{"title":"Pest control gets the CRISPR treatment","authors":"Caroline Seydel","doi":"10.1038/s41587-024-02449-z","DOIUrl":"10.1038/s41587-024-02449-z","url":null,"abstract":"Precision genetic methods are enabling more efficient, environmentally friendly pest control methods for agricultural use as well as stopping the spread of disease.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"42 11","pages":"1633-1636"},"PeriodicalIF":33.1,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41587-024-02449-z.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142487112","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Lei Chang, Yang Xie, Brett Taylor, Zhaoning Wang, Jiachen Sun, Ethan J. Armand, Shreya Mishra, Jie Xu, Melodi Tastemel, Audrey Lie, Zane A. Gibbs, Hannah S. Indralingam, Tuyet M. Tan, Rafael Bejar, Clark C. Chen, Frank B. Furnari, Ming Hu, Bing Ren
{"title":"Droplet Hi-C enables scalable, single-cell profiling of chromatin architecture in heterogeneous tissues","authors":"Lei Chang, Yang Xie, Brett Taylor, Zhaoning Wang, Jiachen Sun, Ethan J. Armand, Shreya Mishra, Jie Xu, Melodi Tastemel, Audrey Lie, Zane A. Gibbs, Hannah S. Indralingam, Tuyet M. Tan, Rafael Bejar, Clark C. Chen, Frank B. Furnari, Ming Hu, Bing Ren","doi":"10.1038/s41587-024-02447-1","DOIUrl":"https://doi.org/10.1038/s41587-024-02447-1","url":null,"abstract":"<p>Current methods for analyzing chromatin architecture are not readily scalable to heterogeneous tissues. Here we introduce Droplet Hi-C, which uses a commercial microfluidic device for high-throughput, single-cell chromatin conformation profiling in droplets. Using Droplet Hi-C, we mapped the chromatin architecture of the mouse cortex and analyzed gene regulatory programs in major cortical cell types. In addition, we used this technique to detect copy number variations, structural variations and extrachromosomal DNA in human glioblastoma, colorectal and blood cancer cells, revealing clonal dynamics and other oncogenic events during treatment. We refined the technique to allow joint profiling of chromatin architecture and transcriptome in single cells, facilitating exploration of the links between chromatin architecture and gene expression in both normal tissues and tumors. Thus, Droplet Hi-C both addresses critical gaps in chromatin analysis of heterogeneous tissues and enhances understanding of gene regulation.</p>","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"193 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142448119","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}
Christian Dörig, Cathy Marulli, Thomas Peskett, Norbert Volkmar, Lorenzo Pantolini, Gabriel Studer, Camilla Paleari, Fabian Frommelt, Torsten Schwede, Natalie de Souza, Yves Barral, Paola Picotti
{"title":"Global profiling of protein complex dynamics with an experimental library of protein interaction markers","authors":"Christian Dörig, Cathy Marulli, Thomas Peskett, Norbert Volkmar, Lorenzo Pantolini, Gabriel Studer, Camilla Paleari, Fabian Frommelt, Torsten Schwede, Natalie de Souza, Yves Barral, Paola Picotti","doi":"10.1038/s41587-024-02432-8","DOIUrl":"https://doi.org/10.1038/s41587-024-02432-8","url":null,"abstract":"<p>Methods to systematically monitor protein complex dynamics are needed. We introduce serial ultrafiltration combined with limited proteolysis-coupled mass spectrometry (FLiP–MS), a structural proteomics workflow that generates a library of peptide markers specific to changes in PPIs by probing differences in protease susceptibility between complex-bound and monomeric forms of proteins. The library includes markers mapping to protein-binding interfaces and markers reporting on structural changes that accompany PPI changes. Integrating the marker library with LiP–MS data allows for global profiling of protein–protein interactions (PPIs) from unfractionated lysates. We apply FLiP–MS to <i>Saccharomyces cerevisiae</i> and probe changes in protein complex dynamics after DNA replication stress, identifying links between Spt-Ada-Gcn5 acetyltransferase activity and the assembly state of several complexes. FLiP–MS enables protein complex dynamics to be probed on any perturbation, proteome-wide, at high throughput, with peptide-level structural resolution and informing on occupancy of binding interfaces, thus providing both global and molecular views of a system under study.</p>","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"20 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142440263","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}
Kai Chen, Hesong Han, Sheng Zhao, Bryant Xu, Boyan Yin, Atip Lawanprasert, Marena Trinidad, Benjamin W. Burgstone, Niren Murthy, Jennifer A. Doudna
