Metagenomi Therapeutics, Inc.
For the period ended Dec 31, 2025. Filed Mar 5, 2026.
View on SEC.govAbout this filing
A company's yearly report to the SEC, with audited financial statements. It is the fullest account a company gives of its business, its finances and the risks it sees.
FY2025 · Filed Mar 5, 2026
What changed in Management’s Discussion and Analysis?
Read the current filingPrevious report: 10-K
Period ended 2024-12-31; filed 2025-03-17.
0000950170-25-040217
Item 7. Management’s Discussion and Analysis of Financial Condition and Results of OperationsCurrent report: 10-K
Period ended 2025-12-31; filed 2026-03-05.
0001193125-26-093976
Item 7. Management’s Discussion and Analysis of Financial Condition and Results of OperationsThe baseline is this issuer’s latest earlier reporting period of the same form that was filed before the current report. A previous 10-Q is a different quarter, not a year-over-year comparison. Amendments are excluded.
Compared 123 previous paragraphs and 119 current paragraphs.
74 unchanged; 25 reworded; 20 added; 23 removed; 1 previous and 0 current paragraphs rearranged.
Tables are not compared: 4 previous and 4 current tables excluded. Dates, whitespace, punctuation and numbering changes are ignored; changes to financial figures remain significant.
A changed paragraph is not evidence that risk increased or decreased. An unchanged paragraph does not establish that risk stayed the same.
Added paragraphs (20)
Current report
Overview
Current report
We are an in vivo genome editing company capitalizing on our proprietary technologies to create curative genetic medicines for patients. We were founded on the science of metagenomics, the study of genetic materials recovered from the natural environment, to discover and develop a suite of novel gene editing tools potentially capable of correcting any type of genetic mutation found anywhere in the human genome. We leverage machine learning and artificial intelligence to enhance our signature gene editing systems. In late 2025, we made the decision to strategically reprioritize our pipeline and discovery efforts to focus our resources on driving forward our lead programs that utilize our most advanced, signature gene-editing capabilities with the highest probability of success while maintaining financial discipline to drive sustainable growth and long-term value. We increased our focus on high-value programs in disease indications with well-understood biology and clearly defined clinical development and regulatory pathways to accelerate programs with the potential to deliver therapeutic benefits of gene editing to patients.
Current report
Wholly Owned Programs
Current report
MGX-001 – Novel, Durable, Site-Specific Genome Integration for Expression of Factor VIII (FVIII)
Current report
MGX-001 is designed to provide curative, life-long protection from bleeding events and joint damage in adults and children with hemophilia A from a single administration. MGX-001 is designed to insert a Factor VIII (“FVIII”) DNA cassette into a “safe harbor location” within an intron of the albumin gene, leveraging the strong native albumin promoter to express FVIII.
Current report
In November 2025, we announced preclinical data from a dose range finding study of MGX-001 in non-human primates (“NHPs”), where MGX-001 demonstrated curative FVIII activity with best-in-class treatment potential. The data also demonstrated clear dose dependency across both the AAV and LNP components of MGX-001, informing our clinical dose-regimen strategy. This data builds upon an earlier study, where we demonstrated durable FVIII activity over an approximately 19-month study in NHPs, with an encouraging safety profile. MGX-001 has also shown no detectable off-target editing in a series of orthogonal assays employed to discover and validate potential off-target sites.
Current report
In the fourth quarter of 2025, we completed a pre-IND meeting for the development of MGX-001. We remain on track for regulatory submission to advance a global clinical program, including an investigational new drug application (“IND”) in the fourth quarter of 2026, and subject to regulatory clearance, initiate clinical trials in 2027.
Current report
MGX-001 Large Gene Integration System for Secreted Protein Deficiency Disorders
Current report
Leveraging the MGX-001 site-specific genome integration system, we are pursuing other secreted protein deficiencies. In late 2025, we demonstrated the curative potential of the MGX-001 large gene integration system in an additional secreted protein disorder, antithrombitin III (“AT-III”) deficiency, in an in vivo study in NHPs.
Current report
Ionis Collaboration
Current report
In November 2022, we entered into a Collaboration and License Agreement with Ionis Pharmaceuticals, Inc. (“Ionis”) to research, develop and commercialize investigational medicines using our genome editing technologies. We are currently in Wave 1 of our collaboration with Ionis Pharmaceuticals, Inc. (“Ionis) focused on four disease targets in cardio metabolic indications. In December 2025, we announced apolipoprotein C-III (“APOC3”) for the treatment of high triglycerides (“HTG”) as the third collaboration target in Wave 1, and we jointly presented NHP preclinical data at the Nature Conference, “Cracking the Code: Nucleic Acid Medicines Coming of Age.” Additional targets in Wave 1 include transthyretin (“TTR”) for transthyretin amyloidosis, angiotensinogen (“AGT”) for refractory hypertension, and one undisclosed program. All four targets in Wave 1 are in the lead optimization phase of development and are designed to achieve protein reduction via gene knockout.
Current report
Initial Public Offering
Current report
ATM Program
Current report
On March 17, 2025, we entered into an Open Market Sale Agreement SM (the “ATM Sales Agreement”) with Jefferies LLC (“Jefferies”), pursuant to which we may issue and sell, from time to time and at our sole discretion, shares of our common stock, through Jefferies as the sales agent, by any method permitted by law deemed to be an “at the market” (“ATM”) offering as defined in Rule 415(a)(4) promulgated under the Securities Act, having an aggregate offering price of up to $75.0 million. We will pay Jefferies a commission fee of up to 3.0% of the gross proceeds of any shares sold through Jefferies under the ATM Sales Agreement, and have also provided Jefferies with customary indemnification and contribution rights. As of December 31, 2025, no shares have been sold under the ATM Sales Agreement.
