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Barthel H, Sébillaud S, Lorcin M, Wolff H, Viton S, Cosnier F, Gaté L, Seidel C. Needlelike, short and thin multi-walled carbon nanotubes: comparison of effects on wild type and p53 +/- rat lungs. Nanotoxicology 2023; 17:270-288. [PMID: 37126100 DOI: 10.1080/17435390.2023.2204933] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Carbon nanotubes (CNTs) are nanomaterials presenting an occupational inhalation risk during production or handling. The International Agency for Research on Cancer classified one CNT, Mitsui-7 (MWNT-7), as 'possibly carcinogenic to humans'. In recognition of their similarities, a proposal has been submitted to the risk assessment committee of ECHA to classify all fibers with 'Fibre Paradigm' (FP)-compatible dimensions as carcinogenic. However, there is a lack of clarity surrounding the toxicity of fibers that do not fit the FP criteria. In this study, we compared the effects of the FP-compatible Mitsui-7, to those of NM-403, a CNT that is too short and thin to fit the paradigm. Female Sprague Dawley rats deficient for p53 (GMO) and wild type (WT) rats were exposed to the two CNTs (0.25 mg/rat/week) by intratracheal instillation. Animals (GMO and WT) were exposed weekly for four consecutive weeks and were sacrificed 3 days or 8 months after the last instillation. Exposure to both CNTs induced acute lung inflammation. However, persistent inflammation at 8 months was only observed in the lungs of rats exposed to NM-403. In addition to the persistent inflammation, NM-403 stimulated hyperplasic changes in rat lungs, and no adenomas or carcinomas were detected. The degree and extent of hyperplasia was significantly more pronounced in GMO rats. These results suggest that CNT not meeting the FP criteria can cause persistent inflammation and hyperplasia. Consequently, their health effects should be carefully assessed.
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Affiliation(s)
- Hélène Barthel
- French Research and Safety Institute for the Prevention of Occupational Accidents and Diseases (INRS), Toxicology and Biomonitoring Division, Vandoeuvre-lès-Nancy, France
- Ingénierie Moléculaire et Physiophatologie Articulaire (IMoPA), Biopôle, Campus Biologie Santé, UMR 7365 CNRS-Université de Lorraine, Vandoeuvre-lès-Nancy, France
| | - Sylvie Sébillaud
- French Research and Safety Institute for the Prevention of Occupational Accidents and Diseases (INRS), Toxicology and Biomonitoring Division, Vandoeuvre-lès-Nancy, France
| | - Mylène Lorcin
- French Research and Safety Institute for the Prevention of Occupational Accidents and Diseases (INRS), Toxicology and Biomonitoring Division, Vandoeuvre-lès-Nancy, France
| | - Henrik Wolff
- Finnish Institute of Occupational Health, Helsinki, Finland
| | - Stéphane Viton
- French Research and Safety Institute for the Prevention of Occupational Accidents and Diseases (INRS), Toxicology and Biomonitoring Division, Vandoeuvre-lès-Nancy, France
| | - Frédéric Cosnier
- French Research and Safety Institute for the Prevention of Occupational Accidents and Diseases (INRS), Toxicology and Biomonitoring Division, Vandoeuvre-lès-Nancy, France
| | - Laurent Gaté
- French Research and Safety Institute for the Prevention of Occupational Accidents and Diseases (INRS), Toxicology and Biomonitoring Division, Vandoeuvre-lès-Nancy, France
| | - Carole Seidel
- French Research and Safety Institute for the Prevention of Occupational Accidents and Diseases (INRS), Toxicology and Biomonitoring Division, Vandoeuvre-lès-Nancy, France
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Ventura C, Torres V, Vieira L, Gomes B, Rodrigues AS, Rueff J, Penque D, Silva MJ. New “Omics” Approaches as Tools to Explore Mechanistic Nanotoxicology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1357:179-194. [DOI: 10.1007/978-3-030-88071-2_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Dai S, Wang Z, Yang Y, Guo T, Li W. Assessment on the lung injury of mice posed by airborne PM 2.5 collected from developing area in China and associated molecular mechanisms by integrated analysis of mRNA-seq and miRNA-seq. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 224:112661. [PMID: 34416640 DOI: 10.1016/j.ecoenv.2021.112661] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/08/2021] [Accepted: 08/13/2021] [Indexed: 02/08/2023]
Abstract
Some epidemiological evidences showed exposure of airborne fine particulate matter (PM2.5) was associated with lung dysfunction. However, the adverse effects of PM2.5 from mid-scale city of China on the respiratory system were unknown. Correspondingly, the mechanisms, especially the epigenetic mechanism regulated by miRNAs, involved in PM2.5-induced lung injury has not been fully understood. In this study, male Balb/C mice were exposed to PM2.5 collected from mid-scale city (Baoji), China for 8 weeks (mean concentration 298.52 ± 25.86 μg/m3 at exposure chamber) using a whole-body exposure system. The carbon component was the main ingredient (45.80%) of PM2.5 followed by ions (43.19%). Meanwhile, the sum concentrations of polycyclic aromatic hydrocarbons (PAHs) and n-alkanes (C18-C33) were 570.48 and 2029.13 ng/m3 in the exposure chamber, respectively. Obvious lung injury including pulmonary inflammation and fibrosis (p < 0.05 compared with the control) were found from PM2.5 exposure group determined by micro-CT and histopathological assays, respectively, suggesting the health risk posed by PM2.5 from mid-scale city of China should be concerned. The integrated analysis between mRNA-seq and miRNA-seq revealed the differentially expression genes in lung tissues were enriched in immune pathways including B cell receptor signaling (p = 0.078) and cell adhesion molecules (CAMs) (p = 0.0068). The expression profiles of the genes and corresponding mRNAs involved into the immune pathways determined by RT-qPCR analysis were consistent with them conducted by transcriptome. Moreover, the expression levels of the proteins (i.e., CD19, CD81, PIK3CD, and CD22) involved into B cell receptor signaling pathway from exposure group were 1.71- to 6.948- folds compared with the control, validating the results of the genes expression profiles. Further, canonical correlation analysis (CCA) and multiple correlation analysis between the target genes and components of PM2.5 documented the organic compounds (i.e., Benzo(a)pyrene (p = 0.012) and octadecane (p = 0.05)) and inorganic elements (i.e., Cl-, Ti, Al, and Zn) was the key environmental factors. Cd19, Pik3cd, and Cd8b1 might be the key genes for lung dysfunction induced by PM2.5 illuminated using interactive analysis (p < 0.05). This work for the first time showed the adverse effects of PM2.5 in mid-scale city in China on respiratory system should be concerned, and the associated epigenetic mechanism regulated by miRNA were revealed. These results may provide new insight into the development of future assessment on the air pollution associated respiratory disease.
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Affiliation(s)
- Shuiping Dai
- National Center for Geriatrics Clinical Medicine Research, Department of Geriatrics and Gerontology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhenglu Wang
- College of oceanography, Hohai University, Nanjing 210098, China
| | - Ying Yang
- Center of Precision Medicine, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tingting Guo
- Center of Precision Medicine, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Weimin Li
- Center of Precision Medicine, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu 610041, China; Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
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Niehof M, Reamon-Buettner SM, Danov O, Hansen T, Sewald K. A modified protocol for successful miRNA profiling in human precision-cut lung slices (PCLS). BMC Res Notes 2021; 14:255. [PMID: 34215333 PMCID: PMC8252208 DOI: 10.1186/s13104-021-05674-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 06/24/2021] [Indexed: 12/11/2022] Open
Abstract
Objective Human precision cut lung slices (PCLS) are widely used as an ex vivo model system for drug discovery and development of new therapies. PCLS reflect the functional heterogeneity of lung tissue and possess relevant lung cell types. We thus determined the use of PCLS in studying non-coding RNAs notably miRNAs, which are important gene regulatory molecules. Since miRNAs play key role as mediators of respiratory diseases, they can serve as valuable prognostic or diagnostic biomarkers, and in therapeutic interventions, of lung diseases. A technical limitation though is the vast amount of agarose in PCLS which impedes (mi)RNA extraction by standard procedures. Here we modified our recently published protocol for RNA isolation from PCLS to enable miRNA readouts. Results The modified method relies on the separation of lysis and precipitation steps, and a clean-up procedure with specific magnetic beads. We obtained successfully quality miRNA amenable for downstream applications such as RTqPCR and whole transcriptome miRNA analysis. Comparison of miRNA profiles in PCLS with published data from human lung, identified all important miRNAs regulated in IPF, COPD, asthma or lung cancer. Therefore, this shows suitability of the method for analyzing miRNA targets and biomarkers in the valuable human PCLS model. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-021-05674-w.
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Affiliation(s)
- Monika Niehof
- Department of Preclinical Pharmacology and In Vitro Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Nikolai-Fuchs-Str. 1, Hannover, 30625, Germany.
| | - Stella Marie Reamon-Buettner
- Department of Preclinical Pharmacology and In Vitro Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Nikolai-Fuchs-Str. 1, Hannover, 30625, Germany
| | - Olga Danov
- Department of Preclinical Pharmacology and In Vitro Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Nikolai-Fuchs-Str. 1, Hannover, 30625, Germany
| | - Tanja Hansen
- Department of Preclinical Pharmacology and In Vitro Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Nikolai-Fuchs-Str. 1, Hannover, 30625, Germany
| | - Katherina Sewald
- Department of Preclinical Pharmacology and In Vitro Toxicology, Fraunhofer Institute for Toxicology and Experimental Medicine, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Nikolai-Fuchs-Str. 1, Hannover, 30625, Germany
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Ye M, Wang S, Sun P, Qie J. Integrated MicroRNA Expression Profile Reveals Dysregulated miR-20a-5p and miR-200a-3p in Liver Fibrosis. BIOMED RESEARCH INTERNATIONAL 2021; 2021:9583932. [PMID: 34235224 PMCID: PMC8218919 DOI: 10.1155/2021/9583932] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 05/27/2021] [Indexed: 12/23/2022]
Abstract
MicroRNAs (miRNAs) have been demonstrated to involve in liver fibrogenesis. However, the miRNA-gene regulation in liver fibrosis is still unclear. Herein, the miRNA expression profile GSE40744 was obtained to analyze the dysregulated miRNAs between liver fibrosis and normal samples. Then, we predicted the target genes of screened miRNAs by miRTarBase, followed by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Then, the protein-protein interaction (PPI) network was constructed to identify the functional miRNA-gene regulatory modules. Furthermore, we verified the hub gene expression using the gene expression profile GSE14323. Finally, 89 DEMs were identified in fibrotic liver samples compared to normal liver samples. The top 3 upregulated DEMs (miR-200b-3p, miR-200a-3p, and miR-182-5p) and downregulated DEMs (miR-20a-5p, miR-194-3p, and miR-148a-3p) were further studied. 516 and 1416 target genes were predicted, respectively. KEGG analysis demonstrated that the predicted genes were enriched in the p53 signaling pathway and hepatitis B, etc. Through constructing a PPI network, the genes with the highest connectivity were identified as hub genes. Of note, most of the hub genes were potentially targeted by miR-20a-5p and miR-200a-3p. Based on the data from GSE14323, the expression of EGFR, STAT3, CTNNB1, and TP53 targeted by miR-200a-3p was significantly downregulated in fibrotic liver samples. Oppositely, the expression of PTEN, MYC, MAPK1, UBC, and CCND1 potentially targeted by miR-20a-5p was significantly upregulated. In conclusion, it is demonstrated that miR-20a-5p and miR-200a-3p were identified as the novel liver fibrosis-associated miRNAs, which may play critical roles in liver fibrogenesis.
