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Zhang S, Niu Q, Zong W, Song Q, Tian S, Wang J, Liu J, Zhang H, Wang Z, Li B. Endotype-driven Co-module mechanisms of danhong injection in the Co-treatment of cardiovascular and cerebrovascular diseases: A modular-based drug and disease integrated analysis. JOURNAL OF ETHNOPHARMACOLOGY 2024; 331:118287. [PMID: 38705429 DOI: 10.1016/j.jep.2024.118287] [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: 12/13/2023] [Revised: 04/18/2024] [Accepted: 05/02/2024] [Indexed: 05/07/2024]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Cardiovascular and cerebrovascular diseases are the leading causes of death worldwide and interact closely with each other. Danhong Injection (DHI) is a widely used preparation for the co-treatment of brain and heart diseases (CTBH). However, the underlying molecular endotype mechanisms of DHI in the CTBH remain unclear. AIM OF THIS STUDY To elucidate the underlying endotype mechanisms of DHI in the CTBH. MATERIALS AND METHODS In this study, we proposed a modular-based disease and drug-integrated analysis (MDDIA) strategy for elucidating the systematic CTBH mechanisms of DHI using high-throughput transcriptome-wide sequencing datasets of DHI in the treatment of patients with stable angina pectoris (SAP) and cerebral infarction (CI). First, we identified drug-targeted modules of DHI and disease modules of SAP and CI based on the gene co-expression networks of DHI therapy and the protein-protein interaction networks of diseases. Moreover, module proximity-based topological analyses were applied to screen CTBH co-module pairs and driver genes of DHI. At the same time, the representative driver genes were validated via in vitro experiments on hypoxia/reoxygenation-related cardiomyocytes and neuronal cell lines of H9C2 and HT22. RESULTS Seven drug-targeted modules of DHI and three disease modules of SAP and CI were identified by co-expression networks. Five modes of modular relationships between the drug and disease modules were distinguished by module proximity-based topological analyses. Moreover, 13 targeted module pairs and 17 driver genes associated with DHI in the CTBH were also screened. Finally, the representative driver genes AKT1, EDN1, and RHO were validated by in vitro experiments. CONCLUSIONS This study, based on clinical sequencing data and modular topological analyses, integrated diseases and drug targets. The CTBH mechanism of DHI may involve the altered expression of certain driver genes (SRC, STAT3, EDN1, CYP1A1, RHO, RELA) through various enriched pathways, including the Wnt signaling pathway.
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Affiliation(s)
- Siqi Zhang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Qikai Niu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Wenjing Zong
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Qi Song
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Siwei Tian
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jingai Wang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jun Liu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Huamin Zhang
- Institute of Basic Theory for Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Zhong Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Bing Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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Zeng Z, Hu J, Xiao G, Liu Y, Jia D, Wu G, Xie C, Li S, Bi X. Integrating network toxicology and molecular docking to explore the toxicity of the environmental pollutant butyl hydroxyanisole: An example of induction of chronic urticaria. Heliyon 2024; 10:e35409. [PMID: 39170477 PMCID: PMC11336633 DOI: 10.1016/j.heliyon.2024.e35409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 07/08/2024] [Accepted: 07/29/2024] [Indexed: 08/23/2024] Open
Abstract
The study aimed to comprehensively investigate environmental pollutants' potential toxicity and underlying molecular mechanisms, focusing on chronic urticaria (CU) induced by butylated hydroxyanisole (BHA) exposure, further drawing public awareness regarding the potential risks of environmental pollutants, applying ChEMBL, STITCH, and SwissTargetPrediction databases to predict the targets of BHA, CTD, GeneCards, and OMIM databases to collect the relevant targets of CU. Ultimately, we identified 81 potential targets of BHA-induced CU and extracted 31 core targets, including TNF, SRC, CASP3, BCL2, IL2, and MMP9. GO and KEGG enrichment analyses revealed that these core targets were predominantly involved in cancer signaling, estrogen and endocrine resistance pathways. Furthermore, molecular docking confirmed the ability of BHA to bind with core targets. The onset and development of CU may result from BHA by affecting multiple immune signaling pathways. Our study elucidated the molecular mechanisms of BHA toxicity and its role in CU induction, providing the basis for preventing and treating chronic urticaria associated with environmental BHA exposure.
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Affiliation(s)
- Zhihao Zeng
- School of the Fifth Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Jiaoting Hu
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Guanlin Xiao
- Guangdong Provincial Engineering and Technology Research Institute of Traditional Chinese Medicine/Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese Medicine, Guangzhou, 510095, China
| | - Yanchang Liu
- School of the Fifth Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Dezheng Jia
- School of the Fifth Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Guangying Wu
- School of the Fifth Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Canhui Xie
- School of the Fifth Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Sumei Li
- Guangdong Provincial Engineering and Technology Research Institute of Traditional Chinese Medicine/Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese Medicine, Guangzhou, 510095, China
| | - Xiaoli Bi
- Guangdong Provincial Engineering and Technology Research Institute of Traditional Chinese Medicine/Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese Medicine, Guangzhou, 510095, China
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Ou Z, Cheng Y, Ma H, Chen K, Lin Q, Chen J, Guo R, Huang Z, Cheng Q, Alaeiilkhchi N, Zhu Q, Huang Z, Jiang H. miR-223 accelerates lipid droplets clearance in microglia following spinal cord injury by upregulating ABCA1. J Transl Med 2024; 22:659. [PMID: 39010173 PMCID: PMC11247820 DOI: 10.1186/s12967-024-05480-5] [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: 01/30/2024] [Accepted: 07/03/2024] [Indexed: 07/17/2024] Open
Abstract
BACKGROUND Spinal cord injury (SCI) is characterized by extensive demyelination and inflammatory responses. Facilitating the clearance of lipid droplets (LDs) within microglia contributes to creating a microenvironment that favors neural recovery and provides essential materials for subsequent remyelination. Therefore, investigating MicroRNAs (miRNAs) that regulate lipid homeostasis after SCI and elucidating their potential mechanisms in promoting LDs clearance in microglia have become focal points of SCI research. METHODS We established a subacute C5 hemicontusion SCI model in mice and performed transcriptomic sequencing on the injury epicenter to identify differentially expressed genes and associated pathways. Confocal imaging was employed to observe LDs accumulation. Multi-omics analyses were conducted to identify differentially expressed mRNA and miRNA post-SCI. Pathway enrichment analysis and protein-protein interaction network construction were performed using bioinformatics methods, revealing miR-223-Abca1 as a crucial miRNA-mRNA pair in lipid metabolism regulation. BV2 microglia cell lines overexpressing miR-223 were engineered, and immunofluorescence staining, western blot, and other techniques were employed to assess LDs accumulation, relevant targets, and inflammatory factor expression, confirming its role in regulating lipid homeostasis in microglia. RESULTS Histopathological results of our hemicontusion SCI model confirmed LDs aggregation at the injury epicenter, predominantly within microglia. Our transcriptomic analysis during the subacute phase of SCI in mice implicated ATP-binding cassette transporter A1 (Abca1) as a pivotal gene in lipid homeostasis, cholesterol efflux and microglial activation. Integrative mRNA-miRNA multi-omics analysis highlighted the crucial role of miR-223 in the neuroinflammation process following SCI, potentially through the regulation of lipid metabolism via Abca1. In vitro experiments using BV2 cells overexpressing miR-223 demonstrated that elevated levels of miR-223 enhance ABCA1 expression in myelin debris and LPS-induced BV2 cells. This promotes myelin debris degradation and LDs clearance, and induces a shift toward an anti-inflammatory M2 phenotype. CONCLUSIONS In summary, our study unveils the critical regulatory role of miR-223 in lipid homeostasis following SCI. The mechanism by which this occurs involves the upregulation of ABCA1 expression, which facilitates LDs clearance and myelin debris degradation, consequently alleviating the lipid burden, and inhibiting inflammatory polarization of microglia. These findings suggest that strategies to enhance miR-223 expression and target ABCA1, thereby augmenting LDs clearance, may emerge as appealing new clinical targets for SCI treatment.
