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Shi YJ, Sheng WJ, Xue MT, Duan FX, Shen L, Ding SQ, Wang QY, Wang R, Lü HZ, Hu JG. Effect of morroniside on the transcriptome profiles of rat in injured spinal cords. Gene 2022; 823:146338. [PMID: 35245640 DOI: 10.1016/j.gene.2022.146338] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/16/2022] [Accepted: 02/11/2022] [Indexed: 12/27/2022]
Abstract
We have previously reported that morroniside promoted motor activity after spinal cord injury (SCI) in rats. However, the mechanism by which morroniside induces recovery of injured spinal cord (SC) remains unknown. In the current study, RNA sequencing (RNA-seq) was employed to evaluate changes of gene expressions at the transcriptional level of the injured spinal cords in morroniside-administrated rats. Principal component analysis, analysis of enriched Gene Ontology (GO), enrichment analyses Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and other bioinformatics analyses were executed to distinguish differentially expressed genes (DEGs). The results of RNA-seq confirmed the anti-inflammatory and anti-apoptotic effects of morroniside on injured SC tissues, and provided the basis for additional research of the mechanisms involving the protective effects of morroniside on SCI.
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Affiliation(s)
- Yu-Jiao Shi
- Department of Clinical Laboratory, The First Affiliated Hospital of Bengbu Medical College, 287 Chang Huai Road, Bengbu 233004, PR China; Anhui Key Laboratory of Tissue Transplantation, Bengbu Medical College, Bengbu 233004, PR China
| | - Wen-Jie Sheng
- Department of Clinical Laboratory, The First Affiliated Hospital of Bengbu Medical College, 287 Chang Huai Road, Bengbu 233004, PR China; Anhui Key Laboratory of Tissue Transplantation, Bengbu Medical College, Bengbu 233004, PR China
| | - Meng-Tong Xue
- Department of Clinical Laboratory, The First Affiliated Hospital of Bengbu Medical College, 287 Chang Huai Road, Bengbu 233004, PR China; Anhui Key Laboratory of Tissue Transplantation, Bengbu Medical College, Bengbu 233004, PR China
| | - Fei-Xiang Duan
- Department of Clinical Laboratory, The First Affiliated Hospital of Bengbu Medical College, 287 Chang Huai Road, Bengbu 233004, PR China; Anhui Key Laboratory of Tissue Transplantation, Bengbu Medical College, Bengbu 233004, PR China
| | - Lin Shen
- Anhui Key Laboratory of Tissue Transplantation, Bengbu Medical College, Bengbu 233004, PR China
| | - Shu-Qin Ding
- Department of Clinical Laboratory, The First Affiliated Hospital of Bengbu Medical College, 287 Chang Huai Road, Bengbu 233004, PR China; Anhui Key Laboratory of Tissue Transplantation, Bengbu Medical College, Bengbu 233004, PR China
| | - Qi-Yi Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Bengbu Medical College, 287 Chang Huai Road, Bengbu 233004, PR China
| | - Rui Wang
- Anhui Key Laboratory of Tissue Transplantation, Bengbu Medical College, Bengbu 233004, PR China
| | - He-Zuo Lü
- Department of Clinical Laboratory, The First Affiliated Hospital of Bengbu Medical College, 287 Chang Huai Road, Bengbu 233004, PR China; Anhui Key Laboratory of Tissue Transplantation, Bengbu Medical College, Bengbu 233004, PR China; Department of Immunology, Bengbu Medical College, Bengbu 233030, PR China.
| | - Jian-Guo Hu
- Department of Clinical Laboratory, The First Affiliated Hospital of Bengbu Medical College, 287 Chang Huai Road, Bengbu 233004, PR China; Anhui Key Laboratory of Tissue Transplantation, Bengbu Medical College, Bengbu 233004, PR China.
