Detecting gene-environment interactions from multiple continuous traits.

MOTIVATION: Genetic variants present differential effects on humans according to various environmental exposures, the so-called "gene-environment interactions" (GxE). Many diseases can be diagnosed with multiple traits, such as obesity, diabetes, and dyslipidemia. I developed a multivariate scale test (MST) for detecting the GxE of a disease with several continuous traits. Given a significant MST result, I continued to search for which trait and which E enriched the GxE signals. Simulation studies were performed to compare MST with the univariate scale test (UST). RESULTS: MST can gain more power than UST because of (1) integrating more traits with GxE information and (2) the less harsh penalty on multiple testing. However, if only few traits account for GxE, MST may lose power due to aggregating non-informative traits into the test statistic. As an example, MST was applied to a discovery set of 93,708 Taiwan Biobank (TWB) individuals and a replication set of 25,200 TWB individuals. From among 2,570,487 SNPs with minor allele frequencies ≥ 5%, MST identified 18 independent variance quantitative trait loci (p < 2.4E-9 in the discovery cohort and p < 2.8E-5 in the replication cohort) and 41 GxE signals (p < 0.00027) based on eight trait domains (including 29 traits). AVAILABILITY: https://github.com/WanYuLin/Multivariate-scale-test-MST. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Genome-wide association study for four measures of epigenetic age acceleration and two epigenetic surrogate markers using DNA methylation data from Taiwan Biobank.

To highlight the genetic architecture for epigenetic aging, McCartney et al. recently identified 137 significant single-nucleotide polymorphisms based on genome-wide association study (GWAS) meta-analyses of four epigenetic clocks and two epigenetic surrogate markers. However, none Asian ancestry studies have been included in this or previous meta-analyses. I performed a GWAS on blood DNA methylation (DNAm) levels of 2309 Taiwan Biobank (TWB) participants. Owing to the fact that the sample size of an individual GWAS of DNAm data is still not large, I adopted the 'prioritized subset analysis' (PSA) method to boost the power of a GWAS. The four epigenetic clocks and the two epigenetic surrogate markers were investigated, respectively. I replicated 21 out of the 137 aging-associated genetic loci by applying the PSA method to the TWB DNAm data. Moreover, I identified five novel loci, including rs117530284 that was associated with the 'epigenetic age acceleration' (EAA) according to Lu et al.'s GrimAge (called 'GrimEAA'). Considering 16 covariates (sex, BMI, smoking status, drinking status, regular exercise, educational attainment and the first 10 ancestry principal components), each 'A' allele of rs117530284 in the IBA57 gene was found to be associated with a 1.5943-year GrimEAA (95% confidence interval = [1.0748, 2.1138]). IBA57 is a protein coding gene and is associated with multiple mitochondrial dysfunctions syndromes. A decline in mitochondrial activity and quality is associated with aging and many age-related diseases. This is one of the first DNAm GWAS for individuals of Asian ancestry.

Factors affecting the distribution of serum anti-müllerian hormone levels among infertile Asian women: a multi-nation, multi-centre, and multi-ethnicity prospective cohort study.

