Integrative analysis of gene expression, DNA methylation, physiological traits, and genetic variation in human skeletal muscle.

We integrate comeasured gene expression and DNA methylation (DNAme) in 265 human skeletal muscle biopsies from the FUSION study with >7 million genetic variants and eight physiological traits: height, waist, weight, waist-hip ratio, body mass index, fasting serum insulin, fasting plasma glucose, and type 2 diabetes. We find hundreds of genes and DNAme sites associated with fasting insulin, waist, and body mass index, as well as thousands of DNAme sites associated with gene expression (eQTM). We find that controlling for heterogeneity in tissue/muscle fiber type reduces the number of physiological trait associations, and that long-range eQTMs (>1 Mb) are reduced when controlling for tissue/muscle fiber type or latent factors. We map genetic regulators (quantitative trait loci; QTLs) of expression (eQTLs) and DNAme (mQTLs). Using Mendelian randomization (MR) and mediation techniques, we leverage these genetic maps to predict 213 causal relationships between expression and DNAme, approximately two-thirds of which predict methylation to causally influence expression. We use MR to integrate FUSION mQTLs, FUSION eQTLs, and GTEx eQTLs for 48 tissues with genetic associations for 534 diseases and quantitative traits. We identify hundreds of genes and thousands of DNAme sites that may drive the reported disease/quantitative trait genetic associations. We identify 300 gene expression MR associations that are present in both FUSION and GTEx skeletal muscle and that show stronger evidence of MR association in skeletal muscle than other tissues, which may partially reflect differences in power across tissues. As one example, we find that increased RXRA muscle expression may decrease lean tissue mass.

Quality of life along the diabetes continuum: a cross-sectional view of health-related quality of life and general health status in middle-aged and older Finns.

PURPOSE: To examine the general health status and health-related quality of life (HRQOL) along the diabetes continuum of middle-aged and older Finns, and to determine the glucose metabolism stage by which the HRQOL has decreased noticeably. METHODS: The cross-sectional sample consisted of 920 persons aged 51-75 from the general population in a single municipality in a rural area of Eastern Finland. Data were adjusted for age, sex, smoking history, current alcohol consumption, employment and marital status. The HRQOL and health status were evaluated using two preference-based HRQOL instruments, 15D and SF-6D, and one health profile instrument, 36-Item Short Form Health Survey (SF-36). RESULTS: Individuals with impaired glucose tolerance (IGT) and type 2 diabetes had noticeably low mean SF-6D, 15D and general health status. The decrease in overall HRQOL was mainly due to a decline in the physical dimensions of HRQOL. The adjusted odds ratios (95% CI) for having noticeably low HRQOL on SF-6D, 15D and general health dimension of SF-36 associated with IGT were 1.95 (1.18-3.25), 1.35 (0.84-2.18) and 2.00 (1.21-3.29), respectively. CONCLUSIONS: The progression along the diabetes continuum was significantly associated with a decrease in HRQOL and health status. Furthermore, the data indicate that when a person is detected to have IGT, the HRQOL and general health status have already diminished noticeably. The prevailing evidence suggests that detection and intervention before a patient develops IGT is essential in order to minimize the loss of quality of life and quality-adjusted life years.

Erectile dysfunction as a predictive indicator of asymptomatic diabetes and prediabetes.

AIMS: Both erectile dysfunction (ED) and diabetes (DM) are common health problems that share risk factors. The aim of this study was to investigate whether ED can predict glucose metabolism dysfunctions in men at the primary care level. METHODS: An 11-year population-based cohort study was conducted in men born between 1933 and 1956. The baseline survey was conducted in 2007-2008, with a follow-up examination 11 years later. The International Index of Erectile Function (IIEF-5) questionnaire was used to assess erectile function. Dysglycemia was evaluated using and a 2-hour oral glucose tolerance test (2hOGTT), in combination with health registry data. RESULTS: At baseline, men with ED but without a history of known DM exhibited a significantly higher prevalence of undetected DM, odds ratio (OR) 4.7 (95 % CI 1.6, 14.4), and preDM, OR 1.9 (1.1, 3.2), compared with men without ED. Over an 11-year follow-up period, a significantly increased cumulative incidence of DM was observed in men who reported symptoms of ED at the start of the study. CONCLUSIONS: The symptoms of ED appear to be an early warning sign of existing DM and preDM and predict an increased risk of developing abnormal glucose metabolism in the future.

