1
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Mukherjee PK, Nguyen QT, Li J, Zhao S, Christensen SM, West GA, Chandra J, Gordon IO, Lin S, Wang J, Mao R, Czarnecki D, Rayan C, Goren I, Banerjee S, Kotak P, Plesec T, Lal S, Fabre T, Asano S, Bound K, Hart K, Park C, Martinez R, Dower K, Wynn TA, Hu S, Naydenov N, Decaris M, Turner S, Holubar SD, Steele SR, Fiocchi C, Ivanov AI, Kravarik KM, Rieder F. Stricturing Crohn's Disease Single-Cell RNA Sequencing Reveals Fibroblast Heterogeneity and Intercellular Interactions. Gastroenterology 2023; 165:1180-1196. [PMID: 37507073 DOI: 10.1053/j.gastro.2023.07.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/22/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023]
Abstract
BACKGROUND & AIMS Fibroblasts play a key role in stricture formation in Crohn's disease (CD) but understanding its pathogenesis requires a systems-level investigation to uncover new treatment targets. We studied full-thickness CD tissues to characterize fibroblast heterogeneity and function by generating the first single-cell RNA sequencing (scRNAseq) atlas of strictured bowel and providing proof of principle for therapeutic target validation. METHODS We performed scRNAseq of 13 fresh full-thickness CD resections containing noninvolved, inflamed nonstrictured, and strictured segments as well as 7 normal non-CD bowel segments. Each segment was separated into mucosa/submucosa or muscularis propria and analyzed separately for a total of 99 tissue samples and 409,001 cells. We validated cadherin-11 (CDH11) as a potential therapeutic target by using whole tissues, isolated intestinal cells, NanoString nCounter, next-generation sequencing, proteomics, and animal models. RESULTS Our integrated dataset revealed fibroblast heterogeneity in strictured CD with the majority of stricture-selective changes detected in the mucosa/submucosa, but not the muscle layer. Cell-cell interaction modeling revealed CXCL14+ as well as MMP/WNT5A+ fibroblasts displaying a central signaling role in CD strictures. CDH11, a fibroblast cell-cell adhesion molecule, was broadly expressed and up-regulated, and its profibrotic function was validated using NanoString nCounter, RNA sequencing, tissue target expression, in vitro gain- and loss-of-function experiments, proteomics, and knock-out and antibody-mediated CDH11 blockade in experimental colitis. CONCLUSIONS A full-thickness bowel scRNAseq atlas revealed previously unrecognized fibroblast heterogeneity and interactions in CD strictures and CDH11 was validated as a potential therapeutic target. These results provide a new resource for a better understanding of CD stricture formation and open potential therapeutic developments. This work has been posted as a preprint on Biorxiv under doi: 10.1101/2023.04.03.534781.
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Affiliation(s)
- Pranab K Mukherjee
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio; Center for Global Translational Inflammatory Bowel Disease Research, Cleveland Clinic, Cleveland, Ohio
| | - Quang Tam Nguyen
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio; Center for Global Translational Inflammatory Bowel Disease Research, Cleveland Clinic, Cleveland, Ohio
| | - Jiannan Li
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Shuai Zhao
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | | | - Gail A West
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Jyotsna Chandra
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio; Center for Global Translational Inflammatory Bowel Disease Research, Cleveland Clinic, Cleveland, Ohio
| | - Ilyssa O Gordon
- Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic Foundation, Cleveland, Ohio; Center for Global Translational Inflammatory Bowel Disease Research, Cleveland Clinic, Cleveland, Ohio
| | - Sinan Lin
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio; Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jie Wang
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio; Henan Key Laboratory of Immunology and Targeted Drug, Xinxiang Medical University, Xinxiang, Henan Province, China
| | - Ren Mao
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio; Department of Gastroenterology and Hepatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Douglas Czarnecki
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Carla Rayan
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Idan Goren
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Suhanti Banerjee
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Prerna Kotak
- Pliant Therapeutics, South San Francisco, California
| | - Thomas Plesec
- Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic Foundation, Cleveland, Ohio; Center for Global Translational Inflammatory Bowel Disease Research, Cleveland Clinic, Cleveland, Ohio
| | - Samir Lal
- Worldwide Research, Development and Medicine, Pfizer Inc, Cambridge, Massachusetts
| | - Thomas Fabre
- Worldwide Research, Development and Medicine, Pfizer Inc, Cambridge, Massachusetts
| | - Shoh Asano
- Worldwide Research, Development and Medicine, Pfizer Inc, Cambridge, Massachusetts
| | - Kathryn Bound
- Worldwide Research, Development and Medicine, Pfizer Inc, Cambridge, Massachusetts
| | - Kevin Hart
- Worldwide Research, Development and Medicine, Pfizer Inc, Cambridge, Massachusetts
| | - Chanyoung Park
- Worldwide Research, Development and Medicine, Pfizer Inc, Cambridge, Massachusetts; Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Robert Martinez
- Worldwide Research, Development and Medicine, Pfizer Inc, Cambridge, Massachusetts
| | - Ken Dower
- Worldwide Research, Development and Medicine, Pfizer Inc, Cambridge, Massachusetts
| | - Thomas A Wynn
- Worldwide Research, Development and Medicine, Pfizer Inc, Cambridge, Massachusetts
| | - Shaomin Hu
- Department of Pathology, Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic Foundation, Cleveland, Ohio; Center for Global Translational Inflammatory Bowel Disease Research, Cleveland Clinic, Cleveland, Ohio
| | - Nayden Naydenov
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | | | - Scott Turner
- Pliant Therapeutics, South San Francisco, California
| | - Stefan D Holubar
- Department of Colorectal Surgery, Digestive Disease and Surgery Institute, Cleveland Clinic, Cleveland, Ohio; Center for Global Translational Inflammatory Bowel Disease Research, Cleveland Clinic, Cleveland, Ohio
| | - Scott R Steele
- Department of Colorectal Surgery, Digestive Disease and Surgery Institute, Cleveland Clinic, Cleveland, Ohio
| | - Claudio Fiocchi
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio; Department of Gastroenterology, Hepatology and Nutrition, Digestive Disease Institute, Cleveland Clinic, Cleveland, Ohio
| | - Andrei I Ivanov
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio; Center for Global Translational Inflammatory Bowel Disease Research, Cleveland Clinic, Cleveland, Ohio
| | - Kellie M Kravarik
- Worldwide Research, Development and Medicine, Pfizer Inc, Cambridge, Massachusetts
| | - Florian Rieder
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio; Department of Gastroenterology, Hepatology and Nutrition, Digestive Disease Institute, Cleveland Clinic, Cleveland, Ohio; Center for Global Translational Inflammatory Bowel Disease Research, Cleveland Clinic, Cleveland, Ohio.
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Wang J, Casimiro-Garcia A, Johnson BG, Duffen J, Cain M, Savary L, Wang S, Nambiar P, Lech M, Zhao S, Xi L, Zhan Y, Olson J, Stejskal JA, Lin H, Zhang B, Martinez RV, Masek-Hammerman K, Schlerman FJ, Dower K. A protein kinase C α and β inhibitor blunts hyperphagia to halt renal function decline and reduces adiposity in a rat model of obesity-driven type 2 diabetes. Sci Rep 2023; 13:16919. [PMID: 37805649 PMCID: PMC10560236 DOI: 10.1038/s41598-023-43759-7] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 09/28/2023] [Indexed: 10/09/2023] Open
Abstract
Type 2 diabetes (T2D) and its complications can have debilitating, sometimes fatal consequences for afflicted individuals. The disease can be difficult to control, and therapeutic strategies to prevent T2D-induced tissue and organ damage are needed. Here we describe the results of administering a potent and selective inhibitor of Protein Kinase C (PKC) family members PKCα and PKCβ, Cmpd 1, in the ZSF1 obese rat model of hyperphagia-induced, obesity-driven T2D. Although our initial intent was to evaluate the effect of PKCα/β inhibition on renal damage in this model setting, Cmpd 1 unexpectedly caused a marked reduction in the hyperphagic response of ZSF1 obese animals. This halted renal function decline but did so indirectly and indistinguishably from a pair feeding comparator group. However, above and beyond this food intake effect, Cmpd 1 lowered overall animal body weights, reduced liver vacuolation, and reduced inguinal adipose tissue (iWAT) mass, inflammation, and adipocyte size. Taken together, Cmpd 1 had strong effects on multiple disease parameters in this obesity-driven rodent model of T2D. Further evaluation for potential translation of PKCα/β inhibition to T2D and obesity in humans is warranted.
