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Wei Z, Zhang W, Du M, Zhong H, Fang X. Widely targeted metabolomic and KEGG analyses of natural deep eutectic solvent-based saponins extraction from Camellia oleifera Abel.: Effects on composition. Food Chem 2024; 450:139333. [PMID: 38636384 DOI: 10.1016/j.foodchem.2024.139333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/20/2024]
Abstract
Camellia saponins are important by-products of Camellia Oleifer Abel. processing. In this study, an eco-friendly method based on natural deep eutectic solvents (NaDESs, proline and glycerol at a molar ratio of 2:5) was established to extract saponins from C.oleifera cakes. The content of saponin (702.22 ± 1.28 mg/g) obtained using NaDES was higher than those extracted using water or methanol. UPLC-Q-TOF MS analysis of chemical structure showed that the difference in the extraction technique alter individual saponins. A widely targeted metabolomic approach and KEGG metabolic pathway analysis showed that the upregulated metabolites in the NaDES-based extract mainly included flavonoids, alkaloids, and phenolic acids; and they were involved in arginine and proline metabolism, metabolic pathways, phenylpropanoid biosynthesis, biosynthesis of secondary metabolites, and flavonoid biosynthesis. The present study proposes a selective substitute for use in the extraction of camellia saponins with composition analysis.
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Affiliation(s)
- Zhenqian Wei
- The Research Institute of Subtropical Forestry, Chinese Academy of Forestry, 73(#), Daqiao Road, Hangzhou City, Zhejiang Province 311400, China
| | - Weiyan Zhang
- The Research Institute of Subtropical Forestry, Chinese Academy of Forestry, 73(#), Daqiao Road, Hangzhou City, Zhejiang Province 311400, China; Food Science and Technology College, Central South University of Forestry & Technology, Changsha City, Hunan Province 410004, China
| | - Menghao Du
- The Research Institute of Subtropical Forestry, Chinese Academy of Forestry, 73(#), Daqiao Road, Hangzhou City, Zhejiang Province 311400, China
| | - Haiyan Zhong
- Food Science and Technology College, Central South University of Forestry & Technology, Changsha City, Hunan Province 410004, China
| | - Xuezhi Fang
- The Research Institute of Subtropical Forestry, Chinese Academy of Forestry, 73(#), Daqiao Road, Hangzhou City, Zhejiang Province 311400, China.
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Zhang Y, Sheng Y, Gao Y, Lin Y, Cheng B, Li H, Zhang L, Xu H. Exploration of the Pathogenesis of Chronic Obstructive Pulmonary Disease Caused by Smoking-Based on Bioinformatics Analysis and In Vitro Experimental Evidence. Toxics 2023; 11:995. [PMID: 38133396 PMCID: PMC10747869 DOI: 10.3390/toxics11120995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/02/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023]
Abstract
This study was aimed at investigating the pathogenesis of chronic obstructive pulmonary disease (COPD) caused by smoking-based on bioinformatics analysis and in vitro experimental evidence. The GEO, GEO2R, TargetScan, miRDB, miRWalk, DAVID, and STRING databases were used for bioinformatics analysis. The mRNA expression and the protein levels were determined by real-time PCR and ELISA. After taking the intersection of the diversified results of the databases, four differentially expressed miRNAs (hsa-miR-146a, hsa-miR-708, hsa-miR-150, and hsa-miR-454) were screened out. Subsequently, a total of 57 target genes of the selected miRNAs were obtained. The results of DAVID analysis showed that the selected miRNAs participated in COPD pathogenesis through long-term potentiation, the TGF-β signaling pathway, the PI3K-Akt signaling pathway, etc. The results of STRING prediction showed that TP53, EP300, and MAPK1 were the key nodes of the PPI network. The results of the confirmatory experiment showed that, compared with the control group, the mRNA expression of ZEB1, MAPK1, EP300, and SP1 were up-regulated, while the expression of MYB was down-regulated and the protein levels of ZEB1, MAPK1, and EP300 were increased. Taken together, miRNAs (hsa-miR-146a, hsa-miR-708, hsa-miR-150, and hsa-miR-454) and their regulated target genes and downstream protein molecules (ZEB1, EP300, and MAPK1) may be closely related to the pathological process of COPD.
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Affiliation(s)
- Yingchi Zhang
- School of Public Health, Ningxia Medical University, Yinchuan 750004, China (Y.S.); (Y.G.); (Y.L.); (H.L.)
- The Key Laboratory of Environmental Factors and Chronic Disease Control, Yinchuan 750004, China
- Xi’an Center for Disease Control and Prevention, Xi’an 710000, China
| | - Yuxin Sheng
- School of Public Health, Ningxia Medical University, Yinchuan 750004, China (Y.S.); (Y.G.); (Y.L.); (H.L.)
- The Key Laboratory of Environmental Factors and Chronic Disease Control, Yinchuan 750004, China
| | - Yanrong Gao
- School of Public Health, Ningxia Medical University, Yinchuan 750004, China (Y.S.); (Y.G.); (Y.L.); (H.L.)
- The Key Laboratory of Environmental Factors and Chronic Disease Control, Yinchuan 750004, China
| | - Yujia Lin
- School of Public Health, Ningxia Medical University, Yinchuan 750004, China (Y.S.); (Y.G.); (Y.L.); (H.L.)
- The Key Laboratory of Environmental Factors and Chronic Disease Control, Yinchuan 750004, China
| | - Bin Cheng
- School of Public Health, Ningxia Medical University, Yinchuan 750004, China (Y.S.); (Y.G.); (Y.L.); (H.L.)
- The Key Laboratory of Environmental Factors and Chronic Disease Control, Yinchuan 750004, China
| | - Hongmei Li
- School of Public Health, Ningxia Medical University, Yinchuan 750004, China (Y.S.); (Y.G.); (Y.L.); (H.L.)
- The Key Laboratory of Environmental Factors and Chronic Disease Control, Yinchuan 750004, China
- The Key Laboratory of Fertility Preservation and Maintenance of the Ministry of Education, Ningxia Medical University, Yinchuan 750004, China
- School of Basic Medicine, Ningxia Medical University, Yinchuan 750004, China
| | - Ling Zhang
- School of Public Health, Ningxia Medical University, Yinchuan 750004, China (Y.S.); (Y.G.); (Y.L.); (H.L.)
- The Key Laboratory of Environmental Factors and Chronic Disease Control, Yinchuan 750004, China
| | - Haiming Xu
- School of Public Health, Ningxia Medical University, Yinchuan 750004, China (Y.S.); (Y.G.); (Y.L.); (H.L.)
- The Key Laboratory of Environmental Factors and Chronic Disease Control, Yinchuan 750004, China
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Gao XM, Zhou XH, Jia MW, Wang XZ, Liu D. Identification of key genes in sepsis by WGCNA. Prev Med 2023; 172:107540. [PMID: 37164163 DOI: 10.1016/j.ypmed.2023.107540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/20/2023] [Accepted: 05/06/2023] [Indexed: 05/12/2023]
Abstract
When the body damages its own tissues in response to an infection, sepsis develops. Medical treatments are limited. It's important to understand the molecular mechanism behind sepsis pathogenesis and identify potential molecular treatment targets. We made two modules based on how genes work together by using WGCNA analysis. The light-green GSE131761 module and the blue GSE137342 module had the strongest links to sepsis. A gene ontology (GO) analysis showed that most of the genes in the lightgreen module were involved in the inflammatory response, specific granule, and immune receptor activity. Most of the genes in the blue module were significantly more likely to have the GO terms proteasomal protein catabolic process, ubiquitin ligase complex, and ubiquitin-like protein transferase activity. The KEGG analysis showed that the genes in module lightgreen were mostly involved in the TNF signaling pathway, while the genes in module blue were mostly involved in the Prion disease pathway. There were two hub genes that were found. In the end, ANKRD22 and VNN1 were singled out as crucial genes. This study used WGCNA to investigate sepsis-associated susceptibility modules and genes. Our study identified two modules and two key genes as essential components in sepsis etiology, which may improve our understanding of its molecular mechanisms.
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Affiliation(s)
| | - Xiu-Hua Zhou
- Department of Critical Care Medicine, The Fourth Affiliated Hospital of China Medical University
| | - Meng-Wei Jia
- Department of Critical Care Medicine, The Fourth Affiliated Hospital of China Medical University
| | - Xiao-Zhuo Wang
- Department of Critical Care Medicine, The Fourth Affiliated Hospital of China Medical University
| | - Dan Liu
- Department of Critical Care Medicine, The Fourth Affiliated Hospital of China Medical University.
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Hao P, Han L, Quan Z, Jin X, Li Y, Wu Y, Zhang X, Wang W, Gao C, Wang L, Wang H, Zhang W, Chang Y, Ding J. Integrative mRNA-miRNA interaction analysis associated with the immune response of Strongylocentrotus intermedius to Vibrio harveyi infection. Fish Shellfish Immunol 2023; 134:108577. [PMID: 36773712 DOI: 10.1016/j.fsi.2023.108577] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 11/08/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Strongylocentrotus intermedius is one of the most economically valuable sea urchin species in China and has experienced mass mortality owing to outbreaks of bacterial diseases such as black mouth disease. This has caused serious economic losses to the sea urchin farming industry. To investigate the immune response mechanism of S. intermedius with different tube feet colors in response to Vibrio harveyi infection, we examined the different tube feet-colored S. intermedius under V. harveyi challenge and compared their transcriptome and microRNA (miRNA) profiles using RNA-Seq. We obtained 1813 differentially expressed genes (DEGs), 28 DE miRNAs, and 303 DE miRNA-DEG pairs in different tube feet-colored S. intermedius under V. harveyi challenge. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that the most significant DEGs were associated with the Notch signaling and phagosome pathways. The target genes of immune-related miRNAs (miR-71, miR-184, miR-193) and genes (CALM1, SPSB4, DMBT, CSRP1) in S. intermedius were predicted and validated. This study provides insight into the molecular mechanisms that regulate genes involved in the immune response of S. intermedius infected with V. harveyi.
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Affiliation(s)
- Pengfei Hao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Lingshu Han
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China; Ningbo University, Ningbo, Zhejiang, 315832, PR China
| | - Zijiao Quan
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Xin Jin
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Yuanxin Li
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Yanglei Wu
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Xianglei Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Wenpei Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Chuang Gao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Luo Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Heng Wang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Weijie Zhang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China
| | - Jun Ding
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, PR China.
