Potentially functional genetic variants in microRNA processing genes and risk of HBV-related hepatocellular carcinoma

Relationship between PIWIL1 gene polymorphisms and epithelial ovarian cancer susceptibility among southern Chinese woman: a three-center case-control study

OBJECTIVE

To investigate the potential correlation between piwi-like RNA-mediated gene silencing 1 (PIWIL1) polymorphisms and susceptibility to epithelial ovarian cancer (EOC).

METHODS

A case-control study was conducted to evaluate the susceptibility of EOC using multinomial logistic regression analysis. The study analyzed the relationship between five functional single nucleotide polymorphisms (SNPs) in the PIWIL1 gene and EOC risk. Genotyping of 288 cases and 361 healthy samples from South China was identified using a TaqMan assay. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to estimate the relationship between the five selected SNPs and EOC susceptibility.

RESULTS

Among the five SNPs analyzed, the rs10848087 G > A and rs7957349 G > C variants significantly increased the susceptibility of EOC, rs10773771 C > T was associated with a decreased risk of EOC, while the rs35997018 and rs1106042 variants were not in Hardy-Weinberg equilibrium (p < 0.05). The rs10848087 G > A was significantly associated with increased risk of EOC in individuals with metastasis, FIGO stage I and III, low and high pathological grade, tumor numbers ≤ 3 and > 3, tumor size > 3 cm and ≤ 3 cm, pregnant more than 3 times, pre-menopausal status, and strong positive expression of ER (estrogen receptor), PR (progesterone receptor), PAX8 (paired-box 8), wild-type p53 (tumor protein 53), WT1 (Wilm's tumor gene), P16 (cyclin-dependent kinase inhibitor 2A). In addition, rs10848087 G > A enhanced the EOC risk of cases with negative/mild positive expression of wild p53 and Ki67, and with or without mutant p53 expression. The rs7957349 G > C variant was linked to an increased risk of EOC in subgroups with certain characteristics, including age equal or less than 53 years, metastasis, clinical stage I, low pathological grade, tumor number, tumor size, pregnant times, post-menopause, pre-menopause, and strong positive expression of wild p53 and Ki67 (Antigen identified by monoclonal antibody Ki-67), as well as without mutant p53 expression. The rs10773771 CT/TT alleles were identified to have a protective effect on EOC in women aged 53 years or older, as well as in cases with metastasis, advanced clinical stage, high pathological grade, multiple tumors, tumor size equal to or less than 3 cm, history of pregnancy, post-menopausal status, and strong positive expression of ER, PR, wild-type p53, PAX8, WT1, P16, and Ki67. Furthermore, rs10773771 CT/TT also showed a protective effect in patients with negative or mildly positive expression of PR, PAX8, wild-type p53, WT1, and P16, as well as positive expression of mutant p53. Compared to the reference haplotype GCG, individuals harboring haplotypes GTG were found to have a significantly decreased susceptibility to EOC. PIWIL1 was significantly expressed in the thyroid, pituitary, and adrenal glands with rs7957349 CC alleles.

CONCLUSIONS

PIWIL1 rs10848087 and rs7957349 were associated with increased risk of EOC, while rs10773771 may have a protective effect against EOC. These genetic variants may serve as potential biomarkers for EOC susceptibility in the South China population.

Pan-Cancer Study on Variants of Canonical miRNA Biogenesis Pathway Components: A Pooled Analysis

