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Meta-Analysis of MS-Based Proteomics Studies Indicates Interferon Regulatory Factor 4 and Nucleobindin1 as Potential Prognostic and Drug Resistance Biomarkers in Diffuse Large B Cell Lymphoma. Cells 2023; 12:cells12010196. [PMID: 36611989 PMCID: PMC9818977 DOI: 10.3390/cells12010196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/20/2022] [Accepted: 12/26/2022] [Indexed: 01/06/2023] Open
Abstract
The prognosis of diffuse large B cell lymphoma (DLBCL) is inaccurately predicted using clinical features and immunohistochemistry (IHC) algorithms. Nomination of a panel of molecules as the target for therapy and predicting prognosis in DLBCL is challenging because of the divergences in the results of molecular studies. Mass spectrometry (MS)-based proteomics in the clinic represents an analytical tool with the potential to improve DLBCL diagnosis and prognosis. Previous proteomics studies using MS-based proteomics identified a wide range of proteins. To achieve a consensus, we reviewed MS-based proteomics studies and extracted the most consistently significantly dysregulated proteins. These proteins were then further explored by analyzing data from other omics fields. Among all significantly regulated proteins, interferon regulatory factor 4 (IRF4) was identified as a potential target by proteomics, genomics, and IHC. Moreover, annexinA5 (ANXA5) and nucleobindin1 (NUCB1) were two of the most up-regulated proteins identified in MS studies. Functional enrichment analysis identified the light zone reactions of the germinal center (LZ-GC) together with cytoskeleton locomotion functions as enriched based on consistent, significantly dysregulated proteins. In this study, we suggest IRF4 and NUCB1 proteins as potential biomarkers that deserve further investigation in the field of DLBCL sub-classification and prognosis.
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Jin Y, Wang W, Wang Q, Zhang Y, Zahid KR, Raza U, Gong Y. Alpha-1-antichymotrypsin as a novel biomarker for diagnosis, prognosis, and therapy prediction in human diseases. Cancer Cell Int 2022; 22:156. [PMID: 35439996 PMCID: PMC9019971 DOI: 10.1186/s12935-022-02572-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 04/06/2022] [Indexed: 12/15/2022] Open
Abstract
The glycoprotein alpha-1-antichymotrypsin (AACT), a serine protease inhibitor, is mainly synthesized in the liver and then secreted into the blood and is involved in the acute phase response, inflammation, and proteolysis. The dysregulation of AACT and its glycosylation levels are associated with tumor progression and recurrence, and could be used as a biomarker for tumor monitoring. In this review, we summarized the expression level, glycosylation modification, and biological characteristics of AACT during inflammation, neurodegenerative or other elderly diseases, and tumorigenesis, as well as, focused on the biological roles of AACT in cancer. The aberrant expression of AACT in cancer might be due to genetic alterations and/or immune by bioinformatics analysis. Moreover, AACT may serve as a diagnostic or prognostic biomarker or therapeutic target in tumors. Furthermore, we found that the expression of AACT was associated with the overall survival of patients with human cancers. Decreased AACT expression was associated with poor survival in patients with liver cancer, increased AACT expression was associated with shorter survival in patients with pancreatic cancer, and decreased AACT expression was associated with shorter survival in patients with early lung cancer. The review confirmed the key roles of AACT in tumorigenesis, suggesting that the glycoprotein AACT may serve as a biomarker for tumor diagnosis and prognosis, and could be a potential therapeutic target for human diseases.
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Affiliation(s)
- Yanxia Jin
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, College of Life Sciences, Hubei Normal University, No. 11 Cihu Road, Huangshi District, Huangshi, 435002, China
| | - Weidong Wang
- College of Life Sciences, Hubei Normal University, No. 11 Cihu Road, Huangshi District, Huangshi, 435002, China.
| | - Qiyun Wang
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, College of Life Sciences, Hubei Normal University, No. 11 Cihu Road, Huangshi District, Huangshi, 435002, China
| | - Yueyang Zhang
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, College of Life Sciences, Hubei Normal University, No. 11 Cihu Road, Huangshi District, Huangshi, 435002, China
| | - Kashif Rafiq Zahid
- Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Science and Oceanography, Carson International Cancer Center, Shenzhen University, Shenzhen, Guangdong, China
| | - Umar Raza
- Department of Biological Sciences, National University of Medical Sciences (NUMS), PWD Campus, Rawalpindi, Pakistan
| | - Yongsheng Gong
- Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, No.26 Daoqian Street, Suzhou, 215002, China.
