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Adler BA, Trinidad MI, Bellieny-Rabelo D, Zhang E, Karp HM, Skopintsev P, Thornton BW, Weissman RF, Yoon P, Chen L, Hessler T, Eggers AR, Colognori D, Boger R, Doherty EE, Tsuchida CA, Tran RV, Hofman L, Shi H, Wasko KM, Zhou Z, Xia C, Al-Shimary MJ, Patel JR, Thomas VCJX, Pattali R, Kan MJ, Vardapetyan A, Yang A, Lahiri A, Maxwell MF, Murdock AG, Ramit GC, Henderson HR, Calvert RW, Bamert R, Knott GJ, Lapinaite A, Pausch P, Cofsky J, Sontheimer EJ, Wiedenheft B, Fineran PC, Brouns SJJ, Sashital DG, Thomas BC, Brown CT, Goltsman DSA, Barrangou R, Siksnys V, Banfield JF, Savage DF, Doudna JA. CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes. Nucleic Acids Res 2024; 52:D590-D596. [PMID: 37889041 PMCID: PMC10767948 DOI: 10.1093/nar/gkad890] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 10/28/2023] Open
Abstract
CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deployed for numerous research, clinical and agricultural applications. However, the immense genetic and biochemical diversity of these proteins in the public domain poses a barrier for researchers seeking to leverage their activities. We present CasPEDIA (http://caspedia.org), the Cas Protein Effector Database of Information and Assessment, a curated encyclopedia that integrates enzymatic classification for hundreds of different Cas enzymes across 27 phylogenetic groups spanning the Cas9, Cas12 and Cas13 families, as well as evolutionarily related IscB and TnpB proteins. All enzymes in CasPEDIA were annotated with a standard workflow based on their primary nuclease activity, target requirements and guide-RNA design constraints. Our functional classification scheme, CasID, is described alongside current phylogenetic classification, allowing users to search related orthologs by enzymatic function and sequence similarity. CasPEDIA is a comprehensive data portal that summarizes and contextualizes enzymatic properties of widely used Cas enzymes, equipping users with valuable resources to foster biotechnological development. CasPEDIA complements phylogenetic Cas nomenclature and enables researchers to leverage the multi-faceted nucleic-acid targeting rules of diverse Class 2 Cas enzymes.
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Affiliation(s)
- Benjamin A Adler
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Marena I Trinidad
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Daniel Bellieny-Rabelo
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Elaine Zhang
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Hannah M Karp
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Petr Skopintsev
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Brittney W Thornton
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Rachel F Weissman
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Peter H Yoon
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - LinXing Chen
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA
| | - Tomas Hessler
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
- EGSB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Amy R Eggers
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - David Colognori
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Ron Boger
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Erin E Doherty
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Connor A Tsuchida
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- University of California, Berkeley - University of California, San Francisco Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ryan V Tran
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Laura Hofman
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Graduate School of Life Sciences, Utrecht University, 3584 CS Utrecht, UT, The Netherlands
| | - Honglue Shi
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
| | - Kevin M Wasko
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Zehan Zhou
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Chenglong Xia
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Muntathar J Al-Shimary
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Jaymin R Patel
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Vienna C J X Thomas
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Rithu Pattali
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Matthew J Kan
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Pediatrics, Division of Allergy, Immunology, and Bone Marrow Transplantation, University of California, San Francisco, CA 94158, USA
| | - Anna Vardapetyan
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Alana Yang
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Arushi Lahiri
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Micaela F Maxwell
- Department of Chemistry and Biochemistry, Hampton University, Hampton, VA 23668, USA
| | - Andrew G Murdock
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Glenn C Ramit
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Hope R Henderson
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Roland W Calvert
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Rebecca S Bamert
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Gavin J Knott
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3168, Australia
| | - Audrone Lapinaite
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA
- Arizona State University-Banner Neurodegenerative Disease Research Center at the Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| | - Patrick Pausch
- LSC-EMBL Partnership Institute for Genome Editing Technologies, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Joshua C Cofsky
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Erik J Sontheimer
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
- Li Weibo Institute for Rare Diseases Research, University of Massachusetts Chan Medical School, Worcester, MA 01655, USA
| | - Blake Wiedenheft
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT 59717, USA
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin 9016, New Zealand
- Genetics Otago, University of Otago, Dunedin 9016, New Zealand
- Bioprotection Aotearoa, University of Otago, Dunedin 9016, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, University of Otago, Dunedin 9016, New Zealand
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, 2629 HZ Delft, Netherlands
- Kavli Institute of Nanoscience, 2629 HZ Delft, The Netherlands
| | - Dipali G Sashital
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | | | | | | | - Rodolphe Barrangou
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27606, USA
| | - Virginius Siksnys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius 10257, Lithuania
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
- EGSB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- The University of Melbourne, Parkville, VIC 3052, Australia
| | - David F Savage
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Gladstone Institutes, University of California, San Francisco, CA 94158, USA
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Affiliation(s)
- Matthew J Kan
- Division of Allergy, Immunology, and Bone Marrow Transplantation, Department of Pediatrics, University of California, San Francisco
- Pediatric Scientist Development Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, San Francisco, California
- Innovative Genomics Institute, University of California, Berkeley
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California, Berkeley
- Department of Molecular and Cell Biology, Department of Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California, Berkeley
- Howard Hughes Medical Institute, University of California, Berkeley
- Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, California
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Kan MJ, Grant LMC, Muña MA, Greenhow TL. Fever Without a Source in an Infant Due to Severe Acute Respiratory Syndrome Coronavirus-2. J Pediatric Infect Dis Soc 2020; 10:49-51. [PMID: 32318729 PMCID: PMC7188112 DOI: 10.1093/jpids/piaa044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 04/17/2020] [Indexed: 01/08/2023]
Abstract
A 5-week-old infant female admitted for fever without a source subsequently tested positive for severe acute respiratory syndrome coronavirus 2. She had a mild hospital course without respiratory distress. This unexpected presentation changed regional hospital screening for coronavirus disease 2019 and personal protective equipment use by medical providers who evaluate febrile infants.
