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Montenegro C, Perdomo-Celis F, Franco MA. Update on Early-Life T Cells: Impact on Oral Rotavirus Vaccines. Viruses 2024; 16:818. [PMID: 38932111 PMCID: PMC11209100 DOI: 10.3390/v16060818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/21/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024] Open
Abstract
Rotavirus infection continues to be a significant public health problem in developing countries, despite the availability of several vaccines. The efficacy of oral rotavirus vaccines in young children may be affected by significant immunological differences between individuals in early life and adults. Therefore, understanding the dynamics of early-life systemic and mucosal immune responses and the factors that affect them is essential to improve the current rotavirus vaccines and develop the next generation of mucosal vaccines. This review focuses on the advances in T-cell development during early life in mice and humans, discussing how immune homeostasis and response to pathogens is established in this period compared to adults. Finally, the review explores how this knowledge of early-life T-cell immunity could be utilized to enhance current and novel rotavirus vaccines.
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Affiliation(s)
| | | | - Manuel A. Franco
- Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá 110221, Colombia; (C.M.); (F.P.-C.)
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2
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Alhamdan F, Koutsogiannaki S, Yuki K. The landscape of immune dysregulation in pediatric sepsis at a single-cell resolution. Clin Immunol 2024; 262:110175. [PMID: 38460893 PMCID: PMC11009045 DOI: 10.1016/j.clim.2024.110175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/09/2024] [Accepted: 02/15/2024] [Indexed: 03/11/2024]
Abstract
Recognizing immune dysregulation as a hallmark of sepsis pathophysiology, leukocytes have attracted major attention of investigation. While adult and pediatric sepsis are clinically distinct, their immunological delineation remains limited. Single cell technologies facilitated the characterization of immune signatures. We tackled to delineate immunological profiles of pediatric sepsis at a single-cell level by analyzing blood samples from six septic children, at both acute and recovery phases, and four healthy children. 16 single-cell transcriptomic datasets were analyzed and compared to adult sepsis dataset. We showed a unique shift in neutrophil subpopulations and functions between acute and recovery phases, along with the regulatory role of resistin. Neutrophil signatures were comparable between adult and pediatric sepsis. Innate-like CD4 T cells were predominantly and uniquely observed in acute phase of pediatric sepsis. Our study serves as a rich source of information about the phenotypic diversity and trajectory of circulating immune cells during pediatric sepsis.
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Affiliation(s)
- Fahd Alhamdan
- Department of Anesthesiology, Critical Care, and Pain Medicine, Cardiac Anesthesia Division, Boston Children's Hospital, USA; Department of Immunology and Anaesthesia, Harvard Medical School, USA; Broad Institute of MIT and Harvard, USA
| | - Sophia Koutsogiannaki
- Department of Anesthesiology, Critical Care, and Pain Medicine, Cardiac Anesthesia Division, Boston Children's Hospital, USA; Department of Immunology and Anaesthesia, Harvard Medical School, USA; Broad Institute of MIT and Harvard, USA.
| | - Koichi Yuki
- Department of Anesthesiology, Critical Care, and Pain Medicine, Cardiac Anesthesia Division, Boston Children's Hospital, USA; Department of Immunology and Anaesthesia, Harvard Medical School, USA; Broad Institute of MIT and Harvard, USA.
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3
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Alhamdan F, Koutsogiannaki S, Yuki K. The landscape of immune dysregulation in pediatric sepsis at a single-cell resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.17.576030. [PMID: 38293080 PMCID: PMC10827142 DOI: 10.1101/2024.01.17.576030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Recognizing immune dysregulation as a hallmark of sepsis pathophysiology, leukocytes have attracted major attention of investigation. While adult and pediatric sepsis are clinically distinct, their immunological delineation remains limited. Breakthrough of single cell technologies facilitated the characterization of immune signatures. We tackled to delineate immunological profiles of pediatric sepsis at a single-cell level by analyzing blood samples from six septic children, at both acute and recovery phases, and four healthy children. 16 single-cell transcriptomic datasets (96,156 cells) were analyzed and compared to adult sepsis dataset. We showed a unique shift in neutrophil subpopulations and functions between acute and recovery phases, along with examining the regulatory role of resistin. Neutrophil signatures were comparable between adult and pediatric sepsis. Innate-like CD4 T cells were predominantly and uniquely observed in acute phase of pediatric sepsis. Our study provides a thorough and comprehensive understanding of immune dysregulation in pediatric sepsis.
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4
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Slysz J, Sinha A, DeBerge M, Singh S, Avgousti H, Lee I, Glinton K, Nagasaka R, Dalal P, Alexandria S, Wai CM, Tellez R, Vescovo M, Sunderraj A, Wang X, Schipma M, Sisk R, Gulati R, Vallejo J, Saigusa R, Lloyd-Jones DM, Lomasney J, Weinberg S, Ho K, Ley K, Giannarelli C, Thorp EB, Feinstein MJ. Single-cell profiling reveals inflammatory polarization of human carotid versus femoral plaque leukocytes. JCI Insight 2023; 8:e171359. [PMID: 37471165 PMCID: PMC10544225 DOI: 10.1172/jci.insight.171359] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 07/17/2023] [Indexed: 07/22/2023] Open
Abstract
Femoral atherosclerotic plaques are less inflammatory than carotid plaques histologically, but limited cell-level data exist regarding comparative immune landscapes and polarization at these sites. We investigated intraplaque leukocyte phenotypes and transcriptional polarization in 49 patients undergoing femoral (n = 23) or carotid (n = 26) endarterectomy using single-cell RNA-Seq (scRNA-Seq; n = 13), flow cytometry (n = 24), and IHC (n = 12). Comparative scRNA-Seq of CD45+-selected leukocytes from femoral (n = 9; 35,265 cells) and carotid (n = 4; 30,655 cells) plaque revealed distinct transcriptional profiles. Inflammatory foam cell-like macrophages and monocytes comprised higher proportions of myeloid cells in carotid plaques, whereas noninflammatory foam cell-like macrophages and LYVE1-overexpressing macrophages comprised higher proportions of myeloid cells in femoral plaque (P < 0.001 for all). A significant comparative excess of CCR2+ macrophages in carotid versus plaque was observed by flow cytometry in a separate validation cohort. B cells were more prevalent and exhibited a comparatively antiinflammatory profile in femoral plaque, whereas cytotoxic CD8+ T cells were more prevalent in carotid plaque. In conclusion, human femoral plaques exhibit distinct macrophage phenotypic and transcriptional profiles as well as diminished CD8+ T cell populations compared with human carotid plaques.
