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Fines DM, Schichnes D, Knight M, Anaya-Sanchez A, Thuong N, Cox J, Stanley SA. Mycobacterial formation of intracellular lipid inclusions is a dynamic process associated with rapid replication. bioRxiv 2023:2023.08.10.552809. [PMID: 37609245 PMCID: PMC10441389 DOI: 10.1101/2023.08.10.552809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Intracellular lipid inclusions (ILI) are triacylglyceride rich organelles produced by mycobacteria thought to serve as energy reservoirs. It is believed that ILI are formed as a result of a dosR mediated transition from replicative growth to non-replicating persistence (NRP). ILI rich Mycobacterium tuberculosis (Mtb) bacilli have been reported during infection and in sputum, establishing their importance in Mtb pathogenesis. Studies conducted in mycobacteria such as Mycobacterium smegmatis, Mycobacterium abscessus, or lab Mtb strains have demonstrated ILI formation in the presence of hypoxic, nitric oxide, nutrient limitation, or low nitrogen stress, conditions believed to emulate the host environment within which Mtb resides. Here, we show that M. marinum and clinical Mtb isolates make ILI during active replication in axenic culture independent of environmental stressors. By tracking ILI formation dynamics we demonstrate that ILI are quickly formed in the presence of fresh media or exogenous fatty acids but are rapidly depleted while bacteria are still actively replicating. We also show that the cell envelope is an alternate site for neutral lipid accumulation observed during stationary phase. In addition, we screen a panel of 60 clinical isolates and observe variation in ILI production during early log phase growth between and among Mtb lineages. Finally, we show that dosR expression level does not strictly correlate with ILI accumulation in fresh clinical isolates. Taken together, our data provide evidence of an active ILI formation pathway in replicating mycobacteria cultured in the absence of stressors, suggesting a decoupling of ILI formation from NRP.
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Van Dis E, Fox DM, Morrison HM, Fines DM, Babirye JP, McCann LH, Rawal S, Cox JS, Stanley SA. IFN-γ-independent control of M. tuberculosis requires CD4 T cell-derived GM-CSF and activation of HIF-1α. PLoS Pathog 2022; 18:e1010721. [PMID: 35877763 PMCID: PMC9352196 DOI: 10.1371/journal.ppat.1010721] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 08/04/2022] [Accepted: 07/01/2022] [Indexed: 11/29/2022] Open
Abstract
The prevailing model of protective immunity to tuberculosis is that CD4 T cells produce the cytokine IFN-γ to activate bactericidal mechanisms in infected macrophages. Although IFN-γ-independent CD4 T cell based control of M. tuberculosis infection has been demonstrated in vivo it is unclear whether CD4 T cells are capable of directly activating macrophages to control infection in the absence of IFN-γ. We developed a co-culture model using CD4 T cells isolated from the lungs of infected mice and M. tuberculosis-infected murine bone marrow-derived macrophages (BMDMs) to investigate mechanisms of CD4 dependent control of infection. We found that even in the absence of IFN-γ signaling, CD4 T cells drive macrophage activation, M1 polarization, and control of infection. This IFN-γ-independent control of infection requires activation of the transcription factor HIF-1α and a shift to aerobic glycolysis in infected macrophages. While HIF-1α activation following IFN-γ stimulation requires nitric oxide, HIF-1α-mediated control in the absence of IFN-γ is nitric oxide-independent, indicating that distinct pathways can activate HIF-1α during infection. We show that CD4 T cell-derived GM-CSF is required for IFN-γ-independent control in BMDMs, but that recombinant GM-CSF is insufficient to control infection in BMDMs or alveolar macrophages and does not rescue the absence of control by GM-CSF-deficient T cells. In contrast, recombinant GM-CSF controls infection in peritoneal macrophages, induces lipid droplet biogenesis, and also requires HIF-1α for control. These results advance our understanding of CD4 T cell-mediated immunity to M. tuberculosis, reveal important differences in immune activation of distinct macrophage types, and outline a novel mechanism for the activation of HIF-1α. We establish a previously unknown functional link between GM-CSF and HIF-1α and provide evidence that CD4 T cell-derived GM-CSF is a potent bactericidal effector.
