Metagenomi, Inc.

Previous wording

In rodent and nonhuman primate studies designed to support MGX-001, we demonstrated significantly higher FVIII activity levels using this bioengineered FVIII construct compared to wild type B-domain deleted FVIII construct, despite similar integration frequencies. These data suggested that incorporating the bioengineered FVIII construct into MGX-001 may enable therapeutic levels of FVIII activity at lower AAV doses, potentially resulting in MGX-001 having improved safety characteristics. Emerging data relating to MGX-001 from additional nonhuman primates using this bioengineered FVIII construct has, to date, demonstrated FVIII activity higher than expected. While we have not received all of the data from the studies, we expect to conduct additional studies and/or consider alternatives to this bioengineered FVIII construct. Based on the current information, we plan to conduct pre-IND and ex-U.S. regulatory meetings in the second half of 2025 and submit IND and clinical trial application (“CTA”) submission in 2026. For more information regarding the risks related to our IND submission and timelines, see “Risks Related to Business, Technology, and Industry” described in Part II, Item 1A, Risk Factors herein.

Current wording

In rodent and NHP studies designed to support MGX-001, we demonstrated significantly higher FVIII activity levels using this bioengineered FVIII construct compared to wild type B-domain deleted FVIII construct, despite similar integration frequencies. These data suggested that incorporating the bioengineered FVIII construct into MGX-001 may enable therapeutic levels of FVIII activity at lower AAV doses, potentially resulting in MGX-001 having improved safety characteristics. Emerging data relating to MGX-001 from additional NHPs using this bioengineered FVIII construct has, to date, demonstrated FVIII activity higher than expected. While we have not received all of the data from the studies, we have commenced additional studies and may consider alternatives to this bioengineered FVIII construct. Based on the current information, we plan to conduct pre-IND and ex-U.S. regulatory meetings in the second half of 2025 and submit IND and clinical trial application (“CTA”) submissions in 2026. For more information regarding the risks related to our IND submission and timelines, see “Risks Related to Business, Technology, and Industry” described in Part II, Item 1A, Risk Factors herein.

Previous wording

Our nucleases can be leveraged as a chassis by adding on additional effector enzymes to create base editors capable of single nucleotide changes in the genome. In October 2024, we demonstrated that our novel Adenine Base Editors (“ABEs”) are potentially targetable to over 95% of the human genome’s base pairs, a significantly wider range of sites than first-generation SpCas9 base editors. Our ABE platform achieved over 95% reproducible and durable triplex protein knockdown in primary T-cells, confirming its highly efficient application for multiplex gene editing. The ABE platform demonstrated highly specific on-target deamination with no detectable translocations and no significant genome composition differences, and the platform demonstrated no adverse effects on cell viability, expansion or other measures of cell health.

Current wording

Our nucleases can be leveraged as a chassis by adding on additional effector enzymes to create base editors capable of single nucleotide changes in the genome. In October 2024, we demonstrated that our novel Adenine Base Editors (“ABEs”) are potentially targetable to over 95% of the human genome’s base pairs, a significantly wider range of sites than first-generation SpCas9 base editors. Our ABE platform achieved greater than 90% editing efficiency simultaneously at seven genomic targets in primary T-cells, confirming its highly efficient application for multiplex gene editing. The ABE platform demonstrated highly specific on-target deamination with no detectable translocations and no significant genome composition differences, and the platform demonstrated no adverse effects on cell viability, expansion or other measures of cell health.

Previous wording

CRISPR Associated Transposase (CAST) systems are a class of genome editing systems that provide directed and programmable genomic integration of large DNA templates (>10,000 base pairs). We recently achievedin vitro proof-of-concept for large gene integration using our potentially industry leading, compact CAST technology. In March 2025, we published our latest findings in Nature Communications describing our novel, compact CAST systems, which demonstrated integration of a large, therapeutically relevant gene into the genome of human cells.

