[Show abstract][Hide abstract] ABSTRACT: Background:
A key focus in cancer research is the discovery of biomarkers that accurately diagnose early lesions in non-invasive tissues. Several studies have identified malignancy-associated DNA methylation changes in blood, yet no general cancer biomarker has been identified to date. Here, we explore the potential of blood DNA methylation as a biomarker of pan-cancer (cancer of multiple different origins) in 41 female cancer discordant monozygotic (MZ) twin-pairs sampled before or after diagnosis using the Illumina HumanMethylation450 BeadChip.
We analysed epigenome-wide DNA methylation profiles in 41 cancer discordant MZ twin-pairs with affected individuals diagnosed with tumours at different single primary sites: the breast, cervix, colon, endometrium, thyroid gland, skin (melanoma), ovary, and pancreas. No significant global differences in whole blood DNA methylation profiles were observed. Epigenome-wide analyses identified one novel pan-cancer differentially methylated position at false discovery rate (FDR) threshold of 10 % (cg02444695, P = 1.8 × 10(-7)) in an intergenic region 70 kb upstream of the SASH1 tumour suppressor gene, and three suggestive signals in COL11A2, AXL, and LINC00340. Replication of the four top-ranked signals in an independent sample of nine cancer-discordant MZ twin-pairs showed a similar direction of association at COL11A2, AXL, and LINC00340, and significantly greater methylation discordance at AXL compared to 480 healthy concordant MZ twin-pairs. The effects at cg02444695 (near SASH1), COL11A2, and LINC00340 were the most promising in biomarker potential because the DNA methylation differences were found to pre-exist in samples obtained prior to diagnosis and were limited to a 5-year period before diagnosis. Gene expression follow-up at the top-ranked signals in 283 healthy individuals showed correlation between blood methylation and gene expression in lymphoblastoid cell lines at PRL, and in the skin tissue at AXL. A significant enrichment of differential DNA methylation was observed in enhancer regions (P = 0.03).
We identified DNA methylation signatures in blood associated with pan-cancer, at or near SASH1, COL11A2, AXL, and LINC00340. Three of these signals were present up to 5 years prior to cancer diagnosis, highlighting the potential clinical utility of whole blood DNA methylation analysis in cancer surveillance.
[Show abstract][Hide abstract] ABSTRACT: Background:
The prevalence of type 2 diabetes (T2D) and obesity has dramatically increased within a few generations, reaching epidemic levels. In addition to genetic risk factors, epigenetic mechanisms triggered by changing environment are investigated for their role in the pathogenesis of these complex diseases. Epigenome-wide association studies (EWASs) have revealed significant associations of T2D, obesity, and BMI with DNA methylation. However, populations from the Middle East, where T2D and obesity rates are highest worldwide, have not been investigated so far.
We performed the first EWAS in an Arab population with T2D and BMI and attempted to replicate 47 EWAS associations previously reported in Caucasians. We used the Illumina Infinium HumanMethylation450 BeadChip to quantify DNA methylation in whole blood DNA from 123 subjects of 15 multigenerational families from Qatar. To investigate the effect of differing genetic background and environment on the epigenetic associations, we further assessed the effect of replicated loci in 810 twins from UK.
Our EWAS suggested a novel association between T2D and cg06721411 (DQX1; p value = 1.18 × 10(-9)). We replicated in the Qatari population seven CpG associations with BMI (SOCS3, p value = 3.99 × 10(-6); SREBF1, p value = 4.33 × 10(-5); SBNO2, p value = 5.87 × 10(-5); CPT1A, p value = 7.99 × 10(-5); PRR5L, p value = 1.85 × 10(-4); cg03078551, intergenic region on chromosome 17; p value = 1.00 × 10(-3); LY6G6E, p value = 1.10 × 10(-3)) and one with T2D (TXNIP, p value = 2.46 × 10(-5)). All the associations were further confirmed in the UK cohort for both BMI and T2D. Meta-analysis increased the significance of the observed associations and revealed strong heterogeneity of the effect sizes (apart from CPT1A), although associations at these loci showed concordant direction in the two populations.
Our study replicated eight known CpG associations with T2D or BMI in an Arab population. Heterogeneity of the effects at all loci except CPT1A between the Qatari and UK studies suggests that the underlying mechanisms might depend on genetic background and environmental pressure. Our EWAS results provide a basis for comparison with other ethnicities.
