Pub Date : 2026-03-11DOI: 10.1038/s41587-026-03022-6
Antony Jozić,Chloé Le Roux,Jeonghwan Kim,Mathieu Berchel,Deepak Kumar Sahel,Emily K Bodi,Michelle Palumbo,Aishwarya Vasudevan,Namratha Turuvekere Vittala Murthy,Yulia Eygeris,Milan Gautam,Elissa Bloom,Anthony P Barnes,Paul-Alain Jaffrès,Gaurav Sahay
Endosomal escape is a central barrier to efficient nucleic acid delivery by lipid nanoparticles (LNPs) and remains challenging to quantify in vivo. We report a library of branched ionizable phospholipids that markedly enhance messenger RNA delivery to the liver. The lead candidate BiP-20 outperformed the clinical benchmark LP01 by eightfold for CRISPR-Cas9 editing of the TTR gene at low dose with rapid pharmacokinetics. To quantify the endosomal escape kinetics of BiP-20, we used LysoTag mice, which allow immunoisolation of liver lysosomes, and our Lysosomal Barcoding method, finding that ~8% of BiP-20 LNPs reach the cytosol within 30 min of administration. Lysosomal proteomics revealed mechanistic regulators of escape and BiP-20-induced alterations in endosomal maturation and recycling pathways. Loss of Rab7, a mediator of late endosomal maturation, increased LNP escape. These findings provide a potent class of ionizable lipids for RNA delivery, a method to quantify endosomal escape in vivo, and mechanistic insight into the endolysosomal determinants of LNP trafficking.
{"title":"In vivo endosomal escape assay identifies mechanisms for efficient hepatic LNP delivery.","authors":"Antony Jozić,Chloé Le Roux,Jeonghwan Kim,Mathieu Berchel,Deepak Kumar Sahel,Emily K Bodi,Michelle Palumbo,Aishwarya Vasudevan,Namratha Turuvekere Vittala Murthy,Yulia Eygeris,Milan Gautam,Elissa Bloom,Anthony P Barnes,Paul-Alain Jaffrès,Gaurav Sahay","doi":"10.1038/s41587-026-03022-6","DOIUrl":"https://doi.org/10.1038/s41587-026-03022-6","url":null,"abstract":"Endosomal escape is a central barrier to efficient nucleic acid delivery by lipid nanoparticles (LNPs) and remains challenging to quantify in vivo. We report a library of branched ionizable phospholipids that markedly enhance messenger RNA delivery to the liver. The lead candidate BiP-20 outperformed the clinical benchmark LP01 by eightfold for CRISPR-Cas9 editing of the TTR gene at low dose with rapid pharmacokinetics. To quantify the endosomal escape kinetics of BiP-20, we used LysoTag mice, which allow immunoisolation of liver lysosomes, and our Lysosomal Barcoding method, finding that ~8% of BiP-20 LNPs reach the cytosol within 30 min of administration. Lysosomal proteomics revealed mechanistic regulators of escape and BiP-20-induced alterations in endosomal maturation and recycling pathways. Loss of Rab7, a mediator of late endosomal maturation, increased LNP escape. These findings provide a potent class of ionizable lipids for RNA delivery, a method to quantify endosomal escape in vivo, and mechanistic insight into the endolysosomal determinants of LNP trafficking.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"30 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2026-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147393855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-11DOI: 10.1038/s41587-026-03059-7
Brittney W Thornton,Rachel F Weissman,Jorge E Rodriguez,Ryan V Tran,Brenda T Duong,Cynthia I Terrace,Ugrappa Nagalakshmi,George Austin,Evan D Groover,Flora Zhiqi Wang,Jung-Un Park,Viktoriya Georgieva,Julia Tartaglia,Myeong-Je Cho,Savithramma P Dinesh-Kumar,Jennifer A Doudna,David F Savage
TnpB is a diverse family of RNA-guided endonucleases associated with prokaryotic transposons. Because of their small size and putative evolutionary relationship to CRISPR-Cas12, TnpB enzymes hold great potential for genome editing. However, most TnpBs lack robust gene-editing activity. Here, we mapped comprehensive sequence-function landscapes of a TnpB ribonucleoprotein using deep mutational scanning and we discovered activating mutations in both the RNA and the protein. Leveraging the protein's mutational landscape, we constructed a combinatorial library of activating mutations, from which we identified two enhanced TnpB variants. These variants increased editing in human cells, Nicotania benthamiana, pepper and rice. While editing efficiencies varied by target site, engineered variants achieved up to 55% insertion and deletion frequencies (a 50-fold increase over wild type) in N. benthamiana, surpassing ISYmu1 (<7%), AsCas12f-HKRA (<9%) and other compact editors. These findings highlight elements critical for regulating TnpB endonuclease activity and demonstrate latent activity accessible through mutation.
