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Chen DP, Wang JC, Liu ZY, Li PL, Chan KW, Wu XN, Yao WDX, Yao T, Kuang DM, Wei Y. miRNome targeting NF-κB signaling orchestrates macrophage-triggered cancer metastasis and recurrence. Mol Ther 2024; 32:1110-1124. [PMID: 38341612 DOI: 10.1016/j.ymthe.2024.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/14/2024] [Accepted: 02/07/2024] [Indexed: 02/12/2024] Open
Abstract
Whether and how tumor intrinsic signature determines macrophage-elicited metastasis remain elusive. Here, we show, in detailed studies of data regarding 7,477 patients of 20 types of human cancers, that only 13.8% ± 2.6%/27.9% ± 3.03% of patients with high macrophage infiltration index exhibit early recurrence/vascular invasion. In parallel, although macrophages enhance the motility of various hepatoma cells, their enhancement intensity is significantly heterogeneous. We identify that the expression of malignant Dicer, a ribonuclease that cleaves miRNA precursors into mature miRNAs, determines macrophage-elicited metastasis. Mechanistically, the downregulation of Dicer in cancer cells leads to defects in miRNome targeting NF-κB signaling, which in turn enhances the ability of cancer cells to respond to macrophage-related inflammatory signals and ultimately promotes metastasis. Importantly, transporting miR-26b-5p, the most potential miRNA targeting NF-κB signaling in hepatocellular carcinoma, can effectively reverse macrophage-elicited metastasis of hepatoma in vivo. Our results provide insights into the crosstalk between Dicer-elicited miRNome and cancer immune microenvironments and suggest that strategies to remodel malignant cell miRNome may overcome pro-tumorigenic activities of inflammatory cells.
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Affiliation(s)
- Dong-Ping Chen
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
| | - Jun-Cheng Wang
- State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Department of Liver Surgery, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Zheng-Yu Liu
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Pei-Lin Li
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ka-Wo Chan
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, Canada
| | - Xiang-Ning Wu
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Wu-De-Xin Yao
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Tingting Yao
- Department of Gynecological Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
| | - Dong-Ming Kuang
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
| | - Yuan Wei
- Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
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Leduc A, Le Guillou S, Laloë D, Herve L, Laubier J, Poton P, Faulconnier Y, Pires J, Gele M, Martin P, Leroux C, Boutinaud M, Le Provost F. MiRNome variations in milk fractions during feed restrictions of different intensities in dairy cows. BMC Genomics 2023; 24:680. [PMID: 37957547 PMCID: PMC10641998 DOI: 10.1186/s12864-023-09769-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND In dairy cows, diet is one factor that can affect their milk production and composition. However, the effect of feed restriction on milk miRNome has not yet been described. Indeed, milk is the body fluid with the highest RNA concentration, which includes numerous microRNA. Its presence in the four different milk fractions, whole milk, fat globules, mammary epithelial cells and extracellular vesicles, is still poorly documented. This study aimed to describe the effects of different feed restrictions on the miRNome composition of different milk fractions. RESULTS Two feed restrictions were applied to lactating dairy cows, one of high intensity and one of moderate intensity. 2,896 mature microRNA were identified in the different milk fractions studied, including 1,493 that were already known in the bovine species. Among the 1,096 microRNA that were sufficiently abundant to be informative, the abundance of 1,027 of them varied between fractions: 36 of those were exclusive to one milk fraction. Feed restriction affected the abundance of 155 microRNA, with whole milk and milk extracellular vesicles being the most affected, whereas milk fat globules and exfoliated mammary epithelial cells were little or not affected at all. The high intensity feed restriction led to more microRNA variations in milk than moderate restriction. The target prediction of known microRNA that varied under feed restriction suggested the modification of some key pathways for lactation related to milk fat and protein metabolisms, cell cycle, and stress responses. CONCLUSIONS This study highlighted that the miRNome of each milk fraction is specific, with mostly the same microRNA composition but with variations in abundance between fractions. These specific miRNomes were affected differently by feed restrictions, the intensity of which appeared to be a major factor modulating milk miRNomes. These findings offer opportunities for future research on the use of milk miRNA as biomarkers of energy status in dairy cows, which is affected by feed restrictions.
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Affiliation(s)
- A Leduc
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France
- PEGASE, INRAE, Institut Agro, 35590, Saint Gilles, France
- Institut de L'Elevage, 75012, Paris, France
| | - S Le Guillou
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France
| | - D Laloë
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France
| | - L Herve
- PEGASE, INRAE, Institut Agro, 35590, Saint Gilles, France
| | - J Laubier
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France
| | - P Poton
- PEGASE, INRAE, Institut Agro, 35590, Saint Gilles, France
| | - Y Faulconnier
- INRAE, Université Clermont Auvergne, VetagroSup, UMRH, Saint-Genès-Champanelle, 63122, France
| | - J Pires
- INRAE, Université Clermont Auvergne, VetagroSup, UMRH, Saint-Genès-Champanelle, 63122, France
| | - M Gele
- Institut de L'Elevage, 75012, Paris, France
| | - P Martin
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France
| | - C Leroux
- INRAE, Université Clermont Auvergne, VetagroSup, UMRH, Saint-Genès-Champanelle, 63122, France
| | - M Boutinaud
- PEGASE, INRAE, Institut Agro, 35590, Saint Gilles, France
| | - F Le Provost
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France.
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Morgunova A, Ibrahim P, Chen GG, Coury SM, Turecki G, Meaney MJ, Gifuni A, Gotlib IH, Nagy C, Ho TC, Flores C. Preparation and processing of dried blood spots for microRNA sequencing. Biol Methods Protoc 2023; 8:bpad020. [PMID: 37901452 PMCID: PMC10603595 DOI: 10.1093/biomethods/bpad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/07/2023] [Accepted: 09/19/2023] [Indexed: 10/31/2023] Open
Abstract
Dried blood spots (DBS) are biological samples commonly collected from newborns and in geographic areas distanced from laboratory settings for the purposes of disease testing and identification. MicroRNAs (miRNAs)-small non-coding RNAs that regulate gene activity at the post-transcriptional level-are emerging as critical markers and mediators of disease, including cancer, infectious diseases, and mental disorders. This protocol describes optimized procedural steps for utilizing DBS as a reliable source of biological material for obtaining peripheral miRNA expression profiles. We outline key practices, such as the method of DBS rehydration that maximizes RNA extraction yield, and the use of degenerate oligonucleotide adapters to mitigate ligase-dependent biases that are associated with small RNA sequencing. The standardization of miRNA readout from DBS offers numerous benefits: cost-effectiveness in sample collection and processing, enhanced reliability and consistency of miRNA profiling, and minimal invasiveness that facilitates repeated testing and retention of participants. The use of DBS-based miRNA sequencing is a promising method to investigate disease mechanisms and to advance personalized medicine.
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Affiliation(s)
- Alice Morgunova
- Integrated Program in Neuroscience, McGill University, Montreal, Quebec H3A 1A1, Canada
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Pascal Ibrahim
- Integrated Program in Neuroscience, McGill University, Montreal, Quebec H3A 1A1, Canada
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec H4H 1R3, Canada
| | - Gary Gang Chen
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec H4H 1R3, Canada
| | - Saché M Coury
- Department of Psychology, Stanford University, Stanford, CA 94305, United States
- Department of Psychology, University of California, Los Angeles, CA 90095, United States
| | - Gustavo Turecki
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec H4H 1R3, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Michael J Meaney
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Neurology and Neurosurgery, Faculty of Medicine, McGill University, Montreal, Quebec H3A 1A1, Canada
- Ludmer Centre for Neuroinformatics and Mental Health, McGill University, Montreal, Quebec H3A 2B4, Canada
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Brenner Centre for Molecular Medicine, Singapore City 138632, Singapore
| | - Anthony Gifuni
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Ian H Gotlib
- Department of Psychology, Stanford University, Stanford, CA 94305, United States
| | - Corina Nagy
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec H4H 1R3, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Tiffany C Ho
- Department of Psychology, Stanford University, Stanford, CA 94305, United States
- Department of Psychology, University of California, Los Angeles, CA 90095, United States
| | - Cecilia Flores
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Neurology and Neurosurgery, Faculty of Medicine, McGill University, Montreal, Quebec H3A 1A1, Canada
- Ludmer Centre for Neuroinformatics and Mental Health, McGill University, Montreal, Quebec H3A 2B4, Canada
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Picó C, Lurbe E, Keijer J, Kopecky J, Landrier JF, Álvarez-Pitti J, Martin JC, Oliver P, Palou A, Palou M, Zouhar P, Ribot J, Rodríguez AM, Sánchez J, Serra F, Bonet ML. Study protocol: Identification and validation of integrative biomarkers of physical activity level and health in children and adolescents (INTEGRActiv). Front Pediatr 2023; 11:1250731. [PMID: 37772038 PMCID: PMC10522911 DOI: 10.3389/fped.2023.1250731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/30/2023] [Indexed: 09/30/2023] Open
Abstract
Background Physical activity (PA) provides health benefits across the lifespan and improves many established cardiovascular risk factors that have a significant impact on overall mortality. However, discrepancies between self-reported and device-based measures of PA make it difficult to obtain consistent results regarding PA and its health effects. Moreover, PA may produce different health effects depending on the type, intensity, duration, and frequency of activities and individual factors such as age, sex, body weight, early life conditions/exposures, etc. Appropriate biomarkers relating the degree of PA level with its effects on health, especially in children and adolescents, are required and missing. The main objective of the INTEGRActiv study is to identify novel useful integrative biomarkers of PA and its effects on the body health in children and adolescents, who represent an important target population to address personalized interventions to improve future metabolic health. Methods/design The study is structured in two phases. First, biomarkers of PA and health will be identified at baseline in a core cohort of 180 volunteers, distributed into two age groups: prepubertal (n = 90), and postpubertal adolescents (n = 90). Each group will include three subgroups (n = 30) with subjects of normal weight, overweight, and obesity, respectively. Identification of new biomarkers will be achieved by combining physical measures (PA and cardiorespiratory and muscular fitness, anthropometry) and molecular measures (cardiovascular risk factors, endocrine markers, cytokines and circulating miRNA in plasma, gene expression profile in blood cells, and metabolomics profiling in plasma). In the second phase, an educational intervention and its follow-up will be carried out in a subgroup of these subjects (60 volunteers), as a first validation step of the identified biomarkers. Discussion The INTEGRActiv study is expected to provide the definition of PA and health-related biomarkers (PA-health biomarkers) in childhood and adolescence. It will allow us to relate biomarkers to factors such as age, sex, body weight, sleep behavior, dietary factors, and pubertal status and to identify how these factors quantitatively affect the biomarkers' responses. Taken together, the INTEGRActiv study approach is expected to help monitor the efficacy of interventions aimed to improve the quality of life of children/adolescents through physical activity. Clinical Trial Registration ClinicalTrials.gov, Identifier NCT05907785.
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Affiliation(s)
- Catalina Picó
- Laboratory of Molecular Biology, Nutrition and Biotechnology (Group of Nutrigenomics, Biomarkers and Risk Evaluation), University of the Balearic Islands (UIB), Palma, Spain
- Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Madrid, Spain
| | - Empar Lurbe
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Madrid, Spain
- Department of Pediatrics (Innovation in Paediatrics and Technologies-iPEDITEC- research group), Fundación de Investigación, Consorcio Hospital General, University of Valencia, Valencia, Spain
| | - Jaap Keijer
- Human and Animal Physiology, Wageningen University, Wageningen, Netherlands
| | - Jan Kopecky
- Laboratory of Adipose Tissue Biology, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Julio Álvarez-Pitti
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Madrid, Spain
- Department of Pediatrics (Innovation in Paediatrics and Technologies-iPEDITEC- research group), Fundación de Investigación, Consorcio Hospital General, University of Valencia, Valencia, Spain
| | | | - Paula Oliver
- Laboratory of Molecular Biology, Nutrition and Biotechnology (Group of Nutrigenomics, Biomarkers and Risk Evaluation), University of the Balearic Islands (UIB), Palma, Spain
- Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Madrid, Spain
| | - Andreu Palou
- Laboratory of Molecular Biology, Nutrition and Biotechnology (Group of Nutrigenomics, Biomarkers and Risk Evaluation), University of the Balearic Islands (UIB), Palma, Spain
- Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Madrid, Spain
| | - Mariona Palou
- Laboratory of Molecular Biology, Nutrition and Biotechnology (Group of Nutrigenomics, Biomarkers and Risk Evaluation), University of the Balearic Islands (UIB), Palma, Spain
- Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Madrid, Spain
| | - Petr Zouhar
- Laboratory of Adipose Tissue Biology, Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Joan Ribot
- Laboratory of Molecular Biology, Nutrition and Biotechnology (Group of Nutrigenomics, Biomarkers and Risk Evaluation), University of the Balearic Islands (UIB), Palma, Spain
- Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Madrid, Spain
| | - Ana M. Rodríguez
- Laboratory of Molecular Biology, Nutrition and Biotechnology (Group of Nutrigenomics, Biomarkers and Risk Evaluation), University of the Balearic Islands (UIB), Palma, Spain
- Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Madrid, Spain
| | - Juana Sánchez
- Laboratory of Molecular Biology, Nutrition and Biotechnology (Group of Nutrigenomics, Biomarkers and Risk Evaluation), University of the Balearic Islands (UIB), Palma, Spain
- Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Madrid, Spain
| | - Francisca Serra
- Laboratory of Molecular Biology, Nutrition and Biotechnology (Group of Nutrigenomics, Biomarkers and Risk Evaluation), University of the Balearic Islands (UIB), Palma, Spain
- Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Madrid, Spain
| | - M. Luisa Bonet
- Laboratory of Molecular Biology, Nutrition and Biotechnology (Group of Nutrigenomics, Biomarkers and Risk Evaluation), University of the Balearic Islands (UIB), Palma, Spain
- Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Madrid, Spain
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Luxen M, Zwiers PJ, Meester F, Jongman RM, Kuiper T, Moser J, Pultar M, Skalicky S, Diendorfer AB, Hackl M, van Meurs M, Molema G. Unique miRNome and transcriptome profiles underlie microvascular heterogeneity in mouse kidney. Am J Physiol Renal Physiol 2023; 325:F299-F316. [PMID: 37410897 PMCID: PMC10511173 DOI: 10.1152/ajprenal.00005.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 06/27/2023] [Accepted: 06/27/2023] [Indexed: 07/08/2023] Open
Abstract
Endothelial cells in blood vessels in the kidney exert different functions depending on the (micro)vascular bed they are located in. The present study aimed to investigate microRNA and mRNA transcription patterns that underlie these differences. We zoomed in on microvascular compartments in the mouse renal cortex by laser microdissecting the microvessels prior to small RNA- and RNA-sequencing analyses. By these means, we characterized microRNA and mRNA transcription profiles of arterioles, glomeruli, peritubular capillaries, and postcapillary venules. Quantitative RT-PCR, in situ hybridization, and immunohistochemistry were used to validate sequencing results. Unique microRNA and mRNA transcription profiles were found in all microvascular compartments, with dedicated marker microRNAs and mRNAs showing enriched transcription in a single microvascular compartment. In situ hybridization validated the localization of microRNAs mmu-miR-140-3p in arterioles, mmu-miR-322-3p in glomeruli, and mmu-miR-451a in postcapillary venules. Immunohistochemical staining showed that von Willebrand factor protein was mainly expressed in arterioles and postcapillary venules, whereas GABRB1 expression was enriched in glomeruli, and IGF1 was enriched in postcapillary venules. More than 550 compartment-specific microRNA-mRNA interaction pairs were identified that carry functional implications for microvascular behavior. In conclusion, our study identified unique microRNA and mRNA transcription patterns in microvascular compartments of the mouse kidney cortex that underlie microvascular heterogeneity. These patterns provide important molecular information for future studies into differential microvascular engagement in health and disease.NEW & NOTEWORTHY Renal endothelial cells display a high level of heterogeneity depending on the (micro)vascular bed they reside in. The molecular basis contributing to these differences is poorly understood yet of high importance to increase understanding of microvascular engagement in the kidney in health and disease. This report describes m(icro)RNA expression profiles of microvascular beds in the mouse renal cortex and uncovers microvascular compartment-specific m(icro)RNAs and miRNA-mRNA pairs, thereby revealing important molecular mechanisms underlying renal microvascular heterogeneity.
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Affiliation(s)
- Matthijs Luxen
- Department of Pathology and Medical Biology, Medical Biology Section, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Critical Care, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Peter J Zwiers
- Department of Pathology and Medical Biology, Medical Biology Section, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Femke Meester
- Department of Pathology and Medical Biology, Medical Biology Section, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Rianne M Jongman
- Department of Pathology and Medical Biology, Medical Biology Section, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Anaesthesiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Timara Kuiper
- Department of Pathology and Medical Biology, Medical Biology Section, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jill Moser
- Department of Pathology and Medical Biology, Medical Biology Section, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Critical Care, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | | | | | | | - Matijs van Meurs
- Department of Pathology and Medical Biology, Medical Biology Section, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
- Department of Critical Care, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Grietje Molema
- Department of Pathology and Medical Biology, Medical Biology Section, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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6
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Elshafie NO, Gribskov M, Lichti NI, Sayedahmed EE, Childress MO, dos Santos AP. miRNome expression analysis in canine diffuse large B-cell lymphoma. Front Oncol 2023; 13:1238613. [PMID: 37711209 PMCID: PMC10499539 DOI: 10.3389/fonc.2023.1238613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/04/2023] [Indexed: 09/16/2023] Open
Abstract
Introduction Lymphoma is a common canine cancer with translational relevance to human disease. Diffuse large B-cell lymphoma (DLBCL) is the most frequent subtype, contributing to almost fifty percent of clinically recognized lymphoma cases. Identifying new biomarkers capable of early diagnosis and monitoring DLBCL is crucial for enhancing remission rates. This research seeks to advance our knowledge of the molecular biology of DLBCL by analyzing the expression of microRNAs, which regulate gene expression by negatively impacting gene expression via targeted RNA degradation or translational repression. The stability and accessibility of microRNAs make them appropriate biomarkers for the diagnosis, prognosis, and monitoring of diseases. Methods We extracted and sequenced microRNAs from ten fresh-frozen lymph node tissue samples (six DLBCL and four non-neoplastic). Results Small RNA sequencing data analysis revealed 35 differently expressed miRNAs (DEMs) compared to controls. RT-qPCR confirmed that 23/35 DEMs in DLBCL were significantly upregulated (n = 14) or downregulated (n = 9). Statistical significance was determined by comparing each miRNA's average expression fold-change (2-Cq) between the DLCBL and healthy groups by applying the unpaired parametric Welch's 2-sample t-test and false discovery rate (FDR). The predicted target genes of the DEMs were mainly enriched in the PI3K-Akt-MAPK pathway. Discussion Our data point to the potential value of miRNA signatures as diagnostic biomarkers and serve as a guideline for subsequent experimental studies to determine the targets and functions of these altered miRNAs in canine DLBCL.
