Cell genomics最新文献_第7页

A genome-wide association study of neonatal metabolites. 新生儿代谢物的全基因组关联研究。

IF 11.1

Cell genomics Pub Date : 2024-10-09 DOI: 10.1016/j.xgen.2024.100668

Quanze He, Hankui Liu, Lu Lu, Qin Zhang, Qi Wang, Benjing Wang, Xiaojuan Wu, Liping Guan, Jun Mao, Ying Xue, Chunhua Zhang, Xinye Cao, Yuxing He, Xiangwen Peng, Huanhuan Peng, Kangrong Zhao, Hong Li, Xin Jin, Lijian Zhao, Jianguo Zhang, Ting Wang

引用次数: 0

The hidden costs of aneuploidy: New insights from yeast. 非整倍体的隐性成本：来自酵母的新见解

IF 11.1

Cell genomics Pub Date : 2024-10-09 DOI: 10.1016/j.xgen.2024.100673

Yuerong Wang, Xian Fu, Yue Shen

引用次数: 0

Unlocking the genetic influence on milk variation and its potential implication for infant health. 揭示基因对牛奶变异的影响及其对婴儿健康的潜在影响。

IF 11.1

Cell genomics Pub Date : 2024-10-09 DOI: 10.1016/j.xgen.2024.100676

Claudia Nussbaum, Sarah Kim-Hellmuth

引用次数: 0

Genome-wide association study of maternal plasma metabolites during pregnancy. 孕期母体血浆代谢物的全基因组关联研究。

IF 11.1

Cell genomics Pub Date : 2024-10-09 DOI: 10.1016/j.xgen.2024.100657

Siyang Liu, Jilong Yao, Liang Lin, Xianmei Lan, Linlin Wu, Xuelian He, Nannan Kong, Yan Li, Yuqing Deng, Jiansheng Xie, Huanhuan Zhu, Xiaoxia Wu, Zilong Li, Likuan Xiong, Yuan Wang, Jinghui Ren, Xuemei Qiu, Weihua Zhao, Ya Gao, Yuanqing Chen, Fengxia Su, Yun Zhou, Weiqiao Rao, Jing Zhang, Guixue Hou, Liping Huang, Linxuan Li, Xinhong Liu, Chao Nie, Liqiong Luo, Mei Zhao, Zengyou Liu, Fang Chen, Shengmou Lin, Lijian Zhao, Qingmei Fu, Dan Jiang, Ye Yin, Xun Xu, Jian Wang, Huanming Yang, Rong Wang, Jianmin Niu, Fengxiang Wei, Xin Jin, Siqi Liu

{"title":"Genome-wide association study of maternal plasma metabolites during pregnancy.","authors":"Siyang Liu, Jilong Yao, Liang Lin, Xianmei Lan, Linlin Wu, Xuelian He, Nannan Kong, Yan Li, Yuqing Deng, Jiansheng Xie, Huanhuan Zhu, Xiaoxia Wu, Zilong Li, Likuan Xiong, Yuan Wang, Jinghui Ren, Xuemei Qiu, Weihua Zhao, Ya Gao, Yuanqing Chen, Fengxia Su, Yun Zhou, Weiqiao Rao, Jing Zhang, Guixue Hou, Liping Huang, Linxuan Li, Xinhong Liu, Chao Nie, Liqiong Luo, Mei Zhao, Zengyou Liu, Fang Chen, Shengmou Lin, Lijian Zhao, Qingmei Fu, Dan Jiang, Ye Yin, Xun Xu, Jian Wang, Huanming Yang, Rong Wang, Jianmin Niu, Fengxiang Wei, Xin Jin, Siqi Liu","doi":"10.1016/j.xgen.2024.100657","DOIUrl":"10.1016/j.xgen.2024.100657","url":null,"abstract":"Metabolites are key indicators of health and therapeutic targets, but their genetic underpinnings during pregnancy-a critical period for human reproduction-are largely unexplored. Using genetic data from non-invasive prenatal testing, we performed a genome-wide association study on 84 metabolites, including 37 amino acids, 24 elements, 13 hormones, and 10 vitamins, involving 34,394 pregnant Chinese women, with sample sizes ranging from 6,394 to 13,392 for specific metabolites. We identified 53 metabolite-gene associations, 23 of which are novel. Significant differences in genetic effects between pregnant and non-pregnant women were observed for 16.7%-100% of these associations, indicating gene-environment interactions. Additionally, 50.94% of genetic associations exhibited pleiotropy among metabolites and between six metabolites and eight pregnancy phenotypes. Mendelian randomization revealed potential causal relationships between seven maternal metabolites and 15 human traits and diseases. These findings provide new insights into the genetic basis of maternal plasma metabolites during pregnancy.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":"4 10","pages":"100657"},"PeriodicalIF":11.1,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11602615/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142402180","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

