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Li X, Michels BE, Tosun OE, Jung J, Kappes J, Ibing S, Nataraj NB, Sahay S, Schneider M, Wörner A, Becki C, Ishaque N, Feuerbach L, Heßling B, Helm D, Will R, Yarden Y, Müller-Decker K, Wiemann S, Körner C. 5’isomiR-183-5p|+2 elicits tumor suppressor activity in a negative feedback loop with E2F1. J Exp Clin Cancer Res 2022; 41:190. [PMID: 35655310 PMCID: PMC9161486 DOI: 10.1186/s13046-022-02380-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 05/04/2022] [Indexed: 12/24/2022] Open
Abstract
Background MicroRNAs (miRNAs) and isomiRs play important roles in tumorigenesis as essential regulators of gene expression. 5’isomiRs exhibit a shifted seed sequence compared to the canonical miRNA, resulting in different target spectra and thereby extending the phenotypic impact of the respective common pre-miRNA. However, for most miRNAs, expression and function of 5’isomiRs have not been studied in detail yet. Therefore, this study aims to investigate the functions of miRNAs and their 5’isomiRs. Methods The expression of 5’isomiRs was assessed in The Cancer Genome Atlas (TCGA) breast cancer patient dataset. Phenotypic effects of miR-183 overexpression in triple-negative breast cancer (TNBC) cell lines were investigated in vitro and in vivo by quantifying migration, proliferation, tumor growth and metastasis. Direct targeting of E2F1 by miR-183-5p|+2 was validated with a 3’UTR luciferase assay and linked to the phenotypes of isomiR overexpression. Results TCGA breast cancer patient data indicated that three variants of miR-183-5p are highly expressed and upregulated, namely miR-183-5p|0, miR-183-5p|+1 and miR-183-5p|+2. However, TNBC cell lines displayed reduced proliferation and invasion upon overexpression of pre-miR-183. While invasion was reduced individually by all three isomiRs, proliferation and cell cycle progression were specifically inhibited by overexpression of miR-183-5p|+2. Proteomic analysis revealed reduced expression of E2F target genes upon overexpression of this isomiR, which could be attributed to direct targeting of E2F1, specifically by miR-183-5p|+2. Knockdown of E2F1 partially phenocopied the effect of miR-183-5p|+2 overexpression on cell proliferation and cell cycle. Gene set enrichment analysis of TCGA and METABRIC patient data indicated that the activity of E2F strongly correlated with the expression of miR-183-5p, suggesting transcriptional regulation of the miRNA by a factor of the E2F family. Indeed, in vitro, expression of miR-183-5p was regulated by E2F1. Hence, miR-183-5p|+2 directly targeting E2F1 appears to be part of a negative feedback loop potentially fine-tuning its activity. Conclusions This study demonstrates that 5’isomiRs originating from the same arm of the same pre-miRNA (i.e. pre-miR-183-5p) may exhibit different functions and thereby collectively contribute to the same phenotype. Here, one of three isomiRs was shown to counteract expression of the pre-miRNA by negatively regulating a transcriptional activator (i.e. E2F1). We speculate that this might be part of a regulatory mechanism to prevent uncontrolled cell proliferation, which is disabled during cancer progression. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13046-022-02380-8.
