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Wang K, Chen Z, Qiao X, Zheng J. LncRNA NORAD regulates the mechanism of the miR-532-3p/Nectin-4 axis in pancreatic cancer cell proliferation and angiogenesis. Toxicol Res (Camb) 2023; 12:425-432. [PMID: 37397924 PMCID: PMC10311138 DOI: 10.1093/toxres/tfad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 02/15/2023] [Accepted: 03/30/2023] [Indexed: 07/04/2023] Open
Abstract
Backgound Pancreatic cancer (PC) is one of the deadliest cancers worldwide, and cell proliferation and angiogenesis play an important role in its occurrence and development. High levels of lncRNANORAD have been detected in many tumors, including PC, yet the effect and mechanism of lncRNA NORAD on PC cell angiogenesis are unexplored. Methods qRT.PCR was applied to quantify lncRNA NORAD and miR-532-3p expression in PC cells, and a dual luciferase reporter gene was used to verify the targeting effects of NORAD, miR-532-3p and Nectin-4. Then, we regulated NORAD and miR-532-3p expression in PC cells and detected their effects on PC cell proliferation and angiogenesis using cloning experiments and HUVEC tube formation experiments. Results LncRNA NORAD was upregulated and miR-532-3p was downregulated in PC cells compared with normal cells. Knockdown of NORAD inhibited PC cell proliferation and angiogenesis. LncRNA NORAD and miR-532-3p competitively bound to promote the expression of the miR-532-3p target gene Nectin-4, thereby promoting proliferation and angiogenesis of PC cells in vitro. Conclusion LncRNA NORAD promotes the proliferation and angiogenesis of PC cells by regulating the miR-532-3p/Nectin-4 axis, which may be a potential biological target in the diagnosis and treatment of clinical PC.
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Affiliation(s)
- Kaiqiong Wang
- Department of Hepatobiliary Surgery, Hainan Provincial People's Hospital, No.19, Xiuhua Road, Haikou, Hainan Province 570311, China
| | - Zhiju Chen
- Department of Gastrointestinal Surgery, Hainan Provincial People’s Hospital, No.19, Xiuhua Road, Haikou, Hainan Province 570311, China
| | - Xin Qiao
- Department of Hepatobiliary Surgery, Hainan Provincial People's Hospital, No.19, Xiuhua Road, Haikou, Hainan Province 570311, China
| | - Jinfang Zheng
- Department of Hepatobiliary Surgery, Hainan Provincial People's Hospital, No.19, Xiuhua Road, Haikou, Hainan Province 570311, China
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Yuan Y, Li N, Fu M, Ye M. Identification of Critical Modules and Biomarkers of Ulcerative Colitis by Using WGCNA. J Inflamm Res 2023; 16:1611-1628. [PMID: 37092131 PMCID: PMC10120594 DOI: 10.2147/jir.s402715] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/28/2023] [Indexed: 04/25/2023] Open
Abstract
Background Ulcerative colitis (UC) is a chronic inflammatory disease of the colon and rectum that has no exact cause and is characterized by relapsing and remitting episodes. We aimed to find biomarkers of UC and its causes. Methods We got GSE73661 from the GEO database and used WGCNA to find DEGs that were expressed in the same way in both normal and UC samples. To identify the co-expression modules, we used Weighted Gene Co-Expression Network Analysis. Next, we selected genes that were both DEGs and parts of main modules. Later, three datasets were used to find the hub genes, and qRT-PCR was utilized to confirm the in-silico findings. Additionally, we analyzed the connection between the hub genes and the filtration of immune cells in UC. Using the databases, we made predictions about the miRNAs and lncRNAs that regulate the hub genes and predicted possible therapeutic drugs. Results We found 822 DEGs and three main modules related to immunity, endoplasmic reticulum, and metabolism. Using another three datasets and human samples to confirm the mRNA expression of these genes in UC patients, XBP1 and PLPP1 were selected as hub genes, and had excellent diagnostic potential. According to the findings of the immune infiltration, patients with UC exhibited a larger proportion of immune cells. And hub genes, particularly XBP1, were closely linked to a number of immune cell infiltrations. Based on the databases and hub genes, a lncRNA-miRNA-mRNA network, including two miRNAs (miR-214-3p and miR-93-5p), two hub genes, and 124 lncRNAs, and potential therapeutic medicine were identified. Conclusion We found two new genes, XBP1 and PLPP1, that are involved in UC and can help diagnose and measure the disease. XBP1 also relates to clinical scores and immune cells. We suggested a gene network and possible drugs based on them.
