Cell genomics最新文献_第10页

Cell type and dynamic state govern genetic regulation of gene expression in heterogeneous differentiating cultures. 在异质分化培养中，细胞类型和动态状态控制着基因表达的遗传调控。

IF 11.1

Cell genomics Pub Date : 2024-12-11 Epub Date: 2024-12-02 DOI: 10.1016/j.xgen.2024.100701

Joshua M Popp, Katherine Rhodes, Radhika Jangi, Mingyuan Li, Kenneth Barr, Karl Tayeb, Alexis Battle, Yoav Gilad

引用次数: 0

Genome-wide chromosome architecture prediction reveals biophysical principles underlying gene structure. 全基因组染色体结构预测揭示了基因结构的生物物理原理。

IF 11.1

Cell genomics Pub Date : 2024-12-11 Epub Date: 2024-11-25 DOI: 10.1016/j.xgen.2024.100698

Michael Chiang, Chris A Brackley, Catherine Naughton, Ryu-Suke Nozawa, Cleis Battaglia, Davide Marenduzzo, Nick Gilbert

{"title":"Genome-wide chromosome architecture prediction reveals biophysical principles underlying gene structure.","authors":"Michael Chiang, Chris A Brackley, Catherine Naughton, Ryu-Suke Nozawa, Cleis Battaglia, Davide Marenduzzo, Nick Gilbert","doi":"10.1016/j.xgen.2024.100698","DOIUrl":"10.1016/j.xgen.2024.100698","url":null,"abstract":"Classical observations suggest a connection between 3D gene structure and function, but testing this hypothesis has been challenging due to technical limitations. To explore this, we developed epigenetic highly predictive heteromorphic polymer (e-HiP-HoP), a model based on genome organization principles to predict the 3D structure of human chromatin. We defined a new 3D structural unit, a \"topos,\" which represents the regulatory landscape around gene promoters. Using GM12878 cells, we predicted the 3D structure of over 10,000 active gene topoi and stored them in the 3DGene database. Data mining revealed folding motifs and their link to Gene Ontology features. We computed a structural diversity score and identified influential nodes-chromatin sites that frequently interact with gene promoters, acting as key regulators. These nodes drive structural diversity and are tied to gene function. e-HiP-HoP provides a framework for modeling high-resolution chromatin structure and a mechanistic basis for chromatin contact networks that link 3D gene structure with function.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100698"},"PeriodicalIF":11.1,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142735179","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

A combined deep learning framework for mammalian m6A site prediction. 哺乳动物 m6A 位点预测的深度学习组合框架。

IF 11.1

Cell genomics Pub Date : 2024-12-11 Epub Date: 2024-11-20 DOI: 10.1016/j.xgen.2024.100697

Rui Fan, Chunmei Cui, Boming Kang, Zecheng Chang, Guoqing Wang, Qinghua Cui

引用次数: 0

Effects of gene dosage on cognitive ability: A function-based association study across brain and non-brain processes. 基因剂量对认知能力的影响：一项基于功能的脑和非脑过程关联研究。

IF 11.1

Cell genomics Pub Date : 2024-12-11 DOI: 10.1016/j.xgen.2024.100721

Guillaume Huguet, Thomas Renne, Cécile Poulain, Alma Dubuc, Kuldeep Kumar, Sayeh Kazem, Worrawat Engchuan, Omar Shanta, Elise Douard, Catherine Proulx, Martineau Jean-Louis, Zohra Saci, Josephine Mollon, Laura M Schultz, Emma E M Knowles, Simon R Cox, David Porteous, Gail Davies, Paul Redmond, Sarah E Harris, Gunter Schumann, Guillaume Dumas, Aurélie Labbe, Zdenka Pausova, Tomas Paus, Stephen W Scherer, Jonathan Sebat, Laura Almasy, David C Glahn, Sébastien Jacquemont

