|REVIEW ARTICLE-BIOMARKER SERIES
|Year : 2021 | Volume
| Issue : 1 | Page : 110-114
NTRK-A narrative review
Ullas Batra1, Shrinidhi Nathany2, Mansi Sharma1
1 Department of Medical Oncology, Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India
2 Department of Molecular Diagnostics, Rajiv Gandhi Cancer Institute and Research Centre, New Delhi, India
|Date of Submission||19-Jan-2021|
|Date of Decision||17-Feb-2021|
|Date of Acceptance||01-Mar-2021|
|Date of Web Publication||26-Mar-2021|
Sector 5 Rohini, Sir Chhotu Ram Marg, New Delhi - 110 085
Source of Support: None, Conflict of Interest: None
Lung cancer diagnostics and therapeutics have witnessed a paradigm shift in the last decade because of the discovery of targetable biomarkers and rapid approvals of the corresponding targeted therapies. The prognosis of biomarker-driven tumors has improved, and hence, testing for the presence of targetable biomarkers is now a mandate according to both national and international recommendations. Apart from the common and canonical alterations in the epidermal growth factor receptor, anaplastic lymphoma kinase, and ROS1 genes, NTRK fusions, although rare, are gaining clinical importance as targetable alterations. With entrectinib and larotrectinib making their way into the phase III trials, a comprehensive knowledge about the biology, molecular diagnostic techniques, ongoing trials, and available drugs for NTRK-fusion-positive lung cancers is essential. Therefore, we performed a narrative review of the already published literature. The PubMed, Embase, and Scopus databases were searched using the keywords “biology of NTRK,” “TRK,” “NTRK” and “NSCLC.” A total of 32 relevant articles were reviewed. In this review, we have described the biology, signaling pathways, detection methods, and treatment for NTRK-fusion-positive cancers.
Keywords: Detection, entrectinib, larotrectinib, NTRK
|How to cite this article:|
Batra U, Nathany S, Sharma M. NTRK-A narrative review. Cancer Res Stat Treat 2021;4:110-4
| Introduction|| |
Lung cancer is a molecularly heterogeneous disease, and the knowledge of biomarker-driven cancers along with the development of molecular targeted therapies has resulted in a dramatic shift in the prognostic landscape of these tumors. Another emerging concept in oncology is that of tissue agnostic therapy, which is defined as treatment that is effective against tumors that harbor a specific genetic alteration, regardless of the site of origin of the tumor. Tissue agnostic markers include the microsatellite instability status, for which pembrolizumab has received fast-tracked approval from the United States Food and Drug Administration (FDA). Similarly, the approval of the first-generation NTRK inhibitors, such as entrectinib and larotrectinib, for use in NTRK-fusion-positive cancers of any histology has led to the inclusion of the NTRK genes in panel-based testing of both rare and common malignancies. In addition, newer drugs like selitrectinib and repotrectinib are also being explored and are currently in clinical trials.,
The NTRK family comprises three genes, namely NTRK1, NTRK2, and NTRK3, which map to the chromosomes 1, 9, and 15, respectively, and encode 3 receptor proteins, namely TRKA, TRKB, and TRKC, respectively. These are transmembrane receptor tyrosine kinases with a high affinity for neurotrophins and are normally implicated in neuronal development and differentiation. NTRK rearrangements were identified 30 years ago in colorectal malignancies, and since then they have been reported in myriad common and rare malignancies. Paradoxically, these are in-frame fusions that often occur in rare malignancies, but are rarely seen in the commonly occurring malignancies. Nevertheless, testing for the presence of NTRK rearrangements is warranted owing to the availability of approved targeted therapies with dramatic responses.
In this narrative review, we have described the associated biology, signaling pathways, spectrum of reported alterations, detection methods, and the management of NTRK-fusion-positive cancers.
| Methods|| |
This is a narrative review of the literature on NTRK-rearranged malignancies. Articles for this review were searched for on the PubMed, Embase, and Scopus databases using the keywords “TRK,” “NTRK,” biology of NTRK,” and “NSCLC.” As this was not a systematic review or meta-analysis, we screened all types of literature, including review articles, original articles, conference proceedings, abstracts, and books. In addition, no inclusion or exclusion criteria were defined. A total of 22 articles were finally included in this review.
| Molecular and Structural Biology|| |
The NTRK1, NTRK2, and NTRK3 genes located on chromosomes 1q23, 9q21, and 15q25, respectively, encode the TRKA, TRKB, and TRKC receptor proteins, respectively, which are normally expressed in the neuronal tissues.
