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Gu W, Eke C, Gonzalez Santiago E, Olaloye O, Konnikova L. Single-cell atlas of the small intestine throughout the human lifespan demonstrates unique features of fetal immune cells. Mucosal Immunol 2024:S1933-0219(24)00031-X. [PMID: 38555026 DOI: 10.1016/j.mucimm.2024.03.011] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/15/2024] [Accepted: 03/23/2024] [Indexed: 04/02/2024]
Abstract
Proper development of mucosal immunity is critical for human health. Over the past decade, it has become evident that in humans, this process begins in utero. However, there are limited data on the unique features and functions of fetal mucosal immune cells. To address this gap, we integrated several single-cell ribonucleic acid sequencing datasets of the human small intestine (SI) to create an SI transcriptional atlas throughout the human life span, ranging from the first trimester to adulthood, with a focus on immune cells. Fetal SI displayed a complex immune landscape comprising innate and adaptive immune cells that exhibited distinct transcriptional programs from postnatal samples, especially compared with pediatric and adult samples. We identified shifts in myeloid populations across gestation and progression of memory T-cell states throughout the human lifespan. In particular, there was a marked shift of memory T cells from those with stem-like properties in the fetal samples to fully differentiated cells with a high expression of activation and effector function genes in adult samples, with neonatal samples containing both features. Finally, we demonstrate that the SI developmental atlas can be used to elucidate improper trajectories linked to mucosal diseases by implicating developmental abnormalities underlying necrotizing enterocolitis, a severe intestinal complication of prematurity. Collectively, our data provide valuable resources and important insights into intestinal immunity that will facilitate regenerative medicine and disease understanding.
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Affiliation(s)
- Weihong Gu
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Chino Eke
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | | | - Oluwabunmi Olaloye
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Liza Konnikova
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA; Department of Obstetrics, Gynecology and Reproductive Science, Yale University School of Medicine, New Haven, CT, USA; Program in Translational Biomedicine, Yale University School of Medicine, New Haven, CT, USA; Program in Human Translational Immunology, Yale University School of Medicine, New Haven, CT, USA.
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2
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Olyha SJ, O'Connor SK, Kribis M, Bucklin ML, Uthaya Kumar DB, Tyler PM, Alam F, Jones KM, Sheikha H, Konnikova L, Lakhani SA, Montgomery RR, Catanzaro J, Du H, DiGiacomo DV, Rothermel H, Moran CJ, Fiedler K, Warner N, Hoppenreijs EPAH, van der Made CI, Hoischen A, Olbrich P, Neth O, Rodríguez-Martínez A, Lucena Soto JM, van Rossum AMC, Dalm VASH, Muise AM, Lucas CL. "Deficiency in ELF4, X-Linked": a Monogenic Disease Entity Resembling Behçet's Syndrome and Inflammatory Bowel Disease. J Clin Immunol 2024; 44:44. [PMID: 38231408 PMCID: PMC10929603 DOI: 10.1007/s10875-023-01610-8] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/27/2023] [Indexed: 01/18/2024]
Abstract
Defining monogenic drivers of autoinflammatory syndromes elucidates mechanisms of disease in patients with these inborn errors of immunity and can facilitate targeted therapeutic interventions. Here, we describe a cohort of patients with a Behçet's- and inflammatory bowel disease (IBD)-like disorder termed "deficiency in ELF4, X-linked" (DEX) affecting males with loss-of-function variants in the ELF4 transcription factor gene located on the X chromosome. An international cohort of fourteen DEX patients was assessed to identify unifying clinical manifestations and diagnostic criteria as well as collate findings informing therapeutic responses. DEX patients exhibit a heterogeneous clinical phenotype including weight loss, oral and gastrointestinal aphthous ulcers, fevers, skin inflammation, gastrointestinal symptoms, arthritis, arthralgia, and myalgia, with findings of increased inflammatory markers, anemia, neutrophilic leukocytosis, thrombocytosis, intermittently low natural killer and class-switched memory B cells, and increased inflammatory cytokines in the serum. Patients have been predominantly treated with anti-inflammatory agents, with the majority of DEX patients treated with biologics targeting TNFα.
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Affiliation(s)
- Sam J Olyha
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Shannon K O'Connor
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Marat Kribis
- Section of Rheumatology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Molly L Bucklin
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | | | - Paul M Tyler
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Faiad Alam
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Kate M Jones
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Hassan Sheikha
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Liza Konnikova
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
- Division of Neonatal and Perinatal Medicine, Yale University School of Medicine, New Haven, CT, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale Medical School, New Haven, CT, USA
- Program in Human and Translational Immunology, Yale University School of Medicine, New Haven, CT, USA
| | - Saquib A Lakhani
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
- Pediatric Genomics Discovery Program, Yale University School of Medicine, New Haven, CT, USA
| | - Ruth R Montgomery
- Section of Rheumatology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jason Catanzaro
- Division of Pediatric Allergy and Clinical Immunology, National Jewish Health, Denver, CO, USA
| | - Hongqiang Du
- National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Child Infection and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
- Department of Rheumatology & Immunology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Daniel V DiGiacomo
- Division of Rheumatology, Allergy and Immunology, Massachusetts General Hospital, Boston, MA, USA
| | - Holly Rothermel
- Division of Pediatric Rheumatology, MassGeneral for Children, Boston, MA, USA
| | - Christopher J Moran
- Division of Pediatric Gastroenterology, MassGeneral for Children, Boston, MA, USA
| | - Karoline Fiedler
- SickKids Inflammatory Bowel Disease Centre, The Hospital for Sick Children, Toronto, ON, Canada
- Cell Biology Program, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
| | - Neil Warner
- Cell Biology Program, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
| | - Esther P A H Hoppenreijs
- Department of Pediatric Rheumatology, Amalia Children's Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Caspar I van der Made
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Peter Olbrich
- Inborn Errors of Immunity Group, Biomedicine Institute of Sevilla (IBiS), CSIC, Seville, Spain
- Pediatric Infectious Diseases, Rheumatology and Immunology Unit, Hospital Universitario Virgen del Rocío, Seville, Spain
- Departamento de Farmacología, Pediatría y Radiología, Universidad de Sevilla, Seville, Spain
| | - Olaf Neth
- Inborn Errors of Immunity Group, Biomedicine Institute of Sevilla (IBiS), CSIC, Seville, Spain
- Pediatric Infectious Diseases, Rheumatology and Immunology Unit, Hospital Universitario Virgen del Rocío, Seville, Spain
| | - Alejandro Rodríguez-Martínez
- Pediatric Gastroenterology, Hepatology and Nutrition Unit, Hospital Universitario Virgen del Rocío, Seville, Spain
| | | | - Annemarie M C van Rossum
- Erasmus MC University Medical Center-Sophia Children's Hospital, Department of Pediatrics, Division of Infectious Diseases and Immunology, Rotterdam, The Netherlands
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Virgil A S H Dalm
- Department of Immunology, Laboratory of Medical Immunology, Erasmus University Medical Centre, Rotterdam, The Netherlands
- Department of Internal Medicine, Division of Allergy & Clinical Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Academic Center for Rare Immunological Diseases (RIDC), Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Aleixo M Muise
- SickKids Inflammatory Bowel Disease Centre, The Hospital for Sick Children, Toronto, ON, Canada
- Cell Biology Program, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Pediatrics, Institute of Medical Science and Biochemistry, University of Toronto, The Hospital for Sick Children, Toronto, ON, Canada
| | - Carrie L Lucas
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
- Program in Human and Translational Immunology, Yale University School of Medicine, New Haven, CT, USA.
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Koren O, Konnikova L, Brodin P, Mysorekar IU, Collado MC. The maternal gut microbiome in pregnancy: implications for the developing immune system. Nat Rev Gastroenterol Hepatol 2024; 21:35-45. [PMID: 38097774 DOI: 10.1038/s41575-023-00864-2] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/20/2023] [Indexed: 01/04/2024]
Abstract
The gut microbiome has important roles in host metabolism and immunity, and microbial dysbiosis affects human physiology and health. Maternal immunity and microbial metabolites during pregnancy, microbial transfer during birth, and transfer of immune factors, microorganisms and metabolites via breastfeeding provide critical sources of early-life microbial and immune training, with important consequences for human health. Only a few studies have directly examined the interactions between the gut microbiome and the immune system during pregnancy, and the subsequent effect on offspring development. In this Review, we aim to describe how the maternal microbiome shapes overall pregnancy-associated maternal, fetal and early neonatal immune systems, focusing on the existing evidence and highlighting current gaps to promote further research.
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Affiliation(s)
- Omry Koren
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Liza Konnikova
- Department of Paediatrics and Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT, USA
| | - Petter Brodin
- Department of Immunology and Inflammation, Imperial College London, London, UK
- Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden
| | - Indira U Mysorekar
- Department of Medicine, Section of Infectious Diseases, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Maria Carmen Collado
- Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Valencia, Spain.
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4
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Mooring M, Yeung GA, Luukkonen P, Liu S, Akbar MW, Zhang GJ, Balogun O, Yu X, Mo R, Nejak-Bowen K, Poyurovsky MV, Booth CJ, Konnikova L, Shulman GI, Yimlamai D. Hepatocyte CYR61 polarizes profibrotic macrophages to orchestrate NASH fibrosis. Sci Transl Med 2023; 15:eade3157. [PMID: 37756381 PMCID: PMC10874639 DOI: 10.1126/scitranslmed.ade3157] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 08/18/2023] [Indexed: 09/29/2023]
Abstract
Obesity is increasing worldwide and leads to a multitude of metabolic diseases, including cardiovascular disease, type 2 diabetes, nonalcoholic fatty liver disease, and nonalcoholic steatohepatitis (NASH). Cysteine-rich angiogenic inducer 61 (CYR61) is associated with the progression of NASH, but it has been described to have anti- and proinflammatory properties. We sought to examine the role of liver CYR61 in NASH progression. CYR61 liver-specific knockout mice on a NASH diet showed improved glucose tolerance, decreased liver inflammation, and reduced fibrosis. CYR61 polarized infiltrating monocytes promoting a proinflammatory/profibrotic phenotype through an IRAK4/SYK/NF-κB signaling cascade. In vitro, CYR61 activated a profibrotic program, including PDGFa/PDGFb expression in macrophages, in an IRAK4/SYK/NF-κB-dependent manner. Furthermore, targeted-antibody blockade reduced CYR61-driven signaling in macrophages in vitro and in vivo, reducing fibrotic development. This study demonstrates that CYR61 is a key driver of liver inflammation and fibrosis in NASH.
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Affiliation(s)
- Meghan Mooring
- Department of Cellular and Molecular Pathology, University of Pittsburgh, School of Medicine; Pittsburgh, Pennsylvania 15261, USA
- Section of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics; Yale School of Medicine; New Haven, Connecticut 06514, USA
- These authors contributed equally to this work
| | - Grace A. Yeung
- Section of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics; Yale School of Medicine; New Haven, Connecticut 06514, USA
- These authors contributed equally to this work
| | - Panu Luukkonen
- Department of Internal Medicine, Yale School of Medicine; New Haven, Connecticut 06514, USA
| | - Silvia Liu
- Department of Pathology, School of Medicine, University of Pittsburgh
- Pittsburgh Liver Research Center, University of Pittsburgh, School of Medicine; Pittsburgh, Pennsylvania 15261, USA
| | - Muhammad Waqas Akbar
- Section of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics; Yale School of Medicine; New Haven, Connecticut 06514, USA
| | - Gary J. Zhang
- Section of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics; Yale School of Medicine; New Haven, Connecticut 06514, USA
| | - Oluwashanu Balogun
- Department of Cellular and Molecular Pathology, University of Pittsburgh, School of Medicine; Pittsburgh, Pennsylvania 15261, USA
- Department of Pathology, School of Medicine, University of Pittsburgh
| | - Xuemei Yu
- Kadmon Corporation, LLC; 450 East 29th Street, New York, New York 10016, USA
| | - Rigen Mo
- Kadmon Corporation, LLC; 450 East 29th Street, New York, New York 10016, USA
| | - Kari Nejak-Bowen
- Department of Cellular and Molecular Pathology, University of Pittsburgh, School of Medicine; Pittsburgh, Pennsylvania 15261, USA
- Department of Pathology, School of Medicine, University of Pittsburgh
- Pittsburgh Liver Research Center, University of Pittsburgh, School of Medicine; Pittsburgh, Pennsylvania 15261, USA
| | - Masha V. Poyurovsky
- Kadmon Corporation, LLC; 450 East 29th Street, New York, New York 10016, USA
| | - Carmen J. Booth
- Department of Comparative Medicine; Yale School of Medicine; New Haven, Connecticut 06514, USA
| | - Liza Konnikova
- Section of Neonatology; Department of Pediatrics; Yale School of Medicine; New Haven, Connecticut 06514, USA
| | - Gerald I. Shulman
- Department of Internal Medicine, Yale School of Medicine; New Haven, Connecticut 06514, USA
- Department of Cellular & Molecular Physiology, Yale School of Medicine; New Haven, Connecticut 06514, USA
| | - Dean Yimlamai
- Department of Cellular and Molecular Pathology, University of Pittsburgh, School of Medicine; Pittsburgh, Pennsylvania 15261, USA
- Section of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics; Yale School of Medicine; New Haven, Connecticut 06514, USA
- Pittsburgh Liver Research Center, University of Pittsburgh, School of Medicine; Pittsburgh, Pennsylvania 15261, USA
- The Yale Liver Center, Yale School of Medicine; New Haven, Connecticut 06514, USA
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5
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Rice TA, Konnikova L. Propionate primes the DC pump in neonates. Immunity 2023; 56:903-905. [PMID: 37163990 DOI: 10.1016/j.immuni.2023.04.006] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 05/12/2023]
Abstract
The protective benefits of breastmilk are well-appreciated, yet lack mechanistic detail. In this issue of Immunity, Sikder et al. reveal how breastmilk-microbiota-derived propionate induces Flt3L expression, dendritic cell maturation, regulatory T cell recruitment, and antiviral immunity in the lung.
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Affiliation(s)
- Tyler A Rice
- Department of Pediatrics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Liza Konnikova
- Department of Pediatrics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Obstetrics, Gynecology and Reproductive Science, Yale School of Medicine, New Haven, CT 06510, USA; Program of Translational Biomedicine, Yale School of Medicine, New Haven, CT 06510, USA; Program of Human and Translational Immunology, Yale School of Medicine, New Haven, CT 06510, USA.
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6
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Egozi A, Olaloye O, Werner L, Silva T, McCourt B, Pierce RW, An X, Wang F, Chen K, Pober JS, Shouval D, Itzkovitz S, Konnikova L. Single-cell atlas of the human neonatal small intestine affected by necrotizing enterocolitis. PLoS Biol 2023; 21:e3002124. [PMID: 37205711 PMCID: PMC10234541 DOI: 10.1371/journal.pbio.3002124] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 06/01/2023] [Accepted: 04/13/2023] [Indexed: 05/21/2023] Open
Abstract
Necrotizing enterocolitis (NEC) is a gastrointestinal complication of premature infants with high rates of morbidity and mortality. A comprehensive view of the cellular changes and aberrant interactions that underlie NEC is lacking. This study aimed at filling in this gap. We combine single-cell RNA sequencing (scRNAseq), T-cell receptor beta (TCRβ) analysis, bulk transcriptomics, and imaging to characterize cell identities, interactions, and zonal changes in NEC. We find an abundance of proinflammatory macrophages, fibroblasts, endothelial cells as well as T cells that exhibit increased TCRβ clonal expansion. Villus tip epithelial cells are reduced in NEC and the remaining epithelial cells up-regulate proinflammatory genes. We establish a detailed map of aberrant epithelial-mesenchymal-immune interactions that are associated with inflammation in NEC mucosa. Our analyses highlight the cellular dysregulations of NEC-associated intestinal tissue and identify potential targets for biomarker discovery and therapeutics.
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Affiliation(s)
- Adi Egozi
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Oluwabunmi Olaloye
- Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Lael Werner
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children’s Medical Center of Israel, Petah Tikva, Israel, affiliated to the Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tatiana Silva
- Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Blake McCourt
- Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Richard W. Pierce
- Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut, United States of America
- Program in Human and Translational Immunology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Xiaojing An
- Department of Medicine, University of Pittsburgh Medical Center Montefiore Hospital, Pittsburgh, Pennsylvania, United States of America
| | - Fujing Wang
- Department of Medicine, University of Pittsburgh Medical Center Montefiore Hospital, Pittsburgh, Pennsylvania, United States of America
| | - Kong Chen
- Department of Medicine, University of Pittsburgh Medical Center Montefiore Hospital, Pittsburgh, Pennsylvania, United States of America
| | - Jordan S. Pober
- Program in Human and Translational Immunology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Dror Shouval
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children’s Medical Center of Israel, Petah Tikva, Israel, affiliated to the Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shalev Itzkovitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Liza Konnikova
- Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut, United States of America
- Program in Human and Translational Immunology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, Connecticut, United States of America
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7
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Gehlhaar A, Shouval D, Santiago EG, Ling G, McCourt B, Werner L, Yerushalmi B, Konnikova L. Immune dysregulation in Glycogen Storage Disease 1b - a CyTOF approach. Res Sq 2023:rs.3.rs-2598829. [PMID: 36865166 PMCID: PMC9980199 DOI: 10.21203/rs.3.rs-2598829/v1] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Glycogen Storage Disease type 1b (GSD1b) is a rare disease manifesting as hypoglycemia, recurrent infections and neutropenia, resulting from deleterious mutations in the SLC37A4 gene encoding the glucose-6-phosphate transporter. The susceptibility to infections is thought to be attributed not only to the neutrophil defect, though extensive immunophenotyping characterization is currently missing. Here we apply a systems immunology approach utilizing Cytometry by Time Of Flight (CyTOF) to map the peripheral immune landscape of 6 GSD1b patients. When compared to control subjects, those with GSD1b had a significant reduction in anti-inflammatory macrophages, CD16+ macrophages, and Natural Killer cells. Additionally, there was a preference towards a central versus an effector memory phenotype in multiple T cell populations, which may suggest that these changes stem from an inability of activated immune cell populations to undergo the appropriate switch to glycolytic metabolism in the hypoglycemic conditions associated with GSD1b. Furthermore, we identified a global reduction of CD123, CD14, CCR4, CD24 and CD11b across several populations and a multi-cluster upregulation of CXCR3, hinting at a potential role of impaired immune cell trafficking in the context of GSD1b. Taken together, our data indicates that that the immune impairment observed in GSD1b patients extends far beyond neutropenia and encompasses innate and adaptive compartments, which may provide novel insights into the pathogenesis of this disorder.
