Work

Retrospective single cell lineage tracing with highly mutable homopolymers

Year: 2026

Type: article

Abstract: Retrospective reconstruction of cell lineages from somatic mutations holds substantial promise for understanding development, tissue homeostasis, and disease. Yet, current approaches are often constrained by low marker density, technical noise, and incomplete molecular readouts that limit the resolution and accuracy of inferred lineages. Here, we present RETrace2, a single-cell dual-omic method for simultaneous lineage tracing and cell-type identification. By identifying and targeting highly mutable homopolymers, which we show are approximately twice as informative as conventional microsatellite repeats, combined with technical improvements to increase marker coverage and reduce experimental errors of reading and amplifying homopolymers, RETrace2 can trace lineage continuously at an estimated resolution of fewer than five cell divisions in microsatellite-unstable organisms. Simultaneously, sparse methylation profiles are obtained from the same cells for cell-type identification. We validate the method using in vitro ground-truth models and demonstrate its utility in vivo by reconstructing multi-organ lineage trees from the brain, kidney and liver of Msh2-deficient mice. Cell lineage reconstruction can reveal developmental histories, but current methods are limited by marker density and accuracy. Here, the authors develop RETrace2, a dual‑omic single‑cell approach that combines highly mutable homopolymer markers with methylation profiling to enable high‑resolution lineage tracing and cell‑type identification.

Source: Nature Communications

DOI: 10.1038/s41467-026-79104-5