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Metcalf GAD. MicroRNAs: circulating biomarkers for the early detection of imperceptible cancers via biosensor and machine-learning advances. Oncogene 2024; 43:2135-2142. [PMID: 38839942 PMCID: PMC11226400 DOI: 10.1038/s41388-024-03076-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/24/2024] [Accepted: 05/29/2024] [Indexed: 06/07/2024]
Abstract
This review explores the topic of microRNAs (miRNAs) for improved early detection of imperceptible cancers, with potential to advance precision medicine and improve patient outcomes. Historical research exploring miRNA's role in cancer detection collectively revealed initial hurdles in identifying specific miRNA signatures for early-stage and difficult-to-detect cancers. Early studies faced challenges in establishing robust biomarker panels and overcoming the heterogeneity of cancer types. Despite this, recent developments have supported the potential of miRNAs as sensitive and specific biomarkers for early cancer detection as well as having demonstrated remarkable potential as diagnostic tools for imperceptible cancers, such as those with elusive symptoms or challenging diagnostic criteria. This review discusses the advent of high-throughput technologies that have enabled comprehensive detection and profiling of unique miRNA signatures associated with early-stage cancers. Furthermore, advancements in bioinformatics and machine-learning techniques are considered, exploring the integration of multi-omics data which have potential to enhance both the accuracy and reliability of miRNA-based cancer detection assays. Finally, perspectives on the continuing development on technologies as well as discussion around challenges that remain, such as the need for standardised protocols and addressing the complex interplay of miRNAs in cancer biology are conferred.
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Affiliation(s)
- Gavin A D Metcalf
- School of Life Sciences, Faculty of Science and Engineering, Anglia Ruskin University, Cambridge, UK.
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2
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Ministrini S, Padro T. MicroRNA in cardiometabolic health and disease: The perspectives of sex, gender and personalised medicine. Eur J Clin Invest 2024; 54:e14223. [PMID: 38623918 DOI: 10.1111/eci.14223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/07/2024] [Accepted: 04/08/2024] [Indexed: 04/17/2024]
Abstract
BACKGROUND Personalized medicine represents a novel and integrative approach that focuses on an individual's genetics and epigenetics, precision medicine, lifestyle and exposures as key players of health status and disease phenotypes. METHODS In this narrative review, we aim to carefully discuss the current knowledge on gender disparities in cardiometabolic diseases, and we consider the sex- specific expression of miRNAs and their role as promising tool in precision medicine. RESULTS Personalised medicine overcomes the restricted care of patient based on a binomial sex approach, by enriching itself with a holistic and dynamic gender integration. Recognized as a major worldwide health emergency, cardiometabolic disorders continue to rise, impacting on health systems and requiring more effective and targeted strategies. Several sex and gender drivers might affect the onset and progression of cardiometabolic disorders in males and females at multiple levels. In this respect, distinct contribution of genetic and epigenetic mechanisms, molecular and physiological pathways, sex hormones, visceral fat and subcutaneous fat and lifestyle lead to differences in disease burden and outcomes in males and females. CONCLUSIONS Sex and gender play a pivotal role in precision medicine because the influence the physiology of each individual and the way they interact with environment from intrauterine life.
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Affiliation(s)
- Stefano Ministrini
- Center for Molecular Cardiology, University of Zurich, Zurich, Switzerland
| | - Teresa Padro
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Barcelona, Spain
- Centro de Investigación Biomédica en Red Cardiovascular (CIBERCV) Instituto de Salud Carlos III, Madrid, Spain
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3
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Kostlivy T, Pesta M, Windrichova J, Skopek P, Klail P, Skalova A, Gal B, Kucera R, Plickova K, Simanek V, Slouka D. The impact of obesity, age, and gender on plasmatic levels of selected glycoprotein biomarkers and miRNA-499 in OSA patients. J Appl Biomed 2024; 22:81-88. [PMID: 38912863 DOI: 10.32725/jab.2024.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 05/06/2024] [Indexed: 06/25/2024] Open
Abstract
BACKGROUND The current obstructive sleep apnea (OSA) diagnostic uses polysomnography or limited polygraphy and requires specialized personnel and technical equipment. Glycoprotein biomarkers and microRNAs are being explored as a possible new method for screening. We aimed to evaluate whether certain biomarkers and microRNA, previously identified as related to OSA, could be influenced by factors such as gender, age, and obesity level in patients with OSA. METHODS In this retrospective analytical study, patients with moderate to severe OSA (n = 130) were compared with the control group. Serum levels of selected biomarkers and microRNA were taken from both groups. The group of OSA patients was then stratified by gender, obesity level, and age to see the possible influence of those variables on biomarker levels. RESULTS Levels of all studied biomarkers - C-reactive protein (CRP), high-sensitivity troponin I (hsTnI), pentraxin-3 (PTX-3), and microRNA-499 were significantly higher in patients with OSA compared to the control group. In the OSA group only hsTnI showed a statistically significant relationship with gender. Levels of CRP and hsTnI showed a significant dependence on the level of obesity. Dependency on age was proven for hsTnI. CRP, PTX-3, and microRNA-499 did not have any statistically significant relationship with age. CONCLUSION We found that serum levels of pentraxin-3 and microRNA-499 in patients with moderate to severe obstructive sleep apnoea are independent of gender, obesity, and age. CRP was affected by the level of obesity and hsTnI was influenced by all 3 variables. We consider these findings important for further research of OSA biomarkers.
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Affiliation(s)
- Tomas Kostlivy
- Charles University, University Hospital in Pilsen, Faculty of Medicine in Pilsen, Department of Otorhinolaryngology, Pilsen, Czech Republic
| | - Martin Pesta
- Charles University, Faculty of Medicine in Pilsen, Department of Biology, Pilsen, Czech Republic
| | - Jindra Windrichova
- Charles University, University Hospital in Pilsen, Faculty of Medicine in Pilsen, Department of Immunochemistry Diagnostics, Pilsen, Czech Republic
| | - Petr Skopek
- Charles University, University Hospital in Pilsen, Faculty of Medicine in Pilsen, Department of Otorhinolaryngology, Pilsen, Czech Republic
| | - Pavel Klail
- Charles University, University Hospital in Pilsen, Faculty of Medicine in Pilsen, Department of Otorhinolaryngology, Pilsen, Czech Republic
| | - Alena Skalova
- Charles University, University Hospital in Pilsen, Faculty of Medicine in Pilsen, Department of Pathology, Pilsen, Czech Republic
| | - Bretislav Gal
- Masaryk University, Faculty of Medicine, Department of Otorhinolaryngology and Head and Neck Surgery, Brno, Czech Republic
| | - Radek Kucera
- Charles University, Faculty of Medicine in Pilsen, Department of Pharmacology and Toxicology, Pilsen, Czech Republic
| | - Krista Plickova
- Charles University, University Hospital in Pilsen, Faculty of Medicine in Pilsen, Department of Pneumology and Phthisiology, Pilsen, Czech Republic
| | - Vaclav Simanek
- Charles University, University Hospital in Pilsen, Faculty of Medicine in Pilsen, Department of Otorhinolaryngology, Pilsen, Czech Republic
| | - David Slouka
- Charles University, University Hospital in Pilsen, Faculty of Medicine in Pilsen, Department of Otorhinolaryngology, Pilsen, Czech Republic
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4
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Azam HMH, Rößling RI, Geithe C, Khan MM, Dinter F, Hanack K, Prüß H, Husse B, Roggenbuck D, Schierack P, Rödiger S. MicroRNA biomarkers as next-generation diagnostic tools for neurodegenerative diseases: a comprehensive review. Front Mol Neurosci 2024; 17:1386735. [PMID: 38883980 PMCID: PMC11177777 DOI: 10.3389/fnmol.2024.1386735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 04/12/2024] [Indexed: 06/18/2024] Open
Abstract
Neurodegenerative diseases (NDs) are characterized by abnormalities within neurons of the brain or spinal cord that gradually lose function, eventually leading to cell death. Upon examination of affected tissue, pathological changes reveal a loss of synapses, misfolded proteins, and activation of immune cells-all indicative of disease progression-before severe clinical symptoms become apparent. Early detection of NDs is crucial for potentially administering targeted medications that may delay disease advancement. Given their complex pathophysiological features and diverse clinical symptoms, there is a pressing need for sensitive and effective diagnostic methods for NDs. Biomarkers such as microRNAs (miRNAs) have been identified as potential tools for detecting these diseases. We explore the pivotal role of miRNAs in the context of NDs, focusing on Alzheimer's disease, Parkinson's disease, Multiple sclerosis, Huntington's disease, and Amyotrophic Lateral Sclerosis. The review delves into the intricate relationship between aging and NDs, highlighting structural and functional alterations in the aging brain and their implications for disease development. It elucidates how miRNAs and RNA-binding proteins are implicated in the pathogenesis of NDs and underscores the importance of investigating their expression and function in aging. Significantly, miRNAs exert substantial influence on post-translational modifications (PTMs), impacting not just the nervous system but a wide array of tissues and cell types as well. Specific miRNAs have been found to target proteins involved in ubiquitination or de-ubiquitination processes, which play a significant role in regulating protein function and stability. We discuss the link between miRNA, PTM, and NDs. Additionally, the review discusses the significance of miRNAs as biomarkers for early disease detection, offering insights into diagnostic strategies.
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Affiliation(s)
- Hafiz Muhammad Husnain Azam
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Rosa Ilse Rößling
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
- Department of Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Christiane Geithe
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, The Brandenburg Medical School Theodor Fontane and the University of Potsdam, Berlin, Germany
| | - Muhammad Moman Khan
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Franziska Dinter
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
- PolyAn GmbH, Berlin, Germany
| | - Katja Hanack
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Harald Prüß
- German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
- Department of Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Britta Husse
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Dirk Roggenbuck
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Peter Schierack
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Stefan Rödiger
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, The Brandenburg Medical School Theodor Fontane and the University of Potsdam, Berlin, Germany
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5
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Giuriato G, Romanelli MG, Bartolini D, Vernillo G, Pedrinolla A, Moro T, Franchi M, Locatelli E, Andani ME, Laginestra FG, Barbi C, Aloisi GF, Cavedon V, Milanese C, Orlandi E, De Simone T, Fochi S, Patuzzo C, Malerba G, Fabene P, Donadelli M, Stabile AM, Pistilli A, Rende M, Galli F, Schena F, Venturelli M. Sex differences in neuromuscular and biological determinants of isometric maximal force. Acta Physiol (Oxf) 2024; 240:e14118. [PMID: 38385696 DOI: 10.1111/apha.14118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/29/2024] [Accepted: 02/09/2024] [Indexed: 02/23/2024]
Abstract
AIM Force expression is characterized by an interplay of biological and molecular determinants that are expected to differentiate males and females in terms of maximal performance. These include muscle characteristics (muscle size, fiber type, contractility), neuromuscular regulation (central and peripheral factors of force expression), and individual genetic factors (miRNAs and gene/protein expression). This research aims to comprehensively assess these physiological variables and their role as determinants of maximal force difference between sexes. METHODS Experimental evaluations include neuromuscular components of isometric contraction, intrinsic muscle characteristics (proteins and fiber type), and some biomarkers associated with muscle function (circulating miRNAs and gut microbiome) in 12 young and healthy males and 12 females. RESULTS Male strength superiority appears to stem primarily from muscle size while muscle fiber-type distribution plays a crucial role in contractile properties. Moderate-to-strong pooled correlations between these muscle parameters were established with specific circulating miRNAs, as well as muscle and plasma proteins. CONCLUSION Muscle size is crucial in explaining the differences in maximal voluntary isometric force generation between males and females with similar fiber type distribution. Potential physiological mechanisms are seen from associations between maximal force, skeletal muscle contractile properties, and biological markers.
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Affiliation(s)
- Gaia Giuriato
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
- Surgical, Medical and Dental Department of Morphological Sciences Related to Transplant, Oncology and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - Maria Grazia Romanelli
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Desirée Bartolini
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Gianluca Vernillo
- Department of Biomedical Sciences for Health, Università degli Studi di Milano, Milan, Italy
- Department of Social Sciences, University of Alberta - Augustana Campus, Camrose, Alberta, Canada
| | - Anna Pedrinolla
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Tatiana Moro
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Martino Franchi
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Elena Locatelli
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Mehran Emadi Andani
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Fabio Giuseppe Laginestra
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
- Department of Anesthesiology, University of Utah, Utah, USA
| | - Chiara Barbi
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Gloria Fiorini Aloisi
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Valentina Cavedon
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Chiara Milanese
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Elisa Orlandi
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Tonia De Simone
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Stefania Fochi
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Cristina Patuzzo
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Giovanni Malerba
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Paolo Fabene
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Massimo Donadelli
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Anna Maria Stabile
- Department of Medicine and Surgery, Section of Human Anatomy, Clinical and Forensic, School of Medicine, University of Perugia, Perugia, Italy
| | - Alessandra Pistilli
- Department of Medicine and Surgery, Section of Human Anatomy, Clinical and Forensic, School of Medicine, University of Perugia, Perugia, Italy
| | - Mario Rende
- Department of Medicine and Surgery, Section of Human Anatomy, Clinical and Forensic, School of Medicine, University of Perugia, Perugia, Italy
| | - Francesco Galli
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Federico Schena
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - Massimo Venturelli
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
- Department of Internal Medicine, University of Utah, Utah, USA
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6
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Alfaifi J. miRNAs Role in Wilms tumor pathogenesis: Signaling pathways interplay. Pathol Res Pract 2024; 256:155254. [PMID: 38460245 DOI: 10.1016/j.prp.2024.155254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/11/2024]
Abstract
Wilms' tumors (WTs) are the most common type of kidney tumor in children, and a negative outlook is generally associated with widespread anaplastic. MicroRNAs (miRNAs) are crucial in the development of WT by regulating the expression of specific genes. There is an increasing amount of research that connects the dysregulation of miRNAs to the development of various renal illnesses. The conditions encompassed are renal fibrosis, renal cancers, and chronic and polycystic kidney disease. Dysregulation of several important miRNAs, either oncogenic or tumor-suppressing, has been found in WT. The present state of knowledge on the involvement of dysregulated miRNAs in the progression of WT is summarized in this review.
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Affiliation(s)
- Jaber Alfaifi
- Department of Child Health, College of Medicine, University of Bisha, Bisha 61922, Saudi Arabia.
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7
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Salama RM, Eissa N, Doghish AS, Abulsoud AI, Abdelmaksoud NM, Mohammed OA, Abdel Mageed SS, Darwish SF. Decoding the secrets of longevity: unraveling nutraceutical and miRNA-Mediated aging pathways and therapeutic strategies. FRONTIERS IN AGING 2024; 5:1373741. [PMID: 38605867 PMCID: PMC11007187 DOI: 10.3389/fragi.2024.1373741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 03/04/2024] [Indexed: 04/13/2024]
Abstract
MicroRNAs (miRNAs) are short RNA molecules that are not involved in coding for proteins. They have a significant function in regulating gene expression after the process of transcription. Their participation in several biological processes has rendered them appealing subjects for investigating age-related disorders. Increasing data indicates that miRNAs can be influenced by dietary variables, such as macronutrients, micronutrients, trace minerals, and nutraceuticals. This review examines the influence of dietary factors and nutraceuticals on the regulation of miRNA in relation to the process of aging. We examine the present comprehension of miRNA disruption in age-related illnesses and emphasize the possibility of dietary manipulation as a means of prevention or treatment. Consolidating animal and human research is essential to validate the significance of dietary miRNA control in living organisms, despite the abundance of information already provided by several studies. This review elucidates the complex interaction among miRNAs, nutrition, and aging, offering valuable insights into promising areas for further research and potential therapies for age-related disorders.
