51
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Ghraichy M, Galson JD, Kovaltsuk A, von Niederhäusern V, Pachlopnik Schmid J, Recher M, Jauch AJ, Miho E, Kelly DF, Deane CM, Trück J. Maturation of the Human Immunoglobulin Heavy Chain Repertoire With Age. Front Immunol 2020; 11:1734. [PMID: 32849618 PMCID: PMC7424015 DOI: 10.3389/fimmu.2020.01734] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/29/2020] [Indexed: 01/01/2023] Open
Abstract
B cells play a central role in adaptive immune processes, mainly through the production of antibodies. The maturation of the B cell system with age is poorly studied. We extensively investigated age-related alterations of naïve and antigen-experienced immunoglobulin heavy chain (IgH) repertoires. The most significant changes were observed in the first 10 years of life, and were characterized by altered immunoglobulin gene usage and an increased frequency of mutated antibodies structurally diverging from their germline precursors. Older age was associated with an increased usage of downstream IgH constant region genes and fewer antibodies with self-reactive properties. As mutations accumulated with age, the frequency of germline-encoded self-reactive antibodies decreased, indicating a possible beneficial role of self-reactive B cells in the developing immune system. Our results suggest a continuous process of change through childhood across a broad range of parameters characterizing IgH repertoires and stress the importance of using well-selected, age-appropriate controls in IgH studies.
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Affiliation(s)
- Marie Ghraichy
- Division of Immunology, University Children's Hospital, University of Zurich, Zurich, Switzerland.,Children's Research Center, University of Zurich, Zurich, Switzerland
| | - Jacob D Galson
- Children's Research Center, University of Zurich, Zurich, Switzerland.,Alchemab Therapeutics Ltd, London, United Kingdom
| | | | - Valentin von Niederhäusern
- Division of Immunology, University Children's Hospital, University of Zurich, Zurich, Switzerland.,Children's Research Center, University of Zurich, Zurich, Switzerland
| | - Jana Pachlopnik Schmid
- Division of Immunology, University Children's Hospital, University of Zurich, Zurich, Switzerland.,Children's Research Center, University of Zurich, Zurich, Switzerland
| | - Mike Recher
- Immunodeficiency Laboratory, Department of Biomedicine, University and University Hospital of Basel, Basel, Switzerland
| | - Annaïse J Jauch
- Immunodeficiency Laboratory, Department of Biomedicine, University and University Hospital of Basel, Basel, Switzerland
| | - Enkelejda Miho
- Institute of Medical Engineering and Medical Informatics, University of Applied Sciences and Arts Northwestern Switzerland FHNW, Muttenz, Switzerland.,SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,aiNET GmbH, Basel, Switzerland
| | - Dominic F Kelly
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, United Kingdom.,Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Charlotte M Deane
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Johannes Trück
- Division of Immunology, University Children's Hospital, University of Zurich, Zurich, Switzerland.,Children's Research Center, University of Zurich, Zurich, Switzerland
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52
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Petrova VN, Sawatsky B, Han AX, Laksono BM, Walz L, Parker E, Pieper K, Anderson CA, de Vries RD, Lanzavecchia A, Kellam P, von Messling V, de Swart RL, Russell CA. Incomplete genetic reconstitution of B cell pools contributes to prolonged immunosuppression after measles. Sci Immunol 2020; 4:4/41/eaay6125. [PMID: 31672862 DOI: 10.1126/sciimmunol.aay6125] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/01/2019] [Indexed: 12/24/2022]
Abstract
Measles is a disease caused by the highly infectious measles virus (MeV) that results in both viremia and lymphopenia. Lymphocyte counts recover shortly after the disappearance of measles-associated rash, but immunosuppression can persist for months to years after infection, resulting in increased incidence of secondary infections. Animal models and in vitro studies have proposed various immunological factors underlying this prolonged immune impairment, but the precise mechanisms operating in humans are unknown. Using B cell receptor (BCR) sequencing of human peripheral blood lymphocytes before and after MeV infection, we identified two immunological consequences from measles underlying immunosuppression: (i) incomplete reconstitution of the naïve B cell pool leading to immunological immaturity and (ii) compromised immune memory to previously encountered pathogens due to depletion of previously expanded B memory clones. Using a surrogate model of measles in ferrets, we investigated the clinical consequences of morbillivirus infection and demonstrated a depletion of vaccine-acquired immunity to influenza virus, leading to a compromised immune recall response and increased disease severity after secondary influenza virus challenge. Our results show that MeV infection causes changes in naïve and memory B lymphocyte diversity that persist after the resolution of clinical disease and thus contribute to compromised immunity to previous infections or vaccinations. This work highlights the importance of MeV vaccination not only for the control of measles but also for the maintenance of herd immunity to other pathogens, which can be compromised after MeV infection.
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Affiliation(s)
| | - Bevan Sawatsky
- Veterinary Medicine Division, Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines and DZIF TTU Emerging Infections, Langen, Germany
| | - Alvin X Han
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Laboratory of Applied Evolutionary Biology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Brigitta M Laksono
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, Netherlands
| | - Lisa Walz
- Veterinary Medicine Division, Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines and DZIF TTU Emerging Infections, Langen, Germany
| | - Edyth Parker
- Laboratory of Applied Evolutionary Biology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Kathrin Pieper
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Carl A Anderson
- Department of Human Genetics, Wellcome Sanger Institute, Cambridge, UK
| | - Rory D de Vries
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, Netherlands
| | - Antonio Lanzavecchia
- Institute for Research in Biomedicine, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Paul Kellam
- Department of Medicine, Division of Infectious Diseases, Imperial College Faculty of Medicine, Wright Fleming Institute, St Mary's Campus, London, UK.,Kymab Ltd., The Bennet Building, Babraham Research Campus, Cambridge, UK
| | - Veronika von Messling
- Veterinary Medicine Division, Paul-Ehrlich-Institut, Federal Institute for Vaccines and Biomedicines and DZIF TTU Emerging Infections, Langen, Germany
| | - Rik L de Swart
- Department of Viroscience, Postgraduate School of Molecular Medicine, Erasmus MC, University Medical Centre Rotterdam, Rotterdam, Netherlands
| | - Colin A Russell
- Laboratory of Applied Evolutionary Biology, Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.
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53
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Abstract
Fetal neurodevelopment in utero is profoundly shaped by both systemic maternal immunity and local processes at the maternal-fetal interface. Immune pathways are a critical participant in the normal physiology of pregnancy and perturbations of maternal immunity due to infections during this period have been increasingly linked to a diverse array of poor neurological outcomes, including diseases that manifest much later in postnatal life. While experimental models of maternal immune activation (MIA) have provided groundbreaking characterizations of the maternal pathways underlying pathogenesis, less commonly examined are the immune factors that serve pathogen-independent developmental functions in the embryo and fetus. In this review, we explore what is known about the in vivo role of immune factors in fetal neurodevelopment during normal pregnancy and provide an overview of how MIA perturbs the proper orchestration of this sequence of events. Finally, we discuss how the dysregulation of immune factors may contribute to the manifestation of a variety of neurological disorders.
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Affiliation(s)
- Alice Lu-Culligan
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, Connecticut 06519, USA
| | - Akiko Iwasaki
- Department of Immunobiology, Yale School of Medicine, Yale University, New Haven, Connecticut 06519, USA.,Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06519, USA; .,Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06519, USA
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54
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Park S, Nixon CE, Miller O, Choi NK, Kurtis JD, Friedman JF, Michelow IC. Impact of Malaria in Pregnancy on Risk of Malaria in Young Children: Systematic Review and Meta-Analyses. J Infect Dis 2020; 222:538-550. [PMID: 32219317 PMCID: PMC7377293 DOI: 10.1093/infdis/jiaa139] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/24/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Our objective was to quantify the risk of acquiring malaria among progeny of women with malaria during pregnancy. METHODS We searched MEDLINE, EMBASE, CINAHL, and the Cochrane Library for eligible prospective studies. The primary predictor was malaria during pregnancy defined as placental malaria, parasitemia, clinical malaria, or pregnancy-associated malaria. Primary outcomes were parasitemia or clinically defined malaria of young children. We performed meta-analyses to pool adjusted risk estimates using a random-effects model. RESULTS Nineteen of 2053 eligible studies met inclusion criteria for the systemic review. Eleven of these studies were quantitative and were included in the meta-analyses. The pooled adjusted odds ratio (aOR) or adjusted hazard ratio (aHR) of malaria during pregnancy for detection of parasitemia in young children were 1.94 (95% confidence interval [CI], 0.93-4.07; P = .08) and 1.46 (95% CI, 1.07-2.00; P < .001), respectively. The pooled aOR or aHR for clinically defined malaria in young children were 2.82 (95% CI, 1.82-4.38; P < .001) and 1.31 (95% CI, 0.96-1.79; P = .09), respectively. CONCLUSIONS Our results confirmed that malaria during pregnancy significantly increased the overall risk of malaria in young children via indeterminate mechanisms and emphasize the urgent need to implement safe and highly effective strategies to prevent malaria during pregnancy.
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Affiliation(s)
- Sangshin Park
- Center for International Health Research, Rhode Island Hospital, Providence, Rhode Island, USA
- Department of Pediatrics, The Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
- Graduate School of Urban Public Health, University of Seoul, Seoul, Republic of Korea
| | - Christina E Nixon
- Center for International Health Research, Rhode Island Hospital, Providence, Rhode Island, USA
- Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Olivia Miller
- Department of Global Health, DePauw University, Greencastle, Indiana, USA
| | - Nam-Kyong Choi
- Department of Health Convergence, Ewha Womans University, Seoul, Republic of Korea
| | - Jonathan D Kurtis
- Center for International Health Research, Rhode Island Hospital, Providence, Rhode Island, USA
- Department of Pathology and Laboratory Medicine, The Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Jennifer F Friedman
- Center for International Health Research, Rhode Island Hospital, Providence, Rhode Island, USA
- Department of Pediatrics, The Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Ian C Michelow
- Center for International Health Research, Rhode Island Hospital, Providence, Rhode Island, USA
- Department of Pediatrics, The Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
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55
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Alberca RW, Pereira NZ, Oliveira LMDS, Gozzi-Silva SC, Sato MN. Pregnancy, Viral Infection, and COVID-19. Front Immunol 2020; 11:1672. [PMID: 32733490 PMCID: PMC7358375 DOI: 10.3389/fimmu.2020.01672] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/23/2020] [Indexed: 12/14/2022] Open
Abstract
Pregnancy comprises a unique immunological condition, to allow fetal development and to protect the host from pathogenic infections. Viral infections during pregnancy can disrupt immunological tolerance and may generate deleterious effects on the fetus. Despite these possible links between pregnancy and infection-induced morbidity, it is unclear how pregnancy interferes with maternal response to some viral pathogens. In this context, the novel coronavirus (SARS-CoV-2) can induce the coronavirus diseases-2019 (COVID-19) in pregnant women. The potential risk of vertical transmission is unclear, babies born from COVID-19-positive mothers seems to have no serious clinical symptoms, the possible mechanisms are discussed, which highlights that checking the children's outcome and more research is warranted. In this review, we investigate the reports concerning viral infections and COVID-19 during pregnancy, to establish a correlation and possible implications of COVID-19 during pregnancy and neonatal's health.
