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An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues
10:41

An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues

Published on: April 5, 2018

Gene expression alterations over large chromosomal regions in cancers include multiple genes unrelated to malignant

Brett G Masayesva1, Patrick Ha, Elizabeth Garrett-Mayer

  • 1Department of Otolaryngology-Head and Neck Surgery, Head and Neck Cancer Research Division, Johns Hopkins Medical Institutions, 720 Rutland Avenue, Baltimore, MD 21205, USA.

Proceedings of the National Academy of Sciences of the United States of America
|May 25, 2004
PubMed

Insights

DNA copy number changes in solid tumors significantly impact gene expression across large chromosomal regions. This study links allelic imbalance on chromosomes 3p and 22q to specific expression alterations in head and neck cancers.

Area of Science:

  • Oncology
  • Genomics
  • Molecular Biology

Background:

  • The correlation between DNA copy number alterations and gene expression across extensive chromosomal segments in solid tumors remains underexplored.
  • Head and neck squamous cell carcinoma (HNSCC) presents a model for investigating these genomic and transcriptomic relationships.

Purpose of the Study:

  • To systematically analyze the relationship between DNA copy number and gene expression across large chromosomal regions in HNSCC.
  • To determine if chromosomal allelic imbalance directly influences gene expression levels in malignant lesions.

Main Methods:

  • Utilized a 12,626-gene expression array to analyze HNSCC and normal oral mucosa.
  • Annotated gene expression data to specific chromosomal loci.
  • Performed microsatellite and chi-squared analyses on chromosomes 3p and 22q for allelic imbalance and expression correlation.

Main Results:

  • Expression alterations correlated with comparative genomic hybridization data.
  • Significant underexpression at 3p and overexpression at 22q were observed in tumors with corresponding allelic imbalance.
  • No significant expression differences were found in tumors lacking allelic imbalance on these specific chromosomal arms.

Conclusions:

  • Loss and gain of chromosomal material in solid tumors can broadly affect gene expression over large regions.
  • Chromosomal instability directly drives gene expression changes, impacting multiple genes, irrespective of their direct role in cancer progression.

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