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Ghasemi T, Khalaj-Kondori M, Hosseinpour Feizi MA, Asadi P. lncRNA-miRNA-mRNA interaction network for colorectal cancer; An in silico analysis. Comput Biol Chem 2020; 89:107370. [PMID: 32932199 DOI: 10.1016/j.compbiolchem.2020.107370] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 05/26/2020] [Accepted: 09/01/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most frequent and diagnosed diseases. Accumulating evidences showed that mRNAs and noncoding RNAs play important regulatory roles in tumorigenesis. Identification and determining the relationship between them can help diagnosis and treatment of cancer. METHODS Here we analyzed three microarray datasets; GSE110715, GSE32323 and GSE21510, to identify differentially expressed lncRNAs and mRNAs in CRC. The adjusted p-value ≤0.05 was considered statistically significant. Gene set enrichment analysis was carried out using DAVID tool. The miRCancer database was searched to obtain differentially expressed miRNAs in colorectal cancer, and the miRDB database was used to attain the targets of the obtained miRNAs. To predict the lncRNA-miRNA interactions we used DIANA-LncBase v2 and RegRNA 2.0. Finally the lncRNA-miRNA-mRNA-signaling pathway network was constructed using Cytoscape v3.1. RESULTS By analyzing the three datasets, a total of 21 mRNAs (15 up- and 6 down-regulated) and 24 lncRNAs (18 up- and 6 down-regulated) were identified as common differentially expressed genes between CRC tumor and marginal tissues. Nevertheless, the constructed lncRNA-miRNA-mRNA-signaling pathway network revealed a convergence on 6 lncRNAs (3 up- and 3 downregulated), 7 mRNAs (2 up- and 5 downregulated) and 6 miRNAs (3 up- and 3 downregulated). We found that dysregulation of lncRNAs such as PCBP1-AS1, UCA1 and SNHG16 could sequester several miRNAs such as hsa-miR-582-5p and hsa-miR-198 and promote the proliferation, invasion and drug resistance of colorectal cancer cells. CONCLUSIONS We introduced a set of lncRNAs, mRNAs and miRNAs differentially expressed in CRC which might be considered for further experimental research as potential biomarkers of CRC development.
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Affiliation(s)
- Tayyebeh Ghasemi
- Dept. of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | | | | | - Parviz Asadi
- Gastroenterology ward, Shahid Mahallati Hospital, Tabriz, Iran
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Jia Y, Tan W, Zhou Y. Transfer RNA-derived small RNAs: potential applications as novel biomarkers for disease diagnosis and prognosis. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1092. [PMID: 33145311 PMCID: PMC7575943 DOI: 10.21037/atm-20-2797] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Transfer RNA-derived small RNA (tsRNA)s are novel non-coding RNAs, expressed in a variety of tissues and organs. Two subtypes of tsRNAs have been reported: tRNA-derived stress-induced RNA (tiRNA)s and tRNA-derived fragment (tRF)s. tsRNAs have been reported to play essential roles and possess different biological functions in a variety of physiological activities. Recently, tsRNAs have been implicated in a large number of diseases, such as cancers (including breast cancer, ovarian cancer, lung cancer, prostate cancer, colorectal cancer, etc.), neurological disorders, viral infections, metabolic diseases and angiogenesis-related diseases. Although the biological functions of tsRNAs are still poorly understood, correlations between dysregulated tsRNA expression and disease development have been recently reported. Additionally, their capabilities as potential biomarkers for disease diagnosis and prognosis have been revealed in clinical studies. In this review, we summarize the current knowledge of tsRNAs, and discuss their potential clinical applications as biomarkers in different diseases. Although the regulation of tsRNAs is similar to miRNAs in regards to the related physiological and pathological processes, the higher stability and expression levels of tsRNAs place them as ideal biomarkers for the diagnosis and prognosis in cancer and other diseases. Therefore, it is worth to verify the possibility and reliability of these reported tsRNAs as potential biomarkers for clinical applications in disease diagnosis and prognosis.
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Affiliation(s)
- Yang Jia
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Wei Tan
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Clinical Research Center of Ophthalmic Disease, Changsha, China
| | - Yedi Zhou
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, China.,Hunan Clinical Research Center of Ophthalmic Disease, Changsha, China
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Masaoutis C, Al Besher S, Koutroulis I, Theocharis S. Exosomes in Nephropathies: A Rich Source of Novel Biomarkers. DISEASE MARKERS 2020; 2020:8897833. [PMID: 32849923 PMCID: PMC7441435 DOI: 10.1155/2020/8897833] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/08/2020] [Accepted: 07/24/2020] [Indexed: 12/12/2022]
Abstract
The biomarkers commonly utilized in diagnostic evaluations of kidney disease suffer from low sensitivity, especially in the early stages of renal damage. On the other hand, obtaining a renal biopsy to augment clinical decision making can lead to potentially serious complications. In order to overcome the shortcomings of currently available diagnostic tools, recent studies suggest that exosomes, cell-secreted extracellular vesicles containing a large array of active molecules to facilitate cell-to-cell communication, may represent a rich source of novel disease biomarkers. Because of their endocytic origin, exosomes carry markers typical for their parent cells, which could permit the localization of biochemical cellular alterations in specific kidney compartments. Different types of exosomes can be isolated from noninvasively obtained biofluids; however, in the context of kidney disease, evidence has emerged on the role of urinary exosomes in the diagnostic and predictive modeling of renal pathology. The current review summarizes the potential application of exosomes in the detection of acute and chronic inflammatory, metabolic, degenerative, and genetic renal diseases.
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Affiliation(s)
- Christos Masaoutis
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 75, Mikras Asias street, Bld 10, Goudi, 11527 Athens, Greece
| | - Samer Al Besher
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 75, Mikras Asias street, Bld 10, Goudi, 11527 Athens, Greece
| | - Ioannis Koutroulis
- Children's National Hospital, Division of Emergency Medicine and Center for Genetic Medicine, George Washington University School of Medicine and Health Sciences, 111 Michigan Ave. NW, Washington, DC 20010, USA
| | - Stamatios Theocharis
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 75, Mikras Asias street, Bld 10, Goudi, 11527 Athens, Greece
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54
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Extracellular vesicles carrying miRNAs in kidney diseases: a systemic review. Clin Exp Nephrol 2020; 24:1103-1121. [DOI: 10.1007/s10157-020-01947-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 07/27/2020] [Indexed: 01/26/2023]
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55
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Emerging Roles of Long Non-Coding RNAs in Renal Fibrosis. Life (Basel) 2020; 10:life10080131. [PMID: 32752143 PMCID: PMC7460436 DOI: 10.3390/life10080131] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/26/2020] [Accepted: 07/29/2020] [Indexed: 12/11/2022] Open
Abstract
Renal fibrosis is an unavoidable consequence that occurs in nearly all of the nephropathies. It is characterized by a superabundant deposition and accumulation of extracellular matrix (ECM). All compartments in the kidney can be affected, including interstitium, glomeruli, vasculature, and other connective tissue, during the pathogenesis of renal fibrosis. The development of this process eventually causes destruction of renal parenchyma and end-stage renal failure, which is a devastating disease that requires renal replacement therapies. Recently, long non-coding RNAs (lncRNAs) have been emerging as key regulators governing gene expression and affecting various biological processes. These versatile roles include transcriptional regulation, organization of nuclear domains, and the regulation of RNA molecules or proteins. Current evidence proposes the involvement of lncRNAs in the pathologic process of kidney fibrosis. In this review, the biological relevance of lncRNAs in renal fibrosis will be clarified as important novel regulators and potential therapeutic targets. The biology, and subsequently the current understanding, of lncRNAs in renal fibrosis are demonstrated—highlighting the involvement of lncRNAs in kidney cell function, phenotype transition, and vascular damage and rarefaction. Finally, we discuss challenges and future prospects of lncRNAs in diagnostic markers and potential therapeutic targets, hoping to further inspire the management of renal fibrosis.
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56
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Tosar JP, Cayota A. Extracellular tRNAs and tRNA-derived fragments. RNA Biol 2020; 17:1149-1167. [PMID: 32070197 PMCID: PMC7549618 DOI: 10.1080/15476286.2020.1729584] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/05/2020] [Accepted: 02/10/2020] [Indexed: 01/08/2023] Open
Abstract
Fragmentation of tRNAs generates a family of small RNAs collectively known as tRNA-derived fragments. These fragments vary in sequence and size but have been shown to regulate many processes involved in cell homoeostasis and adaptations to stress. Additionally, the field of extracellular RNAs (exRNAs) is rapidly growing because exRNAs are a promising source of biomarkers in liquid biopsies, and because exRNAs seem to play key roles in intercellular and interspecies communication. Herein, we review recent descriptions of tRNA-derived fragments in the extracellular space in all domains of life, both in biofluids and in cell culture. The purpose of this review is to find consensus on which tRNA-derived fragments are more prominent in each extracellular fraction (including extracellular vesicles, lipoproteins and ribonucleoprotein complexes). We highlight what is becoming clear and what is still controversial in this field, in order to stimulate future hypothesis-driven studies which could clarify the role of full-length tRNAs and tRNA-derived fragments in the extracellular space.
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Affiliation(s)
- Juan Pablo Tosar
- Analytical Biochemistry Unit, Nuclear Research Center, Faculty of Science, Universidad de la República, Montevideo, Uruguay
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Alfonso Cayota
- Functional Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Department of Medicine, University Hospital, Universidad de la República, Montevideo, Uruguay
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Wu L, Wang Q, Guo F, Ma X, Wang J, Zhao Y, Yan Y, Qin G. Involvement of miR-27a-3p in diabetic nephropathy via affecting renal fibrosis, mitochondrial dysfunction, and endoplasmic reticulum stress. J Cell Physiol 2020; 236:1454-1468. [PMID: 32691413 DOI: 10.1002/jcp.29951] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/19/2020] [Accepted: 07/07/2020] [Indexed: 12/16/2022]
Abstract
Diabetic nephropathy (DN) is acknowledged as a serious chronic complication of diabetes mellitus. Nevertheless, its pathogenesis is complicated and unclear. Thus, in this study, the role of miR-27a-3p-prohibitin/TMBIM6 signaling axis in the progression of DN was elucidated. Type 2 diabetic db/db mice and high glucose (HG)-challenged HK-2 cells were used as in vivo and in vitro models. Our results showed that miR-27a-3p was upregulated and prohibitin or transmembrane BAX inhibitor motif containing 6 (TMBIM6) was downregulated in the kidney tissues of db/db mice and HG-treated HK-2 cells. Silencing miR-27a-3p enhanced the expression of prohibitin and TMBIM6 in the kidney tissues and HK-2 cells. Inhibition of miR-27a-3p improved functional injury, as evidenced by decreased blood glucose, urinary albumin, serum creatinine, and blood urea nitrogen levels. MiR-27a-3p silencing ameliorated renal fibrosis, reflected by reduced profibrogenic genes (e.g., transforming growth factor β1, fibronectin, collagen I and III, and α-smooth muscle actin). Furthermore, inhibition of miR-27a-3p relieved mitochondrial dysfunction in the kidney of db/db mice, including upregulation of mitochondrial membrane potential, complex I and III activities, adenosine triphosphate, and mitochondrial cytochrome C, as well as suppressing reactive oxygen species production. In addition, miR-27a-3p silencing attenuated endoplasmic reticulum (ER) stress, reflected by reduced expression of p-IRE1α, p-eIF2α, XBP1s, and CHOP. Mechanically, we identified prohibitin and TMBIM6 as direct targets of miR-27a-3p. Inhibition of miR-27a-3p protected HG-treated HK-2 cells from apoptosis, extracellular matrix accumulation, mitochondrial dysfunction, and ER stress by regulating prohibitin or TMBIM6. Taken together, we reveal that miR-27a-3p-prohibitin/TMBIM6 signaling axis regulates the progression of DN, which can be a potential therapeutic target.
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Affiliation(s)
- Lina Wu
- Department of Endocrinology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qingzhu Wang
- Department of Endocrinology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Feng Guo
- Department of Endocrinology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaojun Ma
- Department of Endocrinology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jiao Wang
- Department of Endocrinology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yanyan Zhao
- Department of Endocrinology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yushan Yan
- Department of Endocrinology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Guijun Qin
- Department of Endocrinology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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58
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Sinha N, Kumar V, Puri V, Nada R, Rastogi A, Jha V, Puri S. Urinary exosomes: Potential biomarkers for diabetic nephropathy. Nephrology (Carlton) 2020; 25:881-887. [PMID: 32323449 DOI: 10.1111/nep.13720] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 03/04/2020] [Accepted: 04/02/2020] [Indexed: 12/22/2022]
Abstract
Diabetic nephropathy is the most common diabetic complication culminating often into end-stage renal disease. Classically, it is defined by the presence of albuminuria which has limited ability to be detected at early stages but deterioration in kidney function generally precedes albuminuria. This necessitates the development of newer diagnostic assays for diabetic nephropathy to determine the progression of the disease. Kidney associated diseases with non-albuminuria further complicates a timely diagnosis and thus demands an early biomarker. Urinary exosomes, the nanovesicular entities are released by every epithelial cells of the nephron. Their protein or molecular cargo varies in the diseased state which may provide the pathophysiology of the kidney associated diseases. This drives them to be exploited as non-invasive biomarker. This review thus integrates the recent findings on the significance of the urinary exosomes as diagnostic biomarker in kidney-associated diseases, primarily in diabetic nephropathy.
