1
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Li J, Zaslavsky M, Su Y, Guo J, Sikora M, van Unen V, Christophersen A, Chiou SH, Chen L, Li J, Ji X, Wilhelmy J, McSween A, Palanski B, Mallajosyula V, Bracey N, Dhondalay G, Bhamidipati K, Pai J, Kipp L, Dunn J, Hauser S, Oksenberg J, Satpathy A, Robinson WH, Steinmetz L, Khosla C, Utz P, Sollid L, Chien YH, Heath J, Fernandez-Becker N, Nadeau K, Saligrama N, Davis M. Human KIR+ CD8+ T cells target pathogenic T cells in Celiac disease and are active in autoimmune diseases and COVID-19. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.165.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
Previous reports show a small subset of CD8+ T cells expressing Ly49 proteins in mice can suppress autoimmunity in a model of demyelinating disease. Here we find a markedly increased frequency of CD8+ T cells expressing inhibitory Killer cell Immunoglobulin like Receptors (KIR), the human equivalent of the Ly49 family, in the blood and inflamed tissues of various human autoimmune diseases. Increased KIR+ CD8+ T cells in the gut also correlate with disease activity in Celiac disease (CeD) patients. Moreover, KIR+ CD8+ T cells can efficiently eliminate pathogenic gliadin-specific CD4+ T cells from CeD patients’ leukocytes in vitro. Together with gene expression data, this shows that these cells are the likely equivalent of the mouse Ly49+ CD8+ T cells. Furthermore, we observe elevated levels of KIR+ CD8+ T cells, but not CD4+ regulatory T cells, in COVID-19 and influenza-infected patients, and this correlates with disease severity and vasculitis in COVID-19. Single-cell RNA and parallelized TCR sequencing reveals that expanded KIR+ CD8+ T cells from these different diseases and healthy subjects display shared phenotypes and similar T cell receptor sequences. Selective ablation of the murine counterpart in virus-infected mice leads to exacerbated autoimmunity developed after infection. These results characterize a regulatory CD8+ T cell subset in humans which we hypothesize functions to control pathogenic cells in autoimmune and infectious diseases, with important implications for the cellular dynamics and possible therapeutic approaches to suppress unwanted autoimmunity.
Supported by National Institutes of Health U19-AI057229 Howard Hughes Medical Institute Stanford Diabetes Research Center (P30DK116074)
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Li J, Zaslavsky M, Su Y, Guo J, Sikora MJ, van Unen V, Christophersen A, Chiou SH, Chen L, Li J, Ji X, Wilhelmy J, McSween AM, Palanski BA, Mallajosyula VVA, Bracey NA, Dhondalay GKR, Bhamidipati K, Pai J, Kipp LB, Dunn JE, Hauser SL, Oksenberg JR, Satpathy AT, Robinson WH, Dekker CL, Steinmetz LM, Khosla C, Utz PJ, Sollid LM, Chien YH, Heath JR, Fernandez-Becker NQ, Nadeau KC, Saligrama N, Davis MM. KIR +CD8 + T cells suppress pathogenic T cells and are active in autoimmune diseases and COVID-19. Science 2022; 376:eabi9591. [PMID: 35258337 PMCID: PMC8995031 DOI: 10.1126/science.abi9591] [Citation(s) in RCA: 91] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 10/12/2021] [Accepted: 03/01/2022] [Indexed: 12/13/2022]
Abstract
In this work, we find that CD8+ T cells expressing inhibitory killer cell immunoglobulin-like receptors (KIRs) are the human equivalent of Ly49+CD8+ regulatory T cells in mice and are increased in the blood and inflamed tissues of patients with a variety of autoimmune diseases. Moreover, these CD8+ T cells efficiently eliminated pathogenic gliadin-specific CD4+ T cells from the leukocytes of celiac disease patients in vitro. We also find elevated levels of KIR+CD8+ T cells, but not CD4+ regulatory T cells, in COVID-19 patients, correlating with disease severity and vasculitis. Selective ablation of Ly49+CD8+ T cells in virus-infected mice led to autoimmunity after infection. Our results indicate that in both species, these regulatory CD8+ T cells act specifically to suppress pathogenic T cells in autoimmune and infectious diseases.
