PSRTTCA: A new approach for improving the prediction and characterization of tumor T cell antigens using propensity score representation learning
Issued Date
2023-01-01
Resource Type
ISSN
00104825
eISSN
18790534
Scopus ID
2-s2.0-85143841993
Pubmed ID
36481763
Journal Title
Computers in Biology and Medicine
Volume
152
Rights Holder(s)
SCOPUS
Bibliographic Citation
Computers in Biology and Medicine Vol.152 (2023)
Suggested Citation
Charoenkwan P., Pipattanaboon C., Nantasenamat C., Hasan M.M., Moni M.A., Lio P., Shoombuatong W. PSRTTCA: A new approach for improving the prediction and characterization of tumor T cell antigens using propensity score representation learning. Computers in Biology and Medicine Vol.152 (2023). doi:10.1016/j.compbiomed.2022.106368 Retrieved from: https://repository.li.mahidol.ac.th/handle/20.500.14594/81804
Title
PSRTTCA: A new approach for improving the prediction and characterization of tumor T cell antigens using propensity score representation learning
Other Contributor(s)
Abstract
Despite the arsenal of existing cancer therapies, the ongoing recurrence and new cases of cancer pose a serious health concern that necessitates the development of new and effective treatments. Cancer immunotherapy, which uses the body's immune system to combat cancer, is a promising treatment option. As a result, in silico methods for identifying and characterizing tumor T cell antigens (TTCAs) would be useful for better understanding their functional mechanisms. Although few computational methods for TTCA identification have been developed, their lack of model interpretability is a major drawback. Thus, developing computational methods for the effective identification and characterization of TTCAs is a critical endeavor. PSRTTCA, a new machine learning (ML)-based approach for improving the identification and characterization of TTCAs based on their primary sequences, is proposed in this study. Specifically, we introduce a new propensity score representation learning algorithm that allows one to generate various sets of propensity scores of amino acids, dipeptides, and g-gap dipeptides to be TTCAs. To enhance the predictive performance, optimal sets of variant propensity scores were determined and fed into the final meta-predictor (PSRTTCA). Benchmarking results revealed that PSRTTCA was a more precise and promising tool for the identification and characterization of TTCAs than conventional ML classifiers and existing methods. Furthermore, PSR-derived propensities of amino acids in becoming TTCAs are used to reveal the relationship between TTCAs and their informative physicochemical properties in order to provide insights into TTCA characteristics. Finally, a user-friendly online computational platform of PSRTTCA is publicly available at http://pmlabstack.pythonanywhere.com/PSRTTCA. The PSRTTCA predictor is anticipated to facilitate community-wide efforts in accelerating the discovery of novel TTCAs for cancer immunotherapy and other clinical applications.