Abstract A047: Molecular characterization of the malignancies with targetable NTRK gene fusions
Authors: Gatalica Zoran , Swensen Jeffrey , Kimbrough Jeffery , Xiu Joanne 
Published: August 2018

Abstract
Introduction: Targeted inhibitors of neurotropic tyrosine kinases are highly effective in selected patients with gene fusions involving NTRK1, NTRK2, or NTRK3 and are being actively investigated across cancer types. These fusions are consistently detected in rare cancer types (e.g., secretory breast carcinoma/MASC and infantile fibrosarcoma/congenital mesoblastic nephroma), but the occurrence of NTRK gene fusions in common cancer types is largely unexplored. Methods: Formalin-fixed, paraffin-embedded tumor tissues from 11,116 patients (Caris Life Sciences, Phoenix, AZ) were analyzed for 53 gene fusions (Archer FusionPlex) and additional sequencing of the 592 genes (NGS, Illumina). Total mutational load and gene copy number variations were calculated from the NGS results. NTRK protein (monoclonal rabbit antibody EPR17341, Abcam) and PD-L1 expression (SP142 or 22c3 monoclonal antibodies) were detected using immunohistochemistry (IHC). Results: Fusion assay identified 164 cases with a validated gene fusion (1.5% for the cohort), of which 23 cases (0.21% of the entire cohort) had an NTRK gene fusion. All 3 NTRK genes were involved in fusions with 13 different gene partners; TPM3:NTRK1 and ETV6:NTRK3 were the most common (6 cases each). Central nervous system malignancies had the highest frequency of NTRK fusions involving all 3 NTRK genes (11/400 cases, 2.8%), most commonly NTRK2 (7 cases fused with 7 different genes). NTRK2 fusions were exclusively detected in CNS malignancies (mostly GBM). Twelve non-CNS cases with NTRK1 or NTRK3 fusions included carcinomas of the respiratory tract (n=3), colon (n=2), thyroid (n=2), skin and cervix (n=1, each), uterine and soft tissue sarcoma (n=1, each), and one carcinoma of unknown primary (CUP) site. Strong (3+) and uniform (100% of cells) cytoplasmic/membranous expression of NTRK protein characterized NTRK1 fused cases (4 TPM3 and 1 MEF2D); NTRK2 fused cases were variably positive, while ETV6-NTRK3 cases were negative (0/6 cases). Of 23 NTRK fusion positive cases, eight had no other genomic alteration (pathogenic mutations or gene amplifications) which could be considered driving the cancer growth. Total mutational burden varied (1-37 somatic mutations per Mb) and was the highest in two MSI-H cases (CRC: TPM3-NTRK1 and CUP: ETV6-NTRK3). Additionally, PD-L1 expression was detected in 4 cases (lung and colon TPM3-NTRK1, GBM KCTD8-NTRK2 and CUP NTRK3:ETV6). Conclusion: Pathogenic NTRK genes fusions occur in a variety of cancers, but are generally rare (0.1%) outside primary CNS malignancies. NTRK may present as the only actionable target or co-occurring with other potentially targetable alterations (e.g., immune checkpoint inhibitors for PD-L1 positive or MSI-H cases). Uniform strong immunohistochemical staining for pNTRK may be a useful screening tool for NTRK1 gene fusion cancers outside the CNS.
Citation Format: Zoran Gatalica, Jeffrey Swensen, Jeffery Kimbrough, Joanne Xiu. Molecular characterization of the malignancies with targetable NTRK gene fusions [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr A047.