STUDY QUESTION: How do age, ethnicity, and other characteristics affect serum anti-mullerian hormone (AMH) levels in Asian women undergoing fertility treatment? SUMMARY ANSWER: Age, ethnicity, obesity (BMI ≥ 30 kg/m2), and polycystic ovarian syndrome (PCOS) significantly impacted serum AMH levels, with the rate of decrease accelerating as age increased; a concentration of 4.0 ng/ml was the optimal cut-off for diagnosis of PCOS. WHAT IS KNOWN ALREADY: There are significant differences in ovarian reserve among women from different races and ethnicities, and Asian women often have poorer reproductive outcomes during assisted reproductive treatment cycles. STUDY DESIGN, SIZE, DURATION: A population-based multi-nation, multi-centre, multi-ethnicity prospective cohort study of 4613 women was conducted from January 2020 to May 2021. Infertile women of 20-43 years of age were enrolled. The exclusion criteria included: age <20 or >43, non-Asian ethnicity, and missing critical data. PARTICIPANTS/MATERIALS, SETTING, METHODS: Participants were Asian women of Chinese, Japanese, Korean, Thai, Vietnamese, Malay, Indian, and Indonesian ethnicities from 12 IVF centres across Asia. These women were all naïve to ovarian stimulation cycles and attended IVF centres for fertility assessment. The AMH measurement was performed using an AMH automated assay on a clinically validated platform. MAIN RESULTS AND THE ROLE OF CHANCE: A total of 4556 infertile Asian women were included in the final analyses. The mean ± SD for serum AMH concentrations (ng/ml) across specific age groups were: overall, 3.44 ± 2.93; age <30, 4.58 ± 3.16; 30-31, 4.23 ± 3.23; 32-33, 3.90 ± 3.06; 34-35, 3.21 ± 2.65; 36-37, 2.74 ± 2.44; 38-39, 2.30 ± 1.91; 40 and above, 1.67 ± 2.00. The rate of AMH decrease was ∼0.13 ng/ml/year in patients aged 25-33 and 0.31 ng/ml/year in women aged 33-43. The highest rates of PCOS were found in Indians (18.6%), Malays (18.9%), and Vietnamese (17.7%). Age (P < 0.001), ethnicity (P < 0.001), obesity (P = 0.007), PCOS (P < 0.001), and a history of endometrioma cystectomy (P = 0.01) were significantly associated with serum AMH values. Smoking status, pretreatment with GnRH agonist (GnRHa) or the oral contraceptive pill (OCP), freezing-thawing of blood samples, and sampling on Day 2 to Day 5 of the menstrual cycle or randomly did not appear to affect serum AMH levels. An AMH concentration of 4.0 ng/ml was the optimal cut-off for PCOS diagnosis with a sensitivity of 71.7% and specificity of 75.8% (AUC = 0.81, CI 95%: 0.79-0.83; P < 0.001). LIMITATIONS, REASONS FOR CAUTION: The incidence of PCOS was supposedly high in this cohort as some IVF clinics were tertiary referral centres for managing specific fertility issues encountered by women with PCOS. Treatment with GnRHa or OCP before AMH testing was regionally and ethnically confined, mostly in Hong Kong SAR and Japan. Moreover, this reference for serum AMH value is limited to Asian women of the ethnicities examined and may not apply to other ethnicities not included in the study. WIDER IMPLICATIONS OF THE FINDINGS: This is the first study to collate and construct age-specific reference ranges for serum AMH levels using the same bioassay on Asian women of different ethnicities. The findings of this investigation can assist clinicians to counsel and prognosticate about Asian women's ovarian reserve and reproductive potential, thus providing better strategies for personalized fertility interventions. STUDY FUNDING/COMPETING INTEREST(S): This study was technically supported by Ferring Pharmaceuticals and received no specific grant from any funding agency. All authors have no competing interests to disclose. TRIAL REGISTRATION NUMBER: NCT04203355.

Short-Term Effects of a Therapeutic Diet on Biochemical Parameters in Hemodialysis Patients: A Randomized Crossover Trial.

OBJECTIVE: Although unhealthy diets exacerbate nutritional and metabolic derangements in patients with end-stage kidney disease (ESKD), how therapeutic diets that possess a variety of different dietary strategies acutely modify diverse biochemical parameters related to cardiovascular disease remains underexplored. METHODS: Thirty-three adults with end-stage kidney disease undergoing thrice-weekly hemodialysis participated in a randomized crossover trial comparing a therapeutic diet with their usual diets for 7 days, separated by a 4-week washout period. The therapeutic diet was characterized by adequate calorie and protein amounts, natural food ingredients with a low phosphorus-to-protein ratio, higher portions of plant-based food, and high fiber content. The primary outcome measure was the mean difference in the change-from-baseline intact fibroblast growth factor 23 (FGF23) level between the 2 diets. The other outcomes of interest included changes in mineral parameters, uremic toxins, and high-sensitivity C-reactive protein (hs-CRP) levels. RESULTS: Compared with the usual diet, the therapeutic diet lowered intact FGF23 levels (P = .001), decreased serum phosphate levels (P < .001), reduced intact parathyroid hormone (PTH) levels (P = .003), lowered C-terminal FGF23 levels (P = .03), increased serum calcium levels (P = .01), and tended to lower total indoxyl sulfate levels (P = .07) but had no significant effect on hs-CRP levels. Among these changes, reduction in serum phosphate level achieved in 2 days, modifications of intact PTH and calcium levels in 5 days, and reductions in intact and C-terminal FGF23 levels in 7 days of therapeutic diet intervention. CONCLUSION: Within the 1-week intervention period, the dialysis-specific therapeutic diet rapidly reversed mineral abnormalities and tended to decrease total indoxyl sulfate levels in patients undergoing hemodialysis but had no effect on inflammation. Future studies to assess the long-term effects of such therapeutic diets are recommended.

