1
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Mennillo E, Kim YJ, Lee G, Rusu I, Patel RK, Dorman LC, Flynn E, Li S, Bain JL, Andersen C, Rao A, Tamaki S, Tsui J, Shen A, Lotstein ML, Rahim M, Naser M, Bernard-Vazquez F, Eckalbar W, Cho SJ, Beck K, El-Nachef N, Lewin S, Selvig DR, Terdiman JP, Mahadevan U, Oh DY, Fragiadakis GK, Pisco A, Combes AJ, Kattah MG. Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis. Nat Commun 2024; 15:1493. [PMID: 38374043 PMCID: PMC10876948 DOI: 10.1038/s41467-024-45665-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 01/30/2024] [Indexed: 02/21/2024] Open
Abstract
Ulcerative colitis (UC) is driven by immune and stromal subsets, culminating in epithelial injury. Vedolizumab (VDZ) is an anti-integrin antibody that is effective for treating UC. VDZ is known to inhibit lymphocyte trafficking to the intestine, but its broader effects on other cell subsets are less defined. To identify the inflammatory cells that contribute to colitis and are affected by VDZ, we perform single-cell transcriptomic and proteomic analyses of peripheral blood and colonic biopsies in healthy controls and patients with UC on VDZ or other therapies. Here we show that VDZ treatment is associated with alterations in circulating and tissue mononuclear phagocyte (MNP) subsets, along with modest shifts in lymphocytes. Spatial multi-omics of formalin-fixed biopsies demonstrates trends towards increased abundance and proximity of MNP and fibroblast subsets in active colitis. Spatial transcriptomics of archived specimens pre-treatment identifies epithelial-, MNP-, and fibroblast-enriched genes related to VDZ responsiveness, highlighting important roles for these subsets in UC.
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Affiliation(s)
- Elvira Mennillo
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Gyehyun Lee
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Iulia Rusu
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Ravi K Patel
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
| | | | - Emily Flynn
- CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Stephanie Li
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jared L Bain
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Christopher Andersen
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Arjun Rao
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Stanley Tamaki
- CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Jessica Tsui
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Alan Shen
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Madison L Lotstein
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Maha Rahim
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Mohammad Naser
- Biological Imaging Development CoLab, University of California San Francisco, San Francisco, CA, USA
| | | | - Walter Eckalbar
- CoLabs, University of California San Francisco, San Francisco, CA, USA
| | - Soo-Jin Cho
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Kendall Beck
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Najwa El-Nachef
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Sara Lewin
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Daniel R Selvig
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jonathan P Terdiman
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Uma Mahadevan
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - David Y Oh
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Division of Hematology/Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Gabriela K Fragiadakis
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
| | | | - Alexis J Combes
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- CoLabs, University of California San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Michael G Kattah
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
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2
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Mennillo E, Kim YJ, Lee G, Rusu I, Patel RK, Dorman LC, Flynn E, Li S, Bain JL, Andersen C, Rao A, Tamaki S, Tsui J, Shen A, Lotstein ML, Rahim M, Naser M, Bernard-Vazquez F, Eckalbar W, Cho SJ, Beck K, El-Nachef N, Lewin S, Selvig DR, Terdiman JP, Mahadevan U, Oh DY, Fragiadakis GK, Pisco A, Combes AJ, Kattah MG. Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.21.525036. [PMID: 36711576 PMCID: PMC9882264 DOI: 10.1101/2023.01.21.525036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Ulcerative colitis (UC) is driven by immune and stromal subsets, culminating in epithelial injury. Vedolizumab (VDZ) is an anti-integrin antibody that is effective for treating UC. VDZ is known to inhibit lymphocyte trafficking to the intestine, but its broader effects on other cell subsets are less defined. To identify the inflammatory cells that contribute to colitis and are affected by VDZ, we performed single-cell transcriptomic and proteomic analyses of peripheral blood and colonic biopsies in healthy controls and patients with UC on VDZ or other therapies. Here we show that VDZ treatment is associated with alterations in circulating and tissue mononuclear phagocyte (MNP) subsets, along with modest shifts in lymphocytes. Spatial multi-omics of formalin-fixed biopsies demonstrates trends towards increased abundance and proximity of MNP and fibroblast subsets in active colitis. Spatial transcriptomics of archived specimens pre-treatment identifies epithelial-, MNP-, and fibroblast-enriched genes related to VDZ responsiveness, highlighting important roles for these subsets in UC.
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3
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Perlman M, Senger S, Verma S, Carey J, Faherty CS. A foundational approach to culture and analyze malnourished organoids. Gut Microbes 2023; 15:2248713. [PMID: 37724815 PMCID: PMC10512930 DOI: 10.1080/19490976.2023.2248713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 08/07/2023] [Indexed: 09/21/2023] Open
Abstract
The gastrointestinal (GI) epithelium plays a major role in nutrient absorption, barrier formation, and innate immunity. The development of organoid-based methodology has significantly impacted the study of the GI epithelium, particularly in the fields of mucosal biology, immunity, and host-microbe interactions. Various effects on the GI epithelium, such as genetics and nutrition, impact patients and alter disease states. Thus, incorporating these effects into organoid-based models will facilitate a better understanding of disease progression and offer opportunities to evaluate therapeutic candidates. One condition that has a significant effect on the GI epithelium is malnutrition, and studying the mechanistic impacts of malnutrition would enhance our understanding of several pathologies. Therefore, the goal of this study was to begin to develop methodology to generate viable malnourished organoids with accessible techniques and resources that can be used for a wide array of mechanistic studies. By selectively limiting distinct macronutrient components of organoid media, we were able to successfully culture and evaluate malnourished organoids. Genetic and protein-based analyses were used to validate the approach and confirm the presence of known biomarkers of malnutrition. Additionally, as proof-of-concept, we utilized malnourished organoid-derived monolayers to evaluate the effect of malnourishment on barrier formation and the ability of the bacterial pathogen Shigella flexneri to infect the GI epithelium. This work serves as the basis for new and exciting techniques to alter the nutritional state of organoids and investigate the related impacts on the GI epithelium.