[Show abstract][Hide abstract] ABSTRACT: Background:
Frailty is arguably the biggest problem associated with population ageing, and associates with gut
microbiome composition in elderly and care-dependent individuals. Here we characterize frailty associations with
the gut microbiota in a younger community dwelling population, to identify targets for intervention to encourage
We analysed 16S rRNA gene sequence data derived from faecal samples obtained from 728 female twins.
Frailty was quantified using a frailty index (FI). Mixed effects models were used to identify associations with
diversity, operational taxonomic units (OTUs) and taxa. OTU associations were replicated in the Eldermet cohort.
Phenotypes were correlated with modules of OTUs collapsed by co-occurrence.
Frailty negatively associated with alpha diversity of the gut microbiota. Models considering a number of
covariates identified 637 OTUs associated with FI. Twenty-two OTU associations were significant independent of
alpha diversity. Species more abundant with frailty included
OTU was less abundant in frailer individuals, and retained significance in discordant twin
analysis. Sixty OTU associations were replicated in the Eldermet cohort. OTU co-occurrence modules had mutually
exclusive associations between frailty and alpha diversity.
There was a striking negative association between frailty and gut microbiota diversity, underpinned
by specific taxonomic associations. Whether these relationships are causal or consequential is unknown. Nevertheless,
they represent targets for diagnostic surveillance, or for intervention studies to improve vitality in ageing.
Signatures of early frailty in the gut microbiota. Available from: https://www.researchgate.net/publication/291531160_Signatures_of_early_frailty_in_the_gut_microbiota [accessed Feb 3, 2016].
[Show abstract][Hide abstract] ABSTRACT: Leukocyte telomere length (LTL) is considered one of the most predictive markers of biological aging. The aim of this study was to identify novel pathways regulating LTL using a metabolomics approach. To this end, we tested associations between 280 blood metabolites and LTL in 3511 females from TwinsUK and replicated our results in the KORA cohort. We furthermore tested significant metabolites for associations with several aging-related phenotypes, gene expression markers and epigenetic markers to investigate potential underlying pathways. Five metabolites were associated with LTL: Two lysolipids, 1-stearoylglycerophosphoinositol (P=1.6×10-5) and 1-palmitoylglycerophosphoinositol (P=1.6×10-5), were found to be negatively associated with LTL and positively associated with phospholipase A2 expression levels suggesting an involvement of fatty acid metabolism and particularly membrane composition in biological aging. Moreover, two gamma-glutamyl amino acids, gamma-glutamyltyrosine (P=2.5×10-6) and gamma-glutamylphenylalanine (P=1.7×10-5), were negatively correlated with LTL. Both are products of the glutathione cycle and markers for increased oxidative stress. Metabolites were also correlated with functional measures of aging, i.e. higher blood pressure and HDL cholesterol levels and poorer lung, liver and kidney function. Our results suggest an involvement of altered fatty acid metabolism and increased oxidative stress in human biological aging, reflected by LTL and age-related phenotypes of vital organ systems.
[Show abstract][Hide abstract] ABSTRACT: Dickkopf-related protein 1 (DKK1) is a major inhibitor of Wnt signalling pathway but also plays an important role in bone formation. Its circulating levels appear to correlate significantly with plasma levels of inflammatory factors, fractalkine and IL-6. This study, using a large sample of UK twins, showed that the variation of each of these factors and correlation between them was explained by the genetic factors, and indicated possible association with DKK1 gene variants.
DKK1 is involved in the development of several inflammatory conditions related to bone and joint degradation. Our objectives were to explore the genetic contribution (heritability) to circulating DKK1 variation and its correlation with other inflammatory cytokines, interleukin 6 (IL-6) and fractalkine, and to test whether the DKK1 heritability could be attributable to single nucleotide polymorphisms (SNPs) mapped to DKK1, IL-6 and FRCT genes.
The study included a large community-based sample of 4939 women drawn from the general UK population. Plasma samples were analysed for circulating levels of DKK1, IL-6 and fractalkine (FRCT); 65 SNPs of DKK1, IL-6 and FRCT candidate genes, with MAF >0.1, were examined. We applied variance component analysis to evaluate contribution of putative genetic (including above SNPs) and environmental factors to variation of DKK1, and its correlation with IL-6 and FRCT.
