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Huang S, Sun C, Hou Y, Tang Y, Zhu Z, Zhang Z, Zhang Y, Wang L, Zhao Q, Chen MG, Guo Z, Wang D, Ju W, Zhou Q, Wu L, He X. A comprehensive bioinformatics analysis on multiple Gene Expression Omnibus datasets of nonalcoholic fatty liver disease and nonalcoholic steatohepatitis. Sci Rep 2018; 8:7630. [PMID: 29769552 PMCID: PMC5955936 DOI: 10.1038/s41598-018-25658-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/19/2018] [Indexed: 12/12/2022] Open
Abstract
Fatty liver disease is one of the leading causes of chronic damage in western countries. Approximately 25% of adults in the United States have fatty livers in the absence of excessive alcohol consumption, a condition termed nonalcoholic fatty liver disease (NAFLD). Little is known about the prevalence and genetic background of NAFLD or the factors that determine its development. In this study, we used the Gene-Cloud of Biotechnology Information bioinformatics platform to carry out a comprehensive bioinformatics analysis identifying differentially expressed genes (DEGs), key biological processes and intersecting pathways. We imported 3 Gene Expression Omnibus datasets (GSE31803, GSE49541, and GSE63067). Then, we assessed the expression of the DEGs in clinical samples. We found that CD24 was the only gene co-expressed in all 3 datasets. "Glycolysis/gluconeogenesis", "p53 signaling pathway" and "glycine, serine and threonine metabolism" were 3 common pathways related to the fatty liver process. In NAFLD tissues, CD24, COL1A1, LUM, THBS2 and EPHA3 were upregulated, and PZP was downregulated. CD24 is a core gene among these DEGs and have not yet been studied of its impact on NAFLD. Co-expressed genes, common biological processes and intersecting pathways identified in the study might play an important role in NAFLD progression. Further studies are needed to elucidate the mechanism of these potential genes and pathways in NAFLD.
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Affiliation(s)
- Shanzhou Huang
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, 510080, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, 510080, China
| | - Chengjun Sun
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, 510080, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, 510080, China
| | - Yuchen Hou
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, 510080, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, 510080, China
| | - Yunhua Tang
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, 510080, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, 510080, China
| | - Zebin Zhu
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, 510080, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, 510080, China
| | - Zhiheng Zhang
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, 510080, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, 510080, China
| | - Yixi Zhang
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, 510080, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, 510080, China
| | - Linhe Wang
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, 510080, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, 510080, China
| | - Qiang Zhao
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, 510080, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, 510080, China
| | - Mao-Gen Chen
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, 510080, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, 510080, China
| | - Zhiyong Guo
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, 510080, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, 510080, China
| | - Dongping Wang
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, 510080, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, 510080, China
| | - Weiqiang Ju
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, 510080, China
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, 510080, China
| | - Qi Zhou
- Department of General Surgery, Hui Ya Hospital of The First Affiliated Hospital, Sun Yat-sen University, Huizhou, Guangdong, 516081, China.
| | - Linwei Wu
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China.
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, 510080, China.
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, 510080, China.
| | - Xiaoshun He
- Organ Transplant Center, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China.
- Guangdong Provincial Key Laboratory of Organ Donation and Transplant Immunology, Guangzhou, 510080, China.
- Guangdong Provincial International Cooperation Base of Science and Technology (Organ Transplantation), Guangzhou, 510080, China.
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Sugiyama T, Rodriguez RT, McLean GW, Kim SK. Conserved markers of fetal pancreatic epithelium permit prospective isolation of islet progenitor cells by FACS. Proc Natl Acad Sci U S A 2007; 104:175-80. [PMID: 17190805 PMCID: PMC1765430 DOI: 10.1073/pnas.0609490104] [Citation(s) in RCA: 129] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2006] [Indexed: 12/21/2022] Open
Abstract
Prospective isolation and characterization of progenitor cells is a paradigmatic strategy for studies of organ development. However, extraction of viable cells, fractionation of lineages, and in vitro analysis of progenitors from the fetal pancreas in experimental organisms like mice has proved challenging and has not yet been reported for human fetal pancreas. Here, we report isolation of pancreatic islet progenitor cells from fetal mice by FACS. Monoclonal antibodies that recognize cell-surface proteins on candidate stem cells in brain, skin, and other organs enabled separation of major pancreatic cell lineages and isolation of native pancreatic cells expressing neurogenin 3, an established marker of islet progenitors. New in vitro cell culture methods permitted isolated mouse islet progenitors to develop into hormone-expressing endocrine cells. Insulin-producing cells derived in vitro required or expressed factors that regulate fetal beta cell differentiation; thus, the genetic programs normally controlling in vivo mouse islet development are similarly required in our system. Moreover, antibodies that recognize conserved orthologous cell-surface epitopes in human fetal pancreas allowed FACS-based enrichment of candidate islet progenitor cells expressing neurogenin 3. Our studies reveal previously undescribed strategies for prospective purification and analysis of pancreatic endocrine progenitor cells that should accelerate studies of islet development and replacement.
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Affiliation(s)
- Takuya Sugiyama
- *Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329; and
| | - Ryan T. Rodriguez
- *Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329; and
| | - Graeme W. McLean
- *Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329; and
| | - Seung K. Kim
- *Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5329; and
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA 94305-5329
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