Metagenomi Therapeutics, Inc.

Previous wording

You should read the following discussion and analysis of our financial condition and results of operations together with our unaudited condensed financial statements and the related notes thereto included elsewhere in this Quarterly Report on Form 10-Q and our audited consolidated financial statements and notes and Management’s Discussion and Analysis of Financial Condition and Results of Operations, included in our Annual Report on Form 10-K for the year ended December 31, 2025, filed with the SEC on March 5, 2026. 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 under Part II, Item 1A below.

Current wording

You should read the following discussion and analysis of our financial condition and results of operations together with our unaudited condensed financial statements and the related notes thereto included elsewhere in this Quarterly Report on Form 10-Q and our audited financial statements and notes and Management’s Discussion and Analysis of Financial Condition and Results of Operations, included in our Annual Report on Form 10-K for the year ended December 31, 2025, filed with the SEC on March 5, 2026. 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 under Part II, Item 1A below.

Previous wording

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 CRISPR 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 wording

We are an in vivo genome editing company capitalizing on our proprietary technologies to create potentially 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 CRISPR 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.

Previous wording

MGX-001 is designed to provide curative, life-long protection from bleeding events and joint damage in adults and children from a single administration, potentially enabling a new standard of care for the treatment of hemophilia A. MGX-001 is designed to insert a Factor VIII (“FVIII”) gene cassette into a “safe harbor location” within an intron of the albumin gene, leveraging the strong native albumin promoter to express FVIII.

Current wording

MGX-001 is an investigational, one-time genome editing treatment designed to provide curative, life-long protection from bleeding events and joint damage in adults and children, potentially enabling a new standard of care for the treatment of hemophilia A. MGX-001 is designed to site-specifically integrate the Factor VIII (“FVIII”) gene in a “safe harbor” location within an intron of the albumin gene, leveraging the strong native albumin promoter to drive endogenous FVIII expression. MGX-001 consists of an adeno-associated virus (“AAV”) vector that delivers the promoterless FVIII gene cassette as donor DNA, and a lipid nanoparticle (“LNP”) that delivers mRNA encoding our proprietary Type V CRISPR nuclease, MG29-1, together with a guide RNA targeting the albumin gene. MGX-001 represents a departure from prior approved gene therapy for hemophilia A that relied on episomal FVIII expression.

Previous wording

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 wording

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 FVIII activity in the normal physiologic range, with clear dose dependency across both the AAV and LNP components. This data builds upon an earlier study, where we demonstrated durable FVIII activity over approximately 19-months. MGX-001 has also shown no detectable off-target editing in a series of orthogonal assays.

Previous wording

Leveraging the MGX-001 site-specific genome integration system, we are pursuing disease indications which have the potential to be treated by protein replacement via gene insertion. In late 2025, we demonstrated the curative potential of the MGX-001 large gene integration system in a secreted protein disorder, antithrombin III (“AT-III”) deficiency, in an in vivo study in NHPs.

Current wording

We are continuing to evaluate additional disease indications which may be treated by protein replacement via gene insertion leveraging the same site-specific large gene integration at the albumin locus as used in MGX-001. In late 2025, we demonstrated the curative potential of this site-specific large gene integration in a secreted protein disorder, antithrombin III (“AT-III”) deficiency, in an in vivo study in NHPs.

Previous wording

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 June 30, 2026, no shares have been sold under the ATM Sales Agreement.

Current wording

In March 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 September 30, 2026, no shares have been sold under the ATM Sales Agreement.

Previous 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 conflicts in Iran and the Middle East (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 Quarterly Report on Form 10-Q.

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 conflicts in Iran and the Middle East (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, 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 Quarterly Report on Form 10-Q.

Previous 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 consolidated financial statements included in Part II, Item 8 of our Annual Report on Form 10-K for the year ended December 31, 2025.

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 our Annual Report on Form 10-K for the year ended December 31, 2025.