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Affiliation(s)
- Matthew J Kan
- Department of Pediatrics, University of California, San Francisco, San Francisco, California,Alternate contact author: Matthew J. Kan, MD, PhD, 550 6th St Fourth Floor, San Francisco, CA 94143, Phone: 925-588-5750, Fax: 415-476-5354,
| | - Lauren M C Grant
- Department of Pediatrics, University of California, San Francisco, San Francisco, California
| | - Martha A Muña
- Department of Pediatrics, University of California, San Francisco, San Francisco, California
| | - Tara L Greenhow
- Department of Pediatrics, University of California, San Francisco, San Francisco, California,Division of Infectious Diseases, Department of Pediatrics, Kaiser Permanente Northern California, San Francisco, CA,Address Correspondence to: Tara L. Greenhow, 2238 Geary Blvd. San Francisco, CA 94115, Phone: 415-833-9143, Fax: 415-833-4177,
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Yu YRA, Malakhau Y, Yu CHA, Phelan SLJ, Cumming RI, Kan MJ, Mao L, Rajagopal S, Piantadosi CA, Gunn MD. Nonclassical Monocytes Sense Hypoxia, Regulate Pulmonary Vascular Remodeling, and Promote Pulmonary Hypertension. J Immunol 2020; 204:1474-1485. [PMID: 31996456 DOI: 10.4049/jimmunol.1900239] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 12/15/2019] [Indexed: 11/19/2022]
Abstract
An increasing body of evidence suggests that bone marrow-derived myeloid cells play a critical role in the pathophysiology of pulmonary hypertension (PH). However, the true requirement for myeloid cells in PH development has not been demonstrated, and a specific disease-promoting myeloid cell population has not been identified. Using bone marrow chimeras, lineage labeling, and proliferation studies, we determined that, in murine hypoxia-induced PH, Ly6Clo nonclassical monocytes are recruited to small pulmonary arteries and differentiate into pulmonary interstitial macrophages. Accumulation of these nonclassical monocyte-derived pulmonary interstitial macrophages around pulmonary vasculature is associated with increased muscularization of small pulmonary arteries and disease severity. To determine if the sensing of hypoxia by nonclassical monocytes contributes to the development of PH, mice lacking expression of hypoxia-inducible factor-1α in the Ly6Clo monocyte lineage were exposed to hypoxia. In these mice, vascular remodeling and PH severity were significantly reduced. Transcriptome analyses suggest that the Ly6Clo monocyte lineage regulates PH through complement, phagocytosis, Ag presentation, and chemokine/cytokine pathways. Consistent with these murine findings, relative to controls, lungs from pulmonary arterial hypertension patients displayed a significant increase in the frequency of nonclassical monocytes. Taken together, these findings show that, in response to hypoxia, nonclassical monocytes in the lung sense hypoxia, infiltrate small pulmonary arteries, and promote vascular remodeling and development of PH. Our results demonstrate that myeloid cells, specifically cells of the nonclassical monocyte lineage, play a direct role in the pathogenesis of PH.
