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Nath P, Bhuyan K, Bhattacharyya DK, Barah P. ETENLNC: An end to end lncRNA identification and analysis framework to facilitate construction of known and novel lncRNA regulatory networks. Comput Biol Chem 2024; 112:108140. [PMID: 38996755 DOI: 10.1016/j.compbiolchem.2024.108140] [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: 08/31/2023] [Revised: 04/22/2024] [Accepted: 06/26/2024] [Indexed: 07/14/2024]
Abstract
Long non-coding RNAs (lncRNAs) play crucial roles in the regulation of gene expression and maintenance of genomic integrity through various interactions with DNA, RNA, and proteins. The availability of large-scale sequence data from various high-throughput platforms has opened possibilities to identify, predict, and functionally annotate lncRNAs. As a result, there is a growing demand for an integrative computational framework capable of identifying known lncRNAs, predicting novel lncRNAs, and inferring the downstream regulatory interactions of lncRNAs at the genome-scale. We present ETENLNC (End-To-End-Novel-Long-NonCoding), a user-friendly, integrative, open-source, scalable, and modular computational framework for identifying and analyzing lncRNAs from raw RNA-Seq data. ETENLNC employs six stringent filtration steps to identify novel lncRNAs, performs differential expression analysis of mRNA and lncRNA transcripts, and predicts regulatory interactions between lncRNAs, mRNAs, miRNAs, and proteins. We benchmarked ETENLNC against six existing tools and optimized it for desktop workstations and high-performance computing environments using data from three different species. ETENLNC is freely available on GitHub: https://github.com/EvolOMICS-TU/ETENLNC.
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Affiliation(s)
- Prangan Nath
- Department of Molecular Biology and Biotechnology, Tezpur University, Assam 784028, India
| | - Kaveri Bhuyan
- Department of Computer Science and Engineering, Tezpur University, Assam 784028, India; Department of Electrical Engineering, Tezpur University, Assam 784028, India
| | | | - Pankaj Barah
- Department of Molecular Biology and Biotechnology, Tezpur University, Assam 784028, India.
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Wu Z, Zhang H, Chen X, Zhang P, Fang J, Yang S, Chen H, Ji J, Chen L, Zheng Y, Yu D, Zhao Y. miR-145a-5p/SIK1/cAMP-dependent alteration of synaptic structural plasticity drives cognitive impairment induced by coke oven emissions. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 277:116401. [PMID: 38677069 DOI: 10.1016/j.ecoenv.2024.116401] [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: 01/17/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 04/29/2024]
Abstract
Exposure to fine particulate matter (PM) is associated with the neurodegenerative diseases. Coke oven emissions (COEs) in occupational environment are important sources of PM. However, its neurotoxicity is still unclear. Therefore, evaluating the toxicological effects of COE on the nervous system is necessary. In the present study, we constructed mouse models of COE exposure by tracheal instillation. Mice exposed to COE showed signs of cognitive impairment. This was accompanied by a decrease in miR-145a-5p and an increase in SIK1 expression in the hippocampus, along with synaptic structural damage. Our results demonstrated that COE-induced miR-145a-5p downregulation could increase the expression of SIK1 and phosphorylated SIK1, inhibiting the cAMP/PKA/CREB pathway by activating PDE4D, which was associated with reduced synaptic structural plasticity. Furthermore, restoring of miR-145a-5p expression based on COE exposure in HT22 cells could partially reversed the negative effects of COE exposure through the SIK1/PDE4D/cAMP axis. Collectively, our findings link epigenetic regulation with COE-induced neurotoxicity and imply that miR-145a-5p could be an early diagnostic marker for neurological diseases in patients with COE occupational exposure.
