1
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Bouffi C, Wikenheiser-Brokamp KA, Chaturvedi P, Sundaram N, Goddard GR, Wunderlich M, Brown NE, Staab JF, Latanich R, Zachos NC, Holloway EM, Mahe MM, Poling HM, Vales S, Fisher GW, Spence JR, Mulloy JC, Zorn AM, Wells JM, Helmrath MA. In vivo development of immune tissue in human intestinal organoids transplanted into humanized mice. Nat Biotechnol 2023; 41:824-831. [PMID: 36702898 PMCID: PMC10264243 DOI: 10.1038/s41587-022-01558-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 10/07/2022] [Indexed: 01/27/2023]
Abstract
Human intestinal organoids (HIOs) derived from pluripotent stem cells provide a valuable model for investigating human intestinal organogenesis and physiology, but they lack the immune components required to fully recapitulate the complexity of human intestinal biology and diseases. To address this issue and to begin to decipher human intestinal-immune crosstalk during development, we generated HIOs containing immune cells by transplanting HIOs under the kidney capsule of mice with a humanized immune system. We found that human immune cells temporally migrate to the mucosa and form cellular aggregates that resemble human intestinal lymphoid follicles. Moreover, after microbial exposure, epithelial microfold cells are increased in number, leading to immune cell activation determined by the secretion of IgA antibodies in the HIO lumen. This in vivo HIO system with human immune cells provides a framework for future studies on infection- or allergen-driven intestinal diseases.
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Affiliation(s)
- Carine Bouffi
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Kathryn A Wikenheiser-Brokamp
- Division of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pathology and Laboratory Medicine, University of Cincinnati, Cincinnati, OH, USA
| | - Praneet Chaturvedi
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Nambirajan Sundaram
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Gillian R Goddard
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Mark Wunderlich
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Nicole E Brown
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Janet F Staab
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rachel Latanich
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nicholas C Zachos
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Emily M Holloway
- Université de Nantes, Inserm, TENS, The Enteric Nervous System in Gut and Brain Diseases, IMAD, Nantes, France
| | - Maxime M Mahe
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Université de Nantes, Inserm, TENS, The Enteric Nervous System in Gut and Brain Diseases, IMAD, Nantes, France
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Holly M Poling
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Simon Vales
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Garrett W Fisher
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jason R Spence
- Division of Gastroenterology, Department of Internal Medicine, Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI, USA
| | - James C Mulloy
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Aaron M Zorn
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - James M Wells
- Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Michael A Helmrath
- Division of Pediatric General and Thoracic Surgery, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Center for Stem Cell and Organoid Medicine (CuSTOM), Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA.
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2
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Laky K, Kinard JL, Li JM, Moore IN, Lack J, Fischer ER, Kabat J, Latanich R, Zachos NC, Limkar AR, Weissler KA, Thompson RW, Wynn TA, Dietz HC, Guerrerio AL, Frischmeyer-Guerrerio PA. Epithelial-intrinsic defects in TGFβR signaling drive local allergic inflammation manifesting as eosinophilic esophagitis. Sci Immunol 2023; 8:eabp9940. [PMID: 36608150 PMCID: PMC10106118 DOI: 10.1126/sciimmunol.abp9940] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Allergic diseases are a global health challenge. Individuals harboring loss-of-function variants in transforming growth factor-β receptor (TGFβR) genes have an increased prevalence of allergic disorders, including eosinophilic esophagitis. Allergic diseases typically localize to mucosal barriers, implicating epithelial dysfunction as a cardinal feature of allergic disease. Here, we describe an essential role for TGFβ in the control of tissue-specific immune homeostasis that provides mechanistic insight into these clinical associations. Mice expressing a TGFβR1 loss-of-function variant identified in atopic patients spontaneously develop disease that clinically, immunologically, histologically, and transcriptionally recapitulates eosinophilic esophagitis. In vivo and in vitro, TGFβR1 variant-expressing epithelial cells are hyperproliferative, fail to differentiate properly, and overexpress innate proinflammatory mediators, which persist in the absence of lymphocytes or external allergens. Together, our results support the concept that TGFβ plays a fundamental, nonredundant, epithelial cell-intrinsic role in controlling tissue-specific allergic inflammation that is independent of its role in adaptive immunity.
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Affiliation(s)
- Karen Laky
- Food Allergy Research Section, Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jessica L Kinard
- Food Allergy Research Section, Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jenny Min Li
- Food Allergy Research Section, Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ian N Moore
- Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Justin Lack
- Collaborative Bioinformatics Resource, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.,Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Elizabeth R Fischer
- Electron Microscopy Unit, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Juraj Kabat
- Biological Imaging Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rachel Latanich
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Nicholas C Zachos
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Ajinkya R Limkar
- Inflammation Immunobiology Section, Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Katherine A Weissler
- Food Allergy Research Section, Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Robert W Thompson
- Immunopathogenesis Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Thomas A Wynn
- Immunopathogenesis Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Harry C Dietz
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Anthony L Guerrerio
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Pamela A Frischmeyer-Guerrerio
- Food Allergy Research Section, Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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3
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Staab JF, Lemme-Dumit JM, Latanich R, Pasetti MF, Zachos NC. Co-culturing Human Intestinal Enteroid Monolayers with Innate Immune Cells. Methods Mol Biol 2023; 2650:207-223. [PMID: 37310634 DOI: 10.1007/978-1-0716-3076-1_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The coordinated interaction between the intestinal epithelium and immune cells is required to maintain proper barrier function and mucosal host defenses to the harsh external environment of the gut lumen. Complementary to in vivo models, there is a need for practical and reproducible in vitro models that employ primary human cells to confirm and advance our understanding of mucosal immune responses under physiologic and pathophysiologic conditions. Here we describe the methods to co-culture human intestinal stem cell-derived enteroids grown as confluent monolayers on permeable supports with primary human innate immune cells (e.g., monocyte-derived macrophages and polymorphonuclear neutrophils). This co-culture model reconstructs the cellular framework of the human intestinal epithelial-immune niche with distinct apical and basolateral compartments to recreate host responses to luminal and submucosal challenges, respectively. Enteroid-immune co-cultures enable multiple outcome measures to interrogate important biological processes such as epithelial barrier integrity, stem cell biology, cellular plasticity, epithelial-immune cells crosstalk, immune cell effector functions, changes in gene expression (i.e., transcriptomic, proteomic, epigenetic), and host-microbiome interactions.
