Pub Date : 2023-09-12DOI: 10.1038/s41587-023-01941-2
Recent moves of note in and around the biotech and pharma industries.
近期生物技术和制药行业及其周边值得关注的动向。
{"title":"People","authors":"","doi":"10.1038/s41587-023-01941-2","DOIUrl":"10.1038/s41587-023-01941-2","url":null,"abstract":"Recent moves of note in and around the biotech and pharma industries.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"41 9","pages":"1356-1356"},"PeriodicalIF":46.9,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10224683","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}
The COVID-19 pandemic brought mRNA vaccines to market in a short period, pointing the entire drug development field in the direction of mRNA treatment.
{"title":"The global patent landscape of mRNA for diagnosis and therapy","authors":"Mengru Lyu, Jiyuan Chen, Yeheng Peng, Fang Han, Luyao Gong, Jingfei Guo, Lijuan Tian, Yuan Gao","doi":"10.1038/s41587-023-01925-2","DOIUrl":"10.1038/s41587-023-01925-2","url":null,"abstract":"The COVID-19 pandemic brought mRNA vaccines to market in a short period, pointing the entire drug development field in the direction of mRNA treatment.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"41 9","pages":"1193-1199"},"PeriodicalIF":46.9,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10259489","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 : 2023-09-12DOI: 10.1038/s41587-023-01926-1
Julie Chuong
An expert in network dynamics and cell interactions describes her interdisciplinary background, creativity and building community in her lab during a pandemic.
{"title":"Five questions with Mor Nitzan","authors":"Julie Chuong","doi":"10.1038/s41587-023-01926-1","DOIUrl":"10.1038/s41587-023-01926-1","url":null,"abstract":"An expert in network dynamics and cell interactions describes her interdisciplinary background, creativity and building community in her lab during a pandemic.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"41 9","pages":"1355-1355"},"PeriodicalIF":46.9,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10233787","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 : 2023-09-12DOI: 10.1038/s41587-023-01933-2
Abdoallah Sharaf, Charlotte C. Ndiribe, Taiwo Crossby Omotoriogun, Linelle Abueg, Bouabid Badaoui, Fatu J. Badiane Markey, Girish Beedessee, Diaga Diouf, Vincent C. Duru, Chukwuike Ebuzome, Samuel C. Eziuzor, Yasmina Jaufeerally Fakim, Giulio Formenti, Nidhal Ghanmi, Fatma Zahra Guerfali, Isidore Houaga, Justin Eze Ideozu, Sally Mueni Katee, Slimane Khayi, Josiah O. Kuja, Emmanuel Hala Kwon-Ndung, Rose A. Marks, Acclaim M. Moila, Zahra Mungloo-Dilmohamud, Sadik Muzemil, Helen Nigussie, Julian O. Osuji, Verena Ras, Yves H. Tchiechoua, Yedomon Ange Bovys Zoclanclounon, Krystal A. Tolley, Cathrine Ziyomo, Ntanganedzeni Mapholi, Anne W. T. Muigai, Appolinaire Djikeng, ThankGod Echezona Ebenezer
The Open Institute of the African BioGenome Project empowers African scientists and institutions with the skill sets, capacity and infrastructure to advance scientific knowledge and innovation and drive economic growth.