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Affiliation(s)
- Meryl Perlman
- Mucosal Immunology and Biology Research Center, Division of Pediatric Gastroenterology and Nutrition, Massachusetts General Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Stefania Senger
- Mucosal Immunology and Biology Research Center, Division of Pediatric Gastroenterology and Nutrition, Massachusetts General Hospital, Boston, MA, USA
| | - Smriti Verma
- Mucosal Immunology and Biology Research Center, Division of Pediatric Gastroenterology and Nutrition, Massachusetts General Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
| | - James Carey
- Mucosal Immunology and Biology Research Center, Division of Pediatric Gastroenterology and Nutrition, Massachusetts General Hospital, Boston, MA, USA
| | - Christina S. Faherty
- Mucosal Immunology and Biology Research Center, Division of Pediatric Gastroenterology and Nutrition, Massachusetts General Hospital, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
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4
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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] [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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5
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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. RESEARCH SQUARE 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] [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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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] [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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7
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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] [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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8
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Globig AM, Mayer LS, Heeg M, Andrieux G, Ku M, Otto-Mora P, Hipp AV, Zoldan K, Pattekar A, Rana N, Schell C, Boerries M, Hofmann M, Neumann-Haefelin C, Kuellmer A, Schmidt A, Boettler T, Tomov V, Thimme R, Hasselblatt P, Bengsch B. Exhaustion of CD39-Expressing CD8 + T Cells in Crohn's Disease Is Linked to Clinical Outcome. Gastroenterology 2022; 163:965-981.e31. [PMID: 35738329 DOI: 10.1053/j.gastro.2022.06.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 06/07/2022] [Accepted: 06/14/2022] [Indexed: 12/02/2022]
Abstract
BACKGROUND & AIMS Exhaustion of CD8 T cells has been suggested to inform different clinical outcomes in Crohn's disease, but detailed analyses are lacking. This study aimed to identify the role of exhaustion on a single-cell level and identify relevant CD8 T cell populations in Crohn's disease. METHODS Blood and intestinal tissue from 58 patients with Crohn's disease (active disease or remission) were assessed for CD8 T cell expression of exhaustion markers and their cytokine profile by highly multiplexed flow and mass cytometry. Key disease-associated subsets were sorted and analyzed by RNA sequencing. CD39 inhibition assays were performed in vitro. RESULTS Activated CD39+ and CD39+PD-1+ CD8 T cell subsets expressing multiple exhaustion markers were enriched at low frequency in active Crohn's disease. Their cytokine production capacity was inversely linked to the Harvey-Bradshaw Index. Subset-level protein and transcriptome profiling revealed co-existence of effector and exhaustion programs in CD39+ and CD39+ PD-1+CD8 T cells, with CD39+ cells likely originating from the intestine. CD39 enzymatic activity controlled T cell cytokine production. Importantly, transcriptional exhaustion signatures were enriched in remission in CD39-expressing subsets with up-regulation of TOX. Subset-level transcriptomics revealed a CD39-related gene module that is associated with the clinical course. CONCLUSIONS These data showed a role for the exhaustion of peripheral CD39-expressing CD8 T cell subsets in Crohn's disease. Their low frequency illustrated the utility of single-cell cytometry methods for identification of relevant immune populations. Importantly, the link of their exhaustion status to the clinical activity and their specific gene signatures have implications for exhaustion-based personalized medicine approaches.
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Affiliation(s)
- Anna-Maria Globig
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Lena Sophie Mayer
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Maximilian Heeg
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; German Cancer Consortium Partner Site Freiburg, German Cancer Research Center, Heidelberg, Germany
| | - Manching Ku
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Patricia Otto-Mora
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Anna Veronika Hipp
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Katharina Zoldan
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Ajinkya Pattekar
- Department of Medicine, Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Nisha Rana
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Christoph Schell
- Institute for Surgical Pathology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; German Cancer Consortium Partner Site Freiburg, German Cancer Research Center, Heidelberg, Germany
| | - Maike Hofmann
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Christoph Neumann-Haefelin
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Armin Kuellmer
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Arthur Schmidt
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Tobias Boettler
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Vesselin Tomov
- Department of Medicine, Division of Gastroenterology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Robert Thimme
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Peter Hasselblatt
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Bertram Bengsch
- Clinic for Internal Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, University Medical Center Freiburg, Faculty of Medicine, Freiburg, Germany; German Cancer Consortium Partner Site Freiburg, German Cancer Research Center, Heidelberg, Germany; Centre for Biological Signalling Studies (BIOSS) and Centre for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, Freiburg, Germany.
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9
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Elfiky AMI, Hageman IL, Becker MAJ, Verhoeff J, Li Yim AYF, Joustra VW, Mulders L, Fung I, Rioja I, Prinjha RK, Smithers NN, Furze RC, Mander PK, Bell MJ, Buskens CJ, D’Haens GR, Wildenberg ME, de Jonge WJ. A BET Protein Inhibitor Targeting Mononuclear Myeloid Cells Affects Specific Inflammatory Mediators and Pathways in Crohn’s Disease. Cells 2022; 11:cells11182846. [PMID: 36139421 PMCID: PMC9497176 DOI: 10.3390/cells11182846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/08/2022] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Myeloid cells are critical determinants of the sustained inflammation in Crohn’s Disease (CD). Targeting such cells may be an effective therapeutic approach for refractory CD patients. Bromodomain and extra-terminal domain protein inhibitors (iBET) are potent anti-inflammatory agents; however, they also possess wide-ranging toxicities. In the current study, we make use of a BET inhibitor containing an esterase sensitive motif (ESM-iBET), which is cleaved by carboxylesterase-1 (CES1), a highly expressed esterase in mononuclear myeloid cells. Methods: We profiled CES1 protein expression in the intestinal biopsies, peripheral blood, and CD fistula tract (fCD) cells of CD patients using mass cytometry. The anti-inflammatory effect of ESM-iBET or its control (iBET) were evaluated in healthy donor CD14+ monocytes and fCD cells, using cytometric beads assay or RNA-sequencing. Results: CES1 was specifically expressed in monocyte, macrophage, and dendritic cell populations in the intestinal tissue, peripheral blood, and fCD cells of CD patients. ESM-iBET inhibited IL1β, IL6, and TNFα secretion from healthy donor CD14+ monocytes and fCD immune cells, with 10- to 26-fold more potency over iBET in isolated CD14+ monocytes. Transcriptomic analysis revealed that ESM-iBET inhibited multiple inflammatory pathways, including TNF, JAK-STAT, NF-kB, NOD2, and AKT signaling, with superior potency over iBET. Conclusions: We demonstrate specific CES1 expression in mononuclear myeloid cell subsets in peripheral blood and inflamed tissues of CD patients. We report that low dose ESM-iBET accumulates in CES1-expressing cells and exerts robust anti-inflammatory effects, which could be beneficial in refractory CD patients.
