IKZF1 Status Research Articles

Prognosis of pediatric BCP-ALL with IKZF1 deletions and impact of intensive chemotherapy: Results of SCCLG-2016 study.

IKZF1 deletion (IKZF1del) is associated with poor prognosis in B-cell precursor acute lymphoblastic leukemia (BCP-ALL). But the prognosis of IKZF1del combined with other prognostic stratification factors remains unclear. Whether intensified treatment improves BCP-ALL prognosis has not been determined. A retrospective analysis was performed on 1291 pediatric patients diagnosed with BCP-ALL and treated with the South China Children's Leukemia 2016 protocol. Patients were stratified based on IKZF1 status for comparison of characteristics and outcome. Additionally, IKZF1del patients were further divided based on chemotherapy intensity for outcome assessments. The BCP-ALL pediatric patients with IKZF1del in south China showed poorer early response. Notably, the DFS and OS for IKZF1del patients were markedly lower than IKZF1wt group (3-year DFS: 88.7% [95% CI: 83.4%-94.0%] vs. 93.5% [95% CI: 92.0%-94.9%], P = .021; 3-year OS: 90.7% [95% CI: 85.8% to 95.6%] vs. 96.1% [95% CI: 95% to 97.2%, P = .003]), with a concurrent increase in 3-year TRM (6.4% [95% CI: 2.3%-10.5%] vs. 2.9% [95% CI: 1.9%-3.8%], P = .025). However, the 3-year CIR was comparable between the two groups (5.7% [95% CI: 1.8%-9.5%] vs. 3.7% [95% CI: 2.6%-4.7%], P = .138). Subgroup analyses reveal no factor significantly influenced the prognosis of the IKZF1del cohort. Noteworthy, intensive chemotherapy improved DFS from 85.7% ± 4.1% to 94.1% ± 0.7% in IKZF1del group (P = .084). Particularly in BCR::ABL positive subgroup, the 3-year DFS was remarkably improved from 53.6% ± 20.1% with non-intensive chemotherapy to 100% with intensive chemotherapy (P = .026). Pediatric BCP-ALL patients with IKZF1del in South China manifest poor outcomes without independent prognostic significance. While no factor substantially alters the prognosis in the IKZF1del group. Intensified chemotherapy may reduce relapse rates and improve DFS in patients with IKZF1del subset, particularly in IKZFdel patients with BCR::ABL positive.

Prognostic significance and treatment strategies for IKZF1 deletion in pediatric B-cell precursor acute lymphoblastic leukemia

BackgroundThe predictive importance of IKZF1del in pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL) has shown variability across different studies. Thus, the optimal treatment approach for children with IKZF1del BCP-ALL remains contentious, with the ongoing debate surrounding the use of IKZF1del-based high-risk stratification versus a minimal residual disease (MRD)-guided protocol.MethodsIKZF1 status was reliably determined in 804 patients using multiplex ligation-dependent probe amplification (MLPA) data obtained from four hospitals in Fujian, a province of China. In the Chinese Children Leukemia Group (CCLG)-ALL 2008 cohort, IKZF1 status was included in the risk assignment, with all IKZF1del patients receiving a high-risk regimen. Conversely, in the Chinese Children’s Cancer Group (CCCG)-ALL 2015 cohort, IKZF1del was not incorporated into the risk assignment, and patients were treated based on an MRD-guided risk stratification protocol.ResultsIKZF1del was found in 86 patients (86/804, 10.7%) overall and in 30 (30/46, 65.2%) BCR::ABL1-positive patients. Overall, IKZF1del was a poor prognostic predictor for patients, though the significance diminished upon age adjustment, white blood cell (WBC) count at diagnosis, treatment group, and MRD status. In the CCLG-ALL 2008 cohort, IKZF1del conferred a notably lower 5-year overall survival (OS) and event-free survival (EFS) and a significantly higher 5-year cumulative incidence of relapse (CIR) than IKZF1wt. In the CCLG-ALL 2015 cohort, IKZF1del conferred a lower 5-year OS and EFS and a higher 5-year CIR than IKZF1wt, but the differences were insignificant. The IKZF1del patients treated with higher intensity chemotherapy (CCLG-ALL 2008 high-risk regimen) had a markedly lower 5-year OS and EFS compared with those treated with the MRD-guided protocol (CCCG-ALL 2015 protocol). Furthermore, patients treated with the CCLG-ALL 2008 high-risk regimen experienced a higher frequency of serious adverse events (SAEs), especially infection-related SAEs, compared with those treated with the CCCG-ALL 2015 MRD-guided protocol.ConclusionsThe prognostic effect of IKZF1del may vary in different protocols. Compared with higher intensity chemotherapy, the MRD-guided protocol may be a more effective approach to treating BCP-ALL with IKZF1del in children.

Refining risk stratification in paediatric B-acute lymphoblastic leukaemia: Combining IKZF1plus and Day 15 MRD positivity.

This study investigates the potential utility of IKZF1 deletion as an additional high-risk marker for paediatric acute lymphoblastic leukaemia (ALL). The prognostic impact of IKZF1 status, in conjunction with minimal/measurable residual disease (MRD), was evaluated within the MRD-guided TPOG-ALL-2013 protocol using 412 newly diagnosed B-ALL patients aged 1-18. IKZF1 status was determined using multiplex ligation-dependent probe amplification. IKZF1 deletions, when co-occurring with CDKN2A, CDKN2B, PAX5 or PAR1 region deletions in the absence of ERG deletions, were termed IKZF1plus. Both IKZF1 deletion (14.6%) and IKZF1plus (7.8%) independently predicted poorer outcomes in B-ALL. IKZF1plus was observed in 4.1% of Philadelphia-negative ALL, with a significantly lower 5-year event-free survival (53.9%) compared to IKZF1 deletion alone (83.8%) and wild-type IKZF1 (91.3%) (p < 0.0001). Among patients with Day 15 MRD ≥0.01%, provisional high-risk patients with IKZF1plus exhibited the worst outcomes in event-free survival (42.0%), relapse-free survival (48.0%) and overall survival (72.7%) compared to other groups (p < 0.0001). Integration of IKZF1plus and positive Day 15 MRD identified a subgroup of Philadelphia-negative B-ALL with a 50% risk of relapse. This study highlights the importance of assessing IKZF1plus alongside Day 15 MRD positivity to identify patients at increased risk of adverse outcomes, potentially minimizing overtreatment.

