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Castillo Y, Delgadillo NA, Neuta Y, Iniesta M, Sanz M, Herrera D, Pianeta R, Lafaurie GI, Castillo DM. Design and validation of a quantitative polymerase chain reaction test for the identification and quantification of uncultivable bacteria associated with periodontitis. Arch Oral Biol 2023; 154:105758. [PMID: 37419062 DOI: 10.1016/j.archoralbio.2023.105758] [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: 02/13/2023] [Revised: 06/11/2023] [Accepted: 07/02/2023] [Indexed: 07/09/2023]
Abstract
OBJECTIVE This study aimed to standardize a quantitative polymerase chain reaction (qPCR)-based test to identify and quantify the uncultivable bacteria associated with periodontitis. METHODS The standardization of qPCR, the curves for the quantification of Eubacterium saphenum, Eubacterium brachy, Desulfobulbus oralis, and Filifactor alocis were developed by cloning the 16 S rRNA target gene fragment, using the GEMTEasy vector. The qPCRs were validated in 55 subgingival biofilm clinical samples, from different stages of periodontitis and from periodontally healthy/gingivitis individuals, which were previously evaluated by next-generation sequencing (NGS). The results obtained by the two methods were compared by the concordance of Cohen's Kappa index, and sensitivity, specificity, receiver operating characteristic (ROC) curve, and predictive values were established. RESULTS obtained by the two methods were compared using the concordance of Cohen's Kappa index, and sensitivity, specificity, predictive values, and ROC curves were generated. The qPCR test was standardized with efficiencies between 90% and 100% and R2: 0.997-0.999. Concordance between the qPCR and NSG was moderate to F. alocis (agreement 78.2%; kappa 0.56, p < 0.05) and fair to the other microorganisms (agreement 67.27%-72.73; kappa 0.37-0.38, p < 0.05). qPCR exhibited a high sensitivity (82.2-100%) and specificity (100%) for E. brachy, E. saphenum, and F. alocis. Sensitivity was lower to D. oralis. Conversely, qPCR demonstrated higher sensitivity to E. saphenum than NSG (100 vs. 68.1). CONCLUSIONS The uncultivable microorganisms associated with periodontitis, D. oralis, E. brachy, E. saphenum, and F. alocis can be detected and quantified with the newly developed and validates qPCR test.
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Affiliation(s)
- Yormaris Castillo
- Universidad El Bosque, Vicerrectoría de investigaciones, Facultad de Odontología, Unidad de Investigación Básica Oral-UIBO, Bogotá, Colombia
| | - Nathaly Andrea Delgadillo
- Universidad El Bosque, Vicerrectoría de investigaciones, Facultad de Odontología, Unidad de Investigación Básica Oral-UIBO, Bogotá, Colombia
| | - Yineth Neuta
- Universidad El Bosque, Vicerrectoría de investigaciones, Facultad de Odontología, Unidad de Investigación Básica Oral-UIBO, Bogotá, Colombia
| | - Margarita Iniesta
- Complutense University of Madrid, ETEP (Etiology and Therapy of Periodontal and Peri-Implant Diseases) Research Group, School of Dentistry, Madrid, Spain
| | - Mariano Sanz
- Complutense University of Madrid, ETEP (Etiology and Therapy of Periodontal and Peri-Implant Diseases) Research Group, School of Dentistry, Madrid, Spain
| | - David Herrera
- Complutense University of Madrid, ETEP (Etiology and Therapy of Periodontal and Peri-Implant Diseases) Research Group, School of Dentistry, Madrid, Spain
| | - Roquelina Pianeta
- Complutense University of Madrid, ETEP (Etiology and Therapy of Periodontal and Peri-Implant Diseases) Research Group, School of Dentistry, Madrid, Spain; Corporación Universitaria Rafael Núñez, School of Dentistry, Cartagena, Colombia
| | - Gloria Inés Lafaurie
- Universidad El Bosque, Vicerrectoría de investigaciones, Facultad de Odontología, Unidad de Investigación Básica Oral-UIBO, Bogotá, Colombia
| | - Diana Marcela Castillo
- Universidad El Bosque, Vicerrectoría de investigaciones, Facultad de Odontología, Unidad de Investigación Básica Oral-UIBO, Bogotá, Colombia.
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Rhee KH, Yang SA, Pyo MC, Lim JM, Lee KW. MiR-155-5p Elevated by Ochratoxin A Induces Intestinal Fibrosis and Epithelial-to-Mesenchymal Transition through TGF-β Regulated Signaling Pathway In Vitro and In Vivo. Toxins (Basel) 2023; 15:473. [PMID: 37505742 PMCID: PMC10467050 DOI: 10.3390/toxins15070473] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 07/16/2023] [Accepted: 07/19/2023] [Indexed: 07/29/2023] Open
Abstract
Ochratoxin A (OTA) is a mycotoxin that induces fibrosis and epithelial-to-mesenchymal transitions (EMT) in kidneys and livers. It enters our bodies through food consumption, where it is absorbed in the intestines. However, the impact of OTA on the intestines is yet to be studied. MicroRNA (miRNAs) are small non-coding single-stranded RNAs that block the transcription of specific mRNAs and are, therefore, involved in many biochemical processes. Our findings indicate that OTA can induce EMT and intestinal fibrosis both in vivo and in vitro. This study examines the impact of OTA on intestinal toxicity and the role of miRNAs in this process. Following OTA treatment, miR-155-5p was the most elevated miRNA by next-generation sequencing. Our research showed that OTA increased miR-155-5p levels through transforming growth factor β (TGF-β), leading to the development of intestinal fibrosis and EMT. Additionally, the study identified that the modulation of TGF-β and miR-155-5p by OTA is linked to the inhibition of CCAAT/enhancer-binding protein β (C/EBPβ) and Smad2/3 accumulation in the progression of intestinal fibrosis.
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Affiliation(s)
| | | | | | | | - Kwang-Won Lee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea; (K.H.R.); (S.A.Y.); (M.C.P.); (J.-M.L.)
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Peplow P, Martinez B. MicroRNAs as potential biomarkers in temporal lobe epilepsy and mesial temporal lobe epilepsy. Neural Regen Res 2023; 18:716-726. [DOI: 10.4103/1673-5374.354510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Li Z, Xiao H, Li J, Yang Z, Jiang J, Ji J, Peng C, He Y. Graphene Oxide-Based Highly Sensitive Assay of Circulating MicroRNAs for Early Prediction of the Response to Neoadjuvant Chemotherapy in Breast Cancer. Anal Chem 2022; 94:16254-16264. [DOI: 10.1021/acs.analchem.2c04117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zhijia Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Hongtao Xiao
- Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Cancer Hospital affiliated to School of Medicine, University of Electronic Science and Technology of China, Chengdu 610041, China
| | - Junjie Li
- Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Cancer Hospital affiliated to School of Medicine, University of Electronic Science and Technology of China, Chengdu 610041, China
| | - Zhongzhu Yang
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Jun Jiang
- Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Cancer Hospital affiliated to School of Medicine, University of Electronic Science and Technology of China, Chengdu 610041, China
| | - Juan Ji
- Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Cancer Hospital affiliated to School of Medicine, University of Electronic Science and Technology of China, Chengdu 610041, China
| | - Cheng Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yang He
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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5
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Petejova N, Martinek A, Zadrazil J, Klementa V, Pribylova L, Bris R, Kanova M, Sigutova R, Kacirova I, Svagera Z, Bace E, Stejskal D. Expression and 7-day time course of circulating microRNAs in septic patients treated with nephrotoxic antibiotic agents. BMC Nephrol 2022; 23:111. [PMID: 35305556 PMCID: PMC8933949 DOI: 10.1186/s12882-022-02726-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/07/2022] [Indexed: 12/24/2022] Open
Abstract
Background Through regulation of signaling pathways, microRNAs (miRNAs) can be involved in sepsis and associated organ dysfunction. The aims of this study were to track the 7-day time course of blood miRNAs in patients with sepsis treated with vancomycin, gentamicin, or a non-nephrotoxic antibiotic and miRNA associations with neutrophil gelatinase-associated lipokalin (NGAL), creatinine, procalcitonin, interleukin-6, and acute kidney injury (AKI) stage. Methods Of 46 adult patients, 7 were on vancomycin, 20 on gentamicin, and 19 on another antibiotic. Blood samples were collected on days 1, 4, and 7 of treatment, and miRNAs were identified using quantitative reverse transcription PCR. Results The results showed no relationship between miRNA levels and biochemical variables on day 1. By day 7 of gentamicin treatment miR-15a-5p provided good discrimination between AKI and non-AKI (area under curve, 0.828). In patients taking vancomycin, miR-155-5p and miR-192-5p positively correlated with creatinine and NGAL values, and miR-192-5p and miR-423-5p positively correlated with procalcitonin and interleukin-6 in patients treated with a non-nephrotoxic antibiotic. In patients together we found positive correlation between miR-155-5p and miR-423-5p and all biochemical markers. Conclusion The results suggest that these four miRNAs may serve as diagnostic or therapeutic tool in sepsis, renal injury and nephrotoxic treatment. Trial registration ClinicalTrials.gov, ID: NCT04991376. Registered on 27 July 2021.
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Lee SI, Park H, Kim SJ, Lee KW, Shin DY, Son JK, Hong JH, Kim SH, Cho HJ, Park JB, Kim TM. Circulating RNA Profiling in Postreperfusion Plasma From Kidney Transplant Recipients. Transplant Proc 2021; 53:2853-2865. [PMID: 34772491 DOI: 10.1016/j.transproceed.2021.09.044] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/30/2021] [Indexed: 12/29/2022]
Abstract
BACKGROUND Ischemia/reperfusion injury (IRI) is inevitable in kidney transplantation (KT) and may lead to impaired tubular epithelial cell function and reduce graft function and survival. Renal IRI is a complex cellular and molecular event; therefore, investigating the genetic or molecular pathways associated with the early phase of KT would improve our understanding of IRI in KT. MicroRNAs (miRNAs) play a critical role in various pathologic events associated with IRI. METHODS We compared the expression profile of miRNAs extracted from 2 blood plasma samples, 1 from periphery and the other form gonadal veins immediately after reperfusion, in a total 5 cases of KT. RESULTS We observed that the total RNA yield was higher in postreperfusion plasma and that a subset of miRNAs was upregulated (miR-let-7a-3p, miR-143-3p, and miR-214-3p) or downregulated (let-7d-3p, let-7d-3p, miR-1246, miR-1260b, miR-1290, and miR-130b-3p) in postreperfusion plasma. Gene ontology analyses revealed that these subsets target different biological functions. Twenty-four predicted genes were commonly targeted by the upregulated miRNAs, and gene ontology enrichment and pathway analyses revealed that these were associated with various cellular activities such as signal transduction or with components such as exosomes and membranous organelles. CONCLUSION We present 2 subsets of miRNAs that were differentially upregulated or downregulated in postreperfusion plasma. Our findings may enhance our understanding of miRNA-mediated early molecular events related to IRI in KT.
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Affiliation(s)
- Sang In Lee
- Department of Animal Biotechnology, Kyungpook National University, Sangju, Gyeongsangbuk-do, Republic of Korea
| | - Hyojun Park
- School of Medicine, Sungkyunkwan University, Gangnam-gu, Seoul, Republic of Korea
| | - Sung Joo Kim
- School of Medicine, Sungkyunkwan University, Gangnam-gu, Seoul, Republic of Korea; Gennbio Co Ltd, Gangnam-gu, Seoul, Republic of Korea
| | - Kyo Won Lee
- Department of Surgery, Samsung Medical Center, Seoul, Republic of Korea
| | - Du Yeon Shin
- Transplantation Research Center, Stem Cell & Regenerative Medicine Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Jin Kyung Son
- Department of Surgery, Samsung Medical Center, Seoul, Republic of Korea
| | - Ju Hee Hong
- Department of Health Sciences & Technology, Samsung Advanced Institute for Health Sciences & Technology, Graduate School, Sungkyunkwan University, Seoul, Republic of Korea
| | - Seung Han Kim
- Gennbio Co Ltd, Gangnam-gu, Seoul, Republic of Korea
| | - Hye Jin Cho
- Graduate School of International Agricultural Technology, Seoul National University, Gangwon-do, Republic of Korea
| | - Jae Berm Park
- Department of Surgery, Samsung Medical Center, Seoul, Republic of Korea
| | - Tae Min Kim
- Graduate School of International Agricultural Technology, Seoul National University, Gangwon-do, Republic of Korea.
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Schofield AL, Brown JP, Brown J, Wilczynska A, Bell C, Glaab WE, Hackl M, Howell L, Lee S, Dear JW, Remes M, Reeves P, Zhang E, Allmer J, Norris A, Falciani F, Takeshita LY, Seyed Forootan S, Sutton R, Park BK, Goldring C. Systems analysis of miRNA biomarkers to inform drug safety. Arch Toxicol 2021; 95:3475-3495. [PMID: 34510227 PMCID: PMC8492583 DOI: 10.1007/s00204-021-03150-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 08/23/2021] [Indexed: 02/06/2023]
Abstract
microRNAs (miRNAs or miRs) are short non-coding RNA molecules which have been shown to be dysregulated and released into the extracellular milieu as a result of many drug and non-drug-induced pathologies in different organ systems. Consequently, circulating miRs have been proposed as useful biomarkers of many disease states, including drug-induced tissue injury. miRs have shown potential to support or even replace the existing traditional biomarkers of drug-induced toxicity in terms of sensitivity and specificity, and there is some evidence for their improved diagnostic and prognostic value. However, several pre-analytical and analytical challenges, mainly associated with assay standardization, require solutions before circulating miRs can be successfully translated into the clinic. This review will consider the value and potential for the use of circulating miRs in drug-safety assessment and describe a systems approach to the analysis of the miRNAome in the discovery setting, as well as highlighting standardization issues that at this stage prevent their clinical use as biomarkers. Highlighting these challenges will hopefully drive future research into finding appropriate solutions, and eventually circulating miRs may be translated to the clinic where their undoubted biomarker potential can be used to benefit patients in rapid, easy to use, point-of-care test systems.
