New advances of DNA methylation in liver fibrosis, with special emphasis on the crosstalk between microRNAs and DNA methylation machinery

Transcriptional regulation of Glis2 in hepatic fibrosis

The role of Gli-similar 2 (Glis2) in hepatic fibrosis (HF) is controversial. In this study, we focused on the functional and molecular mechanisms involved in the Glis2-mediated activation of hepatic stellate cells (HSCs)-a milestone event leading to HF. The expression levels of Glis2 mRNA and protein were significantly decreased in the liver tissues of patients with severe HF and in mouse fibrotic liver tissues as well as HSCs activated by TGFβ1. Functional studies indicated that upregulated Glis2 significantly inhibited HSC activation and alleviated BDL-induced HF in mice. Downregulation of Glis2 was found to correlate significantly with DNA methylation of the Glis2 promoter mediated by methyltransferase 1 (DNMT1), which restricted the binding of hepatic nuclear factor 1-α (HNF1-α), a liver-specific transcription factor, to Glis2 promoters. In addition, the enrichment of DNMT1 in the Glis2 promoter region was mediated by metastasis-associated lung adenocarcinoma transcriptor-1 (MALAT1) lncRNA, leading to transcriptional silencing of Glis2 and activation of HSCs. In conclusion, our findings reveal that the upregulation of Glis2 can maintain the resting state of HSCs. The decreased expression of Glis2 under pathological conditions may lead to the occurrence and development of HF with the expression silencing of DNA methylation mediated by MALAT1 and DNMT1.

DNA 5mC and RNA m6A modification successively facilitates the initiation and perpetuation stages of HSC activation in liver fibrosis progression

Hepatic stellate cells (HSC) are key effector cells in liver fibrosis. Upon stimulation, the quiescent HSC undergoes complex morphological and functional changes to transdifferentiate into activated collagen-producing myofibroblasts. DNA/RNA methylations (5mC/m6A) are both implicated to participate in hepatic fibrosis, yet their respective roles and specific targets in HSC activation remain elusive. Here, we demonstrate that 5mC is indispensable for the initiation stage of HSC activation (myofibroblast transdifferentiation), whereas m6A is essential for the perpetuation stage of HSC activation (excessive ECM production). Mechanistically, DNA 5mC hypermethylation on the promoter of SOCS3 and PPARγ genes leads to STAT3-mediated metabolic reprogramming and lipid loss in the initiation stage. RNA m6A hypermethylation on the transcripts of major collagen genes enhances the mRNA stability in a YTHDF1-dependent manner, which contributes to massive ECM production. Vitamin A-coupled YTHDF1 siRNA alleviates CCl4-induced liver fibrosis in mice through HSC-specific inhibition of collagen production. HIF-1α, which is transactivated by STAT3, serves as a bridge linking the initiation and the perpetuation stages through transactivating YTHDF1. These findings indicate successive roles of DNA 5mC and RNA m6A modification in the progression of HSC activation, which provides new drug targets for epigenetic therapy of liver fibrosis.

Potential Blood DNA Methylation Biomarker Genes for Diagnosis of Liver Fibrosis in Patients With Biopsy-Proven Non-alcoholic Fatty Liver Disease

Background and objective

This pilot study aimed to identify potential blood DNA methylation (BDM) biomarker genes for the diagnosis of liver fibrosis in non-alcoholic fatty liver disease (NAFLD).

Methods

We included a total of 16 NAFLD patients with significant (SLF, liver fibrosis stage ≥ 2) and 16 patients with non-significant liver fibrosis (NSLF, fibrosis stages 0–1). The association between BDM and liver fibrosis was analyzed. Genes were selected based on a stepwise-filtering with CpG islands containing significant differentially methylated probes.

Results

The two groups of patients were distinguishable through both t-distributed stochastic neighbor embedding (t-SNE) analysis and unsupervised hierarchical clustering analysis based on their BDM status. BDM levels were significantly higher in the NSLF group than in the SLF group. The methylation levels in the island and shelf regions were also significantly higher in the NSLF group, as well as the methylation levels in the first exon, 3′-untranslated region, body, ExonBnd, non-intergenic region, transcription start site (TSS)1500, and TSS200 regions (all p < 0.05). BDM status was associated with greater histological liver fibrosis, but not with age, sex, or other histological features of NAFLD (p < 0.05). The methylation levels of the hypomethylated CpG island region of CISTR, IFT140, and RGS14 genes were increased in the NSLF group compared to the SLF group (all p < 0.05).

