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Zhu G, Zhang C, Wang Y, Wang Y, Li D, Yu X, Zhu W, Fu C, Lou S, Fan L, Ma L, Wang L, Pan Y. Variants in miRNA regulome and their association with the risk of nonsyndromic orofacial clefts. Epigenomics 2020; 12:1109-1121. [PMID: 32408759 DOI: 10.2217/epi-2020-0124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Aim: To investigate the associations between single nucleotide polymorphisms (SNPs) in miRNA regulome and nonsyndromic orofacial clefts. Materials & methods: The associations were evaluated by logistic regression model in stage I (504 cases and 455 controls) and stage II (1500 cases and 1386 controls). Functional experiments including luciferase activity assay, cell apoptosis and proliferation, serum miRNA expression, and mouse embryo RNA sequencing were performed. Results: Rs3830766 in the enhancer of hsa-miR-4260 was associated with cleft lip only (CLO) and enhancer activity. Hsa-miR-4260 expression decreased in the serum of CLO. Overexpression of miR-4260 inhibited cell proliferation and promoted cell apoptosis. UBB was the target gene of hsa-miR-4260. Conclusion: Rs3830766 in the hsa-miR-4260 enhancer that can interact with UBB was relevant to CLO.
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Affiliation(s)
- Guirong Zhu
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Chi Zhang
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Yuting Wang
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Yuli Wang
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Dandan Li
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Xin Yu
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Weihao Zhu
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Chengyi Fu
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Shu Lou
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Liwen Fan
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Lan Ma
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China
| | - Lin Wang
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
| | - Yongchu Pan
- Institute of Stomatology, Nanjing Medical University, Nanjing, PR China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, PR China
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Yang X, Li X, Quan X, Li H, Hao X, Jiang M, Zhou B. Association Between Two Polymorphisms in the Promoter Region of miR-143/miR-145 and the Susceptibility of Lung Cancer in Northeast Chinese Nonsmoking Females. DNA Cell Biol 2019; 38:814-823. [PMID: 31314552 DOI: 10.1089/dna.2019.4796] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Lung cancer is known to cause high mortality and morbidity. The study aimed to explore the association between rs3733845 and rs3733846 polymorphisms in the promoter region of miR-143/145 and the risk of lung cancer among 575 nonsmoking cases and 575 cancer-free controls in a Chinese female population. We genotyped two single nucleotide polymorphisms (SNPs) in the promoter region of miR-143/145 in 575 cases and 575 controls using TaqMan allelic discrimination method. Logistic regression analysis was conducted to assess the association between polymorphisms in the promoter of miR-143/miR-145 and risk of lung cancer females. Crossover analysis was used to explore the interaction between the two SNPs and environmental risk factors (cooking oil fume exposure and passive smoking exposure). The results showed that both rs3733845 and rs3733846 polymorphisms were associated with an increased lung adenocarcinoma risk in dominant model (adjusted odds ratio [OR] = 1.329, 95% confidence intervals [CIs] = 1.026-1.723, p = 0.031 and adjusted OR = 1.450, 95% CI = 1.112-1.890, p = 0.006, respectively). The results of crossover analysis revealed that rs3733845 and rs3733846 risk genotypes along with cooking oil exposure increased lung cancer risk by 1.862-fold and 2.260-fold, respectively (adjusted OR = 1.862, 95% CI = 1.105-3.138, p = 0.020 for rs3733845; adjusted OR = 2.260, 95% CI = 1.354-3.769, p = 0.002 for rs3733846). There was positive multiplicative interaction between the two SNPs and cooking oil fume exposure (adjusted OR = 1.362, 95% CI = 1.078-1.719, p = 0.009 for oil × rs3733845; adjusted OR = 1.399, 95% CI = 1.122-1.745, p = 0.003 for oil × rs3733846). In nonsmoking females, rs3733845 and rs3733846 polymorphisms might be associated with lung adenocarcinoma risk. Moreover, the interactions between the two SNPs and cooking oil fume exposure were statistically significant on a multiplicative scale rather than an addictive scale.
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Affiliation(s)
- Xianglin Yang
- 1Department of Clinical Epidemiology, First Affiliated Hospital, China Medical University, Shenyang, China.,2Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Xuelian Li
- 2Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Xiaowei Quan
- 1Department of Clinical Epidemiology, First Affiliated Hospital, China Medical University, Shenyang, China.,2Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Hang Li
- 1Department of Clinical Epidemiology, First Affiliated Hospital, China Medical University, Shenyang, China.,2Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Xia Hao
- 1Department of Clinical Epidemiology, First Affiliated Hospital, China Medical University, Shenyang, China.,2Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Min Jiang
- 1Department of Clinical Epidemiology, First Affiliated Hospital, China Medical University, Shenyang, China.,2Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
| | - Baosen Zhou
- 1Department of Clinical Epidemiology, First Affiliated Hospital, China Medical University, Shenyang, China.,2Department of Epidemiology, School of Public Health, China Medical University, Shenyang, China
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4
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Guerrero Flórez M, Guerrero Gómez OA, Mena Huertas J, Yépez Chamorro MC. Mapping of microRNAs related to cervical cancer in Latin American human genomic variants. F1000Res 2018; 6:946. [PMID: 37766816 PMCID: PMC10521080 DOI: 10.12688/f1000research.10138.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/05/2018] [Indexed: 09/29/2023] Open
Abstract
Background: MicroRNAs are related to human cancers, including cervical cancer (CC) caused by HPV. In 2018, approximately 56.075 cases and 28.252 deaths from this cancer were registered in Latin America and the Caribbean according to GLOBOCAN reports. The main molecular mechanism of HPV in CC is related to integration of viral DNA into the hosts' genome. However, the different variants in the human genome can result in different integration mechanisms, specifically involving microRNAs (miRNAs). Methods: The miRNAs associated with CC were obtained from literature, the miRNA sequences and four human genome variants (HGV) from Latin American populations were obtained from miRBase and 1000 Genomes Browser, respectively. HPV integration sites near cell cycle regulatory genes were identified. miRNAs were mapped on HGV. miRSNPs were identified in the miRNA sequences located at HPV integration sites on the Latin American HGV. Results: Two hundred seventy-two miRNAs associated with CC were identified in 139 reports from different geographic locations. By mapping with Blast-Like Alignment Tool (BLAT), 2028 binding sites were identified from these miRNAs on the human genome (version GRCh38/hg38); 42 miRNAs were located on unique integration sites; and miR-5095, miR-548c-5p and miR-548d-5p were involved with multiple genes related to the cell cycle. Thirty-seven miRNAs were mapped on the Latin American HGV (PUR, MXL, CLM and PEL), but only miR-11-3p, miR-31-3p, miR-107, miR-133a-3p, miR-133a-5p, miR-133b, miR-215-5p, miR-491-3p, miR-548d-5p and miR-944 were conserved. Conclusions: Ten miRNAs were conserved in the four HGV. In the remaining 27 miRNAs, substitutions, deletions or insertions were observed. These variation patterns can imply differentiated mechanisms towards each genomic variant in human populations because of specific genomic patterns and geographic features. These findings may help in determining susceptibility for CC development. Further identification of cellular genes and signalling pathways involved in CC progression could lead new therapeutic strategies based on miRNAs.