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Demeter A, Jacomin AC, Gul L, Lister A, Lipscombe J, Invernizzi R, Branchu P, Macaulay I, Nezis IP, Kingsley RA, Korcsmaros T, Hautefort I. Computational prediction and experimental validation of Salmonella Typhimurium SopE-mediated fine-tuning of autophagy in intestinal epithelial cells. Front Cell Infect Microbiol 2022; 12:834895. [PMID: 36061866 PMCID: PMC9428466 DOI: 10.3389/fcimb.2022.834895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Macroautophagy is a ubiquitous homeostasis and health-promoting recycling process of eukaryotic cells, targeting misfolded proteins, damaged organelles and intracellular infectious agents. Some intracellular pathogens such as Salmonella enterica serovar Typhimurium hijack this process during pathogenesis. Here we investigate potential protein-protein interactions between host transcription factors and secreted effector proteins of Salmonella and their effect on host gene transcription. A systems-level analysis identified Salmonella effector proteins that had the potential to affect core autophagy gene regulation. The effect of a SPI-1 effector protein, SopE, that was predicted to interact with regulatory proteins of the autophagy process, was investigated to validate our approach. We then confirmed experimentally that SopE can directly bind to SP1, a host transcription factor, which modulates the expression of the autophagy gene MAP1LC3B. We also revealed that SopE might have a double role in the modulation of autophagy: Following initial increase of MAP1LC3B transcription triggered by Salmonella infection, subsequent decrease in MAP1LC3B transcription at 6h post-infection was SopE-dependent. SopE also played a role in modulation of the autophagy flux machinery, in particular MAP1LC3B and p62 autophagy proteins, depending on the level of autophagy already taking place. Upon typical infection of epithelial cells, the autophagic flux is increased. However, when autophagy was chemically induced prior to infection, SopE dampened the autophagic flux. The same was also observed when most of the intracellular Salmonella cells were not associated with the SCV (strain lacking sifA) regardless of the autophagy induction status before infection. We demonstrated how regulatory network analysis can be used to better characterise the impact of pathogenic effector proteins, in this case, Salmonella. This study complements previous work in which we had demonstrated that specific pathogen effectors can affect the autophagy process through direct interaction with autophagy proteins. Here we show that effector proteins can also influence the upstream regulation of the process. Such interdisciplinary studies can increase our understanding of the infection process and point out targets important in intestinal epithelial cell defense.
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Affiliation(s)
- Amanda Demeter
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
- Department of Genetics, Eotvos Lorand University, Budapest, Hungary
| | | | - Lejla Gul
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Ashleigh Lister
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - James Lipscombe
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Rachele Invernizzi
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Priscilla Branchu
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
| | - Iain Macaulay
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Ioannis P. Nezis
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Robert A. Kingsley
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Tamas Korcsmaros
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
- Quadram Institute Bioscience, Norwich Research Park, Norwich, United Kingdom
- Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
- *Correspondence: Tamas Korcsmaros,
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Herrera-Uribe J, Zaldívar-López S, Aguilar C, Entrenas-García C, Bautista R, Claros MG, Garrido JJ. Study of microRNA expression in Salmonella Typhimurium-infected porcine ileum reveals miR-194a-5p as an important regulator of the TLR4-mediated inflammatory response. Vet Res 2022; 53:35. [PMID: 35598011 PMCID: PMC9123658 DOI: 10.1186/s13567-022-01056-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/08/2022] [Indexed: 12/12/2022] Open
Abstract
Infection with Salmonella Typhimurium (S. Typhimurium) is a common cause of food-borne zoonosis leading to acute gastroenteritis in humans and pigs, causing economic losses to producers and farmers, and generating a food security risk. In a previous study, we demonstrated that S. Typhimurium infection produces a severe transcriptional activation of inflammatory processes in ileum. However, little is known regarding how microRNAs regulate this response during infection. Here, small RNA sequencing was used to identify 28 miRNAs differentially expressed (DE) in ileum of S. Typhimurium-infected pigs, which potentially regulate 14 target genes involved in immune system processes such as regulation of cytokine production, monocyte chemotaxis, or cellular response to interferon gamma. Using in vitro functional and gain/loss of function (mimics/CRISPR-Cas system) approaches, we show that porcine miR-194a-5p (homologous to human miR-194-5p) regulates TLR4 gene expression, an important molecule involved in pathogen virulence, recognition and activation of innate immunity in Salmonella infection.