Current report
We expect our research and development expenses will increase substantially as we advance our programs through their planned preclinical and clinical development.
Current report
Benefit from Income Taxes
Current report
Research and development expenses decreased $14.7 million for the year ended December 31, 2025, as compared to the prior year, primarily due to decreases of $6.3 million in employee-related expenses and $4.1 million in stock-based compensation expense primarily due to a decrease in headcount, $3.2 million in research and development supplies and services primarily due to a decrease in lab supplies purchased as a result of the decrease in headcount, and $1.4 million in facilities and allocated overhead, including repairs and maintenance costs and common facilities related expenses allocated to research and development.
Current report
Benefit from Income Taxes
Current report
On March 17, 2025, we entered into the ATM Sales Agreement with Jefferies, pursuant to which we may issue and sell shares of our common stock from time to time and at our sole discretion, through Jefferies as our sales agent, by any method permitted that is deemed to be an “at the market offering” as defined in Rule 415(a)(4) promulgated under the Securities Act having an aggregate offering price of up to $75.0 million. As of December 31, 2025, we have not sold any shares under the ATM Sales Agreement.
Current report
Net cash used in financing activities for the year ended December 31, 2025 was $0.4 million primarily due to a payment of deferred financing costs, partially offset by proceeds from our ESPP.
Removed paragraphs (23)
Previous report
We are a precision genetic medicines company committed to developing curative therapeutics for patients using our proprietary, genome editing toolbox. We are harnessing the power of metagenomics, the study of genetic material recovered from the natural environment, to unlock four billion years of microbial evolution to discover and develop a suite of novel editing tools capable of correcting any type of genetic mutation found anywhere in the genome. Our platform combines artificial intelligence (“AI”), ancestral state reconstruction, and proprietary algorithms run on expansive cloud computing infrastructure to identify novel clustered regularly interspaced short palindromic repeat (“CRISPR”) nucleases and other effector enzymes at high speed. Our comprehensive genome editing toolbox includes systems for making small edits such as programmable nucleases, base editors, and small RNA-mediated integration systems (“RIGS”), as well as large gene integration systems including large template RIGS and CRISPR-associated transposases (“CASTs”). In addition, our toolbox includes ultra-small editing systems that are small enough to be packaged into a single adeno-associated virus (“AAV”) to potentially address extrahepatic therapeutic indications. Together, these tools form a toolbox with the potential to make any desired gene modification – gene knockdown, gene knock-in as well as small and large genomic corrections.
Previous report
Our investigational development program in hemophilia A is a potentially curative therapy designed to provide life-long protection from bleeding events and joint damage in adults and children. In a non-human primate (“NHP”) study, we demonstrated integration of a cynomolgus version of the B-domain deleted wild type Factor VIII (“FVIII”) gene, used to avoid the confounding effects of anti-human FVIII antibodies, and confirmed durable FVIII activity levels in all animals over a 16.5-month period with a data cut-off of November 2024. Durable activity from the FVIII knock-in was achieved with only transient elevation of liver transaminases at the time of dose administrations, and with no other safety findings as of that date and no impact to circulating albumin levels and no significant change in total bilirubin post administrations. In a second NHP study designed to support our lead hemophilia A development candidate, MGX-001, which uses a B-domain deleted bioengineered FVIII construct, we demonstrated significantly higher FVIII activity compared to wild type FVIII, despite similar integration frequency between the bioengineered construct and wild type gene. This data suggests that MGX-001 may enable therapeutic levels of FVIII activity at lower AAV doses, potentially resulting in MGX-001 having improved safety characteristics. In mid 2024, we engaged in regulatory discussions with the U.S. Food and Drug Administration (the “FDA”) and initiated manufacturing activities to support Investigational New Drug (“IND”)-enabling studies and clinical material supply. We plan to conduct pre-IND and ex-U.S. regulatory meetings in 2025 and to complete IND and clinical trial application (“CTA”) filings for MGX-001 in 2026.
Previous report
Our collaboration with Ionis Pharmaceuticals, Inc. (“Ionis”) initially focuses on high value cardiometabolic diseases. In vivo rodent proof-of-concept was achieved in all four wave 1 genetic targets, including transthyretin (“TTR”) for transthyretin amyloidosis and angiotensinogen (“AGT”) for refractory hypertension, as well as two undisclosed programs in significant cardiometabolic indications. Along with our partner Ionis, we are conducting preclinical activities with the plan to nominate one to two development candidates in 2025.
Previous report
We expect our research and development expenses to increase substantially for the foreseeable future as we continue to invest in research and development activities related to developing our platform, including investments in manufacturing, as we advance our programs and conduct clinical trials. The process of conducting the necessary clinical research to obtain regulatory approval is costly and time-consuming, and the successful development of our platform is highly uncertain. As a result, we are unable to determine the duration and completion costs of our research and development projects, the costs of related clinical development costs or when and to what extent we will generate revenue from the commercialization of our platform.