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MESH Headings
- Betacoronavirus
- COVID-19
- Child, Preschool
- Coronavirus Infections/blood
- Coronavirus Infections/immunology
- Coronavirus Infections/transmission
- Coronavirus Infections/virology
- Cytokines/blood
- Female
- Fetal Development/immunology
- Humans
- Infant
- Infant, Newborn
- Infectious Disease Transmission, Vertical
- Mothers
- Pandemics
- Pneumonia, Viral/blood
- Pneumonia, Viral/immunology
- Pneumonia, Viral/transmission
- Pneumonia, Viral/virology
- Pregnancy
- Pregnancy Complications, Infectious/blood
- Pregnancy Complications, Infectious/immunology
- Pregnancy Complications, Infectious/virology
- SARS-CoV-2
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Affiliation(s)
- Ricardo Wesley Alberca
- Laboratory of Dermatology and Immunodeficiencies, LIM-56, Department of Dermatology, School of Medicine and Institute of Tropical Medicine of São Paulo, University of São Paulo, São Paulo, Brazil
| | - Nátalli Zanete Pereira
- Laboratory of Dermatology and Immunodeficiencies, LIM-56, Department of Dermatology, School of Medicine and Institute of Tropical Medicine of São Paulo, University of São Paulo, São Paulo, Brazil
| | - Luanda Mara Da Silva Oliveira
- Laboratory of Dermatology and Immunodeficiencies, LIM-56, Department of Dermatology, School of Medicine and Institute of Tropical Medicine of São Paulo, University of São Paulo, São Paulo, Brazil
| | | | - Maria Notomi Sato
- Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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56
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Martinelli D, Fortunato F, Del Matto G, Iannelli G, Prato R. Post-marketing surveillance study of the DTaP2-IPV-HB-Hib (Hexyon) vaccine administered in preterm infants in the Apulia region, Italy, in 2017. Vaccine 2020; 38:5148-5153. [PMID: 32586764 DOI: 10.1016/j.vaccine.2020.06.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 06/04/2020] [Accepted: 06/10/2020] [Indexed: 10/24/2022]
Abstract
Recommendations in many countries state that preterm infants (PTIs) should receive the same routine immunization schedule and timing as for full-term births, according to their chronological age. Data regarding hexavalent vaccine safety in PTIs are still limited. We conducted a post-marketing surveillance study of the DTaP2-IPV-HB-Hib vaccine administered to PTIs in Apulia region, Italy. We identified PTIs by selecting the hospital discharge records of infants born between January and June 2017 using the DRG and ICD-9-CM codes for preterm birth, and we matched these data with records included in the regional immunization registry. We analyzed coverage and timeliness of vaccination. To investigate adverse events (AEs) after the first dose, we interviewed via phone the parents of PTIs vaccinated with at least one dose of the DTaP2-IPV-HB-Hib vaccine. At the time of our analysis (31.12.2017), 866/936 (92.5%) PTIs received the first dose of hexavalent vaccine and 539/936 (57.6%) were vaccinated by the third month of age, as recommended; 700/866 (80.8%) received the DTaP2-IPV-HB-Hib vaccine. The parents of 339 PTIs vaccinated with the DTaP2-IPV-HB-Hib vaccine reported local pain as the most common reaction (35.7% of the children). Erythema, swelling, induration and nodule were also reported in about 25% of the children. Systemic adverse events were generally rarer than local reactions. No serious AEs were reported. Our findings showed that more than 40% of PTIs received delayed hexavalent vaccination. This study showed a reassuring safety profile of the vaccine in the preterm population and may be considered as a pilot for further real-world studies.
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Affiliation(s)
- Domenico Martinelli
- Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy; Department of Hygiene, Policlinico Riuniti di Foggia, Foggia, Italy
| | - Francesca Fortunato
- Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy; Department of Hygiene, Policlinico Riuniti di Foggia, Foggia, Italy
| | - Giulia Del Matto
- Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy; Department of Hygiene, Policlinico Riuniti di Foggia, Foggia, Italy
| | - Giuseppina Iannelli
- Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy; Department of Hygiene, Policlinico Riuniti di Foggia, Foggia, Italy
| | - Rosa Prato
- Department of Medical and Surgical Sciences, University of Foggia, Foggia, Italy; Department of Hygiene, Policlinico Riuniti di Foggia, Foggia, Italy.
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57
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Han FF, Fan H, Ren LL, Wang HG, Wang C, Ma X, Liu LH, He Q, Guo CL. Profiling the pattern of human TRB/IGH-CDR3 repertoire in liver transplantation patients via high-throughput sequencing analysis. Scand J Immunol 2020; 92:e12912. [PMID: 32458431 DOI: 10.1111/sji.12912] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/29/2020] [Accepted: 05/19/2020] [Indexed: 12/15/2022]
Abstract
Immune processes in liver transplantation remain poorly understood. Acute allograft rejection in liver transplantation is a kind of T cell-mediated inflammatory disease accompanied by inflammatory cell infiltration. However, the effect of acute allograft rejection on the immunological characteristics of TCRs in peripheral blood mononuclear cell is unknown. In this study, we characterized the pattern of the human T cell receptor beta chain (TRB) and immunoglobulin heavy chain (IGH) complementarity-determining region 3 (CDR3) repertoires via high-throughput sequencing in 11 acute allograft rejection (AG) cases, 23 patients with stable allograft liver function (ST) who had liver transplantation performed and 20 healthy controls (HC). The diversity of TRB-CDR3 was significantly reduced in the AG group compared with the ST group and healthy controls (HC). The CDR3 and N-addition length distribution were not significantly different between the AG and ST groups. However, N-addition length distribution was significantly changed compared to HC. It seemed that AG used more short N-additions and healthy people used more long N-additions in TRB-CDR3 repertoire. Our findings suggested that the TRB-CDR3 region of AG had distinctive V gene use compared with that of HC. The characteristics of ST seemed to be in between those of AG and HC although the difference is not significant. Cluster analysis showed that the TRB repertoire could not effectively distinguish AG from ST. This research might give to a better understanding of the immune process of liver transplantation.
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Affiliation(s)
- Fei-Fei Han
- Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Hua Fan
- Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Lu-Lu Ren
- Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Hua-Guang Wang
- Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Chunlin Wang
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
| | - Xu Ma
- Department of Genetics, National Research Institute for Family Planning, Beijing, China.,Graduate School of Peking, Union Medical College, Beijing, China
| | - Li-Hong Liu
- Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Qiang He
- Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Chang-Long Guo
- Department of Genetics, National Research Institute for Family Planning, Beijing, China.,Graduate School of Peking, Union Medical College, Beijing, China
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58
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Park JE, Jardine L, Gottgens B, Teichmann SA, Haniffa M. Prenatal development of human immunity. Science 2020; 368:600-603. [PMID: 32381715 DOI: 10.1126/science.aaz9330] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The blood and immune systems develop in parallel during early prenatal life. Waves of hematopoiesis separated in anatomical space and time give rise to circulating and tissue-resident immune cells. Previous observations have relied on animal models, which differ from humans in both their developmental timeline and exposure to microorganisms. Decoding the composition of the human immune system is now tractable using single-cell multi-omics approaches. Large-scale single-cell genomics, imaging technologies, and the Human Cell Atlas initiative have together enabled a systems-level mapping of the developing human immune system and its emergent properties. Although the precise roles of specific immune cells during development require further investigation, the system as a whole displays malleable and responsive properties according to developmental need and environmental challenge.
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Affiliation(s)
- Jong-Eun Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Laura Jardine
- Biosciences Institute, Newcastle University, Faculty of Medical Sciences, Newcastle upon Tyne NE2 4HH, UK
| | - Berthold Gottgens
- Department of Haematology, University of Cambridge, Cambridge CB2 2XY, UK.,Wellcome and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 2XY, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK. .,Department of Physics/Cavendish Laboratory, University of Cambridge, JJ Thomson Ave., Cambridge CB3 0HE, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK. .,Biosciences Institute, Newcastle University, Faculty of Medical Sciences, Newcastle upon Tyne NE2 4HH, UK.,Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
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59
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Werner L, Lee YN, Rechavi E, Lev A, Yerushalmi B, Ling G, Shah N, Uhlig HH, Weiss B, Somech R, Snapper SB, Shouval DS. Alterations in T and B Cell Receptor Repertoires Patterns in Patients With IL10 Signaling Defects and History of Infantile-Onset IBD. Front Immunol 2020; 11:109. [PMID: 32117262 PMCID: PMC7017840 DOI: 10.3389/fimmu.2020.00109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 01/15/2020] [Indexed: 01/04/2023] Open
Abstract
Patients with loss-of-function mutations in IL10 or IL10 receptor (IL10R) genes develop severe, medical-refractory, infantile-onset inflammatory bowel disease (IBD). We have previously reported significant alterations in innate and adaptive immune responses in these patients. Next generation sequencing platforms enable a comprehensive assessment of T cell receptor (TCR) and B cell receptor (BCR) repertoire patterns. We aimed to characterize TCR and BCR features in peripheral blood of patients with deleterious IL10 signaling defects. DNA was isolated from blood of seven patients with IL10R mutations and one with an IL10 mutation, along with eight controls, and subjected to next generation sequencing of TRB and IgH loci. A significant increase in clonality was observed in both TCR and BCR repertoires in circulating lymphocytes of IL10/IL10R-deficient patients, but to a much greater extent in T cells. Furthermore, short CDR3β length and altered hydrophobicity were demonstrated in T cells of patients, but not in B cells, secondary to lower rates of insertions of nucleotides, but not deletions, at the V-, D-, or J-junctions. We were unable to observe specific T or B clones that were limited only to the patients or among controls. Moreover, the expanded T cells clones were unique to each patient. In conclusion, next generation sequencing of the TCR and BCR is a powerful tool for characterizing the adaptive immune cell phenotype and function in immune-mediated disorders. The oligoclonality observed among IL10/IL10R-deficient patients may suggest specialization of unique clones that likely have a role in mediating tissue damage. Nevertheless, the lack of shared clones between patients provides another piece of evidence that the adaptive immune response in IBD is not triggered against common antigens. Additional studies are required to define the specific antigens that interact with the expanded IL10/IL10R-deficient clones.
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Affiliation(s)
- Lael Werner
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yu Nee Lee
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel
| | - Erez Rechavi
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel
| | - Atar Lev
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel
| | - Baruch Yerushalmi
- Pediatric Gastroenterology Unit, Soroka University Medical Center, Ben Gurion University of the Negev, Be'er Sheva, Israel
| | - Galina Ling
- Pediatric Gastroenterology Unit, Soroka University Medical Center, Ben Gurion University of the Negev, Be'er Sheva, Israel
| | - Neil Shah
- Department of Gastroenterology, Great Ormond Street Hospital, London, United Kingdom
| | - Holm H Uhlig
- Translational Gastroenterology Unit, Nuffield Department of Experimental Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom.,Department of Pediatrics, University of Oxford, Oxford, United Kingdom.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Batia Weiss
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Raz Somech
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Department A, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Immunology Service, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel
| | - Scott B Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Dror S Shouval
- Pediatric Gastroenterology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Centre, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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60
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Radtanakatikanon A, Keller SM, Darzentas N, Moore PF, Folch G, Nguefack Ngoune V, Lefranc MP, Vernau W. Topology and expressed repertoire of the Felis catus T cell receptor loci. BMC Genomics 2020; 21:20. [PMID: 31906850 PMCID: PMC6945721 DOI: 10.1186/s12864-019-6431-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 12/24/2019] [Indexed: 01/26/2023] Open
Abstract
Background The domestic cat (Felis catus) is an important companion animal and is used as a large animal model for human disease. However, the comprehensive study of adaptive immunity in this species is hampered by the lack of data on lymphocyte antigen receptor genes and usage. The objectives of this study were to annotate the feline T cell receptor (TR) loci and to characterize the expressed repertoire in lymphoid organs of normal cats using high-throughput sequencing. Results The Felis catus TRG locus contains 30 genes: 12 TRGV, 12 TRGJ and 6 TRGC, the TRB locus contains 48 genes: 33 TRBV, 2 TRBD, 11 TRBJ, 2 TRBC, the TRD locus contains 19 genes: 11 TRDV, 2 TRDD, 5 TRDJ, 1 TRDC, and the TRA locus contains 127 genes: 62 TRAV, 64 TRAJ, 1 TRAC. Functional feline V genes form monophyletic clades with their orthologs, and clustering of multimember subgroups frequently occurs in V genes located at the 5′ end of TR loci. Recombination signal (RS) sequences of the heptamer and nonamer of functional V and J genes are highly conserved. Analysis of the TRG expressed repertoire showed preferential intra-cassette over inter-cassette rearrangements and dominant usage of the TRGV2–1 and TRGJ1–2 genes. The usage of TRBV genes showed minor bias but TRBJ genes of the second J-C-cluster were more commonly rearranged than TRBJ genes of the first cluster. The TRA/TRD V genes almost exclusively rearranged to J genes within their locus. The TRAV/TRAJ gene usage was relatively balanced while the TRD repertoire was dominated by TRDJ3. Conclusions This is the first description of all TR loci in the cat. The genomic organization of feline TR loci was similar to that of previously described jawed vertebrates (gnathostomata) and is compatible with the birth-and-death model of evolution. The large-scale characterization of feline TR genes provides comprehensive baseline data on immune repertoires in healthy cats and will facilitate the development of improved reagents for the diagnosis of lymphoproliferative diseases in cats. In addition, these data might benefit studies using cats as a large animal model for human disease.
