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Xu Y, Zhu Y, Xu J, Mao H, Li J, Zhu X, Kong X, Zhang J. Analysis of microRNA expression in rat kidneys after VEGF inhibitor treatment under different degrees of hypoxia. Physiol Genomics 2023; 55:504-516. [PMID: 37642276 PMCID: PMC11178269 DOI: 10.1152/physiolgenomics.00023.2023] [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: 03/29/2023] [Revised: 08/24/2023] [Accepted: 08/24/2023] [Indexed: 08/31/2023] Open
Abstract
Previously, we found that the incidence of kidney injury in patients with chronic hypoxia was related to the partial pressure of arterial oxygen. However, at oxygen concentrations that contribute to kidney injury, the changes in the relationship between microRNAs (miRNAs) and the hypoxia-inducible factor-1α (HIF-1α)-vascular endothelial growth factor (VEGF) axis and the key miRNAs involved in this process have not been elucidated. Therefore, we elucidated the relationship between VEGF and kidney injury at different oxygen concentrations and the mechanisms mediated by miRNAs. Sprague-Dawley rats were exposed to normobaric hypoxia and categorized into six groups based on the concentration of the oxygen inhaled and injection of the angiogenesis inhibitor bevacizumab, a humanized anti-VEGF monoclonal antibody. Renal tissue samples were processed to determine pathological and morphological changes and HIF-1α, VEGF, and miRNA expression. We performed a clustering analysis of high-risk pathways and key hub genes. The results were validated using two Gene Expression Omnibus datasets (GSE94717 and GSE30718). As inhaled oxygen concentration decreased, destructive changes in the kidney tissues became more severe. Although the kidney possesses a self-protective mechanism under an intermediate degree of hypoxia (10% O2), bevacizumab injections disrupted this mechanism, and VEGF expression was associated with the ability of the kidney to repair itself. rno-miR-124-3p was identified as a crucial miRNA; a key gene target, Mapk14, was identified during this process. VEGF plays an important role in kidney protection from injury under different hypoxia levels. Specific miRNAs and their target genes may serve as biomarkers that provide new insights into kidney injury treatment.NEW & NOTEWORTHY Renal tolerance to hypoxic environments is limited, and the degree of hypoxia does not show a linear relationship with angiogenesis. VEGF plays an important role in the kidney's self-protective mechanism under different levels of hypoxia. miR-124-3p may be particularly important in kidney repair, and it may modulate VEGF expression through the miR-124-3p/Mapk14 signaling pathway. These microRNAs may serve as biomarkers that provide new insights into kidney injury treatment.
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Affiliation(s)
- Yaya Xu
- Department of Pediatric Critical Care Medicine, Xinhua Hospital, Affiliated to the Medical School of Shanghai Jiaotong University, Shanghai, China
| | - Yueniu Zhu
- Department of Pediatric Critical Care Medicine, Xinhua Hospital, Affiliated to the Medical School of Shanghai Jiaotong University, Shanghai, China
| | - Jiayue Xu
- Department of Pediatric Critical Care Medicine, Xinhua Hospital, Affiliated to the Medical School of Shanghai Jiaotong University, Shanghai, China
| | - Haoyun Mao
- Department of Pediatric Critical Care Medicine, Xinhua Hospital, Affiliated to the Medical School of Shanghai Jiaotong University, Shanghai, China
| | - Jiru Li
- Department of Pediatric Critical Care Medicine, Xinhua Hospital, Affiliated to the Medical School of Shanghai Jiaotong University, Shanghai, China
| | - Xiaodong Zhu
- Department of Pediatric Critical Care Medicine, Xinhua Hospital, Affiliated to the Medical School of Shanghai Jiaotong University, Shanghai, China
| | - Xiangmei Kong
- Department of Pediatric Critical Care Medicine, Xinhua Hospital, Affiliated to the Medical School of Shanghai Jiaotong University, Shanghai, China
| | - Jianhua Zhang
- Department of Pediatric Respiratory Department, Xinhua Hospital, Affiliated to the Medical School of Shanghai Jiaotong University, Shanghai, China
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Zhang Z, Chen L, Liu H, Sun Y, Shui P, Gao J, Wang D, Jiang H, Li Y, Chen K, Hong Y. Gene signature for the prediction of the trajectories of sepsis-induced acute kidney injury. Crit Care 2022; 26:398. [PMID: 36544199 PMCID: PMC9773539 DOI: 10.1186/s13054-022-04234-3] [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: 06/22/2022] [Accepted: 11/10/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Acute kidney injury (AKI) is a common complication in sepsis. However, the trajectories of sepsis-induced AKI and their transcriptional profiles are not well characterized. METHODS Sepsis patients admitted to centres participating in Chinese Multi-omics Advances In Sepsis (CMAISE) from November 2020 to December 2021 were enrolled, and gene expression in peripheral blood mononuclear cells was measured on Day 1. The renal function trajectory was measured by the renal component of the SOFA score (SOFArenal) on Days 1 and 3. Transcriptional profiles on Day 1 were compared between these renal function trajectories, and a support vector machine (SVM) was developed to distinguish transient from persistent AKI. RESULTS A total of 172 sepsis patients were enrolled during the study period. The renal function trajectory was classified into four types: non-AKI (SOFArenal = 0 on Days 1 and 3, n = 50), persistent AKI (SOFArenal > 0 on Days 1 and 3, n = 62), transient AKI (SOFArenal > 0 on Day 1 and SOFArenal = 0 on Day 3, n = 50) and worsening AKI (SOFArenal = 0 on Days 1 and SOFArenal > 0 on Day 3, n = 10). The persistent AKI group showed severe organ dysfunction and prolonged requirements for organ support. The worsening AKI group showed the least organ dysfunction on day 1 but had higher serum lactate and prolonged use of vasopressors than the non-AKI and transient AKI groups. There were 2091 upregulated and 1,902 downregulated genes (adjusted p < 0.05) between the persistent and transient AKI groups, with enrichment in the plasma membrane complex, receptor complex, and T-cell receptor complex. A 43-gene SVM model was developed using the genetic algorithm, which showed significantly greater performance predicting persistent AKI than the model based on clinical variables in a holdout subset (AUC: 0.948 [0.912, 0.984] vs. 0.739 [0.648, 0.830]; p < 0.01 for Delong's test). CONCLUSIONS Our study identified four subtypes of sepsis-induced AKI based on kidney injury trajectories. The landscape of host response aberrations across these subtypes was characterized. An SVM model based on a gene signature was developed to predict renal function trajectories, and showed better performance than the clinical variable-based model. Future studies are warranted to validate the gene model in distinguishing persistent from transient AKI.
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Affiliation(s)
- Zhongheng Zhang
- grid.13402.340000 0004 1759 700XDepartment of Emergency Medicine, Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016 People’s Republic of China
| | - Lin Chen
- grid.13402.340000 0004 1759 700XDepartment of Critical Care Medicine, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, People’s Republic of China
| | - Huiheng Liu
- grid.413280.c0000 0004 0604 9729Emergency Department, Zhongshan Hospital of Xiamen University, Xiamen, Fujian People’s Republic of China
| | - Yujing Sun
- grid.413280.c0000 0004 0604 9729Emergency Department, Zhongshan Hospital of Xiamen University, Xiamen, Fujian People’s Republic of China
| | - Pengfei Shui
- grid.411634.50000 0004 0632 4559Department of Emergency, People’s Hospital of Anji, Anji County, Zhejiang People’s Republic of China
| | - Jian Gao
- Department of Critical Medicine, Pi County Peoples Hospital, Chengdu, People’s Republic of China
| | - Decong Wang
- Department of Critical Medicine, Pi County Peoples Hospital, Chengdu, People’s Republic of China
| | - Huilin Jiang
- grid.412534.5Emergency Department, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Yanling Li
- grid.412534.5Emergency Department, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Kun Chen
- grid.13402.340000 0004 1759 700XDepartment of Critical Care Medicine, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, People’s Republic of China
| | - Yucai Hong
- grid.13402.340000 0004 1759 700XDepartment of Emergency Medicine, Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016 People’s Republic of China
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Yu R, Zhang C. miR-124-Antagonist-Loaded Liposomal Nanoparticles Negatively Regulate the Toll-Like Receptor (TLR)-Signaling Pathway in Alveolar Epithelial Cells in Pulmonary Tuberculosis. J BIOMATER TISS ENG 2022. [DOI: 10.1166/jbt.2022.3195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
miR-124 is intensively expressed in the alveolar epithelial cells of pulmonary tuberculosis. This study focused on exploring the negative regulation of miR-124-antagonist-loaded liposomal nanoparticles on the Toll-like receptor (TLR)-signal transduction pathway in the alveolar epithelial
cells from pulmonary tuberculosis, aiming to provide theoretical evidence for the treatment of pulmonary tuberculosis. The purchased alveolar epithelial cells were grouped into Blank group, Empty-vector group, Bacillus Calmette-Guerin (BCG) group, Nanoparticle+MiR-124 Antagonist group, MiR-124
Antagonist group, and MiR-124 Agonist group. The liposomal nanoparticles were identified. The following aspects were investigated: mRNA level of miR-124, mRNA and protein levels of Myeloid differentiation factor 88 (MyD 88), Toll-like receptor the 6 (TLR 6) and their downstream molecules Nuclear
Factor-κB (NF-κB) and Tumor necrosis factor TNF receptor-associated factor 6 (TRAF 6) secretion level of cytokines (NF-κB, IL-8, IL-1α, TNF-α and IL-6), as well as the regulatory link between miR-124-antagonists with TLR6 and
MyD88. The liposomal nanoparticles were uniform in size, with an average particle size of (35.25±10.58) nm and an average Zeta potential of (−48.55±10.27) mV. The miR-124 level was the strongest in the MiR-124 Agonist group, while being the lowest in the Blank group. The
miR-124 level was relatively higher in the BCG group and Empty-vector group, while being significantly reduced in the Nanoparticle+MiR-124 Antagonist group, which was higher than the Blank group. The miR-124 level in the MiR-124 Antagonist group was higher than that in the Nanoparticle+MiR-124
Antagonist group (P <0.05). The mRNA and protein levels of MyD88, TLR6, NF-κB and TRAF6 were the highest in the MiR-124 Agonist group, while being the lowest in the Blank group. The transcription and translation levels of TRAF6, TLR6, NF-κB and MyD88 were
relatively higher in the BCG group and Empty-vector group, while being significantly reduced in the Nanoparticle+ MiR-124 Antagonist group, which were higher than in the Blank group. The transcription and translation levels of TRAF6, TLR6, NF-κB and MyD88 were in the MiR-124 Antagonist
group were higher than that in the Nanoparticle+MiR-124 Antagonist group (P <0.05). The secretion levels of inflammatory factors (NF-κB, IL-8, IL-1α, TNF-α and IL-6) were the highest in the MiR-124 Agonist group, while being the lowest in the
Blank group. The levels of these inflammatory factors were relatively higher in the BCG group and Empty-vector group, while being significantly reduced in the Nanoparticle+MiR-124 Antagonist group, which were elevated compared to that in the Blank group. The secretion quantities of these inflammatory
factors in the MiR-124 Antagonist group were higher than that in the Nanoparticle+MiR-124 Antagonist group (P <0.05).Dual luciferase experiments indicated that miR-124-antagonists may retard TLR6 and MyD88 to affect the immune response of pulmonary alveolar epithelial cells in
pulmonary tuberculosis. The fluorescence intensity of mutant plasmid was significantly stronger than that of wild-type plasmid (P < 0.05). In the alveolar epithelial cells from pulmonary tuberculosis, the miR-124-antagonistloaded liposomal nanoparticles can significantly reduce the
expression of TLR6 and MyD88, and their downstream molecules (NF-κB and TRAF6), leading to the reduced secretion of the inflammatory factors. As a result, the inflammatory response of lung tissue was alleviated, while the immune function was restored. This regulation was achieved
by the miR-124-antagonist-loaded liposomal nanoparticles via negatively regulating the TLR6/MyD88 pathways.