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Affiliation(s)
- Juber Herrera-Uribe
- Immunogenomics and Molecular Pathogenesis Group, Department of Genetics, Faculty of Veterinary Medicine, University of Córdoba, Córdoba, Spain.,Viral Immunology Group, School of Biochemistry and Immunology, Trinity College Dublin, Trinity Biomedical Sciences Institute, Dublin, Ireland
| | - Sara Zaldívar-López
- Immunogenomics and Molecular Pathogenesis Group, Department of Genetics, Faculty of Veterinary Medicine, University of Córdoba, Córdoba, Spain. .,Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Research Group GA-14, Córdoba, Spain.
| | - Carmen Aguilar
- Immunogenomics and Molecular Pathogenesis Group, Department of Genetics, Faculty of Veterinary Medicine, University of Córdoba, Córdoba, Spain.,Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg, Germany
| | - Carmen Entrenas-García
- Immunogenomics and Molecular Pathogenesis Group, Department of Genetics, Faculty of Veterinary Medicine, University of Córdoba, Córdoba, Spain.,Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Research Group GA-14, Córdoba, Spain
| | - Rocío Bautista
- Andalusian Platform of Bioinformatics-SCBI, University of Málaga, Málaga, Spain
| | - M Gonzalo Claros
- Andalusian Platform of Bioinformatics-SCBI, University of Málaga, Málaga, Spain.,Department of Molecular Biology and Biochemistry, University of Málaga, Málaga, Spain
| | - Juan J Garrido
- Immunogenomics and Molecular Pathogenesis Group, Department of Genetics, Faculty of Veterinary Medicine, University of Córdoba, Córdoba, Spain.,Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Research Group GA-14, Córdoba, Spain
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Mourenza Á, Lorente-Torres B, Durante E, Llano-Verdeja J, Aparicio JF, Fernández-López A, Gil JA, Mateos LM, Letek M. Understanding microRNAs in the Context of Infection to Find New Treatments against Human Bacterial Pathogens. Antibiotics (Basel) 2022; 11:antibiotics11030356. [PMID: 35326819 PMCID: PMC8944844 DOI: 10.3390/antibiotics11030356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/25/2022] [Accepted: 03/04/2022] [Indexed: 02/04/2023] Open
Abstract
The development of RNA-based anti-infectives has gained interest with the successful application of mRNA-based vaccines. Small RNAs are molecules of RNA of <200 nucleotides in length that may control the expression of specific genes. Small RNAs include small interference RNAs (siRNAs), Piwi-interacting RNAs (piRNAs), or microRNAs (miRNAs). Notably, the role of miRNAs on the post-transcriptional regulation of gene expression has been studied in detail in the context of cancer and many other genetic diseases. However, it is also becoming apparent that some human miRNAs possess important antimicrobial roles by silencing host genes essential for the progress of bacterial or viral infections. Therefore, their potential use as novel antimicrobial therapies has gained interest during the last decade. The challenges of the transport and delivery of miRNAs to target cells are important, but recent research with exosomes is overcoming the limitations in RNA-cellular uptake, avoiding their degradation. Therefore, in this review, we have summarised the latest developments in the exosomal delivery of miRNA-based therapies, which may soon be another complementary treatment to pathogen-targeted antibiotics that could help solve the problem caused by multidrug-resistant bacteria.
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Affiliation(s)
- Álvaro Mourenza
- Departamento de Biología Molecular, Área de Microbiología, Universidad de León, 24071 León, Spain; (Á.M.); (B.L.-T.); (E.D.); (J.L.-V.); (J.F.A.); (J.A.G.)
| | - Blanca Lorente-Torres
- Departamento de Biología Molecular, Área de Microbiología, Universidad de León, 24071 León, Spain; (Á.M.); (B.L.-T.); (E.D.); (J.L.-V.); (J.F.A.); (J.A.G.)
| | - Elena Durante
- Departamento de Biología Molecular, Área de Microbiología, Universidad de León, 24071 León, Spain; (Á.M.); (B.L.-T.); (E.D.); (J.L.-V.); (J.F.A.); (J.A.G.)