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Affiliation(s)
- Araya Radtanakatikanon
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA, USA.
| | - Stefan M Keller
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Nikos Darzentas
- Department of Internal Medicine II, University Hospital Schleswig-Holstein, Kiel, Germany.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Peter F Moore
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Géraldine Folch
- IMGT® the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002 CNRS, Université de Montpellier, Montpellier Cedex 5, France
| | - Viviane Nguefack Ngoune
- IMGT® the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002 CNRS, Université de Montpellier, Montpellier Cedex 5, France
| | - Marie-Paule Lefranc
- IMGT® the international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UMR 9002 CNRS, Université de Montpellier, Montpellier Cedex 5, France
| | - William Vernau
- Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, CA, USA
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61
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Sullivan KE. Chromosome 22q11.2 deletion syndrome and DiGeorge syndrome. Immunol Rev 2019; 287:186-201. [PMID: 30565249 DOI: 10.1111/imr.12701] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 07/30/2018] [Indexed: 12/19/2022]
Abstract
Chromosome 22q11.2 deletion syndrome is the most common microdeletion syndrome in humans. The effects are protean and highly variable, making a unified approach difficult. Nevertheless, commonalities have been identified and white papers with recommended evaluations and anticipatory guidance have been published. This review will cover the immune system in detail and discuss both the primary features and the secondary features related to thymic hypoplasia. A brief discussion of the other organ system involvement will be provided for context. The immune system, percolating throughout the body can impact the function of other organs through allergy or autoimmune disease affecting organs in deleterious manners. Our work has shown that the primary effect of thymic hypoplasia is to restrict T cell production. Subsequent homeostatic proliferation and perhaps other factors drive a Th2 polarization, most obvious in adulthood. This contributes to atopic risk in this population. Thymic hypoplasia also contributes to low regulatory T cells and this may be part of the overall increased risk of autoimmunity. Collectively, the effects are complex and often age-dependent. Future goals of improving thymic function or augmenting thymic volume may offer a direct intervention to ameliorate infections, atopy, and autoimmunity.
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Affiliation(s)
- Kathleen E Sullivan
- The Children's Hospital of Philadelphia, The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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62
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Rodriguez M, Porada CD, Almeida-Porada G. Mechanistic Insights into Factor VIII Immune Tolerance Induction via Prenatal Cell Therapy in Hemophilia A. CURRENT STEM CELL REPORTS 2019; 5:145-161. [PMID: 32351874 DOI: 10.1007/s40778-019-00165-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Purpose of Review Prenatal stem cell and gene therapy approaches are amongst the few therapies that can promise the birth of a healthy infant with specific known genetic diseases. This review describes fetal immune cell signaling and its potential influence on donor cell engraftment, and summarizes mechanisms of central T cell tolerance to peripherally-acquired antigen in the context of prenatal therapies for Hemophilia A. Recent Findings During early gestation, different subsets of antigen presenting cells take up peripherally-acquired, non-inherited antigens and induce the deletion of antigen-reactive T-cell precursors in the thymus, demonstrating the potential for using prenatal cell and gene therapies to induce central tolerance to FVIII in the context of prenatal diagnosis/therapy of Hemophilia A. Summary Prenatal cell and gene therapies are promising approaches to treat several genetic disorders including Hemophilia A and B. Understanding the mechanisms of how FVIII-specific tolerance is achieved during ontogeny could help develop novel therapies for HA and better approaches to overcome FVIII inhibitors.
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Affiliation(s)
- Martin Rodriguez
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Christopher D Porada
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Graҫa Almeida-Porada
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston-Salem, NC, USA
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63
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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: 70] [Impact Index Per Article: 14.0] [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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64
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Fleisher TA, Rosenzweig SD. Lymphocyte reference intervals in the era of newborn screening. J Allergy Clin Immunol 2019; 144:1516-1517. [PMID: 31600546 DOI: 10.1016/j.jaci.2019.09.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 09/20/2019] [Indexed: 11/16/2022]
Affiliation(s)
- Thomas A Fleisher
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Md.
| | - Sergio D Rosenzweig
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Md
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65
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Sureshchandra S, Marshall NE, Messaoudi I. Impact of pregravid obesity on maternal and fetal immunity: Fertile grounds for reprogramming. J Leukoc Biol 2019; 106:1035-1050. [PMID: 31483523 DOI: 10.1002/jlb.3ri0619-181r] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/31/2019] [Accepted: 08/01/2019] [Indexed: 12/12/2022] Open
Abstract
Maternal pregravid obesity results in several adverse health outcomes during pregnancy, including increased risk of gestational diabetes, preeclampsia, placental abruption, and complications at delivery. Additionally, pregravid obesity and in utero exposure to high fat diet have been shown to have detrimental effects on fetal programming, predisposing the offspring to adverse cardiometabolic, endocrine, and neurodevelopmental outcomes. More recently, a deeper appreciation for the modulation of offspring immunity and infectious disease-related outcomes by maternal pregravid obesity has emerged. This review will describe currently available animal models for studying the impact of maternal pregravid obesity on fetal immunity and review the data from clinical and animal model studies. We also examine the burden of pregravid obesity on the maternal-fetal interface and the link between placental and systemic inflammation. Finally, we discuss future studies needed to identify key mechanistic underpinnings that link maternal inflammatory changes and fetal cellular reprogramming events.
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Affiliation(s)
- Suhas Sureshchandra
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Nicole E Marshall
- Maternal-Fetal Medicine, Oregon Health and Science University, Portland, Oregon, USA
| | - Ilhem Messaoudi
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
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66
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Ghosn E, Yoshimoto M, Nakauchi H, Weissman IL, Herzenberg LA. Hematopoietic stem cell-independent hematopoiesis and the origins of innate-like B lymphocytes. Development 2019; 146:146/15/dev170571. [PMID: 31371526 DOI: 10.1242/dev.170571] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The current paradigm that a single long-term hematopoietic stem cell can regenerate all components of the mammalian immune system has been challenged by recent findings in mice. These findings show that adult tissue-resident macrophages and innate-like lymphocytes develop early in fetal hematopoiesis from progenitors that emerge prior to, and apparently independently of, conventional long-term hematopoietic stem cells. Here, we discuss these recent findings, which show that an early and distinct wave of hematopoiesis occurs for all major hematopoietic lineages. These data provide evidence that fetal hematopoietic progenitors not derived from the bona fide long-term hematopoietic stem cells give rise to tissue-resident immune cells that persist throughout adulthood. We also discuss recent insights into B lymphocyte development and attempt to synthesize seemingly contradictory recent findings on the origins of innate-like B-1a lymphocytes during fetal hematopoiesis.
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Affiliation(s)
- Eliver Ghosn
- Departments of Medicine and Pediatrics, Lowance Center for Human Immunology, Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Momoko Yoshimoto
- Center for Stem Cell and Regenerative Medicine, Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Hiromitsu Nakauchi
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Irving L Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Leonore A Herzenberg
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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67
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Fike AJ, Kumova OK, Carey AJ. Dissecting the defects in the neonatal CD8 + T-cell response. J Leukoc Biol 2019; 106:1051-1061. [PMID: 31260598 DOI: 10.1002/jlb.5ru0319-105r] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 05/24/2019] [Accepted: 06/10/2019] [Indexed: 12/26/2022] Open
Abstract
The neonatal period presents a complex scenario where the threshold of reactivity toward colonizing microbiota, maternal antigens, autoantigens, and pathogens must be carefully moderated and balanced. CD8+ T cells are critical for the response against intracellular bacteria and viruses, but this immune compartment maintains altered function relative to adult counterparts because of the unique challenges which infants face. Here, we review our current understanding of the factors which may promote the attenuation and altered function of the neonatal CD8+ T-cell response and potential avenues for future study. Specifically, we have focused on the neonatal CD8+ T-cell ontogeny, memory formation, TCR structure and repertoire, TCR inhibitory receptors, and the clinical implications of altered neonatal CD8+ T-cell function. Special emphasis has been placed on examining the response of preterm neonates relative to term neonates and adults.
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Affiliation(s)
- Adam J Fike
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Ogan K Kumova
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
| | - Alison J Carey
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA
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68
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Halkias J, Rackaityte E, Hillman SL, Aran D, Mendoza VF, Marshall LR, MacKenzie TC, Burt TD. CD161 contributes to prenatal immune suppression of IFNγ-producing PLZF+ T cells. J Clin Invest 2019; 129:3562-3577. [PMID: 31145102 DOI: 10.1172/jci125957] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND While the human fetal immune system defaults to a program of tolerance, there is concurrent need for protective immunity to meet the antigenic challenges encountered after birth. Activation of T cells in utero is associated with the fetal inflammatory response with broad implications for the health of the fetus and of the pregnancy. However, the characteristics of the fetal effector T cells that contribute to this process are largely unknown. METHODS We analyzed primary human fetal lymphoid and mucosal tissues and performed phenotypic, functional, and transcriptional analysis to identify T cells with pro-inflammatory potential. The frequency and function of fetal-specific effector T cells was assessed in the cord blood of infants with localized and systemic inflammatory pathologies and compared to healthy term controls. RESULTS We identified a transcriptionally distinct population of CD4+ T cells characterized by expression of the transcription factor Promyelocytic Leukemia Zinc Finger (PLZF). PLZF+ CD4+ T cells were specifically enriched in the fetal intestine, possessed an effector memory phenotype, and rapidly produced pro-inflammatory cytokines. Engagement of the C-type lectin CD161 on these cells inhibited TCR-dependent production of IFNγ in a fetal-specific manner. IFNγ-producing PLZF+ CD4+ T cells were enriched in the cord blood of infants with gastroschisis, a natural model of chronic inflammation originating from the intestine, as well as in preterm birth, suggesting these cells contribute to fetal systemic immune activation. CONCLUSION Our work reveals a fetal-specific program of protective immunity whose dysregulation is associated with fetal and neonatal inflammatory pathologies.
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Affiliation(s)
| | - Elze Rackaityte
- Biomedical Sciences Program, UCSF, San Francisco, California, USA
| | - Sara L Hillman
- Maternal and Fetal Medicine Department, Institute for Women's Health, University College London, London, United Kingdom
| | - Dvir Aran
- Institute for Computational Health Sciences, UCSF, San Francisco, California, USA
| | - Ventura F Mendoza
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, California, USA
| | - Lucy R Marshall
- Division of Infection Immunity and Inflammation, University College London Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Tippi C MacKenzie
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, California, USA.,Department of Surgery, UCSF, San Francisco, California, USA
| | - Trevor D Burt
- Division of Neonatology, Department of Pediatrics, and.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, California, USA
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69
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Konishi H, Komura D, Katoh H, Atsumi S, Koda H, Yamamoto A, Seto Y, Fukayama M, Yamaguchi R, Imoto S, Ishikawa S. Capturing the differences between humoral immunity in the normal and tumor environments from repertoire-seq of B-cell receptors using supervised machine learning. BMC Bioinformatics 2019; 20:267. [PMID: 31138102 PMCID: PMC6537402 DOI: 10.1186/s12859-019-2853-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 04/26/2019] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The recent success of immunotherapy in treating tumors has attracted increasing interest in research related to the adaptive immune system in the tumor microenvironment. Recent advances in next-generation sequencing technology enabled the sequencing of whole T-cell receptors (TCRs) and B-cell receptors (BCRs)/immunoglobulins (Igs) in the tumor microenvironment. Since BCRs/Igs in tumor tissues have high affinities for tumor-specific antigens, the patterns of their amino acid sequences and other sequence-independent features such as the number of somatic hypermutations (SHMs) may differ between the normal and tumor microenvironments. However, given the high diversity of BCRs/Igs and the rarity of recurrent sequences among individuals, it is far more difficult to capture such differences in BCR/Ig sequences than in TCR sequences. The aim of this study was to explore the possibility of discriminating BCRs/Igs in tumor and in normal tissues, by capturing these differences using supervised machine learning methods applied to RNA sequences of BCRs/Igs. RESULTS RNA sequences of BCRs/Igs were obtained from matched normal and tumor specimens from 90 gastric cancer patients. BCR/Ig-features obtained in Rep-Seq were used to classify individual BCR/Ig sequences into normal or tumor classes. Different machine learning models using various features were constructed as well as gradient boosting machine (GBM) classifier combining these models. The results demonstrated that BCR/Ig sequences between normal and tumor microenvironments exhibit their differences. Next, by using a GBM trained to classify individual BCR/Ig sequences, we tried to classify sets of BCR/Ig sequences into normal or tumor classes. As a result, an area under the curve (AUC) value of 0.826 was achieved, suggesting that BCR/Ig repertoires have distinct sequence-level features in normal and tumor tissues. CONCLUSIONS To the best of our knowledge, this is the first study to show that BCR/Ig sequences derived from tumor and normal tissues have globally distinct patterns, and that these tissues can be effectively differentiated using BCR/Ig repertoires.
