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Hernández-Gómez KG, Avila-Nava A, González-Salazar LE, Noriega LG, Serralde-Zúñiga AE, Guizar-Heredia R, Medina-Vera I, Gutiérrez-Solis AL, Torres N, Tovar AR, Guevara-Cruz M. Modulation of MicroRNAs and Exosomal MicroRNAs after Dietary Interventions for Obesity and Insulin Resistance: A Narrative Review. Metabolites 2023; 13:1190. [PMID: 38132872 PMCID: PMC10745452 DOI: 10.3390/metabo13121190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs approximately 22 nucleotides in length. Their main function is to regulate gene expression at the posttranscriptional level by inhibiting the translation of messenger RNAs (mRNAs). miRNAs originate in the cell nucleus from specific genes, where they can perform their function. However, they can also be found in serum, plasma, or other body fluids travelling within vesicles called exosomes and/or bound to proteins or other particles such as lipoproteins. miRNAs can form complexes outside the cell where they are synthesized, mediating paracrine and endocrine communication between different tissues. In this way, they can modulate the gene expression and function of distal cells. It is known that the expression of miRNAs can be affected by multiple factors, such as the nutritional or pathological state of the individual, or even in conditions such as obesity, insulin resistance, or after any dietary intervention. In this review, we will analyse miRNAs whose expression and circulation are affected in conditions of obesity and insulin resistance, as well as the changes generated after a dietary intervention, with the purpose of identifying new possible biomarkers of early response to nutritional treatment in these conditions.
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Affiliation(s)
- Karla G. Hernández-Gómez
- Departamento de Fisiología de la Nutrición, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City 14080, Mexico; (K.G.H.-G.); (L.G.N.); (R.G.-H.); (N.T.)
| | - Azalia Avila-Nava
- Hospital Regional de Alta Especialidad de la Península de Yucatán, Mérida 97130, Mexico; (A.A.-N.); (A.L.G.-S.)
| | - Luis E. González-Salazar
- Servicio de Nutriología Clínica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City 14080, Mexico; (L.E.G.-S.); (A.E.S.-Z.)
| | - Lilia G. Noriega
- Departamento de Fisiología de la Nutrición, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City 14080, Mexico; (K.G.H.-G.); (L.G.N.); (R.G.-H.); (N.T.)
| | - Aurora E. Serralde-Zúñiga
- Servicio de Nutriología Clínica, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City 14080, Mexico; (L.E.G.-S.); (A.E.S.-Z.)
| | - Rocio Guizar-Heredia
- Departamento de Fisiología de la Nutrición, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City 14080, Mexico; (K.G.H.-G.); (L.G.N.); (R.G.-H.); (N.T.)
| | - Isabel Medina-Vera
- Departamento de Metodología de la Investigación, Instituto Nacional de Pediatría, Mexico City 04530, Mexico;
- Escuela de Medicina y Ciencias de la Salud, Tecnológico de Monterrey, 14380 Mexico City, Mexico
| | - Ana Ligia Gutiérrez-Solis
- Hospital Regional de Alta Especialidad de la Península de Yucatán, Mérida 97130, Mexico; (A.A.-N.); (A.L.G.-S.)
| | - Nimbe Torres
- Departamento de Fisiología de la Nutrición, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City 14080, Mexico; (K.G.H.-G.); (L.G.N.); (R.G.-H.); (N.T.)
| | - Armando R. Tovar
- Departamento de Fisiología de la Nutrición, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City 14080, Mexico; (K.G.H.-G.); (L.G.N.); (R.G.-H.); (N.T.)
| | - Martha Guevara-Cruz
- Departamento de Fisiología de la Nutrición, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City 14080, Mexico; (K.G.H.-G.); (L.G.N.); (R.G.-H.); (N.T.)
