Identification and validation of a DNA methylation-driven gene-based prognostic model for clear cell renal cell carcinoma.

BACKGROUND: Clear cell renal cell carcinoma (ccRCC) is a malignant tumor with heterogeneous morphology and poor prognosis. This study aimed to establish a DNA methylation (DNAm)-driven gene-based prognostic model for ccRCC. METHODS: Reduced representation bisulfite sequencing (RRBS) was performed on the DNA extracts from ccRCC patients. We analyzed the RRBS data from 10 pairs of patient samples to screen the candidate CpG sites, then trained and validated an 18-CpG site model, and integrated the clinical characters to establish a Nomogram model for the prognosis or risk evaluation of ccRCC. RESULTS: We identified 2261 DMRs in the promoter region. After DMR selection, 578 candidates were screened, and was correspondence with 408 CpG dinucleotides in the 450 K array. We collected the DNAm profiles of 478 ccRCC samples from TCGA dataset. Using the training set with 319 samples, a prognostic panel of 18 CpGs was determined by univariate Cox regression, LASSO regression, and multivariate Cox proportional hazards regression analyses. We constructed a prognostic model by combining the clinical signatures. In the test set (159 samples) and whole set (478 samples), the Kaplan-Meier plot showed significant differences; and the ROC curve and survival analyses showed AUC greater than 0.7. The Nomogram integrated with clinicopathological characters and methylation risk score had better performance, and the decision curve analyses also showed a beneficial effect. CONCLUSIONS: This work provides insight into the role of hypermethylation in ccRCC. The targets identified might serve as biomarkers for early ccRCC diagnosis and prognosis biomarkers for ccRCC. We believe our findings have implications for better risk stratification and personalized management of this disease.

Phosphofructokinase-M inhibits cell growth via modulating the FOXO3 pathway in renal cell carcinoma cells.

Phosphofructokinase-M (PFKM) is a key enzyme in glycolysis. The expression and activity of PFKM is closely related to the occurrence and development of malignant tumors, but its role in the regulation of renal cell carcinoma (RCC) is still unknown. We found that the expression of PFKM was lower in RCC tumor tissue than in adjacent normal tissues, and that low expression of PFKM was related to the poor overall survival of RCC patients. In addition, our results showed that FOXO3 mediated PFKM inhibited the growth, migration and invasion of RCC cells, suggesting that PFKM is a protective factor for RCC.

Identifying the novel key genes in renal cell carcinoma by bioinformatics analysis and cell experiments.

BACKGROUND: Although major driver gene have been identified, the complex molecular heterogeneity of renal cell cancer (RCC) remains unclear. Therefore, more relevant genes need to be identified to explain the pathogenesis of renal cancer. METHODS: Microarray datasets GSE781, GSE6344, GSE53000 and GSE68417 were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) were identified by employing GEO2R tool, and function enrichment analyses were performed by using DAVID. The protein-protein interaction network (PPI) was constructed and the module analysis was performed using STRING and Cytoscape. Survival analysis was performed using GEPIA. Differential expression was verified in Oncomine. Cell experiments (cell viability assays, transwell migration and invasion assays, wound healing assay, flow cytometry) were utilized to verify the roles of the hub genes on the proliferation of kidney cancer cells (A498 and OSRC-2 cell lines). RESULTS: A total of 215 DEGs were identified from four datasets. Six hub gene (SUCLG1, PCK2, GLDC, SLC12A1, ATP1A1, PDHA1) were identified and the overall survival time of patients with RCC were significantly shorter. The expression levels of these six genes were significantly decreased in six RCC cell lines(A498, OSRC-2, 786- O, Caki-1, ACHN, 769-P) compared to 293t cell line. The expression level of both mRNA and protein of these genes were downregulated in RCC samples compared to those in paracancerous normal tissues. Cell viability assays showed that overexpressions of SUCLG1, PCK2, GLDC significantly decreased proliferation of RCC. Transwell migration, invasion, wound healing assay showed overexpression of three genes(SUCLG1, PCK2, GLDC) significantly inhibited the migration, invasion of RCC. Flow cytometry analysis showed that overexpression of three genes(SUCLG1, PCK2, GLDC) induced G1/S/G2 phase arrest of RCC cells. CONCLUSION: Based on our current findings, it is concluded that SUCLG1, PCK2, GLDC may serve as a potential prognostic marker of RCC.

