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Article ; Online: Enabling Hotspot Detection and Public Health Response to the COVID-19 Pandemic.

Foraker, Randi / Landman, Joshua / Lackey, Ian / Haslam, Matthew D / Antes, Alison L / Goldfarb, Dennis

2022 Volume 19, Page(s) E35

Abstract: Introduction: Public-facing maps of COVID-19 cases, hospital admissions, and deaths are commonly displayed at the state, county, and zip code levels, and low case counts are suppressed to protect confidentiality. Public health authorities are tasked ... ...

Abstract	Introduction: Public-facing maps of COVID-19 cases, hospital admissions, and deaths are commonly displayed at the state, county, and zip code levels, and low case counts are suppressed to protect confidentiality. Public health authorities are tasked with case identification, contact tracing, and canvasing for educational purposes during a pandemic. Given limited resources, authorities would benefit from the ability to tailor their efforts to a particular neighborhood or congregate living facility. Methods: We describe the methods of building a real-time visualization of patients with COVID-19-positive tests, which facilitates timely public health response to the pandemic. We developed an interactive street-level visualization that shows new cases developing over time and resolving after 14 days of infection. Our source data included patient demographics (ie, age, race and ethnicity, and sex), street address of residence, respiratory test results, and date of test. Results: We used colored dots to represent infections. The resulting animation shows where new cases developed in the region and how patterns changed over the course of the pandemic. Users can enlarge specific areas of the map and see street-level detail on residential location of each case and can select from demographic overlays and contour mapping options to see high-level patterns and associations with demographics and chronic disease prevalence as they emerge. Conclusions: Before the development of this tool, local public health departments in our region did not have a means to map cases of disease to the street level and gain real-time insights into the underlying population where hotspots had developed. For privacy reasons, this tool is password-protected and not available to the public. We expect this tool to prove useful to public health departments as they navigate not only COVID-19 pandemic outcomes but also other public health threats, including chronic diseases and communicable disease outbreaks.
MeSH term(s)	COVID-19/epidemiology ; Chronic Disease/epidemiology ; Contact Tracing/methods ; Demography/methods ; Disease Outbreaks/statistics & numerical data ; Hospitalization ; Humans ; Pandemics ; Public Health/methods ; Public Health/statistics & numerical data
Language	English
Publishing date	2022-06-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	2135684-1
ISSN	1545-1151 ; 1545-1151
ISSN (online)	1545-1151
ISSN	1545-1151
DOI	10.5888/pcd19.210425
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Article: A basally active cGAS-STING pathway limits SARS-CoV-2 replication in a subset of ACE2 positive airway cell models.

Puray-Chavez, Maritza / LaPak, Kyle M / Jasuja, Ria / Pan, Jiehong / Xu, Jian / Eschbach, Jenna E / Mohammed, Shawn / Lawson, Dana Q / Wang, Qibo / Brody, Steven L / Major, Michael B / Goldfarb, Dennis / Kutluay, Sebla B

bioRxiv : the preprint server for biology

2024

Abstract: Host factors that define the cellular tropism of SARS-CoV-2 beyond the cognate ACE2 receptor are poorly defined. From a screen of human airway derived cell lines that express varying levels of ACE2/TMPRSS2, we found a subset that express comparably high ... ...

Abstract	Host factors that define the cellular tropism of SARS-CoV-2 beyond the cognate ACE2 receptor are poorly defined. From a screen of human airway derived cell lines that express varying levels of ACE2/TMPRSS2, we found a subset that express comparably high endogenous levels of ACE2 but surprisingly did not support SARS-CoV-2 replication. Here we report that this resistance is mediated by a basally active cGAS-STING pathway culminating in interferon (IFN)-mediated restriction of SARS-CoV-2 replication at a post-entry step. Pharmacological inhibition of JAK1/2, depletion of the IFN-α receptor and cGAS-STING pathway effectors substantially increased SARS-CoV-2 replication in these cell models. While depletion of cGAS or STING was sufficient to reduce the preexisting levels of IFN-stimulated genes (ISGs), SARS-CoV-2 infection in STING knockout cells independently induced ISG expression. Remarkably, SARS-CoV-2-induced ISG expression in STING knockout cell as well as in primary human airway cultures was limited to uninfected bystander cells, demonstrating efficient antagonism of the type I/III IFN-pathway, but not viral sensing or IFN production, in productively infected cells. Of note, SARS-CoV-2-infected primary human airway cells also displayed markedly lower levels of STING expression, raising the possibility that SARS-CoV-2 can target STING expression or preferentially infect cells that express low levels of STING. Finally, ectopic ACE2 overexpression overcame the IFN-mediated blocks, suggesting the ability of SARS-CoV-2 to overcome these possibly saturable blocks to infection. Our study highlights that in addition to viral receptors, basal activation of the cGAS-STING pathway and innate immune defenses may contribute to defining SARS-CoV-2 cellular tropism.
Language	English
Publishing date	2024-01-08
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.01.07.574522
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Article ; Online: TRIM67 regulates exocytic mode and neuronal morphogenesis via SNAP47.