- Escuela de Medicina y Ciencias de la Salud, Tecnológico de Monterrey, 14380 Mexico City, Mexico
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Fei X, Jin M, Yuan Z, Li T, Lu Z, Wang H, Lu J, Quan K, Yang J, He M, Wang T, Wang Y, Wei C. MiRNA-Seq reveals key MicroRNAs involved in fat metabolism of sheep liver. Front Genet 2023; 14:985764. [PMID: 36968587 PMCID: PMC10035661 DOI: 10.3389/fgene.2023.985764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 02/27/2023] [Indexed: 03/11/2023] Open
Abstract
There is a genetic difference between Hu sheep (short/fat-tailed sheep) and Tibetan sheep (short/thin-tailed sheep) in tail type, because of fat metabolism. Previous studies have mainly focused directly on sheep tail fat, which is not the main organ of fat metabolism. The function of miRNAs in sheep liver fat metabolism has not been thoroughly elucidated. In this study, miRNA-Seq was used to identify miRNAs in the liver tissue of three Hu sheep (short/fat-tailed sheep) and three Tibetan sheep (short/thin-tailed sheep) to characterize the differences in fat metabolism of sheep. In our study, Hu sheep was in a control group, we identified 11 differentially expressed miRNAs (DE miRNAs), including six up-regulated miRNAs and five down-regulated miRNAs. Miranda and RNAhybrid were used to predict the target genes of DE miRNAs, obtaining 3,404 target genes. A total of 115 and 67 GO terms as well as 54 and 5 KEGG pathways were significantly (padj < 0.05) enriched for predicted 3,109 target genes of up-regulated and 295 target genes of down-regulated miRNAs, respectively. oar-miR-432 was one of the most up-regulated miRNAs between Hu sheep and Tibetan sheep. And SIRT1 is one of the potential target genes of oar-miR-432. Furthermore, functional validation using the dual-luciferase reporter assay indicated that the up-regulated miRNA; oar-miR-432 potentially targeted sirtuin 1 (SIRT1) expression. Then, the oar-miR-432 mimic transfected into preadipocytes resulted in inhibited expression of SIRT1. This is the first time reported that the expression of SIRT1 gene was regulated by oar-miR-432 in fat metabolism of sheep liver. These results could provide a meaningful theoretical basis for studying the fat metabolism of sheep.
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Affiliation(s)
- Xiaojuan Fei
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Meilin Jin
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zehu Yuan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Taotao Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Huihua Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Lu
- National Animal Husbandry Service, Beijing, China
| | - Kai Quan
- College of Animals Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Junxiang Yang
- Gansu Institute of Animal Husbandry and Veterinary Medicine, Pingliang, China
| | - Maochang He
- Gansu Institute of Animal Husbandry and Veterinary Medicine, Pingliang, China
| | - Tingpu Wang
- College of Bioengineering and Biotechnology, TianShui Normal University, Tianshui, China
| | - Yuqin Wang
- College of Animals Science and Technology, Henan University of Science and Technology, Luoyang, China
- *Correspondence: Caihong Wei, ; Yuqin Wang,
| | - Caihong Wei
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Caihong Wei, ; Yuqin Wang,
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Cai Z, Lu C, He J, Liu L, Zou Y, Zhang Z, Zhu Z, Ge X, Wu A, Jiang T, Zheng H, Peng Y. Identification and characterization of circRNAs encoded by MERS-CoV, SARS-CoV-1 and SARS-CoV-2. Brief Bioinform 2021; 22:1297-1308. [PMID: 33757279 PMCID: PMC7799257 DOI: 10.1093/bib/bbaa334] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/28/2020] [Accepted: 10/23/2020] [Indexed: 12/17/2022] Open
Abstract
The life-threatening coronaviruses MERS-CoV, SARS-CoV-1 and SARS-CoV-2 (SARS-CoV-1/2) have caused and will continue to cause enormous morbidity and mortality to humans. Virus-encoded noncoding RNAs are poorly understood in coronaviruses. Data mining of viral-infection-related RNA-sequencing data has resulted in the identification of 28 754, 720 and 3437 circRNAs encoded by MERS-CoV, SARS-CoV-1 and SARS-CoV-2, respectively. MERS-CoV exhibits much more prominent ability to encode circRNAs in all genomic regions than those of SARS-CoV-1/2. Viral circRNAs typically exhibit low expression levels. Moreover, majority of the viral circRNAs exhibit expressions only in the late stage of viral infection. Analysis of the competitive interactions of viral circRNAs, human miRNAs and mRNAs in MERS-CoV infections reveals that viral circRNAs up-regulated genes related to mRNA splicing and processing in the early stage of viral infection, and regulated genes involved in diverse functions including cancer, metabolism, autophagy, viral infection in the late stage of viral infection. Similar analysis in SARS-CoV-2 infections reveals that its viral circRNAs down-regulated genes associated with metabolic processes of cholesterol, alcohol, fatty acid and up-regulated genes associated with cellular responses to oxidative stress in the late stage of viral infection. A few genes regulated by viral circRNAs from both MERS-CoV and SARS-CoV-2 were enriched in several biological processes such as response to reactive oxygen and centrosome localization. This study provides the first glimpse into viral circRNAs in three deadly coronaviruses and would serve as a valuable resource for further studies of circRNAs in coronaviruses.
