Targeting a proteolytic neo-epitope of CUB-domain containing protein 1 in RAS-driven cancer

Lim, S. A.; Zhou, J.; Martinko, A. J.; Wang, Y.-H.; Filippova, E. V.; Steri, V.; Wang, D.; Remesh, S. G.; Liu, J.; Hann, B.; Kossiakoff, A. A.; Evans, M. J.; Leung, K. K.; Wells, J. A.

doi:10.1101/2021.06.14.448427

bioRxiv · 10.1101/2021.06.14.448427

Targeting a proteolytic neo-epitope of CUB-domain containing protein 1 in RAS-driven cancer

Lim, S. A.·Zhou, J.·Martinko, A. J.·Wang, Y.-H.·Filippova, E. V.·Steri, V.·Wang, D.·Remesh, S. G.·Liu, J.·Hann, B.·Kossiakoff, A. A.·Evans, M. J.·Leung, K. K.·Wells, J. A.

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Abstract

A central challenge for any therapeutic is targeting diseased over normal cells. Proteolysis is frequently upregulated in disease and can generate proteoforms with unique neo-epitopes. We hypothesize that targeting proteolytic neo-epitopes can enable more effective and safer treatments, reflecting a conditional layer of disease-specific regulation. Here, we characterized the precise proteolytic isoforms of CUB domain containing protein 1 (CDCP1), a protein overexpressed and specifically cleaved in RAS-driven cancers. We validated that the N-terminal and C-terminal fragments of CDCP1 remain associated after proteolysis in vitro and on the surface of pancreatic cancer cells. Using a differential phage display strategy, we generated exquisitely selective recombinant antibodies that target cells harboring cleaved CDCP1 and not the full-length form using antibody-drug conjugates or a bi-specific T-cell engagers. We show tumor-specific localization and anti-tumor activity in a syngeneic pancreatic tumor model having superior safety profiles compared to a pan-CDCP1-targeting antibody. Our studies show proteolytic neo-epitopes can provide an orthogonal "AND" gate for disease-specific targeting. One-Sentence SummaryAntibody-based targeting of neo-epitopes generated by disease-associated proteolysis improves the therapeutic index

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Lim, S. A., Zhou, J., Martinko, A. J., Wang, Y.-H., Filippova, E. V., Steri, V., Wang, D., Remesh, S. G., Liu, J., Hann, B., Kossiakoff, A. A., Evans, M. J., Leung, K. K., Wells, J. A.. 2021-06-15. Targeting a proteolytic neo-epitope of CUB-domain containing protein 1 in RAS-driven cancer. https://doi.org/10.1101/2021.06.14.448427

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