Cell genomics最新文献_第2页

Identification of novel type 1 and type 2 diabetes genes by co-localization of human islet eQTL and GWAS variants with colocRedRibbon. 人类胰岛eQTL和GWAS变异与colcredribbon共定位鉴定新型1型和2型糖尿病基因

IF 11.1

Cell genomics Pub Date : 2025-09-16 DOI: 10.1016/j.xgen.2025.101004

Anthony Piron, Florian Szymczak, Lise Folon, Daniel J M Crouch, Theodora Papadopoulou, Maria Lytrivi, Yue Tong, Maria Inês Alvelos, Maikel L Colli, Xiaoyan Yi, Marcin L Pekalski, Konstantinos Hatzikotoulas, Alicia Huerta-Chagoya, Henry J Taylor, Matthieu Defrance, John A Todd, Décio L Eizirik, Josep M Mercader, Miriam Cnop

{"title":"Identification of novel type 1 and type 2 diabetes genes by co-localization of human islet eQTL and GWAS variants with colocRedRibbon.","authors":"Anthony Piron, Florian Szymczak, Lise Folon, Daniel J M Crouch, Theodora Papadopoulou, Maria Lytrivi, Yue Tong, Maria Inês Alvelos, Maikel L Colli, Xiaoyan Yi, Marcin L Pekalski, Konstantinos Hatzikotoulas, Alicia Huerta-Chagoya, Henry J Taylor, Matthieu Defrance, John A Todd, Décio L Eizirik, Josep M Mercader, Miriam Cnop","doi":"10.1016/j.xgen.2025.101004","DOIUrl":"https://doi.org/10.1016/j.xgen.2025.101004","url":null,"abstract":"Over 1,000 genetic variants have been associated with diabetes by genome-wide association studies (GWASs), but for most, their functional impact is unknown; only 7% alter gene expression in pancreatic islets in expression quantitative trait locus (eQTL) studies. To fill this gap, we developed a co-localization pipeline, colocRedRibbon, that prefilters eQTLs by the direction of effect on gene expression and shortlists overlapping eQTL and GWAS variants prior to co-localization. Applying colocRedRibbon to recent diabetes and glycemic trait GWASs, we identified 292 co-localizing gene regions, including 24 co-localizations for type 1 diabetes and 268 for type 2 diabetes and glycemic traits, representing a 4-fold increase. A low-frequency type 2 diabetes protective variant increases islet MYO5C expression, and a type 1 diabetes protective variant increases FUT2 expression. These novel co-localizations advance the understanding of diabetes genetics and its impact on human islet biology. colocRedRibbon has broad applicability to co-localize GWASs and various QTLs.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"101004"},"PeriodicalIF":11.1,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145082523","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

3D chromatin structures precede genome activation in Drosophila embryogenesis. 三维染色质结构先于基因组激活在果蝇胚胎发生。

IF 11.1

Cell genomics Pub Date : 2025-09-15 DOI: 10.1016/j.xgen.2025.101002

Gabriel A Dolsten, Evan M Cofer, Xin Yang Bing, Benjamin Brack, Marcus Curlin, Chandra L Theesfeld, Olga G Troyanskaya, Michael S Levine, Yuri Pritykin

{"title":"3D chromatin structures precede genome activation in Drosophila embryogenesis.","authors":"Gabriel A Dolsten, Evan M Cofer, Xin Yang Bing, Benjamin Brack, Marcus Curlin, Chandra L Theesfeld, Olga G Troyanskaya, Michael S Levine, Yuri Pritykin","doi":"10.1016/j.xgen.2025.101002","DOIUrl":"10.1016/j.xgen.2025.101002","url":null,"abstract":"3D chromatin structure is critical for the regulation of gene expression during development. Here we used Micro-C assays at 100-bp resolution to map genome organization in Drosophila melanogaster throughout the first half of embryogenesis. These high-resolution contact maps reveal fine-scale features such as loops and boundaries delineating topologically associating domains. Notably, we observe that 3D chromatin structures form prior to zygotic genome activation and persist during successive mitotic cycles. Integrative analysis with 149 public chromatin immunoprecipitation sequencing (ChIP-seq) datasets identifies four classes of chromatin structuring elements, including a distinct group enriched for GAGA-associated factor (GAF) and Zelda binding, associated with developmental-gene regulation. These elements are mitotically retained and exhibit sequence and structure similarity between D. melanogaster and D. virilis. We propose that 3D chromatin organization in the pre-cellular embryo facilitates deployment of developmentally regulated genes during Drosophila embryogenesis.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"101002"},"PeriodicalIF":11.1,"publicationDate":"2025-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145076598","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

