Research Papers:

Large-scale in-silico identification of a tumor-specific antigen pool for targeted immunotherapy in triple-negative breast cancer

Jessica Kaufmann, Nicolas Wentzensen, Titus J. Brinker and Niels Grabe _

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Oncotarget. 2019; 10:2515-2529. https://doi.org/10.18632/oncotarget.26808

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Jessica Kaufmann1,2, Nicolas Wentzensen3, Titus J. Brinker4,5 and Niels Grabe1,2

1Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, University of Heidelberg, Heidelberg, Germany

2Medical Oncology Department, Universitätsklinik Heidelberg, National Center for Tumor Diseases (NCT), Heidelberg, Germany

3National Cancer Institute, Division of Cancer Epidemiology & Genetics, Clinical Genetics Branch, NCI Shady Grove, Bethesda, Maryland, USA

4National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Heidelberg, Germany

5Department of Dermatology, University Hospital Heidelberg, Heidelberg, Germany

Correspondence to:

Niels Grabe, email: [email protected]

Keywords: immunotherapy; RNA-seq; triple negative breast cancer; target identification; TCGA

Received: August 31, 2018    Accepted: February 15, 2019    Published: April 02, 2019


Since the advent of cetuximab, clinical cancer treatment has evolved from the standard, relatively nonspecific chemo- and radiotherapy with significant cytotoxic side effects towards immunotherapeutic approaches with selective, target-mechanism-based effects. Antibody therapies as the most successful form of cancer immunotherapy led to approved treatments for specific cancer types with increased patient survival. Thus, the identification of tumor antigens with high immunogenicity is in central focus now. In this study, we applied computational methods to comprehensively discover overexpressed molecular targets with high therapeutic relevance for clinical, immunotherapeutic cancer treatment in triple-negative breast cancer (TNBC). By actively modeling potential negative side effects utilizing expression data of 29 different, normal human tissues, we were able to develop a highly-specific coverage of TNBC patients with RNA targets. We identified here more than 400 potential tumor-specific antigens suitable for targeted therapy, including several already identified as potential targets for TNBC and other solid tumors. A specific cocktail of MAGEB4, CT83, TLX3, ACTL8, PRDM13 achieved almost 94% patient coverage in TNBC. Overall, these results show that our approach can identify and prioritize TNBC targets suitable for targeted therapy. Therefore, our method has the potential to lead to new and more effective immunotherapeutic cancer treatment.

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