A ‘Beyond Genomics’ Approach to Precision Oncology: Development of a Protein Profiling Platform for Tumor and Tumor Organoid Samples


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Christoph Sachse1,Gerrit Erdmann1,Anja Briese1,Przemyslaw Dudys1,Ulrike Pfohl2,Markus Templin3,Christian Regenbrecht4
1NMI TT Pharmaservices,2Institute of Pathology University Clinic Magdeburg,3NMI Natural and Medical Sciences Institute at the University of Tübingen,4Institute of Pathology University Clinic Magdeburg, CELLphenomics GmbH, ASC Oncology GmbH

Abstract

Background

Precision medicine is becoming increasingly important: The common goal of achieving a better response rate by avoiding ineffective therapies has sparked a multitude of different approaches, including the testing of patient-derived tumor tissue cultures for modeling individual patient response, and the use of various molecular pathology techniques for advanced tumor profiling. Well-established genomics methodologies e.g. panel sequencing, however, cannot directly assess cell signaling activity within the tumor cells, as this is defined by the phosphorylation status of cellular signaling pathway networks.

Method

Here we present the development of a robust protein profiling strategy utilizing the DigiWest immuno-assay platform, to obtain data on the status of key cellular signaling networks implicated in cancer, and on proteins targeted by FDA-approved drugs including a number of targeted cancer therapies for EGFR, HER2, PI3K, mTOR, BCR-ABL, ALK and AKT. We compiled a list of relevant pathway nodes and their associated phosphorylation sites that yield activity information on RAS/RAF/ERK, PI3K/AKT and mTOR signaling pathways. Based on this, we validated 242 total and phospho antibodies in a pre-set oncoproteomic DigiWest panel that yields information on the activity of these signaling networks from the receptor level down to transcription factors, apoptosis and proliferation.

Results

This oncoproteomic panel can be utilized for elucidating drug response in pre-clinical cell models, in patient-derived 3d organoid models (PD3Ds, PDOs), or in clinical tumor samples. For example, we show differential effects of PI3K kinase inhibitor copanlisib vs MEK inhibitor trametinib at different stages within their signaling networks in a cell-based model. Also, we tested this panel in PD3D organoids that were subjected to phenotypic growth assays to assess their response to common targeted therapies. Furthermore, we work on evaluating how such an oncoproteomic panel profiling might in the future also contribute to strengthen the rationale for personalized therapy decisions.

Conclusion

Multiplexed DigiWest protein profiling of cell signaling pathway activities yields valuable 'beyond genomics' mechanistic insights in patient-derived tumor organoid models.