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Affiliation(s)
| | - Arjun Sinha
- Division of Cardiology, Department of Medicine
| | | | | | | | - Inhyeok Lee
- Division of Cardiology, Department of Medicine
| | - Kristofor Glinton
- Division of Cardiology, Department of Medicine
- Department of Pathology, and
| | | | | | - Shaina Alexandria
- Department of Preventive Medicine at Northwestern University Feinberg School of Medicine (NUFSM), Chicago, Illinois, USA
| | - Ching Man Wai
- Northwestern University Sequencing Core, Chicago, Illinois, USA
| | - Ricardo Tellez
- Division of Cardiology, Department of Medicine
- Department of Pathology, and
| | | | | | - Xinkun Wang
- Northwestern University Sequencing Core, Chicago, Illinois, USA
| | - Matthew Schipma
- Northwestern University Sequencing Core, Chicago, Illinois, USA
| | - Ryan Sisk
- Division of Cardiology, Department of Medicine
| | - Rishab Gulati
- La Jolla Institute of Immunology, La Jolla, California, USA
| | | | | | - Donald M. Lloyd-Jones
- Division of Cardiology, Department of Medicine
- Department of Preventive Medicine at Northwestern University Feinberg School of Medicine (NUFSM), Chicago, Illinois, USA
| | | | | | - Karen Ho
- Division of Vascular Surgery, NUFSM, Chicago, Illinois, USA
| | - Klaus Ley
- Immunology Center of Georgia, Augusta, Georgia, USA
| | - Chiara Giannarelli
- Department of Medicine and
- Department of Pathology, New York University, New York, New York, USA
| | | | - Matthew J. Feinstein
- Division of Cardiology, Department of Medicine
- Department of Pathology, and
- Department of Preventive Medicine at Northwestern University Feinberg School of Medicine (NUFSM), Chicago, Illinois, USA
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5
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Hartana CA, Broncano PG, Maswabi K, Ajibola G, Moyo S, Mohammed T, Maphorisa C, Makhema J, Powis KM, Lockman S, Burbelo PD, Gao C, Yu XG, Kuritzkes DR, Shapiro R, Lichterfeld M. Immune Modulation of HIV-1 Reservoir Size in Early-Treated Neonates. J Infect Dis 2023; 228:281-286. [PMID: 37201510 PMCID: PMC10420392 DOI: 10.1093/infdis/jiad173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 05/20/2023] Open
Abstract
Immune mechanisms that modulate human immunodeficiency virus-1 (HIV-1) reservoir size in neonates are poorly understood. Using samples from neonates who initiated antiretroviral therapy shortly after birth, we demonstrate that interleukin-8-secreting CD4 T cells, which are selectively expanded in early infancy, are more resistant to HIV-1 infection and inversely correlated with the frequency of intact proviruses at birth. Moreover, newborns with HIV-1 infection displayed a distinct B-cell profile at birth, with reduction of memory B cells and expansion of plasmablasts and transitional B cells; however, B-cell immune perturbations were unrelated to HIV-1 reservoir size and normalized after initiation of antiretroviral therapy. Clinical Trials Registration. NCT02369406.
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Affiliation(s)
- Ciputra Adijaya Hartana
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Pilar Garcia Broncano
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Kenneth Maswabi
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | | | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | | | | | - Joseph Makhema
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Kathleen M Powis
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine and Pediatrics, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Shahin Lockman
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Harvard Medical School, Boston, Massachusetts, USA
| | - Peter D Burbelo
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
| | - Ce Gao
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Xu G Yu
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Daniel R Kuritzkes
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Roger Shapiro
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Mathias Lichterfeld
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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6
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Arif S, Domingo-Vila C, Pollock E, Christakou E, Williams E, Tree TIM. Monitoring islet specific immune responses in type 1 diabetes clinical immunotherapy trials. Front Immunol 2023; 14:1183909. [PMID: 37283770 PMCID: PMC10240960 DOI: 10.3389/fimmu.2023.1183909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/02/2023] [Indexed: 06/08/2023] Open
Abstract
The number of immunotherapeutic clinical trials in type 1 diabetes currently being conducted is expanding, and thus there is a need for robust immune-monitoring assays which are capable of detecting and characterizing islet specific immune responses in peripheral blood. Islet- specific T cells can serve as biomarkers and as such can guide drug selection, dosing regimens and immunological efficacy. Furthermore, these biomarkers can be utilized in patient stratification which can then benchmark suitability for participation in future clinical trials. This review focusses on the commonly used immune-monitoring techniques including multimer and antigen induced marker assays and the potential to combine these with single cell transcriptional profiling which may provide a greater understanding of the mechanisms underlying immuno-intervention. Although challenges remain around some key areas such as the need for harmonizing assays, technological advances mean that multiparametric information derived from a single sample can be used in coordinated efforts to harmonize biomarker discovery and validation. Moreover, the technologies discussed here have the potential to provide a unique insight on the effect of therapies on key players in the pathogenesis of T1D that cannot be obtained using antigen agnostic approaches.
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7
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Lee SW, Lee GW, Kim HO, Cho JH. Shaping Heterogeneity of Naive CD8 + T Cell Pools. Immune Netw 2023; 23:e2. [PMID: 36911807 PMCID: PMC9995989 DOI: 10.4110/in.2023.23.e2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/12/2023] [Accepted: 02/12/2023] [Indexed: 03/07/2023] Open
Abstract
Immune diversification helps protect the host against a myriad of pathogens. CD8+ T cells are essential adaptive immune cells that inhibit the spread of pathogens by inducing apoptosis in infected host cells, ultimately ensuring complete elimination of infectious pathogens and suppressing disease development. Accordingly, numerous studies have been conducted to elucidate the mechanisms underlying CD8+ T cell activation, proliferation, and differentiation into effector and memory cells, and to identify various intrinsic and extrinsic factors regulating these processes. The current knowledge accumulated through these studies has led to a huge breakthrough in understanding the existence of heterogeneity in CD8+ T cell populations during immune response and the principles underlying this heterogeneity. As the heterogeneity in effector/memory phases has been extensively reviewed elsewhere, in the current review, we focus on CD8+ T cells in a "naïve" state, introducing recent studies dealing with the heterogeneity of naive CD8+ T cells and discussing the factors that contribute to such heterogeneity. We also discuss how this heterogeneity contributes to establishing the immense complexity of antigen-specific CD8+ T cell response.