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Affiliation(s)
- Milena Guerrero Flórez
- Department of Biology, University of Nariño, Pasto, Nariño, Colombia
- Department of Biology, Center for Health Studies at the University of Nariño (CESUN), University of Nariño, Pasto, Nariño, Colombia
| | - Olivia Alexandra Guerrero Gómez
- Department of Biology, University of Nariño, Pasto, Nariño, Colombia
- Department of Biology, Center for Health Studies at the University of Nariño (CESUN), University of Nariño, Pasto, Nariño, Colombia
| | - Jaqueline Mena Huertas
- Department of Biology, University of Nariño, Pasto, Nariño, Colombia
- Department of Biology, Center for Health Studies at the University of Nariño (CESUN), University of Nariño, Pasto, Nariño, Colombia
| | - María Clara Yépez Chamorro
- Department of Biology, Center for Health Studies at the University of Nariño (CESUN), University of Nariño, Pasto, Nariño, Colombia
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Fekonja S, Korošec P, Rijavec M, Jeseničnik T, Kunej T. Asthma MicroRNA Regulome Development Using Validated miRNA-Target Interaction Visualization. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2018; 22:607-615. [PMID: 30124362 DOI: 10.1089/omi.2018.0112] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Asthma is a common multifactorial complex disease caused by an interaction of genetic and environmental factors. There are no robust biomarkers or molecular diagnostics for asthma or its detailed phenotypic stratification in the clinic. Regulatory and epigenomic factors are priority candidates for asthma biomarker discovery and translational research because this common disease emerges in association with host/environment interactions. In this context, epigenomic molecular events such as microRNA (miRNA) silencing affect asthma susceptibility and severity. We report here an analysis of the miRNAs in the literature, their targets associated with asthma, and present the findings organized as an miRNA-target network, an miRNA regulome of asthma. The miRNA-target interactions in asthma were extracted from the PubMed and the Web of Science databases, while the miRNA-target network was visualized with the Cytoscape tool. Genomic locations of miRNA and target genes were displayed using the Ensembl Whole Genome tool. We cataloged miRNAs associated with asthma and their experimentally validated targets, retrieving 48 miRNAs associated with asthma, and 54 experimentally validated miRNA targets. Four central molecules involved in 34.5% of all interactions were identified in the network. The miRNA-target pairs were constructed as an asthma-associated miRNA-target regulatory network. The network revealed subnetworks pointing toward potential asthma biomarker candidates. The asthma miRNA regulome reported here offers a strong foundation for future translational research and systems medicine applications for asthma diagnostic and therapeutic innovation. Developed protocol for constructing miRNA regulome could now be used for biomarker development in multifactorial diseases.
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Affiliation(s)
- Simon Fekonja
- 1 Department of Animal Science, Biotechnical Faculty, University of Ljubljana , Domžale, Slovenia
| | - Peter Korošec
- 2 Laboratory for Clinical Immunology and Molecular Genetics, University Clinic of Respiratory and Allergic Diseases Golnick, Golnik, Slovenia
| | - Matija Rijavec
- 2 Laboratory for Clinical Immunology and Molecular Genetics, University Clinic of Respiratory and Allergic Diseases Golnick, Golnik, Slovenia
| | - Taja Jeseničnik
- 3 Agronomy Department, Biotechnical Faculty, University of Ljubljana , Jamnikarjeva, Ljubljana, Slovenia
| | - Tanja Kunej
- 1 Department of Animal Science, Biotechnical Faculty, University of Ljubljana , Domžale, Slovenia
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Vilne B, Schunkert H. Integrating Genes Affecting Coronary Artery Disease in Functional Networks by Multi-OMICs Approach. Front Cardiovasc Med 2018; 5:89. [PMID: 30065929 PMCID: PMC6056735 DOI: 10.3389/fcvm.2018.00089] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 06/22/2018] [Indexed: 12/26/2022] Open
Abstract
Coronary artery disease (CAD) and myocardial infarction (MI) remain among the leading causes of mortality worldwide, urgently demanding a better understanding of disease etiology, and more efficient therapeutic strategies. Genetic predisposition as well as the environment and lifestyle are thought to contribute to disease risk. It is likely that non-linear and complex interactions occur between these multiple factors, involving simultaneous pathological changes in diverse cell types, tissues, and organs, at multiple molecular levels. Recent technological advances have exponentially expanded the breadth of available -omics data, from genome, epigenome, transcriptome, proteome, metabolome to even the microbiome. Integration of multiple layers of information across several -omics domains, i.e., the so-called multi-omics approach, currently holds the promise as a path toward precision medicine. Indeed, a more meaningful interpretation of genotype-phenotype relationships and the development of successful therapeutics tailored to individual patients are urgently needed. In this review, we will summarize recent findings and applications of integrative multi-omics in elucidating the etiology of CAD/MI; with a special focus on established disease susceptibility loci sequentially identified in genome-wide association studies (GWAS) over the last 10 years. Moreover, in addition to the autosomal genome, we will also consider the genetic variation in our “second genome”—the mitochondrial genome. Finally, we will summarize the current challenges in the field and point to future research directions required in order to successfully and effectively apply these approaches for precision medicine.
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Affiliation(s)
- Baiba Vilne
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, Munich, Germany.,Munich Heart Alliance, German Centre for Cardiovascular Research, Munich, Germany
| | - Heribert Schunkert
- Deutsches Herzzentrum München, Klinik für Herz- und Kreislauferkrankungen, Technische Universität München, Munich, Germany.,Munich Heart Alliance, German Centre for Cardiovascular Research, Munich, Germany
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7
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Xie K, Wang C, Qin N, Yang J, Zhu M, Dai J, Jin G, Shen H, Ma H, Hu Z. Genetic variants in regulatory regions of microRNAs are associated with lung cancer risk. Oncotarget 2018; 7:47966-47974. [PMID: 27374108 PMCID: PMC5216992 DOI: 10.18632/oncotarget.10299] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 05/28/2016] [Indexed: 12/12/2022] Open
Abstract
Genetic variants in regulatory regions of some miRNAs might be associated with lung cancer risk and survival. We performed a case-control study including 1341 non-small cell lung cancer (NSCLC) cases and 1982 controls to evaluate the associations of 7 potentially functional polymorphisms in several differently expressed miRNAs with NSCLC risk. Each SNP was also tested for the association with overall survival of 1001 NSCLC patients. We identified that rs9660710 in miR-200b/200a/429 cluster and rs763354 in miR-30a were significantly associated with NSCLC risk [odds ratio (OR) = 1.17, 95% confidence interval (CI) = 1.06–1.30, P = 0.002; OR = 0.88, 95% CI = 0.80–0.98, P = 0.017; respectively]. However, no significant association between variants and NSCLC death risk was observed in survival analysis. Functional annotation showed that both rs9660710 and rs763354 were located in regulatory elements in lung cancer cells. Compared to normal tissues, miR-200a-3p, miR-200a-5p, miR-200b-3p, miR-200b-5p and miR-429 were significantly increased in The Cancer Genome Atlas (TCGA) Lung Adenocarcinoma (LUAD) tumors, whereas miR-30a-3p and miR-30a-5p were significantly decreased in tumors (all P < 0.05). Furthermore, we observed that rs9660710 is an expression quantitative trait locus (eQTL) or methylation eQTL for miR-429 expression in TCGA normal tissues. Our results indicated that rs9660710 in miR-200b/200a/429 cluster and rs763354 in miR-30a might modify the susceptibility to NSCLC.