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Affiliation(s)
- Mu Ye
- Department of General Surgery, Jinshan Hospital, Fudan University, Shanghai 201508, China
| | - Sheng Wang
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Peilong Sun
- Department of General Surgery, Jinshan Hospital, Fudan University, Shanghai 201508, China
| | - Jingbo Qie
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
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González-Palomo AK, Saldaña-Villanueva K, Cortés-García JD, Fernández-Macias JC, Méndez-Rodríguez KB, Pérez Maldonado IN. Effect of silver nanoparticles (AgNPs) exposure on microRNA expression and global DNA methylation in endothelial cells EA.hy926. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2021; 81:103543. [PMID: 33166681 DOI: 10.1016/j.etap.2020.103543] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 10/30/2020] [Accepted: 10/31/2020] [Indexed: 06/11/2023]
Abstract
The aim of this study was to determine the effect of AgNPs on the epigenome of endothelial cells EA.hy926, including the levels of expression of microRNAs (miRNAs) and global DNA methylation patterns. In addition, evaluation of the expression of inflammatory genes and the levels of VCAM-1 protein (miRNA-126 target) was performed. The expression levels of analyzed miRNAs (microRNAs-126, 155 and 146) were reduced significantly and there were not observed changes in inflammatory gene expression. Regarding the levels of protein vascular cell adhesion molecule 1 (VCAM-1), they increase significantly to 0.5 μM AgNPs at 24 h of exposure. As far as DNA methylation is concerned, we found that AgNPs induce a state of global hyper-methylation. In conclusion, it was demonstrated that direct contact between AgNPs and endothelial cells resulted in the dysregulation of highly enriched and vastly functional miRNAs and DNA hypermethylation, that may have multiple effects on endothelium function and integrity.
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Affiliation(s)
- A K González-Palomo
- Laboratorio de Toxicología Molecular, Centro de Investigación Aplicada en Ambiente y Salud (CIAAS), Coordinación para la Innovación y Aplicación de la Ciencia y la Tecnología (CIACYT), Universidad Autónoma de San Luis Potosí, San Luis Potosí, México; Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México.
| | - K Saldaña-Villanueva
- Laboratorio de Toxicología Molecular, Centro de Investigación Aplicada en Ambiente y Salud (CIAAS), Coordinación para la Innovación y Aplicación de la Ciencia y la Tecnología (CIACYT), Universidad Autónoma de San Luis Potosí, San Luis Potosí, México; Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - J D Cortés-García
- Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - J C Fernández-Macias
- Laboratorio de Toxicología Molecular, Centro de Investigación Aplicada en Ambiente y Salud (CIAAS), Coordinación para la Innovación y Aplicación de la Ciencia y la Tecnología (CIACYT), Universidad Autónoma de San Luis Potosí, San Luis Potosí, México; Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - K B Méndez-Rodríguez
- Laboratorio de Toxicología Molecular, Centro de Investigación Aplicada en Ambiente y Salud (CIAAS), Coordinación para la Innovación y Aplicación de la Ciencia y la Tecnología (CIACYT), Universidad Autónoma de San Luis Potosí, San Luis Potosí, México; Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - I N Pérez Maldonado
- Laboratorio de Toxicología Molecular, Centro de Investigación Aplicada en Ambiente y Salud (CIAAS), Coordinación para la Innovación y Aplicación de la Ciencia y la Tecnología (CIACYT), Universidad Autónoma de San Luis Potosí, San Luis Potosí, México; Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
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7
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Falagan-Lotsch P, Murphy CJ. Network-based analysis implies critical roles of microRNAs in the long-term cellular responses to gold nanoparticles. NANOSCALE 2020; 12:21172-21187. [PMID: 32990715 PMCID: PMC7606723 DOI: 10.1039/d0nr04701e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Since gold nanoparticles (AuNPs) have great potential to bring improvements to the biomedical field, their impact on biological systems should be better understood, particularly over the long term, using realistic doses of exposure. MicroRNAs (miRNAs) are small noncoding RNAs that play key roles in the regulation of biological pathways, from development to cellular stress responses. In this study, we performed genome-wide miRNA expression profiling in primary human dermal fibroblasts 20 weeks after chronic and acute (non-chronic) treatments to four AuNPs with different shapes and surface chemistries at a low dose. The exposure condition and AuNP surface chemistry had a significant impact on the modulation of miRNA levels. In addition, a network-based analysis was employed to provide a more complex, systems-level perspective of the miRNA expression changes. In response to the stress caused by AuNPs, miRNA co-expression networks perturbed in cells under non-chronic exposure to AuNPs were enriched for target genes implicated in the suppression of proliferative pathways, possibly in attempt to restore cell homeostasis, while changes in miRNA co-expression networks enriched for target genes related to activation of proliferative and suppression of apoptotic pathways were observed in cells chronically exposed to one specific type of AuNPs. In this case, miRNA dysregulation might be contributing to enforce a new cell phenotype during stress. Our findings suggest that miRNAs exert critical roles in the cellular responses to the stress provoked by a low dose of NPs in the long term and provide a fertile ground for further targeted experimental studies.
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Affiliation(s)
| | - Catherine J. Murphy
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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Sheikhpour M, Naghinejad M, Kasaeian A, Lohrasbi A, Shahraeini SS, Zomorodbakhsh S. The Applications of Carbon Nanotubes in the Diagnosis and Treatment of Lung Cancer: A Critical Review. Int J Nanomedicine 2020; 15:7063-7078. [PMID: 33061368 PMCID: PMC7522408 DOI: 10.2147/ijn.s263238] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/31/2020] [Indexed: 12/14/2022] Open
Abstract
The importance of timely diagnosis and the complete treatment of lung cancer for many people with this deadly disease daily increases due to its high mortality. Diagnosis and treatment with helping the nanoparticles are useful, although they have reasonable harms. This article points out that the side effects of using carbon nanotube (CNT) in this disease treatment process such as inflammation, fibrosis, and carcinogenesis are very problematic. Toxicity can reduce to some extent using the techniques such as functionalizing to proper dimensions as a longer length, more width, and greater curvature. The targeted CNT sensors can be connected to various modified vapors. In this regard, with helping this method, screening makes non-invasive diagnosis possible. Researchers have also found that nanoparticles such as CNTs could be used as carriers to direct drug delivery, especially with chemotherapy drugs. Most of these carriers were multi-wall carbon nanotubes (MWCNT) used for cancerous cell targeting. The results of laboratory and animal researches in the field of diagnosis and treatment became very desirable and hopeful. The collection of researches summarized has highlighted the requirement for a detailed assessment which includes CNT dose, duration, method of induction, etc., to achieve the most controlled conditions for animal and human studies. In the discussion section, 4 contradictory issues are discussed which are invited researchers to do more research to get clearer results.
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Affiliation(s)
- Mojgan Sheikhpour
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Maryam Naghinejad
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Alibakhsh Kasaeian
- Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Armaghan Lohrasbi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Sadegh Shahraeini
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Shahab Zomorodbakhsh
- Department of Chemistry, Mahshahr Branch, Islamic Azad University, Mahshahr, Iran
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Transcriptomics in Toxicogenomics, Part I: Experimental Design, Technologies, Publicly Available Data, and Regulatory Aspects. NANOMATERIALS 2020; 10:nano10040750. [PMID: 32326418 PMCID: PMC7221878 DOI: 10.3390/nano10040750] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 02/07/2023]
Abstract
The starting point of successful hazard assessment is the generation of unbiased and trustworthy data. Conventional toxicity testing deals with extensive observations of phenotypic endpoints in vivo and complementing in vitro models. The increasing development of novel materials and chemical compounds dictates the need for a better understanding of the molecular changes occurring in exposed biological systems. Transcriptomics enables the exploration of organisms' responses to environmental, chemical, and physical agents by observing the molecular alterations in more detail. Toxicogenomics integrates classical toxicology with omics assays, thus allowing the characterization of the mechanism of action (MOA) of chemical compounds, novel small molecules, and engineered nanomaterials (ENMs). Lack of standardization in data generation and analysis currently hampers the full exploitation of toxicogenomics-based evidence in risk assessment. To fill this gap, TGx methods need to take into account appropriate experimental design and possible pitfalls in the transcriptomic analyses as well as data generation and sharing that adhere to the FAIR (Findable, Accessible, Interoperable, and Reusable) principles. In this review, we summarize the recent advancements in the design and analysis of DNA microarray, RNA sequencing (RNA-Seq), and single-cell RNA-Seq (scRNA-Seq) data. We provide guidelines on exposure time, dose and complex endpoint selection, sample quality considerations and sample randomization. Furthermore, we summarize publicly available data resources and highlight applications of TGx data to understand and predict chemical toxicity potential. Additionally, we discuss the efforts to implement TGx into regulatory decision making to promote alternative methods for risk assessment and to support the 3R (reduction, refinement, and replacement) concept. This review is the first part of a three-article series on Transcriptomics in Toxicogenomics. These initial considerations on Experimental Design, Technologies, Publicly Available Data, Regulatory Aspects, are the starting point for further rigorous and reliable data preprocessing and modeling, described in the second and third part of the review series.
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10
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Gene Expression and Epigenetic Changes in Mice Following Inhalation of Copper(II) Oxide Nanoparticles. NANOMATERIALS 2020; 10:nano10030550. [PMID: 32197515 PMCID: PMC7153614 DOI: 10.3390/nano10030550] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/12/2020] [Accepted: 03/17/2020] [Indexed: 12/13/2022]
Abstract
We investigated the transcriptomic response and epigenetic changes in the lungs of mice exposed to inhalation of copper(II) oxide nanoparticles (CuO NPs) (8 × 105 NPs/m3) for periods of 3 days, 2 weeks, 6 weeks, and 3 months. A whole genome transcriptome and miRNA analysis was performed using next generation sequencing. Global DNA methylation was assessed by ELISA. The inhalation resulted in the deregulation of mRNA transcripts: we detected 170, 590, 534, and 1551 differentially expressed transcripts after 3 days, 2 weeks, 6 weeks, and 3 months of inhalation, respectively. Biological processes and pathways affected by inhalation, differed between 3 days exposure (collagen formation) and longer treatments (immune response). Periods of two weeks exposure further induced apoptotic processes, 6 weeks of inhalation affected the cell cycle, and 3 months of treatment impacted the processes related to cell adhesion. The expression of miRNA was not affected by 3 days of inhalation. Prolonged exposure periods modified miRNA levels, although the numbers were relatively low (17, 18, and 38 miRNAs, for periods of 2 weeks, 6 weeks, and 3 months, respectively). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis based on miRNA–mRNA interactions, revealed the deregulation of processes implicated in the immune response and carcinogenesis. Global DNA methylation was not significantly affected in any of the exposure periods. In summary, the inhalation of CuO NPs impacted on both mRNA and miRNA expression. A significant transcriptomic response was already observed after 3 days of exposure. The affected biological processes and pathways indicated the negative impacts on the immune system and potential role in carcinogenesis.
