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Brandes F, Meidert AS, Kirchner B, Yu M, Gebhardt S, Steinlein OK, Dolch ME, Rantner B, Tsilimparis N, Schelling G, Pfaffl MW, Reithmair M. Identification of microRNA biomarkers simultaneously expressed in circulating extracellular vesicles and atherosclerotic plaques. Front Cardiovasc Med 2024; 11:1307832. [PMID: 38725837 PMCID: PMC11079260 DOI: 10.3389/fcvm.2024.1307832] [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: 10/05/2023] [Accepted: 04/08/2024] [Indexed: 05/12/2024] Open
Abstract
Background Atherosclerosis is a widespread disorder of the cardiovascular system. The early detection of plaques by circulating biomarkers is highly clinically relevant to prevent the occurrence of major complications such as stroke or heart attacks. It is known that extracellular vesicles (EVs) are important in intercellular communication in atherosclerotic disorders and carry many components of their cells of origin, including microRNAs (miRNAs). In this study, we test the assumption that miRNAs present in material acquired from plaques in patients undergoing surgery for atherosclerotic carotid artery stenosis are also expressed in circulating EVs obtained from the identical patients. This would allow the adoption of a liquid biopsy approach for the detection of plaques. Methods We studied 22 surgical patients with atherosclerotic carotid arterial stenosis and 28 healthy controls. EVs were isolated from serum by precipitation. miRNA expression profiles of serum-derived EVs were obtained by small RNA sequencing and in plaque material simultaneously acquired from patients. A comparative analysis was performed to identify circulating atherosclerosis-associated miRNAs that are also detectable in plaques. Results Seven miRNAs were found to be differentially regulated in patient serum compared with the serum of healthy controls. Of these, miR-193b-5p, miR-193a-5p, and miR-125a-3p were significantly upregulated in patients compared with that in healthy controls and present in both, circulating EVs and plaque material. An overrepresentation analysis of experimentally validated mRNA targets revealed an increased regulation of inflammation and vascular growth factors, key players in atherosclerosis and plaque formation. Conclusion Our findings suggest that circulating EVs reflect plaque development in patients with symptomatic carotid artery stenosis, which can serve as biomarker candidates for detecting the presence of atherosclerotic plaques.
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Affiliation(s)
- Florian Brandes
- Department of Anesthesiology, LMU University Hospital, LMU Munich, Munich, Germany
| | - Agnes S. Meidert
- Department of Anesthesiology, LMU University Hospital, LMU Munich, Munich, Germany
| | - Benedikt Kirchner
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Mia Yu
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Sonja Gebhardt
- Department of Anaesthesiology, InnKlinikum Altötting, Altötting, Germany
| | - Ortrud K. Steinlein
- Institute of Human Genetics, LMU University Hospital, LMU Munich, Munich, Germany
| | - Michael E. Dolch
- Department of Anaesthesiology, InnKlinikum Altötting, Altötting, Germany
| | - Barbara Rantner
- Department of Vascular Surgery, LMU University Hospital, LMU Munich, Munich, Germany
| | - Nikolaos Tsilimparis
- Department of Vascular Surgery, LMU University Hospital, LMU Munich, Munich, Germany
| | - Gustav Schelling
- Department of Anesthesiology, LMU University Hospital, LMU Munich, Munich, Germany
| | - Michael W. Pfaffl
- Division of Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Marlene Reithmair
- Institute of Human Genetics, LMU University Hospital, LMU Munich, Munich, Germany
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Bharati J, Kumar M, Kumar N, Malhotra A, Singhal PC. MicroRNA193a: An Emerging Mediator of Glomerular Diseases. Biomolecules 2023; 13:1743. [PMID: 38136614 PMCID: PMC10742064 DOI: 10.3390/biom13121743] [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: 10/23/2023] [Revised: 11/30/2023] [Accepted: 12/02/2023] [Indexed: 12/24/2023] Open
Abstract
