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Wei L, Dankwa S, Vijayan K, Smith JD, Kaushansky A. Interrogating endothelial barrier regulation by temporally resolved kinase network generation. Life Sci Alliance 2024; 7:e202302522. [PMID: 38467420 PMCID: PMC10927359 DOI: 10.26508/lsa.202302522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/13/2024] Open
Abstract
Kinases are key players in endothelial barrier regulation, yet their temporal function and regulatory phosphosignaling networks are incompletely understood. We developed a novel methodology, Temporally REsolved KInase Network Generation (TREKING), which combines a 28-kinase inhibitor screen with machine learning and network reconstruction to build time-resolved, functional phosphosignaling networks. We demonstrated the utility of TREKING for identifying pathways mediating barrier integrity after activation by thrombin with or without TNF preconditioning in brain endothelial cells. TREKING predicted over 100 kinases involved in barrier regulation and discerned complex condition-specific pathways. For instance, the MAPK-activated protein kinase 2 (MAPKAPK2/MK2) had early barrier-weakening activity in both inflammatory conditions but late barrier-strengthening activity exclusively with thrombin alone. Using temporal Western blotting, we confirmed that MAPKAPK2/MK2 was differentially phosphorylated under the two inflammatory conditions. We further showed with lentivirus-mediated knockdown of MAPK14/p38α and drug targeting the MAPK14/p38α-MAPKAPK2/MK2 complex that a MAP3K20/ZAK-MAPK14/p38α axis controlled the late activation of MAPKAPK2/MK2 in the thrombin-alone condition. Beyond the MAPKAPK2/MK2 switch, TREKING predicts extensive interconnected networks that control endothelial barrier dynamics.
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Affiliation(s)
- Ling Wei
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Selasi Dankwa
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Kamalakannan Vijayan
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Joseph D Smith
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Alexis Kaushansky
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
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2
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Lahiri SK, Jin F, Zhou Y, Quick AP, Kramm CF, Wang MC, Wehrens XH. Altered myocardial lipid regulation in junctophilin-2-associated familial cardiomyopathies. Life Sci Alliance 2024; 7:e202302330. [PMID: 38438248 PMCID: PMC10912815 DOI: 10.26508/lsa.202302330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/06/2024] Open
Abstract
Myocardial lipid metabolism is critical to normal heart function, whereas altered lipid regulation has been linked to cardiac diseases including cardiomyopathies. Genetic variants in the JPH2 gene can cause hypertrophic cardiomyopathy (HCM) and, in some cases, dilated cardiomyopathy (DCM). In this study, we tested the hypothesis that JPH2 variants identified in patients with HCM and DCM, respectively, cause distinct alterations in myocardial lipid profiles. Echocardiography revealed clinically significant cardiac dysfunction in both knock-in mouse models of cardiomyopathy. Unbiased myocardial lipidomic analysis demonstrated significantly reduced levels of total unsaturated fatty acids, ceramides, and various phospholipids in both mice with HCM and DCM, suggesting a common metabolic alteration in both models. On the contrary, significantly increased di- and triglycerides, and decreased co-enzyme were only found in mice with HCM. Moreover, mice with DCM uniquely exhibited elevated levels of cholesterol ester. Further in-depth analysis revealed significantly altered metabolites from all the lipid classes with either similar or opposing trends in JPH2 mutant mice with HCM or DCM. Together, these studies revealed, for the first time, unique alterations in the cardiac lipid composition-including distinct increases in neutral lipids and decreases in polar membrane lipids-in mice with HCM and DCM were caused by distinct JPH2 variants. These studies may aid the development of novel biomarkers or therapeutics for these inherited disorders.
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Affiliation(s)
- Satadru K Lahiri
- https://ror.org/02pttbw34 Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX, USA
- https://ror.org/02pttbw34 Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, USA
| | - Feng Jin
- https://ror.org/02pttbw34 Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yue Zhou
- https://ror.org/02pttbw34 Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
| | - Ann P Quick
- https://ror.org/02pttbw34 Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX, USA
- https://ror.org/02pttbw34 Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, USA
| | - Carlos F Kramm
- https://ror.org/02pttbw34 Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX, USA
- https://ror.org/02pttbw34 Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, USA
| | - Meng C Wang
- https://ror.org/02pttbw34 Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- https://ror.org/02pttbw34 Huffington Center on Aging, Baylor College of Medicine, Houston, TX, USA
- https://ror.org/02pttbw34 Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX, USA
| | - Xander Ht Wehrens
- https://ror.org/02pttbw34 Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX, USA
- https://ror.org/02pttbw34 Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, USA
- https://ror.org/02pttbw34 Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- https://ror.org/02pttbw34 Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- https://ror.org/02pttbw34 Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- https://ror.org/02pttbw34 Center for Space Medicine, Baylor College of Medicine, Houston, TX, USA
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3
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Ebrahimzadeh T, Basu U, Lutz KC, Gadhvi J, Komarovsky JV, Li Q, Zimmern PE, De Nisco NJ. Inflammatory markers for improved recurrent UTI diagnosis in postmenopausal women. Life Sci Alliance 2024; 7:e202302323. [PMID: 38331474 PMCID: PMC10853434 DOI: 10.26508/lsa.202302323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024] Open
Abstract
Recurrent urinary tract infection (rUTI) severely impacts postmenopausal women. The lack of rapid and accurate diagnostic tools is a major obstacle in rUTI management as current gold standard methods have >24-h diagnostic windows. Work in animal models and limited human cohorts have identified robust inflammatory responses activated during UTI. Consequently, urinary inflammatory cytokines secreted during UTI may function as diagnostic biomarkers. This study aimed to identify urinary cytokines that could accurately diagnose UTI in a controlled cohort of postmenopausal women. Women passing study exclusion criteria were classified into no UTI and active rUTI groups, and urinary cytokine levels were measured by immunoassay. Pro-inflammatory cytokines IL-8, IL-18, IL-1β, and monocyte chemoattractant protein-1 were significantly elevated in the active rUTI group, and anti-inflammatory cytokines IL-13 and IL-4 were elevated in women without UTI. We evaluated cytokine diagnostic performance and found that an IL-8, prostaglandin E2, and IL-13 multivariable model had the lowest misclassification rate and highest sensitivity. Our data identify urinary IL-8, prostaglandin E2, and IL-13 as candidate biomarkers that may be useful in the development of immunoassay-based UTI diagnostics.
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Affiliation(s)
- Tahmineh Ebrahimzadeh
- https://ror.org/049emcs32 Department of Biological Sciences, University of Texas at Dallas, Dallas, TX, USA
| | - Ujjaini Basu
- https://ror.org/049emcs32 Department of Biological Sciences, University of Texas at Dallas, Dallas, TX, USA
| | - Kevin C Lutz
- https://ror.org/049emcs32 Department of Mathematics, University of Texas at Dallas, Dallas, TX, USA
| | - Jashkaran Gadhvi
- https://ror.org/049emcs32 Department of Biological Sciences, University of Texas at Dallas, Dallas, TX, USA
| | - Jessica V Komarovsky
- https://ror.org/049emcs32 Department of Biological Sciences, University of Texas at Dallas, Dallas, TX, USA
| | - Qiwei Li
- https://ror.org/049emcs32 Department of Mathematics, University of Texas at Dallas, Dallas, TX, USA
| | - Philippe E Zimmern
- https://ror.org/05byvp690 Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nicole J De Nisco
- https://ror.org/049emcs32 Department of Biological Sciences, University of Texas at Dallas, Dallas, TX, USA
- https://ror.org/05byvp690 Department of Urology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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4
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VerPlank JJ, Gawron JM, Silvestri NJ, Wrabetz L, Feltri ML. Knockout of PA200 improves proteasomal degradation and myelination in a proteotoxic neuropathy. Life Sci Alliance 2024; 7:e202302349. [PMID: 38320810 PMCID: PMC10847332 DOI: 10.26508/lsa.202302349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
The cellular response to a decrease in protein degradation by 26S proteasomes in chronic diseases is poorly understood. Pharmacological inhibition of proteasomes increases the expression of proteasome subunits and Proteasome Activator 200 (PA200), an alternative proteasome activator. In the S63del mouse model of the peripheral neuropathy Charcot Marie Tooth 1B (CMT1B), proteasomal protein degradation is decreased and proteasome gene expression is increased. Here, we show an increase in PA200 and PA200-bound proteasomes in the peripheral nerves of S63del mice. To test genetically whether the upregulation of PA200 was compensatory, we generated S63del//PA200-/- mice. Unexpectedly, in the sciatic nerves of these mice, there was greater proteasomal protein degradation than in S63del, less polyubiquitinated proteins and markers of the unfolded protein response, and a greater amount of assembled, active 26S proteasomes. These changes were not seen in PA200-/- controls and were therefore specific to the neuropathy. Furthermore, in S63del//PA200-/- mice, myelin thickness and nerve conduction were restored to WT levels. Thus, the upregulation of PA200 is maladaptive in S63del mice and its genetic ablation prevented neuropathy.
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Affiliation(s)
- Jordan Js VerPlank
- https://ror.org/01y64my43 Department of Biochemistry, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Joseph M Gawron
- https://ror.org/01y64my43 Department of Biochemistry, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Nicholas J Silvestri
- Department of Neurology, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Lawrence Wrabetz
- https://ror.org/01y64my43 Department of Biochemistry, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
- Department of Neurology, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Maria Laura Feltri
- https://ror.org/01y64my43 Department of Biochemistry, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
- Department of Neurology, Institute for Myelin and Glia Exploration, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
- IRCCS Neurological Institute "Carlo Besta," Milano, Italy
- Department of Medical Biotechnology and Translational Medicine, Universita' degli Studi di Milano, Milano, Italy
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5
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Hu MC, Reneau JA, Shi M, Takahashi M, Chen G, Mohammadi M, Moe OW. C-terminal fragment of fibroblast growth factor 23 improves heart function in murine models of high intact fibroblast growth factor 23. Am J Physiol Renal Physiol 2024; 326:F584-F599. [PMID: 38299214 DOI: 10.1152/ajprenal.00298.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/24/2024] [Accepted: 01/24/2024] [Indexed: 02/02/2024] Open
Abstract
Cardiovascular disease (CVD) is the major cause of death in chronic kidney disease (CKD) and is associated with high circulating fibroblast growth factor (FGF)23 levels. It is unresolved whether high circulating FGF23 is a mere biomarker or pathogenically contributes to cardiomyopathy. It is also unknown whether the C-terminal FGF23 peptide (cFGF23), a natural FGF23 antagonist proteolyzed from intact FGF23 (iFGF23), retards CKD progression and improves cardiomyopathy. We addressed these questions in three murine models with high endogenous FGF23 and cardiomyopathy. First, we examined wild-type (WT) mice with CKD induced by unilateral ischemia-reperfusion and contralateral nephrectomy followed by a high-phosphate diet. These mice were continuously treated with intraperitoneal implanted osmotic minipumps containing either iFGF23 protein to further escalate FGF23 bioactivity, cFGF23 peptide to block FGF23 signaling, vehicle, or scrambled peptide as negative controls. Exogenous iFGF23 protein given to CKD mice exacerbated pathological cardiac remodeling and CKD progression, whereas cFGF23 treatment improved heart and kidney function, attenuated fibrosis, and increased circulating soluble Klotho. WT mice without renal insult placed on a high-phosphate diet and homozygous Klotho hypomorphic mice, both of whom develop moderate CKD and clear cardiomyopathy, were treated with cFGF23 or vehicle. Mice treated with cFGF23 in both models had improved heart and kidney function and histopathology. Taken together, these data indicate high endogenous iFGF23 is not just a mere biomarker but pathogenically deleterious in CKD and cardiomyopathy. Furthermore, attenuation of FGF23 bioactivity by cFGF23 peptide is a promising therapeutic strategy to protect the kidney and heart from high FGF23 activity.NEW & NOTEWORTHY There is a strong correlation between cardiovascular morbidity and high circulating fibroblast growth factor 23 (FGF23) levels, but causality was never proven. We used a murine chronic kidney disease (CKD) model to show that intact FGF23 (iFGF23) is pathogenic and contributes to both CKD progression and cardiomyopathy. Blockade of FGF23 signaling with a natural proteolytic product of iFGF23, C-terminal FGF23, alleviated kidney and cardiac histology, and function in three separate murine models of high endogenous FGF23.
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Affiliation(s)
- Ming Chang Hu
- Charles and Jane Pak Center of Mineral Metabolism and Clinical Research, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - James A Reneau
- Charles and Jane Pak Center of Mineral Metabolism and Clinical Research, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Mingjun Shi
- Charles and Jane Pak Center of Mineral Metabolism and Clinical Research, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Masaya Takahashi
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, United States
- Department of Radiology, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Gaozhi Chen
- Charles and Jane Pak Center of Mineral Metabolism and Clinical Research, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Moosa Mohammadi
- Charles and Jane Pak Center of Mineral Metabolism and Clinical Research, University of Texas Southwestern Medical Center, Dallas, Texas, United States
| | - Orson W Moe
- Charles and Jane Pak Center of Mineral Metabolism and Clinical Research, University of Texas Southwestern Medical Center, Dallas, Texas, United States
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States
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Sakai T, Choo YY, Mitsuhashi S, Ikebe R, Jeffers A, Idell S, Tucker TA, Ikebe M. Myocardin regulates fibronectin expression and secretion from human pleural mesothelial cells. Am J Physiol Lung Cell Mol Physiol 2024; 326:L419-L430. [PMID: 38349126 DOI: 10.1152/ajplung.00271.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 01/18/2024] [Accepted: 01/26/2024] [Indexed: 03/20/2024] Open
Abstract
During the progression of pleural fibrosis, pleural mesothelial cells (PMCs) undergo a phenotype switching process known as mesothelial-mesenchymal transition (MesoMT). During MesoMT, transformed PMCs become myofibroblasts that produce increased extracellular matrix (ECM) proteins, including collagen and fibronectin (FN1) that is critical to develop fibrosis. Here, we studied the mechanism that regulates FN1 expression in myofibroblasts derived from human pleural mesothelial cells (HPMCs). We found that myocardin (Myocd), a transcriptional coactivator of serum response factor (SRF) and a master regulator of smooth muscle and cardiac muscle differentiation, strongly controls FN1 gene expression. Myocd gene silencing markedly inhibited FN1 expression. FN1 promoter analysis revealed that deletion of the Smad3-binding element diminished FN1 promoter activity, whereas deletion of the putative SRF-binding element increased FN1 promoter activity. Smad3 gene silencing decreased FN1 expression, whereas SRF gene silencing increased FN1 expression. Moreover, SRF competes with Smad3 for binding to Myocd. These results indicate that Myocd activates FN1 expression through Smad3, whereas SRF inhibits FN1 expression in HPMCs. In HPMCs, TGF-β induced Smad3 nuclear localization, and the proximity ligation signal between Myocd and Smad3 was markedly increased after TGF-β stimulation at nucleus, suggesting that TGF-β facilitates nuclear translocation of Smad3 and interaction between Smad3 and Myocd. Moreover, Myocd and Smad3 were coimmunoprecipitated and isolated Myocd and Smad3 proteins directly bound each other. Chromatin immunoprecipitation assays revealed that Myocd interacts with the FN1 promoter at the Smad3-binding consensus sequence. The results indicate that Myocd regulates FN1 gene activation through interaction and activation of the Smad3 transcription factor.NEW & NOTEWORTHY During phenotype switching from mesothelial to mesenchymal, pleural mesothelial cells (PMCs) produce extracellular matrix (ECM) proteins, including collagen and fibronectin (FN1), critical components in the development of fibrosis. Here, we found that myocardin, a transcriptional coactivator of serum response factor (SRF), strongly activates FN1 expression through Smad3, whereas SRF inhibits FN1 expression. This study provides insights about the regulation of FN1 that could lead to the development of novel interventional approaches to prevent pleural fibrosis.