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Affiliation(s)
- Jing Li
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Maxim Zaslavsky
- Program in Computer Science, Stanford University, Stanford, CA, USA
| | - Yapeng Su
- Institute for Systems Biology, Seattle, WA, USA
| | - Jing Guo
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael J. Sikora
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Vincent van Unen
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Asbjørn Christophersen
- K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Immunology, University of Oslo, Oslo, Norway
| | - Shin-Heng Chiou
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Liang Chen
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Jiefu Li
- The Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Xuhuai Ji
- Human Immune Monitoring Center, Stanford University School of Medicine, Stanford, CA, USA
| | - Julie Wilhelmy
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Alana M. McSween
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | | | | | - Nathan A. Bracey
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Gopal Krishna R. Dhondalay
- Sean N. Parker Center for Allergy and Asthma Research, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Kartik Bhamidipati
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Joy Pai
- Program in Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Lucas B. Kipp
- Division of Neuroimmunology, Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey E. Dunn
- Division of Neuroimmunology, Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephen L. Hauser
- Department of Neurology and UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Jorge R. Oksenberg
- Department of Neurology and UCSF Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Ansuman T. Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - William H. Robinson
- VA Palo Alto Health Care System, Palo Alto, CA, USA
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Cornelia L. Dekker
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Lars M. Steinmetz
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Chaitan Khosla
- Department of Chemistry, Stanford University, Stanford, CA, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Stanford ChEM-H, Stanford University, Stanford, CA, USA
| | - Paul J. Utz
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Ludvig M. Sollid
- K.G. Jebsen Coeliac Disease Research Centre, University of Oslo, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Immunology, University of Oslo, Oslo, Norway
- Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Yueh-Hsiu Chien
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - James R. Heath
- Institute for Systems Biology, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | | | - Kari C. Nadeau
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- Sean N. Parker Center for Allergy and Asthma Research, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Naresha Saligrama
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark M. Davis
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
- The Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA
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Li J, Zaslavsky M, Su Y, Sikora MJ, van Unen V, Christophersen A, Chiou SH, Chen L, Li J, Ji X, Wilhelmy J, McSween AM, Palanski BA, Aditya Mallajosyula VV, Dhondalay GKR, Bhamidipati K, Pai J, Kipp LB, Dunn JE, Hauser SL, Oksenberg JR, Satpathy AT, Robinson WH, Steinmetz LM, Khosla C, Utz PJ, Sollid LM, Heath JR, Fernandez-Becker NQ, Nadeau KC, Saligrama N, Davis MM. Human KIR + CD8 + T cells target pathogenic T cells in Celiac disease and are active in autoimmune diseases and COVID-19. bioRxiv 2021:2021.12.23.473930. [PMID: 34981055 PMCID: PMC8722592 DOI: 10.1101/2021.12.23.473930] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
UNLABELLED Previous reports show that Ly49 + CD8 + T cells can suppress autoimmunity in mouse models of autoimmune diseases. Here we find a markedly increased frequency of CD8 + T cells expressing inhibitory Killer cell Immunoglobulin like Receptors (KIR), the human equivalent of the Ly49 family, in the blood and inflamed tissues of various autoimmune diseases. Moreover, KIR + CD8 + T cells can efficiently eliminate pathogenic gliadin-specific CD4 + T cells from Celiac disease (CeD) patients' leukocytes in vitro . Furthermore, we observe elevated levels of KIR + CD8 + T cells, but not CD4 + regulatory T cells, in COVID-19 and influenza-infected patients, and this correlates with disease severity and vasculitis in COVID-19. Expanded KIR + CD8 + T cells from these different diseases display shared phenotypes and similar T cell receptor sequences. These results characterize a regulatory CD8 + T cell subset in humans, broadly active in both autoimmune and infectious diseases, which we hypothesize functions to control self-reactive or otherwise pathogenic T cells. ONE-SENTENCE SUMMARY Here we identified KIR + CD8 + T cells as a regulatory CD8 + T cell subset in humans that suppresses self-reactive or otherwise pathogenic CD4 + T cells.
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Chen W, Baal U, Baal J, Pai J, Vasudevan H, Boreta L, Braunstein S, Raleigh D. Efficacy and Safety of Stereotactic Radiosurgery for Brainstem Metastases: A Systematic Review and Comparative Meta-Analysis. Int J Radiat Oncol Biol Phys 2021. [DOI: 10.1016/j.ijrobp.2021.07.1525] [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: 10/20/2022]
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Nagler A, Kalaora S, Barbolin C, Gangaev A, Ketelaars SLC, Alon M, Pai J, Benedek G, Yahalom-Ronen Y, Erez N, Greenberg P, Yagel G, Peri A, Levin Y, Satpathy AT, Bar-Haim E, Paran N, Kvistborg P, Samuels Y. Identification of presented SARS-CoV-2 HLA class I and HLA class II peptides using HLA peptidomics. Cell Rep 2021; 35:109305. [PMID: 34166618 PMCID: PMC8185308 DOI: 10.1016/j.celrep.2021.109305] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 01/17/2021] [Accepted: 06/03/2021] [Indexed: 02/07/2023] Open
Abstract
The human leukocyte antigen (HLA)-bound viral antigens serve as an immunological signature that can be selectively recognized by T cells. As viruses evolve by acquiring mutations, it is essential to identify a range of presented viral antigens. Using HLA peptidomics, we are able to identify severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-derived peptides presented by highly prevalent HLA class I (HLA-I) molecules by using infected cells as well as overexpression of SARS-CoV-2 genes. We find 26 HLA-I peptides and 36 HLA class II (HLA-II) peptides. Among the identified peptides, some are shared between different cells and some are derived from out-of-frame open reading frames (ORFs). Seven of these peptides were previously shown to be immunogenic, and we identify two additional immunoreactive peptides by using HLA multimer staining. These results may aid the development of the next generation of SARS-CoV-2 vaccines based on presented viral-specific antigens that span several of the viral genes.
