Rearrangement of CRLF2 in B-progenitor– and Down syndrome–associated acute lymphoblastic leukemia

Abstract

AUTHOR CONTRIBUTIONSCGM designed and coordinated the study, designed assays, performed experiments, analyzed data and wrote the manuscript JRC-U generated retroviral vectors and performed Ba/F3 assays LAAP performed JAK sequencing and quantitative PCR assays MLL performed PAR1 deletion genomic PCR WL performed statistical analysis JZ analyzed sequencing data Jing Ma analyzed microarray data EC-S performed flow cytometry and analyzed data RCH and CLW developed FISH assays Julia Meyer performed experiments and analyzed data FMM, AJC and NAH performed FISH assays and analyzed cytogenetic data RTW provided luciferase vectors JC designed subcloning vectors GB and AP provided patient samples SCR performed cytogenetic analysis SPH coordinated studies and sample collection JRD provided patient samples WLC provided patient samples, performed experiments and analyzed data KRR provided samples, performed experiments and analyzed data NIH Public Access Author ManuscriptNat Genet. Author manuscript; available in PMC 2010 May 1. Published in final edited form as:Nat Genet. SUMMARYAneuploidy and translocations are hallmarks of B-progenitor acute lymphoblastic leukemia (ALL), but many patients lack a recurring chromosomal alteration. Here we report a recurring interstitial deletion of the pseudoautosomal region 1 of chromosomes X and Y in B-progenitor ALL that juxtaposes the first, non-coding exon of P2RY8 to the coding region of CRLF2 (which encodes cytokine receptor like factor 2, or thymic stromal lymphopoietin receptor). The P2RY8-CRLF2 fusion was identified in 7% of B-progenitor ALL cases, and was identified in over 50% of ALL cases arising in patients with Down syndrome (53% of 75 cases). CRLF2 alteration was associated with the presence of activating JAK mutations, and expression of P2RY8-CRLF2 together with JAK2 mutants resulted in constitutive Jak-Stat activation and cytokine-independent growth of Ba/F3-IL7R cells, indicating that these two genetic lesions together contribute to leukemogenesis in B-progenitor ALL.Chromosomal alterations are a hallmark of acute lymphoblastic leukemia (ALL), the commonest malignancy of childhood, and include aneuploidy (hyperdiploidy and hypodiploidy) and recurring chromosomal translocations, such as t(12;21) [ETV6-RUNX1], t (1;19) [TCF3-PBX1], t(9;22) [BCR-ABL1] and rearrangement of MLL 1 . These alterations are important events in leukemogenesis and influence response to therapy. However, up to onequarter of childhood ALL cases lack a recurring chromosomal alteration, and the genetic basis of these cases is poorly understood.To identify submicroscopic genetic alterations contributing to the pathogenesis of ALL, we previously performed high resolution profiling of DNA copy number alterations and loss of heterozygosity (LOH) using single nucleotide polymorphism (SNP) microarrays, and identified multiple recurring genetic alterations targeting key cellular pathways including lymphoid development, cell cycle regulation and tumor suppression2 , 3. These alterations included a novel deletio...

Genomic profiling of high-risk acute lymphoblastic leukemia

“…Notably, the V617F mutation commonly observed in the myeloproliferative disorders [57][58][59][60] has not been identified in B-progenitor ALL, although the homolog of JAK2 V617F, JAK1 V658F, has been identified. 61 The presence of JAK mutations was associated with IKZF1 mutations, a BCR-ABL1-like gene expression profile, and poor outcome. Notably, JAK2 mutations (again, most commonly at R683 in the pseudokinase domain) had also recently been reported in up to one-quarter of cases of B-progenitor ALL associated with Down's syndrome [62][63][64] (Table 1); however, most cases in the P9906 high-risk ALL cohort with JAK mutations were cases not associated with Down's syndrome.…”

“…JAK1 pseudokinase mutations have also been described in T-lineage ALL, albeit more commonly in adults than in children. 61,65 The frequency of JAK2 mutations in large cohorts of adult ALL cases has not been determined. Similar to the JAK2 V617F mutation, the JAK1 and JAK2 mutations observed in ALL are transforming in vitro, conferring cytokine-independent growth and constitutive Jak-Stat activation when introduced into Ba/F3 cells (a murine pro-B-cell line) expressing the erythropoietin or thrombopoietin receptors.…”

Targeting the PI3K/AKT/mTOR Signaling Axis in Children with Hematologic Malignancies

“…Recently, using modern genomic techniques, a number of potentially targetable genetic alterations have been identified in a wide variety of signaling pathways, including Jak/Stat, Ras/Raf/Mek/Erk, TP53/RB, and the PI3K/AKT/mTOR pathway. [121][122][123][124] While novel agents targeting these pathways are unlikely to cure ALL individually, the addition of targeted agents to multi-agent cytotoxic backbones has the potential to significantly improve cure rates, as evidenced by markedly improved survival in Ph+ ALL patients when the BCR-ABL kinase inhibitor imatinib was added to a multi-agent chemotherapy backbone. [1] The PI3K/AKT/mTOR pathway can be dysregulated in ALL patients by a number of mechanisms.…”

“…[129] Recently, genetic rearrangements in cytokine receptor-like factor 2 (CRLF2) have been identified in high-risk subsets of pre-B-ALL, affecting up to 10% of patients, and genetic rearrangements in interleukin (IL)-7 receptor α (IL7R) have been identified in pre-B-and pre-T-ALL. [123,130] IL7R heterodimerizes with CRLF2 to form the receptor for thymic stromal-derived lymphoietin (TSLP), a protein that our group had previously demonstrated can stimulate proliferation of pre-B-ALL cells and activate signaling through PI3K/AKT/mTOR. [131] Our group hypothesized that targeting mTOR may be effective in ALL before it was established that the pathway was dysregulated in ALL.…”

Newly diagnosed acute lymphoblastic leukemia in China (I): abnormal genetic patterns in 1346 childhood and adult cases and their comparison with the reports from Western countries

“…The cut-off value of CRLF2 overexpression was identified according to Yoda et al 15 Genomic rearrangement was confirmed by fluorescence in situ hybridization for the detection of breakpoints of IGH@ locus (LSI IGH@ Dual Color Break-Apart Rearrangement Probe, Abbott Diagnostics, Chicago, IL, USA) and involvement of CRLF2 on chromosome X, 16 and genomic PCR for the PAR1 deletion resulting in fusion of P2RY8 --CRLF2 transcript, which was also confirmed by RT-PCR. 17,18 (Supplementary Figure 2).…”