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Gu W, Eke C, Gonzalez Santiago E, Olaloye O, Konnikova L. Single-cell atlas of the small intestine throughout the human lifespan demonstrates unique features of fetal immune cells. Mucosal Immunol 2024; 17:599-617. [PMID: 38555026 DOI: 10.1016/j.mucimm.2024.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/15/2024] [Accepted: 03/23/2024] [Indexed: 04/02/2024]
Abstract
Proper development of mucosal immunity is critical for human health. Over the past decade, it has become evident that in humans, this process begins in utero. However, there are limited data on the unique features and functions of fetal mucosal immune cells. To address this gap, we integrated several single-cell ribonucleic acid sequencing datasets of the human small intestine (SI) to create an SI transcriptional atlas throughout the human life span, ranging from the first trimester to adulthood, with a focus on immune cells. Fetal SI displayed a complex immune landscape comprising innate and adaptive immune cells that exhibited distinct transcriptional programs from postnatal samples, especially compared with pediatric and adult samples. We identified shifts in myeloid populations across gestation and progression of memory T-cell states throughout the human lifespan. In particular, there was a marked shift of memory T cells from those with stem-like properties in the fetal samples to fully differentiated cells with a high expression of activation and effector function genes in adult samples, with neonatal samples containing both features. Finally, we demonstrate that the SI developmental atlas can be used to elucidate improper trajectories linked to mucosal diseases by implicating developmental abnormalities underlying necrotizing enterocolitis, a severe intestinal complication of prematurity. Collectively, our data provide valuable resources and important insights into intestinal immunity that will facilitate regenerative medicine and disease understanding.
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Affiliation(s)
- Weihong Gu
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Chino Eke
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | | | - Oluwabunmi Olaloye
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA
| | - Liza Konnikova
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA; Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA; Department of Obstetrics, Gynecology and Reproductive Science, Yale University School of Medicine, New Haven, CT, USA; Program in Translational Biomedicine, Yale University School of Medicine, New Haven, CT, USA; Program in Human Translational Immunology, Yale University School of Medicine, New Haven, CT, USA.
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2
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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: 9] [Impact Index Per Article: 9.0] [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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3
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Sharma S, Rodrigues PR, Zaher S, Davies LC, Ghazal P. Immune-metabolic adaptations in pregnancy: A potential stepping-stone to sepsis. EBioMedicine 2022; 86:104337. [PMID: 36470829 PMCID: PMC9782817 DOI: 10.1016/j.ebiom.2022.104337] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/30/2022] [Accepted: 10/17/2022] [Indexed: 12/04/2022] Open
Abstract
Physiological shifts during pregnancy predispose women to a higher risk of developing sepsis resulting from a maladapted host-response to infection. Insightful studies have delineated subtle point-changes to the immune system during pregnancy. Here, we present an overlay of these point-changes, asking what changes and when, at a physiological, cellular, and molecular systems-level in the context of sepsis. We identify distinct immune phases in pregnancy delineated by placental hormone-driven changes in homeostasis setpoints of the immune and metabolic systems that subtly mirrors changes observed in sepsis. We propose that pregnancy immune-metabolic setpoint changes impact feedback thresholds that increase risk for a maladapted host-response to infection and thus act as a stepping-stone to sepsis. Defining maternal immune-metabolic setpoint changes is not only vital for tailoring the right diagnostic tools for early management of maternal sepsis but will facilitate an unravelling of the pathophysiological pathways that predispose an individual to sepsis.
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Affiliation(s)
- Simran Sharma
- Project Sepsis, Systems Immunity Research Institute, Cardiff University, Cardiff, CF14 4XN, UK,Department of Obstetrics & Gynaecology, University Hospital of Wales, Cardiff, CF14 4XW, UK,Corresponding author. Department of Obstetrics & Gynaecology, University Hospital of Wales, Cardiff, CF14 4XW, UK.
