Genome-wide DNA methylation profiling in differentiating Crohn’s disease from intestinal tuberculosis

Wu, Hao; Liu, Hongchun; Liu, Hai-Ning; Chen, Yanjie; Liu, Taotao; Shen, Xizhong; Liu, Huan

doi:10.1007/s13258-022-01224-1

Cited by 5 publications

(2 citation statements)

References 44 publications

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“…A systematic review of methylation in inflammatory bowel disease found consistent differential methylation was identified for 256 DMPs in the peripheral blood of IBD patients compared to healthy controls [84]. DNA methylation in the whole blood can also be used to differentiate Crohn's disease from intestinal tuberculosis, which is difficult to achieve clinically [85]. These studies suggest DNA methylation could provide biomarkers for future non-invasive diagnosis.…”

Section: Dna Methylation Biomarkers In Other Autoimmune Diseasesmentioning

confidence: 95%

DNA Methylation Signatures of Response to Conventional Synthetic and Biologic Disease-Modifying Antirheumatic Drugs (DMARDs) in Rheumatoid Arthritis

2023

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Rheumatoid arthritis (RA) is a complex condition that displays heterogeneity in disease severity and response to standard treatments between patients. Failure rates for conventional, target synthetic, and biologic disease-modifying rheumatic drugs (DMARDs) are significant. Although there are models for predicting patient response, they have limited accuracy, require replication/validation, or for samples to be obtained through a synovial biopsy. Thus, currently, there are no prediction methods approved for routine clinical use. Previous research has shown that genetics and environmental factors alone cannot explain the differences in response between patients. Recent studies have demonstrated that deoxyribonucleic acid (DNA) methylation plays an important role in the pathogenesis and disease progression of RA. Importantly, specific DNA methylation profiles associated with response to conventional, target synthetic, and biologic DMARDs have been found in the blood of RA patients and could potentially function as predictive biomarkers. This review will summarize and evaluate the evidence for DNA methylation signatures in treatment response mainly in blood but also learn from the progress made in the diseased tissue in cancer in comparison to RA and autoimmune diseases. We will discuss the benefits and challenges of using DNA methylation signatures as predictive markers and the potential for future progress in this area.

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Section: Dna Methylation Biomarkers In Other Autoimmune Diseasesmentioning

confidence: 95%

DNA Methylation Signatures of Response to Conventional Synthetic and Biologic Disease-Modifying Antirheumatic Drugs (DMARDs) in Rheumatoid Arthritis

2023

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“…Methylation of the VIM and SEPT9 genes had good diagnostic efficacy for colorectal cancer, while hypermethylation of the SFRP2 gene is an early diagnostic feature of colorectal cancer [8][9][10]. In ulcerative colitis (UC), the intestinal epithelium is highly methylated, and the highly methylated ESR-1 and N-33 genes can be used as diagnostic markers for UC [11][12][13][14]. At present, multiomics analysis, a method for comprehensively understanding biological systems through the comprehensive use of multilayer biological data, is also widely used in studying disease mechanisms, diagnosis and other fields.…”

Section: Introductionmentioning

confidence: 99%

Epigenetic Insights Into Necrotizing Enterocolitis: Unraveling Methylation-Regulated Biomarkers

Tian,

Xu,

et al. 2024

Inflammation

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Necrotizing enterocolitis (NEC) is a multifactorial gastrointestinal disease with high morbidity and mortality among premature infants. This study aimed to identify novel methylation-regulated biomarkers in NEC intestinal tissue through multiomics analysis. We analyzed DNA methylation and transcriptome datasets from ileum and colon tissues of patients with NEC. We identify methylation-related differential genes (MrDEGs) based on the rule that the degree of methylation in the promoter region is inversely proportional to RNA transcription. These MrDEGs included ADAP1, GUCA2A, BCL2L14, FUT3, MISP, USH1C, ITGA3, UNC93A and IL22RA1. Single-cell data revealed that MrDEGs were mainly located in the intestinal epithelial part of intestinal tissue. These MrDEGs were verified through Target gene bisulfite sequencing and RT-qPCR. We successfully identified and verified the ADAP1, GUCA2A, IL22RA1 and MISP, primarily expressed in intestinal epithelial villus cells through single-cell data. Through single-gene gene set enrichment analysis, we found that these genes participate mainly in the pathological process of T-cell differentiation and the suppression of intestinal inflammation in NEC. This study enhances our understanding of the pathogenesis of NEC and may promote the development of new precision medicine methods for NEC prediction and diagnosis.

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Epigenetics of Pulmonary Tuberculosis

Gupta,

Gilhotra,

Deopa

et al. 2023

Targeting Epigenetics in Inflammatory Lung Diseases

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Genome-wide DNA methylation profiling in differentiating Crohn’s disease from intestinal tuberculosis

Cited by 5 publications

References 44 publications

DNA Methylation Signatures of Response to Conventional Synthetic and Biologic Disease-Modifying Antirheumatic Drugs (DMARDs) in Rheumatoid Arthritis

DNA Methylation Signatures of Response to Conventional Synthetic and Biologic Disease-Modifying Antirheumatic Drugs (DMARDs) in Rheumatoid Arthritis

Epigenetic Insights Into Necrotizing Enterocolitis: Unraveling Methylation-Regulated Biomarkers

Epigenetics of Pulmonary Tuberculosis

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