Energy output modalities of shockwave lithotripsy in the treatment of urinary stones: escalating or fixed voltage? A systematic review and meta-analysis.

PURPOSE: To compare the effectiveness and safety of escalating and fixed energy output modalities of shockwave lithotripsy (SWL) in the treatment of urinary stones. METHODS: A systematic literature search using PubMed, Embase, Cochrane Library and Web of Science was performed to obtain relevant studies up to December 2018. Summarized mean differences (MDs) and risk differences (RDs) with 95% confidence intervals (CIs) were used for comparing continuous and dichotomous variables, respectively. RESULTS: Six RCTs including 775 patients were identified. In the overall pooled outcomes, no significant difference was detected between escalating and fixed voltage group regarding initial and final success rate (SR) and stone-free status (SFS), auxiliary procedure and complication (hematoma, febrile episode, and pain) rate. However, when shockwave frequency ≥ 90 shocks/min, total shocks per session ≤ 3000, or 1-3 SWL sessions were performed, escalating group was associated with significantly higher SR1 (defined as SFS + fragments ≤ 4 mm); in addition, escalating group brought significantly less hematoma when total shocks per session ≤ 3000. CONCLUSIONS: Escalating voltage SWL offered comparable safety and effectiveness to that of fixed voltage SWL. However, escalating voltage SWL could be recommended in following conditions: (1) shockwave frequency ≥ 90 shocks/min, total shocks per session ≤ 3000, or 1-3 SWL sessions, for better stone removal; (2) total shocks per session ≤ 3000, for less hematoma formation.

Percutaneous nephrolithotomy versus flexible ureteroscopic lithotripsy in the treatment of upper urinary tract stones: a meta-analysis comparing clinical efficacy and safety.

BACKGROUND: Upper urinary tract stones is the most common diseases in urology. Percutaneous nephrolithotomy (PCNL) and ureteroscopic lithotripsy (fURL) are common treatment, but both their efficacy and safety are controversial. Thus we aim to evaluate the efficacy and safety of PCNL and fURL in the treatment of upper urinary tract stones, providing a reference for clinical work. METHODS: PubMed, Web of Science, Embase and CNKI were searched through Apr. 1, 2019 to identify eligible studies. Data were analyzed by using RevMan 5.3 and Stata 12.0 software. Pooled relative risks (RRs) or weighted mean difference (WMD) with 95% confidence intervals (CIs) were calculated using fixed or random effects methods. Publication bias and sensitivity analysis were performed. RESULTS: Four randomized controlled trials (RCTs), fifteen cohort studies involving 1822 patients were included. Stone-free rate of PCNL was significantly high than that of fURL (RR: 1.07; 95% CI: 1.03, 1.12; P = 0.0004). The decline of hemoglobin in PCNL was significantly high than that of fURL (WMD: 1.07; 95% CI: 0.54, 1.61; P < 0.0001). The number of blood transfusion was significantly greater in the PCNL compared to the fURL (RR: 5.04; 95% CI: 1.78, 14.24; P = 0.002). The incidence of postoperative bleeding or hematuria showed greater significantly difference in the PCNL compared to the fURL (RR: 2.72; 95% CI: 1.55, 4.75; P = 0.0005). Operation time, fever, infection, perforation, requiring drug analgesia was not significantly different between two surgical procedures. CONCLUSIONS: In the treatment of upper urinary tract stones, the stones clearance rate of PCNL is higher than fURL, and the safety of fURL is higher than PCNL.

GATA4: Regulation of expression and functions in goat granulosa cells.