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Affiliation(s)
- Zhilin Ou
- Division of Spine Surgery, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Yongquan Cheng
- Division of Spine Surgery, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Hao Ma
- Division of Spine Surgery, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Kai Chen
- The First School of Clinical Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Qiong Lin
- School of Anesthesiology, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Jiayu Chen
- Division of Spine Surgery, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Ruqin Guo
- Division of Spine Surgery, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Zhiping Huang
- Division of Spine Surgery, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Qixian Cheng
- Division of Spine Surgery, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Nima Alaeiilkhchi
- International Collaboration on Repair Discoveries (ICORD), Blusson Spinal Cord Centre, University of British Columbia, Vancouver, Canada
| | - Qingan Zhu
- Division of Spine Surgery, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Zucheng Huang
- Division of Spine Surgery, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China.
| | - Hui Jiang
- Division of Spine Surgery, Department of Orthopaedics, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China.
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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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Mahajan A, Hong J, Krukovets I, Shin J, Tkachenko S, Espinosa-Diez C, Owens GK, Cherepanova OA. Integrative analysis of the lncRNA-miRNA-mRNA interactions in smooth muscle cell phenotypic transitions. Front Genet 2024; 15:1356558. [PMID: 38660676 PMCID: PMC11039880 DOI: 10.3389/fgene.2024.1356558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/25/2024] [Indexed: 04/26/2024] Open
Abstract
Objectives: We previously found that the pluripotency factor OCT4 is reactivated in smooth muscle cells (SMC) in human and mouse atherosclerotic plaques and plays an atheroprotective role. Loss of OCT4 in SMC in vitro was associated with decreases in SMC migration. However, molecular mechanisms responsible for atheroprotective SMC-OCT4-dependent effects remain unknown. Methods: Since studies in embryonic stem cells demonstrated that OCT4 regulates long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), making them candidates for OCT4 effect mediators, we applied an in vitro approach to investigate the interactions between OCT4-regulated lncRNAs, mRNAs, and miRNAs in SMC. We used OCT4 deficient mouse aortic SMC (MASMC) treated with the pro-atherogenic oxidized phospholipid POVPC, which, as we previously demonstrated, suppresses SMC contractile markers and induces SMC migration. Differential expression of lncRNAs, mRNAs, and miRNAs was obtained by lncRNA/mRNA expression array and small-RNA microarray. Long non-coding RNA to mRNA associations were predicted based on their genomic proximity and association with vascular diseases. Given a recently discovered crosstalk between miRNA and lncRNA, we also investigated the association of miRNAs with upregulated/downregulated lncRNA-mRNA pairs. Results: POVPC treatment in SMC resulted in upregulating genes related to the axon guidance and focal adhesion pathways. Knockdown of Oct4 resulted in differential regulation of pathways associated with phagocytosis. Importantly, these results were consistent with our data showing that OCT4 deficiency attenuated POVPC-induced SMC migration and led to increased phagocytosis. Next, we identified several up- or downregulated lncRNA associated with upregulation of the specific mRNA unique for the OCT4 deficient SMC, including upregulation of ENSMUST00000140952-Hoxb5/6 and ENSMUST00000155531-Zfp652 along with downregulation of ENSMUST00000173605-Parp9 and, ENSMUST00000137236-Zmym1. Finally, we found that many of the downregulated miRNAs were associated with cell migration, including miR-196a-1 and miR-10a, targets of upregulated ENSMUST00000140952, and miR-155 and miR-122, targets of upregulated ENSMUST00000155531. Oppositely, the upregulated miRNAs were anti-migratory and pro-phagocytic, such as miR-10a/b and miR-15a/b, targets of downregulated ENSMUST00000173605, and miR-146a/b and miR-15b targets of ENSMUST00000137236. Conclusion: Our integrative analyses of the lncRNA-miRNA-mRNA interactions in SMC indicated novel potential OCT4-dependent mechanisms that may play a role in SMC phenotypic transitions.
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Affiliation(s)
- Aatish Mahajan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Junyoung Hong
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Irene Krukovets
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Junchul Shin
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Svyatoslav Tkachenko
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, United States
| | - Cristina Espinosa-Diez
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, United States
| | - Gary K. Owens
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, United States
| | - Olga A. Cherepanova
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
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Li LD, Zhou Y, Shi SF. Identification and characterization of biomarkers associated with endoplasmic reticulum protein processing in cerebral ischemia-reperfusion injury. PeerJ 2024; 12:e16707. [PMID: 38188159 PMCID: PMC10768662 DOI: 10.7717/peerj.16707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 11/30/2023] [Indexed: 01/09/2024] Open
Abstract
Background Cerebral ischemia (CI), ranking as the second leading global cause of death, is frequently treated by reestablishing blood flow and oxygenation. Paradoxically, this reperfusion can intensify tissue damage, leading to CI-reperfusion injury. This research sought to uncover biomarkers pertaining to protein processing in the endoplasmic reticulum (PER) during CI-reperfusion injury. Methods We utilized the Gene Expression Omnibus (GEO) dataset GSE163614 to discern differentially expressed genes (DEGs) and single out PER-related DEGs. The functions and pathways of these PER-related DEGs were identified via Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Core genes were pinpointed through protein-protein interaction (PPI) networks. Subsequent to this, genes with diagnostic relevance were distinguished using external validation datasets. A single-sample gene-set enrichment analysis (ssGSEA) was undertaken to pinpoint genes with strong associations to hypoxia and apoptosis, suggesting their potential roles as primary inducers of apoptosis in hypoxic conditions during ischemia-reperfusion injuries. Results Our study demonstrated that PER-related genes, specifically ADCY5, CAMK2A, PLCB1, NTRK2, and DLG4, were markedly down-regulated in models, exhibiting a robust association with hypoxia and apoptosis. Conclusion The data indicates that ADCY5, CAMK2A, PLCB1, NTRK2, and DLG4 could be pivotal genes responsible for triggering apoptosis in hypoxic environments during CI-reperfusion injury.
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Affiliation(s)
- Liang-da Li
- Department of Neurology, The People’s Hospital Affiliated to Ningbo University, Ningbo, Zhejiang, China
| | - Yue Zhou
- Department of Neurology, The People’s Hospital Affiliated to Ningbo University, Ningbo, Zhejiang, China
| | - Shan-fen Shi
- Department of Rheumatology, The People’s Hospital Affiliated to Ningbo University, Ningbo, Zhejiang, China
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Molecular docking, network pharmacology and experimental verification to explore the mechanism of Wulongzhiyangwan in the treatment of pruritus. Sci Rep 2023; 13:361. [PMID: 36611103 PMCID: PMC9825397 DOI: 10.1038/s41598-023-27593-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
Wulongzhiyangwan (WLZYW) is a Chinese prescription medicine for the treatment of pruritus, but its mechanism has not been clarified. The purpose of this study was to explore the mechanism of WLZYW in pruritus through network pharmacology analysis and experimental validation. The active components and corresponding targets of WLZYW were obtained from the Traditional Chinese Medicine Systematic Pharmacology (TCMSP) database. Pruritus-related targets were obtained from the GeneCards, TTD (Therapeutic Target Database), and DrugBank databases. The key compounds, core targets, main biological processes and signaling pathways related to WLZYW were identified by constructing and analyzing related networks. The binding affinity between WLZYW components and core targets was validated by AutoDock Vina software. In this study, RBL-2H3 cells were used to construct a degranulation model to simulate histamine-dependent pruritus. 10 chemical constituents, 235 targets and 3606 pruritus-related targets of WLZYW were obtained. Subsequently, 26 core targets were identified through analysis, VEGFA and AKT1 were the main candidates. A pathway enrichment analysis showed that overlapping targets were significantly enriched in the PI3K/AKT signaling pathway. A molecular docking analysis revealed tight binding of VEGF to three core compounds, kaempferol, luteolin and quercetin. Experiments showed that WZLYW inhibited mast cell degranulation, regulated VEGFa mRNA and protein expression levels by inhibiting PI3K/AKT and ERK1/2 signaling pathway activation. The mechanism of WZLYW in pruritus may be regulating VEGFa expression. Network pharmacology assays suggested that WLZYW downregulates VEGFa expression by regulating the PI3K/AKT and ERK1/2 signaling pathways in pruritis treatment.