MicroRNAs (miRNAs) are noncoding small RNAs that regulate the protein expression of coding messenger RNAs. They are used as biomarkers to aid in diagnosing, prognosticating, and surveillance of diseases, especially solid cancers. MiR-193a was shown to be directly pathogenic in an experimental mouse model of focal segmental glomerulosclerosis (FSGS) during the last decade. Its specific binding and downregulation of Wilm's tumor-1 (WT-1), a transcription factor regulating podocyte phenotype, is documented. Also, miR-193a is a regulator switch causing the transdifferentiation of glomerular parietal epithelial cells to a podocyte phenotype in in vitro study. Interaction between miR-193a and apolipoprotein 1 (APOL1) mRNA in glomeruli (filtration units of kidneys) is potentially involved in the pathogenesis of common glomerular diseases. Since the last decade, there has been an increasing interest in the role of miR-193a in glomerular diseases, including diabetic nephropathy and membranous nephropathy, besides FSGS. Considering the lack of biomarkers to manage FSGS and diabetic nephropathy clinically, it is worthwhile to invest in evaluating miR-193a in the pathogenesis of these diseases. What causes the upregulation of miR-193a in FSGS and how the mechanism is different in different glomerular disorders still need to be elucidated. This narrative review highlights the pathogenic mechanisms of miR-193a elevation in various glomerular diseases and its potential use in clinical management.
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Affiliation(s)
- Joyita Bharati
- Feinstein Institute for Medical Research, Manhasset, NY 11030, USA; (J.B.); (M.K.); (N.K.)
- Division of Kidney Diseases and Hypertension, Zucker School of Medicine at Hofstra Northwell Health, Great Neck, NY 11021, USA
| | - Megan Kumar
- Feinstein Institute for Medical Research, Manhasset, NY 11030, USA; (J.B.); (M.K.); (N.K.)
| | - Neil Kumar
- Feinstein Institute for Medical Research, Manhasset, NY 11030, USA; (J.B.); (M.K.); (N.K.)
| | - Ashwani Malhotra
- Feinstein Institute for Medical Research, Manhasset, NY 11030, USA; (J.B.); (M.K.); (N.K.)
| | - Pravin C. Singhal
- Feinstein Institute for Medical Research, Manhasset, NY 11030, USA; (J.B.); (M.K.); (N.K.)
- Division of Kidney Diseases and Hypertension, Zucker School of Medicine at Hofstra Northwell Health, Great Neck, NY 11021, USA
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Yoshida T, Latt KZ, Rosenberg AZ, Shrivastav S, Heymann J, Halushka MK, Winkler CA, Kopp JB. Transcriptomic Analysis of Human Podocytes In Vitro: Effects of Differentiation and APOL1 Genotype. Kidney Int Rep 2022; 8:164-178. [PMID: 36644347 PMCID: PMC9831945 DOI: 10.1016/j.ekir.2022.10.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/03/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Introduction The mechanisms in podocytes that mediate the pathologic effects of the APOL1 high-risk (HR) variants remain incompletely understood, although various molecular and cellular mechanisms have been proposed. We previously established conditionally immortalized human urine-derived podocyte-like epithelial cell (HUPEC) lines to investigate APOL1 HR variant-induced podocytopathy. Methods We conducted comprehensive transcriptomic analysis, including mRNA, microRNA (miRNA), and transfer RNA fragments (tRFs), to characterize the transcriptional profiles in undifferentiated and differentiated HUPEC with APOL1 HR (G1/G2, 2 cell lines) and APOL1 low-risk (LR) (G0/G0, 2 cell lines) genotypes. We reanalyzed single-cell RNA-seq data from urinary podocytes from focal segmental glomerulosclerosis (FSGS) subjects to characterize the effect of APOL1 genotypes on podocyte transcriptomes. Results Differential expression analysis showed that the ribosomal pathway was one of the most enriched pathways, suggesting that altered function of the translation initiation machinery may contribute to APOL1 variant-induced podocyte injury. Expression of genes related to the elongation initiation factor 2 pathway was also enriched in the APOL1 HR urinary podocytes from single-cell RNA-seq, supporting a prior report on the role of this pathway in APOL1-associated cell injury. Expression of microRNA and tRFs were analyzed, and the profile of small RNAs differed by both differentiation status and APOL1 genotype. Conclusion We have profiled the transcriptomic landscape of human podocytes, including mRNA, miRNA, and tRF, to characterize the effects of differentiation and of different APOL1 genotypes. The candidate pathways, miRNAs, and tRFs described here expand understanding of APOL1-associated podocytopathies.
