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Zhang WB, Li J, Li Q, Lu X, Chen JL, Li L, Chen H, Fu W, Chen JC, Lu BJ, Wu H, Sun XX. Endometrial transcriptome profiling of patients with recurrent implantation failure during hormone replacement therapy cycles. Front Endocrinol (Lausanne) 2024; 14:1292723. [PMID: 38352249 PMCID: PMC10863671 DOI: 10.3389/fendo.2023.1292723] [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] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/28/2023] [Indexed: 02/16/2024] Open
Abstract
Background The molecular mechanisms underlying window of implantation (WOI) displacement in patients with recurrent implantation failure (RIF) remain unclear. This study aims to explore the transcriptomic signatures of endometrium with normal and displaced WOIs and to identify the causes of endometrial receptivity (ER) abnormalities and WOI displacement in RIF patients. Methods In this study, 40 RIF patients were recruited and underwent personalized embryo transfer (pET) guided by the predicted results of endometrial receptivity diagnosis (ERD) model. Transcriptome analysis of endometrium from patients with clinical pregnancies after pET was performed to identify differentially expressed genes (DEGs) associated with WOI displacement. Gene expression data from HRT and natural cycle endometrium were compared to identify specific gene expression patterns of ER-related genes during WOI. Results The ERD results indicated that 67.5% of RIF patients (27/40) were non-receptive in the conventional WOI (P+5) of the HRT cycle. The clinical pregnancy rate in RIF patients improved to 65% (26/40) after ERD-guided pET, indicating the effectiveness of transcriptome-based WOI prediction. Among the 26 patients with clinical pregnancy, the gene expression profiles of P+5 endometrium from advanced (n=6), normal (n=10) and delayed (n=10) WOI groups were significantly different from each other. Furthermore, 10 DEGs identified among P+5 endometrium of 3 groups were involved in immunomodulation, transmembrane transport and tissue regeneration, which could accurately classify the endometrium with different WOIs. Additionally, a large number of ER-related genes showed significant correlation and similar gene expression patterns in P+3, P+5, and P+7 endometrium from HRT cycles and LH+5, LH+7, and LH+9 endometrium from natural cycles. Conclusion Our study shows that ER-related genes share similar gene expression patterns during WOI in both natural and HRT cycles, and their aberrant expression is associated with WOI displacements. The improvement of pregnancy outcomes in RIF patients by adjusting ET timing according to ERD results demonstrates the importance of transcriptome-based endometrial receptivity assessment and the clinical efficiency of ERD model.
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Affiliation(s)
- Wen-bi Zhang
- Shanghai Ji Ai Genetics and In vitro Fertilization and Embryo Transfer (IVF-ET) Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Jue Li
- Unimed Biotech (Shanghai) Co., Ltd., Shanghai, China
| | - Qing Li
- Unimed Biotech (Shanghai) Co., Ltd., Shanghai, China
| | - Xiang Lu
- Shanghai Ji Ai Genetics and In vitro Fertilization and Embryo Transfer (IVF-ET) Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Jun-ling Chen
- Shanghai Ji Ai Genetics and In vitro Fertilization and Embryo Transfer (IVF-ET) Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Lu Li
- Shanghai Ji Ai Genetics and In vitro Fertilization and Embryo Transfer (IVF-ET) Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Hua Chen
- Shanghai Ji Ai Genetics and In vitro Fertilization and Embryo Transfer (IVF-ET) Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Wei Fu
- Shanghai Ji Ai Genetics and In vitro Fertilization and Embryo Transfer (IVF-ET) Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | | | - Bing-jie Lu
- Unimed Biotech (Shanghai) Co., Ltd., Shanghai, China
| | - Han Wu
- Unimed Biotech (Shanghai) Co., Ltd., Shanghai, China
| | - Xiao-xi Sun
- Shanghai Ji Ai Genetics and In vitro Fertilization and Embryo Transfer (IVF-ET) Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- Key Laboratory of Female Reproductive Endocrine-Related Diseases, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
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Hu K, Lv L, Huang H, Yin G, Gao J, Liu J, Yang Y, Zeng W, Chen Y, Zhang N, Zhang F, Ma Y, Chen F. A Novel Tree Shrew Model of Chronic Experimental Autoimmune Uveitis and Its Disruptive Application. Front Immunol 2022; 13:889596. [PMID: 35711454 PMCID: PMC9196886 DOI: 10.3389/fimmu.2022.889596] [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: 03/09/2022] [Accepted: 04/29/2022] [Indexed: 11/27/2022] Open
Abstract
Background Previous studies have established several animal models for experimental autoimmune uveitis (EAU) in rodents without the fovea centralis in the human retina. This study aimed to develop and explore the application of a novel EAU model in tree shrews with a cone-dominated retina resembling the human fovea. Methods Tree shrews were clinically and pathologically evaluated for the development and characteristics of EAU immunized with six inter-photoreceptor retinoid-binding proteins (IRBPs). IRBP-specific T-cell proliferation and serum cytokine of tree shrews were evaluated to determine the immune responses. Differentially expressed genes (DEGs) were identified in the eyes of tree shrews with EAU by RNA-sequencing. The disruptive effects of the DEG RGS4 inhibitor CCG 203769 and dihydroartemisinin on the EAU were investigated to evaluate the potential application of tree shrew EAU. Results IRBP1197–1211 and R14 successfully induced chronic EAU with subretinal deposits