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Affiliation(s)
- Sung-Woo Lee
- Medical Research Center for Combinatorial Tumor Immunotherapy, Department of Microbiology and Immunology, Chonnam National University Medical School, Hwasun 58128, Korea.,Immunotherapy Innovation Center, Chonnam National University Medical School, Hwasun 58128, Korea
| | - Gil-Woo Lee
- Medical Research Center for Combinatorial Tumor Immunotherapy, Department of Microbiology and Immunology, Chonnam National University Medical School, Hwasun 58128, Korea.,Immunotherapy Innovation Center, Chonnam National University Medical School, Hwasun 58128, Korea
| | | | - Jae-Ho Cho
- Medical Research Center for Combinatorial Tumor Immunotherapy, Department of Microbiology and Immunology, Chonnam National University Medical School, Hwasun 58128, Korea.,Immunotherapy Innovation Center, Chonnam National University Medical School, Hwasun 58128, Korea.,BioMedical Sciences Graduate Program, Chonnam National University Medical School, Hwasun 58128, Korea
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8
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Dekker L, Sanders E, Lindemans CA, de Koning C, Nierkens S. Naive T Cells in Graft Versus Host Disease and Graft Versus Leukemia: Innocent or Guilty? Front Immunol 2022; 13:893545. [PMID: 35795679 PMCID: PMC9250980 DOI: 10.3389/fimmu.2022.893545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
The outcome of allogeneic hematopoietic cell transplantation (allo-HCT) largely depends on the development and management of graft-versus-host disease (GvHD), infections, and the occurrence of relapse of malignancies. Recent studies showed a lower incidence of chronic GvHD and severe acute GvHD in patients receiving naive T cell depleted grafts compared to patients receiving complete T cell depleted grafts. On the other hand, the incidence of acute GvHD in patients receiving cord blood grafts containing only naive T cells is rather low, while potent graft-versus-leukemia (GvL) responses have been observed. These data suggest the significance of naive T cells as both drivers and regulators of allogeneic reactions. The naive T cell pool was previously thought to be a quiescent, homogenous pool of antigen-inexperienced cells. However, recent studies showed important differences in phenotype, differentiation status, location, and function within the naive T cell population. Therefore, the adequate recovery of these seemingly innocent T cells might be relevant in the imminent allogeneic reactions after allo-HCT. Here, an extensive review on naive T cells and their contribution to the development of GvHD and GvL responses after allo-HCT is provided. In addition, strategies specifically directed to stimulate adequate reconstitution of naive T cells while reducing the risk of GvHD are discussed. A better understanding of the relation between naive T cells and alloreactivity after allo-HCT could provide opportunities to improve GvHD prevention, while maintaining GvL effects to lower relapse risk.
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Affiliation(s)
- Linde Dekker
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
| | - Evy Sanders
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | | | - Coco de Koning
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
| | - Stefan Nierkens
- Princess Máxima Center for Pediatric Oncology, Utrecht, Netherlands
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht, Netherlands
- *Correspondence: Stefan Nierkens,
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9
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Ao YQ, Jiang JH, Gao J, Wang HK, Ding JY. Recent thymic emigrants as the bridge between thymoma and autoimmune diseases. Biochim Biophys Acta Rev Cancer 2022; 1877:188730. [DOI: 10.1016/j.bbcan.2022.188730] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 11/27/2022]
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10
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Sandgaard KS, Gkouleli T, Attenborough T, Adams S, Gibbons D, Holm M, Eisen S, Baxendale H, De Rossi A, Pahwa S, Chain B, Gkazi AS, Klein N. The importance of taking ART appropriately in children and adolescents with HIV-1 to reach the highest capacity of immune function later in life. Front Immunol 2022; 13:860316. [PMID: 35967315 PMCID: PMC9364750 DOI: 10.3389/fimmu.2022.860316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 06/28/2022] [Indexed: 11/26/2022] Open
Abstract
Current antiretroviral therapy (ART) guidelines recommend treating all children with HIV-1 infection. This has changed from the broader use of ART to treat children to improve morbidity and minimise mortality. However, prior to current recommendations, not everyone with HIV-1 received timely treatment. What happens to the paediatric immune system when HIV-1 replication is not appropriately supressed remains unclear. 11 samples from adolescents with HIV-1 on ART and uninfected controls in the UK, aged 12-25 years, were examined; overall, adolescents with CD4+ counts > 500/μl and a viral load < 50 copies/ml were compared with adolescents with CD4+ counts < 500/μl and a viral load > 50 copies/ml at time of sampling. Measurements of thymic output were combined with high throughput next generation sequencing and bioinformatics to systematically organize CD4+ and CD8+ T cell receptor (TCR) repertoires. TCR repertoire diversity, clonal expansions, TCR sequence sharing, and formation of TCR clusters in HIV-1 infected adolescents with successful HIV-1 suppression were compared to adolescents with ineffective HIV-1 suppression. Thymic output and CD4+ T cell numbers were decreased in HIV-1 infected adolescents with poor HIV-1 suppression. A strong homeostatic TCR response, driven by the decreased CD4+ T cell compartment and reduced thymic output was observed in the virally uncontrolled HIV-1-infected adolescents. Formation of abundant robust TCR clusters and structurally related TCRs were found in the adolescents with effective HIV-1 suppression. Numerous CD4+ T cell numbers in the virally controlled adolescents emphasize the importance of high thymic output and formation of robust TCR clusters in the maintenance of HIV-1 suppression. While the profound capacity for immune recovery in children may allow better opportunity to deal with immunological stress, when ART is taken appropriately, this study demonstrates new insights into the unique paediatric immune system and the immunological changes when HIV-1 replication is ongoing.