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Affiliation(s)
- Hiroki Konishi
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033 Japan
- Institute of Medical Science, Health Intelligence Center, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Daisuke Komura
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033 Japan
| | - Hiroto Katoh
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033 Japan
| | - Shinichiro Atsumi
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033 Japan
- Department of Gastrointestinal Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033 Japan
| | - Hirotomo Koda
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033 Japan
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033 Japan
| | - Asami Yamamoto
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033 Japan
| | - Yasuyuki Seto
- Department of Gastrointestinal Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033 Japan
| | - Masashi Fukayama
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033 Japan
| | - Rui Yamaguchi
- Institute of Medical Science, Human Genome Center, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Seiya Imoto
- Institute of Medical Science, Health Intelligence Center, The University of Tokyo, Tokyo, 108-8639 Japan
| | - Shumpei Ishikawa
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033 Japan
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Affiliation(s)
- Ivan K Chinn
- Department of Pediatrics, Section of Immunology, Allergy, and Rheumatology, Baylor College of Medicine, Houston, TX.,Center for Human Immunobiology, Texas Children's Hospital, Houston, TX
| | - Jordan S Orange
- Department of Pediatrics, Columbia University College of Physicians and Surgeons, New York, NY.,New York Presbyterian Morgan Stanley Children's Hospital, New York, NY
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71
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Frizinsky S, Rechavi E, Barel O, Najeeb RH, Greenberger S, Lee YN, Simon AJ, Lev A, Ma CA, Sun G, Blackstone SA, Milner JD, Somech R, Stauber T. Novel MALT1 Mutation Linked to Immunodeficiency, Immune Dysregulation, and an Abnormal T Cell Receptor Repertoire. J Clin Immunol 2019; 39:401-413. [DOI: 10.1007/s10875-019-00629-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 04/09/2019] [Indexed: 02/06/2023]
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72
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Rodriguez-Zhurbenko N, Quach TD, Hopkins TJ, Rothstein TL, Hernandez AM. Human B-1 Cells and B-1 Cell Antibodies Change With Advancing Age. Front Immunol 2019; 10:483. [PMID: 30941130 PMCID: PMC6433875 DOI: 10.3389/fimmu.2019.00483] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 02/22/2019] [Indexed: 12/28/2022] Open
Abstract
Age-related deficits in the immune system have been associated with an increased incidence of infections, autoimmune diseases, and cancer. Human B cell populations change quantitatively and qualitatively in the elderly. However, the function of human B-1 cells, which play critical anti-microbial and housekeeping roles, have not been studied in the older age population. In the present work, we analyzed how the frequency, function and repertoire of human peripheral blood B-1 cells (CD19+CD20+CD27+CD38low/intCD43+) change with age. Our results show that not only the percentage of B-1 cells but also their ability to spontaneously secrete IgM decreased with age. Further, expression levels of the transcription factors XBP-1 and Blimp-1 were significantly lower, while PAX-5, characteristic of non-secreting B cells, was significantly higher, in healthy donors over 65 years (old) as compared to healthy donors between 20 and 45 years (young). To further characterize the B-1 cell population in older individuals, we performed single cell sequencing analysis of IgM heavy chains from healthy young and old donors. We found reduced repertoire diversity of IgM antibodies in B-1 cells from older donors as well as differences in usage of certain VH and DH specific genes, as compared to younger. Overall, our results show impairment of the human B-1 cell population with advancing age, which might impact the quality of life and onset of disease within the elderly population.
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Affiliation(s)
| | - Tam D Quach
- Center for Autoimmune Musculoskeletal and Hematopoietic Diseases, The Feinstein Institute for Medical Research, Manhasset, NY, United States
| | - Thomas J Hopkins
- Center for Oncology and Cell Biology, The Feinstein Institute for Medical Research, Manhasset, NY, United States
| | - Thomas L Rothstein
- Center for Oncology and Cell Biology, The Feinstein Institute for Medical Research, Manhasset, NY, United States.,Center for Immunobiology and Department of Biomedical Sciences, Western Michigan University Homer Stryker MD School of Medicine, Kalamazoo, MI, United States
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73
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Rechavi E, Somech R. Maturation of the immune system in the fetus and the implications for congenital CMV. Best Pract Res Clin Obstet Gynaecol 2019; 60:35-41. [PMID: 30981539 DOI: 10.1016/j.bpobgyn.2019.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 03/01/2019] [Indexed: 12/28/2022]
Abstract
Congenital cytomegalovirus (CMV) infection is the most prevalent and consequential congenital infection, among others, that affects approximately 0.6% of all live births worldwide. Timing of maternal infection and maternal immune status largely determine the likelihood of a symptomatic infection. However, recent studies suggest that the fetal immune system, long perceived as naïve and immature, may also play a role in deciding the outcome of congenital CMV infection. Here, we review the development of four immune cells most pertinent to CMV control in the human fetus. αβT cells, B cells, natural killer (NK) cells, and γδT cells are all present, mature and partially functional in utero, and are capable of mounting some form of response to congenital CMV infection. Whether this response is negligible, effective, or harmful remains an open question. Expanding our knowledge of normal and abnormal immune development could provide clinicians with more accurate tools for the detection, monitoring, and treatment of congenital CMV infection in fetuses.
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Affiliation(s)
- Erez Rechavi
- Pediatric Department A and Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Affiliated with Tel Aviv University, Tel Aviv 6997801, Israel.
| | - Raz Somech
- Pediatric Department A and Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Affiliated with Tel Aviv University, Tel Aviv 6997801, Israel
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74
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Yeo KT, Embury P, Anderson T, Mungai P, Malhotra I, King C, Kazura J, Dent A. HIV, Cytomegalovirus, and Malaria Infections during Pregnancy Lead to Inflammation and Shifts in Memory B Cell Subsets in Kenyan Neonates. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2019; 202:1465-1478. [PMID: 30674575 PMCID: PMC6379806 DOI: 10.4049/jimmunol.1801024] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 12/17/2018] [Indexed: 11/19/2022]
Abstract
Infections during pregnancy can expose the fetus to microbial Ags, leading to inflammation that affects B cell development. Prenatal fetal immune priming may have an important role in infant acquisition of pathogen-specific immunity. We examined plasma proinflammatory biomarkers, the proportions of various B cell subsets, and fetal priming to tetanus vaccination in cord blood from human United States and Kenyan neonates. United States neonates had no identified prenatal infectious exposures, whereas Kenyan neonates examined had congenital CMV or mothers with prenatal HIV or Plasmodium falciparum or no identified infectious exposures. Kenyan neonates had higher levels of IP-10, TNF-α, CRP, sCD14, and BAFF than United States neonates. Among the Kenyan groups, neonates with prenatal infections/infectious exposures had higher levels of cord blood IFN-γ, IL-7, sTNFR1, and sTNFR2 compared with neonates with no infectious exposures. Kenyan neonates had greater proportions of activated memory B cells (MBC) compared with United States neonates. Among the Kenyan groups, HIV-exposed neonates had greater proportions of atypical MBC compared with the other groups. Although HIV-exposed neonates had altered MBC subset distributions, detection of tetanus-specific MBC from cord blood, indicative of fetal priming with tetanus vaccine given to pregnant women, was comparable in HIV-exposed and non-HIV-exposed neonates. These results indicate that the presence of infections during pregnancy induces fetal immune activation with inflammation and increased activated MBC frequencies in neonates. The immunologic significance and long-term health consequences of these differences warrant further investigation.
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Affiliation(s)
- Kee Thai Yeo
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH 44106
- Department of Pediatrics, Rainbow Babies and Children's Hospital, Case Western Reserve University, Cleveland, OH 44106; and
| | - Paula Embury
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH 44106
| | - Timothy Anderson
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH 44106
| | - Peter Mungai
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH 44106
- Division of Vector Borne and Neglected Tropical Diseases, Ministry of Public Health and Sanitation, Nairobi 00200, Kenya
| | - Indu Malhotra
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH 44106
| | - Christopher King
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH 44106
| | - James Kazura
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH 44106
| | - Arlene Dent
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH 44106;
- Department of Pediatrics, Rainbow Babies and Children's Hospital, Case Western Reserve University, Cleveland, OH 44106; and
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75
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New technologies and applications in infant B cell immunology. Curr Opin Immunol 2019; 57:53-57. [PMID: 30825678 DOI: 10.1016/j.coi.2018.12.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 12/21/2018] [Indexed: 12/23/2022]
Abstract
The human immune system changes dramatically with age, and early life exposures to pathogens and environmental antigens begin the formation of immune memory which influences subsequent responses later in life. To study infant immunity, sample-sparing experimental methods that extract maximal data from small samples of blood or other tissues are needed; fortunately, recent developments in high-throughput sequencing and multiplexed labeling and measurement of markers on cells are well-suited to these tasks. Here, we review some recent studies of infant immune responses to infectious disease, highlighting similarities and differences between infants and adults, and identifying important questions for future research. Recent clinical trials in food allergy have revealed the critical role of immunological events in the first year of life that determine an individual's risk of developing peanut allergy; these also warrant thorough evaluation using the new immune monitoring tools.
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76
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Organoid-Induced Differentiation of Conventional T Cells from Human Pluripotent Stem Cells. Cell Stem Cell 2019; 24:376-389.e8. [PMID: 30661959 DOI: 10.1016/j.stem.2018.12.011] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 11/05/2018] [Accepted: 12/13/2018] [Indexed: 11/21/2022]
Abstract
The ability to generate T cells from pluripotent stem cells (PSCs) has the potential to transform autologous T cell immunotherapy by facilitating universal, off-the-shelf cell products. However, differentiation of human PSCs into mature, conventional T cells has been challenging with existing methods. We report that a continuous 3D organoid system induced an orderly sequence of commitment and differentiation from PSC-derived embryonic mesoderm through hematopoietic specification and efficient terminal differentiation to naive CD3+CD8αβ+ and CD3+CD4+ conventional T cells with a diverse T cell receptor (TCR) repertoire. Introduction of an MHC class I-restricted TCR in PSCs produced naive, antigen-specific CD8αβ+ T cells that lacked endogenous TCR expression and showed anti-tumor efficacy in vitro and in vivo. Functional assays and RNA sequencing aligned PSC-derived T cells with primary naive CD8+ T cells. The PSC-artificial thymic organoid (ATO) system presented here is an efficient platform for generating functional, mature T cells from human PSCs.
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77
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Felter S, Kern P, Ryan C. Allergic contact dermatitis: Adequacy of the default 10X assessment factor for human variability to protect infants and children. Regul Toxicol Pharmacol 2018; 99:116-121. [DOI: 10.1016/j.yrtph.2018.09.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 09/08/2018] [Accepted: 09/12/2018] [Indexed: 01/03/2023]
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78
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Breden F, Watson CT. Using High-Throughput Sequencing to Characterize the Development of the Antibody Repertoire During Infections: A Case Study of HIV-1. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1053:245-263. [PMID: 29549643 DOI: 10.1007/978-3-319-72077-7_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
High throughput sequencing (HTS) approaches have only recently been applied to describing the antibody/B-cell repertoire in fine detail, but these data sets have already become critical to the design of vaccines and therapeutics, and monitoring of cancer immunotherapy. As a case study, we describe the potential and present limitations of HTS studies of the Ab repertoire during infection with HIV-1. Most of the present studies restrict their analyses to lineages of specific bnAbs. We discuss future initiatives to expand this type of analysis to more complete repertoires and to improve comparing and sharing of these Ab repertoire data across studies and institutions.
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Affiliation(s)
- Felix Breden
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada.