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Affiliation(s)
- Ju Wang
- Inflammation and Immunology, Pfizer Worldwide Research and Development, Cambridge, MA, USA.
| | | | - Bryce G Johnson
- Inflammation and Immunology, Pfizer Worldwide Research and Development, Cambridge, MA, USA
| | - Jennifer Duffen
- Inflammation and Immunology, Pfizer Worldwide Research and Development, Cambridge, MA, USA
| | - Michael Cain
- Inflammation and Immunology, Pfizer Worldwide Research and Development, Cambridge, MA, USA
- Mediar Therapeutics, Boston, MA, USA
| | - Leigh Savary
- Inflammation and Immunology, Pfizer Worldwide Research and Development, Cambridge, MA, USA
- Instem Life Science Systems Ltd, Mount Ida College, South Hadley, MA, USA
| | - Stephen Wang
- Pharmacokinetics and Drug Metabolism, Pfizer Worldwide Research and Development, Cambridge, MA, USA
- Novartis Gene Therapies, Novartis Institute for Biomedical Research, Cambridge, MA, USA
| | - Prashant Nambiar
- Drug Safety Research and Development, Pfizer Worldwide Research and Development, Cambridge, MA, USA
- Strand Therapeutics, Cambridge, MA, USA
| | - Matthew Lech
- Inflammation and Immunology, Pfizer Worldwide Research and Development, Cambridge, MA, USA
| | - Shanrong Zhao
- Clinical Genetics and Bioinformatics, Pfizer Worldwide Research and Development, Cambridge, MA, USA
- Amunix Pharmaceuticals, San Francisco, CA, USA
| | - Li Xi
- Early Clinical Development, Pfizer Worldwide Research and Development, Cambridge, MA, USA
| | - Yutian Zhan
- Drug Safety Research and Development, Pfizer Worldwide Research and Development, Cambridge, MA, USA
| | - Jennifer Olson
- Drug Safety Research and Development, Pfizer Worldwide Research and Development, Groton, CT, USA
| | - James A Stejskal
- Drug Safety Research and Development, Pfizer Worldwide Research and Development, Groton, CT, USA
- Charles River Laboratories, Shrewsbury, MA, USA
| | - Hank Lin
- Drug Safety Research and Development, Pfizer Worldwide Research and Development, Cambridge, MA, USA
- Sunovion Pharmaceuticals Inc., Marlborough, MA, USA
| | - Baohong Zhang
- Clinical Genetics and Bioinformatics, Pfizer Worldwide Research and Development, Cambridge, MA, USA
- Data Sciences, Biogen, Cambridge, MA, USA
| | - Robert V Martinez
- Inflammation and Immunology, Pfizer Worldwide Research and Development, Cambridge, MA, USA
- Center for Technological Innovation, Pfizer Worldwide Research and Development, San Francisco, CA, USA
| | | | - Franklin J Schlerman
- Inflammation and Immunology, Pfizer Worldwide Research and Development, Cambridge, MA, USA
| | - Ken Dower
- Inflammation and Immunology, Pfizer Worldwide Research and Development, Cambridge, MA, USA.
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Fabre T, Barron AMS, Christensen SM, Asano S, Bound K, Lech MP, Wadsworth MH, Chen X, Wang C, Wang J, McMahon J, Schlerman F, White A, Kravarik KM, Fisher AJ, Borthwick LA, Hart KM, Henderson NC, Wynn TA, Dower K. Identification of a broadly fibrogenic macrophage subset induced by type 3 inflammation. Sci Immunol 2023; 8:eadd8945. [PMID: 37027478 DOI: 10.1126/sciimmunol.add8945] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
Abstract
Macrophages are central orchestrators of the tissue response to injury, with distinct macrophage activation states playing key roles in fibrosis progression and resolution. Identifying key macrophage populations found in human fibrotic tissues could lead to new treatments for fibrosis. Here, we used human liver and lung single-cell RNA sequencing datasets to identify a subset of CD9+TREM2+ macrophages that express SPP1, GPNMB, FABP5, and CD63. In both human and murine hepatic and pulmonary fibrosis, these macrophages were enriched at the outside edges of scarring and adjacent to activated mesenchymal cells. Neutrophils expressing MMP9, which participates in the activation of TGF-β1, and the type 3 cytokines GM-CSF and IL-17A coclustered with these macrophages. In vitro, GM-CSF, IL-17A, and TGF-β1 drive the differentiation of human monocytes into macrophages expressing scar-associated markers. Such differentiated cells could degrade collagen IV but not collagen I and promote TGF-β1-induced collagen I deposition by activated mesenchymal cells. In murine models blocking GM-CSF, IL-17A or TGF-β1 reduced scar-associated macrophage expansion and hepatic or pulmonary fibrosis. Our work identifies a highly specific macrophage population to which we assign a profibrotic role across species and tissues. It further provides a strategy for unbiased discovery, triage, and preclinical validation of therapeutic targets based on this fibrogenic macrophage population.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Ju Wang
- Pfizer Inc., Cambridge, MA, USA
| | | | | | | | | | - Andrew J Fisher
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Lee A Borthwick
- Newcastle Fibrosis Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Neil C Henderson
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Centre for Inflammation Research, the Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
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4
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Mukherjee PK, Nguyen QT, Li J, Zhao S, Christensen SM, West GA, Chandra J, Gordon IO, Lin S, Wang J, Mao R, Czarnecki D, Rayan C, Kotak P, Plesec T, Lal S, Fabre T, Asano S, Bound K, Hart K, Park C, Martinez R, Dower K, Wynn TA, Hu S, Naydenov N, Decaris M, Turner S, Holubar SD, Steele SR, Fiocchi C, Ivanov AI, Kravarik KM, Rieder F. Stricturing Crohn's disease single-cell RNA sequencing reveals fibroblast heterogeneity and intercellular interactions. bioRxiv 2023:2023.04.03.534781. [PMID: 37066202 PMCID: PMC10103967 DOI: 10.1101/2023.04.03.534781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Background Fibroblasts play a key role in stricture formation in Crohn's disease (CD) but understanding it's pathogenesis requires a systems-level investigation to uncover new treatment targets. We studied full thickness CD tissues to characterize fibroblast heterogeneity and function by generating the first single cell RNA sequencing (scRNAseq) atlas of strictured bowel and providing proof of principle for therapeutic target validation. Methods We performed scRNAseq of 13 fresh full thickness CD resections containing non-involved, inflamed non-strictured, and strictured segments as well as 7 normal non-CD bowel segments. Each segment was separated into mucosa/submucosa or muscularis propria and analyzed separately for a total of 99 tissue samples and 409,001 cells. We validated cadherin-11 (CDH11) as a potential therapeutic target by using whole tissues, isolated intestinal cells, NanoString nCounter, next generation sequencing, proteomics and animal models. Results Our integrated dataset revealed fibroblast heterogeneity in strictured CD with the majority of stricture-selective changes detected in the mucosa/submucosa, but not the muscle layer. Cell-cell interaction modeling revealed CXCL14+ as well as MMP/WNT5A+ fibroblasts displaying a central signaling role in CD strictures. CDH11, a fibroblast cell-cell adhesion molecule, was broadly expressed and upregulated, and its pro-fibrotic function was validated by NanoString nCounter, RNA sequencing, tissue target expression, in vitro gain- and loss-of-function experiments, proteomics, and two animal models of experimental colitis. Conclusion A full-thickness bowel scRNAseq atlas revealed previously unrecognized fibroblast heterogeneity and interactions in CD strictures and CDH11 was validated as a potential therapeutic target. These results provide a new resource for a better understanding of CD stricture formation and opens potential therapeutic developments.