and retinal damage in the tree shrews. The immunological characteristics presented the predominant infiltration of microglia/macrophages, dendritic cells, and CD4-T-cells into the uvea and retina and pathogenic T helper (Th) 1 and Th17 responses. The subretinal deposits positively expressed amyloid β-protein (Aβ), CD8, and P2Y purinoceptor 12 (P2RY12). The crucial DEGs in R14-induced EAU, such as P2RY2 and adenylate cyclase 4 (ADCY4), were enriched for several pathways, including inflammatory mediator regulation of transient receptor potential (TRP) channels. The upregulated RGS4 in IRBP-induced EAU was associated with mitogen-activated protein kinase (MAPK) activity. RGS4 inhibition and dihydroartemisinin could significantly alleviate the retinal pathological injuries of IRBP1197-1211-induced EAU by decreasing the expression of CD4 T-cells. Conclusion Our study provides a novel chronic EAU in tree shrews elicited by bovine R14 and tree shrew IRBP1197-1211 characterized by retinal degeneration, retinal damage with subretinal Aβ deposits and microglia/macrophage infiltration, and T-cell response, probably by altering important pathways and genes related to bacterial invasion, inflammatory pain, microglial phagocytosis, and lipid and glucose metabolism. The findings advance the knowledge of the pathogenesis and therapeutics of the fovea-involved visual disturbance in human uveitis.
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Affiliation(s)
- Kaijiao Hu
- Laboratory Animal Center, Chongqing Medical University, Chongqing, China.,Chongqing Engineering Research Center for Rodent Laboratory Animals, Chongqing, China
| | - Longbao Lv
- Laboratory Animal Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Hui Huang
- Laboratory Animal Center, Chongqing Medical University, Chongqing, China.,Chongqing Engineering Research Center for Rodent Laboratory Animals, Chongqing, China
| | - Guangnian Yin
- Laboratory Animal Center, Chongqing Medical University, Chongqing, China.,Chongqing Engineering Research Center for Rodent Laboratory Animals, Chongqing, China.,Department of Clinical Laboratory, the Second Affiliated Hospital of Army Medical University, Chongqing, China
| | - Jie Gao
- Laboratory Animal Center, Chongqing Medical University, Chongqing, China.,Chongqing Engineering Research Center for Rodent Laboratory Animals, Chongqing, China
| | - Jianping Liu
- Department of Pathology, Chongqing Medical University, Chongqing, China
| | - Yaying Yang
- Department of Pathology, Chongqing Medical University, Chongqing, China
| | - Wenxin Zeng
- Laboratory Animal Center, Chongqing Medical University, Chongqing, China.,Chongqing Engineering Research Center for Rodent Laboratory Animals, Chongqing, China
| | - Yan Chen
- Department of Pathology, Chongqing Medical University, Chongqing, China
| | - Ni Zhang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Eye Institute, Chongqing, China
| | - Feiyan Zhang
- Laboratory Animal Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yuhua Ma
- Laboratory Animal Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Feilan Chen
- Laboratory Animal Center, Chongqing Medical University, Chongqing, China.,Chongqing Engineering Research Center for Rodent Laboratory Animals, Chongqing, China
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3
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Liang L, Yan J, Huang X, Zou C, Chen L, Li R, Xie J, Pan M, Zou D, Liu Y. Identification of molecular signatures associated with sleep disorder and Alzheimer's disease. Front Psychiatry 2022; 13:925012. [PMID: 35990086 PMCID: PMC9386361 DOI: 10.3389/fpsyt.2022.925012] [Citation(s) in RCA: 3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Alzheimer's disease (AD) and sleep disorders are both neurodegenerative conditions characterized by impaired or absent sleep. However, potential common pathogenetic mechanisms of these diseases are not well characterized. METHODS Differentially expressed genes (DEGs) were identified using publicly available human gene expression profiles GSE5281 for AD and GSE40562 for sleep disorder. DEGs common to the two datasets were used for enrichment analysis, and we performed multi-scale embedded gene co-expression network analysis (MEGENA) for common DEGs. Fast gene set enrichment analysis (fGSEA) was used to obtain common pathways, while gene set variation analysis (GSVA) was applied to quantify those pathways. Subsequently, we extracted the common genes between module genes identified by MEGENA and genes of the common pathways, and we constructed protein-protein interaction (PPI) networks. The top 10 genes with the highest degree of connectivity were classified as hub genes. Common genes were used to perform Metascape enrichment analysis for functional enrichment. Furthermore, we quantified infiltrating immune cells in patients with AD or sleep disorder and in controls. RESULTS DEGs common to the two disorders were involved in the citrate cycle and the HIF-1 signaling pathway, and several common DEGs were related to signaling pathways regulating the pluripotency of stem cells, as well as 10 other pathways. Using MEGENA, we identified 29 modules and 1,498 module genes in GSE5281, and 55 modules and 1,791 module genes in GSE40562. Hub genes involved in AD and sleep disorder were ATP5A1, ATP5B, COX5A, GAPDH, NDUFA9, NDUFS3, NDUFV2, SOD1, UQCRC1, and UQCRC2. Plasmacytoid dendritic cells and T helper 17 cells had the most extensive infiltration in both AD and sleep disorder. CONCLUSION AD pathology and pathways of neurodegeneration participate in processes contributing in AD and sleep disorder. Hub genes may be worth exploring as potential candidates for targeted therapy of AD and sleep disorder.
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Affiliation(s)
- Lucong Liang
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jing Yan
- Department of Geriatrics, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xiaohua Huang
- Department of Neurology, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Chun Zou
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Liechun Chen
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Rongjie Li
- Department of Geriatrics, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, China.,Department of Geriatrics, The First People's Hospital of Nanning, Nanning, China
| | - Jieqiong Xie
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Mika Pan
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Donghua Zou
- Department of Neurology, The Second Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Ying Liu
- Department of Geriatrics, The Fifth Affiliated Hospital of Guangxi Medical University, Nanning, China.,Department of Geriatrics, The First People's Hospital of Nanning, Nanning, China
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Wu L, Cheng Q, Wen Z, Song Y, Zhu Y, Wang L. IRF1 as a potential biomarker in Mycobacterium tuberculosis infection. J Cell Mol Med 2021; 25:7270-7279. [PMID: 34213077 PMCID: PMC8335664 DOI: 10.1111/jcmm.16756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 01/22/2021] [Revised: 06/01/2021] [Accepted: 06/08/2021] [Indexed: 12/13/2022] Open
Abstract
Pulmonary tuberculosis (PTB) is a major global public health problem. The purpose of this study was to find biomarkers that can be used to diagnose tuberculosis. We used four NCBI GEO data sets to conduct analysis. Among the four data sets, GSE139825 is lung tissue microarray, and GSE83456, GSE19491 and GSE50834 are blood microarray. The differential genes of GSE139825 and GSE83456 were 68 and 226, and intersection genes were 11. Gene ontology (GO) analyses of 11 intersection genes revealed that the changes were mostly enriched in regulation of leucocyte cell-cell adhesion and regulation of T-cell activation. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs revealed that the host response in TB strongly involves cytokine-cytokine receptor interactions and folate biosynthesis. In order to further narrow the range of biomarkers, we used protein-protein interaction to establish a hub gene network of two data sets and a network of 11 candidate genes. Eventually, IRF1 was selected as a biomarker. As validation, IRF1 levels were shown to be up-regulated in patients with TB relative to healthy controls in data sets GSE19491 and GSE50834. Additionally, IRF1 levels were measured in the new patient samples using ELISA. IRF1 was seen to be significantly up-regulated in patients with TB compared with healthy controls with an AUC of 0.801. These results collectively indicate that IRF1 could serve as a new biomarker for the diagnosis of pulmonary tuberculosis.
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Affiliation(s)
- Liwei Wu
- Department of Thoracic SurgeryShanghai Public Health Clinical CenterFudan UniversityShanghaiChina
| | - Qiliang Cheng
- Department of Thoracic SurgeryTuberculosis Hospital of Shaanxi ProvinceXi’anChina
| | - Zilu Wen
- Department of Scientific ResearchShanghai Public Health Clinical CenterFudan UniversityShanghaiChina
| | - Yanzheng Song
- Department of Thoracic SurgeryShanghai Public Health Clinical CenterFudan UniversityShanghaiChina
- TB CenterShanghai Emerging & Re‐emerging Infectious Diseases InstituteShanghaiChina
| | - Yijun Zhu
- Department of Thoracic SurgeryShanghai Public Health Clinical CenterFudan UniversityShanghaiChina
| | - Lin Wang
- Department of Thoracic SurgeryShanghai Public Health Clinical CenterFudan UniversityShanghaiChina
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5
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Sha M, Cao J, Zong ZP, Xu N, Zhang JJ, Tong Y, Xia Q. Identification of genes predicting unfavorable prognosis in hepatitis B virus-associated hepatocellular carcinoma. Ann Transl Med 2021; 9:975. [PMID: 34277775 PMCID: PMC8267317 DOI: 10.21037/atm-21-2085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 05/28/2021] [Indexed: 12/24/2022]
Abstract
Background To identify potential key genes predicting unfavorable prognosis in hepatitis B virus (HBV)-associated hepatocellular carcinoma (HCC). Methods Gene expression profiles of GSE121248, GSE62232, and GSE55092 from the GEO database were obtained and analyzed. Differentially expressed genes (DEGs) between HBV-associated HCC tissues and adjacent normal tissues were screened by the limma package and Venn diagram software. Functional assessment of DEGs was performed by Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). Hub genes were selected by the protein-protein interaction (PPI) network and further validated by GSE14520 clinical data. Results A total of 26 up-regulated genes and 76 down-regulated genes were identified by analyzing three databases. GO and KEGG analysis demonstrated that these genes were involved in cell division, metabolism-related biological processes, the p53 pathway, and the cell cycle, among others. PPI network suggested that 14 hub DEGs (TOP2A, HMMR, DTL, CCNB1, NEK2, PBK, RACGAP1, PRC1, CDK1, RRM2, ECT2, BUB1B, ANLN, and ASPM) were most dysregulated and had potential to distinguish between HBV-associated HCC and noncancerous tissues. Further survival analysis of hub genes demonstrated that high expression of TOP2A was significantly associated with poor clinical outcomes of HBV-associated HCC. Conclusions TOP2A might serve as a key gene for prognosis and as a therapeutic target for HBV-associated HCC.