Crebbp Mutations Are Associated with Slow Minimal Residual Response to Upfront Induction Chemotherapy in Pediatric High-Hyperdiploid B-Cell Precursor Acute Lymphoblastic Leukemia Treated in the AIEOP-BFM ALL 2009 Protocol

Introduction High-hyperdiploidy (HHD) represents the most common cytogenetic abnormality found in B-cell precursor acute lymphoblastic leukemia (B-ALL). Despite the overall good outcome of this entity, up to 15% of patients suffer from disease relapse. Genome-wide ALL studies with next-generation sequencing (NGS) approaches identified a distinct pattern of somatic mutations in HHD ALL, enriched in mutations occurring in genes activating the RAS pathway and in CREBBP gene, especially in relapsed patients. Although several studies have attempted to explore the prognostic significance of these mutations that are potentially susceptible of targeted therapies, their impact in uniformly treated patients with newly diagnosed B-ALL is not well characterized, and there is no consensus on their clinical significance. In this study, we aimed to investigate the frequency of recurrent mutations and to define their prognostic role in the setting of newly diagnosed HHD B-ALL, by using end of induction minimal residual disease (MRD) and event-free survival (EFS). Methods We included 101 consecutive patients, aged between 1-17 years, with newly diagnosed HHD B-ALL and enrolled in the AIEOP-BFM ALL 2009 protocol (NCT01117441). HHD was defined by the presence of a DNA index ≥1.16 and lack of ETV6::RUNX1, BCR::ABL1, KMT2A::AFF1 translocations. Diagnostic leukemia samples of 89 patients were sequenced using a validated clinical NGS panel profiling 39 genes involved in leukemia pathogenesis. Mutations affecting RAS pathway ( NRAS, KRAS, PTPN11, NF1, BRAF) and mutations affecting CREBBP gene were included. In addition, digital multiplex ligation-dependent probe amplification (digital MLPA) analysis for the identification of IKZF1 deletion and IKZF1plus phenotype was evaluable for 67 patients. A Fisher exact test and Wilcoxon rank sum test were used for categorical and continuous variables. MRD was assessed by an IG/TR PCR assay at day +33 of induction (timepoint 1, TP1) and at day +78 (timepoint 2, TP2). EFS was estimated by using Kaplan and Meier method and differences between groups were tested using the log-rank test. Resistance to treatment, relapse, death or second malignant neoplasm were considered as events, whichever occurred first. Results Patients' characteristics according to the presence of studied mutations are shown in Table 1. Mutations affecting RAS pathway and CREBBP occurred in 57.3% and 12.3% of HHD B-ALL patients, respectively. Clonal RAS pathway mutations, defined by variant allele frequency (VAF) ≥25%, were found in 16.8% of cases. Among the 11 patients with mutations of CREBBP, 7 had also a mutation affecting KRAS and the association was significant (p=0.03). Seven patients (10.4%) had deletion of IKZF1, of whom 5 (7.4%) were IKZF1plus. There was no association between any mutations or IKZF1 status and patient presenting characteristics, as including sex, age and WBC counts. MRD was evaluable in 84 patients at the end of induction (TP1). MRD level ≥5x10 -4 was found in 36.4% of patients with CREBBP mutations and in 9.6% of those without, and this association was statistically significant (p=0.02). Additionally, MRD negativity was found in 9.1% and 38.4%, respectively. At TP2, MRD was still detectable in 45.5% of patients with CREBBP mutations compared to 20.6% of those with CREBBP wildtype (p=0.08). Similarly, we observed an association between RAS pathway mutations and MRD at TP1 (p=0.01) with a marked difference in MRD negative patients (21.3% vs 51.4% in patients with and without mutations). No association was observed between MRD level and clonal RAS pathway mutations or IKZF1 status. Despite the association between CREBBP mutations and high MRD at TP1, no significant difference in final high-risk group was found (27.3% vs 11.5%, p=0.17). A total of 8 events were observed, of which 6 were relapses. No impact of any mutations or IKZF1 status in term of 5-years EFS was found in our cohort. Conclusion Our study shows that CREBBP mutations in HHD B-ALL are associated with inferior early response to treatment in terms of MRD level at the end of induction (TP1) but not with worse EFS with our whole current chemotherapy backbone. Therefore, the inclusion of CREBBP mutated patients in very low risk protocols should be carefully evaluated. The validation of these findings is ongoing through the analysis of patients treated by other international study groups adopting different chemotherapy backbones.

Exploring the Heterogeneity of Response to Blinatumomab in High-Risk Philadelphia-Negative B-Cell Precursor Acute Lymphoblastic Leukemia: An Analysis from the QUEST Sub-Study of the Graall-2014/B Trial

Introduction. Adults with Philadelphia (Ph)-negative B-cell precursor acute lymphoblastic leukemia (BCP-ALL) benefit from blinatumomab (BLIN) in first-line consolidation. However, the magnitude of this benefit according to baseline patient and disease characteristics remains largely unexplored. In the GRAALL-2014/B QUEST sub-study, patients with high-risk (HR) features (i.e. post-induction MRD1 ≥10 -4, IKZF1 intragenic deletion, or KMT2A rearrangement) received BLIN during consolidation. Patients eligible to receive an allogeneic hematopoietic stem cell transplant (allo-HSCT) in first complete remission (CR) (i.e. those with late CR, or post-induction MRD1 ≥10 -3, or post-consolidation MRD2 ≥10 -4) received only one BLIN cycle before transplant. A control cohort was established from patients enrolled in the same protocol who exhibited the same HR criteria but did not receive BLIN in first CR. The objective of this analysis was to identify patient- and disease-related factors associated with response to BLIN, and to understand how BLIN influences the outcome after allo-HSCT. Method. Between December 2015 and December 2020, the GRAALL-2014/B trial included 489 patients with Ph-negative BCP-ALL. Among these patients, 266 presented with HR features as defined above and 95 (including 94 evaluable patients) were included in QUEST between October 2018 and December 2020. A control group of 104 patients treated in the same trial, meeting the QUEST eligibility criteria, but not included in QUEST and not exposed to BLIN in CR1 was defined. Results have been presented last year (Boissel et al. ASH Meeting 2022). Here, we investigated which factors were associated with the benefit of BLIN in terms of MRD3 response (1 st post-BLIN MRD) and disease-free-survival (DFS). The most frequently observed genetic entities were included in the analysis (Ph-like, KMT2A-r, low hypodiploidy/near triploidy [HoTr], DUX4-r, ZNF384-r). Results. Patients from the QUEST cohort had a higher chance to be MRD3-negative (&amp;lt;10 -4) when compared to the control cohort (OR, 2.8; 95%CI, 1.3-6.2; p=0.011). Among them, younger patients (&amp;lt;45y), patients with WBC&amp;lt;30 G/L, with poor prednisone response, with IKZF1 deletion or with Ph-like disease had a significantly higher chance to be MRD3-negative after BLIN than after chemotherapy. Among genetic entities, ORs ranged from 1.2 for KMT2A-r to 5.3 for Ph-like BCP-ALL (Figure A). Due to a reduced risk of relapse, patients had a significantly prolonged DFS after BLIN (HR, 0.49; 95%CI, 0.31-0.78; p=0.002), whatever their age (&amp;lt; vs ≥45y), WBC at diagnosis (&amp;lt; vs ≥30 G/L), prednisone response, and MRD1 (&amp;lt;10 -4vs ≥10 -4) (Figure B). Among genetic entities, HR for DFS ranged from 0.21 for DUX4-r to 1.38 for HoTr with none of these differences that reached significance. Patients with IKZF1 deletion had the most significant benefit from BLIN on DFS (HR, 0.21; 95%CI, 0.08-0.52; p=0.001) with a significant interaction between IKZF1 status and the use of BLIN (p=0.011). Patients who received allo-HSCT had a higher chance to be MRD negative before transplant when treated with BLIN (OR, 4.0; 95%CI, 1.4-11.7; p=0.011), however this did not translate into a longer DFS (HR, 0.79; 95%CI, 0.39-1.60). In addition, prior transplant MRD level had a higher impact on post-transplant DFS in the patients exposed to BLIN (HR, 0.28; 95%CI, 0.10-0.79; p=0.017) than in those treated with chemotherapy (HR, 0.74; 95%CI, 0.24-2.27; p=0.60). Conclusion. In adult patients with Ph-negative BCP-ALL who experience an overall benefit of BLIN in consolidation, the present study reveals a heterogeneous landscape of response among genetic entities. Larger prospective studies should further explore this heterogeneity to refine implementation of BLIN in frontline setting.

