Abstract 5726: Pan-cancer proteogenomics expands the landscape of therapeutic targets
Authors: Lei Jonathan T. , Savage Sara R. , Yi Xinpei , Wen Bo , Zhao Hongwei , Somes Lauren K. , Shafer Paul W. , Dou Yongchao , Gao Qiang , Hoyos Valentina , Zhang Bing 
Published: April 2023

Abstract
Background: Molecularly targeted therapies are critical for improving cancer treatment. Since proteins are the targets of these therapies and functional effectors of genomic aberrations, proteogenomics data from the Clinical Proteomics Tumor Analysis Consortium (CPTAC) provides an unprecedented opportunity to characterize existing and future therapeutic targets for cancer treatment.
Approach: CPTAC proteogenomics data from &gt;1000 cancer patients spanning 10 cancer types was used to evaluate current and potential therapeutic targets curated from four databases. Cell line data from DepMap was further integrated to distinguish causations from associations. Computational pipelines were deployed to identify synthetic lethality for targeting tumor suppressor loss and to prioritize tumor associated antigens as immunotherapy targets.
Results: We systematically collected 3050 druggable proteins and classified them into 5 tiers to facilitate different applications such as companion diagnostics, drug repurposing, and new therapy development. Many druggable proteins showed poor mRNA-protein correlation, including secreted proteins and proteins whose abundance was correlated with their interaction partners instead of cognate mRNA, highlighting the necessity of direct proteomic quantification of drug targets. 618 druggable proteins showed both overexpression in tumors compared to normal and significant dependency in CRISPR-Cas9 screens of cell lines of the same lineage. Notably, PAK1, a kinase targeted by investigational drugs, demonstrated both overexpression and dependency in all cancer types. A similar analysis of phosphoproteomics data focusing on known activating sites of druggable proteins further revealed targetable dependencies driven by protein hyperactivation. The phosphosite pS50 on PTPN1, a phosphatase targeted by experimental drugs, was increased in 7 cancer types and PTPN1 demonstrated dependency in related cancer cell lines. Based on tumor proteogenomic data and cell line CRISPR-Cas9 screen data, we identified synthetic lethality for difficult to target tumor suppressor losses, revealing TP53 mutations as a candidate biomarker to select breast cancer patients for CHEK1 inhibition, and endometrial cancer patients for treatment with doxorubicin. We identified 140 proteins whose expression was restricted in normal tissues but abnormal in tumors. Experimental analysis of peptides predicted to have high binding affinity to the most common allotype HLA-A02 for 7 prioritized proteins identified 21 peptides from 5 proteins with both strong binding affinity and immunogenicity which could be further investigated as immunotherapy targets.
Conclusion: We generate a comprehensive resource of protein and peptide targets that covers multiple therapeutic modalities. This unique resource will pave the way for repurposing of currently available drugs and developing new drugs for cancer treatment.
Citation Format: Jonathan T. Lei, Sara R. Savage, Xinpei Yi, Bo Wen, Hongwei Zhao, Lauren K. Somes, Paul W. Shafer, Yongchao Dou, Qiang Gao, Valentina Hoyos, Bing Zhang. Pan-cancer proteogenomics expands the landscape of therapeutic targets. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5726.