Somatic mutations accumulate inexorably in our cells as we age. Most of these mutations are harmless and accumulate passively. Yet, some somatic mutations that occur early in development can cause developmental disorders, and the accumulation of somatic mutations is responsible for cancer and might contribute to ageing. Despite its importance, our understanding of somatic mutation in normal tissues had remained obscure until recently because of technical difficulties in detecting mutations that are present in small numbers of cells.
In the 1990s, studies using p53-immunostaining reported the existence of small groups or clones of a few hundred cells carrying mutations in TP53 in sun-exposed skin [1]. Guided by these clone sizes, in 2015, we used deep targeted sequencing of small biopsies of epidermis to comprehensively detect mutant clones in normal skin from four donors aged 55–73 years [2]. This study revealed many surprises. On average, each cell in sun-exposed skin carried over 10,000 somatic mutations, most of which displayed the distinct signature of ultraviolet mutagenesis. More unexpectedly, we found evidence of positive selection of somatic mutations in at least six cancer genes, revealing that when mutations occur in key cancer genes, proliferation of these cells accelerates, leading to clonal expansions. We found that by middle age, sun-exposed skin is made up of thousands of such clones with one in every four cells carrying a positively selected mutation in a cancer gene.
Although these findings were striking, it seemed likely that sun-exposed skin was an exceptional tissue due to a lifetime of damage by ultraviolet light. To explore this, we then applied an analogous approach to study the mutational landscape in healthy esophagus in individuals ranging from 20 to 75 years of age [3]. To our surprise, we found that although the mutation rate in esophageal epithelium was ten-fold lower than that in sun-exposed skin, consistent with the absence of ultraviolet exposure, positive selection was stronger, leading to clones carrying mutations in cancer genes colonizing the majority of the esophagus by middle age. We detected positive selection driving clonal expansions in at least 14 cancer genes, with a density of several hundred densely packed mutant clones per square centimeter by middle age (Fig. 1). Remarkably, in most of the middle-aged and elderly patients studied, mutations in NOTCH1 and TP53 were found in more than 30% and in 5–20% of the cells, respectively. In an independent study published some weeks later, Yokoyama et al. [4] used exome and genome sequencing of histologically normal esophageal epithelium and reported very similar findings in a larger cohort of 139 healthy donors and cancer patients. The accumulation of somatic mutations was found to be most strongly associated with age [3, 4], with additional effects of heavy smoking and alcohol consumption [4]. This is consistent with the epidemiology of esophageal squamous carcinomas and it offers an early example of how sequencing studies of normal tissues can yield mechanistic insights into the mode of action of epidemiological risk factors.
These studies, together with the discovery of clonal hematopoiesis in blood [5] and recent reports and preprints on other tissues, including endometrium and colon [6,7,8,9,10], are rapidly changing our understanding of somatic mutation in normal human tissues.