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Affiliation(s)
- Rania M. Salama
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Misr International University, Cairo, Egypt
| | - Nermin Eissa
- Department of Biomedical Sciences, College of Health Sciences, Abu Dhabi University, Abu Dhabi, United Arab Emirates
| | - Ahmed S. Doghish
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Cairo, Egypt
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, Egypt
| | - Ahmed I. Abulsoud
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, Egypt
- Biochemistry Department, Faculty of Pharmacy, Heliopolis University, Cairo, Egypt
| | | | - Osama A. Mohammed
- Department of Pharmacology, College of Medicine, University of Bisha, Bisha, Saudi Arabia
| | - Sherif S. Abdel Mageed
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Badr University in Cairo (BUC), Cairo, Egypt
| | - Samar F. Darwish
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Badr University in Cairo (BUC), Cairo, Egypt
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8
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Zhong B, Cui C, Cui Q. Identification and Analysis of Sex-Biased MicroRNAs in Human Diseases. Genes (Basel) 2023; 14:1688. [PMID: 37761827 PMCID: PMC10531062 DOI: 10.3390/genes14091688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/11/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
It is well known that significant differences exist between males and females in both physiology and disease. Thus, it is important to identify and analyze sex-biased miRNAs. However, previous studies investigating sex differences in miRNA expression have predominantly focused on healthy individuals or restricted their analysis to a single disease. Therefore, it is necessary to comprehensively identify and analyze the sex-biased miRNAs in diseases. For this purpose, in this study, we first identified the miRNAs showing sex-biased expression between males and females in diseases based on a number of miRNA expression datasets. Then, we performed a bioinformatics analysis for these sex-biased miRNAs. Notably, our findings revealed that women exhibit a greater number of conserved miRNAs that are highly expressed compared to men, and these miRNAs are implicated in a broader spectrum of diseases. Additionally, we explored the enriched transcription factors, functions, and diseases associated with these sex-biased miRNAs using the miRNA set enrichment analysis tool TAM 2.0. The insights gained from this study could carry implications for endeavors such as precision medicine and possibly pave the way for more targeted and tailored approaches to disease management.
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Affiliation(s)
| | | | - Qinghua Cui
- Department of Biomedical Informatics, Center for Noncoding RNA Medicine, State Key Laboratory of Vascular Homeostasis and Remodeling, School of Basic Medical Sciences, Peking University, 38 Xueyuan Rd, Beijing 100191, China; (B.Z.); (C.C.)
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9
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Curcio R, Poli G, Fabi C, Sugoni C, Pasticci MB, Ferranti R, Rossi M, Folletti I, Sanesi L, Santoni E, Dominioni I, Cavallo M, Morgana G, Mordeglia L, Luca G, Pucci G, Brancorsini S, Vaudo G. Exosomal miR-17-5p, miR-146a-3p, and miR-223-3p Correlate with Radiologic Sequelae in Survivors of COVID-19-Related Acute Respiratory Distress Syndrome. Int J Mol Sci 2023; 24:13037. [PMID: 37685844 PMCID: PMC10488112 DOI: 10.3390/ijms241713037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/16/2023] [Accepted: 08/19/2023] [Indexed: 09/10/2023] Open
Abstract
We investigated the association between circulating microRNAs (miRNAs) potentially involved in the lung inflammatory process and fibrosis development among COVID-19-related acute respiratory distress syndrome (ARDS) survivors. At 4 ± 2 months from clinical recovery, COVID-19-related ARDS survivors matched for age, sex, and clinical characteristics underwent chest high-resolution computerized tomography (HRCT) and were selected based on imaging pattern evolution into fully recovered (N = normal), pulmonary opacities (PO) and fibrosis-like lesions (FL). Based on the previous literature, we performed plasma miRNA profiling of exosomal miRNAs belonging to the NLRP3-inflammasome platform with validated (miR-17-5p, miR-223-3p) and putative targets (miR-146a-5p), miRNAs involved in the post-transcriptional regulation of acute phase cytokines (miR128-3p, miR3168, miR125b-2-3p, miR106a-5p), miRNAs belonging to the NLRP4-inflammasome platform (miR-141-3p) and miRNAs related to post-transcriptional regulation of the fibrosis process (miR-21-5p). miR-17-5p, miR-223-3p, and miR-146a-5p were significantly down-regulated in patients with FL when compared to patients with PO. miR-146a-5p was also down-regulated in patients with FL than in N. The expression of the remaining miRNAs did not differ by group. In patients with long-term pulmonary radiological sequelae following COVID-19-related ARDS, a down-regulation of miR-17-5p, miR-146a-3p, and miR-223-3p correlated to fibrosis development in patients showing persistent hyper-reactivity to inflammatory stimulation. Our results support the hypothesis that NLRP3-Inflammasome could be implicated in the process of fibrotic evolution of COVID-19-associated ARDS.
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Affiliation(s)
- Rosa Curcio
- Unit of Internal Medicine, Santa Maria Terni Hospital, 05100 Terni, Italy
| | - Giulia Poli
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy
| | - Consuelo Fabi
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy
| | - Chiara Sugoni
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy
| | - Maria Bruna Pasticci
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy
- Infectious Diseases Unit, Santa Maria Terni Hospital, 05100 Terni, Italy
| | - Roberto Ferranti
- Unit of Radiology, Santa Maria Terni Hospital, 05100 Terni, Italy
| | - Monica Rossi
- Unit of Radiology, Santa Maria Terni Hospital, 05100 Terni, Italy
| | - Ilenia Folletti
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy
- Section of Occupational Medicine, Santa Maria Terni Hospital, 05100 Terni, Italy
| | - Leandro Sanesi
- Unit of Internal Medicine, Santa Maria Terni Hospital, 05100 Terni, Italy
| | - Edoardo Santoni
- Unit of Internal Medicine, Santa Maria Terni Hospital, 05100 Terni, Italy
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy
| | - Irene Dominioni
- Unit of Internal Medicine, Santa Maria Terni Hospital, 05100 Terni, Italy
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy
| | | | - Giovanni Morgana
- Unit of Internal Medicine, Santa Maria Terni Hospital, 05100 Terni, Italy
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy
| | - Lorenzo Mordeglia
- Unit of Internal Medicine, Santa Maria Terni Hospital, 05100 Terni, Italy
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy
| | - Giovanni Luca
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy
| | - Giacomo Pucci
- Unit of Internal Medicine, Santa Maria Terni Hospital, 05100 Terni, Italy
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy
| | - Stefano Brancorsini
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy
| | - Gaetano Vaudo
- Unit of Internal Medicine, Santa Maria Terni Hospital, 05100 Terni, Italy
- Department of Medicine and Surgery, University of Perugia, 06132 Perugia, Italy
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10
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Kauschke V, Philipp-Gehlhaar M, Schneider J. Expression of microRNAs in leukocytes and serum of asbestosis patients. Eur J Med Res 2023; 28:175. [PMID: 37189132 PMCID: PMC10184414 DOI: 10.1186/s40001-023-01129-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 04/26/2023] [Indexed: 05/17/2023] Open
Abstract
BACKGROUND Although asbestos use is banned in many countries, long latency of asbestos-related diseases like pleural plaques or asbestosis mean it is still a public health issue. People suffering from these diseases have a higher risk of developing mesothelioma or lung cancer, which can progress quickly and aggressively. MicroRNAs were suggested as potential biomarkers in several diseases. However, in asbestosis, blood microRNAs are less explored. Since miR-32-5p, miR-143-3p, miR-145-5p, miR-146b-5p, miR-204-5p and miR-451a are involved in fibrotic processes and in cancer, expression of these microRNAs was analyzed in leukocytes and serum of asbestosis patients. METHODS MicroRNA expression was analyzed in leukocytes and serum of 36 patients (26 affected by pleural plaques and 10 by asbestosis) and 15 healthy controls by real-time RT-PCR. Additionally, data analyses were performed regarding disease severity based on ILO classification. RESULTS MicroRNA miR-146b-5p was significantly down-regulated in leukocytes of patients suffering from pleural plaques with a large effect indicated by η2p = 0.150 and Cohen's f = 0.42, a value of difference of 0.725 and a 95% confidence interval of 0.070-1.381. In patients suffering from asbestosis miR-146b-5p was not significantly regulated. However, data analyses considering disease severity only, revealed that miR-146b-5p was significantly down-regulated in leukocytes of mildly diseased patients compared to controls with a large effect indicated by η2p = 0.178 and Cohen's f = 0.465, a value of difference of 0.848 and a 95% confidence interval of 0.097-1.599. Receiver operating characteristic (ROC) curve and an area under the ROC curve value of 0.757 for miR-146b-5p indicated acceptable discrimination ability between patients suffering from pleural plaques and healthy controls. Less microRNAs were detectable in serum than in leukocytes, showing no significant expression differences in all participants of this study. Moreover, miR-145-5p was regulated significantly differently in leukocytes and serum. An R2 value of 0.004 for miR-145-5p indicated no correlation in microRNA expression between leukocytes and serum. CONCLUSION Leukocytes seem more suitable than serum for microRNA analyses regarding disease and potentially cancer risk assessment of patients suffering from asbestos-related pleural plaques or asbestosis. Long-term studies may reveal whether down-regulation of miR-146b-5p in leukocytes might be an early indicator for an increased cancer risk.
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Affiliation(s)
- Vivien Kauschke
- Institute and Outpatient Clinic of Occupational and Social Medicine, University Hospital of Giessen and Marburg, Aulweg 129, 35392, Giessen, Germany.
| | - Monika Philipp-Gehlhaar
- Institute and Outpatient Clinic of Occupational and Social Medicine, University Hospital of Giessen and Marburg, Aulweg 129, 35392, Giessen, Germany
| | - Joachim Schneider
- Institute and Outpatient Clinic of Occupational and Social Medicine, University Hospital of Giessen and Marburg, Aulweg 129, 35392, Giessen, Germany
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11
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The sheep miRNAome: Characterization and distribution of miRNAs in 21 tissues. Gene X 2023; 851:146998. [DOI: 10.1016/j.gene.2022.146998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/10/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
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12
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Mahdavi Anari SR, Kheirkhah B, Amini K, Roozafzai F. Expression of MicroRNA-155 in Patients with Non-Hodgkin Lymphoma, Coronavirus Disease 2019, or Both: A Cross-Sectional Study. IRANIAN JOURNAL OF MEDICAL SCIENCES 2023; 48:26-34. [PMID: 36688191 PMCID: PMC9843467 DOI: 10.30476/ijms.2022.91669.2282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 11/23/2021] [Accepted: 12/10/2021] [Indexed: 01/24/2023]
Abstract
Background Non-Hodgkin lymphoma (NHL) is the eleventh leading cause of cancer-related death in the world. Diffuse large B-cell lymphoma (DLBCL) is the most common type of NHL. Up to winter 2021-2022, the death toll caused by the coronavirus disease 2019 (COVID-19) has exceeded 5.6 million worldwide. Possible molecular mechanisms involved in the systemic inflammation, and cytokine storm in COVID-19 patients are still not fully understood. MicroRNA-155 (miR-155) plays a role in the post-transcriptional gene regulation of hematopoiesis, oncogenesis, and inflammation. The present study aimed to evaluate the expression of miR-155 in patients with DLBCL and/or COVID-19. Methods A cross-sectional study was conducted from July to December 2020 in Tehran (Iran) to evaluate the expression of miR-155 in adult patients diagnosed with DLBCL and/or COVID-19. The real-time polymerase chain reaction technique was used to evaluate the expression of miR-155 in the sera of 92 adults who were either healthy or suffering from DLBCL and/or COVID-19. Relative quantification of gene expression was calculated in terms of cycle threshold (Ct) value. Data were analyzed using SPSS software, and P<0.05 was considered statistically significant. Results The expression of miR-155 was not associated with the sex or age of the participants. In comparison with healthy individuals (-ΔCt -1.92±0.25), the expression of miR-155 increased in patients with COVID-19 (1.95±0.14), DLBCL (2.25±0.16), or both (4.33±0.65). Conclusion The expression of miR-155 increased in patients with DLBCL and/or COVID-19.
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Affiliation(s)
| | - Babak Kheirkhah
- Department of Biology, Sirjan Branch, Islamic Azad University, Sirjan, Iran,
Department of Microbiology, Kerman Branch, Islamic Azad University, Kerman, Iran
| | - Kumarss Amini
- Department of Microbiology, Saveh Branch, Islamic Azad University, Saveh, Iran
| | - Farzin Roozafzai
- Digestive Diseases Research Institute, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
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13
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Guan S, Yu YN, Li B, Gu H, Chen L, Wang N, Wang B, Liu X, Liu J, Wang Z. Discovery of Drug-Responsive Phenomic Alteration-Related Driver Genes in the Treatment of Coronary Heart Disease. Pharmgenomics Pers Med 2023; 16:201-217. [PMID: 36945217 PMCID: PMC10024908 DOI: 10.2147/pgpm.s398522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/25/2023] [Indexed: 03/17/2023] Open
Abstract
Background The Xueyu Zheng (XYZ) phenome is central to coronary heart disease (CHD), but efforts to detect genetic associations in the XYZ phenome have been disappointing. Methods The phenomic alteration-related genes (PARGs) for the XYZ phenome were screened using |ρ| > 0.4 and p < 0.05 after treatment with Danhong injection at day 14 and day 30. Then, the driver genes for the Protein-Protein Interaction (PPI) networks of the PARGs established using STRING 11.0 were detected using a personalized network control algorithm (PNC). Finally, the molecular correlations of the driver genes with the XYZ phenome were analyzed with the Gene Ontology (GO) biological processes and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways from a holistic viewpoint. Results A total of 525 and 309 PARGs in the XYZ phenome at day 14 and day 30 were identified. These genes were separately enriched in 48 and 35 pathways. Furthermore, five driver genes were detected. These genes were mainly correlated with endoplasmic reticulum stress-mediated apoptosis and autophagy regulation, which could suppress atherosclerosis progression. Conclusion Our study detected the drug-responsive PARGs of the XYZ phenome in CHD and provides an exemplary strategy to investigate the genetic associations among this common phenome and its component symptoms in patients with CHD. Trial Registration ClinicalTrials.gov, NCT01681316; registered on September 7, 2012.
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Affiliation(s)
- Shuang Guan
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, People’s Republic of China
| | - Ya-Nan Yu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, People’s Republic of China
| | - Bing Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, People’s Republic of China
| | - Hao Gu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, People’s Republic of China
| | - Lin Chen
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, People’s Republic of China
| | - Nian Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, People’s Republic of China
| | - Bo Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, People’s Republic of China
| | - Xi Liu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, People’s Republic of China
| | - Jun Liu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, People’s Republic of China
| | - Zhong Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, People’s Republic of China
- Correspondence: Zhong Wang; Jun Liu, Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, No. 16 Nanxiaojie, Dongzhimennei, Beijing, People’s Republic of China, Email ;
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14
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Functional Implications and Clinical Potential of MicroRNAs in Irritable Bowel Syndrome: A Concise Review. Dig Dis Sci 2023; 68:38-53. [PMID: 35507132 PMCID: PMC9066399 DOI: 10.1007/s10620-022-07516-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 04/04/2022] [Indexed: 02/01/2023]
Abstract
MicroRNAs (miRNAs) are tiny (20-24 nucleotides long), non-coding, highly conserved RNA molecules that play a crucial role within the post-transcriptional regulation of gene expression via sequence-specific mechanisms. Since the miRNA transcriptome is involved in multiple molecular processes needed for cellular homeostasis, its altered expression can trigger the development and progression of several human pathologies. In this context, over the last few years, several relevant studies have demonstrated that dysregulated miRNAs affect a wide range of molecular mechanisms associated with irritable bowel syndrome (IBS), a common gastrointestinal disorder. For instance, abnormal miRNA expression in IBS patients is related to the alteration of intestinal permeability, visceral hyperalgesia, inflammatory pathways, and pain sensitivity. Besides, specific miRNAs are differentially expressed in the different subtypes of IBS, and therefore, they might be used as biomarkers for precise diagnosis of these pathological conditions. Accordingly, miRNAs have noteworthy potential as theragnostic targets for IBS. Hence, in this current review, we present an overview of the recent discoveries regarding the clinical relevance of miRNAs in IBS, which might be useful in the future for the development of miRNA-based drugs against this disorder.
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15
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Hamza E, Cosandey J, Gerber V, Koch C, Unger L. The potential of three whole blood microRNAs to predict outcome and monitor treatment response in sarcoid-bearing equids. Vet Res Commun 2023; 47:87-98. [PMID: 35484337 PMCID: PMC9873782 DOI: 10.1007/s11259-022-09930-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/19/2022] [Indexed: 01/28/2023]
Abstract
MicroRNAs (miRNAs) have been proposed as biomarkers for equine sarcoid (ES) disease. In this study, the suitability of three whole blood miRNAs to diagnose ES and to predict and monitor the outcome of therapy was explored. Using reverse transcription-quantitative polymerase chain reaction (RT-qPCR), expression levels of eca-miR-127, eca-miR-379, and eca-miR-432 in whole blood of ES-affected equids before and at least one year after therapy were compared to those of unaffected control equids. Associations of age, sex, species, diagnosis, and therapy outcome with miRNA expression levels were examined using general linear models. In total, 48 ES-affected equids and 47 control equids were recruited. From the affected animals, 31 responded favorably to treatment, and 17 demonstrated a failure of therapy. None of the tested miRNAs were influenced by age. Male equids showed increased expression of eca-miR-127 compared to females and horses showed higher expression levels of eca-miR-379 and eca-miR-432 than donkeys. Eca-miR-127 was confirmed as a diagnostic discriminator between ES-affected and control equids. No difference in miRNA profiles before therapy was found when comparing ES-affected equids with success vs. failure of therapy. Eca-miR-379 and eca-miR-432 decreased over time in horses where therapy was successful, but not in those cases where it failed. Biological variables influence equine whole blood miRNA expression, which may complicate biomarker validation. While none of the tested miRNAs could predict the response to therapy in ES-affected equids and eca-miR-127 showed poor diagnostic accuracy for ES, eca-miR-379 and eca-miR-432 miRNAs might allow refinement of monitoring of success of ES therapy.
