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An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues
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Changes in gene-gene interactions associated with cancer onset and progression are largely independent of changes in

Zainab Arshad1, John F McDonald1

  • 1Integrated Cancer Research Center, School of Biological Sciences, Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, 315 Ferst Drive, Atlanta, GA 30619, USA.

Iscience
|December 17, 2021
PubMed

Insights

Cancer progression involves complex gene interactions, not just individual gene changes. Network analysis reveals reduced complexity in tumors, with stable connections linked to essential functions and new ones to cancer promotion.

Area of Science:

  • Genomics
  • Systems Biology
  • Cancer Research

Background:

  • Cancer development involves genetic alterations.
  • Gene expression changes are key factors in cancer.
  • Gene interactions also play a crucial role in cancer.

Purpose of the Study:

  • To investigate gene-network structural changes during cancer onset and progression.
  • To analyze co-expression patterns across nine cancer types.
  • To understand the role of gene interactions versus gene expression in cancer.

Main Methods:

  • Analysis of gene co-expression networks.
  • Comparison of network structures between normal and tumor tissues.
  • Examination of gene-gene interaction stability and function.
  • Assessment of changes in gene expression relative to network alterations.

Main Results:

  • Network complexity decreases from normal to primary tumor tissues.
  • Early-stage cancers show increased cross-tissue network similarity, which is lost in later stages.
  • Stable gene connections are associated with housekeeping functions.
  • Newly formed interactions are linked to cancer-promoting functions.
  • >90% of network interaction changes occur independently of gene expression changes.

Conclusions:

  • Gene network structure dynamics are critical in cancer.
  • Cancer progression involves significant rewiring of gene interactions.
  • Most gene interaction changes in cancer are not driven by altered gene expression.
Keywords:
Cancer systems biologyClassification DescriptionSystems biologyTranscriptomics

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