Genetics meets epigenetics: Genetic variants that modulate noncoding RNA in cardiovascular diseases

Transcription factor 21 gene and prognosis in a coronary population

INTRODUCTION AND OBJECTIVES

Transcription factor 21 (TCF21) is a member of the basic helix-loop-helix (bHLH) transcription factor family, and is critical for embryogenesis of the heart. It regulates differentiation of epicardium-derived cells into smooth muscle cell (SMC) and fibroblast lineages. The biological role of TCF21 in the progression of atherosclerosis is the subject of debate. The aim of this study was to investigate the impact of the TCF21 rs12190287 gene variant on the prognosis of coronary artery disease (CAD) in a Portuguese population from Madeira island.

METHODS

We analyzed major adverse cardiovascular events (MACE) in 1713 CAD patients, mean age 53.3±7.8, 78.7% male, for 5.0±4.3 years. Genotype and allele distribution between groups with and without MACE was determined. The dominant genetic model (heterozygous GC plus homozygous CC) was used and compared with the wild GG to assess survival probability. Cox regression with risk factors and genetic models assessed variables associated with MACE. Kaplan-Meier analysis was used to estimate survival.

RESULTS

The wild homozygous GG, heterozygous GC and risk CC genotypes were found in 9.5%, 43.2% and 47.3% of the population, respectively. The dominant genetic model remained in the equation as an independent risk factor for MACE (HR 1.41; p=0.033), together with multivessel disease, chronic kidney disease, low physical activity and type 2 diabetes. The C allele in the dominant genetic model showed worse survival (22.5% vs. 44.3%) at 15 years of follow-up.

CONCLUSION

The TCF21 rs12190287 variant is a risk factor for CAD events. This gene may influence fundamental SMC processes in response to vascular stress, accelerating atherosclerosis progression, and may represent a target for future therapies.

Computational and Experimental Analysis of Genetic Variants

Genomics has grown exponentially over the last decade. Common variants are associated with physiological changes through statistical strategies such as Genome-Wide Association Studies (GWAS) and quantitative trail loci (QTL). Rare variants are associated with diseases through extensive filtering tools, including population genomics and trio-based sequencing (parents and probands). However, the genomic associations require follow-up analyses to narrow causal variants, identify genes that are influenced, and to determine the physiological changes. Large quantities of data exist that can be used to connect variants to gene changes, cell types, protein pathways, clinical phenotypes, and animal models that establish physiological genomics. This data combined with bioinformatics including evolutionary analysis, structural insights, and gene regulation can yield testable hypotheses for mechanisms of genomic variants. Molecular biology, biochemistry, cell culture, CRISPR editing, and animal models can test the hypotheses to give molecular variant mechanisms. Variant characterizations can be a significant component of educating future professionals at the undergraduate, graduate, or medical training programs through teaching the basic concepts and terminology of genetics while learning independent research hypothesis design. This article goes through the computational and experimental analysis strategies of variant characterization and provides examples of these tools applied in publications. © 2022 American Physiological Society. Compr Physiol 12:3303-3336, 2022.

EPDR1, Which Is Negatively Regulated by miR-429, Suppresses Epithelial Ovarian Cancer Progression via PI3K/AKT Signaling Pathway

Epithelial ovarian cancer (EOC) is the main pathological type of ovarian cancer. In this study, we found that ependymin-related 1 (EPDR1) was remarkably downregulated in EOC tissues, and low EPDR1 expression was associated with International Federation of Gynecology and Obstetrics (FIGO) stage, metastasis, and poor prognosis. We confirmed that EPDR1 overexpression dramatically suppressed EOC cell proliferation, migration, and invasion in vitro and in vivo. Mechanistically, EPDR1 inhibited EOC tumorigenesis and progression, at least in part, through the repression of the PI3K (Phosphoinositide 3-kinase)/AKT (AKT Serine/Threonine Kinase 1) signaling pathway. Furthermore, the expression and function of EPDR1 were regulated by miR-429, as demonstrated by luciferase reporter assays and rescue experiments. In conclusion, our study validated that EPDR1, negatively regulated by miR-429, played an important role as a tumor-suppressor gene in EOC development via inhibition of the PI3K/AKT pathway. The miR-429/EPDR1 axis might provide novel therapeutic targets for individualized treatment of EOC patients in the future.

