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Jiang Y, Wang W, Tang F, Zhang W, Chen S, Gu X, Chen P, Xu X, Nian B, Li Z, Chen C, Yin H, Su L, Sun H, Chen W, Zhang D, Li Y. Identifying MiR-140-3p as a stable internal reference to normalize MicroRNA qRT-PCR levels of plasma small extracellular vesicles in lung cancer patients. Genomics 2024; 116:110875. [PMID: 38849018 DOI: 10.1016/j.ygeno.2024.110875] [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: 05/31/2023] [Revised: 03/13/2024] [Accepted: 04/12/2024] [Indexed: 06/09/2024]
Abstract
Exploration of a stably expressed gene as a reference is critical for the accurate evaluation of miRNAs isolated from small extracellular vesicles (sEVs). In this study, we analyzed small RNA sequencing on plasma sEV miRNAs in the training dataset (n = 104) and found that miR-140-3p was the most stably expressed candidate reference for sEV miRNAs. We further demonstrated that miR-140-3p expressed most stably in the validation cohort (n = 46) when compared to two other reference miRNAs, miR-451a and miR-1228-3p, and the commonly-used miRNA reference U6. Finally, we compared the capability of miR-140-3p and U6 as the internal reference for sEV miRNA expression by evaluating key miRNAs expression in lung cancer patients and found that miR-140-3p was more suitable as a sEV miRNA reference gene. Taken together, our data indicated miR-140-3p as a stable internal reference miRNA of plasma sEVs to evaluate miRNA expression profiles in lung cancer patients.
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Affiliation(s)
- Yuan Jiang
- Hunan Cancer Hospital & The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, China
| | - Weiwei Wang
- Hunan Cancer Hospital & The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, China
| | - Faqing Tang
- Hunan Cancer Hospital & The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, China
| | - Wei Zhang
- 3D Medicines Inc., Shanghai 201114, China
| | - Sheng Chen
- 3D Medicines Inc., Shanghai 201114, China
| | - Xiumei Gu
- Hunan Cancer Hospital & The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, China
| | - Ping Chen
- Hunan Cancer Hospital & The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, China
| | - Xiaoya Xu
- 3D Medicines Inc., Shanghai 201114, China
| | | | - Zhikuan Li
- 3D Medicines Inc., Shanghai 201114, China
| | | | - Hanbing Yin
- Shenxian People's Hospital, Liaocheng 252411, China
| | - Linlin Su
- Shenxian People's Hospital, Liaocheng 252411, China
| | - Honghou Sun
- Shenxian Maternal and Child Health Hospital, Liaocheng 252499, China
| | - Wei Chen
- 3D Medicines Inc., Shanghai 201114, China
| | | | - Yuejin Li
- Department of Clinical Laboratory, Hui Ya Hospital of The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China.
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Boonkaew B, Satthawiwat N, Pinjaroen N, Chuaypen N, Tangkijvanich P. Circulating Extracellular Vesicle-Derived microRNAs as Novel Diagnostic and Prognostic Biomarkers for Non-Viral-Related Hepatocellular Carcinoma. Int J Mol Sci 2023; 24:16043. [PMID: 38003232 PMCID: PMC10671272 DOI: 10.3390/ijms242216043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 11/26/2023] Open
Abstract
Extracellular vesicle-derived microRNAs (EV-miRNAs) are promising circulating biomarkers for chronic liver disease. In this study, we explored the potential significance of plasma EV-miRNAs in non-hepatitis B-, non-hepatitis C-related HCC (NBNC-HCC). We compared, using the NanoString method, plasma EV-miRNA profiles between NBNC-HCC and control groups including patients with non-alcoholic fatty liver disease (NAFLD) and healthy controls. The differentially expressed EV-miRNAs were validated in another set of plasma samples by qRT-PCR. A total of 66 significantly differentially expressed EV-miRNAs between the HCC and the control groups were identified in the discovery set. In the validation cohort, including plasma samples of 70 NBNC-HCC patients, 70 NAFLD patients, and 35 healthy controls, 5 plasma EV-miRNAs were significantly elevated in HCC, which included miR-19-3p, miR-16-5p, miR-223-3p, miR-30d-5p, and miR-451a. These miRNAs were found to participate in several cancer-related signaling pathways based on bioinformatic analysis. Among them, EV-miR-19-3p exhibited the best diagnostic performance and displayed a high sensitivity for detecting alpha-fetoprotein-negative HCC and early-stage HCC. In multivariate analysis, a high EV-miR-19-3p level was demonstrated as an independently unfavorable predictor of overall survival in patients with NBNC-HCC. In conclusion, our data have indicated, for the first time, that EV-miR-19-3p could serve as a novel circulating biomarker for the diagnosis and prognosis of NBNC-HCC.
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Affiliation(s)
- Bootsakorn Boonkaew
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (B.B.); (N.S.)
| | - Nantawat Satthawiwat
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (B.B.); (N.S.)
| | - Nutcha Pinjaroen
- Department of Radiology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Natthaya Chuaypen
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (B.B.); (N.S.)
| | - Pisit Tangkijvanich
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand; (B.B.); (N.S.)
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3
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Banerjee A, Sriramulu S, Catanzaro R, He F, Chabria Y, Balakrishnan B, Hari S, Ayala A, Muñoz M, Pathak S, Marotta F. Natural Compounds as Integrative Therapy for Liver Protection against Inflammatory and Carcinogenic Mechanisms: From Induction to Molecular Biology Advancement. Curr Mol Med 2023; 23:216-231. [PMID: 35297348 DOI: 10.2174/1566524022666220316102310] [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: 03/11/2021] [Revised: 10/20/2021] [Accepted: 12/25/2021] [Indexed: 02/08/2023]
Abstract
The liver is exposed to several harmful substances that bear the potential to cause excessive liver damage ranging from hepatitis and non-alcoholic fatty liver disease to extreme cases of liver cirrhosis and hepatocellular carcinoma. Liver ailments have been effectively treated from very old times with Chinese medicinal herbal formulations and later also applied by controlled trials in Japan. However, these traditional practices have been hardly well characterized in the past till in the last decades when more qualified studies have been carried out. Modern advances have given rise to specific molecular targets which are specifically good candidates for affecting the intricate mechanisms that play a role at the molecular level. These therapeutic regimens that mainly affect the progression of the disease by inhibiting the gene expression levels or by blocking essential molecular pathways or releasing cytokines may prove to play a vital role in minimizing the tissue damage. This review, therefore, tries to throw light upon the variation in the therapies for the treatment of benign and malignant liver disease from ancient times to the current date. Nonetheless, clinical research exploring the effectiveness of herbal medicines in the treatment of benign chronic liver diseases as well as prevention and treatment of HCC is still warranted.
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Affiliation(s)
- Antara Banerjee
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Chennai 603103, India
| | - Sushmitha Sriramulu
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Chennai 603103, India
| | - Roberto Catanzaro
- Dept of Clinical and Experimental Medicine, Section of Gastroenterology, University of Catania, Catania, Italy
| | - Fang He
- Dept of Nutrition, West China School of Public Health, Sichuan University, Chengdu, China
| | - Yashna Chabria
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Chennai 603103, India
| | | | - Sruthi Hari
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Chennai 603103, India
| | - Antonio Ayala
- Biochemistry and Clinical Biochemistry Department, Faculty of Pharmacy, University of Seville, Spain
| | - Mario Muñoz
- Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Portugal
| | - Surajit Pathak
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Chennai 603103, India
| | - Francesco Marotta
- ReGenera R&D International for Aging Intervention, Milano, Italy and Vitality and Longevity Medical Science Commission, FEMTEC World Federation
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Abstract
Exosomes are extracellular vesicles, which have the ability to convey various types of cargo between cells. Lately, a great amount of interest has been paid to exosomal microRNAs (miRNAs), since much evidence has suggested that the sorting of miRNAs into exosomes is not an accidental process. It has been shown that exosomal miRNAs (exo-miRNAs) are implicated in a variety of cellular processes including (but not limited to) cell migration, apoptosis, proliferation, and autophagy. Exosomes can play a role in cardiovascular diseases and can be used as diagnostic biomarkers for several diseases, especially cancer. Tremendous advances in technology have led to the development of various platforms for miRNA profiling. Each platform has its own limitations and strengths that need to be understood in order to use them properly. In the current review, we summarize some exo-miRNAs that are relevant to exo-miRNA profiling studies and describe new methods used for the measurement of miRNA profiles in different human bodily fluids.