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Affiliation(s)
- Nelly O. Elshafie
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, United States
| | - Michael Gribskov
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Nathanael I. Lichti
- Bindley Bioscience Center, Purdue University, West Lafayette, IN, United States
| | - Ekramy. E. Sayedahmed
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, United States
| | - Michael O. Childress
- Department of Veterinary Clinical Sciences, Purdue University, West Lafayette, IN, United States
| | - Andrea P. dos Santos
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, United States
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7
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Inno R, Laan M. Urinary microRNA profiling in pregnant women identifies placental microRNAs that are candidate biomarkers for monitoring placental health. FEBS Lett 2023. [PMID: 37316461 DOI: 10.1002/1873-3468.14681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/10/2023] [Accepted: 05/25/2023] [Indexed: 06/16/2023]
Abstract
MicroRNAs are among the key modulators of placental transcriptome dynamics. This study aimed at comparative profiling of urinary (sampling at 228-230 gestational days, GD), serum (217-230 GD) and placental (279-286 GD) microRNAs in three healthy pregnant women using miRNome sequencing. Placenta showed significant enrichment of microRNAs compared to serum and urine (1174, 341 and 193, respectively; p<10-5 ). All sample types shared 153 microRNAs, representing candidate biomarkers for placental health. Urine samples contained eight of 56 transcripts from the placenta-specific chromosome 19 microRNA cluster C19MC and one of 91 transcripts (miR-432-5p) from the chromosome 14 cluster C14MC. The data suggest an active filtering at the maternal-fetal interface in passing through only selected microRNAs. Urine represents a valid source to monitor the signature of placenta-expressed microRNAs that are differentially expressed in pregnancy complications.
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Affiliation(s)
- Rain Inno
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, Faculty of Medicine, University of Tartu, Tartu, 50411, Estonia
| | - Maris Laan
- Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, Faculty of Medicine, University of Tartu, Tartu, 50411, Estonia
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8
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Mahto A, Yadav A, P V A, Parida SK, Tyagi AK, Agarwal P. Cytological, transcriptome and miRNome temporal landscapes decode enhancement of rice grain size. BMC Biol 2023; 21:91. [PMID: 37076907 PMCID: PMC10116700 DOI: 10.1186/s12915-023-01577-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 03/27/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND Rice grain size (GS) is an essential agronomic trait. Though several genes and miRNA modules influencing GS are known and seed development transcriptomes analyzed, a comprehensive compendium connecting all possible players is lacking. This study utilizes two contrasting GS indica rice genotypes (small-grained SN and large-grained LGR). Rice seed development involves five stages (S1-S5). Comparative transcriptome and miRNome atlases, substantiated with morphological and cytological studies, from S1-S5 stages and flag leaf have been analyzed to identify GS proponents. RESULTS Histology shows prolonged endosperm development and cell enlargement in LGR. Stand-alone and comparative RNAseq analyses manifest S3 (5-10 days after pollination) stage as crucial for GS enhancement, coherently with cell cycle, endoreduplication, and programmed cell death participating genes. Seed storage protein and carbohydrate accumulation, cytologically and by RNAseq, is shown to be delayed in LGR. Fourteen transcription factor families influence GS. Pathway genes for four phytohormones display opposite patterns of higher expression. A total of 186 genes generated from the transcriptome analyses are located within GS trait-related QTLs deciphered by a cross between SN and LGR. Fourteen miRNA families express specifically in SN or LGR seeds. Eight miRNA-target modules display contrasting expressions amongst SN and LGR, while 26 (SN) and 43 (LGR) modules are differentially expressed in all stages. CONCLUSIONS Integration of all analyses concludes in a "Domino effect" model for GS regulation highlighting chronology and fruition of each event. This study delineates the essence of GS regulation, providing scope for future exploits. The rice grain development database (RGDD) ( www.nipgr.ac.in/RGDD/index.php ; https://doi.org/10.5281/zenodo.7762870 ) has been developed for easy access of data generated in this paper.
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Affiliation(s)
- Arunima Mahto
- National Institute of Plant Genome Research, New Delhi, India
| | - Antima Yadav
- National Institute of Plant Genome Research, New Delhi, India
| | - Aswathi P V
- National Institute of Plant Genome Research, New Delhi, India
| | - Swarup K Parida
- National Institute of Plant Genome Research, New Delhi, India
| | - Akhilesh K Tyagi
- Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | - Pinky Agarwal
- National Institute of Plant Genome Research, New Delhi, India.
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9
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Toor SM, Aldous EK, Parray A, Akhtar N, Al-Sarraj Y, Abdelalim EM, Arredouani A, El-Agnaf O, Thornalley PJ, Pananchikkal SV, Pir GJ, Ayadathil R, Shuaib A, Alajez NM, Albagha OME. Circulating MicroRNA Profiling Identifies Distinct MicroRNA Signatures in Acute Ischemic Stroke and Transient Ischemic Attack Patients. Int J Mol Sci 2022; 24. [PMID: 36613546 DOI: 10.3390/ijms24010108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 12/04/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
Transient ischemic attack (TIA) refers to a momentary neurologic deficit caused by focal cerebral, spinal or retinal ischemic insult. TIA is associated with a high risk of impending acute ischemic stroke (AIS), a neurologic dysfunction characterized by focal cerebral, spinal or retinal infarction. Understanding the differences in molecular pathways in AIS and TIA has merit for deciphering the underlying cause for neuronal deficits with long-term effects and high risks of morbidity and mortality. In this study, we performed comprehensive investigations into the circulating microRNA (miRNA) profiles of AIS (n = 191) and TIA (n = 61) patients. We performed RNA-Seq on serum samples collected within 24 hrs of clinical diagnosis and randomly divided the study populations into discovery and validation cohorts. We identified a panel of 11 differentially regulated miRNAs at FDR < 0.05. Hsa-miR-548c-5p, -20a-5p, -18a-5p, -484, -652-3p, -486-3p, -24-3p, -181a-5p and -222-3p were upregulated, while hsa-miR-500a-3p and -206 were downregulated in AIS patients compared to TIA patients. We also probed the previously validated gene targets of our identified miRNA panel to highlight the molecular pathways affected in AIS. Moreover, we developed a multivariate classifier with potential utilization as a discriminative biomarker for AIS and TIA patients. The underlying molecular pathways in AIS compared to TIA may be explored further in functional studies for therapeutic targeting in clinical translation.
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10
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Di Palo A, Siniscalchi C, Crescente G, De Leo I, Fiorentino A, Pacifico S, Russo A, Potenza N. Effect of Cannabidiolic Acid, N- Trans-Caffeoyltyramine and Cannabisin B from Hemp Seeds on microRNA Expression in Human Neural Cells. Curr Issues Mol Biol 2022; 44:5106-5116. [PMID: 36286061 PMCID: PMC9600072 DOI: 10.3390/cimb44100347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/13/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
Given the increasing interest in bioactive dietary components that can modulate gene expression enhancing human health, three metabolites isolated from hemp seeds-cannabidiolic acid, N-trans-caffeoyltyramine, and cannabisin B-were examined for their ability to change the expression levels of microRNAs in human neural cells. To this end, cultured SH-SY5Y cells were treated with the three compounds and their microRNA content was characterized by next-generation small RNA sequencing. As a result, 31 microRNAs underwent major expression changes, being at least doubled or halved by the treatments. A computational analysis of the biological pathways affected by these microRNAs then showed that some are implicated in neural functions, such as axon guidance, hippocampal signaling, and neurotrophin signaling. Of these, miR-708-5p, miR-181a-5p, miR-190a-5p, miR-199a-5p, and miR-143-3p are known to be involved in Alzheimer's disease and their expression changes are expected to ameliorate neural function. Overall, these results provide new insights into the mechanism of action of hemp seed metabolites and encourage further studies to gain a better understanding of their biological effects on the central nervous system.
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11
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Tanno B, Novelli F, Leonardi S, Merla C, Babini G, Giardullo P, Kadhim M, Traynor D, Medipally DKR, Meade AD, Lyng FM, Tapio S, Marchetti L, Saran A, Pazzaglia S, Mancuso M. MiRNA-Mediated Fibrosis in the Out-of-Target Heart following Partial-Body Irradiation. Cancers (Basel) 2022; 14:cancers14143463. [PMID: 35884524 PMCID: PMC9323333 DOI: 10.3390/cancers14143463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/08/2022] [Accepted: 07/14/2022] [Indexed: 11/16/2022] Open
Abstract
Recent reports have shown a link between radiation exposure and non-cancer diseases such as radiation-induced heart disease (RIHD). Radiation exposures are often inhomogeneous, and out-of-target effects have been studied in terms of cancer risk, but very few studies have been carried out for non-cancer diseases. Here, the role of miRNAs in the pathogenesis of RIHD was investigated. C57Bl/6J female mice were whole- (WBI) or partial-body-irradiated (PBI) with 2 Gy of X-rays or sham-irradiated (SI). In PBI exposure, the lower third of the mouse body was irradiated, while the upper two-thirds were shielded. From all groups, hearts were collected 15 days or 6 months post-irradiation. The MiRNome analysis at 15 days post-irradiation showed that miRNAs, belonging to the myomiR family, were highly differentially expressed in WBI and PBI mouse hearts compared with SI hearts. Raman spectral data collected 15 days and 6 months post-irradiation showed biochemical differences among SI, WBI and PBI mouse hearts. Fibrosis in WBI and PBI mouse hearts, indicated by the increased deposition of collagen and the overexpression of genes involved in myofibroblast activation, was found 6 months post-irradiation. Using an in vitro co-culture system, involving directly irradiated skeletal muscle and unirradiated ventricular cardiac human cells, we propose the role of miR-1/133a as mediators of the abscopal response, suggesting that miRNA-based strategies could be relevant for limiting tissue-dependent reactions in non-directly irradiated tissues.
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Affiliation(s)
- Barbara Tanno
- Laboratory of Biomedical Technologies, Agenzia Nazionale per le Nuove Tecnologie, l’Energia e lo Sviluppo Economico Sostenibile (ENEA), 00123 Rome, Italy; (F.N.); (S.L.); (C.M.); (P.G.); (L.M.); (A.S.); (S.P.)
- Correspondence: (B.T.); (M.M.)
| | - Flavia Novelli
- Laboratory of Biomedical Technologies, Agenzia Nazionale per le Nuove Tecnologie, l’Energia e lo Sviluppo Economico Sostenibile (ENEA), 00123 Rome, Italy; (F.N.); (S.L.); (C.M.); (P.G.); (L.M.); (A.S.); (S.P.)
| | - Simona Leonardi
- Laboratory of Biomedical Technologies, Agenzia Nazionale per le Nuove Tecnologie, l’Energia e lo Sviluppo Economico Sostenibile (ENEA), 00123 Rome, Italy; (F.N.); (S.L.); (C.M.); (P.G.); (L.M.); (A.S.); (S.P.)
| | - Caterina Merla
- Laboratory of Biomedical Technologies, Agenzia Nazionale per le Nuove Tecnologie, l’Energia e lo Sviluppo Economico Sostenibile (ENEA), 00123 Rome, Italy; (F.N.); (S.L.); (C.M.); (P.G.); (L.M.); (A.S.); (S.P.)
| | - Gabriele Babini
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario Agostino Gemelli, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 00168 Rome, Italy;
| | - Paola Giardullo
- Laboratory of Biomedical Technologies, Agenzia Nazionale per le Nuove Tecnologie, l’Energia e lo Sviluppo Economico Sostenibile (ENEA), 00123 Rome, Italy; (F.N.); (S.L.); (C.M.); (P.G.); (L.M.); (A.S.); (S.P.)
| | - Munira Kadhim
- Department of Biological and Medical Sciences, Oxford Brookes University (OBU), Oxford OX3 0BP, UK;
| | - Damien Traynor
- Radiation and Environmental Science Centre, Technological University Dublin, D02 HW71 Dublin, Ireland; (D.T.); (D.K.R.M.); (A.D.M.); (F.M.L.)
| | - Dinesh K. R. Medipally
- Radiation and Environmental Science Centre, Technological University Dublin, D02 HW71 Dublin, Ireland; (D.T.); (D.K.R.M.); (A.D.M.); (F.M.L.)
| | - Aidan D. Meade
- Radiation and Environmental Science Centre, Technological University Dublin, D02 HW71 Dublin, Ireland; (D.T.); (D.K.R.M.); (A.D.M.); (F.M.L.)
| | - Fiona M. Lyng
- Radiation and Environmental Science Centre, Technological University Dublin, D02 HW71 Dublin, Ireland; (D.T.); (D.K.R.M.); (A.D.M.); (F.M.L.)
| | - Soile Tapio
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH (HMGU), Institute of Radiation Biology, D-85764 Neuherberg, Germany;
| | - Luca Marchetti
- Laboratory of Biomedical Technologies, Agenzia Nazionale per le Nuove Tecnologie, l’Energia e lo Sviluppo Economico Sostenibile (ENEA), 00123 Rome, Italy; (F.N.); (S.L.); (C.M.); (P.G.); (L.M.); (A.S.); (S.P.)
- Department of Agricultural and Forestry Sciences, Università della Tuscia, 01100 Viterbo, Italy
| | - Anna Saran
- Laboratory of Biomedical Technologies, Agenzia Nazionale per le Nuove Tecnologie, l’Energia e lo Sviluppo Economico Sostenibile (ENEA), 00123 Rome, Italy; (F.N.); (S.L.); (C.M.); (P.G.); (L.M.); (A.S.); (S.P.)
- Department of Radiation Physics, Guglielmo Marconi University, 00193 Rome, Italy
| | - Simonetta Pazzaglia
- Laboratory of Biomedical Technologies, Agenzia Nazionale per le Nuove Tecnologie, l’Energia e lo Sviluppo Economico Sostenibile (ENEA), 00123 Rome, Italy; (F.N.); (S.L.); (C.M.); (P.G.); (L.M.); (A.S.); (S.P.)
| | - Mariateresa Mancuso
- Laboratory of Biomedical Technologies, Agenzia Nazionale per le Nuove Tecnologie, l’Energia e lo Sviluppo Economico Sostenibile (ENEA), 00123 Rome, Italy; (F.N.); (S.L.); (C.M.); (P.G.); (L.M.); (A.S.); (S.P.)
- Correspondence: (B.T.); (M.M.)
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12
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Louro AF, Paiva MA, Oliveira MR, Kasper KA, Alves PM, Gomes‐Alves P, Serra M. Bioactivity and miRNome Profiling of Native Extracellular Vesicles in Human Induced Pluripotent Stem Cell-Cardiomyocyte Differentiation. Adv Sci (Weinh) 2022; 9:e2104296. [PMID: 35322574 PMCID: PMC9130911 DOI: 10.1002/advs.202104296] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/05/2022] [Indexed: 05/17/2023]
Abstract
Extracellular vesicles (EV) are an attractive therapy to boost cardiac regeneration. Nevertheless, identification of native EV and corresponding cell platform(s) suitable for therapeutic application, is still a challenge. Here, EV are isolated from key stages of the human induced pluripotent stem cell-cardiomyocyte (hiPSC-CM) differentiation and maturation, i.e., from hiPSC (hiPSC-EV), cardiac progenitors, immature and mature cardiomyocytes, with the aim of identifying a promising cell biofactory for EV production, and pinpoint the genetic signatures of bioactive EV. EV secreted by hiPSC and cardiac derivatives show a typical size distribution profile and the expression of specific EV markers. Bioactivity assays show increased tube formation and migration in HUVEC treated with hiPSC-EV compared to EV from committed cell populations. hiPSC-EV also significantly increase cell cycle activity of hiPSC-CM. Global miRNA expression profiles, obtained by small RNA-seq analysis, corroborate an EV-miRNA pattern indicative of stem cell to cardiomyocyte specification, confirming that hiPSC-EV are enriched in pluripotency-associated miRNA with higher in vitro pro-angiogenic and pro-proliferative properties. In particular, a stemness maintenance miRNA cluster upregulated in hiPSC-EV targets the PTEN/PI3K/AKT pathway, involved in cell proliferation and survival. Overall, the findings validate hiPSC as cell biofactories for EV production for cardiac regenerative applications.
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Affiliation(s)
- Ana F. Louro
- iBETInstituto de Biologia Experimental e TecnológicaApartado 12Oeiras2781‐901Portugal
- ITQB‐NOVAInstituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaAv. da RepúblicaOeiras2780‐157Portugal
| | - Marta A. Paiva
- iBETInstituto de Biologia Experimental e TecnológicaApartado 12Oeiras2781‐901Portugal
- ITQB‐NOVAInstituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaAv. da RepúblicaOeiras2780‐157Portugal
| | - Marta R. Oliveira
- iBETInstituto de Biologia Experimental e TecnológicaApartado 12Oeiras2781‐901Portugal
- ITQB‐NOVAInstituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaAv. da RepúblicaOeiras2780‐157Portugal
| | - Katharina A. Kasper
- iBETInstituto de Biologia Experimental e TecnológicaApartado 12Oeiras2781‐901Portugal
- ITQB‐NOVAInstituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaAv. da RepúblicaOeiras2780‐157Portugal
| | - Paula M. Alves
- iBETInstituto de Biologia Experimental e TecnológicaApartado 12Oeiras2781‐901Portugal
- ITQB‐NOVAInstituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaAv. da RepúblicaOeiras2780‐157Portugal
| | - Patrícia Gomes‐Alves
- iBETInstituto de Biologia Experimental e TecnológicaApartado 12Oeiras2781‐901Portugal
- ITQB‐NOVAInstituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaAv. da RepúblicaOeiras2780‐157Portugal
| | - Margarida Serra
- iBETInstituto de Biologia Experimental e TecnológicaApartado 12Oeiras2781‐901Portugal
- ITQB‐NOVAInstituto de Tecnologia Química e Biológica António XavierUniversidade Nova de LisboaAv. da RepúblicaOeiras2780‐157Portugal
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13
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Herrero-Aguayo V, Sáez-Martínez P, Jiménez-Vacas JM, Moreno-Montilla MT, Montero-Hidalgo AJ, Pérez-Gómez JM, López-Canovas JL, Porcel-Pastrana F, Carrasco-Valiente J, Anglada FJ, Gómez-Gómez E, Yubero-Serrano EM, Ibañez-Costa A, Herrera-Martínez AD, Sarmento-Cabral A, Gahete MD, Luque RM. Dysregulation of the miRNome unveils a crosstalk between obesity and prostate cancer: miR-107 asa personalized diagnostic and therapeutic tool. Mol Ther Nucleic Acids 2022; 27:1164-1178. [PMID: 35282415 PMCID: PMC8889365 DOI: 10.1016/j.omtn.2022.02.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/10/2022] [Indexed: 04/12/2023]
Abstract
Prostate-specific antigen (PSA) is the gold-standard marker to screen prostate cancer (PCa) nowadays. Unfortunately, its lack of specificity and sensitivity makes the identification of novel tools to diagnose PCa an urgent medical need. In this context, microRNAs (miRNAs) have emerged as potential sources of non-invasive diagnostic biomarkers in several pathologies. Therefore, this study was aimed at assessing for the first time the dysregulation of the whole plasma miRNome in PCa patients and its putative implication in PCa from a personalized perspective (i.e., obesity condition). Plasma miRNome from a discovery cohort (18 controls and 19 PCa patients) was determined using an Affymetrix-miRNA array, showing that the expression of 104 miRNAs was significantly altered, wherein six exhibited a significant receiver operating characteristic (ROC) curve to distinguish between control and PCa patients (area under the curve [AUC] = 1). Then, a systematic validation using an independent cohort (135 controls and 160 PCa patients) demonstrated that miR-107 was the most profoundly altered miRNA in PCa (AUC = 0.75). Moreover, miR-107 levels significantly outperformed the ability of PSA to distinguish between control and PCa patients and correlated with relevant clinical parameters (i.e., PSA). These differences were more pronounced when considering only obese patients (BMI > 30). Interestingly, miR-107 levels were reduced in PCa tissues versus non-tumor tissues (n = 84) and in PCa cell lines versus non-tumor cells. In vitro miR-107 overexpression altered key aggressiveness features in PCa cells (i.e., proliferation, migration, and tumorospheres formation) and modulated the expression of important genes involved in PCa pathophysiology (i.e., lipid metabolism [i.e., FASN] and splicing process). Altogether, miR-107 might represent a novel and useful personalized diagnostic and prognostic biomarker and a potential therapeutic tool in PCa, especially in obese patients.