FUSE: Improving the estimation and imputation of variant impacts in functional screening. FUSE：改进功能筛选中变异影响的估计和估算。

IF 11.1

Cell genomics Pub Date : 2024-10-09 DOI: 10.1016/j.xgen.2024.100667

Tian Yu, James D Fife, Vineel Bhat, Ivan Adzhubey, Richard Sherwood, Christopher A Cassa

{"title":"FUSE: Improving the estimation and imputation of variant impacts in functional screening.","authors":"Tian Yu, James D Fife, Vineel Bhat, Ivan Adzhubey, Richard Sherwood, Christopher A Cassa","doi":"10.1016/j.xgen.2024.100667","DOIUrl":"10.1016/j.xgen.2024.100667","url":null,"abstract":"Deep mutational scanning enables high-throughput functional assessment of genetic variants. While phenotypic measurements from screening assays generally align with clinical outcomes, experimental noise may affect the accuracy of individual variant estimates. We developed the FUSE (functional substitution estimation) pipeline, which leverages measurements collectively within screening assays to improve the estimation of variant impacts. Drawing data from 115 published functional assays, FUSE assesses the mean functional effect per amino acid position and makes estimates for individual allelic variants. It enhances the correlation of variant functional effects from different assay platforms and increases the classification accuracy of missense variants in ClinVar across 29 genes (area under the receiver operating characteristic [ROC] curve [AUC] from 0.83 to 0.90). In UK Biobank patients with rare missense variants in BRCA1, LDLR, or TP53, FUSE improves the classification accuracy of associated phenotypes. FUSE can also impute variant effects for substitutions not experimentally screened. This approach improves accuracy and broadens the utility of data from functional screening.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":"4 10","pages":"100667"},"PeriodicalIF":11.1,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11602636/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142402203","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

Stable and robust Xi and Y transcriptomes drive cell-type-specific autosomal and Xa responses in vivo and in vitro in four human cell types. 在四种人类细胞类型中，稳定而强大的Xi和Y转录组在体内和体外驱动细胞类型特异的常染色体和Xa反应。

IF 11.1

Cell genomics Pub Date : 2024-09-11 Epub Date: 2024-08-06 DOI: 10.1016/j.xgen.2024.100628

Laura V Blanton, Adrianna K San Roman, Geryl Wood, Ashley Buscetta, Nicole Banks, Helen Skaletsky, Alexander K Godfrey, Thao T Pham, Jennifer F Hughes, Laura G Brown, Paul Kruszka, Angela E Lin, Daniel L Kastner, Maximilian Muenke, David C Page

{"title":"Stable and robust Xi and Y transcriptomes drive cell-type-specific autosomal and Xa responses in vivo and in vitro in four human cell types.","authors":"Laura V Blanton, Adrianna K San Roman, Geryl Wood, Ashley Buscetta, Nicole Banks, Helen Skaletsky, Alexander K Godfrey, Thao T Pham, Jennifer F Hughes, Laura G Brown, Paul Kruszka, Angela E Lin, Daniel L Kastner, Maximilian Muenke, David C Page","doi":"10.1016/j.xgen.2024.100628","DOIUrl":"10.1016/j.xgen.2024.100628","url":null,"abstract":"Recent in vitro studies of human sex chromosome aneuploidy showed that the Xi (\"inactive\" X) and Y chromosomes broadly modulate autosomal and Xa (\"active\" X) gene expression. We tested these findings in vivo. Linear modeling of CD4+ T cells and monocytes from individuals with one to three X chromosomes and zero to two Y chromosomes revealed 82 sex-chromosomal and 344 autosomal genes whose expression changed significantly with Xi and/or Y dosage in vivo. Changes in sex-chromosomal expression were remarkably constant in vivo and in vitro; autosomal responses to Xi and/or Y dosage were largely cell-type specific (∼2.6-fold more variation than sex-chromosomal responses). Targets of the sex-chromosomal transcription factors ZFX and ZFY accounted for a significant fraction of these autosomal responses both in vivo and in vitro. We conclude that the human Xi and Y transcriptomes are surprisingly robust and stable, yet they modulate autosomal and Xa genes in a cell-type-specific fashion.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100628"},"PeriodicalIF":11.1,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11480847/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141903762","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