Adverse events following the first, second and third doses of a COVID-19 vaccine in hemodialysis patients.

BACKGROUND: This study aimed to identify adverse events following the first three doses of COVID-19 vaccines in hemodialysis (HD) patients. Risk factors associated with postvaccination adverse events were explored. METHODS: Postvaccination adverse events in 438 HD patients who received 3 doses of COVID-19 vaccines were prospectively assessed. The adverse events among three doses were compared using generalized linear mixed models. Factors associated with adverse events were assessed with multivariate analyses. RESULTS: The vast majority of participants received Oxford/AstraZeneca ChAdOx1 as their first two doses and Moderna mRNA-1273 as their third dose. Overall, 79%, 50% and 84% of the participants experienced at least one adverse event after their first, second, and third doses, respectively. These adverse events were mostly minor, short-lived and less than 5% reported daily activities being affected. Compared with the first dose, the second dose caused a lower rate of adverse events. Compared with the first dose, the third dose elicited a higher rate of injection site reactions and a lower rate of systemic reactions. Multivariate analyses showed that every 10-year increase of age (odds ratio 0.67, 95% confidence intervals 0.57-0.79) was associated with decreased risk of adverse events, while female sex (2.82, 1.90-4.18) and arteriovenous fistula (1.73, 1.05-2.84) were associated with increased risk of adverse events. Compared with Oxford/AstraZeneca ChAdOx1, Moderna mRNA-1273 was associated with an increased risk of injection site reactions. CONCLUSIONS: COVID-19 vaccination was well tolerated in HD patients. Age, sex, dialysis vascular access and vaccine types were associated with postvaccination adverse events.

Sex-specific autosomal genetic effects across 26 human complex traits.

Previous studies have shown that men and women have different genetic architectures across many traits. However, except waist-to-hip ratio (WHR) and waist circumference (WC), it remains unknown whether the genetic effects of a certain trait are weaker or stronger on men/women. With ~18 000 Taiwan Biobank subjects, we comprehensively investigate sexual heterogeneity in autosomal genetic effects, for traits regarding cardiovascular health, diabetes, kidney, liver, anthropometric profiles, blood, etc. 'Gene-by-sex interactions' (G $\times$ S) were detected in 18 out of 26 traits, each with an interaction P-value (${{P}}_{{INT}}$) less than $0.05/104={0.00048}$, where 104 is the number of tests conducted in this study. The most significant evidence of G $\times$ S was found in WHR (${{P}}_{{INT}}$ = 3.2 $\times{{10}}^{-{55}}$) and WC (${{P}}_{{INT}}$ = 2.3$\times{{10}}^{-{41}}$). As a novel G$\times$S investigation for other traits, we here find that the autosomal genetic effects are weaker on women than on men, for low-density lipoprotein cholesterol (LDL-C), uric acid (UA) and diabetes-related traits such as fasting glucose and glycated hemoglobin. For LDL-C and UA, the evidence of G$\times$S is especially notable in subjects aged less than 50 years, where estrogen can play a role in attenuating the autosomal genetic effects of these two traits. Men and women have systematically distinct environmental contexts caused by hormonal milieu and their specific society roles, which may trigger diverse gene expressions despite the same DNA materials. As many environmental exposures are difficult to collect and quantify, sex can serve as a good surrogate for these factors.

Using angle-selective optical film to enhance the light extraction of a thin-film encapsulated 3D reflective pixel for OLED displays.

Light extraction improvement is still an important issue for active-matrix organic light-emitting diode displays (AMOLEDs). In our previous work, a three-dimensional (3D) reflective pixel configuration embedding the OLED in the concave 3D reflector and patterned high-index filler had been proposed for significant enhancement of the pixel light extraction. In this work, influences of thin film encapsulation (TFE) on light extraction of such reflective 3D OLED pixels are considered as well by simulation studies. Unfortunately, the optical simulation reveals strong reduction of the light extraction efficiency induced by TFE layers. As such, an additional angle-selective optical film structure between the pixel and the encapsulation layers is introduced to control the angular distribution of the light coupled into the encapsulation layers and to solve TFE-induced optical losses. As a result, TFE-induced losses can be substantially reduced to retain much of light extraction efficiency. The results of this study are believed to provide useful insights and guides for developing even more efficient and power-saving AMOLEDs.

