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Xie D, Qian B, Li X. Nucleic acids and proteins carried by exosomes from various sources: Potential role in liver diseases. Front Physiol 2022; 13:957036. [PMID: 36213232 PMCID: PMC9538374 DOI: 10.3389/fphys.2022.957036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/17/2022] [Indexed: 12/24/2022] Open
Abstract
Exosomes are extracellular membrane-encapsulated vesicles that are released into the extracellular space or biological fluids by many cell types through exocytosis. As a newly identified form of intercellular signal communication, exosomes mediate various pathological and physiological processes by exchanging various active substances between cells. The incidence and mortality of liver diseases is increasing worldwide. Therefore, we reviewed recent studies evaluating the role of exosomes from various sources in the diagnosis and treatment of liver diseases.
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Affiliation(s)
- Danna Xie
- The First Clinical Medical College of Lanzhou University, Lanzhou, China
| | - Baolin Qian
- Department of Hepatic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xun Li
- The First Clinical Medical College of Lanzhou University, Lanzhou, China
- Department of General Surgery, the First Hospital of Lanzhou University, Lanzhou, China
- Key Laboratory of Biotherapy and Regenerative Medicine of Gansu Province, Lanzhou, China
- Center for Cancer Prevention and Treatment, School of Medicine, Lanzhou University, Lanzhou, China
- Gansu Provincial Institute of Hepatobiliary and Pancreatic Surgery, Lanzhou, China
- *Correspondence: Xun Li,
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2
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Li D, Chen M, Hong H, Tong W, Ning B. Integrative approaches for studying the role of noncoding RNAs in influencing drug efficacy and toxicity. Expert Opin Drug Metab Toxicol 2022; 18:151-163. [PMID: 35296201 PMCID: PMC9117541 DOI: 10.1080/17425255.2022.2054802] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 03/14/2022] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Drug efficacy and toxicity are important factors for evaluation in drug development. Drug metabolizing enzymes and transporters (DMETs) play an essential role in drug efficacy and toxicity. Noncoding RNAs (ncRNAs) have been implicated to influence inter-individual variations in drug efficacy and safety by regulating DMETs. An efficient strategy is urgently needed to identify and functionally characterize ncRNAs that mediate drug efficacy and toxicity through regulating DMETs. AREAS COVERED We outline an integrative strategy to identify ncRNAs that modulate DMETs. We include reliable tools and databases for computational prediction of ncRNA targets with regard to their advantages and limitations. Various biochemical, molecular, and cellular assays are discussed for in vitro experimental verification of the regulatory function of ncRNAs. In vivo approaches for association of ncRNAs with drug treatment and toxicity are also reviewed. EXPERT OPINION A streamlined integration of computational prediction and wet-lab validation is important to elucidate mechanisms of ncRNAs in the regulation of DMETs related to drug efficacy and safety. Bioinformatic analyses using open-access tools and databases serve as a powerful booster for ncRNA Research in toxicology. Further refinement of computational algorithms and experimental technologies is needed to improve accuracy and efficiency in ncRNA target identification and characterization.
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Affiliation(s)
- Dongying Li
- National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA), Jefferson, AR, USA
| | - Minjun Chen
- National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA), Jefferson, AR, USA
| | - Huixiao Hong
- National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA), Jefferson, AR, USA
| | - Weida Tong
- National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA), Jefferson, AR, USA
| | - Baitang Ning
- National Center for Toxicological Research (NCTR), U.S. Food and Drug Administration (FDA), Jefferson, AR, USA
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Chorley BN, Ellinger-Ziegelbauer H, Tackett M, Simutis FJ, Harrill AH, McDuffie J, Atabakhsh E, Nassirpour R, Whiteley LO, Léonard JF, Carswell GK, Harpur E, Chen CL, Gautier JC. Urinary miRNA Biomarkers of Drug-Induced Kidney Injury and Their Site Specificity Within the Nephron. Toxicol Sci 2021; 180:1-16. [PMID: 33367795 PMCID: PMC7916737 DOI: 10.1093/toxsci/kfaa181] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Drug-induced kidney injury (DIKI) is a major concern in both drug development and clinical practice. There is an unmet need for biomarkers of glomerular damage and more distal renal injury in the loop of Henle and the collecting duct (CD). A cross-laboratory program to identify and characterize urinary microRNA (miRNA) patterns reflecting tissue- or pathology-specific DIKI was conducted. The overall goal was to propose miRNA biomarker candidates for DIKI that could supplement information provided by protein kidney biomarkers in urine. Rats were treated with nephrotoxicants causing injury to distinct nephron segments: the glomerulus, proximal tubule, thick ascending limb (TAL) of the loop of Henle and CD. Meta-analysis identified miR-192-5p as a potential proximal tubule-specific urinary miRNA candidate. This result was supported by data obtained in laser capture microdissection nephron segments showing that miR-192-5p expression was enriched in the proximal tubule. Discriminative miRNAs including miR-221-3p and -222-3p were increased in urine from rats treated with TAL versus proximal tubule toxicants in accordance with their expression localization in the kidney. Urinary miR-210-3p increased up to 40-fold upon treatment with TAL toxicants and was also enriched in laser capture microdissection samples containing TAL and/or CD versus proximal tubule. miR-23a-3p was enriched in the glomerulus and was increased in urine from rats treated with doxorubicin, a glomerular toxicant, but not with toxicants affecting other nephron segments. Taken together these results suggest that urinary miRNA panels sourced from specific nephron regions may be useful to discriminate the pathology of toxicant-induced lesions in the kidney, thereby contributing to DIKI biomarker development needs for industry, clinical, and regulatory use.
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Affiliation(s)
- Brian N Chorley
- U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | | | | | - Frank J Simutis
- Bristol-Myers Squibb Company, New Brunswick, New Jersey 08901, USA
| | - Alison H Harrill
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
| | - James McDuffie
- Janssen Research & Development, LLC, San Diego, California 92121, USA
| | | | - Rounak Nassirpour
- Pfizer Drug Safety Research and Development, Cambridge, Massachusetts 02139, USA
| | - Laurence O Whiteley
- Pfizer Drug Safety Research and Development, Cambridge, Massachusetts 02139, USA
| | | | - Gleta K Carswell
- U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27709, USA
| | - Ernie Harpur
- Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Connie L Chen
- Health and Environmental Sciences Institute, Washington, District of Columbia 20005, USA
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Chorley BN, Atabakhsh E, Doran G, Gautier JC, Ellinger-Ziegelbauer H, Jackson D, Sharapova T, Yuen PST, Church RJ, Couttet P, Froetschl R, McDuffie J, Martinez V, Pande P, Peel L, Rafferty C, Simutis FJ, Harrill AH. Methodological considerations for measuring biofluid-based microRNA biomarkers. Crit Rev Toxicol 2021; 51:264-282. [PMID: 34038674 DOI: 10.1080/10408444.2021.1907530] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNA that regulate the expression of messenger RNA and are implicated in almost all cellular processes. Importantly, miRNAs can be released extracellularly and are stable in these matrices where they may serve as indicators of organ or cell-specific toxicity, disease, and biological status. There has thus been great enthusiasm for developing miRNAs as biomarkers of adverse outcomes for scientific, regulatory, and clinical purposes. Despite advances in measurement capabilities for miRNAs, miRNAs are still not routinely employed as noninvasive biomarkers. This is in part due to the lack of standard approaches for sample preparation and miRNA measurement and uncertainty in their biological interpretation. Members of the microRNA Biomarkers Workgroup within the Health and Environmental Sciences Institute's (HESI) Committee on Emerging Systems Toxicology for the Assessment of Risk (eSTAR) are a consortium of private- and public-sector scientists dedicated to developing miRNAs as applied biomarkers. Here, we explore major impediments to routine acceptance and use of miRNA biomarkers and case examples of successes and deficiencies in development. Finally, we provide insight on miRNA measurement, collection, and analysis tools to provide solid footing for addressing knowledge gaps toward routine biomarker use.
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Affiliation(s)
- Brian N Chorley
- U.S. Environmental Protection Agency, Research Triangle Park, NC, USA
| | | | | | | | | | - David Jackson
- Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - Peter S T Yuen
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Rachel J Church
- Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | | | | | | | | | | | - Lauren Peel
- Health and Environmental Sciences Institute, Washington, DC, USA
| | | | | | - Alison H Harrill
- National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA
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5
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Zhang Y, Zhou J, Liu J, Li S, Zhou S, Zhang C, Wang Y, Shi J, Liu J, Wu Q. RNA-Seq analysis of the protection by Dendrobium nobile alkaloids against carbon tetrachloride hepatotoxicity in mice. Biomed Pharmacother 2021; 137:111307. [PMID: 33561648 DOI: 10.1016/j.biopha.2021.111307] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/30/2020] [Accepted: 12/26/2020] [Indexed: 01/04/2023] Open
Abstract
OBJECTIVE Dendrobium nobile is a genuine Chinese medicine. Dendrobium nobile Lindl. alkaloids (DNLA) protects against CCl4-induced acute liver injury. This study used RNA-Seq to explore the mechanisms. METHODS Mice were pretreated with DNLA (10 and 20 mg/kg, po) for 7 days, and subsequently intoxicated with CCl4 (20 μL/kg, ip for 24 h). Liver RNA was extracted and subjected to RNA-Seq. The bioinformatics, including PCA, GO, KEGG, two-dimensional clustering, Ingenuity Pathways Analysis (IPA), and Illumina BaseSpace Correlation Engine (BSCE) were used to analyze the data. qPCR was performed on selected genes to verify RNA-Seq results. RESULTS DNLA protection against CCl4 hepatotoxicity was confirmed by histopathology. PCA revealed the distinct gene expression patterns between the different treatment groups. GO showed that CCl4 induced the activation, adhesion and proliferation of immune cells. KEGG showed CCl4 induced oxidative stress, diseases and compromised adaptive responses. CCl4 induced differentially expressed genes (DEGs) were identified by DESeq2 with Padj < 0.05 and 2D-clustered with other groups. DNLA reverted CCl4-induced DEGs in a dose-dependent manner. qPCR analysis of S100 g, Sprr1, CCL3/7, Saa2/3, IL1rn, Cox7a2 and Rad15 confirmed RNA-Seq results. IPA showed that CCl4 treatment altered some signaling and metabolic pathways, which were ameliorated or returned to normal following DNLA treatment. The CCl4-activated mitochondrial oxidative phosphorylation was illustrated as an example. IPA Upstream Regulator Analysis further revealed the activated or inhibited molecules and chemicals that are responsible for CCl4-induced DEGs, and DNLA attenuated these changes. BSCE analysis verified that CCl4-induced DEGs were highly correlated with the GEO database of CCl4 hepatotoxicity in rodents, and DNLA dose-dependently attenuated such correlation. CONCLUSION RNA-Seq revealed CCl4-induced DEGs, disruption of canonical pathways, activation or inhibition of upstream regulators, which are highly correlated with database for CCl4 hepatotoxicity. All these changes were attenuated or returned to normal by DNLA, demonstrating the mechanisms for DNLA to protect against CCl4 hepatotoxicity.