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Hao Y, Xu X, Wang Y, Jin F, Tang L, Zheng W, Zhang H, He Z. Comprehensive analysis of immune-related biomarkers and pathways in intracerebral hemorrhage using weighted gene co-expression network analysis and competing endogenous ribonucleic acid. Front Mol Neurosci 2022; 15:955818. [PMID: 36226317 PMCID: PMC9549172 DOI: 10.3389/fnmol.2022.955818] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 08/01/2022] [Indexed: 11/23/2022] Open
Abstract
The immune response is an important part of secondary brain injury following intracerebral hemorrhage (ICH), and is related to neurological deficits and prognosis. The mechanisms underlying the immune response and inflammation are of great significance for brain injury and potential functional restoration; however, the immune-related biomarkers and competing endogenous ribonucleic acid (RNA) (ceRNA) networks in the peripheral blood of ICH patients have not yet been constructed. We collected the peripheral blood from ICH patients and controls to assess their ceRNA profiles using LCHuman ceRNA microarray, and to verify their expression with qRT-PCR. Two-hundred-eleven DElncRNAs and one-hundred-one DEmRNAs were detected in the ceRNA microarray of ICH patients. The results of functional enrichment analysis showed that the immune response was an important part of the pathological process of ICH. Twelve lncRNAs, ten miRNAs, and seven mRNAs were present in our constructed immune-related ceRNA network, combining weighted gene co-expression network analysis (WGCNA). Our study was the first to establish the network of the immune-related ceRNAs derived from WGCNA, and to identify leukemia inhibitory factor (LIF) and B cell lymphoma 2-like 13 (BCL2L13) as pivotal immune-related biomarkers in the peripheral blood of ICH patients, which are likely associated with PI3K-Akt, the MAPK signaling pathway, and oxidative phosphorylation. The MOXD2P-miR-211-3p -LIF and LINC00299-miR-198-BCL2L13 axes were indicated to participate in the immune regulatory mechanism of ICH. The goal of our study was to offer innovative insights into the underlying immune regulatory mechanism and to identify possible immune intervention targets for ICH.
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Affiliation(s)
- Yuehan Hao
- Department of Neurology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xiaoxue Xu
- Department of Neurology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Yuye Wang
- Department of Neurology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Feng Jin
- Department of Neurology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Ling Tang
- Department of Neurology, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Wenxu Zheng
- Department of Geriatric, Dalian Friendship Hospital, Dalian, China
| | - Heyu Zhang
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Diagnosis and Treatment of Major Neurological Diseases, National Key Clinical Department and Key Discipline of Neurology, Guangzhou, China
- *Correspondence: Heyu Zhang,
| | - Zhiyi He
- Department of Neurology, The First Affiliated Hospital of China Medical University, Shenyang, China
- Zhiyi He,
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Riffo-Campos AL, Perez-Hernandez J, Martinez-Arroyo O, Ortega A, Flores-Chova A, Redon J, Cortes R. Biofluid Specificity of Long Non-Coding RNA Profile in Hypertension: Relevance of Exosomal Fraction. Int J Mol Sci 2022; 23:ijms23095199. [PMID: 35563588 PMCID: PMC9101961 DOI: 10.3390/ijms23095199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 11/16/2022] Open
Abstract
Non-coding RNA (ncRNA)-mediated targeting of various genes regulates the molecular mechanisms of the pathogenesis of hypertension (HTN). However, very few circulating long ncRNAs (lncRNAs) have been reported to be altered in essential HTN. The aim of our study was to identify a lncRNA profile in plasma and plasma exosomes associated with urinary albumin excretion in HTN by next-generation sequencing and to assess biological functions enriched in response to albuminuria using GO and KEGG analysis. Plasma exosomes showed higher diversity and fold change of lncRNAs than plasma, and low transcript overlapping was found between the two biofluids. Enrichment analysis identified different biological pathways regulated in plasma or exosome fraction, which were implicated in fatty acid metabolism, extracellular matrix, and mechanisms of sorting ncRNAs into exosomes, while plasma pathways were implicated in genome reorganization, interference with RNA polymerase, and as scaffolds for assembling transcriptional regulators. Our study found a biofluid specific lncRNA profile associated with albuminuria, with higher diversity in exosomal fraction, which identifies several potential targets that may be utilized to study mechanisms of albuminuria and cardiovascular damage.
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Affiliation(s)
- Angela L. Riffo-Campos
- Millennium Nucleus on Sociomedicine (SocioMed) and Vicerrectoría Académica, Universidad de La Frontera, Temuco 4780000, Chile;
- Department of Computer Science, ETSE, University of Valencia, 46010 Valencia, Spain
| | - Javier Perez-Hernandez
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (J.P.-H.); (O.M.-A.); (A.F.-C.); (J.R.)
- Department of Nutrition and Health, Valencian International University (VIU), 46002 Valencia, Spain
- T-Cell Tolerance, Biomarkers and Therapies in Type 1 Diabetes Team, Institut Cochin CNRS, INSERM, Université de Paris Cité, F-75014 Paris, France
| | - Olga Martinez-Arroyo
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (J.P.-H.); (O.M.-A.); (A.F.-C.); (J.R.)
| | - Ana Ortega
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (J.P.-H.); (O.M.-A.); (A.F.-C.); (J.R.)
- Correspondence: (A.O.); (R.C.); Tel.: +34-961973517 (R.C.)
| | - Ana Flores-Chova
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (J.P.-H.); (O.M.-A.); (A.F.-C.); (J.R.)
| | - Josep Redon
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (J.P.-H.); (O.M.-A.); (A.F.-C.); (J.R.)
- Internal Medicine Unit, Hospital Clinico Universitario, 46010 Valencia, Spain
- CIBER of Physiopathology of Obesity and Nutrition (CIBEROBN), Institute of Health Carlos III, Minister of Health, 28029 Madrid, Spain
| | - Raquel Cortes
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (J.P.-H.); (O.M.-A.); (A.F.-C.); (J.R.)
- Correspondence: (A.O.); (R.C.); Tel.: +34-961973517 (R.C.)
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Wang S, Sun Y, Hu S, Lou C, Pan YB. Construction of a lncRNA-associated competing endogenous RNA regulatory network after traumatic brain injury in mouse. Mol Brain 2022; 15:40. [PMID: 35501920 PMCID: PMC9063179 DOI: 10.1186/s13041-022-00925-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 04/19/2022] [Indexed: 12/19/2022] Open
Abstract
Traumatic brain injury (TBI) is a major public health problem worldwide which causes high mortality and disability. Functioning as microRNA (miRNA) sponges, long non-coding RNA (lncRNA) regulates the expression of protein-coding genes in a competing endogenous RNA (ceRNA) network. However, the lncRNA-associated ceRNA in TBI remains unclear. In this study, we processed the raw SRR files of mice cortex samples of sham injury (n = 3) and TBI groups (n = 3) to count files. Then, the expression profiles of lncRNAs and mRNAs were identified, and 86 differentially expressed (DE) lncRNAs and 1201 DEmRNAs between sham and TBI groups were identified. The DEmRNAs were used to perform enrichment analyses. Next, a lncRNA-miRNA-mRNA regulatory ceRNA network was constructed. The network consisted of 23 mRNAs, 5 miRNAs and 2 lncRNAs. The expression alternations of the 5 miRNAs were validated via qRT-PCR. The subnetwork of hub lncRNA Neat1 was extracted. We identified a potential inflammatory associated regulatory axis: Neat1/miR-31-5p/Myd88 axis. The PPI network based on DEmRNA involved in ceRNA network was constructed PPI networks to identify the hub genes. Finally, DElncRNAs and DEmRNAs were selected randomly and validated by qRT-PCR. In conclusion, with the lncRNA-miRNA-mRNA ceRNA network provided above, we can improve our understanding of the regulatory mechanisms and interaction among lncRNAs, miRNAs and mRNAs in TBI process.
