Potential effectiveness of Vitrakvi (Larotrectinib) for treating types of solid tumors carrying NTRK genes and the impact of TRKC mutations

Introduction: NTRK gene fusions have been observed across age groups in a variety of tumor types and are implicated in approximately 1% of all solid tumor cancers. The FDA approved larotrectinib (2018) and entrectinib (2019) for the treatment of TRK fusion cancer in adult and pediatric populations (larotrectinib: all ages; entrectinib: ≥12 years old). Given the rarity of NTRK gene fusions, both approvals were based on trials recruiting small numbers of patients in single arm trials. Characteristics of patients harboring NTRK gene fusions in the real-world setting are limited. This study reports the real-world demographic, clinical, and genomic characteristics in patients harboring an NTRK gene fusion. Methods: A retrospective, observational cohort study of adult patients with a known NTRK gene fusion and diagnosed with any advanced or metastatic solid tumor between January 1, 2016 and December 31, 2019 was conducted. Characteristics and testing patterns were abstracted from patient medical records by 19 medical oncologists (89.5% community-based; 10.5% academic/teaching hospital) across all geographic areas in the US (21.1% Northeast, 10.5% Midwest, 36.8% South, 31.6% West). Descriptive statistics were used to summarize patient characteristics and testing patterns. Results: Among the 110 patients included in the study, the median (range) patient age at advanced/metastatic diagnosis was 62 (39-77) years. The majority of patients (58.2%) were male and white (79.1%). Among the 15 solid tumor types observed, lung (24.5%), cholangiocarcinoma (13.6%), pancreatic (10.9%), and colorectal (10.0%) were reported in at least 10% of the study cohort. Half (50.0%) of patients had an NTRK1 gene fusion, and 27.3% and 20.0% had NTRK3 and NTRK2 gene fusion, respectively. The five most commonly reported NTRK gene fusion partners were ETV6-NTRK3 (13.6%), TPM3-NTRK1 (7.3%), PPL-NTRK1 (4.5%), SQSTM1-NTRK1 (4.5%), and TPM3-NTRK2 (4.5%). Median time from initial cancer diagnosis to NTRK gene fusion testing was 11.5 (interquartile range, 1-149) days. Next generation sequencing was used to identify NTRK gene fusions in 69.1% of patients (8.2% performed as confirmation to immunohistochemistry testing), followed by fluorescent in situ hybridization studies (FISH) in 14.5% of patients and unknown in 16.4% of patients. Conclusion: TRK fusion cancer was most commonly observed in lung, cholangiocarcinoma, pancreatic, and colon cancers. Patients harboring NTRK gene fusions are being identified soon after initial cancer diagnosis across a variety of tumor types and age groups in routine clinical practice. Early detection of NTRK gene fusions can inform the clinician regarding use of TRK inhibitors earlier in the course of disease when indicated. Citation Format: Andrew Klink, Abhishek Kavati, Ruth Antoine, Awa Gassama, Tom Kozlek, Ajeet Gajra. Clinical and genomic characteristics of tropomyosin receptor kinase (TRK) fusion cancer in community oncology practice [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P022.

Detection of Tumor NTRK Gene Fusions to Identify Patients Who May Benefit from Tyrosine Kinase (TRK) Inhibitor Therapy

Oncogenic somatic chromosomal rearrangements involving the NTRK1, NTRK2 or NTRK3 genes (NTRK gene fusions) occur in up to 1% of all solid tumors, and have been reported across a wide range of tumor types. The fusion proteins encoded by such rearranged sequences have constitutively activated TRK tyrosine kinase domains, providing novel therapeutic anticancer targets. The potential clinical effectiveness of TRK inhibition in patients with tumors harboring NTRK gene fusions is being assessed in phase I and II trials of TRK inhibitors, such as larotrectinib and entrectinib. Clinical trial results have demonstrated that larotrectinib is generally well tolerated and has shown high response rates that are durable across tumor types. These data validate NTRK gene fusions as actionable genomic alterations. In this review, we present the clinical data, discuss the different approaches that might be used to routinely screen tumors to indicate the presence of NTRK gene fusions, explore the issue of acquired resistance to TRK inhibition, and reflect on the wider regulatory considerations for tumor site agnostic TRK inhibitor drug development.

