The MIT/DFCI CSBC U54 Center for Systems Biology of Glioblastoma consists of two highly integrated research projects and two shared resource cores. Read details on Project 1 and 2 clicking the project articles below.
In close collaboration with the Project teams, the Biospecimens Core (Sarkaria, Spranger, Burns, Parney, Vaubel) will organize and execute the animal tumor model studies, including PDX, syngeneic, and GEMM models, involving tumor tissue acquisition at various time points of tumor progression, alteration of immune cell repertoire, treatment with anti- epileptics, and assessment of response to immunomodulatory therapies, among others.
Importantly, clinical expertise (Sarkaria, Burns, Parney, Vaubel) within the Biospecimens Core will facilitate the acquisition and initial evaluation of human tumor specimens for downstream analysis and are highly motivated to assess clinical translational potential of potential therapeutic options emerging from Projects 1 and 2. The Biospecimens Core personnel will distribute both animal and human bio-specimens to the relevant scientific personnel. Biological samples, including in vitro co-culture models and in vivo biospecimens obtained from the Biospecimens Core, will be analyzed through our cutting-edge platform in the Analytical Core (Agar, Iavarone, White, Levine, assisted by Elmquist).
This Core will conduct transcriptomic (scNucSeq, bulk RNASeq), immunopeptidomic, proteomic and phosphoproteomic, and metabolomic analyses of each biological sample as needed. As demonstrated in the preliminary data (above in section A5), the Analytical core is fully functioning, able to generate vast amounts of data from single 10-20 micron sections of core biopsies, and has already organized a sample processing and shipment pipeline. The Core will bring in additional technologies (CycIF, CODEX, spatial RNASeq) as needed to validate predictions emerging from our analyses and computational models. Data from the Analytical Core will be accumulated and organized in a FAIR-compliant ‘data lake’ constructed by Dr. Stuart Levine, the Data Manager for our CSBC Center for easy access by all members of the team.
Project 2 – Deciphering the Dynamic Evolution of the Tumor-Immune Interface (Spranger, White, Michor) is co-led by Drs. Spranger and White. Dr. Spranger is a trained immunologist with expertise in T cells and dendritic cells, focusing on immunosuppression in the tumor-immune interface; Dr. White brings expertise in the analysis of signaling networks in brain tumors […]
Project 1 – Deciphering the Dynamic Evolution of the Tumor-Neural Interface (Iavarone, Agar, Michor) is led by Dr. Antonio Iavarone, whose expertise in the classification of glioblastoma tumors has resulted in the identification of novel subtypes, and Dr. Nathalie Agar, whose expertise in spatial metabolomics has enabled quantification of drug distribution and enabled spatial pharmacometabolomics. […]