Hongying Dai

The effect of genotype on methotrexate polyglutamate variability in juvenile idiopathic arthritis and association with drug response

OBJECTIVE The response to and toxicity of methotrexate (MTX) are unpredictable in patients with juvenile idiopathic arthritis (JIA). Intracellular polyglutamation of MTX, assessed by measuring concentrations of MTX polyglutamates (MTXGlu), has been demonstrated to be a promising predictor of drug response. Therefore, this study was aimed at investigating the genetic predictors of MTXGlu variability and associations between MTXGlu and drug response in JIA. METHODS The study was designed as a single-center cross-sectional analysis of patients with JIA who were receiving stable doses of MTX at a tertiary care childrens hospital. After informed consent was obtained from the 104 patients with JIA, blood was withdrawn during routine MTX-screening laboratory testing. Clinical data were collected by chart review. Genotyping for 34 single-nucleotide polymorphisms (SNPs) in 18 genes within the MTX metabolic pathway was performed. An ion-pair chromatographic procedure with mass spectrometric detection was used to measure MTXGlu1-7. RESULTS Analysis and genotyping of MTXGlu was completed in the 104 patients. K-means clustering resulted in 3 distinct patterns of MTX polyglutamation. Cluster 1 had low red blood cell (RBC) MTXGlu concentrations, cluster 2 had moderately high RBC MTXGlu1+2 concentrations, and cluster 3 had high concentrations of MTXGlu, specifically MTXGlu3-5. SNPs in the purine and pyrimidine synthesis pathways, as well as the adenosine pathway, were significantly associated with cluster subtype. The cluster with high concentrations of MTXGlu3-5 was associated with elevated liver enzyme levels on liver function tests (LFTs), and there were higher concentrations of MTXGlu3-5 in children who reported gastrointestinal side effects and had abnormal findings on LFTs. No association was noted between MTXGlu and active arthritis. CONCLUSION MTXGlu remains a potentially useful tool for determining outcomes in patients with JIA being treated with MTX. The genetic predictors of MTXGlu variability may also contribute to a better understanding of the intracellular biotransformation of MTX in these patients.

A modified generalized Fisher method for combining probabilities from dependent tests

Rapid developments in molecular technology have yielded a large amount of high throughput genetic data to understand the mechanism for complex traits. The increase of genetic variants requires hundreds and thousands of statistical tests to be performed simultaneously in analysis, which poses a challenge to control the overall Type I error rate. Combining p-values from multiple hypothesis testing has shown promise for aggregating effects in high-dimensional genetic data analysis. Several p-value combining methods have been developed and applied to genetic data; see Dai et al. (2012b) for a comprehensive review. However, there is a lack of investigations conducted for dependent genetic data, especially for weighted p-value combining methods. Single nucleotide polymorphisms (SNPs) are often correlated due to linkage disequilibrium (LD). Other genetic data, including variants from next generation sequencing, gene expression levels measured by microarray, protein and DNA methylation data, etc. also contain complex correlation structures. Ignoring correlation structures among genetic variants may lead to severe inflation of Type I error rates for omnibus testing of p-values. In this work, we propose modifications to the Lancaster procedure by taking the correlation structure among p-values into account. The weight function in the Lancaster procedure allows meaningful biological information to be incorporated into the statistical analysis, which can increase the power of the statistical testing and/or remove the bias in the process. Extensive empirical assessments demonstrate that the modified Lancaster procedure largely reduces the Type I error rates due to correlation among p-values, and retains considerable power to detect signals among p-values. We applied our method to reassess published renal transplant data, and identified a novel association between B cell pathways and allograft tolerance.

