Landscape of the relationship between type 2 diabetes and coronary heart disease through an integrated gene network analysis

Identification of the susceptible genes and mechanism underlying the comorbid presence of coronary artery disease and rheumatoid arthritis: a network modularization analysis

OBJECTIVE

The comorbidities of coronary artery disease (CAD) and rheumatoid arthritis (RA) are mutual risk factors, which lead to higher mortality, but the biological mechanisms connecting the two remain unclear. Here, we aimed to identify the risk genes for the comorbid presence of these two complex diseases using a network modularization approach, to offer insights into clinical therapy and drug development for these diseases.

METHOD

The expression profile data of patients CAD with and without RA were obtained from the GEO database (GSE110008). Based on the differentially expressed genes (DEGs), weighted gene co-expression network analysis (WGCNA) was used to construct a gene network, detect co-expression modules, and explore their relation to clinical traits. The Zsummary index, gene significance (GS), and module membership (MM) were utilized to screen the important differentiated modules and hub genes. The GO and KEGG pathway enrichment analysis were applied to analyze potential mechanisms.

RESULT

Based on the 278 DEGs obtained, 41 modules were identified, of which 17 and 24 modules were positively and negatively correlated with the comorbid occurrence of CAD and RA (CAD&RA), respectively. Thirteen modules with Zsummary < 2 were found to be the underlying modules, which may be related to CAD&RA. With GS ≥ 0.5 and MM ≥ 0.8, 49 hub genes were identified, such as ADO, ABCA11P, POT1, ZNF141, GPATCH8, ATF6 and MIA3, etc. The area under the curve values of the representative seven hub genes under the three models (LR, KNN, SVM) were greater than 0.88. Enrichment analysis revealed that the biological functions of the targeted modules were mainly involved in cAMP-dependent protein kinase activity, demethylase activity, regulation of calcium ion import, positive regulation of tyrosine, phosphorylation of STAT protein, and tissue migration, etc. CONCLUSION: Thirteen characteristic modules and 49 susceptibility hub genes were identified, and their corresponding molecular functions may reflect the underlying mechanism of CAD&RA, hence providing insights into the development of clinical therapies against these diseases.

Identification of genes associated with sudden cardiac death: a network- and pathway-based approach

Background

Sudden cardiac death (SCD) accounts for a large proportion of the total deaths across different age groups. Although numerous candidate genes related to SCD have been identified by genetic association studies and genome wide association studies (GWAS), the molecular mechanisms underlying SCD are still unclear, and the biological functions and interactions of these genes remain obscure. To clarify this issue, we performed a comprehensive and systematic analysis of SCD-related genes by a network and pathway-based approach.

Methods

By screening the publications deposited in the PubMed and Gene-Cloud Biotechnology Information (GCBI) databases, we collected the genes genetically associated with SCD, which were referred to as the SCD-related gene set (SCDgset). To analyze the biological processes and biochemical pathways of the SCD-related genes, functional analysis was performed. To explore interlinks and interactions of the enriched pathways, pathway crosstalk analysis was implemented. To construct SCD-specific molecular networks, Markov cluster algorithm and Steiner minimal tree algorithm were employed.

Results

We collected 257 genes that were reported to be associated with SCD and summarized them in the SCDgset. Most of the biological processes and biochemical pathways were related to heart diseases, while some of the biological functions may be noncardiac causes of SCD. The enriched pathways could be roughly grouped into two modules. One module was related to calcium signaling pathway and the other was related to MAPK pathway. Moreover, two different SCD-specific molecular networks were inferred, and 23 novel genes potentially associated with SCD were also identified.

Conclusions

In summary, by means of a network and pathway-based methodology, we explored the pathogenetic mechanism underlying SCD. Our results provide valuable information in understanding the pathogenesis of SCD and include novel biomarkers for diagnosing potential patients with heart diseases; these may help in reducing the corresponding risks and even aid in preventing SCD.

