Using a nontargeted metabolomics approach of 447 fasting plasma metabolites, we searched for novel molecular markers that arise before and after hyperglycemia in a large population-based cohort of ...2,204 females (115 type 2 diabetic T2D case subjects, 192 individuals with impaired fasting glucose IFG, and 1,897 control subjects) from TwinsUK. Forty-two metabolites from three major fuel sources (carbohydrates, lipids, and proteins) were found to significantly correlate with T2D after adjusting for multiple testing; of these, 22 were previously reported as associated with T2D or insulin resistance. Fourteen metabolites were found to be associated with IFG. Among the metabolites identified, the branched-chain keto-acid metabolite 3-methyl-2-oxovalerate was the strongest predictive biomarker for IFG after glucose (odds ratio OR 1.65 95% CI 1.39-1.95, P = 8.46 × 10(-9)) and was moderately heritable (h(2) = 0.20). The association was replicated in an independent population (n = 720, OR 1.68 1.34-2.11, P = 6.52 × 10(-6)) and validated in 189 twins with urine metabolomics taken at the same time as plasma (OR 1.87 1.27-2.75, P = 1 × 10(-3)). Results confirm an important role for catabolism of branched-chain amino acids in T2D and IFG. In conclusion, this T2D-IFG biomarker study has surveyed the broadest panel of nontargeted metabolites to date, revealing both novel and known associated metabolites and providing potential novel targets for clinical prediction and a deeper understanding of causal mechanisms.
Ribosome biogenesis is a canonical hallmark of cell growth and proliferation. Here we show that execution of Epithelial-to-Mesenchymal Transition (EMT), a migratory cellular program associated with ...development and tumor metastasis, is fueled by upregulation of ribosome biogenesis during G1/S arrest. This unexpected EMT feature is independent of species and initiating signal, and is accompanied by release of the repressive nucleolar chromatin remodeling complex (NoRC) from rDNA, together with recruitment of the EMT-driving transcription factor Snai1 (Snail1), RNA Polymerase I (Pol I) and the Upstream Binding Factor (UBF). EMT-associated ribosome biogenesis is also coincident with increased nucleolar recruitment of Rictor, an essential component of the EMT-promoting mammalian target of rapamycin complex 2 (mTORC2). Inhibition of rRNA synthesis in vivo differentiates primary tumors to a benign, Estrogen Receptor-alpha (ERα) positive, Rictor-negative phenotype and reduces metastasis. These findings implicate the EMT-associated ribosome biogenesis program with cellular plasticity, de-differentiation, cancer progression and metastatic disease.
Genome-wide association scans with high-throughput metabolic profiling provide unprecedented insights into how genetic variation influences metabolism and complex disease. Here we report the most ...comprehensive exploration of genetic loci influencing human metabolism thus far, comprising 7,824 adult individuals from 2 European population studies. We report genome-wide significant associations at 145 metabolic loci and their biochemical connectivity with more than 400 metabolites in human blood. We extensively characterize the resulting in vivo blueprint of metabolism in human blood by integrating it with information on gene expression, heritability and overlap with known loci for complex disorders, inborn errors of metabolism and pharmacological targets. We further developed a database and web-based resources for data mining and results visualization. Our findings provide new insights into the role of inherited variation in blood metabolic diversity and identify potential new opportunities for drug development and for understanding disease.
Genome-wide association studies (GWAS) with metabolic traits and metabolome-wide association studies (MWAS) with traits of biomedical relevance are powerful tools to identify the contribution of ...genetic, environmental and lifestyle factors to the etiology of complex diseases. Hypothesis-free testing of ratios between all possible metabolite pairs in GWAS and MWAS has proven to be an innovative approach in the discovery of new biologically meaningful associations. The p-gain statistic was introduced as an ad-hoc measure to determine whether a ratio between two metabolite concentrations carries more information than the two corresponding metabolite concentrations alone. So far, only a rule of thumb was applied to determine the significance of the p-gain.
Here we explore the statistical properties of the p-gain through simulation of its density and by sampling of experimental data. We derive critical values of the p-gain for different levels of correlation between metabolite pairs and show that B/(2*α) is a conservative critical value for the p-gain, where α is the level of significance and B the number of tested metabolite pairs.
We show that the p-gain is a well defined measure that can be used to identify statistically significant metabolite ratios in association studies and provide a conservative significance cut-off for the p-gain for use in future association studies with metabolic traits.