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Riffo-Campos AL, Perez-Hernandez J, Ortega A, Martinez-Arroyo O, Flores-Chova A, Redon J, Cortes R. Exosomal and Plasma Non-Coding RNA Signature Associated with Urinary Albumin Excretion in Hypertension. Int J Mol Sci 2022; 23:ijms23020823. [PMID: 35055008 PMCID: PMC8775608 DOI: 10.3390/ijms23020823] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/03/2022] [Accepted: 01/11/2022] [Indexed: 12/13/2022] Open
Abstract
Non-coding RNA (ncRNA), released into circulation or packaged into exosomes, plays important roles in many biological processes in the kidney. The purpose of the present study is to identify a common ncRNA signature associated with early renal damage and its related molecular pathways. Three individual libraries (plasma and urinary exosomes, and total plasma) were prepared from each hypertensive patient (with or without albuminuria) for ncRNA sequencing analysis. Next, an RNA-based transcriptional regulatory network was constructed. The three RNA biotypes with the greatest number of differentially expressed transcripts were long-ncRNA (lncRNA), microRNA (miRNA) and piwi-interacting RNA (piRNAs). We identified a common 24 ncRNA molecular signature related to hypertension-associated urinary albumin excretion, of which lncRNAs were the most representative. In addition, the transcriptional regulatory network showed five lncRNAs (LINC02614, BAALC-AS1, FAM230B, LOC100505824 and LINC01484) and the miR-301a-3p to play a significant role in network organization and targeting critical pathways regulating filtration barrier integrity and tubule reabsorption. Our study found an ncRNA profile associated with albuminuria, independent of biofluid origin (urine or plasma, circulating or in exosomes) that identifies a handful of potential targets, which may be utilized to study mechanisms of albuminuria and cardiovascular damage.
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Affiliation(s)
- Angela L. Riffo-Campos
- Millennium Nucleus on Sociomedicine (SocioMed) and Vicerrectoría Académica, Universidad de La Frontera, Temuco 4780000, Chile;
- Department of Computer Science, ETSE, University of Valencia, 46010 Valencia, Spain
| | - Javier Perez-Hernandez
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (J.P.-H.); (A.O.); (O.M.-A.); (A.F.-C.); (J.R.)
- Departament of Nutrition and Health, Valencian International University (VIU), 46010 Valencia, Spain
- T-Cell Tolerance, Biomarkers and Therapies in Type 1 Diabetes Team, Institut Cochin, CNRS, INSERM, Université de Paris, 75014 Paris, France
| | - Ana Ortega
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (J.P.-H.); (A.O.); (O.M.-A.); (A.F.-C.); (J.R.)
| | - Olga Martinez-Arroyo
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (J.P.-H.); (A.O.); (O.M.-A.); (A.F.-C.); (J.R.)
| | - Ana Flores-Chova
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (J.P.-H.); (A.O.); (O.M.-A.); (A.F.-C.); (J.R.)
| | - Josep Redon
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (J.P.-H.); (A.O.); (O.M.-A.); (A.F.-C.); (J.R.)
- Internal Medicine Unit, Hospital Clinico Universitario, 46010 Valencia, Spain
- CIBER of Physiopathology of Obesity and Nutrition (CIBEROBN), Institute of Health Carlos III, Minister of Health, 28029 Madrid, Spain
| | - Raquel Cortes
- Cardiometabolic and Renal Risk Research Group, INCLIVA Biomedical Research Institute, 46010 Valencia, Spain; (J.P.-H.); (A.O.); (O.M.-A.); (A.F.-C.); (J.R.)
- Correspondence: ; Tel.: +34-961973517
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12
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Study on differential gene expression profile of serum exosomes in patients with acute cerebral infarction. DIGITAL CHINESE MEDICINE 2021. [DOI: 10.1016/j.dcmed.2021.12.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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13
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Zheng Y, Zhang Y, Zhang X, Dang Y, Cheng Y, Hua W, Teng M, Wang S, Lu X. Novel lncRNA-miRNA-mRNA Competing Endogenous RNA Triple Networks Associated Programmed Cell Death in Heart Failure. Front Cardiovasc Med 2021; 8:747449. [PMID: 34692796 PMCID: PMC8528160 DOI: 10.3389/fcvm.2021.747449] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/09/2021] [Indexed: 01/01/2023] Open
Abstract
Objective: Increasing evidence has uncovered the roles of lncRNA-miRNA-mRNA regulatory networks in cardiovascular diseases. However, the crosstalk between ceRNA networks and development of heart failure (HF) remains unclear. This study was to investigate the role of lncRNA-mediated ceRNA networks in the pathophysiological process of HF and its potential regulatory functions on programmed cell death. Methods: We firstly screened the GSE77399, GSE52601 and GSE57338 datasets in the NCBI GEO database for screening differentially expressed lncRNAs, miRNAs and mRNAs. lncRNA-miRNA-mRNA regulatory networks based on the ceRNA theory were subsequently constructed. GO and KEGG enrichment analysis was conducted to predict potential biological functions of mRNAs in ceRNA networks. Differentially expressed mRNAs were then interacted with programmed cell death related genes. lncRNA-mediated ceRNA regulatory pathways on programmed cell death were validated with qRT-PCR testing. Results: Based on our bioinformatic analysis, two lncRNAs, eight miRNAs and 65 mRNAs were extracted to construct two lncRNAs-mediated ceRNA networks in HF. Biological processes and pathways were enriched in extracellular matrix. Seven lncRNA-mediated ceRNA regulatory pathways on programmed cell death, GAS5/miR-345-5p/ADAMTS4, GAS5/miR-18b-5p/AQP3, GAS5/miR-18b-5p/SHISA3, GAS5/miR-18b-5p/C1orf105, GAS5/miR-18b-5p/PLIN2, GAS5/miR-185-5p/LPCAT3, and GAS5/miR-29b-3p/STAT3, were finally validated. Conclusions: Two novel ceRNA regulatory networks in HF were discovered based on our bioinformatic analysis. Based on the interaction and validation analysis, seven lncRNA GAS5-mediated ceRNA regulatory pathways were hypothesized to impact programmed cell death including seven for apoptosis, three for ferroptosis, and one for pyroptosis. Upon which, we provided novel insights and potential research plots for bridging ceRNA regulatory networks and programmed cell death in HF.
