Deciphering liver fibrosis with next generation omics

Abstract

Fibrotic diseases underpin around 45% of all chronic diseases and deaths in the western world. In particular, chronic liver diseases represent a major threat to the public health affecting around 1.5 billion people in the world and accounting for 2 million deaths annually. Hepatic fibrosis is a progressive pathology characterized by a dysregulation of the woundhealing response, resulting in extracellular matrix (ECM) accumulation. Hepatic Stellate cells (HCSs) are the major contributor to ECM deposition in liver diseases. Thus, HSCs are crucial for liver fibrosis progression. Understanding molecular mechanisms of HSC activation is therefore of major interest in study of liver fibrosis. To this end, miRNA sequencing during HCSs activation time-course was employed, which showed significant differences in miRNA expression which may be important for fibrosis progression. 2D cultures are widely used in the study of liver disease. However, they do present limitations, which can be overcome by the use of Bioreactor-cultured Precision cut liver slices (PCLSs) technology developed in our lab. Using this technology, human PCLSs were created and RNA sequencing, proteome and secretome analysis performed. In this thesis, I showed that fibrotic PCLSs present differential gene/protein expression patterns that could be associated with the fibrotic outcome. Previous studies in our lab reported an epigenetic mechanism that generated heritable adaptation in wound healing response in male rats. The adapted rats showed significant fibrogenesis/fibrosis reduction. I was interested in studying the mechanism behind the adaptation. Using omics techniques, I analysed gene expression pattern in adapted livers and differences in DNA methylome and proteome in sperm, as potential mechanism for adaptation transmission. Moreover, I studied the potential of adaptive inheritance transmission via female lineage. This study provides evidence of i) the importance of miRNA during HSCs activation, ii) differential gene/protein expression patterns associated with the fibrotic outcome in human liver, iii) differential gene expression in adapted livers and epigenetic modifications in sperm as a putative mechanism of the adaptive response transmission. This adaptive response was absent in female offspring, suggesting only males can transmit the adaptation.