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Affiliation(s)
- Ahmed M. I. Elfiky
- Tytgat Institute for Liver and Intestinal and Research, Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centers, University of Amsterdam, 1105 BK Amsterdam, The Netherlands
- Immunology Research Unit, GSK Medicines Research Centre, Stevenage SG1 2FX, UK
| | - Ishtu L. Hageman
- Tytgat Institute for Liver and Intestinal and Research, Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centers, University of Amsterdam, 1105 BK Amsterdam, The Netherlands
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Marte A. J. Becker
- Tytgat Institute for Liver and Intestinal and Research, Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centers, University of Amsterdam, 1105 BK Amsterdam, The Netherlands
| | - Jan Verhoeff
- Tytgat Institute for Liver and Intestinal and Research, Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centers, University of Amsterdam, 1105 BK Amsterdam, The Netherlands
- Department of Molecular Cell Biology & Immunology, Amsterdam Infection & Immunity Institute and Cancer Center Amsterdam, Amsterdam University Medical Centers, Free University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Andrew Y. F. Li Yim
- Tytgat Institute for Liver and Intestinal and Research, Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centers, University of Amsterdam, 1105 BK Amsterdam, The Netherlands
- Immunology Research Unit, GSK Medicines Research Centre, Stevenage SG1 2FX, UK
- Genome Diagnostics Laboratory, Department of Clinical Genetics, Amsterdam Reproduction & Development, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Vincent W. Joustra
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Lieven Mulders
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Ivan Fung
- Tytgat Institute for Liver and Intestinal and Research, Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centers, University of Amsterdam, 1105 BK Amsterdam, The Netherlands
| | - Inmaculada Rioja
- Immunology Research Unit, GSK Medicines Research Centre, Stevenage SG1 2FX, UK
| | - Rab K. Prinjha
- Immunology Research Unit, GSK Medicines Research Centre, Stevenage SG1 2FX, UK
| | | | - Rebecca C. Furze
- Immunology Research Unit, GSK Medicines Research Centre, Stevenage SG1 2FX, UK
| | - Palwinder K. Mander
- Immunology Research Unit, GSK Medicines Research Centre, Stevenage SG1 2FX, UK
| | - Matthew J. Bell
- Immunology Research Unit, GSK Medicines Research Centre, Stevenage SG1 2FX, UK
| | - Christianne J. Buskens
- Department of Surgery, Amsterdam UMC, University of Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Geert R. D’Haens
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Amsterdam Gastroenterology Endocrinology Metabolism (AGEM), University of Amsterdam, 1105 AZ Amsterdam, The Netherlands
| | - Manon E. Wildenberg
- Tytgat Institute for Liver and Intestinal and Research, Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centers, University of Amsterdam, 1105 BK Amsterdam, The Netherlands
| | - Wouter J. de Jonge
- Tytgat Institute for Liver and Intestinal and Research, Amsterdam Gastroenterology & Metabolism, Amsterdam University Medical Centers, University of Amsterdam, 1105 BK Amsterdam, The Netherlands
- Department of Surgery, University of Bonn, 53127 Bonn, Germany
- Correspondence: ; Tel.: +31205668163 or +31625387973
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10
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Uniken Venema WTC, Ramírez-Sánchez AD, Bigaeva E, Withoff S, Jonkers I, McIntyre RE, Ghouraba M, Raine T, Weersma RK, Franke L, Festen EAM, van der Wijst MGP. Gut mucosa dissociation protocols influence cell type proportions and single-cell gene expression levels. Sci Rep 2022; 12:9897. [PMID: 35701452 PMCID: PMC9197976 DOI: 10.1038/s41598-022-13812-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 05/27/2022] [Indexed: 01/15/2023] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of the cellular landscape of organs. Most single-cell protocols require fresh material, which limits sample size per experiment, and consequently, introduces batch effects. This is especially true for samples acquired through complex medical procedures, such as intestinal mucosal biopsies. Moreover, the tissue dissociation procedure required for obtaining single cells is a major source of noise; different dissociation procedures applied to different compartments of the tissue induce artificial gene expression differences between cell subsets. To overcome these challenges, we have developed a one-step dissociation protocol and demonstrated its use on cryopreserved gut mucosal biopsies. Using flow cytometry and scRNA-seq analysis, we compared this one-step dissociation protocol with the current gold standard, two-step collagenase digestion, and an adaptation of a recently published alternative, three-step cold-active Bacillus licheniformus protease digestion. Both cell viability and cell type composition were comparable between the one-step and two-step collagenase dissociation, with the former being more time-efficient. The cold protease digestion resulted in equal cell viability, but better preserves the epithelial cell types. Consequently, to analyze the rarer cell types, such as glial cells, larger total biopsy cell numbers are required as input material. The multi-step protocols affected cell types spanning multiple compartments differently. In summary, we show that cryopreserved gut mucosal biopsies can be used to overcome the logistical challenges and batch effects in large scRNA-seq studies. Furthermore, we demonstrate that using cryopreserved biopsies digested using a one-step collagenase protocol enables large-scale scRNA-seq, FACS, organoid generation and intraepithelial lymphocyte expansion.