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Affiliation(s)
- Yu Zheng
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yingjie Zhang
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiu Zhang
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yini Dang
- Department of Gastroenterology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yihui Cheng
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wenjie Hua
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Meiling Teng
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shenrui Wang
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiao Lu
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Wu C, Zhao L, Li X, Xu Y, Guo H, Huang Z, Wang Q, Liu H, Chen D, Zhu M. Integrated Bioinformatics Analysis of Potential mRNA and miRNA Regulatory Networks in Mice With Ischemic Stroke Treated by Electroacupuncture. Front Neurol 2021; 12:719354. [PMID: 34566862 PMCID: PMC8461332 DOI: 10.3389/fneur.2021.719354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/22/2021] [Indexed: 12/02/2022] Open
Abstract
Background: The complicated molecular mechanisms underlying the therapeutic effect of electroacupuncture (EA) on ischemic stroke are still unclear. Recently, more evidence has revealed the essential role of the microRNA (miRNA)–mRNA networks in ischemic stroke. However, a systematic analysis of novel key genes, miRNAs, and miRNA–mRNA networks regulated by EA in ischemic stroke is still absent. Methods: We established a middle cerebral artery occlusion (MCAO) mouse model and performed EA therapy on ischemic stroke mice. Behavior tests and measurement of infarction area were applied to measure the effect of EA treatment. Then, we performed RNA sequencing to analyze differentially expressed genes (DEGs) and functional enrichment between the EA and control groups. In addition, a protein–protein interaction (PPI) network was built, and hub genes were screened by Cytoscape. Upstream miRNAs were predicted by miRTarBase. Then hub genes and predicted miRNAs were verified as key biomarkers by RT-qPCR. Finally, miRNA–mRNA networks were constructed to explore the potential mechanisms of EA in ischemic stroke. Results: Our analysis revealed that EA treatment could significantly alleviate neurological deficits in the affected limbs and reduce infarct area of the MCAO model mice. A total of 174 significant DEGs, including 53 upregulated genes and 121 downregulated genes, were identified between the EA and control groups. Functional enrichment analysis showed that these DEGs were associated with the FOXO signaling pathway, NF-kappa B signaling pathway, T-cell receptor signaling pathway, and other vital pathways. The top 10 genes with the highest degree scores were identified as hub genes based on the degree method, but only seven genes were verified as key genes according to RT-qPCR. Twelve upstream miRNAs were predicted to target the seven key genes. However, only four miRNAs were significantly upregulated and indicated favorable effects of EA treatment. Finally, comprehensive analysis of the results identified the miR-425-5p-Cdk1, mmu-miR-1186b-Prc1, mmu-miR-434-3p-Prc1, and mmu-miR-453-Prc1 miRNA–mRNA networks as key networks that are regulated by EA and linked to ischemic stroke. These networks might mainly take place in neuronal cells regulated by EA in ischemic stroke. Conclusion: In summary, our study identified key DEGs, miRNAs, and miRNA–mRNA regulatory networks that may help to facilitate the understanding of the molecular mechanism underlying the effect of EA treatment on ischemic stroke.
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Affiliation(s)
- Chunxiao Wu
- Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Guangzhou University of Chinese Medicine, Guangdong, China.,The Research Center of Basic Integrative Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Lijun Zhao
- Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Guangzhou University of Chinese Medicine, Guangdong, China
| | - Xinrong Li
- Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Guangzhou University of Chinese Medicine, Guangdong, China
| | - Yingshan Xu
- Clinical Medical of Acupuncture, Moxibustion and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hongji Guo
- Clinical Medical of Acupuncture, Moxibustion and Rehabilitation, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zifeng Huang
- Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Guangzhou University of Chinese Medicine, Guangdong, China
| | - Qizhang Wang
- Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Guangzhou University of Chinese Medicine, Guangdong, China
| | - Helu Liu
- Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Guangzhou University of Chinese Medicine, Guangdong, China
| | - Dongfeng Chen
- The Research Center of Basic Integrative Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Meiling Zhu
- Shenzhen Hospital of Integrated Traditional Chinese and Western Medicine, Guangzhou University of Chinese Medicine, Guangdong, China
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15
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Zhang J, Liu X, Zhou W, Lu S, Wu C, Wu Z, Liu R, Li X, Wu J, Liu Y, Guo S, Jia S, Zhang X, Wang M. Identification of Key Genes Associated With the Process of Hepatitis B Inflammation and Cancer Transformation by Integrated Bioinformatics Analysis. Front Genet 2021; 12:654517. [PMID: 34539726 PMCID: PMC8440810 DOI: 10.3389/fgene.2021.654517] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 06/21/2021] [Indexed: 12/13/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) has become the main cause of cancer death worldwide. More than half of hepatocellular carcinoma developed from hepatitis B virus infection (HBV). The purpose of this study is to find the key genes in the transformation process of liver inflammation and cancer and to inhibit the development of chronic inflammation and the transformation from disease to cancer. Methods Two groups of GEO data (including normal/HBV and HBV/HBV-HCC) were selected for differential expression analysis. The differential expression genes of HBV-HCC in TCGA were verified to coincide with the above genes to obtain overlapping genes. Then, functional enrichment analysis, modular analysis, and survival analysis were carried out on the key genes. Results We identified nine central genes (CDK1, MAD2L1, CCNA2, PTTG1, NEK2) that may be closely related to the transformation of hepatitis B. The survival and prognosis gene markers composed of PTTG1, MAD2L1, RRM2, TPX2, CDK1, NEK2, DEPDC1, and ZWINT were constructed, which performed well in predicting the overall survival rate. Conclusion The findings of this study have certain guiding significance for further research on the transformation of hepatitis B inflammatory cancer, inhibition of chronic inflammation, and molecular targeted therapy of cancer.
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Affiliation(s)
- Jingyuan Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Xinkui Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Wei Zhou
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Shan Lu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Chao Wu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Zhishan Wu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Runping Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Xiaojiaoyang Li
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, China
| | - Jiarui Wu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Yingying Liu
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Siyu Guo
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Shanshan Jia
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Xiaomeng Zhang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Miaomiao Wang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
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Zeng Z, Hu J, Jiang J, Xiao G, Yang R, Li S, Li Y, Huang H, Zhong H, Bi X. Network Pharmacology and Molecular Docking-Based Prediction of the Mechanism of Qianghuo Shengshi Decoction against Rheumatoid Arthritis. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6623912. [PMID: 34527739 PMCID: PMC8437630 DOI: 10.1155/2021/6623912] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 07/18/2021] [Accepted: 08/16/2021] [Indexed: 12/22/2022]
Abstract
Qianghuo Shengshi decoction (QHSSD) is a classical Chinese medicine formula, which is used in clinical practice for the treatment of rheumatoid arthritis (RA) in China. However, the pharmacological mechanism of QHSSD on RA has remained unclear by now. We collected and screened active compounds and its potential targets by the pharmacology platform of Chinese herbal medicines. In addition, the therapeutic targets of RA were obtained and selected from databases. Network construction analyzed that 128 active compounds may act on 87 candidate targets and identified a total of 18 hub targets. GO annotation and KEGG enrichment investigated that the action mechanism underlying the treatment of RA by QHSSD might be involved in cell proliferation, angiogenesis, anti-inflammation, and antioxidation. Finally, molecular docking verification showed that TP53, VEGFA, TNF, EGFR, and NOS3 may be related to the RA treatment and molecular dynamics simulation showed the stability of protein-ligand interactions. In this work, QHSSD might exert therapeutic effect through a multicomponent, multitarget, and multipathway in RA from a holistic aspect, which provides basis for its mechanism of action and subsequent experiments.
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Affiliation(s)
- Zhihao Zeng
- School of the Fifth Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Jiaoting Hu
- Artemisinin Research Center, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Jieyi Jiang
- Guangdong Province Engineering and Technology Research Institute of Traditional Chinese Medicine, Guangzhou 510095, China
- Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese Medicine, Guangzhou 510095, China
| | - Guanlin Xiao
- Guangdong Province Engineering and Technology Research Institute of Traditional Chinese Medicine, Guangzhou 510095, China
- Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese Medicine, Guangzhou 510095, China
| | - Ruipei Yang
- School of the Fifth Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Sumei Li
- Guangdong Province Engineering and Technology Research Institute of Traditional Chinese Medicine, Guangzhou 510095, China
- Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese Medicine, Guangzhou 510095, China
| | - Yangxue Li
- Guangdong Province Engineering and Technology Research Institute of Traditional Chinese Medicine, Guangzhou 510095, China
- Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese Medicine, Guangzhou 510095, China
| | - Huajing Huang
- School of the Fifth Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Huixian Zhong
- School of the Fifth Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
| | - Xiaoli Bi
- School of the Fifth Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510405, China
- Guangdong Province Engineering and Technology Research Institute of Traditional Chinese Medicine, Guangzhou 510095, China
- Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese Medicine, Guangzhou 510095, China
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Khatun MS, Alam MA, Shoombuatong W, Mollah MNH, Kurata H, Hasan MM. Recent development of bioinformatics tools for microRNA target prediction. Curr Med Chem 2021; 29:865-880. [PMID: 34348604 DOI: 10.2174/0929867328666210804090224] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 11/22/2022]
Abstract
MicroRNAs (miRNAs) are central players that regulate the post-transcriptional processes of gene expression. Binding of miRNAs to target mRNAs can repress their translation by inducing the degradation or by inhibiting the translation of the target mRNAs. High-throughput experimental approaches for miRNA target identification are costly and time-consuming, depending on various factors. It is vitally important to develop the bioinformatics methods for accurately predicting miRNA targets. With the increase of RNA sequences in the post-genomic era, bioinformatics methods are being developed for miRNA studies specially for miRNA target prediction. This review summarizes the current development of state-of-the-art bioinformatics tools for miRNA target prediction, points out the progress and limitations of the available miRNA databases, and their working principles. Finally, we discuss the caveat and perspectives of the next-generation algorithms for the prediction of miRNA targets.