The tropomyosin receptor kinase (TRK) family of receptor tyrosine kinases has become a focus of clinical interest because the NTRK genes (NTRK1-3) encoding them have been identified as oncogenic fusion genes in a wide range of different tumor types, including lung cancer. These NTRK gene fusions usually occur at a low frequency below 1%, in non-small cell lung cancer (NSCLC) in 0.1–0.2% of the cases and have been reported across a wide range of tumor types. The TRK fusion proteins encoded by such gene fusions have constitutively activated tyrosine kinase domains and constitute actionable targets for tyrosine kinase inhibitors (TKIs). The first generation TRK TKIs larotrectinib and entrectinib have been investigated in clinical phase I and II trials in solid tumors both in adult and pediatric patients and results have demonstrated high response rates that are durable and with generally good tolerability. This has led to approval of these TRK inhibitors by regulatory authorities in the USA, Europe and Japan as tumor agnostic treatment of advanced or recurrent NTRK fusion-positive cancers in adult and pediatric patients. With a focus on lung cancer, this review gives a background to NTRK fusion genes, presents clinical data for TRK inhibitors and discuss the issue of acquired resistance to TRK inhibition.

The approval of larotrectinib and entrectinib for cancer patients harboring an NTRK gene fusion has represented a milestone in the era of “histology-agnostic” drugs. Among the clinical trials that led to the approval of these two drugs, most of the enrolled patients were affected by soft tissue sarcomas, lung, and salivary gland cancer. However, as next-generation sequencing assays are increasingly available in the clinical setting, health care professionals may be able to detect NTRK gene fusions in patients affected by tumor types under or not represented in the clinical trials. To this aim, we systematically reviewed MEDLINE from its inception to 31 August 2022 for case reports and case series on patients with NTRK gene fusion-positive tumors treated with TRK inhibitors. A virtual cohort of 43 patients was created, excluding those enrolled in the above-mentioned clinical trials. Although our results align with those existing in the literature, various cases of central nervous system tumors were registered in our cohort, confirming the benefit of these agents in this subgroup of patients. Large, multi-institutional registries are needed to provide more information about the efficacy of TRK inhibitors in cancer patients affected by tumor types under or not represented in the clinical trials.

IntroductionNeurotrophic tyrosine receptor kinase (NTRK) gene fusions are oncogenic drivers in various tumor types. Limited data exist on the overall survival (OS) of patients with tumors with NTRK gene fusions and on the co-occurrence of NTRK fusions with other oncogenic drivers. Materials and MethodsThis retrospective study included patients enrolled in the Genomics England 100,000 Genomes Project who had linked clinical data from UK databases. Patients who had undergone tumor whole genome sequencing between March 2016 and July 2019 were included. Patients with and without NTRK fusions were matched. OS was analyzed along with oncogenic alterations in ALK, BRAF, EGFR, ERBB2, KRAS, and ROS1, and tumor mutation burden (TMB) and microsatellite instability (MSI). ResultsOf 15,223 patients analyzed, 38 (0.25%) had NTRK gene fusions in 11 tumor types, the most common were breast cancer, colorectal cancer (CRC), and sarcoma. Median OS was not reached in both the NTRK gene fusion-positive and -negative groups (hazard ratio 1.47, 95% CI 0.39–5.57, P = 0.572). A KRAS mutation was identified in two (5%) patients with NTRK gene fusions, and both had hepatobiliary cancer. High TMB and MSI were both more common in patients with NTRK gene fusions, due to the CRC subset. While there was a higher risk of death in patients with NTRK gene fusions compared to those without, the difference was not statistically significant. ConclusionThis study supports the hypothesis that NTRK gene fusions are primary oncogenic drivers and the co-occurrence of NTRK gene fusions with other oncogenic alterations is rare.