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Affiliation(s)
- Rong Yu
- Department of Tuberculosis, The First Hospital of Changsha, Changsha 410000, Hunan, China
| | - Cai Zhang
- Department of Pediatrics, Brain Hospital of Hunan Province (The Second People’s Hospital of Hunan Province), Changsha 410000, Hunan, China
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Expression of MicroRNAs in Sepsis-Related Organ Dysfunction: A Systematic Review. Int J Mol Sci 2022; 23:ijms23169354. [PMID: 36012630 PMCID: PMC9409129 DOI: 10.3390/ijms23169354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/10/2022] [Accepted: 08/17/2022] [Indexed: 02/06/2023] Open
Abstract
Sepsis is a critical condition characterized by increased levels of pro-inflammatory cytokines and proliferating cells such as neutrophils and macrophages in response to microbial pathogens. Such processes lead to an abnormal inflammatory response and multi-organ failure. MicroRNAs (miRNA) are single-stranded non-coding RNAs with the function of gene regulation. This means that miRNAs are involved in multiple intracellular pathways and thus contribute to or inhibit inflammation. As a result, their variable expression in different tissues and organs may play a key role in regulating the pathophysiological events of sepsis. Thanks to this property, miRNAs may serve as potential diagnostic and prognostic biomarkers in such life-threatening events. In this narrative review, we collect the results of recent studies on the expression of miRNAs in heart, blood, lung, liver, brain, and kidney during sepsis and the molecular processes in which they are involved. In reviewing the literature, we find at least 122 miRNAs and signaling pathways involved in sepsis-related organ dysfunction. This may help clinicians to detect, prevent, and treat sepsis-related organ failures early, although further studies are needed to deepen the knowledge of their potential contribution.
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Antonakos N, Gilbert C, Théroude C, Schrijver IT, Roger T. Modes of action and diagnostic value of miRNAs in sepsis. Front Immunol 2022; 13:951798. [PMID: 35990654 PMCID: PMC9389448 DOI: 10.3389/fimmu.2022.951798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/08/2022] [Indexed: 11/13/2022] Open
Abstract
Sepsis is a clinical syndrome defined as a dysregulated host response to infection resulting in life-threatening organ dysfunction. Sepsis is a major public health concern associated with one in five deaths worldwide. Sepsis is characterized by unbalanced inflammation and profound and sustained immunosuppression, increasing patient susceptibility to secondary infections and mortality. microRNAs (miRNAs) play a central role in the control of many biological processes, and deregulation of their expression has been linked to the development of oncological, cardiovascular, neurodegenerative and metabolic diseases. In this review, we discuss the role of miRNAs in sepsis pathophysiology. Overall, miRNAs are seen as promising biomarkers, and it has been proposed to develop miRNA-based therapies for sepsis. Yet, the picture is not so straightforward because of the versatile and dynamic features of miRNAs. Clearly, more research is needed to clarify the expression and role of miRNAs in sepsis, and to promote the use of miRNAs for sepsis management.
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Xiao S, Liu L, Sun Z, Liu X, Xu J, Guo Z, Yin X, Liao F, Xu J, You Y, Zhang T. Network Pharmacology and Experimental Validation to Explore the Mechanism of Qing-Jin-Hua-Tan-Decoction Against Acute Lung Injury. Front Pharmacol 2022; 13:891889. [PMID: 35873580 PMCID: PMC9304690 DOI: 10.3389/fphar.2022.891889] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/24/2022] [Indexed: 11/29/2022] Open
Abstract
Qing-Jin-Hua-Tan-Decoction (QJHTD), a classic famous Chinese ancient prescription, has been used for treatment of pulmonary diseases since Ming Dynasty. A total of 22 prototype compounds of QJHTD absorbed into rat blood were chosen as candidates for the pharmacological network analysis and molecular docking. The targets from the intersection of compound target and ALI disease targets were used for GO and KEGG enrichment analyses. Molecular docking was adopted to further verify the interactions between 22 components and the top 20 targets with higher degree values in the component–target–pathway network. In vitro experiments were performed to verify the results of network pharmacology using SPR experiments, Western blot experiments, and the PMA-induced neutrophils to produce neutrophil extracellular trap (NET) model. The compound–target–pathway network includes 176 targets and 20 signaling pathways in which the degree of MAPK14, CDK2, EGFR, F2, SRC, and AKT1 is higher than that of other targets and which may be potential disease targets. The biological processes in QJHTD for ALI mainly included protein phosphorylation, response to wounding, response to bacterium, regulation of inflammatory response, and so on. KEGG enrichment analyses revealed multiple signaling pathways, including lipid and atherosclerosis, HIF-1 signaling pathway, renin–angiotensin system, and neutrophil extracellular trap formation. The molecular docking results showed that baicalin, oroxylin A-7-glucuronide, hispidulin-7-O-β-D-glucuronide, wogonoside, baicalein, wogonin, tianshic acid, and mangiferin can be combined with most of the targets, which might be the core components of QJHTD in treatment of ALI. Direct binding ability of baicalein, wogonin, and baicalin to thrombin protein was all micromolar, and their KD values were 11.92 μM, 1.303 μM, and 1.146 μM, respectively, revealed by SPR experiments, and QJHTD could inhibit Src phosphorylation in LPS-activated neutrophils by Western blot experiments. The experimental results of PMA-induced neutrophils to produce NETs indicated that QJHTD could inhibit the production of NETs. This study revealed the active compounds, effective targets, and potential pharmacological mechanisms of QJHTD acting on ALI.
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Affiliation(s)
- Shunli Xiao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lu Liu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhengxiao Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiaoqian Liu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jing Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Zhongyuan Guo
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| | - Xiaojie Yin
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Fulong Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jun Xu
- National and Local United Engineering Laboratory of Modern Preparation and Quality Control Technology of Traditional Chinese Medicine, Tianjin Institute of Pharmaceutical Research, Tianjin, China
| | - Yun You
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- *Correspondence: Yun You, ; Tiejun Zhang,
| | - Tiejun Zhang
- National and Local United Engineering Laboratory of Modern Preparation and Quality Control Technology of Traditional Chinese Medicine, Tianjin Institute of Pharmaceutical Research, Tianjin, China
- *Correspondence: Yun You, ; Tiejun Zhang,
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Chen L, Jin S, Yang M, Gui C, Yuan Y, Dong G, Zeng W, Zeng J, Hu G, Qiao L, Wang J, Xi Y, Sun J, Wang N, Wang M, Xing L, Yang Y, Teng Y, Hou J, Bi Q, Cai H, Zhang G, Hong Y, Zhang Z. Integrated Single Cell and Bulk RNA-Seq Analysis Revealed Immunomodulatory Effects of Ulinastatin in Sepsis: A Multicenter Cohort Study. Front Immunol 2022; 13:882774. [PMID: 35634310 PMCID: PMC9130465 DOI: 10.3389/fimmu.2022.882774] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/04/2022] [Indexed: 11/25/2022] Open
Abstract
Sepsis is a leading cause of morbidity and mortality in the intensive care unit, which is caused by unregulated inflammatory response leading to organ injuries. Ulinastatin (UTI), an immunomodulatory agent, is widely used in clinical practice and is associated with improved outcomes in sepsis. But its underlying mechanisms are largely unknown. Our study integrated bulk and single cell RNA-seq data to systematically explore the potential mechanisms of the effects of UTI in sepsis. After adjusting for potential confounders in the negative binomial regression model, there were more genes being downregulated than being upregulated in the UTI group. These down-regulated genes were enriched in the neutrophil involved immunity such as neutrophil activation and degranulation, indicating the immunomodulatory effects of UTI is mediated via regulation of neutrophil activity. By deconvoluting the bulk RNA-seq samples to obtain fractions of cell types, the Myeloid-derived suppressor cells (MDSC) were significantly expanded in the UTI treated samples. Further cell-cell communication analysis revealed some signaling pathways such as ANEEXIN, GRN and RESISTIN that might be involved in the immunomodulatory effects of UTI. The study provides a comprehensive reference map of transcriptional states of sepsis treated with UTI, as well as a general framework for studying UTI-related mechanisms.