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Kaur J, Saul D, Doolittle ML, Rowsey JL, Vos SJ, Farr JN, Khosla S, Monroe DG. Identification of a suitable endogenous control miRNA in bone aging and senescence. Gene X 2022; 835:146642. [PMID: 35700807 PMCID: PMC9533812 DOI: 10.1016/j.gene.2022.146642] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/15/2022] [Accepted: 06/02/2022] [Indexed: 11/04/2022] Open
Abstract
MicroRNAs (miRNAs) are promising tools as biomarkers and therapeutic agents in various chronic diseases such as osteoporosis, cancers, type I and II diabetes, and cardiovascular diseases. Considering the rising interest in the regulatory role of miRNAs in bone metabolism, aging, and cellular senescence, accurate normalization of qPCR-based miRNA expression data using an optimal endogenous control becomes crucial. We used a systematic approach to select candidate endogenous control miRNAs that exhibit high stability with aging from our miRNA sequence data and literature search. Validation of miRNA expression was performed using qPCR and their comprehensive stability was assessed using the RefFinder tool which is based on four statistical algorithms: GeNorm, NormFinder, BestKeeper, and comparative delta CT. The selected endogenous control was then validated for its stability in mice and human bone tissues, and in bone marrow stromal cells (BMSCs) following induction of senescence and senolytic treatment. Finally, the utility of selected endogenous control versus U6 was tested by using each as a normalizer to measure the expression of miR-34a, a miRNA known to increase with age and senescence. Our results show that Let-7f did not change across the groups with aging, senescence or senolytic treatment, and was the most stable miRNA, whereas U6 was the least stable. Moreover, using Let-7f as a normalizer resulted in significantly increased expression of miR-34a with aging and senescence and decreased expression following senolytic treatment. However, the expression pattern for miR-34a reversed for each of these conditions when U6 was used as a normalizer. We show that optimal endogenous control miRNAs, such as Let-7f, are essential for accurate normalization of miRNA expression data to increase the reliability of results and prevent misinterpretation. Moreover, we present a systematic strategy that is transferrable and can easily be used to identify endogenous control miRNAs in other biological systems and conditions.
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Affiliation(s)
- Japneet Kaur
- Department of Medicine, Division of Endocrinology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA; Robert and Arlene Kogod Center on Aging, Rochester, MN 55905, USA
| | - Dominik Saul
- Department of Medicine, Division of Endocrinology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA; Robert and Arlene Kogod Center on Aging, Rochester, MN 55905, USA
| | - Madison L Doolittle
- Department of Medicine, Division of Endocrinology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA; Robert and Arlene Kogod Center on Aging, Rochester, MN 55905, USA
| | - Jennifer L Rowsey
- Department of Medicine, Division of Endocrinology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA; Robert and Arlene Kogod Center on Aging, Rochester, MN 55905, USA
| | - Stephanie J Vos
- Department of Medicine, Division of Endocrinology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA; Robert and Arlene Kogod Center on Aging, Rochester, MN 55905, USA
| | - Joshua N Farr
- Department of Medicine, Division of Endocrinology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA; Robert and Arlene Kogod Center on Aging, Rochester, MN 55905, USA
| | - Sundeep Khosla
- Department of Medicine, Division of Endocrinology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA; Robert and Arlene Kogod Center on Aging, Rochester, MN 55905, USA
| | - David G Monroe
- Department of Medicine, Division of Endocrinology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA; Robert and Arlene Kogod Center on Aging, Rochester, MN 55905, USA.
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Jia M, Wang Z. MicroRNAs as Biomarkers for Ionizing Radiation Injury. Front Cell Dev Biol 2022; 10:861451. [PMID: 35309926 PMCID: PMC8927810 DOI: 10.3389/fcell.2022.861451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/15/2022] [Indexed: 01/04/2023] Open
Abstract
Accidental radiation exposures such as industrial accidents and nuclear catastrophes pose a threat to human health, and the potential or substantial injury caused by ionizing radiation (IR) from medical treatment that cannot be ignored. Although the mechanisms of IR-induced damage to various organs have been gradually investigated, medical treatment of irradiated individuals is still based on clinical symptoms. Hence, minimally invasive biomarkers that can predict radiation damage are urgently needed for appropriate medical management after radiation exposure. In the field of radiation biomarker, finding molecular biomarkers to assess different levels of radiation damage is an important direction. In recent years, microRNAs have been widely reported as several diseases’ biomarkers, such as cancer and cardiovascular diseases, and microRNAs are also of interest to the ionizing radiation field as radiation response molecules, thus researchers are turning attention to the potential of microRNAs as biomarkers in tumor radiation response and the radiation toxicity prediction of normal tissues. In this review, we summarize the distribution of microRNAs, the progress on research of microRNAs as markers of IR, and make a hypothesis about the origin and destination of microRNAs in vivo after IR.
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Chen W, Li G, Li Z, Zhu J, Wei T, Lei J. Evaluation of plasma exosomal miRNAs as potential diagnostic biomarkers of lymph node metastasis in papillary thyroid carcinoma. Endocrine 2022; 75:846-855. [PMID: 34854020 DOI: 10.1007/s12020-021-02949-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 11/15/2021] [Indexed: 02/08/2023]
Abstract
PURPOSE The early diagnosis of lymph node metastasis (LNM) in papillary thyroid carcinoma (PTC) is clinically important, as it can aid in treatment decision-making and improve prognosis. In the present study, we aimed to identify whether plasma exosomal miRNAs could be potential diagnostic markers of LNM in PTC. METHODS Profiles of plasma exosomal miRNAs were screened using miRNA microarrays. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) was performed in the validation and diagnostic sets to select candidate exosomal miRNAs. Finally, receiver operating characteristic (ROC) curves were generated to evaluate the efficiency of target exosomal miRNAs in distinguishing PTC-N1 patients from PTC-N0 patients. RESULTS In total, 197 miRNAs were found to be differentially expressed in the testing set. Based on the qRT-PCR results, the expression of miR-6774-3p (p < 0.001) and miR-6879-5p (p < 0.001) in the PTC-N1 patients was significantly higher than that in the controls. The AUC values of plasma exosomal miR-6774-3p (0.802; 95% CI, 0.724-0.879) and miR-6879-5p (0.787; 95% CI, 0.706-0.867) and their combination (0.914; 95% CI, 0.865-0.962) were higher than those of the total miRNAs directly isolated from plasma. Moreover, the expression of exosomal miRNAs was stable after treatment with RNase A, prolonged incubation, or repeated freezing and thawing. CONCLUSIONS The two plasma exosomal miRNAs (miR-6774-3p and miR-6879-5p) and their combination could serve as new promising biomarkers for the diagnosis of LNM in PTC patients.
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Affiliation(s)
- Wenjie Chen
- Thyroid Surgery Center, West China Hospital of Sichuan University, Chengdu, 610041, China
- Laboratory of Thyroid and Parathyroid Disease, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Genpeng Li
- Thyroid Surgery Center, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Zhihui Li
- Thyroid Surgery Center, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Jingqiang Zhu
- Thyroid Surgery Center, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Tao Wei
- Thyroid Surgery Center, West China Hospital of Sichuan University, Chengdu, 610041, China
| | - Jianyong Lei
- Thyroid Surgery Center, West China Hospital of Sichuan University, Chengdu, 610041, China.
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8
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Factors influencing circulating microRNAs as biomarkers for liver diseases. Mol Biol Rep 2022; 49:4999-5016. [DOI: 10.1007/s11033-022-07170-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 01/19/2022] [Indexed: 11/09/2022]
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9
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Ragni E, Perucca Orfei C, Viganò M, Valli F, de Girolamo L. Endogenous Controls for the Evaluation of Osteoarthritis-Related miRNAs in Extracellular Vesicles from Bone-Marrow-Derived Mesenchymal Stromal Cells and the Impact of Osteoarthritis Synovial Fluid. Biomolecules 2022; 12:biom12020316. [PMID: 35204816 PMCID: PMC8869367 DOI: 10.3390/biom12020316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 11/16/2022] Open
Abstract
Bone-marrow-derived stromal cells (BMSCs) have emerged as promising therapeutic option for the treatment of osteoarthritis (OA) due to their tissue regenerative and anti-inflammatory features. BMSCs’ clinical potential is mainly ascribed to their released factors and extracellular vesicles (EVs), whose therapeutic portfolio may be modulated by the environment in vivo or specific priming in vitro. Within the array of molecules shaping EVs’ power, miRNAs are considered privileged players. In this frame, a correct EV-miRNA detection and quantification is mandatory to understand and possibly boost BMSCs potential, either when envisioned as cell therapeutics or when proposed as producer of cell-free and clinical grade EVs. The aim of this study is to identify reliable reference genes (RGs) to study miRNAs in BMSC-EVs cultivated under standard or OA synovial fluid (OA-SF). miR-23a-3p and miR-221-3p emerged as the best candidates, respectively. Moreover, when both conditions were analyzed together, miR-24-3p resulted the most stable RGs, allowing for a sharper comparison of EVs content, further validated on the OA-related miRNA-193b-5p. The different RG stability ranking depending on the culturing conditions, as well as its divergence with respect to adipose (ASCs) and amniotic (hAMSCs) MSCs, confirm that miRNA RG selection in EVs is a mandatory step and that the identification of the most reliable candidate is greatly depending on the cell type and culturing/environmental conditions.
