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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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Kiani S, Akhavan-Niaki H, Fattahi S, Kavoosian S, Babaian Jelodar N, Bagheri N, Najafi Zarrini H. Purified sulforaphane from broccoli (Brassica oleracea var. italica) leads to alterations of CDX1 and CDX2 expression and changes in miR-9 and miR-326 levels in human gastric cancer cells. Gene 2018; 678:115-123. [DOI: 10.1016/j.gene.2018.08.026] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 08/06/2018] [Indexed: 02/08/2023]
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3
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Aguennouz M, Lo Giudice C, Licata N, Rodolico C, Musumeci O, Fanin M, Migliorato A, Ragusa M, Macaione V, Di Giorgio RM, Angelini C, Toscano A. MicroRNA signatures predict dysregulated vitamin D receptor and calcium pathways status in limb girdle muscle dystrophies (LGMD) 2A/2B. Cell Biochem Funct 2017; 34:414-22. [PMID: 27558075 DOI: 10.1002/cbf.3202] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 05/12/2016] [Accepted: 06/01/2016] [Indexed: 12/29/2022]
Abstract
miRNA expression profile and predicted pathways involved in selected limb-girdle muscular dystrophy (LGMD)2A/2B patients were investigated. A total of 187 miRNAs were dysregulated in all patients, with six miRNAs showing opposite regulation in LGMD2A versus LGMD2B patients. Silico analysis evidence: (1) a cluster of the dysregulated miRNAs resulted primarily involved in inflammation and calcium metabolism, and (2) two genes predicted as controlled by calcium-assigned miRNAs (Vitamin D Receptor gene and Guanine Nucleotide Binding protein beta polypeptide 1gene) showed an evident upregulation in LGMD2B patients, in accordance with miRNA levels. Our data support alterations in calcium pathway status in LGMD 2A/B, suggesting myofibre calcium imbalance as a potential therapeutic target. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- M Aguennouz
- Department of Clinical and Experimental Medicine, University of Messina, Italy
| | - C Lo Giudice
- Department of Clinical and Experimental Medicine, University of Messina, Italy
| | - N Licata
- Department of Clinical and Experimental Medicine, University of Messina, Italy
| | - C Rodolico
- Department of Clinical and Experimental Medicine, University of Messina, Italy
| | - O Musumeci
- Department of Clinical and Experimental Medicine, University of Messina, Italy
| | - M Fanin
- Neurological Clinic, University of Padua, Italy
| | - A Migliorato
- Department of Clinical and Experimental Medicine, University of Messina, Italy
| | - M Ragusa
- Department of Biomedical and Biotechnological Sciences Biology, Genetics and Bioinformatics Unit, University of Catania, Italy
| | - V Macaione
- Department of Clinical and Experimental Medicine, University of Messina, Italy
| | - R M Di Giorgio
- Department of Clinical and Experimental Medicine, University of Messina, Italy
| | - C Angelini
- Neurological Clinic, University of Padua, Italy
| | - A Toscano
- Department of Clinical and Experimental Medicine, University of Messina, Italy
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Aghaee-Bakhtiari SH, Arefian E, Lau P. miRandb: a resource of online services for miRNA research. Brief Bioinform 2017; 19:254-262. [DOI: 10.1093/bib/bbw109] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Indexed: 12/27/2022] Open
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5
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Lee KH, Lim D, Chiu S, Greenhalgh D, Cho K. Genomic landscapes of endogenous retroviruses unveil intricate genetics of conventional and genetically-engineered laboratory mouse strains. Exp Mol Pathol 2016; 100:248-56. [PMID: 26779669 DOI: 10.1016/j.yexmp.2016.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/09/2016] [Indexed: 11/24/2022]
Abstract
Laboratory strains of mice, both conventional and genetically engineered, have been introduced as critical components of a broad range of studies investigating normal and disease biology. Currently, the genetic identity of laboratory mice is primarily confirmed by surveying polymorphisms in selected sets of "conventional" genes and/or microsatellites in the absence of a single completely sequenced mouse genome. First, we examined variations in the genomic landscapes of transposable repetitive elements, named the TREome, in conventional and genetically engineered mouse strains using murine leukemia virus-type endogenous retroviruses (MLV-ERVs) as a probe. A survey of the genomes from 56 conventional strains revealed strain-specific TREome landscapes, and certain families (e.g., C57BL) of strains were discernible with defined patterns. Interestingly, the TREome landscapes of C3H/HeJ (toll-like receptor-4 [TLR4] mutant) inbred mice were different from its control C3H/HeOuJ (TLR4 wild-type) strain. In addition, a CD14 knock-out strain had a distinct TREome landscape compared to its control/backcross C57BL/6J strain. Second, an examination of superantigen (SAg, a "TREome gene") coding sequences of mouse mammary tumor virus-type ERVs in the genomes of the 46 conventional strains revealed a high diversity, suggesting a potential role of SAgs in strain-specific immune phenotypes. The findings from this study indicate that unexplored and intricate genomic variations exist in laboratory mouse strains, both conventional and genetically engineered. The TREome-based high-resolution genetics surveillance system for laboratory mice would contribute to efficient study design with quality control and accurate data interpretation. This genetics system can be easily adapted to other species ranging from plants to humans.
