Clinical Epigenetics in Gastroenterology

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Human Genomics and Genetic Diseases".

Deadline for manuscript submissions: closed (5 September 2024) | Viewed by 2072

Special Issue Editor


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Guest Editor
Department of Surgery, Yale School of Medicine, New Haven, CT 06520, USA
Interests: appendiceal cancer; epigenetics; translational research; cancer biomarkers; gastrointestinal cancer; precision oncology; epigenetic-specific biomarker
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Special Issue Information

Dear Colleagues,

Clinical epigenetics is a rapidly evolving field that holds great promise for revolutionizing the field of gastroenterology, offering novel insights into disease mechanisms to diagnose, prevent, and enable the development of targeted therapies for various gastrointestinal diseases. This issue explores the role of epigenetics in gastroenterology, highlighting key aspects such as disease mechanisms, diagnostic and prognostic markers, therapeutic strategies, and the role of liquid biopsy approaches in precision medicine.

Environmental factors, diets, and lifestyles are just a few elements that can induce changes in epigenetic mechanisms. Within gastroenterology, pivotal processes like DNA methylation, histone modification, and the regulation of non-coding RNAs (ncRNAs) are instrumental in both the onset and progression of gastrointestinal diseases. Several conditions, including pancreatic cancer, colorectal cancer, inflammatory bowel disease, and other rare diseases, have been associated with distinct epigenetic alterations. For instance, aberrant DNA methylation patterns are commonly observed in multiple gastrointestinal cancers, leading to the silencing of tumor suppressor genes and oncogene activation. Similarly, histone modifications and ncRNA have been implicated in the pathogenesis of inflammatory bowel disease, affecting inflammatory pathways and immune responses.

As research in this area continues to advance, it is expected to significantly impact the management of gastrointestinal diseases, improving patient care and clinical outcomes. Topics can cover but are not limited to the following areas of interest.

  • The interplay of genetics, epigenetics, and the cellular microenvironment.
  • Epigenetic mechanisms in gastrointestinal diseases (epigenetic plasticity, chromatin remodeling, disease heterogeneity, and spatial biology).
  • The epigenetic regulation of immune responses.
  • The integration of clinical epigenetics and systems biology approaches.
  • Epigenetic engineering and its potential application in gastrointestinal diseases.
  • Liquid and tissue biopsy in precision medicine (diagnostic, prognostic, therapeutic targets, surveillance, tissue of origins, and minimal residual diseases).

Dr. Anup R. Sharma
Guest Editor

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Keywords

  • epigenetics
  • gastrointestinal diseases
  • DNA methylation
  • histone modification
  • RNAs
  • diagnostic
  • biomarkers
  • precision medicine
  • pancreatic cancer
  • colorectal cancer
  • inflammatory bowel disease
  • and other rare diseases

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Published Papers (1 paper)

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15 pages, 4213 KiB  
Article
Metabolic Transcriptional Activation in Ulcerative Colitis Identified Through scRNA-seq Analysis
by Christophe Desterke, Yuanji Fu, Raquel Francés and Jorge Mata-Garrido
Genes 2024, 15(11), 1412; https://doi.org/10.3390/genes15111412 - 31 Oct 2024
Viewed by 1611
Abstract
Background: Ulcerative colitis is a chronic inflammatory disease affecting the colon. During chronic inflammation of epithelial cells, lipid metabolism via pro-inflammatory eicosanoids is known to modify the immune response. Methods: Starting from the Mammalian Metabolic Database, the expression of metabolic enzymes was investigated [...] Read more.
Background: Ulcerative colitis is a chronic inflammatory disease affecting the colon. During chronic inflammation of epithelial cells, lipid metabolism via pro-inflammatory eicosanoids is known to modify the immune response. Methods: Starting from the Mammalian Metabolic Database, the expression of metabolic enzymes was investigated in two independent cohorts from transcriptome datasets GSE38713 and GSE11223, which analyzed ulcerative colitis tissue samples from the digestive tract. Results: In the first cohort, 145 differentially expressed enzymes were identified as significantly regulated between ulcerative colitis tissues and normal controls. Overexpressed enzymes were selected to tune an Elastic Net model in the second cohort. Using the best parameters, the model achieved a prediction accuracy for ulcerative colitis with an area under the curve (AUC) of 0.79. Twenty-two metabolic enzymes were found to be commonly overexpressed in both independent cohorts, with decreasing Elastic Net predictive coefficients as follows: LIPG (3.98), PSAT1 (3.69), PGM3 (2.74), CD38 (2.28), BLVRA (1.99), CBR3 (1.94), NT5DC2 (1.76), PHGDH (1.71), GPX7 (1.58), CASP1 (1.56), ASRGL1 (1.4), SOD3 (1.25), CHST2 (0.965), CHST11 (0.95), KYNU (0.94), PLAG2G7 (0.92), SRM (0.87), PTGS2 (0.80), LPIN1 (0.47), ME1 (0.31), PTGDS (0.14), and ADA (0.13). Functional enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database highlighted the main implications of these enzymes in cysteine and methionine metabolism (adjusted p-value = 0.01), arachidonic acid and prostaglandin metabolism (adjusted p-value = 0.01), and carbon metabolism (adjusted p-value = 0.04). A metabolic score based on the transcriptional activation of the validated twenty-two enzymes was found to be significantly greater in Ulcerative colitis samples compared to healthy donor samples (p-value = 1.52 × 10−8). Conclusions: A metabolic expression score was established and reflects the implications of heterogeneous metabolic pathway deregulations in the digestive tract of patients with ulcerative colitis. Full article
(This article belongs to the Special Issue Clinical Epigenetics in Gastroenterology)
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