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Affiliation(s)
- Zhaoxu Wu
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao 266071, China
| | - Heng Zhang
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao 266071, China
| | - Xian Chen
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao 266071, China
| | - Pimei Zhang
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao 266071, China
| | - Jiacheng Fang
- Department of Nutrition, School of Public Health, Qingdao University, Qingdao 266071, China
| | - Shuaishuai Yang
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao 266071, China
| | - Hongguang Chen
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao 266071, China
| | - Jing Ji
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao 266071, China
| | - Lei Chen
- Department of Nutrition, School of Public Health, Qingdao University, Qingdao 266071, China
| | - Yuxin Zheng
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao 266071, China
| | - Dianke Yu
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao 266071, China
| | - Yanjie Zhao
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao 266071, China.
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Liu Y, Li J, Xiong Y, Tan C, Li C, Cao Y, Xie W, Deng Z. Long-term exposure to PM 2.5 leads to mitochondrial damage and differential expression of associated circRNA in rat hepatocytes. Sci Rep 2024; 14:11870. [PMID: 38789588 PMCID: PMC11126672 DOI: 10.1038/s41598-024-62748-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 05/21/2024] [Indexed: 05/26/2024] Open
Abstract
Fine particulate matter (PM2.5) is one of the four major causes of mortality globally. The objective of this study was to investigate the mechanism underlying liver injury following exposure to PM2.5 and the involvement of circRNA in its regulation. A PM2.5 respiratory tract exposure model was established in SPF SD male rats with a dose of 20 mg/kg, and liver tissue of rats in control group and PM2.5-exposed groups rats were detected. The results of ICP-MS showed that Mn, Cu and Ni were enriched in the liver. HE staining showed significant pathological changes in liver tissues of PM2.5-exposed group, transmission electron microscopy showed significant changes in mitochondrial structure of liver cells, and further mitochondrial function detection showed that the PM2.5 exposure resulted in an increase in cell reactive oxygen species content and a decrease in mitochondrial transmembrane potential, while the expression of SOD1 and HO-1 antioxidant oxidase genes was upregulated. Through high-throughput sequencing of circRNAs, we observed a significant down-regulation of 10 and an up-regulation of 17 circRNAs in the PM2.5-exposed groups. The functional enrichment and pathway analyses indicated that the differentially expressed circRNAs by PM2.5 exposure were primarily associated with processes related to protein ubiquitination, zinc ion binding, peroxisome function, and mitochondrial regulation. These findings suggest that the mechanism underlying liver injury induced by PM2.5-exposure may be associated with mitochondrial impairment resulting from the presence of heavy metal constituents. Therefore, this study provides a novel theoretical foundation for investigating the molecular mechanisms underlying liver injury induced by PM2.5 exposure.
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Affiliation(s)
- Ying Liu
- Department of Medical Laboratory, Hunan Provincial People's Hospital, the First Affiliated Hospital of Hunan Normal University, Changsha, 410005, People's Republic of China
| | - Jing Li
- Department of Medical Laboratory, Hunan Provincial People's Hospital, the First Affiliated Hospital of Hunan Normal University, Changsha, 410005, People's Republic of China
| | - Yican Xiong
- Department of Ophthalmology and Stomatology, Hunan Provincial People's Hospital, the First Affiliated Hospital of Hunan Normal University, Changsha, 410005, People's Republic of China
| | - Chaochao Tan
- Department of Medical Laboratory, Hunan Provincial People's Hospital, the First Affiliated Hospital of Hunan Normal University, Changsha, 410005, People's Republic of China
| | - Cunyan Li
- Department of Medical Laboratory, Hunan Provincial People's Hospital, the First Affiliated Hospital of Hunan Normal University, Changsha, 410005, People's Republic of China
| | - Youde Cao
- Department of Medical Laboratory, Hunan Provincial People's Hospital, the First Affiliated Hospital of Hunan Normal University, Changsha, 410005, People's Republic of China
| | - Wanying Xie
- Department of Medical Laboratory, Hunan Provincial People's Hospital, the First Affiliated Hospital of Hunan Normal University, Changsha, 410005, People's Republic of China
| | - Zhonghua Deng
- Department of Medical Laboratory, Hunan Provincial People's Hospital, the First Affiliated Hospital of Hunan Normal University, Changsha, 410005, People's Republic of China.