ONCOLINER: A new solution for monitoring, improving, and harmonizing somatic variant calling across genomic oncology centers. ONCOLINER：用于监测、改进和协调各基因组肿瘤中心体细胞变异调用的新解决方案。

IF 11.1

Cell genomics Pub Date : 2024-09-11 Epub Date: 2024-08-30 DOI: 10.1016/j.xgen.2024.100639

Rodrigo Martín, Nicolás Gaitán, Frédéric Jarlier, Lars Feuerbach, Henri de Soyres, Marc Arbonés, Tom Gutman, Montserrat Puiggròs, Alvaro Ferriz, Asier Gonzalez, Lucía Estelles, Ivo Gut, Salvador Capella-Gutierrez, Lincoln D Stein, Benedikt Brors, Romina Royo, Philippe Hupé, David Torrents

{"title":"ONCOLINER: A new solution for monitoring, improving, and harmonizing somatic variant calling across genomic oncology centers.","authors":"Rodrigo Martín, Nicolás Gaitán, Frédéric Jarlier, Lars Feuerbach, Henri de Soyres, Marc Arbonés, Tom Gutman, Montserrat Puiggròs, Alvaro Ferriz, Asier Gonzalez, Lucía Estelles, Ivo Gut, Salvador Capella-Gutierrez, Lincoln D Stein, Benedikt Brors, Romina Royo, Philippe Hupé, David Torrents","doi":"10.1016/j.xgen.2024.100639","DOIUrl":"10.1016/j.xgen.2024.100639","url":null,"abstract":"The characterization of somatic genomic variation associated with the biology of tumors is fundamental for cancer research and personalized medicine, as it guides the reliability and impact of cancer studies and genomic-based decisions in clinical oncology. However, the quality and scope of tumor genome analysis across cancer research centers and hospitals are currently highly heterogeneous, limiting the consistency of tumor diagnoses across hospitals and the possibilities of data sharing and data integration across studies. With the aim of providing users with actionable and personalized recommendations for the overall enhancement and harmonization of somatic variant identification across research and clinical environments, we have developed ONCOLINER. Using specifically designed mosaic and tumorized genomes for the analysis of recall and precision across somatic SNVs, insertions or deletions (indels), and structural variants (SVs), we demonstrate that ONCOLINER is capable of improving and harmonizing genome analysis across three state-of-the-art variant discovery pipelines in genomic oncology.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100639"},"PeriodicalIF":11.1,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11480849/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142115578","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

Ribosomes unraveled: The path from variant to impact. 解开核糖体：从变异到影响的路径

IF 11.1

Cell genomics Pub Date : 2024-09-11 DOI: 10.1016/j.xgen.2024.100658

Paxton Kostos, Anna Galligos, Jennifer L Gerton

引用次数: 0

ABCA7-dependent induction of neuropeptide Y is required for synaptic resilience in Alzheimer's disease through BDNF/NGFR signaling. 通过 BDNF/NGFR 信号传导，ABCA7 依赖性诱导神经肽 Y 是阿尔茨海默病突触复原力所必需的。

IF 11.1

Cell genomics Pub Date : 2024-09-11 Epub Date: 2024-08-30 DOI: 10.1016/j.xgen.2024.100642

Hüseyin Tayran, Elanur Yilmaz, Prabesh Bhattarai, Yuhao Min, Xue Wang, Yiyi Ma, Ni Wang, Inyoung Jeong, Nastasia Nelson, Nada Kassara, Mehmet Ilyas Cosacak, Ruya Merve Dogru, Dolly Reyes-Dumeyer, Jakob Mørkved Stenersen, Joseph S Reddy, Min Qiao, Delaney Flaherty, Tamil Iniyan Gunasekaran, Zikun Yang, Nathalie Jurisch-Yaksi, Andrew F Teich, Takahisa Kanekiyo, Giuseppe Tosto, Badri N Vardarajan, Özkan İş, Nilüfer Ertekin-Taner, Richard Mayeux, Caghan Kizil

