Genetic Variants in MicroRNAs and Their Binding Sites Are Associated with the Risk of Parkinson Disease

MicroRNAs (miRNAs) are small noncoding RNAs that serve as key regulators of gene expression. They have been shown to be involved in a wide range of biological processes including neurodegenerative diseases. Genetic variants in miRNAs or miRNA‐binding sites on their target genes could affect miRNA function and contribute to disease risk. Here, we investigated the association of miRNA‐related genetic variants with Parkinson disease (PD) using data from the largest GWAS on PD. Of 243 miRNA variants, we identified rs897984:T>C in miR‐4519 (P value = 1.3×10^?5 and OR = 0.93) and rs11651671:A>G in miR‐548at‐5p (P value = 1.1×10^?6 and OR = 1.09) to be associated with PD. We showed that the variant's mutant alleles change the secondary structure and decrease expression level of their related miRNAs. Subsequently, we highlighted target genes that might mediate the effects of miR‐4519 and miR‐548at‐5p on PD. Among them, we experimentally showed that NSF is a direct target of miR‐4519. Furthermore, among 48,844 miRNA‐binding site variants, we found 32 variants (within 13 genes) that are associated with PD. Four of the host genes, CTSB, STX1B, IGSF9B, and HSD3B7, had not previously been reported to be associated with PD. We provide evidence supporting the potential impact of the identified miRNA‐binding site variants on miRNA‐mediated regulation of their host genes.     

Genome‐wide association study of lncRNA polymorphisms with bone mineral density

Recent studies suggested that long noncoding RNAs (lncRNAs) were widely transcribed in the genome, but their potential roles in the genetic complexity of human disorders required further exploration. The purpose of the present study was to explore genetic polymorphisms of lncRNAs associated with bone mineral density (BMD) and its potential value. Based on the lncRNASNP database, 55,906 lncSNPs were selected to conduct a genome‐wide association study meta‐analysis among 11,140 individuals of seven independent studies for BMDs at femoral neck (FN), lumbar spine, and total hip (HIP). Promising results were replicated in Genetic Factors for Osteoporosis Consortium (GEFOS Sequencing, n = 32,965). We found two lncRNA loci that were significantly associated with BMD. MEF2C antisense RNA 1 (MEF2C‐AS1) located at 5q14.3 was significantly associated with FN‐BMD after Bonferroni correction, and the strongest association signal was detected at rs6894139 (P = 3.03 × 10^?9). LOC100506136 rs6465531 located at 7q21.3 showed significant association with HIP‐BMD (P = 7.43 × 10^?7). MEF2C‐AS1 rs6894139 was replicated in GEFOS Sequencing with P‐value of 1.43 × 10^?23. Our results illustrated the important role of polymorphisms in lncRNAs in determining variations of BMD and provided justification and evidence for subsequent functional studies.     

Distinct Patterns of Genetic Variations in Potential Functional Elements in Long Noncoding RNAs

Non‐protein‐coding RNAs have increasingly been shown to be an important class of regulatory RNAs having significant roles in regulation of gene expression. The long noncoding RNA (lncRNA) gene family presently constitutes a large number of noncoding RNA (ncRNA) loci almost equaling the number of protein‐coding genes. Nevertheless, the biological roles and mechanisms of the majority of lncRNAs are poorly understood, with exceptions of a very few well‐studied candidates. The availability of genome‐scale variation datasets, and increasing number of variant loci from genome‐wide association studies falling in lncRNA loci have motivated us to understand the patterns of genomic variations in lncRNA loci, their potential functional correlates, and selection in populations. In the present study, we have performed a comprehensive analysis of genomic variations in lncRNA loci. We analyzed for patterns and distributions of genomic variations with respect to potential functional domains in lncRNAs. The analysis reveals a distinct distribution of variations in subclasses of long ncRNAs and in potential functional domains of lncRNAs. We further examined signals of selections and allele frequencies of these prioritized set of lncRNAs. To the best of our knowledge, this is the first and comprehensive large‐scale analysis of genetic variations in long ncRNAs.     