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Cheng X, Xu X, Zou C, Jiang W. Influence of verapamil on pressure overload-induced ventricular arrhythmias by regulating gene-expression profiles. Cardiovasc J Afr 2022; 33:304-312. [PMID: 35315872 PMCID: PMC10031859 DOI: 10.5830/cvja-2022-010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 02/09/2022] [Indexed: 10/08/2023] Open
Abstract
BACKGROUND Life-threatening ventricular arrhythmias can lead to sudden cardiac death in patients. This study aimed to investigate the changes in gene profiles involved when verapamil (VRP) affects increased wall stress (pressure overload)-induced ventricular arrhythmias, thus revealing the potential causative molecular mechanisms and therapeutic targets through gene-expression identification and functional analysis. METHODS Animal models with wall stress-induced ventricular arrhythmias were established. Low (0.5 mg/kg) and high (1 mg/kg) doses of VRP were administered intravenously 10 minutes before transverse aortic constriction, and average ventricular arrhythmia scores were calculated. Next, we evaluated the molecular role of VRP by characterising differential gene-expression profiles between VRP-pretreated (1 mg/kg) and control groups using RNA-sequencing technology. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were used to reveal molecular function. A protein-protein interaction (PPI) network was then developed. RESULTS VRP exerted its anti-arrhythmic effects in response to increases in left ventricular (LV) afterload. We detected differentially expressed genes (DEGs), of which 36 were upregulated and 1 397 downregulated, between the VRP-pretreated and model groups during acute increases in LV wall stress. GO analysis demonstrated that the DEGs were associated with cytoskeletal protein binding. KEGG analysis showed that enriched pathways were mainly distributed in adherens junctions, actin cytoskeleton regulation and the MAPK signalling pathway. Centralities analysis of the PPI identified Rac1, Grb2, Rbm8a and Mapk1 as hub genes. CONCLUSIONS VRP prevented acute pressure overload-induced ventricular arrhythmias, possibly through the hub genes Rac1, Grb2, Rbm8a and Mapk1 as potential targets of VRP.
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Affiliation(s)
- Xianfeng Cheng
- Department of Cardiac Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China; Department of Cardiac Surgery, Weifang People's Hospital, Weifang, Shandong, China
| | - Xue Xu
- Department of Geriatrics, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China; Department of Cardiology, Peking University People's Hospital, Beijing, China
| | - Chengwei Zou
- Department of Cardiac Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
| | - Weidong Jiang
- Department of Geriatrics, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China.
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Pektaş SD, Kara M, Doğan G, Pektaş MB, Baloğlu MC, Sadi G. Differential Expression and in Silico Functional Analysis of Plasma MicroRNAs in the Pathogenesis of Non-segmental Vitiligo. Indian J Dermatol 2022; 67:705-714. [PMID: 36998849 PMCID: PMC10043660 DOI: 10.4103/ijd.ijd_383_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023] Open
Abstract
Vitiligo is a disease characterized by acquired depigmentation, white macules, and patches on the skin due to the dysfunction of epidermal melanocytes. In this study, we attempt to profile the microRNA (miRNA) expression patterns and predict the potential targets, assessing the biological functions of differentially expressed miRNAs in the blood of generalized vitiligo patients. Peripheral blood samples were taken from all participants, and the expression levels of 89 identified miRNAs were analyzed with real-time quantitative polymerase chain reaction (PCR). The results indicated significant upregulation of six miRNAs and downregulation of 19 miRNAs in the plasma of vitiligo patients. The top three upregulated miRNAs were hsa-miR-451a, hsa-miR-25-3p, and hsa-miR-19a-3p, and the top three downregulated miRNAs were hsa-miR-146a-5p, hsa-miR-940, and hsa-miR-142-3p. Moreover, the miRNA expression profiles of patients with Type 3 and Type 4 phototypes were substantially different in such a way that the patients with Type 3 phototype would be more prone to the emergence of melanoma and cancer. While significant variations in the expression patterns of miRNAs in male and female vitiligo patients were demonstrated, miR-let-7i-5p, miR-19a-3p, miR-25-3p, and miR-451a were commonly upregulated, and miR-142-3p and miR-146a-5p were commonly repressed in both sexes. This study may shed light on the roles of differentially expressed miRNAs in vitiligo patients by examining the miRNA expression patterns and the combined effects of miRNA and their predicted targets.
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Affiliation(s)
- Suzan Demir Pektaş
- Department of Dermatology, Faculty of Medicine, Muğla Sıtkı Koçman University, Mugla, Turkey
| | - Murat Kara
- Department of Dermatology, Faculty of Medicine, Muğla Sıtkı Koçman University, Mugla, Turkey
| | - Gürsoy Doğan
- Department of Dermatology, Faculty of Medicine, Muğla Sıtkı Koçman University, Mugla, Turkey
| | - Mehmet Bilgehan Pektaş
- Department of Pharmacology, Faculty of Medicine, Afyonkarahisar Health Sciences University, Kastamonu, Turkey
| | - Mehmet Cengiz Baloğlu
- Department of Genetics and Bioengineering, Engineering Faculty, Kastamonu University, Kastamonu, Turkey
| | - Gökhan Sadi
- Department of Biology, K. Ö. Science Faculty, Karamanoğlu Mehmetbey University, Karaman, Turkey
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Zhou J, Qiu Y, Zhao J, Wang Y, Zhu N, Wang D, Cui Y, Guo J, Sun T, Ji Y, Wu Z, Zeng P, Li J, Feng X, Hou L, Liu J. The Network of Interactions between the Porcine Epidemic Diarrhea Virus Nucleocapsid and Host Cellular Proteins. Viruses 2022; 14:2269. [PMID: 36298827 DOI: 10.3390/v14102269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 10/14/2022] [Indexed: 11/05/2022] Open
Abstract
Host–virus protein interactions are critical for intracellular viral propagation. Understanding the interactions between cellular and viral proteins may help us develop new antiviral strategies. Porcine epidemic diarrhea virus (PEDV) is a highly contagious coronavirus that causes severe damage to the global swine industry. Here, we employed co-immunoprecipitation and liquid chromatography-mass spectrometry to characterize 426 unique PEDV nucleocapsid (N) protein-binding proteins in infected Vero cells. A protein–protein interaction network (PPI) was created, and gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) database analyses revealed that the PEDV N-bound proteins belong to different cellular pathways, such as nucleic acid binding, ribonucleoprotein complex binding, RNA methyltransferase, and polymerase activities. Interactions of the PEDV N protein with 11 putative proteins: tripartite motif containing 21, DEAD-box RNA helicase 24, G3BP stress granule assembly factor 1, heat shock protein family A member 8, heat shock protein 90 alpha family class B member 1, YTH domain containing 1, nucleolin, Y-box binding protein 1, vimentin, heterogeneous nuclear ribonucleoprotein A2/B1, and karyopherin subunit alpha 1, were further confirmed by in vitro co-immunoprecipitation assay. In summary, studying an interaction network can facilitate the identification of antiviral therapeutic strategies and novel targets for PEDV infection.
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Fan M, Zhang G, Xie M, Liu X, Zhang Q, Wang L. Siglec-15 as a New Perspective Therapy Target in Human Giant Cell Tumor of Bone. Curr Oncol 2022; 29:7655-71. [PMID: 36290882 DOI: 10.3390/curroncol29100605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 01/13/2023] Open
Abstract
The main features of a giant cell tumor of bone (GCTB) are frequent recurrence and aggressive osteolysis, which leads to a poor prognosis in patients. Although the treatment methods for a GCTB, such as scraping and resection, effectively inhibit the disease, the tendency toward malignant transformation remains. Therefore, it is important to identify new treatment methods for a GCTB. In this study, we first found high Siglec-15 expression in GCTB tissues, which was significantly associated with Campanacci staging and tumor recurrence. In Spearman's analysis, Siglec-15 expression was significantly correlated with Ki-67 levels in tumor tissues. In vitro, the mRNA and protein levels of Siglec-15 were high in GCTB stromal cells (Hs737. T), and Siglec-15 knockdown inhibited the biological characteristics of GCTB stromal cells. The RNA sequencing results enabled a prediction of the downstream genes by using the Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and MCODE analyses, and the findings showed that CXCL8 was significantly regulated by Siglec-15 and might be a promising downstream target gene of Siglec-15. Therefore, Siglec-15 may be a potential immunotherapy target for a GCTB.
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Tang Z, Xu W, Zhou Z, Qiao Y, Zheng S, Rong W. Taxonomic and functional alterations in the salivary microbiota of children with and without severe early childhood caries (S-ECC) at the age of 3. PeerJ 2022; 10:e13529. [PMID: 35669952 PMCID: PMC9165595 DOI: 10.7717/peerj.13529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 05/11/2022] [Indexed: 01/17/2023] Open
Abstract
Background Primary dental caries is the most prevalent oral disease among preschool children, which can cause severe damage to teeth and even affect the mental well-being of children. Various studies have demonstrated that the oral microbiome plays a pivotal role in the onset and development of dental caries. However, it remains uncertain about the key microbial markers associated with caries, owing to the limited evidence. Methods Fifteen S-ECC children and fifteen healthy controls were selected from three-year-old children in this study. Their clinical data and oral saliva samples were collected. Shotgun sequencing was conducted to investigate the microbial differences and the relevant functions between the two groups. Results We observed no apparent difference in oral microbial community diversity between the two groups. Still, at the genus/species levels, several characteristic genera/species such as Propionibacterium, Propionibacterium acidifaciens, Prevotella denticola, Streptococcus mutans and Actinomyces sp. oral taxon 448/414 increased significantly in S-ECC children, compared with the oral health group. Furthermore, we found that functional pathways involving glycolysis and acid production, such as starch and sucrose metabolism, fructose and mannose metabolism, glycolysis/gluconeogenesis, were prominently up-regulated in the high-caries group. Conclusions Our study showed that dental caries in children were associated with the alterations in the oral microbiota at the composition and functional levels, which may potentially inspire the exploration of microbial diagnosis or therapeutic treatments.