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Affiliation(s)
- Amy L Schofield
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Buildings, Ashton Street, Liverpool, L69 3GE, UK
| | - Joseph P Brown
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Buildings, Ashton Street, Liverpool, L69 3GE, UK
| | - Jack Brown
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Buildings, Ashton Street, Liverpool, L69 3GE, UK
| | - Ania Wilczynska
- bit.bio, Babraham Research Campus, The Dorothy Hodgkin Building, Cambridge, CB22 3FH, UK
| | - Catherine Bell
- CVRM Safety, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Warren E Glaab
- Merck & Co., Inc, 770 Sumneytown Pike, West Point, PA, 19486, USA
| | | | - Lawrence Howell
- GlaxoSmithKline (GSK), Stevenage, Greater Cambridge Area, UK
| | - Stephen Lee
- ABHI, 1 Duchess St, 4th Floor, Suite 2, London, W1W 6AN, UK
| | - James W Dear
- Centre for Cardiovascular Science, The Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
| | - Mika Remes
- Genomics EMEA, QIAGEN Aarhus, Prismet, Silkeborgvej 2, 8000, Aarhus C, Denmark
| | - Paul Reeves
- Arcis Biotechnology Limited, Suite S07, Techspace One, Sci-tech Daresbury, Keckwick Lane, Daresbury, Warrington, WA4 4AB, UK
| | - Eunice Zhang
- Wolfson Centre for Personalised Medicine, Department of Pharmacology and Therapeutics, University of Liverpool, Crown Street, Liverpool, L69 3BX, UK
| | - Jens Allmer
- Applied Bioinformatics, Bioscience, Wageningen University and Research, Droevendaalsesteeg 4, 6708 PB, Wageningen, The Netherlands
| | - Alan Norris
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Buildings, Ashton Street, Liverpool, L69 3GE, UK
| | - Francesco Falciani
- Computational Biology Facility, MerseyBio, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Louise Y Takeshita
- Computational Biology Facility, MerseyBio, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK
| | - Shiva Seyed Forootan
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Buildings, Ashton Street, Liverpool, L69 3GE, UK
| | - Robert Sutton
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7BE, UK
| | - B Kevin Park
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Buildings, Ashton Street, Liverpool, L69 3GE, UK
| | - Chris Goldring
- MRC Centre for Drug Safety Science, Department of Pharmacology and Therapeutics, University of Liverpool, Sherrington Buildings, Ashton Street, Liverpool, L69 3GE, UK.
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Chorley BN, Ellinger-Ziegelbauer H, Tackett M, Simutis FJ, Harrill AH, McDuffie J, Atabakhsh E, Nassirpour R, Whiteley LO, Léonard JF, Carswell GK, Harpur E, Chen CL, Gautier JC. Urinary miRNA Biomarkers of Drug-Induced Kidney Injury and Their Site Specificity Within the Nephron. Toxicol Sci 2021; 180:1-16. [PMID: 33367795 PMCID: PMC7916737 DOI: 10.1093/toxsci/kfaa181] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Drug-induced kidney injury (DIKI) is a major concern in both drug development and clinical practice. There is an unmet need for biomarkers of glomerular damage and more distal renal injury in the loop of Henle and the collecting duct (CD). A cross-laboratory program to identify and characterize urinary microRNA (miRNA) patterns reflecting tissue- or pathology-specific DIKI was conducted. The overall goal was to propose miRNA biomarker candidates for DIKI that could supplement information provided by protein kidney biomarkers in urine. Rats were treated with nephrotoxicants causing injury to distinct nephron segments: the glomerulus, proximal tubule, thick ascending limb (TAL) of the loop of Henle and CD. Meta-analysis identified miR-192-5p as a potential proximal tubule-specific urinary miRNA candidate. This result was supported by data obtained in laser capture microdissection nephron segments showing that miR-192-5p expression was enriched in the proximal tubule. Discriminative miRNAs including miR-221-3p and -222-3p were increased in urine from rats treated with TAL versus proximal tubule toxicants in accordance with their expression localization in the kidney. Urinary miR-210-3p increased up to 40-fold upon treatment with TAL toxicants and was also enriched in laser capture microdissection samples containing TAL and/or CD versus proximal tubule. miR-23a-3p was enriched in the glomerulus and was increased in urine from rats treated with doxorubicin, a glomerular toxicant, but not with toxicants affecting other nephron segments. Taken together these results suggest that urinary miRNA panels sourced from specific nephron regions may be useful to discriminate the pathology of toxicant-induced lesions in the kidney, thereby contributing to DIKI biomarker development needs for industry, clinical, and regulatory use.
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Affiliation(s)
- Brian N Chorley
- U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | | | | | - Frank J Simutis
- Bristol-Myers Squibb Company, New Brunswick, New Jersey 08901, USA
| | - Alison H Harrill
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
| | - James McDuffie
- Janssen Research & Development, LLC, San Diego, California 92121, USA
| | | | - Rounak Nassirpour
- Pfizer Drug Safety Research and Development, Cambridge, Massachusetts 02139, USA
| | - Laurence O Whiteley
- Pfizer Drug Safety Research and Development, Cambridge, Massachusetts 02139, USA
| | | | - Gleta K Carswell
- U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | - Ernie Harpur
- Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Connie L Chen
- Health and Environmental Sciences Institute, Washington, District of Columbia 20005, USA
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Chen X, Gu L, Cheng X, Xing J, Zhang M. MiR-17-5p downregulation alleviates apoptosis and fibrosis in high glucose-induced human mesangial cells through inactivation of Wnt/β-catenin signaling by targeting KIF23. ENVIRONMENTAL TOXICOLOGY 2021; 36:1702-1712. [PMID: 34014023 DOI: 10.1002/tox.23280] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/28/2021] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
Diabetic nephropathy (DN) remains the major cause of end-stage renal disease. MicroRNAs (miRNAs) have been reported to perform biological functions in many diseases. This investigation elucidated the biological role of miR-17-5p in DN. In this study, high glucose-cultured human mesangial cells (HMCs) were used as a cell model of DN. The miR-17-5p and KIF23 expression was measured by RT-qPCR. Cell apoptosis was detected by flow cytometry. The protein levels of apoptosis markers, fibrosis markers, and Wnt/β-catenin signaling-related genes were assessed using western blotting. The interaction of miR-17-5p with KIF23 was tested by a luciferase reporter assay. We found that miR-17-5p was upregulated in both DN patients and high glucose-treated HMCs. Silencing miR-17-5p attenuated the apoptosis and fibrosis in high glucose-treated HMCs. MiR-17-5p binds to KIF23 3'UTR and negatively regulates KIF23 expression. KIF23 knockdown could suppress the role of miR-17-5p inhibition in high glucose-treated HMCs. Additionally, inhibition of miR-17-5p activated Wnt/β-catenin signaling in HMCs through upregulating KIF23 expression. Suppression of Wnt/β-catenin signaling antagonized the effect of miR-17-5p in HMCs. In conclusion, miR-17-5p inhibition alleviates the apoptosis and fibrosis in high glucose-treated HMCs by targeting KIF23 activating Wnt/β-catenin signaling.
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Affiliation(s)
- Xiaoli Chen
- Department of Endocrinology, The Affiliated Zhangjiagang Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Liyan Gu
- Department of Endocrinology, The Affiliated Zhangjiagang Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Xia Cheng
- Department of Endocrinology, The Affiliated Zhangjiagang Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Jianping Xing
- Department of Endocrinology, The Affiliated Zhangjiagang Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Minxia Zhang
- Department of Endocrinology, The Affiliated Zhangjiagang Hospital of Soochow University, Suzhou, Jiangsu, China
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Shihana F, Wong WKM, Joglekar MV, Mohamed F, Gawarammana IB, Isbister GK, Hardikar AA, Seth D, Buckley NA. Urinary microRNAs as non-invasive biomarkers for toxic acute kidney injury in humans. Sci Rep 2021; 11:9165. [PMID: 33911095 PMCID: PMC8080685 DOI: 10.1038/s41598-021-87918-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 04/05/2021] [Indexed: 12/29/2022] Open
Abstract
MicroRNAs in biofluids are potential biomarkers for detecting kidney and other organ injuries. We profiled microRNAs in urine samples from patients with Russell's viper envenoming or acute self-poisoning following paraquat, glyphosate, or oxalic acid [with and without acute kidney injury (AKI)] and on healthy controls. Discovery analysis profiled for 754 microRNAs using TaqMan OpenArray qPCR with three patients per group (12 samples in each toxic agent). From these, 53 microRNAs were selected and validated in a larger cohort of patients (Russell's viper envenoming = 53, paraquat = 51, glyphosate = 51, oxalic acid = 40) and 27 healthy controls. Urinary microRNAs had significantly higher expression in patients poisoned/envenomed by different nephrotoxic agents in both discovery and validation cohorts. Seven microRNAs discriminated severe AKI patients from no AKI for all four nephrotoxic agents. Four microRNAs (miR-30a-3p, miR-30a-5p, miR-92a, and miR-204) had > 17 fold change (p < 0.0001) and receiver operator characteristics area-under-curve (ROC-AUC) > 0.72. Pathway analysis of target mRNAs of these differentially expressed microRNAs showed association with the regulation of different nephrotoxic signaling pathways. In conclusion, human urinary microRNAs could identify toxic AKI early after acute injury. These urinary microRNAs have potential clinical application as early non-invasive diagnostic AKI biomarkers.
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Affiliation(s)
- Fathima Shihana
- Clinical Pharmacology and Toxicology Research Group, Biomedical Informatics and Digital Health, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.
- South Asian Clinical Toxicology Research Collaboration, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka.
- Centenary Institute of Cancer Medicine and Cell Biology, The University of Sydney, Sydney, NSW, Australia.
| | - Wilson K M Wong
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Campbelltown, NSW, Australia
| | - Mugdha V Joglekar
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Campbelltown, NSW, Australia
| | - Fahim Mohamed
- Clinical Pharmacology and Toxicology Research Group, Biomedical Informatics and Digital Health, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- South Asian Clinical Toxicology Research Collaboration, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka
- Allied Health Sciences, Department of Pharmacy, University of Peradeniya, Peradeniya, Sri Lanka
- Australian Kidney Biomarker Reference Laboratory, Department of Nephrology, Prince of Wales Hospital and Clinical School, University of New South Wales, Sydney, Australia
| | - Indika B Gawarammana
- South Asian Clinical Toxicology Research Collaboration, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka
| | - Geoffrey K Isbister
- Clinical Toxicology Research Group, University of Newcastle, Newcastle, NSW, Australia
| | - Anandwardhan A Hardikar
- Diabetes and Islet Biology Group, School of Medicine, Western Sydney University, Campbelltown, NSW, Australia
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Devanshi Seth
- Centenary Institute of Cancer Medicine and Cell Biology, The University of Sydney, Sydney, NSW, Australia
- Discipline of Clinical Medicine and Addiction Medicine, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Drug Health Services, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Nicholas A Buckley
- Clinical Pharmacology and Toxicology Research Group, Biomedical Informatics and Digital Health, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.
- South Asian Clinical Toxicology Research Collaboration, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka.
- Drug Health Services, Royal Prince Alfred Hospital, Sydney, NSW, Australia.
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11
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Shihana F, Barron ML, Mohamed F, Seth D, Buckley NA. MicroRNAs in toxic acute kidney injury: Systematic scoping review of the current status. Pharmacol Res Perspect 2021; 9:e00695. [PMID: 33600084 PMCID: PMC7891060 DOI: 10.1002/prp2.695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/23/2020] [Accepted: 10/23/2020] [Indexed: 11/14/2022] Open
Abstract
Acute kidney injury induced by nephrotoxic agents is common, increasing in incidence and associated with considerable morbidity and mortality in developing countries. MicroRNAs are stable biomarkers that can be detected in extracellular fluids. This systematic scoping review aims to describe published research on urinary and circulating microRNAs in toxic acute kidney injury in both animal and human studies. We conducted a literature search, using EMBASE and Medline, for articles on urinary and circulating microRNA in nephrotoxic injuries to February 2020. A total of 21 publications studied acute kidney injury from 12 different toxic agents. Cisplatin was the most common nephrotoxic agent (n = 10), followed by antibiotics (n = 4). There were no randomized controlled trials. An increase in urinary miR-218 predicted acute kidney injury in six different studies, suggesting it is a promising biomarker for nephrotoxin-induced acute kidney injury. There were many factors that prevented a more comprehensive synthesis of microRNA performance including highly variable models, no consistent protocols for RNA isolation, cDNA synthesis and PCR amplification, and variability in normalization methods using reference controls. In conclusion, while microRNAs are promising biomarkers to study nephrotoxic acute kidney injury, the replication of most positive findings is not assessable due to deficient reporting of negative outcomes. A very narrow range of poisons have been studied, and more human data are required. In particular, further studies are needed on the most important causes of nephrotoxic injury, such as pesticides, chemicals, snake envenoming, and medicines other than aminoglycosides and cisplatin.