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Qin S, Zeng H, Wu Q, Li Q, Zeeshan M, Ye L, Jiang Y, Zhang R, Jiang X, Li M, Zhang R, Chen W, Chou WC, Dong GH, Li DC, Zeng XW. An integrative analysis of lipidomics and transcriptomics in various mouse brain regions in response to real-ambient PM 2.5 exposure. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 895:165112. [PMID: 37364843 DOI: 10.1016/j.scitotenv.2023.165112] [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: 03/20/2023] [Revised: 06/13/2023] [Accepted: 06/23/2023] [Indexed: 06/28/2023]
Abstract
Exposure to Fine particulate matter (PM2.5) has been associated with various neurological disorders. However, the underlying mechanisms of PM2.5-induced adverse effects on the brain are still not fully defined. Multi-omics analyses could offer novel insights into the mechanisms of PM2.5-induced brain dysfunction. In this study, a real-ambient PM2.5 exposure system was applied to male C57BL/6 mice for 16 weeks, and lipidomics and transcriptomics analysis were performed in four brain regions. The findings revealed that PM2.5 exposure led to 548, 283, 304, and 174 differentially expressed genes (DEGs), as well as 184, 89, 228, and 49 distinctive lipids in the hippocampus, striatum, cerebellum, and olfactory bulb, respectively. Additionally, in most brain regions, PM2.5-induced DEGs were mainly involved in neuroactive ligand-receptor interaction, cytokine-cytokine receptor interaction, and calcium signaling pathway, while PM2.5-altered lipidomic profile were primarily enriched in retrograde endocannabinoid signaling and biosynthesis of unsaturated fatty acids. Importantly, mRNA-lipid correlation networks revealed that PM2.5-altered lipids and DEGs were obviously enriched in pathways involving in bile acid biosynthesis, De novo fatty acid biosynthesis, and saturated fatty acids beta-oxidation in brain regions. Furthermore, multi-omics analyses revealed that the hippocampus was the most sensitive part to PM2.5 exposure. Specifically, dysregulation of Pla2g1b, Pla2g, Alox12, Alox15, and Gpx4 induced by PM2.5 were closely correlated to the disruption of alpha-linolenic acid, arachidonic acid and linoleic acid metabolism in the hippocampus. In summary, our findings highlight differential lipidomic and transcriptional signatures of various brain regions by real-ambient PM2.5 exposure, which will advance our understanding of potential mechanisms of PM2.5-induecd neurotoxicity.
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Affiliation(s)
- Shuangjian Qin
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Guangdong Provincial Engineering Technology Research Center of Environmental and Health risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Huixian Zeng
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Guangdong Provincial Engineering Technology Research Center of Environmental and Health risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Qizhen Wu
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Guangdong Provincial Engineering Technology Research Center of Environmental and Health risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Qingqing Li
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Guangdong Provincial Engineering Technology Research Center of Environmental and Health risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Mohammed Zeeshan
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Guangdong Provincial Engineering Technology Research Center of Environmental and Health risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Lizhu Ye
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Yue Jiang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Rui Zhang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Xinhang Jiang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Miao Li
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Rong Zhang
- Department of Toxicology, School of Public Health, Hebei Medical University, Shijiazhuang 050017, China
| | - Wen Chen
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Wei-Chun Chou
- Center for Environmental and Human Toxicology, Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL 32611, United States
| | - Guang-Hui Dong
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Guangdong Provincial Engineering Technology Research Center of Environmental and Health risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Dao-Chuan Li
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China.
| | - Xiao-Wen Zeng
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Guangdong Provincial Engineering Technology Research Center of Environmental and Health risk Assessment, Department of Occupational and Environmental Health, School of Public Health, Sun Yat-sen University, Guangzhou 510080, China.