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Affiliation(s)
- Katrine Schou Sandgaard
- Infection, Immunity and Inflammation, University College London (UCL) Great Ormond Street Institute of Child Health, London, United Kingdom.,Department of Pediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Triantafylia Gkouleli
- Infection, Immunity and Inflammation, University College London (UCL) Great Ormond Street Institute of Child Health, London, United Kingdom.,University College London (UCL) Zayed Centre for Research into Rare Disease in Children, London, United Kingdom
| | - Teresa Attenborough
- Infection, Immunity and Inflammation, University College London (UCL) Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Stuart Adams
- Genetics and Rare Diseases, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Deena Gibbons
- Peter Gorer Department of Immunobiology, Kings College London, London, United Kingdom
| | - Mette Holm
- Department of Pediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Sarah Eisen
- Tropical Diseases, University College London Hospital, London, United Kingdom
| | - Helen Baxendale
- Clinical Immunology Department, Royal Papworth Hospital, Cambridge, United Kingdom
| | - Anita De Rossi
- Department of Mother and Child Health, University of Padova, Padova, Italy
| | - Savita Pahwa
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, United States
| | - Benny Chain
- University College London (UCL) Division of Infection and Immunity, University College London (UCL) Cruciform Building, London, United Kingdom
| | - Athina S Gkazi
- Genetics and Rare Diseases, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Nigel Klein
- Infection, Immunity and Inflammation, University College London (UCL) Great Ormond Street Institute of Child Health, London, United Kingdom
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11
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Immunization of preterm infants: current evidence and future strategies to individualized approaches. Semin Immunopathol 2022; 44:767-784. [PMID: 35922638 PMCID: PMC9362650 DOI: 10.1007/s00281-022-00957-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 07/08/2022] [Indexed: 12/15/2022]
Abstract
Preterm infants are at particularly high risk for infectious diseases. As this vulnerability extends beyond the neonatal period into childhood and adolescence, preterm infants benefit greatly from infection-preventive measures such as immunizations. However, there is an ongoing discussion about vaccine safety and efficacy due to preterm infants' distinct immunological features. A significant proportion of infants remains un- or under-immunized when discharged from primary hospital stay. Educating health care professionals and parents, promoting maternal immunization and evaluating the potential of new vaccination tools are important means to reduce the overall burden from infectious diseases in preterm infants. In this narrative review, we summarize the current knowledge about vaccinations in premature infants. We discuss the specificities of early life immunity and memory function, including the role of polyreactive B cells, restricted B cell receptor diversity and heterologous immunity mediated by a cross-reactive T cell repertoire. Recently, mechanistic studies indicated that tissue-resident memory (Trm) cell populations including T cells, B cells and macrophages are already established in the fetus. Their role in human early life immunity, however, is not yet understood. Tissue-resident memory T cells, for example, are diminished in airway tissues in neonates as compared to older children or adults. Hence, the ability to make specific recall responses after secondary infectious stimulus is hampered, a phenomenon that is transcriptionally regulated by enhanced expression of T-bet. Furthermore, the microbiome establishment is a dominant factor to shape resident immunity at mucosal surfaces, but it is often disturbed in the context of preterm birth. The proposed function of Trm T cells to remember benign interactions with the microbiome might therefore be reduced which would contribute to an increased risk for sustained inflammation. An improved understanding of Trm interactions may determine novel targets of vaccination, e.g., modulation of T-bet responses and facilitate more individualized approaches to protect preterm babies in the future.
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12
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Sandgaard KS, Margetts B, Attenborough T, Gkouleli T, Adams S, Holm M, Gibb D, Gibbons D, Giaquinto C, De Rossi A, Bamford A, Palma P, Chain B, Gkazi AS, Klein N. Plasticity of the Immune System in Children Following Treatment Interruption in HIV-1 Infection. Front Immunol 2021; 12:643189. [PMID: 34475868 PMCID: PMC8406805 DOI: 10.3389/fimmu.2021.643189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 07/16/2021] [Indexed: 11/13/2022] Open
Abstract
It is intriguing that, unlike adults with HIV-1, children with HIV-1 reach a greater CD4+ T cell recovery following planned treatment cessation. The reasons for the better outcomes in children remain unknown but may be related to increased thymic output and diversity of T cell receptor repertoires. HIV-1 infected children from the PENTA 11 trial tolerated planned treatment interruption without adverse long-term clinical, virological, or immunological consequences, once antiretroviral therapy was re-introduced. This contrasts to treatment interruption trials of HIV-1 infected adults, who had rapid changes in T cells and slow recovery when antiretroviral therapy was restarted. How children can develop such effective immune responses to planned treatment interruption may be critical for future studies. PENTA 11 was a randomized, phase II trial of planned treatment interruptions in HIV-1-infected children (ISRCTN 36694210). In this sub-study, eight patients in long-term follow-up were chosen with CD4+ count>500/ml, viral load <50c/ml at baseline: four patients on treatment interruption and four on continuous treatment. Together with measurements of thymic output, we used high-throughput next generation sequencing and bioinformatics to systematically organize memory CD8+ and naïve CD4+ T cell receptors according to diversity, clonal expansions, sequence sharing, antigen specificity, and T cell receptor similarities following treatment interruption compared to continuous treatment. We observed an increase in thymic output following treatment interruption compared to continuous treatment. This was accompanied by an increase in T cell receptor clonal expansions, increased T cell receptor sharing, and higher sequence similarities between patients, suggesting a more focused T cell receptor repertoire. The low numbers of patients included is a limitation and the data should be interpreted with caution. Nonetheless, the high levels of thymic output and the high diversity of the T cell receptor repertoire in children may be sufficient to reconstitute the T cell immune repertoire and reverse the impact of interruption of antiretroviral therapy. Importantly, the effective T cell receptor repertoires following treatment interruption may inform novel therapeutic strategies in children infected with HIV-1.
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Affiliation(s)
- Katrine Schou Sandgaard
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- Department of Pediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Ben Margetts
- Molecular Haematology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Teresa Attenborough
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- UCL Centre for Computation, Mathematics, and Physics in the Life Sciences and Experimental Biology (CoMPLEX), London, United Kingdom
| | - Triantafylia Gkouleli
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Stuart Adams
- Molecular Haematology, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Mette Holm
- Department of Pediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Diana Gibb
- Medical Research Council Clinical Trials Unit, London, United Kingdom
| | - Deena Gibbons
- Peter Gorer Department of Immunobiology, Kings College London, London, United Kingdom
| | - Carlo Giaquinto
- Department of Mother and Child Health, University of Padova, Padova, Italy
| | - Anita De Rossi
- Section of Oncology and Immunology, Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV – IRCCS, Padova, Italy
| | - Alasdair Bamford
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
- Molecular Haematology, Great Ormond Street Hospital for Children, London, United Kingdom
- Medical Research Council Clinical Trials Unit, London, United Kingdom
| | - Paolo Palma
- Clinical and Research Unit of Clinical Immunology and Vaccinology, Academic Department of Pediatrics, Children Hospital Bambino Gesù - IRCCS, Rome, Italy
| | - Benny Chain
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - Athina S. Gkazi
- Zayed Centre for Research into Rare Disease in Children, University College London, London, United Kingdom
| | - Nigel Klein
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
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13
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Daniel L, Tassery M, Lateur C, Thierry A, Herbelin A, Gombert JM, Barbarin A. Allotransplantation Is Associated With Exacerbation of CD8 T-Cell Senescence: The Particular Place of the Innate CD8 T-Cell Component. Front Immunol 2021; 12:674016. [PMID: 34367138 PMCID: PMC8334557 DOI: 10.3389/fimmu.2021.674016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 06/30/2021] [Indexed: 12/21/2022] Open
Abstract
Immunosenescence is a physiological process that is associated with changes in the immune system, particularly among CD8 T-cells. Recent studies have hypothesized that senescent CD8 T-cells are produced with chronologic age by chronic stimulation, leading to the acquisition of hallmarks of innate-like T-cells. While conventional CD8 T-cells are quite well characterized, CD8 T-cells sharing features of NK cells and memory CD8 T-cells, are a newly described immune cell population. They can be distinguished from conventional CD8 T-cells by their combined expression of panKIR/NKG2A and Eomesodermin (E), a unique phenotype closely associated with IFN-γ production in response to innate stimulation. Here, we first provided new evidence in favor of the innate character of panKIR/NKG2A(+) E(+) CD8 T-cells in normal subjects, documenting their position at an intermediate level in the innateness gradient in terms of both innate IFN-γ production and diminished mitochondrial mass. We also revealed that CD8 E(+) panKIR/NKG2A(+) T-cells, hereafter referred to as Innate E(+) CD8 T-cells, exhibit increased senescent (CD27(-) CD28(-)) phenotype, compared to their conventional memory counterparts. Surprisingly, this phenomenon was not dependent on age. Given that inflammation related to chronic viral infection is known to induce NK-like marker expression and a senescence phenotype among CD8 T-cells, we hypothesized that innate E(+) CD8 T-cells will be preferentially associated with exacerbated cellular senescence in response to chronic alloantigen exposure or CMV infection. Accordingly, in a pilot cohort of stable kidney allotransplant recipients, we observed an increased frequency of the Innate E(+) CD8 T-cell subset, together with an exacerbated senescent phenotype. Importantly, this phenotype cannot be explained by age alone, in clear contrast to their conventional memory counterparts. The senescent phenotype in CD8 T-cells was further increased in cytomegalovirus (CMV) positive serology transplant recipients, suggesting that transplantation and CMV, rather than aging by itself, may promote an exacerbated senescent phenotype of innate CD8 T-cells. In conclusion, we proposed that kidney transplantation, via the setting of inflammatory stimuli of alloantigen exposure and CMV infection, may exogenously age the CD8 T-cell compartment, especially its innate component. The physiopathological consequences of this change in the immune system remain to be elucidated.
