SWATH-based proteomics identified carbonic anhydrase 2 as a potential diagnosis biomarker for nasopharyngeal carcinoma

Luo, Yanzhang; Mok, Tin Seak; Lin, Xiuxian; Zhang, Wanling; Cui, Yizhi; Guo, Jiahui; Chen, Xing; Zhang, Tao; Wang, Tong

doi:10.1038/srep41191

Cited by 30 publications

(33 citation statements)

References 49 publications

(67 reference statements)

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“…The performance of DIA MS is comparable with our previous analysis of nasopharyngeal carcinoma tissues with another DIA platform, SWATH, which identified 1414 proteins across 11 tissue samples (16). In addition, DIA can accurately quantitate the protein abundance (46), and SWATH preferentially detects proteins with lower molecular weights (16). However, we did not observe such a molecular weight preference in this study with the DIA MS analysis by an LTQ Fusion Lumos mass spectrometer.…”

Section: Discussionsupporting

confidence: 78%

“…This led us to report a confident dataset containing .1100 secretory proteins from HS, which represent the deepest secretome coverage of synoviocytes to date, to our knowledge. The performance of DIA MS is comparable with our previous analysis of nasopharyngeal carcinoma tissues with another DIA platform, SWATH, which identified 1414 proteins across 11 tissue samples (16). In addition, DIA can accurately quantitate the protein abundance (46), and SWATH preferentially detects proteins with lower molecular weights (16).…”

Section: Discussionsupporting

confidence: 60%

“…We employed the power law global error mode (PLGEM) algorithm (14) to compare the abundance difference at the proteome level in both phosphoproteome and secretome analyses. We have found this method a useful tool for comparative proteomics per our published work, which addresses the detailed PLGEM method (15,16). A protein was deemed a significantly differentially expressed protein (DEP) when p , 0.05 per PLGEM.…”

Section: Determination Of Differentially Expressed Proteinsmentioning

confidence: 99%

“…The immunoblotting (IB) analysis was performed as we previously described (16). The primary Abs and their working dilution are listed as follows: mouse anti-human proliferating cell nuclear Ag (PCNA) mAb (1:5000; Thermo Fisher Scientific), rabbit anti-human p38 MAPK pAb (1:1000; Cell Signaling Technology, Shanghai, China), rabbit anti-human phospho-p38 MAPK (Thr180/Tyr182) mAb (1:1000; CST), rabbit antihuman JNK1/2 mAb (1:1000; CST), mouse anti-human phospho-SAPK/ JNK (Thr183/Tyr185) mAb, rabbit anti-human ERK1/2 (phospho-T202/ Y204) mAb (1:1000; CST), rabbit anti-human Collagen Type III (C-terminal) pAb (1:1000; Proteintech, Wuhan, China), rabbit anti-human SERPINE2 pAb (1:1000; Proteintech), and rabbit anti-human a-tubulin pAb (1:1000; CST).…”

Section: Immunoblotting Analysismentioning

confidence: 99%

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Deep Coverage Tissue and Cellular Proteomics Revealed IL-1β Can Independently Induce the Secretion of TNF-Associated Proteins from Human Synoviocytes

Tang

Deng

Guo

et al. 2018

The Journal of Immunology

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Synovitis is a key contributor to the inflammatory environment in osteoarthritis (OA) joints. Currently, the biological therapy of OA is not satisfactory in multiple single-target trials on anti-TNF agents, or IL-1 antagonists. Systems biological understanding of the phosphorylation state in OA synovium is warranted to direct further therapeutic strategies. Therefore, in this study, we compared the human synovial phosphoproteome of the OA with the acute joint fracture subjects. We found that OA synovium had significantly more phosphoproteins, and 82 phosphoproteins could only be specifically found in all the OA samples. Differentially expressed proteins of the OA synovium were focusing on endoplasmic reticulum-/Golgi-associated secretion and negative regulation of cell proliferation, which was verified through an IL-1β-treated human synoviocyte (HS) in vitro model. With data-independent acquisition-based mass spectrometry, we found that IL-1β could induce HS to secrete proteins that were significantly associated with the endosomal/vacuolar pathway, endoplasmic reticulum/Golgi secretion, complement activation, and collagen degradation. Especially, we found that while specifically suppressing HS endocytosis, IL-1β could activate the secretion of 25 TNF-associated proteins, and the change of SERPINE2 and COL3A1 secretion was verified by immunoblotting. In conclusion, our results suggest that OA synovium has a polarized phosphoproteome to inhibit proliferation and maintain active secretion of HS, whereas IL-1β alone can transform HS to produce a synovitis-associated secretome, containing numerous TNF-associated secretory proteins in a TNF-independent mode.