All these transmembrane proteins are homologous and comprise three regions, namely the extracellular ligand-binding domain, transmembrane domain, and the intracellular adenosine 5'-triphosphate (ATP)-binding kinase domain. The extracellular domain consists of leucine-rich repeats that are unique to the TRK family of receptors; additionally, it contains the immunoglobulin (Ig)-like C2-type 1 and Ig-like C2-type 2 domains. The kinase domain contains 10 highly conserved tyrosine residues.
Coding exons for NTRK1, the smallest among the three NTRK genes, span 20.7 kb of the genome. NTRK2 and NTRK3 contain exceptionally large introns, as a result of which fusion events involving these two genes may be missed on DNA-based next-generation sequencing (NGS) due to limited coverage.
NTRK fusions and cancer
The first genetic alteration involving an NTRK gene was identified almost 30 years ago in a colon cancer cell line, and was characterized to be a TPM3-NTRK1 fusion transcript. Thereafter, rearrangements involving the NTRK2 and NTRK3 genes were also characterized, and now somatic intra- and inter-chromosomal rearrangements involving these three genes can be identified as the main oncogenic drivers in a wide range of pediatric and adult neoplasia. In almost all the rearrangements involving the NTRK genes, the 5'-promoter region of a gene fuses with the 3' region of the NTRK gene expressed in the tumor. NTRK is a promiscuous gene with more than 80 known fusion partners. A unique feature of rearrangements involving the NTRK genes is that they are in-frame fusions with an intact kinase domain, are oncogenic, and can be targeted with NTRK-directed therapy. A list of known fusion partners in different types of tumors is provided in [Table 1].,,
The fusion protein thus formed, does not contain the extracellular ligand-binding domain of the NTRK genes, and may contain one or more dimerization domains of the 5'-partner. This results in ligand-independent activation of the C-terminal NTRK tyrosine kinase domain, resulting in the constitutive activation of the downstream signaling pathways. A schematic representation of this signaling is depicted in [Figure 1]a and [Figure 1]b.
|Figure 1: (a and b) NTRK signaling: (a): Normal signaling mechanism, (b) Ligand-independent signaling mechanism leading to oncogenesis. (ACRONYMS – NGF: Nerve growth factor, BDNGF: Brain-derived nerve growth factor, TRKA/B/C: Tropomyosin receptor kinase A/B/C, PI3K: Phosphoinositide 3-kinases)|
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NTRK fusions have been reported in around 1% of all the cases of non-small-cell lung cancer (NSCLC). However, unlike other oncogenic drivers known in lung cancer, they do not occur in any clinically enriched population. They are not associated with any specific histology, and have been reported in both adenocarcinomas and squamous cell carcinomas. They are also known to occur in neuroendocrine carcinomas and are independent of the patients' gender and smoking status. In a large retrospective study on 166,067 patients with solid tumors, conducted at the Foundation Medicine Institute, it was observed that NTRK alterations are detected at a higher frequency in patients of Asian descent, are mutually exclusive of other drivers, and have a tumor mutational burden (TMB) similar to the NTRK-negative malignancies; however, the level of expression of the programmed death-ligand 1 and the TMB were higher in NTRK-positive tumors compared to NSCLCs harboring other oncogenic drivers (epidermal growth factor receptor, anaplastic lymphoma kinase [ALK], and ROS1), indicating the potential efficacy of immunotherapy in NTRK-positive tumors. Real-world data on the same are however lacking.
NTRK alterations other than fusions
Genetic alterations other than fusions involving the NTRK genes have been reported, but are extremely rare. These may include mutations, amplifications, and change in mRNA expression. These have been reported in 14.2% (1648 of 11,621) of the cases in a study on adult and pediatric tumors. Genetic alterations other than fusions have been shown to be associated with a lack of response to NTRK-directed therapy, although owing to the rarity of occurrence, there are no large-scale studies validating this observation. Joshi et al. reported more than 12 unique alterations in the form of mutations in patients with leukemia. Amplifications have also been reported in a study by Lee et al., on 1250 tumor samples, of which 28 (2%) were found to have copy number gains. Pasini et al. in their study showed that amplification of the chromosome region 1q21 harboring the NTRK1 gene causes tumor progression. However, the role of NTRK alterations other than fusions is still not validated in terms of the benefit of targeted therapy.
Testing for alterations in NTRK genes
There are recommendations by the European Society for Medical Oncology (ESMO) and the Memorial Sloan Kettering Cancer Center for algorithmic testing of NTRK alterations. Depending on the frequency of occurrence in the tumors, ESMO recommends the use of immunohistochemistry (IHC) followed by polymerase chain reaction (PCR) or NGS in rare tumors with common NTRK fusions, and the reverse in common tumors with rare NTRK fusions. So, in cases of NSCLC, upfront NGS- or PCR-based testing is recommended with the aim of detecting rare alterations, as IHC or single-gene testing may yield false negative results, owing to the limited number of panels and sensitivity.
