The Gene Expression Classifier ALLCatchR Identifies B-cell Precursor ALL Subtypes and Underlying Developmental Trajectories Across Age

Abstract

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.

Refined risk stratification helps guiding transplantation choice in adult BCR::ABL1-positive acute lymphoblastic leukemia

“…It is consistent with previous reports, the non- IKZF1 plus group and IKZF1 plus group enriched in distinct hematopoietic lineage, including B lymphoid/myeloid lineage, early pro-B cells, and pre-B I/II large stages (Fig. 2A–C ) [ 9 , 10 ]. Using multiparameter flow cytometry [ 11 ], similar results at the protein expression level were validated (Fig.…”

“…B ssGSEA score between IKZF1 plus and non- IKZF1 plus group, using gene signatures associated with three transcriptomic classes that correspond to early pro-B, pro-B and pre-B I differentiation stages in Kim et al [ 9 ]. C ssGSEA score between IKZF1 plus and non- IKZF1 plus group, using seven B lymphopoiesis stage-specific gene sets identified by Beder et al [ 10 ]. D Box plots illustrating expression of B lymphoid and myeloid lineage antigens between IKZF1 plus and non- IKZF1 plus group, as measured by multiparameter flow cytometry ( n = 135, 2 patients without flow cytometry results).…”

Mutational and transcriptional landscape of pediatric B-cell precursor lymphoblastic lymphoma

“…Count matrices were generated by implementing the featurecounts function from the Rsubread v1.6.4 package. Transcript per million (TPM) normalized data was used to predict subtypes using the ALLCatchR classifier 20 . Subtypes were assigned by integrating information coming from aneuploidies, fusions, single nucleotides variants (SNVs) and ALLCatchR prediction.…”

“…(not assigned). For those cases with missing experimental data but assigned to a subtype with "high-confidence" by ALLCatchR 20 , the ALLCatchR prediction was used as final subtype.…”

“…Samples for which lack of experimental data prevented subtype definition were labelled as “n.a.” (not assigned). For those cases with missing experimental data but assigned to a subtype with “high-confidence” by ALLCatchR 20 , the ALLCatchR prediction was used as final subtype.…”