NTRK2 (Neurotrophic tyrosine kinase, receptor, type 2)

2007-12-01   Nadia Gabellini  

University of Padua, Department of Biological Chemistry, Viale G. Colombo, 3; 35131, Padua, Italy

Identity

HGNC
LOCATION
9q21.33
LOCUSID
ALIAS
DEE58,EIEE58,GP145-TrkB,OBHD,TRKB,trk-B
FUSION GENES

DNA/RNA

Atlas Image
Figure 1: The horizontal bar represents NTRK2 gene (355,039 bp). Vertical bars depict the exons 1-24 (red: translated regions, blue: 5 and 3 UTR regions).
Table 1: NTRK2 exons and size (bp).

Description

NTRK2 gene is comprised between 86,473,286-86,828,325 bp of chromosome 9, with plus strand orientation. The start codon is located on exon 5. Alternative stop codons are placed on terminal exons 16, 19 and 24.

Transcription

According to AceView (NCBI), six alternative promoters may control transcription of the complex NTRK2 locus. There are at least 18 mRNA variants supported by cDNA clones, potentially encoding 12 complete proteins. Variants may include 8 different terminal exons with alternative polyadenylation sites. Truncation at the 5 end or 3 end, alternative splicing, intron retention, occurrence of 5 cassette exons, and different exon boundaries introduce additional differences.
Five confirmed mRNA variants (a, b, c, d, e) are reported (NCBI accessions: NM_006180.3; NM_001007097.1; NM_001018064.1; NM_001018065.1; NM_001018066.1). The mRNA variant (a) encodes the full-length protein; variant (c) is slightly shorter excluding the small internal exon 17. Of particular importance are the truncated isoforms lacking the catalytic tyrosine kinase domain generated by the inclusion of alternate terminal exon 16 (b) or exon 19 (d) and (e).

Pseudogene

None

Proteins

Note

Three TrkB isoforms are reported by UniProt/Swiss-Prot:
1. The long isoform TrkB, including the tyrosine kinase domain (ID Q16620-1; variant c).
2. The truncated isoform TrkB-T1 lacking the tyrosine kinase domain (ID Q16620-2; variant b).
3. The truncated isoform TrkB-T-Shc lacking the tyrosine kinase domain but retaining the Shc site (ID Q16620-3; variant e).
Atlas Image
The predicted domains of TrkB (variant c): Signal Peptide (SP, AA 1-31); Leucine Rich Repeat N-Terminal domain (LRRNT, AA 31-65); Leucine-rich Repeats (LRR, AA 72-93, 96-117, 116-138); Leucine Rich Repeat C-Terminal domain (LRRCT, AA 148-195); Immunoglobulin C-2 Type 1 domain (IGC2-1, AA 197-282); Immunoglobulin C-2-type 2 domain (IGC2-2, AA 295-365); Transmembrane (TM, AA 431-454); the Protein Kinase domain (TyrKc, AA 538-807). In addition the site of interaction with SHC1 (Shc, AA 516) and with Phospho-Lipase C-gamma-1 (AA PLC-gamma, 817) are indicated.

Description

The unprocessed precursor of the full-length TrkB (a) consists of 838 AA. Variant (c) excludes 16 AA of unknown function, located downstream of the transmembrane segment.
The N-terminal portion (AA 32-430) is potentially extracellular and includes several N-glycosylation sites (AA 67, 121, 254). It follows a single transmembrane segment (AA 432-454). The C-terminal portion is cytosolic (AA 455-822) and comprises the Protein Kinase domain. This region includes the ATP binding site (AA 544-552) and several sites of autophosphorylation such as Tyr-516/702/706/707/817 (AA position refers to variant c).
The truncated Trkb-T1 (b) is composed of 477 AA. TrkB-T-Shc variants d and e consist of 553 AA and 537 AA, respectively. Truncated isoforms TrkB-T1 and TrkB-T-Shc include C-terminal sequence variations of 10 and 9 AA, respectively.