Single nucleotide polymorphisms in genes involved in microRNA processing/maturation and release may deregulate the microRNAome expression levels. We aimed to assess the relationship between miRNA machinery genetic variants and human cancer risk using integrative bioinformatics analyses to identify the role of these genes in cancer aggressiveness. Mutations of 8176 pan-cancer samples were retrieved from 33 studies in "TCGA" database, and a Cox regression model for survival was performed. Next, 22 computationally identified variants within 11 genes were selected based on their high citation rate and MAF. Relevant articles through March 2020 were included. Pooled estimates under the five genetic association models were calculated. Publication bias and heterogeneity between articles were evaluated. Trial Sequential Analysis (TSA) was applied to assess the power and reliability of the draw conclusions. TCGA patients with different cancer types revealed significant alterations in miRNA machinery genes, with mutation frequency ranging from 0.6-13% of samples. RAN was associated with LN metastasis, while TARBP2 and PIWIL1 gene mutations exhibited better overall survival. In the meta-analysis, 45 articles (74,593 cases and 89,198 controls) met the eligibility criteria. Pooled analysis revealed an increased cancer risk with DROSHArs10719*G, RANrs3803012*G, DGCR8rs417309*A, and GEMIN3rs197414*A. In contrast, both DICER1rs1057035*T and GEMIN4rs2743048*G conferred protection against developing cancer. TSA showed the cumulative evidence is inadequate, and the addition of further primary studies is necessary. This study suggests a potential role of miRNA biogenesis genes in cancer development/prognosis. Further functional studies may reveal biological explanations for the differential risks of the machinery variants in different cancer types.

PIWI-interacting RNAs in cancer: Biogenesis, function, and clinical significance

PIWI-interacting RNAs (piRNAs) are a less-studied class of small non-coding RNAs approximately 24–31 nucleotides in length. They express in germline and somatic cells and form complexes with PIWI proteins to exert regulatory effects. New studies show that piRNAs are aberrantly expressed in various cancers. In this review, we focus on those piRNAs that are associated with cancer hallmarks such as proliferation, invasion, and chemoresistance and discuss their potential as biomarkers for cancer diagnosis and prognosis.

Association of MicroRNA Biogenesis Genes Polymorphisms with Risk of Large Artery Atherosclerosis Stroke

Convincing evidence has shown that microRNAs (miRNAs) are involved in the pathogenesis of stroke. This study aimed to examine whether miRNA biogenesis genes polymorphisms are associated with risk of large artery atherosclerosis (LAA) stroke. Three polymorphisms (DROSHA rs10719 T>C, RAN rs3803012 A>G, and PIWIL1 rs10773771 C>T) were screened by certain criteria. A total of 1,785 (710 cases and 1,075 controls) study subjects were included in this study. We found that rs10773771 CC genotype was associated with a decreased risk of LAA stroke (CC vs. TT/CT: OR 0.63, 95% CI 0.46-0.86, P = 3 × 10^-3). In silico analysis suggested that rs10773771 can change the mRNA secondary structure of PIWIL1 and affect the binding of the miRNAs and regulatory motifs to the 3'-UTR of PIWIL1. Expression quantitative trait loci analysis showed that rs10773771 could change the expression of PIWIL1 in human skin (P = 1.534 × 10^-10) and thyroid tissues (P = 4.869 × 10^-6). These findings suggested that PIWIL1 rs10773771 may be associated with a decreased risk of LAA stroke.

Integrated bioinformatic analysis of RNA binding proteins in hepatocellular carcinoma

RNA binding proteins (RBPs) are aberrantly expressed in a tissue-specific manner across many tumors. These proteins, which play a vital role in post-transcriptional gene regulation, are involved in RNA splicing, maturation, transport, stability, degradation, and translation. We set out to establish an accurate risk score model based on RBPs to estimate prognosis in hepatocellular carcinoma (HCC). RNA-sequencing data, proteomic data and corresponding clinical information were acquired from the Cancer Genome Atlas database and the Clinical Proteomic Tumor Analysis Consortium database respectively. We identified 406 differentially expressed RBPs between HCC tumor and normal tissues at the transcriptional and protein level. Overall, 11 RBPs (BRIX1, DYNC1H1, GTPBP4, PRKDC, RAN, RBM19, SF3B4, SMG5, SPATS2, TAF9, and THOC5) were selected to establish a risk score model. We divided HCC patients into low-risk and high-risk groups based on the median of risk score values. The survival analysis indicated that patients in the high-risk group had poorer overall survival compared to patients in the low-risk group. Our study demonstrated that 11 RBPs were associated with the overall survival of HCC patients. These RBPs may represent potential drug targets and can help optimize future clinical treatment.