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8
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Olaloye O, Eke C, Jolteus A, Konnikova L. Single cell analysis via mass cytometry of spontaneous intestinal perforation reveals alterations in small intestinal innate and adaptive mucosal immunity. Front Immunol 2023; 14:995558. [PMID: 36825028 PMCID: PMC9941693 DOI: 10.3389/fimmu.2023.995558] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 01/18/2023] [Indexed: 02/10/2023] Open
Abstract
Introduction Spontaneous intestinal perforation (SIP) is a poorly understood severe gastrointestinal complications of prematurity which is poorly understood. Extremely premature infants born prior to 28 weeks' gestation develop a localized perforation of the terminal ileum during the first week of life and therapy involves surgery and cessation of enteral feeds. Little is known regardj g the impact of mucosal immune dysfunction on disease pathogenesis. Methods We performed mass cytometry time of flight (CyTOF) of small intestinal mucosa of patients with SIP (Gestational age (GA) 24 - 27 weeks, n=8) compared to patients who had surgery for non-SIP conditions (neonatal (GA >36 weeks, n=5 ) and fetal intestine from elective terminations (GA 18-21 weeks, n=4). CyTOF analysis after stimulation of T cells with PMA/Ionomycin was also performed. Results We noted changes in innate and adaptive mucosal immunity in SIP. SIP mucosa had an expansion of ckit+ neutrophils, an influx of naïve CD4 and CD8 T cells and a reduction of effector memory T cells. SIP T cells were characterized by reduced CCR6 and CXCR3 expression and increased interferon gamma expression after stimulation. Discussion These findings suggest that previously unrecognized immune dysregulation is associated with SIP and should be explored in future studies.
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Affiliation(s)
- Oluwabunmi Olaloye
- Department of Pediatrics, Yale University, New Haven, CT, United States
- Division of Neonatal and Perinatal Medicine Yale University, New Haven, CT, United States
| | - Chino Eke
- Department of Pediatrics, Yale University, New Haven, CT, United States
| | - Abigail Jolteus
- Department of Pediatrics, Yale University, New Haven, CT, United States
| | - Liza Konnikova
- Department of Pediatrics, Yale University, New Haven, CT, United States
- Division of Neonatal and Perinatal Medicine Yale University, New Haven, CT, United States
- Department of Obstetrics, Gynecology, and Reproductive Sciences, New Haven, CT, United States
- Program in Human and Translational Immunology, Yale University, New Haven, CT, United States
- *Correspondence: Liza Konnikova,
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9
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Kennedy KM, de Goffau MC, Perez-Muñoz ME, Arrieta MC, Bäckhed F, Bork P, Braun T, Bushman FD, Dore J, de Vos WM, Earl AM, Eisen JA, Elovitz MA, Ganal-Vonarburg SC, Gänzle MG, Garrett WS, Hall LJ, Hornef MW, Huttenhower C, Konnikova L, Lebeer S, Macpherson AJ, Massey RC, McHardy AC, Koren O, Lawley TD, Ley RE, O'Mahony L, O'Toole PW, Pamer EG, Parkhill J, Raes J, Rattei T, Salonen A, Segal E, Segata N, Shanahan F, Sloboda DM, Smith GCS, Sokol H, Spector TD, Surette MG, Tannock GW, Walker AW, Yassour M, Walter J. Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies. Nature 2023; 613:639-649. [PMID: 36697862 DOI: 10.1038/s41586-022-05546-8] [Citation(s) in RCA: 94] [Impact Index Per Article: 94.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/09/2022] [Indexed: 01/26/2023]
Abstract
Whether the human fetus and the prenatal intrauterine environment (amniotic fluid and placenta) are stably colonized by microbial communities in a healthy pregnancy remains a subject of debate. Here we evaluate recent studies that characterized microbial populations in human fetuses from the perspectives of reproductive biology, microbial ecology, bioinformatics, immunology, clinical microbiology and gnotobiology, and assess possible mechanisms by which the fetus might interact with microorganisms. Our analysis indicates that the detected microbial signals are likely the result of contamination during the clinical procedures to obtain fetal samples or during DNA extraction and DNA sequencing. Furthermore, the existence of live and replicating microbial populations in healthy fetal tissues is not compatible with fundamental concepts of immunology, clinical microbiology and the derivation of germ-free mammals. These conclusions are important to our understanding of human immune development and illustrate common pitfalls in the microbial analyses of many other low-biomass environments. The pursuit of a fetal microbiome serves as a cautionary example of the challenges of sequence-based microbiome studies when biomass is low or absent, and emphasizes the need for a trans-disciplinary approach that goes beyond contamination controls by also incorporating biological, ecological and mechanistic concepts.
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Affiliation(s)
- Katherine M Kennedy
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Marcus C de Goffau
- Tytgat Institute for Liver and Intestinal Research, Amsterdam University Medical Centers, Amsterdam, The Netherlands
- Department of Vascular Medicine, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
- Wellcome Sanger Institute, Cambridge, UK
| | - Maria Elisa Perez-Muñoz
- Department of Agriculture, Food and Nutrition Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Marie-Claire Arrieta
- International Microbiome Center, University of Calgary, Calgary, Alberta, Canada
| | - Fredrik Bäckhed
- The Wallenberg Laboratory, Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Physiology, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, Berlin, Germany
- Yonsei Frontier Lab (YFL), Yonsei University, Seoul, South Korea
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Thorsten Braun
- Department of Obstetrics and Experimental Obstetrics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Frederic D Bushman
- Department of Microbiology Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Joel Dore
- Université Paris-Saclay, INRAE, MetaGenoPolis, AgroParisTech, MICALIS, Jouy-en-Josas, France
| | - Willem M de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Boston, MA, USA
| | - Jonathan A Eisen
- Department of Evolution and Ecology, University of California, Davis, Davis, CA, USA
- Department of Medical Microbiology and Immunology, University of California, Davis, Davis, CA, USA
- UC Davis Genome Center, University of California, Davis, Davis, CA, USA
| | - Michal A Elovitz
- Maternal and Child Health Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Stephanie C Ganal-Vonarburg
- Universitätsklinik für Viszerale Chirurgie und Medizin, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Michael G Gänzle
- Department of Agriculture, Food and Nutrition Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Wendy S Garrett
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Harvard T.H. Chan Microbiome in Public Health Center, Boston, MA, USA
- Department of Medicine and Division of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lindsay J Hall
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
- Chair of Intestinal Microbiome, ZIEL-Institute for Food and Health, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Mathias W Hornef
- Institute of Medical Microbiology, RWTH University Hospital, Aachen, Germany
| | - Curtis Huttenhower
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Liza Konnikova
- Departments of Pediatrics and Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Sarah Lebeer
- Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Andrew J Macpherson
- Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Ruth C Massey
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Alice Carolyn McHardy
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany
- German Center for Infection Research (DZIF), Hannover Braunschweig site, Braunschweig, Germany
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Trevor D Lawley
- Department of Vascular Medicine, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Liam O'Mahony
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
- Department of Medicine, University College Cork, Cork, Ireland
| | - Paul W O'Toole
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Eric G Pamer
- Duchossois Family Institute, University of Chicago, Chicago, IL, USA
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Jeroen Raes
- VIB Center for Microbiology, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Thomas Rattei
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Anne Salonen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Eran Segal
- Weizmann Institute of Science, Rehovot, Israel
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
- European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Fergus Shanahan
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Medicine, University College Cork, Cork, Ireland
| | - Deborah M Sloboda
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
- Department of Obstetrics and Gynecology, McMaster University, Hamilton, Ontario, Canada
| | - Gordon C S Smith
- Department of Obstetrics and Gynaecology, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Harry Sokol
- Gastroenterology Department, AP-HP, Saint Antoine Hospital, Centre de Recherche Saint-Antoine, CRSA, INSERM and Sorbonne Université, Paris, France
- Paris Center for Microbiome Medicine (PaCeMM), Fédération Hospitalo-Universitaire, Paris, France
- Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy en Josas, France
| | - Tim D Spector
- Department of Twin Research, King's College London, London, UK
| | - Michael G Surette
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Gerald W Tannock
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alan W Walker
- Gut Health Group, Rowett Institute, University of Aberdeen, Aberdeen, UK
| | - Moran Yassour
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Microbiology and Molecular Genetics, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jens Walter
- APC Microbiome Ireland, University College Cork, Cork, Ireland.
- School of Microbiology, University College Cork, Cork, Ireland.
- Department of Medicine, University College Cork, Cork, Ireland.
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10
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Sultan M, Adawi M, Kol N, McCourt B, Adawi I, Baram L, Tal N, Werner L, Lev A, Snapper SB, Barel O, Konnikova L, Somech R, Shouval DS. RIPK1 mutations causing infantile-onset IBD with inflammatory and fistulizing features. Front Immunol 2022; 13:1041315. [PMID: 36466854 PMCID: PMC9716469 DOI: 10.3389/fimmu.2022.1041315] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 10/04/2022] [Indexed: 08/13/2023] Open
Abstract
PURPOSE Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) is an important regulator of necroptosis and inflammatory responses. We present the clinical features, genetic analysis and immune work-up of two patients with infantile-onset inflammatory bowel disease (IBD) resulting from RIPK1 mutations. METHODS Whole exome and Sanger sequencing was performed in two IBD patients. Mass cytometry time of flight (CyTOF) was conducted for in-depth immunophenotyping on one of the patient's peripheral blood mononuclear cells, and compared to control subjects and patients with Crohn's disease. RESULTS The patients presented with severe colitis and perianal fistulas in the first months of life, without severe/atypical infections. Genetic studies identified pathogenic genetic variants in RIPK1 (Patient 1, A c.1934C>T missense mutation in Exon 11; Patient 2, c.580G>A missense mutation residing in Exon 4). Protein modeling demonstrated that the mutation in Patient 1 displaces a water molecule, potentially disrupting the local environment, and the mutation in Patient 2 may lead to disruption of the packing and conformation of the kinase domain. Immunofluorescence RIPK1 staining in rectal biopsies demonstrated no expression for Patient 1 and minimal expression for Patient 2, compared to controls and patients with active Crohn's disease. Using CyTOF unbiased clustering analysis, we identified peripheral immune dysregulation in one of these patients, characterized by an increase in IFNγ CD8+ T cells along with a decrease in monocytes, dendritic cells and B cells. Moreover, RIPK1-deficient patient's immune cells exhibited decreased IL-6 production in response to lipopolysaccharide (LPS) across multiple cell types including T cells, B cells and innate immune cells. CONCLUSIONS Mutations in RIPK1 should be considered in very young patients presenting with colitis and perianal fistulas. Given RIPK1's role in inflammasome activation, but also in epithelial cells, it is unclear whether IL1 blockade or allogeneic hematopoietic stem cell transplantation can suppress or cure the hyper-inflammatory response in these patients. Additional studies in humans are required to better define the role of RIPK1 in regulating intestinal immune responses, and how treatment can be optimized for patients with RIPK1 deficiency.
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Affiliation(s)
- Mutaz Sultan
- Department of Pediatrics, Faculty of Medicine, Makassed Hospital, Al-Quds University, Jerusalem, Palestine
| | - Mohammad Adawi
- Department of Pediatrics, Faculty of Medicine, Makassed Hospital, Al-Quds University, Jerusalem, Palestine
| | - Nitzan Kol
- The Genomic Unit, Sheba Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel
- Wohl Institute of Translational Medicine, Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Blake McCourt
- Department of Pediatrics, Yale Medical School, New Haven, CT, United States
- Department of Obstetrics, Gynecology and Reproductive Sciences, Human and Translational Immunology, Yale Medical School, New Haven, CT, United States
| | - Ihda Adawi
- Department of Pediatrics, Faculty of Medicine, Makassed Hospital, Al-Quds University, Jerusalem, Palestine
| | - Liran Baram
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children’s Medical Center of Israel, Petah Tiqwa, Israel
| | - Noa Tal
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children’s Medical Center of Israel, Petah Tiqwa, Israel
| | - Lael Werner
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children’s Medical Center of Israel, Petah Tiqwa, Israel
| | - Atar Lev
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Pediatric Immunology Service, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat Gan, Israel
- Pediatric Department Ward A, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat Gan, Israel
- Jeffrey Modell Foundation Center, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat Gan, Israel
| | - Scott B. Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston, MA, United States
- Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Ortal Barel
- The Genomic Unit, Sheba Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel
- Wohl Institute of Translational Medicine, Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Liza Konnikova
- Department of Pediatrics, Yale Medical School, New Haven, CT, United States
- Department of Obstetrics, Gynecology and Reproductive Sciences, Human and Translational Immunology, Yale Medical School, New Haven, CT, United States
| | - Raz Somech
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Pediatric Immunology Service, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat Gan, Israel
- Pediatric Department Ward A, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat Gan, Israel
- Jeffrey Modell Foundation Center, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Ramat Gan, Israel
| | - Dror S. Shouval
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Institute of Gastroenterology, Nutrition and Liver Diseases, Schneider Children’s Medical Center of Israel, Petah Tiqwa, Israel
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11
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Gehlhaar A, Inala A, Llivichuzhca-Loja D, Silva TN, Adegboye CY, O’Connell AE, Konnikova L. Insights into the Role of Commensal-Specific T Cells in Intestinal Inflammation. J Inflamm Res 2022; 15:1873-1887. [PMID: 35342295 PMCID: PMC8943607 DOI: 10.2147/jir.s288288] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/19/2022] [Indexed: 12/21/2022] Open
Abstract
Trillions of microorganisms exist in the human intestine as commensals and contribute to homeostasis through their interactions with the immune system. In this review, we use previous evidence from published papers to elucidate the involvement of commensal-specific T cells (CSTCs) in regulating intestinal inflammatory responses. CSTCs are generated centrally in the thymus or peripherally at mucosal interfaces and present as CD4+ or CD8+ T cells. Bacteria, fungi, and even viruses act commensally with humans, warranting consideration of CSTCs in this critical relationship. Dysregulation of this immunological balance can result in both intestinal inflammation or damaging autoimmune responses elsewhere in the body. Given the relative novelty of CSTCs in the literature, we aim to introduce the importance of their role in maintaining immune homeostasis at barrier sites such as the intestine.
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Affiliation(s)
- Arne Gehlhaar
- Department of Pediatrics, Yale University, New Haven, CT, USA
| | - Ashwin Inala
- Department of Pediatrics, Yale University, New Haven, CT, USA
| | | | - Tatiana N Silva
- Department of Pediatrics, Yale University, New Haven, CT, USA
| | - Comfort Y Adegboye
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, MA, USA
| | - Amy E O’Connell
- Division of Newborn Medicine, Boston Children’s Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Correspondence: Amy E O’Connell, Division of Newborn Medicine, Boston Children’s Hospital, 300 Longwood Ave, Boston, MA, USA, Tel +1 617 919-2358, Email
| | - Liza Konnikova
- Department of Pediatrics, Yale University, New Haven, CT, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University, New Haven, CT, USA
- Program in Human and Translational Immunology, Yale University, New Haven, CT, USA
- Liza Konnikova, Department of Pediatrics, Yale University, 375 Congress Ave, LSOG 405B, New Haven, CT, USA, Tel +1 203 737-8016, Email
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12
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Toothaker JM, Olaloye O, McCourt BT, McCourt CC, Silva TN, Case RM, Liu P, Yimlamai D, Tseng G, Konnikova L. Immune landscape of human placental villi using single-cell analysis. Development 2022; 149:274057. [PMID: 35050308 PMCID: PMC8935213 DOI: 10.1242/dev.200013] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 07/19/2021] [Accepted: 12/30/2021] [Indexed: 12/19/2022]
Abstract
Maintenance of a healthy pregnancy is reliant on a successful balance between the fetal and maternal immune systems. Although the maternal mechanisms responsible have been well studied, those used by the fetal immune system remain poorly understood. Using suspension mass cytometry and various imaging modalities, we report a complex immune system within the mid-gestation (17-23 weeks) human placental villi (PV). Consistent with recent reports in other fetal organs, T cells with memory phenotypes, although rare in abundance, were detected within the PV tissue and vasculature. Moreover, we determined that T cells isolated from PV samples may be more proliferative after T cell receptor stimulation than adult T cells at baseline. Collectively, we identified multiple subtypes of fetal immune cells within the PV and specifically highlight the enhanced proliferative capacity of fetal PV T cells.