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Affiliation(s)
- Erik Van Dis
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, Berkeley, California, United States of America
| | - Douglas M. Fox
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, Berkeley, California, United States of America
| | - Huntly M. Morrison
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, Berkeley, California, United States of America
| | - Daniel M. Fines
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, Berkeley, California, United States of America
| | - Janet Peace Babirye
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, Berkeley, California, United States of America
| | - Lily H. McCann
- School of Public Health, Division of Infectious Diseases and Vaccinology, University of California, Berkeley, Berkeley, California, United States of America
| | - Sagar Rawal
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, Berkeley, California, United States of America
| | - Jeffery S. Cox
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, Berkeley, California, United States of America
| | - Sarah A. Stanley
- Department of Molecular and Cell Biology, Division of Immunology and Pathogenesis, University of California, Berkeley, Berkeley, California, United States of America
- School of Public Health, Division of Infectious Diseases and Vaccinology, University of California, Berkeley, Berkeley, California, United States of America
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Biering SB, Van Dis E, Wehri E, Yamashiro LH, Nguyenla X, Dugast-Darzacq C, Graham TGW, Stroumza JR, Golovkine GR, Roberts AW, Fines DM, Spradlin JN, Ward CC, Bajaj T, Dovala D, Schulze-Gamen U, Bajaj R, Fox DM, Ott M, Murthy N, Nomura DK, Schaletzky J, Stanley SA. Screening a Library of FDA-Approved and Bioactive Compounds for Antiviral Activity against SARS-CoV-2. ACS Infect Dis 2021; 7:2337-2351. [PMID: 34129317 PMCID: PMC8231672 DOI: 10.1021/acsinfecdis.1c00017] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Indexed: 01/18/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has emerged as a major global health threat. The COVID-19 pandemic has resulted in over 168 million cases and 3.4 million deaths to date, while the number of cases continues to rise. With limited therapeutic options, the identification of safe and effective therapeutics is urgently needed. The repurposing of known clinical compounds holds the potential for rapid identification of drugs effective against SARS-CoV-2. Here, we utilized a library of FDA-approved and well-studied preclinical and clinical compounds to screen for antivirals against SARS-CoV-2 in human pulmonary epithelial cells. We identified 13 compounds that exhibit potent antiviral activity across multiple orthogonal assays. Hits include known antivirals, compounds with anti-inflammatory activity, and compounds targeting host pathways such as kinases and proteases critical for SARS-CoV-2 replication. We identified seven compounds not previously reported to have activity against SARS-CoV-2, including B02, a human RAD51 inhibitor. We further demonstrated that B02 exhibits synergy with remdesivir, the only antiviral approved by the FDA to treat COVID-19, highlighting the potential for combination therapy. Taken together, our comparative compound screening strategy highlights the potential of drug repurposing screens to identify novel starting points for development of effective antiviral mono- or combination therapies to treat COVID-19.
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Affiliation(s)
- Scott B. Biering
- School of Public Health, Division of Infectious
Diseases and Vaccinology, University of California, Berkeley,
Berkeley, California 94720, United States
| | - Erik Van Dis
- Department of Molecular and Cell Biology, Division of
Immunology and Pathogenesis, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Eddie Wehri
- The Henry Wheeler Center for Emerging and
Neglected Diseases, 344 Li Ka Shing, Berkeley, California 94720,
United States
| | - Livia H. Yamashiro
- School of Public Health, Division of Infectious
Diseases and Vaccinology, University of California, Berkeley,
Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, Division of
Immunology and Pathogenesis, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Xammy Nguyenla
- School of Public Health, Division of Infectious
Diseases and Vaccinology, University of California, Berkeley,
Berkeley, California 94720, United States
| | - Claire Dugast-Darzacq
- Department of Molecular and Cell Biology, Division of
Biochemistry, Biophysics and Structural Biology, University of California,
Berkeley, Berkeley, California 94720, United
States
| | - Thomas G. W. Graham
- Department of Molecular and Cell Biology, Division of
Biochemistry, Biophysics and Structural Biology, University of California,
Berkeley, Berkeley, California 94720, United
States
| | - Julien R. Stroumza
- The Henry Wheeler Center for Emerging and
Neglected Diseases, 344 Li Ka Shing, Berkeley, California 94720,
United States
| | - Guillaume R. Golovkine
- Department of Molecular and Cell Biology, Division of
Immunology and Pathogenesis, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Allison W. Roberts
- Department of Molecular and Cell Biology, Division of