Identifying the RNA signatures of coronary artery disease from combined lncRNA and mRNA expression profiles

Coronary artery disease (CAD) is the most common cardiovascular disease. CAD research has greatly progressed during the past decade. mRNA is a traditional and popular pipeline to investigate various disease, including CAD. Compared with mRNA, lncRNA has better stability and thus may serve as a better disease indicator in blood. Investigating potential CAD-related lncRNAs and mRNAs will greatly contribute to the diagnosis and treatment of CAD. In this study, a computational analysis was conducted on patients with CAD by using a comprehensive transcription dataset with combined mRNA and lncRNA expression data. Several machine learning algorithms, including feature selection methods and classification algorithms, were applied to screen for the most CAD-related RNA molecules. Decision rules were also reported to provide a quantitative description about the effect of these RNA molecules on CAD progression. These new findings (CAD-related RNA molecules and rules) can help understand mRNA and lncRNA expression levels in CAD.

A Comprehensive Survey of Tools and Software for Active Subnetwork Identification

A recent focus of computational biology has been to integrate the complementary information available in molecular profiles as well as in multiple network databases in order to identify connected regions that show significant changes under different conditions. This allows for capturing dynamic and condition-specific mechanisms of the underlying phenomena and disease stages. Here we review 22 such integrative approaches for active module identification published over the last decade. This article only focuses on tools that are currently available for use and are well-maintained. We compare these methods focusing on their primary features, integrative abilities, network structures, mathematical models, and implementations. We also provide real-world scenarios in which these methods have been successfully applied, as well as highlight outstanding challenges in the field that remain to be addressed. The main objective of this review is to help potential users and researchers to choose the best method that is suitable for their data and analysis purpose.

Mice deficient in AKAP13 (BRX) develop compulsive-like behavior and increased body weight

OBJECTIVE

Hormonal contributions to the sex-dependent development of both obsessive-compulsive disorder (OCD) and obesity have been described, but the underlying mechanisms are incompletely understood. A-kinase anchoring protein 13 (AKAP13) significantly augments ligand-dependent activation of estrogen receptors alpha and beta. The hypothalamus and pituitary gland are implicated in the development and exacerbation of OCD and obesity and have strong AKAP13 expression. The AKAP13 localization pattern observed in these key brain regions together with its effects on sex steroid action suggest a potential role for AKAP13 in compulsive-like behaviors. Here we tested the role of AKAP13 in compulsive-like behavior and body weight using an Akap13 haploinsufficient murine model.

MATERIALS AND METHODS

Targeted deletion of the Akap13 gene generated haploinsufficient (Akap13+/-) mice in a C57BL6/J genetic background. Established behavioral assays were conducted, video recorded, and scored blindly to assess compulsive-like behavior based on genotype and gender. Tests included: marble-burying, grooming, open- field and elevated plus-maze. Brain and body weights were also obtained. Mean levels of test outcomes were compared using multi-way ANOVA to test for genotype, sex, genotype*sex, and genotype*sex*age interaction effects with Bonferroni adjustment for multiple comparisons, to further explain any significant interactions.

RESULTS

The marble-burying and grooming assays revealed significant sex-dependent increases in perseverative, compulsive-like behaviors in female Akap13 haploinsufficient mice compared to female wild type (WT) mice by demonstrating increased marble-burying activity (p = .0025) and a trend towards increased grooming behavior (p = .06). Male Akap13 haploinsufficient mice exhibited no behavioral changes (p > 0.05). Elevated plus-maze and open-field test results showed no overt anxiety-like behavior in Akap13 haploinsufficient mice irrespective of sex (p > 0.05, both). No differences in brain weight were found in Akap13 haploinsufficient mice compared to WT mice (p > 0.05). However, female Akap13 haploinsufficient mice weighed more than female WT mice in the 4 to <7 months age range (p = .0051). Male Akap13 haploinsufficient mice showed no differences in weight compared to male WT mice (p = >0.05) at any age range examined.

