Dissecting single-cell genomes through the clonal organoid technique

Abstract

Genomics: Culturing mini-organs improves the accuracy of single-cell sequencing The combination of three-dimensional tissue culturing and the latest DNA sequencing methods is allowing researchers to track genetic changes in single cells in ways that were previously impossible. A team led by Young Seok Ju from the Korea Advanced Institute of Science and Technology in Daejeon, South Korea, review some common techniques by which biologists catalog mutations at single-cell resolution. The most precise and informative, they suggest, involves first growing cells in the laboratory in three-dimensional aggregates known as organoids, which mimic tissue structures in the body, before running genome-sequencing assays. Although the tissue culturing adds extra work, the authors maintain that the additional biological material that organoids provide yields the most accurate mutational profile of the cells under investigation, which is of value in many research settings. The revolution in genome sequencing technologies has enabled the comprehensive detection of genomic variations in human cells, including inherited germline polymorphisms, de novo mutations, and postzygotic mutations. When these technologies are combined with techniques for isolating and expanding single-cell DNA, the landscape of somatic mosaicism in an individual body can be systematically revealed at a single-cell resolution. Here, we summarize three strategies (whole-genome amplification, microdissection of clonal patches in the tissue, and in vitro clonal expansion of single cells) that are currently applied for single-cell mutational analyses. Among these approaches, in vitro clonal expansion, particularly via adult stem cell-derived organoid culture technologies, yields the most sensitive and precise catalog of somatic mutations in single cells. Moreover, because it produces living mutant cells, downstream validation experiments and multiomics profiling are possible. Through the synergistic combination of organoid culture and genome sequencing, researchers can track genome changes at a single-cell resolution, which will lead to new discoveries that were previously impossible.