{"title":"Effects of gene dosage on cognitive ability: A function-based association study across brain and non-brain processes.","authors":"Guillaume Huguet, Thomas Renne, Cécile Poulain, Alma Dubuc, Kuldeep Kumar, Sayeh Kazem, Worrawat Engchuan, Omar Shanta, Elise Douard, Catherine Proulx, Martineau Jean-Louis, Zohra Saci, Josephine Mollon, Laura M Schultz, Emma E M Knowles, Simon R Cox, David Porteous, Gail Davies, Paul Redmond, Sarah E Harris, Gunter Schumann, Guillaume Dumas, Aurélie Labbe, Zdenka Pausova, Tomas Paus, Stephen W Scherer, Jonathan Sebat, Laura Almasy, David C Glahn, Sébastien Jacquemont","doi":"10.1016/j.xgen.2024.100721","DOIUrl":"10.1016/j.xgen.2024.100721","url":null,"abstract":"Copy-number variants (CNVs) that increase the risk for neurodevelopmental disorders also affect cognitive ability. However, such CNVs remain challenging to study due to their scarcity, limiting our understanding of gene-dosage-sensitive biological processes linked to cognitive ability. We performed a genome-wide association study (GWAS) in 258,292 individuals, which identified-for the first time-a duplication at 2q12.3 associated with higher cognitive performance. We developed a functional-burden analysis, which tested the association between cognition and CNVs disrupting 6,502 gene sets biologically defined across tissues, cell types, and ontologies. Among those, 864 gene sets were associated with cognition, and effect sizes of deletion and duplication were negatively correlated. The latter suggested that functions across all biological processes were sensitive to either deletions (e.g., subcortical regions, postsynaptic) or duplications (e.g., cerebral cortex, presynaptic). Associations between non-brain tissues and cognition were driven partly by constrained genes, which may shed light on medical comorbidities in neurodevelopmental disorders.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":"4 12","pages":"100721"},"PeriodicalIF":11.1,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11701252/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142820147","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

Deciphering proteins in Alzheimer's disease: A new Mendelian randomization method integrated with AlphaFold3 for 3D structure prediction. 解码阿尔茨海默病中的蛋白质：一种新的孟德尔随机化方法与AlphaFold3相结合，用于3D结构预测。

IF 11.1

Cell genomics Pub Date : 2024-12-11 Epub Date: 2024-12-04 DOI: 10.1016/j.xgen.2024.100700

Minhao Yao, Gary W Miller, Badri N Vardarajan, Andrea A Baccarelli, Zijian Guo, Zhonghua Liu

{"title":"Deciphering proteins in Alzheimer's disease: A new Mendelian randomization method integrated with AlphaFold3 for 3D structure prediction.","authors":"Minhao Yao, Gary W Miller, Badri N Vardarajan, Andrea A Baccarelli, Zijian Guo, Zhonghua Liu","doi":"10.1016/j.xgen.2024.100700","DOIUrl":"10.1016/j.xgen.2024.100700","url":null,"abstract":"Hidden confounding biases hinder identifying causal protein biomarkers for Alzheimer's disease in non-randomized studies. While Mendelian randomization (MR) can mitigate these biases using protein quantitative trait loci (pQTLs) as instrumental variables, some pQTLs violate core assumptions, leading to biased conclusions. To address this, we propose MR-SPI, a novel MR method that selects valid pQTL instruments using Leo Tolstoy's Anna Karenina principle and performs robust post-selection inference. Integrating MR-SPI with AlphaFold3, we developed a computational pipeline to identify causal protein biomarkers and predict 3D structural changes. Applied to genome-wide proteomics data from 54,306 UK Biobank participants and 455,258 subjects (71,880 cases and 383,378 controls) for a genome-wide association study of Alzheimer's disease, we identified seven proteins (TREM2, PILRB, PILRA, EPHA1, CD33, RET, and CD55) with structural alterations due to missense mutations. These findings offer insights into the etiology and potential drug targets for Alzheimer's disease.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100700"},"PeriodicalIF":11.1,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142787878","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

scTrends: A living review of commercial single-cell and spatial 'omic technologies. scTrends：商业单细胞和空间'omic'技术的动态回顾。