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Affiliation(s)
- Werna T C Uniken Venema
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Aarón D Ramírez-Sánchez
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Emilia Bigaeva
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Sebo Withoff
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Iris Jonkers
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | | | | | - Tim Raine
- Department of Gastroenterology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Rinse K Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Eleonora A M Festen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Monique G P van der Wijst
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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11
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Loke P, Lee SC, Oyesola OO. Effects of helminths on the human immune response and the microbiome. Mucosal Immunol 2022; 15:1224-1233. [PMID: 35732819 DOI: 10.1038/s41385-022-00532-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/17/2022] [Accepted: 05/22/2022] [Indexed: 02/04/2023]
Abstract
Helminths have evolved sophisticated immune regulating mechanisms to prevent rejection by their mammalian host. Our understanding of how the human immune system responds to these parasites remains poor compared to mouse models of infection and this limits our ability to develop vaccines as well as harness their unique properties as therapeutic strategies against inflammatory disorders. Here, we review how recent studies on human challenge infections, self-infected individuals, travelers, and endemic populations have improved our understanding of human type 2 immunity and its effects on the microbiome. The heterogeneity of responses between individuals and the limited access to tissue samples beyond the peripheral blood are challenges that limit human studies on helminths, but also provide opportunities to transform our understanding of human immunology. Organoids and single-cell sequencing are exciting new tools for immunological analysis that may aid this pursuit. Learning about the genetic and immunological basis of resistance, tolerance, and pathogenesis to helminth infections may thus uncover mechanisms that can be utilized for therapeutic purposes.
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Affiliation(s)
- P'ng Loke
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Soo Ching Lee
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Oyebola O Oyesola
- Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
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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] [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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Insulin is expressed by enteroendocrine cells during human fetal development. Nat Med 2021; 27:2104-2107. [PMID: 34887578 DOI: 10.1038/s41591-021-01586-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 10/22/2021] [Indexed: 12/23/2022]
Abstract
Generation of beta cells via transdifferentiation of other cell types is a promising avenue for the treatment of diabetes. Here we reconstruct a single-cell atlas of the human fetal and neonatal small intestine. We identify a subset of fetal enteroendocrine K/L cells that express high levels of insulin and other beta cell genes. Our findings highlight a potential extra-pancreatic source of beta cells and expose its molecular blueprint.
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14
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Perrone F, Zilbauer M. Biobanking of human gut organoids for translational research. Exp Mol Med 2021; 53:1451-1458. [PMID: 34663935 PMCID: PMC8569164 DOI: 10.1038/s12276-021-00606-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/10/2021] [Accepted: 03/03/2021] [Indexed: 12/23/2022] Open
Abstract
The development of human organoid culture models has led to unprecedented opportunities to generate self-organizing, three-dimensional miniature organs that closely mimic in vivo conditions. The ability to expand, culture, and bank such organoids now provide researchers with the opportunity to generate next-generation living biobanks, which will substantially contribute to translational research in a wide range of areas, including drug discovery and testing, regenerative medicine as well as the development of a personalized treatment approach. However, compared to traditional tissue repositories, the generation of a living organoid biobank requires a much higher level of coordination, additional resources, and scientific expertise. In this short review, we discuss the opportunities and challenges associated with the generation of a living organoid biobank. Focusing on human intestinal organoids, we highlight some of the key aspects that need to be considered and provide an outlook for future development in this exciting field.
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Affiliation(s)
- Francesca Perrone
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Matthias Zilbauer
- Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK.
- Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's, Cambridge, UK.
- Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK.
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15
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Moreira TG, Mangani D, Cox LM, Leibowitz J, Lobo ELC, Oliveira MA, Gauthier CD, Nakagaki BN, Willocq V, Song A, Guo L, Lima DCA, Murugaiyan G, Butovsky O, Gabriely G, Anderson AC, Rezende RM, Faria AMC, Weiner HL. PD-L1 + and XCR1 + dendritic cells are region-specific regulators of gut homeostasis. Nat Commun 2021; 12:4907. [PMID: 34389726 PMCID: PMC8363668 DOI: 10.1038/s41467-021-25115-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 07/26/2021] [Indexed: 12/12/2022] Open
Abstract
The intestinal mucosa constitutes an environment of closely regulated immune cells. Dendritic cells (DC) interact with the gut microbiome and antigens and are important in maintaining gut homeostasis. Here, we investigate DC transcriptome, phenotype and function in five anatomical locations of the gut lamina propria (LP) which constitute different antigenic environments. We show that DC from distinct gut LP compartments induce distinct T cell differentiation and cytokine secretion. We also find that PD-L1+ DC in the duodenal LP and XCR1+ DC in the colonic LP comprise distinct tolerogenic DC subsets that are crucial for gut homeostasis. Mice lacking PD-L1+ and XCR1+ DC have a proinflammatory gut milieu associated with an increase in Th1/Th17 cells and a decrease in Treg cells and have exacerbated disease in the models of 5-FU-induced mucositis and DSS-induced colitis. Our findings identify PD-L1+ and XCR1+ DC as region-specific physiologic regulators of intestinal homeostasis.
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Affiliation(s)
- Thais G Moreira
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Davide Mangani
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Laura M Cox
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jeffrey Leibowitz
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Eduardo L C Lobo
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mariana A Oliveira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Christian D Gauthier
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brenda N Nakagaki
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Valerie Willocq
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Anya Song
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lydia Guo
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - David C A Lima
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Gopal Murugaiyan
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Oleg Butovsky
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Galina Gabriely
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ana C Anderson
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Rafael M Rezende
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ana Maria C Faria
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Howard L Weiner
- Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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16
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Fava A, Raychaudhuri S, Rao DA. The Power of Systems Biology: Insights on Lupus Nephritis from the Accelerating Medicines Partnership. Rheum Dis Clin North Am 2021; 47:335-350. [PMID: 34215367 DOI: 10.1016/j.rdc.2021.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The Accelerating Medicines Partnership (AMP) SLE Network united resources from academic centers, government, nonprofit, and industry to accelerate discovery in lupus nephritis (LN). The AMP SLE Network developed a set of protocols for high-throughput analyses to systematically study kidney tissue, urine, and blood in LN. This article summarizes approaches and results from phase 1 of AMP SLE Network effort, including single cell RNA-seq analysis of LN kidney biopsies, cellular and proteomic studies of LN urine, and mass cytometry immunophenotyping of blood cells. This work provides a framework to guide studies of the clinical implications of active cellular/molecular pathways in LN.