PersonALL: a genetic scoring guide for personalized risk assessment in pediatric B-cell precursor acute lymphoblastic leukemia

BackgroundRecurrent genetic lesions provide basis for risk assessment in pediatric acute lymphoblastic leukemia (ALL). However, current prognostic classifiers rely on a limited number of predefined sets of alterations.MethodsDisease-relevant copy number aberrations (CNAs) were screened genome-wide in 260 children with B-cell precursor ALL. Results were integrated with cytogenetic data to improve risk assessment.ResultsCNAs were detected in 93.8% (n = 244) of the patients. First, cytogenetic profiles were combined with IKZF1 status (IKZF1normal, IKZF1del and IKZF1plus) and three prognostic subgroups were distinguished with significantly different 5-year event-free survival (EFS) rates, IKAROS-low (n = 215): 86.3%, IKAROS-medium (n = 27): 57.4% and IKAROS-high (n = 18): 37.5%. Second, contribution of genetic aberrations to the clinical outcome was assessed and an aberration-specific score was assigned to each prognostically relevant alteration. By aggregating the scores of aberrations emerging in individual patients, personalized cumulative values were calculated and used for defining four prognostic subgroups with distinct clinical outcomes. Two favorable subgroups included 60% of patients (n = 157) with a 5-year EFS of 96.3% (excellent risk, n = 105) and 87.2% (good risk, n = 52), respectively; while 40% of patients (n = 103) showed high (n = 74) or ultra-poor (n = 29) risk profile (5-year EFS: 67.4% and 39.0%, respectively).ConclusionsPersonALL, our conceptually novel prognostic classifier considers all combinations of co-segregating genetic alterations, providing a highly personalized patient stratification.

The Prognostic Effect of IKZF1 Deletions in ETV6::RUNX1 and High Hyperdiploid Childhood Acute Lymphoblastic Leukemia

Acute lymphoblastic leukemia (ALL) is the most prevalent childhood malignancy and recent cure rates approach 90% on first line therapy. IKZF1 deletions have been reported as an unfavorable prognostic factor and are rare in ETV6::RUNX1 and high hyperdiploid (HeH) ALL, the two cytogenetic subgroups with the most favorable prognosis. Due to its rarity, the prognostic effect of IKZF1deletions within this subset of patients remains unclear. Therefore, we assessed the prognostic impact of IKZF1deletions in 939 ETV6::RUNX1 and 968 HeH ALL patients. We performed this retrospective analysis on data of children and adolescents of 1-18 years with B-cell precursor ALL diagnosed in 1991-2016 and treated on one of 16 trials from 9 study groups, of which 6 were minimal residual disease (MRD) guided. Cytogenetic, fluorescence in-situ hybridization, and RT-PCR analyses of pre-treatment bone marrow samples to determine ploidy and fusion gene status were performed locally. Trials using MRD for risk stratification applied either PCR or flow cytometry analyses. The IKZF1 status was determined by multiplex ligation-dependent probe amplification by each individual study group. 3% of ETV6::RUNX1 (n=26) cases had an IKZF1 deletion; this affected survival adversely overall (5-year event free survival [EFS]: 79% vs. 92%, p = 0.02) (Table 1). However, in minimal residual disease (MRD) guided protocols, IKZF1 did not affect outcome in ETV6::RUNX1 cases ( 5-year EFS: 100% vs. 93%, p = 0.34) (Table 1). 9% of HeH cases had an IKZF1 deletion (n=85); this adversely affected survival overall (5-year EFS: 76% vs. 89%, p = 0.006), and in MRD-guided protocols (73% vs. 88%, p = 0.004) (Table 1). Multivariate cox regression showed that IKZF1deletions negatively affected survival independent of sex, age, and white blood cell count at diagnosis in HeH ALL (Hazard ratio of EFS [95% CI]: 2.00 [1.20-3.30]) (Table 1). As the prognostic effect of IKZF1 deletions has been shown to vary by MRD risk group, we examined the prognostic effect of IKZF1deletions in HeH cases with detectable MRD <5% at end of induction in more detail. Of these cases, 10% carried an IKZF1deletion (n=34) which negatively affected outcome (5-year EFS: 78% vs. 92%, p = 0.01) Multivariate cox regression showed that IKZF1deletions negatively affected survival independent of sex, age, and white blood cell count at diagnosis in this intermediate MRD HeH ALL (Hazard ratio of EFS [95% CI]: 2.90 [1.20-6.80]). However, cases with an IKZF1 deletion had significantly higher MRD values than their wild-type counterparts (p = 0.03, Figure 1). In conclusion, our analysis of a large composite cohort consisting of 16 trials shows that IKZF1deletions do not affect survival in ETV6::RUNX1 ALL when treated on MRD-guided protocols. In contrast, our data shows that in HeH ALL IKZF1deletions are associated with lower survival rates, higher relapse rates, and higher MRD values. Future results of current trials such as the ALLTogether will likely reveal whether risk stratification predominantly reliant on MRD is adequate for HeH patients or whether stratification by copy number alteration profile, including IKZF1 status, or by other methods would be more suitable. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Chemotherapy or Hematopoietic Stem Cell Transplantation in B-Lineage Acute Lymphoblastic Leukemia Patients Based on IKZF1 and MRD Status

