Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2016 Feb;6(2):154-65.
doi: 10.1158/2159-8290.CD-15-0913. Epub 2015 Nov 13.

Diverse and Targetable Kinase Alterations Drive Histiocytic Neoplasms

Affiliations
Free PMC article

Diverse and Targetable Kinase Alterations Drive Histiocytic Neoplasms

Eli L Diamond et al. Cancer Discov. .
Free PMC article

Abstract

Histiocytic neoplasms are clonal, hematopoietic disorders characterized by an accumulation of abnormal, monocyte-derived dendritic cells or macrophages in Langerhans cell histiocytosis (LCH) and non-Langerhans cell histiocytosis (non-LCH), respectively. The discovery of BRAF(V600E) mutations in approximately 50% of these patients provided the first molecular therapeutic target in histiocytosis. However, recurrent driving mutations in the majority of patients with BRAF(V600E)-wild-type non-LCH are unknown, and recurrent cooperating mutations in non-MAP kinase pathways are undefined for the histiocytic neoplasms. Through combined whole-exome and transcriptome sequencing, we identified recurrent kinase fusions involving BRAF, ALK, and NTRK1, as well as recurrent, activating MAP2K1 and ARAF mutations in patients with BRAF(V600E)-wild-type non-LCH. In addition to MAP kinase pathway lesions, recurrently altered genes involving diverse cellular pathways were identified. Treatment of patients with MAP2K1- and ARAF-mutated non-LCH using MEK and RAF inhibitors, respectively, resulted in clinical efficacy, demonstrating the importance of detecting and targeting diverse kinase alterations in these disorders.

Significance: We provide the first description of kinase fusions in systemic histiocytic neoplasms and activating ARAF and MAP2K1 mutations in non-Langerhans histiocytic neoplasms. Refractory patients with MAP2K1- and ARAF-mutant histiocytoses had clinical responses to MEK inhibition and sorafenib, respectively, highlighting the importance of comprehensive genomic analysis of these disorders.

Conflict of interest statement

Conflict of Interest Disclosure Statement:

P.J.S., V.A.M., J.S.R., and S.M.A. are employees of Foundation Medicine Inc. and have equity interest. Otherwise, the authors declare no competing financial interests.