Defining Risk Factors for Red Man Syndrome in Children and Adults

Background: Red man syndrome (RMS) is a well-known adverse reaction that occurs in pediatric patients receiving vancomycin, yet reported prevalence is varied, and characteristics and risk factors are not well understood. Our objective was to determine the prevalence, characteristics and risk factors for RMS in pediatric patients receiving vancomycin, including contributing genetic factors. Methods: A multicenter retrospective study of 546 subjects (0.5–21 years) who received at least 1 dose of intravenous vancomycin was conducted. Demographic and symptom data were collected through chart review and parent/nurse report. Genotype analysis included 10 single nucleotide polymorphisms in the histamine pathway. Results: RMS was observed in 77 (14%) subjects receiving vancomycin. Forty percent of subjects with RMS symptoms developed rash, pruritis and flushing, without hypotension. Antecedent antihistamine use was identified as a risk factor for RMS (P < 0.001). Multivariate regression analysis identified age > 2 years (P = 0.008), previous RMS (P < 0.001), vancomycin dose (P = 0.02) and vancomycin concentration (P = 0.017) as RMS risk factors, whereas African American race was protective (P = 0.011). We observed an apparent association between RMS and a single nucleotide polymorphism in the diamine oxidasegene (P = 0.044); however, no associations were revealed by multifactor dimensionality reduction analysis. Conclusions: RMS is a common adverse event in children receiving vancomycin. Identified risk factors are Caucasian ethnicity, age≥ 2 years, previous RMS history, vancomycin dose ≥ 10 mg/kg, vancomycin concentration ≥ 5 mg/mL and antecedent antihistamine use. Known genetic variants in histamine metabolism or receptors do not appear to be substantial contributors to risk of RMS.

Red blood cell folate concentrations and polyglutamate distribution in juvenile arthritis: predictors of folate variability.

Objective Methotrexate (MTX) has several enzymatic targets in the folate pathway. To better understand the variability in response to MTX, we characterized the interindividual variability of intracellular folate pools in children with juvenile arthritis (JA) and determined clinical and genetic contributors to this variability. Study design This exploratory single-center cross-sectional study evaluated 93 patients with JA not currently receiving MTX. Whole blood, plasma, and erythrocyte folate concentrations were determined after deconjugation and analyzed through reversed-phase separation and stable isotope dilution tandem mass spectrometry. Folate polyglutamates were measured in red blood cell lysates using an ion-pair reversed phase chromatography tandem mass spectrometry method. Results Intracellular concentrations of 5-methyl-tetrahydrofolate (5-CH3-THF) and 5,10-methenyl-tetrahydrofolate varied approximately 20-fold and 80-fold, respectively. The polyglutamated forms of 5-CH3-THF as a percentage of total 5-CH3-THF (5-CH3-THFGlun) were also measured. Hierarchical clustering of 5-CH3-THFGlun revealed two groups, each with two distinct clusters. There was an inverse relationship between 5-CH3-THFGlun chain length and plasma 5-CH3-THF concentrations. A subgroup of patients with a historical intolerance to MTX had significantly lower cellular folate concentrations (P<0.0001). In univariate analyses, clinical variables including sex, age, and folate supplementation in addition to variations in MTHFR, MTR, and SLC25A32 were associated with differential intracellular folate redox concentrations. Multivariate analysis further supported the association of single nucleotide polymorphisms in SLC25A32, MTHFR, and MTR with variability in intracellular 5-CH3-THF and 5,10-methenyl-tetrahydrofolate concentrations, respectively. Conclusion Measurement of intracellular folate isoforms may contribute toward a better understanding of individual MTX effects in JA. Clinical variables in addition to genotypic differences beyond MTHFR may additionally explain differential intracellular folate concentrations and variable responses to MTX.

Mining social media data for opinion polarities about electronic cigarettes

Background There is an ongoing debate about harm and benefit of e-cigarettes, usage of which has rapidly increased in recent years. By separating non-commercial (organic) tweets from commercial tweets, we seek to evaluate the general publics attitudes towards e-cigarettes. Methods We collected tweets containing the words ‘e-cig’, ‘e-cigarette’, ‘e-liquid’, ‘vape’, ‘vaping’, ‘vapor’ and ‘vaporizer’ from 23 July to 14 October 2015 (n=757 167). A multilabel Naïve Bayes model was constructed to classify tweets into 5 polarities (against, support, neutral, commercial, irrelevant). We further analysed the prevalence of e-cigarette tweets, geographic variations in these tweets and the impact of socioeconomic factors on the public attitudes towards e-cigarettes. Results Opinions from organic tweets about e-cigarettes were mixed (against 17.7%, support 10.8% and neutral 19.4%). The organic—against tweets delivered strong educational information about the risks of e-cigarette use and advocated for the general public, especially youth, to stop vaping. However, the organic—against tweets were outnumbered by commercial tweets and organic—support tweets by a ratio of over 1 to 3. Higher prevalence of organic tweets was associated with states with higher education rates (r=0.60, p<0.0001), higher percentage of black and African-American population (r=0.34, p=0.01), and higher median household income (r=0.33, p=0.02). The support rates for e-cigarettes were associated with states with fewer persons under 18 years old (r=−0.33, p=0.02) and a higher percentage of female population (r=0.3, p=0.02). Conclusions The organic—against tweets raised public awareness of potential health risks and could aid in preventing non-smokers, adolescents and young adults from using e-cigarettes. Opinion polarities about e-cigarettes from social networks could be highly influential to the general public, especially youth. Further educational campaigns should include measuring their effectiveness.