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Affiliation(s)
- Yen-Rei A Yu
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Duke University School of Medicine, Durham, NC 27710;
| | - Yuryi Malakhau
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Duke University School of Medicine, Durham, NC 27710
| | - Chen-Hsin A Yu
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC 27710
| | - Stefan-Laural J Phelan
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Duke University School of Medicine, Durham, NC 27710
| | - R Ian Cumming
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Duke University School of Medicine, Durham, NC 27710
| | - Matthew J Kan
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94115; and
| | - Lan Mao
- Division of Cardiology, Department of Medicine, Duke University School of Medicine, Durham, NC 27710
| | - Sudarshan Rajagopal
- Division of Cardiology, Department of Medicine, Duke University School of Medicine, Durham, NC 27710
| | - Claude A Piantadosi
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Duke University School of Medicine, Durham, NC 27710
| | - Michael D Gunn
- Division of Cardiology, Department of Medicine, Duke University School of Medicine, Durham, NC 27710
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Paik H, Kan MJ, Rappoport N, Hadley D, Sirota M, Chen B, Manber U, Cho SB, Butte AJ. Tracing diagnosis trajectories over millions of patients reveal an unexpected risk in schizophrenia. Sci Data 2019; 6:201. [PMID: 31615985 PMCID: PMC6794302 DOI: 10.1038/s41597-019-0220-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 04/03/2019] [Accepted: 09/27/2019] [Indexed: 02/07/2023] Open
Abstract
The identification of novel disease associations using big-data for patient care has had limited success. In this study, we created a longitudinal disease network of traced readmissions (disease trajectories), merging data from over 10.4 million inpatients through the Healthcare Cost and Utilization Project, which allowed the representation of disease progression mapping over 300 diseases. From these disease trajectories, we discovered an interesting association between schizophrenia and rhabdomyolysis, a rare muscle disease (incidence < 1E-04) (relative risk, 2.21 [1.80-2.71, confidence interval = 0.95], P-value 9.54E-15). We validated this association by using independent electronic medical records from over 830,000 patients at the University of California, San Francisco (UCSF) medical center. A case review of 29 rhabdomyolysis incidents in schizophrenia patients at UCSF demonstrated that 62% are idiopathic, without the use of any drug known to lead to this adverse event, suggesting a warning to physicians to watch for this unexpected risk of schizophrenia. Large-scale analysis of disease trajectories can help physicians understand potential sequential events in their patients.
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Affiliation(s)
- Hyojung Paik
- Bakar Computational Health Sciences Institute, University of California, San Francisco, 550 16th Street, San Francisco, CA, 9414, USA
- Department of Pediatrics, University of California, San Francisco, 550 16th Street, San Francisco, CA, 94143, USA
- Korea Institute of Science and Technology Information, Center for Supercomputing Application, Division of Supercomputing, Daejeon, 34141, South Korea
- National Institute of Health, Division of Bio-Medical Informatics, Center for Genome Science, OHTAC, 187 Osongsaengmyeong2(i)-ro, Gangoe-myeon, Cheongwon-gun, ChoongchungBuk-do, South Korea
| | - Matthew J Kan
- Bakar Computational Health Sciences Institute, University of California, San Francisco, 550 16th Street, San Francisco, CA, 9414, USA
- Department of Pediatrics, University of California, San Francisco, 550 16th Street, San Francisco, CA, 94143, USA
| | - Nadav Rappoport
- Bakar Computational Health Sciences Institute, University of California, San Francisco, 550 16th Street, San Francisco, CA, 9414, USA
- Department of Pediatrics, University of California, San Francisco, 550 16th Street, San Francisco, CA, 94143, USA
| | - Dexter Hadley
- Bakar Computational Health Sciences Institute, University of California, San Francisco, 550 16th Street, San Francisco, CA, 9414, USA
- Department of Pediatrics, University of California, San Francisco, 550 16th Street, San Francisco, CA, 94143, USA
| | - Marina Sirota
- Bakar Computational Health Sciences Institute, University of California, San Francisco, 550 16th Street, San Francisco, CA, 9414, USA
- Department of Pediatrics, University of California, San Francisco, 550 16th Street, San Francisco, CA, 94143, USA
| | - Bin Chen
- Bakar Computational Health Sciences Institute, University of California, San Francisco, 550 16th Street, San Francisco, CA, 9414, USA
- Department of Pediatrics, University of California, San Francisco, 550 16th Street, San Francisco, CA, 94143, USA
| | - Udi Manber
- Bakar Computational Health Sciences Institute, University of California, San Francisco, 550 16th Street, San Francisco, CA, 9414, USA
- Department of Medicine, University of California, San Francisco, 505 Parnassus Avenue, San Francisco, CA, 94143, USA
| | - Seong Beom Cho
- National Institute of Health, Division of Bio-Medical Informatics, Center for Genome Science, OHTAC, 187 Osongsaengmyeong2(i)-ro, Gangoe-myeon, Cheongwon-gun, ChoongchungBuk-do, South Korea.
| | - Atul J Butte
- Bakar Computational Health Sciences Institute, University of California, San Francisco, 550 16th Street, San Francisco, CA, 9414, USA.
- Department of Pediatrics, University of California, San Francisco, 550 16th Street, San Francisco, CA, 94143, USA.
