Novel risk prediction models for deep vein thrombosis after thoracotomy and thoracoscopic lung cancer resections, involving coagulation and immune function.

The main focus of this study was to compare the predictive value of coagulation, fibrinolysis, thromboelastography, stress response, and immune function in predicting the incidence of deep venous thrombosis (DVT) in lung cancer (LC) patients undergoing thoracoscopic LC resection vs thoracotomy LC resection. To do that, a prospective, single-center, case-control study involving 460 LC patients was conducted. The risk indicators affecting patients with DVT after LC resection in the testing cohort were determined using logistic regression and receiver operator characteristic (ROC) analyses. One validation cohort was used to assess the risk prediction models. DVT incidence was higher in the thoracoscopic group (18.7%) than in the thoracotomy group (11.2%) in the testing cohort (χ 2 = 4.116, P = 0.042). The final model to predict the incidence of DVT after thoracoscopic LC excision (1 day after surgery) was as follows: Logit(P) = 9.378 - 0.061(R-value) - 0.109(K value) + 0.374(α angle) + 0.403(MA) + 0.298(FIB) + 0.406(D-D) + 0.190(MDA) - 0.097(CD4+/CD8+). For thoracotomy LC resection, the final model (3 days after operation) was: Logit(P) = -2.463 - 0.026(R-value) - 0.143(K value) + 0.402(α angle) + 0.198(D-D) + 0.237(MDA) + 0.409(SOD). In the validation cohort, this risk prediction model continued to demonstrate good predictive performance. As a result, the predictive accuracy of postoperative DVT in patients who underwent thoracoscopic LC resection and thoracotomy LC resection was improved by risk prediction models.

Parsimonious model for mass-univariate vertexwise analysis.

Purpose: Covariance between gray-matter measurements can reflect structural or functional brain networks though it has also been shown to be influenced by confounding factors (e.g., age, head size, and scanner), which could lead to lower mapping precision (increased size of associated clusters) and create distal false positives associations in mass-univariate vertexwise analyses. Approach: We evaluated this concern by performing state-of-the-art mass-univariate analyses (general linear model, GLM) on traits simulated from real vertex-wise gray matter data (including cortical and subcortical thickness and surface area). We contrasted the results with those from linear mixed models (LMMs), which have been shown to overcome similar issues in omics association studies. Results: We showed that when performed on a large sample ( N = 8662 , UK Biobank), GLMs yielded greatly inflated false positive rate (cluster false discovery rate > 0.6 ). We showed that LMMs resulted in more parsimonious results: smaller clusters and reduced false positive rate but at a cost of increased computation. Next, we performed mass-univariate association analyses on five real UKB traits (age, sex, BMI, fluid intelligence, and smoking status) and LMM yielded fewer and more localized associations. We identified 19 significant clusters displaying small associations with age, sex, and BMI, which suggest a complex architecture of at least dozens of associated areas with those phenotypes. Conclusions: The published literature could contain a large proportion of redundant (possibly confounded) associations that are largely prevented using LMMs. The parsimony of LMMs results from controlling for the joint effect of all vertices, which prevents local and distal redundant associations from reaching significance.

miR-141-3p Reduces Cell Migration and Proliferation in an In Vitro Modelof Atherosclerosis by Targeting Wnt5a.

BACKGROUND: Atherosclerosis (AS) is a type of chronic vascular disease that is also a leading cause of numerous cardiovascular diseases in humans. The biomolecules responsible for the roles of microRNA (miR)-141-3p during AS development are less understood. METHODS: The relation between Wnt5a and miR-141-3p was predicted using bioinformatics software TargetScan 7.1, and confirmed via dual luciferase reporter assay. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) and immunoblotting were conducted for examining miR-141-3p and Wingless and Int-1 (Wnt)5a expression levels. Additionally, transwell migration and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assays were conducted for analyzing cell migration and proliferation, respectively. RESULTS: miR-141-3p was decreased in oxidized low-density lipoprotein (ox-LDL)-treated human vascular smooth muscle cells (VSMCs). Pretreatment with miR-141-3p mimic inhibited cell migration and proliferation in ox-LDL-induced VSMCs. Wnt5a was verified to act as the target of miR-141-3p in VSMCs. pcDNA3-Wnt5a partially reversed the effects of miR-141-3p mimic in ox-LDL-stimulated VSMCs. CONCLUSION: miR-141-3p mimic decreased the damage in an AS model by targeting Wnt5a, thereby presenting a novel potential therapeutic target for treating AS.