Putative genetic factors explained 42.2 ± 2 % of the total variation of circulating DKK1 levels, and were also significant for fractalkine and IL-6 variations. Most importantly, we report significant phenotypic (0.208 ± 0.006–0.459 ± 0.007) and genetic (0.338 ± 0.069–0.617 ± 0.033) correlations between these molecules. We found evidence suggestive of association between the DKK1 and its structural genes variants.
Circulating DKK1 levels correlated significantly with levels of IL-6 and FRCT, known risk factors for several inflammatory processes suggesting a potential role of DKK1 in inflammation and tissue injury. Our results suggest the contribution of genetic factors in inter-individual variation of DKK1 levels in human population. However, further studies are required to determine genetic polymorphisms affecting DKK1 variation and its correlation with IL-6 and FRCT.
Full-text · Article · Jan 2016 · Osteoporosis International
[Show abstract][Hide abstract] ABSTRACT: Objective:
Proton pump inhibitors (PPIs) are drugs used to suppress gastric acid production and treat GI disorders such as peptic ulcers and gastro-oesophageal reflux. They have been considered low risk, have been widely adopted, and are often over-prescribed. Recent studies have identified an increased risk of enteric and other infections with their use. Small studies have identified possible associations between PPI use and GI microbiota, but this has yet to be carried out on a large population-based cohort.
We investigated the association between PPI usage and the gut microbiome using 16S ribosomal RNA amplification from faecal samples of 1827 healthy twins, replicating results within unpublished data from an interventional study.
We identified a significantly lower abundance in gut commensals and lower microbial diversity in PPI users, with an associated significant increase in the abundance of oral and upper GI tract commensals. In particular, significant increases were observed in Streptococcaceae. These associations were replicated in an independent interventional study and in a paired analysis between 70 monozygotic twin pairs who were discordant for PPI use. We propose that the observed changes result from the removal of the low pH barrier between upper GI tract bacteria and the lower gut.
Our findings describe a significant impact of PPIs on the gut microbiome and should caution over-use of PPIs, and warrant further investigation into the mechanisms and their clinical consequences.
[Show abstract][Hide abstract] ABSTRACT: Objective:
Mal-alignment is associated with knee osteoarthritis however, the optimal anatomic axis (AA) knee alignment measurement on a standard limb radiograph (SLR) is unknown. This study compares one-point (1P) and two-point (2P) AA methods using 3 knee joint centre locations and examines cross-sectional associations with symptomatic radiographic knee osteoarthritis (SRKOA), radiographic knee osteoarthritis (RKOA) and knee pain.
AA alignment was measured 6 different ways using KneeMorf software on 1058 SLRs from 584 women in the Chingford Study. Cross-sectional associations with principal outcome SRKOA combined with greatest reproducibility determined the optimal 1P and 2P AA method. Appropriate varus/neutral/valgus alignment categories were established using logistic regression with generalised estimating equation models fitted with restricted cubic spline function.
The tibial plateau centre displayed greatest reproducibility and associations with SRKOA. As mean 1P and 2P values differed by > 2°, new alignment categories were generated for 1P: varus <178°, neutral 178 -182°, valgus >182° and for 2P methods: varus <180°, neutral 180 - 185°, valgus >185°. Varus versus neutral alignment was associated with a near 2-fold increase in SRKOA and RKOA, and valgus versus neutral for RKOA using 2P method. Non-significant associations were seen for 1P method for SRKOA, RKOA and knee pain.
AA alignment was associated with SRKOA and the tibial plateau centre had the strongest association. Differences in AA alignment when 1P versus 2P methods were compared indicated bespoke alignment categories were necessary. Further replication and validation with mechanical axis alignment comparison is required.
Preview · Article · Dec 2015 · Osteoarthritis and Cartilage
[Show abstract][Hide abstract] ABSTRACT: Recently, we have begun to realize that the billions of microorganisms living in symbiosis with us have an influence on disease. Evidence is mounting that the alimentary tract microbiome, in particular, influences both host metabolic potential and its innate and adaptive immune system. Inflammatory states characterize many bone and joint diseases of ageing. This prompts a thesis that the gut microbiome could alter the inflammatory state of the individual and directly influence the development of these common and burdensome clinical problems. As the microbiome is easily modifiable this could have major therapeutic impact. This perspective discusses evidence to date on the role of the microbiome and the highly prevalent age-related disorders of osteoporosis, osteoarthritis, gout, rheumatoid arthritis, sarcopenia and frailty. It also reviews data on the effects of probiotics and prebiotic interventions in animal and human models. Despite suggestive findings, research to date is not conclusive, and we identify priorities for research to substantiate and translate findings. This article is protected by copyright. All rights reserved.