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Affiliation(s)
- Zhe Tang
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology, Beijing, China
| | - Wenyi Xu
- Beijing QuantiHealth Technology Co., Ltd., Beijing QuantiHealth Technology Co., Ltd., Beijing, China
| | - Zhifang Zhou
- Department of Stomatology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Yanchun Qiao
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology, Beijing, China
| | - Shuguo Zheng
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology, Beijing, China
| | - Wensheng Rong
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology, Beijing, China
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Guo J, Zhang S, Wang J, Zhang P, Lu T, Zhang L. Hinokiflavone Inhibits Growth of Esophageal Squamous Cancer By Inducing Apoptosis via Regulation of the PI3K/AKT/mTOR Signaling Pathway. Front Oncol 2022; 12:833719. [PMID: 35178352 PMCID: PMC8844566 DOI: 10.3389/fonc.2022.833719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 01/10/2022] [Indexed: 12/24/2022] Open
Abstract
Background Globally, esophageal cancer ranks as the seventh most common cancer. Esophageal squamous cell carcinoma (ESCC) is one of its major histological types. ESCC accounts for the vast majority of cases in China, and the mortality rate is high. Cisplatin, the standard adjuvant chemotherapy drug for ESCC, has a modest response rate due to the development of drug resistance. Hinokiflavone (HF) is a natural biflavonoid compound with anti-melanoma activity. However, its anti-tumor effect on ESCC and the underlying mechanisms remain largely unknown. Methods The ESCC cell lines KYSE150 and TE14 were used. The cell counting kit-8 assay and flow cytometry analysis, along with colony formation, EdU, wound healing, and Transwell migration assays, were performed to assess cell characteristics (viability, migration, invasion, and apoptosis) following treatment with HF. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), western blotting, and molecular docking were used to investigate the pathways potentially modulated by HF. In vivo anti-tumor effects of HF were also investigated using a mouse xenograft model. Results Our findings revealed that HF inhibited ESCC cell proliferation. Hoechst 33342 staining, annexin V-FITC/PI staining, and western blotting confirmed that HF causes caspase-dependent apoptosis. KEGG pathway enrichment analysis and western blotting indicated that the PI3K/AKT/mTOR pathway played an important role in the process of HF-induced apoptosis. Furthermore, HF effectively impaired the migration and invasion abilities of KYSE150 cells and downregulated the expression of the matrix metalloproteinases (MMP) MMP2 and MMP9. HF inhibited tumor growth and exhibited minimal toxicity in the organs of the KYSE150 xenograft model. Conclusion This is the first study to demonstrate the inhibition of ESCC growth and progression by HF. The underlying mechanism is through blocking the PI3K/AKT/mTOR signaling pathway, thereby inhibiting cell proliferation and inducing apoptosis. HF can be used as a complementary/alternative agent for ESCC therapy.
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Affiliation(s)
- Jida Guo
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
| | - Shengqiang Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
| | - Jun Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
| | - Pengfei Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
| | - Tong Lu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
| | - Linyou Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
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Zhu F, Zuo L, Hu R, Wang J, Yang Z, Qi X, Feng L. A ten-genes-based diagnostic signature for atherosclerosis. BMC Cardiovasc Disord 2021; 21:513. [PMID: 34688276 PMCID: PMC8540101 DOI: 10.1186/s12872-021-02323-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 10/12/2021] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Atherosclerosis is the leading cause of cardiovascular disease with a high mortality worldwide. Understanding the atherosclerosis pathogenesis and identification of efficient diagnostic signatures remain major problems of modern medicine. This study aims to screen the potential diagnostic genes for atherosclerosis. METHODS We downloaded the gene chip data of 135 peripheral blood samples, including 57 samples with atherosclerosis and 78 healthy subjects from GEO database (Accession Number: GSE20129). The weighted gene co-expression network analysis was applied to identify atherosclerosis-related genes. Functional enrichment analysis was conducted by using the clusterProfiler R package. The interaction pairs of proteins encoded by atherosclerosis-related genes were screened using STRING database, and the interaction network was further optimized with the cytoHubba plug-in of Cytoscape software. RESULTS The logistic regression diagnostic model was constructed to predict normal and atherosclerosis samples. A gene module which included 532 genes related to the occurrence of atherosclerosis were screened. Functional enrichment analysis basing on the 532 genes identified 235 significantly enriched GO terms and 44 significantly enriched KEGG pathways. The top 50 hub genes of the protein-protein interaction network were identified. The final logistic regression diagnostic model was established by the optimal 10 key genes, which could distinguish atherosclerosis samples from normal samples. CONCLUSIONS A predictive model based on 10 potential atherosclerosis-related genes was obtained, which should shed light on the diagnostic research of atherosclerosis.
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Affiliation(s)
- Feng Zhu
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China.,Department of Traditional Chinese Medicine, Hebei North University, Zhangjiakou City, Hebei Province, China.,Department of Cardiology, Tianjin Union Medical Center, Tianjin, China
| | - Lili Zuo
- Department of Neonatal, ZiBo Maternal and Child Health Hospital, Zibo City, Shandong Province, China
| | - Rui Hu
- Center for Drug Monitoring and Evaluation Department, Center for Drug Monitoring and Evaluation in Zhangjiakou, Zhangjiakou City, Hebei Province, China
| | - Jin Wang
- Department of Cardiovascular Disease, ZiBo Hospital of Traditional Chinese Medicine, Zibo City, Shandong Province, China
| | - Zhihua Yang
- Graduate School, Tianjin University of Traditional Chinese Medicine, Tianjin, China.,First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xin Qi
- Department of Cardiology, Tianjin Union Medical Center, Tianjin, China
| | - Limin Feng
- Department of Cardiology, The Second Affiliated Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin, China.
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12
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Zhou D, Wan J, Luo J. Construction and Validation of Prognostic Markers of Liver Cancer Based on Autophagy Genes. Anticancer Agents Med Chem 2021; 21:1921-1930. [PMID: 33781194 DOI: 10.2174/1871520621666210329100052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 02/15/2021] [Accepted: 03/01/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Liver cancer is one of the most common diseases in the world. At present, the mechanism of autophagy genes in liver cancer is not very clear. Therefore, it is meaningful to study the role and the prognostic value of autophagy genes in liver cancer. OBJECTIVE The purpose of this study is to conduct a bioinformatics analysis of autophagy genes related to primary liver cancer for establishing a prognostic model of primary liver cancer based on autophagy genes. METHODS We identified autophagy genes related to the prognosis of liver cancer through bioinformatics methods. RESULTS Through difference analysis, 31 differential autophagy genes were screened out and then analyzed by GO and KEGG analysis. At the same time, we built a PPI network. For optimizing the evaluation of the prognosis of liver cancer patients, we integrated multiple autophagy genes, after which a prognostic model was established. By using univariate cox regression analysis, 15 autophagy genes related to prognosis were screened out. Then we included these 15 genes into the Least Absolute Shrinkage and Selection Operator (LASSO) and performed a multi-factor cox regression analysis on the 9 selected genes for constructing a prognostic model. The risk score of each patient, who participated in the establishing of the model, was calculated based on 4 genes (BIRC5, HSP8, SQSTM1, and TMEM74). Then the patients were divided into high-risk groups and low-risk groups. In the multivariate cox regression analysis, the risk score was assessed by the independent prognostic factors (HR = 1.872, 95% CI = 1.544 - 2.196, p < 0.001). Survival analysis showed that the survival time of the low-risk group was significantly longer than that of the high-risk group. By combining clinical characteristics and autophagy genes, we constructed a nomogram for predicting the prognosis. The external dataset GSE14520 proved that the nomogram has a good prediction for individual patients with primary liver cancer. CONCLUSION This study provided potential autophagy-related markers for liver cancer patients to predict their prognosis and reveal part of the molecular mechanism of liver cancer autophagy. At the same time, certain gene pathways and protein pathways related to autophagy may provide some inspiration for the development of anticancer drugs.
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Affiliation(s)
- Dawei Zhou
- School of Medical Imaging, Xu Zhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Juncheng Wan
- School of Medical Imaging, Xu Zhou Medical University, Xuzhou, Jiangsu, 221004, China
| | - Jiang Luo
- School of Medical Imaging, Xu Zhou Medical University, Xuzhou, Jiangsu, 221004, China
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Zhai Z, Tao X, Alami MM, Shu S, Wang X. Network Pharmacology and Molecular Docking Combined to Analyze the Molecular and Pharmacological Mechanism of Pinellia ternata in the Treatment of Hypertension. Curr Issues Mol Biol 2021; 43:65-78. [PMID: 34062719 DOI: 10.3390/cimb43010006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 04/21/2021] [Accepted: 04/24/2021] [Indexed: 12/13/2022] Open
Abstract
Hypertension is a cardiovascular disease that causes great harm to health and life, affecting the function of important organs and accompanied by a variety of secondary diseases, which need to be treated with drugs for a long time. P. ternata alone or combination with western medicine has played an important role in traditional Chinese medicine. Although P. ternata is used clinically to treat hypertension, its functional molecular mechanism and pharmacological mechanism have not been elucidated. Therefore, in this study, the potentially effective components, and targets of P. ternata in the treatment of hypertension were screened by the method of network pharmacology, and the mechanism of P. ternata in the treatment of hypertension was analyzed by constructing a component-target relationship network, PPI interaction network, targets’ function analysis, and molecular docking. In the study, 12 potentially effective components and 88 targets were screened, and 3 potential protein modules were found and analyzed after constructing a PPI network using targets. In addition, 10 targets were selected as core targets of the PPI network. After that, the targets were analyzed by Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Finally, the molecular docking method is used to study the interaction between the targets and the active components. The above evidence shows that the mechanism of P. ternata in the treatment of hypertension is complicated, as it acts in many ways, mainly by affecting nerve signal transmission, cell proliferation, and apoptosis, calcium channels, and so on. The binding between targets and active components mainly depends on Pi bonds and hydrogen bonds. Using the method of network pharmacology and molecular docking to analyze the mechanism of P. ternata in the treatment of hypertension will help to provide a better scientific basis for the combined use of traditional Chinese medicine and western medicine, and will better help to improve the quality of P. ternata and point out its direction.
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14
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Wu X, Yang W, Gou XH, Xu XY, Lu N, Jian SN, Han YJ, Lv TS, Luo LZ. A study of the proteomic expression in patients with complicated parapneumonic pleural effusion. Arch Med Sci 2021; 19:1270-1280. [PMID: 37732066 PMCID: PMC10507766 DOI: 10.5114/aoms/132885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 01/27/2021] [Indexed: 09/22/2023] Open
Abstract
Introduction The present study aimed to investigate the differences in the proteomic expression between uncomplicated parapneumonic pleural effusion (UPPE) and complicated parapneumonic pleural effusion (CPPE). Material and methods There were 10 patients with UPPE and 10 patients with CPPE. These patients were combined due to the complication of pleural effusion and further divided into group A and group B. An LC-MS analysis was conducted with the extraction of high-abundance proteins, and proteins with 1.5-fold or higher difference multiples were identified as differential proteins. Then, gene ontology (GO) and KEGG analyses were conducted on the differential proteins between the groups. Results Compared with the UPPE group, there were 38 upregulated proteins and 29 downregulated proteins in the CPPE group. The GO analysis revealed that the CPPE group had enhanced expressions in monosaccharide biosynthesis, glucose catabolism, fructose-6-phosphate glycolysis, glucose-6-phosphate glycolysis, and NADH regeneration as well as reduced expressions in fibrinogen complexes, protein polymerization, and coagulation. Moreover, the KEGG analysis showed that the CPPE group had enhanced expressions in amino acid synthesis, the HIF-1 signalling pathway, and glycolysis/glycoisogenesis and decreased expressions in platelet activation and complement activation. Conclusions In pleural effusion in patients with CPPE, there are enhanced expressions of proteins concerning glucose and amino acid metabolism, NADH regeneration, and HIF-1 signalling pathways together with decreased expressions of proteins concerning protein polymerization, blood coagulation, platelet activation, and complement activation.
