Neurotrophic Tyrosine Kinase 1 – NTRK Fusions

The neurotrophic tyrosine receptor kinases are a family of genes (NTRK1, NTRK2, and NTRK3) that encode the proteins TrkA, TrkB, and TrkC, respectively. They function as receptors that span the cell membrane, sensing extracellular signals, like the binding of neurotrophin molecules, and transferring the signal to the cell’s intracellular environment through kinase activity. Trk receptors are particularly essential to neuronal development.1, 2 The aberrant expression of rearranged NTRK genes, encoding Trk fusion proteins, has been detected in a wide range of cancers (e.g., salivary gland cancer, colon cancer, lung cancer, thyroid cancer, breast cancer) and suggests that signaling by these receptors may be important in the regulation of tumor cell proliferation, differentiation, and/or apoptosis in the subset of patients whose tumors harbor such gene fusions (see Table 1). It is thought that an NTRK fusion that joins the kinase portion of the gene to various N-terminal partners (as described below) results in their constitutive activation in a ligand-independent manner.1,2

NTRK1

One of the first receptor kinases found to be involved in a fusion event that led to the development of cancer was neurotrophic tyrosine receptor kinase type 1 (NTRK1), which encodes the protein TrkA. This gene was originally identified as a fusion oncogene in colon carcinoma.3,4 TrkA is a 140 kDa glycoprotein comprised of an extracellular (N-terminal) ligand-binding domain, a transmembrane domain, and an intracellular tyrosine kinase domain.4 Upon binding to its ligand, nerve growth factor (NGF), TrkA dimerizes and undergoes autophosphorylation of its intracellular domain. This results in subsequent activation of intracellular signaling molecules, including RAS, phosphatidylinositol-3-kinase (PI3K), and mitogen-activated protein kinase (MAPK), thus stimulating cellular proliferation, differentiation, and survival.4,5

Abnormal expression of the TrkA protein was recently identified in tumor and liver metastases of a patient with colorectal cancer who was refractory to standard therapy. Molecular characterization unveiled a novel fusion between the LMNA and NTRK1 genes within chromosome 1, resulting in the formation of a fusion oncogene (LMNANTRK1) with transforming potential.6 The patient was treated with a Trk inhibitor, entrectinib, and achieved a partial response, which was maintained for approximately 5 months (March 2014 – July 2014). This was the first clinical evidence of efficacy for therapeutic inhibition of TrkA using a Trk inhibitor in a solid tumor.6

In lung cancer patients, one study identified NTRK1 rearrangements in 3 of 91 patients with lung adenocarcinoma (3.3%), and this study also identified 2 additional gene fusion partners for NTRK1: MPRIP and CD74, both of which resulted in constitutive activation of the resulting fusion kinase and were also oncogenic (Table 1). 7 As in colorectal cancer, there is also evidence for therapeutic inhibition of lung tumors with NTRK1 rearrangements; during Phase I trials, one patient with metastatic lung cancer harboring an NTRK1 rearrangement displayed a partial response to entrectinib, including a complete response for all brain metastases.8

NTRK1 fusion events are now being more widely screened for and increasingly recognized across multiple cancer types. A recent survey of Northeastern US patients with pediatric papillary thyroid carcinoma (N=28), for example, identified a single patient (4%) with diffuse follicular papillary thyroid cancer (PTC) harboring a fusion between the gene translocated promoter region (TPR) and NTRK1.9 Another recent study identified the previously described LMNANTRK1 and a fusion between tropomyosin 3 TPM3NTRK1 fusion genes in a total of 3 of 147 patients (2%) from a Korean colon cancer population using next-generation RNA sequencing.10 This study found that tumors harboring these NTRK1 gene rearrangements did not have somatic mutations in other oncogenes like KRAS, NRAS, or PIK3CA, and both fusion proteins were shown to be oncogenic, as their expression in NIH3T3 cells resulted in transformation and tumor formation in immunocompromised mice.10 In a sampling of 140 Spitzoid skin neoplasms, which included 75 Spitz naevi, 32 atypical Spitz tumors, and 33 Spitzoid melanomas, NTRK1 rearrangements were detected in a total of 16.4% of the samples (23 patients), with 8, 8, and 7 patients, respectively, harboring rearrangements in the respective tumor types.11