- L’Università di Urbino Carlo Bo, Via Aurelio Saffi, 2, 61029 Urbino, Italy
| | - Jesús Llano-Verdeja
- Departamento de Biología Molecular, Área de Microbiología, Universidad de León, 24071 León, Spain; (Á.M.); (B.L.-T.); (E.D.); (J.L.-V.); (J.F.A.); (J.A.G.)
| | - Jesús F. Aparicio
- Departamento de Biología Molecular, Área de Microbiología, Universidad de León, 24071 León, Spain; (Á.M.); (B.L.-T.); (E.D.); (J.L.-V.); (J.F.A.); (J.A.G.)
| | - Arsenio Fernández-López
- Departamento de Biología Molecular, Área de Biología Celular, Universidad de León, 24071 León, Spain;
- Instituto de Biomedicina (IBIOMED), Universidad de León, 24071 León, Spain
- Neural Therapies SL, Campus de Vegazana s/n, 24071 León, Spain
| | - José A. Gil
- Departamento de Biología Molecular, Área de Microbiología, Universidad de León, 24071 León, Spain; (Á.M.); (B.L.-T.); (E.D.); (J.L.-V.); (J.F.A.); (J.A.G.)
- Instituto de Biología Molecular, Genómica y Proteómica (INBIOMIC), Universidad de León, 24071 León, Spain
| | - Luis M. Mateos
- Departamento de Biología Molecular, Área de Microbiología, Universidad de León, 24071 León, Spain; (Á.M.); (B.L.-T.); (E.D.); (J.L.-V.); (J.F.A.); (J.A.G.)
- Instituto de Biología Molecular, Genómica y Proteómica (INBIOMIC), Universidad de León, 24071 León, Spain
- Correspondence: (L.M.M.); (M.L.)
| | - Michal Letek
- Departamento de Biología Molecular, Área de Microbiología, Universidad de León, 24071 León, Spain; (Á.M.); (B.L.-T.); (E.D.); (J.L.-V.); (J.F.A.); (J.A.G.)
- Instituto de Desarrollo Ganadero y Sanidad Animal (INDEGSAL), Universidad de León, 24071 León, Spain
- Correspondence: (L.M.M.); (M.L.)
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Xie H, Lv S, Wang Z, Yuan X. E2F transcription factor 1 elevates cyclin D1 expression by suppressing transcription of microRNA-107 to augment progression of glioma. Brain Behav 2021; 11:e2399. [PMID: 34758200 PMCID: PMC8671784 DOI: 10.1002/brb3.2399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Dysregulation of microRNAs has been frequently implicated in the progression of human diseases, including glioma. This study aims to explore the interaction between E2F transcription factor 1 (E2F1) and miR-107 in the progression of glioma. METHODS Expression of miR-107 in glioma tissues and cells was examined. Putative binding sites between E2F1 and the promoter region of miR-107, and between miR-107 and cyclin D1 (CCND1) mRNA were predicted via bioinformatic systems and validated via chromatin immunoprecipitation and luciferase reporter gene assays. Altered expression of miR-107, E2F1, and CCND1 was introduced in A172 and T98G cells to examine their roles in cell growth and the activity of the Wnt/β-catenin signaling. In vivo experiments were performed by injecting cells in nude mice. RESULTS miR-107 was poorly expressed, whereas E2F1 and CCND1 were highly expressed in glioma tissues and cells. E2F1 bound to the promoter region of miR-107 to induce transcriptional repression, and miR-107 directly bound to CCND1 mRNA to reduce its expression. Overexpression of miR-107 reduced proliferation, migration and invasion, and augmented apoptosis of glioma cells, and it reduced activity of the Wnt/β-catenin pathway. The anti-tumorigenic roles of miR-107 were blocked by E2F1 or CCND1 overexpression. Similar results were reproduced in vivo where miR-107 overexpression or E2F1 inhibition blocked tumor growth in nude mice. CONCLUSION This study suggested that E2F1 reduces miR-107 transcription to induce CCND1 upregulation, which leads to progression of glioma via Wnt/β-catenin signaling activation.
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Affiliation(s)
- Huan Xie
- Department of Clinical Medicine, Jiangxi Health Vocational College, Nanchang, P. R. China
| | - Shigang Lv
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, P. R. China
| | - Zhaozhen Wang
- Department of Clinical Medicine, Jiangxi Health Vocational College, Nanchang, P. R. China
| | - Xinzhang Yuan
- Department of Clinical Medicine, Jiangxi Health Vocational College, Nanchang, P. R. China
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