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Affiliation(s)
- Yifan Yuan
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, 430071, China
- Hubei Clinical Centre and Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, 430071, China
| | - Na Li
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, 430071, China
- Hubei Clinical Centre and Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, 430071, China
| | - Mingyue Fu
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, 430071, China
- Hubei Clinical Centre and Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, 430071, China
| | - Mei Ye
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, 430071, China
- Hubei Clinical Centre and Key Laboratory of Intestinal and Colorectal Diseases, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, 430071, China
- Correspondence: Mei Ye, Email
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Genetic and Epigenetic Etiology of Inflammatory Bowel Disease: An Update. Genes (Basel) 2022; 13:genes13122388. [PMID: 36553655 PMCID: PMC9778199 DOI: 10.3390/genes13122388] [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: 11/17/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic disease with periods of exacerbation and remission of the disease. The etiology of IBD is not fully understood. Many studies point to the presence of genetic, immunological, environmental, and microbiological factors and the interactions between them in the occurrence of IBD. The review looks at genetic factors in the context of both IBD predisposition and pharmacogenetics.
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Jimenez-Rondan FR, Ruggiero CH, Cousins RJ. Long Noncoding RNA, MicroRNA, Zn Transporter Zip14 (Slc39a14) and Inflammation in Mice. Nutrients 2022; 14:nu14235114. [PMID: 36501144 PMCID: PMC9740689 DOI: 10.3390/nu14235114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/17/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
Integration of non-coding RNAs and miRNAs with physiological processes in animals, including nutrient metabolism, is an important new focus. Twenty-three transporter proteins control cellular zinc homeostasis. The transporter Zip14 (Slc39a14) responds to proinflammatory stimuli. Using enterocyte-specific Zip14 knockout mice and RNA-sequencing and quantitative polymerase chain reaction (qPCR), we conducted transcriptome profiling of proximal small intestine, where Zip14 is highly expressed, using RNA from whole intestine tissue, isolated intestinal epithelial cells (IECs) and intestinal organoids. H19, U90926, Meg3, Bvht, Pvt1, Neat1 and miR-7027 were among the most highly expressed genes. Enterocyte-specific deletion of Zip14 demonstrated tissue specific expression, as such these changes were not observed with skeletal muscle. Chromatin immunoprecipitation (ChIP) assays of chromatin from isolated intestinal epithelial cells showed that enterocyte-specific Zip14 deletion enhanced binding of proinflammatory transcription factors (TFs) signal transducer and activator of transcription 3 (STAT3) and nuclear factor kappa beta (NF-ĸβ) to promoters of H19, Meg3 and U90926. We conclude enterocyte-specific ablation of Zip14 restricts changes in those RNAs to the intestine. Binding of proinflammatory TFs, NF-ĸβ and STAT3 to the H19, Meg3 and U90926 promoters is consistent with a model where Zip14 ablation, leads to increased TF occupancy, allowing epigenetic regulation of specific lncRNA genes.
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Li Y, Tang M, Zhang FJ, Huang Y, Zhang J, Li J, Wang Y, Yang J, Zhu S. Screening of ulcerative colitis biomarkers and potential pathways based on weighted gene co-expression network, machine learning and ceRNA hypothesis. Hereditas 2022; 159:42. [PMID: 36419192 PMCID: PMC9685902 DOI: 10.1186/s41065-022-00259-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 11/12/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Ulcerative colitis (UC) refers to an intractable intestinal inflammatory disease. Its increasing incidence rate imposes a huge burden on patients and society. The UC etiology has not been determined, so screening potential biomarkers is critical to preventing disease progression and selecting optimal therapeutic strategies more effectively. METHODS The microarray datasets of intestinal mucosal biopsy of UC patients were selected from the GEO database, and integrated with R language to screen differentially expressed genes and draw proteins interaction network diagrams. GO, KEGG, DO and GSEA enrichment analyses were performed to explore their biological functions. Through machine learning and WGCNA analysis, targets that can be used as UC potential biomarkers are screened out. ROC curves were drawn to verify the reliability of the results and predicted the mechanism of marker genes from the aspects of immune cell infiltration, co-expression analysis, and competitive endogenous network (ceRNA). RESULTS Two datasets GSE75214 and GSE87466 were integrated for screening, and a total of 107 differentially expressed genes were obtained. They were mainly related to biological functions such as humoral immune response and inflammatory response. Further screened out five marker genes, and found that they were associated with M0 macrophages, quiescent mast cells, M2 macrophages, and activated NK cells in terms of immune cell infiltration. The co-expression network found significant co-expression relationships between 54 miRNAs and 5 marker genes. According to the ceRNA hypothesis, NEAT1-miR-342-3p/miR-650-SLC6A14, NEAT1-miR-650-IRAK3, and XIST-miR-342-3p-IRAK3 axes were found as potential regulatory pathways in UC. CONCLUSION This study screened out five biomarkers that can be used for the diagnosis and treatment of UC, namely SLC6A14, TIMP1, IRAK3, HMGCS2, and APOBEC3B. Confirmed that they play a role in the occurrence and development of UC at the level of immune infiltration, and proposed a potential RNA regulatory pathway that controls the progression of UC.