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2
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Li Y, Yuan P, Fan S, Zhai B, Li S, Li H, Zhang Y, Li W, Sun G, Han R, Tian Y, Liu X, Jiang R, Li G, Kang X. miR-30a-3p can inhibit the proliferation and promote the differentiation of chicken primary myoblasts. Br Poult Sci 2022; 63:475-483. [PMID: 35275038 DOI: 10.1080/00071668.2022.2050674] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
1. Chicken muscle is an important factor in meat quality and its development is controlled by a complex regulatory network.2. The following study examined the expression of miR-30a-3p in Gushi chicken breast muscle tissue and found that it was differentially expressed at different embryonic stages, reaching a peak in the 14-day-old embryo (E14).3. The effect of miR-30a-3p on chicken primary myoblasts (CPMs) was explored. Results from both cell counting kit-8 (CCK-8) and 5-ethynyl-2'-deoxyuridine (EdU) showed that this can inhibit the proliferation of myoblasts, and through cell cycle experiments, the inhibition of myoblast proliferation was found, which may be due to G0/G1 arrest in the cell cycle.4. The effect of miR-30a-3p on the differentiation of myoblasts was studied. The results showed that miR-30a-3p can promote the expression of MYOD, myogenin (MYOG), and myosin heavy chain (MYHC) genes to promote the differentiation of myoblasts. Through MYHC protein immunofluorescence experiments, it was found that miR-30a-3p can effectively increase the area of myotubes.5. Finally, mRNA transcriptome data was analysed, which showed that miR-30a-3p has 51 potential target genes. Among them, forkhead box O3 (FOXO3), ankyrin repeat domain 1 (ANKRD1), and insulin-induced 1 (INSIG1) genes were differentially expressed at different developmental stages and were enriched in Gene Ontology (GO) terms, such as cell differentiation and cellular developmental process. The data showed that tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein gamma (YWHAG), BUB1 mitotic checkpoint serine/threonine kinase (BUB1), and growth arrest and DNA damage-inducible 45 (GADD45) genes were enriched in the cell cycle pathway.6. It can be speculated that miR-30a-3p plays roles through these genes in myoblast development. This research provides information for further improving knowledge of the chicken muscle development regulation network.
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Affiliation(s)
- Yuanfang Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Pengtao Yuan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Shengxin Fan
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Bin Zhai
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Shuaihao Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Hongtai Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yanhua Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Wenting Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Guirong Sun
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Ruili Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Ruirui Jiang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Guoxi Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.,Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
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Feng J, Wei T, Cui X, Wei R, Hong T. Identification of key genes and pathways in mild and severe nonalcoholic fatty liver disease by integrative analysis. Chronic Dis Transl Med 2021; 7:276-286. [PMID: 34786546 PMCID: PMC8579024 DOI: 10.1016/j.cdtm.2021.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Indexed: 12/13/2022] Open
Abstract
Background The global prevalence of nonalcoholic fatty liver disease (NAFLD) is increasing. The pathogenesis of NAFLD is multifaceted, and the underlying mechanisms are elusive. We conducted data mining analysis to gain a better insight into the disease and to identify the hub genes associated with the progression of NAFLD. Methods The dataset GSE49541, containing the profile of 40 samples representing mild stages of NAFLD and 32 samples representing advanced stages of NAFLD, was acquired from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified using the R programming language. The Database for Annotation, Visualization and Integrated Discovery (DAVID) online tool and Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database were used to perform the enrichment analysis and construct protein–protein interaction (PPI) networks, respectively. Subsequently, transcription factor networks and key modules were identified. The hub genes were validated in a mice model of high fat diet (HFD)-induced NAFLD and in cultured HepG2 cells by real-time quantitative PCR. Results Based on the GSE49541 dataset, 57 DEGs were selected and enriched in chemokine activity and cellular component, including the extracellular region. Twelve transcription factors associated with DEGs were indicated from PPI analysis. Upregulated expression of five hub genes (SOX9, CCL20, CXCL1, CD24, and CHST4), which were identified from the dataset, was also observed in the livers of HFD-induced NAFLD mice and in HepG2 cells exposed to palmitic acid or advanced glycation end products. Conclusion The hub genes SOX9, CCL20, CXCL1, CD24, and CHST4 are involved in the aggravation of NAFLD. Our results offer new insights into the underlying mechanism of NAFLD progression.
