1
|
Li K, Zheng J, Liu H, Gao Q, Yang M, Tang J, Wang H, Li S, Sun Y, Chang X. Whole-transcriptome sequencing revealed differentially expressed mRNAs and non-coding RNAs played crucial roles in NiONPs-induced liver fibrosis. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 248:114308. [PMID: 36410144 DOI: 10.1016/j.ecoenv.2022.114308] [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: 08/09/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Nickel oxide nanoparticles (NiONPs) induced liver fibrosis, while its mechanisms associated with transcriptome remained unclear. This study aimed to investigate the roles of differentially expressed (DE) messenger RNAs (mRNAs) and non-coding RNAs (ncRNAs) in NiONPs-induced liver fibrosis, and further confirm whether JNK/c-Jun pathway enriched by the DE RNAs was involved in the regulation of the disease. A liver fibrosis rat model was established by intratracheal perfusion of NiONPs twice a week for 9 weeks. Whole-transcriptome sequencing was applied to obtain expression profiles of mRNAs, long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs) in the model rat and control liver tissues. Comparing the RNA expression profiles of the model and control liver tissues, we identified 324 DE mRNAs, 129 DE lncRNAs, 24 DE miRNAs and 33 DE circRNAs, and the potential interactions among them were revealed by constructing two co-expression networks, including lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA networks. Using RT-qPCR, we verified the sequencing results of some RNAs in the networks and obtained similar expression profiles, indicating our sequencing results were reliable and referable. Through Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, we predicted the biological functions and signaling pathways potentially related to NiONPs-induced liver fibrosis, such as "positive regulation of JNK cascade", "inflammatory response", "transcription factor binding", and MAPK, Wnt, PI3K-Akt signaling pathways. JNK/c-Jun pathway, a subclass of MAPK signal, was selected for further investigation because it was significantly enriched by fibrosis-related DE genes and activated in animal models. In vitro, we detected the cytotoxicity of NiONPs on LX-2 cells and treated the cells with 5 μg/ml NiONPs for 12 h. The results showed NiONPs induced the up-regulated protein expression of fibrotic factors collagen-1a1 (Col-1a1) and matrix metalloproteinas2 (MMP2) and JNK/c-Jun pathway activation. While these effects were reversed after JNK/c-Jun pathway was blocked by SP600125 (JNK pathway inhibitor), indicating the pathway was involved in NiONPs-induced excessive collagen formation. In conclusion, our results revealed the DE mRNAs and ncRNAs played crucial roles in NiONPs-induced liver fibrosis, and JNK/c-Jun pathway mediated the development of the disease.
Collapse
Affiliation(s)
- Kun Li
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Jinfa Zheng
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Han Liu
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Qing Gao
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Mengmeng Yang
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Jiarong Tang
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Hui Wang
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Sheng Li
- Department of Public Health, The First People's Hospital of Lanzhou City, Lanzhou 730000, China
| | - Yingbiao Sun
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China.
| | - Xuhong Chang
- Department of Toxicology, School of Public Health, Lanzhou University, Lanzhou 730000, China.
| |
Collapse
|
2
|
Huang C, Leng D, Zheng P, Deng M, Li L, Wu G, Sun B, Zhang XD. Comprehensive transcriptome analysis of peripheral blood unravels key lncRNAs implicated in ABPA and asthma. PeerJ 2021; 9:e11453. [PMID: 34221710 PMCID: PMC8236232 DOI: 10.7717/peerj.11453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/23/2021] [Indexed: 11/20/2022] Open
Abstract
Allergic bronchopulmonary aspergillosis (ABPA) is a complex hypersensitivity lung disease caused by a fungus known as Aspergillus fumigatus. It complicates and aggravates asthma. Despite their potential associations, the underlying mechanisms of asthma developing into ABPA remain obscure. Here we performed an integrative transcriptome analysis based on three types of human peripheral blood, which derived from ABPA patients, asthmatic patients and health controls, aiming to identify crucial lncRNAs implicated in ABPA and asthma. Initially, a high-confidence dataset of lncRNAs was identified using a stringent filtering pipeline. A comparative mutational analysis revealed no significant difference among these samples. Differential expression analysis disclosed several immune-related mRNAs and lncRNAs differentially expressed in ABPA and asthma. For each disease, three sub-networks were established using differential network analysis. Many key lncRNAs implicated in ABPA and asthma were identified, respectively, i.e., AL139423.1-201, AC106028.4-201, HNRNPUL1-210, PUF60-218 and SREBF1-208. Our analysis indicated that these lncRNAs exhibits in the loss-of-function networks, and the expression of which were repressed in the occurrences of both diseases, implying their important roles in the immune-related processes in response to the occurrence of both diseases. Above all, our analysis proposed a new point of view to explore the relationship between ABPA and asthma, which might provide new clues to unveil the pathogenic mechanisms for both diseases.