{"title":"Engineered TnpB genome editors for plants and human cells identified by ribonucleoprotein mutational scanning.","authors":"Brittney W Thornton,Rachel F Weissman,Jorge E Rodriguez,Ryan V Tran,Brenda T Duong,Cynthia I Terrace,Ugrappa Nagalakshmi,George Austin,Evan D Groover,Flora Zhiqi Wang,Jung-Un Park,Viktoriya Georgieva,Julia Tartaglia,Myeong-Je Cho,Savithramma P Dinesh-Kumar,Jennifer A Doudna,David F Savage","doi":"10.1038/s41587-026-03059-7","DOIUrl":"https://doi.org/10.1038/s41587-026-03059-7","url":null,"abstract":"TnpB is a diverse family of RNA-guided endonucleases associated with prokaryotic transposons. Because of their small size and putative evolutionary relationship to CRISPR-Cas12, TnpB enzymes hold great potential for genome editing. However, most TnpBs lack robust gene-editing activity. Here, we mapped comprehensive sequence-function landscapes of a TnpB ribonucleoprotein using deep mutational scanning and we discovered activating mutations in both the RNA and the protein. Leveraging the protein's mutational landscape, we constructed a combinatorial library of activating mutations, from which we identified two enhanced TnpB variants. These variants increased editing in human cells, Nicotania benthamiana, pepper and rice. While editing efficiencies varied by target site, engineered variants achieved up to 55% insertion and deletion frequencies (a 50-fold increase over wild type) in N. benthamiana, surpassing ISYmu1 (<7%), AsCas12f-HKRA (<9%) and other compact editors. These findings highlight elements critical for regulating TnpB endonuclease activity and demonstrate latent activity accessible through mutation.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"9 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2026-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147393852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-10DOI: 10.1038/s41587-026-03018-2
Patrick A Ott
Transformational advances in genomic sequencing capabilities, vastly improved HLA class I epitope prediction algorithms and powerful delivery platforms have facilitated the clinical development of vaccines targeting neoantigens encoded by tumor mutations. Early clinical trials indicate that vaccination against neoantigens can induce robust and durable T cell immunity that may persist for decades. mRNA vaccines, originally developed for cancer applications, have demonstrated considerable promise due to their efficacy and scalable production, as evidenced during the SARS-CoV-2 pandemic. However, the optimal cancer vaccine platform and delivery strategy is not yet known, as current approaches have not been compared head-to-head and substantial technological advances to improve immunogenicity and potentially clinical efficacy are achievable. For example, lipid-based formulations, while necessary for the effective delivery of mRNA vaccines, may also improve the immunogenicity of peptides and other delivery strategies. Here we review the current state of neoantigen vaccines in the clinic and highlight emerging opportunities for advancement in the field.
{"title":"The promises and challenges of neoantigen cancer vaccines.","authors":"Patrick A Ott","doi":"10.1038/s41587-026-03018-2","DOIUrl":"https://doi.org/10.1038/s41587-026-03018-2","url":null,"abstract":"Transformational advances in genomic sequencing capabilities, vastly improved HLA class I epitope prediction algorithms and powerful delivery platforms have facilitated the clinical development of vaccines targeting neoantigens encoded by tumor mutations. Early clinical trials indicate that vaccination against neoantigens can induce robust and durable T cell immunity that may persist for decades. mRNA vaccines, originally developed for cancer applications, have demonstrated considerable promise due to their efficacy and scalable production, as evidenced during the SARS-CoV-2 pandemic. However, the optimal cancer vaccine platform and delivery strategy is not yet known, as current approaches have not been compared head-to-head and substantial technological advances to improve immunogenicity and potentially clinical efficacy are achievable. For example, lipid-based formulations, while necessary for the effective delivery of mRNA vaccines, may also improve the immunogenicity of peptides and other delivery strategies. Here we review the current state of neoantigen vaccines in the clinic and highlight emerging opportunities for advancement in the field.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"188 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2026-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147383364","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-10DOI: 10.1038/s41587-026-03069-5
Melanie Senior,Ricardo Grieshaber-Bouyer
{"title":"B cell depletion in autoimmune disease: in vivo CAR-T or T cell engagers?","authors":"Melanie Senior,Ricardo Grieshaber-Bouyer","doi":"10.1038/s41587-026-03069-5","DOIUrl":"https://doi.org/10.1038/s41587-026-03069-5","url":null,"abstract":"","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"16 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2026-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147383302","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Cellular metabolites have emerged as noncanonical RNA caps. Despite its early discovery as an RNA cap, the dephospho-CoA (dpCoA) cap remains largely uncharacterized because of a lack of detection technologies. Here we use biochemical and structural analysis to identify Arabidopsis NUDT11 as a specific decapping enzyme toward dpCoA-RNA. Leveraging this specificity, we develop biochemical and transcriptomic methods to quantify and profile dpCoA-RNA across the genome, revealing that dpCoA-RNAs exist across species and exhibit tissue-specific and/or condition-specific variations. In Arabidopsis, dpCoA-RNAs possess distinct transcription start sites and respond more rapidly to high light intensity as compared to 7-methylguanosine (m7G)-capped RNAs. Moreover, Arabidopsis dpCoA-RNAs can reach up to 15% of m7G-capped RNAs in abundance and are associated with translating ribosomes. We further demonstrate that an in vitro transcribed dpCoA-RNA is translated in human cells. This study uncovers a dynamic dpCoA cap that may potentially influence gene expression and establishes a toolkit for future investigations.
