Nature biotechnology最新文献

NIS-Seq enables cell-type-agnostic optical perturbation screening

IF 46.9 1区生物学

Nature biotechnology Pub Date : 2024-12-19 DOI: 10.1038/s41587-024-02516-5

Caroline I. Fandrey, Marius Jentzsch, Peter Konopka, Alexander Hoch, Katja Blumenstock, Afraa Zackria, Salie Maasewerd, Marta Lovotti, Dorothee J. Lapp, Florian N. Gohr, Piotr Suwara, Jędrzej Świeżewski, Lukas Rossnagel, Fabienne Gobs, Maia Cristodaro, Lina Muhandes, Rayk Behrendt, Martin C. Lam, Klaus J. Walgenbach, Tobias Bald, Florian I. Schmidt, Eicke Latz, Jonathan L. Schmid-Burgk

{"title":"NIS-Seq enables cell-type-agnostic optical perturbation screening","authors":"Caroline I. Fandrey, Marius Jentzsch, Peter Konopka, Alexander Hoch, Katja Blumenstock, Afraa Zackria, Salie Maasewerd, Marta Lovotti, Dorothee J. Lapp, Florian N. Gohr, Piotr Suwara, Jędrzej Świeżewski, Lukas Rossnagel, Fabienne Gobs, Maia Cristodaro, Lina Muhandes, Rayk Behrendt, Martin C. Lam, Klaus J. Walgenbach, Tobias Bald, Florian I. Schmidt, Eicke Latz, Jonathan L. Schmid-Burgk","doi":"10.1038/s41587-024-02516-5","DOIUrl":"https://doi.org/10.1038/s41587-024-02516-5","url":null,"abstract":"Optical pooled screening offers a broader-scale alternative to enrichment-based perturbation screening, using fluorescence microscopy to correlate phenotypes and perturbations across single cells. Previous methods work well in large, transcriptionally active cell lines, because they rely on cytosolic detection of endogenously expressed barcoded transcripts; however, they are limited by reliable cell segmentation, cytosol size, transcriptional activity and cell density. Nuclear In-Situ Sequencing (NIS-Seq) expands this technology by creating bright sequencing signals directly from nuclear genomic DNA to screen nucleated cells at high density and high library complexity. By inserting an inverted phage promoter downstream of the single guide RNA (sgRNA), many RNA copies of the sgRNA can be generated and sequenced independently of cellular transcription. In this study, we benchmarked NIS-Seq across eight cell types from two species and performed four genome-scale optical perturbation screens, identifying key players of inflammation-related cellular pathways. Finally, we performed a small-scale pooled optical screen in primary human macrophages from blood of healthy donors and demonstrated barcode identification in lentivirally transduced human skin tissue.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"40 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2024-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142849637","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}

引用次数: 0

CRISPR-StAR enables high-resolution genetic screening in complex in vivo models

IF 46.9 1区生物学

Nature biotechnology Pub Date : 2024-12-16 DOI: 10.1038/s41587-024-02512-9

Esther C. H. Uijttewaal, Joonsun Lee, Annika Charlotte Sell, Naomi Botay, Gintautas Vainorius, Maria Novatchkova, Juliane Baar, Jiaye Yang, Tobias Potzler, Sophie van der Leij, Christopher Lowden, Julia Sinner, Anais Elewaut, Milanka Gavrilovic, Anna Obenauf, Daniel Schramek, Ulrich Elling

{"title":"CRISPR-StAR enables high-resolution genetic screening in complex in vivo models","authors":"Esther C. H. Uijttewaal, Joonsun Lee, Annika Charlotte Sell, Naomi Botay, Gintautas Vainorius, Maria Novatchkova, Juliane Baar, Jiaye Yang, Tobias Potzler, Sophie van der Leij, Christopher Lowden, Julia Sinner, Anais Elewaut, Milanka Gavrilovic, Anna Obenauf, Daniel Schramek, Ulrich Elling","doi":"10.1038/s41587-024-02512-9","DOIUrl":"https://doi.org/10.1038/s41587-024-02512-9","url":null,"abstract":"Pooled genetic screening with CRISPR–Cas9 has enabled genome-wide, high-resolution mapping of genes to phenotypes, but assessing the effect of a given genetic perturbation requires evaluation of each single guide RNA (sgRNA) in hundreds of cells to counter stochastic genetic drift and obtain robust results. However, resolution is limited in complex, heterogeneous models, such as organoids or tumors transplanted into mice, because achieving sufficient representation requires impractical scaling. This is due to bottleneck effects and biological heterogeneity of cell populations. Here we introduce CRISPR-StAR, a screening method that uses internal controls generated by activating sgRNAs in only half the progeny of each cell subsequent to re-expansion of the cell clone. Our method overcomes both intrinsic and extrinsic heterogeneity as well as genetic drift in bottlenecks by generating clonal, single-cell-derived intrinsic controls. We use CRISPR-StAR to identify in-vivo-specific genetic dependencies in a genome-wide screen in mouse melanoma. Benchmarking against conventional screening demonstrates the improved data quality provided by this technology.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"63 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2024-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142825185","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}