Immunology and Pathogenesis, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Daniel M. Fines
- Department of Molecular and Cell Biology, Division of
Immunology and Pathogenesis, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Jessica N. Spradlin
- Departments of Chemistry, Molecular and Cell Biology,
and Nutritional Sciences and Toxicology, University of California,
Berkeley, Berkeley, California 94720, United
States
| | - Carl C. Ward
- Departments of Chemistry, Molecular and Cell Biology,
and Nutritional Sciences and Toxicology, University of California,
Berkeley, Berkeley, California 94720, United
States
| | - Teena Bajaj
- Department of Bioengineering, University of
California, Berkeley, Berkeley, California 94720, United
States
| | - Dustin Dovala
- Novartis Institutes for BioMedical
Research, Emeryville, California 94608, United
States
| | - Ursula Schulze-Gamen
- QBI Coronavirus Research Group Structural Biology
Consortium, University of California, San Francisco, California
94158, United States
| | - Ruchika Bajaj
- Department of Bioengineering and Therapeutic Sciences,
University of California, San Francisco, San Francisco,
California 94158, United States
| | - Douglas M. Fox
- School of Public Health, Division of Infectious
Diseases and Vaccinology, University of California, Berkeley,
Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, Division of
Immunology and Pathogenesis, University of California,
Berkeley, Berkeley, California 94720, United States
| | - Melanie Ott
- Department of Medicine, Medical Scientist Training
Program, Biomedical Sciences Graduate Program, University of California, San
Francisco, San Francisco, California 94143, United
States
- J. David Gladstone
Institutes, San Francisco, California 94158, United
States
| | - Niren Murthy
- Department of Bioengineering, University of
California, Berkeley, Berkeley, California 94720, United
States
- Innovative Genomics Institute
(IGI), 2151 Berkeley Way, Berkeley, California 94704, United
States
| | - Daniel K. Nomura
- Departments of Chemistry, Molecular and Cell Biology,
and Nutritional Sciences and Toxicology, University of California,
Berkeley, Berkeley, California 94720, United
States
| | - Julia Schaletzky
- The Henry Wheeler Center for Emerging and
Neglected Diseases, 344 Li Ka Shing, Berkeley, California 94720,
United States
| | - Sarah A. Stanley
- School of Public Health, Division of Infectious
Diseases and Vaccinology, University of California, Berkeley,
Berkeley, California 94720, United States
- Department of Molecular and Cell Biology, Division of
Immunology and Pathogenesis, University of California,
Berkeley, Berkeley, California 94720, United States
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Agrawal AA, Hastings AP, Fines DM, Bogdanowicz S, Huber M. Insect herbivory and plant adaptation in an early successional community*. Evolution 2018; 72:1020-1033. [DOI: 10.1111/evo.13451] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 02/04/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Anurag A. Agrawal
- Department of Ecology and Evolutionary Biology Cornell University Ithaca New York 14853
- Department of Entomology Cornell University Ithaca New York 14853
| | - Amy P. Hastings
- Department of Ecology and Evolutionary Biology Cornell University Ithaca New York 14853
| | - Daniel M. Fines
- Department of Ecology and Evolutionary Biology Cornell University Ithaca New York 14853
| | - Steve Bogdanowicz
- Department of Ecology and Evolutionary Biology Cornell University Ithaca New York 14853
| | - Meret Huber
- Department of Biochemistry Max‐Planck Institute for Chemical Ecology Jena Germany
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Donnelly CJ, Zhang PW, Pham JT, Heusler AR, Mistry NA, Vidensky S, Daley EL, Poth EM, Hoover B, Fines DM, Maragakis N, Tienari PJ, Petrucelli L, Traynor BJ, Wang J, Rigo F, Bennett CF, Blackshaw S, Sattler R, Rothstein JD. RNA toxicity from the ALS/FTD C9ORF72 expansion is mitigated by antisense intervention. Neuron 2013; 80:415-28. [PMID: 24139042 PMCID: PMC4098943 DOI: 10.1016/j.neuron.2013.10.015] [Citation(s) in RCA: 682] [Impact Index Per Article: 62.0] [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] [Accepted: 10/02/2013] [Indexed: 12/11/2022]
Abstract
A hexanucleotide GGGGCC repeat expansion in the noncoding region of the C9ORF72 gene is the most common genetic abnormality in familial and sporadic amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The function of the C9ORF72 protein is unknown, as is the mechanism by which the repeat expansion could cause disease. Induced pluripotent stem cell (iPSC)-differentiated neurons from C9ORF72 ALS patients revealed disease-specific (1) intranuclear GGGGCCexp RNA foci, (2) dysregulated gene expression, (3) sequestration of GGGGCCexp RNA binding protein ADARB2, and (4) susceptibility to excitotoxicity. These pathological and pathogenic characteristics were confirmed in ALS brain and were mitigated with antisense oligonucleotide (ASO) therapeutics to the C9ORF72 transcript or repeat expansion despite the presence of repeat-associated non-ATG translation (RAN) products. These data indicate a toxic RNA gain-of-function mechanism as a cause of C9ORF72 ALS and provide candidate antisense therapeutics and candidate human pharmacodynamic markers for therapy.