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Affiliation(s)
- Enrico Ragni
- Laboratorio di Biotecnologie Applicate all’Ortopedia, IRCCS Istituto Ortopedico Galeazzi, Via R. Galeazzi 4, I-20161 Milan, Italy; (E.R.); (C.P.O.); (M.V.)
| | - Carlotta Perucca Orfei
- Laboratorio di Biotecnologie Applicate all’Ortopedia, IRCCS Istituto Ortopedico Galeazzi, Via R. Galeazzi 4, I-20161 Milan, Italy; (E.R.); (C.P.O.); (M.V.)
| | - Marco Viganò
- Laboratorio di Biotecnologie Applicate all’Ortopedia, IRCCS Istituto Ortopedico Galeazzi, Via R. Galeazzi 4, I-20161 Milan, Italy; (E.R.); (C.P.O.); (M.V.)
| | - Federico Valli
- Chirurgia Articolare Sostitutiva e Chirurgia Ortopedica (CASCO), IRCCS Istituto Ortopedico Galeazzi, Via R. Galeazzi 4, I-20161 Milan, Italy;
| | - Laura de Girolamo
- Laboratorio di Biotecnologie Applicate all’Ortopedia, IRCCS Istituto Ortopedico Galeazzi, Via R. Galeazzi 4, I-20161 Milan, Italy; (E.R.); (C.P.O.); (M.V.)
- Correspondence: ; Tel.: +39-02-66214059
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XU L, SONG JD. Crocin reversed the antitumor effects through up-regulation of MicroRNA-181a in cervical cancer cells. FOOD SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1590/fst.09422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Lina XU
- The Affiliated Hospital of Inner Mongolia Medical University, China
| | - Jian-Dong SONG
- The Affiliated Hospital of Inner Mongolia Medical University, China
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11
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Cukovic D, Bagla S, Ukasik D, Stemmer PM, Jena BP, Naik AR, Sood S, Asano E, Luat A, Chugani DC, Dombkowski AA. Exosomes in Epilepsy of Tuberous Sclerosis Complex: Carriers of Pro-Inflammatory MicroRNAs. Noncoding RNA 2021; 7:ncrna7030040. [PMID: 34287356 PMCID: PMC8293460 DOI: 10.3390/ncrna7030040] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/30/2021] [Accepted: 07/03/2021] [Indexed: 01/14/2023] Open
Abstract
Exosomes are a class of small, secreted extracellular vesicles (EV) that have recently gained considerable attention for their role in normal cellular function, disease processes and potential as biomarkers. Exosomes serve as intercellular messengers and carry molecular cargo that can alter gene expression and the phenotype of recipient cells. Here, we investigated alterations of microRNA cargo in exosomes secreted by epileptogenic tissue in tuberous sclerosis complex (TSC), a multi-system genetic disorder that includes brain lesions known as tubers. Approximately 90% of TSC patients suffer from seizures that originate from tubers, and ~60% are resistant to antiseizure drugs. It is unknown why some tubers cause seizures while others do not, and the molecular basis of drug-resistant epilepsy is not well understood. It is believed that neuroinflammation is involved, and characterization of this mechanism may be key to disrupting the "vicious cycle" between seizures, neuroinflammation, and increased seizure susceptibility. We isolated exosomes from epileptogenic and non-epileptogenic TSC tubers, and we identified differences in their microRNA cargo using small RNA-seq. We identified 12 microRNAs (including miR-142-3p, miR-223-3p and miR-21-5p) that are significantly increased in epileptogenic tubers and contain nucleic acid motifs that activate toll-like receptors (TLR7/8), initiating a neuroinflammatory cascade. Exosomes from epileptogenic tissue caused induction of key pathways in cultured cells, including innate immune signaling (TLR), inflammatory response and key signaling nodes SQSTM1 (p62) and CDKN1A (p21). Genes induced in vitro were also significantly upregulated in epileptogenic tissue. These results provide new evidence on the role of exosomes and non-coding RNA cargo in the neuroinflammatory cascade of epilepsy and may help advance the development of novel biomarkers and therapeutic approaches for the treatment of drug-resistant epilepsy.
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Affiliation(s)
- Daniela Cukovic
- Department of Pediatrics, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (D.C.); (S.B.); (E.A.)
| | - Shruti Bagla
- Department of Pediatrics, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (D.C.); (S.B.); (E.A.)
| | - Dylan Ukasik
- Translational Neurosciences Program, Wayne State University, Detroit, MI 48201, USA;
| | - Paul M. Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201, USA;
| | - Bhanu P. Jena
- Department of Physiology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (B.P.J.); (A.R.N.)
| | - Akshata R. Naik
- Department of Physiology, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (B.P.J.); (A.R.N.)
| | - Sandeep Sood
- Department of Neurosurgery, School of Medicine, Wayne State University, Detroit, MI 48201, USA;
| | - Eishi Asano
- Department of Pediatrics, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (D.C.); (S.B.); (E.A.)
- Translational Neurosciences Program, Wayne State University, Detroit, MI 48201, USA;
- Department of Neurology, School of Medicine, Wayne State University, Detroit, MI 48201, USA;
| | - Aimee Luat
- Department of Neurology, School of Medicine, Wayne State University, Detroit, MI 48201, USA;
- Department of Pediatrics, Central Michigan University, Mt Pleasant, MI 48858, USA
| | - Diane C. Chugani
- Departments of Communication Sciences and Disorders, and Chemistry and Biochemistry, University of Delaware, Newark, DE 19713, USA;
| | - Alan A. Dombkowski
- Department of Pediatrics, School of Medicine, Wayne State University, Detroit, MI 48201, USA; (D.C.); (S.B.); (E.A.)
- Translational Neurosciences Program, Wayne State University, Detroit, MI 48201, USA;
- Correspondence: ; Tel.: +1-(313)-745-6381
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12
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Garcia A, Dunoyer-Geindre S, Fontana P. Do miRNAs Have a Role in Platelet Function Regulation? Hamostaseologie 2021; 41:217-224. [PMID: 34192780 DOI: 10.1055/a-1478-2105] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of non-coding RNAs known to repress mRNA translation and subsequent protein production. miRNAs are predicted to modulate many targets and are involved in regulating various cellular processes. Identifying their role in cell function regulation may allow circulating miRNAs to be used as diagnostic or prognostic markers of various diseases. Increasing numbers of clinical studies have shown associations between circulating miRNA levels and platelet reactivity or the recurrence of cardiovascular events. However, these studies differed regarding population selection, sample types used, miRNA quantification procedures, and platelet function assays. Furthermore, they often lacked functional validation of the miRNA identified in such studies. The latter step is essential to identifying causal relationships and understanding if and how miRNAs regulate platelet function. This review describes recent advances in translational research dedicated to identifying miRNAs' roles in platelet function regulation.
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Affiliation(s)
- A Garcia
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - P Fontana
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Division of Angiology and Haemostasis, Geneva University Hospitals, Geneva, Switzerland
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miREV: An Online Database and Tool to Uncover Potential Reference RNAs and Biomarkers in Small-RNA Sequencing Data Sets from Extracellular Vesicles Enriched Samples. J Mol Biol 2021; 433:167070. [PMID: 34052284 DOI: 10.1016/j.jmb.2021.167070] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 05/11/2021] [Accepted: 05/22/2021] [Indexed: 02/06/2023]
Abstract
Extracellular vesicles (EVs) are nano-sized, membrane-enclosed vesicles released by cells for intercellular communication. EVs are involved in pathological processes and miRNAs in EVs have gained interest as easily accessible biomolecules in liquid biopsies for diagnostic purposes. To validate potential miRNA biomarker, transcriptome analyses must be carried out to detect suitable reference miRNAs. miREV is a database with over 400 miRNA sequencing data sets and helps the researcher to find suitable reference miRNAs for their individual experimental setup. The researcher can put together a specific sample set in miREV, which is similar to his own experimental concept in order to find the most suitable references. This allows to run validation experiments without having to carry out a complex and costly transcriptome analysis priorly. Additional read count tables of each generated sample set are downloadable for further analysis. miREV is freely available at https://www.physio.wzw.tum.de/mirev/.