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Affiliation(s)
- Jessica M. Toothaker
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15213, USA,Department of Pediatrics, Yale University, New Haven, CT 06510, USA
| | | | - Blake T. McCourt
- Department of Pediatrics, Yale University, New Haven, CT 06510, USA
| | - Collin C. McCourt
- Department of Pediatrics, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15219, USA
| | - Tatiana N. Silva
- Department of Pediatrics, Yale University, New Haven, CT 06510, USA
| | - Rebecca M. Case
- Department of Pediatrics, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA 15219, USA
| | - Peng Liu
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Dean Yimlamai
- Department of Pediatrics, Yale University, New Haven, CT 06510, USA
| | - George Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Liza Konnikova
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15213, USA,Department of Pediatrics, Yale University, New Haven, CT 06510, USA,Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University, New Haven, CT 06519, USA,Program in Human and Translational Immunology, Yale University, New Haven, CT 06519, USA,Author for correspondence ()
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13
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Kennedy KM, Bellissimo CJ, Breznik JA, Barrett J, Braun T, Bushman FD, De Goffau M, Elovitz MA, Heimesaat MM, Konnikova L, Koren O, Parry S, Rossi L, Segata N, Simmons RA, Surette MG, Walter J, Sloboda DM. Over-celling fetal microbial exposure. Cell 2021; 184:5839-5841. [PMID: 34822779 DOI: 10.1016/j.cell.2021.10.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/05/2021] [Accepted: 10/26/2021] [Indexed: 12/21/2022]
Affiliation(s)
- Katherine M Kennedy
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada; Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Christian J Bellissimo
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada; Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Jessica A Breznik
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada; Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Jon Barrett
- Department of Obstetrics and Gynecology, McMaster University, Hamilton, ON, Canada
| | - Thorsten Braun
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Obstetrics and 'Experimental Obstetrics', Berlin, Germany
| | - Frederic D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marcus De Goffau
- Department of Vascular Medicine, Amsterdam University Medical Center, University of Amsterdam, 1105 AZ Amsterdam, the Netherlands; Wellcome Sanger Institute, Cambridge, UK
| | - Michal A Elovitz
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Maternal and Child Health Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Center for Research on Reproduction and Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Markus M Heimesaat
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Department of Obstetrics and 'Experimental Obstetrics', Berlin, Germany; Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Micro-biology, Infectious Diseases and Immunology, Berlin, Germany
| | - Liza Konnikova
- Department of Pediatrics, Department of Obstetrics, Gynecology and Reproductive Sciences, Human and Translational Immunology, Yale Medical School, New Haven, CT, USA
| | - Omry Koren
- The Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Samuel Parry
- Maternal and Child Health Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Laura Rossi
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada; Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Nicola Segata
- Department CIBIO, University of Trento, Trento, Italy
| | - Rebecca A Simmons
- Center for Research on Reproduction and Women's Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Division of Neonatology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michael G Surette
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada; Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada; Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Jens Walter
- APC Microbiome Ireland, School of Microbiology and Department of Medicine, University College Cork - National University of Ireland, Cork, Ireland
| | - Deborah M Sloboda
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada; Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, ON, Canada; Department of Obstetrics and Gynecology, McMaster University, Hamilton, ON, Canada; Department of Pediatrics, McMaster University, Hamilton, ON, Canada.
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14
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Chen A, Jiang Y, Li Z, Wu L, Santiago U, Zou H, Cai C, Sharma V, Guan Y, McCarl LH, Ma J, Wu YL, Michel J, Shi Y, Konnikova L, Amankulor NM, Zinn PO, Kohanbash G, Agnihotri S, Lu S, Lu X, Sun D, Gittes GK, Wang Q, Xiao X, Yimlamai D, Pollack IF, Camacho CJ, Hu B. Chitinase-3-like 1 protein complexes modulate macrophage-mediated immune suppression in glioblastoma. J Clin Invest 2021; 131:e147552. [PMID: 34228644 DOI: 10.1172/jci147552] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 06/22/2021] [Indexed: 12/16/2022] Open
Affiliation(s)
- Apeng Chen
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yinan Jiang
- John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Pediatric Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Zhengwei Li
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Neurosurgery, Zhongnan Hospital, Wuhan University, Wuhan, Hubei, China
| | - Lingxiang Wu
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
| | | | - Han Zou
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Chunhui Cai
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Vaibhav Sharma
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yongchang Guan
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Neurosurgery, The Fourth Hospital of China Medical University, Shenyang, Liaoning, China
| | - Lauren H McCarl
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jie Ma
- John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Pediatric Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Yijen L Wu
- John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Developmental Biology and
| | - Joshua Michel
- John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yi Shi
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Liza Konnikova
- Section of Neonatal, Perinatal Medicine, Department of Pediatrics and Obstetrics, Gynecology, and Reproductive Sciences, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Nduka M Amankulor
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Pascal O Zinn
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Gary Kohanbash
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Sameer Agnihotri
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Songjian Lu
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Xinghua Lu
- Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Dandan Sun
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - George K Gittes
- John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Pediatric Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Qianghu Wang
- Department of Bioinformatics, Nanjing Medical University, Nanjing, China
| | - Xiangwei Xiao
- John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Pediatric Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Dean Yimlamai
- Section of Pediatric Gastroenterology and Hepatology, Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Ian F Pollack
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | | | - Baoli Hu
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,John G. Rangos Sr. Research Center, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Cancer Biology Program, UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
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15
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Olaloye OO, Liu P, Toothaker JM, McCourt BT, McCourt CC, Xiao J, Prochaska E, Shaffer S, Werner L, Gringauz J, Good M, Goldsmith JD, An X, Wang F, Snapper SB, Shouval D, Chen K, Tseng G, Konnikova L. CD16+CD163+ monocytes traffic to sites of inflammation during necrotizing enterocolitis in premature infants. J Exp Med 2021; 218:212478. [PMID: 34269788 PMCID: PMC8289692 DOI: 10.1084/jem.20200344] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 02/08/2021] [Accepted: 06/07/2021] [Indexed: 11/30/2022] Open
Abstract
Necrotizing enterocolitis (NEC) is a severe gastrointestinal complication of prematurity. Using suspension and imaging mass cytometry coupled with single-cell RNA sequencing, we demonstrate severe inflammation in patients with NEC. NEC mucosa could be subtyped by an influx of three distinct neutrophil phenotypes (immature, newly emigrated, and aged). Furthermore, CD16+CD163+ monocytes/Mϕ, correlated with newly emigrated neutrophils, were specifically enriched in NEC mucosa, found adjacent to the blood vessels, and increased in circulation of infants with surgical NEC, suggesting trafficking from the periphery to areas of inflammation. NEC-specific monocytes/Mϕ transcribed inflammatory genes, including TREM1, IL1A, IL1B, and calprotectin, and neutrophil recruitment genes IL8, CXCL1, CXCL2, CXCL5 and had enrichment of gene sets in pathways involved in chemotaxis, migration, phagocytosis, and reactive oxygen species generation. In summary, we identify a novel subtype of inflammatory monocytes/Mϕ associated with NEC that should be further evaluated as a potential biomarker of surgical NEC and a target for the development of NEC-specific therapeutics.
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Affiliation(s)
| | - Peng Liu
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA
| | | | - Blake T McCourt
- Department of Pediatrics, Yale Medical School, New Haven, CT
| | - Collin C McCourt
- Department of Pediatrics, University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh, Pittsburgh, PA
| | - Jenny Xiao
- Department of Biology, University of Pittsburgh, Pittsburgh, PA
| | - Erica Prochaska
- Division of Infectious Diseases, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Spenser Shaffer
- Division of Newborn Medicine, University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh, Pittsburgh, PA
| | - Lael Werner
- Institute of Gastroenterology, Nutrition and Liver Disease, Schneider Children's Medical Center of Israel, Petah Tiqwa, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | | | - Jordan Gringauz
- Department of Medicine, Boston Children's Hospital, Boston, MA
| | - Misty Good
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO
| | | | - Xiaojing An
- Department of Medicine, University of Pittsburgh Medical Center Montefiore Hospital, Pittsburgh, PA
| | - Fujing Wang
- Department of Medicine, University of Pittsburgh Medical Center Montefiore Hospital, Pittsburgh, PA
| | - Scott B Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA
| | - Dror Shouval
- Institute of Gastroenterology, Nutrition and Liver Disease, Schneider Children's Medical Center of Israel, Petah Tiqwa, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Kong Chen
- Department of Medicine, University of Pittsburgh Medical Center Montefiore Hospital, Pittsburgh, PA
| | - George Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA
| | - Liza Konnikova
- Department of Pediatrics, Yale Medical School, New Haven, CT.,Department of Immunology, University of Pittsburgh, Pittsburgh, PA.,Division of Newborn Medicine, University of Pittsburgh Medical Center, Children's Hospital of Pittsburgh, Pittsburgh, PA.,Division of Reproductive Sciences, Yale University, New Haven, CT.,Program in Human and Translational Immunology Yale University, New Haven, CT
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16
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Muller K, Xiao J, Putra J, Rothstein R, McCourt C, Konnikova L, Lisovsky M. Lymphocytic Esophagitis With Predominance of CD4 T Cells and Expansion of Th1 Cells Is Associated With Achalasia. Am J Clin Pathol 2021; 156:278-287. [PMID: 33609026 DOI: 10.1093/ajcp/aqaa239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 11/12/2022] Open
Abstract
OBJECTIVES Although histologic features in biopsies suggesting a possibility of achalasia would be helpful diagnostically, such features remain unknown. The goal of this study was to explore the prevalence, histologic features, and immunophenotype of lymphocytic esophagitis (LyE) in achalasia biopsies. METHODS The study group consisted of 57 patients with achalasia. Controls comprised 52 patients with severe gastroesophageal reflux disease (GERD) and normal esophageal motility. CD4/CD8 immunophenotype of lymphocytes was analyzed by immunohistochemistry. RESULTS LyE was identified in 30% (17/57) of patients with achalasia and 6% (3/52) of patients with GERD, indicating a strong association with achalasia (odds ratio, 6.94; 95% confidence interval, 1.90-25.38). LyE was focal in 59% (10/17) of the cases and diffuse in 41% (7/17). CD4 T-cell predominance over CD8 T cells was observed in 88% of patients with achalasia and LyE. T helper 1 (Th1) cells, but not T helper 2 cells, were expanded in CD4 T cells; in the absence of evident infection, this was compatible with the role of Th1 cells in organ-specific autoimmunity. CONCLUSIONS Achalasia should be considered in the differential diagnosis of clinical entities associated with CD4-predominant LyE. Additional studies to explore the significance of Th1 cells in achalasia-associated LyE are warranted.
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Affiliation(s)
- Kristen Muller
- Department of Pathology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Jenny Xiao
- Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Juan Putra
- Department of Pathology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Richard Rothstein
- Section of Gastroenterology and Hepatology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Collin McCourt
- Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Liza Konnikova
- Department of Pediatrics, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mikhail Lisovsky
- Department of Pathology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
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17
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Koutroumpakis F, Phillips AE, Yadav D, Machicado JD, Ahsan M, Ramos Rivers C, Tan X, Schwartz M, Proksell S, Johnston E, Dueker J, Hashash JG, Barrie A, Harrison J, Dunn MA, Konnikova L, Hartman DJ, Din H, Babichenko D, Tang G, Binion DG. Serum IgG4 Subclass Deficiency Defines a Distinct, Commonly Encountered, Severe Inflammatory Bowel Disease Subtype. Inflamm Bowel Dis 2021; 27:855-863. [PMID: 32879976 DOI: 10.1093/ibd/izaa230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Immunoglobulin G subclass 4 (IgG4) is hypothesized to play an immunomodulatory role, downregulating humoral immune responses. The role of this anti-inflammatory molecule in inflammatory bowel disease (IBD) has not been fully characterized. We sought to define alterations in serum IgG4 in patients with IBD and their association with multiyear disease severity. METHODS We analyzed metadata derived from curated electronic health records from consented patients with IBD prospectively followed at a tertiary center over a 10-year time period. Patients with IBD with IgG4 serum levels available formed the study population. Demographics and multiyear clinical data were collected and analyzed. We stratified patients with IBD with low, normal, or high serum IgG4 levels. RESULTS We found IgG4 characterized in 1193 patients with IBD and low IgG4 levels in 233 patients (20%) and elevated IgG4 levels in 61 patients (5%). An IgG4 deficiency did not significantly correlate with other antibody deficiencies. In a multiple Poisson regression analysis, low IgG4 was associated with more years on biologic agents (P = 0.002) and steroids (P = 0.049) and more hospital admissions (P < 0.001), clinic visits (P = 0.010), outpatient antibiotic prescriptions (P < 0.001), and CD-related surgeries (P = 0.011) during the study period after controlling for certain confounders. Elevated IgG4 was only associated with primary sclerosing cholangitis (P = 0.011). A cohort of patients with IgG4-deficient severe IBD received intravenous Ig replacement therapy, which benefited and was continued in 10 out of 11 individuals. CONCLUSIONS An IgG4 subclass deficiency, distinct from other antibody deficiencies, occurred commonly in a referral IBD population and was associated with multiple markers of disease severity. This is the first association of IgG4 subclass deficiency with an inflammatory disease process. Further work is needed to define the mechanistic role of IgG4 deficiency in this severe IBD subgroup.
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Affiliation(s)
- Filippos Koutroumpakis
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States
| | - Anna Evans Phillips
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States
| | - Dhiraj Yadav
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States
| | - Jorge D Machicado
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic Health System, Eau Claire, Wisconsin, United States
| | - Maaz Ahsan
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States
| | - Claudia Ramos Rivers
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States
| | - Xiaoqing Tan
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Marc Schwartz
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States
| | - Siobhan Proksell
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States
| | - Elyse Johnston
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States
| | - Jeffrey Dueker
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States
| | - Jana G Hashash
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States
| | - Arthur Barrie
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States
| | - Janet Harrison
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States
| | - Michael A Dunn
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States
| | - Liza Konnikova
- Department of Pediatrics, Division of Newborn Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States
| | - Douglas J Hartman
- Department of Pathology, Division of Anatomic Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Hasieb Din
- Internal Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States
| | - Dmitriy Babichenko
- School of Information Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Gong Tang
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - David G Binion
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States
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18
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Lu-Culligan A, Chavan AR, Vijayakumar P, Irshaid L, Courchaine EM, Milano KM, Tang Z, Pope SD, Song E, Vogels CBF, Lu-Culligan WJ, Campbell KH, Casanovas-Massana A, Bermejo S, Toothaker JM, Lee HJ, Liu F, Schulz W, Fournier J, Muenker MC, Moore AJ, Konnikova L, Neugebauer KM, Ring A, Grubaugh ND, Ko AI, Morotti R, Guller S, Kliman HJ, Iwasaki A, Farhadian SF. Maternal respiratory SARS-CoV-2 infection in pregnancy is associated with a robust inflammatory response at the maternal-fetal interface. Med 2021; 2:591-610.e10. [PMID: 33969332 PMCID: PMC8084634 DOI: 10.1016/j.medj.2021.04.016] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/01/2021] [Accepted: 04/16/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND Pregnant women are at increased risk for severe outcomes from coronavirus disease 2019 (COVID-19), but the pathophysiology underlying this increased morbidity and its potential effect on the developing fetus is not well understood. METHODS We assessed placental histology, ACE2 expression, and viral and immune dynamics at the term placenta in pregnant women with and without respiratory severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. FINDINGS The majority (13 of 15) of placentas analyzed had no detectable viral RNA. ACE2 was detected by immunohistochemistry in syncytiotrophoblast cells of the normal placenta during early pregnancy but was rarely seen in healthy placentas at full term, suggesting that low ACE2 expression may protect the term placenta from viral infection. Using immortalized cell lines and primary isolated placental cells, we found that cytotrophoblasts, the trophoblast stem cells and precursors to syncytiotrophoblasts, rather than syncytiotrophoblasts or Hofbauer cells, are most vulnerable to SARS-CoV-2 infection in vitro. To better understand potential immune mechanisms shielding placental cells from infection in vivo, we performed bulk and single-cell transcriptomics analyses and found that the maternal-fetal interface of SARS-CoV-2-infected women exhibited robust immune responses, including increased activation of natural killer (NK) and T cells, increased expression of interferon-related genes, as well as markers associated with pregnancy complications such as preeclampsia. CONCLUSIONS SARS-CoV-2 infection in late pregnancy is associated with immune activation at the maternal-fetal interface even in the absence of detectable local viral invasion. FUNDING NIH (T32GM007205, F30HD093350, K23MH118999, R01AI157488, U01DA040588) and Fast Grant funding support from Emergent Ventures at the Mercatus Center.
