Cell genomics最新文献_第5页

Empowering integrative and collaborative exploration of single-cell and spatial multimodal data with SGS genome browser. 利用SGS基因组浏览器增强单细胞和空间多模态数据的整合和协作探索能力。

IF 11.1

Cell genomics Pub Date : 2025-05-14 Epub Date: 2025-04-14 DOI: 10.1016/j.xgen.2025.100848

Tingting Xia, Jiahe Sun, Yongjiang Luo, Hailong Guo, Yudi Mao, Ling Xu, Fang Lu, Yi Wang

{"title":"Empowering integrative and collaborative exploration of single-cell and spatial multimodal data with SGS genome browser.","authors":"Tingting Xia, Jiahe Sun, Yongjiang Luo, Hailong Guo, Yudi Mao, Ling Xu, Fang Lu, Yi Wang","doi":"10.1016/j.xgen.2025.100848","DOIUrl":"10.1016/j.xgen.2025.100848","url":null,"abstract":"Recent advancements in single-cell and spatial omics technologies have generated a large amount of complex, high-dimensional data, which poses significant challenges to visualization tools. We introduce SGS (single-cell and spatial genomics system), a user-friendly, collaborative, and versatile browser designed for visualizing single-cell and spatial multimodal data. SGS excels in the integrative visualization of complex multimodal data, offering an innovative genome browser, flexible visualization modes, and 3D spatially resolved transcriptomics (SRT) data visualization capabilities. Notably, SGS empowers users with advanced capabilities for comparative visualization through features like scCompare, scMultiView, and the dual-chromosome mode. It supports a variety of data formats and is compatible with established analysis tools, enabling collaborative data exploration and visualization without programming. Overall, SGS is a comprehensive browser that enables researchers to unlock novel insights from multimodal data.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100848"},"PeriodicalIF":11.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143324/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144042225","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

α2 adrenoceptors, cold-induced vasoconstriction, and Raynaud's phenomenon. α2肾上腺素受体、冷致血管收缩和雷诺现象。

IF 11.1

Cell genomics Pub Date : 2025-05-14 DOI: 10.1016/j.xgen.2025.100884

Nicholas A Flavahan

引用次数: 0

Perceptual and technical barriers in sharing and formatting metadata accompanying omics studies. 组学研究中共享和格式化元数据的感知和技术障碍。

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Cell genomics Pub Date : 2025-05-14 Epub Date: 2025-04-10 DOI: 10.1016/j.xgen.2025.100845

Yu-Ning Huang, Viorel Munteanu, Michael I Love, Cynthia Flaire Ronkowski, Dhrithi Deshpande, Annie Wong-Beringer, Russell Corbett-Detig, Mihai Dimian, Jason H Moore, Lana X Garmire, T B K Reddy, Atul J Butte, Mark D Robinson, Eleazar Eskin, Malak S Abedalthagafi, Serghei Mangul

{"title":"Perceptual and technical barriers in sharing and formatting metadata accompanying omics studies.","authors":"Yu-Ning Huang, Viorel Munteanu, Michael I Love, Cynthia Flaire Ronkowski, Dhrithi Deshpande, Annie Wong-Beringer, Russell Corbett-Detig, Mihai Dimian, Jason H Moore, Lana X Garmire, T B K Reddy, Atul J Butte, Mark D Robinson, Eleazar Eskin, Malak S Abedalthagafi, Serghei Mangul","doi":"10.1016/j.xgen.2025.100845","DOIUrl":"10.1016/j.xgen.2025.100845","url":null,"abstract":"Metadata, or \"data about data,\" is essential for organizing, understanding, and managing large-scale omics datasets. It enhances data discovery, integration, and interpretation, enabling reproducibility, reusability, and secondary analysis. However, metadata sharing remains hindered by perceptual and technical barriers, including the lack of uniform standards, privacy concerns, study design limitations, insufficient incentives, inadequate infrastructure, and a shortage of trained personnel. These challenges compromise data reliability and obstruct integrative meta-analyses. Addressing these issues requires standardization, education, stronger roles for journals and funding agencies, and improved incentives and infrastructure. Looking ahead, emerging technologies such as artificial intelligence and machine learning may offer promising solutions to automate metadata processes, increasing accuracy and scalability. Fostering a collaborative culture of metadata sharing will maximize the value of omics data, accelerating innovation and scientific discovery.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100845"},"PeriodicalIF":11.1,"publicationDate":"2025-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12143318/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144065378","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