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Gao YN, Min L, Yang X, Wang JQ, Zheng N. The coexistence of aflatoxin M1 and ochratoxin A induced intestinal barrier disruption via the regulation of key differentially expressed microRNAs and long non-coding RNAs in BALB/c mice. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 264:115428. [PMID: 37688864 DOI: 10.1016/j.ecoenv.2023.115428] [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: 05/25/2023] [Revised: 08/07/2023] [Accepted: 08/30/2023] [Indexed: 09/11/2023]
Abstract
Food safety can be seriously threatened by the existence of both aflatoxin M1 (AFM1) and ochratoxin A (OTA) in milk and corresponding products. The importance of intestine integrity in preserving human health is widely understood in vitro, but the fundamental processes by which AFM1 and OTA cause disruption of the intestinal barrier are as yet unknown, especially in vivo. Based on the analysis of the whole transcriptome of BALB/c mice, the competing endogenous RNA (ceRNA) regulation network was obtained in the current study. Each of 12 mice were separated into five treatments: saline solution treatment, 1.0% DMSO vehicle control treatment, 3.0 mg/kg b.w. individual AFM1 treatment (AFM1), 3.0 mg/kg b.w. individual OTA treatment (OTA), and combined mycotoxins treatment (AFM1 +OTA). The study period lasted 28 days. The jejunum tissue was collected for the histological assessment and whole transcriptome analysis, and the whole blood was collected, and determination of serum biochemical indicators. The phenotypic results demonstrated that AFM1 and OTA caused intestinal barrier disruption via an increased apoptosis level and decreased expression of tight junction (TJ) proteins. The ceRNA network demonstrated that AFM1 and OTA induced cell apoptosis through activating the expression of DUSP9 and suppressing the expression of PLA2G2D, which were regulated by differentially expressed microRNAs (DEmiRNAs) (miR-124-y, miR-194-z, miR-224-x, and miR-452-x) and differentially expressed long non-coding RNAs (DElncRNAs) (FUT8 and GPR31C). And AFM1 and OTA decreased TJ proteins via inhibiting the expression of PAK6, which was regulated by several important DEmiRNAs and DElncRNAs. These DE RNAs in intestinal integrity were involved in MAPK and Ras signaling pathway. Overall, our findings expand the current knowledge regarding the potential mechanisms of intestinal integrity disruption brought on by AFM1 and OTA in vivo.
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Affiliation(s)
- Ya-Nan Gao
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Li Min
- Ministry of Agriculture Key Laboratory of Animal Nutrition and Feed Science in South China, Guangdong Public Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Xue Yang
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jia-Qi Wang
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Nan Zheng
- Key Laboratory of Quality & Safety Control for Milk and Dairy Products of Ministry of Agriculture and Rural Affairs, Laboratory of Quality and Safety Risk Assessment for Dairy Products of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Zhang L, Shen Y, Wang Z, Li X, Xia W, Fan X, Su L, Wang D. Comprehensive analysis of exosomal circRNA, lncRNA, and mRNA profiles to identify the potential RNAs involved in the pathogenesis of venous malformation. J Oral Pathol Med 2023. [PMID: 36807323 DOI: 10.1111/jop.13416] [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: 10/22/2022] [Revised: 01/11/2023] [Accepted: 01/30/2023] [Indexed: 02/22/2023]
Abstract
BACKGROUND Venous malformation (VM) is a kind of congenital vascular anomaly with a high incidence of recurrence, detailed pathogenesis and standard treatment of VM still lack now. Increasing evidence showed exosomal RNA plays a pivotal role in various diseases. However, the underlying mechanism of VM based on the potential differentially exosomal RNAs remains unclear. METHODS Comparative high-throughput sequencing with serum exosomes from three VM patients and three healthy donors was used to explore differentially expressed (DE) circRNAs, DE lncRNAs, and DE mRNAs involving the formation of VM. We identified and verified DE circRNAs, DE lncRNAs, and DE mRNAs via qRT-PCR assay. We explored the potential functions of these exosomal DE non-coding RNAs via performing further Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis. Besides, circRNA/lncRNA-miRNA-mRNA linkages were also constructed to find their potential relationships in VM. RESULTS A total of 121 circRNAs, 53 lncRNAs, and 42 mRNAs (|log2 FC| ≥ 2.0, FDR <0.05, n = 3) were determined to be differentially expressed. QRT-PCR validated that these top-changed DE circRNAs, lncRNAs, and mRNAs had significant expression changes. Functional studies demonstrated that DE circRNAs play a pivotal role in thyroid hormone signaling pathway, DE lncRNAs function as a key regulator in MAPK signaling pathway and DE miRNAs participate in the process of hepatocellular carcinoma mostly. CONCLUSION Our study comprehensively depicted exosomal DE non-coding RNAs networks related to the pathogenesis of VM which can provide new insight into, a novel target for treating VM.