Ternary-code DNA methylation dynamics: A new era for scalable mapping. 三元代码DNA甲基化动力学：可扩展映射的新时代。

IF 11.1

Cell genomics Pub Date : 2025-09-10 DOI: 10.1016/j.xgen.2025.101006

Yubin Zhou, Yun Huang

引用次数: 0

Genetic history and adaptation of Eurasian wild boars inform livestock breeding. 欧亚野猪的遗传历史和适应性为家畜育种提供了信息。

IF 11.1

Cell genomics Pub Date : 2025-09-10 DOI: 10.1016/j.xgen.2025.101008

Ji Yang, Wen-Tian Wei, Meng-Hua Li

引用次数: 0

Exploring genetic adaptation and microbial dynamics in engineered anaerobic ecosystems via strain-level metagenomics. 通过菌株水平宏基因组学探索工程厌氧生态系统的遗传适应和微生物动力学。

IF 11.1

Cell genomics Pub Date : 2025-09-10 Epub Date: 2025-07-15 DOI: 10.1016/j.xgen.2025.100949

Gabriele Ghiotto, Aikaterini Xirostylidou, Maria Gaspari, Panagiotis G Kougias, Stefano Campanaro, Laura Treu

{"title":"Exploring genetic adaptation and microbial dynamics in engineered anaerobic ecosystems via strain-level metagenomics.","authors":"Gabriele Ghiotto, Aikaterini Xirostylidou, Maria Gaspari, Panagiotis G Kougias, Stefano Campanaro, Laura Treu","doi":"10.1016/j.xgen.2025.100949","DOIUrl":"10.1016/j.xgen.2025.100949","url":null,"abstract":"Genetic heterogeneity exists within all microbial populations, with sympatric cells of the same species often exhibiting single-nucleotide variations that influence phenotypic traits, including metabolic efficiency. However, the evolutionary dynamics of these strain-level differences in response to environmental stress remain poorly understood. Here, we present a first-of-its-kind study tracking the adaptive evolution of an anaerobic, carbon-fixing microbiota under a controlled engineered ecosystem focused on carbon dioxide bioconversion into methane. Leveraging strain-resolved metagenomics with an ad hoc variant calling and phasing approach, we mapped mutation trajectories and observed that the two dominant Methanothermobacter species maintained distinct sweeping haplotypes over time, most likely due to niche-specific metabolic roles. By combining population genetic statistics and peptide reconstruction, mer and mcrB genes emerged as potential drivers of archaeal strain-level competition. These findings pave the way for targeted engineering of microbial communities to enhance bioconversion efficiency, with significant implications for sustainable energy and carbon management in anaerobic systems.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100949"},"PeriodicalIF":11.1,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144651381","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

Human genetic variation reveals FCRL3 is a lymphocyte receptor for Yersinia pestis. 人类遗传变异显示FCRL3是鼠疫耶尔森菌的淋巴细胞受体。

IF 11.1

Cell genomics Pub Date : 2025-09-10 Epub Date: 2025-06-09 DOI: 10.1016/j.xgen.2025.100917

Rachel M Keener, Sam Shi, Trisha Dalapati, Liuyang Wang, Nicolás M Reinoso-Vizcaino, Micah A Luftig, Samuel I Miller, Timothy J Wilson, Dennis C Ko

引用次数: 0

Single-cell proteomics using mass spectrometry. 单细胞蛋白质组学使用质谱法。

IF 11.1

Cell genomics Pub Date : 2025-09-10 Epub Date: 2025-08-20 DOI: 10.1016/j.xgen.2025.100973

Amanda Momenzadeh, Jesse G Meyer

引用次数: 0

Landscape and m⁶A post-transcriptional regulation of soybean proteome. 大豆蛋白质组的景观和m6A转录后调控。

IF 11.1

Cell genomics Pub Date : 2025-09-10 Epub Date: 2025-07-07 DOI: 10.1016/j.xgen.2025.100926

Qing Yang, Zhi-Yang Hou, Linxia Li, Leili Wang, Shang-Tong Li, Yaping Li, Xuemin Zhang, Huanwei Huang, Yunzhuo Ke, Xiaofei Ma, Zexuan Wu, Zhi Liu, Xiaolei Shi, Chaofan Liu, Chen Meng, Hai Du, Mingxun Chen, Xiaofeng Gu, Zhe Yan, Faming Wang, Xiao Luo, Long Yan, Zhe Liang

引用次数: 0

The extracellular vesicle transcriptome provides tissue-specific functional genomic annotation relevant to disease susceptibility in obesity. 细胞外囊泡转录组提供了与肥胖疾病易感性相关的组织特异性功能基因组注释。