Previously, we reported strong influences of genetic variants on metabolic phenotypes, some of them with clinical relevance. Here, we hypothesize that DNA methylation may have an important and ...potentially independent effect on human metabolism. To test this hypothesis, we conducted what is to the best of our knowledge the first epigenome-wide association study (EWAS) between DNA methylation and metabolic traits (metabotypes) in human blood. We assess 649 blood metabolic traits from 1814 participants of the Kooperative Gesundheitsforschung in der Region Augsburg (KORA) population study for association with methylation of 457 004 CpG sites, determined on the Infinium HumanMethylation450 BeadChip platform. Using the EWAS approach, we identified two types of methylome-metabotype associations. One type is driven by an underlying genetic effect; the other type is independent of genetic variation and potentially driven by common environmental and life-style-dependent factors. We report eight CpG loci at genome-wide significance that have a genetic variant as confounder (P = 3.9 × 10(-20) to 2.0 × 10(-108), r(2) = 0.036 to 0.221). Seven loci display CpG site-specific associations to metabotypes, but do not exhibit any underlying genetic signals (P = 9.2 × 10(-14) to 2.7 × 10(-27), r(2) = 0.008 to 0.107). We further identify several groups of CpG loci that associate with a same metabotype, such as 4-vinylphenol sulfate and 4-androsten-3-beta,17-beta-diol disulfate. In these cases, the association between CpG-methylation and metabotype is likely the result of a common external environmental factor, including smoking. Our study shows that analysis of EWAS with large numbers of metabolic traits in large population cohorts are, in principle, feasible. Taken together, our data suggest that DNA methylation plays an important role in regulating human metabolism.
To characterise the influence of the fat free mass on the metabolite profile in serum samples from participants of the population-based KORA (Cooperative Health Research in the Region of Augsburg) S4 ...study.
Analyses were based on metabolite profile from 965 participants of the S4 and 890 weight-stable subjects of its seven-year follow-up study (KORA F4). 190 different serum metabolites were quantified in a targeted approach including amino acids, acylcarnitines, phosphatidylcholines (PCs), sphingomyelins and hexose. Associations between metabolite concentrations and the fat free mass index (FFMI) were analysed using adjusted linear regression models. To draw conclusions on enzymatic reactions, intra-metabolite class ratios were explored. Pairwise relationships among metabolites were investigated and illustrated by means of Gaussian graphical models (GGMs).
We found 339 significant associations between FFMI and various metabolites in KORA S4. Among the most prominent associations (p-values 4.75 × 10(-16)-8.95 × 10(-06)) with higher FFMI were increasing concentrations of the branched chained amino acids (BCAAs), ratios of BCAAs to glucogenic amino acids, and carnitine concentrations. For various PCs, a decrease in chain length or in saturation of the fatty acid moieties could be observed with increasing FFMI, as well as an overall shift from acyl-alkyl PCs to diacyl PCs. These findings were reproduced in KORA F4. The established GGMs supported the regression results and provided a comprehensive picture of the relationships between metabolites. In a sub-analysis, most of the discovered associations did not exist in obese subjects in contrast to non-obese subjects, possibly indicating derangements in skeletal muscle metabolism.
A set of serum metabolites strongly associated with FFMI was identified and a network explaining the relationships among metabolites was established. These results offer a novel and more complete picture of the FFMI effects on serum metabolites in a data-driven network.
In this study, micro-level data from wood energy producers in Hedmark County were gathered and analysed. The aim was to find how much greenhouse gas (GHG) emissions various kinds of wood energy cause ...(not only CO
2, but also CH
4 and N
2O), which energy they substitute, their potential to reduce GHG emissions, and the major sources of uncertainty. The method was life cycle assessment. Six types of wood energy were studied: fuel wood, sawdust, pellets, briquettes, demolition wood, and bark.
GHG emissions over the life cycle of the wood energy types in this study are 2–19% of the emissions from a comparable source of energy. The lowest figure is for demolition wood substituting oil in large combustion facilities, the highest for fuel wood used in dwellings to substitute electricity produced by coal-based power plants.
Avoided GHG emissions per m
3 wood used for energy were from 0.210 to 0.640
tonne CO
2-equivalents. Related to GWh energy produced, avoided GHG emissions were from 250 to 360
tonne CO
2-equivalents. Avoided GHG emissions per tonne CO
2 in the wood are 0.28–0.70 tonne CO
2-equivalents. The most important factors were technology used for combustion, which energy that is substituted, densities, and heating values. Inputs concerning harvest, transport, and production of the wood energy are not important.
Overall, taking the uncertainties into account there is not much difference in avoided GHG emissions for the different kinds of wood energy.
Abstract
STUDY QUESTION
How did general practitioners (GPs) (family physicians) manage infertility in females and males in primary care between 2000 and 2016?
SUMMARY ANSWER
The number of GP ...infertility consultations for females increased 1.6 folds during the study period, with 42.9% of consultations resulting in a referral to a fertility clinic or specialist, compared to a 3-fold increase in the number of consultations for men, with 21.5% of consultations resulting in a referral.
WHAT IS KNOWN ALREADY
Infertility affects one in six couples and is expected to increase with the trend to later childbearing and reports of declining sperm counts. Despite GPs often being the first contact for infertile people, very limited information is available on the management of infertility in primary care.
STUDY DESIGN, SIZE, DURATION
Data from the Bettering the Evaluation and Care of Health programme were used, which is a national study of Australian primary care (general practice) clinical activity based on 1000 ever-changing, randomly selected GPs involved in 100 000 GP–patient consultations per year between 2000 and 2016.
