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

A microRNA-microRNA crosstalk network inferred from genome-wide single nucleotide polymorphism variants in natural populations of Arabidopsis thaliana

To adapt to variable natural conditions, plants have evolved several strategies to respond to different environmental stresses. MicroRNA (miRNA)-mediated gene regulation is one of such strategies. Variants, e.g., single nucleotide polymorphisms (SNPs) within the mature miRNAs or their target sites may cause the alteration of regulatory networks and serious phenotype changes. In this study, we proposed a novel approach to construct a miRNA-miRNA crosstalk network in Arabidopsis thaliana based on the notion that two cooperative miRNAs toward common targets are under a strong pressure to be inherited together across ecotypes. By performing a genome-wide scan of the SNPs within the mature miRNAs and their target sites, we defined a "regulation fate profile" to describe a miRNA-target regulation being static (kept) or dynamic (gained or lost) across 1,135 ecotypes compared with the reference genome of Col-0. The cooperative miRNA pairs were identified by estimating the similarity of their regulation fate profiles toward the common targets. The reliability of the cooperative miRNA pairs was supported by solid expressional correlation, high PPImiRFS scores, and similar stress responses. Different combinations of static and dynamic miRNA-target regulations account for the cooperative miRNA pairs acting on various biological characteristics of miRNA conservation, expression, homology, and stress response. Interestingly, the targets that are co-regulated dynamically by both cooperative miRNAs are more likely to be responsive to stress. Hence, stress-related genes probably bear selective pressures in a certain group of ecotypes, in which miRNA regulations on the stress genes reprogram. Finally, three case studies showed that reprogramming miRNA-miRNA crosstalk toward the targets in specific ecotypes was associated with these ecotypes' climatic variables and geographical locations. Our study highlights the potential of miRNA-miRNA crosstalk as a genetic basis underlying environmental adaptation in natural populations.

Computationally Modeling ncRNA-ncRNA Crosstalk

Our understanding of complex gene regulatory networks have been improved by the discovery of ncRNA-ncRNA crosstalk in normal and disease-specific physiological conditions. Previous studies have proposed numerous approaches for constructing ncRNA-ncRNA networks via ncRNA-mRNA regulation, functional information, or phenomics alone, or by combining heterogeneous data. Furthermore, it has been shown that ncRNA-ncRNA crosstalk can be rewired in different tissues or specific diseases. Therefore, it is necessary to integrate transcriptome data to construct context-specific ncRNA-ncRNA networks. In this chapter, we elucidated the commonly used ncRNA-ncRNA network modeling methods, and highlighted the need to integrate heterogeneous multi-mics data. Finally, we suggest future directions for studies of ncRNAs crosstalk. This comprehensive description and discussion elucidated in this chapter will provide constructive insights into ncRNA-ncRNA crosstalk.

Correlations of MicroRNA-21 Gene Polymorphisms With Chemosensitivity and Prognosis of Cervical Cancer

BACKGROUND

We investigated correlations of miR-21 gene polymorphisms including rs1292037 (A > G) and rs13137 (A > T) with the chemosensitivity to cisplatin plus paclitaxel, and prognosis before cervical cancer (CC) surgery, which may provide a novel target for prevention and treatment of CC.

MATERIALS AND METHODS

A total of 165 patients with CC were divided into 2 groups, a sensitive group and resistance group. Gene polymorphisms of rs1292037 (A > G) and rs13137 (A > T) were detected respectively. Logistic and Cox multivariate regression analyses were used to explore factors that influence resistance to cisplatin plus paclitaxel.

RESULTS

rs1292037 (A > G) locus AG, GG, AG + GG and G allele in miR-21 gene may increase chemoresistance to cisplatin plus paclitaxel in CC. The risk factors of prognosis included rs1292037 (A > G) locus, tumor stage, maximum lesion diameter and lymph node metastasis (hazard ratio [HR] = 1.819, 95% CI = 1.127-2.935; HR = 1.504, 95% CI = 1.070-2.114; HR = 1.671, 95% CI = 1.038-2.689; HR = 3.043, 95% CI = 1.783-5.193). The influencing factors of resistance to cisplatin plus paclitaxel included maximum lesion diameter, tumor stage, lymph node metastasis and rs1292037 (odds ratio [OR] = 14.047, 95% CI = 5.694-34.653; OR = 5.873, 95% CI = 3.104-11.110; OR = 3.574, 95% CI = 1.554-8.216; OR = 2.449, 95% CI = 1.052-5.705).

CONCLUSIONS

rs1292037 (A > G) locus are associated with the chemoresistance to cisplatin plus paclitaxel and prognosis of patients with CC. In addition to that, the G allele at rs1292037 (A > G) locus increases the risk of preoperative chemoresistance to cisplatin plus paclitaxel and is a poor prognostic factor for patients with CC.

miRNA-miRNA crosstalk: from genomics to phenomics

The discovery of microRNA (miRNA)-miRNA crosstalk has greatly improved our understanding of complex gene regulatory networks in normal and disease-specific physiological conditions. Numerous approaches have been proposed for modeling miRNA-miRNA networks based on genomic sequences, miRNA-mRNA regulation, functional information and phenomics alone, or by integrating heterogeneous data. In addition, it is expected that miRNA-miRNA crosstalk can be reprogrammed in different tissues or specific diseases. Thus, transcriptome data have also been integrated to construct context-specific miRNA-miRNA networks. In this review, we summarize the state-of-the-art miRNA-miRNA network modeling methods, which range from genomics to phenomics, where we focus on the need to integrate heterogeneous types of omics data. Finally, we suggest future directions for studies of crosstalk of noncoding RNAs. This comprehensive summarization and discussion elucidated in this work provide constructive insights into miRNA-miRNA crosstalk.