The Advisory Board was held on December 24, 2021. The molecular genetic research lead specialists and national lead oncologists discussed issues of diagnosis of NTRK gene translocations in patients with non-small cell lung cancer (NSCLC), as well as current opportunities for the treatment of patients with NSCLC caused by NTRK gene fusions. The experts reaffirmed the necessity to identify timely patients with NSCLC caused by NTRK gene fusions, as the correct diagnosis of the disease, including the use of modern diagnostic methods of NTRK gene fusion (NGS is the most sensitive and specific method) determines the success of patient treatment. In this regard, it is critical that physicians know the advantages and disadvantages of each molecular diagnostic method used to have the opportunity to choose the best approach in each clinical case. In order to have a clear, well-functioning strategy for managing patients with suspected NSCLC caused by NTRK gene fusion, it is necessary to use molecular genetic tests, as well as include TRK inhibitors (in particular, the drug larotrectinib; at the time publication of the Resolution, the drug larotrectinib is not registered in the territory of the Russian Federation) in the clinical guidelines for the treatment of lung cancer. Larotrectinib is a highly selective tropomyosin receptor kinase (TRK) inhibitor. The clinical studies on larotrectinib have demonstrated high response rates and durable responses in adults and children with tumours associated with NTRK gene fusions, including primary CNS tumours and brain metastases. The objective response rate observed with larotrectinib was 79%, with 16% achieving a complete response and 64% achieving a partial response. At the same time, the median progression-free survival on larotrectinib was 28.3 months, and the median overall survival was 44.4 months.

Chromosomal rearrangements of NTRK1-3 resulting in gene fusions (NTRK gene fusions) have been clinically validated as oncogenic drivers in a wide range of human cancers. Typically, NTRK gene fusions involve both inter- and intrachromosomal fusions of the 5' regions of a variety of genes with the 3' regions of NTRK genes leading to TRK fusion proteins with constitutive, ligand-independent activation of the intrinsic tyrosine kinase. The incidence of NTRK gene fusions can range from the majority of cases in certain rare cancers to lower rates in a wide range of more common cancers. Two small-molecule TRK inhibitors have recently received regulatory approval for the treatment of patients with solid tumors harboring NTRK gene fusions, including the selective TRK inhibitor larotrectinib and the TRK/ROS1/ALK multikinase inhibitor entrectinib. In this review, we consider the practicalities of detecting tumors harboring NTRK gene fusions, the pharmacologic properties of TRK inhibitors currently in clinical development, the clinical evidence for larotrectinib and entrectinib efficacy, and possible resistance mechanisms.