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Rivera PD, Hanamsagar R, Kan MJ, Tran PK, Stewart D, Jo YC, Gunn M, Bilbo SD. Removal of microglial-specific MyD88 signaling alters dentate gyrus doublecortin and enhances opioid addiction-like behaviors. Brain Behav Immun 2019; 76:104-115. [PMID: 30447281 PMCID: PMC6348129 DOI: 10.1016/j.bbi.2018.11.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [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: 07/24/2018] [Revised: 11/09/2018] [Accepted: 11/13/2018] [Indexed: 12/15/2022] Open
Abstract
Drugs of abuse promote a potent immune response in central nervous system (CNS) via the activation of microglia and astrocytes. However, the molecular mechanisms underlying microglial activation during addiction are not well known. We developed and functionally characterized a novel transgenic mouse (Cx3cr1-CreBTtg/0:MyD88f/f [Cretg/0]) wherein the immune signaling adaptor gene, MyD88, was specifically deleted in microglia. To test the downstream effects of loss of microglia-specific MyD88 signaling in morphine addiction, Cretg/0 and Cre0/0 mice were tested for reward learning, extinction, and reinstatement using a conditioned place preference (CPP) paradigm. There were no differences in drug acquisition, but Cretg/0 mice had prolonged extinction and enhanced reinstatement compared to Cre0/0 controls. Furthermore, morphine-treated Cretg/0 mice showed increased doublecortin (DCX) signal relative to Cre0/0 control mice in the hippocampus, indicative of increased number of immature neurons. Additionally, there was an increase in colocalization of microglial lysosomal marker CD68 with DCX+cells in morphine-treated Cretg/0 mice but not in Cre0/0 or drug-naїve mice, suggesting a specific role for microglial MyD88 signaling in neuronal phagocytosis in the hippocampus. Our results show that MyD88 deletion in microglia may negatively impact maturing neurons within the adult hippocampus and thus reward memories, suggesting a novel protective role for microglia in opioid addiction.
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Affiliation(s)
- Phillip D Rivera
- Program in Neuroscience, Harvard Medical School, Boston, MA, USA; Department of Pediatrics, Lurie Center for Autism, MassGeneral Hospital for Children, Boston, MA, USA; Department of Psychology & Neuroscience, Duke University, Durham, NC, USA; Department of Biology, Hope College, Holland, MI, USA
| | - Richa Hanamsagar
- Program in Neuroscience, Harvard Medical School, Boston, MA, USA; Department of Pediatrics, Lurie Center for Autism, MassGeneral Hospital for Children, Boston, MA, USA; Department of Psychology & Neuroscience, Duke University, Durham, NC, USA
| | - Matthew J Kan
- Department of Immunology, Duke University Medical Center, Durham, NC, USA; Department of Medicine, Duke University Medical Center, Durham, NC, USA; Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Phuong K Tran
- Department of Pediatrics, Lurie Center for Autism, MassGeneral Hospital for Children, Boston, MA, USA; Department of Psychology & Neuroscience, Duke University, Durham, NC, USA
| | - David Stewart
- Department of Psychology & Neuroscience, Duke University, Durham, NC, USA
| | - Young Chan Jo
- Program in Neuroscience, Harvard Medical School, Boston, MA, USA; Department of Pediatrics, Lurie Center for Autism, MassGeneral Hospital for Children, Boston, MA, USA
| | - Michael Gunn
- Department of Immunology, Duke University Medical Center, Durham, NC, USA; Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Staci D Bilbo
- Program in Neuroscience, Harvard Medical School, Boston, MA, USA; Department of Pediatrics, Lurie Center for Autism, MassGeneral Hospital for Children, Boston, MA, USA; Department of Psychology & Neuroscience, Duke University, Durham, NC, USA.
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Zalocusky KA, Kan MJ, Hu Z, Dunn P, Thomson E, Wiser J, Bhattacharya S, Butte AJ. The 10,000 Immunomes Project: Building a Resource for Human Immunology. Cell Rep 2018; 25:1995. [PMID: 30428364 DOI: 10.1016/j.celrep.2018.11.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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Zalocusky KA, Kan MJ, Hu Z, Dunn P, Thomson E, Wiser J, Bhattacharya S, Butte AJ. The 10,000 Immunomes Project: Building a Resource for Human Immunology. Cell Rep 2018; 25:513-522.e3. [PMID: 30304689 PMCID: PMC6263160 DOI: 10.1016/j.celrep.2018.09.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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] [Received: 01/08/2018] [Revised: 05/01/2018] [Accepted: 09/07/2018] [Indexed: 02/06/2023] Open
Abstract
There is increasing appreciation that the immune system plays critical roles not only in the traditional domains of infection and inflammation but also in many areas of biology, including tumorigenesis, metabolism, and even neurobiology. However, one of the major barriers for understanding human immunological mechanisms is that immune assays have not been reproducibly characterized for a sufficiently large and diverse healthy human cohort. Here, we present the 10,000 Immunomes Project (10KIP), a framework for growing a diverse human immunology reference, from ImmPort, a publicly available resource of subject-level immunology data. Although some measurement types are sparse in the presently deposited ImmPort database, the extant data allow for a diversity of robust comparisons. Using 10KIP, we describe variations in serum cytokines and leukocytes by age, race, and sex; define a baseline cell-cytokine network; and describe immunologic changes in pregnancy. All data in the resource are available for visualization and download at http://10kimmunomes.org/.
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Affiliation(s)
- Kelly A Zalocusky
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Matthew J Kan
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Zicheng Hu
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Patrick Dunn
- Information Systems Health IT, Northrop Grumman, Rockville, MD 20850, USA
| | - Elizabeth Thomson
- Information Systems Health IT, Northrop Grumman, Rockville, MD 20850, USA
| | - Jeffrey Wiser
- Information Systems Health IT, Northrop Grumman, Rockville, MD 20850, USA
| | - Sanchita Bhattacharya
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Atul J Butte
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA; Department of Pediatrics, University of California, San Francisco, San Francisco, CA 94158, USA.
