Poster Presentation 36th Lorne Cancer Conference 2024

Identification of a novel NTRK2 activating internal tandem duplication in paediatric CNS neuroblastoma (#237)

Lauren M Brown 1 2 , Loretta MS Lau 1 2 3 , Steve Foresto 4 , Fatimah Jalud 5 6 , Teresa Sadras 5 6 , Pablo Acera Mateos 1 2 , Antoine De Weck 1 2 , Pamela Ajuyah 1 , Paulette Barahona 1 , Marie Wong 1 , Chelsea Mayoh 1 2 , Mark J Cowley 1 2 , Paul G Ekert 1 2 5 6 7
  1. Children's Cancer Institute, UNSW Sydney, NSW, Australia
  2. School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia
  3. Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
  4. Queensland Children's Hospital, Brisbane, QLD, Australia
  5. Peter MacCallum Cancer Centre, Parkville, VIC, Australia
  6. The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
  7. University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia

Personalised medicine programs like the Zero Childhood Cancer Program (ZERO) perform molecular analysis of individual patient tumours to identify targeted treatment options for childhood cancer patients. The comprehensive and unbiased sequencing approaches that ZERO employs, including whole genome sequencing (WGS) and RNA sequencing (RNAseq), enables detection of novel structural variants (SVs) that may be cryptic to standard cytogenetic techniques or panel sequencing approaches. Identification of receptor tyrosine kinase (RTK) activating variants is a high priority given the availability and remarkable success of RTK inhibitors. TRK family kinases (encoded by NTRK1, NTRK2, and NTRK3) are activated in cancer by a range of mechanisms, including gene amplification, mutation, and gene fusions. In paediatric cancers, NTRK fusions are enriched in rare tumour types, including infantile fibrosarcoma and infant high-grade glioma, and are sensitive to TRK inhibition, notably with larotrectinib.

Here we describe a novel internal tandem duplication (ITD) in NTRK2, encoding TRKB, in a ZERO patient with CNS neuroblastoma. This SV was detected by WGS and was notably missed by RNAseq-based gene fusion and SV detection. The ITD spans exons 10-13 of NTRK2, is in-frame, and includes the juxtamembrane and transmembrane protein domains.

We have overexpressed NTRK2 ITD, as well as wild-type NTRK2 and an established NTRK2-activating fusion, SPECC1L-NTRK2, in the interleukin-3 (IL-3)-dependent cell line, Ba/F3, and the neuroblastoma cell line, SH-SY5Y. We show that like SPECC1L-NTRK2, NTRK2 ITD can promote IL-3 independent cell survival and proliferation of Ba/F3 cells through constitutive activation of TRKB signalling. Conversely, wild-type NTRK2 overexpression was insufficient to transform cells to IL-3 independence. Importantly, we show that cells transformed by NTRK2 ITD were specifically sensitive to TRK inhibitors, including larotrectinib.

While ITDs have been described in other RTK genes, notably FGFR1 and FLT3, structurally these have involved the kinase domain or the juxtamembrane domain. This is the first report of an ITD that spans the transmembrane domain of an RTK, characterising an additional mechanism by which RTKs can be activated in cancer. This study highlights the value of unbiased WGS approaches to identify novel SVs and identifies another class of patients that may benefit from RTK inhibitor therapy.