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. 2019 Nov;7(11):1748-1754.
doi: 10.1158/2326-6066.CIR-19-0107. Epub 2019 Sep 16.

Direct Detection and Quantification of Neoantigens

Qing Wang #  1   2 , Jacqueline Douglass #  3   2 , Michael S Hwang  3   2 , Emily Han-Chung Hsiue  3   2 , Brian J Mog  3   2 , Ming Zhang  3   2 , Nickolas Papadopoulos  3   2 , Kenneth W Kinzler  3   2 , Shibin Zhou  1   2 , Bert Vogelstein  1   2
Affiliations

Direct Detection and Quantification of Neoantigens

Qing Wang et al. Cancer Immunol Res. 2019 Nov.

Abstract

Many immunotherapeutic approaches under development rely on T-cell recognition of cancer-derived peptides bound to human leukocyte antigen molecules on the cell surface. Direct experimental demonstration that such peptides are processed and bound is currently challenging. Here, we describe a method that meets this challenge. The method entailed an optimized immunoprecipitation protocol coupled with two-dimensional chromatography and mass spectrometry. The ability to detect and quantify minute amounts of predefined antigens should be useful both for basic research in tumor immunology and for the development of rationally designed cancer vaccines.

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Conflict of interest statement

Conflict of Interest Statement

Bert Vogelstein and Kenneth W. Kinzler are founder of Personal Genome Diagnostics and Thrive and advisors of Sysmex, Eisai, CAGE, Neophore. BV is also an advisor to Nexus. Nickolas Papadopolous and Shibin Zhou are founders of Personal Genome Diagnostics and Thrive. These companies and others have licensed technologies related to the work described in this paper from Johns Hopkins University. Some of these licenses are associated with equity or royalty payments to the afore-mentioned individuals. Additional patent applications on the work described in this paper may be filed by Johns Hopkins University. The terms of these arrangements are being managed by Johns Hopkins University in accordance with its conflict of interest policies.

Figures

Fig.1
Fig.1
Schematic of MANA-SRM pipeline. Cells were lysed and HLA-binding peptides were enriched through immuno-precipitation with an antibody targeting HLA molecules. HLA molecules together with their presented peptides were eluted and dissociated. The eluate containing the neo-antigenic peptide was filtered where only short peptides (MW<3 kDa) were allowed to pass through. The filtered peptide sample was lyophilized and made ready for MANA-SRM analysis with additional improvements through HILIC-based cleanup and the D-Red strategy (see details in Materials and Methods).
See this image and copyright information in PMC

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