Our research determines molecular mechanisms regulating epithelial plasticity, including differentiation, stem cell behaviors, and cancer. Within this context, our three areas of focus include 1) intracellular pH dynamics, 2) regulation of actin filament architectures, and 3) lysosome pH dynamics.
Intracellular pH (pHi) dynamics
A major aspect our research program is determining in molecular detail how pHi dynamics regulates cell behaviors, with a focus on epithelial plasticity. Although pHi was previously thought to be relatively constant as a homeostatic mechanism, we now know that pHi changes during normal cell cycle progression, cell migration, and cell differentiation. Moreover, pHi is dysregulated in diseases, including being constitutively increased in cancers, which as we describe enables a range of cancer cell behaviors, including increased proliferation, tumorigenesis, metabolic reprogramming and metastasis (Webb et al., 2011 Nat Rev Cancer 11:671; White et al., 2017 J Cell Sci 130:663-669). The molecular mechanisms mediating pHi-regulated cell behaviors, however, remain understudied and largely unknown. Our work bridges protein structure and electrostatics with cell biology to reveal how pHi dynamics regulates cell behaviors through protonation of titrating amino acids as a post-translational modification to regulate protein structure and function (Schönichen et al., 2013 Ann Rev Biophys. 42:289). We resolved in molecular detail the design principles and functional significance of endogenous pH sensors (Fig.1) with activities or binding kinetics regulated within the narrow pHi range, 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), 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, β-catenin regulating epithelial plasticity (White et al., 2018 J Cell Biol 217:3965) as well as tau binding to microtubules (Charafeddine et al., 2019 J Biol Chem. 294:8779), transcription factor-DNA binding selectivity (Kisor et al., 2025 Nucleic Acids Res 53:gkaf474) and a gain in pH sensing by charge-changing somatic mutations in cancers (White et al, 2017 Sci Signaling . We are also 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; Webb et al., 2017 J Cell Biol 216:2305) and the retention of recurring somatic mutations (White et al., 2017 Sci Signaling 10(495). pii: eaam9931). For differentiation programs, we found that increased pHi is necessary for adult and embryonic stem cell differentiation and lineage specification (Ulmschneider et al., 2016 J. Cell Biol 215:345; Benitez et al., 2019 Dev Biol. 452:127; Liu, et al., 2023 Nat Commun 4:3745).
Regulation of actin filament architectures
An additional focus is on how actin filament dynamics and architectures regulate epithelial plasticity. Our work on actin filament dynamics has focused on regulated actin architectures 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) and EMT (Haynes et al., 2011 Mol Biol Cell 22:4750; Rana et al., 2015 J Cell Sci 128:1083; Rana et al., 2018 Mol Biol Cell 29:1465) as well as new modes for activation of the Arp2/3 complex (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). Additional work includes resolving roles for actin dynamics in mouse and human embryonic stem cell differentiation (Aloisio and Barber 2022 Stem Cell Reports 17:1318; Meyer et al., 2024 eLife 13:e89725) (Fig. 2).
Lysosome pH dynamics
A recent new direction is addressing questions on the role of lysosome pH (pHlys) dynamics in cancers and neurodegenerative disorders. These studies include generating the first genetically encoded and ratiometric pHlys biosensor, pHLARE, (Webb, et al., 2021 Mol Biol Cell 32:131) (Fig. 3) and determining increased pHlys and lysosome dynamics in induced pluripotent stem cells (iPSCs) derived from patients with frontotemporal dementia (Infante-Tadeo and Barber, 2025 Mol Biol Cell mbcE24120539).