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9
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Bhattacharya S, Li J, Sockell A, Kan MJ, Bava FA, Chen SC, Ávila-Arcos MC, Ji X, Smith E, Asadi NB, Lachman RS, Lam HYK, Bustamante CD, Butte AJ, Nolan GP. Whole-genome sequencing of Atacama skeleton shows novel mutations linked with dysplasia. Genome Res 2018; 28:423-431. [PMID: 29567674 PMCID: PMC5880234 DOI: 10.1101/gr.223693.117] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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: 04/21/2017] [Accepted: 02/21/2018] [Indexed: 12/30/2022]
Abstract
Over a decade ago, the Atacama humanoid skeleton (Ata) was discovered in the Atacama region of Chile. The Ata specimen carried a strange phenotype-6-in stature, fewer than expected ribs, elongated cranium, and accelerated bone age-leading to speculation that this was a preserved nonhuman primate, human fetus harboring genetic mutations, or even an extraterrestrial. We previously reported that it was human by DNA analysis with an estimated bone age of about 6-8 yr at the time of demise. To determine the possible genetic drivers of the observed morphology, DNA from the specimen was subjected to whole-genome sequencing using the Illumina HiSeq platform with an average 11.5× coverage of 101-bp, paired-end reads. In total, 3,356,569 single nucleotide variations (SNVs) were found as compared to the human reference genome, 518,365 insertions and deletions (indels), and 1047 structural variations (SVs) were detected. Here, we present the detailed whole-genome analysis showing that Ata is a female of human origin, likely of Chilean descent, and its genome harbors mutations in genes (COL1A1, COL2A1, KMT2D, FLNB, ATR, TRIP11, PCNT) previously linked with diseases of small stature, rib anomalies, cranial malformations, premature joint fusion, and osteochondrodysplasia (also known as skeletal dysplasia). Together, these findings provide a molecular characterization of Ata's peculiar phenotype, which likely results from multiple known and novel putative gene mutations affecting bone development and ossification.
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Affiliation(s)
- Sanchita Bhattacharya
- Institute for Computational Health Sciences, University of California San Francisco, San Francisco, California 94158, USA
| | - Jian Li
- Roche Sequencing Solutions, Belmont, California 94002, USA
| | - Alexandra Sockell
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Matthew J Kan
- Institute for Computational Health Sciences, University of California San Francisco, San Francisco, California 94158, USA
| | - Felice A Bava
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, California 94305, USA
| | - Shann-Ching Chen
- Institute for Computational Health Sciences, University of California San Francisco, San Francisco, California 94158, USA
| | - María C Ávila-Arcos
- International Laboratory for Human Genome Research, National Autonomous University of Mexico (UNAM) Santiago de Querétaro, Querétaro 76230, Mexico
| | - Xuhuai Ji
- Human Immune Monitoring Center and Functional Genomics Facility, Stanford University, Stanford, California 94305, USA
| | - Emery Smith
- Ultra Intelligence Corporation, Boulder, Colorado 80301, USA
| | - Narges B Asadi
- Roche Sequencing Solutions, Belmont, California 94002, USA
| | - Ralph S Lachman
- Department of Pediatric Radiology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Hugo Y K Lam
- Roche Sequencing Solutions, Belmont, California 94002, USA
| | - Carlos D Bustamante
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Atul J Butte
- Institute for Computational Health Sciences, University of California San Francisco, San Francisco, California 94158, USA
| | - Garry P Nolan
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, California 94305, USA
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10
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Kan MJ, Zalocusky K, Hu Z, Dunn P, Thomson E, Wiser J, Bhattacharya S, Butte A. The 10,000 Immunomes Project: A Resource for Human Immunology. J Allergy Clin Immunol 2018. [DOI: 10.1016/j.jaci.2017.12.857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Mastria EM, Cai LY, Kan MJ, Li X, Schaal JL, Fiering S, Gunn MD, Dewhirst MW, Nair SK, Chilkoti A. Nanoparticle formulation improves doxorubicin efficacy by enhancing host antitumor immunity. J Control Release 2017; 269:364-373. [PMID: 29146246 DOI: 10.1016/j.jconrel.2017.11.021] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 10/15/2017] [Accepted: 11/11/2017] [Indexed: 12/14/2022]
Abstract
Strategies that enhance the host antitumor immune response promise to revolutionize cancer therapy. Optimally mobilizing the immune system will likely require a multi-pronged approach to overcome the resistance developed by tumors to therapy. Recently, it has become recognized that doxorubicin can contribute to re-establishing host antitumor immunity through the generation of immunogenic cell death. However, the potential for delivery strategies to further enhance the immunological effects of doxorubicin has not been adequately examined. We report herein that Chimeric Polypeptide Doxorubicin (CP-Dox), a nanoparticle formulation of doxorubicin, enhances antitumor immunity. Compared to free doxorubicin, a single intravenous (IV) administration of CP-Dox at the maximum tolerated dose increases the infiltration of leukocytes into the tumor, slowing tumor growth and preventing metastasis in poorly immunogenic 4T1 mammary carcinoma. We demonstrate that the full efficacy of CP-Dox is dependent on CD8+ T cells and IFN-γ. CP-dox treatment also repolarized intratumoral myeloid cells towards an antitumor phenotype. These findings demonstrate that a nanoparticle drug is distinct from the free drug in its ability to productively stimulate antitumor immunity. Our study strongly argues for the use of antitumor immunotherapies combined with nanoparticle-packaged chemotherapy.
