Polygenic regression uncovers trait-relevant cellular contexts through pathway activation transformation of single-cell RNA sequencing data

doi:10.1016/j.xgen.2023.100383

科研成果详情

题名	Polygenic regression uncovers trait-relevant cellular contexts through pathway activation transformation of single-cell RNA sequencing data
作者	Ma, Yunlong1,2; Deng, Chunyu 3; Zhou, Yijun 1,2; Zhang, Yaru1,2; Qiu, Fei1; Jiang, Dingping1; Zheng, Gongwei1; Li, Jingjing 1; Shuai, Jianwei 2; Zhang, Yan 3; Yang, Jian 4,5; Su, Jianzhong1,2
发表日期	2023-09-13
发表期刊	Cell genomics 影响因子和分区
语种	英语
原始文献类型	Journal Article ; Article
关键词	GWAS genetic variants risk genes single-cell RNA sequencing trait-relevant cell types
其他关键词	MOLECULAR NETWORKS ; HETEROGENEITY ; TECHNOLOGIES ; REVEALS ; GENES ; RISK
摘要	Advances in single-cell RNA sequencing (scRNA-seq) techniques have accelerated functional interpretation of disease-associated variants discovered from genome-wide association studies (GWASs). However, identification of trait-relevant cell populations is often impeded by inherent technical noise and high sparsity in scRNA-seq data. Here, we developed scPagwas, a computational approach that uncovers trait-relevant cellular context by integrating pathway activation transformation of scRNA-seq data and GWAS summary statistics. scPagwas effectively prioritizes trait-relevant genes, which facilitates identification of trait-relevant cell types/populations with high accuracy in extensive simulated and real datasets. Cellular-level association results identified a novel subpopulation of naive CD8+ T cells related to COVID-19 severity and oligodendrocyte progenitor cell and microglia subsets with critical pathways by which genetic variants influence Alzheimer's disease. Overall, our approach provides new insights for the discovery of trait-relevant cell types and improves the mechanistic understanding of disease variants from a pathway perspective
资助项目	Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang[2021R01013];Scientific Research Foundation for Talents of Wenzhou Medical University[KYQD20201001];Westlake Education Foundation[101566022001];Westlake Laboratory of Life Sciences and Biomedicine[202208013];National Natural Science Foundation of China[32200535,61871294,82172882];Science Foundation of Zhejiang Province[LR19C060001];
出版者	ELSEVIER
ISSN	2666-979X
卷号	3 期号:9
DOI	10.1016/j.xgen.2023.100383
页数	21
WOS类目	Cell Biology ; Genetics & Heredity
WOS研究方向	Cell Biology ; Genetics & Heredity
WOS记录号	WOS:001100041100001
收录类别	PUBMED ; SCOPUS ; ESCI
在线发表日期	2023-09
URL	查看原文
PubMed ID	37719150
SCOPUSEID	2-s2.0-85170250498
通讯作者地址	[Zhang, Yan]School of Life Science and Technology,Harbin Institute of Technology,Heilongjiang,Harbin,150080,China ; [Yang, Jian]School of Life Sciences,Westlake University,Zhejiang,Hangzhou,310012,China ; [Su, Jianzhong]School of Biomedical Engineering,School of OphthalmoFlogy & Optometry and Eye Hospital,Wenzhou Medical University,Zhejiang,Wenzhou,325027,China
Scopus学科分类	Biochemistry, Genetics and Molecular Biology (miscellaneous);Genetics
引用统计
文献类型	期刊论文
条目标识符	https://kms.wmu.edu.cn/handle/3ETUA0LF/182928
专题	仁济学院_眼视光、生物医学工程学部
通讯作者	Zhang, Yan; Yang, Jian; Su, Jianzhong
作者单位	1.School of Biomedical Engineering,School of OphthalmoFlogy & Optometry and Eye Hospital,Wenzhou Medical University,Zhejiang,Wenzhou,325027,China; 2.Oujiang Laboratory,Zhejiang Lab for Regenerative Medicine,Vision and Brain Health,Zhejiang,Wenzhou,325101,China; 3.School of Life Science and Technology,Harbin Institute of Technology,Heilongjiang,Harbin,150080,China; 4.School of Life Sciences,Westlake University,Zhejiang,Hangzhou,310012,China; 5.Westlake Laboratory of Life Sciences and Biomedicine,Zhejiang,Hangzhou,310024,China
第一作者单位	仁济学院_眼视光、生物医学工程学部
通讯作者单位	仁济学院_眼视光、生物医学工程学部
第一作者的第一单位	仁济学院_眼视光、生物医学工程学部
推荐引用方式 GB/T 7714	Ma, Yunlong,Deng, Chunyu,Zhou, Yijun,et al. Polygenic regression uncovers trait-relevant cellular contexts through pathway activation transformation of single-cell RNA sequencing data[J]. Cell genomics,2023,3(9).
APA	Ma, Yunlong., Deng, Chunyu., Zhou, Yijun., Zhang, Yaru., Qiu, Fei., ... & Su, Jianzhong. (2023). Polygenic regression uncovers trait-relevant cellular contexts through pathway activation transformation of single-cell RNA sequencing data. Cell genomics, 3(9).
MLA	Ma, Yunlong,et al."Polygenic regression uncovers trait-relevant cellular contexts through pathway activation transformation of single-cell RNA sequencing data".Cell genomics 3.9(2023).