Cotinine in human placenta predicts induction of gene expression in fetal tissues.

Maternal cigarette smoking during pregnancy is associated with increased risk of perinatal morbidity and mortality. However, the mechanisms underlying adverse birth outcomes following prenatal exposure to cigarette smoke remain unknown due, in part, to the absence or unreliability of information regarding maternal cigarette smoke exposure during pregnancy. Our goal was to determine if placental cotinine could be a reliable biomarker of fetal cigarette smoke exposure during pregnancy. Cotinine levels were determined in placentas from 47 women who reported smoking during pregnancy and from 10 women who denied cigarette smoke exposure. Cotinine levels were significantly higher in placentas from women reporting cigarette smoking (median = 27.2 ng/g) versus women who reported no smoke exposure (2.3 ng/g, P < 0.001). Receiver operating characteristic curve analysis identified an optimal cut point of 7.5 ng/g (sensitivity = 78.7%, specificity = 100%) to classify placenta samples from mothers who smoked versus those from mothers who did not. Among 415 placentas for which maternal cigarette smoking status was unavailable, 167 had cotinine levels > 7.5 ng/g and would be considered positive for cigarette smoke exposure. Data from quantitative reverse-transcription polymerase chain reaction analyses demonstrated that in utero cigarette smoke exposure predicted by cotinine in placenta is associated with changes in the expression of xenobiotic-metabolizing enzymes in fetal tissues. CYP1A1 mRNA in fetal lung and liver tissue and CYP1B1 mRNA in fetal lung tissue were significantly induced when cotinine was detected in placenta. These findings indicate that cotinine in placenta is a reliable biomarker for fetal exposure and response to maternal cigarette smoking during pregnancy.

Risk score modeling of multiple gene to gene interactions using aggregated-multifactor dimensionality reduction

BackgroundMultifactor Dimensionality Reduction (MDR) has been widely applied to detect gene-gene (GxG) interactions associated with complex diseases. Existing MDR methods summarize disease risk by a dichotomous predisposing model (high-risk/low-risk) from one optimal GxG interaction, which does not take the accumulated effects from multiple GxG interactions into account.ResultsWe propose an Aggregated-Multifactor Dimensionality Reduction (A-MDR) method that exhaustively searches for and detects significant GxG interactions to generate an epistasis enriched gene network. An aggregated epistasis enriched risk score, which takes into account multiple GxG interactions simultaneously, replaces the dichotomous predisposing risk variable and provides higher resolution in the quantification of disease susceptibility. We evaluate this new A-MDR approach in a broad range of simulations. Also, we present the results of an application of the A-MDR method to a data set derived from Juvenile Idiopathic Arthritis patients treated with methotrexate (MTX) that revealed several GxG interactions in the folate pathway that were associated with treatment response. The epistasis enriched risk score that pooled information from 82 significant GxG interactions distinguished MTX responders from non-responders with 82% accuracy.ConclusionsThe proposed A-MDR is innovative in the MDR framework to investigate aggregated effects among GxG interactions. New measures (pOR, pRR and pChi) are proposed to detect multiple GxG interactions.

Effects of perinatal cocaine exposure on open field behavior and the response to corticotropin releasing hormone (CRH) in rat offspring