Association between genetic variants in DICER1 and cancer risk: An updated meta-analysis

Dysfunctions in mechanisms of gene regulation based on RNA interference are recognized as a common feature of the molecular basis of cancer pathogenesis. Therefore, as one of the crucial components of the machinery involved in the biogenesis of both siRNAs and microRNA molecules, DICER was recognized as one of the candidates for the research in the field of carcinogenesis. Due to their potential functional properties, several genetic variants located within DICER1 gene were analyzed for their possible association with the susceptibility to cancer through case-control studies. In order to elucidate their effect on the overall cancer risk, we conducted an updated meta-analysis of all eligible association studies. The publications were selected based on PubMed database search, while OpenMeta-analyst and MetaGenyo software were used for quantitative data synthesis. Statistically significant results were found for the association of rs1057035 with the overall cancer risk under multiple genetic models (P_{CT vs. TT} < 0.001, OR_{CT vs. TT} = 0.870, 95% CI = 0.812-0.933; P_allelic = 0.009, OR_allelic = 0.896, 95% CI = 0.825-0.973; P_dom < 0.001, OR_dom = 0.874, 95% CI = 0.817-0.934; P_overdom = 0.004, OR_overdom = 0.858, 95% CI = 0.773-0.953). Other selected genetic variants within DICER1, rs13078, rs1209904 and rs3742330, did not show the association with the overall susceptibility to malignant diseases. We conclude that rs1057035 may represent a potential biomarker associated with the risk of developing cancer, which requires a confirmation in a larger set of studies.

Association of microRNA biosynthesis genes XPO5 and RAN polymorphisms with cancer susceptibility: Bayesian hierarchical meta-analysis

XPO5/RAN-GTP complex mediates the nuclear transport of pre-miRNAs in the miRNA processing system, its altered expression is indicated to be correlated with cancer risk. Several studies have inspected the association between XPO5 or RAN polymorphisms and the risk of various cancers, but the findings remain controversial. A Bayesian hierarchical meta-analysis was carried out to review and analyze the effect of XPO5 and RAN polymorphisms on cancer risk. The association was estimated by calculating the logarithm of odds ratio (Log OR) and 95% credible interval (95% CrI). The expression quantitative trait loci (eQTL) analysis was used for in silico functional validation of the identified significant susceptibility loci. Consequently, 38 case-control studies (from 27 citations) with 27,459 cancer cases and 25,151controls were included in the meta-analysis of the five most prevalent SNPs (rs11077 A/C, rs2257082 G/A, rs3803012 A/G, rs14035 C/T, rs3809142 C/T). In the XPO5 gene rs11077 SNP, the minor C allele significantly increased the risk of cancer (Log OR = 0.120, 95% CrI = 0.013, 0.241), and a strong association between rs11077 SNP and cancer risk was also found in the dominant model (CC + AC vs. AA: Log OR = 0.132, 95% CrI = 0.009, 0.275). In addition, the minor GG genotype allele of the RAN gene rs3803012 SNP significantly increased the cancer risk (Log OR = 0.707, 95% CrI = 0.059, 1.385). Statistically significant associations between rs3803012 SNP and cancer risk were also observed in the recessive model (GG vs. AG + AA: Log OR = 0.708, 95% CrI = 0.059, 1.359). Furthermore, the eQTL analysis revealed that rs11077 SNP was significantly correlated with XPO5 mRNA expression, which provided additional biological basis for the observed positive association. Our results suggest that XPO5 rs11077 may be a possible functional susceptibility locus for cancer risk.

A Systematic Review and Meta-Analysis for the Association of Gene Polymorphisms in RAN with Cancer Risk