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Integrative characterization of MYC RNA-binding function. MYC rna结合功能的综合表征。

IF 11.1

Cell genomics Pub Date : 2025-05-13 DOI: 10.1016/j.xgen.2025.100878

Sihan Li, Zehua Wang, Xiaofei Wang, Yifei Wang, Dhamotharan Pattarayan, Yu Zhang, Phuong Nguyen, Avishek Bhuniya, Yuang Chen, Haozhe Huang, Yixian Huang, Luxuan Wang, Junmei Wang, Song Li, Min Zhang, Yang Liu, Nara Lee, Da Yang

引用次数: 0

Systematic analysis of nonsense variants uncovers peptide release rate as a novel modifier of nonsense-mediated mRNA decay. 无义变异的系统分析揭示了肽释放率作为无义介导的mRNA衰变的新修饰因子。

IF 11.1

Cell genomics Pub Date : 2025-05-13 DOI: 10.1016/j.xgen.2025.100882

Divya Kolakada, Rui Fu, Nikita Biziaev, Alexey Shuvalov, Mlana Lore, Amy E Campbell, Michael A Cortázar, Marcin P Sajek, Jay R Hesselberth, Neelanjan Mukherjee, Elena Alkalaeva, Zeynep H Coban-Akdemir, Sujatha Jagannathan

{"title":"Systematic analysis of nonsense variants uncovers peptide release rate as a novel modifier of nonsense-mediated mRNA decay.","authors":"Divya Kolakada, Rui Fu, Nikita Biziaev, Alexey Shuvalov, Mlana Lore, Amy E Campbell, Michael A Cortázar, Marcin P Sajek, Jay R Hesselberth, Neelanjan Mukherjee, Elena Alkalaeva, Zeynep H Coban-Akdemir, Sujatha Jagannathan","doi":"10.1016/j.xgen.2025.100882","DOIUrl":"10.1016/j.xgen.2025.100882","url":null,"abstract":"The phenotypic impact of nonsense variants is determined by nonsense-mediated mRNA decay (NMD), which degrades transcripts with premature termination codons (PTCs). Despite the clinical importance of nonsense variants, transcript-specific and context-dependent variations in NMD activity remain poorly understood. Here, we show that the amino acid preceding the PTC strongly influences NMD activity. Glycine codons promote robust NMD efficiency and show striking enrichment before PTCs but are depleted before normal termination codons. Glycine-PTC enrichment is particularly pronounced in genes tolerant to loss-of-function variants, suggesting efficient elimination of truncated proteins from nonessential genes. We further demonstrate that the peptide release rate during translation termination is an important determinant of NMD activity. We propose a \"window of opportunity\" model where translation termination kinetics modulate NMD activity. By revealing how sequence context shapes NMD activity through translation termination dynamics, our findings provide a mechanistic framework for improved clinical interpretation of nonsense variants.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100882"},"PeriodicalIF":11.1,"publicationDate":"2025-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144112930","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Binding domain mutations provide insight into CTCF's relationship with chromatin and its contribution to gene regulation. 结合域突变提供了CTCF与染色质的关系及其对基因调控的贡献。

IF 11.1

Cell genomics Pub Date : 2025-04-09 Epub Date: 2025-03-20 DOI: 10.1016/j.xgen.2025.100813

Catherine Do, Guimei Jiang, Giulia Cova, Christos C Katsifis, Domenic N Narducci, Theodore Sakellaropoulos, Raphael Vidal, Priscillia Lhoumaud, Aristotelis Tsirigos, Faye Fara D Regis, Nata Kakabadze, Elphege P Nora, Marcus Noyes, Anders S Hansen, Jane A Skok