Terpene Chain Length Affects the Base Pairing Discrimination of S-geranyl-2-thiouridine in RNA Duplex

Geranylation is a hydrophobic modification discovered in several bacteria tRNAs with the function of promoting codon bias during translation. However, why nature selects this C10-geranyl group remains a question. We conduct synthesis, UV-thermal denaturation, and molecular simulation studies in RNA duplexes and reveal possible reasons behind this natural selection. Among methyl-(C1), dimethylallyl-(C5), geranyl-(C10), and farnesyl-(C15) modified 2-thiouridines, only geranyl-group promotes U:G over U:A pair. Molecular simulation shows all the modified terpene groups point to the minor groove of RNA duplexes. The discrimination between U:G and U:A pairs derives from the difference in hydrogen bonding and interactions of the chain with the hydrophobic area in the minor groove. Geranyl group has perfect length to discriminate U:G and U:A pairs, whereas the others are either too long or too short to achieve the same behavior. This work indicates that geranyl group cannot be replaced by other terpene groups in promoting codon-specificity.

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Geranyl group on ges²U has perfect length to enhance binding to G over A in RNA

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Other ges²U analogues has no pairing preference between G or A

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MD shows the molecular dynamic behavior of different terpene chains in RNA duplex

Association of Genetic Variation in the 3'UTR of LHX6, IMMP2L, and AADAC With Tourette Syndrome

Background: Tourette Syndrome (TS) is a neurodevelopmental disorder that presents with motor and vocal tics early in childhood. The aim of this study was to investigate genetic variants in the 3' untranslated region (3'UTR) of TS candidate genes with a putative link to microRNA (miRNA) mediated regulation or gene expression. Methods: We used an in silico approach to identify 32 variants in the 3'UTR of 18 candidate genes putatively changing the binding site for miRNAs. In a sample composed of TS cases and controls (n = 290), as well as TS family trios (n = 148), we performed transmission disequilibrium test (TDT) and meta-analysis. Results: We found positive association of rs3750486 in the LIM homeobox 6 (LHX6) gene (p = 0.021) and rs7795011 in the inner mitochondrial membrane peptidase subunit 2 (IMMP2L) gene (p = 0.029) with TS in our meta-analysis. The TDT showed an over-transmission of the A allele of rs1042201 in the arylacetamide deacetylase (AADAC) gene in TS patients (p = 0.029). Conclusion: This preliminary study provides further support for the involvement of LHX6, IMMP2L, and AADAC genes, as well as epigenetic mechanisms, such as altered miRNA mediated gene expression regulation in the etiology of TS.

Identification of differentially expressed long non-coding RNAs associated with dilated cardiomyopathy using integrated bioinformatics approaches

The aim of this study was to identify novel long non-coding RNA (lncRNA) biomarkers associated with dilated cardiomyopathy (DCM) and reveal the potential molecular mechanisms of DCM development using bioinformatics approaches. The array data of GSE5406, including 108 DCM samples and 16 non-failing control samples, were obtained from the Gene Expression Omnibus database. The differentially expressed lncRNAs were identified using limma package in R. Pearson's correlation analyses were performed between the differentially expressed lncRNAs and protein-coding genes based on their expression levels. Pathway enrichment of these lncRNAs was conducted based on the significantly co-expressed genes. From the receiver operating characteristic (ROC) curve, the area under the ROC curve (AUC) value was obtained and used for evaluating discriminatory ability. IDI2-AS1 and XIST were differentially expressed in DCM patients. A total of 510 co-expressed genes were identified. The enriched functions and pathways of the co-expressed genes mainly included NADH dehydrogenase activity, cardiac muscle contraction, and oxidative phosphorylation. The ROC curve analysis indicated that the two lncRNAs have favorable diagnostic values in DCM. The AUC values of XIST, IDI2-AS1, and the combination of XIST and IDI2-AS1 were 0.733 (95% CI: 0.646-0.809), 0.796 (95% CI: 0.715-0.863), and 0.823 (95% CI: 0.745-0.886), respectively. This study identified IDI2-AS1 and XIST lncRNAs and related pathways involved in the pathogenesis of DCM, thus providing potential diagnostic and therapeutic targets for DCM.

