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Yang TH, Syu GD, Chen CS, Chen GR, Jhong SE, Lin PH, Lin PC, Wang YC, Shah P, Tseng YY, Wu WS. BAPCP: A comprehensive and user-friendly web tool for identifying biomarkers from protein microarray technologies. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2024; 254:108260. [PMID: 38878357 DOI: 10.1016/j.cmpb.2024.108260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 04/06/2024] [Accepted: 05/29/2024] [Indexed: 07/28/2024]
Abstract
BACKGROUND AND OBJECTIVE Proteome microarrays are one of the popular high-throughput screening methods for large-scale investigation of protein interactions in cells. These interactions can be measured on protein chips when coupled with fluorescence-labeled probes, helping indicate potential biomarkers or discover drugs. Several computational tools were developed to help analyze the protein chip results. However, existing tools fail to provide a user-friendly interface for biologists and present only one or two data analysis methods suitable for limited experimental designs, restricting the use cases. METHODS In order to facilitate the biomarker examination using protein chips, we implemented a user-friendly and comprehensive web tool called BAPCP (Biomarker Analysis tool for Protein Chip Platforms) in this research to deal with diverse chip data distributions. RESULTS BAPCP is well integrated with standard chip result files and includes 7 data normalization methods and 7 custom-designed quality control/differential analysis filters for biomarker extraction among experiment groups. Moreover, it can handle cost-efficient chip designs that repeat several blocks/samples within one single slide. Using experiments of the human coronavirus (HCoV) protein microarray and the E. coli proteome chip that helps study the immune response of Kawasaki disease as examples, we demonstrated that BAPCP can accelerate the time-consuming week-long manual biomarker identification process to merely 3 min. CONCLUSIONS The developed BAPCP tool provides substantial analysis support for protein interaction studies and conforms to the necessity of expanding computer usage and exchanging information in bioscience and medicine. The web service of BAPCP is available at https://cosbi.ee.ncku.edu.tw/BAPCP/.
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Affiliation(s)
- Tzu-Hsien Yang
- Department of Biomedical Engineering, National Cheng Kung University, No. 1, University Road, 701 Tainan, Taiwan; Medical Device Innovation Center, National Cheng Kung University, No. 1, University Road, Tainan City 701, Taiwan.
| | - Guan-Da Syu
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, No. 1, University Road, 701 Tainan, Taiwan; Medical Device Innovation Center, National Cheng Kung University, No. 1, University Road, Tainan City 701, Taiwan; International Center for Wound Repair and Regeneration, National Cheng Kung University, No. 1, University Road, Tainan 701, Taiwan.
| | - Chien-Sheng Chen
- Department of Food Safety/Hygiene and Risk Management, National Cheng Kung University, No. 1, University Road, 701 Tainan, Taiwan.
| | - Guan-Ru Chen
- Department of Electrical Engineering, National Cheng Kung University, No. 1, University Road, 701 Tainan, Taiwan.
| | - Song-En Jhong
- Department of Electrical Engineering, National Cheng Kung University, No. 1, University Road, 701 Tainan, Taiwan.
| | - Po-Heng Lin
- Department of Electrical Engineering, National Cheng Kung University, No. 1, University Road, 701 Tainan, Taiwan.
| | - Pei-Chun Lin
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, No. 1, University Road, 701 Tainan, Taiwan.
| | - Yun-Cih Wang
- Department of Electrical Engineering, National Cheng Kung University, No. 1, University Road, 701 Tainan, Taiwan.
| | - Pramod Shah
- Institute of Systems Biology and Bioinformatics, Department of Biomedical Sciences and Engineering, College of Health Sciences and Technology, National Central University, No. 300, Zhongda Rd., Zhongli District, 320317 Taoyuan, Taiwan.
| | - Yan-Yuan Tseng
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, MI 48201, USA.
| | - Wei-Sheng Wu
- Department of Electrical Engineering, National Cheng Kung University, No. 1, University Road, 701 Tainan, Taiwan.