{"title":"Binding domain mutations provide insight into CTCF's relationship with chromatin and its contribution to gene regulation.","authors":"Catherine Do, Guimei Jiang, Giulia Cova, Christos C Katsifis, Domenic N Narducci, Theodore Sakellaropoulos, Raphael Vidal, Priscillia Lhoumaud, Aristotelis Tsirigos, Faye Fara D Regis, Nata Kakabadze, Elphege P Nora, Marcus Noyes, Anders S Hansen, Jane A Skok","doi":"10.1016/j.xgen.2025.100813","DOIUrl":"10.1016/j.xgen.2025.100813","url":null,"abstract":"Here we used a series of CTCF mutations to explore CTCF's relationship with chromatin and its contribution to gene regulation. CTCF's impact depends on the genomic context of bound sites and the unique binding properties of WT and mutant CTCF proteins. Specifically, CTCF's signal strength is linked to changes in accessibility, and the ability to block cohesin is linked to its binding stability. Multivariate modeling reveals that both CTCF and accessibility contribute independently to cohesin binding and insulation, but CTCF signal strength has a stronger effect. CTCF and chromatin have a bidirectional relationship such that at CTCF sites, accessibility is reduced in a cohesin-dependent, mutant-specific fashion. In addition, each mutant alters TF binding and accessibility in an indirect manner, changes which impart the most influence on rewiring transcriptional networks and the cell's ability to differentiate. Collectively, the mutant perturbations provide a rich resource for determining CTCF's site-specific effects.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100813"},"PeriodicalIF":11.1,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12008812/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143675086","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

High-throughput screening of human genetic variants by pooled prime editing. 利用聚合引物编辑技术高通量筛选人类遗传变异。

IF 11.1

Cell genomics Pub Date : 2025-04-09 Epub Date: 2025-03-21 DOI: 10.1016/j.xgen.2025.100814

Michael Herger, Christina M Kajba, Megan Buckley, Ana Cunha, Molly Strom, Gregory M Findlay

{"title":"High-throughput screening of human genetic variants by pooled prime editing.","authors":"Michael Herger, Christina M Kajba, Megan Buckley, Ana Cunha, Molly Strom, Gregory M Findlay","doi":"10.1016/j.xgen.2025.100814","DOIUrl":"10.1016/j.xgen.2025.100814","url":null,"abstract":"Multiplexed assays of variant effect (MAVEs) enable scalable functional assessment of human genetic variants. However, established MAVEs are limited by exogenous expression of variants or constraints of genome editing. Here, we introduce a pooled prime editing (PE) platform to scalably assay variants in their endogenous context. We first improve efficiency of PE in HAP1 cells, defining optimal prime editing guide RNA (pegRNA) designs and establishing enrichment of edited cells via co-selection. We next demonstrate negative selection screening by testing over 7,500 pegRNAs targeting SMARCB1 and observing depletion of efficiently installed loss-of-function (LoF) variants. We then screen for LoF variants in MLH1 via 6-thioguanine selection, testing 65.3% of all possible SNVs in a 200-bp region including exon 10 and 362 non-coding variants from ClinVar spanning a 60-kb region. The platform's overall accuracy for discriminating pathogenic variants indicates that it will be highly valuable for identifying new variants underlying diverse human phenotypes across large genomic regions.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100814"},"PeriodicalIF":11.1,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12008803/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143694606","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Cross-ancestry analyses of Chinese and European populations reveal insights into the genetic architecture and disease implication of metabolites. 中国和欧洲人群的跨祖先分析揭示了代谢物的遗传结构和疾病含义。

IF 11.1

Cell genomics Pub Date : 2025-04-09 Epub Date: 2025-03-20 DOI: 10.1016/j.xgen.2025.100810

Chenhao Lin, Mingfeng Xia, Yuxiang Dai, Qingxia Huang, Zhonghan Sun, Guoqing Zhang, Ruijin Luo, Qianqian Peng, Jinxi Li, Xiaofeng Wang, Huandong Lin, Xin Gao, Huiru Tang, Xia Shen, Sijia Wang, Li Jin, Xingjie Hao, Yan Zheng