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Affiliation(s)
- Alice Lu-Culligan
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Arun R Chavan
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Pavithra Vijayakumar
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Lina Irshaid
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Edward M Courchaine
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Kristin M Milano
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Zhonghua Tang
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Scott D Pope
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Eric Song
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - William J Lu-Culligan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Katherine H Campbell
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Arnau Casanovas-Massana
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Santos Bermejo
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jessica M Toothaker
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hannah J Lee
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Feimei Liu
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Wade Schulz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - John Fournier
- Section of Infectious Diseases, Department of Medicine, Yale School of Medicine, New Haven, CT, USA
| | - M Catherine Muenker
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Adam J Moore
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Liza Konnikova
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Aaron Ring
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Raffaella Morotti
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Seth Guller
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Harvey J Kliman
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Molecular, Cellular and Developmental Biology, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Shelli F Farhadian
- Section of Infectious Diseases, Department of Medicine, Yale School of Medicine, New Haven, CT, USA
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19
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Konnikova L, Robinson TO, Owings AH, Shirley JF, Davis E, Tang Y, Wall S, Li J, Hasan MH, Gharaibeh RZ, Mendoza Alvarez LB, Ryan LK, Doty A, Chovanec JF, O'Connell MP, Grunes DE, Daley WP, Mayer E, Chang L, Liu J, Snapper SB, Milner JD, Glover SC, Lyons JJ. Small intestinal immunopathology and GI-associated antibody formation in hereditary alpha-tryptasemia. J Allergy Clin Immunol 2021; 148:813-821.e7. [PMID: 33865872 DOI: 10.1016/j.jaci.2021.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 11/13/2020] [Revised: 03/09/2021] [Accepted: 04/01/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND Hereditary alpha-tryptasemia (HαT) is characterized by elevated basal serum tryptase due to increased copies of the TPSAB1 gene. Individuals with HαT frequently present with multisystem complaints, including anaphylaxis and seemingly functional gastrointestinal (GI) symptoms. OBJECTIVE We sought to determine the prevalence of HαT in an irritable bowel syndrome cohort and associated immunologic characteristics that may distinguish patients with HαT from patients without HαT. METHODS Tryptase genotyping by droplet digital PCR, flow cytometry, cytometry by time-of-flight, immunohistochemistry, and other molecular biology techniques was used. RESULTS HαT prevalence in a large irritable bowel syndrome cohort was 5% (N = 8/158). Immunophenotyping of HαT PBMCs (N ≥ 27) revealed increased total and class-switched memory B cells. In the small bowel, expansion of tissue mast cells with expression of CD203c, HLA-DR, and FcεRI, higher intestinal epithelial cell pyroptosis, and increased class-switched memory B cells were observed. IgG profiles in sera from individuals with HαT (N = 21) significantly differed from those in individuals with quiescent Crohn disease (N = 20) and non-HαT controls (N = 19), with increased antibodies directed against GI-associated proteins identified in individuals with HαT. CONCLUSIONS Increased mast cell number and intestinal epithelial cell pyroptosis in the small intestine, and class-switched memory B cells in both the gut and peripheral blood associated with IgG reactive to GI-related proteins, distinguish HαT from functional GI disease. These innate and adaptive immunologic findings identified in association with HαT are suggestive of subclinical intestinal inflammation in symptomatic individuals.
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Affiliation(s)
- Liza Konnikova
- Division of Newborn Medicine, Boston Children's Hospital, Boston, Mass; Department of Pediatrics, Children's Hospital of UPMC, Pittsburgh, Pa; Department of Pediatrics, Yale University School of Medicine, New Haven, Conn
| | - Tanya O Robinson
- Division of Digestive Diseases, Department of Medicine, University of Mississippi Medical Center, Jackson, Miss
| | - Anna H Owings
- Division of Digestive Diseases, Department of Medicine, University of Mississippi Medical Center, Jackson, Miss
| | - James F Shirley
- Division of Gastroenterology, Department of Medicine, University of Florida, Gainesville, Fla
| | - Elisabeth Davis
- Division of Gastroenterology, Department of Medicine, University of Arkansas for Medical Sciences, Little Rock, Ark
| | - Ying Tang
- Division of Gastroenterology, Department of Medicine, University of Florida, Gainesville, Fla; Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, Mass
| | - Sarah Wall
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, Mass
| | - Jian Li
- Division of Gastroenterology, Department of Medicine, University of Florida, Gainesville, Fla
| | - Mohammad H Hasan
- Division of Digestive Diseases, Department of Medicine, University of Mississippi Medical Center, Jackson, Miss
| | - Raad Z Gharaibeh
- Division of Gastroenterology, Department of Medicine, University of Florida, Gainesville, Fla
| | - Lybil B Mendoza Alvarez
- Division of Pediatric Gastroenterology, Department of Pediatrics, University of Florida, Gainesville, Fla
| | - Lisa K Ryan
- Division of Infectious Disease, Department of Medicine, University of Florida, Gainesville, Fla
| | - Andria Doty
- Interdisciplinary Center for Biotechnology Research Cytometry Core, University of Florida, Gainesville, Fla
| | - Jack F Chovanec
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Michael P O'Connell
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Dianne E Grunes
- Department of Pathology, University of Mississippi Medical Center, Jackson, Miss
| | - William P Daley
- Department of Pathology, University of Mississippi Medical Center, Jackson, Miss
| | - Emeran Mayer
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, UCLA, Los Angeles, Calif
| | - Lin Chang
- Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, UCLA, Los Angeles, Calif
| | - Julia Liu
- Morehouse School of Medicine, Atlanta, Ga
| | - Scott B Snapper
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Boston, Mass
| | - Joshua D Milner
- Division of Allergy, Immunology and Rheumatology, Columbia University Medical Center, New York, NY
| | - Sarah C Glover
- Division of Digestive Diseases, Department of Medicine, University of Mississippi Medical Center, Jackson, Miss; Division of Gastroenterology, Department of Medicine, University of Florida, Gainesville, Fla.
| | - Jonathan J Lyons
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md.
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20
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Lu-Culligan A, Chavan AR, Vijayakumar P, Irshaid L, Courchaine EM, Milano KM, Tang Z, Pope SD, Song E, Vogels CB, Lu-Culligan WJ, Campbell KH, Casanovas-Massana A, Bermejo S, Toothaker JM, Lee HJ, Liu F, Schulz W, Fournier J, Muenker MC, Moore AJ, Konnikova L, Neugebauer KM, Ring A, Grubaugh ND, Ko AI, Morotti R, Guller S, Kliman HJ, Iwasaki A, Farhadian SF. SARS-CoV-2 infection in pregnancy is associated with robust inflammatory response at the maternal-fetal interface. medRxiv 2021:2021.01.25.21250452. [PMID: 33532791 PMCID: PMC7852242 DOI: 10.1101/2021.01.25.21250452] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Pregnant women appear to be at increased risk for severe outcomes associated with COVID-19, but the pathophysiology underlying this increased morbidity and its potential impact on the developing fetus is not well understood. In this study of pregnant women with and without COVID-19, we assessed viral and immune dynamics at the placenta during maternal SARS-CoV-2 infection. Amongst uninfected women, ACE2 was detected by immunohistochemistry in syncytiotrophoblast cells of the normal placenta during early pregnancy but was rarely seen in healthy placentas at full term. Term placentas from women infected with SARS-CoV-2, however, displayed a significant increase in ACE2 levels. Using immortalized cell lines and primary isolated placental cells, we determined the vulnerability of various placental cell types to direct infection by SARS-CoV-2 in vitro. Yet, despite the susceptibility of placental cells to SARS-CoV-2 infection, viral RNA was detected in the placentas of only a subset (~13%) of women in this cohort. Through single cell transcriptomic analyses, we found that the maternal-fetal interface of SARS-CoV-2-infected women exhibited markers associated with pregnancy complications, such as preeclampsia, and robust immune responses, including increased activation of placental NK and T cells and increased expression of interferon-related genes. Overall, this study suggests that SARS-CoV-2 is associated with immune activation at the maternal-fetal interface even in the absence of detectable local viral invasion. While this likely represents a protective mechanism shielding the placenta from infection, inflammatory changes in the placenta may also contribute to poor pregnancy outcomes and thus warrant further investigation.
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Affiliation(s)
- Alice Lu-Culligan
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Arun R. Chavan
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Pavithra Vijayakumar
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Lina Irshaid
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Edward M. Courchaine
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Kristin M. Milano
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Zhonghua Tang
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Scott D. Pope
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Eric Song
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Chantal B.F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - William J. Lu-Culligan
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Department of Cell Biology, Yale School of Medicine, New Haven, CT, USA
| | - Katherine H. Campbell
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Arnau Casanovas-Massana
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Santos Bermejo
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Jessica M. Toothaker
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hannah J. Lee
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Feimei Liu
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Wade Schulz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - John Fournier
- Section of Infectious Diseases, Department of Medicine, Yale School of Medicine, New Haven, CT, USA
| | - M. Catherine Muenker
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Adam J. Moore
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | - Liza Konnikova
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA
| | - Karla M. Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Aaron Ring
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Albert I. Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Raffaella Morotti
- Department of Pathology, Yale School of Medicine, New Haven, CT, USA
| | - Seth Guller
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Harvey J. Kliman
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Yale School of Medicine, New Haven, CT, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Molecular, Cellular and Developmental Biology, New Haven, CT, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Shelli F. Farhadian
- Section of Infectious Diseases, Department of Medicine, Yale School of Medicine, New Haven, CT, USA
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21
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Pantalone JM, Liu S, Olaloye OO, Prochaska EC, Yanowitz T, Riley MM, Buland JR, Brozanski BS, Good M, Konnikova L. Gestational Age-Specific Complete Blood Count Signatures in Necrotizing Enterocolitis. Front Pediatr 2021; 9:604899. [PMID: 33718296 PMCID: PMC7952609 DOI: 10.3389/fped.2021.604899] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/29/2021] [Indexed: 12/18/2022] Open
Abstract
Objective: Necrotizing enterocolitis (NEC) is characterized by peripheral cell abnormalities, yet few studies have analyzed the complete blood count (CBC) specifically by gestational age (GA). Our objective was to describe GA-specific immune abnormalities in NEC through a comprehensive analysis of the CBC differential. Methods: Using a cohort of 246 infants (177 cases, 69 controls) admitted to neonatal intensive care units at a single institution, we retrospectively analyzed CBCs around illness onset in NEC cases compared with controls. Cases included surgical NEC (S-NEC, 34.5%) and medical NEC (M-NEC, 65.5%). Infants were divided into those born at GA <33 and ≥33 weeks. Differences in CBC values were described as absolute and percent changes at NEC onset from baseline and at antibiotic completion after NEC. We used machine learning algorithms based on the CBC at NEC to generate predictive models for diagnosis. Results: At NEC onset, there was an acute drop in monocytes and lymphocytes along with a rise in bands in S-NEC infants born <33 weeks compared with M-NEC. In comparison, both M-NEC and S-NEC ≥33 weeks had a percent drop in neutrophils at diagnosis compared with controls. At antibiotic completion, monocytes in S-NEC <33 weeks significantly rose compared with M-NEC, yet for S-NEC ≥33 weeks, bands significantly dropped compared with M-NEC. Predictive modeling was able to accurately predict S-NEC from M-NEC and controls. Conclusion: There are discrete leukocyte patterns in NEC based on GA. The CBC at diagnosis may be useful in identifying patients who will require surgery.
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Affiliation(s)
- Julia M Pantalone
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Silvia Liu
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Oluwabunmi O Olaloye
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Pediatrics, Yale School of Medicine, New Haven, CT, United States
| | - Erica C Prochaska
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, United States.,Division of Infectious Diseases, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Toby Yanowitz
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Melissa M Riley
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States
| | - Justin R Buland
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States
| | - Beverly S Brozanski
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States
| | - Misty Good
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States
| | - Liza Konnikova
- University of Pittsburgh School of Medicine, Pittsburgh, PA, United States.,Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Pediatrics, Yale School of Medicine, New Haven, CT, United States.,Department of Immunology, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, United States
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22
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Mirizio E, Liu C, Yan Q, Waltermire J, Mandel R, Schollaert KL, Konnikova L, Wang X, Chen W, Torok KS. Genetic Signatures From RNA Sequencing of Pediatric Localized Scleroderma Skin. Front Pediatr 2021; 9:669116. [PMID: 34164359 PMCID: PMC8215272 DOI: 10.3389/fped.2021.669116] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/12/2021] [Indexed: 01/02/2023] Open
Abstract
The purpose of this study was to explore the skin transcriptional profile in pediatric localized scleroderma (LS) to provide a better understanding of the altered immune and fibrotic pathways promoting disease. LS is a progressive disease of the skin and underlying tissue that causes significant functional disability and disfigurement, especially in developing children. RNA sequencing (RNAseq) technology allows for improved understanding of relevant cellular expression through transcriptome analysis of phases during LS disease progression (more active/inflammatory vs. inactive/fibrotic) and also permits the use of RNA extracted from existing paraffin-embedded skin tissue, which is important in pediatrics. A strong correlation was observed between the comparison of genes expressed between fresh (RNAlater) and paraffinized skin in healthy and LS subjects, supporting the use of paraffinized tissue. LS gene signatures compared to healthy controls showed a distinct expression of an inflammatory response gene signature (IRGS) composed of IFNγ-, IFNα-, and TNFα-associated genes. GSEA© enrichment analysis showed that the IRGS, including interferon-inducible chemokines such as CXCL9, CXCL10, CXCL11, and IFNγ itself, was more highly expressed in LS patients with more inflammatory lesions. The use of paraffinized skin for sequencing was proven to be an effective substitute for fresh skin by comparing gene expression profiles. The prevalence of the IFNγ signature in the lesion biopsies of active LS patients indicates that these genes reflect clinical activity parameters and may be the promoters of early, inflammatory disease.
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Affiliation(s)
- Emily Mirizio
- Division of Rheumatology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, United States
| | - Christopher Liu
- Division of Rheumatology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, United States
| | - Qi Yan
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, United States
| | - Julia Waltermire
- Division of Rheumatology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, United States
| | - Roosha Mandel
- Division of Rheumatology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, United States
| | - Kaila L Schollaert
- Division of Rheumatology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, United States
| | - Liza Konnikova
- Division of Neonatal Medicine, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, United States
| | - Xinjun Wang
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, United States
| | - Wei Chen
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh Medical Center (UPMC) Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, United States
| | - Kathryn S Torok
- Division of Rheumatology, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA, United States.,Clinical and Translational Science Institute, University of Pittsburgh, Pittsburgh, PA, United States
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23
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Li Y, Toothaker JM, Ben-Simon S, Ozeri L, Schweitzer R, McCourt BT, McCourt CC, Werner L, Snapper SB, Shouval DS, Khatib S, Koren O, Agnihorti S, Tseng G, Konnikova L. In utero human intestine harbors unique metabolome, including bacterial metabolites. JCI Insight 2020; 5:138751. [PMID: 33001863 PMCID: PMC7710283 DOI: 10.1172/jci.insight.138751] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/23/2020] [Indexed: 12/13/2022] Open
Abstract
Symbiotic microbial colonization through the establishment of the intestinal microbiome is critical to many intestinal functions, including nutrient metabolism, intestinal barrier integrity, and immune regulation. Recent studies suggest that education of intestinal immunity may be ongoing in utero. However, the drivers of this process are unknown. The microbiome and its byproducts are one potential source. Whether a fetal intestinal microbiome exists is controversial, and whether microbially derived metabolites are present in utero is unknown. Here, we aimed to determine whether bacterial DNA and microbially derived metabolites can be detected in second trimester human intestinal samples. Although we were unable to amplify bacterial DNA from fetal intestines, we report a fetal metabolomic intestinal profile with an abundance of bacterially derived and host-derived metabolites commonly produced in response to microbiota. Though we did not directly assess their source and function, we hypothesize that these microbial-associated metabolites either come from the maternal microbiome and are vertically transmitted to the fetus to prime the fetal immune system and prepare the gastrointestinal tract for postnatal microbial encounters or are produced locally by bacteria that were below our detection threshold. A unique human fetal metabolomic intestinal profile is reported with an abundance of bacterially derived metabolites.
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Affiliation(s)
| | - Jessica M Toothaker
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Shira Ben-Simon
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Lital Ozeri
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | - Ron Schweitzer
- Analytical Chemistry Laboratory, Tel-Hai College, Upper Galilee, Israel
| | - Blake T McCourt
- Department of Pediatrics, Yale University, New Haven, Connecticut, USA
| | - Collin C McCourt
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Lael Werner
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Scott B Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Dror S Shouval
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Soliman Khatib
- Analytical Chemistry Laboratory, Tel-Hai College, Upper Galilee, Israel.,Department of Natural Compounds and Analytical Chemistry, Migal Galilee Research Institute, Kiryat Shmona, Israel
| | - Omry Koren
- Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel
| | | | | | - Liza Konnikova
- Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Pediatrics, Yale University, New Haven, Connecticut, USA.,Department of Pediatrics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Developmental Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Division of Reproductive Sciences and.,Program in Human and Translational Immunology, Yale University, New Haven, Connecticut, USA
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24
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Vardi I, Chermesh I, Werner L, Barel O, Freund T, McCourt C, Fisher Y, Pinsker M, Javasky E, Weiss B, Rechavi G, Hagin D, Snapper SB, Somech R, Konnikova L, Shouval DS. Monogenic Inflammatory Bowel Disease: It's Never Too Late to Make a Diagnosis. Front Immunol 2020; 11:1775. [PMID: 33013830 PMCID: PMC7509434 DOI: 10.3389/fimmu.2020.01775] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/02/2020] [Indexed: 12/19/2022] Open
Abstract
Background: More than 50 different monogenic disorders have been identified as directly causing inflammatory bowel diseases, typically manifesting in the first years of life. We present the clinical course and immunological work-up of an adult patient who presented in adolescent years with an atypical gastrointestinal phenotype and was diagnosed more than two decades later with a monogenic disorder with important therapeutic implications. Methods: Whole exome sequencing was performed in a 37-years-old patient with a history of diarrhea since adolescence. Sanger sequencing was used to validate the suspected variant. Mass cytometry (CyTOF) and flow cytometry were conducted on peripheral blood mononuclear cells for deep immunophenotyping. Next-generation sequencing of the TCRB and IgH was performed for global immune repertoire analysis of circulating lymphocytes. Results: We identified a novel deleterious c.1455C>A (p.Y485X) mutation in LRBA. CyTOF studies demonstrated significant changes in immune landscape in the LRBA-deficient patient, including an increase in myeloid derived suppressor cells and double-negative T cells, decreased B cells, low ratio of naïve:memory T cells, and reduced capacity of T cells to secrete various cytokines following stimulation, including tumor necrosis factor alpha (TNF-α) and interferon gamma (IFN-γ). In addition, this patient exhibited low frequency of regulatory T cells, with a reduction in their CTLA4 expression and interleukin (IL)-10 secretion. Finally, we show marked oligoclonal expansion of specific B- and T-cell clones in the peripheral blood of the LRBA-deficient patient. Conclusions: LRBA deficiency is characterized by marked immunological changes in innate and adaptive immune cells. This case highlights the importance of advanced genetic studies in patients with a unique phenotype, regardless of their age at presentation.
