1
|
Shen CY, Chang WH, Chen YJ, Weng CW, Regmi P, Kier MKK, Su KY, Chang GC, Chen JS, Chen YJ, Yu SL. Tissue Proteogenomic Landscape Reveals the Role of Uncharacterized SEL1L3 in Progression and Immunotherapy Response in Lung Adenocarcinoma. J Proteome Res 2022; 22:1056-1070. [PMID: 36349894 DOI: 10.1021/acs.jproteome.2c00382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The fundamental pursuit to complete the human proteome atlas and the unmet clinical needs in lung adenocarcinoma have prompted us to study the functional role of uncharacterized proteins and explore their implications in cancer biology. In this study, we characterized SEL1L3, a previously uncharacterized protein encoded from chromosome 4 as a dysregulated protein in lung adenocarcinoma from the large-scale tissue proteogenomics data set established using the cohort of Taiwan Cancer Moonshot. SEL1L3 was expressed in abundance in the tumor parts compared with paired adjacent normal tissues in 90% of the lung adenocarcinoma patients in our cohorts. Moreover, survival analysis revealed the association of SEL1L3 with better clinical outcomes. Intriguingly, silencing of SEL1L3 imposed a reduction in cell viability and activation of ER stress response pathways, indicating a role of SEL1L3 in the regulation of cell stress. Furthermore, the immune profiles of patients with higher SEL1L3 expression were corroborated with its active role in immunophenotype and favorable clinical outcomes in lung adenocarcinoma. Taken together, our study revealed that SEL1L3 might play a vital role in the regulation of cell stress, interaction with cancer cells and the immune microenvironment. Our research findings provide promising insights for further investigation of its molecular signaling network and also suggest SEL1L3 as a potential emerging adjuvant for immunotherapy in lung adenocarcinoma.
Collapse
Affiliation(s)
- Chi-Ya Shen
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei10048, Taiwan
| | - Wen-Hsin Chang
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, University of California─Davis, Davis, California95616, United States.,Division of Nephrology, Department of Internal Medicine, University of California─Davis, Davis, California95616, United States
| | - Yi-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei11529, Taiwan
| | - Chia-Wei Weng
- Institute of Medicine, Chung Shan Medical University, Taichung40201, Taiwan
| | - Prabha Regmi
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei10048, Taiwan
| | - Mickiela K K Kier
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei10048, Taiwan
| | - Kang-Yi Su
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei10048, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital, Taipei10002, Taiwan
| | - Gee-Chen Chang
- Division of Pulmonary Medicine, Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung40201, Taiwan
| | - Jin-Shing Chen
- Department of Surgery, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei10002, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei11529, Taiwan
| | - Sung-Liang Yu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei10048, Taiwan.,Department of Laboratory Medicine, National Taiwan University Hospital, Taipei10002, Taiwan.,Institute of Medical Device and Imaging, College of Medicine, National Taiwan University, Taipei10051, Taiwan.,Graduate Institute of Pathology, College of Medicine, National Taiwan University, Taipei10051, Taiwan.,Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei10002, Taiwan
| |
Collapse
|
2
|
Chen Q, Zhang Y, Zhang K, Liu J, Pan H, Wang X, Li S, Hu D, Lin Z, Zhao Y, Hou G, Guan F, Li H, Liu S, Ren Y. Profiling the Bisecting N-acetylglucosamine Modification in Amniotic Membrane via Mass Spectrometry. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:648-656. [PMID: 35123071 PMCID: PMC9880894 DOI: 10.1016/j.gpb.2021.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/30/2021] [Accepted: 10/11/2021] [Indexed: 01/31/2023]
Abstract
Bisecting N-acetylglucosamine (GlcNAc), a GlcNAc linked to the core β-mannose residue via a β1,4 linkage, is a special type of N-glycosylation that has been reported to be involved in various biological processes, such as cell adhesion and fetal development. This N-glycan structure is abundant in human trophoblasts, which is postulated to be resistant to natural killer cell-mediated cytotoxicity, enabling a mother to nourish a fetus without rejection. In this study, we hypothesized that the human amniotic membrane, which serves as the last barrier for the fetus, may also express bisected-type glycans. To test this hypothesis, glycomic analysis of the human amniotic membrane was performed, and bisected N-glycans were detected. Furthermore, our proteomic data, which have been previously employed to explore human missing proteins, were analyzed and the presence of bisecting GlcNAc-modified peptides was confirmed. A total of 41 glycoproteins with 43 glycopeptides were found to possess a bisecting GlcNAc, and 25 of these glycoproteins were reported to exhibit this type of modification for the first time. These results provide insights into the potential roles of bisecting GlcNAc modification in the human amniotic membrane, and can be beneficial to functional studies on glycoproteins with bisecting GlcNAc modifications and functional studies on immune suppression in human placenta.
Collapse
Affiliation(s)
| | | | | | - Jie Liu
- BGI-Shenzhen, Shenzhen 518083, China
| | | | | | - Siqi Li
- BGI-Shenzhen, Shenzhen 518083, China
| | - Dandan Hu
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Yun Zhao
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Feng Guan
- Joint International Research Laboratory of Glycobiology and Medical Chemistry, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Hong Li
- Shenzhen Seventh People's Hospital, Shenzhen 518081, China
| | - Siqi Liu
- BGI-Shenzhen, Shenzhen 518083, China,Corresponding authors.
| | - Yan Ren
- BGI-Shenzhen, Shenzhen 518083, China,Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China,Corresponding authors.
| |
Collapse
|
3
|
Muroski JM, Fu JY, Nguyen HH, Wofford NQ, Mouttaki H, James KL, McInerney MJ, Gunsalus RP, Loo JA, Ogorzalek Loo RR. The acyl-proteome of Syntrophus aciditrophicus reveals metabolic relationships in benzoate degradation. Mol Cell Proteomics 2022; 21:100215. [PMID: 35189333 PMCID: PMC8942843 DOI: 10.1016/j.mcpro.2022.100215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 01/13/2022] [Accepted: 02/17/2022] [Indexed: 11/08/2022] Open
Abstract
Syntrophus aciditrophicus is a model syntrophic bacterium that degrades fatty and aromatic acids into acetate, CO2, formate, and H2 that are utilized by methanogens and other hydrogen-consuming microbes. S. aciditrophicus benzoate degradation proceeds by a multistep pathway with many intermediate reactive acyl-coenzyme A species (RACS) that can potentially Nε-acylate lysine residues. Herein, we describe the identification and characterization of acyl-lysine modifications that correspond to RACS in the benzoate degradation pathway. The amounts of modified peptides are sufficient to analyze the post-translational modifications without antibody enrichment, enabling a range of acylations located, presumably, on the most extensively acylated proteins throughout the proteome to be studied. Seven types of acyl modifications were identified, six of which correspond directly to RACS that are intermediates in the benzoate degradation pathway including 3-hydroxypimeloylation, a modification first identified in this system. Indeed, benzoate-degrading enzymes are heavily represented among the acylated proteins. A total of 125 sites were identified in 60 proteins. Functional deacylase enzymes are present in the proteome, indicating a potential regulatory system/mechanism by which S. aciditrophicus modulates acylation. Uniquely, Nε-acyl-lysine RACS are highly abundant in these syntrophic bacteria, raising the compelling possibility that post-translational modifications modulate benzoate degradation in this and potentially other, syntrophic bacteria. Our results outline candidates for further study of how acylations impact syntrophic consortia. Abundant lysine modifications in microbes enable unbiased global acylation profiling. Seven types of acyl modifications are found; six from benzoate degradation intermediates. Benzoate-degrading enzymes are prominent among the 60 acylated proteins. Abundant acylation/active deacylases suggest PTMs modulate syntrophic metabolism.
