Identification of the differentially expressed proteins in nasopharyngeal carcinoma by proteomics

Rong, Dongxiu; Lin, Xiuxian; Luo, Yanzhang; Mok, Tin Seak; Wang, Qing; Wang, Haiyan; Zhang, Tao

doi:10.21037/tcr.2019.11.14

Cited by 4 publications

(1 citation statement)

References 27 publications

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“…It is therefore clinically important to identify potential tumor markers that influence the progression and prognostic assessment of nasopharyngeal cancer. Rong et al (2020) performed a proteomics detection of 30 nasopharyngeal cancer samples and 30 normal control nasopharyngeal tissues via SWATH‐MS and identified 1415 differentially expressed proteins. The SWATH‐MS data were verified via SILAC and LC–MS.…”

Section: Application Of the Lfq Proteomics Technology For Malignant T...mentioning

confidence: 99%

Advances in the application of label‐free quantitative proteomics techniques in malignancy research

Meng

Liu

Guan

2023

Biomedical Chromatography

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Proteomics is the scientific discipline that deals with the protein composition of cells, tissues, and organisms and their patterns of change. It is considered an invaluable tool for tackling many challenges faced in medicine and biology. Among the available approaches, label‐free quantitative proteomics techniques are extensively used to study malignant tumors due to their low cost, simple operation, and short cycle time. Therefore, it provides a novel approach to explore the pathogenesis, diagnostic markers, and targeted drugs of malignant tumors. Here, we summarize the research progress and potential of label‐free quantitative proteomics and discuss the application of such techniques in the research on malignancies.

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Section: Application Of the Lfq Proteomics Technology For Malignant T...mentioning

confidence: 99%

Advances in the application of label‐free quantitative proteomics techniques in malignancy research

Meng

Liu

Guan

2023

Biomedical Chromatography

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Application of two-dimensional difference gel electrophoresis to identify protein changes between center, margin, and adjacent non-tumor tissues obtained from non-small-cell lung cancer with adenocarcinoma or squamous cell carcinoma subtype

et al. 2022

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Lung cancer is responsible for the most cancer-related mortality worldwide and the mechanism of its development is poorly understood. Proteomics has become a powerful tool offering vital knowledge related to cancer development. Using a two-dimensional difference gel electrophoresis (2D-DIGE) approach, we sought to compare tissue samples from non-small-cell lung cancer (NSCLC) patients taken from the tumor center and tumor margin. Two subtypes of NSCLC, adenocarcinoma (ADC) and squamous cell carcinoma (SCC) were compared. Data are available via ProteomeXchange with identifier PXD032736 and PXD032962 for ADC and SCC, respectively. For ADC proteins, 26 significant canonical pathways were identified, including Rho signaling pathways, a semaphorin neuronal repulsive signaling pathway, and epithelial adherens junction signaling. For SCC proteins, nine significant canonical pathways were identified, including hypoxia-inducible factor-1α signaling, thyroid hormone biosynthesis, and phagosome maturation. Proteins differentiating the tumor center and tumor margin were linked to cancer invasion and progression, including cell migration, adhesion and invasion, cytoskeletal structure, protein folding, anaerobic metabolism, tumor angiogenesis, EMC transition, epithelial adherens junctions, and inflammatory responses. In conclusion, we identified several proteins that are important for the better characterization of tumor development and molecular specificity of both lung cancer subtypes. We also identified proteins that may be important as biomarkers and/or targets for anticancer therapy.

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A Proteomic Analysis of Nasopharyngeal Carcinoma in a Moroccan Subpopulation

Reffai,

Hori,

Adusumilli

et al. 2024

Cancers

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Background: Nasopharyngeal carcinoma (NPC) is a distinct cancer of the head and neck that is highly prevalent in Southeast Asia and North Africa. Though an extensive analysis of environmental and genetic contributors has been performed, very little is known about the proteome of this disease. A proteomic analysis of formalin-fixed paraffin-embedded (FFPE) tissues can provide valuable information on protein expression and molecular patterns for both increasing our understanding of the disease and for biomarker discovery. To date, very few NPC proteomic studies have been performed, and none focused on patients from Morocco and North Africa. Methods: Label-free Liquid Chromatography–Tandem Mass Spectrometry (LC-MS/MS) was used to perform a proteomic analysis of FFPE tissue samples from a cohort of 41 NPC tumor samples of Morocco and North Africa origins. The LC-MS/MS data from this cohort were analyzed alongside 21 healthy controls using MaxQuant 2.4.2.0. A differential expression analysis was performed using the MSstats package in R. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotations were carried out using the DAVID bioinformatic tool. Results: 3341 proteins were identified across our NPC cases, revealing three main clusters and five DEPs with prognostic significance. The sex disparity of NPC was investigated from a proteomic perspective in which 59 DEPs were found between males and females, with significantly enriched terms associated with the immune response and gene expression. Furthermore, 26 DEPs were observed between patients with early and advanced stages of NPC with a significant cluster related to the immune response, implicating up-regulated DEPs such as IGHA, IGKC, and VAT1. Across both datasets, 6532 proteins were quantified between NPC patients and healthy controls. Among them, 1507 differentially expressed proteins (DEPs) were observed. GO and KEGG pathway analyses showed enriched terms of DEPs related to increased cellular activity, cell proliferation, and survival. PI3K and MAPK proteins as well as RAC1 BCL2 and PPIA were found to be overexpressed between cancer tissues and healthy controls. EBV infection was also one of the enriched pathways implicating its latent genes like LMP1 and LMP2 that activate several proteins and signaling pathways including NF-Kappa B, MAPK, and JAK-STAT pathways. Conclusion: Our findings unveil the proteomic landscape of NPC for the first time in the Moroccan population. These studies additionally may provide a foundation for identifying potential biomarkers. Further research is still needed to help develop tools for the early diagnosis and treatment of NPC in Moroccan and North African populations.

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Identification of the differentially expressed proteins in nasopharyngeal carcinoma by proteomics

Cited by 4 publications

References 27 publications

Advances in the application of label‐free quantitative proteomics techniques in malignancy research

Advances in the application of label‐free quantitative proteomics techniques in malignancy research

Application of two-dimensional difference gel electrophoresis to identify protein changes between center, margin, and adjacent non-tumor tissues obtained from non-small-cell lung cancer with adenocarcinoma or squamous cell carcinoma subtype

A Proteomic Analysis of Nasopharyngeal Carcinoma in a Moroccan Subpopulation

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