The health-related quality-of-life impact of nocturnal awakenings in the middle-aged and older Finnish population.

PURPOSE: The aim of the study is to examine the health-related quality-of-life (HRQOL) impact of the nocturnal awakenings and the duration of the sleep in the Finnish middle-aged and older population. METHODS: Cross-sectional sample consisted of 823 community-dwelling persons aged 55-75 living in a single municipality in a rural area of Eastern Finland. Frequency of the nocturnal awakenings was dichotomized as reporting "frequent," if the participant reported subjectively awakening "often" or "very often," and "infrequent" if the participant reported awakening "sometimes" or less frequently. HRQOL was measured with a preference-based HRQOL-index instrument, 15D. Analyses were adjusted for gender, BMI, morbidities, depression, employment and marital status, current smoking and drinking, exercise, recommendation to exercise from a health care professional, and subjective opinion about own exercise habits. RESULTS: Frequent nocturnal awakenings had statistically and clinically significant negative impact on HRQOL, the mean (SE) adjusted marginal HRQOL impact being -0.0416 (0.006). More than 10 and less than 6.5 h of daily sleep were associated with higher probability of having low HRQOL, adjusted odd ratios (95 % CI) being 2.65 (1.11-6.33) and 2.65 (1.55-4.52), respectively. However, the changes in daily sleep duration did not have noticeable influence on the significance or magnitude of the negative HRQOL impact of the frequent nocturnal awakenings. CONCLUSIONS: Nocturnal awakenings displayed a strong independent association with decreased HRQOL. The findings suggest that both clinicians and researchers should pay closer attention to nocturnal awakenings and other sleep problems in order to find ways to improve the quality of life in individuals with such conditions.

Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation.

Skeletal muscle, the largest human organ by weight, is relevant to several polygenic metabolic traits and diseases including type 2 diabetes (T2D). Identifying genetic mechanisms underlying these traits requires pinpointing the relevant cell types, regulatory elements, target genes, and causal variants. Here, we used genetic multiplexing to generate population-scale single nucleus (sn) chromatin accessibility (snATAC-seq) and transcriptome (snRNA-seq) maps across 287 frozen human skeletal muscle biopsies representing 456,880 nuclei. We identified 13 cell types that collectively represented 983,155 ATAC summits. We integrated genetic variation to discover 6,866 expression quantitative trait loci (eQTL) and 100,928 chromatin accessibility QTL (caQTL) (5% FDR) across the five most abundant cell types, cataloging caQTL peaks that atlas-level snATAC maps often miss. We identified 1,973 eGenes colocalized with caQTL and used mediation analyses to construct causal directional maps for chromatin accessibility and gene expression. 3,378 genome-wide association study (GWAS) signals across 43 relevant traits colocalized with sn-e/caQTL, 52% in a cell-specific manner. 77% of GWAS signals colocalized with caQTL and not eQTL, highlighting the critical importance of population-scale chromatin profiling for GWAS functional studies. GWAS-caQTL colocalization showed distinct cell-specific regulatory paradigms. For example, a C2CD4A/B T2D GWAS signal colocalized with caQTL in muscle fibers and multiple chromatin loop models nominated VPS13C, a glucose uptake gene. Sequence of the caQTL peak overlapping caSNP rs7163757 showed allelic regulatory activity differences in a human myocyte cell line massively parallel reporter assay. These results illuminate the genetic regulatory architecture of human skeletal muscle at high-resolution epigenomic, transcriptomic, and cell state scales and serve as a template for population-scale multi-omic mapping in complex tissues and traits.

Ocular surface health of the Finnish elderly population.

