Proinflammatory cytokine IFN-γ, lncRNA BANCR and the occurrence of coronary artery disease

Distinct circulating cytokine levels in patients with angiography-proven coronary artery disease compared to disease-free controls

Background

Systemic inflammation has a critical role in the development of symptomatic coronary artery disease (CAD). Identification of inflammatory pathways may provide a platform for novel therapeutic approaches. We sought to determine whether there are differences in circulating cytokine profiles between patients with CAD and disease-free controls as well as according to the severity of the disease.

Methods

Case-control study's population consisted of 452 patients who underwent diagnostic invasive coronary angiography due to clinical indications. We measured the serum concentrations of 48 circulating cytokines. Extent of CAD was assessed using the SYNTAX Score in 116 patients. Cytokine differences between groups were tested using Mann-Whitney U test and associations with CAD were explored using a logistic regression model.

Results

Overall, 310 patients had angiographically verified CAD whereas 142 had no angiographically-detected coronary atherosclerosis. In multivariable logistic regression models adjusted for age, sex, hypertension, atrial fibrillation, history of smoking and treatment for diabetes and hyperlipidemia, increased levels of interleukin 9 (OR 1.359, 95%CI 1.046-1.766, p = 0.022), IL-17 (1.491, 95%CI 1.115-1.994, p = 0.007) and tumor necrosis factor alpha (TNF-α) (OR 1.440, 95%CI 1.089-1.904, p = 0.011) were independently associated with CAD. Patients with SYNTAX Score>22 had increased levels of stromal cell-derived factor 1 alfa (SDF-1α), beta-nerve growth factor (β-NGF), IL-3 and decreased level of IL-17 compared to those with score ≤22 when adjusted for smoking and use of beta-blockers.

Conclusions

Patients with CAD have distinct circulating cytokine profiles compared to disease-free controls. Distinct cytokines may have pivotal roles at different stages of coronary atherosclerosis. ClinicalTrials.gov Identifier: NCT03444259 (https://clinicaltrials.gov/study/NCT03444259).

Variations in the interferon and TLR3 genes may be associated with susceptibility to systemic lupus erythematosus and its clinical presentation

The study aimed to explore the pontential impact of 10 polymorphisms within IFN-α, IFN-β1, IFN-γ and TLR3 genes on SLE phenotype and susceptibility and to study the relationship between specific genotypes and clinics. Whole blood samples from SLE patients and healthy controls was obtained. DNA was extracted from the peripheral blood by the QIAamp DNA Blood Mini Kit (Qiagen). The quality and quantity of isolated DNA was estimated by the Quawell Q5000 spectrophotometer. We genotyped SLE patients and healthy subjects using real-time PCR (QuantStudio 5 thermocycler). The study suggests that IFN-γ rs2069705, IFN-γ rs2069718 and IFN-α rs3758236 polymorphisms have a protective role in SLE. We observed relations between TLR3 rs3775292, IFN-β1 rs7873167, IFN-γ rs2069705, TLR3 rs3775291 and TLR3 rs5743305 polymorphisms and clinical picture of SLE patients. We found associations between the IFN-α rs3758236, IFN-γ rs2069705, IFN-γ rs2069718, IFN-γ rs1861493 and IFN-β1 rs10964831 polymorphisms and the clinical manifestation of the SLE and/or its comorbidities. We perceived links between IFN-γ rs2069705, IFN-γ rs2069718, IFN-γ rs1861493, TLR3 rs3775291, TLR3 rs3775292 and TLR3 rs5743305 polymorphisms and the occurrence of autoantibodies. Our study presented the relationship between IFN and TLR gene polymorphisms with SLE susceptibility, phenotype and autoantibodies profile. This study propose that polymorphisms within interferons and TLR3 genes can be engaged in the SLE pathogenesis and course.