IF 11.1

Cell genomics Pub Date : 2024-12-11 DOI: 10.1016/j.xgen.2024.100723

Joachim De Jonghe, James W Opzoomer, Amaia Vilas-Zornoza, Benedikt S Nilges, Peter Crane, Marco Vicari, Hower Lee, David Lara-Astiaso, Torsten Gross, Jörg Morf, Kim Schneider, Juliana Cudini, Lorenzo Ramos-Mucci, Dylan Mooijman, Katarína Tiklová, Sergio Marco Salas, Christoffer Mattsson Langseth, Nachiket D Kashikar, Denis Schapiro, Joakim Lundeberg, Mats Nilsson, Alex K Shalek, Adam P Cribbs, Jake P Taylor-King

{"title":"scTrends: A living review of commercial single-cell and spatial 'omic technologies.","authors":"Joachim De Jonghe, James W Opzoomer, Amaia Vilas-Zornoza, Benedikt S Nilges, Peter Crane, Marco Vicari, Hower Lee, David Lara-Astiaso, Torsten Gross, Jörg Morf, Kim Schneider, Juliana Cudini, Lorenzo Ramos-Mucci, Dylan Mooijman, Katarína Tiklová, Sergio Marco Salas, Christoffer Mattsson Langseth, Nachiket D Kashikar, Denis Schapiro, Joakim Lundeberg, Mats Nilsson, Alex K Shalek, Adam P Cribbs, Jake P Taylor-King","doi":"10.1016/j.xgen.2024.100723","DOIUrl":"10.1016/j.xgen.2024.100723","url":null,"abstract":"Understanding the rapidly evolving landscape of single-cell and spatial omic technologies is crucial for advancing biomedical research and drug development. We provide a living review of both mature and emerging commercial platforms, highlighting key methodologies and trends shaping the field. This review spans from foundational single-cell technologies such as microfluidics and plate-based methods to newer approaches like combinatorial indexing; on the spatial side, we consider next-generation sequencing and imaging-based spatial transcriptomics. Finally, we highlight emerging methodologies that may fundamentally expand the scope for data generation within pharmaceutical research, creating opportunities to discover and validate novel drug mechanisms. Overall, this review serves as a critical resource for navigating the commercialization and application of single-cell and spatial omic technologies in pharmaceutical and academic research.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":"4 12","pages":"100723"},"PeriodicalIF":11.1,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11701258/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142820152","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

Single-nucleus multi-omics analyses reveal cellular and molecular innovations in the anterior cingulate cortex during primate evolution. 单核多组学分析揭示了灵长类动物进化过程中前扣带皮层的细胞和分子创新。

IF 11.1

Cell genomics Pub Date : 2024-12-11 Epub Date: 2024-12-03 DOI: 10.1016/j.xgen.2024.100703

Jiamiao Yuan, Kangning Dong, Haixu Wu, Xuerui Zeng, Xingyan Liu, Yan Liu, Jiapei Dai, Jichao Yin, Yongjie Chen, Yongbo Guo, Wenhao Luo, Na Liu, Yan Sun, Shihua Zhang, Bing Su

