The potential of PIK3CA, KRAS, BRAF, and APC hotspot mutations as a non-invasive detection method for colorectal cancer

Abstract

Background: Early diagnosis of colorectal cancer (CRC) can lead to prompt treatment modalities. Circulating cell-free DNA (cfDNA) analysis provides an alternative non-invasive procedure for the study of the molecular profiles of the corresponding tumor tissue. In this study, we aimed to investigate PIK3CA, KRAS, BRAF, and APC hotspot mutations in CRC tumor tissue, besides evaluating the diagnostic performance of KRAS, BRAF, and PIK3CA mutations in the plasma cfDNA.

Method: Primary CRC tissue samples and paired plasma samples were collected from 70 patients. After DNA extraction, PCR-direct sequencing was used to screen for mutations in PIK3CA exon 9 and APC exon 15 in tumor tissues. Amplification Refractory Mutation System (ARMS)-quantitative PCR (qPCR) was used to evaluate KRAS codon 12 and 13, BRAF V600E, and PIK3CA exon 9 hotspot mutations.

Results: PIK3CA exon 9 hotspot mutations were detected in 47.1% of tumor tissues and 20% of paired plasma cfDNA samples by ARMS-qPCR method, while Sanger sequencing did not identify any mutation in PIK3CA exon 9. The KRAS exon 2 mutations were detected in 71.4% and 34.3% of tumor tissue samples and paired plasma cfDNA respectively. BRAF V600E mutation was observed in 17.1% and 4.3% of tissue DNA and plasma cfDNA respectively. A panel of PIK3CA, KRAS, and BRAF showed a sensitivity of 61% and a specificity of 100% (AUC = 0.803). APC hotspot mutations were observed in 76.8% of CRC tissue samples. APC mutations were not analyzed in the plasma samples. The co-existence of KRAS/PIK3CA/APC gene mutations encompassed the highest frequency among all combinations of mutations. BRAF and PIK3CA mutations were significantly more frequent in older patients.

Conclusion: We demonstrated that a panel consisting of PIK3CA, KRAS, and BRAF mutations showed good diagnostic performance for detecting CRC in the plasma cfDNA.

Keywords: APC, (Adenomatous polyposis coli); BRAF, (v-Raf murine sarcoma viral oncogene homolog B); Biomarker; Cell free DNA; Colorectal neoplasm; KRAS, (Kirsten rat sarcoma viral oncogene homolog); Liquid biopsy; Mutation; PIK3CA, (phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha).