Shawn Davidson (LSI Fellow): "Probing metabolic heterogeneity with imaging mass spectrometry."
Abstract: Nutrient requirements for cancer cells are different from those of most normal cells. Understanding these differences and the factors that are responsible for creating different metabolic dependencies is critical to understanding the basic requirements of rapid proliferation and identifying potential therapeutic vulnerabilities. In particular, oncogene status, tissue-of-origin, cell-of-origin, and microenvironmental factors all can contribute to defining these requirements, but methods to characterize which dependencies exist in various physiological settings are lacking. Here, we couple stable-isotope infusions of nutrients in animal models of cancer and analyze normal tumors in situ with imaging mass spectrometry to better understand the active metabolic pathways of cells in normal tissues compared to tumors. We demonstrate regional differences in metabolism as a functional of spatial location and describe metabolic phenotypes and nutrient utilization of normal cells, tumor cells, and immune cells found within the tumor.
Joao Raimundo (Levine Lab): "Looking for the operator: How GAGA elements may mediate long range promoter-enhancer communication and timing of gene expression."
Transcriptional enhancers are short segments of DNA that can mediate patterns of gene expression in space and time. To activate gene expression a promoter and an enhancer have to come into physical proximity, which can happen over long distances and even across chromosomes. The organization of metazoan genomes into topologically associating domains helps to compartmentalize genes and reduce some of the distances between regulatory elements and promoters. Recent studies indicate that diminishing of TAD organization, by depleting CTCF, cohesin proteins or deleting insulator DNA binding sites in vertebrates, affects the expression of only a small subset of genes, suggesting that there may be other more relevant factors bridging the interactions between enhancers and promoters.
In Drosophila, the DNA binding protein GAGA factor (GAF) binds to GAGA repeats and has been associated with a general role in nucleosome displacement and in regulating the levels of paused polymerase in a wide variety of promoters. GAF binding is also enriched in distal enhancers across the Drosophila genome and has been shown earlier to be able to form loops between two DNA sequences suggesting that its pleiotropic regulatory role may involve an architecture function by bridging distal enhancers to their respective promoters.
We are currently investigating whether GAGA DNA binding motifs can mediate long range promoter-enhancer communication in Drosophila and which aspects of transcription are affected when this communication is disrupted.