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Affiliation(s)
- Andrea Fava
- Division of Rheumatology, Johns Hopkins University, 1830 East Monument Street, Suite 7500, Baltimore, MD 21205, USA.
| | - Soumya Raychaudhuri
- Division of Rheumatology, Inflammation, Immunity, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Center for Data Sciences, Brigham and Women's Hospital, Building for Transformative Medicine, 60 Fenwood Road, Boston, MA 02115, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester, UK. https://twitter.com/soumya_boston
| | - Deepak A Rao
- Division of Rheumatology, Inflammation, Immunity, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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17
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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: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [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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18
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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] [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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19
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An intestinal organoid-based platform that recreates susceptibility to T-cell-mediated tissue injury. Blood 2021; 135:2388-2401. [PMID: 32232483 DOI: 10.1182/blood.2019004116] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 02/29/2020] [Indexed: 12/13/2022] Open
Abstract
A goal in precision medicine is to use patient-derived material to predict disease course and intervention outcomes. Here, we use mechanistic observations in a preclinical animal model to design an ex vivo platform that recreates genetic susceptibility to T-cell-mediated damage. Intestinal graft-versus-host disease (GVHD) is a life-threatening complication of allogeneic hematopoietic cell transplantation. We found that intestinal GVHD in mice deficient in Atg16L1, an autophagy gene that is polymorphic in humans, is reversed by inhibiting necroptosis. We further show that cocultured allogeneic T cells kill Atg16L1-mutant intestinal organoids from mice, which was associated with an aberrant epithelial interferon signature. Using this information, we demonstrate that pharmacologically inhibiting necroptosis or interferon signaling protects human organoids derived from individuals harboring a common ATG16L1 variant from allogeneic T-cell attack. Our study provides a roadmap for applying findings in animal models to individualized therapy that targets affected tissues.
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20
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Pattekar A, Mayer LS, Lau CW, Liu C, Palko O, Bewtra M, Consortium HPAP, Lindesmith LC, Brewer-Jensen PD, Baric RS, Betts MR, Naji A, Wherry EJ, Tomov VT. Norovirus-Specific CD8 + T Cell Responses in Human Blood and Tissues. Cell Mol Gastroenterol Hepatol 2021; 11:1267-1289. [PMID: 33444817 PMCID: PMC8010716 DOI: 10.1016/j.jcmgh.2020.12.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/26/2020] [Accepted: 12/15/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Noroviruses (NoVs) are the leading cause of acute gastroenteritis worldwide and are associated with significant morbidity and mortality. Moreover, an asymptomatic carrier state can persist following acute infection, promoting NoV spread and evolution. Thus, defining immune correlates of NoV protection and persistence is needed to guide the development of future vaccines and limit viral spread. Whereas antibody responses following NoV infection or vaccination have been studied extensively, cellular immunity has received less attention. Data from the mouse NoV model suggest that T cells are critical for preventing persistence and achieving viral clearance, but little is known about NoV-specific T-cell immunity in humans, particularly at mucosal sites. METHODS We screened peripheral blood mononuclear cells from 3 volunteers with an overlapping NoV peptide library. We then used HLA-peptide tetramers to track virus-specific CD8+ T cells in peripheral, lymphoid, and intestinal tissues. Tetramer+ cells were further characterized using markers for cellular trafficking, exhaustion, cytotoxicity, and proliferation. RESULTS We defined 7 HLA-restricted immunodominant class I epitopes that were highly conserved across pandemic strains from genogroup II.4. NoV-specific CD8+ T cells with central, effector, or tissue-resident memory phenotypes were present at all sites and were especially abundant in the intestinal lamina propria. The properties and differentiation states of tetramer+ cells varied across donors and epitopes. CONCLUSIONS Our findings are an important step toward defining the breadth, distribution, and properties of human NoV T-cell immunity. Moreover, the molecular tools we have developed can be used to evaluate future vaccines and engineer novel cellular therapeutics.
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Affiliation(s)
- Ajinkya Pattekar
- Department of Medicine, Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Lena S. Mayer
- Department of Medicine, Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania,Department of Medicine II: Gastroenterology, Hepatology, Endocrinology, and Infectious Disease, University Medical Center Freiburg, Freiburg, Germany
| | - Chi Wai Lau
- Department of Medicine, Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Chengyang Liu
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Olesya Palko
- Department of Medicine, Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania,Department of Orthopedic Surgery, Montefiore Medical Center, Bronx, New York
| | - Meenakshi Bewtra
- Department of Medicine, Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania,Center for Clinical Epidemiology and Biostatistics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Lisa C. Lindesmith
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina
| | - Paul D. Brewer-Jensen
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina
| | - Ralph S. Baric
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina
| | - Michael R. Betts
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ali Naji
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - E. John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania,Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania,Parker Institute for Cancer Immunotherapy, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Vesselin T. Tomov
- Department of Medicine, Division of Gastroenterology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania,Institute for Immunology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania,Correspondence Address correspondence to: Vesselin Tomov, MD, PhD, Department of Medicine, Division of Gastroenterology, University of Pennsylvania, Perelman School of Medicine, 421 Curie Boulevard, BRB 313, Philadelphia, Pennsylvania 19103. fax: (215) 349-5915.