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Affiliation(s)
- Lin Chen
- Department of Critical Care Medicine, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Senjun Jin
- Department of Emergency, Zhejiang Provincial People’s Hospital, People’s Hospital of Hangzhou Medical College, Hangzhou, China
| | - Min Yang
- The 2nd Department of Intensive Care Unit, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Chunmei Gui
- Department of Critical Care Medicine, The First People’s Hospital of Changde City, Changde, China
| | - Yingpu Yuan
- Department of Critical Care Medicine, The First People’s Hospital of Changde City, Changde, China
| | - Guangtao Dong
- Department of Emergency Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Weizhong Zeng
- Department of Critical Care Medicine, Zhuzhou Central Hospital, Zhuzhou, China
| | - Jing Zeng
- Department of Critical Care Medicine, Zhuzhou Central Hospital, Zhuzhou, China
| | - Guoxin Hu
- Emergency Department, Shengli Oilfield Central Hospital, Dongying, China
| | - Lujun Qiao
- Emergency Department, Shengli Oilfield Central Hospital, Dongying, China
| | - Jinhua Wang
- Department of Critical Care Medicine, The Second Affiliated Hospital of Xi’an Medical University, Xi’an, China
| | - Yonglin Xi
- Department of Critical Care Medicine, The Second Affiliated Hospital of Xi’an Medical University, Xi’an, China
| | - Jian Sun
- Department of Critical Care Medicine, Lishui Center Hospital, Lishui, China
| | - Nan Wang
- Department of Critical Care Medicine, The Fourth Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, China
| | - Minmin Wang
- Department of Critical Care Medicine, The Fourth Affiliated Hospital of Anhui Medical University, Anhui Medical University, Hefei, China
| | - Lifeng Xing
- Department of Emergency Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yi Yang
- Department of Emergency Medicine, The Second Hospital of Jiaxing, Jiaxing, China
| | - Yan Teng
- Department of Critical Care Medicine, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Junxia Hou
- Department of Critical Care Medicine, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Qiaojie Bi
- Department of Emergency, Qingdao Municipal Hospital, QingDao University School of Medicine, Qingdao, China
| | - Huabo Cai
- Department of Emergency Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Gensheng Zhang
- Department of Critical Care Medicine, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yucai Hong
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Department of Emergency Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhongheng Zhang
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Department of Emergency Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Moubarak RS, Koetz-Ploch L, Mullokandov G, Gaziel A, de Pablos-Aragoneses A, Argibay D, Kleffman K, Sokolova E, Berwick M, Thomas NE, Osman I, Brown BD, Hernando E. In Vivo miRNA Decoy Screen Reveals miR-124a as a Suppressor of Melanoma Metastasis. Front Oncol 2022; 12:852952. [PMID: 35480113 PMCID: PMC9036958 DOI: 10.3389/fonc.2022.852952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/24/2022] [Indexed: 11/30/2022] Open
Abstract
Melanoma is a highly prevalent cancer with an increasing incidence worldwide and high metastatic potential. Brain metastasis is a major complication of the disease, as more than 50% of metastatic melanoma patients eventually develop intracranial disease. MicroRNAs (miRNAs) have been found to play an important role in the tumorigenicity of different cancers and have potential as markers of disease outcome. Identification of relevant miRNAs has generally stemmed from miRNA profiling studies of cells or tissues, but these approaches may have missed miRNAs with relevant functions that are expressed in subfractions of cancer cells. We performed an unbiased in vivo screen to identify miRNAs with potential functions as metastasis suppressors using a lentiviral library of miRNA decoys. Notably, we found that a significant fraction of melanomas that metastasized to the brain carried a decoy for miR-124a, a miRNA that is highly expressed in the brain/neurons. Additional loss- and gain-of-function in vivo validation studies confirmed miR-124a as a suppressor of melanoma metastasis and particularly of brain metastasis. miR-124a overexpression did not inhibit tumor growth in vivo, underscoring that miR-124a specifically controls processes required for melanoma metastatic growth, such as seeding and growth post-extravasation. Finally, we provide proof of principle of this miRNA as a promising therapeutic agent by showing its ability to impair metastatic growth of melanoma cells seeded in distal organs. Our efforts shed light on miR-124a as an antimetastatic agent, which could be leveraged therapeutically to impair metastatic growth and improve patient survival.
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Affiliation(s)
- Rana S. Moubarak
- Department of Pathology, New York University (NYU) School of Medicine, New York, NY, United States
- Interdisciplinary Melanoma Cooperative Group (IMCG), New York University (NYU) Cancer Institute, New York, NY, United States
- Laura and Isaac Perlmutter Cancer Center, New York University (NYU) Langone Health, New York, NY, United States
| | - Lisa Koetz-Ploch
- Department of Pathology, New York University (NYU) School of Medicine, New York, NY, United States
- Interdisciplinary Melanoma Cooperative Group (IMCG), New York University (NYU) Cancer Institute, New York, NY, United States
| | - Gavriel Mullokandov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Avital Gaziel
- Department of Pathology, New York University (NYU) School of Medicine, New York, NY, United States
- Interdisciplinary Melanoma Cooperative Group (IMCG), New York University (NYU) Cancer Institute, New York, NY, United States
| | - Ana de Pablos-Aragoneses
- Department of Pathology, New York University (NYU) School of Medicine, New York, NY, United States
- Interdisciplinary Melanoma Cooperative Group (IMCG), New York University (NYU) Cancer Institute, New York, NY, United States
| | - Diana Argibay
- Department of Pathology, New York University (NYU) School of Medicine, New York, NY, United States
- Interdisciplinary Melanoma Cooperative Group (IMCG), New York University (NYU) Cancer Institute, New York, NY, United States
| | - Kevin Kleffman
- Department of Pathology, New York University (NYU) School of Medicine, New York, NY, United States
- Interdisciplinary Melanoma Cooperative Group (IMCG), New York University (NYU) Cancer Institute, New York, NY, United States
| | - Elena Sokolova
- Department of Pathology, New York University (NYU) School of Medicine, New York, NY, United States
- Interdisciplinary Melanoma Cooperative Group (IMCG), New York University (NYU) Cancer Institute, New York, NY, United States
| | - Marianne Berwick
- Division of Epidemiology, Biostatistics and Preventive Medicine, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, United States
| | - Nancy E. Thomas
- Department of Dermatology, University of North Carolina, Chapel Hill, NC, United States
| | - Iman Osman
- Interdisciplinary Melanoma Cooperative Group (IMCG), New York University (NYU) Cancer Institute, New York, NY, United States
- Laura and Isaac Perlmutter Cancer Center, New York University (NYU) Langone Health, New York, NY, United States
- Ronald O. Perelman Department of Dermatology, New York University (NYU) School of Medicine, New York, NY, United States
| | - Brian D. Brown
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Eva Hernando
- Department of Pathology, New York University (NYU) School of Medicine, New York, NY, United States
- Interdisciplinary Melanoma Cooperative Group (IMCG), New York University (NYU) Cancer Institute, New York, NY, United States
- Laura and Isaac Perlmutter Cancer Center, New York University (NYU) Langone Health, New York, NY, United States
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9
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Zhou Q, He DX, Deng YL, Wang CL, Zhang LL, Jiang FM, IRAKOZE L, Liang ZA. MiR-124-3p targeting PDE4B attenuates LPS-induced ALI through the TLR4/NF-κB signaling pathway. Int Immunopharmacol 2022; 105:108540. [DOI: 10.1016/j.intimp.2022.108540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/31/2021] [Accepted: 01/10/2022] [Indexed: 12/14/2022]
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10
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You J, Li H, Fan P, Yang X, Wei Y, Zheng L, Li Z, Yi C. Inspiration for COVID-19 Treatment: Network Analysis and Experimental Validation of Baicalin for Cytokine Storm. Front Pharmacol 2022; 13:853496. [PMID: 35350754 PMCID: PMC8957998 DOI: 10.3389/fphar.2022.853496] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 02/21/2022] [Indexed: 02/05/2023] Open
Abstract
Background: Cytokine storm (CS) is a systemic inflammatory syndrome and a major cause of multi-organ failure and even death in COVID-19 patients. With the increasing number of COVID-19 patients, there is an urgent need to develop effective therapeutic strategies for CS. Baicalin is an anti-inflammatory and antiviral traditional Chinese medicine. In the present study, we aimed to evaluate the therapeutic mechanism of baicalin against CS through network analysis and experimental validation, and to detect key targets of CS that may bind closely to baicalin through molecular docking. Method: Access to potential targets of baicalin and CS in public databases. We constructed the protein-protein interaction (PPI) network of baicalin and CS by Cytoscape 9.0 software and performed network topology analysis of the potential targets. Then, the hub target was identified by molecular docking technique and validated in the CS model. Finally, GO and KEGG pathway functional enrichment analysis of common targets were confirmed using R language, and the location of overlapping targets in key pathways was queried via KEGG Mapper. Result: A total of 86 overlapping targets of baicalin and CS were identified, among which MAPK14, IL2, FGF2, CASP3, PTGS2, PIK3CA, EGFR, and TNF were the core targets. Moreover, it was found that baicalin bound most closely to TNF through molecular docking, and demonstrated that baicalin can effectively inhibit the elevation of TNF-α in vitro and in vivo. Furthermore, bioenrichment analysis revealed that the TNF signaling pathway and IL-17 signaling pathway may be potential key pathways for baicalin to treat CS. Conclusion: Based on this study, baicalin was identified as a potential drug for the alleviation of CS, and the possible key targets and pathways of baicalin for the treatment of CS were elucidated to reveal the main pharmacological mechanisms.