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Affiliation(s)
- Vicente Herrero-Aguayo
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Edificio IMIBIC, Av. Menéndez Pidal s/n, 14004 Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, 14014 Córdoba, Spain
- Hospital Universitario Reina Sofía (HURS), 14004 Córdoba, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), 28019 Madrid, Spain
| | - Prudencio Sáez-Martínez
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Edificio IMIBIC, Av. Menéndez Pidal s/n, 14004 Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, 14014 Córdoba, Spain
- Hospital Universitario Reina Sofía (HURS), 14004 Córdoba, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), 28019 Madrid, Spain
| | - Juan M. Jiménez-Vacas
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Edificio IMIBIC, Av. Menéndez Pidal s/n, 14004 Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, 14014 Córdoba, Spain
- Hospital Universitario Reina Sofía (HURS), 14004 Córdoba, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), 28019 Madrid, Spain
| | - M. Trinidad Moreno-Montilla
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Edificio IMIBIC, Av. Menéndez Pidal s/n, 14004 Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, 14014 Córdoba, Spain
- Hospital Universitario Reina Sofía (HURS), 14004 Córdoba, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), 28019 Madrid, Spain
| | - Antonio J. Montero-Hidalgo
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Edificio IMIBIC, Av. Menéndez Pidal s/n, 14004 Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, 14014 Córdoba, Spain
- Hospital Universitario Reina Sofía (HURS), 14004 Córdoba, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), 28019 Madrid, Spain
| | - Jesús M. Pérez-Gómez
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Edificio IMIBIC, Av. Menéndez Pidal s/n, 14004 Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, 14014 Córdoba, Spain
- Hospital Universitario Reina Sofía (HURS), 14004 Córdoba, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), 28019 Madrid, Spain
| | - Juan L. López-Canovas
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Edificio IMIBIC, Av. Menéndez Pidal s/n, 14004 Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, 14014 Córdoba, Spain
- Hospital Universitario Reina Sofía (HURS), 14004 Córdoba, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), 28019 Madrid, Spain
| | - Francisco Porcel-Pastrana
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Edificio IMIBIC, Av. Menéndez Pidal s/n, 14004 Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, 14014 Córdoba, Spain
- Hospital Universitario Reina Sofía (HURS), 14004 Córdoba, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), 28019 Madrid, Spain
| | - Julia Carrasco-Valiente
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Edificio IMIBIC, Av. Menéndez Pidal s/n, 14004 Córdoba, Spain
- Hospital Universitario Reina Sofía (HURS), 14004 Córdoba, Spain
- Urology Service, HURS/IMIBIC, 14004 Córdoba, Spain
| | - Francisco J. Anglada
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Edificio IMIBIC, Av. Menéndez Pidal s/n, 14004 Córdoba, Spain
- Hospital Universitario Reina Sofía (HURS), 14004 Córdoba, Spain
- Urology Service, HURS/IMIBIC, 14004 Córdoba, Spain
| | - Enrique Gómez-Gómez
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Edificio IMIBIC, Av. Menéndez Pidal s/n, 14004 Córdoba, Spain
- Hospital Universitario Reina Sofía (HURS), 14004 Córdoba, Spain
- Urology Service, HURS/IMIBIC, 14004 Córdoba, Spain
| | - Elena M. Yubero-Serrano
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Edificio IMIBIC, Av. Menéndez Pidal s/n, 14004 Córdoba, Spain
- Hospital Universitario Reina Sofía (HURS), 14004 Córdoba, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), 28019 Madrid, Spain
- Lipids and Atherosclerosis Unit, HURS/IMIBIC, 14004 Córdoba, Spain
| | - Alejandro Ibañez-Costa
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Edificio IMIBIC, Av. Menéndez Pidal s/n, 14004 Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, 14014 Córdoba, Spain
- Hospital Universitario Reina Sofía (HURS), 14004 Córdoba, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), 28019 Madrid, Spain
| | - Aura D. Herrera-Martínez
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Edificio IMIBIC, Av. Menéndez Pidal s/n, 14004 Córdoba, Spain
- Hospital Universitario Reina Sofía (HURS), 14004 Córdoba, Spain
- Endocrinology and Nutrition Service, HURS/IMIBIC, 14004 Córdoba, Spain
| | - André Sarmento-Cabral
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Edificio IMIBIC, Av. Menéndez Pidal s/n, 14004 Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, 14014 Córdoba, Spain
- Hospital Universitario Reina Sofía (HURS), 14004 Córdoba, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), 28019 Madrid, Spain
| | - Manuel D. Gahete
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Edificio IMIBIC, Av. Menéndez Pidal s/n, 14004 Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, 14014 Córdoba, Spain
- Hospital Universitario Reina Sofía (HURS), 14004 Córdoba, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), 28019 Madrid, Spain
- Corresponding author Manuel D. Gahete, Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Edificio IMIBIC, Av. Menéndez Pidal s/n, 14004 Córdoba, Spain.
| | - Raúl M. Luque
- Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Edificio IMIBIC, Av. Menéndez Pidal s/n, 14004 Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, 14014 Córdoba, Spain
- Hospital Universitario Reina Sofía (HURS), 14004 Córdoba, Spain
- Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición, (CIBERobn), 28019 Madrid, Spain
- Corresponding author Raúl M. Luque, Maimonides Institute for Biomedical Research of Córdoba (IMIBIC), Edificio IMIBIC, Av. Menéndez Pidal s/n, 14004 Córdoba, Spain.
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14
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Pazzaglia S, Tanno B, De Stefano I, Giardullo P, Leonardi S, Merla C, Babini G, Tuncay Cagatay S, Mayah A, Kadhim M, Lyng FM, von Toerne C, Khan ZN, Subedi P, Tapio S, Saran A, Mancuso M. Micro-RNA and Proteomic Profiles of Plasma-Derived Exosomes from Irradiated Mice Reveal Molecular Changes Preventing Apoptosis in Neonatal Cerebellum. Int J Mol Sci 2022; 23:ijms23042169. [PMID: 35216284 PMCID: PMC8878539 DOI: 10.3390/ijms23042169] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/04/2022] [Accepted: 02/11/2022] [Indexed: 12/12/2022] Open
Abstract
Cell communication via exosomes is capable of influencing cell fate in stress situations such as exposure to ionizing radiation. In vitro and in vivo studies have shown that exosomes might play a role in out-of-target radiation effects by carrying molecular signaling mediators of radiation damage, as well as opposite protective functions resulting in resistance to radiotherapy. However, a global understanding of exosomes and their radiation-induced regulation, especially within the context of an intact mammalian organism, has been lacking. In this in vivo study, we demonstrate that, compared to sham-irradiated (SI) mice, a distinct pattern of proteins and miRNAs is found packaged into circulating plasma exosomes after whole-body and partial-body irradiation (WBI and PBI) with 2 Gy X-rays. A high number of deregulated proteins (59% of WBI and 67% of PBI) was found in the exosomes of irradiated mice. In total, 57 and 13 miRNAs were deregulated in WBI and PBI groups, respectively, suggesting that the miRNA cargo is influenced by the tissue volume exposed to radiation. In addition, five miRNAs (miR-99b-3p, miR-200a-3p, miR-200a, miR-182-5p, miR-182) were commonly overexpressed in the exosomes from the WBI and PBI groups. In this study, particular emphasis was also given to the determination of the in vivo effect of exosome transfer by intracranial injection in the highly radiosensitive neonatal cerebellum at postnatal day 3. In accordance with a major overall anti-apoptotic function of the commonly deregulated miRNAs, here, we report that exosomes from the plasma of irradiated mice, especially in the case of WBI, prevent radiation-induced apoptosis, thus holding promise for exosome-based future therapeutic applications against radiation injury.
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Affiliation(s)
- Simonetta Pazzaglia
- Laboratory of Biomedical Technologies, Agenzia Nazionale per le Nuove Tecnologie, l’Energia e lo Sviluppo Economico Sostenibile (ENEA), 00123 Rome, Italy; (B.T.); (I.D.S.); (P.G.); (S.L.); (C.M.); (A.S.)
- Correspondence: (S.P.); (M.M.)
| | - Barbara Tanno
- Laboratory of Biomedical Technologies, Agenzia Nazionale per le Nuove Tecnologie, l’Energia e lo Sviluppo Economico Sostenibile (ENEA), 00123 Rome, Italy; (B.T.); (I.D.S.); (P.G.); (S.L.); (C.M.); (A.S.)
| | - Ilaria De Stefano
- Laboratory of Biomedical Technologies, Agenzia Nazionale per le Nuove Tecnologie, l’Energia e lo Sviluppo Economico Sostenibile (ENEA), 00123 Rome, Italy; (B.T.); (I.D.S.); (P.G.); (S.L.); (C.M.); (A.S.)
| | - Paola Giardullo
- Laboratory of Biomedical Technologies, Agenzia Nazionale per le Nuove Tecnologie, l’Energia e lo Sviluppo Economico Sostenibile (ENEA), 00123 Rome, Italy; (B.T.); (I.D.S.); (P.G.); (S.L.); (C.M.); (A.S.)
| | - Simona Leonardi
- Laboratory of Biomedical Technologies, Agenzia Nazionale per le Nuove Tecnologie, l’Energia e lo Sviluppo Economico Sostenibile (ENEA), 00123 Rome, Italy; (B.T.); (I.D.S.); (P.G.); (S.L.); (C.M.); (A.S.)
| | - Caterina Merla
- Laboratory of Biomedical Technologies, Agenzia Nazionale per le Nuove Tecnologie, l’Energia e lo Sviluppo Economico Sostenibile (ENEA), 00123 Rome, Italy; (B.T.); (I.D.S.); (P.G.); (S.L.); (C.M.); (A.S.)
| | - Gabriele Babini
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), 00168 Rome, Italy;
| | - Seda Tuncay Cagatay
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK; (S.T.C.); (A.M.); (M.K.)
| | - Ammar Mayah
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK; (S.T.C.); (A.M.); (M.K.)
| | - Munira Kadhim
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, UK; (S.T.C.); (A.M.); (M.K.)
| | - Fiona M. Lyng
- FOCAS Research Institute, Technological University Dublin (TU Dublin), D07 EWV4 Dublin, Ireland;
| | - Christine von Toerne
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH (HMGU), Institute of Radiation Biology, 85764, Neuherberg, Germany; (C.v.T.); (Z.N.K.); (P.S.); (S.T.)
| | - Zohaib N. Khan
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH (HMGU), Institute of Radiation Biology, 85764, Neuherberg, Germany; (C.v.T.); (Z.N.K.); (P.S.); (S.T.)
| | - Prabal Subedi
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH (HMGU), Institute of Radiation Biology, 85764, Neuherberg, Germany; (C.v.T.); (Z.N.K.); (P.S.); (S.T.)
| | - Soile Tapio
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH (HMGU), Institute of Radiation Biology, 85764, Neuherberg, Germany; (C.v.T.); (Z.N.K.); (P.S.); (S.T.)
| | - Anna Saran
- Laboratory of Biomedical Technologies, Agenzia Nazionale per le Nuove Tecnologie, l’Energia e lo Sviluppo Economico Sostenibile (ENEA), 00123 Rome, Italy; (B.T.); (I.D.S.); (P.G.); (S.L.); (C.M.); (A.S.)
| | - Mariateresa Mancuso
- Laboratory of Biomedical Technologies, Agenzia Nazionale per le Nuove Tecnologie, l’Energia e lo Sviluppo Economico Sostenibile (ENEA), 00123 Rome, Italy; (B.T.); (I.D.S.); (P.G.); (S.L.); (C.M.); (A.S.)
- Correspondence: (S.P.); (M.M.)
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15
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Flowers AE, Gonzalez TL, Joshi NV, Eisman LE, Clark EL, Buttle RA, Sauro E, DiPentino R, Lin Y, Wu D, Wang Y, Santiskulvong C, Tang J, Lee B, Sun T, Chan JL, Wang ET, Jefferies C, Lawrenson K, Zhu Y, Afshar Y, Tseng HR, Williams J, Pisarska MD. Sex differences in microRNA expression in first and third trimester human placenta†. Biol Reprod 2021; 106:551-567. [PMID: 35040930 DOI: 10.1093/biolre/ioab221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 11/09/2021] [Accepted: 12/04/2021] [Indexed: 12/13/2022] Open
Abstract
Maternal and fetal pregnancy outcomes related to placental function vary based on fetal sex, which may be due to sexually dimorphic epigenetic regulation of RNA expression. We identified sexually dimorphic miRNA expression throughout gestation in human placentae. Next-generation sequencing identified miRNA expression profiles in first and third trimester uncomplicated pregnancies using tissue obtained at chorionic villous sampling (n = 113) and parturition (n = 47). Sequencing analysis identified 986 expressed mature miRNAs from female and male placentae at first and third trimester (baseMean>10). Of these, 11 sexually dimorphic (FDR < 0.05) miRNAs were identified in the first and 4 in the third trimester, all upregulated in females, including miR-361-5p, significant in both trimesters. Sex-specific analyses across gestation identified 677 differentially expressed (DE) miRNAs at FDR < 0.05 and baseMean>10, with 508 DE miRNAs in common between female-specific and male-specific analysis (269 upregulated in first trimester, 239 upregulated in third trimester). Of those, miR-4483 had the highest fold changes across gestation. There were 62.5% more female exclusive differences with fold change>2 across gestation than male exclusive (52 miRNAs vs 32 miRNAs), indicating miRNA expression across human gestation is sexually dimorphic. Pathway enrichment analysis identified significant pathways that were differentially regulated in first and third trimester as well as across gestation. This work provides the normative sex dimorphic miRNA atlas in first and third trimester, as well as the sex-independent and sex-specific placenta miRNA atlas across gestation, which may be used to identify biomarkers of placental function and direct functional studies investigating placental sex differences.
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Affiliation(s)
- Amy E Flowers
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Tania L Gonzalez
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Nikhil V Joshi
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Laura E Eisman
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ekaterina L Clark
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Rae A Buttle
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Erica Sauro
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Rosemarie DiPentino
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yayu Lin
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Di Wu
- Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yizhou Wang
- Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Chintda Santiskulvong
- CS Cancer Applied Genomics Shared Resource, CS Cancer, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jie Tang
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Bora Lee
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Tianyanxin Sun
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jessica L Chan
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Erica T Wang
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Caroline Jefferies
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kate Lawrenson
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yazhen Zhu
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yalda Afshar
- David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Hsian-Rong Tseng
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - John Williams
- David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Margareta D Pisarska
- Department of Obstetrics and Gynecology, Division of Reproductive Endocrinology and Infertility, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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16
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Abstract
Depression is an effect of complex interactions between genetic, epigenetic and environmental factors. It is well established that stress responses are associated with multiple modest and often dynamic molecular changes in the homeostatic balance, rather than with a single genetic factor that has a strong phenotypic penetration. As depression is a multifaceted phenotype, it is important to study biochemical pathways that can regulate the overall allostasis of the brain. One such biological system that has the potential to fine-tune a multitude of diverse molecular processes is RNA interference (RNAi). RNAi is an epigenetic process showing a very low level of evolutionary diversity, and relies on the posttranscriptional regulation of gene expression using, in the case of mammals, primarily short (17–23 nucleotides) noncoding RNA transcripts called microRNAs (miRNA). In this review, our objective was to examine, summarize and discuss recent advances in the field of biomedical and clinical research on the role of miRNA-mediated regulation of gene expression in the development of depression. We focused on studies investigating post-mortem brain tissue of individuals with depression, as well as research aiming to elucidate the biomarker potential of miRNAs in depression and antidepressant response.
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17
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Re M, Tomasetti M, Monaco F, Amati M, Rubini C, Foschini MP, Sollini G, Gioacchini FM, Pasquini E, Santarelli L. NGS-based miRNome identifies miR-449 cluster as marker of malignant transformation of sinonasal inverted papilloma. Oral Oncol 2021; 122:105554. [PMID: 34653751 DOI: 10.1016/j.oraloncology.2021.105554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/14/2021] [Accepted: 09/25/2021] [Indexed: 11/30/2022]
Abstract
OBJECTIVE identification of the miRNA expression profile in sinonasal inverted papilloma (SNIP) as a tool to evaluate the risk of transformation into sinonasal squamous cell carcinoma (SNSCC). MATERIALS AND METHODS paired tumour tissues and adjacent normal tissues were obtained from SNIP and SNSCC patients who had undergone surgical resection and used for next-generation sequencing (NGS)-based miRNome analysis. SNIP tissues with concomitant dysplasia (SNIP-DISP) were used as malignant transition samples. By comparing the deregulated miRNAs in SNIP and SNSCC, an miRNA cluster was identified and its physio- and clinical-pathological value was predicted. RESULTS NGS identified 54 miRNAs significantly down- and upregulated in SNIP. Among them, the miR-449 cluster was upregulated in SNIP and could differentiate the benign tumour from normal tissue. Notably, the miR-449 cluster was found to be significantly underexpressed in SNSCC, and the cluster markedly changed in SNIP during the malignant transition into SNSCC. miRNA enrichment analysis and GO analysis revealed that miR-449 is involved in apoptotic and cell proliferation pathways. CONCLUSIONS Our findings suggest that miR-449 may be involved in the molecular pathogenesis of SNIP and its malignant transformation into SNSCC. miR-449 might therefore be a useful tumour biomarker in patients with SNIP and may also have the potential to be used as a tool for detecting and monitoring the course of the possible malignant transformation.