Purpose： We aimed to investigate the outcomes of different post-remission treatment choices based on IKZF1 detection by RT-PCR and dynamic measurable residual disease (MRD) by multiparameter flow cytometry in B-ALL. Prospectively confirm the role of MRD and IKZF1 deletion as a significant predictor of post-remission treatment, replacing the definition of clinical risk categories for patients after complete remission (CR). Patients and Methods： There were 202 patients with B-ALL enrolled in this registry-based cohort study including 99 who received chemotherapy (CMT), and 103 allogeneic stem cell transplantation (allo-SCT). The primary endpoint was the 5-year overall survival (OS), event-free survival (EFS), and cumulative incidence of relapse (CIR). Subgroup analyses were performed based on IKZF1deletion and dynamic MRD 14,24,45 days after induction therapy. Results： In subgroups of patients with IKZF1wt and MRD negative patients， the 5-year overall survival (OS), event-free survival (EFS), and cumulative incidence of relapse(CIR) probabilities for patients assigned to chemotherapy were 67.6%, 55.2%,36.5% and 71.4%,60.7%,28.6%, for those assigned to HSCT respectively. In subgroups of patients with IZKF1 del or MRD positive patients after CR, with OS, EFS, and CIR rates for patients assigned to chemotherapy were 30.1%, 10.3% and76.2%, and 71.8%, 39.8%, and 43.7%for those assigned to HSCT, respectively. Conclusion： The results thus suggest a clear distinction between HSCT and CMT inIKZF1del or MRD positive Patients. While IKZF1wt patients and MRD negative had significant differences. Affected patients should thus be carefully monitored for IKZF1 and minimal residual disease to decide on the post-remission treatment after CR.

Impact of IKZF1 Deletions in the Prognosis of Childhood Acute Lymphoblastic Leukemia in Argentina.

Simple SummaryAn association of deletions in the IKZF1 gene (IKZF1del) with poor prognosis in acute lymphoblastic leukemia (ALL) has been demonstrated. However, the co-occurrence of IKZF1del with deletions in other genes (IKZF1plus) seems to better define prognosis. Our aim was to analyze the influence of IKZF1del and/or IKZF1plus profiles on the survival of children with ALL. We analyzed 1023 eligible cases who were classified into three subsets: IKZF1not-del: IKZF1-not-deleted (n = 835), IKZF1del: IKZF1deleted (n = 94) and IKZF1plus: IKZF1del plus deletion of other genes (n = 94). Leukemia-free-survival probability (standard deviation) (LFSp(SE)) was 75 (2)% for IKZF1not-del, 51 (6)% for IKZF1del and 48 (6)% for IKZF1plus (p-value < 0.00001). The LFSp(SE) according to ALL-IC risk-group stratification showed a statistically significant difference within Intermediate-Risk patients, LFSp (SE) being 77 (2)% for IKZF1not-del, 61 (10)% for IKZF1del and 54 (7)% for IKZF1plus (p-value = 0.0005). The LFSp(SE) of the high-risk group was: 61 (4)% IKZF1not-del, 38 (8)% IKZF1del and 35 (9)% IKZF1plus (p-value = 0.0102). Thus, the IKZF1 status was shown to define a population of patients with a poor outcome, mainly in those with intermediate risk. However, not-significant differences were observed between the LFSp of IKZF1del versus IKZF1plus groups. The study of the IKZF1 status should be incorporated into the risk-group stratification of pediatric ALL.An association of deletions in the IKZF1 gene (IKZF1del) with poor prognosis in acute lymphoblastic leukemia (ALL) has been demonstrated. Additional deletions in other genes (IKZF1plus) define different IKZF1del subsets. We analyzed the influence of IKZF1del and/or IKZF1plus in the survival of children with ALL. From October 2009 to July 2021, 1055 bone marrow samples from patients with ALL were processed by Multiplex ligation-dependent probe amplification (MLPA). Of them, 28 patients died during induction and 4 were lost-in-follow-up, resulting in an eligible 1023 cases. All patients were treated according to ALLIC-BFM-2009-protocol. Patients were classified into three subsets: IKZF1not-deleted (IKZFF1not-del), IKZF1deleted (IKZF1del) and IKZF1del plus deletion of PAX5, CDKN2A, CDKN2B and/or alterations in CRLF2 with ERG-not-deleted (IKZF1plus). The LFSp and SE were calculated with the Kaplan–Meier calculation and compared with a log-rank test. From the 1023 eligible patients, 835 (81.6%) were defined as IKZF1not-del, 94 (9.2%) as IKZF1del and 94 (9.2%) as IKZF1plus. Of them, 100 (9.8%) corresponded to Standard-Risk (SRG), 629 (61.5%) to Intermediate-Risk (IRG) and 294 (28.7%) to High-Risk (HRG) groups. LFSp(SE) was 7 5(2)% for IKZF1not-del, 51 (6)% for IKZF1del and 48 (6)% for IKZF1plus (p-value < 0.00001). LFSp(SE) according to the risk groups was: in SRG, 91 (4)% for IKZF1not-del, 50 (35)% IKZF1del and 100% IKZF1plus (p-value = ns); in IRG, 77 (2)% IKZF1not-del, 61 (10)% IKZF1del and 54 (7)% IKZF1plus (p-value = 0.0005) and in HRG, 61 (4)% IKZF1not-del, 38 (8)% IKZF1del and 35 (9)% IKZF1plus (p-value = 0.0102). The IKZF1 status defines a population of patients with a poor outcome, mainly in IRG. No differences were observed between IKZF1del versus IKZF1plus. MLPA studies should be incorporated into the risk-group stratification of pediatric ALL.

CRLF2 overexpression defines an immature-like subgroup which is rescued through restoration of the PRC2 function in T-cell precursor acute lymphoblastic leukemia.