NTRK2

TrkB, which is encoded by the NTRK2 gene, was identified in 1991 to be a functional receptor for brain-derived neurotrophic factor (BDNF) and neurotrophin 3 (NT-3), but unlike TrkA, it does not bind to NGF.12,13 When expressed in cell lines, TrkB has been shown to regulate cellular effects for both BDNF and NT-3, although NT-3 is the weaker of the 2 known ligands.12,13 Like TrkA, ligand binding to TrkB causes dimerization and autophosphorylation of its catalytic domain, resulting in the activation of multiple intracellular signaling pathways, including the RAS-MAPK, phospholipase-C gamma (PLCg), and PI3K pathways, which mediate its cellular effects.2 Some of the implicated roles for altered TrkB signaling in cancer include its role in suppressing anoikis, or apoptosis in response to loss of cell matrix interaction (thereby promoting a more invasive phenotype), and a potential role of the BDNF/TrkB-signaling axis in overcoming resistance to other cancer therapies, such as epidermal growth factor receptor (EGFR) inhibitors, as previously observed in colon cancer cells.14,15

Like NTRK1, gene fusion events involving NTRK2 are also becoming increasingly recognized in various cancers. Two novel NTRK2 rearrangements were identified in a study conducted by the International Cancer Genome Consortium and PedBrain Tumor Project, which examined 96 pilocytic astrocytomas, the most common form of childhood brain tumor.16 In both cases, expression of the aberrant fusion kinase resulted in ligand-independent dimerization and constitutive activation of the kinase.16 Data from the Cancer Genome Atlas has also recorded novel fusions involving NTRK2 in lung adenocarcinoma, squamous cell head and neck cancer, and low-grade glioma (Table 1).

NTRK3

TrkC, encoded by NTRK3, is the primary receptor for NT-3, and like TrkB and TrkA, it mediates the effects of its ligand on neuronal growth and differentiation during development.2 In 1998, a fusion between the NTRK3 gene and an ets-type transcription factor (ETV6, also called TEL) was reported in congenital fibrosarcoma (CFS). This fusion transcript encoded a protein with a helix-loop-helix (HLH) domain, believed to be involved in dimerization, fused to the protein tyrosine kinase domain of TrkC.18.19 The resultant fusion protein was subsequently shown to result in dysregulation of downstream signaling pathways.18, 20

In 2003, a fusion between ETV6 and the NTRK3 gene was also found to be expressed in human secretory breast cancers (SBC), a rare but clinically distinct subtype of breast cancer.17 Transcripts for this fusion were detected in 11 of 12 SBC cases (92%).17 In a recent survey of Northeastern US patients with pediatric papillary thyroid carcinoma (PTC; N=28), a total of 6 patients (22%) with varying PTC phenotypes were found to harbor an NTRK3 fusion, most commonly with the ETV6 gene (n=5 of 6 cases, 1 unknown fusion partner).9 Interestingly, the high incidence (26% overall) of NTRK1 and NTRK3 rearrangements in the pediatric PTC population in this study (overall 26%) was notably higher than that reported by The Cancer Genome Atlas (TCGA) for adult PTC, as well as that observed in sporadic and radiation-induced PTCs.9

The STARTRK-2 trial is enrolling patients with NTRK, ROS1, and ALK fusions.

More information is available at www.startrktrials.com.

Table 1: Examples of Known NTRK Gene Fusions in Cancer7, 8, 10, 11, 17, 18, 21, 22
NTRK Kinase Gene Cancer Type
NTRK1 Colorectal cancer
Papillary thyroid cancer
Non small cell lung cancer
Soft tissue sarcoma
Pediatric glioma
Breast cancers
Gallbladder cancer
Cholangiocarcinoma
Spitzoid melanoma
Glioblastoma multiforme
Astrocytoma
Pancreatic cancer
Uterine carcinoma
NTRK2 Squamous cell head and neck
Pilocytic astrocytoma
Pediatric and adult glioma
Colorectal cancer
Non-small cell lung cancer
NTRK3 Adult and pediatric papillary thyroid cancer
Sarcoma
Salivary gland tumors
Mammary analog secretory carcinoma (MASC)
Pediatric and adult glioma

 