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Affiliation(s)
- Zena Cai
- College of Biology, Hunan University
| | - Congyu Lu
- College of Biology, Hunan University
| | | | - Li Liu
- Hunan Yuelu mountain data science and Technology Research Institute Co., Ltd, Changsha, China
| | | | | | | | - Xingyi Ge
- College of Biology, Hunan University
| | - Aiping Wu
- Suzhou Institute of Systems Medicine
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Cai Z, Fan Y, Zhang Z, Lu C, Zhu Z, Jiang T, Shan T, Peng Y. VirusCircBase: a database of virus circular RNAs. Brief Bioinform 2020; 22:2182-2190. [PMID: 32349124 DOI: 10.1093/bib/bbaa052] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/12/2020] [Accepted: 03/16/2020] [Indexed: 12/11/2022] Open
Abstract
Circular RNAs (circRNAs) are covalently closed long noncoding RNAs critical in diverse cellular activities and multiple human diseases. Several cancer-related viral circRNAs have been identified in double-stranded DNA viruses (dsDNA), yet no systematic study about the viral circRNAs has been reported. Herein, we have performed a systematic survey of 11 924 circRNAs from 23 viral species by computational prediction of viral circRNAs from viral-infection-related RNA sequencing data. Besides the dsDNA viruses, our study has also revealed lots of circRNAs in single-stranded RNA viruses and retro-transcribing viruses, such as the Zika virus, the Influenza A virus, the Zaire ebolavirus, and the Human immunodeficiency virus 1. Most viral circRNAs had reverse complementary sequences or repeated sequences at the flanking sequences of the back-splice sites. Most viral circRNAs only expressed in a specific cell line or tissue in a specific species. Functional enrichment analysis indicated that the viral circRNAs from dsDNA viruses were involved in KEGG pathways associated with cancer. All viral circRNAs presented in the current study were stored and organized in VirusCircBase, which is freely available at http://www.computationalbiology.cn/ViruscircBase/home.html and is the first virus circRNA database. VirusCircBase forms the fundamental atlas for the further exploration and investigation of viral circRNAs in the context of public health.
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Seclaman E, Balacescu L, Balacescu O, Bejinar C, Udrescu M, Marian C, Sirbu IO, Anghel A. MicroRNAs mediate liver transcriptome changes upon soy diet intervention in mice. J Cell Mol Med 2019; 23:2263-2267. [PMID: 30618122 PMCID: PMC6378209 DOI: 10.1111/jcmm.14140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 12/11/2018] [Accepted: 12/14/2018] [Indexed: 01/07/2023] Open
Abstract
Soy‐based diets have triggered the interest of the research community due to their beneficial effects on a wide variety of pathologies like breast and prostate cancer, diabetes and atherosclerosis. However, the molecular details underlying these effects are far from being completely understood; several recent attempts have been made to elucidate the soy‐induced liver transcriptome changes in different animal models. Here we used Next Generation Sequencing to identify a set of microRNAs specifically modulated by short‐term soy‐enriched diet in young male mice and estimated their impact on the liver transcriptome assessed by microarray. Clustering and topological community detection (CTCD) network analysis of STRING generated interactions of transcriptome data led to the identification of four topological communities of genes characteristically altered and putatively targeted by microRNAs upon soy diet intervention.
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Affiliation(s)
- Edward Seclaman
- Department of Biochemistry and Pharmacology, University of Medicine and Pharmacy "Victor Babes" Timisoara, Timisoara, Romania
| | - Loredana Balacescu
- Department of Functional Genomics, Proteomics and Experimental Pathology, The Oncology Institute "Prof. Dr. Ion Chiricuta", Cluj-Napoca, Romania
| | - Ovidiu Balacescu
- Department of Functional Genomics, Proteomics and Experimental Pathology, The Oncology Institute "Prof. Dr. Ion Chiricuta", Cluj-Napoca, Romania
| | - Cristina Bejinar
- Department of Biochemistry and Pharmacology, University of Medicine and Pharmacy "Victor Babes" Timisoara, Timisoara, Romania
| | - Mihai Udrescu
- Department of Computer and Information Technology, Politehnica University of Timisoara, Timisoara, Romania
| | - Catalin Marian
- Department of Biochemistry and Pharmacology, University of Medicine and Pharmacy "Victor Babes" Timisoara, Timisoara, Romania
| | - Ioan Ovidiu Sirbu
- Department of Biochemistry and Pharmacology, University of Medicine and Pharmacy "Victor Babes" Timisoara, Timisoara, Romania
| | - Andrei Anghel
- Department of Biochemistry and Pharmacology, University of Medicine and Pharmacy "Victor Babes" Timisoara, Timisoara, Romania
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