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Affiliation(s)
- Janet F Staab
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jose M Lemme-Dumit
- Department of Pediatrics, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Rachel Latanich
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marcela F Pasetti
- Department of Pediatrics, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Nicholas C Zachos
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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4
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Staab J, Doucet M, Latanich R, Lencer WI, Zachos NC. Coronin 1A is Uniquely Expressed in the Human Follicle Associated Epithelium and is Required For Human M Cell Maturation and Function. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r6087] [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: 11/11/2022]
Affiliation(s)
- Janet Staab
- Johns Hopkins University School of MedicineBaltimoreMD
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5
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Abstract
Human intestinal enteroids derived from adult stem cells offer a relevant ex vivo system to study biological processes of the human gut. They recreate cellular and functional features of the intestinal epithelium of the small intestine (enteroids) or colon (colonoids) albeit limited by the lack of associated cell types that help maintain tissue homeostasis and respond to external challenges. In the gut, innate immune cells interact with the epithelium, support barrier function, and deploy effector functions. We have established a co-culture system of enteroid/colonoid monolayers and underlying macrophages and polymorphonuclear neutrophils to recapitulate the cellular framework of the human intestinal epithelial niche. Enteroids are generated from biopsies or resected tissue from any segment of the human gut and maintained in long-term cultures as three-dimensional structures through supplementation of stem cell growth factors. Immune cells are isolated from fresh human whole blood or frozen peripheral blood mononuclear cells (PBMC). Monocytes from PBMC are differentiated into macrophages by cytokine stimulation prior to co-culture. The methods are divided into the two main components of the model: (1) generating enteroid/colonoid monolayers and isolating immune cells and (2) assembly of enteroid/colonoid-immune cell co-cultures with separate apical and basolateral compartments. Co-cultures containing macrophages can be maintained for 48 hr while those involving neutrophils, due to their shorter life span, remain viable for 4 hr. Enteroid-immune co-cultures enable multiple outcome measures, including transepithelial resistance, production of cytokines/chemokines, phenotypic analysis of immune cells, tissue immunofluorescence imaging, protein or mRNA expression, antigen or microbe uptake, and other cellular functions. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Seeding enteroid fragments onto Transwells for monolayer formation Alternate Protocol: Seeding enteroid fragments for monolayer formation using trituration Basic Protocol 2: Isolation of monocytes and derivation of immune cells from human peripheral blood Basic Protocol 3: Isolation of neutrophils from human peripheral blood Basic Protocol 4: Assembly of enteroid/macrophage or enteroid/neutrophil co-culture.
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Affiliation(s)
- Janet F Staab
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jose M Lemme-Dumit
- Department of Pediatrics, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland
| | - Rachel Latanich
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Marcella F Pasetti
- Department of Pediatrics, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland
| | - Nicholas C Zachos
- Department of Medicine, Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, Maryland
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6
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Wang E, Thombre R, Shah Y, Latanich R, Wang J. G-Quadruplexes as pathogenic drivers in neurodegenerative disorders. Nucleic Acids Res 2021; 49:4816-4830. [PMID: 33784396 PMCID: PMC8136783 DOI: 10.1093/nar/gkab164] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 02/20/2021] [Accepted: 03/29/2021] [Indexed: 12/12/2022] Open
Abstract
G-quadruplexes (G4s), higher-order DNA and RNA secondary structures featuring guanine-rich nucleic acid sequences with various conformations, are widely distributed in the human genome. These structural motifs are known to participate in basic cellular processes, including transcription, splicing, and translation, and their functions related to health and disease are becoming increasingly recognized. In this review, we summarize the landscape of G4s involved in major neurodegenerative disorders, describing the genes that contain G4-forming sequences and proteins that have high affinity for G4-containing elements. The functions of G4s are diverse, with potentially protective or deleterious effects in the pathogenic cascades of various neurological diseases. While the studies of the functions of G4s in vivo, including those involved in pathophysiology, are still in their early stages, we will nevertheless discuss the evidence pointing to their biological relevance. A better understanding of this unique structural element in the biological context is important for unveiling its potential roles in the pathogenesis of diseases such as neurodegeneration and for designing new diagnostic and therapeutic strategies.
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Affiliation(s)
- Ernest Wang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore MD, 21205, USA.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Ravi Thombre
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore MD, 21205, USA.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Yajas Shah
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore MD, 21205, USA.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Rachel Latanich
- Department of Medicine, Division of Gastroenterology and Hepatology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jiou Wang
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore MD, 21205, USA.,Department of Neuroscience, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
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7
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Vergara C, Duggal P, Thio CL, Valencia A, O'Brien TR, Latanich R, Timp W, Johnson EO, Kral AH, Mangia A, Goedert JJ, Piazzola V, Mehta SH, Kirk GD, Peters MG, Donfield SM, Edlin BR, Busch MP, Alexander G, Murphy EL, Kim AY, Lauer GM, Chung RT, Cramp ME, Cox AL, Khakoo SI, Rosen HR, Alric L, Wheelan SJ, Wojcik GL, Thomas DL, Taub MA. Correction: Multi-ancestry fine mapping of interferon lambda and the outcome of acute hepatitis C virus infection. Genes Immun 2020; 21:420. [PMID: 33230236 DOI: 10.1038/s41435-020-00119-z] [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: 11/09/2022]
Affiliation(s)
- Candelaria Vergara
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.
