Pan-TRK immunohistochemistry as a tool in the screening for NTRK gene fusions in cancer patients

Therapy with TRK inhibitors is a tumor-agnostic treatment directed against specific molecular changes rather than cancer type. NTRK fusions are rare in most prevalent cancers, accounting for less than 0.5% of cases. However, there is a group of rare cancers in which NTRK fusion is more prevalent. These include secretory carcinoma of the breast and salivary gland, childhood sarcomas, such as infantile fibrosarcoma, and cellular and mixed congenital mesoblastic nephroblastoma. The most common rearrangement pertains to NTRK3 and the most common fusion gene is ETV6. Identifying patients with NTRK gene fusions who would likely benefit from targeted therapy with TRK inhibitors requires practical diagnostic tools and an appropriate management strategy of diagnostic trajectory. The fusions can be detected by molecular biology techniques or pan-TRK immunohistochemistry. The latter detects NTRK1/2/3 gene fusions independently of the resulting fusion gene but does not determine which of them has been rearranged or what the fusion partner is. The sensitivity and specificity of the method reach 97% and 100%, respectively. Other advantages include the relatively low cost, short duration of examination, and broad accessibility of immunohistochemistry laboratories. These characteristics make this method a useful screening tool for detecting patients with NTRK gene fusions

Multidisciplinary consensus on optimising the detection of NTRK gene alterations in tumours

Fusions de gens; Oncologia molecular; NeoplàsiaFusiones de genes; Oncología molecular; NeoplasiaGene fusions; Molecular oncology; NeoplasmThe recent identification of rearrangements of neurotrophic tyrosine receptor kinase (NTRK) genes and the development of specific fusion protein inhibitors, such as larotrectinib and entrectinib, have revolutionised the diagnostic and clinical management of patients presenting with tumours with these alterations. Tumours that harbour NTRK fusions are found in both adults and children; and they are either rare tumours with common NTRK fusions that may be diagnostic, or more prevalent tumours with rare NTRK fusions. To assess currently available evidence on this matter, three key Spanish medical societies (the Spanish Society of Medical Oncology (SEOM), the Spanish Society of Pathological Anatomy (SEAP), and the Spanish Society of Paediatric Haematology and Oncology (SEHOP) have brought together a group of experts to develop a consensus document that includes guidelines on the diagnostic, clinical, and therapeutic aspects of NTRK-fusion tumours. This document also discusses the challenges related to the routine detection of these genetic alterations in a mostly public Health Care System.SEOM, SEAP and SEHOP have received financial support for this project in the form of unrestricted collaboration in the logistics of expert meeting from Bayer and Roche

Potential Novel Therapy Targets in Neuroendocrine Carcinomas of the Breast.

Neuroendocrine carcinoma (NEC) of the breast is a rare, special type of breast cancer, reportedly constituting 2% to 5% of all breast cancers. Although breast NEC does not have a specific targeted therapy, several new targeted therapies based on specific biomarkers were recently investigated in the NEC of lung and in other types of breast carcinoma, which may provide guidance to their feasibility in breast NEC. Twenty breast NECs were profiled for biomarkers of therapy including antibody-drug conjugates (DLL3, TROP-2, and FOLR1), histone deacetylase (H3K36Me3) inhibitors, tropomyosin receptor kinases (NTRK1/2/3 gene fusions) targeted inhibitors, alkylating agents (MGMT), and immune checkpoint inhibitors (PD-L1, TMB, and MSI) using immunohistochemistry and DNA/RNA next-generation sequencing assays. Predictive expression of TROP-2, FOLR1, and H3K36Me3 were detected in different subsets of tumors and may pave the way for development of novel targeted therapies in some patients with breast NECs. There was no evidence of DLL3 expression, NTRK gene fusions, or MGMT hypermethylation. No biomarkers predictive of immune checkpoint inhibitor efficacy (programmed death-ligand 1 expression, tumor mutational burden, microsatellite instability) were identified. FGFR and CCND1 gene amplifications were detected in isolated cases. This study identified several potential targets for novel therapies in breast NEC, including farletuzumab and mirvetuximab soravtansine (FOLR1), sacituzumab govitecan (TROP-2), and HDAC inhibitors (H3K36Me3). In some cases, CCND1 gene amplification may indicate the usefulness of investigational therapies. The reported results should serve as an early indication of potential clinical relevance in selected patients with breast NEC

Real-time PCR expression profile of all receptor and non-receptor tyrosine kinases in prostate cancer

Objectives: Tyrosine kinases (TKs) represent a group of enzymes that play a key role in the development of cancer. They act as important relay points affecting proliferation, differentiation, cell motility and apoptosis. Consequently, they are the focus of studies investigating the molecular basis of tumour development and progress. For the first time, we show the gene expression signature of all TKs in prostate cancer. Methods: The expression of 89 TKs was examined in prostatic tissue by real-time PCR (i.e. TaqMan Low Density Array). Tissue sampling, RNA isolation and cDNA synthesis were meticulously standardized. Cancer specimens of defined histological grades were compared to benign tissue. Expression data was processed using a combination of different software solutions to take on the problems of normalization and statistics. Results: We identified six TK genes with a significant increase (ABL2: +3.46-fold) or decrease (FGFR2: -3.46-fold, FGFR4: -4.59-fold, NTRK1: -4.38-fold, NTRK3: -6.04-fold, ROR2: -3.765-fold; p=0,009-0,018) in gene expression. Commercially available antibodies for immunohistochemistry worked well for FGFR2 and ABL2 and confirmed our data on the protein level. Conclusions: Our results underline the potential of an all-TK expression array in cancer and point out a number of TKs that are markedly dysregulated. Especially the overexpression of ABL2 is a finding of high clinical interest, as it provides a rational molecular background for the successful application of imatinib mesylate in prostate cancer. </p

Investigation of the sarcoma fusion gene landscape through targeted sequencing of archived patient samples

Fusion genes are known to be key diagnostic, prognostic and therapeutic targets in blood cancers. However in sarcoma, the fusion gene landscape has yet to be fully elucidated due to the heterogeneity of fusion gene partners and rarity of the samples. Current fusion gene diagnostics are only able to detect presence of the fusion and are unable to identify novel fusion gene partners or splice isoforms. Therefore to expand on the knowledge of fusion genes in sarcoma, my study aims to sequence RNA from archived sarcoma patient samples by targeting a panel of 255 genes known to be involved in fusion. Through targeted sequencing, accurate fusion gene detection can be achieved along with information on novel fusion gene partners or splice junctions. Finally gene expression analysis was performed to gain insight into the transcriptome of sarcoma and identify the relationship of fusion genes to clinical prognostic markers. In this study, RNA was sourced from formalin fixed paraffin embedded (FFPE) samples, which is often degraded and chemically modified. However based on quality assessment, fusion gene detection could still be carried out in libraries as small as 1 million reads. Fusion genes were found to be identified in 44% (43/98) of patient samples with 38 of these fusions consistent with those reported in literature. Novel fusion isoforms were also found to contain different breakpoints but retain the same protein domains as the recurrent fusion isoform. Through gene expression analysis of fusion positive and negative Ewing’s sarcoma, it was found that 52% of differentially expressed protein coding isoforms contained fewer regulatory elements compared to the principal isoform of the gene. This suggests that presence of the fusion in Ewing’s sarcoma may be related to eased expression of certain genes. To identify any other links fusion genes may have to gene expression, levels of prognostic immune markers were compared to fusion type. While fusion type did not appear to be associated with expression of these immune genes, varying expression levels between samples may potentially act as a predictor for immunotherapy success