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Affiliation(s)
- Ya Zhang
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnocentric of Ministry of Education, Zunyi Medical University, Zunyi, China.
| | - Jinxin Zhou
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnocentric of Ministry of Education, Zunyi Medical University, Zunyi, China.
| | - Jiajia Liu
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnocentric of Ministry of Education, Zunyi Medical University, Zunyi, China.
| | - Shujun Li
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnocentric of Ministry of Education, Zunyi Medical University, Zunyi, China.
| | - Shaoyu Zhou
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnocentric of Ministry of Education, Zunyi Medical University, Zunyi, China.
| | - Chengchen Zhang
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnocentric of Ministry of Education, Zunyi Medical University, Zunyi, China.
| | - Yan Wang
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnocentric of Ministry of Education, Zunyi Medical University, Zunyi, China.
| | - Jingshan Shi
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnocentric of Ministry of Education, Zunyi Medical University, Zunyi, China.
| | - Jie Liu
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnocentric of Ministry of Education, Zunyi Medical University, Zunyi, China.
| | - Qin Wu
- Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnocentric of Ministry of Education, Zunyi Medical University, Zunyi, China.
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Zhao L, Wang Y, Zhang Y. The potential diagnostic and therapeutic applications of exosomes in drug-induced liver injury. Toxicol Lett 2020; 337:68-77. [PMID: 33259895 DOI: 10.1016/j.toxlet.2020.11.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 11/02/2020] [Accepted: 11/24/2020] [Indexed: 12/13/2022]
Abstract
Drug-induced liver injury (DILI) has gradually become a global public medical problem, which can be caused by more than 1000 currently available drugs. Unfortunately, the diagnosis and treatment of DILI are limited and imperfect. Exosomes can be secreted by a variety of cells and tissues in the body, rich in cell-type specific proteins, nucleic acids and lipids, which has been widely studied as an important intercellular communication vehicle in liver diseases. Emerging data suggest that circulating exosomes and their cargos can be used as minimally-invasive sources of potential molecular biomarkers for the early detection, monitoring and evaluation of DILI. Exosomes in the urine were also found to contain proteins or RNAs that were indicative of DILI. In addition, exosomes derived from mesenchymal stem cell or hepatocyte are considered potential therapeutic agents to promote liver regenerative responses, modulate inflammatory response and deduce hepatocytes apoptosis. Based on the current findings, we suggest the potential applications of exosomes as biomarkers and therapeutics for DILI.
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Affiliation(s)
- Lanlan Zhao
- Department of Gerontology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yuezhi Wang
- Department of Gerontology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yu Zhang
- Department of Gerontology, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.
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Azparren-Angulo M, Royo F, Gonzalez E, Liebana M, Brotons B, Berganza J, Goñi-de-Cerio F, Manicardi N, Abad-Jordà L, Gracia-Sancho J, Falcon-Perez JM. Extracellular vesicles in hepatology: Physiological role, involvement in pathogenesis, and therapeutic opportunities. Pharmacol Ther 2020; 218:107683. [PMID: 32961265 DOI: 10.1016/j.pharmthera.2020.107683] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/09/2020] [Indexed: 02/06/2023]
Abstract
Since the first descriptions of hepatocyte-released exosome-like vesicles in 2008, the number of publications describing Extracellular Vesicles (EVs) released by liver cells in the context of hepatic physiology and pathology has grown exponentially. This growing interest highlights both the importance that cell-to-cell communication has in the organization of multicellular organisms from a physiological point of view, as well as the opportunity that these circulating organelles offer in diagnostics and therapeutics. In the present review, we summarize systematically and comprehensively the myriad of works that appeared in the last decade and lighted the discussion about the best opportunities for using EVs in liver disease therapeutics.
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Affiliation(s)
- Maria Azparren-Angulo
- Exosomes Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Bizkaia 48160, Spain
| | - Felix Royo
- Exosomes Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Bizkaia 48160, Spain; Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Esperanza Gonzalez
- Exosomes Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Bizkaia 48160, Spain
| | - Marc Liebana
- Exosomes Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Bizkaia 48160, Spain
| | - Bruno Brotons
- Exosomes Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Bizkaia 48160, Spain
| | - Jesús Berganza
- GAIKER Technology Centre, Basque Research and Technology Alliance (BRTA), Parque Tecnológico, Edificio 202, 48170 Zamudio, Bizkaia, Spain
| | - Felipe Goñi-de-Cerio
- GAIKER Technology Centre, Basque Research and Technology Alliance (BRTA), Parque Tecnológico, Edificio 202, 48170 Zamudio, Bizkaia, Spain
| | - Nicoló Manicardi
- Liver Vascular Biology Research Group, Barcelona Hepatic Hemodynamic Unit, IDIBAPS, CIBEREHD, Barcelona, Spain
| | - Laia Abad-Jordà
- Liver Vascular Biology Research Group, Barcelona Hepatic Hemodynamic Unit, IDIBAPS, CIBEREHD, Barcelona, Spain
| | - Jordi Gracia-Sancho
- Liver Vascular Biology Research Group, Barcelona Hepatic Hemodynamic Unit, IDIBAPS, CIBEREHD, Barcelona, Spain; Hepatology, Department of Biomedical Research, Inselspital & University of Bern, Switzerland
| | - Juan M Falcon-Perez
- Exosomes Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Derio, Bizkaia 48160, Spain; Centro de Investigación Biomédica en Red de enfermedades hepáticas y digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid 28029, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia 48015, Spain.
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Chen CK, Liao J, Li MS, Khoo BL. Urine biopsy technologies: Cancer and beyond. Theranostics 2020; 10:7872-7888. [PMID: 32685026 PMCID: PMC7359094 DOI: 10.7150/thno.44634] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 06/02/2020] [Indexed: 12/18/2022] Open
Abstract
Since the discovery of circulating tumor cells in 1869, technological advances in the study of biomarkers from liquid biopsy have made it possible to diagnose disease in a less invasive way. Although blood-based liquid biopsy has been used extensively for the detection of solid tumors and immune diseases, the potential of urine-based liquid biopsy has not been fully explored. Advancements in technologies for the harvesting and analysis of biomarkers are providing new opportunities for the characterization of other disease types. Liquid biopsy markers such as exfoliated bladder cancer cells, cell-free DNA (cfDNA), and exosomes have the potential to change the nature of disease management and care, as they allow a cost-effective and convenient mode of patient monitoring throughout treatment. In this review, we addressed the advancement of research in the field of disease detection for the key liquid biopsy markers such as cancer cells, cfDNA, and exosomes, with an emphasis on urine-based liquid biopsy. First, we highlighted key technologies that were widely available and used extensively for clinical urine sample analysis. Next, we presented recent technological developments in cell and genetic research, with implications for the detection of other types of diseases, besides cancer. We then concluded with some discussions on these areas, emphasizing the role of microfluidics and artificial intelligence in advancing point-of-care applications. We believe that the benefits of urine biopsy provide diagnostic development potential, which will pave opportunities for new ways to guide treatment selections and facilitate precision disease therapies.
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Affiliation(s)
| | | | | | - Bee Luan Khoo
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, China
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Carreiro S, Marvel-Coen J, Lee R, Chapman B, Ambros V. Circulating microRNA Profiles in Acetaminophen Toxicity. J Med Toxicol 2020; 16:177-187. [PMID: 31792846 PMCID: PMC7099119 DOI: 10.1007/s13181-019-00739-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/05/2019] [Accepted: 09/11/2019] [Indexed: 12/19/2022] Open
Abstract
INTRODUCTION Acetaminophen toxicity has been associated with elevation of microRNAs. The present study was to evaluate overall microRNA profiles and previously identified microRNAs to differentiate acetaminophen (APAP) toxicity from other causes of transaminase elevation. METHODS This was an observational study of adults with presumed acetaminophen toxicity at presentation. Serum samples were collected every 12 hours during hospitalization. Total miRNAs were extracted from plasma and levels of 327 microRNAs were quantified using real-time polymerase chain reaction. A standard measure of miRNA expression (delta-delta cycle threshold) was calculated for each microRNAs. A two-level cluster analysis was performed using a random k-means algorithm. Demographic and clinical characteristics of each cluster were compared using ANOVA, Wilcoxon rank sum, Kruskal-Wallis, and chi-square tests. Performance of specific miRNAs of interest was also evaluated. RESULTS Twenty-seven subjects were enrolled (21 with a final diagnosis of acetaminophen toxicity), and a total of 61 samples were analyzed. Five clusters were identified, two of which demonstrated clear clinical patterns and included specific elevated miRNAs previously reported to be elevated in APAP toxicity patients. Features associated with clusters 1 and 5 included confirmed acetaminophen toxicity, high peak alanine aminotransferase, and late presentation. Clusters 2-4 contained lower peak microRNAs, lower peak alanine aminotransferase, and heterogeneous clinical characteristics. CONCLUSIONS Severe cases of acetaminophen toxicity showed two distinct patterns of microRNA elevation which were similar to previous work, while less severe cases were difficult to distinguish from non-acetaminophen-associated cases. Further work is needed to incorporate microRNA profiles into the diagnostic algorithm of acetaminophen toxicity.
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Affiliation(s)
- Stephanie Carreiro
- Department of Emergency Medicine, Division of Medical Toxicology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA.
| | - James Marvel-Coen
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Rosalind Lee
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Brittany Chapman
- Department of Emergency Medicine, Division of Medical Toxicology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA
| | - Victor Ambros
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
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10
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Liu Y, Jing R, Wen Z, Li M. Narrowing the Gap Between In Vitro and In Vivo Genetic Profiles by Deconvoluting Toxicogenomic Data In Silico. Front Pharmacol 2020; 10:1489. [PMID: 31992983 PMCID: PMC6964707 DOI: 10.3389/fphar.2019.01489] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 11/18/2019] [Indexed: 01/09/2023] Open
Abstract
Toxicogenomics (TGx) is a powerful method to evaluate toxicity and is widely used in both in vivo and in vitro assays. For in vivo TGx, reduction, refinement, and replacement represent the unremitting pursuit of live-animal tests, but in vitro assays, as alternatives, usually demonstrate poor correlation with real in vivo assays. In living subjects, in addition to drug effects, inner-environmental reactions also affect genetic variation, and these two factors are further jointly reflected in gene abundance. Thus, finding a strategy to factorize inner-environmental factor from in vivo assays based on gene expression levels and to further utilize in vitro data to better simulate in vivo data is needed. We proposed a strategy based on post-modified non-negative matrix factorization, which can estimate the gene expression profiles and contents of major factors in samples. The applicability of the strategy was first verified, and the strategy was then utilized to simulate in vivo data by correcting in vitro data. The similarities between real in vivo data and simulated data (single-dose 0.72, repeat-doses 0.75) were higher than those observed when directly comparing real in vivo data with in vitro data (single-dose 0.56, repeat-doses 0.70). Moreover, by keeping environment-related factor, a simulation can always be generated by using in vitro data to provide potential substitutions for in vivo TGx and to reduce the launch of live-animal tests.
