The unexpected landscape of in vivo somatic mutation in a human epithelial cell lineage

Abstract

Few data exist on somatic mutation in the epithelial cell lineages that play a central role in human biology and disease. To delineate the "landscape" of somatic mutation in a human epithelial cell lineage, we determined the frequency and molecular nature of somatic mutations occurring in vivo in the X-linked HPRT gene of kidney tubular epithelial cells. Kidney epithelial mutants were frequent (range 0.5 to 4.2 x 10(-4)) and contained a high proportion of unreported HPRT base substitutions, -1-bp deletions and multiple mutations. This spectrum of somatic mutation differed from HPRT mutations identified in human peripheral blood T lymphocytes and from germ-line HPRT mutations identified in Lesch-Nyhan syndrome or hyperuricemia patients. Our results indicate that DNA damage and mutagenesis may have unusual or mechanistically interesting features in kidney tubular epithelium, and that somatic mutation may play a more important role in human kidney disease than has been previously appreciated.

Figure 1

Newly identified human somatic HPRT −1-bp deletions and base substitutions in kidney tubular epithelial cells. The central rectangle represents the HPRT ORF with previously unreported single base deletions shown above and base substitutions below the rectangle. Exon boundaries are indicated by vertical lines in the cDNA; individual exons are numbered. Deleted or substituted bases are indicated together with the mutation position in the human HPRT cDNA, where the A of the cDNA ATG start codon is position 1. Gray shading indicates substitutions that identify mutable sites. Changes are given by using the sense (coding) strand of human HPRT cDNA as a reference.

Figure 2

Distribution of multiple mutations in the human HPRT gene. (A) The probability distribution for distances between pairs of mutations occurring uniformly and independently across the portion of the human HPRT gene containing the nine HPRT exons (expected hypothetical distribution) is shown as a filled triangle falling monotonically from shortest and longest distances. In contrast, the distribution of pairs of mutations that fall in or immediately adjacent to one or more HPRT exon (expected observable distribution) is highly nonuniform, as indicated by the jagged line. (B) Proportion of multiple mutation pairs from kidney and peripheral blood T lymphocytes (23) as a function of distance between mutations versus expectation from A. The distribution of distances between mutations differed from expectation for kidney (P < 4 × 10 ⁻⁴) although not for T lymphocytes (P = 0.15; results not shown), as did the proportion of closely spaced kidney mutations separated by <15 bp (*, P = 0.004, versus 0.07–0.96 for other length classes).