PURPOSE: The aim of this study was to describe the clinical ocular surface characteristics in a population-based sample of Finnish elderly people. METHODS: This cross-sectional study included 601 subjects (335 females, 266 males) born between the years 1933-1956 and living in Savitaipale, Finland. Ocular surface health was evaluated using a comprehensive set of diagnostic tests. Previous dry eye (DE) diagnosis and history of drug treatment of DE were also recorded. Differences between sexes were estimated with Wilcoxon rank sum test and Fisher's exact test. RESULTS: Overall, 10% and 33% of people displayed signs of DE and ocular surface disease (OSD), respectively, and 30% had been previously diagnosed with DE and 36% used some form of drugs for DE. Men displayed more severe signs of meibomian gland dysfunction, blepharitis and conjunctival redness (p < 0.001), while women had higher scores in corneal staining (p = 0.005) and OSD Index (p < 0.001). CONCLUSION: Signs of OSD and DE are common among the Finnish elderly population. However, the diagnosis is affected by the diagnostic criteria used and significant differences exist between sexes. Although women were more frequently diagnosed with DE and OSD and experienced more ocular surface irritation, men had more often lid and meibomian gland-related issues. The current diagnostic criteria of DE pose a risk of misclassifying men, who commonly display less severe symptoms in comparison with women yet exhibit more severe clinical signs associated especially with the lid margin.

A Natural History of Erectile Dysfunction in Elderly Men: A Population-Based, Twelve-Year Prospective Study.

There is a wide variation in the development and course of erectile dysfunction (ED) in men, which confirms the need for prospective studies. We conducted a cross-sectional analysis among the general male population at the baseline (n = 359) and in a follow-up survey (n = 218) 12 years later. The prospective 12-year study included 189 men. ED was assessed using the International Index of Erectile Function questionnaire. The mean age of the participants was 62.0 years at the baseline, while at the 12-year follow-up it was 71.6 years. The crude prevalence of ED was 61.6% at the baseline and 78.9% at the follow-up, and the prevalence tended to increase with age. All of the men aged 75 years or more had at least mild ED. The incidence of ED in every thousand person years was 53.5. A total of 54.5% of the men experienced ED progression, while 39.2% reported no changes in erectile function, and 6.3% experienced ED regression during the 12-year study. The likelihood of ED progression was higher in the older compared with younger age group (odds ratio, OR 5.2 (95% CI: 1.1-26.2)), and the likelihood of ED regression was lower among men with increased depression symptoms (OR 0.3 (95% CI: 0.1-0.6)) and among men with a decreased interest in their sexual life (OR 0.1 (95% CI: 0.0-0.6)). Lifestyle factors such as the consumption of alcohol and smoking were not significantly associated with ED.

Elevated One-Hour Post-Load Glucose Is Independently Associated with Albuminuria: A Cross-Sectional Population Study.

The purpose of this study was to examine and compare the associations between albuminuria and fasting (FPG), 1 h post-load (1 h PG) and 2 h post-load plasma glucose (2 h PG) in an oral glucose tolerance test (OGTT). A total of 496 people free of known diabetes (mean age 72 years) participated in the examinations including the OGTT with plasma glucose measurements at 0, 1, and 2 h and levels of HbA1c. Albuminuria was determined by the urinary albumin-to-creatinine ratio and was defined as ≥3.0 mg/mmol. Compared with those without albuminuria, participants with albuminuria had significantly higher 1 h PG and 2 h PG levels, but not FPG or HbA1c levels. An elevated 1 h PG increased the estimated odds ratio of albuminuria more than three times in people with prediabetic 1 h PG (8.6-11.5 mmol/L: OR 3.60; 95% CI 1.70-7.64) and diabetic 1 h PG (≥11.6 mmol/L: OR 3.05; 95% CI 1.29-7.23). After adjusting for blood pressure and age, the association of elevated 1 h PG with albuminuria remained significant. Prediabetic or diabetic FPG, 2 h PG, or HbA1c did not have a statistically significant association with albuminuria. These findings suggest that 1 h PG seems to be the best glycemic parameter and is useful in recognizing persons with an elevated risk of early kidney disease due to hyperglycemia.

Variations in the G6PC2/ABCB11 genomic region are associated with fasting glucose levels.

Identifying the genetic variants that regulate fasting glucose concentrations may further our understanding of the pathogenesis of diabetes. We therefore investigated the association of fasting glucose levels with SNPs in 2 genome-wide scans including a total of 5,088 nondiabetic individuals from Finland and Sardinia. We found a significant association between the SNP rs563694 and fasting glucose concentrations (P = 3.5 x 10(-7)). This association was further investigated in an additional 18,436 nondiabetic individuals of mixed European descent from 7 different studies. The combined P value for association in these follow-up samples was 6.9 x 10(-26), and combining results from all studies resulted in an overall P value for association of 6.4 x 10(-33). Across these studies, fasting glucose concentrations increased 0.01-0.16 mM with each copy of the major allele, accounting for approximately 1% of the total variation in fasting glucose. The rs563694 SNP is located between the genes glucose-6-phosphatase catalytic subunit 2 (G6PC2) and ATP-binding cassette, subfamily B (MDR/TAP), member 11 (ABCB11). Our results in combination with data reported in the literature suggest that G6PC2, a glucose-6-phosphatase almost exclusively expressed in pancreatic islet cells, may underlie variation in fasting glucose, though it is possible that ABCB11, which is expressed primarily in liver, may also contribute to such variation.