Conclusion

BDM may stratify NAFLD patients with significant and non-significant liver fibrosis. The CISTR, IFT140, and RGS14 genes are potential novel candidate BDM biomarkers for liver fibrosis and these pilot data suggest further work on BDM biomarkers is warranted.

Characterization of body composition and liver epigenetic markers during periods of negative energy balance and subsequent compensatory growth in postpubertal beef bulls

This study aimed to characterize the effects of dietary restriction and subsequent re-alimentation on body composition and hepatic gene expression of epigenetic markers of DNA methylation, RNA m6A methylation, and histone acetylation in the liver of postpubertal beef bulls. Twelve Angus × Hereford crossbred bulls (n = 6, 23 ± 0.55 mo [young bulls], 558 ± 6.1 kg; and n = 6, 47 ± 1.2 mo [mature bulls], 740 ± 30.5 kg) were submitted to two dietary regimes per offering of the same hay: low plane of nutrition (90 d) and compensatory growth (90 d). Each animal acted as its own control and were fed Beardless wheat (Triticum aestivum) hay and mineral mix during the trial. Statistical analyses were performed using SAS 9.4 following a pre-post repeated measures design. Bulls in negative energy balance (NEB) decreased (P < 0.001) empty body weight (EBW; 23.1% [-139.1 kg]), empty body fat (EBF; 39.8% [-85.4 kg]), and empty body protein (EBP; 14.9% [-13.5 kg]) and fully recovered at the end of the trial. Body fat accounted for 77.1% of daily changes in body energy status, whereas body protein accounted for only 22.9% (P < 0.001). Relative abundance of epigenetic markers transcripts was analyzed via qPCR. Bulls at NEB tended (P ≤ 0.097) to increase gene expression of epigenetic markers of RNA m6A methylation (METTL14, VIRMA, and WTAP) and increased (P ≤ 0.050) the gene expression of epigenetic markers of DNA methylation (DNMT3A) and histone-acetylation (SIRT3 and SIRT7). Young bulls had a tendency (P ≤ 0.072) of higher RNA m6A methylation, VIRMA, and WTAP than mature bulls. Effect of diet × age interaction was not detected (P ≥ 0.137) for METTL14, VIRMA, WTAP, DNMT3A, SIRT3, or SIRT7. Younger bulls tended to have greater RNA m6A methylation levels than mature bulls, indicating that, while contemporaneously fed the same diet during periods of undernourishment followed by compensatory growth, age has an impact on this epigenetic mechanism. In conclusion, metabolic status seems to carry a greater impact on regulating bovine hepatic epigenetic mechanisms that modulate gene transcription, such as DNA methylation and histone acetylation, than on epigenetic mechanisms that regulate gene translation, such as RNA m6A methylation. During periods of undernourishment followed by compensatory growth, body fat pools appear to change more dynamically and are easily detected having a greater impact on epigenetic markers that modulate hepatic gene transcription rather than translation.

Integrated analysis of differentially expressed genes, differentially methylated genes, and natural compounds in hepatitis C virus-induced cirrhosis

Objective

To identify key genes in hepatitis C virus (HCV)-induced cirrhosis and to predict effective drugs for its treatment.

Methods

Three datasets were used to screen for differentially expressed genes (DEGs) and differentially methylated genes (DMGs) in HCV-induced cirrhosis. DEGs were subjected to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses using the clusterProfiler R package. Their respective protein–protein interaction (PPI) networks were constructed using Cytoscape. Cross analysis of DEGs and DMGs was performed to identify the genetic landscape of HCV-induced cirrhosis, and five genes were validated by receiver operating characteristic curve analysis. Molecular autodocking between ISG15 and natural products was performed using AutoDock Tool 1.5.6.

Results

A total of 357 DEGs and 8,830 DMGs were identified. DEG functional analysis identified several pathways involved in the pathogenesis of HCV-induced cirrhosis. Cross analysis of DEGs and DMGs identified 212 genes, and PPI network analysis identified 25 hub genes. Finally, five genes including ISG15 were identified and confirmed in dataset GSE36411. Artesunate and betulinic acid were shown to have a strong binding affinity to ISG15.