CONCLUSION

Akap13 haploinsufficiency led to sex-dependent, compulsive-like behavioral changes in a murine model. Interestingly, Akap13 haploinsufficiency also led to a sex-dependent increase in body weight. These results revealed a requirement for AKAP13 in murine behavior, particularly in female mice, and is the first report of AKAP13 involvement in murine behavior. Future studies may examine the involvement of AKAP13 in the pathophysiology of OCD in female humans and may contribute to a better understanding of the role of AKAP13 and sex hormones in the development and exacerbation of OCD.

Polymorphisms/Mutations in A-Kinase Anchoring Proteins (AKAPs): Role in the Cardiovascular System

A-kinase anchoring proteins (AKAPs) belong to a family of scaffolding proteins that bind to protein kinase A (PKA) by definition and a variety of crucial proteins, including kinases, phosphatases, and phosphodiesterases. By scaffolding these proteins together, AKAPs build a "signalosome" at specific subcellular locations and compartmentalize PKA signaling. Thus, AKAPs are important for signal transduction after upstream activation of receptors ensuring accuracy and precision of intracellular PKA-dependent signaling pathways. Since their discovery in the 1980s, AKAPs have been studied extensively in the heart and have been proven essential in mediating cyclic adenosine monophosphate (cAMP)-PKA signaling. Although expression of AKAPs in the heart is very low, cardiac-specific knock-outs of several AKAPs have a noteworthy cardiac phenotype. Moreover, single nucleotide polymorphisms and genetic mutations in crucial cardiac proteins play a substantial role in the pathophysiology of cardiovascular diseases (CVDs). Despite the significant role of AKAPs in the cardiovascular system, a limited amount of research has focused on the role of genetic polymorphisms and/or mutations in AKAPs in increasing the risk of CVDs. This review attempts to overview the available literature on the polymorphisms/mutations in AKAPs and their effects on human health with a special focus on CVDs.

Critical assessment of health disparities across subpopulation groups through a social determinants of health perspective: The case of type 2 diabetes patients

BACKGROUND

Studies on diabetes have shown that population subgroups have varying rates of medical events and related procedures; however, existing studies have investigated either medical events or procedures, and hence, it is unknown whether disparities exist between medical events and procedures.

PURPOSE

The objective of this study is to investigate how diabetes-related medical events and procedures are different across population subgroups through a social determinants of health (SDH) perspective.

METHODS

Because the purpose of this manuscript is to explore whether statistically significant health disparities exist across population subgroups regarding diabetes patients' medical events and procedures, group difference test methods were employed. Diabetes patients' data were drawn from the Cerner Health Facts® data warehouse.

RESULTS

The study revealed systematic disparities across population subgroups regarding medical events and procedures. The most significant disparities were connected with smoking status, alcohol use, type of insurance, age, marital status, and gender.

CONCLUSIONS

Some population subgroups have higher rates of medical events and yet receive lower rates of treatments, and such disparities are systematic. Socially constructed behaviors and structurally discriminating public policies in part contribute to such systematic health disparities across population subgroups.

Analysis of the Relationship Between ADIPOR1 Variants and the Susceptibility of Chronic Metabolic Diseases in a Northeast Han Chinese Population

Objective: Shared genetic variants in ADIPOR1 have been identified as closely related to coronary artery disease (CAD), type 2 diabetes (T2D), and T2D with CAD susceptibility, suggesting that these variants are strong candidates for the common soil hypothesis. Therefore, it is essential to analyze the relationship between ADIPOR1 variants and the susceptibility to CAD, T2D, and T2D with CAD in other populations.

Materials and Methods: A case–control study was conducted which included three case cohorts [CAD (n = 316), T2D (n = 295), T2D with CAD (n = 302)], and a control cohort (n = 268) from a population in northeast China. Six ADIPOR1 single-nucleotide polymorphisms were genotyped by high-resolution melting and polymerase chain reaction–restriction fragment length polymorphism.

