Decoding Disease Persistence in Pediatric Acute Lymphoblastic Leukemia One Single Cell at a Time
Imbach, Kathleen Jane
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In order to understand the biological and molecular mechanisms underlying disease resistance to therapy in pediatric acute lymphoblastic leukemia (ALL), we performed an investigation utilizing single-cell RNA-sequencing (scRNA-seq) on the 10X Genomics Chromium platform. Bone marrow samples from seven patients were collected, four of whom exhibited measurable residual disease (MRD) after induction therapy, and three patients who did not. Cells from bone marrow tissue were extracted from each patient at the time of diagnosis, prior to treatment efforts. Leukemic cells were separated from peripheral immune cells using flow cytometry and ~1000 single cells were sequenced from each patients’ cell populations. The goal of this study was to discern how the immune and leukemic cell populations and gene expression therein vary at the time of diagnosis between patients who do or do not respond to induction. Our results demonstrate a comparative increase in immune exhaustion signatures in the immune cells of MRD-positive patients, corroborating previous findings that implicate the role of exhaustion in resistant disease. We also show a discrepancy of cell cycle states in the leukemic cell compartment according to disease outcome, with an enrichment of blasts from MRD-negative patients exhibiting genetic signatures of S- and G2/M-phase.