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Affiliation(s)
- Iddo Vardi
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Genomic Unit, Sheba Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel.,Sheba Medical Center, Wohl Institute of Translational Medicine, Ramat Gan, Israel
| | - Irit Chermesh
- Department of Gastroenterology, Rambam Health Care Campus, Affiliated With Technion-Israel Institute of Technology, Haifa, Israel
| | - Lael Werner
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ortal Barel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Genomic Unit, Sheba Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel.,Sheba Medical Center, Wohl Institute of Translational Medicine, Ramat Gan, Israel
| | - Tal Freund
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Allergy and Clinical Immunology Unit, Department of Medicine, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Collin McCourt
- Division of Newborn Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - Yael Fisher
- Institute of Pathology, Rambam Health Care Campus, Affiliated With Technion-Israel Institute of Technology, Haifa, Israel
| | - Marina Pinsker
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel.,Institute of Nanotechnology and Advanced Materials, Bar Ilan University, Ramat Gan, Israel
| | - Elisheva Javasky
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Genomic Unit, Sheba Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel.,Sheba Medical Center, Wohl Institute of Translational Medicine, Ramat Gan, Israel
| | - Batia Weiss
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Gideon Rechavi
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Genomic Unit, Sheba Cancer Research Center, Sheba Medical Center, Ramat Gan, Israel.,Sheba Medical Center, Wohl Institute of Translational Medicine, Ramat Gan, Israel
| | - David Hagin
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Allergy and Clinical Immunology Unit, Department of Medicine, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Scott B Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, United States.,Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Raz Somech
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel.,Pediatric Department Ward A, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel.,Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
| | - Liza Konnikova
- Division of Newborn Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, United States.,Department of Immunology, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Dror S Shouval
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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25
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Wen L, Javed TA, Dobbs AK, Brown R, Niu M, Li L, Khalid A, Barakat MT, Xiao X, Yimlamai D, Konnikova L, Yu M, Byersdorfer CA, Husain SZ. The Protective Effects of Calcineurin on Pancreatitis in Mice Depend on the Cellular Source. Gastroenterology 2020; 159:1036-1050.e8. [PMID: 32445858 PMCID: PMC7502475 DOI: 10.1053/j.gastro.2020.05.051] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 02/27/2020] [Revised: 04/30/2020] [Accepted: 05/14/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND & AIMS Calcineurin is a ubiquitously expressed central Ca2+-responsive signaling molecule that mediates acute pancreatitis, but little is known about its effects. We compared the effects of calcineurin expression by hematopoietic cells vs pancreas in mouse models of pancreatitis and pancreatitis-associated lung inflammation. METHODS We performed studies with mice with hematopoietic-specific or pancreas-specific deletion of protein phosphatase 3, regulatory subunit B, alpha isoform (PPP3R1, also called CNB1), in mice with deletion of CNB1 (Cnb1UBC△/△) and in the corresponding controls for each deletion of CNB1. Acute pancreatitis was induced in mice by administration of caerulein or high-pressure infusion of radiocontrast into biliopancreatic ducts; some mice were also given intraductal infusions of an adeno-associated virus vector that expressed nuclear factor of activated T -cells (NFAT)-luciferase into pancreas. Pancreas, bone marrow, liver, kidney, heart, and lung were collected and analyzed by histopathology, immunohistochemistry, and immunoblots; levels of cytokines were measured in serum. Mouse and human primary pancreatic acinar cells were transfected with a vector that expressed NFAT-luciferase and incubated with an agent that blocks interaction of NFAT with calcineurin; cells were analyzed by immunofluorescence. Calcineurin-mediated neutrophil chemotaxis and reactive oxygen species production were measured in neutrophils from mice. RESULTS Mice with hematopoietic-specific deletion of CNB1 developed the same level of local pancreatic inflammation as control mice after administration of caerulein or infusion of radiocontrast into biliopancreatic ducts. Cnb1UBC△/△ mice or mice with pancreas-specific deletion of CNB1 developed less severe pancreatitis and reduced pancreatic inflammation after administration of caerulein or infusion of radiocontrast into biliopancreatic ducts compared with control mice. NFAT was activated in pancreas of Swiss Webster mice given caerulein or infusions of radiocontrast into biliopancreatic ducts. Blocking the interaction between calcineurin and NFAT did not reduce pancreatic acinar cell necrosis in response to caerulein or infusions of radiocontrast. Mice with hematopoietic-specific deletion of CNB1 (but not mice with pancreas-specific deletion of CNB1) had reduced infiltration of lung tissues by neutrophils. Neutrophil chemotaxis and production of reactive oxygen species were decreased after incubation with a calcineurin inhibitor. CONCLUSIONS Hematopoietic and neutrophil expression of calcineurin promotes pancreatitis-associated lung inflammation, whereas pancreatic calcineurin promotes local pancreatic inflammation. The findings indicate that the protective effects of blocking or deleting calcineurin on pancreatitis are mediated by the source of its expression. This information should be used in the development of strategies to inhibit calcineurin for the prevention of pancreatitis and pancreatitis-associated lung inflammation.
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Affiliation(s)
- Li Wen
- Department of Gastroenterology and Shanghai Key Laboratory of Pancreatic Disease, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Tanveer A Javed
- Division of Pediatric Gastroenterology, University of Pittsburgh School of Medicine and the Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Andrea K Dobbs
- Division of Blood and Marrow Transplantation and Cellular Therapies, University of Pittsburgh School of Medicine and the Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Rebecca Brown
- Division of Blood and Marrow Transplantation and Cellular Therapies, University of Pittsburgh School of Medicine and the Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Mengya Niu
- Department of Gastroenterology and Shanghai Key Laboratory of Pancreatic Disease, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liwen Li
- University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Asna Khalid
- Division of Pediatric Gastroenterology, Department of Pediatrics, Stanford University, Palo Alto, California
| | - Monique T Barakat
- Division of Pediatric Gastroenterology, Department of Pediatrics, Stanford University, Palo Alto, California; Department of Medicine, Stanford University, Palo Alto, California
| | - Xiangwei Xiao
- Division of Pediatric Surgery, University of Pittsburgh School of Medicine and the Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Dean Yimlamai
- Division of Pediatric Gastroenterology, University of Pittsburgh School of Medicine and the Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Liza Konnikova
- Division of Newborn Medicine, Department of Pediatrics, University of Pittsburgh School of Medicine and the Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Mang Yu
- Division of Pediatric Gastroenterology, Department of Pediatrics, Stanford University, Palo Alto, California
| | - Craig A Byersdorfer
- Division of Blood and Marrow Transplantation and Cellular Therapies, University of Pittsburgh School of Medicine and the Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Sohail Z Husain
- Division of Pediatric Gastroenterology, Department of Pediatrics, Stanford University, Palo Alto, California.
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26
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Mitsialis V, Wall S, Liu P, Ordovas-Montanes J, Parmet T, Vukovic M, Spencer D, Field M, McCourt C, Toothaker J, Bousvaros A, Shalek AK, Kean L, Horwitz B, Goldsmith J, Tseng G, Snapper SB, Konnikova L. Single-Cell Analyses of Colon and Blood Reveal Distinct Immune Cell Signatures of Ulcerative Colitis and Crohn's Disease. Gastroenterology 2020; 159:591-608.e10. [PMID: 32428507 PMCID: PMC8166295 DOI: 10.1053/j.gastro.2020.04.074] [Citation(s) in RCA: 135] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/07/2020] [Accepted: 04/24/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Studies are needed to determine the mechanisms of mucosal dysregulation in patients with inflammatory bowel diseases (IBDs) and differences in inflammatory responses of patients with ulcerative colitis (UC) vs Crohn's disease (CD). We used mass cytometry (CyTOF) to characterize and compare immune cell populations in the mucosa and blood from patients with IBD and without IBD (controls) at single-cell resolution. METHODS We performed CyTOF analysis of colonic mucosa samples (n = 87) and peripheral blood mononuclear cells (n = 85) from patients with active or inactive UC or CD and controls. We also performed single-cell RNA sequencing, flow cytometry, and RNA in situ hybridization analyses to validate key findings. We used random forest modeling to identify differences in signatures across subject groups. RESULTS Compared with controls, colonic mucosa samples from patients with IBD had increased abundances of HLA-DR+CD38+ T cells, including T-regulatory cells that produce inflammatory cytokines; CXCR3+ plasmablasts; and IL1B+ macrophages and monocytes. Colonic mucosa samples from patients with UC were characterized by expansion of IL17A+ CD161+ effector memory T cells and IL17A+ T-regulatory cells; expansion of HLA-DR+CD56+ granulocytes; and reductions in type 3 innate lymphoid cells. Mucosal samples from patients with active CD were characterized by IL1B+HLA-DR+CD38+ T cells, IL1B+TNF+IFNG+ naïve B cells, IL1B+ dendritic cells (DCs), and IL1B+ plasmacytoid DCs. Peripheral blood mononuclear cells from patients with active CD differed from those of active UC in that the peripheral blood mononuclear cells from patients with CD had increased IL1B+ T-regulatory cells, IL1B+ DCs and IL1B+ plasmacytoid DCs, IL1B+ monocytes, and fewer group 1 innate lymphoid cells. Random forest modeling differentiated active UC from active CD in colonic mucosa and blood samples; top discriminating features included many of the cellular populations identified above. CONCLUSIONS We used single-cell technologies to identify immune cell populations specific to mucosa and blood samples from patients with active or inactive CD and UC and controls. This information might be used to develop therapies that target specific cell populations in patients with different types of IBD.
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Affiliation(s)
- Vanessa Mitsialis
- Division of Gastroenterology, Brigham and Women’s Hospital, Boston, MA 02115, USA,Division of Gastroenterology, Hepatology and Nutrition, Boston, MA 02115, USA
| | - Sarah Wall
- Division of Gastroenterology, Hepatology and Nutrition, Boston, MA 02115, USA
| | - Peng Liu
- Department of Biostatistics University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Jose Ordovas-Montanes
- Division of Gastroenterology, Hepatology and Nutrition, Boston, MA 02115, USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA 02139 USA,Harvard Stem Cell Institute, Cambridge, MA, USA 02138 USA
| | - Tamar Parmet
- Division of Gastroenterology, Hepatology and Nutrition, Boston, MA 02115, USA
| | - Marko Vukovic
- Institute for Medical Engineering and Science (IMES), MIT, Cambridge, MA, 02139 USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA 02139 USA,Harvard Stem Cell Institute, Cambridge, MA, USA 02138 USA,Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, 02139 USA,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139 USA
| | - Dennis Spencer
- Division of Gastroenterology, Hepatology and Nutrition, Boston, MA 02115, USA
| | - Michael Field
- Division of Gastroenterology, Hepatology and Nutrition, Boston, MA 02115, USA
| | - Collin McCourt
- Broad Institute of MIT and Harvard, Cambridge, MA, USA 02139 USA
| | | | - Athos Bousvaros
- Division of Gastroenterology, Hepatology and Nutrition, Boston, MA 02115, USA
| | - BCH IBD Center
- BCH IBD Center: Sonia Ballal, MD, Silvana Bonilla, MD, MS, Rima Fawaz, MD, Laurie N. Fishman, MD, Alejandro Flores, MD, Victor Fox, MD, Amit S. Grover, MB, BCh BAO, Leslie Higuchi, MD, Susanna Huh, MD, Stacy Kahn, MD, Christine Lee, MD, Munir Mobassaleh, MD, Jodie Ouahed, MD, Randi G. Pleskow, MD, Brian Regan, DO, Paul A. Rufo, MD, MMSc, Sabina Sabharwal, MD, Jared Silverstein, MD, Menno Verhave, MD, Anne Wolf, MD, Lori Zimmerman, MD, Naamah Zitomersky, MD
| | - BWH Crohn’s and Colitis Center
- BWH Crohn’s and Colitis Center: Jessica R. Allegretti, MD, MPH, Punyanganie De Silva, MD, MPH, Sonia Friedman, MD, Matthew Hamilton, MD, Joshua Korzenik, MD, Frederick Makrauer, MD, Beth-Ann Norton, MS, RN, ANP-BC, Rachel W. Winter, MD, MPH
| | - Alex K. Shalek
- Institute for Medical Engineering and Science (IMES), MIT, Cambridge, MA, 02139 USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA 02139 USA,Harvard Stem Cell Institute, Cambridge, MA, USA 02138 USA,Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA, 02139 USA,Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139 USA
| | - Leslie Kean
- Division of Hematology Oncology Boston Children’s Hospital, Boston, MA 02115, USA
| | - Bruce Horwitz
- Division of Gastroenterology, Hepatology and Nutrition, Boston, MA 02115, USA
| | | | - George Tseng
- Department of Biostatistics University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Scott B. Snapper
- Division of Gastroenterology, Brigham and Women’s Hospital, Boston, MA 02115, USA,Division of Gastroenterology, Hepatology and Nutrition, Boston, MA 02115, USA
| | - Liza Konnikova
- Division of Newborn Medicine, Boston Children's Hospital, Boston, Massachusetts; Department of Pediatrics, University of Pittsburgh Medical Center Children's Hospital, Pittsburgh, Pennsylvania; Department of Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania; Department of Developmental Biology University of Pittsburgh, Pittsburgh, Pennsylvania; Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut.
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27
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Ziv A, Werner L, Konnikova L, Awad A, Jeske T, Hastreiter M, Mitsialis V, Stauber T, Wall S, Kotlarz D, Klein C, Snapper SB, Tzfati Y, Weiss B, Somech R, Shouval DS. An RTEL1 Mutation Links to Infantile-Onset Ulcerative Colitis and Severe Immunodeficiency. J Clin Immunol 2020; 40:1010-1019. [PMID: 32710398 DOI: 10.1007/s10875-020-00829-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 07/16/2020] [Indexed: 12/27/2022]
Abstract
PURPOSE More than 50 different monogenic disorders causing inflammatory bowel disease (IBD) have been identified. Our goal was to characterize the clinical phenotype, genetic workup, and immunologic alterations in an Ashkenazi Jewish patient that presented during infancy with ulcerative colitis and unique clinical manifestations. METHODS Immune workup and whole-exome sequencing were performed, along with Sanger sequencing for confirmation. Next-generation sequencing of the TCRB and IgH was conducted for immune repertoire analysis. Telomere length was evaluated by in-gel hybridization assay. Mass cytometry was performed on patient's peripheral blood mononuclear cells, and compared with control subjects and patients with UC. RESULTS The patient presented in infancy with failure to thrive and dysmorphic features, consistent with a diagnosis of dyskeratosis congenita and Hoyeraal-Hreidarsson syndrome. Severe ulcerative colitis manifested in the first year of life and proceeded to the development of a primary immunodeficiency, presenting as Pneumocystis jiroveci pneumonia and hypogammaglobulinemia. Genetic studies identified a deleterious homozygous C.3791G>A missense mutation in the helicase regulator of telomere elongation 1 (RTEL1), leading to short telomeres in the index patient. Immune repertoire studies showed polyclonal T and B cell receptor distribution, while mass cytometry analysis demonstrated marked immunological alterations, including a predominance of naïve T cells, paucity of B cells, and a decrease in various innate immune subsets. CONCLUSIONS RTEL1 mutations are associated with significant alterations in immune landscape and can manifest with infantile-onset IBD. A high index of suspicion is required in Ashkenazi Jewish families where the carriage rate of the C.3791G>A variant is high.
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Affiliation(s)
- Alma Ziv
- Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lael Werner
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Liza Konnikova
- Division of Newborn Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Aya Awad
- Department of Genetics, The Silberman Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tim Jeske
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Maximilian Hastreiter
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Vanessa Mitsialis
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Tali Stauber
- Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
- Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
| | - Sarah Wall
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
| | - Daniel Kotlarz
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Christoph Klein
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Scott B Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Yehuda Tzfati
- Department of Genetics, The Silberman Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Batia Weiss
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Raz Somech
- Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
- Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
| | - Dror S Shouval
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel.