Epigenetic Regulation of Alternative mRNA Splicing in Dilated Cardiomyopathy

In recent years, the genetic architecture of dilated cardiomyopathy (DCM) has been more thoroughly elucidated. However, there is still insufficient knowledge on the modifiers and regulatory principles that lead to the failure of myocardial function. The current study investigates the association of epigenome-wide DNA methylation and alternative splicing, both of which are important regulatory principles in DCM. We analyzed screening and replication cohorts of cases and controls and identified distinct transcriptomic patterns in the myocardium that differ significantly, and we identified a strong association of intronic DNA methylation and flanking exons usage (p < 2 × 10^-16). By combining differential exon usage (DEU) and differential methylation regions (DMR), we found a significant change of regulation in important sarcomeric and other DCM-associated pathways. Interestingly, inverse regulation of Titin antisense non-coding RNA transcript splicing and DNA methylation of a locus reciprocal to TTN substantiate these findings and indicate an additional role for non-protein-coding transcripts. In summary, this study highlights for the first time the close interrelationship between genetic imprinting by DNA methylation and the transport of this epigenetic information towards the dynamic mRNA splicing landscape. This expands our knowledge of the genome-environment interaction in DCM besides simple gene expression regulation.

RNA sequencing discloses the genome‑wide profile of long noncoding RNAs in dilated cardiomyopathy

Dilated cardiomyopathy (DCM) is a common type of non‑ischemic cardiomyopathy, of which the underlying mechanisms have not yet been fully elucidated. Long noncoding RNAs (lncRNAs) have been reported to serve crucial physiological roles in various cardiac diseases. However, the genome‑wide expression profile of lncRNAs remains to be elucidated in DCM. In the present study, a case‑control study was performed to identify expression deviations in circulating lncRNAs between patients with DCM and controls by RNA sequencing. Partial dysregulated lncRNAs were validated by reverse transcription‑polymerase chain reaction. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes pathway, and lncRNA‑messenger RNA (mRNA) co‑expression network analyses were employed to probe potential functions of these dysregulated lncRNAs in DCM. Comparison between 8 DCM and 8 control samples demonstrated that there were alterations in the expression levels of 988 lncRNAs and 1,418 mRNAs in total. The dysregulated lncRNAs were found to be mainly associated with system development, organ morphogenesis and metabolic regulation in terms of 'biological processes'. Furthermore, the analysis revealed that the gap junction pathway, phagosome, and dilated and hypertrophic cardiomyopathy pathways may serve crucial roles in the development of DCM. The lncRNA‑mRNA co‑expression network also suggested that the target genes of the lncRNAs were different in patients with DCM as compared with those in the controls. In conclusion, the present study revealed the genome‑wide profile of circulating lncRNAs in DCM by RNA sequencing, and explored the potential functions of these lncRNAs in DCM using bioinformatics analysis. These findings provide a theoretical foundation for future studies of lncRNAs in DCM.

Association between a MIR499A polymorphism and diabetic neuropathy in type 2 diabetes

AIMS

Diabetic polyneuropathy (DPN) and cardiovascular autonomic neuropathy (CAN) affect a large percentage of diabetic people and impact severely on quality of life. As it seems that miRNAs and their variations might play a role in these complications, we investigated whether the rs3746444 SNP in the MIR499A gene could be associated with susceptibility to DPN and/or CAN.

METHODS

We analyzed 150 participants with type 2 diabetes. DNA was extracted from peripheral blood samples and genotyping was performed by TaqMan genotyping assay. Cardiovascular tests, MNSI-Q and MDNS for neuropathic symptoms and signs, VPT, and thermal thresholds were used for CAN and DPN assessment. We performed a genotype-phenotype correlation analysis.

RESULTS

We observed that the GG genotype was associated with a higher risk of developing CAN (P=0.002 and OR=16.08, P=0.0005 and OR=35.02, for early and confirmed CAN, respectively) and DPN (P=0.037 and OR=6.56), after correction for BMI, sex, age, HbA1c and disease duration. Moreover, the GG genotype was associated with worse values of MDNS (P=0.017), VPT (P=0.01), thermal thresholds (P=0.01), and CAN score (P<0.001). A logistic multivariate analysis confirmed that MIR499A GG genotype, disease duration and HbA1c contributed to early CAN (R²=0.26), while the same variables and age contributed to DPN (R²=0.21). With a multiple linear regression, we observed that GG genotype (P=0.001) and disease duration (P=0.035) were the main variables contributing to the CAN score (R²=0.35).