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5
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Winkler A, Sun W, De S, Jiao A, Sharif MN, Symanowicz PT, Athale S, Shin JH, Wang J, Jacobson BA, Ramsey SJ, Dower K, Andreyeva T, Liu H, Hegen M, Homer BL, Brodfuehrer J, Tilley M, Gilbert SA, Danto SI, Beebe JJ, Barnes BJ, Pascual V, Lin LL, Kilty I, Fleming M, Rao VR. The Interleukin-1 Receptor-Associated Kinase 4 Inhibitor PF-06650833 Blocks Inflammation in Preclinical Models of Rheumatic Disease and in Humans Enrolled in a Randomized Clinical Trial. Arthritis Rheumatol 2021; 73:2206-2218. [PMID: 34423919 PMCID: PMC8671219 DOI: 10.1002/art.41953] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 08/17/2021] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To investigate the role of PF-06650833, a highly potent and selective small-molecule inhibitor of interleukin-1-associated kinase 4 (IRAK4), in autoimmune pathophysiology in vitro, in vivo, and in the clinical setting. METHODS Rheumatoid arthritis (RA) inflammatory pathophysiology was modeled in vitro through 1) stimulation of primary human macrophages with anti-citrullinated protein antibody immune complexes (ICs), 2) RA fibroblast-like synoviocyte (FLS) cultures stimulated with Toll-like receptor (TLR) ligands, as well as 3) additional human primary cell cocultures exposed to inflammatory stimuli. Systemic lupus erythematosus (SLE) pathophysiology was simulated in human neutrophils, dendritic cells, B cells, and peripheral blood mononuclear cells stimulated with TLR ligands and SLE patient ICs. PF-06650833 was evaluated in vivo in the rat collagen-induced arthritis (CIA) model and the mouse pristane-induced and MRL/lpr models of lupus. Finally, RNA sequencing data generated with whole blood samples from a phase I multiple-ascending-dose clinical trial of PF-06650833 were used to test in vivo human pharmacology. RESULTS In vitro, PF-06650833 inhibited human primary cell inflammatory responses to physiologically relevant stimuli generated with RA and SLE patient plasma. In vivo, PF-06650833 reduced circulating autoantibody levels in the pristane-induced and MRL/lpr murine models of lupus and protected against CIA in rats. In a phase I clinical trial (NCT02485769), PF-06650833 demonstrated in vivo pharmacologic action pertinent to SLE by reducing whole blood interferon gene signature expression in healthy volunteers. CONCLUSION These data demonstrate that inhibition of IRAK4 kinase activity can reduce levels of inflammation markers in humans and provide confidence in the rationale for clinical development of IRAK4 inhibitors for rheumatologic indications.
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Affiliation(s)
| | | | - Saurav De
- The Feinstein Institute, Manhasset, New York
| | | | | | | | - Shruti Athale
- Baylor Institute for Immunology Research, Dallas, Texas
| | | | - Ju Wang
- Pfizer, Cambridge, Massachusetts
| | | | | | | | | | - Heng Liu
- Pfizer, Cambridge, Massachusetts
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6
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Abstract
This symposium synopsis summarizes key results from a 41-week study of diabetic nephropathy (DN) in the type 2 diabetic ZSF1 fa/faCP rat model. During this study, we conducted longitudinal analysis of biomarkers, renal histopathology, ultrastructural assessment, renal quantitative image analysis, and transcriptome analysis of glomerular-enriched tissue. We concluded that there is translational value for using the ZSF1 rat model in mechanistic and therapeutic intervention efficacy studies for type 2 DN.
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Affiliation(s)
- Bruce L. Homer
- Drug Safety, Pfizer Worldwide Research and Development, Cambridge, Massachusetts, USA
| | - Ken Dower
- Inflammation and Immunology, Pfizer Worldwide Research and Development, Cambridge, Massachusetts, USA
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7
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Zhang C, Dower K, Zhang B, Martinez RV, Lin LL, Zhao S. Computational identification and validation of alternative splicing in ZSF1 rat RNA-seq data, a preclinical model for type 2 diabetic nephropathy. Sci Rep 2018; 8:7624. [PMID: 29769602 PMCID: PMC5955895 DOI: 10.1038/s41598-018-26035-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 04/26/2018] [Indexed: 12/11/2022] Open
Abstract
Obese ZSF1 rats exhibit spontaneous time-dependent diabetic nephropathy and are considered to be a highly relevant animal model of progressive human diabetic kidney disease. We previously identified gene expression changes between disease and control animals across six time points from 12 to 41 weeks. In this study, the same data were analysed at the isoform and exon levels to reveal additional disease mechanisms that may be governed by alternative splicing. Our analyses identified alternative splicing patterns in genes that may be implicated in disease pathogenesis (such as Shc1, Serpinc1, Epb4.1l5, and Il-33), which would have been overlooked in standard gene-level analysis. The alternatively spliced genes were enriched in pathways related to cell adhesion, cell–cell interactions/junctions, and cytoskeleton signalling, whereas the differentially expressed genes were enriched in pathways related to immune response, G protein-coupled receptor, and cAMP signalling. Our findings indicate that additional mechanistic insights can be gained from exon- and isoform-level data analyses over standard gene-level analysis. Considering alternative splicing is poorly conserved between rodents and humans, it is noted that this work is not translational, but the point holds true that additional insights can be gained from alternative splicing analysis of RNA-seq data.
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Affiliation(s)
- Chi Zhang
- Precision Medicine, Early Clinical Development, Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA
| | - Ken Dower
- Inflammation & Immunology Research Unit, Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA
| | - Baohong Zhang
- Precision Medicine, Early Clinical Development, Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA
| | - Robert V Martinez
- Inflammation & Immunology Research Unit, Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA
| | - Lih-Ling Lin
- Inflammation & Immunology Research Unit, Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA
| | - Shanrong Zhao
- Precision Medicine, Early Clinical Development, Pfizer Worldwide Research and Development, Cambridge, MA, 02139, USA.
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Hall J, Brault A, Vincent F, Weng S, Wang H, Dumlao D, Aulabaugh A, Aivazian D, Castro D, Chen M, Culp J, Dower K, Gardner J, Hawrylik S, Golenbock D, Hepworth D, Horn M, Jones L, Jones P, Latz E, Li J, Lin LL, Lin W, Lin D, Lovering F, Niljanskul N, Nistler R, Pierce B, Plotnikova O, Schmitt D, Shanker S, Smith J, Snyder W, Subashi T, Trujillo J, Tyminski E, Wang G, Wong J, Lefker B, Dakin L, Leach K. Discovery of PF-06928215 as a high affinity inhibitor of cGAS enabled by a novel fluorescence polarization assay. PLoS One 2017; 12:e0184843. [PMID: 28934246 PMCID: PMC5608272 DOI: 10.1371/journal.pone.0184843] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/31/2017] [Indexed: 12/30/2022] Open
Abstract
Cyclic GMP-AMP synthase (cGAS) initiates the innate immune system in response to cytosolic dsDNA. After binding and activation from dsDNA, cGAS uses ATP and GTP to synthesize 2', 3' -cGAMP (cGAMP), a cyclic dinucleotide second messenger with mixed 2'-5' and 3'-5' phosphodiester bonds. Inappropriate stimulation of cGAS has been implicated in autoimmune disease such as systemic lupus erythematosus, thus inhibition of cGAS may be of therapeutic benefit in some diseases; however, the size and polarity of the cGAS active site makes it a challenging target for the development of conventional substrate-competitive inhibitors. We report here the development of a high affinity (KD = 200 nM) inhibitor from a low affinity fragment hit with supporting biochemical and structural data showing these molecules bind to the cGAS active site. We also report a new high throughput cGAS fluorescence polarization (FP)-based assay to enable the rapid identification and optimization of cGAS inhibitors. This FP assay uses Cy5-labelled cGAMP in combination with a novel high affinity monoclonal antibody that specifically recognizes cGAMP with no cross reactivity to cAMP, cGMP, ATP, or GTP. Given its role in the innate immune response, cGAS is a promising therapeutic target for autoinflammatory disease. Our results demonstrate its druggability, provide a high affinity tool compound, and establish a high throughput assay for the identification of next generation cGAS inhibitors.