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Affiliation(s)
- Massimo Re
- Department of Clinical and Molecular Sciences, Section of Otorhinolaryngology, Polytechnic University of Marche, Ancona, Italy.
| | - Marco Tomasetti
- Department of Clinical and Molecular Sciences, Section of Occupational Medicine, Polytechnic University of Marche, Ancona, Italy
| | - Federica Monaco
- Department of Clinical and Molecular Sciences, Section of Occupational Medicine, Polytechnic University of Marche, Ancona, Italy
| | - Monica Amati
- Department of Clinical and Molecular Sciences, Section of Occupational Medicine, Polytechnic University of Marche, Ancona, Italy
| | - Corrado Rubini
- Department of Biomedical Sciences and Public Health, Section of Anatomical Pathology, Polytechnic University of Marche, Ancona, Italy
| | - Maria P Foschini
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Section of Anatomic Pathology, Bellaria Hospital, Bologna, Italy
| | - Giacomo Sollini
- Surgical Department, ENT Metropolitan Unit, Bellaria & Budrio Hospital, Bologna, Italy
| | - Federico Maria Gioacchini
- Department of Clinical and Molecular Sciences, Section of Otorhinolaryngology, Polytechnic University of Marche, Ancona, Italy
| | - Ernesto Pasquini
- Surgical Department, ENT Metropolitan Unit, Bellaria & Budrio Hospital, Bologna, Italy
| | - Lory Santarelli
- Department of Clinical and Molecular Sciences, Section of Occupational Medicine, Polytechnic University of Marche, Ancona, Italy
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18
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Corrêa S, Lopes FP, Panis C, Basili T, Binato R, Abdelhay E. miRNome Profiling Reveals Shared Features in Breast Cancer Subtypes and Highlights miRNAs That Potentially Regulate MYB and EZH2 Expression. Front Oncol 2021; 11:710919. [PMID: 34646766 PMCID: PMC8502886 DOI: 10.3389/fonc.2021.710919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 08/30/2021] [Indexed: 01/03/2023] Open
Abstract
Breast cancer (BC) has been extensively studied, as it is one of the more commonly diagnosed cancer types worldwide. The study of miRNAs has increased what is known about the complexity of pathways and signaling and has identified potential biomarkers and therapeutic targets. Thus, miRNome profiling could provide important information regarding the molecular mechanisms involved in BC. On average, more than 430 miRNAs were identified as differentially expressed between BC cell lines and normal breast HMEC cells. From these, 110 miRNAs were common to BC subtypes. The miRNome enrichment analysis and interaction maps highlighted epigenetic-related pathways shared by all BC cell lines and revealed potential miRNA targets. Quantitative evaluation of BC patient samples and GETx/TCGA-BRCA datasets confirmed MYB and EZH2 as potential targets from BC miRNome. Moreover, overall survival was impacted by EZH2 expression. The expression of 15 miRNAs, selected according to aggressiveness of BC subtypes, was confirmed in TCGA-BRCA dataset. Of these miRNAs, miRNA-mRNA interaction prediction revealed 7 novel or underexplored miRNAs in BC: miR-1271-5p, miR-130a-5p, and miR-134 as MYB regulators and miR-138-5p, miR-455-3p, miR-487a, and miR-487b as EZH2 regulators. Herein, we report a novel molecular miRNA signature for BC and identify potential miRNA/mRNAs involved in disease subtypes.
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Affiliation(s)
- Stephany Corrêa
- Centro de Transplante de Medula Óssea (CEMO), Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil
| | - Francisco P Lopes
- Grupo de Biologia do Desenvolvimento e Sistemas Dinâmicos, Universidade Federal do Rio de Janeiro (UFRJ), Duque de Caxias, Brazil
| | - Carolina Panis
- Laboratório de Biologia de Tumores, Universidade Estadual do Oeste do Paraná (UNIOESTE), Francisco Beltrão, Brazil
| | - Thais Basili
- Centro de Transplante de Medula Óssea (CEMO), Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Renata Binato
- Centro de Transplante de Medula Óssea (CEMO), Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil
| | - Eliana Abdelhay
- Centro de Transplante de Medula Óssea (CEMO), Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil
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19
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Re M, Tomasetti M, Monaco F, Amati M, Rubini C, Sollini G, Bajraktari A, Gioacchini FM, Santarelli L, Pasquini E. MiRNome analysis identifying miR-205 and miR-449a as biomarkers of disease progression in intestinal-type sinonasal adenocarcinoma. Head Neck 2021; 44:18-33. [PMID: 34647653 PMCID: PMC9292973 DOI: 10.1002/hed.26894] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 09/02/2021] [Accepted: 09/30/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Patients with intestinal-type sinonasal adenocarcinoma (ITAC) have an unfavorable prognosis, and new diagnostic and therapeutic approaches are needed to improve clinical management. METHODS Next-generation sequencing-based miRNome analysis was performed on 43 ITAC patients who underwent surgical resection, and microRNA (miRNA) data were obtained from 35 cases. Four miRNAs were identified, and their expression levels were detected by reverse-transcription quantitative polymerase chain reaction and related to the relevant patient outcome. Overall survival and disease-free survival rates were evaluated through the Kaplan-Meier method and log-rank test, and multivariate analysis was performed by means of Cox proportional hazard analysis. RESULTS High levels of miR-205 and miR-34c/miR-449 cluster expression were associated with an increased recurrence risk and, therefore, a worse prognosis. Multivariate analysis confirmed that miR-205 and miR-449 were significant prognostic predictors. CONCLUSIONS A high expression of miR-205 and miR-449 is independent predictors of poor survival for ITAC patients.
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Affiliation(s)
- Massimo Re
- Department of Clinical and Molecular Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Marco Tomasetti
- Department of Clinical and Molecular Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Federica Monaco
- Department of Clinical and Molecular Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Monica Amati
- Department of Clinical and Molecular Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Corrado Rubini
- Department of Biomedical Sciences and Public Health, Anatomy Pathology and Histopathology Section, Polytechnic University of Marche, Ancona, Italy
| | | | - Arisa Bajraktari
- Department of Clinical and Molecular Sciences, Polytechnic University of Marche, Ancona, Italy
| | | | - Lory Santarelli
- Department of Clinical and Molecular Sciences, Polytechnic University of Marche, Ancona, Italy
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20
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Li B, Yang J, Gong Y, Xiao Y, Zeng Q, Xu K, Duan Y, He J, He J, Ma H. Integrated Analysis of Liver Transcriptome, miRNA, and Proteome of Chinese Indigenous Breed Ningxiang Pig in Three Developmental Stages Uncovers Significant miRNA-mRNA-Protein Networks in Lipid Metabolism. Front Genet 2021; 12:709521. [PMID: 34603377 PMCID: PMC8481880 DOI: 10.3389/fgene.2021.709521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/19/2021] [Indexed: 11/13/2022] Open
Abstract
Liver is an important metabolic organ of mammals. During each transitional period of life, liver metabolism is programmed by a complex molecular regulatory system for multiple physiological functions, many pathways of which are regulated by hormones and cytokines, nuclear receptors, and transcription factors. To gain a comprehensive and unbiased molecular understanding of liver growth and development in Ningxiang pigs, we analyzed the mRNA, microRNA (miRNA), and proteomes of the livers of Ningxiang pigs during lactation, nursery, and fattening periods. A total of 22,411 genes (19,653 known mRNAs and 2758 novel mRNAs), 1122 miRNAs (384 known miRNAs and 738 novel miRNAs), and 1123 unique proteins with medium and high abundance were identified by high-throughput sequencing and mass spectrometry. We show that the differences in transcriptional, post-transcriptional, or protein levels were readily identified by comparing different time periods, providing evidence that functional changes that may occur during liver development are widespread. In addition, we found many overlapping differentially expressed genes (DEGs)/differentially expressed miRNAs (DEMs)/differentially expressed proteins (DEPs) related to glycolipid metabolism in any group comparison. These overlapping DEGs/DEMs/DGPs may play an important role in functional transformation during liver development. Short Time-series Expression Miner (STEM) analysis revealed multiple expression patterns of mRNA, miRNA, and protein in the liver. Furthermore, several diverse key Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including immune defense, glycolipid metabolism, protein transport and uptake, and cell proliferation and development, were identified by combined analysis of DEGs and DGPs. A number of predicted miRNA–mRNA–protein pairs were found and validated by qRT-PCR and parallel reaction monitoring (PRM) assays. The results provide new and important information about the genetic breeding of Ningxiang pigs, which represents a foundation for further understanding the molecular regulatory mechanisms of dynamic development of liver tissue, functional transformation, and lipid metabolism.
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Affiliation(s)
- Biao Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Jinzeng Yang
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Yan Gong
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Yu Xiao
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Qinghua Zeng
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China.,Ningxiang Pig Farm of Dalong Livestock Technology Co., Ltd., Ningxiang, China
| | - Kang Xu
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agroecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences (CAS), Changsha, China
| | - Yehui Duan
- Laboratory of Animal Nutritional Physiology and Metabolic Process, Key Laboratory of Agroecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences (CAS), Changsha, China
| | - Jianhua He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Jun He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
| | - Haiming Ma
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, China
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Núñez-Acuña G, Valenzuela-Muñoz V, Valenzuela-Miranda D, Gallardo-Escárate C. Comprehensive Transcriptome Analyses in Sea Louse Reveal Novel Delousing Drug Responses Through MicroRNA regulation. Mar Biotechnol (NY) 2021; 23:710-723. [PMID: 34564738 DOI: 10.1007/s10126-021-10058-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
The role of miRNAs in pharmacological responses through gene regulation related to drug metabolism and the detoxification system has recently been determined for terrestrial species. However, studies on marine ectoparasites have scarcely been conducted to investigate the molecular mechanisms of pesticide resistance. Herein, we explored the sea louse Caligus rogercresseyi miRNome responses exposed to delousing drugs and the interplaying with coding/non-coding RNAs. Drug sensitivity in sea lice was tested by in vitro bioassays for the pesticides azamethiphos, deltamethrin, and cypermethrin. Ectoparasites strains with contrasting susceptibility to these compounds were used. Small-RNA sequencing was conducted, identifying 2776 novel annotated miRNAs, where 163 mature miRNAs were differentially expressed in response to the drug testing. Notably, putative binding sites for miRNAs were found in the ADME genes associated with the drugs' absorption, distribution, metabolism, and excretion. Interactions between the miRNAs and long non-coding RNAs (lncRNAs) were also found, suggesting putative molecular gene regulation mechanisms. This study reports putative miRNAs correlated to the coding/non-coding RNAs modulation, revealing novel pharmacological mechanisms associated with drug resistance in sea lice species.
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Affiliation(s)
- Gustavo Núñez-Acuña
- Interdisciplinary Center for Aquaculture Research, University of Concepción, O'Higgins 1695, Concepción, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Center of Biotechnology, Barrio Universitario S/N, Concepción, Chile
| | - Valentina Valenzuela-Muñoz
- Interdisciplinary Center for Aquaculture Research, University of Concepción, O'Higgins 1695, Concepción, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Center of Biotechnology, Barrio Universitario S/N, Concepción, Chile
| | - Diego Valenzuela-Miranda
- Interdisciplinary Center for Aquaculture Research, University of Concepción, O'Higgins 1695, Concepción, Chile
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Center of Biotechnology, Barrio Universitario S/N, Concepción, Chile
| | - Cristian Gallardo-Escárate
- Interdisciplinary Center for Aquaculture Research, University of Concepción, O'Higgins 1695, Concepción, Chile.
- Laboratory of Biotechnology and Aquatic Genomics, Department of Oceanography, Center of Biotechnology, Barrio Universitario S/N, Concepción, Chile.
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Zelli V, Compagnoni C, Capelli R, Corrente A, Cornice J, Vecchiotti D, Di Padova M, Zazzeroni F, Alesse E, Tessitore A. Emerging Role of isomiRs in Cancer: State of the Art and Recent Advances. Genes (Basel) 2021; 12:genes12091447. [PMID: 34573429 PMCID: PMC8469436 DOI: 10.3390/genes12091447] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 12/12/2022] Open
Abstract
The advent of Next Generation Sequencing technologies brought with it the discovery of several microRNA (miRNA) variants of heterogeneous lengths and/or sequences. Initially ascribed to sequencing errors/artifacts, these isoforms, named isomiRs, are now considered non-canonical variants that originate from physiological processes affecting the canonical miRNA biogenesis. To date, accurate IsomiRs abundance, biological activity, and functions are not completely understood; however, the study of isomiR biology is an area of great interest due to their high frequency in the human miRNome, their putative functions in cooperating with the canonical miRNAs, and potential for exhibiting novel functional roles. The discovery of isomiRs highlighted the complexity of the small RNA transcriptional landscape in several diseases, including cancer. In this field, the study of isomiRs could provide further insights into the miRNA biology and its implication in oncogenesis, possibly providing putative new cancer diagnostic, prognostic, and predictive biomarkers as well. In this review, a comprehensive overview of the state of research on isomiRs in different cancer types, including the most common tumors such as breast cancer, colorectal cancer, melanoma, and prostate cancer, as well as in the less frequent tumors, as for example brain tumors and hematological malignancies, will be summarized and discussed.
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Affiliation(s)
- Veronica Zelli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
- Center for Molecular Diagnostics and Advanced Therapies, University of L’Aquila, Via Petrini, 67100 L’Aquila, Italy
| | - Chiara Compagnoni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Roberta Capelli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Alessandra Corrente
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Jessica Cornice
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Davide Vecchiotti
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Monica Di Padova
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Francesca Zazzeroni
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Edoardo Alesse
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
| | - Alessandra Tessitore
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, Via Vetoio, 67100 L’Aquila, Italy; (V.Z.); (C.C.); (R.C.); (A.C.); (J.C.); (D.V.); (M.D.P.); (F.Z.); (E.A.)
- Center for Molecular Diagnostics and Advanced Therapies, University of L’Aquila, Via Petrini, 67100 L’Aquila, Italy
- Correspondence: ; Tel.: +39-0862433518; Fax: +39-0862433131
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23
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Pedroza DA, Ramirez M, Rajamanickam V, Subramani R, Margolis V, Gurbuz T, Estrada A, Lakshmanaswamy R. miRNome and Functional Network Analysis of PGRMC1 Regulated miRNA Target Genes Identify Pathways and Biological Functions Associated With Triple Negative Breast Cancer. Front Oncol 2021; 11:710337. [PMID: 34350123 PMCID: PMC8327780 DOI: 10.3389/fonc.2021.710337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 06/24/2021] [Indexed: 12/14/2022] Open
Abstract
Background Increased expression of the progesterone receptor membrane component 1, a heme and progesterone binding protein, is frequently found in triple negative breast cancer tissue. The basis for the expression of PGRMC1 and its regulation on cellular signaling mechanisms remain largely unknown. Therefore, we aim to study microRNAs that target selective genes and mechanisms that are regulated by PGRMC1 in TNBCs. Methods To identify altered miRNAs, whole human miRNome profiling was performed following AG-205 treatment and PGRMC1 silencing. Network analysis identified miRNA target genes while KEGG, REACTOME and Gene ontology were used to explore altered signaling pathways, biological processes, and molecular functions. Results KEGG term pathway analysis revealed that upregulated miRNAs target specific genes that are involved in signaling pathways that play a major role in carcinogenesis. While multiple downregulated miRNAs are known oncogenes and have been previously demonstrated to be overexpressed in a variety of cancers. Overlapping miRNA target genes associated with KEGG term pathways were identified and overexpression/amplification of these genes was observed in invasive breast carcinoma tissue from TCGA. Further, the top two genes (CCND1 and YWHAZ) which are highly genetically altered are also associated with poorer overall survival. Conclusions Thus, our data demonstrates that therapeutic targeting of PGRMC1 in aggressive breast cancers leads to the activation of miRNAs that target overexpressed genes and deactivation of miRNAs that have oncogenic potential.
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Affiliation(s)
- Diego A Pedroza
- Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
| | - Matthew Ramirez
- Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
| | - Venkatesh Rajamanickam
- Earle A. Chiles Research Institute, Providence Cancer Institute, Portland, OR, United States
| | - Ramadevi Subramani
- Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States.,Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
| | - Victoria Margolis
- Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
| | - Tugba Gurbuz
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
| | - Adriana Estrada
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
| | - Rajkumar Lakshmanaswamy
- Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States.,Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX, United States
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24
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Gonzalez TL, Eisman LE, Joshi NV, Flowers AE, Wu D, Wang Y, Santiskulvong C, Tang J, Buttle RA, Sauro E, Clark EL, DiPentino R, Jefferies CA, Chan JL, Lin Y, Zhu Y, Afshar Y, Tseng HR, Taylor K, Williams J, Pisarska MD. High-throughput miRNA sequencing of the human placenta: expression throughout gestation. Epigenomics 2021; 13:995-1012. [PMID: 34030457 PMCID: PMC8244582 DOI: 10.2217/epi-2021-0055] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/29/2021] [Indexed: 12/11/2022] Open
Abstract
Aim: To understand miRNA changes across gestation in healthy human placentae. This is essential before miRNAs can be used as biomarkers or prognostic indicators during pregnancy. Materials & methods: Using next-generation sequencing, we characterize the normative human placenta miRNome in first (n = 113) and third trimester (n = 47). Results & conclusion: There are 801 miRNAs expressed in both first and third trimester, including 182 with similar expression across gestation (p ≥ 0.05, fold change ≤2) and 180 significantly different (false discovery rate <0.05, fold change >2). Of placenta-specific miRNA clusters, chromosome 14 miRNA cluster decreases across gestation and chromosome 19 miRNA cluster is overall highly expressed. Chromosome 13 clusters are upregulated in first trimester. This work provides a rich atlas of healthy pregnancies to direct functional studies investigating the epigenetic differences in first and third trimester placentae.