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Affiliation(s)
- Jia You
- Department of Oncology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Huawei Li
- Department of Oncology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Peng Fan
- Department of Respiratory and Critical Care Medicine, Chongqing Traditional Chinese Medicine Hospital, Chongqing, China
| | - Xi Yang
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yuanfeng Wei
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Lingnan Zheng
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Zhaojun Li
- Department of Radiation Oncology, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Cheng Yi
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
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11
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Luo X, Lu W, Zhao J, Hu J, Chen E, Fu S, Fu Q. Identification of the TF-miRNA-mRNA co-regulatory networks involved in sepsis. Funct Integr Genomics 2022; 22:481-489. [PMID: 35322335 DOI: 10.1007/s10142-022-00843-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 03/06/2022] [Accepted: 03/07/2022] [Indexed: 11/26/2022]
Abstract
Sepsis is a life-threatening medical condition caused by a dysregulated host response to infection. Recent studies have found that the expression of miRNAs is associated with the pathogenesis of sepsis and septic shock. Our study aimed to reveal which miRNAs may be involved in the dysregulated immune response in sepsis and how these miRNAs interact with transcription factors (TFs) using a computational approach with in vitro validation studies. To determine the network of TFs, miRNAs, and target genes involved in sepsis, GEO datasets GSE94717 and GSE131761 were used to identify differentially expressed miRNAs and DEGs. TargetScan and miRWalk databases were used to predict biological targets that overlap with the identified DEGs of differentially expressed miRNAs. The TransmiR database was used to predict the differential miRNA TFs that overlap with the identified DEGs. The TF-miRNA-mRNA network was constructed and visualized. Finally, qRT-PCR was used to verify the expression of TFs and miRNA in HUVECs. Between the healthy and sepsis groups, there were 146 upregulated and 98 downregulated DEGs in the GSE131761 dataset, and there were 1 upregulated and 183 downregulated DEMs in the GSE94717 dataset. A regulatory network of the TF-miRna target genes was established. According to the experimental results, RUNX3 was found to be downregulated while MAPK14 was upregulated, which corroborates the result of the computational expression analysis. In a HUVECs model, miR-19b-1-5p and miR-5009-5p were found to be significantly downregulated. Other TFs and miRNAs did not correlate with our bioinformatics expression analysis. We constructed a TF-miRNA-target gene regulatory network and identified potential treatment targets RUNX3, MAPK14, miR-19b-1-5p, and miR-5009-5p. This information provides an initial basis for understanding the complex sepsis regulatory mechanisms.
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Affiliation(s)
- Xiaoqian Luo
- The Department of SICU, The Second Affiliated Hospital of Zhejiang University School of Medicine, Jiefang street 88th, Hangzhou, 310009, Zhejiang Province, China
| | - Weina Lu
- The Department of SICU, The Second Affiliated Hospital of Zhejiang University School of Medicine, Jiefang street 88th, Hangzhou, 310009, Zhejiang Province, China
| | - Jianfeng Zhao
- The Department of SICU, The First Affiliated Hospital, Zhejiang University School of Medicine, Qingchun street 79th, Hangzhou, 310003, Zhejiang Province, China
| | - Jun Hu
- The Department of SICU, The Second Affiliated Hospital of Zhejiang University School of Medicine, Jiefang street 88th, Hangzhou, 310009, Zhejiang Province, China
| | - Enjiang Chen
- The Department of SICU, The Second Affiliated Hospital of Zhejiang University School of Medicine, Jiefang street 88th, Hangzhou, 310009, Zhejiang Province, China
| | - Shi Fu
- The Department of SICU, The First Affiliated Hospital, Zhejiang University School of Medicine, Qingchun street 79th, Hangzhou, 310003, Zhejiang Province, China
| | - Qinghui Fu
- The Department of SICU, The First Affiliated Hospital, Zhejiang University School of Medicine, Qingchun street 79th, Hangzhou, 310003, Zhejiang Province, China.
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12
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Wu X, Li W, Luo Z, Chen Y. The molecular mechanism of Ligusticum wallichii for improving idiopathic pulmonary fibrosis: A network pharmacology and molecular docking study. Medicine (Baltimore) 2022; 101:e28787. [PMID: 35147109 PMCID: PMC8830865 DOI: 10.1097/md.0000000000028787] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/21/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND At present, there was no evidence that any drugs other than lung transplantation can effectively treat Idiopathic Pulmonary Fibrosis (IPF). Ligusticum wallichii, or Chinese name Chuan xiong has been widely used in different fibrosis fields. Our aim is to use network pharmacology and molecular docking to explore the pharmacological mechanism of the Traditional Chinese medicine (TCM) Ligusticum wallichii to improve IPF. MATERIALS AND METHODS The main chemical components and targets of Ligusticum wallichii were obtained from TCMSP, Swiss Target Prediction and Phammapper databases, and the targets were uniformly regulated in the Uniprot protein database after the combination. The main targets of IPF were obtained through Gencards, OMIM, TTD and DRUGBANK databases, and protein interaction analysis was carried out by using String to build PPI network. Metascape platform was used to analyze its involved biological processes and pathways, and Cytoscape3.8.2 software was used to construct "component-IPF target-pathway" network. And molecular docking verification was conducted through Auto Dock software. RESULTS The active ingredients of Ligusticum wallichii were Myricanone, Wallichilide, Perlolyrine, Senkyunone, Mandenol, Sitosterol and FA. The core targets for it to improve IPF were MAPK1, MAPK14, SRC, BCL2L1, MDM2, PTGS2, TGFB2, F2, MMP2, MMP9, and so on. The molecular docking verification showed that the molecular docking affinity of the core active compounds in Ligusticum wallichii (Myricanone, wallichilide, Perlolyrine) was <0 with MAPK1, MAPK14, and SRC. Perlolyrine has the strongest molecular docking ability, and its docking ability with SRC (-6.59 kJ/mol) is particularly prominent. Its biological pathway to improve IPF was mainly acted on the pathways in cancer, proteoglycans in cancer, and endocrine resistance, etc. CONCLUSIONS This study preliminarily identified the various molecular targets and multiple pathways of Ligusticum wallichii to improve IPF.
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Wu M, Huang Z, Huang W, Lin M, Liu W, Liu K, Li C. microRNA-124-3p attenuates myocardial injury in sepsis via modulating SP1/HDAC4/HIF-1α axis. Cell Death Dis 2022; 8:40. [PMID: 35091534 PMCID: PMC8799658 DOI: 10.1038/s41420-021-00763-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 10/08/2021] [Accepted: 10/14/2021] [Indexed: 12/13/2022]
Abstract
Sepsis-induced cardiac dysfunction can lead to death in sepsis. In this case, we targeted to explore in detail the relative mechanism of microRNA (miR)-124-3p in sepsis-induced myocardial injury via the specific protein 1/histone deacetylase 4/hypoxia-inducing factor 1α (SP1/HDAC4/HIF-1α) axis. Septic rats were modeled by cecal ligation puncture while in vitro septic cardiomyocyte H9C2 were induced by lipopolysaccharide (LPS). miR-124-3p/SP1/HDAC4/HIF-1α expression levels in myocardial tissues of septic rats and LPS-treated H9C2 cells were measured. miR-124-3p overexpression and SP1 silencing assays were implemented on LPS-treated H9C2 cells to explore theirs actions in inflammation, oxidative stress and cell apoptosis. The interactions of miR-124-3p, SP1, and HDAC4 were testified. miR-124-3p was lowly expressed while SP1, HDAC4, and HIF-1α were highly expressed in sepsis. Upregulation of miR-124-3p ameliorated inflammation, oxidative stress, and apoptosis of LPS-treated H9C2 cells. Silencing SP1 improved LPS-induced damage to cardiomyocytes. miR-124-3p targeted SP1 and HDAC4 interacted with SP1. SP1 overexpression antagonized miR-124-3p upregulation-induced improvements in LPS-induced cardiomyocyte damage. This study illustrates that miR-124-3p improves myocardial injury in septic rats through targeted regulation of SP1 to mediate HDAC4/HIF-1α.
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14
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Fan Y, Han Q, Li J, Ye G, Zhang X, Xu T, Li H. Revealing potential diagnostic gene biomarkers of septic shock based on machine learning analysis. BMC Infect Dis 2022; 22:65. [PMID: 35045818 PMCID: PMC8772133 DOI: 10.1186/s12879-022-07056-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 01/07/2022] [Indexed: 12/26/2022] Open
Abstract
Background Sepsis is an inflammatory response caused by infection with pathogenic microorganisms. The body shock caused by it is called septic shock. In view of this, we aimed to identify potential diagnostic gene biomarkers of the disease. Material and methods Firstly, mRNAs expression data sets of septic shock were retrieved and downloaded from the GEO (Gene Expression Omnibus) database for differential expression analysis. Functional enrichment analysis was then used to identify the biological function of DEmRNAs (differentially expressed mRNAs). Machine learning analysis was used to determine the diagnostic gene biomarkers for septic shock. Thirdly, RT-PCR (real-time polymerase chain reaction) verification was performed. Lastly, GSE65682 data set was utilized to further perform diagnostic and prognostic analysis of identified superlative diagnostic gene biomarkers. Results A total of 843 DEmRNAs, including 458 up-regulated and 385 down-regulated DEmRNAs were obtained in septic shock. 15 superlative diagnostic gene biomarkers (such as RAB13, KIF1B, CLEC5A, FCER1A, CACNA2D3, DUSP3, HMGN3, MGST1 and ARHGEF18) for septic shock were identified by machine learning analysis. RF (random forests), SVM (support vector machine) and DT (decision tree) models were used to construct classification models. The accuracy of the DT, SVM and RF models were very high. Interestingly, the RF model had the highest accuracy. It is worth mentioning that ARHGEF18 and FCER1A were related to survival. CACNA2D3 and DUSP3 participated in MAPK signaling pathway to regulate septic shock. Conclusion Identified diagnostic gene biomarkers may be helpful in the diagnosis and therapy of patients with septic shock. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-022-07056-4.