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Affiliation(s)
- Ying Li
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, College of Traditional Chinese Medicine, Jinan, China ,grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, The First College for Clinical Medicine, Jinan, China
| | - Mengyao Tang
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, College of Innovation and Research of Traditional Chinese Medicine, Jinan, 250000 China
| | - Feng Jun Zhang
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, College of Traditional Chinese Medicine, Jinan, China ,grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, The First College for Clinical Medicine, Jinan, China
| | - Yihan Huang
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, College of Traditional Chinese Medicine, Jinan, China
| | - Jing Zhang
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, College of Traditional Chinese Medicine, Jinan, China
| | - Junqi Li
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, College of Traditional Chinese Medicine, Jinan, China
| | - Yunpeng Wang
- grid.479672.9Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Department of Gastroenterology, Jinan, China
| | - Jinguang Yang
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, The First College for Clinical Medicine, Jinan, China
| | - Shu Zhu
- grid.464402.00000 0000 9459 9325Shandong University of Traditional Chinese Medicine, College of Innovation and Research of Traditional Chinese Medicine, Jinan, 250000 China
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Song Y, Nie L, Wang M, Liao W, Huan C, Jia Z, Wei D, Liu P, Fan K, Mao Z, Wang C, Huo W. Differential Expression of lncRNA-miRNA-mRNA and Their Related Functional Networks in New-Onset Type 2 Diabetes Mellitus among Chinese Rural Adults. Genes (Basel) 2022; 13:genes13112073. [PMID: 36360309 PMCID: PMC9690016 DOI: 10.3390/genes13112073] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022] Open
Abstract
Increasing evidence suggested that the expression and inter-regulation of long noncoding RNA (lncRNA), microRNA (miRNA), and messenger RNA (mRNA) were related to the development of diabetes. Based on bioinformatics analysis, this study aimed to comprehensively analyze the dysregulated RNA molecules related to new-onset type 2 diabetes mellitus (T2DM). Twenty-four patients with new-onset T2DM were included as cases, and sex- and age-matched participants were included as controls. The differentially expressed lncRNAs, miRNAs, and mRNAs between the two groups were screened by RNA sequencing. LncRNA-miRNA-mRNA network and enrichment analysis were used to reveal the RNA molecules that were potentially associated with T2DM and their early changes. A total of 123 lncRNAs, 49 miRNAs, and 312 mRNAs were differentially expressed in the new-onset T2DM (fold change ≥ 1.5 and p value < 0.05). Functional analysis revealed that differentially expressed RNAs were likely to play essential roles in diabetes-related pathways. In addition, the protein–protein interaction (PPI) network screened multiple hub mRNAs, and lncRNA-miRNA-mRNA networks showed that a single miRNA could be related to multiple lncRNAs, and then they coregulated more mRNAs. SLC25A4, PLCB1, AGTR2, PRKN, and SCD5 were shown to be important mRNAs in T2DM, and miR-199b-5p, miR-202-5p, miR-548o-3p as well as miR-1255b-5p could be involved in their regulation. In conclusion, several new and previously identified dysregulated lncRNAs, miRNAs, and mRNAs were found to be vital biomarkers in T2DM. Their alterations and interactions could modulate the pathophysiology of T2DM. Those findings may provide new insights into the molecular mechanisms underlying the development of T2DM.
