Elucidating the hepatic ecosystem and factors that drive liver postnatal development and tumorigenesis by single cell RNA-sequencing
Liver is the major metabolic organ. We analyzed single cell RNA-sequencing (scRNA-seq) data collected from mouse liver to study its postnatal development and tumorigenesis. The postnatal development and maturation of liver are inadequately understood. We analyzed 52,834 single cell transcriptomes collected at postnatal day 1, 3, 7, 21 and 56. We observed unexpectedly high levels of hepatocyte heterogeneity in the developing liver and progressive construction of the zonated metabolic functions from pericentral to periportal hepatocytes, which was orchestrated with development of sinusoid endothelial, stellate and Kupffer cells. Trajectory and gene regulatory analyses captured 36 transcription factors, including a circadian regulator Bhlhe40, in programming liver development. Remarkably, we identified a special group of macrophages enriched at day 7 with a hybrid phenotype of macrophages and endothelial cells, which may regulate sinusoidal construction and regulatory T (Treg) cell function. For tumorigenesis, we show that Myc-driven hepatocellular carcinoma (HCC) was dramatically aggravated in mice with hepatocyte-specific Ptpn11/Shp2 deletion. However, Myc-induced tumors developed selectively from the rare Shp2-positive hepatocytes in Shp2-deficent liver, and Myc-driven oncogenesis depended on an intact Ras-Erk signaling ensued by Shp2 to sustain Myc stability. Despite a stringent requirement of Shp2 cell-autonomously, Shp2 deletion induced an immune-suppressive environment, resulting in defective clearance of tumor-initiating cells and aggressive tumor progression. The basal Wnt/beta-catenin signaling was upregulated in Shp2-deficient liver, which was further augmented by Myc transfection. Ablating Ctnnb1 suppressed Myc-induced HCC in Shp2-deficient livers, revealing an essential role of beta-catenin. Consistently, Myc overexpression and CTNNB1 mutations were frequently co-detected in HCC patients with poor prognosis. These data elucidate complex mechanisms of liver tumorigenesis driven by cell-intrinsic oncogenic signaling in cooperation with environmental tumor-promoting factors generated by disrupting the specific oncogenic pathway.