3081 Background: Tropomyosin receptor kinase A (TrkA) is a protein encoded by the NTRK1 gene. Upregulation of TrkA signal transduction pathways, which can be caused by either NTRK1 gene fusions or intact TrkA protein overexpression, are oncogenic for multiple tumor types. This is clinically validated by demonstrated efficacy of ATP-competitive pan-TrkA/B/C inhibitors, larotrectinib and entrectinib for treatment of advanced solid tumors harboring NTRK1/2/3 gene fusions. VMD-928 is the first oral small-molecule TrkA (NTRK1) selective inhibitor with differentiated allosteric (ATP non-competitive) and irreversible mechanisms of action, acting as a molecular glue which sticks two TrkA proteins together and dose-dependently inhibits TrkA functions and downstream effectors, e.g. activated ERK, a hallmark of cancer. We conducted a first time in human phase 1 trial and completed the dose escalation phase. Methods: This is an open label, Phase 1 study investigating oral VMD-928 in adults with advanced solid tumors or lymphoma. The primary objective is to assess the safety and tolerability of VMD-928 and determine the recommended phase 2 dose. Secondary objectives include characterizing the pharmacokinetics (PK) and pharmacodynamics as well as assessing antitumor activity. Results: Non-biomarker-selected patients (n = 20) were accrued to 4 dose escalation cohorts ranging from 300 mg/day to 2400 mg/day. Three patients were accrued to the 2400 mg dose level with one DLT of elevated bilirubin, AST and ALT. The trough concentrations (Ctrough, ng/mL) ranged from 5.3 to 727. The dose was de-escalated to 1200 mg per day in divided doses and fifteen heavily pretreated patients were accrued with the following tumor types: adenoid cystic carcinoma, cholangiocarcinoma, lung cancer, pancreatic cancer, parotid, and squamous cell carcinoma of head and neck. There were no DLT’s at this dose and one patient with adenoid cystic carcinoma had prolonged stable disease. Common adverse events related to therapy were dark stool (35%), elevated liver enzymes (25%, primarily at 2400 mg/day), fatigue, nausea or vomiting, and decreased appetite (20% each). Conclusions: VMD-928 was well tolerated with mainly gastrointestinal side effects. The recommended phase 2 dose (RP2D) is 600 mg twice (1200 mg) per day. The study is currently accruing in expansion cohorts to evaluate efficacy in biomarker-selected patients with tumors of TrkA protein overexpression. Tumor types with reported high TrkA protein expression including thymic carcinoma (98% with TrkA protein expression without NTRK1/2/3 gene fusions), mesothelioma (81%), squamous cell carcinoma of head and neck (80%), ovarian (80%), hepatocellular (72%), and squamous cell carcinoma of the lung (71%) are being accrued. Clinical trial information: NCT03556228.

604TiP ON-TRK: A non-interventional study of larotrectinib in patients with TRK fusion cancer

Larotrectinib in adult patients with solid tumours: a multi-centre, open-label, phase I dose-escalation study

Introduction: A variety of alterations in NTRK genes have been identified in various cancers, including amplifications, rearrangements, deletions, splice variants as well as fusions. Larotrectinib is a highly selective TRK inhibitor that is active in patients (pts) with TRK fusion cancer. Here, we report post hoc efficacy and safety outcomes of larotrectinib treatment in pts with cancer and NTRK gene fusions (Fusion) vs those with Non-fusion alterations. Methods: Data were pooled from three clinical trials of adult and pediatric pts with TRK fusion cancer treated with larotrectinib (NCT02122913, NCT02576431, NCT02637687). NTRK gene status was assessed using local molecular testing; two studies (NCT02122913 and NCT02637687) initially enrolled pts regardless of TRK fusion status. Efficacy outcomes included objective response rate (ORR), assessed by investigators using RECIST 1.1, duration of response (DOR), progression-free survival (PFS), and overall survival (OS). Adverse events (AEs) were also assessed. The data cut-off was February 19, 2019. Results: This analysis included 159 pts (153 evaluable for efficacy) with NTRK fusions, with 17 different tumor types, and 73 Non-fusion pts with various genomic alterations, with 25 different tumor types. NTRK alterations reported in the Non-fusion pts included point mutations in 8 pts, amplifications in 7, rearrangements in 4 and deletions in 1. The ORR was 79% (95% confidence interval [CI] 72-85) in the Fusion group, with complete responses (CR) in 24 (16%), partial responses (PR) in 97 (63%), stable disease (SD) in 19 (12%), and progressive disease (PD) in 9 (6%). Median DOR was 35.2 months (95% CI 22.8-not estimable [NE]). In the Non-fusion group treated with larotrectinib, there were no responses except for one pt with NTRK1 amplification who had a PR of short duration (3.7 months); 17 Non-fusion pts (23%) had SD and 48 (66%) had PD as best response. Similarly, differences were seen in survival endpoints between pts in the overall Fusion and Non-fusion groups: median PFS 28.3 mo vs 1.8 mo and median OS 44.4 mo vs 10.7 mo, respectively. Median time of treatment was 7.9 months in the Fusion group and 1.7 months in the Non-fusion group. Incidences of Grade 3 or 4 AEs were lower in the Fusion group (49%) vs the Non-fusion group (58%). Discontinuation due to AEs occurred in 6% of pts in the Fusion group vs 25% in the Non-fusion group. Conclusion: Larotrectinib is highly efficacious in pts with TRK fusion cancer and has demonstrated durable responses. Pts with other NTRK alterations, including point mutations and amplifications, had only limited benefit from larotrectinib. Citation Format: David S. Hong, Afshin Dowlati, Howard Burris, Edward Chu, Marcia S. Brose, Anna F. Farago, Cornelis M. van Tilburg, Shivaani Kummar, Leo Mascarenhas, John A. Reeves, Marion Rudolph, Patricia Maeda, Barrett H. Childs, Theodore W. Laetsch, Alexander Drilon. Efficacy and safety of larotrectinib in patients with cancer and NTRK gene fusions or other alterations [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr CT062.