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Affiliation(s)
- Tsuyoshi Sakai
- Department of Cellular and Molecular Biology, University of Texas at Tyler Health Science Center, Tyler, Texas, United States
| | - Young-Yeon Choo
- Department of Cellular and Molecular Biology, University of Texas at Tyler Health Science Center, Tyler, Texas, United States
| | - Shinya Mitsuhashi
- Department of Cellular and Molecular Biology, University of Texas at Tyler Health Science Center, Tyler, Texas, United States
| | - Reiko Ikebe
- Department of Cellular and Molecular Biology, University of Texas at Tyler Health Science Center, Tyler, Texas, United States
| | - Ann Jeffers
- Department of Cellular and Molecular Biology, University of Texas at Tyler Health Science Center, Tyler, Texas, United States
| | - Steven Idell
- Department of Cellular and Molecular Biology, University of Texas at Tyler Health Science Center, Tyler, Texas, United States
| | - Torry A Tucker
- Department of Cellular and Molecular Biology, University of Texas at Tyler Health Science Center, Tyler, Texas, United States
| | - Mitsuo Ikebe
- Department of Cellular and Molecular Biology, University of Texas at Tyler Health Science Center, Tyler, Texas, United States
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7
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Zuke JD, Burton BM. From isotopically labeled DNA to fluorescently labeled dynamic pili: building a mechanistic model of DNA transport to the cytoplasmic membrane. Microbiol Mol Biol Rev 2024; 88:e0012523. [PMID: 38466096 DOI: 10.1128/mmbr.00125-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024] Open
Abstract
SUMMARYNatural competence, the physiological state wherein bacteria produce proteins that mediate extracellular DNA transport into the cytosol and the subsequent recombination of DNA into the genome, is conserved across the bacterial domain. DNA must successfully translocate across formidable permeability barriers during import, including the cell membrane(s) and the cell wall, that are normally impermeable to large DNA polymers. This review will examine the mechanisms underlying DNA transport from the extracellular space to the cytoplasmic membrane. First, the challenges inherent to DNA movement through the cell periphery will be discussed to provide context for DNA transport during natural competence. The following sections will trace the development of a comprehensive model for DNA translocation to the cytoplasmic membrane, highlighting the crucial studies performed over the last century that have contributed to building contemporary DNA import models. Finally, this review will conclude by reflecting on what is still unknown about the process and the possible solutions to overcome these limitations.
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Affiliation(s)
- Jason D Zuke
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Briana M Burton
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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8
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Ortiz SC, Hull CM. Biogenesis, germination, and pathogenesis of Cryptococcus spores. Microbiol Mol Biol Rev 2024; 88:e0019623. [PMID: 38440970 DOI: 10.1128/mmbr.00196-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024] Open
Abstract
SUMMARYSpores are primary infectious propagules for the majority of human fungal pathogens; however, relatively little is known about their fundamental biology. One strategy to address this deficiency has been to develop the basidiospores of Cryptococcus into a model for pathogenic spore biology. Here, we provide an update on the state of the field with a comprehensive review of the data generated from the study of Cryptococcus basidiospores from their formation (sporulation) and differentiation (germination) to their roles in pathogenesis. Importantly, we provide support for the presence of basidiospores in nature, define the key characteristics that distinguish basidiospores from yeast cells, and clarify their likely roles as infectious particles. This review is intended to demonstrate the importance of basidiospores in the field of Cryptococcus research and provide a solid foundation from which researchers who wish to study sexual spores in any fungal system can launch their studies.
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Affiliation(s)
- Sébastien C Ortiz
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Christina M Hull
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
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9
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Reza MI, Kumar A, Pabelick CM, Britt RD, Prakash YS, Sathish V. Downregulation of protein phosphatase 2Aα in asthmatic airway smooth muscle. Am J Physiol Lung Cell Mol Physiol 2024. [PMID: 38529552 DOI: 10.1152/ajplung.00050.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 03/21/2024] [Indexed: 03/27/2024] Open
Abstract
Airway smooth muscle cell (ASM) is renowned for its involvement in airway hyperresponsiveness through impaired ASM relaxation and bronchoconstriction in asthma which poses a significant challenge in the field. Recent studies have explored different targets in ASM to alleviate airway hyperresponsiveness, however, a sizeable portion of asthmatics still experience poor control. In our study, we explored protein phosphatase 2A (PP2A) in ASM as it has been reported to regulate cellular contractility by controlling intracellular calcium ([Ca2+]i), ion channels, and respective regulatory proteins. We obtained human ASM cells and lung tissues from healthy and asthmatic patients and evaluated PP2A expression using RNA Seq data, immunofluorescence, and immunoblotting. We further investigated the functional importance of PP2A by determining its role in bronchoconstriction using mouse bronchus and human ASM [Ca2+]i regulation. We found ubiquitous expression of PP2A isoforms in human ASM with PP2Aα being predominantly expressed. Interestingly, PP2Aα was significantly downregulated in asthmatic tissue and human ASM exposed to pro-inflammatory cytokines. Functionally, PP2Aα activation inhibited acetylcholine or methacholine induced bronchial contraction in mouse bronchus and further potentiated isoproterenol-induced bronchial relaxation. Mechanistically, PP2Aα activation inhibited histamine evoked [Ca2+]i response and myosin light chain (MLC) phosphorylation in the presence of interleukin-13 (IL-13) in human ASM cells. To conclude, we for the first time established the PP2A signaling in ASM which can be further explored to develop novel therapeutics to alleviate airway hyperresponsiveness in asthma.
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Affiliation(s)
- Mohammad Irshad Reza
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND, United States
| | - Ashish Kumar
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND, United States
| | - Christina M Pabelick
- Department of Anesthesiology and Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, United States
| | - Rodney D Britt
- Center for Perinatal Research, Nationwide Children's Hospital, Columbus, OH, United States
| | - Y S Prakash
- Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, MN, United States
| | - Venkatachalem Sathish
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND, United States
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10
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Challita EJ, Bhamla MS. Unifying fluidic excretion across life from cicadas to elephants. Proc Natl Acad Sci U S A 2024; 121:e2317878121. [PMID: 38466877 DOI: 10.1073/pnas.2317878121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 01/30/2024] [Indexed: 03/13/2024] Open
Abstract
Can insects weighing mere grams challenge our current understanding of fluid dynamics in urination, jetting fluids like their larger mammalian counterparts? Current fluid urination models, predominantly formulated for mammals, suggest that jetting is confined to animals over 3 kg, owing to viscous and surface tension constraints at microscales. Our findings defy this paradigm by demonstrating that cicadas-weighing just 2 g-possess the capability for jetting fluids through remarkably small orifices. Using dimensional analysis, we introduce a unifying fluid dynamics scaling framework that accommodates a broad range of taxa, from surface-tension-dominated insects to inertia and gravity-reliant mammals. This study not only refines our understanding of fluid excretion across various species but also highlights its potential relevance in diverse fields such as ecology, evolutionary biology, and biofluid dynamics.
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Affiliation(s)
- Elio J Challita
- Chemical & Biomolecular Engineering, Georgia Institute of Technology, Georgia 30332, Atlanta
| | - M Saad Bhamla
- Chemical & Biomolecular Engineering, Georgia Institute of Technology, Georgia 30332, Atlanta
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11
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Chareyre S, Li X, Anjuwon-Foster BR, Updegrove TB, Clifford S, Brogan AP, Su Y, Zhang L, Chen J, Shroff H, Ramamurthi KS. Cell division machinery drives cell-specific gene activation during differentiation in Bacillus subtilis. Proc Natl Acad Sci U S A 2024; 121:e2400584121. [PMID: 38502707 DOI: 10.1073/pnas.2400584121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 02/22/2024] [Indexed: 03/21/2024] Open
Abstract
When faced with starvation, the bacterium Bacillus subtilis transforms itself into a dormant cell type called a "spore". Sporulation initiates with an asymmetric division event, which requires the relocation of the core divisome components FtsA and FtsZ, after which the sigma factor σF is exclusively activated in the smaller daughter cell. Compartment-specific activation of σF requires the SpoIIE phosphatase, which displays a biased localization on one side of the asymmetric division septum and associates with the structural protein DivIVA, but the mechanism by which this preferential localization is achieved is unclear. Here, we isolated a variant of DivIVA that indiscriminately activates σF in both daughter cells due to promiscuous localization of SpoIIE, which was corrected by overproduction of FtsA and FtsZ. We propose that the core components of the redeployed cell division machinery drive the asymmetric localization of DivIVA and SpoIIE to trigger the initiation of the sporulation program.
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Affiliation(s)
- Sylvia Chareyre
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Xuesong Li
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD 20892
- HHMI, Ashburn, VA 20147
| | | | - Taylor B Updegrove
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Sarah Clifford
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Anna P Brogan
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Yijun Su
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD 20892
- HHMI, Ashburn, VA 20147
| | - Lixia Zhang
- Advanced Imaging and Microscopy Resource, NIH, Bethesda, MD 20892
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, NIH, Bethesda, MD 20892
| | - Hari Shroff
- Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD 20892
- HHMI, Ashburn, VA 20147
| | - Kumaran S Ramamurthi
- Laboratory of Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892
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12
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Dombach JL, Christensen GL, Allgood SC, Quintana JLJ, Detweiler CS. Inhibition of multiple staphylococcal growth states by a small molecule that disrupts membrane fluidity and voltage. mSphere 2024; 9:e0077223. [PMID: 38445864 DOI: 10.1128/msphere.00772-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/26/2024] [Indexed: 03/07/2024] Open
Abstract
New molecular approaches to disrupting bacterial infections are needed. The bacterial cell membrane is an essential structure with diverse potential lipid and protein targets for antimicrobials. While rapid lysis of the bacterial cell membrane kills bacteria, lytic compounds are generally toxic to whole animals. In contrast, compounds that subtly damage the bacterial cell membrane could disable a microbe, facilitating pathogen clearance by the immune system with limited compound toxicity. A previously described small molecule, D66, terminates Salmonella enterica serotype Typhimurium (S. Typhimurium) infection of macrophages and reduces tissue colonization in mice. The compound dissipates bacterial inner membrane voltage without rapid cell lysis under broth conditions that permeabilize the outer membrane or disable efflux pumps. In standard media, the cell envelope protects Gram-negative bacteria from D66. We evaluated the activity of D66 in Gram-positive bacteria because their distinct envelope structure, specifically the absence of an outer membrane, could facilitate mechanism of action studies. We observed that D66 inhibited Gram-positive bacterial cell growth, rapidly increased Staphylococcus aureus membrane fluidity, and disrupted membrane voltage while barrier function remained intact. The compound also prevented planktonic staphylococcus from forming biofilms and a disturbed three-dimensional structure in 1-day-old biofilms. D66 furthermore reduced the survival of staphylococcal persister cells and of intracellular S. aureus. These data indicate that staphylococcal cells in multiple growth states germane to infection are susceptible to changes in lipid packing and membrane conductivity. Thus, agents that subtly damage bacterial cell membranes could have utility in preventing or treating disease.IMPORTANCEAn underutilized potential antibacterial target is the cell membrane, which supports or associates with approximately half of bacterial proteins and has a phospholipid makeup distinct from mammalian cell membranes. Previously, an experimental small molecule, D66, was shown to subtly damage Gram-negative bacterial cell membranes and to disrupt infection of mammalian cells. Here, we show that D66 increases the fluidity of Gram-positive bacterial cell membranes, dissipates membrane voltage, and inhibits the human pathogen Staphylococcus aureus in several infection-relevant growth states. Thus, compounds that cause membrane damage without lysing cells could be useful for mitigating infections caused by S. aureus.
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Affiliation(s)
- Jamie L Dombach
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Grace L Christensen
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Samual C Allgood
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Joaquin L J Quintana
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Corrella S Detweiler
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
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13
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Sutherland CA, Prigozhin DM, Monroe JG, Krasileva KV. High allelic diversity in Arabidopsis NLRs is associated with distinct genomic features. EMBO Rep 2024:10.1038/s44319-024-00122-9. [PMID: 38528170 DOI: 10.1038/s44319-024-00122-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/27/2024] Open
Abstract
Plants rely on Nucleotide-binding, Leucine-rich repeat Receptors (NLRs) for pathogen recognition. Highly variable NLRs (hvNLRs) show remarkable intraspecies diversity, while their low-variability paralogs (non-hvNLRs) are conserved between ecotypes. At a population level, hvNLRs provide new pathogen-recognition specificities, but the association between allelic diversity and genomic and epigenomic features has not been established. Our investigation of NLRs in Arabidopsis Col-0 has revealed that hvNLRs show higher expression, less gene body cytosine methylation, and closer proximity to transposable elements than non-hvNLRs. hvNLRs show elevated synonymous and nonsynonymous nucleotide diversity and are in chromatin states associated with an increased probability of mutation. Diversifying selection maintains variability at a subset of codons of hvNLRs, while purifying selection maintains conservation at non-hvNLRs. How these features are established and maintained, and whether they contribute to the observed diversity of hvNLRs is key to understanding the evolution of plant innate immune receptors.
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Affiliation(s)
- Chandler A Sutherland
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Daniil M Prigozhin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - J Grey Monroe
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616, USA
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA.
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14
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Boda AR, Liu AJ, Castro-Pando S, Whitfield BT, Molldrem JJ, Al-Atrash G, Di Francesco ME, Jones P, Ager CR, Curran MA. Identification of Nonfunctional Alternatively Spliced Isoforms of STING in Human Acute Myeloid Leukemia. Cancer Res Commun 2024; 4:911-918. [PMID: 38477596 PMCID: PMC10962316 DOI: 10.1158/2767-9764.crc-24-0095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/14/2024]
Abstract
Lack of robust activation of Stimulator of Interferon Genes (STING) pathway and subsequent induction of type I IFN responses is considered a barrier to antitumor immunity in acute myeloid leukemia (AML). Using common human AML cell lines as in vitro tools to evaluate the efficacy of novel STING agonists, we found most AML lines to be poor producers of IFNs upon exposure to extremely potent agonists, suggesting cell-intrinsic suppression of STING signaling may occur. We observed unexpected patterns of response that did not correlate with levels of STING pathway components or of known enzymes associated with resistance. To identify a genetic basis for these observations, we cloned and sequenced STING from the cDNA of human AML cell lines and found both frequent mutations and deviations from normal RNA splicing. We identified two novel spliced isoforms of STING in these lines and validated their expression in primary human AML samples. When transduced into reporter cells, these novel STING isoforms exhibited complete insensitivity to agonist stimulation. These observations identify alternative splicing as a mechanism of STING pathway suppression and suggest that most AML silences the STING pathway through direct modification rather than through engagement of external inhibitory factors. SIGNIFICANCE We find that AML acquires resistance to innate immune activation via the STING pathway through aberrant splicing of the STING transcript including two novel forms described herein that act as dominant negatives. These data broaden understanding of how cancers evolve STING resistance, and suggest that the AML tumor microenvironment, not the cancer cell, should be the target of therapeutic interventions to activate STING.