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Affiliation(s)
- Xin Wu
- The Second Department of Respiration, Baoding No.1 Central Hospital, HeBei, China
| | - Wei Yang
- The Second Department of Respiration, Baoding No.1 Central Hospital, HeBei, China
| | - Xiao-Hua Gou
- The Second Department of Respiration, Baoding No.1 Central Hospital, HeBei, China
| | - Xiao-Yun Xu
- The Second Department of Respiration, Baoding No.1 Central Hospital, HeBei, China
| | - Na Lu
- Department of Respiration, Lixian County Hospital, HeBei, China
| | - Shi-Ning Jian
- The Second Department of Respiration, Baoding No.1 Central Hospital, HeBei, China
| | - Yu-Jie Han
- The Second Department of Respiration, Baoding No.1 Central Hospital, HeBei, China
| | - Tong-Shuai Lv
- The Second Department of Respiration, Baoding No.1 Central Hospital, HeBei, China
| | - Li-Zhu Luo
- The Second Department of Respiration, Baoding No.1 Central Hospital, HeBei, China
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Sun JL, Zhao LL, He K, Liu Q, Luo J, Zhang DM, Liang J, Liao L, Ma JD, Yang S. MicroRNA regulation in hypoxic environments: differential expression of microRNAs in the liver of largemouth bass (Micropterus salmoides). Fish Physiol Biochem 2020; 46:2227-2242. [PMID: 32948974 DOI: 10.1007/s10695-020-00877-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 09/08/2020] [Indexed: 06/11/2023]
Abstract
Environmental changes in intensive aquaculture commonly lead to hypoxic stress for cultured largemouth bass (Micropterus salmoides). To better to understand the hypoxic stress response mechanisms, the miRNA expression profiles of the livers of largemouth bass exposed for 24 h to three different dissolved oxygen levels (7.0 ± 0.2 mg/L as control, 3.0 ± 0.2 mg/L and 1.2 ± 0.2 mg/L) were compared. In this study, a total of 266 known miRNAs were identified, 84 of which were differentially expressed compared with the control group. Thirteen of the differentially expressed miRNAs (miR-15b-5p, miR-30a-3p, miR-133a-3p, miR-19d-5p, miR-1288-3p, miR456, miR-96-5p, miR-23a-3p, miR-23b-5p, miR-214, miR-24, miR-20a-3p, and miR-2188-5p) were significantly enriched in VEGF signaling pathway, MAPK signaling pathway, and phosphatidylinositol signaling system. These miRNAs were significantly downregulated during stress, especially after a 4-h exposure to hypoxia. In contrast, their target genes (vegfa, pla2g4a, raf1a, pik3c2a, clam2a, inpp1, pi4k2b, mtmr14, ip6k, itpkca, map3k7, and Jun) were significant upregulated after 4 h of hypoxic stress. Moreover, two potential hypoxia-tolerance signal transduction pathways (MAPK signaling pathway and phosphatidylinositol signaling system) were revealed, both of which may play important roles in responding to acute hypoxic stress. We see that miRNAs played an important role in regulating gene expression related to physiological responses to hypoxia. Potential functional network regulated by miRNAs under hypoixic stress in the liver of largemouth bass (Micropterus salmoides). Blue boxes indicated that the expression of miRNA or target genes were down-regulated. Red boxes indicated that the expression of miRNA or target genes wasere up-regulated.
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Affiliation(s)
- Jun Long Sun
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan University, Haikou, 570228, Hainan, China
| | - Liu Lan Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Kuo He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qiao Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jie Luo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Dong Mei Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Ji Liang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Lei Liao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Ji Deng Ma
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Song Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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Li H, Huang X, Li W, Lu Y, Dai X, Zhou Z, Li Q. MicroRNA comparison between poplar and larch provides insight into the different mechanism of wood formation. Plant Cell Rep 2020; 39:1199-1217. [PMID: 32577818 DOI: 10.1007/s00299-020-02559-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 06/12/2020] [Indexed: 05/22/2023]
Abstract
MiRNA transcriptome analysis of different tissues in poplar and larch suggests variant roles of miRNAs in regulating wood formation between two kinds of phyla. Poplar and larch belong to two different phyla. Both are ecological woody species and major resources for wood-related industrial applications. However, wood properties are different between these two species and the molecular basis is largely unknown. In this study, we performed high-throughput sequencing of microRNAs (miRNAs) in the three tissues, xylem, phloem and leaf of Populus alba × Populus glandulosa and Larix kaempferi. Differentially expressed miRNA (DEmiRNA) analysis identified 85 xylem-specific miRNAs in P. alba × P. glandulosa and 158 xylem-specific miRNAs in L. kaempferi. Among 36 common miRNAs, 12 were conserved between the two species. GO and KEGG analyses of the miRNA target genes showed similar metabolism in two species. Through KEGG and BLASTN, we predicted target genes of xylem differentially expressed (DEmiRNA) in the wood formation-related pathways and located DEmiRNAs in these pathways. A network was built for wood formation-related DEmiRNAs, their target genes and orthologous genes in Arabidopsis thaliana. Comparison of DEmiRNA and target gene annotation between P. alba × P. glandulosa and L. kaempferi suggested the different functions of DEmiRNAs and divergent mechanism in wood formation between two species, providing knowledge to understand wood formation mechanism in gymnosperm and angiosperm woody plants.
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Affiliation(s)
- Hui Li
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xiong Huang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Wanfeng Li
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Yan Lu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Xinren Dai
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China.
| | - Zaizhi Zhou
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China.
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
- Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
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Yu XZ, Lu CJ, Tang S, Zhang Q. Transcriptomic analysis of cytochrome P450 genes and pathways involved in chromium toxicity in Oryza sativa. Ecotoxicology 2020; 29:503-513. [PMID: 31119592 DOI: 10.1007/s10646-019-02046-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/19/2019] [Indexed: 06/09/2023]
Abstract
In plants, cytochrome P450 monooxygenase (CYP) plays an important role in detoxifying xenobiotic chemicals and coordinating abiotic stresses. Agilent 44 K rice microarray has been used to focus on the transcriptional profile of osCYP genes in rice seedling exposed to Cr solution containing K2CrO4 or Cr(NO3)3. Our study showed that expression profiles of 264 osCYP genes identified were tissue, dose and stimulus specific in rice seedlings. Comparative genomics analysis revealed that more differentially expressed osCYP genes were discovered in roots than in shoots under both Cr exposures. Results from Venn diagram analysis of differentially expressed osCYP genes demonstrated that there were common osCYP genes and unique osCYP genes present in different rice tissue as well as in different Cr treatments, which may control and/or regulate involvement of different CYP isoenzymes under Cr exposure individually or combinedly. KEGG analysis indicated that significant up- and down-regulated osCYP genes in rice tissues were chiefly related to "biosynthesis of secondary metabolites". However, involvements of osCYP genes mapped in the "biosynthesis of secondary metabolites" were tissue and dose specific, implying their distinctly responsive and adaptive mechanisms during Cr exposure. Overall, our findings are evident to describe and clarify their individual roles of specific osCYP genes in regulating involvement of CYP isoforms in Cr detoxification by rice seedlings.
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Affiliation(s)
- Xiao-Zhang Yu
- College of Environmental Science & Engineering, Guilin University of Technology, 541004, Guilin, P. R. China.
| | - Chun-Jiao Lu
- College of Environmental Science & Engineering, Guilin University of Technology, 541004, Guilin, P. R. China
| | - Shen Tang
- College of Environmental Science & Engineering, Guilin University of Technology, 541004, Guilin, P. R. China
| | - Qing Zhang
- College of Environmental Science & Engineering, Guilin University of Technology, 541004, Guilin, P. R. China
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Sun J, Liu Q, Zhao L, Cui C, Wu H, Liao L, Tang G, Yang S, Yang S. Potential regulation by miRNAs on glucose metabolism in liver of common carp (Cyprinus carpio) at different temperatures. Comp Biochem Physiol Part D Genomics Proteomics 2019; 32:100628. [PMID: 31677400 DOI: 10.1016/j.cbd.2019.100628] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 09/13/2019] [Accepted: 09/13/2019] [Indexed: 12/12/2022]
Abstract
Water temperature can affect the metabolism of fish. Common carp (Cyprinus carpio) is a representative eurythermic fish that can survive at a wide range of ambient temperatures, allowing it to live in an extensive geographical range. The goal of this work was to study the glucose metabolism of common carp at different temperatures and determine the miRNAs involved in the regulation of glucose metabolism. We determined the indicators related to glucose metabolism after long-term temperature stress and constructed nine small RNA libraries of livers under different temperature stress (5 °C, 17 °C, and 30 °C, with three biological replicates for each temperature), and subjected these samples to high-throughput sequencing. A positive relationship was observed between weight gain rate (WGR) and temperature increase after 18 days of temperature stress. However, the glucose level in the plasma maintained a gentle decrease. Unexpectedly, liver lactic acid levels were elevated in HTG (high temperature group) and LTG (low temperature group). Six down-regulated miRNAs (miR-122, miR-30b, miR-15b-5p, miR-20a-5p, miR-1, and miR-7b) were identified as involved in the regulation of glycolysis. Twelve genes were predicted as targets of these miRNAs, and these genes are in pathways related to pyruvate metabolism, glycolysis/gluconeogenesis, and the citrate cycle (TCA cycle). The results allowed prediction of a potential regulatory network of miRNAs involved in the regulation of glycolysis. The target genes of six down-regulated miRNAs were up-regulated under temperature stress, including Aldolase C, fructose-bisphosphate, b (ALDOCB), multiple inositol-polyphosphate phosphatase 1 (MINPP1), phosphoenolpyruvate carboxykinase 1 (PCK1), pyruvate dehydrogenase E1 alpha 1 (PDHA1), aldehyde dehydrogenase 9 family member A1a (ALDH9A1A), Acetyl-coenzyme A synthetase (ACSS), lactate dehydrogenase b (LDH-b), and glyoxylate reductase/hydroxypyruvate reductase (GRHPR). Other key genes of glycolysis, glucose transporter 1 (GLUT-1), pyruvate kinase PKM (PKM), and mitochondrial pyruvate carrier (MPC) were significantly up-regulated in LTG and HTG. Overall, the results suggest that miRNAs maintain their energy requirements by regulating glycolysis and play an important role in the molecular response to cold and heat stress of common carp. These data provide the foundation for further studies of the role of miRNAs in environmental adaptation in fish.
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Affiliation(s)
- JunLong Sun
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Qiao Liu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - LiuLan Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Can Cui
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Hao Wu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Lei Liao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Gang Tang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - ShiYong Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Song Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.