Previous wording

Comparison of the Three and Six Months Ended June 30, 2026 and 2025

Current wording

Comparison of the Three and Nine Months Ended September 30, 2026 and 2025

Previous wording

Collaboration revenue decreased $11.6 million for the six months ended June 30, 2026, as compared to the corresponding prior year period, due to decreases of $11.2 million in revenue related to the Ionis Agreement and $0.4 million in revenue related to the Affini-T Agreement.

Current wording

Collaboration revenue decreased $6.5 million for the three months ended September 30, 2026, as compared to the corresponding prior year period, due to decreases of $6.4 million in revenue related to the Ionis Agreement and $0.1 million in revenue related to the Affini-T Agreement.

Previous wording

Collaboration revenue decreased $8.8 million for the three months ended June 30, 2026, as compared to the corresponding prior year period, due to decreases of $8.5 million in revenue related to the Ionis Agreement, partially due to timing of work performed and a $2.6 million cumulative catch-up adjustment recorded during the three months ended June 30, 2026 due to the modification of the agreement to perform new research services for one of the Wave 1 targets, and $0.3 million in revenue related to the Affini-T Agreement.

Current wording

Collaboration revenue decreased $18.1 million for the nine months ended September 30, 2026, as compared to the corresponding prior year period, due to decreases of $17.5 million in revenue related to the Ionis Agreement, partially due to a $2.6 million cumulative catch-up adjustment recorded during the nine months ended September 30, 2026 due to the modification of the agreement to perform new research services for one of the Wave 1 targets, and $0.6 million in revenue related to the Affini-T Agreement.

Previous wording

Total research and development expense decreased $5.8 million for thesix months ended June 30, 2026, as compared to the corresponding prior year period, primarily due to decreases of $5.8 million in employee-related expenses, $1.4 million in facilities and overhead costs and $1.0 million in stock-based compensation expense, partially offset by an increase of $2.3 million in research and development supplies and services.

Current wording

Total research and development expense decreased $7.8 million for thethree months ended September 30, 2026, as compared to the corresponding prior year period, primarily due to decreases of $4.9 million in research and development supplies and services, $2.3 million in employee-related expenses, $0.7 million in facilities and overhead costs and $0.4 million in stock-based compensation expense, partially offset by an increase of $0.6 million in professional services and consulting costs.

Previous wording

Total research and development expense for thethree months ended June 30, 2026 was consistent with the corresponding prior year period, primarily due to decreases of $2.5 million in employee-related expenses, $0.6 million in stock-based compensation expense and $0.5 million in facilities and overhead costs, offset by an increase of $3.4 million in research and development supplies and services.

Current wording

Total research and development expense decreased $13.6 million for thenine months ended September 30, 2026, as compared to the corresponding prior year period, primarily due to decreases of $8.1 million in employee-related expenses, $2.6 million in research and development supplies and services, $2.1 million in facilities and overhead costs and $1.4 million in stock-based compensation expense, partially offset by an increase of $0.6 million in professional services and consulting costs.

Previous wording

Total general and administrative expense decreased $1.0 million for thethree months ended June 30, 2026, as compared to the corresponding prior year period, primarily related to decreases of $0.4 million in stock-based compensation expense, $0.2 million in employee-related expenses, $0.2 million in facilities and overhead costs and $0.1 million in professional services and consulting costs.

Current wording

Total general and administrative expense decreased $0.6 million for thenine months ended September 30, 2026, as compared to the corresponding prior year period, primarily related to decreases of $1.2 million in stock-based compensation expense and $0.9 million in employee-related expenses, partially offset by $1.2 million in litigation settlement expense, net, and an increase of $0.4 million in professional services and consulting costs.

Previous wording

Total other income (expense), net increased $0.2 million for thethree months ended June 30, 2026, as compared to the corresponding prior year period, primarily related to a loss from the change in fair value of our long-term investment in Affini-T in the prior year period, partially offset by a decrease of $1.2 million in interest income.