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Affiliation(s)
- Jin Feng
- Department of Endocrinology and Metabolism, Peking University Third Hospital, Beijing 100191, China
| | - Tianjiao Wei
- Department of Endocrinology and Metabolism, Peking University Third Hospital, Beijing 100191, China
| | - Xiaona Cui
- Department of Endocrinology and Metabolism, Peking University Third Hospital, Beijing 100191, China
| | - Rui Wei
- Department of Endocrinology and Metabolism, Peking University Third Hospital, Beijing 100191, China
| | - Tianpei Hong
- Department of Endocrinology and Metabolism, Peking University Third Hospital, Beijing 100191, China
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Hozhabri H, Lashkari A, Razavi SM, Mohammadian A. Integration of gene expression data identifies key genes and pathways in colorectal cancer. Med Oncol 2021; 38:7. [PMID: 33411100 DOI: 10.1007/s12032-020-01448-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 11/21/2020] [Indexed: 12/16/2022]
Abstract
Colorectal cancer (CRC) is one of the most common malignant tumor and prevalent cause of cancer-related death worldwide. In this study, we analyzed the gene expression profiles of patients with CRC with the aim of better understanding the molecular mechanism and key genes in CRC. Four gene expression profiles including, GSE9348, GSE41328, GSE41657, and GSE113513 were downloaded from GEO database. The data were processed using R programming language, in which 319 common differentially expressed genes including 94 up-regulated and 225 down-regulated were identified. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses were conducted to find the most significant enriched pathways in CRC. Based on the GO and KEGG pathway analysis, the most important dysregulated pathways were regulation of cell proliferation, biocarbonate transport, Wnt, and IL-17 signaling pathways, and nitrogen metabolism. The protein-protein interaction (PPI) network of the DEGs was constructed using Cytoscape software and hub genes including MYC, CXCL1, CD44, MMP1, and CXCL12 were identified as the most critical hub genes. The present study enhances our understanding of the molecular mechanisms of the CRC, which might potentially be applied in the treatment strategies of CRC as molecular targets and diagnostic biomarkers.
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Affiliation(s)
- Hossein Hozhabri
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
| | - Ali Lashkari
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Seyed-Morteza Razavi
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran.,Salari Institute of Cognitive and Behavioral Disorders (SICBD), Karaj, Alborz, Iran.,Systems Biology Research Lab, Bioinformatics Group, Systems Biology of Next Generation Company (SBNGC), Qom, Iran
| | - Ali Mohammadian
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
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5
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Ghulam A, Lei X, Guo M, Bian C. A Review of Pathway Databases and Related Methods Analysis. Curr Bioinform 2020. [DOI: 10.2174/1574893614666191018162505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Pathway analysis integrates most of the computational tools for the investigation of
high-level and complex human diseases. In the field of bioinformatics research, biological pathways
analysis is an important part of systems biology. The molecular complexities of biological
pathways are difficult to understand in human diseases, which can be explored through pathway
analysis. In this review, we describe essential information related to pathway databases and their
mechanisms, algorithms and methods. In the pathway database analysis, we present a brief introduction
on how to gain knowledge from fundamental pathway data in regard to specific human
pathways and how to use pathway databases and pathway analysis to predict diseases during an
experiment. We also provide detailed information related to computational tools that are used in
complex pathway data analysis, the roles of these tools in the bioinformatics field and how to store
the pathway data. We illustrate various methodological difficulties that are faced during pathway
analysis. The main ideas and techniques for the pathway-based examination approaches are presented.