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Affiliation(s)
- Eric M Mastria
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Leon Y Cai
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Matthew J Kan
- Department of Immunology, Duke University Medical Center, Durham, NC, USA
| | - Xinghai Li
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Jeffrey L Schaal
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Steven Fiering
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth, Hanover, NH, USA; Norris Cotton Cancer Center, Lebanon, NH, USA
| | - Michael D Gunn
- Department of Immunology, Duke University Medical Center, Durham, NC, USA; Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Mark W Dewhirst
- Department of Biomedical Engineering, Duke University, Durham, NC, USA; Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Smita K Nair
- Department of Surgery, Duke University Medical Center, Durham, NC, USA; Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC, USA; Center for Biologically Inspired Materials and Materials Systems, Duke University, Durham, NC, USA.
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12
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Rudemiller NP, Patel MB, Zhang JD, Jeffs AD, Karlovich NS, Griffiths R, Kan MJ, Buckley AF, Gunn MD, Crowley SD. C-C Motif Chemokine 5 Attenuates Angiotensin II-Dependent Kidney Injury by Limiting Renal Macrophage Infiltration. Am J Pathol 2016; 186:2846-2856. [PMID: 27640148 DOI: 10.1016/j.ajpath.2016.07.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 07/12/2016] [Accepted: 07/19/2016] [Indexed: 12/24/2022]
Abstract
Inappropriate activation of the renin angiotensin system (RAS) is a key contributor to the pathogenesis of essential hypertension. During RAS activation, infiltration of immune cells into the kidney exacerbates hypertension and renal injury. However, the mechanisms underpinning the accumulation of mononuclear cells in the kidney after RAS stimulation remain unclear. C-C motif chemokine 5 (CCL5) drives recruitment of macrophages and T lymphocytes into injured tissues, and we have found that RAS activation induces CCL5 expression in the kidney during the pathogenesis of hypertension and renal fibrosis. We therefore evaluated the contribution of CCL5 to renal damage and fibrosis in hypertensive and normotensive models of RAS stimulation. Surprisingly, during angiotensin II-induced hypertension, CCL5-deficient (knockout, KO) mice exhibited markedly augmented kidney damage, macrophage infiltration, and expression of proinflammatory macrophage cytokines compared with wild-type controls. When subjected to the normotensive unilateral ureteral obstruction model of endogenous RAS activation, CCL5 KO mice similarly developed more severe renal fibrosis and greater accumulation of macrophages in the kidney, congruent with enhanced renal expression of the macrophage chemokine CCL2. In turn, pharmacologic inhibition of CCL2 abrogated the differences between CCL5 KO and wild-type mice in kidney fibrosis and macrophage infiltration after unilateral ureteral obstruction. These data indicate that CCL5 paradoxically limits macrophage accumulation in the injured kidney during RAS activation by constraining the proinflammatory actions of CCL2.
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Affiliation(s)
- Nathan P Rudemiller
- Division of Nephrology, Department of Medicine, Duke University Medical Center, Durham, North Carolina; Durham VA Medical Center, Durham, North Carolina
| | - Mehul B Patel
- Division of Nephrology, Department of Medicine, Duke University Medical Center, Durham, North Carolina; Durham VA Medical Center, Durham, North Carolina
| | - Jian-Dong Zhang
- Division of Nephrology, Department of Medicine, Duke University Medical Center, Durham, North Carolina; Durham VA Medical Center, Durham, North Carolina
| | - Alexander D Jeffs
- Division of Nephrology, Department of Medicine, Duke University Medical Center, Durham, North Carolina; Durham VA Medical Center, Durham, North Carolina
| | - Norah S Karlovich
- Division of Nephrology, Department of Medicine, Duke University Medical Center, Durham, North Carolina; Durham VA Medical Center, Durham, North Carolina
| | - Robert Griffiths
- Division of Nephrology, Department of Medicine, Duke University Medical Center, Durham, North Carolina; Durham VA Medical Center, Durham, North Carolina
| | - Matthew J Kan
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Anne F Buckley
- Department of Pathology, Duke University Medical Center, Durham, North Carolina
| | - Michael D Gunn
- Division of Cardiology, Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | - Steven D Crowley
- Division of Nephrology, Department of Medicine, Duke University Medical Center, Durham, North Carolina; Durham VA Medical Center, Durham, North Carolina.