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Affiliation(s)
- Fathima Shihana
- Clinical Pharmacology and Toxicology Research GroupDiscipline of PharmacologyFaculty of Medicine and HealthThe University of SydneySydneyNSWAustralia
- South Asian Clinical Toxicology of Research CollaborationFaculty of MedicineUniversity of PeradeniyaPeradeniyaSri Lanka
| | - Melissa L. Barron
- Department of PharmacyFaculty of Allied Health SciencesUniversity of PeradeniyaPeradeniyaSri Lanka
| | - Fahim Mohamed
- Clinical Pharmacology and Toxicology Research GroupDiscipline of PharmacologyFaculty of Medicine and HealthThe University of SydneySydneyNSWAustralia
- South Asian Clinical Toxicology of Research CollaborationFaculty of MedicineUniversity of PeradeniyaPeradeniyaSri Lanka
- Department of PharmacyFaculty of Allied Health SciencesUniversity of PeradeniyaPeradeniyaSri Lanka
| | - Devanshi Seth
- Discipline of Clinical Medicine & Addiction MedicineFaculty of Medicine and HealthThe University of SydneySydneyNSWAustralia
- Drug Health ServicesRoyal Prince Alfred HospitalCamperdownNSWAustralia
- The Centenary Institute of Cancer Medicine & Cell BiologyThe University of SydneySydneyNSWAustralia
| | - Nicholas A. Buckley
- Clinical Pharmacology and Toxicology Research GroupDiscipline of PharmacologyFaculty of Medicine and HealthThe University of SydneySydneyNSWAustralia
- South Asian Clinical Toxicology of Research CollaborationFaculty of MedicineUniversity of PeradeniyaPeradeniyaSri Lanka
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12
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Zhu Y, Zhu Y, Liu Y, Liu Y, Chen X. Long noncoding RNA metastasis-associated lung adenocarcinoma transcript 1 correlates with microRNA-125b/microRNA-146a/microRNA-203 and predicts 2-year restenosis risk in coronary heart disease patients. Biomark Med 2021; 15:257-271. [PMID: 33565328 DOI: 10.2217/bmm-2020-0715] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: To investigate correlations of long noncoding RNA metastasis-associated lung adenocarcinoma transcript 1 (lnc-MALAT1) and its target microRNAs with clinical features and restenosis risk in coronary heart disease (CHD) patients post drug-eluting stent-percutaneous coronary intervention (DES-PCI). Materials & methods: A total of 274 CHD patients undergoing DES-PCI were enrolled, pre-operative plasma samples were obtained to detect lnc-MALAT1, miR-125b, miR-146a, miR-203 by RT-qPCR; 2-year restenosis was determined by quantitative coronary angiography. Results: Lnc-MALAT1 negatively correlated with miR-125b, miR-146a and miR-203. Furthermore, lnc-MALAT1, miR-125b, miR-146a and miR-203 correlated with diabetes mellitus, hyperuricemia, lesion properties, cholesterol, inflammation and cardiac function indexes. Additionally, lnc-MALAT1 was increased, while miR-125b and miR-146a were decreased in patients with 2-year restenosis than patients without 2-year restenosis; however, miR-203 did not differ. Conclusion: Lnc-MALAT1 and its target miRNAs might help manage restenosis risk in CHD patients post DES-PCI.
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Affiliation(s)
- Yankuo Zhu
- Department of Cardiology, People's Hospital of Mudan, Heze, PR China
| | - Yinchuan Zhu
- Department of Vasculocardiology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, PR. China
| | - Yingchao Liu
- Department of Clinical Laboratory, The Second People's Hospital of Liaocheng, The Second Hospital of Liaocheng Affiliated to Shandong First Medical University, Linqing, PR China
| | - Yanru Liu
- Department of Cardiology, People's Hospital of Mudan, Heze, PR China
| | - Xiaoyu Chen
- Department of Clinical Laboratory, People's Hospital of Mudan, Heze, PR China
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13
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Jeon BS, Lee SH, Hwang SR, Yi H, Bang JH, Tham NTT, Lee HK, Woo GH, Kang HG, Ku HO. Identification of urinary microRNA biomarkers for in vivo gentamicin-induced nephrotoxicity models. J Vet Sci 2020; 21:e81. [PMID: 33263228 PMCID: PMC7710462 DOI: 10.4142/jvs.2020.21.e81] [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: 04/30/2020] [Revised: 08/20/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Although previous in vivo studies explored urinary microRNA (miRNA), there is no agreement on nephrotoxicity-specific miRNA biomarkers. OBJECTIVES In this study, we assessed whether urinary miRNAs could be employed as biomarkers for nephrotoxicity. METHODS For this, literature-based candidate miRNAs were identified by reviewing the previous studies. Female Sprague-Dawley rats received subcutaneous injections of a single dose or repeated doses (3 consecutive days) of gentamicin (GEN; 137 or 412 mg/kg). The expression of miRNAs was analyzed by real-time reverse transcription-polymerase chain reaction in 16 h pooled urine from GEN-treated rats. RESULTS GEN-induced acute kidney injury was confirmed by the presence of tubular necrosis. We identified let-7g-5p, miR-21-3p, 26b-3p, 192-5p, and 378a-3p significantly upregulated in the urine of GEN-treated rats with the appearance of the necrosis in proximal tubules. Specifically, miR-26-3p, 192-5p, and 378a-3p with highly expressed levels in urine of rats with GEN-induced acute tubular injury were considered to have sensitivities comparable to clinical biomarkers, such as blood urea nitrogen, serum creatinine, and urinary kidney injury molecule protein. CONCLUSIONS These results indicated the potential involvement of urinary miRNAs in chemical-induced nephrotoxicity, suggesting that certain miRNAs could serve as biomarkers for acute nephrotoxicity.
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Affiliation(s)
- Byung Suk Jeon
- Toxicological Evaluation Laboratory, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Soo Ho Lee
- Toxicological Evaluation Laboratory, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - So Ryeon Hwang
- Toxicological Evaluation Laboratory, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Hee Yi
- Toxicological Evaluation Laboratory, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Ji Hyun Bang
- Toxicological Evaluation Laboratory, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Nga Thi Thu Tham
- Toxicological Evaluation Laboratory, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Hyun Kyoung Lee
- Animal Pathodiagnostic Laboratory, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Gye Hyeong Woo
- Department of Clinical Laboratory Science, Semyung University, Jecheon 27136, Korea
| | - Hwan Goo Kang
- Department of Clinical Laboratory Science, Semyung University, Jecheon 27136, Korea.
| | - Hyun Ok Ku
- Toxicological Evaluation Laboratory, Animal and Plant Quarantine Agency, Gimcheon 39660, Korea.
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14
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Shihana F, Mohamed F, Joglekar MV, Hardikar AA, Seth D, Buckley NA. Urinary versus serum microRNAs in human oxalic acid poisoning: Contrasting signals and performance. Toxicol Lett 2020; 334:21-26. [PMID: 32910981 DOI: 10.1016/j.toxlet.2020.09.003] [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: 07/03/2020] [Revised: 08/25/2020] [Accepted: 09/03/2020] [Indexed: 11/28/2022]
Abstract
MicroRNAs are key regulators of the normal kidney function and development, and altered in acute kidney injury (AKI). However, there is a lack of studies comparing serum and urine miRNA expression in toxic AKI in humans. We aimed to compare the global signature of urinary and serum microRNAs, with and without kidney injury, after human oxalic acid poisoning. We profiled urinary microRNAs in patients who ingested oxalic acid and developed no injury (No AKI n = 3), moderate injury (AKIN2 n = 3) or severe injury (AKIN3 n = 3) and healthy controls (n = 3). We validated a signature of 30 urinary microRNAs identified in the discovery profiling, in a second cohort of individuals exposed to oxalic acid (No AKI n = 15, AKIN2 n=11 & AKIN3 n= 18) and healthy controls (n=-27) and we compared the results with previously published serum data. Global profiling in toxic AKI patients showed a higher expression of urinary microRNAs and lower expression of serum microRNAs. Most urine microRNA in the validation cohort were significantly upregulated (25/30, fold change >2.8 and p < 0.05) in AKIN2/3 patients compared to No AKI. Four urinary microRNAs (miR-191, miR-19b, miR-20a and miR-30b) had good diagnostic performance (AUC greater than 0.8) to predict AKIN2/3 between 4-8 hours post ingestion. Poisoning irrespective of AKI led to significantly lower expression of many microRNAs in serum but relatively few changes in urinary miRNA expression. In conclusion, urinary microRNA signature provides a stronger measure of AKI in oxalic acid poisoning compared to serum microRNA. Kidney injury has the greatest impact on urinary microRNA, while poisoning itself was better reflected in serum miRNA. Plasma and urinary microRNAs signatures provide complementary information in toxic kidney injury.
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Affiliation(s)
- Fathima Shihana
- The University of Sydney, Clinical Pharmacology and Toxicology Research Group, Discipline of Pharmacology, Faculty of Medicine and Health, Sydney, NSW, Australia; University of Peradeniya, South Asian Clinical Toxicology of Research Collaboration, Faculty of Medicine, Peradeniya, Sri Lanka.
| | - Fahim Mohamed
- The University of Sydney, Clinical Pharmacology and Toxicology Research Group, Discipline of Pharmacology, Faculty of Medicine and Health, Sydney, NSW, Australia; University of Peradeniya, South Asian Clinical Toxicology of Research Collaboration, Faculty of Medicine, Peradeniya, Sri Lanka; University of Peradeniya, Faculty of Allied Health Sciences, Department of Pharmacy, Peradeniya, Sri Lanka
| | - Mugdha V Joglekar
- The University of Sydney, Diabetes and Islet Biology Group, NHMRC Clinical Trials Centre, Faculty of Medicine & Health, NSW, Australia
| | - Anandwardhan A Hardikar
- The University of Sydney, Diabetes and Islet Biology Group, NHMRC Clinical Trials Centre, Faculty of Medicine & Health, NSW, Australia.
| | - Devanshi Seth
- The University of Sydney, Discipline of Clinical Medicine & Addiction Medicine, Faculty of Medicine & Health, NSW, Australia; Drug Health Services, Royal Prince Alfred Hospital, Camperdown, NSW, Australia; The University of Sydney The Centenary Institute of Cancer Medicine & Cell Biology, NSW, Australia
| | - Nicholas A Buckley
- The University of Sydney, Clinical Pharmacology and Toxicology Research Group, Discipline of Pharmacology, Faculty of Medicine and Health, Sydney, NSW, Australia; University of Peradeniya, South Asian Clinical Toxicology of Research Collaboration, Faculty of Medicine, Peradeniya, Sri Lanka
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15
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Brandenburger T, Lorenzen JM. Diagnostic and Therapeutic Potential of microRNAs in Acute Kidney Injury. Front Pharmacol 2020; 11:657. [PMID: 32477132 PMCID: PMC7240101 DOI: 10.3389/fphar.2020.00657] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 04/22/2020] [Indexed: 01/22/2023] Open
Abstract
During hospital stay, about 20% of adult patients experience an episode of acute kidney injury (AKI), which is characterized by a rapid decrease in kidney function. Diagnostic tools regarding early diagnosis of kidney dysfunction prior to AKI and markers of renal recovery are not available. Additionally, there is no therapeutic option for the treatment of AKI. Thus, better and more specific diagnostic and therapeutic options are urgently needed in daily clinical practice. NoncodingRNAs (ncRNAs) have come into focus of research in the context of AKI in the last decade. The best characterized group of ncRNAs are microRNAs (miRNAs). An increasing body of literature has shown that miRNAs are involved in the pathogenesis of AKI and that they are promising future tools in the diagnosis and therapy of AKI. However, there are obstacles to be overcome before miRNAs can be transferred to patient care. This review will give an overview of our current knowledge of miRNA involvement in the context of AKI while critically evaluating their diagnostic and therapeutic potential.
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Affiliation(s)
- Timo Brandenburger
- Department of Anesthesiology, University Hospital Duesseldorf, Duesseldorf, Germany
| | - Johan M Lorenzen
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
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16
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Branco GP, Valieris R, Povoa LV, Araújo LFD, Fernandes GR, Souza JESD, Amorim MGD, Ferreira ENE, Silva ITD, Nunes DN, Dias-Neto E. A comparison between SOLiD 5500XLand Ion Torrent PGM-derived miRNA expression profiles in two breast cell lines. Genet Mol Biol 2020; 43:e20180351. [PMID: 32352476 PMCID: PMC7201575 DOI: 10.1590/1678-4685-gmb-2018-0351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 06/06/2019] [Indexed: 11/22/2022] Open
Abstract
Next-generation sequencing (NGS) platforms allow the analysis of hundreds of
millions of molecules in a single sequencing run, revolutionizing many research
areas. NGS-based microRNA studies enable expression quantification in
unprecedented scale without the limitations of closed-platforms. Yet, whereas a
massive amount of data produced by these platforms is available, comparisons of
quantification/discovery capabilities between platforms are still lacking. Here
we compare two NGS-platforms: SOLiD and PGM, by evaluating their microRNA
identification/quantification capabilities using two breast-derived cell-lines.
A high expression correlation (R2 > 0.9) was achieved, encompassing 97% of
the miRNAs, and the few discrepancies in miRNA counts were attributable to
molecules that have very low expression. Quantification divergences indicative
of artefactual representation were seen for 14 miRNAs (higher in SOLiD-reads)
and another 10 miRNAs more abundant in PGM-data. An inspection of these revealed
an increased and statistically significant count of uracyls and uracyl-stretches
for PGM-enriched miRNAs, compared to SOLiD and to the miRBase. In parallel,
adenines and adenine-stretches were enriched for SOLiDderived miRNA reads. We
conclude that, whereas both platforms are overall consistent and can be used
interchangeably for microRNA expression studies, particular sequence features
appear to be indicative of specific platform bias, and their presence in
microRNAs should be considered for database-analyses.