We provide the list of pathway databases and analytical tools. This review will serve as a
helpful manual for pathway analysis databases.
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Affiliation(s)
- Ali Ghulam
- School of Computer Science, Shaanxi Normal University, Xian, China
| | - Xiujuan Lei
- School of Computer Science, Shaanxi Normal University, Xian, China
| | - Min Guo
- School of Computer Science, Shaanxi Normal University, Xian, China
| | - Chen Bian
- School of Computer Science, Shaanxi Normal University, Xian, China
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6
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Cavalcante BGN, Lacerda RHW, Assis IO, Bezamat M, Modesto A, Vieira AR. Talon Cusp Associates With MMP2 in a Cohort of Individuals Born With Oral Clefts. Cleft Palate Craniofac J 2020; 58:597-602. [PMID: 32935555 DOI: 10.1177/1055665620958569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVE The aim of this study was to use dental development as a tool to subphenotype oral clefts and investigate the association of MMP2 with dentin-pulp complex anomalies, in order to identify dental anomalies that are a part of a "cleft syndrome." DESIGN Two hundred and ninety individuals born with cleft lip and palate were evaluated and several clinical features, such as cleft completeness or incompleteness, laterality, and presence of dental anomalies were used to assess each individual's cleft status. We tested for overrepresentation of MMP2 single nucleotide polymorphism rs9923304 alleles depending on individuals having certain dental anomalies. Chi-square and Fisher exact tests were used in all comparisons (α = .05). RESULTS All individuals studied had at least one dental anomaly outside the cleft area. Significant differences between individuals born with clefts with and without talon cusp (P = .04) were observed for the frequency of the MMP2 less common allele. CONCLUSION All individuals born with cleft lip and palate had alterations of the dentition, and a quarter to half of the individuals had alterations of the internal anatomy of their teeth, which further indicates that dental anomalies can be considered as an extended phenotype for clefts. MMP2 was associated with talon cusp in individuals born with oral clefts.
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Affiliation(s)
- Bianca G N Cavalcante
- Graduate Program in Dentistry and Center for Treatment of Cleft Lip and Palate, University Hospital Lauro Wanderley, 123204Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Rosa Helena W Lacerda
- Graduate Program in Dentistry and Center for Treatment of Cleft Lip and Palate, University Hospital Lauro Wanderley, 123204Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Ionária O Assis
- Graduate Program in Dentistry and Center for Treatment of Cleft Lip and Palate, University Hospital Lauro Wanderley, 123204Universidade Federal da Paraíba, João Pessoa, Brazil
| | - Mariana Bezamat
- Department of Oral Biology, School of Dental Medicine, 6614University of Pittsburgh, Pittsburgh, PA, USA
| | - Adriana Modesto
- Department of Pediatric Dentistry, School of Dental Medicine, 6614University of Pittsburgh, Pittsburgh, PA, USA
| | - Alexandre R Vieira
- Department of Oral Biology, School of Dental Medicine, 6614University of Pittsburgh, Pittsburgh, PA, USA.,Graduate Program in Dentistry, 123204Universidade Federal da Paraíba, João Pessoa, Brazil
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Chen J, Chen YQ, Wang SN, Duan FX, Shi YJ, Ding SQ, Hu JG, Lü HZ. Effect of VX‑765 on the transcriptome profile of mice spinal cords with acute injury. Mol Med Rep 2020; 22:33-42. [PMID: 32377730 PMCID: PMC7248530 DOI: 10.3892/mmr.2020.11129] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 11/18/2019] [Indexed: 12/12/2022] Open
Abstract