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14
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Garcia A, Dunoyer-Geindre S, Fish RJ, Neerman-Arbez M, Reny JL, Fontana P. Methods to Investigate miRNA Function: Focus on Platelet Reactivity. Thromb Haemost 2021; 121:409-421. [PMID: 33124028 PMCID: PMC8263142 DOI: 10.1055/s-0040-1718730] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/08/2020] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs modulating protein production. They are key players in regulation of cell function and are considered as biomarkers in several diseases. The identification of the proteins they regulate, and their impact on cell physiology, may delineate their role as diagnostic or prognostic markers and identify new therapeutic strategies. During the last 3 decades, development of a large panel of techniques has given rise to multiple models dedicated to the study of miRNAs. Since plasma samples are easily accessible, circulating miRNAs can be studied in clinical trials. To quantify miRNAs in numerous plasma samples, the choice of extraction and purification techniques, as well as normalization procedures, are important for comparisons of miRNA levels in populations and over time. Recent advances in bioinformatics provide tools to identify putative miRNAs targets that can then be validated with dedicated assays. In vitro and in vivo approaches aim to functionally validate candidate miRNAs from correlations and to understand their impact on cellular processes. This review describes the advantages and pitfalls of the available techniques for translational research to study miRNAs with a focus on their role in regulating platelet reactivity.
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Affiliation(s)
- Alix Garcia
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - Richard J. Fish
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Marguerite Neerman-Arbez
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
- iGE3, Institute of Genetics and Genomics in Geneva, Geneva, Switzerland
| | - Jean-Luc Reny
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of General Internal Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Pierre Fontana
- Geneva Platelet Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Division of Angiology and Haemostasis, Geneva University Hospitals, Geneva, Switzerland
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15
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Zivko C, Fuhrmann G, Luciani P. Liver-derived extracellular vesicles: A cell by cell overview to isolation and characterization practices. Biochim Biophys Acta Gen Subj 2021; 1865:129559. [DOI: 10.1016/j.bbagen.2020.129559] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/16/2020] [Accepted: 02/11/2020] [Indexed: 02/08/2023]
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16
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Ragni E, Colombini A, De Luca P, Libonati F, Viganò M, Perucca Orfei C, Zagra L, de Girolamo L. miR-103a-3p and miR-22-5p Are Reliable Reference Genes in Extracellular Vesicles From Cartilage, Adipose Tissue, and Bone Marrow Cells. Front Bioeng Biotechnol 2021; 9:632440. [PMID: 33659243 PMCID: PMC7917212 DOI: 10.3389/fbioe.2021.632440] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/18/2021] [Indexed: 12/14/2022] Open
Abstract
Cartilage cells (CCs), adipose tissue (ASC)- and bone marrow (BMSC)-derived mesenchymal stromal cells (MSCs) have been shown as promising candidates for the treatment of osteoarthritis (OA). Despite their adaptive ability, exposure to chronic catabolic and inflammatory processes can limit their survival and healing potential. An attractive cell-free alternative or complementary strategy is represented by their secreted extracellular vesicles (EVs), having homeostatic properties on OA chondrocytes and synovial cells. In view of clinical translation, a thorough characterization of the shuttled therapeutic molecules, like miRNAs, is greatly needed to fingerprint and develop the most effective EV formulation for OA treatment. To date, a crucial pitfall is given by the lack of EV-miRNA-associated reference genes (RGs) for the reliable quantification and comparison among different therapeutic EV-based therapeutic products. In this study, the stability of 12 putative miRNA RGs (let-7a-5p, miR-16-5p, miR-22-5p, miR-23a-3p, miR-26a-5p, miR-29a-5p, miR-101-3p, miR-103a-3p, miR-221-3p, miR-423-5p, miR-425-5p and miR-660-5p), already proposed by literature in EV products from alternative sources, was assessed in EVs isolated from three donor-matched ASCs, BMSCs, and CCs through geNorm, NormFinder, BestKeeper, and ΔCt algorithms and the geometric mean of rankings. ASC-EVs and BMSC-EVs shared more similar molecular signatures than cartilage-derived EVs, although overall miR-103a-3p consistently ranked as the first and miR-22-5p as the second most stable EV-miRNA RG, whereas miR-221-3p behaved poorly. Further, to emphasize the impact of incorrect RG choice, the abundance of four OA-therapeutic miRNAs (miR-93-5p, miR-125b-5p, miR-455-3p, and miR-27b-3p) was compared. The use of miR-221-3p led to less accurate EV fingerprinting and, when applied to sift therapeutic potency prediction, to misleading indication of the most appropriate clinical product. In conclusion, miR-103a-3p and miR-22-5p will represent reliable RGs for the quantification of miRNAs embedded in MSC- and CC-EVs, a mandatory step for the molecular definition and comparison of the clinical potency of these innovative cell-free-based therapeutic products for OA in particular, as well as for a wider array of regenerative-medicine-based approaches.
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Affiliation(s)
- Enrico Ragni
- IRCCS Istituto Ortopedico Galeazzi, Laboratorio di Biotecnologie Applicate all'Ortopedia, Milan, Italy
| | - Alessandra Colombini
- IRCCS Istituto Ortopedico Galeazzi, Laboratorio di Biotecnologie Applicate all'Ortopedia, Milan, Italy
| | - Paola De Luca
- IRCCS Istituto Ortopedico Galeazzi, Laboratorio di Biotecnologie Applicate all'Ortopedia, Milan, Italy
| | - Francesca Libonati
- IRCCS Istituto Ortopedico Galeazzi, Laboratorio di Biotecnologie Applicate all'Ortopedia, Milan, Italy
| | - Marco Viganò
- IRCCS Istituto Ortopedico Galeazzi, Laboratorio di Biotecnologie Applicate all'Ortopedia, Milan, Italy
| | - Carlotta Perucca Orfei
- IRCCS Istituto Ortopedico Galeazzi, Laboratorio di Biotecnologie Applicate all'Ortopedia, Milan, Italy
| | - Luigi Zagra
- IRCCS Istituto Ortopedico Galeazzi, Hip Department, Milan, Italy
| | - Laura de Girolamo
- IRCCS Istituto Ortopedico Galeazzi, Laboratorio di Biotecnologie Applicate all'Ortopedia, Milan, Italy
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17
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Dai Y, Cao Y, Köhler J, Lu A, Xu S, Wang H. Unbiased RNA-Seq-driven identification and validation of reference genes for quantitative RT-PCR analyses of pooled cancer exosomes. BMC Genomics 2021; 22:27. [PMID: 33407103 PMCID: PMC7789813 DOI: 10.1186/s12864-020-07318-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 12/09/2020] [Indexed: 01/08/2023] Open
Abstract
Background Exosomes are extracellular vesicles (EVs) derived from endocytic compartments of eukaryotic cells which contain various biomolecules like mRNAs or miRNAs. Exosomes influence the biologic behaviour and progression of malignancies and are promising candidates as non-invasive diagnostic biomarkers or as targets for therapeutic interventions. Usually, quantitative real-time polymerase chain reaction (qRT-PCR) is used to assess gene expression in cancer exosomes, however, the ideal reference genes for normalization yet remain to be identified. Results In this study, we performed an unbiased analysis of high-throughput mRNA and miRNA-sequencing data from exosomes of patients with various cancer types and identify candidate reference genes and miRNAs in cancer exosomes. The expression stability of these candidate reference genes was evaluated by the coefficient of variation “CV” and the average expression stability value “M”. We subsequently validated these candidate reference genes in exosomes from an independent cohort of ovarian cancer patients and healthy control individuals by qRT-PCR. Conclusions Our study identifies OAZ1 and hsa-miR-6835-3p as the most reliable individual reference genes for mRNA and miRNA quantification, respectively. For superior accuracy, we recommend the use of a combination of reference genes - OAZ1/SERF2/MPP1 for mRNA and hsa-miR-6835-3p/hsa-miR-4468-3p for miRNA analyses.
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Affiliation(s)
- Yao Dai
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Yumeng Cao
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jens Köhler
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Aiping Lu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Shaohua Xu
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Haiyun Wang
- Department of Gynecology, Shanghai First Maternity and Infant Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
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Yang L, Wei C, Li Y, He X, He M. miR-224 is an early-stage biomarker of hepatocellular carcinoma with miR-224 and miR-125b as prognostic biomarkers. Biomark Med 2020; 14:1485-1500. [PMID: 33155836 DOI: 10.2217/bmm-2020-0099] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Aim: The aim was to systematically investigate the miRNA biomarkers for early diagnosis of hepatocellular carcinoma (HCC). Materials & methods: A systematic review and meta-analysis of miRNA expression in HCC were performed. Results: A total of 4903 cases from 30 original studies were comprehensively analyzed. The sensitivity and specificity of miR-224 in discriminating early-stage HCC patients from benign lesion patients were 0.868 and 0.792, which were superior to α-fetoprotein. Combined miR-224 with α-fetoprotein, the sensitivity and specificity were increased to 0.882 and 0.808. Prognostic survival analysis showed low expression of miR-125b and high expression of miR-224 were associated with poor prognosis. Conclusion: miR-224 had a prominent diagnostic efficiency in early-stage HCC, with miR-224 and miR-125b being valuable in the prognostic diagnosis.
