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Yin DE, Palin AC, Lombo TB, Mahon RN, Poon B, Wu DY, Atala A, Brooks KM, Chen S, Coyne CB, D’Souza MP, Fackler OT, Furler O’Brien RL, Garcia-de-Alba C, Jean-Philippe P, Karn J, Majji S, Muotri AR, Ozulumba T, Sakatis MZ, Schlesinger LS, Singh A, Spiegel HM, Struble E, Sung K, Tagle DA, Thacker VV, Tidball AM, Varthakavi V, Vunjak-Novakovic G, Wagar LE, Yeung CK, Ndhlovu LC, Ott M. 3D human tissue models and microphysiological systems for HIV and related comorbidities. Trends Biotechnol 2024; 42:526-543. [PMID: 38071144 PMCID: PMC11065605 DOI: 10.1016/j.tibtech.2023.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/22/2023] [Accepted: 10/24/2023] [Indexed: 03/03/2024]
Abstract
Three-dimensional (3D) human tissue models/microphysiological systems (e.g., organs-on-chips, organoids, and tissue explants) model HIV and related comorbidities and have potential to address critical questions, including characterization of viral reservoirs, insufficient innate and adaptive immune responses, biomarker discovery and evaluation, medical complexity with comorbidities (e.g., tuberculosis and SARS-CoV-2), and protection and transmission during pregnancy and birth. Composed of multiple primary or stem cell-derived cell types organized in a dedicated 3D space, these systems hold unique promise for better reproducing human physiology, advancing therapeutic development, and bridging the human-animal model translational gap. Here, we discuss the promises and achievements with 3D human tissue models in HIV and comorbidity research, along with remaining barriers with respect to cell biology, virology, immunology, and regulatory issues.
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Palin AC, Alter G, Crotty S, Ellebedy AH, Lane MC, Lee FEH, Locci M, Malaspina A, Mallia C, McElrath MJ, Pulendran B, Singh A, D'Souza MP. Author Correction: The persistence of memory: defining, engineering, and measuring vaccine durability. Nat Immunol 2023; 24:200. [PMID: 36572838 DOI: 10.1038/s41590-022-01414-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Amy C Palin
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Shane Crotty
- Center for Infectious Diseases and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Ali H Ellebedy
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.,Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St Louis, MO, USA.,The Andrew M. and Jane M. Bursky Center for Human Immunology & Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA
| | - M Chelsea Lane
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - F Eun-Hyung Lee
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA, USA.,Lowance Center for Human Immunology, Emory University, Atlanta, Georgia, USA
| | - Michela Locci
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Angela Malaspina
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Conrad Mallia
- Division of Allergy, Immunology, and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Anjali Singh
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - M Patricia D'Souza
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.
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Palin AC, Alter G, Crotty S, Ellebedy AH, Lane MC, Lee FEH, Locci M, Malaspina A, Mallia C, McElrath MJ, Pulendran B, Singh A, D'Souza MP. The persistence of memory: defining, engineering, and measuring vaccine durability. Nat Immunol 2022; 23:1665-1668. [PMID: 36456737 PMCID: PMC9916179 DOI: 10.1038/s41590-022-01359-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Affiliation(s)
- Amy C Palin
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA
| | - Shane Crotty
- Center for Infectious Diseases and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Ali H Ellebedy
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.,Center for Vaccines and Immunity to Microbial Pathogens, Washington University School of Medicine, St Louis, MO, USA.,The Andrew M. and Jane M. Bursky Center for Human Immunology & Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA
| | - M Chelsea Lane
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - F Eun-Hyung Lee
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA, USA.,Lowance Center for Human Immunology, Emory University, Atlanta, Georgia, USA
| | - Michela Locci
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Angela Malaspina
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Conrad Mallia
- Division of Allergy, Immunology, and Transplantation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - M Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Bali Pulendran
- Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Anjali Singh
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - M Patricia D'Souza
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.
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D'Souza MP, Palin AC, Calder T, Golding H, Kleinstein SH, Milliken EL, O'Connor D, Tomaras G, Warren J, Boggiano C. Mind the gap from research laboratory to clinic: Challenges and opportunities for next-generation assays in human diseases. Vaccine 2021; 39:5233-5239. [PMID: 34366145 PMCID: PMC8343370 DOI: 10.1016/j.vaccine.2021.07.071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 07/24/2021] [Accepted: 07/26/2021] [Indexed: 11/16/2022]
Abstract
Modern vaccinology has experienced major conceptual and technological advances over the past 30 years. These include atomic-level structures driving immunogen design, new vaccine delivery methods, powerful adjuvants, and novel animal models. In addition, utilizing advanced assays to learn how the immune system senses a pathogen and orchestrates protective immunity has been critical in the design of effective vaccines and therapeutics. The National Institute of Allergy and Infectious Diseases of the National Institutes of Health convened a workshop in September 2020 focused on next generation assays for vaccine development (Table 1). The workshop focused on four critical pathogens: severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) and human immunodeficiency virus (HIV)—which have no licensed vaccines—and tuberculosis (TB) and influenza—both of which are in critical need of improved vaccines. The goal was to share progress and lessons learned, and to identify any commonalities that can be leveraged to design vaccines and therapeutics.