引用次数: 0

Toward a safer and more secure US bioeconomy

IF 46.9 1区生物学

Nature biotechnology Pub Date : 2024-12-16 DOI: 10.1038/s41587-024-02519-2

Matthew C. Watson, Kunal J. Rambhia, Meghan J. Seltzer, Sarah R. Carter, Rebecca L. Moritz, Aurelia Attal-Juncqua, James Diggans, John Dileo

引用次数: 0

The devolution of biosimilars regulations

IF 46.9 1区生物学

Nature biotechnology Pub Date : 2024-12-16 DOI: 10.1038/s41587-024-02497-5

Erik Doevendans, Peter van Meer, Huub Schellekens

引用次数: 0

A general system for targeting MHC class II–antigen complex via a single adaptable loop

IF 46.9 1区生物学

Nature biotechnology Pub Date : 2024-12-13 DOI: 10.1038/s41587-024-02466-y

Haotian Du, Jingjia Liu, Kevin M. Jude, Xinbo Yang, Ying Li, Braxton Bell, Hongli Yang, Audrey Kassardjian, Wyatt Blackson, Ali Mobedi, Udit Parekh, R. Andres Parra Sperberg, Jean-Philippe Julien, Elizabeth D. Mellins, K. Christopher Garcia, Po-Ssu Huang

{"title":"A general system for targeting MHC class II–antigen complex via a single adaptable loop","authors":"Haotian Du, Jingjia Liu, Kevin M. Jude, Xinbo Yang, Ying Li, Braxton Bell, Hongli Yang, Audrey Kassardjian, Wyatt Blackson, Ali Mobedi, Udit Parekh, R. Andres Parra Sperberg, Jean-Philippe Julien, Elizabeth D. Mellins, K. Christopher Garcia, Po-Ssu Huang","doi":"10.1038/s41587-024-02466-y","DOIUrl":"https://doi.org/10.1038/s41587-024-02466-y","url":null,"abstract":"Major histocompatibility complex class II (MHCII) bound to a peptide antigen mediates interactions between CD4+ T cells and antigen-presenting cells. Targeting peptide–MHCII with T cell antigen receptors (TCRs) and TCR-like antibodies has shown promise for autoimmune diseases and microbiome tolerance. To develop a general targeting approach, we introduce targeted recognition of antigen–MHC complex reporter for MHCII (TRACeR-II) for the rapid development of peptide-specific MHCII binders. TRACeR-II binders have a small helical bundle scaffold and use a single loop to recognize peptide–MHCII, which offers versatility and enables structural modeling of the interactions to target MHCII antigens. We demonstrate rapid generation of TRACeR-II binders to multiple molecules with affinities in the low-nanomolar to low-micromolar range, comparable to best-in-class TCRs and antibodies. Through computational protein design, we created specific binding sequences in silico from only the sequence of a severe acute respiratory syndrome coronavirus 2 peptide. TRACeR-II provides a straightforward approach to target antigen–MHCII without relying on combinatorial selection on complementarity-determining region loops.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"352 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142815480","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}

引用次数: 0

Biopharma deals get smaller and earlier

IF 46.9 1区生物学

Nature biotechnology Pub Date : 2024-12-13 DOI: 10.1038/s41587-024-02506-7

引用次数: 0

A synthetic scaffold to target peptide–MHC complexes

IF 46.9 1区生物学

Nature biotechnology Pub Date : 2024-12-13 DOI: 10.1038/s41587-024-02513-8

Pallavi A. Balivada, Stephanie A. Gaglione, Michael E. Birnbaum

引用次数: 0

Targeting peptide antigens using a multiallelic MHC I-binding system

IF 46.9 1区生物学

Nature biotechnology Pub Date : 2024-12-13 DOI: 10.1038/s41587-024-02505-8

Haotian Du, Leena Mallik, Daniel Hwang, Yi Sun, Chengzi Kaku, Daniel Hoces, Shirley M. Sun, Reem Ghinnagow, Stephen D. Carro, Hoang Anh T. Phan, Sagar Gupta, Wyatt Blackson, Hyejin Lee, Christian A. Choe, Devin Dersh, Jingjia Liu, Braxton Bell, Hongli Yang, Georgia F. Papadaki, Michael C. Young, Emily Zhou, Gina El Nesr, Kimia Dasteh Goli, Laurence C. Eisenlohr, Andy J. Minn, Rogelio A. Hernandez-Lopez, Joseph G. Jardine, Nikolaos G. Sgourakis, Po-Ssu Huang

