Analysis of NTRK Alterations in Pan-Cancer Adult and Pediatric Malignancies: Implications for NTRK-Targeted Therapeutics

Abstract

Purpose: Fusions that involve neurotrophic-tropomyosin receptor kinase (NTRK) genes are known drivers of oncogenesis. Therapies that target these ultra-rare, constitutionally active NTRK fusions have been remarkably effective. Herein, we analyze the prevalence of the full array of NTRK alterations-fusions, mutations, copy number alterations, and increased transcript expression-in diverse adult and pediatric tumor types to understand the landscape of NTRK aberrations in cancer.

Methods: We assessed 13,467 samples available from The Cancer Genome Atlas (adult tumors) and the St Jude PeCan database (pediatric tumors) for the prevalence of NTRK fusions, as well as associated genomic and transcriptomic co-aberrations in different tumor types.

Results: NTRK fusions were observed in 0.31% of adult tumors and in 0.34% of pediatric tumors. The most common gene partners were NTRK3 (0.16% of adult tumors) followed by NTRK1 (0.14% of pediatric tumors). NTRK fusions were found more commonly in pediatric melanoma (11.1% of samples), pediatric glioma (3.97%), and adult thyroid cancers (2.34%). Additional genomic and transcriptomic NTRK alterations- mutation, amplification, and mRNA overexpression-occurred in 14.2% of samples, whereas the frequency of alterations that implicated NTRK ligands and the NTRK co-receptor (p75NTR) ranged from 3.8% to 5.4%. Among 31 adult samples carrying NTRK fusions, co-alterations occurred often and usually involved the downstream phosphoinositide-3-kinase signaling pathway, cell-cycle machinery, other tyrosine-kinase receptors, and mitogen-activated protein kinase signals.

Conclusion: Whereas NTRK fusions are exceedingly rare, other NTRK abnormalities affect 14% of patients with cancer. Affecting these alterations has not yet been achievable in cancer. Genomic co-alterations occur frequently with NTRK fusions, but it is not known if co-targeting them can attenuate primary or secondary resistance to NTRK inhibitors.

Fig 1.

Neurotrophic-tropomyosin receptor tyrosine kinase (NTRK) receptor signaling pathway and inhibitors. The ligands nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), neurotrophin 3 (NT-3), and NT-4 bind to their receptors, namely NTRK1 (tropomyosin receptor kinase A or TrkA), NTRK2 (tropomyosin receptor kinase B or TrkB), and NTRK3 (tropomyosin receptor kinase C or TrkC). These receptors are under the regulation of the co-receptor p75 neurotrophin receptor (p75^NTR). The binding of the ligand to the receptor promotes to the dimerization of the receptor and its subsequent intracellular phosphorylation. Several signaling cascades are further activated—phospholipase Cγ (PLC-γ), mitogen-activated protein kinase (MAPK), and phosphoinositide-3-kinase (PI3K) —and are converging to protumorigenic cell processes, such as proliferation, survival invasion, or differentiation. The hyperactivation of the NTRK signaling pathway induced by NTRK alterations—fusions or point mutations—can be overcome by the use of NTRK antagonists (eg, ANA-12 and cyclotraxin B) or small-molecule tyrosine kinase inhibitors (eg, larotrectinib and entrectinib). For now, only small-molecule tyrosine kinase inhibitors are used in the clinic.

Fig 2.

Distribution of molecular alterations leading to the hyperactivation of the neurotrophic-tropomyosin receptor tyrosine kinase (NTRK) signaling pathway in human tumors (N = 11,621 samples with comprehensive molecular data). All samples that presented a nonsilent mutation, gene copy amplification, gene fusion, or mRNA overexpression of NTRK receptors (NTRK1, NTRK2, and NTRK3), co-receptor (p75^NTR), or ligands (nerve growth factor [NGF], brain-derived neurotrophic factor [BDNF], neurotrophin 3 [NT-3], and NT-4) were retrieved from a large adult and pediatric pan-cancer cohort (The Cancer Genome Atlas and St Jude’s PeCan databases; N = 11,621samples). Among the NTRK fusion cases (n = 31 from TCGA cohort), four cases had concomitant alteration within the genes that code the NTRK pathway members—ligands, co-receptor, and receptors—as follows: low-grade glioma, NTRK3 fusion plus NTF3 amplification (n = 1); low-grade glioma, NTRK1 fusion plus NTRK1 amplification (n = 1); glioblastoma, NTRK1 fusion plus NTRK1 amplification (n = 1); head and neck squamous cell carcinoma, NTRK3 fusion plus NTRK3 amplification (n = 1).

Fig 3.

Co-alterations associated with neurotrophic-tropomyosin receptor tyrosine kinase (NTRK) fusions in adult tumors (from The Cancer Genome Atlas). All samples that presented a gene fusion of NTRK receptors—NTRK1, NTRK2, and NTRK3—were retrieved from a large adult pan-cancer cohort (The Cancer Genome Atlas database; n = 9,966 samples). Among 31 patients with NTRK fusions, some patients also harbored co-alterations that can lead to tumorigenesis. Those co-alterations include TP53-associated genes, cell cycle–associated genes, tyrosine kinase families, and mitogen-activated protein kinase (MAPK) and phosphoinositide-3-kinase (PI3K) signaling alterations.

Fig A1.

Association of neurotrophic-tropomyosin receptor tyrosine kinase (NTRK) fusions and NTRK mRNA overexpression in adult tumors.

Fig A2.

Association of neurotrophic-tropomyosin receptor tyrosine kinase (NTRK) fusions and mutational burden in adult tumors. The mutational burden corresponds to the total number of nonsynonymous mutations detected by whole-exome sequencing in each sample.