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, USA
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79
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Galindo-Sevilla N, Mancilla-Ramírez J. T-cell tolerance as a potential effect of congenital leishmaniasis on offspring immunity. Parasite Immunol 2018; 41:e12540. [PMID: 29888463 DOI: 10.1111/pim.12540] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 05/29/2018] [Indexed: 12/16/2022]
Abstract
Congenital transmission of leishmaniasis is recognized in cases detected by passive surveillance. Most cases are from low-resource countries, limiting the study of several important aspects of this route of infection, including the offspring's immune response. Studies on natural and experimentally infected animals suggest that parasites might be transmitted to the embryo or foetus at any time during pregnancy. As immune system undergoes sequential stages of development, an infection before the time of self-recognition could lead to central tolerance, making an individual specifically tolerant and susceptible to infection. In the alternative scenario, infection after self-recognition would allow the proper development of T-lymphocyte clones in response to Leishmania antigens, providing resistance to the disease. Newborns undergo a transient period of low expression of several immune surface molecules and a naïve adaptive immune response with no memory, which together might contribute to slow elimination of the parasite over several months. This insight is a proposed independent mechanism of the previously proven T-cell exhaustion and must be investigated. Analyses of infected placenta, cord blood and infant immunity are required for a better understanding of immunity in congenital leishmaniasis infection.
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Affiliation(s)
- N Galindo-Sevilla
- Departamento de Infectología e Inmunología, Instituto Nacional de Perinatología, Secretaria de Salud, Mexico City, Mexico
| | - J Mancilla-Ramírez
- Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City, Mexico.,Hospital de la Mujer, Secretaria de Salud, Mexico City, Mexico
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80
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Tirosh I, Yamazaki Y, Frugoni F, Ververs FA, Allenspach EJ, Zhang Y, Burns S, Al-Herz W, Noroski L, Walter JE, Gennery AR, van der Burg M, Notarangelo LD, Lee YN. Recombination activity of human recombination-activating gene 2 (RAG2) mutations and correlation with clinical phenotype. J Allergy Clin Immunol 2018; 143:726-735. [PMID: 29772310 DOI: 10.1016/j.jaci.2018.04.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Revised: 04/22/2018] [Accepted: 04/27/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND Mutations in recombination-activating gene (RAG) 1 and RAG2 are associated with a broad range of clinical and immunologic phenotypes in human subjects. OBJECTIVE Using a flow cytometry-based assay, we aimed to measure the recombinase activity of naturally occurring RAG2 mutant proteins and to correlate our results with the severity of the clinical and immunologic phenotype. METHODS Abelson virus-transformed Rag2-/- pro-B cells engineered to contain an inverted green fluorescent protein (GFP) cassette flanked by recombination signal sequences were transduced with retroviruses encoding either wild-type or 41 naturally occurring RAG2 variants. Bicistronic vectors were used to introduce compound heterozygous RAG2 variants. The percentage of GFP-expressing cells was evaluated by using flow cytometry, and high-throughput sequencing was used to analyze rearrangements at the endogenous immunoglobulin heavy chain (Igh) locus. RESULTS The RAG2 variants showed a wide range of recombination activity. Mutations associated with severe combined immunodeficiency and Omenn syndrome had significantly lower activity than those detected in patients with less severe clinical presentations. Four variants (P253R, F386L, N474S, and M502V) previously thought to be pathogenic were found to have wild-type levels of activity. Use of bicistronic vectors permitted us to assess more carefully the effect of compound heterozygous mutations, with good correlation between GFP expression and the number and diversity of Igh rearrangements. CONCLUSIONS Our data support genotype-phenotype correlation in the setting of RAG2 deficiency. The assay described can be used to define the possible disease-causing role of novel RAG2 variants and might help predict the severity of the clinical phenotype.
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Affiliation(s)
- Irit Tirosh
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, Mass
| | - Yasuhiro Yamazaki
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Francesco Frugoni
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, Mass
| | - Francesca A Ververs
- Division of Immunology, Boston Children's Hospital, Harvard Medical School, Boston, Mass
| | - Eric J Allenspach
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Wash; Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Wash
| | - Yu Zhang
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Siobhan Burns
- Institute for Immunity and Transplantation, University College London, London, United Kingdom; Department of Immunology, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Waleed Al-Herz
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Lenora Noroski
- Division of Allergy and Immunology, Baylor College of Medicine, Texas Children's Hospital, Houston, Tex
| | - Jolan E Walter
- Division of Pediatric Allergy/Immunology, University of South Florida and Johns Hopkins All Children's Hospital, St Petersburg, Fla
| | - Andrew R Gennery
- Department of Pediatric Immunology, Newcastle Upon Tyne Hospital, NHS Foundation Trust, United Kingdom and Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Mirjam van der Burg
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md.
| | - Yu Nee Lee
- Pediatric Department A and the Immunology Service, "Edmond and Lily Safra" Children's Hospital, Jeffrey Modell Foundation Center, Sheba Medical Center, Tel Hashomer, Ramat-Gan and Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.
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81
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Waltari E, Jia M, Jiang CS, Lu H, Huang J, Fernandez C, Finzi A, Kaufmann DE, Markowitz M, Tsuji M, Wu X. 5' Rapid Amplification of cDNA Ends and Illumina MiSeq Reveals B Cell Receptor Features in Healthy Adults, Adults With Chronic HIV-1 Infection, Cord Blood, and Humanized Mice. Front Immunol 2018; 9:628. [PMID: 29632541 PMCID: PMC5879793 DOI: 10.3389/fimmu.2018.00628] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 03/13/2018] [Indexed: 12/17/2022] Open
Abstract
Using 5′ rapid amplification of cDNA ends, Illumina MiSeq, and basic flow cytometry, we systematically analyzed the expressed B cell receptor (BCR) repertoire in 14 healthy adult PBMCs, 5 HIV-1+ adult PBMCs, 5 cord blood samples, and 3 HIS-CD4/B mice, examining the full-length variable region of μ, γ, α, κ, and λ chains for V-gene usage, somatic hypermutation (SHM), and CDR3 length. Adding to the known repertoire of healthy adults, Illumina MiSeq consistently detected small fractions of reads with high mutation frequencies including hypermutated μ reads, and reads with long CDR3s. Additionally, the less studied IgA repertoire displayed similar characteristics to that of IgG. Compared to healthy adults, the five HIV-1 chronically infected adults displayed elevated mutation frequencies for all μ, γ, α, κ, and λ chains examined and slightly longer CDR3 lengths for γ, α, and λ. To evaluate the reconstituted human BCR sequences in a humanized mouse model, we analyzed cord blood and HIS-CD4/B mice, which all lacked the typical SHM seen in the adult reference. Furthermore, MiSeq revealed identical unmutated IgM sequences derived from separate cell aliquots, thus for the first time demonstrating rare clonal members of unmutated IgM B cells by sequencing.
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Affiliation(s)
- Eric Waltari
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, United States
| | - Manxue Jia
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, United States
| | - Caroline S Jiang
- Hospital Biostatistics, The Rockefeller University, New York, NY, United States
| | - Hong Lu
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, United States
| | - Jing Huang
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, United States
| | - Cristina Fernandez
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, United States
| | - Andrés Finzi
- Centre de Recherche du CHUM, Université de Montréal, Montreal, QC, Canada
| | - Daniel E Kaufmann
- Centre de Recherche du CHUM, Université de Montréal, Montreal, QC, Canada.,Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery (CHAVI-ID), La Jolla, CA, United States
| | - Martin Markowitz
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, United States
| | - Moriya Tsuji
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, United States
| | - Xueling Wu
- Aaron Diamond AIDS Research Center, Affiliate of The Rockefeller University, New York, NY, United States
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82
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Goodwin E, Gilman MSA, Wrapp D, Chen M, Ngwuta JO, Moin SM, Bai P, Sivasubramanian A, Connor RI, Wright PF, Graham BS, McLellan JS, Walker LM. Infants Infected with Respiratory Syncytial Virus Generate Potent Neutralizing Antibodies that Lack Somatic Hypermutation. Immunity 2018; 48:339-349.e5. [PMID: 29396163 PMCID: PMC6005179 DOI: 10.1016/j.immuni.2018.01.005] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 11/03/2017] [Accepted: 12/29/2017] [Indexed: 11/17/2022]
Abstract
Respiratory syncytial virus (RSV) is a leading cause of infant mortality, and there are currently no licensed vaccines to protect this vulnerable population. A comprehensive understanding of infant antibody responses to natural RSV infection would facilitate vaccine development. Here, we isolated more than 450 RSV fusion glycoprotein (F)-specific antibodies from 7 RSV-infected infants and found that half of the antibodies recognized only two antigenic sites. Antibodies targeting both sites showed convergent sequence features, and structural studies revealed the molecular basis for their recognition of RSV F. A subset of antibodies targeting one of these sites displayed potent neutralizing activity despite lacking somatic mutations, and similar antibodies were detected in RSV-naive B cell repertoires, suggesting that expansion of these B cells in infants may be possible with suitably designed vaccine antigens. Collectively, our results provide fundamental insights into infant antibody responses and a framework for the rational design of age-specific RSV vaccines.
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Affiliation(s)
| | - Morgan S A Gilman
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Daniel Wrapp
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Man Chen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Joan O Ngwuta
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Syed M Moin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Patricia Bai
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | | | - Ruth I Connor
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Peter F Wright
- Department of Pediatrics, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA
| | - Barney S Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Jason S McLellan
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755, USA.
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83
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Jiang Q, Liu Y, Xu B, Zheng W, Xiang X, Tang X, Dong H, Chen Y, Wang C, Deng G, Mao Q, Shang X, Wu Y. Analysis of T cell receptor repertoire in monozygotic twins concordant and discordant for chronic hepatitis B infection. Biochem Biophys Res Commun 2018; 497:153-159. [PMID: 29438710 DOI: 10.1016/j.bbrc.2018.02.043] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 02/05/2018] [Indexed: 12/12/2022]
Abstract
Due to their identical inheritance and shared surroundings, identical twins have been the recommended group for studying the susceptibility and prognosis of diseases. Here, CD8+ T cell receptor beta (TCRβ) chains were analyzed by high-throughput sequencing in three pairs of healthy identical twins and chronic hepatitis B patients. The data showed a high level of similarity in the TCR repertoire of each pair in terms of average TCR Vβ segment expression and frequency of the complementary determining region 3 (CDR3) pattern and skewed or oligoclonal clonotypes. Notably, the level of similarity in TCR Vβ expression between the twins appeared to be independent of the consistency or inconsistency of chronic HBV infection, although the detailed CDR3 pattern and frequency were related to disease prognosis. There were more immunodominant clonotypes in patients with HBV antigen seroconversion, which showed an increased abundance. These immunodominant clonotypes may be used as favorable prognostic biomarkers and potential targets for immunotherapy. Thus, delineating the CD8+ T cell repertoire of identical twins with concordant chronic viral infections provides a promising means to screen protective TCR genes for immunotherapy.
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Affiliation(s)
- Qiong Jiang
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China
| | - Yao Liu
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China
| | - Baoyan Xu
- Institute of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing 400038, PR China
| | - Wenhong Zheng
- Department of Health, Third Military Medical University, Chongqing 400038, PR China
| | - Xiaomei Xiang
- Institute of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing 400038, PR China
| | - Xiaoqin Tang
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China
| | - Hui Dong
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China
| | - Yongwen Chen
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China
| | - Chenhui Wang
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China
| | - Guohong Deng
- Institute of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing 400038, PR China
| | - Qing Mao
- Institute of Infectious Diseases, Southwest Hospital, Third Military Medical University, Chongqing 400038, PR China
| | - Xiaoyun Shang
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China.
| | - Yuzhang Wu
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China.
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84
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Ma KY, He C, Wendel BS, Williams CM, Xiao J, Yang H, Jiang N. Immune Repertoire Sequencing Using Molecular Identifiers Enables Accurate Clonality Discovery and Clone Size Quantification. Front Immunol 2018; 9:33. [PMID: 29467754 PMCID: PMC5808239 DOI: 10.3389/fimmu.2018.00033] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 01/04/2018] [Indexed: 11/13/2022] Open
Abstract
Unique molecular identifiers (MIDs) have been demonstrated to effectively improve immune repertoire sequencing (IR-seq) accuracy, especially to identify somatic hypermutations in antibody repertoire sequencing. However, evaluating the sensitivity to detect rare T cells and the degree of clonal expansion in IR-seq has been difficult due to the lack of knowledge of T cell receptor (TCR) RNA molecule copy number and a generalized approach to estimate T cell clone size from TCR RNA molecule quantification. This limited the application of TCR repertoire sequencing (TCR-seq) in clinical settings, such as detecting minimal residual disease in lymphoid malignancies after treatment, evaluating effectiveness of vaccination and assessing degree of infection. Here, we describe using an MID Clustering-based IR-Seq (MIDCIRS) method to quantitatively study TCR RNA molecule copy number and clonality in T cells. First, we demonstrated the necessity of performing MID sub-clustering to eliminate erroneous sequences. Further, we showed that MIDCIRS enables a sensitive detection of a single cell in as many as one million naïve T cells and an accurate estimation of the degree of T cell clonal expression. The demonstrated accuracy, sensitivity, and wide dynamic range of MIDCIRS TCR-seq provide foundations for future applications in both basic research and clinical settings.