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21
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FitzPatrick MEB, Provine NM, Garner LC, Powell K, Amini A, Irwin SL, Ferry H, Ambrose T, Friend P, Vrakas G, Reddy S, Soilleux E, Klenerman P, Allan PJ. Human intestinal tissue-resident memory T cells comprise transcriptionally and functionally distinct subsets. Cell Rep 2021; 34:108661. [PMID: 33472060 PMCID: PMC7816164 DOI: 10.1016/j.celrep.2020.108661] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 10/14/2020] [Accepted: 12/22/2020] [Indexed: 01/07/2023] Open
Abstract
Tissue-resident memory T (TRM) cells provide key adaptive immune responses in infection, cancer, and autoimmunity. However, transcriptional heterogeneity of human intestinal TRM cells remains undefined. Here, we investigate transcriptional and functional heterogeneity of human TRM cells through study of donor-derived TRM cells from intestinal transplant recipients. Single-cell transcriptional profiling identifies two transcriptional states of CD8+ TRM cells, delineated by ITGAE and ITGB2 expression. We define a transcriptional signature discriminating these populations, including differential expression of cytotoxicity- and residency-associated genes. Flow cytometry of recipient-derived cells infiltrating the graft, and lymphocytes from healthy gut, confirm these CD8+ TRM phenotypes. CD8+ CD69+CD103+ TRM cells produce interleukin-2 (IL-2) and demonstrate greater polyfunctional cytokine production, whereas β2-integrin+CD69+CD103− TRM cells have higher granzyme expression. Analysis of intestinal CD4+ T cells identifies several parallels, including a β2-integrin+ population. Together, these results describe the transcriptional, phenotypic, and functional heterogeneity of human intestinal CD4+ and CD8+ TRM cells. Human intestinal transplants were used to identify bona fide TRM cells Single-cell RNA sequencing identifies two distinct CD8+ TRM subsets CD103+CD69+ and CD103−CD69+ TRM cell subsets show distinct localization and function β2-integrin is highly expressed on CD103− TRM cells
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Affiliation(s)
- Michael E B FitzPatrick
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Nicholas M Provine
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Lucy C Garner
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Kate Powell
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
| | - Ali Amini
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Sophie L Irwin
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Helen Ferry
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Tim Ambrose
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Peter Friend
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford OX3 9DU, UK; Oxford Transplant Centre, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK
| | - Georgios Vrakas
- Oxford Transplant Centre, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK
| | - Srikanth Reddy
- Oxford Transplant Centre, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK
| | - Elizabeth Soilleux
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Paul Klenerman
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK; Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK; NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK.
| | - Philip J Allan
- Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford OX3 9DU, UK; Oxford Transplant Centre, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK; NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK
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22
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Tran F, Klein C, Arlt A, Imm S, Knappe E, Simmons A, Rosenstiel P, Seibler P. Stem Cells and Organoid Technology in Precision Medicine in Inflammation: Are We There Yet? Front Immunol 2020; 11:573562. [PMID: 33408713 PMCID: PMC7779798 DOI: 10.3389/fimmu.2020.573562] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/19/2020] [Indexed: 12/12/2022] Open
Abstract
Individualised cellular models of disease are a key tool for precision medicine to recapitulate chronic inflammatory processes. Organoid models can be derived from induced pluripotent stem cells (iPSCs) or from primary stem cells ex vivo. These models have been emerging over the past decade and have been used to reconstruct the respective organ-specific physiology and pathology, at an unsurpassed depth. In cancer research, patient-derived cancer organoids opened new perspectives in predicting therapy response and provided novel insights into tumour biology. In precision medicine of chronic inflammatory disorders, stem-cell based organoid models are currently being evaluated in pre-clinical pharmacodynamic studies (clinical studies in a dish) and are employed in clinical studies, e.g., by re-transplanting autologous epithelial organoids to re-establish intestinal barrier integrity. A particularly exciting feature of iPSC systems is their ability to provide insights into organ systems and inflammatory disease processes, which cannot be monitored with clinical biopsies, such as immune reactions in neurodegenerative disorders. Refinement of differentiation protocols, and next-generation co-culturing methods, aimed at generating self-organised, complex tissues in vitro, will be the next logical steps. In this mini-review, we critically discuss the current state-of-the-art stem cell and organoid technologies, as well as their future impact, potential and promises in combating immune-mediated chronic diseases.
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Affiliation(s)
- Florian Tran
- Institute of Clinical Molecular Biology, University of Kiel, Kiel, Germany.,Klinik für Innere Medizin I, Universitätsklinikum Schleswig-Holstein, Kiel, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Alexander Arlt
- Klinik für Innere Medizin I, Universitätsklinikum Schleswig-Holstein, Kiel, Germany.,University Department for Gastroenterology, Klinikum Oldenburg AöR, European Medical School (EMS), Oldenburg, Germany
| | - Simon Imm
- Institute of Clinical Molecular Biology, University of Kiel, Kiel, Germany
| | - Evelyn Knappe
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Alison Simmons
- MRC Human Immunology Unit (MRC), University of Oxford, Oxford, United Kingdom.,Translational Gastroenterology Unit, University of Oxford, Oxford, United Kingdom
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, University of Kiel, Kiel, Germany
| | - Philip Seibler
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
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23
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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] [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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24
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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: 156] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [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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25
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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: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [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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26
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Tyler CJ, Guzman M, Lundborg LR, Yeasmin S, Perez-Jeldres T, Yarur A, Behm B, Dulai PS, Patel D, Bamias G, Rivera-Nieves J. Inherent Immune Cell Variation Within Colonic Segments Presents Challenges for Clinical Trial Design. J Crohns Colitis 2020; 14:1364-1377. [PMID: 32239151 PMCID: PMC7533898 DOI: 10.1093/ecco-jcc/jjaa067] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND AIMS Intestinal biopsy sampling during IBD trials represents a valuable adjunct strategy for understanding drug responses at the tissue level. Given the length and distinctive embryonic origins of the proximal and distal colon, we investigated whether inherent regional differences of immune cell composition could introduce confounders when sampling different disease stages, or pre/post drug administration. Here, we capitalise on novel mass cytometry technology to perform deep immunophenotyping of distinct healthy colonic segments, using the limited numbers of biopsies that can be harvested from patients. METHODS Biopsies [2.8 mm] were collected from the caecum, transverse colon, descending colon, and rectum of normal volunteers. Intestinal leukocytes were isolated, stained with a panel of 37 antibodies, and mass cytometry data acquired. RESULTS Site-specific patterns of leukocyte localisation were observed. The proximal colon featured increased CD8+ T cells [particularly resident memory], monocytes, and CD19+ B cells. Conversely, the distal colon and rectum tissues exhibited enrichment for CD4+ T cells and antibody-secreting cells. The transverse colon displayed increased abundance of both γδ T cells and NK cells. Subsets of leukocyte lineages also displayed gradients of expression along the colon length. CONCLUSIONS Our results show an inherent regional immune cell variation within colonic segments, indicating that regional mucosal signatures must be considered when assessing disease stages or the prospective effects of trial drugs on leukocyte subsets. Precise protocols for intestinal sampling must be implemented to allow for the proper interpretation of potential differences observed within leukocyte lineages present in the colonic lamina propria.
