The Gene Expression Classifier ALLCatchR Identifies B-cell Precursor ALL Subtypes and Underlying Developmental...

Area of Science:

• Computational biology and bioinformatics
• Hematology and oncology
• Molecular diagnostics

Background:

• Current B-cell precursor acute lymphoblastic leukemia (BCP-ALL) classifications rely on genomic drivers, but systematic gene expression analysis is less advanced.
• Transcriptome sequencing (RNA-Seq) is established for identifying driver aberrations, yet robust methods for gene expression-based subtyping are needed.

Purpose of the Study:

• To develop ALLCatchR, a machine learning classifier for accurate molecular subtyping of BCP-ALL using RNA-Seq gene expression data.
• To enable routine application of RNA-Seq for BCP-ALL diagnostics and provide novel insights into developmental trajectories.

Main Methods:

• Developed ALLCatchR, a machine learning classifier trained on 1869 BCP-ALL transcriptome profiles across four cohorts.
• Validated ALLCatchR on three independent hold-out cohorts (n=1018), assessing accuracy, sensitivity, and specificity for subtype allocation.
• Established a novel RNA-Seq reference of human B-lymphopoiesis from FACS-sorted healthy bone marrow progenitor stages.

Main Results:

• ALLCatchR achieved 95.7% overall accuracy in subtype allocation across independent cohorts, with high-confidence predictions in 83.7% of samples.
• The classifier outperformed existing tools and identified novel driver candidates, with only 1.2% of samples remaining unclassified.
• Projection of BCP-ALL samples onto the normal lymphopoiesis trajectory revealed shared proximity patterns, offering a new framework for developmental comparisons.

Conclusions:

• ALLCatchR provides a systematic and accurate RNA-Seq-based approach for BCP-ALL molecular subtyping, enhancing diagnostic capabilities.
• The tool facilitates routine RNA-Seq application in BCP-ALL diagnostics, improving subtype allocation and providing novel insights into disease biology.
• The integration of a normal lymphopoiesis reference trajectory offers a framework for understanding BCP-ALL developmental origins and classifications.