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15
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Zhang X, Tang X, Pan L, Li Y, Li J, Li C. Elevated lncRNA-UCA1 upregulates EZH2 to promote inflammatory response in sepsis-induced pneumonia via inhibiting HOXA1. Carcinogenesis 2022; 43:371-381. [PMID: 35018436 DOI: 10.1093/carcin/bgac004] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 12/13/2021] [Accepted: 01/07/2022] [Indexed: 11/13/2022] Open
Abstract
Sepsis is characterized by a dysregulated inflammatory response. We aimed to explore the role of the long non-coding RNA urothelial carcinoma associated 1 (lncRNA UCA1)/enhancer of zeste homolog 2 (EZH2)/homeobox A1 (HOXA1) axis in sepsis-induced pneumonia. The sepsis rat models and RLE-6TN cellular sepsis-induced pneumonia models were established using ligation and puncture (CLP) and lipopolysaccharide (LPS). The expression of UCA1, EZH2 and HOXA1 in rat lung tissues and RLE-6TN cells was detected. Then, the CLP rats were respectively treated with UCA1 up-regulation or UCA1 silencing, EZH2 overexpression to measure their roles in the pathology, apoptosis, inflammation and NF-κB mRNA and phosphorylated NF-κB p-65 levels in CLP rat lung tissues. The cells were subjected to same treatment to examine the effects of UCA1, EZH2 and HOXA1 on viability, apoptosis, inflammation and NF-κB mRNA and phosphorylated NF-κB p-65 levels in LPS-induced RLE-6TN cells. The interactions among UCA1, EZH2 and HOXA1 were identified. UCA1 and EZH2 were upregulated while HOXA1 was downregulated in CLP rat lung tissues and LPS-induced RLE-6TN cells. Elevated UCA1 or increased EZH2 aggravated pathology and promoted apoptosis, inflammation and NF-κB mRNA and phosphorylated NF-κB p-65 levels in CLP rat lung tissues, and inhibited viability while facilitated apoptosis, inflammation and NF-κB mRNA and phosphorylated NF-κB p-65 levels in LPS-induced RLE-6TN cells. UCA1 inhibition exerted contrary effects. Silenced EZH2 reversed the effects of UCA1 elevation on sepsis-induced pneumonia. UCA1 targeted EZH2 that interacted with HOXA1. UCA1 overexpression upregulates EZH2 to repress HOXA1 expression, thus aggravating the progression of sepsis-induced pneumonia, which could be alleviated by EZH2 inhibition.
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Affiliation(s)
- Xiaoqin Zhang
- Department of Intensive Care Unit, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Xuemei Tang
- Department of Intensive Care Unit, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Lingai Pan
- Department of Intensive Care Unit, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Yongheng Li
- Department of neurosurgery, Medical Center Hospital of QiongLai City, Chengdu 611530, China
| | - Junlei Li
- Department of Intensive Care Unit, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Chunling Li
- Department of Intensive Care Unit, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu 611731, China
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Ghafouri-Fard S, Khoshbakht T, Hussen BM, Taheri M, Arefian N. Regulatory Role of Non-Coding RNAs on Immune Responses During Sepsis. Front Immunol 2021; 12:798713. [PMID: 34956235 PMCID: PMC8695688 DOI: 10.3389/fimmu.2021.798713] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 11/19/2021] [Indexed: 12/22/2022] Open
Abstract
Sepsis is resulted from a systemic inflammatory response to bacterial, viral, or fungal agents. The induced inflammatory response by these microorganisms can lead to multiple organ system failure with devastating consequences. Recent studies have shown altered expressions of several non-coding RNAs such as long non-coding RNAs (lncRNAs), microRNAs (miRNAs) and circular RNAs (circRNAs) during sepsis. These transcripts have also been found to participate in the pathogenesis of multiple organ system failure through different mechanisms. NEAT1, MALAT1, THRIL, XIST, MIAT and TUG1 are among lncRNAs that participate in the pathoetiology of sepsis-related complications. miR-21, miR-155, miR-15a-5p, miR-494-3p, miR-218, miR-122, miR-208a-5p, miR-328 and miR-218 are examples of miRNAs participating in these complications. Finally, tens of circRNAs such as circC3P1, hsa_circRNA_104484, hsa_circRNA_104670 and circVMA21 and circ-PRKCI have been found to affect pathogenesis of sepsis. In the current review, we describe the role of these three classes of noncoding RNAs in the pathoetiology of sepsis-related complications.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Tayyebeh Khoshbakht
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Iraq.,Center of Research and Strategic Studies, Lebanese French University, Erbil, Iraq
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Normohammad Arefian
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Jia X, Huang J, Wu B, Yang M, Xu W. A Competitive Endogenous RNA Network Based on Differentially Expressed lncRNA in Lipopolysaccharide-Induced Acute Lung Injury in Mice. Front Genet 2021; 12:745715. [PMID: 34917127 PMCID: PMC8669720 DOI: 10.3389/fgene.2021.745715] [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: 07/28/2021] [Accepted: 10/14/2021] [Indexed: 12/03/2022] Open
Abstract
Non-coding RNAs have remarkable roles in acute lung injury (ALI) initiation. Nevertheless, the significance of long non-coding RNAs (lncRNAs) in ALI is still unknown. Herein, we purposed to identify potential key genes in ALI and create a competitive endogenous RNA (ceRNA) modulatory network to uncover possible molecular mechanisms that affect lung injury. We generated a lipopolysaccharide-triggered ALI mouse model, whose lung tissue was subjected to RNA sequencing, and then we conducted bioinformatics analysis to select genes showing differential expression (DE) and to build a lncRNA-miRNA (microRNA)- mRNA (messenger RNA) modulatory network. Besides, GO along with KEGG assessments were conducted to identify major biological processes and pathways, respectively, involved in ALI. Then, RT-qPCR assay was employed to verify levels of major RNAs. A protein-protein interaction (PPI) network was created using the Search Tool for the Retrieval of Interacting Genes (STRING) database, and the hub genes were obtained with the Molecular Complex Detection plugin. Finally, a key ceRNA subnetwork was built from major genes and their docking sites. Overall, a total of 8,610 lncRNAs were identified in the normal and LPS groups. Based on the 308 DE lncRNAs [p-value < 0.05, |log2 (fold change) | > 1] and 3,357 DE mRNAs [p-value < 0.05, |log2 (fold change) | > 1], lncRNA-miRNA and miRNA-mRNA pairs were predicted using miRanda. The lncRNA-miRNA-mRNA network was created from 175 lncRNAs, 22 miRNAs, and 209 mRNAs in ALI. The RT-qPCR data keep in step with the RNA sequencing data. GO along with KEGG analyses illustrated that DE mRNAs in this network were mainly bound up with the inflammatory response, developmental process, cell differentiation, cell proliferation, apoptosis, and the NF-kappa B, PI3K-Akt, HIF-1, MAPK, Jak-STAT, and Notch signaling pathways. A PPI network on the basis of the 209 genes was established, and three hub genes (Nkx2-1, Tbx2, and Atf5) were obtained from the network. Additionally, a lncRNA-miRNA-hub gene subnetwork was built from 15 lncRNAs, 3 miRNAs, and 3 mRNAs. Herein, novel ideas are presented to expand our knowledge on the regulation mechanisms of lncRNA-related ceRNAs in the pathogenesis of ALI.
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Affiliation(s)
- Xianxian Jia
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jinhui Huang
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Bo Wu
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Miao Yang
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Wei Xu
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
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Wang Y, Wang X, Zhang H, Han B, Ye Y, Zhang M, Wang Y, Xue J, Wang C. Transforming Growth Factor-β1 Promotes M1 Alveolar Macrophage Polarization in Acute Lung Injury by Up-Regulating DNMT1 to Mediate the microRNA-124/PELI1/IRF5 Axis. Front Cell Infect Microbiol 2021; 11:693981. [PMID: 34504806 PMCID: PMC8421846 DOI: 10.3389/fcimb.2021.693981] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/29/2021] [Indexed: 12/12/2022] Open
Abstract
Objective Macrophages function as key orchestrators in the pathogenesis of acute lung injury (ALI). The current study sets out to investigate the molecular mechanism of transforming growth factor-β (TGFβ1) in the regulation of M1 alveolar macrophage polarization in ALI by modulating DNA methyltransferase 1 (DNMT1), along with the microRNA (miR)-124/Pellino 1 (PELI1)/interferon regulatory factor 5 (IRF5) axis. Methods First, ALI mouse models were established, and the proportion of M1 and M2 macrophages in mouse lung tissues was detected using flow cytometry. The targeting relationship between miR-124 and PELI1 was verified with the help of a dual luciferase gene reporter assay. Following TGFβ1 knockdown, RT-qPCR and Western blot assay were performed to analyze the expression patterns of TGFβ1, DNMT1, miR-124, and PELI1 and M1/M2 polarization markers in the lung tissues of ALI mice. Immunofluorescence was further employed to detect nuclear translocation of IRF5 in macrophages. Results The polarization of M1 macrophages was found to be positively correlated with the severity of lung injury. TGFβ1, DNMT1, PELI1 were highly expressed, while miR-124 was down-regulated in ALI mice, and IRF5 was primarily distributed in the nucleus. TGFβ1 promoted the polarization of M1 alveolar macrophages by up-regulating DNMT1. Furthermore, DNMT1 down-regulated the expression of miR-124, which led to enhancement of M1 alveolar macrophage polarization. Meanwhile, over-expression of miR-124 inhibited the nuclear translocation of IRF5 and suppressed M1 alveolar macrophage polarization. On the other hand, over-expression of PELI1 reversed the above trends. Conclusion Collectively, our findings indicated that TGFβ1 can promote the expression of DNMT1, which down-regulates miR-124 to activate PELI1 and nuclear translocation of IRF5, thereby aggravating ALI in mice.