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
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Abstract
MOTIVATION Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq), couples the measurement of surface marker proteins with simultaneous sequencing of mRNA at single cell level, which brings accurate cell surface phenotyping to single-cell transcriptomics. Unfortunately, multiplets in CITE-seq datasets create artificial cell types (ACT) and complicate the automation of cell surface phenotyping. RESULTS We propose CITE-sort, an artificial-cell-type aware surface marker clustering method for CITE-seq. CITE-sort is aware of and is robust to multiplet-induced ACT. We benchmarked CITE-sort with real and simulated CITE-seq datasets and compared CITE-sort against canonical clustering methods. We show that CITE-sort produces the best clustering performance across the board. CITE-sort not only accurately identifies real biological cell types (BCT) but also consistently and reliably separates multiplet-induced artificial-cell-type droplet clusters from real BCT droplet clusters. In addition, CITE-sort organizes its clustering process with a binary tree, which facilitates easy interpretation and verification of its clustering result and simplifies cell-type annotation with domain knowledge in CITE-seq. AVAILABILITY AND IMPLEMENTATION http://github.com/QiuyuLian/CITE-sort. SUPPLEMENTARY INFORMATION Supplementary data is available at Bioinformatics online.
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Affiliation(s)
- Qiuyu Lian
- MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua University, Beijing 100084, China
- Department of Pediatrics, School of Medicine, University of Pittsburgh, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Hongyi Xin
- Department of Pediatrics, School of Medicine, University of Pittsburgh, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
- University of Michigan-Shanghai Jiao Tong University Joint Institute, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jianzhu Ma
- Department of Biochemistry and Computer Science, Purdue University, West Lafayette, IA 47907, USA
| | - Liza Konnikova
- Department of Pediatrics, School of Medicine, University of Pittsburgh, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Wei Chen
- Department of Pediatrics, School of Medicine, University of Pittsburgh, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Jin Gu
- MOE Key Laboratory of Bioinformatics, BNRIST Bioinformatics Division, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Kong Chen
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
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29
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Toothaker JM, Presicce P, Cappelletti M, Stras SF, McCourt CC, Chougnet CA, Kallapur SG, Konnikova L. Immune Cells in the Placental Villi Contribute to Intra-amniotic Inflammation. Front Immunol 2020; 11:866. [PMID: 32528468 PMCID: PMC7256198 DOI: 10.3389/fimmu.2020.00866] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/15/2020] [Indexed: 01/22/2023] Open
Abstract
Intra-amniotic (IA) inflammation is associated with significant morbidities for both the mother and the fetus. Prior studies have illustrated many of the effects of IA inflammation on the uterine lining (decidua) and membranous layers of the placenta at the fetal–maternal interface. However, much less is known about the immunological response occurring within the villous placenta. Using a rhesus macaque model of lipopolysaccharide (LPS)-induced IA inflammation, we showed that pregnancy-matched choriodecidua and villi have distinct immunological profiles in rhesus pregnancies. In the choriodecidua, we show that the abundance of neutrophils, multiple populations of antigen-presenting cells, and two populations of natural killer (NK) cells changes with prenatal IA LPS exposure. In contrast, in immune cells within the villous placenta we observed alterations in the abundance of B cells, monocytes, and CD8 T cells. Prior work has illustrated that IA inflammation leads to an increase in tumor necrosis factor alpha (TNFα) at the fetal–maternal interface. In this study, pretreatment with a TNFα blockade partially reversed inflammation in the placental villi. Furthermore, we report that immune cells in the villous placenta sensed LPS during our experimental window, and subsequently activated T cells to produce proinflammatory cytokines. Moreover, this study is the first report of memory T cells in third-trimester non-human primate placental villi and provides evidence that manipulation of immune cells in the villi at the fetal–maternal interface should be considered as a potential therapeutic target for IA inflammation.
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Affiliation(s)
- Jessica M Toothaker
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Pietro Presicce
- Divisions of Neonatology and Developmental Biology, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA, United States
| | - Monica Cappelletti
- Divisions of Neonatology and Developmental Biology, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA, United States
| | - Stephanie F Stras
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, United States.,Division of Newborn Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - Collin C McCourt
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, United States.,Division of Newborn Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, United States
| | - Claire A Chougnet
- Division of Immunobiology, Cincinnati Children's Hospital Research Foundation, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Suhas G Kallapur
- Divisions of Neonatology and Developmental Biology, David Geffen School of Medicine at the University of California, Los Angeles, Los Angeles, CA, United States
| | - Liza Konnikova
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, United States.,Division of Newborn Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, United States.,Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, United States.,Department of Pediatrics, Yale University, New Haven, CT, United States
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30
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Liu P, Liu S, Fang Y, Xue X, Zou J, Tseng G, Konnikova L. Recent Advances in Computer-Assisted Algorithms for Cell Subtype Identification of Cytometry Data. Front Cell Dev Biol 2020; 8:234. [PMID: 32411698 PMCID: PMC7198724 DOI: 10.3389/fcell.2020.00234] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 03/20/2020] [Indexed: 11/13/2022] Open
Abstract
The progress in the field of high-dimensional cytometry has greatly increased the number of markers that can be simultaneously analyzed producing datasets with large numbers of parameters. Traditional biaxial manual gating might not be optimal for such datasets. To overcome this, a large number of automated tools have been developed to aid with cellular clustering of multi-dimensional datasets. Here were review two large categories of such tools; unsupervised and supervised clustering tools. After a thorough review of the popularity and use of each of the available unsupervised clustering tools, we focus on the top six tools to discuss their advantages and limitations. Furthermore, we employ a publicly available dataset to directly compare the usability, speed, and relative effectiveness of the available unsupervised and supervised tools. Finally, we discuss the current challenges for existing methods and future direction for the new generation of cell type identification approaches.
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Affiliation(s)
- Peng Liu
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Silvia Liu
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, United States
| | - Yusi Fang
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Xiangning Xue
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Jian Zou
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, United States
| | - George Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, United States
| | - Liza Konnikova
- Department of Pediatrics, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, United States
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, United States
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31
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Stras SF, Werner L, Toothaker JM, Olaloye OO, Oldham AL, McCourt CC, Lee YN, Rechavi E, Shouval DS, Konnikova L. Maturation of the Human Intestinal Immune System Occurs Early in Fetal Development. Dev Cell 2019; 51:357-373.e5. [PMID: 31607651 DOI: 10.1016/j.devcel.2019.09.008] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [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: 03/17/2019] [Revised: 06/16/2019] [Accepted: 09/10/2019] [Indexed: 02/07/2023]
Abstract
There are limited data on fetal and early life development of human intestinal immunity. Using mass cytometry (CyTOF) and next-generation sequencing of B and T cell receptor (BCR and TCR) repertoires, we demonstrate complex intestinal immunity from 16 weeks' gestational age (GA). Both BCR and TCR repertoires are diverse with CDRH and CDR3β length increasing with advancing GA. The difference-from-germline, CDR insertions and/or deletions, similarly occur in utero for TCR but not BCR, suggesting earlier mucosal T than B cell maturity. Innate immunity is dominated by macrophages, dendritic cells (DCs), innate lymphoid cells (ILCs), and natural killer (NK) cells. Follicular and transitional B cells are enriched in fetuses while CD69+IgM+ B cells are abundant in infants. Both CD4+ and CD8+ T cells are abundant, capable of secreting cytokines and are phenotypically of the tissue resident memory state in utero. Our data provide the foundation for a 2nd trimester and infant intestinal immune atlas and suggest that a complex innate and adaptive immune landscape exists significantly earlier than previously reported.
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Affiliation(s)
- Stephanie F Stras
- Division of Newborn Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Lael Werner
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer 52621, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Jessica M Toothaker
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Oluwabunmi O Olaloye
- Division of Newborn Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Austin L Oldham
- Division of Newborn Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Collin C McCourt
- Division of Newborn Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Yu Nee Lee
- Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer 52621, Israel; Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer 52621, Israel; Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer 52621, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Erez Rechavi
- Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer 52621, Israel; Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer 52621, Israel; Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer 52621, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Dror S Shouval
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer 52621, Israel; Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel.
| | - Liza Konnikova
- Division of Newborn Medicine, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA; Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA.
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32
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Kurolap A, Eshach Adiv O, Konnikova L, Werner L, Gonzaga-Jauregui C, Steinberg M, Mitsialis V, Mory A, Nunberg MY, Wall S, Shaoul R, Overton JD, Shuldiner AR, Zohar Y, Paperna T, Snapper SB, Shouval DS, Baris Feldman H. A Unique Presentation of Infantile-Onset Colitis and Eosinophilic Disease without Recurrent Infections Resulting from a Novel Homozygous CARMIL2 Variant. J Clin Immunol 2019; 39:430-439. [PMID: 31079270 DOI: 10.1007/s10875-019-00631-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 04/14/2019] [Indexed: 11/26/2022]
Abstract
PURPOSE This study aimed to characterize the clinical phenotype, genetic basis, and consequent immunological phenotype of a boy with severe infantile-onset colitis and eosinophilic gastrointestinal disease, and no evidence of recurrent or severe infections. METHODS Trio whole-exome sequencing (WES) was utilized for pathogenic variant discovery. Western blot (WB) and immunohistochemical (IHC) staining were used for protein expression analyses. Immunological workup included in vitro T cell studies, flow cytometry, and CyTOF analysis. RESULTS WES revealed a homozygous variant in the capping protein regulator and myosin 1 linker 2 (CARMIL2) gene: c.1590C>A; p.Asn530Lys which co-segregated with the disease in the nuclear family. WB and IHC analyses demonstrated reduced protein levels in patient's cells compared with controls. Moreover, comprehensive immunological workup revealed severely diminished blood-borne regulatory T cell (Treg) frequency and impaired in vitro CD4+ T cell proliferation and Treg generation. CyTOF analysis showed significant shifts in the patient's innate and adaptive immune cells compared with healthy controls and ulcerative colitis patients. CONCLUSIONS Pathogenic variants in CARMIL2 have been implicated in an immunodeficiency syndrome characterized by recurrent infections, occasionally with concurrent chronic diarrhea. We show that CARMIL2-immunodeficiency is associated with significant alterations in the landscape of immune populations in a patient with prominent gastrointestinal disease. This case provides evidence that CARMIL2 should be a candidate gene when diagnosing children with very early onset inflammatory and eosinophilic gastrointestinal disorders, even when signs of immunodeficiency are not observed.
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Affiliation(s)
- Alina Kurolap
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Orly Eshach Adiv
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- Pediatric Gastroenterology, Rambam Health Care Campus, Haifa, Israel
| | - Liza Konnikova
- Devision of Newborn Medicine, Department of Pediatrics, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, PA, USA
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Lael Werner
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Maya Steinberg
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel
| | - Vanessa Mitsialis
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Adi Mory
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel
| | - Moran Y Nunberg
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sarah Wall
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
| | - Ron Shaoul
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- Pediatric Gastroenterology, Rambam Health Care Campus, Haifa, Israel
| | | | | | - Yaniv Zohar
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
- Institute of Pathology, Rambam Health Care Campus, Haifa, Israel
| | - Tamar Paperna
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel
| | - Scott B Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women's Hospital, Boston, MA, USA
| | - Dror S Shouval
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hagit Baris Feldman
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel.
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel.
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33
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Goettel JA, Kotlarz D, Emani R, Canavan JB, Konnikova L, Illig D, Frei SM, Field M, Kowalik M, Peng K, Gringauz J, Mitsialis V, Wall SM, Tsou A, Griffith AE, Huang Y, Friedman JR, Towne JE, Plevy SE, O'Hara Hall A, Snapper SB. Low-Dose Interleukin-2 Ameliorates Colitis in a Preclinical Humanized Mouse Model. Cell Mol Gastroenterol Hepatol 2019; 8:193-195. [PMID: 31078723 PMCID: PMC6661391 DOI: 10.1016/j.jcmgh.2019.05.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 05/02/2019] [Accepted: 05/03/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Jeremy A Goettel
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, Massachusetts; Department of Pediatrics, Harvard Medical School, Boston, Massachusetts.
| | - Daniel Kotlarz
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, Massachusetts; Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Rohini Emani
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, Massachusetts; Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - James B Canavan
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, Massachusetts; Department of Pediatrics, Harvard Medical School, Boston, Massachusetts; Division of Gastroenterology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Liza Konnikova
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, Massachusetts; Department of Pediatrics, Harvard Medical School, Boston, Massachusetts; Department of Pediatric and Newborn Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - David Illig
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, Massachusetts
| | - Sandra M Frei
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, Massachusetts; Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Michael Field
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, Massachusetts
| | - Matthew Kowalik
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, Massachusetts; Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Kaiyue Peng
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, Massachusetts; Department of Gastroenterology, Children's Hospital of Fudan University, Shanghai, China
| | - Jordan Gringauz
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, Massachusetts
| | - Vanessa Mitsialis
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, Massachusetts; Department of Pediatrics, Harvard Medical School, Boston, Massachusetts; Division of Gastroenterology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Sarah M Wall
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, Massachusetts
| | - Amy Tsou
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, Massachusetts; Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Alexandra E Griffith
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, Massachusetts
| | - Ying Huang
- Department of Gastroenterology, Children's Hospital of Fudan University, Shanghai, China
| | | | | | - Scott E Plevy
- Janssen Research & Development, Spring House, Pennsylvania
| | | | - Scott B Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, Massachusetts; Department of Pediatrics, Harvard Medical School, Boston, Massachusetts; Division of Gastroenterology, Brigham and Women's Hospital, Boston, Massachusetts.
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Konnikova L, Stras S, Werner L, Toothaker J, Oldham A, Shouval D. High-dimensional immune atlas of second trimester human intestinal immunity. The Journal of Immunology 2019. [DOI: 10.4049/jimmunol.202.supp.67.12] [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: 01/03/2023]
Abstract
Abstract
It has long been postulated that newborn’s immune system is immature. To this end, a third of neonatal deaths are due to infections. Similarly, newborns tend to have reduced immune responses to vaccines. Nevertheless, most newborns are healthy. There is limited direct human studies focusing on utero fetal mucosal immune development. Therefore, there is a critical need to investigate fetal mucosal immunity. Using cytometry time of flight (CyTOF) and next-generation sequencing of B and T-cell receptor (B/TCR) repertoires of small (S) and large intestines (LI), we show that intestinal immunity is diverse and functional as early as 16 weeks gestation (GA). Similarly, BCR and TCR repertoires are as diverse in early fetal as in full term samples, though an increase in CDR3β length and distance-from-germline correlates with advanced GA. Innate immunity is dominated by antigen presenting cells, including CD103+DCs, innate lymphoid cells and natural killer cells. B-cells are also present in all tissue examined, with follicular and transitional B-cells enriched in the fetal and CD69+IgM+B-cell in neonatal tissue. Finally, there is high complexity in T-cells, representing >50% of immune cells with similar frequencies at all developmental stages and locations studied. Contrary to our assumption, the majority of T-cells are of central and effector memory subsets. Even more surprisingly, functional tissue resident memory T-cells are abundant and functional in fetal and neonatal samples. Our data provide the foundation for a mucosal immune atlas of second trimester human development and challenge the paradigm that the neonatal immune system is immature, suggesting that development occurs significantly earlier than previously reported.
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Affiliation(s)
| | | | - Lael Werner
- 2Edmond and Lily Safra Children’s Hospital, Israel
| | | | | | - Dror Shouval
- 2Edmond and Lily Safra Children’s Hospital, Israel
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35
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Biswas A, Shouval DS, Griffith A, Goettel JA, Field M, Kang YH, Konnikova L, Janssen E, Redhu NS, Thrasher AJ, Chatila T, Kuchroo VK, Geha RS, Notarangelo LD, Pai SY, Horwitz BH, Snapper SB. WASP-mediated regulation of anti-inflammatory macrophages is IL-10 dependent and is critical for intestinal homeostasis. Nat Commun 2018; 9:1779. [PMID: 29725003 PMCID: PMC5934380 DOI: 10.1038/s41467-018-03670-6] [Citation(s) in RCA: 35] [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: 05/31/2017] [Accepted: 03/03/2018] [Indexed: 01/01/2023] Open
Abstract
Mutations in Wiskott–Aldrich syndrome protein (WASP) cause autoimmune sequelae including colitis. Yet, how WASP mediates mucosal homeostasis is not fully understood. Here we show that WASP-mediated regulation of anti-inflammatory macrophages is critical for mucosal homeostasis and immune tolerance. The generation and function of anti-inflammatory macrophages are defective in both human and mice in the absence of WASP. Expression of WASP specifically in macrophages, but not in dendritic cells, is critical for regulation of colitis development. Importantly, transfer of WT anti-inflammatory macrophages prevents the development of colitis. DOCK8-deficient macrophages phenocopy the altered macrophage properties associated with WASP deficiency. Mechanistically, we show that both WASP and DOCK8 regulates macrophage function by modulating IL-10-dependent STAT3 phosphorylation. Overall, our study indicates that anti-inflammatory macrophage function and mucosal immune tolerance require both WASP and DOCK8, and that IL-10 signalling modulates a WASP-DOCK8 complex. Deficiency in Wiskott-Aldrich syndrome protein (WASP) has been associated with autoimmune colitis, but the underlying mechanism is still unclear. Here the authors show that WASP deficiency is associated with defective WASP/DOCK8 complex formation, altered IL-10 signalling, and impaired anti-inflammatory macrophage functions.
