Our research program addresses questions on fundamental biological processes across scales, from molecules to cells to tissues. Our current focus is on the regulation of epithelial plasticity, including differentiation and cancer behaviors. Within this context we are determining how protein behaviors and cell functions are regulated by intracellular pH (pHi) and actin filament dynamics.

Cancer cells have a higher pHi than normal cells, which as we describe enables metastatic progression (Webb et al., 2011 Nat Rev Cancer 11:671). However, we have limited understanding of how this occurs at the molecular level and can be exploited to limit disease progression. We have unique expertise to resolve regulation by pHi dynamics at molecular, cellular and tissue scales by bridging structural and cell biology. Through our 10-year collaboration with Matthew Jacobson, a computational biologist, we have shown how protonation functions as a post-translational modification to regulate protein structure and function (Schonichen et al., 2013 Ann Rev Biophys 42:289). We showed in molecular detail how increased pHi is necessary for directed cell migration by identifying the design principles and functional significance of selective pH sensors, including guanine nucleotide exchange factors regulating cell polarity (Frantz et al., 2007 J Cell Biol 179:403), cofilin controlling actin assemblies (Frantz et al., 2008 J Cell Biol 183:865, and talin (Srivastava et al., 2008 Proc Natl Acad Sci 105:14436) and the focal adhesion kinase FAK (Choi et al., 2013 J Cell Biol 202:849) controlling cell-substrate adhesion. We are now addressing questions on how increased pHi enables tumorigenic behaviors (Grillo-Hill et al., 2015 eLife 4:e03270), glycolytic enzymes for metabolic programming (Webb et al., 2015 Nature 523:111) and the selection and retention of specific somatic mutations. Contributing to these studies is our distinct and unique expertise in investigating pHi dynamics and pHi-regulated cell processes combined with innovative approaches, including optogenetic tools for modulating pHi, genetically encoded biosensors to rigorously quantify pHi dynamics in single cells and in vivo, and computational programs for identifying titrating networks of ionizable residues in proteins as well as amino acid mutation signatures in cancer databases.

In addition to cancer, dysregulated pHi is seen in other human diseases and our recent work investigates how lysosomal and cytosolic pH dynamics contributes to Alzheimer’s pathologies. For differentiation programs, we found that increased pHi is necessary for epithelial to mesenchymal transition (EMT) and embryonic stem cell differentiation. 

Our work on actin filament remodeling focuses on regulated actin dynamics in cell migration (Denker et al., 2002 J Cell Biol 159:1087; Patel and Barber, 2005 J Cell Biol 169:321; Baumgartner et al., 2006 PNAS 103:13391; Frantz et al., 2008 J Cell Biol 183:865), in EMT (Haynes et al., 2011 Mol Biol Cell 22:4750). We also identified a new mode for activation of the Arp2/3 complex by phosphorylation of the Arp2 subunit, including a molecular understanding of how phosphorylation regulates conformational changes in Arp2/3 complex subunit orientation, kinases activating the complex and cellular behaviors dependent on phosphorylated Arp2 (LeClaire et al., 2008 J Cell Biol 182:647; Narayanan et al., PLoS Comput Biol 7:e1002226; LeClaire et al., 2015 J Cell Biol 208:161). Our current work shows that Arp2/3 complex activity is necessary for differentiation of mouse embryonic stem cells, including nuclear events for transcriptional regulation.