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Affiliation(s)
- Akash R. Boda
- Immunology Program, The University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, Texas
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Arthur J. Liu
- Immunology Program, The University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, Texas
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Susana Castro-Pando
- Immunology Program, The University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, Texas
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Benjamin T. Whitfield
- Immunology Program, The University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, Texas
| | - Jeffrey J. Molldrem
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Gheath Al-Atrash
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Maria Emilia Di Francesco
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Philip Jones
- Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Casey R. Ager
- Department of Immunology, The Mayo Clinic, Scottsdale, Arizona
| | - Michael A. Curran
- Immunology Program, The University of Texas MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, Texas
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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15
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Spasic M, Ogayo ER, Parsons AM, Mittendorf EA, van Galen P, McAllister SS. Spectral Flow Cytometry Methods and Pipelines for Comprehensive Immunoprofiling of Human Peripheral Blood and Bone Marrow. Cancer Res Commun 2024; 4:895-910. [PMID: 38466569 PMCID: PMC10962315 DOI: 10.1158/2767-9764.crc-23-0357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/20/2023] [Accepted: 03/05/2024] [Indexed: 03/13/2024]
Abstract
Profiling hematopoietic and immune cells provides important information about disease risk, disease status, and therapeutic responses. Spectral flow cytometry enables high-dimensional single-cell evaluation of large cohorts in a high-throughput manner. Here, we designed, optimized, and implemented new methods for deep immunophenotyping of human peripheral blood and bone marrow by spectral flow cytometry. Two blood antibody panels capture 48 cell-surface markers to assess more than 58 cell phenotypes, including subsets of T cells, B cells, monocytes, natural killer (NK) cells, and dendritic cells, and their respective markers of exhaustion, activation, and differentiation in less than 2 mL of blood. A bone marrow antibody panel captures 32 markers for 35 cell phenotypes, including stem/progenitor populations, T-cell subsets, dendritic cells, NK cells, and myeloid cells in a single tube. We adapted and developed innovative flow cytometric analysis algorithms, originally developed for single-cell genomics, to improve data integration and visualization. We also highlight technical considerations for users to ensure data fidelity. Our protocol and analysis pipeline accurately identifies rare cell types, discerns differences in cell abundance and phenotype across donors, and shows concordant immune landscape trends in patients with known hematologic malignancy. SIGNIFICANCE This study introduces optimized methods and analysis algorithms that enhance capabilities in comprehensive immunophenotyping of human blood and bone marrow using spectral flow cytometry. This approach facilitates detection of rare cell types, enables measurement of cell variations across donors, and provides proof-of-concept in identifying known hematologic malignancies. By unlocking complexities of hematopoietic and immune landscapes at the single-cell level, this advancement holds potential for understanding disease states and therapeutic responses.
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Affiliation(s)
- Milos Spasic
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Esther R. Ogayo
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, Massachusetts
| | - Adrienne M. Parsons
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Elizabeth A. Mittendorf
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, Massachusetts
| | - Peter van Galen
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Harvard Stem Cell Institute, Cambridge, Massachusetts
- Ludwig Center at Harvard, Harvard Medical School, Boston, Massachusetts
| | - Sandra S. McAllister
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
- Harvard Stem Cell Institute, Cambridge, Massachusetts
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16
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Wu DH, Senyo SE. Scratching beneath the surface: IL4Rα blockade and the progression from myocardial ischemic injury to heart failure. Am J Physiol Heart Circ Physiol 2024. [PMID: 38517226 DOI: 10.1152/ajpheart.00150.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 03/15/2024] [Indexed: 03/23/2024]
Affiliation(s)
- Douglas H Wu
- Biomedical Engineering, Case Western Reserve University, Cleveland, OH, United States
| | - Samuel E Senyo
- Biomecical Engineering, Case Western Reserve University, Cleveland, OH, United States
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17
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Kuzminov A. Bacterial nucleoid is a riddle wrapped in a mystery inside an enigma. J Bacteriol 2024; 206:e0021123. [PMID: 38358278 DOI: 10.1128/jb.00211-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024] Open
Abstract
Bacterial chromosome, the nucleoid, is traditionally modeled as a rosette of DNA mega-loops, organized around proteinaceous central scaffold by nucleoid-associated proteins (NAPs), and mixed with the cytoplasm by transcription and translation. Electron microscopy of fixed cells confirms dispersal of the cloud-like nucleoid within the ribosome-filled cytoplasm. Here, I discuss evidence that the nucleoid in live cells forms DNA phase separate from riboprotein phase, the "riboid." I argue that the nucleoid-riboid interphase, where DNA interacts with NAPs, transcribing RNA polymerases, nascent transcripts, and ssRNA chaperones, forms the transcription zone. An active part of phase separation, transcription zone enforces segregation of the centrally positioned information phase (the nucleoid) from the surrounding action phase (the riboid), where translation happens, protein accumulates, and metabolism occurs. I speculate that HU NAP mostly tiles up the nucleoid periphery-facilitating DNA mobility but also supporting transcription in the interphase. Besides extruding plectonemically supercoiled DNA mega-loops, condensins could compact them into solenoids of uniform rings, while HU could support rigidity and rotation of these DNA rings. The two-phase cytoplasm arrangement allows the bacterial cell to organize the central dogma activities, where (from the cell center to its periphery) DNA replicates and segregates, DNA is transcribed, nascent mRNA is handed over to ribosomes, mRNA is translated into proteins, and finally, the used mRNA is recycled into nucleotides at the inner membrane. The resulting information-action conveyor, with one activity naturally leading to the next one, explains the efficiency of prokaryotic cell design-even though its main intracellular transportation mode is free diffusion.
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Affiliation(s)
- Andrei Kuzminov
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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18
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Kosakowski HL, Saadon-Grosman N, Du J, Eldaief MC, Buckner RL. Human Striatal Association Megaclusters. J Neurophysiol 2024. [PMID: 38505898 DOI: 10.1152/jn.00387.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 03/13/2024] [Indexed: 03/21/2024] Open
Abstract
The striatum receives projections from multiple regions of the cerebral cortex consistent with the role of the basal ganglia in diverse motor, affective, and cognitive functions. Within the striatum, the caudate receives projections from association cortex including multiple distinct regions of prefrontal cortex. Building on recent insights about the details of how juxtaposed cortical networks are specialized for distinct aspects of higher-order cognition, we revisited caudate organization using within-individual precision neuroimaging initially in two intensively scanned individuals (each scanned 31 times). Results revealed that the caudate has side-by-side regions that are coupled to at least five distinct distributed association networks, paralleling the organization observed in the cerebral cortex. We refer to these spatial groupings of regions as striatal association megaclusters. Correlation maps from closely juxtaposed seed regions placed within the megaclusters recapitulated the five distinct cerebral networks including their multiple spatially distributed regions. Striatal association megaclusters were explored in 15 additional participants (each scanned at least 8 times) finding that their presence generalizes to new participants. Analysis of the laterality of the regions within the megaclusters further revealed that they possess asymmetries paralleling their cortical counterparts. For example, caudate regions linked to the language network were left-lateralized. These results extend the general notion of parallel specialized basal ganglia circuits, with the additional discovery that even within the caudate, there is fine-grained separation of multiple distinct higher-order networks that reflect the organization and lateralization found in the cerebral cortex.
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Affiliation(s)
| | | | - Jingnan Du
- Department of Psychology, Harvard University, Cambridge, MA, United States
| | - Mark C Eldaief
- Department of Psychiatry, Harvard University, Cambridge, MA, United States
| | - Randy L Buckner
- Department of Psychology, Harvard University, Cambridge, MA, United States
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19
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Martins M, Nooruzzaman M, Cunningham JL, Ye C, Caserta LC, Jackson N, Martinez-Sobrido L, Fang Y, Diel DG. The SARS-CoV-2 Spike is a virulence determinant and plays a major role on the attenuated phenotype of Omicron virus in a feline model of infection. J Virol 2024; 98:e0190223. [PMID: 38421180 PMCID: PMC10949471 DOI: 10.1128/jvi.01902-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/22/2024] [Indexed: 03/02/2024] Open
Abstract
The role of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.1 Spike (S) on disease pathogenesis was investigated. For this, we generated recombinant viruses harboring the S D614G mutation (rWA1-D614G) and the Omicron BA.1 S gene (rWA1-Omi-S) in the backbone of the ancestral SARS-CoV-2 WA1 strain genome. The recombinant viruses were characterized in vitro and in vivo. Viral entry, cell-cell fusion, plaque size, and the replication kinetics of the rWA1-Omi-S virus were markedly impaired when compared to the rWA1-D614G virus, demonstrating a lower fusogenicity and ability to spread cell-to-cell of rWA1-Omi-S. To assess the contribution of the Omicron BA.1 S protein to SARS-CoV-2 pathogenesis, the pathogenicity of rWA1-D614G and rWA1-Omi-S viruses was compared in a feline model. While the rWA1-D614G-inoculated cats were lethargic and showed increased body temperatures on days 2 and 3 post-infection (pi), rWA1-Omi-S-inoculated cats remained subclinical and gained weight throughout the 14-day experimental period. Animals inoculated with rWA1-D614G presented higher infectious virus shedding in nasal secretions, when compared to rWA1-Omi-S-inoculated animals. In addition, tissue replication of the rWA1-Omi-S was markedly reduced compared to the rWA1-D614G, as evidenced by lower viral load in tissues on days 3 and 5 pi. Histologic examination of the nasal turbinate and lungs revealed intense inflammatory infiltration in rWA1-D614G-inoculated animals, whereas rWA1-Omi-S-inoculated cats presented only mild to modest inflammation. Together, these results demonstrate that the S protein is a major virulence determinant for SARS-CoV-2 playing a major role for the attenuated phenotype of the Omicron virus. IMPORTANCE We have demonstrated that the Omicron BA.1.1 variant presents lower pathogenicity when compared to D614G (B.1) lineage in a feline model of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. There are over 50 mutations across the Omicron genome, of which more than two-thirds are present in the Spike (S) protein. To assess the role of the Omicron BA.1 S on virus pathogenesis, recombinant viruses harboring the S D614G mutation (rWA1-D614G) and the Omicron BA.1 Spike gene (rWA1-Omi-S) in the backbone of the ancestral SARS-CoV-2 WA1 were generated. While the Omicron BA.1 S promoted early entry into cells, it led to impaired fusogenic activity and cell-cell spread. Infection studies with the recombinant viruses in a relevant naturally susceptible feline model of SARS-CoV-2 infection here revealed an attenuated phenotype of rWA1-Omi-S, demonstrating that the Omi-S is a major determinant of the attenuated disease phenotype of Omicron strains.
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Affiliation(s)
- Mathias Martins
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Mohammed Nooruzzaman
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Jessie Lee Cunningham
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Chengjin Ye
- Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Leonardo Cardia Caserta
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | | | | | - Ying Fang
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Diego G. Diel
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
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20
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Jensen CC, Peifer M. Too old for hide-and-seek; cell maturation reveals hidden apical junctional organization. Proc Natl Acad Sci U S A 2024; 121:e2401735121. [PMID: 38466856 PMCID: PMC10962932 DOI: 10.1073/pnas.2401735121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024] Open
Affiliation(s)
- Corbin C. Jensen
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
| | - Mark Peifer
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC27599
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21
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Hanna DA, Diessl J, Guha A, Kumar R, Andren A, Lyssiotis C, Banerjee R. H 2S preconditioning induces long-lived perturbations in O 2 metabolism. Proc Natl Acad Sci U S A 2024; 121:e2319473121. [PMID: 38478695 PMCID: PMC10962982 DOI: 10.1073/pnas.2319473121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/30/2024] [Indexed: 03/26/2024] Open
Abstract
Hydrogen sulfide exposure in moderate doses can induce profound but reversible hypometabolism in mammals. At a cellular level, H2S inhibits the electron transport chain (ETC), augments aerobic glycolysis, and glutamine-dependent carbon utilization via reductive carboxylation; however, the durability of these changes is unknown. We report that despite its volatility, H2S preconditioning increases P50(O2), the O2 pressure for half-maximal cellular respiration, and has pleiotropic effects on oxidative metabolism that persist up to 24 to 48 h later. Notably, cyanide, another complex IV inhibitor, does not induce this type of metabolic memory. Sulfide-mediated prolonged fractional inhibition of complex IV by H2S is modulated by sulfide quinone oxidoreductase, which commits sulfide to oxidative catabolism. Since induced hypometabolism can be beneficial in disease settings that involve insufficient or interrupted blood flow, our study has important implications for attenuating reperfusion-induced ischemic injury and/or prolonging the shelf life of biologics like platelets.
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Affiliation(s)
- David A. Hanna
- Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, MI48109-0600
| | - Jutta Diessl
- Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, MI48109-0600
| | - Arkajit Guha
- Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, MI48109-0600
| | - Roshan Kumar
- Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, MI48109-0600
| | - Anthony Andren
- Department of Molecular and Integrative Physiology, University of Michigan Medical Center, Ann Arbor, MI48109-0600
| | - Costas Lyssiotis
- Department of Molecular and Integrative Physiology, University of Michigan Medical Center, Ann Arbor, MI48109-0600
- Department of Internal Medicine, University of Michigan Medical Center, Ann Arbor, MI48109-0600
- Department of Rogel Cancer Center, University of Michigan Medical Center, Ann Arbor, MI48109-0600
| | - Ruma Banerjee
- Department of Biological Chemistry, University of Michigan Medical Center, Ann Arbor, MI48109-0600
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22
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Patterson B, Dinkele R, Gessner S, Koch A, Hoosen Z, January V, Leonard B, McKerry A, Seldon R, Vazi A, Hermans S, Cobelens F, Warner DF, Wood R. Aerosolization of viable Mycobacterium tuberculosis bacilli by tuberculosis clinic attendees independent of sputum-Xpert Ultra status. Proc Natl Acad Sci U S A 2024; 121:e2314813121. [PMID: 38470917 PMCID: PMC10962937 DOI: 10.1073/pnas.2314813121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 02/01/2024] [Indexed: 03/14/2024] Open
Abstract
Potential Mycobacterium tuberculosis (Mtb) transmission during different pulmonary tuberculosis (TB) disease states is poorly understood. We quantified viable aerosolized Mtb from TB clinic attendees following diagnosis and through six months' follow-up thereafter. Presumptive TB patients (n=102) were classified by laboratory, radiological, and clinical features into Group A: Sputum-Xpert Ultra-positive TB (n=52), Group B: Sputum-Xpert Ultra-negative TB (n=20), or Group C: TB undiagnosed (n=30). All groups were assessed for Mtb bioaerosol release at baseline, and subsequently at 2 wk, 2 mo, and 6 mo. Groups A and B were notified to the national TB program and received standard anti-TB chemotherapy; Mtb was isolated from 92% and 90% at presentation, 87% and 74% at 2 wk, 54% and 44% at 2 mo and 32% and 20% at 6 mo, respectively. Surprisingly, similar numbers were detected in Group C not initiating TB treatment: 93%, 70%, 48% and 22% at the same timepoints. A temporal association was observed between Mtb bioaerosol release and TB symptoms in all three groups. Persistence of Mtb bioaerosol positivity was observed in ~30% of participants irrespective of TB chemotherapy. Captured Mtb bacilli were predominantly acid-fast stain-negative and poorly culturable; however, three bioaerosol samples yielded sufficient biomass following culture for whole-genome sequencing, revealing two different Mtb lineages. Detection of viable aerosolized Mtb in clinic attendees, independent of TB diagnosis, suggests that unidentified Mtb transmitters might contribute a significant attributable proportion of community exposure. Additional longitudinal studies with sputum culture-positive and -negative control participants are required to investigate this possibility.