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Affiliation(s)
- Justin Hall
- Medicine Design, Pfizer, Groton, Connecticut, United States of America
| | - Amy Brault
- Medicine Design, Pfizer, Groton, Connecticut, United States of America
| | - Fabien Vincent
- Medicine Design, Pfizer, Groton, Connecticut, United States of America
| | - Shawn Weng
- Pfizer Centers for Therapeutic Innovation (CTI), Boston, Massachusetts, United States of America
| | - Hong Wang
- Medicine Design, Pfizer, Groton, Connecticut, United States of America
| | - Darren Dumlao
- Medicine Design, Pfizer, Groton, Connecticut, United States of America
| | - Ann Aulabaugh
- Medicine Design, Pfizer, Groton, Connecticut, United States of America
| | - Dikran Aivazian
- Pfizer Centers for Therapeutic Innovation (CTI), San Diego, California, United States of America
| | - Dana Castro
- Pfizer Centers for Therapeutic Innovation (CTI), San Diego, California, United States of America
| | - Ming Chen
- Medicine Design, Pfizer, Groton, Connecticut, United States of America
| | - Jeffrey Culp
- Medicine Design, Pfizer, Groton, Connecticut, United States of America
| | - Ken Dower
- Inflammation and Immunology, Pfizer, Cambridge, Massachusetts, United States of America
| | - Joseph Gardner
- External Research Solutions, Pfizer, Groton, Connecticut, United States of America
| | - Steven Hawrylik
- Medicine Design, Pfizer, Groton, Connecticut, United States of America
| | - Douglas Golenbock
- University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - David Hepworth
- Medicine Design, Pfizer, Cambridge, Massachusetts, United States of America
| | - Mark Horn
- Pfizer Centers for Therapeutic Innovation (CTI), San Diego, California, United States of America
| | - Lyn Jones
- Medicine Design, Pfizer, Cambridge, Massachusetts, United States of America
| | - Peter Jones
- Medicine Design, Pfizer, Cambridge, Massachusetts, United States of America
| | - Eicke Latz
- University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Institute of Innate Immunity, University Hospitals Bonn, Bonn, Germany
| | - Jing Li
- Medicine Design, Pfizer, Cambridge, Massachusetts, United States of America
| | - Lih-Ling Lin
- Inflammation and Immunology, Pfizer, Cambridge, Massachusetts, United States of America
| | - Wen Lin
- Medicine Design, Pfizer, Groton, Connecticut, United States of America
| | - David Lin
- Medicine Design, Pfizer, Groton, Connecticut, United States of America
| | - Frank Lovering
- Medicine Design, Pfizer, Cambridge, Massachusetts, United States of America
| | | | - Ryan Nistler
- Pfizer Centers for Therapeutic Innovation (CTI), Boston, Massachusetts, United States of America
| | - Betsy Pierce
- Medicine Design, Pfizer, Groton, Connecticut, United States of America
| | - Olga Plotnikova
- Medicine Design, Pfizer, Groton, Connecticut, United States of America
| | - Daniel Schmitt
- Medicine Design, Pfizer, Groton, Connecticut, United States of America
| | - Suman Shanker
- Medicine Design, Pfizer, Groton, Connecticut, United States of America
| | - James Smith
- Medicine Design, Pfizer, Groton, Connecticut, United States of America
| | - William Snyder
- Pfizer Centers for Therapeutic Innovation (CTI), San Diego, California, United States of America
| | - Timothy Subashi
- Medicine Design, Pfizer, Groton, Connecticut, United States of America
| | - John Trujillo
- Medicine Design, Pfizer, Groton, Connecticut, United States of America
| | - Edyta Tyminski
- Pfizer Centers for Therapeutic Innovation (CTI), Boston, Massachusetts, United States of America
| | - Guoxing Wang
- Pfizer Centers for Therapeutic Innovation (CTI), Boston, Massachusetts, United States of America
| | - Jimson Wong
- Medicine Design, Pfizer, Groton, Connecticut, United States of America
| | - Bruce Lefker
- Medicine Design, Pfizer, Cambridge, Massachusetts, United States of America
| | - Leslie Dakin
- Medicine Design, Pfizer, Cambridge, Massachusetts, United States of America
| | - Karen Leach
- Pfizer Centers for Therapeutic Innovation (CTI), Boston, Massachusetts, United States of America
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9
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Dower K, Zhao S, Schlerman FJ, Savary L, Campanholle G, Johnson BG, Xi L, Nguyen V, Zhan Y, Lech MP, Wang J, Nie Q, Karsdal MA, Genovese F, Boucher G, Brown TP, Zhang B, Homer BL, Martinez RV. High resolution molecular and histological analysis of renal disease progression in ZSF1 fa/faCP rats, a model of type 2 diabetic nephropathy. PLoS One 2017; 12:e0181861. [PMID: 28746409 PMCID: PMC5529026 DOI: 10.1371/journal.pone.0181861] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 07/07/2017] [Indexed: 02/07/2023] Open
Abstract
ZSF1 rats exhibit spontaneous nephropathy secondary to obesity, hypertension, and diabetes, and have gained interest as a model system with potentially high translational value to progressive human disease. To thoroughly characterize this model, and to better understand how closely it recapitulates human disease, we performed a high resolution longitudinal analysis of renal disease progression in ZSF1 rats spanning from early disease to end stage renal disease. Analyses included metabolic endpoints, renal histology and ultrastructure, evaluation of a urinary biomarker of fibrosis, and transcriptome analysis of glomerular-enriched tissue over the course of disease. Our findings support the translational value of the ZSF1 rat model, and are provided here to assist researchers in the determination of the model’s suitability for testing a particular mechanism of interest, the design of therapeutic intervention studies, and the identification of new targets and biomarkers for type 2 diabetic nephropathy.
