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

Lower Intake of Saturated Fatty Acids Is Associated with Improved Lipid Profile in a 6-Year-Old Nationally Representative Population.

To access publisher's full text version of this article, please click on the hyperlink in Additional Links field or click on the hyperlink at the top of the page marked DownloadTo strengthen the organization of new national dietary surveys and interventions in childhood, our aim was to study macronutrient intake and blood lipid profile at 6 years of age by comparing results from two earlier population-based cohorts. Subjects were n = 131 and n = 162 in the years 2001-2002 and 2011-2012, respectively. Three-day weighed food records were used to estimate diet and calculate nutrient intake. Total cholesterol, HDL-cholesterol and triacylglycerol were measured in serum and LDL-cholesterol was calculated. The average intake of saturated fatty acids (SFA) and trans FA was lower in 2011-2012 than 2001-2002 (13.3E% vs. 14.7E%, p < 0.001, and 0.8E% vs. 1.4E%, p < 0.001, respectively), replaced by a higher intake of unsaturated fatty acids. Total cholesterol and LDL-cholesterol were significantly lower in 2011-2012 than 2001-2002 (4.6 vs. 4.4 mmol/L, p = 0.003 and 2.8 vs. 2.5 mmol/L, p < 0.001, respectively). In a multiple linear regression model, one E% increase in SFA intake was related to a 0.03 mmol/L increase in LDL cholesterol (p = 0.04). A lower intake of saturated and trans fatty acids, replaced by unsaturated fatty acids, may have contributed to an improved lipid profile in a healthy 6-year-old population. Biological data for analysis of blood lipids are important in national dietary surveys in healthy children to monitor important health outcomes of interventions

Accumulation of Progerin Affects the Symmetry of Cell Division and Is Associated with Impaired Wnt Signaling and the Mislocalization of Nuclear Envelope Proteins

Hutchinson-Gilford progeria syndrome (HGPS) is the result of a defective form of the lamin A protein called progerin. While progerin is known to disrupt the properties of the nuclear lamina, the underlying mechanisms responsible for the pathophysiology of HGPS remain less clear. Previous studies in our laboratory have shown that progerin expression in murine epidermal basal cells results in impaired stratification and halted development of the skin. Stratification and differentiation of the epidermis is regulated by asymmetric stem cell division. Here, we show that expression of progerin impairs the ability of stem cells to maintain tissue homeostasis as a result of altered cell division. Quantification of basal skin cells showed an increase in symmetric cell division that correlated with progerin accumulation in HGPS mice. Investigation of the mechanisms underlying this phenomenon revealed a putative role of Wnt/beta-catenin signaling. Further analysis suggested an alteration in the nuclear translocation of beta-catenin involving the inner and outer nuclear membrane proteins, emerin and nesprin-2. Taken together, our results suggest a direct involvement of progerin in the transmission of Wnt signaling and normal stem cell division. These insights into the molecular mechanisms of progerin may help develop new treatment strategies for HGPS.Peer reviewe

Assessment of osteoarthritis candidate genes in a meta-analysis of nine genome-wide association studies

OBJECTIVE: To assess candidate genes for association with osteoarthritis (OA) and identify promising genetic factors and, secondarily, to assess the candidate gene approach in OA. METHODS: A total of 199 candidate genes for association with OA were identified using Human Genome Epidemiology (HuGE) Navigator. All of their single-nucleotide polymorphisms (SNPs) with an allele frequency of >5% were assessed by fixed-effects meta-analysis of 9 genome-wide association studies (GWAS) that included 5,636 patients with knee OA and 16,972 control subjects and 4,349 patients with hip OA and 17,836 control subjects of European ancestry. An additional 5,921 individuals were genotyped for significantly associated SNPs in the meta-analysis. After correction for the number of independent tests, P values less than 1.58 × 10(-5) were considered significant. RESULTS: SNPs at only 2 of the 199 candidate genes (COL11A1 and VEGF) were associated with OA in the meta-analysis. Two SNPs in COL11A1 showed association with hip OA in the combined analysis: rs4907986 (P = 1.29 × 10(-5) , odds ratio [OR] 1.12, 95% confidence interval [95% CI] 1.06-1.17) and rs1241164 (P = 1.47 × 10(-5) , OR 0.82, 95% CI 0.74-0.89). The sex-stratified analysis also showed association of COL11A1 SNP rs4908291 in women (P = 1.29 × 10(-5) , OR 0.87, 95% CI 0.82-0.92); this SNP showed linkage disequilibrium with rs4907986. A single SNP of VEGF, rs833058, showed association with hip OA in men (P = 1.35 × 10(-5) , OR 0.85, 95% CI 0.79-0.91). After additional samples were genotyped, association at one of the COL11A1 signals was reinforced, whereas association at VEGF was slightly weakened. CONCLUSION: Two candidate genes, COL11A1 and VEGF, were significantly associated with OA in this focused meta-analysis. The remaining candidate genes were not associated

Germline sequence variants in TGM3 and RGS22 confer risk of basal cell carcinoma.

