From genome sequencing to the discovery of potential biomarkers in liver disease

Abstract

Chronic liver disease progresses through several stages, fatty liver, steatohepatitis, cirrhosis, and eventually, it leads to hepatocellular carcinoma (HCC) over a long period of time. Since a large proportion of patients with HCC are accompanied by cirrhosis, it is considered to be an important factor in the diagnosis of liver cancer. This is because cirrhosis leads to an irreversible harmful effect, but the early stages of chronic liver disease could be reversed to a healthy state. Therefore, the discovery of biomarkers that could identify the early stages of chronic liver disease is important to prevent serious liver damage. Biomarker discovery at liver cancer and cirrhosis has enhanced the development of sequencing technology. Next generation sequencing (NGS) is one of the representative technical innovations in the biological field in the recent decades and it is the most important thing to design for research on what type of sequencing methods are suitable and how to handle the analysis steps for data integration. In this review, we comprehensively summarized NGS techniques for identifying genome, transcriptome, DNA methylome and 3D/4D chromatin structure, and introduced framework of processing data set and integrating multi-omics data for uncovering biomarkers.

Polydatin: A Critical Promising Natural Agent for Liver Protection via Antioxidative Stress

“…However, the detail molecular mechanisms were not thoroughly explored. Modern research methods such as genomics, metabolomics, proteomics, and metagenomics can be used to conduct more in-depth investigations on the corresponding mechanisms of PD on liver diseases, which provide strong support and theoretical basis for the subsequent clinical research and ultimately developed this natural compound to a new drug for liver disorders [ 114 – 116 ]. Secondly, although researchers have concentrated on LD 50 of PD, the study of reproductive, carcinogenic, and teratogenic toxicity was not involved.…”

Epigenetic Biomarkers for the Diagnosis and Treatment of Liver Disease

“…In this sense, great efforts have been made to better understand the molecular and cellular mechanisms implicated in the progression of CLD. Over the last decade, next-generation sequencing technologies have been used to identify the most frequent mutations, DNA copy variations, and changes in gene expression that contribute to hepatocarcinogenesis [ 29 , 30 , 31 , 32 , 33 , 34 , 35 ].…”

Identification of Molecular Subgroups in Liver Cirrhosis by Gene Expression Profiles

“…Therefore, it is essential to find biomarkers to identify the early stage of chronic liver disease to prevent severe liver damage. The discovery of biomarkers for liver cancer and liver cirrhosis has promoted sequencing technology development, and high-throughput sequencing is one of the representative technological innovations in the biological field in recent decades (4). Recently, many studies have been conducted to clarify the pathogenesis of liver cirrhosis based on the experimental data of microarray and highthroughput sequencing (5)(6)(7)(8).…”