Single-cell Technologies Provide Novel Insights into Liver Physiology and Pathology

被引:1
作者
Chen, Guanzi [1 ]
Xu, Wenli [1 ]
Long, Zhicong [1 ]
Chong, Yutian [1 ]
Lin, Bingliang [1 ,2 ]
Jie, Yusheng [1 ,2 ]
机构
[1] Sun Yat Sen Univ, Affiliated Hosp 3, Dept Infect Dis, Guangzhou, Guangdong, Peoples R China
[2] Sun Yat Sen Univ, Affiliated Hosp 3, Dept Infect Dis, Guangzhou 510630, Guangdong, Peoples R China
基金
中国国家自然科学基金;
关键词
Single-cell technology; Normal liver; Chronic liver disease; Hepato-cellular carcinoma; Acute-on-chronic liver failure; RNA-SEQ; GENE-EXPRESSION; HETEROGENEITY; LANDSCAPE; INFERENCE; TISSUES; MARKER; ATLAS;
D O I
10.14218/JCTH.2023.00224
中图分类号
R57 [消化系及腹部疾病];
学科分类号
摘要
The liver is the largest glandular organ in the body and has a unique distribution of cells and biomolecules. However, the treatment outcome of end-stage liver disease is extremely poor. Single-cell sequencing is a new advanced and powerful technique for identifying rare cell populations and biomolecules by analyzing the characteristics of gene expression between individual cells. These cells and biomolecules might be used as potential targets for immunotherapy of liver diseases and contribute to the development of precise individualized treatment. Compared to whole-tissue RNA sequencing, single-cell RNA sequencing (scRNA-seq) or other single-cell histological techniques have solved the problem of cell population heterogeneity and characterize molecular changes associated with liver diseases with higher accuracy and resolution. In this review, we comprehensively summarized single-cell approaches including transcriptomic, spatial transcriptomic, immunomic, proteomic, epigenomic, and multiomic technologies, and described their application in liver physiology and pathology. We also discussed advanced techniques and recent studies in the field of single-cell; our review might provide new insights into the pathophysiological mechanisms of the liver to achieve precise and individualized treatment of liver diseases.
引用
收藏
页码:79 / 90
页数:12
相关论文
共 116 条
[31]   Single-cell RNA sequencing shows the immunosuppressive landscape and tumor heterogeneity of HBV-associated hepatocellular carcinoma [J].
Ho, Daniel Wai-Hung ;
Tsui, Yu-Man ;
Chan, Lo-Kong ;
Sze, Karen Man-Fong ;
Zhang, Xin ;
Cheu, Jacinth Wing-Sum ;
Chiu, Yung-Tuen ;
Lee, Joyce Man-Fong ;
Chan, Albert Chi-Yan ;
Cheung, Elaine Tin-Yan ;
Yau, Derek Tsz-Wai ;
Chia, Nam-Hung ;
Lo, Irene Lai-Oi ;
Sham, Pak-Chung ;
Cheung, Tan-To ;
Wong, Carmen Chak-Lui ;
Ng, Irene Oi-Lin .
NATURE COMMUNICATIONS, 2021, 12 (01)
[32]   Integrating Spatial Transcriptomics and Single-Cell RNA-seq Reveals the Gene Expression Profling of the Human Embryonic Liver [J].
Hou, Xianliang ;
Yang, Yane ;
Li, Ping ;
Zeng, Zhipeng ;
Hu, Wenlong ;
Zhe, Ruilian ;
Liu, Xinqiong ;
Tang, Donge ;
Ou, Minglin ;
Dai, Yong .
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY, 2021, 9
[33]   Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas [J].
Hou, Yu ;
Guo, Huahu ;
Cao, Chen ;
Li, Xianlong ;
Hu, Boqiang ;
Zhu, Ping ;
Wu, Xinglong ;
Wen, Lu ;
Tang, Fuchou ;
Huang, Yanyi ;
Peng, Jirun .
CELL RESEARCH, 2016, 26 (03) :304-319
[34]   A spatial vascular transcriptomic, proteomic, and phosphoproteomic atlas unveils an angiocrine Tie-Wnt signaling axis in the liver [J].