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19
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Wang L, Tang S, Wang Z, Chen H, Rajcha SS, Qian J. The administration of dexmedetomidine changes microRNA expression profiling of rat hearts. Biomed Pharmacother 2019; 120:109463. [PMID: 31541882 DOI: 10.1016/j.biopha.2019.109463] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 09/11/2019] [Accepted: 09/12/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Dexmedetomidine is widely used for perioperative and ICU patients. microRNAs (miRNAs) function as regulators of gene expression. The aim of the study was to assay expression profiling of microRNA in rat hearts following administration of dexmedetomidine. METHODS In this study 6 rats were randomly divided into two groups (n = 3): dexmedetomidine group and control group. The rats of dexmedetomidine group were intraperitoneally given dexmedetomidine in a dose of 100 μg/kg whereas the rats in control group were administered normal saline intraperitoneally. The hearts were excised 30 min after the administration of dexmedetomidine or normal saline under anesthesia. The samples were analyzed for differentially expressed microRNAs with Exiqon miRNA Array. The differentially expressed microRNAs were confirmed by using qRT-PCR. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to find the target genes and signaling pathways of the aberrantly expressed miRNAs. RESULTS Six microRNAs were identified to be significantly expressed, among of which, five microRNAs (miRNA-434-3p, miRNA-3596d, miRNA-496-5p, miRNA-7a-2-3p and miRNA-702-3p) were up-regulated and 1 microRNA (miRNA-208b-3p) down-regulated compared to those of control group. The aberrantly expressed microRNAs were further validated by Quantitative Real Time-Polymerase Chain Reaction (qRT-PCR). GO and KEGG analyses were used to identify target genes and the signaling pathways. CONCLUSIONS The use of dexmedetomidine is associated with differentially expressed microRNAs which may be involved in cardioprotection following administration of dexmedetomidine.
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Affiliation(s)
- Lingyan Wang
- Department of Anesthesiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, China
| | - Shumiao Tang
- Department of Anesthesiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, China
| | - Zhuoran Wang
- Department of Anesthesiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, China
| | - Hongmei Chen
- Department of Anesthesiology, Kunming Angel Women's & Children's Hospital, Kunming, Yunnan Province, China
| | - Shiva Sunder Rajcha
- Department of Anesthesiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, China
| | - Jinqiao Qian
- Department of Anesthesiology, First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, China.
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He F, Wang X, Ren H, Yuan M, Sun L. Association between ACE gene polymorphism and carotid stenosisand and construction of related gene regulatory networks. Saudi J Biol Sci 2019; 26:2000-2005. [PMID: 31889785 PMCID: PMC6923473 DOI: 10.1016/j.sjbs.2019.08.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 08/13/2019] [Accepted: 08/27/2019] [Indexed: 11/16/2022] Open
Abstract
Objective To investigate the association between DD, ID and II genotypes of ACE gene and carotid stenosis, and to construct a network of ACE-related genes regulating carotid stenosis. Approaches Meta-analysis was used to study the association between three genotypes DD, ID and II of carotid stenosis susceptibility gene ACE; functional annotation of ACE gene was conducted by GO analysis; and a network of ACE-related genes that regulate the mechanisms of carotid stenosis was established. Results Meta-analysis showed that DD and II genotypes of ACE gene were associated with carotid stenosis. GO analysis showed that the main biological processes involved in ACE include: the process of transforming angiotensinogen into mature angiotensin; angiotensin’s mediation of the brain's response to alcohol consumption and thirst control; any chemical reaction involving the regulation of angiotensin; and the process of catalyzing the release of a C-terminal dipeptide from a polypeptide chain. A network of ACE gene regulation of carotid stenosis was constructed in combination with KEGG analysis. Conclusion The ACE gene is a susceptibility gene for carotid stenosis. Through the functional annotation and pathway analysis of ACE gene, an ACE gene-involved carotid stenosis regulatory mechanisms network was constructed.
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Affiliation(s)
- Feng He
- Neurosurgery, Xinxiang Central Hospital, Xinxiang 453000, China
| | - Xiying Wang
- Department of Nursing, Xinxiang Central Hospital, Xinxiang 453000, China
| | - Huimin Ren
- Neurosurgery, Xinxiang Central Hospital, Xinxiang 453000, China
| | - Min Yuan
- Neurosurgery, Xinxiang Central Hospital, Xinxiang 453000, China
| | - Laiguang Sun
- Neurosurgery, Xinxiang Central Hospital, Xinxiang 453000, China
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Kang H, Liang QJ, Hu R, Li ZH, Liu Y, Wang WN. Integrative mRNA-miRNA interaction analysis associated with the immune response of Epinephelus coioddes to Vibrio alginolyticus infection. Fish Shellfish Immunol 2019; 90:404-412. [PMID: 31077847 DOI: 10.1016/j.fsi.2019.05.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/29/2019] [Accepted: 05/04/2019] [Indexed: 06/09/2023]
Abstract
MicroRNAs (miRNAs) are a kind of small non-coding RNAs that have been reported to play a vital role in mediating host-pathogen interactions. High-throughput sequencing technology was applied to identify and illuminate mRNAs and miRNAs from grouper infected with Vibrio alginolyticus. The KEGG pathway enrichment analysis showed that the most significate DEGs are associated with Toll-like receptor signaling pathway and NOD-like receptor signaling pathway. We obtained 374 known miRNAs and 116 novel miRNAs. During them, there are 31 up-regulated miRNAs and 93 down-regulated miRNAs. miRNA-mRNA GO and KEGG analysis show that there are 90 miRNAs associated with the immune system. The target genes of immune-related miRNAs (miR-142, miR-146, miR-150, miR-155, miR-203, miR-205, miR-24, miR-31) and genes (CD80, IL-2, AMPK, PI3K) in Epinephelus coioddes were predicted and validated. This study provides an opportunity to further understanding the molecular mechanisms especially the immune system of miRNA regulation in Epinephelus coioddes host-pathogen interactions.
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Affiliation(s)
- Huan Kang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education, College of Life Science, South China Normal University, Guangzhou, 510631, PR China
| | - Qing-Jian Liang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education, College of Life Science, South China Normal University, Guangzhou, 510631, PR China
| | - Rui Hu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education, College of Life Science, South China Normal University, Guangzhou, 510631, PR China
| | - Zhong-Hua Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education, College of Life Science, South China Normal University, Guangzhou, 510631, PR China
| | - Yuan Liu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education, College of Life Science, South China Normal University, Guangzhou, 510631, PR China
| | - Wei-Na Wang
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory for Healthy and Safe Aquaculture, Key Laboratory of Ecology and Environmental Science in Guangdong Higher Education, College of Life Science, South China Normal University, Guangzhou, 510631, PR China.
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22
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Ali N, Gong H, Giwa AS, Yuan Q, Wang K. Metagenomic analysis and characterization of acidogenic microbiome and effect of pH on organic acid production. Arch Microbiol 2019; 201:1163-1171. [PMID: 31172250 DOI: 10.1007/s00203-019-01676-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 05/02/2019] [Accepted: 05/11/2019] [Indexed: 01/14/2023]
Abstract
Organic acid production including lactate and acetate is an economically attractive technology that has gained momentum worldwide over the past years. These series of action need to be performed by an esoteric and complex microbial community, in which different members have distinct roles in the establishment of a collective organization. In this study, we analyzed the bioma from bioreactors with various pH conditions of 4.0, 5.0 and 6.0 (R1, R2 and R3), respectively, involved in acidogenic digestion for stable production of various organic acids by means of high-throughput Illumina sequencing, disclosing thousands of genes and extracting more than 53 microbial genomes. At pH 5.0, the hydrolysis reaction was enhanced and thus the lactic acid fermentation was stably improved to 45.96 mm/L and acetic acid to 73.77 mm/L. R2 was found with the most suitable pH condition for stable organic acids production as Lactobacilli and Bifidobacteria were the major members. Both the members have the key roles in heterofermentation and produce higher transcripts of key encoding enzymes involved in the dominant heterofermentation pathways.
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Affiliation(s)
- Nasir Ali
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.,Qingdao Institute of Bioenergy and Bioprocess Technology, University of Chinese Academy of Sciences, Qingdao, 266101, Shandong Province, People's Republic of China
| | - Hui Gong
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Abdulmoseen Segun Giwa
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Quan Yuan
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Kaijun Wang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China.
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23
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Hong M, Jiang A, Li N, Li W, Shi H, Storey KB, Ding L. Comparative analysis of the liver transcriptome in the red-eared slider Trachemys scripta elegans under chronic salinity stress. PeerJ 2019; 7:e6538. [PMID: 30923649 PMCID: PMC6431541 DOI: 10.7717/peerj.6538] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 01/29/2019] [Indexed: 01/27/2023] Open
Abstract
The red-eared slider (Trachemys scripta elegans), identified as one of the 100 most invasive species in the world, is a freshwater turtle originally from the eastern United States and northeastern Mexico. Field investigations have shown that T. s. elegans can survive and lay eggs in saline habitats. In order to understand the molecular mechanisms of salinity adaptation, high-throughput RNA-Seq was utilized to identify the changes in gene expression profiles in the liver of T. s. elegans in response to elevated salinity. We exposed individuals to 0, 5, or 15 psu (practical salinity units) for 30 days. A total of 157.21 million reads were obtained and assembled into 205138 unigenes with an average length of 620 bp and N50 of 964 bp. Of these, 1019 DEGs (differentially expressed genes) were found in the comparison of 0 vs. 5 psu, 1194 DEGs in 0 vs. 15 psu and 1180 DEGs in 5 vs. 15 psu, which are mainly related to macromolecule metabolic process, ion transport, oxidoreductase activity and generation of precursor metabolites and energy by GO (Gene Ontology) enrichment analyses. T. s. elegans can adapt itself into salinity by balancing the entry of sodium and chloride ions via the up-regulation expression genes of ion transport (potassium voltage-gated channel subfamily H member 5, KCNH5; erine/threonine-protein kinase 32, STK32; salt-inducible kinase 1, SIK1; adiponectin, ACDC), and by accumulating plasma urea and free amino acid via the up-regulation expression genes of amino acid metabolism (ornithine decarboxylase antizyme 3, OAZ3; glutamine synthetase, GLUL; asparaginase-like protein 1b, ASRGL; L-amino-acid oxidase-like, LAAO; sodium-dependent neutral amino acid transporter B, SLC6A15s; amino acid permease, SLC7A9) in response to osmotic regulation. An investment of energy to maintain their homeostatic balance is required to salinity adaptation, therefore, the genes related to energy production and conversion (F-ATPase protein 6, ATP6; cytochrome c oxidase subunit I, COX1; cytochrome c oxidase subunit III, COX3; cytochrome b, CYTb; cytochrome P450 17A1, CYP17A1) were up-regulated with the increase of gene expression associated with lipid metabolism (apolipoprotein E precursor, APoE; coenzyme Q-binding protein, CoQ10; high-density lipoprotein particle, SAA) and carbohydrate metabolism (HK, MIP). These findings improve our understanding of the underlying molecular mechanisms involved in salinity adaptation and provide general guidance to illuminate the invasion potential of T. s. elegans into saline environments.