LncRNA RP1-276N6.2 Expression and RP1-276N6.2 Gene Polymorphisms Contribute to the Risk of Coronary Artery Disease in Chinese Han Population

Long noncoding RNAs (lncRNAs) have been implicated in coronary artery disease (CAD) processes. However, the relationship between the gene polymorphisms of lncRNA RP1-276N6.2 as a novel molecule and susceptibility to CAD remains unclear. In our case-control study, 949 CAD patients and 892 healthy controls were genotyped using the TaqMan genotyping assay. The quantitative real-time polymerase chain reaction and enzyme-linked immunosorbent assay were performed to examine the expression levels of RP1-276N6.2 and SLC22A3(OCT3). We observed that CAD patients had significantly lower RP1-276N6.2 levels than those healthy participants (p < 0.05). Compared to the wild-type genotype, the rs611950 T allele and the rs10499313 AG genotype and G allele significantly increased the premature CAD risk (p = 0.02, p = 0.002, and p = 0.01, respectively), while the rs505000 G allele reduced this risk (p = 0.01); moreover, the rs505000 CG genotype significantly enhanced the delayed CAD risk (p = 0.03), and the rs505000 G allele reduced the expression levels of RP1-276N6.2 and SLC22A3 (p < 0.05 and p < 0.05, respectively). In addition, RP1-276N6.2 positively regulated the mRNA and secreted protein levels of SLC22A3 (p < 0.05). In conclusion, the RP1-276N6.2 gene polymorphisms were closely associated with CAD risk. LncRNA RP1-276N6.2 may be a potential genetic target for CAD early diagnosis and treatment.

Correlation of apolipoprotein A‐I with T cell subsets and interferon‐ү in coronary artery disease

Background

The association of Apolipoprotein A‐I (APOAI) with T cell subsets and interferon‐ү (IFN‐γ) in patients with coronary artery disease (CAD) has been not reported. Thus, this study aimed to investigate the association of APOAI with T cell subsets and IFN‐γ in CAD.

Methods

This study included a total of 107 patients with CAD including acute coronary syndrome and chronic coronary syndrome. T cell subsets, and CD3‐CD56+ natural killer cells were quantified by flow cytometric analysis. The serum concentrations of IFN‐ү were measured by enzyme‐linked immunosorbent assay. Lipid profiles, C‐reactive protein (CRP), and fibrinogen were measured in the clinical laboratory. Clinical data was obtained duration hospitalization.

Results

The CD4+ T cells were higher in patients of the low‐APOAI group (<median: 1.2 mmol/L) than in patients of the high‐APOAI group(≥median: 1.2 mmol/L) (p < .05). The CD8+ T cells were lower in patients of the low APOAI group than in patients of the high‐APOAI group (p < .05). APOAI was inversely associated with CD4+ T cells, IFN‐γ, and was positively associated with CD8+ T cells (p < .05). No correlation was observed between CD3 + CD56+ cells, regulatory T cells (Tregs), and CD3‐CD56+ natural killer cells and APOAI (p > .05). The high‐density lipoprotein cholesterol (HDL‐C) was also inversely associated with CD4+ T cells (p < .05), and positively associated with CD8+ T cells (p < .05). Lastly, APOA1 and HDL‐C did not correlated with fibrinogen and CRP (p > .05).

Conclusion

The present study demonstrated the correlation of APOAI with T cell subsets and IFN‐γ in CAD. These results provided novel information for the regulatory action between APOAI and T cell subsets and inflammatory immunity in CAD.

GCN-GENE: A novel method for prediction of coronary heart disease-related genes

Coronary heart disease is the most common heart disease, it can induce myocardial infarction, and the cause of the disease has a lot to do with life and eating habits. The results of a large number of epidemiological studies at home and abroad show that the incidence of coronary heart disease has an obvious familial tendency. However, little is known about the genetic factors of coronary heart disease. Although genome-wide association analysis and gene knockout experiments have found some genes related to coronary heart disease, there are still a large number of genes potentially related to coronary heart disease that have not been discovered. If it is confirmed by biological experimental means, the time and money cost is too high. Therefore, it is urgent to identify genes related to coronary heart disease on a large scale by computational means, so as to conduct targeted biological experimental verification. This paper proposes a deep learning method based on biological networks for the identification of coronary heart disease-related genes. We constructed gene interaction networks and extracted gene expression levels in different tissues as features. Through the association information and expression characteristics between genes, we constructed a model of coronary heart disease-related genes. Through cross-validation, we found that our proposed GCN-GENE that has AUC as 0.75 and AUPR as 0.78, which is more accurate than other methods and is a reliable method for predicting coronary heart disease-related genes.