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Affiliation(s)
- Ken Dower
- Inflammation and Immunology, Pfizer Worldwide Research and Development, Cambridge, Massachusetts, United States of America
- * E-mail: (KD); (RVM)
| | - Shanrong Zhao
- Clinical Bioinformatics, Early Clinical Development, Pfizer Worldwide Research and Development, Cambridge, Massachusetts, United States of America
| | - Franklin J. Schlerman
- Inflammation and Immunology, Pfizer Worldwide Research and Development, Cambridge, Massachusetts, United States of America
| | - Leigh Savary
- Drug Safety, Pfizer Worldwide Research and Development, Andover, Massachusetts, United States of America
| | - Gabriela Campanholle
- Inflammation and Immunology, Pfizer Worldwide Research and Development, Cambridge, Massachusetts, United States of America
| | - Bryce G. Johnson
- Inflammation and Immunology, Pfizer Worldwide Research and Development, Cambridge, Massachusetts, United States of America
| | - Li Xi
- Clinical Bioinformatics, Early Clinical Development, Pfizer Worldwide Research and Development, Cambridge, Massachusetts, United States of America
| | - Vuong Nguyen
- Drug Safety, Pfizer Worldwide Research and Development, Andover, Massachusetts, United States of America
| | - Yutian Zhan
- Drug Safety, Pfizer Worldwide Research and Development, Andover, Massachusetts, United States of America
| | - Matthew P. Lech
- Inflammation and Immunology, Pfizer Worldwide Research and Development, Cambridge, Massachusetts, United States of America
| | - Ju Wang
- Inflammation and Immunology, Pfizer Worldwide Research and Development, Cambridge, Massachusetts, United States of America
| | - Qing Nie
- Drug Safety, Pfizer Worldwide Research and Development, Andover, Massachusetts, United States of America
| | | | | | - Germaine Boucher
- Drug Safety, Pfizer Worldwide Research and Development, Groton, Connecticut, United States of America
| | - Thomas P. Brown
- Drug Safety, Pfizer Worldwide Research and Development, Groton, Connecticut, United States of America
| | - Baohong Zhang
- Clinical Bioinformatics, Early Clinical Development, Pfizer Worldwide Research and Development, Cambridge, Massachusetts, United States of America
| | - Bruce L. Homer
- Drug Safety, Pfizer Worldwide Research and Development, Andover, Massachusetts, United States of America
| | - Robert V. Martinez
- Inflammation and Immunology, Pfizer Worldwide Research and Development, Cambridge, Massachusetts, United States of America
- * E-mail: (KD); (RVM)
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10
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Lee KL, Ambler CM, Anderson DR, Boscoe BP, Bree AG, Brodfuehrer JI, Chang JS, Choi C, Chung S, Curran KJ, Day JE, Dehnhardt CM, Dower K, Drozda SE, Frisbie RK, Gavrin LK, Goldberg JA, Han S, Hegen M, Hepworth D, Hope HR, Kamtekar S, Kilty IC, Lee A, Lin LL, Lovering FE, Lowe MD, Mathias JP, Morgan HM, Murphy EA, Papaioannou N, Patny A, Pierce BS, Rao VR, Saiah E, Samardjiev IJ, Samas BM, Shen MWH, Shin JH, Soutter HH, Strohbach JW, Symanowicz PT, Thomason JR, Trzupek JD, Vargas R, Vincent F, Yan J, Zapf CW, Wright SW. Discovery of Clinical Candidate 1-{[(2S,3S,4S)-3-Ethyl-4-fluoro-5-oxopyrrolidin-2-yl]methoxy}-7-methoxyisoquinoline-6-carboxamide (PF-06650833), a Potent, Selective Inhibitor of Interleukin-1 Receptor Associated Kinase 4 (IRAK4), by Fragment-Based Drug Design. J Med Chem 2017; 60:5521-5542. [PMID: 28498658 DOI: 10.1021/acs.jmedchem.7b00231] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Through fragment-based drug design focused on engaging the active site of IRAK4 and leveraging three-dimensional topology in a ligand-efficient manner, a micromolar hit identified from a screen of a Pfizer fragment library was optimized to afford IRAK4 inhibitors with nanomolar potency in cellular assays. The medicinal chemistry effort featured the judicious placement of lipophilicity, informed by co-crystal structures with IRAK4 and optimization of ADME properties to deliver clinical candidate PF-06650833 (compound 40). This compound displays a 5-unit increase in lipophilic efficiency from the fragment hit, excellent kinase selectivity, and pharmacokinetic properties suitable for oral administration.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Heidi M Morgan
- Worldwide Medicinal Chemistry, Pfizer Inc. , 1070 Science Center Drive, San Diego, California 92121, United States
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jiangli Yan
- Worldwide Medicinal Chemistry, Pfizer Inc. , 1070 Science Center Drive, San Diego, California 92121, United States
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11
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Primiano MJ, Lefker BA, Bowman MR, Bree AG, Hubeau C, Bonin PD, Mangan M, Dower K, Monks BG, Cushing L, Wang S, Guzova J, Jiao A, Lin LL, Latz E, Hepworth D, Hall JP. Efficacy and Pharmacology of the NLRP3 Inflammasome Inhibitor CP-456,773 (CRID3) in Murine Models of Dermal and Pulmonary Inflammation. J I 2016; 197:2421-33. [DOI: 10.4049/jimmunol.1600035] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 07/12/2016] [Indexed: 01/12/2023]
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12
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Filone CM, Dower K, Cowley GS, Hensley LE, Connor JH. Probing the virus host interaction in high containment: an approach using pooled short hairpin RNA. Assay Drug Dev Technol 2015; 13:34-43. [PMID: 25646658 DOI: 10.1089/adt.2014.613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The study of viruses in high containment offers unique challenges for technology-intense approaches. These approaches include high-throughput screening for small-molecule antivirals and genetic perturbation-based screens for host factors required for viral replication. Here, we describe the use of whole-genome scale pooled short hairpin RNA (shRNA) libraries to screen for host factors necessary for viral infection at BSL2, and the transition of this technique into the BSL4 environment. Pooled screening provides a unique way to circumvent many of the technological challenges associated with other high-throughput screening approaches in high containment. Our pooled screening approach identified host factors involved in the replication of orthopoxviruses (Vaccinia and Monkeypox) and filoviruses (Ebola and Marburg) under conditions that enable straightforward screen-to-follow-up approaches.
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Affiliation(s)
- Claire Marie Filone
- 1 National Emerging Infectious Diseases Laboratory, Boston University School of Medicine , Boston, Massachusetts
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13
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Abstract
Poxviruses are a family of double stranded DNA viruses that include active human pathogens such as monkeypox, molluscum contagiousum, and Contagalo virus. The family also includes the smallpox virus, Variola. Due to the complexity of poxvirus replication, many questions still remain regarding their gene expression strategy. In this article we describe the conceptualization and usage of recombinant vaccinia viruses that enable real-time measurement of single and multiple stages of viral gene expression in a high-throughput format. This is enabled through the use of spectrally distinct fluorescent proteins as reporters for each of three stages of viral replication. These viruses provide a high signal-to-noise ratio while retaining stage specific expression patterns, enabling plate-based assays and microscopic observations of virus propagation and replication. These tools have uses for antiviral discovery, studies of the virus-host interaction, and evolutionary biology.
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Affiliation(s)
- Daniel K Rozelle
- Department of Microbiology, Boston University School of Medicine
| | | | - Ken Dower
- Department of Microbiology, Boston University School of Medicine
| | - John H Connor
- Department of Microbiology, Boston University School of Medicine;
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14
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Cushing L, Stochaj W, Siegel M, Czerwinski R, Dower K, Wright Q, Hirschfield M, Casanova JL, Picard C, Puel A, Lin LL, Rao VR. Interleukin 1/Toll-like receptor-induced autophosphorylation activates interleukin 1 receptor-associated kinase 4 and controls cytokine induction in a cell type-specific manner. J Biol Chem 2014; 289:10865-10875. [PMID: 24567333 DOI: 10.1074/jbc.m113.544809] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
IRAK4 is a central kinase in innate immunity, but the role of its kinase activity is controversial. The mechanism of activation for IRAK4 is currently unknown, and little is known about the role of IRAK4 kinase in cytokine production, particularly in different human cell types. We show IRAK4 autophosphorylation occurs by an intermolecular reaction and that autophosphorylation is required for full catalytic activity of the kinase. Phosphorylation of any two of the residues Thr-342, Thr-345, and Ser-346 is required for full activity, and the death domain regulates the activation of IRAK4. Using antibodies against activated IRAK4, we demonstrate that IRAK4 becomes phosphorylated in human cells following stimulation by IL-1R and Toll-like receptor agonists, which can be blocked pharmacologically by a dual inhibitor of IRAK4 and IRAK1. Interestingly, in dermal fibroblasts, although complete inhibition of IRAK4 kinase activity does not inhibit IL-1-induced IL-6 production, NF-κB, or MAPK activation, there is complete ablation of these processes in IRAK4-deficient cells. In contrast, the inhibition of IRAK kinase activity in primary human monocytes reduces R848-induced IL-6 production with minimal effect on NF-κB or MAPK activation. Taken together, these studies define the mechanism of IRAK4 activation and highlight the differential role of IRAK4 kinase activity in different human cell types as well as the distinct roles IRAK4 scaffolding and kinase functions play.
