Somatic mutations in healthy cells and age-associated diseases

Aging is a complex process that affects all living organisms. As we age, the biological functions are affected, resulting in a decline of the tissue and possibly age-related diseases. Several environmental and genetic factors have been suggested to contribute to aging. Among these factors, a progressive loss of genome integrity, caused by the occurrence of somatic mutations, is proposed as a cause of deterioration of cellular functions. The aim of this thesis was to analyze the effect of somatic mutations in healthy cells and analyze the contribution of somatic mutations to age-related diseases.

In paper I, we showed that satellite cells, stem cells of the skeletal muscle, accumulate 13 somatic mutations per genome per year during adult life. Although genes expressed in the skeletal muscle were protected from mutations by the DNA repair machinery, we observed that this protection was less efficient at increased age, resulting in higher mutation load in the exons of old compared to young satellite cells. A somatic mutation identified in a satellite cell was also detected in a small percentage of the cells of the muscle biopsy, suggesting that somatic mutations propagate from satellite cells to the differentiated muscle during adult age and might contribute to its age-related decline.

In paper II, we created a genetic atlas of somatic mutations in healthy cells from different tissues based on newly generated and publicly-available sequencing data. In contrast to the current view of a tissue-specific mutational profile, several cell types showed the same mutational profile despite coming from different tissues. Furthermore, two distinct cell types from the same tissue showed different mutational profiles and rates of mutation accumulation. Thanks to these data, we identified multiple factors influencing mutagen exposure and consequent mutational profiles. These factors include the cell´s localization within the tissue, the degree of differentiation and the presence of a protective stem cell niche. In addition, we identified an epithelial cell of the kidney that shows a unique distribution of mutations, characterized by mutation enrichment in highly transcribed genes. This pattern increases the chances of mutating a cancer-driver gene and is in agreement with an increased predisposition to cancer in this cell type. Finally, our analyses provide evidence of a decline of DNA-repair with aging.

In paper III, we identified somatic mutations in the brain of Alzheimer´s disease (AD) patients. Using ultra-deep sequencing and tailored bioinformatics analysis, we could detect low-frequency variants in bulk tissue. In total, 2.86 Mb of candidate genes and AD-linked genomic regions were included in the study, and 11 somatic single nucleotide variants (SNVs) were identified in AD brains, but none in non-AD brains. One variant was validated and predicted to affect transcription factor binding sites upstream of the CD55 gene, possibly contributing to AD through the regulation of the complement system.

In paper IV, we showed that patients with end-stage chronic kidney disease (CKD) express progerin within their arterial media, the same mutated form of the protein lamin A found in premature aging patients. Importantly, we could identify the mutation that causes progeria, the LMNA c.1824C>T, in DNA extracted from the arteries. In total, we could identify the progerin protein or the mutation in 34 of the 40 CKD patients. DNA damage and increased proliferation were detected in the CKD patients, indicating extensive vascular regeneration. Our result suggests that progenitor cells carrying LMNA c.1824C>T contribute to the vascular pathology and thereby to the disease progression observed in CKD patients.

In conclusion, the work presented in this thesis provides a new understanding of the contribution of mutation accumulation in healthy cells with possible implications for aging and age-associated diseases.

List of scientific papers

I. Somatic mutagenesis in satellite cells associates with human skeletal muscle aging. Irene Franco, Anna Johansson, Karl Olsson, Peter Vrtačnik, Pär Lundin, Hafdis T. Helgadottir, Malin Larsson, Gwladys Revêchon, Carla Bosia, Andrea Pagnani, Paolo Provero, Thomas Gustafsson, Helen Fischer, Maria Eriksson. Nature Communications. 2018 Feb 23;9(1):800.
https://doi.org/10.1038/s41467-018-03244-6

II. Basal and mutagen-driven somatic mutagenesis shapes the genome of healthy human cells. Irene Franco*, Hafdis T. Helgadottir*, Aldo Moggio, Malin Larsson, Peter Vrtačnik, Anna Johansson, Nina Norgren, Pär Lundin, David Mas-Ponte, Johan Nordström, Torbjörn Lundgren, Peter Stenvinkel, Lars Wennberg, Fran Supek, Maria Eriksson. *Equal contribution. [Submitted]

III. Somatic mutation that affects transcription factor binding upstream of CD55 in the temporal cortex of a late-onset Alzheimer disease patient. Hafdis T. Helgadottir, Pär Lundin, Emelie Wallén Arzt, Anna-Karin Lindström, Caroline Graff, Maria Eriksson. Human Molecular Genetics. 2019 Aug 15;28(16):2675-2685.
https://doi.org/10.1093/hmg/ddz085

IV. The Hutchinson-Gilford progeria syndrome mutation, LMNA c.1824C>T, is a somatic mutation in patients with chronic kidney disease. Hafdis T. Helgadottir*, Nikenza Viceconte*, Anna Witasp, Agustin Sola Carvajal, Gwladys Revêchon, Daniel Whisenant, Ece Somuncular, Anne-Sofie Johansson, Emelie Wallén Arzt, Anders Thorell, Anne Babler, Susanne Ziegler, Dagmara McGuinness, Sidinh Luc, Rafael Kramann, Paul G. Shiels, Annika Wernerson, Peter Stenvinkel, Maria Eriksson. *Equal contribution. [Manuscript]