Functional implications of the CpG island methylation in the pathogenesis of celiac disease

Molecular regulation of whole genome DNA methylation in heat stress response of dairy cows

BACKGROUND

Heat stress seriously affects the production and health of dairy cows and is a key factor limiting the sustainable development of the dairy industry. DNA methylation serves as an important epigenetic regulatory mechanism closely associated with an animal's response to heat stress. However, the specific molecular mechanism of DNA methylation in cows' heat stress response is not fully understood.

RESULTS

In this study, whole genome bisulfite sequencing analysis of blood identified 49861 specific differentially methylated regions corresponding to 7613 differentially methylated genes between spring and summer dairy cows. Among them, 4069 the promoter region of differentially methylated genes were significantly enriched in key biological pathways such as substance transport, reactive oxygen species metabolism, signal transduction, and energy metabolism. By integrating the expression data of 4069 promoter differentially methylated genes, 157 genes were further screened, and their DNA methylation levels were negatively correlated with gene expression. The changes in DNLZ, GNAS, and SMAD5 genes were most significant, and network analysis showed that DNLZ gene has high connectivity in the protein-protein interaction network, indicating its potential key function in heat stress response. Experimental verification shows that under heat stress conditions, the methylation level of CpG islands in the promoter region of DNLZ gene significantly increases, and its methylation level is significantly negatively correlated with gene expression level. The Dual-luciferase reporter assays using constructs containing the DNLZ promoter reporter gene experiment further confirms that promoter methylation significantly inhibits DNLZ transcriptional activity, and the higher the degree of methylation, the stronger the inhibitory effect.

CONCLUSIONS

The research results provide new insights into the mechanism of heat stress-related DNA methylation in dairy cows, clarify the key roles of genes such as DNLZ, and provide potential target genes and epigenetic markers for the cultivation of heat-resistant dairy cows.

Gut dysbiosis: cause or consequence of intestinal inflammation in celiac disease?

INTRODUCTION

Celiac disease (CeD) is an immune-mediated condition that occurs in genetically predisposed individuals ingesting gluten. It is characterized by enteropathy leading to both gastrointestinal and extra-intestinal symptoms. The prevalence of CeD has increased world-wide. Evidence suggests that genetic predisposition and exposure to gluten are necessary but not sufficient for CeD onset, implying that other unknown factors are at play in its pathogenesis.

AREAS COVERED

This review summarizes the current knowledge on the contribution of the gut microbiota to CeD pathogenesis, aiming to address the question of whether it is the cause or consequence of the celiac enteropathy. We reviewed the current literature (studies published in PubMed database between 2007 and 2023), linking gut microbiota dysbiosis and CeD, focusing specifically on prospective birth cohorts' studies and discussing how multi-omics and artificial intelligence (AI) could transform the diagnosis of CeD in a personalized medicine approach.

EXPERT OPINION

A multi-omic approach will allow for better clarification of the pivotal role of the microbiome in epigenetically triggering CeD pathogenesis. Further, the combination of multi-omics results with AI would pave the way to an improved CeD diagnosis and to the identification of new personalized therapeutic interventions.

LINE-1 hypomethylation characterizes the inflammatory response in coeliac disease associated-intestinal mucosa and small bowel adenocarcinomas