| | - Patricia R.S. Rodrigues
- Project Sepsis, Systems Immunity Research Institute, Cardiff University, Cardiff, CF14 4XN, UK
| | - Summia Zaher
- Project Sepsis, Systems Immunity Research Institute, Cardiff University, Cardiff, CF14 4XN, UK,Department of Obstetrics & Gynaecology, University Hospital of Wales, Cardiff, CF14 4XW, UK
| | - Luke C. Davies
- Project Sepsis, Systems Immunity Research Institute, Cardiff University, Cardiff, CF14 4XN, UK,Biomedical Sciences Unit, Swansea University Medical School, Singleton Park, Swansea, SA2 8PP, UK
| | - Peter Ghazal
- Project Sepsis, Systems Immunity Research Institute, Cardiff University, Cardiff, CF14 4XN, UK,Corresponding author. Systems Immunity Research Institute, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
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Genome-Wide Patterns of Homozygosity Reveal the Conservation Status in Five Italian Goat Populations. Animals (Basel) 2021; 11:ani11061510. [PMID: 34071004 PMCID: PMC8224610 DOI: 10.3390/ani11061510] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary In the local populations, the increase in inbreeding is a relevant problem for the reduction in production, reproduction, and adaptive traits. The application of genomic technologies has facilitated the assessment of inbreeding in these populations. The current study aims to investigate the patterns of homozygosity in five Italian local goat populations. The results showed the different selection histories and breeding schemes of these goat populations. The analysis also indicated the importance of this information to avoid future loss of diversity and to produce information for designing optimal breeding and conservation programs. Abstract The application of genomic technologies has facilitated the assessment of genomic inbreeding based on single nucleotide polymorphisms (SNPs). In this study, we computed several runs of homozygosity (ROH) parameters to investigate the patterns of homozygosity using Illumina Goat SNP50 in five Italian local populations: Argentata dell’Etna (N = 48), Derivata di Siria (N = 32), Girgentana (N = 59), Maltese (N = 16) and Messinese (N = 22). The ROH results showed well-defined differences among the populations. A total of 3687 ROH segments >2 Mb were detected in the whole sample. The Argentata dell’Etna and Messinese were the populations with the lowest mean number of ROH and inbreeding coefficient values, which reflect admixture and gene flow. In the Girgentana, we identified an ROH pattern related with recent inbreeding that can endanger the viability of the breed due to reduced population size. The genomes of Derivata di Siria and Maltese breeds showed the presence of long ROH (>16 Mb) that could seriously impact the overall biological fitness of these breeds. Moreover, the results confirmed that ROH parameters are in agreement with the known demography of these populations and highlighted the different selection histories and breeding schemes of these goat populations. In the analysis of ROH islands, we detected harbored genes involved with important traits, such as for milk yield, reproduction, and immune response, and are consistent with the phenotypic traits of the studied goat populations. Finally, the results of this study can be used for implementing conservation programs for these local populations in order to avoid further loss of genetic diversity and to preserve the production and fitness traits. In view of this, the availability of genomic data is a fundamental resource.
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Lutckii A, Strunz B, Zhirkov A, Filipovich O, Rukoiatkina E, Gusev D, Lobzin Y, Fischler B, Aleman S, Sällberg M, Björkström NK. Evidence for B cell maturation but not trained immunity in uninfected infants exposed to hepatitis C virus. Gut 2020; 69:2203-2213. [PMID: 32341018 DOI: 10.1136/gutjnl-2019-320269] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 03/11/2020] [Accepted: 04/03/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVES Vertical transmission of hepatitis C virus (HCV) is rare compared with other chronic viral infections, despite that newborns have an immature, and possibly more susceptible, immune system. It further remains unclear to what extent prenatal and perinatal exposure to HCV affects immune system development in neonates. DESIGN To address this, we studied B cells, innate immune cells and soluble factors in a cohort of 62 children that were either unexposed, exposed uninfected or infected with HCV. Forty of these infants were followed longitudinally from birth up until 18 months of age. RESULTS As expected, evidence for B cell maturation was observed with increased age in children, whereas few age-related changes were noticed among innate immune cells. HCV-infected children had a high frequency of HCV-specific IgG-secreting B cells. Such a response was also detected in some exposed but uninfected children but not in uninfected controls. Consistent with this, both HCV-exposed uninfected and HCV-infected infants had evidence of early B cell immune maturation with an increased proportion of IgA-positive plasma cells and upregulated CD40 expression. In contrast, actual HCV viraemia, but not mere exposure, led to alterations within myeloid immune cell populations, natural killer (NK) cells and a distinct soluble factor profile with increased levels of inflammatory cytokines and chemokines. CONCLUSION Our data reveal that exposure to, and infection with, HCV causes disparate effects on adaptive B cells and innate immune cell such as myeloid cells and NK cells in infants.