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13
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Colton CA, Puranam RS, Vitek MP, Kan MJ. P2‐127: Immune‐Mediated Nutrient Deprivation and Metabolic Disruption in an Alzheimer's Disease Mouse Model. Alzheimers Dement 2016. [DOI: 10.1016/j.jalz.2016.06.1497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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14
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Yu YRA, O’Koren EG, Hotten DF, Kan MJ, Kopin D, Nelson ER, Que L, Gunn MD. A Protocol for the Comprehensive Flow Cytometric Analysis of Immune Cells in Normal and Inflamed Murine Non-Lymphoid Tissues. PLoS One 2016; 11:e0150606. [PMID: 26938654 PMCID: PMC4777539 DOI: 10.1371/journal.pone.0150606] [Citation(s) in RCA: 252] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 02/16/2016] [Indexed: 11/18/2022] Open
Abstract
Flow cytometry is used extensively to examine immune cells in non-lymphoid tissues. However, a method of flow cytometric analysis that is both comprehensive and widely applicable has not been described. We developed a protocol for the flow cytometric analysis of non-lymphoid tissues, including methods of tissue preparation, a 10-fluorochrome panel for cell staining, and a standardized gating strategy, that allows the simultaneous identification and quantification of all major immune cell types in a variety of normal and inflamed non-lymphoid tissues. We demonstrate that our basic protocol minimizes cell loss, reliably distinguishes macrophages from dendritic cells (DC), and identifies all major granulocytic and mononuclear phagocytic cell types. This protocol is able to accurately quantify 11 distinct immune cell types, including T cells, B cells, NK cells, neutrophils, eosinophils, inflammatory monocytes, resident monocytes, alveolar macrophages, resident/interstitial macrophages, CD11b- DC, and CD11b+ DC, in normal lung, heart, liver, kidney, intestine, skin, eyes, and mammary gland. We also characterized the expression patterns of several commonly used myeloid and macrophage markers. This basic protocol can be expanded to identify additional cell types such as mast cells, basophils, and plasmacytoid DC, or perform detailed phenotyping of specific cell types. In examining models of primary and metastatic mammary tumors, this protocol allowed the identification of several distinct tumor associated macrophage phenotypes, the appearance of which was highly specific to individual tumor cell lines. This protocol provides a valuable tool to examine immune cell repertoires and follow immune responses in a wide variety of tissues and experimental conditions.
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Affiliation(s)
- Yen-Rei A. Yu
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
| | - Emily G. O’Koren
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Danielle F. Hotten
- Department of Medicine, Division of Cardiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Matthew J. Kan
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - David Kopin
- School of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Erik R. Nelson
- Department of Molecular & Integrative Physiology, University of Illinois, Champaign, Illinois, United States of America
| | - Loretta Que
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Michael D. Gunn
- Department of Medicine, Division of Cardiology, Duke University Medical Center, Durham, North Carolina, United States of America
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15
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Keum S, Lee HK, Chu PL, Kan MJ, Huang MN, Gallione CJ, Gunn MD, Lo DC, Marchuk DA. Natural genetic variation of integrin alpha L (Itgal) modulates ischemic brain injury in stroke. PLoS Genet 2013; 9:e1003807. [PMID: 24130503 PMCID: PMC3794904 DOI: 10.1371/journal.pgen.1003807] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [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: 03/11/2013] [Accepted: 08/05/2013] [Indexed: 11/18/2022] Open
Abstract
During ischemic stroke, occlusion of the cerebrovasculature causes neuronal cell death (infarction), but naturally occurring genetic factors modulating infarction have been difficult to identify in human populations. In a surgically induced mouse model of ischemic stroke, we have previously mapped Civq1 to distal chromosome 7 as a quantitative trait locus determining infarct volume. In this study, genome-wide association mapping using 32 inbred mouse strains and an additional linkage scan for infarct volume confirmed that the size of the infarct is determined by ancestral alleles of the causative gene(s). The genetically isolated Civq1 locus in reciprocal recombinant congenic mice refined the critical interval and demonstrated that infarct size is determined by both vascular (collateral vessel anatomy) and non-vascular (neuroprotection) effects. Through the use of interval-specific SNP haplotype analysis, we further refined the Civq1 locus and identified integrin alpha L (Itgal) as one of the causative genes for Civq1. Itgal is the only gene that exhibits both strain-specific amino acid substitutions and expression differences. Coding SNPs, a 5-bp insertion in exon 30b, and increased mRNA and protein expression of a splice variant of the gene (Itgal-003, ENSMUST00000120857), all segregate with infarct volume. Mice lacking Itgal show increased neuronal cell death in both ex vivo brain slice and in vivo focal cerebral ischemia. Our data demonstrate that sequence variation in Itgal modulates ischemic brain injury, and that infarct volume is determined by both vascular and non-vascular mechanisms.