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Khaliullin TO, Yanamala N, Newman MS, Kisin ER, Fatkhutdinova LM, Shvedova AA. Comparative analysis of lung and blood transcriptomes in mice exposed to multi-walled carbon nanotubes. Toxicol Appl Pharmacol 2020; 390:114898. [PMID: 31978390 DOI: 10.1016/j.taap.2020.114898] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/16/2020] [Accepted: 01/21/2020] [Indexed: 12/16/2022]
Abstract
Pulmonary exposure to multi-walled carbon nanotubes (MWCNT) causes inflammation, fibroproliferation, immunotoxicity, and systemic responses in rodents. However, the search for representative biomarkers of exposure is an ongoing endeavor. Whole blood gene expression profiling is a promising new approach for the identification of novel disease biomarkers. We asked if the whole blood transcriptome reflects pathology-specific changes in lung gene expression caused by MWCNT. To answer this question, we performed mRNA sequencing analysis of the whole blood and lung in mice administered MWCNT or vehicle solution via pharyngeal aspiration and sacrificed 56 days later. The pattern of lung mRNA expression as determined using Ingenuity Pathway Analysis (IPA) was indicative of continued inflammation, immune cell trafficking, phagocytosis, and adaptive immune responses. Simultaneously, innate immunity-related transcripts (Plunc, Bpifb1, Reg3g) and cancer-related pathways were downregulated. IPA analysis of the differentially expressed genes in the whole blood suggested increased hematopoiesis, predicted activation of cancer/tumor development pathways, and atopy. There were several common upregulated genes between whole blood and lungs, important for adaptive immune responses: Cxcr1, Cd72, Sharpin, and Slc11a1. Trim24, important for TH2 cell effector function, was downregulated in both datasets. Hla-dqa1 mRNA was upregulated in the lungs and downregulated in the blood, as was Lilrb4, which controls the reactivity of immune response. "Cancer" disease category had opposing activation status in the two datasets, while the only commonality was "Hypersensitivity". Transcriptome changes occurring in the lungs did not produce a completely replicable pattern in whole blood; however, specific systemic responses may be shared between transcriptomic profiles.
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Affiliation(s)
- Timur O Khaliullin
- Department of Physiology and Pharmacology, West Virginia University, Morgantown, WV, USA; Health Effects Laboratory Division, NIOSH, CDC, Morgantown, WV, USA.
| | - Naveena Yanamala
- Health Effects Laboratory Division, NIOSH, CDC, Morgantown, WV, USA.
| | - Mackenzie S Newman
- Department of Physiology and Pharmacology, West Virginia University, Morgantown, WV, USA.
| | - Elena R Kisin
- Health Effects Laboratory Division, NIOSH, CDC, Morgantown, WV, USA.
| | - Liliya M Fatkhutdinova
- Department of Hygiene and Occupational Medicine, Kazan State Medical University, Kazan, Russia
| | - Anna A Shvedova
- Department of Physiology and Pharmacology, West Virginia University, Morgantown, WV, USA; Health Effects Laboratory Division, NIOSH, CDC, Morgantown, WV, USA.
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12
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Guo NL, Poh TY, Pirela S, Farcas MT, Chotirmall SH, Tham WK, Adav SS, Ye Q, Wei Y, Shen S, Christiani DC, Ng KW, Thomas T, Qian Y, Demokritou P. Integrated Transcriptomics, Metabolomics, and Lipidomics Profiling in Rat Lung, Blood, and Serum for Assessment of Laser Printer-Emitted Nanoparticle Inhalation Exposure-Induced Disease Risks. Int J Mol Sci 2019; 20:E6348. [PMID: 31888290 PMCID: PMC6940784 DOI: 10.3390/ijms20246348] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 12/12/2019] [Accepted: 12/13/2019] [Indexed: 12/13/2022] Open
Abstract
Laser printer-emitted nanoparticles (PEPs) generated from toners during printing represent one of the most common types of life cycle released particulate matter from nano-enabled products. Toxicological assessment of PEPs is therefore important for occupational and consumer health protection. Our group recently reported exposure to PEPs induces adverse cardiovascular responses including hypertension and arrythmia via monitoring left ventricular pressure and electrocardiogram in rats. This study employed genome-wide mRNA and miRNA profiling in rat lung and blood integrated with metabolomics and lipidomics profiling in rat serum to identify biomarkers for assessing PEPs-induced disease risks. Whole-body inhalation of PEPs perturbed transcriptional activities associated with cardiovascular dysfunction, metabolic syndrome, and neural disorders at every observed time point in both rat lung and blood during the 21 days of exposure. Furthermore, the systematic analysis revealed PEPs-induced transcriptomic changes linking to other disease risks in rats, including diabetes, congenital defects, auto-recessive disorders, physical deformation, and carcinogenesis. The results were also confirmed with global metabolomics profiling in rat serum. Among the validated metabolites and lipids, linoleic acid, arachidonic acid, docosahexanoic acid, and histidine showed significant variation in PEPs-exposed rat serum. Overall, the identified PEPs-induced dysregulated genes, molecular pathways and functions, and miRNA-mediated transcriptional activities provide important insights into the disease mechanisms. The discovered important mRNAs, miRNAs, lipids and metabolites may serve as candidate biomarkers for future occupational and medical surveillance studies. To the best of our knowledge, this is the first study systematically integrating in vivo, transcriptomics, metabolomics, and lipidomics to assess PEPs inhalation exposure-induced disease risks using a rat model.
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Affiliation(s)
- Nancy Lan Guo
- West Virginia University Cancer Institute/School of Public Health, West Virginia University, Morgantown, WV 26506, USA;
| | - Tuang Yeow Poh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore; (T.Y.P.); (S.H.C.); (S.S.); (D.C.C.)
| | - Sandra Pirela
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T. H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA; (S.P.); (K.W.N.); (P.D.)
| | - Mariana T. Farcas
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA; (M.T.F.); (Y.Q.)
| | - Sanjay H. Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore; (T.Y.P.); (S.H.C.); (S.S.); (D.C.C.)
| | - Wai Kin Tham
- Singapore Phenome Centre, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore; (W.K.T.); (S.S.A.)
| | - Sunil S. Adav
- Singapore Phenome Centre, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 636921, Singapore; (W.K.T.); (S.S.A.)
| | - Qing Ye
- West Virginia University Cancer Institute/School of Public Health, West Virginia University, Morgantown, WV 26506, USA;
| | - Yongyue Wei
- Key Lab for Modern Toxicology, Department of Epidemiology and Biostatistics and Ministry of Education (MOE), School of Public Health, Nanjing Medical University, Nanjing 210029, China;
| | - Sipeng Shen
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore; (T.Y.P.); (S.H.C.); (S.S.); (D.C.C.)
| | - David C. Christiani
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore; (T.Y.P.); (S.H.C.); (S.S.); (D.C.C.)
| | - Kee Woei Ng
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T. H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA; (S.P.); (K.W.N.); (P.D.)
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
- Environmental Chemistry and Materials Centre, Nanyang Environment & Water Research Institute, Singapore 637141, Singapore
| | - Treye Thomas
- Office of Hazard Identification and Reduction, U.S. Consumer Product Safety Commission, Rockville, MD 20814, USA;
| | - Yong Qian
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA; (M.T.F.); (Y.Q.)
| | - Philip Demokritou
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T. H. Chan School of Public Health, Harvard University, Boston, MA 02115, USA; (S.P.); (K.W.N.); (P.D.)
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13
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Kabadi PK, Rodd AL, Simmons AE, Messier NJ, Hurt RH, Kane AB. A novel human 3D lung microtissue model for nanoparticle-induced cell-matrix alterations. Part Fibre Toxicol 2019; 16:15. [PMID: 30943996 PMCID: PMC6448215 DOI: 10.1186/s12989-019-0298-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 03/15/2019] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Multi-walled carbon nanotubes (MWCNT) have been shown to elicit the release of inflammatory and pro-fibrotic mediators, as well as histopathological changes in lungs of exposed animals. Current standards for testing MWCNTs and other nanoparticles (NPs) rely on low-throughput in vivo studies to assess acute and chronic toxicity and potential hazard to humans. Several alternative testing approaches utilizing two-dimensional (2D) in vitro assays to screen engineered NPs have reported conflicting results between in vitro and in vivo assays. Compared to conventional 2D in vitro or in vivo animal model systems, three-dimensional (3D) in vitro platforms have been shown to more closely recapitulate human physiology, providing a relevant, more efficient strategy for evaluating acute toxicity and chronic outcomes in a tiered nanomaterial toxicity testing paradigm. RESULTS As inhalation is an important route of nanomaterial exposure, human lung fibroblasts and epithelial cells were co-cultured with macrophages to form scaffold-free 3D lung microtissues. Microtissues were exposed to multi-walled carbon nanotubes, M120 carbon black nanoparticles or crocidolite asbestos fibers for 4 or 7 days, then collected for characterization of microtissue viability, tissue morphology, and expression of genes and selected proteins associated with inflammation and extracellular matrix remodeling. Our data demonstrate the utility of 3D microtissues in predicting chronic pulmonary endpoints following exposure to MWCNTs or asbestos fibers. These test nanomaterials were incorporated into 3D human lung microtissues as visualized using light microscopy. Differential expression of genes involved in acute inflammation and extracellular matrix remodeling was detected using PCR arrays and confirmed using qRT-PCR analysis and Luminex assays of selected genes and proteins. CONCLUSION 3D lung microtissues provide an alternative testing platform for assessing nanomaterial-induced cell-matrix alterations and delineation of toxicity pathways, moving towards a more predictive and physiologically relevant approach for in vitro NP toxicity testing.
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Affiliation(s)
- Pranita K Kabadi
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, 02912, USA.,AstraZeneca, Gaithersburg, MD, 20878, USA
| | - April L Rodd
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, 02912, USA.
| | - Alysha E Simmons
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, 02912, USA
| | - Norma J Messier
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, 02912, USA
| | - Robert H Hurt
- School of Engineering, Brown University, Providence, Rhode Island, 02912, USA
| | - Agnes B Kane
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, 02912, USA.
