Project 2: Deciphering the Dynamic Evolution of the Tumor-Immune Interface

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ABSTRACT – PROJECT 2 The central premise of our CSBC MIT/DFCI Center for Systems Biology in Glioblastoma is that high-content systems-level measurement techniques, employed across a variety of scales (molecular-cellular-tissue) with cell-type specific and spatial resolution, and combined with data integration, data deconvolution, and computational modeling, will enable the identification of critical pathways and networks regulating tumor progression and therapeutic resistance, while also providing biomarkers reflecting tumor state and efficacy of improved therapeutic strategies. This project aims to apply this same premise to the tumor-immune interface, defining the molecular pathways and networks underlying the dynamic evolution of the immunosuppressive state of GBM tumors. To this end, we have designed a multi-tiered project, with the foundation based on carefully controlled co-evolution of the tumor-immune interface in co-culture model systems in vitro, with temporal systems-level multi-omic analysis of molecular nodes in specific cell types provided by experimental and computational deconvolution. Computational modeling of this data coupled to quantitative phenotypic data will yield predictions as to nodes, pathways, and networks associated with altered immune and tumor states that will be experimentally verified. In the second Aim, we extend these studies to multiple GEMM and syngeneic murine models to query the tumor-immune interface in vivo, with spatial and temporal systems-level analysis at different time points of tumor development and in response to therapy. We also use this Aim to interrogate the role of different immune cells in mediating the evolution of the tumor-immune interface by engineering mice lacking various immune cell types and repeating the above studies. Computational modeling of these data connect molecular networks with dynamic evolution in the more complex in vivo environment. Finally, in the third Aim of this project, we extend these analyses to geographically distinct regions of human GBM tumors through systems- level analysis of spatially-guided core biopsies. These human tumor specimens provide ‘ground truth’ data for our computational models and enable development of quantitative models predicting the therapeutic impact of different treatment strategies. Together, this project will yield unprecedented systems-level molecular insight into the tumor-immune interface, enabling identification of novel therapeutic targets to abrogate the immunosuppressive nature of GBM tumors.