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Affiliation(s)
- Benjamin Patterson
- Amsterdam Institute for Global Health and Development, University of Amsterdam, Amsterdam1105, The Netherlands
| | - Ryan Dinkele
- South African Medical Research Council, National Health Laboratory Service, University of Cape Town Molecular Mycobacteriology Research Unit & Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town7925, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town7925, South Africa
| | - Sophia Gessner
- South African Medical Research Council, National Health Laboratory Service, University of Cape Town Molecular Mycobacteriology Research Unit & Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town7925, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town7925, South Africa
| | - Anastasia Koch
- South African Medical Research Council, National Health Laboratory Service, University of Cape Town Molecular Mycobacteriology Research Unit & Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town7925, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town7925, South Africa
| | - Zeenat Hoosen
- Aerobiology and TB Research Unit, Desmond Tutu Health Foundation, Cape Town7975, South Africa
| | - Vanessa January
- Aerobiology and TB Research Unit, Desmond Tutu Health Foundation, Cape Town7975, South Africa
| | - Bryan Leonard
- Aerobiology and TB Research Unit, Desmond Tutu Health Foundation, Cape Town7975, South Africa
| | - Andrea McKerry
- Aerobiology and TB Research Unit, Desmond Tutu Health Foundation, Cape Town7975, South Africa
| | - Ronnett Seldon
- Aerobiology and TB Research Unit, Desmond Tutu Health Foundation, Cape Town7975, South Africa
| | - Andiswa Vazi
- Aerobiology and TB Research Unit, Desmond Tutu Health Foundation, Cape Town7975, South Africa
| | - Sabine Hermans
- Amsterdam Institute for Global Health and Development, University of Amsterdam, Amsterdam1105, The Netherlands
| | - Frank Cobelens
- Amsterdam Institute for Global Health and Development, University of Amsterdam, Amsterdam1105, The Netherlands
| | - Digby F. Warner
- South African Medical Research Council, National Health Laboratory Service, University of Cape Town Molecular Mycobacteriology Research Unit & Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town7925, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town7925, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, Faculty of Health Sciences, University of Cape Town, Cape Town7925, South Africa
| | - Robin Wood
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town7925, South Africa
- Aerobiology and TB Research Unit, Desmond Tutu Health Foundation, Cape Town7975, South Africa
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Uprety T, Yu J, Nogales A, Naveed A, Yu H, Chen X, Liu Y, Bowman AS, Martinez-Sobrido L, Parrish CR, Melikyan GB, Wang D, Li F. Influenza D virus utilizes both 9- O-acetylated N-acetylneuraminic and 9- O-acetylated N-glycolylneuraminic acids as functional entry receptors. J Virol 2024; 98:e0004224. [PMID: 38376198 PMCID: PMC10949506 DOI: 10.1128/jvi.00042-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 01/20/2024] [Indexed: 02/21/2024] Open
Abstract
Influenza D virus (IDV) utilizes bovines as a primary reservoir with periodical spillover to other hosts. We have previously demonstrated that IDV binds both 9-O-acetylated N-acetylneuraminic acid (Neu5,9Ac2) and 9-O-acetylated N-glycolylneuraminic acid (Neu5Gc9Ac). Bovines produce both Neu5,9Ac2 and Neu5Gc9Ac, while humans are genetically unable to synthesize Neu5Gc9Ac. 9-O-Acetylation of sialic acids is catalyzed by CASD1 via a covalent acetyl-enzyme intermediate. To characterize the role of Neu5,9Ac2 and Neu5Gc9Ac in IDV infection and determine which form of 9-O-acetylated sialic acids drives IDV entry, we took advantage of a CASD1 knockout (KO) MDCK cell line and carried out feeding experiments using synthetic 9-O-acetyl sialic acids in combination with the single-round and multi-round IDV infection assays. The data from our studies show that (i) CASD1 KO cells are resistant to IDV infection and lack of IDV binding to the cell surface is responsible for the failure of IDV replication; (ii) feeding CASD1 KO cells with Neu5,9Ac2 or Neu5Gc9Ac resulted in a dose-dependent rescue of IDV infectivity; and (iii) diverse IDVs replicated robustly in CASD1 KO cells fed with either Neu5,9Ac2 or Neu5Gc9Ac at a level similar to that in wild-type cells with a functional CASD1. These data demonstrate that IDV can utilize Neu5,9Ac2- or non-human Neu5Gc9Ac-containing glycan receptor for infection. Our findings provide evidence that IDV has acquired the ability to infect and transmit among agricultural animals that are enriched in Neu5Gc9Ac, in addition to posing a zoonotic risk to humans expressing only Neu5,9Ac2.IMPORTANCEInfluenza D virus (IDV) has emerged as a multiple-species-infecting pathogen with bovines as a primary reservoir. Little is known about the functional receptor that drives IDV entry and promotes its cross-species spillover potential among different hosts. Here, we demonstrated that IDV binds exclusively to 9-O-acetylated N-acetylneuraminic acid (Neu5,9Ac2) and non-human 9-O-acetylated N-glycolylneuraminic acid (Neu5Gc9Ac) and utilizes both for entry and infection. This ability in effective engagement of both 9-O-acetylated sialic acids as functional receptors for infection provides an evolutionary advantage to IDV for expanding its host range. This finding also indicates that IDV has the potential to emerge in humans because Neu5,9Ac2 is ubiquitously expressed in human tissues, including lung. Thus, results of our study highlight a need for continued surveillance of IDV in humans, as well as for further investigation of its biology and cross-species transmission mechanism.
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Affiliation(s)
- Tirth Uprety
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, USA
| | - Jieshi Yu
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, USA
| | - Aitor Nogales
- Centro de Investigación en Sanidad Animal, INIA-CSIC. Madrid, Madrid, Spain
| | - Ahsan Naveed
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, USA
| | - Hai Yu
- Department of Chemistry, University of California, Davis, California, USA
| | - Xi Chen
- Department of Chemistry, University of California, Davis, California, USA
| | | | - Andrew S. Bowman
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | | | - Colin R. Parrish
- College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | | | - Dan Wang
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, USA
| | - Feng Li
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, USA
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Miles J, Lozano GL, Rajendhran J, Stabb EV, Handelsman J, Broderick NA. Massively parallel mutant selection identifies genetic determinants of Pseudomonas aeruginosa colonization of Drosophila melanogaster. mSystems 2024; 9:e0131723. [PMID: 38380971 PMCID: PMC10949475 DOI: 10.1128/msystems.01317-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/06/2024] [Indexed: 02/22/2024] Open
Abstract
Pseudomonas aeruginosa is recognized for its ability to colonize diverse habitats and cause disease in a variety of hosts, including plants, invertebrates, and mammals. Understanding how this bacterium is able to occupy wide-ranging niches is important for deciphering its ecology. We used transposon sequencing [Tn-Seq, also known as insertion sequencing (INSeq)] to identify genes in P. aeruginosa that contribute to fitness during the colonization of Drosophila melanogaster. Our results reveal a suite of critical factors, including those that contribute to polysaccharide production, DNA repair, metabolism, and respiration. Comparison of candidate genes with fitness determinants discovered in previous studies on P. aeruginosa identified several genes required for colonization and virulence determinants that are conserved across hosts and tissues. This analysis provides evidence for both the conservation of function of several genes across systems, as well as host-specific functions. These findings, which represent the first use of transposon sequencing of a gut pathogen in Drosophila, demonstrate the power of Tn-Seq in the fly model system and advance the existing knowledge of intestinal pathogenesis by D. melanogaster, revealing bacterial colonization determinants that contribute to a comprehensive portrait of P. aeruginosa lifestyles across habitats.IMPORTANCEDrosophila melanogaster is a powerful model for understanding host-pathogen interactions. Research with this system has yielded notable insights into mechanisms of host immunity and defense, many of which emerged from the analysis of bacterial mutants defective for well-characterized virulence factors. These foundational studies-and advances in high-throughput sequencing of transposon mutants-support unbiased screens of bacterial mutants in the fly. To investigate mechanisms of host-pathogen interplay and exploit the tractability of this model host, we used a high-throughput, genome-wide mutant analysis to find genes that enable the pathogen P. aeruginosa to colonize the fly. Our analysis reveals critical mediators of P. aeruginosa establishment in its host, some of which are required across fly and mouse systems. These findings demonstrate the utility of massively parallel mutant analysis and provide a platform for aligning the fly toolkit with comprehensive bacterial genomics.
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Affiliation(s)
- Jessica Miles
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
- Graduate Program in Microbiology, Yale University, New Haven, Connecticut, USA
| | - Gabriel L. Lozano
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Jeyaprakash Rajendhran
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Eric V. Stabb
- Department of Biological Sciences, University of Illinois Chicago, Chicago, Illinois, USA
| | - Jo Handelsman
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
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25
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Witwit H, Khafaji R, Salaniwal A, Kim AS, Cubitt B, Jackson N, Ye C, Weiss SR, Martinez-Sobrido L, de la Torre JC. Activation of protein kinase receptor (PKR) plays a pro-viral role in mammarenavirus-infected cells. J Virol 2024; 98:e0188323. [PMID: 38376197 PMCID: PMC10949842 DOI: 10.1128/jvi.01883-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/26/2024] [Indexed: 02/21/2024] Open
Abstract
Many viruses, including mammarenaviruses, have evolved mechanisms to counteract different components of the host cell innate immunity, which is required to facilitate robust virus multiplication. The double-stranded RNA (dsRNA) sensor protein kinase receptor (PKR) pathway plays a critical role in the cell anti-viral response. Whether PKR can restrict the multiplication of the Old World mammarenavirus lymphocytic choriomeningitis virus (LCMV) and the mechanisms by which LCMV may counteract the anti-viral functions of PKR have not yet been investigated. Here we present evidence that LCMV infection results in very limited levels of PKR activation, but LCMV multiplication is enhanced in the absence of PKR. In contrast, infection with a recombinant LCMV with a mutation affecting the 3'-5' exonuclease (ExoN) activity of the viral nucleoprotein resulted in robust PKR activation in the absence of detectable levels of dsRNA, which was associated with severely restricted virus multiplication that was alleviated in the absence of PKR. However, pharmacological inhibition of PKR activation resulted in reduced levels of LCMV multiplication. These findings uncovered a complex role of the PKR pathway in LCMV-infected cells involving both pro- and anti-viral activities.IMPORTANCEAs with many other viruses, the prototypic Old World mammarenavirus LCMV can interfere with the host cell innate immune response to infection, which includes the dsRNA sensor PKR pathway. A detailed understanding of LCMV-PKR interactions can provide novel insights about mammarenavirus-host cell interactions and facilitate the development of effective anti-viral strategies against human pathogenic mammarenaviruses. In the present work, we present evidence that LCMV multiplication is enhanced in PKR-deficient cells, but pharmacological inhibition of PKR activation unexpectedly resulted in severely restricted propagation of LCMV. Likewise, we document a robust PKR activation in LCMV-infected cells in the absence of detectable levels of dsRNA. Our findings have revealed a complex role of the PKR pathway during LCMV infection and uncovered the activation of PKR as a druggable target for the development of anti-viral drugs against human pathogenic mammarenaviruses.
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Affiliation(s)
- Haydar Witwit
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
| | - Roaa Khafaji
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
| | - Arul Salaniwal
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
| | - Arthur S. Kim
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA
| | - Beatrice Cubitt
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
| | | | - Chengjin Ye
- Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Susan R. Weiss
- Department of Microbiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | | | - Juan Carlos de la Torre
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, California, USA
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26
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Mao J, Griniasty I, Teoh HK, Ramesh R, Yang R, Transtrum MK, Sethna JP, Chaudhari P. The training process of many deep networks explores the same low-dimensional manifold. Proc Natl Acad Sci U S A 2024; 121:e2310002121. [PMID: 38470929 PMCID: PMC10962999 DOI: 10.1073/pnas.2310002121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 02/12/2024] [Indexed: 03/14/2024] Open
Abstract
We develop information-geometric techniques to analyze the trajectories of the predictions of deep networks during training. By examining the underlying high-dimensional probabilistic models, we reveal that the training process explores an effectively low-dimensional manifold. Networks with a wide range of architectures, sizes, trained using different optimization methods, regularization techniques, data augmentation techniques, and weight initializations lie on the same manifold in the prediction space. We study the details of this manifold to find that networks with different architectures follow distinguishable trajectories, but other factors have a minimal influence; larger networks train along a similar manifold as that of smaller networks, just faster; and networks initialized at very different parts of the prediction space converge to the solution along a similar manifold.
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Affiliation(s)
- Jialin Mao
- Applied Mathematics and Computational Sciences, University of Pennsylvania, Philadelphia, PA19104
| | - Itay Griniasty
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY14853
| | - Han Kheng Teoh
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY14853
| | - Rahul Ramesh
- Department of Computer and Information Science, University of Pennsylvania, Philadelphia, PA19104
| | - Rubing Yang
- Applied Mathematics and Computational Sciences, University of Pennsylvania, Philadelphia, PA19104
| | - Mark K. Transtrum
- Department of Physics and Astronomy, Brigham Young University, Provo, UT84604
| | - James P. Sethna
- Laboratory of Atomic and Solid State Physics, Cornell University, Ithaca, NY14853
| | - Pratik Chaudhari
- Department of Electrical and Systems Engineering, University of Pennsylvania, Philadelphia, PA19104
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27
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Iram T, Garcia MA, Amand J, Kaur A, Atkins M, Iyer M, Lam M, Ambiel N, Jorgens DM, Keller A, Wyss-Coray T, Kern F, Zuchero JB. SRF transcriptionally regulates the oligodendrocyte cytoskeleton during CNS myelination. Proc Natl Acad Sci U S A 2024; 121:e2307250121. [PMID: 38483990 PMCID: PMC10962977 DOI: 10.1073/pnas.2307250121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 02/10/2024] [Indexed: 03/19/2024] Open
Abstract
Myelination of neuronal axons is essential for nervous system development. Myelination requires dramatic cytoskeletal dynamics in oligodendrocytes, but how actin is regulated during myelination is poorly understood. We recently identified serum response factor (SRF)-a transcription factor known to regulate expression of actin and actin regulators in other cell types-as a critical driver of myelination in the aged brain. Yet, a major gap remains in understanding the mechanistic role of SRF in oligodendrocyte lineage cells. Here, we show that SRF is required cell autonomously in oligodendrocytes for myelination during development. Combining ChIP-seq with RNA-seq identifies SRF-target genes in oligodendrocyte precursor cells and oligodendrocytes that include actin and other key cytoskeletal genes. Accordingly, SRF knockout oligodendrocytes exhibit dramatically reduced actin filament levels early in differentiation, consistent with its role in actin-dependent myelin sheath initiation. Surprisingly, oligodendrocyte-restricted loss of SRF results in upregulation of gene signatures associated with aging and neurodegenerative diseases. Together, our findings identify SRF as a transcriptional regulator that controls the expression of cytoskeletal genes required in oligodendrocytes for myelination. This study identifies an essential pathway regulating oligodendrocyte biology with high relevance to brain development, aging, and disease.