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Affiliation(s)
- Yuan Liu
- College of Chemistry, Sichuan University, Chengdu, China
| | - Runyu Jing
- College of Cybersecurity, Sichuan University, Chengdu, China
| | - Zhining Wen
- College of Chemistry, Sichuan University, Chengdu, China
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu, China
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11
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Kuna L, Bozic I, Kizivat T, Bojanic K, Mrso M, Kralj E, Smolic R, Wu GY, Smolic M. Models of Drug Induced Liver Injury (DILI) - Current Issues and Future Perspectives. Curr Drug Metab 2018; 19:830-838. [PMID: 29788883 PMCID: PMC6174638 DOI: 10.2174/1389200219666180523095355] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 03/20/2018] [Accepted: 03/28/2018] [Indexed: 12/13/2022]
Abstract
Background: Drug-induced Liver Injury (DILI) is an important cause of acute liver failure cases in the United States, and remains a common cause of withdrawal of drugs in both preclinical and clinical phases. Methods: A structured search of bibliographic databases – Web of Science Core Collection, Scopus and Medline for peer-reviewed articles on models of DILI was performed. The reference lists of relevant studies was prepared and a citation search for the included studies was carried out. In addition, the characteristics of screened studies were described. Results: One hundred and six articles about the existing knowledge of appropriate models to study DILI in vitro and in vivo with special focus on hepatic cell models, variations of 3D co-cultures, animal models, databases and predictive modeling and translational biomarkers developed to understand the mechanisms and pathophysiology of DILI are described. Conclusion: Besides descriptions of current applications of existing modeling systems, associated advantages and limitations of each modeling system and future directions for research development are discussed as well.
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Affiliation(s)
- Lucija Kuna
- Department of Chemistry and Biochemistry, Faculty of Dental Medicine and Health, J. J. Strossmayer University of Osijek, Crkvena 21, 31000 Osijek, Croatia
| | - Ivana Bozic
- Department of Pharmacology, Faculty of Medicine, J. J. Strossmayer University of Osijek, J. Huttlera 4, 31000 Osijek, Croatia
| | - Tomislav Kizivat
- Department of Pharmacology, Faculty of Medicine, J. J. Strossmayer University of Osijek, J. Huttlera 4, 31000 Osijek, Croatia
| | - Kristina Bojanic
- Department of Pharmacology, Faculty of Medicine, J. J. Strossmayer University of Osijek, J. Huttlera 4, 31000 Osijek, Croatia
| | - Margareta Mrso
- Department of Pharmacology, Faculty of Medicine, J. J. Strossmayer University of Osijek, J. Huttlera 4, 31000 Osijek, Croatia
| | - Edgar Kralj
- Inspecto, LLC, Martina Divalta 193, 31000 Osijek, Croatia
| | - Robert Smolic
- Department of Pharmacology, Faculty of Medicine, J. J. Strossmayer University of Osijek, J. Huttlera 4, 31000 Osijek, Croatia
| | - George Y Wu
- Department of Medicine, Division of Gastroenterology-Hepatology, University of Connecticut Health Center, Farmington, CT, United States
| | - Martina Smolic
- Department of Pharmacology, Faculty of Medicine, J. J. Strossmayer University of Osijek, J. Huttlera 4, 31000 Osijek, Croatia.,Department of Pharmacology, Faculty Of Dental Medicine and Health, J. J. Strossmayer University of Osijek, Crkvena 21, 31000 Osijek, Croatia
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12
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Jia L, Zhang D, Huang H, Zhou Y, Zhou S, Guo J. Triazophos-induced toxicity in zebrafish: miRNA-217 inhibits nup43. Toxicol Res (Camb) 2018; 7:913-922. [PMID: 30310668 PMCID: PMC6116809 DOI: 10.1039/c8tx00065d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/29/2018] [Indexed: 11/21/2022] Open
Abstract
Triazophos is a highly toxic organophosphorus pesticide, causing acute toxicity to brain tissue, and neurotoxicity and embryotoxicity to animals. Therefore, triazophos is considered as a public health problem due to its acute hazard index. MicroRNAs (miRNAs), a class of endogenous noncoding RNAs, can regulate the expression of target gene(s) by mediating mRNA cleavage or translational repression in organisms exposed to environmental chemicals. We found that nup43 is targeted by miR-217, which was significantly regulated in adult zebrafish (Danio rerio) exposed to triazophos (phenyl-1,2,4-triazolyl-3-(o,o-diethyl thionophosphate)). The expression of nup43 in both mRNA and protein levels was downregulated in a dose-dependent manner upon stimulation with triazophos. A dual luciferase reporter assay demonstrated that miR-217 interacted with the 3'-untranslated regions (3'-UTR) of nup43. The expression of nup43 in both mRNA and protein level was reduced in ZF4 cells when transfected with an miR-217 mimic, but increased when transfected with an miR-217 inhibitor. As a result, nup43 is targeted by miR-217 upon triazophos exposure. We suggest that miR-217 could be a potential toxicological biomarker for triazophos.
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Affiliation(s)
- Longlue Jia
- College of Life Sciences , Zhejiang Sci-Tech University , Hangzhou , 310018 , China .
| | - Danyan Zhang
- College of Life Sciences , Zhejiang Sci-Tech University , Hangzhou , 310018 , China .
| | - Hannian Huang
- Department of Applied Engineering , Zhejiang Economic & Trade Polytechnic , Hangzhou , 310018 , China
| | - Yongyong Zhou
- College of Life Sciences , Zhejiang Sci-Tech University , Hangzhou , 310018 , China .
| | - Shengli Zhou
- Environmental Monitoring Center of Zhejiang Province , Hangzhou , 310015 , China
| | - Jiangfeng Guo
- College of Life Sciences , Zhejiang Sci-Tech University , Hangzhou , 310018 , China .
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13
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Krauskopf J, Kleinjans JC, de Kok TM. Circulating MicroRNAs as Novel Biomarkers of Drug-Induced Liver Injury in Humans. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/978-1-4939-7677-5_28] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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14
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Battista C, Howell BA, Siler SQ, Watkins PB. An Introduction to DILIsym® Software, a Mechanistic Mathematical Representation of Drug-Induced Liver Injury. ACTA ACUST UNITED AC 2018. [DOI: 10.1007/978-1-4939-7677-5_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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15
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Liu Z, Delavan B, Roberts R, Tong W. Transcriptional Responses Reveal Similarities Between Preclinical Rat Liver Testing Systems. Front Genet 2018; 9:74. [PMID: 29616076 PMCID: PMC5870427 DOI: 10.3389/fgene.2018.00074] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 02/19/2018] [Indexed: 01/03/2023] Open
Abstract
Toxicogenomics (TGx) is an important tool to gain an enhanced understanding of toxicity at the molecular level. Previously, we developed a pair ranking (PRank) method to assess in vitro to in vivo extrapolation (IVIVE) using toxicogenomic datasets from the Open Toxicogenomics Project-Genomics Assisted Toxicity Evaluation System (TG-GATEs) database. With this method, we investiagted three important questions that were not addressed in our previous study: (1) is a 1-day in vivo short-term assay able to replace the 28-day standard and expensive toxicological assay? (2) are some biological processes more conservative across different preclinical testing systems than others? and (3) do these preclinical testing systems have the similar resolution in differentiating drugs by their therapeutic uses? For question 1, a high similarity was noted (PRank score = 0.90), indicating the potential utility of shorter term in vivo studies to predict outcome in longer term and more expensive in vivo model systems. There was a moderate similarity between rat primary hepatocytes and in vivo repeat-dose studies (PRank score = 0.71) but a low similarity (PRank score = 0.56) between rat primary hepatocytes and in vivo single dose studies. To address question 2, we limited the analysis to gene sets relevant to specific toxicogenomic pathways and we found that pathways such as lipid metabolism were consistently over-represented in all three assay systems. For question 3, all three preclinical assay systems could distinguish compounds from different therapeutic categories. This suggests that any noted differences in assay systems was biological process-dependent and furthermore that all three systems have utility in assessing drug responses within a certain drug class. In conclusion, this comparison of three commonly used rat TGx systems provides useful information in utility and application of TGx assays.
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Affiliation(s)
- Zhichao Liu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, United States
| | - Brian Delavan
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, United States.,Department of Biosciences, University of Arkansas at Little Rock, Little Rock, AR, United States
| | - Ruth Roberts
- ApconiX, Alderley Edge, United Kingdom.,Department of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, United States
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16
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Lin H, Ewing LE, Koturbash I, Gurley BJ, Miousse IR. MicroRNAs as biomarkers for liver injury: Current knowledge, challenges and future prospects. Food Chem Toxicol 2017; 110:229-239. [PMID: 29042291 PMCID: PMC6693868 DOI: 10.1016/j.fct.2017.10.026] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 10/02/2017] [Accepted: 10/14/2017] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) are short regulatory RNAs that are involved in various biological processes that regulate gene expression posttranscriptionally. Changes in miRNA expression can be detected in many physiological and pathological events, such as liver injury. Drug induced liver injury is a life threatening condition that frequently requires organ transplantation. Hepatotoxicity is also one of the major causes of drug failure in clinical trials and of drug withdrawal from the market. The profiling of miRNA expression shows great promise in monitoring liver injury, in the prediction of outcome in patients, and in the identification of liver-reactive compounds in toxicological assessment. Recent studies have demonstrated organ-specificity of some miRNAs (i.e., miR-122), which are released into biological fluids as a result of hepatocyte damage. This attests to the potential of miRNAs as noninvasive biomarkers to detect liver toxicity. This review presents information on miRNA signatures of hepatotoxicity and on the application of promising miRNA biomarkers in preclinical safety assessment. We further discuss the technical challenges associated with these emerging biomarkers for early diagnosis and detection of hepatotoxicity.
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Affiliation(s)
- Haixia Lin
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, United States.
| | - Laura E Ewing
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, United States; Department of Pharmacology and Toxicology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, United States.
| | - Igor Koturbash
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, United States.
| | - Bill J Gurley
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR, 72223, United States.
| | - Isabelle R Miousse
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, United States.
