Genomic Analysis to Predict Response to Neoadjuvant Chemoradiation Therapy in Rectal Cancer

Abstract

The role of preoperative chemoradiation therapy is well established in the treatment of locally advanced rectal cancer. However, there remains significant heterogeneity in response to CRT, with only 50% of patients having some degree of response to neoadjuvant therapy. Currently, there is no established method to identify the subset of patients that do not response to treatment. Therefore, the purpose of this study was to utilize next generation DNA sequencing to assess for variants among a panel of 160 cancer-related genes to identify gene signatures among patients with pathologic complete response (pCR) compared to patients with no response (NR). A cohort of patients treated with neoadjuvant CRT followed by definitive surgery were selected from our clinical database and pathology archive (N=16). The pCR group included patients who had no evidence of residual tumor on pathologic assessment (N=8). In contrast, the NR group included patients who had >50% original tumor on final assessment. Tumor DNA was extracted from formalin-fixed paraffin-embedded tissue and libraries constructed with Comprehensive Cancer Panel (Qiagen). Sequencing was performed with Illumina NextSeq 500 and alignment was achieved using Biomedical Genomics Workbench with subsequent analysis with Ingenuity Variant Analysis. A comparison of the pretreatment biopsies from non-responders (n=8) versus complete responders (n=8) identified 178 individual variants in 71 genes. However, of these only 2 variants were found in more than one non-responder which were absent in all the complete responders. These variants were found in KDM6A and DNMT3A. Pathway analysis of all the variants found in non-responders identified “colorectal cancer metastasis signaling” as being highly altered. Analysis at the gene level identified 27 variants in 11 genes that were altered in the non-responder compared to the responders. There genes were CTNNB1, PIK3CA, APC, ECT2L, MET, ABL1, ATM, KRAS, AKT1, TP53 and EP300. Several of these genes were represented in the “epithelial-mesenchymal transition pathway”. This preliminary study has identified mutated genes which are present in the pretreatment biopsies of rectal cancer patients who do not respond to neoadjuvant chemoradiation. Genes involved in DNA repair, cell survival and epithelial-mesenchymal transition were amongst the genes altered. Several drug targets including PIK3CA, MET and DNA damage response may offer new avenues for combination therapy for these patients.