Combination of microRNA expression profiling with genome-wide SNP genotyping to construct a coronary artery disease-related miRNA-miRNA synergistic network

Hua, Lin; Xia, Hong; Zhou, Ping; Li, Dongguo; Li, Lin

doi:10.5582/bst.2014.01031

Cited by 12 publications

(12 citation statements)

References 40 publications

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“…The largest set is the BART miRNAs, which consists of 40 miRNAs that are expressed in all forms during EBV infection, promoting viral latency or cancer development by targeting both viral and cellular genes (65)(66)(67). Many studies have reported that polymorphisms in human miRNAs or genetic variations in miRNA-binding sites in the 3= untranslated region (UTR) of human genes influence cancer susceptibility or promote cancer progression, affecting prognosis (68). In this study, several variations in EBV miRNAs were found; especially, polymorphisms in the mature miRNA EBV-miR-BART19-5p might influence minimum free energy or potency and stability during binding to the 3= UTR of target genes.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Analysis of 18 Epstein-Barr Viruses Isolated from Primary Nasopharyngeal Carcinoma Biopsy Specimens

Zeng

et al. 2017

J Virol

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Epstein-Barr virus (EBV) is a ubiquitous gammaherpesvirus that is highly prevalent in almost all human populations and is associated with many human cancers, such as nasopharyngeal carcinoma (NPC), Hodgkin's disease, and gastric carcinoma. However, in these EBV-associated cancers, only NPC exhibits remarkable ethnic and geographic distribution. We hypothesized that EBV genomic variations might contribute to the pathogenesis of different human cancers in different geographic areas. In this study, we collected 18 NPC biopsy specimens from the Hunan Province in southern China and assembled 18 NPC biopsy specimen-derived EBV (NPC-EBV) genomes, designated HN1 to HN18. This was achieved through target enrichment of EBV DNA by hybridization, followed by next-generation sequencing, to reveal sequence diversity. These EBV genomes harbored 20,570 variations totally, including 20,328 substitutions, 88 insertions, and 154 deletions, compared to the EBV reference genome. Phylogenetic analysis revealed that all NPC-EBV genomes were distinct from other EBV genomes. Furthermore, HN1 to HN18 had some nonsynonymous variations in EBV genes including genes encoding latent, early lytic, and tegument proteins, such as substitutions within transmembrane domains 1 and 3 of LMP1, FoP_duplication, and zf-AD domains of ENBA1, in addition to aberrations in noncoding regions, especially in BamHI A rightward transcript microRNAs. These variations might have potential biological significance. In conclusion, we reported a genome-wide view of sequence variation in EBV isolated from primary NPC biopsy specimens obtained from the Hunan Province. This might contribute to further understanding of how genomic variations contribute to carcinogenesis, which would impact the treatment of EBV-associated cancer. Nasopharyngeal carcinoma (NPC) is highly associated with Epstein-Barr virus (EBV) infection and exhibits remarkable ethnic and geographic distribution. Hunan Province in southern China has a high incidence rate of NPCs. Here, we report 18 novel EBV genome sequences from viruses isolated from primary NPC biopsy specimens in this region, revealing whole-genome sequence diversity.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Analysis of 18 Epstein-Barr Viruses Isolated from Primary Nasopharyngeal Carcinoma Biopsy Specimens

Zeng

et al. 2017

J Virol

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“…Recent advances in genetic research have systematically identified and analyzed human polymorphisms in miRNAs and/or miRNA target sites (22,23). However, the majority of these studies focus on SNPs in the target sites and their effects on disease-related miRNAs (8,(22)(23)(24). One of these studies has mentioned the interplay effects between miRNAs' SNP and target gene SNPs in disease (24).…”

Section: Introductionmentioning

confidence: 99%

“…However, the majority of these studies focus on SNPs in the target sites and their effects on disease-related miRNAs (8,(22)(23)(24). One of these studies has mentioned the interplay effects between miRNAs' SNP and target gene SNPs in disease (24). There are currently no data regarding the role of miRNA polymorphisms in CAD pathogenesis.…”

Section: Introductionmentioning

confidence: 99%

miRNA polymorphisms (miR-146a, miR-149, miR-196a2 and miR-499) are associated with the risk of coronary artery disease