| | - Priya Duggal
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Chloe L Thio
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ana Valencia
- Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Universidad Pontificia Bolivariana, Medellin, Colombia
| | - Thomas R O'Brien
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rachel Latanich
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Winston Timp
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Alex H Kral
- RTI International, Research Triangle Park, NC, USA
| | - Alessandra Mangia
- Liver Unit IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - James J Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Valeria Piazzola
- Liver Unit IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Shruti H Mehta
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Gregory D Kirk
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Marion G Peters
- Division of Gastroenterology, Department of Medicine, School of Medicine, University of California, San Francisco, CA, USA
| | | | - Brian R Edlin
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Michael P Busch
- Vitalant Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Graeme Alexander
- The Royal Free Hospital, University College London Institute for Liver and Digestive Health, London, UK
| | - Edward L Murphy
- Vitalant Research Institute, University of California San Francisco, San Francisco, CA, USA
| | - Arthur Y Kim
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Georg M Lauer
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Raymond T Chung
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Andrea L Cox
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Salim I Khakoo
- Southampton General Hospital, University of Southampton, Southampton, UK
| | | | - Laurent Alric
- Department of Internal Medicine and Digestive Diseases, Centre Hospitalier Universitaire Rangueil, UMR 152, Institut de Recherche pour le Développement Toulouse 3 University, Toulouse, France
| | - Sarah J Wheelan
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.,Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Genevieve L Wojcik
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - David L Thomas
- Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Margaret A Taub
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
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8
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Vergara C, Duggal P, Thio CL, Valencia A, O’Brien TR, Latanich R, Timp W, Johnson EO, Kral AH, Mangia A, Goedert JJ, Piazzola V, Mehta SH, Kirk GD, Peters MG, Donfield SM, Edlin BR, Busch MP, Alexander G, Murphy EL, Kim AY, Lauer GM, Chung RT, Cramp ME, Cox AL, Khakoo SI, Rosen HR, Alric L, Wheelan SJ, Wojcik GL, Thomas DL, Taub MA. Multi-ancestry fine mapping of interferon lambda and the outcome of acute hepatitis C virus infection. Genes Immun 2020; 21:348-359. [PMID: 33116245 PMCID: PMC7657970 DOI: 10.1038/s41435-020-00115-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 07/15/2019] [Revised: 10/08/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023]
Abstract
Clearance of acute infection with hepatitis C virus (HCV) is associated with the chr19q13.13 region containing the rs368234815 (TT/ΔG) polymorphism. We fine-mapped this region to detect possible causal variants that may contribute to HCV clearance. First, we performed sequencing of IFNL1-IFNL4 region in 64 individuals sampled according to rs368234815 genotype: TT/clearance (N = 16) and ΔG/persistent (N = 15) (genotype-outcome concordant) or TT/persistent (N = 19) and ΔG/clearance (N = 14) (discordant). 25 SNPs had a difference in counts of alternative allele >5 between clearance and persistence individuals. Then, we evaluated those markers in an association analysis of HCV clearance conditioning on rs368234815 in two groups of European (692 clearance/1 025 persistence) and African ancestry (320 clearance/1 515 persistence) individuals. 10/25 variants were associated (P < 0.05) in the conditioned analysis leaded by rs4803221 (P value = 4.9 × 10-04) and rs8099917 (P value = 5.5 × 10-04). In the European ancestry group, individuals with the haplotype rs368234815ΔG/rs4803221C were 1.7× more likely to clear than those with the rs368234815ΔG/rs4803221G haplotype (P value = 3.6 × 10-05). For another nearby SNP, the haplotype of rs368234815ΔG/rs8099917T was associated with HCV clearance compared to rs368234815ΔG/rs8099917G (OR: 1.6, P value = 1.8 × 10-04). We identified four possible causal variants: rs368234815, rs12982533, rs10612351 and rs4803221. Our results suggest a main signal of association represented by rs368234815, with contributions from rs4803221, and/or nearby SNPs including rs8099917.
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Affiliation(s)
- Candelaria Vergara
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD. USA
| | - Priya Duggal
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD. USA
| | - Chloe L. Thio
- Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Ana Valencia
- Johns Hopkins University, School of Medicine, Baltimore, MD, USA,Universidad Pontificia Bolivariana, Medellin, Colombia
| | - Thomas R. O’Brien
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rachel Latanich
- Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Winston Timp
- Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | | | - Alex H. Kral
- RTI International, Research Triangle Park, NC. USA
| | - Alessandra Mangia
- Liver Unit IRCCS “Casa Sollievo della Sofferenza”, San Giovanni Rotondo, Italy
| | - James J. Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD. USA
| | - Valeria Piazzola
- Liver Unit IRCCS “Casa Sollievo della Sofferenza”, San Giovanni Rotondo, Italy
| | - Shruti H. Mehta
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD. USA
| | - Gregory D. Kirk
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD. USA
| | - Marion G. Peters
- Department of Gastroenterology, University of California, San Francisco, CA., USA
| | | | - Brian R. Edlin
- Centers for Disease Control and Prevention, Atlanta, GA., USA
| | - Michael P. Busch
- University of California San Francisco and Vitalant Research Institute, San Francisco, CA., USA
| | - Graeme Alexander
- University College London Institute for Liver and Digestive Health, The Royal Free Hospital, London, UK
| | - Edward L. Murphy
- University of California San Francisco and Vitalant Research Institute, San Francisco, CA., USA
| | - Arthur Y. Kim
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA. USA
| | - Georg M. Lauer
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA.,USA
| | - Raymond T. Chung
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA.,USA
| | | | - Andrea L. Cox
- Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Salim I. Khakoo
- University of Southampton, Southampton General Hospital, Southampton, UK
| | | | - Laurent Alric
- Department of Internal Medicine and Digestive Diseases, Centre Hospitalier Universitaire Rangueil, UMR 152, Institut de Recherche pour le Développement Toulouse 3 University, France
| | - Sarah J. Wheelan
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD. USA.,Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Genevieve L. Wojcik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA., USA
| | - David L. Thomas
- Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Margaret A. Taub
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD. USA
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9
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Falade-Nwulia O, Hackman J, Mehta S, Sulkowski M, Latkin C, Thomas D, Downing Z, Latanich R, Kirk G, Laeyendecker O, Ray S. A22 Phylogenetic clustering of hepatitis C virus infection among people who inject drugs in Baltimore. Virus Evol 2019. [PMCID: PMC6736145 DOI: 10.1093/ve/vez002.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The availability of effective, oral direct acting antivirals for hepatitis C virus (HCV) treatment has fueled optimism for HCV elimination through treatment as prevention (TasP) among people who inject drugs (PWID). Identifying characteristics of individuals in transmission networks would provide critical information for the development and implementation of effective, targeted HCV TasP strategies. The AIDS linked to the IntraVenous Experience (ALIVE) cohort has followed PWID in Baltimore since 1988. Sequencing of the HCV core/E1 region (342 nucleotides) was performed on HCV viremic samples from the most recent study visit attended by ALIVE participants between August, 2005 and December, 2016. Outgroup sequences were retrieved from GenBank through a BLAST search for HCV sequences similar to study sequences to support identification of ‘local clusters’ and were aligned to study sequences using Clustal O. Phylogenetic trees were inferred for each of HCV subtype 1a and 1b separately through maximum likelihood analysis implemented in the MEGA X software using the Tamura-Nei model with gamma distribution and invariant sites. Nucleotide substitution model selection was based on the corrected Akaike information criterion scores of various models in MEGA. Robustness of the resulting tree was assessed by bootstrapping with 1,000 replicates. Clusters were identified using ClusterPicker software (70% bootstrap threshold and 0.05 maximum genetic distance threshold). Sensitivity analyses were performed by varying the genetic distance threshold between 0.025 and 0.05 to determine the effect on identification of factors associated with clustering. HCV infection clustering was defined as > 2 participants with HCV genome sequences satisfying 70 per cent bootstrap and 0.05 genetic threshold distance requirement for sequence similarity. Logistic regression was used to assess sociodemographic factors associated with being in an HCV cluster. Among 512 HCV genotype 1 viremic PWID, HCV subtype prevalence was 83 per cent genotype 1a and 17 per cent genotype 1b. The median age of participants was 54 years, 68 per cent male, 87 per cent Black, and 38 per cent HIV infected. Overall, 9 per cent (n = 44) were grouped into 21 clusters, consisting of 20 pairs and 1 triad. Of the 425 genotype 1a and 87 genotype 1b samples evaluated, 8 per cent (n = 33) and 13 per cent (n = 11) respectively, were in clusters. In unadjusted analyses, membership in a cluster, was associated with younger age (odds ratio (OR) 1.5 [95% confidence interval (CI) 1.1–2.1] per 10 year age decrease); female sex (OR 2.8 [95% CI 1.5–5.3]), HIV infection (OR 4.9 [95% CI 2.5–9.9]), and living in East Baltimore (versus outside East Baltimore, OR 2.0 [95% CI 1.0–3.9]). In adjusted analyses, female sex (OR 2.0 [95% CI 1.0–3.9] and HIV infection (OR 5.4 [95% CI 2.6–11.1] remained independently associated with being in an HCV infection cluster. HIV-infected PWID and their networks should be prioritized for HCV treatment and prevention interventions given an increased likelihood of transmission in these groups.