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Affiliation(s)
- Leah Cushing
- Inflammation and Remodeling Research Unit, Pfizer Research, Cambridge, Massachusetts 02140
| | - Wayne Stochaj
- Global Biological Technology, Pfizer Research, Cambridge, Massachusetts 02140
| | - Marshall Siegel
- Pfizer Chemical Technologies Section, Pearl River, New York 10965
| | - Robert Czerwinski
- Inflammation and Remodeling Research Unit, Pfizer Research, Cambridge, Massachusetts 02140
| | - Ken Dower
- Inflammation and Remodeling Research Unit, Pfizer Research, Cambridge, Massachusetts 02140
| | - Quentin Wright
- Inflammation and Remodeling Research Unit, Pfizer Research, Cambridge, Massachusetts 02140
| | - Margaret Hirschfield
- Inflammation and Remodeling Research Unit, Pfizer Research, Cambridge, Massachusetts 02140
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases Howard Hughes Medical Institute, Rockefeller University, New York, New York 10065; Howard Hughes Medical Institute, Rockefeller University, New York, New York 10065; Pediatric Hematology-Immunology Unit, Assistance Publique Hôpitaux de Paris, Necker Hospital, Paris 75015, France; Laboratory of Human Genetics of Infectious Diseases, Imagine Institute, Assistance Publique Hôpitaux de Paris, Necker Hospital, Paris 75015, France; University of Paris at Descartes, Paris 75006, France
| | - Capucine Picard
- Laboratory of Human Genetics of Infectious Diseases, Imagine Institute, Assistance Publique Hôpitaux de Paris, Necker Hospital, Paris 75015, France; Study Center for Primary Immunodeficiencies, Assistance Publique Hôpitaux de Paris, Necker Hospital, Paris 75015, France; University of Paris at Descartes, Paris 75006, France
| | - Anne Puel
- St. Giles Laboratory of Human Genetics of Infectious Diseases Howard Hughes Medical Institute, Rockefeller University, New York, New York 10065; Laboratory of Human Genetics of Infectious Diseases, Imagine Institute, Assistance Publique Hôpitaux de Paris, Necker Hospital, Paris 75015, France; University of Paris at Descartes, Paris 75006, France
| | - Lih-Ling Lin
- Inflammation and Remodeling Research Unit, Pfizer Research, Cambridge, Massachusetts 02140.
| | - Vikram R Rao
- Inflammation and Remodeling Research Unit, Pfizer Research, Cambridge, Massachusetts 02140.
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15
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Filone CM, Caballero IS, Dower K, Mendillo ML, Cowley GS, Santagata S, Rozelle DK, Yen J, Rubins KH, Hacohen N, Root DE, Hensley LE, Connor J. The master regulator of the cellular stress response (HSF1) is critical for orthopoxvirus infection. PLoS Pathog 2014; 10:e1003904. [PMID: 24516381 PMCID: PMC3916389 DOI: 10.1371/journal.ppat.1003904] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [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: 06/14/2013] [Accepted: 12/12/2013] [Indexed: 12/17/2022] Open
Abstract
The genus Orthopoxviridae contains a diverse group of human pathogens including monkeypox, smallpox and vaccinia. These viruses are presumed to be less dependent on host functions than other DNA viruses because they have large genomes and replicate in the cytoplasm, but a detailed understanding of the host factors required by orthopoxviruses is lacking. To address this topic, we performed an unbiased, genome-wide pooled RNAi screen targeting over 17,000 human genes to identify the host factors that support orthopoxvirus infection. We used secondary and tertiary assays to validate our screen results. One of the strongest hits was heat shock factor 1 (HSF1), the ancient master regulator of the cytoprotective heat-shock response. In investigating the behavior of HSF1 during vaccinia infection, we found that HSF1 was phosphorylated, translocated to the nucleus, and increased transcription of HSF1 target genes. Activation of HSF1 was supportive for virus replication, as RNAi knockdown and HSF1 small molecule inhibition prevented orthopoxvirus infection. Consistent with its role as a transcriptional activator, inhibition of several HSF1 targets also blocked vaccinia virus replication. These data show that orthopoxviruses co-opt host transcriptional responses for their own benefit, thereby effectively extending their functional genome to include genes residing within the host DNA. The dependence on HSF1 and its chaperone network offers multiple opportunities for antiviral drug development.
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Affiliation(s)
- Claire Marie Filone
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
- United States Army Medical Research Institute of Infectious Diseases, Virology Division, Fort Detrick, Maryland, United States of America
- * E-mail:
| | - Ignacio S. Caballero
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Ken Dower
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Marc L. Mendillo
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Glenn S. Cowley
- The Broad Institute, Cambridge Massachusetts, United States of America
| | - Sandro Santagata
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Daniel K. Rozelle
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Judy Yen
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Kathleen H. Rubins
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Nir Hacohen
- The Broad Institute, Cambridge Massachusetts, United States of America
| | - David E. Root
- The Broad Institute, Cambridge Massachusetts, United States of America
| | - Lisa E. Hensley
- United States Army Medical Research Institute of Infectious Diseases, Virology Division, Fort Detrick, Maryland, United States of America
| | - John Connor
- Department of Microbiology, Boston University School of Medicine, Boston, Massachusetts, United States of America
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16
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Luong M, Zhang Y, Chamberlain T, Zhou T, Wright JF, Dower K, Hall JP. Stimulation of TLR4 by recombinant HSP70 requires structural integrity of the HSP70 protein itself. J Inflamm (Lond) 2012; 9:11. [PMID: 22448747 PMCID: PMC3355006 DOI: 10.1186/1476-9255-9-11] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Accepted: 03/26/2012] [Indexed: 12/24/2022]
Abstract
BACKGROUND Toll-like receptor 4 (TLR4) is activated by bacterial endotoxin, a prototypical pathogen-associated molecular pattern (PAMP). It has been suggested that TLR4 can also be activated by damage-associated molecular pattern (DAMP) proteins such as HSP70. It remains a challenge to provide unequivocal evidence that DAMP proteins themselves play a role in TLR4 activation, as the DAMP proteins used are often contaminated with endotoxin and other TLR ligands introduced during protein expression and/or purification. RESULTS Here we report that the activation of TLR4 on primary human macrophage cultures by recombinant HSP70 is not solely due to contaminating endotoxin. Polymyxin B pretreatment of HSP70 preparations to neutralize contaminating endotoxin caused significant reductions in the amount of TNF-α induced by the recombinant protein as determined by ELISA. However, digestion of HSP70 with Proteinase K-agarose beads also dramatically reduced the TNF-α response of macrophages to HSP70, while leaving levels of contaminating endotoxin largely unchanged relative to controls. CONCLUSIONS These results indicate that the stimulatory effect of recombinant HSP70 requires both the presence of endotoxin and structural integrity of the heat shock protein itself.
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Affiliation(s)
- Michael Luong
- Inflammation and Remodeling Research Unit, Pfizer, Cambridge, Massachusetts, USA.
