IL-7 Receptor Mutations and Steroid Resistance in Pediatric T cell Acute Lymphoblastic Leukemia: A Genome Sequencing Study

Abstract

BackgroundPediatric acute lymphoblastic leukemia (ALL) is the most common childhood cancer and the leading cause of cancer-related mortality in children. T cell ALL (T-ALL) represents about 15% of pediatric ALL cases and is considered a high-risk disease. T-ALL is often associated with resistance to treatment, including steroids, which are currently the cornerstone for treating ALL; moreover, initial steroid response strongly predicts survival and cure. However, the cellular mechanisms underlying steroid resistance in T-ALL patients are poorly understood. In this study, we combined various genomic datasets in order to identify candidate genetic mechanisms underlying steroid resistance in children undergoing T-ALL treatment.Methods and FindingsWe performed whole genome sequencing on paired pre-treatment (diagnostic) and post-treatment (remission) samples from 13 patients, and targeted exome sequencing of pre-treatment samples from 69 additional T-ALL patients. We then integrated mutation data with copy number data for 151 mutated genes, and this integrated dataset was tested for associations of mutations with clinical outcomes and in vitro drug response. Our analysis revealed that mutations in JAK1 and KRAS, two genes encoding components of the interleukin 7 receptor (IL7R) signaling pathway, were associated with steroid resistance and poor outcome. We then sequenced JAK1, KRAS, and other genes in this pathway, including IL7R, JAK3, NF1, NRAS, and AKT, in these 69 T-ALL patients and a further 77 T-ALL patients. We identified mutations in 32% (47/146) of patients, the majority of whom had a specific T-ALL subtype (early thymic progenitor ALL or TLX). Based on the outcomes of these patients and their prednisolone responsiveness measured in vitro, we then confirmed that these mutations were associated with both steroid resistance and poor outcome.To explore how these mutations in IL7R signaling pathway genes cause steroid resistance and subsequent poor outcome, we expressed wild-type and mutant IL7R signaling molecules in two steroid-sensitive T-ALL cell lines (SUPT1 and P12 Ichikawa cells) using inducible lentiviral expression constructs. We found that expressing mutant IL7R, JAK1, or NRAS, or wild-type NRAS or AKT, specifically induced steroid resistance without affecting sensitivity to vincristine or L-asparaginase. In contrast, wild-type IL7R, JAK1, and JAK3, as well as mutant JAK3 and mutant AKT, had no effect. We then performed a functional study to examine the mechanisms underlying steroid resistance and found that, rather than changing the steroid receptor’s ability to activate downstream targets, steroid resistance was associated with strong activation of MEK-ERK and AKT, downstream components of the IL7R signaling pathway, thereby inducing a robust antiapoptotic response by upregulating MCL1 and BCLXL expression. Both the MEK-ERK and AKT pathways also inactivate BIM, an essential molecule for steroid-induced cell death, and inhibit GSK3B, an important regulator of proapoptotic BIM. Importantly, treating our...

Mutant JAK3 signaling is increased by loss of wild-type JAK3 or by acquisition of secondary JAK3 mutations in T-ALL

“…2,9,10,[14][15][16] Detailed analysis of our next-generation sequencing data 9,10,18 revealed that 14 of 41 JAK3-mutant T-ALLs have either a homozygous JAK3 mutation or 2 different JAK3 mutations ( Figure 1A). In a recently published exome sequencing study, 3 of 20 JAK3-mutant T-ALL patient cases were reported to harbor 2 JAK3 mutations.…”

“…11,12 Between 10% and 16% of patients with T-ALL carry at least 1 mutation in JAK3. 2,9,10,[14][15][16] A more detailed analysis presented here shows that up to a third of these patient cases harbor a second JAK3 mutation, and we investigated the biological significance of having multiple JAK3 mutations.…”

Overcoming Steroid Resistance in T Cell Acute Lymphoblastic Leukemia

“…In this issue of PLOS Medicine , Jules Meijerink and colleagues [4] integrated next-generation sequencing data and genome-wide copy number profiles with ex vivo drug sensitivity and clinical outcome in a large panel of primary T-ALL specimens obtained at diagnosis. Interestingly, the authors found that mutations in the interleukin 7 receptor (IL7R) signaling pathway, including JAK1 and KRAS mutations, were significantly associated with prednisolone resistance and reduced survival in an initial discovery cohort of 69 primary T-ALL samples.…”

CD47 agonist peptide PKHB1 induces immunogenic cell death in T‐cell acute lymphoblastic leukemia cells

“…The 5‐year survival rate in adults is about 30%‐50% compared to 90% in children . ALL can affect B cells (B‐ALL) or T cells (T‐ALL); T‐ALL has a high risk of relapse as a result of acquired therapy resistance . Chemoresistance is one of the most important reasons for failure in cancer treatments.…”