As an important component of miRNA processing genes, RAN gene encodes the ras-related nuclear protein, which is a unique member of the Ras superfamily of GTPases. The mutations in RAN gene are very likely to play a critical role in pathology-related changes to miRNA transport and expression and thus participate in tumor genesis and development. Currently, accumulating studies have explored the association between RAN SNPs and cancer risk. However, the results are conflicting. In the present study, we performed a systematic review for the association of RAN SNPs with overall cancer risk. Meanwhile, a meta-analysis was conducted based on available data, aiming at clarifying the association between RAN SNPs and cancer susceptibility. After literature search and data extraction, 17 studies containing four RAN SNPs were involved in the systematic review. And 12 studies with two highly studied SNPs (RAN rs14035 C>T and rs3803012 A>G) were included in the final meta-analysis, consisting of 7662 cases and 9807 controls. The results showed that the rs14035 polymorphism was linked to a decreased cancer risk in overall subjects and hospital-based (HB) subgroup, while the rs3803012 polymorphism conferred to an increased cancer risk in overall subjects and population-based (PB) subgroup. Our findings suggested that the two SNPs had the potential to be predictive biomarkers for cancer risk. The study would provide novel clues for the identification of miRNA-related genetic biomarkers applied to predicting cancer susceptibility.

Genetic variants in microRNA biogenesis genes as novel indicators for secondary growth in Populus

MicroRNAs (miRNAs) function as key regulators of complex traits, but how genetic alterations in miRNA biogenesis genes (miRBGs) affect quantitative variation has not been elucidated. We conducted transcript analyses and association genetics to investigate how miRBGs, miRNA genes (MIRNAs) and their respective targets contribute to secondary growth in a natural population of 435 Populus tomentosa individuals. This analysis identified 29 843 common single-nucleotide polymorphisms (SNPs; frequency > 0.10) within 682 genes (80 miRBGs, 152 MIRNAs, and 457 miRNA targets). Single-SNP association analysis found SNPs in 234 candidate genes exhibited significant additive/dominant effects on phenotypes. Among these, specific candidates that associated with the same traits produced 791 miRBG-MIRNA-target combinations, suggesting possible genetic miRBG-MIRNA and MIRNA-target interactions, providing an important clue for the regulatory mechanisms of miRBGs. Multi-SNP association found 4672 epistatic pairs involving 578 genes that showed significant associations with traits and identified 106 miRBG-MIRNA-target combinations. Two multi-hierarchical networks were constructed based on correlations of miRBG-miRNA and miRNA-target expression to further probe the mechanisms of trait diversity underlying changes in miRBGs. Our study opens avenues for the investigation of miRNA function in perennial plants and underscored miRBGs as potentially modulating quantitative variation in traits.

Association of miRNA biosynthesis genes DROSHA and DGCR8 polymorphisms with cancer susceptibility: a systematic review and meta-analysis

Single nucleotide polymorphisms (SNPs) in miRNA biosynthesis genes DROSHA and DGCR8 were indicated to be correlated with cancer risk. We comprehensively reviewed and analyzed the effect of DROSHA and DGCR8 polymorphisms on cancer risk. Eligible articles were selected according to a series of inclusion and exclusion criteria. Consequently, ten case–control studies (from nine citations) with 4265 cancer cases and 4349 controls were involved in a meta-analysis of seven most prevalent SNPs (rs10719 T/C, rs6877842 G/C, rs2291109 A/T, rs642321 C/T, rs3757 G/A, rs417309 G/A, rs1640299 T/G). Our findings demonstrated that the rs417309 SNP in DGCR8 was significantly associated with an elevated risk of overall cancer in every genetic model. In stratified analysis, correlations of DROSHA rs10719 and rs6877842 SNPs were observed in Asian and laryngeal cancer subgroups, respectively. Moreover, associations of the rs417309 SNP could also be found in numerous subgroups including: Asian and Caucasian population subgroups; laryngeal and breast cancer subgroups; population-based (PB) and hospital-based (HB) subgroups. In conclusion, the DROSHA rs10719, rs6877842 SNPs, and DGCR8 rs417309 SNP play pivotal roles in cancerogenesis and may be potential biomarkers for cancer-forewarning.