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Affiliation(s)
- Yongqi Wang
- Department of Anesthesiology, The First Hospital of Lanzhou University, Lanzhou, China
| | - Xiaoqing Wang
- Department of Anesthesiology, The First Hospital of Lanzhou University, Lanzhou, China
| | - Hong Zhang
- Department of Anesthesiology, The First Hospital of Lanzhou University, Lanzhou, China
| | - Biao Han
- Department of Thoracic Surgery, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yuanmei Ye
- Department of Anesthesiology, The First Hospital of Lanzhou University, Lanzhou, China
| | - Mengjie Zhang
- Department of Anesthesiology, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yingbin Wang
- Department of Anesthesiology, Lanzhou University Second Hospital, Lanzhou, China
| | - Jianjun Xue
- Department of Anesthesiology, Gansu Provincial Hospital of TCM, Lanzhou, China
| | - Chun'ai Wang
- Department of Anesthesiology, Gansu Provincial Hospital of TCM, Lanzhou, China
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Genome-Wide Analysis of LncRNA in Bovine Mammary Epithelial Cell Injuries Induced by Escherichia Coli and Staphylococcus Aureus. Int J Mol Sci 2021; 22:ijms22189719. [PMID: 34575880 PMCID: PMC8470725 DOI: 10.3390/ijms22189719] [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: 07/28/2021] [Revised: 08/11/2021] [Accepted: 09/04/2021] [Indexed: 12/19/2022] Open
Abstract
Escherichia coli and Staphylococcus aureus are two common pathogenic microorganisms that cause mastitis in dairy cows. They can cause clinical mastitis and subclinical mastitis. In recent studies, lncRNAs have been found to play an important role in the immune responses triggered by microbial inducers. However, the actions of lncRNAs in bovine mastitis remain unclear. The purpose of this study was to investigate the effects of bovine mammary epithelial cell injuries induced by treatment with E. coli and S. aureus, and to explore the lncRNA profile on cell injuries. The lncRNA transcriptome analysis showed a total of 2597 lncRNAs. There were 2234 lncRNAs differentially expressed in the E. coli group and 2334 in the S. aureus group. Moreover, we found that the E. coli and S. aureus groups of maternal genes targeted signaling pathways with similar functions according to KEGG and GO analyses. Two lncRNA-miRNA-mRNA interaction networks were constructed in order to predict the potential molecular mechanisms of regulation in the cell injuries. We believe that this is the first report demonstrating the dysregulation of lncRNAs in cells upon E. coli and S. aureus infections, suggesting that they have the potential to become important diagnostic markers and to provide novel insights into controlling and preventing mastitis.
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Huang Q, Chen L, Bai Q, Tong T, Zhou Y, Li Z, Lu C, Chen S, Chen L. The roles of microRNAs played in lung diseases via regulating cell apoptosis. Mol Cell Biochem 2021; 476:4265-4275. [PMID: 34398353 DOI: 10.1007/s11010-021-04242-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 08/10/2021] [Indexed: 01/24/2023]
Abstract
MicroRNAs (miRNAs) are a type of endogenous non-coding short-chain RNA, which plays a crucial role in the regulation of many essential cellular functions, including cellular migration, proliferation, invasion, autophagy, oxidative stress, apoptosis, and differentiation. The lung can be damaged by pathogenic microorganisms, as well as physical or chemical factors. Research has confirmed that miRNAs and lung cell apoptosis can affect the development and progression of several lung diseases. This article reviews the role of miRNAs in the development of lung disease through regulating host cell apoptosis.
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Affiliation(s)
- Qiaoling Huang
- Department of Public Health Laboratory Sciences, College of Public Health, Hengyang Medical School, University of South China, 28 West Changsheng Rd, Hengyang, 421001, Hunan, China.,Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, College of Public Health, University of South China, 28 West Changsheng Rd, Hengyang, 421001, Hunan, China
| | - Li Chen
- Department of Public Health Laboratory Sciences, College of Public Health, Hengyang Medical School, University of South China, 28 West Changsheng Rd, Hengyang, 421001, Hunan, China.,Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, College of Public Health, University of South China, 28 West Changsheng Rd, Hengyang, 421001, Hunan, China
| | - Qinqin Bai
- Department of Public Health Laboratory Sciences, College of Public Health, Hengyang Medical School, University of South China, 28 West Changsheng Rd, Hengyang, 421001, Hunan, China.,Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, College of Public Health, University of South China, 28 West Changsheng Rd, Hengyang, 421001, Hunan, China
| | - Ting Tong
- Department of Public Health Laboratory Sciences, College of Public Health, Hengyang Medical School, University of South China, 28 West Changsheng Rd, Hengyang, 421001, Hunan, China.,Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, College of Public Health, University of South China, 28 West Changsheng Rd, Hengyang, 421001, Hunan, China
| | - You Zhou
- Department of Public Health Laboratory Sciences, College of Public Health, Hengyang Medical School, University of South China, 28 West Changsheng Rd, Hengyang, 421001, Hunan, China.,Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, College of Public Health, University of South China, 28 West Changsheng Rd, Hengyang, 421001, Hunan, China
| | - Zhongyu Li
- Hengyang Medical School, University of South China, 28 West Changsheng Rd, Hengyang, 421001, Hunan, China
| | - Chunxue Lu
- Hengyang Medical School, University of South China, 28 West Changsheng Rd, Hengyang, 421001, Hunan, China
| | - Shenghua Chen
- Hengyang Medical School, University of South China, 28 West Changsheng Rd, Hengyang, 421001, Hunan, China.
| | - Lili Chen
- Department of Public Health Laboratory Sciences, College of Public Health, Hengyang Medical School, University of South China, 28 West Changsheng Rd, Hengyang, 421001, Hunan, China. .,Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, College of Public Health, University of South China, 28 West Changsheng Rd, Hengyang, 421001, Hunan, China.
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21
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Zhang R, Chen L, Huang F, Wang X, Li C. Long non-coding RNA NEAT1 promotes lipopolysaccharide-induced acute lung injury by regulating miR-424-5p/MAPK14 axis. Genes Genomics 2021; 43:815-827. [PMID: 33904112 DOI: 10.1007/s13258-021-01103-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 04/12/2021] [Indexed: 12/21/2022]
Abstract
BACKGROUND Many long non-coding RNAs (lncRNAs) have been suggested to play critical roles in acute lung injury (ALI) pathogenesis, including lncRNA nuclear enriched abundant transcript 1 (NEAT1). OBJECTIVE We aimed to further elucidate the functions and molecular mechanism of NEAT1 in ALI. METHODS Human pulmonary alveolar epithelial cells (HPAEpiCs) stimulated by lipopolysaccharide (LPS) were served as a cellular model of ALI. Cell viability and cell apoptosis were determined by cell counting kit-8 (CCK-8) assay and flow cytometry, respectively. The expression of NEAT1, microRNA-424-5p (miR-424-5p), and mitogen-activated protein kinase 14 (MAPK14) was measured by quantitative real-time polymerase chain reaction (qRT-PCR) or western blot analysis. Caspase activity was determined by caspase activity kit. The inflammatory responses were evaluated using enzyme-linked immunosorbent assay (ELISA). The oxidative stress factors were analyzed by corresponding kits. RESULTS NEAT1 was upregulated in LPS-stimulated HPAEpiCs. NEAT1 knockdown weakened LPS-induced injury by inhibiting apoptosis, inflammation and oxidative stress in HPAEpiCs. Moreover, miR-424-5p was a direct target of NEAT1, and its knockdown reversed the effects caused by NEAT1 knockdown in LPS-induced HPAEpiCs. Furthermore, MAPK14 was a downstream target of miR-424-5p, and its overexpression attenuated the effects of miR-424-5p on reduction of LPS-induced injury in HPAEpiCs. Besides, NEAT1 acted as a sponge of miR-424-5p to regulate MAPK14 expression. CONCLUSION NEAT1 knockdown alleviated LPS-induced injury of HPAEpiCs by regulating miR-424-5p/MAPK14 axis, which provided a potential therapeutic target for the treatment of ALI.
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Affiliation(s)
- Rui Zhang
- Department of Paediatrics, Suizhou Hospital, Hubei University of Medicine, Long Men Street 60th, Zeng Du District, Suizhou, 441300, Hubei, China
| | - Lina Chen
- Department of Paediatrics, Suizhou Hospital, Hubei University of Medicine, Long Men Street 60th, Zeng Du District, Suizhou, 441300, Hubei, China
| | - Fei Huang
- Department of Paediatrics, Suizhou Hospital, Hubei University of Medicine, Long Men Street 60th, Zeng Du District, Suizhou, 441300, Hubei, China
| | - Xiaorong Wang
- Department of Paediatrics, Suizhou Hospital, Hubei University of Medicine, Long Men Street 60th, Zeng Du District, Suizhou, 441300, Hubei, China
| | - Cuihong Li
- Department of Paediatrics, Suizhou Hospital, Hubei University of Medicine, Long Men Street 60th, Zeng Du District, Suizhou, 441300, Hubei, China.