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Affiliation(s)
- Amlan Biswas
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts, 02115, USA.,Department of Pediatrics, Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts, 02115, USA.,VEO-IBD Consortium, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Dror S Shouval
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts, 02115, USA.,VEO-IBD Consortium, 300 Longwood Avenue, Boston, MA, 02115, USA.,Division of Pediatric Gastroenterology and Nutrition, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, 52621, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Alexandra Griffith
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts, 02115, USA.,VEO-IBD Consortium, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Jeremy A Goettel
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts, 02115, USA.,Department of Pediatrics, Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts, 02115, USA.,VEO-IBD Consortium, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Michael Field
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts, 02115, USA.,VEO-IBD Consortium, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Yu Hui Kang
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts, 02115, USA.,Department of Pediatrics, Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts, 02115, USA.,VEO-IBD Consortium, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Liza Konnikova
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts, 02115, USA.,Department of Pediatrics, Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts, 02115, USA.,VEO-IBD Consortium, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Erin Janssen
- Department of Pediatrics, Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts, 02115, USA.,Division of Immunology, Boston Children's Hospital, Boston, 1 Blackfan Circle, Massachusetts, 02115, USA
| | - Naresh Singh Redhu
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts, 02115, USA.,Department of Pediatrics, Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts, 02115, USA.,VEO-IBD Consortium, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Adrian J Thrasher
- Great Ormond Street Hospital NHS Trust, London and Institute of Child Health, University College London, 30 Guilford Street, London, WC1N 1EH, UK
| | - Talal Chatila
- Department of Pediatrics, Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts, 02115, USA.,Division of Immunology, Boston Children's Hospital, Boston, 1 Blackfan Circle, Massachusetts, 02115, USA
| | - Vijay K Kuchroo
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, 60 Fenwood Road, Boston, Massachusetts, 02115, USA
| | - Raif S Geha
- Department of Pediatrics, Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts, 02115, USA.,Division of Immunology, Boston Children's Hospital, Boston, 1 Blackfan Circle, Massachusetts, 02115, USA
| | - Luigi D Notarangelo
- Clinical Immunology and Microbiology, NIAID, National Institutes of Health, 10 Center Drive, MSC 1456, Bethesda, Maryland, 20892-9806, USA
| | - Sung-Yun Pai
- Division of Hematology-Oncology, Boston Children's Hospital Boston, 1 Blackfan Circle, Boston, Massachusetts, 02115, USA
| | - Bruce H Horwitz
- Department of Pediatrics, Harvard Medical School, 25 Shattuck Street, Boston, Massachusetts, 02115, USA.,VEO-IBD Consortium, 300 Longwood Avenue, Boston, MA, 02115, USA.,Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, 02115, Massachusetts, USA.,Division of Emergency Medicine, Boston Children's Hospital, Boston, 300 Longwood Avenue, Boston, Massacusetts, 02115, USA
| | - Scott B Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, 300 Longwood Avenue, Boston, Massachusetts, 02115, USA. .,VEO-IBD Consortium, 300 Longwood Avenue, Boston, MA, 02115, USA. .,Division of Gastroenterology, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, 75 Francis Street, Boston, Massachusetts, 02115, USA.
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36
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Sallis BF, Erkert L, Moñino-Romero S, Acar U, Wu R, Konnikova L, Lexmond WS, Hamilton MJ, Dunn WA, Szepfalusi Z, Vanderhoof JA, Snapper SB, Turner JR, Goldsmith JD, Spencer LA, Nurko S, Fiebiger E. An algorithm for the classification of mRNA patterns in eosinophilic esophagitis: Integration of machine learning. J Allergy Clin Immunol 2018; 141:1354-1364.e9. [PMID: 29273402 PMCID: PMC6425755 DOI: 10.1016/j.jaci.2017.11.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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: 06/22/2017] [Revised: 11/17/2017] [Accepted: 11/30/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND Diagnostic evaluation of eosinophilic esophagitis (EoE) remains difficult, particularly the assessment of the patient's allergic status. OBJECTIVE This study sought to establish an automated medical algorithm to assist in the evaluation of EoE. METHODS Machine learning techniques were used to establish a diagnostic probability score for EoE, p(EoE), based on esophageal mRNA transcript patterns from biopsies of patients with EoE, gastroesophageal reflux disease and controls. Dimensionality reduction in the training set established weighted factors, which were confirmed by immunohistochemistry. Following weighted factor analysis, p(EoE) was determined by random forest classification. Accuracy was tested in an external test set, and predictive power was assessed with equivocal patients. Esophageal IgE production was quantified with epsilon germ line (IGHE) transcripts and correlated with serum IgE and the Th2-type mRNA profile to establish an IGHE score for tissue allergy. RESULTS In the primary analysis, a 3-class statistical model generated a p(EoE) score based on common characteristics of the inflammatory EoE profile. A p(EoE) ≥ 25 successfully identified EoE with high accuracy (sensitivity: 90.9%, specificity: 93.2%, area under the curve: 0.985) and improved diagnosis of equivocal cases by 84.6%. The p(EoE) changed in response to therapy. A secondary analysis loop in EoE patients defined an IGHE score of ≥37.5 for a patient subpopulation with increased esophageal allergic inflammation. CONCLUSIONS The development of intelligent data analysis from a machine learning perspective provides exciting opportunities to improve diagnostic precision and improve patient care in EoE. The p(EoE) and the IGHE score are steps toward the development of decision trees to define EoE subpopulations and, consequently, will facilitate individualized therapy.
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Affiliation(s)
- Benjamin F. Sallis
- Department of Pediatrics, Division of Gastroenterology,
Hepatology and Nutrition, Medical University of Vienna.,Department of Medicine, Harvard Medical School, Medical
University of Vienna
| | - Lena Erkert
- Department of Pediatrics, Division of Gastroenterology,
Hepatology and Nutrition, Medical University of Vienna
| | - Sherezade Moñino-Romero
- Department of Pediatrics, Division of Gastroenterology,
Hepatology and Nutrition, Medical University of Vienna.,Department of Pediatrics and Adolescent Medicine, Medical
University of Vienna
| | - Utkucan Acar
- Department of Pediatrics, Division of Gastroenterology,
Hepatology and Nutrition, Medical University of Vienna.,Department of Medicine, Harvard Medical School, Medical
University of Vienna
| | - Rina Wu
- Department of Pediatrics, Division of Gastroenterology,
Hepatology and Nutrition, Medical University of Vienna
| | - Liza Konnikova
- Department of Pediatrics, Division of Gastroenterology,
Hepatology and Nutrition, Medical University of Vienna.,Department of Medicine, Harvard Medical School, Medical
University of Vienna
| | - Willem S. Lexmond
- Department of Pediatrics, Division of Gastroenterology,
Hepatology and Nutrition, Medical University of Vienna.,Department of Medicine, Harvard Medical School, Medical
University of Vienna
| | - Matthew J. Hamilton
- Department of Medicine, Harvard Medical School, Medical
University of Vienna.,Department of Pathology, Medical University of
Vienna.,Division of Gastroenterology, Hepatology, and Endoscopy,
Brigham and Women’s Hospital; Medical University of Vienna
| | - W. Augustine Dunn
- Department of Pediatrics, Division of Gastroenterology,
Hepatology and Nutrition, Medical University of Vienna.,Department of Medicine, Harvard Medical School, Medical
University of Vienna
| | - Zsolt Szepfalusi
- Department of Pediatrics and Adolescent Medicine, Medical
University of Vienna
| | - Jon A. Vanderhoof
- Department of Pediatrics, Division of Gastroenterology,
Hepatology and Nutrition, Medical University of Vienna
| | - Scott B. Snapper
- Department of Pediatrics, Division of Gastroenterology,
Hepatology and Nutrition, Medical University of Vienna.,Department of Medicine, Harvard Medical School, Medical
University of Vienna
| | - Jerrold R. Turner
- Department of Pathology, Medical University of
Vienna.,Division of Gastroenterology, Hepatology, and Endoscopy,
Brigham and Women’s Hospital; Medical University of Vienna
| | - Jeffrey D. Goldsmith
- Department of Pathology, Boston Children’s Hospital,
Medical University of Vienna
| | - Lisa A. Spencer
- Department of Medicine, Harvard Medical School, Medical
University of Vienna.,Department of Medicine, Division of Allergy and
Inflammation, Beth Israel Deaconess Medical Center, Boston, Medical University of
Vienna
| | - Samuel Nurko
- Department of Pediatrics, Division of Gastroenterology,
Hepatology and Nutrition, Medical University of Vienna.,Department of Medicine, Harvard Medical School, Medical
University of Vienna
| | - Edda Fiebiger
- Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, Mass; Department of Medicine, Harvard Medical School, Boston, Mass.
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Kotlarz D, Marquardt B, Barøy T, Lee WS, Konnikova L, Hollizeck S, Magg T, Lehle AS, Walz C, Borggraefe I, Hauck F, Bufler P, Conca R, Wall SM, Schumacher EM, Misceo D, Frengen E, Bentsen BS, Uhlig HH, Hopfner KP, Muise AM, Snapper SB, Strømme P, Klein C. Human TGF-β1 deficiency causes severe inflammatory bowel disease and encephalopathy. Nat Genet 2018; 50:344-348. [PMID: 29483653 PMCID: PMC6309869 DOI: 10.1038/s41588-018-0063-6] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 01/12/2018] [Indexed: 12/11/2022]
Abstract
Transforming growth factor (TGF)-β1 (encoded by TGFB1) is the prototypic member of the TGF-β family of 33 proteins that orchestrate embryogenesis, development and tissue homeostasis1,2. Following its discovery 3 , enormous interest and numerous controversies have emerged about the role of TGF-β in coordinating the balance of pro- and anti-oncogenic properties4,5, pro- and anti-inflammatory effects 6 , or pro- and anti-fibrinogenic characteristics 7 . Here we describe three individuals from two pedigrees with biallelic loss-of-function mutations in the TGFB1 gene who presented with severe infantile inflammatory bowel disease (IBD) and central nervous system (CNS) disease associated with epilepsy, brain atrophy and posterior leukoencephalopathy. The proteins encoded by the mutated TGFB1 alleles were characterized by impaired secretion, function or stability of the TGF-β1-LAP complex, which is suggestive of perturbed bioavailability of TGF-β1. Our study shows that TGF-β1 has a critical and nonredundant role in the development and homeostasis of intestinal immunity and the CNS in humans.
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Affiliation(s)
- Daniel Kotlarz
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital LMU Munich, Munich, Germany
| | - Benjamin Marquardt
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital LMU Munich, Munich, Germany
| | - Tuva Barøy
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Way S Lee
- Department of Pediatrics, University Malaya Medical Center, Kuala Lumpur, Malaysia
| | - Liza Konnikova
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Department of Pediatric and Newborn Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Sebastian Hollizeck
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital LMU Munich, Munich, Germany
| | - Thomas Magg
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital LMU Munich, Munich, Germany
| | - Anna S Lehle
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital LMU Munich, Munich, Germany
| | - Christoph Walz
- Institute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ingo Borggraefe
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital LMU Munich, Munich, Germany
| | - Fabian Hauck
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital LMU Munich, Munich, Germany
| | - Philip Bufler
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital LMU Munich, Munich, Germany
| | - Raffaele Conca
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital LMU Munich, Munich, Germany
| | - Sarah M Wall
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
| | - Eva M Schumacher
- Division of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Doriana Misceo
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Eirik Frengen
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Beint S Bentsen
- Division of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
- Department of Pediatric Research, Pediatric Liver Kidney Alimentary Nutrition and Transplantation Research Group, Oslo University Hospital, Oslo, Norway
| | - Holm H Uhlig
- Translational Gastroenterology Unit and Department of Pediatrics, University of Oxford, Oxford, UK
| | - Karl-Peter Hopfner
- Department of Biochemistry and Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Aleixo M Muise
- SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, University of Toronto, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Scott B Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Brigham and Women's Hospital, Boston, MA, USA
| | - Petter Strømme
- Faculty of Medicine, University of Oslo, Oslo, Norway
- Division of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo, Norway
| | - Christoph Klein
- Dr. von Hauner Children's Hospital, Department of Pediatrics, University Hospital LMU Munich, Munich, Germany.
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38
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Shouval DS, Konnikova L, Griffith AE, Wall SM, Biswas A, Werner L, Nunberg M, Kammermeier J, Goettel JA, Anand R, Chen H, Weiss B, Li J, Loizides A, Yerushalmi B, Yanagi T, Beier R, Conklin LS, Ebens CL, Santos FGMS, Sherlock M, Goldsmith JD, Kotlarz D, Glover SC, Shah N, Bousvaros A, Uhlig HH, Muise AM, Klein C, Snapper SB. Enhanced TH17 Responses in Patients with IL10 Receptor Deficiency and Infantile-onset IBD. Inflamm Bowel Dis 2017; 23:1950-1961. [PMID: 29023267 DOI: 10.1097/mib.0000000000001270] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
BACKGROUND IL10 receptor (IL10R) deficiency causes severe infantile-onset inflammatory bowel disease. Intact IL10R-dependent signals have been shown to be important for innate and adaptive immune cell functions in mice. We have previously reported a key role of IL10 in the generation and function of human anti-inflammatory macrophages. Independent of innate immune cell defects, the aim of the current study was to determine the role of IL10R signaling in regulating human CD4 T-cell function. METHODS Peripheral blood mononuclear cells and intestinal biopsies cells were collected from IL10/IL10R-deficient patients and controls. Frequencies of CD4 T-cell subsets, naive T-cell proliferation, regulatory T cell (Treg)-mediated suppression, and Treg and TH17 generation were determined by flow cytometry. Transcriptional profiling was performed by NanoString and quantitative real-time polymerase chain reaction. RNA in situ hybridization was used to determine the quantities of various transcripts in intestinal mucosa. RESULTS Analysis of 16 IL10- and IL10R-deficient patients demonstrated similar frequencies of peripheral blood and intestinal Tregs, compared with control subjects. In addition, in vitro Treg suppression of CD4 T-cell proliferation and generation of Treg were not dependent on IL10R signaling. However, IL10R-deficient T naive cells exhibited higher proliferative capacity, a strong TH17 signature, and an increase in polarization toward TH17 cells, compared with controls. Moreover, the frequency of TH17 cells was increased in the colon and ileum of IL10R-deficient patients. Finally, we show that stimulation of IL10R-deficient Tregs in the presence of IL1β leads to enhanced production of IL17A. CONCLUSIONS IL10R signaling regulates TH17 polarization and T-cell proliferation in humans but is not required for the generation and in vitro suppression of Tregs. Therapies targeting the TH17 axis might be beneficial for IL10- and IL10R-deficient patients as a bridge to allogeneic hematopoietic stem cell transplantation.
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Affiliation(s)
- Dror S Shouval
- 1Division of Pediatric Gastroenterology and Nutrition, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Ramat-Gan, Israel; 2Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; 3Department of Pediatrics, Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, Massachusetts; 4VEO-IBD Consortium; 5Department of Pediatrics and Newborn Medicine, Brigham and Women's Hospital, Boston, Massachusetts; 6Harvard Medical School, Boston, Massachusetts; 7Great Ormond Street Hospital London, London, England; 8Translational Gastroenterology Unit, University of Oxford, Oxford, England; 9Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Florida, Gainesville, Florida; 10Division of Gastroenterology and Nutrition, The Children's Hospital at Montefiore, Bronx, New York; 11Pediatric Gastroenterology Unit, Soroka University Medical Center and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel; 12Department of Pediatrics, Kurume University School of Medicine, Kurume, Japan; 13Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany; 14Department of Gastroenterology, Children's National Medical Center, Washington, DC; 15Division of Pediatric Hematology and Oncology, University of Michigan, Ann Arbor, Michigan; 16Hospital das Clınicas, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; 17Division of Gastroenterology, McMaster Children's Hospital, West Hamilton, Ontario, Canada; 18Dr von Hauner Children's Hospital, Ludwig-Maximilians-University, Munich, Germany; 19Division of Pathology, Boston Children's Hospital, Boston, Massachusetts; 20Department of Pediatrics, University of Oxford, Oxford, England; 21Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada; 22Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Toronto, Hospital for Sick Children, Toronto, Ontario, Canada; 23Department of Biochemistry, Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada; and 24Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women's Hospital, Boston, Massachusetts
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39
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Abstract
Antibiotic treatment alters the composition and metabolic function of the intestinal microbiota. These alterations may contribute to the pathogenesis of necrotizing enterocolitis (NEC) and antibiotic-associated diarrhea (AAD). Recent studies are beginning to unravel the contribution of specific groups of microbes and their metabolic pathways to these diseases. Probiotics or other microbiota-targeted therapies may provide effect strategies to prevent and treat NEC and AAD.