Expression

NTRK2 gene is preferentially expressed in brain, spinal cord, cranial and spinal ganglia. Expression is most prominent in the following brain regions: amygdale, caudate nucleus, cerebellum, choroid plexus, corpus callosum, cortex, hippocampus, hypothalamus and thalamus. In addition, a variety of cranial structures such as eyes, ophthalmic nerves, various facial districts and vestibular system indicate significant expression. Lower expression is described in several other tissues such as heart, kidney, lung, ovaries, pancreas, pituitary gland, prostate, salivary glands, skeletal muscle, spleen, thymus and thyroid.
Isoforms TrkB and TrkB-T1 are expressed in brain as well as in several peripheral areas, whereas TrkB-T-Shc is primarily expressed in brain.
AceView (NCBI) analysis of cDNA clones supports the expression pattern suggested by the evaluation of mRNA described above. In addition suggests elevated expression in several tumor tissues.

Localisation

Neuronal activity promotes TrkB translocation from intracellular vesicles to the plasma membrane where it becomes available for neurotrophins. The N-terminal segment is extracellular and is involved in neurotrophin binding and cell adhesion. A single transmembrane segment is located in the central portion of the polypeptide. The C-terminal segment is intracellular and comprises the protein kinase domain.

Function

TrkB specifically binds brain-derived neurotrophic factor (BDNF) and neurotrophin 4/5. It can also bind neurotrophin-3 with low affinity but it excludes nerve growth factor (NGF). Neurotrophin binding triggers receptor dimerization and consequent trans-phosphorylation of tyrosine residues of the TyrKc domain. Phosphorylated receptor undergoes conformational changes, which promote the recruitment of intracellular substrates such SHC1, PI-3 kinase, and PLC-gamma-1. The signaling cascades consequently activated support neuronal survival during development and following injuries, promote neuronal differentiation and maintenance, control short-term and long-term synaptic activity. TrkB can also form heterodimers with the pan-neurotrophin receptor p75NTR or with truncated TrkB. This influences the establishment of specific connections with signaling pathways.

Homology

TrkB belongs to the large family of protein kinase comprising a conserved kinase domain. It is included in the subfamily of tyrosine protein kinase. For the presence of a highly conserved intracellular TyrKc domain it is most related to growth factor receptors, and particularly to the neurotrophic factor receptors TrkA and TrkC. The homology with tyrosine kinase receptors is extended to the IGC-2 and LRRs domains, however, these are also present in cell-adhesion molecules.

Mutations

Germinal

Heterozygous missense mutations leading to substitution of highly conserved residues have been linked to Obesity, Hyperphagia and Developmental Delay.
Recurrent SNPs of the NTRK2 locus are associated with Eating Disorders (Anorexia and Bulimia nervosa).

Somatic

Tumor-specific mutations in the kinase domain have been identified in Colorectal Cancer cells.

Implicated in

Entity name
Various diseases
Disease
Obesity, Hyperphagia and Developmental Delay. Neuroblastomas, Pancreatic Ductal Adenocarcinomas, Wilmss tumors, Colorectal Cancer.
Oncogenesis
Overexpression of full-length TrkB is generally associated with malignant transformation. Excessive TrkB signaling through MAPK, PI3K and mTOR pathways support tumor development and metastasis. In highly malignant tumors the overexpression of TrkB enhances angiogenesis and invasive potential by upregulating VEGF and matrix proteases. Furthermore TrkB overcomes apoptosis caused by loss of cell-matrix interactions (anoikis), which is a natural barrier to metastasis.
In contrast with the oncogenic activity of TrkB, the truncated isoforms TrkB-T1 and TrkB-T-Shc, lacking the tyrosine kinase domain, behave as dominant-negative inhibitors and counteract tumor growth.

Breakpoints

Atlas Image

Article Bibliography

Pubmed IDLast YearTitleAuthors

Other Information

Locus ID:

NCBI: 4915
MIM: 600456
HGNC: 8032
Ensembl: ENSG00000148053

Variants:

dbSNP: 4915
ClinVar: 4915
TCGA: ENSG00000148053
COSMIC: NTRK2

RNA/Proteins

Gene IDTranscript IDUniprot
ENSG00000148053ENST00000277120Q16620
ENSG00000148053ENST00000277120A0A024R230
ENSG00000148053ENST00000304053Q16620
ENSG00000148053ENST00000323115Q16620
ENSG00000148053ENST00000323115Q548C2
ENSG00000148053ENST00000359847Q16620
ENSG00000148053ENST00000359847Q5VWE5
ENSG00000148053ENST00000376208Q16620
ENSG00000148053ENST00000376213Q16620
ENSG00000148053ENST00000376213Q548C2
ENSG00000148053ENST00000376214Q16620
ENSG00000148053ENST00000376214A0A024R230
ENSG00000148053ENST00000395882Q16620
ENSG00000148053ENST00000395882Q5VWE5