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Affiliation(s)
- Meng Sha
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Cao
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhi-Peng Zong
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ning Xu
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jian-Jun Zhang
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Tong
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qiang Xia
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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Dong B, Chai M, Chen H, Feng Q, Jin R, Hu S. Screening and verifying key genes with poor prognosis in colon cancer through bioinformatics analysis. Transl Cancer Res 2020; 9:6720-6732. [PMID: 35117282 PMCID: PMC8797306 DOI: 10.21037/tcr-20-2309] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/30/2020] [Indexed: 12/17/2022]
Abstract
Background Colon cancer (CC) is one of the tumors with high morbidity and mortality in the world, and has a trend of younger generation. The molecular level of CC has not been fully elaborated. The purpose of this study is to screen and identify important genes with poor prognosis and their mechanisms at different levels. Methods GSE74602 and GSE10972 gene expression profiles were downloaded from the Gene Expression Omnibus (GEO) database. There were 58 normal tissues and 58 CC tissues. Differentially expressed genes (DEGs) were screened out by using the GEO2R tool and Venn diagram. Then, the DAVID online database was used to perform the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Six hub genes with the highest correlation were screened out after the modular analysis of the protein-protein interaction (PPI) network by using Cytoscape’s MCODE plug-in. Finally, the overall survival of key hub genes and potential pathways were verified in GEPIA and UALCAN database. Results A total of 78 up-regulated DEGs were enriched in the mitotic nuclear division, cell division, cell proliferation, anaphase-promoting complex-dependent catabolic process and G2/M transition of the mitotic cell cycle. In total, 130 down-regulated DEGs were enriched in muscle contraction, bicarbonate transport, cellular response to zinc ion, negative regulation of growth, negative regulation of leukocyte apoptotic process and one-carbon metabolic process. CDK1, CCNB1, CDC20, AURKA, CCNA2 and TOP2A were the top six hub genes, mainly enriched in cell cycle pathways. Among them, CCNB1, CDK1, CDC20, CCNA2 were enriched in the G2/M phase. GEPIA and UALCAN database confirmed that CCNA2 and CCNB1 had a significant relationship with the poor prognosis of CC patients. Meanwhile, there was a positive correlation between the two. Conclusions Screening out genes with abnormal expression in CC help understand the initiation and progression of CC at the molecular level and explore candidate biomarkers for diagnosis, treatment and prognosis.
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Affiliation(s)
- Buyuan Dong
- Department of Gastroenterology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Mengyu Chai
- Department of Respiratory, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Hao Chen
- Department of Gastroenterology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Qian Feng
- Department of Gastroenterology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Rong Jin
- Department of Epidemiology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Sunkuan Hu
- Department of Gastroenterology, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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Li Z, Liu J, Wang W, Zhao Y, Yang D, Geng X. Investigation of hub genes involved in diabetic nephropathy using biological informatics methods. Ann Transl Med 2020; 8:1087. [PMID: 33145306 PMCID: PMC7575993 DOI: 10.21037/atm-20-5647] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background The aim of this study was to find genes with significantly aberrant expression in diabetic nephropathy (DN) and determine their underlying mechanisms. Methods GSE30528 and GSE1009 were obtained by querying the Gene Expression Omnibus (GEO) database. The difference in target gene expression between normal renal tissues and kidney tissues in patients with DN was screened by using the GEO2R tool. Using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) database, differentially expressed genes (DEGs) were analysed by Gene Ontology (GO) annotation and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. Then, the protein-protein interactions (PPIs) of DEGs were analyzed by Cytoscape with the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database, and the hub genes in this PPI network were recognized by centrality analysis. Results There were 110 genes with significant expression differences between normal and DN tissues. The differences in gene expression involved many functions and expression pathways, such as the formation of the extracellular matrix and the construction of the extracellular domain. The correlation analysis and subgroup analysis of 14 hub genes and the clinical characteristics of DN showed that CTGF, ALB, PDPN, FLT1, IGF1, WT1, GJA1, IGFBP2, FGF9, BMP2, FGF1, BMP7, VEGFA, and TGFBR3 may be involved in the progression of DN. Conclusions We confirmed the differentially expressed hub genes and other genes which may be the novel biomarker and target candidates in DN.