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Affiliation(s)
- Tania L Gonzalez
- Department of Obstetrics & Gynecology, Center for Reproductive Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Laura E Eisman
- Department of Obstetrics & Gynecology, Center for Reproductive Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Nikhil V Joshi
- Department of Obstetrics & Gynecology, Center for Reproductive Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Amy E Flowers
- Department of Obstetrics & Gynecology, Center for Reproductive Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Di Wu
- Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Yizhou Wang
- Genomics Core, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Chintda Santiskulvong
- CS Cancer Applied Genomics Shared Resource, CS Cancer, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jie Tang
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Rae A Buttle
- Department of Obstetrics & Gynecology, Center for Reproductive Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Erica Sauro
- Department of Obstetrics & Gynecology, Center for Reproductive Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Ekaterina L Clark
- Department of Obstetrics & Gynecology, Center for Reproductive Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Rosemarie DiPentino
- Department of Obstetrics & Gynecology, Center for Reproductive Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Caroline A Jefferies
- Division of Rheumatology, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jessica L Chan
- Department of Obstetrics & Gynecology, Center for Reproductive Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Yayu Lin
- Department of Obstetrics & Gynecology, Center for Reproductive Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Yazhen Zhu
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular & Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
| | - Yalda Afshar
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Hsian-Rong Tseng
- California NanoSystems Institute, Crump Institute for Molecular Imaging, Department of Molecular & Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
| | - Kent Taylor
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- The Institute for Translational Genomics & Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - John Williams
- Department of Obstetrics & Gynecology, Center for Reproductive Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Margareta D Pisarska
- Department of Obstetrics & Gynecology, Center for Reproductive Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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25
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Soffritti I, D'Accolti M, Ravegnini G, Arcangeletti MC, Maccari C, De Conto F, Calderaro A, Caselli E. Modulation of microRNome by Human Cytomegalovirus and Human Herpesvirus 6 Infection in Human Dermal Fibroblasts: Possible Significance in the Induction of Fibrosis in Systemic Sclerosis. Cells 2021; 10:1060. [PMID: 33946985 DOI: 10.3390/cells10051060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 02/07/2023] Open
Abstract
Human cytomegalovirus (HCMV) and Human herpesvirus 6 (HHV-6) have been reportedly suggested as triggers of the onset and/or progression of systemic sclerosis (SSc), a severe autoimmune disorder characterized by multi-organ fibrosis. The etiology and pathogenesis of SSc are still largely unknown but virological and immunological observations support a role for these beta-herpesviruses, and we recently observed a direct impact of HCMV and HHV-6 infection on the expression of cell factors associated with fibrosis at the cell level. Since miRNA expression has been found profoundly deregulated at the tissue level, here we aimed to investigate the impact on cell microRNome (miRNome) of HCMV and HHV-6 infection in in vitro infected primary human dermal fibroblasts, which represent one of the main SSc target cells. The analysis, performed by Taqman arrays detecting and quantifying 754 microRNAs (miRNAs), showed that both herpesviruses significantly modulated miRNA expression in infected cells, with evident early and late effects and deep modulation (>10 fold) of >40 miRNAs at each time post infection, including those previously recognized for their key function in fibrosis. The correlation between these in vitro results with in vivo observations is strongly suggestive of a role of HCMV and/or HHV-6 in the multistep pathogenesis of fibrosis in SSc and in the induction of fibrosis-signaling pathways finally leading to tissue fibrosis. The identification of specific miRNAs may open the way to their use as biomarkers for SSc diagnosis, assessment of disease progression and possible antifibrotic therapies.
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26
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Li C, Lu L, Qi Z, Zhu Y, Su F, Zhao P, Dong H. Transcriptome and miRNome Analysis Provide New Insight Into Host Lipid Accumulation, Innate Immunity, and Viral Persistence in Hepatitis C Virus Infection in vitro. Front Microbiol 2020; 11:535673. [PMID: 33101221 PMCID: PMC7555709 DOI: 10.3389/fmicb.2020.535673] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 09/14/2020] [Indexed: 12/17/2022] Open
Abstract
Hepatitis C virus (HCV)-host cell interaction during infection disturbs cellular homeostasis and culminates in pathological consequences. The processes could be first embodied in gene expression of HCV-infected cells. Here, we investigated transcriptome and miRNA expression (miRNome) alterations in HCV-infected Huh7 cells at 12, 36, and 60 h after infection to systematically explore host responses. The number of deregulated genes in the HCV-infected cells increased with infection duration. The altered biological processes at 36 h were mainly associated with stress and inflammatory response, whereas the most enriched processes at 60 h were predominantly linked to lipid metabolism. Notably, the key genes that participated in lipogenesis were downregulated, and conversely, the genes implicated in fatty acid beta-oxidation were upregulated. Reduced expression of the key genes involved in lipoprotein assembly and secretion pointed to a decreased requirement for and export of lipids, leading to lipid accumulation in HCV-infected hepatocytes. Fluctuation in the expression of host factors, innate immunity genes and transcription factors provided insight into host-directed mechanisms to control viral replication. Furthermore, miRNome presented a comprehensive expression profile of miRNAs in HCV-infected Huh7 cells. The integrated analysis of transcriptome and miRNome suggested that deregulated miR-483, miR-1303, miR-1260a, miR-27a∗, and miR-21∗ directly regulated lipid metabolical genes at 60 h. The decreased miR-122 at 60 h was indirectly involved in lipid metabolism and is expected to attenuate rampant replication of HCV and potentially contribute to viral persistence. Our results will help to gain a comprehensive understanding of the molecular mechanisms implicated in HCV-induced pathogenesis.
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Affiliation(s)
- Chong Li
- Cancer Institute, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lungen Lu
- Shanghai Key Laboratory of Pancreatic Diseases, Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhongtian Qi
- Department of Microbiology, Second Military Medical University, Shanghai, China
| | - Yongqiang Zhu
- Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Fengtao Su
- Cancer Institute, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ping Zhao
- Department of Microbiology, Second Military Medical University, Shanghai, China
| | - Hui Dong
- Shanghai Key Laboratory of Pancreatic Diseases, Department of Gastroenterology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Ayala-Suárez R, Díez-Fuertes F, Calonge E, De La Torre Tarazona HE, Gracia-Ruíz de Alda M, Capa L, Alcamí J. Insight in miRNome of Long-Term Non-Progressors and Elite Controllers Exposes Potential RNAi Role in Restraining HIV-1 Infection. J Clin Med 2020; 9:jcm9082452. [PMID: 32751854 PMCID: PMC7464121 DOI: 10.3390/jcm9082452] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/17/2020] [Accepted: 07/29/2020] [Indexed: 12/14/2022] Open
Abstract
Long-term non-progressors (LTNP) and elite controllers (EC) represent spontaneous natural models of efficient HIV-1 response in the absence of treatment. The main purposes of this work are to describe the miRNome of HIV-1 infected patients with different extreme phenotypes and identify potentially altered pathways regulated by differentially expressed (DE) miRNAs. The miRNomes from peripheral blood mononuclear cells (PBMCs) of dual phenotype EC-LTNP or LTNP with detectable viremia and HIV-infected patients with typical progression before and after treatment, were obtained through miRNA-Seq and compared among them. The administration of treatment produces 18 DE miRNAs in typical progressors. LTNP condition shows 14 DE miRNA when compared to typical progressors, allowing LTNP phenotype differentiation. A set of four miRNAs: miR-144-3p, miR-18a-5p, miR-451a, and miR-324 is strongly downregulated in LTNP and related to protein regulation as AKT, mTOR, ERK or IKK, involved in immune response pathways. Deregulation of 28 miRNA is observed between EC-LTNP and viremic-LTNP, including previously described anti-HIV miRNAs: miR-29a, associated with LTNP phenotype, and miR-155, targeting different pre-integration complexes such as ADAM10 and TNPO3. A holistic perspective of the changes observed in the miRNome of patients with different phenotypes of HIV-control and non-progression is provided.
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Affiliation(s)
- Rubén Ayala-Suárez
- AIDS Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, 28220 Madrid, Spain; (R.A.-S.); (E.C.); (H.E.D.L.T.T.); (L.C.)
| | - Francisco Díez-Fuertes
- AIDS Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, 28220 Madrid, Spain; (R.A.-S.); (E.C.); (H.E.D.L.T.T.); (L.C.)
- HIV Unit, Hospital Clínic de Barcelona, 08036 Barcelona, Spain
- Correspondence: (F.D.-F.); (J.A.); Tel.: +34-91-822-3234 (F.D.-F.); +34-91-822-3943 (J.A.)
| | - Esther Calonge
- AIDS Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, 28220 Madrid, Spain; (R.A.-S.); (E.C.); (H.E.D.L.T.T.); (L.C.)
| | - Humberto Erick De La Torre Tarazona
- AIDS Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, 28220 Madrid, Spain; (R.A.-S.); (E.C.); (H.E.D.L.T.T.); (L.C.)
| | - María Gracia-Ruíz de Alda
- Sección de Enfermedades Infecciosas, Medicina Interna, Complejo Hospitalario de Navarra, 31008 Pamplona, Spain;
| | - Laura Capa
- AIDS Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, 28220 Madrid, Spain; (R.A.-S.); (E.C.); (H.E.D.L.T.T.); (L.C.)
| | - José Alcamí
- AIDS Immunopathology Unit, National Center for Microbiology, Institute of Health Carlos III, Majadahonda, 28220 Madrid, Spain; (R.A.-S.); (E.C.); (H.E.D.L.T.T.); (L.C.)
- HIV Unit, Hospital Clínic de Barcelona, 08036 Barcelona, Spain
- Correspondence: (F.D.-F.); (J.A.); Tel.: +34-91-822-3234 (F.D.-F.); +34-91-822-3943 (J.A.)
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28
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Walbrecq G, Lecha O, Gaigneaux A, Fougeras MR, Philippidou D, Margue C, Tetsi Nomigni M, Bernardin F, Dittmar G, Behrmann I, Kreis S. Hypoxia-Induced Adaptations of miRNomes and Proteomes in Melanoma Cells and Their Secreted Extracellular Vesicles. Cancers (Basel) 2020; 12:cancers12030692. [PMID: 32183388 PMCID: PMC7140034 DOI: 10.3390/cancers12030692] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 03/12/2020] [Indexed: 12/13/2022] Open
Abstract
Reduced levels of intratumoural oxygen are associated with hypoxia-induced pro-oncogenic events such as invasion, metabolic reprogramming, epithelial–mesenchymal transition, metastasis and resistance to therapy, all favouring cancer progression. Small extracellular vesicles (EV) shuttle various cargos (proteins, miRNAs, DNA and others). Tumour-derived EVs can be taken up by neighbouring or distant cells in the tumour microenvironment, thus facilitating intercellular communication. The quantity of extracellular vesicle secretion and their composition can vary with changing microenvironmental conditions and disease states. Here, we investigated in melanoma cells the influence of hypoxia on the content and number of secreted EVs. Whole miRNome and proteome profiling revealed distinct expression patterns in normoxic or hypoxic growth conditions. Apart from the well-known miR-210, we identified miR-1290 as a novel hypoxia-associated microRNA, which was highly abundant in hypoxic EVs. On the other hand, miR-23a-5p and -23b-5p were consistently downregulated in hypoxic conditions, while the protein levels of the miR-23a/b-5p-predicted target IPO11 were concomitantly upregulated. Furthermore, hypoxic melanoma EVs exhibit a signature consisting of six proteins (AKR7A2, DDX39B, EIF3C, FARSA, PRMT5, VARS), which were significantly associated with a poor prognosis for melanoma patients, indicating that proteins and/or miRNAs secreted by cancer cells may be exploited as biomarkers.
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Affiliation(s)
- Geoffroy Walbrecq
- Department of Life Sciences and Medicine, University of Luxembourg, 6, avenue du Swing, L-4367 Belvaux, Luxembourg; (G.W.); (O.L.); (A.G.); (D.P.); (C.M.); (M.T.N.); (G.D.); (I.B.)
| | - Odile Lecha
- Department of Life Sciences and Medicine, University of Luxembourg, 6, avenue du Swing, L-4367 Belvaux, Luxembourg; (G.W.); (O.L.); (A.G.); (D.P.); (C.M.); (M.T.N.); (G.D.); (I.B.)
| | - Anthoula Gaigneaux
- Department of Life Sciences and Medicine, University of Luxembourg, 6, avenue du Swing, L-4367 Belvaux, Luxembourg; (G.W.); (O.L.); (A.G.); (D.P.); (C.M.); (M.T.N.); (G.D.); (I.B.)
| | - Miriam R. Fougeras
- Proteomics of Cellular Signaling, Quantitative Biology Unit, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, L-1445 Strassen, Luxembourg; (M.R.F.)
- Doctoral School in Science and Engineering (DSSE), Faculty of Science, Technology and Medicine, University of Luxembourg, 2 avenue de l’Université, L-4365 Esch-sur-Alzette, Luxembourg
| | - Demetra Philippidou
- Department of Life Sciences and Medicine, University of Luxembourg, 6, avenue du Swing, L-4367 Belvaux, Luxembourg; (G.W.); (O.L.); (A.G.); (D.P.); (C.M.); (M.T.N.); (G.D.); (I.B.)
| | - Christiane Margue
- Department of Life Sciences and Medicine, University of Luxembourg, 6, avenue du Swing, L-4367 Belvaux, Luxembourg; (G.W.); (O.L.); (A.G.); (D.P.); (C.M.); (M.T.N.); (G.D.); (I.B.)
| | - Milène Tetsi Nomigni
- Department of Life Sciences and Medicine, University of Luxembourg, 6, avenue du Swing, L-4367 Belvaux, Luxembourg; (G.W.); (O.L.); (A.G.); (D.P.); (C.M.); (M.T.N.); (G.D.); (I.B.)
| | - François Bernardin
- Proteomics of Cellular Signaling, Quantitative Biology Unit, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, L-1445 Strassen, Luxembourg; (M.R.F.)
| | - Gunnar Dittmar
- Department of Life Sciences and Medicine, University of Luxembourg, 6, avenue du Swing, L-4367 Belvaux, Luxembourg; (G.W.); (O.L.); (A.G.); (D.P.); (C.M.); (M.T.N.); (G.D.); (I.B.)
- Proteomics of Cellular Signaling, Quantitative Biology Unit, Luxembourg Institute of Health, 1A-B, rue Thomas Edison, L-1445 Strassen, Luxembourg; (M.R.F.)
| | - Iris Behrmann
- Department of Life Sciences and Medicine, University of Luxembourg, 6, avenue du Swing, L-4367 Belvaux, Luxembourg; (G.W.); (O.L.); (A.G.); (D.P.); (C.M.); (M.T.N.); (G.D.); (I.B.)
| | - Stephanie Kreis
- Department of Life Sciences and Medicine, University of Luxembourg, 6, avenue du Swing, L-4367 Belvaux, Luxembourg; (G.W.); (O.L.); (A.G.); (D.P.); (C.M.); (M.T.N.); (G.D.); (I.B.)
- Correspondence:
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Neou M, Villa C, Armignacco R, Jouinot A, Raffin-Sanson ML, Septier A, Letourneur F, Diry S, Diedisheim M, Izac B, Gaspar C, Perlemoine K, Verjus V, Bernier M, Boulin A, Emile JF, Bertagna X, Jaffrezic F, Laloe D, Baussart B, Bertherat J, Gaillard S, Assié G. Pangenomic Classification of Pituitary Neuroendocrine Tumors. Cancer Cell 2020; 37:123-134.e5. [PMID: 31883967 DOI: 10.1016/j.ccell.2019.11.002] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 10/07/2019] [Accepted: 11/21/2019] [Indexed: 12/14/2022]
Abstract
Pituitary neuroendocrine tumors (PitNETs) are common, with five main histological subtypes: lactotroph, somatotroph, and thyrotroph (POU1F1/PIT1 lineage); corticotroph (TBX19/TPIT lineage); and gonadotroph (NR5A1/SF1 lineage). We report a comprehensive pangenomic classification of PitNETs. PitNETs from POU1F1/PIT1 lineage showed an epigenetic signature of diffuse DNA hypomethylation, with transposable elements expression and chromosomal instability (except for GNAS-mutated somatotrophs). In TPIT lineage, corticotrophs were divided into three classes: the USP8-mutated with overt secretion, the USP8-wild-type with increased invasiveness and increased epithelial-mesenchymal transition, and the large silent tumors with gonadotroph transdifferentiation. Unexpected expression of gonadotroph markers was also found in GNAS-wild-type somatotrophs (SF1 expression), challenging the current definition of SF1/gonadotroph lineage. This classification improves our understanding and affects the clinical stratification of patients with PitNETs.
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Affiliation(s)
- Mario Neou
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes-Université de Paris, 75006 Paris, France
| | - Chiara Villa
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes-Université de Paris, 75006 Paris, France; Department of Pathological Cytology and Anatomy, Foch Hospital, 92151 Suresnes, France; Department of Endocrinology, Sart Tilman B35, 4000 Liège, Belgium
| | - Roberta Armignacco
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes-Université de Paris, 75006 Paris, France
| | - Anne Jouinot
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes-Université de Paris, 75006 Paris, France
| | - Marie-Laure Raffin-Sanson
- Department of Endocrinology, Hôpital Ambroise Paré, Assistance Publique-Hôpitaux de Paris, 92100 Boulogne Billancourt, France; UE4340, Université de Versailles Saint-Quentin-en-Yvelines Montigny-le-Bretonneux, 78000 Versailles, France
| | - Amandine Septier
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes-Université de Paris, 75006 Paris, France
| | - Franck Letourneur
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes-Université de Paris, 75006 Paris, France; Plate-Forme Séquençage et Génomique (Genom'IC), INSERM U1016, Institut Cochin, 75014 Paris, France
| | - Ségolène Diry
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes-Université de Paris, 75006 Paris, France
| | - Marc Diedisheim
- Department of Diabetology, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, 75014 Paris, France
| | - Brigitte Izac
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes-Université de Paris, 75006 Paris, France; Plate-Forme Séquençage et Génomique (Genom'IC), INSERM U1016, Institut Cochin, 75014 Paris, France
| | - Cassandra Gaspar
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes-Université de Paris, 75006 Paris, France; Sorbonne Université, Inserm, UMS PASS, Plateforme Post-génomique de la Pitié-Salpêtrière, P3S, 75013 Paris, France
| | - Karine Perlemoine
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes-Université de Paris, 75006 Paris, France
| | - Victoria Verjus
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes-Université de Paris, 75006 Paris, France
| | - Michèle Bernier
- Department of Pathological Cytology and Anatomy, Foch Hospital, 92151 Suresnes, France
| | - Anne Boulin
- Department of Diagnostic and Interventional Neuroradiology, Foch Hospital, 92151 Suresnes, France
| | - Jean-François Emile
- Department of Pathology, Ambroise Paré, Assistance Publique-Hôpitaux de Paris, 92100 Boulogne Billancourt, France
| | - Xavier Bertagna
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes-Université de Paris, 75006 Paris, France; Department of Endocrinology, Center for Rare Adrenal Diseases, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, 75014 Paris, France
| | - Florence Jaffrezic
- INRA, UMR 1313 GABI, Université Paris Saclay, AgroParisTech, 78352 Jouy-en-Josas, France
| | - Denis Laloe
- INRA, UMR 1313 GABI, Université Paris Saclay, AgroParisTech, 78352 Jouy-en-Josas, France
| | | | - Jérôme Bertherat
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes-Université de Paris, 75006 Paris, France; Department of Endocrinology, Center for Rare Adrenal Diseases, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, 75014 Paris, France
| | - Stephan Gaillard
- Department of Neurosurgery, Foch Hospital, 92151 Suresnes, France
| | - Guillaume Assié
- INSERM U1016, Institut Cochin, 75014 Paris, France; CNRS UMR 8104, 75014 Paris, France; Université Paris Descartes-Université de Paris, 75006 Paris, France; Department of Endocrinology, Center for Rare Adrenal Diseases, Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, 75014 Paris, France.