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Affiliation(s)
| | - Renan Valieris
- A.C.Camargo Cancer Center, Laboratório de Biologia Computacional, São Paulo, SP, Brazil
| | - Lucas Venezian Povoa
- A.C.Camargo Cancer Center, Laboratório de Biologia Computacional, São Paulo, SP, Brazil.,Instituto Tecnológico de Aeronáutica, Divisão de Ciências Computacionais, Grupo de Inteligência Artificial e Robótica, São José dos Campos, SP, Brazil.,Instituto Federal de Educação, Ciência e Tecnologia de São Paulo, Caraguatatuba, SP, Brazil
| | | | | | | | - Maria Galli de Amorim
- A.C.Camargo Cancer Center, Laboratório de Genômica Médica, CIPE, São Paulo, SP, Brazil
| | - Elisa Napolitano E Ferreira
- A.C.Camargo Cancer Center, Laboratório de Genômica e Biologia, CIPE, São Paulo, SP, Brazil.,Grupo Fleury Pesquisa e Desenvolvimento, São Paulo, SP, Brazil
| | - Israel Tojal da Silva
- A.C.Camargo Cancer Center, Laboratório de Biologia Computacional, São Paulo, SP, Brazil
| | - Diana Noronha Nunes
- A.C.Camargo Cancer Center, Laboratório de Genômica Médica, CIPE, São Paulo, SP, Brazil
| | - Emmanuel Dias-Neto
- A.C.Camargo Cancer Center, Laboratório de Genômica Médica, CIPE, São Paulo, SP, Brazil.,Universidade de São Paulo, Faculdade de Medicina, Departamento & Instituto de Psiquiatria, Laboratório de Neurociências Alzira Denise Hertzog Silva (LIM-27), São Paulo, SP, Brazil
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17
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Tsai YC, Kuo MC, Hung WW, Wu LY, Wu PH, Chang WA, Kuo PL, Hsu YL. High Glucose Induces Mesangial Cell Apoptosis through miR-15b-5p and Promotes Diabetic Nephropathy by Extracellular Vesicle Delivery. Mol Ther 2020; 28:963-974. [PMID: 31991106 DOI: 10.1016/j.ymthe.2020.01.014] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 01/02/2020] [Accepted: 01/03/2020] [Indexed: 12/12/2022] Open
Abstract
Diabetic nephropathy (DN) is an increasing threat to human health and is regarded as an important public issue. The pathophysiologic mechanisms of DN are complicated. The initiating molecular events triggering the loss function in mesangial cells (MCs) in DN are not well known. In this cross-disciplinary study, transcriptome analysis of high glucose (HG)-treated mouse MCs (MMCs) using next-generation sequencing and systematic bioinformatics analyses indicated that miR-15b-5p and its downstream target B cell lymphoma 2 (BCL-2) contribute to HG-induced apoptosis in MMCs. HG elevated miR-15b-5p expression, which in turn decreased the translation of BCL-2, leading to MMC apoptosis under HG. Apoptosis of MCs was enhanced in the presence of extracellular vesicles isolated from the urine of type 2 diabetic patients with high levels of miR-15b-5p. Furthermore, increased levels of urinary miR-15b-5p were found in db/db mice and type 2 diabetic patients, and such levels correlated with low baseline kidney function and rapid decline in kidney function during a mean of follow-up period of 2.4 ± 0.1 years. Therefore, miR-15b-5p induced mesangial cells apoptosis by targeting BCL-2 under HG. miR-15b-5p has the potential to predict kidney injury in DN. Blocking the miR-15b-5p epigenetic regulatory network could be a potential therapeutic strategy to prevent mesangial apoptosis in DN.
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Affiliation(s)
- Yi-Chun Tsai
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Faculty of Renal Care, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of General Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of Nephrology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan; Cohort Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Mei-Chuan Kuo
- Faculty of Renal Care, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of Nephrology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wei-Wen Hung
- Division of Endocrinology and Metabolism, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ling-Yu Wu
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ping-Hsun Wu
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of Nephrology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan; Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wei-An Chang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of Pulmonary and Critical Care Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Po-Lin Kuo
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ya-Ling Hsu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung, Taiwan.
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18
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Abstract
Next generation sequencing (NGS) represents several powerful platforms that have revolutionized RNA and DNA analysis. The parallel sequencing of millions of DNA molecules can provide mechanistic insights into toxicology and provide new avenues for biomarker discovery with growing relevance for risk assessment. The evolution of NGS technologies has improved over the last decade with increased sensitivity and accuracy to foster new biomarker assays from tissue, blood and other biofluids. NGS sequencing technologies can identify transcriptional changes and genomic targets with base pair precision in response to chemical exposure. Further, there are several exciting movements within the toxicology community that incorporate NGS platforms into new strategies for more rapid toxicological characterizations. These include the Tox21 in vitro high throughput transcriptomic screening program, development of organotypic spheroids, alternative animal models, mining archival tissues, liquid biopsy and epigenomics. This review will describe NGS-based technologies, demonstrate how they can be used as tools for target discovery in tissue and blood, and suggest how they might be applied for risk assessment.
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Affiliation(s)
- B Alex Merrick
- Molecular and Genomic Toxicology Group, Biomolecular Screening Branch, Division National Toxicology Program, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, Ph: 919-541-1531,
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19
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Glineur SF, Hanon E, Dremier S, Snelling S, Berteau C, De Ron P, Nogueira da Costa A. Assessment of a Urinary Kidney MicroRNA Panel as Potential Nephron Segment-Specific Biomarkers of Subacute Renal Toxicity in Preclinical Rat Models. Toxicol Sci 2019; 166:409-419. [PMID: 30169741 DOI: 10.1093/toxsci/kfy213] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Drug-induced kidney injury (DIKI) remains a significant concern during drug development. Whereas FDA-endorsed urinary protein biomarkers encounter limitations including the lack of translatability, there is a considerable interest surrounding the application of microRNAs (miRNAs) in the renal biomarker space. Current knowledge about the value of these novel biomarkers for subacute preclinical rodent studies is still sparse. In this work, Wistar rats were treated with three nephrotoxic compounds-cisplatin (CIS, proximal tubule, 2.5 mg/kg, intraperitoneal [i.p.]), puromycin (PUR, glomerulus, 20/10 mg/kg, i.p.) and N-phenylanthranylic acid (NPAA, collecting ducts, 500 mg/kg, per os)-for up to 28 days to evaluate the performance of a panel of 68 urinary miRNAs as potential nephron segment-specific biomarkers. Out of these 68 kidney injury associated-miRNAs, our selection strategy ultimately revealed rno-miR-34c-5p significantly dysregulated after CIS single administration, and rno-miR-335 and rno-miR-155-5p significantly dysregulated after PUR treatment. In contrast, NPAA daily administration strongly altered the expression profile of 28 miRNAs, with rno-miR-210-3p displaying the most robust changes. A thorough evaluation showed that these miRNA candidates could complement urinary protein biomarkers to detect CIS- or PUR-induced kidney injury in a subacute setting, with a mechanistic (based on rno-miR-34c-5p) and/or a kidney injury detection potential. Our results also provide the first evidence that urinary miRNAs could enhance the detection of collecting duct damage. Overall, these data improve our understanding of the utility of urinary miRNAs as DIKI biomarkers in a subacute DIKI preclinical setting and support the value of using urinary biomarker panels comprising proteins and miRNAs.
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Affiliation(s)
- Stéphanie F Glineur
- Investigative Toxicology, Development Science, UCB Biopharma SPRL, B-1420 Braine L'Alleud, Belgium.,Medvet, AML Lab BVBA, E. Vloorstraat 9, B-2020 Antwerpen, Belgium
| | - Etienne Hanon
- Bio Data Analysis, New Medicines Therapeutics, UCB Biopharma SPRL, B-1420 Braine L'Alleud, Belgium
| | - Sarah Dremier
- Investigative Toxicology, Development Science, UCB Biopharma SPRL, B-1420 Braine L'Alleud, Belgium.,Head HTS & In Vitro Pharmacology, Ogeda SA, 47 Rue Adrienne Bolland, 6041 Gosselies, Belgium
| | - Sara Snelling
- Investigative Toxicology, Development Science, UCB Biopharma SPRL, B-1420 Braine L'Alleud, Belgium.,Immunology, Abzena, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Caroline Berteau
- Investigative Toxicology, Development Science, UCB Biopharma SPRL, B-1420 Braine L'Alleud, Belgium.,School of Medicine, Leeds Institute of Biomedical and Clinical Sciences, University of Leeds, LS9 7FT, UK
| | - Pierrette De Ron
- Investigative Toxicology, Development Science, UCB Biopharma SPRL, B-1420 Braine L'Alleud, Belgium
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20
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Human Circulating miRNAs Real-time qRT-PCR-based Analysis: An Overview of Endogenous Reference Genes Used for Data Normalization. Int J Mol Sci 2019; 20:ijms20184353. [PMID: 31491899 PMCID: PMC6769746 DOI: 10.3390/ijms20184353] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/30/2019] [Accepted: 09/02/2019] [Indexed: 12/16/2022] Open
Abstract
miRNAs are small non-coding RNAs of about 18–25 nucleotides that negatively regulate gene expression at the post-transcriptional level. It was reported that a deregulation of their expression patterns correlates to the onset and progression of various diseases. Recently, these molecules have been identified in a great plethora of biological fluids, and have also been proposed as potential diagnostic and prognostic biomarkers. Actually, real time quantitative polymerase chain reaction is the most widely used approach for circulating miRNAs (c-miRNAs) expression profiling. Nevertheless, the debate on the choice of the most suitable endogenous reference genes for c-miRNAs expression levels normalization is still open. In this regard, numerous research groups are focusing their efforts upon identifying specific, highly stable, endogenous c-mRNAs. The aim of this review is to provide an overview on the reference genes currently used in the study of various pathologies, offering to researchers the opportunity to select the appropriate molecules for c-miRNA levels normalization, when their choosing is based upon literature data.
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21
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Xu L, Luo H, Wang R, Wu WW, Phue JN, Shen RF, Juhl H, Wu L, Alterovitz WL, Simonyan V, Pelosof L, Rosenberg AS. Novel reference genes in colorectal cancer identify a distinct subset of high stage tumors and their associated histologically normal colonic tissues. BMC MEDICAL GENETICS 2019; 20:138. [PMID: 31409279 PMCID: PMC6693228 DOI: 10.1186/s12881-019-0867-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 07/29/2019] [Indexed: 12/20/2022]
Abstract
Background Reference genes are often interchangeably called housekeeping genes due to 1) the essential cellular functions their proteins provide and 2) their constitutive expression across a range of normal and pathophysiological conditions. However, given the proliferative drive of malignant cells, many reference genes such as beta-actin (ACTB) and glyceraldehyde-3-phosphate-dehydrogenase (GAPDH) which play critical roles in cell membrane organization and glycolysis, may be dysregulated in tumors versus their corresponding normal controls Methods Because Next Generation Sequencing (NGS) technology has several advantages over hybridization-based technologies, such as independent detection and quantitation of transcription levels, greater sensitivity, and increased dynamic range, we evaluated colorectal cancers (CRC) and their histologically normal tissue counterparts by NGS to evaluate the expression of 21 “classical” reference genes used as normalization standards for PCR based methods. Seventy-nine paired tissue samples of CRC and their patient matched healthy colonic tissues were subjected to NGS analysis of their mRNAs. Results We affirmed that 17 out of 21 classical reference genes had upregulated expression in tumors compared to normal colonic epithelial tissue and dramatically so in some cases. Indeed, tumors were distinguished from normal controls in both unsupervised hierarchical clustering analyses (HCA) and principal component analyses (PCA). We then identified 42 novel potential reference genes with minimal coefficients of variation (CV) across 79 CRC tumor pairs. Though largely consistently expressed across tumors and normal control tissues, a subset of high stage tumors (HSTs) as well as some normal tissue samples (HSNs) located adjacent to these HSTs demonstrated dysregulated expression, thus identifying a subset of tumors with a potentially distinct and aggressive biological profile. Conclusion While classical CRC reference genes were found to be differentially expressed between tumors and normal controls, novel reference genes, identified via NGS, were more consistently expressed across malignant and normal colonic tissues. Nonetheless, a subset of HST had profound dysregulation of such genes as did many of the histologically normal tissues adjacent to such HSTs, indicating that the HSTs so distinguished may have unique biological properties and that their histologically normal tissues likely harbor a small population of microscopically undetected but metabolically active tumors. Electronic supplementary material The online version of this article (10.1186/s12881-019-0867-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lai Xu
- OBP/DBRR-III, CDER, FDA, Silver Spring, MD, 20993, USA. .,Office of Hematology and Oncology Products CDER, FDA, Silver Spring, MD, 20993, USA. .,, Silver Spring, USA.
| | - Helen Luo
- OBP/DBRR-III, CDER, FDA, Silver Spring, MD, 20993, USA
| | - Rong Wang
- OBP/DBRR-III, CDER, FDA, Silver Spring, MD, 20993, USA
| | - Wells W Wu
- Facility for Biotechnology Resources CBER, FDA, Silver Spring, MD, 20993, USA
| | - Je-Nie Phue
- Facility for Biotechnology Resources CBER, FDA, Silver Spring, MD, 20993, USA
| | - Rong-Fong Shen
- Facility for Biotechnology Resources CBER, FDA, Silver Spring, MD, 20993, USA
| | | | - Leihong Wu
- OCS/NCTR/DBB, FDA, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | | | | | - Lorraine Pelosof
- Office of Hematology and Oncology Products CDER, FDA, Silver Spring, MD, 20993, USA
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Brandenburger T, Salgado Somoza A, Devaux Y, Lorenzen JM. Noncoding RNAs in acute kidney injury. Kidney Int 2019; 94:870-881. [PMID: 30348304 DOI: 10.1016/j.kint.2018.06.033] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/30/2018] [Accepted: 06/11/2018] [Indexed: 02/09/2023]
Abstract
Acute kidney injury (AKI) is an important health issue concerning ∼50% of patients treated in intensive care units. AKI mainly occurs after sepsis, acute ischemia, nephrotoxicity, or hypoxia and leads to severe damage of the kidney and to an increased risk of mortality. The diagnosis of AKI is currently based on creatinine urea levels and diuresis. Yet, novel markers may improve the accuracy of this diagnosis at an early stage of the disease, thereby allowing early prevention and therapy, ultimately leading to a reduction in the need for renal replacement therapy and decreased mortality. Non-protein-coding RNAs or noncoding RNAs are central players in development and disease. They are important regulatory molecules that allow a fine-tuning of gene expression and protein synthesis. This regulation is necessary to maintain homeostasis, and its dysregulation is often associated with disease development. Noncoding RNAs are present in the kidney and in body fluids and their expression is modulated during AKI. This review article assembles the current knowledge of the role of noncoding RNAs, including microRNAs, long noncoding RNAs and circular RNAs, in the pathogenesis of AKI. Their potential as biomarkers and therapeutic targets as well as the challenges to translate research findings to clinical application are discussed. Although microRNAs have entered clinical testing, preclinical and clinical trials are needed before long noncoding RNAs and circular RNAs may be considered as useful biomarkers or therapeutic targets of AKI.