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Affiliation(s)
- Yu Song
- Department of Occupational and Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Luting Nie
- Department of Occupational and Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Mian Wang
- Department of Occupational and Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Wei Liao
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Changsheng Huan
- Department of Occupational and Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Zexin Jia
- Department of Occupational and Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Dandan Wei
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Pengling Liu
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Keliang Fan
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Zhenxing Mao
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Chongjian Wang
- Department of Epidemiology and Biostatistics, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Wenqian Huo
- Department of Occupational and Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou 450001, China
- Correspondence: ; Tel.: +86-371-67781452; Fax: +86-371-67781868
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Feng S, Xu Z, Zhang Z, Mo Y, Deng Y, Li L, Fei S, Wu J, Wang K, Zhang Q, Song J, Zhou R. RNA-Seq approach to investigate the effects of melatonin on bone marrow-derived dendritic cells from dextran sodium sulfate-induced colitis mice. Toxicology 2022; 481:153354. [DOI: 10.1016/j.tox.2022.153354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/30/2022] [Accepted: 10/14/2022] [Indexed: 11/16/2022]
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Dong L, Zhang R, Huang Q, Shen Y, Li H, Yu S, Wu Q. Construction, bioinformatics analysis, and validation of competitive endogenous RNA networks in ulcerative colitis. Front Genet 2022; 13:951243. [PMID: 36061211 PMCID: PMC9428148 DOI: 10.3389/fgene.2022.951243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 07/06/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Ulcerative colitis (UC) is a common chronic disease of the digestive system. Recently, competitive endogenous RNAs (ceRNAs) have been increasingly used to reveal key mechanisms for the pathogenesis and treatment of UC. However, the role of ceRNA in UC pathogenesis has not been fully clarified. This study aimed to explore the mechanism of the lncRNA-miRNA-mRNA ceRNA network in UC and identify potential biomarkers and therapeutic targets. Materials and Methods: An integrative analysis of mRNA, microRNA (miRNA), and long non-coding RNA (lncRNA) files downloaded from the Gene Expression Omnibus (GEO) was performed. Differentially expressed mRNA (DE-mRNAs), miRNA (DE-miRNAs), and lncRNA (DE-lncRNAs) were investigated between the normal and UC groups by the limma package. A weighted correlation network analysis (WGCNA) was used to identify the relative model for constructing the ceRNA network, and, concurrently, miRWalk and DIANA-LncBase databases were used for target prediction. Consecutively, the Gene Ontology (GO), Kyoto encyclopedia of genes and genomes (KEGG) pathway, and Reactome pathway enrichment analyses, protein-protein interaction (PPI) network, Cytohubba, and ClueGO were performed to identify hub genes. Additionally, we examined the immune infiltration characteristics of UC and the correlation between hub genes and immune cells using the immuCellAI database. Finally, the expression of potential biomarkers of ceRNA was validated via qRT-PCR in an experimental UC model induced by dextran sulfate sodium (DSS). Result: The ceRNA network was constructed by combining four mRNAs, two miRNAs, and two lncRNAs, and the receiver operating characteristic (ROC) analysis showed that two mRNAs (CTLA4 and STAT1) had high diagnostic accuracy (area under the curve [AUC] > 0.9). Furthermore, CTLA4 up-regulation was positively correlated with the infiltration of immune cells. Finally, as a result of this DSS-induced experimental UC model, CTLA4, MIAT, and several associate genes expression were consistent with the results of previous bioinformatics analysis, which proved our hypothesis. Conclusion: The investigation of the ceRNA network in this study could provide insight into UC pathogenesis. CTLA4, which has immune-related properties, can be a potential biomarker in UC, and MIAT/miR-422a/CTLA4 ceRNA networks may play important roles in UC.
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Affiliation(s)
- Longcong Dong
- Acupuncture and Tuina College, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Ruibin Zhang
- Acupuncture and Tuina College, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qin Huang
- Acupuncture and Tuina College, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yuan Shen
- Acupuncture and Tuina College, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Hongying Li
- Acupuncture and Tuina College, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shuguang Yu
- Acupuncture and Tuina College, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Qiaofeng Wu
- Acupuncture and Tuina College, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Acupuncture and Chronobiology Key Laboratory of Sichuan Province, Chengdu, China
- *Correspondence: Qiaofeng Wu,
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Yao W, Liu M, Chen X, You L, Ma Y, Hileuskaya K. Effects of UV/H 2O 2 degradation and step gradient ethanol precipitation on Sargassum fusiforme polysaccharides: Physicochemical characterization and protective effects against intestinal epithelial injury. Food Res Int 2022; 155:111093. [PMID: 35400466 DOI: 10.1016/j.foodres.2022.111093] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 11/18/2022]
Abstract
In this study, the degraded purified fraction from Sargassum fusiforme polysaccharides (SFP), named DSFP, was produced by the treatment of ultraviolet/hydrogen peroxide (UV/H2O2) degradation and step gradient ethanol precipitation. Results showed that the treatment significantly reduced the molecular weight of polysaccharides, from 282.83 kDa to 18.54 kDa, and influenced their surface morphology and roughness. SFP and DSFP were typical sulfated polysaccharides, mainly composed of fucose, galacturonic acid, glucuronic acid, galactose, and mannose. Both SFP and DSFP increased cell migration during intestinal epithelial wound healing and stimulated the cell cycle progression by promoting the transition from G0/G1 to S phase in the rat intestine epithelium cells (IEC-6). But DSFP had a stronger positive effect on wound healing and cell migration than SFP. It reinforced the intestinal barrier function and attenuated lipopolysaccharides-induced intestinal inflammation. DSFP significantly downregulated the expression of Toll-like receptor 4, tumor necrosis factor-α, interleukin-6, interleukin-1β, and inducible nitric oxide synthase by 53.14%, 92.41%, 66.01%, 68.24%, and 78.09%, respectively, and upregulated that of interleukin-10 by 2.48 folds when compared to the model. Therefore, the treatment (UV/H2O2 degradation and step gradient ethanol precipitation) could effectively improve the protective effects against intestinal epithelial injury.
