Measures of genetic diversification in somatic tissues at bulk and single cell resolution suggest sources of unknown stochasticity

Abstract

AbstractIntra-tissue genetic heterogeneity is universal to both healthy and cancerous tissues. It emerges from the stochastic accumulation of somatic mutations throughout development and homeostasis. By combining population genetics theory and genomic information, genetic heterogeneity can be exploited to infer tissue organisation and dynamicsin vivo. However, many basic quantities, for example the dynamics of tissue specific stem cells remain difficult to quantify precisely. Here we show that single cell and bulk sequencing data inform on different aspects of the underlying stochastic processes. Bulk derived variant allele frequency spectra (VAF) show transitions from growing to constant stem cell populations with age in samples of healthy oesophagus epithelium. Single-cell mutational burden distributions allow a sample size independent measure of mutation and proliferation rates. Mutation rates in adult haematopietic stem cells are higher compared to inferences during development, suggesting additional proliferation independent effects. Furthermore, single cell derived VAF spectra contain information on the number of tissue specific stem cells. In haematopiesis, we find approximately 2 × 105HSCs, if all stem cells divide symmetrically. However, the single cell mutational burden distribution is over-dispersed compared to a model of Poisson distributed random mutations suggesting currently unknown processes induce additional stochasticity. Possible candidates for these processes may be occasional bursts of stem cell divisions, potentially in response to injury, or non-constant mutation rates either through environmental exposures or cell intrinsic variation.