Identification of a hepatocyte stem cell and its niche in liver homeostasis

Summary: RNAseq analysis of Axin2+ hepatocyte stem cells versus Axin2- mature hepatocytes shows that Axin2+ cells have a distinct gene expression profile compared to Axin2- hepatocytes. Methods: Hepatocytes were isolated from 8 week old Axin2rtTA;TetO-H2B-GFP mice (n = 3) given doxycycline in drinking water for 7 days. After removal of non-parenchymal cells, the hepatocytes were sorted into GFP+ versus GFP- populations by FACS. mRNA was isolated and RNAseq profiles were generated using Illumina HiSeq 2000. The reads were mapped to the mouse genome (mm10) using TopHat (v2.0.11) and differential gene expression analysis was performed using CuffDiff (v.2.2.2). Results: We mapped about 60 million sequence reads per sample to the mouse genome (build mm10) and identified more than 30,000 transcripts in the Axin2+ and Axin2- cell populations. Differential gene expression analysis using CuffDiff identified 96 genes with signficantly different expression levels between the two populations. Several of these were confirmed by RNA in situ and qRT-PCR analysis. mRNA profiles of Axin2+ and Axin2- cells from uninjured adult mouse liver were analysed by deep sequencing, in triplicate, using Illumina HiSeq 2000.