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Affiliation(s)
- Zhanting Li
- Department of Nephrology, Xi'an International Medical Center Hospital, Xi'an, China
| | - Jianxin Liu
- Physical Examination Section, Qinhuangdao Jungong Hospital, Qinhuangdao, China
| | - Weiwei Wang
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | - Dengfeng Yang
- Department of Laboratory Medicine, Mianxian Hospital, Mianxian, China
| | - Xiaodong Geng
- Medical School of Chinese PLA, Chinese PLA General Hospital, Beijing, China.,Kidney Diagnostic and Therapeutic Center of the Chinese PLA, Beidaihe Rehabilitation and Recuperation Center of the Chinese PLA, Qinhuangdao, China
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Yin G, Zeng W, Hu K, Gao J, Liu J, Chen Y, Chen F. Parental Uveitis Influences Offspring With an Increased Susceptibility to the Experimental Autoimmune Uveitis. Front Immunol 2020; 11:1053. [PMID: 32612602 PMCID: PMC7308830 DOI: 10.3389/fimmu.2020.01053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 02/21/2020] [Accepted: 04/30/2020] [Indexed: 01/02/2023] Open
Abstract
Purpose: Previous studies have shown that parental abnormal physiological conditions such as inflammation, stress, and obesity can be transferred to offspring. The purpose of this study was to investigate the impact of parental uveitis on the development and susceptibility to experimental autoimmune uveitis (EAU) in offspring. Methods: Parental male and female B10RIII mice were immunized with interphotoreceptor retinoid binding protein (IRBP) 161–180 in complete Freund's adjuvant and were immediately allowed to mate. Gross examination of the offspring gestated with EAU was performed to determine the influence of parental uveitis on offspring development after birth. Gene expression profiles were analyzed in the affected eyes of offspring under EAU to identify differentially expressed genes (DEGs). Adult offspring were given 5, 25, and 50 μg IRBP161−180 to compare their susceptibility to EAU. Immunized mice were clinically and pathologically evaluated for the development of EAU. Ag-specific T-cell proliferation and IL-17 production from spleens and lymph nodes were evaluated on day 14 or 35 after immunization. Results: Hair loss, delay of eye opening, and swollen spleens in the offspring from parents with uveitis were observed from day 14 to 39 after birth. DEGs were involved in the immune system process, muscle system process, and cell development. The altered antigen processing and presentation, cell adhesion molecules, and phagosome in the eyes of the offspring from uveitis-affected parents were enriched. Offspring gestated with EAU showed a susceptibility to EAU and an earlier onset and higher severity of EAU compared to the control group mice. IRBP-specific lymphocyte proliferation and IL-17 production were observed in the EAU offspring with exposure to parental uveitis. Conclusions: The results suggest that mouse parents with uveitis can increase their offspring's susceptibility to EAU, probably through altering cell adhesion molecules and antigen processing and presentation related to the T-cell proliferation and Th17 response.
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Affiliation(s)
- Guangnian Yin
- Laboratory Animal Center, Chongqing Medical University, Chongqing, China.,Chongqing Engineering Research Center for Rodent Laboratory Animals, Chongqing Medical University, Chongqing, China
| | - Wenxin Zeng
- Laboratory Animal Center, Chongqing Medical University, Chongqing, China.,Chongqing Engineering Research Center for Rodent Laboratory Animals, Chongqing Medical University, Chongqing, China
| | - Kaijiao Hu
- Laboratory Animal Center, Chongqing Medical University, Chongqing, China.,Chongqing Engineering Research Center for Rodent Laboratory Animals, Chongqing Medical University, Chongqing, China
| | - Jie Gao
- Laboratory Animal Center, Chongqing Medical University, Chongqing, China.,Chongqing Engineering Research Center for Rodent Laboratory Animals, Chongqing Medical University, Chongqing, China
| | - Jianping Liu
- Pathology Department, Chongqing Medical University, Chongqing, China
| | - Yan Chen
- College of Pharmacy, Chongqing Medical and Pharmaceutical College, Chongqing, China
| | - Feilan Chen
- Laboratory Animal Center, Chongqing Medical University, Chongqing, China.,Chongqing Engineering Research Center for Rodent Laboratory Animals, Chongqing Medical University, Chongqing, China
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9
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Liu G, Zhao Y, Chen H, Jia J, Cheng X, Wang F, Ji Q, Thorne RF, Chen S, Liu X. Analysis of Differentially Expressed Genes in a Chinese Cohort of Esophageal Squamous Cell Carcinoma. J Cancer 2020; 11:3783-3793. [PMID: 32328183 PMCID: PMC7171491 DOI: 10.7150/jca.40850] [Citation(s) in RCA: 2] [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: 10/02/2019] [Accepted: 03/27/2020] [Indexed: 01/23/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is a leading malignancy in China with both high incidence and mortality. Towards improving outcomes, clinically-relevant biomarkers are urgently needed for use as prognostic and treatment targets. Herein we applied RNA-seq for deep sequencing of ten matched pairs of ESCC and adjacent non-cancerous tissues (NT) from Chinese patients. Transcriptomic data mapped to approximately 64% of all annotated genes with 2,047 and 708 unigenes being differentially up-regulated and down-regulated, respectively, between ESCCs and NT samples (p<0.05). Dividing cases by pathological grade revealed significant differentially expressed genes (DEG) between ESCC and NT in both low and high differentiation cases (p<0.05) whereas gene expression differences were not significantly different between high and low differentiation ESCC tissues (p=0.053). Moreover, the majority of ESCC and NT tissues formed clusters in principal component analyses. The veracity of the DEG list was validated in a larger cohort of 45 patient samples, with down-regulated CLIC3, up-regulated CLIC4 and unchanged expression of CLIC2 confirmed in ESCC using quantitative PCR and Western blotting. Our data reveal both previously identified ESCC biomarkers along with novel candidates and represent a ready resource of DEGs in ESCC for further investigation.