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Affiliation(s)
- Adi Nagler
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Shelly Kalaora
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Chaya Barbolin
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Anastasia Gangaev
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, the Netherlands
| | - Steven L C Ketelaars
- Division of Molecular Oncology and Immunology, the Netherlands Cancer Institute, the Netherlands
| | - Michal Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Joy Pai
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Gil Benedek
- Tissue Typing and Immunogenetics Unit, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Yfat Yahalom-Ronen
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Noam Erez
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Polina Greenberg
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Gal Yagel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Aviyah Peri
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yishai Levin
- The de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Erez Bar-Haim
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Nir Paran
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Pia Kvistborg
- Tissue Typing and Immunogenetics Unit, Hadassah Medical Organization and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Yardena Samuels
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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Baker J, Qureshi Z, Durrani S, Cao S, Bo N, Pai J, Ellison M, Rawlings L, Sigua N, Manchanda S, Khan B. Assessing physician-patient communication around sleep experience, habits and behaviors through a novel Sleeplife® application-a pilot, feasibility study. Sleep Med 2019. [DOI: 10.1016/j.sleep.2019.11.061] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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7
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Cohen YZ, Lorenzi JCC, Krassnig L, Barton JP, Burke L, Pai J, Lu CL, Mendoza P, Oliveira TY, Sleckman C, Millard K, Butler AL, Dizon JP, Belblidia SA, Witmer-Pack M, Shimeliovich I, Gulick RM, Seaman MS, Jankovic M, Caskey M, Nussenzweig MC. Relationship between latent and rebound viruses in a clinical trial of anti-HIV-1 antibody 3BNC117. J Exp Med 2018; 215:2311-2324. [PMID: 30072495 PMCID: PMC6122972 DOI: 10.1084/jem.20180936] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [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: 05/18/2018] [Revised: 06/19/2018] [Accepted: 07/17/2018] [Indexed: 11/04/2022] Open
Abstract
A clinical trial was performed to evaluate 3BNC117, a potent anti-HIV-1 antibody, in infected individuals during suppressive antiretroviral therapy and subsequent analytical treatment interruption (ATI). The circulating reservoir was evaluated by quantitative and qualitative viral outgrowth assay (Q2VOA) at entry and after 6 mo. There were no significant quantitative changes in the size of the reservoir before ATI, and the composition of circulating reservoir clones varied in a manner that did not correlate with 3BNC117 sensitivity. 3BNC117 binding site amino acid variants found in rebound viruses preexisted in the latent reservoir. However, only 3 of 217 rebound viruses were identical to 868 latent viruses isolated by Q2VOA and near full-length sequencing. Instead, 63% of the rebound viruses appeared to be recombinants, even in individuals with 3BNC117-resistant reservoir viruses. In conclusion, viruses emerging during ATI in individuals treated with 3BNC117 are not the dominant species found in the circulating latent reservoir, but frequently appear to represent recombinants of latent viruses.
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Affiliation(s)
- Yehuda Z Cohen
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Julio C C Lorenzi
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Lisa Krassnig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - John P Barton
- Department of Physics and Astronomy, University of California, Riverside, CA
| | - Leah Burke
- Division of Infectious Diseases, Weill Cornell Medicine, New York, NY
| | - Joy Pai
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Ching-Lan Lu
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Pilar Mendoza
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | | | - Katrina Millard
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Allison L Butler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Juan P Dizon
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Shiraz A Belblidia
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Maggi Witmer-Pack
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Irina Shimeliovich
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Roy M Gulick
- Division of Infectious Diseases, Weill Cornell Medicine, New York, NY
| | - Michael S Seaman
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA
| | - Mila Jankovic
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY .,Howard Hughes Medical Institute, Chevy Chase, MD
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Jacko M, Weyn-Vanhentenryck SM, Smerdon JW, Yan R, Feng H, Williams DJ, Pai J, Xu K, Wichterle H, Zhang C. Rbfox Splicing Factors Promote Neuronal Maturation and Axon Initial Segment Assembly. Neuron 2018; 97:853-868.e6. [PMID: 29398366 PMCID: PMC5823762 DOI: 10.1016/j.neuron.2018.01.020] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 08/28/2017] [Accepted: 01/08/2018] [Indexed: 12/22/2022]
Abstract
Neuronal maturation requires dramatic morphological and functional changes, but the molecular mechanisms governing this process are not well understood. Here, we studied the role of Rbfox1, Rbfox2, and Rbfox3 proteins, a family of tissue-specific splicing regulators mutated in multiple neurodevelopmental disorders. We generated Rbfox triple knockout (tKO) ventral spinal neurons to define a comprehensive network of alternative exons under Rbfox regulation and to investigate their functional importance in the developing neurons. Rbfox tKO neurons exhibit defects in alternative splicing of many cytoskeletal, membrane, and synaptic proteins, and display immature electrophysiological activity. The axon initial segment (AIS), a subcellular structure important for action potential initiation, is diminished upon Rbfox depletion. We identified an Rbfox-regulated splicing switch in ankyrin G, the AIS "interaction hub" protein, that regulates ankyrin G-beta spectrin affinity and AIS assembly. Our data show that the Rbfox-regulated splicing program plays a crucial role in structural and functional maturation of postmitotic neurons.
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Affiliation(s)
- Martin Jacko
- Departments of Systems Biology and Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA; Departments of Pathology and Cell Biology, Neurology, and Neuroscience, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA
| | - Sebastien M Weyn-Vanhentenryck
- Departments of Systems Biology and Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - John W Smerdon
- Departments of Pathology and Cell Biology, Neurology, and Neuroscience, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA; Department of Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA
| | - Rui Yan
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Huijuan Feng
- Departments of Systems Biology and Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA; MOE Key Laboratory of Bioinformatics and Bioinformatics Division, TNLIST/Department of Automation, Tsinghua University, Beijing 100084, China
| | - Damian J Williams
- Columbia University Stem Cell Core Facility, Department of Rehabilitation and Regenerative Medicine, New York, NY 10032, USA
| | - Joy Pai
- Departments of Systems Biology and Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Hynek Wichterle
- Departments of Pathology and Cell Biology, Neurology, and Neuroscience, Center for Motor Neuron Biology and Disease, Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA.
| | - Chaolin Zhang
- Departments of Systems Biology and Biochemistry and Molecular Biophysics, Center for Motor Neuron Biology and Disease, Columbia University, New York, NY 10032, USA.