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Affiliation(s)
| | - Jada Hackman
- National Institute of Allergy and Infectious Diseases, Baltimore, MD, USA
| | | | | | - Carl Latkin
- Johns Hopkins University, Baltimore, MD, USA
| | | | | | | | | | | | - Stuart Ray
- Johns Hopkins University, Baltimore, MD, USA
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10
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Vergara C, Thio CL, Johnson E, Kral AH, O'Brien TR, Goedert JJ, Mangia A, Piazzolla V, Mehta SH, Kirk GD, Kim AY, Lauer GM, Chung RT, Cox AL, Peters MG, Khakoo SI, Alric L, Cramp ME, Donfield SM, Edlin BR, Busch MP, Alexander G, Rosen HR, Murphy EL, Latanich R, Wojcik GL, Taub MA, Valencia A, Thomas DL, Duggal P. Multi-Ancestry Genome-Wide Association Study of Spontaneous Clearance of Hepatitis C Virus. Gastroenterology 2019; 156:1496-1507.e7. [PMID: 30593799 PMCID: PMC6788806 DOI: 10.1053/j.gastro.2018.12.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 12/05/2018] [Accepted: 12/19/2018] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Spontaneous clearance of hepatitis C virus (HCV) occurs in approximately 30% of infected persons and less often in populations of African ancestry. Variants in major histocompatibility complex (MHC) and in interferon lambda genes are associated with spontaneous HCV clearance, but there have been few studies of these variants in persons of African ancestry. We performed a dense multi-ancestry genome-wide association study of spontaneous clearance of HCV, focusing on individuals of African ancestry. METHODS We performed genotype analyses of 4423 people from 3 ancestry groups: 2201 persons of African ancestry (445 with HCV clearance and 1756 with HCV persistence), 1739 persons of European ancestry (701 with HCV clearance and 1036 with HCV persistence), and 486 multi-ancestry Hispanic persons (173 with HCV clearance and 313 with HCV persistence). Samples were genotyped using Illumina (San Diego, CA) arrays and statistically imputed to the 1000 Genomes Project. For each ancestry group, the association of single-nucleotide polymorphisms with HCV clearance was tested by log-additive analysis, and then a meta-analysis was performed. RESULTS In the meta-analysis, significant associations with HCV clearance were confirmed at the interferon lambda gene locus IFNL4-IFNL3 (19q13.2) (P = 5.99 × 10-50) and the MHC locus 6p21.32 (P = 1.15 × 10-21). We also associated HCV clearance with polymorphisms in the G-protein-coupled receptor 158 gene (GPR158) at 10p12.1 (P = 1.80 × 10-07). These 3 loci had independent, additive effects of HCV clearance, and account for 6.8% and 5.9% of the variance of HCV clearance in persons of European and African ancestry, respectively. Persons of African or European ancestry carrying all 6 variants were 24-fold and 11-fold, respectively, more likely to clear HCV infection compared with individuals carrying none or 1 of the clearance-associated variants. CONCLUSIONS In a meta-analysis of data from 3 studies, we found variants in MHC genes, IFNL4-IFNL3, and GPR158 to increase odds of HCV clearance in patients of European and African ancestry. These findings could increase our understanding of immune response to and clearance of HCV infection.
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Affiliation(s)
| | - Chloe L Thio
- Johns Hopkins University, School of Medicine, Baltimore, Maryland
| | - Eric Johnson
- Research Triangle Institute International, Research Triangle Park, North Carolina; Atlanta, Georgia; San Francisco, California
| | - Alex H Kral
- Research Triangle Institute International, Research Triangle Park, North Carolina; Atlanta, Georgia; San Francisco, California
| | - Thomas R O'Brien
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - James J Goedert
- Liver Unit Istituto Di Ricovero e Cura a Carattere Scientifico "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Alessandra Mangia
- Liver Unit Istituto Di Ricovero e Cura a Carattere Scientifico "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Valeria Piazzolla
- Liver Unit Istituto Di Ricovero e Cura a Carattere Scientifico "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Shruti H Mehta
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland
| | - Gregory D Kirk
- Johns Hopkins University, School of Medicine, Baltimore, Maryland; Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland
| | - Arthur Y Kim
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Georg M Lauer
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Raymond T Chung
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Andrea L Cox
- Johns Hopkins University, School of Medicine, Baltimore, Maryland
| | - Marion G Peters
- Division of Gastroenterology, Department of Medicine, School of Medicine, University of California, San Francisco, California
| | - Salim I Khakoo
- University of Southampton, Southampton General Hospital, Southampton, UK
| | - Laurent Alric
- Department of Internal Medicine and Digestive Diseases, Centre Hospitalier Universitaire Purpan, UMR 152, Institut de Recherche pour le Développement Toulouse 3 University, France
| | | | | | - Brian R Edlin
- State University of New York Downstate College of Medicine, Brooklyn, New York
| | - Michael P Busch
- University of California and Vitalant Research Institute, San Francisco, California
| | - Graeme Alexander
- University College London Institute for Liver and Digestive Health, The Royal Free Hospital, London, UK
| | | | - Edward L Murphy
- University of California and Vitalant Research Institute, San Francisco, California
| | - Rachel Latanich
- Johns Hopkins University, School of Medicine, Baltimore, Maryland
| | - Genevieve L Wojcik
- Department of Genetics, Stanford University School of Medicine, Stanford, California
| | - Margaret A Taub
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland
| | - Ana Valencia
- Johns Hopkins University, School of Medicine, Baltimore, Maryland; Universidad Pontificia Bolivariana, Medellin, Colombia
| | - David L Thomas
- Johns Hopkins University, School of Medicine, Baltimore, Maryland
| | - Priya Duggal
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland.