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Affiliation(s)
- Kaipeng Xie
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center of Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Cheng Wang
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center of Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Na Qin
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center of Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Jianshui Yang
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center of Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Meng Zhu
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center of Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Juncheng Dai
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center of Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Guangfu Jin
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center of Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center of Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Hongxia Ma
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center of Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center of Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, School of Public Health, Nanjing Medical University, Nanjing, 211166, China
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8
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Ghaffarzadeh M, Ghaedi H, Alipoor B, Omrani MD, Kazerouni F, Shanaki M, Labbaf A, Pashaiefar H, Rahimipour A. Association of MiR-149 (RS2292832) Variant with the Risk of Coronary Artery Disease. J Med Biochem 2017; 36:251-258. [PMID: 30568542 PMCID: PMC6287219 DOI: 10.1515/jomb-2017-0005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 12/24/2016] [Indexed: 12/20/2022] Open
Abstract
Background Coronary artery disease (CAD) is the most common cause of mortality and disability from incommunicable disease in the world. Although the association between the single nucleotide polymorphisms (SNPs) in protein-coding genes and the risk of CAD has been investigated extensively, very few heart-disease associated studies concerning the SNPs in miRNA genes have been reported. The present study was performed to elucidate the association between the pre-microRNA-149 (miR-149) SNP rs2292832 and the risk of CAD in an Iranian population. Methods Polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) were performed to identify the genotypes of the miR-149 SNP rs2292832 in 421 unrelated subjects (272 with CAD and 149 controls). Results Our analysis revealed that the TT genotype was more frequent in CAD patients than control subjects (P=0.02) implying that TT genotype should be considered as a risk factor in CAD development (TT vs. TC+CC p=0.02, OR=1.88). Conclusions The present study suggests that rs2292832-TT in pre-miR-149 is associated with CAD in an Iranian population.
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Affiliation(s)
- Maryam Ghaffarzadeh
- Department of Medical Lab Technology, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Ghaedi
- Department of Medical Lab Technology, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Behnam Alipoor
- Department of Laboratory Sciences, Faculty of Paramedicine, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Mir Davood Omrani
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Faranak Kazerouni
- Department of Medical Lab Technology, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehrnoosh Shanaki
- Department of Medical Lab Technology, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Afsaneh Labbaf
- Department of Medical Lab Technology, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Pashaiefar
- Medical Genetics Department, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Rahimipour
- Department of Medical Lab Technology, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Xie K, Chen M, Zhu M, Wang C, Qin N, Liang C, Song C, Dai J, Jin G, Shen H, Lin D, Ma H, Hu Z. A polymorphism in miR-1262 regulatory region confers the risk of lung cancer in Chinese population. Int J Cancer 2017; 141:958-966. [PMID: 28510306 DOI: 10.1002/ijc.30788] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Revised: 04/09/2017] [Accepted: 05/05/2017] [Indexed: 12/27/2022]
Abstract
It has been proposed that the majority of disease-associated loci identified by genome-wide association studies (GWAS) are enriched in non-coding regions, such as the promoter, enhancer or non-coding RNA genes. Thus, we performed a two-stage case-control study to systematically evaluate the association of genetic variants in miRNA regulatory regions (promoter and enhancer) with lung cancer risk in 7,763 subjects (discovery stage: 2,331 cases and 3,077 controls; validation stage: 1,065 cases and 1,290 controls). As a result, we identified that rs12740674 (C > T) in miR-1262 enhancer was significantly associated with the increased risk of lung cancer (additive model in discovery stage: adjusted OR = 1.31, 95%CI = 1.13-1.53, p = 3.846 × 10-4 in Nanjing GWAS; adjusted OR = 1.20, 95%CI = 1.00-1.44, p = 0.041 in Beijing GWAS; validation stage: adjusted OR = 1.20, 95%CI = 1.03-1.41, p = 0.024). In meta-analysis, the p value for the association between rs12740674 and lung cancer risk reached 6.204 × 10-6 (adjusted OR = 1.24, 95%CI = 1.13-1.36). Using 3DSNP database, The Cancer Genome Atlas (TCGA) data and functional assays, we observed that the risk T allele of rs12740674 reduced the expression level of miR-1262 in lung tissue through chromosomal looping, and overexpression of miR-1262 inhibited lung cancer cell proliferation probably through targeting the expression levels of ULK1 and RAB3D. Our findings confirmed the important role that genetic variants of noncoding sequence play in lung cancer susceptibility and indicated that rs12740674 in miR-1262 may be biologically relevant to lung carcinogenesis.
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Affiliation(s)
- Kaipeng Xie
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China.,Nanjing Maternal and Child Health Institute, Nanjing Maternal and Child Health Care Hospital, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, 210004, China
| | - Mengxi Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Meng Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Cheng Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Na Qin
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Cheng Liang
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Ci Song
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Juncheng Dai
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Guangfu Jin
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Dongxin Lin
- State Key Laboratory of Molecular Oncology and Department of Etiology and Carcinogenesis, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Hongxia Ma
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, 211166, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University, Nanjing, 211166, China
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10
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Ghanbari M, Erkeland SJ, Xu L, Colijn JM, Franco OH, Dehghan A, Klaver CCW, Meester-Smoor MA. Genetic variants in microRNAs and their binding sites within gene 3'UTRs associate with susceptibility to age-related macular degeneration. Hum Mutat 2017; 38:827-838. [PMID: 28397307 DOI: 10.1002/humu.23226] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/06/2017] [Accepted: 04/06/2017] [Indexed: 01/06/2023]
Abstract
Age-related macular degeneration (AMD), the leading cause of blindness in the elderly, is a complex disease that results from multiple genetic and environmental factors. MicroRNAs (miRNAs) are small noncoding RNAs that post-transcriptionally regulate target mRNAs and are frequently implicated in human diseases. Here, we investigated the association of genetic variants in miRNAs and miRNA-binding sites within gene 3'-untranslated regions (3'UTRs) with AMD using data from the largest AMD genome-wide association study. First, we identified three variants in miRNAs significantly associated with AMD. These include rs2168518:G>A in the miR-4513 seed sequence, rs41292412:C>T in pre-miR-122/miR-3591, and rs4351242:C>T in the terminal-loop of pre-miR-3135b. We demonstrated that these variants reduce expression levels of the mature miRNAs in vitro and pointed the target genes that may mediate downstream effects of these miRNAs in AMD. Second, we identified 54 variants (in 31 genes) in miRNA-binding sites associated with AMD. Based on stringent prioritization criteria, we highlighted the variants that are more likely to have an impact on the miRNA-target interactions. Further, we selected rs4151672:C>T within the CFB 3'UTR and experimentally showed that while miR-210-5p downregulates expression of CFB, the variant decreases miR-210-5p-mediated repression of CFB. Together, our findings support the notion that miRNAs may play a role in AMD.