{"title":"Single-nucleus multi-omics analyses reveal cellular and molecular innovations in the anterior cingulate cortex during primate evolution.","authors":"Jiamiao Yuan, Kangning Dong, Haixu Wu, Xuerui Zeng, Xingyan Liu, Yan Liu, Jiapei Dai, Jichao Yin, Yongjie Chen, Yongbo Guo, Wenhao Luo, Na Liu, Yan Sun, Shihua Zhang, Bing Su","doi":"10.1016/j.xgen.2024.100703","DOIUrl":"10.1016/j.xgen.2024.100703","url":null,"abstract":"The anterior cingulate cortex (ACC) of the human brain is involved in higher-level cognitive functions such as emotion and self-awareness. We generated profiles of human and macaque ACC gene expression and chromatin accessibility at single-nucleus resolution. We characterized the conserved patterns of gene expression, chromatin accessibility, and transcription factor binding in different cell types. Combining the published mouse data, we discovered the molecular identities and cell-lineage origin of the primate von Economo neurons (VENs). Our in vitro and in vivo experiments identified a group of primate-shared and human-specific VEN marker genes, such as PCSK6, ADAMTSL3, and CDHR3, potentially contributing to VEN morphogenesis. We demonstrated that the human-specific sequence changes account for the cellular and functional innovations in the ACC during primate evolution and human origin. These findings provide new insights into understanding the cellular composition and molecular regulation of ACC and its evolutionary role in shaping human-owned higher cognitive skills.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100703"},"PeriodicalIF":11.1,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142781866","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

AI techniques have facilitated the understanding of epitranscriptome distribution. 人工智能技术有助于了解表观转录组的分布。

IF 11.1

Cell genomics Pub Date : 2024-12-11 DOI: 10.1016/j.xgen.2024.100718

Daiyun Huang, Jia Meng, Kunqi Chen

引用次数: 0

Adult single-nucleus neuronal transcriptomes of insulin signaling mutants reveal regulators of behavior and learning. 胰岛素信号突变体的成人单核神经元转录组揭示了行为和学习的调节因子。

IF 11.1

Cell genomics Pub Date : 2024-12-11 Epub Date: 2024-12-04 DOI: 10.1016/j.xgen.2024.100720

Jonathan St Ange, Yifei Weng, Rachel Kaletsky, Morgan E Stevenson, Rebecca S Moore, Shiyi Zhou, Coleen T Murphy

{"title":"Adult single-nucleus neuronal transcriptomes of insulin signaling mutants reveal regulators of behavior and learning.","authors":"Jonathan St Ange, Yifei Weng, Rachel Kaletsky, Morgan E Stevenson, Rebecca S Moore, Shiyi Zhou, Coleen T Murphy","doi":"10.1016/j.xgen.2024.100720","DOIUrl":"10.1016/j.xgen.2024.100720","url":null,"abstract":"Gene expression in individual neurons can change during development to adulthood and can have large effects on behavior. Additionally, the insulin/insulin-like signaling (IIS) pathway regulates many of the adult functions of Caenorhabditis elegans, including learning and memory, via transcriptional changes. We used the deep resolution of single-nucleus RNA sequencing to define the adult transcriptome of each neuron in wild-type and daf-2 mutants, revealing expression differences between L4 larval and adult neurons in chemoreceptors, synaptic genes, and learning/memory genes. We used these data to identify adult new AWC-specific regulators of chemosensory function that emerge upon adulthood. daf-2 gene expression changes correlate with improved cognitive functions, particularly in the AWC sensory neuron that controls learning and associative memory; behavioral assays of AWC-specific daf-2 genes revealed their roles in cognitive function. Combining technology and functional validation, we identified conserved genes that function in specific adult neurons to control behavior, including learning and memory.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100720"},"PeriodicalIF":11.1,"publicationDate":"2024-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142787866","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

Characterizing the genetic architecture of drug response using gene-context interaction methods. 利用基因-环境相互作用方法表征药物反应的遗传结构。

IF 11.1

Cell genomics Pub Date : 2024-12-11 Epub Date: 2024-12-04 DOI: 10.1016/j.xgen.2024.100722

Michal Sadowski, Mike Thompson, Joel Mefford, Tanushree Haldar, Akinyemi Oni-Orisan, Richard Border, Ali Pazokitoroudi, Na Cai, Julien F Ayroles, Sriram Sankararaman, Andy W Dahl, Noah Zaitlen

引用次数: 0