MicroRNA-Related Polymorphisms in Infectious Diseases-Tiny Changes With a Huge Impact on Viral Infections and Potential Clinical Applications

MicroRNAs (miRNAs) are single-stranded sequences of non-coding RNA with approximately 22 nucleotides that act posttranscriptionally on gene expression. miRNAs are important gene regulators in physiological contexts, but they also impact the pathogenesis of various diseases. The role of miRNAs in viral infections has been explored by different authors in both population-based as well as in functional studies. However, the effect of miRNA polymorphisms on the susceptibility to viral infections and on the clinical course of these diseases is still an emerging topic. Thus, this review will compile and organize the findings described in studies that evaluated the effects of genetic variations on miRNA genes and on their binding sites, in the context of human viral diseases. In addition to discussing the basic aspects of miRNAs biology, we will cover the studies that investigated miRNA polymorphisms in infections caused by hepatitis B virus, hepatitis C virus, human immunodeficiency virus, Epstein–Barr virus, and human papillomavirus. Finally, emerging topics concerning the importance of miRNA genetic variants will be presented, focusing on the context of viral infectious diseases.

Genetic variant in DICER gene is associated with prognosis of hepatocellular carcinoma in a Chinese cohort

AIM

MicroRNAs (miRNAs) function as gene regulators and play crucial roles in the pathogenesis and prognosis of hepatocellular carcinoma (HCC). Genetic variants in miRNA processing genes may affect miRNA expression and contribute to HCC risk and survival. We hypothesized that single nucleotide polymorphisms (SNPs) in miRNA processing genes may be associated with HCC susceptibility and prognosis. The study aims to verify whether this hypothesis is right or not.

METHODS

We first genotyped the selected three SNPs in miRNA processing genes (RAN rs3803012 A>G, HIWI rs10773771 T>C, and DICER rs1057035 T>C) in 312 HCC patients and 320 cancer-free controls using the TaqMan assay, and evaluated the associations of the three SNPs with HCC risk. We also investigated the effect of the three SNPs on the overall survival of 312 HCC patients.

RESULTS

There were no significant associations between the three SNPs (RAN rs3803012 A>G, HIWI rs10773771 T>C, and DICER rs1057035 T>C) and HCC risk. However, HCC patients carrying DICER rs1057035 CT + CC genotypes had significantly longer median survival time (log-rank, P = 0.018) and decreased death risk (adjusted hazard ratio = 0.68; 95% confidence interval, 0.49-0.95; P = 0.022) than patients with rs1057035 TT genotypes. The DICER rs1057035 genotype was an independent protective factor for HCC survival (CT + CC vs. TT: hazard ratio = 0.72; 95% confidence interval, 0.55-0.96; P = 0.031).

CONCLUSION

This study provides evidence that DICER rs1057035 T>C polymorphism may be a prognostic biomarker for HCC patients.

MicroRNA biogenesis pathway genes polymorphisms and cancer risk: a systematic review and meta-analysis

MicroRNAs (miRNAs) may promote the development and progression of human cancers. Therefore, components of the miRNA biogenesis pathway may play critical roles in human cancer. Single nucleotide polymorphisms (SNPs) or mutations in genes involved in the miRNA biogenesis pathway may alter levels of gene expression, affecting disease susceptibility. Results of previous studies on genetic variants in the miRNA biogenesis pathway and cancer risk were inconsistent. Therefore, a meta-analysis is needed to assess the associations of these genetic variants with human cancer risk. We searched for relevant articles from PubMed, Web of Science, CNKI, and CBM through Jun 21, 2016. In total, 21 case-control articles met all of the inclusion criteria for the study. Significant associations were observed between cancer risk and the DGCR8polymorphism rs417309 G >A (OR 1.22, 95% CI [1.04-1.42]), as well as the DICER1 polymorphism rs1057035 TT (OR 1.13, 95% CI [1.05-1.22]). These SNPs exhibit high potential as novel diagnostic markers. Future studies with larger sample sizes and more refined analyses are needed to shed more light on these findings.

Autophagy and microRNA in hepatitis B virus-related hepatocellular carcinoma

Approximately 350 million people worldwide are chronically infected by hepatitis B virus (HBV). HBV causes severe liver diseases including cirrhosis and hepatocellular carcinoma (HCC). In about 25% of affected patients, HBV infection proceeds to HCC. Therefore, the mechanisms by which HBV affects the host cell to promote viral replication and its pathogenesis have been the subject of intensive research efforts. Emerging evidence indicates that both autophagy and microRNAs (miRNAs) are involved in HBV replication and HBV-related hepatocarcinogenesis. In this review, we summarize how HBV induces autophagy, the role of autophagy in HBV infection, and HBV-related tumorigenesis. We further discuss the emerging roles of miRNAs in HBV infection and how HBV affects miRNAs biogenesis. The accumulating knowledge pertaining to autophagy and miRNAs in HBV replication and its pathogenesis may lead to the development of novel strategies against HBV infection and HBV-related HCC tumorigenesis.