Previous report
Benefit (Provision) for Income Taxes
Previous report
Research and development expenses were $109.2 million for the year ended December 31, 2024, compared to $94.4 million for the year ended December 31, 2023. The increase of $14.8 million was primarily due to an increase of $5.5 million in stock-based compensation expense in addition to $2.7 million in other employee-related expenses, an increase of $3.0 million in facilities and allocated overhead, including rent, repairs and maintenance costs, depreciation, common facilities and information technology related expenses allocated to research and development due to expansion of our research and development operations, and an increase of $3.1 million in research and development supplies and services related to external costs to support our research and preclinical development activities and manufacturing activities to support the MGX-001 program in hemophilia A. The increase in stock-based compensation and employee-related expenses was due to an increase in the average headcount, the issuance of annual equity awards to existing employees, and a one-time acceleration of stock-based compensation expense related to profits interests units that were canceled without a concurrent grant of a replacement award during the Reorganization and were accounted for as a repurchase for no consideration during the year ended December 31, 2024
Previous report
Benefit (Provision) for Income Taxes
Previous report
Net cash provided by financing activities for the year ended December 31, 2023 was $1.0 million, which consisted of $4.3 million of net cash proceeds from our issuance of Series B-1 preferred redeemable convertible preferred stock, partially offset by $3.3 million of payments of IPO costs.
Previous report
We issued profits interests units to our employees, consultants and our board of managers prior to our IPO. In connection with the Reorganization, all outstanding unvested profits interests were exchanged for unvested restricted common stock. Prior to July 31, 2023, we used the Black-Scholes option-pricing model to determine the grant date fair value of profits interests. Beginning on July 31, 2023, the grant date fair value of profits interests issued and modified was estimated using the valuation model based on the Probability Weighted Expected Return Method (“PWERM”) with the estimated equity fair value allocated via the distribution waterfall in accordance with the amendment to the LLC Agreement to all outstanding redeemable convertible preferred units, common units and profits interests.
Previous report
Determination of the Fair Value of our Common Units Issued Prior to our IPO
Previous report
As there was no public market for our common units prior to the IPO, the estimated fair value of our common units was determined by our board of managers as of the date of each award grant with input from management, considering our most recently available third-party valuations of common unit, and our board of managers’ assessment of additional objective and subjective factors that it believed were relevant and which may have changed from the date of the most recent valuation through the date of the grant. These third-party valuations were performed in accordance with the guidance outlined in the American Institute of Certified Public Accountants’ Accounting and Valuation Guide, Valuation of Privately-Held-Company Equity Securities Issued as Compensation (the “Practice Aid”).
Previous report
In accordance with the Practice Aid, we determined the hybrid method was the most appropriate method for determining the fair value of our common units based on our stage of development and other relevant factors. The hybrid method is a PWERM, where the equity value in one or more scenarios is calculated using an option-pricing method (“OPM”). The PWERM is a scenario-based methodology that estimates the fair value of common unit based upon an analysis of future values for the company, assuming various outcomes. The common unit value is based on the probability-weighted present value of expected future investment returns considering each of the possible outcomes available as well as the rights of each class of members’ units. The future value of the common unit under each outcome is discounted back to the valuation date at an appropriate risk-adjusted discount rate and probability weighted to arrive at an indication of value for the common unit. A discount for lack of marketability of the common unit is then applied to arrive at an indication of value for the common unit. In addition to considering the results of independent third-party valuations, our board of managers considered various objective and subjective factors to determine the thresholds for the profits interests as of each grant date, including:
Previous report
the prices at which we sold shares of redeemable convertible preferred units and the superior rights and preferences of the redeemable convertible preferred units relative to our common units at the time of each grant;
Previous report
the progress of our research and development programs;
Previous report
milestones achieved by us;
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the state of the industry and the economy;
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our stage of development and commercialization and our business strategy;
Previous report
external market conditions affecting the biopharmaceutical industry and trends within the biopharmaceutical industry;
Previous report
our financial position, including cash on hand, and our historical and forecasted performance and operating results;
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the lack of an active public market for our common stock and our preferred stock;
Previous report
the likelihood of achieving a liquidity event, such as an initial public offering (“IPO”), or our sale in light of prevailing market conditions; and
Previous report
the analysis of IPOs and the market performance of similar companies in the biopharmaceutical industry.
Previous report
The assumptions underlying these valuations are highly complex and subjective and represent management’s best estimates, which involved inherent uncertainties and the application of management’s judgment. As a result, if we had used significantly different assumptions or estimates, the fair value of our common unit and our unit-based compensation expense could be materially different.
Reworded paragraphs (25)
Previous wording
You should read the following discussion and analysis of our financial condition and results of operations together with our consolidated financial statements and the related notes included elsewhere in this Annual Report on Form 10-K. As discussed in the section titled “Special Note Regarding Forward-Looking Statements,” the following discussion and analysis contains forward-looking statements that involve risks and uncertainties, such as statements regarding our plans, objectives, expectations, intentions and projections. Our actual results could differ materially from those discussed in these forward-looking statements. Factors that could cause or contribute to such differences include, but are not limited to, those discussed in the “Risk Factors” section of this Annual Report on Form 10-K. Our historical results are not necessarily indicative of the results that may be expected for any period in the future.
Current wording
You should read the following discussion and analysis of our financial condition and results of operations together with our financial statements and the related notes included elsewhere in this Annual Report on Form 10-K. As discussed in the section titled “Special Note Regarding Forward-Looking Statements,” the following discussion and analysis contains forward-looking statements that involve risks and uncertainties, such as statements regarding our plans, objectives, expectations, intentions and projections. Our actual results could differ materially from those discussed in these forward-looking statements. Factors that could cause or contribute to such differences include, but are not limited to, those discussed in the “Risk Factors” section of this Annual Report on Form 10-K. Our historical results are not necessarily indicative of the results that may be expected for any period in the future.