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11
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Veenhuis RT, Kwaa AK, Garliss CC, Latanich R, Salgado M, Pohlmeyer CW, Nobles CL, Gregg J, Scully EP, Bailey JR, Bushman FD, Blankson JN. Long-term remission despite clonal expansion of replication-competent HIV-1 isolates. JCI Insight 2018; 3:122795. [PMID: 30232278 DOI: 10.1172/jci.insight.122795] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/07/2018] [Indexed: 11/17/2022] Open
Abstract
Clonal expansion of T cells harboring replication-competent virus has recently been demonstrated in patients on suppressive antiretroviral therapy (ART) regimens. However, there has not been direct evidence of this phenomenon in settings of natural control, including in posttreatment controllers who maintain control of viral replication after treatment when ART is discontinued. We present a case of an individual who has had undetectable viral loads for more than 15 years following the cessation of ART. Using near-full-genome sequence analysis, we demonstrate that 9 of 12 replication-competent isolates cultured from this subject were identical and that this identity was maintained 6 months later. A similar pattern of replication-competent virus clonality was seen in a treatment-naive HLA-B*57 elite controller. In both cases, we show that CD8+ T cells are capable of suppressing the replication of the clonally expanded viruses in vitro. Our data suggest that, while clonal expansion of replication-competent virus can present a barrier to viral eradication, these viral isolates remain susceptible to HIV-specific immune responses and can be controlled in patients with long-term suppression of viral replication.
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Affiliation(s)
- Rebecca T Veenhuis
- Department of Medicine and.,Department of Molecular and Comparative Pathobiology, Center for AIDS Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | | | | | | | - Christopher L Nobles
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - John Gregg
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | | | | | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Joel N Blankson
- Department of Medicine and.,Department of Molecular and Comparative Pathobiology, Center for AIDS Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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12
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Huang H, Duggal P, Thio CL, Latanich R, Goedert JJ, Mangia A, Cox AL, Kirk GD, Mehta S, Aneja J, Alric L, Donfield SM, Cramp ME, Khakoo SI, Tobler LH, Busch M, Alexander GJ, Rosen HR, Edlin BR, Segal FP, Lauer GM, Thomas DL, Daly MJ, Chung RT, Kim AY. Fine-mapping of genetic loci driving spontaneous clearance of hepatitis C virus infection. Sci Rep 2017; 7:15843. [PMID: 29158528 PMCID: PMC5696522 DOI: 10.1038/s41598-017-16011-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 05/09/2017] [Accepted: 11/06/2017] [Indexed: 12/17/2022] Open
Abstract
Approximately three quarters of acute hepatitis C (HCV) infections evolve to a chronic state, while one quarter are spontaneously cleared. Genetic predispositions strongly contribute to the development of chronicity. We have conducted a genome-wide association study to identify genomic variants underlying HCV spontaneous clearance using ImmunoChip in European and African ancestries. We confirmed two previously reported significant associations, in the IL28B/IFNL4 and the major histocompatibility complex (MHC) regions, with spontaneous clearance in the European population. We further fine-mapped the association in the MHC to a region of about 50 kilo base pairs, down from 1 mega base pairs in the previous study. Additional analyses suggested that the association in MHC is stronger in samples from North America than those from Europe.
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Affiliation(s)
- Hailiang Huang
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Priya Duggal
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Chloe L Thio
- Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Rachel Latanich
- Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - James J Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, 20852, USA
| | - Alessandra Mangia
- IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
| | - Andrea L Cox
- Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Gregory D Kirk
- Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Shruti Mehta
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Jasneet Aneja
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Laurent Alric
- Department of Medicine, Purpan Hospital, University of Toulouse III, Toulouse, France
| | | | - Matthew E Cramp
- South West Liver Unit, Plymouth Hospitals NHS Trust, Plymouth, United Kingdom
| | - Salim I Khakoo
- Henry Welcome Laboratories, Southampton General Hospital, Southampton, UK
| | - Leslie H Tobler
- University of California and Blood Systems Research Institute, San Francisco, CA, 94118, USA
| | - Michael Busch
- University of California and Blood Systems Research Institute, San Francisco, CA, 94118, USA
| | - Graeme J Alexander
- Cambridge University Hospitals NHS Foundation Trust and Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Hugo R Rosen
- University of Colorado, Aurora, Colorado, 90045, United States
| | - Brian R Edlin
- State University of New York Downstate College of Medicine, Brooklyn, New York, USA
| | - Florencia P Segal
- Brigham and Women's Hospital, 75 Francis Street, Boston, MA, 02115, USA
| | - Georg M Lauer
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - David L Thomas
- Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, 02114, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Raymond T Chung
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.
| | - Arthur Y Kim
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.
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13
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Vergara C, Thio C, Latanich R, Cox AL, Kirk GD, Mehta SH, Busch M, Murphy EL, Villacres MC, Peters MG, French AL, Golub E, Eron J, Lahiri CD, Shrestha S, Gustafson D, Young M, Anastos K, Aouizerat B, Kim AY, Lauer G, Thomas DL, Duggal P. Genetic basis for variation in plasma IL-18 levels in persons with chronic hepatitis C virus and human immunodeficiency virus-1 infections. Genes Immun 2017; 18:82-87. [PMID: 28300059 PMCID: PMC5408324 DOI: 10.1038/gene.2017.2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 09/26/2016] [Revised: 11/07/2016] [Accepted: 11/08/2016] [Indexed: 12/27/2022]
Abstract
Inflammasomes are multi-protein complexes integrating pathogen-triggered signaling leading to the generation of pro-inflammatory cytokines, including interleukin-18 (IL-18). Hepatitis C virus (HCV) and human immunodeficiency virus-1 (HIV) infections are associated with elevated IL-18, suggesting inflammasome activation. However, there is marked person-to-person variation in the inflammasome response to HCV and HIV. We hypothesized that host genetics may explain this variation. To test this, we analyzed the associations of plasma IL-18 levels and polymorphisms in 10 genes in the inflammasome cascade. 1538 participants with active HIV and/or HCV infection in 3 ancestry groups are included. Samples were genotyped using the Illumina Omni 1-quad and Omni 2.5 arrays. Linear regression analyses were performed to test the association of variants with logIL-18 including HCV and HIV infection status and HIV-RNA, in each ancestry group and then meta-analyzed. Eleven highly correlated SNPs (r2=0.98-1) in the IL18-BCO2 region were significantly associated with logIL-18; Each T allele of rs80011693 confers a decrease of 0.06 log pg/mL of IL-18 after adjusting for covariates (rs80011693; rs111311302 β=-0.06, P-value=2.7×10-4). In conclusion, genetic variation in IL18 is associated with IL-18 production in response to HIV and HCV infection and may explain variability in the inflammatory outcomes of chronic viral infections.