Expression (GTEx)

0
10
20
30
40
50
60
70
80

Pathways

PathwaySourceExternal ID
MAPK signaling pathwayKEGGko04010
MAPK signaling pathwayKEGGhsa04010
Neurotrophin signaling pathwayKEGGko04722
Neurotrophin signaling pathwayKEGGhsa04722
AlcoholismKEGGhsa05034
AlcoholismKEGGko05034
Signal TransductionREACTOMER-HSA-162582
Signalling by NGFREACTOMER-HSA-166520
NGF signalling via TRKA from the plasma membraneREACTOMER-HSA-187037
Activation of TRKA receptorsREACTOMER-HSA-187015
NGF-independant TRKA activationREACTOMER-HSA-187024

Protein levels (Protein atlas)

Not detected
Low
Medium
High

PharmGKB

Entity IDNameTypeEvidenceAssociationPKPDPMIDs
PA166182733larotrectinib sulfateChemicalLabelAnnotationassociated
PA166190161entrectinibChemicalLabelAnnotationassociated
PA444460Heroin DependenceDiseaseClinicalAnnotationassociatedPD23651024
PA445043Opioid-Related DisordersDiseaseClinicalAnnotationassociatedPD23651024
PA447199Bipolar DisorderDiseaseClinicalAnnotationassociatedPD21047205
PA447216SchizophreniaDiseaseClinicalAnnotationassociatedPD25751398
PA447321Depressive Disorder, MajorDiseaseClinicalAnnotation, VariantAnnotationambiguousPD27378793, 28244805
PA449061clozapineChemicalClinicalAnnotationassociatedPD25751398
PA450243lithiumChemicalClinicalAnnotation, Literature, MultilinkAnnotationassociatedPD21047205, 24885933
PA450401methadoneChemicalClinicalAnnotationassociatedPD23651024
PA452229antidepressantsChemicalClinicalAnnotation, VariantAnnotationambiguousPD27378793, 28244805

References

Pubmed IDYearTitleCitations
380082092024TrkB/BDNF signaling pathway and its small molecular agonists in CNS injury.1
384807832024Targeting the NTSR2/TrkB oncogenic pathway in chronic lymphocytic leukemia.0
385617342024Childhood urbanicity is associated with emotional episodic memory-related striatal function and common variation in NTRK2.0
380082092024TrkB/BDNF signaling pathway and its small molecular agonists in CNS injury.1
384807832024Targeting the NTSR2/TrkB oncogenic pathway in chronic lymphocytic leukemia.0
385617342024Childhood urbanicity is associated with emotional episodic memory-related striatal function and common variation in NTRK2.0
366824192023nNOS-induced tyrosine nitration of TRKB impairs BDNF signaling and restrains neuronal plasticity.0
369391202023Spitz Tumor With SQSTM1::NTRK2 Fusion: A Clinicopathological Study of 5 Cases.2
372528442023DRD1 signaling modulates TrkB turnover and BDNF sensitivity in direct pathway striatal medium spiny neurons.4
375085142023BDNF/TrkB Is a Crucial Regulator in the Inflammation-Mediated Odontoblastic Differentiation of Dental Pulp Stem Cells.4
377264922023miR-603 promotes cell proliferation and differentiation by targeting TrkB in acute promyelocytic leukemia.0
377494502023TrkB inhibition of DJ-1 degradation promotes the growth and maintenance of cancer stem cell characteristics in hepatocellular carcinoma.0
380029802023Association between NTRK2 Polymorphisms, Hippocampal Volumes and Treatment Resistance in Major Depressive Disorder.0
366824192023nNOS-induced tyrosine nitration of TRKB impairs BDNF signaling and restrains neuronal plasticity.0
369391202023Spitz Tumor With SQSTM1::NTRK2 Fusion: A Clinicopathological Study of 5 Cases.2

Citation

Nadia Gabellini

NTRK2 (Neurotrophic tyrosine kinase, receptor, type 2)

Atlas Genet Cytogenet Oncol Haematol. 2007-12-01

Online version: http://atlasgeneticsoncology.org/gene/41589/gene-explorer/css/lib/gene-fusions-explorer/