Previous studies have shown that caspase-1 plays an important role in the acute inflammatory response of spinal cord injury (SCI). VX‑765, a novel and irreversible caspase‑1 inhibitor, has been reported to effectively intervene in inflammation. However, the effect of VX‑765 on genome‑wide transcription in acutely injured spinal cords remains unknown. Therefore, in the present study, RNA‑sequencing (RNA‑Seq) was used to analyze the effect of VX‑765 on the local expression of gene transcription 8 h following injury. The differentially expressed genes (DEGs) underwent enrichment analysis of functions and pathways by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses, respectively. Parallel analysis of western blot confirmed that VX‑765 can effectively inhibit the expression and activation of caspase‑1. RNA‑Seq showed that VX‑765 treatment resulted in 1,137 upregulated and 1,762 downregulated DEGs. These downregulated DEGs and their associated signaling pathways, such as focal adhesion, cytokine‑cytokine receptor interaction, leukocyte transendothelial migration, extracellular matrix‑receptor interaction, phosphatidylinositol 3‑kinase‑protein kinase B, Rap1 and hypoxia inducible factor‑1 signaling pathway, are mainly associated with inflammatory response, local hypoxia, macrophage differentiation, adhesion migration and apoptosis of local cells. This suggests that the application of VX‑765 in the acute phase can improve the local microenvironment of SCI by inhibiting caspase‑1. However, whether VX‑765 can be used as a therapeutic drug for SCI requires further exploration. The sequence data have been deposited into the Sequence Read Archive (https://www.ncbi.nlm.nih.gov/sra/PRJNA548970).
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Affiliation(s)
- Jing Chen
- Clinical Laboratory, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Yu-Qing Chen
- Clinical Laboratory, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Sai-Nan Wang
- Clinical Laboratory, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Fei-Xiang Duan
- Clinical Laboratory, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Yu-Jiao Shi
- Clinical Laboratory, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Shu-Qin Ding
- Clinical Laboratory, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - Jian-Guo Hu
- Clinical Laboratory, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
| | - He-Zuo Lü
- Clinical Laboratory, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui 233004, P.R. China
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Zhang YX, Wang SN, Chen J, Hu JG, Lü HZ. A transcriptomic study of probenecid on injured spinal cords in mice. PeerJ 2020; 8:e8367. [PMID: 31921518 PMCID: PMC6944129 DOI: 10.7717/peerj.8367] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 12/06/2019] [Indexed: 11/20/2022] Open
Abstract
Background Recent studies have found that probenecid has neuroprotective and reparative effects on central nervous system injuries. However, its effect on genome-wide transcription in acute spinal cord injury (SCI) remains unknown. In the present study, RNA sequencing (RNA-Seq) is used to analyze the effect of probenecid on the local expression of gene transcription 8 h after spinal injury. Methods An Infinite Horizon impactor was used to perform contusive SCI in mice. The SCI model was made by using a rod (1.3 mm diameter) with a force of 50 Kdynes. Sham-operated mice only received a laminectomy without contusive injury. The injured mice were randomly assigned into either the control (SCI_C) or probenecid injection (SCI_P) group. In the latter group, the probenecid drug was intraperitoneally injected (0.5 mg/kg) immediately following injury. Eight hours after the injury or laminectomy, the spinal cords were removed from the mice in both groups. The total RNAs were extracted and purified for library preparation and transcriptome sequencing. Differential gene expressions (DEGs) of the three groups-sham, SCI_C and SCI_P-were analyzed using a DESeq software. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs were performed using a GOseq R package and KOBAS software. Real-time quantitative reverse-transcriptase polymerase chain reaction was used to validate RNA-Seq results. Results RNA-Seq showed that, compared to the SCI_C group, the number of DEGs was 641 in the SCI_P group (286 upregulated and 355 downregulated). According to GO analysis, DEGs were most enriched in extracellular matrix (ECM), collagen trimer, protein bounding and sequence specific DNA binding. KEGG analysis showed that the most enriched pathways included: cell adhesion molecules, Leukocyte transendothelial migration, ECM-receptor interactions, PI3K-Akt signaling pathways, hematopoietic cell lineages, focal adhesions, the Rap1 signaling pathway, etc. The sequence data have been deposited into the Sequence Read Archive (https://www.ncbi.nlm.nih.gov/sra/PRJNA554464).
