Abstract A133: Genetic heterogeneity in rectal cancer: Identification of subpopulations of tumor cells resistant to neoadjuvant CRT.
Authors: Bettoni Fabiana , Donnard Elisa R. , Correa Bruna R. S. , Asprino Paula F. , Koyama Fernanda C. , Felício Natália M. , Hessel Bruna H. , Galante Pedro A. F. , Camargo Anamaria A. , Habr-Gama Angelita , Perez Rodrigo O. 
Published: August 2014

One of the benefits of neoadjuvant chemotherapy and radiation therapy (CRT) for the management of rectal cancer is tumor downstaging that can ultimately lead to complete tumor regression (known as complete pathological response - pCR). In a previous study using PET/CT imaging to assess tumor response to CRT, 50% of rectal cancers showed a continuous decrease in metabolic activity (estimated by standard uptake value measurements) between 6 and 12 weeks from CRT completion. However the remaining 50% of the cases showed increased metabolic activity within that period. We reasoned that the increased metabolic activity observed in these later patients could be determined by the clonal expansion of a genetically distinct subpopulation of tumor cells resistant to CRT. To address this question we performed exome sequencing and mutation detection analysis on normal tissue, primary tumor and residual tumor from one patient with rectal cancer that exhibited an increase in metabolic activity after CRT. Approximately, 15Gb of unambiguously mapped sequences were generated for each normal tissue and residual tumor and 25Gb of mapped sequences were generated for primary tumor. Over 51% of the bases mapped to the targeted regions, resulting in an average fold-coverage of 30X. Captured sequences mapped to the reference human genome were then used for the detection of SNPs and non-synonymous somatic point mutations in all three samples from this patient. Approximately 30,000 single nucleotide variants (SNVs) were identified in each sample and most of the SNVs were common to all samples. As expected, the majority of these common inherited variants (96%) have already been described in dbSNP. To identify non-synonymous somatic mutations occurring in primary and residual tumor samples, we excluded those present in the normal sample and those already described as a known SNP in dbSNP. Noteworthy, a significant number of non-synonymous somatic mutations were exclusively found in the primary and residual tumor samples revealing a high degree of tumor genetic heterogeneity. A total of 80 non-synonymous somatic mutations were present in both samples, and for these mutations we determined the mutant allele frequency (number of reads representing the mutation/total number of reads covering the mutated base) in the primary and the residual tumor. We then searched for mutations with significantly different allele frequencies in the two samples, as these mutations would likely represent genetically distinct subpopulations of tumor cells selected during CRT. Functional analysis of these mutations and mutated genes will be presented, providing new insights into the molecular events influencing response to neoadjuvant CRT in rectal cancer.

Citation Information: Mol Cancer Ther 2013;12(11 Suppl):A133.

Citation Format: Fabiana Bettoni, Elisa R. Donnard, Bruna R. S. Correa, Paula F. Asprino, Fernanda C. Koyama, Natália M. Felício, Bruna H. Hessel, Pedro A. F. Galante, Anamaria A. Camargo, Angelita Habr-Gama, Rodrigo O. Perez. Genetic heterogeneity in rectal cancer: Identification of subpopulations of tumor cells resistant to neoadjuvant CRT. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr A133.