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 consolidated 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, 2023, filed with the SEC on March 27, 2024. 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 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, 2024, filed with the SEC on March 17, 2025. 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

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”). These tools form a toolbox that can potentially make any desired gene modification – gene knock-down, gene knock-in as well as small and large genetic changes. In addition, our toolbox includes ultra small editing systems that are small enough to be packaged into a single adeno-associated virus (“AAV”) to address extrahepatic therapeutic indications. All elements of our toolbox are wholly owned, and we have constructed a broad patent estate that protects our intellectual property. We anticipate that our toolbox will continue to expand as we discover, interrogate, and optimize our novel editing systems.

Current wording

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”). These tools form a toolbox that can potentially make any desired gene modification ranging from gene knock-down, gene knock-in as well as small and large genetic changes. In addition, our toolbox includes ultra small editing systems which have the potential to be packaged into a single adeno-associated virus (“AAV”) to address extrahepatic therapeutic indications. All elements of our toolbox are wholly-owned, and we have constructed a broad patent estate that protects our intellectual property, which we expect will continue to expand as we discover, interrogate, and optimize our novel editing systems.

Previous wording

We are taking a stepwise approach deploying our genome editing toolbox to prosecute a genetic medicine therapeutic development strategy across a broad array of diseases and target organs including liver, central nervous system, muscle, kidney, and lung, matching the right tool to each specific target.

Current wording

We are taking a stepwise approach, deploying our genome editing toolbox to develop potentially curative therapies for patients across a broad array of diseases and target organs including the liver, central nervous system, muscle, kidney, and lung, matching the right tool to each specific target. Our lead programs are selected to both address important diseases and establish new standards in targetability, precision, efficiency, and scope of editing capabilities. We are focused onin vivo gene editing for our wholly owned pipeline, while pursuing technology out-licensing forex vivo cell therapy, where next generation genome editing systems are an important enabler of novel therapies. We believe our therapeutic programs are well-positioned to leverage the clinical, regulatory, and manufacturing advancements made to date across gene therapy, gene editing, and delivery modalities to accelerate progression to clinical trials and potential approval.

Previous wording

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.

Current wording

Our investigational development program in hemophilia A, MGX-001, is a potentially curative therapy designed to provide life-long protection from bleeding events and joint damage in adults and children. Our approach 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 in an approach that is not expected to have deleterious effects. This unique design differentiates from gene therapies that deliver the FVIII gene in an episomal location thereby increasing the risk of dilution from cell division, cell death, and episomal transcriptional silencing. Our FVIII knock-in approach is designed to provide stable expression and clinically relevant circulating levels of FVIII, even at low integration rates because of the strength of the albumin promoter.

Previous wording

Our program is designed to insert a Factor VIII (“FVIII”) DNA cassette into a “safe harbor location,” within an intron of the albumin gene that is not expected to have deleterious effects. FVIII expression is then driven off the strength of the native albumin promoter. Our lead hemophilia A genome editing strategy has two components. A lipid nanoparticle (“LNP”) is designed to deliver mRNA along with a gRNA to the liver in order to produce a highly efficient and specific nuclease that creates a precise cut at the albumin safe harbor gene locus. Additionally, an adeno-associated virus (“AAV”) vector that is designed to deliver the donor template FVIII DNA that becomes inserted into the nuclease cut site by a naturally occurring DNA repair process called non-homologous end joining.

Current wording

Our lead hemophilia A genome editing strategy has two components. A lipid nanoparticle (“LNP”) is designed to deliver mRNA along with a gRNA to the liver in order to produce a highly efficient and specific nuclease that creates a precise cut at the albumin safe harbor gene locus. Additionally, an adeno-associated virus (“AAV”) vector is designed to deliver the donor template FVIII DNA that becomes inserted into the nuclease cut site by a naturally occurring DNA repair process called non-homologous end joining.

Previous wording

In an ongoing non-human primate (“NHP”) study, we demonstrated integration of a surrogate cynomolgus-FVIII cassette (used to avoid immune response that would occur with a foreign human FVIII protein) and confirmed durable FVIII activity levels over a twelve-month period, as of the September 2024 data cutoff. Treatment was generally well tolerated with findings limited to moderate transient elevation of liver transaminases following AAV and LNP administration. There were no notable findings in total bilirubin or albumin levels or adverse clinical observations.