Knockdown of lncRNA H19 alleviates ox-LDL-induced HCAECs inflammation and injury by mediating miR-20a-5p/HDAC4 axis

BACKGROUND

Coronary artery disease (CAD) seriously disturbs the life of people. LncRNA H19 is reported to promote the progression of CAD; Nevertheless, the detailed mechanism by which H19 modulates CAD development is unclear.

METHODS

Clinical samples of CAD patients were collected, meanwhile we established in vitro and in vivo models of CAD by treating HCAECs with ox-LDL and feeding ApoE^-/- mice with high fat diets (HFD). MTT assay was adopted to assess the cell viability. Transwell detection was applied to test the migration, and apoptosis was tested by flow cytometry. The levels of inflammatory cytokines were examined by ELISA. The relation among H19, miR-20a-5p and HDAC4 was explored by dual luciferase reporter and RIP assay.

RESULTS

H19 and HDAC4 levels were elevated, while miR-20a-5p was reduced in plasma of CAD patients and ox-LDL-treated HCAECs. ox-LDL increased H19 level and induced apoptosis and inflammation in HCAECs, while silencing of H19 rescued this phenomenon. In addition, the level of H19 was negatively correlated with miR-20a-5p, and miR-20a-5p inhibitor restored the effect of H19 silencing on HCAECs function. HDAC4 was the downstream mRNA of miR-20a-5p, and miR-20a-5p upregulation reversed ox-LDL-induced HCAECs injury through targeting HDAC4. Furthermore, H19 silencing significantly alleviated the coronary atherosclerotic plaques and inhibited the inflammatory responses in vivo.

CONCLUSIONS

We proved that knockdown of H19 alleviated ox-LDL-induced HCAECs injury via miR-20a-5p/HDAC4 axis, which might provide a new tactics against CAD.

Risk Prediction of Coronary Artery Stenosis in Patients with Coronary Heart Disease Based on Logistic Regression and Artificial Neural Network

Objective

Coronary heart disease (CHD) is considered an inflammatory relative disease. This study is aimed at analyzing the health information of serum interferon in CHD based on logistic regression and artificial neural network (ANN) model.

Method

A total of 155 CHD patients diagnosed by coronary angiography in our department from January 2017 to March 2020 were included. All patients were randomly divided into a training set (n = 108) and a test set (n = 47). Logistic regression and ANN models were constructed using the training set data. The predictive factors of coronary artery stenosis were screened, and the predictive effect of the model was evaluated by using the test set data. All the health information of participants was collected. Expressions of serum IFN-γ, MIG, and IP-10 were detected by double antibody sandwich ELISA. Spearman linear correlation analysis determined the relationship between the interferon and degree of stenosis. The logistic regression model was used to evaluate independent risk factors of CHD.

Result

The Spearman correlation analysis showed that the degree of stenosis was positively correlated with serum IFN-γ, MIG, and IP-10 levels. The logistic regression analysis and ANN model showed that the MIG and IP-10 were independent predictors of Gensini score: MIG (95% CI: 0.876~0.934, P < 0.001) and IP-10 (95% CI: 1.009~1.039, P < 0.001). There was no statistically significant difference between the logistic regression and the ANN model (P > 0.05).

Conclusion

The logistic regression model and ANN model have similar predictive performance for coronary artery stenosis risk factors in patients with CHD. In patients with CHD, the expression levels of IFN-γ, IP-10, and MIG are positively correlated with the degree of stenosis. The IP-10 and MIG are independent risk factors for coronary artery stenosis.