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Affiliation(s)
- Timo Brandenburger
- Department of Anesthesiology, University Hospital Duesseldorf, Duesseldorf, Germany.
| | - Antonio Salgado Somoza
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Yvan Devaux
- Cardiovascular Research Unit, Department of Population Health, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Johan M Lorenzen
- Division of Nephrology, University Hospital Zurich, Zurich, Switzerland
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Kalbolandi SM, Gorji AV, Babaahmadi-Rezaei H, Mansouri E. Luteolin confers renoprotection against ischemia-reperfusion injury via involving Nrf2 pathway and regulating miR320. Mol Biol Rep 2019; 46:4039-4047. [PMID: 31089916 DOI: 10.1007/s11033-019-04853-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 05/02/2019] [Indexed: 01/12/2023]
Abstract
This work aims to evaluate the renoprotective effect of luteolin on expression of Nrf2 and miR320 in ischemia-reperfusion (I/R) injury in rats. Thirty rats were randomly divided into five groups; control, Luteolin (50 mg/kg), ischemia-reperfusion (I/R), DMSO (0/1%) + I/R and Luteolin+I/R, (n = 6 each). Administration of luteolin and DMSO was carried out by gavage for 3 days before renal I/R. Then, the rats were subjected to bilateral renal ischemia for 45 min and followed by reperfusion for 2 h. All rats were killed and the renal function, histological changes, oxidative stress degree, in all of groups were evaluated. In addition, the effects of luteolin on renal expression of Nrf2 and miR320 were examined by immunohistochemistry and real time- PCR. Luteolin significantly improved the creatinine (Cr) and blood urea nitrogen (BUN) levels in Luteolin + I/R group compared to I/R group (p < 0.001 and p < 0.001 respectively). Reduction of enzymatic activity of superoxide dismutase, glutathione peroxidase and catalase in I/R and DMSO + I/R groups, was significantly improved by Luteolin (p < 0.05) in Luteolin + I/R group. Pre-treatment with luteolin also resulted in significant reduction in tissue MDA level (p < 0.001), Nrf2 (p < 0.001) and miR320 expression (P < 0.05) that were increased by renal I/R. Also, the rats pretreated with luteolin had nearly normal structure of the kidney. These results indicate that luteolin protects the kidney against I/R injury via reducing oxidative stress, increasing antioxidant enzymes and reducing expression of Nrf2 and miR320.
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Affiliation(s)
- Sanaz Moradi Kalbolandi
- Department of Anatomical Sciences, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Armita Valizadeh Gorji
- Cellular and Molecular Research Center, Department of Anatomical Sciences, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Hossein Babaahmadi-Rezaei
- Atherosclerosis Research Center, Department of Clinical Biochemistry, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Esrafil Mansouri
- Cellular and Molecular Research Center, Department of Anatomical Sciences, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, 61335, Iran.
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Liu Z, Wang Y, Shu S, Cai J, Tang C, Dong Z. Non-coding RNAs in kidney injury and repair. Am J Physiol Cell Physiol 2019; 317:C177-C188. [PMID: 30969781 DOI: 10.1152/ajpcell.00048.2019] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Acute kidney injury (AKI) is a major kidney disease featured by a rapid decline of renal function. Pathologically, AKI is characterized by tubular epithelial cell injury and death. Besides its acute consequence, AKI contributes critically to the development and progression of chronic kidney disease (CKD). After AKI, surviving tubular cells regenerate to repair. Normal repair restores tubular integrity, while maladaptive or incomplete repair results in renal fibrosis and eventually CKD. Non-coding RNAs (ncRNAs) are functional RNA molecules that are transcribed from DNA but not translated into proteins, which mainly include microRNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), small nucleolar RNAs (snoRNAs), and tRNAs. Accumulating evidence suggests that ncRNAs play important roles in kidney injury and repair. In this review, we summarize the recent advances in the understanding of the roles of ncRNAs, especially miRNAs and lncRNAs in kidney injury and repair, discuss the potential application of ncRNAs as biomarkers of AKI as well as therapeutic targets for treating AKI and impeding AKI-CKD transition, and highlight the future research directions of ncRNAs in kidney injury and repair.
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Affiliation(s)
- Zhiwen Liu
- Department of Nephrology, The Key Laboratory of Kidney Disease and Blood Purification of Hunan Province, Second Xiangya Hospital at Central South University , Changsha , China
| | - Ying Wang
- Department of Nephrology, The Key Laboratory of Kidney Disease and Blood Purification of Hunan Province, Second Xiangya Hospital at Central South University , Changsha , China
| | - Shaoqun Shu
- Department of Nephrology, The Key Laboratory of Kidney Disease and Blood Purification of Hunan Province, Second Xiangya Hospital at Central South University , Changsha , China
| | - Juan Cai
- Department of Nephrology, The Key Laboratory of Kidney Disease and Blood Purification of Hunan Province, Second Xiangya Hospital at Central South University , Changsha , China
| | - Chengyuan Tang
- Department of Nephrology, The Key Laboratory of Kidney Disease and Blood Purification of Hunan Province, Second Xiangya Hospital at Central South University , Changsha , China
| | - Zheng Dong
- Department of Nephrology, The Key Laboratory of Kidney Disease and Blood Purification of Hunan Province, Second Xiangya Hospital at Central South University , Changsha , China.,Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University and Charlie Norwood Veterans Affairs Medical Center , Augusta, Georgia
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25
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Urinary biomarker evaluation for early detection of gentamycin-induced acute kidney injury. Toxicol Lett 2019; 300:73-80. [DOI: 10.1016/j.toxlet.2018.10.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 10/19/2018] [Accepted: 10/22/2018] [Indexed: 12/20/2022]
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Abstract
While infecting humans and other mammals, Leishmania spp. are obligate intracellular parasites. Therefore, for the purpose of therapeutic intervention and the study of infectivity, the relevant form of Leishmania spp. is the intracellular amastigote. Therefore, monitoring intracellular parasite load is an essential requirement in many fields of Leishmania research. Real-time quantitative PCR is a highly accurate technique for the detection and quantification of parasite burden in in vitro or in vivo infection experiments. The quantification of DNA for standard curves shows linearity over a 5 to 6-log concentration range indicating the high sensitivity of the method. Moreover, qPCR allows for the simultaneous quantification of host and parasite DNA in the same reaction, thereby allowing for an assessment of relative parasite load for basic research, but also for low- to medium-throughput compound screening. The method also allows to analyze late stages of in vitro infections where host cells and parasites have detached from surfaces and escape microscopy-based assays.
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Affiliation(s)
- Eugenia Bifeld
- Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany.
- altona Diagnostics GmbH, Hamburg, Germany.
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27
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The Interaction of miR-378i-Skp2 Regulates Cell Senescence in Diabetic Nephropathy. J Clin Med 2018; 7:jcm7120468. [PMID: 30469549 PMCID: PMC6306775 DOI: 10.3390/jcm7120468] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 11/15/2018] [Accepted: 11/20/2018] [Indexed: 12/18/2022] Open
Abstract
Diabetic nephropathy (DN) is the major cause of end stage renal disease. Proximal tubular epithelial cell (PTEC) injury occurs early in diabetic kidney, and it is correlated with consequent renal failure. Cellular senescence participates in the pathophysiology of DN, but its role remains unclear. We conducted a cross-disciplinary study, including human, in vivo, and in vitro studies, to explore the novel molecular mechanisms of PTEC senescence in DN. We found that HG induced cell senescence in PTECs, supported by enhanced β-galactosidase staining, p53 and p27 expression, and reduced cyclin E levels. Transcriptome analysis of PTECs from a type 2 diabetic patient and a normal individual using next generation sequencing (NGS) and systematic bioinformatics analyses indicated that miR-378i and its downstream target S-phase kinase protein 2 (Skp2) contribute to HG-induced senescence in PTECs. High glucose (HG) elevated miR-378i expression in PTECs, and miR-378i transfection reduced Skp2 expression. Urinary miR-378i levels were elevated in both db/db mice and type 2 diabetic patients, whereas decreased Skp2 levels were shown in proximal tubule of db/db mice and human DN. Moreover, urinary miR-378i levels were positively correlated with urinary senescence-associated secretory phenotype cytokines and renal function in in vivo and human study. This study demonstrates that the interaction between miR-378i and Skp2 regulates PTEC senescence of DN. miR-378i has the potential to predict renal injury in DN. These findings suggest future applications in both therapy and in predicting renal dysfunction of DN.
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28
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McDuffie JE. Brief Overview: Assessment of Compound-induced Acute Kidney Injury Using Animal Models, Biomarkers, and In Vitro Platforms. Toxicol Pathol 2018; 46:978-990. [PMID: 30392454 DOI: 10.1177/0192623318807679] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The inability to unequivocally predict translatable drug-induced kidney injury in nonclinical studies during pharmacological development is evidenced by drug attrition in human clinical trials. Eight urinary proteins have been qualified as renal safety biomarkers for limited context of use in nonclinical drug development studies in rats. Formal qualification of human renal safety biomarkers is pending the submission of data from prospective clinical trials and analyses of biomarker performance to the Food and Drug Administration and European Medicines Agency by the Foundation for the National Institutes of Health and Predictive Safety Testing Consortium's Nephrotoxicity Working Group. In vitro kidney platforms may be leveraged to investigate the potential risk of compound-induced acute kidney injury and/or dysfunction. The early assessment of drug-related kidney safety profiles using biomarker-level changes in animal models and in vitro platforms could significantly reduce renal safety-related drug attrition; yet, there are no well-validated in vitro systems to enable comprehensive investigations of compound-induced nephrotoxicity. Thus, histopathology remains the gold standard for diagnosing nephron-specific damage. Traditional and emerging biomarker panels should be combined with histopathology and/or cytopathology to enable early identification of compound-induced kidney injury.
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Affiliation(s)
- James E McDuffie
- Mechanistic & Investigative Toxicology, Janssen Research & Development, LLC, San Diego, California, USA
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29
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Tsai YC, Kuo PL, Hung WW, Wu LY, Wu PH, Chang WA, Kuo MC, Hsu YL. Angpt2 Induces Mesangial Cell Apoptosis through the MicroRNA-33-5p-SOCS5 Loop in Diabetic Nephropathy. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 13:543-555. [PMID: 30414568 PMCID: PMC6226567 DOI: 10.1016/j.omtn.2018.10.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 09/30/2018] [Accepted: 10/03/2018] [Indexed: 02/03/2023]
Abstract
Diabetic nephropathy (DN) is the leading cause of end-stage renal disease. Mesangial cell (MC) loss is correlated with worsening renal function in DN. Disturbance of angiopoietin (Angpt)/Tie ligand-receptor system causes inflammation and abnormal angiogenesis. This association between elevated circulating Angpt2 and poor renal outcome has been in DN patients. However, the pathogenic role of Angpt2 in the MCs remains unknown. We found serum Angpt2 levels were elevated in type 2 diabetes mellitus (DM) patients and db/db mice, which correlated with albuminuria. Angpt2 synergistically induced MC apoptosis under high glucose (HG), and miR-33-5p regulated Angpt2-inducing MC apoptosis treated with HG. Loss of miR-33-5p increased suppressor of cytokine signaling 5 (SOCS5), leading to the inhibition of Janus kinase 1 and signal transducer and activator of transcription 3 signaling transduction. Elevated expression of SOCS5 was found in the MCs in kidney sections of both db/db mice and type 2 DM patients. Decreased miR-33-5p levels were found in the urine of db/db mice and type 2 DM patients, and miR-33-55p levels negatively correlated with albuminuria. Angpt2 leads to MC apoptosis via the miR-33-5p-SOCS5 loop in DN. miR-33-5p is predictive of kidney injury in DN. These findings may provide future applications in predicting renal dysfunction and the therapeutic potential of DN.
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Affiliation(s)
- Yi-Chun Tsai
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Faculty of Renal Care, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of General Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Division of Nephrology, Department of Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Po-Lin Kuo
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wei-Wen Hung
- Division of Endocrinology and Metabolism, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Ling-Yu Wu
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ping-Hsun Wu
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of Nephrology, Department of Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Wei-An Chang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of Pulmonary and Critical Care Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Mei-Chuan Kuo
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Faculty of Renal Care, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of Nephrology, Department of Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.
| | - Ya-Ling Hsu
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
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30
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Suter-Dick L, Mauch L, Ramp D, Caj M, Vormann MK, Hutter S, Lanz HL, Vriend J, Masereeuw R, Wilmer MJ. Combining Extracellular miRNA Determination with Microfluidic 3D Cell Cultures for the Assessment of Nephrotoxicity: a Proof of Concept Study. AAPS JOURNAL 2018; 20:86. [PMID: 30039346 DOI: 10.1208/s12248-018-0245-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 06/25/2018] [Indexed: 12/31/2022]
Abstract
Drug-induced kidney injury is often observed in the clinics and can lead to long-term organ failure. In this work, we evaluated a novel in vitro system that aims at detecting whether compounds can cause renal proximal tubule damage in man. For this, we implemented organotypic cultures of human conditionally immortalized proximal tubule epithelial cells overexpressing the organic anion transporter 1 (ciPTEC-OAT1) in a three-channel OrganoPlate under microfluidic conditions. Cells were exposed to four known nephrotoxicants (cisplatin, tenofovir, cyclosporine A, and tobramycin). The effect on cell viability and NAG release into the medium was determined. A novel panel of four miRNAs (mir-21, mir-29a, mir-34a, and mir-192) was selected as potential biomarkers of proximal tubule damage. After nephrotoxicant treatment, miRNA levels in culture medium were earlier indicators than cell viability (WST-8 assay) and outperformed NAG for proximal tubule damage. In particular, mir-29a, mir-34a, and mir-192 were highly reproducible between experiments and across compounds, whereas mir-21 showed more variability. Moreover, similar data were obtained in two different laboratories, underlining the reproducibility and technical transferability of the results, a key requirement for the implementation of novel biomarkers. In conclusion, the selected miRNAs behaved like sensitive biomarkers of damage to tubular epithelial cells caused by several nephrotoxicity mechanisms. This biomarker panel, in combination with the 3D cultures of ciPTEC-OAT1 in the OrganoPlate, represents a novel tool for in vitro nephrotoxicity detection. These results pave the way for the application of miRNAs in longitudinal, time-course in vitro toxicity studies.