Studied microRNA gene expression in human hepatocellular carcinoma by microRNA microarray techniques

AIM: To achieve a better understanding of the molecular mechanisms of microRNA expression changes involved in hepatocellular carcinoma.

METHODS: In this research process, patients were not treated with antivirals, immunosuppressants or immunomodulators for at least 6 mo before collecting serum. The study population was composed of 35 outpatient hepatitis B virus (HBV) cases and 12 healthy control cases from the Affiliated Hospital of Inner Mongolia Medical University (Inner Mongolia, China) from July 2013 to April 2014. The 35 HBV cases were divided into two groups: a hepatocirrhosis group with 20 cases and a liver cancer group with 15 cases. All 35 cases carried HBsAg. The diagnostic criteria followed the European Association for the Study of the Liver 2012 (EASL2012) standards. MicroRNA (miRNA) was extracted from a control group of patients, a group with hepatocirrhosis and a group with liver cancer and its quality was analyzed using the human V2 microRNA expression beadchip. Cluster analysis and a radar chart were then applied to the miRNA changes.

RESULTS: The miRNA-qualified rate of human serum samples was 93%. The concentration of a single sample was > 200 ng/μL and the volume was > 5 μL. All miRNA serum samples were uncontaminated by the genome. The Mann-Whitney test showed significant differences in miRNA between each group, with a detection P-value of < 0.05. Illumina software was set up with Diff Score set to ± 13, meaning that P = 0.001.There were significant changes in miRNA expression between the three groups. miRNA-183 was the most up-regulated, followed by miRNA-373. miRNA-129 and miRNA-188 were both strongly down-regulated and miRNA-378 was down-regulated a small amount. The liver cancer group had greater changes, which indicated that changes in miRNA expression levels were caused by hepatocirrhosis. The liver cancer disease course then further increased these changes. In the pentagon created by these five miRNAs, three groups showed significant deviation. The liver cancer group had a bigger deviation trend. The chart indicated that miRNA expression changes occurred in the hepatocirrhosis group, which increased in the liver cancer disease course and were irreversible.

CONCLUSION: There was a significant relationship between the irreversible up-regulation of miRNA-183/373 and down-regulation of miRNA-129/188/378 and incidences of hepatocirrhosis and liver cancer.

MicroRNAs as biomarkers for hepatocellular carcinoma diagnosis and prognosis

Hepatocellular carcinoma (HCC) is the fifth most common cancer in the world, and it is the second leading cause of cancer-related deaths. Despite improvements in HCC therapy, the overall survival rate is still very low because of the late detection of the tumors. Thus, early detection of HCC offers the best chance of survival for patients. MicroRNAs (miRNAs) are evolutionarily conserved small noncoding RNAs involved in the regulation of gene expression and protein translation. Many studies have shown that they played a very important role in cancer progresses and outcomes. The aberrant expression of miRNAs is common in various human malignancies and it modulates cancer-associated genomic regions or fragile sites. As for the relationship between miRNAs and HCC, several studies have demonstrated that the aberrant expression of specific miRNAs can be detected in HCC patients' serum and plasma or HCC cells and tissues, and miRNAs have shown great promise as diagnostic and prognostic markers for HCC. In the present review, we discussed the applications of miRNAs as biomarkers for HCC diagnosis and prognosis, and the association between miRNAs polymorphisms and the risk of HCC as well.

Connecting rules from paired miRNA and mRNA expression data sets of HCV patients to detect both inverse and positive regulatory relationships

BACKGROUND

Intensive research based on the inverse expression relationship has been undertaken to discover the miRNA-mRNA regulatory modules involved in the infection of Hepatitis C virus (HCV), the leading cause of chronic liver diseases. However, biological studies in other fields have found that inverse expression relationship is not the only regulatory relationship between miRNAs and their targets, and some miRNAs can positively regulate a mRNA by binding at the 5' UTR of the mRNA.