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Affiliation(s)
- Gang Liu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450003, China.,Biology Department, School of Life Sciences, Anhui Medical University, Hefei, 230032, China
| | - Yuan Zhao
- Department of Thoracic Surgery, the First Affiliated Hospital, Anhui Medical University, Hefei 230032, China
| | - Huili Chen
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450003, China
| | - Jinru Jia
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450003, China
| | - Xiaomin Cheng
- Biology Department, School of Life Sciences, Anhui Medical University, Hefei, 230032, China
| | - Fengjie Wang
- Biology Department, School of Life Sciences, Anhui Medical University, Hefei, 230032, China
| | - Qiang Ji
- Biology Department, School of Life Sciences, Anhui Medical University, Hefei, 230032, China
| | - Rick F Thorne
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450003, China
| | - Song Chen
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450003, China.,Institute of Medicinal Biotechnology, Jiangsu College of Nursing, Huai'an, 223005, China
| | - Xiaoying Liu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, 450003, China.,Biology Department, School of Life Sciences, Anhui Medical University, Hefei, 230032, China
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10
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Fu Y, Dong T, Tan L, Yin D, Zhang M, Zhao G, Ye M, Wu R. Identification of Shoot Differentiation-Related Genes in Populus euphratica Oliv. Genes (Basel) 2019; 10:genes10121034. [PMID: 31835855 PMCID: PMC6947848 DOI: 10.3390/genes10121034] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 10/03/2019] [Revised: 11/25/2019] [Accepted: 12/09/2019] [Indexed: 12/30/2022] Open
Abstract
De novo shoot regeneration is one of the important manifestations of cell totipotency in organogenesis, which reflects a survival strategy organism evolved when facing natural selection. Compared with tissue regeneration, and somatic embryogenesis, de novo shoot regeneration denotes a shoot regeneration process directly from detatched or injured tissues of plant. Studies on plant shoot regeneration had identified key genes mediating shoot regeneration. However, knowledge was derived from Arabidopsis; the regeneration capacity is hugely distinct among species. To achieve a comprehensive understanding of the shoot regeneration mechanism from tree species, we select four genetic lines of Populus euphratica from a natural population to be sequenced at transcriptome level. On the basis of the large difference of differentiation capacity, between the highly differentiated (HD) and low differentiated (LD) groups, the analysis of differential expression identified 4920 differentially expressed genes (DEGs), which were revealed in five groups of expression patterns by clustering analysis. Enrichment showed crucial pathways involved in regulation of regeneration difference, including “plant hormone signal transduction”, “cell differentiation”, "cellular response to auxin stimulus", and “auxin-activated signaling pathway”. The expression of nine genes reported to be associated with shoot regeneration was validated using quantitative real-time PCR (qRT-PCR). For the specificity of regeneration mechanism with P. euphratica, large amount of DEGs involved in "plant-pathogen interaction", ubiquitin-26S proteosome mediated proteolysis pathway, stress-responsive DEGs, and senescence-associated DEGs were summarized to possibly account for the differentiation difference with distinct genotypes of P. euphratica. The result in this study helps screening of key regulators in mediating the shoot differentiation. The transcriptomic characteristic in P. euphratica further enhances our understanding of key processes affecting the regeneration capacity of de novo shoots among distinct species.