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Affiliation(s)
- Mst Shamima Khatun
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502. Japan
| | - Md Ashad Alam
- Tulane Center for Biomedical Informatics and Genomics, Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112. United States
| | - Watshara Shoombuatong
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700. Thailand
| | - Md Nurul Haque Mollah
- Laboratory of Bioinformatics, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh. 5Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083. Japan
| | - Hiroyuki Kurata
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502. Japan
| | - Md Mehedi Hasan
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502. Japan
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Fu M, Guo J, Zhao Y, Zhang Y, Zhang Y, Wang Z, Hou Z. Characteristics of Fall-Related Fractures in Older Adults with Cerebrovascular Disease: A Cross-Sectional Study. Clin Interv Aging 2021; 16:1337-1346. [PMID: 34285478 PMCID: PMC8286076 DOI: 10.2147/cia.s316739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/25/2021] [Indexed: 11/23/2022] Open
Abstract
PURPOSE Limited information exists on fall-related fractures in older adults with cerebrovascular disease. This study aimed to determine the characteristics of older adults with cerebrovascular disease who sustained fall-related fractures and identify the associated risk factors for perioperative complications. PATIENTS AND METHODS This was a cross-sectional study, which included patients with cerebrovascular disease who sustained fractures between Jan. 2017 and Dec. 2019. The collected data included demographics (age and gender), time and place of fracture occurrence, mechanism of injury, fracture location, type of cerebrovascular disease, complications, and comorbidities. RESULTS A total of 768 patients with 815 fractures were included; there were 253 males and 515 females, with an average age of 78.3 years. For either males or females, 80-84 years was the most commonly involved age group. Most (61.0%) patients had their fractures occurring at home and most fractures (70.7%) occurred during the daytime. Most were hip fractures and limb weakness; instability-related falls were the most common cause of fracture, making a proportion of 34.5%. Patients who suffered falls were mainly combining ischemic cerebrovascular disease. Most (85.9%) patients presented with at least one comorbid disease and the perioperative complication rate was 76.9% in total cases. Age≥80 (OR: 1.772, 95% CI: 1.236-2.540) and the number of comorbidities≥3 (OR: 1.606, 95% CI: 1.035-2.494) were found independently associated with complications, while the type of cerebrovascular disease, fracture location, and comorbidities of prior fragility fracture and respiratory disease were not significantly correlated with complications. CONCLUSION Our findings highlighted that more focus on improved physical function explored in intervention setting and the importance of primary home prevention measures seems justified in China and maybe other countries as well. It is the first study that presented the epidemiological characteristics of older adults with cerebrovascular disease who later experienced a fracture.
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Affiliation(s)
- Mingming Fu
- Department of Geriatric Orthopedics, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, People’s Republic of China
| | - Junfei Guo
- Department of Orthopaedic Surgery, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050051, People’s Republic of China
| | - Yuqi Zhao
- Department of Geriatric Orthopedics, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, People’s Republic of China
| | - Yaqian Zhang
- Department of Geriatric Orthopedics, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, People’s Republic of China
| | - Yingze Zhang
- Department of Orthopaedic Surgery, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050051, People’s Republic of China
- NHC Key Laboratory of Intelligent Orthopeadic Equipment (The Third Hospital of Hebei Medical University), Shijiazhuang, Hebei, 050051, People's Republic of China
- Chinese Academy of Engineering, Beijing, 100088, People’s Republic of China
| | - Zhiqian Wang
- Department of Geriatric Orthopedics, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, People’s Republic of China
| | - Zhiyong Hou
- Department of Orthopaedic Surgery, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050051, People’s Republic of China
- NHC Key Laboratory of Intelligent Orthopeadic Equipment (The Third Hospital of Hebei Medical University), Shijiazhuang, Hebei, 050051, People's Republic of China
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Wang D, Xiong T, Yu W, Liu B, Wang J, Xiao K, She Q. Predicting the Key Genes Involved in Aortic Valve Calcification Through Integrated Bioinformatics Analysis. Front Genet 2021; 12:650213. [PMID: 34046056 PMCID: PMC8144713 DOI: 10.3389/fgene.2021.650213] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/05/2021] [Indexed: 11/17/2022] Open
Abstract
Background: Valvular heart disease is obtaining growing attention in the cardiovascular field and it is believed that calcific aortic valve disease (CAVD) is the most common valvular heart disease (VHD) in the world. CAVD does not have a fully effective treatment to delay its progression and the specific molecular mechanism of aortic valve calcification remains unclear. Materials and Methods: We obtained the gene expression datasets GSE12644 and GSE51472 from the public comprehensive free database GEO. Then, a series of bioinformatics methods, such as GO and KEGG analysis, STING online tool, Cytoscape software, were used to identify differentially expressed genes in CAVD and healthy controls, construct a PPI network, and then identify key genes. In addition, immune infiltration analysis was used via CIBERSORT to observe the expression of various immune cells in CAVD. Results: A total of 144 differential expression genes were identified in the CAVD samples in comparison with the control samples, including 49 up-regulated genes and 95 down-regulated genes. GO analysis of DEGs were most observably enriched in the immune response, signal transduction, inflammatory response, proteolysis, innate immune response, and apoptotic process. The KEGG analysis revealed that the enrichment of DEGs in CAVD were remarkably observed in the chemokine signaling pathway, cytokine-cytokine receptor interaction, and PI3K-Akt signaling pathway. Chemokines CXCL13, CCL19, CCL8, CXCL8, CXCL16, MMP9, CCL18, CXCL5, VCAM1, and PPBP were identified as the hub genes of CAVD. It was macrophages that accounted for the maximal proportion among these immune cells. The expression of macrophages M0, B cells memory, and Plasma cells were higher in the CAVD valves than in healthy valves, however, the expression of B cells naïve, NK cells activated, and macrophages M2 were lower. Conclusion: We detected that chemokines CXCL13, CXCL8, CXCL16, and CXCL5, and CCL19, CCL8, and CCL18 are the most important markers of aortic valve disease. The regulatory macrophages M0, plasma cells, B cells memory, B cells naïve, NK cells activated, and macrophages M2 are probably related to the occurrence and the advancement of aortic valve stenosis. These identified chemokines and these immune cells may interact with a subtle adjustment relationship in the development of calcification in CAVD.