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Affiliation(s)
- Lauren Daniel
- Inserm U1082, Poitiers, France.,Université de Poitiers, Poitiers, France
| | - Marion Tassery
- Service de Néphrologie, Hémodialyse et Transplantation, CHU de Poitiers, Poitiers, France
| | - Clara Lateur
- Service d'Immunologie et Inflammation, CHU de Poitiers, Poitiers, France
| | - Antoine Thierry
- Inserm U1082, Poitiers, France.,Université de Poitiers, Poitiers, France.,Service de Néphrologie, Hémodialyse et Transplantation, CHU de Poitiers, Poitiers, France
| | - André Herbelin
- Inserm U1082, Poitiers, France.,Université de Poitiers, Poitiers, France
| | - Jean-Marc Gombert
- Inserm U1082, Poitiers, France.,Université de Poitiers, Poitiers, France.,Service d'Immunologie et Inflammation, CHU de Poitiers, Poitiers, France
| | - Alice Barbarin
- Inserm U1082, Poitiers, France.,CHU de Poitiers, Poitiers, France
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14
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Semmes EC, Chen JL, Goswami R, Burt TD, Permar SR, Fouda GG. Understanding Early-Life Adaptive Immunity to Guide Interventions for Pediatric Health. Front Immunol 2021; 11:595297. [PMID: 33552052 PMCID: PMC7858666 DOI: 10.3389/fimmu.2020.595297] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 12/04/2020] [Indexed: 01/16/2023] Open
Abstract
Infants are capable of mounting adaptive immune responses, but their ability to develop long-lasting immunity is limited. Understanding the particularities of the neonatal adaptive immune system is therefore critical to guide the design of immune-based interventions, including vaccines, in early life. In this review, we present a thorough summary of T cell, B cell, and humoral immunity in early life and discuss infant adaptive immune responses to pathogens and vaccines. We focus on the differences between T and B cell responses in early life and adulthood, which hinder the generation of long-lasting adaptive immune responses in infancy. We discuss how knowledge of early life adaptive immunity can be applied when developing vaccine strategies for this unique period of immune development. In particular, we emphasize the use of novel vaccine adjuvants and optimization of infant vaccine schedules. We also propose integrating maternal and infant immunization strategies to ensure optimal neonatal protection through passive maternal antibody transfer while avoiding hindering infant vaccine responses. Our review highlights that the infant adaptive immune system is functionally distinct and uniquely regulated compared to later life and that these particularities should be considered when designing interventions to promote pediatric health.
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Affiliation(s)
- Eleanor C. Semmes
- Duke Human Vaccine Institute, Duke University, Durham, NC, United States
- Medical Scientist Training Program, Duke University, Durham, NC, United States
- Children’s Health and Discovery Initiative, Department of Pediatrics, Duke University, Durham, NC, United States
| | - Jui-Lin Chen
- Duke Human Vaccine Institute, Duke University, Durham, NC, United States
| | - Ria Goswami
- Duke Human Vaccine Institute, Duke University, Durham, NC, United States
| | - Trevor D. Burt
- Children’s Health and Discovery Initiative, Department of Pediatrics, Duke University, Durham, NC, United States
- Division of Neonatology, Department of Pediatrics, Duke University, Durham, NC, United States
| | - Sallie R. Permar
- Duke Human Vaccine Institute, Duke University, Durham, NC, United States
- Children’s Health and Discovery Initiative, Department of Pediatrics, Duke University, Durham, NC, United States
| | - Genevieve G. Fouda
- Duke Human Vaccine Institute, Duke University, Durham, NC, United States
- Children’s Health and Discovery Initiative, Department of Pediatrics, Duke University, Durham, NC, United States
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15
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Interleukin-8 as a candidate for thymoma identification and recurrence surveillance. Nat Commun 2020; 11:4881. [PMID: 32985506 PMCID: PMC7522267 DOI: 10.1038/s41467-020-18697-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 09/04/2020] [Indexed: 01/09/2023] Open
Abstract
Thymoma is the most common tumor of the anterior mediastinum. Routine imaging methods such as computed tomography or magnetic resonance imaging often lead to misdiagnosis between thymoma and other thymic abnormalities. Therefore, urgently needed is to develop a new diagnostic strategy. Here we identify interleukin-8 (IL-8) as a biomarker for auxiliary diagnosis of thymoma. We find that IL-8 levels in naïve T cells are markedly elevated in patients with thymoma compared to those with other thymic tumors. IL-8 levels in naive T cells are significantly decreased after surgical resection in thymoma patients, and rise again when thymoma recurs. A receiver operating characteristic curve analysis shows that IL-8 evaluation performs well in thymoma identification, with high specificities and sensitivities. We also observe significant clinical relevance between IL-8 levels in naïve T cells and clinicopathological features. In conclusion, our study suggests that IL-8 is a biomarker for thymoma identification and recurrence surveillance. Imaging methods, such as CT or MRI, cannot provide accurate diagnosis between malignant thymomas and other thymic abnormalities. Here the authors show that the levels of IL-8 in circulating naive T cells are elevated in patients with thymoma compared with other thymic masses, proposing IL-8 as a candidate biomarker for thymoma diagnosis and recurrence surveillance.
