Remodeling of the immune microenvironment is linked to adverse outcome in pediatric T cell acute lymphoblastic leukemia

Changes in the immune microenvironment are frequent in cancers occurring in adult patients, yet our understanding of the pediatric cancer immune microenvironment and its clinical relevance is limited. We investigate the immune microenvironment in pediatric T cell acute lymphoblastic leukemia (T-ALL), using single-cell CITE-seq and immune repertoire analyses. We identify a T-ALL subgroup characterized by a remodeled immune microenvironment, which is associated with adverse clinical outcome in minimal residual disease low patients. This adverse immune landscape is dominated by the presence of a population of non-malignant CD4-CD8-TCRab T cells that interact with CXCL16 expressing non-classical monocytes. Leukemia cell intrinsic transcriptional rewiring in these patients is associated with activation of Rap1 signaling. Inhibiting Rap1 signaling results in increased sensitivity to the BCL2/BCL-XL inhibitor navitoclax. Our study provides insights into the immune microenvironment of pediatric hematologic malignancies, forming the basis for identifying novel (immuno)therapeutic targets and risk stratification for treatment. Single-cell multi-omics (CITE-seq (RNA-seq + ADT-seq), TCR-seq and BCR-seq (5' 10x Genomics)) of primary human bone marrow and peripheral blood CD45+ mononuclear cells of 4 normal donors and 15 pediatric T-ALL patients at diagnosis (n=15), short-term treatment (n=8) and remission (n=6). T-ALL patient samples were separated into CD45++ immune cells and CD45+CD7+ leukemia cells by flow-based sorting and subsequently pooled to increase immune-leukemia cell ratio. This study is registered under dbGaP: phs004269.v1.p1. Low-input RNA-seq (Smart-seq2) of CD8+ T-cells cultured in the absence and presence of 100ng/ml CXCL16.