Several TRK inhibitors have demonstrated clinical efficacy in patients with solid tumors harboring NTRK gene fusions. However, the natural history and prognostic implications of NTRK fusions in solid tumors remain unknown. A cohort of 77 MD Anderson Cancer Center patients (MDACC) with NTRK gene fusions was identified and retrospectively compared to a second cohort from the Cancer Genome Atlas (TCGA) database. Due to paucity of events in early stage cancers and lack of TCGA data in rare tumors, 25 randomly selected MDACC patients were matched to 122 TCGA patients without NTRK gene fusion. Next we assessed the associations between NTRK gene fusion and overall (OS) and progression-free survivals (PFS). Among the 77 MDACC patients with NTRK gene fusions, 18 NTRK fusion partners were identified. There were insufficient OS events for analysis in the matched cohort. PFS was not significantly different (p = 0.49) between the NTRK-fusion positive MDACC patients (median PFS 786weeks, 95% CI 317-NE) and the NTRK-fusion negative TCGA patients (median PFS NE). The adjusted hazard ratio comparing TCGA patients to MDACC patients was HR = 0.72 (95% CI: 0.23-2.33), which trended towards a reduced rate of progression or death experienced by TCGA patients. This study did not identify statistically significant associations between NTRK fusion and PFS. Nonsignificant trends estimated increases in the risk of progression or death events for patients with NTRK fusions when compared to matched controls. Our findings help illuminate the influence of NTRK fusions on the natural history of a variety of solid tumors.

BackgroundNeurotrophic tyrosine receptor kinase (NTRK) gene fusions are oncogenic drivers in various tumor types. While NTRK gene fusions are predictive of benefit from tropomyosin receptor kinase inhibitors regardless of tumor type, the prognostic significance of NTRK gene fusions in a pan-tumor setting remains unclear.ObjectiveThis study evaluated the characteristics and prognosis of tropomyosin receptor kinase fusion cancer in the real-world setting.Patients and MethodsThis retrospective study used a de-identified clinico-genomic database and included patients with cancer who had comprehensive genomic profiling between January 2011 and July 2018. Patients were classified as having cancer with NTRK gene fusions or NTRK wild-type genes. Patients were matched with a 1:4 ratio (NTRK fusion:NTRK wild-type) using the Mahalanobis distance method on demographic and clinical characteristics, including age and Eastern Cooperative Oncology Group performance status. Descriptive analysis of clinical and molecular characteristics was conducted. Kaplan–Meier estimator and Cox regression were used for overall survival analysis.ResultsMedian overall survival was 12.5 months (95% confidence interval 9.5–not estimable) and 16.5 months (95% confidence interval 12.5–22.5) in the NTRK gene fusion (n = 27) and NTRK wild-type cohorts (n = 107), respectively (hazard ratio 1.44; 95% confidence interval 0.61–3.37; p = 0.648). Co-occurrence of select targetable biomarkers including ALK, BRAF, ERBB2, EGFR, ROS1, and KRAS was lower in cancers with NTRK gene fusions than in NTRK wild-type cancers.ConclusionsAlthough the hazard ratio for overall survival suggested a higher risk of death for patients with NTRK gene fusions, the difference was not statistically significant. Co-occurrence of NTRK gene fusions and other actionable biomarkers was uncommon.Supplementary InformationThe online version contains supplementary material available at 10.1007/s11523-021-00815-4.