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Affiliation(s)
- E. Hamza
- Swiss Institute of Equine Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, Switzerland ,Departement of Zoonoses, Faculty of Veterinary Medicine, Cairo University, Cairo, Egypt
| | - J. Cosandey
- Swiss Institute of Equine Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - V. Gerber
- Swiss Institute of Equine Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - C. Koch
- Swiss Institute of Equine Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - L. Unger
- Swiss Institute of Equine Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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16
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MiR-371a-5p Positively Associates with Hepatocellular Carcinoma Malignancy but Sensitizes Cancer Cells to Oxaliplatin by Suppressing BECN1-Dependent Autophagy. Life (Basel) 2022; 12:life12101651. [DOI: 10.3390/life12101651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/07/2022] [Accepted: 10/17/2022] [Indexed: 01/27/2023] Open
Abstract
Oxaliplatin (OXA)-based chemotherapy demonstrates active efficacy in advanced hepatocellular carcinoma (HCC), while resistance development limits its clinical efficacy. Thus, identifying resistance-related molecules and underlying mechanisms contributes to improving the therapeutic efficacy of HCC patients. MicroRNA-371a-5p (MiR-371a-5p) fulfills an important function in tumor progression. However, little is known about the effect of miR-371a-5p on chemotherapy response. In this study, quantitative real-time polymerase chain reaction, Western blot and immunohistochemistry were used to determine the expression levels of miR-371a-5p, BECN1 and autophagy-related proteins in HCC cells, tissues and serum. The luciferase reporter assay was used to assess the directly suppressive effect of miR-371a-5p on BECN1 mRNA translation. Moreover, gain- and loss-of-function assays and rescue assays were used to evaluate the mediated effect of BECN1-dependent autophagy on the role of miR-371a-5p in the response of HCC cells to OXA. We found that miR-371a-5p was significantly up-regulated in HCC tissues and serum from patients, whereas BECN1 protein was down-regulated in HCC tissues compared to the corresponding controls. We also found that there was a negative correlation between the two molecules in HCC tissues. In addition, we found that miR-371a-5p expression was positively associated with malignant characteristics of HCC and BECN1 protein expression is negatively associated. Contrary to this, we found that miR-371a-5p enhances and BECN1 attenuates the response of HCC cells to OXA. Importantly, the enhanced effect of miR-371a-5p on the response of HCC cells to OXA could be reduced by re-expression of non-targetable BECN1, and then the reduced effect was restored following bafilomycin A treatment. Taken together, we identified a dual role of miR-371a-5p in HCC malignant characteristics and the response of HCC cells to oxaliplatin. Importantly, we reveal that miR-371a-5p enhances oxaliplatin response by target suppression of BECN1-dependent autophagy.
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17
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Comprehensive microRNA-seq transcriptomic profiling across 11 organs, 4 ages, and 2 sexes of Fischer 344 rats. Sci Data 2022; 9:201. [PMID: 35551205 PMCID: PMC9098487 DOI: 10.1038/s41597-022-01285-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 03/04/2022] [Indexed: 11/08/2022] Open
Abstract
Rat is one of the most widely-used models in chemical safety evaluation and biomedical research. However, the knowledge about its microRNA (miRNA) expression patterns across multiple organs and various developmental stages is still limited. Here, we constructed a comprehensive rat miRNA expression BodyMap using a diverse collection of 320 RNA samples from 11 organs of both sexes of juvenile, adolescent, adult and aged Fischer 344 rats with four biological replicates per group. Following the Illumina TruSeq Small RNA protocol, an average of 5.1 million 50 bp single-end reads was generated per sample, yielding a total of 1.6 billion reads. The quality of the resulting miRNA-seq data was deemed to be high from raw sequences, mapped sequences, and biological reproducibility. Importantly, aliquots of the same RNA samples have previously been used to construct the mRNA BodyMap. The currently presented miRNA-seq dataset along with the existing mRNA-seq dataset from the same RNA samples provides a unique resource for studying the expression characteristics of existing and novel miRNAs, and for integrative analysis of miRNA-mRNA interactions, thereby facilitating better utilization of rats for biomarker discovery.
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18
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Radiation therapy for triple-negative breast cancer: emerging role of microRNAs as biomarkers and radiosensitivity modifiers. A systematic review. Breast Cancer Res Treat 2022; 193:265-279. [PMID: 35397079 DOI: 10.1007/s10549-022-06533-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 01/19/2022] [Indexed: 11/02/2022]
Abstract
PURPOSE Radiation therapy (RT) for triple-negative breast cancer (TNBC) treatment is currently delivered in the adjuvant setting and is under investigation as a booster of neoadjuvant treatments. However, TNBC radioresistance remains an obstacle, so new biomarkers are needed to select patients for any integration of RT in the TNBC therapy sequence. MicroRNAs (miRs) are important regulators of gene expression, involved in cancer response to ionizing radiation (IR) and assessable by tumor tissue or liquid biopsy. This systematic review aimed to evaluate the relationships between miRs and response to radiation in TNBC, as well as their potential predictive and prognostic values. METHODS A thorough review of studies related to miRs and RT in TNBC was performed on PubMed, EMBASE, and Web of Science. We searched for original English articles that involved dysregulation of miRs in response to IR on TNBC-related preclinical and clinical studies. After a rigorous selection, 44 studies were chosen for further analysis. RESULTS Thirty-five miRs were identified to be TNBC related, out of which 21 were downregulated, 13 upregulated, and 2 had a double-side expression in this cancer. Expression modulation of many of these miRs is radiosensitizing, among which miR-7, -27a, -34a, -122, and let-7 are most studied, still only in experimental models. The miRs reported as most influencing/reflecting TNBC response to IR are miR-7, -27a, -155, -205, -211, and -221, whereas miR-21, -33a, -139-5p, and -210 are associated with TNBC patient outcome after RT. CONCLUSION miRs are emerging biomarkers and radiosensitizers in TNBC, worth further investigation. Dynamic assessment of circulating miRs could improve monitoring and TNBC RT efficacy, which are of particular interest in the neoadjuvant and the high-risk patients' settings.
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19
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Liu G, Liu X, Yang Y. Comparative transcriptome analysis of miRNA in hydronephrosis male children caused by ureteropelvic junction obstruction with or without renal functional injury. PeerJ 2022; 10:e12962. [PMID: 35237468 PMCID: PMC8884061 DOI: 10.7717/peerj.12962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 01/27/2022] [Indexed: 01/11/2023] Open
Abstract
MicroRNAs (miRNAs or miRs) are non-coding RNAs that contribute to pathological processes of various kidney diseases. Renal function injury represents a final common outcome of congenital obstructive nephropathy and has attracted a great deal of attention. However the molecular mechanisms are still not fully established. In this study, we compared transcriptome sequencing data of miRNAs of renal tissues from congenital hydronephrosis children with or without renal functional injury, in order to better understand whether microRNAs could play important roles in renal functional injury after ureteropelvic junction obstruction. A total of 22 microRNAs with significant changes in their expression were identified. Five microRNAs were up-regulated and 17 microRNAs were down-regulated in the renal tissues of the hydronephrosis patients with renal function injury compared with those without renal function injury. MicroRNA target genes were predicted by three major online miRNA target prediction algorithms, and all these mRNAs were used to perform the gene ontology analysis and Kyoto Encyclopedia of Gene and Genomes pathway analysis. Then, twelve candidate human and rat homologous miRNAs were selected for validation using RT-qPCR in vitro and in vivo; only miR-187-3p had a trend identical to that detected by the sequencing results among the human tissues, in vivo and in vitro experimental models. In addition, we found that the change of miR-187-3p in vivo was consistent with results in vitro models and showed a decrease trend in time dependence. These results provided a detailed catalog of candidate miRNAs to investigate their regulatory role in renal injury of congenital hydronephrosis, indicating that they may serve as candidate biomarkers or therapeutic targets in the future.
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Affiliation(s)
- Ge Liu
- Urology Division, Pediatric Surgery Department, Shengjing Hospital of China Medical University, Shenyang, Liaoning, People’s Republic of China
| | - Xin Liu
- Urology Division, Pediatric Surgery Department, Shengjing Hospital of China Medical University, Shenyang, Liaoning, People’s Republic of China
| | - Yi Yang
- Urology Division, Pediatric Surgery Department, Shengjing Hospital of China Medical University, Shenyang, Liaoning, People’s Republic of China
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20
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Wojtusik J, Curry E, Roth TL. Rhinoceros Serum microRNAs: Identification, Characterization, and Evaluation of Potential Iron Overload Biomarkers. Front Vet Sci 2021; 8:711576. [PMID: 34977204 PMCID: PMC8716540 DOI: 10.3389/fvets.2021.711576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 11/17/2021] [Indexed: 11/13/2022] Open
Abstract
Iron overload disorder (IOD) in critically endangered Sumatran (Dicerorhinus sumatrensis) and black (Diceros bicornis) rhinoceros is an over-accumulation of iron in organs which may exacerbate other diseases and indicate metabolic disturbances. IOD in rhinos is not well understood and diagnostics and therapeutics are limited in effectiveness. MicroRNAs (miRNAs) are small non-coding RNAs capable of altering protein synthesis. miRNA expression responds to physiological states and could serve as the basis for development of diagnostics and therapeutics. This study aimed to identify miRNAs differentially expressed among healthy rhinos and those afflicted with IOD or other diseases ("unhealthy"), and assess expression of select miRNAs to evaluate their potential as biomarkers of IOD. miRNAs in serum of black (n = 11 samples; five individuals) and Sumatran (n = 7 samples; four individuals) rhinos, representing individuals categorized as healthy (n = 9), unhealthy (n = 5), and afflicted by IOD (n = 3) were sequenced. In total, 715 miRNAs were identified, of which 160 were novel, 131 were specific to black rhinos, and 108 were specific to Sumatran rhinos. Additionally, 95 miRNAs were specific to healthy individuals, 31 specific to unhealthy, and 63 were specific to IOD individuals. Among healthy, unhealthy, and IOD states, 21 miRNAs were differentially expressed (P ≤ 0.01). Five known miRNAs (let-7g, miR-16b, miR-30e, miR-143, and miR-146a) were selected for further assessment via RT-qPCR in serum from black (n = 61 samples; seven individuals) and Sumatran (n = 38 samples; five individuals) rhinos. let-7g, miR-30e, and miR-143 all showed significant increased expression (P ≤ 0.05) during IOD (between 1 and 2 years prior to death) and late IOD (within 1 year of death) compared to healthy and unhealthy individuals. miR-16b expression increased (P ≤ 0.05) in late IOD, but was not different among IOD, healthy, and unhealthy states (P > 0.05). Expression of miR-146a increased in IOD and late IOD as compared to unhealthy samples (P ≤ 0.05) but was not different from the healthy state (P > 0.05). Selected serum miRNAs of black and Sumatran rhinos, in particular let-7g, miR-30e, and miR-143, could therefore provide a tool for advancing rhino IOD diagnostics that should be further investigated.
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Affiliation(s)
- Jessye Wojtusik
- Center for Conservation and Research of Endangered Wildlife (CREW), Cincinnati Zoo and Botanical Garden, Cincinnati, OH, United States
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21
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Francavilla A, Gagliardi A, Piaggeschi G, Tarallo S, Cordero F, Pensa RG, Impeduglia A, Caviglia GP, Ribaldone DG, Gallo G, Grioni S, Ferrero G, Pardini B, Naccarati A. Faecal miRNA profiles associated with age, sex, BMI, and lifestyle habits in healthy individuals. Sci Rep 2021; 11:20645. [PMID: 34667192 PMCID: PMC8526833 DOI: 10.1038/s41598-021-00014-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/05/2021] [Indexed: 12/14/2022] Open
Abstract
For their stability and detectability faecal microRNAs represent promising molecules with potential clinical interest as non-invasive diagnostic and prognostic biomarkers. However, there is no evidence on how stool miRNA profiles change according to an individual’s age, sex, and body mass index (BMI) or how lifestyle habits influence the expression levels of these molecules. We explored the relationship between the stool miRNA levels and common traits (sex, age, BMI, and menopausal status) or lifestyle habits (physical activity, smoking status, coffee, and alcohol consumption) as derived by a self-reported questionnaire, using small RNA-sequencing data of samples from 335 healthy subjects. We detected 151 differentially expressed miRNAs associated with one variable and 52 associated with at least two. Differences in miR-638 levels were associated with age, sex, BMI, and smoking status. The highest number of differentially expressed miRNAs was associated with BMI (n = 92) and smoking status (n = 84), with several miRNAs shared between them. Functional enrichment analyses revealed the involvement of the miRNA target genes in pathways coherent with the analysed variables. Our findings suggest that miRNA profiles in stool may reflect common traits and lifestyle habits and should be considered in relation to disease and association studies based on faecal miRNA expression.
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Affiliation(s)
- Antonio Francavilla
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Turin, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Amedeo Gagliardi
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Turin, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Giulia Piaggeschi
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Turin, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Sonia Tarallo
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Turin, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | | | - Ruggero G Pensa
- Department of Computer Science, University of Turin, Turin, Italy
| | | | - Gian Paolo Caviglia
- Division of Gastroenterology, Department of Medical Sciences, University of Turin, Turin, Italy
| | | | - Gaetano Gallo
- Department of Medical and Surgical Sciences, University of Catanzaro, Catanzaro, Italy
| | - Sara Grioni
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale Dei Tumori Di Milano, Milan, Italy
| | - Giulio Ferrero
- Department of Computer Science, University of Turin, Turin, Italy.,Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Barbara Pardini
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Turin, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Alessio Naccarati
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Candiolo, Turin, Italy. .,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy.
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Tutino V, De Nunzio V, Milella RA, Gasparro M, Cisternino AM, Gigante I, Lanzilotta E, Iacovazzi PA, Lippolis A, Lippolis T, Caruso MG, Notarnicola M. Impact of Fresh Table Grape Intake on Circulating microRNAs Levels in Healthy Subjects: A Significant Modulation of Gastrointestinal Cancer-Related Pathways. Mol Nutr Food Res 2021; 65:e2100428. [PMID: 34495579 DOI: 10.1002/mnfr.202100428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/23/2021] [Indexed: 12/11/2022]
Abstract
SCOPE The study aims to investigate the effects of fresh table grape consumption in healthy subjects on circulating levels of the most common human microRNAs (miRNAs). The regulatory network governed by these modulated miRNAs is also investigated. METHODS AND RESULTS Autumn Royal table grape, used in this study, is chosen for its high polyphenolic content and antioxidant properties. The study is a randomized controlled trial, in which 40 consecutive subjects are recruited on a voluntary basis and randomly assigned to two groups of the study, the control group, receiving only dietary recommendations and a grape group receiving a daily dose of 5 g of fresh table grape per kg of body weight for 21 days. All analyses are performed at baseline and after 21 days of dietary treatment. Circulating miRNAs levels are detected by Real-Time quantitative PCR (RT-qPCR) followed by bioinformatic functional analysis. The study identifies 20 circulating miRNAs differentially expressed in healthy subjects after grape intake, and in particular, 18 of 20 are down-regulated and 2 are up-regulated. CONCLUSION The dietary intake of table grape affects circulating miRNAs levels in healthy subjects, particularly the miRNAs related to pathways involved in counteracting cancer development, including gastrointestinal cancers.
