Epigenetics of alcohol-related liver diseases

Abstract

Alcohol-related liver disease (ARLD) is a primary cause of chronic liver disease in the United States. Despite advances in the diagnosis and management of ARLD, it remains a major public health problem associated with significant morbidity and mortality, emphasising the need to adopt novel approaches to the study of ARLD and its complications. Epigenetic changes are increasingly being recognised as contributing to the pathogenesis of multiple disease states. Harnessing the power of innovative technologies for the study of epigenetics (e.g., next-generation sequencing, DNA methylation assays, histone modification profiling and computational techniques like machine learning) has resulted in a seismic shift in our understanding of the pathophysiology of ARLD. Knowledge of these techniques and advances is of paramount importance for the practicing hepatologist and researchers alike. Accordingly, in this review article we will summarise the current knowledge about alcohol-induced epigenetic alterations in the context of ARLD, including but not limited to, DNA hyper/hypo methylation, histone modifications, changes in non-coding RNA, 3D chromatin architecture and enhancer-promoter interactions. Additionally, we will discuss the state-of-the-art techniques used in the study of ARLD (e.g. single-cell sequencing). We will also highlight the epigenetic regulation of chemokines and their proinflammatory role in the context of ARLD. Lastly, we will examine the clinical applications of epigenetics in the diagnosis and management of ARLD.

Keywords: 3C, chromosome conformation capture; 4C, chromosome conformation capture-on-chip; AH, alcohol-related hepatitis; ARLD, alcohol-related liver disease; ASH, alcohol-related steatohepatitis; ATAC, assay for transposase-accessible chromatin; Acetylation; Alcohol liver disease; BET, bromodomain and extraterminal motif; BETi, BET inhibitor; BRD, bromodomain; CCL2, C-C motif chemokine ligand 2; CTCF, CCCTC-binding factor; CXCL, C-X-C motif chemokine ligand; Chromatin architecture; Computational biology; DNA methylation; DNMT, DNA methyltransferase; E-P, enhancer-promoter; Epidrugs; Epigenetics; FKBP5, FK506-binding protein 5; HCC, hepatocellular carcinoma; HDAC, histone deacetylase; HIF1α, hypoxia inducible factor-1α; HMGB1, high-mobility group box protein 1; HNF4α, hepatocyte nuclear factor 4α; HSC, hepatic stellate cell; Hi-C, chromosome capture followed by high-throughput sequencing; Histones; IL, interleukin; LPS, lipopolysaccharide; MALAT1, metastasis-associated lung adenocarcinoma transcript 1; MECP2, methyl-CpG binding protein 2; NAFLD, non-alcohol-related fatty liver disease; PPARG, peroxisome proliferator activated receptor-γ; SAA, salvianolic acid A; SIRT, sirtuin; SREBPs, sterol regulatory element-binding proteins; Single cell epigenome; TAD, topologically associating domain; TEAD, TEA domain transcription factor; TLR, Toll-like receptor; TNF, tumour necrosis factor; YAP, Yes-associated protein; lncRNA, long non-coding RNA; miRNA, microRNA.

Fig. 1

The epigenetic modifiers: writers, readers, and erasers. DNA methylation is mediated by DNMT (writer). Methyl groups (M) are attached to CpG dinucleotide islands, reversed by TET (eraser). MECP2 (reader) recognises methyl groups and represses expression of associated genes. Histone methylation is mediated by HMT (writer). KDM and PADI4 (erasers) remove methyl groups from lysine and arginine, respectively. Tudor/PHD/chromodomain (readers) recognise methylated histones. Histone acetylation is mediated by HAT (writer) and reversed by HDAC (eraser). Acetyl groups are recognised by bromodomains (readers). Non-coding RNAs interact with the different epigenic modifiers and modulate their function. circRNA, circular RNA; DNMT, DNA methyltransferase; HAT, histone acetyltransferase; HDAC, histone deacetylase; HMT, histone methyltransferase; KDM, lysine demethylase; lncRNA, long non-coding RNA; MECP2, methyl-CpG binding protein 2; miRNA, microRNA; ncRNA, non-coding RNA; PADI4, peptidyl arginine deiminase 4; PHD, plant homeodomain; TET, ten eleven translocation.