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Affiliation(s)
- Mohsen Ghanbari
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Stefan J Erkeland
- Department of Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Lei Xu
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Johanna M Colijn
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Oscar H Franco
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
| | - Caroline C W Klaver
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Ophthalmology, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Magda A Meester-Smoor
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
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11
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Assmann TS, Duarte GCK, Brondani LA, de Freitas PHO, Martins ÉM, Canani LH, Crispim D. Polymorphisms in genes encoding miR-155 and miR-146a are associated with protection to type 1 diabetes mellitus. Acta Diabetol 2017; 54:433-441. [PMID: 28101643 DOI: 10.1007/s00592-016-0961-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 12/28/2016] [Indexed: 12/18/2022]
Abstract
AIMS Type 1 diabetes mellitus (T1DM) is characterized by severe autoimmune destruction of pancreatic beta-cells. The triggering of autoimmunity against beta-cells is probably caused by a combination of environmental and genetic risk factors. Even though much is known about the genetic of T1DM, more information is needed to completely unravel this tangled disease. MicroRNAs (miRNAs) are a class of small noncoding RNAs molecules that negatively regulate gene expression by inducing target mRNA cleavage or by inhibiting protein translation. Abnormal miRNA expressions have been described in autoimmune diseases and T1DM. Polymorphisms in genes codifying miRNAs may alter the expression of the corresponding miRNA and, thus, confer susceptibility for a given disease. Therefore, the aim of this study was to investigate whether polymorphisms in genes encoding miR-155, miR-146a, and miR-375 are associated with T1DM. METHODS Frequencies of the miRNA-146a rs2910164, miRNA-155 rs767649 and miRNA-375 rs6715345 polymorphisms were analyzed in 490 T1DM patients and in 469 nondiabetic subjects. RESULTS The miR-146a rs2910164 and miR-155 rs767649 polymorphisms were associated with protection for T1DM, and the strongest association was observed for the dominant model [odds ratio (OR) = 0.557 95% CI 0.355-0.874 and OR = 0.508, 95% CI 0.265-0.973, respectively, after adjustment for age, ethnicity, and risk HLA loci]. However, miR-375 rs6715345 frequencies did not differ between cases and controls. CONCLUSION MiR-146a rs2910164 and miR-155 rs767649 polymorphisms were associated with protection for T1DM.
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Affiliation(s)
- Taís S Assmann
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, prédio 12, 4° andar, Porto Alegre, Rio Grande do Sul, 90035-003, Brazil
- Postgraduation Program in Medical Sciences: Endocrinology, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Guilherme C K Duarte
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, prédio 12, 4° andar, Porto Alegre, Rio Grande do Sul, 90035-003, Brazil
- Postgraduation Program in Medical Sciences: Endocrinology, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Letícia A Brondani
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, prédio 12, 4° andar, Porto Alegre, Rio Grande do Sul, 90035-003, Brazil
| | - Pedro H O de Freitas
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, prédio 12, 4° andar, Porto Alegre, Rio Grande do Sul, 90035-003, Brazil
| | - Égina M Martins
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, prédio 12, 4° andar, Porto Alegre, Rio Grande do Sul, 90035-003, Brazil
| | - Luís H Canani
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, prédio 12, 4° andar, Porto Alegre, Rio Grande do Sul, 90035-003, Brazil
- Postgraduation Program in Medical Sciences: Endocrinology, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Daisy Crispim
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Rua Ramiro Barcelos 2350, prédio 12, 4° andar, Porto Alegre, Rio Grande do Sul, 90035-003, Brazil.
- Postgraduation Program in Medical Sciences: Endocrinology, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.
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12
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Bastami M, Nariman-Saleh-Fam Z, Saadatian Z, Nariman-Saleh-Fam L, Omrani MD, Ghaderian SMH, Masotti A. The miRNA targetome of coronary artery disease is perturbed by functional polymorphisms identified and prioritized by in-depth bioinformatics analyses exploiting genome-wide association studies. Gene 2016; 594:74-81. [DOI: 10.1016/j.gene.2016.08.054] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Revised: 08/27/2016] [Accepted: 08/31/2016] [Indexed: 12/22/2022]
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13
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A functional variant in miR-155 regulation region contributes to lung cancer risk and survival. Oncotarget 2016; 6:42781-92. [PMID: 26543233 PMCID: PMC4767470 DOI: 10.18632/oncotarget.5840] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 10/16/2015] [Indexed: 12/19/2022] Open
Abstract
Emerging evidence suggested that upregulation of miR-155 could serve as a promising marker for the diagnosis and prognosis of non-small cell lung cancer (NSCLC). In the present study, we genotyped rs767649 (A > T) located in miR-155 regulation region in 1341 cases and 1982 controls, and analyzed the associations of rs767649 with NSCLC risk and survival. Consequently, rs767649 exhibited the significant associations with the risk (adjusted OR = 1.12, 95% CI = 1.01–1.24, P = 0.031) and prognosis of NSCLC (adjusted HR = 1.17, 95% CI = 1.03–1.32, P = 0.014). Meanwhile, rs767649 specifically interacted with radio-chemotherapy (Pint = 0.013), and patients with both the rs767649-TT genotype and radio-chemotherapy had the highest hazard ratio (adjusted HR = 1.65, 95% CI = 1.26–2.16, P < 0.001). Furthermore, using functional assays and The Cancer Genome Atlas (TCGA) Lung Adenocarcinoma (LUAD) dataset, we found that rs767649 variant allele could increase the transcriptional activity of miR-155, which in turn facilitated tumor growth and metastasis by inhibiting HBP1, TJP1, SMAD5 and PRKAR1A expression. Our findings suggested that rs767649 A > T might contribute to the increased risk and poor prognosis of NSCLC, highlighting the importance of rs767649 in the prevention and therapy of NSCLC.
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14
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Freiesleben S, Hecker M, Zettl UK, Fuellen G, Taher L. Analysis of microRNA and Gene Expression Profiles in Multiple Sclerosis: Integrating Interaction Data to Uncover Regulatory Mechanisms. Sci Rep 2016; 6:34512. [PMID: 27694855 PMCID: PMC5046091 DOI: 10.1038/srep34512] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/15/2016] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) have been reported to contribute to the pathophysiology of multiple sclerosis (MS), an inflammatory disorder of the central nervous system. Here, we propose a new consensus-based strategy to analyse and integrate miRNA and gene expression data in MS as well as other publically available data to gain a deeper understanding of the role of miRNAs in MS and to overcome the challenges posed by studies with limited patient sample sizes. We processed and analysed microarray datasets, and compared the expression of genes and miRNAs in the blood of MS patients and controls. We then used our consensus and integration approach to construct two molecular networks dysregulated in MS: a miRNA- and a gene-based network. We identified 18 differentially expressed (DE) miRNAs and 128 DE genes that may contribute to the regulatory alterations behind MS. The miRNAs were linked to immunological and neurological pathways, and we exposed let-7b-5p and miR-345-5p as promising blood-derived disease biomarkers in MS. The results suggest that DE miRNAs are more informative than DE genes in uncovering pathways potentially involved in MS. Our findings provide novel insights into the regulatory mechanisms and networks underlying MS.