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Affiliation(s)
- Laura Suter-Dick
- School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Gründenstrasse 40, 4132, Muttenz, Switzerland.
| | - L Mauch
- School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Gründenstrasse 40, 4132, Muttenz, Switzerland
| | - D Ramp
- School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Gründenstrasse 40, 4132, Muttenz, Switzerland
| | - M Caj
- School of Life Sciences, University of Applied Sciences Northwestern Switzerland, Gründenstrasse 40, 4132, Muttenz, Switzerland
| | - M K Vormann
- MIMETAS B.V., JH Oortweg 19, 2333 CH, Leiden, The Netherlands
| | - S Hutter
- MIMETAS B.V., JH Oortweg 19, 2333 CH, Leiden, The Netherlands
| | - H L Lanz
- MIMETAS B.V., JH Oortweg 19, 2333 CH, Leiden, The Netherlands
| | - J Vriend
- Department of Pharmacology and Toxicology, Radboudumc, P.O. box 9101, 6500 HB, Nijmegen, The Netherlands
| | - R Masereeuw
- Div. Pharmacology, Department of Pharmaceutical Sciences, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - M J Wilmer
- Department of Pharmacology and Toxicology, Radboudumc, P.O. box 9101, 6500 HB, Nijmegen, The Netherlands
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Zhang L, Masetti G, Colucci G, Salvi M, Covelli D, Eckstein A, Kaiser U, Draman MS, Muller I, Ludgate M, Lucini L, Biscarini F. Combining micro-RNA and protein sequencing to detect robust biomarkers for Graves' disease and orbitopathy. Sci Rep 2018; 8:8386. [PMID: 29849043 PMCID: PMC5976672 DOI: 10.1038/s41598-018-26700-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/15/2018] [Indexed: 12/12/2022] Open
Abstract
Graves’ Disease (GD) is an autoimmune condition in which thyroid-stimulating antibodies (TRAB) mimic thyroid-stimulating hormone function causing hyperthyroidism. 5% of GD patients develop inflammatory Graves’ orbitopathy (GO) characterized by proptosis and attendant sight problems. A major challenge is to identify which GD patients are most likely to develop GO and has relied on TRAB measurement. We screened sera/plasma from 14 GD, 19 GO and 13 healthy controls using high-throughput proteomics and miRNA sequencing (Illumina’s HiSeq2000 and Agilent-6550 Funnel quadrupole-time-of-flight mass spectrometry) to identify potential biomarkers for diagnosis or prognosis evaluation. Euclidean distances and differential expression (DE) based on miRNA and protein quantification were analysed by multidimensional scaling (MDS) and multinomial regression respectively. We detected 3025 miRNAs and 1886 proteins and MDS revealed good separation of the 3 groups. Biomarkers were identified by combined DE and Lasso-penalized predictive models; accuracy of predictions was 0.86 (±0:18), and 5 miRNA and 20 proteins were found including Zonulin, Alpha-2 macroglobulin, Beta-2 glycoprotein 1 and Fibronectin. Functional analysis identified relevant metabolic pathways, including hippo signaling, bacterial invasion of epithelial cells and mRNA surveillance. Proteomic and miRNA analyses, combined with robust bioinformatics, identified circulating biomarkers applicable to diagnose GD, predict GO disease status and optimize patient management.
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Affiliation(s)
- Lei Zhang
- Cardiff University, School of Medicine, Division of Infection & Immunity, Cardiff, UK
| | - Giulia Masetti
- Cardiff University, School of Medicine, Division of Infection & Immunity, Cardiff, UK.,Parco Tecnologico Padano, Bioinformatics Unit, Lodi, Italy
| | - Giuseppe Colucci
- Università degli Studi di Milano, Fondazione Ca' Granda IRCCS, Department of Clinical Sciences and Community Health, Milan, Italy
| | - Mario Salvi
- Università degli Studi di Milano, Fondazione Ca' Granda IRCCS, Department of Clinical Sciences and Community Health, Milan, Italy
| | - Danila Covelli
- Università degli Studi di Milano, Fondazione Ca' Granda IRCCS, Department of Clinical Sciences and Community Health, Milan, Italy
| | - Anja Eckstein
- University Hospital Essen/University of Duisburg-Essen, Department of Ophthalmology, Essen, Germany
| | - Ulrike Kaiser
- University Hospital Essen/University of Duisburg-Essen, Department of Ophthalmology, Essen, Germany
| | - Mohd Shazli Draman
- Cardiff University, School of Medicine, Division of Infection & Immunity, Cardiff, UK
| | - Ilaria Muller
- Cardiff University, School of Medicine, Division of Infection & Immunity, Cardiff, UK
| | - Marian Ludgate
- Cardiff University, School of Medicine, Division of Infection & Immunity, Cardiff, UK
| | - Luigi Lucini
- Università Cattolica del Sacro Cuore, Department for Sustainable food process, Piacenza, Italy
| | - Filippo Biscarini
- Cardiff University, School of Medicine, Division of Infection & Immunity, Cardiff, UK. .,CNR (National Council for Research), Institute of Biology and Biotechnology in Agriculture (IBBA), Milan, Italy.
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32
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Lyu LL, Feng Y, Liu BC. Urinary Biomarkers for Chronic Kidney Disease with a Focus on Gene Transcript. Chin Med J (Engl) 2018; 130:2251-2256. [PMID: 28875962 PMCID: PMC5598339 DOI: 10.4103/0366-6999.213965] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Objective: In the upcoming era of precision medicine, searching for the early, noninvasive biomarkers has been the cornerstone and major challenge in the management of chronic kidney disease (CKD). Urine contains rich biological information which could be the ideal source for noninvasive biomarkers of CKD. This review will discuss the recent advance in urinary biomarker. Data Sources: This review was based on data in articles published in the PubMed databases up to June 20, 2017, with the following keywords: “Chronic kidney disease”, “Biomarker”, and “Urine”. Study Selection: Original articles and important reviews on urinary biomarker were selected for this review. Results: Urinary biomarker studies of CKD mainly focused on urine sediment, supernatant, and urinary extracellular vesicles. The gene transcript (microRNA [miRNA], messenger RNA [mRNA]) biomarkers have been recently shown with diagnostic potential for CKD reflecting kidney function and histological change. However, challenges regarding technique and data analysis need to be resolved before translation to clinic. Conclusions: Different fractions of urine contain rich information for biomarker discovery, among which urine (extracellular vesicles) mRNA, miRNA, might represent promising biomarker for CKD.
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Affiliation(s)
- Lin-Li Lyu
- Department of Nephrology, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, Jiangsu 210009, China
| | - Ye Feng
- Department of Nephrology, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, Jiangsu 210009, China
| | - Bi-Cheng Liu
- Department of Nephrology, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, Jiangsu 210009, China
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Brogaard L, Larsen LE, Heegaard PMH, Anthon C, Gorodkin J, Dürrwald R, Skovgaard K. IFN-λ and microRNAs are important modulators of the pulmonary innate immune response against influenza A (H1N2) infection in pigs. PLoS One 2018; 13:e0194765. [PMID: 29677213 PMCID: PMC5909910 DOI: 10.1371/journal.pone.0194765] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 02/02/2018] [Indexed: 11/19/2022] Open
Abstract
The innate immune system is paramount in the response to and clearance of influenza A virus (IAV) infection in non-immune individuals. Known factors include type I and III interferons and antiviral pathogen recognition receptors, and the cascades of antiviral and pro- and anti-inflammatory gene expression they induce. MicroRNAs (miRNAs) are increasingly recognized to participate in post-transcriptional modulation of these responses, but the temporal dynamics of how these players of the antiviral innate immune response collaborate to combat infection remain poorly characterized. We quantified the expression of miRNAs and protein coding genes in the lungs of pigs 1, 3, and 14 days after challenge with swine IAV (H1N2). Through RT-qPCR we observed a 400-fold relative increase in IFN-λ3 gene expression on day 1 after challenge, and a strong interferon-mediated antiviral response was observed on days 1 and 3 accompanied by up-regulation of genes related to the pro-inflammatory response and apoptosis. Using small RNA sequencing and qPCR validation we found 27 miRNAs that were differentially expressed after challenge, with the highest number of regulated miRNAs observed on day 3. In contrast, the number of protein coding genes found to be regulated due to IAV infection peaked on day 1. Pulmonary miRNAs may thus be aimed at fine-tuning the initial rapid inflammatory response after IAV infection. Specifically, we found five miRNAs (ssc-miR-15a, ssc-miR-18a, ssc-miR-21, ssc-miR-29b, and hsa-miR-590-3p)-four known porcine miRNAs and one novel porcine miRNA candidate-to be potential modulators of viral pathogen recognition and apoptosis. A total of 11 miRNAs remained differentially expressed 14 days after challenge, at which point the infection had cleared. In conclusion, the results suggested a role for miRNAs both during acute infection as well as later, with the potential to influence lung homeostasis and susceptibility to secondary infections in the lungs of pigs after IAV infection.
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Affiliation(s)
- Louise Brogaard
- Section for Protein Science and Signaling Biology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
- * E-mail:
| | - Lars E. Larsen
- Division of Diagnostics and Scientific Advice–Virology, National Veterinary Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Peter M. H. Heegaard
- Section for Protein Science and Signaling Biology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Christian Anthon
- Center for non-coding RNA in Technology and Health (RTH), Department of Veterinary and Animal Science, University of Copenhagen, Frederiksberg, Denmark
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health (RTH), Department of Veterinary and Animal Science, University of Copenhagen, Frederiksberg, Denmark
| | - Ralf Dürrwald
- Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Kerstin Skovgaard
- Section for Protein Science and Signaling Biology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
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Strauss P, Marti HP, Beisland C, Scherer A, Lysne V, Leh S, Flatberg A, Koch E, Beisvag V, Landolt L, Skogstrand T, Eikrem Ø. Expanding the Utilization of Formalin-Fixed, Paraffin-Embedded Archives: Feasibility of miR-Seq for Disease Exploration and Biomarker Development from Biopsies with Clear Cell Renal Cell Carcinoma. Int J Mol Sci 2018. [PMID: 29534467 PMCID: PMC5877664 DOI: 10.3390/ijms19030803] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Novel predictive tools for clear cell renal cell carcinoma (ccRCC) are urgently needed. MicroRNAs (miRNAs) have been increasingly investigated for their predictive value, and formalin-fixed paraffin-embedded biopsy archives may potentially be a valuable source of miRNA sequencing material, as they remain an underused resource. Core biopsies of both cancerous and adjacent normal tissues were obtained from patients (n = 12) undergoing nephrectomy. After small RNA-seq, several analyses were performed, including classifier evaluation, obesity-related inquiries, survival analysis using publicly available datasets, comparisons to the current literature and ingenuity pathway analyses. In a comparison of tumour vs. normal, 182 miRNAs were found with significant differential expression; miR-155 was of particular interest as it classified all ccRCC samples correctly and correlated well with tumour size (R² = 0.83); miR-155 also predicted poor survival with hazard ratios of 2.58 and 1.81 in two different TCGA (The Cancer Genome Atlas) datasets in a univariate model. However, in a multivariate Cox regression analysis including age, sex, cancer stage and histological grade, miR-155 was not a statistically significant survival predictor. In conclusion, formalin-fixed paraffin-embedded biopsy tissues are a viable source of miRNA-sequencing material. Our results further support a role for miR-155 as a promising cancer classifier and potentially as a therapeutic target in ccRCC that merits further investigation.
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Affiliation(s)
- Philipp Strauss
- Department of Clinical Medicine, University of Bergen, 5021 Bergen, Norway; (P.S.); (H.-P.M.); (C.B.); (S.L.); (E.K.); (L.L.)
| | - Hans-Peter Marti
- Department of Clinical Medicine, University of Bergen, 5021 Bergen, Norway; (P.S.); (H.-P.M.); (C.B.); (S.L.); (E.K.); (L.L.)
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
| | - Christian Beisland
- Department of Clinical Medicine, University of Bergen, 5021 Bergen, Norway; (P.S.); (H.-P.M.); (C.B.); (S.L.); (E.K.); (L.L.)
- Department of Urology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Andreas Scherer
- Spheromics, 81100 Kontiolahti, Finland;
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, 00100 Helsinki, Finland
| | - Vegard Lysne
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway;
| | - Sabine Leh
- Department of Clinical Medicine, University of Bergen, 5021 Bergen, Norway; (P.S.); (H.-P.M.); (C.B.); (S.L.); (E.K.); (L.L.)