Promoter-anchored chromatin interactions predicted from genetic analysis of epigenomic data.

Promoter-anchored chromatin interactions (PAIs) play a pivotal role in transcriptional regulation. Current high-throughput technologies for detecting PAIs, such as promoter capture Hi-C, are not scalable to large cohorts. Here, we present an analytical approach that uses summary-level data from cohort-based DNA methylation (DNAm) quantitative trait locus (mQTL) studies to predict PAIs. Using mQTL data from human peripheral blood ([Formula: see text]), we predict 34,797 PAIs which show strong overlap with the chromatin contacts identified by previous experimental assays. The promoter-interacting DNAm sites are enriched in enhancers or near expression QTLs. Genes whose promoters are involved in PAIs are more actively expressed, and gene pairs with promoter-promoter interactions are enriched for co-expression. Integration of the predicted PAIs with GWAS data highlight interactions among 601 DNAm sites associated with 15 complex traits. This study demonstrates the use of mQTL data to predict PAIs and provides insights into the role of PAIs in complex trait variation.

Analysis of DNA methylation associates the cystine-glutamate antiporter SLC7A11 with risk of Parkinson's disease.

An improved understanding of etiological mechanisms in Parkinson's disease (PD) is urgently needed because the number of affected individuals is projected to increase rapidly as populations age. We present results from a blood-based methylome-wide association study of PD involving meta-analysis of 229 K CpG probes in 1,132 cases and 999 controls from two independent cohorts. We identify two previously unreported epigenome-wide significant associations with PD, including cg06690548 on chromosome 4. We demonstrate that cg06690548 hypermethylation in PD is associated with down-regulation of the SLC7A11 gene and show this is consistent with an environmental exposure, as opposed to medications or genetic factors with effects on DNA methylation or gene expression. These findings are notable because SLC7A11 codes for a cysteine-glutamate anti-porter regulating levels of the antioxidant glutathione, and it is a known target of the environmental neurotoxin ß-methylamino-L-alanine (BMAA). Our study identifies the SLC7A11 gene as a plausible biological target in PD.

Effects of TNFR1 gene silencing on early apoptosis of marbofloxacin-treated chondrocytes from juvenile dogs.

Quinolones (QNs)-induced cartilaginous lesions in juvenile animals by chondrocyte apoptosis is an important toxic effect, which results in the restriction of their use in pediatrics. However, limited data about QNs chondrotoxicity are available for evaluation of the potential toxicity in both animals and human cartilage. To explore whether tumor necrosis factor/its receptor (TNF/TNFR1) signaling pathway is involved in the early apoptosis of marbofloxacin-induced chondrocytes, canine juvenile chondrocytes were treated with 0, 20, 50 and 100 µg/mL marbofloxacin. Results showed that the apoptosis rates of the chondrocytes at 2, 8 and 24 h were significantly increased in a concentration- and time-dependent manner (P < 0.05). The mRNA levels of apoptosis-related factors in TNF/TNFR1 signaling pathways and the protein levels of TNFα and TNFR1 were increased in canine chondrocytes treated with 20-100 µg/mL marbofloxacin (P < 0.05) while TNFR1 gene silencing significantly decreased the chondrocyte apoptosis and inhibited the mRNA expression of TNF/TNFR1 downstream signaling molecules after 100 µg/mL marbofloxacin treatment at 8 h (P < 0.01). It was confirmed that activated TNF/TNFR1 signaling pathway may play a leading role in the early apoptosis of marbofloxacin-induced canine juvenile chondrocytes, which is helpful for clinical estimation or prevention of the risk of QNs.

Genome-wide association analyses of risk tolerance and risky behaviors in over 1 million individuals identify hundreds of loci and shared genetic influences.