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14
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Kong Z, Zhou C, Li B, Jiao J, Chen L, Ren A, Jie H, Tan Z. Integrative plasma proteomic and microRNA analysis of Jersey cattle in response to high-altitude hypoxia. J Dairy Sci 2019; 102:4606-4618. [PMID: 30879823 DOI: 10.3168/jds.2018-15515] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 01/02/2019] [Indexed: 12/15/2022]
Abstract
Blood has been widely collected and analyzed for diagnosing and monitoring diseases in humans and animals; a range of plasma proteins and peptide can be used as biomarkers to describe pathological or physiological status. Changes in the environment such as high-altitude hypoxia (HAH) can lead to adaptive changes in the blood system of mammals. However, the adaptation mechanism induced by HAH remains unclear. In this study, we used 12 multiparous Jersey cattle (400 ± 35 kg, average 3 yr old, dry period). We applied an iTRAQ (isobaric tags for relative and absolute quantitation) proteomics approach and microRNA (miRNA) microarray to explore differences in the plasma proteomic and miRNA profiles of Jersey cattle exposed to HAH conditions in Nyingchi, Tibet (altitude 3,000 m) and HAH-free conditions in Shenyang, China (altitude 50 m). Such quantitative proteomic strategies are suitable for accurate and comprehensive prediction of miRNA targets. In total, 264 differentially expressed proteins (127 upregulated, fold-change >1.2; 137 downregulated, fold-change <0.8) and 47 differential miRNAs (25 upregulated, fold-change >2; 22 downregulated, fold-change <0.5) were observed in the HAH-stressed group compared with the HAH-free group. Integrative analysis of proteomic and miRNA profiles demonstrated that the biological processes associated with differentially expressed proteins were immune response, complement system, and conjugation system. Integrative analysis of canonical pathways showed that most were associated with acute phase response signaling (z-score = -0.125), liver X receptor/retinoid X receptor (LXR/RXR) activation pathway (z-score = 1.134), coagulation system (z-score = -0.943), and complement system (z-score = -0.632). The current results indicated that Jersey cattle exposed to HAH could adapt to that condition through regulation of inflammatory homeostasis by inhibiting the acute phase response, coagulation system, and complement system and promoting LXR/RXR activation.
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Affiliation(s)
- Zhiwei Kong
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan 410125, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Chuanshe Zhou
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan 410125, China; Hunan Co-Innovation Center of Safety Animal Production (CICSAP), Changsha, Hunan 410128, China.
| | - Bin Li
- Institute of Animal Husbandry and Veterinary, Tibet Autonomous Regional Academy of Agricultural Sciences, State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850000, China.
| | - Jinzhen Jiao
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan 410125, China; Hunan Co-Innovation Center of Safety Animal Production (CICSAP), Changsha, Hunan 410128, China
| | - Liang Chen
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan 410125, China; College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Ao Ren
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan 410125, China; College of Animal Science and Technology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Hongdong Jie
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan 410125, China
| | - Zhiliang Tan
- CAS Key Laboratory for Agro-Ecological Processes in Subtropical Region, National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, South-Central Experimental Station of Animal Nutrition and Feed Science in Ministry of Agriculture, Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan 410125, China; Hunan Co-Innovation Center of Safety Animal Production (CICSAP), Changsha, Hunan 410128, China
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15
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Schulte P, Leso V, Niang M, Iavicoli I. Biological monitoring of workers exposed to engineered nanomaterials. Toxicol Lett 2018; 298:112-124. [PMID: 29920308 PMCID: PMC6239923 DOI: 10.1016/j.toxlet.2018.06.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/29/2018] [Accepted: 06/08/2018] [Indexed: 12/27/2022]
Abstract
As the number of nanomaterial workers increase there is need to consider whether biomonitoring of exposure should be used as a routine risk management tool. Currently, no biomonitoring of nanomaterials is mandated by authoritative or regulatory agencies. However, there is a growing knowledge base to support such biomonitoring, but further research is needed as are investigations of priorities for biomonitoring. That research should be focused on validation of biomarkers of exposure and effect. Some biomarkers of effect are generally nonspecific. These biomarkers need further interpretation before they should be used. Overall biomonitoring of nanomaterial workers may be important to supplement risk assessment and risk management efforts.
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Affiliation(s)
- P Schulte
- National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, 1090 Tusculum Avenue, MS C-14, Cincinnati, OH 45226, USA.
| | - V Leso
- Department of Public Health, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
| | - M Niang
- University of Cincinnati, Cincinnati, OH, USA
| | - I Iavicoli
- Department of Public Health, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
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16
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Arnoldussen YJ, Skaug V, Aleksandersen M, Ropstad E, Anmarkrud KH, Einarsdottir E, Chin-Lin F, Granum Bjørklund C, Kasem M, Eilertsen E, Apte RN, Zienolddiny S. Inflammation in the pleural cavity following injection of multi-walled carbon nanotubes is dependent on their characteristics and the presence of IL-1 genes. Nanotoxicology 2018; 12:522-538. [PMID: 29742950 DOI: 10.1080/17435390.2018.1465139] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Upon inhalation, multi-walled carbon nanotubes (MWCNTs) may reach the subpleura and pleural spaces, and induce pleural inflammation and/or mesothelioma in humans. However, the mechanisms of MWCNT-induced pathology after direct intrapleural injections are still only partly elucidated. In particular, a role of the proinflammatory interleukin-1 (IL-1) cytokines in pleural inflammation has so far not been published. We examined the MWCNT-induced pleural inflammation, gene expression abnormalities, and the modifying role of IL-1α and β cytokines following intrapleural injection of two types of MWCNTs (CNT-1 and CNT-2) compared with crocidolite asbestos in IL-1 wild-type (WT) and IL-1α/β KO (IL1-KO) mice. Histopathological examination of the pleura 28 days post-exposure revealed mesothelial cell hyperplasia, leukocyte infiltration, and fibrosis occurring in the CNT-1 (Mitsui-7)-exposed group. The pleura of these mice also showed the greatest changes in mRNA and miRNA expression levels, closely followed by CNT-2. In addition, the CNT-1-exposed group also presented the greatest infiltrations of leukocytes and proliferation of fibrous tissue. WT mice were more prone to development of sustained inflammation and fibrosis than IL1-KO mice. Prominent differences in genetic and epigenetic changes were also observed between the two genotypes. In conclusion, the fibrotic response to MWCNTs in the pleura depends on the particles' physico-chemical properties and on the presence or absence of the IL-1 genes. Furthermore, we found that CNT-1 was the most potent inducer of inflammatory responses, followed by CNT-2 and crocidolite asbestos.
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Affiliation(s)
- Yke Jildouw Arnoldussen
- a Department of Biological and Chemical Work Environment , National Institute of Occupational Health , Oslo , Norway
| | - Vidar Skaug
- a Department of Biological and Chemical Work Environment , National Institute of Occupational Health , Oslo , Norway
| | - Mona Aleksandersen
- b Department of Basic Sciences and Aquatic Medicine , Faculty of Veterinary Medicine, Norwegian University of Life Sciences , Oslo , Norway
| | - Erik Ropstad
- c Department of Production Animal Clinical Sciences , Faculty of Veterinary Medicine, Norwegian University of Life Sciences , Oslo , Norway
| | - Kristine Haugen Anmarkrud
- a Department of Biological and Chemical Work Environment , National Institute of Occupational Health , Oslo , Norway
| | - Elin Einarsdottir
- a Department of Biological and Chemical Work Environment , National Institute of Occupational Health , Oslo , Norway
| | - Fang Chin-Lin
- a Department of Biological and Chemical Work Environment , National Institute of Occupational Health , Oslo , Norway
| | - Cesilie Granum Bjørklund
- c Department of Production Animal Clinical Sciences , Faculty of Veterinary Medicine, Norwegian University of Life Sciences , Oslo , Norway
| | - Mayes Kasem
- a Department of Biological and Chemical Work Environment , National Institute of Occupational Health , Oslo , Norway
| | - Einar Eilertsen
- a Department of Biological and Chemical Work Environment , National Institute of Occupational Health , Oslo , Norway
| | - Ron N Apte
- d The Shraga Segal Department of Microbiology, Immunology, and Genetics, The Faculty of Health Sciences , Ben Gurion University of the Negev , Beer Sheva , Israel
| | - Shanbeh Zienolddiny
- a Department of Biological and Chemical Work Environment , National Institute of Occupational Health , Oslo , Norway
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17
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Ventura C, Sousa-Uva A, Lavinha J, Silva MJ. Conventional and novel “omics”-based approaches to the study of carbon nanotubes pulmonary toxicity. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2018; 59:334-362. [PMID: 29481700 DOI: 10.1002/em.22177] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 01/05/2018] [Accepted: 01/21/2018] [Indexed: 02/05/2023]
Affiliation(s)
- Célia Ventura
- Departamento de Genética Humana; Instituto Nacional de Saúde Doutor Ricardo Jorge (INSA); Lisboa Portugal
- Departamento de Saúde Ocupacional e Ambiental; Escola Nacional de Saúde Pública, Universidade NOVA de Lisboa (UNL); Lisboa Portugal
- Center for Toxicogenomics and Human Health (ToxOmics), NOVA Medical School-FCM, UNL; Lisboa Portugal
| | - António Sousa-Uva
- Departamento de Saúde Ocupacional e Ambiental; Escola Nacional de Saúde Pública, Universidade NOVA de Lisboa (UNL); Lisboa Portugal
- CISP - Public Health Research Center; Lisboa Portugal
| | - João Lavinha
- Departamento de Genética Humana; Instituto Nacional de Saúde Doutor Ricardo Jorge (INSA); Lisboa Portugal
| | - Maria João Silva
- Departamento de Genética Humana; Instituto Nacional de Saúde Doutor Ricardo Jorge (INSA); Lisboa Portugal
- Center for Toxicogenomics and Human Health (ToxOmics), NOVA Medical School-FCM, UNL; Lisboa Portugal
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18
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Li X, Lv Y, Gao N, Sun H, Lu R, Yang H, Zhang C, Meng Q, Wu S, Li AQ, Xia Y, Chen R. microRNA-802/Rnd3 pathway imposes on carcinogenesis and metastasis of fine particulate matter exposure. Oncotarget 2018; 7:35026-43. [PMID: 27144337 PMCID: PMC5085207 DOI: 10.18632/oncotarget.9019] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/10/2016] [Indexed: 12/14/2022] Open
Abstract
Recent studies have linked ambient fine particulate matter (PM2.5) to increased lung cancer mortality and morbidity. However, the underlying mechanism causing the adverse effects of PM2.5 is less clear. In the present study, post-transcriptional profiling was used to explore biological pathways involved in PM2.5-induced pulmonary disorders. The carcinogenesis and metastasis of PM2.5 exposure were evaluated by long-term PM2.5 exposure tests. We observed dysregulation of actin in A549 cells line and dysplasia in the lungs of mice exposed to PM2.5. Both PM2.5-exposed cells and animals showed increased Rnd3 expression levels. Moreover, miR-802 mimics rescued actin disorganization in vitro and alveolitis in vivo. Long-term exposure to PM2.5 promoted carcinogenesis and metastasis of pulmonary cells. Decreased miR-802 expression levels in the serum samples of PM2.5-treated mice and individuals from moderately polluted cities were observed. Increased Rnd3 expression levels in lung cancers tissues have been identified by a genome database TCGA, and have been linked to less overall survival probabilities of lung cancer patients. Our findings suggest that dysregulation of actin cytoskeleton and down-regulation of miR-802 expression might be the underlying mechanism involved in the adverse effects of PM2.5 exposure. In addition, long-term exposure to PM2.5 demonstrated strong associations with malignant pulmonary disorders.