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17
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Loiodice S, Nogueira da Costa A, Atienzar F. Current trends in in silico, in vitro toxicology, and safety biomarkers in early drug development. Drug Chem Toxicol 2017; 42:113-121. [DOI: 10.1080/01480545.2017.1400044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Simon Loiodice
- Department of Non-Clinical Development, UCB Biopharma SPRL, Braine-l’Alleud, Belgium
| | | | - Franck Atienzar
- Department of Non-Clinical Development, UCB Biopharma SPRL, Braine-l’Alleud, Belgium
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18
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Multiple microRNAs function as self-protective modules in acetaminophen-induced hepatotoxicity in humans. Arch Toxicol 2017; 92:845-858. [PMID: 29067470 DOI: 10.1007/s00204-017-2090-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 10/05/2017] [Indexed: 12/12/2022]
Abstract
Acetaminophen (APAP) overdose is the leading cause of acute liver failure. Yet the mechanisms underlying adaptive tolerance toward APAP-induced liver injury are not fully understood. To better understand molecular mechanisms contributing to adaptive tolerance to APAP is an underpinning foundation for APAP-related precision medicine. In the current study, the mRNA and microRNA (miRNA) expression profiles derived from next generation sequencing data for APAP-treated (5 and 10 mM) HepaRG cells and controls were analyzed systematically. Putative miRNAs targeting key dysregulated genes involved in APAP hepatotoxicity were selected using in silico prediction algorithms, un-biased gene ontology, and network analyses. Luciferase reporter assays, RNA electrophoresis mobility shift assays, and miRNA pull-down assays were performed to investigate the role of miRNAs affecting the expression of dysregulated genes. Levels of selected miRNAs were measured in serum samples obtained from children with APAP overdose (58.6-559.4 mg/kg) and from healthy controls. As results, 2758 differentially expressed genes and 47 miRNAs were identified. Four of these miRNAs (hsa-miR-224-5p, hsa-miR-320a, hsa-miR-449a, and hsa-miR-877-5p) suppressed drug metabolizing enzyme (DME) levels involved in APAP-induced liver injury by downregulating HNF1A, HNF4A and NR1I2 expression. Exogenous transfection of these miRNAs into HepaRG cells effectively rescued them from APAP toxicity, as indicated by decreased alanine aminotransferase levels. Importantly, hsa-miR-320a and hsa-miR-877-5p levels were significantly elevated in serum samples obtained from children with APAP overdose compared to health controls. Collectively, these data indicate that hsa-miR-224-5p, hsa-miR-320a, hsa-miR-449a, and hsa-miR-877-5p suppress DME expression involved in APAP-induced hepatotoxicity and they contribute to an adaptive response in hepatocytes.
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19
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Cho YE, Im EJ, Moon PG, Mezey E, Song BJ, Baek MC. Increased liver-specific proteins in circulating extracellular vesicles as potential biomarkers for drug- and alcohol-induced liver injury. PLoS One 2017; 12:e0172463. [PMID: 28225807 PMCID: PMC5321292 DOI: 10.1371/journal.pone.0172463] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 02/06/2017] [Indexed: 12/21/2022] Open
Abstract
Drug- and alcohol-induced liver injury are a leading cause of liver failure and transplantation. Emerging evidence suggests that extracellular vesicles (EVs) are a source of biomarkers because they contain unique proteins reflecting the identity and tissue-specific origin of the EV proteins. This study aimed to determine whether potentially hepatotoxic agents, such as acetaminophen (APAP) and binge alcohol, can increase the amounts of circulating EVs and evaluate liver-specific EV proteins as potential biomarkers for liver injury. The circulating EVs, isolated from plasma of APAP-exposed, ethanol-fed mice, or alcoholic hepatitis patients versus normal control counterparts, were characterized by proteomics and biochemical methods. Liver specific EV proteins were analyzed by immunoblots and ELISA. The amounts of total and liver-specific proteins in circulating EVs from APAP-treated mice significantly increased in a dose- and time-dependent manner. Proteomic analysis of EVs from APAP-exposed mice revealed that the amounts of liver-specific and/or hepatotoxic proteins were increased compared to those of controls. Additionally, the increased protein amounts in EVs following APAP exposure returned to basal levels when mice were treated with N-acetylcysteine or glutathione. Similar results of increased amounts and liver-specific proteins in circulating EVs were also observed in mice exposed to hepatotoxic doses of thioacetamide or d-galactosamine but not by non-hepatotoxic penicillin or myotoxic bupivacaine. Additionally, binge ethanol exposure significantly elevated liver-specific proteins in circulating EVs from mice and alcoholics with alcoholic hepatitis, compared to control counterparts. These results indicate that circulating EVs in drug- and alcohol-mediated hepatic injury contain liver-specific proteins that could serve as specific biomarkers for hepatotoxicity.
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Affiliation(s)
- Young-Eun Cho
- Department of Molecular Medicine, Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
- Section of Molecular Pharmacology and Toxicology, Laboratory of Membrane Biochemistry and Biophysics, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, Maryland, United States of America
| | - Eun-Ju Im
- Department of Molecular Medicine, Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Pyong-Gon Moon
- Department of Molecular Medicine, Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Esteban Mezey
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Byoung-Joon Song
- Section of Molecular Pharmacology and Toxicology, Laboratory of Membrane Biochemistry and Biophysics, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, Maryland, United States of America
| | - Moon-Chang Baek
- Department of Molecular Medicine, Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
- * E-mail:
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20
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Gao Y, Cao Z, Yang X, Abdelmegeed MA, Sun J, Chen S, Beger RD, Davis K, Salminen WF, Song BJ, Mendrick DL, Yu LR. Proteomic analysis of acetaminophen-induced hepatotoxicity and identification of heme oxygenase 1 as a potential plasma biomarker of liver injury. Proteomics Clin Appl 2016; 11. [PMID: 27634590 DOI: 10.1002/prca.201600123] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 09/02/2016] [Accepted: 09/13/2016] [Indexed: 02/06/2023]
Abstract
PURPOSE Overdose of acetaminophen (APAP) is a major cause of acute liver failure. This study was aimed to identify pathways related to hepatotoxicity and potential biomarkers of liver injury. EXPERIMENTAL DESIGN Rats were treated with low (100 mg/kg) and high (1250 mg/kg) doses of APAP, and liver tissues at 6 and 24 h post-treatment were analyzed using a proteomic approach of 16O/18O labeling and 2D-LC-MS/MS. RESULTS Molecular pathways evolved progressively from scattered and less significant perturbations to more focused and significant alterations in a dose- and time-dependent manner upon APAP treatment. Imbalanced expression of hemeoxygenase 1 (HMOX1) and biliverdin reductase A (BLVRA) was associated with hepatotoxicity. Protein abundance changes of a total of 31 proteins were uniquely correlated to liver damage, among which a dramatic increase of HMOX1 levels in plasma was observed. Liver injury-associated significant elevation of plasma HMOX1 was further validated in mice treated with APAP. CONCLUSIONS AND CLINICAL RELEVANCE This study unveiled molecular changes associated with APAP-induced liver toxicity at the pathway levels and identified HMOX1 as a potential plasma biomarker of liver injury.
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Affiliation(s)
- Yuan Gao
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Zhijun Cao
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Xi Yang
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Mohamed A Abdelmegeed
- Laboratory of Membrane Biochemistry and Biophysics, National Institute on Alcohol Abuse and Alcoholism, Bethesda, MD, USA
| | - Jinchun Sun
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Si Chen
- Division of Biochemical Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Richard D Beger
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Kelly Davis
- Toxicologic Pathology Associates, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - William F Salminen
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Byoung-Joon Song
- Laboratory of Membrane Biochemistry and Biophysics, National Institute on Alcohol Abuse and Alcoholism, Bethesda, MD, USA
| | - Donna L Mendrick
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Li-Rong Yu
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
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Mitsugi R, Itoh T, Fujiwara R. MicroRNA-877-5p is involved in the trovafloxacin-induced liver injury. Toxicol Lett 2016; 263:34-43. [PMID: 27713024 DOI: 10.1016/j.toxlet.2016.10.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 08/26/2016] [Accepted: 10/02/2016] [Indexed: 12/21/2022]
Abstract
Trovafloxacin develops severe hepatotoxicity; however, the underlying mechanism of the trovafloxacin-induced liver injury has not been cleared. It has been shown that microRNAs (miRNAs) can be involved in the development of drug-induced liver injuries. We performed a miRNA microarray analysis to identify hepatic miRNAs that were induced or reduced by trovafloxacin in mice. It was demonstrated that miR-877-5p was the most increased miRNA in the mouse liver 24h after the trovafloxacin administration. To investigate the role of miR-877-5p in the liver, we established miR-877-5p-overexpressed HepG2 cells. Microarray analysis detected altered expressions in 2077 (>2-fold) and 1547 (<0.5-fold) genes in the miR-877-5p overexpressing cells compared to the mock cells. Especially, SLCO4C1, PEPCK, MT1M, HIST1H2BM, LGI1, and PLA2G2A were markedly increased or decreased in the miR-877-5p overexpressing cells. We conducted a correlation analysis between the expression levels of miR-877-5p and the six genes in eight miR-877-5p stably-expressed clones. It was shown that the PEPCK expression levels were correlated with miR-877-5p expression levels. PEPCK is associated with development of apoptotic cell death; therefore, the increased miR- 877-5p-induced PEPCK can be a trigger that is involved in the development of trovafloxacin-induced liver injury.
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Affiliation(s)
- Ryo Mitsugi
- School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Tomoo Itoh
- School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan
| | - Ryoichi Fujiwara
- School of Pharmacy, Kitasato University, 5-9-1 Shirokane, Minato-ku, Tokyo 108-8641, Japan.
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22
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Robles-Díaz M, Medina-Caliz I, Stephens C, Andrade RJ, Lucena MI. Biomarkers in DILI: One More Step Forward. Front Pharmacol 2016; 7:267. [PMID: 27597831 PMCID: PMC4992729 DOI: 10.3389/fphar.2016.00267] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 08/08/2016] [Indexed: 12/11/2022] Open
Abstract
Despite being relatively rare, drug-induced liver injury (DILI) is a serious condition, both for the individual patient due to the risk of acute liver failure, and for the drug development industry and regulatory agencies due to associations with drug development attritions, black box warnings, and postmarketing withdrawals. A major limitation in DILI diagnosis and prediction is the current lack of specific biomarkers. Despite refined usage of traditional liver biomarkers in DILI, reliable disease outcome predictions are still difficult to make. These limitations have driven the growing interest in developing new more sensitive and specific DILI biomarkers, which can improve early DILI prediction, diagnosis, and course of action. Several promising DILI biomarker candidates have been discovered to date, including mechanistic-based biomarker candidates such as glutamate dehydrogenase, high-mobility group box 1 protein and keratin-18, which can also provide information on the injury mechanism of different causative agents. Furthermore, microRNAs have received much attention lately as potential non-invasive DILI biomarker candidates, in particular miR-122. Advances in “omics” technologies offer a new approach for biomarker exploration studies. The ability to screen a large number of molecules (e.g., metabolites, proteins, or DNA) simultaneously enables the identification of ‘toxicity signatures,’ which may be used to enhance preclinical safety assessments and disease diagnostics. Omics-based studies can also provide information on the underlying mechanisms of distinct forms of DILI that may further facilitate the identification of early diagnostic biomarkers and safer implementation of personalized medicine. In this review, we summarize recent advances in the area of DILI biomarker studies.