GATA4 plays a pivotal role in the reproductive processes of mammals. However, the research on GATA4 in goat ovary is limited. This study aimed to study the expression and function of GATA4 in goat ovary. Utilizing real-time PCR and western blot analysis, we studied the expression and regulatory mechanisms of GATA4 in goat ovary and granulosa cells (GCs). We found that GATA4 was expressed in all follicle types in the goat ovary, with significantly higher levels in GCs of larger follicles (>3 mm) compared to those in smaller follicles (<3 mm). Additionally, we demonstrated that human chorionic gonadotrophin (hCG) induced GATA4 mRNA expression via the activation of PKA, MEK, p38 MAPK, PKC, and PI3K pathways in vitro. Our study also showed that hCG suppressed the levels of miR-200b and miR-429, which in turn directly target GATA4, thereby modulating the basal and hCG-induced expression of GATA4. Functionally, we examined the effect of siRNA-mediated GATA4 knockdown on cell proliferation and hormone secretion in goat GCs. Our results revealed that knockdown of GATA4, miR-200b, and miR-429 suppressed cell proliferation. Moreover, knockdown of GATA4 decreased estradiol and progesterone production by inhibiting the promoter activities of CYP11A1, CYP19A1, HSD3B, and StAR. Collectively, our findings suggest a critical involvement of GATA4 in regulating goat GC survival and steroidogenesis.

ZnO nanoparticles induce melanoma-like lesions via recruiting dermal dendritic cells in barrier-damaged skin in mice.

ZnO nanoparticles (NPs) are used in skin treatments and cosmetics, the toxicity of long-term and continuous exposure to ZnO NPs is unknown. Mice with epidermal barrier dysfunction revealed melanoma-like lesions after continuous exposure to ZnO NPs. However, the effects of metallic NPs on the skin microenvironment and immune system remain poorly understood. Mice with epidermal barrier failure were given continuous exposure to ZnO NPs for 7 weeks. The malignant transformation of melanocytes was induced with ZnO NPs 2.5 µg/ml for 72 h exposure. The supernatant of the culture medium from dendritic cells after being exposed to 10 µg/ml ZnO NPs for 24 h was applied to melanocytes to explore the effect of recruitment of DCs. The expressure of ZnO NPs resulted in a tendency of malignant transformation of melanocytes, the recruitment of DCs induces this process by produce inflammatory factors such as TNF-α. These DC-produced inflammatory factors, which were induced by ZnO NP exposure, increased the production of matrix metalloproteinases in melanocytes and expedited the malignant transformation process. Our findings revealed that the disrupted cutaneous microenvironment by ZnO NPs penetrated directly promoted the malignant transformation of melanocytes, which process also indirectly enhanced by the TNF-αsecreted from the recruited DCs.

Mitochondrial phosphoenolpyruvate carboxykinase inhibits kidney renal clear cell carcinoma malignant progression, leading to cell energy metabolism imbalance.

Mitochondrial phosphoenolpyruvate carboxykinase (PCK2) is a key gluconeogenesis enzyme. Its differential expression is related to kidney renal clear cell carcinoma (KIRC) malignancy, possibly by influencing energy metabolism. Therefore, it is possible that PKC2 plays a significant part in the emergence and progression of KIRC. To systematically and comprehensively identify the significance of PCK2 in KIRC, we further studied PCK2 in terms of its relationship to clinical features and various clinical subgroups' prognoses. Moreover, we verified the effect of PCK2 and KIRC cells using experimental methods. PCR and western blotting analyses confirmed PCK2 expression in KIRC cell lines and tissues. As a cell model, we constructed cells that overexpress PCK2. Proliferation was detected by EdU experiments. Scratch tests and transwell assays were used, respectively, to analyze cell migration and invasion. Mass spectrometry detected energy metabolite expression in KIRC cells. The findings revealed that KIRC patients with lower levels of PCK2 expression exhibited shorter progression-free intervals, shorter disease-specific survival, and shorter overall survival. The experimental results showed that compared with 293t, PCK2 was downregulated in three KIRC lines (OSRC-2, 786-O, and A498). Relative to surrounding tissues, PCK2 was downregulated in KIRC. PCK2 overexpression inhibited KIRC cell proliferation, migration, and invasion and upregulated energy metabolite expression. Mass spectrometry revealed that thiamine pyrophosphate, cyclic AMP, beta-D-fructose 6-phosphate, lactate, flavin mononucleotide, NAD, NADP, and D-glucose 6-phosphate were upregulated. PCK2 has the potential to serve as both a diagnostic and prognostic molecular biomarker for KIRC, as well as an independent prognostic risk factor for KIRC. It is hoped that PCK2 will emerge as a therapeutic target for KIRC.