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Affiliation(s)
- Tal Iram
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA94305
- Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA94305
| | - Miguel A. Garcia
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA94305
| | - Jérémy Amand
- Department of Clinical Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland–Helmholtz Centre for Infection Research, Saarland University Campus, Saarbrücken66123, Germany
- Clinical Bioinformatics, Saarland University, Saarbrücken66123, Germany
| | - Achint Kaur
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA94305
- Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA94305
| | - Micaiah Atkins
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA94305
- Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA94305
| | - Manasi Iyer
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA94305
| | - Mable Lam
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA94305
| | - Nicholas Ambiel
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA94305
| | | | - Andreas Keller
- Department of Clinical Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland–Helmholtz Centre for Infection Research, Saarland University Campus, Saarbrücken66123, Germany
- Clinical Bioinformatics, Saarland University, Saarbrücken66123, Germany
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA94305
- Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA94305
| | - Fabian Kern
- Department of Clinical Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland–Helmholtz Centre for Infection Research, Saarland University Campus, Saarbrücken66123, Germany
- Clinical Bioinformatics, Saarland University, Saarbrücken66123, Germany
| | - J. Bradley Zuchero
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA94305
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28
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Oguntuyo KY, Haas GD, Azarm KD, Stevens CS, Brambilla L, Kowdle SS, Avanzato VA, Pryce R, Freiberg AN, Bowden TA, Lee B. Structure-guided mutagenesis of Henipavirus receptor-binding proteins reveals molecular determinants of receptor usage and antibody-binding epitopes. J Virol 2024; 98:e0183823. [PMID: 38426726 PMCID: PMC10949843 DOI: 10.1128/jvi.01838-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/05/2024] [Indexed: 03/02/2024] Open
Abstract
Nipah virus (NiV) is a highly lethal, zoonotic Henipavirus (HNV) that causes respiratory and neurological signs and symptoms in humans. Similar to other paramyxoviruses, HNVs mediate entry into host cells through the concerted actions of two surface glycoproteins: a receptor-binding protein (RBP) that mediates attachment and a fusion glycoprotein (F) that triggers fusion in an RBP-dependent manner. NiV uses ephrin-B2 (EFNB2) and ephrin-B3 (EFNB3) as entry receptors. Ghana virus (GhV), a novel HNV identified in a Ghanaian bat, uses EFNB2 but not EFNB3. In this study, we employ a structure-informed approach to identify receptor-interfacing residues and systematically introduce GhV-RBP residues into a NiV-RBP backbone to uncover the molecular determinants of EFNB3 usage. We reveal two regions that severely impair EFNB3 binding by NiV-RBP and EFNB3-mediated entry by NiV pseudotyped viral particles. Further analyses uncovered two-point mutations (NiVN557SGhV and NiVY581TGhV) pivotal for this phenotype. Moreover, we identify NiV interaction with Y120 of EFNB3 as important for the usage of this receptor. Beyond these EFNB3-related findings, we reveal two domains that restrict GhV binding of EFNB2, confirm the HNV-head as an immunodominant target for polyclonal and monoclonal antibodies, and describe putative epitopes for GhV- and NiV-specific monoclonal antibodies. Cumulatively, the work presented here generates useful reagents and tools that shed insight to residues important for NiV usage of EFNB3, reveal regions critical for GhV binding of EFNB2, and describe putative HNV antibody-binding epitopes. IMPORTANCE Hendra virus and Nipah virus (NiV) are lethal, zoonotic Henipaviruses (HNVs) that cause respiratory and neurological clinical features in humans. Since their initial outbreaks in the 1990s, several novel HNVs have been discovered worldwide, including Ghana virus. Additionally, there is serological evidence of zoonotic transmission, lending way to concerns about future outbreaks. HNV infection of cells is mediated by the receptor-binding protein (RBP) and the Fusion protein (F). The work presented here identifies NiV RBP amino acids important for the usage of ephrin-B3 (EFNB3), a receptor highly expressed in neurons and predicted to be important for neurological clinical features caused by NiV. This study also characterizes epitopes recognized by antibodies against divergent HNV RBPs. Together, this sheds insight to amino acids critical for HNV receptor usage and antibody binding, which is valuable for future studies investigating determinants of viral pathogenesis and developing antibody therapies.
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Affiliation(s)
| | - Griffin D. Haas
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kristopher D. Azarm
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Christian S. Stevens
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Luca Brambilla
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Shreyas S. Kowdle
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Victoria A. Avanzato
- Division of Structural Biology, Wellcome Center for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Rhys Pryce
- Division of Structural Biology, Wellcome Center for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Thomas A. Bowden
- Division of Structural Biology, Wellcome Center for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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29
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Fenton AD, Archin N, Turner AM, Joseph S, Moeser M, Margolis DM, Browne EP. A novel high-throughput microwell outgrowth assay for HIV-infected cells. J Virol 2024; 98:e0179823. [PMID: 38376258 PMCID: PMC10949454 DOI: 10.1128/jvi.01798-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/12/2024] [Indexed: 02/21/2024] Open
Abstract
Although antiretroviral therapy (ART) is effective at suppressing HIV replication, a viral reservoir persists that can reseed infection if ART is interrupted. Curing HIV will require elimination or containment of this reservoir, but the size of the HIV reservoir is highly variable between individuals. To evaluate the size of the HIV reservoir, several assays have been developed, including PCR-based assays for viral DNA, the intact proviral DNA assay, and the quantitative viral outgrowth assay (QVOA). QVOA is the gold standard assay for measuring inducible replication-competent proviruses, but this assay is technically challenging and time-consuming. To begin progress toward a more rapid and less laborious tool for quantifying cells infected with replication-competent HIV, we developed the Microwell Outgrowth Assay, in which infected CD4 T cells are co-cultured with an HIV-detecting reporter cell line in a polydimethylsiloxane (PDMS)/polystyrene array of nanoliter-sized wells. Transmission of HIV from infected cells to the reporter cell line induces fluorescent reporter protein expression that is detected by automated scanning across the array. Using this approach, we were able to detect HIV-infected cells from ART-naïve people with HIV (PWH) and from PWH on ART with large reservoirs. Furthermore, we demonstrate that infected cells can be recovered from individual rafts and used to analyze the diversity of viral sequences. Although additional development and optimization will be required for quantifying the reservoir in PWH with small latent reservoirs, this assay may be a useful prototype for microwell assays of infected cells.IMPORTANCEMeasuring the size of the HIV reservoir in people with HIV (PWH) will be important for determining the impact of HIV cure strategies. However, measuring this reservoir is challenging. We report a new method for quantifying HIV-infected cells that involves culturing cells from PWH in an array of microwells with a cell line that detects HIV infection. We show that this approach can detect rare HIV-infected cells and derive detailed virus sequence information for each infected cell.
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Affiliation(s)
- Anthony D. Fenton
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nancie Archin
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Anne-Marie Turner
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sarah Joseph
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Matthew Moeser
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David M. Margolis
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Edward P. Browne
- Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- UNC HIV Cure Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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Yang Q, Barbachano-Guerrero A, Fairchild LM, Rowland TJ, Dowell RD, Allen MA, Warren CJ, Sawyer SL. Macrophages derived from human induced pluripotent stem cells (iPSCs) serve as a high-fidelity cellular model for investigating HIV-1, dengue, and influenza viruses. J Virol 2024; 98:e0156323. [PMID: 38323811 PMCID: PMC10949493 DOI: 10.1128/jvi.01563-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 01/08/2024] [Indexed: 02/08/2024] Open
Abstract
Macrophages are important target cells for diverse viruses and thus represent a valuable system for studying virus biology. Isolation of primary human macrophages is done by culture of dissociated tissues or from differentiated blood monocytes, but these methods are both time consuming and result in low numbers of recovered macrophages. Here, we explore whether macrophages derived from human induced pluripotent stem cells (iPSCs)-which proliferate indefinitely and potentially provide unlimited starting material-could serve as a faithful model system for studying virus biology. Human iPSC-derived monocytes were differentiated into macrophages and then infected with HIV-1, dengue virus, or influenza virus as model human viruses. We show that iPSC-derived macrophages support the replication of these viruses with kinetics and phenotypes similar to human blood monocyte-derived macrophages. These iPSC-derived macrophages were virtually indistinguishable from human blood monocyte-derived macrophages based on surface marker expression (flow cytometry), transcriptomics (RNA sequencing), and chromatin accessibility profiling. iPSC lines were additionally generated from non-human primate (chimpanzee) fibroblasts. When challenged with dengue virus, human and chimpanzee iPSC-derived macrophages show differential susceptibility to infection, thus providing a valuable resource for studying the species-tropism of viruses. We also show that blood- and iPSC-derived macrophages both restrict influenza virus at a late stage of the virus lifecycle. Collectively, our results substantiate iPSC-derived macrophages as an alternative to blood monocyte-derived macrophages for the study of virus biology. IMPORTANCE Macrophages have complex relationships with viruses: while macrophages aid in the removal of pathogenic viruses from the body, macrophages are also manipulated by some viruses to serve as vessels for viral replication, dissemination, and long-term persistence. Here, we show that iPSC-derived macrophages are an excellent model that can be exploited in virology.
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Affiliation(s)
- Qing Yang
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | | | - Laurence M. Fairchild
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Teisha J. Rowland
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Robin D. Dowell
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Linda Crnic Institute for Down Syndrome Boulder Branch, BioFrontiers Institute, Boulder, Colorado, USA
- Department of Computer Science, University of Colorado Boulder, Boulder, Colorado, USA
| | - Mary A. Allen
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
- Linda Crnic Institute for Down Syndrome, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- Linda Crnic Institute for Down Syndrome Boulder Branch, BioFrontiers Institute, Boulder, Colorado, USA
| | - Cody J. Warren
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio, USA
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio, USA
- Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA
- Viruses and Emerging Pathogens Program, Infectious Diseases Institute, The Ohio State University, Columbus, Ohio, USA
| | - Sara L. Sawyer
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, USA
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31
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Schmitz KS, Handrejk K, Liepina L, Bauer L, Haas GD, van Puijfelik F, Veldhuis Kroeze EJB, Riekstina M, Strautmanis J, Cao H, Verdijk RM, GeurtsvanKessel CH, van Boheemen S, van Riel D, Lee B, Porotto M, de Swart RL, de Vries RD. Functional properties of measles virus proteins derived from a subacute sclerosing panencephalitis patient who received repeated remdesivir treatments. J Virol 2024; 98:e0187423. [PMID: 38329336 PMCID: PMC10949486 DOI: 10.1128/jvi.01874-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/16/2024] [Indexed: 02/09/2024] Open
Abstract
Subacute sclerosing panencephalitis (SSPE) is a rare but fatal late neurological complication of measles, caused by persistent measles virus (MeV) infection of the central nervous system. There are no drugs approved for the treatment of SSPE. Here, we followed the clinical progression of a 5-year-old SSPE patient after treatment with the nucleoside analog remdesivir, conducted a post-mortem evaluation of the patient's brain, and characterized the MeV detected in the brain. The quality of life of the patient transiently improved after the first two courses of remdesivir, but a third course had no further clinical effect, and the patient eventually succumbed to his condition. Post-mortem evaluation of the brain displayed histopathological changes including loss of neurons and demyelination paired with abundant presence of MeV RNA-positive cells throughout the brain. Next-generation sequencing of RNA isolated from the brain revealed a complete MeV genome with mutations that are typically detected in SSPE, characterized by a hypermutated M gene. Additional mutations were detected in the polymerase (L) gene, which were not associated with resistance to remdesivir. Functional characterization showed that mutations in the F gene led to a hyperfusogenic phenotype predominantly mediated by N465I. Additionally, recombinant wild-type-based MeV with the SSPE-F gene or the F gene with the N465I mutation was no longer lymphotropic but instead efficiently disseminated in neural cultures. Altogether, this case encourages further investigation of remdesivir as a potential treatment of SSPE and highlights the necessity to functionally understand SSPE-causing MeV.IMPORTANCEMeasles virus (MeV) causes acute, systemic disease and remains an important cause of morbidity and mortality in humans. Despite the lack of known entry receptors in the brain, MeV can persistently infect the brain causing the rare but fatal neurological disorder subacute sclerosing panencephalitis (SSPE). SSPE-causing MeVs are characterized by a hypermutated genome and a hyperfusogenic F protein that facilitates the rapid spread of MeV throughout the brain. No treatment against SSPE is available, but the nucleoside analog remdesivir was recently demonstrated to be effective against MeV in vitro. We show that treatment of an SSPE patient with remdesivir led to transient clinical improvement and did not induce viral escape mutants, encouraging the future use of remdesivir in SSPE patients. Functional characterization of the viral proteins sheds light on the shared properties of SSPE-causing MeVs and further contributes to understanding how those viruses cause disease.
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Affiliation(s)
| | - Kim Handrejk
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Lelde Liepina
- Clinic for Pediatric Neurology and Neurosurgery, Children’s Clinical University Hospital, Riga, Latvia
| | - Lisa Bauer
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Griffin D. Haas
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | | | - Marta Riekstina
- Department of Pathology, Children’s Clinical University Hospital, Riga, Latvia
| | - Jurgis Strautmanis
- Clinic for Pediatric Neurology and Neurosurgery, Children’s Clinical University Hospital, Riga, Latvia
| | - Huyen Cao
- Departments of Clinical Research, Biometrics, and Virology, Gilead Sciences, Inc., Foster City, California, USA
| | - Robert M. Verdijk
- Department of Pathology, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | | | - Debby van Riel
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Matteo Porotto
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
- Center for Host–Pathogen Interaction, Columbia University Irving Medical Center, New York, New York, USA
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, Caserta, Italy
| | - Rik L. de Swart
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Rory D. de Vries
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands
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Chesnokova LS, Mosher BS, Fulkerson HL, Nam HW, Shakya AK, Yurochko AD. Distinct early role of PTEN regulation during HCMV infection of monocytes. Proc Natl Acad Sci U S A 2024; 121:e2312290121. [PMID: 38483999 PMCID: PMC10962971 DOI: 10.1073/pnas.2312290121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/01/2023] [Indexed: 03/19/2024] Open
Abstract
Human cytomegalovirus (HCMV) infection of monocytes is essential for viral dissemination and persistence. We previously identified that HCMV entry/internalization and subsequent productive infection of this clinically relevant cell type is distinct when compared to other infected cells. We showed that internalization and productive infection required activation of epidermal growth factor receptor (EGFR) and integrin/c-Src, via binding of viral glycoprotein B to EGFR, and the pentamer complex to β1/β3 integrins. To understand how virus attachment drives entry, we compared infection of monocytes with viruses containing the pentamer vs. those without the pentamer and then used a phosphoproteomic screen to identify potential phosphorylated proteins that influence HCMV entry and trafficking. The screen revealed that the most prominent pentamer-biased phosphorylated protein was the lipid- and protein-phosphatase phosphatase and tensin homolog (PTEN). PTEN knockdown with siRNA or PTEN inhibition with a PTEN inhibitor decreased pentamer-mediated HCMV entry, without affecting trimer-mediated entry. Inhibition of PTEN activity affected lipid metabolism and interfered with the onset of the endocytic processes required for HCMV entry. PTEN inactivation was sufficient to rescue pentamer-null HCMV from lysosomal degradation. We next examined dephosphorylation of a PTEN substrate Rab7, a regulator of endosomal maturation. Inhibition of PTEN activity prevented dephosphorylation of Rab7. Phosphorylated Rab7, in turn, blocked early endosome to late endosome maturation and promoted nuclear localization of the virus and productive infection.