- Department of Pathology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Arnar Flatberg
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway; (A.F.); (V.B.)
| | - Even Koch
- Department of Clinical Medicine, University of Bergen, 5021 Bergen, Norway; (P.S.); (H.-P.M.); (C.B.); (S.L.); (E.K.); (L.L.)
| | - Vidar Beisvag
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491 Trondheim, Norway; (A.F.); (V.B.)
| | - Lea Landolt
- Department of Clinical Medicine, University of Bergen, 5021 Bergen, Norway; (P.S.); (H.-P.M.); (C.B.); (S.L.); (E.K.); (L.L.)
| | - Trude Skogstrand
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
- Department of Biomedicine, University of Bergen, 5021 Bergen, Norway;
| | - Øystein Eikrem
- Department of Clinical Medicine, University of Bergen, 5021 Bergen, Norway; (P.S.); (H.-P.M.); (C.B.); (S.L.); (E.K.); (L.L.)
- Department of Medicine, Haukeland University Hospital, 5021 Bergen, Norway
- Correspondence: ; Tel.: +47-4544-6008
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Iguchi T, Niino N, Tamai S, Sakurai K, Mori K. Absolute Quantification of Plasma MicroRNA Levels in Cynomolgus Monkeys, Using Quantitative Real-time Reverse Transcription PCR. J Vis Exp 2018. [PMID: 29553521 DOI: 10.3791/56850] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
RT-qPCR is one of the most common methods to assess individual target miRNAs. MiRNAs levels are generally measured relative to a reference sample. This approach is appropriate for examining physiological changes in target gene expression levels. However, absolute quantification using better statistical analysis is preferable for a comprehensive assessment of gene expression levels. Absolute quantification is still not in common use. This report describes a protocol for measuring the absolute levels of plasma miRNA, using RT-qPCR with or without pre-amplification. A fixed volume (200 µL) of EDTA-plasma was prepared from the blood collected from the femoral vein of conscious cynomolgus monkeys (n = 50). Total RNA was extracted using commercially available system. Plasma miRNAs were quantified by probe-based RT-qPCR assays which contains miRNA-specific forward/reverse PCR primer and probe. Standard curves for absolute quantification were generated using commercially available synthetic RNA oligonucleotides. A synthetic cel-miR-238 was used as an external control for normalization and quality assessment. The miRNAs that showed quantification cycle (Cq) values above 35 were pre-amplified prior to the qPCR step. Among the 8 miRNAs examined, miR-122, miR-133a, and miR-192 were detectable without pre-amplification, whereas miR-1, miR-206, and miR-499a required pre-amplification because of their low expression levels. MiR-208a and miR-208b were not detectable even after pre-amplification. Sample processing efficiency was evaluated by the Cq values of the spiked cel-miR-238. In this assay method, technical variation was estimated to be less than 3-fold and the lower limit of quantification (LLOQ) was 102 copy/µL, for most of the examined miRNAs. This protocol provides a better estimate of the quantity of plasma miRNAs, and allows quality assessment of corresponding data from different studies. Considering the low number of miRNAs in body fluids, pre-amplification is useful to enhance detection of poorly expressed miRNAs.
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Affiliation(s)
- Takuma Iguchi
- Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd.;
| | - Noriyo Niino
- Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd
| | - Satoshi Tamai
- Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd
| | - Ken Sakurai
- Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd
| | - Kazuhiko Mori
- Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd
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Blondal T, Brunetto MR, Cavallone D, Mikkelsen M, Thorsen M, Mang Y, Pinheiro H, Bonino F, Mouritzen P. Genome-Wide Comparison of Next-Generation Sequencing and qPCR Platforms for microRNA Profiling in Serum. Methods Mol Biol 2018; 1580:21-44. [PMID: 28439824 DOI: 10.1007/978-1-4939-6866-4_3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
This study compares next-generation sequencing (NGS) technologies that have been optimized specifically for biofluid samples, with more established qPCR-based methods for profiling microRNAs in biofluids. The same patient serum samples were analyzed by NGS and qPCR, and differences in the serum microRNA profile between HBV and HCV infected patients were investigated. While there was overall good agreement between NGS and qPCR, there were some differences between the platforms, highlighting the importance of validation.
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Affiliation(s)
| | - Maurizia Rossana Brunetto
- Hepatology Unit and Laboratory of Molecular Genetics and Pathology of Hepatitis Viruses, Reference Center of the Tuscany Region for Chronic Liver Disease and Cancer, University Hospital of Pisa, Pisa, Italy
| | - Daniela Cavallone
- Hepatology Unit and Laboratory of Molecular Genetics and Pathology of Hepatitis Viruses, Reference Center of the Tuscany Region for Chronic Liver Disease and Cancer, University Hospital of Pisa, Pisa, Italy
| | | | | | | | | | - Ferruccio Bonino
- Hepatology Unit and Laboratory of Molecular Genetics and Pathology of Hepatitis Viruses, Reference Center of the Tuscany Region for Chronic Liver Disease and Cancer, University Hospital of Pisa, Pisa, Italy
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Zou YF, Zhang W. Role of microRNA in the detection, progression, and intervention of acute kidney injury. Exp Biol Med (Maywood) 2017; 243:129-136. [PMID: 29264947 DOI: 10.1177/1535370217749472] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Acute kidney injury, characterized by sharply decreased renal function, is a common and important complication in hospitalized patients. The pathological mechanism of acute kidney injury is mainly related to immune activation and inflammation. Given the high morbidity and mortality rates of hospitalized patients with acute kidney injury, the identification of biomarkers useful for assessing risk, making an early diagnosis, evaluating the prognosis, and classifying the injury severity is urgently needed. Furthermore, investigation into the development of acute kidney injury and potential therapeutic targets is required. While microRNA was first discovered in Caenorhabditis elegans, Gary Ruvkun's laboratory identified the first microRNA target gene. Together, these two important findings confirmed the existence of a novel post-transcriptional gene regulatory mechanism. Considering that serum creatinine tests often fail in the early detection of AKI, testing for microRNAs as early diagnostic biomarkers has shown great potential. Numerous studies have identified microRNAs that can serve as biomarkers for the detection of acute kidney injury. In addition, as microRNAs can control the expression of multiple proteins through hundreds or thousands of targets influencing multiple signaling pathways, the number of studies on the functions of microRNAs in AKI progression is increasing. Here, we mainly focus on research into microRNAs as biomarkers and explorations of their functions in acute kidney injury. Impact statement Firstly, we have discussed the potential advantages and limitations of miRNA as biomarkers. Secondly, we have summarized the role of miRNA in the progress of AKI. Finally, we have made a vision of miRNA's potential and advantages as therapeutic target intervention AKI.
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Affiliation(s)
- Yan-Fang Zou
- Department of Nephrology, 66281 School of Medicine, Ruijin Hospital, Shanghai Jiao Tong University , Shanghai 200025, PR China
| | - Wen Zhang
- Department of Nephrology, 66281 School of Medicine, Ruijin Hospital, Shanghai Jiao Tong University , Shanghai 200025, PR China
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Genome-wide Profiling of Urinary Extracellular Vesicle microRNAs Associated With Diabetic Nephropathy in Type 1 Diabetes. Kidney Int Rep 2017; 3:555-572. [PMID: 29854963 PMCID: PMC5976846 DOI: 10.1016/j.ekir.2017.11.019] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 11/15/2017] [Accepted: 11/27/2017] [Indexed: 01/01/2023] Open
Abstract
Introduction Diabetic nephropathy (DN) is a form of progressive kidney disease that often leads to end-stage renal disease (ESRD). It is initiated by microvascular complications due to diabetes. Although microalbuminuria (MA) is the earliest clinical indication of DN among patients with type 1 diabetes (T1D), it lacks the sensitivity and specificity to detect the early onset of DN. Recently, microRNAs (miRNAs) have emerged as critical regulators in diabetes as well as various forms of kidney disease, including renal fibrosis, acute kidney injury, and progressive kidney disease. Additionally, circulating extracellular miRNAs, especially miRNAs packaged in extracellular vesicles (EVs), have garnered significant attention as potential noninvasive biomarkers for various diseases and health conditions. Methods As part of the University of Pittsburgh Epidemiology of Diabetes Complications (EDC) study, urine was collected from individuals with T1D with various grades of DN or MA (normal, overt, intermittent, and persistent) over a decade at prespecified intervals. We isolated EVs from urine and analyzed the small-RNA using NextGen sequencing. Results We identified a set of miRNAs that are enriched in urinary EVs compared with EV-depleted samples, and identified a number of miRNAs showing concentration changes associated with DN occurrence, MA status, and other variables, such as hemoglobin A1c levels. Conclusion Many of the miRNAs associated with DN occurrence or MA status directly target pathways associated with renal fibrosis (including transforming growth factor-β and phosphatase and tensin homolog), which is one of the major contributors to the pathology of DN. These miRNAs are potential biomarkers for DN and MA.
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Schraml E, Hackl M, Grillari J. MicroRNAs and toxicology: A love marriage. Toxicol Rep 2017; 4:634-636. [PMID: 29214146 PMCID: PMC5695539 DOI: 10.1016/j.toxrep.2017.11.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 10/16/2017] [Accepted: 11/10/2017] [Indexed: 12/14/2022] Open
Abstract
Circulating microRNAs can serve as novel toxicological biomarkers. MicroRNAs are non-invasive biomarkers for early detection of tissue injury. MicroRNAs regulate gene activity in tissues exposed to toxic substances. They are novel tools for identifying and monitoring safety risks in drug development. MicroRNA are highly-conserved and potentially useful in preclinical animal studies.
With the dawn of personalized medicine, secreted microRNAs (miRNAs) have come into the very focus of biomarker development for various diseases. MiRNAs fulfil key requirements of diagnostic tools such as i) non or minimally invasive accessibility, ii) robust, standardized and non-expensive quantitative analysis, iii) rapid turnaround of the test result and iv) most importantly because they provide a comprehensive snapshot of the ongoing physiologic processes in cells and tissues that package and release miRNAs into cell-free space. These characteristics have also established circulating miRNAs as promising biomarker candidates for toxicological studies, where they are used as biomarkers of drug-, or chemical-induced tissue injury for safety assessment. The tissue-specificity and early release of circulating miRNAs upon tissue injury, when damage is still reversible, are main factors for their clinical utility in toxicology. Here we summarize in brief, current knowledge of this field.
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Affiliation(s)
| | | | - Johannes Grillari
- TAmiRNA GmbH, Muthgasse 18, 1190, Wien, Austria.,Christian Doppler Labor für Biotechnologie der Hautalterung, Department für Biotechnologie, BOKU Universität für Bodenkultur, Muthgasse 18, 1190, Wien, Austria.,Austrian Cluster for Tissue Regeneration, Austria
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40
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Baraniuk JN, Shivapurkar N. Exercise - induced changes in cerebrospinal fluid miRNAs in Gulf War Illness, Chronic Fatigue Syndrome and sedentary control subjects. Sci Rep 2017; 7:15338. [PMID: 29127316 PMCID: PMC5681566 DOI: 10.1038/s41598-017-15383-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 10/11/2017] [Indexed: 01/06/2023] Open
Abstract
Gulf War Illness (GWI) and Chronic Fatigue Syndrome (CFS) have similar profiles of pain, fatigue, cognitive dysfunction and exertional exhaustion. Post-exertional malaise suggests exercise alters central nervous system functions. Lumbar punctures were performed in GWI, CFS and control subjects after (i) overnight rest (nonexercise) or (ii) submaximal bicycle exercise. Exercise induced postural tachycardia in one third of GWI subjects (Stress Test Activated Reversible Tachycardia, START). The remainder were Stress Test Originated Phantom Perception (STOPP) subjects. MicroRNAs (miRNA) in cerebrospinal fluid were amplified by quantitative PCR. Levels were equivalent between nonexercise GWI (n = 22), CFS (n = 43) and control (n = 22) groups. After exercise, START (n = 22) had significantly lower miR-22-3p than control (n = 15) and STOPP (n = 42), but higher miR-9-3p than STOPP. All post-exercise groups had significantly reduced miR-328 and miR-608 compared to nonexercise groups; these may be markers of exercise effects on the brain. Six miRNAs were significantly elevated and 12 diminished in post-exercise START, STOPP and control compared to nonexercise groups. CFS had 12 diminished miRNAs after exercise. Despite symptom overlap of CFS, GWI and other illnesses in their differential diagnosis, exercise-induced miRNA patterns in cerebrospinal fluid indicated distinct mechanisms for post-exertional malaise in CFS and START and STOPP phenotypes of GWI.
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Affiliation(s)
- James N Baraniuk
- Division of Rheumatology, Immunology and Allergy, Department of Medicine, Georgetown University, Washington, District of Columbia, United States of America.
| | - Narayan Shivapurkar
- Division of Rheumatology, Immunology and Allergy, Department of Medicine, Georgetown University, Washington, District of Columbia, United States of America
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Kevill JL, Highfield A, Mordecai GJ, Martin SJ, Schroeder DC. ABC Assay: Method Development and Application to Quantify the Role of Three DWV Master Variants in Overwinter Colony Losses of European Honey Bees. Viruses 2017; 9:v9110314. [PMID: 29077069 PMCID: PMC5707521 DOI: 10.3390/v9110314] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 10/24/2017] [Accepted: 10/25/2017] [Indexed: 02/05/2023] Open
Abstract
Deformed wing virus (DWV) is one of the most prevalent honey bee viral pathogens in the world. Typical of many RNA viruses, DWV is a quasi-species, which is comprised of a large number of different variants, currently consisting of three master variants: Type A, B, and C. Little is known about the impact of each variant or combinations of variants upon the biology of individual hosts. Therefore, we have developed a new set of master variant-specific DWV primers and a set of standards that allow for the quantification of each of the master variants. Competitive reverse transcriptase polymerase chain reaction (RT-PCR) experimental design confirms that each new DWV primer set is specific to the retrospective master variant. The sensitivity of the ABC assay is dependent on whether DNA or RNA is used as the template and whether other master variants are present in the sample. Comparison of the overall proportions of each master variant within a sample of known diversity, as confirmed by next-generation sequence (NGS) data, validates the efficiency of the ABC assay. The ABC assay was used on archived material from a Devon overwintering colony loss (OCL) 2006-2007 study; further implicating DWV type A and, for the first time, possibly C in the untimely collapse of honey bee colonies. Moreover, in this study DWV type B was not associated with OCL. The use of the ABC assay will allow researchers to quickly and cost effectively pre-screen for the presence of DWV master variants in honey bees.