Rs2262251 in lncRNA RP11‐462G12.2 is associated with nonsyndromic cleft lip with/without cleft palate

Nonsyndromic cleft lip with/without cleft palate (NSCL/P) is one of the most common human congenital defects. Rs2262251 (G>C) in long noncoding RNA (lncRNA) RP11‐462G12.2 is in high linkage disequilibrium with rs8049367, which was identified in our previous genome‐wide association study on NSCL/P, and is a potential causative single‐nucleotide polymorphism (SNP) for NSCL/P. To test these hypotheses, rs2262251 was evaluated in another cohort of 1,314 cases and 1,259 controls. Rs2262251 was associated with NSCL/P risk (p = .003). However, no association was detected for cleft palate only. SNP rs2262251 affected the structure and expression of lncRNA RP11‐462G12.2 in HEK293 and HEPM cells and in lip tissues from patients with NSCL/P. Overexpression of the rs2262251 G allele contributed to reducing the number of cells in the G0/G1 phase, inhibiting cell apoptosis, and promoting cell proliferation in vitro. The rs2262251 C allele regulated the expression of miR‐744‐5p and its target gene IQSEC2, both of which were expressed in human lip tissues, and showed reverse correlation during mouse lip development. Taken together, these findings suggest that rs2262251 is associated with the risk of NSCL/P and participates in a lncRNA–miRNA–mRNA regulatory axis in which miR‐744‐5p and IQSEC2 combine to control NSCL/P development.     

Functional variant in microRNA‐196a2 contributes to the susceptibility of congenital heart disease in a Chinese population

Hox gene clusters play an important role during cardiac septation to valve formation in different species, and the miR‐196a‐HOXB8‐Sonic hedgehog signaling pathway is of particular interest. Recently, we found that a genetic variant of rs11614913 in the miR‐196a2 sequence could alter mature miR‐196a expression and target mRNA binding; this observation led us to hypothesize that rs11614913 might influence susceptibility to sporadic congenital heart disease (CHD). We conducted a three‐stage case–control study of CHD in Chinese to test our hypothesis by genotyping miR‐196a2 rs11614913 and three other pre‐miRNA SNPs (miR‐146a rs2910164, miR‐149 rs2292832, and miR‐499 rs3746444) in 1,324 CHD cases and 1,783 non‐CHD controls. We found that rs11614913 CC was associated with a significantly increased risk of CHD in all three stages combined (P=6.81×10^?6). In a genotype–phenotype correlation analysis using 29 cardiac tissue samples of CHD, rs11614913 CC was associated with significantly increased mature miR‐196a expression (P=0.001). In vitro binding assays further revealed that the rs11614913 variant affects HOXB8 binding to mature miR‐196a. This is the first study to indicate that miR‐196a2 rs11614913 plays a role in sporadic CHD susceptibility. Hum Mutat 30:1–6, 2009. © 2009 Wiley‐Liss, Inc.     

CDKN2A,NF2, and JUN are dysregulated among other genes by miRNAs in malignant mesothelioma—A miRNA microarray analysis

Malignant mesothelioma (MM) is an aggressive cancer arising from mesothelial cells, mainly due to former asbestos exposure. Little is known about the microRNA (miRNA) expression of MM. miRNAs are small noncoding RNAs, which play an essential role in the regulation of gene expression. This study was carried out to analyze the miRNA expression profile of 17 MM samples using miRNA microarray. The analysis distinguished the overall miRNA expression profiles of tumor tissue and normal mesothelium. Differentially expressed miRNAs were found in tumor samples compared with normal sample. Twelve of them, let‐7b*, miR‐1228*, miR‐195*, miR‐30b*, miR‐32*, miR‐345, miR‐483‐3p, miR‐584, miR‐595, miR‐615‐3p, and miR‐885‐3p, were highly expressed whereas the remaining nine, let‐7e*, miR‐144*, miR‐203, miR‐340*, miR‐34a*, miR‐423, miR‐582, miR‐7‐1*, and miR‐9, were unexpressed or had severely reduced expression levels. Target genes for these miRNAs include the most frequently affected genes in MM such as CDKN2A, NF2, JUN, HGF, and PDGFA. Many of the miRNAs were located in chromosomal areas known to be deleted or gained in MM such as 8q24, 1p36, and 14q32. Furthermore, we could identify specific miRNAs for each histopathological subtype of MM. Regarding risk factors such as smoking status and asbestos exposure, significantly differentially expressed miRNAs were identified in smokers versus nonsmokers (miR‐379, miR‐301a, miR‐299‐3p, miR‐455‐3p, and miR‐127‐3p), but not in asbestos‐exposed patients versus nonexposed ones. This could be related to the method of assessment of asbestos exposure as asbestos remains to be the main contributor to the development of MM. © 2009 Wiley‐Liss,Inc.     