Urbina, Fabio L / Menon, Shalini / Goldfarb, Dennis / Edwards, Reginald / Ben Major, M / Brennwald, Patrick / Gupton, Stephanie L

Cell reports

2022 Volume 34, Issue 6, Page(s) 108743

Abstract: Neuronal morphogenesis involves dramatic plasma membrane expansion, fueled by soluble N-ethylmaleimide-sensitive factor attachment protein eceptors (SNARE)-mediated exocytosis. Distinct fusion modes described at synapses include full-vesicle fusion (FVF) ...

Abstract	Neuronal morphogenesis involves dramatic plasma membrane expansion, fueled by soluble N-ethylmaleimide-sensitive factor attachment protein eceptors (SNARE)-mediated exocytosis. Distinct fusion modes described at synapses include full-vesicle fusion (FVF) and kiss-and-run fusion (KNR). During FVF, lumenal cargo is secreted and vesicle membrane incorporates into the plasma membrane. During KNR, a transient fusion pore secretes cargo but closes without membrane addition. In contrast, fusion modes are not described in developing neurons. Here, we resolve individual exocytic events in developing murine cortical neurons and use classification tools to identify four distinguishable fusion modes: two FVF-like modes that insert membrane material and two KNR-like modes that do not. Discrete fluorescence profiles suggest distinct behavior of the fusion pore. Simulations and experiments agree that FVF-like exocytosis provides sufficient membrane material for morphogenesis. We find the E3 ubiquitin ligase TRIM67 promotes FVF-like exocytosis in part by limiting incorporation of the Qb/Qc SNARE SNAP47 into SNARE complexes and, thus, SNAP47 involvement in exocytosis.
MeSH term(s)	Animals ; Cytoskeletal Proteins/genetics ; Cytoskeletal Proteins/metabolism ; Exocytosis ; Female ; Mice ; Mice, Knockout ; Neurogenesis ; Qb-SNARE Proteins/genetics ; Qb-SNARE Proteins/metabolism ; Qc-SNARE Proteins/genetics ; Qc-SNARE Proteins/metabolism ; SNARE Proteins/genetics ; SNARE Proteins/metabolism ; Synapses/genetics ; Synapses/metabolism ; Tripartite Motif Proteins/genetics ; Tripartite Motif Proteins/metabolism
Chemical Substances	Cytoskeletal Proteins ; Qb-SNARE Proteins ; Qc-SNARE Proteins ; SNARE Proteins ; Snap47 protein, mouse ; TRIM67 protein, mouse ; Tripartite Motif Proteins
Language	English
Publishing date	2022-02-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2021.108743
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Article ; Online: The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases.

Berginski, Matthew E / Moret, Nienke / Liu, Changchang / Goldfarb, Dennis / Sorger, Peter K / Gomez, Shawn M

Nucleic acids research

2020 Volume 49, Issue D1, Page(s) D529–D535

Abstract: Kinases 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 ... ...

Abstract	Kinases 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.
MeSH term(s)	Gene Expression Regulation, Enzymologic ; Internet ; Knowledge Bases ; Phosphotransferases/metabolism
Chemical Substances	Phosphotransferases (EC 2.7.-)
Language	English
Publishing date	2020-10-20
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkaa853
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Article ; Online: The ubiquitylome of developing cortical neurons.

Menon, Shalini / Goldfarb, Dennis / Cousins, Emily M / Major, M Ben / Gupton, Stephanie L

microPublication biology

2020 Volume 2020

Language	English
Publishing date	2020-11-28
Publishing country	United States
Document type	Journal Article
ISSN	2578-9430
ISSN (online)	2578-9430
DOI	10.17912/micropub.biology.000333
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Article: Biophysical Mechanism of Allosteric Regulation of Actin Capping Protein.

Mooren, Olivia L / Stuchell-Brereton, Melissa D / McConnell, Patrick / Yan, Chenbo / Wilkerson, Emily M / Goldfarb, Dennis / Cooper, John A / Sept, David / Soranno, Andrea

bioRxiv : the preprint server for biology

2023

Abstract: Actin capping protein (CP) can be regulated by steric and allosteric mechanisms. The molecular mechanism of the allosteric regulation at a biophysical level includes linkage between the binding sites for three ligands: F-actin, Capping-Protein- ... ...