Inverso, Donato ;
Shi, Jingjing ;
Lee, Ki Hong ;
Jakab, Moritz ;
Ben-Moshe, Shani ;
Kulkarni, Shubhada R. ;
Schneider, Martin ;
Wang, Guanxiong ;
Komeili, Marziyeh ;
Velez, Paula Argos ;
Riedel, Maria ;
Spegg, Carleen ;
Ruppert, Thomas ;
Schaeffer-Reiss, Christine ;
Helm, Dominic ;
Singh, Indrabahadur ;
Boutros, Michael ;
Chintharlapalli, Sudhakar ;
Heikenwalder, Mathias ;
Itzkovitz, Shalev ;
Augustin, Hellmut G. .
DEVELOPMENTAL CELL, 2021, 56 (11) :1677-+
[35]   Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types [J].
Jaitin, Diego Adhemar ;
Kenigsberg, Ephraim ;
Keren-Shaul, Hadas ;
Elefant, Naama ;
Paul, Franziska ;
Zaretsky, Irina ;
Mildner, Alexander ;
Cohen, Nadav ;
Jung, Steffen ;
Tanay, Amos ;
Amit, Ido .
SCIENCE, 2014, 343 (6172) :776-779
[36]   A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade [J].
Jerby-Arnon, Livnat ;
Shah, Parin ;
Cuoco, Michael S. ;
Rodman, Christopher ;
Su, Mei-Ju ;
Melms, Johannes C. ;
Leeson, Rachel ;
Kanodia, Abhay ;
Mei, Shaolin ;
Lin, Jia-Ren ;
Wang, Shu ;
Rabasha, Bokang ;
Liu, David ;
Zhang, Gao ;
Margolais, Claire ;
Ashenberg, Orr ;
Ott, Patrick A. ;
Buchbinder, Elizabeth I. ;
Haq, Rizwan ;
Hodi, F. Stephen ;
Boland, Genevieve M. ;
Sullivan, Ryan J. ;
Frederick, Dennie T. ;
Miao, Benchun ;
Moll, Tabea ;
Flaherty, Keith T. ;
Herlyn, Meenhard ;
Jenkins, Russell W. ;
Thummalapalli, Rohit ;
Kowalczyk, Monika S. ;
Canadas, Israel ;
Schilling, Bastian ;
Cartwright, Adam N. R. ;
Luoma, Adrienne M. ;
Malu, Shruti ;
Hwu, Patrick ;
Bernatchez, Chantale ;
Forget, Marie-Andree ;
Barbie, David A. ;
Shalek, Alex K. ;
Tirosh, Itay ;
Sorger, Peter K. ;
Wucherpfennig, Kai ;
Van Allen, Eliezer M. ;
Schadendorf, Dirk ;
Johnson, Bruce E. ;
Rotem, Asaf ;
Rozenblatt-Rosen, Orit ;
Garraway, Levi A. ;
Yoon, Charles H. .
CELL, 2018, 175 (04) :984-+
[37]   Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples [J].
Jin, Wenfei ;
Tang, Qingsong ;
Wan, Mimi ;
Cui, Kairong ;
Zhang, Yi ;
Ren, Gang ;
Ni, Bing ;
Sklar, Jeffrey ;
Przytycka, Teresa M. ;
Childs, Richard ;
Levens, David ;
Zhao, Keji .
NATURE, 2015, 528 (7580) :142-+
[38]   Molecular and cellular mechanisms of liver fibrosis and its regression [J].
Kisseleva, Tatiana ;
Brenner, David .
NATURE REVIEWS GASTROENTEROLOGY & HEPATOLOGY, 2021, 18 (03) :151-166
[39]   Profiling single-cell histone modifications using indexing chromatin immunocleavage sequencing [J].
Ku, Wai Lim ;
Pan, Lixia ;
Cao, Yaqiang ;
Gao, Weiwu ;
Zhao, Keji .
GENOME RESEARCH, 2021, 31 (10) :1831-1842
[40]   Beyond bulk: a review of single cell transcriptomics methodologies and applications [J].
Kulkarni, Ashwinikumar ;
Anderson, Ashley G. ;
Merullo, Devin P. ;
Konopka, Genevieve .
CURRENT OPINION IN BIOTECHNOLOGY, 2019, 58 :129-136