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Affiliation(s)
- Xiaobo Li
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Yang Lv
- Department of Histology and Embryology, Hebei North University, Zhangjiakou, 075000, China
| | - Na Gao
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Hao Sun
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Runze Lu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Hongbao Yang
- Center for Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing, 211198, China
| | - Chengcheng Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Qingtao Meng
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Shenshen Wu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China
| | - Ai-Qun Li
- School of Public Health, Medical College, Wuhan University of Science and Technology, Wuhan, 430081, China
| | - Yankai Xia
- Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 210009, China
| | - Rui Chen
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing 210009, China.,State Key Laboratory of Bioelectronics, Southeast University, Nanjing, 210096, China
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19
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Shin DY, Jeong MH, Bang IJ, Kim HR, Chung KH. MicroRNA regulatory networks reflective of polyhexamethylene guanidine phosphate-induced fibrosis in A549 human alveolar adenocarcinoma cells. Toxicol Lett 2018; 287:49-58. [PMID: 29337256 DOI: 10.1016/j.toxlet.2018.01.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/26/2017] [Accepted: 01/11/2018] [Indexed: 12/28/2022]
Abstract
Polyhexamethylene guanidine phosphate (PHMG-phosphate), an active component of humidifier disinfectant, is suspected to be a major cause of pulmonary fibrosis. Fibrosis, induced by recurrent epithelial damage, is significantly affected by epigenetic regulation, including microRNAs (miRNAs). The aim of this study was to investigate the fibrogenic mechanisms of PHMG-phosphate through the profiling of miRNAs and their target genes. A549 cells were treated with 0.75 μg/mL PHMG-phosphate for 24 and 48 h and miRNA microarray expression analysis was conducted. The putative mRNA targets of the miRNAs were identified and subjected to Gene Ontology analysis. After exposure to PHMG-phosphate for 24 and 48 h, 46 and 33 miRNAs, respectively, showed a significant change in expression over 1.5-fold compared with the control. The integrated analysis of miRNA and mRNA microarray results revealed the putative targets that were prominently enriched were associated with the epithelial-mesenchymal transition (EMT), cell cycle changes, and apoptosis. The dose-dependent induction of EMT by PHMG-phosphate exposure was confirmed by western blot. We identified 13 putative EMT-related targets that may play a role in PHMG-phosphate-induced fibrosis according to the Comparative Toxicogenomic Database. Our findings contribute to the comprehension of the fibrogenic mechanism of PHMG-phosphate and will aid further study on PHMG-phosphate-induced toxicity.
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Affiliation(s)
- Da Young Shin
- School of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi-do, 16419, Republic of Korea
| | - Mi Ho Jeong
- School of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi-do, 16419, Republic of Korea
| | - In Jae Bang
- School of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi-do, 16419, Republic of Korea
| | - Ha Ryong Kim
- College of Pharmacy, Catholic University of Daegu, Gyeongsan, Gyeongsangbuk-do, 38430, Republic of Korea.
| | - Kyu Hyuck Chung
- School of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi-do, 16419, Republic of Korea.
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20
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Nymark P, Rieswijk L, Ehrhart F, Jeliazkova N, Tsiliki G, Sarimveis H, Evelo CT, Hongisto V, Kohonen P, Willighagen E, Grafström RC. A Data Fusion Pipeline for Generating and Enriching Adverse Outcome Pathway Descriptions. Toxicol Sci 2017; 162:264-275. [DOI: 10.1093/toxsci/kfx252] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Penny Nymark
- Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
- Department of Toxicology, Misvik Biology, 20520 Turku, Finland
| | - Linda Rieswijk
- Department of Bioinformatics, NUTRIM, Maastricht University, 6200MD Maastricht, The Netherlands
- Division of Environmental Health Sciences, School of Public Health, University of California, 94720-7360 Berkeley, California, United States
| | - Friederike Ehrhart
- Department of Bioinformatics, NUTRIM, Maastricht University, 6200MD Maastricht, The Netherlands
| | | | - Georgia Tsiliki
- School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece
- Institute for the Management of Information Systems, ATHENA Research and Innovation Centre, 151 25 Athens, Greece
| | - Haralambos Sarimveis
- School of Chemical Engineering, National Technical University of Athens, 157 80 Athens, Greece
| | - Chris T Evelo
- Department of Bioinformatics, NUTRIM, Maastricht University, 6200MD Maastricht, The Netherlands
| | - Vesa Hongisto
- Department of Toxicology, Misvik Biology, 20520 Turku, Finland
| | - Pekka Kohonen
- Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
- Department of Toxicology, Misvik Biology, 20520 Turku, Finland
| | - Egon Willighagen
- Department of Bioinformatics, NUTRIM, Maastricht University, 6200MD Maastricht, The Netherlands
| | - Roland C Grafström
- Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
- Department of Toxicology, Misvik Biology, 20520 Turku, Finland
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21
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Williams A, Halappanavar S. Application of bi-clustering of gene expression data and gene set enrichment analysis methods to identify potentially disease causing nanomaterials. Data Brief 2017; 15:933-940. [PMID: 29159232 PMCID: PMC5683856 DOI: 10.1016/j.dib.2017.10.060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 10/23/2017] [Indexed: 01/24/2023] Open
Abstract
This article contains data related to the research article ‘Application of bi-clustering of gene expression data and gene set enrichment analysis methods to identify potentially disease causing nanomaterials’ (Williams and Halappanavar, 2015) [1]. The presence of diverse types of nanomaterials (NMs) in commerce has grown significantly in the past decade and as a result, human exposure to these materials in the environment is inevitable. The traditional toxicity testing approaches that are reliant on animals are both time- and cost- intensive; employing which, it is not possible to complete the challenging task of safety assessment of NMs currently on the market in a timely manner. Thus, there is an urgent need for comprehensive understanding of the biological behavior of NMs, and efficient toxicity screening tools that will enable the development of predictive toxicology paradigms suited to rapidly assessing the human health impacts of exposure to NMs. In an effort to predict the long term health impacts of acute exposure to NMs, in Williams and Halappanavar (2015) [1], we applied bi-clustering and gene set enrichment analysis methods to derive essential features of altered lung transcriptome following exposure to NMs that are associated with lung-specific diseases. Several datasets from public microarray repositories describing pulmonary diseases in mouse models following exposure to a variety of substances were examined and functionally related bi-clusters showing similar gene expression profiles were identified. The identified bi-clusters were then used to conduct a gene set enrichment analysis on lung gene expression profiles derived from mice exposed to nano-titanium dioxide, carbon black or carbon nanotubes (nano-TiO2, CB and CNTs) to determine the disease significance of these data-driven gene sets. The results of the analysis correctly identified all NMs to be inflammogenic, and only CB and CNTs as potentially fibrogenic. Here, we elaborate on the details of the statistical methods and algorithms used to derive the disease relevant gene signatures. These details will enable other investigators to use the gene signature in future Gene Set Enrichment Analysis studies involving NMs or as features for clustering and classifying NMs of diverse properties.
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Affiliation(s)
- Andrew Williams
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, Canada K1A 0K9
| | - Sabina Halappanavar
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, Ontario, Canada K1A 0K9
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22
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Yanamala N, Orandle MS, Kodali VK, Bishop L, Zeidler-Erdely PC, Roberts JR, Castranova V, Erdely A. Sparse Supervised Classification Methods Predict and Characterize Nanomaterial Exposures: Independent Markers of MWCNT Exposures. Toxicol Pathol 2017; 46:14-27. [PMID: 28934917 DOI: 10.1177/0192623317730575] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Recent experimental evidence indicates significant pulmonary toxicity of multiwalled carbon nanotubes (MWCNTs), such as inflammation, interstitial fibrosis, granuloma formation, and carcinogenicity. Although numerous studies explored the adverse potential of various CNTs, their comparability is often limited. This is due to differences in administered dose, physicochemical characteristics, exposure methods, and end points monitored. Here, we addressed the problem through sparse classification method, a supervised machine learning approach that can reduce the noise contained in redundant variables for discriminating among MWCNT-exposed and MWCNT-unexposed groups. A panel of proteins measured from bronchoalveolar lavage fluid (BAL) samples was used to predict exposure to various MWCNT and determine markers that are attributable to MWCNT exposure and toxicity in mice. Using sparse support vector machine-based classification technique, we identified a small subset of proteins clearly distinguishing each exposure. Macrophage-derived chemokine (MDC/CCL22), in particular, was associated with various MWCNT exposures and was independent of exposure method employed, that is, oropharyngeal aspiration versus inhalation exposure. Sustained expression of some of the selected protein markers identified also suggests their potential role in MWCNT-induced toxicity and proposes hypotheses for future mechanistic studies. Such approaches can be used more broadly for nanomaterial risk profiling studies to evaluate decisions related to dose/time-response relationships that could delineate experimental variables from exposure markers.
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Affiliation(s)
- Naveena Yanamala
- 1 Exposure Assessment Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, West Virginia, USA
| | - Marlene S Orandle
- 2 Pathology & Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, West Virginia, USA
| | - Vamsi K Kodali
- 2 Pathology & Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, West Virginia, USA
| | - Lindsey Bishop
- 2 Pathology & Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, West Virginia, USA
| | - Patti C Zeidler-Erdely
- 2 Pathology & Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, West Virginia, USA
| | - Jenny R Roberts
- 3 Allergy and Clinical Immunology Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, West Virginia, USA
| | - Vincent Castranova
- 4 Department of Pharmaceutical Sciences, West Virginia University, Morgantown, West Virginia, USA
| | - Aaron Erdely
- 2 Pathology & Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, West Virginia, USA
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23
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Chen W, Zhao W, Yang A, Xu A, Wang H, Cong M, Liu T, Wang P, You H. Integrated analysis of microRNA and gene expression profiles reveals a functional regulatory module associated with liver fibrosis. Gene 2017; 636:87-95. [PMID: 28919164 DOI: 10.1016/j.gene.2017.09.027] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 07/13/2017] [Accepted: 09/13/2017] [Indexed: 02/06/2023]
Abstract
BACKGROUND Liver fibrosis, characterized with the excessive accumulation of extracellular matrix (ECM) proteins, represents the final common pathway of chronic liver inflammation. Ever-increasing evidence indicates microRNAs (miRNAs) dysregulation has important implications in the different stages of liver fibrosis. However, our knowledge of miRNA-gene regulation details pertaining to such disease remains unclear. METHODS The publicly available Gene Expression Omnibus (GEO) datasets of patients suffered from cirrhosis were extracted for integrated analysis. Differentially expressed miRNAs (DEMs) and genes (DEGs) were identified using GEO2R web tool. Putative target gene prediction of DEMs was carried out using the intersection of five major algorithms: DIANA-microT, TargetScan, miRanda, PICTAR5 and miRWalk. Functional miRNA-gene regulatory network (FMGRN) was constructed based on the computational target predictions at the sequence level and the inverse expression relationships between DEMs and DEGs. DAVID web server was selected to perform KEGG pathway enrichment analysis. Functional miRNA-gene regulatory module was generated based on the biological interpretation. Internal connections among genes in liver fibrosis-related module were determined using String database. MiRNA-gene regulatory modules related to liver fibrosis were experimentally verified in recombinant human TGFβ1 stimulated and specific miRNA inhibitor treated LX-2 cells. RESULTS We totally identified 85 and 923 dysregulated miRNAs and genes in liver cirrhosis biopsy samples compared to their normal controls. All evident miRNA-gene pairs were identified and assembled into FMGRN which consisted of 990 regulations between 51 miRNAs and 275 genes, forming two big sub-networks that were defined as down-network and up-network, respectively. KEGG pathway enrichment analysis revealed that up-network was prominently involved in several KEGG pathways, in which "Focal adhesion", "PI3K-Akt signaling pathway" and "ECM-receptor interaction" were remarked significant (adjusted p<0.001). Genes enriched in these pathways coupled with their regulatory miRNAs formed a functional miRNA-gene regulatory module that contains 7 miRNAs, 22 genes and 42 miRNA-gene connections. Gene interaction analysis based on String database revealed that 8 out of 22 genes were highly clustered. Finally, we experimentally confirmed a functional regulatory module containing 5 miRNAs (miR-130b-3p, miR-148a-3p, miR-345-5p, miR-378a-3p, and miR-422a) and 6 genes (COL6A1, COL6A2, COL6A3, PIK3R3, COL1A1, CCND2) associated with liver fibrosis. CONCLUSIONS Our integrated analysis of miRNA and gene expression profiles highlighted a functional miRNA-gene regulatory module associated with liver fibrosis, which, to some extent, may provide important clues to better understand the underlying pathogenesis of liver fibrosis.