miR‐29b and miR‐125a regulate podoplanin and suppress invasion in glioblastoma

Glioblastoma is the most frequent and malignant brain tumor, characterized by an elevated capacity for cellular proliferation and invasion. Recently, it was demonstrated that podoplanin membrane sialo‐glycoprotein encoded by PDPN gene is over‐expressed and related to cellular invasion in astrocytic tumors; however the mechanisms of regulation are still unknown. MicroRNAs are noncoding RNAs that regulate gene expression and several biological processes and diseases, including cancer. Nevertheless, their roles in invasion, proliferation, and apoptosis of glioblastoma are not completely understood. In this study, we focused on miR‐29b and miR‐125a, which were predicted to regulate PDPN, and demonstrated that these microRNAs directly target the 3′ untranslated region of PDPN and inhibit invasion, apoptosis, and proliferation of glioblastomas. Furthermore, we report that miR‐29b and miR‐125a are downregulated in glioblastomas and also in CD133‐positive cells. Taken together, these results suggest that miR‐29b and miR‐125a represent potential therapeutic targets in glioblastoma. © 2010 Wiley‐Liss, Inc.     

GWAS and network analysis of co‐occurring nicotine and alcohol dependence identifies significantly associated alleles and network

Alcohol dependence (AD) and nicotine dependence (ND) co‐occur frequently (AD+ND). We integrated SNP‐based, gene‐based, and protein–protein interaction network analyses to identify shared risk genes or gene subnetworks for AD+ND in African Americans (AAs, N = 2,094) and European Americans (EAs, N = 1,207). The DSM‐IV criterion counts for AD and ND were modeled as two dependent variables in a multivariate linear mixed model, and analyzed separately for the two populations. The most significant SNP was rs6579845 in EAs (p < 1.29 × 10^?8) in GM2A, which encodes GM2 ganglioside activator, and is a cis‐expression quantitative locus that affects GM2A expression in blood and brain tissues. However, this SNP was not replicated in our another small sample (N = 678). We identified a subnetwork of 24 genes that contributed to the AD+ND criterion counts. In the gene‐set analysis for the subnetwork in an independent sample, the Study of Addiction: Genetics and Environment project (predominately EAs), these 24 genes as a set differed in AD+ND versus control subjects in EAs (p = .041). Functional enrichment analysis for this subnetwork revealed that the gene enrichment involved primarily nerve growth factor pathways, and cocaine and amphetamine addiction. In conclusion, we identified a genome‐wide significant variant at GM2A and a gene subnetwork underlying the genetic trait of shared AD+ND. These results increase our understanding of the shared (pleiotropic) genetic risk that underlies AD+ND.     

The Role of microRNA‐146a (miR‐146a) and its Target IL‐1R‐Associated Kinase (IRAK1) in Psoriatic Arthritis Susceptibility

MicroRNAs have shown different expression patterns in immune diseases. The present study explores the association of miRNA‐146a variant rs2910164 and of two IRAK1 (target of miR‐146a) polymorphisms rs3027898 and rs1059703 with psoriasic arthritis (PsA). Twenty‐nine PsA and 66 controls were enrolled in the study. To study if the statistical significant differences between patients with PsA and controls are independent to psoriasis, we expanded the study in 49 patients with ankylosing spondylitis (AS). Strong statistical significant difference was observed in IRAK1 rs3027898 polymorphism distribution between patients with PsA and controls (P = 0.003), as between patients with AS and controls (P < 0.001). Marginally significant difference was observed in distribution of IRAK1 rs1059703 genotypes between patients with PsA and controls (P = 0.058), but no difference was observed in miRNA‐146a rs2910164 distribution (P = 0.394). This is the first study that addresses IRAK1 rs3027898 polymorphism association with PsA susceptibility, but further studies could help to understand the extent of the proposed association.