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Affiliation(s)
- Michael A. Silverman
- Division of Infectious Diseases, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, and Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104
| | - Liza Konnikova
- Department of Pediatric and Newborn Medicine, Brigham and Women’s Hospital, Boston, MA 02115 and Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Jeffrey S. Gerber
- Center for Pediatric Clinical Effectiveness, Division of Infectious Diseases, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104 and Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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40
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Shouval DS, Biswas A, Kang YH, Griffith AE, Konnikova L, Mascanfroni ID, Redhu NS, Frei SM, Field M, Doty AL, Goldsmith JD, Bhan AK, Loizides A, Weiss B, Yerushalmi B, Yanagi T, Lui X, Quintana FJ, Muise AM, Klein C, Horwitz BH, Glover SC, Bousvaros A, Snapper SB. Interleukin 1β Mediates Intestinal Inflammation in Mice and Patients With Interleukin 10 Receptor Deficiency. Gastroenterology 2016; 151:1100-1104. [PMID: 27693323 PMCID: PMC5124405 DOI: 10.1053/j.gastro.2016.08.055] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 08/10/2016] [Accepted: 08/24/2016] [Indexed: 12/02/2022]
Abstract
Interleukin 10 receptor (IL10R)-deficient mice develop spontaneous colitis and, similarly, patients with loss-of-function mutations in IL10R develop severe infant-onset inflammatory bowel disease. Loss of IL10R signaling in mouse and human macrophages is associated with increased production of interleukin 1β. We demonstrated that innate immune production of IL1β mediates colitis in IL10R-deficient mice. Transfer of Il1r1-/- CD4+ T cells into Rag1-/-/Il10rb-/- mice reduced the severity of their colitis (compared to mice that received CD4+ T cells that express IL1R), accompanied by decreased production of interferon gamma, tumor necrosis factor-α, and IL17A. In macrophages from mice without disruption of IL10R signaling or from healthy humans (controls), incubation with IL10 reduced canonical activation of the inflammasome and production of IL1β through transcriptional and post-translational regulation of NLRP3. Lipopolysaccharide and adenosine triphosphate stimulation of macrophages from Il10rb-/- mice or IL10R-deficient patients resulted in increased production of IL1β. Moreover, in human IL10R-deficient macrophages, lipopolysaccharide stimulation alone triggered IL1β secretion via non-canonical, caspase 8-dependent activation of the inflammasome. We treated 2 IL10R-deficient patients with severe and treatment-refractory infant-onset inflammatory bowel disease with the IL1-receptor antagonist anakinra. Both patients had marked clinical, endoscopic, and histologic responses after 4-7 weeks. This treatment served as successful bridge to allogeneic hematopoietic stem cell transplantation in 1 patient. Our findings indicate that loss of IL10 signaling leads to intestinal inflammation, at least in part, through increased production of IL1 by innate immune cells, leading to activation of CD4+ T cells. Agents that block IL1 signaling might be used to treat patients with inflammatory bowel disease resulting from IL10R deficiency.
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Affiliation(s)
- Dror S. Shouval
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA,Harvard Medical School, Boston, MA, USA,Division of Pediatric Gastroenterology and Nutrition, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel Hashomer, Israel,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel,VEO-IBD International Consortium, Division of Gastroenterology, Brigham and Women's Hospital, Boston, MA, USA
| | - Amlan Biswas
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA,Harvard Medical School, Boston, MA, USA,VEO-IBD International Consortium, Division of Gastroenterology, Brigham and Women's Hospital, Boston, MA, USA
| | - Yu Hui Kang
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA,Harvard Medical School, Boston, MA, USA
| | - Alexandra E. Griffith
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA,VEO-IBD International Consortium, Division of Gastroenterology, Brigham and Women's Hospital, Boston, MA, USA
| | - Liza Konnikova
- Harvard Medical School, Boston, MA, USA,Divsion of Newborn Medicine, Brigham and Women's Hospital, Boston, MA, USA,VEO-IBD International Consortium, Division of Gastroenterology, Brigham and Women's Hospital, Boston, MA, USA
| | - Ivan D. Mascanfroni
- Harvard Medical School, Boston, MA, USA,Ann Romney Center for Neurological Diseases, Brigham and Women's Hospital, Boston, MA, USA
| | - Naresh S. Redhu
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA,Harvard Medical School, Boston, MA, USA
| | - Sandra M. Frei
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA,Harvard Medical School, Boston, MA, USA
| | - Michael Field
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA,VEO-IBD International Consortium, Division of Gastroenterology, Brigham and Women's Hospital, Boston, MA, USA
| | - Andria L. Doty
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Immunology and Laboratory Medicine and, University of Florida, FL, USA
| | - Jeffrey D. Goldsmith
- Harvard Medical School, Boston, MA, USA,Department of Pathology, Boston Children's Hospital, Boston, MA, USA
| | - Atul K. Bhan
- Harvard Medical School, Boston, MA, USA,Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Anthony Loizides
- Division of Gastroenterology and Nutrition, The Children’s Hospital at Montefiore, Bronx, NY, USA,VEO-IBD International Consortium, Division of Gastroenterology, Brigham and Women's Hospital, Boston, MA, USA
| | - Batia Weiss
- Division of Pediatric Gastroenterology and Nutrition, Edmond and Lily Safra Children’s Hospital, Sheba Medical Center, Tel Hashomer, Israel,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel,VEO-IBD International Consortium, Division of Gastroenterology, Brigham and Women's Hospital, Boston, MA, USA
| | - Baruch Yerushalmi
- Pediatric Gastroenterology Unit, Soroka University Medical Center and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel,VEO-IBD International Consortium, Division of Gastroenterology, Brigham and Women's Hospital, Boston, MA, USA
| | - Tadahiro Yanagi
- Department of Pediatrics, Kurume University School of Medicine, Kurume, Japan,VEO-IBD International Consortium, Division of Gastroenterology, Brigham and Women's Hospital, Boston, MA, USA
| | - Xiuli Lui
- Department of Pathology, Immunology and Laboratory Medicine and, University of Florida, FL, USA
| | - Francisco J. Quintana
- Harvard Medical School, Boston, MA, USA,Ann Romney Center for Neurological Diseases, Brigham and Women's Hospital, Boston, MA, USA
| | - Aleixo M. Muise
- Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada,Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Toronto, Hospital for Sick Children, Toronto, ON, Canada,Institute of Medical Science, and Department of Biochemistry, University of Toronto, Toronto, ON, Canada,VEO-IBD International Consortium, Division of Gastroenterology, Brigham and Women's Hospital, Boston, MA, USA
| | - Christoph Klein
- Dr von Hauner Children’s Hospital, Ludwig-Maximilians-University, Munich, Germany,VEO-IBD International Consortium, Division of Gastroenterology, Brigham and Women's Hospital, Boston, MA, USA
| | - Bruce H. Horwitz
- Harvard Medical School, Boston, MA, USA,Department of Pathology Brigham and Women's Hospital, Boston, MA, USA,VEO-IBD International Consortium, Division of Gastroenterology, Brigham and Women's Hospital, Boston, MA, USA
| | - Sarah C. Glover
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, Immunology and Laboratory Medicine and, University of Florida, FL, USA,VEO-IBD International Consortium, Division of Gastroenterology, Brigham and Women's Hospital, Boston, MA, USA
| | - Athos Bousvaros
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA,Harvard Medical School, Boston, MA, USA,VEO-IBD International Consortium, Division of Gastroenterology, Brigham and Women's Hospital, Boston, MA, USA
| | - Scott B. Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA,Harvard Medical School, Boston, MA, USA,VEO-IBD International Consortium, Division of Gastroenterology, Brigham and Women's Hospital, Boston, MA, USA,Corresponding Author: Scott B. Snapper, M.D., Ph.D., Wolpow Family Chair in IBD Treatment and Research, Director, Inflammatory Bowel Disease Center, Division of Gastroenterology, Boston Children’s Hospital, 300 Longwood Ave, Enders Building 670, Boston, MA 02115, USA, Phone: 617-919-4973, Fax: 617-730-0498,
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Sefik E, Geva-Zatorsky N, Oh S, Konnikova L, Zemmour D, McGuire AM, Burzyn D, Ortiz-Lopez A, Lobera M, Yang J, Ghosh S, Earl A, Snapper SB, Jupp R, Kasper D, Mathis D, Benoist C. MUCOSAL IMMUNOLOGY. Individual intestinal symbionts induce a distinct population of RORγ⁺ regulatory T cells. Science 2015; 349:993-7. [PMID: 26272906 DOI: 10.1126/science.aaa9420] [Citation(s) in RCA: 602] [Impact Index Per Article: 66.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 07/22/2015] [Indexed: 12/18/2022]
Abstract
T regulatory cells that express the transcription factor Foxp3 (Foxp3(+) T(regs)) promote tissue homeostasis in several settings. We now report that symbiotic members of the human gut microbiota induce a distinct T(reg) population in the mouse colon, which constrains immuno-inflammatory responses. This induction—which we find to map to a broad, but specific, array of individual bacterial species—requires the transcription factor Rorγ, paradoxically, in that Rorγ is thought to antagonize FoxP3 and to promote T helper 17 (T(H)17) cell differentiation. Rorγ's transcriptional footprint differs in colonic T(regs) and T(H)17 cells and controls important effector molecules. Rorγ, and the T(regs) that express it, contribute substantially to regulating colonic T(H)1/T(H)17 inflammation. Thus, the marked context-specificity of Rorγ results in very different outcomes even in closely related cell types.
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Affiliation(s)
- Esen Sefik
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston 02115, MA, USA
| | - Naama Geva-Zatorsky
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston 02115, MA, USA
| | - Sungwhan Oh
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston 02115, MA, USA
| | - Liza Konnikova
- Division of Gastroenterology and Hepatology, Brigham and Women's Hospital, Boston, MA 02115, USA, and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - David Zemmour
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston 02115, MA, USA
| | | | - Dalia Burzyn
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston 02115, MA, USA
| | - Adriana Ortiz-Lopez
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston 02115, MA, USA
| | - Mercedes Lobera
- Tempero Pharmaceuticals, a GSK Company, Cambridge, MA 02115, USA
| | - Jianfei Yang
- Tempero Pharmaceuticals, a GSK Company, Cambridge, MA 02115, USA
| | - Shomir Ghosh
- Tempero Pharmaceuticals, a GSK Company, Cambridge, MA 02115, USA
| | - Ashlee Earl
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Scott B Snapper
- Division of Gastroenterology and Hepatology, Brigham and Women's Hospital, Boston, MA 02115, USA, and Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Ray Jupp
- UCB Pharma, Slough, Berkshire, UK
| | - Dennis Kasper
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston 02115, MA, USA
| | - Diane Mathis
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston 02115, MA, USA. Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA.
| | - Christophe Benoist
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston 02115, MA, USA. Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA.
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Rhein LM, Konnikova L, McGeachey A, Pruchniewski M, Smith VC. The role of pulmonary follow-up in reducing health care utilization in infants with bronchopulmonary dysplasia. Clin Pediatr (Phila) 2012; 51:645-50. [PMID: 22492835 DOI: 10.1177/0009922812439242] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
OBJECTIVE To determine whether pulmonary follow-up affects rates of rehospitalization and visitations to emergency departments (EDs) in preterm infants with bronchopulmonary dysplasia (BPD). METHODS In this retrospective cohort study, the authors identified all preterm infants born at ≤ 32 weeks' gestation with at least one outpatient visit to a pulmonary follow-up clinic at Children's Hospital Boston or a high-risk primary neurodevelopmental follow-up clinic for preterm infants. ED visits and rehospitalizations were identified through electronic medical records. RESULTS Infants with pulmonary follow-up compared with infants without pulmonary follow-up were, respectively, younger (mean gestational age 26.3 ± 2.3 vs 28.3 ± 2.3 weeks, P < .0001), smaller at birth (birth weight <1200 g, 87.6% vs 57.2%, P < .0001), and needed more supplemental oxygen (55.7% vs 2.6%, P < .0001) and diuretics (65.8% vs 4.7%, P < .001) at the time of discharge from the neonatal intensive care unit. Although rates of rehospitalization were higher in infants with pulmonary follow-up, rates of visits to an ED for respiratory causes were not statistically significant. After controlling for baseline differences in both groups, the rates of rehospitalization or ED visits were the same for both groups. CONCLUSIONS Despite differences in lung disease status in infants with and without pulmonary follow-up, the rates of health care utilization were the same in both groups. Pulmonary follow-up may decrease the expected higher rates of ED visits and hospitalizations in preterm infants with more severe lung disease.
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Konnikova L, Simeone MC, Kruger MM, Kotecki M, Cochran BH. Signal transducer and activator of transcription 3 (STAT3) regulates human telomerase reverse transcriptase (hTERT) expression in human cancer and primary cells. Cancer Res 2005; 65:6516-20. [PMID: 16061629 DOI: 10.1158/0008-5472.can-05-0924] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Signal transducer and activator of transcription 3 (STAT3) is a transcription factor that plays a critical role in cytokine and growth factor signaling and is frequently activated in human tumors. Human telomerase reverse transcriptase (hTERT) is also often overexpressed in tumor cells and mediates cellular immortalization. Here we report that STAT3 directly regulates the expression of hTERT in a variety of human cancer cells. Moreover, STAT3 activity is required for the survival of many human tumors, and hTERT expression contributes to the survival of STAT3-dependent tumor cells. In addition, we find that growth factors and cytokines stimulate hTERT expression in primary human cells in a STAT3-dependent manner. Thus, STAT3 is a key regulator of hTERT expression in both normal and tumor cells.
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Affiliation(s)
- Liza Konnikova
- Department of Physiology, Tufts University, Boston, Massachusetts 02111, USA
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Yimlamai D, Konnikova L, Moss LG, Jay DG. The zebrafish down syndrome cell adhesion molecule is involved in cell movement during embryogenesis. Dev Biol 2005; 279:44-57. [PMID: 15708557 DOI: 10.1016/j.ydbio.2004.12.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [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: 06/08/2004] [Revised: 11/30/2004] [Accepted: 12/01/2004] [Indexed: 10/26/2022]
Abstract
The Down syndrome cell adhesion molecule (Dscam) is a protein overexpressed in the brains of Down syndrome patients and implicated in mental retardation. Dscam is involved in axon guidance and branching in Drosophila, but cellular roles in vertebrates have yet to be elucidated. To understand its role in vertebrate development, we cloned the zebrafish homolog of Dscam and showed that it shares high amino acid identity and structure with the mammalian homologs. Zebrafish dscam is highly expressed in developing neurons, similar to what has been described in Drosophila and mouse. When dscam expression is diminished by morpholino injection, embryos display few neurons and their axons do not enter stereotyped pathways. Zebrafish dscam is also present at early embryonic stages including blastulation and gastrulation. Its loss results in early morphogenetic defects. dscam knockdown results in impaired cell movement during epiboly as well as in subsequent stages. We propose that migrating cells utilize dscam to remodel the developing embryo.
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Affiliation(s)
- Dean Yimlamai
- Cellular and Molecular Physiology, Tufts University School of Medicine, 136 Harrison Avenue, M and V 709, Boston, MA 02111, USA
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Konnikova L, Kotecki M, Kruger MM, Cochran BH. Knockdown of STAT3 expression by RNAi induces apoptosis in astrocytoma cells. BMC Cancer 2003; 3:23. [PMID: 13678425 PMCID: PMC212316 DOI: 10.1186/1471-2407-3-23] [Citation(s) in RCA: 178] [Impact Index Per Article: 8.5] [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: 07/14/2003] [Accepted: 09/17/2003] [Indexed: 12/11/2022] Open
Abstract
Background Astrocytomas are the most common type of primary central nervous system tumors. They are frequently associated with genetic mutations that deregulate cell cycle and render these tumors resistant to apoptosis. STAT3, signal transducer and activator of transcription 3, participates in several human cancers by inducing cell proliferation and inhibiting apoptosis and is frequently activated in astrocytomas. Methods RNA interference was used to knockdown STAT3 expression in human astrocytes and astrocytoma cell lines. The effect of STAT3 knockdown on apoptosis, cell proliferation, and gene expression was then assessed by standard methods. Results We have found that STAT3 is constitutively activated in several human astrocytoma cell lines. Knockdown of STAT3 expression by siRNA induces morphologic and biochemical changes consistent with apoptosis in several astrocytoma cell lines, but not in primary human astrocytes. Moreover, STAT3 is required for the expression of the antiapoptotic genes survivin and Bcl-xL in the A172 glioblastoma cell line. Conclusion These results show that STAT3 is required for the survival of some astrocytomas. These studies suggest STAT3 siRNA could be a useful therapeutic agent for the treatment of astrocytomas.
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Affiliation(s)
- Liza Konnikova
- Department of Physiology, Tufts University School of Medicine 136 Harrison Ave., Boston, Massachusetts, 02111, USA
| | - Maciej Kotecki
- Department of Physiology, Tufts University School of Medicine 136 Harrison Ave., Boston, Massachusetts, 02111, USA
| | - Mathew M Kruger
- Department of Physiology, Tufts University School of Medicine 136 Harrison Ave., Boston, Massachusetts, 02111, USA
| | - Brent H Cochran
- Department of Physiology, Tufts University School of Medicine 136 Harrison Ave., Boston, Massachusetts, 02111, USA
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Konnikova L, Harvey-Wilkes K, Marino T, Craigo S, Nielsen HC. Clinical dilemma in triplet pregnancy: when is it appropriate to intervene for a jeopardized fetus? J Perinatol 2003; 23:229-34. [PMID: 12732861 DOI: 10.1038/sj.jp.7210888] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
OBJECTIVE To determine gestational age-specific risks of intervening to "rescue" a compromised fetus in triplet pregnancies. STUDY DESIGN We analyzed retrospectively triplet pregnancies managed at New England Medical Center (July 1992-May 2000; n=97 pregnancies). For each week in gestation, we compared the chance of at least one of three infants developing complications of prematurity in Scenario A (delivery at that gestation to rescue the jeopardized fetus) with the chance of at least one of two infants from Scenario B (allowing the jeopardized fetus to die in utero to prolong pregnancy) developing that complication later in gestation. RESULTS We observed a decreased risk of at least one infant developing a specific complication in Scenario B than in Scenario A for all complications studied. CONCLUSIONS Comparison of triplet outcomes with the two surviving older newborns identifies important changes in risk between 25 and 32 weeks. These data enable physicians and parents to weigh acceptable risks with benefits.
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Affiliation(s)
- Liza Konnikova
- Department of Pediatrics, Floating Hospital for Children, New England Medical Center, Boston, MA 02111, USA
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