New generation sequencing of targeted genes in the classical and the variant form of hairy cell leukemia highlights mutations in epigenetic regulation genes.

Elsa Maitre,Edouard Cornet,Fabrice Jardin,Xavier Troussard,Brigitte Sola,Philippe Bertrand,Catherine Maingonnat,Pierre-Julien Viailly,Dina Naguib,Véronique Salaün,Margaux Wiber,Gandhi Damaj

doi:10.18632/oncotarget.25601

Abstract

Classical hairy cell leukemia (HCL-c) is a rare lymphoid neoplasm. BRAFV600E mutation, detected in more than 80% of the cases, is described as a driver mutation, but additional genetic abnormalities appear to be necessary for the disease progression. For cases of HCL-c harboring a wild-type BRAF gene, the differential diagnosis of the variant form of HCL (HCL-v) or splenic diffuse red pulp lymphoma (SDRPL) is complex. We selected a panel of 21 relevant genes based on a literature review of whole exome sequencing studies (BRAF, MAP2K1, DUSP2, MAPK15, ARID1A, ARID1B, EZH2, KDM6A, CREBBP, TP53, CDKN1B, XPO1, KLF2, CXCR4, NOTH1, NOTCH2, MYD88, ANXA1, U2AF1, BCOR, and ABCA8). We analyzed 20 HCL-c and 4 HCL-v patients. The analysis of diagnostic samples mutations in BRAF (n = 18), KLF2 (n = 4), MAP2K1 (n = 3), KDM6A (n = 2), CDKN1B (n = 2), ARID1A (n = 2), CREBBP (n = 2) NOTCH1 (n = 1) and ARID1B (n = 1). BRAFV600E was found in 90% (18/20) of HCL-c patients. In HCL-c patients with BRAFV600E, other mutations were found in 33% (6/18) of cases. All 4 HCL-v patients had mutations in epigenetic regulatory genes: KDM6A (n = 2), CREBBP (n = 1) or ARID1A (n = 1). The analysis of sequential samples (at diagnosis and relapse) from 5 patients (2 HCL-c and 3 HCL-v), showed the presence of 2 new subclonal mutations (BCORE1430X and XPO1E571K) in one patient and variations of the mutated allele frequency in 2 other cases. In the HCL-v disease, we described new mutations targeting KDM6A that encode a lysine demethylase protein. This opens new perspectives for personalized medicine for this group of patients.

Highlights

Classical Hairy cell leukemia (HCL-c) is a rare lymphoid neoplasm with an incidence rate estimated at 0.3 per 100,000 people in United States between 2011 and 2012, and 0.2 per 100,000 people for the variant form of Hairy cell leukemia (HCL-v) [1]
We selected a panel of 21 relevant genes based on a literature review of whole exome sequencing studies (BRAF, MAP2K1, DUSP2, MAPK15, ARID1A, ARID1B, EZH2, KDM6A, CREBBP, TP53, CDKN1B, XPO1, KLF2, CXCR4, NOTH1, NOTCH2, MYD88, ANXA1, U2AF1, BCOR, and ABCA8)
35 non-synonymous single nucleotide variants (SNV) were validated with a range of 0–3 variants per samples (Figure 1 and Supplementary Table 5)

Summary

Introduction

Classical Hairy cell leukemia (HCL-c) is a rare lymphoid neoplasm with an incidence rate estimated at 0.3 per 100,000 people in United States between 2011 and 2012, and 0.2 per 100,000 people for the variant form of Hairy cell leukemia (HCL-v) [1]. The diagnosis of HCL-c is based on the typical hairy morphology of lymphocytes and the identification of BRAFV600E mutation [2,3,4]. The BRAFV600E mutation has been described as a driver mutation and detected in the hematopoietic stem cells (HSC) from HCL-c patients [5]. Tumor hairy cells display additional genetic alterations that are absent in HSC harboring BRAFV600E. Whole-exome sequencing (WES) studies have highlighted www.oncotarget.com additional BRAFV600E single nucleotide variants (SNV) [4, 6,7,8]. Some of these SNVs are probably passenger mutations, but others, because of their recurrence, appear to be more relevant to the disease

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