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Affiliation(s)
- Valeria Tutino
- Laboratory of Nutritional Biochemistry, National Institute of Gastroenterology "S. de Bellis" Research Hospital, Castellana Grotte (Ba), 70013, Italy
| | - Valentina De Nunzio
- Laboratory of Nutritional Biochemistry, National Institute of Gastroenterology "S. de Bellis" Research Hospital, Castellana Grotte (Ba), 70013, Italy
| | - Rosa Anna Milella
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics, Turi, Bari, 70010, Italy
| | - Marica Gasparro
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics, Turi, Bari, 70010, Italy
| | - Anna Maria Cisternino
- Ambulatory of Clinical Nutrition, National Institute of Gastroenterology "S. de Bellis" Research Hospital, Castellana Grotte (Ba), 70013, Italy
| | - Isabella Gigante
- Laboratory of Nutritional Biochemistry, National Institute of Gastroenterology "S. de Bellis" Research Hospital, Castellana Grotte (Ba), 70013, Italy
| | - Elsa Lanzilotta
- Laboratory of Clinical Pathology, National Institute of Gastroenterology "S. de Bellis" Research Hospital, Castellana Grotte (Ba), 70013, Italy
| | - Palma Aurelia Iacovazzi
- Laboratory of Clinical Pathology, National Institute of Gastroenterology "S. de Bellis" Research Hospital, Castellana Grotte (Ba), 70013, Italy
| | - Antonio Lippolis
- Laboratory of Clinical Pathology, National Institute of Gastroenterology "S. de Bellis" Research Hospital, Castellana Grotte (Ba), 70013, Italy
| | - Tamara Lippolis
- Laboratory of Nutritional Biochemistry, National Institute of Gastroenterology "S. de Bellis" Research Hospital, Castellana Grotte (Ba), 70013, Italy
| | - Maria Gabriella Caruso
- Ambulatory of Clinical Nutrition, National Institute of Gastroenterology "S. de Bellis" Research Hospital, Castellana Grotte (Ba), 70013, Italy
| | - Maria Notarnicola
- Laboratory of Nutritional Biochemistry, National Institute of Gastroenterology "S. de Bellis" Research Hospital, Castellana Grotte (Ba), 70013, Italy
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23
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Liu J, Li DD, Dong W, Liu YQ, Wu Y, Tang DX, Zhang FC, Qiu M, Hua Q, He JY, Li J, Du B, Du TH, Niu LL, Jiang XJ, Cui B, Chen JB, Wang YG, Wang HR, Yu Q, He J, Mao YL, Bin XF, Deng Y, Tian YD, Han QH, Liu DJ, Duan LQ, Zhao MJ, Zhang CY, Dai HY, Li ZH, Xiao Y, Hu YZ, Huang XY, Xing K, Jiang X, Liu CF, An J, Li FC, Tao T, Jiang JF, Yang Y, Dong YR, Zhang L, Fu G, Li Y, Huang SW, Dou LP, Sun LJ, Zhao YQ, Li J, Xia Y, Liu J, Liu F, He WJ, Li Y, Tan JC, Lin Y, Zhou YB, Yang JF, Ma GQ, Chen HJ, Liu HP, Liu ZW, Liu JX, Luo XJ, Bin XH, Yu YN, Dang HX, Li B, Teng F, Qiao WM, Zhu XL, Chen BW, Chen QG, Shen CT, Wang YY, Chen YD, Wang Z. Detection of an anti-angina therapeutic module in the effective population treated by a multi-target drug Danhong injection: a randomized trial. Signal Transduct Target Ther 2021; 6:329. [PMID: 34471087 PMCID: PMC8410855 DOI: 10.1038/s41392-021-00741-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 12/12/2022] Open
Abstract
It’s a challenge for detecting the therapeutic targets of a polypharmacological drug from variations in the responsed networks in the differentiated populations with complex diseases, as stable coronary heart disease. Here, in an adaptive, 31-center, randomized, double-blind trial involving 920 patients with moderate symptomatic stable angina treated by 14-day Danhong injection(DHI), a kind of polypharmacological drug with high quality control, or placebo (0.9% saline), with 76-day following-up, we firstly confirmed that DHI could increase the proportion of patients with clinically significant changes on angina-frequency assessed by Seattle Angina Questionnaire (ΔSAQ-AF ≥ 20) (12.78% at Day 30, 95% confidence interval [CI] 5.86–19.71%, P = 0.0003, 13.82% at Day 60, 95% CI 6.82–20.82%, P = 0.0001 and 8.95% at Day 90, 95% CI 2.06–15.85%, P = 0.01). We also found that there were no significant differences in new-onset major vascular events (P = 0.8502) and serious adverse events (P = 0.9105) between DHI and placebo. After performing the RNA sequencing in 62 selected patients, we developed a systemic modular approach to identify differentially expressed modules (DEMs) of DHI with the Zsummary value less than 0 compared with the control group, calculated by weighted gene co-expression network analysis (WGCNA), and sketched out the basic framework on a modular map with 25 functional modules targeted by DHI. Furthermore, the effective therapeutic module (ETM), defined as the highest correlation value with the phenotype alteration (ΔSAQ-AF, the change in SAQ-AF at Day 30 from baseline) calculated by WGCNA, was identified in the population with the best effect (ΔSAQ-AF ≥ 40), which is related to anticoagulation and regulation of cholesterol metabolism. We assessed the modular flexibility of this ETM using the global topological D value based on Euclidean distance, which is correlated with phenotype alteration (r2: 0.8204, P = 0.019) by linear regression. Our study identified the anti-angina therapeutic module in the effective population treated by the multi-target drug. Modular methods facilitate the discovery of network pharmacological mechanisms and the advancement of precision medicine. (ClinicalTrials.gov identifier: NCT01681316).
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Affiliation(s)
- Jun Liu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Dan-Dan Li
- Department of Cardiology, Chinese PLA General Hospital, Beijing, China
| | - Wei Dong
- Department of Cardiology, Chinese PLA General Hospital, Beijing, China
| | - Yu-Qi Liu
- Department of Cardiology, Chinese PLA General Hospital, Beijing, China
| | - Yang Wu
- Department of Cardiology, Dongfang Hospital Affiliated to Beijing University of Chinese Medicine, Beijing, China
| | - Da-Xuan Tang
- Department of Cardiology, Dongfang Hospital Affiliated to Beijing University of Chinese Medicine, Beijing, China
| | - Fu-Chun Zhang
- Department of Geratology, Peking University Third Hospital, Beijing, China
| | - Meng Qiu
- Department of Geratology, Peking University Third Hospital, Beijing, China
| | - Qi Hua
- Department of Cardiology, Xuan Wu Hospital, Capital Medical University, Beijing, China
| | - Jing-Yu He
- Department of Cardiology, Xuan Wu Hospital, Capital Medical University, Beijing, China
| | - Jun Li
- Department of Cardiology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Bai Du
- Department of Cardiology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ting-Hai Du
- Department of Cardiology, First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan, China
| | - Lin-Lin Niu
- Department of Cardiology, First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan, China
| | - Xue-Jun Jiang
- Department of Cardiology, Wuhan University Renmin Hospital, Wuhan, Hubei, China
| | - Bo Cui
- Department of Cardiology, Wuhan University Renmin Hospital, Wuhan, Hubei, China
| | - Jiang-Bin Chen
- Department of Cardiology, Wuhan University Renmin Hospital, Wuhan, Hubei, China
| | - Yang-Gan Wang
- Department of Cardiology, Wuhan University Zhongnan Hospital, Wuhan, Hubei, China
| | - Hai-Rong Wang
- Department of Cardiology, Wuhan University Zhongnan Hospital, Wuhan, Hubei, China
| | - Qin Yu
- Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China
| | - Jing He
- Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning, China
| | - Yi-Lin Mao
- Department of Cardiology, Second Affiliated Hospital to Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Xiao-Fang Bin
- Department of Cardiology, Second Affiliated Hospital to Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Yue Deng
- Department of Cardiology, First Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Yu-Dan Tian
- Department of Cardiology, First Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Qing-Hua Han
- Department of Cardiology, First Affiliated Hospital to Shanxi Medical University, Taiyuan, Shanxi, China
| | - Da-Jin Liu
- Department of Cardiology, First Affiliated Hospital to Shanxi Medical University, Taiyuan, Shanxi, China
| | - Li-Qin Duan
- Department of Cardiology, First Affiliated Hospital to Shanxi Medical University, Taiyuan, Shanxi, China
| | - Ming-Jun Zhao
- Department of Cardiology, Affiliated Hospital of Shanxi University of Chinese Medicine, Xianyang, Shanxi, China
| | - Cui-Ying Zhang
- Department of Cardiology, Affiliated Hospital of Shanxi University of Chinese Medicine, Xianyang, Shanxi, China
| | - Hai-Ying Dai
- Department of Cardiology, Changsha Central Hospital, Changsha, Hunan, China
| | - Ze-Hua Li
- Department of Cardiology, Changsha Central Hospital, Changsha, Hunan, China
| | - Ying Xiao
- Department of Cardiology, Changsha Central Hospital, Changsha, Hunan, China
| | - You-Zhi Hu
- Department of Cardiology, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, Hubei, China
| | - Xiao-Yu Huang
- Department of Cardiology, Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, Hubei, China
| | - Kun Xing
- Department of Cardiology, Shanxi Provincial People's Hospital, Xi'an, Shanxi, China
| | - Xin Jiang
- Department of Cardiology, Shanxi Provincial People's Hospital, Xi'an, Shanxi, China
| | - Chao-Feng Liu
- Department of Cardiology, Shanxi Province Hospital of Traditional Chinese Medicine, Xi'an, Shanxi, China
| | - Jing An
- Department of Cardiology, Shanxi Province Hospital of Traditional Chinese Medicine, Xi'an, Shanxi, China
| | - Feng-Chun Li
- Department of Cardiology, Xi'an City Hospital of Traditional Chinese Medicine, Xi'an, Shanxi, China
| | - Tao Tao
- Department of Cardiology, Xi'an City Hospital of Traditional Chinese Medicine, Xi'an, Shanxi, China
| | - Jin-Fa Jiang
- Department of Cardiology, Shanghai Tongji Hospital, Shanghai, China
| | - Ying Yang
- Department of Cardiology, Shanghai Tongji Hospital, Shanghai, China
| | - Yao-Rong Dong
- Department of Cardiology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai, China
| | - Lei Zhang
- Department of Cardiology, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai, China
| | - Guang Fu
- Department of Cardiology, The First Hospital of Changsha, Changsha, Hunan, China
| | - Ying Li
- Department of Cardiology, The First Hospital of Changsha, Changsha, Hunan, China
| | - Shu-Wei Huang
- Department of Cardiology, Xinhua Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Li-Ping Dou
- Department of Cardiology, Xinhua Hospital of Zhejiang Province, Hangzhou, Zhejiang, China
| | - Lan-Jun Sun
- Department of Cardiology, Second Affiliated Hospital of Tianjin University of Traditional Chinese Medicine, Zengchan Dao, Tianjin, China
| | - Ying-Qiang Zhao
- Department of Cardiology, Second Affiliated Hospital of Tianjin University of Traditional Chinese Medicine, Zengchan Dao, Tianjin, China
| | - Jie Li
- Department of Cardiology, Second Affiliated Hospital of Tianjin University of Traditional Chinese Medicine, Zengchan Dao, Tianjin, China
| | - Yun Xia
- Department of Chinese medicine, Shanghai Tenth People's Hospital, Shanghai, China
| | - Jun Liu
- Department of Chinese medicine, Shanghai Tenth People's Hospital, Shanghai, China
| | - Fan Liu
- Department of Cardiology, Chongqing City Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Wen-Jin He
- Department of Cardiology, Chongqing City Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Ying Li
- Department of Cardiology, Chongqing City Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Jian-Cong Tan
- Department of Cardiology, Third People's Hospital of Chongqing, Chongqing, China
| | - Yang Lin
- Department of Cardiology, Third People's Hospital of Chongqing, Chongqing, China
| | - Ya-Bin Zhou
- Department of Cardiology, First Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin, Heilongjiang, China
| | - Jian-Fei Yang
- Department of Cardiology, First Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin, Heilongjiang, China
| | - Guo-Qing Ma
- Department of Cardiology, Second Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin, Heilongjiang, China
| | - Hui-Jun Chen
- Department of Cardiology, Second Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin, Heilongjiang, China
| | - He-Ping Liu
- Department of Cardiology, Jilin Province People's Hospital, Changchun, Jilin, China
| | - Zong-Wu Liu
- Department of Cardiology, Jilin Province People's Hospital, Changchun, Jilin, China
| | - Jian-Xiong Liu
- Department of Cardiology, Chengdu Second People's Hospital, Chengdu, Sichuan, China
| | - Xiao-Jia Luo
- Department of Cardiology, Chengdu Second People's Hospital, Chengdu, Sichuan, China
| | - Xiao-Hong Bin
- Department of Cardiology, Chengdu Second People's Hospital, Chengdu, Sichuan, China
| | - Ya-Nan Yu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Hai-Xia Dang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China.,China Academy of Chinese Medical Sciences, Beijing, China
| | - Bing Li
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China.,Institute of Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Fei Teng
- Beijing Genomics Institute (Shenzhen), Shenzhen, Guangdong, China
| | - Wang-Min Qiao
- Beijing Genomics Institute (Shenzhen), Shenzhen, Guangdong, China
| | - Xiao-Long Zhu
- Beijing Genomics Institute (Shenzhen), Shenzhen, Guangdong, China
| | - Bing-Wei Chen
- School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Qi-Guang Chen
- School of Public Health, Southeast University, Nanjing, Jiangsu, China
| | - Chun-Ti Shen
- Changzhou Hospital of Traditional Chinese Medicine, Changzhou, Jiangsu, China
| | - Yong-Yan Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China.
| | - Yun-Dai Chen
- Department of Cardiology, Chinese PLA General Hospital, Beijing, China.
| | - Zhong Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China.
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24
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Abu-Halima M, Becker LS, Ayesh BM, Baus SL, Hamza A, Fischer U, Hammadeh M, Keller A, Meese E. Characterization of micro-RNA in women with different ovarian reserve. Sci Rep 2021; 11:13351. [PMID: 34172798 PMCID: PMC8233349 DOI: 10.1038/s41598-021-92901-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 06/08/2021] [Indexed: 12/11/2022] Open
Abstract
Women undergoing infertility treatment are routinely subjected to one or more tests of ovarian reserve. Therefore, an adequate assessment of the ovarian reserve is necessary for the treatment. In this study, we aimed to characterize the potential role of microRNAs (miRNAs) as biomarkers for women with different ovarian reserves. A total of 159 women were recruited in the study and classified according to their anti-Müllerian hormone (AMH) level into three groups: (1) low ovarian reserve (LAMH, n = 39), (2) normal ovarian reserve (NAMH, n = 80), and (3) high ovarian reserve (HAMH, n = 40). SurePrint Human miRNA array screening and reverse transcription-quantitative PCR (RT-qPCR) were respectively employed to screen and validate the miRNA abundance level in the three tested groups. Compared with NAMH, the abundance level of 34 and 98 miRNAs was found to be significantly altered in LAMH and HAMH, respectively. The abundance level of miRNAs was further validated by RT-qPCR in both, the screening samples as well as in an independent set of validation samples. The abundance levels of the validated miRNAs were significantly correlated with the AMH level. The best AUC value for the prediction of the increase and decrease in the AMH level was obtained for the miR-100-5p and miR-21-5p, respectively. The level of miRNAs abundance correlates with the level of AMH, which may serve as a tool for identifying women with a different ovarian reserve and may help to lay the ground for the development of novel diagnostic approaches.