PARTICIPANTS/MATERIALS, SETTING, METHODS
Females and males aged 18–49 years attending GPs for the management of infertility were included in the study. Details recorded by GPs included patient characteristics, problems managed and management actions (including counselling/education, imaging, pathology, medications and referrals to specialists and fertility clinics). Analyses included trends in the rates of infertility consultations by sex of patient, descriptive and univariate analyses of patient characteristics and management actions and multivariate logistic regression to determine which patient and GP characteristics were independently associated with increased rates of infertility management and referrals.
MAIN RESULTS AND THE ROLE OF CHANCE
The rate of infertility consultations per capita increased 1.6 folds for women (17.7–28.3 per 1000 women aged 18–49 years) and 3 folds for men over the time period (3.4–10.2 per 1000 men aged 18–49 years). Referral to a fertility clinic or relevant specialist occurred in 42.9% of female infertility consultations and 21.5% of male infertility consultations. After controlling for age and other patient characteristics, being aged in their 30s, not having income assistance, attending primary care in later years of the study and coming from a non-English-speaking background, were associated with an increased likelihood of infertility being managed in primary care. In female patients, holding a Commonwealth concession card (indicating low income), living in a remote area and having a female GP all indicated a lower adjusted odds of referral to a fertility clinic or specialist.
LIMITATIONS, REASONS FOR CAUTION
Data are lacking for the period of infertility and infertility diagnosis, which would provide a more complete picture of the epidemiology of treatment-seeking behaviour for infertility. Australia’s universal insurance scheme provides residents with access to a GP, and therefore these findings may not be generalizable to other settings.
WIDER IMPLICATIONS OF THE FINDINGS
This study informs public policy on how infertility is managed in primary care in different patient groups. Whether the management actions taken and rates of secondary referral to a fertility clinic or specialist are appropriate warrants further investigation. The development of clinical practice guidelines for the management of infertility would provide a standardized approach to advice, investigations, treatment and referral pathways in primary care.
STUDY FUNDING/COMPETING INTEREST(S)
This paper is part of a study being funded by an Australian National Health and Medical Research Council project grant APP1104543. G.C. reports that she is an employee of The University of New South Wales (UNSW) and Director of the National Perinatal Epidemiology and Statistics Unit (NPESU), UNSW. The NPESU manages the Australian and New Zealand Assisted Reproductive Technology Database on behalf of the Fertility Society of Australia. W.L. reports being a part-time paid employee and minor shareholder of Virtus Health, a fertility company. R.N. reports being a small unitholder in a fertility company, receiving grants for research from Merck and Ferring and speaker travel grants from Merck.
TRIAL REGISTRATION NUMBER
NA
Cancer stem cells (CSCs) are a major cause of tumor therapy failure. This is mainly attributed to increased DNA repair capacity and immune escape. Recent studies have shown that functional DNA repair
...homologous recombination (HR) prevents radiation-induced accumulation of DNA in the cytoplasm, thereby inhibiting the intracellular immune response. However, it is unclear whether CSCs can suppress radiation-induced cytoplasmic dsDNA formation. Here, we show that the increased radioresistance of ALDH1-positive breast cancer stem cells (BCSCs) in S phase is mediated by both enhanced DNA double-strand break repair and improved replication fork protection due to HR. Both HR-mediated processes lead to suppression of radiation-induced replication stress and consequently reduction of cytoplasmic dsDNA. The amount of cytoplasmic dsDNA correlated significantly with BCSC content (p=0.0002). This clearly indicates that HR-dependent avoidance of radiation-induced replication stress mediates radioresistance and contributes to its immune evasion. Consistent with this, enhancement of replication stress by inhibition of ataxia telangiectasia and RAD3 related (ATR) resulted in significant radiosensitization (SER37 increase 1.7-2.8 Gy, p<0.0001). Therefore, disruption of HR-mediated processes, particularly in replication, opens a CSC-specific radiosensitization option by enhancing their intracellular immune response.
The ubiquitin specific protease 7 (USP7) is a deubiquitinating enzyme with numerous substrates. Aberrant expression of USP7 is associated with tumor progression. This study aims to investigate how a ...deregulated USP7 expression affects chromosomal instability and prognosis of breast cancer patients in silico and radiosensitivity and DNA repair in breast cancer cells in vitro. The investigations in silico were performed using overall survival and USP7 mRNA expression data of breast cancer patients. The results showed that a high USP7 expression was associated with increased chromosomal instability and decreased overall survival. The in vitro experiments were performed in a luminal and a triple-negative breast cancer cell line. Proliferation, DNA repair, DNA replication stress, and survival after USP7 overexpression or inhibition and irradiation were analyzed. Both, USP7 inhibition and overexpression resulted in decreased cellular survival, distinct radiosensitization and an increased number of residual DNA double-strand breaks in the S phase following irradiation. RAD51 recruitment and base incorporation were decreased after USP7 inhibition plus irradiation and more single-stranded DNA was detected. The results show that deregulation of USP7 activity disrupts DNA repair in the S phase by increasing DNA replication stress and presents USP7 as a promising target to overcome the radioresistance of breast tumors.
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