Collapse
|
4
|
Liu YC, Huang YT, Chen CJ. Development of a high-pH reversed-phase well plate for peptide fractionation and deep proteome analysis of cells and exosomes. Anal Bioanal Chem 2022; 414:2513-2522. [PMID: 35099582 DOI: 10.1007/s00216-022-03892-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/27/2021] [Accepted: 01/10/2022] [Indexed: 11/01/2022]
Abstract
The complexity of the proteome often limits the number of identified proteins in the nanoflow LC-MS (nanoLC-MS) analysis of samples. Therefore, peptide fractionation is essential for reducing the sample complexity and improving the proteome coverage. In this study, to achieve high-pH reversed-phase (RP)-well plate fractionation for high-throughput proteomics analysis, C18 particles were coated on a 96-well plate, and the sample-loading processes were optimized for high-pH fractionation. The sample capacity of the high-pH RP-well plate was estimated to be ~6 μg of protein. There were 1.85- and 1.71-fold increases in the number of protein groups and peptides identified, respectively, with high-pH RP-well plate fractionation, compared to those without fractionation. In addition, with alkaline C18 well plate fractionation, exosome markers could be detected using ~1 μg of a protein digest of exosomes by microflow LC-MS (microLC-MS). These results illustrate that high-pH RP-well plate fractionation has superior sensitivity and effectiveness in preparing trace amounts of proteins for deep proteome analysis.
Collapse
Affiliation(s)
- Yu-Ching Liu
- Graduate Institute of Integrated Medicine, China Medical University, Taichung, Taiwan.,Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | | | - Chao-Jung Chen
- Graduate Institute of Integrated Medicine, China Medical University, Taichung, Taiwan. .,Proteomics Core Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan.
| |
Collapse
|
5
|
Sun J, Shi J, Wang Y, Wu S, Zhao L, Li Y, Wang H, Chang L, Lyu Z, Wu J, Liu F, Li W, He F, Zhang Y, Xu P. Open-pFind Enhances the Identification of Missing Proteins from Human Testis Tissue. J Proteome Res 2019; 18:4189-4196. [DOI: 10.1021/acs.jproteome.9b00376] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Jinshuai Sun
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Jiahui Shi
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Yihao Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Shujia Wu
- Key Laboratory of Combinational Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Science, Wuhan University, Wuhan 430072, China
| | - Liping Zhao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- Guizhou University School of Medicine, Guiyang 550025, China
| | - Yanchang Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Hong Wang
- School of Public Health, North China University Science and Technology, Tangshan 063210, China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Zhitang Lyu
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Junzhu Wu
- Key Laboratory of Combinational Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Science, Wuhan University, Wuhan 430072, China
| | - Fengsong Liu
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Wenjun Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yao Zhang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
- Key Laboratory of Combinational Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Science, Wuhan University, Wuhan 430072, China
- Guizhou University School of Medicine, Guiyang 550025, China
| |
Collapse
|
6
|
Sun J, Shi J, Wang Y, Chen Y, Li Y, Kong D, Chang L, Liu F, Lv Z, Zhou Y, He F, Zhang Y, Xu P. Multiproteases Combined with High-pH Reverse-Phase Separation Strategy Verified Fourteen Missing Proteins in Human Testis Tissue. J Proteome Res 2018; 17:4171-4177. [PMID: 30280576 DOI: 10.1021/acs.jproteome.8b00397] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Subsequent to conducting the Chromosome-Centric Human Proteome Project, we have focused on human testis-enriched missing proteins (MPs) since 2015. For protein coverage to be enhanced, a multiprotease strategy was used for separation of samples by 10% SDS-PAGE. For the separating efficiency to be improved, a high-pH reverse phase (RP) separation strategy was applied to fractionate complex samples in this study. A total of 11,558 proteins was identified, which is the largest proteome data set for single human tissue sample so far. On the basis of this large-scale data set, we verified 14 MPs (PE2) in neXtProt (2018-01) after spectrum quality analysis, isobaric post-translational modification, and single amino acid variant filtering, and synthesized peptide matching. Tissue expression analysis showed that 3 of 14 MPs were testis-specific proteins. Functional analysis showed that 10 of 14 MPs were closely related to liver tumor, liver carcinoma, and hepatocellular carcinoma. Another 100 MPs were listed as candidates but required additional verification information. All MS data sets have been deposited into the ProteomeXchange with the identifier PXD009737.
