Abstract C61: Genetic alterations in the TP53 genomic region of African American and Caucasian colorectal cancers
Authors: Salazar-Gonzalez Jesus F. , Salazar Maria G. , Putcha Balananda Dhurjati Kumar , Partridge Edward E. , Fouad Mona N. , Upender Manne 
Published: May 2015

Abstract
Purpose: In the US, colorectal cancer (CRC) is the second leading cause of cancer-related deaths and the third most common cancer in both men and women. CRC affects African Americans (AAs) disproportionately, relative to non-Hispanic Caucasians (CAs). Data from our prior studies indicate that the p53 codon 72 polymorphism is disproportionately higher in AAs compared to CAs [Clin Cancer Res; 15(14); 2406–-2416. 2009]. It is also evident that genetic human diversity is due not only to single nucleotide polymorphisms (SNPs), but also to structural variants or retrotransposons. Retrotransposons induce mutations, near or within genes by several mechanisms: insertions, deletions, duplications, copy number variants, inversions, or translocations, all of which expand human diversity and possibly alter cancer susceptibility. Thus, our objectives are to establish genomic profiles of the p53 tumor suppressor (TP53) region of CRCs of AA and CA patients to identify race/ethnic-specific alterations that are associated with ancestry, and to develop a DNA sequencing protocol to delineate AA and CA patient profiles using this complex genomic region (∼19 Kb).
Methods: Genomic DNA was extracted from 4 frozen tissue samples (2 CRCs and their corresponding normal pairs) and 4 (2 CRCs/normal pairs) formalin-fixed, paraffin-embedded (FFPE) tissues. For the DNA of two CRC patients (one tumor/normal pair each of AA and CA patients), the complete TP53 gene (∼19 Kb, including exons and introns) was amplified by PCR in two halves, followed by Illumina next-generation sequencing and comparison to the human genome 19 reference sequence. For each patient, paired normal (benign/control) and tumor tissue DNAs were compared.
Results: TheTP53 gene was amplified from DNA extracted from all 4 frozen CRC tissues, but not from the 4 FFPE tissues. Sequence comparisons of normal versus tumor DNA revealed 80 single nucleotide polymorphisms (SNPs). Most (96%, n=77) located within introns. Of these, 34 were shared by AA and CA patients. In contrast, 8 SNPs were detected only in a CA patient, and 13 others were present only in an AA patient. Two SNPs found in our AA patient were absent in our CA patient and in the publicly available HapMap database of CAs, suggesting that these SNPs reflect African ancestry. Also, 22 SNPs were exclusively present in the CA tumor, whereas only 3 SNPs were unique to the AA tumor. These findings deserve further investigation.
Conclusions: We developed PCR protocols that should allow us to conduct a comprehensive mutational profiling of coding and non-coding regions of the TP53 genomic region in DNA isolated from frozen tissues. Comparison of genetic alteration profiles of TP53 in AAs and CAs will aid in determining the race/ethnicity of CRC patients. These studies were supported by a Charles Barkley Foundation grant though the UAB MHRC and a pre-pilot project of the UAB/TU/MSM Partnership grant, U54-CA 118948.
Citation Format: Jesus F. Salazar-Gonzalez, Maria G. Salazar, Balananda Dhurjati Kumar Putcha, Edward E. Partridge, Mona N. Fouad, Manne Upender. Genetic alterations in the TP53 genomic region of African American and Caucasian colorectal cancers. [abstract]. In: Proceedings of the Sixth AACR Conference: The Science of Cancer Health Disparities; Dec 6–9, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2014;23(11 Suppl):Abstract nr C61. doi:10.1158/1538-7755.DISP13-C61