An Integrative Network Approach to Identify Common Genes for the Therapeutics in Tuberculosis and Its Overlapping Non-Communicable Diseases

Tuberculosis (TB) is the leading cause of death from a single infectious agent. The estimated total global TB deaths in 2019 were 1.4 million. The decline in TB incidence rate is very slow, while the burden of noncommunicable diseases (NCDs) is exponentially increasing in low- and middle-income countries, where the prevention and treatment of TB disease remains a great burden, and there is enough empirical evidence (scientific evidence) to justify a greater research emphasis on the syndemic interaction between TB and NCDs. The current study was proposed to build a disease-gene network based on overlapping TB with NCDs (overlapping means genes involved in TB and other/s NCDs), such as Parkinson’s disease, cardiovascular disease, diabetes mellitus, rheumatoid arthritis, and lung cancer. We compared the TB-associated genes with genes of its overlapping NCDs to determine the gene-disease relationship. Next, we constructed the gene interaction network of disease-genes by integrating curated and experimentally validated interactions in humans and find the 13 highly clustered modules in the network, which contains a total of 86 hub genes that are commonly associated with TB and its overlapping NCDs, which are largely involved in the Inflammatory response, cellular response to cytokine stimulus, response to cytokine, cytokine-mediated signaling pathway, defense response, response to stress and immune system process. Moreover, the identified hub genes and their respective drugs were exploited to build a bipartite network that assists in deciphering the drug-target interaction, highlighting the influential roles of these drugs on apparently unrelated targets and pathways. Targeting these hub proteins by using drugs combination or drug repurposing approaches will improve the clinical conditions in comorbidity, enhance the potency of a few drugs, and give a synergistic effect with better outcomes. Thus, understanding the Mycobacterium tuberculosis (Mtb) infection and associated NCDs is a high priority to contain its short and long-term effects on human health. Our network-based analysis opens a new horizon for more personalized treatment, drug-repurposing opportunities, investigates new targets, multidrug treatment, and can uncover several side effects of unrelated drugs for TB and its overlapping NCDs.

Expression of lncRNA-ANRIL before and after Treatment and Its Predictive Value for Short-Term Survival in Patients with Coronary Heart Disease

This study aimed at observing the expression of lncRNA-ANRIL (ANRIL) before and after treatment and its predictive value for short-term survival in patients with coronary heart disease (CHD). Altogether, 112 patients with CHD admitted to the hospital were enrolled as a study group (SG), which was divided into a pretreatment study group (preSG) and a posttreatment study group (postSG). Further 72 healthy people undergoing physical examinations during the same period were enrolled as a control group (CG). Peripheral blood was collected from the subjects in the three groups, to detect the expression level of serum ANRIL using quantitative reverse transcription PCR (qRT-PCR). A receiver operating characteristic (ROC) curve was plotted to evaluate the diagnostic value of ANRIL for CHD. Kaplan-Meier survival curves were plotted to analyze 3-year survival rates in high- and low-ANRIL expression groups. Cox regression was conducted to analyze independent risk factors affecting the patients. The expression level of serum ANRIL in preSG was significantly lower than those in CG and postSG (P < 0.05). According to the ROC curve, the area under the curve (AUC) of serum ANRIL for diagnosing CHD in CG was 0.894 and the optimal cutoff value was 0.639, with the sensitivity of 86.61% and the specificity of 93.67%. According to the survival curves, the 3-year overall survival rate in the high-ANRIL expression group was significantly lower than that in the low-expression group (P < 0.05). History of smoking, high total cholesterol (TC), high triglyceride (TG), high homocysteine (Hcy), and ANRIL expression were independent prognostic factors affecting the overall survival time of the patients (P < 0.05). ANRIL is poorly expressed in the peripheral blood of patients with CHD. Its detection has good sensitivity and specificity for diagnosing the disease, and its expression may be related to the poor prognosis of the patients.

Identifying a Serum Exosomal-Associated lncRNA/circRNA-miRNA-mRNA Network in Coronary Heart Disease

Background

Accumulating evidence supports the importance of noncoding RNAs and exosomes in coronary heart disease (CHD). However, exosomal-associated competing endogenous RNA- (ceRNA-) mediated regulatory mechanisms in CHD are largely unexplored. The present study aimed to explore exosomal-associated ceRNA networks in CHD.