Collapse
Affiliation(s)
- Jinshuai Sun
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences , Hebei University , Baoding , Hebei 071002 , China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Jiahui Shi
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences , Hebei University , Baoding , Hebei 071002 , China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Yihao Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Yang Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Yanchang Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Degang Kong
- Department of Hepatopancreatobiliary Surgery , The Second Affiliated Hospital of Tianjin Medical University , Tianjin 300211 , China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Fengsong Liu
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences , Hebei University , Baoding , Hebei 071002 , China
| | - Zhitang Lv
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences , Hebei University , Baoding , Hebei 071002 , China
| | - Yue Zhou
- Demo Laboratory of Thermofisher Scientific China , Shanghai 200120 , China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Yao Zhang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences , Sun Yat-Sen University , Guangzhou 510275 , China
| | - Ping Xu
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences , Hebei University , Baoding , Hebei 071002 , China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing) , Beijing Institute of Lifeomics , Beijing 102206 , China.,Key Laboratory of Combinational Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Science , Wuhan University , Wuhan 430072 , China
| |
Collapse
|
7
|
Zhang Y, Lin Z, Hao P, Hou K, Sui Y, Zhang K, He Y, Li H, Yang H, Liu S, Ren Y. Improvement of Peptide Separation for Exploring the Missing Proteins Localized on Membranes. J Proteome Res 2018; 17:4152-4159. [DOI: 10.1021/acs.jproteome.8b00409] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuanliang Zhang
- BGI-Shenzhen, Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China
| | - Zhilong Lin
- BGI-Shenzhen, Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China
| | - Piliang Hao
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Kexia Hou
- The Second Maternal and Child Health Care Center of Huangdao District, 236 Fuchunjiang Road, Qingdao 266555, Shandong, China
| | - Yuanyuan Sui
- The Second Maternal and Child Health Care Center of Huangdao District, 236 Fuchunjiang Road, Qingdao 266555, Shandong, China
| | - Keren Zhang
- BGI-Shenzhen, Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China
| | - Yanbin He
- BGI-Shenzhen, Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China
| | - Hong Li
- Pulmonary Function Room, Shenzhen Seventh People’s Hospital, 2010 Wutong Road, Yantian District, Shenzhen, Guangdong 518081, China
| | - Huanming Yang
- BGI-Shenzhen, Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Siqi Liu
- BGI-Shenzhen, Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China
| | - Yan Ren
- BGI-Shenzhen, Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China
| |
Collapse
|
8
|
He C, Sun J, Shi J, Wang Y, Zhao J, Wu S, Chang L, Gao H, Liu F, Lv Z, He F, Zhang Y, Xu P. Digging for Missing Proteins Using Low-Molecular-Weight Protein Enrichment and a “Mirror Protease” Strategy. J Proteome Res 2018; 17:4178-4185. [DOI: 10.1021/acs.jproteome.8b00398] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Cuitong He
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102206, China
| | - Jinshuai Sun
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102206, China
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Jiahui Shi
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102206, China
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Yihao Wang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102206, China
| | - Jialing Zhao
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102206, China
- Key Laboratory of Combinational Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Science, Wuhan University, Wuhan 430072, China
| | - Shujia Wu
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102206, China
- Key Laboratory of Combinational Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Science, Wuhan University, Wuhan 430072, China
| | - Lei Chang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102206, China
| | - Huiying Gao
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102206, China
| | - Fengsong Liu
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Zhitang Lv
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Fuchu He
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102206, China
| | - Yao Zhang
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102206, China
| | - Ping Xu
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102206, China
- Hebei Province Key Lab of Research and Application on Microbial Diversity, College of Life Sciences, Hebei University, Baoding, Hebei 071002, China
- Key Laboratory of Combinational Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, School of Pharmaceutical Science, Wuhan University, Wuhan 430072, China
| |
Collapse
|
9
|
Weldemariam MM, Han CL, Shekari F, Kitata RB, Chuang CY, Hsu WT, Kuo HC, Choong WK, Sung TY, He FC, Chung MCM, Salekdeh GH, Chen YJ. Subcellular Proteome Landscape of Human Embryonic Stem Cells Revealed Missing Membrane Proteins. J Proteome Res 2018; 17:4138-4151. [DOI: 10.1021/acs.jproteome.8b00407] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Mehari Muuz Weldemariam
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 112, Taiwan
| | - Chia-Li Han
- Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, College of Pharmacy, Taipei Medical University, Taipei 110, Taiwan
| | - Faezeh Shekari
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | | | - Ching-Yu Chuang
- Genomics Research Center, Academia Sinica, Taiepei 115, Taiwan
| | | | | | | | | | - Fu-Chu He
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing, 102206 China
| | - Maxey Ching Ming Chung
- Department of Biochemistry, Yong Loo Lin School of Medicine, NUS, 14 Science Drive 4, singapore, 117543 Singpore
| | - Ghasem Hosseini Salekdeh
- Department of Molecular Systems Biology at Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
- Department of Molecular Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization, Karaj, Iran
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan
- Department of Chemistry, National Taiwan University, Taipei 112, Taiwan
| |
Collapse
|
10
|
Chang IS, Sy LK, Cao B, Lum CT, Kwong WL, Fung YME, Lok CN, Che CM. Shotgun Proteomics and Quantitative Pathway Analysis of the Mechanisms of Action of Dehydroeffusol, a Bioactive Phytochemical with Anticancer Activity from Juncus effusus. J Proteome Res 2018; 17:2470-2479. [PMID: 29812950 DOI: 10.1021/acs.jproteome.8b00227] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dehydroeffusol (DHE) is a phenanthrene isolated from the Chinese medicinal plant Juncus effusus. Biological evaluation of DHE reveals in vitro and in vivo anticancer effects. We performed a shotgun proteomic analysis using liquid chromatography-tandem mass spectrometry to investigate the changes in the protein profiles in cancer cells upon DHE treatment. DHE affected cancer-associated signaling pathways, including NF-κB, β-catenin, and endoplasmic reticulum stress. Through quantitative pathway and key node analysis of the proteomics data, activating transcription factor 2 (ATF-2) and c-Jun kinase (JNK) were found to be the key components in DHE's modulated biological pathways. Based on the pathway analysis as well as chemical similarity to estradiol, DHE is proposed to be a phytoestrogen. The proteomic, bioinformatic, and chemoinformatic analyses were further verified with individual cell-based experiments. Our study demonstrates a workflow for identifying the mechanisms of action of DHE through shotgun proteomic analysis.
