Deciphering Genetic Alterations of Hairy Cell Leukemia and Hairy Cell Leukemia-like Disorders in 98 Patients

Abstract

Hairy cell leukemia (cHCL) patients have, in most cases, a specific clinical and biological presentation with splenomegaly, anemia, leukopenia, neutropenia, monocytopenia and/or thrombocytopenia, identification of hairy cells that express CD103, CD123, CD25, CD11c and identification of the V600E mutation in the B-Raf proto-oncogene (BRAF) in 90% of cases. Monocytopenia is absent in vHCL and SDRPL patients and the abnormal cells do not express CD25 or CD123 and do not present the BRAF^V600E mutation. Ten percent of cHCL patients are BRAF^WT and the distinction between cHCL and HCL-like disorders including the variant form of HCL (vHCL) and splenic diffuse red pulp lymphoma (SDRPL) can be challenging. We performed deep sequencing in a large cohort of 84 cHCL and 16 HCL-like disorders to improve insights into the pathogenesis of the diseases. BRAF mutations were detected in 76/82 patients of cHCL (93%) and additional mutations were identified in Krüppel-like Factor 2 (KLF2) in 19 patients (23%) or CDKN1B in 6 patients (7.5%). Some KLF2 genetic alterations were localized on the cytidine deaminase (AID) consensus motif, suggesting AID-induced mutations. When analyzing sequential samples, a clonal evolution was identified in half of the cHCL patients (6/12 pts). Among the 16 patients with HCL-like disorders, we observed an enrichment of MAP2K1 mutations in vHCL/SDRPL (3/5 pts) and genes involved in the epigenetic regulation (KDM6A, EZH2, CREBBP, ARID1A) (3/5 pts). Furthermore, MAP2K1 mutations were associated with a bad prognosis and a shorter time to next treatment (TTNT) and progression-free survival (PFS), independently of the HCL classification.

Keywords: BRAF; HCL; KLF2; MAP2K1; genetic alterations; hairy cell leukemia; hairy cell leukemia variant (vHCL); hairy cell leukemia-like disorders; splenic diffuse red pulp lymphoma (SDRPL).

Figure 1

(A) Classification of the variants (n = 220) in the overall cohort (135 samples). (B) Top10 mutated genes in the overall cohort (n = 135 samples). (C) Waterfall representation for the unique patients (n = 98). When several samples were available for one patient, the first sample was used.

Figure 2

Fish-plot representation of UPN-45 showing clonal evolution of the mutations along the progression of the disease. The patient received interferon during five years; then 2-CDA at relapse 1 (R1) and 2 (R2), pentostatin at R3, 4 cycles of rituximab (R4), BRAF-inhibitor: vemurafenib (R5), and anti-CD22 immunotoxin moxetumomab-pasudotox (R6). No sample was obtained at R2 and R4. R1: Relapse 1 (165 months); R3: Relapse 3 (226 months); R5: Relapse 3 +237 months; R6: Relapse 6 +309 months.

Figure 3

(A) Lolliplot representation of KLF2 mutations, excluding synonymous and deep intronic mutations. In green, missense mutations of the two domains: COG5048, conserved protein domain family COG5048, including zinc-finger proteins and Zf-H2C2_2, zinc-finger double domains. (B) transition–transversion plot of the KLF2 mutation. Intronic and synonymous mutations are included.

Figure 3

(A) Lolliplot representation of KLF2 mutations, excluding synonymous and deep intronic mutations. In green, missense mutations of the two domains: COG5048, conserved protein domain family COG5048, including zinc-finger proteins and Zf-H2C2_2, zinc-finger double domains. (B) transition–transversion plot of the KLF2 mutation. Intronic and synonymous mutations are included.

Figure 4

Enrichment of a specific mutated gene in the three different sub-groups.

Figure 5

Survival analysis of the MAP2K1 mutation on TTNT (A), PFS (B) and OS (C), Kaplan–Meier representation, comparison by log-rank.

Figure 5

Survival analysis of the MAP2K1 mutation on TTNT (A), PFS (B) and OS (C), Kaplan–Meier representation, comparison by log-rank.