Single-cell RNA sequencing reveals the mediatory role of cancer-associated fibroblast PTN in hepatitis B virus cirrhosis-HCC progression.

BACKGROUND: Cancer-associated fibroblasts (CAFs) are essential stromal components in the tumor microenvironment of hepatocellular carcinoma (HCC). Hepatitis B virus (HBV) infection induces pathological changes such as liver fibrosis/cirrhosis and HCC. The aim of this research was to explore the novel mediators of CAFs to modulate HBV cirrhosis-HCC progression. METHODS: The single-cell transcriptome data of HCC were divided into subsets, and the significant subset related to fibrotic cells, along with biological function, and clinical information of HCC was revealed by integrated data analyses. The cell communication, cells communicated weight analysis of signaling pathways, and key genes in signaling pathways analysis of significant CAFs subclasses were conducted to discover the novel gene of CAFs. Bioinformatics, vitro and HBV transfection assays were used to verify the novel gene is an important target for promoting the progression HBV cirrhosis-HCC progression. RESULTS: Fibroblasts derived from HCC single-cell data could be separated into three cell subclasses (CAF0-2), of which CAF2 was associated with the HCC clinical information. Fibroblasts have opposite developmental trajectories to immune B cells and CD8 + T cells. CAF0-2 had strong interaction with B cells and CD8 + T cells, especially CAF2 had the highest interaction frequency and weight with B cells and CD8 + T cells. Moreover, PTN participated in CAF2-related pathways involved in the regulation of cell communication, and the interactions among CAF2 and PTN contributed the most to B cells and CD8 + T cells. Furthermore, the genes of PTN, SDC1, and NCL from PTN signaling were highest expression in CAF2, B cells, and CD8 + T cells, respectively, and the interaction of PTN- SDC1 and PTN- NCL contributed most to the interaction of CAF2- B cells and CAF2-CD8 + T cells. Bioinformatics and vitro experiments confirm PTN was upregulated in HCC and promoted the proliferation of tumor cells, and HBV infection could initiate PTN to perform cirrhosis-HCC progression. CONCLUSION: Our findings revealed CAF was associated with hepatocarcinogenesis, and the functional importance of B cells and CD8 + T cells in modulating CAF in HCC. Importantly, PTN maybe a novel mediator of CAF to mediate HBV cirrhosis-HCC progression.

Integrated single-nucleus sequencing and spatial architecture analysis identified distinct injured-proximal tubular types in calculi rats.

BACKGROUND: Urolithiasis with high prevalence and recurrence rate, has impacts on kidney injury in patients, becomes a socioeconomic and healthcare problem in worldwide. However, the biology of kidney with crystal formation and proximal tubular injury remains essentially unclear. The present study aims to evaluate the cell biology and immune-communications in urolithiasis mediated kidney injury, to provide new insights in the kidney stone treatment and prevention. RESULTS: We identified 3 distinct injured-proximal tubular cell types based on the differentially expression injury markers (Havcr1 and lcn2) and functional solute carriers (slc34a3, slc22a8, slc38a3 and slc7a13), and characterized 4 main immune cell types in kidney and one undefined cell population, where F13a1+/high/CD163+/high monocyte & macrophage and Sirpa/Fcgr1a/Fcgr2a+/high granulocyte were the most enriched. We performed intercellular crosstalk analysis based on the snRNA-seq data and explored the potential immunomodulation of calculi stone formation, and founded that the interaction between ligand Gas6 and its receptors (Gas6-Axl, Gas6-Mertk) was specifically observed in the injured-PT1 cells, but not injured-PT2 and -PT3 cells. The interaction of Ptn-Plxnb2 was only observed between the injured-PT3 cells and its receptor enriched cells. CONCLUSIONS: Present study comprehensively characterized the gene expression profile in the calculi rat kidney at single nucleus level, identified novel marker genes for all cell types of rat kidney, and determined 3 distinct sub-population of injured-PT clusters, as well as intercellular communication between injured-PTs and immune cells. Our collection of data provides a reliable resource and reference for studies on renal cell biology and kidney disease.