Current wording

In a non-human primate (“NHP”) study, we demonstrated integration of a surrogate cynomolgus-FVIII cassette (used to avoid immune response that would occur with a foreign human FVIII protein) and confirmed durable and therapeutically relevant FVIII activity levels over an approximately nineteen-month period. Plasma FVIII activity levels correlated with gene integration frequency measured in the liver at termination. Treatment was generally well tolerated with findings limited to moderate transient elevation of liver transaminases following AAV and LNP administration. There were no notable findings in total bilirubin or albumin levels.

Previous wording

This early NHP study was conducted without the benefit of several subsequent optimizations of the therapeutic candidate designed to enhance safety and efficacy in the clinic. Following our meeting with the FDA to align on key aspects of our planned IND submission, in August 2024, we nominated a lead development candidate, MGX-001. For the development candidate MGX-001, the company selected a bioengineered FVIII construct.

Current wording

This early NHP study was conducted without the benefit of several subsequent optimizations of the therapeutic candidate designed to enhance safety and efficacy in the clinic. Following our meeting with the FDA to align on key aspects of our planned IND submission, in August 2024, we nominated a lead development candidate, MGX-001. For the development candidate MGX-001, we selected a bioengineered B-domain deleted FVIII construct (a “bioengineered FVIII construct”).

Previous wording

All four therapeutic targets in Wave 1 of our collaboration with Ionis Pharmaceuticals, Inc. (“Ionis”) focus on high value cardiometabolic diseases and are advancing in lead optimization. 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.

Current wording

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. All four therapeutic targets in Wave 1 of our collaboration with Ionis focus on cardiometabolic diseases and are in lead optimization. In vivo rodent proof-of-concept was achieved in all four wave 1 genetic targets in 2024, including transthyretin (“TTR”) for transthyretin amyloidosis and angiotensinogen (“AGT”) for refractory hypertension, as well as two undisclosed programs. In partnership with Ionis, we plan to nominate one to two development candidates from the Wave 1 targets and disclose the remaining two therapeutic indications in 2025. In 2026, we plan to initiate IND-enabling activities for the development candidates nominated in 2025, and nominate additional development candidates from the remaining Wave 1 targets.

Previous wording

We believe our metagenomics-based, AI-enhanced discovery approach will allow us to achieve our goal of having the most effective genome editing tools to address any genetic disease anywhere in the human genome. In August 2024, we presented a poster at the CRISPR Frontiers conference at Cold Spring Harbor Laboratory titled “Unlocking the Therapeutic Potential of Compact SMART Nucleases through Ancestral Reconstruction, Structure-Guided Engineering, and Generative AI” which demonstrated how our metagenomics-informed synthetic sequence generation, including ancestral sequence reconstruction and generative AI techniques, potentially enable rapid development of novel programmable CRISPR nuclease- and base editing systems.

Current wording

We believe our metagenomics-based, AI-enhanced, discovery approach will allow us to achieve our goal of having highly effective genome editing tools to address any genetic disease by editing anywhere in the human genome. We have demonstrated how our metagenomics-informedde novo sequence generation approach, which includes using ancestral sequence reconstruction and generative AI techniques, can be used together with structure-guided engineering methods to potentially expand therapeutic applications.

Previous wording

To date, we have identified thousands of novel CRISPR type II, type V and highly efficient ultra-small (SMall Arginine-Rich sysTems or SMART) nucleases, expanding the collection of known programmable nucleases by mining our proprietary metagenomics database. This allows us to potentially select the ideal nuclease for targeting any given gene in a site-specific manner, overcoming a major limitation of first-generation CRISPR/Cas9 systems.

Current wording

To date, we have identified thousands of novel CRISPR nucleases, expanding the collection of known programmable nucleases by mining our proprietary metagenomics database. This allows us to potentially select the ideal nuclease for targeting any given gene in a site-specific manner, overcoming a major limitation of first-generation CRISPR/Cas9 systems. We recently demonstrated technological advancements to address unmet needs for therapeutic applications ofin vivo gene editing beyond the liver using our novel nucleases, including single-AAV delivery to a central nervous system (“CNS”) target, a key milestone towards addressing neurological disorders. We achievedin vivo proof-of-concept for CNS editing with a single blood-brain-barrier penetrating AAV, which may enable treatments with systemic injections and provide a more tolerable treatment for patients. Furthermore, based on data generated to date, we believe our SMall Arginine-Rich sysTems (SMART) genome editing systems, which are small enough to be packaged into standard AAV vectors, even when additional effector domains are included for base editing, potentially enable a differentiated therapeutic approach for extrahepatic targets.