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Affiliation(s)
- Wei Chen
- Experimental and Translational Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China; Beijing Key Laboratory of Tolerance Induction and Organ Protection in Transplantation, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Wenshan Zhao
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Translational Medicine in Liver Cirrhosis, National Clinical Research Center of Digestive Diseases, Beijing, China
| | - Aiting Yang
- Experimental and Translational Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China; Beijing Key Laboratory of Tolerance Induction and Organ Protection in Transplantation, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Anjian Xu
- Experimental and Translational Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China; Beijing Key Laboratory of Tolerance Induction and Organ Protection in Transplantation, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Huan Wang
- Experimental and Translational Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China; Beijing Key Laboratory of Tolerance Induction and Organ Protection in Transplantation, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Min Cong
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Translational Medicine in Liver Cirrhosis, National Clinical Research Center of Digestive Diseases, Beijing, China
| | - Tianhui Liu
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Translational Medicine in Liver Cirrhosis, National Clinical Research Center of Digestive Diseases, Beijing, China
| | - Ping Wang
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Translational Medicine in Liver Cirrhosis, National Clinical Research Center of Digestive Diseases, Beijing, China
| | - Hong You
- Experimental and Translational Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing, China; Beijing Key Laboratory of Tolerance Induction and Organ Protection in Transplantation, Beijing Friendship Hospital, Capital Medical University, Beijing, China; Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing Key Laboratory of Translational Medicine in Liver Cirrhosis, National Clinical Research Center of Digestive Diseases, Beijing, China.
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24
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Huang Z, Chen M, Zhang J, Sheng Y, Ji L. Integrative analysis of hepatic microRNA and mRNA to identify potential biological pathways associated with monocrotaline-induced liver injury in mice. Toxicol Appl Pharmacol 2017; 333:35-42. [PMID: 28818515 DOI: 10.1016/j.taap.2017.08.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 08/05/2017] [Accepted: 08/11/2017] [Indexed: 01/22/2023]
Abstract
Pyrrolizidine alkaloids (PAs) are a type of natural hepatotoxic compounds. Monocrotaline (MCT), belongs to PAs, is a main compound distributed in medicinal herb Crotalaria ferruginea Grah. ex Benth. This study aims to identify the potential biological signaling pathway associated with MCT-induced liver injury by analyzing the integrative altered hepatic microRNA (miRNA) and mRNA expression profile. C57BL/6 mice were orally given with MCT (270, 330mg/kg). Serum alanine/aspartate aminotransferase (ALT/AST) activity, total bilirubin (TBil) amount and liver histological evaluation showed the liver injury induced by MCT. Results of miRNA chip analysis showed that the hepatic expression of 15 miRNAs (whose signal intensity>200) was significantly altered in MCT-treated mice, and among them total 11 miRNAs passed further validation by using Real-time PCR assay. Results of mRNA chip analysis demonstrated that the hepatic expression of 569 genes was up-regulated and of other 417 genes was down-regulated in MCT-treated mice. There are total 426 predicted target genes of those above altered 11 miRNAs, and among them total 10 genes were also altered in mice treated with both MCT (270mg/kg) and MCT (330mg/kg) from the results of mRNA chip. Among these above 10 genes, total 8 genes passed further validation by using Real-time PCR assay. Only 1 biological signaling pathway was annotated by using those above 8 genes, which is phagosome. In conclusion, this study demonstrated the integrative altered expression profile of liver miRNA and mRNA, and identified that innate immunity may be critically involved in MCT-induced liver injury in mice.
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Affiliation(s)
- Zhenlin Huang
- Shanghai Key Laboratory for Complex Prescription, MOE Key Laboratory for Standardization of Chinese Medicines, and SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Minwei Chen
- Shanghai Key Laboratory for Complex Prescription, MOE Key Laboratory for Standardization of Chinese Medicines, and SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jiaqi Zhang
- Shanghai Key Laboratory for Complex Prescription, MOE Key Laboratory for Standardization of Chinese Medicines, and SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Yuchen Sheng
- Center for Drug Safety Evaluation and Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Lili Ji
- Shanghai Key Laboratory for Complex Prescription, MOE Key Laboratory for Standardization of Chinese Medicines, and SATCM Key Laboratory for New Resources and Quality Evaluation of Chinese Medicines, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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25
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Kinaret P, Marwah V, Fortino V, Ilves M, Wolff H, Ruokolainen L, Auvinen P, Savolainen K, Alenius H, Greco D. Network Analysis Reveals Similar Transcriptomic Responses to Intrinsic Properties of Carbon Nanomaterials in Vitro and in Vivo. ACS NANO 2017; 11:3786-3796. [PMID: 28380293 DOI: 10.1021/acsnano.6b08650] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Understanding the complex molecular alterations related to engineered nanomaterial (ENM) exposure is essential for carrying out toxicity assessment. Current experimental paradigms rely on both in vitro and in vivo exposure setups that often are difficult to compare, resulting in questioning the real efficacy of cell models to mimic more complex exposure scenarios at the organism level. Here, we have systematically investigated transcriptomic responses of the THP-1 macrophage cell line and lung tissues of mice, after exposure to several carbon nanomaterials (CNMs). Under the assumption that the CNM exposure related molecular alterations are mixtures of signals related to their intrinsic properties, we inferred networks of responding genes, whose expression levels are coordinately altered in response to specific CNM intrinsic properties. We observed only a minute overlap between the sets of intrinsic property-correlated genes at different exposure scenarios, suggesting specific transcriptional programs working in different exposure scenarios. However, when the effects of the CNM were investigated at the level of significantly altered molecular functions, a broader picture of substantial commonality emerged. Our results imply that in vitro exposures can efficiently recapitulate the complex molecular functions altered in vivo. In this study, altered molecular pathways in response to specific CNM intrinsic properties have been systematically characterized from transcriptomic data generated from multiple exposure setups. Our computational approach to the analysis of network response modules further revealed similarities between in vitro and in vivo exposures that could not be detected by traditional analysis of transcriptomics data. Our analytical strategy also opens a possibility to look for pathways of toxicity and understanding the molecular and cellular responses identified across predefined biological themes.
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Affiliation(s)
| | | | | | | | - Henrik Wolff
- Finnish Institute of Occupational Health , Helsinki, Finland 00251
| | | | | | - Kai Savolainen
- Finnish Institute of Occupational Health , Helsinki, Finland 00251
| | - Harri Alenius
- Institute of Environmental Medicine (IMM), Karolinska Institutet , 171 77 Stockholm, Sweden
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26
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Bornholdt J, Saber AT, Lilje B, Boyd M, Jørgensen M, Chen Y, Vitezic M, Jacobsen NR, Poulsen SS, Berthing T, Bressendorff S, Vitting-Seerup K, Andersson R, Hougaard KS, Yauk CL, Halappanavar S, Wallin H, Vogel U, Sandelin A. Identification of Gene Transcription Start Sites and Enhancers Responding to Pulmonary Carbon Nanotube Exposure in Vivo. ACS NANO 2017; 11:3597-3613. [PMID: 28345861 DOI: 10.1021/acsnano.6b07533] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Increased use of nanomaterials in industry, medicine, and consumer products has raised concerns over their toxicity. To ensure safe use of nanomaterials, understanding their biological effects at the molecular level is crucial. In particular, the regulatory mechanisms responsible for the cascade of genes activated by nanomaterial exposure are not well-characterized. To this end, we profiled the genome-wide usage of gene transcription start sites and linked active enhancer regions in lungs of C57BL/6 mice 24 h after intratracheal instillation of a single dose of the multiwalled carbon nanotube (MWCNT) Mitsui-7. Our results revealed a massive gene regulatory response, where expression of key inflammatory genes (e.g., Csf3, Il24, and Fgf23) was increased >100-fold 24 h after Mitsui-7 exposure. Many of the Mitsui-7-responsive transcription start sites were alternative transcription start sites for known genes, and the number of alternative transcription start sites used in a given gene was correlated with overall Mitsui-7 response. Strikingly, genes that were up-regulated after Mitsui-7 exposure only through their main annotated transcription start site were linked to inflammatory and defense responses, while genes up-regulated only through alternative transcription start sites were functionally heterogeneous and not inflammation-associated. Furthermore, we identified almost 12 000 active enhancers, many of which were Mitsui-7-responsive, and we identified similarly responding putative target genes. Overall, our study provides the location and activity of Mitsui-7-induced enhancers and transcription start sites, providing a useful resource for targeted experiments elucidating the biological effects of nanomaterials and the identification of biomarkers for early detection of MWCNT-induced inflammation.
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Affiliation(s)
- Jette Bornholdt
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
| | | | - Berit Lilje
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
| | - Mette Boyd
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
| | - Mette Jørgensen
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
| | - Yun Chen
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
| | - Morana Vitezic
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
| | | | - Sarah Søs Poulsen
- National Research Centre for the Working Environment , 2100 Copenhagen, Denmark
| | - Trine Berthing
- National Research Centre for the Working Environment , 2100 Copenhagen, Denmark
| | - Simon Bressendorff
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
| | - Kristoffer Vitting-Seerup
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
| | - Robin Andersson
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
| | | | - Carole L Yauk
- Environmental and Radiation Health Sciences Directorate, Health Canada , Ottawa, Ontario K1A 0K9, Canada
| | - Sabina Halappanavar
- Environmental and Radiation Health Sciences Directorate, Health Canada , Ottawa, Ontario K1A 0K9, Canada
| | - Håkan Wallin
- National Research Centre for the Working Environment , 2100 Copenhagen, Denmark
- Department of Public Health, University of Copenhagen , 2200 Copenhagen, Denmark
| | - Ulla Vogel
- National Research Centre for the Working Environment , 2100 Copenhagen, Denmark
- Department of Micro and Nanotechnology, Technical University of Denmark , 2800 Kongens Lyngby, Denmark
| | - Albin Sandelin
- The Bioinformatics Centre, Department of Biology University of Copenhagen , 2200 Copenhagen, Denmark
- Biotech Research and Innovation Centre, University of Copenhagen , 2200 Copenhagen, Denmark
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27
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Chen Z, Wang Q, Asmani M, Li Y, Liu C, Li C, Lippmann JM, Wu Y, Zhao R. Lung Microtissue Array to Screen the Fibrogenic Potential of Carbon Nanotubes. Sci Rep 2016; 6:31304. [PMID: 27510174 PMCID: PMC4980669 DOI: 10.1038/srep31304] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 07/18/2016] [Indexed: 12/25/2022] Open
Abstract
Due to their excellent physical and chemical characteristics, multi-wall carbon nanotubes (MWCNT) have the potential to be used in structural composites, conductive materials, sensors, drug delivery and medical imaging. However, because of their small-size and light-weight, the applications of MWCNT also raise health concerns. In vivo animal studies have shown that MWCNT cause biomechanical and genetic alterations in the lung tissue which lead to lung fibrosis. To screen the fibrogenic risk factor of specific types of MWCNT, we developed a human lung microtissue array device that allows real-time and in-situ readout of the biomechanical properties of the engineered lung microtissue upon MWCNT insult. We showed that the higher the MWCNT concentration, the more severe cytotoxicity was observed. More importantly, short type MWCNT at low concentration of 50 ng/ml stimulated microtissue formation and contraction force generation, and caused substantial increase in the fibrogenic marker miR-21 expression, indicating the high fibrogenic potential of this specific carbon nanotube type and concentration. The presented microtissue array system provides a powerful tool for high-throughput examination of the therapeutic and toxicological effects of target compounds in realistic tissue environment.
