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      Absolute quantification of tumor antigens using embedded MHC-I isotopologue calibrants

      brief-report

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          Abstract

          Absolute quantification measurements (copies per cell) of peptide major histocompatibility complex (pMHC) antigens are necessary to inform targeted immunotherapy drug design; however, existing methods for absolute quantification have critical limitations. Here, we present a platform termed SureQuant-IsoMHC, utilizing a series of pMHC isotopologues and internal standard-triggered targeted mass spectrometry to generate an embedded multipoint calibration curve to determine endogenous pMHC concentrations for a panel of 18 tumor antigens. We apply SureQuant-IsoMHC to measure changes in expression of our target panel in a melanoma cell line treated with a MEK inhibitor and translate this approach to estimate antigen concentrations in melanoma tumor biopsies.

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          Skyline: an open source document editor for creating and analyzing targeted proteomics experiments.

          Brendan Maclean, Daniela Tomazela, Nicholas Shulman … (2010)
          Skyline is a Windows client application for targeted proteomics method creation and quantitative data analysis. It is open source and freely available for academic and commercial use. The Skyline user interface simplifies the development of mass spectrometer methods and the analysis of data from targeted proteomics experiments performed using selected reaction monitoring (SRM). Skyline supports using and creating MS/MS spectral libraries from a wide variety of sources to choose SRM filters and verify results based on previously observed ion trap data. Skyline exports transition lists to and imports the native output files from Agilent, Applied Biosystems, Thermo Fisher Scientific and Waters triple quadrupole instruments, seamlessly connecting mass spectrometer output back to the experimental design document. The fast and compact Skyline file format is easily shared, even for experiments requiring many sample injections. A rich array of graphs displays results and provides powerful tools for inspecting data integrity as data are acquired, helping instrument operators to identify problems early. The Skyline dynamic report designer exports tabular data from the Skyline document model for in-depth analysis with common statistical tools. Single-click, self-updating web installation is available at http://proteome.gs.washington.edu/software/skyline. This web site also provides access to instructional videos, a support board, an issues list and a link to the source code project.
          Article 0 comments Cited 821 times – based on 0 reviews     Review now
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            Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry

            Michal Bassani-Sternberg, Eva Bräunlein, Richard Klar … (2016)
            Although mutations may represent attractive targets for immunotherapy, direct identification of mutated peptide ligands isolated from human leucocyte antigens (HLA) on the surface of native tumour tissue has so far not been successful. Using advanced mass spectrometry (MS) analysis, we survey the melanoma-associated immunopeptidome to a depth of 95,500 patient-presented peptides. We thereby discover a large spectrum of attractive target antigen candidates including cancer testis antigens and phosphopeptides. Most importantly, we identify peptide ligands presented on native tumour tissue samples harbouring somatic mutations. Four of eleven mutated ligands prove to be immunogenic by neoantigen-specific T-cell responses. Moreover, tumour-reactive T cells with specificity for selected neoantigens identified by MS are detected in the patient's tumour and peripheral blood. We conclude that direct identification of mutated peptide ligands from primary tumour material by MS is possible and yields true neoepitopes with high relevance for immunotherapeutic strategies in cancer.
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              Monoclonal TCR-redirected tumor cell killing.

              Nathaniel Liddy, Giovanna Bossi, Katherine J. Adams … (2012)
              T cell immunity can potentially eradicate malignant cells and lead to clinical remission in a minority of patients with cancer. In the majority of these individuals, however, there is a failure of the specific T cell receptor (TCR)–mediated immune recognition and activation process. Here we describe the engineering and characterization of new reagents termed immune-mobilizing monoclonal TCRs against cancer (ImmTACs). Four such ImmTACs, each comprising a distinct tumor-associated epitope-specific monoclonal TCR with picomolar affinity fused to a humanized cluster of differentiation 3 (CD3)-specific single-chain antibody fragment (scFv), effectively redirected T cells to kill cancer cells expressing extremely low surface epitope densities. Furthermore, these reagents potently suppressed tumor growth in vivo. Thus, ImmTACs overcome immune tolerance to cancer and represent a new approach to tumor immunotherapy.
              Article 0 comments Cited 131 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Proc Natl Acad Sci U S A
                Journal ID (iso-abbrev): Proc Natl Acad Sci U S A
                Journal ID (hwp): pnas
                Journal ID (publisher-id): PNAS
                Title: Proceedings of the National Academy of Sciences of the United States of America
                Publisher: National Academy of Sciences
                ISSN (Print): 0027-8424
                ISSN (Electronic): 1091-6490
                Publication date (Print): 14 September 2021
                Publication date (Electronic): 08 September 2021
                Publication date PMC-release: 08 September 2021
                Volume: 118
                Issue: 37
                Electronic Location Identifier: e2111173118
                Affiliations
                [1] aDepartment of Biological Engineering, Koch Institute for Integrative Cancer Research, Center for Precision Cancer Medicine, Massachusetts Institute of Technology , Cambridge, MA 02139;
                [2] bThermo Fisher Scientific , San Jose, CA 95134;
                [3] cThermo Fisher Scientific , Rockford, IL 61101;
                [4] dThermo Fisher Scientific , Precision Medicine Science Center, Cambridge, MA 02139;
                [5] eDivision of Surgical Oncology, Massachusetts General Hospital, Harvard Medical School , Boston, MA 02114
                Author notes
                1To whom correspondence may be addressed. Email: fwhite@ 123456mit.edu .

                Edited by K. Christopher Garcia, Stanford University, Stanford, CA, and approved August 2, 2021 (received for review June 22, 2021)

                Author contributions: L.E.S., A.S.G., B.P., S.G., D.T.F., G.M.B., R.J.S., and F.M.W. designed research; L.E.S. and D.T.F. performed research; B.P. and S.G. contributed new reagents/analytic tools; L.E.S. analyzed data; and L.E.S., A.S.G., B.P., S.G., D.T.F., G.M.B., R.J.S., and F.M.W. wrote the paper.

                Article
                Publisher ID: 202111173
                DOI: 10.1073/pnas.2111173118
                PMC ID: 8449407
                PubMed ID: 34497125
                SO-VID: 6798f12e-5146-4199-87f3-260309f7a4ad
                Copyright © Copyright © 2021 the Author(s). Published by PNAS.
                License:

                This open access article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND).

                History
                Date accepted : 02 August 2021
                Page count
                Pages: 3
                Funding
                Funded by: HHS | National Institutes of Health (NIH) 100000002
                Award ID: U54CA210180
                Award Recipient : Lauren E Stopfer Award Recipient : Forest M White
                Funded by: HHS | National Institutes of Health (NIH) 100000002
                Award ID: U01CA238720
                Award Recipient : Lauren E Stopfer Award Recipient : Forest M White
                Funded by: HHS | National Institutes of Health (NIH) 100000002
                Award ID: T32-ES007020
                Award Recipient : Lauren E Stopfer Award Recipient : Forest M White
                Categories
                Subject: 420
                Subject: 524
                Subject: Biological Sciences
                Subject: Immunology and Inflammation
                Series title: Brief Report

                Keywords: mhc class i,immunopeptidomics,antigen presentation
                Data availability:
                Keywords: mhc class i, immunopeptidomics, antigen presentation

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