Introduction: Targeted inhibitors of neurotropic tyrosine kinases are highly effective in selected patients with gene fusions involving NTRK1, NTRK2, or NTRK3 and are being actively investigated across cancer types. These fusions are consistently detected in rare cancer types (e.g., secretory breast carcinoma/MASC and infantile fibrosarcoma/congenital mesoblastic nephroma), but the occurrence of NTRK gene fusions in common cancer types is largely unexplored. Methods: Formalin-fixed, paraffin-embedded tumor tissues from 11,116 patients (Caris Life Sciences, Phoenix, AZ) were analyzed for 53 gene fusions (Archer FusionPlex) and additional sequencing of the 592 genes (NGS, Illumina). Total mutational load and gene copy number variations were calculated from the NGS results. NTRK protein (monoclonal rabbit antibody EPR17341, Abcam) and PD-L1 expression (SP142 or 22c3 monoclonal antibodies) were detected using immunohistochemistry (IHC). Results: Fusion assay identified 164 cases with a validated gene fusion (1.5% for the cohort), of which 23 cases (0.21% of the entire cohort) had an NTRK gene fusion. All 3 NTRK genes were involved in fusions with 13 different gene partners; TPM3:NTRK1 and ETV6:NTRK3 were the most common (6 cases each). Central nervous system malignancies had the highest frequency of NTRK fusions involving all 3 NTRK genes (11/400 cases, 2.8%), most commonly NTRK2 (7 cases fused with 7 different genes). NTRK2 fusions were exclusively detected in CNS malignancies (mostly GBM). Twelve non-CNS cases with NTRK1 or NTRK3 fusions included carcinomas of the respiratory tract (n=3), colon (n=2), thyroid (n=2), skin and cervix (n=1, each), uterine and soft tissue sarcoma (n=1, each), and one carcinoma of unknown primary (CUP) site. Strong (3+) and uniform (100% of cells) cytoplasmic/membranous expression of NTRK protein characterized NTRK1 fused cases (4 TPM3 and 1 MEF2D); NTRK2 fused cases were variably positive, while ETV6-NTRK3 cases were negative (0/6 cases). Of 23 NTRK fusion positive cases, eight had no other genomic alteration (pathogenic mutations or gene amplifications) which could be considered driving the cancer growth. Total mutational burden varied (1-37 somatic mutations per Mb) and was the highest in two MSI-H cases (CRC: TPM3-NTRK1 and CUP: ETV6-NTRK3). Additionally, PD-L1 expression was detected in 4 cases (lung and colon TPM3-NTRK1, GBM KCTD8-NTRK2 and CUP NTRK3:ETV6). Conclusion: Pathogenic NTRK genes fusions occur in a variety of cancers, but are generally rare (0.1%) outside primary CNS malignancies. NTRK may present as the only actionable target or co-occurring with other potentially targetable alterations (e.g., immune checkpoint inhibitors for PD-L1 positive or MSI-H cases). Uniform strong immunohistochemical staining for pNTRK may be a useful screening tool for NTRK1 gene fusion cancers outside the CNS. Citation Format: Zoran Gatalica, Jeffrey Swensen, Jeffery Kimbrough, Joanne Xiu. Molecular characterization of the malignancies with targetable NTRK gene fusions [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr A047.