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Affiliation(s)
- Nisha Sinha
- Centre for Stem Cell & Tissue Engineering and Excellence in Biomedical Sciences, Punjab University, Chandigarh, India.,Department of Nephrology, Post Graduate Institute of Medical Education & Research, Chandigarh, India
| | - Vivek Kumar
- Department of Nephrology, Post Graduate Institute of Medical Education & Research, Chandigarh, India
| | - Veena Puri
- Centre for Systems Biology & Bioinformatics, Punjab University, Chandigarh, India
| | - Ritambhra Nada
- Department of Histopathology, Post Graduate Institute of Medical Education & Research, Chandigarh, India
| | - Ashu Rastogi
- Department of Endocrinology and Metabolism, Post Graduate Institute of Medical Education & Research, Chandigarh, India
| | - Vivekanand Jha
- George Institute for Global Health, UNSW, India. George Institute for Global Health, University of Oxford, Oxford, UK. Manipal Academy of Higher Education, Manipal, India
| | - Sanjeev Puri
- Department of Biotechnology, University Institute of Engineering & Technology (UIET), Punjab University, Chandigarh, India
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59
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Ramanathan K, Padmanabhan G. MiRNAs as potential biomarker of kidney diseases: A review. Cell Biochem Funct 2020; 38:990-1005. [PMID: 32500596 DOI: 10.1002/cbf.3555] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 03/15/2020] [Accepted: 05/03/2020] [Indexed: 12/17/2022]
Abstract
MicroRNAs (miRNAs) are 22 nucleotides short, non-coding and tissue-specific single-stranded RNA which modulates target gene expression. Presently, shreds of evidence confirmed that miRNAs play a key role in kidney pathophysiology. The objectives of the present review are to summarize new research data towards the latest developments in the potential use of miRNAs as a diagnostic biomarker for kidney diseases. This holistic information will update the existing knowledge of kidney disease biomarkers. "miRNA profile for Diabetic Kidney disease, Acute kidney injury, Renal fibrosis, hemodialysis, transplants, FSGS, IgAN, etc." are the search keywords which have been used in this review. The search outcome gave an exciting insightful perception of miRNAs competence as a biomarker. Also it is observed that various samples as plasma, urine and biopsies were used for profiling the miRNA expression. The miRNAs were not only used for diagnostic biomarkers but also for therapeutic targets. Each kidney disease showed different miRNAs expression profile and few miRNAs quite common with some kidney diseases. miRNAs are simple and efficient diagnostic biomarkers for kidney diseases.
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Affiliation(s)
- Kumaresan Ramanathan
- Department of Medical Biochemistry, Division of Biomedical Sciences, School of Medicine, College of Health Sciences, Mekelle University (Ayder Campus), Mekelle, Ethiopia
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60
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Clinical decision support system to predict chronic kidney disease: A fuzzy expert system approach. Int J Med Inform 2020; 138:104134. [PMID: 32298972 DOI: 10.1016/j.ijmedinf.2020.104134] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 03/01/2020] [Accepted: 03/24/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND OBJECTIVES Diagnosis and early intervention of chronic kidney disease are essential to prevent loss of kidney function and a large amount of financial resources. To this end, we developed a fuzzy logic-based expert system for diagnosis and prediction of chronic kidney disease and evaluate its robustness against noisy data. METHODS At first, we identified the diagnostic parameters and risk factors through a literature review and a survey of 18 nephrologists. Depending on the features selected, a set of fuzzy rules for the prediction of chronic kidney disease was determined by reviewing the literature, guidelines and consulting with nephrologists. Fuzzy expert system was developed using MATLAB software and Mamdani Inference System. Finally, the fuzzy expert system was evaluated using data extracted from 216 randomly selected medical records of patients with and without chronic kidney disease. We added noisy data to our dataset and compare the performance of the system on original and noisy datasets. RESULTS We selected 16 parameters for the prediction of chronic kidney disease. The accuracy, sensitivity, and specificity of the final system were 92.13 %, 95.37 %, and 88.88 %, respectively. The area under the curve was 0.92 and the Kappa coefficient was 0.84, indicating a very high correlation between the system diagnosis and the final diagnosis recorded in the medical records. The performance of the system on noisy input variables indicated that in the worse scenario, the accuracy, sensitivity, and specificity of the system decreased only by 4.43 %, 7.48 %, and 5.41 %, respectively. CONCLUSION Considering the desirable performance of the proposed expert system, the system can be useful in the prediction of chronic kidney disease.
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61
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Zhong G, Wang K, Li J, Xiao S, Wei W, Liu J. Determination of Serum Exosomal H19 as a Noninvasive Biomarker for Breast Cancer Diagnosis. Onco Targets Ther 2020; 13:2563-2571. [PMID: 32273726 PMCID: PMC7109356 DOI: 10.2147/ott.s243601] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 03/12/2020] [Indexed: 12/19/2022] Open
Abstract
Purpose There is an urgent need for new biomarkers for the diagnosis of breast cancer. Exosomes can communicate with cells through transport molecules, including long-chain noncoding RNA (lncRNA), which is considered as a promising noninvasive biomarker. Here, we aimed to determine the potential of long noncoding RNA (lncRNA) H19 in the circulating exosomes for the diagnosis of breast cancer (BC). Materials and Methods We measured the levels of lncRNA H19 in serum-derived exosomes from patients with breast cancer (BC) or benign breast disease (BBD) and healthy subjects, using quantitative real-time PCR. H19 levels were also measured for pre-operative and post-operative patients. Receiver operating characteristic curve was constructed, and the area under the curve (AUC) was calculated to determine the applicability of exosomal H19 levels as biomarkers in BC. The relationship between H19 relative expression and clinical features of BC patients was also analyzed. Results Exosomal H19 expression levels were upregulated in patients with BC compared to that in patients with BBD and healthy controls (BC vs BBD, P < 0.001; BC vs healthy subjects, P < 0.001). The median serum exosomal H19 levels were significantly lower in post-operative than that in the pre-operative patients (P < 0.001). The AUC for exosomal H19 analysis was 0.870 (95% CI: 0.774–0.966) with a sensitivity of 87.0% and specificity of 70.6%, which was higher than the AUCs for CA15-3 and CEA, ie, 0.822 and 0.811, respectively. Moreover, exosomal H19 expression levels were associated with lymph node metastasis (P = 0.039), distant metastasis (P = 0.008), TNM stages (P = 0.022), ER (P=0.009), PR (P = 0.018), and Her-2 (P = 0.021). Conclusion Our results indicated that serum exosomal H19 acts as a novel biomarker for the diagnosis of BC.
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Affiliation(s)
- Guobin Zhong
- Department of Breast Surgery, Guangxi Medical University Cancer Hospital, Nanning, People's Republic of China
| | - Keqiong Wang
- Department of Breast Surgery, Guangxi Medical University Cancer Hospital, Nanning, People's Republic of China
| | - Jiawei Li
- Department of Breast Surgery, Guangxi Medical University Cancer Hospital, Nanning, People's Republic of China
| | - Shuzhe Xiao
- Department of Pediatrics, Guangzhou First Municipal People's Hospital, Guangzhou, People's Republic of China
| | - Wei Wei
- Department of Breast Surgery, Guangxi Medical University Cancer Hospital, Nanning, People's Republic of China
| | - Jianlun Liu
- Department of Breast Surgery, Guangxi Medical University Cancer Hospital, Nanning, China; Department of General Surgery, The Langdong Hospital of Guangxi Medical University, Nanning, People's Republic of China
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62
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Zhao Q, Yan T, Chopp M, Venkat P, Chen J. Brain-kidney interaction: Renal dysfunction following ischemic stroke. J Cereb Blood Flow Metab 2020; 40:246-262. [PMID: 31766979 PMCID: PMC7370616 DOI: 10.1177/0271678x19890931] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Stroke is a leading cause of mortality and morbidity, with long-term debilitating effects. Accumulating evidence from experimental studies as well as observational studies in patients suggests a cross talk between the brain and kidney after stroke. Stroke may lead to kidney dysfunction which can adversely impact patient outcome. In this review article, we discuss the epidemiology and mechanisms of brain–kidney interaction following ischemic stroke. Specifically, we discuss the role of the central autonomic network, autoregulation, inflammatory and immune responses, the role of extracellular vesicles and their cargo microRNA, in mediating brain–kidney interaction following stroke. Understanding the bidirectional nature of interaction between the brain and kidney after cerebral injury would have clinical implications for the treatment of stroke and overall patient outcome.
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Affiliation(s)
- Qiang Zhao
- Tianjin Neurological Institute, Neurology, Tianjin Medical University General Hospital, Tianjin, China
| | - Tao Yan
- Tianjin Neurological Institute, Neurology, Tianjin Medical University General Hospital, Tianjin, China
| | - Michael Chopp
- Department of Neurology, Henry Ford Hospital, Detroit, MI, USA.,Department of Physics, Oakland University, Rochester, MI, USA
| | - Poornima Venkat
- Department of Neurology, Henry Ford Hospital, Detroit, MI, USA
| | - Jieli Chen
- Department of Neurology, Henry Ford Hospital, Detroit, MI, USA
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63
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Su Z, Frost EL, Lammert CR, Przanowska RK, Lukens JR, Dutta A. tRNA-derived fragments and microRNAs in the maternal-fetal interface of a mouse maternal-immune-activation autism model. RNA Biol 2020; 17:1183-1195. [PMID: 31983265 DOI: 10.1080/15476286.2020.1721047] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
tRNA-derived small fragments (tRFs) and tRNA halves have emerging functions in different biological pathways, such as regulating gene expression, protein translation, retrotransposon activity, transgenerational epigenetic changes and response to environmental stress. However, small RNAs like tRFs and microRNAs in the maternal-fetal interface during gestation have not been studied extensively. Here we investigated the small RNA composition of mouse placenta/decidua, which represents the interface where the mother communicates with the foetus, to determine whether there are specific differences in tRFs and microRNAs during fetal development and in response to maternal immune activation (MIA). Global tRF expression pattern, just like microRNAs, can distinguish tissue types among placenta/decidua, fetal brain and fetal liver. In particular, 5' tRNA halves from tRNAGly, tRNAGlu, tRNAVal and tRNALys are abundantly expressed in the normal mouse placenta/decidua. Moreover, tRF and microRNA levels in the maternal-fetal interface change dynamically over the course of embryonic development. To see if stress alters non-coding RNA expression at the maternal-fetal interface, we treated pregnant mice with a viral infection mimetic, which has been shown to promote autism-related phenotypes in the offspring. Acute changes in the levels of specific tRFs and microRNAs were observed 3-6 h after MIA and are suppressed thereafter. A group of 5' tRNA halves is down-regulated by MIA, whereas a group of 18-nucleotide tRF-3a is up-regulated. In conclusion, tRFs show tissue-specificity, developmental changes and acute response to environmental stress, opening the possibility of them having a role in the fetal response to MIA.
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Affiliation(s)
- Zhangli Su
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia , Charlottesville, VA, USA
| | - Elizabeth L Frost
- Center for Brain Immunology and Glia, Department of Neuroscience, School of Medicine, University of Virginia , Charlottesville, VA, USA
| | - Catherine R Lammert
- Center for Brain Immunology and Glia, Department of Neuroscience, School of Medicine, University of Virginia , Charlottesville, VA, USA
| | - Roza K Przanowska
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia , Charlottesville, VA, USA
| | - John R Lukens
- Center for Brain Immunology and Glia, Department of Neuroscience, School of Medicine, University of Virginia , Charlottesville, VA, USA
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia , Charlottesville, VA, USA
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Thongboonkerd V. Roles for Exosome in Various Kidney Diseases and Disorders. Front Pharmacol 2020; 10:1655. [PMID: 32082158 PMCID: PMC7005210 DOI: 10.3389/fphar.2019.01655] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 12/17/2019] [Indexed: 12/13/2022] Open
Abstract
Exosome is a nanoscale vesicle with a size range of 30–100 nm. It is secreted from cell to extracellular space by exocytosis after fusion of multivesicular body (MVB) (formed by endocytic vesicles) with plasma membrane. Exosome plays several important roles in cellular homeostasis and intercellular communications. During the last two decades, exosome has acquired a wide attention to explore its additional roles in various aspects of cell biology and function in several organ systems. For the kidney, several lines of evidence have demonstrated 1that exosome is involved in the renal physiology and pathogenic mechanisms of various kidney diseases/disorders. This article summarizes roles of the exosome as the potential source of biomarkers, pathogenic molecules, and therapeutic biologics that have been extensively investigated in many kidney diseases/disorders, including lupus nephritis (LN), other glomerular diseases, acute kidney injury (AKI), diabetic nephropathy (DN), as well as in the process of renal fibrosis and chronic kidney disease (CKD) progression, in addition to polycystic kidney disease (PKD), kidney transplantation, and renal cell carcinoma (RCC). Moreover, the most recent evidence has shown its emerging role in kidney stone disease (or nephrolithiasis), involving inflammasome activation and inflammatory cascade frequently found in kidney stone pathogenesis.
