Related Experiment Video

Updated: Jan 12, 2026

Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer
07:50

Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer

Published on: September 18, 2020

6.1K

Integrative methylation and transcriptomic analysis reveals key genes linking cellular senescence and metabolic

Xiaochen Ma1, Lu Chen2, Chenhe Yi1

  • 1Department of General Surgery, Hepatobiliary Surgery Center, Huashan Hospital & Cancer Metastasis Institute, Fudan University, Shanghai, China.

Bioscience Trends
|November 3, 2025
PubMed

Insights

This study uncovers a five-gene signature linking epigenomic changes to cellular senescence and metabolic reprogramming in colorectal liver metastasis (CRLM). This molecular hub may serve as a biomarker for patient stratification and targeted therapies.

Area of Science:

  • Oncology
  • Genomics
  • Epigenetics

Background:

  • Colorectal liver metastasis (CRLM) is a significant cause of cancer mortality.
  • The interplay between cellular senescence, metabolic reprogramming, and epigenomic alterations in CRLM is not well understood.

Purpose of the Study:

  • To identify key genes and pathways involved in the epigenomic rewiring of CRLM.
  • To discover a molecular signature for potential use in patient stratification and therapeutic strategies.

Main Methods:

  • Integrated genome-wide DNA methylation and RNA-seq data from paired primary tumors and liver metastases.
  • Applied machine learning (LASSO + SVM-RFE) to identify a gene signature.
  • Performed gene-set enrichment and immune deconvolution analyses.

Main Results:

  • Identified a five-gene signature (CXCL1, SERPINE1, NDRG1, SRM, GATM) associated with CRLM, characterized by hypomethylation and overexpression.
  • These genes are implicated in pathways like oxidative phosphorylation and focal adhesion.
  • Signature genes correlated with immunosuppressive immune cells and modulated chemo-resistance.

Conclusions:

  • A five-gene epigenetic-transcriptomic signature is identified in colorectal liver metastasis.
  • This signature holds potential as a biomarker for patient stratification and combination therapy development.
Keywords:
DNA hypomethylationchemoresistanceimmunosuppressive microenvironmentmachine-learning signaturepolyamine metabolism

More Related Videos

Molecular Profiling of the Invasive Tumor Microenvironment in a 3-Dimensional Model of Colorectal Cancer Cells and Ex vivo Fibroblasts10:33

Molecular Profiling of the Invasive Tumor Microenvironment in a 3-Dimensional Model of Colorectal Cancer Cells and Ex vivo Fibroblasts

Published on: April 29, 2014

11.4K
A Robust Discovery Platform for the Identification of Novel Mediators of Melanoma Metastasis07:41

A Robust Discovery Platform for the Identification of Novel Mediators of Melanoma Metastasis

Published on: March 8, 2022

2.8K

Related Concept Videos

Epigenetic Regulation01:37

Epigenetic Regulation

Epigenetic changes alter the physical structure of the DNA without changing the genetic sequence and often regulate whether genes are turned on or off. This regulation ensures that each cell produces only proteins necessary for its function. For example, proteins that promote bone growth are not produced in muscle cells. Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
X-chromosome...
3.7K
Epigenetic Regulation01:46

Epigenetic Regulation

Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
33.4K
PI3K/mTOR/AKT Signaling Pathway01:22

PI3K/mTOR/AKT Signaling Pathway

The mammalian target of rapamycin  (mTOR) is a serine/threonine kinase that regulates growth, proliferation, and cell survival in response to hormones, growth factors, or nutrient availability. This kinase exists in two structurally and functionally distinct forms: mTOR complex 1  (mTORC1) and mTOR complex 2  (mTORC2). The first form (mTORC1) is composed of a rapamycin-sensitive Raptor and proline-rich Akt substrate, PRAS40. In contrast,  mTORC2 consists of a...
5.3K
mTOR Signaling and Cancer Progression03:03

mTOR Signaling and Cancer Progression

The mammalian target of rapamycin or mTOR protein was discovered in 1994 due to its direct interaction with rapamycin. The protein gets its name from a yeast homolog called TOR. The mTOR protein complex in mammalian cells plays a major role in balancing anabolic processes such as the synthesis of proteins, lipids, and nucleotides and catabolic processes, such as autophagy in response to environmental cues, such as availability of nutrients and growth factors.
The mTOR pathway or the...
4.6K