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Section: Discussionsupporting

confidence: 78%

Section: Discussionsupporting

confidence: 60%

Section: Determination Of Differentially Expressed Proteinsmentioning

confidence: 99%

Section: Immunoblotting Analysismentioning

confidence: 99%

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Deep Coverage Tissue and Cellular Proteomics Revealed IL-1β Can Independently Induce the Secretion of TNF-Associated Proteins from Human Synoviocytes

Tang

Deng

Guo

et al. 2018

The Journal of Immunology

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“…SWATH has been successfully applied to qualitative and quantitative analyses of proteomics. 35,36 and metabolomics. 37,38 …”

Section: Introductionmentioning

confidence: 99%

Data-Independent Mass Spectrometry Approach for Screening and Identification of DNA Adducts

2017

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Long-term exposures to environmental toxicants and endogenous electrophiles are causative factors for human diseases including cancer. DNA adducts reflect the internal exposure to genotoxicants and can serve as biomarkers for risk assessment. Liquid chromatography-multistage mass spectrometry (LC-MSn) is the most common method for biomonitoring DNA adducts, generally targeting single exposures and measuring up to several adducts. However, the data often provide limited evidence for a role of a chemical in the etiology of cancer. An “untargeted” method is required that captures global exposures to chemicals, by simultaneously detecting their DNA adducts in the genome; some of which may induce cancer-causing mutations. We established a wide selected ion monitoring tandem mass spectrometry (Wide-SIM/MS2) screening method utilizing ultra-performance-LC nanoelectrospray ionization Orbitrap MSn with on-line trapping to enrich bulky, non-polar adducts. Wide-SIM scan events are followed by MS2 scans to screen for modified nucleosides by co-eluting peaks containing precursor and fragment ions differing by -116.0473 Da, attributed to the neutral loss of deoxyribose. Wide-SIM/MS2 was shown to be superior in sensitivity, specificity, and breadth of adduct coverage to other tested adductomic methods with detection possible at adduct levels as low as 4 per 109 nucleotides. Wide-SIM/MS2 data can be analyzed in a “targeted” fashion by generation of extracted ion chromatograms or in an “untargeted” fashion where a chromatographic peak-picking algorithm can be used to detect putative DNA adducts. Wide-SIM/MS2 successfully detected DNA adducts, derived from chemicals in the diet and traditional medicines and from lipid peroxidation products, in human prostate and renal specimens.

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SWATH‐MS and MRM: Quantification of Ras‐related proteins in HIV‐1 infected and methamphetamine‐exposed human monocyte‐derived macrophages (hMDM)

et al. 2021

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HIV‐1 infection of macrophages is a multistep and multifactorial process that has been shown to be enhanced by exposure to methamphetamine (Meth). In this study, we sought to identify the underlying mechanisms of this effect by quantifying the effect of Meth on the proteome of HIV‐1‐infected macrophages using sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH‐MS) approach. The analyses identified several members of the Rab family of proteins as being dysregulated by Meth treatment, which was confirmed by bioinformatic analyses that indicated substantial alteration of vesicular transport pathways. Validation of the SWATH‐MS was performed using an MRM based approach, which confirmed that Meth exposure affects expression of the Rab proteins. However, the pattern of expression changes were highly dynamic, and displayed high donor‐to‐donor variability. Surprisingly a similar phenomenon was observed for Actin. Our results demonstrate that Meth affects vesicular transport pathways, suggesting a possible molecular mechanism underlying its effect on HIV infection hMDM and a potential broader effect of Meth on cellular homeostasis.

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SWATH-based proteomics identified carbonic anhydrase 2 as a potential diagnosis biomarker for nasopharyngeal carcinoma

Cited by 30 publications

References 49 publications

Deep Coverage Tissue and Cellular Proteomics Revealed IL-1β Can Independently Induce the Secretion of TNF-Associated Proteins from Human Synoviocytes

Deep Coverage Tissue and Cellular Proteomics Revealed IL-1β Can Independently Induce the Secretion of TNF-Associated Proteins from Human Synoviocytes

Data-Independent Mass Spectrometry Approach for Screening and Identification of DNA Adducts

SWATH‐MS and MRM: Quantification of Ras‐related proteins in HIV‐1 infected and methamphetamine‐exposed human monocyte‐derived macrophages (hMDM)

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