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Time series proteome profile analysis reveals a protective role of citrate synthase in angiotensin II-induced atrial fibrillation. J Hypertens 2022; 40:765-775. [PMID: 35013064 PMCID: PMC8901035 DOI: 10.1097/hjh.0000000000003075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND Angiotensin (Ang) II and elevated blood pressure are considered to be the main risk factors for atrial fibrillation. However, the proteome profiles and key mediators/signaling pathways involved in the development of Ang II-induced atrial fibrillation remain unclear. METHODS Male wild-type C57BL/6 mice (10-week old) were infused with Ang II (2000 ng/kg per min) for 1, 2, or 3 weeks, respectively. Time series proteome profiling of atrial tissues was performed using isobaric tags for relative and absolute quantitation and liquid chromatography coupled with tandem mass spectrometry. RESULTS We identified a total of 1566 differentially expressed proteins (DEPs) in the atrial tissues at weeks 1, 2, and 3 after Ang II infusion. These DEPs were predominantly involved in mitochondrial oxidation-reduction and tricarboxylic acid cycle in Ang II-infused atria. Moreover, coexpression network analysis revealed that citrate synthase, a rate-limiting enzyme in the tricarboxylic acid cycle, was localized at the center of the mitochondrial oxidation-reduction process, and its expression was significantly downreguated in Ang II-infused atria at different time points. Cardiomyocyte-specific overexpresion of citrate synthase markedly reduced atrial fibrillation susceptibility and atrial remodeling in mice. These beneficial effects were associated with increased ATP production and mitochondrial oxidative phosphorylation system complexes I-V expression and inhibition of oxidative stress. CONCLUSION The current study defines the dynamic changes of the DEPs involved in Ang II-induced atrial fibrillation, and identifies that citrate synthase plays a protective role in regulating atrial fibrillation development, and increased citrate synthase expression may represent a potential therapeutic option for atrial fibrillation treatment.
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Santos S, Obukhov Y, Nekhai S, Pushkarsky T, Brichacek B, Bukrinsky M, Iordanskiy S. Cellular minichromosome maintenance complex component 5 (MCM5) is incorporated into HIV-1 virions and modulates viral replication in the newly infected cells. Virology 2016; 497:11-22. [PMID: 27414250 PMCID: PMC5079758 DOI: 10.1016/j.virol.2016.06.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 06/22/2016] [Accepted: 06/28/2016] [Indexed: 12/01/2022]
Abstract
The post-entry events of HIV-1 infection occur within reverse transcription complexes derived from the viral cores entering the target cell. HIV-1 cores contain host proteins incorporated from virus-producing cells. In this report, we show that MCM5, a subunit of the hexameric minichromosome maintenance (MCM) DNA helicase complex, associates with Gag polyprotein and is incorporated into HIV-1 virions. The progeny virions depleted of MCM5 demonstrated reduced reverse transcription in newly infected cells, but integration and subsequent replication steps were not affected. Interestingly, increased packaging of MCM5 into the virions also led to reduced reverse transcription, but here viral replication was impaired. Our data suggest that incorporation of physiological amounts of MCM5 promotes aberrant reverse transcription, leading to partial incapacitation of cDNA, whereas increased MCM5 abundance leads to reduced reverse transcription and infection. Therefore, MCM5 has the properties of an inhibitory factor that interferes with production of an integration-competent cDNA product.