Conclusion

Our study provides novel insights into the mechanisms of HCV-induced cirrhosis which could lead to the identification of new therapeutics.

Epigenetic Biomarkers for the Diagnosis and Treatment of Liver Disease

Research in the last decades has demonstrated the relevance of epigenetics in controlling gene expression to maintain cell homeostasis, and the important role played by epigenome alterations in disease development. Moreover, the reversibility of epigenetic marks can be harnessed as a therapeutic strategy, and epigenetic marks can be used as diagnosis biomarkers. Epigenetic alterations in DNA methylation, histone post-translational modifications (PTMs), and non-coding RNA (ncRNA) expression have been associated with the process of hepatocarcinogenesis. Here, we summarize epigenetic alterations involved in the pathogenesis of chronic liver disease (CLD), particularly focusing on DNA methylation. We also discuss their utility as epigenetic biomarkers in liquid biopsy for the diagnosis and prognosis of hepatocellular carcinoma (HCC). Finally, we discuss the potential of epigenetic therapeutic strategies for HCC treatment.

The interaction between microRNA-152 and DNA methyltransferase-1 as an epigenetic prognostic biomarker in HCV-induced liver cirrhosis and HCC patients

The necessity for early detection and hence improving the outcome of treatment of hepatocellular carcinoma (HCC) is critical especially in Hepatitis C virus (HCV)-Genotype 4 induced cases. In our current work, we examined the miRNA-152 and DNMT-1 expression in chronic liver disease (CLD) due to HCV genotype 4 infection with/without cirrhosis and HCC patients as an attempt to evaluate the potential benefits of these new circulating, noninvasive, prognostic, epigenetic markers for liver cirrhosis and carcinogenesis of Egyptian patients. Eighty subjects were included in this study, divided into two groups; group I (40 patients) were classified into subgroup Ia (CLD without cirrhosis, n = 18) and subgroup Ib (CLD with cirrhosis, n = 22), group II (CLD patients with HCC, n = 20), and control (Healthy volunteer, n = 20). The expression of miRNA-152 and DNMT-1 genes were analyzed using Real-Time PCR. MiRNA-152 showed a persistent and significant downregulation in all diseased groups, which was in consistence with the progression of the disease toward the HCC stage. DNMT-1 showed upregulation in all diseased groups when compared to control and subgroup Ia. The miRNA-152 was shown to correlate inversely with DNMT-1 in subgroup Ia, Ib and group II (r = -0.557, p < 0.01), (r = -0.850, p < 0.001) and (r = -0.544, p < 0.02) respectively. In addition, miRNA-152 and DNMT-1 showed a diagnostic ability to discriminate between cases of cirrhosis and HCC against CLD without cirrhosis (p < 0.01), while DNMT-1 did not, except between HCC and cirrhotic cases. Furthermore, both genes can be considered as predictor and prognostic parameters for cirrhosis (OR = 1.041, p = 0.043) and (OR = 1.039, p = 0.04) respectively, while miRNA-152 alone is proved as a prognostic marker for HCC (OR = 1.003, p = 0.044). Finally, the persistent reverse correlation between miRNA-152 with DNMT-1 prompts their use as noninvasive prognostic biomarkers for HCV induced liver cirrhosis and HCC in HCV Genotype 4 patients.

