@article{jeffries_gomez_macdonald_gamcsik_2022, title={Direct Detection of Glutathione Biosynthesis, Conjugation, Depletion and Recovery in Intact Hepatoma Cells}, volume={23}, ISSN={["1422-0067"]}, DOI={10.3390/ijms23094733}, abstractNote={Nuclear magnetic resonance (NMR) spectroscopy was used to monitor glutathione metabolism in alginate-encapsulated JM-1 hepatoma cells perfused with growth media containing [3,3′-13C2]-cystine. After 20 h of perfusion with labeled medium, the 13C NMR spectrum is dominated by the signal from the 13C-labeled glutathione. Once 13C-labeled, the high intensity of the glutathione resonance allows the acquisition of subsequent spectra in 1.2 min intervals. At this temporal resolution, the detailed kinetics of glutathione metabolism can be monitored as the thiol alkylating agent monobromobimane (mBBr) is added to the perfusate. The addition of a bolus dose of mBBr results in rapid diminution of the resonance for 13C-labeled glutathione due to a loss of this metabolite through alkylation by mBBr. As the glutathione resonance decreases, a new resonance due to the production of intracellular glutathione-bimane conjugate is detectable. After clearance of the mBBr dose from the cells, intracellular glutathione repletion is then observed by a restoration of the 13C-glutathione signal along with wash-out of the conjugate. These data demonstrate that standard NMR techniques can directly monitor intracellular processes such as glutathione depletion with a time resolution of approximately < 2 min.}, number={9}, journal={INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES}, author={Jeffries, Rex E. and Gomez, Shawn M. and Macdonald, Jeffrey M. and Gamcsik, Michael P.}, year={2022}, month={May} }
 @article{kirchoff_gomez_2022, title={EMBER: multi-label prediction of kinase-substrate phosphorylation events through deep learning}, ISSN={["1460-2059"]}, DOI={10.1093/bioinformatics/btac083}, abstractNote={Abstract
               
                  Motivation
                  Kinase-catalyzed phosphorylation of proteins forms the backbone of signal transduction within the cell, enabling the coordination of numerous processes such as the cell cycle, apoptosis, and differentiation. Although on the order of 105 phosphorylation events have been described, we know the specific kinase performing these functions for <5% of cases. The ability to predict which kinases initiate specific individual phosphorylation events has the potential to greatly enhance the design of downstream experimental studies, while simultaneously creating a preliminary map of the broader phosphorylation network that controls cellular signaling.
               
               
                  Results
                  We describe Embedding-based multi-label prediction of phosphorylation events (EMBER), a deep learning method that integrates kinase phylogenetic information and motif-dissimilarity information into a multi-label classification model for the prediction of kinase–motif phosphorylation events. Unlike previous deep learning methods that perform single-label classification, we restate the task of kinase–motif phosphorylation prediction as a multi-label problem, allowing us to train a single unified model rather than a separate model for each of the 134 kinase families. We utilize a Siamese neural network to generate novel vector representations, or an embedding, of peptide motif sequences, and we compare our novel embedding to a previously proposed peptide embedding. Our motif vector representations are used, along with one-hot encoded motif sequences, as input to a classification neural network while also leveraging kinase phylogenetic relationships into our model via a kinase phylogeny-weighted loss function. Results suggest that this approach holds significant promise for improving the known map of phosphorylation relationships that underlie kinome signaling.
               
               
                  Availability and implementation
                  The data and code underlying this article are available in a GitHub repository at https://github.com/gomezlab/EMBER.
               
               
                  Supplementary information
                  Supplementary data are available at Bioinformatics online.