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Affiliation(s)
- Teruhiko Yoshida
- Kidney Disease Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA,Correspondence: Teruhiko Yoshida, Kidney Disease Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, 10 Center Drive, 3N104, Bethesda, Maryland 20892-1268, USA.
| | - Khun Zaw Latt
- Kidney Disease Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Avi Z. Rosenberg
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Shashi Shrivastav
- Kidney Disease Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Jurgen Heymann
- Kidney Disease Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Marc K. Halushka
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Cheryl A. Winkler
- Frederick National Laboratory for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
| | - Jeffrey B. Kopp
- Kidney Disease Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, USA
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Xu N, Liu J, Li X. Lupus nephritis: The regulatory interplay between epigenetic and MicroRNAs. Front Physiol 2022; 13:925416. [PMID: 36187762 PMCID: PMC9523357 DOI: 10.3389/fphys.2022.925416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs (miRNAs) are endogenous, small, non-coding RNA molecules that act as epigenetic modifiers to regulate the protein levels of target messenger RNAs without altering their genetic sequences. The highly complex role of miRNAs in the epigenetics of lupus nephritis (LN) is increasingly being recognized. DNA methylation and histone modifications are focal points of epigenetic research. miRNAs play a critical role in renal development and physiology, and dysregulation may result in abnormal renal cell proliferation, inflammation, and fibrosis of the kidneys in LN. However, epigenetic and miRNA-mediated regulation are not mutually exclusive. Further research has established a link between miRNA expression and epigenetic regulation in various disorders, including LN. This review summarizes the most recent evidence regarding the interaction between miRNAs and epigenetics in LN and highlights potential therapeutic and diagnostic targets.
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Affiliation(s)
- Ning Xu
- School of Clinical Medicine, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Jie Liu
- School of Clinical Medicine, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Xiangling Li
- Department of Nephrology, Affiliated Hospital of Weifang Medical University, Weifang, China
- *Correspondence: Xiangling Li,
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3D Modeling of Non-coding RNA Interactions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1385:281-317. [DOI: 10.1007/978-3-031-08356-3_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Horx P, Geyer A. High five! Methyl probes at five ring positions of phenylalanine explore the hydrophobic core dynamics of zinc finger miniproteins. Chem Sci 2021; 12:11455-11463. [PMID: 34667551 PMCID: PMC8447250 DOI: 10.1039/d1sc02346b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/22/2021] [Indexed: 12/02/2022] Open
Abstract
The elucidation of internal dynamics in proteins is essential for the understanding of their stability and functionality. Breaking the symmetry of the degenerate rotation of the phenyl side chain provides additional structural information and allows a detailed description of the dynamics. Based on this concept, we propose a combination of synthetic and computational methods, to study the rotational mobility of the Phe ring in a sensitive zinc finger motif. The systematic methyl hopping around the phenylalanine ring yields o-, m-, p-tolyl and xylyl side chains that provide a vast array of additional NOE contacts, allowing the precise determination of the orientation of the aromatic ring. MD simulations and metadynamics complement these findings and facilitate the generation of free energy profiles for each derivative. Previous studies used a wide temperature window in combination with NMR spectroscopy to elucidate the side chain mobility of stable proteins. The zinc finger moiety exhibits a limited thermodynamic stability in a temperature range of only 40 K, making this approach impractical for this compound class. Therefore, we have developed a method that can be applied even to thermolabile systems and facilitates the detailed investigation of protein dynamics.
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Affiliation(s)
- Philip Horx
- Philipps-University Marburg 35043 Marburg Germany
| | - Armin Geyer
- Philipps-University Marburg 35043 Marburg Germany
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