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Affiliation(s)
- Lichao Yang
- School of Public Health, Guangxi Medical University, Nanning 530021, China
| | - Chunmeng Wei
- Nanning Municipal Center for Disease Control & Prevention, Nanning 530021, China
| | - Yasi Li
- College of Global Public Health, New York University, NY 10003, USA
| | - Xiao He
- School of Public Health, Guilin Medical School, Guilin 541100, China
| | - Min He
- School of Public Health, Guangxi Medical University, Nanning 530021, China.,Key Laboratory of High-Incidence Tumor Prevention & Treatment (Guangxi Medical University), Ministry of Education, Nanning 530021, China.,Laboratory Animal Center, Guangxi Medical University, Nanning 530021, China
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19
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Narita M, Nishida H, Asahina R, Nakata K, Yano H, Dickinson PJ, Tanaka T, Akiyoshi H, Maeda S, Kamishina H. Expression of microRNAs in plasma and in extracellular vesicles derived from plasma for dogs with glioma and dogs with other brain diseases. Am J Vet Res 2020; 81:355-360. [PMID: 32228257 DOI: 10.2460/ajvr.81.4.355] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To measure expression of microRNAs (miRNAs) in plasma and in extracellular vesicles (EVs) derived from plasma for dogs with glioma and dogs with other brain diseases. SAMPLE Plasma samples from 11 dogs with glioma and 19 control dogs with various other brain diseases. PROCEDURES EVs were isolated from plasma samples by means of ultracentrifugation. Expression of 4 candidate reference miRNAs (let-7a, miR-16, miR-26a, and miR-103) and 4 candidate target miRNAs (miR-15b, miR-21, miR-155, and miR-342-3p) was quantified with reverse transcription PCR assays. Three software programs were used to select the most suitable reference miRNAs from among the 4 candidate reference miRNAs. Expression of the 4 target miRNAs was then calculated relative to expression of the reference genes in plasma and EVs, and relative expression was compared between dogs with glioma and control dogs with other brain diseases. RESULTS The most suitable reference miRNAs were miR-16 for plasma and let-7a for EVs. Relative expression of miR-15b in plasma and in EVs was significantly higher in dogs with glioma than in control dogs. Relative expression of miR-342-3p in EVs was significantly higher in dogs with glioma than in control dogs. CONCLUSIONS AND CLINICAL RELEVANCE Results suggested that miR-15b and miR-342-3p have potential as noninvasive biomarkers for differentiating glioma from other intracranial diseases in dogs. However, more extensive analysis of expression in specific glioma subtypes and grades, compared with expression in more defined control populations, will be necessary to assess their clinical relevance.
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20
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Cai P, Mu Y, Olveda RM, Ross AG, Olveda DU, McManus DP. Serum Exosomal miRNAs for Grading Hepatic Fibrosis Due to Schistosomiasis. Int J Mol Sci 2020; 21:ijms21103560. [PMID: 32443549 PMCID: PMC7278994 DOI: 10.3390/ijms21103560] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/11/2020] [Accepted: 05/14/2020] [Indexed: 02/07/2023] Open
Abstract
Chronic infection with Schistosoma japonicum or Schistosoma mansoni results in hepatic fibrosis of the human host. The staging of fibrosis is crucial for prognosis and to determine the need for treatment of patients with schistosomiasis. This study aimed to determine whether there is a correlation between the levels of serum exosomal micro-ribonucleic acids (miRNAs) (exomiRs) and fibrosis progression in schistosomiasis. Reference gene (RG) validation was initially carried out for the analysis of serum exomiRs expression in staging liver fibrosis caused by schistosome infection. The expression levels of liver fibrosis-associated exomiRs in serum were determined in a murine schistosomiasis model and in a cohort of Filipino schistosomiasis japonica patients (n = 104) with different liver fibrosis grades. Of twelve RG candidates validated, miR-103a-3p and miR-425-5p were determined to be the most stable genes in the murine schistosomiasis model and subjects from the schistosomiasis-endemic area, respectively. The temporal expression profiles of nine fibrosis-associated serum exomiRs, as well as their correlations with the liver pathologies, were determined in C57BL/6 mice during S. japonicum infection. The serum levels of three exomiRs (miR-92a-3p, miR-146a-5p and miR-532-5p) were able to distinguish subjects with fibrosis grades I-III from those with no fibrosis, but only the serum level of exosomal miR-146a-5p showed potential for distinguishing patients with mild (grades 0–I) versus severe fibrosis (grades II–III). The current data imply that serum exomiRs can be a supplementary tool for grading liver fibrosis in hepatosplenic schistosomiasis with moderate accuracy.
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Affiliation(s)
- Pengfei Cai
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane 4006, Australia;
- Correspondence: (P.C.); (D.P.M.); Tel.: +61-7-3362-0406 (P.C.); +61-7-3362-0401 (D.P.M.)
| | - Yi Mu
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane 4006, Australia;
| | - Remigio M. Olveda
- Department of Health, Research Institute for Tropical Medicine, Manila 1781, Philippines;
| | - Allen G. Ross
- Menzies Health Institute Queensland, Griffith University, Gold Coast 4222, Australia; (A.G.R.); (D.U.O.)
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka 1212, Bangladesh
| | - David U. Olveda
- Menzies Health Institute Queensland, Griffith University, Gold Coast 4222, Australia; (A.G.R.); (D.U.O.)
| | - Donald P. McManus
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane 4006, Australia;
- Correspondence: (P.C.); (D.P.M.); Tel.: +61-7-3362-0406 (P.C.); +61-7-3362-0401 (D.P.M.)
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21
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miRNA Reference Genes in Extracellular Vesicles Released from Amniotic Membrane-Derived Mesenchymal Stromal Cells. Pharmaceutics 2020; 12:pharmaceutics12040347. [PMID: 32290510 PMCID: PMC7238137 DOI: 10.3390/pharmaceutics12040347] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 12/17/2022] Open
Abstract
Human amniotic membrane and amniotic membrane-derived mesenchymal stromal cells (hAMSCs) have produced promising results in regenerative medicine, especially for the treatment of inflammatory-based diseases and for different injuries including those in the orthopedic field such as tendon disorders. hAMSCs have been proposed to exert their anti-inflammatory and healing potential via secreted factors, both free and conveyed within extracellular vesicles (EVs). In particular, EV miRNAs are considered privileged players due to their impact on target cells and tissues, and their future use as therapeutic molecules is being intensely investigated. In this view, EV-miRNA quantification in either research or future clinical products has emerged as a crucial paradigm, although, to date, largely unsolved due to lack of reliable reference genes (RGs). In this study, a panel of thirteen putative miRNA RGs (let-7a-5p, miR-16-5p, miR-22-5p, miR-23a-3p, miR-26a-5p, miR-29a-5p, miR-101-3p, miR-103a-3p, miR-221-3p, miR-423-5p, miR-425-5p, miR-660-5p and U6 snRNA) that were identified in different EV types was assessed in hAMSC-EVs. A validated experimental pipeline was followed, sifting the output of four largely accepted algorithms for RG prediction (geNorm, NormFinder, BestKeeper and ΔCt method). Out of nine RGs constitutively expressed across all EV isolates, miR-101-3p and miR-22-5p resulted in the most stable RGs, whereas miR-423-5p and U6 snRNA performed poorly. miR-22-5p was also previously reported to be a reliable RG in adipose-derived MSC-EVs, suggesting its suitability across samples isolated from different MSC types. Further, to shed light on the impact of incorrect RG choice, the level of five tendon-related miRNAs (miR-29a-3p, miR-135a-5p, miR-146a-5p, miR-337-3p, let-7d-5p) was compared among hAMSC-EVs isolates. The use of miR-423-5p and U6 snRNA did not allow a correct quantification of miRNA incorporation in EVs, leading to less accurate fingerprinting and, if used for potency prediction, misleading indication of the most appropriate clinical batch. These results emphasize the crucial importance of RG choice for EV-miRNAs in hAMSCs studies and contribute to the identification of reliable RGs such as miR-101-3p and miR-22-5p to be validated in other MSC-EVs related fields.