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Affiliation(s)
- Zhaowei Chen
- State University of New York at Buffalo, Department of Biomedical Engineering, Buffalo, New York, 14260, USA
| | - Qixin Wang
- State University of New York at Buffalo, Department of Biomedical Engineering, Buffalo, New York, 14260, USA
| | - Mohammadnabi Asmani
- State University of New York at Buffalo, Department of Biomedical Engineering, Buffalo, New York, 14260, USA
| | - Yan Li
- State University of New York at Buffalo, Department of Biomedical Engineering, Buffalo, New York, 14260, USA
| | - Chang Liu
- State University of New York at Buffalo, Department of Biomedical Engineering, Buffalo, New York, 14260, USA
| | - Changning Li
- State University of New York at Buffalo, Department of Biomedical Engineering, Buffalo, New York, 14260, USA.,State University of New York at Buffalo, Department of Chemical and Biological Engineering, Buffalo, New York, 14260, USA
| | - Julian M Lippmann
- State University of New York at Buffalo, Department of Biomedical Engineering, Buffalo, New York, 14260, USA
| | - Yun Wu
- State University of New York at Buffalo, Department of Biomedical Engineering, Buffalo, New York, 14260, USA
| | - Ruogang Zhao
- State University of New York at Buffalo, Department of Biomedical Engineering, Buffalo, New York, 14260, USA
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28
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Shi H, Zhang G, Wang J, Wang Z, Liu X, Cheng L, Li W. Studying Dynamic Features in Myocardial Infarction Progression by Integrating miRNA-Transcription Factor Co-Regulatory Networks and Time-Series RNA Expression Data from Peripheral Blood Mononuclear Cells. PLoS One 2016; 11:e0158638. [PMID: 27367417 PMCID: PMC4930172 DOI: 10.1371/journal.pone.0158638] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Accepted: 06/20/2016] [Indexed: 12/22/2022] Open
Abstract
Myocardial infarction (MI) is a serious heart disease and a leading cause of mortality and morbidity worldwide. Although some molecules (genes, miRNAs and transcription factors (TFs)) associated with MI have been studied in a specific pathological context, their dynamic characteristics in gene expressions, biological functions and regulatory interactions in MI progression have not been fully elucidated to date. In the current study, we analyzed time-series RNA expression data from peripheral blood mononuclear cells. We observed that significantly differentially expressed genes were sharply up- or down-regulated in the acute phase of MI, and then changed slowly until the chronic phase. Biological functions involved at each stage of MI were identified. Additionally, dynamic miRNA–TF co-regulatory networks were constructed based on the significantly differentially expressed genes and miRNA–TF co-regulatory motifs, and the dynamic interplay of miRNAs, TFs and target genes were investigated. Finally, a new panel of candidate diagnostic biomarkers (STAT3 and ICAM1) was identified to have discriminatory capability for patients with or without MI, especially the patients with or without recurrent events. The results of the present study not only shed new light on the understanding underlying regulatory mechanisms involved in MI progression, but also contribute to the discovery of true diagnostic biomarkers for MI.
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Affiliation(s)
- Hongbo Shi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, PR China
| | - Guangde Zhang
- Department of Cardiology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, PR China
| | - Jing Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, PR China
| | - Zhenzhen Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, PR China
| | - Xiaoxia Liu
- Department of Cardiology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, PR China
| | - Liang Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, 150081, PR China
| | - Weimin Li
- Department of Cardiology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, PR China
- * E-mail:
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29
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Yang Z, Li Q, Yao S, Zhang G, Xue R, Li G, Wang Y, Wang S, Wu R, Gao H. Down-Regulation of miR-19a as a Biomarker for Early Detection of Silicosis. Anat Rec (Hoboken) 2016; 299:1300-7. [PMID: 27312312 DOI: 10.1002/ar.23381] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 03/30/2016] [Accepted: 04/16/2016] [Indexed: 12/19/2022]
Abstract
The accumulated data indicate that there is significant genetic heterogeneity underlying the etiology of silicosis. Recent reports have revealed that microRNAs (miRNAs) play an important role in regulating pulmonary fibrosis. This study, therefore, aimed to identify some miRNAs as biomarkers for silicosis, and to explore the early diagnostic value of biomarkers for silicosis. Total RNAs were collected from the peripheral blood leukocytes of 23 silicosis patients and 23 healthy controls, the different miRNAs were screened using microarrays. The potential biomarker miRNAs were identified by quantitative real-time polymerase chain reaction (qPCR) and receiver operating characteristic (ROC) curves. Eighteen differential miRNAs in leukocytes were up-regulated and twenty differential miRNAs were down-regulated in the silicosis group, compared with the control group. The expression levels of miR-181a and miR-19a were 0.8854 ± 0.1037 and 0.2929 ± 0.0342 by the relative quantitation method 2(-△△CT) of qPCR, respectively. The sensitivity and specificity for miR-181a at a cut-off value of 1.8917 were 70% and 75%, respectively, whereas, those for miR-19a at a cut-off value of 3.6828 were 95% and 95%, respectively. Thus, miR-19a in peripheral blood leukocyte could be used as an effective biomarker for silicosis. Anat Rec, 299:1300-1307, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Zhen Yang
- Tianjin Key Laboratory for Prevention and Control of Occupational and Environmental Hazard, No. 1 Huizhihuan Road, Dongli District, Tianjin, 300309, China.,Institute of Medical Equipment, Academy of Military Medical Sciences of Chinese People's Libration Army, 106 Wan Dong Road, Hedong District, Tianjin, 300163, China.,Department of Hygiene, Logistics College of Chinese People's Armed Police Forces, 1 Huizhihuan Road, Dongli District, Tianjin, 300309, China
| | - Qian Li
- Tianjin Key Laboratory for Prevention and Control of Occupational and Environmental Hazard, No. 1 Huizhihuan Road, Dongli District, Tianjin, 300309, China
| | - Sanqiao Yao
- School of Public Health, Xinxiang Medical University, 601 Jinsui Road, Hongqi District, Henan, 453003, China
| | - Ge Zhang
- Tianjin Key Laboratory for Prevention and Control of Occupational and Environmental Hazard, No. 1 Huizhihuan Road, Dongli District, Tianjin, 300309, China
| | - Rong Xue
- Tianjin Key Laboratory for Prevention and Control of Occupational and Environmental Hazard, No. 1 Huizhihuan Road, Dongli District, Tianjin, 300309, China
| | - Guoliang Li
- Tianjin Key Laboratory for Prevention and Control of Occupational and Environmental Hazard, No. 1 Huizhihuan Road, Dongli District, Tianjin, 300309, China.,Department of Hygiene, Logistics College of Chinese People's Armed Police Forces, 1 Huizhihuan Road, Dongli District, Tianjin, 300309, China
| | - Yizheng Wang
- Tianjin Key Laboratory for Prevention and Control of Occupational and Environmental Hazard, No. 1 Huizhihuan Road, Dongli District, Tianjin, 300309, China.,Department of Hygiene, Logistics College of Chinese People's Armed Police Forces, 1 Huizhihuan Road, Dongli District, Tianjin, 300309, China
| | - Shixin Wang
- Tianjin Key Laboratory for Prevention and Control of Occupational and Environmental Hazard, No. 1 Huizhihuan Road, Dongli District, Tianjin, 300309, China
| | - Ruichang Wu
- Institute of Medical Equipment, Academy of Military Medical Sciences of Chinese People's Libration Army, 106 Wan Dong Road, Hedong District, Tianjin, 300163, China
| | - Hongsheng Gao
- Tianjin Key Laboratory for Prevention and Control of Occupational and Environmental Hazard, No. 1 Huizhihuan Road, Dongli District, Tianjin, 300309, China.,Department of Hygiene, Logistics College of Chinese People's Armed Police Forces, 1 Huizhihuan Road, Dongli District, Tianjin, 300309, China
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Labib S, Williams A, Yauk CL, Nikota JK, Wallin H, Vogel U, Halappanavar S. Nano-risk Science: application of toxicogenomics in an adverse outcome pathway framework for risk assessment of multi-walled carbon nanotubes. Part Fibre Toxicol 2016; 13:15. [PMID: 26979667 PMCID: PMC4792104 DOI: 10.1186/s12989-016-0125-9] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/01/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND A diverse class of engineered nanomaterials (ENMs) exhibiting a wide array of physical-chemical properties that are associated with toxicological effects in experimental animals is in commercial use. However, an integrated framework for human health risk assessment (HHRA) of ENMs has yet to be established. Rodent 2-year cancer bioassays, clinical chemistry, and histopathological endpoints are still considered the 'gold standard' for detecting substance-induced toxicity in animal models. However, the use of data derived from alternative toxicological tools, such as genome-wide expression profiling and in vitro high-throughput assays, are gaining acceptance by the regulatory community for hazard identification and for understanding the underlying mode-of-action. Here, we conducted a case study to evaluate the application of global gene expression data in deriving pathway-based points of departure (PODs) for multi-walled carbon nanotube (MWCNT)-induced lung fibrosis, a non-cancer endpoint of regulatory importance. METHODS Gene expression profiles from the lungs of mice exposed to three individual MWCNTs with different physical-chemical properties were used within the framework of an adverse outcome pathway (AOP) for lung fibrosis to identify key biological events linking MWCNT exposure to lung fibrosis. Significantly perturbed pathways were categorized along the key events described in the AOP. Benchmark doses (BMDs) were calculated for each perturbed pathway and were used to derive transcriptional BMDs for each MWCNT. RESULTS Similar biological pathways were perturbed by the different MWCNT types across the doses and post-exposure time points studied. The pathway BMD values showed a time-dependent trend, with lower BMDs for pathways perturbed at the earlier post-exposure time points (24 h, 3d). The transcriptional BMDs were compared to the apical BMDs derived by the National Institute for Occupational Safety and Health (NIOSH) using alveolar septal thickness and fibrotic lesions endpoints. We found that regardless of the type of MWCNT, the BMD values for pathways associated with fibrosis were 14.0-30.4 μg/mouse, which are comparable to the BMDs derived by NIOSH for MWCNT-induced lung fibrotic lesions (21.0-27.1 μg/mouse). CONCLUSIONS The results demonstrate that transcriptomic data can be used to as an effective mechanism-based method to derive acceptable levels of exposure to nanomaterials in product development when epidemiological data are unavailable.
