Cell circuits regulate responses to external stimuli, such as heat or pathogens. To investigate cellular response, we have the ability to measure mRNA levels, splice isoforms, protein levels, and post-translation modifications. An example of this type of circuitry analysis includes measuring and interpreting all of these parameters over a time course, following stimulation of mouse bone marrow-derived dendritic cells with bacterial lipopolysaccharides (LPS) endotoxin.
The CCP also focuses on deciphering the regulatory circuit that controls chromatin organization and maintenance in various stem cell types to determine their functional influence on a cell expression signature and phenotype. Studies of stable cell maintenance are being conducted in leukemia stem cells, hematopoietic stem cells, and mouse embryonic stem cells.
The CCP is assembling a technological and computational toolbox for regulatory circuit reconstruction. This effort includes working with emerging technologies, as well as developing computational tools for circuit modeling and visualization.
Techniques broadly used are various systematic perturbations (e.g. CRISPRs, shRNAs), single cell sequencing, ChIP-seq, and affinity-based proteomics to measure at the global and draft level scales.
Current explorations into the molecular underpinnings of cell circuitry are leveraging multiple data types including expression profiling and epigenetic analysis leveraging RNA-seq and CHiP-Seq coupled with molecular markers and cellular phenotypes. Data exploration ais enabled by visualization and analysis tools including IGV, GenomeSpace, Trinity, Scripture, and Bioconductor.
Differentiation of a cell into a more specialized cell type is directed by cellular circuits. The CCP is developing an unbiased reconstruction of genetic and molecular networks that direct cell differentiation in various human cell circuitry systems, such as Th17 immune cells and brain neuronal cell nuclei.
The CCP is engaged in numerous multidisciplinary projects in other model systems (e.g. fly, zebrafish, yeast) that aim to determine how complex molecular circuits function and evolve in response to genetic and environmental changes, cellular differentiation, evolution and disease.