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Aydinoglu F. Elucidating the regulatory roles of microRNAs in maize (Zea mays L.) leaf growth response to chilling stress. Planta 2020; 251:38. [PMID: 31907623 DOI: 10.1007/s00425-019-03331-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/18/2019] [Indexed: 05/18/2023]
Abstract
MAIN CONCLUSION: miRNAs control leaf size of maize crop during chilling stress tolerance by regulating developmentally important transcriptional factors and sustaining redox homeostasis of cells. Chilling temperature (0-15 °C) is a major constraint for the cultivation of maize (Zea mays) which inhibits the early growth of maize leading to reduction in leaf size. Growth and development take place in meristem, elongation, and mature zones that are linearly located along the leaf base to tip. To prevent shortening of leaf caused by chilling, this study aims to elucidate the regulatory roles of microRNA (miRNA) genes in the controlling process switching between growth and developmental stages. In this respect, hybrid maize ADA313 seedlings were treated to the chilling temperature which caused 26% and 29% reduction in the final leaf length and a decline in cell production of the fourth leaf. The flow cytometry data integrated with the expression analysis of cell cycle genes indicated that the reason for the decline was a failure proceeding from G2/M rather than G1/S. Through an miRNome analysis of 321 known maize miRNAs, 24, 6, and 20 miRNAs were assigned to putative meristem, elongation, and mature zones, respectively according to their chilling response. To gain deeper insight into decreased cell production, in silico, target prediction analysis was performed for meristem specific miRNAs. Among the miRNAs, miR160, miR319, miR395, miR396, miR408, miR528, and miR1432 were selected for confirming the potential of negative regulation with their predicted targets by qRT-PCR. These findings indicated evidence for improvement of growth and yield under chilling stress of the maize.
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Affiliation(s)
- Fatma Aydinoglu
- Molecular Biology and Genetics Department, Gebze Technical University, Kocaeli, Turkey.
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31
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Gasiulė S, Dreize N, Kaupinis A, Ražanskas R, Čiupas L, Stankevičius V, Kapustina Ž, Laurinavičius A, Valius M, Vilkaitis G. Molecular Insights into miRNA-Driven Resistance to 5-Fluorouracil and Oxaliplatin Chemotherapy: miR-23b Modulates the Epithelial–Mesenchymal Transition of Colorectal Cancer Cells. J Clin Med 2019; 8:E2115. [PMID: 31810268 DOI: 10.3390/jcm8122115] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 02/07/2023] Open
Abstract
Although treatment of colorectal cancer with 5-florouracil and oxaliplatin is widely used, it is frequently followed by a relapse. Therefore, there is an urgent need for profound understanding of chemotherapy resistance mechanisms as well as the profiling of predictive markers for individualized treatment. In this study, we identified the changes in 14 miRNAs in 5-fluouracil and 40 miRNAs in oxaliplatin-resistant cell lines by miRNA sequencing. The decrease in miR-224-5p expression in the 5-fluorouracil-resistant cells correlated with drug insensitivity due to its overexpression-induced drug-dependent apoptosis. On the other hand, the miR-23b/27b/24-1 cluster was overexpressed in oxaliplatin-resistant cells. The knockout of miR-23b led to the partial restoration of oxaliplatin susceptibility, showing the essential role of miR-23b in the development of drug resistance by this cluster. Proteomic analysis identified target genes of miR-23b and showed that endothelial–mesenchymal transition (EMT) was implicated in oxaliplatin insensibility. Data revealed that EMT markers, such as vimentin and SNAI2, were expressed moderately higher in the oxaliplatin-resistant cells and their expression increased further in the less drug-resistant cells, which had miR-23b knockout. This establishes that the balance of EMT contributes to the drug resistance, showing the importance of the miR-23b-mediated fine-tuning of EMT in oxaliplatin-resistant cancer cells.
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Pereira A, Moreira F, Vinasco-Sandoval T, Cunha A, Vidal A, Ribeiro-dos-Santos AM, Pinto P, Magalhães L, Assumpção M, Demachki S, Santos S, Assumpção P, Ribeiro-dos-Santos Â. miRNome Reveals New Insights Into the Molecular Biology of Field Cancerization in Gastric Cancer. Front Genet 2019; 10:592. [PMID: 31275362 PMCID: PMC6593062 DOI: 10.3389/fgene.2019.00592] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 06/04/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) play an important role in gastric carcinogenesis and have been associated with gastric field cancerization; however, their role is not fully understood in this process. We performed the miRNome sequencing of non-cancerous, adjacent to tumor and gastric cancer samples to understand the involvement of these small RNAs in gastric field cancerization. METHODS We analyzed samples of patients without cancer as control (non-cancerous gastric samples) and adjacent to cancer and gastric cancer paired samples, and considered miRNAs with |log2(fold change)| > 2 and Padj < 0.05 to be statistically significant. The identification of target genes, functional analysis and enrichment in KEGG pathways were realized in the TargetCompare, miRTargetLink, and DAVID tools. We also performed receiver operating characteristic (ROC) curves and miRNAs that had an AUC > 0.85 were considered to be potential biomarkers. RESULTS We found 14 miRNAs exclusively deregulated in gastric cancer, of which six have potential diagnostic value for advanced disease. Nine miRNAs with known tumor suppressor activities (TS-miRs) were deregulated exclusively in adjacent tissue. Of these, five have potential diagnostic value for the early stages of gastric cancer. Functional analysis of these TS-miRs revealed that they regulate important cellular signaling pathways (PI3K-Akt, HIF-1, Ras, Rap1, ErbB, and MAPK signaling pathways), that are involved in gastric carcinogenesis. Seven miRNAs were differentially expressed in both gastric cancer and adjacent regarding to non-cancerous tissues; among them, hsa-miR-200a-3p and hsa-miR-873-5p have potential diagnostic value for early and advanced stages of the disease. Only hsa-miR-196a-5p was differentially expressed between adjacent to cancer and gastric cancer tissues. In addition, the other miRNAs identified in this study were not differentially expressed between adjacent to cancer and gastric cancer, suggesting that these tissues are very similar and that share these molecular changes. CONCLUSION Our results show that gastric cancer and adjacent tissues have a similar miRNA expression profile, indicating that studied miRNAs are intimately associated with field cancerization in gastric cancer. The overexpression of TS-miRs in adjacent tissues may be a barrier against tumorigenesis within these pre-cancerous conditions prior to the eventual formation or relapse of a tumor. Additionally, these miRNAs have a great accuracy in discriminating non-cancerous from adjacent to tumor and cancer tissues and can be potentially useful as biomarkers for gastric cancer.
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Affiliation(s)
- Adenilson Pereira
- Laboratory of Human and Medical Genetics, Institute of Biological Sciences, Graduate Program of Genetics and Molecular Biology, Federal University of Pará, Belém, Brazil
- Research Center on Oncology, Graduate Program of Oncology and Medical Science, Federal University of Pará, Belém, Brazil
| | - Fabiano Moreira
- Laboratory of Human and Medical Genetics, Institute of Biological Sciences, Graduate Program of Genetics and Molecular Biology, Federal University of Pará, Belém, Brazil
- Research Center on Oncology, Graduate Program of Oncology and Medical Science, Federal University of Pará, Belém, Brazil
| | - Tatiana Vinasco-Sandoval
- Research Center on Oncology, Graduate Program of Oncology and Medical Science, Federal University of Pará, Belém, Brazil
| | - Adenard Cunha
- Research Center on Oncology, Graduate Program of Oncology and Medical Science, Federal University of Pará, Belém, Brazil
| | - Amanda Vidal
- Research Center on Oncology, Graduate Program of Oncology and Medical Science, Federal University of Pará, Belém, Brazil
| | - André M. Ribeiro-dos-Santos
- Laboratory of Human and Medical Genetics, Institute of Biological Sciences, Graduate Program of Genetics and Molecular Biology, Federal University of Pará, Belém, Brazil
| | - Pablo Pinto
- Laboratory of Human and Medical Genetics, Institute of Biological Sciences, Graduate Program of Genetics and Molecular Biology, Federal University of Pará, Belém, Brazil
| | - Leandro Magalhães
- Laboratory of Human and Medical Genetics, Institute of Biological Sciences, Graduate Program of Genetics and Molecular Biology, Federal University of Pará, Belém, Brazil
| | - Mônica Assumpção
- Research Center on Oncology, Graduate Program of Oncology and Medical Science, Federal University of Pará, Belém, Brazil
| | - Samia Demachki
- Research Center on Oncology, Graduate Program of Oncology and Medical Science, Federal University of Pará, Belém, Brazil
| | - Sidney Santos
- Laboratory of Human and Medical Genetics, Institute of Biological Sciences, Graduate Program of Genetics and Molecular Biology, Federal University of Pará, Belém, Brazil
- Research Center on Oncology, Graduate Program of Oncology and Medical Science, Federal University of Pará, Belém, Brazil
| | - Paulo Assumpção
- Research Center on Oncology, Graduate Program of Oncology and Medical Science, Federal University of Pará, Belém, Brazil
| | - Ândrea Ribeiro-dos-Santos
- Laboratory of Human and Medical Genetics, Institute of Biological Sciences, Graduate Program of Genetics and Molecular Biology, Federal University of Pará, Belém, Brazil
- Research Center on Oncology, Graduate Program of Oncology and Medical Science, Federal University of Pará, Belém, Brazil
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Lee S, Temple FT, Dawson PA. Kidney microRNA profile in pregnant mice reveals molecular insights into kidney adaptation to pregnancy: A pilot study. Mol Genet Metab Rep 2019; 20:100486. [PMID: 31249785 PMCID: PMC6587019 DOI: 10.1016/j.ymgmr.2019.100486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 06/12/2019] [Indexed: 02/06/2023] Open
Abstract
The maternal kidneys undergo numerous physiological changes during pregnancy to maintain a healthy pregnancy for mother and child. Over the past decade, interest in microRNAs (miRNAs) for regulating gene expression during pregnancy has expanded. However, the role of miRNAs in modulating kidney physiology during pregnancy has not been extensively investigated. In this study, miRNome profiling suggested differential expression of 163 miRNAs (of 887 miRNAs detected) in the kidneys from pregnant mice at 6.5 days gestation when compared to non-pregnant female mice, of which 35 and 128 miRNAs were potentially down- and up-regulated, respectively. We performed network and pathway analyses of the >1700 potential mRNA targets of the differentially expressed miRNAs using MiRNet, Gene Ontology, Reactome and KEGG analyses. The mRNA targets were over-represented in numerous cellular signalling pathways, including cellular protective responses. In addition, we explored 13 and 29 potential differentially expressed miRNAs to have putative binding sites in the Slc13a1 and Slc26a1 sulfate transporter mRNAs, respectively, and that decreased levels of mir-466k may potentially explain the increased expression of these sulfate transporters in early mouse gestation. Collectively, this study suggests altered expression levels of miRNAs during mouse gestation, which provides pilot data for future investigations into the molecular events that modulate kidney adaptsation to pregnancy.
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Affiliation(s)
- Soohyun Lee
- Mater Research Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Fergal Thomas Temple
- Mater Research Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Paul Anthony Dawson
- Mater Research Institute, University of Queensland, Brisbane, Queensland, Australia
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Logotheti S, Marquardt S, Pützer BM. p73-Governed miRNA Networks: Translating Bioinformatics Approaches to Therapeutic Solutions for Cancer Metastasis. Methods Mol Biol 2019; 1912:33-52. [PMID: 30635889 DOI: 10.1007/978-1-4939-8982-9_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The transcription factor p73 synthesizes a large number of isoforms and presents high structural and functional homology with p53, a well-known tumor suppressor and a famous "Holy Grail" of anticancer targeting. p73 has attracted increasing attention mainly because (a) unlike p53, p73 is rarely mutated in cancer, (b) some p73 isoforms can inhibit all hallmarks of cancer, and (c) it has the ability to mimic oncosuppressive functions of p53, even in p53-mutated cells. These attributes render p73 and its downstream pathways appealing for therapeutic targeting, especially in mutant p53-driven cancers. p73 functions are, at least partly, mediated by microRNAs (miRNAs), which constitute nodal components of p73-governed networks. p73 not only regulates transcription of crucial miRNA genes, but is also predicted to affect miRNA populations in a transcription-independent manner by developing protein-protein interactions with components of the miRNA processing machinery. This combined effect of p73, both in miRNA transcription and maturation, appears to be isoform-dependent and can result in a systemic switch of cell miRNomes toward either an anti-oncogenic or oncogenic outcome. In this review, we combine literature search with bioinformatics approaches to reconstruct the p73-governed miRNA network and discuss how these crosstalks may be exploited to develop next-generation therapeutics.
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Denham J, Gray AJ, Scott-Hamilton J, Hagstrom AD, Murphy AJ. Small non-coding RNAs are altered by short-term sprint interval training in men. Physiol Rep 2019; 6:e13653. [PMID: 29611322 PMCID: PMC5880879 DOI: 10.14814/phy2.13653] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 02/22/2018] [Accepted: 02/23/2018] [Indexed: 12/17/2022] Open
Abstract
Small non-coding RNAs (ncRNAs) are emerging as important molecules for normal biological processes and are deregulated in disease. Exercise training is a powerful therapeutic strategy that prevents cardiometabolic disease and improves cardiorespiratory fitness and performance. Despite the known systemic health benefits of exercise training, the underlying molecular mechanisms are incompletely understood. Recent evidence suggests a role for epigenetic mechanisms, such as microRNAs, but whether other small ncRNAs are modulated by chronic exercise training is unknown. Here, we used small RNA sequencing to explore whether sprint interval training (SIT) controls the abundance of circulating small ncRNAs in human whole blood samples. Ten healthy men performed SIT three times a week for 6 weeks. After training, subjects showed marked improvements in maximal oxygen consumption and cycling performance with concurrent changes to the abundance of diverse species of circulating small ncRNAs (n = 1266 small ncRNAs, n = 13 microRNAs, q < 0.05). Twelve microRNAs altered by 6 weeks of SIT were ubiquitously expressed microRNAs and two regulated important signaling pathways, including p53, thyroid hormone and cell cycle signaling. MicroRNAs altered by 6 weeks of SIT were unchanged after a single session of SIT (n = 24, all P > 0.05). Relative to older individuals, younger subjects exhibited an increased acute SIT-induced fold change in miR-1301-3p (P = 0.02) - a microRNA predicted to target mRNAs involved in alternative splicing, phosphoprotein and chromosomal rearrangement processes (all P < 0.001). Our findings indicate many species of circulating small ncRNAs are modulated by exercise training and that they could control signaling pathways responsible for health benefits achieved from exercise.
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Affiliation(s)
- Joshua Denham
- School of Science and Technology, University of New England, Armidale, New South Wales, Australia
| | - Adrian J Gray
- School of Science and Technology, University of New England, Armidale, New South Wales, Australia
| | - John Scott-Hamilton
- School of Health, University of New England, Armidale, New South Wales, Australia
| | - Amanda D Hagstrom
- School of Science and Technology, University of New England, Armidale, New South Wales, Australia
| | - Aron J Murphy
- School of Science and Technology, University of New England, Armidale, New South Wales, Australia.,School of Environmental and Rural Science, University of New England, Armidale, New South Wales, Australia
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Almenar-Pérez E, Sánchez-Fito T, Ovejero T, Nathanson L, Oltra E. Impact of Polypharmacy on Candidate Biomarker miRNomes for the Diagnosis of Fibromyalgia and Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: Striking Back on Treatments. Pharmaceutics 2019; 11:pharmaceutics11030126. [PMID: 30889846 PMCID: PMC6471415 DOI: 10.3390/pharmaceutics11030126] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 02/26/2019] [Accepted: 03/05/2019] [Indexed: 12/14/2022] Open
Abstract
Fibromyalgia (FM) and myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) are diseases of unknown etiology presenting complex and often overlapping symptomatology. Despite promising advances on the study of miRNomes of these diseases, no validated molecular diagnostic biomarker yet exists. Since FM and ME/CFS patient treatments commonly include polypharmacy, it is of concern that biomarker miRNAs are masked by drug interactions. Aiming at discriminating between drug-effects and true disease-associated differential miRNA expression, we evaluated the potential impact of commonly prescribed drugs on disease miRNomes, as reported by the literature. By using the web search tools SM2miR, Pharmaco-miR, and repoDB, we found a list of commonly prescribed drugs that impact FM and ME/CFS miRNomes and therefore could be interfering in the process of biomarker discovery. On another end, disease-associated miRNomes may incline a patient’s response to treatment and toxicity. Here, we explored treatments for diseases in general that could be affected by FM and ME/CFS miRNomes, finding a long list of them, including treatments for lymphoma, a type of cancer affecting ME/CFS patients at a higher rate than healthy population. We conclude that FM and ME/CFS miRNomes could help refine pharmacogenomic/pharmacoepigenomic analysis to elevate future personalized medicine and precision medicine programs in the clinic.
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Affiliation(s)
- Eloy Almenar-Pérez
- Escuela de Doctorado, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain.
| | - Teresa Sánchez-Fito
- Escuela de Doctorado, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain.
| | - Tamara Ovejero
- School of Medicine, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain.
| | - Lubov Nathanson
- Kiran C Patel College of Osteopathic Medicine, Nova Southeastern University, Ft Lauderdale, FL 33314, USA.
- Institute for Neuro Immune Medicine, Nova Southeastern University, Ft Lauderdale, FL 33314, USA.
| | - Elisa Oltra
- School of Medicine, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain.
- Unidad Mixta CIPF-UCV, Centro de Investigación Príncipe Felipe, 46012 Valencia, Spain.
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Misso G, Zarone MR, Lombardi A, Grimaldi A, Cossu AM, Ferri C, Russo M, Vuoso DC, Luce A, Kawasaki H, Di Martino MT, Virgilio A, Festa A, Galeone A, De Rosa G, Irace C, Donadelli M, Necas A, Amler E, Tagliaferri P, Tassone P, Caraglia M. miR-125b Upregulates miR-34a and Sequentially Activates Stress Adaption and Cell Death Mechanisms in Multiple Myeloma. Mol Ther Nucleic Acids 2019; 16:391-406. [PMID: 31009917 PMCID: PMC6479071 DOI: 10.1016/j.omtn.2019.02.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 02/26/2019] [Accepted: 02/26/2019] [Indexed: 12/12/2022]
Abstract
miR-125b, ubiquitously expressed and frequently dysregulated in several tumors, has gained special interest in the field of cancer research, displaying either oncogenic or oncosuppressor potential based on tumor type. We have previously demonstrated its tumor-suppressive role in multiple myeloma (MM), but the analysis of molecular mechanisms needs additional investigation. The purpose of this study was to explore the effects of miR-125b and its chemically modified analogs in modulating cell viability and cancer-associated molecular pathways, also focusing on the functional aspects of stress adaptation (autophagy and senescence), as well as programmed cell death (apoptosis). Based on the well-known low microRNA (miRNA) stability in therapeutic application, we designed chemically modified miR-125b mimics, laying the bases for their subsequent investigation in in vivo models. Our study clearly confirmed an oncosuppressive function depending on the repression of multiple targets, and it allowed the identification, for the first time, of miR-125b-dependent miR-34a stimulation as a possible consequence of the inhibitory role on the interleukin-6 receptor (IL-6R)/signal transducer and activator of transcription 3 (STAT3)/miR-34a feedback loop. Moreover, we identified a pattern of miR-125b-co-regulated miRNAs, shedding light on possible new players of anti-MM activity. Finally, functional studies also revealed a sequential activation of senescence, autophagy, and apoptosis, thus indicating, for the first two processes, an early cytoprotective and inhibitory role from apoptosis activation.