References

  1. Nakagawara A. Trk receptor tyrosine kinases: a bridge between cancer and neural development. Cancer Lett. 2001; 169(2):107-114.
  1. Thiele CJ, Li Z, McKee AE. On Trk–the TrkB signal transduction pathway is an increasingly important target in cancer biology. Clin Cancer Res. 2009; 15(19):5962-5967.
  1. Shaw AT, Hsu PP, Awad MM, Engelman JA. Tyrosine kinase gene rearrangements in epithelial malignancies. Nat Rev Cancer. 2013; 13(11):772-787.
  1. Greco A, Miranda C, Pierotti MA. Rearrangements of NTRK1 gene in papillary thyroid carcinoma. Mol Cell Endocrinol. 2010; 321(1):44-49.
  1. Kaplan DR, Miller FD. Neurotrophin signal transduction in the nervous system. Curr Opin Neurobiol. 2000; 10(3): 381-391.
  1. Sartore-Bianchi A, Ardinia E, Bosotti R, et al. Sensitivity to Entrectinib Associated With a Novel LMNANTRK1 Gene Fusion in Metastatic Colorectal Cancer. J Natl Cancer Inst. 2016; 108(1): djv306
  1. Vaishnavi A, Capelletti M, Le AT, et al. Oncogenic and drug sensitive NTRK1 rearrangements in lung cancer. Nat Med. 2013;19(11):1469–1472.
  1. Farago AF, Le LP, Zheng Z, et al. Durable Clinical Response to Entrectinib in NTRK1 -Rearranged Non-Small Cell Lung Cancer. J Thorac Oncol. 2015;10(12):1670-1674.
  1. Prasad ML, Vyas M, Horne MJ, et al. NTRK fusion oncogenes in pediatric papillary thyroid carcinoma in northeast United States. Cancer. 2016 Jan 19. doi: 10.1002/cncr.29887. [Epub ahead of print]
  1. Park DY, Choi C, Shin E, et al. NTRK1 fusions for the therapeutic intervention of Korean patients with colon cancer. Oncotarget. 2015. doi: 10.18632/oncotarget.6724. [Epub ahead of print]
  1. Wiesner T, He J, Yelensky R, et al. Kinase fusions are frequent in Spitz tumours and spitzoid melanomas. Nat Commun. 2014; 5:3116. doi: 10.1038/ncomms4116.
  1. Squinto SP, Stitt TN, Aldrich TH, et al. TrkB encodes a functional receptor for brain-derived neurotrophic factor and neurotrophin-3 but not nerve growth factor. Cell. 1991; 65(5):885-893. [Need to order]
  1. Klein R, Nanduri V, Jing SA, et al. The trkB tyrosine protein kinase is a receptor for brain-derived neurotrophic factor and neurotrophin-3. Cell. 1991; 66(2): 395-403.
  1. Douma S, Van Laar T, Zevenhoven J, Meuwissen R, Van Garderen E, Peeper DS. Suppression of anoikis and induction of metastasis by the neurotrophic receptor TrkB. Nature. 2004;430(7003):1034-1039.
  1. de Farias CB, Heinen TE, dos Santos RP, Abujamra AL, Schwartsmann G, Roesler R. BDNF/TrkB signaling protects HT-29 human colon cancer cells from EGFR inhibition. Biochem Biophys Res Commun. 2012; 425(2): 328-332.
  1. Jones DT, Hutter B, Jäger N, et al; International Cancer Genome Consortium PedBrain Tumor Project. Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma. Nat Genet. 2013; 45(8):927-932.
  1. Tognon, C. et al. Expression of the ETV6-NTRK3 gene fusion as a primary event in human secretory breast carcinoma. Cancer Cell. 2002; 2, 367–376.
  1. Knezevich SR, McFadden DE, Tao W, Lim JF, Sorensen PH. A novel ETV6NTRK3 gene fusion in congenital fibrosarcoma. Nat Genet. 1998; 18(2):184-187.
  1. Jin W, Yun C, Hobbie A, Martin MJ, Sorensen PH, Kim SJ. Cellular transformation and activation of the phosphoinositide-3-kinase-Akt cascade by the ETV6NTRK3 chimeric tyrosine kinase requires c-Src. Cancer Res. 2007; 67(7):3192-3200.
  1. Tognon C, Garnett M, Kenward E, Kay R, Morrison K, Sorensen PH. The chimeric protein tyrosine kinase ETV6NTRK3 requires both Ras-Erk1/2 and PI3-kinase-Akt signaling for fibroblast transformation. Cancer Res. 2001; 61(24):8909-8916.
  1. Stransky N, Cerami E, Schalm S, Kim JL, Lengauer C. The landscape of kinase fusions in cancer. Nat Commun. 2014;5: 4846. doi: 10.1038/ncomms5846.
  1. Doebele RC, Davis LE, Vaishnavi A, et al. An Oncogenic NTRK Fusion in a Patient with Soft-Tissue Sarcoma with Response to the Tropomyosin-Related Kinase Inhibitor LOXO-101. Cancer Discov. 2015; 5(10):1049-1057.

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