Children with Philadelphia chromosome-positive acute lymphoblastic leukemia (Ph-positive ALL) have a poor prognosis, and there is no consensus on the optimal treatment for this variant of ALL.We reviewed the medical records of patients with Ph-positive ALL who were treated with intensive chemotherapy, with or without bone marrow transplantation, by 10 study groups or large single institutions from 1986 to 1996. Data on 326 children and young adults, who ranged in age from 0.4 to 19.9 years (median, 8.1), were analyzed to determine the rate of complete remission and the probability of event-free, disease-free and overall survival according to standard prognostic factors and type of treatment.The 267 patients who achieved a complete remission after induction chemotherapy (82 percent) were stratified into three subgroups according to the age and leukocyte count at the time of diagnosis: those with the best prognosis (a leukocyte count of less than 50,000 per cubic millimeter and an age of less than 10 years; 95 patients); those with an intermediate prognosis (intermediate-risk features; 92 patients); and those with the worst prognosis (a leukocyte count of more than 100,000 per cubic millimeter; 80 patients). The estimates of disease-free survival at five years (+/-SE) were 49+/-5 percent) for patients with the best prognosis), 30+/-5 percent (for those with an intermediate prognosis), and 20+/-5 percent (for those with the worst prognosis) (P<0.001 for the overall comparison). We also found that transplantation of bone marrow from an HLA-matched related donor offered significantly greater benefit than intensive chemotherapy alone in terms of protecting patients from relapse or other adverse events (relative risk, 0.3; 95 percent confidence interval, 0.2 to 0.5; P<0.001). This finding was consistent in all three groups.Unlike the usual type of all, Ph-positive ALL is associated with a poor prognosis. Nevertheless, in some patients with favorable prognosis features, the disease can be be controlled by intensive chemotherapy. Transplantation of bone marrow from an HLA-matched related donor is superior to other types of transplantation and to intensive chemotherapy alone in prolonging initial complete remissions.
Current classifications (World Health Organization-HAEM5/ICC) define up to 26 molecular B-cell precursor acute lymphoblastic leukemia (BCP-ALL) disease subtypes by genomic driver aberrations and corresponding gene expression signatures. Identification of driver aberrations by transcriptome sequencing (RNA-Seq) is well established, while systematic approaches for gene expression analysis are less advanced. Therefore, we developed ALLCatchR, a machine learning-based classifier using RNA-Seq gene expression data to allocate BCP-ALL samples to all 21 gene expression-defined molecular subtypes. Trained on n = 1869 transcriptome profiles with established subtype definitions (4 cohorts; 55% pediatric / 45% adult), ALLCatchR allowed subtype allocation in 3 independent hold-out cohorts (n = 1018; 75% pediatric / 25% adult) with 95.7% accuracy (averaged sensitivity across subtypes: 91.1% / specificity: 99.8%). High-confidence predictions were achieved in 83.7% of samples with 98.9% accuracy. Only 1.2% of samples remained unclassified. ALLCatchR outperformed existing tools and identified novel driver candidates in previously unassigned samples. Additional modules provided predictions of samples blast counts, patient’s sex, and immunophenotype, allowing the imputation in cases where these information are missing. We established a novel RNA-Seq reference of human B-lymphopoiesis using 7 FACS-sorted progenitor stages from healthy bone marrow donors. Implementation in ALLCatchR enabled projection of BCP-ALL samples to this trajectory. This identified shared proximity patterns of BCP-ALL subtypes to normal lymphopoiesis stages, extending immunophenotypic classifications with a novel framework for developmental comparisons of BCP-ALL. ALLCatchR enables RNA-Seq routine application for BCP-ALL diagnostics with systematic gene expression analysis for accurate subtype allocation and novel insights into underlying developmental trajectories.