Results: We confirmed that the shared variant, rs3737884*G, in ADIPOR1 is associated with CAD, T2D, and T2D with CAD (p-value range: 6.54E-6–1.82E-5, odds ratio [OR] range: 1.770–1.844) and that rs16850797*C is associated with T2D and T2D with CAD (p-value range: 0.001–0.001, OR range: 1.529–1.571). We also found that a novel shared variant, rs7514221*C, is associated with an increased susceptibility to CAD, T2D, and T2D with CAD (p-value range: 0.002–0.004, OR range: 1.194–2.382) in this population.

Conclusions:ADPOR1 variants, rs3737884*G and rs7514221*C, may be shared risk factors associated with CAD, T2D, and T2D with CAD in a population of northeast China.

Association of seven thrombotic pathway gene CpG-SNPs with coronary heart disease

OBJECTIVES

Coronary heart disease (CHD) has been considered a thromboembolic arterial diseases. The aim of this case-control study was to explore whether the CpG-SNPs of the thrombotic pathway genes contributed to the risk of CHD.

METHODS AND MATERIALS

A total of 784 CHD patients and 738 healthy controls were recruited in the current association study, which evaluated 7 CpG-SNPs of the thrombotic pathway genes. The CpG-SNPs included THBS4 rs17878919, CYP2C19 rs12773342, P2RY12 rs1491974, ITGA2 rs26680, FGB rs2227389, F7 rs510317 and F5 rs2269648. SNP genotyping was performed with a Sequenom Mass Spectrometry Genetic Analyzer.

RESULTS

Our results demonstrated that CYP2C19 rs12773342 polymorphism was significantly associated with CHD in the recessive model (χ(2)=5.41, df=1, P=0.020, OR=1.455, 95% CI=1.060-1.996). A breakdown analysis by age showed that the association of CYP2C19 rs12773342 with CHD was mainly found in individuals aged 55-65 (genotype: χ(2)=7.93, df=2, P=0.019; allele: χ(2)=4.45, df=1, P=0.035). In addition, we also observed a significant association between F7 rs510317 polymorphism and CHD in males (genotype: χ(2)=7.24, df=2, P=0.027). There was no significant association with CHD for the remaining CpG-SNPs.

CONCLUSION

Our results supported that the CYP2C19 rs12773342 and F7 rs510317 polymorphisms were associated with CHD in the Han Chinese population.

Prediabetes is associated with HNF-4 α P2 promoter polymorphism rs1884613: a case-control study in Han Chinese population and an updated meta-analysis

BACKGROUND

Controversy remains for the association between hepatocyte nuclear factor 4α (HNF-4α) P2 promoter polymorphism rs1884613 and type 2 diabetes (T2D). There was no association test of this polymorphism with prediabetes and T2D in the Chinese population. Moreover, an updated meta-analysis in various ethnic groups is needed to establish the contribution of rs1884613 to T2D risk.

METHODS

Using the Sequenom MassARRAY platform approach, we genotyped rs1884613 of HNF-4α in the P2 promoter region among 490 T2D patients, 471 individuals with prediabetes, and 575 healthy controls. All the individuals were recruited from 16 community health service centers in Nanshan district in Shenzhen province. Using STATA 11.0 software, meta-analysis was performed to summarize the overall contribution of rs1884613 to T2D risk.

RESULTS

Polymorphism rs1884613 was associated with genetic susceptibility to prediabetes in the whole samples (OR = 1.40, 95% CI = 1.16-1.68, P = 0.0001) and the female subgrouped samples (OR = 1.48, 95% CI = 1.14-1.92, P = 0.003) after adjusting for age and body mass index (BMI). In contrast, there was no association of rs1884613 with T2D in the whole samples and male in our case-control study and meta-analysis.

CONCLUSIONS

Our results suggest that rs1884613 contributes to susceptibility to prediabetes, whereas this polymorphism may not play an important role in the development of T2D.