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We are analyzing https://www.nature.com/articles/s41467-020-16588-9.

Title:
Multiplexed relative and absolute quantitative immunopeptidomics reveals MHC I repertoire alterations induced by CDK4/6 inhibition | Nature Communications
Description:
Peptides bound to class I major histocompatibility complexes (MHC) play a critical role in immune cell recognition and can trigger an antitumor immune response in cancer. Surface MHC levels can be modulated by anticancer agents, altering immunity. However, understanding the peptide repertoire’s response to treatment remains challenging and is limited by quantitative mass spectrometry-based strategies lacking normalization controls. We describe an experimental platform that leverages recombinant heavy isotope-coded peptide MHCs (hipMHCs) and multiplex isotope tagging to quantify peptide repertoire alterations using low sample input. HipMHCs improve quantitative accuracy of peptide repertoire changes by normalizing for variation across analyses and enable absolute quantification using internal calibrants to determine copies per cell of MHC antigens, which can inform immunotherapy design. Applying this platform in melanoma cell lines to profile the immunopeptidome response to CDK4/6 inhibition and interferon-γ — known modulators of antigen presentation — uncovers treatment-specific alterations, connecting the intracellular response to extracellular immune presentation. Immunopeptidomics allows identifying the cellular repertoire of MHC-bound peptides, but quantifying them remains challenging. Here, the authors present a method to efficiently generate internal peptide MHC standards and calibration curves, facilitating relative and absolute quantitative immunopeptidomics.
Website Age:
30 years and 10 months (reg. 1994-08-11).

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Keywords {🔍}

peptides, pubmed, cell, data, article, fig, cells, peptide, google, scholar, cas, pmhc, quantification, palbociclib, supplementary, analyses, samples, skmel, treatment, expression, source, significantly, hipmhc, analysis, tmt, mhc, cancer, hipmhcs, sample, enriched, cdk, absolute, response, lines, proteins, central, nature, quantitative, correction, class, repertoire, mass, presentation, pmhcs, ifnγ, gene, antigen, performed, biological, relative,

Topics {✒️}

nature portfolio privacy policy advertising pgc-1α-responsive genes involved ice-cold phosphate-buffered saline resulting libraries heavy-isotope-coded synthetic peptides reporting summary integrative cancer research demand heavy-isotope-labeled pmhcs reprints multiplexed nature subsequent lc-ms/ms analysis heavy-isotope-labeled mhc peptides uv-mediated ligand exchange ifn-γ-induced pmhc alterations traditional data-dependent acquisition phosphotyrosine-based-phosphoproteomics scaled bruker miroflex maldi-tof recombinant adenovirus-infected hepatocytes tmt-labeled mda-mb-231 cells cyclin d-dependent kinases nature 548 nature 543 nature mass spectrometry-based identification heavy-isotope-labeled leucine heavy leucine-coded peptides enzyme-linked immunosorbent assay dna double-strand breaks engineered tcr-based therapies c-terminal carboxyl groups 40 nt single-end reads author information authors t-cell-mediated elimination low-dose-treated skmel5 cells uv-mediated peptide exchange27 mhc-bound peptide epitopes genome-wide experimental datasets observe c-terminal amidation 10 ng ml−1 ifn-γ protein–protein association networks research design small-molecule cdk4/6 inhibitor uv-mediated peptide exchange social media half-maximal inhibitory concentrations performed lc-ms/ms analysis tmt-labeled data sets high-dose palbociclib showed

Schema {🗺️}

WebPage:
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         headline:Multiplexed relative and absolute quantitative immunopeptidomics reveals MHC I repertoire alterations induced by CDK4/6 inhibition
         description:Peptides bound to class I major histocompatibility complexes (MHC) play a critical role in immune cell recognition and can trigger an antitumor immune response in cancer. Surface MHC levels can be modulated by anticancer agents, altering immunity. However, understanding the peptide repertoire’s response to treatment remains challenging and is limited by quantitative mass spectrometry-based strategies lacking normalization controls. We describe an experimental platform that leverages recombinant heavy isotope-coded peptide MHCs (hipMHCs) and multiplex isotope tagging to quantify peptide repertoire alterations using low sample input. HipMHCs improve quantitative accuracy of peptide repertoire changes by normalizing for variation across analyses and enable absolute quantification using internal calibrants to determine copies per cell of MHC antigens, which can inform immunotherapy design. Applying this platform in melanoma cell lines to profile the immunopeptidome response to CDK4/6 inhibition and interferon-γ — known modulators of antigen presentation — uncovers treatment-specific alterations, connecting the intracellular response to extracellular immune presentation. Immunopeptidomics allows identifying the cellular repertoire of MHC-bound peptides, but quantifying them remains challenging. Here, the authors present a method to efficiently generate internal peptide MHC standards and calibration curves, facilitating relative and absolute quantitative immunopeptidomics.
         datePublished:2020-06-02T00:00:00Z
         dateModified:2020-06-02T00:00:00Z
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            MHC class I
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            Science
            Humanities and Social Sciences
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      headline:Multiplexed relative and absolute quantitative immunopeptidomics reveals MHC I repertoire alterations induced by CDK4/6 inhibition
      description:Peptides bound to class I major histocompatibility complexes (MHC) play a critical role in immune cell recognition and can trigger an antitumor immune response in cancer. Surface MHC levels can be modulated by anticancer agents, altering immunity. However, understanding the peptide repertoire’s response to treatment remains challenging and is limited by quantitative mass spectrometry-based strategies lacking normalization controls. We describe an experimental platform that leverages recombinant heavy isotope-coded peptide MHCs (hipMHCs) and multiplex isotope tagging to quantify peptide repertoire alterations using low sample input. HipMHCs improve quantitative accuracy of peptide repertoire changes by normalizing for variation across analyses and enable absolute quantification using internal calibrants to determine copies per cell of MHC antigens, which can inform immunotherapy design. Applying this platform in melanoma cell lines to profile the immunopeptidome response to CDK4/6 inhibition and interferon-γ — known modulators of antigen presentation — uncovers treatment-specific alterations, connecting the intracellular response to extracellular immune presentation. Immunopeptidomics allows identifying the cellular repertoire of MHC-bound peptides, but quantifying them remains challenging. Here, the authors present a method to efficiently generate internal peptide MHC standards and calibration curves, facilitating relative and absolute quantitative immunopeptidomics.
      datePublished:2020-06-02T00:00:00Z
      dateModified:2020-06-02T00:00:00Z
      pageStart:1
      pageEnd:14
      license:http://creativecommons.org/licenses/by/4.0/
      sameAs:https://doi.org/10.1038/s41467-020-16588-9
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         Mass spectrometry
         Melanoma
         MHC class I
         Peptides
         Proteomics
         Science
         Humanities and Social Sciences
         multidisciplinary
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      name:Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, USA
      name:Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, USA
      name:Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, USA
      name:Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, USA
      name:Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, USA
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