Abstract	Actin capping protein (CP) can be regulated by steric and allosteric mechanisms. The molecular mechanism of the allosteric regulation at a biophysical level includes linkage between the binding sites for three ligands: F-actin, Capping-Protein-Interacting (CPI) motifs, and V-1/myotrophin, based on biochemical functional studies and solvent accessibility experiments. Here, we investigated the mechanism of allosteric regulation at the atomic level using single-molecule Förster resonance energy transfer (FRET) and molecular dynamics (MD) to assess the conformational and structural dynamics of CP in response to linked-binding site ligands. In the absence of ligand, both single-molecule FRET and MD revealed two distinct conformations of CP in solution; previous crystallographic studies revealed only one. CPI-motif peptide association induced conformational changes within CP that propagate in one direction, while V-1 association induced conformational changes in the opposite direction. Comparing CPI-motif peptides from different proteins, we identified variations in CP conformations and dynamics that are specific to each CPI motif. MD simulations for CP alone and in complex with a CPI motif and V-1 reveal atomistic details of the conformational changes. Analysis of the interaction of CP with wildtype (wt) and chimeric CPI-motif peptides using single-molecule FRET, isothermal calorimetry (ITC) and MD simulation indicated that conformational and affinity differences are intrinsic to the C-terminal portion of the CPI-motif. We conclude that allosteric regulation of CP involves changes in conformation that disseminate across the protein to link distinct binding-site functions. Our results provide novel insights into the biophysical mechanism of the allosteric regulation of CP.
Language	English
Publishing date	2023-08-17
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.08.16.553570
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Article ; Online: Protein Kinase Signaling Networks Driven by Oncogenic Gq/11 in Uveal Melanoma Identified by Phosphoproteomic and Bioinformatic Analyses.

Onken, Michael D / Erdmann-Gilmore, Petra / Zhang, Qiang / Thapa, Kisan / King, Emily / Kaltenbronn, Kevin M / Noda, Sarah E / Makepeace, Carol M / Goldfarb, Dennis / Babur, Özgün / Townsend, R Reid / Blumer, Kendall J

Molecular & cellular proteomics : MCP

2023 Volume 22, Issue 11, Page(s) 100649

Abstract: Metastatic uveal melanoma (UM) patients typically survive only 2 to 3 years because effective therapy does not yet exist. Here, to facilitate the discovery of therapeutic targets in UM, we have identified protein kinase signaling mechanisms elicited by ... ...

Abstract	Metastatic uveal melanoma (UM) patients typically survive only 2 to 3 years because effective therapy does not yet exist. Here, to facilitate the discovery of therapeutic targets in UM, we have identified protein kinase signaling mechanisms elicited by the drivers in 90% of UM tumors: mutant constitutively active G protein α-subunits encoded by GNAQ (Gq) or GNA11 (G11). We used the highly specific Gq/11 inhibitor FR900359 (FR) to elucidate signaling networks that drive proliferation, metabolic reprogramming, and dedifferentiation of UM cells. We determined the effects of FR on the proteome and phosphoproteome of UM cells as indicated by bioinformatic analyses with CausalPath and site-specific gene set enrichment analysis. We found that inhibition of oncogenic Gq/11 caused deactivation of PKC, Erk, and the cyclin-dependent kinases CDK1 and CDK2 that drive proliferation. Inhibition of oncogenic Gq/11 in UM cells with low metastatic risk relieved inhibitory phosphorylation of polycomb-repressive complex subunits that regulate melanocytic redifferentiation. Site-specific gene set enrichment analysis, unsupervised analysis, and functional studies indicated that mTORC1 and 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2 drive metabolic reprogramming in UM cells. Together, these results identified protein kinase signaling networks driven by oncogenic Gq/11 that regulate critical aspects of UM cell biology and provide targets for therapeutic investigation.
MeSH term(s)	Humans ; GTP-Binding Protein alpha Subunits, Gq-G11/genetics ; GTP-Binding Protein alpha Subunits, Gq-G11/metabolism ; GTP-Binding Protein alpha Subunits, Gq-G11/pharmacology ; Cell Proliferation ; Uveal Neoplasms/genetics ; Uveal Neoplasms/metabolism ; Uveal Neoplasms/pathology ; Protein Kinase C/metabolism ; Computational Biology ; Mutation
Chemical Substances	GTP-Binding Protein alpha Subunits, Gq-G11 (EC 3.6.5.1) ; Protein Kinase C (EC 2.7.11.13)
Language	English
Publishing date	2023-09-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	2075924-1
ISSN	1535-9484 ; 1535-9476
ISSN (online)	1535-9484
ISSN	1535-9476
DOI	10.1016/j.mcpro.2023.100649
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Article ; Online: Biophysical Mechanism of Allosteric Regulation of Actin Capping Protein.