High expression of RNF169 is associated with poor prognosis in pancreatic adenocarcinoma by regulating tumour immune infiltration.

Background: Pancreatic adenocarcinoma (PAAD) is a highly deadly and aggressive tumour with a poor prognosis. However, the prognostic value of RNF169 and its related mechanisms in PAAD have not been elucidated. In this study, we aimed to explore prognosis-related genes, especially RNF169 in PAAD and to identify novel potential prognostic predictors of PAAD. Methods: The GEPIA and UALCAN databases were used to investigate the expression and prognostic value of RNF169 in PAAD. The correlation between RNF169 expression and immune infiltration was determined by using TIMER and TISIDB. Correlation analysis with starBase was performed to identify a potential regulatory axis of lncRNA-miRNA-RNF169. Results: The data showed that the level of RNF169 mRNA expression in PAAD tissues was higher than that in normal tissues. High RNF169 expression was correlated with poor prognosis in PAAD. In addition, analysis with the TISIDB and TIMER databases revealed that RNF169 expression was positively correlated with tumour immune infiltration in PAAD. Correlation analysis suggested that the long non-coding RNA (lncRNA) AL049555.1 and the microRNA (miRNA) hsa-miR-324-5p were involved in the expression of RNF169, composing a potential regulatory axis to control the progression of PAAD. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that RNF169 plays a role in PAAD through pathways such as TNF, Hippo, JAK-STAT and Toll-like receptor signaling. Conclusion: In summary, the upregulation of RNF169 expression mediated by ncRNAs might influence immune cell infiltration in the microenvironment; thus, it can be used as a prognostic biomarker and a potential therapeutic target in PAAD.

Inhibition of LIM kinase reduces contraction and proliferation in bladder smooth muscle.

Overactive bladder (OAB) is the most bothersome symptom in lower urinary tract symptoms (LUTS). Current pharmacologic treatment aims to inhibit detrusor contraction; however, shows unsatisfied efficacy and high discontinuation rate. LIM kinases (LIMKs) promote smooth muscle contraction in the prostate; however, their function in the bladder smooth muscle remains unclear. Here, we studied effects of the LIMK inhibitors on bladder smooth muscle contraction and proliferation both in vitro and in vivo experiments. Bladder expressions of LIMKs are elevated in OAB rat detrusor tissues. Two LIMK inhibitors, SR7826 and LIMKi3, inhibit contraction of human detrusor strip, and cause actin filament breakdown, as well as cell proliferation reduction in cultured human bladder smooth muscle cells (HBSMCs), paralleled by reduced cofilin phosphorylation. Silencing of LIMK1 and LIMK2 in HBSMCs resulted in breakdown of actin filaments and decreased cell proliferation. Treatment with SR7826 or LIMKi3 decreased micturition frequency and bladder detrusor hypertrophy in rats with bladder outlet obstruction. Our study suggests that LIMKs may promote contraction and proliferation in the bladder smooth muscle, which could be inhibited by small molecule LIMK inhibitors. LIMK inhibitors could be a potential therapeutic strategy for OAB- related LUTS.

The clinicopathological and prognostic value of PD-L1 in urothelial carcinoma: a meta-analysis.

