A New t(7;9)(p12;q34) Involving NOTCH1 and IKZF1 in Pediatric T-Cell Lymphoblastic Lymphoma
Authors: Baleydier Frederic Paul , Amruthalingam Esther , Ansari Marc , Rougemont Anne-Laure , Hediger David , Tchinda Joelle 
Published: December 2023

Background

Notch1 pathway activation is demonstrated in approximately 50% of T-cell acute lymphoblastic leukemias/lymphomas (T-ALL/LL) mainly by the presence of activating somatic mutations of NOTCH1 involving homodimerization and/or PEST (proline, glutamic acid, serine, threonine) domains. The oncogenic role of NOTCH1 was however primarily described with the characterization of the recurrent although rare t(7;9)(q34;q34). By positioning the coding region of the intracellular part of Notch1 (ICN1) under the control of the TCR beta-gene promoter, this translocation generates a truncated Notch1 receptor resulting in constitutive activation of the Notch1 pathway, independent of ligand binding. In murine models ICN1 is much more pro-oncogenic than NOTCH1 activating mutations. While several retrospective studies identified NOTCH1 activating mutations as an independent good-prognostic factor in human T-ALL/LL, search for truncated ICN1 in NOTCH1 wild-type patients was usually not performed/considered.

Aim

To describe and characterize a new translocation in a pediatric patient with T-LL.

Method

Somatic cytogenetics of blastic T-cells from diagnosis was explored by conventional karyotype. A specific fluorescence in situ hybridization (FISH) Breakapart probe was designed to explore the NOTCH1 locus on chromosome 9q34. Targeted locus amplification based sequencing (TLA) using genomic DNA was used to confirm/determine the partners involved in the new fusion found. Targeted RNA-sequencing using the Illumina TruSight RNA Fusion Panel was used to determine the putative transcript produced by the fusion.

Results

The patient, a 14-year-old young female, was diagnosed with stage 3 T-LL characterized by a large mediastinal mass with massive pleural effusion. Flow cytometry demonstrated a CD7+, CD1a+, CD4+/CD8+ double positive phenotype corresponding to EGIL type III T-LL. Conventional karyotype on T-lymphoblastic cells showed two clonal abnormalities, a deletion del(6)(q13q22) and a translocation t(7;9)(p12;q34) in 10 metaphases analyzed. Involvement of NOTCH1 in this new t(7;9)(p12;q34) was confirmed by molecular cytogenetics using a FISH Breakapart probe targeting the NOTCH1 locus. Targeted locus amplification based sequencing (TLA) revealed IKZF1 as the fusion partner involved in this new fusion. DNA sequencing revealed a predictive fusion between the intracellular domain of NOTCH1 (ICN1; breakpoint in intron 26 (NM_017617.5)) and IKF1 (breakpoint in intron 5 (NM_006060)). The targeted RNA-sequencing performed on the pleural effusion confirmed an in frame NOTCH1-IKZF1 fusion transcript. Sequencing of exons 26-27 and 34 of NOTCH1 showed wild-type alleles. After a swift response to the induction phase, the patient is in complete remission one year after completing her treatment according to the EuroLB-02 protocol.

Summary/perspectives

This new t(7;9)(p12;q34) involving ICN1 illustrates the importance to look for ICN1 more extensively in parallel to NOTCH1/FBXW7 mutations in the screening of Notch1 activation pathway in T-ALL/LL specially in the event of a stratification on Notch1 status for treatment. As both NOTCH1 and IKZF1 are major actors of normal T-cell differentiation/proliferation, the oncogenic role of the fusion NOTCH1::IKZF1 in T-ALL/LL deserves a better understanding in a larger population and will be further explored.