Previous wording
We previously operated as a Delaware limited liability company under the name Metagenomi Technologies, LLC (“Metagenomi LLC”). On January 24, 2024, we completed a series of transactions pursuant to which Metagenomi LLC merged with and into its wholly-owned subsidiary Metagenomi, Inc., a Delaware corporation, with Metagenomi, Inc. (“Metagenomi” or the “Company”) continuing as the surviving corporation (the “Reorganization”). In connection with the Reorganization, (i) all of the outstanding common unitholders of Metagenomi LLC received shares of common stock of Metagenomi, Inc., (ii) all of the outstanding redeemable convertible preferred unitholders of Metagenomi LLC received shares of redeemable convertible preferred stock of
Current wording
We previously operated as a Delaware limited liability company under the name Metagenomi Technologies, LLC (“Metagenomi LLC”). On January 24, 2024, we completed a series of transactions pursuant to which Metagenomi LLC merged with and into its wholly-owned subsidiary Metagenomi, Inc., a Delaware corporation, with Metagenomi, Inc. continuing as the surviving corporation (the “Reorganization”). In connection with the Reorganization, (i) all of the outstanding common unitholders of Metagenomi LLC received shares of common stock of Metagenomi, Inc., (ii) all of the outstanding redeemable convertible preferred unitholders of Metagenomi LLC received shares of redeemable convertible preferred stock of Metagenomi, Inc. with the same rights and privileges and (iii) certain holders of profits interests in Metagenomi LLC received shares of common stock or unvested restricted common stock in Metagenomi, Inc. as determined by the applicable provisions of the Amended and Restated Limited Liability Company Agreement in effect immediately prior to the Reorganization. In connection with the Reorganization, by operation of law, Metagenomi, Inc. acquired all assets of Metagenomi LLC, and assumed all of its liabilities and obligations. The Reorganization was a non-taxable transaction to Metagenomi, Inc. for U.S. income tax purposes.
Previous wording
On January 26, 2024, following the Reorganization, Metagenomi, Inc. effected a reverse stock split of the shares of common stock at a ratio of 1-for-1.74692 (the “Reverse Stock Split”). Immediately prior to the closing of the IPO, each share of Metagenomi, Inc.’s redeemable convertible preferred stock then outstanding converted into 23,935,594 shares of common stock.
Current wording
On January 26, 2024, following the Reorganization, Metagenomi, Inc. effected a reverse stock split of the shares of common stock at a ratio of 1-for-1.74692 (the “Reverse Stock Split”). Immediately prior to the closing of the IPO, all of the then-outstanding shares of redeemable convertible preferred stock converted into 23,935,594 shares of common stock.
Previous wording
Unfavorable conditions in the economy in the United States and abroad may negatively affect the growth of our business and our results of operations. For example, macroeconomic events, including, inflationary pressures, interest rate and currency rate fluctuations, increased U.S. trade tariffs and trade disputes with other countries, economic slowdown or recession, banking instability, monetary policy changes, geopolitical tensions or the outbreak of hostilities or war, including from the ongoing Russia-Ukraine conflict, the current conflict in Israel and Gaza (including any escalation or expansion) and increasing tensions between China and Taiwan, have led to economic uncertainty and volatility globally. The effect of macroeconomic conditions may not be fully reflected in our results of operations until future periods. To date, the macroeconomic trends discussed above have not had a material adverse impact on our business, financial condition or results of operations. If, however, economic uncertainty increases or the global economy worsens, our business, financial condition and results of operations may be harmed. For further discussion of the potential impacts of macroeconomic events on our business, financial condition, and operating results, refer to the section titled “Risk Factors” included elsewhere in this Annual Report on Form 10-K.
Current wording
Unfavorable conditions in the economy in the United States (“U.S.”) and abroad may negatively affect the growth of our business and our results of operations. For example, macroeconomic events, including, inflationary pressures, interest rate and currency rate fluctuations, increased U.S. trade tariffs, reciprocal and retaliatory tariffs from other countries, and trade disputes with other countries, new laws and regulations enacted by the Trump administration, including, but not limited to, the One Big Beautiful Bill Act (the “OBBBA”), economic slowdown or recession, banking instability, monetary policy changes, geopolitical tensions or the outbreak of hostilities or war, including from the ongoing Russia-Ukraine conflict, the current conflict in Israel and Gaza (including any escalation or expansion), the current conflict in Venezuela and increasing tensions between China and Taiwan, have led to economic uncertainty and volatility globally. The effect of macroeconomic conditions may not be fully reflected in our results of operations until future periods. To date, the macroeconomic trends discussed above have not had a material adverse impact on our business, financial condition or results of operations, but we continue to monitor these developments closely. If, however, economic uncertainty increases or the global economy worsens, our business, financial condition and results of operations may be harmed. For further discussion of the potential impacts of macroeconomic events on our business, financial condition, and operating results, refer to the section titled “Risk Factors” included elsewhere in this Annual Report on Form 10-K.