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Mayer CT, Gazumyan A, Kara EE, Gitlin AD, Golijanin J, Viant C, Pai J, Oliveira TY, Wang Q, Escolano A, Medina-Ramirez M, Sanders RW, Nussenzweig MC. The microanatomic segregation of selection by apoptosis in the germinal center. Science 2017; 358:science.aao2602. [PMID: 28935768 DOI: 10.1126/science.aao2602] [Citation(s) in RCA: 168] [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] [Received: 06/30/2017] [Accepted: 08/29/2017] [Indexed: 01/04/2023]
Abstract
B cells undergo rapid cell division and affinity maturation in anatomically distinct sites in lymphoid organs called germinal centers (GCs). Homeostasis is maintained in part by B cell apoptosis. However, the precise contribution of apoptosis to GC biology and selection is not well defined. We developed apoptosis-indicator mice and used them to visualize, purify, and characterize dying GC B cells. Apoptosis is prevalent in the GC, with up to half of all GC B cells dying every 6 hours. Moreover, programmed cell death is differentially regulated in the light zone and the dark zone: Light-zone B cells die by default if they are not positively selected, whereas dark-zone cells die when their antigen receptors are damaged by activation-induced cytidine deaminase.
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Affiliation(s)
- Christian T Mayer
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Ervin E Kara
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Alexander D Gitlin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Jovana Golijanin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Charlotte Viant
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Joy Pai
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Qiao Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Amelia Escolano
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Max Medina-Ramirez
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, Netherlands
| | - Rogier W Sanders
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, 1105 AZ Amsterdam, Netherlands.,Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY 10065, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA. .,Howard Hughes Medical Institute (HHMI), The Rockefeller University, New York, NY 10065, USA
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10
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Robbiani DF, Bozzacco L, Keeffe JR, Khouri R, Olsen PC, Gazumyan A, Schaefer-Babajew D, Avila-Rios S, Nogueira L, Patel R, Azzopardi SA, Uhl LFK, Saeed M, Sevilla-Reyes EE, Agudelo M, Yao KH, Golijanin J, Gristick HB, Lee YE, Hurley A, Caskey M, Pai J, Oliveira T, Wunder EA, Sacramento G, Nery N, Orge C, Costa F, Reis MG, Thomas NM, Eisenreich T, Weinberger DM, de Almeida ARP, West AP, Rice CM, Bjorkman PJ, Reyes-Teran G, Ko AI, MacDonald MR, Nussenzweig MC. Recurrent Potent Human Neutralizing Antibodies to Zika Virus in Brazil and Mexico. Cell 2017; 169:597-609.e11. [PMID: 28475892 PMCID: PMC5492969 DOI: 10.1016/j.cell.2017.04.024] [Citation(s) in RCA: 237] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 04/17/2017] [Accepted: 04/17/2017] [Indexed: 01/20/2023]
Abstract
Antibodies to Zika virus (ZIKV) can be protective. To examine the antibody response in individuals who develop high titers of anti-ZIKV antibodies, we screened cohorts in Brazil and Mexico for ZIKV envelope domain III (ZEDIII) binding and neutralization. We find that serologic reactivity to dengue 1 virus (DENV1) EDIII before ZIKV exposure is associated with increased ZIKV neutralizing titers after exposure. Antibody cloning shows that donors with high ZIKV neutralizing antibody titers have expanded clones of memory B cells that express the same immunoglobulin VH3-23/VK1-5 genes. These recurring antibodies cross-react with DENV1, but not other flaviviruses, neutralize both DENV1 and ZIKV, and protect mice against ZIKV challenge. Structural analyses reveal the mechanism of recognition of the ZEDIII lateral ridge by VH3-23/VK1-5 antibodies. Serologic testing shows that antibodies to this region correlate with serum neutralizing activity to ZIKV. Thus, high neutralizing responses to ZIKV are associated with pre-existing reactivity to DENV1 in humans.
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Affiliation(s)
- Davide F Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA.
| | - Leonia Bozzacco
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Jennifer R Keeffe
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ricardo Khouri
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz/MS, Salvador, Bahia CEP 40296-710, Brazil
| | - Priscilla C Olsen
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Anna Gazumyan
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | | | | | - Lilian Nogueira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Roshni Patel
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Stephanie A Azzopardi
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Lion F K Uhl
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Mohsan Saeed
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | | | - Marianna Agudelo
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Kai-Hui Yao
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Jovana Golijanin
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Harry B Gristick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yu E Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Arlene Hurley
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Joy Pai
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Thiago Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Elsio A Wunder
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz/MS, Salvador, Bahia CEP 40296-710, Brazil; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06520, USA
| | - Gielson Sacramento
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz/MS, Salvador, Bahia CEP 40296-710, Brazil
| | - Nivison Nery
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz/MS, Salvador, Bahia CEP 40296-710, Brazil
| | - Cibele Orge
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz/MS, Salvador, Bahia CEP 40296-710, Brazil
| | - Federico Costa
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz/MS, Salvador, Bahia CEP 40296-710, Brazil; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06520, USA; Faculdade de Medicina da Bahia and Instituto da Saúde Coletiva, Universidade Federal da Bahia, Salvador, Bahia CEP 40296-710, Brazil
| | - Mitermayer G Reis
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz/MS, Salvador, Bahia CEP 40296-710, Brazil; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06520, USA; Faculdade de Medicina da Bahia and Instituto da Saúde Coletiva, Universidade Federal da Bahia, Salvador, Bahia CEP 40296-710, Brazil
| | - Neena M Thomas
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Thomas Eisenreich
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Daniel M Weinberger
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06520, USA
| | - Antonio R P de Almeida
- Faculdade de Medicina da Bahia and Instituto da Saúde Coletiva, Universidade Federal da Bahia, Salvador, Bahia CEP 40296-710, Brazil
| | - Anthony P West
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Pamela J Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Albert I Ko
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz/MS, Salvador, Bahia CEP 40296-710, Brazil; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06520, USA
| | - Margaret R MacDonald
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA.