Pathological mechanisms and therapeutic outlooks for arthrofibrosis

Arthrofibrosis is a fibrotic joint disorder that begins with an inflammatory reaction to insults such as injury, surgery and infection. Excessive extracellular matrix and adhesions contract pouches, bursae and tendons, cause pain and prevent a normal range of joint motion, with devastating consequences for patient quality of life. Arthrofibrosis affects people of all ages, with published rates varying. The risk factors and best management strategies are largely unknown due to a poor understanding of the pathology and lack of diagnostic biomarkers. However, current research into the pathogenesis of fibrosis in organs now informs the understanding of arthrofibrosis. The process begins when stress signals stimulate immune cells. The resulting cascade of cytokines and mediators drives fibroblasts to differentiate into myofibroblasts, which secrete fibrillar collagens and transforming growth factor-β (TGF-β). Positive feedback networks then dysregulate processes that normally terminate healing processes. We propose two subtypes of arthrofibrosis occur: active arthrofibrosis and residual arthrofibrosis. In the latter the fibrogenic processes have resolved but the joint remains stiff. The best therapeutic approach for each subtype may differ significantly. Treatment typically involves surgery, however, a pharmacological approach to correct dysregulated cell signalling could be more effective. Recent research shows that myofibroblasts are capable of reversing differentiation, and understanding the mechanisms of pathogenesis and resolution will be essential for the development of cell-based treatments. Therapies with significant promise are currently available, with more in development, including those that inhibit TGF-β signalling and epigenetic modifications. This review focuses on pathogenesis of sterile arthrofibrosis and therapeutic treatments.

Alcohol or Not: A Review Comparing Initial Mechanisms, Contributing Factors, and Liver Transplantation Outcomes Between Alcoholic and Nonalcoholic Steatohepatitis

Chronic liver diseases take many forms; alcohol-related liver disease (ALD) and nonalcoholic fatty liver disease (NAFLD) are two common illnesses that potentially lead to cirrhosis, liver failure, and liver cancer. It is estimated that a quarter of heavy drinkers develop ALD and the same portion of people without heavy drinking habits have NAFLD. Alcohol intake is regularly used to differentiate NAFLD from ALD; however, diagnosis based on the discrimination threshold may be suboptimal when facing an obese patient with a high level of alcohol exposure. Therefore, understanding the common and/or different mechanism(s) driving each disease is extremely important. The ‘two-hit’ or ‘multi-hit’ hypothesis is used to explain the pathogenesis of both diseases. The ‘first hit’ refers to developing steatosis, the accumulation of fat components in the liver, and the ‘second hits’ are factors leading to oxidative stress, inflammation, and fibrosis, such as metabolic syndromes (e.g., morbid obesity, hyperglycaemia, hyperlipidaemia, disturbed circadian cycles, and altered intestinal microbiota) and environmental toxins (e.g., cigarette smoke and pollutants). Heritable factors also affect the probability and disease progression of both ALD and NAFLD. Whereas PNPLA3 and TM6SF2 variants are influential genetic risk factors for the diseases, epigenetic factors, such as DNA methylation, post-translational histone modifications, and small non-coding RNA, are of paramount importance. Moreover, considering that both ALD and NAFLD patients may eventually develop end-stage liver disease and require liver transplantation, the authors extensively investigated the worldwide outcomes from original literature for these two aetiologies, and the results showed no obvious differences in post-transplantation survival between them. Precise percentage determination of these two aetiologies contributing to steatohepatitis and its secondary injuries in the future would allow for better strategies for therapeutic and preventive intervention.

Epigenetic differences of chronic hepatitis B in different TCM syndromes: Protocol for a case-control, non-interventional, observational clinical study

INTRODUCTION

Chronic hepatitis B is a serious disease causing serious harm to the human health. Chinese medicine has its unique advantages in the clinical prevention and treatment, while the syndrome of Chinese medicine lacks the understanding at the micro level. There are some theoretical commonalities between the epigenetics and traditional Chinese medicine (TCM) syndromes. The biological basis of chronic hepatitis B (CHB) syndrome differentiation from the perspective of epigenetics is of great significance to diagnose and prevent the diseases.

METHODS

This protocol is a case-control, noninterventional, observational clinical study. Patients with CHB for spleen-stomach damp heat and liver depression and spleen deficiency, with 12 each and 11 healthy volunteers were recruited. Peripheral venous blood was collected from the participants. DNA methylated transferase, genomic DNA methylated spectrum, methylated DNA binding protein MeCP2, chronic infection of hepatitis B virus with methylated related proteins, and miRNA target genes were analyzed.

OBJECTIVES

From the perspective of DNA methylation epigenetics, "DNA methylation-miRNA-Target gene" is the main line, which further reveals the essence of TCM syndrome. To improve the level of TCM clinical syndrome differentiation and the clinical efficacy of TCM, especially in the study of TCM syndromes of CHB, discovering its underlying biological signature is necessary.

TRIAL REGISTRATION

Clinical Trials Registration: ChiCTR1800017365, registered 26 July 2018.

