Single Cell RNA Sequencing in NASH.
10× Genomics
Fibrosis
Macrophages
Myeloid immune cells
NAFLD
NASH
Single cell RNA sequencing (scRNA-seq)
Transcriptomics
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2022
2022
Historique:
entrez:
25
2
2022
pubmed:
26
2
2022
medline:
3
3
2022
Statut:
ppublish
Résumé
Single cell RNA sequencing (scRNA-seq) allows to uncover cellular heterogeneity and the identification of novel subpopulations. In non-alcoholic steatohepatitis (NASH), scRNA-seq is particularly powerful to understand non-parenchymal cell heterogeneity in the liver, e.g. for inflammatory cells. Myeloid immune cells, particularly macrophages, play a critical role in response of the innate immune system and significantly contribute to the progression of fatty liver disease. Due to their high heterogeneity and complex phenotypes, their functional role in health and disease is difficult to analyze. Here, we describe the isolation and analysis of myeloid cell populations from mouse liver using microdroplet-based scRNA-seq. This approach allows the identification and characterization of different hepatic cell types, exemplified here by hepatic macrophage populations, as well as analyses of differentially expressed genes between samples (e.g., cells from healthy or NASH livers).
Identifiants
pubmed: 35212995
doi: 10.1007/978-1-0716-2128-8_15
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
181-202Informations de copyright
© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
Références
Krenkel O, Tacke F (2017) Liver macrophages in tissue homeostasis and disease. Nat Rev Immunol 17(5):306–321
doi: 10.1038/nri.2017.11
Weston CJ, Zimmermann HW, Adams DH (2019) The role of myeloid-derived cells in the progression of liver disease. Front Immunol 10:893
doi: 10.3389/fimmu.2019.00893
Krenkel O, Hundertmark J, Abdallah AT et al (2020) Myeloid cells in liver and bone marrow acquire a functionally distinct inflammatory phenotype during obesity-related steatohepatitis. Gut 69(3):551–563
doi: 10.1136/gutjnl-2019-318382
Saviano A, Henderson NC, Baumert TF (2020) Single-cell genomics and spatial transcriptomics: discovery of novel cell states and cellular interactions in liver physiology and disease biology. J Hepatol 73(5):1219–1230
doi: 10.1016/j.jhep.2020.06.004
Xiong X, Kuang H, Ansari S et al (2019) Landscape of intercellular crosstalk in healthy and NASH liver revealed by single-cell secretome gene analysis. Mol Cell 75(3):644–660.e645
doi: 10.1016/j.molcel.2019.07.028
Ramachandran P, Dobie R, Wilson-Kanamori JR et al (2019) Resolving the fibrotic niche of human liver cirrhosis at single-cell level. Nature 575(7783):512–518
doi: 10.1038/s41586-019-1631-3
Zheng GX, Terry JM, Belgrader P et al (2017) Massively parallel digital transcriptional profiling of single cells. Nat Commun 8:14049
doi: 10.1038/ncomms14049
Stuart T, Butler A, Hoffman P et al (2019) Comprehensive integration of single-cell data. Cell 177:1888–1902.e1821
doi: 10.1016/j.cell.2019.05.031
Liberzon A, Birger C, Thorvaldsdottir H et al (2015) The molecular signatures database (MSigDB) hallmark gene set collection. Cell Syst 1:417–425
doi: 10.1016/j.cels.2015.12.004
Yu G, Wang LG, Han Y et al (2012) clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16(5):284–287
doi: 10.1089/omi.2011.0118