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Affiliation(s)
- Masood Abu-Halima
- Institute of Human Genetics, Saarland University, 66421, Homburg, Saar, Germany.
| | - Lea Simone Becker
- Institute of Human Genetics, Saarland University, 66421, Homburg, Saar, Germany
| | - Basim M Ayesh
- Department of Laboratory Medical Sciences, Alaqsa University, Gaza, Palestine
| | - Simona Lucia Baus
- Department of Obstetrics and Gynecology, Saarland University, 66421, Homburg, Saar, Germany
| | - Amer Hamza
- Department of Obstetrics and Gynecology, Saarland University, 66421, Homburg, Saar, Germany.,Kantonspital Baden, Im Ergel 1, 5400, Baden, Switzerland
| | - Ulrike Fischer
- Institute of Human Genetics, Saarland University, 66421, Homburg, Saar, Germany
| | - Mohamad Hammadeh
- Department of Obstetrics and Gynecology, Saarland University, 66421, Homburg, Saar, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbruecken, Germany
| | - Eckart Meese
- Institute of Human Genetics, Saarland University, 66421, Homburg, Saar, Germany
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25
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Munchel S, Rohrback S, Randise-Hinchliff C, Kinnings S, Deshmukh S, Alla N, Tan C, Kia A, Greene G, Leety L, Rhoa M, Yeats S, Saul M, Chou J, Bianco K, O'Shea K, Bujold E, Norwitz E, Wapner R, Saade G, Kaper F. Circulating transcripts in maternal blood reflect a molecular signature of early-onset preeclampsia. Sci Transl Med 2021; 12:12/550/eaaz0131. [PMID: 32611681 DOI: 10.1126/scitranslmed.aaz0131] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/07/2019] [Accepted: 06/08/2020] [Indexed: 12/13/2022]
Abstract
Circulating RNA (C-RNA) is continually released into the bloodstream from tissues throughout the body, offering an opportunity to noninvasively monitor all aspects of pregnancy health from conception to birth. We asked whether C-RNA analysis could robustly detect aberrations in patients diagnosed with preeclampsia (PE), a prevalent and potentially fatal pregnancy complication. As an initial examination, we sequenced the circulating transcriptome from 40 pregnancies at the time of severe, early-onset PE diagnosis and 73 gestational age-matched controls. Differential expression analysis identified 30 transcripts with gene ontology annotations and tissue expression patterns consistent with the placental dysfunction, impaired fetal development, and maternal immune and cardiovascular system dysregulation characteristic of PE. Furthermore, machine learning identified combinations of 49 C-RNA transcripts that classified an independent cohort of patients (early-onset PE, n = 12; control, n = 12) with 85 to 89% accuracy. C-RNA may thus hold promise for improving the diagnosis and identification of at-risk pregnancies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Emmanuel Bujold
- Department of Obstetrics and Gynecology and Department of Social and Preventive Medicine, Faculty of Medicine, Université Laval, Quebec City, Quebec G1V 086, Canada
| | - Errol Norwitz
- Department of Obstetrics and Gynecology and the Mother Infant Research Institute, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Ronald Wapner
- Department of Obstetrics and Gynecology, Columbia University Medical Center, New York, NY 10032, USA
| | - George Saade
- Department of Obstetrics and Gynecology, University of Texas Medical Branch, Galveston, TX 77555, USA
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26
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Chorley BN, Atabakhsh E, Doran G, Gautier JC, Ellinger-Ziegelbauer H, Jackson D, Sharapova T, Yuen PST, Church RJ, Couttet P, Froetschl R, McDuffie J, Martinez V, Pande P, Peel L, Rafferty C, Simutis FJ, Harrill AH. Methodological considerations for measuring biofluid-based microRNA biomarkers. Crit Rev Toxicol 2021; 51:264-282. [PMID: 34038674 DOI: 10.1080/10408444.2021.1907530] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNA that regulate the expression of messenger RNA and are implicated in almost all cellular processes. Importantly, miRNAs can be released extracellularly and are stable in these matrices where they may serve as indicators of organ or cell-specific toxicity, disease, and biological status. There has thus been great enthusiasm for developing miRNAs as biomarkers of adverse outcomes for scientific, regulatory, and clinical purposes. Despite advances in measurement capabilities for miRNAs, miRNAs are still not routinely employed as noninvasive biomarkers. This is in part due to the lack of standard approaches for sample preparation and miRNA measurement and uncertainty in their biological interpretation. Members of the microRNA Biomarkers Workgroup within the Health and Environmental Sciences Institute's (HESI) Committee on Emerging Systems Toxicology for the Assessment of Risk (eSTAR) are a consortium of private- and public-sector scientists dedicated to developing miRNAs as applied biomarkers. Here, we explore major impediments to routine acceptance and use of miRNA biomarkers and case examples of successes and deficiencies in development. Finally, we provide insight on miRNA measurement, collection, and analysis tools to provide solid footing for addressing knowledge gaps toward routine biomarker use.
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Affiliation(s)
- Brian N Chorley
- U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | | | | | | | | | - David Jackson
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - Peter S T Yuen
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Rachel J Church
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | | | | | | | | | | | - Lauren Peel
- Health and Environmental Sciences Institute, Washington, DC, USA
| | | | | | - Alison H Harrill
- National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
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27
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Haupt S, Haupt Y. Cancer and Tumour Suppressor p53 Encounters at the Juncture of Sex Disparity. Front Genet 2021; 12:632719. [PMID: 33664771 PMCID: PMC7920968 DOI: 10.3389/fgene.2021.632719] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/26/2021] [Indexed: 12/12/2022] Open
Abstract
There are many differences in cancer manifestation between men and women. New understanding of the origin of these point to fundamental distinctions in the genetic code and its demise. Tumour suppressor protein p53 is the chief operating officer of cancer defence and critically acts to safeguard against sustained DNA damaged. P53 cannot be ignored in cancer sex disparity. In this review we discuss the greater prevalence and associated death rates for non-reproductive cancers in males. The major tumour suppressor protein p53, encoded in the TP53 gene is our chosen context. It is fitting to ask why somatic TP53 mutation incidence is estimated to be disproportionately higher among males in the population for these types of cancers compared with females? We scrutinised the literature for evidence of predisposing genetic and epigenetic alterations that may explain this sex bias. Our second approach was to explore whether redox activity, either externally imposed or inherent to males and females, may define distinct risks that could contribute to the clear cancer sex disparities.
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Affiliation(s)
- Sue Haupt
- Tumor Suppression Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia.,Department of Clinical Pathology, University of Melbourne, Parkville, VIC, Australia
| | - Ygal Haupt
- Tumor Suppression Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia.,Department of Clinical Pathology, University of Melbourne, Parkville, VIC, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, Australia
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28
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Vergallo A, Lista S, Zhao Y, Lemercier P, Teipel SJ, Potier MC, Habert MO, Dubois B, Lukiw WJ, Hampel H. MiRNA-15b and miRNA-125b are associated with regional Aβ-PET and FDG-PET uptake in cognitively normal individuals with subjective memory complaints. Transl Psychiatry 2021; 11:78. [PMID: 33504764 PMCID: PMC7840941 DOI: 10.1038/s41398-020-01184-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/07/2020] [Accepted: 12/15/2020] [Indexed: 01/30/2023] Open
Abstract
There is substantial experimental evidence for dysregulation of several microRNA (miRNA) expression levels in Alzheimer's disease (AD). MiRNAs modulate critical brain intracellular signaling pathways and are associated with AD core pathophysiological mechanisms. First, we conducted a real-time quantitative PCR-based pilot study to identify a set of brain-enriched miRNAs in a monocentric cohort of cognitively normal individuals with subjective memory complaints, a condition associated with increased risk of AD. Second, we investigated the impact of age, sex, and the Apolipoprotein E ε4 (APOE ε4) allele, on the identified miRNA plasma concentrations. In addition, we explored the cross-sectional and longitudinal association of the miRNAs plasma concentrations with regional brain metabolic uptake using amyloid-β (Aβ)-positron emission tomography (Aβ-PET) and 18F-fluorodeoxyglucose-PET (18F-FDG-PET). We identified a set of six brain-enriched miRNAs-miRNA-125b, miRNA-146a, miRNA-15b, miRNA-148a, miRNA-26b, and miRNA-100. Age, sex, and APOE ε4 allele were not associated with individual miRNA abundance. MiRNA-15b concentrations were significantly lower in the Aβ-PET-positive compared to Aβ-PET-negative individuals. Furthermore, we found a positive effect of the miRNA-15b*time interaction on regional metabolic 18F-FDG-PET uptake in the left hippocampus. Plasma miRNA-125b concentrations, as well as the miRNA-125b*time interaction (over a 2-year follow-up), were negatively associated with regional Aβ-PET standard uptake value ratio in the right anterior cingulate cortex. At baseline, we found a significantly negative association between plasma miRNA-125b concentrations and 18F-FDG-PET uptake in specific brain regions. In an asymptomatic at-risk population for AD, we show significant associations between plasma concentrations of miRNA-125b and miRNA-15b with core neuroimaging biomarkers of AD pathophysiology. Our results, coupled with existing experimental evidence, suggest a potential protective anti-Aβ effect of miRNA-15b and a biological link between miRNA-125b and Aβ-independent neurotoxic pathways.
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Affiliation(s)
- Andrea Vergallo
- Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Boulevard de l'hôpital, F-75013, Paris, France.
| | - Simone Lista
- Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Boulevard de l’hôpital, F-75013 Paris, France ,grid.411439.a0000 0001 2150 9058Brain & Spine Institute (ICM), INSERM U 1127, CNRS UMR 7225, Boulevard de l’hôpital, F-75013 Paris, France ,grid.411439.a0000 0001 2150 9058Institute of Memory and Alzheimer’s Disease (IM2A), Department of Neurology, Pitié-Salpêtrière Hospital, AP-HP, Boulevard de l’hôpital, F-75013 Paris, France
| | - Yuhai Zhao
- grid.279863.10000 0000 8954 1233LSU Neuroscience Center, Louisiana State University Health Science Center, New Orleans, LA 70112 USA ,grid.279863.10000 0000 8954 1233Department of Cell Biology and Anatomy, Louisiana State University Health Science Center, New Orleans, LA 70112 USA
| | - Pablo Lemercier
- Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Boulevard de l’hôpital, F-75013 Paris, France ,grid.411439.a0000 0001 2150 9058Brain & Spine Institute (ICM), INSERM U 1127, CNRS UMR 7225, Boulevard de l’hôpital, F-75013 Paris, France ,grid.411439.a0000 0001 2150 9058Institute of Memory and Alzheimer’s Disease (IM2A), Department of Neurology, Pitié-Salpêtrière Hospital, AP-HP, Boulevard de l’hôpital, F-75013 Paris, France
| | - Stefan J. Teipel
- grid.424247.30000 0004 0438 0426German Center for Neurodegenerative Diseases (DZNE), Rostock, Germany ,grid.10493.3f0000000121858338Department of Psychosomatic Medicine, University Medicine Rostock, Rostock, Germany
| | - Marie-Claude Potier
- grid.411439.a0000 0001 2150 9058ICM Institut du Cerveau et de la Moelle épinière, CNRS UMR7225, INSERM U1127, UPMC, Hôpital de la Pitié-Salpêtrière, 47 Bd de l’Hôpital, F-75013 Paris, France
| | - Marie-Odile Habert
- grid.503298.50000 0004 0370 0969Sorbonne Université, CNRS, INSERM, Laboratoire d’Imagerie Biomédicale, F-75013 Paris, France ,Centre pour l’Acquisition et le Traitement des Images (www.cati-neuroimaging.com), Paris, France ,grid.411439.a0000 0001 2150 9058AP-HP, Hôpital Pitié-Salpêtrière, Département de Médecine Nucléaire, F-75013 Paris, France
| | - Bruno Dubois
- Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Boulevard de l’hôpital, F-75013 Paris, France ,grid.411439.a0000 0001 2150 9058Brain & Spine Institute (ICM), INSERM U 1127, CNRS UMR 7225, Boulevard de l’hôpital, F-75013 Paris, France ,grid.411439.a0000 0001 2150 9058Institute of Memory and Alzheimer’s Disease (IM2A), Department of Neurology, Pitié-Salpêtrière Hospital, AP-HP, Boulevard de l’hôpital, F-75013 Paris, France
| | - Walter J. Lukiw
- Alchem Biotech Research, Toronto, ON M5S 1A8 Canada ,grid.279863.10000 0000 8954 1233Department of Ophthalmology, LSU Neuroscience Center, Louisiana State University Health Science Center, New Orleans, LA 70112 USA ,grid.279863.10000 0000 8954 1233Department Neurology, LSU Neuroscience Center Louisiana State University Health Science Center, New Orleans, LA 70112 USA
| | - Harald Hampel
- Sorbonne University, GRC n° 21, Alzheimer Precision Medicine (APM), AP-HP, Pitié-Salpêtrière Hospital, Boulevard de l’hôpital, F-75013 Paris, France
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Unger L, Abril C, Gerber V, Jagannathan V, Koch C, Hamza E. Diagnostic potential of three serum microRNAs as biomarkers for equine sarcoid disease in horses and donkeys. J Vet Intern Med 2021; 35:610-619. [PMID: 33415768 PMCID: PMC7848377 DOI: 10.1111/jvim.16027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are potential biomarkers for equine sarcoids (ES). OBJECTIVES To assess eca-miR-331, eca-miR-100, and eca-miR-1 as serum biomarkers for ES disease. ANIMALS Sixty-eight ES cases (56 horses, 12 donkeys), 69 tumor-free controls (60 horses, 9 donkeys), and 20 horses with other skin tumors. METHODS For this case-control study, expression of serum eca-miR-331, eca-miR-100, and eca-miR-1 in ES-affected equids was compared to tumor-free age-, sex-, and breed-matched control horses and donkeys with other skin tumors using reverse transcription quantitative PCR (polymerase chain reaction) for relative miRNA quantification. Biological, preanalytical, and clinical variable influences on miRNA expression were examined. Receiver operator characteristic (ROC) curve analyses were used to determine differences in miRNA expression between groups. RESULTS The expression of eca-miR-100 was affected by age (P = .003) and expression of eca-miR-100 and eca-miR-1 were affected by hemolysis (both P < .001). Eca-miR-331 was unaffected by biological variation, hemolysis, ES type, and disease severity. Eca-miR-331 concentrations were higher in ES-affected compared to tumor-free controls (P = .002). The ROC curve analysis indicated an area under the curve of 0.65 (P = .002) with a sensitivity of 60%, specificity of 71%, and positive and negative likelihood ratios of 2.1 and 0.56, respectively, to diagnose ES. Eca-miR-331 expression did not discriminate between horses with ES and other skin tumors. Expression of eca-miR-100 and eca-miR-1 was not different between groups. CONCLUSIONS AND CLINICAL IMPORTANCE Serum eca-miR-331 expression is neither sensitive nor specific enough as a single ES biomarker. If combined with other miRNAs, it may be helpful for ES diagnosis.
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Affiliation(s)
- Lucia Unger
- Department of Clinical Veterinary Medicine, Swiss Institute of Equine Medicine (ISME), Vetsuisse Faculty, University of Bern, and Agroscope, Bern, Switzerland
| | - Carlos Abril
- Institute of Virology and Immunology, University of Bern, Bern, Switzerland
| | - Vinzenz Gerber
- Department of Clinical Veterinary Medicine, Swiss Institute of Equine Medicine (ISME), Vetsuisse Faculty, University of Bern, and Agroscope, Bern, Switzerland
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Christoph Koch
- Department of Clinical Veterinary Medicine, Swiss Institute of Equine Medicine (ISME), Vetsuisse Faculty, University of Bern, and Agroscope, Bern, Switzerland
| | - Eman Hamza
- Department of Clinical Veterinary Medicine, Swiss Institute of Equine Medicine (ISME), Vetsuisse Faculty, University of Bern, and Agroscope, Bern, Switzerland
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Liu T, Gatto NM, Chen Z, Qiu H, Lee G, Duerksen-Hughes P, Fraser G, Wang C. Vegetarian diets, circulating miRNA expression and healthspan in subjects living in the Blue Zone. PRECISION CLINICAL MEDICINE 2021; 3:245-259. [PMID: 33391847 PMCID: PMC7757436 DOI: 10.1093/pcmedi/pbaa037] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 10/11/2020] [Accepted: 10/18/2020] [Indexed: 12/21/2022] Open
Abstract
A long-term vegetarian diet plays a role in the longevity and maintenance of the healthspan, but the underlying mechanisms for these observations are largely unknown. Particularly, it is not known whether a long-term vegetarian dietary pattern may affect the circulating miRNA expression in such a way as to modulate the healthspan. The Adventist Health Study-2 (AHS-2) cohort includes a large number of older adults who primarily follow vegetarian dietary patterns and reside in Loma Linda, California, one of five “Blue Zones” in the world in which a higher proportion of the population enjoys a longer than average lifespan. We performed miRNA-seq in 96 subjects selected from the AHS-2 cohort with different dietary patterns. We identified several differentially expressed miRNAs between vegetarians and non-vegetarians, which are involved in immune response and cytokine signaling, cell growth and proliferation as well as age-related diseases such as cardiovascular diseases and neurodegenerative diseases. Overall, our study showed that a vegetarian diet modulates aging-associated circulating miRNAs in a sex-dependent manner of differential expression for certain miRNAs, which may be related in a beneficial manner to the healthspan. Further investigation is needed to validate these miRNAs as potential biomarkers for diet-modulated longevity in humans.