No preview · Article · Dec 2015 · Journal of bone and mineral research: the official journal of the American Society for Bone and Mineral Research
[Show abstract][Hide abstract] ABSTRACT: Lung function measures are used in the diagnosis of chronic obstructive pulmonary disease. In 38,199 European ancestry individuals, we studied genome-wide association of forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC) and FEV1/FVC with 1000 Genomes Project (phase 1)-imputed genotypes and followed up top associations in 54,550 Europeans. We identify 14 novel loci (P<5 × 10-8) in or near ENSA, RNU5F-1, KCNS3, AK097794, ASTN2, LHX3, CCDC91, TBX3, TRIP11, RIN3, TEKT5, LTBP4, MN1 and AP1S2, and two novel signals at known loci NPNT and GPR126, providing a basis for new understanding of the genetic determinants of these traits and pulmonary diseases in which they are altered.
Full-text · Article · Dec 2015 · Nature Communications
[Show abstract][Hide abstract] ABSTRACT: We investigated whether expression of genes previously implicated in arterial stiffening associates with cross-sectional and longitudinal measures of arterial stiffness. Women from the Twins UK cohort (n=470, aged 39-81 years) had gene expression in lymphoblastoid cell lines measured using an Illumina microarray. Arterial stiffness was measured by carotid-femoral pulse wave velocity and carotid distensibility. A subsample (n=121) of women had repeat vascular measures after a mean±SD follow-up of 4.3±1.4 years. Associations of arterial phenotypes with gene expression levels were examined for 52 genes identified from previous association studies. The gene transcript most closely associated with pulse wave velocity in cross-sectional analysis was ectonucleotide pyrophosphatase/phosphodiesterase (P=0.012). Pleiotropic genetic effects accounted for 14% of the phenotypic correlation between ectonucleotide pyrophosphatase/phosphodiesterase expression and pulse wave velocity. Progression of pulse wave velocity during the follow-up period best related to expression of ectonucleotide pyrophosphatase/phosphodiesterase (β=0.19, P=0.008) and collagen type IV α 1 (β=0.32, P<0.0001). Gene transcripts most closely related to change in carotid distensibility during the follow-up period were endothelial nitric oxide synthase (β=-0.20, P=0.005), angiotensin-converting enzyme (β=-0.15, P=0.035), and B-cell CLL/lymphoma11B (β=0.18, P=0.010). Expression levels of angiotensin-converting enzyme also related to progression in carotid diameter (β=0.21, P=0.012). Expression levels of ectonucleotide pyrophosphatase/phosphodiesterase, involved in arterial calcification, and collagen type IV α 1, involved in collagen formation, correlate with aortic stiffening. These genes may be functional mediators of arterial stiffening.
[Show abstract][Hide abstract] ABSTRACT: Low birth weight (LBW) can have an impact on health outcomes in later life, especially in relation to pre-disposition to metabolic disease. Several studies suggest that LBW resulting from restricted intrauterine growth leaves a footprint on DNA methylation in utero, and this influence likely persists into adulthood. To investigate this further, we performed epigenome-wide association analyses of blood DNA methylation using Infinium HumanMethylation450 BeadChip profiles in 71 adult monozygotic (MZ) twin pairs who were extremely discordant for birth weight. A signal mapping to the IGF1R gene (cg12562232, p = 2.62 × 10-8), was significantly associated with birth weight discordance at a genome-wide false-discovery rate (FDR) of 0.05. We pursued replication in three additional independent datasets of birth weight discordant MZ pairs and observed the same direction of association, but the results were not significant. However, a meta-analysis across the four independent samples, in total 216 birth-weight discordant MZ twin pairs, showed a significant positive association between birth weight and DNA methylation differences at IGF1R (random-effects meta-analysis p = .04), and the effect was particularly pronounced in older twins (random-effects meta-analysis p = .008, 98 older birth-weight discordant MZ twin pairs). The results suggest that severe intra-uterine growth differences (birth weight discordance >20%) are associated with methylation changes in the IGF1R gene in adulthood, independent of genetic effects.