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Affiliation(s)
- Yu-Xin Zhang
- Clinical Laboratory, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China.,Anhui Key Laboratory of Tissue Transplantation, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China.,Department of Biochemistry and Molecular Biology, Bengbu Medical College, Bengbu, China
| | - Sai-Nan Wang
- Clinical Laboratory, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China.,Anhui Key Laboratory of Tissue Transplantation, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Jing Chen
- Clinical Laboratory, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China.,Anhui Key Laboratory of Tissue Transplantation, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Jian-Guo Hu
- Clinical Laboratory, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China.,Anhui Key Laboratory of Tissue Transplantation, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - He-Zuo Lü
- Clinical Laboratory, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China.,Anhui Key Laboratory of Tissue Transplantation, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
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Lu W, Li N, Liao F. Identification of Key Genes and Pathways in Pancreatic Cancer Gene Expression Profile by Integrative Analysis. Genes (Basel) 2019; 10:genes10080612. [PMID: 31412643 PMCID: PMC6722756 DOI: 10.3390/genes10080612] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 07/31/2019] [Accepted: 08/07/2019] [Indexed: 12/15/2022] Open
Abstract
Background: Pancreatic cancer is one of the malignant tumors that threaten human health. Methods: The gene expression profiles of GSE15471, GSE19650, GSE32676 and GSE71989 were downloaded from the gene expression omnibus database including pancreatic cancer and normal samples. The differentially expressed genes between the two types of samples were identified with the Limma package using R language. The gene ontology functional and pathway enrichment analyses of differentially-expressed genes were performed by the DAVID software followed by the construction of a protein–protein interaction network. Hub gene identification was performed by the plug-in cytoHubba in cytoscape software, and the reliability and survival analysis of hub genes was carried out in The Cancer Genome Atlas gene expression data. Results: The 138 differentially expressed genes were significantly enriched in biological processes including cell migration, cell adhesion and several pathways, mainly associated with extracellular matrix-receptor interaction and focal adhesion pathway in pancreatic cancer. The top hub genes, namely thrombospondin 1, DNA topoisomerase II alpha, syndecan 1, maternal embryonic leucine zipper kinase and proto-oncogene receptor tyrosine kinase Met were identified from the protein–protein interaction network. The expression levels of hub genes were consistent with data obtained in The Cancer Genome Atlas. DNA topoisomerase II alpha, syndecan 1, maternal embryonic leucine zipper kinase and proto-oncogene receptor tyrosine kinase Met were significantly linked with poor survival in pancreatic adenocarcinoma. Conclusions: These hub genes may be used as potential targets for pancreatic cancer diagnosis and treatment.
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Affiliation(s)
- Wenzong Lu
- Department of Biomedical Engineering, College of Electronic and Information Engineering, Xi'an Technological University, Xi'an 710021, China.
