June 30, 2025 was driven primarily by the following uses of cash:

• $104.5 million net loss;

• $6.7 million change in accrued expenses and other current liabilities;

• $2.4 million change in deferred revenue — related party;

These were offset by:

• $10.7 million of non-cash amounts included in net loss, which primarily consisted of stock-based compensation expense, non-cash lease expense, depreciation expense, and change in fair value of short-term investment — related party;

• $2.1 million change in lease liabilities

• $1.7 million change in accrued expenses and other current liabilities;

• $1.5 million change in accounts payable.

Net cash used in operating activities for the three months ended March 31, 2024 was driven primarily by the following uses of cash:

These were offset by $21.3 million of non-cash amounts included in net loss, which primarily consisted of stock-based compensation expense, non-cash lease expense, depreciation expense, and change in fair value of short-term investment — related party.

Net cash used in operating activities for the six months ended June 30, 2024 was driven primarily by the following uses of cash:

• $101.1 million net loss;

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• $9.2 million change in accounts payable;

• $4.5 million change in accrued expenses and other current liabilities;

• $5.7 million change in lease liabilities;

• $3.9 million change in accrued expenses and other current liabilities;

• $2.5 million change in prepaid and other current assets.

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Investing Activities

Net cash used in investing activities for the three months ended March 31, 2025 was driven primarily by the following:

Net cash used in investing activities for the six months ended June 30, 2025 was driven primarily by the following:

• $41.0 million of purchases of marketable securities, net of maturities;

• $4.0 million of purchases of property and equipment.

Net cash used in investing activities for the three months ended March 31, 2024 was driven primarily by the following:

Net cash used in investing activities for the six months ended June 30, 2024 was driven primarily by the following:

• $25.9 million of purchases of marketable securities, net of maturities;

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Financing Activities

Net cash provided by financing activities for the three months ended March 31, 2025 was driven by $6.0 million of proceeds received under our agreement with Cystic Fibrosis Foundation.

Net cash provided by financing activities for the three months ended March 31, 2024 was driven primarily by the following:

• $132.1 million of proceeds from issuances of common stock in the our February 2024 public offering;

Net cash provided by financing activities for the six months ended June 30, 2025 was driven by $6.0 million of proceeds received under our agreement with Cystic Fibrosis Foundation.

Net cash provided by financing activities for the six months ended June 30, 2024 was driven primarily by the following:

• $132.1 million of proceeds from issuances of common stock in our February 2024 public offering;

• $18.8 million of proceeds from issuance of pre-funded warrants contemporaneous with our February 2024 public offering;

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We expect our expenses to increase in connection with our ongoing activities, particularly as we advance the preclinical activities and studies and initiate clinical trials.

In addition, if we obtain regulatory approval for any product candidates, we expect to incur significant expenses related to product sales, marketing, and distribution to the extent that such sales, marketing and distribution are not the responsibility of potential collaborators.

In addition, if we obtain regulatory approval for any product candidates, we expect to incur significant expenses related to product sales, marketing, and distribution to the extent that such sales,

marketing and distribution are not the responsibility of potential collaborators.

Further, we have incurred, and expect to continue to incur, costs associated with operating as a public company.

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For more information, refer to the section titled “Risk Factors” in our Annual Report on Form 10-K for the year ended December 31, 2024, and the “Risk Factors” section of subsequent Quarterly Reports on Form 10-Q.

We believe our existing cash, cash equivalents, and investments, will be sufficient to fund our operating expenses and capital expenditure requirements into the first half of 2026.

We believe our existing cash, cash equivalents, and investments, including funds from our August 2025 offering, will be sufficient to fund our operating expenses and capital expenditure requirements into 2027.

We have based this estimate on assumptions that may prove to be wrong, and we could exhaust our available capital resources sooner than we expect.

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• identify product candidates;

• evaluate strategic alternatives and potential partnership opportunities for PM359, including our ability to execute and realize the anticipated benefits of any strategic alternatives we may pursue;

• develop, maintain, expand and protect our intellectual property portfolio and defend intellectual property-related claims;

• maintain existing collaborations or strategic relationships and identify and enter into future license agreements and collaborations with third parties;

• initiate preclinical testing and clinical trials for our future product candidates we identify;

• develop, maintain, expand and protect our intellectual property portfolio;

• further develop our Prime Editing platform;

• hire additional research, clinical and scientific personnel.

• hire additional personnel to support our strategic priorities.

If we receive regulatory approval for any of our product candidates, we expect to incur significant commercialization expenses related to product manufacturing, sales, marketing and distribution, depending on where we choose to commercialize ourselves.

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To the extent that we raise additional capital through the sale of equity or convertible debt securities, ownership interest may be materially diluted, and the terms of such securities could include liquidation or other preferences that adversely affect your rights as a common stockholder.

Debt financing and preferred equity financing, if available, may involve agreements that include restrictive covenants that limit our ability to take specified actions, such as incurring additional debt, making capital expenditures or declaring dividends.

Debt and equity financing, if available, may involve agreements that include restrictive covenants that limit our ability to take specified actions, such as incurring additional debt, making capital expenditures or declaring dividends.

If we raise funds through collaborations, strategic alliances or marketing, or distribution or licensing arrangements with third parties, we may have to relinquish valuable rights to our technologies, any future revenue streams, research programs or product candidates or grant licenses on terms that may not be favorable to us.

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These contracts generally provide for termination on notice, and therefore are cancellable contracts and not included in the table of contractual obligations and commitments.

During the three months ended March 31, 2025, except for the minimum lease commitments disclosed in Note 6, Leases , to the unaudited condensed consolidated financial statements in this Quarterly Report on Form 10-Q, there were no significant changes to our contractual obligations and commitments described under Management’s Discussion and Analysis of Financial Condition and Results of Operations in our Annual Report on Form 10-K for the year ended December 31, 2024.

During the six months ended June 30, 2025, except for the minimum lease commitments disclosed in Note 6, Leases , to the unaudited condensed consolidated financial statements in this Quarterly Report on Form 10-Q, there

were no significant changes to our contractual obligations and commitments described under Management’s Discussion and Analysis of Financial Condition and Results of Operations in our Annual Report on Form 10-K for the year ended December 31, 2024.

Critical Accounting Policies and Significant Judgments and Estimates

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Actual results may differ from these estimates.

During the three months ended March 31, 2025, there were no material changes to our critical accounting policies and significant judgements described under Management’s Discussion and Analysis of Critical Accounting Policies and Significant Judgments and Estimates which are included in our Annual Report on Form 10-K for the year ended December 31, 2024.

During the six months ended June 30, 2025, there were no material changes to our critical accounting policies and significant judgements described under Management’s Discussion and Analysis of Critical Accounting Policies and Significant Judgments and Estimates which are included in our Annual Report on Form 10-K for the year ended December 31, 2024.

Recently Issued and Adopted Accounting Pronouncements

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Compared sentence by sentence after normalising whitespace, quotation marks, case and digits, so re-formatting and restated figures do not read as changed language. Wording changes appear as one removal and one addition. The current filing and the prior one are authoritative.

What changed 10-Q

Item 1. Financial Statements