Fig. 2

Role of ncRNA in alcohol-related liver disease. NcRNAs are a group of RNA molecules of various length that are not translated into protein. The role of miRNA in the pathogenesis of alcohol-related liver disease has been reviewed extensively over the years.^,,, , , , Dysregulation of miRNAs in alcohol-related liver disease is linked to the development of steatosis (yellow circle), inflammation via recruitment of inflammatory cells (blue circle), fibrosis (blue lines) and HCC (green circle). The associated table shows examples of dysregulated miRNAs in alcohol-related liver disease and their role in its pathogenesis. References (miR-21,, , miR-26a, miR-27a,^, miR-29, miR-34a,, , miR-122,^,, mir155,^,, , , miR-125b, miR-182,^, miR-126, miR-200a, miR-181b-3p, miR-214, miR-199, miR-217, miR-223, miR-291b, miR-378¹⁸⁸). EMT, epithelial-mesenchymal transition; HCC, hepatocellular carcinoma; ncRNA, non-coding RNA.

Fig. 3

Chromosome conformation capture (3C) methods study the interactions between genetic loci in 3D structure. 3C methods study the interactions between genetic loci in 3D structure. These 3D interactions can be hundreds or thousands of bases to megabases apart in sequence and can heavily regulate gene expression. Most 3C assays share the same basic principles, mainly the fixation of genomic DNA-DNA and DNA-protein interactions through chemical crosslinking. The DNA is then digested, proteins disassociated, and the crosslinked fragments are ligated. Fragments are sequenced and mapped onto the genome to localise these interactions, 3C, chromosome conformation capture; 4C, chromosome conformation capture-on-chip; 5C, carbon copy chromosome conformation capture; ChIA-PET, chromatin interaction analysis by paired-end tag sequencing; CTCF, CCCTC-binding factor; Hi-C, chromosome capture followed by high-throughput sequencing.

Fig. 4

ChromHMM model and chromatin transcriptional states. “ChromHMM model based on melanoma tumour samples. Emission profile from a 15-State LearnModel based on the 6 histone modifications studied. ChromHMM identifies functionally distinct chromatin states representing both repressive and active domains, such as polycomb repression (State 1), heterochromatic repression (State 5), active transcription (State 8 and 9) and active enhancers (State 13 and 14).” (From Terranova et al.¹⁰⁶).

Fig. 5

Chromatin interactions around CXCL super-enhancer and co-induced gene promoter clusters. (A) TNF-α–induced SE and its interaction with the promoters of gene clusters, including IL-8, CXCL1, CXCL2, and CXCL3. CTCF, NF-κB p65, and BRD4 peaks are observed at the super-enhancer and the promoters of all these genes. (B) A snapshot of ENCODE data on the same gene loci. Chromatin immunoprecipitation-sequencing of CTCF in HUVEC shows the proximity of CTCF binding sites to the transcription start sites of all CXCL genes. BRD, bromodomain-containing; ChIP-Seq, chromatin immunoprecipitation-sequencing; CTCF, CCCTC-binding factor; CXCL, C-X-C motif chemokine ligand; HUVEC, human umbilical vein endothelial cell; IL8, interleukin-8; SE, super-enhancer.

Fig. 6

Epidrugs in alcohol-related liver disease. Based on their mechanism of action, epidrugs can be divided into 8 broad categories: DNMTi, HATi, HDACi, HMTi, histone demethylase inhibitor, proteins binding to methylated histones inhibitor, proteins binding to acetylated histones inhibitor, and ncRNAs (such as antisense-RNAs, small interfering RNAs, and miRNAs). Ac, acetyl group; BETi, bromodomain and extraterminal motif inhibitor; circRNA, circular RNA; DNMT(i), DNA methyltransferase (inhibitor); HAT(i), histone acetyltransferase (inhibitor); HDAC(i), histone deacetylase; HMT(i), histone methyltransferase (inhibitor); KDM, lysine demethylase; lncRNA, long non-coding RNA; MECP2, methyl-CpG binding protein 2; miRNA, microRNA; ncRNA, non-coding RNA; PADI4, peptidyl arginine deiminase 4; PHD, plant homeodomain; PRMT, protein arginine methyltransferase; TET, ten eleven translocation.