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Affiliation(s)
- Wanzi Yao
- School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong 510640, China; Research Institute for Food Nutrition and Human Health (111 Center), Guangzhou, Guangdong 510640, China
| | - Mengyuan Liu
- School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong 510640, China; Research Institute for Food Nutrition and Human Health (111 Center), Guangzhou, Guangdong 510640, China
| | - Xiaoyong Chen
- School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong 510640, China; Research Institute for Food Nutrition and Human Health (111 Center), Guangzhou, Guangdong 510640, China
| | - Lijun You
- School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong 510640, China; Research Institute for Food Nutrition and Human Health (111 Center), Guangzhou, Guangdong 510640, China.
| | - Yongxuan Ma
- Sericultural & Agri-Food Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong 510610, China
| | - Kseniya Hileuskaya
- Institute of Chemistry of New Materials of National Academy of Science of Belarus
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Identification of Immune-Related lncRNA Pairs and Construction and Validation of a New Prognostic Signature of Colon Cancer. Can J Gastroenterol Hepatol 2022; 2022:5827544. [PMID: 35399646 PMCID: PMC8986404 DOI: 10.1155/2022/5827544] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND More and more evidence has shown that immune-related long noncoding ribonucleic acid (irlncRNAs) is a potential prognostic factor for colon cancer. The relevant gene pair pattern can improve the sensitivity of the prognostic model. Therefore, our present study aimed to identify irlncRNA Pairs and construct and validate a new prognostic signature in colon cancer. METHODS We downloaded the expression matrix of mRNA and lncRNA of patients with colon cancer and their clinical information from the public TCGA database. We obtained immune genes from the ImmPort database. Coexpression analysis was performed to identify irlncRNAs. We built an irlncRNA pair matrix by comparing the expression levels of each lncRNA pair in a cycle. Univariate Cox regression analysis, LASSO penalized regression analysis, and multivariate Cox regression analysis were performed to determine the final variables to construct the prognostic risk score model (a new signature). We draw the receiver operating characteristic (ROC) curves of the signature and clinical characteristics and determine the optimal cutoff value by the optimal Akaike Information Criterion (AIC) value. Based on the optimal cutoff value of the ROC curve of the signature, colon cancer patients were divided into the high- and low-risk groups. Then, the signature was evaluated by clinicopathological features, tumor-infiltrating immune cells, checkpoint-related biomarkers, targeted therapy, and chemotherapy. RESULTS We identified 8 lncRNA pairs including AC103740.1|LEF1-AS1, LINC02391|AC053503.5, WWC2-AS2|AL355916.2, AC104090.1|NEURL1-AS1, AC099524.1|AL161908.1, AC074011.1|AL078601.2, AL355916.2|LINC01723, and AP003392.4|LINC00598 from 71 differently expressed irlncRNAs. We constructed a prognostic risk score model (a new signature) using these optimal eight irlncRNA pairs. ROC curve analysis revealed that the highest AUC value of the signature was 0.776 at 1 year, with the optimal cutoff value of 1.283. Our present study also showed that the constructed signature could accurately identify adverse survival outcomes, prognostic clinicopathological features, and specify tumor invasion status. The expression of immune checkpoint-related genes and chemical drug sensitivity were related to different risk groups. CONCLUSION In our present study, we constructed a new irlncRNA signature of colon cancer based on the irlncRNA pairs instead of the special expression level of lncRNA. We found this signature had not only good prognostic value but also certain clinical value, which might provide a new insight into the treatment and prognosis of colon cancer.