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Affiliation(s)
- Liming Zhang
- Vascular Anomaly Center, Department of Interventional Therapy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuchen Shen
- Vascular Anomaly Center, Department of Interventional Therapy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhenfeng Wang
- Vascular Anomaly Center, Department of Interventional Therapy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao Li
- Vascular Anomaly Center, Department of Interventional Therapy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Weiya Xia
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xindong Fan
- Vascular Anomaly Center, Department of Interventional Therapy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lixin Su
- Vascular Anomaly Center, Department of Interventional Therapy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Fengcheng Hospital of Feng Xian District, Fengcheng Branch, Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Deming Wang
- Vascular Anomaly Center, Department of Interventional Therapy, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Ran W, Liang N, Yuan R, Wang Z, Gao J. Identification of Potential Key circRNAs in Aged Mice With Postoperative Delirium. Front Mol Neurosci 2022; 15:836534. [PMID: 35493320 PMCID: PMC9047966 DOI: 10.3389/fnmol.2022.836534] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/01/2022] [Indexed: 11/24/2022] Open
Abstract
Postoperative delirium (POD) is a common postoperative complication in elderly patients and seriously affects postoperative recovery. The exact mechanism of POD is still unclear. Therefore, it is necessary to explore the mechanism of POD in transcriptional regulation. At present, circRNAs have been proven to play an important role in a variety of mental health and cognitive disorders, such as Alzheimer’s disease, depression and schizophrenia. To reveal the effect of circRNA on POD, we used microarray to analyze the differential expression profiles of circRNAs in the hippocampus of 12-month-old mice between the tibial fracture and control groups. A total of 1,4236 circRNAs were identified. Compared with the control group, there were 500 circRNAs with increased expression and 187 with decreased expression. The accuracy of the microarray data was further verified by qRT–PCR. Finally, GO enrichment and KEGG pathway analyses indicated that changes in axon orientation, ubiquitin-mediated proteolysis, glutamate synapses, the estrogen signaling pathway, the RAS signaling pathway and other systems may be important potential pathological mechanisms in the progression of POD. In particular, we found that the HOMER1 gene and its transcript mmu_circRNA_26701 are specifically expressed in the glutamate synapse, which may provide new clues and intervention targets for the progression of this refractory disease.