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Affiliation(s)
- Sarah Labib
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON K1A 0K9 Canada
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON K1A 0K9 Canada
| | - Carole L. Yauk
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON K1A 0K9 Canada
| | - Jake K. Nikota
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON K1A 0K9 Canada
| | - Håkan Wallin
- National Research Centre for the Working Environment, Lerso Parkallé 105, DK-2100 Copenhagen, Denmark
- Department of Public Health, University of Copenhagen, DK-1353 Copenhagen K, Denmark
| | - Ulla Vogel
- National Research Centre for the Working Environment, Lerso Parkallé 105, DK-2100 Copenhagen, Denmark
- Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Kgs Lyngby, Denmark
| | - Sabina Halappanavar
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON K1A 0K9 Canada
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Fatkhutdinova LM, Khaliullin TO, Vasil'yeva OL, Zalyalov RR, Mustafin IG, Kisin ER, Birch ME, Yanamala N, Shvedova AA. Fibrosis biomarkers in workers exposed to MWCNTs. Toxicol Appl Pharmacol 2016; 299:125-31. [PMID: 26902652 DOI: 10.1016/j.taap.2016.02.016] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 02/17/2016] [Accepted: 02/18/2016] [Indexed: 12/14/2022]
Abstract
Multi-walled carbon nanotubes (MWCNT) with their unique physico-chemical properties offer numerous technological advantages and are projected to drive the next generation of manufacturing growth. As MWCNT have already found utility in different industries including construction, engineering, energy production, space exploration and biomedicine, large quantities of MWCNT may reach the environment and inadvertently lead to human exposure. This necessitates the urgent assessment of their potential health effects in humans. The current study was carried out at NanotechCenter Ltd. Enterprise (Tambov, Russia) where large-scale manufacturing of MWCNT along with relatively high occupational exposure levels was reported. The goal of this small cross-sectional study was to evaluate potential biomarkers during occupational exposure to MWCNT. All air samples were collected at the workplaces from both specific areas and personal breathing zones using filter-based devices to quantitate elemental carbon and perform particle analysis by TEM. Biological fluids of nasal lavage, induced sputum and blood serum were obtained from MWCNT-exposed and non-exposed workers for assessment of inflammatory and fibrotic markers. It was found that exposure to MWCNTs caused significant increase in IL-1β, IL6, TNF-α, inflammatory cytokines and KL-6, a serological biomarker for interstitial lung disease in collected sputum samples. Moreover, the level of TGF-β1 was increased in serum obtained from young exposed workers. Overall, the results from this study revealed accumulation of inflammatory and fibrotic biomarkers in biofluids of workers manufacturing MWCNTs. Therefore, the biomarkers analyzed should be considered for the assessment of health effects of occupational exposure to MWCNT in cross-sectional epidemiological studies.
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Affiliation(s)
| | - Timur O Khaliullin
- Kazan State Medical University, ul. Butlerova 49, Kazan 420012, Russia; Department of Physiology & Pharmacology, WVU, Morgantown, WV, USA.
| | - Olga L Vasil'yeva
- Kazan State Medical University, ul. Butlerova 49, Kazan 420012, Russia.
| | - Ramil R Zalyalov
- Kazan State Medical University, ul. Butlerova 49, Kazan 420012, Russia.
| | - Ilshat G Mustafin
- Kazan State Medical University, ul. Butlerova 49, Kazan 420012, Russia.
| | - Elena R Kisin
- National Institute for Occupational Safety and Health, Morgantown, WV, USA.
| | - M Eileen Birch
- National Institute for Occupational Safety and Health, Cincinnati, OH, USA.
| | - Naveena Yanamala
- National Institute for Occupational Safety and Health, Morgantown, WV, USA.
| | - Anna A Shvedova
- National Institute for Occupational Safety and Health, Morgantown, WV, USA; Department of Physiology & Pharmacology, WVU, Morgantown, WV, USA.
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32
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Snyder-Talkington BN, Dong C, Sargent LM, Porter DW, Staska LM, Hubbs AF, Raese R, McKinney W, Chen BT, Battelli L, Lowry DT, Reynolds SH, Castranova V, Qian Y, Guo NL. mRNAs and miRNAs in whole blood associated with lung hyperplasia, fibrosis, and bronchiolo-alveolar adenoma and adenocarcinoma after multi-walled carbon nanotube inhalation exposure in mice. J Appl Toxicol 2016; 36:161-74. [PMID: 25926378 PMCID: PMC4418205 DOI: 10.1002/jat.3157] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 03/02/2015] [Accepted: 03/03/2015] [Indexed: 12/28/2022]
Abstract
Inhalation exposure to multi-walled carbon nanotubes (MWCNT) in mice results in inflammation, fibrosis and the promotion of lung adenocarcinoma; however, the molecular basis behind these pathologies is unknown. This study determined global mRNA and miRNA profiles in whole blood from mice exposed by inhalation to MWCNT that correlated with the presence of lung hyperplasia, fibrosis, and bronchiolo-alveolar adenoma and adenocarcinoma. Six-week-old, male, B6C3F1 mice received a single intraperitoneal injection of either the DNA-damaging agent methylcholanthrene (MCA, 10 µg g(-1) body weight) or vehicle (corn oil). One week after injections, mice were exposed by inhalation to MWCNT (5 mg m(-3), 5 hours per day, 5 days per week) or filtered air (control) for a total of 15 days. At 17 months post-exposure, mice were euthanized and examined for the development of pathological changes in the lung, and whole blood was collected and analyzed using microarray analysis for global mRNA and miRNA expression. Numerous mRNAs and miRNAs in the blood were significantly up- or down-regulated in animals developing pathological changes in the lung after MCA/corn oil administration followed by MWCNT/air inhalation, including fcrl5 and miR-122-5p in the presence of hyperplasia, mthfd2 and miR-206-3p in the presence of fibrosis, fam178a and miR-130a-3p in the presence of bronchiolo-alveolar adenoma, and il7r and miR-210-3p in the presence of bronchiolo-alveolar adenocarcinoma, among others. The changes in miRNA and mRNA expression, and their respective regulatory networks, identified in this study may potentially serve as blood biomarkers for MWCNT-induced lung pathological changes.
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Affiliation(s)
- Brandi N. Snyder-Talkington
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | - Chunlin Dong
- Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506-9300, USA
| | - Linda M. Sargent
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | - Dale W. Porter
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | | | - Ann F. Hubbs
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | - Rebecca Raese
- Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506-9300, USA
| | - Walter McKinney
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | - Bean T. Chen
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | - Lori Battelli
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | - David T. Lowry
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | - Steven H. Reynolds
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | - Vincent Castranova
- Department of Basic Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, WV 26506, USA
| | - Yong Qian
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | - Nancy L. Guo
- Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506-9300, USA
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Malur A, Barna BP, Patel J, McPeek M, Wingard CJ, Dobbs L, Thomassen MJ. Exposure to a Mycobacterial Antigen, ESAT-6, Exacerbates Granulomatous and Fibrotic Changes in a Multiwall Carbon Nanotube Model of Chronic Pulmonary Disease. ACTA ACUST UNITED AC 2015; 6. [PMID: 27019768 DOI: 10.4172/2157-7439.1000340] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Recent studies suggest additive effects of environmental pollutants and microbial antigens on respiratory disease. We established a granuloma model in which instilled multiwall carbon nanotubes (MWCNT) elicit granulomatous pathology. We hypothesized that mycobacterial antigen ESAT-6, a T cell activator associated with tuberculosis and sarcoidosis, might alter pathology. Wild-type C57Bl/6 mice received MWCNT with or without ESAT-6 peptide. Controls received vehicle (surfactant-PBS) or ESAT-6 alone. Mice were evaluated 60 days later for granulomas, fibrosis, and bronchoalveolar lavage (BAL) cell expression of inflammatory mediators (CCL2, MMP-12, and Osteopontin). Results indicated increased granulomas, fibrosis, and inflammatory mediators in mice receiving the combination of MWCNT+ESAT-6 compared to MWCNT or vehicle alone. ESAT-6 alone showed no significant effect on these pathological endpoints. However, CD3 (+) lymphocyte infiltration of lung tissue increased with MWCNT+ESAT-6 versus MWCNT alone. Findings suggest that concurrent exposure to microbial antigen and MWCNT exacerbates chronic pulmonary disease.
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Li S, Xue C, Yuan Y, Zhang R, Wang Y, Wang Y, Yu B, Liu J, Ding F, Yang Y, Gu X. The transcriptional landscape of dorsal root ganglia after sciatic nerve transection. Sci Rep 2015; 5:16888. [PMID: 26576491 PMCID: PMC4649668 DOI: 10.1038/srep16888] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 10/21/2015] [Indexed: 11/12/2022] Open
Abstract
Following peripheral nerve injury, transcriptional responses are orchestrated to regulate the expression of numerous genes in the lesioned nerve, thus activating the intrinsic regeneration program. To better understand the molecular regulation of peripheral nerve regeneration, we aimed at investigating the transcriptional landscape of dorsal root ganglia (DRGs) after sciatic nerve transection in rats. The cDNA microarray analysis was used to identify thousands of genes that were differentially expressed at different time points post nerve injury (PNI). The results from Euclidean distance matrix, principal component analysis, and hierarchical clustering indicated that 2 nodal transitions in temporal gene expressions could segregate 3 distinct transcriptional phases within the period of 14 d PNI. The 3 phases were designated as “a stress response phase”, “a pre-regeneration phase”, and “a regeneration phase”, respectively, by referring to morphological observation of post-nerve-injury changes. The gene ontology (GO) analysis revealed the distinct features of biological process, cellular component, and molecular function at each transcriptional phase. Moreover, Ingenuity Pathway Analysis suggested that differentially expressed genes, mainly transcription factors and genes associated with neurite/axon growth, might be integrated into regulatory networks to mediate the regulation of peripheral nerve regeneration in a highly cooperative manner.
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Affiliation(s)
- Shiying Li
- Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, JS 226001, China
| | - Chengbin Xue
- Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, JS 226001, China
| | - Ying Yuan
- Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, JS 226001, China
| | - Ruirui Zhang
- Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, JS 226001, China
| | - Yaxian Wang
- Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, JS 226001, China
| | - Yongjun Wang
- Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, JS 226001, China
| | - Bin Yu
- Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, JS 226001, China
| | - Jie Liu
- Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, JS 226001, China
| | - Fei Ding
- Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, JS 226001, China
| | - Yuming Yang
- Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, JS 226001, China
| | - Xiaosong Gu
- Jiangsu Key Laboratory of Neuroregeneration, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, JS 226001, China
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35
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Fukunaga S, Kakehashi A, Sumida K, Kushida M, Asano H, Gi M, Wanibuchi H. Integrative analyses of miRNA and proteomics identify potential biological pathways associated with onset of pulmonary fibrosis in the bleomycin rat model. Toxicol Appl Pharmacol 2015; 286:188-97. [DOI: 10.1016/j.taap.2015.04.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 04/15/2015] [Accepted: 04/22/2015] [Indexed: 02/07/2023]
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