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Affiliation(s)
- C Vergara
- School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - C Thio
- School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - R Latanich
- School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - A L Cox
- School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - G D Kirk
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - S H Mehta
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - M Busch
- University of California, San Francisco, CA, USA
| | - E L Murphy
- University of California, San Francisco, CA, USA.,Blood Systems Research Institute, San Francisco, CA, USA
| | - M C Villacres
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - M G Peters
- Blood Systems Research Institute, San Francisco, CA, USA
| | - A L French
- CORE Center/Stroger Hospital of Cook County, Chicago, IL, USA
| | - E Golub
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - J Eron
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - C D Lahiri
- School of Medicine, Emory University, Atlanta, GA, USA
| | - S Shrestha
- The University of Alabama at Birmingham, AL, USA
| | - D Gustafson
- State University of New York-Downstate Medical Center, New York, NY, USA
| | - M Young
- Georgetown University Medical Center, Washington, DC, USA
| | - K Anastos
- Albert Einstein College of Medicine and Montefiore Medical Center, New York, NY, USA
| | - B Aouizerat
- Bluestone Center for Clinical Research, New York University, New York, NY, USA.,Department of Oral and Maxillofacial Surgery, New York University, New York, NY, USA
| | - A Y Kim
- Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - G Lauer
- Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - D L Thomas
- School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - P Duggal
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
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14
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Kurbanov F, Kim Y, Latanich R, Chaudhari P, El-Diwany R, Knabel M, Kandathil AJ, Cameron A, Cox A, Jang YY, Thomas DL, Balagopal A. IFNL3 genotype is associated with differential induction of IFNL3 in primary human hepatocytes. Antivir Ther 2015; 20:805-14. [PMID: 26109548 PMCID: PMC4821403 DOI: 10.3851/imp2974] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2015] [Indexed: 12/17/2022]
Abstract
BACKGROUND Lambda interferons (IFNLs) have potent antiviral activity against HCV, and polymorphisms within the IFNL gene cluster near the IFNL3 gene strongly predict spontaneous- and treatment-related HCV infection outcomes. The mechanism(s) linking IFNL polymorphisms and HCV control is currently elusive. METHODS IFNL induction was studied in primary human hepatocytes (PHH) from 18 human donors, peripheral blood mononuclear cells (PBMCs) from 18 human donors, multiple cell lines and induced pluripotent stem cell-derived hepatocyte-like cells (iPSC-hepatocytes) from 7 human donors. After stimulation with intracellular RNA and infectious HCV, quantitative PCR (qPCR) primers and probes were designed to distinguish and quantify closely related IFNL messenger (m)RNAs from IFNL1, IFNL2 and IFNL3. RESULTS PHH demonstrated the most potent induction of IFNLs, although had lower pre-stimulation levels compared to PBMCs, monocytes and cell lines. PHH stimulation with cytoplasmic poly I:C induced >1,000-fold expression of IFNL1, IFNL2 and IFNL3. PHH from donors who were homozygous for the favourable IFNL3 allele (IFNL3-CC) had higher IFNL3 induction compared to PHH from IFNL3-TT donors (P=0.03). Baseline IFNL mRNA expression and induction was also tested in iPSC-hepatocytes: iPSC-hepatocytes had significantly higher baseline expression of IFNLs compared to PHH (P<0.0001), and IFNL3 induction was marginally different in iPSC-hepatocytes by IFNL genotype (P=0.07). CONCLUSIONS Hepatocytes express IFNLs when stimulated by a synthetic viral RNA that signals the cell through the cytoplasm. IFNL induction may be greater in persons with the favourable IFNL3 allele. These data provide insight into the strong linkage between IFNL3 genetics and control of HCV infection.
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Affiliation(s)
- Fuat Kurbanov
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Yonghak Kim
- Stem Cell Biology Laboratory, Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Rachel Latanich
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Pooja Chaudhari
- Stem Cell Biology Laboratory, Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ramy El-Diwany
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Matt Knabel
- Division of Transplant Surgery, Department of Surgery, Johns Hopkins School of Medicine, Baltimore, MD USA
| | - Abraham J Kandathil
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Andrew Cameron
- Division of Transplant Surgery, Department of Surgery, Johns Hopkins School of Medicine, Baltimore, MD USA
| | - Andrea Cox
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Yoon-Young Jang
- Stem Cell Biology Laboratory, Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - David L Thomas
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ashwin Balagopal
- Division of Infectious Diseases, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
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15
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Osburn WO, Snider AE, Wells BL, Latanich R, Bailey JR, Thomas DL, Cox AL, Ray SC. Clearance of hepatitis C infection is associated with the early appearance of broad neutralizing antibody responses. Hepatology 2014; 59:2140-51. [PMID: 24425349 PMCID: PMC4043926 DOI: 10.1002/hep.27013] [Citation(s) in RCA: 197] [Impact Index Per Article: 19.7] [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: 09/30/2014] [Accepted: 01/10/2014] [Indexed: 12/12/2022]
Abstract
UNLABELLED The contribution of humoral immune responses to spontaneous control of hepatitis C virus (HCV) infection remains unclear. We assessed neutralizing antibody (nAb) responses during acute HCV infection to determine whether infection outcome is associated with the nAb response, specifically, its timing or breadth (neutralization of multiple genotype-matched variants). A representative genotype 1 HCV pseudoparticle (HCVpp) library, consisting of 19 genetically distinct genotype 1 HCVpp that comprise the natural variability of genotype 1 E1E2 sequences, was used to assess anti-genotype 1 nAb responses during acute infection in at-risk persons followed prospectively. Neutralization of individual library HCVpp by the last viremic plasma sample obtained before clearance was compared to either 1-year post-initial viremia or clearance time-matched specimens obtained from subjects developing persistent infection. In persistently infected persons nAb responses were delayed then progressively broadened, whereas in persons who controlled viremia broader responses were detected early and contracted after clearance of viremia. Surprisingly, the breadth of anti-genotype 1 nAb responses was not dependent on subjects' infection genotype. Also, individual library HCVpp neutralization sensitivity was not associated with any known E2 sequence determinants. Interestingly, two single nucleotide polymorphisms in the HLA-DQ locus were associated with nAb breadth. CONCLUSION Control of HCV infection is associated with more rapid development of a broad nAb response, independent of the infection viral genotype, providing further evidence for the role of nAb in controlling HCV infection and the potential benefit of generating broad anti-HCV nAb responses by vaccination.