Integrated Modules Analysis to Explore the Molecular Mechanisms of Phlegm-Stasis Cementation Syndrome with Ischemic Heart Disease

Background: Ischemic heart disease (IHD) has been the leading cause of death for several decades globally, IHD patients usually hold the symptoms of phlegm-stasis cementation syndrome (PSCS) as significant complications. However, the underlying molecular mechanisms of PSCS complicated with IHD have not yet been fully elucidated. Materials and Methods: Network medicine methods were utilized to elucidate the underlying molecular mechanisms of IHD phenotypes. Firstly, high-quality IHD-associated genes from both human curated disease-gene association database and biomedical literatures were integrated. Secondly, the IHD disease modules were obtained by dissecting the protein-protein interaction (PPI) topological modules in the String V9.1 database and the mapping of IHD-associated genes to the PPI topological modules. After that, molecular functional analyses (e.g., Gene Ontology and pathway enrichment analyses) for these IHD disease modules were conducted. Finally, the PSCS syndrome modules were identified by mapping the PSCS related symptom-genes to the IHD disease modules, which were further validated by both pharmacological and physiological evidences derived from published literatures. Results: The total of 1,056 high-quality IHD-associated genes were integrated and evaluated. In addition, eight IHD disease modules (the PPI sub-networks significantly relevant to IHD) were identified, in which two disease modules were relevant to PSCS syndrome (i.e., two PSCS syndrome modules). These two modules had enriched pathways on Toll-like receptor signaling pathway (hsa04620) and Renin-angiotensin system (hsa04614), with the molecular functions of angiotensin maturation (GO:0002003) and response to bacterium (GO:0009617), which had been validated by classical Chinese herbal formulas-related targets, IHD-related drug targets, and the phenotype features derived from human phenotype ontology (HPO) and published biomedical literatures. Conclusion: A network medicine-based approach was proposed to identify the underlying molecular modules of PSCS complicated with IHD, which could be used for interpreting the pharmacological mechanisms of well-established Chinese herbal formulas (e.g., Tao Hong Si Wu Tang, Dan Shen Yin, Hunag Lian Wen Dan Tang and Gua Lou Xie Bai Ban Xia Tang). In addition, these results delivered novel understandings of the molecular network mechanisms of IHD phenotype subtypes with PSCS complications, which would be both insightful for IHD precision medicine and the integration of disease and TCM syndrome diagnoses.

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

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 de novo 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.IMPORTANCE 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.

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

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.

Identifying miRNA synergistic regulatory networks in heterogeneous human data via network motifs

Understanding the synergism of multiple microRNAs (miRNAs) in gene regulation can provide important insights into the mechanisms of complex human diseases caused by miRNA regulation. Therefore, it is important to identify miRNA synergism and study miRNA characteristics in miRNA synergistic regulatory networks. A number of methods have been proposed to identify miRNA synergism. However, most of the methods only use downstream target genes of miRNAs to infer miRNA synergism when miRNAs can also be regulated by upstream transcription factors (TFs) at the transcriptional level. Additionally, most methods are based on statistical associations identified from data without considering the causal nature of gene regulation. In this paper, we present a causality based framework, called mirSRN (miRNA synergistic regulatory network), to infer miRNA synergism in human molecular systems by considering both downstream miRNA targets and upstream TF regulation. We apply the proposed framework to two real world datasets and discover that almost all the top 10 miRNAs with the largest node degree in the mirSRNs are associated with different human diseases, including cancer, and that the mirSRNs are approximately scale-free and small-world networks. We also find that most miRNAs in the networks are frequently synergistic with other miRNAs, and miRNAs related to the same disease are likely to be synergistic and in a cluster linked to a biological function. Synergistic miRNA pairs show higher co-expression level, and may have potential functional relationships indicating collaboration between the miRNAs. Functional validation of the identified synergistic miRNAs demonstrates that these miRNAs cause different kinds of diseases. These results deepen our understanding of the biological meaning of miRNA synergism.

Dermatoglyphs in Coronary Artery Disease Among Ningxia Population of North China

BACKGROUND

Coronary artery disease (CAD) is an enormous health problem in the world. Dermatoglyphs are cutaneous ridges on the fingers, palms, and soles, formed by genetic regulation and control during early intrauterine life. The Dermatoglyphic traits do not change significantly as the growth of the age. They may be the phenotypic characters of individual genes and represent the predisposition to certain diseases.

AIMS AND OBJECTIVES

The study was carried out to document characteristic dermatoglyphic patterns in coronary artery disease which could be useful in early diagnosis of the disease.

MATERIALS AND METHODS

Dermatoglyphic study of 258 male (129 coronary artery disease cases and 129 normal subjects) of Ningxia China were studied in the present cross-sectional study. It involved the digital patterns, ATD angles, A-B ridge counts on the hands. Chi-square test, t-test were used for the statistical analysis in this study.

RESULTS

The overall frequency of whorls was higher followed by loop and arch in both two groups. It was observed that there was significant difference of digital frequency of whorls and ulnar loops in patients in both hands as compared to controls (p≤0.01). The mean value of finger ridge counts, total ridge counts were similar between two groups. The A-B ridge counts were significantly higher in coronary artery disease compared with controls on the right palm (p≤0.01). However, the mean ATD angle values were significantly higher in cases than those of in normal on both hands (p<0.05).

CONCLUSION

Abnormally high A-B ridge count, ATD angles and the frequency of whorls are characteristic dermatoglyphic patterns of coronary artery disease. Dermatoglyphics may have an important role in early diagnosis of coronary artery disease in future.