Previous wording
As part of our strategy, we have entered into collaborations with third parties for one or more of our programs or product candidates we may develop. For example, in June 2022, we entered into a Development, Option and License Agreement with Affini-T Therapeutics, Inc. (“Affini-T”) (the “Affini-T Agreement”) to develop and commercialize gene edited T-cell receptor (“TCR”)-based therapeutic products exclusively in the field of treatment, prevention or diagnosis of any human cancer using products with any engineered primary TCR alpha/beta T cells and non-exclusively in the field of treatment, prevention or diagnosis of any human cancer using products with certain other engineered immune cells worldwide, and in November 2022, we entered into a Collaboration and License Agreement with Ionis to research, develop and commercialize investigational medicines using genome editing technologies. In October 2021, we entered into a Strategic Collaboration and License Agreement (the “Moderna Agreement”) with ModernaTx, Inc. (“Moderna”), focused on advancing new genome editing system for in vivo human therapeutic applications, and in April 2024, we and Moderna mutually terminated the Moderna Agreement. Refer to Note 7 in our consolidated financial statements included in Part II, Item 8 of this Annual Report on Form 10-K for additional information related to the terms of the agreements between us and our collaborators.
Current wording
As part of our strategy, we have entered into license and collaboration agreements with third parties for one or more of our programs or product candidates we may develop. For example, in September 2025, we entered into the Acuitas License Agreement to license certain Acuitas LNP technology, including LNP patents, formulation processes, and analytical characterization methods for manufacturing products that incorporate our company's proprietary genome editing constructs formulated with Acuitas LNP technology, to research, develop, sell, and commercialize certain licensed products in connection with a single target. In November 2022, we entered into a Collaboration and License Agreement with Ionis to research, develop and commercialize investigational medicines using our genome editing technologies. Refer to Note 7, “Significant Agreements”, in our financial statements included in Part II, Item 8 of this Annual Report on Form 10-K for additional information related to the terms of the agreements between us and our collaborators.
Previous wording
To date, all of our revenue consists of collaboration revenue, earned from collaboration agreements with Moderna (prior to the termination of the Moderna Agreement), Ionis and Affini-T. These agreements may include the following types of promised goods or services: (i) grants of licenses; (ii) performance of research and development services and (iii) participation on joint research and/or development committees. They also may include options to obtain licenses to our intellectual property or to extend the term of the research activities. Our revenues under such collaboration agreements were $52.3 million and $44.8 million for the years ended December 31, 2024 and 2023, respectively.
Current wording
To date, all of our revenue consists of collaboration revenue, earned from collaboration agreements with Moderna (prior to the termination of the Moderna Agreement), Ionis and Affini-T (prior to the termination of the Affini-T Agreement). These agreements may include the following types of promised goods or services: (i) grants of licenses; (ii) performance of research and development services and (iii) participation on joint research and/or development committees. They also may include options to obtain licenses to our intellectual property or to extend the term of the research activities. Our revenues under such collaboration agreements were $25.2 million and $52.3 million for the years ended December 31, 2025 and 2024, respectively.
Previous wording
For additional information about our revenue recognition policy related to our collaboration agreements, refer to Note 2 in our consolidated financial statements included in Part II, Item 8 of this Annual Report on Form 10-K.
Current wording
For additional information about our revenue recognition policy related to our collaboration agreements, refer to Note 2, “Summary of Significant Accounting Policies”, in our financial statements included in Part II, Item 8 of this Annual Report on Form 10-K.
Previous wording
We anticipate that our general and administrative expenses will increase in the future as we increase our headcount to support development of our platform and our continued research activities. We also anticipate that we will incur increased accounting, audit, legal, regulatory, compliance and director and officer insurance costs as well as investor and public relations expenses associated with being a public company. We also expect our intellectual property expenses to increase as we expand our intellectual property portfolio.
Current wording
We anticipate that our general and administrative expenses will increase in the future to support our increased research and development activities. We also expect to continue to incur costs associated with being a public company and maintaining controls over financial reporting, including costs of accounting, audit, legal, regulatory and tax-related services associated with maintaining compliance with Nasdaq and SEC requirements, director and officer insurance costs, and investor and public relations costs.
Previous wording
Metagenomi LLC was taxed under the provisions of Subchapter K — Partners and Partnerships of the Internal Revenue Code. Under those provisions, Metagenomi LLC does not pay federal or state corporate income taxes on its taxable income. Instead, each member includes net operating income or loss for Metagenomi LLC on its individual return. Metagenomi is a corporation for tax purposes and is subject to income taxes. Prior to the Reorganization, Metagenomi was a wholly-owned subsidiary of Metagenomi LLC. After the Reorganization, Metagenomi continues as the surviving corporation.
Current wording
Prior to the Reorganization, Metagenomi LLC was taxed under the provisions of Subchapter K — Partners and Partnerships of the Internal Revenue Code. Under those provisions, Metagenomi LLC did not pay federal or state corporate income taxes on its taxable income. Instead, each member included net operating income or loss for Metagenomi LLC on its individual return. After the Reorganization and name change, Metagenomi Therapeutics, Inc. is a corporation for tax purposes and is subject to income taxes.
Previous wording
As of December 31, 2024, we had net operating loss carryforwards of $45.6 million and $118.3 million for federal and state income tax purposes, respectively, available to reduce future taxable income, if any. The federal net operating loss carryforwards do not expire. State net operating loss carryforwards begin expiring in 2037. As of December 31, 2024, we had state research and development credit carryforwards of $4.5 million, which do not expire. As of December 31, 2024, we had zero federal research and development credit carryforwards.
