Abstract 4773: Quantitative HLA-peptidomics by XPRESIDENT - differential quantitation of naturally processed HLA-restricted peptides for cancer immunotherapy development (2010)

Abstract Development of cancer immunotherapeutics aiming to induce the immune system's T-cell arm to fight cancer might be substantially improved by a profound knowledge of human leukocyte antigen (HLA)-bound peptide presentation levels on primary malignant tissues. This information is relevant for peptide vaccines in particular as well as for any other type of T-cell vaccine based on molecular entities such as protein, DNA or RNA. This kind of quantitative data has not been available on an “omics”-scale before, because common quantitation methods have so far mostly relied on differential chemical labeling strategies requiring that all samples to be compared are processed within a single experiment, which severely limited the possible scale of such investigations. For the first time our new approach allows the identification and selection of relevant over-presented peptide vaccine candidates based on direct relative quantitation of HLA-restricted peptide levels on cancer tissues in comparison to several different non-cancerous tissues and organs. This was achieved by the development of label-free differential quantitation using liquid chromatography-coupled mass spectrometry data processed by a proprietary data analysis pipeline, combining algorithms for sequence identification, spectral clustering, ion counting, and normalization. The approach can be applied to peptides from any HLA class I allele and routine quantitation has already been performed for two very common alleles and several different tumor entities. Extensive validation experiments confirmed the accuracy of our results. The normalization strategy was corroborated by measurements of beta-2 microglobulin levels in tissue lysates by western blotting. More than 9,500 different peptides have been quantified on 50 cancer and 35 non-cancerous samples so far. Significance scores for over-presentation within individual cancer entities as well as average presentation levels including confidence intervals for every single peptide and sample were established. Peptides exclusively presented on tumor tissue and peptides over-presented in tumor versus non-cancerous tissues and organs have been identified. To summarize, XPRESIDENT has the power to routinely identify relevant HLA-bound peptide antigens from primary tissue specimens quantitatively on a large scale. This information can not only be used for the development of peptide vaccines but is also highly valuable for molecularly defined immunomonitoring and identification of new antigens for any immunotherapeutic strategy in which HLA-restricted antigenic determinants function as targets, such as a variety of subunit vaccines or adoptive T-cell transfer approaches in cancer or infectious diseases. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4773.