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Affiliation(s)
- Visith Thongboonkerd
- Medical Proteomics Unit, Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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Zhou Q, Chen W, Yu XQ. Long non-coding RNAs as novel diagnostic and therapeutic targets in kidney disease. Chronic Dis Transl Med 2020; 5:252-257. [PMID: 32055784 PMCID: PMC7005109 DOI: 10.1016/j.cdtm.2019.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Indexed: 12/11/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have critical roles in the development of many diseases including kidney disease. An increasing number of studies have shown that lncRNAs are involved in kidney development and that their dysregulation can result in distinct disease processes, including acute kidney injury (AKI), chronic kidney disease (CKD), and renal cell carcinoma (RCC). Understanding the roles of lncRNAs in kidney disease may provide new diagnostic and therapeutic opportunities in the clinic. This review provides an overview of lncRNA characteristics, biological function and discusses specific studies that provide insight into the function and potential application of lncRNAs in kidney disease treatment.
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Affiliation(s)
- Qin Zhou
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China.,National Health Commission Key Laboratory of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China.,Guangdong Provincial Key Laboratory of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Wei Chen
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China.,National Health Commission Key Laboratory of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China.,Guangdong Provincial Key Laboratory of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Xue-Qing Yu
- Department of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China.,National Health Commission Key Laboratory of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China.,Guangdong Provincial Key Laboratory of Nephrology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China.,Guangdong General Hospital, Guangzhou, Guangdong, 510080, China
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Wang J, Chai L, Lu Y, Lu H, Liu Y, Zhang Y. Attenuation of mTOR Signaling Is the Major Response Element in the Rescue Pathway of Chronic Kidney Disease in Rats. Neuroimmunomodulation 2020; 27:9-18. [PMID: 32526762 DOI: 10.1159/000505095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 11/28/2019] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Modern lifestyle changes and the interlinking of non-communicable diseases result in the development of chronic kidney disease (CKD). While research has focused on attenuating the CKD, the role of mTOR in the progression of CKD is still unclear. OBJECTIVES The current investigation was undertaken to study the role of mTOR-mediated signaling in CKD using Wistar male rats and adenine-induced CKD as an experimental model. METHOD The animals were divided into 3 groups, representing control, CKD, and rapamycin-pretreated rats. At the end of the experimental period, blood biochemical indexes on kidney function and expression levels of fibrotic markers, including TGF-β, PAI-1, α-smooth muscle action, fibronectin, CTGF, and collagen-1, were analyzed. In addition, kidney injury markers such as kim-1, cystatin-C, NAG, and NGAL, indicating a progressive fibrotic response, were also studied. RESULTS The results suggest that mTOR inhibition significantly attenuated the induction of fibrosis, with restored serum creatinine and blood urea nitrogen levels. Intriguingly, the microRNA (miRNA) analysis revealed an increased expression of miR-193-5p, miR-221, miR-212, and miR-183-5p in CKD, while an increased mRNA expression of anti-inflammatory cytokines and reduced level of pS6K with attenuated miRNA was found in rapamycin-treated rats compared to the CKD animals. CONCLUSION Activation of mTOR is the major responsive element with activation of miRNAs as an elementary role in the progression of kidney disease. Hence, targeting mTOR would be a possible strategy of treatment for CKD.
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Affiliation(s)
- Jing Wang
- Department of Nephrology, Xingtai People's Hospital, Xingtai, China
| | - Lichao Chai
- Department of Nuclear Medicine, Xingtai People's Hospital, Xingtai, China,
| | - Yi Lu
- Department of Endocrinology, Xingtai People's Hospital, Xingtai, China
| | - Hua Lu
- Department of Nephrology, Xingtai People's Hospital, Xingtai, China
| | - Yanling Liu
- Department of Nephrology, Xingtai People's Hospital, Xingtai, China
| | - Yingying Zhang
- Department of Oncology, Affiliated Hospital of Hebei University of Engineering, Handan, China
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Li Y, Yin Z, Fan J, Zhang S, Yang W. The roles of exosomal miRNAs and lncRNAs in lung diseases. Signal Transduct Target Ther 2019; 4:47. [PMID: 31728212 PMCID: PMC6851157 DOI: 10.1038/s41392-019-0080-7] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/15/2019] [Accepted: 09/15/2019] [Indexed: 12/11/2022] Open
Abstract
An increasing number of studies have reported that exosomes released from various cells can serve as mediators of information exchange between different cells. With further exploration of exosome content, a more accurate molecular mechanism involved in the process of cell-to-cell communication has been revealed; specifically, microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) are shuttled by exosomes. In addition, exosomal miRNAs and lncRNAs may play vital roles in the pathogenesis of several respiratory diseases, such as chronic obstructive pulmonary disease (COPD), lung cancer, and asthma. Consequently, exosomal miRNAs and lncRNAs show promise as diagnostic biomarkers and therapeutic targets in several lung diseases. This review will summarize recent knowledge about the roles of exosomal miRNAs and lncRNAs in lung diseases, which has shed light on the discovery of novel diagnostic methods and treatments for these disorders. Because there is almost no published literature about exosomal lncRNAs in COPD, asthma, interstitial lung disease, or tuberculosis, we summarize the roles of exosomal lncRNAs only in lung cancer in the second section. This may inspire some new ideas for researchers who are interested in whether lncRNAs shuttled by exosomes may play roles in other lung diseases.
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Affiliation(s)
- Yang Li
- Key Laboratory of Respiratory Diseases of the Ministry of Health, Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022 Wuhan, China
| | - Zhengrong Yin
- Key Laboratory of Respiratory Diseases of the Ministry of Health, Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022 Wuhan, China
| | - Jinshuo Fan
- Key Laboratory of Respiratory Diseases of the Ministry of Health, Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022 Wuhan, China
| | - Siyu Zhang
- Key Laboratory of Respiratory Diseases of the Ministry of Health, Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022 Wuhan, China
| | - Weibing Yang
- Key Laboratory of Respiratory Diseases of the Ministry of Health, Department of Respiratory and Critical Care Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1277 Jiefang Avenue, 430022 Wuhan, China
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Dhama K, Latheef SK, Dadar M, Samad HA, Munjal A, Khandia R, Karthik K, Tiwari R, Yatoo MI, Bhatt P, Chakraborty S, Singh KP, Iqbal HMN, Chaicumpa W, Joshi SK. Biomarkers in Stress Related Diseases/Disorders: Diagnostic, Prognostic, and Therapeutic Values. Front Mol Biosci 2019; 6:91. [PMID: 31750312 PMCID: PMC6843074 DOI: 10.3389/fmolb.2019.00091] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 09/11/2019] [Indexed: 02/05/2023] Open
Abstract
Various internal and external factors negatively affect the homeostatic equilibrium of organisms at the molecular to the whole-body level, inducing the so-called state of stress. Stress affects an organism's welfare status and induces energy-consuming mechanisms to combat the subsequent ill effects; thus, the individual may be immunocompromised, making them vulnerable to pathogens. The information presented here has been extensively reviewed, compiled, and analyzed from authenticated published resources available on Medline, PubMed, PubMed Central, Science Direct, and other scientific databases. Stress levels can be monitored by the quantitative and qualitative measurement of biomarkers. Potential markers of stress include thermal stress markers, such as heat shock proteins (HSPs), innate immune markers, such as Acute Phase Proteins (APPs), oxidative stress markers, and chemical secretions in the saliva and urine. In addition, stress biomarkers also play critical roles in the prognosis of stress-related diseases and disorders, and therapy guidance. Moreover, different components have been identified as potent mediators of cardiovascular, central nervous system, hepatic, and nephrological disorders, which can also be employed to evaluate these conditions precisely, but with stringent validation and specificity. Considerable scientific advances have been made in the detection, quantitation, and application of these biomarkers. The present review describes the current progress of identifying biomarkers, their prognostic, and therapeutic values.
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Affiliation(s)
- Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Shyma K. Latheef
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Maryam Dadar
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran
| | - Hari Abdul Samad
- Division of Physiology and Climatology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Ashok Munjal
- Department of Genetics, Barkatullah University, Bhopal, India
| | - Rekha Khandia
- Department of Genetics, Barkatullah University, Bhopal, India
| | - Kumaragurubaran Karthik
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, UP Pandit Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan, Mathura, India
| | - Mohd. Iqbal Yatoo
- Division of Veterinary Clinical Complex, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Prakash Bhatt
- Teaching Veterinary Clinical Complex, College of Veterinary and Animal Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, India
| | - Sandip Chakraborty
- Department of Veterinary Microbiology, College of Veterinary Sciences and Animal Husbandry, Agartala, India
| | - Karam Pal Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Hafiz M. N. Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Wanpen Chaicumpa
- Department of Parasitology, Faculty of Medicine, Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Sunil Kumar Joshi
- Division of Hematology, Oncology and Bone Marrow Transplantation, Department of Microbiology & Immunology, Department of Pediatrics, University of Miami School of Medicine, Miami, FL, United States
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Dhama K, Latheef SK, Dadar M, Samad HA, Munjal A, Khandia R, Karthik K, Tiwari R, Yatoo MI, Bhatt P, Chakraborty S, Singh KP, Iqbal HMN, Chaicumpa W, Joshi SK. Biomarkers in Stress Related Diseases/Disorders: Diagnostic, Prognostic, and Therapeutic Values. Front Mol Biosci 2019. [PMID: 31750312 DOI: 10.3389/fmolb.2019.0009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Various internal and external factors negatively affect the homeostatic equilibrium of organisms at the molecular to the whole-body level, inducing the so-called state of stress. Stress affects an organism's welfare status and induces energy-consuming mechanisms to combat the subsequent ill effects; thus, the individual may be immunocompromised, making them vulnerable to pathogens. The information presented here has been extensively reviewed, compiled, and analyzed from authenticated published resources available on Medline, PubMed, PubMed Central, Science Direct, and other scientific databases. Stress levels can be monitored by the quantitative and qualitative measurement of biomarkers. Potential markers of stress include thermal stress markers, such as heat shock proteins (HSPs), innate immune markers, such as Acute Phase Proteins (APPs), oxidative stress markers, and chemical secretions in the saliva and urine. In addition, stress biomarkers also play critical roles in the prognosis of stress-related diseases and disorders, and therapy guidance. Moreover, different components have been identified as potent mediators of cardiovascular, central nervous system, hepatic, and nephrological disorders, which can also be employed to evaluate these conditions precisely, but with stringent validation and specificity. Considerable scientific advances have been made in the detection, quantitation, and application of these biomarkers. The present review describes the current progress of identifying biomarkers, their prognostic, and therapeutic values.
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Affiliation(s)
- Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Shyma K Latheef
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Maryam Dadar
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization, Karaj, Iran
| | - Hari Abdul Samad
- Division of Physiology and Climatology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Ashok Munjal
- Department of Genetics, Barkatullah University, Bhopal, India
| | - Rekha Khandia
- Department of Genetics, Barkatullah University, Bhopal, India
| | - Kumaragurubaran Karthik
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, India
| | - Ruchi Tiwari
- Department of Veterinary Microbiology and Immunology, College of Veterinary Sciences, UP Pandit Deen Dayal Upadhayay Pashu Chikitsa Vigyan Vishwavidyalay Evum Go-Anusandhan Sansthan, Mathura, India
| | - Mohd Iqbal Yatoo
- Division of Veterinary Clinical Complex, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Prakash Bhatt
- Teaching Veterinary Clinical Complex, College of Veterinary and Animal Sciences, Govind Ballabh Pant University of Agriculture and Technology, Pantnagar, India
| | - Sandip Chakraborty
- Department of Veterinary Microbiology, College of Veterinary Sciences and Animal Husbandry, Agartala, India
| | - Karam Pal Singh
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Wanpen Chaicumpa
- Department of Parasitology, Faculty of Medicine, Center of Research Excellence on Therapeutic Proteins and Antibody Engineering, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Sunil Kumar Joshi
- Division of Hematology, Oncology and Bone Marrow Transplantation, Department of Microbiology & Immunology, Department of Pediatrics, University of Miami School of Medicine, Miami, FL, United States
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Wang X, Gu H, Palma-Duran SA, Fierro A, Jasbi P, Shi X, Bresette W, Tasevska N. Influence of Storage Conditions and Preservatives on Metabolite Fingerprints in Urine. Metabolites 2019; 9:metabo9100203. [PMID: 31569767 PMCID: PMC6836253 DOI: 10.3390/metabo9100203] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/12/2019] [Accepted: 09/18/2019] [Indexed: 12/15/2022] Open
Abstract
Human urine, which is rich in metabolites, provides valuable approaches for biomarker measurement. Maintaining the stability of metabolites in urine is critical for accurate and reliable research results and subsequent interpretation. In this study, the effect of storage temperature (4, 22, and 40 °C), storage time (24 and 48 h), and use of preservatives (boric acid (BA), thymol) and para-aminobenzoic acid (PABA) on urinary metabolites in the pooled urine samples from 20 participants was systematically investigated using large-scale targeted liquid chromatography tandem mass spectrometry (LC-MS/MS)-based metabolomics. Statistical analysis of 158 reliably detected metabolites showed that metabolites in urine with no preservative remained stable at 4 °C for 24 and 48 h as well as at 22 °C for 24 h, but significant metabolite differences were observed in urine stored at 22 °C for 48 h and at 40 °C. The mere addition of BA caused metabolite changes. Thymol was observed to be effective in maintaining metabolite stability in urine in all the conditions designed, most likely due to the inhibitory effect of thymol on urine microbiota. Our results provide valuable urine preservation guidance during sample storage, which is essential for obtaining reliable, accurate, and reproducible analytical results from urine samples.