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Affiliation(s)
- Christopher J Tyler
- Inflammatory Bowel Disease Center, Division of Gastroenterology, University of California San Diego, La Jolla, CA, USA,San Diego VA Medical Center, San Diego, CA, USA
| | - Mauricio Guzman
- Inflammatory Bowel Disease Center, Division of Gastroenterology, University of California San Diego, La Jolla, CA, USA,San Diego VA Medical Center, San Diego, CA, USA
| | - Luke R Lundborg
- Inflammatory Bowel Disease Center, Division of Gastroenterology, University of California San Diego, La Jolla, CA, USA,San Diego VA Medical Center, San Diego, CA, USA
| | - Shaila Yeasmin
- Inflammatory Bowel Disease Center, Division of Gastroenterology, University of California San Diego, La Jolla, CA, USA,San Diego VA Medical Center, San Diego, CA, USA
| | - Tamara Perez-Jeldres
- Universidad Católica de Chile, Santiago, Chile,Hospital San Borja Arriarán, Santiago, Chile
| | - Andres Yarur
- Division of Gastroenterology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Brian Behm
- Division of Gastroenterology, University of Virginia, Charlottesville, VI, USA
| | | | - Derek Patel
- San Diego VA Medical Center, San Diego, CA, USA
| | - Giorgos Bamias
- GI Unit, 3rd Academic Department of Internal Medicine, National and Kapodistrian University of Athens, Sotiria Hospital, Athens, Greece
| | - Jesús Rivera-Nieves
- Inflammatory Bowel Disease Center, Division of Gastroenterology, University of California San Diego, La Jolla, CA, USA,San Diego VA Medical Center, San Diego, CA, USA,Corresponding author: Jesús Rivera-Nieves, MD, Inflammatory Bowel Disease Center, Division of Gastroenterology, University of California San Diego, 9500 Gilman Drive Bldg. BRF-II Rm. 4A32, San Diego, CA 92093-0063. Tel.: 858.534.5495; fax: 858.246.1788;
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27
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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] [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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28
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Taylor DM, Aronow BJ, Tan K, Bernt K, Salomonis N, Greene CS, Frolova A, Henrickson SE, Wells A, Pei L, Jaiswal JK, Whitsett J, Hamilton KE, MacParland SA, Kelsen J, Heuckeroth RO, Potter SS, Vella LA, Terry NA, Ghanem LR, Kennedy BC, Helbig I, Sullivan KE, Castelo-Soccio L, Kreigstein A, Herse F, Nawijn MC, Koppelman GH, Haendel M, Harris NL, Rokita JL, Zhang Y, Regev A, Rozenblatt-Rosen O, Rood JE, Tickle TL, Vento-Tormo R, Alimohamed S, Lek M, Mar JC, Loomes KM, Barrett DM, Uapinyoying P, Beggs AH, Agrawal PB, Chen YW, Muir AB, Garmire LX, Snapper SB, Nazarian J, Seeholzer SH, Fazelinia H, Singh LN, Faryabi RB, Raman P, Dawany N, Xie HM, Devkota B, Diskin SJ, Anderson SA, Rappaport EF, Peranteau W, Wikenheiser-Brokamp KA, Teichmann S, Wallace D, Peng T, Ding YY, Kim MS, Xing Y, Kong SW, Bönnemann CG, Mandl KD, White PS. The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution. Dev Cell 2019; 49:10-29. [PMID: 30930166 PMCID: PMC6616346 DOI: 10.1016/j.devcel.2019.03.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 02/11/2019] [Accepted: 03/01/2019] [Indexed: 12/15/2022]
Abstract
Single-cell gene expression analyses of mammalian tissues have uncovered profound stage-specific molecular regulatory phenomena that have changed the understanding of unique cell types and signaling pathways critical for lineage determination, morphogenesis, and growth. We discuss here the case for a Pediatric Cell Atlas as part of the Human Cell Atlas consortium to provide single-cell profiles and spatial characterization of gene expression across human tissues and organs. Such data will complement adult and developmentally focused HCA projects to provide a rich cytogenomic framework for understanding not only pediatric health and disease but also environmental and genetic impacts across the human lifespan.