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16
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Davenport MP, Smith NL, Rudd BD. Building a T cell compartment: how immune cell development shapes function. Nat Rev Immunol 2020; 20:499-506. [PMID: 32493982 DOI: 10.1038/s41577-020-0332-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2020] [Indexed: 02/06/2023]
Abstract
We are just beginning to understand the diversity of the peripheral T cell compartment, which arises from the specialization of different T cell subsets and the plasticity of individual naive T cells to adopt different fates. Although the progeny of a single T cell can differentiate into many phenotypes following infection, individual T cells are biased towards particular phenotypes. These biases are typically ascribed to random factors that occur during and after antigenic stimulation. However, the T cell compartment does not remain static with age, and shifting immune challenges during ontogeny give rise to T cells with distinct functional properties. Here, we argue that the developmental history of naive T cells creates a 'hidden layer' of diversity that persists into adulthood. Insight into this diversity can provide a new perspective on immunity and immunotherapy across the lifespan.
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Affiliation(s)
- Miles P Davenport
- Kirby Institute for Infection and Immunity, University of New South Wales Australia, Sydney, New South Wales, Australia.
| | - Norah L Smith
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Brian D Rudd
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
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17
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Rackaityte E, Halkias J. Mechanisms of Fetal T Cell Tolerance and Immune Regulation. Front Immunol 2020; 11:588. [PMID: 32328065 PMCID: PMC7160249 DOI: 10.3389/fimmu.2020.00588] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/13/2020] [Indexed: 12/19/2022] Open
Abstract
The developing human fetus generates both tolerogenic and protective immune responses in response to the unique requirements of gestation. Thus, a successful human pregnancy depends on a fine balance between two opposing immunological forces: the semi-allogeneic fetus learns to tolerate both self- and maternal- antigens and, in parallel, develops protective immunity in preparation for birth. This critical window of immune development bridges prenatal immune tolerance with the need for postnatal environmental protection, resulting in a vulnerable neonatal period with heightened risk of infection. The fetal immune system is highly specialized to mediate this transition and thus serves a different function from that of the adult. Adaptive immune memory is already evident in the fetal intestine. Fetal T cells with pro-inflammatory potential are born in a tolerogenic environment and are tightly controlled by both cell-intrinsic and -extrinsic mechanisms, suggesting that compartmentalization and specialization, rather than immaturity, define the fetal immune system. Dysregulation of fetal tolerance generates an inflammatory response with deleterious effects to the pregnancy. This review aims to discuss the recent advances in our understanding of the cellular and molecular composition of fetal adaptive immunity and the mechanisms that govern T cell development and function. We also discuss the tolerance promoting environment that impacts fetal immunity and the consequences of its breakdown. A greater understanding of fetal mechanisms of immune activation and regulation has the potential to uncover novel paradigms of immune balance which may be leveraged to develop therapies for transplantation, autoimmune disease, and birth-associated inflammatory pathologies.
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Affiliation(s)
- Elze Rackaityte
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, United States
| | - Joanna Halkias
- Division of Neonatology, Department of Pediatrics, University of California, San Francisco, San Francisco, CA, United States.,Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, UCSF, San Francisco, CA, United States
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18
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Deeke JM, Gagnon-Bartsch JA. Stably expressed genes in single-cell RNA sequencing. J Bioinform Comput Biol 2020; 18:2040004. [DOI: 10.1142/s0219720020400041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Motivation: In single-cell RNA-sequencing (scRNA-seq) experiments, RNA transcripts are extracted and measured from isolated cells to understand gene expression at the cellular level. Measurements from this technology are affected by many technical artifacts, including batch effects. In analogous bulk gene expression experiments, external references, e.g. synthetic gene spike-ins often from the External RNA Controls Consortium (ERCC), may be incorporated to the experimental protocol for use in adjusting measurements for technical artifacts. In scRNA-seq experiments, the use of external spike-ins is controversial due to dissimilarities with endogenous genes and uncertainty about sufficient precision of their introduction. Instead, endogenous genes with highly stable expression could be used as references within scRNA-seq to help normalize the data. First, however, a specific notion of stable expression at the single-cell level needs to be formulated; genes could be stable in absolute expression, in proportion to cell volume, or in proportion to total gene expression. Different types of stable genes will be useful for different normalizations and will need different methods for discovery. Results: We compile gene sets whose products are associated with cellular structures and record these gene sets for future reuse and analysis. We find that genes whose final products are associated with the cytosolic ribosome have expressions that are highly stable with respect to the total RNA content. Notably, these genes appear to be stable in bulk measurements as well. Supplementary information: Supplementary data are available through GitHub (johanngb/sc-stable).
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Affiliation(s)
- Julie M. Deeke
- Department of Statistics, University of Michigan, 1085 South University Ave, Ann Arbor, MI 48109, USA
| | - Johann A. Gagnon-Bartsch
- Department of Statistics, University of Michigan, 1085 South University Ave, Ann Arbor, MI 48109, USA
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19
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Kamdar S, Hutchinson R, Laing A, Stacey F, Ansbro K, Millar MR, Costeloe K, Wade WG, Fleming P, Gibbons DL. Perinatal inflammation influences but does not arrest rapid immune development in preterm babies. Nat Commun 2020; 11:1284. [PMID: 32152273 PMCID: PMC7062833 DOI: 10.1038/s41467-020-14923-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 02/11/2020] [Indexed: 02/07/2023] Open
Abstract
Infection and infection-related complications are important causes of death and morbidity following preterm birth. Despite this risk, there is limited understanding of the development of the immune system in those born prematurely, and of how this development is influenced by perinatal factors. Here we prospectively and longitudinally follow a cohort of babies born before 32 weeks of gestation. We demonstrate that preterm babies, including those born extremely prematurely (<28 weeks), are capable of rapidly acquiring some adult levels of immune functionality, in which immune maturation occurs independently of the developing heterogeneous microbiome. By contrast, we observe a reduced percentage of CXCL8-producing T cells, but comparable levels of TNF-producing T cells, from babies exposed to in utero or postnatal infection, which precedes an unstable post-natal clinical course. These data show that rapid immune development is possible in preterm babies, but distinct identifiable differences in functionality may predict subsequent infection mediated outcomes.
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Affiliation(s)
- S Kamdar
- Peter Gorer Department of Immunobiology, King's College London, London, SE1 9RT, UK
| | - R Hutchinson
- Department of Neonatology, Homerton University Hospital, London, UK
- Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - A Laing
- Peter Gorer Department of Immunobiology, King's College London, London, SE1 9RT, UK
| | - F Stacey
- Department of Neonatology, Homerton University Hospital, London, UK
| | - K Ansbro
- Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
- University of Sheffield, Sheffield, UK
| | - M R Millar
- Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - K Costeloe
- Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - W G Wade
- Faculty of Dentistry, Oral and Craniofacial Sciences, Centre for Host-Microbiome Interactions, King's College London, London, UK
| | - P Fleming
- Department of Neonatology, Homerton University Hospital, London, UK
- Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - D L Gibbons
- Peter Gorer Department of Immunobiology, King's College London, London, SE1 9RT, UK.