22-year trends in dysglycemia and body mass index: A population-based cohort study in Savitaipale, Finland.

AIMS: We describe a 22-year prospective observational population-based study that determined the prevalence and incidence of type 2 diabetes (T2D) and intermediate hyperglycaemia (IH), obesity, hypertension, and disorders of lipid metabolism in a middle-age population in the Finnish municipality of Savitaipale. METHODS: 1151 people participated in the baseline survey in 1996-1999, following two follow-up examinations, in 2007-2008 and 2018-2019. Follow-up studies comprised clinical measurements, 2-h oral glucose tolerance test and other biochemistry, questionnaires, and registry data. RESULTS: The prevalence of T2D quadrupled to 27% and the proportion of normoglycemic people decreased from 73% to 44% while IH increased only slightly during the 22-year follow-up. A large proportion of people who died between the surveys were diabetic. The mean body mass index (BMI) did not, whereas mean waist circumference increased significantly, by 5-6 cm (P = 0.001) during the 22 years. Systolic blood pressure increased by 13-15 mmHg from baseline (P = 0.0001) but diastolic blood pressure did not. The mean plasma levels of total and LDL-cholesterol decreased 10.8% and 8.9% in women (P = 0.001), 21.5% and 22.2% in men (P = 0.001), respectively, while HDL-cholesterol and triglycerides remained stable. The proportion of those achieving targets in the treatment of dyslipidaemia increased significantly (P < 0.001). CONCLUSIONS: In this 22-year prospective follow-up study of in middle-aged Europeans with high participation rates, the progression of dysglycaemia to overt diabetes with aging was rapid, even without a significant change in BMI.

Interactions between genetic variation and cellular environment in skeletal muscle gene expression.

From whole organisms to individual cells, responses to environmental conditions are influenced by genetic makeup, where the effect of genetic variation on a trait depends on the environmental context. RNA-sequencing quantifies gene expression as a molecular trait, and is capable of capturing both genetic and environmental effects. In this study, we explore opportunities of using allele-specific expression (ASE) to discover cis-acting genotype-environment interactions (GxE)-genetic effects on gene expression that depend on an environmental condition. Treating 17 common, clinical traits as approximations of the cellular environment of 267 skeletal muscle biopsies, we identify 10 candidate environmental response expression quantitative trait loci (reQTLs) across 6 traits (12 unique gene-environment trait pairs; 10% FDR per trait) including sex, systolic blood pressure, and low-density lipoprotein cholesterol. Although using ASE is in principle a promising approach to detect GxE effects, replication of such signals can be challenging as validation requires harmonization of environmental traits across cohorts and a sufficient sampling of heterozygotes for a transcribed SNP. Comprehensive discovery and replication will require large human transcriptome datasets, or the integration of multiple transcribed SNPs, coupled with standardized clinical phenotyping.

Late pregnancy blood pressure in nulliparas and subsequent abnormal glucose tolerance.

A growing body of evidence indicates that pregnancy-induced hypertension can be associated with features of insulin resistance. However, the impact of lower than hypertension-levels of blood pressure in pregnancy on the subsequent risk of developing abnormal glucose tolerance (AGT), has not been examined. We investigated women born in the years 1933-1956 and living in the municipality of Savitaipale, Finland, in May 1996. Prevalence of AGT was assessed by using oral glucose tolerance tests (OGTT). A retrospective chart review was carried out with regard to 216 nulliparas to obtain late pregnancy blood pressures. Logistic regression analyses showed that, after adjusting for body mass index (BMI) and age at OGTT, as well as for the number of subsequent pregnancies and the use of antihypertensive medication for PIH, 1 mmHg increase in systolic and diastolic blood pressure at late pregnancy in nulliparas increased the probability for AGT later in life 1.04-fold (OR, 1.04; 95% confidence interval, 1.00-1.09) and 1.06-fold (OR, 1.06; 95% confidence interval, 1.02-1.11), respectively. The results of this study suggest that not only hypertension but also less elevated levels of blood pressure during late pregnancy in nulliparas may be used as a predictor of subsequent AGT.