Genome-wide analysis of DNA methylation in human peripheral leukocytes identifies potential biomarkers of nonalcoholic fatty liver disease

The aim of the present study was to uncover the role of leukocytic DNA methylation in the evaluation of nonalcoholic fatty liver disease (NAFLD). Patients with biopsy-proven NAFLD (n=35) and normal controls (n=30) were recruited from Chinese Han population. Their DNA methylation in peripheral leukocytes was subjected to genome-wide profiling. The association between differential methylation of CpG sites and NAFLD was further investigated on the basis of histopathological classification, bioinformatics, and pyrosequencing. A panel of 863 differentially methylated CpG sites dominated by global hypomethylation, characterized the NAFLD patients. Hypomethylated CpG sites of Acyl-CoA synthetase long-chain family member 4 (ACSL4) (cg15536552) and carnitine palmitoyltransferase 1C (CPT1C) (cg21604803) associated with the increased risk of NAFLD [cg15536552, odds ratio (OR): 11.44, 95% confidence interval (CI): 1.04‑125.37, P=0.046; cg21604803, OR: 6.57, 95% CI: 1.02-42.15, P=0.047] at cut-off β-values of <3.36 (ACSL4 cg15536552) and <3.54 (CPT1C cg21604803), respectively, after the adjustment of age, sex, body mass index (BMI) and homeostasis model assessment of insulin resistant (HOMA-IR). Their methylation levels also served as biomarkers of NAFLD (ACSL4 cg15536552, AUC: 0.80, 95% CI: 0.62-0.98, P=0.009; CPT1C cg21604803, AUC: 0.78, 95% CI: 0.65-0.91, P=0.001). Pathologically, lowered methylation level (β-values <3.26) of ACSL4 (cg15536552) conferred susceptibility to nonalcoholic steatohepatitis (NASH). Taken together, genome-wide hypomethylation of peripheral leukocytes may differentiate NAFLD patients from normal controls. The leukocytic hypomethylated ACSL4 (cg15536552) was suggested to be a biomarker for the pathological characteristics of NAFLD.

miRNA-34b is directly involved in the aging of macrophages

BACKGROUND

MicroRNAs (miRNAs) are a class of short noncoding RNA that play important regulatory roles in living organisms. These RNA molecules are implicated in the development and progression of malignant diseases such as cancer and are closely associated with cell aging. Findings demonstrating that microRNA is associated with aging in macrophages have nevertheless rarely been reported.

AIMS

This study's objective was to investigate if miRNA-34 is linked to aging process of macrophages.

METHODS

We built a cell aging model in mouse RAW264.7 macrophages using D-galactose and determined the expression levels of miRNA-34a, miRNA-34b, and miRNA-34c in aging and normal macrophages by fluorescence quantitative polymerase chain reaction (q-PCR). We predicted a target gene of miRNA-34 using biological information techniques and constructed the recombinant plasmid pGL3-E2f3 for the putative target gene E2f3.

RESULTS

The expression level of miRNA-34b was 5.23 times higher in aging macrophages than in normal macrophages. The luciferase activity decreased by nearly 50 % in cells transfected with miRNA-34b mimics, while no significant decrease in luciferase activity was noted in cells transfected with the miRNA-34b inhibitor or unrelated sequences.

DISCUSSION

Our findings provide the groundwork for further research into the molecular mechanisms whereby miRNA-34b regulates the aging of macrophages.

CONCLUSIONS

miRNA-34b is associated with the aging of RAW264.7 macrophages, and E2f3 is a target gene of miRNA-34b.

Mechanisms and treatment of liver fibrosis

Hepatic fibrosis is a characteristic consequence of multiple chronic liver injuries. However, there are currently no specific drugs that can effectively reverse or prevent liver fibrosis progression. Liver fibrosis is a complex pathological process attributable to a variety of cytokines and molecular pathways. Therefore, further exploring the cellular and molecular mechanisms of liver fibrosis, unearthing specific anti-fibrosis targeted therapies and translation of the potential findings into clinical treatment are of great significance.