No preview · Article · Nov 2015 · Twin Research and Human Genetics
[Show abstract][Hide abstract] ABSTRACT: Background:
Many observational studies have shown a protective effect of physical activity on cognitive ageing, but interventional studies have been less convincing. This may be due to short time scales of interventions, suboptimal interventional regimes or lack of lasting effect. Confounding through common genetic and developmental causes is also possible.
We aimed to test whether muscle fitness (measured by leg power) could predict cognitive change in a healthy older population over a 10-year time interval, how this performed alongside other predictors of cognitive ageing, and whether this effect was confounded by factors shared by twins. In addition, we investigated whether differences in leg power were predictive of differences in brain structure and function after 12 years of follow-up in identical twin pairs.
A total of 324 healthy female twins (average age at baseline 55, range 43-73) performed the Cambridge Neuropsychological Test Automated Battery (CANTAB) at two time points 10 years apart. Linear regression modelling was used to assess the relationships between baseline leg power, physical activity and subsequent cognitive change, adjusting comprehensively for baseline covariates (including heart disease, diabetes, blood pressure, fasting blood glucose, lipids, diet, body habitus, smoking and alcohol habits, reading IQ, socioeconomic status and birthweight). A discordant twin approach was used to adjust for factors shared by twins. A subset of monozygotic pairs then underwent magnetic resonance imaging. The relationship between muscle fitness and brain structure and function was assessed using linear regression modelling and paired t tests.
A striking protective relationship was found between muscle fitness (leg power) and both 10-year cognitive change [fully adjusted model standardised β-coefficient (Stdβ) = 0.174, p = 0.002] and subsequent total grey matter (Stdβ = 0.362, p = 0.005). These effects were robust in discordant twin analyses, where within-pair difference in physical fitness was also predictive of within-pair difference in lateral ventricle size. There was a weak independent effect of self-reported physical activity.
Leg power predicts both cognitive ageing and global brain structure, despite controlling for common genetics and early life environment shared by twins. Interventions targeted to improve leg power in the long term may help reach a universal goal of healthy cognitive ageing.
[Show abstract][Hide abstract] ABSTRACT: Introduction:
Despite recent discoveries of germline and somatic mutations in melanoma, naevus count remains the most important risk factor for melanoma. Counting naevi on the whole body is time consuming. In order to identify patients at risk for melanoma, many studies have used naevus count on selected body sites as a proxy for total body naevus count.
The most predictive body site for total naevus count was assessed in a cohort of female healthy twins. This finding was replicated on a control group from UK a case-control study and a prediction model was after performed. The area under the receiver operating characteristics curve was used to evaluate the best cut off for the prediction of having more than 50 or 100 total body naevus counts.
3694 female twins were included. The total body naevus count showed a steady decline after the age of 30 (p<0.001). The most predictive sites for total body naevus count were the arms and legs: the adjusted correlation coefficients were 0.50 and 0.51 (p<0.001) for right and left arm respectively and 0.49 and 0.48 for right and left arm respectively (p<0.001). The arm remained the most predictive site for total body naevus counts when replicated in a control population including both sexes. In the twin study, women with more than 11 naevi on the right arm were approximately 9 times more likely to have more than 100 naevi (OR =9.38, 95% CI: 6.71-13.11).
The ability to estimate total body naevus count quickly by counting naevi on one arm could be a very useful tool in assessing melanoma risk in primary care. This article is protected by copyright. All rights reserved.
No preview · Article · Oct 2015 · British Journal of Dermatology
[Show abstract][Hide abstract] ABSTRACT: Genetic association studies have identified 21 loci associated with atopic dermatitis risk predominantly in populations of European ancestry. To identify further susceptibility loci for this common, complex skin disease, we performed a meta-analysis of >15 million genetic variants in 21,399 cases and 95,464 controls from populations of European, African, Japanese and Latino ancestry, followed by replication in 32,059 cases and 228,628 controls from 18 studies. We identified ten new risk loci, bringing the total number of known atopic dermatitis risk loci to 31 (with new secondary signals at four of these loci). Notably, the new loci include candidate genes with roles in the regulation of innate host defenses and T cell function, underscoring the important contribution of (auto)immune mechanisms to atopic dermatitis pathogenesis.