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Affiliation(s)
- Anton Lutckii
- Department of Laboratory Medicine, Karolinska institutet, Stockholm, Sweden.,Pediatric Research and Clinical Center for Infectious Diseases, Saint Petersburg, Russian Federation
| | - Benedikt Strunz
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Anton Zhirkov
- Pediatric Research and Clinical Center for Infectious Diseases, Saint Petersburg, Russian Federation
| | - Olga Filipovich
- North-Western State Medical University named after I.I.Mechnikov, Saint Petersburg, Russian Federation
| | - Elena Rukoiatkina
- Maternity Hospital No 16, Saint Petersburg, Russian Federation.,Department of Pediatrics, Gynecology and Female Reproductology, Saint Petersburg State Pediatric Medical University, Saint Petersburg, Russian Federation
| | - Denis Gusev
- Center for Prevention and Control of AIDS and Infectious Diseases, Saint Petersburg, Russian Federation
| | - Yuriy Lobzin
- Pediatric Research and Clinical Center for Infectious Diseases, Saint Petersburg, Russian Federation
| | - Björn Fischler
- Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden.,Department of Pediatrics, Karolinska University Hospital, Stockholm, Sweden
| | - Soo Aleman
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden.,Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Matti Sällberg
- Department of Laboratory Medicine, Karolinska institutet, Stockholm, Sweden
| | - Niklas K Björkström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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Leite GGF, Scicluna BP, van der Poll T, Salomão R. Genetic signature related to heme-hemoglobin metabolism pathway in sepsis secondary to pneumonia. NPJ Syst Biol Appl 2019; 5:26. [PMID: 31396396 PMCID: PMC6672010 DOI: 10.1038/s41540-019-0105-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 07/12/2019] [Indexed: 02/07/2023] Open
Abstract
Sepsis is defined as a life-threatening organ dysfunction caused by a dysregulated inflammatory response to pathogens. Bioinformatics and transcriptomics studies contribute to get a better understanding of the pathogenesis of sepsis. These studies revealed differentially expressed genes (DEGs) in sepsis involved in several pathways. Here we investigated the gene expression profiles of blood leukocytes using three microarray datasets of sepsis secondary to pneumonia, focusing on the heme/hemoglobin metabolism pathway. We demonstrate that the heme/hemoglobin metabolism pathway was found to be enriched in these three cohorts with four common genes (ALAS2, AHSP, HBD, and CA1). Several studies show that these four genes are involved in the cytoprotection of non-erythrocyte cells in response to different stress conditions. The upregulation of heme/hemoglobin metabolism in sepsis might be a protective response of white cells to the hostile environment present in septic patients (follow-up samples).
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Affiliation(s)
- Giuseppe Gianini Figuerêido Leite
- Division of Infectious Diseases, Department of Medicine, Hospital São Paulo, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, São Paulo, Brazil
| | - Brendon P. Scicluna
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Center of Infection and Immunity Amsterdam, Amsterdam University Medical Centers, location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Tom van der Poll
- Center for Experimental and Molecular Medicine, Amsterdam University Medical Centers, location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Center of Infection and Immunity Amsterdam, Amsterdam University Medical Centers, location Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Reinaldo Salomão
- Division of Infectious Diseases, Department of Medicine, Hospital São Paulo, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, São Paulo, Brazil
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7
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Brizić I, Hiršl L, Britt WJ, Krmpotić A, Jonjić S. Immune responses to congenital cytomegalovirus infection. Microbes Infect 2017; 20:543-551. [PMID: 29287989 DOI: 10.1016/j.micinf.2017.12.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/15/2017] [Accepted: 12/19/2017] [Indexed: 12/15/2022]
Abstract
Human cytomegalovirus (HCMV) is the most common cause of viral infection acquired in utero. Even though the infection has been studied for several decades, immune determinants important for virus control and mechanisms of long-term sequelae caused by infection are still insufficiently characterized. Animal models of congenital HCMV infection provide unique opportunity to study various aspects of human disease. In this review, we summarize current knowledge on the role of immune system in congenital CMV infection, with emphasis on lessons learned from mouse model of congenital CMV infection.
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Affiliation(s)
- Ilija Brizić
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia; Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Lea Hiršl
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia; Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - William J Britt
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA; Department of Pediatrics Infectious Disease, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Astrid Krmpotić
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
| | - Stipan Jonjić
- Department of Histology and Embryology, Faculty of Medicine, University of Rijeka, Rijeka, Croatia; Center for Proteomics, Faculty of Medicine, University of Rijeka, Rijeka, Croatia.
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