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Topological velocity inference from spatial transcriptomic data 从空间转录组数据推断拓扑速度
IF 46.9 1区 生物学
Nature biotechnology Pub Date : 2025-07-16 DOI: 10.1038/s41587-025-02688-8
Yichen Gu, Jialin Liu, Kun H. Lee, Chen Li, Lu Lu, Jaimee Moline, Renxiang Guan, Joshua D. Welch
{"title":"Topological velocity inference from spatial transcriptomic data","authors":"Yichen Gu, Jialin Liu, Kun H. Lee, Chen Li, Lu Lu, Jaimee Moline, Renxiang Guan, Joshua D. Welch","doi":"10.1038/s41587-025-02688-8","DOIUrl":"https://doi.org/10.1038/s41587-025-02688-8","url":null,"abstract":"<p>Incorporating space and time into models of cell fate transition will be a key step toward characterizing how interactions among neighboring cells, local niche factors and cell migration contribute to tissue development. Here we propose Topological Velocity Inference (TopoVelo), a model for jointly inferring spatial and temporal dynamics of cell fate transition from spatial transcriptomic data. TopoVelo extends the RNA velocity framework to model single-cell gene expression dynamics of an entire tissue with spatially coupled differential equations. TopoVelo estimates cell velocity from developing mouse cerebral cortex, learns interpretable spatial cell state dependencies that correlate with the expression of ligand–receptor genes and reveals spatial signatures of mouse neural tube closure. Finally, we generate Slide-seq data from an in vitro model of human development and use TopoVelo to study the spatial patterns of early differentiation. Our work introduces a new dimension into the study of cell fate transitions and lays a foundation for modeling the collective dynamics of cells comprising an entire tissue.</p>","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"84 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144639830","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
Mapping cell fate transition in space and time 绘制细胞命运在空间和时间上的转变
IF 46.9 1区 生物学
Nature biotechnology Pub Date : 2025-07-16 DOI: 10.1038/s41587-025-02704-x
{"title":"Mapping cell fate transition in space and time","authors":"","doi":"10.1038/s41587-025-02704-x","DOIUrl":"https://doi.org/10.1038/s41587-025-02704-x","url":null,"abstract":"Cells in a tissue influence each other through physical and chemical cues as they differentiate to their final fates and migrate through space. A new technique integrates spatial transcriptomic data with the dynamics of RNA transcription and splicing across an entire tissue to model the directions of cell differentiation and migration.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"24 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144639828","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
Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper 利用SingleM和矶鹞对宏基因组数据中的微生物种类进行综合分类鉴定
IF 46.9 1区 生物学
Nature biotechnology Pub Date : 2025-07-16 DOI: 10.1038/s41587-025-02738-1
Ben J. Woodcroft, Samuel T. N. Aroney, Rossen Zhao, Mitchell Cunningham, Joshua A. M. Mitchell, Rizky Nurdiansyah, Linda Blackall, Gene W. Tyson
{"title":"Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper","authors":"Ben J. Woodcroft, Samuel T. N. Aroney, Rossen Zhao, Mitchell Cunningham, Joshua A. M. Mitchell, Rizky Nurdiansyah, Linda Blackall, Gene W. Tyson","doi":"10.1038/s41587-025-02738-1","DOIUrl":"https://doi.org/10.1038/s41587-025-02738-1","url":null,"abstract":"<p>Determining the taxonomy and relative abundance of microorganisms in metagenomic data remains technically challenging. Here we present ‘SingleM’, which estimates community composition using conserved regions within universal marker genes. By accurately incorporating species lacking genomic representation, we show that unknown species dominate in most environmental microbial communities. Our website ‘Sandpiper’ collates microbial community profiles from 248,559 publicly available metagenomes.</p>","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"669 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144639831","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
Clinical trials gain intelligence 临床试验获得智慧
IF 46.9 1区 生物学
Nature biotechnology Pub Date : 2025-07-15 DOI: 10.1038/s41587-025-02754-1
{"title":"Clinical trials gain intelligence","authors":"","doi":"10.1038/s41587-025-02754-1","DOIUrl":"https://doi.org/10.1038/s41587-025-02754-1","url":null,"abstract":"As governments around the world begin to embrace artificial intelligence in healthcare, clinical trials are entering a new phase — faster, smarter and more inclusive. With regulatory momentum building to adapt new technologies, artificial intelligence is no longer just a promise for the future but a powerful tool reshaping how trials are designed, conducted and analyzed today.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"94 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144629931","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
Biotech news from around the world 来自世界各地的生物技术新闻
IF 46.9 1区 生物学
Nature biotechnology Pub Date : 2025-07-15 DOI: 10.1038/s41587-025-02749-y
