Scalable methylome-transcriptome profiling resolves clonal organization in human hematopoiesis

Human tissue maintenance and remodeling can be better understood by linking clonal ancestry to molecular state. Researchers have developed Droplet-MT, a method for simultaneous transcriptome and methylome profiling of up to 10,000 cells per library. By analyzing methylation epimutations, mutation-independent clonal reconstruction becomes possible from high-coverage methylomes.

Reference-based label transfer assigns cells to known clones with just 0.2% CpG coverage, cutting down on sequencing costs. This approach allows for the aggregation of somatic variants, providing genetic annotations without the need for additional single-cell genotyping.

Using this technique, researchers analyzed 21,000 paired profiles from healthy blood samples and patients with acute myeloid leukemia. The framework successfully identified small and expanded clones with diverse lineage outputs. In leukemia cases, the method distinguished alterations in malignant clonal abundance, state remodeling within persistent clones, and the recovery of healthy polyclonal hematopoiesis.

Notably, malignant monocytes remained transcriptionally and epigenetically distinct from healthy and recovery-associated cells even after treatment-related remodeling. Droplet-MT provides a scalable solution for analyzing human tissues by connecting clonal organization with molecular state and enabling retrospective genetic annotation.