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA.
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Wang Q, Kieffer-Kwon KR, Oliveira TY, Mayer CT, Yao K, Pai J, Cao Z, Dose M, Casellas R, Jankovic M, Nussenzweig MC, Robbiani DF. The cell cycle restricts activation-induced cytidine deaminase activity to early G1. J Exp Med 2016; 214:49-58. [PMID: 27998928 PMCID: PMC5206505 DOI: 10.1084/jem.20161649] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [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: 09/29/2016] [Revised: 10/21/2016] [Accepted: 11/22/2016] [Indexed: 02/02/2023] Open
Abstract
Wang et al. show that antibody gene deamination by activation-induced cytidine deaminase (AID) is restricted to a short time window in early G1 as a result of AID’s transient nuclear localization and accessibility of the target sites. Activation-induced cytidine deaminase (AID) converts cytosine into uracil to initiate somatic hypermutation (SHM) and class switch recombination (CSR) of antibody genes. In addition, this enzyme produces DNA lesions at off-target sites that lead to mutations and chromosome translocations. However, AID is mostly cytoplasmic, and how and exactly when it accesses nuclear DNA remains enigmatic. Here, we show that AID is transiently in spatial contact with genomic DNA from the time the nuclear membrane breaks down in prometaphase until early G1, when it is actively exported into the cytoplasm. Consistent with this observation, the immunoglobulin (Igh) gene deamination as measured by uracil accumulation occurs primarily in early G1 after chromosomes decondense. Altering the timing of cell cycle–regulated AID nuclear residence increases DNA damage at off-target sites. Thus, the cell cycle–controlled breakdown and reassembly of the nuclear membrane and the restoration of transcription after mitosis constitute an essential time window for AID-induced deamination, and provide a novel DNA damage mechanism restricted to early G1.
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Affiliation(s)
- Qiao Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
| | - Kyong-Rim Kieffer-Kwon
- Genomics and Immunity, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892.,Center of Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Thiago Y Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
| | - Christian T Mayer
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
| | - Kaihui Yao
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
| | - Joy Pai
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
| | - Zhen Cao
- Weill Cornell Medical College and Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Marei Dose
- Genomics and Immunity, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892.,Center of Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Rafael Casellas
- Genomics and Immunity, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892.,Center of Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Mila Jankovic
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065 .,Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065
| | - Davide F Robbiani
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065
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Park KH, Pai J, Song DG, Sim DW, Park HJ, Lee JH, Jeong KY, Pan CH, Shin I, Park JW. Ranitidine-induced anaphylaxis: clinical features, cross-reactivity, and skin testing. Clin Exp Allergy 2016; 46:631-9. [PMID: 26764898 DOI: 10.1111/cea.12708] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [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: 08/18/2015] [Revised: 11/05/2015] [Accepted: 12/13/2015] [Indexed: 12/11/2022]
Abstract
BACKGROUND Histamine H2 receptor antagonists are commonly prescribed medications and are known to be well tolerated. However, 99 cases of ranitidine-induced anaphylaxis occurred in Korea from 2007 to 2014. OBJECTIVE The purpose of this study was to determine the incidence, clinical features, and diagnostic methods for ranitidine-induced anaphylaxis. METHODS Ranitidine-related pharmacovigilance data from 2007 to 2014 were reviewed. Adverse drug reactions with causal relationships were selected, and clinical manifestations, outcomes, and drug-related information were assessed. For further investigation, 8 years of pharmacovigilance data were collected at a single centre. Twenty-three patients participated in in vivo and in vitro studies. Skin tests, oral provocation tests, and laboratory tests were performed, including tests using other kinds of histamine H2 receptor antagonists. RESULTS Over 7 years, 584 patients suffered adverse reactions to ranitidine. The most common manifestation was cutaneous symptoms. Among them, 99 patients (17.0%) experienced anaphylaxis. In a single-centre study, skin prick tests were positive in 91.7% of ranitidine-induced anaphylaxis patients (11/12); the optimal concentration was 20 mg/mL. Detection of ranitidine-specific immunoglobulin E failed. Cimetidine and proton pump inhibitors showed no cross-reactivity with ranitidine based on the skin prick test, oral provocation test, or clinical determination. Surprisingly, 82.6% of patients reintroduced ranitidine and re-experienced the same adverse reactions because ranitidine was not considered the culprit drug. CONCLUSIONS AND CLINICAL RELEVANCE Although ranitidine is known as a safe drug, it can also cause diverse adverse reactions, including anaphylaxis. This study demonstrates the need to pay attention to adverse reactions to ranitidine and consider ranitidine as a cause of anaphylaxis.