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Affiliation(s)
- Sherry Freiesleben
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, University of Rostock, Rostock, Germany
| | - Michael Hecker
- Department of Neurology, Division of Neuroimmunology, University of Rostock, Rostock, Germany
| | - Uwe Klaus Zettl
- Department of Neurology, Division of Neuroimmunology, University of Rostock, Rostock, Germany
| | - Georg Fuellen
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, University of Rostock, Rostock, Germany
- Interdisciplinary Faculty, University of Rostock, Rostock, Germany
| | - Leila Taher
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, University of Rostock, Rostock, Germany
- Division of Bioinformatics, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
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15
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Schizophrenia risk variants affecting microRNA function and site-specific regulation of NT5C2 by miR-206. Eur Neuropsychopharmacol 2016; 26:1522-1526. [PMID: 27424800 DOI: 10.1016/j.euroneuro.2016.06.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 05/25/2016] [Accepted: 06/18/2016] [Indexed: 01/12/2023]
Abstract
Despite the identification of numerous schizophrenia-associated genetic variants, few have been examined functionally to identify and characterize the causal variants. To mitigate this, we aimed at identifying functional variants affecting miRNA function. Using data from a large-scale genome-wide association study of schizophrenia, we looked for schizophrenia risk variants altering either miRNA binding sites, miRNA genes, promoters for miRNA genes, or variants that were expression quantitative trait loci (eQTLs) for miRNA genes. We hereby identified several potentially functional variants relating to miRNA function with our top finding being a schizophrenia protective allele that disrupts miR-206׳s binding to NT5C2 thus leading to increased expression of this gene. A subsequent experimental follow-up of the variant using a luciferase-based reporter assay confirmed that the allele disrupts the binding. Our study therefore suggests that miR-206 may contribute to schizophrenia risk through allele-dependent regulation of the genome-wide significant gene NT5C2.
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16
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Ghaedi H, Bastami M, Jahani MM, Alipoor B, Tabasinezhad M, Ghaderi O, Nariman-Saleh-Fam Z, Mirfakhraie R, Movafagh A, Omrani MD, Masotti A. A Bioinformatics Approach to the Identification of Variants Associated with Type 1 and Type 2 Diabetes Mellitus that Reside in Functionally Validated miRNAs Binding Sites. Biochem Genet 2016; 54:211-221. [DOI: 10.1007/s10528-016-9713-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 01/18/2016] [Indexed: 12/29/2022]
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17
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Bhattacharya A, Cui Y. SomamiR 2.0: a database of cancer somatic mutations altering microRNA-ceRNA interactions. Nucleic Acids Res 2015; 44:D1005-10. [PMID: 26578591 PMCID: PMC4702864 DOI: 10.1093/nar/gkv1220] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 10/28/2015] [Indexed: 12/14/2022] Open
Abstract
SomamiR 2.0 (http://compbio.uthsc.edu/SomamiR) is a database of cancer somatic mutations in microRNAs (miRNA) and their target sites that potentially alter the interactions between miRNAs and competing endogenous RNAs (ceRNA) including mRNAs, circular RNAs (circRNA) and long noncoding RNAs (lncRNA). Here, we describe the recent major updates to the SomamiR database. We expanded the scope of the database by including somatic mutations that impact the interactions between miRNAs and two classes of non-coding RNAs, circRNAs and lncRNAs. Recently, a large number of miRNA target sites have been discovered by newly emerged high-throughput technologies for mapping the miRNA interactome. We have mapped 388 247 somatic mutations to the experimentally identified miRNA target sites. The updated database also includes a list of somatic mutations in the miRNA seed regions, which contain the most important guiding information for miRNA target recognition. A recently developed webserver, miR2GO, was integrated with the database to provide a seamless pipeline for assessing functional impacts of somatic mutations in miRNA seed regions. Data and functions from multiple sources including biological pathways and genome-wide association studies were updated and integrated with SomamiR 2.0 to make it a better platform for functional analysis of somatic mutations altering miRNA–ceRNA interactions.
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Affiliation(s)
- Anindya Bhattacharya
- Machine Intelligence Unit, Indian Statistical Institute, Kolkata, WB 700108, India
| | - Yan Cui
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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18
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Kutchko KM, Sanders W, Ziehr B, Phillips G, Solem A, Halvorsen M, Weeks KM, Moorman N, Laederach A. Multiple conformations are a conserved and regulatory feature of the RB1 5' UTR. RNA (NEW YORK, N.Y.) 2015; 21:1274-85. [PMID: 25999316 PMCID: PMC4478346 DOI: 10.1261/rna.049221.114] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Accepted: 03/27/2015] [Indexed: 05/22/2023]
Abstract
Folding to a well-defined conformation is essential for the function of structured ribonucleic acids (RNAs) like the ribosome and tRNA. Structured elements in the untranslated regions (UTRs) of specific messenger RNAs (mRNAs) are known to control expression. The importance of unstructured regions adopting multiple conformations, however, is still poorly understood. High-resolution SHAPE-directed Boltzmann suboptimal sampling of the Homo sapiens Retinoblastoma 1 (RB1) 5' UTR yields three distinct conformations compatible with the experimental data. Private single nucleotide variants (SNVs) identified in two patients with retinoblastoma each collapse the structural ensemble to a single but distinct well-defined conformation. The RB1 5' UTRs from Bos taurus (cow) and Trichechus manatus latirostris (manatee) are divergent in sequence from H. sapiens (human) yet maintain structural compatibility with high-probability base pairs. SHAPE chemical probing of the cow and manatee RB1 5' UTRs reveals that they also adopt multiple conformations. Luciferase reporter assays reveal that 5' UTR mutations alter RB1 expression. In a traditional model of disease, causative SNVs disrupt a key structural element in the RNA. For the subset of patients with heritable retinoblastoma-associated SNVs in the RB1 5' UTR, the absence of multiple structures is likely causative of the cancer. Our data therefore suggest that selective pressure will favor multiple conformations in eukaryotic UTRs to regulate expression.
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Affiliation(s)
- Katrina M Kutchko
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Wes Sanders
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
| | - Ben Ziehr
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599, USA Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Gabriela Phillips
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
| | - Amanda Solem
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
| | - Matthew Halvorsen
- Institute for Genomic Medicine, Columbia University Medical Center, New York, New York 10032, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
| | - Nathaniel Moorman
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599, USA Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3290, USA
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19
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Solem AC, Halvorsen M, Ramos SBV, Laederach A. The potential of the riboSNitch in personalized medicine. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:517-32. [PMID: 26115028 PMCID: PMC4543445 DOI: 10.1002/wrna.1291] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 03/25/2015] [Accepted: 05/13/2015] [Indexed: 01/28/2023]
Abstract
RNA conformation plays a significant role in stability, ligand binding, transcription, and translation. Single nucleotide variants (SNVs) have the potential to disrupt specific structural elements because RNA folds in a sequence-specific manner. A riboSNitch is an element of RNA structure with a specific function that is disrupted by an SNV or a single nucleotide polymorphism (SNP; or polymorphism; SNVs occur with low frequency in the population, <1%). The riboSNitch is analogous to a riboswitch, where binding of a small molecule rather than mutation alters the structure of the RNA to control gene regulation. RiboSNitches are particularly relevant to interpreting the results of genome-wide association studies (GWAS). Often GWAS identify SNPs associated with a phenotype mapping to noncoding regions of the genome. Because a majority of the human genome is transcribed, significant subsets of GWAS SNPs are putative riboSNitches. The extent to which the transcriptome is tolerant of SNP-induced structure change is still poorly understood. Recent advances in ultra high-throughput structure probing begin to reveal the structural complexities of mutation-induced structure change. This review summarizes our current understanding of SNV and SNP-induced structure change in the human transcriptome and discusses the importance of riboSNitch discovery in interpreting GWAS results and massive sequencing projects.