Current wording
As of December 31, 2025, we had net operating loss carryforwards of $175.3 million and $213.5 million for federal and state income tax purposes, respectively, available to reduce future taxable income, if any. The federal net operating loss carryforwards do not expire. State net operating loss carryforwards begin expiring in 2037. As of December 31, 2025, we had $3.3 million federal research and development credit carryforwards, which begin expiring in 2045. As of December 31, 2025, we had state research and development credit carryforwards of $6.1 million, which do not expire.
Previous wording
A valuation allowance is provided for deferred tax assets where the recoverability of the assets is uncertain. The determination to provide a valuation allowance is dependent upon the assessment of whether it is more likely than not that sufficient future taxable income will be generated to utilize the deferred tax assets. Based on the weight of the available evidence, which includes our consolidated entities’ historical operating losses and forecast of future losses, we have provided a full valuation allowance against the deferred tax assets resulting from the tax loss and credits carried forward.
Current wording
A valuation allowance is provided for deferred tax assets where the recoverability of the assets is uncertain. The determination to provide a valuation allowance is dependent upon the assessment of whether it is more likely than not that sufficient future taxable income will be generated to utilize the deferred tax assets. Based on the weight of the available evidence, which includes our entities’ historical operating losses and forecast of future losses, we have provided a full valuation allowance against the deferred tax assets resulting from the tax loss and credits carried forward.
Previous wording
Collaboration revenue increased by $7.5 million, from $44.8 million for the year ended December 31, 2023 to $52.3 million for the year ended December 31, 2024. The increase in collaboration revenue for the year ended December 31, 2024 was primarily driven by an $8.5 million increase in revenue related to the Ionis Agreement as we performed more services and a $0.6 million increase in revenue related to the Moderna Agreement due to the recognition of all remaining deferred revenue during the year ended December 31, 2024, offset by a $1.6 million decrease in revenue related to the Affini-T Agreement.
Current wording
Collaboration revenue decreased $27.1 million for the year ended December 31, 2025, as compared to the prior year, primarily driven by a $18.7 million decrease in revenue related to the Moderna Agreement due to the recognition of all remaining deferred revenue upon termination of the Agreement during the year ended December 31, 2024, a $5.8 million decrease in revenue related to the Ionis Agreement due to the timing of work performed and a $2.6 million decrease in revenue related to the Affini-T Agreement.
Previous wording
General and administrative expenses were $32.0 million for the year ended December 31, 2024, compared to $28.8 million for the year ended December 31, 2023. The increase of $3.2 million was primarily related to an increase of $3.8 million in stock-based compensation expense in addition to $0.7 million in other employee-related expenses, as a result of increased headcount and the issuance of annual equity awards to existing employees, an increase of $0.8 million in facilities and allocated overhead, offset by a decrease of $2.1 million in professional services and consulting costs.
Current wording
General and administrative expenses decreased $5.2 million for the year ended December 31, 2025, as compared to the prior year, primarily related to decreases of $2.5 million in professional services and consulting costs primarily as more of this work is now performed in-house, $1.3 million in employee-related expenses and $0.3 million in stock-based compensation expense primarily due to a decrease in headcount and $1.1 million in facilities and allocated overhead.
Previous wording
Total other income, net, decreased by $12.9 million, from $18.3 million for the year ended December 31, 2023 to $5.3 million for the year ended December 31, 2024. The decrease in other income, net, was primarily due to a net change in the fair value of our long-term investment in Affini-T in which the Company recognized a loss of $9.2 million during the year ended December 31, 2024, and a gain of $2.9 million during the year ended December 31, 2023.
Current wording
Total other income, net, increased $2.8 million for the year ended December 31, 2025, as compared to the prior year, primarily due to a net change in the fair value of our long-term investment in Affini-T in which the Company recognized a loss of $1.3 million during the year ended December 31, 2025 compared to a loss of $9.2 million during the year ended December 31, 2024, partially offset by a $5.3 million decrease in interest income.
Previous wording
Provision for income taxes decreased by $13.5 million for the year ended December 31, 2024, from a provision for income taxes of $8.0 million for the year ended December 31, 2023, to a benefit for income taxes of $5.5 million for the year ended December 31, 2024. The benefit for income taxes for the year ended December 31, 2024 was primarily due to our intention to elect to carry back the 2024 research and development credit to the prior year, in addition to a return to provision adjustment related to the prior year return. The provision for income taxes for the year ended December 31, 2023 was mainly due to our taxable income related to an upfront payment received under the Ionis Agreement and capitalization of research and development expenses under the Internal Revenue Code Section 174 (“Section 174”).
Current wording
Benefit from income taxes decreased by $5.5 million for the year ended December 31, 2025, as compared to the prior year. The benefit for income taxes for the year ended December 31, 2025 was primarily due to a return to provision adjustment related to the prior year return. The benefit from income taxes for the year ended December 31, 2024 was primarily due to our intention to elect to carry back the 2024 research and development credit to the prior year, in addition to a return to provision adjustment related to the prior year return.
Previous wording
Since our inception, we have historically funded our operations primarily through sales of our redeemable convertible preferred units and convertible promissory notes, which generated approximately $351.7 million in aggregate gross proceeds, in addition to net proceeds of approximately $80.7 million received in February 2024 upon the closing of our IPO. Additionally, through December 31, 2024, we received approximately $120.0 million upfront cash payments from collaboration and licensing agreements.