Current wording

Total other income (expense), net decreased $1.1 million for thethree months ended September 30, 2026, as compared to the corresponding prior year period, primarily related to a decrease of $1.2 million in interest income.

Previous wording

Total other income (expense), net decreased $1.2 million for thesix months ended June 30, 2026, as compared to the corresponding prior year period, primarily related to a decrease of $2.6 million in interest income, partially offset by a loss from the change in fair value of our long-term investment in Affini-T in the prior year period.

Current wording

Total other income (expense), net decreased $2.3 million for thenine months ended September 30, 2026, as compared to the corresponding prior year period, primarily related to a decrease of $3.7 million in interest income, partially offset by a loss from the change in fair value of our long-term investment in Affini-T in the prior year period.

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 $87.9 million and $78.1 million for the years ended December 31, 2025 and 2024, respectively, and $50.5 million and $44.9 million for the six months ended June 30, 2026 and 2025, respectively. As of June 30, 2026, we had an accumulated deficit of $361.4 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, and $71.7 million and $65.3 million for the nine months ended September 30, 2026 and 2025, respectively. As of September 30, 2026, we had an accumulated deficit of $382.5 million.

Previous wording

As of June 30, 2026, we had $120.7 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 Quarterly Report on Form 10-Q. 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 September 30, 2026, we had $101.7 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 Quarterly Report on Form 10-Q. 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 six months ended June 30, 2026, was $40.7 million and consisted primarily of our net loss of $50.5 million and changes in our net operating assets and liabilities of $0.3 million, partially offset by net non-cash charges of $10.1 million. The net change in operating assets and liabilities consisted primarily of a decrease of $2.9 million in operating lease liabilities, partially offset by increases of $0.9 million in accrued expenses and other current liabilities, $1.1 million in accounts payable and $0.8 million in prepaid expenses and other assets. The net non-cash charges consisted primarily of $4.8 million in stock-based compensation expense, $2.7 million in non-cash lease expense and $2.5 million of depreciation expense, partially offset by $0.6 million in accretion of discounts on available-for-sale marketable securities and $0.6 million in impairment of right of use assets.

Current wording

Net cash used in operating activities for the nine months ended September 30, 2026, was $59.8 million and consisted primarily of our net loss of $71.7 million and changes in our net operating assets and liabilities of $2.5 million, partially offset by net non-cash charges of $14.4 million. The net change in operating assets and liabilities consisted primarily of a decrease of $4.4 million in operating lease liabilities, a decrease of $2.7 million in deferred revenue as we recognized revenue under our collaboration agreements, a decrease of $0.7 million in accounts payable due to the timing of invoices and payments and an increase of $4.6 million in prepaid expenses and other assets, primarily related to the insurance receivable recorded in connection with the litigation settlement, partially offset by an increase of $9.5 million in accrued expenses and other current liabilities primarily related to the litigation settlement. The net non-cash charges consisted primarily of $6.6 million in stock-based compensation expense, $4.1 million in non-cash lease expense, $3.8 million of depreciation expense and $0.6 million in impairment of right of use assets, partially offset by $0.7 million in accretion of discounts on available-for-sale marketable securities.

Previous wording

Net cash used in operating activities for the six months ended June 30, 2025, was $44.1 million and consisted primarily of our net loss of $44.9 million and changes in our net operating assets and liabilities of $10.2 million, partially offset by net non-cash charges of $11.1 million. The net change in operating assets and liabilities consisted primarily of a decrease of $10.4 million in deferred revenue as we recognized revenue under our collaboration agreements, a decrease of $2.5 million in accrued expenses and other current liabilities, a decrease of $2.8 million in operating lease liabilities, partially offset by a decrease of $2.7 million in prepaid expenses and other current assets and an increase of $2.3 million accounts payable due to the timing of payments to our vendors. The net non-cash charges consisted primarily of $6.1 million in stock-based compensation expense, $2.7 million of depreciation expense, $2.7 million in non-cash lease expense, $1.3 million change in fair value related to our investment in Affini-T, partially offset by $1.8 million in accretion of discounts on available-for-sale marketable securities.