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Affiliation(s)
- K H Park
- Division of Allergy and Immunology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea.,Institute of Allergy, Yonsei University College of Medicine, Seoul, Korea
| | - J Pai
- Department of Chemistry, Yonsei University, Seoul, Korea
| | - D-G Song
- Laboratory of Biomodulation, KIST Gangneung Institute of Natural Products, Gangneung, Korea
| | - D W Sim
- Division of Allergy and Immunology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea.,Institute of Allergy, Yonsei University College of Medicine, Seoul, Korea
| | - H J Park
- Division of Allergy and Immunology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea.,Institute of Allergy, Yonsei University College of Medicine, Seoul, Korea
| | - J-H Lee
- Division of Allergy and Immunology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea.,Institute of Allergy, Yonsei University College of Medicine, Seoul, Korea
| | - K Y Jeong
- Institute of Allergy, Yonsei University College of Medicine, Seoul, Korea
| | - C-H Pan
- Laboratory of Biomodulation, KIST Gangneung Institute of Natural Products, Gangneung, Korea.,Department of Biological Chemistry, Korea University of Science and Technology (UST), Daejeon, Korea
| | - I Shin
- Department of Chemistry, Yonsei University, Seoul, Korea
| | - J-W Park
- Division of Allergy and Immunology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea.,Institute of Allergy, Yonsei University College of Medicine, Seoul, Korea
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Pai J, Behr S, Anwar M. Radiographic and Biochemical Predictors of Outcome After Stereotactic Body Radiation Therapy in HCC With Poor Liver Function. Int J Radiat Oncol Biol Phys 2016. [DOI: 10.1016/j.ijrobp.2016.06.1057] [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: 10/20/2022]
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Osmundson E, Newman A, Bratman S, Klass D, Zhou L, Pai J, Longacre T, Alizadeh A, Koong A, Diehn M. Circulating Tumor DNA as a Biomarker for Pancreatic Adenocarcinoma. Int J Radiat Oncol Biol Phys 2014. [DOI: 10.1016/j.ijrobp.2014.05.2354] [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: 11/27/2022]
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15
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Pai J, Wang Z, Shaffer J, Gibbs I, Chang D, Koong A, Chang S, Harsh G, Li G, Soltys S. Brain Metastases and Resection Cavities From Colorectal Carcinoma Treated With Stereotactic Radiosurgery Have Poor Local Control Compared to Noncolorectal Histology. Int J Radiat Oncol Biol Phys 2013. [DOI: 10.1016/j.ijrobp.2013.06.415] [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: 11/29/2022]
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16
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Pai J, Chiu W, Shultz D, Graber M, Columbo L, Wild A, Kumar R, Herman J, Chang D, Koong A. Plasma SPARC Following Stereotactic Body Radiation Therapy (SBRT) Predicts for Progression-Free Survival in Locally-Advanced Pancreatic Cancer. Int J Radiat Oncol Biol Phys 2013. [DOI: 10.1016/j.ijrobp.2013.06.1771] [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: 11/28/2022]
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17
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Chou Y, Gau J, Liu J, Yu Y, Pai J, Hsiao L, Hong Y, Liu C, Chen P, Tzeng C. Leukocytosis in Polycythemia Vera and Splenomegaly in Essential Thrombocythemia Are Independent Risk Factors of Hemorrhage. Ann Oncol 2012. [DOI: 10.1016/s0923-7534(20)33643-7] [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: 10/25/2022] Open
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Kader H, Ansbacher W, Popescu C, Panadés M, Pai J, Nguyen D, Truong P. 625 poster PROSPECTIVE STUDY OF PARTIAL BREAST IRRADIATION USING HIGH DOSE RATE INTERSTITIAL BRACHYTHERAPY: SEVEN-YEAR OUTCOMES. Radiother Oncol 2011. [DOI: 10.1016/s0167-8140(11)70747-2] [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: 11/26/2022]
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Burgess S, Thompson SG, Burgess S, Thompson SG, Andrews G, Samani NJ, Hall A, Whincup P, Morris R, Lawlor DA, Davey Smith G, Timpson N, Ebrahim S, Ben-Shlomo Y, Davey Smith G, Timpson N, Brown M, Ricketts S, Sandhu M, Reiner A, Psaty B, Lange L, Cushman M, Hung J, Thompson P, Beilby J, Warrington N, Palmer LJ, Nordestgaard BG, Tybjaerg-Hansen A, Zacho J, Wu C, Lowe G, Tzoulaki I, Kumari M, Sandhu M, Yamamoto JF, Chiodini B, Franzosi M, Hankey GJ, Jamrozik K, Palmer L, Rimm E, Pai J, Psaty B, Heckbert S, Bis J, Anand S, Engert J, Collins R, Clarke R, Melander O, Berglund G, Ladenvall P, Johansson L, Jansson JH, Hallmans G, Hingorani A, Humphries S, Rimm E, Manson J, Pai J, Watkins H, Clarke R, Hopewell J, Saleheen D, Frossard R, Danesh J, Sattar N, Robertson M, Shepherd J, Schaefer E, Hofman A, Witteman JCM, Kardys I, Ben-Shlomo Y, Davey Smith G, Timpson N, de Faire U, Bennet A, Sattar N, Ford I, Packard C, Kumari M, Manson J, Lawlor DA, Davey Smith G, Anand S, Collins R, Casas JP, Danesh J, Davey Smith G, Franzosi M, Hingorani A, Lawlor DA, Manson J, Nordestgaard BG, Samani NJ, Sandhu M, Smeeth L, Wensley F, Anand S, Bowden J, Burgess S, Casas JP, Di Angelantonio E, Engert J, Gao P, Shah T, Smeeth L, Thompson SG, Verzilli C, Walker M, Whittaker J, Hingorani A, Danesh J. Bayesian methods for meta-analysis of causal relationships estimated using genetic instrumental variables. Stat Med 2010; 29:1298-311. [PMID: 20209660 DOI: 10.1002/sim.3843] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Genetic markers can be used as instrumental variables, in an analogous way to randomization in a clinical trial, to estimate the causal relationship between a phenotype and an outcome variable. Our purpose is to extend the existing methods for such Mendelian randomization studies to the context of multiple genetic markers measured in multiple studies, based on the analysis of individual participant data. First, for a single genetic marker in one study, we show that the usual ratio of coefficients approach can be reformulated as a regression with heterogeneous error in the explanatory variable. This can be implemented using a Bayesian approach, which is next extended to include multiple genetic markers. We then propose a hierarchical model for undertaking a meta-analysis of multiple studies, in which it is not necessary that the same genetic markers are measured in each study. This provides an overall estimate of the causal relationship between the phenotype and the outcome, and an assessment of its heterogeneity across studies. As an example, we estimate the causal relationship of blood concentrations of C-reactive protein on fibrinogen levels using data from 11 studies. These methods provide a flexible framework for efficient estimation of causal relationships derived from multiple studies. Issues discussed include weak instrument bias, analysis of binary outcome data such as disease risk, missing genetic data, and the use of haplotypes.
