Mechanisms of treatment escape in childhood B-cell leukemia

In childhood acute lymphoblastic leukemia (ALL), relapse is the main cause of treatment failure. Most relapses occur within non-high risk groups, suggesting inadequate risk stratification in current protocols for a subset of patients.In this project, we have studied tumor cell treatment escape and the selectionprocess that results in disease relapse, both with respect to selection of genetic traits, as well as selection of cell states that are favorable for cancer cell survival.

While unimodal single-cell transcriptomics have been widely applied in human and animal tissues, their application to patient derived cells of malignant origin, such as leukemic cells, remain challenging, as samples have to be processed freshly, or have to be cryopreserved using crystal-inhibiting additives and stored in liquid nitrogen. Additionally, unimodal sequencing methods cannot capture phenotypic changes within genetically distinct clones, which motivates the use of multi-omic methods. Direct nuclear tagmentation and RNA-seq(DNTR-seq) (Zachariadis et al., Mol. Cell 2020), developed by the Enge lab, is one such multi-modal method and allows for joint transcriptome-wide expression analysis (RNA-seq) and whole genome sequencing (DNA-seq) in single cells from human primary tissues. This enables us to follow clonal evolution and compare how phenotypes change, making it possible to study treatment escape in ALL.

In this project, we sequenced and analysed 14 225 cells from 15 patients across different timepoints (initial diagnosis, during treatment and at relapse) and found evidence that the mechanisms that allow for treatment persistence and the mechanisms that drive relapse are fundamentally decoupled. This means that the processes that allow leukemic cells to rapidly proliferate appear to be distinct from those that confer survival under acute therapeutic stress, and only rarely depend on selection of genetic traits. Importantly, we found that aspecific and highly predictive cell state is associated with blast cellpersistence during induction treatment. Importantly, the persistence cell state predates treatment which suggests that selection is responsible for the emergence of the state. Specific cell surface markers are associated with the cell state, opening up the possibility of selective combination treatment using antibody-based therapy.

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