Tracing the transformation of hematopoietic stem cells into leukemic cells using single-cell multi-omics

Cancer is a leading cause of death worldwide. While most cells have a limited lifespan, cancer stem cells can self-renew indefinitely and are thought to drive disease initiation, progression, and relapse. A major challenge in the development of chemotherapies is the necessity to specifically target these cancer-driving stem cells while sparing their healthy counterparts, which are phenotypically very similar. While non-genetic heterogeneity and the presence of stem cell hierarchies have significant clinical implications, the genetic het-erogeneity that contributes to a cancer’s ability to resist drug treatment represents a major obstacle in devising effective therapeutics. Using acute myeloid leukemia as a model system, we investigate the transformation of healthy hematopoietic stem cells into cancer stem cells. By combining single-cell transcriptomics and mutation-based lineage tracing, we single out the putative cancer "cells-of-origin" and pinpoint the mutations that precede and drive oncogenic transformation. We first apply single-cell transcriptomics to classify blood cells according to their differentiation state and cell type. Then using mutations detected in RNA, we identify healthy, pre-leukemic, and leukemic clones to create maps of their evolutionary trajectories and elucidate the patterns in clonal structure underlying leukemia. Taken together, we characterize blood cancer stem cells with high transcriptomic resolution. We further demonstrate the ability to detect clonal mitochondrial and nuclear mutations in single cells, allowing for the computational delineation of the order in which mutations arose, the assignment of cells to clones, and the discovery of novel clones. This approach also identifies differentiation blocks and unique gene-expression profiles present in leukemic stem cells. These achievements highlight the utility of single-cell sequencing technologies in answering fundamental questions in the field of cancer biology and beyond