Ahmed Mawlawi

Bioinformatics Specialization · Cohort 2026

Dissecting Intra-Individual Tumor Heterogeneity in Childhood Leukemia: A Single-Cell Analysis of Maturation States and Ribosomal Expression

Childhood acute lymphoblastic leukemia (cALL) is characterized by the disrupted maturation and clonal expansion of bone marrow lymphoid precursors. While standard bulk sequencing stratifies patients into broad cytogenetic subtypes, it averages out transcriptional signals, masking intra-tumor heterogeneity and minor subclonal populations that drive therapeutic resistance and disease relapse. In this study, we developed an end-to-end single-cell RNA sequencing (scRNA-seq) pipeline to reproduce and advance the transcriptomic findings of Caron et al. (2020) [2], with a dedicated downstream focus on a High Hyperdiploid (HHD) patient sample. By implementing strict per-sample quality filtering and restricting downstream clustering to resting G1-phase cancer cells (n=16,731), we eliminated confounding cell-cycle variability while preserving true intra-individual biological diversity. Replacing manual canonical marker evaluation with automated SingleR reference mapping against the Human Primary Cell Atlas, we identified two distinct intra-tumor subclones in patient HHD_1 (Subclone 9, n=1,020; Subclone 11, n=679), demonstrating an early Pro-B (CD34+) to mature B-cell developmental transition. Non-linear LOESS trajectory modeling and Euclidean distance projections confirmed an inverse relationship between developmental pseudotime and ribosomal protein gene expression (RPS/RPL). Differential expression via MAST [3] and Gene Ontology enrichment via goseq [4] independently validated that subclonal divergence is predominantly driven by translation initiation and ribosome assembly pathways (padj<10-6). These findings establish that leukemic maturation arrest locks immature subclones into a hyper-active translational state, identifying developmental and metabolic heterogeneity as core features of cALL pathology.

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