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Transcriptome complexity in intravascular NK/T-cell lymphoma
  1. Kohei Fujikura1,2,
  2. Makoto Yoshida1,
  3. Kazuma Uesaka3
  1. 1 Department of Pathology, Kobe City Medical Center General Hospital, Kobe, Japan
  2. 2 Department of Diagnostic Pathology, Kobe University Graduate School of Medicine, Kobe, Japan
  3. 3 Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
  1. Correspondence to Kohei Fujikura, Department of Pathology, Kobe city medical center general hospital, Kobe 650-0047, Japan; kfuji{at}med.kobe-u.ac.jp

Abstract

Aims Intravascular NK/T-cell lymphoma (IVNKTCL) is a rare disease, which is characterised by exclusive growth of large cells within the lumen of small vessels, Epstein–Barr virus infection and somatic mutations in epigenetic regulator genes. Here, we elucidate the transcriptomic complexity of IVNKTCL.

Methods IVNKTCL cases were retrieved from a single-centre cohort of 25 intravascular lymphomas. RNA-seq and whole exome sequencing (WES) were performed to analyse transcriptomic abnormalities and mutations in splicing factors.

Results Approximately 88% of the total reads from the RNA-seq were considered exonic, while the remaining reads (12%) were mapped to intronic or intergenic regions. We detected 28,941 alternative splicing events, some of which would produce abnormal proteins rarely found in normal cells. The detected events also included tumour-specific splicing alterations in oncogenes and tumour suppressors (e.g., HRAS, MDM2 and VEGFA). WES identified premature termination mutations or copy number losses in a total of 15 splicing regulator genes, including SF3B5, SRSF12 and TNPO3.

Conclusions This study raises the possibility that IVNKTCL may be driven by multiple complex regulatory loops, including non-exonic expression and aberrant splicing, in addition to defects in epigenetic regulation.

  • lymphoma
  • histopathology
  • haematology
  • genetics
  • molecular pathology
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Footnotes

  • Handling editor Runjan Chetty.

  • Contributors KF designed the study, performed the experiments and wrote the manuscript. MY collected clinical data. KU assisted bioinformatic analysis. All authors read and approved the submitted version of manuscript.

  • Funding This study was supported by the Kasahara Cancer Research Fund (H28 to KF).

  • Competing interests None declared.

  • Patient consent for publication Not required.

  • Ethics approval This study was approved by the institutional ethics committee of Kobe City Medical Center General Hospital.

  • Provenance and peer review Not commissioned; externally peer reviewed.

  • Data availability statement Sequence data are available upon request.

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