Current wording
Since our inception, we have historically funded our operations primarily through sales of our redeemable convertible preferred units and convertible promissory notes, which generated approximately $351.7 million in aggregate gross proceeds, in addition to net proceeds of approximately $80.7 million received in February 2024 upon the closing of our IPO. Additionally, through December 31, 2025, we received approximately $120.0 million in upfront cash payments from collaboration and licensing agreements.
Previous wording
We have incurred significant operating losses since inception and we expect to continue to incur substantial losses for the foreseeable future. Our net losses were $78.1 million and $68.3 million for the years ended December 31, 2024 and 2023, respectively. As of December 31, 2024, we had an accumulated deficit of $223.0 million.
Current wording
We have incurred significant operating losses since inception and we expect to continue to incur substantial losses for the foreseeable future. Our net losses were $87.9 million and $78.1 million for the years ended December 31, 2025 and 2024, respectively. As of December 31, 2025, we had an accumulated deficit of $310.9 million.
Previous wording
the impact of the COVID-19 pandemic, as well as other factors, including inflation, economic uncertainty and geopolitical tensions, which may exacerbate the magnitude of the factors discussed above.
Current wording
the impact of health epidemics, pandemics, and other widespread outbreaks of contagious disease, as well as other factors, including inflation, economic uncertainty and geopolitical tensions, which may exacerbate the magnitude of the factors discussed above.
Previous wording
As of December 31, 2024, we had $248.3 million in cash, cash equivalents and available-for-sale marketable securities. Based on our current operating plan, we estimate that our existing cash, cash equivalents and available-for-sale marketable securities will be sufficient to fund our projected operating expenses and capital expenditure requirements for at least the next 12 months from the date of issuance of this Annual Report on Form 10-K. 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. See “Liquidity and Capital Resources” and “Risk Factors—Risks Related To Our Financial Position and Need for Additional Capital.” We expect that we will require additional funding to: continue our current research development activities; develop, maintain, expand and protect our intellectual property portfolio; further develop our platform; and hire additional research, clinical and scientific personnel. 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 our products.
Current wording
As of December 31, 2025, we had $160.8 million in cash, cash equivalents and available-for-sale marketable securities. Based on our current operating plan, we estimate that our existing cash, cash equivalents and available-for-sale marketable securities will be sufficient to fund our projected operating expenses and capital expenditure requirements for at least the next 12 months from the date of issuance of this Annual Report on Form 10-K. 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. See “Liquidity and Capital Resources” and “Risk Factors—Risks Related To Our Financial Position and Need for Additional Capital.” We expect that we will require additional funding to continue our current research development activities; develop, maintain, expand and protect our intellectual property portfolio; further develop our platform; and hire additional research, clinical and scientific personnel. 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 our products.
Previous wording
Net cash used in operating activities for the year ended December 31, 2023 was $91.4 million and consisted primarily of our net loss of $68.3 million, a net reduction of $26.4 million in our net operating assets and liabilities, and decreased by non-cash charges of $3.3 million. The net change in our net operating assets and liabilities primarily consisted of a $30.3 million decrease in deferred revenue and collaboration advances as we recognized revenue under our collaboration agreements, a $2.5 million increase in accounts receivable related to the Affini-T Agreement and the Moderna Agreement, a $1.2 million decrease in operating lease liabilities due to recurring payments under the existing lease agreements, and a $1.1 million increase in prepaid expenses and other assets, all partially offset by a $4.0 million increase in other non-current liabilities, a $1.7 million increase in income tax payable due to additional tax expense, a $1.6 million increase in accrued expenses and other current liabilities and a $1.3 million decrease in contract assets related to the Affini-T Agreement. The net non-cash charges consisted of $6.9 million stock-based compensation expense, $4.2 million non-cash lease expense and $4.2 million depreciation expense, all partially offset by $8.5 million credit related to amortization of the discounts on available-for-sale marketable securities, $2.9 million increase in fair value of our investments in Affini-T and $0.7 million amortization of non-cash collaboration revenue related to the Affini-T Agreement.
Current wording
Net cash used in operating activities was $88.9 million for the year ended December 31, 2025 and consisted primarily of our net loss of $87.9 million and changes in our net operating assets and liabilities of $22.1 million, partially offset by net non-cash charges of $21.1 million. The net change in our operating assets and liabilities consisted primarily of a decrease of $21.1 million in deferred revenue as we recognized revenue based on work performed under our collaboration agreements, a decrease of $5.6 million in operating lease liabilities due to recurring payments under the existing lease agreements and a decrease $1.6 million in accrued expenses and other current liabilities, partially offset by a decrease of $4.3 million in prepaid expenses and other current assets primarily due to a decrease in other current assets as we received our 2023 tax refund, an increase of $1.1 million in accounts payable and a decrease of $1.0 million in accounts receivable. The net non-cash charges consisted primarily of $11.9 million in stock-based compensation expense, $5.3 million of depreciation expense, $5.3 million in non-cash lease expense, a $1.3 million charge related to the fair value of our investments in Affini-T and a $0.5 million loss on the write-off of fixed assets, partially offset by $3.0 million in amortization of discounts on available-for-sale marketable securities.
Previous wording
Net cash provided by investing activities for the year ended December 31, 2023 was $45.7 million, which consisted of $55.5 million in net maturities of available-for-sale marketable securities, offset by $9.8 million of purchases of property and equipment.
Current wording
Net cash provided by investing activities for the year ended December 31, 2025 was $103.5 million primarily due to net maturities of available-for-sale securities of $104.1 million, partially offset by purchases of property and equipment of $0.6 million.