{"title":"ABCA7-dependent induction of neuropeptide Y is required for synaptic resilience in Alzheimer's disease through BDNF/NGFR signaling.","authors":"Hüseyin Tayran, Elanur Yilmaz, Prabesh Bhattarai, Yuhao Min, Xue Wang, Yiyi Ma, Ni Wang, Inyoung Jeong, Nastasia Nelson, Nada Kassara, Mehmet Ilyas Cosacak, Ruya Merve Dogru, Dolly Reyes-Dumeyer, Jakob Mørkved Stenersen, Joseph S Reddy, Min Qiao, Delaney Flaherty, Tamil Iniyan Gunasekaran, Zikun Yang, Nathalie Jurisch-Yaksi, Andrew F Teich, Takahisa Kanekiyo, Giuseppe Tosto, Badri N Vardarajan, Özkan İş, Nilüfer Ertekin-Taner, Richard Mayeux, Caghan Kizil","doi":"10.1016/j.xgen.2024.100642","DOIUrl":"10.1016/j.xgen.2024.100642","url":null,"abstract":"Genetic variants in ABCA7, an Alzheimer's disease (AD)-associated gene, elevate AD risk, yet its functional relevance to the etiology is unclear. We generated a CRISPR-Cas9-mediated abca7 knockout zebrafish to explore ABCA7's role in AD. Single-cell transcriptomics in heterozygous abca7+/- knockout combined with Aβ42 toxicity revealed that ABCA7 is crucial for neuropeptide Y (NPY), brain-derived neurotrophic factor (BDNF), and nerve growth factor receptor (NGFR) expressions, which are crucial for synaptic integrity, astroglial proliferation, and microglial prevalence. Impaired NPY induction decreased BDNF and synaptic density, which are rescuable with ectopic NPY. In induced pluripotent stem cell-derived human neurons exposed to Aβ42, ABCA7-/- suppresses NPY. Clinical data showed reduced NPY in AD correlated with elevated Braak stages, genetic variants in NPY associated with AD, and epigenetic changes in NPY, NGFR, and BDNF promoters linked to ABCA7 variants. Therefore, ABCA7-dependent NPY signaling via BDNF-NGFR maintains synaptic integrity, implicating its impairment in increased AD risk through reduced brain resilience.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":" ","pages":"100642"},"PeriodicalIF":11.1,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11480862/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142115575","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

Long genetic and social isolation in Neanderthals before their extinction. 尼安德特人灭绝前的长期遗传和社会隔离。

IF 11.1

Cell genomics Pub Date : 2024-09-11 DOI: 10.1016/j.xgen.2024.100593

Ludovic Slimak, Tharsika Vimala, Andaine Seguin-Orlando, Laure Metz, Clément Zanolli, Renaud Joannes-Boyau, Marine Frouin, Lee J Arnold, Martina Demuro, Thibaut Devièse, Daniel Comeskey, Michael Buckley, Hubert Camus, Xavier Muth, Jason E Lewis, Hervé Bocherens, Pascale Yvorra, Christophe Tenailleau, Benjamin Duployer, Hélène Coqueugniot, Olivier Dutour, Thomas Higham, Martin Sikora

{"title":"Long genetic and social isolation in Neanderthals before their extinction.","authors":"Ludovic Slimak, Tharsika Vimala, Andaine Seguin-Orlando, Laure Metz, Clément Zanolli, Renaud Joannes-Boyau, Marine Frouin, Lee J Arnold, Martina Demuro, Thibaut Devièse, Daniel Comeskey, Michael Buckley, Hubert Camus, Xavier Muth, Jason E Lewis, Hervé Bocherens, Pascale Yvorra, Christophe Tenailleau, Benjamin Duployer, Hélène Coqueugniot, Olivier Dutour, Thomas Higham, Martin Sikora","doi":"10.1016/j.xgen.2024.100593","DOIUrl":"10.1016/j.xgen.2024.100593","url":null,"abstract":"Neanderthal genomes have been recovered from sites across Eurasia, painting an increasingly complex picture of their populations' structure that mostly indicates that late European Neanderthals belonged to a single metapopulation with no significant evidence of population structure. Here, we report the discovery of a late Neanderthal individual, nicknamed \"Thorin,\" from Grotte Mandrin in Mediterranean France, and his genome. These dentognathic fossils, including a rare example of distomolars, are associated with a rich archeological record of Neanderthal final technological traditions in this region ∼50-42 thousand years ago. Thorin's genome reveals a relatively early divergence of ∼105 ka with other late Neanderthals. Thorin belonged to a population with a small group size that showed no genetic introgression with other known late European Neanderthals, revealing some 50 ka of genetic isolation of his lineage despite them living in neighboring regions. These results have important implications for resolving competing hypotheses about causes of the disappearance of the Neanderthals.","PeriodicalId":72539,"journal":{"name":"Cell genomics","volume":"4 9","pages":"100593"},"PeriodicalIF":11.1,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11480857/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142302300","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