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20
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Abstract
Neonatal CD4+ and CD8+ T cells have historically been characterized as immature or defective. However, recent studies prompt a reinterpretation of the functions of neonatal T cells. Rather than a population of cells always falling short of expectations set by their adult counterparts, neonatal T cells are gaining recognition as a distinct population of lymphocytes well suited for the rapidly changing environment in early life. In this review, I will highlight new evidence indicating that neonatal T cells are not inert or less potent versions of adult T cells but instead are a broadly reactive layer of T cells poised to quickly develop into regulatory or effector cells, depending on the needs of the host. In this way, neonatal T cells are well adapted to provide fast-acting immune protection against foreign pathogens, while also sustaining tolerance to self-antigens.
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Affiliation(s)
- Brian D Rudd
- Department of Microbiology and Immunology, Cornell University, Ithaca, New York 14853, USA;
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21
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Isozaki A, Mikami H, Hiramatsu K, Sakuma S, Kasai Y, Iino T, Yamano T, Yasumoto A, Oguchi Y, Suzuki N, Shirasaki Y, Endo T, Ito T, Hiraki K, Yamada M, Matsusaka S, Hayakawa T, Fukuzawa H, Yatomi Y, Arai F, Di Carlo D, Nakagawa A, Hoshino Y, Hosokawa Y, Uemura S, Sugimura T, Ozeki Y, Nitta N, Goda K. A practical guide to intelligent image-activated cell sorting. Nat Protoc 2019; 14:2370-2415. [PMID: 31278398 DOI: 10.1038/s41596-019-0183-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 04/18/2019] [Indexed: 02/08/2023]
Abstract
Intelligent image-activated cell sorting (iIACS) is a machine-intelligence technology that performs real-time intelligent image-based sorting of single cells with high throughput. iIACS extends beyond the capabilities of fluorescence-activated cell sorting (FACS) from fluorescence intensity profiles of cells to multidimensional images, thereby enabling high-content sorting of cells or cell clusters with unique spatial chemical and morphological traits. Therefore, iIACS serves as an integral part of holistic single-cell analysis by enabling direct links between population-level analysis (flow cytometry), cell-level analysis (microscopy), and gene-level analysis (sequencing). Specifically, iIACS is based on a seamless integration of high-throughput cell microscopy (e.g., multicolor fluorescence imaging, bright-field imaging), cell focusing, cell sorting, and deep learning on a hybrid software-hardware data management infrastructure, enabling real-time automated operation for data acquisition, data processing, intelligent decision making, and actuation. Here, we provide a practical guide to iIACS that describes how to design, build, characterize, and use an iIACS machine. The guide includes the consideration of several important design parameters, such as throughput, sensitivity, dynamic range, image quality, sort purity, and sort yield; the development and integration of optical, microfluidic, electrical, computational, and mechanical components; and the characterization and practical usage of the integrated system. Assuming that all components are readily available, a team of several researchers experienced in optics, electronics, digital signal processing, microfluidics, mechatronics, and flow cytometry can complete this protocol in ~3 months.
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Affiliation(s)
- Akihiro Isozaki
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
| | - Hideharu Mikami
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
| | | | - Shinya Sakuma
- Department of Micro-Nano Mechanical Science and Engineering, Nagoya University, Nagoya, Japan
| | - Yusuke Kasai
- Department of Micro-Nano Mechanical Science and Engineering, Nagoya University, Nagoya, Japan
| | - Takanori Iino
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Tokyo, Japan
| | - Takashi Yamano
- Laboratory of Applied Molecular Microbiology, Kyoto University, Kyoto, Japan
| | - Atsushi Yasumoto
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yusuke Oguchi
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
| | - Nobutake Suzuki
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
| | | | | | - Takuro Ito
- Department of Chemistry, The University of Tokyo, Tokyo, Japan.,Japan Science and Technology Agency, Saitama, Japan
| | - Kei Hiraki
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
| | - Makoto Yamada
- Department of Intelligence Science and Technology, Graduate School of Informatics, Kyoto University, Kyoto, Japan
| | - Satoshi Matsusaka
- Clinical Research and Regional Innovation, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Takeshi Hayakawa
- Department of Precision Mechanics, Chuo University, Tokyo, Japan
| | - Hideya Fukuzawa
- Laboratory of Applied Molecular Microbiology, Kyoto University, Kyoto, Japan
| | - Yutaka Yatomi
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Fumihito Arai
- Department of Micro-Nano Mechanical Science and Engineering, Nagoya University, Nagoya, Japan
| | - Dino Di Carlo
- Department of Chemistry, The University of Tokyo, Tokyo, Japan.,Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Mechanical Engineering, University of California, Los Angeles, Los Angeles, CA, USA.,California NanoSystems Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Atsuhiro Nakagawa
- Department of Neurosurgery, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Yu Hoshino
- Department of Chemical Engineering, Kyushu University, Fukuoka, Japan
| | - Yoichiroh Hosokawa
- Division of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Sotaro Uemura
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
| | - Takeaki Sugimura
- Department of Chemistry, The University of Tokyo, Tokyo, Japan.,Japan Science and Technology Agency, Saitama, Japan
| | - Yasuyuki Ozeki
- Department of Electrical Engineering and Information Systems, The University of Tokyo, Tokyo, Japan
| | - Nao Nitta
- Department of Chemistry, The University of Tokyo, Tokyo, Japan.,Japan Science and Technology Agency, Saitama, Japan
| | - Keisuke Goda
- Department of Chemistry, The University of Tokyo, Tokyo, Japan. .,Japan Science and Technology Agency, Saitama, Japan. .,Department of Electrical Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
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22
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Miller MM, Barik S, Cattin-Roy AN, Ukah TK, Hoeman CM, Zaghouani H. A New IRF-1-Driven Apoptotic Pathway Triggered by IL-4/IL-13 Kills Neonatal Th1 Cells and Weakens Protection against Viral Infection. THE JOURNAL OF IMMUNOLOGY 2019; 202:3173-3186. [PMID: 30996000 DOI: 10.4049/jimmunol.1800943] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 03/21/2019] [Indexed: 11/19/2022]
Abstract
Early life immune responses are deficient in Th1 lymphocytes that compromise neonatal vaccination. We found that IL-4 and IL-13 engage a developmentally expressed IL-4Rα/IL-13Rα1 heteroreceptor to endow IFN regulatory factor 1 (IRF-1) with apoptotic functions, which redirect murine neonatal Th1 reactivation to cell death. IL-4/IL-13-induced STAT6 phosphorylation serves to enhance IRF-1 transcription and promotes its egress from the nucleus. In the cytoplasm, IRF-1 can no longer serve as an anti-viral transcription factor but, instead, colocalizes with Bim and instigates the mitochondrial, or intrinsic, death pathway. The new pivotal function of IRF-1 in the death of neonatal Th1 cells stems from the ability of its gene to bind STAT6 for enhanced transcription and the proficiency of its protein to precipitate Bim-driven apoptosis. This cytokine-induced, IRF-1-mediated developmental death network weakens neonatal Th1 responses during early life vaccination and increases susceptibility to viral infection.
