Genome wide analysis of DNA copy number neutral loss of heterozygosity (CNNLOH) and its relation to gene expression in esophageal squamous cell carcinoma

Nan Hu,Howard H Yang,Ti Ding,Maxwell P Lee,Philip R Taylor,Alisa M Goldstein,Robert J Clifford,Chaoyu Wang

doi:10.1186/1471-2164-11-576

Abstract

BackgroundGenomic instability plays an important role in human cancers. We previously characterized genomic instability in esophageal squamous cell carcinomas (ESCC) in terms of loss of heterozygosity (LOH) and copy number (CN) changes in tumors using the Affymetrix GeneChip Human Mapping 500K array in 30 cases from a high-risk region of China. In the current study we focused on copy number neutral (CN = 2) LOH (CNNLOH) and its relation to gene expression in ESCC.ResultsOverall we found that 70% of all LOH observed was CNNLOH. Ninety percent of ESCCs showed CNNLOH (median frequency in cases = 60%) and this was the most common type of LOH in two-thirds of cases. CNNLOH occurred on all 39 autosomal chromosome arms, with highest frequencies on 19p (100%), 5p (96%), 2p (95%), and 20q (95%). In contrast, LOH with CN loss represented 19% of all LOH, occurred in just half of ESCCs (median frequency in cases = 0%), and was most frequent on 3p (56%), 5q (47%), and 21q (41%). LOH with CN gain was 11% of all LOH, occurred in 93% of ESCCs (median frequency in cases = 13%), and was most common on 20p (82%), 8q (74%), and 3q (42%). To examine the effect of genomic instability on gene expression, we evaluated RNA profiles from 17 pairs of matched normal and tumor samples (a subset of the 30 ESCCs) using Affymetrix U133A 2.0 arrays. In CN neutral regions, expression of 168 genes (containing 1976 SNPs) differed significantly in tumors with LOH versus tumors without LOH, including 101 genes that were up-regulated and 67 that were down-regulated.ConclusionOur results indicate that CNNLOH has a profound impact on gene expression in ESCC, which in turn may affect tumor development.

Highlights

Genomic instability plays an important role in human cancers
Not every gene will map to every sample - in a particular sample, a gene may map to a gap between LOHCN regions. (ii) we identified genes for which at least two of the 17 esophageal squamous cell carcinomas (ESCC) samples with expression data were loss of heterozygosity (LOH) negative and at least two samples were LOH positive. (iii) We performed two-sided unpaired t-tests comparing the log2 fold changes for a probe set in LOH positive and LOH negative samples
In the present study we determined copy number and loss of heterozygosity (LOH) status in DNA isolated from germ-line and micro-dissected tumor and matched adjacent normal samples from 30 ESCC patients using the Affymetrix 500 K single nucleotide polymorphism (SNP) array

Summary

Introduction

We previously characterized genomic instability in esophageal squamous cell carcinomas (ESCC) in terms of loss of heterozygosity (LOH) and copy number (CN) changes in tumors using the Affymetrix GeneChip Human Mapping 500K array in 30 cases from a high-risk region of China. We identified several regions of LOH and CN alteration in ESCC using microsatellite markers and lowand high-density SNP arrays [22,23,24,25,26,27], where the majority of ESCC patients from this high-risk population were found to have high genomic instability and high frequency of LOH on several chromosome arms. Expression of BRCA2 was often increased (unpublished data)

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