Cell lineage tracing in human epithelial tissues using mitochondrial DNA mutations as clonal markers

The study of cell lineages through heritable genetic lineage tracing is well established in experimental animals, particularly mice. While such techniques are not feasible in humans, we have taken advantage of the fact that the mitochondrial genome is highly prone to nonpathogenic mutations and such mutations can be used as clonal markers to identify stem cell derived clonal populations in human tissue sections. A mitochondrial DNA ( mtDNA ) mutation can spread by a stochastic process through the several copies of the circular genome in a single mitochondrion, and then through the many mitochondria in a single cell, a process called ‘genetic drift.’ This process takes many years and so is likely to occur only in stem cells, but once established, the fate of stem cell progeny can be followed. A cell having at least 80% of its mtDNA genomes bearing the mutation results in a demonstrable deficiency in mtDNA‐encoded cytochrome c oxidase ( CCO ), optimally detected in frozen tissue sections by dual‐color histochemistry, whereby CCO activity stains brown and CCO deficiency is highlighted by subsequent succinate dehydrogenase activity, staining the CCO ‐deficient areas blue. Cells with CCO deficiency can be laser captured and subsequent mtDNA sequencing can ascertain the nature of the mutation. If all cells in a CCO ‐deficient area have an identical mutation, then a clonal population has been identified; the chances of the same mutation initially arising in separate cells are highly improbable. The technique lends itself to the study of both normal epithelia and can answer several questions in tumor biology. WIREs Dev Biol 2016, 5:103–117. doi: 10.1002/wdev.203 This article is categorized under: Adult Stem Cells, Tissue Renewal, and Regeneration > Methods and Principles Adult Stem Cells, Tissue Renewal, and Regeneration > Tissue Stem Cells and Niches Adult Stem Cells, Tissue Renewal, and Regeneration > Stem Cells and Disease