Current wording

CAST systems are a class of genome editing systems that provide directed and programmable genomic integration of large DNA templates (>10,000 base pairs). We recently achievedin vitro proof-of-concept for large gene integration using our potentially industry leading, compact CAST technology. In March 2025, we published our latest findings in Nature Communications describing our novel, compact CAST systems, which demonstrated integration of a large, therapeutically relevant gene into the genome of human cells.

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, 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, 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 recently enacted 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) 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

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. 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 our 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 forin vivo human therapeutic applications, and in April 2024, we and Moderna mutually terminated the Moderna Agreement. Refer to Note 7 in our condensed financial statements included elsewhere in this Quarterly Report on Form 10-Q 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 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. 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 our 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 forin vivo human therapeutic applications, and in April 2024, we and Moderna mutually terminated the Moderna Agreement. Refer to Note 7, “Significant Agreements,” in our condensed financial statements included elsewhere in this Quarterly Report on Form 10-Q 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 $4.1 million for the three months ended March 31, 2025 and $11.2 million for the three months ended March 31, 2024.

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. 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 $8.5 million and $12.6 million for the three and six months ended June 30, 2025, respectively, and $20.0 million and $31.2 million for the three and six months ended June 30, 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 our Annual Report on Form 10-K for the year ended December 31, 2024.

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 consolidated financial statements included in Part II, Item 8 of our Annual Report on Form 10-K for the year ended December 31, 2024.

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

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

Current wording

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

Previous wording

Collaboration revenue decreased by $7.0 million, from $11.2 million for the three months ended March 31, 2024 to $4.1 million for the three months ended March 31, 2025. The decrease in collaboration revenue for the three months ended March 31, 2025, was primarily driven by a $2.8 million decrease in revenue related to the Moderna Agreement due to the recognition of all remaining deferred revenue during the year ended December 31, 2024 as a result of the Termination Agreement, a $4.1 million decrease in revenue related to the Ionis Agreement and a $0.1 million decrease in revenue related to the Affini-T Agreement.

Current wording

Collaboration revenue decreased by $11.5 million for the three months ended June 30, 2025, as compared to the corresponding prior year period, primarily due to a $15.9 million decrease in revenue related to the Moderna Agreement due to the recognition of all remaining deferred revenue during the year ended December 31, 2024 as a result of the Termination Agreement and a $0.7 million decrease in revenue related to the Affini-T Agreement, partially offset bya $5.1 million increase in revenue related to the Ionis Agreement.

Previous wording

General and administrative expenses were $6.8 million for the three months ended March 31, 2025, compared to $8.8 million for the three months ended March 31, 2024. The decrease of $1.9 million was primarily related to a decrease of $1.3 million in professional services and consulting costs, a decrease of $0.7 million in other employee-related expenses, and a decrease of $0.5 million in facilities and allocated overhead, offset by an increase of $0.6 million in stock-based compensation expense.

Current wording

General and administrative expenses decreased $1.6 million for the three months ended June 30, 2025, as compared to the corresponding prior year period, primarily related to decreases of $0.4 million in professional services and consulting costs, $0.4 million in employee-related expenses, $0.4 million in stock-based compensation expense, and $0.3 million in facilities and overhead costs.

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, and $25.0 million and $25.1 million for the three months ended March 31, 2025 and 2024, respectively. As of March 31, 2025, we had an accumulated deficit of $248.0 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 $78.1 million and $68.3 million for the years ended December 31, 2024 and 2023, respectively, and $44.9 million and $35.9 million for the six months ended June 30, 2025 and 2024, respectively. As of June 30, 2025, we had an accumulated deficit of $267.9 million.

Previous wording

As of March 31, 2025, we had $226.0 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 June 30, 2025, we had $205.0 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 was $22.8 million for the three months ended March 31, 2025, and consisted primarily of our net loss of $25.0 million and changes in our net operating assets and liabilities of $2.3 million, offset by net non-cash charges of $4.5 million. The net change in operating assets and liabilities consisted primarily of a decrease of $3.0 million in deferred revenue as we recognized revenue under our collaboration agreements, a decrease of $2.6 million in accrued expenses and other current liabilities, a decrease of $1.4 million in operating lease liabilities and a decrease of $2.2 million in prepaid expenses and other current assets, offset by an increase of $2.2 million in accounts payable due to the timing of payments to our vendors. The net non-cash charges consisted primarily of $2.9 million in stock-based compensation expense, $1.4 million of depreciation expense, $1.3 million in non-cash lease expense, partially offset by $1.0 million in accretion of discounts on available-for-sale marketable securities and $0.1 million in amortization of non-cash collaboration revenue related to the Affini-T Agreement.

