Whole-genome profiling of primary cutaneous anaplastic large cell lymphoma

Haematologica. 2022 Jul 1;107(7):1619-1632. doi: 10.3324/haematol.2020.263251.

Abstract

Primary cutaneous anaplastic large cell lymphoma (pcALCL), a hematological neoplasm caused by skin-homing CD30+ malignant T cells, is part of the spectrum of primary cutaneous CD30+ lymphoproliferative disorders. To date, only a small number of molecular alterations have been described in pcALCL and, so far, no clear unifying theme that could explain the pathogenetic origin of the disease has emerged among patients. In order to clarify the pathogenetic basis of pcALCL, we performed high-resolution genetic profiling (genome/transcriptome) of this lymphoma (n=12) by using whole-genome sequencing, whole-exome sequencing and RNA sequencing. Our study, which uncovered novel genomic rearrangements, copy number alterations and small-scale mutations underlying this malignancy, revealed that the cell cycle, T-cell physiology regulation, transcription and signaling via the PI-3-K, MAPK and G-protein pathways are cellular processes commonly impacted by molecular alterations in patients with pcALCL. Recurrent events affecting cancer-associated genes included deletion of PRDM1 and TNFRSF14, gain of EZH2 and TNFRSF8, small-scale mutations in LRP1B, PDPK1 and PIK3R1 and rearrangements involving GPS2, LINC-PINT and TNK1. Consistent with the genomic data, transcriptome analysis uncovered upregulation of signal transduction routes associated with the PI-3-K, MAPK and G-protein pathways (e.g., ERK, phospholipase C, AKT). Our molecular findings suggest that inhibition of proliferation-promoting pathways altered in pcALCL (particularly PI-3-K/AKT signaling) should be explored as potential alternative therapy for patients with this lymphoma, especially, for cases that do not respond to first-line skin-directed therapies or with extracutaneous disease.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 3-Phosphoinositide-Dependent Protein Kinases
  • Fetal Proteins
  • Humans
  • Ki-1 Antigen
  • Lymphoma, Large-Cell, Anaplastic* / genetics
  • Lymphoma, Large-Cell, Anaplastic* / pathology
  • Lymphoma, Primary Cutaneous Anaplastic Large Cell*
  • Lymphoproliferative Disorders* / pathology
  • Protein-Tyrosine Kinases
  • Proto-Oncogene Proteins c-akt
  • Skin Neoplasms* / metabolism

Substances

  • Fetal Proteins
  • Ki-1 Antigen
  • Protein-Tyrosine Kinases
  • TNK1 protein, human
  • 3-Phosphoinositide-Dependent Protein Kinases
  • PDPK1 protein, human
  • Proto-Oncogene Proteins c-akt

Grants and funding

Funding: This study was funded by the Dutch Cancer Society (KWF, grant UL2013-6104), the Netherlands Organization for Health Research and Development (ZonMw, grant 40-43500-98-4027/435004503), Takeda Nederland B.V. and the Foundation for Pathological Research and Development (S.P.O.O., grant SPOO-2016003).