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Affiliation(s)
- William O. Osburn
- Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD 21205
| | - Anna E. Snider
- Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD 21205
| | - Brittany L. Wells
- Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD 21205
| | - Rachel Latanich
- Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD 21205
| | - Justin R. Bailey
- Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD 21205
| | - David L. Thomas
- Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD 21205
| | - Andrea L. Cox
- Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD 21205
| | - Stuart C. Ray
- Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD 21205
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16
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Chattergoon MA, Latanich R, Quinn J, Winter ME, Buckheit RW, Blankson JN, Pardoll D, Cox AL. HIV and HCV activate the inflammasome in monocytes and macrophages via endosomal Toll-like receptors without induction of type 1 interferon. PLoS Pathog 2014; 10:e1004082. [PMID: 24788318 PMCID: PMC4006909 DOI: 10.1371/journal.ppat.1004082] [Citation(s) in RCA: 137] [Impact Index Per Article: 13.7] [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: 10/28/2013] [Accepted: 03/07/2014] [Indexed: 02/07/2023] Open
Abstract
Innate immune sensing of viral infection results in type I interferon (IFN) production and inflammasome activation. Type I IFNs, primarily IFN-α and IFN-β, are produced by all cell types upon virus infection and promote an antiviral state in surrounding cells by inducing the expression of IFN-stimulated genes. Type I IFN production is mediated by Toll-like receptor (TLR) 3 in HCV infected hepatocytes. Type I IFNs are also produced by plasmacytoid dendritic cells (pDC) after sensing of HIV and HCV through TLR7 in the absence of productive pDC infection. Inflammasomes are multi-protein cytosolic complexes that integrate several pathogen-triggered signaling cascades ultimately leading to caspase-1 activation and generation pro-inflammatory cytokines including interleukin (IL)-18 and IL-1β. Here, we demonstrate that HIV and HCV activate the inflammasome, but not Type I IFN production, in monocytes and macrophages in an infection-independent process that requires clathrin-mediated endocytosis and recognition of the virus by distinct endosomal TLRs. Knockdown of each endosomal TLR in primary monocytes by RNA interference reveals that inflammasome activation in these cells results from HIV sensing by TLR8 and HCV recognition by TLR7. Despite its critical role in type I IFN production by pDCs stimulated with HIV, TLR7 is not required for inflammasome activation by HIV. Similarly, HCV activation of the inflammasome in monocytes does not require TLR3 or its downstream signaling adaptor TICAM-1, while this pathway leads to type I IFN in infected hepatocytes. Monocytes and macrophages do not produce type I IFN upon TLR8 or TLR7 sensing of HIV or HCV, respectively. These findings reveal a novel infection-independent mechanism for chronic viral induction of key anti-viral programs and demonstrate distinct TLR utilization by different cell types for activation of the type I IFN vs. inflammasome pathways of inflammation. Pathogens are detected by the immune system in multiple ways that initiate responses to control infection. Two systems of first line defense against viruses are 1) the production of Type I interferons and 2) production of the cytokines IL-1β and IL-18 by the inflammasome. Type I interferons promote an antiviral state in the infected host. Inflammasome cytokines induce inflammation, modulate adaptive immune responses, and have direct antiviral effects. While both are produced in response to the chronic human viral infections HIV and HCV, we demonstrate here that inflammasome activation does not require cell infection and that the mechanisms for viral sensing as well as cell types in which sensing occurs are distinct between the two viruses and between the type I interferon vs. inflammasome systems. The relative amount of sensing via these different mechanisms may affect the balance between antiviral and inflammatory responses to chronic infection.
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Affiliation(s)
- Michael A. Chattergoon
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Rachel Latanich
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jeffrey Quinn
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Matthew E. Winter
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Robert W. Buckheit
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Joel N. Blankson
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Drew Pardoll
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Andrea L. Cox
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail:
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17
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Wojcik G, Latanich R, Mosbruger T, Astemborski J, Kirk GD, Mehta SH, Goedert JJ, Kim AY, Seaberg EC, Busch M, Thomas DL, Duggal P, Thio CL. Variants in HAVCR1 gene region contribute to hepatitis C persistence in African Americans. J Infect Dis 2013; 209:355-9. [PMID: 23964107 DOI: 10.1093/infdis/jit444] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
To confirm previously identified polymorphisms in HAVCR1 that were associated with persistent hepatitis C virus (HCV) infection in individuals of African and of European descent, we studied 165 subjects of African descent and 635 subjects of European descent. Because the association was only confirmed in subjects of African descent (rs6880859; odds ratio, 2.42; P = .01), we then used 379 subjects of African descent (142 with spontaneous HCV clearance) to fine-map HAVCR1. rs111511318 was strongly associated with HCV persistence after adjusting for IL28B and HLA (adjusted P = 8.8 × 10(-4)), as was one 81-kb haplotype (adjusted P = .0006). The HAVCR1 genomic region is an independent genetic determinant of HCV persistence in individuals of African descent.
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Affiliation(s)
- Genevieve Wojcik
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore
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18
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Duggal P, Thio CL, Wojcik GL, Goedert JJ, Mangia A, Latanich R, Kim AY, Lauer GM, Chung RT, Peters MG, Kirk GD, Mehta SH, Cox AL, Khakoo SI, Alric L, Cramp ME, Donfield SM, Edlin BR, Tobler LH, Busch MP, Alexander G, Rosen HR, Gao X, Abdel-Hamid M, Apps R, Carrington M, Thomas DL. Genome-wide association study of spontaneous resolution of hepatitis C virus infection: data from multiple cohorts. Ann Intern Med 2013; 158:235-45. [PMID: 23420232 PMCID: PMC3638215 DOI: 10.7326/0003-4819-158-4-201302190-00003] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
UNLABELLED Chinese translation BACKGROUND Hepatitis C virus (HCV) infections occur worldwide and either spontaneously resolve or persist and markedly increase the person's lifetime risk for cirrhosis and hepatocellular carcinoma. Although HCV persistence occurs more often in persons of African ancestry and persons with genetic variants near interleukin-28B (IL-28B), the genetic basis is not well-understood. OBJECTIVE To evaluate the host genetic basis for spontaneous resolution of HCV infection. DESIGN 2-stage, genome-wide association study. SETTING 13 international multicenter study sites. PATIENTS 919 persons with serum HCV antibodies but no HCV RNA (spontaneous resolution) and 1482 persons with serum HCV antibodies and HCV RNA (persistence). MEASUREMENTS Frequencies of 792 721 single nucleotide polymorphisms (SNPs). RESULTS Differences in allele frequencies between persons with spontaneous resolution and persistence were identified on chromosomes 19q13.13 and 6p21.32. On chromosome 19, allele frequency differences localized near IL-28B and included rs12979860 (overall per-allele OR, 0.45; P = 2.17 × 10-30) and 10 additional SNPs spanning 55 000 base pairs. On chromosome 6, allele frequency differences localized near genes for HLA class II and included rs4273729 (overall per-allele OR, 0.59; P = 1.71 × 10-16) near DQB1*03:01 and an additional 116 SNPs spanning 1 090 000 base pairs. The associations in chromosomes 19 and 6 were independent and additive and explain an estimated 14.9% (95% CI, 8.5% to 22.6%) and 15.8% (CI, 4.4% to 31.0%) of the variation in HCV resolution in persons of European and African ancestry, respectively. Replication of the chromosome 6 SNP, rs4272729, in an additional 745 persons confirmed the findings (P = 0.015). LIMITATION Epigenetic effects were not studied. CONCLUSION IL-28B and HLA class II are independently associated with spontaneous resolution of HCV infection, and SNPs marking IL-28B and DQB1*03:01 may explain approximately 15% of spontaneous resolution of HCV infection.
