Fusion-Negative NTRK Overexpression Exhibit Biological Relevance in Colorectal Cancer: Implications for Prediction of Responses to Kinase Inhibitors

Background/Objectives: The aims of this study are to define the roles of the neurotrophic tyrosine receptor kinase genes NTRK1, NTRK2 and NTRK3 (NTRK1/2/3) in CRC and to determine the clinicopathological, molecular, cancer signalling and potential predictive significances of NTRK1/2/3 expression in CRC, irrespective of NTRK gene fusion. Methods: Standard statistical tests in SPSS were utilised to interrogate the associations and correlations between NTRK1/2/3 expression and clinicopathological, molecular and genomic features in two CRC cohorts. NTRK1/2/3 expression deregulation was also investigated using correlation and regression analyses. Furthermore, gene set enrichment analysis (GSEA) and pathway/drug ontology enrichment analysis (POEA/DOEA) were utilised to interrogate the enrichment of cancer signalling pathways, as well as NTRK and other tyrosine kinase inhibitor response in the CRC cohorts. Results: Whilst NTRK1 expression was higher in the CRC subset with microsatellite instability, NTRK2/3 expression was preferentially overexpressed in the microsatellite stable subsets. Moreover, there was differential NTRK1/2/3 expression with respect to clinicopathological and molecular/genomic indices. In addition, this study demonstrated that NTRK1/2/3 expression was deregulated by a combination of copy number alterations (NTRK2), aberrant methylation (NTRK1/2/3) and potentially and cryptic gene fusion (NTRK3). Furthermore, GSEA and POEA demonstrated that NTRK1/2/3-high CRC subsets exhibited enrichment of and cross-talks among the NTRK signalling pathways, as well as of known cancer signalling pathways. The GSEA and DOEA showed that NTRK signalling was enriched for kinase inhibitors responses, representing evidence that NTRK1/2/3 expression may serve as biomarkers for multiple kinase inhibitors, including entrectinib—the tissue-agnostic kinase inhibitor for cancers with NTRK gene fusions. Conclusions: The results demonstrated that fusion-negative NTRK signalling may be active in CRC and may contribute to the molecular pathogenesis and biology of the disease. The results also demonstrated that the NTRK1/2/3 expression may be predictive multiple kinase inhibitors.