Methods

Data from 6 CHD patients and 32 normal controls were downloaded from the ExoRBase database. CHD and normal controls were compared by screening differentially expressed mRNAs (DEMs), lncRNAs (DELs), and circRNAs (DECs) in serum exosomes. MicroRNAs (miRNAs) targeting DEMs were predicted using the Targetscan and miRanda databases, and miRNAs targeted by DELs and DECs were predicted using the miRcode and starBase databases, respectively. The biological functions and related signaling pathways of DEMs were analyzed using the David and KOBAS databases. Subsequently, a protein-protein interaction (PPI) network was established to screen out on which hub genes enrichment analyses should be performed, and a ceRNA network (lncRNA/circRNA-miRNA-mRNA) was constructed to elucidate ceRNA axes in CHD.

Results

A total of 312 DEMs, 43 DELs, and 85 DECs were identified between CHD patients and normal controls. Functional enrichment analysis showed that DEMs were significantly enriched in “chromatin silencing at rDNA,” “telomere organization,” and “negative regulation of gene expression, epigenetic.” PPI network analysis showed that 25 hub DEMs were closely related to CHD, of which ubiquitin C (UBC) was the most important. Hub genes were mainly enriched in “cellular protein metabolic process” functions. The exosomal-associated ceRNA regulatory network incorporated 48 DEMs, 73 predicted miRNAs, 10 DELs, and 15 DECs. The LncRNA/circRNA-miRNA-mRNA interaction axes (RPL7AP11/hsa-miR-17-5p/UBC and RPL7AP11/hsa-miR-20b-5p/UBC) were obtained from the network.

Conclusions

Our findings provide a novel perspective on the potential role of exosomal-associated ceRNA network regulation of the pathogenesis of CHD.

Analysis on the Expression and Prognostic Value of LncRNA FAF in Patients with Coronary Heart Disease

Objective

To investigate the expression and prognostic value of LncRNA FAF in patients with coronary heart disease. Patients and Methods. 97 patients with coronary heart disease who came to our hospital were selected as the research group (RG), and 97 healthy people who came to our hospital for physical examination during the same period were selected as the control group (CG). The serum LncRNA FAF, plasma homocysteine (HCY), lipoprotein A (Lp-a), serum tumor necrosis factor α (TNF-α), and high-sensitivity C-reactive protein (hsCRP) in the two groups of patients were detected, and their correlations were analyzed. Then, the predictive value and risk factors of FAF for poor prognosis of patients with coronary heart disease were analyzed.

Results

The expression of LncRNA FAF in the serum of patients in the RG was significantly lower than that in the CG, and the expressions of HCY, Lp-a, TNF-α, and hsCRP were significantly higher than those in the CG (p <0.05). The AUC of FAF in the diagnosis of coronary heart disease was more than 0.9. FAF was negatively correlated with the coronary lesion vessels, HCY, Lp-a, TNF-α, and hsCRP expressions in patients with coronary heart disease (p < 0.05). The ROC of FAF for predicting poor prognosis in patients with coronary heart disease was greater than 0.9. Low expression of FAF; high expressions of HCY, Lp-a, and hsCRP; and increase of coronary lesion vessels were independent risk factors for poor prognosis in patients with coronary heart disease.

Conclusions

LncRNA FAF was lowly expressed in the serum of patients with coronary heart disease, and it was of high value in the diagnosis and prediction of poor prognosis of coronary heart disease. It was also an independent risk factor for poor prognosis of patients with coronary heart disease and may be a potential target for diagnosis and treatment of coronary heart disease.

High BANCR expression is associated with worse prognosis in human malignant carcinomas: an updated systematic review and meta-analysis

Background

BRAF-activated noncoding RNA (BANCR) is aberrantly expressed in various tumor tissues and has been confirmed to function as a tumor suppressor or oncogene in many types of cancers. Considering the conflicting results and insufficient sampling, a meta-analysis was performed to explore the prognostic value of BANCR in various carcinomas.