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Affiliation(s)
- Mercedes Robles-Díaz
- Unidad de Gestión Clínica de Aparato Digestivo, Servicio de Farmacología Clínica, Instituto de Investigación Biomédica de Málaga, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas Málaga, Spain
| | - Inmaculada Medina-Caliz
- Unidad de Gestión Clínica de Aparato Digestivo, Servicio de Farmacología Clínica, Instituto de Investigación Biomédica de Málaga, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas Málaga, Spain
| | - Camilla Stephens
- Unidad de Gestión Clínica de Aparato Digestivo, Servicio de Farmacología Clínica, Instituto de Investigación Biomédica de Málaga, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas Málaga, Spain
| | - Raúl J Andrade
- Unidad de Gestión Clínica de Aparato Digestivo, Servicio de Farmacología Clínica, Instituto de Investigación Biomédica de Málaga, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas Málaga, Spain
| | - M Isabel Lucena
- Unidad de Gestión Clínica de Aparato Digestivo, Servicio de Farmacología Clínica, Instituto de Investigación Biomédica de Málaga, Hospital Universitario Virgen de la Victoria, Universidad de Málaga, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas Málaga, Spain
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23
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Harrill AH, McCullough SD, Wood CE, Kahle JJ, Chorley BN. MicroRNA Biomarkers of Toxicity in Biological Matrices. Toxicol Sci 2016; 152:264-72. [DOI: 10.1093/toxsci/kfw090] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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24
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Wolenski FS, Shah P, Sano T, Shinozawa T, Bernard H, Gallacher MJ, Wyllie SD, Varrone G, Cicia LA, Carsillo ME, Fisher CD, Ottinger SE, Koenig E, Kirby PJ. Identification of microRNA biomarker candidates in urine and plasma from rats with kidney or liver damage. J Appl Toxicol 2016; 37:278-286. [PMID: 27397436 PMCID: PMC5298042 DOI: 10.1002/jat.3358] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/19/2016] [Accepted: 05/24/2016] [Indexed: 12/20/2022]
Abstract
MicroRNAs (miRNA) are short single‐stranded RNA sequences that have a role in the post‐transcriptional regulation of genes. The identification of tissue specific or enriched miRNAs has great potential as novel safety biomarkers. One longstanding goal is to associate the increase of miRNA in biofluids (e.g., plasma and urine) with tissue‐specific damage. Next‐generation sequencing (miR‐seq) was used to analyze changes in miRNA profiles of tissue, plasma and urine samples of rats treated with either a nephrotoxicant (cisplatin) or one of two hepatotoxicants (acetaminophen [APAP] or carbon tetrachloride [CCL4]). Analyses with traditional serum chemistry and histopathology confirmed that toxicant‐induced organ damage was specific. In animals treated with cisplatin, levels of five miRNAs were significantly altered in the kidney, 14 in plasma and six in urine. In APAP‐treated animals, five miRNAs were altered in the liver, 74 in plasma and six in urine; for CCL4 the changes were five, 20 and 6, respectively. Cisplatin treatment caused an elevation of miR‐378a in the urine, confirming the findings of other similar studies. There were 17 in common miRNAs elevated in the plasma after treatment with either APAP or CCL4. Four of these (miR‐122, −802, −31a and −365) are known to be enriched in the livers of rats. Interestingly, the increase of serum miR‐802 in both hepatotoxicant treatments was comparable to that of the well‐known liver damage marker miR‐122. Taken together, comparative analysis of urine and plasma miRNAs demonstrated their utility as biomarkers of organ injury. Copyright © 2016 The Authors. Journal of Applied Toxicology published by John Wiley & Sons Ltd. MicroRNAs (miRNA) have great potential as novel safety biomarkers. Next‐generation sequencing was used to analyze changes in miRNA profiles of tissue, plasma and urine samples of rats treated with either a nephrotoxicant (cisplatin) or one of two hepatotoxicants (acetaminophen or carbon tetrachloride). Cisplatin treatment caused an elevation of miR‐378a in the urine, confirming the findings of other similar studies. Treatment with either acetaminophen or carbon tetrachloride caused a serum elevation of four liver‐enriched miRNAs (miR‐122, −802, −31a and −365).
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Affiliation(s)
- Francis S Wolenski
- Drug Safety Research & Evaluation, Millennium Pharmaceuticals, Inc., a wholly owned subsidiary of Takeda Pharmaceutical Company Limited, Cambridge, MA, 02139, USA
| | - Pooja Shah
- Molecular Pathology, Millennium Pharmaceuticals, Inc, a wholly owned subsidiary of Takeda Pharmaceutical Company Limited, Cambridge, MA, 02139, USA
| | - Tomoya Sano
- Drug Safety Research Laboratories, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, 251-8555, Japan
| | - Tadahiro Shinozawa
- Drug Safety Research Laboratories, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, 251-8555, Japan
| | - Hugues Bernard
- Molecular Pathology, Millennium Pharmaceuticals, Inc, a wholly owned subsidiary of Takeda Pharmaceutical Company Limited, Cambridge, MA, 02139, USA
| | - Matt J Gallacher
- Drug Safety Research & Evaluation, Millennium Pharmaceuticals, Inc., a wholly owned subsidiary of Takeda Pharmaceutical Company Limited, Cambridge, MA, 02139, USA
| | - Shylah D Wyllie
- Drug Safety Research & Evaluation, Millennium Pharmaceuticals, Inc., a wholly owned subsidiary of Takeda Pharmaceutical Company Limited, Cambridge, MA, 02139, USA
| | - Georgianna Varrone
- Drug Safety Research & Evaluation, Millennium Pharmaceuticals, Inc., a wholly owned subsidiary of Takeda Pharmaceutical Company Limited, Cambridge, MA, 02139, USA
| | - Lisa A Cicia
- Drug Safety Research & Evaluation, Millennium Pharmaceuticals, Inc., a wholly owned subsidiary of Takeda Pharmaceutical Company Limited, Cambridge, MA, 02139, USA
| | - Mary E Carsillo
- Drug Safety Research & Evaluation, Millennium Pharmaceuticals, Inc., a wholly owned subsidiary of Takeda Pharmaceutical Company Limited, Cambridge, MA, 02139, USA
| | - Craig D Fisher
- Drug Safety Research & Evaluation, Millennium Pharmaceuticals, Inc., a wholly owned subsidiary of Takeda Pharmaceutical Company Limited, Cambridge, MA, 02139, USA
| | - Sean E Ottinger
- Drug Safety Research & Evaluation, Millennium Pharmaceuticals, Inc., a wholly owned subsidiary of Takeda Pharmaceutical Company Limited, Cambridge, MA, 02139, USA
| | - Erik Koenig
- Molecular Pathology, Millennium Pharmaceuticals, Inc, a wholly owned subsidiary of Takeda Pharmaceutical Company Limited, Cambridge, MA, 02139, USA
| | - Patrick J Kirby
- Drug Safety Research & Evaluation, Millennium Pharmaceuticals, Inc., a wholly owned subsidiary of Takeda Pharmaceutical Company Limited, Cambridge, MA, 02139, USA
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Abstract
Drug-induced kidney injury (DIKI) is a severe complication in hospitalized patients associated with higher probabilities of developing progressive chronic kidney disease or end-stage renal diseases. Furthermore, DIKI is a problem during preclinical and clinical phases of drug development leading to high rates of project terminations. Understanding the molecular perturbations caused by DIKI would pave the way for a new class of therapeutics to mitigate the damage. Yet, another approach to ameliorate DIKI is identifying sensitive and specific translational biomarkers that outperform the current diagnostic analytes like serum creatinine and facilitate early diagnosis. MicroRNAs (miRNAs), a class of non-coding RNAs, are increasingly being recognized to have a two-pronged approach toward DIKI management: 1) miRNAs have a regulatory role in gene expression and signaling pathways thereby making them novel interventional targets and 2) miRNAs enable diagnosis and prognosis of DIKI because of their stable presence in biofluids. In this review, apart from summarizing the literature on miRNAs in DIKI, we report small RNA sequencing results showing miRNA expression profiles at baseline in normal kidney samples from mice and humans. Additionally, we also compared the miRNA expression in biopsies of normal human kidneys to patients with acute tubular necrosis, and found 76 miRNAs significantly downregulated and 47 miRNAs upregulated (FDR adjusted p<0.05, +/-2-fold change). In summary, we highlight the transformative potential of miRNAs in therapeutics and translational medicine with a focus on drug-induced kidney damage.
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Affiliation(s)
- Mira Pavkovic
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, United States; Department of Medicine, Renal Division, Brigham and Women's Hospital, Boston, MA, United States
| | - Vishal S Vaidya
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, United States; Department of Medicine, Renal Division, Brigham and Women's Hospital, Boston, MA, United States; Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, United States.
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Urinary miR-16 transactivated by C/EBPβ reduces kidney function after ischemia/reperfusion-induced injury. Sci Rep 2016; 6:27945. [PMID: 27297958 PMCID: PMC4906401 DOI: 10.1038/srep27945] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/26/2016] [Indexed: 12/15/2022] Open
Abstract
Ischemia-reperfusion (I/R) induced acute kidney injury (AKI) is regulated by transcriptional factors and microRNAs (miRs). However, modulation of miRs by transcriptional factors has not been characterized in AKI. Here, we found that urinary miR-16 was 100-fold higher in AKI patients. MiR-16 was detected earlier than creatinine in mouse after I/R. Using TargetScan, the 3′UTR of B-cell lymphoma 2 (BCL-2) was found complementary to miR-16 to decrease the fluorescent reporter activity. Overexpression of miR-16 in mice significantly attenuated renal function and increased TUNEL activity in epithelium tubule cells. The CCAAT enhancer binding protein beta (C/EBP-β) increased the expression of miR-16 after I/R injury. The ChIP and luciferase promoter assay indicated that about −1.0 kb to −0.5 kb upstream of miR-16 genome promoter region containing C/EBP-β binding motif transcriptionally regulated miR-16 expression. Meanwhile, the level of pri-miR-16 was higher in mice infected with lentivirus containing C/EBP-β compared with wild-type (WT) mice and overexpression of C/EBP-β in the kidney of WT mice reduced kidney function, increased kidney apoptosis, and elevated urinary miR-16 level. Our results indicated that miR-16 was transactivated by C/EBP-β resulting in aggravated I/R induced AKI and that urinary miR-16 may serve as a potential biomarker for AKI.