IF 11.1

Cell genomics Pub Date : 2025-09-10 Epub Date: 2025-07-15 DOI: 10.1016/j.xgen.2025.100925

Emeli Chatterjee, Michael J Betti, Quanhu Sheng, Phillip Lin, Margo P Emont, Guoping Li, Kaushik Amancherla, Marta Garcia-Contreras, Priyanka Gokulnath, Worawan B Limpitikul, Olivia Rosina Whittaker, Kathy Luong, Christopher Azzam, Denise Gee, Matthew Hutter, Karen Flanders, Parul Sahu, Charles R Flynn, Jonathan Brown, Danxia Yu, Evan D Rosen, Kendall Van-Keuren Jensen, Eric R Gamazon, Ravi Shah, Saumya Das

{"title":"The extracellular vesicle transcriptome provides tissue-specific functional genomic annotation relevant to disease susceptibility in obesity.","authors":"Emeli Chatterjee, Michael J Betti, Quanhu Sheng, Phillip Lin, Margo P Emont, Guoping Li, Kaushik Amancherla, Marta Garcia-Contreras, Priyanka Gokulnath, Worawan B Limpitikul, Olivia Rosina Whittaker, Kathy Luong, Christopher Azzam, Denise Gee, Matthew Hutter, Karen Flanders, Parul Sahu, Charles R Flynn, Jonathan Brown, Danxia Yu, Evan D Rosen, Kendall Van-Keuren Jensen, Eric R Gamazon, Ravi Shah, Saumya Das","doi":"10.1016/j.xgen.2025.100925","DOIUrl":"10.1016/j.xgen.2025.100925","url":null,"abstract":"We characterized circulating extracellular vesicles (EVs) in obese and lean humans, identifying transcriptional cargo differentially expressed in obesity (277 unique genes; false discovery rate < 10%). Since circulating EVs may have broad origin, we compared this obesity EV transcriptome with expression from human visceral-adipose-tissue-derived EVs from freshly collected and cultured biopsies from the same obese individuals, observing high concordance. Using a comprehensive set of adipose-specific epigenomic and chromatin conformation assays, we found that the differentially expressed transcripts from the EVs were those regulated in adipose by body mass index-associated SNPs (p < 5 × 10-8) from a large-scale genome-wide association study (GWAS). Using a phenome-wide association study of the regulatory SNPs for the EV-derived transcripts, we identified a substantial enrichment for inflammatory phenotypes, including type 2 diabetes. Collectively, these findings represent the convergence of the GWAS (genetics), epigenomics (transcript regulation), and EV (liquid biopsy) fields, enabling powerful future genomic studies of complex diseases.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100925"},"PeriodicalIF":11.1,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144651382","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

OmicsTweezer: A distribution-independent cell deconvolution model for multi-omics Data. OmicsTweezer：多组学数据的分布无关细胞反卷积模型。

IF 11.1

Cell genomics Pub Date : 2025-09-10 Epub Date: 2025-07-16 DOI: 10.1016/j.xgen.2025.100950

Xinxing Yang, Faming Zhao, Tao Ren, Canping Chen, Katelyn T Byrne, Alexey V Danilov, Rosalie C Sears, Peter S Nelson, Lisa M Coussens, Gordon B Mills, Zheng Xia

{"title":"OmicsTweezer: A distribution-independent cell deconvolution model for multi-omics Data.","authors":"Xinxing Yang, Faming Zhao, Tao Ren, Canping Chen, Katelyn T Byrne, Alexey V Danilov, Rosalie C Sears, Peter S Nelson, Lisa M Coussens, Gordon B Mills, Zheng Xia","doi":"10.1016/j.xgen.2025.100950","DOIUrl":"10.1016/j.xgen.2025.100950","url":null,"abstract":"Cell deconvolution estimates cell type proportions from bulk omics data, enabling insights into tissue microenvironments and disease. However, practical applications are often hindered by batch effects between bulk data and referenced single-cell data, a challenge that is frequently overlooked. To address this discrepancy, we developed OmicsTweezer, a distribution-independent cell deconvolution model. By integrating optimal transport with deep learning, OmicsTweezer aligns simulated and real data in a shared latent space, effectively mitigating data shifts and inter-omics distribution differences. OmicsTweezer is versatile, capable of deconvolving bulk RNA-seq, bulk proteomics, and spatial transcriptomics. Extensive evaluations on simulated and real-world datasets demonstrate its robustness and accuracy. Furthermore, applications in prostate and colon cancer showcase OmicsTweezer's ability to identify biologically meaningful cell types. As a unified deconvolution framework for multi-omics data, OmicsTweezer offers an efficient and powerful tool for studying disease microenvironments.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100950"},"PeriodicalIF":11.1,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144661143","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