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Affiliation(s)
- Priya Duggal
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Chloe L. Thio
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Genevieve L. Wojcik
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - James J. Goedert
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Alessandra Mangia
- Liver Unit IRCCS “Casa Sollievo della Sofferenza”, 71013 San Giovanni Rotondo, Italy
| | - Rachel Latanich
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Arthur Y. Kim
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Warren 1019A, 55 Fruit Street, Boston MA, USA
- Ragon Institute of Harvard, Boston, MA, USA
| | - Georg M. Lauer
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Warren 1019A, 55 Fruit Street, Boston MA, USA
- Ragon Institute of Harvard, Boston, MA, USA
| | - Raymond T. Chung
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Warren 1019A, 55 Fruit Street, Boston MA, USA
- Ragon Institute of Harvard, Boston, MA, USA
| | - Marion G. Peters
- University of California San Francisco, 513 Parnassus Ave S357, San Francisco, CA, USA
| | - Greg D. Kirk
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Shruti H. Mehta
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Andrea L. Cox
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Salim I. Khakoo
- University of Southampton, Mailpoint 811, Level E South Academic Block, Southampton General Hospital, Tremona Road, Southampton, UK
| | | | | | | | | | - Leslie H Tobler
- Viral Reference Laboratory and Repository Core, Blood Systems Research Institute, San Francisco, CA, USA
| | - Michael P. Busch
- Viral Reference Laboratory and Repository Core, Blood Systems Research Institute, San Francisco, CA, USA
| | - Graeme Alexander
- Division of Gastroenetrology & Hepatology, University Department of Medicine, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke’s Hospital, Hill’s Road, Cambridge,, CB2 0QQ, United Kingdom
| | - Hugo R. Rosen
- Department of Medicine, University of Colorado, Denver, Colorado, USA
| | - Xiaojiang Gao
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Mohamed Abdel-Hamid
- Department of Microbiology and Immunology, Faculty of Medicine, Minia University and Director, Viral Hepatitis Research Lab National Hepatology and Tropical Disease Research Institute
| | - Richard Apps
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Mary Carrington
- Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | - David L. Thomas
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Kurbanov F, Abdel-Hamid M, Latanich R, Astemborski J, Mohamed M, Mikhail NMH, El-Daly M, El-Kafrawy S, Thomas DL, Thio CL. Genetic polymorphism in IL28B is associated with spontaneous clearance of hepatitis C virus genotype 4 infection in an Egyptian cohort. J Infect Dis 2011; 204:1391-4. [PMID: 21933876 PMCID: PMC3182308 DOI: 10.1093/infdis/jir536] [Citation(s) in RCA: 43] [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: 02/15/2011] [Accepted: 06/13/2011] [Indexed: 12/14/2022] Open
Abstract
Single-nucleotide polymorphisms (SNPs) around IL28B are associated with spontaneous hepatitis C virus (HCV) clearance of genotypes 1 and 3 in white and African-American populations. This study investigated whether the IL28B SNP (rs12979860) is associated with spontaneous clearance of HCV, principally genotype 4, in 162 Egyptians (80 with clearance). The protective C allele was more common in those with spontaneous clearance (76.3% vs 57.9%; P = .0006). Individuals with clearance were 3.4 (95% confidence interval, 1.8-6.5) times more likely to have C/C genotype. Thus, IL28B plays a role in spontaneous clearance of HCV genotype 4 in North Africa.
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Affiliation(s)
- Fuat Kurbanov
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Mohamed Abdel-Hamid
- Faculty of Medicine, Department of Microbiology and Immunology, Minia University
| | - Rachel Latanich
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland
| | | | | | - Nabiel MH Mikhail
- Deptartment of Biostatistics and Cancer Epidemiology, South Egypt Cancer Institute, Assuit University, Asyut
| | - Mai El-Daly
- Clinical Pathology Department, Molecular Biology Unit, National Liver Institute, Menophyia, Egypt
| | - Sherif El-Kafrawy
- Clinical Pathology Department, Molecular Biology Unit, National Liver Institute, Menophyia, Egypt
| | - David L. Thomas
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Chloe L. Thio
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland
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20
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Chattergoon MA, Levine JS, Latanich R, Osburn WO, Thomas DL, Cox AL. High plasma interleukin-18 levels mark the acute phase of hepatitis C virus infection. J Infect Dis 2011; 204:1730-40. [PMID: 21984735 DOI: 10.1093/infdis/jir642] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Proinflammatory cytokines play a critical role in antiviral immune responses. Large-scale genome studies have found correlations between single-nucleotide polymorphisms (SNPs) in the interleukin (IL) 18 promoter and spontaneous control of hepatitis C virus (HCV), suggesting a role in clearance. METHODS Plasma IL-18, IL-1β, IL-6, IL-8, IL-12, interferon-γ, tumor necrosis factor-α, alanine aminotransferase (ALT), and HCV RNA levels were assessed longitudinally in subjects with known dates of HCV acquisition and analyzed according to IL-18 SNPs and outcome, either spontaneous clearance (SC) (n = 13) or persistent infection (PI) (n = 25). RESULTS No significant change in plasma proinflammatory cytokine expression was observed with the exception of IL-18, which increased in every subject with initial detection of HCV RNA. In every SC subject, IL-18 returned to the preinfection baseline concomitant with HCV control. In PI subjects, IL-18 declined following the acute phase of infection but remained above the preinfection baseline throughout chronic infection and did not correlate with HCV RNA or ALT levels. CONCLUSIONS Plasma IL-18 was an early and the most reliably detected host response to HCV infection measured in blood. Reduced IL-18 production with transition to chronic infection without correlation with HCV RNA or ALT levels suggests modulation of the innate response with persistent infection.
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Affiliation(s)
- Michael A Chattergoon
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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