Collapse
Affiliation(s)
- Chen Huang
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, Macau University of Science and Technology, Macau, SAR, China, Macau, China.,Stat Key laboratory of Quality Research in Chinese Medicine, Macau Institute For Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, SAR, China, Macau, China
| | - Dongliang Leng
- Faculty of Health and Science, University of Macau, Macao, Macau
| | - Peiyan Zheng
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Center of Respiratory Disease, Guangzhou Institute of Respiratory, Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Min Deng
- Faculty of Health and Science, University of Macau, Macao, Macau
| | - Lu Li
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Center of Respiratory Disease, Guangzhou Institute of Respiratory, Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Ge Wu
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Center of Respiratory Disease, Guangzhou Institute of Respiratory, Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Baoqing Sun
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Center of Respiratory Disease, Guangzhou Institute of Respiratory, Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | | |
Collapse
|
3
|
Karri K, Waxman DJ. Widespread Dysregulation of Long Noncoding Genes Associated With Fatty Acid Metabolism, Cell Division, and Immune Response Gene Networks in Xenobiotic-exposed Rat Liver. Toxicol Sci 2020; 174:291-310. [PMID: 31926019 PMCID: PMC7098378 DOI: 10.1093/toxsci/kfaa001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Xenobiotic exposure dysregulates hundreds of protein-coding genes in mammalian liver, impacting many physiological processes and inducing diverse toxicological responses. Little is known about xenobiotic effects on long noncoding RNAs (lncRNAs), many of which have important regulatory functions. Here, we present a computational framework to discover liver-expressed, xenobiotic-responsive lncRNAs (xeno-lncs) with strong functional, gene regulatory potential and elucidate the impact of xenobiotic exposure on their gene regulatory networks. We assembled the long noncoding transcriptome of xenobiotic-exposed rat liver using RNA-seq datasets from male rats treated with 27 individual chemicals, representing 7 mechanisms of action (MOAs). Ortholog analysis was combined with coexpression data and causal inference methods to infer lncRNA function and deduce gene regulatory networks, including causal effects of lncRNAs on protein-coding gene expression and biological pathways. We discovered > 1400 liver-expressed xeno-lncs, many with human and/or mouse orthologs. Xenobiotics representing different MOAs often regulated common xeno-lnc targets: 123 xeno-lncs were dysregulated by ≥ 10 chemicals, and 5 xeno-lncs responded to ≥ 20 of the 27 chemicals investigated; 81 other xeno-lncs served as MOA-selective markers of xenobiotic exposure. Xeno-lnc-protein-coding gene coexpression regulatory network analysis identified xeno-lncs closely associated with exposure-induced perturbations of hepatic fatty acid metabolism, cell division, or immune response pathways, and with apoptosis or cirrhosis. We also identified hub and bottleneck lncRNAs, which are expected to be key regulators of gene expression. This work elucidates extensive networks of xeno-lnc-protein-coding gene interactions and provides a framework for understanding the widespread transcriptome-altering actions of foreign chemicals in a key-responsive mammalian tissue.
Collapse
Affiliation(s)
- Kritika Karri
- Department of Biology and Bioinformatics Program, Boston University, Boston, Massachusetts
| | - David J Waxman
- Department of Biology and Bioinformatics Program, Boston University, Boston, Massachusetts
| |
Collapse
|