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Affiliation(s)
- Kang-Hoon Lee
- Department of Surgery, University of California, Davis, and Shriners Hospitals for Children Northern California, Sacramento, CA 95817, United States
| | - Debora Lim
- Department of Surgery, University of California, Davis, and Shriners Hospitals for Children Northern California, Sacramento, CA 95817, United States
| | - Sophia Chiu
- Department of Surgery, University of California, Davis, and Shriners Hospitals for Children Northern California, Sacramento, CA 95817, United States
| | - David Greenhalgh
- Department of Surgery, University of California, Davis, and Shriners Hospitals for Children Northern California, Sacramento, CA 95817, United States
| | - Kiho Cho
- Department of Surgery, University of California, Davis, and Shriners Hospitals for Children Northern California, Sacramento, CA 95817, United States.
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6
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Hommers LG, Domschke K, Deckert J. Heterogeneity and individuality: microRNAs in mental disorders. J Neural Transm (Vienna) 2014; 122:79-97. [PMID: 25395183 DOI: 10.1007/s00702-014-1338-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 11/07/2014] [Indexed: 12/21/2022]
Abstract
MicroRNAs are about 22 nucleotide long single-stranded RNA molecules, negatively regulating gene expression of a single gene or a gene network. In neural tissues, they have been implicated in developmental and neuroplasticity-related processes, such as neurogenesis, differentiation, apoptosis and long-term potentiation. Their molecular mode of action is reminiscent of findings of genome-wide association studies in mental disorders, unable to attribute the risk of disease to a specific gene, but rather to multiple genes, gene-networks and gene-environment interaction. As such, microRNAs are an attractive target for research. Here, we review clinical studies conducted in humans on microRNAs in mental disorders with a particular focus on schizophrenia, bipolar disorder, major depressive disorder and anxiety disorders. The majority of clinical studies have focused on schizophrenia. The most robust finding has been reported for rs1625579 located in MIR137HG, which was associated with schizophrenia on a genome-wide level. Concerning bipolar disorder, major depression and anxiety disorders, promising results have been published, but only a considerably smaller number of clinical studies is available and genome-wide association studies did not suggest a direct link to microRNAs so far. Expression of microRNAs as biomarkers of mental disorders and treatment response is currently emerging with preliminary results. Larger-scaled genetic and functional studies along with translational research are needed to enhance our understanding of microRNAs in mental disorders. These studies will aid in disentangling the complex genetic nature of these disorders and possibly contribute to the development of novel, individualized diagnostic and therapeutic approaches.
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Affiliation(s)
- Leif G Hommers
- Center of Mental Health, Department of Psychiatry, Psychosomatics and Psychotherapy, University Hospital Würzburg, Füchsleinstrasse 15, 97080, Würzburg, Germany,
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Mu W, Zhang W. Molecular Approaches, Models, and Techniques in Pharmacogenomic Research and Development. Pharmacogenomics 2013. [DOI: 10.1016/b978-0-12-391918-2.00008-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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8
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Pietrzykowski AZ. Coinciding revolutions: how discovery of non-coding DNA and RNA can change our understanding of addiction. Front Genet 2012; 3:271. [PMID: 23189086 PMCID: PMC3505015 DOI: 10.3389/fgene.2012.00271] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 11/07/2012] [Indexed: 12/01/2022] Open
Affiliation(s)
- Andrzej Z Pietrzykowski
- Laboratory of Adaptation, Reward, and Addiction, Department of Animal Sciences, Department of Genetics, Rutgers University , New Brunswick, NJ, USA
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Jenkins RB, Xiao Y, Sicotte H, Decker PA, Kollmeyer TM, Hansen HM, Kosel ML, Zheng S, Walsh KM, Rice T, Bracci P, McCoy LS, Smirnov I, Patoka JS, Hsuang G, Wiemels JL, Tihan T, Pico AR, Prados MD, Chang SM, Berger MS, Caron AA, Fink SR, Halder C, Rynearson AL, Fridley BL, Buckner JC, O'Neill BP, Giannini C, Lachance DH, Wiencke JK, Eckel-Passow JE, Wrensch MR. A low-frequency variant at 8q24.21 is strongly associated with risk of oligodendroglial tumors and astrocytomas with IDH1 or IDH2 mutation. Nat Genet 2012; 44:1122-5. [PMID: 22922872 PMCID: PMC3600846 DOI: 10.1038/ng.2388] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 07/25/2012] [Indexed: 12/13/2022]
Abstract
Variants at 8q24.21 have been shown to be associated with glioma development. By means of tag SNP genotyping and imputation, pooled next-generation sequencing using long-range PCR and subsequent validation SNP genotyping, we identified seven low-frequency SNPs at 8q24.21 that were strongly associated with glioma risk (P=1×10(-25) to 1×10(-14)). The most strongly associated SNP, rs55705857, remained highly significant after individual adjustment for the other top six SNPs and two previously published SNPs. After stratifying by histological and tumor genetic subtype, the most significant associations of rs55705857 were with oligodendroglial tumors and gliomas with mutant IDH1 or IDH2 (odds ratio (OR)=5.1, P=1.1×10(-31) and OR=4.8, P=6.6×10(-22), respectively). Strong associations were observed for astrocytomas with mutated IDH1 or IDH2 (grades 2-4) (OR=5.16-6.66, P=4.7×10(-12) to 2.2×10(-8)) but not for astrocytomas with wild-type IDH1 and IDH2 (smallest P=0.26). The conserved sequence block that includes rs55705857 is consistently modeled as a microRNA.
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Affiliation(s)
- Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic College of Medicine, Rochester, Minnesota, USA.
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