               }, journal={BIOINFORMATICS}, author={Kirchoff, Kathryn E. and Gomez, Shawn M.}, year={2022}, month={Feb} }
 @article{mestril_kim_hinman_gomez_allbritton_2021, title={Stem/Proliferative and Differentiated Cells within Primary Murine Colonic Epithelium Display Distinct Intracellular Free Ca2+ Signal Codes}, ISSN={["2192-2659"]}, DOI={10.1002/adhm.202101318}, abstractNote={AbstractThe second messenger, intracellular free calcium (Ca2+), acts to transduce mitogenic and differentiation signals incoming to the colonic epithelium. A self‐renewing monolayer of primary murine colonic epithelial cells is formed over a soft, transparent hydrogel matrix for the scalable analysis of intracellular Ca2+ transients. Cultures that are enriched for stem/proliferative cells exhibit repetitive, high frequency (≈25 peaks h−1), and short pulse width (≈25 s) Ca2+ transients. Upon cell differentiation the transient frequency declines by 50% and pulse width widens by 200%. Metabolites and growth factors that are known to modulate stem cell proliferation and differentiation through Wnt and Notch signaling pathways, including CHIR‐99021, N‐[(3,5‐Difluorophenyl)acetyl]‐L‐alanyl‐2‐phenylglycine‐1,1‐dimethylethyl ester (DAPT), bone morphogenetic proteins (BMPs), and butyrate, also modulate Ca2+ oscillation patterns in a consistent manner. Increasing the stiffness of the supportive matrix from 200 Pa to 3 GPa shifts Ca2+ transient patterns toward those resembling differentiated cells. The ability to monitor Ca2+ oscillations with the spatial and temporal resolution offered by this platform, combined with its amenability to high‐content screens, provides a powerful tool for investigating real‐time communication within a wide range of primary tissues in addition to the colonic epithelium.}, journal={ADVANCED HEALTHCARE MATERIALS}, author={Mestril, Sebastian and Kim, Raehyun and Hinman, Samuel S. and Gomez, Shawn M. and Allbritton, Nancy L.}, year={2021}, month={Sep} }
 @article{berginski_moret_liu_goldfarb_sorger_gomez_2021, title={The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases}, volume={49}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gkaa853}, abstractNote={AbstractKinases form the backbone of numerous cell signaling pathways, with their dysfunction similarly implicated in multiple pathologies. Further facilitated by their druggability, kinases are a major focus of therapeutic development efforts in diseases such as cancer, infectious disease and autoimmune disorders. While their importance is clear, the role or biological function of nearly one-third of kinases is largely unknown. Here, we describe a data resource, the Dark Kinase Knowledgebase (DKK; https://darkkinome.org), that is specifically focused on providing data and reagents for these understudied kinases to the broader research community. Supported through NIH’s Illuminating the Druggable Genome (IDG) Program, the DKK is focused on data and knowledge generation for 162 poorly studied or ‘dark’ kinases. Types of data provided through the DKK include parallel reaction monitoring (PRM) peptides for quantitative proteomics, protein interactions, NanoBRET reagents, and kinase-specific compounds. Higher-level data is similarly being generated and consolidated such as tissue gene expression profiles and, longer-term, functional relationships derived through perturbation studies. Associated web tools that help investigators interrogate both internal and external data are also provided through the site. As an evolving resource, the DKK seeks to continually support and enhance knowledge on these potentially high-impact druggable targets.}, number={D1}, journal={NUCLEIC ACIDS RESEARCH}, author={Berginski, Matthew E. and Moret, Nienke and Liu, Changchang and Goldfarb, Dennis and Sorger, Peter K. and Gomez, Shawn M.}, year={2021}, month={Jan}, pages={D529–D535} }