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Danesh J, Erqou S, Walker M, Thompson SG, Tipping R, Ford C, Pressel S, Walldius G, Jungner I, Folsom AR, Chambless LE, Knuiman M, Whincup PH, Wannamethee SG, Morris RW, Willeit J, Kiechl S, Santer P, Mayr A, Wald N, Ebrahim S, Lawlor DA, Yarnell JWG, Gallacher J, Casiglia E, Tikhonoff V, Nietert PJ, Sutherland SE, Bachman DL, Keil JE, Cushman M, Psaty BM, Tracy RP, Tybjaerg-Hansen A, Nordestgaard BG, Frikke-Schmidt R, Giampaoli S, Palmieri L, Panico S, Vanuzzo D, Pilotto L, Simons L, McCallum J, Friedlander Y, Fowkes FGR, Lee AJ, Smith FB, Taylor J, Guralnik J, Phillips C, Wallace R, Blazer D, Khaw KT, Jansson JH, Donfrancesco C, Salomaa V, Harald K, Jousilahti P, Vartiainen E, Woodward M, D'Agostino RB, Wolf PA, Vasan RS, Pencina MJ, Bladbjerg EM, Jorgensen T, Moller L, Jespersen J, Dankner R, Chetrit A, Lubin F, Rosengren A, Wilhelmsen L, Lappas G, Eriksson H, Bjorkelund C, Cremer P, Nagel D, Tilvis R, Strandberg T, Rodriguez B, Bouter LM, Heine RJ, Dekker JM, Nijpels G, Stehouwer CDA, Rimm E, Pai J, Sato S, Iso H, Kitamura A, Noda H, Goldbourt U, Salomaa V, Salonen JT, Nyyssönen K, Tuomainen TP, Deeg D, Poppelaars JL, Meade T, Cooper J, Hedblad B, Berglund G, Engstrom G, Döring A, Koenig W, Meisinger C, Mraz W, Kuller L, Selmer R, Tverdal A, Nystad W, Gillum R, Mussolino M, Hankinson S, Manson J, De Stavola B, Knottenbelt C, Cooper JA, Bauer KA, Rosenberg RD, Sato S, Naito Y, Holme I, Nakagawa H, Miura H, Ducimetiere P, Jouven X, Crespo C, Garcia-Palmieri M, Amouyel P, Arveiler D, Evans A, Ferrieres J, Schulte H, Assmann G, Shepherd J, Packard C, Sattar N, Cantin B, Lamarche B, Després JP, Dagenais GR, Barrett-Connor E, Wingard D, Bettencourt R, Gudnason V, Aspelund T, Sigurdsson G, Thorsson B, Trevisan M, Witteman J, Kardys I, Breteler M, Hofman A, Tunstall-Pedoe H, Tavendale R, Lowe GDO, Ben-Shlomo Y, Howard BV, Zhang Y, Best L, Umans J, Onat A, Meade TW, Njolstad I, Mathiesen E, Lochen ML, Wilsgaard T, Gaziano JM, Stampfer M, Ridker P, Ulmer H, Diem G, Concin H, Rodeghiero F, Tosetto A, Brunner E, Shipley M, Buring J, Cobbe SM, Ford I, Robertson M, He Y, Ibanez AM, Feskens EJM, Kromhout D, Collins R, Di Angelantonio E, Kaptoge S, Lewington S, Orfei L, Pennells L, Perry P, Ray K, Sarwar N, Scherman M, Thompson A, Watson S, Wensley F, White IR, Wood AM. The Emerging Risk Factors Collaboration: analysis of individual data on lipid, inflammatory and other markers in over 1.1 million participants in 104 prospective studies of cardiovascular diseases. Eur J Epidemiol 2007; 22:839-69. [PMID: 17876711 DOI: 10.1007/s10654-007-9165-7] [Citation(s) in RCA: 132] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2007] [Accepted: 07/02/2007] [Indexed: 01/22/2023]
Abstract
Many long-term prospective studies have reported on associations of cardiovascular diseases with circulating lipid markers and/or inflammatory markers. Studies have not, however, generally been designed to provide reliable estimates under different circumstances and to correct for within-person variability. The Emerging Risk Factors Collaboration has established a central database on over 1.1 million participants from 104 prospective population-based studies, in which subsets have information on lipid and inflammatory markers, other characteristics, as well as major cardiovascular morbidity and cause-specific mortality. Information on repeat measurements on relevant characteristics has been collected in approximately 340,000 participants to enable estimation of and correction for within-person variability. Re-analysis of individual data will yield up to approximately 69,000 incident fatal or nonfatal first ever major cardiovascular outcomes recorded during about 11.7 million person years at risk. The primary analyses will involve age-specific regression models in people without known baseline cardiovascular disease in relation to fatal or nonfatal first ever coronary heart disease outcomes. This initiative will characterize more precisely and in greater detail than has previously been possible the shape and strength of the age- and sex-specific associations of several lipid and inflammatory markers with incident coronary heart disease outcomes (and, secondarily, with other incident cardiovascular outcomes) under a wide range of circumstances. It will, therefore, help to determine to what extent such associations are independent from possible confounding factors and to what extent such markers (separately and in combination) provide incremental predictive value.
