1
|
Balasubramanian S, Perumal E. Integrated in silico analysis of transcriptomic alterations in nanoparticle toxicity across human and mouse models. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 949:174897. [PMID: 39053559 DOI: 10.1016/j.scitotenv.2024.174897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/17/2024] [Accepted: 07/17/2024] [Indexed: 07/27/2024]
Abstract
Nanoparticles, due to their exceptional physicochemical properties are used in our day-to-day environment. They are currently not regulated which might lead to increased levels in the biological systems causing adverse effects. However, the overall mechanism behind nanotoxicity remains elusive. Previously, we analysed the transcriptome datasets of copper oxide nanoparticles using in silico tools and identified IL-17, chemokine signaling pathway, and cytokine-cytokine receptor interaction as the key pathways altered. Based on the findings, we hypothesized a common pathway could be involved in transition metal oxide nanoparticles toxicity irrespective of the variables. Further, there could be unique transcriptome changes between metal oxide nanoparticles and other nanoparticles. To accomplish this, the overall transcriptome datasets of nanoparticles consisting of microarray and RNA-Seq were obtained. >90 studies for 17 different nanoparticles, performed in humans, rats, and mice were assessed. After initial screening, 24 mouse studies (with 196 datasets) and 34 human studies (with 200 datasets) were used for further analyses. The common genes that are dysregulated upon NPs exposure were identified for human and mouse datasets separately. Further, an overrepresentation functional enrichment analysis was performed. The common genes, their gene ontology, gene-gene, and protein-protein interactions were assessed. The overall results suggest that IL-17 and its related pathways might be commonly altered in nanoparticle exposure with lung as one of the major organs affected.
Collapse
Affiliation(s)
- Satheeswaran Balasubramanian
- Molecular Toxicology Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu 641046, India
| | - Ekambaram Perumal
- Molecular Toxicology Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu 641046, India.
| |
Collapse
|
2
|
Liu L, Yu Z, Ma Q, Yu J, Gong Z, Deng G, Wu X. LncRNA NR_003508 Suppresses Mycobacterium tuberculosis-Induced Programmed Necrosis via Sponging miR-346-3p to Regulate RIPK1. Int J Mol Sci 2023; 24:ijms24098016. [PMID: 37175724 PMCID: PMC10179217 DOI: 10.3390/ijms24098016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Emerging evidence suggests that long non-coding RNAs (LncRNAs) are involved in Mtb-induced programmed necrosis. Among these LncRNAs, LncRNA NR_003508 is associated with LPS-induced acute respiratory distress syndrome. However, whether LncRNA NR_003508 contributes to Mtb-induced programmed necrosis remains undocumented. Firstly, the expression of LncRNA NR_003508 was determined using RT-qPCR and FISH. The protein expression of RIPK1, p-RIPK1, RIPK3, p-RIPK3, MLKL, and p-MLKL was measured by Western blot in RAW264.7 and mouse lung tissues. Furthermore, luciferase reporter assays and bioinformatics were used to predict specific miRNA (miR-346-3p) and mRNA (RIPK1) regulated by LncRNA NR_003508. In addition, RT-qPCR was used to detect the RIPK1 expression in TB patients and healthy peripheral blood. The flow cytometry assay was performed to detect cell necrosis rates. Here we show that BCG infection-induced cell necrosis and increased LncRNA NR_003508 expression. si-NR_003508 inhibited BCG/H37Rv-induced programmed necrosis in vitro or in vivo. Functionally, LncRNA NR_003508 has been verified as a ceRNA for absorbing miR-346-3p, which targets RIPK1. Moreover, RIPK1 expression was elevated in the peripheral blood of TB patients compared with healthy people. Knockdown of LncRNA NR_003508 or miR-346-3p overexpression suppresses cell necrosis rate and ROS accumulation in RAW264.7 cells. In conclusion, LncRNA NR_003508 functions as a positive regulator of Mtb-induced programmed necrosis via sponging miR-346-3p to regulate RIPK1. Our findings may provide a promising therapeutic target for tuberculosis.