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Affiliation(s)
- Ke-Yue Ma
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States
| | - Chenfeng He
- Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Ben S Wendel
- McKetta Department of Chemical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Chad M Williams
- Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Jun Xiao
- ImmuDX, LLC, Austin, TX, United States
| | - Hui Yang
- School of Life Sciences, Northwestern Polytechnical University, Xi'an, Shaanxi, China.,Research Center of Special Environmental Biomechanics & Medical Engineering, Xi'an, Shaanxi, China
| | - Ning Jiang
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, United States.,Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, United States
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85
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Carey AJ, Hope JL, Mueller YM, Fike AJ, Kumova OK, van Zessen DBH, Steegers EAP, van der Burg M, Katsikis PD. Public Clonotypes and Convergent Recombination Characterize the Naïve CD8 + T-Cell Receptor Repertoire of Extremely Preterm Neonates. Front Immunol 2017; 8:1859. [PMID: 29312340 PMCID: PMC5742125 DOI: 10.3389/fimmu.2017.01859] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 12/07/2017] [Indexed: 01/03/2023] Open
Abstract
Respiratory support improvements have aided survival of premature neonates, but infection susceptibility remains a predominant problem. We previously reported that neonatal mice have a rapidly evolving T-cell receptor (TCR) repertoire that impairs CD8+ T cell immunity. To understand the impact of prematurity on the human CD8+ TCR repertoire, we performed next-generation sequencing of the complementarity-determining region 3 (CDR3) from the rearranged TCR variable beta (Vβ) in sorted, naïve CD8+ T cells from extremely preterm neonates (23–27 weeks gestation), term neonates (37–41 weeks gestation), children (16–56 months), and adults (25–50 years old). Strikingly, preterm neonates had an increased frequency of public clonotypes shared between unrelated individuals. Public clonotypes identified in preterm infants were encoded by germline gene sequences, and some of these clonotypes persisted into adulthood. The preterm neonatal naïve CD8+ TCR repertoire exhibited convergent recombination, characterized by different nucleotide sequences encoding the same amino acid CDR3 sequence. As determined by Pielou’s evenness and iChao1 metrics, extremely preterm neonates have less clonality, and a much lower bound for the number of unique TCR within an individual preterm neonate, which indicates a less rich and diverse repertoire, as compared to term neonates, children, and adults. This suggests that T cell selection in the preterm neonate may be less stringent or different. Our analysis is the first to compare the TCR repertoire of naïve CD8+ T cells between viable preterm neonates and term neonates. We find preterm neonates have a repertoire immaturity which potentially contributes to their increased infection susceptibility. A developmentally regulated, evenly distributed repertoire in preterm neonates may lead to the inclusion of public TCR CDR3β sequences that overlap between unrelated individuals in the preterm repertoire.
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Affiliation(s)
- Alison J Carey
- Department of Pediatrics, Drexel University College of Medicine, Philadelphia, PA, United States.,Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Jennifer L Hope
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States.,Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Yvonne M Mueller
- Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Adam J Fike
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - Ogan K Kumova
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, United States
| | - David B H van Zessen
- Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands.,Department of Bioinformatics, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Eric A P Steegers
- Department of Obstetrics and Gynecology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Mirjam van der Burg
- Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Peter D Katsikis
- Department of Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
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86
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Jenmalm MC. The mother-offspring dyad: microbial transmission, immune interactions and allergy development. J Intern Med 2017; 282:484-495. [PMID: 28727206 DOI: 10.1111/joim.12652] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The increasing prevalence of allergy in affluent countries may be caused by reduced intensity and diversity of microbial stimulation, resulting in abnormal postnatal immune maturation. Most studies investigating the underlying immunomodulatory mechanisms have focused on postnatal microbial exposure, for example demonstrating that the gut microbiota differs in composition and diversity during the first months of life in children who later do or do not develop allergic disease. However, it is also becoming increasingly evident that the maternal microbial environment during pregnancy is important in childhood immune programming, and the first microbial encounters may occur already in utero. During pregnancy, there is a close immunological interaction between the mother and her offspring, which provides important opportunities for the maternal microbial environment to influence the immune development of the child. In support of this theory, combined pre- and postnatal supplementations seem to be crucial for the preventive effect of probiotics on infant eczema. Here, the influence of microbial and immune interactions within the mother-offspring dyad on childhood allergy development will be discussed. In addition, how perinatal transmission of microbes and immunomodulatory factors from mother to offspring may shape appropriate immune maturation during infancy and beyond, potentially via epigenetic mechanisms, will be examined. Deeper understanding of these interactions between the maternal and offspring microbiome and immunity is needed to identify efficacious preventive measures to combat the allergy epidemic.
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Affiliation(s)
- M C Jenmalm
- Department of Clinical and Experimental Medicine, Unit of Autoimmunity and Immune Regulation, Linköping University, Linköping, Sweden.,International Inflammation (in-FLAME) Network of the World Universities Network, Sydney, NSW, Australia
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87
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Mokhtari S, Colletti EJ, Atala A, Zanjani ED, Porada CD, Almeida-Porada G. Boosting Hematopoietic Engraftment after in Utero Transplantation through Vascular Niche Manipulation. Stem Cell Reports 2017; 6:957-969. [PMID: 27304918 PMCID: PMC4912311 DOI: 10.1016/j.stemcr.2016.05.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 05/17/2016] [Accepted: 05/18/2016] [Indexed: 02/07/2023] Open
Abstract
In utero hematopoietic stem/progenitor cell transplantation (IUHSCT) has only been fully successful in the treatment of congenital immunodeficiency diseases. Using sheep as a large animal model of IUHSCT, we demonstrate that administration of CD146+CXCL12+VEGFR2+ or CD146+CXCL12+VEGFR2− cells prior to, or in combination with, hematopoietic stem/progenitor cells (HSC), results in robust CXCL12 production within the fetal marrow environment, and significantly increases the levels of hematopoietic engraftment. While in the fetal recipient, donor-derived HSC were found to reside within the trabecular bone, the increased expression of VEGFR2 in the microvasculature of CD146+CXCL12+VEGFR2+ transplanted animals enhanced levels of donor-derived hematopoietic cells in circulation. These studies provide important insights into IUHSCT biology, and demonstrate the feasibility of enhancing HSC engraftment to levels that would likely be therapeutic in many candidate diseases for IUHSCT. After IUHSCT, HSC engraft in the trabecular bone of the metaphysis CD146++(+/−) cells engraft in diaphysis and make hematopoiesis-supporting cytokines Donor cell-derived CXCL12 and VEGFR2 significantly increase HSC engraftment IUHSCT of CD146+CXCL12+VEGFR2+ cells prior to HSC could be curative in several diseases
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Affiliation(s)
- Saloomeh Mokhtari
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, 391 Technology Way, Winston-Salem, NC 27157-1083, USA
| | - Evan J Colletti
- Experimental Station, University of Nevada Reno, Reno, NV 89503, USA
| | - Anthony Atala
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, 391 Technology Way, Winston-Salem, NC 27157-1083, USA
| | - Esmail D Zanjani
- Experimental Station, University of Nevada Reno, Reno, NV 89503, USA
| | - Christopher D Porada
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, 391 Technology Way, Winston-Salem, NC 27157-1083, USA
| | - Graça Almeida-Porada
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, 391 Technology Way, Winston-Salem, NC 27157-1083, USA.
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88
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Rechavi E, Lev A, Simon AJ, Stauber T, Daas S, Saraf-Levy T, Broides A, Nahum A, Marcus N, Hanna S, Stepensky P, Toker O, Dalal I, Etzioni A, Almashanu S, Somech R. First Year of Israeli Newborn Screening for Severe Combined Immunodeficiency-Clinical Achievements and Insights. Front Immunol 2017; 8:1448. [PMID: 29167666 PMCID: PMC5682633 DOI: 10.3389/fimmu.2017.01448] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 10/17/2017] [Indexed: 11/29/2022] Open
Abstract
Severe combined immunodeficiency (SCID), the most severe form of T cell immunodeficiency, is detectable through quantification of T cell receptor excision circles (TRECs) in dried blood spots obtained at birth. Herein, we describe the results of the first year of the Israeli SCID newborn screening (NBS) program. This important, life-saving screening test is available at no cost for every newborn in Israel. Eight SCID patients were diagnosed through the NBS program in its first year, revealing an incidence of 1:22,500 births in the Israeli population. Consanguine marriages and Muslim ethnic origin were found to be a risk factor in affected newborns, and a founder effect was detected for both IL7Rα and DCLRE1C deficiency SCID. Lymphocyte subset analysis and TREC quantification in the peripheral blood appear to be sufficient for confirmation of typical and leaky SCID and ruling out false positive (FP) results. Detection of secondary targets (infants with non-SCID lymphopenia) did not significantly affect the management or outcomes of these infants in our cohort. In the general, non-immunodeficient population, TREC rises along with gestational age and birth weight, and is significantly higher in females and the firstborn of twin pairs. Low TREC correlates with both gestational age and birth weight in extremely premature newborns. Additionally, the rate of TREC increase per week consistently accelerates with gestational age. Together, these findings mandate a lower cutoff or a more lenient screening algorithm for extremely premature infants, in order to reduce the high rate of FPs within this group. A significant surge in TREC values was observed between 28 and 30 weeks of gestation, where median TREC copy numbers rise by 50% over 2 weeks. These findings suggest a maturational step in T cell development around week 29 gestation, and imply moderate to late preterms should be screened with the same cutoff as term infants. The SCID NBS program is still in its infancy, but is already bearing fruit in the early detection and improved outcomes of children with SCID in Israel and other countries.
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Affiliation(s)
- Erez Rechavi
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Atar Lev
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amos J Simon
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Tali Stauber
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Suha Daas
- The National Center for Newborn Screening, Israel Ministry of Health, Tel-HaShomer, Israel
| | - Talia Saraf-Levy
- The National Center for Newborn Screening, Israel Ministry of Health, Tel-HaShomer, Israel
| | - Arnon Broides
- Pediatric Immunology Clinic, Soroka University Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,The Jeffrey Modell Foundation Israeli Network for Primary Immunodeficiency, New York, NY, United States
| | - Amit Nahum
- Pediatric Immunology Clinic, Soroka University Medical Center, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.,The Jeffrey Modell Foundation Israeli Network for Primary Immunodeficiency, New York, NY, United States
| | - Nufar Marcus
- The Jeffrey Modell Foundation Israeli Network for Primary Immunodeficiency, New York, NY, United States.,Allergy and Immunology Unit, Schneider Children's Medical Center of Israel, Felsenstein Medical Research Center, Petach Tikva, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Suhair Hanna
- The Jeffrey Modell Foundation Israeli Network for Primary Immunodeficiency, New York, NY, United States.,Ruth Children Hospital, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Polina Stepensky
- The Jeffrey Modell Foundation Israeli Network for Primary Immunodeficiency, New York, NY, United States.,Bone Marrow Transplantation Department, Hadassah Hebrew University Medical Center, Hadassah-Hebrew University Medical School, Jerusalem, Israel
| | - Ori Toker
- The Jeffrey Modell Foundation Israeli Network for Primary Immunodeficiency, New York, NY, United States.,Allergy and Clinical Immunology Clinic, Department of Pediatrics, Shaare Zedek Medical Center, Hadassah-Hebrew University Medical School, Jerusalem, Israel
| | - Ilan Dalal
- The Jeffrey Modell Foundation Israeli Network for Primary Immunodeficiency, New York, NY, United States.,Pediatric Allergy Unit, Wolfson Medical Center, Holon, Israel.,Pediatric Department, Wolfson Medical Center, Holon, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amos Etzioni
- The Jeffrey Modell Foundation Israeli Network for Primary Immunodeficiency, New York, NY, United States.,Ruth Children Hospital, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Shlomo Almashanu
- The National Center for Newborn Screening, Israel Ministry of Health, Tel-HaShomer, Israel
| | - Raz Somech
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Jeffrey Modell Foundation Israeli Network for Primary Immunodeficiency, New York, NY, United States.,The National Lab for Diagnosing SCID - The Israeli Newborn Screening Program, Israel Ministry of Health, Tel-Hashomer, Israel
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89
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Breden F, Luning Prak ET, Peters B, Rubelt F, Schramm CA, Busse CE, Vander Heiden JA, Christley S, Bukhari SAC, Thorogood A, Matsen Iv FA, Wine Y, Laserson U, Klatzmann D, Douek DC, Lefranc MP, Collins AM, Bubela T, Kleinstein SH, Watson CT, Cowell LG, Scott JK, Kepler TB. Reproducibility and Reuse of Adaptive Immune Receptor Repertoire Data. Front Immunol 2017; 8:1418. [PMID: 29163494 PMCID: PMC5671925 DOI: 10.3389/fimmu.2017.01418] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/12/2017] [Indexed: 12/22/2022] Open
Abstract
High-throughput sequencing (HTS) of immunoglobulin (B-cell receptor, antibody) and T-cell receptor repertoires has increased dramatically since the technique was introduced in 2009 (1–3). This experimental approach explores the maturation of the adaptive immune system and its response to antigens, pathogens, and disease conditions in exquisite detail. It holds significant promise for diagnostic and therapy-guiding applications. New technology often spreads rapidly, sometimes more rapidly than the understanding of how to make the products of that technology reliable, reproducible, or usable by others. As complex technologies have developed, scientific communities have come together to adopt common standards, protocols, and policies for generating and sharing data sets, such as the MIAME protocols developed for microarray experiments. The Adaptive Immune Receptor Repertoire (AIRR) Community formed in 2015 to address similar issues for HTS data of immune repertoires. The purpose of this perspective is to provide an overview of the AIRR Community’s founding principles and present the progress that the AIRR Community has made in developing standards of practice and data sharing protocols. Finally, and most important, we invite all interested parties to join this effort to facilitate sharing and use of these powerful data sets (join@airr-community.org).
