Analysis of somatic mutations identifies signs of selection during in vitro aging of primary dermal fibroblasts

• Published in: Aging cell Vol. 18; no. 6; pp. e13010 - n/a
• Main Authors: Narisu, Narisu, Rothwell, Rebecca, Vrtačnik, Peter, Rodríguez, Sofía, Didion, John, Zöllner, Sebastian, Erdos, Michael R., Collins, Francis S., Eriksson, Maria
• Format: Journal Article
• Language: English
• Published: England John Wiley & Sons, Inc 01.12.2019; John Wiley and Sons Inc
• Subjects: Adolescent; Age; Aged, 80 and over; Aging; aging cell; Alleles; Analysis; BRCA2 protein; Cell culture; cell mosaicism; Cells, Cultured; Cellular Senescence - genetics; Child; Child, Preschool; Complementation; DNA - genetics; Exons; Female; Fibroblasts; Fibroblasts - cytology; Fibroblasts - metabolism; Gene frequency; Genes; Genetic aspects; Genetic drift; genome instability; Humans; Male; Mathematical models; molecular biology of aging; Mutation; Nucleotide sequence; Original; Positive selection; Progeria; Sequence Analysis, RNA; Skin - cytology; Skin - metabolism; somatic mutation; tissue heterogeneity; Xeroderma pigmentosum; tissue heterogeneity; genome instability; molecular biology of aging; positive selection; cell mosaicism; aging cell; somatic mutation
• ISSN: 1474-9718; 1474-9726; 1474-9726
• DOI: 10.1111/acel.13010

Somatic mutations are critical for cancer development and may play a role in age‐related functional decline. Here, we used deep sequencing to analyze the prevalence of somatic mutations during in vitro cell aging. Primary dermal fibroblasts from healthy subjects of young and advanced age, from Hutchinson–Gilford progeria syndrome and from xeroderma pigmentosum complementation groups A and C, were first restricted in number and then expanded in vitro. DNA was obtained from cells pre‐ and post‐expansion and sequenced at high depth (1656× mean coverage), over a cumulative 290 kb target region, including the exons of 44 aging‐related genes. Allele frequencies of 58 somatic mutations differed between the pre‐ and post‐cell culture expansion passages. Mathematical modeling revealed that the frequency change of three of the 58 mutations was unlikely to be explained by genetic drift alone, indicative of positive selection. Two of these three mutations, CDKN2A c.53C>T (T18M) and ERCC8 c.*772T>A, were identified in cells from a patient with XPA. The allele frequency of the CDKN2A mutation increased from 0% to 55.3% with increasing cell culture passage. The third mutation, BRCA2 c.6222C>T (H2074H), was identified in a sample from a healthy individual of advanced age. However, further validation of the three mutations suggests that other unmeasured variants probably provide the selective advantage in these cells. Our results reinforce the notions that somatic mutations occur during aging and that some are under positive selection, supporting the model of increased tissue heterogeneity with increased age. De novo somatic mutations are identified in vitro cell culture experiments. We discover three mutations in aging‐related genes displaying signs of positive selection, supporting the model of increased tissue heterogeneity with increased age.