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22
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Sun J, Xin K, Leng C, Ge J. Down-regulation of SNHG16 alleviates the acute lung injury in sepsis rats through miR-128-3p/HMGB3 axis. BMC Pulm Med 2021; 21:191. [PMID: 34092219 PMCID: PMC8180123 DOI: 10.1186/s12890-021-01552-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/10/2021] [Indexed: 02/08/2023] Open
Abstract
Background Long noncoding RNAs contribute to various inflammatory diseases, including sepsis. We explore the role of small nucleolar RNA host gene 16 (SNHG16) in sepsis-mediated acute lung injury (ALI) and inflammation. Methods A sepsis-induced ALI rat model was constructed by the cecal ligation and perforation method. The profiles of SNHG16, miR-128-3p, and high-mobility group box 3 (HMGB3) were monitored by quantitative reverse transcription PCR and Western blot. The pathologic changes of lung tissues were evaluated by Hematoxylin–Eosin staining, immunohistochemistry, and dry and wet method. Meanwhile, the pro-inflammatory factors and proteins were determined by ELISA and Western blot. In contrast, a sepsis model in BEAS-2B was induced with lipopolysaccharide (LPS) to verify the effects of SNHG16/miR-128-3p/HMGB3 on lung epithelial cell viability and apoptosis. Results As a result, SNHG16 and HMGB3 were up-regulated, while miR-128-3p was down-regulated in sepsis-induced ALI both in vivo and in vitro. Inhibiting SNHG16 reduced the apoptosis and inflammation in the sepsis-induced ALI model. Overexpressing SNHG16 promoted LPS-mediated lung epithelial apoptosis and inhibited cell viability and inflammation, while miR-128-3p had the opposite effects. Mechanistically, SNHG16 targeted miR-128-3p and attenuated its expression, while miR-128-3p targeted the 3′ untranslated region of HMGB3. Conclusions Overall, down-regulating SNHG16 alleviated the sepsis-mediated ALI by regulating miR-128-3p/HMGB3. Supplementary Information The online version contains supplementary material available at 10.1186/s12890-021-01552-0.
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Affiliation(s)
- Junli Sun
- General ICU, Luoyang Central Hospital Affiliated To Zhengzhou University, 288 Zhongzhou Middle Road, Luoyang, 471009, Henan, China.
| | - Keke Xin
- General ICU, Luoyang Central Hospital Affiliated To Zhengzhou University, 288 Zhongzhou Middle Road, Luoyang, 471009, Henan, China
| | - Chenghui Leng
- General ICU, Luoyang Central Hospital Affiliated To Zhengzhou University, 288 Zhongzhou Middle Road, Luoyang, 471009, Henan, China
| | - Jianlin Ge
- General ICU, Luoyang Central Hospital Affiliated To Zhengzhou University, 288 Zhongzhou Middle Road, Luoyang, 471009, Henan, China
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23
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Zhang X, Cui Y, Ding X, Liu S, Han B, Duan X, Zhang H, Sun T. Analysis of mRNA‑lncRNA and mRNA‑lncRNA-pathway co‑expression networks based on WGCNA in developing pediatric sepsis. Bioengineered 2021; 12:1457-1470. [PMID: 33949285 PMCID: PMC8806204 DOI: 10.1080/21655979.2021.1908029] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Pediatric sepsis is a great threat to death worldwide. However, the pathogenesis has not been clearly understood until now in sepsis. This study identified differentially expressed mRNAs and lncRNAs based on Gene Expression Omnibus (GEO) database. And the weighted gene co-expression network analysis (WGCNA) was performed to explore co-expression modules associated with pediatric sepsis. Then, Gene Ontology (GO), KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway, mRNA‑lncRNA and mRNA‑lncRNA-pathway co-expression network analysis was conducted in selected significant module. A total of 1941 mRNAs and 225 lncRNAs were used to conduct WGCNA. And turquoise module was selected as a significant module that was associated with particular traits. The mRNAs functions associated with many vital processes were also shown by GO and KEGG pathway analysis in the turquoise module. Finally, 15 mRNAs (MAPK14, ITGAM, HK3, ALOX5, CR1, HCK, NCF4, PYGL, FLOT1, CARD6, NLRC4, SH3GLB1, PGS1, RAB31, LTB4R) and 4 lncRNAs (GSEC, NONHSAT160878.1, XR_926068.1 and RARA-AS1) were selected as hub genes in mRNA‑lncRNA-Pathway co-expression network. We identified 15 mRNAs and 4 lncRNAs as diagnostic markers, which have potential functions in pediatric sepsis. Our study provides more directions to study the molecular mechanism of pediatric sepsis.Abbreviations: mRNA: messenger RNA; lncRNA: long noncoding RNAs; GEO: Gene Expression Omnibus; WGCNA: weighted gene co-expression network analysis; GO: Gene Ontology; KEGG: Kyoto Encyclopedia of Genes and Genomes; SIRS: systemic inflammatory response syndrome; TOM: topological overlap measure; BP: biological process; MF: molecular function; CC: cellular component; ROC: receiver operating characteristic curve; AUC: area under curve; MAPK14: Mitogen-activated protein kinase 14; ALI: acute lung injury; ITGAM: Integrin subunit alpha M; HK3: Hexokinase 3; LPS: lipopolysaccharide; 5-LO: 5-lipoxygenase; LTs: leukotrienes; LTB4R: leukotriene B4 receptor.
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Affiliation(s)
- Xiaojuan Zhang
- General ICU, Zhengzhou Key Laboratory of Sepsis, Henan Engineering Research Center for Critical Care Medicine, the First Affiliated Hospital of Zhengzhou University, Henan Key Laboratory of Critical Care Medicine, Zhengzhou, China
| | - Yuqing Cui
- General ICU, Zhengzhou Key Laboratory of Sepsis, Henan Engineering Research Center for Critical Care Medicine, the First Affiliated Hospital of Zhengzhou University, Henan Key Laboratory of Critical Care Medicine, Zhengzhou, China
| | - Xianfei Ding
- General ICU, Zhengzhou Key Laboratory of Sepsis, Henan Engineering Research Center for Critical Care Medicine, the First Affiliated Hospital of Zhengzhou University, Henan Key Laboratory of Critical Care Medicine, Zhengzhou, China
| | - Shaohua Liu
- General ICU, Zhengzhou Key Laboratory of Sepsis, Henan Engineering Research Center for Critical Care Medicine, the First Affiliated Hospital of Zhengzhou University, Henan Key Laboratory of Critical Care Medicine, Zhengzhou, China
| | - Bing Han
- General ICU, Zhengzhou Key Laboratory of Sepsis, Henan Engineering Research Center for Critical Care Medicine, the First Affiliated Hospital of Zhengzhou University, Henan Key Laboratory of Critical Care Medicine, Zhengzhou, China
| | - Xiaoguang Duan
- General ICU, Zhengzhou Key Laboratory of Sepsis, Henan Engineering Research Center for Critical Care Medicine, the First Affiliated Hospital of Zhengzhou University, Henan Key Laboratory of Critical Care Medicine, Zhengzhou, China
| | - Haibo Zhang
- Interdepartmental Division of Critical Care Medicine, Departments of Anesthesia and Physiology, University of Toronto, Toronto, Canada
| | - Tongwen Sun
- General ICU, Zhengzhou Key Laboratory of Sepsis, Henan Engineering Research Center for Critical Care Medicine, the First Affiliated Hospital of Zhengzhou University, Henan Key Laboratory of Critical Care Medicine, Zhengzhou, China
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24
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Zhu Y, Wang Y, Xing S, Xiong J. Blocking SNHG14 Antagonizes Lipopolysaccharides-Induced Acute Lung Injury via SNHG14/miR-124-3p Axis. J Surg Res 2021; 263:140-150. [PMID: 33652176 DOI: 10.1016/j.jss.2020.10.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 09/15/2020] [Accepted: 10/31/2020] [Indexed: 12/30/2022]
Abstract
BACKGROUND Emerging evidence show that long noncoding RNAs (lncRNAs) are crucial regulators in pathophysiology of acute lung injury (ALI). Small nucleolar RNA host gene 14 (SNHG14) is a novel oncogenic lncRNA, and has been associated with inflammation-related cell injuries. Thus, we wondered the role and mechanism of SNHG14 in lipopolysaccharides (LPS)-induced ALI cell model. METHODS Expression of SNHG14, miRNA (miR)-124-3p, and transforming growth factor β type 2 receptor (TGFBR2) was detected by RT-qPCR and western blotting. Cell apoptosis was determined by methyl thiazolyl tetrazolium assay, flow cytometry, western blotting, and lactate dehydrogenase activity kit. Inflammation was measured by enzyme-linked immunosorbent assay. The interaction among SNHG14, miR-124-3p, and TGFBR2 was validated by dual-luciferase reporter assay and RNA immunoprecipitation. RESULTS LPS administration attenuated human lung epithelial cell viability and B-cell lymphoma-2 expression, but augmented apoptosis rate, cleaved-caspase-3 expression, lactate dehydrogenase activity, and secretions of tumor necrosis factor-α, interleukin-1β, and IL-6 in A549 cells. Thus, LPS induced A549 cells apoptosis and inflammation, wherein SNHG14 was upregulated and miR-124-3p was downregulated. However, silencing SNHG14 could suppress LPS-induced apoptosis and inflammation depending on upregulating miR-124-3p via target binding. Similarly, overexpressing miR-124-3p attenuated LPS-induced A549 cells injury through inhibiting its downstream target TGFBR2. Furthermore, SNHG14 knockdown could also affect TGFBR2 expression via miR-124-3p. CONCLUSIONS SNHG14 knockdown prevents A549 cells from LPS-induced apoptosis and inflammation through regulating miR-124-3p and TGFBR2, suggesting a novel SNHG14/miR-124-3p/TGFBR2 circuit in alveolar epithelial cells on the set of ALI.