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Affiliation(s)
- Sehoon Keum
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Han Kyu Lee
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Pei-Lun Chu
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Matthew J. Kan
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Min-Nung Huang
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Carol J. Gallione
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Michael D. Gunn
- Department of Immunology, Duke University Medical Center, Durham, North Carolina, United States of America
- Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Donald C. Lo
- Center for Drug Discovery and Department of Neurobiology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Douglas A. Marchuk
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
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16
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Cain DW, O'Koren EG, Kan MJ, Womble M, Sempowski GD, Hopper K, Gunn MD, Kelsoe G. Identification of a tissue-specific, C/EBPβ-dependent pathway of differentiation for murine peritoneal macrophages. J Immunol 2013; 191:4665-75. [PMID: 24078688 DOI: 10.4049/jimmunol.1300581] [Citation(s) in RCA: 134] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Macrophages and dendritic cells (DC) are distributed throughout the body and play important roles in pathogen detection and tissue homeostasis. In tissues, resident macrophages exhibit distinct phenotypes and activities, yet the transcriptional pathways that specify tissue-specific macrophages are largely unknown. We investigated the functions and origins of two peritoneal macrophage populations in mice: small and large peritoneal macrophages (SPM and LPM, respectively). SPM and LPM differ in their ability to phagocytose apoptotic cells, as well as in the production of cytokines in response to LPS. In steady-state conditions, SPM are sustained by circulating precursors, whereas LPM are maintained independently of hematopoiesis; however, both populations are replenished by bone marrow precursors following radiation injury. Transcription factor analysis revealed that SPM and LPM express abundant CCAAT/enhancer binding protein (C/EBP)-β. Cebpb(-/-) mice exhibit elevated numbers of SPM-like cells but lack functional LPM. Alveolar macrophages are also missing in Cebpb(-/-) mice, although macrophage populations in the spleen, kidney, skin, mesenteric lymph nodes, and liver are normal. Adoptive transfer of SPM into Cebpb(-/-) mice results in SPM differentiation into LPM, yet donor SPM do not generate LPM after transfer into C/EBPβ-sufficient mice, suggesting that endogenous LPM inhibit differentiation by SPM. We conclude that C/EBPβ plays an intrinsic, tissue-restricted role in the generation of resident macrophages.
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Affiliation(s)
- Derek W Cain
- Department of Immunology, Duke University, Durham, NC 27710
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17
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Meyer EH, Wurbel MA, Staton TL, Pichavant M, Kan MJ, Savage PB, DeKruyff RH, Butcher EC, Campbell JJ, Umetsu DT. iNKT cells require CCR4 to localize to the airways and to induce airway hyperreactivity. J Immunol 2007; 179:4661-71. [PMID: 17878364 PMCID: PMC2564604 DOI: 10.4049/jimmunol.179.7.4661] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
iNKT cells are required for the induction of airway hyperreactivity (AHR), a cardinal feature of asthma, but how iNKT cells traffic to the lungs to induce AHR has not been previously studied. Using several models of asthma, we demonstrated that iNKT cells required the chemokine receptor CCR4 for pulmonary localization and for the induction of AHR. In both allergen-induced and glycolipid-induced models of AHR, wild-type but not CCR4-/- mice developed AHR. Furthermore, adoptive transfer of wild-type but not CCR4-/- iNKT cells reconstituted AHR in iNKT cell-deficient mice. Moreover, we specifically tracked CCR4-/- vs wild-type iNKT cells in CCR4-/-:wild-type mixed BM chimeric mice in the resting state, and when AHR was induced by protein allergen or glycolipid. Using this unique model, we showed that both iNKT cells and conventional T cells required CCR4 for competitive localization into the bronchoalveolar lavage/airways compartment. These results establish for the first time that the pulmonary localization of iNKT cells critical for the induction of AHR requires CCR4 expression by iNKT cells.
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Affiliation(s)
- Everett H. Meyer
- Division of Immunology, Karp Laboratories, Children’s Hospital, Harvard Medical School, Boston, MA 02115
- Immunology Program and School of Medicine, Stanford University, Stanford, CA 94305
| | - Marc-André Wurbel
- Department of Pathology, Harvard Medical School, Boston, MA 02115
- Department of Dermatology, Harvard Medical School, Boston, MA 02115
- Department of Dermatology, Brigham and Women’s Hospital, Boston, MA 02115
| | - Tracy L. Staton
- Immunology Program and School of Medicine, Stanford University, Stanford, CA 94305
| | - Muriel Pichavant
- Division of Immunology, Karp Laboratories, Children’s Hospital, Harvard Medical School, Boston, MA 02115
| | - Matthew J. Kan
- Division of Immunology, Karp Laboratories, Children’s Hospital, Harvard Medical School, Boston, MA 02115
| | - Paul B. Savage
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - Rosemarie H. DeKruyff
- Division of Immunology, Karp Laboratories, Children’s Hospital, Harvard Medical School, Boston, MA 02115
- Immunology Program and School of Medicine, Stanford University, Stanford, CA 94305
| | - Eugene C. Butcher
- Immunology Program and School of Medicine, Stanford University, Stanford, CA 94305
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305
| | - James J. Campbell
- Department of Pathology, Harvard Medical School, Boston, MA 02115
- Department of Dermatology, Harvard Medical School, Boston, MA 02115
- Department of Dermatology, Brigham and Women’s Hospital, Boston, MA 02115
| | - Dale T. Umetsu
- Division of Immunology, Karp Laboratories, Children’s Hospital, Harvard Medical School, Boston, MA 02115
- Immunology Program and School of Medicine, Stanford University, Stanford, CA 94305
- Address correspondence and reprint requests to Dr. Dale T. Umetsu, Division of Immunology, Karp Laboratories, Children’s Hospital, Harvard Medical School, Room 10127, One Blackfan Circle, Boston, MA 02115. E-mail address:
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