Current Research and Scholarly Interests
Areas of research in the Rohatgi Lab:
1. The Hedgehog and WNT pathways, two cell-cell communication systems that regulate the formation of most tissues during development. These same pathways play central roles in tissue stem-cell function and organ regeneration in adults. Defects in these systems are associated with degenerative conditions and cancer.
2. Signal transduction at the primary cilium and the mechanism of cilia-associated human diseases. Primary cilia are solitary hair-like projections found on most cells in our bodies that function as critical hubs for signal transduction pathways (such as Hedgehog). Over fifty human genetic diseases, called “ciliopathies,” are caused by defects in cilia. Patients with ciliopathies can show phenotypes in nearly all organ systems, suffering from abnormalities ranging from birth defects to obesity.
3. Regulation of signaling pathways by endogenous lipids. The landscape of endogenous small-molecules and their biological functions remains a terra incognita, one that provides many opportunities to discover new regulatory layers in signaling pathways.
4. Phase separation in signal transduction. The formation of reversible, membrane-less compartments in cells by the segregation of proteins into liquid phases, hydrogels or amyloid-like assemblies is an emerging principle of cellular organization, with broad implications for areas that include signaling at the cell surface, stress response pathways, and neuro-degeneration.
5. Cellular responses to osmolar stresses. Maintaining a stable concentration of intracellular macromolecules and ions in a fluctuating environment is a universal challenge to homeostasis faced by all cells. In our own bodies, cells of the kidney and cells in inflammatory environments face tissue osmolality levels that are 3-fold higher than blood!
Strategies:
1. CRISPR/Cas9-based genome-wide, loss-of-function screens targeting signaling pathways.
•Enhancer and suppressor screens to comprehensively identify pathway components.
•Synthetic screens to identify the genetic vulnerabilities of cells carrying mutations in human oncogenes and tumor suppressor genes.
•Screens based on complex, physiological read-outs of signaling, such as differentiation.
2. Protein biochemistry: proteomics, structure-guided analysis, activity-based purification and cell-free reconstitution of signaling reactions in extracts and using purified components.
3. Chemical Biology: new probes to assay the interactions between proteins and small molecules.
4. Imaging: Live-cell imaging with innovative optical probes and genetically-encoded reporters to monitor the temporal and spatial progression of signaling, the quantitative phase separation behavior of proteins, and the dynamic, signal-regulated trafficking of proteins.
5. Collaborations: With experts in structural biology (Christian Siebold, Oxford, Elife 2013, 2016 and Nature 2016), genome-wide screening (Jan Carette, Stanford, Elife and Cancer Research 2016), protein and genome evolution (L. Aravind, NIH, Dev Cell 2014 and 2018), and developmental biology (James Briscoe, Francis Crick Institute, Dev Cell 2018).