CRLF2 overexpression has been described as a biomarker of poor prognosis in T-cell acute lymphoblastic leukemia (T-ALL). In the present study, we aimed to unravel the genomic profile underlying CRLF2 overexpression (CRLF2-high) by analyzing RNA-seq, WES, and SNP-array data from 264 T-ALL patients and five cell lines deposited on the TARGET initiative, Cancer Cell Line Encyclopedia and Gene Expression Omnibus. These data allowed us to delineate the genomic landscape of CRLF2-high in T-ALL, which was associated with PTEN, JAK3, PHF6, EZH2, and RUNX1 mutations. We also observed an enrichment of CRLF2-high in early T-precursor (ETP)-ALL (23.08% vs. 4.02%, P=7.579e-06 ) and a very similar gene upregulation profile between these two entities. The inhibition of BET (iBET) proteins is a strategy previously demonstrated to reverse the gene upregulation pattern of ETP cells through restoration of polycomb repressive complex 2 (PRC2) activity. While CRLF2 expression was rescued by using this strategy in LOUCY (untreated vs. iBET P =0.0095, DMSO vs. iBET P=0.0286), a classical ETP-ALL cell line, PRC2 loss was not sufficient to promote CRLF2 upregulation in JURKAT, a more mature T-ALL cell line. Considering the role of IKZF1 in CRLF2 regulation and in recruitment of PCR2, we evaluated IKZF1 status according to CRLF2-expression subgroups. We identified that IKZF1 transcripts with intron retention were upregulated in the CRLF2-high subgroup. Here, we delineated the gene expression profile of CRLF2-high T-ALL samples and unraveled the crucial role of PRC2 in CRLF2 regulation in ETP-ALL.

Modeling IKZF1 lesions in B-ALL reveals distinct chemosensitivity patterns and potential therapeutic vulnerabilities

AbstractIKAROS family zinc finger 1 (IKZF1) alterations represent a diverse group of genetic lesions that are associated with an increased risk of relapse in B-cell acute lymphoblastic leukemia. Due to the heterogeneity of concomitant lesions, it remains unclear how IKZF1 abnormalities directly affect cell function and therapy resistance, and whether their consideration as a prognostic indicator is valuable in improving outcome. CRISPR/Cas9 strategies were used to engineer multiple panels of isogeneic lymphoid leukemia cell lines with a spectrum of IKZF1 lesions to measure changes in chemosensitivity, gene expression, cell cycle, and in vivo engraftment that can be linked to loss of IKAROS protein. IKZF1 knockout and heterozygous null cells displayed relative resistance to a number of common therapies for B-cell acute lymphoblastic leukemia, including dexamethasone, asparaginase, and daunorubicin. Transcription profiling revealed a stem/myeloid cell–like phenotype and JAK/STAT upregulation after IKAROS loss. A CRISPR homology-directed repair strategy was also used to knock-in the dominant-negative IK6 isoform into the endogenous locus, and a similar drug resistance profile, with the exception of retained dexamethasone sensitivity, was observed. Interestingly, IKZF1 knockout and IK6 knock-in cells both have significantly increased sensitivity to cytarabine, likely owing to marked downregulation of SAMHD1 after IKZF1 knockout. Both types of IKZF1 lesions decreased the survival time of xenograft mice, with higher numbers of circulating blasts and increased organ infiltration. Given these findings, exact specification of IKZF1 status in patients may be a beneficial addition to risk stratification and could inform therapy.

IKZF1 Deletions as a Prognostic Factor in Costa Rican Patients With Pediatric B-Cell Acute Lymphoblastic Leukemia.

The IKZF1 gene encodes for Ikaros, a transcriptional factor in B-cell development. Deletions in this gene have been associated with a worse prognosis in B-cell acute lymphoblastic leukemia (B-ALL). We evaluated the presence of these alterations in all Costa Rican pediatric patients diagnosed with B-ALL between 2011 and 2014, treated with a modified Berlin-Frankfurt-Münster therapeutic protocol. Multiplex polymerase chain reaction with 2 detection methods (agarose gel and gene scanning) was used to detect intragenic deletions and multiplex ligation-dependent probe amplification for whole-gene deletions. Differences between groups (normal vs. deleted IKZF1) were analyzed by the χ test, the Kaplan-Meier test was used to calculate relapse-free survival and overall survival, and Cox regression was performed for multivariant analysis. Minimum follow-up was 4.5 years. Incidence of IKZF1 deletions was 12.9% (n=20), with an equal amount of intragenic and complete gene deletions. Adverse karyotype (P=0.048), high-risk category (P=0.030), occurrence of relapse (P=0.021), and medullar relapse (P=0.011) were statistically associated with the presence of deletions in IKZF1. Relapse-free survival at 54 months was lower in patients harboring an IKZF1 deletion than that in patients with IKZF1-wt (40.0% vs. 66.7%; P=0.014). Patients with B-ALL and IKZF1 deletions, showed a poorer relapse-free survival, in comparison with patients with IKZF1-wt, suggesting that IKZF1 status is an independent prognostic factor for pediatric patients with B-ALL.

Minimal Residual Disease and IKZF1 As Predictors of Relapse, and Increased Treatment Related Mortality in Down Syndrome Acute Lymphoblastic Leukemia: A Unique and Large International Matched Case-Control Study

