Proteomic identification of an MHC-binding peptidome from pancreas and breast cancer cell lines

Antwi, Kwasi; Hanavan, Paul D.; Myers, Cheryl; Ruiz, Yvette; Thompson, Eric J.; Lake, Douglas F.

doi:10.1016/j.molimm.2009.06.021

Cited by 26 publications

(19 citation statements)

References 26 publications

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“…Until recently, MAE was used to isolate MHC class I peptides from various cell lines, bone-marrow-derived dendritic cells, and primary thymocytes (5,38,39,48,50). The MAE approach is cell-surface-specific and can be repeated over time from the same cell population, e.g.…”

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confidence: 99%

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Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry*

Caron

Kowalewski

Koh

et al. 2015

Molecular & Cellular Proteomics

190

118

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The myriad of peptides presented at the cell surface by class I and class II major histocompatibility complex (MHC) molecules are referred to as the immunopeptidome and are of great importance for basic and translational science. For basic science, the immunopeptidome is a critical component for understanding the immune system; for translational science, exact knowledge of the immunopeptidome can directly fuel and guide the development of next-generation vaccines and immunotherapies against autoimmunity, infectious diseases, and cancers. In this mini-review, we summarize established isolation techniques as well as emerging mass spectrometry-based platforms (i.e. SWATH-MS) to identify and quantify MHC-associated peptides. We also highlight selected biological applications and discuss important current technical limitations that need to be solved to accelerate the development of this field. Molecular & Cellular

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confidence: 99%

“…Due to high consumption of affinity matrix, this isolation technique typically requires in-house production of mAb from hybridoma cell lines. Of note, papain digestion has also been used in combination with the IP method to cleave and subsequently isolate cell surface MHCpeptide complexes (50,56).…”

mentioning

confidence: 99%

Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry*

Caron

Kowalewski

Koh

et al. 2015

Molecular & Cellular Proteomics

190

118

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“…Currently, the best established methodology is using anti-HLA monoclonal antibody to immunoprecipitation of HLA-peptide complexes from detergent solubilized tumor lysates, followed by epitopes elution from HLA complex, and purification and concentration of the short peptides [30]. In particular, pan-HLA class I or pan-HLA class II monoclonal antibodies can be used, and different HLA allele-specific antibodies are also available.…”

Section: Mass Spectrometry Based Methodsmentioning

confidence: 99%

The Prediction and Function of Neoantigen in Oncobiology

Cui¹

2017

Proceedings of the 2017 International Conference on Material Science, Energy and Environmental Engineering (MSEEE 2017)

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Abstract.Recent clinical data clearly demonstrated that patient's own immune system has great potential in controlling the progression of many human cancers. Neoantigen is the foundation of tumor immunology for it is the "marker" for mature autologous T lymphocytes to distinguish tumor cells and normal cells. So identification of neoantigen is an important work in both fundamental studies and clinical immunotherapies. Neoantigen is patient-specific, it is derived from tumor genome somatic mutations in protein coding region. Identification of neoantigen is a laborious work before, but recent technological innovations have made this measurement easier and faster, though still not perfect. Now, numerous neoantigen based clinical trials are being carried out around the world by both academic institutes and companies, some have achieved exciting results.

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“…Before then, many studies used various mass spectrometers to profile T-cell epitopes on cells of interest (reviewed in [45]). In brief, a typical procedure for MHC-bound peptide profiling includes the use of a huge number of cells, such as 10 7 -10 9 cells for class I MHC [46,47] and 10 9 -10 10 cells for MHCII [48,49]. After the cell lysis, MHC molecules with peptides bound therewith are usually purified from the mixture by specific antibodies [46] and then the peptides of interest are eluted from the complex in acidic conditions and isolated from proteins by ultrafiltration [45].…”

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confidence: 99%

“…After the cell lysis, MHC molecules with peptides bound therewith are usually purified from the mixture by specific antibodies [46] and then the peptides of interest are eluted from the complex in acidic conditions and isolated from proteins by ultrafiltration [45]. In the former method, the peptides were recovered from intact cells by mild acidic elution [47,50]. However, in recent articles, the researchers have used an affinity capture method to enrich the sample with the MHC molecules [45].…”

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confidence: 99%

Proteogenomics meets cancer immunology: mass spectrometric discovery and analysis of neoantigens

Polyakova

Kuznetsova

Moshkovskii³

2015

Expert Review of Proteomics

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Cancer proteogenomics is an emerging field that aims to identify and quantify protein sequence changes associated with the cancer genome. Besides being involved in cancer development and progression, such protein variants may serve as neoantigens, which provide the T-cell response against tumors. Mass spectrometry-based proteogenomics may be a promising tool for finding neoantigens in individual specimens. It is partly based on a technical background accumulated from mass spectrometric studies of peptide ligands of major histocompatibility complex proteins. Examples of the use of mass spectrometry in neoantigen identification are reviewed in this article. Some experimental workflows are discussed, which may use shotgun and targeted proteomics for translational human studies of neoepitopes, such as cancer vaccine development and checkpoint therapy response prediction.

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Proteomic identification of an MHC-binding peptidome from pancreas and breast cancer cell lines

Cited by 26 publications

References 26 publications

Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry*

Analysis of Major Histocompatibility Complex (MHC) Immunopeptidomes Using Mass Spectrometry*

The Prediction and Function of Neoantigen in Oncobiology

Proteogenomics meets cancer immunology: mass spectrometric discovery and analysis of neoantigens

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