Constitutive Function of the Ikaros Transcription Factor in Primary Leukemia Cells from Pediatric Newly Diagnosed High-Risk and Relapsed B-precursor ALL Patients

Fatih M Uckun,Anoush Shahidzadeh,Sanjive Qazi,Amanda Termuhlen,Hong Ma,Rita Ishkhanian,Paul S Gaynon,Martha Arellano,Pablo Menendez

doi:10.1371/journal.pone.0080732

Abstract

We examined the constitutive function of the Ikaros (IK) transcription factor in blast cells from pediatric B-precursor acute lymphoblastic leukemia (BPL) patients using multiple assay platforms and bioinformatics tools. We found no evidence of diminished IK expression or function for primary cells from high-risk BPL patients including a Philadelphia chromosome (Ph)+ subset. Relapse clones as well as very aggressive in vivo clonogenic leukemic B-cell precursors isolated from spleens of xenografted NOD/SCID mice that developed overt leukemia after inoculation with primary leukemic cells of patients with BPL invariably and abundantly expressed intact IK protein. These results demonstrate that a lost or diminished IK function is not a characteristic feature of leukemic cells in Ph+ or Ph- high-risk BPL.

Highlights

Ikaros (IK) is a zinc finger (ZF)-containing sequence-specific DNA-binding protein encoded by the IKZF1 gene
Representative IKZF1 Exon 4-specific qPCR amplification plots are depicted in Figure 2, Panels E-H. These results demonstrate that IKZF1 deletions are not consistent abnormalities in pediatric high-risk B-precursor ALL (BPL) and they are not signature characteristics of pediatric Philadelphia chromosome (Ph)+ BPL, as previously reported [3]
In order to gain further insights into the incidence and biological significance of IKZF1 deletions, we examined the expression levels of IKZF1 transcripts in primary leukemic cells from 327 pediatric Ph- BPL patients in side by side comparison with 123 pediatric Ph+ BPL cases and 74 normal bone marrow specimens obtained from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database GSE13159 and GSE13351

Summary

Introduction

Ikaros (IK) is a zinc finger (ZF)-containing sequence-specific DNA-binding protein encoded by the IKZF1 gene. It plays a pivotal role in immune homeostasis through transcriptional regulation of the earliest stages of lymphocyte ontogeny and differentiation by both (a) gene transcriptional activation via efficient transcription initiation and elongation as well as (b) repression [1]. The reported SNP array based IKZF1 deletion data were not accompanied by functional data on expression levels of IK target genes or EMSA of IK-specific DNA binding activity in nuclear extracts to support the functional IK deficiency proposal [3,4]. A more recent report by Palmi et al suggested that the prognostic significance of IKZF1 deletions is markedly enhanced when additional copy number abnormalities involving other genes are present [7], which prompts the hypothesis that the observed association of IKZF1 deletions with poor treatment outcome may stem from a profound underlying genomic instability rather than lost or diminished IK function

Objectives

Methods

Results

Conclusion