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Affiliation(s)
- Xinchen Wang
- Jiangxi Key Laboratory for Mass Spectrometry and Instrumentation, East China University of Technology, Nanchang 330013, China.
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA.
| | - Haiwei Gu
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA.
| | | | - Andres Fierro
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA.
| | - Paniz Jasbi
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA.
| | - Xiaojian Shi
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA.
| | - William Bresette
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA.
| | - Natasha Tasevska
- College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA.
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71
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Kołat D, Hammouz R, Bednarek AK, Płuciennik E. Exosomes as carriers transporting long non‑coding RNAs: Molecular characteristics and their function in cancer (Review). Mol Med Rep 2019; 20:851-862. [PMID: 31173220 PMCID: PMC6625196 DOI: 10.3892/mmr.2019.10340] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 05/09/2019] [Indexed: 02/07/2023] Open
Abstract
Long non‑coding RNAs (lncRNAs) comprise a sizeable class of non‑coding RNAs with a length of over 200 base pairs. Little is known about their biological function, although over 20,000 lncRNAs have been annotated in the human genome. Through a diverse range of mechanisms, their primary function is in the regulation of the transcription of protein‑coding genes. lncRNA transcriptional activation can result from a group of nucleus‑retained and chromatin‑associated lncRNAs, which function as scaffolds in the cis/trans recruitment of transcription factors, co‑activators or chromatin remodelers, and/or promoter enhancers. Exosomes are released as extracellular vesicles and they are produced by endocytic pathways. Their synthesis is initiated by various processes including ceramide synthesis, release of intracellular Ca2+ or acid‑base balance disorders. Prior to vesicle creation, selective cargo loading occurs in the Endosomal Sorting Complex Required for Transport. Participation of endosomal sorting proteins such as tetraspanins or specific sumoylated proteins required for transport has been indicated in research. The endosomal‑sorting complex consists of four components, these induce the formation of multivesicular bodies and the induction of membrane deformation to form exosomes. Nanovesicles could be formed inside multivesicular bodies to allow transport outside the cell or digestion in lysosomes. The molecular content of exosomes is more heterogenic than its synthesis process, with different cargoes being examined inside vesicles with regard to the type or stage of cancers. This paper will review the importance of lncRNAs as crucial molecular content of exosomes, indicating its involvement in tumour suppression, pro‑tumorigenic events and the development of novel therapeutic approaches in the near future. Further studies of their mechanisms of function are essential, as well as overcoming several challenges to gain a clearer insight to the approaches for the best clinical application.
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Affiliation(s)
- Damian Kołat
- Faculty of Biomedical Sciences and Postgraduate Education, Medical University of Łódź, 90-752 Łódź, Poland
| | - Raneem Hammouz
- Department of Molecular Carcinogenesis, Medical University of Łódź, 90-752 Łódź, Poland
| | - Andrzej K. Bednarek
- Department of Molecular Carcinogenesis, Medical University of Łódź, 90-752 Łódź, Poland
| | - Elżbieta Płuciennik
- Department of Molecular Carcinogenesis, Medical University of Łódź, 90-752 Łódź, Poland
- Correspondence to: Dr Elżbieta Płuciennik, Department of Molecular Carcinogenesis, Medical University of Łódź, Zeligowskiego 7/9, 90-752 Łódź, Poland, E-mail:
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Kelemen E, Danis J, Göblös A, Bata-Csörgő Z, Széll M. Exosomal long non-coding RNAs as biomarkers in human diseases. EJIFCC 2019; 30:224-236. [PMID: 31263395 PMCID: PMC6599197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The intensive study of extracellular vesicles was started about a decade ago revealing alterations of their amount and content to several cellular stimuli, highly depending on the releasing cell type. Exosomes, a type of extracellular vesicles, are released by every cell type and are present in most body fluids, what makes them attractive targets of biomarker research. Several studies have indicated that their content - including proteins and coding, as well as non-coding nucleic acids - could represent the disease state and serves as specific disease biomarkers. Out of these molecules, a special interest was gained by long non-coding RNAs (lncRNAs). Just as exosomes, lncRNAs are specific to their cell of origin and often specific to diseases, also found extracellularly, mainly contained in extracellular vesicles. Thus, recent efforts in biomarker research has turned to circulating exosomal lncRNAs, which might lead to the development of highly specific disease markers. Here we summarize the current knowledge on disease-associated exosomal long non-coding RNAs. The intensive studies in this area have revealed numerous potential targets for biomarkers, and highlighted the potential of their combination with other exosomal markers to represent a highly sensitive and specific diagnostic tool. However, we believe that additional functional data on both exosomes and lncRNAs are necessary for understanding their deregulation in diseases and developing their use as diagnostic approaches.
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Affiliation(s)
- Evelyn Kelemen
- Department of Dermatology and Allergology, Research Institute of Translational Biomedicine, University of Szeged, Hungary
| | - Judit Danis
- Department of Dermatology and Allergology, Research Institute of Translational Biomedicine, University of Szeged, Hungary,MTA-SZTE Dermatological Research Group, Szeged, Hungary
| | - Anikó Göblös
- Department of Dermatology and Allergology, Research Institute of Translational Biomedicine, University of Szeged, Hungary,MTA-SZTE Dermatological Research Group, Szeged, Hungary
| | - Zsuzsanna Bata-Csörgő
- Department of Dermatology and Allergology, Research Institute of Translational Biomedicine, University of Szeged, Hungary,MTA-SZTE Dermatological Research Group, Szeged, Hungary
| | - Márta Széll
- MTA-SZTE Dermatological Research Group, Szeged, Hungary, Department of Medical Genetics, University of Szeged, Hungary,Corresponding author: Márta Széll Department of Medical Genetics University of Szeged Somogyi B. u 4. Szeged, 6720 Hungary Phone: +36-62-54-51-34 E-mail:
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Aitbaev KA, Murkamilov IT, Fomin VV. Circulating microRNAs as potential biomarkers of chronic kidney disease. TERAPEVT ARKH 2019; 91:131-136. [DOI: 10.26442/00403660.2019.06.000046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Indexed: 11/22/2022]
Abstract
Chronic kidney disease (CKD) is a supra - nosological term that reflects the progressive nature of chronic kidney diseases, which are based on the mechanisms of nephrosclerosis. Diagnosis of CKD at the earliest stages is of great importance, because it allows, by using therapeutic agents, to slow the progression of renal dysfunction and the development of cardiovascular complications. However, the currently available methods for diagnosing renal function impairment, including the determination of endogenous creatinine clearance, can detect renal dysfunction too late, when around 40-50% of the renal parenchyma is already reversibly or irreversibly damaged. In this regard, there is an active search for new, more sensitive and specific biomarkers for early diagnosis of CKD. Recent studies in cellular and animal models of CKD have demonstrated the important role of microRNA, a new class of posttranscriptional regulators of gene expression, in physiology and pathophysiology of kidneys. In particular, it has been shown that their expression profile in blood or urine can reflect changes in cells involved in a particular pathological process, since these cells can secrete a specific population of microRNAs, for example, through secretion of microRNA-containing exosomes. This gave grounds for considering increased or decreased expression of individual microRNAs in renal tissue or biological fluids (including urine) as new biomarkers for the diagnosis and monitoring of CKD. This review presents the results of recent experimental and clinical studies on these issues.
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Dieter C, Assmann TS, Costa AR, Canani LH, de Souza BM, Bauer AC, Crispim D. MiR-30e-5p and MiR-15a-5p Expressions in Plasma and Urine of Type 1 Diabetic Patients With Diabetic Kidney Disease. Front Genet 2019; 10:563. [PMID: 31249597 PMCID: PMC6582252 DOI: 10.3389/fgene.2019.00563] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 05/29/2019] [Indexed: 01/29/2023] Open
Abstract
Introduction Diabetic kidney disease (DKD) is a common microvascular complication that affects 40% of patients with diabetes mellitus (DM). Emerging evidence suggests a role for several microRNAs (miRNAs) in the development of DKD. In this context, miR-15a-5p and miR-30e-5p have been shown to regulate the expression of the uncoupling protein 2 (UCP2), a mitochondrial protein that decreases reactive oxygen species (ROS) formation by the mitochondria. Since ROS overproduction is a key contributor to the pathogenesis of DKD, dysregulation of these two miRNAs could be involved in DKD pathogenesis. Thus, the aim of this study was to compare the expressions of miR-15a-5p and miR-30e-5p in type 1 DM (T1DM) patients with DKD (cases) and without this complication (controls), and to perform bioinformatics analyses to investigate their putative targets and biological pathways under their regulation. Methods MiR-15a-5p and miR-30e-5p expressions were analyzed in plasma and urine of 17 T1DM controls and 23 DKD cases (12 with moderate DKD and 11 with severe DKD) using qPCR. Bioinformatics analyses were performed in Cytoscape software. Results MiR-30e-5p expression was downregulated in plasma of patients with moderate and severe DKD compared to T1DM controls. Moreover, this miRNA was also downregulated in urine of patients with severe DKD compared to the other groups. No difference was found in miR-15a-5p expression between groups. Bioinformatics analyses indicated that miR-30e-5p and miR-15a-5p regulate various genes that participate in pathways related to angiogenesis, apoptosis, cell differentiation, oxidative stress, and hypoxia. Conclusion MiR-30e-5p seems to be downregulated in plasma and urine of patients with DKD.
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Affiliation(s)
- Cristine Dieter
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Post-Graduate Program in Medical Sciences: Endocrinology, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Taís Silveira Assmann
- Department of Food Science and Physiology, School of Pharmacy and Nutrition, University of Navarra, Pamplona, Spain
| | | | - Luís Henrique Canani
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Post-Graduate Program in Medical Sciences: Endocrinology, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Bianca Marmontel de Souza
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Post-Graduate Program in Medical Sciences: Endocrinology, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Andrea Carla Bauer
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Post-Graduate Program in Medical Sciences: Endocrinology, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Nephrology Division, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Daisy Crispim
- Endocrine Division, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Post-Graduate Program in Medical Sciences: Endocrinology, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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Mussack V, Wittmann G, Pfaffl MW. Comparing small urinary extracellular vesicle purification methods with a view to RNA sequencing-Enabling robust and non-invasive biomarker research. BIOMOLECULAR DETECTION AND QUANTIFICATION 2019; 17:100089. [PMID: 31194192 PMCID: PMC6554496 DOI: 10.1016/j.bdq.2019.100089] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/27/2019] [Accepted: 04/10/2019] [Indexed: 01/10/2023]
Abstract
Small extracellular vesicles (EVs) are 50–200 nm sized mediators in intercellular communication that reflect both physiological and pathophysiological changes of their parental cells. Thus, EVs hold great potential for biomarker detection. However, reliable purification methods for the downstream screening of the microRNA (miRNA) cargo carried within urinary EVs by small RNA sequencing have yet to be established. To address this knowledge gap, RNA extracted from human urinary EVs obtained by five different urinary EV purification methods (spin column chromatography, immunoaffinity, membrane affinity, precipitation and ultracentrifugation combined with density gradient) was analyzed by small RNA sequencing. Urinary EVs were further characterized by nanoparticle tracking analysis, Western blot analysis and transmission electron microscopy. Comprehensive EV characterization established significant method-dependent differences in size and concentration as well as variances in protein composition of isolated vesicles. Even though all purification methods captured enough total RNA to allow small RNA sequencing, method-dependent differences were also observed with respect to library sizes, mapping distributions, number of miRNA reads and diversity of transcripts. Whereas EVs obtained by immunoaffinity yielded the purest subset of small EVs, highly comparable with results attained by ultracentrifugation combined with density gradient, precipitation and membrane affinity, sample purification by spin column chromatography indicated a tendency to isolate different subtypes of small EVs, which might also carry a distinct subset of miRNAs. Based on our results, different EV purification methods seem to preferentially isolate different subtypes of EVs with varying efficiencies. As a consequence, sequencing experiments and resulting miRNA profiles were also affected. Hence, the selection of a specific EV isolation method has to satisfy the respective research question and should be well considered. In strict adherence with the MISEV (minimal information for studies of extracellular vesicles) guidelines, the importance of a combined evaluation of biophysical and proteomic EV characteristics alongside transcriptomic results was clearly demonstrated in this present study.