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Affiliation(s)
- Tiantian Liu
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
| | - Nicole M Gatto
- School of Community and Global Health, Claremont Graduate University, Claremont, CA 91711, USA
| | - Zhong Chen
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
| | - Hongyu Qiu
- Center of Molecular and Translational Medicine, Institution of Biomedical Science, Georgia State University, Atlanta, GA 30303, USA
| | - Grace Lee
- Department of Psychology, School of Behavioral Health, Loma Linda University, Loma Linda, CA 92350, USA
| | - Penelope Duerksen-Hughes
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
| | - Gary Fraser
- School of Public Health, Loma Linda University, Loma Linda, CA 92350, USA
| | - Charles Wang
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA 92350, USA
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Pawlina-Tyszko K, Oczkowicz M, Gurgul A, Szmatoła T, Bugno-Poniewierska M. MicroRNA profiling of the pig periaqueductal grey (PAG) region reveals candidates potentially related to sex-dependent differences. Biol Sex Differ 2020; 11:67. [PMID: 33451362 PMCID: PMC7809845 DOI: 10.1186/s13293-020-00343-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/17/2020] [Indexed: 11/10/2022] Open
Abstract
Background MicroRNAs indirectly orchestrate myriads of essential biological processes. A wide diversity of miRNAs of the neurodevelopmental importance characterizes the brain tissue, which, however, exhibits region-specific miRNA profile differences. One of the most conservative regions of the brain is periaqueductal grey (PAG) playing vital roles in significant functions of this organ, also those observed to be sex-influenced. The domestic pig is an important livestock species but is also believed to be an excellent human model. This is of particular importance for neurological research because of the similarity of pig and human brains as well as difficult access to human samples. However, the pig PAG profile has not been characterized so far. Moreover, molecular bases of sex differences connected with brain functioning, including miRNA expression profiles, have not been fully deciphered yet. Methods Thus, in this study, we applied next-generation sequencing to characterize pig PAG expressed microRNAs. Furthermore, we performed differential expression analysis between females and males to identify changes of the miRNA profile and reveal candidates underlying sex-related differences. Results As a result, known brain-enriched, and new miRNAs which will expand the available profile, were identified. The downstream analysis revealed 38 miRNAs being differentially expressed (DE) between female and male samples. Subsequent pathway analysis showed that they enrich processes vital for neuron growth and functioning, such as long-term depression and axon guidance. Among the identified sex-influenced miRNAs were also those associated with the PAG physiology and diseases related to this region. Conclusions The obtained results broaden the knowledge on the porcine PAG miRNAome, along with its dynamism reflected in different isomiR signatures. Moreover, they indicate possible mechanisms associated with sex-influenced differences mediated via miRNAs in the PAG functioning. They also provide candidate miRNAs for further research concerning, i.e., sex-related bases of physiological and pathological processes occurring in the nervous system. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13293-020-00343-2.
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Affiliation(s)
- Klaudia Pawlina-Tyszko
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Kraków, Poland.
| | - Maria Oczkowicz
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Kraków, Poland
| | - Artur Gurgul
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Kraków, Poland.,Center for Experimental and Innovative Medicine, University of Agriculture in Kraków, Rędzina 1c, 30-248, Kraków, Poland
| | - Tomasz Szmatoła
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Kraków, Poland.,Center for Experimental and Innovative Medicine, University of Agriculture in Kraków, Rędzina 1c, 30-248, Kraków, Poland
| | - Monika Bugno-Poniewierska
- Department of Animal Reproduction, Anatomy and Genomics, University of Agriculture in Kraków, al. Mickiewicza 24/28, 30-059, Kraków, Poland
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Fehlmann T, Lehallier B, Schaum N, Hahn O, Kahraman M, Li Y, Grammes N, Geffers L, Backes C, Balling R, Kern F, Krüger R, Lammert F, Ludwig N, Meder B, Fromm B, Maetzler W, Berg D, Brockmann K, Deuschle C, von Thaler AK, Eschweiler GW, Milman S, Barziliai N, Reichert M, Wyss-Coray T, Meese E, Keller A. Common diseases alter the physiological age-related blood microRNA profile. Nat Commun 2020; 11:5958. [PMID: 33235214 PMCID: PMC7686493 DOI: 10.1038/s41467-020-19665-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023] Open
Abstract
Aging is a key risk factor for chronic diseases of the elderly. MicroRNAs regulate post-transcriptional gene silencing through base-pair binding on their target mRNAs. We identified nonlinear changes in age-related microRNAs by analyzing whole blood from 1334 healthy individuals. We observed a larger influence of the age as compared to the sex and provide evidence for a shift to the 5' mature form of miRNAs in healthy aging. The addition of 3059 diseased patients uncovered pan-disease and disease-specific alterations in aging profiles. Disease biomarker sets for all diseases were different between young and old patients. Computational deconvolution of whole-blood miRNAs into blood cell types suggests that cell intrinsic gene expression changes may impart greater significance than cell abundance changes to the whole blood miRNA profile. Altogether, these data provide a foundation for understanding the relationship between healthy aging and disease, and for the development of age-specific disease biomarkers.
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Affiliation(s)
- Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Benoit Lehallier
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Nicholas Schaum
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Oliver Hahn
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Mustafa Kahraman
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Yongping Li
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Nadja Grammes
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Lars Geffers
- Luxembourg Center for Systems Biomedicine, 4362, Esch-sur-Alzette, Luxemburg
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Rudi Balling
- Luxembourg Center for Systems Biomedicine, 4362, Esch-sur-Alzette, Luxemburg
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), 1445, Strassen, Luxemburg
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg, 1210, Luxembourg, Luxemburg
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Rejko Krüger
- Luxembourg Center for Systems Biomedicine, 4362, Esch-sur-Alzette, Luxemburg
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), 1445, Strassen, Luxemburg
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg, 1210, Luxembourg, Luxemburg
| | - Frank Lammert
- Internal Medicine, Saarland University, 66421, Homburg, Germany
| | - Nicole Ludwig
- Human Genetics, Saarland University, 66421, Homburg, Germany
| | - Benjamin Meder
- Internal Medicine, University Hospital Heidelberg, 69120, Heidelberg, Germany
| | - Bastian Fromm
- Department of Molecular Biosciences, Stockholm University, 11418, Stockholm, Sweden
| | - Walter Maetzler
- Department of Neurology, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
| | - Daniela Berg
- Department of Neurology, Christian-Albrechts-Universität zu Kiel, 24105, Kiel, Germany
| | | | | | | | - Gerhard W Eschweiler
- Geriatric Center and the Department of Psychiatry and Psychotherapy, University Hospital Tübingen, 72076, Tübingen, Germany
| | - Sofiya Milman
- The Institute for Aging Research, Albert Einstein College of Medicine, New York, NY, 10461, USA
| | - Nir Barziliai
- The Institute for Aging Research, Albert Einstein College of Medicine, New York, NY, 10461, USA
| | | | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA
| | - Eckart Meese
- Human Genetics, Saarland University, 66421, Homburg, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany.
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, 94305, USA.
- Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123, Saarbrücken, Germany.
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The Physiological MicroRNA Landscape in Nipple Aspirate Fluid: Differences and Similarities with Breast Tissue, Breast Milk, Plasma and Serum. Int J Mol Sci 2020; 21:ijms21228466. [PMID: 33187146 PMCID: PMC7696615 DOI: 10.3390/ijms21228466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 02/06/2023] Open
Abstract
Background: MicroRNAs (miRNAs) target 60% of human messenger RNAs and can be detected in tissues and biofluids without loss of stability during sample processing, making them highly appraised upcoming biomarkers for evaluation of disease. However, reporting of the abundantly expressed miRNAs in healthy samples is often surpassed. Here, we characterized for the first time the physiological miRNA landscape in a biofluid of the healthy breast: nipple aspirate fluid (NAF), and compared NAF miRNA expression patterns with publically available miRNA expression profiles of healthy breast tissue, breast milk, plasma and serum. Methods: MiRNA RT-qPCR profiling of NAF (n = 41) and serum (n = 23) samples from two healthy female cohorts was performed using the TaqMan OpenArray Human Advanced MicroRNA 754-Panel. MiRNA quantification data based on non-targeted or multi-targeted profiling techniques for breast tissue, breast milk, plasma and serum were retrieved from the literature by means of a systematic search. MiRNAs from each individual study were orderly ranked between 1 and 50, combined into an overall ranking per sample type and compared. Results: NAF expressed 11 unique miRNAs and shared 21/50 miRNAs with breast tissue. Seven miRNAs were shared between the five sample types. Overlap between sample types varied between 42% and 62%. Highly ranked NAF miRNAs have established roles in breast carcinogenesis. Conclusion: This is the first study to characterize and compare the unique physiological NAF-derived miRNA landscape with the physiological expression pattern in breast tissue, breast milk, plasma and serum. Breast-specific sources did not mutually overlap more than with systemic sources. Given their established role in carcinogenesis, NAF miRNA assessment could be a valuable tool in breast tumor diagnostics.
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Tang H, Gao Y, Li Z, Miao Y, Huang Z, Liu X, Xie L, Li H, Wen W, Zheng Y, Su W. The noncoding and coding transcriptional landscape of the peripheral immune response in patients with COVID-19. Clin Transl Med 2020; 10:e200. [PMID: 33135345 PMCID: PMC7548099 DOI: 10.1002/ctm2.200] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND COVID-19 is currently a global pandemic, but the response of human immune system to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection remains unclear. Noncoding RNAs serve as immune regulators and thus may play a critical role in disease progression. METHODS We performed multi-transcriptome sequencing of both noncoding RNAs and mRNAs isolated from the red blood cell depleted whole blood of moderate and severe COVID-19 patients. The functions of noncoding RNAs were validated by analyses of the expression of downstream mRNAs. We further utilized the single-cell RNA-seq data of COVID-19 patients from Wilk et al. and Chua et al. to characterize noncoding RNA functions in different cell types. RESULTS We defined four types of microRNAs with different expression tendencies that could serve as biomarkers for COVID-19 progress. We also identified miR-146a-5p, miR-21-5p, miR-142-3p, and miR-15b-5p as potential contributors to the disease pathogenesis, possibly serving as biomarkers of severe COVID-19 and as candidate therapeutic targets. In addition, the transcriptome profiles consistently suggested hyperactivation of the immune response, loss of T-cell function, and immune dysregulation in severe patients. CONCLUSIONS Collectively, these findings provide a comprehensive view of the noncoding and coding transcriptional landscape of peripheral immune cells during COVID-19, furthering our understanding and offering novel insights into COVID-19 pathogenesis.
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Affiliation(s)
- Hao Tang
- Department of Respiratory and Critical Care Medicine Changzheng HospitalSecond Military Medical UniversityShanghaiChina
- Department of Critical CareWuhan Huo Shen Shan HospitalHubeiChina
| | - Yuehan Gao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic CenterSun Yat‐sen UniversityGuangzhouChina
| | - Zhaohuai Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic CenterSun Yat‐sen UniversityGuangzhouChina
| | - Yushan Miao
- Department of Respiratory and Critical Care Medicine Changzheng HospitalSecond Military Medical UniversityShanghaiChina
| | - Zhaohao Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic CenterSun Yat‐sen UniversityGuangzhouChina
| | - Xiuxing Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic CenterSun Yat‐sen UniversityGuangzhouChina
| | - Lihui Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic CenterSun Yat‐sen UniversityGuangzhouChina
| | - He Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic CenterSun Yat‐sen UniversityGuangzhouChina
| | - Wen Wen
- National Center for Liver CancerSecond Military Medical UniversityShanghaiChina
| | - Yingfeng Zheng
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic CenterSun Yat‐sen UniversityGuangzhouChina
| | - Wenru Su
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic CenterSun Yat‐sen UniversityGuangzhouChina
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Fazmin IT, Achercouk Z, Edling CE, Said A, Jeevaratnam K. Circulating microRNA as a Biomarker for Coronary Artery Disease. Biomolecules 2020; 10:E1354. [PMID: 32977454 PMCID: PMC7598281 DOI: 10.3390/biom10101354] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/15/2020] [Accepted: 09/19/2020] [Indexed: 12/14/2022] Open
Abstract
Coronary artery disease (CAD) is the leading cause of sudden cardiac death in adults, and new methods of predicting disease and risk-stratifying patients will help guide intervention in order to reduce this burden. Current CAD detection involves multiple modalities, but the consideration of other biomarkers will help improve reliability. The aim of this narrative review is to help researchers and clinicians appreciate the growing relevance of miRNA in CAD and its potential as a biomarker, and also to suggest useful miRNA that may be targets for future study. We sourced information from several databases, namely PubMed, Scopus, and Google Scholar, when collating evidentiary information. MicroRNAs (miRNA) are short, noncoding RNAs that are relevant in cardiovascular physiology and pathophysiology, playing roles in cardiac hypertrophy, maintenance of vascular tone, and responses to vascular injury. CAD is associated with changes in miRNA expression profiles, and so are its risk factors, such as abnormal lipid metabolism and inflammation. Thus, they may potentially be biomarkers of CAD. Nevertheless, there are limitations in using miRNA. These include cost and the presence of several confounding factors that may affect miRNA profiles. Furthermore, there is difficulty in the normalisation of miRNA values between published studies, due to pre-analytical variations in samples.
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Affiliation(s)
- Ibrahim T. Fazmin
- Faculty of Health and Medical Science, University of Surrey, Guildford GU2 7AL, UK; (I.T.F.); (Z.A.); (C.E.E.)
- School of Clinical Medicine, University of Cambridge, Cambridge CB2 1TN, UK
| | - Zakaria Achercouk
- Faculty of Health and Medical Science, University of Surrey, Guildford GU2 7AL, UK; (I.T.F.); (Z.A.); (C.E.E.)
| | - Charlotte E. Edling
- Faculty of Health and Medical Science, University of Surrey, Guildford GU2 7AL, UK; (I.T.F.); (Z.A.); (C.E.E.)
| | - Asri Said
- School of Medicine, University Malaysia Sarawak, Kota Samarahan 94300, Sarawak, Malaysia;
| | - Kamalan Jeevaratnam
- Faculty of Health and Medical Science, University of Surrey, Guildford GU2 7AL, UK; (I.T.F.); (Z.A.); (C.E.E.)
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36
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Shah V, Shah J. Recent trends in targeting miRNAs for cancer therapy. J Pharm Pharmacol 2020; 72:1732-1749. [PMID: 32783235 DOI: 10.1111/jphp.13351] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/12/2020] [Accepted: 07/15/2020] [Indexed: 12/19/2022]
Abstract
OBJECTIVES MicroRNAs (miRNAs) are a type of small noncoding RNA employed by the cells for gene regulation. A single miRNA, typically 22 nucleotides in length, can regulate the expression of numerous genes. Over the past decade, the study of miRNA biology in the context of cancer has led to the development of new diagnostic and therapeutic opportunities. KEY FINDINGS MicroRNA dysregulation is commonly associated with cancer, in part because miRNAs are actively involved in the mechanisms like genomic instabilities, aberrant transcriptional control, altered epigenetic regulation and biogenesis machinery defects. MicroRNAs can regulate oncogenes or tumour suppressor genes and thus when altered can lead to tumorigenesis. Expression profiling of miRNAs has boosted the possibilities of application of miRNAs as potential cancer biomarkers and therapeutic targets, although the feasibility of these approaches will require further validation. SUMMARY In this review, we will focus on how miRNAs regulate tumour development and the potential applications of targeting miRNAs for cancer therapy.
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Affiliation(s)
- Vandit Shah
- Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat, India
| | - Jigna Shah
- Institute of Pharmacy, Nirma University, Ahmedabad, Gujarat, India
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37
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The Role of microRNAs in Organismal and Skin Aging. Int J Mol Sci 2020; 21:ijms21155281. [PMID: 32722415 PMCID: PMC7432402 DOI: 10.3390/ijms21155281] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 07/11/2020] [Accepted: 07/23/2020] [Indexed: 12/12/2022] Open
Abstract
The aging process starts directly after birth and lasts for the entire lifespan; it manifests itself with a decline in an organism’s ability to adapt and is linked to the development of age-related diseases that eventually lead to premature death. This review aims to explore how microRNAs (miRNAs) are involved in skin functioning and aging. Recent evidence has suggested that miRNAs regulate all aspects of cutaneous biogenesis, functionality, and aging. It has been noted that some miRNAs were down-regulated in long-lived individuals, such as let-7, miR-17, and miR-34 (known as longevity-related miRNAs). They are conserved in humans and presumably promote lifespan prolongation; conversely, they are up-regulated in age-related diseases, like cancers. The analysis of the age-associated cutaneous miRNAs revealed the increased expression of miR-130, miR-138, and miR-181a/b in keratinocytes during replicative senescence. These miRNAs affected cell proliferation pathways via targeting the p63 and Sirtuin 1 mRNAs. Notably, miR-181a was also implicated in skin immunosenescence, represented by the Langerhans cells. Dermal fibroblasts also expressed increased the levels of the biomarkers of aging that affect telomere maintenance and all phases of the cellular life cycle, such as let-7, miR-23a-3p, 34a-5p, miR-125a, miR-181a-5p, and miR-221/222-3p. Among them, the miR-34 family, stimulated by ultraviolet B irradiation, deteriorates collagen in the extracellular matrix due to the activation of the matrix metalloproteinases and thereby potentiates wrinkle formation. In addition to the pro-aging effects of miRNAs, the plausible antiaging activity of miR-146a that antagonized the UVA-induced inhibition of proliferation and suppressed aging-related genes (e.g., p21WAF-1, p16, and p53) through targeting Smad4 has also been noticed. Nevertheless, the role of miRNAs in skin aging is still not fully elucidated and needs to be further discovered and explained.