 @article{urbina_gomez_gupton_2018, title={Spatiotemporal organization of exocytosis emerges during neuronal shape change}, volume={217}, ISSN={["1540-8140"]}, DOI={10.1083/jcb.201709064}, abstractNote={Neurite elongation and branching in developing neurons requires plasmalemma expansion, hypothesized to occur primarily via exocytosis. We posited that exocytosis in developing neurons and nonneuronal cells would exhibit distinct spatiotemporal organization. We exploited total internal reflection fluorescence microscopy to image vesicle-associated membrane protein (VAMP)–pHluorin—mediated exocytosis in mouse embryonic cortical neurons and interphase melanoma cells, and developed computer-vision software and statistical tools to uncover spatiotemporal aspects of exocytosis. Vesicle fusion behavior differed between vesicle types, cell types, developmental stages, and extracellular environments. Experiment-based mathematical calculations indicated that VAMP2-mediated vesicle fusion supplied excess material for the plasma membrane expansion that occurred early in neuronal morphogenesis, which was balanced by clathrin-mediated endocytosis. Spatial statistics uncovered distinct spatiotemporal regulation of exocytosis in the soma and neurites of developing neurons that was modulated by developmental stage, exposure to the guidance cue netrin-1, and the brain-enriched ubiquitin ligase tripartite motif 9. In melanoma cells, exocytosis occurred less frequently, with distinct spatial clustering patterns.}, number={3}, journal={JOURNAL OF CELL BIOLOGY}, author={Urbina, Fabio L. and Gomez, Shawn M. and Gupton, Stephanie L.}, year={2018}, month={Mar}, pages={1113–1128} }
 @article{oprea_bologa_brunak_campbell_gan_gaulton_gomez_guha_hersey_holmes_et al._2018, title={Unexplored therapeutic opportunities in the human genome}, volume={17}, ISSN={["1474-1784"]}, DOI={10.1038/nrd.2018.14}, abstractNote={In 2014, the Illuminating the Druggable Genome programme was launched to promote the exploration of currently understudied but potentially druggable proteins. This article discusses how the systematic collection and processing of a wide array of biological and chemical data as part of this programme has enabled the development of evidence-based criteria for tracking the target development level of human proteins, which indicates a substantial knowledge deficit for approximately one out of three proteins in the human proteome. It also highlights the nature of the unexplored therapeutic opportunities for major protein families. A large proportion of biomedical research and the development of therapeutics is focused on a small fraction of the human genome. In a strategic effort to map the knowledge gaps around proteins encoded by the human genome and to promote the exploration of currently understudied, but potentially druggable, proteins, the US National Institutes of Health launched the Illuminating the Druggable Genome (IDG) initiative in 2014. In this article, we discuss how the systematic collection and processing of a wide array of genomic, proteomic, chemical and disease-related resource data by the IDG Knowledge Management Center have enabled the development of evidence-based criteria for tracking the target development level (TDL) of human proteins, which indicates a substantial knowledge deficit for approximately one out of three proteins in the human proteome. We then present spotlights on the TDL categories as well as key drug target classes, including G protein-coupled receptors, protein kinases and ion channels, which illustrate the nature of the unexplored opportunities for biomedical research and therapeutic development.}, number={5}, journal={NATURE REVIEWS DRUG DISCOVERY}, author={Oprea, Tudor I. and Bologa, Cristian G. and Brunak, Soren and Campbell, Allen and Gan, Gregory N. and Gaulton, Anna and Gomez, Shawn M. and Guha, Rajarshi and Hersey, Anne and Holmes, Jayme and et al.}, year={2018}, month={May}, pages={317–332} }
 @article{dickinson_meyer_pawlak_gomez_jaspers_allbritton_2015, title={Analysis of sphingosine kinase activity in single natural killer cells from peripheral blood}, volume={7}, ISSN={["1757-9708"]}, DOI={10.1039/c5ib00007f}, abstractNote={Heterogeneity of sphingosine kinase (SK) pathway activity in natural killer (NK) cells may enable cells to respond effectively to a diverse array of pathogens as well as incipient tumor cells.}, number={4}, journal={INTEGRATIVE BIOLOGY}, author={Dickinson, Alexandra J. and Meyer, Megan and Pawlak, Erica A. and Gomez, Shawn and Jaspers, Ilona and Allbritton, Nancy L.}, year={2015}, month={Apr}, pages={392–401} }