To access publisher's full text version of this article. Please click on the hyperlink in Additional Links field.To search for new sequence variants that confer risk of cutaneous basal cell carcinoma (BCC), we conducted a genome-wide association study of 38.5 million single nucleotide polymorphisms (SNPs) and small indels identified through whole-genome sequencing of 2230 Icelanders. We imputed genotypes for 4208 BCC patients and 109 408 controls using Illumina SNP chip typing data, carried out association tests and replicated the findings in independent population samples. We found new BCC susceptibility loci at TGM3 (rs214782[G], P = 5.5 × 10(-17), OR = 1.29) and RGS22 (rs7006527[C], P = 8.7 × 10(-13), OR = 0.77). TGM3 encodes transglutaminase type 3, which plays a key role in production of the cornified envelope during epidermal differentiation.Red Tematica de Investigacion Cooperative en Cancer RD06/0020/1054 Danish Cancer Society "Europe Against Cancer": European Prospective Investigation into Cancer and Nutrition (EPIC) deCODE Genetics/AMGE

Genome-wide association and Mendelian randomisation analysis provide insights into the pathogenesis of heart failure

Heart failure (HF) is a leading cause of morbidity and mortality worldwide. A small proportion of HF cases are attributable to monogenic cardiomyopathies and existing genome-wide association studies (GWAS) have yielded only limited insights, leaving the observed heritability of HF largely unexplained. We report results from a GWAS meta-analysis of HF comprising 47,309 cases and 930,014 controls. Twelve independent variants at 11 genomic loci are associated with HF, all of which demonstrate one or more associations with coronary artery disease (CAD), atrial fibrillation, or reduced left ventricular function, suggesting shared genetic aetiology. Functional analysis of non-CAD-associated loci implicate genes involved in cardiac development (MYOZ1, SYNPO2L), protein homoeostasis (BAG3), and cellular senescence (CDKN1A). Mendelian randomisation analysis supports causal roles for several HF risk factors, and demonstrates CAD-independent effects for atrial fibrillation, body mass index, and hypertension. These findings extend our knowledge of the pathways underlying HF and may inform new therapeutic strategies

Lower Intake of Saturated Fatty Acids Is Associated with Improved Lipid Profile in a 6-Year-Old Nationally Representative Population

To strengthen the organization of new national dietary surveys and interventions in childhood, our aim was to study macronutrient intake and blood lipid profile at 6 years of age by comparing results from two earlier population-based cohorts. Subjects were n = 131 and n = 162 in the years 2001–2002 and 2011–2012, respectively. Three-day weighed food records were used to estimate diet and calculate nutrient intake. Total cholesterol, HDL-cholesterol and triacylglycerol were measured in serum and LDL-cholesterol was calculated. The average intake of saturated fatty acids (SFA) and trans FA was lower in 2011–2012 than 2001–2002 (13.3E% vs. 14.7E%, p < 0.001, and 0.8E% vs. 1.4E%, p < 0.001, respectively), replaced by a higher intake of unsaturated fatty acids. Total cholesterol and LDL-cholesterol were significantly lower in 2011–2012 than 2001–2002 (4.6 vs. 4.4 mmol/L, p = 0.003 and 2.8 vs. 2.5 mmol/L, p < 0.001, respectively). In a multiple linear regression model, one E% increase in SFA intake was related to a 0.03 mmol/L increase in LDL cholesterol (p = 0.04). A lower intake of saturated and trans fatty acids, replaced by unsaturated fatty acids, may have contributed to an improved lipid profile in a healthy 6-year-old population. Biological data for analysis of blood lipids are important in national dietary surveys in healthy children to monitor important health outcomes of interventions

Unravelling genetic variants of a swedish family with high risk of prostate cancer

Abstract Background Prostate cancer is the most prevalent cancer in men worldwide. It is a polygenic disease with a substantial proportion of heritability. Identification of novel candidate biomarkers is crucial for clinical cancer prevention and the development of therapeutic strategies. Here, we describe the analysis of rare and common genetic variants that can predispose to the development of prostate cancer. Methods Whole-genome sequencing was performed on germline DNA of five Swedish siblings which were diagnosed with prostate cancer. The high-risk variants were identified setting the minor allele frequency  10 and if tested in PRACTICAL, OR > 1.5, while the low-risk variants were identified minor allele frequency > 0.01, CADD > 10 and if tested in PRACTICAL, OR > 1.1. Results We identified 38 candidate high-risk gene variants and 332 candidate low-risk gene variants, where 2 and 14 variants were in coding regions, respectively, that were shared by the brothers with prostate cancer. Conclusions This study expanded the knowledge of potential risk factor candidates involved in hereditary and familial prostate cancer. Our findings can be beneficial when applying targeted screening in families with a high risk of developing the disease