Transcriptomics of Congenital Hepatic Fibrosis in Autosomal Recessive Polycystic Kidney Disease Using PCK Rats

Abstract

Congenital hepatic fibrosis/Autosomal recessive polycystic kidney disease (CHF/ARPKD) is an inherited neonatal disease induced by mutations in the PKHD1 gene and characterized by cysts and robust pericystic fibrosis in the liver and kidneys. The PCK rat is an excellent animal model that carries a Pkhd1 mutation and exhibits similar pathophysiology. We performed RNA-Seq analysis on liver samples from PCK rats over a time course of postnatal day (PND) 15, 20, 30, and 90 using age-matched Sprague Dawley (SD) rats as controls to characterize molecular mechanisms of CHF/ARPKD pathogenesis. A comprehensive gene expression analysis identified 1298 differentially expressed genes (DEGs) between PCK and SD rats. The genes overexpressed in the PCK rats at PND30 and 90 were involved cell migration (e.g., Lamc2, Tgfb2, and Plet1), cell adhesion (e.g., Spp1, Adgrg1, and Cd44), and wound healing (e.g., Plat, Celsr1, Tpm1). Connective tissue growth factor (Ctgf) and platelet-derived growth factor (Pdgfb), two genes associated with fibrosis, were upregulated in PCK rats at all time points. Genes associated with MHC class I molecules (e.g., RT1-A2) or involved in ribosome assembly (e.g., Pes1) were significantly downregulated in PCK rats. Upstream regulator analysis showed activation of proteins involved tissue growth (MTPN) inflammation (STAT family members), chromatin remodeling (BRG1), reduction in fibrosis (SMAD7), and inhibition of proteins involved in hepatic differentiation (HNF4α). Immunofluorescence staining revealed that cyst wall epithelium cells also express hepatic progenitor cell markers. The increase in mRNAs of four top upregulated genes, including Reg3b, Aoc1, Tm4sf20, and Cdx2, was confirmed at the protein level using immunohistochemistry. In conclusion, these studies indicate that a combination of increased inflammation, cell migration, wound healing, decreased antifibrotic gene expression, and inhibition of hepatic function are the major underlying pathogenic mechanisms in CHF/ARPKD.