<p>We present single-cell transcriptome and surface protein expression (CITE-seq) data from four healthy donors and fifteen pediatric T cell acute lymphoblastic leukemia (T-ALL) patients at diagnosis and at different treatment timepoints (days 1 – 6 and at time of remission). Mononuclear cells from peripheral blood (PB; longitudinal) or bone marrow (BM; diagnosis only) were isolated and <a href="https://www.ncbi.nlm.nih.gov/gene/5788">CD45</a>high immune cells and CD45dim<a href="https://www.ncbi.nlm.nih.gov/datasets/gene/924/">CD7</a>+ malignant cells were sorted and subsequently pooled to enrich for immune cells. For comparison,CD45high immune cells from four healthy donors were also sorted. Single-cell sequencing of the transcriptome and surface protein expression (204 antibodies) was performed using the 10x Genomics platform.</p><p>Multiomics analyses resulted in the identification of a T-ALL subgroup characterized by a remodeled immune microenvironment at initial diagnosis. This immune landscape is dominated by the presence of non-malignant <a href="https://www.ncbi.nlm.nih.gov/datasets/gene/920/">CD4</a>-<a href="https://www.ncbi.nlm.nih.gov/datasets/gene/925/">CD8</a>-TCRab T cells that interact with <a href="https://www.ncbi.nlm.nih.gov/datasets/gene/58191/">CXCL16</a> expressing non-classical monocytes. Leukemia cell intrinsic transcriptional rewiring in these patients is associated with activation of <a href="https://www.ncbi.nlm.nih.gov/datasets/gene/5906/">Rap1</a> signaling.</p>

Single-Cell Multiomics of the Immune Microenvironment in T-Cell Acute Lymphoblastic Leukemia