Collapse
Affiliation(s)
- I-Sheng Chang
- Department of Chemistry, Chemical Biology Center and State Key Laboratory of Synthetic Chemistry , The University of Hong Kong , Hong Kong , China
| | - Lai-King Sy
- Department of Chemistry, Chemical Biology Center and State Key Laboratory of Synthetic Chemistry , The University of Hong Kong , Hong Kong , China
| | - Bei Cao
- Department of Chemistry, Chemical Biology Center and State Key Laboratory of Synthetic Chemistry , The University of Hong Kong , Hong Kong , China
| | - Ching Tung Lum
- Department of Chemistry, Chemical Biology Center and State Key Laboratory of Synthetic Chemistry , The University of Hong Kong , Hong Kong , China
| | - Wai-Lun Kwong
- Department of Chemistry, Chemical Biology Center and State Key Laboratory of Synthetic Chemistry , The University of Hong Kong , Hong Kong , China
| | - Yi-Man Eva Fung
- Department of Chemistry, Chemical Biology Center and State Key Laboratory of Synthetic Chemistry , The University of Hong Kong , Hong Kong , China
| | - Chun-Nam Lok
- Department of Chemistry, Chemical Biology Center and State Key Laboratory of Synthetic Chemistry , The University of Hong Kong , Hong Kong , China
| | - Chi-Ming Che
- Department of Chemistry, Chemical Biology Center and State Key Laboratory of Synthetic Chemistry , The University of Hong Kong , Hong Kong , China
| |
Collapse
|
11
|
Putri DU, Feng PH, Hsu YH, Lee KY, Jiang FW, Kuo LW, Chen YJ, Han CL. Chemotherapy Immunophenoprofiles in Non-Small-Cell Lung Cancer by Personalized Membrane Proteomics. Proteomics Clin Appl 2018; 12. [PMID: 29278294 DOI: 10.1002/prca.201700040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 11/26/2017] [Indexed: 12/13/2022]
Abstract
OBJECTIVES No study has addressed how the immune status at the molecular level is affected by first-line pemetrexed and cisplatin (PEM-CIS) combination therapy in patients with non-small-cell lung cancer (NSCLC). Thus, we aimed to identify the immune status from membrane proteome alterations in patients with NSCLC upon PEM-CIS treatment. METHODS The paired peripheral blood mononuclear cells (PBMCs) were collected from four patients with lung adenocarcinoma before and after the first regimen of PEM-CIS treatment and applied quantitative membrane proteomics analysis. RESULT In the personalized PBMC membrane proteome profiles, 2424 proteins were identified as displaying patient-specific responsive patterns. We discovered an elevated neutrophil activity and a more suppressive T-cell phenotype with the downregulation of cytotoxic T lymphocyte antigen 4 degradation and the upregulation of type 2 T-helper and T-regulatory cells in the patient with the highest progression-free survival (PFS) of 14.5 months. Patients with a PFS of 2 months showed higher expressions of T-cell subsets, MHC class II pathways, and T-cell receptor signaling, which indicated an activated immune status. CONCLUSION AND CLINICAL RELEVANCE Without the additional isolation of specific immune cell populations, our study demonstrated that PEM-CIS chemotherapy altered patients' immune system in terms of neutrophils, T cells, and antigen presentation pathways.
Collapse
Affiliation(s)
- Denise Utami Putri
- International PhD Program in Medicine, Taipei Medical University, Taipei, Taiwan.,Graduate Program, Faculty of Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Po-Hao Feng
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei, Taiwan.,Division of Pulmonary Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yuu-Hueih Hsu
- Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Kang-Yun Lee
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei, Taiwan.,Division of Pulmonary Medicine, Taipei Medical University, Taipei, Taiwan
| | - Feng-Wen Jiang
- Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Lu-Wei Kuo
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chia-Li Han
- Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| |
Collapse
|
12
|
Yang MH, Chen WJ, Fu YS, Huang B, Tsai WC, Arthur Chen YM, Lin PC, Yuan CH, Tyan YC. Utilizing glycine N-methyltransferasegene knockout mice as a model for identification of missing proteins in hepatocellular carcinoma. Oncotarget 2017; 9:442-452. [PMID: 29416626 PMCID: PMC5787479 DOI: 10.18632/oncotarget.23064] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 11/13/2017] [Indexed: 11/25/2022] Open
Abstract
Glycine N-methyltransferase is a tumor suppressor gene for hepatocellular carcinoma, which can activate DNA methylation by inducing the S-adenosylmethionine to S-adenosylhomocystine. Previous studies have indicated that the expression of Glycine N-methyltransferase is inhibited in hepatocellular carcinoma. To confirm and identify missing proteins, the pathologic analysis of the tumor-bearing mice will provide critical histologic information. Such a mouse model is applied as a screening tool for hepatocellular carcinoma as well as a strategy for missing protein discovery. In this study we designed an analysis platform using the human proteome atlas to compare the possible missing proteins to human whole chromosomes. This will integrate the information from animal studies to establish an optimal technique in the missing protein biomarker discovery.
Collapse
Affiliation(s)
- Ming-Hui Yang
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wan-Jou Chen
- Department of Medical Imaging and Radiological Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yaw-Syan Fu
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Bin Huang
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wan-Chi Tsai
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yi-Ming Arthur Chen
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan.,Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Po-Chiao Lin
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Cheng-Hui Yuan
- Mass Spectrometry Laboratory, Department of Chemistry, National University of Singapore, Singapore
| | - Yu-Chang Tyan
- Center for Infectious Disease and Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan.,Department of Medical Imaging and Radiological Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan.,Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.,Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung, Taiwan.,Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| |
Collapse
|
13
|
Elguoshy A, Hirao Y, Xu B, Saito S, Quadery AF, Yamamoto K, Mitsui T, Yamamoto T. Identification and Validation of Human Missing Proteins and Peptides in Public Proteome Databases: Data Mining Strategy. J Proteome Res 2017; 16:4403-4414. [PMID: 28980472 DOI: 10.1021/acs.jproteome.7b00423] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In an attempt to complete human proteome project (HPP), Chromosome-Centric Human Proteome Project (C-HPP) launched the journey of missing protein (MP) investigation in 2012. However, 2579 and 572 protein entries in the neXtProt (2017-1) are still considered as missing and uncertain proteins, respectively. Thus, in this study, we proposed a pipeline to analyze, identify, and validate human missing and uncertain proteins in open-access transcriptomics and proteomics databases. Analysis of RNA expression pattern for missing proteins in Human protein Atlas showed that 28% of them, such as Olfactory receptor 1I1 ( O60431 ), had no RNA expression, suggesting the necessity to consider uncommon tissues for transcriptomic and proteomic studies. Interestingly, 21% had elevated expression level in a particular tissue (tissue-enriched proteins), indicating the importance of targeting such proteins in their elevated tissues. Additionally, the analysis of RNA expression level for missing proteins showed that 95% had no or low expression level (0-10 transcripts per million), indicating that low abundance is one of the major obstacles facing the detection of missing proteins. Moreover, missing proteins are predicted to generate fewer predicted unique tryptic peptides than the identified proteins. Searching for these predicted unique tryptic peptides that correspond to missing and uncertain proteins in the experimental peptide list of open-access MS-based databases (PA, GPM) resulted in the detection of 402 missing and 19 uncertain proteins with at least two unique peptides (≥9 aa) at <(5 × 10-4)% FDR. Finally, matching the native spectra for the experimentally detected peptides with their SRMAtlas synthetic counterparts at three transition sources (QQQ, QTOF, QTRAP) gave us an opportunity to validate 41 missing proteins by ≥2 proteotypic peptides.
