Detection of gene fusion transcripts in Peripheral T-cell Lymphoma using a multiplexed targeted sequencing assay.

Abstract

The genetic basis of peripheral T-cell lymphoma (PTCL) is complex and encompasses several recurrent fusion transcripts discovered over the past years by means of massive parallel sequencing. However, there is currently no affordable and rapid technology for their simultaneous detection in clinical samples. Here, we developed a multiplex ligation-dependent RT-PCR-based assay followed by high-throughput sequencing, to detect 33 known PTCL associated fusion transcripts. ALK fusion transcripts were detected in 15/16 ALK-positive anaplastic large cell lymphoma (ALCL). The latter case was further characterized by a novel SATB1_ALK fusion transcript. Among 239 other PTCL representative of 9 entities, non-ALK fusion transcripts were detected in 24 samples, mostly of follicular helper T cell (TFH) derivation. The most frequent non-ALK fusion transcript was ICOS_CD28 in 9 TFH-PTCL, 1 PTCL not otherwise specified (NOS) and 1 adult T-cell leukemia/lymphoma (ATLL), followed by VAV1 rearrangements with multiple partners (STAP2, THAP4, MYO1F, CD28) in 5 samples (3 PTCL-NOS, 2 TFH-PTCL). The other rearrangements were CTLA4_CD28 (1 TFH-PTCL), ITK_SYK (2 TFH-PTCL), ITK_FER (1 TFH-PTCL), IKZF2_ERBB4 (1 TFH-PTCL, 1 ATLL) and TP63_TBL1XR1 (1 ALK-negative ALCL). All fusions detected by our assay were validated by conventional RT-PCR and Sanger sequencing in 30 samples with adequate material. The simplicity and robustness of this targeted multiplex assay make it an attractive tool for the characterization of these heterogeneous diseases.