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Affiliation(s)
- Deanne M Taylor
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, and the Department of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - Bruce J Aronow
- Department of Biomedical Informatics, University of Cincinnati College of Medicine, and Cincinnati Children's Hospital Medical Center, Division of Biomedical Informatics, Cincinnati, OH 45229, USA.
| | - Kai Tan
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, and the Department of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - Kathrin Bernt
- Division of Oncology, Department of Pediatrics, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nathan Salomonis
- Department of Biomedical Informatics, University of Cincinnati College of Medicine, and Cincinnati Children's Hospital Medical Center, Division of Biomedical Informatics, Cincinnati, OH 45229, USA
| | - Casey S Greene
- Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Philadelphia, PA 19102, USA; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alina Frolova
- Institute of Molecular Biology and Genetics, National Academy of Science of Ukraine, Kyiv 03143, Ukraine
| | - Sarah E Henrickson
- Division of Allergy Immunology, Department of Pediatrics, The Children's Hospital of Philadelphia and the Institute for Immunology, the University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Andrew Wells
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Liming Pei
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jyoti K Jaiswal
- Department of Genomics and Precision Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC, USA; Center for Genetic Medicine Research, Children's National Medical Center, NW, Washington, DC, 20010-2970, USA
| | - Jeffrey Whitsett
- Cincinnati Children's Hospital Medical Center, Section of Neonatology, Perinatal and Pulmonary Biology, Perinatal Institute, Cincinnati, OH 45229, USA
| | - Kathryn E Hamilton
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Sonya A MacParland
- Multi-Organ Transplant Program, Toronto General Hospital Research Institute, Departments of Laboratory Medicine and Pathobiology and Immunology, University of Toronto, Toronto, ON, Canada
| | - Judith Kelsen
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Robert O Heuckeroth
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - S Steven Potter
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Laura A Vella
- Division of Infectious Diseases, Department of Pediatrics, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Natalie A Terry
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Louis R Ghanem
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Benjamin C Kennedy
- Division of Neurosurgery, Department of Surgery, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Ingo Helbig
- Division of Neurology, Department of Pediatrics, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kathleen E Sullivan
- Division of Allergy Immunology, Department of Pediatrics, The Children's Hospital of Philadelphia and the Institute for Immunology, the University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Leslie Castelo-Soccio
- Department of Pediatrics, Section of Dermatology, The Children's Hospital of Philadelphia and University of Pennsylvania Perleman School of Medicine, Philadelphia, PA 19104, USA
| | - Arnold Kreigstein
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Florian Herse
- Experimental and Clinical Research Center, A Joint Cooperation Between the Charité Medical Faculty and the Max-Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Martijn C Nawijn
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, and Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands
| | - Gerard H Koppelman
- University of Groningen, University Medical Center Groningen, Beatrix Children's Hospital, Department of Pediatric Pulmonology and Pediatric Allergology, and Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands
| | - Melissa Haendel
- Oregon Clinical & Translational Research Institute, Oregon Health & Science University, Portland, OR, USA; Linus Pauling Institute, Oregon State University, Corvallis, OR, USA
| | - Nomi L Harris
- Environmental Genomics and Systems Biology Division, E. O. Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jo Lynne Rokita
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yuanchao Zhang
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Koch Institure of Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jennifer E Rood
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Timothy L Tickle
- Data Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, South Cambridgeshire CB10 1SA, UK
| | - Saif Alimohamed
- Department of Biomedical Informatics, University of Cincinnati College of Medicine, and Cincinnati Children's Hospital Medical Center, Division of Biomedical Informatics, Cincinnati, OH 45229, USA
| | - Monkol Lek
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520-8005, USA
| | - Jessica C Mar
- Australian Institute for Bioengineering and Nanotechnology, the University of Queensland, Brisbane, QLD 4072, Australia
| | - Kathleen M Loomes
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - David M Barrett
- Division of Oncology, Department of Pediatrics, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Prech Uapinyoying
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA; Center for Genetic Medicine Research, Children's National Medical Center, NW, Washington, DC, 20010-2970, USA
| | - Alan H Beggs
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Pankaj B Agrawal
- The Manton Center for Orphan Disease Research, Divisions of Newborn Medicine and of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Yi-Wen Chen
- Department of Genomics and Precision Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC, USA; Center for Genetic Medicine Research, Children's National Medical Center, NW, Washington, DC, 20010-2970, USA
| | - Amanda B Muir
- Division of Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Lana X Garmire
- Department of Computational Medicine & Bioinformatics, The University of Michigan Medical School, University of Michigan, Ann Arbor, MI, USA
| | - Scott B Snapper
- Division of Gastroenterology, Hepatology, and Nutrition, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Javad Nazarian
- Department of Genomics and Precision Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC, USA; Center for Genetic Medicine Research, Children's National Medical Center, NW, Washington, DC, 20010-2970, USA
| | - Steven H Seeholzer
- Protein and Proteomics Core Facility, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Hossein Fazelinia
- Protein and Proteomics Core Facility, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Larry N Singh
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Robert B Faryabi
- Department of Pathology and Laboratory Medicine, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Pichai Raman
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Noor Dawany
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Hongbo Michael Xie
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Batsal Devkota
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sharon J Diskin
- Division of Oncology, Department of Pediatrics, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Stewart A Anderson
- Department of Psychiatry, The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Eric F Rappaport
- Nucleic Acid PCR Core Facility, The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA 19104, USA
| | - William Peranteau
- Department of Surgery, Division of General, Thoracic, and Fetal Surgery, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kathryn A Wikenheiser-Brokamp
- Department of Pathology & Laboratory Medicine, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Divisions of Pathology & Laboratory Medicine and Pulmonary Biology in the Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Sarah Teichmann
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, South Cambridgeshire CB10 1SA, UK; European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, South Cambridgeshire CB10 1SA, UK; Cavendish Laboratory, Theory of Condensed Matter, 19 JJ Thomson Ave, Cambridge CB3 1SA, UK
| | - Douglas Wallace
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Genetics, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Tao Peng
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, and the Department of Pediatrics, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Yang-Yang Ding
- Division of Oncology, Department of Pediatrics, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Man S Kim
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yi Xing
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia and The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sek Won Kong
- Computational Health Informatics Program, Boston Children's Hospital, Departments of Biomedical Informatics and Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Carsten G Bönnemann
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA; Department of Genomics and Precision Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Kenneth D Mandl
- Computational Health Informatics Program, Boston Children's Hospital, Departments of Biomedical Informatics and Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Peter S White
- Department of Biomedical Informatics, University of Cincinnati College of Medicine, and Cincinnati Children's Hospital Medical Center, Division of Biomedical Informatics, Cincinnati, OH 45229, USA
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