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Affiliation(s)
- Steven Santos
- George Washington University School of Medicine and Health Sciences, Department of Microbiology, Immunology and Tropical Medicine, 2300 I Street NW, Ross Hall, Washington, DC 20037, USA
| | - Yuri Obukhov
- Howard University College of Medicine, Department of Medicine, Center for Sickle Cell Disease, 1840 7th Street N.W., Washington DC 20001, USA; Howard University College of Medicine, RCMI Proteomics Core Facility, 1840 7th Street N.W., Washington DC 20001, USA
| | - Sergei Nekhai
- Howard University College of Medicine, Department of Medicine, Center for Sickle Cell Disease, 1840 7th Street N.W., Washington DC 20001, USA; Howard University College of Medicine, RCMI Proteomics Core Facility, 1840 7th Street N.W., Washington DC 20001, USA
| | - Tatiana Pushkarsky
- George Washington University School of Medicine and Health Sciences, Department of Microbiology, Immunology and Tropical Medicine, 2300 I Street NW, Ross Hall, Washington, DC 20037, USA
| | - Beda Brichacek
- George Washington University School of Medicine and Health Sciences, Department of Microbiology, Immunology and Tropical Medicine, 2300 I Street NW, Ross Hall, Washington, DC 20037, USA
| | - Michael Bukrinsky
- George Washington University School of Medicine and Health Sciences, Department of Microbiology, Immunology and Tropical Medicine, 2300 I Street NW, Ross Hall, Washington, DC 20037, USA.
| | - Sergey Iordanskiy
- George Washington University School of Medicine and Health Sciences, Department of Microbiology, Immunology and Tropical Medicine, 2300 I Street NW, Ross Hall, Washington, DC 20037, USA
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Santos S, Obukhov Y, Nekhai S, Bukrinsky M, Iordanskiy S. Virus-producing cells determine the host protein profiles of HIV-1 virion cores. Retrovirology 2012; 9:65. [PMID: 22889230 PMCID: PMC3432596 DOI: 10.1186/1742-4690-9-65] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 07/15/2012] [Indexed: 11/10/2022] Open
Abstract
Background Upon HIV entry into target cells, viral cores are released and rearranged into reverse transcription complexes (RTCs), which support reverse transcription and also protect and transport viral cDNA to the site of integration. RTCs are composed of viral and cellular proteins that originate from both target and producer cells, the latter entering the target cell within the viral core. However, the proteome of HIV-1 viral cores in the context of the type of producer cells has not yet been characterized. Results We examined the proteomic profiles of the cores purified from HIV-1 NL4-3 virions assembled in Sup-T1 cells (T lymphocytes), PMA and vitamin D3 activated THP1 (model of macrophages, mMΦ), and non-activated THP1 cells (model of monocytes, mMN) and assessed potential involvement of identified proteins in the early stages of infection using gene ontology information and data from genome-wide screens on proteins important for HIV-1 replication. We identified 202 cellular proteins incorporated in the viral cores (T cells: 125, mMΦ: 110, mMN: 90) with the overlap between these sets limited to 42 proteins. The groups of RNA binding (29), DNA binding (17), cytoskeleton (15), cytoskeleton regulation (21), chaperone (18), vesicular trafficking-associated (12) and ubiquitin-proteasome pathway-associated proteins (9) were most numerous. Cores of the virions from SupT1 cells contained twice as many RNA binding proteins as cores of THP1-derived virus, whereas cores of virions from mMΦ and mMN were enriched in components of cytoskeleton and vesicular transport machinery, most probably due to differences in virion assembly pathways between these cells. Spectra of chaperones, cytoskeletal proteins and ubiquitin-proteasome pathway components were similar between viral cores from different cell types, whereas DNA-binding and especially RNA-binding proteins were highly diverse. Western blot analysis showed that within the group of overlapping proteins, the level of incorporation of some RNA binding (RHA and HELIC2) and DNA binding proteins (MCM5 and Ku80) in the viral cores from T cells was higher than in the cores from both mMΦ and mMN and did not correlate with the abundance of these proteins in virus producing cells. Conclusions Profiles of host proteins packaged in the cores of HIV-1 virions depend on the type of virus producing cell. The pool of proteins present in the cores of all virions is likely to contain factors important for viral functions. Incorporation ratio of certain RNA- and DNA-binding proteins suggests their more efficient, non-random packaging into virions in T cells than in mMΦ and mMN.
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Affiliation(s)
- Steven Santos
- Department of Microbiology, Immunology and Tropical Medicine, George Washington University School of Medicine and Health Sciences, 2300 I Street NW, Ross Hall, Washington, DC 20037, USA
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