INTRODUCTION Down syndrome patients with acute lymphoblastic leukemia (DS ALL) are less likely to have a favorable (cyto)genetic subtype and are at higher risk of relapse and treatment-related mortality (TRM) than non-DS ALL (Buitenkamp et al., Blood 2014). At present, the independent predictive value of minimal residual disease (MRD) is unclear and may be biased by an unequal distribution of (cyto)genetic risk groups among DS ALL and non-DS ALL patients. This study was aimed to decipher the prognostic implications of MRD and IKZF1 deletions and the frequency of TRM in a matched cohort of DS ALL cases and non-DS ALL controls. METHODS Each DS ALL patient was matched to 3 non-DS ALL patients based on treatment protocol, induction treatment, cytogenetic subtype, IKZF1 status, age (cutoff at 10 years), and white blood cell count (cutoff at 50,000 cells/µl). For MRD analysis, matching was only on induction treatment and excluded the MRD-guided treatment arm; for survival analyses, matching included the MRD-guided treatment arm, thus resulting in two separately matched cohorts. Patients who died during induction were excluded from matching. Absolute MRD levels were measured with RQ-PCR, log-transformed and analyzed with a multilevel mixed-effects linear regression model. Matched Cox proportional hazard regression models were used to analyze event-free survival (EFS), overall-survival (OS), relapse-free survival (RFS) and mortality in remission as surrogate for TRM. RESULTS Patients treated between 2002 and 2018 on Dutch DCOG-ALL10/11 trials, Australian ANZCHOG-ALL8 and AIEOP-BFM-ALL2009 trials, and UKALL2003 trial were included, resulting in 160 DS ALL and 5313 non-DS ALL patients. Out of these 160 DS ALL patients, 13 died during induction versus 42/5313 non-DS ALL patients (8.1% versus 0.8%, p&amp;lt;0.0001). Exclusion of induction deaths and patients with missing IKZF1 or MRD data, resulted in 110 DS ALL matched to study MRD differences (1 DS ALL could not be matched and was excluded), and 93 DS ALL matched to analyze survival (ALL11 was excluded due to short follow-up; 3 DS ALL could not be matched and were excluded). In the matched cohort, 22% (24/110) had favorable cytogenetics, 19% (21/110) had an IKZF1 deletion, 26% (29/110) were ≥10 years, and 17% (19/110) had a WBC ≥50,000 cells/µl. Only 3 cases (2 DS, 1 non-DS) did not achieve complete remission (excluding induction deaths). Median follow-up time of survivors was 7.1 years. The MRD levels did not differ between DS ALL and matched non-DS ALL patients at end of induction (p=0.96) nor when analyzed over time (p=0.43). In accordance, the 5-yr RFS did not differ between DS ALL and matched non-DS ALL patients (85 ± 4% versus 89 ± 2%, p=0.09). The 5-yr TRM of patients in remission was higher in DS ALL compared to non-DS ALL (11 ± 3% versus 3 ± 1%, p=0.001). In line, 5-yr EFS was lower in DS ALL compared to non-DS ALL patients (74 ± 5% versus 86 ± 2%, p=0.0007), as was 5-yr OS (77 ± 5% versus 93 ± 2%, p=0.0001). Multivariable analysis revealed that IKZF1 deletion can discriminate DS ALL patients at high risk of relapse (RFS: HR&amp;gt;3, 95% CI=1-12, p=0.05). The effect of IKZF1 deletion was stronger in DS ALL patients than in the non-DS ALL patients in our cohort. CONCLUSION The MRD levels did not differ between DS ALL and non-DS ALL patients when matched for (cyto)genetics and other risk factors. In accordance, the overall relapse rate of DS ALL patients did not differ from that of matched non-DS ALL patients. Similar to non-DS ALL, IKZF1 deletion is an adverse risk factor for DS-ALL, indicating the need for treatment aimed at reducing the high relapse risk. DS ALL patients suffer more frequently from death in induction and from treatment while in remission, which jeopardizes treatment intensification. Therefore, the efficacy of targeted, less toxic therapies such as immunotherapies should be assessed in DS ALL. Disclosures van der Velden: Jansen: Research Funding; BD Biosciences: Research Funding; Amgen: Honoraria, Research Funding. Pieters:jazz farmaceuticals: Consultancy; medac: Consultancy. Zwaan:Celgene: Consultancy, Research Funding; Pfizer: Research Funding; BMS: Research Funding; Janssen: Consultancy; Servier: Consultancy; Roche: Consultancy; Incyte: Consultancy; Sanofi: Consultancy; Jazz Pharmaceuticals: Other: Travel support; Daiichi Sankyo: Consultancy.

Prognostic Significance of IKZF1, PAX5, and CDKN2A Deletions in Patients with Philadelphia Chromosome-Positive Acute Lymphoblastic Leukemia Treated with Hyper-CVAD/MA with Dasatinib or Ponatinib

Prognostic Significance of IKZF1, PAX5, and CDKN2A Deletions in Patients with Philadelphia Chromosome-Positive Acute Lymphoblastic Leukemia Treated with Hyper-CVAD/MA with Dasatinib or Ponatinib

Application of Real-Time PCR for the Detection of BCR-ABL1-like Group in Pediatric Acute Lymphoblastic Leukemia Patients

Background. In 2016 WHO classification of myeloid neoplasms and acute leukemias a new provisional entity ‘B-lymphoblastic leukemia/lymphoma, BCR-ABL1-like’ has been introduced. Two current strategies of BCR-ABL1-like ALL detection are based on gene expression profile revealed either by microarray ('BCR-ABL-like') or by NGS / patented TaqMan low-density array (TLDA) ('Ph-like'). Although both techniques and not widely applicable. Aims. To find out whether expression profile based on combined expression data of 5 genes assessed by real-time PCR can be used for the identification of BCR-ABL1-like pediatric ALL patients. Methods. The study was done on initial bone marrow samples of 147 primary pediatric BCP-ALL patients. Positive cohort included 10 BCR-ABL1-positive ALL patients, negative cohort consisted of 59 cases with known structural or numerical aberrations. Among them there were 21 patients with high hyperdiploidy, 1 low hypodploid, 1 near tetraploid and 1 iAMP21 cases, 23 patients with translocation t(12;21)(p13;q22), 5 cases with t(1;19)(q23;p13), 1 case with t(9;11)(p22;q23) and 6 Down syndrome (DS-ALL) patients. The rest 78 cases were called 'B-others' ALL and designated as training cohort. According to the previously published data (R. Harvey et al. ASH 2013 abs #826.) we picked 5 genes (IGJ, SPATS2L, MUC4, CRLF2, CA6) those expressions were estimated by real-time PCR. ΔCt method was applied in relation to ABL1 expression. In case of having expression results similar to BCR-ABL1-positive cases, patients with BCR-ABL1-negative ALL were attributed as BCR-ABL1-like ALL. In 113 patients we evaluated IKZF1 status by MLPA using P335 kit (MRC-Holland). Presence of ABL1, ABL2, CRLF2, IgH, JAK2, PDGFRb/CSFR1 gene rearrangements were done by FISH. Prognostic significance of BCR-ABL-like profile was estimated in 66 ‘B-others’ patients uniformly treated according to the ALL-MB 2008 protocol. Informed consent was obtained in all cases. Results. Hierarchical cluster analysis and principal component analysis showed that 16 examined samples were clustered together with 9 BCR-ABL1-positive ones. Among them there were 3 DS patients, 1 iAMP21, 1 t(12;21) cases and 11 patients from ‘B-other’ group. IKZF1 deletions and high CRLF2 expression were more frequent in BCR-ABL1-like group in comparison to non-BCR-ABL1-like (67% vs 11%, and 40% vs 6%, correspondingly; p<0.001 in both cases). Among 9 BCR-ABL1-like cases which were assessed by FISH, JAK2 rearrangements were found in 2, CRLF2 in 4 (2 cases of CRLF2-IgH and 2 CRLF2-P2RY8). In 3 patients none of the tested gene rearrangements were revealed. We did not detect any tyrosine kinase fusion genes in 64 non-BCR-ABL-like ‘B-other’ patients (p<0.001). BCR-ABL1-like profile was associated with female gender (80% vs. 57% p=0.011), high initial WBC (≥30*10^9/L) (67% vs. 18%, p=0.001), M3 bone marrow status on day 15 of induction remission (27% vs. 4%, p=0.010). BCR-ABL1-like ALL patients more often were stratified to high-risk group (40% vs. 9%, p=0.001). EFS of BCR-ABL1-like patients was remarkably lower in comparison to non-BCR-ABL1-like ‘B-other’ patients enrolled into ALL-MB 2008 protocol (0.28±0.17 vs. 0.93±0.04, p<0.0001) while cumulative incidence of relapse was significantly higher (0.57±0.19 vs. 0.02±0.02, p<0.0001) with median of follow-up period 4.9 years. The worst outcome was noted in case of combination of BCR-ABL1-like profile and IKZF1 deletions (EFS 0.00), while patients with isolated BCR-ABL1-like profile doing much better (EFS 0.67±0.22). Poor EOI flow-MRD response (>0.1%) together with BCR-ABL1-like profile identified a group of patients with dismal outcome (EFS 0.00 vs 0.88±0.11, p<0.001). Overall accuracy of our BCR-ABL1-like profile for relapse prediction in ‘B-other’ group on ALL-MB 2008 protocol was 0.939 (95% CI 0.881-0.997), for risk of unfavorable event 0.909 (95% CI 0.840-0.978). Conclusion. Thus, we showed that described real-time PCR technology based on expression data of 5 genes allowed to detect the BCR-ABL1-like ALL patients with similar clinical characteristics, genetic parameters and treatment outcome to ones revealed by microarray, NGS or TLDA techniques. We believe that detection of BCR-ABL1-like profile by PCR can be used as fast and easy screening method in ‘B-other’ ALL for the further identification of tyrosine kinase fusion genes or other targetable lesions by NGS or FISH within this group only. DisclosuresNo relevant conflicts of interest to declare.