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Key Words
- A, spin column chromatography
- ANOVA, analysis of variance
- Ago2, argonaute-2 protein
- B, immunoaffinity
- Biomarker
- C, membrane affinity
- D, precipitation
- DGE, differential gene expression
- DTT, dithiothreitol
- E, ultracentrifugation combined with density gradient
- EV(s), extracellular vesicle(s)
- Extracellular vesicles
- FM, fluorescent mode
- Human
- MISEV, minimal information for studies of extracellular vesicles
- NTA, nanoparticle tracking analysis
- PC, principal component
- RIN, RNA integrity number
- RNA-Seq, RNA sequencing
- SM, scattering mode
- Small RNA sequencing
- TEM, transmission electron microscopy
- UCrea, urinary creatinine
- Urine
- mIgG, murine immunoglobulin G
- mRNA, messenger RNA
- miRNA, microRNA
- microRNA
- nm, nanometer(s)
- nt, nucleotide(s)
- rRNA, ribosomal RNA
- snRNA, small nuclear RNA
- snoRNA, small nucleolar RNA
- tRNA, transfer RNA
- uEVs, urinary extracellular vesicles
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Affiliation(s)
- Veronika Mussack
- Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Weihenstephaner Berg 3, 85354, Freising, Germany
| | - Georg Wittmann
- Department for Transfusion Medicine, Cell therapeutics and Haemostaseology, University Hospital LMU, Marchioninistraße 15, 81377, Munich, Germany
| | - Michael W Pfaffl
- Animal Physiology and Immunology, School of Life Sciences Weihenstephan, Technical University of Munich, Weihenstephaner Berg 3, 85354, Freising, Germany
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76
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Non-Coding RNAs as New Therapeutic Targets in the Context of Renal Fibrosis. Int J Mol Sci 2019; 20:ijms20081977. [PMID: 31018516 PMCID: PMC6515288 DOI: 10.3390/ijms20081977] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 04/19/2019] [Accepted: 04/20/2019] [Indexed: 12/15/2022] Open
Abstract
Fibrosis, or tissue scarring, is defined as the excessive, persistent and destructive accumulation of extracellular matrix components in response to chronic tissue injury. Renal fibrosis represents the final stage of most chronic kidney diseases and contributes to the progressive and irreversible decline in kidney function. Limited therapeutic options are available and the molecular mechanisms governing the renal fibrosis process are complex and remain poorly understood. Recently, the role of non-coding RNAs, and in particular microRNAs (miRNAs), has been described in kidney fibrosis. Seminal studies have highlighted their potential importance as new therapeutic targets and innovative diagnostic and/or prognostic biomarkers. This review will summarize recent scientific advances and will discuss potential clinical applications as well as future research directions.
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77
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Joilin G, Leigh PN, Newbury SF, Hafezparast M. An Overview of MicroRNAs as Biomarkers of ALS. Front Neurol 2019; 10:186. [PMID: 30899244 PMCID: PMC6416171 DOI: 10.3389/fneur.2019.00186] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 02/13/2019] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS; MND, motor neuron disease) is a debilitating neurodegenerative disease affecting 4.5 per 100,000 people per year around the world. There is currently no cure for this disease, and its causes are relatively unknown. Diagnosis is based on a battery of clinical tests up to a year after symptom onset, with no robust markers of diagnosis or disease progression currently identified. A major thrust of current research is to identify potential non-invasive markers (“biomarkers”) in body fluids such as blood and/or cerebrospinal fluid (CSF) to use for diagnostic or prognostic purposes. Non-coding RNAs (ncRNAs), including microRNAs (miRNAs), are found at detectable and stable levels in blood and other bodily fluids. Specific ncRNAs can vary in levels between ALS patients and non-ALS controls without the disease. In this review, we will provide an overview of early findings, demonstrate the potential of this new class as biomarkers, and discuss future challenges and opportunities taking this forward to help patients with ALS.
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Affiliation(s)
- Greig Joilin
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - P Nigel Leigh
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Sarah F Newbury
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Majid Hafezparast
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
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Abstract
Chronic kidney disease is currently assessed by estimated glomerular filtration rate, a mathematical construct based on creatinine or creatinine and cystatin concentration. Creatinine-based equations have improved with standardization efforts and the Modification of Diet in Renal Disease Study (MDRD) and CKD-Epidemiology Collaboration Study (CKD-EPI). Because the measurement of creatinine is subject to interference from non-GFR determinants, alternative markers have long been sought. These have included cystatin C and low molecular weight proteins like β2-microglobulin and beta trace protein. Tubular disease often occurs before glomerular filtration is impaired and investigators have investigated the excretion of other low molecular weight proteins such as Neutrophil Gelatinase-Associated Lipocalin (NGAL) and Kidney Injury Molecule-1 and N-acetyl-β-d-glucosaminidase. While preliminary, there is some evidence linking these analytes with GFR, disease stage and mortality. Although asymmetrical dimethyl arginine, an inhibitor of nitric oxide, has been shown to be associated with progression of renal disease, symmetric dimethyl arginine may be a better marker. Recent work has also explored the potential of microRNA (miRNA) analysis and metabolomics studies to further elucidate this complex pathophysiologic disease process. Investigators hope to improve our ability to detect CKD by the use of test panels, i.e., various marker combinations thereof. Unfortunately, most of these markers lack standardization unlike traditional measures that rely on creatinine and cystatin C measurement.
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79
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Ichii O, Ohta H, Horino T, Nakamura T, Hosotani M, Mizoguchi T, Morishita K, Nakamura K, Sasaki N, Takiguchi M, Sato R, Oyamada K, Elewa YHA, Kon Y. Urinary Exosome-Derived microRNAs Reflecting the Changes in Renal Function in Cats. Front Vet Sci 2018; 5:289. [PMID: 30525049 PMCID: PMC6262179 DOI: 10.3389/fvets.2018.00289] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 10/31/2018] [Indexed: 12/22/2022] Open
Abstract
Increased incidence of kidney disease (KD) is a common concern in human and companion animals. Cats, in particular, are highly susceptible to KD. Novel KD biomarkers would help to address these problems. Therefore, we are focusing on microRNA, a highly conserved nucleic acid, as a KD biomarker for various animals. We previously reported that altered levels of urinary exosome (UExo)-derived microRNAs indicate renal pathologies in dogs. This study comprehensively examined UExo-derived microRNAs, which reflected the KD status in cats. The examined cats were divided into two groups: normal renal function (NR) and KD. Based on our previous data in dogs and cats, as well as the present data on UExo-derived microRNAs in cats by next-generation sequencing, let-7b, let-7f, miR-10a, miR-10b, miR-21a, miR-22, miR-26a, miR-27b, miR-146a, miR-181a, miR-191, and miR-486a were identified as biomarker candidates. In summary, the levels of UExo-derived let-7b, miR-22, and miR-26a significantly decreased in cats with KD from the early stages of the disease. UExo-derived miRNA levels normalized to urinary creatinine or total RNA of miR-21a was significantly higher in the KD group. Importantly, the ratio of UExo-derived miR-21a to let-7b showed a significant and strongest correlation with serum creatinine (ρ = 0.751), blood urea nitrogen (ρ = 0.754), and urinary creatinine (ρ = −0.421) among all examined indices. Further, the ratio of miR-181a to let-7b or miR-10b significantly correlated with the progression of renal dysfunction in the KD group. Thus, we identified that UExo-derived microRNAs in cats, and their raw and normalized levels could indicate altered renal function.
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Affiliation(s)
- Osamu Ichii
- Laboratory of Anatomy, Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Hiroshi Ohta
- Laboratory of Veterinary Internal Medicine, Department of Veterinary Clinical Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Taro Horino
- Department of Endocrinology, Metabolism and Nephrology, Kochi Medical School, Kochi University, Nankoku, Japan
| | - Teppei Nakamura
- Laboratory of Anatomy, Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan.,Section of Biological Safety Research, Chitose Laboratory, Japan Food Research Laboratories, Chitose, Japan
| | - Marina Hosotani
- Laboratory of Anatomy, Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Tatsuya Mizoguchi
- Laboratory of Anatomy, Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Keitaro Morishita
- Veterinary Teaching Hospital, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Kensuke Nakamura
- Organization for Promotion of Tenure Track, University of Miyazaki, Miyazaki, Japan
| | - Noboru Sasaki
- Laboratory of Veterinary Internal Medicine, Department of Veterinary Clinical Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Mitsuyoshi Takiguchi
- Laboratory of Veterinary Internal Medicine, Department of Veterinary Clinical Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Ryo Sato
- Matsubara Animal Hospital, Matsubara, Japan
| | | | - Yaser Hosny Ali Elewa
- Laboratory of Anatomy, Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan.,Department of Histology and Cytology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Yasuhiro Kon
- Laboratory of Anatomy, Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
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80
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Chen T, Wang C, Yu H, Ding M, Zhang C, Lu X, Zhang CY, Zhang C. Increased urinary exosomal microRNAs in children with idiopathic nephrotic syndrome. EBioMedicine 2018; 39:552-561. [PMID: 30467011 PMCID: PMC6355644 DOI: 10.1016/j.ebiom.2018.11.018] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 11/07/2018] [Accepted: 11/10/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Urinary exosomal miRNAs are gaining increasing attention for their potential as ideal non-invasive biomarkers for kidney diseases; however, little is known about their diagnostic ability for paediatric nephrotic syndrome (NS). This study explored the clinical value of urinary exosomal miRNAs for paediatric idiopathic NS. METHODS Urine samples were collected from 129 NS children and 126 age-/sex-matched healthy controls. The miRNA profile of urinary exosomes was analysed by high-throughput Illumina sequencing via synthesis (SBS) technology followed by verification with a quantitative reverse-transcription polymerase chain reaction (RT-qPCR) assay arranged in two independent cohorts. Additionally, paired urine samples from 65 of these patients were collected before and after treatment. FINDINGS The Illumina SBS identified 30 markedly increased urinary exosomal miRNAs in NS children compared with controls (≥ 5-fold, P < .05). Fifteen miRNAs were selected for further investigation, of which 5 (miR-194-5p, miR-146b-5p, miR-378a-3p, miR-23b-3p and miR-30a-5p) were verified by RT-qPCR to be significantly and steadily increased in NS (> 3-fold, P < .01) and markedly reduced during the clinical remission period (P < .001). Moreover, the concentrations of miR-194-5p and miR-23b-3p were significantly positively correlated with the urine protein content and were markedly higher in the high urine protein group than in the low urine protein group (P < .001 and P < .01, respectively). INTERPRETATIONS We identified 5 altered urinary exosomal miRNAs in NS children with disease progression and treatment. These urinary exosomal miRNAs could be promising and non-invasive potential biomarker candidates for diagnosing, monitoring and stratifying paediatric NS. FUND: National Natural Science Foundation of China; Fund of State Key Laboratory of Analytical Chemistry for Life Science; National Basic Research Programme of China; Foundation of Jiangsu Provincial Medical Youth Talent.
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Affiliation(s)
- Tingting Chen
- Department of Clinical Laboratory, Jinling Hospital, Nanjing School of Clinical Medicine, Southern Medical University, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing, China; State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advance Research Institute of Life Sciences, Nanjing University, School of Life Sciences, Nanjing, China
| | - Cheng Wang
- Department of Clinical Laboratory, Jinling Hospital, Nanjing School of Clinical Medicine, Southern Medical University, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing, China; State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advance Research Institute of Life Sciences, Nanjing University, School of Life Sciences, Nanjing, China
| | - Hanqing Yu
- Department of Clinical Laboratory, Nanjing Children's Hospital, Nanjing, China
| | - Meng Ding
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advance Research Institute of Life Sciences, Nanjing University, School of Life Sciences, Nanjing, China
| | - Cuiping Zhang
- Department of Clinical Laboratory, Jinling Hospital, Nanjing School of Clinical Medicine, Southern Medical University, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing, China
| | - Xiaolan Lu
- Department of Clinical Laboratory, Jinling Hospital, Nanjing School of Clinical Medicine, Southern Medical University, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing, China; State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advance Research Institute of Life Sciences, Nanjing University, School of Life Sciences, Nanjing, China
| | - Chen-Yu Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advance Research Institute of Life Sciences, Nanjing University, School of Life Sciences, Nanjing, China.
| | - Chunni Zhang
- Department of Clinical Laboratory, Jinling Hospital, Nanjing School of Clinical Medicine, Southern Medical University, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing, China; State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, Advance Research Institute of Life Sciences, Nanjing University, School of Life Sciences, Nanjing, China.
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81
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Cañadas-Garre M, Anderson K, McGoldrick J, Maxwell AP, McKnight AJ. Genomic approaches in the search for molecular biomarkers in chronic kidney disease. J Transl Med 2018; 16:292. [PMID: 30359254 PMCID: PMC6203198 DOI: 10.1186/s12967-018-1664-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 10/14/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Chronic kidney disease (CKD) is recognised as a global public health problem, more prevalent in older persons and associated with multiple co-morbidities. Diabetes mellitus and hypertension are common aetiologies for CKD, but IgA glomerulonephritis, membranous glomerulonephritis, lupus nephritis and autosomal dominant polycystic kidney disease are also common causes of CKD. MAIN BODY Conventional biomarkers for CKD involving the use of estimated glomerular filtration rate (eGFR) derived from four variables (serum creatinine, age, gender and ethnicity) are recommended by clinical guidelines for the evaluation, classification, and stratification of CKD. However, these clinical biomarkers present some limitations, especially for early stages of CKD, elderly individuals, extreme body mass index values (serum creatinine), or are influenced by inflammation, steroid treatment and thyroid dysfunction (serum cystatin C). There is therefore a need to identify additional non-invasive biomarkers that are useful in clinical practice to help improve CKD diagnosis, inform prognosis and guide therapeutic management. CONCLUSION CKD is a multifactorial disease with associated genetic and environmental risk factors. Hence, many studies have employed genetic, epigenetic and transcriptomic approaches to identify biomarkers for kidney disease. In this review, we have summarised the most important studies in humans investigating genomic biomarkers for CKD in the last decade. Several genes, including UMOD, SHROOM3 and ELMO1 have been strongly associated with renal diseases, and some of their traits, such as eGFR and serum creatinine. The role of epigenetic and transcriptomic biomarkers in CKD and related diseases is still unclear. The combination of multiple biomarkers into classifiers, including genomic, and/or epigenomic, may give a more complete picture of kidney diseases.