Humans vary substantially in their willingness to take risks. In a combined sample of over 1 million individuals, we conducted genome-wide association studies (GWAS) of general risk tolerance, adventurousness, and risky behaviors in the driving, drinking, smoking, and sexual domains. Across all GWAS, we identified hundreds of associated loci, including 99 loci associated with general risk tolerance. We report evidence of substantial shared genetic influences across risk tolerance and the risky behaviors: 46 of the 99 general risk tolerance loci contain a lead SNP for at least one of our other GWAS, and general risk tolerance is genetically correlated ([Formula: see text] ~ 0.25 to 0.50) with a range of risky behaviors. Bioinformatics analyses imply that genes near SNPs associated with general risk tolerance are highly expressed in brain tissues and point to a role for glutamatergic and GABAergic neurotransmission. We found no evidence of enrichment for genes previously hypothesized to relate to risk tolerance.

An epigenome-wide association study of sex-specific chronological ageing.

BACKGROUND: Advanced age is associated with cognitive and physical decline and is a major risk factor for a multitude of disorders. There is also a gap in life expectancy between males and females. DNA methylation differences have been shown to be associated with both age and sex. Here, we investigate age-by-sex differences in blood-based DNA methylation in an unrelated cohort of 2586 individuals between the ages of 18 and 87 years, with replication in a further 4450 individuals between the ages of 18 and 93 years. METHODS: Linear regression models were applied, with stringent genome-wide significance thresholds (p < 3.6 × 10-8) used in both the discovery and replication data. A second, highly conservative mixed linear model method that better controls the false-positive rate was also applied, using the same genome-wide significance thresholds. RESULTS: Using the linear regression method, 52 autosomal and 597 X-linked CpG sites, mapping to 251 unique genes, replicated with concordant effect size directions in the age-by-sex interaction analysis. The site with the greatest difference mapped to GAGE10, an X-linked gene. Here, DNA methylation levels remained stable across the male adult age range (DNA methylation by age r = 0.02) but decreased across female adult age range (DNA methylation by age r = - 0.61). One site (cg23722529) with a significant age-by-sex interaction also had a quantitative trait locus (rs17321482) that is a genome-wide significant variant for prostate cancer. The mixed linear model method identified 11 CpG sites associated with the age-by-sex interaction. CONCLUSION: The majority of differences in age-associated DNA methylation trajectories between sexes are present on the X chromosome. Several of these differences occur within genes that have been implicated in sexually dimorphic traits.

Role of glutamine in the mediation of E-cadherin, p120-catenin and inflammation in ventilator-induced lung injury.

BACKGROUND: Ventilator-induced lung injury (VILI) is commonly associated with barrier dysfunction and inflammation reaction. Glutamine could ameliorate VILI, but its role has not been fully elucidated. This study examined the relationship between inflammatory cytokines (interleukin [IL]-6, tumor necrosis factor [TNF]-α, and IL-10) and adherens junctions (E-cadherin, p120-catenin), which were ameliorated by glutamine in VILI, both in vitro and in vivo. METHODS: For the in vivo study, 30 healthy C57BL/6 mice weighing 25-30 g were randomly divided into five groups with random number table (n = 6 in each group): control (Group C); low tidal volume (Group L); low tidal volume + glutamine (Group L + G); high tidal volume (Group H); and high tidal volume + glutamine (Group H + G). Mice in all groups, except Group C, underwent mechanical ventilation for 4 h. For the in vitro study, mouse lung epithelial 12 (MLE-12) cells pretreated with glutamine underwent cyclic stretching at 20% for 4 h. Cell lysate and lung tissue were obtained to detect the junction proteins, inflammatory cytokines, and lung pathological changes by the Western blotting, cytokine assay, hematoxylin and eosin staining, and immunofluorescence. RESULTS: In vivo, compared with Group C, total cell counts (t = -28.182, P < 0.01), the percentage of neutrophils (t = -28.095, P < 0.01), IL-6 (t = -28.296, P < 0.01), and TNF-α (t = -19.812, P < 0.01) in bronchoalveolar lavage (BAL) fluid, lung injury scores (t = -6.708, P < 0.01), and the wet-to-dry ratio (t = -15.595, P < 0.01) were increased in Group H; IL-10 in BAL fluid (t = 9.093, P < 0.01) and the expression of E-cadherin (t = 10.044, P < 0.01) and p120-catenin (t = 13.218, P < 0.01) were decreased in Group H. Compared with Group H, total cell counts (t = 14.844, P < 0.01), the percentage of neutrophils (t = 18.077, P < 0.01), IL-6 (t = 18.007, P < 0.01), and TNF-α (t = 10.171, P < 0.01) in BAL fluid were decreased in Group H + G; IL-10 in BAL fluid (t = -7.531, P < 0.01) and the expression of E-cadherin (t = -14.814, P < 0.01) and p120-catenin (t = -9.114, P < 0.01) were increased in Group H + G. In vitro, compared with the nonstretching group, the levels of IL-6 (t = -21.111, P < 0.01) and TNF-α (t = -15.270, P < 0.01) were increased in the 20% cyclic stretching group; the levels of IL-10 (t = 5.450, P < 0.01) and the expression of E-cadherin (t = 17.736, P < 0.01) and p120-catenin (t = 16.136, P < 0.01) were decreased in the 20% cyclic stretching group. Compared with the stretching group, the levels of IL-6 (t = 11.818, P < 0.01) and TNF-α (t = 8.631, P < 0.01) decreased in the glutamine group; the levels of IL-10 (t = -3.203, P < 0.05) and the expression of E-cadherin (t = -13.567, P < 0.01) and p120-catenin (t = -10.013, P < 0.01) were increased in the glutamine group. CONCLUSIONS: High tidal volume mechanical ventilation and 20% cyclic stretching could cause VILI. Glutamine regulates VILI by improving cytokines and increasing the adherens junctions, protein E-cadherin and p120-catenin, to enhance the epithelial barrier function.