Interpreting the Evidence of Body Mass Index in Relation to Mental Health Status in Community-Dwelling Older Adults.

INTRODUCTION: Maintaining a better physical and mental health status is an important issue for older adults in their later life. Thus, the study's purpose was to evaluate the association between body mass index (BMI) and mental health status in older adults aged 65 years old or above residing in communities of Taipei City, Taiwan. METHODS: We carried out secondary data analysis with data from a volunteer-based health examination project for older adults >65 years old residing in Taipei City from 2006 to 2010 with a retrospective study design. BMI, calculated by standardized measuring procedures for height and weight, and mental health status, evaluated by 5-item Brief Symptom Rating Scale (BSRS-5), were collected at their first visits of health examination. A BSRS-5 score ≥6 was considered an inferior mental health status for the outcome. In statistical analysis, univariable and multivariable logistic regressions were adopted to estimate the relative risk of inferior mental health status, treating BMI as the major exposure of interest. RESULTS: A total of 90,576 subjects were involved, with a mean age of 73.38 years old (SD = 6.64 years) and 49.21% females. With confounders controlled, compared to normal or overweight (23 ≤ BMI <30), an adjusted OR of 1.23 (95% CI: 1.18, 1.29) on inferior mental health status was detected for the underweight group (BMI <23) significantly. Adjusted OR for those obese (BMI ≧30) was 0.87 (95% CI: 0.79, 0.96). Significantly elevated ORs of underweight were found for both genders, but the significantly protective effect of obese was only detected for females. CONCLUSION: Keeping an appropriate weight or even being overweighted might be beneficial for older adults dwelling in the community, especially for males.

Associations of five obesity indicators with cognitive performance in 30,697 Taiwan Biobank participants.

BACKGROUND: Obesity adversely influences the central nervous system and cognitive functions. However, the relationship between various obesity indicators and cognitive performance remains controversial. It is unclear which obesity indicator is more relevant to cognitive impairment. METHODS: The Taiwan Biobank (TWB) administered the Chinese version of the Mini-Mental State Examination (MMSE) to 30,697 participants (12,094 males and 18,603 females) aged 60 to 70 years. A total of 3,454 (11.25%) individuals with MMSE < = 24 were classified as having poor cognitive performance. This cross-sectional study investigates the associations of five obesity indicators with cognitive performance. Five separate logistic regression models were fitted for males and another five for females. Covariates adjusted in all models included age, smoking status, drinking status, regular exercise, chronic disease status (diabetes, cardiovascular diseases, heart diseases, stroke, or Parkinson's disease), depression status, blood pressure level, total cholesterol, fasting glucose, and educational attainment. The five obesity indicators included body mass index (BMI), body fat percentage (BFP), waist circumference (WC), hip circumference (HC), and waist-hip ratio (WHR). RESULTS: Abdominal obesity defined by WHR was significantly associated with poor cognitive performance. Male WHR > = 0.90 had a higher risk of poor cognitive performance than male WHR < 0.90 (odds ratio [OR] = 1.233; p = 0.007); female WHR > = 0.85 had an increased risk of poor cognitive performance compared with female WHR < 0.85 (OR = 1.221; p = 3.9E-4). HC and general obesity (defined by BMI and BFP) were not significantly associated with cognitive performance. CONCLUSION: The results consistently agreed that preventing abdominal obesity is associated with better cognitive performance in both males and females.

Performing different kinds of physical exercise differentially attenuates the genetic effects on obesity measures: Evidence from 18,424 Taiwan Biobank participants.