{"title":"Bridging the gap in African biodiversity genomics and bioinformatics","authors":"Abdoallah Sharaf, Charlotte C. Ndiribe, Taiwo Crossby Omotoriogun, Linelle Abueg, Bouabid Badaoui, Fatu J. Badiane Markey, Girish Beedessee, Diaga Diouf, Vincent C. Duru, Chukwuike Ebuzome, Samuel C. Eziuzor, Yasmina Jaufeerally Fakim, Giulio Formenti, Nidhal Ghanmi, Fatma Zahra Guerfali, Isidore Houaga, Justin Eze Ideozu, Sally Mueni Katee, Slimane Khayi, Josiah O. Kuja, Emmanuel Hala Kwon-Ndung, Rose A. Marks, Acclaim M. Moila, Zahra Mungloo-Dilmohamud, Sadik Muzemil, Helen Nigussie, Julian O. Osuji, Verena Ras, Yves H. Tchiechoua, Yedomon Ange Bovys Zoclanclounon, Krystal A. Tolley, Cathrine Ziyomo, Ntanganedzeni Mapholi, Anne W. T. Muigai, Appolinaire Djikeng, ThankGod Echezona Ebenezer","doi":"10.1038/s41587-023-01933-2","DOIUrl":"10.1038/s41587-023-01933-2","url":null,"abstract":"The Open Institute of the African BioGenome Project empowers African scientists and institutions with the skill sets, capacity and infrastructure to advance scientific knowledge and innovation and drive economic growth.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"41 9","pages":"1348-1354"},"PeriodicalIF":46.9,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10233793","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 : 2023-09-12DOI: 10.1038/s41587-023-01968-5
Cell lines from human samples have historically benefitted scientific research but continue to raise questions about consent.
从人体样本中提取的细胞系历来有益于科学研究，但也不断引发有关同意与否的问题。
{"title":"When are your cells no longer your own?","authors":"","doi":"10.1038/s41587-023-01968-5","DOIUrl":"10.1038/s41587-023-01968-5","url":null,"abstract":"Cell lines from human samples have historically benefitted scientific research but continue to raise questions about consent.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"41 9","pages":"1177-1177"},"PeriodicalIF":46.9,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41587-023-01968-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10233794","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}
Pub Date : 2023-09-11DOI: 10.1038/s41587-023-01930-5
BugSigDB is a community-editable wiki that harmonizes how key microbial differential abundance methods and results are reported, identifying rare and common patterns across the literature of published host-associated microbiome studies.
{"title":"BugSigDB — a database for identifying unusual abundance patterns in human microbiome studies","authors":"","doi":"10.1038/s41587-023-01930-5","DOIUrl":"10.1038/s41587-023-01930-5","url":null,"abstract":"BugSigDB is a community-editable wiki that harmonizes how key microbial differential abundance methods and results are reported, identifying rare and common patterns across the literature of published host-associated microbiome studies.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"42 5","pages":"708-709"},"PeriodicalIF":46.9,"publicationDate":"2023-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10212108","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 : 2023-09-11DOI: 10.1038/s41587-023-01872-y
Ludwig Geistlinger, Chloe Mirzayi, Fatima Zohra, Rimsha Azhar, Shaimaa Elsafoury, Clare Grieve, Jennifer Wokaty, Samuel David Gamboa-Tuz, Pratyay Sengupta, Issac Hecht, Aarthi Ravikrishnan, Rafael S. Gonçalves, Eric Franzosa, Karthik Raman, Vincent Carey, Jennifer B. Dowd, Heidi E. Jones, Sean Davis, Nicola Segata, Curtis Huttenhower, Levi Waldron
The literature of human and other host-associated microbiome studies is expanding rapidly, but systematic comparisons among published results of host-associated microbiome signatures of differential abundance remain difficult. We present BugSigDB, a community-editable database of manually curated microbial signatures from published differential abundance studies accompanied by information on study geography, health outcomes, host body site and experimental, epidemiological and statistical methods using controlled vocabulary. The initial release of the database contains >2,500 manually curated signatures from >600 published studies on three host species, enabling high-throughput analysis of signature similarity, taxon enrichment, co-occurrence and coexclusion and consensus signatures. These data allow assessment of microbiome differential abundance within and across experimental conditions, environments or body sites. Database-wide analysis reveals experimental conditions with the highest level of consistency in signatures reported by independent studies and identifies commonalities among disease-associated signatures, including frequent introgression of oral pathobionts into the gut. A database of microbial signatures is used for systematic comparison of differential abundance patterns.