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Specific circulating microRNAs during hepatitis E infection can serve as indicator for chronic hepatitis E. Sci Rep 2020; 10:5337. [PMID: 32210284 PMCID: PMC7093451 DOI: 10.1038/s41598-020-62159-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 03/10/2020] [Indexed: 12/20/2022] Open
Abstract
Hepatitis E virus (HEV) genotypes 3 and 4 (HEV-3, HEV-4) infections are an emerging public health issue in industrialized countries. HEV-3 and −4 are usually self-limiting but can progress to chronic hepatitis E in immunocompromised individuals. The molecular mechanisms involved in persistent infections are poorly understood. Micro RNAs (miRNAs) can regulate viral pathogenesis and can serve as novel disease biomarkers. We aimed to explore the modulation of serum miRNAs in patients with acute (AHE) and chronic (CHE) hepatitis E. Both AHE- and CHE-patients exhibited high viral loads (median 3.23E + 05 IU/mL and 2.11E + 06 IU/mL, respectively) with HEV-3c being the predominant HEV-genotype. Expression analysis of liver-specific serum miRNAs was performed using real-time PCR. miR-99a-5p, miR-122-5p, and miR-125b-5p were upregulated in AHE (4.70–5.28 fold) and CHE patients (2.28–6.34 fold), compared to HEV-negative controls. Notably, miR-192-5p was increased 2.57 fold while miR-125b-5p was decreased 0.35 fold in CHE but not in AHE patients. Furthermore, decreased miR-122-5p expression significantly correlates with reduced liver transaminases in CHE patients. To our knowledge, this marks the first investigation concerning the regulation of circulating liver-specific miRNAs in acute and chronic HEV infections. We found that miR-125b-5p, miR-192-5p, and miR-99a-5p may prove useful in the diagnosis of chronic hepatitis E.
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Pagacz K, Kucharski P, Smyczynska U, Grabia S, Chowdhury D, Fendler W. A systemic approach to screening high-throughput RT-qPCR data for a suitable set of reference circulating miRNAs. BMC Genomics 2020; 21:111. [PMID: 32005151 PMCID: PMC6995162 DOI: 10.1186/s12864-020-6530-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 01/22/2020] [Indexed: 12/12/2022] Open
Abstract
Background The consensus on how to choose a reference gene for serum or plasma miRNA expression qPCR studies has not been reached and none of the potential candidates have yet been convincingly validated. We proposed a new in silico approach of finding a suitable reference for human, circulating miRNAs and identified a new set of endogenous reference miRNA based on miRNA profiling experiments from Gene Expression Omnibus. We used 3 known normalization algorithms (NormFinder, BestKeeper, GeNorm) to calculate a new normalization score. We searched for a universal set of endogenous miRNAs and validated our findings on 2 new datasets using our approach. Results We discovered and validated a set of 13 miRNAs (miR-222, miR-92a, miR-27a, miR-17, miR-24, miR-320a, miR-25, miR-126, miR-19b, miR-199a-3p, miR-30b, miR-30c, miR-374a) that can be used to create a reliable reference combination of 3 miRNAs. We showed that on average the mean of 3 miRNAs (p = 0.0002) and 2 miRNAs (p = 0.0031) were a better reference than single miRNA. The arithmetic means of 3 miRNAs: miR-24, miR-222 and miR-27a was shown to be the most stable combination of 3 miRNAs in validation sets. Conclusions No single miRNA was suitable as a universal reference in serum miRNA qPCR profiling, but it was possible to designate a set of miRNAs, which consistently contributed to most stable combinations.
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Affiliation(s)
- Konrad Pagacz
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, Lodz, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Przemyslaw Kucharski
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, Lodz, Poland.,Institute of Applied Computer Science, Lodz University of Technology, Lodz, Poland
| | - Urszula Smyczynska
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, Lodz, Poland
| | - Szymon Grabia
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, Lodz, Poland.,Institute of Applied Computer Science, Lodz University of Technology, Lodz, Poland
| | | | - Wojciech Fendler
- Department of Biostatistics and Translational Medicine, Medical University of Lodz, Lodz, Poland. .,Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA.
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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: 71] [Impact Index Per Article: 14.2] [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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25
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Madadi S, Schwarzenbach H, Lorenzen J, Soleimani M. MicroRNA expression studies: challenge of selecting reliable reference controls for data normalization. Cell Mol Life Sci 2019; 76:3497-3514. [PMID: 31089747 PMCID: PMC11105490 DOI: 10.1007/s00018-019-03136-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 04/13/2019] [Accepted: 05/06/2019] [Indexed: 02/06/2023]
Abstract
Accurate determination of microRNA expression levels is a prerequisite in using these small non-coding RNA molecules as novel biomarkers in disease diagnosis and prognosis. Quantitative PCR is the method of choice for measuring the expression levels of microRNAs. However, a major obstacle that affects the reliability of results is the lack of validated reference controls for data normalization. Various non-coding RNAs have previously been used as reference controls, but their use may lead to variations and lack of comparability of microRNA data among the studies. Despite the growing number of studies investigating microRNA profiles to discriminate between healthy and disease stages, robust reference controls for data normalization have so far not been established. In the present article, we provide an overview of different reference controls used in various diseases, and highlight the urgent need for the identification of suitable reference controls to produce reliable data. Our analysis shows, among others, that RNU6 is not an ideal normalizer in studies using patient material from different diseases. Finally, our article tries to disclose the challenges to find a reference control which is uniformly and stably expressed across all body tissues, fluids, and diseases.
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Affiliation(s)
- Soheil Madadi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Heidi Schwarzenbach
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Johan Lorenzen
- Department of Nephrology, University Hospital Zürich, Zurich, Switzerland
| | - Meysam Soleimani
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Hamadan University of Medical Sciences, Hamadan, Iran.
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Narita M, Nishida H, Asahina R, Nakata K, Yano H, Ueda T, Inden M, Akiyoshi H, Maeda S, Kamishina H. Identification of reference genes for microRNAs of extracellular vesicles isolated from plasma samples of healthy dogs by ultracentrifugation, precipitation, and membrane affinity chromatography methods. Am J Vet Res 2019; 80:449-454. [PMID: 31034274 DOI: 10.2460/ajvr.80.5.449] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To compare ultracentrifugation, precipitation, and membrane affinity chromatography methods for isolation of extracellular vesicles (EVs) from canine plasma samples and to identify suitable reference genes for incorporation into a quantitative reverse transcription PCR assay of microRNA expression in plasma EVs of healthy dogs. ANIMALS 6 healthy Beagles. PROCEDURES Plasma samples were obtained from each dog, and EVs were isolated from 0.3 mL of these samples via ultracentrifugation, precipitation, and membrane-affinity chromatographic methods. Nanoparticle tracking analysis was performed to determine the concentration and size distribution of EVs isolated by the ultracentrifugation method. Expression levels (cycle threshold values) of 4 microRNAs (let-7a, miR-16, miR-26a, and miR-103) were then compared by means of quantitative reverse transcription PCR assay. Three statistical programs were used to identify the microRNAs most suitable for use as reference genes. RESULTS Results indicated that ultracentrifugation was the most stable of all 3 methods for isolating microRNAs from 0.3 mL of plasma. Nanoparticle tracking revealed that EV samples obtained by the ultracentrifugation method contained a mean ± SD of approximately 1.59 × 1010 vesicles/mL ± 4.2 × 108 vesicles/mL. Of the 4 microRNAs in plasma EVs isolated by ultracentrifugation, miR-103 was the most stable. CONCLUSIONS AND CLINICAL RELEVANCE The ultracentrifugation method has potential as a stable method for isolating EVs from canine plasma samples with a high recovery rate, and miR-103 may provide the most stable reference gene for normalizing microRNA expression data pertaining to plasma EVs isolated by ultracentrifugation.
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miR-22-5p and miR-29a-5p Are Reliable Reference Genes for Analyzing Extracellular Vesicle-Associated miRNAs in Adipose-Derived Mesenchymal Stem Cells and Are Stable under Inflammatory Priming Mimicking Osteoarthritis Condition. Stem Cell Rev Rep 2019; 15:743-754. [DOI: 10.1007/s12015-019-09899-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Ragni E, De Luca P, Perucca Orfei C, Colombini A, Viganò M, Lugano G, Bollati V, de Girolamo L. Insights into Inflammatory Priming of Adipose-Derived Mesenchymal Stem Cells: Validation of Extracellular Vesicles-Embedded miRNA Reference Genes as A Crucial Step for Donor Selection. Cells 2019; 8:cells8040369. [PMID: 31018576 PMCID: PMC6523846 DOI: 10.3390/cells8040369] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 04/19/2019] [Accepted: 04/21/2019] [Indexed: 12/22/2022] Open
Abstract
Mesenchymal stem cells (MSCs) are promising tools for cell-based therapies due to their homing to injury sites, where they secrete bioactive factors such as cytokines, lipids, and nucleic acids, either free or conveyed within extracellular vesicles (EVs). Depending on the local environment, MSCs’ therapeutic value may be modulated, determining their fate and cell behavior. Inflammatory signals may induce critical changes on both the phenotype and secretory portfolio. Intriguingly, in animal models resembling joint diseases as osteoarthritis (OA), inflammatory priming enhanced the healing capacity of MSC-derived EVs. In this work, we selected miRNA reference genes (RGs) from the literature (let-7a-5p, miR-16-5p, miR-23a-3p, miR-26a-5p, miR-101-3p, miR-103a-3p, miR-221-3p, miR-423-5p, miR-425-5p, U6 snRNA), using EVs isolated from adipose-derived MSCs (ASCs) primed with IFNγ (iASCs). geNorm, NormFinder, BestKeeper, and ΔCt methods identified miR-26a-5p/16-5p as the most stable, while miR-103a-rp/425-5p performed poorly. Our results were validated on miRNAs involved in OA cartilage trophism. Only a proper normalization strategy reliably identified the differences between donors, a critical factor to empower the therapeutic value of future off-the-shelf MSC-EV isolates. In conclusion, the proposed pipeline increases the accuracy of MSC-EVs embedded miRNAs assessment, and help predicting donor variability for precision medicine approaches.