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Zhang X, Gu J, Zhao C, Hu Y, Zhang B, Wang J, Lv H, Ji X, Wang S. Sweeteners Maintain Epithelial Barrier Function Through the miR-15b/RECK/MMP-9 Axis, Remodel Microbial Homeostasis, and Attenuate Dextran Sodium Sulfate-Induced Colitis in Mice. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:171-183. [PMID: 34962394 DOI: 10.1021/acs.jafc.1c06788] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Non-nutritive sweeteners are the most widely used food additives designed to provide sweetness and reduce caloric intake. Studies have confirmed a link between sweeteners and colitis, yet supporting scientific data remain exiguous and controversial. In this study, three common sweeteners (Saccharin sodium, Stevioside, and Sucralose) in acceptable daily intake dosage were added to water in order to determine their effects on dextran sodium sulfate-induced colitis in mice. Our results show that the three sweeteners meliorate colitis to varying degrees─Saccharin exerts the most pronounced effect, followed by Stevioside and Sucralose. Intake of sweeteners alleviates colitis symptoms, alters gut microbiota, reshapes the TH17/Treg balance, protects the intestinal barrier, and reduces inflammation. Most significantly, sweeteners can enhance the abundance of Mucispirillum and Alistipes, which are conducive to colitis recovery, and upregulate the expression of E-cadherin through the miR-15b/RECK/MMP-9 axis to improve intestinal barrier integrity. Moreover, by inhibiting the MMP-9/AKT/NF-κB pathway, inflammation is relieved, as reflected in the restoration of the Th17/Treg balance. Our results link the consumption of sweeteners to the remission of colitis, which provides new scientific evidence for the safe use of sweeteners.
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Affiliation(s)
- Xuejiao Zhang
- School of Medicine, Nankai University, Tianjin 300071, China
- College of Food Science and Technology, Hebei Agricultural University, Baoding 071000, China
| | - Jiaxin Gu
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Congying Zhao
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Yaozhong Hu
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Bowei Zhang
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Jin Wang
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Huan Lv
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Xuemeng Ji
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Shuo Wang
- School of Medicine, Nankai University, Tianjin 300071, China
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12
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Ye C, Zhu S, Yuan J. Construction of ceRNA Network to Reveal Potential Biomarkers in Crohn's Disease and Validation in a TNBS Induced Mice Model. J Inflamm Res 2021; 14:6447-6459. [PMID: 34880646 PMCID: PMC8648272 DOI: 10.2147/jir.s338053] [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: 09/13/2021] [Accepted: 11/12/2021] [Indexed: 12/15/2022] Open
Abstract
Purpose We aimed to construct a competing endogenous RNA (ceRNA) network and explore the potential biomarkers in Crohn's disease (CD) via bioinformatics analysis. Validation of candidate biomarkers in a 2,4,6-trinitrobenzene sulfonic acid (TNBS) induced experimental colitis model and ceRNA network in an HCT116 cell line was also an aim, along with purposing to reveal the pathogenesis of CD. Methods GSE102134 and GSE67106 datasets were obtained and used to screen the differentially expressed genes. WCGNA was applied to identify the relative model to construct the ceRNA network. Furthermore, the relationship between candidate gene and immune infiltration was investigated. Then, the expression of potential biomarkers was validated via qRT-PCR in a TNBS induced experimental colitis model. Finally, the ceRNA network was confirmed by RNAi experiments in an HCT116 cell line. Results The ceRNA network, consisting of four lncRNAs, four miRNAs, and eight mRNAs, was constructed and the ROC analysis showed four mRNAs (PTGS2, LPL, STAT1, and TRIB2) had high diagnostic accuracy (AUC>0.9). In addition, upregulated PTGS2 was positively correlated with immune cell infiltration, including Natural killer cells, exhausted T-cells, monocytes, and Dendritic cells. The outcome of this TNBS induced experimental colitis model verified that the expression of PTGS2 and mir-429 was consistent with results of previous bioinformatics analysis. Furthermore, the predicted ceRNA network MIR3142HG/mir-429/PTGS2 were validated via RNA interference. Knockout of MIR3142HG decreased the mRNA level of PTGS2, whereas inhibition of mir-429 increased the mRNA level of PTGS2 in the HCT116 cell line. Conclusion The exploration of the ceRNA network in this work might contribute to understanding the pathogenesis of CD. The constructed MIR3142HG/mir-429/PTGS2 ceRNA network may play a role in CD, and PTGS2 can be a potential immune-related biomarker in CD.