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Affiliation(s)
- Liudmila S. Chesnokova
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center Shreveport, Shreveport, LA71103
- Center for Applied Immunology and Pathological Processes, Louisiana State University Health Sciences Center Shreveport, Shreveport, LA71103
| | - Bailey S. Mosher
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center Shreveport, Shreveport, LA71103
- Center for Applied Immunology and Pathological Processes, Louisiana State University Health Sciences Center Shreveport, Shreveport, LA71103
| | - Heather L. Fulkerson
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center Shreveport, Shreveport, LA71103
- Center for Cardiovascular Diseases and Sciences, Louisiana State University Health Sciences Center Shreveport, Shreveport, LA71103
| | - Hyung W. Nam
- Department of Pharmacology, Toxicology, and Neuroscience, Louisiana State University Health Sciences Center Shreveport, Shreveport, LA71103
| | - Akhalesh K. Shakya
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center Shreveport, Shreveport, LA71103
| | - Andrew D. Yurochko
- Department of Microbiology and Immunology, Louisiana State University Health Sciences Center Shreveport, Shreveport, LA71103
- Center for Applied Immunology and Pathological Processes, Louisiana State University Health Sciences Center Shreveport, Shreveport, LA71103
- Center for Cardiovascular Diseases and Sciences, Louisiana State University Health Sciences Center Shreveport, Shreveport, LA71103
- Feist-Weller Cancer Center, Louisiana State University Health Sciences Center Shreveport, Shreveport, LA 71103, Shreveport, LA71103
- Center for Excellence in Arthritis and Rheumatology, Louisiana State University Health Sciences Center Shreveport, Shreveport, LA71103
- Center of Excellence for Emerging Viral Threats, Louisiana State University Health Sciences Center Shreveport, Shreveport, LA71103
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Lohani SC, Ramer-Tait AE, Li Q. High-fat diet feeding exacerbates HIV-1 rectal transmission. mSystems 2024; 9:e0132223. [PMID: 38303112 PMCID: PMC10949459 DOI: 10.1128/msystems.01322-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 01/07/2024] [Indexed: 02/03/2024] Open
Abstract
High-fat diet (HFD) is well known to impact various aspects of gut health and has been associated with many diseases and inflammation. However, the impact of HFD feeding on HIV-1 rectal transmission has not yet been well addressed. With an increasing threat of HIV-1 infection in men who have sex with men (MSM), where the rectal route is the primary mode of infection, it is imperative to understand the impact of HFD on gut microbiota and inflammation and consequently, its effect on HIV-1 rectal transmission. Here, we utilized our double humanized bone marrow, liver, thymus (dHu-BLT) mouse model to assess the impact of HFD feeding on the host's susceptibility to HIV-1 rectal transmission. We found that feeding an HFD successfully altered the gut microbial composition within 3 weeks in the dHu-BLT mouse model. In addition, levels of inflammatory mediators, specifically IL-12p70, IP-10, ICAM-1, and fecal calprotectin, were significantly higher in HFD-fed mice compared to control mice on a regular chow diet. We also observed that significantly different inflammatory markers (IL-12p70 and ICAM-1) were negatively correlated with the number of observed ASVs, Shannon diversity, and Faith's diversity in the HFD-fed group. Notably, when repeatedly challenged with a low dose of HIV-1 via a rectal route, mice receiving an HFD were significantly more susceptible to HIV-1 rectal infection than control mice. Together, these results underscore the impact of HFD feeding on the gut microbiota and inflammation and suggest the significance of diet-induced gut microbial dysbiosis and inflammation in promoting viral infection.IMPORTANCEHFD induces gut microbial dysbiosis and inflammation and has been associated with many infections and disease progression; however, its impact on HIV-1 rectal transmission is largely unknown. Given the increasing threat of HIV-1 incidence in men who have sex with men (MSM), it has become crucial to comprehend the impact of factors associated with gut health, like HFD consumption, on host susceptibility to HIV-1 rectal transmission. This is particularly important since anal intercourse remains the primary mode of HIV transmission within the MSM group. In this study, utilizing our unique mouse model, featuring both the human immune system and gut microbiota, we showed that HFD feeding led to gut microbial dysbiosis, induced inflammation, and increased HIV-1 rectal transmission. Collectively, our study highlights the significant impact of HFD on gut microbiota and inflammation and suggests an HFD consumption as a potential risk factor for promoting HIV-1 rectal susceptibility.
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Affiliation(s)
- Saroj Chandra Lohani
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Amanda E. Ramer-Tait
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Qingsheng Li
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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Dufault-Thompson K, Jiang X. Annotating microbial functions with ProkFunFind. mSystems 2024; 9:e0003624. [PMID: 38364094 PMCID: PMC10949468 DOI: 10.1128/msystems.00036-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 01/22/2024] [Indexed: 02/18/2024] Open
Abstract
Analyzing microbial genomes has become an essential part of microbiology research, giving valuable insights into the functions and evolution of microbial species. Identifying genes of interest and assigning putative annotations to those genes is a central task in genome analysis, and a plethora of tools and approaches have been developed for this task. The ProkFunFind tool was developed to bridge the gap between these various annotation approaches, providing a flexible and customizable search approach to annotate microbial functions. ProkFunFind is designed around hierarchical definitions of biological functions, where individual genes can be identified using heterogeneous search terms consisting of sequences, profile hidden Markov models, protein domains, and orthology groups. This flexible and customizable search approach allows for searches to be tailored to specific biological functions, and the search results are output in multiple formats to facilitate downstream analyses. The utility of the ProkFunFind search tool was demonstrated through its application in searching for bacterial flagella, which are complex organelles composed of multiple genes. Overall, ProkFunFind provides an accessible and flexible way to integrate multiple types of annotation and sequence data while annotating biological functions in microbial genomes.IMPORTANCEGenome sequencing and analysis are increasingly important parts of microbiology, providing a way to predict metabolic functions, identify virulence factors, and understand the evolution of microbes. The expanded use of genome sequencing has also brought an abundance of search and annotation methods, but integrating the information from these different methods can be challenging and is often done through ad hoc approaches. To bridge the gap between different types of annotations, we developed ProkFunFind, a flexible and customizable search tool incorporating multiple search approaches and annotation types to annotate microbial functions. We demonstrated the utility of ProkFunFind by searching for gene clusters encoding flagellar genes using a combination of different annotation types and searches. Overall, ProkFunFind provides a reproducible and flexible way to identify gene clusters of interest, facilitating the meaningful analysis of new and existing microbial genomes.
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Affiliation(s)
| | - Xiaofang Jiang
- National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
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35
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Balakrishnan S, Adolph M, Tsai MS, Akizuki T, Gallagher K, Cortez D, Chazin WJ. Structure of RADX and mechanism for regulation of RAD51 nucleofilaments. Proc Natl Acad Sci U S A 2024; 121:e2316491121. [PMID: 38466836 PMCID: PMC10962997 DOI: 10.1073/pnas.2316491121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/07/2024] [Indexed: 03/13/2024] Open
Abstract
Replication fork reversal is a fundamental process required for resolution of encounters with DNA damage. A key step in the stabilization and eventual resolution of reversed forks is formation of RAD51 nucleoprotein filaments on exposed single strand DNA (ssDNA). To avoid genome instability, RAD51 filaments are tightly controlled by a variety of positive and negative regulators. RADX (RPA-related RAD51-antagonist on the X chromosome) is a recently discovered negative regulator that binds tightly to ssDNA, directly interacts with RAD51, and regulates replication fork reversal and stabilization in a context-dependent manner. Here, we present a structure-based investigation of RADX's mechanism of action. Mass photometry experiments showed that RADX forms multiple oligomeric states in a concentration-dependent manner, with a predominance of trimers in the presence of ssDNA. The structure of RADX, which has no structurally characterized orthologs, was determined ab initio by cryo-electron microscopy (cryo-EM) from maps in the 2 to 4 Å range. The structure reveals the molecular basis for RADX oligomerization and the coupled multi-valent binding of ssDNA binding. The interaction of RADX with RAD51 filaments was imaged by negative stain EM, which showed a RADX oligomer at the end of filaments. Based on these results, we propose a model in which RADX functions by capping and restricting the end of RAD51 filaments.
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Affiliation(s)
- Swati Balakrishnan
- Center for Structural Biology, Vanderbilt University, Nashville, TN37240
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37237
| | - Madison Adolph
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37237
| | - Miaw-Sheue Tsai
- Biological Systems and Bioengineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA94720
| | - Tae Akizuki
- Center for Structural Biology, Vanderbilt University, Nashville, TN37240
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37237
| | - Kaitlyn Gallagher
- Center for Structural Biology, Vanderbilt University, Nashville, TN37240
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37237
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37237
| | - Walter J. Chazin
- Center for Structural Biology, Vanderbilt University, Nashville, TN37240
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN37237
- Department of Chemistry, Vanderbilt University, Nashville, TN37235
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36
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Yan Q, Gomis Perez C, Karatekin E. Cell membrane tension gradients, membrane flows and cellular processes. Physiology (Bethesda) 2024. [PMID: 38501962 DOI: 10.1152/physiol.00007.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/18/2024] [Indexed: 03/20/2024] Open
Abstract
Cell membrane tension affects and is affected by many fundamental cellular processes, yet it is poorly understood. Recent experiments show that membrane tension can propagate at vastly different speeds in different cell types, reflecting physiological adaptations. Here we briefly review the current knowledge about membrane tension gradients, membrane flows, and their physiological context.
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Affiliation(s)
- Qi Yan
- Cellular and Molecular Physiology, Yale University, West Haven, CT, United States
| | - Carolina Gomis Perez
- Cellular and Molecular Physiology, Yale University, West haven, CT, United States
| | - Erdem Karatekin
- Cellular and Molecular Phyisoloty, Yale University, West Haven, CT, United States
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Godthi A, Min S, Das S, Cruz-Corchado J, Deonarine A, Misel-Wuchter K, Issuree PD, Prahlad V. Neuronal IL-17 controls Caenorhabditis elegans developmental diapause through CEP-1/p53. Proc Natl Acad Sci U S A 2024; 121:e2315248121. [PMID: 38483995 PMCID: PMC10963014 DOI: 10.1073/pnas.2315248121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 02/06/2024] [Indexed: 03/19/2024] Open
Abstract
During metazoan development, how cell division and metabolic programs are coordinated with nutrient availability remains unclear. Here, we show that nutrient availability signaled by the neuronal cytokine, ILC-17.1, switches Caenorhabditis elegans development between reproductive growth and dormancy by controlling the activity of the tumor suppressor p53 ortholog, CEP-1. Specifically, upon food availability, ILC-17.1 signaling by amphid neurons promotes glucose utilization and suppresses CEP-1/p53 to allow growth. In the absence of ILC-17.1, CEP-1/p53 is activated, up-regulates cell-cycle inhibitors, decreases phosphofructokinase and cytochrome C expression, and causes larvae to arrest as stress-resistant, quiescent dauers. We propose a model whereby ILC-17.1 signaling links nutrient availability and energy metabolism to cell cycle progression through CEP-1/p53. These studies describe ancestral functions of IL-17 s and the p53 family of proteins and are relevant to our understanding of neuroimmune mechanisms in cancer. They also reveal a DNA damage-independent function of CEP-1/p53 in invertebrate development and support the existence of a previously undescribed C. elegans dauer pathway.
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Affiliation(s)
- Abhishiktha Godthi
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY14263
- Department of Biology, The University of Iowa, Iowa City, IA52242-1324
| | - Sehee Min
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY14263
- Department of Biology, The University of Iowa, Iowa City, IA52242-1324
| | - Srijit Das
- Department of Biology, The University of Iowa, Iowa City, IA52242-1324
| | - Johnny Cruz-Corchado
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY14263
- Department of Biology, The University of Iowa, Iowa City, IA52242-1324
| | - Andrew Deonarine
- Department of Biology, The University of Iowa, Iowa City, IA52242-1324
| | - Kara Misel-Wuchter
- Department of Internal Medicine, The University of Iowa, Iowa City, IA52242
| | - Priya D. Issuree
- Department of Internal Medicine, The University of Iowa, Iowa City, IA52242
| | - Veena Prahlad
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY14263
- Department of Biology, The University of Iowa, Iowa City, IA52242-1324
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Ranjitkar S, Krajewski D, Garcia C, Tedeschi C, Polukort SH, Rovatti J, Mire M, Blesso CN, Jellison E, Schneider SS, Ryan JJ, Mathias CB. IL-10 Differentially Promotes Mast Cell Responsiveness to IL-33, Resulting in Enhancement of Type 2 Inflammation and Suppression of Neutrophilia. J Immunol 2024:ji2300884. [PMID: 38497670 DOI: 10.4049/jimmunol.2300884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/26/2024] [Indexed: 03/19/2024]
Abstract
Mast cells (MCs) play critical roles in the establishment of allergic diseases. We recently demonstrated an unexpected, proinflammatory role for IL-10 in regulating MC responses. IL-10 enhanced MC activation and promoted IgE-dependent responses during food allergy. However, whether these effects extend to IgE-independent stimuli is not clear. In this article, we demonstrate that IL-10 plays a critical role in driving IL-33-mediated MC responses. IL-10 stimulation enhanced MC expansion and degranulation, ST2 expression, IL-13 production, and phospho-relA upregulation in IL-33-treated cells while suppressing TNF-α. These effects were partly dependent on endogenous IL-10 and further amplified in MCs coactivated with both IL-33 and IgE/Ag. IL-10's divergent effects also extended in vivo. In a MC-dependent model of IL-33-induced neutrophilia, IL-10 treatment enhanced MC responsiveness, leading to suppression of neutrophils and decreased TNF-α. In contrast, during IL-33-induced type 2 inflammation, IL-10 priming exacerbated MC activity, resulting in MC recruitment to various tissues, enhanced ST2 expression, induction of hypothermia, recruitment of eosinophils, and increased MCPT-1 and IL-13 levels. Our data elucidate an important role for IL-10 as an augmenter of IL-33-mediated MC responses, with implications during both allergic diseases and other MC-dependent disorders. IL-10 induction is routinely used as a prognostic marker of disease improvement. Our data suggest instead that IL-10 can enhance ST2 responsiveness in IL-33-activated MCs, with the potential to both aggravate or suppress disease severity depending on the inflammatory context.
