Integrated mate-pair and RNA sequencing identifies novel, targetable gene fusions in peripheral T-cell lymphoma

Abstract

Peripheral T-cell lymphomas (PTCLs) represent a heterogeneous group of T-cell malignancies that generally demonstrate aggressive clinical behavior, often are refractory to standard therapy, and remain significantly understudied. The most common World Health Organization subtype is PTCL, not otherwise specified (NOS), essentially a “wastebasket” category because of inadequate understanding to assign cases to a more specific diagnostic entity. Identification of novel fusion genes has contributed significantly to improving the classification, biologic understanding, and therapeutic targeting of PTCLs. Here, we integrated mate-pair DNA and RNA next-generation sequencing to identify chromosomal rearrangements encoding expressed fusion transcripts in PTCL, NOS. Two of 11 cases had novel fusions involving VAV1, encoding a truncated form of the VAV1 guanine nucleotide exchange factor important in T-cell receptor signaling. Fluorescence in situ hybridization studies identified VAV1 rearrangements in 10 of 148 PTCLs (7%). These were observed exclusively in PTCL, NOS (11%) and anaplastic large cell lymphoma (11%). In vitro, ectopic expression of a VAV1 fusion promoted cell growth and migration in a RAC1-dependent manner. This growth was inhibited by azathioprine, a clinically available RAC1 inhibitor. We also identified novel kinase gene fusions, ITK-FER and IKZF2-ERBB4, as candidate therapeutic targets that show similarities to known recurrent oncogenic ITK-SYK fusions and ERBB4 transcript variants in PTCLs, respectively. Additional novel and potentially clinically relevant fusions also were discovered. Together, these findings identify VAV1 fusions as recurrent and targetable events in PTCLs and highlight the potential for clinical sequencing to guide individualized therapy approaches for this group of aggressive malignancies.

Peripheral T-cell lymphoma, not otherwise specified

“…[9][10][11] For this reason, the former follicular variant of PTCL-NOS has been moved to the new T-follicular helper-lymphoma category in the 2016 WHO classification. 12 Recurrent gene fusions of VAV1, which encodes a critical component of the T-cell receptor signaling, have been recently described in a relevant proportion of PTCL-NOS and ALCL, 13 along with rearrangements of ITK with genes such as SYK, FER, and ERBB4; this suggests their possible role in regulating cell growth and in ultimately driving T-cell lymphomagenesis 14 as well as representing potential targets for therapy to be extensively exploited in rationally designed clinical trials. TP63 rearrangements have also been recurrently found in PTCL-NOS and ALCL characterized by high proliferation indices and more severe prognosis.…”

Toward the Integration of Mate Pair and RNA Sequencing to Identify Gene Fusions in Cancer Research: A Mini Review

“…It has been reported in the literature that a combined approach tends to overcome many of the limitations found when the methods are applied separately [16]. MPseq and RNAseq have successfully identified fusions in peripheral T-cell Lymphoma (PTCL) [17]. One of the important points in this paper is that structural rearrangements predicted by MPseq do not necessarily involve genes nor expressed genes as fusion partners.…”

“…One of the important points in this paper is that structural rearrangements predicted by MPseq do not necessarily involve genes nor expressed genes as fusion partners. On the other hand, RNAseq tends to identify expressed gene fusions [17].…”

Recent Progress in the Understanding of Angioimmunoblastic T-cell Lymphoma

“…57 An ITK-SYK fusion gene generated by the translocation t(5;9)(q33;q22) was identified predominantly in FTCL (FTCL 18% 11 -38%; 58 all PTCL-NOS, 17% 58 ). The expression of the ITK-SYK fusion gene was reported to constitutively activate TCR signaling.…”

“…56,57 VAV1 fusion genes and in-frame deletions are thought to be activating mutations by disrupting intramolecular autoinhibition.…”