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Affiliation(s)
- Chenglin Ye
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Sizhe Zhu
- Department of Clinical Immunology, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, Hubei, People's Republic of China
| | - Jingping Yuan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, Hubei, People's Republic of China
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The Role of lncRNAs in Regulating the Intestinal Mucosal Mechanical Barrier. BIOMED RESEARCH INTERNATIONAL 2021; 2021:2294942. [PMID: 34820453 PMCID: PMC8608538 DOI: 10.1155/2021/2294942] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/29/2021] [Accepted: 10/27/2021] [Indexed: 12/18/2022]
Abstract
lncRNA is a transcript that is more than 200 bp in length. Currently, evidence has shown that lncRNA is of great significance in cell activity, involved in epigenetics, gene transcription, chromatin regulation, etc. The existence of an intestinal mucosal mechanical barrier hinders the invasion of pathogenic bacteria and toxins, maintaining the stability of the intestinal environment. Serious destruction or dysfunction of the mechanical barrier often leads to intestinal diseases. This review first summarizes the ability of lncRNAs to regulate the intestinal mucosal mechanical barrier. We then discussed how lncRNAs participate in various intestinal diseases by regulating the intestinal mucosal mechanical barrier. Finally, we envision its potential as a new marker for diagnosing and treating intestinal inflammatory diseases.
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14
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Ma YS, Yang XL, Liu YS, Ding H, Wu JJ, Shi Y, Jia CY, Lu GX, Zhang DD, Wang HM, Wang PY, Yu F, Lv ZW, Wang GR, Liu JB, Fu D. Long non-coding RNA NORAD promotes pancreatic cancer stem cell proliferation and self-renewal by blocking microRNA-202-5p-mediated ANP32E inhibition. J Transl Med 2021; 19:400. [PMID: 34551785 PMCID: PMC8456629 DOI: 10.1186/s12967-021-03052-5] [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: 02/15/2021] [Accepted: 08/24/2021] [Indexed: 02/08/2023] Open
Abstract
Background Cancer stem cells (CSCs) are key regulators in the processes of tumor initiation, progression, and recurrence. The mechanism that maintains their stemness remains enigmatic, although the role of several long noncoding RNAs (lncRNAs) has been highlighted in the pancreatic cancer stem cells (PCSCs). In this study, we first established that PCSCs overexpressing lncRNA NORAD, and then investigated the effects of NORAD on the maintenance of PCSC stemness. Methods Expression of lncRNA NORAD, miR-202-5p and ANP32E in PC tissues and cell lines was quantified after RNA isolation. Dual-luciferase reporter assay, RNA pull-down and RIP assays were performed to verify the interactions among NORAD, miR-202-5p and ANP32E. We then carried out gain- and loss-of function of miR-202-5p, ANP32E and NORAD in PANC-1 cell line, followed by measurement of the aldehyde dehydrogenase activity, cell viability, apoptosis, cell cycle distribution, colony formation, self-renewal ability and tumorigenicity of PC cells. Results LncRNA NORAD and ANP32E were upregulated in PC tissues and cells, whereas the miR-202-5p level was down-regulated. LncRNA NORAD competitively bound to miR-202-5p, and promoted the expression of the miR-202-5p target gene ANP32E thereby promoting PC cell viability, proliferation, and self-renewal ability in vitro, as well as facilitating tumorigenesis of PCSCs in vivo. Conclusion Overall, lncRNA NORAD upregulates ANP32E expression by competitively binding to miR-202-5, which accelerates the proliferation and self-renewal of PCSCs. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-03052-5.