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Affiliation(s)
- Saurav Ranjitkar
- Department of Nutritional Sciences, University of Connecticut, Storrs, CT
| | - Dylan Krajewski
- Department of Pharmaceutical and Administrative Sciences, Western New England University, Springfield, MA
| | - Chelsea Garcia
- Department of Nutritional Sciences, University of Connecticut, Storrs, CT
| | - Caitlin Tedeschi
- Department of Nutritional Sciences, University of Connecticut, Storrs, CT
| | - Stephanie H Polukort
- Department of Pharmaceutical and Administrative Sciences, Western New England University, Springfield, MA
| | - Jeffrey Rovatti
- Department of Pharmaceutical and Administrative Sciences, Western New England University, Springfield, MA
| | - Mohamed Mire
- Department of Pharmaceutical and Administrative Sciences, Western New England University, Springfield, MA
| | | | - Evan Jellison
- Department of Immunology, University of Connecticut, Farmington, CT
| | - Sallie S Schneider
- Pioneer Valley Life Sciences Institute, Baystate Medical Center, Springfield, MA
| | - John J Ryan
- Department of Biology, Virginia Commonwealth University, Richmond, VA
| | - Clinton B Mathias
- Department of Nutritional Sciences, University of Connecticut, Storrs, CT
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Karanth S, Osazuwa-Peters OL, Wilson LE, Previs RA, Rahman F, Huang B, Pisu M, Liang M, Ward KC, Schymura MJ, Berchuck A, Akinyemiju TF. Health Care Access Dimensions and Racial Disparities in End-of-Life Care Quality among Patients with Ovarian Cancer. Cancer Res Commun 2024; 4:811-821. [PMID: 38441644 PMCID: PMC10946308 DOI: 10.1158/2767-9764.crc-23-0283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/22/2023] [Accepted: 02/15/2024] [Indexed: 03/20/2024]
Abstract
This study investigated the association between health care access (HCA) dimensions and racial disparities in end-of-life (EOL) care quality among non-Hispanic Black (NHB), non-Hispanic White (NHW), and Hispanic patients with ovarian cancer. This retrospective cohort study used the Surveillance, Epidemiology, and End Results-linked Medicare data for women diagnosed with ovarian cancer from 2008 to 2015, ages 65 years and older. Health care affordability, accessibility, and availability measures were assessed at the census tract or regional levels, and associations between these measures and quality of EOL care were examined using multivariable-adjusted regression models, as appropriate. The final sample included 4,646 women [mean age (SD), 77.5 (7.0) years]; 87.4% NHW, 6.9% NHB, and 5.7% Hispanic. In the multivariable-adjusted models, affordability was associated with a decreased risk of intensive care unit stay [adjusted relative risk (aRR) 0.90, 95% confidence interval (CI): 0.83-0.98] and in-hospital death (aRR 0.91, 95% CI: 0.84-0.98). After adjustment for HCA dimensions, NHB patients had lower-quality EOL care compared with NHW patients, defined as: increased risk of hospitalization in the last 30 days of life (aRR 1.16, 95% CI: 1.03-1.30), no hospice care (aRR 1.23, 95% CI: 1.04-1.44), in-hospital death (aRR 1.27, 95% CI: 1.03-1.57), and higher counts of poor-quality EOL care outcomes (count ratio:1.19, 95% CI: 1.04-1.36). HCA dimensions were strong predictors of EOL care quality; however, racial disparities persisted, suggesting that additional drivers of these disparities remain to be identified. SIGNIFICANCE Among patients with ovarian cancer, Black patients had lower-quality EOL care, even after adjusting for three structural barriers to HCA, namely affordability, availability, and accessibility. This suggests an important need to investigate the roles of yet unexplored barriers to HCA such as accommodation and acceptability, as drivers of poor-quality EOL care among Black patients with ovarian cancer.
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Affiliation(s)
- Shama Karanth
- UF Health Cancer Center, University of Florida, Gainesville, Florida
| | | | - Lauren E. Wilson
- Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina
| | - Rebecca A. Previs
- Division of Gynecologic Oncology, Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina
| | - Fariha Rahman
- Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina
| | - Bin Huang
- Department of Biostatistics and Kentucky Cancer Registry, Univ of Kentucky, Lexington, Kentucky
| | - Maria Pisu
- Division of Preventive Medicine and O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama
| | - Margaret Liang
- Division of Gynecologic Oncology, Department of Obstetrics & Gynecology, and O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama
| | - Kevin C. Ward
- Georgia Cancer Registry, Emory University, Atlanta, Georgia
| | - Maria J. Schymura
- New York State Cancer Registry, New York State Department of Health, Albany, New York
| | - Andrew Berchuck
- Division of Gynecologic Oncology, Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina
| | - Tomi F. Akinyemiju
- Department of Population Health Sciences, Duke University School of Medicine, Durham, North Carolina
- Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina
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40
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Miskin RP, DiPersio CM. Roles for integrin α3β1 in regulating the ability of epithelial cells to modulate the microenvironment during normal and pathological tissue remodeling. Am J Physiol Cell Physiol 2024. [PMID: 38497112 DOI: 10.1152/ajpcell.00128.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 03/08/2024] [Indexed: 03/19/2024]
Abstract
Integrin receptors for the extracellular matrix activate intracellular signaling pathways that are critical for tissue development, homeostasis, and regeneration/repair, and their loss or dysregulation contributes to many developmental defects and tissue pathologies. This review will focus on tissue remodeling roles for integrin α3β1, a receptor for laminins found in the basement membranes that underlie epithelial cell layers. As a paradigm, we will discuss literature that supports a role for α3β1 in promoting ability of epidermal keratinocytes to modify their tissue microenvironment during skin development, wound healing or tumorigenesis. Preclinical and clinical studies have shown that this role depends largely on ability of α3β1 to govern the keratinocyte's repertoire of secreted proteins, or the "secretome", including (1) matrix proteins and proteases involved in matrix remodeling and (2) paracrine-acting growth factors/cytokines that stimulate other cells with important tissue remodeling functions (e.g., endothelial cells, fibroblasts, inflammatory cells). Moreover, α3β1 signaling controls gene expression that helps epithelial cells carry out these functions, including genes that encode secreted matrix proteins, proteases, growth factors, or cytokines. We will review what is known about α3β1-dependent gene regulation through both transcription and post-transcriptional mRNA stability. Regarding the latter, we will discuss examples of α3β1-dependent alternative splicing or alternative polyadenylation that prevents inclusion of cis-acting mRNA sequences that would otherwise target the transcript for degradation via nonsense-mediated decay or destabilizing AU-rich elements in the 3'-UTR. Finally, we will discuss prospects and anticipated challenges of exploiting α3β1 as a clinical target for the treatment of cancer or wound healing.
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Affiliation(s)
| | - C Michael DiPersio
- Department of Surgery / Department of Molecular & Cellular Physiology, albany medical center, Albany, NY, United States
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41
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Butenas ALE, Flax JS, Carroll RJ, Chuwonganant CS, Baranczuk AM, Copp SW. Sex differences in the purinergic 2 receptor mediated blood pressure response to treadmill exercise in rats with simulated peripheral artery disease. Am J Physiol Regul Integr Comp Physiol 2024. [PMID: 38497127 DOI: 10.1152/ajpregu.00010.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
We investigated the role played by ATP sensitive purinergic 2 (P2) receptors in evoking the pressor response to treadmill exercise in male and female rats with and without femoral arteries that were ligated for ~72 hours to induce simulated peripheral artery disease (PAD). We hypothesized that PPADS (P2 receptor antagonist, 10 mg i.v.) would reduce the pressor response to four minutes of treadmill exercise (15 m×min-1, 1° incline) and steady-state exercise plasma norepinephrine (NE) values in male and female rats, and that the magnitude of effect of PPADS would be greater in rats with simulated PAD ("ligated") than in sham-operated rats. In males, PPADS significantly reduced the difference between steady-state exercise and baseline mean arterial pressure (ΔMAP) response to treadmill exercise in sham (n=8, pre-PPADS: 12±2, post-PPADS: 1±5 mmHg; P=0.037) and ligated (n=4; pre-PPADS: 20±2, post-PPADS: 11±3 mmHg; P=0.028) rats with a similar magnitude of effect observed between groups (P=0.720). In females, PPADS had no effect on the ∆MAP response to treadmill exercise in sham (n=6, pre-PPADS: 9±2, post-PPADS: 7±2 mmHg; P=0.448) or ligated (n=6, pre-PPADS: 15±2, post-PPADS: 16±3 mmHg; P=0.684) rats. When NE values were grouped by sex independent of ligation/sham status, PPADS significantly reduced plasma NE in male (P=0.016) and female (P=0.027) rats. The data indicate that P2 receptors contribute to the sympathetic response to exercise in both male and female rats, but that the sympathoexcitatory role for P2 receptors translates into an obligatory role in the blood pressure response to exercise in male but not female rats.
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Affiliation(s)
- Alec L E Butenas
- Department of Kinesiology, Kansas State University, Manhattan, KS, United States
| | - Joseph S Flax
- Department of Kinesiology, Kansas State University, United States
| | - Raimi J Carroll
- Department of Kinesiology, Kansas State University, United States
| | | | - Ashley M Baranczuk
- Department of Kinesiology, Kansas State University, Manhattan, KS, United States
| | - Steven W Copp
- Department of Kinesiology, Kansas State University, United States
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Du J, DiNicola LM, Angeli PA, Saadon-Grosman N, Sun W, Kaiser S, Ladopoulou J, Xue A, Yeo BTT, Eldaief MC, Buckner RL. Organization of the Human Cerebral Cortex Estimated Within Individuals: Networks, Global Topography, and Function. J Neurophysiol 2024. [PMID: 38489238 DOI: 10.1152/jn.00308.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 02/16/2024] [Indexed: 03/17/2024] Open
Abstract
The cerebral cortex is populated by specialized regions that are organized into networks. Here we estimated networks from functional MRI (fMRI) data in intensively sampled participants. The procedure was developed in two participants (scanned 31 times) and then prospectively applied to 15 participants (scanned 8-11 times). Analysis of the networks revealed a global organization. Locally organized first-order sensory and motor networks were surrounded by spatially adjacent second-order networks that linked to distant regions. Third-order networks possessed regions distributed widely throughout association cortex. Regions of distinct third-order networks displayed side-by-side juxtapositions with a pattern that repeated across multiple cortical zones. We refer to these as Supra-Areal Association Megaclusters (SAAMs). Within each SAAM, two candidate control regions were adjacent to three separate domain-specialized regions. Response properties were explored with task data. The somatomotor and visual networks responded to body movements and visual stimulation, respectively. Second-order networks responded to transients in an oddball detection task, consistent with a role in orienting to salient events. The third-order networks, including distinct regions within each SAAM, showed two levels of functional specialization. Regions linked to candidate control networks responded to working memory load across multiple stimulus domains. The remaining regions dissociated across language, social, and spatial / episodic processing domains. These results suggest progressively higher-order networks nest outwards from primary sensory and motor cortices. Within the apex zones of association cortex, there is specialization that repeatedly divides domain-flexible from domain-specialized regions. We discuss implications of these findings including how repeating organizational motifs may emerge during development.
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Affiliation(s)
- Jingnan Du
- Department of Psychology, Harvard University, Cambridge, MA, United States
| | - Lauren M DiNicola
- Department of Psychology, Harvard University, Cambridge, MA, United States
| | - Peter A Angeli
- Department of Psychology, Harvard University, Cambridge, MA, United States
| | | | - Wendy Sun
- Division of Medical Sciences, Harvard University, Cambridge, MA, United States
| | - Stephanie Kaiser
- Department of Psychology, Harvard University, Cambridge, MA, United States
| | - Joanna Ladopoulou
- Department of Psychology, Harvard University, Cambridge, MA, United States
| | - Aihuiping Xue
- Electrical and Computer Engineering, National University of Singapore, Singapore, Singapore
| | - B T Thomas Yeo
- Electrical and Computer Engineering, National University of Singapore, Singapore, Singapore
| | - Mark C Eldaief
- Department of Psychiatry, Harvard University, Cambridge, MA, United States
| | - Randy L Buckner
- Department of Psychology, Harvard University, Cambridge, MA, United States
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Nazari I, Feinstein MJ. Evolving mechanisms and presentations of cardiovascular disease in people with HIV: implications for management. Clin Microbiol Rev 2024; 37:e0009822. [PMID: 38299802 PMCID: PMC10938901 DOI: 10.1128/cmr.00098-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024] Open
Abstract
SUMMARYPeople with HIV (PWH) are at elevated risk for cardiovascular diseases (CVDs), including myocardial infarction, heart failure, and sudden cardiac death, among other CVD manifestations. Chronic immune dysregulation resulting in persistent inflammation is common among PWH, particularly those with sustained viremia and impaired CD4+ T cell recovery. This inflammatory milieu is a major contributor to CVDs among PWH, in concert with common comorbidities (such as dyslipidemia and smoking) and, to a lesser extent, off-target effects of antiretroviral therapy. In this review, we discuss the clinical and mechanistic evidence surrounding heightened CVD risks among PWH, implications for specific CVD manifestations, and practical guidance for management in the setting of evolving data.
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Affiliation(s)
- Ilana Nazari
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Matthew J. Feinstein
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Cardiology in the Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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44
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Puumala E, Fallah S, Robbins N, Cowen LE. Advancements and challenges in antifungal therapeutic development. Clin Microbiol Rev 2024; 37:e0014223. [PMID: 38294218 PMCID: PMC10938895 DOI: 10.1128/cmr.00142-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024] Open
Abstract
SUMMARYOver recent decades, the global burden of fungal disease has expanded dramatically. It is estimated that fungal disease kills approximately 1.5 million individuals annually; however, the true worldwide burden of fungal infection is thought to be higher due to existing gaps in diagnostics and clinical understanding of mycotic disease. The development of resistance to antifungals across diverse pathogenic fungal genera is an increasingly common and devastating phenomenon due to the dearth of available antifungal classes. These factors necessitate a coordinated response by researchers, clinicians, public health agencies, and the pharmaceutical industry to develop new antifungal strategies, as the burden of fungal disease continues to grow. This review provides a comprehensive overview of the new antifungal therapeutics currently in clinical trials, highlighting their spectra of activity and progress toward clinical implementation. We also profile up-and-coming intracellular proteins and pathways primed for the development of novel antifungals targeting their activity. Ultimately, we aim to emphasize the importance of increased investment into antifungal therapeutics in the current continually evolving landscape of infectious disease.
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Affiliation(s)
- Emily Puumala
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Sara Fallah
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Leah E. Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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45
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Uddin MJ, Thompson B, Leslie JL, Fishman C, Sol-Church K, Kumar P, Petri WA. Investigating the impact of antibiotic-induced dysbiosis on protection from Clostridium difficile colitis by mouse colonic innate lymphoid cells. mBio 2024; 15:e0333823. [PMID: 38376154 DOI: 10.1128/mbio.03338-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/18/2024] [Indexed: 02/21/2024] Open
Abstract
Innate lymphoid cells (ILCs) play a critical role in maintaining intestinal health in homeostatic and diseased conditions. During Clostridium difficile infection (CDI), IL-33 activates ILC2 to protect from colonic damage and mortality. The function of IL-33 and ILC is tightly regulated by the intestinal microbiota. We set out to determine the impact of antibiotic-induced disruption of the microbiome on ILC function. Our goal was to understand antibiotic-induced changes in ILC function on susceptibility to C. difficile colitis in a mouse model. We utilized high-throughput single-cell RNAseq to investigate the phenotypic features of colonic ILC at baseline, after antibiotic administration with or without IL-33 treatment. We identified a heterogeneous landscape of colonic ILCs with gene signatures of inflammatory, anti-inflammatory, migratory, progenitor, plastic, and antigen-presenting ILCs. Antibiotic treatment decreased ILC2 while coordinately increasing ILC1 and ILC3 phenotypes. Notably, Ifng+, Ccl5+, and Il23r+ ILC increased after antibiotics. IL-33 treatment counteracted the antibiotic effect by downregulating ILC1 and ILC3 and activating ILC2. In addition, IL-33 treatment markedly induced the expression of type 2 genes, including Areg and Il5. Finally, we identified amphiregulin, produced by ILC2, as protective during C. difficile infection. Together, our data expand our understanding of how antibiotics induce susceptibility to C. difficile colitis through their impact on ILC subsets and function.IMPORTANCEClostridium difficile infection (CDI) accounts for around 500,000 symptomatic cases and over 20,000 deaths annually in the United States alone. A major risk factor of CDI is antibiotic-induced dysbiosis of the gut. Microbiota-regulated IL-33 and innate lymphoid cells (ILCs) are important in determining the outcomes of C. difficile infection. Understanding how antibiotic and IL-33 treatment alter the phenotype of colon ILCs is important to identify potential therapeutics. Here, we performed single-cell RNAseq of mouse colon ILCs collected at baseline, after antibiotic treatment, and after IL-33 treatment. We identified heterogeneous subpopulations of all three ILC subtypes in the mouse colon. Our analysis revealed several potential pathways of antibiotic-mediated increased susceptibility to intestinal infection. Our discovery that Areg is abundantly expressed by ILCs, and the protection of mice from CDI by amphiregulin treatment, suggests that the amphiregulin-epidermal growth factor receptor pathway is a potential therapeutic target for treating intestinal colitis.
