Comparison of mitochondrial mutation spectra in ageing human colonic epithelium and disease: absence of evidence for purifying selection in somatic mitochondrial DNA point mutations

Abstract

Human ageing has been predicted to be caused by the accumulation of molecular damage in cells and tissues. Somatic mitochondrial DNA (mtDNA) mutations have been documented in a number of ageing tissues and have been shown to be associated with cellular mitochondrial dysfunction. It is unknown whether there are selective constraints, which have been shown to occur in the germline, on the occurrence and expansion of these mtDNA mutations within individual somatic cells. Here we compared the pattern and spectrum of mutations observed in ageing human colon to those observed in the general population (germline variants) and those associated with primary mtDNA disease. The pathogenicity of the protein encoding mutations was predicted using a computational programme, MutPred, and the scores obtained for the three groups compared. We show that the mutations associated with ageing are randomly distributed throughout the genome, are more frequently non-synonymous or frameshift mutations than the general population, and are significantly more pathogenic than population variants. Mutations associated with primary mtDNA disease were significantly more pathogenic than ageing or population mutations. These data provide little evidence for any selective constraints on the occurrence and expansion of mtDNA mutations in somatic cells of the human colon during human ageing in contrast to germline mutations seen in the general population.

Figure 1. Gene location and types of mutations observed in ageing, population, and disease.

A: Gene location of mutations. Data are represented as the percentage of the total coding region mutations. Contingency analysis with Bonferroni correction for multiple testing was carried out on the frequencies of the changes in each gene type (ageing n = 117, population n = 182, disease n = 176). Thresholds for statistical significance are; ***<0.0003, ** 0.003, * = 0.017. B: Types of changes observed in ageing, population and disease. Data are represented as the percentage of the total coding region mutations. Contingency analysis with Bonferroni correction for multiple testing was carried out on the frequencies of the changes in each mutational category. Thresholds for statistical significance are; ***<0.0003, ** 0.003, * = 0.017.

Figure 2. Genetic consequences of mutations observed in ageing, population, and disease.

A: The percentage of changes which predict synonymous, non-synonymous and premature termination codons or frameshifts in protein encoding genes. Contingency analysis with Bonferroni correction for multiple testing was carried out on the frequencies of the changes in each gene type (ageing n = 81, population n = 155, disease n = 76). Thresholds for statistical significance are; ***<0.0003, ** 0.003, * = 0.017. B: Frequency of termination codon and frameshift mutations in inherited and sporadic disease-causing mtDNA mutations. Chi-squared analysis showed a significantly higher frequency such mutations in sporadic than inherited cases (p = 0.003).

Figure 3. MutPred pathogenicity scores of mtDNA mutations in ageing, populations, disease, and all possible mtDNA mutations.

A: The distribution of pathogenicity scores in ageing, populations, disease and all possible mutations. Results of Wilcoxon rank sum analysis are shown. With six tests, the threshold for significance is 0.05/6 = 0.008, ** = p<0.0017, *** = p<0.00017. B: The distribution of pathogenicity scores including synonymous mtDNA mutations which were assigned a pathogenicity score of 0, in ageing, population and disease. Results of Wilcoxon rank sum analysis are shown. With three tests the threshold for significance is 0.05/3 = 0.017, ** = p<0.003, *** = p<0.0003. C: The distribution of pathogenicity scores in sporadic and inherited disease-causing mtDNA mutations. Results of Wilcoxon rank sum test are shown,* p<0.05.