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Affiliation(s)
- Christopher J. Donnelly
- Department of Neurology, Johns Hopkins University, 855 N Wolfe Street, Rangos 2–270, Baltimore, MD 21205, USA
- Brain Science Institute, Johns Hopkins University, 855 N Wolfe Street, Rangos 2–270, Baltimore, MD 21205, USA
| | - Ping-Wu Zhang
- Department of Neurology, Johns Hopkins University, 855 N Wolfe Street, Rangos 2–270, Baltimore, MD 21205, USA
- Brain Science Institute, Johns Hopkins University, 855 N Wolfe Street, Rangos 2–270, Baltimore, MD 21205, USA
| | - Jacqueline T. Pham
- Department of Cellular and Molecular Medicine, Johns Hopkins University, 855 N Wolfe Street, Rangos 2–270, Baltimore, MD 21205, USA
| | - Aaron R. Heusler
- Department of Biochemistry and Molecular Biology, Johns Hopkins University, 855 N Wolfe Street, Rangos 2–270, Baltimore, MD 21205, USA
| | - Nipun A. Mistry
- Department of Neurology, Johns Hopkins University, 855 N Wolfe Street, Rangos 2–270, Baltimore, MD 21205, USA
- Brain Science Institute, Johns Hopkins University, 855 N Wolfe Street, Rangos 2–270, Baltimore, MD 21205, USA
| | - Svetlana Vidensky
- Department of Neurology, Johns Hopkins University, 855 N Wolfe Street, Rangos 2–270, Baltimore, MD 21205, USA
- Brain Science Institute, Johns Hopkins University, 855 N Wolfe Street, Rangos 2–270, Baltimore, MD 21205, USA
| | - Elizabeth L. Daley
- Department of Neurology, Johns Hopkins University, 855 N Wolfe Street, Rangos 2–270, Baltimore, MD 21205, USA
- Brain Science Institute, Johns Hopkins University, 855 N Wolfe Street, Rangos 2–270, Baltimore, MD 21205, USA
| | - Erin M. Poth
- Department of Neuroscience, Johns Hopkins University, 855 N Wolfe Street, Rangos 2–270, Baltimore, MD 21205, USA
| | - Benjamin Hoover
- Department of Neurology, Johns Hopkins University, 855 N Wolfe Street, Rangos 2–270, Baltimore, MD 21205, USA
- Brain Science Institute, Johns Hopkins University, 855 N Wolfe Street, Rangos 2–270, Baltimore, MD 21205, USA
| | - Daniel M. Fines
- Department of Neurology, Johns Hopkins University, 855 N Wolfe Street, Rangos 2–270, Baltimore, MD 21205, USA
- Brain Science Institute, Johns Hopkins University, 855 N Wolfe Street, Rangos 2–270, Baltimore, MD 21205, USA
| | - Nicholas Maragakis
- Department of Neurology, Johns Hopkins University, 855 N Wolfe Street, Rangos 2–270, Baltimore, MD 21205, USA
| | - Pentti J. Tienari
- Biomedicum, Research Programs Unit, Molecular Neurology, University of Helsinki; Helsinki University Central Hospital, Department of Neurology, Haartmaninkatu 8, FIN-00290 Helsinki, Finland
| | - Leonard Petrucelli
- Department of Molecular Neuroscience, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL 32224, USA
| | - Bryan J. Traynor
- Department of Neurology, Johns Hopkins University, 855 N Wolfe Street, Rangos 2–270, Baltimore, MD 21205, USA
- Laboratory of Neurogenetics, National Institute on Aging, National Institute of Health, 35 Convent Drive, Room 1A-1000, Bethesda, MD 20892, USA
| | - Jiou Wang
- Department of Neuroscience, Johns Hopkins University, 855 N Wolfe Street, Rangos 2–270, Baltimore, MD 21205, USA
- Department of Biochemistry and Molecular Biology, Johns Hopkins University, 855 N Wolfe Street, Rangos 2–270, Baltimore, MD 21205, USA
| | - Frank Rigo
- Isis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - C. Frank Bennett
- Isis Pharmaceuticals, 2855 Gazelle Court, Carlsbad, CA 92010, USA
| | - Seth Blackshaw
- Department of Neuroscience, Johns Hopkins University, 855 N Wolfe Street, Rangos 2–270, Baltimore, MD 21205, USA
| | - Rita Sattler
- Department of Neurology, Johns Hopkins University, 855 N Wolfe Street, Rangos 2–270, Baltimore, MD 21205, USA
- Brain Science Institute, Johns Hopkins University, 855 N Wolfe Street, Rangos 2–270, Baltimore, MD 21205, USA
| | - Jeffrey D. Rothstein
- Department of Neurology, Johns Hopkins University, 855 N Wolfe Street, Rangos 2–270, Baltimore, MD 21205, USA
- Department of Neuroscience, Johns Hopkins University, 855 N Wolfe Street, Rangos 2–270, Baltimore, MD 21205, USA
- Department of Cellular and Molecular Medicine, Johns Hopkins University, 855 N Wolfe Street, Rangos 2–270, Baltimore, MD 21205, USA
- Brain Science Institute, Johns Hopkins University, 855 N Wolfe Street, Rangos 2–270, Baltimore, MD 21205, USA
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