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Yamashita Y, Asakura M, Mitsugi R, Fujii H, Nagai K, Atsuda K, Itoh T, Fujiwara R. MicroRNA expression in the vildagliptin-treated two- and three-dimensional HepG2 cells. Drug Metab Pharmacokinet 2016; 31:201-9. [DOI: 10.1016/j.dmpk.2016.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 02/24/2016] [Accepted: 02/24/2016] [Indexed: 12/14/2022]
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Song L, Zhang Z, Zhang J, Zhu X, He L, Shi Z, Gao L, Feng F. Ratio of microRNA-122/155 in isoniazid-induced acute liver injury in mice. Exp Ther Med 2016; 12:889-894. [PMID: 27446292 PMCID: PMC4950840 DOI: 10.3892/etm.2016.3375] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 01/15/2016] [Indexed: 12/13/2022] Open
Abstract
Liver injury is a major hindrance to the treatment of tuberculosis (TB) patients due to the primary side effects associated with anti-TB drugs. Several investigations have identified sensitive biomarkers for the early diagnosis of anti-TB drug-induced liver injury (ADLI), including the use of microRNAs (miRNAs/miRs). However, the association between miR-122/155 and ADLI remains unknown. Thus, the present study used reverse transcription-quantitative polymerase chain reaction to observe changes in tissue miR-122/155 expression levels during the course of liver injury in mice. Liver injury was induced by the administration of isoniazid (INH), a first-line anti-TB drug. miR-122/155 expression levels were quantified at seven time points throughout 1 day (0.25, 0.75, 1.5, 6, 12, 18 and 24 h) based on the pharmacokinetics of INH in mice. Notably, over the timecourse of INH-induced liver injury, the tissue miR-122 expression level significantly decreased at 0.25 h, which is the peak concentration time of INH, compared with the control group (P<0.05). The change was more rapid than that of the serum aminotransferase and miR-155, which were significantly increased at 0.75 h. In addition, the pathological score correlated with the ratio of miR-122/miR-155 (r=−0.779; P<0.01). In conclusion, the miR-122/155 ratio may be utilized as a sensitive biomarker for ADLI, which could contribute to the early diagnosis of patients following anti-TB treatment.
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Affiliation(s)
- Lei Song
- Key Laboratory of Coal Mine Health and Safety, School of Public Health, North China University of Science and Technology, Tangshan, Hebei 063000, P.R. China; Bayan Nur Center for Disease Control and Prevention, Bayan Nur, Inner Mongolia 015000, P.R. China
| | - Zhongrui Zhang
- Key Laboratory of Coal Mine Health and Safety, School of Public Health, North China University of Science and Technology, Tangshan, Hebei 063000, P.R. China
| | - Jinling Zhang
- Key Laboratory of Coal Mine Health and Safety, School of Public Health, North China University of Science and Technology, Tangshan, Hebei 063000, P.R. China
| | - Xuebin Zhu
- Key Laboratory of Coal Mine Health and Safety, School of Public Health, North China University of Science and Technology, Tangshan, Hebei 063000, P.R. China
| | - Lei He
- Key Laboratory of Coal Mine Health and Safety, School of Public Health, North China University of Science and Technology, Tangshan, Hebei 063000, P.R. China
| | - Zhe Shi
- Key Laboratory of Coal Mine Health and Safety, School of Public Health, North China University of Science and Technology, Tangshan, Hebei 063000, P.R. China
| | - Li Gao
- Key Laboratory of Coal Mine Health and Safety, School of Public Health, North China University of Science and Technology, Tangshan, Hebei 063000, P.R. China
| | - Fumin Feng
- Key Laboratory of Coal Mine Health and Safety, School of Public Health, North China University of Science and Technology, Tangshan, Hebei 063000, P.R. China
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29
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Weldon BA, Shubin SP, Smith MN, Workman T, Artemenko A, Griffith WC, Thompson B, Faustman EM. Urinary microRNAs as potential biomarkers of pesticide exposure. Toxicol Appl Pharmacol 2016; 312:19-25. [PMID: 26826490 DOI: 10.1016/j.taap.2016.01.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 01/20/2016] [Accepted: 01/26/2016] [Indexed: 01/26/2023]
Abstract
MicroRNAs (miRNAs) are post-transcriptional regulators that silence messenger RNAs. Because miRNAs are stable at room temperature and long-lived, they have been proposed as molecular biomarkers to monitor disease and exposure status. While urinary miRNAs have been used clinically as potential diagnostic markers for kidney and bladder cancers and other diseases, their utility in non-clinical settings has yet to be fully developed. Our goal was to investigate the potential for urinary miRNAs to act as biomarkers of pesticide exposure and early biological response by identifying the miRNAs present in urine from 27 parent/child, farmworker/non-farmworker pairs (16FW/11NFW) collected during two agricultural seasons (thinning and post-harvest) and characterizing the between- and within-individual variability of these miRNA epigenetic regulators. MiRNAs were isolated from archived urine samples and identified using PCR arrays. Comparisons were made between age, households, season, and occupation. Of 384 miRNAs investigated, 297 (77%) were detectable in at least one sample. Seven miRNAs were detected in at least 50% of the samples, and one miRNA was present in 96% of the samples. Principal components and hierarchical clustering analyses indicate significant differences in miRNA profiles between farmworker and non-farmworker adults as well as between seasons. Six miRNAs were observed to be positively associated with farmworkers status during the post-harvest season. Expression of five of these miRNA trended towards a positive dose response relationship with organophosphate pesticide metabolites in farmworkers. These results suggest that miRNAs may be novel biomarkers of pesticide exposure and early biological response.
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Affiliation(s)
- Brittany A Weldon
- Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, United States; Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States
| | - Sara Pacheco Shubin
- Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, United States; Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States
| | - Marissa N Smith
- Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, United States; Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States
| | - Tomomi Workman
- Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, United States; Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States
| | - Alexander Artemenko
- Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, United States; Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States
| | - William C Griffith
- Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, United States; Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States
| | - Beti Thompson
- Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Elaine M Faustman
- Institute for Risk Analysis and Risk Communication, University of Washington, Seattle, WA, United States; Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States.
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30
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Falcon-Perez JM, Royo F. Circulating RNA: looking at the liver through a frosted glass. Biomarkers 2015; 20:339-54. [DOI: 10.3109/1354750x.2015.1101785] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- J. M. Falcon-Perez
- Metabolomics Unit, CIC bioGUNE, CIBERehd, Technology Park of Bizkaia, Derio, Bizkaia, Spain and
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - F. Royo
- Metabolomics Unit, CIC bioGUNE, CIBERehd, Technology Park of Bizkaia, Derio, Bizkaia, Spain and
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31
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Krauskopf J, Verheijen M, Kleinjans JC, de Kok TM, Caiment F. Development and regulatory application of microRNA biomarkers. Biomark Med 2015; 9:1137-51. [PMID: 26502281 DOI: 10.2217/bmm.15.50] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs, a class of regulatory small non-coding RNAs, are emerging as promising biomarkers for different health outcomes. Due to their tissue specificity, stability in extracellular space and high conservation between preclinical test species, applications of novel miRNA-based biomarkers for drug safety testing regarding hepatotoxicity and cardiotoxicity are investigated. Furthermore, miRNA expression is altered by environmental exposure such as cigarette smoke or polychlorinated biphenyls. As a consequence, miRNAs potentially influence tumor suppressor genes and oncogenes and may influence carcinogenesis. This has raised the interest in the use of miRNA profiles for health risk assessment. This review summarizes the recent developments in miRNA research with focus on biomarkers for drug safety testing and biomarkers for health outcomes related to environmental exposures.
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Affiliation(s)
- Julian Krauskopf
- Department of Toxicogenomics, Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Marcha Verheijen
- Department of Toxicogenomics, Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Jos C Kleinjans
- Department of Toxicogenomics, Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Theo M de Kok
- Department of Toxicogenomics, Maastricht University, 6200 MD Maastricht, The Netherlands
| | - Florian Caiment
- Department of Toxicogenomics, Maastricht University, 6200 MD Maastricht, The Netherlands
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32
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Wang W, Shi Q, Mattes WB, Mendrick DL, Yang X. Translating extracellular microRNA into clinical biomarkers for drug-induced toxicity: from high-throughput profiling to validation. Biomark Med 2015; 9:1177-88. [PMID: 26501984 DOI: 10.2217/bmm.15.86] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Over the past 5 years, extracellular microRNAs (miRNAs) are being vigorously explored as injury biomarkers, including drug-induced cardiotoxicity, hepatotoxicity and nephrotoxicity. Currently, the development of miRNAs as clinical biomarkers has been hindered by the lack of standardization. Therefore, extracellular miRNA-based biomarkers have not been embraced as diagnostic tools. Each platform has its strengths and weaknesses when working with low-input-amount RNA samples from body fluids; the selection of a miRNA quantification approach should be based on the study design. The following review provides a summary of the extracellular miRNA release and stability in body fluids, performances of different miRNA quantification platforms, existing clinical gold standards for drug-induced tissue damage and translation of the miRNA biomarkers from the nonclinical to clinical setting.
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Affiliation(s)
- Wenjun Wang
- College of Life Science, South-Central University for Nationalities, Wuhan 430074, PR China.,Division of Systems Biology, National Center for Toxicological Research, Food & Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Qiang Shi
- Division of Systems Biology, National Center for Toxicological Research, Food & Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Williams B Mattes
- Division of Systems Biology, National Center for Toxicological Research, Food & Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Donna L Mendrick
- Division of Systems Biology, National Center for Toxicological Research, Food & Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Xi Yang
- Division of Systems Biology, National Center for Toxicological Research, Food & Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
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33
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Beger RD, Bhattacharyya S, Yang X, Gill PS, Schnackenberg LK, Sun J, James LP. Translational biomarkers of acetaminophen-induced acute liver injury. Arch Toxicol 2015; 89:1497-522. [PMID: 25983262 PMCID: PMC4551536 DOI: 10.1007/s00204-015-1519-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 04/21/2015] [Indexed: 12/17/2022]
Abstract
Acetaminophen (APAP) is a commonly used analgesic drug that can cause liver injury, liver necrosis and liver failure. APAP-induced liver injury is associated with glutathione depletion, the formation of APAP protein adducts, the generation of reactive oxygen and nitrogen species and mitochondrial injury. The systems biology omics technologies (transcriptomics, proteomics and metabolomics) have been used to discover potential translational biomarkers of liver injury. The following review provides a summary of the systems biology discovery process, analytical validation of biomarkers and translation of omics biomarkers from the nonclinical to clinical setting in APAP-induced liver injury.
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Affiliation(s)
- Richard D Beger
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, USA,
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Patel SAA, Gooderham NJ. IL6 Mediates Immune and Colorectal Cancer Cell Cross-talk via miR-21 and miR-29b. Mol Cancer Res 2015; 13:1502-8. [PMID: 26184038 DOI: 10.1158/1541-7786.mcr-15-0147] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 07/06/2015] [Indexed: 01/08/2023]
Abstract
UNLABELLED Tumors are surrounded and infiltrated by a variety of stromal cell types, including fibroblasts, immune cells, and vascular endothelial cells, which interact with malignant cells to generate the tumor microenvironment (TME). This complex environment is thought to be regulated by the tumor in order to promote its survival and progression and thus constitutes a potential target for cancer therapy. However, intercellular communication within the microenvironment is not yet well understood. The current study investigates the mechanism by which cancer and immune cells communicate using an in vitro coculture model. It is demonstrated that IL6, a proinflammatory cytokine, secreted by immune cells promotes colorectal cancer cell invasiveness. In addition, in the presence of IL6, the cancer cells were able to secrete circulating miRNAs miR-21 and miR-29b to further induce immune cell IL6 production. Activated immune cells were also found to release miR-21 into the TME. Taken together, these mechanistic findings provide a better understanding of intercellular communication between immune and cancer cells in the TME and offer insight into some of the key players that mediate this cross-talk. IMPLICATIONS This study demonstrates that cocultured cancer and immune cells communicate via IL6 and circulating miRNAs to sustain chronic inflammation and promote prometastatic cancer cell behavior. In addition, critical players are identified that mediate intercellular communication in the TME and suggest possible therapeutic approaches that target the microenvironment.