Collapse
Affiliation(s)
- Amr Elguoshy
- Biofluid and Biomarker Center, Niigata University , Niigata 950-2181, Japan.,Graduate School of Science and Technology, Niigata University , Niigata 950-2181, Japan.,Biotechnology Department - Faculty of Agriculture, Al-azhar University , Cairo 11651, Egypt
| | - Yoshitoshi Hirao
- Biofluid and Biomarker Center, Niigata University , Niigata 950-2181, Japan
| | - Bo Xu
- Biofluid and Biomarker Center, Niigata University , Niigata 950-2181, Japan
| | - Suguru Saito
- Biofluid and Biomarker Center, Niigata University , Niigata 950-2181, Japan
| | - Ali F Quadery
- Biofluid and Biomarker Center, Niigata University , Niigata 950-2181, Japan
| | - Keiko Yamamoto
- Biofluid and Biomarker Center, Niigata University , Niigata 950-2181, Japan
| | - Toshiaki Mitsui
- Graduate School of Science and Technology, Niigata University , Niigata 950-2181, Japan
| | - Tadashi Yamamoto
- Biofluid and Biomarker Center, Niigata University , Niigata 950-2181, Japan
| | | |
Collapse
|
14
|
Poverennaya EV, Ilgisonis EV, Ponomarenko EA, Kopylov AT, Zgoda VG, Radko SP, Lisitsa AV, Archakov AI. Why Are the Correlations between mRNA and Protein Levels so Low among the 275 Predicted Protein-Coding Genes on Human Chromosome 18? J Proteome Res 2017; 16:4311-4318. [PMID: 28956606 DOI: 10.1021/acs.jproteome.7b00348] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work targeted (selected reaction monitoring, SRM, PASSEL: PASS00697) and panoramic (shotgun LC-MS/MS, PRIDE: PXD00244) mass-spectrometric methods as well as transcriptomic analysis of the same samples using RNA-Seq and PCR methods (SRA experiment IDs: SRX341198, SRX267708, SRX395473, SRX390071) were applied for quantification of chromosome 18 encoded transcripts and proteins in human liver and HepG2 cells. The obtained data was used for the estimation of quantitative mRNA-protein ratios for the 275 genes of the selected chromosome in the selected tissues. The impact of methodological limitations of existing analytical proteomic methods on gene-specific mRNA-protein ratios and possible ways of overcoming these limitations for detection of missing proteins are also discussed.
Collapse
Affiliation(s)
| | | | | | | | - Victor G Zgoda
- Institute of Biomedical Chemistry RAS , 119121 Moscow, Russia
| | - Sergey P Radko
- Institute of Biomedical Chemistry RAS , 119121 Moscow, Russia
| | | | | |
Collapse
|
15
|
Zhao Q, Fang F, Shan Y, Sui Z, Zhao B, Liang Z, Zhang L, Zhang Y. In-Depth Proteome Coverage by Improving Efficiency for Membrane Proteome Analysis. Anal Chem 2017; 89:5179-5185. [DOI: 10.1021/acs.analchem.6b04232] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Qun Zhao
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Fei Fang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yichu Shan
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Zhigang Sui
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Baofeng Zhao
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Zhen Liang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Lihua Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Yukui Zhang
- Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| |
Collapse
|
16
|
Nagao H, Nishizawa H, Bamba T, Nakayama Y, Isozumi N, Nagamori S, Kanai Y, Tanaka Y, Kita S, Fukuda S, Funahashi T, Maeda N, Fukusaki E, Shimomura I. Increased Dynamics of Tricarboxylic Acid Cycle and Glutamate Synthesis in Obese Adipose Tissue: IN VIVO METABOLIC TURNOVER ANALYSIS. J Biol Chem 2017; 292:4469-4483. [PMID: 28119455 DOI: 10.1074/jbc.m116.770172] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 01/06/2017] [Indexed: 01/20/2023] Open
Abstract
Obesity is closely associated with various metabolic disorders. However, little is known about abnormalities in the metabolic change of obese adipose tissue. Here we use static metabolic analysis and in vivo metabolic turnover analysis to assess metabolic dynamics in obese mice. The static metabolic analyses showed that glutamate and constitutive metabolites of the TCA cycle were increased in the white adipose tissue (WAT) of ob/ob and diet-induced obesity mice but not in the liver or skeletal muscle of these obese mice. Moreover, in vivo metabolic turnover analyses demonstrated that these glucose-derived metabolites were dynamically and specifically produced in obese WAT compared with lean WAT. Glutamate rise in obese WAT was associated with down-regulation of glutamate aspartate transporter (GLAST), a major glutamate transporter for adipocytes, and low uptake of glutamate into adipose tissue. In adipocytes, glutamate treatment reduced adiponectin secretion and insulin-mediated glucose uptake and phosphorylation of Akt. These data suggest that a high intra-adipocyte glutamate level potentially relates to adipocyte dysfunction in obesity. This study provides novel insights into metabolic dysfunction in obesity through comprehensive application of in vivo metabolic turnover analysis in two obese animal models.
Collapse
Affiliation(s)
| | | | - Takeshi Bamba
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yasumune Nakayama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | | | | | | | | | - Shunbun Kita
- From the Departments of Metabolic Medicine.,Metabolism and Atherosclerosis, Graduate School of Medicine, and
| | | | - Tohru Funahashi
- From the Departments of Metabolic Medicine.,Metabolism and Atherosclerosis, Graduate School of Medicine, and
| | - Norikazu Maeda
- From the Departments of Metabolic Medicine.,Metabolism and Atherosclerosis, Graduate School of Medicine, and
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | | |
Collapse
|
17
|
Ruprecht B, Zecha J, Zolg DP, Kuster B. High pH Reversed-Phase Micro-Columns for Simple, Sensitive, and Efficient Fractionation of Proteome and (TMT labeled) Phosphoproteome Digests. Methods Mol Biol 2017; 1550:83-98. [PMID: 28188525 DOI: 10.1007/978-1-4939-6747-6_8] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Despite recent advances in mass spectrometric sequencing speed and improved sensitivity, the in-depth analysis of proteomes still widely relies on off-line peptide separation and fractionation to deal with the enormous molecular complexity of shotgun digested proteomes. While a multitude of methods has been established for off-line peptide separation using HPLC columns, their use can be limited particularly when sample quantities are scarce. In this protocol, we describe an approach which combines high pH reversed-phase peptide separation into few fractions in StageTip micro-columns. This miniaturized sample preparation method enhances peptide recovery and hence improves sensitivity. This is particularly useful when working with limited sample amounts obtained from e.g., phosphopeptide enrichments or tissue biopsies. Essentially the same approach can also be applied for multiplexed analysis using tandem mass tags (TMT) and can be parallelized in order to deliver the required throughput. Here, we provide a step-by-step protocol for TMT6plex labeling of peptides, the construction of StageTips, sample fractionation and pooling schemes adjusted to different types of analytes, mass spectrometric sample measurement, and downstream data processing using MaxQuant. To illustrate the expected results using this protocol, we provide results from an unlabeled and a TMT6plex labeled phosphopeptide sample leading to the identification of >17,000 phosphopeptides in 8 h (Q Exactive HF) and >23,000 TMT6plex labeled phosphopeptides (Q Exactive Plus) in 12 h of measurement time. Importantly, this protocol is equally applicable to the fractionation of full proteome digests.