Mooren, Olivia L / Stuchell-Brereton, Melissa D / McConnell, Patrick / Yan, Chenbo / Wilkerson, Emily M / Goldfarb, Dennis / Cooper, John A / Sept, David / Soranno, Andrea

Journal of molecular biology

2023 Volume 435, Issue 24, Page(s) 168342

Abstract	Actin capping protein (CP) can be regulated by steric and allosteric mechanisms. The molecular mechanism of the allosteric regulation at a biophysical level includes linkage between the binding sites for three ligands: F-actin, Capping-Protein-Interacting (CPI) motifs, and V-1/myotrophin, based on biochemical functional studies and solvent accessibility experiments. Here, we investigated the mechanism of allosteric regulation at the atomic level using single-molecule Förster resonance energy transfer (FRET) and molecular dynamics (MD) to assess the conformational and structural dynamics of CP in response to linked-binding site ligands. In the absence of ligand, both single-molecule FRET and MD revealed two distinct conformations of CP in solution; previous crystallographic studies revealed only one. Interaction with CPI-motif peptides induced conformations within CP that bring the cap and stalk closer, while interaction with V-1 moves them away from one another. Comparing CPI-motif peptides from different proteins, we identified variations in CP conformations and dynamics that are specific to each CPI motif. MD simulations for CP alone and in complex with a CPI motif and V-1 reveal atomistic details of the conformational changes. Analysis of the interaction of CP with wild-type (wt) and chimeric CPI-motif peptides using single-molecule FRET, isothermal calorimetry (ITC) and MD simulation indicated that conformational and affinity differences are intrinsic to the C-terminal portion of the CPI motif. We conclude that allosteric regulation of CP involves changes in conformation that disseminate across the protein to link distinct binding-site functions. Our results provide novel insights into the biophysical mechanism of the allosteric regulation of CP.
MeSH term(s)	Actin Capping Proteins/chemistry ; Protein Binding ; Allosteric Regulation ; Actins/metabolism ; Peptides/chemistry
Chemical Substances	Actin Capping Proteins ; Actins ; Peptides
Language	English
Publishing date	2023-11-02
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2023.168342
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Article ; Online: A basally active cGAS-STING pathway limits SARS-CoV-2 replication in a subset of ACE2 positive airway cell models

Puray-Chavez, Maritza / LaPak, Kyle M. / Jasuja, Ria / Pan, Jiehong / Xu, Jian / Eschbach, Jenna E. / Mohammed, Shawn / Lawson, Dana Q. / Wang, Qibo / Brody, Steven L. / Major, Michael B. / Goldfarb, Dennis / Kutluay, Sebla B.

bioRxiv

Abstract	Host factors that define the cellular tropism of SARS-CoV-2 beyond the cognate ACE2 receptor are poorly defined. From a screen of human airway derived cell lines that express varying levels of ACE2/TMPRSS2, we found a subset that express comparably high endogenous levels of ACE2 but surprisingly did not support SARS-CoV-2 replication. Here we report that this resistance is mediated by a basally active cGAS-STING pathway culminating in interferon (IFN)-mediated restriction of SARS-CoV-2 replication at a post-entry step. Pharmacological inhibition of JAK1/2, depletion of the IFN-alpha; receptor and cGAS-STING pathway effectors substantially increased SARS-CoV-2 replication in these cell models. While depletion of cGAS or STING was sufficient to reduce the preexisting levels of IFN-stimulated genes (ISGs), SARS-CoV-2 infection in STING knockout cells independently induced ISG expression. Remarkably, SARS-CoV-2-induced ISG expression in STING knockout cell as well as in primary human airway cultures was limited to uninfected bystander cells, demonstrating efficient antagonism of the type I/III IFN-pathway, but not viral sensing or IFN production, in productively infected cells. Of note, SARS-CoV-2-infected primary human airway cells also displayed markedly lower levels of STING expression, raising the possibility that SARS-CoV-2 can target STING expression or preferentially infect cells that express low levels of STING. Finally, ectopic ACE2 overexpression overcame the IFN-mediated blocks, suggesting the ability of SARS-CoV-2 to overcome these possibly saturable blocks to infection. Our study highlights that in addition to viral receptors, basal activation of the cGAS-STING pathway and innate immune defenses may contribute to defining SARS-CoV-2 cellular tropism.
Keywords	covid19
Language	English
Publishing date	2024-01-08
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2024.01.07.574522
Database	COVID19

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Article ; Online: Positive Cooperativity in Substrate Binding by Human Thymidylate Synthase.

Bonin, Jeffrey P / Sapienza, Paul J / Wilkerson, Emily / Goldfarb, Dennis / Wang, Li / Herring, Laura / Chen, Xian / Major, Michael B / Lee, Andrew L

Biophysical journal

2021 Volume 120, Issue 18, Page(s) 4137

Language	English
Publishing date	2021-08-24
Publishing country	United States
Document type	Published Erratum
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2021.08.023
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