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Affiliation(s)
- Felix Breden
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Eline T Luning Prak
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Florian Rubelt
- Department of Microbiology and Immunology, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, United States
| | - Chaim A Schramm
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Christian E Busse
- Division of B Cell Immunology, Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | - Jason A Vander Heiden
- Department of Neurology, Yale University School of Medicine, New Haven, CT, United States
| | - Scott Christley
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | | | - Adrian Thorogood
- entre of Genomics and Policy, McGill University, Montreal, QC, Canada
| | - Frederick A Matsen Iv
- Public Health Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Yariv Wine
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Uri Laserson
- Department of Genetics and Genome Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - David Klatzmann
- Immunology-Immunopathology-Immunotherapy (i3 & i2B), Sorbonne Université, Paris, France
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Marie-Paule Lefranc
- IMGT, LIGM, Institut de Génétique Humaine IGH, CNRS, University of Montpellier, Montpellier, France
| | - Andrew M Collins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW, Australia
| | - Tania Bubela
- Faculty of Health Sciences, Simon Fraser University, Burnaby, BC, Canada
| | - Steven H Kleinstein
- Department of Pathology, Yale University School of Medicine, New Haven, CT, United States
| | - Corey T Watson
- Department of Biochemistry and Molecular Genetics, University of Louisville School of Medicine, Louisville, KY, United States
| | - Lindsay G Cowell
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Jamie K Scott
- Faculty of Health Sciences, Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, Boston, MA, United States.,Department of Mathematics and Statistics, Boston University, Boston, MA, United States
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90
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Tassi Yunga S, Kayatani AK, Fogako J, Leke RJI, Leke RGF, Taylor DW. Timing of the human prenatal antibody response to Plasmodium falciparum antigens. PLoS One 2017; 12:e0184571. [PMID: 28950009 PMCID: PMC5614534 DOI: 10.1371/journal.pone.0184571] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 08/25/2017] [Indexed: 12/27/2022] Open
Abstract
Plasmodium falciparum (Pf)-specific T- and B-cell responses may be present at birth; however, when during fetal development antibodies are produced is unknown. Accordingly, cord blood samples from 232 preterm (20–37 weeks of gestation) and 450 term (≥37 weeks) babies were screened for IgM to Pf blood-stage antigens MSP1, MSP2, AMA1, EBA175 and RESA. Overall, 25% [95% CI = 22–28%] of the 682 newborns were positive for IgM to ≥1 Pf antigens with the earliest response occurring at 22 weeks. Interestingly, the odds of being positive for cord blood Pf IgM decreased with gestational age (adjusted OR [95% CI] at 20–31 weeks = 2.55 [1.14–5.85] and at 32–36 weeks = 1.97 [0.92–4.29], with ≥37 weeks as reference); however, preterm and term newborns had similar levels of Pf IgM and recognized a comparable breadth of antigens. Having cord blood Pf IgM was associated with placental malaria (adjusted OR [95% CI] = 2.37 [1.25–4.54]). To determine if in utero exposure occurred via transplacental transfer of Pf-IgG immune complexes (IC), IC containing MSP1 and MSP2 were measured in plasma of 242 mother-newborn pairs. Among newborns of IC-positive mothers (77/242), the proportion of cord samples with Pf IC increased with gestational age but was not associated with Pf IgM, suggesting that fetal B cells early in gestation had not been primed by IC. Finally, when cord mononuclear cells from 64 term newborns were cultured in vitro, only 11% (7/64) of supernatants had Pf IgM; whereas, 95% (61/64) contained secreted Pf IgG. These data suggest fetal B cells are capable of making Pf-specific IgM from early in the second trimester and undergo isotype switching to IgG towards term.
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Affiliation(s)
- Samuel Tassi Yunga
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Alexander K. Kayatani
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Josephine Fogako
- The Biotechnology Center, University of Yaoundé 1, Yaoundé, Cameroon
| | - Robert J. I. Leke
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | - Rose G. F. Leke
- The Biotechnology Center, University of Yaoundé 1, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé 1, Yaoundé, Cameroon
| | - Diane W. Taylor
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
- * E-mail:
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91
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Wendel BS, He C, Qu M, Wu D, Hernandez SM, Ma KY, Liu EW, Xiao J, Crompton PD, Pierce SK, Ren P, Chen K, Jiang N. Accurate immune repertoire sequencing reveals malaria infection driven antibody lineage diversification in young children. Nat Commun 2017; 8:531. [PMID: 28912592 PMCID: PMC5599618 DOI: 10.1038/s41467-017-00645-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/15/2017] [Indexed: 12/03/2022] Open
Abstract
Accurately measuring antibody repertoire sequence composition in a small amount of blood is challenging yet important for understanding repertoire responses to infection and vaccination. We develop molecular identifier clustering-based immune repertoire sequencing (MIDCIRS) and use it to study age-related antibody repertoire development and diversification before and during acute malaria in infants (< 12 months old) and toddlers (12-47 months old) with 4-8 ml of blood. Here, we show this accurate and high-coverage repertoire-sequencing method can use as few as 1000 naive B cells. Unexpectedly, we discover high levels of somatic hypermutation in infants as young as 3 months old. Antibody clonal lineage analysis reveals that somatic hypermutation levels are increased in both infants and toddlers upon infection, and memory B cells isolated from individuals who previously experienced malaria continue to induce somatic hypermutations upon malaria rechallenge. These results highlight the potential of antibody repertoire diversification in infants and toddlers.Somatic hypermutation of antibodies can occur in infants but are difficult to track. Here the authors present a new method called MIDCIRS for deep quantitative repertoire sequencing with few cells, and show infants as young as 3 months can expand antibody lineage complexity in response to malaria infection.
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Affiliation(s)
- Ben S Wendel
- McKetta Department of Chemical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Chenfeng He
- Department of Biomedical engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Mingjuan Qu
- Department of Biomedical engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, 78712, USA
- School of Life Sciences, Ludong University, Yantai, Shandong, 264025, China
| | - Di Wu
- Department of Biomedical engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Stefany M Hernandez
- McKetta Department of Chemical Engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Ke-Yue Ma
- Institute for Cellular and Molecular Biology, College of Natural Sciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Eugene W Liu
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
- Parasitic Diseases Branch, Division of Parasitic Diseases and Malaria, Center for Global Health, Atlanta, 30329, GA, USA
| | - Jun Xiao
- ImmuDX, LLC, Austin, TX, 78750, USA
| | - Peter D Crompton
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Susan K Pierce
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Pengyu Ren
- Department of Biomedical engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Keke Chen
- Department of Computer Science and Engineering, Wright State University, Dayton, OH, 45435, USA
| | - Ning Jiang
- Department of Biomedical engineering, Cockrell School of Engineering, University of Texas at Austin, Austin, TX, 78712, USA.
- Institute for Cellular and Molecular Biology, College of Natural Sciences, University of Texas at Austin, Austin, TX, 78712, USA.
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92
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Protecting the Newborn and Young Infant from Infectious Diseases: Lessons from Immune Ontogeny. Immunity 2017; 46:350-363. [PMID: 28329702 DOI: 10.1016/j.immuni.2017.03.009] [Citation(s) in RCA: 257] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 12/20/2016] [Accepted: 03/06/2017] [Indexed: 12/14/2022]
Abstract
Infections in the first year of life are common and often severe. The newborn host demonstrates both quantitative and qualitative differences to the adult in nearly all aspects of immunity, which at least partially explain the increased susceptibility to infection. Here we discuss how differences in susceptibility to infection result not out of a state of immaturity, but rather reflect adaptation to the particular demands placed on the immune system in early life. We review the mechanisms underlying host defense in the very young, and discuss how specific developmental demands increase the risk of particular infectious diseases. In this context, we discuss how this plasticity, i.e. the capacity to adapt to demands encountered in early life, also provides the potential to leverage protection of the young against infection and disease through a number of interventions.
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93
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In utero development of memory T cells. Semin Immunopathol 2017; 39:585-592. [DOI: 10.1007/s00281-017-0650-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 08/07/2017] [Indexed: 12/24/2022]
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94
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Rowe JH, Stadinski BD, Henderson LA, Ott de Bruin L, Delmonte O, Lee YN, de la Morena MT, Goyal RK, Hayward A, Huang CH, Kanariou M, King A, Kuijpers TW, Soh JY, Neven B, Walter JE, Huseby ES, Notarangelo LD. Abnormalities of T-cell receptor repertoire in CD4 + regulatory and conventional T cells in patients with RAG mutations: Implications for autoimmunity. J Allergy Clin Immunol 2017; 140:1739-1743.e7. [PMID: 28864286 DOI: 10.1016/j.jaci.2017.08.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 07/07/2017] [Accepted: 08/01/2017] [Indexed: 10/18/2022]
Affiliation(s)
- Jared H Rowe
- Division of Immunology, Boston Children's Hospital, Boston, Mass
| | - Brian D Stadinski
- Department of Pathology, University of Massachusetts Medical School, Worcester, Mass
| | | | | | - Ottavia Delmonte
- Division of Immunology, Boston Children's Hospital, Boston, Mass
| | - Yu Nee Lee
- Pediatric Department A and the Immunology Service, "Edmond and Lily Safra" Children's Hospital, Jeffrey Modell Foundation Center, Sheba Medical Center, Tel Hashomer, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - M Teresa de la Morena
- Division of Allergy and Immunology, University of Texas, Southwestern Medical Center, Dallas, Tex
| | - Rakesh K Goyal
- Division of Hematology/Oncology/BMT, Children's Mercy Hospital & Clinics, Kansas City, Mo
| | | | - Chiung-Hui Huang
- Department of Pediatrics, National University of Singapore, Singapore
| | - Maria Kanariou
- Department of Immunology-Histocompatibility, "Aghia Sophia" Children's Hospital, Athens, Greece
| | - Alejandra King
- Division of Pediatric Immunology, Hospital Luis Calvo Mackenna, Santiago, Chile
| | - Taco W Kuijpers
- Department of Pediatric Hematology, Immunology and Infectious Diseases, Emma Children's Hospital, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Jian Yi Soh
- Department of Pediatrics, National University of Singapore, Singapore
| | - Benedicte Neven
- Pediatric Hematology-Immunology Department, Hospital Necker-Enfants Malades, AP-HP, Paris Descartes University, Sorbonne-Paris-Cité, Institut Imagine, Paris, France
| | - Jolan E Walter
- Division of Pediatric Allergy/Immunology, University of South Florida at Johns Hopkins All Children's Hospital, St Petersburg, Fla
| | - Eric S Huseby
- Department of Pathology, University of Massachusetts Medical School, Worcester, Mass
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md.