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Affiliation(s)
- Amanda C Solem
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Matthew Halvorsen
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Silvia B V Ramos
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA
| | - Alain Laederach
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA.,Bioinformatics and Computational Biology Program, University of North Carolina, Chapel Hill, NC, USA
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20
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GRAAE LISETTE, PADDOCK SILVIA, BELIN ANDREACARMINE. ReMo-SNPs: a new software tool for identification of polymorphisms in regions and motifs genome-wide. Genet Res (Camb) 2015; 97:e8. [PMID: 25882789 PMCID: PMC6863641 DOI: 10.1017/s0016672315000051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Revised: 02/23/2015] [Accepted: 02/25/2015] [Indexed: 12/13/2022] Open
Abstract
Studies of complex genetic diseases have revealed many risk factors of small effect, but the combined amount of heritability explained is still low. Genome-wide association studies are often underpowered to identify true effects because of the very large number of parallel tests. There is, therefore, a great need to generate data sets that are enriched for those markers that have an increased a priori chance of being functional, such as markers in genomic regions involved in gene regulation. ReMo-SNPs is a computational program developed to aid researchers in the process of selecting functional SNPs for association analyses in user-specified regions and/or motifs genome-wide. The useful feature of automatic selection of genotyped markers in the user-provided material makes the output data ready to be used in a following association study. In this article we describe the program and its functions. We also validate the program by including an example study on three different transcription factors and results from an association study on two psychiatric phenotypes. The flexibility of the ReMo-SNPs program enables the user to study any region or sequence of interest, without limitation to transcription factor binding regions and motifs. The program is freely available at: http://www.neuro.ki.se/ReMo-SNPs/.
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Affiliation(s)
- LISETTE GRAAE
- Department of Neuroscience, Karolinska Institutet, Retzius väg 8, 171 77 Stockholm
| | | | - ANDREA CARMINE BELIN
- Department of Neuroscience, Karolinska Institutet, Retzius väg 8, 171 77 Stockholm
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21
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Maxwell EK, Campbell JD, Spira A, Baxevanis AD. SubmiRine: assessing variants in microRNA targets using clinical genomic data sets. Nucleic Acids Res 2015; 43:3886-98. [PMID: 25813044 PMCID: PMC4417167 DOI: 10.1093/nar/gkv256] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 03/13/2015] [Indexed: 01/05/2023] Open
Abstract
MicroRNAs (miRNAs) regulate gene expression by binding to partially complementary sequences on target mRNA transcripts, thereby causing their degradation, deadenylation, or inhibiting their translation. Genomic variants can alter miRNA regulation by modifying miRNA target sites, and multiple human disease phenotypes have been linked to such miRNA target site variants (miR-TSVs). However, systematic genome-wide identification of functional miR-TSVs is difficult due to high false positive rates; functional miRNA recognition sequences can be as short as six nucleotides, with the human genome encoding thousands of miRNAs. Furthermore, while large-scale clinical genomic data sets are becoming increasingly commonplace, existing miR-TSV prediction methods are not designed to analyze these data. Here, we present an open-source tool called SubmiRine that is designed to perform efficient miR-TSV prediction systematically on variants identified in novel clinical genomic data sets. Most importantly, SubmiRine allows for the prioritization of predicted miR-TSVs according to their relative probability of being functional. We present the results of SubmiRine using integrated clinical genomic data from a large-scale cohort study on chronic obstructive pulmonary disease (COPD), making a number of high-scoring, novel miR-TSV predictions. We also demonstrate SubmiRine's ability to predict and prioritize known miR-TSVs that have undergone experimental validation in previous studies.
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Affiliation(s)
- Evan K Maxwell
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA Bioinformatics Program, Boston University, Boston, MA 02215, USA
| | - Joshua D Campbell
- Bioinformatics Program, Boston University, Boston, MA 02215, USA Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA 02215, USA
| | - Avrum Spira
- Bioinformatics Program, Boston University, Boston, MA 02215, USA Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA 02215, USA
| | - Andreas D Baxevanis
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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22
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Susceptibility variants in the CD58 gene locus point to a role of microRNA-548ac in the pathogenesis of multiple sclerosis. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2015; 763:161-7. [DOI: 10.1016/j.mrrev.2014.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 10/06/2014] [Accepted: 10/07/2014] [Indexed: 11/18/2022]
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23
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Franceschini N, Hu Y, Reiner AP, Buyske S, Nalls M, Yanek LR, Li Y, Hindorff LA, Cole SA, Howard BV, Stafford JM, Carty CL, Sethupathy P, Martin LW, Lin DY, Johnson KC, Becker LC, North KE, Dehghan A, Bis JC, Liu Y, Greenland P, Manson JE, Maeda N, Garcia M, Harris TB, Becker DM, O'Donnell C, Heiss G, Kooperberg C, Boerwinkle E. Prospective associations of coronary heart disease loci in African Americans using the MetaboChip: the PAGE study. PLoS One 2014; 9:e113203. [PMID: 25542012 PMCID: PMC4277270 DOI: 10.1371/journal.pone.0113203] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 10/20/2014] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Coronary heart disease (CHD) is a leading cause of morbidity and mortality in African Americans. However, there is a paucity of studies assessing genetic determinants of CHD in African Americans. We examined the association of published variants in CHD loci with incident CHD, attempted to fine map these loci, and characterize novel variants influencing CHD risk in African Americans. METHODS AND RESULTS Up to 8,201 African Americans (including 546 first CHD events) were genotyped using the MetaboChip array in the Atherosclerosis Risk in Communities (ARIC) study and Women's Health Initiative (WHI). We tested associations using Cox proportional hazard models in sex- and study-stratified analyses and combined results using meta-analysis. Among 44 validated CHD loci available in the array, we replicated and fine-mapped the SORT1 locus, and showed same direction of effects as reported in studies of individuals of European ancestry for SNPs in 22 additional published loci. We also identified a SNP achieving array wide significance (MYC: rs2070583, allele frequency 0.02, P = 8.1 × 10(-8)), but the association did not replicate in an additional 8,059 African Americans (577 events) from the WHI, HealthABC and GeneSTAR studies, and in a meta-analysis of 5 cohort studies of European ancestry (24,024 individuals including 1,570 cases of MI and 2,406 cases of CHD) from the CHARGE Consortium. CONCLUSIONS Our findings suggest that some CHD loci previously identified in individuals of European ancestry may be relevant to incident CHD in African Americans.