Abstract Acute lymphoblastic leukemia (ALL) arises from the uncontrolled proliferation of precursor B or T cells (B- or T-ALL). Novel immunotherapies are urgently needed to reduce polychemotherapy-related toxicities and to target relapsed/refractory disease. The Interleukin 7 receptor (IL7R) plays a pivotal role in the development of ALL through mutations leading to constitutive activation of the oncogenic IL7R pathway or through overexpression of the receptor. The IL7Rα chain (CD127)-targeting antibody OSE-127 is a full antagonist of the IL7R pathway with an excellent safety profile (NCT03980080), currently evaluated in phase 2 trials in inflammatory and autoimmune diseases (NCT04882007, NCT04605978). We previously reported in vivo efficacy of OSE-127 in CD127+ ALL patient-derived xenografts (PDXs) and synergy with standard of care polychemotherapy, but we had not evaluated CD127 protein expression in ALL patient cells. Moreover, the mechanism of action underlying OSE-127’s anti-leukemic activity remained to be fully elucidated. Here we show that CD127 is expressed by >84% ALL patients and that OSE-127 efficiently targets CD127 not only via its IL7R antagonist activity but also through macrophage-mediated antibody dependent phagocytosis (ADCP). First, CD127 surface expression was prospectively measured by flow cytometry in 372 diagnostic ALL patient samples. We detected CD127-positivity (defined as ≥10% CD127+ blasts) in 84.4% (314/372) cases, of which 39.5% (147/372) were CD127hi (≥ 50% CD127+ blasts). CD127 expression was higher in T- than in B-ALL. Among B-ALL, highest expression was detected in E2A-PBX1+ and BCR-ABL-like ALLs. Mechanistically, OSE-127 blocked STAT5 phosphorylation in IL7-responsive ALL-PDX cells, leading to decreased cell survival and proliferation. Surprisingly, we detected high in vivo efficacy of OSE-127 therapy in IL7-unresponsive PDXs (e.g., unable to induce phosphorylation of STAT5 upon ex vivo IL7 stimulation or with IL7R mutation-induced constitutive phosphorylation of STAT5). We uncovered that OSE-127 induced macrophage-mediated ADCP of CD127+ ALL cells in vitro. Accordingly, treatment of IL7-unresponsive, but OSE-127-sensitive models with an OSE-127-LALAPG variant (conserving IL7R-antagonistic properties but lacking ADCP activity due to Fc-inactivating mutations) did not impact leukemia development, thereby substantiating that ADCP contributes to the anti-leukemic efficacy of OSE-127. In fact, ADCP levels induced by OSE-127 treatment in vitro correlated with its capacity to reduce ALL blasts in the blood of PDX mice in vivo. Altogether, through its dual mode of action, OSE-127 may represent a powerful novel immunotherapy option for ALL patients, including cases with dysregulated IL7R signaling, particularly in combination with standard of care polychemotherapy. Citation Format: Irene Baccelli, Lennart Lenk, Anna Laqua, Dorothee Winterberg, Anna Dietterle, Frederique Corallo, Julien Taurelle, Emma Narbeburu, Beat Bornhauser, Jean-Pierre Bourquin, Fotini Vogiatzi, Simon Raffel, Martin Schrappe, Gunnar Cario, Monika Brüggemann, Denis M Schewe, Nicolas Poirier. CD127 is expressed by acute lymphoblastic leukemias and is efficiently targeted by the IL7R-antagonist OSE-127 through macrophage-mediated antibody dependent phagocytosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2957.
Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer. Leukemic cells are characterized by structural and numeric genomic aberrations, which strongly correlate with prognosis and clinical outcome. A proportion of ALLs cannot be assigned to a distinct subgroup and are classified as B-other. Within this group the IKZF1plus-profile was described as a copy-number based and MRD-dependent stratification profile with very poor prognosis. It is unknown so far, if this profile presents as a surrogate for other unidentified underlying variants. Using optical genome mapping (OGM), a method to detect all types structural variants, we retrospectively investigated IKZF1del/plus-ALL samples and searched for genomic aberrations driving or contributing to the poor prognosis for these patients. Applying OGM we detected several recurrent stratification markers associated with poor prognosis such as a ETV6::ABL1 fusion (ins(12;9)), a PAX5::JAK2 fusion (inv(9)), a EBF1:PDGFRB fusion (t(5;5)). Additionally, we identified a novel NPAT::JAK2 fusion resulting from a t(9;11). Our preliminary data show that IKZF1del/plus-ALL carry additional markers that might be the drivers of the disease.
The increasing volume and intricacy of sequencing data, along with other clinical and diagnostic data, like drug responses and measurable residual disease, creates challenges for efficient clinical comprehension and interpretation. Using paediatric B-cell precursor acute lymphoblastic leukaemia (BCP-ALL) as a use case, we present an artificial intelligence (AI)-assisted clinical framework clinALL that integrates genomic and clinical data into a user-friendly interface to support routine diagnostics and reveal translational insights for hematologic neoplasia.