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38
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Keller A, Fehlmann T, Backes C, Kern F, Gislefoss R, Langseth H, Rounge TB, Ludwig N, Meese E. Competitive learning suggests circulating miRNA profiles for cancers decades prior to diagnosis. RNA Biol 2020; 17:1416-1426. [PMID: 32456538 DOI: 10.1080/15476286.2020.1771945] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs are regulators of gene expressionand may be key markers in liquid biopsy.Early diagnosis is an effective means to increase patients' overall survival. We generated genome-wide miRNA profiles from serum of patients and controls from the population-based Janus Serum Bank (JSB) and analysed them by bioinformatics and artificial intelligence approaches. JSB contains sera from 318,628 originally healthy persons, more than 96,000 of whom developed cancer. We selected 210 serum samples from patients with lung, colon or breast cancer at three time points prior to diagnosis (up to 32 years prior to diagnosis with median 5 years interval between TPs), one time-point after diagnosis and from individually matched controls. The controls were matched on age and year of all pre-diagnostic sampling time-points for the corresponding case. Using ANOVA we report 70 significantly deregulated markers (adjusted p-value<0.05). The driver for the significance was the diagnostic time point (miR-575, miR-6821-5p, miR-630 with adjusted p-values<10-10). Further, 91miRNAs were differently expressed in pre-diagnostic samples as compared to controls (nominal p < 0.05). Self-organized maps (SOMs)indicated larges effects in lung cancer samples while breast cancer samples showed the least pronounced changes. SOMsalsohighlighted cancer and time point specific miRNA dys-regulation. Intriguingly, a detailed breakdown of the results highlighted that 51% of all miRNAs were highly specific, either for a time-point or a cancer entity. Pathway analysis highlighted 12 pathways including Hipo signalling and ABC transporters.Our results indicate that tumours may be indicated by serum miRNAs decades prior the clinical manifestation.
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Affiliation(s)
- Andreas Keller
- Department of Clinical Bioinformatics, Saarland University , Saarbrücken, Germany.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine , Stanford, CA, USA
| | - Tobias Fehlmann
- Department of Clinical Bioinformatics, Saarland University , Saarbrücken, Germany
| | - Christina Backes
- Department of Clinical Bioinformatics, Saarland University , Saarbrücken, Germany
| | - Fabian Kern
- Department of Clinical Bioinformatics, Saarland University , Saarbrücken, Germany
| | - Randi Gislefoss
- Department of Research, Cancer Registry of Norway , Oslo, Norway
| | - Hilde Langseth
- Department of Research, Cancer Registry of Norway , Oslo, Norway.,Department of Epidemiology and Biostatistics, Imperial College London , London, UK
| | - Trine B Rounge
- Department of Research, Cancer Registry of Norway , Oslo, Norway.,Department of Informatics, University of Oslo , Oslo, Norway
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University , Homburg/Saar, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University , Homburg/Saar, Germany
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39
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Le DH, Tran TTH. RWRMTN: a tool for predicting disease-associated microRNAs based on a microRNA-target gene network. BMC Bioinformatics 2020; 21:244. [PMID: 32539680 PMCID: PMC7296691 DOI: 10.1186/s12859-020-03578-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 06/01/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The misregulation of microRNA (miRNA) has been shown to cause diseases. Recently, we have proposed a computational method based on a random walk framework on a miRNA-target gene network to predict disease-associated miRNAs. The prediction performance of our method is better than that of some existing state-of-the-art network- and machine learning-based methods since it exploits the mutual regulation between miRNAs and their target genes in the miRNA-target gene interaction networks. RESULTS To facilitate the use of this method, we have developed a Cytoscape app, named RWRMTN, to predict disease-associated miRNAs. RWRMTN can work on any miRNA-target gene network. Highly ranked miRNAs are supported with evidence from the literature. They then can also be visualized based on the rankings and in relationships with the query disease and their target genes. In addition, automation functions are also integrated, which allow RWRMTN to be used in workflows from external environments. We demonstrate the ability of RWRMTN in predicting breast and lung cancer-associated miRNAs via workflows in Cytoscape and other environments. CONCLUSIONS Considering a few computational methods have been developed as software tools for convenient uses, RWRMTN is among the first GUI-based tools for the prediction of disease-associated miRNAs which can be used in workflows in different environments.
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Affiliation(s)
- Duc-Hau Le
- Department of Computational Biomedicine, Vingroup Big Data Institute, No 7, Bang Lang 1 Street, Viet Hung Ward, Long Bien District, Hanoi, Vietnam.
| | - Trang T H Tran
- Department of Computational Biomedicine, Vingroup Big Data Institute, No 7, Bang Lang 1 Street, Viet Hung Ward, Long Bien District, Hanoi, Vietnam
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40
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Chen C, Wu Y, Li M, Cui C, Zhao Y, Sun X, Wang Y, Liu C, Wu H, Zhong X, Kermode AG, Peng L, Qiu W. Different Exosomal microRNA Profile in Aquaporin-4 Antibody Positive Neuromyelitis Optica Spectrum Disorders. Front Immunol 2020; 11:1064. [PMID: 32547558 PMCID: PMC7274160 DOI: 10.3389/fimmu.2020.01064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Accepted: 05/04/2020] [Indexed: 12/29/2022] Open
Abstract
Neuromyelitis optica spectrum disorders (NMOSD) and multiple sclerosis (MS) are inflammatory demyelinating diseases of the central nervous system. Exosomal microRNAs (miRNAs) are emerging biomarkers for demyelinating diseases. In this study, 52 aquaporin-4 antibody serum-positive NMOSD patients, 18 relapsing-remitting multiple sclerosis (RRMS) patients and 17 healthy controls (HCs) were included for the next-generation sequencing (NGS). To validate the NGS results, the valuable miRNAs were selected for validation by real-time quantitative polymerase chain reaction in another cohort of patients, comprising 31 NMOSD patients and 14 HCs. In addition, these miRNAs were also validated in a longitudinal study. NGS data revealed the exosomal miRNAs profile in NMOSD patients was different from HCs. Among those potential exosomal miRNAs which can distinguish NMOSD status, hsa-miR-122-3p and hsa-miR-200a-5p were the most abundant miRNAs. In addition, hsa-miR-122-3p and hsa-miR-200a-5p were significantly upregulated in the serum exosome of relapsing NMOSD compared with that in remitting NMOSD. Hsa-miR-122-3p and hsa-miR-200a-5p had positive correlations with disease severity in NMOSD patients. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that the MAPK, Wnt and Ras signaling pathways were enriched. Further biological function analysis demonstrated that these two miRNAs might be involved in the immunoregulation of NMOSD pathogenesis. Our results indicated that miRNAs delivered by exosomes could be applied as potential biomarkers for NMOSD.
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Affiliation(s)
- Chen Chen
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yunting Wu
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Miaochang Li
- Department of Neurology, Zhaoqing No. 1 People's Hospital, Zhaoqing, China
| | - Chunping Cui
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yipeng Zhao
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaobo Sun
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yuge Wang
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Chunxin Liu
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Haotian Wu
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaonan Zhong
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Allan G Kermode
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.,Centre for Neuromuscular and Neurological Disorders, University of Western Australia, Perth, WA, Australia.,Department of Neurology, Sir Charles Gairdner Hospital, Queen Elizabeth II Medical Centre, Perth, WA, Australia.,Institute of Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia
| | - Lisheng Peng
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wei Qiu
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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41
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Ye Z, Sun B, Xiao Z. Machine learning identifies 10 feature miRNAs for lung squamous cell carcinoma. Gene 2020; 749:144669. [PMID: 32298761 DOI: 10.1016/j.gene.2020.144669] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 04/07/2020] [Accepted: 04/11/2020] [Indexed: 12/24/2022]
Abstract
Lung squamous cell carcinoma (LUSC) is a common type of malignancy. The mechanism behind its tumor progression is not clear yet. The aim of this study is to use machine learning to identify the feature miRNAs, which can be reliably used as biomarkers for diagnosis LUSC. We downloaded microRNA expression data and clinical data from The Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus(GEO) database to identify differences in microRNA expression of primary tumor tissues and para-carcinoma tissues from LUSC. Construction of miRNA-mRNA interaction network, GO, KEGG pathway analysis and Kaplan-Meier survival analysis were used to explore the biological functions of the identified microRNAs. 21 feature miRNAs were identified between lung SCC tumor tissues and para-carcinoma tissues with the support of SVM and PCA methods. Among them, ten feature miRNAs: mir-143, mir-100, mir-101-1, mir-101-2, mir-182, mir-183, mir-205, mir-21, mir-30a, mir30-d were identified which could be used as a feature group to separate the cancer tissues from the adjacent tissues ultimately, and cross-validation of the obtained data showed that it can achieve extremely high accuracy and recall rate. Using KEGG, Reactome, GO databases, these 10 miRNAs and their target genes were found to be highly correlated with cancer. Survival analysis found that this group of miRNAs had a significant relationship with the survival rate of cancer patients, and the expression was significantly different between tumor tissues and healthy tissues. The dysregulated feature miRNAs might be involved in the pathology of LUSC and could be used as potential diagnostic biomarkers or therapeutic targets for LUSC.
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Affiliation(s)
- Zheng Ye
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Bo Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Zhongdang Xiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China.
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42
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Horváth M, Horváthová V, Hájek P, Štěchovský C, Honěk J, Šenolt L, Veselka J. MicroRNA-331 and microRNA-151-3p as biomarkers in patients with ST-segment elevation myocardial infarction. Sci Rep 2020; 10:5845. [PMID: 32246100 PMCID: PMC7125297 DOI: 10.1038/s41598-020-62835-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 03/19/2020] [Indexed: 12/04/2022] Open
Abstract
We sought to analyse plasma levels of peripheral blood microRNAs (miRs) as biomarkers of ST-segment-elevation myocardial infarction (STEMI) due to type-1 myocardial infarction as a model situation of vulnerable plaque (VP) rupture. Samples of 20 patients with STEMI were compared both with a group of patients without angina pectoris in whom coronary angiogram did not reveal coronary atherosclerotic disease (no coronary atherosclerosis-NCA) and a group of patients with stable angina pectoris and at least one significant coronary artery stenosis (stable coronary artery disease-SCAD). This study design allowed us to identify miRs deregulated in the setting of acute coronary artery occlusion due to VP rupture. Based on an initial large scale miR assay screening, we selected a total of 12 miRs (three study miRs and nine controls) that were tested in the study. Two of the study miRs (miR-331 and miR-151-3p) significantly distinguished STEMI patients from the control groups, while ROC analysis confirmed their suitability as biomarkers. Importantly, this was observed in patients presenting early with STEMI, even before the markers of myocardial necrosis (cardiac troponin I, miR-208 and miR-499) were elevated, which suggests that the origin of miR-331 and miR-151-3p might be in the VP. In conclusion, the study provides two novel biomarkers observed in STEMI, which may be associated with plaque rupture.
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Affiliation(s)
- Martin Horváth
- Department of Cardiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic.
| | - Veronika Horváthová
- Faculty of Science, Charles University, Prague, Czech Republic
- Department of Rheumatology, Charles University, 1st Faculty of Medicine and Rheumatology Institute, Prague, Czech Republic
| | - Petr Hájek
- Department of Cardiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
| | - Cyril Štěchovský
- Department of Cardiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
| | - Jakub Honěk
- Department of Cardiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
| | - Ladislav Šenolt
- Department of Rheumatology, Charles University, 1st Faculty of Medicine and Rheumatology Institute, Prague, Czech Republic
| | - Josef Veselka
- Department of Cardiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
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43
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Barraclough JY, Joan M, Joglekar MV, Hardikar AA, Patel S. MicroRNAs as Prognostic Markers in Acute Coronary Syndrome Patients-A Systematic Review. Cells 2019; 8:cells8121572. [PMID: 31817254 PMCID: PMC6952952 DOI: 10.3390/cells8121572] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/23/2019] [Accepted: 12/02/2019] [Indexed: 01/09/2023] Open
Abstract
Background: The potential utility of microRNAs (miRNAs) in the diagnosis, prognosis, and treatment of multiple disease states has been an area of great interest since their discovery. In patients with cardiovascular disease, there is a large pool of literature amassed from the last decade assessing their diagnostic and prognostic potential. This systematic review sought to determine whether existing literature supports the use of miRNAs as prognostic markers after an Acute Coronary Syndrome (ACS) presentation. Methods: A systematic review of published articles from 2005–2019 using MEDLINE and EMBASE databases was undertaken independently by two reviewers. Studies addressing prognosis in an ACS population yielded 32 studies and 2 systematic reviews. Results/conclusion: 23 prospective studies reported significant differences in miRNA levels and 16 compared the predictive power of miRNAs. The most common miRNAs assessed included miR-133a, -208b, -21, -1, -34a, -150, and -423, shown to be involved in cell differentiation, apoptosis, and angiogenesis. Barriers to the use of miRNAs as prognostic markers include bias in miRNA selection, small sample size, variable normalization of data, and adjustment for confounders. Therefore, findings from this systematic review do not support the use of miRNAs for prognostication post-ACS beyond traditional cardiovascular risk factors, existing risk scores, and stratifications tools.
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Affiliation(s)
- Jennifer Y Barraclough
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney 2050, Australia
- Sydney Medical School, The University of Sydney, Sydney 2050, Australia
- Heart Research Institute, Sydney 2042, Australia
| | - Michelyn Joan
- Sydney Medical School, The University of Sydney, Sydney 2050, Australia
| | - Mugdha V Joglekar
- NHMRC Clinical Trials Centre, Faculty of Medicine and Health, The University of Sydney, Sydney 2050, Australia
| | - Anandwardhan A Hardikar
- NHMRC Clinical Trials Centre, Faculty of Medicine and Health, The University of Sydney, Sydney 2050, Australia
| | - Sanjay Patel
- Department of Cardiology, Royal Prince Alfred Hospital, Sydney 2050, Australia
- Sydney Medical School, The University of Sydney, Sydney 2050, Australia
- Heart Research Institute, Sydney 2042, Australia
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44
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Ludwig N, Fehlmann T, Kern F, Gogol M, Maetzler W, Deutscher S, Gurlit S, Schulte C, von Thaler AK, Deuschle C, Metzger F, Berg D, Suenkel U, Keller V, Backes C, Lenhof HP, Meese E, Keller A. Machine Learning to Detect Alzheimer's Disease from Circulating Non-coding RNAs. GENOMICS PROTEOMICS & BIOINFORMATICS 2019; 17:430-440. [PMID: 31809862 PMCID: PMC6943763 DOI: 10.1016/j.gpb.2019.09.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 08/26/2019] [Accepted: 10/07/2019] [Indexed: 12/11/2022]
Abstract
Blood-borne small non-coding (sncRNAs) are among the prominent candidates for blood-based diagnostic tests. Often, high-throughput approaches are applied to discover biomarker signatures. These have to be validated in larger cohorts and evaluated by adequate statistical learning approaches. Previously, we published high-throughput sequencing based microRNA (miRNA) signatures in Alzheimer’s disease (AD) patients in the United States (US) and Germany. Here, we determined abundance levels of 21 known circulating miRNAs in 465 individuals encompassing AD patients and controls by RT-qPCR. We computed models to assess the relation between miRNA expression and phenotypes, gender, age, or disease severity (Mini-Mental State Examination; MMSE). Of the 21 miRNAs, expression levels of 20 miRNAs were consistently de-regulated in the US and German cohorts. 18 miRNAs were significantly correlated with neurodegeneration (Benjamini-Hochberg adjusted P < 0.05) with highest significance for miR-532-5p (Benjamini-Hochberg adjusted P = 4.8 × 10−30). Machine learning models reached an area under the curve (AUC) value of 87.6% in differentiating AD patients from controls. Further, ten miRNAs were significantly correlated with MMSE, in particular miR-26a/26b-5p (adjusted P = 0.0002). Interestingly, the miRNAs with lower abundance in AD were enriched in monocytes and T-helper cells, while those up-regulated in AD were enriched in serum, exosomes, cytotoxic t-cells, and B-cells. Our study represents the next important step in translational research for a miRNA-based AD test.