The prognostic value of programed death-ligand 1 (PD-L1) in urothelial carcinoma (UC) has been assessed in previous studies, while the results remain controversial and heterogeneous. Therefore, we performed this meta-analysis to explore the prognostic effect of PD-L1 in patients with UC. PubMed, Embase and Web of Science were searched to identify the studies. Hazard ratios (HR) with 95% confidence interval (95% CI) and clinicopathological factors were extracted from included studies. A total of 1819 patients with UC from 11 published studies were incorporated. The results of meta-analysis showed that positive PD-L1 expression was significantly associated with poorer overall survival (OS) (HR 1.59, 95% CI 1.05-2.40) and disease-free survival (DFS) (HR 1.83, 95% CI 1.03-3.25), but not recurrence-free survival. Moreover, in the subgroup analysis, significant associations between PD-L1 expression and OS or DFS were found in bladder UC, the cutoff value of positive expression of PD-L1 ≥ 5% and the expression of PD-L1 on the tumor cell membrane. Interestingly, positive PD-L1 expression was correlated with poorer pathological T stage (OR 2.03, 95% CI 1.46-2.82). Our meta-analysis implies that PD-L1 might be a valuable biomarker of poor prognosis for UC, especially bladder UC, although further large-scale and well-designed studies are warranted to verify the prognostic value of PD-L1 for UC.

Association between vasectomy and risk of testicular cancer: A systematic review and meta-analysis.

OBJECTIVES: A number of researchers have reported that vasectomy is a risk factor for testicular cancer. However, this conclusion is inconsistent with a number of other published articles. Hence, we conducted this meta-analysis to assess whether vasectomy increases the risk of testicular cancer. MATERIALS AND METHODS: We identified all related studies by searching the PubMed, Embase, and Cochrane Library database from January 01, 1980 to June 01, 2017. The Newcastle-Ottawa Scale (NOS) checklist was used to assess all included non-randomized studies. Summarized odds ratios (ORs) and 95% confidence intervals (CIs) were used to assess the difference in outcomes between case and control groups. Subgroup analyses were performed according to the study design and country. RESULTS: A total of eight studies (2176 testicular cancer patients) were included in this systematic review and meta-analysis. Six articles were case-control studies, and two were cohort studies. The pooled estimate of the OR was 1.10 (95% CI: 0.93-1.30) based on the eight studies in a fixed effects model. Two subgroup analyses were performed according to the study design and country. The results were consistent with the overall findings. Publication bias was detected by Begg's test and Egger's test and p values > 0.05, respectively. CONCLUSIONS: Our meta-analysis suggested that there was no association between vasectomy and the development of testicular cancer. More high-quality studies are warranted to further explore the association between vasectomy and risk of testicular cancer.

The prognostic value of HOXA13 in solid tumors: A meta-analysis.

PURPOSE: The prognostic value of homeobox (HOX) A13 (HOXA13) in cancer remains uncertain due to limitations of sample size and discrete outcome in previous studies. We performed this meta-analysis to explore the prognostic effect of HOXA13 in patients with solid tumors. METHODS: PubMed, Embase, and Web of Science were searched to identify eligible studies. Hazard ratios (HR) with 95% confidence interval (95%CI) and clinicopathological factors were extracted. Subgroup analysis according to cancer type, sample size and analysis method were also performed. RESULTS: A total of 844 patients with solid tumor from 9 eligible studies were incorporated in the meta-analysis. We found that high HOXA13 expression level was significantly associated with poor overall survival (OS) in human cancer (HR = 2.23; 95%CI: 1.74-2.85), and significantly related to poorer histological grade (odds ratio (OR) = 2.03, 95%CI: 1.40-2.96), positive lymph node metastasis (OR = 1.96, 95%CI: 1.26-3.02) and more advanced tumor-node-metastasis (TNM) stage (OR = 3.92, 95%CI: 2.46-6.22). CONCLUSION: Our meta-analysis suggests that HOXA13 might be a valuable biomarker of poor prognosis and a potential therapeutic target for human solid tumors.

Association Between Apolipoprotein B XbaI Polymorphism and Coronary Heart Disease in Han Chinese Population: A Meta-Analysis.