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Affiliation(s)
- Dinghui Wang
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Tianhua Xiong
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Wenlong Yu
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Bin Liu
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jing Wang
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Kaihu Xiao
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qiang She
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Wang D, Wang L, Han J, Zhang Z, Fang B, Chen F. Bioinformatics-Based Analysis of the lncRNA-miRNA-mRNA Network and TF Regulatory Network to Explore the Regulation Mechanism in Spinal Cord Ischemia/Reperfusion Injury. Front Genet 2021; 12:650180. [PMID: 33986769 PMCID: PMC8110913 DOI: 10.3389/fgene.2021.650180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/29/2021] [Indexed: 11/28/2022] Open
Abstract
Background Spinal cord ischemia/reperfusion injury (SCII) is a catastrophic complication involved with cardiovascular, spine, and thoracic surgeries and can lead to paraplegia. Nevertheless, the molecular mechanism of SCII remain ill-defined. Methods Expression profiling (GSE138966) data were obtained from GEO database. Then, differentially expressed (DE) lncRNAs and DEmRNAs were screened out with p < 0.05, and | fold change| > 1.5. Aberrant miRNAs expression in SCII was obtained from PubMed. Functional enrichment analysis of overlapping DEmRNAs between predicted mRNAs in miRDB database and DEmRNAs obtained from GSE138966 was performed using cluster Profiler R package. The lncRNA-miRNA-mRNA competitive endogenous RNA (ceRNA) network was established in light of ceRNA theory. The key lncRNAs in the ceRNA network were identified by topological analysis. Subsequently, key lncRNAs related ceRNA-pathway network and transcription factors (TFs)-mRNAs network were constructed. Simultaneously, the expression levels of hub genes were measured via qRT-PCR. Results The results in this study indicated that 76 miRNAs, 1373 lncRNAs, and 4813 mRNAs were differentially expressed in SCII. A SCII-related ceRNA network was constructed with 154 ncRNAs, 139 mRNAs, and 51 miRNAs. According topological analysis, six lncRNAs (NONRATT019236.2, NONRATT009530.2, NONRATT026999.2, TCONS_00032391, NONRATT023112.2, and NONRATT021956.2) were selected to establish the ceRNA-pathway network, and then two candidate hub lncRNAs (NONRATT009530.2 and NONRATT026999.2) were identified. Subsequently, two lncRNA-miRNA-mRNA regulatory axes were identified. NONRATT026999.2 and NONRATT009530.2 might involve SCII via miR-20b-5p/Map3k8 axis based on the complex ceRNA network. SP1 and Hnf4a acting as important TFs might regulate Map3k8. Furthermore, qRT-PCR results showed that the NONRATT009530.2, NONRATT026999.2, Map3k8, Hfn4a, and SP1 were significantly upregulated in SCII of rats, while the miR-20b-5p was downregulated. Conclusion Our results offer a new insight to understand the ceRNA regulation mechanism in SCII and identify highlighted lncRNA-miRNA-mRNA axes and two key TFs as potential targets for prevention and treatment of SCII.
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Affiliation(s)
- Dan Wang
- Department of Anesthesiology, The First Hospital of China Medical University, Shenyang, China
| | - Limei Wang
- Department of Anesthesiology, The First Hospital of China Medical University, Shenyang, China
| | - Jie Han
- Department of Anesthesiology, The First Hospital of China Medical University, Shenyang, China
| | - Zaili Zhang
- Department of Anesthesiology, The First Hospital of China Medical University, Shenyang, China
| | - Bo Fang
- Department of Anesthesiology, The First Hospital of China Medical University, Shenyang, China
| | - Fengshou Chen
- Department of Anesthesiology, The First Hospital of China Medical University, Shenyang, China
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Hou G, Zhao X, Li L, Yang Q, Liu X, Huang C, Lu R, Chen R, Wang Y, Jiang B, Yu J. SUMOylation of YTHDF2 promotes mRNA degradation and cancer progression by increasing its binding affinity with m6A-modified mRNAs. Nucleic Acids Res 2021; 49:2859-2877. [PMID: 33577677 PMCID: PMC7969013 DOI: 10.1093/nar/gkab065] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 01/23/2021] [Accepted: 01/27/2021] [Indexed: 12/19/2022] Open
Abstract
N 6-Methyladenosine (m6A) is the most abundant modification within diverse RNAs including mRNAs and lncRNAs and is regulated by a reversible process with important biological functions. Human YTH domain family 2 (YTHDF2) selectively recognized m6A-RNAs to regulate degradation. However, the possible regulation of YTHDF2 by protein post-translational modification remains unknown. Here, we show that YTHDF2 is SUMOylated in vivo and in vitro at the major site of K571, which can be induced by hypoxia while reduced by oxidative stress and SUMOylation inhibitors. SUMOylation of YTHDF2 has little impact on its ubiquitination and localization, but significantly increases its binding affinity of m6A-modified mRNAs and subsequently results in deregulated gene expressions which accounts for cancer progression. Moreover, Disease-free survival analysis of patients with lung adenocarcinoma derived from TCGA dataset reveals that higher expression of YTHDF2 together with higher expression of SUMO1 predicts poor prognosis. Our works uncover a new regulatory mechanism for YTHDF2 recognition of m6A-RNAs and highlight the importance of YTHDF2 SUMOylation in post-transcriptional gene expression regulation and cancer progression.
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Affiliation(s)
- Guofang Hou
- State Key Laboratory of Oncogenes and Related Genes, Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Department of Oncology, Shanghai 9th People's Hospital, Shanghai Jiao Tong University School of Medicine, 280 Mohe Road, Shanghai 201999, China
| | - Xian Zhao
- State Key Laboratory of Oncogenes and Related Genes, Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lian Li
- State Key Laboratory of Oncogenes and Related Genes, Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Qianqian Yang
- State Key Laboratory of Oncogenes and Related Genes, Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiaojia Liu
- State Key Laboratory of Oncogenes and Related Genes, Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Caihu Huang
- State Key Laboratory of Oncogenes and Related Genes, Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Runhui Lu
- State Key Laboratory of Oncogenes and Related Genes, Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ran Chen
- State Key Laboratory of Oncogenes and Related Genes, Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yanli Wang
- State Key Laboratory of Oncogenes and Related Genes, Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Bin Jiang
- Department of Oncology, Shanghai 9th People's Hospital, Shanghai Jiao Tong University School of Medicine, 280 Mohe Road, Shanghai 201999, China
| | - Jianxiu Yu
- State Key Laboratory of Oncogenes and Related Genes, Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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Gao L, Zhao Y, Ma X, Zhang L. Integrated analysis of lncRNA-miRNA-mRNA ceRNA network and the potential prognosis indicators in sarcomas. BMC Med Genomics 2021; 14:67. [PMID: 33653335 PMCID: PMC7927383 DOI: 10.1186/s12920-021-00918-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 02/22/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Competitive endogenous RNA (ceRNA) networks have revealed a new mechanism of interaction between RNAs, and play crucial roles in multiple biological processes and development of neoplasms. They might serve as diagnostic and prognosis markers as well as therapeutic targets. METHODS In this work, we identified differentially expressed mRNAs (DEGs), lncRNAs (DELs) and miRNAs (DEMs) in sarcomas by comparing the gene expression profiles between sarcoma and normal muscle samples in Gene Expression Omnibus (GEO) datasets. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analyses were applied to investigate the primary functions of the overlapped DEGs. Then, lncRNA-miRNA and miRNA-mRNA interactions were predicted, and the ceRNA regulatory network was constructed using Cytoscape software. In addition, the protein-protein interaction (PPI) network and survival analysis were performed. RESULTS A total of 1296 DEGs were identified in sarcoma samples by combining the GO and KEGG enrichment analyses, 338 DELs were discovered after the probes were reannotated, and 36 DEMs were ascertained through intersecting two different expression miRNAs sets. Further, through target gene prediction, a lncRNA-miRNA-mRNA ceRNA network that contained 113 mRNAs, 69 lncRNAs and 29 miRNAs was constructed. The PPI network identified the six most significant hub proteins. Survival analysis revealed that seven mRNAs, four miRNAs and one lncRNA were associated with overall survival of sarcoma patients. CONCLUSIONS Overall, we constructed a ceRNA network in sarcomas, which might provide insights for further research on the molecular mechanism and potential prognosis biomarkers.
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Affiliation(s)
- Lu Gao
- College of Medicine, Southwest Jiaotong University, Chengdu, 610031, Sichuan, China
- Department of Oncology, The General Hospital of Western Theater Command, Chengdu, 610083, Sichuan, China
| | - Yu Zhao
- Department of Oncology, The General Hospital of Western Theater Command, Chengdu, 610083, Sichuan, China
| | - Xuelei Ma
- Department of Biotherapy, West China Hospital and State Key Laboratory of Biotherapy, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Ling Zhang
- Department of Oncology, The General Hospital of Western Theater Command, Chengdu, 610083, Sichuan, China.