| | - Ning Li
- Department of Biomedical Engineering, College of Electronic and Information Engineering, Xi'an Technological University, Xi'an 710021, China
| | - Fuyuan Liao
- Department of Biomedical Engineering, College of Electronic and Information Engineering, Xi'an Technological University, Xi'an 710021, China
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10
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Chen J, Wu Y, Duan FX, Wang SN, Guo XY, Ding SQ, Zhou JH, Hu JG, Lü HZ. Effect of M2 macrophage adoptive transfer on transcriptome profile of injured spinal cords in rats. Exp Biol Med (Maywood) 2019; 244:880-892. [PMID: 31159561 DOI: 10.1177/1535370219854668] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The previous studies showed that alternatively activated anti-inflammatory macrophage (M2) adoptive immunity can improve the proportion of local M2 cells and play the neuroprotective effect after spinal cord injury (SCI). Its molecular mechanism is not yet very clear. Therefore, this study aims to analyze the effect of the M2 adoptive transfer on the local expression of gene transcription. Sprague-Dawley (SD) rats were used for culture of macrophages and establishment of SCI models. After SCI, the polarized M2 macrophages were transferred to the injured rats by tail vein injection. Seven days after operation, the differentially expressed genes (DEGs) in the spinal cords were analyzed by RNA-sequencing (RNA-Seq). Then, the functional enrichment analysis and pathways were performed by using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), respectively. RNA-Seq showed that M2 adoptive immunity can down-regulate many well-studied gene expressions associated with signaling pathways of inflammatory, such as antigen processing and presentation, phagosome, cell adhesion molecules, natural killer cell-mediated cytotoxicity, endocytosis, proteasome, and Toll-like receptor signaling pathway. These may explain the mechanism of our previous adoptive immunization of M2 cells to provide neuroprotection for SCI. In addition, a novel pathway, retinoic acid-inducible gene-1 (RIG-I)-like receptor signaling pathway was found to be involved in the pathological process of SCI and the response to M2 adoptive immunity as well. This will provide a new explanation for the pathological mechanism of SCI and a new theoretical and experimental basis for its clinical treatment. The raw Illumina data are available at http://www.ncbi.nlm.nih.gov/sra (accession number PRJNA517238). Impact statement This research aimed to analyze the effect of M2 macrophage adoptive transfer on the local expression of gene transcription after SCI by RNA-Seq. The results showed that M2 adoptive immunity can down-regulate many well-studied gene expressions associated with signaling pathways of inflammatory. These may explain the mechanism of our previous adoptive immunization of M2 cells to provide neuroprotection for SCI. In addition, a novel pathway, RIG-I-like receptor signaling pathway was also found to involve in the pathological process of SCI and the response to M2 adoptive immunity. This will provide a new explanation for the pathological mechanism of SCI and a new theoretical and experimental basis for its clinical treatment.
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Affiliation(s)
- Jing Chen
- 1 Clinical Laboratory, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China.,2 Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China.,3 Department of Immunology, Bengbu Medical College, Anhui 233030, PR China
| | - Yan Wu
- 1 Clinical Laboratory, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China.,2 Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China.,3 Department of Immunology, Bengbu Medical College, Anhui 233030, PR China
| | - Fei-Xiang Duan
- 1 Clinical Laboratory, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China.,2 Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China
| | - Sai-Nan Wang
- 1 Clinical Laboratory, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China.,2 Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China.,3 Department of Immunology, Bengbu Medical College, Anhui 233030, PR China
| | - Xue-Yan Guo
- 1 Clinical Laboratory, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China.,2 Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China
| | - Shu-Qin Ding
- 1 Clinical Laboratory, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China.,2 Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China
| | - Ji-Hong Zhou
- 3 Department of Immunology, Bengbu Medical College, Anhui 233030, PR China
| | - Jian-Guo Hu
- 1 Clinical Laboratory, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China.,2 Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China
| | - He-Zuo Lü
- 1 Clinical Laboratory, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China.,2 Anhui Key Laboratory of Tissue Transplantation, the First Affiliated Hospital of Bengbu Medical College, Anhui 233004, PR China.,3 Department of Immunology, Bengbu Medical College, Anhui 233030, PR China
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CEA: Combination-based gene set functional enrichment analysis. Sci Rep 2018; 8:13085. [PMID: 30166636 PMCID: PMC6117355 DOI: 10.1038/s41598-018-31396-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 08/10/2018] [Indexed: 02/08/2023] Open
Abstract
Functional enrichment analysis is a fundamental and challenging task in bioinformatics. Most of the current enrichment analysis approaches individually evaluate functional terms and often output a list of enriched terms with high similarity and redundancy, which makes it difficult for downstream studies to extract the underlying biological interpretation. In this paper, we proposed a novel framework to assess the performance of combination-based enrichment analysis. Using this framework, we formulated the enrichment analysis as a multi-objective combinatorial optimization problem and developed the CEA (Combination-based Enrichment Analysis) method. CEA provides the whole landscape of term combinations; therefore, it is a good benchmark for evaluating the current state-of-the-art combination-based functional enrichment methods in a comprehensive manner. We tested the effectiveness of CEA on four published microarray datasets. Enriched functional terms identified by CEA not only involve crucial biological processes of related diseases, but also have much less redundancy and can serve as a preferable representation for the enriched terms found by traditional single-term-based methods. CEA has been implemented in the R package CopTea and is available at http://github.com/wulingyun/CopTea/.