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Affiliation(s)
- Yaru Fu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Y.F.); (T.D.); (L.T.); (D.Y.); (M.Z.); (G.Z.); (R.W.)
| | - Tianyu Dong
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Y.F.); (T.D.); (L.T.); (D.Y.); (M.Z.); (G.Z.); (R.W.)
| | - Lizhi Tan
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Y.F.); (T.D.); (L.T.); (D.Y.); (M.Z.); (G.Z.); (R.W.)
| | - Danni Yin
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Y.F.); (T.D.); (L.T.); (D.Y.); (M.Z.); (G.Z.); (R.W.)
| | - Miaomiao Zhang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Y.F.); (T.D.); (L.T.); (D.Y.); (M.Z.); (G.Z.); (R.W.)
| | - Guomiao Zhao
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Y.F.); (T.D.); (L.T.); (D.Y.); (M.Z.); (G.Z.); (R.W.)
| | - Meixia Ye
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Y.F.); (T.D.); (L.T.); (D.Y.); (M.Z.); (G.Z.); (R.W.)
- Correspondence: ; Tel.: +86-10-6233-7061
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China; (Y.F.); (T.D.); (L.T.); (D.Y.); (M.Z.); (G.Z.); (R.W.)
- Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA 17033, USA
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11
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Wang H, Xie Q, Ou-Yang W, Zhang M. Integrative analyses of genes associated with idiopathic pulmonary fibrosis. J Cell Biochem 2019; 120:8648-8660. [PMID: 30506760 DOI: 10.1002/jcb.28153] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 09/07/2018] [Accepted: 11/09/2018] [Indexed: 01/24/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF), characterized by irreversible scarring and progressive destruction of the lung tissue, is one of the most common types of idiopathic interstitial pneumonia worldwide. However, there are no reliable candidates for curative therapies. Hence, elucidation of the mechanisms of IPF genesis and exploration of potential biomarkers and prognostic indicators are essential for accurate diagnosis and treatment of IPF. Recently, efficient microarray and bioinformatics analyses have promoted an understanding of the molecular mechanisms of disease occurrence and development, which is necessary to explore genetic alternations and identify potential diagnostic biomarkers. However, high false-positive rates results have been observed based on single microarray datasets. In the current study, we performed a comprehensive analysis of the differential expression, biological functions, and interactions of IPF-related genes. Three publicly available microarray datasets including 54 IPF samples and 34 normal samples were integrated by performing gene set enrichment analysis and analyzing differentially expressed genes (DEGs). Our results identified 350 DEGs genetically associated with IPF. Gene ontology analyses revealed that the changes in the modules were mostly enriched in the positive regulation of smooth muscle cell proliferation, positive regulation of inflammatory responses, and the extracellular space. Kyoto encyclopedia of genes and genomes enrichment analysis of DEGs revealed that IPF involves the TNF signaling pathway, NOD-like receptor signaling pathway, and PPAR signaling pathway. To identify key genes related to IPF in the protein-protein interaction network, 20 hub genes were screened out with highest scores. Our results provided a framework for developing new pathological molecular networks related to specific diseases in silico.
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Affiliation(s)
- Huimei Wang
- Department of Integrative Medicine and Neurobiology, State Key Laboratory of Medical Neurobiology, Institute of Brain Science, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, PR China
| | - Qiqi Xie
- Department of Orthopaedics, Second Hospital of Lanzhou University, Lanzhou, Gansu, PR China
| | - Wen Ou-Yang
- The Second Clinical Medical College, Zhujiang Hospital, Southern Medical University, Guangzhou, PR China
| | - Mingwei Zhang
- Department of Radiotherapy, First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, PR China
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12
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Zhang J, Wang J, Jiang W, Liu J, Yang S, Gai J, Li Y. Identification and Analysis of NaHCO 3 Stress Responsive Genes in Wild Soybean ( Glycine soja) Roots by RNA-seq. Front Plant Sci 2016; 7:1842. [PMID: 28018382 PMCID: PMC5161042 DOI: 10.3389/fpls.2016.01842] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 11/22/2016] [Indexed: 05/25/2023]
Abstract
Soil alkalinity is a major abiotic constraint to crop productivity and quality. Wild soybean (Glycine soja) is considered to be more stress-tolerant than cultivated soybean (G. max), and has considerable genetic variation for increasing alkalinity tolerance of soybean. In this study, we analyzed the transcriptome profile in the roots of an alkalinity tolerant wild soybean variety N24852 at 12 and 24 h after 90 mM NaHCO3 stress by RNA-sequencing. Compared with the controls, a total of 449 differentially expressed genes (DEGs) were identified, including 95 and 140 up-regulated genes, and 108 and 135 down-regulated genes at 12 and 24 h after NaHCO3 treatment, respectively. Quantitative RT-PCR analysis of 14 DEGs showed a high consistency with their expression profiles by RNA-sequencing. Gene Ontology (GO) terms related to transcription factors and transporters were significantly enriched in the up-regulated genes at 12 and 24 h after NaHCO3 stress, respectively. Nuclear factor Y subunit A transcription factors were enriched at 12 h after NaHCO3 stress, and high percentages of basic helix-loop-helix, ethylene-responsive factor, Trihelix, and zinc finger (C2H2, C3H) transcription factors were found at both 12 and 24 h after NaHCO3 stress. Genes related to ion transporters such as ABC transporter, aluminum activated malate transporter, glutamate receptor, nitrate transporter/proton dependent oligopeptide family, and S-type anion channel were enriched in up-regulated DEGs at 24 h after NaHCO3 treatment, implying their roles in maintaining ion homeostasis in soybean roots under alkalinity. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis showed "phenylpropanoid biosynthesis" and "phenylalanine metabolism" pathways might participate in soybean response to alkalinity. This study provides a foundation to further investigate the functions of NaHCO3 stress-responsive genes and the molecular basis of soybean tolerance to alkalinity.