Epigenetic repression of long non-coding RNA MEG3 mediated by DNMT1 represses the p53 pathway in gliomas

Epigenetic regulation plays a significant role in gliomas. However, how methylation and long non-coding RNA (lncRNA) cooperates to regulate gliomas progression is largely unknown. In this investigation we showed that the downregulation of MEG3 expression due to hypermethylation of MEG3 was observed in gliomas tissues. Treatment of glioma cells with the DNA methylation inhibitor 5-Aza-2'-deoxycytidine (5-AzadC) decreased aberrant hypermethylation of the MEG3 promoter and prevented the loss of MEG3 expression. In addition, DNMT1 was involved in MEG3 promoter methylation, and was inversely correlated with MEG3 expression in gliomas. The inhibition of DNMT1 repressed the proliferation, clone formation, and induced apoptosis in glioma cells. Importantly, the inhibition of DNMT1 contributed to the activation of p53 pathways in gliomas cells. These results suggest that DNMT1-mediated MEG3 hypermethylation caused the loss of MEG3 expression, followed by the inhibition of the p53 pathways in gliomas.

PNPO Deficiency and Cirrhosis: Expanding the Clinical Phenotype?

We report the case of a 4-year-old boy with pyridoxamine 5-phosphate oxidase deficiency, now the second reported case to develop hepatic cirrhosis. He presented with an encephalopathy in the first 1.5 h of life and received a first dose of PLP at 40 h of life. PNPO gene sequencing identified homozygosity for a novel variant in exon 7, c.637C>T (p.Pro213Ser). Persistent elevations in alanine transferase and aspartate transferase combined with an echogenic liver on ultrasound prompted performance of a liver biopsy which demonstrated hepatic cirrhosis. This is the second reported case of hepatic cirrhosis in PNPO deficiency. The pathogenesis is unclear but may be related to epigenetic activation of purinergic signaling in the hepatic stellate cells. PNPO deficiency may in time prove to be a suitable candidate for consideration of therapeutic orthotropic liver transplantation in select patients.

Role and mechanisms of DNA methylation in liver diseases

DNA methylation plays an important role in disease development, cell differentiation, embryonic development, and environmental adaptation by regulating gene transcription, gene imprinting and X chromosome inactivation and defending from invasion of exogenous genetic material. DNA methylation is a hot topic in the study of epigenetics. Numerous studies have demonstrated that DNA methylation plays an important role in the occurrence and development of liver diseases, and it influences the process of liver diseases through regulation of the activation and expression of genes related to lipid metabolism, inflammation, and cell proliferation in liver cells. In this review, we will review the recent progress in understanding the role and mechanisms of DNA methylation in alcoholic liver disease, nonalcoholic fatty liver disease, viral hepatitis, liver fibrosis and hepatocellular carcinoma, with an aim to provide a theoretical basis for the treatment of liver diseases and drug development.

The wound healing, chronic fibrosis, and cancer progression triad

For decades tumors have been recognized as "wounds that do not heal." Besides the commonalities that tumors and wounded tissues share, the process of wound healing also portrays similar characteristics with chronic fibrosis. In this review, we suggest a tight interrelationship, which is governed as a concurrence of cellular and microenvironmental reactivity among wound healing, chronic fibrosis, and cancer development/progression (i.e., the WHFC triad). It is clear that the same cell types, as well as soluble and matrix elements that drive wound healing (including regeneration) via distinct signaling pathways, also fuel chronic fibrosis and tumor progression. Hence, here we review the relationship between fibrosis and cancer through the lens of wound healing.

Advances in research of epigenetic regulation in liver fibrosis

Liver fibrosis is a pathological repair process in response to chronic injury caused by various etiologies in the liver. Imbalance between the expression of pro-fibrosis genes and anti-fibrosis genes play a pivotal role in hepatic fibrosis. The important path of reversing liver fibrosis is the early diagnosis and effective treatment. Epigenetic modifications have been considered an initial event in the development of hepatic fibrosis. Epigenetic regulatory mechanisms in liver fibrosis are intricate, including DNA methylation, histone modification, and microRNAs (miRNAs). Recently, many researchers have studied the effect of fibrosis-related gene expression at the epigenetic level on hepatic stellate cell activation and myofibroblast differentiation in hepatic fibrosis. This review discusses the epigenetic regulation in liver fibrosis, with an aim to provide new insights into the early non-invasive diagnosis, condition assessment and targeted therapy of this disease.