Comparative Analysis of Copy Number Variations in Ulcerative Colitis Associated and Sporadic Colorectal Neoplasia

Shivakumar, BM and Chakrabarty, Sanjiban and Rotti, Harish and Venu, Seenappa and Rao, Lakshmi and Geetha, Vasudevan and Kini, Hema and Pai, Ganesh C and Satyamoorthy, K (2016) Comparative Analysis of Copy Number Variations in Ulcerative Colitis Associated and Sporadic Colorectal Neoplasia. BMC Cancer, 16 (1). pp. 271-282. ISSN 1471-2407

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Abstract

Background: The incidence of and mortality from colorectal cancers (CRC) can be reduced by early detection.Currently there is a lack of established markers to detect early neoplastic changes. We aimed to identify the copy number variations (CNVs) and the associated genes which could be potential markers for the detection of neoplasia in both ulcerative colitis-associated neoplasia (UC-CRN) and sporadic colorectal neoplasia (S-CRN).Methods: We employed array comparative genome hybridization (aCGH) to identify CNVs in tissue samples of UC nonprogressor, progressor and sporadic CRC. Select genes within these CNV regions as a panel of markers were validated using quantitative real time PCR (qRT-PCR) method along with the microsatellite instability (MSI) in an independent cohort of samples. Immunohistochemistry (IHC) analysis was also performed.Results: Integrated analysis showed 10 overlapping CNV regions between UC-Progressor and S-CRN, with the 8q and 12p regions showing greater overlap. The qRT-PCR based panel of MYC, MYCN, CCND1, CCND2, EGFR and FNDC3A was successful in detecting neoplasia with an overall accuracy of 54 % in S-CRN compared to that of 29 % in UC neoplastic samples. IHC study showed that p53 and CCND1 were significantly overexpressed with an increasing frequency from pre- eoplastic to neoplastic stages. EGFR and AMACR were expressed only in the neoplastic conditions.Conclusion: CNVs that are common and unique to both UC-associated and sporadic colorectal neoplasm could be the key players driving carcinogenesis. Comparative analysis of CNVs provides testable driver aberrations but needs further evaluation in larger cohorts of samples. These markers may help in developing more effective neoplasia-detection strategies during screening and surveillance programs.

Item Type: Article
Uncontrolled Keywords: Colorectal cancer; Ulcerative colitis; aCGH; Copy number variations; Quantitative RT-PCR; IHC
Subjects: Medicine > KMC Manipal > Gastroenterology
Life Sciences > MLSC Manipal
Medicine > KMC Mangalore > Pathology
Medicine > KMC Manipal > Pathology
Depositing User: KMC Library
Date Deposited: 01 Jul 2016 08:58
Last Modified: 07 Jan 2017 16:04
URI: http://eprints.manipal.edu/id/eprint/146452

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