Synergism of FAK and tyrosine kinase inhibition in Ph+ B-ALL

BCR-ABL1+ B progenitor acute lymphoblastic leukemia (Ph+ B-ALL) is an aggressive disease that frequently responds poorly to currently available therapies. Alterations in IKZF1, which encodes the lymphoid transcription factor Ikaros, are present in over 80% of Ph+ ALL and are associated with a stem cell-like phenotype, aberrant adhesion molecule expression and signaling, leukemic cell adhesion to the bone marrow stem cell niche, and poor outcome. Here, we show that FAK1 is upregulated in Ph+ B-ALL with further overexpression in IKZF1-altered cells and that the FAK inhibitor VS-4718 potently inhibits aberrant FAK signaling and leukemic cell adhesion, potentiating responsiveness to tyrosine kinase inhibitors, inducing cure in vivo. Thus, targeting FAK with VS-4718 is an attractive approach to overcome the deleterious effects of FAK overexpression in Ph+ B-ALL, particularly in abrogating the adhesive phenotype induced by Ikaros alterations, and warrants evaluation in clinical trials for Ph+ B-ALL, regardless of IKZF1 status.

Ikaros Gene Deletion Significantly Predicts Relapse in Pediatric B-ALL Patients with Low End-Induction Minimal Residual Disease

Background:Deletions in the Ikaros gene (IKZF1) have been associated with a poor outcome in pediatric B-ALL, but the interaction of IKZF1 deletions with other established prognostic factors, such as minimal residual disease (MRD), is still under investigation. Here we report the IKZF1 deletion status of 405 patients (pts) with acute lymphoblastic leukemia (ALL) and its association with other presenting features, end-induction MRD, and outcome.Methods:Between 2005-2011, 794 eligible pts (aged 1-18 yrs) with newly diagnosed pediatric ALL (B-ALL: 697; T-ALL: 97) were enrolled on DFCI ALL Consortium Protocol 05-001. End-induction MRD was assessed prospectively on all pts by allele-specific oligonucleotide-PCR assay. DNA was extracted from archived diagnostic blood or bone marrow samples from 399 B-ALL and 6 T-ALL pts with sufficient available material. Using a commercially available kit (SALSA MLPA P202 IKZF1, MRC-Holland), IKZF1 deletion status was assessed by multiplex ligation-dependent probe amplification (MLPA). Event free survival (EFS) and relapse free survival (RFS) were estimated using the method of Kaplan and Meier.Results:IKZF1 deletion was detected in 69 (17%) of the 405 evaluated pts. IKZF1 deletion was more common in pts over 10 years old (p<0.0001), males (p=0.05), Hispanic/Latinos (p=0.002) and those with presenting white blood cell count (WBC) at diagnosis ≥ 50K/ul (p<0.0001). IKZF1 deletions were detected in 7 of 13 (54%) pts with the Philadelphia chromosome (Ph+). Significantly more IKZF1 pts experienced induction failure (7% vs 1%, p=0.009) and relapse (25% vs 7%, p<0.0001) than pts without IKZF1 deletions. There was no difference in rates of treatment-related mortality. With a median follow-up of 5.3 years, the 5-year event free survival (EFS) for patients without IKZF1 deletion was 87% and 61% for those with IKZF1 deletion (p<0.0001; Figure 1). There was no significant difference in EFS based on type of IKZF1 deletion: 1) deletions of exons 4-7 or 4-8 (42% of cases, 5-yr EFS 51%) or 2) whole gene (49% of cases, 5-yr EFS 69%) (p=0.23).315 Ph-negative B-ALL pts achieving complete remission (CR) had assessable end-induction MRD. Significantly more IKZF1 non-deleted pts had low MRD compared with IKZF1-deleted pts (95% vs 82%, p=0.006). For the 293 MRD-low pts, relapse occurred in 7% of IKZF1 non-deleted and 24% of IKZF1-deleted pts (p=0.004); for 22 MRD-high pts (all of whom received intensified therapy), there was no significant difference in relapse between IKZF1 non-deleted and IKZF1-deleted pts (21% vs 37%, p=0.62). The 5-yr relapse-free survival (RFS) was significantly worse for MRD-low pts with IKZF1 deletions versus those without these deletions (Figure 1). In multivariable analysis, IKZF1 status, but not MRD, was significantly associated with RFS for Ph-negative B-ALL pts. (Table 1)Conclusions:IKZF1 deletion is associated with higher rates of induction failure and relapse, and is a significant predictor of inferior outcome in pediatric B-ALL. IKZF1 deletion was associated with significantly higher rates of relapse in Ph-negative B-ALL patients with low end-induction MRD, and thus may be useful factor to consider when stratifying treatment intensity in this subset of pts. We conclude that IKZF1 deletion should be incorporated into risk stratification for pediatric B-ALL.Table 1Prognostic Factors for RFS for B-ALL, Ph-negative pts with evaluable end-induction MRDUnivariateMultivariableHR [95% CI]p-valueHR [95% CI]p-valueAge, ≥10 vs <101.40 [0.68-2.91]0.361.19 [0.56-2.51]0.65IKZF1, del vs. not3.23 [1.61-6.45]0.00092.53 [1.20-5.30]0.01MRD, high vs. low2.51 [1.04-6.03]0.041.63 [0.64-4.11]0.30WBC, ≥50 vs. <502.50 [1.27-4.94]0.0081.99 [0.98-4.03]0.06[HR=Hazard ratio] [Display omitted] [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Tumor Suppressors BTG1 and IKZF1 Cooperate during Mouse Leukemia Development and Impact Relapse Rate in Childhood Acute Lymphoblastic Leukemia