Collapse
Affiliation(s)
- Li Liu
- Key Lab of Ministry of Education for Protection and Utilization of Special Biological Resources in Western China, Ningxia University, Yinchuan 750021, China
- School of Life Science, Ningxia University, Yinchuan 750021, China
| | - Zhirui Yu
- Key Lab of Ministry of Education for Protection and Utilization of Special Biological Resources in Western China, Ningxia University, Yinchuan 750021, China
- School of Life Science, Ningxia University, Yinchuan 750021, China
| | - Qinmei Ma
- Key Lab of Ministry of Education for Protection and Utilization of Special Biological Resources in Western China, Ningxia University, Yinchuan 750021, China
- School of Life Science, Ningxia University, Yinchuan 750021, China
| | - Jialin Yu
- Key Lab of Ministry of Education for Protection and Utilization of Special Biological Resources in Western China, Ningxia University, Yinchuan 750021, China
- School of Life Science, Ningxia University, Yinchuan 750021, China
| | - Zhaoqian Gong
- Key Lab of Ministry of Education for Protection and Utilization of Special Biological Resources in Western China, Ningxia University, Yinchuan 750021, China
- School of Life Science, Ningxia University, Yinchuan 750021, China
| | - Guangcun Deng
- Key Lab of Ministry of Education for Protection and Utilization of Special Biological Resources in Western China, Ningxia University, Yinchuan 750021, China
- School of Life Science, Ningxia University, Yinchuan 750021, China
| | - Xiaoling Wu
- Key Lab of Ministry of Education for Protection and Utilization of Special Biological Resources in Western China, Ningxia University, Yinchuan 750021, China
- School of Life Science, Ningxia University, Yinchuan 750021, China
| |
Collapse
|
3
|
miR-346-3p promotes osteoclastogenesis via inhibiting TRAF3 gene. In Vitro Cell Dev Biol Anim 2020; 56:533-542. [PMID: 32839904 DOI: 10.1007/s11626-020-00479-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 06/30/2020] [Indexed: 01/30/2023]
Abstract
MicroRNAs (miRNAs) modulate gene expression and regulate many physiological and pathological conditions. However, their modulation and effect in osteoclastogenesis remain unknown. In this study, we investigated the role of miR-346-3p in regulating the osteoclast differentiation from RAW264.7 cells. We used the miRNA microarray assay, miR-346-3p mimic transfection, tartrate resistant acid phosphatase (TRAP) staining, bone resorption assay, qRT-PCR, and western blot. Our results showed that the expression of miR-346-3p was significantly upregulated during osteoclast differentiation. Further, by transfecting cells with miR-346-3p mimic, we observed an increased number of TRAP-positive multinucleated cells, increased pit area caused by bone resorption, and enhanced expression of osteoclast-specific genes and proteins. Conversely, miR-346-3p inhibition attenuated the osteoclast differentiation and function. Software-mediated prediction and validation using luciferase reporter assay showed that TRAF3, a negative regulator of osteoclast differentiation, was inhibited by miR-346-3p overexpression. Our results showed that miR-346-3p directly targeted TRAF3 mRNA via binding to its 3'-UTR and inhibited the expression of TRAF3 protein. Taken together, our results revealed that miR-346-3p promotes the regulation of osteoclastogenesis by suppressing the TRAF3 gene. In conclusion, miR-346-3p could be a novel therapeutic target for bone loss-related pathogenesis.
Collapse
|
4
|
Lin CW, Jan MS, Kuo JHS. The microRNA expression profiles in extracellular vesicles from HeLa cancer cells in response to cationic lipid- or polyethylenimine-mediated gene delivery. J Drug Target 2018; 27:94-102. [DOI: 10.1080/1061186x.2018.1491977] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Chia-Wei Lin
- Institute of Biochemistry, Microbiology and Immunology, Taichung, Taiwan
| | - Ming-Shiou Jan
- Institute of Biochemistry, Microbiology and Immunology, Taichung, Taiwan
- Immunology Research Center, Medical College of Chung Shan Medical University, Taichung, Taiwan
- Division of Allergy, Immunology, and Rheumatology, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Jung-Hua Steven Kuo
- Department of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan, Taiwan
| |
Collapse
|
5
|
Wang S, Gu K. Insulin-like growth factor 1 inhibits autophagy of human colorectal carcinoma drug-resistant cells via the protein kinase B/mammalian target of rapamycin signaling pathway. Mol Med Rep 2017; 17:2952-2956. [PMID: 29257307 PMCID: PMC5783513 DOI: 10.3892/mmr.2017.8272] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 03/30/2017] [Indexed: 12/26/2022] Open
Abstract
Insulin-like growth factor 1 (IGF-1) is reported to inhibit autophagy of human colorectal carcinoma cells (HCT); however, little is known regarding the mechanisms underlying the inhibitory effect of IGF-1 on autophagy in HCT resistant strains. The present study aimed to analyze the inhibitory effect of IGF-1 on the autophagy of HCT resistant strains and its potential underlying mechanisms. The viability and apoptosis of HCT-8 colon cancer cells were analyzed, and expression levels of relevant genes and proteins were investigated using reverse transcription-quantitative polymerase chain reaction and western blot analysis, respectively. Treatment of cells with IGF-1 induced apoptosis. IGF-1 treatment activated protein kinase B (AKT), which may inhibit autophagy via the AKT/mammalian target of rapamycin signaling pathway. Following inhibition of autophagy, drug resistant cells became sensitive to apoptosis induced by 5-fluorouracil.
