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Tang J, Shen X, Ouyang H, Luo W, Huang Y, Tian Y, Zhang X. Transcriptome analysis of pituitary gland revealed candidate genes and gene networks regulating the growth and development in goose. Anim Biotechnol 2020; 33:429-439. [PMID: 32779547 DOI: 10.1080/10495398.2020.1801457] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Goose is important meat poultry and its growth and development has always been the focus of attention, but the regulation mechanisms of genes and gene network underlying growth and development of goose are still unclear. Three males of large-size Shitou goose and three males of small size Wuzong goose at 5 weeks of age were used for transcriptome analysis with deep sequencing. After slaughter, their pituitary gland was taken for RNA-seq. A total of 290 DEGs were identified by fold change ≥2 and false discovery rate (FDR) <0.05, where there were 148 upregulated genes and 142 downregulated genes in Shitou goose compared to Wuzong goose. Results also showed that the DEGs related to insulin signaling pathway could increase protein synthesis and fat production, and the interaction network of DEGs was mainly related to development, endocrine system, inflammatory diseases, tissue damage and abnormality. The DEGs involved in the growth and function of the pituitary organs may regulate the growth and development of the body by affecting the synthesis and secretion of pituitary hormones. The results of this study will help to understand the regulatory mechanism of goose growth and development.
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Affiliation(s)
- Jun Tang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China.,College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China.,Guangdong Province Key Laboratory of Waterfowl Healthy Breeding, Guangzhou, Guangdong, China
| | - Xu Shen
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China.,Guangdong Province Key Laboratory of Waterfowl Healthy Breeding, Guangzhou, Guangdong, China
| | - Hongjia Ouyang
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China.,Guangdong Province Key Laboratory of Waterfowl Healthy Breeding, Guangzhou, Guangdong, China
| | - Wen Luo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yunmao Huang
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China.,Guangdong Province Key Laboratory of Waterfowl Healthy Breeding, Guangzhou, Guangdong, China
| | - Yunbo Tian
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China.,Guangdong Province Key Laboratory of Waterfowl Healthy Breeding, Guangzhou, Guangdong, China
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
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Weinguny M, Klanert G, Eisenhut P, Jonsson A, Ivansson D, Lövgren A, Borth N. Directed evolution approach to enhance efficiency and speed of outgrowth during single cell subcloning of Chinese Hamster Ovary cells. Comput Struct Biotechnol J 2020; 18:1320-1329. [PMID: 32612755 PMCID: PMC7306589 DOI: 10.1016/j.csbj.2020.05.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/16/2020] [Accepted: 05/17/2020] [Indexed: 01/08/2023] Open
Abstract
Chinese Hamster Ovary (CHO) cells are the working horse of the pharmaceutical industry. To obtain high producing cell clones and to satisfy regulatory requirements single cell cloning is a necessary step in cell line development. However, it is also a tedious, labor intensive and expensive process. Here we show an easy way to enhance subclonability using subcloning by single cell sorting itself as the selection pressure, resulting in improved subcloning performance of three different host cell lines. These improvements in subclonability also lead to an enhanced cellular growth behavior during standard batch culture. RNA-seq was performed to shed light on the underlying mechanisms, showing that there is little overlap in differentially expressed genes or associated pathways between the cell lines, each finding their individual strategy for optimization. However, in all three cell lines pathways associated with the extracellular matrix were found to be enriched, indicating that cells struggle predominantly with their microenvironment and possibly lack of cell-to-cell contact. The observed small overlap may hint that there are multiple ways for a cell line to achieve a certain phenotype due to numerous genetic and subsequently metabolic redundancies.
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Key Words
- CHO
- CHO cells
- CHO, Chinese hamster ovary
- Cell line development
- Cell sorting
- Chinese Hamster Ovary Cells
- CoI, clusters of interest
- DE, directed evolved
- Directed Evolution
- ECM, extracellular matrix
- ES, enrichment score
- FACS
- FACS, fluorescent-activated cell sorting
- Fluorescent-activated cell sorting
- GSEA, gene set analysis
- Growth enhancement
- Growth improvement
- LDC, limiting dilution cloning
- NES, negative enrichment score
- PC, principal component
- PCA, principal component analysis
- POI, product of interest
- RNA Sequencing
- RNA-Seq
- RNA-Seq, RNA sequencing
- SCC, single cell cloning
- Single Cell Cloning
- Single Cell Subcloning
- Subcloning
- lfcSE, logfoldstandard error
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Affiliation(s)
- Marcus Weinguny
- ACIB Gmbh, Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | - Gerald Klanert
- ACIB Gmbh, Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Peter Eisenhut
- ACIB Gmbh, Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
| | | | | | | | - Nicole Borth
- ACIB Gmbh, Austrian Centre of Industrial Biotechnology, Vienna, Austria
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Vienna, Austria
- Corresponding author at: Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria.
