Genomic drivers and an immune-cold microenvironment are associated with relapse in Chinese pediatric B-ALL

Background: Relapse remains a major challenge in pediatric B-cell Acute Lymphoblastic Leukemia (B-ALL). This study aims to identify the specific genomic and cellular markers that drive treatment failure and are associated with relapse and poor Event-Free Survival (EFS) in Chinese pediatric B-ALL patients. Methods: We performed an integrated multi-omic analysis on a cohort of 105 Chinese pediatric B-ALL patients, including 13 EFS Event (relapse plus died) cases. The cohort was profiled using ultra-deep gene panel sequencing (N=87), single-cell RNA-sequencing (scRNA-seq, N=52), and VDJ-sequencing (N=40). We integrated genomic, transcriptomic, and immune repertoire data to identify biomarkers associated with relapse and EFS. Associations were tested using Fisher's Exact Test, the Wilcoxon rank-sum test, and Cox regression. Results: Our scRNA-seq and VDJ-seq analyses revealed the cellular landscape of relapse. We found a positive correlation between B-ALL blast proportion and BCR clonality and a negative correlation between T-cell proportion and TCR clonality (p=0.041). Notably, relapsed patients showed a higher BCR clonality but a highly polyclonal TCR repertoire, suggesting immune failure. We identified that mutations in a curated panel of ALL-Drivers was significantly associated with relapse status (p=0.033) and a higher B-ALL blast percentage (p=0.013). And the higher ALL-Drivers VAF burden phenotype correlates with relapse status (p=0.006). The non-relapse patients were found exhibited an “immune-hot" phenotype, characterized by significantly higher T-cell exhaustion and cytotoxicity scores (p<0.001). This state of active immune engagement is associated with PD-1/PD-L1 pathway. Relapse was associated with an "immune-cold" state, lacking this active T-cell engagement. Finally, survival analysis and KM plot confirmed the prognostic significance of these findings. The presence of an ALL-Driver is significantly associated with poor Event-Free Survival (p=0.021). Conclusion: Our findings reveal a biological pathway to poor prognosis. ALL-Drivers are linked to a high B-ALL blasts burden. This high-risk state is strongly correlated with patient relapse and is characterized by an "immune-cold" microenvironment, defined by the absence of the PD-L1 mediated T-cell exhaustion and cytotoxicity signature seen in non-relapsed patients.