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Yli-Hietanen J, Ylipää A, Yli-Harja O. Cancer research in the era of next-generation sequencing and big data calls for intelligent modeling. CHINESE JOURNAL OF CANCER 2015; 34:423-6. [PMID: 25963029 PMCID: PMC4593335 DOI: 10.1186/s40880-015-0008-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 12/10/2014] [Indexed: 11/12/2022]
Abstract
We examine the role of big data and machine learning in cancer research. We describe an example in cancer research where gene-level data from The Cancer Genome Atlas (TCGA) consortium is interpreted using a pathway-level model. As the complexity of computational models increases, their sample requirements grow exponentially. This growth stems from the fact that the number of combinations of variables grows exponentially as the number of variables increases. Thus, a large sample size is needed. The number of variables in a computational model can be reduced by incorporating biological knowledge. One particularly successful way of doing this is by using available gene regulatory, signaling, metabolic, or context-specific pathway information. We conclude that the incorporation of existing biological knowledge is essential for the progress in using big data for cancer research.
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Affiliation(s)
- Jari Yli-Hietanen
- Department of Signal Processing, Tampere University of Technology, P. O. Box 553, Tampere, 33101, Finland.
| | - Antti Ylipää
- Department of Signal Processing, Tampere University of Technology, P. O. Box 553, Tampere, 33101, Finland.
| | - Olli Yli-Harja
- Department of Signal Processing, Tampere University of Technology, P. O. Box 553, Tampere, 33101, Finland.
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CoCiter: an efficient tool to infer gene function by assessing the significance of literature co-citation. PLoS One 2013; 8:e74074. [PMID: 24086311 PMCID: PMC3781068 DOI: 10.1371/journal.pone.0074074] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 07/30/2013] [Indexed: 01/17/2023] Open
Abstract
A routine approach to inferring functions for a gene set is by using function enrichment analysis based on GO, KEGG or other curated terms and pathways. However, such analysis requires the existence of overlapping genes between the query gene set and those annotated by GO/KEGG. Furthermore, GO/KEGG databases only maintain a very restricted vocabulary. Here, we have developed a tool called "CoCiter" based on literature co-citations to address the limitations in conventional function enrichment analysis. Co-citation analysis is widely used in ranking articles and predicting protein-protein interactions (PPIs). Our algorithm can further assess the co-citation significance of a gene set with any other user-defined gene sets, or with free terms. We show that compared with the traditional approaches, CoCiter is a more accurate and flexible function enrichment analysis method. CoCiter is freely available at www.picb.ac.cn/hanlab/cociter/.
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Zhou X. Cancer bioinformatics: detection of chromatin states, SNP-containing motifs, and functional enrichment modules. CHINESE JOURNAL OF CANCER 2013; 32:153-4. [PMID: 23544450 PMCID: PMC3845569 DOI: 10.5732/cjc.013.10045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In this editorial preface, I briefly review cancer bioinformatics and introduce the four articles in this special issue highlighting important applications of the field: detection of chromatin states; detection of SNP-containing motifs and association with transcription factor-binding sites; improvements in functional enrichment modules; and gene association studies on aging and cancer. We expect this issue to provide bioinformatics scientists, cancer biologists, and clinical doctors with a better understanding of how cancer bioinformatics can be used to identify candidate biomarkers and targets and to conduct functional analysis.
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