RESULTS

This work focuses on the detection of both inverse and positive regulatory relationships from a paired miRNA and mRNA expression data set of HCV patients through a 'change-to-change' method which can derive connected discriminatory rules. Our study uncovered many novel miRNA-mRNA regulatory modules. In particular, it was revealed that GFRA2 is positively regulated by miR-557, miR-765 and miR-17-3p that probably bind at different locations of the 5' UTR of this mRNA. The expression relationship between GFRA2 and any of these three miRNAs has not been studied before, although separate research for this gene and these miRNAs have all drawn conclusions linked to hepatocellular carcinoma. This suggests that the binding of mRNA GFRA2 with miR-557, miR-765, or miR-17-3p, or their combinations, is worthy of further investigation by experimentation. We also report another mRNA QKI which has a strong inverse expression relationship with miR-129 and miR-493-3p which may bind at the 3' UTR of QKI with a perfect sequence match. Furthermore, the interaction between hsa-miR-129-5p (previous ID: hsa-miR-129) and QKI is supported with CLIP-Seq data from starBase. Our method can be easily extended for the expression data analysis of other diseases.

CONCLUSION

Our rule discovery method is useful for integrating binding information and expression profile for identifying HCV miRNA-mRNA regulatory modules and can be applied to the study of the expression profiles of other complex human diseases.

Circulating miRNAs: roles in cancer diagnosis, prognosis and therapy

MicroRNAs (miRNAs) belong to a class of small non-coding RNAs that regulate numerous biological processes by targeting a broad set of messenger RNAs. Recently, miRNAs have been detected in remarkably stable forms in many types of body fluids. A comparison between cancer patients and healthy individuals has clearly shown that certain types of circulating miRNAs are associated with cancer initiation and progression. Research on miRNA-based biomarkers has witnessed phenomenal growth, owing to the non-invasive nature of miRNA-based screening assays and their sensitivity and specificity in detecting cancers. Consequently, a considerable effort has been devoted to identify suitable miRNAs for cancer diagnosis and also decode the information carried by circulating miRNAs. This review highlights the current studies that focus on the identification of circulating miRNA-based diagnostic and prognostic markers, for the most prevalent types of cancer. Additionally, the review also provides an insight into the putative functions of miRNAs, and attempts to delineate the mechanisms through which they are released into the bloodstream. Moreover, methodologies and strategies for identification of circulating miRNAs in cancers are summarized. Finally, potential strategies for circulating miRNA-based cancer therapies are proposed.

Complex interactions between microRNAs and hepatitis B/C viruses

MicroRNAs (miRNAs) are a class of small noncoding RNAs that post-transcriptionally regulate the expression of many target genes via mRNA degradation or translation inhibition. Many studies have shown that miRNAs are involved in the modulation of gene expression and replication of hepatitis B virus (HBV) and hepatitis C virus (HCV) and play a pivotal role in host-virus interactions. Increasing evidence also demonstrates that viral infection leads to alteration of the miRNA expression profile in hepatic tissues or circulation. The deregulated miRNAs participate in hepatocellular carcinoma (HCC) initiation and progression by functioning as oncogenes or tumor suppressor genes by targeting various genes involved in cancer-related signaling pathways. The distinct expression pattern of miRNAs may be a useful marker for the diagnosis and prognosis of virus-related diseases considering the limitation of currently used biomarkers. Moreover, the role of deregulated miRNA in host-virus interactions and HCC development suggested that miRNAs may serve as therapeutic targets or as tools. In this review, we summarize the recent findings about the deregulation and the role of miRNAs during HBV/HCV infection and HCC development, and we discuss the possible mechanism of action of miRNAs in the pathogenesis of virus-related diseases. Furthermore, we discuss the potential of using miRNAs as markers for diagnosis and prognosis as well as therapeutic targets and drugs.

miRNAs affect the development of hepatocellular carcinoma via dysregulation of their biogenesis and expression