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Affiliation(s)
- M. Cañadas-Garre
- Epidemiology and Public Health Research Group, Centre for Public Health, Belfast City Hospital, Queen’s University of Belfast, c/o University Floor, Level A, Tower Block, Lisburn Road, Belfast, BT9 7AB Northern Ireland UK
| | - K. Anderson
- Epidemiology and Public Health Research Group, Centre for Public Health, Belfast City Hospital, Queen’s University of Belfast, c/o University Floor, Level A, Tower Block, Lisburn Road, Belfast, BT9 7AB Northern Ireland UK
| | - J. McGoldrick
- Epidemiology and Public Health Research Group, Centre for Public Health, Belfast City Hospital, Queen’s University of Belfast, c/o University Floor, Level A, Tower Block, Lisburn Road, Belfast, BT9 7AB Northern Ireland UK
| | - A. P. Maxwell
- Epidemiology and Public Health Research Group, Centre for Public Health, Belfast City Hospital, Queen’s University of Belfast, c/o University Floor, Level A, Tower Block, Lisburn Road, Belfast, BT9 7AB Northern Ireland UK
- Regional Nephrology Unit, Belfast City Hospital, Belfast, UK
| | - A. J. McKnight
- Epidemiology and Public Health Research Group, Centre for Public Health, Belfast City Hospital, Queen’s University of Belfast, c/o University Floor, Level A, Tower Block, Lisburn Road, Belfast, BT9 7AB Northern Ireland UK
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82
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Gholaminejad A, Abdul Tehrani H, Gholami Fesharaki M. Identification of candidate microRNA biomarkers in renal fibrosis: a meta-analysis of profiling studies. Biomarkers 2018; 23:713-724. [DOI: 10.1080/1354750x.2018.1488275] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Alieh Gholaminejad
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hossein Abdul Tehrani
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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83
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Vall-Palomar M, Arévalo J, Ariceta G, Meseguer A. Establishment of urinary exosome-like vesicles isolation protocol for FHHNC patients and evaluation of different exosomal RNA extraction methods. J Transl Med 2018; 16:278. [PMID: 30305086 PMCID: PMC6180391 DOI: 10.1186/s12967-018-1651-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/01/2018] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Molecular and cellular pathophysiological events occurring in the majority of rare kidney diseases remain to be elucidated. Familial hypomagnesemia with hypercalciuria and nephrocalcinosis (FHHNC) is a rare autosomal recessive disorder caused by mutations in either CLDN16 or CLDN19 genes. This disease is characterized by massive urinary wasting of magnesium and calcium, osmosis deregulation and polyuria. Patients with p.G20D homozygous mutation in CLDN19 gene exhibit different progression to kidney failure suggesting that beyond the pathogenic mutation itself, other molecular events are favoring disease progression. Due to the fact that biopsy is not clinically indicated in these patients, urinary exosome-like vesicles (uEVs) can be envisioned as a valuable non-invasive source of information of events occurring in the kidney. Exosome research has increased notably to identify novel disease biomarkers but there is no consensus standardized protocols for uEVs isolation in patients with polyuria. For this reason, this work was aimed to evaluate and refine different uEVs isolation methods based on differential centrifugation, the gold standard method. RESULTS Characterization by NTA, cryo-TEM and immunoblotting techniques identified the most appropriate protocol to obtain the highest yield and purest uEVs enriched fraction possible from urine control samples and FHHNC patients. Moreover, we tested five different RNA extraction methods and evaluated the miRNA expression pattern by qRT-PCR. CONCLUSIONS In summary, we have standardized the conditions to proceed with the identification of differentially expressed miRNAs in uEVs of FHHNC patients, or other renal diseases characterized by polyuria.
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Affiliation(s)
- M. Vall-Palomar
- Fisiopatologia Renal, Centre d’Investigacions en Bioquímica i Biologia Molecular (CIBBIM), Institut de Recerca Vall d’Hebron (VHIR), Barcelona, Spain
| | - J. Arévalo
- Fisiopatologia Renal, Centre d’Investigacions en Bioquímica i Biologia Molecular (CIBBIM), Institut de Recerca Vall d’Hebron (VHIR), Barcelona, Spain
| | - G. Ariceta
- Fisiopatologia Renal, Centre d’Investigacions en Bioquímica i Biologia Molecular (CIBBIM), Institut de Recerca Vall d’Hebron (VHIR), Barcelona, Spain
- Nefrologia Pediàtrica, Hospital Universitari Vall d’Hebron (HUVH), Barcelona, Spain
| | - A. Meseguer
- Fisiopatologia Renal, Centre d’Investigacions en Bioquímica i Biologia Molecular (CIBBIM), Institut de Recerca Vall d’Hebron (VHIR), Barcelona, Spain
- Departament de Bioquímica i Biologia Molecular, Unitat de Bioquímica de Medicina, Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
- Red de Investigación Renal (REDINREN), Instituto de Salud Carlos III-FEDER, Madrid, Spain
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84
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Liu Z, Cauvi DM, Bernardino EMA, Lara B, Lizardo RE, Hawisher D, Bickler S, De Maio A. Isolation and characterization of human urine extracellular vesicles. Cell Stress Chaperones 2018; 23:943-953. [PMID: 29796787 PMCID: PMC6111092 DOI: 10.1007/s12192-018-0902-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/16/2018] [Accepted: 04/17/2018] [Indexed: 12/13/2022] Open
Abstract
Extracellular vesicles (ECV) reflect physiological or pathological conditions, emerging as potential biomarkers for disease. They can be obtained from a variety of body fluids, particularly urine that is an ideal source because it can be obtained in great quantities, recurrently and with minimal intervention. However, the characterization of urine ECV is challenging because the preparation is usually contaminated with soluble proteins, such as uromodulin (UMOD) or Tamm-Horsfall glycoprotein that forms large extracellular filaments co-sedimenting with ECV. We developed a method to obtain human urine ECV free of UMOD by the addition of ZnSO4 prior to vesicle isolation by differential centrifugation. Treatment with ZnSO4 did not affect the size and concentration of the vesicle preparation and preserved the storage of the samples at low temperatures. We did not observe a variation in the number of vesicles isolated during different times of the day or different days between different donors. The glycoprotein pattern of urine ECV was characterized by binding to concanavalin A (Con A) and mass spectroscopy. Several markers were found, including dipeptidyl peptidase IV (CD26), vacuolar protein sorting factor 4A (VPS4A) and dipeptidase 1 (DPEP1), and galectin 3 binding protein (G3-BP). The levels of VPS4A and DPEP1 were similar in ECV preparations obtained from several donors of both sexes. Con A binding pattern and monosaccharide composition were also comparable between subjects. In summary, our method for the isolation of highly pure ECV derived from human urine is likely to help in the use of these vesicles as potential biomarkers.
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Affiliation(s)
- Zhanguo Liu
- Department of Surgery, School of Medicine University of California San Diego, 9500 Gilman Drive, #0739, La Jolla, CA, 92093-0739, USA
- Department of Critical Care Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - David M Cauvi
- Department of Surgery, School of Medicine University of California San Diego, 9500 Gilman Drive, #0739, La Jolla, CA, 92093-0739, USA
| | - Erika M A Bernardino
- Department of Surgery, School of Medicine University of California San Diego, 9500 Gilman Drive, #0739, La Jolla, CA, 92093-0739, USA
| | - Bernardo Lara
- Department of Surgery, School of Medicine University of California San Diego, 9500 Gilman Drive, #0739, La Jolla, CA, 92093-0739, USA
| | | | - Dennis Hawisher
- Department of Surgery, School of Medicine University of California San Diego, 9500 Gilman Drive, #0739, La Jolla, CA, 92093-0739, USA
| | - Stephen Bickler
- Department of Surgery, School of Medicine University of California San Diego, 9500 Gilman Drive, #0739, La Jolla, CA, 92093-0739, USA
| | - Antonio De Maio
- Department of Surgery, School of Medicine University of California San Diego, 9500 Gilman Drive, #0739, La Jolla, CA, 92093-0739, USA.
- Department of Neurosciences, School of Medicine University of California San Diego, La Jolla, CA, USA.
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85
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Feng Y, Lv LL, Wu WJ, Li ZL, Chen J, Ni HF, Zhou LT, Tang TT, Wang FM, Wang B, Chen PS, Crowley SD, Liu BC. Urinary Exosomes and Exosomal CCL2 mRNA as Biomarkers of Active Histologic Injury in IgA Nephropathy. THE AMERICAN JOURNAL OF PATHOLOGY 2018; 188:2542-2552. [PMID: 30142333 DOI: 10.1016/j.ajpath.2018.07.017] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/03/2018] [Accepted: 07/24/2018] [Indexed: 01/21/2023]
Abstract
IgA nephropathy (IgAN) features variable renal pathology and a heterogeneous clinical course. Our aim was to search noninvasive biomarkers from urinary exosomes for IgAN patients; membrane nephropathy and minimal change disease were included as other glomerulopathy controls. Transmission electron microscopy and nanoparticle tracking analysis confirmed the size and morphology characteristic of urinary exosomes. Exosome markers (Alix and CD63) as well as renal cell markers [aquaporin 2 (AQP2) and nephrin] were detected, which indicate the renal origin of urinary exosomes. Exosome excretion was increased markedly in IgAN patients compared with controls and correlated with levels of proteinuria and tubular injury. More important, urinary exosome excretion correlated with greater histologic activity (mesangial hypercellularity, crescents, and endocapillary hypercellularity). Profiling of the inflammation-related mRNA revealed that exosomal chemokine (C-C motif) ligand 2 (CCL2) was up-regulated in IgAN patients. In a validation study, CCL2 was exclusively highly expressed in IgAN patients compared with healthy controls as well as minimal change disease and membrane nephropathy patients. Also, a correlation between exosomal CCL2 and estimated glomerular filtration rate levels was found in IgAN. Exosomal CCL2 was correlated with tubulointerstitial inflammation and C3 deposition. High CCL2 levels at the time of renal biopsy were associated with subsequent deterioration in renal function. Thus, urinary exosomes and exosomal CCL2 mRNA are promising biomarkers reflecting active renal histologic injury and renal function deterioration in IgAN.
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Affiliation(s)
- Ye Feng
- Institute of Nephrology, Zhongda Hospital, Southeast University School of Medicine, Nanjing, China
| | - Lin-Li Lv
- Institute of Nephrology, Zhongda Hospital, Southeast University School of Medicine, Nanjing, China.
| | - Wei-Jun Wu
- Institute of Nephrology, Zhongda Hospital, Southeast University School of Medicine, Nanjing, China
| | - Zuo-Lin Li
- Institute of Nephrology, Zhongda Hospital, Southeast University School of Medicine, Nanjing, China
| | - Jun Chen
- Institute of Nephrology, Zhongda Hospital, Southeast University School of Medicine, Nanjing, China
| | - Hai-Feng Ni
- Institute of Nephrology, Zhongda Hospital, Southeast University School of Medicine, Nanjing, China
| | - Le-Ting Zhou
- Institute of Nephrology, Zhongda Hospital, Southeast University School of Medicine, Nanjing, China
| | - Tao-Tao Tang
- Institute of Nephrology, Zhongda Hospital, Southeast University School of Medicine, Nanjing, China
| | - Feng-Mei Wang
- Institute of Nephrology, Zhongda Hospital, Southeast University School of Medicine, Nanjing, China
| | - Bin Wang
- Institute of Nephrology, Zhongda Hospital, Southeast University School of Medicine, Nanjing, China
| | - Ping-Sheng Chen
- Institute of Nephrology, Zhongda Hospital, Southeast University School of Medicine, Nanjing, China
| | - Steven D Crowley
- Division of Nephrology, Department of Medicine, Duke University, Durham VA Medical Centers, Durham, North Carolina
| | - Bi-Cheng Liu
- Institute of Nephrology, Zhongda Hospital, Southeast University School of Medicine, Nanjing, China.
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86
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Srivastava A, Moxley K, Ruskin R, Dhanasekaran DN, Zhao YD, Ramesh R. A Non-invasive Liquid Biopsy Screening of Urine-Derived Exosomes for miRNAs as Biomarkers in Endometrial Cancer Patients. AAPS J 2018. [PMID: 29987691 DOI: 10.1208/s12248-018-0220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Exosomes have great potential to serve as a source of diagnostic and prognostic biomarkers for endometrial cancer (EC). Urine-derived exosomes from patients with EC and patients with symptoms of EC, but without established EC, were used to evaluate a unique miRNA expression profile. Of the 84 miRNA studied, 57 were amplified in qPCR, suggesting the differential packaging of miRNA in exosomes. Further, hsa-miR-200c-3p was identified to be enriched the most. Various bioinformatics and in silico tools were used to evaluate the biological significance of hsa-miR-200c-3p in EC. We conclude that differential miRNA in exosomes can be utilized for discovery of biomarker signatures and EC diagnosis; hsa-miR-200c-3p is one such candidate. Urine-derived exosomes pave the way for the development of non-invasive biomarkers.
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Affiliation(s)
- Akhil Srivastava
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.,Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Katherine Moxley
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.,Department of Gynecology Oncology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Rachel Ruskin
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.,Department of Gynecology Oncology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Danny Natarajan Dhanasekaran
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.,Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Yan Daniel Zhao
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.,Department of Biostatistics and Epidemiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Rajagopal Ramesh
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA. .,Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA. .,Graduate Program in Biomedical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA. .,Department of Pathology, Stanton L. Young Biomedical Research Center, Suite 1403, 975 N.E., 10th Street, Oklahoma City, Oklahoma, 73104, USA.
