From genomic spectrum of NTRK genes to adverse effects of its inhibitors, a comprehensive genome-based and real-world pharmacovigilance analysis

Abstract

Introduction: The discovery of neurotrophic tyrosine receptor kinase (NTRK) gene fusions has facilitated the development of precision oncology. Two first-generation NTRK inhibitors (larotrectinib and entrectinib) are currently approved for the treatment of patients with solid tumors harboring NTRK gene fusions. Nevertheless, comprehensive NTRK profiling at the pan-cancer genomic level and real-world studies pertaining to the adverse events of NTRK inhibitors are lacking. Methods: We characterize the genome of NTRK at the pan-cancer level through multi-omics databases such as The Cancer Genome Atlas (TCGA). Through the FDA Adverse Event Reporting System (FAERS) database, we collect reports of entrectinib and larotrectinib-induced adverse events and perform a pharmacovigilance analysis using various disproportionality methods. Results: NTRK1/2/3 expression is lower in most tumor tissues, while they have higher methylation levels. NTRK gene expression has prognostic value in some cancer types, such as breast invasive carcinoma (BRCA). The cancer type with highest NTRK alteration frequency is skin cutaneous melanoma (SKCM) (31.98%). Thyroid carcinoma (THCA) has the largest number of NTRK fusion cases, and the most common fusion pair is ETV6-NTRK3. Adverse drug events (ADEs) obtained from the FAERS database for larotrectinib and entrectinib are 524 and 563, respectively. At the System Organ Class (SOC) level, both drugs have positive signal value for "nervous system disorder". Other positive signals for entrectinib include "cardiac disorders", "metabolism and nutrition disorders", while for larotrectinib, it is "hepatobiliary disorders". The unexpected signals are also listed in detail. ADEs of the two NTRK inhibitors mainly occur in the first month. The median onset time of ADEs for entrectinib and larotrectinib was 16 days (interquartile range [IQR] 6-86.5) and 44 days ([IQR] 7-136), respectively. Conclusion: Our analysis provides a broad molecular view of the NTRK family. The real-world adverse drug event analysis of entrectinib and larotrectinib contributes to more refined medication management.

Keywords: FAERS; NTRK; adverse drug event; entrectinib; gene fusion; larotrectinib; pharmacovigilance.

FIGURE 1

A flow chart of the whole study. In part I, we acquired NTRK expression profiling data and conducted an analysis of its mRNA expression, methylation, and CNV (step 1). Subsequently, we delved into the genomic alterations of NTRK, co-mutation pathways (step 2), and emphasized NTRK fusions (step 3). The part II involved a comprehensive review of the clinical trials of NTRK inhibitors (step 4). In part III, a safety assessment of the first-generation NTRK inhibitors was carried out utilizing real-world ADE reports sourced from the FAERS database (step 5). This encompassed data cleaning, baseline information description, signal detection, and time to onset analysis. Furthermore, we provided a summarization of the interrelationships between the three different data sources (top right of figure). CNV, copy number variation; FAERS, FDA Adverse Event Reporting System; SOC, System Organ Class; PT, preferred term; ADE, adverse drug event; PS, primary suspect.

FIGURE 2

Genomic characterization of NTRK genes at the pan-cancer level. (A). Differential mRNA expression of NTRK1/2/3 in tumor and corresponding normal tissues. Gene expression is compared after Log2 (TPM+1) transformed. (B). Bubble plots demonstrate the correlation between NTRK genes expression and methylation levels. The bubble size positively correlates with the significance of FDR. The black outline border indicates FDR≤0.05. (C). Bubble plots depict the methylation differences of NTRK genes between tumor and normal samples. Blue dots and red color indicate methylation downregulation and upregulation in tumors, respectively. (D). Figure summarizes the correlations between CNV and NTRK genes expression in pan-cancer. (E). Percentage of cancers in which NTRK1/2/3 expression has a potential impact on pathway activity is shown. Pathway A and I represent activation or inhibition of this pathway. (F). Pie chart showing the percentage of different types of CNV in NTRK1/2/3 in a given cancer, with different colors representing different CNV types. (G). The relationship between NTRK genes expression and patient prognosis (OS, DSS, PFI) in pan-cancer. TPM, transcripts per million; FDR, false discovery rate; CNV, copy number variation; OS, overall survival; DSS, disease-specific survival; PFI, progression-free interval. *p < 0.05. **p < 0.01. ***p < 0.001. ns, no significance.

FIGURE 3

Genomic alterations of the NTRK genes at the pan-cancer level. (A). The alteration frequency of NTRK genes across 32 TCGA tumor types. (B). Amino acid mutation of in TCGA cancers. The GO and KEGG enrichment analyses of differentially altered genes between NTRK-gene-altered and unaltered groups are visualized using circular subgroup plot (C) and chord plot (D). GO, gene ontology; BP, biological process; CC, cellular component; MF, molecular function; KEGG, Kyoto Encyclopedia of Genes and Genomes.

FIGURE 4

This chart shows the top biomarkers most frequently included in clinical trials investigating larotrectinib (A) and entrectinib (B), and the types of cancers associated with those biomarkers. (C). Current clinical trial status of larotrectinib and entrectinib.

FIGURE 5

Signal detection at the SOC level. (A). Annual distribution of ADE reports of the two first-generation NTRK inhibitors (entrectinib, blue; larotrectinib, red), from 2019 Q1 to 2023 Q1. (B). Number of ADE reports for entrectinib and larotrectinib at the SOC level. (C). The bar scale graph shows the percentage of ADEs at the SOC level. The ROR values and their corresponding 95% confidence intervals for larotrectinib (D) and entrectinib (E) are displayed for different levels of SOC. ADEs, adverse drug events; SOC, System Organ Class; Q1, first quarter; ROR, reporting odds ratio.

FIGURE 6

Comparison of signal values of the two first-generation NTRK inhibitors for ADEs at the PT level. All positive signals for entrectinib (A) and larotrectinib (B) are ranked by case number. (C). Intersection of positive signals of two drugs. All positive signals for entrectinib (D) and larotrectinib (E) are ranked by IC025 value. An asterisk indicates that the signal is not indicated in the drug instruction. PRR, proportional reporting ratio; PT, preferred term; IC, information component; IC025, the lower limit of the 95% confidence interval of IC.

FIGURE 7

Time to onset (TTO) analysis (counted in days). Box plot of the TTO at the SOC level for entrectinib (A) and larotrectinib (B). Bold bar within the stick: median TTO; Lower end of the stick: 1/4 quantile of the TTO; Upper end of the stick: 3/4 quantile of the TTO. Number and proportion of all TTO reports in different time periods for entrectinib (C) and larotrectinib (D). Weibull distribution test of TTO for entrectinib (E) and larotrectinib (F). A TTO of 0 days signifies that the adverse event occurred on the same day as the start of treatment. IQR, interquartile range.