Previous wording

The chassis of our nucleases can be leveraged by adding on additional effector enzymes to create base editors capable of single nucleotide changes in the genome. In October 2024, we presented a poster at the European Society of Gene and Cell Therapy’s 31st Annual Congress titled “Efficient and specific genome editing with metagenomics-derived base editor for human therapeutic applications.” We showcased that our novel Adenine Base Editor (“ABE”) was 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. Our ABE demonstrated highly specific on-target deamination with minimum-to-no indel formation, and genome-wide analyses confirmed no detectable translocations and no significant genomic composition differences when compared to unedited cells.

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 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.

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, rising inflation, tensions in U.S.-China relations, the COVID-19 pandemic, the U.S. Federal Reserve raising interest rates, recent and potential future disruptions in access to bank deposits and lending commitments due to bank failures and the effects of the ongoing geopolitical conflict in Ukraine and the Israel-Hamas war, 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 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, 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. (“Affini-T”) (the “Affini-T Agreement”) to develop and commercialize gene edited 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 forin vivo human therapeutic applications, and in April 2024, we and Moderna mutually terminated the Moderna Agreement. Refer to Note 7 in our condensed consolidated 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 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 $11.5 million and $42.7 million for the three and nine months ended September 30, 2024, respectively, and $12.4 million and $32.4 million for the three and nine months ended September 30, 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. 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.

Previous wording

The largest component of our total operating expenses since our inception has been research and development activities. Research and development expenses consist primarily of compensation and benefits for research and development employees, including stock-based compensation; the costs of acquiring research and development supplies and services; manufacturing process development costs; the research and development expenses that we share with our collaboration partners for co-development programs; other outside services and consulting costs; and allocated facilities, information technology and overhead expenses. Research and development costs are expensed as incurred.

Current wording

The largest component of our total operating expenses since our inception has been research and development activities. Research and development expenses consist primarily of personnel costs for research and development employees, including stock-based compensation; the costs of acquiring research and development supplies and services; manufacturing process development costs; the research and development expenses that we share with our collaboration partners for co-development programs; other outside services and consulting costs; and allocated facilities, information technology and overhead expenses. Research and development costs are expensed as incurred.

Previous wording

Comparison of the Three and Nine Months Ended September 30, 2024 and 2023

Current wording

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

Previous wording

Our revenue consists of collaboration revenue recognized under our agreements with Moderna (prior to the termination of the Moderna Agreement), Affini-T and Ionis. We recognize revenue as the performance obligations are satisfied. Collaboration revenue decreased by $0.8 million, from $12.4 million for the three months ended September 30, 2023 to $11.5 million for the three months ended September 30, 2024 and increased by $10.3 million, from $32.4 million for the nine months ended September 30, 2023 to $42.7 million for the nine months ended September 30, 2024. The decrease in collaboration revenue for the three months ended September 30, 2024 was primarily driven by a $5.3 million decrease in revenue related to the Termination Agreement, offset by a $3.9 million increase in revenue related to the Ionis Agreement as we performed more services and a $0.5 million increase in revenue related to the Affini-T Agreement. The increase in collaboration revenue for the nine months ended September 30, 2024 was primarily driven by a $6.6 million increase in revenue related to the Ionis Agreement as we performed more services and a $4.5 million increase in revenue related to the Moderna Agreement mainly due to the recognition of all remaining deferred revenue during the nine months ended September 30, 2024, offset by a $0.8 million decrease in revenue related to the Affini-T Agreement.

Current 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.

Previous wording

General and administrative expenses were $24.9 million for the nine months ended September 30, 2024, compared to $21.0 million for the nine months ended September 30, 2023. The increase of $3.9 million was primarily related to an increase of $4.6 million in employee-related expenses, including stock-based compensation expense, as a result of increased headcount and the issuance of annual equity awards to existing employees and an increase of $0.8 million in facilities and allocated overhead, offset by a decrease of $1.5 million in professional service fees and other costs.

Current 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.

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 $68.3 million and $43.6 million for the years ended December 31, 2023 and 2022, respectively, and $54.7 million and $49.0 million for the nine months ended September 30, 2024 and 2023, respectively. As of September 30, 2024, we had an accumulated deficit of $199.6 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 $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.