Meta-analysis identifies five novel loci associated with endometriosis highlighting key genes involved in hormone metabolism.

Endometriosis is a heritable hormone-dependent gynecological disorder, associated with severe pelvic pain and reduced fertility; however, its molecular mechanisms remain largely unknown. Here we perform a meta-analysis of 11 genome-wide association case-control data sets, totalling 17,045 endometriosis cases and 191,596 controls. In addition to replicating previously reported loci, we identify five novel loci significantly associated with endometriosis risk (P<5 × 10-8), implicating genes involved in sex steroid hormone pathways (FN1, CCDC170, ESR1, SYNE1 and FSHB). Conditional analysis identified five secondary association signals, including two at the ESR1 locus, resulting in 19 independent single nucleotide polymorphisms (SNPs) robustly associated with endometriosis, which together explain up to 5.19% of variance in endometriosis. These results highlight novel variants in or near specific genes with important roles in sex steroid hormone signalling and function, and offer unique opportunities for more targeted functional research efforts.

TNF/TNFR1 pathway and endoplasmic reticulum stress are involved in ofloxacin-induced apoptosis of juvenile canine chondrocytes.

BACKGROUND AND PURPOSE: Quinolones cause obvious cartilaginous lesions in juvenile animals by chondrocyte apoptosis, which results in the restriction of their use in pediatric and adolescent patients. Studies showed that chondrocytes can be induced to produce TNFα, and the cisternae of the endoplasmic reticulum in quinolone-treated chondrocytes become dilated. We investigated whether TNF/TNFR1 pathway and endoplasmic reticulum stress (ERs) are involved in ofloxacin (a typical quinolone)-induced apoptosis of juvenile canine chondrocytes. EXPERIMENTAL APPROACH: Canine juvenile chondrocytes were treated with ofloxacin. Cell survival and apoptosis rates were determined with MTT method and flow cytometry, respectively. The gene expression levels of the related signaling molecules (TNFα, TNFR1, TRADD, FADD and caspase-8) in death receptor pathways and main apoptosis-related molecules (calpain, caspase-12, GADD153 and GRP78) in ERs were measured by qRT-PCR. The gene expression of TNFR1 was suppressed with its siRNA. The protein levels of TNFα, TNFR1 and caspase-12 were assayed using Western blotting. KEY RESULTS: The survival rates decreased while apoptosis rates increased after the chondrocytes were treated with ofloxacin. The mRNA levels of the measured apoptosis-related molecules in death receptor pathways and ERs, and the protein levels of TNFα, TNFR1 and caspase-12 increased after the chondrocytes were exposed to ofloxacin. The downregulated mRNA expressions of TNFR1, Caspase-8 and TRADD, and the decreased apoptosis rates of the ofloxacin-treated chondrocytes occurred after TNFR1-siRNA interference. CONCLUSIONS AND IMPLICATIONS: Ofloxacin-induced chondrocyte apoptosis in a time- and concentration-dependent fashion. TNF/TNFR1 pathway and ERs are involved in ofloxacin-induced apoptosis of juvenile canine chondrocytes in the early stage.