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Zhang P, Rasheed M, Liang J, Wang C, Feng L, Chen Z. Emerging Potential of Exosomal Non-coding RNA in Parkinson’s Disease: A Review. Front Aging Neurosci 2022; 14:819836. [PMID: 35360206 PMCID: PMC8960858 DOI: 10.3389/fnagi.2022.819836] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/07/2022] [Indexed: 12/13/2022] Open
Abstract
Exosomes are extracellular vesicles that are released by cells and circulate freely in body fluids. Under physiological and pathological conditions, they serve as cargo for various biological substances such as nucleotides (DNA, RNA, ncRNA), lipids, and proteins. Recently, exosomes have been revealed to have an important role in the pathophysiology of several neurodegenerative illnesses, including Parkinson’s disease (PD). When secreted from damaged neurons, these exosomes are enriched in non-coding RNAs (e.g., miRNAs, lncRNAs, and circRNAs) and display wide distribution characteristics in the brain and periphery, bridging the gap between normal neuronal function and disease pathology. However, the current status of ncRNAs carried in exosomes regulating neuroprotection and PD pathogenesis lacks a systematic summary. Therefore, this review discussed the significance of ncRNAs exosomes in maintaining the normal neuron function and their pathogenic role in PD progression. Additionally, we have emphasized the importance of ncRNAs exosomes as potential non-invasive diagnostic and screening agents for the early detection of PD. Moreover, bioengineered exosomes are proposed to be used as drug carriers for targeted delivery of RNA interference molecules across the blood-brain barrier without immune system interference. Overall, this review highlighted the diverse characteristics of ncRNA exosomes, which may aid researchers in characterizing future exosome-based biomarkers for early PD diagnosis and tailored PD medicines.
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Affiliation(s)
- Peng Zhang
- School of Mechanical Engineering and Automation, Beihang University, Beijing, China
| | - Madiha Rasheed
- School of Life Sciences, Beijing Institute of Technology, Beijing, China
| | - Junhan Liang
- School of Life Sciences, Beijing Institute of Technology, Beijing, China
| | - Chaolei Wang
- School of Life Sciences, Beijing Institute of Technology, Beijing, China
| | - Lin Feng
- School of Mechanical Engineering and Automation, Beihang University, Beijing, China
- Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing, China
- *Correspondence: Lin Feng,
| | - Zixuan Chen
- School of Life Sciences, Beijing Institute of Technology, Beijing, China
- Zixuan Chen,
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9
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Liang M, Zhang Y, Gan S, Liu Y, Li H, Liu Q, Liu H, Zhou Z, Wu H, Chen G, Wu Z. Identifying lncRNA- and Transcription Factor-Associated Regulatory Networks in the Cortex of Rats With Deep Hypothermic Circulatory Arrest. Front Genet 2021; 12:746757. [PMID: 34976005 PMCID: PMC8719624 DOI: 10.3389/fgene.2021.746757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 11/30/2021] [Indexed: 11/19/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) are involved in the mechanism underlying cerebral dysfunction after deep hypothermic circulatory arrest (DHCA), although the exact details have not been elucidated. To explore the expression profiles of lncRNAs and miRNAs in DHCA cerebral injury, we determined the lncRNA, miRNA and mRNA expression profiles in the cerebral cortex of DHCA and sham rats. First, a rat model of DHCA was established, and high-throughput sequencing was performed to analyze the differentially expressed RNAs (DERNAs). Then, the principal functions of the significantly deregulated genes were identified using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Expression networks (lncRNAs-miRNAs-mRNAs and transcription factors (TFs)-miRNAs-mRNAs) were also established. Finally, the expression of DERNAs was confirmed by quantitative real-time PCR (RT-qPCR). We identified 89 lncRNAs, 45 miRNAs and 59 mRNAs between the DHCA and sham groups and constructed a comprehensive competitive endogenous RNAs (ceRNAs) network. A TF-miRNA-mRNA regulatory network was also established. Finally, we predicted that Lcorl-miR-200a-3p-Ttr, BRD4-Ccl2 and Ep300-miR-200b-3p-Tmem72 may participate in the pathogenesis of DHCA cerebral injury.