Long interspersed nuclear elements 1 (LINE-1) are the most abundant and the only autonomous mobile elements in the human genome. When their epigenetic repression is removed, it can lead to disease, such as autoimmune diseases and cancer. Coeliac disease (CeD) is an immune-mediated disease triggered by an abnormal T-cell response to dietary gluten and a predisposing condition of small bowel adenocarcinoma (SBA), frequently characterized by epigenetic alterations. The aim of this work was to assess LINE-1 methylation by bisulphite pyrosequencing and NanoString® gene transcription analysis in 38 CeD-SBAs compared with 25 SBAs associated with Crohn's disease (CrD-SBAs) and 25 sporadic SBAs (S-SBA). Both analyses were also performed in duodenal mucosae from 12 untreated CeD patients (UCD) and 19 treated CeD patients (TCD), and in 11 samples of normal intestinal mucosa to better investigate the role of LINE-1 deregulation in CeD and in CeD-SBA. A significant loss of LINE-1 methylation was observed in CeD-SBAs and in mucosae from UCD patients (with very similar methylation levels) compared with controls. By contrast, a restoration of normal LINE-1 methylation levels was found in TCD mucosae after a strict gluten-free diet. LINE-1 hypomethylation does not lead to expression of ORF1 and ORF2, with the only exception being for one CeD-SBA. The expression analysis of enzymes modulating DNA methylation and inflammatory genes confirmed that CeD-SBA shared a very similar expression profile of UCD mucosae showing a strong upregulation of genes involved in inflammation, immune response, and T-cell activity compared with TCD mucosae. For the first time, this work demonstrates that loss of DNA methylation is an intrinsic epigenetic feature of CeD, accompanying the immune response as a reversible mechanism in patients following a strict gluten-free diet, and suggests the possible role of LINE-1 hypomethylation in promoting cell adaptability during the gliadin-related inflammatory process. © 2024 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Research progress and applications of epigenetic biomarkers in cancer

Epigenetic changes are heritable changes in gene expression without changes in the nucleotide sequence of genes. Epigenetic changes play an important role in the development of cancer and in the process of malignancy metastasis. Previous studies have shown that abnormal epigenetic changes can be used as biomarkers for disease status and disease prediction. The reversibility and controllability of epigenetic modification changes also provide new strategies for early disease prevention and treatment. In addition, corresponding drug development has also reached the clinical stage. In this paper, we will discuss the recent progress and application status of tumor epigenetic biomarkers from three perspectives: DNA methylation, non-coding RNA, and histone modification, in order to provide new opportunities for additional tumor research and applications.

The connection between epigenetics and gut microbiota-current perspective

Both the epigenetic changes and gut microbiota (GM) have attracted a growing interest in establishing effective diagnostics and potential therapeutic strategies for a number of diseases. These disorders include metabolic, central nervous system-related diseases, autoimmune, and gastrointestinal infections (GI). Despite the number of studies, there is no extensive review that connects the epigenetics modifications and GM as biomarkers that could confer effective diagnostics and confer treatment options. To this end, this review hopes to give detailed information on connecting the modifications in epigenetic and GM. An updated and detailed information on the connection between the epigenetics factors and GM that influence diseases are given. In addition, the review showed some associations between the epigenetics to the maternal GM and offspring health. Finally, the limitations of the concept and prospects into this new emerging discipline were also looked into. Although this review elucidated on the maternal diet and response to offspring health with respect to GM and epigenetic modifications, there still exist various limitations to this newly emerging discipline. In addition to integrating complementary multi-omics data, longitudinal sampling will aid with the identification of functional mechanisms that may serve as therapeutic targets. To this end, this review gave a detailed perspective into harnessing disease diagnostics, prevention and treatment options through epigenetics and GM.

Malignancies in Patients with Celiac Disease: Diagnostic Challenges and Molecular Advances

Celiac disease (CD) is a multiorgan autoimmune disorder of the chronic intestinal disease group characterized by duodenal inflammation in genetically predisposed individuals, precipitated by gluten ingestion. The pathogenesis of celiac disease is now widely studied, overcoming the limits of the purely autoimmune concept and explaining its hereditability. The genomic profiling of this condition has led to the discovery of numerous genes involved in interleukin signaling and immune-related pathways. The spectrum of disease manifestations is not limited to the gastrointestinal tract, and a significant number of studies have considered the possible association between CD and neoplasms. Patients with CD are found to be at increased risk of developing malignancies, with a particular predisposition of certain types of intestinal cancer, lymphomas, and oropharyngeal cancers. This can be partially explained by common cancer hallmarks present in these patients. The study of gut microbiota, microRNAs, and DNA methylation is evolving to find the any possible missing links between CD and cancer incidence in these patients. However, the literature is extremely mixed and, therefore, our understanding of the biological interplay between CD and cancer remains limited, with significant implications in terms of clinical management and screening protocols. In this review article, we seek to provide a comprehensive overview of the genomics, epigenomics, and transcriptomics data on CD and its relation to the most frequent types of neoplasms that may occur in these patients.