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Affiliation(s)
- Saroor A A Patel
- Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Nigel J Gooderham
- Surgery and Cancer, Imperial College London, London, United Kingdom.
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35
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Toska E, Zagorsky R, Figler B, Cheng F. Transcriptomic studies on liver toxicity of acetaminophen. Drug Dev Res 2015; 75:419-23. [PMID: 25195586 DOI: 10.1002/ddr.21227] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Acetaminophen is widely used as a pain reliever and to reduce fever. At high doses, it can cause severe hepatotoxicity. Acetaminophen overdose has become the leading cause of acute liver failure in the US. The mechanisms for acetaminophen-induced liver injury are unclear. Transcriptomic studies can identify the changes in expression of thousands of genes when exposed to supratherapeutic doses of acetaminophen. These studies elucidated the mechanism of acetaminophen-induced hepatotoxicity and also provide insight into future development of diagnosis and treatment options for acetaminophen-induced acute liver failure. The following is a brief overview of some recent transcriptomic studies and gene-expression-based prediction models on liver toxicity induced by acetaminophen.
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Affiliation(s)
- Endrit Toska
- Department of Pharmaceutical Science, College of Pharmacy, University of South Florida, Tampa, FL, 33612, USA
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Kobayashi A, Kondo K, Sugai S. [Investigation of Predisposition Biomarkers to Identify Risk Factors for Drug-induced Liver Injury in Humans: Analyses of Endogenous Metabolites in an Animal Model Mimicking Human Responders to APAP-induced Hepatotoxicity]. YAKUGAKU ZASSHI 2015; 135:655-62. [PMID: 25948298 DOI: 10.1248/yakushi.14-00230-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Drug-induced liver injury is a main reason of regulatory action pertaining to drugs, including restrictions to clinical indications and withdrawal from the marketplace. Acetaminophen (APAP) is a commonly used and effective analgesic/antipyretic agent and relatively safe drug even in long-term treatment. However, it is known that APAP at therapeutic doses may cause hepatotoxicity in some individuals. Hence great efforts have been made to identify risk factors for APAP-induced chronic hepatotoxicity. We investigated the contribution of undernourishment to susceptibility to APAP-induced chronic hepatotoxicity using an animal model. We employed daytime restricted fed (RF) rats as a modified-nutritional state model for human APAP-induced hepatotoxicity. RF and ad libitum fed (ALF) rats were given APAP at 0, 300, and 500 mg/kg for 3 months. Plasma and urinary glutathione-related metabolomes and liver function parameters were measured during the dosing period. Endogenous metabolites forming at different levels between the RF and ALF rats could be potential predisposition biomarkers for APAP-induced hepatotoxicity. In addition, RF rats were considered a useful model to estimate the contribution of nutritional state of patients to APAP-induced chronic hepatotoxicity. In this article we report our current research focusing on nutritional state as risk factor for APAP-induced chronic hepatotoxicity and our findings of hepatotoxicity biomarkers.
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Affiliation(s)
- Akio Kobayashi
- Toxicology Research Lab., Central Pharmaceutical Research Institute, JAPAN TOBACCO INC
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37
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Marrone AK, Beland FA, Pogribny IP. The role for microRNAs in drug toxicity and in safety assessment. Expert Opin Drug Metab Toxicol 2015; 11:601-11. [PMID: 25739314 DOI: 10.1517/17425255.2015.1021687] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Adverse drug reactions present significant challenges that impact pharmaceutical development and are major burdens to public health services worldwide. In response to this need, the field of toxicology is rapidly expanding to identify key pathways involved in drug toxicity. AREAS COVERED MicroRNAs (miRNAs) are a class of small evolutionary conserved endogenous non-coding RNAs that regulate the translation of protein-coding genes. A wide range of toxicants alter miRNA levels in target organs and these altered miRNAs can also be detected in easily accessible biological fluids. This, combined with an early miRNA response to toxic insults and miRNA stability, substantiates the potential for these small molecules to be useful biomarkers for drug safety assessment. EXPERT OPINION miRNAs are early indicators and useful tools to detect drug-induced toxicity. Incorporation of miRNA profiling into the drug safety testing process will complement currently used techniques and may substantially enhance drug safety. With the increasing interests in translational research, the field of miRNA biomarker research will continue to expand and become an important part of the investigation of human drug toxicity.
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Affiliation(s)
- April K Marrone
- FDA-National Center for Toxicological Research, Division of Biochemical Toxicology , Jefferson, AR , USA
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38
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Yang X, Salminen WF, Shi Q, Greenhaw J, Gill PS, Bhattacharyya S, Beger RD, Mendrick DL, Mattes WB, James LP. Potential of extracellular microRNAs as biomarkers of acetaminophen toxicity in children. Toxicol Appl Pharmacol 2015; 284:180-7. [PMID: 25708609 DOI: 10.1016/j.taap.2015.02.013] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 02/11/2015] [Accepted: 02/13/2015] [Indexed: 01/02/2023]
Abstract
UNLABELLED Developing biomarkers for detecting acetaminophen (APAP) toxicity has been widely investigated. Recent studies of adults with APAP-induced liver injury have reported human serum microRNA-122 (miR-122) as a novel biomarker of APAP-induced liver injury. The goal of this study was to examine extracellular microRNAs (miRNAs) as potential biomarkers for APAP liver injury in children. Global levels of serum and urine miRNAs were examined in three pediatric subgroups: 1) healthy children (n=10), 2) hospitalized children receiving therapeutic doses of APAP (n=10) and 3) children hospitalized for APAP overdose (n=8). Out of 147 miRNAs detected in the APAP overdose group, eight showed significantly increased median levels in serum (miR-122, -375, -423-5p, -30d-5p, -125b-5p, -4732-5p, -204-5p, and -574-3p), compared to the other groups. Analysis of urine samples from the same patients had significantly increased median levels of four miRNAs (miR-375, -940, -9-3p and -302a) compared to the other groups. Importantly, correlation of peak serum APAP protein adduct levels (an indicator of the oxidation of APAP to the reactive metabolite N-acetyl-para-quinone imine) with peak miRNA levels showed that the highest correlation was observed for serum miR-122 (R=0.94; p<0.01) followed by miR-375 (R=0.70; p=0.05). CONCLUSION Our findings demonstrate that miRNAs are increased in children with APAP toxicity and correlate with APAP protein adducts, suggesting a potential role as biomarkers of APAP toxicity.
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Affiliation(s)
- Xi Yang
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, USA.
| | - William F Salminen
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, USA.
| | - Qiang Shi
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, USA.
| | - James Greenhaw
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, USA.
| | - Pritmohinder S Gill
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Clinical Pharmacology and Toxicology Section, Arkansas Children's Hospital, Little Rock, AR, USA.
| | - Sudeepa Bhattacharyya
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Clinical Pharmacology and Toxicology Section, Arkansas Children's Hospital, Little Rock, AR, USA.
| | - Richard D Beger
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, USA.
| | - Donna L Mendrick
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, USA.
| | - William B Mattes
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, USA.
| | - Laura P James
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Clinical Pharmacology and Toxicology Section, Arkansas Children's Hospital, Little Rock, AR, USA.
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39
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Wang Y, Chen T, Tong W. miRNAs and their application in drug-induced liver injury. Biomark Med 2014; 8:161-72. [PMID: 24521012 DOI: 10.2217/bmm.13.147] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The complex miRNA regulatory network plays an important role in diverse biological activities of physiopathological processes. In addition to the discovery of and research on the extracellular miRNAs detected in multiple biofluids, the properties of tissue specificity and high stability underlie the great potential of these small miRNAs to serve as translational biomarkers for various diseases in the clinical setting, including in drug-induced liver injury. In this review, we describe the major technologies currently used and challenges in miRNA measurement and provide information on major bioinformatics resources available for current miRNA research. We also discuss novel findings in liver disease and highlight the potential of miRNAs for clinical and basic research as translational biomarkers for drug-induced liver injury.
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Affiliation(s)
- Yuping Wang
- Division of Bioinformatics & Biostatistics, National Center for Toxicological Research, US FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
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Pavkovic M, Riefke B, Ellinger-Ziegelbauer H. Urinary microRNA profiling for identification of biomarkers after cisplatin-induced kidney injury. Toxicology 2014; 324:147-57. [DOI: 10.1016/j.tox.2014.05.005] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 04/24/2014] [Accepted: 05/14/2014] [Indexed: 11/25/2022]
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41
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Kanki M, Moriguchi A, Sasaki D, Mitori H, Yamada A, Unami A, Miyamae Y. Identification of urinary miRNA biomarkers for detecting cisplatin-induced proximal tubular injury in rats. Toxicology 2014; 324:158-68. [DOI: 10.1016/j.tox.2014.05.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 04/19/2014] [Accepted: 05/14/2014] [Indexed: 11/16/2022]
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42
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Li LM, Wang D, Zen K. MicroRNAs in Drug-induced Liver Injury. J Clin Transl Hepatol 2014; 2:162-9. [PMID: 26357624 PMCID: PMC4521241 DOI: 10.14218/jcth.2014.00015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 08/02/2014] [Accepted: 08/04/2014] [Indexed: 12/12/2022] Open
Abstract
Drug-induced liver injury (DILI) is a leading cause of acute liver failure, and a major reason for the recall of marketed drugs. Detection of potential liver injury is a challenge for clinical management and preclinical drug safety studies, as well as a great obstacle to the development of new, effective and safe drugs. Currently, serum levels of alanine and aspartate aminotransferases are the gold standard for evaluating liver injury. However, these levels are assessed by nonspecific, insensitive, and non-predictive tests, and often result in false-positive results. Therefore, there is an urgent need for better DILI biomarkers to guide risk assessment and patient management. The discovery of microRNAs (miRNAs) as a new class of gene expression regulators has triggered an explosion of research, particularly on the measurement of miRNAs in various body fluids as biomarkers for many human diseases. The properties of miRNA-based biomarkers, such as tissue specificity and high stability and sensitivity, suggest they could be used as novel, minimally invasive and stable DILI biomarkers. In the current review, we summarize recent progress concerning the role of miRNAs in diagnosing and monitoring both clinical and preclinical DILI, and discuss the main advantages and challenges of miRNAs as novel DILI biomarkers.