{"title":"Targeting peptide antigens using a multiallelic MHC I-binding system","authors":"Haotian Du, Leena Mallik, Daniel Hwang, Yi Sun, Chengzi Kaku, Daniel Hoces, Shirley M. Sun, Reem Ghinnagow, Stephen D. Carro, Hoang Anh T. Phan, Sagar Gupta, Wyatt Blackson, Hyejin Lee, Christian A. Choe, Devin Dersh, Jingjia Liu, Braxton Bell, Hongli Yang, Georgia F. Papadaki, Michael C. Young, Emily Zhou, Gina El Nesr, Kimia Dasteh Goli, Laurence C. Eisenlohr, Andy J. Minn, Rogelio A. Hernandez-Lopez, Joseph G. Jardine, Nikolaos G. Sgourakis, Po-Ssu Huang","doi":"10.1038/s41587-024-02505-8","DOIUrl":"https://doi.org/10.1038/s41587-024-02505-8","url":null,"abstract":"Identifying highly specific T cell receptors (TCRs) or antibodies against epitopic peptides presented by class I major histocompatibility complex (MHC I) proteins remains a bottleneck in the development of targeted therapeutics. Here, we introduce targeted recognition of antigen–MHC complex reporter for MHC I (TRACeR-I), a generalizable platform for targeting peptides on polymorphic HLA-A*, HLA-B* and HLA-C* allotypes while overcoming the cross-reactivity challenges of TCRs. Our TRACeR–MHC I co-crystal structure reveals a unique antigen recognition mechanism, with TRACeR forming extensive contacts across the entire peptide length to confer single-residue specificity at the accessible positions. We demonstrate rapid screening of TRACeR-I against a panel of disease-relevant HLAs with peptides derived from human viruses (human immunodeficiency virus, Epstein–Barr virus and severe acute respiratory syndrome coronavirus 2), and oncoproteins (Kirsten rat sarcoma virus, paired-like homeobox 2b and New York esophageal squamous cell carcinoma 1). TRACeR-based bispecific T cell engagers and chimeric antigen receptor T cells exhibit on-target killing of tumor cells with high efficacy in the low nanomolar range. Our platform empowers the development of broadly applicable MHC I-targeting molecules for research, diagnostic and therapeutic applications.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"15 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2024-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142815481","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}

引用次数: 0

Efficient non-viral immune cell engineering using circular single-stranded DNA-mediated genomic integration

IF 46.9 1区生物学

Nature biotechnology Pub Date : 2024-12-11 DOI: 10.1038/s41587-024-02504-9

Keqiang Xie, Jakob Starzyk, Ishita Majumdar, Jiao Wang, Katerina Rincones, Thao Tran, Danna Lee, Sarah Niemi, John Famiglietti, Bernhard Suter, Richard Shan, Hao Wu

{"title":"Efficient non-viral immune cell engineering using circular single-stranded DNA-mediated genomic integration","authors":"Keqiang Xie, Jakob Starzyk, Ishita Majumdar, Jiao Wang, Katerina Rincones, Thao Tran, Danna Lee, Sarah Niemi, John Famiglietti, Bernhard Suter, Richard Shan, Hao Wu","doi":"10.1038/s41587-024-02504-9","DOIUrl":"https://doi.org/10.1038/s41587-024-02504-9","url":null,"abstract":"The use of adeno-associated viruses (AAVs) as donors for homology-directed repair (HDR)-mediated genome engineering is limited by safety issues, manufacturing constraints and restricted packaging limits. Non-viral targeted genetic knock-ins rely primarily on double-stranded DNA (dsDNA) and linear single-stranded DNA (lssDNA) donors. dsDNA is known to have low efficiency and high cytotoxicity, while lssDNA is challenging for scaled manufacture. In this study, we developed a non-viral genome writing catalyst (GATALYST) system that allows production of circular single-stranded DNAs (cssDNAs) up to approximately 20 kilobases as donor templates for highly efficient precision transgene integration. cssDNA donors enable knock-in efficiency of up to 70% in induced pluripotent stem cells (iPSCs) and improved efficiency in multiple clinically relevant primary immune cell types and at multiple genomic loci implicated for clinical applications with various nuclease editor systems. The high precision and efficiency in chimeric antigen receptor (CAR)-T and natural killer (NK) cells, improved safety, payload flexibility and scalable manufacturability of cssDNA shows potential for future applications of genome engineering.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"25 6 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142805096","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}

引用次数: 0

BioNTech boosts oncology pipeline with China buy

IF 33.1 1区生物学

Nature biotechnology Pub Date : 2024-12-11 DOI: 10.1038/s41587-024-02518-3

引用次数: 0