Single-cell genomics and spatial transcriptomics: Discovery of novel cell states and cellular interactions in liver physiology and disease biology.

Journal of Hepatology
Antonio SavianoThomas F Baumert

Abstract

Transcriptome analysis enables the study of gene expression in human tissues and is a valuable tool to characterise liver function and gene expression dynamics during liver disease, as well as to identify prognostic markers or signatures, and to facilitate discovery of new therapeutic targets. In contrast to whole tissue RNA sequencing analysis, single-cell RNA-sequencing (scRNA-seq) and spatial transcriptomics enables the study of transcriptional activity at the single cell or spatial level. ScRNA-seq has paved the way for the discovery of previously unknown cell types and subtypes in normal and diseased liver, facilitating the study of rare cells (such as liver progenitor cells) and the functional roles of non-parenchymal cells in chronic liver disease and cancer. By adding spatial information to scRNA-seq data, spatial transcriptomics has transformed our understanding of tissue functional organisation and cell-to-cell interactions in situ. These approaches have recently been applied to investigate liver regeneration, organisation and function of hepatocytes and non-parenchymal cells, and to profile the single cell landscape of chronic liver diseases and cancer. Herein, we review the principles and technologies behind scRNA-s...Continue Reading

Citations

Oct 27, 2020·American Journal of Physiology. Endocrinology and Metabolism·Sung Rye ParkJun Hee Lee
Feb 23, 2021·Frontiers in Immunology·Armando Andres Roca SuarezJoachim Lupberger
Apr 4, 2021·Cancers·María ArechederraCarmen Berasain
Feb 28, 2021·Annual Review of Immunology·Xianwen RenZemin Zhang
May 8, 2021·Briefings in Bioinformatics·Philip DaviesDaniel Hebenstreit
May 25, 2021·JHEP Reports : Innovation in Hepatology·Valéry L PayenAdil El Taghdouini
Mar 17, 2021·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·James CarterScott L Friedman
Jun 20, 2021·Nature Reviews. Genetics·Sophia K LongoPaul A Khavari
Nov 13, 2021·Frontiers in Genetics·Brianna M Paisley, Yunlong Liu
Dec 24, 2021·American Journal of Physiology. Gastrointestinal and Liver Physiology·Enis KostallariVijay H Shah
Dec 20, 2021·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Scott L Friedman, Massimo Pinzani
Jan 28, 2022·Clinical and Translational Medicine·Xiaoxia LiuXiangdong Wang
Feb 1, 2022·Current Opinion in Gastroenterology·Alix BruneauFrank Tacke

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Methods Mentioned

BETA
dissect
scRNA-seq
PCR
in vitro transcription
FACS
RNA-seq

Software Mentioned

Smart
seq
ScRNA
NovoSpaRc
Seq2
Drop

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