- Core B: Genomics and Immune Monitoring Shared Resource Core The application of next generation sequencing to cancer genomics has already had broad-based application to this disease and has greatly enriched our understanding of DNA- and RNA-level alterations that occur in the course of disease onset and progression, and in response and resistance to therapies, among others. Recent efforts to apply next generation sequencing to cancer have been focused on characterization of the immune system's response to cancers. These new methods are dependent upon performing appropriate preparatory methods prior to the read-out from NGS, and especially upon computational and algorithmic evaluation of the resulting data set. In addition to NGS, the application of selection by immune cell-specific antibodies by cytometry, followed by time-of-flight mass spectrometry, have been combined in mass cytometry instrumentation that has tremendously enhanced our characterization of the immune microenvironment in cancer, especially when these data are integrated with single cell transcriptome-based evaluation of the tumor immune microenvironment. Our Genomics and Immune Monitoring Shared Resource Core will apply these cutting-edge approaches to characterization of the immunome in our mouse models-focused immunotherapy studies, in efforts to enhance the individual projects proposed in the U54. In particular, using exome sequencing data and paired tumor RNAseq data, we will evaluate the immunogenic epitopes (both shared and neoantigens) of different cancer models, enabling our U54 investigators to track specific anti-tumor T cell responses in their models. RNAseq data also can report changes in gene expression levels for known immunomodulatory genes, providing specific information about treatment-related gene expression changes, and provides a means of characterizing immune infiltrating cells and their changes in response to immunotherapy by data deconvolution. Integration of mass cytometry data, alone and integrated with single cell transcriptome data, will provide further granularity about the nature and types of immune cell infiltration and persistence in the context of durability of response to therapy. Finally, the results from immune infiltrate analyses will be compared to conventional pathology staining results and to Nanostring nCounter-based immune profiling assay results, thereby shaping a strong evidence base for the changes elicited by the different therapeutic approaches being investigated. We also plan to evaluate changes in the T-cell receptor (TCR) repertoire in the context of immunotherapy treatments with our co-investigators. Taken together, these foundational discovery efforts set the stage for future human clinical trials of our innovative approaches and provide the basis for devising accompanying clinical companion diagnostic and immune response monitoring assays.