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 September 30, 2024, we had $274.6 million in cash, cash equivalents and available-for-sale marketable securities. We believe that our existing cash, cash equivalents and available-for-sale marketable securities will be sufficient to fund our current operating plan for at least the next 12 months. 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 into 2027. We have based this estimate on assumptions that may prove to be wrong, and we could exhaust our available capital resources sooner than we expect. 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 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.

Previous wording

Net cash used in operating activities was $82.8 million for the nine months ended September 30, 2024 and consisted primarily of our net loss of $54.7 million and changes in our net operating assets and liabilities of $44.2 million, partially offset by net non-cash charges of $16.1 million. The net change in operating assets and liabilities consisted primarily of a decrease of $38.4 million in deferred revenue as we recognized revenue under our collaboration agreements, a decrease of $3.3 million in income tax payable due to payment of our 2023 income tax liability, a decrease of $2.2 million in operating lease liabilities, a decrease of $2.0 million in other non-current liabilities and an increase of $1.2 million in prepaid expenses and other current assets, offset by a decrease of $1.9 million in accounts receivable related to the Affini-T Agreement and the Moderna Agreement and an increase of $1.5 million in accounts payable due to the timing of payments to our vendors. The net non-cash charges consisted primarily of $12.8 million in stock-based compensation expense, $3.9 million of depreciation expense, $3.4 million in non-cash lease expense, and a $2.1 million charge related to the fair value of our investments in Affini-T, partially offset by $4.8 million in amortization of discounts on available-for-sale marketable securities and $1.6 million in amortization of non-cash collaboration revenue related to the Affini-T Agreement.

Current 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.

Previous wording

Net cash used in operating activities for the nine months ended September 30, 2023 was $70.8 million and consisted primarily of our net loss of $49.0 million and changes in our net operating assets and liabilities of $22.1 million, partially offset by net non-cash charges of $0.2 million. The changes in our net operating assets and liabilities consisted primarily of a decrease of $25.0 million in deferred revenue and collaboration advances as we recognized revenue under our collaboration agreements, an increase of $3.9 million in accounts receivable related to the Affini-T Agreement and the Moderna Agreement and a $1.0 million decrease in operating lease liabilities due to recurring payments under the existing lease agreements, partially offset by a $2.4 million increase in accounts payable due to the timing of payments to our vendors, a $2.4 million increase in other non-current liabilities, a $1.3 million decrease in contract assets related to the Affini-T Agreement, a $0.7 million increase in accrued expenses and other liabilities and a $0.6 million increase in income tax payable due to additional tax expense. The net non-cash charges consisted primarily of $4.5 million in stock-based compensation expense, $3.1 million in non-cash lease expense and $3.0 million of depreciation expense, offset by $6.9 million credit related to amortization of the discount on our available-for-sale marketable securities, $2.9 million increase in the fair value of our investments in Affini-T and $0.7 million in amortization of non-cash collaboration revenue related to the Affini-T Agreement.

Current 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.

Previous wording

Net cash used in investing activities for the nine months ended September 30, 2024 was $116.7 million primarily due to net purchases of available-for-sale marketable securities of $113.6 million and purchases of property and equipment of $2.8 million.

Current 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.

Previous wording

Net cash used in investing activities for the nine months ended September 30, 2023 was $14.9 million due to net purchases of available-for-sale marketable securities of $6.8 million and purchases of property and equipment of $8.1 million.

Current 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.

Previous wording

Net cash provided by financing activities for the nine months ended September 30, 2024 was $84.0 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 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.

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 nine months ended September 30, 2024, 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, 2023, filed with the SEC on March 27, 2024.

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 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.

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

Previous wording

Our management’s discussion and analysis of our financial condition and results of operations is based on our financial statements, which have been prepared in accordance with generally accepted accounting principles (“GAAP”). The preparation of these financial statements requires us to make estimates and assumptions that affect the reported amounts of assets and liabilities and the disclosure of contingent assets and liabilities at the date of the financial statements, as well as thereported revenue generated and expenses incurred during the reporting periods. On an ongoing basis, we evaluate our estimates and judgments, including but not limited to those related to revenue recognition under our collaboration agreements, accrued research and development costs, 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 underthe 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.

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 underthe 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.

Previous wording

During the nine months ended September 30, 2024, 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, 2023.

Current 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.