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Quantitative proteomics analysis of differentially expressed proteins in activated B-cell-like diffuse large B-cell lymphoma using quantitative proteomics. Pathol Res Pract 2019; 215:152528. [DOI: 10.1016/j.prp.2019.152528] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 06/10/2019] [Accepted: 07/05/2019] [Indexed: 12/31/2022]
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Supraphysiological Levels of Oxygen Exposure During the Neonatal Period Impairs Signaling Pathways Required for Learning and Memory. Sci Rep 2018; 8:9914. [PMID: 29967535 PMCID: PMC6028393 DOI: 10.1038/s41598-018-28220-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 06/04/2018] [Indexed: 12/31/2022] Open
Abstract
Preterm infants often require prolonged oxygen supplementation and are at high risk of neurodevelopmental impairment. We recently reported that adult mice exposed to neonatal hyperoxia (postnatal day [P] 2 to 14) had spatial navigation memory deficits associated with hippocampal shrinkage. The mechanisms by which early oxidative stress impair neurodevelopment are not known. Our objective was to identify early hyperoxia-induced alterations in hippocampal receptors and signaling pathways necessary for memory formation. We evaluated C57BL/6 mouse pups at P14, exposed to either 85% oxygen or air from P2 to 14. We performed targeted analysis of hippocampal ligand-gated ion channels and proteins necessary for memory formation, and global bioinformatic analysis of differentially expressed hippocampal genes and proteins. Hyperoxia decreased hippocampal mGLU7, TrkB, AKT, ERK2, mTORC1, RPS6, and EIF4E and increased α3, α5, and ɤ2 subunits of GABAA receptor and PTEN proteins, although changes in gene expression were not always concordant. Bioinformatic analysis indicated dysfunction in mitochondria and global protein synthesis and translational processes. In conclusion, supraphysiological oxygen exposure reduced proteins necessary for hippocampus-dependent memory formation and may adversely impact hippocampal mitochondrial function and global protein synthesis. These early hippocampal changes may account for memory deficits seen in preterm survivors following prolonged oxygen supplementation.
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Xu N, Ma C, Ou J, Sun WW, Zhou L, Hu H, Liu XM. Comparative Proteomic Analysis of Three Chinese Hamster Ovary (CHO) Host Cells. Biochem Eng J 2017; 124:122-129. [PMID: 28736500 DOI: 10.1016/j.bej.2017.05.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Chinese hamster ovary (CHO) cells have been widely used to express heterologous genes and produce therapeutic proteins in biopharmaceutical industry. Different CHO host cells have distinct cell growth rates and protein expression characteristics. In this study, the expression of about 1,307 host proteins in three sublines, i.e. CHO K1, CHO S and CHO/dihydrofolate reductase (dhfr)- , were investigated and compared using proteomic analysis. The proteins involved in cell growth, glycolysis, tricarboxylic acid cycle, transcription, translation and glycosylation were quantitated using Liquid chromatography tandem-mass spectrometry (LC-MS/MS). The key host cell proteins that regulate the kinetics of cell growth and the magnitude of protein expression levels were identified. Furthermore, several rational cell engineering strategies on how to combine the desired features of fast cell growth and efficient production of therapeutic proteins into one new super CHO host cell have been proposed.
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Affiliation(s)
- Ningning Xu
- Department of Biomedical Engineering, University of Alabama at Birmingham (UAB), 1670 University Blvd, Birmingham, AL 35233, USA
| | - Chao Ma
- Department of Biomedical Engineering, University of Alabama at Birmingham (UAB), 1670 University Blvd, Birmingham, AL 35233, USA
| | - Jianfa Ou
- Department of Biomedical Engineering, University of Alabama at Birmingham (UAB), 1670 University Blvd, Birmingham, AL 35233, USA
| | - Wanqi Wendy Sun
- Department of Chemical and Biological Engineering, The University of Alabama (UA), 245 7th Avenue, Tuscaloosa, AL 35401, USA
| | - Lufang Zhou
- Departments of Medicine and Biomedical Engineering, University of Alabama at Birmingham (UAB), 703 19 Street South and 1530 3 Avenue South, Birmingham, AL 35294, USA
| | - Hui Hu
- Department of Microbiology, University of Alabama at Birmingham (UAB), 845 19 Street South, Birmingham AL 35294, USA
| | - Xiaoguang Margaret Liu
- Department of Biomedical Engineering, University of Alabama at Birmingham (UAB), 1670 University Blvd, Birmingham, AL 35233, USA
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Galicia N, Dégano R, Díez P, González-González M, Góngora R, Ibarrola N, Fuentes M. CSF analysis for protein biomarker identification in patients with leptomeningeal metastases from CNS lymphoma. Expert Rev Proteomics 2017; 14:363-372. [DOI: 10.1080/14789450.2017.1307106] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- N. Galicia
- Proteomics Unit, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
| | - R. Dégano
- Proteomics Unit, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
| | - P. Díez
- Proteomics Unit, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
- Department of Medicine and General Service of Cytometry, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
| | - M. González-González
- Proteomics Unit, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
- Department of Medicine and General Service of Cytometry, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
| | - R. Góngora
- Department of Medicine and General Service of Cytometry, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
| | - N. Ibarrola
- Proteomics Unit, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
| | - M. Fuentes
- Proteomics Unit, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
- Department of Medicine and General Service of Cytometry, Cancer Research Centre, IBSAL, University of Salamanca-CSIC, Salamanca, Spain
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