Collapse
Affiliation(s)
- Benjamin Ruprecht
- Technische Universität München, Emil Erlenmeyer Forum 5, 85354, Freising, Germany
- Center for Integrated Protein Science Munich (CIPSM), Freising, Germany
| | - Jana Zecha
- Technische Universität München, Emil Erlenmeyer Forum 5, 85354, Freising, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniel P Zolg
- Technische Universität München, Emil Erlenmeyer Forum 5, 85354, Freising, Germany
| | - Bernhard Kuster
- Technische Universität München, Emil Erlenmeyer Forum 5, 85354, Freising, Germany.
- Center for Integrated Protein Science Munich (CIPSM), Freising, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Bavarian Bimolecular Mass Spectrometry Center, Technische Universität München, Freising, Germany.
| |
Collapse
|
18
|
Zhang X. Detergents: Friends not foes for high-performance membrane proteomics toward precision medicine. Proteomics 2016; 17. [PMID: 27633951 DOI: 10.1002/pmic.201600209] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 07/31/2016] [Accepted: 09/13/2016] [Indexed: 01/05/2023]
Abstract
Precision medicine, particularly therapeutics, emphasizes the atomic-precise, dynamic, and systems visualization of human membrane proteins and their endogenous modifiers. For years, bottom-up proteomics has grappled with removing and avoiding detergents, yet faltered at the therapeutic-pivotal membrane proteins, which have been tackled by classical approaches and are known for decades refractory to single-phase aqueous or organic denaturants. Hydrophobicity and aggregation commonly challenge tissue and cell lysates, biofluids, and enriched samples. Frequently, expected membrane proteins and peptides are not identified by shotgun bottom-up proteomics, let alone robust quantitation. This review argues the cause of this proteomic crisis is not detergents per se, but the choice of detergents. Recently, inclusion of compatible detergents for membrane protein extraction and digestion has revealed stark improvements in both quantitative and structural proteomics. This review analyzes detergent properties behind recent proteomic advances, and proposes that rational use of detergents may reconcile outstanding membrane proteomics dilemmas, enabling ultradeep coverage and minimal artifacts for robust protein and endogenous PTM measurements. The simplicity of detergent tools confers bottom-up membrane proteomics the sophistication toward precision medicine.
Collapse
Affiliation(s)
- Xi Zhang
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
19
|
Wei W, Luo W, Wu F, Peng X, Zhang Y, Zhang M, Zhao Y, Su N, Qi Y, Chen L, Zhang Y, Wen B, He F, Xu P. Deep Coverage Proteomics Identifies More Low-Abundance Missing Proteins in Human Testis Tissue with Q-Exactive HF Mass Spectrometer. J Proteome Res 2016; 15:3988-3997. [PMID: 27535590 DOI: 10.1021/acs.jproteome.6b00390] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Since 2012, missing proteins (MPs) investigation has been one of the critical missions of Chromosome-Centric Human Proteome Project (C-HPP) through various biochemical strategies. On the basis of our previous testis MPs study, faster scanning and higher resolution mass-spectrometry-based proteomics might be conducive to MPs exploration, especially for low-abundance proteins. In this study, Q-Exactive HF (HF) was used to survey proteins from the same testis tissues separated by two separating methods (tricine- and glycine-SDS-PAGE), as previously described. A total of 8526 proteins were identified, of which more low-abundance proteins were uniquely detected in HF data but not in our previous LTQ Orbitrap Velos (Velos) reanalysis data. Further transcriptomics analysis showed that these uniquely identified proteins by HF also had lower expression at the mRNA level. Of the 81 total identified MPs, 74 and 39 proteins were listed as MPs in HF and Velos data sets, respectively. Among the above MPs, 47 proteins (43 neXtProt PE2 and 4 PE3) were ranked as confirmed MPs after verifying with the stringent spectra match and isobaric and single amino acid variants filtering. Functional investigation of these 47 MPs revealed that 11 MPs were testis-specific proteins and 7 MPs were involved in spermatogenesis process. Therefore, we concluded that higher scanning speed and resolution of HF might be factors for improving the low-abundance MP identification in future C-HPP studies. All mass-spectrometry data from this study have been deposited in the ProteomeXchange with identifier PXD004092.
Collapse
Affiliation(s)
- Wei Wei
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, Beijing Institute of Radiation Medicine , Beijing 102206, China
| | - Weijia Luo
- Graduate School, Anhui Medical University , Hefei 230032, China
| | - Feilin Wu
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, Beijing Institute of Radiation Medicine , Beijing 102206, China.,Life Science College, Southwest Forestry University , Kunming, 650224, China
| | - Xuehui Peng
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, Beijing Institute of Radiation Medicine , Beijing 102206, China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of the Ministry of Education, School of Pharmaceutical Sciences, Wuhan University , Wuhan 430072, China
| | - Yao Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, Beijing Institute of Radiation Medicine , Beijing 102206, China.,Institute of Microbiology , Chinese Academy of Science, Beijing 100101, China
| | - Manli Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, Beijing Institute of Radiation Medicine , Beijing 102206, China
| | - Yan Zhao
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, Beijing Institute of Radiation Medicine , Beijing 102206, China
| | - Na Su
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, Beijing Institute of Radiation Medicine , Beijing 102206, China
| | - YingZi Qi
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, Beijing Institute of Radiation Medicine , Beijing 102206, China
| | - Lingsheng Chen
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, Beijing Institute of Radiation Medicine , Beijing 102206, China
| | - Yangjun Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, Beijing Institute of Radiation Medicine , Beijing 102206, China
| | - Bo Wen
- BGI-Shenzhen , Shenzhen 518083, China
| | - Fuchu He
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, Beijing Institute of Radiation Medicine , Beijing 102206, China
| | - Ping Xu
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Proteome Research Center, National Engineering Research Center for Protein Drugs, Beijing Institute of Radiation Medicine , Beijing 102206, China.,Graduate School, Anhui Medical University , Hefei 230032, China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of the Ministry of Education, School of Pharmaceutical Sciences, Wuhan University , Wuhan 430072, China
| |
Collapse
|
20
|
Vandenbrouck Y, Lane L, Carapito C, Duek P, Rondel K, Bruley C, Macron C, Gonzalez de Peredo A, Couté Y, Chaoui K, Com E, Gateau A, Hesse AM, Marcellin M, Méar L, Mouton-Barbosa E, Robin T, Burlet-Schiltz O, Cianferani S, Ferro M, Fréour T, Lindskog C, Garin J, Pineau C. Looking for Missing Proteins in the Proteome of Human Spermatozoa: An Update. J Proteome Res 2016; 15:3998-4019. [PMID: 27444420 DOI: 10.1021/acs.jproteome.6b00400] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The Chromosome-Centric Human Proteome Project (C-HPP) aims to identify "missing" proteins in the neXtProt knowledgebase. We present an in-depth proteomics analysis of the human sperm proteome to identify testis-enriched missing proteins. Using protein extraction procedures and LC-MS/MS analysis, we detected 235 proteins (PE2-PE4) for which no previous evidence of protein expression was annotated. Through LC-MS/MS and LC-PRM analysis, data mining, and immunohistochemistry, we confirmed the expression of 206 missing proteins (PE2-PE4) in line with current HPP guidelines (version 2.0). Parallel reaction monitoring acquisition and sythetic heavy labeled peptides targeted 36 ≪one-hit wonder≫ candidates selected based on prior peptide spectrum match assessment. 24 were validated with additional predicted and specifically targeted peptides. Evidence was found for 16 more missing proteins using immunohistochemistry on human testis sections. The expression pattern for some of these proteins was specific to the testis, and they could possibly be valuable markers with fertility assessment applications. Strong evidence was also found of four "uncertain" proteins (PE5); their status should be re-examined. We show how using a range of sample preparation techniques combined with MS-based analysis, expert knowledge, and complementary antibody-based techniques can produce data of interest to the community. All MS/MS data are available via ProteomeXchange under identifier PXD003947. In addition to contributing to the C-HPP, we hope these data will stimulate continued exploration of the sperm proteome.