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87
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Srivastava A, Moxley K, Ruskin R, Dhanasekaran DN, Zhao YD, Ramesh R. A Non-invasive Liquid Biopsy Screening of Urine-Derived Exosomes for miRNAs as Biomarkers in Endometrial Cancer Patients. AAPS JOURNAL 2018; 20:82. [PMID: 29987691 DOI: 10.1208/s12248-018-0220-y] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 03/16/2018] [Indexed: 12/18/2022]
Abstract
Exosomes have great potential to serve as a source of diagnostic and prognostic biomarkers for endometrial cancer (EC). Urine-derived exosomes from patients with EC and patients with symptoms of EC, but without established EC, were used to evaluate a unique miRNA expression profile. Of the 84 miRNA studied, 57 were amplified in qPCR, suggesting the differential packaging of miRNA in exosomes. Further, hsa-miR-200c-3p was identified to be enriched the most. Various bioinformatics and in silico tools were used to evaluate the biological significance of hsa-miR-200c-3p in EC. We conclude that differential miRNA in exosomes can be utilized for discovery of biomarker signatures and EC diagnosis; hsa-miR-200c-3p is one such candidate. Urine-derived exosomes pave the way for the development of non-invasive biomarkers.
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Affiliation(s)
- Akhil Srivastava
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.,Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Katherine Moxley
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.,Department of Gynecology Oncology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Rachel Ruskin
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.,Department of Gynecology Oncology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Danny Natarajan Dhanasekaran
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.,Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Yan Daniel Zhao
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA.,Department of Biostatistics and Epidemiology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Rajagopal Ramesh
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA. .,Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA. .,Graduate Program in Biomedical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA. .,Department of Pathology, Stanton L. Young Biomedical Research Center, Suite 1403, 975 N.E., 10th Street, Oklahoma City, Oklahoma, 73104, USA.
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88
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Pre-Analytical Handling Conditions and Small RNA Recovery from Urine for miRNA Profiling. J Mol Diagn 2018; 20:565-571. [PMID: 29936254 DOI: 10.1016/j.jmoldx.2018.04.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 03/19/2018] [Accepted: 04/30/2018] [Indexed: 12/24/2022] Open
Abstract
There are currently no standardized protocols for pre-analytical handling of urine to best preserve small RNA for miRNA profiling studies. miRNA is an attractive candidate as a potential biomarker because of the high level of stability in body fluids and its ability to be quantified on multiple high-throughput platforms. We present a comparison of small RNA recovery and stability in urine under alternate pre-analytical handling conditions and extend recommendations on what conditions optimize yield of miRNA from cell-free urine and urine extracellular vesicles (EVs). Using an affinity slurry for isolation of small RNA from urine, we found that urine samples held at room temperature (20°C) for up to 8 hours before processing yield the highest amounts of intact small RNAs from EVs. Some miRNA is lost from urine samples when held 2°C to 4°C and/or frozen before EV isolation, likely because of EV entrapment in uromodulin precipitates. However, we found that a simple 5-minute incubation of urine containing cold-induced precipitate at 37°C resolubilizes much of this precipitate and results in an increased recovery of EVs and miRNAs. Finally, small RNA integrity can be compromised when whole urine is held at 37°C for as little as 4 hours and is not conducive to efficient miRNA profiling.
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89
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Xu H, Chen Y, Dong X, Wang X. Serum Exosomal Long Noncoding RNAs ENSG00000258332.1 and LINC00635 for the Diagnosis and Prognosis of Hepatocellular Carcinoma. Cancer Epidemiol Biomarkers Prev 2018; 27:710-716. [PMID: 29650788 DOI: 10.1158/1055-9965.epi-17-0770] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 12/09/2017] [Accepted: 04/02/2018] [Indexed: 12/18/2022] Open
Abstract
Background: Increasing studies suggest that long noncoding RNAs (lncRNAs) are involved in carcinogenesis of human cancers and might be used as diagnostic biomarkers for cancers.Methods: A total of 301 participants were recruited in the first part of the study, including a hepatocellular carcinoma (HCC) group (n = 60), liver cirrhosis (LC) group (n = 85), chronic hepatitis B (CHB) group (n = 96), and healthy subjects (n = 60). In the second part, we collected 55 HCC patients, 60 CHB patients, and 60 healthy subjects as an independent cohort to validate the ability of the experiential lncRNAs for identifying HCC from CHB. A commercial kit was used to isolate serum exosomes and total RNA. The relative levels of lnRNAs and GAPDH mRNA were measured with TaqMan PCR.Results: The results showed that the levels of ENSG00000258332.1 and LINC00635 in the HCC group were significantly higher than those in the other groups (all P < 0.05). A high ENSG00000258332.1 level in HCC was associated with portal vein tumor emboli, lymph node metastasis, TNM stage, and overall survival (OS; all P < 0.05), and a high LINC00635 level was related to lymph node metastasis, TNM stage, and OS (all P < 0.05). ENSG00000258332.1 discriminated HCC from CHB, gaining an area under the ROC curve (AUC) of 0.719 (cutoff value of 1.345); LINC00635 gained an AUC of 0.750 (cutoff value of 1.690). Furthermore, the AUC for the combination of the 2 lncRNAs and serum AFP (cutoff value of 20 μg/L) was 0.894. The abilities of the 2 lncRNAs for identifying HCC from CHB were validated by an independent cohort.Conclusions: The results suggested that the combination of serum exosomal ENSG00000258332.1, LINC00635, and AFP may be a valuable assay in diagnosis and prognosis of HCC.Impact: Our data will shed light on exosomal lncRNAs as biomarkers for HCC. Cancer Epidemiol Biomarkers Prev; 27(6); 710-6. ©2018 AACR.
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Affiliation(s)
- Hong Xu
- Department of Laboratory Medicine, Hangzhou First People's Hospital, Hangzhou, China
| | - Yueming Chen
- Department of Laboratory Medicine, Hangzhou First People's Hospital, Hangzhou, China.
| | - Xueyan Dong
- Department of Laboratory Medicine, Hangzhou First People's Hospital, Hangzhou, China
| | - Xianjun Wang
- Department of Laboratory Medicine, Hangzhou First People's Hospital, Hangzhou, China
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90
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Zhong Z, Rosenow M, Xiao N, Spetzler D. Profiling plasma extracellular vesicle by pluronic block-copolymer based enrichment method unveils features associated with breast cancer aggression, metastasis and invasion. J Extracell Vesicles 2018; 7:1458574. [PMID: 29696079 PMCID: PMC5912199 DOI: 10.1080/20013078.2018.1458574] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 03/17/2018] [Indexed: 12/12/2022] Open
Abstract
Extracellular vesicle (EV)-based liquid biopsies have been proposed to be a readily obtainable biological substrate recently for both profiling and diagnostics purposes. Development of a fast and reliable preparation protocol to enrich such small particles could accelerate the discovery of informative, disease-related biomarkers. Though multiple EV enrichment protocols are available, in terms of efficiency, reproducibility and simplicity, precipitation-based methods are most amenable to studies with large numbers of subjects. However, the selectivity of the precipitation becomes critical. Here, we present a simple plasma EV enrichment protocol based on pluronic block copolymer. The enriched plasma EV was able to be verified by multiple platforms. Our results showed that the particles enriched from plasma by the copolymer were EV size vesicles with membrane structure; proteomic profiling showed that EV-related proteins were significantly enriched, while high-abundant plasma proteins were significantly reduced in comparison to other precipitation-based enrichment methods. Next-generation sequencing confirmed the existence of various RNA species that have been observed in EVs from previous studies. Small RNA sequencing showed enriched species compared to the corresponding plasma. Moreover, plasma EVs enriched from 20 advanced breast cancer patients and 20 age-matched non-cancer controls were profiled by semi-quantitative mass spectrometry. Protein features were further screened by EV proteomic profiles generated from four breast cancer cell lines, and then selected in cross-validation models. A total of 60 protein features that highly contributed in model prediction were identified. Interestingly, a large portion of these features were associated with breast cancer aggression, metastasis as well as invasion, consistent with the advanced clinical stage of the patients. In summary, we have developed a plasma EV enrichment method with improved precipitation selectivity and it might be suitable for larger-scale discovery studies.
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Affiliation(s)
- Zhenyu Zhong
- Caris Life Sciences, Phoenix, AZ, USA.,Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ, USA
| | | | - Nick Xiao
- Caris Life Sciences, Phoenix, AZ, USA
| | - David Spetzler
- Caris Life Sciences, Phoenix, AZ, USA.,Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, AZ, USA
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91
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Whole-Transcriptome Sequencing: a Powerful Tool for Vascular Tissue Engineering and Endothelial Mechanobiology. High Throughput 2018; 7:ht7010005. [PMID: 29485616 PMCID: PMC5876531 DOI: 10.3390/ht7010005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 02/18/2018] [Accepted: 02/19/2018] [Indexed: 02/07/2023] Open
Abstract
Among applicable high-throughput techniques in cardiovascular biology, whole-transcriptome sequencing is of particular use. By utilizing RNA that is isolated from virtually all cells and tissues, the entire transcriptome can be evaluated. In comparison with other high-throughput approaches, RNA sequencing is characterized by a relatively low-cost and large data output, which permits a comprehensive analysis of spatiotemporal variation in the gene expression profile. Both shear stress and cyclic strain exert hemodynamic force upon the arterial endothelium and are considered to be crucial determinants of endothelial physiology. Laminar blood flow results in a high shear stress that promotes atheroresistant endothelial phenotype, while a turbulent, oscillatory flow yields a pathologically low shear stress that disturbs endothelial homeostasis, making respective arterial segments prone to atherosclerosis. Severe atherosclerosis significantly impairs blood supply to the organs and frequently requires bypass surgery or an arterial replacement surgery that requires tissue-engineered vascular grafts. To provide insight into patterns of gene expression in endothelial cells in native or bioartificial arteries under different biomechanical conditions, this article discusses applications of whole-transcriptome sequencing in endothelial mechanobiology and vascular tissue engineering.
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92
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Ichii O, Horino T. MicroRNAs associated with the development of kidney diseases in humans and animals. J Toxicol Pathol 2018; 31:23-34. [PMID: 29479137 PMCID: PMC5820100 DOI: 10.1293/tox.2017-0051] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 09/10/2017] [Indexed: 12/20/2022] Open
Abstract
Mature microRNAs (miRNAs) are single-stranded RNAs with approximately 18-25 bases, and their sequences are highly conserved among animals. miRNAs act as posttranscriptional regulators by binding mRNAs, and their main function involves the degradation of their target mRNAs. Recent studies revealed altered expression of miRNAs in the kidneys during the progression of acute kidney injury (AKI) and chronic kidney disease (CKD) in humans and experimental rodent models by using high-throughput screening techniques including microarray and small RNA sequencing. Particularly, miR-21 seems to be strongly associated with renal pathogenesis both in the glomerulus and tubulointerstitium. Furthermore, abundant evidence has been gathered showing the involvement of miRNAs in renal fibrosis. Because of the complex morphofunctional organization of the mammalian kidneys, it is crucial both to determine the exact localization of the kidney cells that express the miRNAs, which has been addressed mainly using in situ hybridization methods, and to identify precisely which mRNAs are bound and degraded by these miRNAs, which has been studied mostly through in vitro analysis. To discover novel biomarker candidates, miRNA levels in urine supernatant, sediment, and exosomal fraction were comprehensively investigated in different types of kidney disease, including drug-induced AKI, ischemia-induced AKI, diabetic nephropathy, lupus nephritis, and IgA nephropathy. Recent studies also demonstrated the therapeutic effect of miRNA and/or anti-miRNA administrations. The intent of this review is to illustrate the state-of-the-art research in the field of miRNAs associated with renal pathogenesis, especially focusing on AKI and CKD in humans and animal models.
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Affiliation(s)
- Osamu Ichii
- Laboratory of Anatomy, Department of Basic Veterinary
Sciences, Faculty of Veterinary Medicine, Hokkaido University, Kita 18-Nishi 9, Kita-ku,
Sapporo, Hokkaido 060-0818, Japan
| | - Taro Horino
- Laboratory of Anatomy, Department of Basic Veterinary
Sciences, Faculty of Veterinary Medicine, Hokkaido University, Kita 18-Nishi 9, Kita-ku,
Sapporo, Hokkaido 060-0818, Japan
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93
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Renal fibrosis: Recent translational aspects. Matrix Biol 2017; 68-69:318-332. [PMID: 29292218 DOI: 10.1016/j.matbio.2017.12.013] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/15/2017] [Accepted: 12/21/2017] [Indexed: 01/14/2023]
Abstract
Renal fibrogenesis is the common final pathway to all renal injuries that consequently leads to Chronic Kidney Disease (CKD). Renal fibrogenesis corresponds to the replacement of renal functional tissue by extra-cellular matrix proteins, mainly collagens, that ultimately impairs kidney function. Blockade of the renin angiotensin system by Angiotensin Converting Enzyme inhibitors (ACEi) or Angiotensin Receptor Blockers (ARBs) was the first strategy that proved efficient to blunt the development of renal fibrogenesis independently of its systemic action on blood pressure. Although this strategy has been published 20years ago, there is to date no novel therapeutic targets that are both safe and efficient in hindering renal fibrogenesis and CKD in humans, nor there is any new biomarker to precisely quantify this process. In our review, we will focus on the most recent pathways leading to fibrogenesis which have a high therapeutic potential in humans and on the most promising biomarkers of renal fibrosis.