{"title":"Lung and liver editing by lipid nanoparticle delivery of a stable CRISPR–Cas9 ribonucleoprotein","authors":"Kai Chen, Hesong Han, Sheng Zhao, Bryant Xu, Boyan Yin, Atip Lawanprasert, Marena Trinidad, Benjamin W. Burgstone, Niren Murthy, Jennifer A. Doudna","doi":"10.1038/s41587-024-02437-3","DOIUrl":"https://doi.org/10.1038/s41587-024-02437-3","url":null,"abstract":"<p>Lipid nanoparticle (LNP) delivery of clustered regularly interspaced short palindromic repeat (CRISPR) ribonucleoproteins (RNPs) could enable high-efficiency, low-toxicity and scalable in vivo genome editing if efficacious RNP–LNP complexes can be reliably produced. Here we engineer a thermostable Cas9 from <i>Geobacillus stearothermophilus</i> (GeoCas9) to generate iGeoCas9 variants capable of >100× more genome editing of cells and organs compared with the native GeoCas9 enzyme. Furthermore, iGeoCas9 RNP–LNP complexes edit a variety of cell types and induce homology-directed repair in cells receiving codelivered single-stranded DNA templates. Using tissue-selective LNP formulations, we observe genome-editing levels of 16‒37% in the liver and lungs of reporter mice that receive single intravenous injections of iGeoCas9 RNP–LNPs. In addition, iGeoCas9 RNPs complexed to biodegradable LNPs edit the disease-causing <i>SFTPC</i> gene in lung tissue with 19% average efficiency, representing a major improvement over genome-editing levels observed previously using viral or nonviral delivery strategies. These results show that thermostable Cas9 RNP–LNP complexes can expand the therapeutic potential of genome editing.</p>","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"31 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142440260","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}
{"title":"People","authors":"","doi":"10.1038/s41587-024-02421-x","DOIUrl":"10.1038/s41587-024-02421-x","url":null,"abstract":"Recent moves of note in and around the biotech and pharma industries.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"42 10","pages":"1622-1622"},"PeriodicalIF":33.1,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142431541","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}
Maima Matin, Dalibor Hrg, Olena Litvinova, Małgorzata Łysek-Gładysinska, Agnieszka Wierzbicka, Jarosław Olav Horbańczuk, Artur Jóźwik, Atanas G. Atanasov
{"title":"The global patent landscape of functional food innovation","authors":"Maima Matin, Dalibor Hrg, Olena Litvinova, Małgorzata Łysek-Gładysinska, Agnieszka Wierzbicka, Jarosław Olav Horbańczuk, Artur Jóźwik, Atanas G. Atanasov","doi":"10.1038/s41587-024-02410-0","DOIUrl":"10.1038/s41587-024-02410-0","url":null,"abstract":"An analysis of patent documents reveals a trend of increasing interest in functional food innovations that may aid future decision-making in research, business and policymaking.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"42 10","pages":"1493-1497"},"PeriodicalIF":33.1,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142431545","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}
{"title":"The European Innovation Council supports innovative portfolios in health biotech","authors":"Iordanis Arzimanoglou","doi":"10.1038/s41587-024-02416-8","DOIUrl":"10.1038/s41587-024-02416-8","url":null,"abstract":"The European Innovation Council aims to catalyze the formation and growth of science-based businesses in Europe through highly targeted initiatives, actively managed innovative portfolios and a stepped funding pathway of grants and equity investment.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"42 10","pages":"1488-1492"},"PeriodicalIF":33.1,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142431544","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}
Victoria Bartek, Daria Ferro, Flaura Winston, Mark Kessel
{"title":"Accessible training for academic clinicians and researchers to address the need for academic entrepreneurs","authors":"Victoria Bartek, Daria Ferro, Flaura Winston, Mark Kessel","doi":"10.1038/s41587-024-02417-7","DOIUrl":"10.1038/s41587-024-02417-7","url":null,"abstract":"A short course in the fundamentals of academic entrepreneurship is a feasible way to train scientists and physicians from varied backgrounds and experience.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"42 10","pages":"1618-1620"},"PeriodicalIF":33.1,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41587-024-02417-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142431543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Biotech news from around the world","authors":"","doi":"10.1038/s41587-024-02436-4","DOIUrl":"10.1038/s41587-024-02436-4","url":null,"abstract":"","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"42 10","pages":"1480-1480"},"PeriodicalIF":33.1,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142431540","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}
{"title":"Editor’s pick: Switch Therapeutics","authors":"Iris Marchal","doi":"10.1038/s41587-024-02423-9","DOIUrl":"10.1038/s41587-024-02423-9","url":null,"abstract":"Each year, Nature Biotechnology highlights companies that have received sizeable early-stage funding in the previous year. Switch Therapeutics is rethinking cell-type specificity, building precision RNAi therapeutics for the brain.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"42 10","pages":"1486-1487"},"PeriodicalIF":33.1,"publicationDate":"2024-10-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142431460","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}