Preprint-biorxiv, 2020
Nature 2020

Short Summary: In this manuscript we utilize single cell DNA-sequencing to evaluate clonal abundance and mutation order in patient samples ranging from clonal hematopoiesis to relapsed/refractory leukemia. We combined scDNA-seq with oligonucleotide conjugated antibodies to resolve how genotype influences differentiation/immunophenotype.

Abstract: Myeloid malignancies, including acute myeloid leukaemia (AML), arise from the expansion of haematopoietic stem and progenitor cells that acquire somatic mutations. Bulk molecular profiling has suggested that mutations are acquired in a stepwise fashion: mutant genes with high variant allele frequencies appear early in leukaemogenesis, and mutations with lower variant allele frequencies are thought to be acquired later1-3. Although bulk sequencing can provide information about leukaemia biology and prognosis, it cannot distinguish which mutations occur in the same clone(s), accurately measure clonal complexity, or definitively elucidate the order of mutations. To delineate the clonal framework of myeloid malignancies, we performed single-cell mutational profiling on 146 samples from 123 patients. Here we show that AML is dominated by a small number of clones, which frequently harbour co-occurring mutations in epigenetic regulators. Conversely, mutations in signalling genes often occur more than once in distinct subclones, consistent with increasing clonal diversity. We mapped clonal trajectories for each sample and uncovered combinations of mutations that synergized to promote clonal expansion and dominance. Finally, we combined protein expression with mutational analysis to map somatic genotype and clonal architecture with immunophenotype. Our findings provide insights into the pathogenesis of myeloid transformation and how clonal complexity evolves with disease progression.

Recommended citation: Miles LA*, Bowman RL*, Merlinsky TR, Csete IS, Ooi AT, Durruthy-Durruthy R, Bowman M, Famulare C, Patel MA, Mendez P, Ainali C, Demaree B, Delley CL, Abate AR, Manivannan M, Sahu S, Goldberg AD, Bolton KL, Zehir A, Rampal R, Carroll MP, Meyer SE, Viny AD, Levine RL. "Single-cell mutation analysis of clonal evolution in myeloid malignancies." Nature. 2020 Nov;587(7834):477-482.