Deletions and mutations affecting transcription factor IKZF1 are associated with increased relapse risk and poor outcome in B cell precursor acute lymphoblastic leukemia (BCP-ALL). However, additional genetic events may either enhance or negate the effects of IKZF1 on prognosis. We observed that deletions of the gene encoding the transcriptional coregulator BTG1 frequently co-occured with loss of IKZF1 function, suggesting a synergistic role for these events during leukemia development or progression. Targeted deletion of Btg1 predisposed both Btg1+/- and Btg1-/- mice to T cell malignancies, similar to what has been observed in Ikzf1 heterozygous knockout animals. Hence, while somatic single single-copy losses of either BTG1 and IKZF1 in the patient are predominantly found in BCP-ALL, targeted deletion of these genes in the mouse gives rise to T cell malignancies.To establish whether loss of BTG1 function affected the tumor suppressive role of IKZF1, the Btg1 knockout allele was crossed onto mice heterozygous for a loss-of-function Ikzf1 allele. Leukemia penetrance in these compound mice increased in a Btg1 dose-dependent manner. These leukemias were characterized by clonal TCRb rearrangement and aggressive infiltration into secondary organs, indicating synergistic roles for these tumor suppressors during mouse leukemia development.To investigate the effects of combined IKZF1/BTG1 loss in human BCP-ALL, we examined a large pediatric cohort of BCP-ALL cases, and found that the combined presence of BTG1 and IKZF1 deletions was associated with a markedly higher incidence of relapse, relative to IKZF1-deleted cases without BTG1 aberrations. Similar to BTG1 copy number losses, deletions in EBF1, PAX5, RB1 and CDKN2A/B appeared to be selectively enriched in IKZF1 deleted ALL. However, in contrast to BTG1, none of these other copy number alterations affected relapse incidence or outcome in this patient group. In conclusion, our data demonstrate synergy between the tumor suppressors BTG1 and IKZF1 during mouse leukemia development while the combined (single copy) loss of these two tumor suppressors identifies a patient group with an extremely poor outcome.Event free survival in a cohort of 514 children newly diagnosed with BCP-ALL, divided into four categories based on IKZF1 and BTG1 deletion status. [Display omitted] DisclosuresPieters:Eusa Pharma: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees.

Effect of IKZF1 deletions on signal transduction pathways in Philadelphia chromosome negative pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL).

BackgroundIKZF1 deletions are an unfavorable prognostic factor in children with Philadelphia chromosome positive (Ph+) as well as negative (Ph−) acute lymphoblastic leukemia (ALL). Although IKZF1 deletions occur in 10–15% of Ph− ALL cases, effects of IKZF1 deletions on signaling pathways in this group have not been extensively studied. Therefore, in this study we aimed to study the effect of IKZF1 deletions on active signal transduction pathways.MethodsMultiplex ligation-dependent probe amplification (MLPA) was used to determine IKZF1 deletions and other copy number alterations in 109 pediatric B-Cell Precursor ALL (BCP-ALL) patients. Kinase activity profiling of 45 primary Ph− BCP-ALL patients (31 IKZF1 wild type patients and 14 patients harboring an IKZF1 alteration) and western blot analysis of 14 pediatric BCP-ALL samples was performed to determine active signal transduction pathways.ResultsUnsupervised hierarchical cluster analysis of kinome profiles of 45 pediatric Ph− ALL cases showed no clustering based on IKZF1 status. Comparing the phosphorylation intensities of peptides associated with signaling pathways known to be involved in BCP-ALL maintenance, we did not observe differences between the two groups. Western blot analysis of 14 pediatric BCP-ALL samples showed large variations in phosphorylation levels between the different ALL samples, independent of IKZF1 status.ConclusionsBased on these results we conclude that, although IKZF1 deletions appear to be an important clinical prognostic factor, we were unable to identify a unique IKZF1 dependent protein expression signature in pediatric Ph− ALL and consequently no specific targets for future therapy of Ph−IKZF1 deleted BCP-ALL could be identified.Electronic supplementary materialThe online version of this article (doi:10.1186/s40164-015-0017-y) contains supplementary material, which is available to authorized users.

The clinical impact of IKZF1 deletions in paediatric B-cell precursor acute lymphoblastic leukaemia is independent of minimal residual disease stratification in Nordic Society for Paediatric Haematology and Oncology treatment protocols used between 1992 and 2013.

Paediatric B-cell precursor acute lymphoblastic leukaemias (BCP ALL) with IKZF1 deletions (∆IKZF1) are associated with a poor outcome. However, there are conflicting data as to whether ∆IKZF1 is an independent risk factor if minimal residual disease (MRD) and other copy number alterations also are taken into account. We investigated 334 paediatric BCP ALL, diagnosed 1992-2013 and treated according to Nordic Society for Paediatric Haematology and Oncology ALL protocols, with known IKZF1 status based on either single nucleotide polymorphism array (N=218) or multiplex ligation-dependent probe amplification (N=116) analyses. ∆IKZF1, found in 15%, was associated with inferior 10-year probabilities of event-free (60% vs. 83%; P<0·001) and overall survival (pOS; 73% vs. 89%; P=0·001). Adjusting for known risk factors, including white blood cell (WBC) count and MRD, ∆IKZF1 was the strongest independent factor for relapse and death. ∆IKZF1 was present in 27% of cases with non-informative cytogenetics ('BCP-other') and a poor 10-year pOS was particularly pronounced in this group (58% vs. 90%; P<0·001). Importantly, neither MRD nor WBC count predicted events in the ∆IKZF1-positive cases. Co-occurrence of pseudoautosomal region 1 (PAR1) deletions in Xp22.33/Yp11.32 (P2RY8-CRLF2) and ∆IKZF1 increased the risk of relapse (75% vs. 30% for cases with only ∆IKZF1; P=0·045), indicating that BCP-other ALL with both P2RY8-CRLF2 and ∆IKZF1 constitutes a particularly high-risk group.