Obesity is a worldwide health problem that is closely linked to many metabolic disorders. Regular physical exercise has been found to attenuate the genetic predisposition to obesity. However, it remains unknown what kinds of exercise can modify the genetic risk of obesity. This study included 18,424 unrelated Han Chinese adults aged 30-70 years who participated in the Taiwan Biobank (TWB). A total of 5 obesity measures were investigated here, including body mass index (BMI), body fat percentage (BFP), waist circumference (WC), hip circumference (HC), and waist-to-hip ratio (WHR). Because there have been no large genome-wide association studies on obesity for Han Chinese, we used the TWB internal weights to construct genetic risk scores (GRSs) for each obesity measure, and then test the significance of GRS-by-exercise interactions. The significance level throughout this work was set at 0.05/550 = 9.1x10-5 because a total of 550 tests were performed. Performing regular exercise was found to attenuate the genetic effects on 4 obesity measures, including BMI, BFP, WC, and HC. Among the 18 kinds of self-reported regular exercise, 6 mitigated the genetic effects on at least one obesity measure. Regular jogging blunted the genetic effects on BMI, BFP, and HC. Mountain climbing, walking, exercise walking, international standard dancing, and a longer practice of yoga also attenuated the genetic effects on BMI. Exercises such as cycling, stretching exercise, swimming, dance dance revolution, and qigong were not found to modify the genetic effects on any obesity measure. Across all 5 obesity measures, regular jogging consistently presented the most significant interactions with GRSs. Our findings show that the genetic effects on obesity measures can be decreased to various extents by performing different kinds of exercise. The benefits of regular physical exercise are more impactful in subjects who are more predisposed to obesity.

Polygenic approaches to detect gene-environment interactions when external information is unavailable.

The exploration of 'gene-environment interactions' (G × E) is important for disease prediction and prevention. The scientific community usually uses external information to construct a genetic risk score (GRS), and then tests the interaction between this GRS and an environmental factor (E). However, external genome-wide association studies (GWAS) are not always available, especially for non-Caucasian ethnicity. Although GRS is an analysis tool to detect G × E in GWAS, its performance remains unclear when there is no external information. Our 'adaptive combination of Bayes factors method' (ADABF) can aggregate G × E signals and test the significance of G × E by a polygenic test. We here explore a powerful polygenic approach for G × E when external information is unavailable, by comparing our ADABF with the GRS based on marginal effects of SNPs (GRS-M) and GRS based on SNP × E interactions (GRS-I). ADABF is the most powerful method in the absence of SNP main effects, whereas GRS-M is generally the best test when single-nucleotide polymorphisms main effects exist. GRS-I is the least powerful test due to its data-splitting strategy. Furthermore, we apply these methods to Taiwan Biobank data. ADABF and GRS-M identified gene × alcohol and gene × smoking interactions on blood pressure (BP). BP-increasing alleles elevate more BP in drinkers (smokers) than in nondrinkers (nonsmokers). This work provides guidance to choose a polygenic approach to detect G × E when external information is unavailable.

Acute effects of dietary phosphorus intake on markers of mineral metabolism in hemodialysis patients: post hoc analysis of a randomized crossover trial.

BACKGROUND: Long-term dietary phosphorus excess influences disturbances in mineral metabolism, but it is unclear how rapidly the mineral metabolism responds to short-term dietary change in dialysis populations. METHODS: This was a post hoc analysis of a randomized crossover trial that evaluated the short-term effects of low-phosphorus diets on mineral parameters in hemodialysis patients. Within a 9-day period, we obtained a total of 4 repeated measurements for each participant regarding dietary intake parameters, including calorie, phosphorus, and calcium intake, and markers of mineral metabolism, including phosphate, calcium, intact parathyroid hormone (iPTH), intact fibroblast growth factor 23 (iFGF23), and C-terminal fibroblast growth factor 23 (cFGF23). The correlations between dietary phosphorus intake and serum mineral parameters were assessed by using mixed-effects models. RESULTS: Thirty-four patients were analyzed. In the fully adjusted model, we found that an increase in dietary phosphorus intake of 100 mg was associated with an increase in serum phosphate of 0.3 mg/dL (95% confidence intervals [CI], 0.2-0.4, p < .001), a decrease in serum calcium of 0.06 mg/dL (95% CI, -0.11 to -0.01, p = .01), an increase in iPTH of 5.4% (95% CI, 1.4-9.3, p = .01), and an increase in iFGF23 of 5.0% (95% CI, 2.0-8.0, p = .001). Dietary phosphorus intake was not related to cFGF23. CONCLUSIONS: Increased dietary phosphorus intake acutely increases serum phosphate, iPTH, and iFGF23 levels and decreases serum calcium levels, highlighting the important role of daily fluctuations of dietary habits in disturbed mineral homeostasis in hemodialysis patients.

Effects of indoor residual spraying and outdoor larval control on Anopheles coluzzii from São Tomé and Príncipe, two islands with pre-eliminated malaria.

