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Enhancing proteasomal processing improves survival for a peptide vaccine used to treat glioblastoma

Fidanza, Mario and Gupta, Puja and Sayana, Anin and Shanker, Varun and Pahlke, Svenja-Maria and Vu, Brandon and Krantz, Fanny and Azameera, Aruna and Wong, Nicollette and Anne, Navya and Xia, Yuanxuan and Rong, Jiming and Anne, Avani and Skirboll, Stephen and Lim, Michael and Wong, Albert J. (2021) Enhancing proteasomal processing improves survival for a peptide vaccine used to treat glioblastoma. Science Translational Medicine, 13 (598). Art. No. eaax4100. ISSN 1946-6234. doi:10.1126/scitranslmed.aax4100.

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Despite its essential role in antigen presentation, enhancing proteasomal processing is an unexploited strategy for improving vaccines. pepVIII, an anticancer vaccine targeting EGFRvIII, has been tested in several trials for glioblastoma. We examined 20 peptides in silico and experimentally, which showed that a tyrosine substitution (Y6-pepVIII) maximizes proteasome cleavage and survival in a subcutaneous tumor model in mice. In an intracranial glioma model, Y6-pepVIII showed a 62 and 31% improvement in median survival compared to control animals and pepVIII-vaccinated mice. Y6-pepVIII vaccination altered tumor-infiltrating lymphocyte subsets and expression of PD-1 on intratumoral T cells. Combination with anti–PD-1 therapy cured 45% of the Y6-pepVIII–vaccinated mice but was ineffective for pepVIII-treated mice. Liquid chromatography–tandem mass spectrometry analysis of proteasome-digested pepVIII and Y6-pepVIII revealed that most fragments were similar but more abundant in Y6-pepVIII digests and 77% resulted from proteasome-catalyzed peptide splicing (PCPS). We identified 10 peptides that bound human and murine MHC class I. Nine were PCPS products and only one peptide was colinear with EGFRvIII, indicating that PCPS fragments may be a component of MHC class I recognition. Despite not being colinear with EGFRvIII, two of three PCPS products tested were capable of increasing survival when administered independently as vaccines. We hypothesize that the immune response to a vaccine represents the collective contribution from multiple PCPS and linear products. Our work suggests a strategy to increase proteasomal processing of a vaccine that results in an augmented immune response and enhanced survival in mice.

Item Type:Article
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URLURL TypeDescription Materials
Fidanza, Mario0000-0002-6436-2874
Sayana, Anin0000-0002-9713-6654
Shanker, Varun0000-0003-4443-9229
Pahlke, Svenja-Maria0000-0001-5955-1673
Rong, Jiming0000-0003-1379-6856
Lim, Michael0000-0003-0523-3076
Wong, Albert J.0000-0001-9102-8129
Additional Information:© 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Submitted 21 March 2019; Resubmitted 24 August 2020; Accepted 18 March 2021; Published 16 June 2021. We thank R. Winant, M. Eckhardt, and A. Chien for assistance with the MALDI-TOF studies as well as R. Leib and F. Liu and the Stanford Proteomics facility for assistance with the LC-MS/MS analysis. We also thank B. F. de Silva, T. M. Lucena, and V. Pieri for assistance with ELISA studies and L.-S. Perez for providing the CT2A(vIII) cell lines. This work was funded by California Institute of Regenerative Medicine (TRAN1-08522 and DISC2COVID19-11941 to A.J.W.). Author contributions: M.F. performed intracranial tumor model studies, CTL and TIL assays, and the checkpoint inhibitor studies with assistance from Y.X. and M.L. M.F. wrote the manuscript with assistance from A.S., V.S., and A.J.W. S.-M.P. performed the peptide modeling and, with M.F., also performed the in silico analysis. S.-M.P. and P.G. performed T2 binding assays. A.Azameera., N.A., and B.V. performed the in silico analysis and T2 assays. P.G. performed subcutaneous tumor studies with assistance from F.K., B.V. and J.R. Proteasome digestion assays were performed by P.G. with collaboration from S.-M.P. and A.Azameera. A.S. and V.S. analyzed proteasome fragments with further analysis done in conjunction with N.W., A. Anne, S.S., and A.J.W. A.J.W. conceived the study, supervised the project, and edited the manuscript. Competing interests: M.L. reports research support from Arbor, BMS, Accuray, DNAtrix, Tocagen, Biohaven, and Kyrin-Kyowa. M.L. is a consultant to Tocagen, SQZ Technologies, VBI, InCephalo Therapeutics, Pyramid Bio, and Stryker. Two U.S. patents related to this work have been issued to A.J.W. (#6,224,868, “Reagent and processes for targeting mutant epidermal growth factor receptors,” and #9,694,060, “Peptide vaccines based on the EGFRvIII sequence for the treatment of tumors”). The authors declare that they have no other competing interests. Data and materials availability: The atomic coordinates for the pepVIII and Y6-pepVIII models are available in the Model Archive database under the archive numbers ma-7c64k and ma-5s4ct, respectively. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRoteomics IDEntifications (PRIDE) repository (submission no. 1-20190227-11204). All data associated with this study are present in the paper or the Supplementary Materials.
Funding AgencyGrant Number
California Institute of Regenerative MedicineTRAN1-08522
California Institute of Regenerative MedicineDISC2COVID19-11941
California Institute for Regenerative MedicineUNSPECIFIED
Issue or Number:598
Record Number:CaltechAUTHORS:20210621-152256841
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Official Citation:M. Fidanza, P. Gupta, A. Sayana, V. Shanker, S.-M. Pahlke, B. Vu, F. Krantz, A. Azameera, N. Wong, N. Anne, Y. Xia, J. Rong, A. Anne, S. Skirboll, M. Lim, A. J. Wong, Enhancing proteasomal processing improves survival for a peptide vaccine used to treat glioblastoma. Sci. Transl. Med. 13, eaax4100 (2021)
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:109503
Deposited By: Tony Diaz
Deposited On:21 Jun 2021 18:00
Last Modified:21 Jun 2021 18:00

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