{"title":"Biotech news from around the world","authors":"","doi":"10.1038/s41587-025-02749-y","DOIUrl":"https://doi.org/10.1038/s41587-025-02749-y","url":null,"abstract":"<p>Poland launches its national hub for the Horizon Europe Mission to improve cancer diagnosis and treatment, the first of a planned network of hubs connecting all Horizon countries. The €725 million ($837 million), European Union-funded Horizon Cancer Mission will encourage cancer research with the goal of improving the lives of more three million people affected by cancer by 2030.</p><p>BioNTech announces a 10-year investment of up to £1 billion ($1.4 billion), one of the biggest investments in the history of UK life sciences, to fund new research and AI centers in London and Cambridge. The agreement, backed by up to £129 million ($176) in government support, forms part of thePlan for Change, the government’s mission to boost economic growth in every part of the country.</p>","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"670 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144630237","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
The strength and importance of government-funded patents for approved drugs 政府资助的药物专利的力量和重要性
IF 46.9 1区 生物学
Nature biotechnology Pub Date : 2025-07-15 DOI: 10.1038/s41587-025-02724-7
Sarah M. E. Gabriele, Matthew J. Martin, Aaron S. Kesselheim, S. Sean Tu
{"title":"The strength and importance of government-funded patents for approved drugs","authors":"Sarah M. E. Gabriele, Matthew J. Martin, Aaron S. Kesselheim, S. Sean Tu","doi":"10.1038/s41587-025-02724-7","DOIUrl":"https://doi.org/10.1038/s41587-025-02724-7","url":null,"abstract":"Understanding the strength and importance of US government-sponsored patents can help to limit high drug prices as well as constitute a justification to enact reasonable pricing clauses and exercise march-in rights.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"11 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144630141","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
Vascular organoids recover blood flow in vivo 类血管器官在体内恢复血液流动
IF 46.9 1区 生物学
Nature biotechnology Pub Date : 2025-07-15 DOI: 10.1038/s41587-025-02747-0
Iris Marchal
{"title":"Vascular organoids recover blood flow in vivo","authors":"Iris Marchal","doi":"10.1038/s41587-025-02747-0","DOIUrl":"https://doi.org/10.1038/s41587-025-02747-0","url":null,"abstract":"<p>Developing vascular organoids (VOs) that faithfully mimic human blood vessels is difficult because both endothelial and mural cells need to be co-differentiated and stably maintained in an organized structure. Existing models offer limited control over cellular composition and incomplete maturation. Now, in <i>Cell Stem Cell</i>, Gong et al. describe a protocol to generate functional VOs in 5 days that engraft in vivo, which provides potential clinical utility.</p><p>Building on previously developed protocols, the authors created VOs by transiently activating the transcription factors (TFs) ETV2 and NKX3.1 to enable the co-differentiation of an endothelial and a mural compartment from induced pluripotent stem cells. By expressing the TFs using chemically modified mRNA, the VOs could be produced without a genetic footprint. Although VOs did not need exogenous extracellular matrix to grow, embedding them in hydrogel led to enhanced vascular maturation that resulted in the formation of larger, structured vessels. Single-cell transcriptomics showed that VOs contained heterogeneous vascular cell populations, and changing the duration of TF activation could influence endothelial phenotypes.</p>","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"15 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144630240","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
A new impact framework for investors in life sciences bridges financial returns and patient outcomes 为生命科学投资者提供的一个新的影响框架将财务回报与患者结果联系起来
IF 46.9 1区 生物学
Nature biotechnology Pub Date : 2025-07-15 DOI: 10.1038/s41587-025-02726-5
Philip Brainin
{"title":"A new impact framework for investors in life sciences bridges financial returns and patient outcomes","authors":"Philip Brainin","doi":"10.1038/s41587-025-02726-5","DOIUrl":"https://doi.org/10.1038/s41587-025-02726-5","url":null,"abstract":"A new model for quantifying the impact of capital investments in life science interventions could help investors, policymakers and healthcare stakeholders to assess, monitor and optimize the societal impact of their investments.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"96 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144630294","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
De-extinction: debate continues around tech to ‘resurrect’ lost species 反灭绝：围绕技术“复活”灭绝物种的争论仍在继续
IF 46.9 1区 生物学
Nature biotechnology Pub Date : 2025-07-15 DOI: 10.1038/s41587-025-02745-2
{"title":"De-extinction: debate continues around tech to ‘resurrect’ lost species","authors":"","doi":"10.1038/s41587-025-02745-2","DOIUrl":"https://doi.org/10.1038/s41587-025-02745-2","url":null,"abstract":"Experts disagree about the extent to which hybrids based on dire wolves reflect the original extinct species, and the broader role of de-extinction technologies in ecosystem restoration.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"670 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144630289","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
Radiopharmaceuticals 放射性药物
IF 46.9 1区 生物学
Nature biotechnology Pub Date : 2025-07-15 DOI: 10.1038/s41587-025-02728-3
{"title":"Radiopharmaceuticals","authors":"","doi":"10.1038/s41587-025-02728-3","DOIUrl":"https://doi.org/10.1038/s41587-025-02728-3","url":null,"abstract":"Recent patents relating to radiopharmaceutical compositions, preparation methods and delivery systems.","PeriodicalId":19084,"journal":{"name":"Nature biotechnology","volume":"93 1","pages":""},"PeriodicalIF":46.9,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144630239","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
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