Clinical Multigene Panel Sequencing Identifies Distinct Mutational Association Patterns in Metastatic Colorectal Cancer.

Francesca Belardinilli,Angela Gradilone,Carlo Capalbo,Francesco Pepe,Pasquale Sibilio,Umberto Malapelle,Francesca Fabretti,Giancarlo Troncone,Mahdavian Yasaman,Pasquale Pisapia,Arianna Nicolussi,Paola Infante,Domenico Raimondo,Carlotta Liccardi,Gianluca Canettieri,Anna Coppa,Sonia Coni,Silvia Mezi,Valentina Magri,Edoardo Milanetti,Marialaura Petroni,Stefano Di Giulio,Caterina Bonfiglio,Paola Paci

doi:10.3389/fonc.2020.00560

Abstract

Extensive molecular characterization of human colorectal cancer (CRC) via Next Generation Sequencing (NGS) indicated that genetic or epigenetic dysregulation of a relevant, but limited, number of molecular pathways typically occurs in this tumor. The molecular picture of the disease is significantly complicated by the frequent occurrence of individually rare genetic aberrations, which expand tumor heterogeneity. Inter- and intratumor molecular heterogeneity is very likely responsible for the remarkable individual variability in the response to conventional and target-driven first-line therapies, in metastatic CRC (mCRC) patients, whose median overall survival remains unsatisfactory. Implementation of an extensive molecular characterization of mCRC in the clinical routine does not yet appear feasible on a large scale, while multigene panel sequencing of most commonly mutated oncogene/oncosuppressor hotspots is more easily achievable. Here, we report that clinical multigene panel sequencing performed for anti-EGFR therapy predictive purposes in 639 formalin-fixed paraffin-embedded (FFPE) mCRC specimens revealed previously unknown pairwise mutation associations and a high proportion of cases carrying actionable gene mutations. Most importantly, a simple principal component analysis directed the delineation of a new molecular stratification of mCRC patients in eight groups characterized by non-random, specific mutational association patterns (MAPs), aggregating samples with similar biology. These data were validated on a The Cancer Genome Atlas (TCGA) CRC dataset. The proposed stratification may provide great opportunities to direct more informed therapeutic decisions in the majority of mCRC cases.

Highlights

Colorectal carcinoma (CRC) is one of the most commonly diagnosed cancers worldwide [1, 2]
We report that a clinical genomic profiling via multigene panel sequencing allowed identification of pairwise mutation associations and eight distinct mutational association patterns (MAPs), providing great opportunities to direct more informed therapeutic decisions, in the majority of metastatic CRC (mCRC) cases
While mutations in the EGFR tyrosine-kinase domain are mutually exclusive with KRAS mutations and are positive predictive biomarkers for the efficacy of tyrosine kinase inhibitors in non-small cell lung cancer (NSCLC) [34, 47], these mutations are rare and scarcely relevant in predicting responses to antibodybased anti-EGFR therapy, in mCRC [48]. 8/11 EGFR mutation occurring in our mCRC cohort coexist with KRAS mutations

Summary

INTRODUCTION

Colorectal carcinoma (CRC) is one of the most commonly diagnosed cancers worldwide [1, 2]. We introduced a 22 multigene panel sequencing, which includes the clinically relevant RAS and BRAF hotspots, as a routine for the predictive selection of mCRC patients to be subjected to anti-EGFR therapy [25,26,27,28,29,30,31,32]. This implementation allowed us to accumulate a large dataset to ask the question of whether application of multigene panel sequencing to the standard diagnostics of mCRC could provide clinically useful information, with no extra-costs in terms of turnaround time and money. We employed the R package TCGAbiolinks [40] to retrieve patient’s Microsatellite Instability (MSI) status from the legacy archive of GDC data portal (https://portal.gdc.cancer.gov/)

RESULTS

DISCUSSION

ETHICS STATEMENT