OBJECTIVE: To examine the association between apolipoprotein B (ApoB) XbaI polymorphisms (rs693) and coronary heart disease (CHD) risk among the Han Chinese population by systematically analyzing multiple independent studies. METHODS: The Hardy-Weinberg equilibrium test was applied to check genetic equilibrium among genotypes for the selected literatures. The quality of the studies was assessed by using the NewcastleOttawa Scale. Power analysis was performed with Power and Precision V4 software. A fixed or random effect model was used on the basis of heterogeneity. Publication bias was quantified and examined with Begg's funnel plot test and Egger's linear regression test. The meta-analysis was performed by Stata 12.0 software. RESULTS: A total of 10 eligible association studies were included in this meta-analysis, and the pooled sample consisted of 1195 CHD patients and 1178 health controls. No consistent inference regarding publication bias for the included studies was obtained by using the two above-mentioned methods. The pooled odds ratios (95% confidence intervals [CIs]) for X(-) versus X(+) allele and X(+)X(+) + X(+)X(-) versus X(-)X(-) genotype were 2.25 (1.40-3.62) and 2.21 (1.39-3.50), respectively. CONCLUSIONS: This meta-analysis indicated that ApoB XbaI allele confers a significant risk towards the development of CHD among the Han Chinese population.

Association between apolipoprotein B EcoRI polymorphisms and coronary heart disease : A meta-analysis.

OBJECTIVE: The study was carried out to examine the association between apolipoprotein B (ApoB) EcoRI polymorphism (E- vs. E+) (rs1042031) and coronary heart disease (CHD) risk by systematically analyzing multiple independent studies. METHODS: The Hardy-Weinberg equilibrium (HWE) test was applied to assess genotype frequency distribution in healthy controls. The quality of the studies was assessed using the Newcastle-Ottawa scale (NOS). Power analysis was performed with Power and Precision V4 software. A fixed effect model was used because no deviation from homogeneity was found. Publication bias was quantified and examined with Begg's funnel plot test and Egger's linear regression method. The meta-analysis was performed by Stata 12.0 software. RESULTS: A total of 21 eligible association studies were merged in this meta-analysis and the pooled sample consisted of 2994 CHD patients and 3258 healthy controls. No significant publication bias and heterogeneity were observed in these studies. The pooled odds ratio (OR) and 95% confidence interval (CI) of E- vs. E+ were 1.18 (1.06-1.32). The pooled OR (95% CI) of E+ E- + E- E- vs. E+ E+ was 1.18 (1.04-1.34). CONCLUSIONS: This meta-analysis indicated that ApoB EcoRI confers a moderate risk for CHD and the E- allele at this locus might be a susceptibility allele for the development of CHD.

Identification of Risk Pathways and Functional Modules for Coronary Artery Disease Based on Genome-wide SNP Data.

Coronary artery disease (CAD) is a complex human disease, involving multiple genes and their nonlinear interactions, which often act in a modular fashion. Genome-wide single nucleotide polymorphism (SNP) profiling provides an effective technique to unravel these underlying genetic interplays or their functional involvements for CAD. This study aimed to identify the susceptible pathways and modules for CAD based on SNP omics. First, the Wellcome Trust Case Control Consortium (WTCCC) SNP datasets of CAD and control samples were used to assess the joint effect of multiple genetic variants at the pathway level, using logistic kernel machine regression model. Then, an expanded genetic network was constructed by integrating statistical gene-gene interactions involved in these susceptible pathways with their protein-protein interaction (PPI) knowledge. Finally, risk functional modules were identified by decomposition of the network. Of 276 KEGG pathways analyzed, 6 pathways were found to have a significant effect on CAD. Other than glycerolipid metabolism, glycosaminoglycan biosynthesis, and cardiac muscle contraction pathways, three pathways related to other diseases were also revealed, including Alzheimer's disease, non-alcoholic fatty liver disease, and Huntington's disease. A genetic epistatic network of 95 genes was further constructed using the abovementioned integrative approach. Of 10 functional modules derived from the network, 6 have been annotated to phospholipase C activity and cell adhesion molecule binding, which also have known functional involvement in Alzheimer's disease. These findings indicate an overlap of the underlying molecular mechanisms between CAD and Alzheimer's disease, thus providing new insights into the molecular basis for CAD and its molecular relationships with other diseases.