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94
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Isolation and characterization of urinary extracellular vesicles: implications for biomarker discovery. Nat Rev Nephrol 2017. [PMID: 29081510 DOI: 10.1038/nrneph.2017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Urine is a valuable diagnostic medium and, with the discovery of urinary extracellular vesicles, is viewed as a dynamic bioactive fluid. Extracellular vesicles are lipid-enclosed structures that can be classified into three categories: exosomes, microvesicles (or ectosomes) and apoptotic bodies. This classification is based on the mechanisms by which membrane vesicles are formed: fusion of multivesicular bodies with the plasma membranes (exosomes), budding of vesicles directly from the plasma membrane (microvesicles) or those shed from dying cells (apoptotic bodies). During their formation, urinary extracellular vesicles incorporate various cell-specific components (proteins, lipids and nucleic acids) that can be transferred to target cells. The rigour needed for comparative studies has fueled the search for optimal approaches for their isolation, purification, and characterization. RNA, the newest extracellular vesicle component to be discovered, has received substantial attention as an extracellular vesicle therapeutic, and compelling evidence suggests that ex vivo manipulation of microRNA composition may have uses in the treatment of kidney disorders. The results of these studies are building the case that urinary extracellular vesicles act as mediators of renal pathophysiology. As the field of extracellular vesicle studies is burgeoning, this Review focuses on primary data obtained from studies of human urine rather than on data from studies of laboratory animals or cultured immortalized cells.
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95
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Isolation and characterization of urinary extracellular vesicles: implications for biomarker discovery. Nat Rev Nephrol 2017; 13:731-749. [PMID: 29081510 DOI: 10.1038/nrneph.2017.148] [Citation(s) in RCA: 305] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Urine is a valuable diagnostic medium and, with the discovery of urinary extracellular vesicles, is viewed as a dynamic bioactive fluid. Extracellular vesicles are lipid-enclosed structures that can be classified into three categories: exosomes, microvesicles (or ectosomes) and apoptotic bodies. This classification is based on the mechanisms by which membrane vesicles are formed: fusion of multivesicular bodies with the plasma membranes (exosomes), budding of vesicles directly from the plasma membrane (microvesicles) or those shed from dying cells (apoptotic bodies). During their formation, urinary extracellular vesicles incorporate various cell-specific components (proteins, lipids and nucleic acids) that can be transferred to target cells. The rigour needed for comparative studies has fueled the search for optimal approaches for their isolation, purification, and characterization. RNA, the newest extracellular vesicle component to be discovered, has received substantial attention as an extracellular vesicle therapeutic, and compelling evidence suggests that ex vivo manipulation of microRNA composition may have uses in the treatment of kidney disorders. The results of these studies are building the case that urinary extracellular vesicles act as mediators of renal pathophysiology. As the field of extracellular vesicle studies is burgeoning, this Review focuses on primary data obtained from studies of human urine rather than on data from studies of laboratory animals or cultured immortalized cells.
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96
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Hosohata K. Biomarkers for Chronic Kidney Disease Associated with High Salt Intake. Int J Mol Sci 2017; 18:ijms18102080. [PMID: 28973979 PMCID: PMC5666762 DOI: 10.3390/ijms18102080] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 09/25/2017] [Accepted: 09/29/2017] [Indexed: 12/31/2022] Open
Abstract
High salt intake has been related to the development to chronic kidney disease (CKD) as well as hypertension. In its early stages, symptoms of CKD are usually not apparent, especially those that are induced in a “silent” manner in normotensive individuals, thereby providing a need for some kind of urinary biomarker to detect injury at an early stage. Because traditional renal biomarkers such as serum creatinine are insensitive, it is difficult to detect kidney injury induced by a high-salt diet, especially in normotensive individuals. Recently, several new biomarkers for damage of renal tubular epithelia such as neutrophil gelatinase-associated lipocalin (NGAL) and kidney injury molecule-1 (Kim-1) have been identified. Previously, we found a novel renal biomarker, urinary vanin-1, in several animal models with renal tubular injury. However, there are few studies about early biomarkers of the progression to CKD associated with a high-salt diet. This review presents some new insights about these novel biomarkers for CKD in normotensives and hypertensives under a high salt intake. Interestingly, our recent reports using spontaneously hypertensive rats (SHR) and normotensive Wistar Kyoto rats (WKY) fed a high-salt diet revealed that urinary vanin-1 and NGAL are earlier biomarkers of renal tubular damage in SHR and WKY, whereas urinary Kim-1 is only useful as a biomarker of salt-induced renal injury in SHR. Clinical studies will be needed to clarify these findings.
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Affiliation(s)
- Keiko Hosohata
- Education and Research Center for Clinical Pharmacy, Osaka University of Pharmaceutical Sciences, Osaka 569-1094, Japan.
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97
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Xie Y, Jia Y, Cuihua X, Hu F, Xue M, Xue Y. Urinary Exosomal MicroRNA Profiling in Incipient Type 2 Diabetic Kidney Disease. J Diabetes Res 2017; 2017:6978984. [PMID: 29038788 PMCID: PMC5605810 DOI: 10.1155/2017/6978984] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 06/19/2017] [Accepted: 06/28/2017] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Albuminuria is an early sign but not a strong predictor of diabetic kidney disease (DKD). Owing to their high stability, urinary exosomal miRNAs can be useful predictors of the progression of early-stage DKD to renal failure; fluid biopsies are ideal for detecting abnormalities in these miRNAs. The aim of this study was to identify novel differentially expressed miRNAs as urine biomarkers for type 2 DKD by comparing between patients of type 2 diabetes (T2D) with and without macroalbuminuria. METHODS Ten patients with T2D, including five who had no renal disease and five with macroalbuminuria (DKD G1-2A3), were selected for this study. Exosome- (UExo-) derived miRNA profiles were used to identify candidate biomarkers, a subset of which was verified using quantitative reverse transcription PCR. RESULTS A total of 496 UExo-derived miRNA species were found to be differentially expressed (>2-fold) in patients with DKD, compared to those with T2D. A validation analysis revealed that three miRNAs (miR-362-3p, miR-877-3p, and miR-150-5p) were upregulated and one (miR-15a-5p) was downregulated. These miRNAs might regulate DKD through p53, mTOR, and AMPK pathways. CONCLUSIONS In conclusion, UExo-derived miRNAs were altered in type 2 DKD. MiR-362-3p, miR-877-3p, miR-150-5p, and miR-15a-5p might be novel biomarkers for incipient DKD.
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Affiliation(s)
- Yijun Xie
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Yijie Jia
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Xie Cuihua
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Fang Hu
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Meng Xue
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Yaoming Xue
- Department of Endocrinology and Metabolism, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
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98
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Rysz J, Gluba-Brzózka A, Franczyk B, Jabłonowski Z, Ciałkowska-Rysz A. Novel Biomarkers in the Diagnosis of Chronic Kidney Disease and the Prediction of Its Outcome. Int J Mol Sci 2017; 18:E1702. [PMID: 28777303 PMCID: PMC5578092 DOI: 10.3390/ijms18081702] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 07/17/2017] [Accepted: 07/26/2017] [Indexed: 02/07/2023] Open
Abstract
In its early stages, symptoms of chronic kidney disease (CKD) are usually not apparent. Significant reduction of the kidney function is the first obvious sign of disease. If diagnosed early (stages 1 to 3), the progression of CKD can be altered and complications reduced. In stages 4 and 5 extensive kidney damage is observed, which usually results in end-stage renal failure. Currently, the diagnosis of CKD is made usually on the levels of blood urea and serum creatinine (sCr), however, sCr has been shown to be lacking high predictive value. Due to the development of genomics, epigenetics, transcriptomics, proteomics, and metabolomics, the introduction of novel techniques will allow for the identification of novel biomarkers in renal diseases. This review presents some new possible biomarkers in the diagnosis of CKD and in the prediction of outcome, including asymmetric dimethylarginine (ADMA), symmetric dimethylarginine (SDMA), uromodulin, kidney injury molecule-1 (KIM-1), neutrophil gelatinase-associated lipocalin (NGAL), miRNA, ncRNA, and lincRNA biomarkers and proteomic and metabolomic biomarkers. Complicated pathomechanisms of CKD development and progression require not a single marker but their combination in order to mirror all types of alterations occurring in the course of this disease. It seems that in the not so distant future, conventional markers may be exchanged for new ones, however, confirmation of their efficacy, sensitivity and specificity as well as the reduction of analysis costs are required.
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Affiliation(s)
- Jacek Rysz
- Department of Nephrology, Hypertension and Family Medicine, Medical University of Lodz, Zeromskiego 113, 90-549 Lodz, Poland.
| | - Anna Gluba-Brzózka
- Department of Nephrology, Hypertension and Family Medicine, WAM Teaching Hospital, Zeromskiego 113, 90-549 Lodz, Poland.
| | - Beata Franczyk
- Department of Nephrology, Hypertension and Family Medicine, Medical University of Lodz, Zeromskiego 113, 90-549 Lodz, Poland.
| | - Zbigniew Jabłonowski
- I Department of Urology, Medical University of Lodz, Zeromskiego 113, 90-549 Lodz, Poland.
| | - Aleksandra Ciałkowska-Rysz
- Palliative Medicine Unit, Chair of Oncology, Medical University of Lodz, Zeromskiego 113, 90-549 Lodz, Poland.
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Kumar A, Rimando AM, Levenson AS. Resveratrol and pterostilbene as a microRNA-mediated chemopreventive and therapeutic strategy in prostate cancer. Ann N Y Acad Sci 2017; 1403:15-26. [PMID: 28662290 DOI: 10.1111/nyas.13372] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/07/2017] [Accepted: 04/10/2017] [Indexed: 12/23/2022]
Abstract
Growing evidence indicates that deregulation of the epigenetic machinery comprising the microRNA (miRNA) network is a critical factor in the progression of various diseases, including cancer. Concurrently, dietary phytochemicals are being intensively studied for their miRNA-mediated health-beneficial properties, such as anti-inflammatory, cardioprotective, antioxidative, and anticancer properties. Available experimental data have suggested that dietary polyphenols may be effective miRNA-modulating chemopreventive and therapeutic agents. Moreover, noninvasive detection of changes in miRNA expression in liquid biopsies opens enormous possibilities for their clinical utilization as novel prognostic and predictive biomarkers. In our published studies, we identified resveratrol-regulated miRNA profiles in prostate cancer. Resveratrol downregulated the phosphatase and tensin homolog (PTEN)-targeting members of the oncogenic miR-17 family of miRNAs, which are overexpressed in prostate cancer. We have functionally validated the miRNA-mediated ability of resveratrol and its potent analog pterostilbene to rescue the tumor suppressor activity of PTEN in vitro and in vivo. Taken together, our findings implicate the use of resveratrol and its analogs as an attractive miRNA-mediated chemopreventive and therapeutic strategy in prostate cancer and the use of circulating miRNAs as potential predictive biomarkers for clinical development.
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Affiliation(s)
- Avinash Kumar
- Arnold and Marie Schwartz College of Pharmacy and Health Sciences, Long Island University, Brooklyn, New York
| | - Agnes M Rimando
- United States Department of Agriculture, Agricultural Research Service, Natural Products Utilization Research Unit, Oxford, Mississippi
| | - Anait S Levenson
- Arnold and Marie Schwartz College of Pharmacy and Health Sciences, Long Island University, Brooklyn, New York
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Abstract
Extracellular vesicles are a heterogeneous population of microparticles released by virtually all living cells which have been recently widely investigated in different biological fields. They are typically composed of two primary types (exosomes and microvesicles) and are recently commanding increasing attention as mediators of cellular signaling. Indeed, these vesicles can affect recipient cells by carrying and delivering complex cargos of biomolecules (including proteins, lipids and nucleic acids), protected from enzymatic degradation in the environment. Their importance has been demonstrated in the pathophysiology of several organs, in particular in kidney, where different cell types secrete extracellular vesicles that mediate their communication with downstream urinary tract cells. Over the past few years, evidence has been shown that vesicles participate in kidney development and normal physiology. Moreover, EVs are widely demonstrated to be implicated in cellular signaling during renal regenerative and pathological processes. Although many EV mechanisms are still poorly understood, in particular in kidney, the discovery of their role could help to shed light on renal biological processes which are so far elusive. Lastly, extracellular vesicles secreted by renal cells gather in urine, thus becoming a great resource for disease or recovery markers and a promising non-invasive diagnostic instrument for renal disease. In the present review, we discuss the most recent findings on the role of extracellular vesicles in renal physiopathology and their potential implication in diagnosis and therapy.
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Affiliation(s)
| | - Chiara Gai
- Stem Cell Laboratory, Department of Medical Sciences, University of TurinTurin, Italy
| | - Benedetta Bussolati
- Department of Molecular Biotechnology and Health Sciences, University of TurinTurin, Italy
| | - Giovanni Camussi
- Stem Cell Laboratory, Department of Medical Sciences, University of TurinTurin, Italy
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