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Affiliation(s)
- Gabriella Misso
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli," 80138 Naples, Italy.
| | - Mayra Rachele Zarone
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli," 80138 Naples, Italy
| | - Angela Lombardi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli," 80138 Naples, Italy
| | - Anna Grimaldi
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli," 80138 Naples, Italy
| | - Alessia Maria Cossu
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli," 80138 Naples, Italy; IRGS, Biogem, Molecular and Precision Oncology Laboratory, Via Camporeale, 83031 Ariano Irpino, Italy
| | - Carmela Ferri
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli," 80138 Naples, Italy
| | - Margherita Russo
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli," 80138 Naples, Italy
| | - Daniela Cristina Vuoso
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli," 80138 Naples, Italy
| | - Amalia Luce
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli," 80138 Naples, Italy
| | - Hiromichi Kawasaki
- Drug Discovery Laboratory, Wakunaga Pharmaceutical Co., Ltd., Hiroshima, Japan
| | - Maria Teresa Di Martino
- Department of Experimental and Clinical Medicine, University Magna Græcia of Catanzaro, Salvatore Venuta University Campus, 88100 Catanzaro, Italy.
| | - Antonella Virgilio
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Agostino Festa
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli," 80138 Naples, Italy
| | - Aldo Galeone
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Giuseppe De Rosa
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Carlo Irace
- Department of Pharmacy, School of Medicine, University of Naples Federico II, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Massimo Donadelli
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy
| | - Alois Necas
- CEITEC - Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno, Brno, Czech Republic
| | - Evzen Amler
- Second Medical Faculty, Charles University in Prague, Prague, Czech Republic
| | - Pierosandro Tagliaferri
- Department of Experimental and Clinical Medicine, University Magna Græcia of Catanzaro, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
| | - Pierfrancesco Tassone
- Department of Experimental and Clinical Medicine, University Magna Græcia of Catanzaro, Salvatore Venuta University Campus, 88100 Catanzaro, Italy
| | - Michele Caraglia
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli," 80138 Naples, Italy; IRGS, Biogem, Molecular and Precision Oncology Laboratory, Via Camporeale, 83031 Ariano Irpino, Italy.
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Aydinoglu F, Lucas SJ. Identification and expression profiles of putative leaf growth related microRNAs in maize (Zea mays L.) hybrid ADA313. Gene 2018; 690:57-67. [PMID: 30597233 DOI: 10.1016/j.gene.2018.12.042] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 10/17/2018] [Accepted: 12/13/2018] [Indexed: 02/06/2023]
Abstract
Throughout the plant life cycle, growth of new leaves is governed by cell division and cell expansion. During steady-state growth of the maize leaf, these processes are spatially separated between the meristem zone, consisting of dividing cells at the leaf base, the elongation zone, consisting of expanding cells moving upwards from the meristem, and the mature zone containing differentiated mature cells. Increased leaf size can be achieved through increasing cell number or cell size, for example by manipulating the genes controlling the transition between those zones. In this study, microRNA (miRNA) genes, which are a class of endogenous small, non-coding gene regulatory RNAs, were investigated in the growth zones, to gain insight into their role in the transition between cell division and cell expansion. A genome-wide survey was conducted using a miRNA-microarray and 59 miRNA genes were detected to be differentially expressed between the growth zones. miR160, miR166, miR168, miR172, miR319 and miR390 families were significantly up-regulated in the meristem relative to the elongation and mature zones. In contrast, expression of the miR167 and miR396 families was lower in the meristem and higher in the mature zone. Therefore, these were considered to be candidate growth-regulated miRNAs that control cell division processes indirectly by repressing target genes. The miR156, miR166, miR167, miR399, miR408 and miR2275 families were expressed most highly in the elongation zone, and so were classified as elongation-specific, with possible roles in switching from cell division to cell elongation during leaf differentiation. In silico target prediction analysis showed that these miRNAs target several transcription factors and metabolic genes, and a reciprocal relationship between the expression levels of miR319 and miR396 and their targets was confirmed by qRT-PCR. Furthermore, 12 candidate novel miRNAs were identified from the microarray data and computationally verified. Three out of twelve were also validated by qRT-PCR. These findings provide important information regarding the regulatory functions of miRNAs in controlling progression of growth mechanisms.
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Affiliation(s)
- Fatma Aydinoglu
- Gebze Technical University, Molecular Biology and Genetics Department, Kocaeli, Turkey.
| | - Stuart James Lucas
- Sabanci University Nanotechnology Research & Application Center (SUNUM), Istanbul, Turkey
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Agapito-Tenfen SZ, Vilperte V, Traavik TI, Nodari RO. Systematic miRNome profiling reveals differential microRNAs in transgenic maize metabolism. Environ Sci Eur 2018; 30:37. [PMID: 30294516 PMCID: PMC6153861 DOI: 10.1186/s12302-018-0168-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/11/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND While some genetically modified organisms (GMOs) are created to produce new double-stranded RNA molecules (dsRNA), in others, such molecules may occur as an unintended effect of the genetic engineering process. Furthermore, GMOs might produce naturally occurring dsRNA molecules in higher or lower quantities than its non-transgenic counterpart. This study is the first to use high-throughput technology to characterize the miRNome of commercialized GM maize events and to investigate potential alterations in miRNA regulatory networks. RESULTS Thirteen different conserved miRNAs were found to be dys-regulated in GM samples. The insecticide Bt GM variety had the most distinct miRNome. These miRNAs target a range of endogenous transcripts, such as transcription factors and nucleic acid binding domains, which play key molecular functions in basic genetic regulation. In addition, we have identified 20 potential novel miRNAs with target transcripts involved in lipid metabolism in maize. isomiRs were also found in 96 conserved miRNAs sequences, as well as potential transgenic miRNA sequences, which both can be a source of potential off-target effects in the plant genome. We have also provided information on technical limitations and when to carry on additional in vivo experimental testing. CONCLUSIONS These findings do not reveal hazards per se but show that robust and reproducible miRNA profiling technique can strengthen the assessment of risk by detecting any new intended and unintended dsRNA molecules, regardless of the outcome, at any stage of GMO development.
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Affiliation(s)
| | - Vinicius Vilperte
- Departamento de Fitotecnia, Universidade Federal de Santa Catarina, Florianópolis, 88034000 Brazil
- Present Address: Institute for Plant Genetics, Faculty of Natural Sciences, Leibniz University of Hannover, 30419 Hannover, Germany
| | - Terje Ingemar Traavik
- GenØk–Centre for Biosafety, Forskningsparken i Breivika, Sykehusveien 23, 9294 Tromsø, Norway
| | - Rubens Onofre Nodari
- Departamento de Fitotecnia, Universidade Federal de Santa Catarina, Florianópolis, 88034000 Brazil
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Nam RK, Wallis CJD, Amemiya Y, Benatar T, Seth A. Identification of a Novel MicroRNA Panel Associated with Metastasis Following Radical Prostatectomy for Prostate Cancer. Anticancer Res 2018; 38:5027-5034. [PMID: 30194146 DOI: 10.21873/anticanres.12821] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 08/17/2018] [Accepted: 08/19/2018] [Indexed: 11/10/2022]
Abstract
BACKGROUND/AIM This is a case control study designed to identify one or more novel microRNA sequences associated with metastasis following radical prostatectomy for clinically localized prostate cancer. MATERIALS AND METHODS Samples were obtained from patients with clinical evidence of metastatic disease following surgery (cases) and patients who showed no evidence of metastasis or biochemical recurrence at least 5 years following surgery (controls) as identified from a single-center, institutional database. Cases and controls were matched for tumor grade and duration of follow-up. RESULTS Whole miRNome analysis identified 2,792 expressed miRNAs in 19 patient pairs. The 497 miRNA sequences with reads per million over 10, were used for analysis, bootstrapping with backward selection identified a panel of 5-miRNA (miR-17-3p, miR-27a-3p, miR-200a-3p, miR-375, and miR-376b-3p) with a risk score strongly associated with metastasis (AUC=89.5%, 95%CI=79.5-99.5%). Methodologically, most studies use the magnitude of differential expression with or without clinical judgement for selection of predictors for inclusion in panels. In order to strengthen the predictive model, a selection strategy was employed, bootstrapping with automated backwards selection, which relied on the strength of association for inclusion. CONCLUSION A genome-wide analysis of microRNA expression identified a panel of 5 miRNAs strongly associated with prostate cancer metastasis following radical prostatectomy.
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Affiliation(s)
- Robert K Nam
- Division of Urology, Sunnybrook Health Sciences Centre, Sunnybrook Research Institute, University of Toronto, Toronto, Canada
| | - Christopher J D Wallis
- Division of Urology, Sunnybrook Health Sciences Centre, Sunnybrook Research Institute, University of Toronto, Toronto, Canada
| | - Yutaka Amemiya
- Sunnybrook Research Institute Genomics Facility, Toronto, Canada
| | - Tania Benatar
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Platform Biological Sciences, Sunnybrook Health Sciences Centre, Sunnybrook Research Institute, University of Toronto, Toronto, Canada
| | - Arun Seth
- Sunnybrook Research Institute Genomics Facility, Toronto, Canada .,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Platform Biological Sciences, Sunnybrook Health Sciences Centre, Sunnybrook Research Institute, University of Toronto, Toronto, Canada.,Faculty of Dentistry, University of Toronto, Toronto, Canada
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Chokeshaiusaha K, Sananmuang T, Puthier D, Nguyen C. An innovative approach to predict immune-associated genes mutually targeted by cow and human milk microRNAs expression profiles. Vet World 2018; 11:1203-1209. [PMID: 30410222 PMCID: PMC6200572 DOI: 10.14202/vetworld.2018.1203-1209] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 07/16/2018] [Indexed: 12/21/2022] Open
Abstract
Aim: Milk is rich in miRNAs - the endogenous small non-coding RNA responsible for gene post-transcriptional silencing. Milk miRNAs were previously evidenced to affect consumer’s immune response. While most studies relied on a few well-characterized milk miRNAs to relate their immunoregulatory roles on target genes among mammals, this study introduced a procedure to predict the target genes based on overall milk miRNA expression profiles - the miRNome data of cow and human. Materials and Methods: Cow and human milk miRNome expression datasets of cow and human milk lipids at 2, 4, and 6 months of lactation periods were preprocessed and predicted for their target genes using TargetScanHuman. Enrichment analysis was performed using target genes to extract the immune-associated gene ontology (GO) terms shared between the two species. The genes within these terms with more than 50 different miRNAs of each species targeting were selected and reviewed for their immunological functions. Results: A total of 146 and 129 miRNAs were identified in cow and human milk with several miRNAs reproduced from other previous reports. Enrichment analysis revealed nine immune-related GO terms shared between cow and human (adjusted p≤0.01). There were 14 genes related to these terms with more than 50 miRNA genes of each species targeting them. These genes were evidenced for their major roles in lymphocyte stimulation and differentiation. Conclusion: A novel procedure to determine mutual immune-associated genes targeted by milk miRNAs was demonstrated using cow and human milk miRNome data. As far as we know, this was the 1st time that milk miRNA target genes had been identified based on such cross-species approach. Hopefully, the introduced strategy should hereby facilitate a variety of cross-species miRNA studies in the future.
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Affiliation(s)
- Kaj Chokeshaiusaha
- Department of Veterinary Science, Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-OK, Chonburi, Thailand
| | - Thanida Sananmuang
- Department of Veterinary Science, Faculty of Veterinary Medicine, Rajamangala University of Technology Tawan-OK, Chonburi, Thailand
| | - Denis Puthier
- Aix-Marseille Université, INSERM UMR 1090, TAGC, Marseille, France
| | - Catherine Nguyen
- Aix-Marseille Université, INSERM UMR 1090, TAGC, Marseille, France
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Ishikawa D, Diekmann U, Fiedler J, Just A, Thum T, Lenzen S, Naujok O. miRNome Profiling of Purified Endoderm and Mesoderm Differentiated from hESCs Reveals Functions of miR-483-3p and miR-1263 for Cell-Fate Decisions. Stem Cell Reports 2018; 9:1588-1603. [PMID: 29141233 PMCID: PMC5688239 DOI: 10.1016/j.stemcr.2017.10.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 10/12/2017] [Accepted: 10/12/2017] [Indexed: 12/20/2022] Open
Abstract
Pluripotent stem cells hold great promise for regenerative medicine since they can differentiate into all somatic cells. MicroRNAs (miRNAs) could be important for the regulation of these cell-fate decisions. Profiling of miRNAs revealed 19 differentially expressed miRNAs in the endoderm and 29 in the mesoderm when analyzing FACS-purified cells derived from human embryonic stem cells. The mesodermal-enriched miR-483-3p was identified as an important regulator for the generation of mesodermal PDGFRA+ paraxial cells. Repression of its target PGAM1 significantly increased the number of PDGFRA+ cells. Furthermore, miR-483-3p, miR-199a-3p, and miR-214-3p might also have functions for the mesodermal progenitors. The endoderm-specific miR-489-3p and miR-1263 accelerated and increased endoderm differentiation upon overexpression. KLF4 was identified as a target of miR-1263. RNAi-mediated downregulation of KLF4 partially mimicked miR-1263 overexpression. Thus, the effects of this miRNA were mediated by facilitating differentiation through destabilization of pluripotency along with other not yet defined targets.
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Affiliation(s)
- Daichi Ishikawa
- Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany; Department of Surgery, Tokushima University, 3-18-15, Kuramoto, Tokushima 770-8503, Japan
| | - Ulf Diekmann
- Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Jan Fiedler
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Annette Just
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Thomas Thum
- Institute of Molecular and Translational Therapeutic Strategies (IMTTS), Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany; National Heart and Lung Institute, Imperial College London, Sydney Street, London SW3 6NP, UK
| | - Sigurd Lenzen
- Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Ortwin Naujok
- Institute of Clinical Biochemistry, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany.
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Pedersen NJ, Jensen DH, Lelkaitis G, Kiss K, Charabi BW, Ullum H, Specht L, Schmidt AY, Nielsen FC, von Buchwald C. MicroRNA-based classifiers for diagnosis of oral cavity squamous cell carcinoma in tissue and plasma. Oral Oncol 2018; 83:46-52. [PMID: 30098778 DOI: 10.1016/j.oraloncology.2018.05.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 04/27/2018] [Accepted: 05/25/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND MicroRNAs (miRNAs) hold promise as diagnostic cancer biomarkers. Here we aimed to define the miRNome in oral squamous cell carcinoma (OSCC) and normal oral mucosa (NOM), and to identify and validate new diagnostic miRNAs and miRNA combinations in formalin-fixed paraffin-embedded (FFPE) tissue samples and plasma samples. METHODS We performed next-generation miRNA sequencing in FFPE tissue samples of OSCC (n = 80) and NOM (n = 8). Our findings were validated by quantitative polymerase chain reaction (qPCR) analysis of OSCC (n = 195) and NOM (n = 103) FFPE tissue samples, and plasma samples from OSCC patients (n = 55) and healthy persons (n = 18). RESULTS The OSCC miRNome included 567 miRNAs, 66 of which were differentially expressed between OSCC and NOM. Using qPCR data, we constructed receiver operating curves to classify patients as NOM or OSCC based on miRNA combinations. The area under the curve was of 0.92 from FFPE tissue (miR-204-5p, miR-370, miR-1307, miR-193b-3p, and miR-144-5p), and 1.0 from plasma samples (miR-30a-5p and miR-769-5p). Model calibration and discrimination were evaluated using 10-fold cross-validation. CONCLUSIONS Analysis of the miRNome from many OSCC cases improves our knowledge of the importance of individual miRNAs and their predictive potential in OSCC. We successfully identified miRNA classifiers in FFPE OSCC tissue and plasma with a high discriminatory ability between OSCC and NOM. The proposed combination of miR-30a-5p and miR-769-5p in plasma from OSCC patients could serve as a minimal invasive biomarker for diagnosis and control of T-site recurrences.
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Affiliation(s)
- Nicklas Juel Pedersen
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - David Hebbelstrup Jensen
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Giedrius Lelkaitis
- Department of Pathology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Katalin Kiss
- Department of Pathology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Birgitte Wittenborg Charabi
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Ullum
- Department of Clinical Immunology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Lena Specht
- Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Ane Yde Schmidt
- Centre for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Finn Cilius Nielsen
- Centre for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Christian von Buchwald
- Department of Otorhinolaryngology, Head and Neck Surgery and Audiology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.
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Granata S, Santoro G, Masola V, Tomei P, Sallustio F, Pontrelli P, Accetturo M, Antonucci N, Carratù P, Lupo A, Zaza G. In Vitro Identification of New Transcriptomic and miRNomic Profiles Associated with Pulmonary Fibrosis Induced by High Doses Everolimus: Looking for New Pathogenetic Markers and Therapeutic Targets. Int J Mol Sci 2018; 19:ijms19041250. [PMID: 29677166 PMCID: PMC5979287 DOI: 10.3390/ijms19041250] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/17/2018] [Accepted: 04/17/2018] [Indexed: 12/24/2022] Open
Abstract
The administration of Everolimus (EVE), a mTOR inhibitor used in transplantation and cancer, is often associated with adverse effects including pulmonary fibrosis. Although the underlying mechanism is not fully clarified, this condition could be in part caused by epithelial to mesenchymal transition (EMT) of airway cells. To improve our knowledge, primary bronchial epithelial cells (BE63/3) were treated with EVE (5 and 100 nM) for 24 h. EMT markers (α-SMA, vimentin, fibronectin) were measured by RT-PCR. Transepithelial resistance was measured by Millicell-ERS ohmmeter. mRNA and microRNA profiling were performed by Illumina and Agilent kit, respectively. Only high dose EVE increased EMT markers and reduced the transepithelial resistance of BE63/3. Bioinformatics showed 125 de-regulated genes that, according to enrichment analysis, were implicated in collagen synthesis/metabolism. Connective tissue growth factor (CTGF) was one of the higher up-regulated mRNA. Five nM EVE was ineffective on the pro-fibrotic machinery. Additionally, 3 miRNAs resulted hyper-expressed after 100 nM EVE and able to regulate 31 of the genes selected by the transcriptomic analysis (including CTGF). RT-PCR and western blot for MMP12 and CTGF validated high-throughput results. Our results revealed a complex biological network implicated in EVE-related pulmonary fibrosis and underlined new potential disease biomarkers and therapeutic targets.