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Ren J, Gu C, Yang Y, Xue J, Sun Y, Jian F, Chen D, Bian L, Sun Q. TSP-1 is downregulated and inversely correlates with miR-449c expression in Cushing's disease. J Cell Mol Med 2019; 23:4097-4110. [PMID: 31016850 PMCID: PMC6533510 DOI: 10.1111/jcmm.14297] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 01/29/2019] [Accepted: 03/04/2019] [Indexed: 12/11/2022] Open
Abstract
The pathogenesis of Cushing's disease, which is caused by pituitary corticotroph adenoma, remains to be studied. Secreted angioinhibitory factor thrombospondin-1 (TSP-1) is an adhesive glycoprotein that mediates cell-to-cell and cell-to-matrix interactions and is associated with platelet aggregation, angiogenesis and tumorigenesis. We have found that the expression of TSP-1 is significantly lower in human pituitary corticotroph tumours compared with normal adenohypophysis. This study aims to elucidate the role of TSP-1 in regulating the tumour function of pituitary adenomas. Forced overexpression of TSP-1 in a murine AtT20 pituitary corticotroph tumour cell line decreased corticotroph precursor hormone proopiomelanocortin (POMC) transcription and adrenocorticotropic hormone (ACTH) secretion. Functional studies showed that TSP-1 overexpression in pituitary adenoma cells suppressed proliferation, migration and invasion. We have demonstrated that TSP-1 is a direct target of miR-449c. Further study showed that miR-449c activity enhanced tumorigenesis by directly inhibiting TSP-1 expression. Low expression of lncTHBS1, along with low expression of TSP-1, was associated with the high expression of miR-449c in Cushing's disease patients. Furthermore, RNA-immunoprecipitation associates miR-449c with lncTHBS1 suggesting that lncTHBS1 might be a negative regulator of miR-449c. Taken together, this study has demonstrated that lncTHBS1 might function as competing endogenous RNA for miR-449c, which could suppress the development of Cushing's disease.
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Affiliation(s)
- Jie Ren
- Department of Neurosurgery, Ruijin HospitalShanghai Jiaotong University School of MedicineShanghaiP.R. China
| | - Changwei Gu
- Department of Neurosurgery, Ruijin Hospital, Luwan BranchShanghai Jiaotong University School of MedicineShanghaiP.R. China
| | - Yong Yang
- Department of NeurosurgeryGuangdong General Hospital, Guangdong Academy of Medical SciencesGuangzhouChina
| | - Jun Xue
- Department of Neurosurgery, Ruijin HospitalShanghai Jiaotong University School of MedicineShanghaiP.R. China
| | - Yuhao Sun
- Department of Neurosurgery, Ruijin HospitalShanghai Jiaotong University School of MedicineShanghaiP.R. China
| | - Fangfang Jian
- Department of Obstetrics and Gynecology, Ruijin HospitalShanghai Jiaotong University School of MedicineShanghaiP.R. China
| | - Dongjiang Chen
- Department of Neurosurgery, McKnight Brain InstituteUniversity of FloridaGainesvilleFlorida
| | - Liuguan Bian
- Department of Neurosurgery, Ruijin HospitalShanghai Jiaotong University School of MedicineShanghaiP.R. China
| | - Qingfang Sun
- Department of Neurosurgery, Ruijin HospitalShanghai Jiaotong University School of MedicineShanghaiP.R. China
- Department of Neurosurgery, Ruijin Hospital, Luwan BranchShanghai Jiaotong University School of MedicineShanghaiP.R. China
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Feng J, Zhang Q, Zhou Y, Yu S, Hong L, Zhao S, Yang J, Wan H, Xu G, Zhang Y, Li C. Integration of Proteomics and Metabolomics Revealed Metabolite-Protein Networks in ACTH-Secreting Pituitary Adenoma. Front Endocrinol (Lausanne) 2018; 9:678. [PMID: 30532734 PMCID: PMC6266547 DOI: 10.3389/fendo.2018.00678] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 10/29/2018] [Indexed: 12/20/2022] Open
Abstract
An effective treatment for the management of adrenocorticotropic hormone-secreting pituitary adenomas (ACTH-PA) is currently lacking, although surgery is a treatment option. We have integrated information obtained at the metabolomic and proteomic levels to identify critical networks and signaling pathways that may play important roles in the metabolic regulation of ACTH-PA and therefore hopefully represent potential therapeutic targets. Six ACTH-PAs and seven normal pituitary glands were investigated via gas chromatography-mass spectrometry (GC-MS) analysis for metabolomics. Five ACTH-PAs and five normal pituitary glands were subjected to proteomics analysis via nano liquid chromatography tandem-mass spectrometry (nanoLC-MS/MS). The joint pathway analysis and network analysis was performed using MetaboAnalyst 3.0. software. There were significant differences of metabolites and protein expression levels between the ACTH-PAs and normal pituitary glands. A proteomic analysis identified 417 differentially expressed proteins that were significantly enriched in the Myc signaling pathway. The protein-metabolite joint pathway analysis showed that differentially expressed proteins and metabolites were significantly enriched in glycolysis/gluconeogenesis, pyruvate metabolism, citrate cycle (TCA cycle), and the fatty acid metabolism pathway in ACTH-PA. The protein-metabolite molecular interaction network identified from the metabolomics and proteomics investigation resulted in four subnetworks. Ten nodes in subnetwork 1 were the most significantly enriched in cell amino acid metabolism and pyrimidine nucleotide metabolism. Additionally, the metabolite-gene-disease interaction network established nine subnetworks. Ninety-two nodes in subnetwork 1 were the most significantly enriched in carboxylic acid metabolism and organic acid metabolism. The present study clarified the pathway networks that function in ACTH-PA. Our results demonstrated the presence of downregulated glycolysis and fatty acid synthesis in this tumor type. We also revealed that the Myc signaling pathway significantly participated in the metabolic changes and tumorigenesis of ACTH-PA. This data may provide biomarkers for ACTH-PA diagnosis and monitoring, and could also lead to the development of novel strategies for treating pituitary adenomas.
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Affiliation(s)
- Jie Feng
- Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Beijing Institute for Brain Disorders, Brain Tumor Center, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Qi Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yang Zhou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Shenyuan Yu
- Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Lichuan Hong
- Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Sida Zhao
- Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jingjing Yang
- Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Hong Wan
- Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Yazhuo Zhang
- Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Beijing Institute for Brain Disorders, Brain Tumor Center, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Chuzhong Li
- Beijing Neurosurgical Institute, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Beijing Institute for Brain Disorders, Brain Tumor Center, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- *Correspondence: Chuzhong Li
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