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Affiliation(s)
- Nora Franceschini
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Yijuan Hu
- Department of Biostatistics and Bioinformatics, Emory University, Atlanta, Georgia, United States of America
| | - Alex P. Reiner
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Steven Buyske
- Department of Statistics & Biostatistics, Rutgers University, Piscataway, New Jersey, United States of America
| | - Mike Nalls
- Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, Maryland, United States of America
| | - Lisa R. Yanek
- Division of General Internal Medicine, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Yun Li
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Lucia A. Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, NIH, Bethesda, Maryland, United States of America
| | - Shelley A. Cole
- Department of Genetics, Southwest Foundation for Biomedical Research, San Antonio, Texas, United States of America
| | - Barbara V. Howard
- MedStar Health Research Institute, Hyattsville, Maryland, United States of America
| | - Jeanette M. Stafford
- Department of Biostatistical Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Cara L. Carty
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Praveen Sethupathy
- Department of Genetics Lineberger Comprehensive Cancer Center School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Lisa W. Martin
- Cardiovascular Institute, the George Washington University, Washington, D. C., United States of America
| | - Dan-Yu Lin
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Karen C. Johnson
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Lewis C. Becker
- Division of General Internal Medicine, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Kari E. North
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
- UNC Center for Genome Sciences, Chapel Hill, North Carolina, United States of America
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Joshua C. Bis
- Cardiovascular Health Research Unit and Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Yongmei Liu
- Center for Human Genomics, Department of Epidemiology and Prevention, Wake Forest School of Medicine, Winston Salem, North Carolina, Tennessee, United States of America
| | - Philip Greenland
- Departments of Preventive Medicine and Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - JoAnn E. Manson
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Nobuyo Maeda
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Melissa Garcia
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, NIH, Bethesda, Maryland, United States of America
| | - Tamara B. Harris
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, NIH, Bethesda, Maryland, United States of America
| | - Diane M. Becker
- Division of General Internal Medicine, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Health Policy and Management, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Christopher O'Donnell
- National Heart, Lung and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, United States of America
| | - Gerardo Heiss
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Eric Boerwinkle
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
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Obsteter J, Dovc P, Kunej T. Genetic variability of microRNA regulome in human. Mol Genet Genomic Med 2014; 3:30-9. [PMID: 25629077 PMCID: PMC4299713 DOI: 10.1002/mgg3.110] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 07/19/2014] [Accepted: 07/31/2014] [Indexed: 11/05/2022] Open
Abstract
MicroRNAs are currently being extensively studied due to their important role as post-transcriptional regulators. During miRNA biogenesis, precursors undergo two cleavage steps performed by Drosha-DGCR8 (Microprocessor) cleaving of pri-miRNA to produce pre-miRNA and Dicer-mediated cleaving to create mature miRNA. Genetic variants within human miRNA regulome have been shown to influence miRNA expression, target interaction and to affect the phenotype. In this study, we reviewed the literature, existing bioinformatics tools and catalogs associated with polymorphic miRNA regulome, and organized them into four categories: (1) polymorphisms located within miRNA genes (miR-SNPs), (2) transcription factor-binding sites/miRNA regulatory regions (miR-rSNPs), (3) miRNA target sites (miR-TS-SNPs), and 4. miRNA silencing machinery (miR-SM-SNPs). Since the miR-SM-SNPs have not been systematically studied yet, we have collected polymorphisms associated with miRNA silencing machinery. We have developed two catalogs containing genetic variability within: (1) genes encoding three main catalytic components of the silencing machinery, DROSHA, DGCR8, and DICER1; (2) miRNA genes itself, overlapping Drosha and Dicer cleavage sites. The developed resource of polymorphisms is available online (http://www.integratomics-time.com/miRNA-regulome) and will be useful for further functional studies and development of biomarkers associated with diseases and phenotypic traits.
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Affiliation(s)
- Jana Obsteter
- University of Ljubljana, Biotechnical Faculty, Department of Animal Science Groblje 3, 1230, Domzale, Slovenia
| | - Peter Dovc
- University of Ljubljana, Biotechnical Faculty, Department of Animal Science Groblje 3, 1230, Domzale, Slovenia
| | - Tanja Kunej
- University of Ljubljana, Biotechnical Faculty, Department of Animal Science Groblje 3, 1230, Domzale, Slovenia
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Pivarcsi A, Ståhle M, Sonkoly E. Genetic polymorphisms altering microRNA activity in psoriasis - a key to solve the puzzle of missing heritability? Exp Dermatol 2014; 23:620-4. [DOI: 10.1111/exd.12469] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2014] [Indexed: 12/15/2022]
Affiliation(s)
- Andor Pivarcsi
- Unit of Dermatology and Venerology; Department of Medicine; Karolinska Institutet; Stockholm Sweden
| | - Mona Ståhle
- Unit of Dermatology and Venerology; Department of Medicine; Karolinska Institutet; Stockholm Sweden
| | - Enikő Sonkoly
- Unit of Dermatology and Venerology; Department of Medicine; Karolinska Institutet; Stockholm Sweden
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26
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Rawlings-Goss RA, Campbell MC, Tishkoff SA. Global population-specific variation in miRNA associated with cancer risk and clinical biomarkers. BMC Med Genomics 2014; 7:53. [PMID: 25169894 PMCID: PMC4159108 DOI: 10.1186/1755-8794-7-53] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Accepted: 08/12/2014] [Indexed: 12/30/2022] Open
Abstract
Background MiRNA expression profiling is being actively investigated as a clinical biomarker and diagnostic tool to detect multiple cancer types and stages as well as other complex diseases. Initial investigations, however, have not comprehensively taken into account genetic variability affecting miRNA expression and/or function in populations of different ethnic backgrounds. Therefore, more complete surveys of miRNA genetic variability are needed to assess global patterns of miRNA variation within and between diverse human populations and their effect on clinically relevant miRNA genes. Methods Genetic variation in 1524 miRNA genes was examined using whole genome sequencing (60x coverage) in a panel of 69 unrelated individuals from 14 global populations, including European, Asian and African populations. Results We identified 33 previously undescribed miRNA variants, and 31 miRNA containing variants that are globally population-differentiated in frequency between African and non-African populations (PD-miRNA). The top 1% of PD-miRNA were significantly enriched for regulation of genes involved in glucose/insulin metabolism and cell division (p < 10−7), most significantly the mitosis pathway, which is strongly linked to cancer onset. Overall, we identify 7 PD-miRNAs that are currently implicated as cancer biomarkers or diagnostics: hsa-mir-202, hsa-mir-423, hsa-mir-196a-2, hsa-mir-520h, hsa-mir-647, hsa-mir-943, and hsa-mir-1908. Notably, hsa-mir-202, a potential breast cancer biomarker, was found to show significantly high allele frequency differentiation at SNP rs12355840, which is known to affect miRNA expression levels in vivo and subsequently breast cancer mortality. Conclusion MiRNA expression profiles represent a promising new category of disease biomarkers. However, population specific genetic variation can affect the prevalence and baseline expression of these miRNAs in diverse populations. Consequently, miRNA genetic and expression level variation among ethnic groups may be contributing in part to health disparities observed in multiple forms of cancer, specifically breast cancer, and will be an essential consideration when assessing the utility of miRNA biomarkers for the clinic.