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Affiliation(s)
- Jessica L Kevill
- School of Environment and Life Sciences, The University of Salford, Manchester M5 4WT, UK.
| | - Andrea Highfield
- Viral Ecology, Marine Biological Association, Plymouth PL1 2PB, UK.
| | - Gideon J Mordecai
- Viral Ecology, Marine Biological Association, Plymouth PL1 2PB, UK.
- Department of Earth, Ocean and Atmospheric Sciences and Biodiversity Research Centre, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| | - Stephen J Martin
- School of Environment and Life Sciences, The University of Salford, Manchester M5 4WT, UK.
| | - Declan C Schroeder
- Viral Ecology, Marine Biological Association, Plymouth PL1 2PB, UK.
- School of Biological Sciences, University of Reading, Reading RG6 6LA, UK.
- Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St Paul, MN 55108, USA.
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Balacescu O, Petrut B, Tudoran O, Feflea D, Balacescu L, Anghel A, Sirbu IO, Seclaman E, Marian C. Urinary microRNAs for prostate cancer diagnosis, prognosis, and treatment response: are we there yet? WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [DOI: 10.1002/wrna.1438] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 06/27/2017] [Accepted: 07/18/2017] [Indexed: 12/28/2022]
Affiliation(s)
- Ovidiu Balacescu
- Department of Functional Genomics, Proteomics and Experimental Pathology; The Oncology Institute “Prof. Dr. Ion Chiricuta”; Cluj-Napoca Romania
| | - Bogdan Petrut
- Department of Urology; The Oncology Institute “Prof. Dr. Ion Chiricuta”; Cluj-Napoca Romania
| | - Oana Tudoran
- Department of Functional Genomics, Proteomics and Experimental Pathology; The Oncology Institute “Prof. Dr. Ion Chiricuta”; Cluj-Napoca Romania
| | - Dragos Feflea
- Department of Urology; The Oncology Institute “Prof. Dr. Ion Chiricuta”; Cluj-Napoca Romania
| | - Loredana Balacescu
- Department of Functional Genomics, Proteomics and Experimental Pathology; The Oncology Institute “Prof. Dr. Ion Chiricuta”; Cluj-Napoca Romania
| | - Andrei Anghel
- Department of Biochemistry & Pharmacology; Victor Babes University of Medicine and Pharmacy; Timisoara Romania
| | - Ioan O. Sirbu
- Department of Biochemistry & Pharmacology; Victor Babes University of Medicine and Pharmacy; Timisoara Romania
| | - Edward Seclaman
- Department of Biochemistry & Pharmacology; Victor Babes University of Medicine and Pharmacy; Timisoara Romania
| | - Catalin Marian
- Department of Biochemistry & Pharmacology; Victor Babes University of Medicine and Pharmacy; Timisoara Romania
- Division of Cancer Prevention and Control; The Ohio State University Comprehensive Cancer Center; Columbus OH USA
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Bencurova P, Baloun J, Musilova K, Radova L, Tichy B, Pail M, Zeman M, Brichtova E, Hermanova M, Pospisilova S, Mraz M, Brazdil M. MicroRNA and mesial temporal lobe epilepsy with hippocampal sclerosis: Whole miRNome profiling of human hippocampus. Epilepsia 2017; 58:1782-1793. [PMID: 28815576 DOI: 10.1111/epi.13870] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2017] [Indexed: 12/19/2022]
Abstract
OBJECTIVE Mesial temporal lobe epilepsy (mTLE) is a severe neurological disorder characterized by recurrent seizures. mTLE is frequently accompanied by neurodegeneration in the hippocampus resulting in hippocampal sclerosis (HS), the most common morphological correlate of drug resistance in mTLE patients. Incomplete knowledge of pathological changes in mTLE+HS complicates its therapy. The pathological mechanism underlying mTLE+HS may involve abnormal gene expression regulation, including posttranscriptional networks involving microRNAs (miRNAs). miRNA expression deregulation has been reported in various disorders, including epilepsy. However, the miRNA profile of mTLE+HS is not completely known and needs to be addressed. METHODS Here, we have focused on hippocampal miRNA profiling in 33 mTLE+HS patients and nine postmortem controls to reveal abnormally expressed miRNAs. In this study, we significantly reduced technology-related bias (the most common source of false positivity in miRNA profiling data) by combining two different miRNA profiling methods, namely next generation sequencing and miRNA-specific quantitative real-time polymerase chain reaction. RESULTS These methods combined have identified and validated 20 miRNAs with altered expression in the human epileptic hippocampus; 19 miRNAs were up-regulated and one down-regulated in mTLE+HS patients. Nine of these miRNAs have not been previously associated with epilepsy, and 19 aberrantly expressed miRNAs potentially regulate the targets and pathways linked with epilepsy (such as potassium channels, γ-aminobutyric acid, neurotrophin signaling, and axon guidance). SIGNIFICANCE This study extends current knowledge of miRNA-mediated gene expression regulation in mTLE+HS by identifying miRNAs with altered expression in mTLE+HS, including nine novel abnormally expressed miRNAs and their putative targets. These observations further encourage the potential of microRNA-based biomarkers or therapies.
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Affiliation(s)
- Petra Bencurova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Neurology, Brno Epilepsy Center, St. Anne's University Hospital, Brno, Czech Republic.,Medical Faculty of Masaryk University, Brno, Czech Republic
| | - Jiri Baloun
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Neurology, Brno Epilepsy Center, St. Anne's University Hospital, Brno, Czech Republic.,Medical Faculty of Masaryk University, Brno, Czech Republic
| | - Katerina Musilova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Medical Faculty of Masaryk University, Brno, Czech Republic
| | - Lenka Radova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Boris Tichy
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Martin Pail
- Department of Neurology, Brno Epilepsy Center, St. Anne's University Hospital, Brno, Czech Republic.,Medical Faculty of Masaryk University, Brno, Czech Republic
| | - Martin Zeman
- Medical Faculty of Masaryk University, Brno, Czech Republic.,Department of Forensic Medicine, St. Anne's University Hospital, Brno, Czech Republic
| | - Eva Brichtova
- Medical Faculty of Masaryk University, Brno, Czech Republic.,Department of Neurosurgery, St. Anne's University Hospital, Brno, Czech Republic
| | - Marketa Hermanova
- Medical Faculty of Masaryk University, Brno, Czech Republic.,First Department of Pathological Anatomy, St. Anne's University Hospital, Brno, Czech Republic
| | - Sarka Pospisilova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Marek Mraz
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Milan Brazdil
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Neurology, Brno Epilepsy Center, St. Anne's University Hospital, Brno, Czech Republic.,Medical Faculty of Masaryk University, Brno, Czech Republic
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Personalized Medicine: New Perspectives for the Diagnosis and the Treatment of Renal Diseases. Int J Mol Sci 2017; 18:ijms18061248. [PMID: 28604601 PMCID: PMC5486071 DOI: 10.3390/ijms18061248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/19/2017] [Accepted: 05/27/2017] [Indexed: 12/29/2022] Open
Abstract
The prevalence of renal diseases is rising and reaching 5-15% of the adult population. Renal damage is associated with disturbances of body homeostasis and the loss of equilibrium between exogenous and endogenous elements including drugs and metabolites. Studies indicate that renal diseases are influenced not only by environmental but also by genetic factors. In some cases the disease is caused by mutation in a single gene and at that time severity depends on the presence of one or two mutated alleles. In other cases, renal disease is associated with the presence of alteration within a gene or genes, but environmental factors are also necessary for the development of disease. Therefore, it seems that the analysis of genetic aspects should be a natural component of clinical and experimental studies. The goal of personalized medicine is to determine the right drug, for the right patient, at the right time. Whole-genome examinations may help to change the approach to the disease and the patient resulting in the creation of "personalized medicine" with new diagnostic and treatment strategies designed on the basis of genetic background of each individual. The identification of high-risk patients in pharmacogenomics analyses will help to avoid many unwarranted side effects while optimizing treatment efficacy for individual patients. Personalized therapies for kidney diseases are still at the preliminary stage mainly due to high costs of such analyses and the complex nature of human genome. This review will focus on several areas of interest: renal disease pathogenesis, diagnosis, treatment, rate of progression and the prediction of prognosis.
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van de Vrie M, Deegens JK, Eikmans M, van der Vlag J, Hilbrands LB. Urinary MicroRNA as Biomarker in Renal Transplantation. Am J Transplant 2017; 17:1160-1166. [PMID: 27743494 PMCID: PMC5434819 DOI: 10.1111/ajt.14082] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 09/30/2016] [Accepted: 10/02/2016] [Indexed: 01/25/2023]
Abstract
Urine represents a noninvasive source in which proteins and nucleic acids can be assessed. Such analytes may function as biomarkers to monitor kidney graft pathology at every desired frequency, thereby providing a time window to prevent graft damage by therapeutic intervention. Recently, several proteins have been measured in urine as markers of graft injury. However, the specificity is limited, and measuring urinary proteins generally lacks the potential to predict early kidney graft damage. Currently, urinary mRNA and microRNA are being investigated to evaluate the prognostic value of changes in gene expression during the initial stages of graft damage. At such time point, a change in treatment regimen and dosage is expected to have maximum potency to minimize future decline in graft function. Both mRNA and microRNAs have shown promising results in both detection and prediction of graft injury. An advantage of microRNAs compared to mRNA molecules is their stability, a characteristic that is beneficial when working with urine samples. In this review, we provide the current state of urinary biomarkers in renal transplantation, with a focus on urinary microRNA. In addition, we discuss the methods used to study urinary microRNA expression.
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Affiliation(s)
- M. van de Vrie
- Department of NephrologyRadboud University Medical CenterNijmegenthe Netherlands
| | - J. K. Deegens
- Department of NephrologyRadboud University Medical CenterNijmegenthe Netherlands
| | - M. Eikmans
- Department of ImmunohematologyLeiden University Medical CenterLeidenthe Netherlands
| | - J. van der Vlag
- Department of NephrologyRadboud University Medical CenterNijmegenthe Netherlands
| | - L. B. Hilbrands
- Department of NephrologyRadboud University Medical CenterNijmegenthe Netherlands
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Hypoxia-Related Tumor Acidosis Affects MicroRNA Expression Pattern in Prostate and Breast Tumor Cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 977:119-124. [DOI: 10.1007/978-3-319-55231-6_16] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Next-Generation Sequencing to Investigate Urinary microRNAs from Macaca fascicularis (Cynomolgus Monkey). Methods Mol Biol 2017; 1641:349-378. [PMID: 28748475 DOI: 10.1007/978-1-4939-7172-5_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Advanced sequencing technologies like next-generation sequencing (NGS) not only detect microRNAs (miRNAs) in biological samples but also facilitate de novo identification of miRNAs. Using an Ion Torrent's Ion Proton System, here we described miRNAs sequencing of urine samples collected from Macaca fascicularis (Cynomolgus monkey) to investigate miRNAs as potential novel biomarkers of nephrotoxicity in this species. Urinary miRNA sequencing methodologies described here include (a) urinary exosomal RNA isolation, (b) sequencing library preparation, (c) sequencing template preparation, and (d) template library sequencing using Ion Proton System. The sequencing method presented in this study serves as a valuable resource in the identification of novel urinary miRNAs in M. fascicularis.
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Daneshpour M, Omidfar K, Ghanbarian H. A novel electrochemical nanobiosensor for the ultrasensitive and specific detection of femtomolar-level gastric cancer biomarker miRNA-106a. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2016; 7:2023-2036. [PMID: 28144550 PMCID: PMC5238648 DOI: 10.3762/bjnano.7.193] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/23/2016] [Indexed: 06/06/2023]
Abstract
Gastric cancer (GC) is the second leading cause of cancer-related deaths all over the world. miR-106a is a circulatory oncogenic microRNA (miRNA), which overexpresses in various malignancies, especially in GC. In this study, an ultrasensitive electrochemical nanobiosensor was developed for the detection of miR-106a using a double-specific probe methodology and a gold-magnetic nanocomposite as tracing tag. The successful modification of the electrode and hybridization with the target miRNA were confirmed by electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV) methods. Differential pulse voltammetry (DPV) was used for quantitative evaluation of miR-106a via recording the reduction peak current of gold nanoparticles. The electrochemical signal had a linear relationship with the concentration of the target miRNA ranging from 1 × 10-3 pM to 1 × 103 pM, and the detection limit was 3 × 10-4 pM. The proposed miRNA-nanobiosensor showed remarkable selectivity, high specificity, agreeable storage stability, and great performance in real sample investigation with no pretreatment or amplification. Consequently, our biosensing strategy offers such a promising application to be used for clinical early detection of GC and additionally the screen of any miRNA sequence.
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Affiliation(s)
- Maryam Daneshpour
- Biotechnology Department, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kobra Omidfar
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Hossein Ghanbarian
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Nephron segment specific microRNA biomarkers of pre-clinical drug-induced renal toxicity: Opportunities and challenges. Toxicol Appl Pharmacol 2016; 312:34-41. [DOI: 10.1016/j.taap.2016.01.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/19/2016] [Accepted: 01/27/2016] [Indexed: 12/11/2022]
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Güçlü A, Koçak C, Koçak FE, Akçılar R, Dodurga Y, Akçılar A, Seçme M. Micro RNA-320 as a novel potential biomarker in renal ischemia reperfusion. Ren Fail 2016; 38:1468-1475. [DOI: 10.1080/0886022x.2016.1227915] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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