BACKGROUND: Vector control is a key component of malaria prevention. Two major vector control strategies have been implemented in São Tomé and Príncipe (STP), indoor residual spraying (IRS) and outdoor larval control using Bacillus thuringiensis israelensis (Bti). This study evaluated post-intervention effects of control strategies on vector population density, composition, and knockdown resistance mutation, and their implications for malaria epidemiology in STP. METHODS: Mosquitoes were collected by indoor and outdoor human landing catches and mosquito light traps in seven districts. Mosquito density was calculated by numbers of captured adult mosquitoes/house/working hour. Mitochondrial cytochrome c oxidase subunit I (COI) was PCR amplified and sequenced to understand the spatial-temporal population composition of malaria vector in STP. Knockdown resistance L1014F mutation was detected using allele-specific PCR. To estimate the malaria transmission risks in STP, a negative binomial regression model was constructed. The response variable was monthly incidence, and the explanatory variables were area, rainfall, entomological inoculation rate (EIR), and kdr mutation frequency. RESULTS: Malaria vector in STP is exophilic Anopheles coluzzii with significant population differentiation between Príncipe and São Tomé (mean FST = 0.16, p < 0.001). Both vector genetic diversity and knockdown resistance mutation were relatively low in Príncipe (mean of kdr frequency = 15.82%) compared to São Tomé (mean of kdr frequency = 44.77%). Annual malaria incidence rate in STP had been rapidly controlled from 37 to 2.1% by three rounds of country-wide IRS from 2004 to 2007. Long-term application of Bti since 2007 kept the mosquito density under 10 mosquitoes/house/hr/month, and malaria incidence rate under 5% after 2008, except for a rising that occurred in 2012 (incidence rate = 6.9%). Risk factors of area (São Tomé compared to Príncipe), rainfall, outdoor EIR, and kdr mutation frequency could significantly increase malaria incidence by 9.33-11.50, 1.25, 1.07, and 1.06 fold, respectively. CONCLUSIONS: Indoor residual spraying could rapidly decrease Anopheles density and malaria incidence in STP. Outdoor larval control using Bti is a sustainable approach for controlling local vector with exophilic feature and insecticide resistance problem. Vector control interventions should be intensified especially at the north-eastern part of São Tomé to minimize impacts of outbreaks.

Impact of cardiac reverse remodeling after cardiac resynchronization therapy assessed by myocardial perfusion imaging on ventricular arrhythmia.

BACKGROUND: Although cardiac resynchronization therapy (CRT) has been a useful treatment of heart failure, patients with CRT are still in risk of sudden cardiac death due to ventricular arrhythmia. The aim of this study was to investigate the impact of cardiac reverse remodeling after CRT on the prevalence of ventricular tachycardia or fibrillation (VT/VF). METHODS AND RESULTS: Forty-one heart failure patients (26 men, age 66 ± 10 years), who were implanted with CRT for at least 12 months, were enrolled. All patients received myocardial perfusion imaging (MPI) under CRT pacing to evaluate left ventricle (LV) function, dyssynchrony, and scar. VT/VF episodes during the follow-up period after MPI were recorded by the CRT devices. Sixteen patients (N = 16/41, 39%) were found to have VT/VF. Multivariate Cox regression analysis and receiver operating characteristic curve analysis showed that five risk factors were significant predictors of VT/VF, including increased left ventricle ejection fraction (LVEF) by ≤7% after CRT, low LVEF after CRT (≤30%), change of intrinsic QRS duration (iQRSd) by ≤7 ms, wide iQRSd after CRT (≥121 ms), and high systolic dyssynchrony after CRT (phase standard deviation ≥45.6°). For those patients with all of the 5 risk factors, 85.7% or more developed VT/VF. CONCLUSIONS: The characteristics of cardiac reverse remodeling after CRT as assessed by MPI are associated with the prevalence of ventricular arrhythmia.

Nuclear magnetic resonance- and mass spectrometry-based metabolomics to study maleic acid toxicity from repeated dose exposure in rats.