Figures

Figure 1
Figure 1. Mutational profiles of systemic histiocytic neoplasm patients and recurrent MAP2K1 and ARAF mutations in non-Langerhans histiocytic neoplasms
(A) Results of whole exome and transcriptome sequencing of Langerhans and non-Langerhans cell histiocytic (non-LCH) neoplasms. Each patient is represented in one column. Diagnosis (Langerhans Cell Histiocytosis or Erdheim-Chester Disease), age category, and sequencing method are in the first 3 rows. Somatic mutations identified are in the lower rows and subdivided based on mutations known to activate kinases, affect the JNK/p38 MAP kinase pathway, or involve a diverse array of co-occurring pathways (as shown on right hand label). Only mutations identified in >1 sample and selected other mutations are shown. (B) Mutational analysis of NRAS, KRAS, MAP2K1, ARAF, and PIK3CA from archival, formalin-fixed, paraffin embedded tissue from BRAFV600E-wildtype patients with a spectrum of non-LCH neoplasms. Diagnosis and percent histiocyte content per section is shown in the first 2 rows. (C) Diagram of MAP2K1 mutations identified by WES, RNA-seq, and targeted sequencing approaches in this study. (D) Diagram of activating ARAF mutations identified by WES, RNA-seq, and targeted sequencing approaches in the study. (E) Western blot analysis of pERK1/2, pMEK1/2, and controls in 293T cells transfected with vector, wildtype FLAG-MEK1, or various FLAG-MEK1 mutant cDNAs along with HA-tagged ERK2.
Figure 2
Figure 2. Kinase fusions in non-Langerhans cell systemic histiocytic (non-LCH) neoplasms
(A) Illustration of the RNF11-BRAF fusion with Sanger sequencing confirmation. (B) BRAF FISH break-apart probes revealing an isolated green signal confirming translocation of BRAF. (C) Effect of stable expression of BRAF wildtype, BRAFV600E, RNF11-BRAF, or an empty vector on MAP kinase and AKT signaling and (D) cytokine-independent growth of Ba/F3 cells. Mean viable cell number post-IL-3 withdrawal from a triplicate experiment is shown. Error bars indicate standard deviation of mean. (E) CellTiter-Glo luminescent viability IC50 results from 3 independent experiments of Ba/F3 cells from (D) exposed to MEK inhibitor GDC-0973, vemurafenib, or sorafenib. Log10 IC50 values are on y-axis. Error bars indicate standard error of mean. (F) Illustration of the CLIP2-BRAF fusion with Sanger sequencing confirmation identified in histiocytic ovarian infiltrates in a patient with Erdheim-Chester Disease. (G) Illustration of the KIF5B-ALK fusion with Sanger sequencing confirmation. (H) ALK FISH break-apart probe reveals an isolated red signal confirming the translocation of ALK. (I) Effect of KIF5B-ALK expression on ALK, STAT3, MEK1/2, ERK1/2, and AKT signaling in serum-starved Ba/F3 cells. (J) Effect of expression of KIF5B-ALK on cytokine-independent growth in Ba/F3 cells. Mean viable cell number post-IL-3 withdrawal from triplicate experiment is shown. Error bars indicate standard deviation of mean. (K) CellTiter-Glo luminescent viability IC50 results from 3 independent experiments of Ba/F3 cells from (J) exposed to crizotinib or alectinib. Log10 IC50 values on y-axis. Error bars indicate standard error of mean. (L) Illustration of a second KIF5B-ALK fusion identified in the liver lesions of a 50-year-old ECD patient involving exons 1–24 of KIF5B and 20–29 of ALK. (M) IHC of NTRK1 (top left) and CD68 (top right) in skin lesions of the LMNA-NTRK1 fusion index patient (400x magnification; scale bar = 50 μm) and illustration of the LMNA-NTRK1 fusion (bottom).
Figure 3
Figure 3. Gene expression analysis of histiocytic neoplasms by RNA-seq
(A) Unsupervised hierarchical clustering of the top 1% most differentially expressed genes in 7 LCH and 6 non-LCH lesions presented in a heat map. (B) Gene expression by RNA-seq of 6 out of the 159 genes from (A), which encode proteins currently known to differentiate these diseases in clinical diagnosis. (C) Enrichment plots of gene sets differentially enriched in LCH (n=4) or non-LCH (n=3) as detected by Gene Set Enrichment Analysis (analysis restricted to those samples with BRAF alterations only). (D) Eleven lineage-defining genes with enriched expression in LCH (4 cases) or non-LCH samples (3 cases) with BRAF kinase alterations.
Figure 4
Figure 4. Therapeutic efficacy of MEK and RAF inhibition in patients with MAP2K1- and ARAF-mutant systemic histiocytic neoplasms
(A) Axial FDG-PET scans pre-trametinib and 4-weeks post-trametinib in a MAP2K1K57N ECD patient with histiocytic infiltration of kidneys (top) and spermatic cord (bottom). (B) Creatinine and platelet counts in same patient pre- and post-trametinib therapy (green line indicates boundary of normal values). (C) PET scan pre-cobimetinib and 4-weeks post-cobimetinib of a MAP2K1Q56P-mutant ECD patient with disease infiltration in facial sinuses, heart, and kidneys. (D) Axial brain MRI of ARAFS214A- mutant ECD patient with histiocytic infiltration of retina and optic nerves. MRI images show optic nerve infiltration (arrows) pre- and 6-weeks post-sorafenib (top). Retinal fundoscopic photographs from the same time points (bottom) reveal improvement in retinal infiltrates with sorafenib treatment. (E) Ratio of concentration of ARAFS214A:ARAF wildtype in plasma cell-free DNA with sorafenib treatment.

Similar articles

See all similar articles

Cited by 72 articles

See all "Cited by" articles

Publication types

MeSH terms

LinkOut - more resources

Feedback