Current wording

Net cash used in operating activities was $44.1 million for the six months ended June 30, 2025, and consisted primarily of our net loss of $44.9 million and changes in our net operating assets and liabilities of $10.2 million, 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, and 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 in 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.

Previous wording

Net cash used in operating activities for the three months ended March 31, 2024, was $29.9 million and consisted primarily of our net loss of $25.1 million and changes in our net operating assets and liabilities of $10.9 million, partially offset by net non-cash charges of $6.2 million. The changes in our net 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 $3.0 million decrease in accrued expenses and other liabilities primarily related to payout of the 2024 annual bonus, and a $0.9 million increase in prepaid expenses and other assets, offset by an increase of $3.2 million in accounts payable due to the timing of payments to our vendors. The net non-cash charges consisted primarily of $5.1 million in stock-based compensation expense, $1.1 million in non-cash lease expense and $1.3 million of depreciation expense, partially offset by $1.2 million in amortization of discounts on available-for-sale marketable securities.

Current wording

Net cash used in operating activities for the six months ended June 30, 2024, was $56.2 million and consisted primarily of our net loss of $35.9 million and changes in our net operating assets and liabilities of $31.7 million, partially offset by net non-cash charges of $11.4 million. The changes in our net operating assets and liabilities consisted primarily of a decrease of $29.4 million in deferred revenue as we recognized revenue under our collaboration agreements, a $0.3 million increase in accrued expenses and other liabilities primarily related to payout of the 2024 annual bonus, and a $0.3 million increase in prepaid expenses and other assets, offset by an increase of $1.7 million in accounts payable due to the timing of payments to our vendors. The net non-cash charges consisted primarily of $9.6 million in stock-based compensation expense, $2.3 million in non-cash lease expense, and $2.6 million of depreciation expense, partially offset by $3.2 million in amortization of discounts on available-for-sale marketable securities.

Previous wording

Net cash provided by investing activities for the three months ended March 31, 2025, was $24.7 million primarily due to net maturities of available-for-sale marketable securities of $25.0 million, partially offset purchases of property and equipment of $0.3 million.

Current 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.

Previous wording

Net cash used in investing activities for the three months ended March 31, 2024, was $94.7 million due to net purchases of available-for-sale marketable securities of $93.8 million and purchases of property and equipment of $0.9 million.

Current wording

Net cash used in investing activities for the six months ended June 30, 2024, was $107.8 million due to net purchases of available-for-sale marketable securities of $106.2 million and purchases of property and equipment of $1.6 million.

Previous wording

Net cash used in financing activities for the three months ended March 31, 2025, was $0.1 million due to a payment of deferred financing costs.

Current wording

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

Previous wording

Net cash provided by financing activities for the three months ended March 31, 2024, was $86.5 million due to net proceeds from the issuance of our common stock in our IPO, net of issuance costs paid during the period.

Current wording

Net cash provided by financing activities for the six months ended June 30, 2024, was $84.5 million due to net proceeds from the issuance of our common stock in our IPO, net of issuance costs paid during the period.

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 three months ended March 31, 2025, 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, 2024, filed with the SEC on March 17, 2025.

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 six months ended June 30, 2025, 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, 2024, filed with the SEC on March 17, 2025.

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 condensed financial statements included elsewhere in this Quarterly Report on Form 10-Q.

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 condensed financial statements included elsewhere in this Quarterly Report on Form 10-Q.

Previous wording

During the three months ended March 31, 2025, 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, 2024.

Current wording

During the six months ended June 30, 2025, 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, 2024.