Maleic acid (MA), a chemical intermediate used in many consumer and industrial products, was intentionally adulterated in a variety of starch-based foods and instigated food safety incidents in Asia. We aim to elucidate possible mechanisms of MA toxicity after repeated exposure by (1) determining the changes of metabolic profile using 1 H nuclear magnetic resonance spectroscopy and multivariate analysis, and (2) investigating the occurrence of oxidative stress using liquid chromatography tandem mass spectrometry by using Sprague-Dawley rat urine samples. Adult male rats were subjected to a 28 day subchronic study (0, 6, 20 and 60 mg kg-1 ) via oral gavage. Urine was collected twice a day on days 0, 7, 14, 21 and 28; organs underwent histopathological examination. Changes in body weight and relative kidney weights in medium- and high-dose groups were significantly different compared to controls. Morphological alterations were evident in the kidneys and liver. Metabolomic results demonstrated that MA exposure increases the urinary concentrations of 8-hydroxy-2'-deoxyguanosine, 8-nitroguanine and 8-iso-prostaglandin F2α ; levels of acetoacetate, hippurate, alanine and acetate demonstrated time- and dose-dependent variations in the treatment groups. Findings suggest that MA consumption escalates oxidative damage, membrane lipid destruction and disrupt energy metabolism. These aforementioned changes in biomarkers and endogenous metabolites elucidate and assist in characterizing the possible mechanisms by which MA induces nephro- and hepatotoxicity.

Melatonin set out to ER stress signaling thwarts epithelial mesenchymal transition and peritoneal dissemination via calpain-mediated C/EBPß and NFκB cleavage.

Peritoneal dissemination of tumor has high mortality and is associated with the loss of epithelial features, acquisition of motile mesenchymal morphology characteristics, and invasive properties by tumor cells. Melatonin is an endogenously produced molecule in all plant species that is known to exert antitumor activity, but to date, its underlying mechanisms and antiperitoneal metastasis efficacy is not well defined. This study determined the antiperitoneal dissemination potential of melatonin in vivo and assessed its association with the inhibition of epithelial-to-mesenchymal transition (EMT) signaling mechanism by endoplasmic reticulum (ER) stress, which may be a major molecular mechanism of melatonin against cancer. The results demonstrate that melatonin inhibited peritoneal metastasis in vivo and activated ER stress in Cignal ERSE Reporter Assay, organelle structure in transmission electron microscopy images, calpain activity, and protein biomarkers like p-elf2α. Moreover, the overexpression of transcription factor C/EBPß in gastric cancer interacted with NFκB and further regulates COX-2 expression. These were dissociated and downregulated by melatonin, as proven by immunofluorescence imaging, immunoprecipitation, EMSA, and ChIP assay. Melatonin or gene silencing of C/EBPß decreased the EMT protein markers (E-cadherin, Snail, and Slug) and Wnt/beta-catenin activity by Topflash activity, and increased ER stress markers. In an animal study, the results of melatonin therapy were consistent with those of in vitro findings and attenuated systemic proangiogenesis factor production. In conclusion, C/EBPß and NFκB inhibition by melatonin may impede both gastric tumor growth and peritoneal dissemination by inducing ER stress and inhibiting EMT.

Rare-Variant Kernel Machine Test for Longitudinal Data from Population and Family Samples.

OBJECTIVE: The kernel machine (KM) test reportedly performs well in the set-based association test of rare variants. Many studies have been conducted to measure phenotypes at multiple time points, but the standard KM methodology has only been available for phenotypes at a single time point. In addition, family-based designs have been widely used in genetic association studies; therefore, the data analysis method used must appropriately handle familial relatedness. A rare-variant test does not currently exist for longitudinal data from family samples. Therefore, in this paper, we aim to introduce an association test for rare variants, which includes multiple longitudinal phenotype measurements for either population or family samples. METHODS: This approach uses KM regression based on the linear mixed model framework and is applicable to longitudinal data from either population (L-KM) or family samples (LF-KM). RESULTS: In our population-based simulation studies, L-KM has good control of Type I error rate and increased power in all the scenarios we considered compared with other competing methods. Conversely, in the family-based simulation studies, we found an inflated Type I error rate when L-KM was applied directly to the family samples, whereas LF-KM retained the desired Type I error rate and had the best power performance overall. Finally, we illustrate the utility of our proposed LF-KM approach by analyzing data from an association study between rare variants and blood pressure from the Genetic Analysis Workshop 18 (GAW18). CONCLUSION: We propose a method for rare-variant association testing in population and family samples using phenotypes measured at multiple time points for each subject. The proposed method has the best power performance compared to competing approaches in our simulation study.

