Core2: Transcriptomics and Chromatin Structure

Genomic and Chromatin Analysis Core (Core B): SUMMARY The Genomic and Chromatin Analysis Core (Core B) will provide services to Projects 1 and 2, in collaboration with Core A, focusing on the role of alterations in transcriptional patterns induced by intravascular stress and extravasation on extravascular survival, dormancy, and outgrowth. GCC will be responsible for analyzing transcriptional and chromatin events that are affected by and may affect tumor cell vascular and transmigration processes isolated in Projects 1 and 2. GCC will deploy state-of-the-art technologies, including single-cell mRNA sequencing, genome mapping (e.g., Hi-C), and the nanoscale imaging of chromatin structural and molecular states, and these results will be used for computational modeling of the mechanical properties and the signaling pathways involved in mechano-adaptation and chromatin perturbation (Core A). In the bloodstream and during extravasation, tumor cells are exposed to a variety of physical stressors, including mechanical damage due to shear stress and passage through narrow capillaries with substantial nuclear deformations. It is not fully understood how mechanical stress and the resulting chromatin derangement and transcriptional alterations affect the ability of tumor cells to form metastases, lead to aggressive disease, develop dormancy, and foster their overall survival ability. Core B will provide genomic and chromatin analyses that will enable the Projects to begin addressing these long-standing questions on the consequences of mechano-adaptation in metastasis. Core B will leverage single- cell mRNA sequencing for transcription analysis as well as genome mapping (Hi-C, whenever possible, or Low- input Hi-C) and a unique suite of nanoscale imaging technologies (3-D chromatin scanning transmission electron tomography, optical single-molecule nanoscopy, and optical spectroscopic nanosensing) for chromatin conformation analysis on cells generated by the model systems in the Projects. Furthermore, the data on chromatin structure, including genome mapping and chromatin conformation imaging, will be provided to Core A to enable the modeling of the mechanical and phenotypic properties of metastasizing tumor cells. Beyond the scope of the U54 Center and upon completion of the Projects, the normalization of transcriptional reprogramming might be explored for therapeutic targeting of metastasis.