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This study applied differential gene expression analysis to ovarian cancer samples from four GEO-derived datasets, followed by functional annotation and pathway analysis, protein localization and gene expression assessment, and oncogenicity and network analyses. A total of 153 differentially expressed genes were found, including 60 plasma-membrane protein–encoding genes suitable as CAR-T-cell antigens. Among them, 21 were predicted oncogenes, with nine proteins central to the network. Key oncogenic-pathway genes included MUC1, CXCR4, EPCAM, RACGAP1, UBE2C, PRAME, SORT1, JUP, and CLDN3, supporting them as recommended CAR-T antigens for ovarian cancer immunotherapy.",{"@graph":69,"@context":127},[70,84,106],{"@type":71,"itemListElement":72},"BreadcrumbList",[73,77,79,82],{"item":74,"name":75,"@type":76,"position":8},"https://docshare.wps.com","Home","ListItem",{"item":78,"name":9,"@type":76,"position":14},"https://docshare.wps.com/document/",{"item":80,"name":40,"@type":76,"position":81},"https://docshare.wps.com/document/research-report/",3,{"item":83,"name":65,"@type":76,"position":19},"https://docshare.wps.com/document/discovery-of-differentially-expressed-proteins-for-car-t-therapy-of-ovarian-cancers-with-a-bioinformatics-analysis/328526/",{"url":83,"name":65,"@type":85,"image":86,"author":91,"headline":65,"publisher":94,"fileFormat":97,"inLanguage":63,"description":67,"dateModified":98,"datePublished":99,"encodingFormat":97,"isAccessibleForFree":100,"interactionStatistic":101},"DigitalDocument",{"url":87,"@type":88,"width":89,"height":90},"https://docshare.wps.com/thumbnails/discovery-of-differentially-expressed-proteins-for-car-t-therapy-of-ovarian-cancers-with-a-bioinformatics-analysis/328526.png","ImageObject",300,407,{"name":92,"@type":93},"Oliver","Person",{"url":74,"name":95,"@type":96},"DocShare","Organization","application/pdf","2026-10-23","2026-09-21",true,{"@type":102,"interactionType":103,"userInteractionCount":105},"InteractionCounter",{"@type":104},"ViewAction",11,{"@type":107,"mainEntity":108},"FAQPage",[109,115,119,123],{"name":110,"@type":111,"acceptedAnswer":112},"Why are target antigens important for CAR-T cell therapy in ovarian cancer?","Question",{"text":113,"@type":114},"Target antigens are necessary for CAR-T cells to recognize and attack cancer cells. 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Timothy Qiu1,5,6  \n1 International Ph. D. Program in Cell Therapy and Regenerative Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan  \n2 Faculty of Medicine and Health Sciences, Universitas Muhammadiyah Makassar, Makassar 90221, Indonesia 3School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan  \n4 PhD Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan  \n5 Department of Obstetrics and Gynecology, Taipei Medical University Hospital, Taipei 11031, Taiwan 6 Department of Obstetrics and Gynecology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110301, Taiwan  \nCorrespondence to: J. Timothy Qiu; email: [191010@h.tmu.edu.tw](191010@h.tmu.edu.tw)  \nKeywords: chimeric antigen receptor (CAR)-T cell, ovarian cancer, differentially expressed gene (DEG), protein-protein interaction (PPI) network, CAR-T-cell antigen  \nReceived: December 15, 2023 Accepted: March 7, 2024 Published: July 18, 2024  \nCopyright: © 2024 Anurogo et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.  \nABSTRACT  \nTarget antigens are crucial for developing chimeric antigen receptor (CAR)-T cells, but their application to ovarian cancers is limited. This study aimed to identify potential genes as CAR-T-cell antigen candidates for ovarian cancers. A differential gene expression analysis was performed on ovarian cancer samples from four datasets obtained from the GEO datasets. Functional annotation, pathway analysis, protein localization, and gene expression analysis were conducted using various datasets and tools. An oncogenicity analysis and network analysis were also performed. In total, 153 differentially expressed genes were identified in ovarian cancer samples, with 60 differentially expressed genes expressing plasma membrane proteins suitable for CART-cell antigens. Among them, 21 plasma membrane proteins were predicted to be oncogenes in ovarian cancers, with nine proteins playing crucial roles in the network. Key genes identified in the oncogenic pathways of ovarian cancers included MUC1, CXCR4, EPCAM, RACGAP1, UBE2C, PRAME, SORT1, JUP, and CLDN3, suggesting them as recommended antigens for CAR-T-cell therapy for ovarian cancers. This study sheds light on potential targets for immunotherapy in ovarian cancers.  \nINTRODUCTION  \nA chimeric antigen receptor for T cells was developed by Zelig Eshhar in 1993 before being developed to increase its effectiveness and potential as an anti-tumor therapy [1] . One of the most influential and specific methods of immune therapy is chimeric antigen receptor (CAR)-T cell therapies. CAR-T-cell therapies have emerged atthe forefront of these advancements, demonstrating remarkable potential in transforming cancer treatment  \nparadigms [2] . CAR-T-cell therapy has emerged as a promising immunotherapeutic strategy for managing various malignancies. These engineered T cells are designed to recognize and destroy cancer cells expressing specific antigens, bypassing major histocompatibility complex (MHC) restrictions associated with conventional T-cell activation. Despite the success of CAR-T cell therapy in hematologic malignancies, its potential in solid tumors, such as ovarian cancer (OC), is yet to be fully realized. Key challenges include the identification of  \n11409  \ntarget antigens that are highly and specifically expressed by tumor cells but ","cbCailJPvRx3VxtM","https://ap.wps.com/l/cbCailJPvRx3VxtM","pdf",3175425,25,"English","# Introduction\n## Background on CAR-T cell therapy and ovarian cancer challenges\n# Abstract\n## Study purpose and bioinformatics workflow\n## Key findings: DEGs, plasma membrane proteins, oncogene predictions\n## Recommended CAR-T antigens","[{\"question\":\"Why are target antigens important for CAR-T cell therapy in ovarian cancer?\",\"answer\":\"Target antigens are necessary for CAR-T cells to recognize and attack cancer cells. For ovarian cancer, suitable antigens have been limited, restricting broader application of CAR-T approaches.\"},{\"question\":\"What bioinformatics analyses were performed to identify CAR-T-cell antigen candidates?\",\"answer\":\"The study conducted differential gene expression analysis on four GEO-derived datasets, then performed functional annotation, pathway analysis, protein localization and gene expression analysis, followed by oncogenicity and network analyses.\"},{\"question\":\"What key results were obtained from the analysis?\",\"answer\":\"The study identified 153 differentially expressed genes, including 60 plasma membrane protein–encoding genes suitable for CAR-T-cell antigens. It further predicted 21 plasma membrane proteins as oncogenes, with nine central network proteins.\"},{\"question\":\"Which genes were highlighted as recommended CAR-T-cell antigens for ovarian cancer?\",\"answer\":\"The recommended key genes included MUC1, CXCR4, EPCAM, RACGAP1, UBE2C, PRAME, SORT1, JUP, and CLDN3, based on their roles in oncogenic pathways and the network analysis.\"}]","Discovery of differentially expressed proteins for CAR-T therapy of ovarian cancers with a bioinformatics analysis | PDF",1789980062,63]