The pathogenesis of hepatocellular carcinoma (HCC) is not fully understood, which has affected the early diagnosis and treatment of HCC and the survival time of patients. MicroRNAs (miRNAs) are a class of evolutionarily conserved small, non-coding RNAs, which regulate the expression of various genes post-transcriptionally. Emerging evidence indicates that the key enzymes involved in the miRNA biosynthesis pathway and some tumor-specific miRNAs are widely deregulated or upregulated in HCC and closely associated with the occurrence and development of various cancers, including HCC. Early studies have shown that miRNAs have critical roles in HCC progression by targeting many critical protein-coding genes, thereby contributing to the promotion of cell proliferation; the avoidance of apoptosis, inducing via angiogenesis; and the activation of invasion and metastasis pathways. Experimental data indicate that discovery of increasing numbers of aberrantly expressed miRNAs has opened up a new field for investigating the molecular mechanism of HCC progression. In this review, we describe the current knowledge about the roles and validated targets of miRNAs in the above pathways that are known to be hallmarks of HCC, and we also describe the influence of genetic variations in miRNA biosynthesis and genes.

Effects of common polymorphisms rs2910164 in miR-146a and rs11614913 in miR-196a2 on susceptibility to colorectal cancer: a systematic review meta-analysis

PURPOSE

Emerging evidence has shown that single nucleotide polymorphisms occurred in microRNAs may contribute to the development of colorectal cancer (CRC). rs2910164 in miR-146a and rs11614913 in miR-196a2 are suggested to be associated with the susceptibility to CRC, but individually published studies revealed inconclusive results. To systematically summarize the possible correlationship between these polymorphisms and CRC risk, we performed this meta-analysis.

METHODS

We retrieved the relevant articles of the associations between these two microRNA polymorphisms and susceptibility to CRC for the period up to July 1, 2013. A total of seven articles were identified with 2,143 cases and 2,457 controls for miR-146a rs2910164, 1,594 cases and 2,252 controls for miR-196a2 rs11614913. Odds ratio and 95 % confidence interval were calculated to investigate the strength of the association.

RESULTS

The pooled analysis showed that miR-146a rs2910164 did not reveal any correlation with CRC susceptibility. However, a decreased risk was observed between miR-196a2 rs11614913 and CRC in all genetic models.

CONCLUSION

Our current meta-analysis demonstrates that miR-196a2 rs11614913 most likely contributes to decreased risk of CRC, whereas miR-146a rs2910164 may not be associated with the susceptibility to CRC.

New insights on the role of epigenetic alterations in hepatocellular carcinoma

Emerging evidence assigns to epigenetic mechanisms heritable differences in gene function that come into being during cell development or via the effect of environmental factors. Epigenetic deregulation is strongly involved in the development of hepatocellular carcinoma (HCC). It includes changes in methionine metabolism, promoter hypermethylation, or increased proteasomal degradation of oncosuppressors, as well as posttranscriptional deregulation by microRNA or messenger RNA (mRNA) binding proteins. Alterations in the methylation of the promoter of methyl adenosyltransferase MAT1A and MAT2A genes in HCC result in decreased S-adenosylmethionine levels, global DNA hypomethylation, and deregulation of signal transduction pathways linked to methionine metabolism and methyl adenosyltransferases activity. Changes in S-adenosylmethionine levels may also depend on MAT1A mRNA destabilization associated with MAT2A mRNA stabilization by specific proteins. Decrease in MAT1A expression has also been attributed to miRNA upregulation in HCC. A complex deregulation of miRNAs is also strongly involved in hepatocarcinogenesis, with up-regulation of different miRNAs targeting oncosuppressor genes and down-regulation of miRNAs targeting genes involved in cell-cycle and signal transduction control. Oncosuppressor gene down-regulation in HCC is also induced by promoter hypermethylation or posttranslational deregulation, leading to proteasomal degradation. The role of epigenetic changes in hepatocarcinogenesis has recently suggested new promising therapeutic approaches for HCC on the basis of the administration of methylating agents, inhibition of methyl adenosyltransferases, and restoration of the expression of tumor-suppressor miRNAs.