Integrated Analysis of Copy Number Variation and Genome-Wide Expression Profiling in Colorectal Cancer Tissues

Roslan Harun,Hassan Ashktorab,Nur Zarina Ali Hassan,Teow Kok Sin,Norfilza Mohd Mokhtar,Isa Mohamed Rose,Rahman Jamal,Ismail Sagap

doi:10.1371/journal.pone.0092553

Abstract

Integrative analyses of multiple genomic datasets for selected samples can provide better insight into the overall data and can enhance our knowledge of cancer. The objective of this study was to elucidate the association between copy number variation (CNV) and gene expression in colorectal cancer (CRC) samples and their corresponding non-cancerous tissues. Sixty-four paired CRC samples from the same patients were subjected to CNV profiling using the Illumina HumanOmni1-Quad assay, and validation was performed using multiplex ligation probe amplification method. Genome-wide expression profiling was performed on 15 paired samples from the same group of patients using the Affymetrix Human Gene 1.0 ST array. Significant genes obtained from both array results were then overlapped. To identify molecular pathways, the data were mapped to the KEGG database. Whole genome CNV analysis that compared primary tumor and non-cancerous epithelium revealed gains in 1638 genes and losses in 36 genes. Significant gains were mostly found in chromosome 20 at position 20q12 with a frequency of 45.31% in tumor samples. Examples of genes that were associated at this cytoband were PTPRT, EMILIN3 and CHD6. The highest number of losses was detected at chromosome 8, position 8p23.2 with 17.19% occurrence in all tumor samples. Among the genes found at this cytoband were CSMD1 and DLC1. Genome-wide expression profiling showed 709 genes to be up-regulated and 699 genes to be down-regulated in CRC compared to non-cancerous samples. Integration of these two datasets identified 56 overlapping genes, which were located in chromosomes 8, 20 and 22. MLPA confirmed that the CRC samples had the highest gains in chromosome 20 compared to the reference samples. Interpretation of the CNV data in the context of the transcriptome via integrative analyses may provide more in-depth knowledge of the genomic landscape of CRC.

Highlights

Colorectal cancer is a major health concern, with more than a million individuals diagnosed every year worldwide [1]
One common form of structural variants due to chromosomal instability (CIN) is known as copy number variations (CNVs), which is defined as a gain or loss of copies of DNA segments that are larger than 1 kb in length when compared to a reference genome [6]
Of the 8722 genomic segments in all samples, we narrowed down our analysis to 2212 CNV regions that corresponded to the autosomes that showed amplifications (Table S1)

Summary

Introduction

Colorectal cancer is a major health concern, with more than a million individuals diagnosed every year worldwide [1]. This cancer is among the top three of all cancers that lead to death worldwide [2]. Aneuploidy is a consequence of CIN that leads to the gain or loss of whole or parts of chromosomal regions [5], and it may cause structural complexity that leads to genomic instability. One common form of structural variants due to CIN is known as copy number variations (CNVs), which is defined as a gain or loss of copies of DNA segments that are larger than 1 kb in length when compared to a reference genome [6]. It has been suggested that transcriptional changes correspond to CNVs and alterations in gene dosage can be correlated with changes in expression level [7]

Objectives

Methods

Results

Conclusion