Previous reports indicate that prenatal cocaine exposure alters specific behaviors and hypothalamic-pituitary-adrenal axis (HPA) function in the offspring. In most previous studies, cocaine was given via subcutaneous injections. However intravenous administration more closely mimics human cocaine abuse during pregnancy. Therefore, we investigated the effects of prenatal cocaine exposure via intravenous injection to the mothers on open field behavior and HPA axis function of the offspring. We hypothesized that prenatal cocaine exposure decreases immobility in a novel environment, and enhances the HPA response to stress. Dams received cocaine (COC) or vehicle (control, CON) intravenously from gestation day 8 to postnatal day (PD) 5. Behaviors were recorded in the open field on PD 28 (weanlings). As expected, perinatally cocaine-exposed offspring spent less time immobile and had a longer latency to entering the center zone. No other behavioral activities were different between the groups. On PD 43-50, adolescent male and female offspring received either corticotropin releasing hormone (CRH) or saline intravenously. Plasma adrenocorticotropic hormone (ACTH) and corticosterone (CORT) levels were determined before, and up to 60 min after injection. COC-exposed offspring of both sexes had higher basal CORT levels. Prenatal cocaine enhanced the CORT response to CRH/saline injections up to 60 min in males but not in females. These novel results show that perinatal administration of cocaine in a manner that most closely mimics human cocaine use has long-term effects on the offsprings behavioral response to stress and on HPA axis functions.

Geographic density and proximity of vape shops to colleges in the USA

Background Vape shops have been spreading rapidly in the USA since 2008, catering to the fast-growing market for electronic cigarettes. Little is known about the geographic density and proximity of vape shops near colleges. Methods Names and addresses of vape shops were collected from 3 online directories: Yelp.com, Yellowpages.com and Guidetovaping.com. We identified the prevalence of US-based vape shops and their density and proximity to colleges using a geographic information system. General linear model and negative binomial regression were performed to examine the factors associated with proximity and density of vape shops near colleges. Results We identified 9945 vape shops in the USA as of December 2015, a nearly threefold increase from 2013. Among the 2755 colleges included in this study, 66.5% had at least 1 vape shop within a 3-mile radius. The median proximity of the nearest vape shop to each college/university was 1.8 miles. Proximity increased by student population, private as compared to public institutions, and location (city vs rural). Within a 1-mile radius, colleges with smoke-free campus policies had a lower density of vape shops (RR=0.6, p=0.002) than those without smoke-free campus policies. Private institutions had a higher density of vape shops (RR=7.8, p<0.0001) than did public institutions. Colleges with campus housing had a lower density of vape shops (RR=0.4, p<0.0001) than those without campus housing, and colleges located in cities had a much higher density of vape shops than those located in rural areas (RR=6.6, p<0.0001). Smoke-free and e-cigarette-free campus policies had significant interactions with college type (private vs public) and campus housing in reducing vape shop density. Conclusions Vape shops are more likely to be located near private institutions and colleges in cities as opposed to rural areas. Smoke-free and e-cigarette-free campus policies have had significant effects in reducing the density of vape shops but have not reduced the proximity of vape shops to colleges. Regulations on the sale and advertisement of e-cigarettes to youth and young adults are critically needed.

Sleep problems and functional disability in children with functional gastrointestinal disorders: An examination of the potential mediating effects of physical and emotional symptoms

BackgroundSleep disturbances are increasingly recognized as a common problem for children and adolescents with chronic pain conditions, but little is known about the prevalence, type, and impact of sleep problems in pediatric functional gastrointestinal disorders (FGIDs). The objectives of the current study were two-fold: 1) to describe the pattern of sleep disturbances reported in a large sample of children and adolescents with FGIDs; and, 2) to explore the impact of sleep by examining the inter-relationships between sleep disturbance, physical symptoms, emotional problems, and functional disability in this population.MethodsOver a 3-year period, 283 children aged 8–17 years who were diagnosed with an FGID and a primary caretaker independently completed questionnaires regarding sleep, emotional functioning, physical symptoms, and functional disability during an initial evaluation for chronic abdominal pain at a pediatric tertiary care center. A verbal review of systems also was collected at that time. Descriptive statistics were used to characterize the pattern of sleep disturbances reported, while structural equation modeling (SEM) was employed to test theorized meditational relationships between sleep and functional disability through physical and emotional symptoms.ResultsClinically significant elevations in sleep problems were found in 45% of the sample, with difficulties related to sleep onset and maintenance being most common. No difference was seen by specific FGID or by sex, although adolescents were more likely to have sleep onset issues than younger children. Sleep problems were positively associated with functional disability and physical symptoms fully mediated this relationship. Emotional symptoms, while associated with sleep problems, evidenced no direct link to functional disability.ConclusionsSleep problems are common in pediatric FGIDs and are associated with functional disability through their impact on physical symptoms. Treatments targeting sleep are likely to be beneficial in improving physical symptoms and, ultimately, daily function in pediatric FGIDs.