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New protein engineering-based tools and technologies for characterizing cell surface proteolysis in cancer cells for novel neo-epitope biomarkers and drug targets

Award Number: R01CA248323
ORGANIZATION: NATIONAL CANCER INSTITUTE
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 04/01/2020
PERIOD OF PERFORMANCE END DATE: 03/31/2025

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New protein engineering-based tools and technologies for characterizing cell surface proteolysis in cancer cells for novel neo-epitope biomarkers and drug targets - Project Summary Extracellular proteolysis is a hallmark of cancer. Proteolysis has major functional consequences for remodeling cell surface proteins and matrix including receptor activation and shedding of receptor extracellular domains. Of the more than 600 human proteases, over half are on the cell surface or secreted reflecting their significance for processing the extracellular space. Yet we understand very little about the targets for cell surface proteolysis (CSP), the proteases responsible, and resulting neo- cleaved products that could serve as new biomarkers or drug targets. What has been missing are robust technologies for unbiased identification of the CSP targets, their specific sites of cleavage, the proteases responsible for promoting disease, and the generation of neo-epitope specific antibodies. My group has engineered a novel peptide ligase, called subtiligase, and shown it robustly labels sites of proteolysis of soluble proteins. Our preliminary data show that this powerful tool can be used to determine the targets and precise sites of cleavage for CSP. We propose this novel CSP technology can be used to determine CSP signatures in cancer. We will initially focus on KRAS, the most dominant oncogene, especially in pancreatic cancer. We will determine KRAS- induced proteolysis in isogenic pancreatic cell lines, with and without mutant KRAS, grown in hypoxic and normoxic conditions in the context of two- and three-dimensional culture. We will identify the surface proteases up-regulated using cell surface capture (CSC) proteomics and confirm their activities using CRISPRi or small molecule inhibitors. We will characterize their specificities using new substrate phage technology coupled with NGS and match these to neo-epitopes we discover. Lastly, we will further exploit differential antibody phage display selection technology, and generate antibodies specific to the cleaved forms of various identified targets, including CDCP1. We will develop important technologies for new neo-epitope biomarkers and potential immune-oncology reagents for the characterization of these important cleavage events. Impact: Our studies will provide robust protein engineering-based technologies for unbiased insights into how CSP remodels cells, the proteases responsible, and actionable oncogene specific neo-epitopes to generate antibodies as potential biomarkers and therapeutics. We believe these approaches will be generally applicable to characterizing proteolysis in other solid tumor cancers.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2025 ( Subtotal = $404,177 )
2025	2025	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94103	SAN FRANCISCO	USA	Cancer Detection and Diagnosis Research	000	6	3/17/2025	COMPETING CONTINUATION	$404,177
2025	2024	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94103	SAN FRANCISCO	USA	Cancer Detection and Diagnosis Research	001	5	6/26/2025	NON-COMPETING CONTINUATION	$0
														Subtotal = $404,177

Issue Date FY: 2024 ( Subtotal = $345,184 )
2024	2024	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94103	SAN FRANCISCO	USA	Cancer Detection and Diagnosis Research	000	5	2/23/2024	NON-COMPETING CONTINUATION	$327,016
2024	2024	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94103	SAN FRANCISCO	USA	Cancer Detection and Diagnosis Research	001	5	4/16/2024	NON-COMPETING CONTINUATION	$18,168
														Subtotal = $345,184

Issue Date FY: 2023 ( Subtotal = $356,084 )
2023	2023	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Cancer Detection and Diagnosis Research	000	4	3/14/2023	NON-COMPETING CONTINUATION	$356,084
														Subtotal = $356,084

Issue Date FY: 2022 ( Subtotal = $356,084 )
2022	2022	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Cancer Detection and Diagnosis Research	001	3	5/3/2022	NON-COMPETING CONTINUATION	$29,069
2022	2022	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Cancer Detection and Diagnosis Research	000	3	3/2/2022	NON-COMPETING CONTINUATION	$327,015
														Subtotal = $356,084

Issue Date FY: 2021 ( Subtotal = $363,351 )
2021	2021	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Cancer Detection and Diagnosis Research	000	2	3/15/2021	NON-COMPETING CONTINUATION	$363,351
														Subtotal = $363,351

Issue Date FY: 2020 ( Subtotal = $362,803 )
2020	2020	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Cancer Detection and Diagnosis Research	000	1	2/7/2020	NEW	$362,803
														Subtotal = $362,803

Grand Total All Awards = $2,187,683

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New protein engineering-based tools and technologies for characterizing cell surface proteolysis in cancer cells for novel neo-epitope biomarkers and drug targets

Award Number: R01CA248323

ORGANIZATION: NATIONAL CANCER INSTITUTE

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 04/01/2020

PERIOD OF PERFORMANCE END DATE: 03/31/2025

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