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Affiliation(s)
- Simona Granata
- Renal Unit, Department of Medicine, University of Verona, Piazzale Stefani 1, 37126 Verona, Italy.
| | - Gloria Santoro
- Renal Unit, Department of Medicine, University of Verona, Piazzale Stefani 1, 37126 Verona, Italy.
| | - Valentina Masola
- Renal Unit, Department of Medicine, University of Verona, Piazzale Stefani 1, 37126 Verona, Italy.
| | - Paola Tomei
- Renal Unit, Department of Medicine, University of Verona, Piazzale Stefani 1, 37126 Verona, Italy.
| | - Fabio Sallustio
- Department of Emergency and Organ Transplantation, University of Bari "Aldo Moro", Piazza Giulio Cesare 11, 70124 Bari, Italy.
- Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari "Aldo Moro", Piazza Giulio Cesare 11, 70124 Bari, Italy.
| | - Paola Pontrelli
- Department of Emergency and Organ Transplantation, University of Bari "Aldo Moro", Piazza Giulio Cesare 11, 70124 Bari, Italy.
| | - Matteo Accetturo
- Department of Emergency and Organ Transplantation, University of Bari "Aldo Moro", Piazza Giulio Cesare 11, 70124 Bari, Italy.
| | - Nadia Antonucci
- Renal Unit, Department of Medicine, University of Verona, Piazzale Stefani 1, 37126 Verona, Italy.
| | - Pierluigi Carratù
- Department of Respiratory Diseases, University of Bari "Aldo Moro", Piazza Giulio Cesare 11, 70124 Bari, Italy.
| | - Antonio Lupo
- Renal Unit, Department of Medicine, University of Verona, Piazzale Stefani 1, 37126 Verona, Italy.
| | - Gianluigi Zaza
- Renal Unit, Department of Medicine, University of Verona, Piazzale Stefani 1, 37126 Verona, Italy.
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Benoit C, Doubi-Kadmiri S, Benigni X, Crepin D, Riffault L, Poizat G, Vacher CM, Taouis M, Baroin-Tourancheau A, Amar L. miRNA Long-Term Response to Early Metabolic Environmental Challenge in Hypothalamic Arcuate Nucleus. Front Mol Neurosci 2018; 11:90. [PMID: 29643765 PMCID: PMC5882837 DOI: 10.3389/fnmol.2018.00090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 03/08/2018] [Indexed: 11/13/2022] Open
Abstract
Epidemiological reports and studies using rodent models indicate that early exposure to nutrient and/or hormonal challenges can reprogram metabolism at adulthood. Hypothalamic arcuate nucleus (ARC) integrates peripheral and central signals to adequately regulate energy homeostasis. microRNAs (miRNAs) participate in the control of gene expression of large regulatory networks including many signaling pathways involved in epigenetics regulations. Here, we have characterized and compared the miRNA population of ARC of adult male rats continuously exposed to a balanced metabolic environment to the one of adult male rats exposed to an unbalanced high-fat/high-carbohydrate/moderate-protein metabolic environment during the perinatal period and/or at adulthood that consequently displayed hyperinsulinemia and/or hyperleptinemia. We identified more than 400 miRNA species in ARC of adult male rats. By comparing the miRNA content of six biological replicates in each of the four perinatal/adult environments/rat groups, we identified the 10 miRNAs specified by clusters miR-96/182/183, miR-141/200c, and miR-200a/200b/429 as miRNAs of systematic and uncommonly high variation of expression. This uncommon variation of expression may underlie high individual differences in aging disease susceptibilities. By comparing the miRNA content of the adult ARC between the rat groups, we showed that the miRNA population was not affected by the unbalanced adult environment while, in contrast, the expression of 11 miRNAs was repeatedly impacted by the perinatal unbalanced environment. Our data revealed a miRNA response of adult ARC to early metabolic environmental challenge.
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Affiliation(s)
- Charlotte Benoit
- Centre National de la Recherche Scientifique UMR 9197/Institut de Neurosciences, Université Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Soraya Doubi-Kadmiri
- Centre National de la Recherche Scientifique UMR 9197/Institut de Neurosciences, Université Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Xavier Benigni
- Centre National de la Recherche Scientifique UMR 9197/Institut de Neurosciences, Université Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Delphine Crepin
- Centre National de la Recherche Scientifique UMR 9197/Institut de Neurosciences, Université Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Laure Riffault
- Centre National de la Recherche Scientifique UMR 9197/Institut de Neurosciences, Université Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Ghislaine Poizat
- Centre National de la Recherche Scientifique UMR 9197/Institut de Neurosciences, Université Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Claire-Marie Vacher
- Centre National de la Recherche Scientifique UMR 9197/Institut de Neurosciences, Université Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Mohammed Taouis
- Centre National de la Recherche Scientifique UMR 9197/Institut de Neurosciences, Université Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Anne Baroin-Tourancheau
- Centre National de la Recherche Scientifique UMR 9197/Institut de Neurosciences, Université Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Laurence Amar
- Centre National de la Recherche Scientifique UMR 9197/Institut de Neurosciences, Université Paris-Sud, Université Paris-Saclay, Orsay, France
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Salgado CG, Pinto P, Bouth RC, Gobbo AR, Messias ACC, Sandoval TV, Dos Santos AMR, Moreira FC, Vidal AF, Goulart LR, Barreto JG, da Silva MB, Frade MAC, Spencer JS, Santos S, Ribeiro-Dos-Santos Â. miRNome Expression Analysis Reveals New Players on Leprosy Immune Physiopathology. Front Immunol 2018; 9:463. [PMID: 29593724 PMCID: PMC5854644 DOI: 10.3389/fimmu.2018.00463] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 02/21/2018] [Indexed: 12/31/2022] Open
Abstract
Leprosy remains as a public health problem and its physiopathology is still not fully understood. MicroRNAs (miRNA) are small RNA non-coding that can interfere with mRNA to regulate gene expression. A few studies using DNA chip microarrays have explored the expression of miRNA in leprosy patients using a predetermined set of genes as targets, providing interesting findings regarding the regulation of immune genes. However, using a predetermined set of genes restricted the possibility of finding new miRNAs that might be involved in different mechanisms of disease. Thus, we examined the miRNome of tuberculoid (TT) and lepromatous (LL) patients using both blood and lesional biopsies from classical leprosy patients (LP) who visited the Dr. Marcello Candia Reference Unit in Sanitary Dermatology in the State of Pará and compared them with healthy subjects. Using a set of tools to correlate significantly differentially expressed miRNAs with their gene targets, we identified possible interactions and networks of miRNAs that might be involved in leprosy immunophysiopathology. Using this approach, we showed that the leprosy miRNA profile in blood is distinct from that in lesional skin as well as that four main groups of genes are the targets of leprosy miRNA: (1) recognition and phagocytosis, with activation of immune effector cells, where the immunosuppressant profile of LL and immunoresponsive profile of TT are clearly affected by miRNA expression; (2) apoptosis, with supportive data for an antiapoptotic leprosy profile based on BCL2, MCL1, and CASP8 expression; (3) Schwann cells (SCs), demyelination and epithelial–mesenchymal transition (EMT), supporting a role for different developmental or differentiation gene families, such as Sox, Zeb, and Hox; and (4) loss of sensation and neuropathic pain, revealing that RHOA, ROCK1, SIGMAR1, and aquaporin-1 (AQP1) may be involved in the loss of sensation or leprosy pain, indicating possible new therapeutic targets. Additionally, AQP1 may also be involved in skin dryness and loss of elasticity, which are well known signs of leprosy but with unrecognized physiopathology. In sum, miRNA expression reveals new aspects of leprosy immunophysiopathology, especially on the regulation of the immune system, apoptosis, SC demyelination, EMT, and neuropathic pain.
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Affiliation(s)
- Claudio Guedes Salgado
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Marituba, Brazil
| | - Pablo Pinto
- Laboratório de Genética Humana e Médica, ICB, UFPA, Belém, Brazil.,Núcleo de Pesquisas em Oncologia (NPO), UFPA, Belém, Brazil
| | - Raquel Carvalho Bouth
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Marituba, Brazil
| | - Angélica Rita Gobbo
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Marituba, Brazil
| | - Ana Caroline Cunha Messias
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Marituba, Brazil
| | | | | | | | | | - Luiz Ricardo Goulart
- Laboratório de Nanobiotecnologia, Instituto de Genética e Bioquímica, Universidade Federal de Uberlândia (UFU), Uberlândia, Brazil
| | - Josafá Gonçalves Barreto
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Marituba, Brazil.,Laboratório de Epidemiologia Espacial (LabEE), Campus Castanhal, UFPA, Belém, Brazil
| | - Moisés Batista da Silva
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas (ICB), Universidade Federal do Pará (UFPA), Marituba, Brazil
| | - Marco Andrey Cipriani Frade
- Divisão de Dermatologia, Departamento de Clínica Médica da Faculdade de Medicina de Ribeirão Preto, USP, Ribeirão Preto, Brazil
| | - John Stewart Spencer
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
| | - Sidney Santos
- Laboratório de Genética Humana e Médica, ICB, UFPA, Belém, Brazil.,Núcleo de Pesquisas em Oncologia (NPO), UFPA, Belém, Brazil
| | - Ândrea Ribeiro-Dos-Santos
- Laboratório de Genética Humana e Médica, ICB, UFPA, Belém, Brazil.,Núcleo de Pesquisas em Oncologia (NPO), UFPA, Belém, Brazil
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D'Argenio V, Del Monaco V, Paparo L, De Palma FDE, Nocerino R, D'Alessio F, Visconte F, Discepolo V, Del Vecchio L, Salvatore F, Berni Canani R. Altered miR-193a-5p expression in children with cow's milk allergy. Allergy 2018; 73:379-386. [PMID: 28857182 DOI: 10.1111/all.13299] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2017] [Indexed: 12/20/2022]
Abstract
BACKGROUND Cow's milk allergy (CMA) is one of the most common food allergies in children. Epigenetic mechanisms have been suggested to play a role in CMA pathogenesis. We have shown that DNA methylation of Th1/Th2 cytokine genes and FoxP3 affects CMA disease course. Preliminary evidence suggests that also the miRNome could be implicated in the pathogenesis of allergy. Main study outcome was to comparatively evaluate miRNome in children with CMA and in healthy controls. METHODS Peripheral blood mononuclear cells were obtained from children aged 4-18 months: 10 CMA patients, 9 CMA patients who outgrew CMA, and 11 healthy controls. Small RNA libraries were sequenced using a next-generation sequencing-based approach. Functional assessment of IL-4 expression was also performed. RESULTS Among the miRNAs differently expressed, 2 were upregulated and 14 were downregulated in children with active CMA compared to healthy controls. miR-193a-5p resulted the most downregulated miRNA in children with active CMA compared to healthy controls. The predicted targets of miR-193a-5p resulted upregulated in CMA patients compared to healthy controls. Peripheral blood CD4+ T cells transfected with a miR193a-5 inhibitor showed a significant upregulation of IL-4 mRNA and its protein expression. Children who outgrew CMA showed miRNA-193a-5p level, and its related targets expression, similar to that observed in healthy controls. CONCLUSIONS Our results suggest that miR-193a-5p is a post-transcriptional regulator of IL-4 expression and could have a role in IgE-mediated CMA. This miRNA could be a novel diagnostic and therapeutic target for this common form of food allergy in childhood.
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Affiliation(s)
- V. D'Argenio
- CEINGE-Biotecnologie Avanzate s.c.ar.l.; Naples Italy
- Department of Molecular Medicine and Medical Biotechnologies; University of Naples Federico II; Naples Italy
| | - V. Del Monaco
- CEINGE-Biotecnologie Avanzate s.c.ar.l.; Naples Italy
| | - L. Paparo
- Department of Translational Medical Science; University of Naples Federico II; Naples Italy
| | | | - R. Nocerino
- Department of Translational Medical Science; University of Naples Federico II; Naples Italy
| | - F. D'Alessio
- CEINGE-Biotecnologie Avanzate s.c.ar.l.; Naples Italy
| | - F. Visconte
- CEINGE-Biotecnologie Avanzate s.c.ar.l.; Naples Italy
- Department of Molecular Medicine and Medical Biotechnologies; University of Naples Federico II; Naples Italy
| | - V. Discepolo
- CEINGE-Biotecnologie Avanzate s.c.ar.l.; Naples Italy
- Department of Translational Medical Science; University of Naples Federico II; Naples Italy
| | - L. Del Vecchio
- CEINGE-Biotecnologie Avanzate s.c.ar.l.; Naples Italy
- Department of Molecular Medicine and Medical Biotechnologies; University of Naples Federico II; Naples Italy
| | - F. Salvatore
- CEINGE-Biotecnologie Avanzate s.c.ar.l.; Naples Italy
- Department of Molecular Medicine and Medical Biotechnologies; University of Naples Federico II; Naples Italy
- IRCCS-Fondazione SDN; Naples Italy
| | - R. Berni Canani
- CEINGE-Biotecnologie Avanzate s.c.ar.l.; Naples Italy
- Department of Translational Medical Science; University of Naples Federico II; Naples Italy
- European Laboratory for the Investigation of Food-Induced Diseases; University of Naples Federico II; Naples Italy
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48
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Kuryłowicz A, Wicik Z, Owczarz M, Jonas MI, Kotlarek M, Świerniak M, Lisik W, Jonas M, Noszczyk B, Puzianowska-Kuźnicka M. NGS Reveals Molecular Pathways Affected by Obesity and Weight Loss-Related Changes in miRNA Levels in Adipose Tissue. Int J Mol Sci 2017; 19:E66. [PMID: 29280944 DOI: 10.3390/ijms19010066] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 12/22/2017] [Accepted: 12/24/2017] [Indexed: 12/22/2022] Open
Abstract
Both obesity and weight loss may cause molecular changes in adipose tissue. This study aimed to characterize changes in adipose tissue miRNome in order to identify molecular pathways affected by obesity and weight changes. Next generation sequencing (NGS) was applied to identify microRNAs (miRNAs) differentially expressed in 47 samples of visceral (VAT) and subcutaneous (SAT) adipose tissues from normal-weight (N), obese (O) and obese after surgery-induced weight loss (PO) individuals. Subsequently miRNA expression was validated by real-time PCR in 197 adipose tissues and bioinformatics analysis performed to identify molecular pathways affected by obesity-related changes in miRNA expression. NGS identified 344 miRNAs expressed in adipose tissues with ≥5 reads per million. Using >2 and <−2 fold change as cut-offs we showed that the expression of 54 miRNAs differed significantly between VAT-O and SAT-O. Equally, between SAT-O and SAT-N, the expression of 20 miRNAs differed significantly, between SAT-PO and SAT-N the expression of 79 miRNAs differed significantly, and between SAT-PO and SAT-O, the expression of 61 miRNAs differed significantly. Ontological analyses disclosed several molecular pathways regulated by these miRNAs in adipose tissue. NGS-based miRNome analysis characterized changes of the miRNA profile of adipose tissue, which are associated with changes of weight possibly responsible for a differential regulation of molecular pathways in adipose tissue when the individual is obese and after the individual has lost weight.
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49
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Borghini A, Foffa I, Pulignani S, Vecoli C, Ait-Ali L, Andreassi MG. miRNome Profiling in Bicuspid Aortic Valve-Associated Aortopathy by Next-Generation Sequencing. Int J Mol Sci 2017; 18:E2498. [PMID: 29165337 DOI: 10.3390/ijms18112498] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 11/20/2017] [Accepted: 11/20/2017] [Indexed: 01/05/2023] Open
Abstract
The molecular mechanisms underlying thoracic aortic aneurysm (TAA) in patients with bicuspid aortic valve (BAV) are incompletely characterized. MicroRNAs (miRNAs) may play a major role in the different pathogenesis of aortopathy. We sought to employ next-generation sequencing to analyze the entire miRNome in TAA tissue from patients with BAV and tricuspid aortic valve (TAV). In the discovery stage, small RNA sequencing was performed using the Illumina MiSeq platform in 13 TAA tissue samples (seven patients with BAV and six with TAV). Gene ontology (GO) and KEGG pathway analysis were used to identify key pathways and biological functions. Validation analysis was performed by qRT-PCR in an independent cohort of 30 patients with BAV (26 males; 59.5 ± 12 years) and 30 patients with TAV (16 males; 68.5 ± 9.5 years). Bioinformatic analysis identified a total of 489 known mature miRNAs and five novel miRNAs. Compared to TAV samples, 12 known miRNAs were found to be differentially expressed in BAV, including two up-regulated and 10 down-regulated (FDR-adjusted p-value ≤ 0.05 and fold change ≥ 1.5). GO and KEGG pathway enrichment analysis (FDR-adjusted p-value < 0.05) identified different target genes and pathways linked to BAV and aneurysm formation, including Hippo signaling pathway, ErbB signaling, TGF-beta signaling and focal adhesion. Validation analysis of selected miRNAs confirmed the significant down-regulation of miR-424-3p (p = 0.01) and miR-3688-3p (p = 0.03) in BAV patients as compared to TAV patients. Our study provided the first in-depth screening of the whole miRNome in TAA specimens and identified specific dysregulated miRNAs in BAV patients.
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50
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Baumgart M, Barth E, Savino A, Groth M, Koch P, Petzold A, Arisi I, Platzer M, Marz M, Cellerino A. A miRNA catalogue and ncRNA annotation of the short-living fish Nothobranchius furzeri. BMC Genomics 2017; 18:693. [PMID: 28874118 PMCID: PMC5584509 DOI: 10.1186/s12864-017-3951-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 07/20/2017] [Indexed: 12/22/2022] Open
Abstract
Background The short-lived fish Nothobranchius furzeri is the shortest-lived vertebrate that can be cultured in captivity and was recently established as a model organism for aging research. Small non-coding RNAs, especially miRNAs, are implicated in age dependent control of gene expression. Results Here, we present a comprehensive catalogue of miRNAs and several other non-coding RNA classes (ncRNAs) for Nothobranchius furzeri. Analyzing multiple small RNA-Seq libraries, we show most of these identified miRNAs are expressed in at least one of seven Nothobranchius species. Additionally, duplication and clustering of N. furzeri miRNAs was analyzed and compared to the four fish species Danio rerio, Oryzias latipes, Gasterosteus aculeatus and Takifugu rubripes. A peculiar characteristic of N. furzeri, as compared to other teleosts, was a duplication of the miR-29 cluster. Conclusion The completeness of the catalogue we provide is comparable to that of the zebrafish. This catalogue represents a basis to investigate the role of miRNAs in aging and development in this species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3951-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mario Baumgart
- Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany
| | - Emanuel Barth
- Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany.,Bioinformatics/High Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743, Jena, Germany
| | | | - Marco Groth
- Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany
| | - Philipp Koch
- Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany
| | | | - Ivan Arisi
- European Brain Research Institute (EBRI), Rome, Italy
| | - Matthias Platzer
- Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany
| | - Manja Marz
- Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany. .,Bioinformatics/High Throughput Analysis, Friedrich Schiller University Jena, Leutragraben 1, 07743, Jena, Germany.
| | - Alessandro Cellerino
- Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany. .,Laboratory of Biology, Scuola Normale Superiore, 56126, Pisa, Italy.
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