IHC with a pan-TRK antibody is commercially available, and may be used as a screening tool. However, variability in the staining patterns of the different TRK proteins is a disadvantage and may result in both false negative and false positive results.
Interphase fluorescence in situ hybridization (FISH) using break-apart probes may be used; however, the assay cannot be multiplexed, and hence, will require three reactions per sample, leading to tissue depletion, along with the inherent user-dependent problems of FISH.
Reverse transcription PCR is another technique that is widely used for the detection of fusions across many malignancies. However, in case of NTRK, with so many known fusion partners and many chromosomal breakpoints, this technique may not be able to detect all the known fusion variants, resulting in a higher rate of false negative results.
NGS serves as a one-stop solution; RNA sequencing can detect a wide range of fusions and the simultaneous DNA sequencing can detect other non-fusion genetic alterations. DNA-based detection of fusions by NGS has also been tested and can be used in order to account for both intronic and exonic breakpoints. However, all centers may not have the informatics support for complex genomic data analysis. A comparison of various testing methods for NTRK fusions, with their advantages and disadvantages is presented in [Table 2].
|Table 2: Comparison of immunohistochemistry, fluorescence in situ hybridization, and next-generation sequencing for detection of NTRK fusions|
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Relevance of identifying NTRK-positive tumors
Many small molecule inhibitors of the kinase domain of the TRK proteins have been developed and are in various phases of clinical trials. In July 2017, entrectinib was designated an orphan drug by the FDA for the treatment of TRKA/TRKB/TRKC-positive NSCLC and colorectal cancer. Larotrectinib activity has been evaluated in three trials: a phase-I trial in adults (NCT02122913), a phase-I/II trial in pediatric patients (SCOUT, NCT02637687), and a phase-II trial involving adults and adolescents (NAVIGATE, NCT02576431). Larotrectinib was approved by the FDA in November 2018 for many adult and pediatric solid tumors that are NTRK-fusion-positive and meet the prescribing criteria for the same.
A few multi-target tyrosine kinase inhibitors (TKIs), with variable inhibitory activity against the TRK proteins, which are approved for other biomarker-driven cancers have also been used. Crizotinib, which was originally developed and approved for ALK/ROS1-rearranged lung cancers; cabozantinib, originally approved for renal cell carcinoma; ponatinib for chronic myeloid leukemia; and nintedanib for idiopathic pulmonary fibrosis are well-known examples. However, the responses to these drugs are not well characterized as the affinity of the drugs for the TRK receptors varies leading to variable outcomes. Some other drugs are in development and these include lestaurtinib, which inhibits TRK, JAK2, and FLT3 and merestinib, which originally was described as a MET inhibitor but has recently been found to cause multi-kinase inhibition. A summary of the drugs targeting NTRK fusions along with their reported responses is presented in [Table 3].
Resistance mutations in NTRK kinase domain
Analogous to other TKIs, resistance, especially acquired, may eventually develop against NTRK TKIs. This may occur due to alterations in the ATP-binding site of the kinase domain of the TRK protein, including solvent-front mutations, gatekeeper mutations, and xDFG-motif substitutions in the activation loop. Solvent-front mutations in NTRK1 include p. G595R and p. G667C mutations, and in NTRK3 include p. G623C. Second-generation TKIs like selitrectinib and repotrectinib can overcome these mechanisms of resistance.
Future perspectives and interpretations
This is a narrative review which describes the biology, pathology, genomics, and clinical relevance of testing for NTRK gene rearrangement across solid organ malignancies. However, our review is limited by the fact that we did not perform a meta-analysis or systematic review reporting. Our review summarizes the different alterations which can occur in the NTRK family of genes, along with various diagnostic modalities available for testing, which may serve as a valuable aid to the treating clinician. The rarity of occurrence of this alteration requires panel-based testing as per recommendations. Developing newer modalities relevant to economically constrained setups may prove beneficial in future. In addition, developing artificial intelligence-based models with fair accuracy to predict the alteration may be a step forward in the ever-evolving field of oncogenomics.
| Conclusion|| |
NTRK fusions are rare genetic alterations that can be found in common malignancies, and the approval of targeted therapies like larotrectinib and entrectinib mandate the testing of these alterations for optimal therapeutic decision making. Various diagnostic techniques are available for the detection of alterations in the NTRK genes. However, in the real world, NGS despite being a one-stop solution may not always be feasible. Therefore, initial screening with IHC is recommended in all cancers that are known to harbor these alterations.
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Conflicts of interest
There are no conflicts of interest.
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[Table 1], [Table 2], [Table 3]