Collapse
Affiliation(s)
- Shuomin Wang
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230032, P.R. China
| | - Kangsheng Gu
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230032, P.R. China
| |
Collapse
|
6
|
Liu C, Zhang C, Yang J, Geng X, Du H, Ji X, Zhao H. Screening circular RNA expression patterns following focal cerebral ischemia in mice. Oncotarget 2017; 8:86535-86547. [PMID: 29156814 PMCID: PMC5689704 DOI: 10.18632/oncotarget.21238] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/07/2017] [Indexed: 12/31/2022] Open
Abstract
Circular RNAs (circRNAs) have been demonstrated to act as microRNA (miRNA) sponges and they play important roles in regulating gene expression through a circRNA-miRNA-gene pathway. The specific roles of circRNAs in the pathogenesis of cerebral ischemia, however, are still unclear. Thus, the aim of this study is to determine circRNA expression profiles in the ischemic brain after stroke, which was induced by 45 min of transient middle cerebral artery occlusion (MCAO). The results from the circRNA microarrays revealed that 1027 circRNAs were significantly altered 48 hours after reperfusion in the ischemic brain compared with the sham group. Among them, 914 circRNAs were significantly upregulated, and the remaining 113 were significantly downregulated. In addition, the expressions of the three selected circRNAs, mmu_circRNA_40001, mmu_circRNA_013120, and mmu_circRNA_40806, were verified using quantitative real-time polymerase chain reaction (qRT-PCR). After predicting their target genes, the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) analyses were further used to predict the associated significant cell signaling pathways and functions. The results show that the most enriched pathways are associated with the Rap1 signaling pathway and the Hippo signaling pathway, which regulate cell survival and death. Finally, we constructed an interaction network of circRNA-miRNA-target genes, including 13 miRNAs and their corresponding genes, indicating that changes in circRNA are associated with genes related with brain injury and recovery. In conclusion, circRNAs are complicated in the pathological development of brain injury after stroke, suggesting novel diagnostic and therapeutic targets for stroke therapy.
Collapse
Affiliation(s)
- Cuiying Liu
- China-America Institute of Neuroscience, Beijing Luhe Hospital, Capital Medical University, Beijing, China
| | - Chencheng Zhang
- China-America Institute of Neuroscience, Beijing Luhe Hospital, Capital Medical University, Beijing, China
| | - Jian Yang
- China-America Institute of Neuroscience, Beijing Luhe Hospital, Capital Medical University, Beijing, China
| | - Xiaokun Geng
- China-America Institute of Neuroscience, Beijing Luhe Hospital, Capital Medical University, Beijing, China.,Department of Neurology, Beijing Luhe Hospital, Capital Medical University, Beijing, China
| | - Huishan Du
- China-America Institute of Neuroscience, Beijing Luhe Hospital, Capital Medical University, Beijing, China.,Department of Neurology, Beijing Luhe Hospital, Capital Medical University, Beijing, China
| | - Xunming Ji
- China-America Institute of Neuroscience, Beijing Luhe Hospital, Capital Medical University, Beijing, China.,Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Heng Zhao
- China-America Institute of Neuroscience, Beijing Luhe Hospital, Capital Medical University, Beijing, China.,Department of Neurosurgery, Stanford University, Stanford, CA, USA
| |
Collapse
|
7
|
Lin CW, Jan MS, Kuo JHS. The vector-related influences of autophagic microRNA delivery by Lipofectamine 2000 and polyethylenimine 25K on mouse embryonic fibroblast cells. Eur J Pharm Sci 2017; 101:11-21. [DOI: 10.1016/j.ejps.2017.01.031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 01/24/2017] [Accepted: 01/24/2017] [Indexed: 10/20/2022]
|