Current wording

Net cash used in operating activities for the nine months ended September 30, 2025, was $65.3 million and consisted primarily of our net loss of $65.3 million and changes in our net operating assets and liabilities of $15.8 million, partially offset by net non-cash charges of $15.8 million. The net change in operating assets and liabilities consisted primarily of decreases of $18.0 million in deferred revenue as we recognized revenue under our collaboration agreements and $4.1 million in operating lease liabilities, partially offset by a decrease of $3.8 million in prepaid expenses and other current assets and an increase of $1.5 million in accrued expenses and other current liabilities. The net non-cash charges consisted primarily of $9.2 million in stock-based compensation expense, $4.0 million of depreciation expense, $3.9 million in non-cash lease expense, $1.3 million change in fair value related to our investment in Affini-T, partially offset by $2.5 million in accretion of discounts on available-for-sale marketable securities.

Previous wording

Net cash provided by investing activities for the six months ended June 30, 2026, was $37.2 million primarily due to net maturities of available-for-sale marketable securities of $37.3 million.

Current wording

Net cash provided by investing activities for the nine months ended September 30, 2026, was $53.3 million primarily due to net maturities of available-for-sale marketable securities of $53.4 million.

Previous wording

Net cash provided by investing activities for the six months ended June 30, 2025, was $43.8 million primarily due to net maturities of available-for-sale marketable securities of $44.2 million.

Current wording

Net cash provided by investing activities for the nine months ended September 30, 2025, was $71.2 million primarily due to net maturities of available-for-sale marketable securities of $71.6 million.

Previous wording

Net cash provided by financing activities for the six months ended June 30, 2026, was less than $0.1 million due toproceeds from our ESPP, partially offset bypayment of deferred financing costs.

Current wording

Net cash provided by financing activities for the nine months ended September 30, 2026, was less than $0.1 million due toproceeds from our ESPP, partially offset bypayment of deferred financing costs.

Previous wording

Net cash used in financing activities for the six months ended June 30, 2025, was $0.2 million due to payment of deferred financing costs.

Current wording

Net cash used in financing activities for the nine months ended September 30, 2025, was $0.4 million due to payment of deferred financing costs.

Previous wording

Our material cash requirements include our contractual obligations for our leased office and laboratory space under three lease agreements and one vivarium lease agreement. During the six months ended June 30, 2026, there were no material changes outside the ordinary course of our business to our material cash requirements described under “Management’s Discussion and Analysis of Financial Condition and Results of Operations” included in our Annual Report on Form 10-K for the year ended December 31, 2025, filed with the SEC on March 5, 2026.

Current wording

Our material cash requirements include our contractual obligations for our leased office and laboratory space under three lease agreements and one vivarium lease agreement. During the nine months ended September 30, 2026, there were no material changes outside the ordinary course of our business to our material cash requirements described under “Management’s Discussion and Analysis of Financial Condition and Results of Operations” included in our Annual Report on Form 10-K for the year ended December 31, 2025, filed with the SEC on March 5, 2026.

Previous wording

During the six months ended June 30, 2026, there were no material changes to our critical accounting estimates or in the methodology used for estimates from those described in “Management’s Discussion and Analysis of Financial Condition and Results of Operations” included in our Annual Report on Form 10-K for the year ended December 31, 2025.

Current wording

During the nine months ended September 30, 2026, there were no material changes to our critical accounting estimates or in the methodology used for estimates from those described in “Management’s Discussion and Analysis of Financial Condition and Results of Operations” included in our Annual Report on Form 10-K for the year ended December 31, 2025.