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Xiong Y, Tang X, Meng Q, Zhang H. Differential expression analysis of the broiler tracheal proteins responsible for the immune response and muscle contraction induced by high concentration of ammonia using iTRAQ-coupled 2D LC-MS/MS. SCIENCE CHINA. LIFE SCIENCES 2016; 59:1166-1176. [PMID: 27761697 PMCID: PMC7089013 DOI: 10.1007/s11427-016-0202-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 08/22/2016] [Indexed: 01/21/2023]
Abstract
Ammonia has been considered the contaminant primarily responsible for respiratory disease in poultry. Even though it can cause tracheal lesions, its adverse effects on the trachea have not been sufficiently studied. The present study investigated tracheal changes in Arbor Acres broilers (Gallus gallus) induced by high concentration of ammonia using isobaric tag for relative and absolute quantification (iTRAQ)-based proteome analysis. In total, 3,706 proteins within false discovery rate of 1% were identified, including 119 significantly differentially expressed proteins. Functional analysis revealed that proteins related to immune response and muscle contraction were significantly enriched. With respect to the immune response, up-regulated proteins (like FGA) were pro-inflammatory, while down-regulated proteins participated in antigen processing and antigen presenting (like MYO1G), immunoglobulin and cathelicidin production (like fowlicidin-2), and immunodeficiency (like PTPRC). Regarding muscle contraction, all differentially expressed proteins (like TPM1) were up-regulated. An over-expression of mucin, which is a common feature of airway disease, was also observed. Additionally, the transcriptional alterations of 6 selected proteins were analyzed by quantitative RT-PCR. Overall, proteomic changes suggested the onset of airway obstruction and diminished host defense in trachea after ammonia exposure. These results may serve as a valuable reference for future interventions against ammonia toxicity.
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Affiliation(s)
- Yan Xiong
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiangfang Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qingshi Meng
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Yu H, Wang F, Lin L, Cao W, Liu Y, Qin L, Lu H, He F, Shen H, Yang P. Mapping and analyzing the human liver proteome: progress and potential. Expert Rev Proteomics 2016; 13:833-43. [PMID: 27448621 DOI: 10.1080/14789450.2016.1213132] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION The liver is an important organ in humans. Hepatocellular carcinoma (HCC) is one of the deadliest cancers in the world. Progress in the Human Liver Proteome Project (HLPP) has improved understanding of the liver and the liver cancer proteome. AREAS COVERED Here, we summarize the recent progress in liver proteome modification profiles, proteomic studies in liver cancer, proteomic study in the search for novel liver cancer biomarkers and drug targets, and progress of the Chromosome Centric Human Proteome Project (CHPP) in the past five years in the Institutes of Biomedical Sciences (IBS) of Fudan University. Expert commentary: Recent advances and findings discussed here provide great promise of improving the outcome of patients with liver cancer.
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Affiliation(s)
- Hongxiu Yu
- a Department of Systems Biology for Medicine, School of Basic Medical Sciences , Fudan University , Shanghai , China.,b Minhang Hospital and Institutes of Biomedical Sciences , Fudan University , Shanghai , China
| | - Fang Wang
- a Department of Systems Biology for Medicine, School of Basic Medical Sciences , Fudan University , Shanghai , China
| | - Ling Lin
- a Department of Systems Biology for Medicine, School of Basic Medical Sciences , Fudan University , Shanghai , China
| | - Weiqian Cao
- a Department of Systems Biology for Medicine, School of Basic Medical Sciences , Fudan University , Shanghai , China
| | - Yinkun Liu
- c China Liver Cancer Institute, Zhongshan Hospital , Fudan University , Shanghai , China
| | - Lunxiu Qin
- c China Liver Cancer Institute, Zhongshan Hospital , Fudan University , Shanghai , China
| | - Haojie Lu
- b Minhang Hospital and Institutes of Biomedical Sciences , Fudan University , Shanghai , China
| | - Fuchu He
- d State Key Laboratory of Proteomics, Beijing Proteome Research Center , Beijing Institute of Radiation Medicine , Beijing , China
| | - Huali Shen
- a Department of Systems Biology for Medicine, School of Basic Medical Sciences , Fudan University , Shanghai , China.,b Minhang Hospital and Institutes of Biomedical Sciences , Fudan University , Shanghai , China
| | - Pengyuan Yang
- a Department of Systems Biology for Medicine, School of Basic Medical Sciences , Fudan University , Shanghai , China.,b Minhang Hospital and Institutes of Biomedical Sciences , Fudan University , Shanghai , China
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Chang Z, Gu L. Is the mission to identify all the human proteins achievable?--Commenting on the human proteome draft maps. SCIENCE CHINA. LIFE SCIENCES 2014; 57:1039-1040. [PMID: 25216708 DOI: 10.1007/s11427-014-4738-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Accepted: 08/12/2014] [Indexed: 06/03/2023]
Affiliation(s)
- ZengYi Chang
- Center for Protein Science, State Key Laboratory of Protein and Plant Gene Studies, School of Life Sciences, Center for History and Philosophy of Science, Peking University, Beijing, 100871, China,
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Rapid development of proteomics in China: from the perspective of the Human Liver Proteome Project and technology development. SCIENCE CHINA-LIFE SCIENCES 2014; 57:1162-71. [PMID: 25119674 DOI: 10.1007/s11427-014-4714-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 07/01/2014] [Indexed: 12/17/2022]
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Fu X, Shi X, Yan L, Zhang H, Chang Z. In vivo substrate diversity and preference of small heat shock protein IbpB as revealed by using a genetically incorporated photo-cross-linker. J Biol Chem 2013; 288:31646-54. [PMID: 24045939 DOI: 10.1074/jbc.m113.501817] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Small heat shock proteins (sHSPs), as ubiquitous molecular chaperones found in all forms of life, are known to be able to protect cells against stresses and suppress the aggregation of a variety of model substrate proteins under in vitro conditions. Nevertheless, it is poorly understood what natural substrate proteins are protected by sHSPs in living cells. Here, by using a genetically incorporated photo-cross-linker (p-benzoyl-l-phenylalanine), we identified a total of 95 and 54 natural substrate proteins of IbpB (an sHSP from Escherichia coli) in living cells with and without heat shock, respectively. Functional profiling of these proteins (110 in total) suggests that IbpB, although binding to a wide range of cellular proteins, has a remarkable substrate preference for translation-related proteins (e.g. ribosomal proteins and amino-acyl tRNA synthetases) and moderate preference for metabolic enzymes. Furthermore, these two classes of proteins were found to be more prone to aggregation and/or inactivation in cells lacking IbpB under stress conditions (e.g. heat shock). Together, our in vivo data offer novel insights into the chaperone function of IbpB, or sHSPs in general, and suggest that the preferential protection on the protein synthesis machine and metabolic enzymes may dominantly contribute to the well known protective effect of sHSPs on cell survival against stresses.
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Affiliation(s)
- Xinmiao Fu
- From the State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871 and
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