Does Future Diabetes Risk Impair Current Quality of Life? A Cross-Sectional Study of Health-Related Quality of Life in Relation to the Finnish Diabetes Risk Score (FINDRISC).

OBJECTIVES: Present study examines the relationship between the estimated risk of developing type 2 diabetes (T2D) and health-related quality of life (HRQoL). We quantify the association between Finnish Diabetes Risk Score (FINDRISC) and HRQoL, and examine the potential use of FINDRISC as tool to evaluate HRQoL indirectly. METHODS: We conducted a cross-sectional study comprising 707 Finnish people without a diagnosis of T2D between the ages of 51 and 75 years. The risk of developing T2D was assessed using the validated and widely used FINDRISC (range 0-26 points), and quality of life was measured using two preference-based HRQoL instruments (15D and SF-6D) and one health profile instrument (SF-36). Effects of the individual FINDRISC items and demographic and clinical characteristics, such as co-morbidities, on HRQoL were studied using multivariable Tobit regression models. RESULTS: Low HRQoL was significantly and directly associated with the estimated risk of developing T2D. An approximate 4-5 point change in FINDRISC score was observed to be associated with clinically noticeable changes in the preference-based instrument HRQoL index scores. The association between HRQoL and the risk of developing T2D was also observed for most dimensions of HRQoL in all applied HRQoL instruments. Overall, old age, lack of physical activity, obesity, and history of high blood glucose were the FINDRISC factors most prominently associated with lower HRQoL. CONCLUSIONS: The findings may help the health care professionals to substantiate the possible improvement in glucose metabolism and HRQoL potentially achieved by lifestyle changes, and better convince people at high risk of T2D to take action towards healthier lifestyle habits. FINDRISC may also provide an accurate proxy for HRQoL, and thus by estimating the risk of T2D with the FINDRISC, information about patients' HRQoL may also be obtained indirectly, when it is not feasible to use HRQoL instruments.

The genetic regulatory signature of type 2 diabetes in human skeletal muscle.

Type 2 diabetes (T2D) results from the combined effects of genetic and environmental factors on multiple tissues over time. Of the >100 variants associated with T2D and related traits in genome-wide association studies (GWAS), >90% occur in non-coding regions, suggesting a strong regulatory component to T2D risk. Here to understand how T2D status, metabolic traits and genetic variation influence gene expression, we analyse skeletal muscle biopsies from 271 well-phenotyped Finnish participants with glucose tolerance ranging from normal to newly diagnosed T2D. We perform high-depth strand-specific mRNA-sequencing and dense genotyping. Computational integration of these data with epigenome data, including ATAC-seq on skeletal muscle, and transcriptome data across diverse tissues reveals that the tissue-specific genetic regulatory architecture of skeletal muscle is highly enriched in muscle stretch/super enhancers, including some that overlap T2D GWAS variants. In one such example, T2D risk alleles residing in a muscle stretch/super enhancer are linked to increased expression and alternative splicing of muscle-specific isoforms of ANK1.

A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants.

Identifying the genetic variants that increase the risk of type 2 diabetes (T2D) in humans has been a formidable challenge. Adopting a genome-wide association strategy, we genotyped 1161 Finnish T2D cases and 1174 Finnish normal glucose-tolerant (NGT) controls with >315,000 single-nucleotide polymorphisms (SNPs) and imputed genotypes for an additional >2 million autosomal SNPs. We carried out association analysis with these SNPs to identify genetic variants that predispose to T2D, compared our T2D association results with the results of two similar studies, and genotyped 80 SNPs in an additional 1215 Finnish T2D cases and 1258 Finnish NGT controls. We identify T2D-associated variants in an intergenic region of chromosome 11p12, contribute to the identification of T2D-associated variants near the genes IGF2BP2 and CDKAL1 and the region of CDKN2A and CDKN2B, and confirm that variants near TCF7L2, SLC30A8, HHEX, FTO, PPARG, and KCNJ11 are associated with T2D risk. This brings the number of T2D loci now confidently identified to at least 10.