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Affiliation(s)
- Meiling Hong
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, Hainan, China
| | - Aiping Jiang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, Hainan, China
| | - Na Li
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, Hainan, China
| | - Weihao Li
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, Hainan, China
| | - Haitao Shi
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, Hainan, China.,Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | | | - Li Ding
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, College of Life Sciences, Hainan Normal University, Haikou, Hainan, China
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24
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Zhang X, Wang X, Wu J, Peng J, Deng X, Shen Y, Yang C, Yuan J, Zou Y. The diagnostic values of circulating miRNAs for hypertension and bioinformatics analysis. Biosci Rep 2018; 38:BSR20180525. [PMID: 29961674 DOI: 10.1042/BSR20180525] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/08/2018] [Accepted: 06/22/2018] [Indexed: 12/19/2022] Open
Abstract
Few studies have compared the performances of those reported miRNAs as biomarkers for hypertension in a same cohort, we aimed to comprehensively examine the performances of those reported miRNAs as biomarkers for hypertension and identify the genes and pathways targetted by these miRNAs. Serum samples were collected from patients hospitalized for hypertension in Zhongshan Hospital. Gene expressions of 25 miRNAs were compared between hypertension and normal groups. Receiver operating characteristic (ROC) curves were used to evaluate the accuracy of those miRNAs as biomarkers for hypertension. miRWALK2.0 and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis were performed to predict the target genes and pathways of selected miRNAs. A total of 164 participants were enrolled, amongst which 53 were patients with hypertension, 111 were normal population. MiR-122-5p (area under curve (AUC): 0.750), miR-199a-3p (AUC: 0.744), miR-208a-3p (AUC: 0.743), miR-423-5p (AUC: 0.740), and miR-223-5p (AUC: 0.718) showed better performance than others, and the best performance was the combination of miR-199a-3p, miR-208a-3p, miR-122-5p, and miR-223-3p (AUC: 0.80). Pathway analysis revealed that 94 pathways enriched with genes targetted by miR-199a-3p, miR-208a-3p, miR-122-5p, miR-223-5p. FoxO signaling was enriched with genes targetted by all the three miRNAs (miR-199a-3p, miR-208a-3p, miR-122-5p). The combination of miR-199a-3p, miR-208a-3p, miR-122-5p, and miR-223-3p has a good diagnostic performance for hypertension, and multitudes of possible mechanisms/pathways through which dysregulation of these miRNAs may impact risk of hypertension.
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25
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Gurunathan S, Qasim M, Park C, Yoo H, Kim JH, Hong K. Cytotoxic Potential and Molecular Pathway Analysis of Silver Nanoparticles in Human Colon Cancer Cells HCT116. Int J Mol Sci 2018; 19:E2269. [PMID: 30072642 PMCID: PMC6121495 DOI: 10.3390/ijms19082269] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 07/29/2018] [Accepted: 07/30/2018] [Indexed: 12/12/2022] Open
Abstract
Silver nanoparticles (AgNPs) have gained attention for use in cancer therapy. In this study, AgNPs were biosynthesized using naringenin. We investigated the anti-colon cancer activities of biogenic AgNPs through transcriptome analysis using RNA sequencing, and the mechanisms of AgNPs in regulating colon cancer cell growth. The synthesized AgNPs were characterized using UV⁻visible spectroscopy (UV⁻vis), X-ray diffraction (XRD), Fourier-transform infrared spectroscopy (FTIR), dynamic light scattering (DLS), and transmission electron microscopy (TEM). The AgNPs were spherical with sizes of 2⁻10 nm. Cytotoxicity assays indicated that the AgNPs in HCT116 colorectal cancer cells were very effective at low concentrations. The viability and proliferation of colon cancer cells treated with 5 µg/mL biogenic AgNPs were reduced by 50%. Increased lactate dehydrogenase leakage (LDH), reactive oxygen species (ROS) generation, malondialdehyde (MDA), and decreased dead-cell protease activity and ATP generation were observed. This impaired mitochondrial function and DNA damage led to cell death. The AgNPs upregulated and downregulated the most highly ranked biological processes of oxidation⁻reduction and cell-cycle regulation, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that AgNPs upregulated GADD45G in the p53 pathway. Thus, the AgNP tumor suppressive effects were mediated by cell apoptosis following DNA damage, as well as by mitochondrial dysfunction and cell-cycle arrest following aberrant regulation of p53 effector proteins. It is of interest to mention that, to the best of our knowledge, this study is the first report demonstrating cellular responses and molecular pathways analysis of AgNPs in HCT116 colorectal cancer cells.
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Affiliation(s)
- Sangiliyandi Gurunathan
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Muhammad Qasim
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Chanhyeok Park
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Hyunjin Yoo
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Jin-Hoi Kim
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
| | - Kwonho Hong
- Department of Stem Cell and Regenerative Biotechnology and Humanized Pig Center (SRC), Konkuk Institute of Technology, Konkuk University, Seoul 05029, Korea.
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26
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Xu D, Xu Y, Ning N, Cui Q, Liu Z, Wang X, Liu D, Chen H, Kong MG. Alteration of metabolite profiling by cold atmospheric plasma treatment in human myeloma cells. Cancer Cell Int 2018; 18:42. [PMID: 29568236 PMCID: PMC5859683 DOI: 10.1186/s12935-018-0541-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 03/14/2018] [Indexed: 12/17/2022] Open
Abstract
Background Despite new progress of chemotherapy in multiple myeloma (MM) clinical treatment, MM is still a refractory disease and new technology is needed to improve the outcomes and prolong the survival. Cold atmospheric plasma is a rapidly developed technology in recent years, which has been widely applied in biomedicine. Although plasma could efficiently inactivate various tumor cells, the effects of plasma on tumor cell metabolism have not been studied yet. Methods In this study, we investigated the metabolite profiling of He plasma treatment on myeloma tumor cells by gas-chromatography time-of-flight (GC-TOF) mass-spectrometry. Meanwhile, by bioinformatic analysis such as GO and KEGG analysis we try to figure out the metabolism pathway that was significantly affected by gas plasma treatment. Results By GC-TOF mass-spectrometry, 573 signals were detected and evaluated using PCA and OPLS-DA. By KEGG analysis we listed all the differential metabolites and further classified into different metabolic pathways. The results showed that beta-alanine metabolism pathway was the most significant change after He gas plasma treatment in myeloma cells. Besides, propanoate metabolism and linoleic acid metabolism should also be concerned during gas plasma treatment of cancer cells. Conclusions Cold atmospheric plasma treatment could significantly alter the metabolite profiling of myeloma tumor cells, among which, the beta-alanine metabolism pathway is the most susceptible to He gas plasma treatment. Electronic supplementary material The online version of this article (10.1186/s12935-018-0541-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dehui Xu
- 1State Key Laboratory of Electrical Insulation and Power Equipment, Centre for Plasma Biomedicine, Xi'an Jiaotong University, Xi'an, 710049 Shaanxi People's Republic of China
| | - Yujing Xu
- 1State Key Laboratory of Electrical Insulation and Power Equipment, Centre for Plasma Biomedicine, Xi'an Jiaotong University, Xi'an, 710049 Shaanxi People's Republic of China
| | - Ning Ning
- 2The School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049 Shaanxi People's Republic of China
| | - Qingjie Cui
- 2The School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049 Shaanxi People's Republic of China
| | - Zhijie Liu
- 1State Key Laboratory of Electrical Insulation and Power Equipment, Centre for Plasma Biomedicine, Xi'an Jiaotong University, Xi'an, 710049 Shaanxi People's Republic of China
| | - Xiaohua Wang
- 1State Key Laboratory of Electrical Insulation and Power Equipment, Centre for Plasma Biomedicine, Xi'an Jiaotong University, Xi'an, 710049 Shaanxi People's Republic of China
| | - Dingxin Liu
- 1State Key Laboratory of Electrical Insulation and Power Equipment, Centre for Plasma Biomedicine, Xi'an Jiaotong University, Xi'an, 710049 Shaanxi People's Republic of China
| | - Hailan Chen
- 3Frank Reidy Center for Bioelectrics, Old Dominion University, Norfolk, VA 23508 USA
| | - Michael G Kong
- 1State Key Laboratory of Electrical Insulation and Power Equipment, Centre for Plasma Biomedicine, Xi'an Jiaotong University, Xi'an, 710049 Shaanxi People's Republic of China.,3Frank Reidy Center for Bioelectrics, Old Dominion University, Norfolk, VA 23508 USA.,4Department of Electrical and Computer Engineering, Old Dominion University, Norfolk, VA 23529 USA
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27
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Strainiene E, Binkis M, Urnikyte S, Stankevicius V, Sasnauskiene A, Kundrotas G, Kazlauskas A, Suziedelis K. Microenvironment dependent gene expression signatures in reprogrammed human colon normal and cancer cell lines. BMC Cancer 2018; 18:222. [PMID: 29482503 PMCID: PMC5827990 DOI: 10.1186/s12885-018-4145-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 02/19/2018] [Indexed: 12/14/2022] Open
Abstract
Background Since the first evidence suggesting existence of stem-like cancer cells, the process of cells reprogramming to the stem cell state remains as an attractive tool for cancer stemness research. Current knowledge in the field of cancer stemness, indicates that the microenvironment is a fundamental regulator of cell behavior. With regard to this, we investigated the changes of genome wide gene expression in reprogrammed human colon normal epithelial CRL-1831 and colon carcinoma DLD1 cell lines grown under more physiologically relevant three-dimensional (3D) cell culture microenvironment compared to 2D monolayer. Methods Whole genome gene expression changes were evaluated in both cell lines cultured under 3D conditions over a 2D monolayer by gene expression microarray analysis. To evaluate the biological significance of gene expression changes, we performed pathway enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Gene network analysis was used to study relationships between differentially expressed genes (DEGs) in functional categories by the GeneMANIA Cytoscape toolkit. Results In total, we identified 3228 and 2654 differentially expressed genes (DEGs) for colon normal and cancer reprogrammed cell lines, respectively. Furthermore, the expression of 1097 genes was commonly regulated in both cell lines. KEGG enrichment analysis revealed that in total 129 and 101 pathways for iPSC-CRL-1831 and for CSC-DLD1, respectively, were enriched. Next, we grouped these pathways into three functional categories: cancer transformation/metastasis, cell interaction, and stemness. β-catenin (CTNNB1) was confirmed as a hub gene of all three functional categories. Conclusions Our present findings suggest common pathways between reprogrammed human colon normal epithelium (iPSC-CRL-1831) and adenocarcinoma (CSC-DLD1) cells grown under 3D microenvironment. In addition, we demonstrated that pathways important for cancer transformation and tumor metastatic activity are altered both in normal and cancer stem-like cells during the transfer from 2D to 3D culture conditions. Thus, we indicate the potential of cell culture models enriched in normal and cancer stem-like cells for the identification of new therapeutic targets in cancer treatment. Electronic supplementary material The online version of this article (10.1186/s12885-018-4145-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Egle Strainiene
- National Cancer Institute, Santariskiu 1, 08660, Vilnius, LT, Lithuania. .,Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, Vilnius, Lithuania.