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Affiliation(s)
- Mindy M Miller
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia MO 65212
| | - Subhasis Barik
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia MO 65212
| | - Alexis N Cattin-Roy
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia MO 65212
| | - Tobechukwu K Ukah
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia MO 65212
| | - Christine M Hoeman
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia MO 65212
| | - Habib Zaghouani
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia MO 65212; .,Department of Child Health, University of Missouri School of Medicine, Columbia MO 65212; and.,Department of Neurology, University of Missouri School of Medicine, Columbia MO 65212
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23
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Wu J, Gong RL, Hu QF, Chen XT, Zhao W, Chen TX. Immunoregulatory effect of human β-defensin 1 on neonatal cord blood monocyte-derived dendritic cells and T cells. Mol Immunol 2019; 109:99-107. [PMID: 30921683 DOI: 10.1016/j.molimm.2019.03.007] [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: 10/31/2018] [Revised: 03/11/2019] [Accepted: 03/15/2019] [Indexed: 12/31/2022]
Abstract
The relationship between breastfeeding and infant health has been well elucidated in past decades. Our previous study has shown that human β-defensin 1 (hBD-1) in human breast milk plays a protective role in reducing the incidence of upper respiratory infection in infants younger than 6 months. In the present study, we aim to reveal the mechanism underlying the protective role of hBD-1 by focusing on its immunoregulatory function in neonates. Cord blood (CB) from newborns' umbilical cords, which can simulate many of the neonatal symptoms, was used to study the immunomodulatory role of hBD-1 in neonates in vitro. Our results showed that hBD-1 promotes the GM-CSF- and IL-4-driven differentiation of neonatal umbilical CB monocytes to immature dendritic cells (DCs) and the final maturation of CB monocyte-derived DCs (moDCs) induced by LPS but not inflammatory cytokine production. In addition, hBD-1 inhibits apoptosis in neonatal moDCs through CCR6, which might be a possible mechanism of the hBD-1-induced phenotypes in moDCs. Furthermore, we found that hBD-1 promotes the proliferation and activation, but not the maturation, of neonatal CB CD4 + T cells. These results extend the immunoregulatory effects of hBD-1 and provide a potential mechanism for the protective role of hBD-1 in early infants, which will inform the development of infant nutrition, novel vaccines and anti-infective strategies in the future.
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Affiliation(s)
- Jing Wu
- Division of Immunology, Institute of Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Ruo-Lan Gong
- Division of Immunology, Institute of Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Qing-Feng Hu
- Division of Immunology, Institute of Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Xu-Ting Chen
- Division of Immunology, Institute of Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Wei Zhao
- Division of Allergy and Immunology, Department of Pediatrics, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - Tong-Xin Chen
- Department of Rheumatology/Immunology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China; Division of Immunology, Institute of Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China.
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Challenges in Developing Protein Secretion Assays at a Single-Cell Level. Methods Mol Biol 2019; 1808:1-7. [PMID: 29956169 DOI: 10.1007/978-1-4939-8567-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
In addition to direct physical interactions between/among cells, the secretion of humoral factors from living cells is a critical process for cell-cell communications. A well-known extracellular signaling event is mediated by immune cell cytokines/chemokines. Because cell-cell communication is crucial in immune cell sociology, protein secretion assays first attracted a broad range of immunology interests. Now that we have entered an era of systems biology, cell-cell interactions mediated by secreted molecules should be revisited to understand the dynamics and homeostasis of the cell society as a whole. Of more importance, recent advances in detection and microfluidics technologies enable us to monitor protein secretion in real time rather than as a snapshot from the past, which gives us an opportunity to more deeply understand the logic of mammalian cell sociology. This chapter reviews the recent progress in and future direction of protein secretion assays, particularly from a mammalian cell sociology viewpoint.
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Visger CJ, Wong GKS, Zhang Y, Soltis PS, Soltis DE. Divergent gene expression levels between diploid and autotetraploid Tolmiea relative to the total transcriptome, the cell, and biomass. AMERICAN JOURNAL OF BOTANY 2019; 106:280-291. [PMID: 30779448 DOI: 10.1002/ajb2.1239] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 12/03/2018] [Indexed: 05/28/2023]
Abstract
PREMISE OF THE STUDY Studies of gene expression and polyploidy are typically restricted to characterizing differences in transcript concentration. Using diploid and autotetraploid Tolmiea, we present an integrated approach for cross-ploidy comparisons that account for differences in transcriptome size and cell density and make multiple comparisons of transcript abundance. METHODS We use RNA spike-in standards in concert with cell size and density to identify and correct for differences in transcriptome size and compare levels of gene expression across multiple scales: per transcriptome, per cell, and per biomass. KEY RESULTS In total, ~17% of all loci were identified as differentially expressed (DEGs) between the diploid and autopolyploid species. The per-transcriptome normalization, the method researchers typically use, captured the fewest DEGs (58% of total DEGs) and failed to detect any DEGs not found by the alternative normalizations. When transcript abundance was normalized per biomass and per cell, ~66% and ~82% of the total DEGs were recovered, respectively. The discrepancy between per-transcriptome and per-cell recovery of DEGs occurs because per-transcriptome normalizations are concentration-based and therefore blind to differences in transcriptome size. CONCLUSIONS While each normalization enables valid comparisons at biologically relevant scales, a holistic comparison of multiple normalizations provides additional explanatory power not available from any single approach. Notably, autotetraploid loci tend to conserve diploid-like transcript abundance per biomass through increased gene expression per cell, and these loci are enriched for photosynthesis-related functions.
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Affiliation(s)
- Clayton J Visger
- Department of Biological Sciences, California State University Sacramento, Sacramento, CA, 95819, USA
| | - Gane K-S Wong
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- Beijing Genomics Institute-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Yong Zhang
- Beijing Genomics Institute-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
- Shenzhen Hua Han Gene Co. Ltd., 7F Jian An Shan Hai Building, No. 8000, Shennan Road, Futian District, Shenzhen, 518040, China
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
- Genetics Institute, University of Florida, Gainesville, FL, 32610, USA
- Biodiversity Institute, University of Florida, Gainesville, FL, 32611, USA
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
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