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  • Writer's pictureDženita Omerkić Dautovic, MSc & Dr Edin Hamzić

Exploring the Role of NTRK Gene and NTRK Gene Fusions

This is the first blog post in a series of posts focused on the NTRK gene. In this first blog post, we would like to describe the NTRK gene and its role shortly. This blog post is followed by one more post covering the topic of NTRK Gene Inhibitors.

What Is the NTRK Gene? What Is the Function of NTRK?

The Neurotrophic Receptor Tyrosine Kinase 1 (NTRK1) gene is located on chromosome 1. It encodes a protein Tropomyosin receptor kinase A (TrkA), a member of the neurotrophic TRK family. It is a membrane-bound receptor that has a role in neurotrophin binding and is responsible for the phosphorylation of itself and other members of the mitogen-activated protein kinase (MAPK) pathway. In addition, TrkA is vital in cell differentiation processes and sensory neuron subtypes' specification.

The term "neurotrophic" refers to anything that promotes the growth, survival, and differentiation of neurons (nerve cells) in the nervous system. "Neuro-" comes from the Greek word for "nerve," and "trophic" comes from the Greek word for "nourishment." Therefore, neurotrophic substances or factors nourish or support the growth and maintenance of neurons. These substances can include proteins, growth factors, and other molecules interacting with neurons and their surrounding cells to help regulate their development, function, and repair.

What Is the NTRK Gene Family, and What Are the Members of the NTRK Gene Family?

The NTRK gene family is a family of neurotrophic tyrosine kinase receptors that contains three members; besides the NTRK1 gene mentioned above, there are also NTRK2 and NTRK3 genes. In addition, the genes from the NTRK gene family, NTRK1, NTRK2, and NTRK3, encode Tropomyosin receptor kinase proteins TrkA, TrkB, and TrkC, respectively.

What Cellular Processes Do NTRK Gene Family Proteins Regulate or Are Involved In, and Why Are They Important?

The TrkA protein is one of the critical elements of the MAPK pathway involved in B cell differentiation, aging, axon guidance, cellular response to nerve growth factor stimulus, cellular response to nicotine, circadian rhythm, and more [citation].

The NTRK1, NTRK2, and NTRK3 genes are essential as they regulate the proliferation and survival of nerve cells. However, the NTRK gene fusions lead to the disruption of these pathways, thus leading to the uncontrolled proliferation of cancer cells.

The MAPK (mitogen-activated protein kinase) pathway is a critical signaling pathway that plays an essential role in many cellular processes, including cell proliferation, differentiation, survival, and death. The MAPK pathway is activated in response to various extracellular signals, such as growth factors, cytokines, and stressors.
The MAPK pathway involves several physiological and pathological processes, including embryonic development, immune response, inflammation, and cancer. The dysregulation of this pathway has been implicated in many diseases, including cancer, autoimmune disorders, and neurodegenerative diseases.

The NTRK Gene & Gene Fusions

Alterations in the NTRK gene lead to changes in the TrkA kinase, which further disrupts the processes mentioned in the above sections of this blog post, as well as:

  1. The detection of mechanical stimulus involved in pain perception

  2. Ephrin receptor signaling

  3. Learning or memory

  4. Mechanoreceptor differentiation

  5. Multicellular organism development

  6. Negative regulation of apoptosis

  7. Cell population proliferation

  8. Neuron apoptosis regulation

  9. Nerve growth factor signaling, and

  10. And neurotrophin Trk receptor signaling pathway [citation].

In addition, mutations in the NTRK gene have been associated with the following diseases:

  1. Congenital insensitivity to pain

  2. Anhidrosis

  3. Self-mutilating behavior

  4. Cognitive disability, and

  5. Cancer [citation].

The most common alterations in the NTRK are gene fusions.

What Is Gene Fusion? What Are the Functional Consequences of Gene Fusions?

A gene fusion is a phenomenon where two genes are joined so that they are transcribed and translated as a single-unit protein. This single-unit protein is also called fusion protein. These fusion proteins contain complete or incomplete parts of two normal proteins originating from fused genes. [citation].

Regarding functional consequences of gene fusions, the function of the proteins encoded by individual genes is disrupted, and fusion proteins tend to cause adverse consequences in the body [citation]. To learn more about gene fusion, check my short blog post here.

What Are the Most Common NTRK Gene Fusions? What Do NTRK Gene Fusions Cause?

NTRK gene fusions are rare but can occur in any of the three NTRK genes. NTRK gene fusions are random events due to breakages and translocations of segments containing NTRK1, NTRK2, and NTRK3 occurring in chromosomes 1, 9, and 15, respectively [citation].

NTRK gene fusions were found to be a causative agent for cancer, thus, are termed oncogenic. Fusions are more common in NTRK1 and NTRK3 genes and less frequent in the NTRK2 gene [citation].