| | - Mindaugas Binkis
- National Cancer Institute, Santariskiu 1, 08660, Vilnius, LT, Lithuania.,Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Silvija Urnikyte
- National Cancer Institute, Santariskiu 1, 08660, Vilnius, LT, Lithuania.,Department of Chemistry and Bioengineering, Vilnius Gediminas Technical University, Vilnius, Lithuania
| | - Vaidotas Stankevicius
- National Cancer Institute, Santariskiu 1, 08660, Vilnius, LT, Lithuania.,Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Ausra Sasnauskiene
- Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | | | - Andrius Kazlauskas
- Department of Ophthalmology, Harvard Medical School, Schepens Eye Research Institute and Massachusetts Eye and Ear Infirmary, Boston, MA, 02114, USA
| | - Kestutis Suziedelis
- National Cancer Institute, Santariskiu 1, 08660, Vilnius, LT, Lithuania. .,Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
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Hou L, Gu W, Zhu H, Yao W, Wang W, Meng Q. Spiroplasma eriocheiris induces mouse 3T6-Swiss albino cell apoptosis that associated with the infection mechanism. Mol Immunol 2017; 91:75-85. [PMID: 28889064 DOI: 10.1016/j.molimm.2017.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 07/31/2017] [Accepted: 08/07/2017] [Indexed: 11/20/2022]
Abstract
Spiroplasma eriocheiris is a novel pathogen similar to the Spiroplasma mirum and also had an ability to infect the newborn mice and caused cataract. Our study was designed to study how S. eriocheiris infects mouse 3T6-Swiss albino cells and to elucidate the cellular molecular pathogenesis of Spiroplasma. FCM analysis and MTT analysis clearly shown that S. eriocheiris could induce 3T6 cell apoptosis and cause cell viability decreased seriously. Immunofluorescence experiments and TEM analysis shown that S. eriocheiris can invade 3T6 cells and form typical inclusion bodies and exhibit vacuolization in vitro. S. eriocheiris-oxytetracycline protection assay show that the infective bacteria already were detected at 1h post infection, and sharply increased at 12h after the bacteria infection. To further study the infection mechanism of S. eriocheiris, global mRNA and microRNA (miRNA) expression profiling were analyzed after the cells infected with the bacteria. A total of 619 non-redundant annotated transcripts (183 up-regulated and 436 down-regulated) and 22 miRNAs (8 up-regulated and 14 down-regulated) were differential expression after 6h S. eriocheiris infection compared to control group. Integrated analysis shown that homologous genes from differential expression miRNA targets and the differential expression genes of the mRNA microarray were major focused on two important pathways focal adhesion and MAPK signaling pathway. To validate the results of microarray, eight focal adhesion (β-Catenin, Parvin, Grb2 and ERK) and MAPK signaling pathway (FGFR, Grb2, ERK, MKK3, p38 and JNK) genes and the housekeeping gene GAPDH were assayed by qPCR and Western blot to confirm the results. Eight miRNAs (miR-143-3p, miR-214-5p, miR-322-3p, miR-328-5p, miR-351-5p, miR-466h-5p, miR-503-5p and miR-30c-1-3p) and the housekeeping gene U6 miRNA were assayed by qPCR to confirm the results of microarray. All the results help us better understand the infection mechanism of S. eriocheiris.
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Affiliation(s)
- Libo Hou
- Jiangsu Key Laboratory for Microbes & Functional Genomics and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China
| | - Wei Gu
- Jiangsu Key Laboratory for Microbes & Functional Genomics and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China
| | - Huanxi Zhu
- Jiangsu Key Laboratory for Microbes & Functional Genomics and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China
| | - Wei Yao
- Jiangsu Key Laboratory for Microbes & Functional Genomics and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China
| | - Wen Wang
- Jiangsu Key Laboratory for Microbes & Functional Genomics and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China
| | - Qingguo Meng
- Jiangsu Key Laboratory for Microbes & Functional Genomics and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University, 1 Wenyuan Road, Nanjing 210046, China; Co-Innovation Center for Marine Bio-Industry Technology of Jiangsu Province, Lianyungang, Jiangsu 222005, China.
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Abstract
Objective To identify potential genes that may be involved in lipid metabolism in rats after treatment with aqueous extract of Arctium lappa L (burdock). Methods Rats were randomly divided into six groups: (i) control (standard diet); (ii) model group (high-fat diet only); (iii) high-fat diet and low-dose aqueous burdock root extract (2 g/kg); (iv) high-fat diet and moderate-dose aqueous burdock root extract (4 g/kg); (v) high-fat diet and high-dose aqueous burdock root extract (8 g/kg); and (vi) a positive control group exposed to a high-fat diet and simvastatin (10 mg/kg). Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis was performed to find the potential candidate genes involved in the modulation of blood lipids by treatment with aqueous burdock root extract. Results Burdock root extract reduced body weight and cholesterol levels in rats. KEGG analysis revealed 113 genes that were involved in metabolic pathways. Of these, 27 potential genes associated with blood lipid metabolism were identified. Conclusions Aqueous extract of burdock root reduced body weight and cholesterol in rats, possibly by modulating the differential expression of genes.
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Affiliation(s)
- Bo Hou
- 1 Department of Cardiology, Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| | - Wencheng Wang
- 2 Qingdao Municipal Centre for Disease Control and Prevention, Qingdao, Shandong Province, China
| | - Hui Gao
- 3 Department of Pharmacology, Qingdao University Medical College, Qingdao, Shandong Province, China
| | - Shanglang Cai
- 1 Department of Cardiology, Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| | - Chunbo Wang
- 3 Department of Pharmacology, Qingdao University Medical College, Qingdao, Shandong Province, China
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Hao Y, Shan G, Nan K. Establishment of apoptotic regulatory network for genetic markers of colorectal cancer. Saudi J Biol Sci 2017; 24:466-476. [PMID: 28386169 PMCID: PMC5372377 DOI: 10.1016/j.sjbs.2017.01.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 12/25/2016] [Accepted: 01/06/2017] [Indexed: 11/30/2022] Open
Abstract
Our purpose is to screen out genetic markers applicable to early diagnosis for colorectal cancer and to establish apoptotic regulatory network model for colorectal cancer, thereby providing theoretical evidence and targeted therapy for early diagnosis of colorectal cancer. Taking databases including CNKI, VIP, Wanfang data, Pub Med, and MEDLINE as main sources of literature retrieval, literatures associated with genetic markers applied to early diagnosis of colorectal cancer were searched to perform comprehensive and quantitative analysis by Meta analysis, hence screening genetic markers used in early diagnosis of colorectal cancer. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were employed to establish apoptotic regulatory network model based on screened genetic markers, and then verification experiment was conducted. Through Meta analysis, seven genetic markers were screened out, including WWOX, K-ras, COX-2, p53, APC, DCC and PTEN, among which DCC shows highest diagnostic efficiency. GO analysis of genetic markers found that six genetic markers played role in biological process, molecular function and cellular component. It was indicated in apoptotic regulatory network built by KEGG analysis and verification experiment that WWOX could promote tumor cell apoptotic in colorectal cancer and elevate expression level of p53. The apoptotic regulatory model of colorectal cancer established in this study provides clinically theoretical evidence and targeted therapy for early diagnosis of colorectal cancer.
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Affiliation(s)
- Yibin Hao
- Department of Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710077, China
- Department of Oncological Radiotherapy, People’s Hospital of Zhengzhou, Zhengzhou 450003, China
| | - Guoyong Shan
- Department of Oncological Radiotherapy, People’s Hospital of Zhengzhou, Zhengzhou 450003, China
| | - Kejun Nan
- Department of Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710077, China
- Corresponding author.
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Stankevicius V, Vasauskas G, Noreikiene R, Kuodyte K, Valius M, Suziedelis K. Extracellular Matrix-dependent Pathways in Colorectal Cancer Cell Lines Reveal Potential Targets for Anticancer Therapies. Anticancer Res 2017; 36:4559-67. [PMID: 27630296 DOI: 10.21873/anticanres.11004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 08/18/2016] [Indexed: 11/10/2022]
Abstract
BACKGROUND Cancer cells grown in a 3D culture are more resistant to anticancer therapy treatment compared to those in a monolayer 2D culture. Emerging evidence has suggested that the key reasons for increased cell survival could be gene expression changes in cell-extracellular matrix (ECM) interaction-dependent manner. MATERIALS AND METHODS Global gene-expression changes were obtained in human colorectal carcinoma HT29 and DLD1 cell lines between 2D and laminin-rich (lr) ECM 3D growth conditions by gene-expression microarray analysis. The most significantly altered functional categories were revealed by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. RESULTS The microarray data revealed that 841 and 1190 genes were differentially expressed in colorectal carcinoma DLD1 and HT29 cells. KEGG analysis indicated that the most significantly altered categories were cell adhesion, mitogen-activated protein kinase and immune response. CONCLUSION Our results indicate altered pathways related to cancer development and progression and suggest potential ECM-regulated targets for the development of anticancer therapies.