{"title":"BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures","authors":"Ludwig Geistlinger, Chloe Mirzayi, Fatima Zohra, Rimsha Azhar, Shaimaa Elsafoury, Clare Grieve, Jennifer Wokaty, Samuel David Gamboa-Tuz, Pratyay Sengupta, Issac Hecht, Aarthi Ravikrishnan, Rafael S. Gonçalves, Eric Franzosa, Karthik Raman, Vincent Carey, Jennifer B. Dowd, Heidi E. Jones, Sean Davis, Nicola Segata, Curtis Huttenhower, Levi Waldron","doi":"10.1038/s41587-023-01872-y","DOIUrl":"10.1038/s41587-023-01872-y","url":null,"abstract":"The literature of human and other host-associated microbiome studies is expanding rapidly, but systematic comparisons among published results of host-associated microbiome signatures of differential abundance remain difficult. We present BugSigDB, a community-editable database of manually curated microbial signatures from published differential abundance studies accompanied by information on study geography, health outcomes, host body site and experimental, epidemiological and statistical methods using controlled vocabulary. The initial release of the database contains >2,500 manually curated signatures from >600 published studies on three host species, enabling high-throughput analysis of signature similarity, taxon enrichment, co-occurrence and coexclusion and consensus signatures. These data allow assessment of microbiome differential abundance within and across experimental conditions, environments or body sites. Database-wide analysis reveals experimental conditions with the highest level of consistency in signatures reported by independent studies and identifies commonalities among disease-associated signatures, including frequent introgression of oral pathobionts into the gut. A database of microbial signatures is used for systematic comparison of differential abundance patterns.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"42 5","pages":"790-802"},"PeriodicalIF":46.9,"publicationDate":"2023-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11098749/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10212109","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}
Pub Date : 2023-09-11DOI: 10.1038/s41587-023-01949-8
Heon Seok Kim, Susan M. Grimes, Tianqi Chen, Anuja Sathe, Billy T. Lau, Gue-Ho Hwang, Sangsu Bae, Hanlee P. Ji
Genome sequencing studies have identified numerous cancer mutations across a wide spectrum of tumor types, but determining the phenotypic consequence of these mutations remains a challenge. Here, we developed a high-throughput, multiplexed single-cell technology called TISCC-seq to engineer predesignated mutations in cells using CRISPR base editors, directly delineate their genotype among individual cells and determine each mutation’s transcriptional phenotype. Long-read sequencing of the target gene’s transcript identifies the engineered mutations, and the transcriptome profile from the same set of cells is simultaneously analyzed by short-read sequencing. Through integration, we determine the mutations’ genotype and expression phenotype at single-cell resolution. Using cell lines, we engineer and evaluate the impact of >100 TP53 mutations on gene expression. Based on the single-cell gene expression, we classify the mutations as having a functionally significant phenotype. Engineered cancer mutations are linked with phenotypes in a multiplexed single-cell technology.
{"title":"Direct measurement of engineered cancer mutations and their transcriptional phenotypes in single cells","authors":"Heon Seok Kim, Susan M. Grimes, Tianqi Chen, Anuja Sathe, Billy T. Lau, Gue-Ho Hwang, Sangsu Bae, Hanlee P. Ji","doi":"10.1038/s41587-023-01949-8","DOIUrl":"10.1038/s41587-023-01949-8","url":null,"abstract":"Genome sequencing studies have identified numerous cancer mutations across a wide spectrum of tumor types, but determining the phenotypic consequence of these mutations remains a challenge. Here, we developed a high-throughput, multiplexed single-cell technology called TISCC-seq to engineer predesignated mutations in cells using CRISPR base editors, directly delineate their genotype among individual cells and determine each mutation’s transcriptional phenotype. Long-read sequencing of the target gene’s transcript identifies the engineered mutations, and the transcriptome profile from the same set of cells is simultaneously analyzed by short-read sequencing. Through integration, we determine the mutations’ genotype and expression phenotype at single-cell resolution. Using cell lines, we engineer and evaluate the impact of >100 TP53 mutations on gene expression. Based on the single-cell gene expression, we classify the mutations as having a functionally significant phenotype. Engineered cancer mutations are linked with phenotypes in a multiplexed single-cell technology.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"42 8","pages":"1254-1262"},"PeriodicalIF":33.1,"publicationDate":"2023-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41587-023-01949-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10212107","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}
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