CONCLUSIONS

We described for the first time that the MIR499A genetic variation could be involved in diabetic neuropathies susceptibility. In particular, patients carrying the rs3746444 GG genotype had a higher risk of CAN development, together with a more severe form of CAN.

Biomarkers in cardiovascular disease: Statistical assessment and section on key novel heart failure biomarkers

Cardiovascular disease (CVD) is a leading cause of death worldwide and continues to increase in prevalence compared to previous decades, in part because of the aging of the world population. Atherosclerotic CVD starts at a very young age and progresses over time allowing sufficient time for screening and early detection of the condition. Advances in biomarker research and developments related to CVD over the past 30 years have led to more sensitive screening methods, a greater emphasis on its early detection and diagnosis, and improved treatments resulting in more favorable clinical outcomes in the community. However, the use of biomarkers for different purposes in CVD remains an important area of research that has been explored by scientists over the years and many new developments are still underway. Therefore, a detailed description of all CVD biomarkers that are currently been used or investigated for future use in the field of cardiovascular medicine is out of scope for any review article. In the present review, we do not intend to replicate the information from previous exhaustive review on biomarkers, but highlight key statistical and clinical issues with an emphasis on methods to evaluate the incremental yield of biomarkers, including their clinical utility, a prerequisite before any putative novel biomarker is utilized in clinical practice. In addition, we will summarize information regarding recent novel heart failure biomarkers in current practice, which are undergoing scrutiny before they can be available for clinical use, and their impact on clinical outcomes.

Multi-omics analysis reveals regulators of the response to PDGF-BB treatment in pulmonary artery smooth muscle cells

Background

Pulmonary arterial hypertension (PAH) is a lethal disease with pronounced narrowing of pulmonary vessels due to abnormal cell proliferation. The platelet-derived growth factor BB (PDGF-BB) is well known as a potent mitogen for smooth muscle cell proliferation. To better understand how this growth factor regulates pulmonary arterial smooth muscle cells (PASMCs) proliferation, we sought to characterize the response to PDGF-BB stimulation at system-wide levels, including the transcriptome and proteome.

Results

In this study, we identified 1611 mRNAs (transcriptome), 207 proteins (proteome) differentially expressed in response to PDGF-BB stimulation in PASMCs based on RNA-sequencing and isobaric tags for relative and absolute quantification (iTRAQ) assay. Transcription factor (TF)-target network analysis revealed that PDGF-BB regulated gene expression potentially via TFs including HIF1A, JUN, EST1, ETS1, SMAD1, FOS, SP1, STAT1, LEF1 and CEBPB. Among them, SMAD1-involved BMPR2/SMADs axis plays a significant role in PAH development. Interestingly, we observed that the expression of BMPR2 was decreased in both mRNA and protein level in response to PDGF-BB. Further study revealed that BMPR2 is the direct target of miR-376b that is up-regulated upon PDGF-BB treatment. Finally, EdU incorporation assay showed that miR-376b promoted proliferation of PASMCs.

Conclusion

This integrated analysis of PDGF-BB-regulated transcriptome and proteome was performed for the first time in normal PASMCs, which revealed a crosstalk between PDGF signaling and BMPR2/SMADs axis. Further study demonstrated that PDGF-BB-induced miR-376b upregulation mediated the downregulation of BMPR2, which led to expression change of its downstream targets and promoted proliferation of PASMCs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3122-3) contains supplementary material, which is available to authorized users.