{"title":"Cross-ancestry analyses of Chinese and European populations reveal insights into the genetic architecture and disease implication of metabolites.","authors":"Chenhao Lin, Mingfeng Xia, Yuxiang Dai, Qingxia Huang, Zhonghan Sun, Guoqing Zhang, Ruijin Luo, Qianqian Peng, Jinxi Li, Xiaofeng Wang, Huandong Lin, Xin Gao, Huiru Tang, Xia Shen, Sijia Wang, Li Jin, Xingjie Hao, Yan Zheng","doi":"10.1016/j.xgen.2025.100810","DOIUrl":"10.1016/j.xgen.2025.100810","url":null,"abstract":"Differential susceptibilities to various diseases and corresponding metabolite variations have been documented across diverse ethnic populations, but the genetic determinants of these disparities remain unclear. Here, we performed large-scale genome-wide association studies of 171 directly quantifiable metabolites from a nuclear magnetic resonance-based metabolomics platform in 10,792 Han Chinese individuals. We identified 15 variant-metabolite associations, eight of which were successfully replicated in an independent Chinese population (n = 4,480). By cross-ancestry meta-analysis integrating 213,397 European individuals from the UK Biobank, we identified 228 additional variant-metabolite associations and improved fine-mapping precision. Moreover, two-sample Mendelian randomization analyses revealed evidence that genetically predicted levels of triglycerides in high-density lipoprotein were associated with a higher risk of coronary artery disease and that of glycine with a lower risk of heart failure in both ancestries. These findings enhance our understanding of the shared and specific genetic architecture of metabolites as well as their roles in complex diseases across populations.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100810"},"PeriodicalIF":11.1,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12008806/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143675087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Proteome-wide assessment of differential missense variant clustering in neurodevelopmental disorders and cancer. 神经发育障碍和癌症中差异错义变异聚类的蛋白质组范围评估。

IF 11.1

Cell genomics Pub Date : 2025-04-09 Epub Date: 2025-03-11 DOI: 10.1016/j.xgen.2025.100807

Jeffrey K Ng, Yilin Chen, Titilope M Akinwe, Hillary B Heins, Elvisa Mehinovic, Yoonhoo Chang, David H Gutmann, Christina A Gurnett, Zachary L Payne, Juana G Manuel, Rachel Karchin, Tychele N Turner

{"title":"Proteome-wide assessment of differential missense variant clustering in neurodevelopmental disorders and cancer.","authors":"Jeffrey K Ng, Yilin Chen, Titilope M Akinwe, Hillary B Heins, Elvisa Mehinovic, Yoonhoo Chang, David H Gutmann, Christina A Gurnett, Zachary L Payne, Juana G Manuel, Rachel Karchin, Tychele N Turner","doi":"10.1016/j.xgen.2025.100807","DOIUrl":"10.1016/j.xgen.2025.100807","url":null,"abstract":"Prior studies examining genomic variants suggest that some proteins contribute to both neurodevelopmental disorders (NDDs) and cancer. While there are several potential etiologies, here, we hypothesize that missense variation in proteins occurs in different clustering patterns, resulting in distinct phenotypic outcomes. This concept was first explored in 1D protein space and expanded using 3D protein structure models. Missense de novo variants were examined from 39,883 families with NDDs and missense somatic variants from 10,543 sequenced tumors covering five The Cancer Genome Atlas (TCGA) cancer types and two Catalog of Somatic Mutations in Cancer (COSMIC) pan-cancer aggregates of tissue types. We find 18 proteins with differential missense variation clustering in NDDs compared to cancers and 19 in cancers relative to NDDs. These proteins may be important for detailed assessments in thinking of future prognostic and therapeutic applications. We establish a framework for interpreting missense patterns in NDDs and cancer, using advances in 3D protein structure prediction.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100807"},"PeriodicalIF":11.1,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12008811/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143617854","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Meet the author: Tychele N. Turner, PhD. 认识一下作者：Tychele N. Turner博士。

IF 11.1

Cell genomics Pub Date : 2025-04-09 DOI: 10.1016/j.xgen.2025.100843

Tychele N Turner

引用次数: 0