{"title":"Quantification and transcriptome profiling reveal abundant, dynamic and translatable dephospho-CoA-capped RNAs","authors":"Hao Hu, Qiyue Zhang, Xuan Ma, Hsu-Feng Chu, Han Wang, Yiwen Guo, Yuze Bai, Qianyu Wang, Zehao Li, Jiayi Zhao, Huiyuan Lin, Chenjiang You, Xing Li, Liang Tong, Xuemei Chen","doi":"10.1038/s41587-026-03040-4","DOIUrl":"https://doi.org/10.1038/s41587-026-03040-4","url":null,"abstract":"Cellular metabolites have emerged as noncanonical RNA caps. Despite its early discovery as an RNA cap, the dephospho-CoA (dpCoA) cap remains largely uncharacterized because of a lack of detection technologies. Here we use biochemical and structural analysis to identify Arabidopsis NUDT11 as a specific decapping enzyme toward dpCoA-RNA. Leveraging this specificity, we develop biochemical and transcriptomic methods to quantify and profile dpCoA-RNA across the genome, revealing that dpCoA-RNAs exist across species and exhibit tissue-specific and/or condition-specific variations. In Arabidopsis, dpCoA-RNAs possess distinct transcription start sites and respond more rapidly to high light intensity as compared to 7-methylguanosine (m7G)-capped RNAs. Moreover, Arabidopsis dpCoA-RNAs can reach up to 15% of m7G-capped RNAs in abundance and are associated with translating ribosomes. We further demonstrate that an in vitro transcribed dpCoA-RNA is translated in human cells. This study uncovers a dynamic dpCoA cap that may potentially influence gene expression and establishes a toolkit for future investigations.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"1 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2026-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147346840","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-03DOI: 10.1038/s41587-026-03052-0
Erik Alexandersson,Thies Marten Heick,Anna Chailyan,Sisse Marquina-Jongberg,Thomas de Bang,Claus Felby
{"title":"Sharing big data for sustainable agri-food innovation.","authors":"Erik Alexandersson,Thies Marten Heick,Anna Chailyan,Sisse Marquina-Jongberg,Thomas de Bang,Claus Felby","doi":"10.1038/s41587-026-03052-0","DOIUrl":"https://doi.org/10.1038/s41587-026-03052-0","url":null,"abstract":"","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"42 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2026-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147346458","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-02DOI: 10.1038/s41587-026-03056-w
Stanley T Crooke,Andrew W Lo
{"title":"Establishing a commercial solution for extremely rare genetic diseases.","authors":"Stanley T Crooke,Andrew W Lo","doi":"10.1038/s41587-026-03056-w","DOIUrl":"https://doi.org/10.1038/s41587-026-03056-w","url":null,"abstract":"","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"65 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2026-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147329353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01DOI: 10.1038/s41587-026-03070-y
Iris Marchal
{"title":"In vivo base editing reverses a neurodevelopmental disorder.","authors":"Iris Marchal","doi":"10.1038/s41587-026-03070-y","DOIUrl":"https://doi.org/10.1038/s41587-026-03070-y","url":null,"abstract":"","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"16 1","pages":"369"},"PeriodicalIF":46.9,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147471394","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2026-03-01DOI: 10.1038/s41587-026-03027-1
Iris Marchal
{"title":"Biotech building from a venture capitalist perspective.","authors":"Iris Marchal","doi":"10.1038/s41587-026-03027-1","DOIUrl":"https://doi.org/10.1038/s41587-026-03027-1","url":null,"abstract":"","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"44 3","pages":"350-353"},"PeriodicalIF":41.7,"publicationDate":"2026-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147474587","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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