IKAROS Deletions Dictate a Unique Gene Expression Signature in Patients with Adult B-Cell Acute Lymphoblastic Leukemia

Abstract

Background Deletions of IKAROS ( IKZF1 ) frequently occur in B-cell precursor acute lymphoblastic leukemia (B-ALL) but the mechanisms by which they influence pathogenesis are unclear. To address this issue, a cohort of 144 adult B-ALL patients (106 BCR-ABL1 -positive and 38 B-ALL negative for known molecular rearrangements) was screened for IKZF1 deletions by single nucleotide polymorphism (SNP) arrays; a sub-cohort of these patients (44%) was then analyzed for gene expression profiling. Principal Findings Total or partial deletions of IKZF1 were more frequent in BCR-ABL1 -positive than in BCR-ABL1 -negative B-ALL cases (75% vs 58%, respectively, p = 0.04). Comparison of the gene expression signatures of patients carrying IKZF1 deletion vs those without showed a unique signature featured by down-regulation of B-cell lineage and DNA repair genes and up-regulation of genes involved in cell cycle, JAK-STAT signalling and stem cell self-renewal. Through chromatin immunoprecipitation and luciferase reporter assays we corroborated these findings both in vivo and in vitro , showing that Ikaros deleted isoforms lacked the ability to directly regulate a large group of the genes in the signature, such as IGLL1 , BLK , EBF1 , MSH2, BUB3, ETV6, YES1, CDKN1A (p21), CDKN2C (p18) and MCL1 . Conclusions Here we identified and validated for the first time molecular pathways specifically controlled by IKZF1 , shedding light into IKZF1 role in B-ALL pathogenesis.

Impact of IKZF1 deletions on long-term outcomes of allo-SCT following imatinib-based chemotherapy in adult Philadelphia chromosome-positive ALL

“…IKZF1 deletions were identified in 93 of 118 patients (78.8%), which is within range of other cohorts. [19][20][21][22][23][24][25]36,37 In this cohort of patients, on the basis of speed of good molecular response and its persistence in response to imatinib-based chemotherapy, IKZF1 Figure 3. Influence of IKZF1 deletions on CIR and DFS according to MRD kinetics.…”

“…We classified patients with IKZF1 deletions into three functional subtypes based on quantities and localizations of Ikaros proteins: (1) dominant-negative deletions (deletions involving at least exons 4-7 (Δ4-7), which lead to the expression of dominantnegative Ikaros isoform due to the loss of DNA binding domains; Δ4-7 deletions and/or monoallelic-null deletions), (2) haploinsufficient deletions (monoallelic-null deletions of the whole gene (complete deletions) or partial deletions affecting exon 2 or exon 8, which lead to haploinsufficiency with reduced protein levels of Ikaros) and (3) biallelic-null deletions (deletions of two null alleles, which lead to the absence of Ikaros protein). [19][20][21][22]24,25 MRD monitoring MRD monitoring for BCR-ABL1 transcripts was centrally evaluated by RQ-PCR (4.5 log sensitivity) through handling of BM samples from all patients (Research Institute of Molecular Genetics, The Catholic University of Korea, Seoul, Korea). Details of methods for MRD assessment were previously described.…”

“…[16][17][18] Among these abnormalities, deletions of the IKZF1 gene, which encodes the lymphoid transcription factor Ikaros, have received the most attention due to their frequency in BCP-ALL, particularly Phpositive ALL (approximately 70%). [19][20][21][22][23][24][25] Using different sample composition and treatment protocols in a chemotherapy setting, several studies have shown that IKZF1 deletions were significantly associated with an increased relapse rate and poor outcome in childhood BCP-ALL. [26][27][28][29][30][31] This predictive value is frequently independent of other known risk factors, suggesting that testing for IKZF1 status at time of diagnosis is warranted.…”

Transcriptional regulation of the Ikzf1 locus

“…Finally, point mutations that abolish the DNA binding activity of IKAROS and also generate dominant negative IKAROS protein isoforms have been reported in association with acute lymphoblastic leukemias. 13,[37][38][39] Mutations in the IKZF1 locus occurring in the highly conserved Ikzf1 regulatory regions may interfere with Ikaros expression and provide a mechanism of leukemia development.…”

Ikzf1 Deletions Are Independent Prognostic Factor in Pediatric B-Cell Precursor Acute Lymphoblastic Leukemia

“…Делеции могут затрагивать как весь ген IKZF1, так и отдельные его экзоны (так называемые фокальные делеции). Наибо-лее часто встречаются делеции экзонов 4-7, реже то-тальные делеции гена (экзоны [1][2][3][4][5][6][7][8], еще реже делеции экзонов 2-7, 4-8, 2-3, 2-8 (даны в порядке убывания частоты) [10,[15][16][17] (рис. 1в).…”