Methods

A comprehensive literature search of PubMed, Web of Science, EMBASE, Cochrane Library and the China National Knowledge Infrastructure (CNKI) was conducted to collect relevant articles.

Results

The pooled results showed a strong relationship between high BANCR expression and poor overall survival (OS) (HR (hazard ratio) =1.60, 95% confidence interval (CI): 1.19–2.15, P = 0.002) and recurrence-free survival (RFS) (HR = 1.53, 95% CI: 1.27–1.85, P < 0.00001). In addition, high BANCR expression predicted advanced tumor stage (OR (odds ratio) =2.39, 95% CI: 1.26–4.53, P = 0.008), presence of lymph node metastasis (OR = 2.03, 95% CI: 1.08–3.83, P = 0.03), positive distant metastasis (OR = 3.08, 95% CI: 1.92–4.96, P < 0.00001) and larger tumor sizes (OR = 1.63, 95% CI: 1.09–2.46, P = 0.02). However, no associations were found for smoking status (OR = 1.01, 95% CI: 0.65–1.56, P = 0.98), age (OR = 0.88, 95% CI: 0.71–1.09, P = 0.236) and sex (OR = 0.91, 95% CI: 0.72–1.16, P = 0.469). The sensitivity analysis of OS showed that the results of each publication were almost consistent with the combined results, and the merged results have high robustness and reliability.

Conclusions

The results showed that elevated BANCR expression was associated with unfavorable prognosis for most cancer patients, and BANCR could serve as a promising therapeutic target and independent prognostic predictor in most of cancer types.

Reconstruction of a lncRNA-Associated ceRNA Network in Endothelial Cells under Circumferential Stress

Background

Numerous studies have highlighted that long noncoding RNA (lncRNA) can indirectly regulate the expression of mRNAs by binding to microRNA (miRNA). LncRNA-associated ceRNA networks play a vital role in the initiation and progression of several pathological mechanisms. However, the lncRNA-miRNA-mRNA ceRNA network in endothelial cells under cyclic stretch is seldom studied.

Methods

The miRNA, mRNA, and lncRNA expression profiles of 6 human umbilical vein endothelial cells (HUVECs) under circumferential stress were obtained by next-generation sequencing (NGS). We identified the differential expression of miRNAs, mRNAs, and lncRNAs using the R software package GDCRNATools. Cytoscape was adopted to construct a lncRNA-miRNA-mRNA ceRNA network. In addition, through GO and KEGG pathway annotations, we analyzed gene functions and their related pathways. We also adopted ELISA and TUNEL to investigate the effect of si-NEAT1 on endothelial inflammation and apoptosis.

Results

We recognized a total of 32978 lncRNAs, 1046 miRNAs, and 31958 mRNAs in 6 samples; among them, 155 different expressed lncRNAs, 74 different expressed miRNAs, and 960 different mRNAs were adopted. Based on the established theory, the ceRNA network was composed of 13 lncRNAs, 44 miRNAs, and 115 mRNAs. We constructed and visualized a lncRNA-miRNA-mRNA network, and the top 20 nodes are identified after calculating their degrees. The nodes with most degrees in three kinds of RNAs are hsa-miR-4739, NEAT1, and MAP3K2. Functional analysis showed that different biological processes enriched in biological regulation, response to stimulus and cell communication. Pathway analysis was mainly enriched in longevity regulating, cell cycle, mTOR, and FoxO signaling pathway. Circumferential stress can significantly downregulate NEAT1, and after transducing si-NEAT1 for 24 h, inflammatory cytokine IL-6 and MCP-1 were significantly increased; furthermore, fewer TUNEL-positive cells were found in the si-NEAT1 treated group.

Conclusions

The establishing of a ceRNA network can help further understand the mechanism of vein graft failure. Our data demonstrated that NEAT1 may be a core factor among the mechanical stress factors and that cyclic stress can significantly reduce expression of NEAT1, give rise to inflammation in the early stage of endothelial dysfunction, and promote EC apoptosis, which may play an essential role in vein graft failure.