Taipei Medical University Institutional Repository:Item 987654321/62401
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    Title: Development of Data-Independent Acquisition-mass spectrometry strategy for immunopeptidomics analysis
    Development of Data-Independent Acquisition-mass spectrometry strategy for immunopeptidomics analysis
    Authors: HOA, VO THANH
    Contributors: 臨床基因體學暨蛋白質體學碩士學位學程
    Chia-Li Han
    Keywords: Data-independent-acquisition;mass spectrometry;proteogenomics;neoantigen;human leukocyte antigen
    Date: 2022-07-07
    Issue Date: 2022-12-29 11:09:21 (UTC+8)
    Abstract: Antigen presentation by the human leukocyte antigen proteins plays a critical role in the regulation of the immune system to trigger antitumor response in cancer. By targeting neoantigens, tumor destruction via anticancer T-cell responses will be achieved without causing damage to normal tissues. Data-independent-acquisition mass spectrometry (DIA-MS) emerges as an effective method for detecting low-abundance proteins by collecting fragment ion spectra regardless of precursor ion intensities, which subsequently facilitates the detection of neoantigen. However, the application of DIA-MS in neoantigen detection is challenging because of the limited spectral library, resulting in few identifications. Therefore, the aim of our study is to optimize the DIA-MS platform to leverage HLA-binding peptides and potential neoantigen identification. Two lung cancer cell lines, H1975 cells and CRISPR9-edited H1975 cells with additional EGFR C797S mutation are our study model. Firstly, we expanded the experimental peptide spectral library to a total of 4,746 peptides by including the spectra identified from the reported mono-HLA allelic cell lines and our immunoprecipitation experiments. Secondly, we constructed a virtual spectral library that combines the predicted spectra of putative 23,404 mutant and 542,444 wild-type peptides. Third, we generated a hybrid spectral library by integrating the experimental and virtual libraries to aid the identification of 570 HLA-binding peptides and 102 mutant peptides in both cells. Further functional analysis of the mutant peptides suggested FVLEDPTLL peptide derived from I83V mutation of Adenylate Cyclase 2 as a potential neoantigen in lung cancer. We expect that this DIA-MS platform will be a powerful tool for enhancing neoantigen discovery and fostering personalized treatment upon clinical application.
    Description: 碩士
    指導教授:Chia-Li Han
    委員:Chia-Li Han
    委員:San-Yuan Wang
    委員:I-Lin Tsai
    Data Type: thesis
    Appears in Collections:[Master Program for Clinical Pharmacogenomics and Pharmacoproteomics] Dissertations/Theses

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