COMPUTATIONAL ASSESSMENT OF GENOMIC AND FUNCTIONAL HETEROGENEITY IN ACUTE MYELOID LEUKAEMIA

Acute myeloid leukaemia (AML) is the most diffused leukaemia in adults and represents a disease with an urgent medical need as 50-60% of patients relapse within 3 years after diagnosis. Intra-tumour heterogeneity (ITH), both at biological and genetic level, is a crucial feature of AMLs which results necessary for tumour maintenance and drug resistance. From the biological side, AML is hierarchically organised, with, at the top level, leukaemia stem cells (LSCs), a rare cell population having self-renewal, differentiation and quiescence properties. Quiescent LSCs can be less sensitive to radiation and chemotherapy acting as a source for leukaemia relapse. Genetically, AMLs harbour patient-specific combinations of different driver mutations, which are organised within individual cases in sub-clones with distinct fitness. In our experimental plan, we hypothesised that clonal evolution dynamics of relapsing AMLs are characterised by the selective expansion of quiescent low-frequency sub-clones present within the primary LSC population, which serve as the genomic and functional reservoir of the tumour. We performed whole-exome sequencing (WES) and longitudinal clonal evolution analyses of i) a cohort of 30 AML patients, ii) xenotransplanted human leukaemias and iii) functionally isolated leukaemic subpopulations with diverse proliferation histories. We identified 3 clonal evolution patterns in our cohort: stable, “gain of clones” and “loss of clones”, at relapse. We dissected the evolutionary dynamics of the “gain of clones” group performing high sensitivity sequencing (HSS) and found low frequency sub-clonal mutations in primary AML, some of which were selected and expanded after chemotherapy. We lead back the origin of these sub-clones within the quiescent leukaemic subpopulation. Furthermore, we assessed transcriptional ITH of leukaemic subpopulations with diverse proliferation histories of two patients’ xenografts by single cell (sc) RNA sequencing and identified a set of markers genes potentially associated with leukaemogenesis and quiescence. All together our findings point out that the clonal architecture of primary AML is more complex than what previously thought and are the first direct proof showing that relapsing AMLs are shaped by expansion of low-frequency preexisting clones. These clones appear to be sustained by the quiescent LSC pool. We expect that the outcome of our studies will provide new insights into the mechanisms of disease progression and treatment response in AML, and potentially points toward novel therapeutic approaches.