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95
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Holodick NE, Rodríguez-Zhurbenko N, Hernández AM. Defining Natural Antibodies. Front Immunol 2017; 8:872. [PMID: 28798747 PMCID: PMC5526850 DOI: 10.3389/fimmu.2017.00872] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 07/10/2017] [Indexed: 01/05/2023] Open
Abstract
The traditional definition of natural antibodies (NAbs) states that these antibodies are present prior to the body encountering cognate antigen, providing a first line of defense against infection thereby, allowing time for a specific antibody response to be mounted. The literature has a seemingly common definition of NAbs; however, as our knowledge of antibodies and B cells is refined, re-evaluation of the common definition of Nabs may be required. Defining Nabs becomes important as the function of NAb production is used to define B cell subsets (1) and as these important molecules are shown to play numerous roles in the immune system (Figure 1). Herein, we aim to briefly summarize our current knowledge of NAbs in the context of initiating a discussion within the field of how such an important and multifaceted group of molecules should be defined.
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Affiliation(s)
- Nichol E Holodick
- Department of Biomedical Sciences, Center for Immunobiology, Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI, United States
| | - Nely Rodríguez-Zhurbenko
- Natural Antibodies Group, Tumor Immunology Division, Center of Molecular Immunology, Havana, Cuba
| | - Ana María Hernández
- Natural Antibodies Group, Tumor Immunology Division, Center of Molecular Immunology, Havana, Cuba
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96
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Pogorelyy MV, Elhanati Y, Marcou Q, Sycheva AL, Komech EA, Nazarov VI, Britanova OV, Chudakov DM, Mamedov IZ, Lebedev YB, Mora T, Walczak AM. Persisting fetal clonotypes influence the structure and overlap of adult human T cell receptor repertoires. PLoS Comput Biol 2017; 13:e1005572. [PMID: 28683116 PMCID: PMC5500008 DOI: 10.1371/journal.pcbi.1005572] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 05/14/2017] [Indexed: 11/30/2022] Open
Abstract
The diversity of T-cell receptors recognizing foreign pathogens is generated through a highly stochastic recombination process, making the independent production of the same sequence rare. Yet unrelated individuals do share receptors, which together constitute a "public" repertoire of abundant clonotypes. The TCR repertoire is initially formed prenatally, when the enzyme inserting random nucleotides is downregulated, producing a limited diversity subset. By statistically analyzing deep sequencing T-cell repertoire data from twins, unrelated individuals of various ages, and cord blood, we show that T-cell clones generated before birth persist and maintain high abundances in adult organisms for decades, slowly decaying with age. Our results suggest that large, low-diversity public clones are created during pre-natal life, and survive over long periods, providing the basis of the public repertoire.
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Affiliation(s)
- Mikhail V. Pogorelyy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Yuval Elhanati
- Laboratoire de physique théorique, CNRS, UPMC and École normale supérieure, Paris, France
| | - Quentin Marcou
- Laboratoire de physique théorique, CNRS, UPMC and École normale supérieure, Paris, France
| | | | - Ekaterina A. Komech
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Vadim I. Nazarov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Olga V. Britanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
- Pirogov Russian National Research Medical University, Moscow, Russian Federation
- Masaryk University, Central European Institute of Technology, Brno, Czech Republic
| | - Dmitriy M. Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
- Pirogov Russian National Research Medical University, Moscow, Russian Federation
- Masaryk University, Central European Institute of Technology, Brno, Czech Republic
| | - Ilgar Z. Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Yury B. Lebedev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Thierry Mora
- Laboratoire de physique statistique, CNRS, UPMC and École normale supérieure, Paris, France
| | - Aleksandra M. Walczak
- Laboratoire de physique théorique, CNRS, UPMC and École normale supérieure, Paris, France
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97
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Roy A, Bystry V, Bohn G, Goudevenou K, Reigl T, Papaioannou M, Krejci A, O'Byrne S, Chaidos A, Grioni A, Darzentas N, Roberts IAG, Karadimitris A. High resolution IgH repertoire analysis reveals fetal liver as the likely origin of life-long, innate B lymphopoiesis in humans. Clin Immunol 2017. [PMID: 28645875 PMCID: PMC5678457 DOI: 10.1016/j.clim.2017.06.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The ontogeny of the natural, public IgM repertoire remains incompletely explored. Here, high-resolution immunogenetic analysis of B cells from (unrelated) fetal, child, and adult samples, shows that although fetal liver (FL) and bone marrow (FBM) IgM repertoires are equally diversified, FL is the main source of IgM natural immunity during the 2nd trimester. Strikingly, 0.25% of all prenatal clonotypes, comprising 18.7% of the expressed repertoire, are shared with the postnatal samples, consistent with persisting fetal IgM + B cells being a source of natural IgM repertoire in adult life. Further, the origins of specific stereotypic IgM + B cell receptors associated with chronic lymphocytic leukemia, can be traced back to fetal B cell lymphopoiesis, suggesting that persisting fetal B cells can be subject to malignant transformation late in life. Overall, these novel data provide unique insights into the ontogeny of physiological and malignant B lymphopoiesis that spans the human lifetime. Second trimester human fetal liver and fetal bone marrow B-cells have IgM repertoires that are equally diversified Human fetal liver B-cells are the main source of innate, natural IgM responses CLL-associated, stereotypic B cell receptors are detected in fetal IgM repertoire
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Affiliation(s)
- Anindita Roy
- Department of Paediatrics, University of Oxford, Brno, Czech Republic
| | - Vojtech Bystry
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Georg Bohn
- Centre for Haematology, Department of Medicine, Imperial College London, Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, UK
| | - Katerina Goudevenou
- Centre for Haematology, Department of Medicine, Imperial College London, Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, UK
| | - Tomas Reigl
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Maria Papaioannou
- Centre for Haematology, Department of Medicine, Imperial College London, Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, UK
| | - Adam Krejci
- Centre for Haematology, Department of Medicine, Imperial College London, Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, UK; RECAMO, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Sorcha O'Byrne
- Department of Paediatrics, University of Oxford, Brno, Czech Republic
| | - Aristeidis Chaidos
- Centre for Haematology, Department of Medicine, Imperial College London, Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, UK
| | - Andrea Grioni
- Department of Paediatrics, University of Oxford, Brno, Czech Republic; Centro Ricerca Tettamanti, Clinica Pediatrica, Università di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, Monza, Italy
| | - Nikos Darzentas
- CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Irene A G Roberts
- Department of Paediatrics, University of Oxford, Brno, Czech Republic; MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford and BRC Blood Theme, NIHR Oxford Biomedical Centre, Oxford, UK.
| | - Anastasios Karadimitris
- Centre for Haematology, Department of Medicine, Imperial College London, Imperial College Healthcare NHS Trust, Hammersmith Hospital, London, UK.
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98
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Rechavi E, Somech R. Survival of the fetus: fetal B and T cell receptor repertoire development. Semin Immunopathol 2017; 39:577-583. [PMID: 28466095 DOI: 10.1007/s00281-017-0626-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 04/04/2017] [Indexed: 12/29/2022]
Abstract
A mature and diverse T and B cell receptor repertoire is a prerequisite for immunocompetence. In light of its increased susceptibility to infection, the human fetus has long been considered deficient in this regard. However, data accumulated since the 1990s and in earnest in the past couple of years paints a more complicated picture. As we describe in this review, mechanisms responsible for generating a diverse receptor repertoire, such as somatic recombination, class switch recombination, and somatic hypermutation, are all operational to surprising extents in the growing fetus. The composition of the fetal repertoire differs from that of adults, with preferential usage of certain variable (V), diversity (D), and joining (J) gene segments and a shorter complementarity determining (CDR3) region, primarily due to decreased terminal deoxynucleotidyl transferase (TdT) expression. Both T and B cell receptor repertoires are extremely diverse by the end of the second trimester, and in the case of T cells, are capable of responding to an invading pathogen with in utero clonal expansion. Thus, it would appear as though the T and B cell receptor repertoires are not a hindrance towards immunocompetence of the newborn. Our improved understanding of fetal receptor repertoire development is already bearing fruit in the early diagnosis of primary immunodeficiencies (PID) and may help clarify the pathogenesis of congenital infections, recurrent abortions, and autoimmune disorders in the near future.
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Affiliation(s)
- Erez Rechavi
- Pediatric Department A and Immunology Service, Jeffrey Modell Foundation Center, "Edmond and Lily Safra" Children's Hospital, Sheba Medical Center, Tel Hashomer, Sackler School of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Raz Somech
- Pediatric Department A and Immunology Service, Jeffrey Modell Foundation Center, "Edmond and Lily Safra" Children's Hospital, Sheba Medical Center, Tel Hashomer, Sackler School of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel.
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99
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Allenspach EJ, Finn LS, Rendi MH, Eken A, Singh AK, Oukka M, Taylor SD, Altman MC, Fligner CL, Ochs HD, Rawlings DJ, Torgerson TR. Absence of functional fetal regulatory T cells in humans causes in utero organ-specific autoimmunity. J Allergy Clin Immunol 2017; 140:616-619.e7. [PMID: 28322850 DOI: 10.1016/j.jaci.2017.02.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 02/11/2017] [Accepted: 02/14/2017] [Indexed: 02/01/2023]
Affiliation(s)
- Eric J Allenspach
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Wash; Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Wash
| | - Laura S Finn
- Department of Laboratories, Seattle Children's Hospital, Seattle, Wash; Department of Pathology, University of Washington School of Medicine, Seattle, Wash
| | - Mara H Rendi
- Department of Pathology, University of Washington School of Medicine, Seattle, Wash
| | - Ahmet Eken
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Wash
| | - Akhilesh K Singh
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Wash
| | - Mohamed Oukka
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Wash
| | - Sean D Taylor
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Wash
| | - Matthew C Altman
- Benaroya Research Institute, Seattle, Wash; Department of Medicine, University of Washington School of Medicine, Seattle, Wash
| | - Corinne L Fligner
- Department of Pathology, University of Washington School of Medicine, Seattle, Wash; Department of Laboratory Medicine, University of Washington School of Medicine, Seattle, Wash
| | - Hans D Ochs
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Wash; Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Wash
| | - David J Rawlings
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Wash; Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Wash
| | - Troy R Torgerson
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Wash; Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Wash.
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100
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Borghesi A, Stronati M, Fellay J. Neonatal Group B Streptococcal Disease in Otherwise Healthy Infants: Failure of Specific Neonatal Immune Responses. Front Immunol 2017; 8:215. [PMID: 28326082 PMCID: PMC5339282 DOI: 10.3389/fimmu.2017.00215] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/15/2017] [Indexed: 12/26/2022] Open
Abstract
Only a small proportion of newborn infants exposed to a pathogenic microorganism develop overt infection. Susceptibility to infection in preterm infants and infants with known comorbidities has a likely multifactorial origin and can be often attributed to the concurrence of iatrogenic factors, environmental determinants, underlying pathogenic processes, and probably genetic predisposition. Conversely, infection occurring in otherwise healthy full-term newborn infants is unexplained in most cases. Microbial virulence factors and the unique characteristics of the neonatal immune system only partially account for the interindividual variability in the neonatal immune responses to pathogens. We here suggest that neonatal infection occurring in otherwise healthy infants is caused by a failure of the specific protective immunity to the microorganism. To explain infection in term and preterm infants, we propose an extension of the previously proposed model of the genetic architecture of infectious diseases in humans. We then focus on group B streptococcus (GBS) disease, the best characterized neonatal infection, and outline the potential molecular mechanisms underlying the selective failure of the immune responses against GBS. In light of the recent discoveries of pathogen-specific primary immunodeficiencies and of the role of anticytokine autoantibodies in increasing susceptibility to specific infections, we hypothesize that GBS disease occurring in otherwise healthy infants could reflect an immunodeficiency caused either by rare genetic defects in the infant or by transmitted maternal neutralizing antibodies. These hypotheses are consistent with available epidemiological data, with clinical and epidemiological observations, and with the state of the art of neonatal physiology and disease. Studies should now be designed to comprehensively search for genetic or immunological factors involved in susceptibility to severe neonatal infections.
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Affiliation(s)
- Alessandro Borghesi
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Neonatal Intensive Care Unit, San Matteo Hospital, Pavia, Italy
| | - Mauro Stronati
- Neonatal Intensive Care Unit, San Matteo Hospital, Pavia, Italy
| | - Jacques Fellay
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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