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Affiliation(s)
- Mengya Liang
- Department of Cardiac Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Yi Zhang
- NHC Key Laboratory of Assisted Circulation, Sun Yat-Sen University, Guangzhou, China
| | - Shuangjiao Gan
- NHC Key Laboratory of Assisted Circulation, Sun Yat-Sen University, Guangzhou, China
| | - Yunqi Liu
- Department of Cardiac Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Huayang Li
- NHC Key Laboratory of Assisted Circulation, Sun Yat-Sen University, Guangzhou, China
| | - Quan Liu
- NHC Key Laboratory of Assisted Circulation, Sun Yat-Sen University, Guangzhou, China
| | - Haoliang Liu
- NHC Key Laboratory of Assisted Circulation, Sun Yat-Sen University, Guangzhou, China
| | - Zhuoming Zhou
- NHC Key Laboratory of Assisted Circulation, Sun Yat-Sen University, Guangzhou, China
| | - Huawei Wu
- Department of Neurobiology, Physiology and Behavior, College of Biological Sciences, University of California, Davis, CA, United States
| | - Guangxian Chen
- Department of Cardiac Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Zhongkai Wu
- Department of Cardiac Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
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10
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Protein profiling reveals potential isomiR-associated cross-talks among RNAs in cholangiocarcinoma. Comput Struct Biotechnol J 2021; 19:5722-5734. [PMID: 34745457 PMCID: PMC8551523 DOI: 10.1016/j.csbj.2021.10.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 09/29/2021] [Accepted: 10/10/2021] [Indexed: 12/04/2022] Open
Abstract
Protein profiling identified crucial genes that were used to screen related ncRNAs. Both miRNAs and isomiRs were involved in coding-non-coding RNA regulatory network. IsomiR-associated ceRNA networks implied the complex interactions among RNAs.
Cholangiocarcinomas (CCAs) are tumors that arise from the cholangiocytes. Although some genes have been shown with important roles in pathological process, interactions or cross-talks among different RNAs are important to understand the detailed molecular mechanisms in cancer development, especially discussing cross-talks among isomiRs and other RNAs. Herein, to characterize crucial genes in CCA, the protein expression profile was performed to survey potential crucial mRNAs and related non-coding RNAs (ncRNAs) in mRNA-ncRNA network, mainly including miRNAs/isomiRs and lncRNAs. Deregulated mRNAs were firstly obtained if consistent expression patterns were found at protein and mRNA levels, and related miRNAs/isomiRs were screened according to regulatory relationships. Diverse isomiRs from a given miRNA locus also contributed to interactions between the small RNAs and target mRNAs, and miRNAs were further used to survey related lncRNAs to expand the interactions. Thus, several groups of RNAs were constructed as candidate competitive endogenous RNA (ceRNA) networks. Finally, we found that RAB11FIP1:miR-101-3p:MIR3142HG may be a potential ceRNA network, and the interactions among them may be more complex due to variety of isomiRs. Simultaneously, RAB11FIP1 and miR-194-5p were also detected other related lncRNAs (FBXL19-AS1, SNHG1 and PVT1) that may be crucial in coding-non-coding RNA regulatory network. Our results show that diverse isomiRs with sequence and expression heterogeneities contribute to ceRNA regulatory network that may have crucial roles in CCA, which will expand our understanding of interactions among diverse RNAs and their contributions in cancer development.
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Key Words
- BLCA, bladder urothelial carcinoma
- BRCA, breast invasive carcinoma
- CHOL, cholangiocarcinoma
- COAD, colon adenocarcinoma
- Cholangiocarcinoma (CCA)
- Cross-talk
- ESCA, esophageal carcinoma
- HNSC, head and neck squamous cell carcinoma
- KICH, kidney chromophobe
- KIRC, Kidney renal clear cell carcinoma
- KIRP, kidney renal papillary cell carcinoma
- LIHC, liver hepatocellular carcinoma
- LUAD, lung adenocarcinoma
- LUSC, lung squamous cell carcinoma
- Long non-coding RNA (lncRNA)
- PRAD, prostate adenocarcinoma
- Protein profiling
- STAD, stomach adenocarcinoma
- THCA, thyroid carcinoma
- UCEC, uterine corpus endometrial carcinoma
- isomiR
- microRNA (miRNA)
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