Previous wording
As of December 31, 2024, we leased our office and laboratory space under three lease agreements and one vivarium lease agreement. Remaining lease obligations under our non-cancellable leases were $63.4 million as of December 31, 2024, including $10.4 million payable through December 31, 2025 and $53.0 million for the reminder of the leases’ terms. For additional information on our leases and timing of future lease payments refer to Note 8 in our consolidated financial statements included in Part II, Item 8 of this Annual Report on Form 10-K.
Current wording
As of December 31, 2025, we leased our office and laboratory space under three lease agreements and one vivarium lease agreement. Remaining lease obligations under our non-cancelable leases were $53.5 million as of December 31, 2025, including $10.2 million payable through December 31, 2026 and $43.3 million for the remainder of the leases’ terms. For additional information on our leases and timing of future lease payments refer to Note 8, “Commitments and Contingencies”, in our financial statements included in Part II, Item 8 of this Annual Report on Form 10-K.
Previous wording
A description of recently issued accounting pronouncements that may potentially impact our financial position, results of operations or cash flows is disclosed in Note 2 to our consolidated financial statements included elsewhere in Part II, Item 8 of this Annual Report on Form 10-K.
Current wording
A description of recently issued accounting pronouncements that may potentially impact our financial position, results of operations or cash flows is disclosed in Note 2, “Summary of Significant Accounting Policies”, to our financial statements included elsewhere in Part II, Item 8 of this Annual Report on Form 10-K.
Previous wording
On an ongoing basis, we evaluate our estimates and judgments, including but not limited to those related to revenue recognition under our collaboration agreements, the fair value of common stock and stock-based compensation expense, the valuation of deferred tax assets, and uncertain income tax positions. These estimates and assumptions are monitored and analyzed by us for changes in facts and circumstances, and material changes in these estimates and assumptions could occur in the future. Our estimates are based on our historical experience and on various other factors that we believe are reasonable under the circumstances, the results of which form the basis for making judgments about the carrying value of assets and liabilities that are not readily apparent from other sources. Changes in estimates are reflected in reported results for the period in which they become known. Actual results may differ from these estimates under different assumptions or conditions. While our significant accounting policies are described in more detail in Note 2 to our consolidated financial statements included in Part II, Item 8 of this Annual Report on Form 10-K, we believe that the following accounting policies are those most critical to the judgments and estimates used in the preparation of our financial statements.
Current wording
On an ongoing basis, we evaluate our estimates and judgments, including but not limited to those related to revenue recognition under our collaboration agreements, stock-based compensation expense, the valuation of deferred tax assets, and uncertain income tax positions. These estimates and assumptions are monitored and analyzed by us for changes in facts and circumstances, and material changes in these estimates and assumptions could occur in the future. Our estimates are based on our historical experience and on various other factors that we believe are reasonable under the circumstances, the results of which form the basis for making judgments about the carrying value of assets and liabilities that are not readily apparent from other sources. Changes in estimates are reflected in reported results for the period in which they become known. Actual results may differ from these estimates under different assumptions or conditions. While our significant accounting policies are described in more detail in Note 2, “Summary of Significant Accounting Policies”, to our financial statements included in Part II, Item 8 of this Annual Report on Form 10-K, we believe that the following accounting policies are those most critical to the judgments and estimates used in the preparation of our financial statements.
Previous wording
Metagenomi, Inc., our wholly-owned subsidiary, accounts for income taxes using the asset and liability method. We recognize deferred tax assets and liabilities for the expected future tax consequences of events that have been included in our consolidated financial statements or tax returns. Deferred tax assets and liabilities are determined based on the difference between the accounting and tax basis of assets and liabilities using enacted tax rates in effect for the year in which the differences are expected to reverse. A valuation allowance is established for deferred tax assets for which it is more likely than not that some portion or all of the deferred tax assets will not be realized. We assess the need for a valuation allowance against our deferred tax assets based on all available evidence, including scheduled reversals of deferred tax liabilities, projected future taxable income, tax planning strategies, results of recent operations, and our historical earnings experience by taxing jurisdiction. Significant judgment is required in making this assessment.
Current wording
Metagenomi Therapeutics, Inc. accounts for income taxes using the asset and liability method. We recognize deferred tax assets and liabilities for the expected future tax consequences of events that have been included in our financial statements or tax returns. Deferred tax assets and liabilities are determined based on the difference between the accounting and tax basis of assets and liabilities using enacted tax rates in effect for the year in which the differences are expected to reverse. A valuation allowance is established for deferred tax assets for which it is more likely than not that some portion or all of the deferred tax assets will not be realized. We assess the need for a valuation allowance against our deferred tax assets based on all available evidence, including scheduled reversals of deferred tax liabilities, projected future taxable income, tax planning strategies, results of recent operations, and our historical earnings experience by taxing jurisdiction. Significant judgment is required in making this assessment.
Rearranged previous paragraphs (1)
Previous report — wording carried elsewhere
Metagenomi, Inc. with the same rights and privileges and (iii) certain holders of profits interests in Metagenomi LLC received shares of common stock or unvested restricted common stock in Metagenomi, Inc. as determined by the applicable provisions of the Amended and Restated Limited Liability Company Agreement in effect immediately prior to the Reorganization. In connection with the Reorganization, by operation of law, Metagenomi, Inc. acquired all assets of Metagenomi LLC, and assumed all of its liabilities and obligations. The Reorganization was a non-taxable transaction to Metagenomi, Inc. for U.S. income tax purposes.