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Allen RT, Pai J, Bovard K, Hunter WJ, Agrawal DK. Immunogold staining for Bcl-xL and morphological analysis of rat and human vascular smooth muscle cells undergoing apoptosis induced by c-myc or staurosporine. Scanning 1998; 20:207-208. [PMID: 9604385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
MESH Headings
- Animals
- Apoptosis/drug effects
- Apoptosis/genetics
- Humans
- Immunohistochemistry
- Insulin-Like Growth Factor I/analysis
- Microscopy, Electron, Scanning/methods
- Microscopy, Electron, Scanning Transmission/methods
- Microscopy, Video/methods
- Muscle, Smooth, Vascular/drug effects
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/ultrastructure
- Proto-Oncogene Proteins c-bcl-2/analysis
- Proto-Oncogene Proteins c-myc/metabolism
- Rats
- Staurosporine/pharmacology
- bcl-X Protein
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Affiliation(s)
- R T Allen
- Department of Medicine, Creighton University School of Medicine, Omaha, Nebraska, USA
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Abstract
Chlamydia pneumoniae, a respiratory pathogen, has been associated with occlusive vascular disease, including atherosclerosis and intimal hyperplasia, through seroepidemiologic studies. Furthermore, using immunohistochemistry (IHC), polymerase chain reaction (PCR), transmission electron microscopy (TEM), and in situ hybridization, this association has been reconfirmed by detecting this organism in atherosclerotic vascular tissue. This review summarizes and critically analyzes these findings and also discusses various mechanisms of how Chlamydia pneumoniae could be involved in the pathogenesis of occlusive vascular disease. Although more studies are needed to reproduce these results and, possibly, uncover a mechanism, the current literature fails to include detailed methodologies for studying Chlamydia pneumoniae. Therefore, to provide a general standard, we have also outlined specific protocols for IHC, PCR, and TEM. These protocols incorporate essential components from various studies and are presented in a concise and easily adaptable format.
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Affiliation(s)
- J Pai
- Department of Internal Medicine, Creighton University School of Medicine, Omaha, Nebraska 68178, USA
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Passfall J, Pai J, Spies KP, Haller H, Luft FC. Effect of water and bicarbonate loading in patients with chronic renal failure. Clin Nephrol 1997; 47:92-8. [PMID: 9049456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Animal studies suggest that alkalinization and increased intake of free water both serve to decrease the rate of progression in chronic renal failure. However, clinicians have been reluctant to apply either strategy because of concerns regarding volume overload and water intoxication. We tested the effects of 2 1 daily water supplementation, with either an electrolyte-poor or a HCO3-rich (47.5 mmol/1) water in 11 patients with chronic renal failure (creatinine clearance 10 +/- 5 ml/min). The patients were brought into balance on a diet containing 80 mmol/24 h Na+, 80 mmol/24 h Cl- and 70 mmol/24 h K+. After a 3-day equilibration period, the patients were randomized to one or the other regimen for 7 days. After a 3-day washout period, the alternate regimen was given for another 7 days. Neither regimen led to weight gain or hyponatremia. The supplemental 95 mmol/24 h HCO3- lowered the serum Cl- concentration and raised the serum HCO3- concentration, as well as the pH value, to normal. Creatinine clearance and protein excretion were not affected. Serum beta 2-microglobulin concentrations decreased with the NaHCO3-containing water. Na+/H(+)-antiporter activity was not consistently influenced since an order effect of the regimens was apparent. We conclude that 2 1/24 h water and NaHCO3 supplementation is well tolerated, causes no deleterious effects, and may evoke improvement in patients with chronic renal failure.
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Affiliation(s)
- J Passfall
- Franz Volhard Clinic, Humboldt University of Berlin, Germany
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Abstract
The phospholipase D-inhibitory activity of a methanol extract from the leaves of a New Zealand plant, Myrsine australis, has been attributed to two new saponins 1 and 2. Compound 1 was assigned as 3-0-[-beta-D-xylopyranosyl-(1-->2)-0-beta-D-glucopyranosyl-(1-->4)- -[0-beta-D -glucopyranosyl-(1-->2)]-alpha-L-arabinosyl]-16alpha-hydroxy-+ ++13beta,28-epoxyoleanane and 2 as 3beta-0-[-beta-rhamnopyranosyl-(1-->2)-0-beta-D-glucopyranosyl-(1-->4)-[ 0-beta-D-glucopranosyl]-alpha-L-arabinopyranosyl]-16alpha -hydroxy-13beta, 28-epoxyleanane. Compounds 1 and 2 showed IC50 values of 3 and 2 microM, respectively, versus phorbol 12-myrisate-13-acetate-stimulated phosphlipase D in human promyelocytic leukemic (HL-60) cells. Compounds 1 and 2 also inhibited fMLP (formyl-Met-Leu-Phe) stimulated phospholipase D with IC50 values of 8 and 24 microM, respectively.
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Affiliation(s)
- V R Hegde
- Schering-Plough Research Institute, Kenilworth, New Jersey 07033, USA
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