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27
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Vencken SF, Sethupathy P, Blackshields G, Spillane C, Elbaruni S, Sheils O, Gallagher MF, O'Leary JJ. An integrated analysis of the SOX2 microRNA response program in human pluripotent and nullipotent stem cell lines. BMC Genomics 2014; 15:711. [PMID: 25156079 PMCID: PMC4162954 DOI: 10.1186/1471-2164-15-711] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Accepted: 07/15/2014] [Indexed: 12/13/2022] Open
Abstract
Background SOX2 is a core component of the transcriptional network responsible for maintaining embryonal carcinoma cells (ECCs) in a pluripotent, undifferentiated state of self-renewal. As such, SOX2 is an oncogenic transcription factor and crucial cancer stem cell (CSC) biomarker in embryonal carcinoma and, as more recently found, in the stem-like cancer cell component of many other malignancies. SOX2 is furthermore a crucial factor in the maintenance of adult stem cell phenotypes and has additional roles in cell fate determination. The SOX2-linked microRNA (miRNA) transcriptome and regulome has not yet been fully defined in human pluripotent cells or CSCs. To improve our understanding of the SOX2-linked miRNA regulatory network as a contribution to the phenotype of these cell types, we used high-throughput differential miRNA and gene expression analysis combined with existing genome-wide SOX2 chromatin immunoprecipitation (ChIP) data to map the SOX2 miRNA transcriptome in two human embryonal carcinoma cell (hECC) lines. Results Whole-microRNAome and genome analysis of SOX2-silenced hECCs revealed many miRNAs regulated by SOX2, including several with highly characterised functions in both cancer and embryonic stem cell (ESC) biology. We subsequently performed genome-wide differential expression analysis and applied a Monte Carlo simulation algorithm and target prediction to identify a SOX2-linked miRNA regulome, which was strongly enriched with epithelial-to-mesenchymal transition (EMT) markers. Additionally, several deregulated miRNAs important to EMT processes had SOX2 binding sites in their promoter regions. Conclusion In ESC-like CSCs, SOX2 regulates a large miRNA network that regulates and interlinks the expression of crucial genes involved in EMT. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-711) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sebastian F Vencken
- Department of Histopathology, Trinity College Dublin, Sir Patrick Dun Research Laboratory, St, James's Hospital, Dublin, Ireland.
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28
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Abstract
MicroRNAs (miRNAs) are important regulators of gene expression and translation. The genetic variants altering miRNA targets have been associated with many diseases. Here we systematically mapped the human genetic polymorphisms that may affect miRNA-mRNA interactions in the autoimmune thyroid disease (AITD) pathway. We also mapped the polymorphic miRNA target sites in the genes that have been linked to AITDs or other thyroid-related diseases/phenotypes in genome-wide association studies (GWAS). These genetic polymorphisms may potentially contribute to the pathogenesis of AITDs and other thyroid diseases. The polymorphic miRNA-mRNA interactions we mapped in the AITD pathway and the GWAS-informed thyroid disease loci may provide insights into the possible miRNA-mediated molecular mechanisms through which genetic variants assert their influences on thyroid diseases and phenotypes.
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Affiliation(s)
- Yan Cui
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center , Memphis, TN , USA and
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29
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Chemonges S, Tung JP, Fraser JF. Proteogenomics of selective susceptibility to endotoxin using circulating acute phase biomarkers and bioassay development in sheep: a review. Proteome Sci 2014; 12:12. [PMID: 24580811 PMCID: PMC3946179 DOI: 10.1186/1477-5956-12-12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 02/24/2014] [Indexed: 02/06/2023] Open
Abstract
Scientists have injected endotoxin into animals to investigate and understand various pathologies and novel therapies for several decades. Recent observations have shown that there is selective susceptibility to Escherichia coli lipopolysaccharide (LPS) endotoxin in sheep, despite having similar breed characteristics. The reason behind this difference is unknown, and has prompted studies aiming to explain the variation by proteogenomic characterisation of circulating acute phase biomarkers. It is hypothesised that genetic trait, biochemical, immunological and inflammation marker patterns contribute in defining and predicting mammalian response to LPS. This review discusses the effects of endotoxin and host responses, genetic basis of innate defences, activation of the acute phase response (APR) following experimental LPS challenge, and the current approaches employed in detecting novel biomarkers including acute phase proteins (APP) and micro-ribonucleic acids (miRNAs) in serum or plasma. miRNAs are novel targets for elucidating molecular mechanisms of disease because of their differential expression during pathological, and in healthy states. Changes in miRNA profiles during a disease challenge may be reflected in plasma. Studies show that gel-based two-dimensional electrophoresis (2-DE) coupled with either matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF MS) or liquid chromatography–mass spectrometry (LC-MS/MS) are currently the most used methods for proteome characterisation. Further evidence suggests that proteomic investigations are preferentially shifting from 2-DE to non-gel based LC-MS/MS coupled with data extraction by sequential window acquisition of all theoretical fragment-ion spectra (SWATH) approaches that are able to identify a wider range of proteins. Enzyme-linked immunosorbent assay (ELISA), quantitative real-time polymerase chain reaction (qRT-PCR), and most recently proteomic methods have been used to quantify low abundance proteins such as cytokines. qRT-PCR and next generation sequencing (NGS) are used for the characterisation of miRNA. Proteogenomic approaches for detecting APP and novel miRNA profiling are essential in understanding the selective resistance to endotoxin in sheep. The results of these methods could help in understanding similar pathology in humans. It might also be helpful in the development of physiological and diagnostic screening assays for determining experimental inclusion and endpoints, and in clinical trials in future.
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Affiliation(s)
- Saul Chemonges
- The Institute of Health and Biomedical Innovation (IHBI), Queensland University of Technology, Brisbane, QLD, Australia.
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Bhattacharya A, Ziebarth JD, Cui Y. PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways. Nucleic Acids Res 2013; 42:D86-91. [PMID: 24163105 PMCID: PMC3965097 DOI: 10.1093/nar/gkt1028] [Citation(s) in RCA: 243] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Polymorphisms in microRNAs (miRNAs) and their target sites (PolymiRTS) are known to disrupt miRNA function, leading to the development of disease and variation in physiological and behavioral phenotypes. Here, we describe recent updates to the PolymiRTS database (http://compbio.uthsc.edu/miRSNP), an integrated platform for analyzing the functional impact of genetic polymorphisms in miRNA seed regions and miRNA target sites. Recent advances in genomic technologies have made it possible to identify miRNA–mRNA binding sites from direct mapping experiments such as CLASH (cross linking, ligation and sequencing of hybrids). We have integrated data from CLASH experiments in the PolymiRTS database to provide more complete and accurate miRNA–mRNA interactions. Other significant new features include (i) small insertions and deletions in miRNA seed regions and miRNA target sites, (ii) TargetScan context + score differences for assessing the impact of polymorphic miRNA–mRNA interactions and (iii) biological pathways. The browse and search pages of PolymiRTS allow users to explore the relations between the PolymiRTSs and gene expression traits, physiological and behavioral phenotypes, human diseases and biological pathways.
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Affiliation(s)
- Anindya Bhattacharya
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA and Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
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