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Affiliation(s)
- Nicole Ludwig
- Department of Human Genetics, Saarland University, 66421 Homburg/Saar, Germany
| | - Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Manfred Gogol
- Institut für Gerontologie, Universität Heidelberg, 69047 Heidelberg, Germany
| | - Walter Maetzler
- Department of Neurology, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany; Center for Neurology and Hertie Institute for Clinical Brain Research, Department of Neurodegeneration, University of Tuebingen, 72074 Tuebingen, Germany; German Center for Neurodegenerative Diseases (DZNE), 72076 Tuebingen, Germany
| | - Stephanie Deutscher
- Department of Human Genetics, Saarland University, 66421 Homburg/Saar, Germany
| | - Simone Gurlit
- Department of Anesthesiology and Intensive Care, St. Franziskus Hospital Muenster, 48145 Muenster, Germany
| | - Claudia Schulte
- Center for Neurology and Hertie Institute for Clinical Brain Research, Department of Neurodegeneration, University of Tuebingen, 72074 Tuebingen, Germany; German Center for Neurodegenerative Diseases (DZNE), 72076 Tuebingen, Germany
| | - Anna-Katharina von Thaler
- Center for Neurology and Hertie Institute for Clinical Brain Research, Department of Neurodegeneration, University of Tuebingen, 72074 Tuebingen, Germany; German Center for Neurodegenerative Diseases (DZNE), 72076 Tuebingen, Germany
| | - Christian Deuschle
- Center for Neurology and Hertie Institute for Clinical Brain Research, Department of Neurodegeneration, University of Tuebingen, 72074 Tuebingen, Germany; German Center for Neurodegenerative Diseases (DZNE), 72076 Tuebingen, Germany
| | - Florian Metzger
- Department of Psychiatry and Psychotherapy, University Hospital Tuebingen, 72016 Tuebingen, Germany
| | - Daniela Berg
- Department of Neurology, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany; Center for Neurology and Hertie Institute for Clinical Brain Research, Department of Neurodegeneration, University of Tuebingen, 72074 Tuebingen, Germany; German Center for Neurodegenerative Diseases (DZNE), 72076 Tuebingen, Germany
| | - Ulrike Suenkel
- Center for Neurology and Hertie Institute for Clinical Brain Research, Department of Neurodegeneration, University of Tuebingen, 72074 Tuebingen, Germany; German Center for Neurodegenerative Diseases (DZNE), 72076 Tuebingen, Germany
| | - Verena Keller
- Department of Medicine II, Saarland University Medical Center, 66421 Homburg/Saar, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Hans-Peter Lenhof
- Center for Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, 66421 Homburg/Saar, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany; Center for Bioinformatics, Saarland Informatics Campus, 66123 Saarbrücken, Germany.
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45
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Fehlmann T, Backes C, Pirritano M, Laufer T, Galata V, Kern F, Kahraman M, Gasparoni G, Ludwig N, Lenhof HP, Gregersen HA, Francke R, Meese E, Simon M, Keller A. The sncRNA Zoo: a repository for circulating small noncoding RNAs in animals. Nucleic Acids Res 2019; 47:4431-4441. [PMID: 30937442 PMCID: PMC6511844 DOI: 10.1093/nar/gkz227] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 03/29/2019] [Indexed: 12/12/2022] Open
Abstract
The repertoire of small noncoding RNAs (sncRNAs), particularly miRNAs, in animals is considered to be evolutionarily conserved. Studies on sncRNAs are often largely based on homology-based information, relying on genomic sequence similarity and excluding actual expression data. To obtain information on sncRNA expression (including miRNAs, snoRNAs, YRNAs and tRNAs), we performed low-input-volume next-generation sequencing of 500 pg of RNA from 21 animals at two German zoological gardens. Notably, none of the species under investigation were previously annotated in any miRNA reference database. Sequencing was performed on blood cells as they are amongst the most accessible, stable and abundant sources of the different sncRNA classes. We evaluated and compared the composition and nature of sncRNAs across the different species by computational approaches. While the distribution of sncRNAs in the different RNA classes varied significantly, general evolutionary patterns were maintained. In particular, miRNA sequences and expression were found to be even more conserved than previously assumed. To make the results available for other researchers, all data, including expression profiles at the species and family levels, and different tools for viewing, filtering and searching the data are freely available in the online resource ASRA (Animal sncRNA Atlas) at https://www.ccb.uni-saarland.de/asra/.
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Affiliation(s)
- Tobias Fehlmann
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Christina Backes
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Marcello Pirritano
- Molecular Cell Dynamics, Center for Human and Molecular Biology, Saarland University, 66123 Saarbrücken, Germany.,Molecular Cell Biology and Microbiology, University of Wuppertal, 42097 Wuppertal, Germany
| | - Thomas Laufer
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Hummingbird Diagnostics GmbH, 69120 Heidelberg, Germany
| | - Valentina Galata
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Kern
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Mustafa Kahraman
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Hummingbird Diagnostics GmbH, 69120 Heidelberg, Germany
| | - Gilles Gasparoni
- Department of Genetics, Center for Human and Molecular Biology, Saarland University, 66123 Saarbrücken, Germany
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University Hospital, 66421 Homburg, Germany
| | - Hans-Peter Lenhof
- Chair for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | | | | | - Eckart Meese
- Department of Human Genetics, Saarland University Hospital, 66421 Homburg, Germany
| | - Martin Simon
- Molecular Cell Dynamics, Center for Human and Molecular Biology, Saarland University, 66123 Saarbrücken, Germany.,Molecular Cell Biology and Microbiology, University of Wuppertal, 42097 Wuppertal, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany.,Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
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46
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Ouwens KG, Jansen R, Nivard MG, van Dongen J, Frieser MJ, Hottenga JJ, Arindrarto W, Claringbould A, van Iterson M, Mei H, Franke L, Heijmans BT, A C 't Hoen P, van Meurs J, Brooks AI, Penninx BWJH, Boomsma DI. A characterization of cis- and trans-heritability of RNA-Seq-based gene expression. Eur J Hum Genet 2019; 28:253-263. [PMID: 31558840 DOI: 10.1038/s41431-019-0511-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 07/21/2019] [Accepted: 08/12/2019] [Indexed: 01/19/2023] Open
Abstract
Insights into individual differences in gene expression and its heritability (h2) can help in understanding pathways from DNA to phenotype. We estimated the heritability of gene expression of 52,844 genes measured in whole blood in the largest twin RNA-Seq sample to date (1497 individuals including 459 monozygotic twin pairs and 150 dizygotic twin pairs) from classical twin modeling and identity-by-state-based approaches. We estimated for each gene h2total, composed of cis-heritability (h2cis, the variance explained by single nucleotide polymorphisms in the cis-window of the gene), and trans-heritability (h2res, the residual variance explained by all other genome-wide variants). Mean h2total was 0.26, which was significantly higher than heritability estimates earlier found in a microarray-based study using largely overlapping (>60%) RNA samples (mean h2 = 0.14, p = 6.15 × 10-258). Mean h2cis was 0.06 and strongly correlated with beta of the top cis expression quantitative loci (eQTL, ρ = 0.76, p < 10-308) and with estimates from earlier RNA-Seq-based studies. Mean h2res was 0.20 and correlated with the beta of the corresponding trans-eQTL (ρ = 0.04, p < 1.89 × 10-3) and was significantly higher for genes involved in cytokine-cytokine interactions (p = 4.22 × 10-15), many other immune system pathways, and genes identified in genome-wide association studies for various traits including behavioral disorders and cancer. This study provides a thorough characterization of cis- and trans-h2 estimates of gene expression, which is of value for interpretation of GWAS and gene expression studies.
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Affiliation(s)
- Klaasjan G Ouwens
- Department of Biological Psychology, Amsterdam Public Health research institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| | - Rick Jansen
- Department of Psychiatry, Amsterdam Public Health and Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Michel G Nivard
- Department of Biological Psychology, Amsterdam Public Health research institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Jenny van Dongen
- Department of Biological Psychology, Amsterdam Public Health research institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Maia J Frieser
- Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, USA.,Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, USA
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, Amsterdam Public Health research institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Wibowo Arindrarto
- Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Annique Claringbould
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Maarten van Iterson
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.,Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center Nijmegen, Nijmegen, the Netherlands
| | - Joyce van Meurs
- Department of Internal Medicine, ErasmusMC, Rotterdam, The Netherlands
| | - Andrew I Brooks
- Department of Genetics and the Human Genetics Institute, RUCDR Infinite Biologics, Rutgers University, New Brunswick, NJ, USA
| | | | - Brenda W J H Penninx
- Department of Psychiatry, Amsterdam Public Health and Amsterdam Neuroscience, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Amsterdam Public Health research institute, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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47
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Kinser HE, Pincus Z. MicroRNAs as modulators of longevity and the aging process. Hum Genet 2019; 139:291-308. [PMID: 31297598 DOI: 10.1007/s00439-019-02046-0] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/05/2019] [Indexed: 12/22/2022]
Abstract
MicroRNAs (miRNAs) are short, non-coding RNAs that post-transcriptionally repress translation or induce mRNA degradation of target transcripts through sequence-specific binding. miRNAs target hundreds of transcripts to regulate diverse biological pathways and processes, including aging. Many microRNAs are differentially expressed during aging, generating interest in their use as aging biomarkers and roles as regulators of the aging process. In the invertebrates Caenorhabditis elegans and Drosophila, a number of miRNAs have been found to both positive and negatively modulate longevity through canonical aging pathways. Recent studies have also shown that miRNAs regulate age-associated processes and pathologies in a diverse array of mammalian tissues, including brain, heart, bone, and muscle. The review will present an overview of these studies, highlighting the role of individual miRNAs as biomarkers of aging and regulators of longevity and tissue-specific aging processes.
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Affiliation(s)
- Holly E Kinser
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, USA
| | - Zachary Pincus
- Department of Developmental Biology and Department of Genetics, Washington University in St. Louis, St. Louis, USA.
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48
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Ludwig N, Hecksteden A, Kahraman M, Fehlmann T, Laufer T, Kern F, Meyer T, Meese E, Keller A, Backes C. Spring is in the air: seasonal profiles indicate vernal change of miRNA activity. RNA Biol 2019; 16:1034-1043. [PMID: 31035857 DOI: 10.1080/15476286.2019.1612217] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The envisioned application of miRNAs as diagnostic or prognostic biomarkers calls for an in-depth understanding of their distribution and variability in different physiological states. While effects with respect to ethnic origin, age, or gender are known, the inter-individual variability of miRNAs across the four seasons remained largely hidden. We sequentially profiled the complete repertoire of blood-borne miRNAs for 25 physiologically normal individuals in spring, summer, fall, and winter (altogether 95 samples) and validated the results on 292 individuals (919 samples collected with the Mitra home sampling device) by RT-qPCR. Principal variance component analysis suggests that the largest variability observed in miRNA expression is due to individual variability and the individuals' gender. But the results also highlight a deviation of miRNA activity in samples collected during spring time. Following adjustment for multiple testing, remarkable differences are observed between spring and fall (77 miRNAs). The two most dys-regulated miRNAs were miR-181c-5p and miR-106b-5p (adjusted p-value of 0.007). Other significant miRNAs include miR-140-3p, miR-21-3p, and let-7c-5p. The dys-regulation was validated by RT-qPCR. Systems biology analysis further provides strong evidence for the immunological origin of the signals: dys-regulated miRNAs are enriched in CD56 cells and belong to various signalling and immune-system-related pathways. Our data suggest that besides known confounding factors such as age and sex, also the season in which a test is conducted might have a considerable influence on the expression of blood-borne miRNAs and subsequently might interfere with diagnosis based on such signatures.
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Affiliation(s)
- Nicole Ludwig
- a Department of Human Genetics , Saarland University Hospital , Homburg , Germany.,b Center for Human and Molecular Biology , Saarland University , Homburg , Germany
| | - Anne Hecksteden
- c Department of Sports Medicine , Saarland University , Saarbrücken , Germany
| | - Mustafa Kahraman
- d Chair for Clinical Bioinformatics , Saarland University , Saarbrücken , Germany.,e Hummingbird Diagnostics GmbH , Heidelberg , Germany
| | - Tobias Fehlmann
- d Chair for Clinical Bioinformatics , Saarland University , Saarbrücken , Germany
| | - Thomas Laufer
- d Chair for Clinical Bioinformatics , Saarland University , Saarbrücken , Germany.,e Hummingbird Diagnostics GmbH , Heidelberg , Germany
| | - Fabian Kern
- d Chair for Clinical Bioinformatics , Saarland University , Saarbrücken , Germany
| | - Tim Meyer
- c Department of Sports Medicine , Saarland University , Saarbrücken , Germany
| | - Eckart Meese
- a Department of Human Genetics , Saarland University Hospital , Homburg , Germany
| | - Andreas Keller
- d Chair for Clinical Bioinformatics , Saarland University , Saarbrücken , Germany
| | - Christina Backes
- d Chair for Clinical Bioinformatics , Saarland University , Saarbrücken , Germany
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49
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Circulating small non-coding RNAs associated with age, sex, smoking, body mass and physical activity. Sci Rep 2018; 8:17650. [PMID: 30518766 PMCID: PMC6281647 DOI: 10.1038/s41598-018-35974-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 11/13/2018] [Indexed: 12/15/2022] Open
Abstract
Small non-coding RNAs (sncRNA) are regulators of cell functions and circulating sncRNAs from the majority of RNA classes are potential non-invasive biomarkers. Understanding how common traits influence ncRNA expression is essential for assessing their biomarker potential. In this study, we identify associations between sncRNA expression and common traits (sex, age, self-reported smoking, body mass, self-reported physical activity). We used RNAseq data from 526 serum samples from the Janus Serum Bank and traits from health examination surveys. Ageing showed the strongest association with sncRNA expression, both in terms of statistical significance and number of RNAs, regardless of RNA class. piRNAs were abundant in the serum samples and they were associated to sex. Interestingly, smoking cessation generally restored RNA expression to non-smoking levels, although for some sncRNAs smoking-related expression levels persisted. Pathway analysis suggests that smoking-related sncRNAs target the cholinergic synapses and may therefore potentially play a role in smoking addiction. Our results show that common traits influence circulating sncRNA expression. It is clear that sncRNA biomarker analyses should be adjusted for age and sex. In addition, for specific sncRNAs, analyses should also be adjusted for body mass, smoking, physical activity and technical factors.
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50
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Unger L, Jagannathan V, Pacholewska A, Leeb T, Gerber V. Differences in miRNA differential expression in whole blood between horses with sarcoid regression and progression. J Vet Intern Med 2018; 33:241-250. [PMID: 30506726 PMCID: PMC6335546 DOI: 10.1111/jvim.15375] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 11/06/2018] [Indexed: 12/20/2022] Open
Abstract
Background Currently no methods are available to predict the clinical outcome of individual horses with equine sarcoid (ES) disease. Objective To investigate if whole blood microRNA (miRNA) profiles can predict the long‐term development of ES tumors. Animals Five horses with regression and 5 with progression of ES lesions monitored over 5‐7 years and 5 control horses free of ES for at least 5 years. Methods For this cohort study, RNA extracted from whole blood samples from the regression, progression, and control groups was used for high throughput sequencing. Known and novel miRNAs were identified using miRDeep2 and differential expression analysis was carried out by the DESeq2 algorithm. Target gene and pathway prediction as well as enrichment and network analyses were conducted using TarBase, mirPath, and metaCore from GeneGo. Results Fourteen miRNAs were differentially expressed between regression and progression groups after accounting for the control condition: 4 miRNAs (28.6%) were upregulated and 10 miRNAs (71.4%) were downregulated with >2‐fold change. Seven of the 10 downregulated miRNAs are encoded in an miRNA cluster on equine chromosome 24, homologous to the well‐known 14q32 cluster in humans. Their target genes show enrichment for pathways involved in viral carcinogenesis. Conclusions and Clinical Importance Whole blood miRNA expression profiles are associated with long‐term ES growth in horses and warrant further validation as prognostic biomarkers in a larger study cohort. Deregulation of miRNAs on equine chromosome 24 might represent a trigger for ES development.
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Affiliation(s)
- Lucia Unger
- Swiss Institute of Equine Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Alicja Pacholewska
- Swiss Institute of Equine Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Vinzenz Gerber
- Swiss Institute of Equine Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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