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17
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Dower K, Rubins KH, Hensley LE, Connor JH. Development of Vaccinia reporter viruses for rapid, high content analysis of viral function at all stages of gene expression. Antiviral Res 2011; 91:72-80. [PMID: 21569797 PMCID: PMC3177160 DOI: 10.1016/j.antiviral.2011.04.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 04/20/2011] [Accepted: 04/27/2011] [Indexed: 01/25/2023]
Abstract
Vaccinia virus is the prototypical orthopoxvirus of Poxviridae, a family of viruses that includes the human pathogens Variola (smallpox) and Monkeypox. Core viral functions are conserved among orthopoxviruses, and consequently Vaccinia is routinely used to study poxvirus biology and screen for novel antiviral compounds. Here we describe the development of a series of fluorescent protein-based reporter Vaccinia viruses that provide unprecedented resolution for tracking viral function. The reporter viruses are divided into two sets: (1) single reporter viruses that utilize temporally regulated early, intermediate, or late viral promoters; and (2) multi-reporter viruses that utilize multiple temporally regulated promoters. Promoter and reporter combinations were chosen that yielded high signal-to-background for stage-specific viral outputs. We provide examples for how these viruses can be used in the rapid and accurate monitoring of Vaccinia function and drug action.
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Affiliation(s)
- Ken Dower
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
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18
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Kuai J, Gregory B, Hill A, Pittman DD, Feldman JL, Brown T, Carito B, O'Toole M, Ramsey R, Adolfsson O, Shields KM, Dower K, Hall JP, Kurdi Y, Beech JT, Nanchahal J, Feldmann M, Foxwell BM, Brennan FM, Winkler DG, Lin LL. TREM-1 expression is increased in the synovium of rheumatoid arthritis patients and induces the expression of pro-inflammatory cytokines. Rheumatology (Oxford) 2009; 48:1352-8. [PMID: 19713442 DOI: 10.1093/rheumatology/kep235] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES To investigate the expression and function of triggering receptor expressed on myeloid cells-1 (TREM-1) in the synovium of human RA patients as well as the level of soluble TREM-1 in the plasma of RA patients. METHODS Twenty-four RA synovial samples were analysed by gene expression oligonucleotide microarrays. Expression levels of TREM-1 mRNA in murine CIA paws were determined by quantitative PCR (qPCR). TREM-1 protein expression was detected by immunohistochemistry in five RA synovial samples and two OA synovial samples. TREM-1-positive cells from five RA synovial tissues were analysed by FACS staining to determine the cell type. Activation of TREM-1 was tested in five RA synovial samples. Soluble TREM-1 was measured in serum from 32 RA patients. RESULTS The expression of TREM-1 mRNA was found to increase 6.5-fold in RA synovial samples, whereas it was increased 132-fold in CIA paws. Increased numbers of TREM-1-positive cells were seen in RA synovium sections and these cells co-expressed CD14. Using a TREM-1-activating cross-linking antibody in RA synovial cultures, multiple pro-inflammatory cytokines were induced. The average amount of soluble TREM-1 in plasma from RA patients was found to be higher than that in plasma from healthy volunteers. CONCLUSIONS These findings suggest that the presence of high levels of functionally active TREM-1 in RA synovium may contribute to the development or maintenance of RA, or both. Inhibiting TREM-1 activity may, therefore, have a therapeutic effect on RA. High levels of soluble TREM-1 in the plasma of RA patients compared with healthy volunteers may indicate disease activity.
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Affiliation(s)
- Jun Kuai
- Department of Inflammation, Wyeth Research, 200 Cambridge Park Drive, Cambridge, MA 02140, USA
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19
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Dower K, Ellis DK, Saraf K, Jelinsky SA, Lin LL. Innate Immune Responses to TREM-1 Activation: Overlap, Divergence, and Positive and Negative Cross-Talk with Bacterial Lipopolysaccharide. J Immunol 2008; 180:3520-34. [DOI: 10.4049/jimmunol.180.5.3520] [Citation(s) in RCA: 134] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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20
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Abruzzi KC, Belostotsky DA, Chekanova JA, Dower K, Rosbash M. 3'-end formation signals modulate the association of genes with the nuclear periphery as well as mRNP dot formation. EMBO J 2006; 25:4253-62. [PMID: 16946703 PMCID: PMC1570430 DOI: 10.1038/sj.emboj.7601305] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [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: 04/07/2006] [Accepted: 08/02/2006] [Indexed: 11/09/2022] Open
Abstract
Multiple studies indicate that mRNA processing defects cause mRNAs to accumulate in discrete nuclear foci or dots, in mammalian cells as well as yeast. To investigate this phenomenon, we have studied a series of GAL reporter constructs integrated into the yeast genome adjacent to an array of TetR-GFP-bound TetO sites. mRNA within dots is predominantly post-transcriptional, and dots are adjacent to but distinct from their transcription site. These reporter genes also localize to the nuclear periphery upon gene induction, like their endogenous GAL counterparts. Surprisingly, this peripheral localization persists long after transcriptional shutoff, and there is a comparable persistence of the RNA in the dots. Moreover, dot disappearance and gene delocalization from the nuclear periphery occur with similar kinetics after transcriptional shutoff. Both kinetics depend in turn on reporter gene 3'-end formation signals. Our experiments indicate that gene association with the nuclear periphery does not require ongoing transcription and suggest that the mRNPs within dots may make a major contribution to the gene-nuclear periphery tether.
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Affiliation(s)
- Katharine C Abruzzi
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, MA, USA
| | - Dmitry A Belostotsky
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, MA, USA
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA
| | - Julia A Chekanova
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, MA, USA
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA
| | - Ken Dower
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, MA, USA
| | - Michael Rosbash
- Howard Hughes Medical Institute and Department of Biology, Brandeis University, Waltham, MA, USA
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA
- Department of Biology, Howard Hughes Medical Institute, Brandeis University, 415 South Street, Waltham, MA 02454, USA. Tel.: +1 781 736 3160; Fax: +1 781 736 3164; E-mail:
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21
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Abstract
Nonsense-mediated decay (NMD) is a eukaryotic regulatory process that degrades mRNAs with premature termination codons (PTCs). Although NMD is a translation-dependent process, there is evidence from mammalian systems that PTC recognition and mRNA degradation takes place in association with nuclei. Consistent with this notion, degradation of mammalian PTC-containing mRNAs occurs when they are bound by the cap binding complex (CBC) during a "pioneer" round of translation. Moreover, there are reports indicating that a PTC can trigger other nuclear events such as alternative splicing, abnormal 3' end processing, and accumulation of pre-mRNA at transcription sites. To examine whether a PTC can elicit similar nuclear events in yeast, we used RNA export-defective mutants to sequester mRNAs within nuclei. The results indicate that nuclear PTC-containing yeast RNAs are NMD insensitive. We also observed by fluorescent in situ hybridization that there was no PTC effect on mRNA accumulated at the site of transcription. Finally, we show that yeast NMD occurs minimally if at all on CBC-bound transcripts, arguing against a CBC-mediated pioneer round of translation in yeast. The data taken together indicate that there are no direct consequences of a PTC within the yeast nucleus.
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Affiliation(s)
- Nicolas Kuperwasser
- Howard Hughes Medical Institute, Department of Biology, Brandeis University, 415 South St., Waltham, MA 02454, USA
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22
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Abstract
To investigate the role of 3' end formation in yeast mRNA export, we replaced the mRNA cleavage and polyadenylation signal with a self-cleaving hammerhead ribozyme element. The resulting RNA is unadenylated and accumulates near its site of synthesis. Nonetheless, a significant fraction of this RNA reaches the cytoplasm. Nuclear accumulation was relieved by insertion of a stretch of DNA-encoded adenosine residues immediately upstream of the ribozyme element (a synthetic A tail). This indicates that a 3' stretch of adenosines can promote export, independently of cleavage and polyadenylation. We further show that a synthetic A tail-containing RNA is unaffected in 3' end formation mutant strains, in which a normally cleaved and polyadenylated RNA accumulates within nuclei. Our results support a model in which a polyA tail contributes to efficient mRNA progression away from the gene, most likely through the action of the yeast polyA-tail binding protein Pab1p.