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Affiliation(s)
- Enrico Ragni
- IRCCS Istituto Ortopedico Galeazzi, Laboratorio di Biotecnologie Applicate all'Ortopedia, I-20161 Milan, Italy.
| | - Paola De Luca
- IRCCS Istituto Ortopedico Galeazzi, Laboratorio di Biotecnologie Applicate all'Ortopedia, I-20161 Milan, Italy.
| | - Carlotta Perucca Orfei
- IRCCS Istituto Ortopedico Galeazzi, Laboratorio di Biotecnologie Applicate all'Ortopedia, I-20161 Milan, Italy.
| | - Alessandra Colombini
- IRCCS Istituto Ortopedico Galeazzi, Laboratorio di Biotecnologie Applicate all'Ortopedia, I-20161 Milan, Italy.
| | - Marco Viganò
- IRCCS Istituto Ortopedico Galeazzi, Laboratorio di Biotecnologie Applicate all'Ortopedia, I-20161 Milan, Italy.
| | - Gaia Lugano
- IRCCS Istituto Ortopedico Galeazzi, Laboratorio di Biotecnologie Applicate all'Ortopedia, I-20161 Milan, Italy.
| | - Valentina Bollati
- University of Milan, EPIGET-Epidemiology, Epigenetics and Toxicology Lab, Department of Clinical Sciences and Community Health, I-20122 Milan, Italy.
| | - Laura de Girolamo
- IRCCS Istituto Ortopedico Galeazzi, Laboratorio di Biotecnologie Applicate all'Ortopedia, I-20161 Milan, Italy.
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Madadi S, Soleimani M. The crucial need of internal control validation in the normalization of circulating microRNAs. Dig Liver Dis 2019; 51:610-611. [PMID: 30824410 DOI: 10.1016/j.dld.2019.01.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 01/12/2019] [Accepted: 01/15/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Soheil Madadi
- School of Pharmacy, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Meysam Soleimani
- School of Pharmacy, Hamadan University of Medical Sciences, Hamadan, Iran.
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Identification of miRNA Reference Genes in Extracellular Vesicles from Adipose Derived Mesenchymal Stem Cells for Studying Osteoarthritis. Int J Mol Sci 2019; 20:ijms20051108. [PMID: 30841483 PMCID: PMC6429322 DOI: 10.3390/ijms20051108] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 02/27/2019] [Accepted: 02/28/2019] [Indexed: 02/07/2023] Open
Abstract
Osteoarthritis (OA) leads to chronic pain and disability, and traditional conservative treatments are not effective in the long term. The intra-articular injection of mesenchymal stem cells (MSCs) is considered a novel therapy for OA whose efficacy mainly relies on the adaptive release of paracrine molecules which are either soluble or extracellular vesicles (EVs) embedded. The correct quantification of EV-miRNAs using reliable reference genes (RGs) is a crucial step in optimizing this future therapeutic cell-free approach. The purpose of this study is to rate the stabilities of literature-selected proposed RGs for EV-miRNAs in adipose derived-MSCs (ASCs). EVs were isolated by ultracentrifugation from ASCs cultured with or without inflammatory priming mimicking OA synovial fluid condition. Expression of putative RGs (let-7a-5p, miR-16-5p, miR-23a-3p, miR-26a-5p, miR-101-3p, miR-103a-3p, miR-221-3p, miR-423-5p, miR-425-5p, U6 snRNA) was scored by using the algorithms geNorm, NormFinder, BestKeeper and ΔCt method. miR-16a-5p/miR-23a-3p yielded the most stable RGs, whereas let-7a-5p/miR-425-5p performed poorly. Outcomes were validated by qRT-PCR on miR-146a-5p, reported to be ASC-EVs enriched and involved in OA. Incorrect RG selection affected the evaluation of miR-146a-5p abundance and modulation by inflammation, with both values resulting strongly donor-dependent. Our findings demonstrated that an integrated approach of multiple algorithms is necessary to identify reliable, stable RGs for ASC-EVs miRNAs evaluation. A correct approach would increase the accuracy of embedded molecule assessments aimed to develop therapeutic strategies for the treatment of OA based on EVs.
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31
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The utility of serum exosomal microRNAs in hepatocellular carcinoma. Biomed Pharmacother 2019; 111:1221-1227. [PMID: 30841435 DOI: 10.1016/j.biopha.2018.12.131] [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: 09/14/2018] [Revised: 12/26/2018] [Accepted: 12/30/2018] [Indexed: 12/31/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common types of cancer worldwide and the third most common cause of cancer-associated deaths each year. Due to the invasive, fast growth and insidious onset of HCC, most patients are diagnosed at an advanced stage, reducing the effectiveness of radical surgery. Therefore, effective early detection and diagnostic methods are crucial for improving the treatment and prognosis of HCC patients. Exosomes are 40- to 100-nm-sized vesicles that are released from many cell types into the extracellular space, and extensive evidence has suggested that exosomes are involved in the occurrence and development of HCC. Recently, the presence of microRNAs (miRNAs) in exosomes has been verified. Such miRNAs can be internalized by neighboring or distant cells to subsequently regulate multiple target genes in recipient cells at the posttranscriptional level and affect the processes of cell proliferation, differentiation and apoptosis. Herein, we summarize the current knowledge about the potential utility of serum exosomal miRNAs in the diagnosis and treatment of HCC.
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32
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Pan JH, Zhou H, Zhao XX, Ding H, Li W, Qin L, Pan YL. Role of exosomes and exosomal microRNAs in hepatocellular carcinoma: Potential in diagnosis and antitumour treatments (Review). Int J Mol Med 2018; 41:1809-1816. [PMID: 29328436 PMCID: PMC5810235 DOI: 10.3892/ijmm.2018.3383] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 01/03/2018] [Indexed: 02/06/2023] Open
Abstract
Communication between hepatocellular carcinoma (HCC) cells and their environment is essential for the development and progression of HCC. Exosomes, which are microvesicles secreted by a number of cell types, are carriers of intercellular information and regulate the tumour microenvironment. Studies have demonstrated that exosomes are involved in the communication between HCC cells, endothelial cells and stem cells, and that they serve important roles in the metastasis and invasion, immune evasion and immunotherapy of HCC. In addition, the mechanism of HCC-derived exosome-mediated microRNA (miRNA) transfer is important in the environmental modulation of HCC growth and progression. As exosomes can be used for detecting and monitoring HCC, they can potentially serve as specific biomarkers for early-stage tumours and the tumour metastasis of HCC. Moreover, mesenchymal stem cell-derived exosomes can be transfected with miRNAs to inhibit HCC development. Therefore, as nucleic acid delivery vehicles, exosomes show a tremendous potential for effective treatment against HCC. In the present review, recent advances in our understanding of the source, composition and function of exosomes in HCC, and their potential value in the early diagnosis and treatment of HCC, are summarized.
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Affiliation(s)
- Jing-Hua Pan
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Hong Zhou
- Department of Gynecology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Xiao-Xu Zhao
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Hui Ding
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Wei Li
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Li Qin
- Department of Histology and Embryology, Medical School of Jinan University, Guangzhou, Guangdong 510632, P.R. China
| | - Yun-Long Pan
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong 510632, P.R. China
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33
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Extracellular vesicles: Novel mediator for cell to cell communications in liver pathogenesis. Mol Aspects Med 2017; 60:115-122. [PMID: 29122679 DOI: 10.1016/j.mam.2017.11.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 11/01/2017] [Accepted: 11/02/2017] [Indexed: 12/17/2022]
Abstract
Extracellular vesicles (EVs) are membrane derived nanometer-sized vesicles. EVs are released by normal, diseased, and transformed cells in vitro and in vivo, and carry lipids, proteins, mRNAs, non-coding RNAs, and even DNA out of cells. Transferring biological information via EVs to neighboring cells and inter-cellular communication not only maintain physiological functions, but also involve in the pathogenesis of several diseases, including cancer. The aim of this review is to discuss the emerging role of EVs in viral hepatitis, non-alcoholic or alcoholic liver disease and liver cancers. We summarize what is known about exosome biogenesis, and role in liver disease progression, and discuss the potential clinical applications of EVs as predictive biomarkers and therapeutic modalities.