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Affiliation(s)
| | | | - Ke Zen
- Correspondence to: Ke Zen, Nanjing University School of Life Sciences, 22 Hankou Road, Nanjing, Jiangsu 210093, China. E-mail:
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Identification of a metabolic biomarker panel in rats for prediction of acute and idiosyncratic hepatotoxicity. Comput Struct Biotechnol J 2014; 10:78-89. [PMID: 25379137 PMCID: PMC4204381 DOI: 10.1016/j.csbj.2014.08.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
It has been estimated that 10% of acute liver failure is due to “idiosyncratic hepatotoxicity”. The inability to identify such compounds with classical preclinical markers of hepatotoxicity has driven the need to discover a mechanism-based biomarker panel for hepatotoxicity. Seven compounds were included in this study: two overt hepatotoxicants (acetaminophen and carbon tetrachloride), two idiosyncratic hepatotoxicants (felbamate and dantrolene), and three non-hepatotoxicants (meloxicam, penicillin and metformin). Male Sprague–Dawley rats were orally gavaged with a single dose of vehicle, low dose or high dose of the compounds. At 6 h and 24 h post-dosing, blood was collected for metabolomics and clinical chemistry analyses, while organs were collected for histopathology analysis. Forty-one metabolites from previous hepatotoxicity studies were semi-quantified and were used to build models to predict hepatotoxicity. The selected metabolites were involved in various pathways, which have been noted to be linked to the underlying mechanisms of hepatotoxicity. PLS models based on all 41 metabolite or smaller subsets of 6 (6 h), 7 (24 h) and 20 (6 h and 24 h) metabolites resulted in models with an accuracy of at least 97.4% for the hold-out test set and 100% for training sets. When applied to the external test sets, the PLS models predicted that 1 of 9 rats at both 6 h and 24 h treated with idiosyncratic liver toxicants was exposed to a hepatotoxic chemical. In conclusion, the biomarker panel might provide information that along with other endpoint data (e.g., transcriptomics and proteomics) may diagnose acute and idiosyncratic hepatotoxicity in a clinical setting.
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Wang Z, Li X. The role of noncoding RNA in hepatocellular carcinoma. Gland Surg 2014; 2:25-9. [PMID: 25083452 DOI: 10.3978/j.issn.2227-684x.2013.02.07] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 02/25/2013] [Indexed: 12/13/2022]
Abstract
Increasing noncoding RNAs (ncRNAs) were found to show abnormal expression patterns in various human cancers. Based on their length, ncRNAs are briefly divided into two categories. Transcripts that are shorter than 200 nucleotides are recognized as short/small noncoding RNAs and greater than 200 nucleotides as long noncoding RNAs (lncRNAs). Short/small noncoding RNAs include microRNAs, piRNAs, snoRNAs, and endogenous siRNAs. Numerous studies have revealed that these short/small ncRNA play important roles in multiple biological processes and tumorigenesis. In contrast to small ncRNAs, long noncoding RNAs are much less known concerning their functions in human cancers especially in hepatocellular carcinoma (HCC). In this review, we highlight recent progress regarding HCC development, tumorigenesis, metastasis, clinical implication, as well as the role in the risk of HBV infection.
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Affiliation(s)
- Zhuolu Wang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
| | - Xinying Li
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha 410008, People's Republic of China
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45
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Gooderham N, Koufaris C. Using microRNA profiles to predict and evaluate hepatic carcinogenic potential. Toxicol Lett 2014; 228:127-32. [DOI: 10.1016/j.toxlet.2014.04.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 04/17/2014] [Accepted: 04/20/2014] [Indexed: 01/17/2023]
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46
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Khan SR, Baghdasarian A, Fahlman RP, Michail K, Siraki AG. Current status and future prospects of toxicogenomics in drug discovery. Drug Discov Today 2014; 19:562-78. [DOI: 10.1016/j.drudis.2013.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 09/27/2013] [Accepted: 11/01/2013] [Indexed: 01/03/2023]
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47
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Perez A, Loizaga A, Arceo R, Lacasa I, Rabade A, Zorroza K, Mosen-Ansorena D, Gonzalez E, Aransay AM, Falcon-Perez JM, Unda-Urzaiz M, Royo F. A Pilot Study on the Potential of RNA-Associated to Urinary Vesicles as a Suitable Non-Invasive Source for Diagnostic Purposes in Bladder Cancer. Cancers (Basel) 2014; 6:179-92. [PMID: 24458310 PMCID: PMC3980604 DOI: 10.3390/cancers6010179] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 12/20/2013] [Accepted: 01/13/2014] [Indexed: 12/26/2022] Open
Abstract
Bladder cancer is one of the most common cancers and, together with prostate carcinoma, accounts for the majority of the malignancies of the genitourinary tract. Since prognosis ameliorates with early detection, it will be beneficial to have a repertoire of diagnostic markers that could complement the current diagnosis protocols. Recently, cell-secreted extracellular vesicles have received great interest as a source of low invasive disease biomarkers because they are found in many body fluids, including urine. The current work describes a pilot study to generate an array-based catalogue of mRNA associated to urinary vesicles, and also a comparison with samples obtained from bladder cancer patients. After an analysis of presence/absence of transcripts in bladder cancer EVs, a list of genes was selected for further validation using PCR technique. We found four genes differentially expressed in cancer samples. LASS2 and GALNT1 were present in cancer patients, while ARHGEF39 and FOXO3 were found only in non-cancer urinary vesicles. Previous studies have pointed to the involvement of those genes in tumour progression and metastasis.
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Affiliation(s)
- Amparo Perez
- Urology Service, Basurto University Hospital, Bilbao 48013, Bizkaia, Spain; E-Mails: (A.P.); (A.L.); (R.A.); (I.L.); (A.R.); (M.U.-U.)
| | - Ana Loizaga
- Urology Service, Basurto University Hospital, Bilbao 48013, Bizkaia, Spain; E-Mails: (A.P.); (A.L.); (R.A.); (I.L.); (A.R.); (M.U.-U.)
| | - Raquel Arceo
- Urology Service, Basurto University Hospital, Bilbao 48013, Bizkaia, Spain; E-Mails: (A.P.); (A.L.); (R.A.); (I.L.); (A.R.); (M.U.-U.)
| | - Isabel Lacasa
- Urology Service, Basurto University Hospital, Bilbao 48013, Bizkaia, Spain; E-Mails: (A.P.); (A.L.); (R.A.); (I.L.); (A.R.); (M.U.-U.)
| | - Ainara Rabade
- Urology Service, Basurto University Hospital, Bilbao 48013, Bizkaia, Spain; E-Mails: (A.P.); (A.L.); (R.A.); (I.L.); (A.R.); (M.U.-U.)
| | - Kerman Zorroza
- Basque Foundation for Health Innovation and Research (BIOEF), DNA Laboratory, Basurto Hospital, Bilbao 48013, Bizkaia, Spain; E-Mail:
| | - David Mosen-Ansorena
- Genome Analysis Platform, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, Derio 48160, Bizkaia, Spain; E-Mails: (D.M.-A); (A.M.A.)
| | - Esperanza Gonzalez
- Metabolomics Unit, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, Derio 48160, Bizkaia, Spain; E-Mails: (E.G.); (J.M.F.-P.)
| | - Ana M. Aransay
- Genome Analysis Platform, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, Derio 48160, Bizkaia, Spain; E-Mails: (D.M.-A); (A.M.A.)
| | - Juan M. Falcon-Perez
- Metabolomics Unit, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, Derio 48160, Bizkaia, Spain; E-Mails: (E.G.); (J.M.F.-P.)
- IKERBASQUE, Basque Foundation for Science, Bilbao 48011, Bizkaia, Spain; E-Mail:
| | - Miguel Unda-Urzaiz
- Urology Service, Basurto University Hospital, Bilbao 48013, Bizkaia, Spain; E-Mails: (A.P.); (A.L.); (R.A.); (I.L.); (A.R.); (M.U.-U.)
| | - Felix Royo
- Metabolomics Unit, CIC bioGUNE, CIBERehd, Bizkaia Technology Park, Derio 48160, Bizkaia, Spain; E-Mails: (E.G.); (J.M.F.-P.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +34-944-061-325; Fax: +34-944-061-301
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Yang X, Weng Z, Mendrick DL, Shi Q. Circulating extracellular vesicles as a potential source of new biomarkers of drug-induced liver injury. Toxicol Lett 2014; 225:401-6. [PMID: 24462978 DOI: 10.1016/j.toxlet.2014.01.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 01/07/2014] [Accepted: 01/08/2014] [Indexed: 12/11/2022]
Abstract
Like most cell types, hepatocytes constantly produce extracellular vesicles (EVs) such as exosomes and microvesicles that are released into the circulation to transport signaling molecules and cellular waste. Circulating EVs are being vigorously explored as biomarkers of diseases and toxicities, including drug-induced liver injury (DILI). Emerging data suggest that (a) blood-borne EVs contain liver-specific mRNAs and microRNAs (miRNAs), (b) the levels can be remarkably elevated in response to DILI, and (c) the increases correlate well with classical measures of liver damage. The expression profile of mRNAs in EVs and the compartmentalization of miRNAs within EVs or other blood fractions were found to be indicative of the offending drug involved in DILI, thus providing more informative assessment of liver injury than using alanine aminotransferase alone. EVs in the urine and cell culture medium were also found to contain proteins or mRNAs that were indicative of DILI. However, major improvements in EV isolation methods are needed for the discovery, evaluation, and quantification of possible DILI biomarkers in circulating EVs.
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Affiliation(s)
- Xi Yang
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Zuquan Weng
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Donna L Mendrick
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Qiang Shi
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
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Church RJ, McDuffie JE, Sonee M, Otieno M, Ma JY, Liu X, Watkins PB, Harrill AH. MicroRNA-34c-3p is an early predictive biomarker for doxorubicin-induced glomerular injury progression in male Sprague-Dawley rats. Toxicol Res (Camb) 2014. [DOI: 10.1039/c4tx00051j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Increased microRNA-34c-3p appeared as a novel biomarker for doxorubicin nephrotoxicity in rats; alterations showed greater specificity than and comparable sensitivity to albuminuria for early prediction of glomerular injury.
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Affiliation(s)
| | - J. Eric McDuffie
- Preclinical Development and Safety
- Janssen Research & Development
- LLC
- San Diego, USA
| | - Manisha Sonee
- Preclinical Development and Safety
- Janssen Research & Development
- LLC
- Spring House, USA
| | - Monicah Otieno
- Preclinical Development and Safety
- Janssen Research & Development
- LLC
- Spring House, USA
| | - Jing Ying Ma
- Preclinical Development and Safety
- Janssen Research & Development
- LLC
- San Diego, USA
| | - Xuejun Liu
- Immunology Systems Pharmacology and Biomarkers
- Janssen Research & Development
- LLC
- San Diego, USA
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50
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Osaki M, Kosaka N, Okada F, Ochiya T. Circulating MicroRNAs in Drug Safety Assessment for Hepatic and Cardiovascular Toxicity: The Latest Biomarker Frontier? Mol Diagn Ther 2013; 18:121-6. [DOI: 10.1007/s40291-013-0065-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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