Measuring Longitudinal Genome-wide Clonal Evolution of Pediatric Acute Lymphoblastic Leukemia at Single-Cell...

Area of Science:

• Genomics
• Cancer Biology
• Pediatric Oncology

Background:

• Acute lymphoblastic leukemia (pALL) in children is often curable with multi-year chemotherapy, but treatment failure suggests drug susceptibility variations.
• Bulk sequencing shows limited genetic variants in pALL, masking true single-cell diversity.

Purpose of the Study:

• To investigate the extent of genetic heterogeneity in pediatric acute lymphoblastic leukemia (pALL) at the single-cell level.
• To understand how pre-existing genetic diversity influences chemotherapy response in pALL.

Main Methods:

• Employed error-corrected bulk sequencing, single-cell exome sequencing, and primary template-directed amplification (PTA)-enabled single-cell genome sequencing.
• Conducted PTA-based phylogenetic analysis on over 150 single-cell genomes from four pALL patients.

Main Results:

• Discovered substantial genetic diversity within individual pALL cells, with significantly more mutations per cell than detected in bulk samples.
• Identified multiple independent ras clones in some ETV6-RUNX1 samples and APOBEC-driven mutagenesis signatures.
• Revealed heritable phenotypes linked to genetic alterations and preferential selection of low-frequency clones during chemotherapy.

Conclusions:

• pALL exhibits previously undetected genetic diversity, with mutations influencing treatment response.
• Understanding single-cell genetic evolution provides a framework for developing more effective pALL therapies.