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Affiliation(s)
- Md Jashim Uddin
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Brandon Thompson
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Jhansi L Leslie
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia, USA
- Arcus Biosciences, Hayward, California, USA
| | - Casey Fishman
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Katia Sol-Church
- Genome Analysis and Technology Core, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Pankaj Kumar
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - William A Petri
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia, USA
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Ciudad MT, Quevedo R, Lamorte S, Jin R, Nzirorera N, Koritzinsky M, McGaha TL. Dabrafenib Alters MDSC Differentiation and Function by Activation of GCN2. Cancer Res Commun 2024; 4:765-784. [PMID: 38421883 PMCID: PMC10936428 DOI: 10.1158/2767-9764.crc-23-0376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 12/12/2023] [Accepted: 02/27/2024] [Indexed: 03/02/2024]
Abstract
The effect of targeted therapeutics on anticancer immune responses is poorly understood. The BRAF inhibitor dabrafenib has been reported to activate the integrated stress response (ISR) kinase GCN2, and the therapeutic effect has been partially attributed to GCN2 activation. Because ISR signaling is a key component of myeloid-derived suppressor cell (MDSC) development and function, we measured the effect of dabrafenib on MDSC differentiation and suppressive activity. Our data showed that dabrafenib attenuated MDSC ability to suppress T-cell activity, which was associated with a GCN2-dependent block of the transition from monocytic progenitor to polymorphonuclear (PMN)-MDSCs and proliferative arrest resulting in PMN-MDSC loss. Transcriptional profiling revealed that dabrafenib-driven GCN2 activation altered metabolic features in MDSCs enhancing oxidative respiration, and attenuated transcriptional programs required for PMN development. Moreover, we observed a broad downregulation of transcriptional networks associated with PMN developmental pathways, and increased activity of transcriptional regulons driven by Atf5, Mafg, and Zbtb7a. This transcriptional program alteration underlies the basis for PMN-MDSC developmental arrest, skewing immature MDSC development toward monocytic lineage cells. In vivo, we observed a pronounced reduction in PMN-MDSCs in dabrafenib-treated tumor-bearing mice suggesting that dabrafenib impacts MDSC populations systemically and locally, in the tumor immune infiltrate. Thus, our data reveal transcriptional networks that govern MDSC developmental programs, and the impact of GCN2 stress signaling on the innate immune landscape in tumors, providing novel insight into potentially beneficial off-target effects of dabrafenib. SIGNIFICANCE An important, but poorly understood, aspect of targeted therapeutics for cancer is the effect on antitumor immune responses. This article shows that off-target effects of dabrafenib activating the kinase GCN2 impact MDSC development and function reducing PMN-MDSCs in vitro and in vivo. This has important implications for our understanding of how this BRAF inhibitor impacts tumor growth and provides novel therapeutic target and combination possibilities.
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Affiliation(s)
- M. Teresa Ciudad
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Immunology, University of Toronto, Toronto, Canada
| | - Rene Quevedo
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Immunology, University of Toronto, Toronto, Canada
| | - Sara Lamorte
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Immunology, University of Toronto, Toronto, Canada
| | - Robbie Jin
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Immunology, University of Toronto, Toronto, Canada
| | - Nadine Nzirorera
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Immunology, University of Toronto, Toronto, Canada
| | - Marianne Koritzinsky
- Princess Margaret Cancer Center, University Health Network, Toronto, Canada
- Institute of Medical Science, University of Toronto, Toronto, Canada
- Department of Radiation Oncology, University of Toronto, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Tracy L. McGaha
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Immunology, University of Toronto, Toronto, Canada
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Singh N, Rolandelli A, O’Neal AJ, Butler LR, Samaddar S, Laukaitis-Yousey HJ, Butnaru M, Mohr SE, Perrimon N, Pedra JHF. Genetic manipulation of an Ixodes scapularis cell line. mBio 2024; 15:e0247923. [PMID: 38380961 PMCID: PMC10936194 DOI: 10.1128/mbio.02479-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/08/2024] [Indexed: 02/22/2024] Open
Abstract
Although genetic manipulation is one of the hallmarks of model organisms, its applicability to non-model species has remained difficult due to our limited understanding of their fundamental biology. For instance, manipulation of a cell line originated from the black-legged tick Ixodes scapularis, an arthropod that serves as a vector for several human pathogens, has yet to be established. Here, we demonstrate the successful genetic modification of the commonly used tick ISE6 line through ectopic expression and clustered regularly interspaced palindromic repeats [(CRISPR)/CRISPR-associated protein 9 (Cas9)] genome editing. We performed ectopic expression using nucleofection and attained CRISPR-Cas9 editing via homology-dependent recombination. Targeting the E3 ubiquitin ligase x-linked inhibitor of apoptosis (xiap) and its substrate p47 led to an alteration in molecular signaling within the immune deficiency network and increased infection of the rickettsial agent Anaplasma phagocytophilum in I. scapularis ISE6 cells. Collectively, our findings complement techniques for the genetic engineering of I. scapularis ticks, which currently limit efficient and scalable molecular genetic screens in vivo.IMPORTANCEGenetic engineering in arachnids has lagged compared to insects, largely because of substantial differences in their biology. This study unveils the implementation of ectopic expression and CRISPR-Cas9 gene editing in a tick cell line. We introduced fluorescently tagged proteins in ISE6 cells and edited its genome via homology-dependent recombination. We ablated the expression of xiap and p47, two signaling molecules present in the immune deficiency (IMD) pathway of Ixodes scapularis. Impairment of the tick IMD pathway, an analogous network of the tumor necrosis factor receptor in mammals, led to enhanced infection of the rickettsial agent Anaplasma phagocytophilum. Altogether, our findings provide a critical technical resource to the scientific community to enable a deeper understanding of biological circuits in the black-legged tick I. scapularis.
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Affiliation(s)
- Nisha Singh
- Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Agustin Rolandelli
- Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Anya J. O’Neal
- Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - L. Rainer Butler
- Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Sourabh Samaddar
- Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Hanna J. Laukaitis-Yousey
- Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Matthew Butnaru
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Stephanie E. Mohr
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Joao H. F. Pedra
- Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
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48
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Sodroski CN, Oh HS, Chou SF, Knipe DM. Sp1 facilitates continued HSV-1 gene expression in the absence of key viral transactivators. mBio 2024; 15:e0347923. [PMID: 38349188 PMCID: PMC10936440 DOI: 10.1128/mbio.03479-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 03/14/2024] Open
Abstract
Productive replication of herpes simplex virus (HSV) relies upon a well-ordered transcriptional cascade flowing from immediate-early (IE) to early (E) to late (L) gene products. While several virus-encoded transcriptional activators are involved in this process, IE and E gene promoters also contain multiple binding sites for the ubiquitously expressed cellular transcription factor Sp1. Sp1 has been previously implicated in activating HSV-1 gene transcription downstream of these sites, but why Sp1-binding sites are maintained in the promoters of genes activated by virus-encoded activators remains unclear. We hypothesized that Sp1 enables continued HSV-1 transcription and replication when viral transactivators are limited. We used a depletion-based approach in human foreskin fibroblasts to investigate the specific contribution of Sp1 to the initiation and progression of the HSV-1 lytic gene cascade. We found that Sp1 increased viral transcript levels, protein expression, and replication following infection with VP16- or ICP0-deficient viruses but had little to no effect on rescued viruses or during wild-type (WT) HSV-1 infection. Moreover, Sp1 promoted WT virus transcription and replication following interferon treatment of fibroblasts and thus may contribute to viral immune evasion. Interestingly, we observed reduced expression of Sp1 and Sp1-family transcription factors in differentiated sensory neurons compared to undifferentiated cells, suggesting that reduced Sp1 levels may also contribute to HSV-1 latent infection. Overall, these findings indicate that Sp1 can promote HSV-1 gene expression in the absence of key viral transactivators; thus, HSV-1 may use Sp1 to maintain its gene expression and replication under adverse conditions.IMPORTANCEHerpes simplex virus (HSV) is a common human pathogen that actively replicates in the epithelia but can persist for the lifetime of the infected host via a stable, latent infection in neurons. A key feature of the HSV replication cycle is a complex transcriptional program in which virus and host-cell factors coordinate to regulate expression of the viral gene products necessary for continued viral replication. Multiple binding sites for the cellular transcription factor Sp1 are located in the promoters of HSV-1 genes, but how Sp1 binding contributes to transcription and replication of wild-type virus is not fully understood. In this study, we identified a specific role for Sp1 in maintaining HSV-1 gene transcription under adverse conditions, as when virus-encoded transcriptional activators were absent or limited. Preservation of Sp1-binding sites in HSV-1 gene promoters may thus benefit the virus as it navigates diverse cell types and host-cell conditions during infection.
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Affiliation(s)
- Catherine N. Sodroski
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
- Program in Virology, Harvard Medical School, Boston, Massachusetts, USA
| | - Hyung Suk Oh
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Shu-Fan Chou
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - David M. Knipe
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
- Program in Virology, Harvard Medical School, Boston, Massachusetts, USA
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Zeng Q, Antia A, Casorla-Perez LA, Puray-Chavez M, Kutluay SB, Ciorba MA, Ding S. Calpain-2 mediates SARS-CoV-2 entry via regulating ACE2 levels. mBio 2024; 15:e0228723. [PMID: 38349185 PMCID: PMC10936414 DOI: 10.1128/mbio.02287-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 01/03/2024] [Indexed: 02/15/2024] Open
Abstract
Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, much effort has been dedicated to identifying effective antivirals against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A number of calpain inhibitors show excellent antiviral activities against SARS-CoV-2 by targeting the viral main protease (Mpro), which plays an essential role in processing viral polyproteins. In this study, we found that calpain inhibitors potently inhibited the infection of a chimeric vesicular stomatitis virus (VSV) encoding the SARS-CoV-2 spike protein but not Mpro. In contrast, calpain inhibitors did not exhibit antiviral activities toward the wild-type VSV with its native glycoprotein. Genetic knockout of calpain-2 by CRISPR/Cas9 conferred resistance of the host cells to the chimeric VSV-SARS-CoV-2 virus and a clinical isolate of wild-type SARS-CoV-2. Mechanistically, calpain-2 facilitates SARS-CoV-2 spike protein-mediated cell attachment by positively regulating the cell surface levels of ACE2. These results highlight an Mpro-independent pathway targeted by calpain inhibitors for efficient viral inhibition. We also identify calpain-2 as a novel host factor and a potential therapeutic target responsible for SARS-CoV-2 infection at the entry step. IMPORTANCE Many efforts in small-molecule screens have been made to counter SARS-CoV-2 infection by targeting the viral main protease, the major element that processes viral proteins after translation. Here, we discovered that calpain inhibitors further block SARS-CoV-2 infection in a main protease-independent manner. We identified the host cysteine protease calpain-2 as an important positive regulator of the cell surface levels of SARS-CoV-2 cellular receptor ACE2 and, thus, a facilitator of viral infection. By either pharmacological inhibition or genetic knockout of calpain-2, the SARS-CoV-2 binding to host cells is blocked and viral infection is decreased. Our findings highlight a novel mechanism of ACE2 regulation, which presents a potential new therapeutic target. Since calpain inhibitors also potently interfere with the viral main protease, our data also provide a mechanistic understanding of the potential use of calpain inhibitors as dual inhibitors (entry and replication) in the clinical setting of COVID-19 diseases. Our findings bring mechanistic insights into the cellular process of SARS-CoV-2 entry and offer a novel explanation to the mechanism of activities of calpain inhibitors.
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Affiliation(s)
- Qiru Zeng
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Avan Antia
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Luis Alberto Casorla-Perez
- Division of Gastroenterology, Department of Medicine, Inflammatory Bowel Diseases Center, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Maritza Puray-Chavez
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Sebla B. Kutluay
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Matthew A. Ciorba
- Division of Gastroenterology, Department of Medicine, Inflammatory Bowel Diseases Center, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Siyuan Ding
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
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50
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Marques AD, Graham-Wooten J, Fitzgerald AS, Sobel Leonard A, Cook EJ, Everett JK, Rodino KG, Moncla LH, Kelly BJ, Collman RG, Bushman FD. SARS-CoV-2 evolution during prolonged infection in immunocompromised patients. mBio 2024; 15:e0011024. [PMID: 38364100 PMCID: PMC10936176 DOI: 10.1128/mbio.00110-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/18/2024] Open
Abstract
Prolonged infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in immunocompromised patients provides an opportunity for viral evolution, potentially leading to the generation of new pathogenic variants. To investigate the pathways of viral evolution, we carried out a study on five patients experiencing prolonged SARS-CoV-2 infection (quantitative polymerase chain reaction-positive for 79-203 days) who were immunocompromised due to treatment for lymphoma or solid organ transplantation. For each timepoint analyzed, we generated at least two independent viral genome sequences to assess the heterogeneity and control for sequencing error. Four of the five patients likely had prolonged infection; the fifth apparently experienced a reinfection. The rates of accumulation of substitutions in the viral genome per day were higher in hospitalized patients with prolonged infection than those estimated for the community background. The spike coding region accumulated a significantly greater number of unique mutations than other viral coding regions, and the mutation density was higher. Two patients were treated with monoclonal antibodies (bebtelovimab and sotrovimab); by the next sampled timepoint, each virus population showed substitutions associated with monoclonal antibody resistance as the dominant forms (spike K444N and spike E340D). All patients received remdesivir, but remdesivir-resistant substitutions were not detected. These data thus help elucidate the trends of emergence, evolution, and selection of mutational variants within long-term infected immunocompromised individuals. IMPORTANCE SARS-CoV-2 is responsible for a global pandemic, driven in part by the emergence of new viral variants. Where do these new variants come from? One model is that long-term viral persistence in infected individuals allows for viral evolution in response to host pressures, resulting in viruses more likely to replicate efficiently in humans. In this study, we characterize replication in several hospitalized and long-term infected individuals, documenting efficient pathways of viral evolution.
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Affiliation(s)
- Andrew D. Marques
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jevon Graham-Wooten
- Division of Pulmonary, Allergy, and Critical Care, Philadelphia, Pennsylvania, USA
| | | | - Ashley Sobel Leonard
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Emma J. Cook
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John K. Everett
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kyle G. Rodino
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Louise H. Moncla
- Department of Pathobiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Brendan J. Kelly
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ronald G. Collman
- Division of Pulmonary, Allergy, and Critical Care, Philadelphia, Pennsylvania, USA
| | - Frederic D. Bushman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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