Aberrant IKZF1 gene as relapse predictor in standard-risk pediatric patients with B-cell precursor acute lymphoblastic leukaemia

INTRODUCTION

Worldwide, the B-cell precursor acute lymphoblastic leukaemia (BCP-ALL) treatment protocols are based on risk-adaptive therapy, that is on the search for biological markers for stratification by risk groups for optimal management. Depending on the treatment protocol, deletions and overexpression of non-functional IKZF1 isoforms act as relapse predictors in ALL. We investigated the IKZF1 gene aberrations as the substantive marker for predicting the development of relapse or adverse events when using risk stratification from ALL-MB-2002/2008 protocols.

METHODS

We retrospectively analysed the bone marrow samples collected from 202 newly diagnosed patients with BCP-ALL harbouring IKZF1 aberrations.

RESULTS

In patients of intermediate- and high-risk the presence of IKZF1 aberrations contributed to the delayed clearance of blast cells on the 15th and 36th day of induction therapy, but there was not a significant effect on relapse rate. The comparative analysis demonstrated that standard-risk patients with IKZF1 aberrations have a much higher 5-years cumulative incidence of relapse (66.7 ± 22.7% vs. 11.6 ± 2.9% in the group with normal gene status, p < 0.001) in contrast to intermediate- and high-risk groups. In the competing risk model of relapse, IKZF1 aberrations determine a high risk of relapse only in standard-risk patients (p = 0.025), and it was not significant for patients of other risk groups (p = 0.284 for intermediate, and 0.408 for high-risk groups).

CONCLUSION

Our findings support that IKZF1 aberrations are a crucial relapse predictor in standard-risk patients with BCP-ALL, who practically have no significant markers to assess the prognosis during the primary diagnosis.

Comparison of the blood, bone marrow, and cerebrospinal fluid metabolomes in children with b-cell acute lymphoblastic leukemia

Metabolomics may shed light on treatment response in childhood acute lymphoblastic leukemia (ALL), however, most assessments have analyzed bone marrow or cerebrospinal fluid (CSF), which are not collected during all phases of therapy. Blood is collected frequently and with fewer risks, but it is unclear whether findings from marrow or CSF biomarker studies may translate. We profiled end-induction plasma, marrow, and CSF from N = 10 children with B-ALL using liquid chromatography-mass spectrometry. We estimated correlations between plasma and marrow/CSF metabolite abundances detected in ≥ 3 patients using Spearman rank correlation coefficients (r_s). Most marrow metabolites were detected in plasma (N = 661; 81%), and we observed moderate-to-strong correlations (median r_s 0.62, interquartile range [IQR] 0.29–0.83). We detected 328 CSF metabolites in plasma (90%); plasma-CSF correlations were weaker (median r_s 0.37, IQR 0.07–0.70). We observed plasma-marrow correlations for metabolites in pathways associated with end-induction residual disease (pyruvate, asparagine) and plasma-CSF correlations for a biomarker of fatigue (gamma-glutamylglutamine). There is considerable overlap between the plasma, marrow, and CSF metabolomes, and we observed strong correlations for biomarkers of clinically relevant phenotypes. Plasma may be suitable for biomarker studies in B-ALL.

Association of Combined Focal 22q11.22 Deletion and IKZF1 Alterations With Outcomes in Childhood Acute Lymphoblastic Leukemia

Importance

Alterations in the IKZF1 gene drive B-cell acute lymphoblastic leukemia (B-ALL) but are not routinely used to stratify patients by risk because of inconsistent associations with outcomes. We describe a novel deletion in 22q11.22 that was consistently associated with very poor outcomes in patients with B-ALL with IKZF1 alterations.

Objective

To determine whether focal deletions within the λ variable chain region in chromosome 22q11.22 were associated with patients with B-ALL with IKZF1 alterations with the highest risk of relapse and/or death.

Design, Setting, and Participants

This cohort study included 1310 primarily high-risk pediatric patients with B-ALL who were taken from 6 independent clinical cohorts, consisting of 3 multicenter cohorts (AALL0232 [2004-2011], P9906 [2000-2003], and patients with Down syndrome who were pooled from national and international studies) and 3 single-institution cohorts (University of Utah [Salt Lake City], Children's Hospital of Philadelphia [Philadelphia, Pennsylvania], and St. Jude Children's Hospital [Memphis, Tennessee]). Data analysis began in 2011 using patients from the older studies first, and data analysis concluded in 2021.

Exposures

Focal 22q11.22 deletions.

Main Outcomes and Measures

Event-free and overall survival was investigated. The hypothesis that 22q11.22 deletions stratified the prognostic effect of IKZF1 alterations was formulated while investigating nearby deletions in VPREB1 in 2 initial cohorts (n = 270). Four additional cohorts were then obtained to further study this association (n = 1040).

Results

This study of 1310 patients with B-ALL (717 male [56.1%] and 562 female patients [43.9%]) found that focal 22q11.22 deletions are frequent (518 of 1310 [39.5%]) in B-ALL and inconsistent with physiologic V(D)J recombination. A total of 299 of 1310 patients with B-ALL had IKZF1 alterations. Among patients with IKZF1 alterations, more than half shared concomitant focal 22q11.22 deletions (159 of 299 [53.0%]). Patients with combined IKZF1 alterations and 22q11.22 deletions had worse outcomes compared with patients with IKZF1 alterations and wild-type 22q11.22 alleles in every cohort examined (combined cohorts: 5-year event-free survival rates, 43.3% vs 68.5%; hazard ratio [HR], 2.18; 95% CI, 1.54-3.07; P < .001; 5-year overall survival rates, 66.9% vs 83.9%; HR, 2.05; 95% CI, 1.32-3.21; P = .001). While 22q11.22 deletions were not prognostic in patients with wild-type IKZF1 , concomitant 22q11.22 deletions in patients with IKZF1 alterations stratified outcomes across additional risk groups, including patients who met the IKZF1plus criteria, and maintained independent significance in multivariate analysis for event-free survival (HR, 2.05; 95% CI, 1.27-3.29; P = .003) and overall survival (HR, 1.83; 95% CI, 1.01-3.34; P = .05).