From Genetics to Epigenetics: New Perspectives in Tourette Syndrome Research

Gilles de la Tourette Syndrome (TS) is a neurodevelopmental disorder marked by the appearance of multiple involuntary motor and vocal tics. TS presents high comorbidity rates with other disorders such as attention deficit hyperactivity disorder (ADHD) and obsessive compulsive disorder (OCD). TS is highly heritable and has a complex polygenic background. However, environmental factors also play a role in the manifestation of symptoms. Different epigenetic mechanisms may represent the link between these two causalities. Epigenetic regulation has been shown to have an impact in the development of many neuropsychiatric disorders, however very little is known about its effects on Tourette Syndrome. This review provides a summary of the recent findings in genetic background of TS, followed by an overview on different epigenetic mechanisms, such as DNA methylation, histone modifications, and non-coding RNAs in the regulation of gene expression. Epigenetic studies in other neurological and psychiatric disorders are discussed along with the TS-related epigenetic findings available in the literature to date. Moreover, we are proposing that some general epigenetic mechanisms seen in other neuropsychiatric disorders may also play a role in the pathogenesis of TS.

Long noncoding RNAs: Novel molecules in cardiovascular biology, disease and regeneration

Remarkable breakthroughs made in genomic technologies have facilitated the discovery of thousands of novel transcripts that do not template protein synthesis. Numerous RNAs termed as long noncoding RNAs (lncRNAs) generated from this pervasive transcription function vividly in gene regulatory networks and a variety of biological and cellular processes. Here, we make a brief description of the known and putative functions of lncRNAs in cardiovascular biology and disease. The association between lncRNAs and stem cells mediated cardiomyocytes differentiation and neovascularization is discussed then. It will provide a new clue for further studies on these novel molecules in cardiovascular disease and bring bright prospects for their future applications in cardiac regenerative medicine.

Epigenetics and obesity cardiomyopathy: From pathophysiology to prevention and management

Uncorrected obesity has been associated with cardiac hypertrophy and contractile dysfunction. Several mechanisms for this cardiomyopathy have been identified, including oxidative stress, autophagy, adrenergic and renin-angiotensin aldosterone overflow. Another process that may regulate effects of obesity is epigenetics, which refers to the heritable alterations in gene expression or cellular phenotype that are not encoded on the DNA sequence. Advances in epigenome profiling have greatly improved the understanding of the epigenome in obesity, where environmental exposures during early life result in an increased health risk later on in life. Several mechanisms, including histone modification, DNA methylation and non-coding RNAs, have been reported in obesity and can cause transcriptional suppression or activation, depending on the location within the gene, contributing to obesity-induced complications. Through epigenetic modifications, the fetus may be prone to detrimental insults, leading to cardiac sequelae later in life. Important links between epigenetics and obesity include nutrition, exercise, adiposity, inflammation, insulin sensitivity and hepatic steatosis. Genome-wide studies have identified altered DNA methylation patterns in pancreatic islets, skeletal muscle and adipose tissues from obese subjects compared with non-obese controls. In addition, aging and intrauterine environment are associated with differential DNA methylation. Given the intense research on the molecular mechanisms of the etiology of obesity and its complications, this review will provide insights into the current understanding of epigenetics and pharmacological and non-pharmacological (such as exercise) interventions targeting epigenetics as they relate to treatment of obesity and its complications. Particular focus will be on DNA methylation, histone modification and non-coding RNAs.

Differential lncRNA‑mRNA co‑expression network analysis revealing the potential regulatory roles of lncRNAs in myocardial infarction

Previous studies have reported that long, non-coding RNAs (lncRNAs) are important in cardiovascular disease. However, the lncRNAs involved in myocardial infarction and their detailed mechanism have not been well characterized. In the present study, an affymetrix microarray associated with myocardial infarction was re-annotated, following which a myocardial infarction-related differential lncRNA-mRNA co-expression network (MILMN) was constructed. Subsequently, pathway enrichment analysis was used for all the mRNAs in the MILMN, and an lncRNA-pathway network was constructed. It was found that the mRNAs were predominantly involved in certain cardiovascular disease-associated pathway, for example the dilated cardiomyopathy and mitogen-activated protein kinase signaling pathway. Finally, a total of 39 key lncRNAs were identified, which regulate crucial pathways in myocardial infarction. Through pathway analysis of these 39 key lncRNAs, the novel function of an annotated lncRNAs-H19 was predicted, which may regulate apoptosis signal-regulating kinase, which is a protein that promotes pathological cardiac remodeling following myocardial infarction. The results of the present study not only provide potential non-coding RNA biomarkers, but also provide further insights into understanding the molecular mechanism of lncRNAs.