Sung

Kim

Yang

et al. 2016

Molecular Medicine Reports

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Small non‑coding microRNAs (miRNAs) are not only important for heart and vascular development but are also important in cardiovascular pathophysiology and diseases, such as ischemia and atherosclerosis‑related diseases. However, the effect of miR‑146a, miR‑149, miR‑196a2 and miR‑499 polymorphisms on coronary artery disease (CAD) susceptibility remain unknown. The aim of the present study was to examine the genotype frequencies of miR‑146a, miR‑149, miR‑196a2 and miR‑499 polymorphisms in patients with CAD, and assess their clinical applications for diagnosing and monitoring CAD. Using polymerase chain reaction‑amplified DNA, microRNA polymorphisms were analyzed in 522 patients with CAD and 535 control subjects. The miR‑149 rs2292832 C>T and miR‑196a2 rs11614913 T>C polymorphisms were shown to be significantly associated with CAD prevalence. In subgroup analyses according to disease severity, the miR‑146a rs2910164GG genotype was significantly associated with CAD risk in the stent ≥2 group. In addition, miR‑146aG/‑149T/‑196a2C/‑499 G allele combination was significantly associated with CAD prevalence (G‑T‑C‑G and G‑C‑C‑G of miR‑146a/‑149/‑196a2/‑499). The combination genotypes of miR‑146aGG/149TC+CC and miR‑149CC/196a2TC were significantly associated with CAD incidence. In subgroup analyses, miR‑146a rs2910164 C>G increased the risk of developing CAD in non‑smoking, hypertensive and nondiabetic subgroups. Furthermore, miR‑149 rs2292832 C>T and miR‑196a2 rs11614913 T>C was shown to increase CAD risk in females and patients aged >63 years old. The miR‑149T allele, miR‑196a2C allele and miR‑146aG/‑149T/‑196a2C/‑499 G allele combination were associated with CAD pathogenesis. The combined effects of environmental factor and genotype combination of miRNA polymorphisms may contribute to CAD prevalence.

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“…A miRNA-miRNA co-regulation network in lung cancer was identified using a progressive data refining approach20. Similarly, miRNA expression profiling along with a genome-wide SNP approach was used to create a miRNA-miRNA synergistic network to study coronary artery disease41. miRNA-miRNA interactions were also identified in esophageal cancer using K-clique analysis on a bipartite network consisting of miRNAs and subpathways42.…”

Section: Discussionmentioning

confidence: 99%

miRsig: a consensus-based network inference methodology to identify pan-cancer miRNA-miRNA interaction signatures

Nalluri

Barh

Azevedo

et al. 2017

Sci Rep

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Decoding the patterns of miRNA regulation in diseases are important to properly realize its potential in diagnostic, prog- nostic, and therapeutic applications. Only a handful of studies computationally predict possible miRNA-miRNA interactions; hence, such interactions require a thorough investigation to understand their role in disease progression. In this paper, we design a novel computational pipeline to predict the common signature/core sets of miRNA-miRNA interactions for different diseases using network inference algorithms on the miRNA-disease expression profiles; the individual predictions of these algorithms were then merged using a consensus-based approach to predict miRNA-miRNA associations. We next selected the miRNA-miRNA associations across particular diseases to generate the corresponding disease-specific miRNA-interaction networks. Next, graph intersection analysis was performed on these networks for multiple diseases to identify the common signature/core sets of miRNA interactions. We applied this pipeline to identify the common signature of miRNA-miRNA inter- actions for cancers. The identified signatures when validated using a manual literature search from PubMed Central and the PhenomiR database, show strong relevance with the respective cancers, providing an indirect proof of the high accuracy of our methodology. We developed miRsig, an online tool for analysis and visualization of the disease-specific signature/core miRNA-miRNA interactions, available at: http://bnet.egr.vcu.edu/miRsig.

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Combination of microRNA expression profiling with genome-wide SNP genotyping to construct a coronary artery disease-related miRNA-miRNA synergistic network

Cited by 12 publications

References 40 publications

Genome-Wide Analysis of 18 Epstein-Barr Viruses Isolated from Primary Nasopharyngeal Carcinoma Biopsy Specimens

Genome-Wide Analysis of 18 Epstein-Barr Viruses Isolated from Primary Nasopharyngeal Carcinoma Biopsy Specimens

miRNA polymorphisms (miR-146a, miR-149, miR-196a2 and miR-499) are associated with the risk of coronary artery disease

miRsig: a consensus-based network inference methodology to identify pan-cancer miRNA-miRNA interaction signatures

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