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MESH Headings
- Base Sequence
- Cell Nucleus/metabolism
- Green Fluorescent Proteins/genetics
- Green Fluorescent Proteins/metabolism
- In Situ Hybridization, Fluorescence
- Models, Biological
- Mutation
- Poly A/chemistry
- Poly A/genetics
- Poly A/metabolism
- Poly(A)-Binding Proteins/genetics
- Poly(A)-Binding Proteins/metabolism
- RNA, Catalytic/metabolism
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Transcription, Genetic
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Affiliation(s)
- Ken Dower
- Howard Hughes Medical Institute, Department of Biology, Brandeis University, 415 South Street, Waltham, MA 02454, USA
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23
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Abstract
Eukaryotic mRNA is processed by enzymes and packaged with proteins within nuclei to generate functional messenger ribonucleoprotein (mRNP) particles. Processing and packaging factors can interact with mRNA cotranscriptionally to form an early mRNP. Erroneous mRNP formation leads to nuclear retention and degradation of the mRNA. It therefore appears that one function of cotranscriptional mRNP assembly is to discard aberrant mRNPs early in their biogenesis. Cotranscriptional mRNP assembly may also enable the transcription machinery to respond to improper mRNP formation.
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Affiliation(s)
- Torben Heick Jensen
- Department of Molecular Biology, Aarhus University, C.F. Møllers Alle, Building 130, 8000 Aarhus C., Denmark.
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24
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Libri D, Dower K, Boulay J, Thomsen R, Rosbash M, Jensen TH. Interactions between mRNA export commitment, 3'-end quality control, and nuclear degradation. Mol Cell Biol 2002; 22:8254-66. [PMID: 12417728 PMCID: PMC134070 DOI: 10.1128/mcb.22.23.8254-8266.2002] [Citation(s) in RCA: 197] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several aspects of eukaryotic mRNA processing are linked to transcription. In Saccharomyces cerevisiae, overexpression of the mRNA export factor Sub2p suppresses the growth defect of hpr1 null cells, yet the protein Hpr1p and the associated THO protein complex are implicated in transcriptional elongation. Indeed, we find that a pool of heat shock HSP104 transcripts are 3'-end truncated in THO complex mutant as well as sub2 mutant backgrounds. Surprisingly, however, this defect can be suppressed by deletion of the 3'-5' exonuclease Rrp6p. This indicates that incomplete RNAs result from nuclear degradation rather than from a failure to efficiently elongate transcription. RNAs that are not degraded are retained at the transcription site in a Rrp6p-dependent manner. Interestingly, the addition of a RRP6 deletion to sub2 or to THO complex mutants shows a strong synthetic growth phenotype, suggesting that the failure to retain and/or degrade defective mRNAs is deleterious. mRNAs produced in the 3'-end processing mutants rna14-3 and rna15-2, as well as an RNA harboring a 3' end generated by a self-cleaving hammerhead ribozyme, are also retained in Rrp6p-dependent transcription site foci. Taken together, our results show that several classes of defective RNPs are subject to a quality control step that impedes release from transcription site foci and suggest that suboptimal messenger ribonucleoprotein assembly leads to RNA degradation by Rrp6p.
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Affiliation(s)
- Domenico Libri
- Centre National de la Recherche Scientifique, Centre de Genetique Moleculaire, 91190 Gif-sur-Yvette, France.
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25
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Abstract
We have characterized transcripts synthesized in vivo by bacteriophage T7 RNA polymerase to investigate yeast mRNA processing. T7 transcripts are not capped, consistent with capping being tightly coupled to RNA polymerase II (pol II) transcription. In contrast to higher eukaryotic non-pol II transcripts, yeast T7 transcripts are spliced as well as cleaved and polyadenylated. However, T7 and pol II transcripts are affected differently in cleavage and polyadenylation mutant strains, indicating that pol II may have a role in yeast 3' end formation. T7 transcripts with 3' ends directed by a polyadenylation signal are exported from the nucleus, and this export is dependent on the canonical cleavage and polyadenylation machinery. Importantly, transcripts with T7 terminator-directed 3' ends are unadenylated and predominantly nuclear in wild-type cells. Our results suggest that transcription by pol II is required for neither the nuclear export of an in vivo-transcribed mRNA nor for the retention of transcripts with aberrant 3' ends. Moreover, proper 3' end formation may be necessary and sufficient to promote mRNA export in yeast.
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Affiliation(s)
- Ken Dower
- Howard Hughes Medical Institute, Department of Biology, Brandeis University, Waltham, Massachusetts 02454, USA
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26
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Li D, Dower K, Ma Y, Tian Y, Benjamin TL. A tumor host range selection procedure identifies p150(sal2) as a target of polyoma virus large T antigen. Proc Natl Acad Sci U S A 2001; 98:14619-24. [PMID: 11734654 PMCID: PMC64731 DOI: 10.1073/pnas.251447198] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [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] [Indexed: 11/18/2022] Open
Abstract
Cancer cells may undergo loss or alterations in functions that certain viruses normally target to promote virus replication. Virus mutants that have lost the targeting function(s) should be able to grow in such cancer cells but not in normal cells. A "tumor host range" (t-hr) selection procedure has been devised and applied to polyoma virus based on this rationale. Studies of one t-hr mutant have led to the identification of the mSal2 gene product (p150(sal2)) as a binding partner of the large T antigen. mSal2 encodes a multizinc finger protein and putative transcription factor homologous to the Drosophila homeotic gene Spalt. The t-hr mutant encodes an altered large T protein that fails to interact with p150(sal2) and is defective in replication and tumor induction in newborn mice.
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Affiliation(s)
- D Li
- Department of Pathology, Harvard Medical School, Boston, MA 02115, USA
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27
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Vainberg IE, Dower K, Rosbash M. Nuclear export of heat shock and non-heat-shock mRNA occurs via similar pathways. Mol Cell Biol 2000; 20:3996-4005. [PMID: 10805742 PMCID: PMC85767 DOI: 10.1128/mcb.20.11.3996-4005.2000] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [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: 11/08/1999] [Accepted: 03/08/2000] [Indexed: 11/20/2022] Open
Abstract
Several studies of the yeast Saccharomyces cerevisiae support differential regulation of heat shock mRNA (hs mRNA) and non-hs mRNA nuclear export during stress. These include the finding that hs mRNA export at 42 degrees C is inhibited in the absence of the nucleoporinlike protein Rip1p (also called Nup42p) (C. A. Saavedra, C. M. Hammell, C. V. Heath, and C. N. Cole, Genes Dev. 11:2845-2856, 1997; F. Stutz, J. Kantor, D. Zhang, T. McCarthy, M. Neville, and M. Rosbash, Genes Dev. 11:2857-2868, 1997). However, the results reported in this paper provide little evidence for selective non-hs mRNA retention or selective hs mRNA export under heat shock conditions. First, we do not detect a block to non-hs mRNA export at 42 degrees C in a wild-type strain. Second, hs mRNA export appears to be mediated by the Ran system and several other factors previously reported to be important for general mRNA export. Third, the export of non-hs mRNA as well as hs mRNA is inhibited in the absence of Rip1p at 42 degrees C. As a corollary, we find no evidence for cis-acting hs mRNA sequences that promote transport during heat shock. Taken together, our data suggest that a shift to 42 degrees C in the absence of Rip1p impacts a late stage of transport affecting most if not all mRNA.
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Affiliation(s)
- I E Vainberg
- Department of Biology, Howard Hughes Medical Institute, MS008 Brandeis University, Waltham, Massachusetts 02454, USA
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