Immune Dysregulation and State-Transition Transcriptomic Signatures Underlying Pediatric Chronic Myeloid Leukemia Pathogenesis

Abstract Chronic myeloid leukemia (CML) accounts for approximately 2% of all leukemias in children under 15 and 9% in adolescents aged 15 to 19. Compared to older adults, children and young adults with CML often present with more aggressive clinical features, such as elevated white blood counts and splenomegaly. Despite significant advances in understanding the molecular biology of adult CML, much less is known about pediatric CML, including the long-term effects of tyrosine kinase inhibitor (TKI) therapy in younger patients. This knowledge gap underscores a critical need to elucidate the molecular pathogenesis of pediatric CML to guide the development of novel age-specific targeted therapies, particularly for relapsed or progressive cases. Although both pediatric and adult CML patients harbor the BCR::ABL1 fusion gene, accumulating evidence suggests that additional age-related molecular and immunological features may shape the distinct pathogenesis of pediatric CML. To investigate these differences, we performed high-throughput bulk RNA sequencing of bone marrow-derived CD34+cells from 10 pediatric (ages 9-13) and 10 adult (ages 33-62) CML patients with chronic phase of CML (CML-CP), alongside age-matched healthy controls. Transcriptomic analysis revealed clear distinctions between pediatric and adult CML, including differential expression of Rho-GTPase pathway genes and alterations in B cell development and metabolic pathways. Single-cell RNA sequencing further identified significant differences in hematopoietic progenitor cell populations, particularly a marked loss of CD34+ pro-B cells in pediatric CML, and downregulation of HLA-related genes in pediatric CD34+ CML cells. Given that loss of HLA-DR expression is a known mechanism of immune escape and correlates with reduced T cell infiltration and poorer clinical outcomes, we assessed its functional relevance by co-culturing HLA-DR+ (MOLM-1, MOLM-6) and HLA-DR- (K562) CML cell lines with healthy, activated T cells. HLA-DR+ cells were significantly more susceptible to T cell-mediated apoptosis, indicating that HLA-DR downregulation may facilitate immune evasion and support CML cell survival in pediatric patients. In parallel, principal component analysis (PCA) and state-transition modeling of bulk RNA-seq data revealed that adult and pediatric disease are characterized by distinct transcriptome states, driven by unique gene sets. Notably, pediatric CML showed a diminished role for metabolic rewiring compared to adult CML, with gene set enrichment analysis (GSEA) highlighting inflammatory and heme metabolism signatures uniquely enriched in pediatric CML samples. Together, these findings demonstrate that pediatric CML is a biologically distinct disease, marked by altered immune regulation, loss of B cell precursors, and reduced HLA expression that may contribute to immune escape. These molecular features likely corroborate the clinical differences observed between pediatric and adult CML patients and support the importance of developing age-specific therapeutic strategies. Further investigation of these age-related transcriptomic and immune signatures may yield predictive biomarkers aimed at selectively targeting CD34+ CML cells.