Conclusions and Relevance

This cohort study suggests that 22q11.22 deletions identify patients with B-ALL and IKZF1 alterations who have very poor outcomes and may offer a new genetic biomarker to further refine B-ALL risk stratification and treatment strategies.

Increased Toxicity Among Adolescents and Young Adults Compared with Children Hospitalized with Acute Lymphoblastic Leukemia at Children's Hospitals in the United States

Purpose: Adolescent and young adult (AYA) patients (15-39 years old) with acute lymphoblastic leukemia (ALL) have less favorable outcomes and higher treatment-related mortality as compared with older children with ALL. Minimal data exist regarding how well AYA patients tolerate the intensity of chemotherapy at doses and regimens designed for children, and the toxicities suffered by this population at children's hospitals have not been thoroughly characterized. Methods: Pediatric Health Information Systems database was queried to analyze health care outcomes in pediatric (ages 10-14) and AYA patients (ages 15-39) with ALL hospitalized between January 1999 and December 2014. We extracted relevant ICD-9 data for each patient related to grades 3 or 4 toxicities as outlined by the NCI. Results: A total of 5345 hospital admissions met inclusion criteria, representing 4046 unique patients. Of these admissions, 2195 (41.1%) were in the AYA age group, and the remainder were in the 10-14-year-old group. AYA patients had a significantly higher incidence of intensive care unit stay but no difference in median hospital stay nor mortality. AYA patients had increased toxicities in almost every organ system as compared with older children. Conclusions: In this large multicenter US database study, we found an overall increased number of toxicities among AYA patients with ALL in children's hospitals. Compared with children between the ages of 10 and 15, AYA patients developed disproportionately higher toxicities from drugs commonly used in pediatric protocols for ALL. Prospective studies are needed to assess whether dose modifications for certain chemotherapeutics may improve the toxicity profile and health care burden of AYA patients with ALL treated in children's hospitals.

A validated novel continuous prognostic index to deliver stratified medicine in pediatric acute lymphoblastic leukemia

Risk stratification is essential for the delivery of optimal treatment in childhood acute lymphoblastic leukemia. However, current risk stratification algorithms dichotomize variables and apply risk factors independently, which may incorrectly assume identical associations across biologically heterogeneous subsets and reduce statistical power. Accordingly, we developed and validated a prognostic index (PIUKALL) that integrates multiple risk factors and uses continuous data. We created discovery (n = 2405) and validation (n = 2313) cohorts using data from 4 recent trials (UKALL2003, COALL-03, DCOG-ALL10, and NOPHO-ALL2008). Using the discovery cohort, multivariate Cox regression modeling defined a minimal model including white cell count at diagnosis, pretreatment cytogenetics, and end-of-induction minimal residual disease. Using this model, we defined PIUKALL as a continuous variable that assigns personalized risk scores. PIUKALL correlated with risk of relapse and was validated in an independent cohort. Using PIUKALL to risk stratify patients improved the concordance index for all end points compared with traditional algorithms. We used PIUKALL to define 4 clinically relevant risk groups that had differential relapse rates at 5 years and were similar between the 2 cohorts (discovery: low, 3% [95% confidence interval (CI), 2%-4%]; standard, 8% [95% CI, 6%-10%]; intermediate, 17% [95% CI, 14%-21%]; and high, 48% [95% CI, 36%-60%; validation: low, 4% [95% CI, 3%-6%]; standard, 9% [95% CI, 6%-12%]; intermediate, 17% [95% CI, 14%-21%]; and high, 35% [95% CI, 24%-48%]). Analysis of the area under the curve confirmed the PIUKALL groups were significantly better at predicting outcome than algorithms employed in each trial. PIUKALL provides an accurate method for predicting outcome and more flexible method for defining risk groups in future studies.

IKZF1 alterations in acute lymphoblastic leukemia: The good, the bad and the ugly

Advances in genomics have deepened our understanding of the biology of acute lymphoblastic leukemia (ALL), defined novel molecular leukemia subtypes, discovered new prognostic biomarkers and paved the way to emerging molecularly targeted therapeutic avenues. Since its discovery, IKZF1 has generated significant interest within the leukemia scientific community.IKZF1 plays a critical role in lymphoid development and its alterations cooperate to mediate leukemogenesis. IKZF1 alterations are present in approximately 15% of childhood ALL, rise in prevalence among adults with ALL and become highly enriched within kinase-driven ALL. A cumulating body of literature has highlighted the adverse prognostic impact of IKZF1 alterations in both Philadelphia chromosome (Ph)-negative and Ph-driven ALL. IKZF1 alterations thus emerge as an important prognostic biomarker in ALL. This article aims to provide a state-of-the-art review focusing on the prognostic clinical relevance of IKZF1 alterations in ALL, as well as current and future therapeutic strategies targeting IKZF1-altered ALL.