Collapse
Affiliation(s)
- Yves Vandenbrouck
- CEA, DRF, BIG, Laboratoire de Biologie à Grande Echelle, 17 rue des martyrs, Grenoble F-38054, France.,Inserm U1038 , 17, rue des Martyrs, Grenoble F-38054, France.,Université de Grenoble , Grenoble F-38054, France
| | - Lydie Lane
- Department of Human Protein Sciences, Faculty of Medicine, University of Geneva , 1, rue Michel-Servet, 1211 Geneva 4, Switzerland.,CALIPHO Group, SIB-Swiss Institute of Bioinformatics, CMU , rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS UMR7178, 25 Rue Becquerel, 67087 Strasbourg, France
| | - Paula Duek
- CALIPHO Group, SIB-Swiss Institute of Bioinformatics, CMU , rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland
| | - Karine Rondel
- Protim, Inserm U1085, Irset, Campus de Beaulieu, Rennes 35042, France
| | - Christophe Bruley
- CEA, DRF, BIG, Laboratoire de Biologie à Grande Echelle, 17 rue des martyrs, Grenoble F-38054, France.,Inserm U1038 , 17, rue des Martyrs, Grenoble F-38054, France.,Université de Grenoble , Grenoble F-38054, France
| | - Charlotte Macron
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS UMR7178, 25 Rue Becquerel, 67087 Strasbourg, France
| | - Anne Gonzalez de Peredo
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Yohann Couté
- CEA, DRF, BIG, Laboratoire de Biologie à Grande Echelle, 17 rue des martyrs, Grenoble F-38054, France.,Inserm U1038 , 17, rue des Martyrs, Grenoble F-38054, France.,Université de Grenoble , Grenoble F-38054, France
| | - Karima Chaoui
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Emmanuelle Com
- Protim, Inserm U1085, Irset, Campus de Beaulieu, Rennes 35042, France
| | - Alain Gateau
- CALIPHO Group, SIB-Swiss Institute of Bioinformatics, CMU , rue Michel-Servet 1, CH-1211 Geneva 4, Switzerland
| | - Anne-Marie Hesse
- CEA, DRF, BIG, Laboratoire de Biologie à Grande Echelle, 17 rue des martyrs, Grenoble F-38054, France.,Inserm U1038 , 17, rue des Martyrs, Grenoble F-38054, France.,Université de Grenoble , Grenoble F-38054, France
| | - Marlene Marcellin
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Loren Méar
- Protim, Inserm U1085, Irset, Campus de Beaulieu, Rennes 35042, France
| | - Emmanuelle Mouton-Barbosa
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Thibault Robin
- Proteome Informatics Group, Centre Universitaire d'Informatique , Route de Drize 7, 1227 Carouge, CH, Switzerland
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Sarah Cianferani
- Laboratoire de Spectrométrie de Masse BioOrganique (LSMBO), IPHC, Université de Strasbourg, CNRS UMR7178, 25 Rue Becquerel, 67087 Strasbourg, France
| | - Myriam Ferro
- CEA, DRF, BIG, Laboratoire de Biologie à Grande Echelle, 17 rue des martyrs, Grenoble F-38054, France.,Inserm U1038 , 17, rue des Martyrs, Grenoble F-38054, France.,Université de Grenoble , Grenoble F-38054, France
| | - Thomas Fréour
- Service de Médecine de la Reproduction, CHU de Nantes , 38 boulevard Jean Monnet, 44093 Nantes cedex, France.,INSERM UMR1064 , Nantes 44093, France
| | - Cecilia Lindskog
- CEA, DRF, BIG, Laboratoire de Biologie à Grande Echelle, 17 rue des martyrs, Grenoble F-38054, France.,Inserm U1038 , 17, rue des Martyrs, Grenoble F-38054, France
| | - Jérôme Garin
- CEA, DRF, BIG, Laboratoire de Biologie à Grande Echelle, 17 rue des martyrs, Grenoble F-38054, France.,Inserm U1038 , 17, rue des Martyrs, Grenoble F-38054, France.,Université de Grenoble , Grenoble F-38054, France
| | - Charles Pineau
- Protim, Inserm U1085, Irset, Campus de Beaulieu, Rennes 35042, France
| |
Collapse
|
21
|
Elguoshy A, Magdeldin S, Xu B, Hirao Y, Zhang Y, Kinoshita N, Takisawa Y, Nameta M, Yamamoto K, El-Refy A, El-Fiky F, Yamamoto T. Why are they missing? : Bioinformatics characterization of missing human proteins. J Proteomics 2016; 149:7-14. [PMID: 27535355 DOI: 10.1016/j.jprot.2016.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 07/17/2016] [Accepted: 08/08/2016] [Indexed: 12/19/2022]
Abstract
NeXtProt is a web-based protein knowledge platform that supports research on human proteins. NeXtProt (release 2015-04-28) lists 20,060 proteins, among them, 3373 canonical proteins (16.8%) lack credible experimental evidence at protein level (PE2:PE5). Therefore, they are considered as "missing proteins". A comprehensive bioinformatic workflow has been proposed to analyze these "missing" proteins. The aims of current study were to analyze physicochemical properties, existence and distribution of the tryptic cleavage sites, and to pinpoint the signature peptides of the missing proteins. Our findings showed that 23.7% of missing proteins were hydrophobic proteins possessing transmembrane domains (TMD). Also, forty missing entries generate tryptic peptides were either out of mass detection range (>30aa) or mapped to different proteins (<9aa). Additionally, 21% of missing entries didn't generate any unique tryptic peptides. In silico endopeptidase combination strategy increased the possibility of missing proteins identification. Coherently, using both mature protein database and signal peptidome database could be a promising option to identify some missing proteins by targeting their unique N-terminal tryptic peptide from mature protein database and or C-terminus tryptic peptide from signal peptidome database. In conclusion, Identification of missing protein requires additional consideration during sample preparation, extraction, digestion and data analysis to increase its incidence of identification.