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Yang Y, Yao G, Yue W, Zhang S, Wu J. Transcriptome profiling reveals differential gene expression in proanthocyanidin biosynthesis associated with red/green skin color mutant of pear (Pyrus communis L.). Front Plant Sci 2015; 6:795. [PMID: 26483812 PMCID: PMC4588701 DOI: 10.3389/fpls.2015.00795] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 09/13/2015] [Indexed: 05/03/2023]
Abstract
Anthocyanin concentration is the key determinant for red skin color in pear fruit. However, the molecular basis for development of red skin is complicated and has not been well-understood thus far. "Starkrimson" (Pyrus communis L.), an introduced red pear cultivated in the north of China and its green mutant provides a desirable red/green pair for identification of candidate genes involved in color variation. Here, we sequenced and annotated the transcriptome for the red/green color mutant at three stages of development using Illumina RNA-seq technology. The total number of mapped reads ranged from 26 to 46 million in six libraries. About 70.11-71.95% of clean reads could be mapped to the reference genome. Compared with green colored fruit, a total of 2230 differentially expressed genes (DEGs) were identified in red fruit. Gene Ontology (GO) terms were defined for 4886 differential transcripts involved in 15 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Three DEGs were identified as candidate genes in the flavonoid pathway, LAR, ANR, and C3H. Tellingly, higher expression was found for genes encoding ANR and LAR in the green color mutant, promoting the proanthocyanidin (PA) pathway and leading to lower anthocyanin. MYB-binding cis-motifs were identified in the promoter region of LAR and ANR. Based on these findings, we speculate that the regulation of PA biosynthesis might be a key factor for this red/green color mutant. Besides the known MYB and MADS transcription families, two new families, AP2 and WRKY, were identified as having high correlation with anthocyanin biosynthesis in red skinned pear. In addition, qRT-PCR was used to confirm the transcriptome results for 17 DEGs, high correlation of gene expression, further proved that AP2 and WARK regulated the anthocyanin biosynthesis in red skinned "Starkrimson," and ANR and LAR promote PA biosynthesis and contribute to the green skinned variant. This study can serve as a valuable new resource laying a solid foundation for functional gene identification in the anthocyanin pathway of red-skinned pear and provide a good reference for relevant research on molecular mechanisms of color variation in other pear species.
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Affiliation(s)
- Yanan Yang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural UniversityNanjing, China
| | - Gaifang Yao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural UniversityNanjing, China
| | - Wenquan Yue
- Pear Fruit Research Centre, Changli Institute of Pomology, Hebei Academy of Agriculture and Forestry SciencesChangli, China
| | - Shaoling Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural UniversityNanjing, China
| | - Jun Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural UniversityNanjing, China
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14
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Li J, Liu B, Cheng F, Wang X, Aarts MGM, Wu J. Expression profiling reveals functionally redundant multiple-copy genes related to zinc, iron and cadmium responses in Brassica rapa. New Phytol 2014; 203:182-94. [PMID: 24738937 DOI: 10.1111/nph.12803] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [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: 12/22/2013] [Accepted: 02/28/2014] [Indexed: 05/20/2023]
Abstract
Genes underlying environmental adaptability tend to be over-retained in polyploid plant species. Zinc deficiency (ZnD) and iron deficiency (FeD), excess Zn (ZnE) and cadmium exposure (CdE) are major environmental problems for crop cultivation, but little is known about the differential expression of duplicated genes upon these stress conditions. Applying Tag-Seq technology to leaves of Brassica rapa grown under FeD, ZnD, ZnE or CdE conditions, with normal conditions as a control, we examined global gene expression changes and compared the expression patterns of multiple paralogs. We identified 812, 543, 331 and 447 differentially expressed genes under FeD, ZnD, ZnE and CdE conditions, respectively, in B. rapa leaves. Genes involved in regulatory networks centered on the transcription factors bHLH038 or bHLH100 were differentially expressed under (ZnE-induced) FeD. Further analysis revealed that genes associated with Zn, Fe and Cd responses tended to be over-retained in the B. rapa genome. Most of these multiple-copy genes showed the same direction of expression change under stress conditions. We conclude that the duplicated genes involved in trace element responses in B. rapa are functionally redundant, making the regulatory network more complex in B. rapa than in Arabidopsis thaliana.
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Affiliation(s)
- Jimeng Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Zhongguancun Southern Street 12, 100081, Beijing, China; Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, the Netherlands
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