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LncRNA TINCR favors tumorigenesis via STAT3-TINCR-EGFR-feedback loop by recruiting DNMT1 and acting as a competing endogenous RNA in human breast cancer. Cell Death Dis 2021; 12:83. [PMID: 33446634 PMCID: PMC7809450 DOI: 10.1038/s41419-020-03188-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 10/20/2020] [Accepted: 10/23/2020] [Indexed: 12/18/2022]
Abstract
The long noncoding RNA (lncRNA) TINCR has recently been found to be associated with the progression of human malignancies, but the molecular mechanism of TINCR action remains elusive, particularly in breast cancer. The oncogenic role of TINCR was examined in vitro and in vivo in breast cancer. Next, the interaction between TINCR, DNMT1, and miR-503-5p methylation was explored. Moreover, the mechanism by which TINCR enhances EGFR expression and downstream signaling via an RNA–RNA interaction was comprehensively investigated. Furthermore, upstream transcriptional regulation of TINCR expression by STAT3 was examined by performing chromatin immunoprecipitation. Finally, feedback signaling in the STAT3–TINCR–EGFR downstream cascade was also investigated. TINCR is upregulated in human breast cancer tissues, and TINCR knockdown suppresses tumorigenesis in vitro and in vivo. Mechanistically, TINCR recruits DNMT1 to the miR-503-5p locus promoter, which increases the methylation and suppresses the transcriptional expression of miR-503-5p. Furthermore, TINCR also functions as a competing endogenous RNA to upregulate EGFR expression by sponging miR-503-5p. In addition, TINCR stimulates JAK2–STAT3 signaling downstream from EGFR, and STAT3 reciprocally enhances the transcriptional expression of TINCR. Our findings broaden the current understanding of the diverse manners in which TINCR functions in cancer biology. The newly identified STAT3–TINCR–EGFR-feedback loop could serve as a potential therapeutic target for human cancer.
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Integrated Analysis of Hub Genes and miRNAs in Dilated Cardiomyopathy. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8925420. [PMID: 33015184 PMCID: PMC7512046 DOI: 10.1155/2020/8925420] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/10/2020] [Accepted: 08/17/2020] [Indexed: 12/15/2022]
Abstract
Purpose The aim of this study is to identify hub genes and miRNAs by the miRNA-mRNA interaction network in dilated cardiomyopathy (DCM) disease. Methods The differentially expressed miRNAs (DEMis) and mRNAs (DEMs) were selected using data of DCM patients downloaded from the GEO database (GSE112556 and GSE3585). Gene Ontology (GO) pathway analysis and transcription factor enrichment analysis were used for selecting DEMis, and the target mRNAs of DEMis were filtered by using miRDB, miRTarBase, and TargetScan. Cytoscape software was used to visualize the network between miRNAs and mRNAs and calculate the hub genes. GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were used to analyze the mRNAs in the regulatory network. Results A total of 9 DEMis and 281 DEMs were selected, from which we reconstructed the miRNA-mRNA network consisting of 7 miRNAs and 51 mRNAs. The top 10 nodes, miR-144-3p, miR-363-3p, miR-9-3p, miR-21-3p, miR-144-5p, miR-338-3p, ID4 (inhibitor of DNA binding/differentiation 4), miR-770-5p, PIK3R1 (p85α regulatory subunit of phosphoinositide 3-kinase (PI3K)), and FN1 (fibronectin 1), were identified as important regulators. Conclusions The study uncovered several important hub genes and miRNAs involved in the pathogenesis of DCM, among which, the miR-144-3p/FN1 and miR-9-3p/FN1 pathways may play an important role in myocardial fibrosis, which can help identify the etiology of DCM, and provide potential therapeutic targets.
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Zhang J, Liu X, Zhou W, Cheng G, Wu J, Guo S, Jia S, Liu Y, Li B, Zhang X, Wang M. A bioinformatics investigation into molecular mechanism of Yinzhihuang granules for treating hepatitis B by network pharmacology and molecular docking verification. Sci Rep 2020; 10:11448. [PMID: 32651427 PMCID: PMC7351787 DOI: 10.1038/s41598-020-68224-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/22/2020] [Indexed: 12/17/2022] Open
Abstract
Yinzhihuang granules (YZHG) is a patented Chinese medicine for the treatment of hepatitis B. This study aimed to investigate the intrinsic mechanisms of YZHG in the treatment of hepatitis B and to provide new evidence and insights for its clinical application. The chemical compounds of YZHG were searched in the CNKI and PUBMED databases, and their putative targets were then predicted through a search of the SuperPred and Swiss Target Prediction databases. In addition, the targets of hepatitis B were obtained from TTD, PharmGKB and DisGeNET. The abovementioned data were visualized using Cytoscape 3.7.1, and network construction identified a total of 13 potential targets of YZHG in the treatment of hepatitis B. Molecular docking verification showed that CDK6, CDK2, TP53 and BRCA1 might be strongly correlated with hepatitis B treatment. Furthermore, GO and KEGG analyses indicated that the treatment of hepatitis B by YZHG might be related to positive regulation of transcription, positive regulation of gene expression, the hepatitis B pathway and the viral carcinogenesis pathway. Network pharmacology intuitively shows the multicomponent, multitarget and multichannel pharmacological effects of YZHG in the treatment of hepatitis B and provides a scientific basis for its mechanism of action.
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Affiliation(s)
- Jingyuan Zhang
- Beijing University of Chinese Medicine, Beijing, 100102, China
| | - Xinkui Liu
- Beijing University of Chinese Medicine, Beijing, 100102, China
| | - Wei Zhou
- Beijing University of Chinese Medicine, Beijing, 100102, China
| | - Guoliang Cheng
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Linyi, 276000, China
| | - Jiarui Wu
- Beijing University of Chinese Medicine, Beijing, 100102, China.
| | - Siyu Guo
- Beijing University of Chinese Medicine, Beijing, 100102, China
| | - Shanshan Jia
- Beijing University of Chinese Medicine, Beijing, 100102, China
| | - Yingying Liu
- Beijing University of Chinese Medicine, Beijing, 100102, China
| | - Bingbing Li
- State Key Laboratory of Generic Manufacture Technology of Chinese Traditional Medicine, Linyi, 276000, China
| | - Xiaomeng Zhang
- Beijing University of Chinese Medicine, Beijing, 100102, China
| | - Miaomiao Wang
- Beijing University of Chinese Medicine, Beijing, 100102, China
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Comprehensive analysis of competitive endogenous RNAs network reveals potential prognostic lncRNAs in gastric cancer. Heliyon 2020; 6:e03978. [PMID: 32455175 PMCID: PMC7235626 DOI: 10.1016/j.heliyon.2020.e03978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/13/2020] [Accepted: 05/11/2020] [Indexed: 01/17/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are key regulators of a range of human diseases, including various cancers, with multiple previous studies having explored lncRNA dysregulation in the context of gastric cancer (GC). The present study sought to expand upon these previous results by downloading lncRNA, mRNA, and microRNA (miRNA) expression profiles derived from 180 GC tissues and 24 normal control tissues within the Cancer Genome Atlas (TCGA) database. These datasets were then interrogated to identify GC-related differentially expressed (DE) RNAs (|fold change| ≥ 2, FDR< 0.01), leading to the identification of 1946 DE lncRNAs, 123 DE miRNAs, and 3159 DE mRNAs. These results were then used to generate a putative GC-related competitive endogenous RNA (ceRNA) network composed of 131 lncRNAs, 9 miRNAs, and 78 mRNAs. Subsequent survival analyses based upon this network revealed 17 of these lncRNAs to be significantly associated with GC patient survival (P < 0.05). Further multivariable Cox regression and lasso analyses allowed for the construction of an 8-lncRNA risk score that was able to effectively predict GC patient survival with good discriminative ability. The Kaplan-Meier Plotter database further confirmed that network hub genes that were related to these 8 lncRNAs were associated with GC patient prognosis (P < 0.05). As the ceRNA network in the present study was constructed with a focus on both disease stage and differential gene expression, it represents a key resource that will offer valuable insights into the mechanistic roles of ceRNA pathways in GC development and progression.
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