A Sequence Kernel Association Test for Dichotomous Traits in Family Samples under a Generalized Linear Mixed Model.

OBJECTIVE: The existing methods for identifying multiple rare variants underlying complex diseases in family samples are underpowered. Therefore, we aim to develop a new set-based method for an association study of dichotomous traits in family samples. METHODS: We introduce a framework for testing the association of genetic variants with diseases in family samples based on a generalized linear mixed model. Our proposed method is based on a kernel machine regression and can be viewed as an extension of the sequence kernel association test (SKAT and famSKAT) for application to family data with dichotomous traits (F-SKAT). RESULTS: Our simulation studies show that the original SKAT has inflated type I error rates when applied directly to family data. By contrast, our proposed F-SKAT has the correct type I error rate. Furthermore, in all of the considered scenarios, F-SKAT, which uses all family data, has higher power than both SKAT, which uses only unrelated individuals from the family data, and another method, which uses all family data. CONCLUSION: We propose a set-based association test that can be used to analyze family data with dichotomous phenotypes while handling genetic variants with the same or opposite directions of effects as well as any types of family relationships.

Kernel-machine testing coupled with a rank-truncation method for genetic pathway analysis.

Traditional genome-wide association studies (GWASs) usually focus on single-marker analysis, which only accesses marginal effects. Pathway analysis, on the other hand, considers biological pathway gene marker hierarchical structure and therefore provides additional insights into the genetic architecture underlining complex diseases. Recently, a number of methods for pathway analysis have been proposed to assess the significance of a biological pathway from a collection of single-nucleotide polymorphisms. In this study, we propose a novel approach for pathway analysis that assesses the effects of genes using the sequence kernel association test and the effects of pathways using an extended adaptive rank truncated product statistic. It has been increasingly recognized that complex diseases are caused by both common and rare variants. We propose a new weighting scheme for genetic variants across the whole allelic frequency spectrum to be analyzed together without any form of frequency cutoff for defining rare variants. The proposed approach is flexible. It is applicable to both binary and continuous traits, and incorporating covariates is easy. Furthermore, it can be readily applied to GWAS data, exome-sequencing data, and deep resequencing data. We evaluate the new approach on data simulated under comprehensive scenarios and show that it has the highest power in most of the scenarios while maintaining the correct type I error rate. We also apply our proposed methodology to data from a study of the association between bipolar disorder and candidate pathways from Wellcome Trust Case Control Consortium (WTCCC) to show its utility.

Establishment of a trimodality analytical platform for tracing, imaging and quantification of gold nanoparticles in animals by radiotracer techniques.

This study aims to establish a (198)Au-radiotracer technique for in vivo tracing, rapid quantification, and ex vivo visualization of PEGylated gold nanoparticles (GNPs) in animals, organs and tissue dissections. The advantages of GNPs lie in its superior optical property, biocompatibility and versatile conjugation chemistry, which are promising to develop diagnostic probes and drug delivery systems. (198)Au is used as a radiotracer because it simultaneously emits beta and gamma radiations with proper energy and half-life; therefore, (198)Au can be used for bioanalytical purposes. The (198)Au-tagged radioactive gold nanoparticles ((198)Au-GNPs) were prepared simply by irradiating the GNPs in a nuclear reactor through the (197)Au(n,γ)(198)Au reaction and subsequently the (198)Au-GNPs were subjected to surface modification with polyethylene glycol to form PEGylated (198)Au-GNPs. The (198)Au-GNPs retained physicochemical properties that were the same as those of GNP before neutron irradiation. Pharmacokinetic and biodisposition studies were performed by intravenously injecting three types of (198)Au-GNPs with or without PEGylation into mice; the γ radiation in blood specimens and dissected organs was then measured. The (198)Au-radiotracer technique enables rapid quantification freed from tedious sample preparation and shows more than 95% recovery of injected GNPs. Clinical gamma scintigraphy was proved feasible to explore spatial- and temporal-resolved biodisposition of (198)Au-GNPs in living animals. Moreover, autoradiography, which recorded beta particles from (198)Au, enabled visualizing the heterogeneous biodisposition of (198)Au-GNPs in different microenvironments and tissues. In this study, the (198)Au-radiotracer technique facilitated creating a trimodality analytical platform for tracing, quantifying and imaging GNPs in animals.