Collapse
Affiliation(s)
- Amr Elguoshy
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan; Biotechnology Department, Faculty of Agriculture, Al-Azhar University, Cairo 11682, Egypt
| | - Sameh Magdeldin
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan; Department of Physiology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Bo Xu
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan
| | - Yoshitoshi Hirao
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan
| | - Ying Zhang
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan
| | - Naohiko Kinoshita
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan
| | - Yusuke Takisawa
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan
| | - Masaaki Nameta
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan
| | - Keiko Yamamoto
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan
| | - Ali El-Refy
- Biotechnology Department, Faculty of Agriculture, Al-Azhar University, Cairo 11682, Egypt
| | - Fawzy El-Fiky
- Biotechnology Department, Faculty of Agriculture, Al-Azhar University, Cairo 11682, Egypt
| | - Tadashi Yamamoto
- Biofluid Biomarker Center, Institute of Social innovation and Co-operation, Niigata University, Niigata 951-2181, Japan.
| |
Collapse
|
22
|
Paik YK, Omenn GS, Overall CM, Deutsch EW, Hancock WS. Recent Advances in the Chromosome-Centric Human Proteome Project: Missing Proteins in the Spot Light. J Proteome Res 2016; 14:3409-14. [PMID: 26337862 DOI: 10.1021/acs.jproteome.5b00785] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Young-Ki Paik
- Yonsei Proteome Research Center, Yonsei University , Seoul 120-749, Korea
| | - Gilbert S Omenn
- Center for Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, Michigan 48109, United States.,Yonsei Proteome Research Center, Yonsei University , Seoul 120-749, Korea
| | - Christopher M Overall
- Department of Biochemistry and Molecular Biology, University of British Columbia , Vancouver, British Columbia V6T 1Z3, Canada.,Yonsei Proteome Research Center, Yonsei University , Seoul 120-749, Korea
| | - Eric W Deutsch
- Institute for Systems Biology , Seattle, Washington 98109, United States.,Yonsei Proteome Research Center, Yonsei University , Seoul 120-749, Korea
| | - William S Hancock
- Department of Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States.,Yonsei Proteome Research Center, Yonsei University , Seoul 120-749, Korea
| |
Collapse
|
23
|
Yee KMP, Feener EP, Madigan M, Jackson NJ, Gao BB, Ross-Cisneros FN, Provis J, Aiello LP, Sadun AA, Sebag J. Proteomic Analysis of Embryonic and Young Human Vitreous. Invest Ophthalmol Vis Sci 2016; 56:7036-42. [PMID: 26529037 DOI: 10.1167/iovs.15-16809] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
PURPOSE The proteomic profile of vitreous from second-trimester human embryos and young adults was characterized using mass spectrometry and analyzed for changes in protein levels that may relate to structural changes occurring during this time. This vitreous proteome was compared to previous reports to confirm proteins already identified and reveal novel ones. METHODS Vitreous from 17 human embryos aged 14 to 20 weeks gestation (WG) and from a 12-, a 14-, a 15-, and a 28-year-old was individually analyzed using tandem mass spectrometry-based proteomics. Peptide spectral count associations with embryonic age were assessed using a general linear model of fold changes and Spearman's rank correlation. Differences between embryonic and young adult vitreous proteomes were also compared. Immunohistochemistry was used to evaluate three proteins in five additional fetal (10-18 WG) human eyes. RESULTS There were 1217 proteins identified in fetal and young adult human vitreous, 206 after quantile normalization and variance filtering. In embryos, the peptide counts of 37 proteins changed significantly from 14 to 20 WG: 75.7% increased, 24.3% decreased. Immunohistochemistry confirmed the absence of clusterin and cadherin in 10 and 14 WG eyes and their presence at 18 WG. Comparing embryonic to young adult vitreous, 47 proteins were significantly higher or lower. A total of 768 proteins not previously identified in the literature are presented. CONCLUSIONS Proteins previously unreported in the human vitreous were identified. The human vitreous proteome undergoes significant changes during embryogenesis and young adulthood. A number of protein levels change considerably during the second trimester, with the majority decreasing.
Collapse
Affiliation(s)
- Kenneth M P Yee
- VMR Institute for Vitreous Macula Retina, Huntington Beach, California, United States 2Doheny Eye Institute, Los Angeles, California, United States
| | - Edward P Feener
- Beetham Eye Institute, Joslin Diabetes Center, Boston, Massachusetts, United States
| | - Michele Madigan
- School of Optometry and Vision Science, University of New South Wales, Sydney, Australia 5Save Sight Institute, University of Sydney, Sydney, Australia
| | - Nicholas J Jackson
- Department of Medicine Statistics Core, David Geffen School of Medicine at UCLA, Los Angeles, California, United States
| | - Ben-Bo Gao
- Beetham Eye Institute, Joslin Diabetes Center, Boston, Massachusetts, United States
| | | | - Jan Provis
- John Curtin School of Medical Research, Canberra, Australia 8Australian National University, Canberra, Australia
| | - Lloyd Paul Aiello
- Beetham Eye Institute, Joslin Diabetes Center, Boston, Massachusetts, United States 9Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, United States
| | - Alfredo A Sadun
- Doheny Eye Institute, Los Angeles, California, United States 10Department of Ophthalmology, David Geffen School of Medicine at UCLA, Los Angeles, California, United States
| | - J Sebag
- VMR Institute for Vitreous Macula Retina, Huntington Beach, California, United States 2Doheny Eye Institute, Los Angeles, California, United States
| |
Collapse
|