NTRK gene fusions are found in less than 1% of all tumors,i.e., secretory breast cancer, colorectal cancer, mammary analog secretory carcinoma, infantile fibrosarcoma, high-grade pediatric glioma, spitzoid melanoma, papillary thyroid carcinoma, and others [citation].

How Do We Test for the NTRK Gene Fusions? What Type of Technology Is Used for Testing NTRK Gene Fusions?

NTRK gene fusions are tested by using various molecular technologies.

In the case of the NTRK gene, technologies used for testing NTRK gene fusion are:

  1. DNA sequencing, including First-generation and Next-generation sequencing (NGS)

  2. Immunohistochemistry (IHC)

  3. Fluorescence in situ hybridization (FISH), and

  4. Reverse Transcriptase Polymerase chain reaction (RT-PCR) [citation]

NTRK gene fusion testing is used to pinpoint individuals with NTRK gene fusions, making them eligible for therapies targeting these changes [citation].

NGS detects known and novel fusions with breakpoints in DNA or RNA; IHC serves for detecting Trk proteins; FISH detects gene rearrangements in DNA that may create a fusion transcript; and PCR detects known fusion transcripts in RNA.

What Are the Most Common NTRK Mutations That Are Associated With Cancer?

Gene fusion is the most common NTRK mutation associated with cancer. Recurrent NTRK1 and NTRK2 gene fusions have been identified in glioblastoma, cholangiocarcinoma, and high-grade pediatric glioma [citation].

NTRK1 and NTRK3 gene fusions were found in papillary thyroid cancer and glioblastoma [citation].

NTRK genes can also fuse with genes outside of their family and form fusion proteins that are causative agents of cancer [citation].

Some of those fusions are:

  • PAN3-NTRK2 is a gene fusion between Poly(A) Specific Ribonuclease Subunit (PAN3) and the NTRK2 gene found in head and neck squamous cell carcinoma.

  • AFAP1-NTRK2 is a gene fusion between Actin Filament Associated Protein 1 (AFAP1) and the NTRK2 gene, and it was found in low-grade glioma.

  • TRIM24-NTRK2 is a gene fusion between Tripartite Motif Containing 24 (TRIM24) and the NTRK2 gene, and it was found in lung adenocarcinoma.

  • TPM3-NTRK1 is a gene fusion between Tropomyosin 3 (TPM3) and the NTRK1 gene, found in sarcoma and thyroid cancer [citation].

What Is the NTRK NGS Fusion Profile? How Do You Test for NTRK Gene Fusion?

NTRK gene fusion testing can be done using an NGS panel that detects known and novel fusions, NTRK1, NTRK2, and NTRK3, genes with known and novel fusion partners [citation]. The test evaluated formalin-fixed paraffin-embedded tumor slides from patients with advanced solid tumors for rearrangements in the target regions of NTRK1, NTRK2, and NTRK3 to identify gene candidates for therapy. The assay uses sequencing methodologies to identify fusions in the target regions [citation]. If a sequence corresponding to a fusion between two NTRK genes is detected, the sample is denoted as positive for NTRK fusion. NTRK testing is the same as NTRK gene fusion testing, aiming to detect NTRK fusions using NGS technologies.

What are the FDA-approved tests for the detection of NTRK gene alterations?

The most important FDA-approved tests used for the detection of NTRK gene fusions are:

  1. FoundationOne CDx: This is an NGS test that analyzes the entire coding region of over 300 cancer-related genes, including NTRK1, NTRK2, and NTRK3, to identify genomic alterations, including gene fusions. This test is approved for use in solid tumors.

  2. Oncomine Dx Target Test: This is an NGS test that analyzes DNA and RNA from tumor samples to identify genomic alterations, including NTRK gene fusions, in 23 cancer-related genes. This test is approved for use in solid tumors.

  3. FISH (fluorescence in situ hybridization) assays: These are laboratory tests that detect NTRK gene fusions by using fluorescently labeled probes to detect specific DNA sequences in tumor samples. The Vysis ALK Break Apart FISH Probe Kit is approved for detecting NTRK gene fusions in solid tumors.

What Is Pan TRK? Is Pan TRK the Same as NTRK?

Pan-TRK is an effective IHC method that is time-efficient and tissue-efficient in screening for NTRK fusion, especially in driver-negative malignancies. This method used a Pan-TRK antibody to detect the C-terminal region of the tropomyosin receptor kinase (TRK) proteins A, B, and C, which are functional products of NTRK1, 2, and 3 [citation]. Pan-TRK has the same overall aim and outcome as NTRK fusion testing; the difference is that pan-TRK detects NTRK fusions by detecting aberrant protein products, while NTRK testing aims to detect gene fusions directly. In addition, the Pan-TRK IHC method can determine whether translation occurs for novel NTRK rearrangements [citation].

If you are interested in Tropomyosin receptor kinase (TRK) inhibitors, please check out our second blog.


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