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Affiliation(s)
- Yuanbin Zhu
- Department of Respiratory, Linyi Central Hospital, Linyi, Shandong, China
| | - Yingying Wang
- Department of Respiratory, Linyi Central Hospital, Linyi, Shandong, China
| | - Shigang Xing
- Department of Respiratory, Linyi Central Hospital, Linyi, Shandong, China
| | - Jie Xiong
- Department of Respiratory, Linyi Central Hospital, Linyi, Shandong, China.
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25
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Gao X, Yang Q, Zhang S, Huang X, Yan Z, Wang P, Luo R, Wang W, Xie K, Gun S. Epigenetic upregulation of ssc-miR-124a following treatment with Clostridium perfringens beta2-toxin attenuates both apoptosis and inflammation in intestinal porcine epithelial cells. Arch Biochem Biophys 2021; 701:108806. [PMID: 33587903 DOI: 10.1016/j.abb.2021.108806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 12/19/2022]
Abstract
Clostridium perfringens (C. perfringens) is a globally recognized zoonotic pathogen. It has been reported that the beta2-toxin produced by C. perfringens can cause a variety of gastrointestinal diseases and even systemic inflammation. MicroRNA-124a (miR-124a) has been reported to play important roles in the host response to pathogenic infection. Although C. perfringens beta2-toxin induced injury in intestinal porcine epithelial (IPEC-J2) cells has been established, the underlying molecular mechanism is not completely unraveled. Here we show that a significant upregulation of ssc-miR-124a in IPEC-J2 cells after beta2-toxin stimulation was associated with the MiR-124A-1 and MiR-124A-2 gene promoter demethylation status. Importantly, overexpression of ssc-miR-124a significantly increased cell proliferation and decreased apoptosis and cytotoxicity in beta2-toxin treated IPEC-J2 cells. Transfection of IPEC-J2 cells with ssc-miR-124a mimic suppressed beta2-toxin induced inflammation. On the contrary, ssc-miR-124a inhibitor promoted aggravation of cell apoptosis and excessive damage. Furthermore, rho-associated coiled-coil-containing protein kinase 1 (ROCK1) was identified as the direct target gene of ssc-miR-124a in IPEC-J2 cells and its siRNA transfection reversed the promotion of apoptosis and aggravation of cellular damage induced by ssc-miR-124a inhibitor. Overall, we speculated that the miR-124A-1/2 gene was epigenetically regulated in IPEC-J2 cells after beta2-toxin treatment. Upregulation of ssc-miR-124a may restrain ROCK1, and attenuate apoptosis and inflammation induced by beta2-toxin that prevent IPEC-J2 cells from severe damages. We discover a new molecular mechanism by which IPEC-J2 cells counteract beta2-toxin-induced damage through the ssc-miR-124a/ROCK1 axis partially.
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Affiliation(s)
- Xiaoli Gao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Qiaoli Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Shengwei Zhang
- Farmer Education and Training Work Station of Gansu Province, Lanzhou, 730070, China
| | - Xiaoyu Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Zunqiang Yan
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Pengfei Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Ruirui Luo
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Wei Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Kaihui Xie
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Shuangbao Gun
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China; Gansu Research Center for Swine Production Engineering and Technology, Lanzhou, 730070, China.
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26
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Down-regulation of miR-let-7e attenuates LPS-induced acute lung injury in mice via inhibiting pulmonary inflammation by targeting SCOS1/NF-κB pathway. Biosci Rep 2021; 41:227104. [PMID: 33392621 PMCID: PMC7785041 DOI: 10.1042/bsr20201089] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 12/26/2022] Open
Abstract
Excessive pulmonary inflammatory response is critical in the development of acute lung injury (ALI). Previously, microRNAs (miRNAs) have been recognized as an important regulator of inflammation in various diseases. However, the effects and mechanisms of miRNAs on inflammatory response in ALI remain unclear. Herein, we tried to screen miRNAs in the processes of ALI and elucidate the potential mechanism. Using a microarray assay, microRNA let-7e (let-7e) was chose as our target for its reported suppressive roles in several inflammatory diseases. Down-regulation of let-7e by antagomiR-let-7e injection attenuated LPS-induced acute lung injury. We also found that antagomiR-let-7e could obviously improve the survival rate in ALI mice. Moreover, antagomiR-let-7e treatment reduced the production of proinflammatory cytokines (i.e., TNF-α, IL-1β and IL-6) in bronchoalveolar lavage fluid (BALF) of LPS-induced ALI mice. Luciferase reporter assays confirmed that suppressor of cytokine signaling 1 (SOCS1), a powerful attenuator of nuclear factor kappa B (NF-κB) signaling pathway, was directly targeted and suppressed by let-7e in RAW264.7 cells. In addition, it was further observed that SOCS1 was down-regulated, and inversely correlated with let-7e expression levels in lung tissues of ALI mice. Finally, down-regulation of let-7e suppressed the activation of NF-κB pathway, as evidenced by the reduction of p-IκBα, and nuclear p-p65 expressions in ALI mice. Collectively, our findings indicate that let-7e antagomir protects mice against LPS-induced lung injury via repressing the pulmonary inflammation though regulation of SOCS1/NF-κB pathway, and let-7e may act as a potential therapeutic target for ALI.
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27
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Xiu MX, Liu ZT, Tang J. Screening and identification of key regulatory connections and immune cell infiltration characteristics for lung transplant rejection using mucosal biopsies. Int Immunopharmacol 2020; 87:106827. [PMID: 32791489 PMCID: PMC7417178 DOI: 10.1016/j.intimp.2020.106827] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/03/2020] [Accepted: 07/20/2020] [Indexed: 02/06/2023]
Abstract
This study aimed to explore key regulatory connections underlying lung transplant rejection. The differentially expressed genes (DEGs) between rejection and stable lung transplantation (LTx) samples were screened using R package limma, followed by functional enrichment analysis and protein-protein interaction network construction. Subsequently, a global triple network, including miRNAs, mRNAs, and transcription factors (TFs), was constructed. Furthermore, immune cell infiltration characteristics were analyzed to investigate the molecular immunology of lung transplant rejection. Finally, potential drug-target interactions were generated. In brief, 739 DEGs were found between rejection and stable LTx samples. PTPRC, IL-6, ITGAM, CD86, TLR8, TYROBP, CXCL10, ITGB2, and CCR5 were defined as hub genes. Eight TFs, including STAT1, SPIB, NFKB1, SPI1, STAT5A, RUNX1, VENTX, and BATF, and five miRNAs, including miR-335-5p, miR-26b-5p, miR-124-3p, miR-1-3p, and miR-155-5p, were involved in regulating hub genes. The immune cell infiltration analysis revealed higher proportions of activated memory CD4 T cells, follicular helper T cells, γδ T cells, monocytes, M1 and M2 macrophages, and eosinophils in rejection samples, besides lower proportions of resting memory CD4 T cells, regulatory T cells, activated NK cells, M0 macrophages, and resting mast cells. This study provided a comprehensive perspective of the molecular co-regulatory network underlying lung transplant rejection.
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Affiliation(s)
- Meng-Xi Xiu
- Medical School of Nanchang University, Nanchang, PR China
| | - Zu-Ting Liu
- Medical School of Nanchang University, Nanchang, PR China
| | - Jian Tang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang 330006, PR China.
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28
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Wang J, Zhao Q. Linc02381 Exacerbates Rheumatoid Arthritis Through Adsorbing miR-590-5p and Activating the Mitogen-Activated Protein Kinase Signaling Pathway in Rheumatoid arthritis-fibroblast-like synoviocytes. Cell Transplant 2020; 29:963689720938023. [PMID: 32608996 PMCID: PMC7563894 DOI: 10.1177/0963689720938023] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/17/2020] [Accepted: 06/01/2020] [Indexed: 12/29/2022] Open
Abstract
Rheumatoid arthritis (RA) is a chronic systemic autoimmune disease. New evidence suggested that linc02381 suppressed colorectal cancer progression by regulating PI3 K signaling pathway, but the role of linc02381 in other diseases, such as RA, remains unclear. This study aimed to reveal the mechanism of linc02381 in RA progression. In vivo and in vitro, we found that linc02381 was upregulated in RA synovial tissues or RA fibroblast-like synoviocytes (RA-FLSs, P < 0.01), which were detected by quantitative real-time polymerase chain reaction. Cell Counting Kit-8, EDU, and Transwell assays revealed that linc02381 overexpression enhanced cell proliferation and invasion, and linc02381 knockdown inhibited cell proliferation and invasion in FLSs. Moreover, the results of bioinformatics analysis, luciferase reporter gene assay, and pull-down assay verified that linc02381 could directly bind with miR-590-5p. MiR-590-5p was downregulated in RA-FLSs, and overexpression of linc02381 suppressed expression of miR-590-5p that post-transcriptionally suppressed the expression of mitogen-activated protein kinase kinase 3 (MAP2K3), and overexpression of miR-590-5p reversed the effect of linc02381 overexpression on MAP2K3 expression. MiR-590-5p inhibitor reversed the inhibition effect of linc02381 knockdown on proliferation and invasion of FLSs, which enhanced expression of MAP2K3, and activation of p38 and AP-1 in the MAPK signaling pathway. In summary, linc02381 was upregulated in RA synovial tissues and RA-FLSs, and it exacerbated RA by adsorbing miR-590-5p to activate the MAPK signaling pathway.
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Affiliation(s)
- Jing Wang
- Department of Rheumatology and Immunology, Huaihe Hospital of Henan University, Kaifeng, People’s Republic of China
| | - Qing Zhao
- Department of Rheumatology and Immunology, Huaihe Hospital of Henan University, Kaifeng, People’s Republic of China
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