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Affiliation(s)
- Yu-Shui Ma
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, No. 301, Yanchang Middle Road, Jing'an District, Shanghai, 200072, China.,Cancer Institute, Affiliated Tumor Hospital of Nantong University, Nantong, 226631, China
| | - Xiao-Li Yang
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, No. 301, Yanchang Middle Road, Jing'an District, Shanghai, 200072, China
| | - Yu-Shan Liu
- Department of Pathology, Affiliated Tumor Hospital of Nantong University, Nantong, 226631, China
| | - Hua Ding
- Department of Radiotherapy, Affiliated Tumor Hospital of Nantong University, Nantong, 226631, China
| | - Jian-Jun Wu
- Nantong Haimen Yuelai Health Centre, Haimen, 226100, China
| | - Yi Shi
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, No. 301, Yanchang Middle Road, Jing'an District, Shanghai, 200072, China.,Cancer Institute, Affiliated Tumor Hospital of Nantong University, Nantong, 226631, China
| | - Cheng-You Jia
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, No. 301, Yanchang Middle Road, Jing'an District, Shanghai, 200072, China
| | - Gai-Xia Lu
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, No. 301, Yanchang Middle Road, Jing'an District, Shanghai, 200072, China
| | - Dan-Dan Zhang
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, No. 301, Yanchang Middle Road, Jing'an District, Shanghai, 200072, China
| | - Hui-Min Wang
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, No. 301, Yanchang Middle Road, Jing'an District, Shanghai, 200072, China
| | - Pei-Yao Wang
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, No. 301, Yanchang Middle Road, Jing'an District, Shanghai, 200072, China
| | - Fei Yu
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, No. 301, Yanchang Middle Road, Jing'an District, Shanghai, 200072, China
| | - Zhong-Wei Lv
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, No. 301, Yanchang Middle Road, Jing'an District, Shanghai, 200072, China
| | - Gao-Ren Wang
- Cancer Institute, Affiliated Tumor Hospital of Nantong University, Nantong, 226631, China.
| | - Ji-Bin Liu
- Cancer Institute, Affiliated Tumor Hospital of Nantong University, Nantong, 226631, China.
| | - Da Fu
- Department of Nuclear Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, No. 301, Yanchang Middle Road, Jing'an District, Shanghai, 200072, China.
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15
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He R, Wu S, Gao R, Chen J, Peng Q, Hu H, Zhu L, Du Y, Sun W, Ma X, Zhang H, Cui Z, Wang H, Martin BN, Wang Y, Zhang CJ, Wang C. Identification of a Long Noncoding RNA TRAF3IP2-AS1 as Key Regulator of IL-17 Signaling through the SRSF10-IRF1-Act1 Axis in Autoimmune Diseases. THE JOURNAL OF IMMUNOLOGY 2021; 206:2353-2365. [PMID: 33941656 DOI: 10.4049/jimmunol.2001223] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/16/2021] [Indexed: 01/25/2023]
Abstract
IL-17A plays an essential role in the pathogenesis of many autoimmune diseases, including psoriasis and multiple sclerosis. Act1 is a critical adaptor in the IL-17A signaling pathway. In this study, we report that an anti-sense long noncoding RNA, TRAF3IP2-AS1, regulates Act1 expression and IL-17A signaling by recruiting SRSF10, which downregulates the expression of IRF1, a transcriptional factor of Act1. Interestingly, we found that a psoriasis-susceptible variant of TRAF3IP2-AS1 A4165G (rs13210247) is a gain-of-function mutant. Furthermore, we identified a mouse gene E130307A14-Rik that is homologous to TRAF3IP2-AS1 and has a similar ability to regulate Act1 expression and IL-17A signaling. Importantly, treatment with lentiviruses expressing E130307A14-Rik or SRSF10 yielded therapeutic effects in mouse models of psoriasis and experimental autoimmune encephalomyelitis. These findings suggest that TRAF3IP2-AS1 and/or SRSF10 may represent attractive therapeutic targets in the treatment of IL-17-related autoimmune diseases, such as psoriasis and multiple sclerosis.
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Affiliation(s)
- Ruirui He
- Key Laboratory of Molecular Biophysics of the Ministry of Education, National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Songfang Wu
- Shanghai Xuhui Central Hospital/Zhongshan-Xuhui Hospital, Fudan University, Shanghai, People's Republic of China.,Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Ru Gao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jianwen Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Qianwen Peng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Huijun Hu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Liwen Zhu
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine at Shanghai, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Yanyun Du
- Key Laboratory of Molecular Biophysics of the Ministry of Education, National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Wanwei Sun
- Key Laboratory of Molecular Biophysics of the Ministry of Education, National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaojian Ma
- Key Laboratory of Molecular Biophysics of the Ministry of Education, National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Huazhi Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Zhihui Cui
- Key Laboratory of Molecular Biophysics of the Ministry of Education, National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Heping Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Bradley N Martin
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Yueying Wang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine at Shanghai, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China
| | - Cun-Jin Zhang
- Department of Neurology of Nanjing Drum Tower Hospital, Medical School and the State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, Jiangsu, China
| | - Chenhui Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China .,Wuhan Institute of Biotechnology, Wuhan, China
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