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34
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Moris D, Beal EW, Chakedis J, Burkhart RA, Schmidt C, Dillhoff M, Zhang X, Theocharis S, Pawlik TM. Role of exosomes in treatment of hepatocellular carcinoma. Surg Oncol 2017; 26:219-228. [DOI: 10.1016/j.suronc.2017.04.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 04/24/2017] [Indexed: 02/07/2023]
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35
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Circulating exosomal microRNAs as prognostic biomarkers for non-small-cell lung cancer. Oncotarget 2017; 8:13048-13058. [PMID: 28055956 PMCID: PMC5355076 DOI: 10.18632/oncotarget.14369] [Citation(s) in RCA: 187] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 12/05/2016] [Indexed: 12/12/2022] Open
Abstract
Exosomal miRNAs are proposed as excellent candidate biomarkers for clinical applications. However, little is known about their potential roles as prognostic biomarkers in lung cancer. In this study, we explored the prognostic value of plasma exosomal microRNAs (miRNAs) for non-small-cell lung cancer (NSCLC). Using a quantitative polymerase chain reaction (qPCR) array panel, we analyzed 84 plasma exosomal miRNAs in 10 lung adenocarcinoma patients and 10 matched healthy controls. The qPCR array showed 30 aberrantly expressed exosomal miRNAs. Nine candidate miRNAs were selected based on differential expression and previous reports for further evaluating their prognostic roles in 196 NSCLC patients. Elevated levels of exosomal miR-23b-3p, miR-10b-5p and miR-21-5p were independently associated with poor overall survival (with hazard ratio [95% confidence interval]: 2.42 (1.45 - 4.04), P = 0.001; 2.22 (1.18 - 4.16), P = 0.013; 2.12 (1.28 - 3.49), P = 0.003, respectively). When compared to the clinical prognostic variables only model, adding the three exosomal miRNA signatures significantly improved survival predictive accuracy with an increase of time-dependent area under the receiver operating characteristic curve from 0.88 to 0.91 (P=0.015). Our results indicated that plasma exosomal miR-23b-3p, miR-10b-5p and miR-21-5p are promising non-invasive prognostic biomarkers of NSCLC.
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36
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Wang S, Wang JQ, Lv XW. Exosomal miRNAs as biomarkers in the diagnosis of liver disease. Biomark Med 2017; 11:491-501. [PMID: 28598214 DOI: 10.2217/bmm-2017-0011] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Liver disease is a primary cause of liver-related morbidity and mortality worldwide. Currently, histological examination is the gold standard for diagnosis and classification of liver disease; however, due to its several drawbacks, including the risk of complications and sampling variability, noninvasive diagnostic options are favorable. Exosomal miRNAs have recently been considered as an important source of medical biomarkers due to being widely distributed in body fluids. This review summarizes existing concepts related to the origin, mode of transportation and possible functions of exosomal miRNAs, and recent findings on the role of exosomal miRNAs in liver diseases and development of exosomal miRNA-based diagnostic biomarkers in the primary forms of liver diseases.
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Affiliation(s)
- Sheng Wang
- School of Pharmacy, Anhui Medical University, Hefei 230032, China.,Institute for Liver Disease of Anhui Medical University, Anhui Medical University, Hefei 230032, China.,The Key Laboratory of Anti-inflammatory and Immune medicines, Ministry of Education, Anhui Medical University, Hefei 230032, China
| | - Jian-Qing Wang
- Department of Pharmacology, The Second Hospital of Anhui Medical University, Hefei 230601, China
| | - Xiong-Wen Lv
- School of Pharmacy, Anhui Medical University, Hefei 230032, China.,Institute for Liver Disease of Anhui Medical University, Anhui Medical University, Hefei 230032, China.,The Key Laboratory of Anti-inflammatory and Immune medicines, Ministry of Education, Anhui Medical University, Hefei 230032, China
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37
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Occhipinti G, Giulietti M, Principato G, Piva F. The choice of endogenous controls in exosomal microRNA assessments from biofluids. Tumour Biol 2016; 37:11657-11665. [PMID: 27438704 DOI: 10.1007/s13277-016-5164-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 07/12/2016] [Indexed: 01/02/2023] Open
Abstract
The assessment of differentially expressed microRNAs in patients and healthy controls is important to identify potential tumor biomarkers. Recently, it has been shown that the microRNA levels in exosomes are more correlated with the clinical-pathological variables than vesicle-free microRNAs (miRNAs) in biofluids; therefore, there is an increasing interest in these specific evaluations. However, these measurements can be affected by experimental problems that not always are evaluated and/or by inadequate procedural choices. In particular, exosome isolation and miRNA extraction procedures are crucial to avoid contaminations, and even the choice of the most suitable purity controls is important. Moreover, a stable endogenous RNA should be used for normalization of miRNA expression obtained by reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) in order to make these measures comparable among different samples. A rushed choice of the endogenous control can bias study conclusions without revealing inconsistencies. Unfortunately, a few studies systematically identified the best normalizer for their specific experimental context. Instead, sometimes, the normalization procedures were performed in a disputable way or the normalizer choices simply based on the previous literature. Here, we reviewed the studies where the exosomal miRNA profiling was assessed in human biofluids to point out the adopted procedures and the specific endogenous controls chosen for normalization.
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Affiliation(s)
- G Occhipinti
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - M Giulietti
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - G Principato
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - F Piva
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy.
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Zhou X, Qu Z, Zhu C, Lin Z, Huo Y, Wang X, Wang J, Li B. Identification of urinary microRNA biomarkers for detection of gentamicin-induced acute kidney injury in rats. Regul Toxicol Pharmacol 2016; 78:78-84. [PMID: 27074385 DOI: 10.1016/j.yrtph.2016.04.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/06/2016] [Accepted: 04/07/2016] [Indexed: 11/17/2022]
Abstract
MicroRNAs (miRNAs) have been recently recognized as promising non-invasive biomarkers for detecting the organ injuries. To further understand the sensibility and reliability of miRNA measurements in urine sample for predicting drug-induced early nephrotoxicity, a global urinary miRNA expression analysis was performed in the rodent models with gentamicin-induced acute kidney injury (AKI). Male Wistar rats were daily administrated with gentamicin (0, 60, and 120 mg/kg) for up to 10 days by intraperitoneal injection, and the miRNA profiling of animal urine samples were subsequently analyzed using TaqMan(®) Array Rodent miRNA Cards. The results showed that four miRNAs (mmu-miR-138-5p, mmu-miR-1971, mmu-miR-218-1-3p, and rno-miR-489) were continuously increased in urine samples since day 4 after administration with gentamicin, which was not reflected by the standard markers such as serum creatinine (Cr) and urea nitrogen (BUN). Furthermore, other nine urinary miRNAs were increased in both 60 and 120 mg/kg groups on day 8. Receiver operator characteristics analysis demonstrated that the performance of these miRNAs with time- or dose-dependent increases were comparable to standard biomarkers (i.e. serum Cr and BUN), suggesting that the urinary miRNA panel can be used as potential biomarkers for the detection of gentamicin-induced AKI in rats. Moreover, the computer prediction analysis showed that these differentially expressed miRNAs were potentially targeted to many genes, which were mainly associated with the regulation of metabolic process and signaling. These data will improve the understanding and prediction of toxicology processes induced by nephrotoxicants.
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Affiliation(s)
- Xiaobing Zhou
- National Center for Safety Evaluation of Drugs, National Institutes of Food and Drug Control, Hongda Middle Street A8, Beijing Economic and Technological Development Area, Beijing, 100176, China
| | - Zhe Qu
- National Center for Safety Evaluation of Drugs, National Institutes of Food and Drug Control, Hongda Middle Street A8, Beijing Economic and Technological Development Area, Beijing, 100176, China
| | - Cong Zhu
- National Center for Safety Evaluation of Drugs, National Institutes of Food and Drug Control, Hongda Middle Street A8, Beijing Economic and Technological Development Area, Beijing, 100176, China
| | - Zhi Lin
- National Center for Safety Evaluation of Drugs, National Institutes of Food and Drug Control, Hongda Middle Street A8, Beijing Economic and Technological Development Area, Beijing, 100176, China
| | - Yan Huo
- National Center for Safety Evaluation of Drugs, National Institutes of Food and Drug Control, Hongda Middle Street A8, Beijing Economic and Technological Development Area, Beijing, 100176, China
| | - Xue Wang
- National Center for Safety Evaluation of Drugs, National Institutes of Food and Drug Control, Hongda Middle Street A8, Beijing Economic and Technological Development Area, Beijing, 100176, China
| | - Jufeng Wang
- National Center for Safety Evaluation of Drugs, National Institutes of Food and Drug Control, Hongda Middle Street A8, Beijing Economic and Technological Development Area, Beijing, 100176, China
| | - Bo Li
- National Center for Safety Evaluation of Drugs, National Institutes of Food and Drug Control, Hongda Middle Street A8, Beijing Economic and Technological Development Area, Beijing, 100176, China.
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