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Affiliation(s)
- Vaidotas Stankevicius
- Laboratory of Molecular Oncology, National Cancer Institute, Vilnius, Lithuania Department of Biochemistry and Molecular Biology, Faculty of Natural Sciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Gintautas Vasauskas
- Laboratory of Molecular Oncology, National Cancer Institute, Vilnius, Lithuania Department of Biochemistry and Molecular Biology, Faculty of Natural Sciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Rimante Noreikiene
- Laboratory of Molecular Oncology, National Cancer Institute, Vilnius, Lithuania Department of Biochemistry and Molecular Biology, Faculty of Natural Sciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Karolina Kuodyte
- Laboratory of Molecular Oncology, National Cancer Institute, Vilnius, Lithuania Department of Biochemistry and Molecular Biology, Faculty of Natural Sciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Mindaugas Valius
- Proteomics Center, Vilnius University Institute of Biochemistry, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Kestutis Suziedelis
- Laboratory of Molecular Oncology, National Cancer Institute, Vilnius, Lithuania Department of Biochemistry and Molecular Biology, Faculty of Natural Sciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
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Tian T, Chen C, Yang F, Tang J, Pei J, Shi B, Zhang N, Zhang J. Establishment of apoptotic regulatory network for genetic markers of colorectal cancer and optimal selection of traditional Chinese medicine target. Saudi J Biol Sci 2017; 24:634-643. [PMID: 28386190 PMCID: PMC5372422 DOI: 10.1016/j.sjbs.2017.01.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/28/2016] [Accepted: 01/07/2017] [Indexed: 01/02/2023] Open
Abstract
The paper aimed to screen out genetic markers applicable to early diagnosis for colorectal cancer and establish apoptotic regulatory network model for colorectal cancer, and to analyze the current situation of traditional Chinese medicine (TCM) target, thereby providing theoretical evidence for early diagnosis and targeted therapy of colorectal cancer. Taking databases including CNKI, VIP, Wanfang data, Pub Med, and MEDLINE as main sources of literature retrieval, literatures associated with genetic markers that are applied to early diagnosis of colorectal cancer were searched and performed comprehensive and quantitative analysis by Meta analysis, hence screening genetic markers used in early diagnosis of colorectal cancer. KEGG analysis was employed to establish apoptotic regulatory network model based on screened genetic markers, and optimization was conducted on TCM targets. Through Meta analysis, seven genetic markers were screened out, including WWOX, K-ras, COX-2, P53, APC, DCC and PTEN, among which DCC has the highest diagnostic efficiency. Apoptotic regulatory network was built by KEGG analysis. Currently, it was reported that TCM has regulatory function on gene locus in apoptotic regulatory network. The apoptotic regulatory model of colorectal cancer established in this study provides theoretical evidence for early diagnosis and TCM targeted therapy of colorectal cancer in clinic.
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Affiliation(s)
- Tongde Tian
- Integrated TCM and Western Medicine Department, Cancer Hospital Affiliated to Zhengzhou University, No. 127 Dongming Rd., Zhengzhou, Henan Province 450008, China
| | - Chuanliang Chen
- Hospital Office, People's Hospital of Zhengzhou University, No. 7 Weiwu Rd., Zhengzhou, Henan Province 450003, China
| | - Feng Yang
- Integrated TCM and Western Medicine Department, Cancer Hospital Affiliated to Zhengzhou University, No. 127 Dongming Rd., Zhengzhou, Henan Province 450008, China
| | - Jingwen Tang
- Integrated TCM and Western Medicine Department, Cancer Hospital Affiliated to Zhengzhou University, No. 127 Dongming Rd., Zhengzhou, Henan Province 450008, China
| | - Junwen Pei
- Integrated TCM and Western Medicine Department, Cancer Hospital Affiliated to Zhengzhou University, No. 127 Dongming Rd., Zhengzhou, Henan Province 450008, China
| | - Bian Shi
- Integrated TCM and Western Medicine Department, Cancer Hospital Affiliated to Zhengzhou University, No. 127 Dongming Rd., Zhengzhou, Henan Province 450008, China
| | - Ning Zhang
- Medical Engineering Technology and Data Mining Institute of Zhengzhou University, No. 100 Science Ave., Gaoxin Dist., Zhengzhou, Henan Province 450001, China
| | - Jianhua Zhang
- Medical Engineering Technology and Data Mining Institute of Zhengzhou University, No. 100 Science Ave., Gaoxin Dist., Zhengzhou, Henan Province 450001, China
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Zhan C, Yan L, Wang L, Jiang W, Zhang Y, Xi J, Jin Y, Chen L, Shi Y, Lin Z, Wang Q. Landscape of expression profiles in esophageal carcinoma by The Cancer Genome Atlas data. Dis Esophagus 2016; 29:920-928. [PMID: 26402921 DOI: 10.1111/dote.12416] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this study, we explored the gene and microRNA (miRNA) expressions profile of esophageal carcinoma. The expression data for messenger RNAs and miRNAs in normal and cancerous esophageal tissues were obtained from the Cancer Genome Atlas database and then the differentially expressed genes and miRNAs were identified. As a result, we identified 2962 genes and 45 miRNAs differentially expressed in esophageal carcinoma compared with normal esophageal tissues. Subsequently, the altered gene functions and signaling pathways were investigated using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, and these differentially expressed genes were significantly enriched in the cell cycle, cell migration, mitogen-activated protein kinase (MAPK) and toll-like receptor signaling pathway, and so on. Then the regulatory relationships between the differentially expressed miRNAs and genes were examined with Targetscan and Miranda, and the potential target sites of transcription factors (TFs) in the promoter regions of these miRNAs and genes were identified using the TRANSFAC database. Finally the TF-miRNA-gene network in esophageal cancer was established, summarizing the regulatory links among the TFs, differentially expressed miRNAs and differentially expressed genes. Factors such as core promoter-binding protein (CPBP), nuclear factor of activated T-cells 1 (NFAT-1), miR-30c-5p, were located in the central hub of this network, highlighting their vital roles in esophageal tumorigenesis. These findings may extend our understanding of the molecular mechanisms underlying esophageal carcinoma and promote new perspectives for prevention, diagnosis and treatment.
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Affiliation(s)
- C Zhan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - L Yan
- Department of Radiation Oncology, Eye & ENT Hospital, Fudan University, Shanghai, China
| | - L Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - W Jiang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Y Zhang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - J Xi
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Y Jin
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - L Chen
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Y Shi
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Z Lin
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Q Wang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
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Zhang WW, Sun XF, Tong HL, Wang YH, Li SF, Yan YQ, Li GP. Effect of differentiation on microRNA expression in bovine skeletal muscle satellite cells by deep sequencing. Cell Mol Biol Lett 2016; 21:8. [PMID: 28536611 PMCID: PMC5415838 DOI: 10.1186/s11658-016-0009-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 09/25/2015] [Indexed: 01/01/2023] Open
Abstract
Background The differentiation of skeletal muscle-derived satellite cells (MDSCs) is important in controlling muscle growth, improving livestock muscle quality, and healing of muscle-related disease. MicroRNAs (miRNAs) are a class of gene expression regulatory factors, which play critical roles in the regulation of muscle cell differentiation. This study aimed to compare the expression profile of miRNAs in MDSC differentiation, and to investigate the miRNAs which are involved in MDSC differentiation. Method Total RNA was extracted from MDSCs at three different stages of differentiation (MDSC-P, MDSC-D1 and MDSC-D3, representing 0, 1 and 3 days after differentiation, respectively), and used to construct small RNA libraries for RNA sequencing (RNA-seq). Results The results showed that in total 617 miRNAs, including 53 novel miRNA candidates, were identified. There were 9 up-expressed, 165 down-expressed, and 15 up-expressed, 145 down-expressed in MDSC-D1 and MDSC-D3, respectively, compared to those in MDSC-P. Also, 17 up-expressed, 55 down-expressed miRNAs were observed in MDSC-D3 compared to those in MDSC-D1. All known miRNAs belong to 237 miRNA gene families. Furthermore, we observed some sequence variants and base edits of the miRNAs. GO and KEGG pathway analysis showed that the majority of target genes regulated by miRNAs were involved in cellular metabolism, pathways in cancer, actin cytoskeleton regulation and the MAPK signaling pathway. Regarding the 53 novel miRNAs, there were 7 up-expressed, 31 down-expressed, and 8 up-expressed, 26 down-expressed in MDSC-D1 and MDSC-D3, respectively, compared to those in MDSC-P. The expression levels of 12 selected miRNA genes detected by RT-qPCR were consistent with those generated by deep sequencing. Conclusions This study confirmed the authenticity of 564 known miRNAs and identified 53 novel miRNAs which were involved in MDSC differentiation. The identification of novel miRNAs has significantly expanded the repertoire of bovine miRNAs and could contribute to advances in understanding muscle development in cattle. Electronic supplementary material The online version of this article (doi:10.1186/s11658-016-0009-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wei Wei Zhang
- The Laboratory of Cell and Development, Northeast Agricultural University, Mucai Street 59, Xiangfang District, Harbin, 150030 Heilongjiang China.,College of Life Sciences and Agriculture & Forestry, Qiqihar University, Qiqihar, Heilongjiang 161006 China
| | - Xiao Feng Sun
- The Laboratory of Cell and Development, Northeast Agricultural University, Mucai Street 59, Xiangfang District, Harbin, 150030 Heilongjiang China
| | - Hui Li Tong
- The Laboratory of Cell and Development, Northeast Agricultural University, Mucai Street 59, Xiangfang District, Harbin, 150030 Heilongjiang China
| | - Ya Hui Wang
- The Laboratory of Cell and Development, Northeast Agricultural University, Mucai Street 59, Xiangfang District, Harbin, 150030 Heilongjiang China
| | - Shu Feng Li
- The Laboratory of Cell and Development, Northeast Agricultural University, Mucai Street 59, Xiangfang District, Harbin, 150030 Heilongjiang China
| | - Yun Qin Yan
- The Laboratory of Cell and Development, Northeast Agricultural University, Mucai Street 59, Xiangfang District, Harbin, 150030 Heilongjiang China
| | - Guang Peng Li
- The Key Laboratory of Mammal Reproductive Biology and Biotechnology Ministry of Education, Inner Mongolia University, Hohhot, 010021 China
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Yan L, Zhan C, Wang S, Wang S, Guo L. Genetic analysis of radiation-specific biomarkers in sinonasal squamous cell carcinomas. Tumour Biol 2016; 37:12001-9. [PMID: 27164935 DOI: 10.1007/s13277-016-5057-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/11/2015] [Indexed: 12/14/2022] Open
Abstract
The aim of this study was to investigate the differences in the gene expression profiles of radiation-sensitive (RS) and radiation-resistant (RR) sinonasal squamous cell carcinoma (SNSCC) and to identify prognostic markers for the radiation reaction of SNSCC. We first examined the differentially expressed genes (DEGs) in RS and RR SNSCC tissues by analyzing clinical samples with GeneChip Human Transcriptome Array 2.0 (HTA 2.0).To understand the functional significance of the molecular changes, we examined the DEGs with Gene Ontology (GO) and pathway analyses to identify the core genes. The expression of several core genes (CCND2, COL5A2, GADD45B, and THBS2) was confirmed with reverse transcription quantitative PCR (RT-qPCR) in a larger series of tissues. We identified 208 DEGs, of which 76 were upregulated and 132 downregulated in the RS tissues relative to the RR tissues. The DEGs were mainly involved in the regulation of cell proliferation, the NF-kappaB signaling pathway, the cell adhesion molecule signaling pathway, and the extracellular matrix-receptor interaction signaling pathway. RT-qPCR confirmed that the CCND2, COL5A2, GADD45B, and THBS2 genes were significantly differentially expressed in the RS and RR tissues, consistent with the GeneChip data. These results extend our understanding of the molecular mechanisms underlying the sensitivity of SNSCC to radiation. The DEGs are involved in the differential response to radiation therapy and the dysregulated core genes identified in this study can be used to predict radiation sensitivity in SNSCC.
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