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Healthy Esophageal Tissue Often Marked by Cancer-Related Mutations

NEW YORK (GenomeWeb) – A new study suggests cells in healthy esophageal skin tissue can progressively acquire a wide-range of cancer-related mutations with age, leading to mutant clones in more than half of the tissue tested by midlife.

"After studying the genetics, we were shocked to see that the healthy esophagus was riddled with mutations," senior author Philip Jones, a researcher with the Wellcome Trust Sanger Institute, said in a statement. "We discovered that by the time an individual reaches middle age, they probably have more mutant than normal cells."

Jones and his colleagues from the Sanger Institute and the University of Cambridge performed ultra-deep targeted sequencing on dozens of cancer genes, and uncovered somatic mutations in more than 800 normal esophageal epithelial tissue samples from nine deceased organ transplant donors ranging in age from 20 to 75. Their results revealed a rise in somatic mutations in these genes as individuals aged, coupled with positive selection for cellular clones marked by mutations in 14 of the genes assessed.

The study, published online today in Science, "emphasizes how little we know about somatic evolution within normal tissues, a fundamental process that is likely to take place to varying degrees in every tissue of every species," Jones and his co-authors wrote. "Better understanding of the extent of somatic mutation and selection across tissues, in health and disease promises to provide insights into the origins of cancer and aging."

In particular, the team noted that NOTCH1 gene mutations were particularly prominent in the normal esophageal tissues tested, outpacing the rate of NOTCH1 mutations described in esophageal cancer samples.

"[W]e were surprised to find that a gene commonly associated with esophageal cancer, NOTCH1, was more mutated in normal cells than cancer cells," co-first author Joanna Fowler, a Sanger Institute researcher, said in a statement. "These results suggest that scientists may need to rethink the role of some cancer genes in the light of sequencing normal tissues."

The researchers focused on 74 cancer genes for their analyses, generating 870-fold average coverage for each of the 844 normal esophageal epithelium samples. They also did whole-genome sequencing to a depth of 37-fold, on average, to assess 21 of the samples containing large clonal populations in the initial sequencing data.

Using its analytical algorithm, the team uncovered more than 8,900 somatic mutations and 6,935 independent mutation events — alterations that included more cancer-associated variants than those described in normal, sun-exposed skin in samples from middle-aged individuals, despite far lower mutation rates overall.

Across the 14 recurrently mutated genes under positive selection, the researchers noted that 11 genes have previously been classified as esophageal squamous cell carcinoma drivers. In NOTCH1 alone, they identified 2,055 distinct coding mutations, most of which were non-synonymous.

In addition to the age-related rise in somatic mutations in the esophagus, the team noted that mutation selection strength seemed to differ from one individual to the next. With the genome-wide data, meanwhile, the group got a look at the mutational signatures present in the tissue, providing potential clues to the mutagenic processes that might have produced the alterations.

"Given the importance of these mutations to cancer, it is remarkable that we have been unaware of the extent of this phenomenon until now," Sanger researcher Iñigo Martincorena, the study's co-first author, added in a statement. "While the work sheds light on early cancer development, it also raises many questions about how these mutations may contribute to ageing and other diseases, opening interesting avenues for future research."