A Multi-Omics Approach to Liver Diseases: Integration of Single Nuclei Transcriptomics with Proteomics and HiCap Bulk Data in Human Liver

The liver is the largest solid organ and a primary metabolic hub. In recent years, intact cell nuclei were used to perform single-nuclei RNA-seq (snRNA-seq) for tissues difficult to dissociate and for flash-frozen archived tissue samples to discover unknown and rare cell subpopulations. In this stud...

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Veröffentlicht in:	Omics (Larchmont, N.Y.) N.Y.), 2020-04, Vol.24 (4), p.18-194
Hauptverfasser:	Cavalli, Marco, Diamanti, Klev, Pan, Gang, Spalinskas, Rapolas, Kumar, Chanchal, Deshmukh, Atul Shahaji, Mann, Matthias, Sahlén, Pelin, Komorowski, Jan, Wadelius, Claes
Format:	Artikel
Sprache:	eng
Schlagworte:	ADAMTS protein ADAMTS2 protein albumin apoa2 gene B-Lymphocytes - cytology B-Lymphocytes - metabolism biological marker c3 gene cadherin cadherin 11 Carcinoma, Hepatocellular - genetics Carcinoma, Hepatocellular - metabolism Carcinoma, Hepatocellular - pathology CD163 antigen CD74 antigen Cell Nucleus - genetics Cell Nucleus - metabolism collagen type 3 collagen type 6 Computational Biology - methods controlled study cystic fibrosis transmembrane conductance regulator dcn gene dihydropyrimidine dehydrogenase Endothelial Cells - cytology Endothelial Cells - metabolism enhancer region epithelial cell adhesion molecule eps2 gene f5 gene f8 gene fgb gene fgl1 gene fibroblast growth factor 1 fluorouracil g6pc gene gene Gene Expression Regulation gene identification glucose transporter 1 glucose transporter 2 Hepatic Stellate Cells - cytology Hepatic Stellate Cells - metabolism Hepatocytes - cytology Hepatocytes - metabolism High-Throughput Nucleotide Sequencing human human cell human chromosome human liver human tissue Humans interleukin 18 intron Killer Cells, Natural - cytology Killer Cells, Natural - metabolism Kupffer Cells - cytology Kupffer Cells - metabolism lamb1 gene Liver - cytology Liver - metabolism liver cell carcinoma Liver Neoplasms - genetics Liver Neoplasms - metabolism Liver Neoplasms - pathology liver parenchyma lrp2 gene marker gene mass spectrometry messenger RNA multi-omics data integration multiomics mup3 gene myo1f gene nostrin oit3 gene pck1 gene plekhg1 gene plg gene priority journal promoter region proteome proteomics ptprb gene RNA conformation RNA sequencing single nucleotide polymorphism Single-Cell Analysis - methods small nuclear RNA snRNA-seq somatomedin binding protein 3 spp1 gene T-Lymphocytes - cytology T-Lymphocytes - metabolism transcription factor Sox4 transcription factor Sox9 Transcriptome transcriptomics unclassified drug vasculotropin receptor 1
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Zusammenfassung:	The liver is the largest solid organ and a primary metabolic hub. In recent years, intact cell nuclei were used to perform single-nuclei RNA-seq (snRNA-seq) for tissues difficult to dissociate and for flash-frozen archived tissue samples to discover unknown and rare cell subpopulations. In this study, we performed snRNA-seq of a liver sample to identify subpopulations of cells based on nuclear transcriptomics. In 4282 single nuclei, we detected, on average, 1377 active genes and we identified seven major cell types. We integrated data from 94,286 distal interactions ( p
ISSN:	1557-8100 1536-2310 1557-8100
DOI:	10.1089/omi.2019.0215