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Affiliation(s)
- M Patricia D'Souza
- Vaccine Clinical Research Branch, Vaccine Research Program, Division of AIDS, National Institute of Allergy and Infectious Diseases, Rockville, MD, USA.
| | - Amy C Palin
- Vaccine Clinical Research Branch, Vaccine Research Program, Division of AIDS, National Institute of Allergy and Infectious Diseases, Rockville, MD, USA
| | - Thomas Calder
- Office of the Director, Vaccine Research Program, Division of AIDS, National Institute of Allergy and Infectious Diseases, Rockville, MD, USA
| | - Hana Golding
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Steven H Kleinstein
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Pathology and Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | | | - David O'Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Georgia Tomaras
- Duke Human Vaccine Institute, Duke University, Durham, NC, USA
| | - Jon Warren
- Pre-clinical Research and Development Branch, Vaccine Research Program, Division of AIDS, National Institute of Allergy and Infectious Diseases, Rockville, MD, USA
| | - Cesar Boggiano
- Pre-clinical Research and Development Branch, Vaccine Research Program, Division of AIDS, National Institute of Allergy and Infectious Diseases, Rockville, MD, USA
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Ohigashi I, Tanaka Y, Kondo K, Fujimori S, Kondo H, Palin AC, Hoffmann V, Kozai M, Matsushita Y, Uda S, Motosugi R, Hamazaki J, Kubota H, Murata S, Tanaka K, Katagiri T, Kosako H, Takahama Y. Trans-omics Impact of Thymoproteasome in Cortical Thymic Epithelial Cells. Cell Rep 2020; 29:2901-2916.e6. [PMID: 31775054 PMCID: PMC6897492 DOI: 10.1016/j.celrep.2019.10.079] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 08/27/2019] [Accepted: 10/18/2019] [Indexed: 12/19/2022] Open
Abstract
The thymic function to produce self-protective and self-tolerant T cells is chiefly mediated by cortical thymic epithelial cells (cTECs) and medullary TECs (mTECs). Recent studies including single-cell transcriptomic analyses have highlighted a rich diversity in functional mTEC subpopulations. Because of their limited cellularity, however, the biochemical characterization of TECs, including the proteomic profiling of cTECs and mTECs, has remained unestablished. Utilizing genetically modified mice that carry enlarged but functional thymuses, here we show a combination of proteomic and transcriptomic profiles for cTECs and mTECs, which identified signature molecules that characterize a developmental and functional contrast between cTECs and mTECs. Our results reveal a highly specific impact of the thymoproteasome on proteasome subunit composition in cTECs and provide an integrated trans-omics platform for further exploration of thymus biology. Ohigashi et al. show that the use of cyclin D1-transgenic mice allows quantitative proteomic analysis of cortical and medullary thymic epithelial cells (TECs). Results provide a trans-omics platform for further exploration of TEC biology and reveal the specific impact of the thymoproteasome on proteasome subunit composition in cortical TECs.
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Affiliation(s)
- Izumi Ohigashi
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, Tokushima 770-8503, Japan
| | - Yu Tanaka
- Experimental Immunology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Kenta Kondo
- Experimental Immunology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sayumi Fujimori
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, Tokushima 770-8503, Japan
| | - Hiroyuki Kondo
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, Tokushima 770-8503, Japan
| | - Amy C Palin
- Experimental Immunology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Victoria Hoffmann
- Division of Veterinary Resources, Office of Research Services, NIH, Bethesda, MD 20892, USA
| | - Mina Kozai
- Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, Tokushima 770-8503, Japan
| | - Yosuke Matsushita
- Division of Genome Medicine, Institute of Advanced Medical Sciences, University of Tokushima, Tokushima 770-8503, Japan
| | - Shinsuke Uda
- Division of Integrated Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Ryo Motosugi
- Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Jun Hamazaki
- Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hiroyuki Kubota
- Division of Integrated Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Shigeo Murata
- Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Keiji Tanaka
- Tokyo Metropolitan Institute for Medical Science, Tokyo 156-8506, Japan
| | - Toyomasa Katagiri
- Division of Genome Medicine, Institute of Advanced Medical Sciences, University of Tokushima, Tokushima 770-8503, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, University of Tokushima, Tokushima 770-8503, Japan
| | - Yousuke Takahama
- Experimental Immunology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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Abstract
The role of co-receptor molecules in the generation of inducible regulatory T cells (iTregs) remains incompletely defined. In this issue of Immunity, Henderson et al. (2015) show that CD5 regulates iTreg cell induction by rendering emerging iTreg cells refractory to signals mediated by effector-differentiating cytokines.
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Affiliation(s)
- Amy C Palin
- Eunice Kennedy Shriver, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul E Love
- Eunice Kennedy Shriver, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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Palin AC, Ramachandran V, Acharya S, Lewis DB. Human neonatal naive CD4+ T cells have enhanced activation-dependent signaling regulated by the microRNA miR-181a. J Immunol 2013; 190:2682-91. [PMID: 23408835 DOI: 10.4049/jimmunol.1202534] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Compared with older children and adults, human neonates have reduced and delayed CD4(+) T cell immunity to certain pathogens, but the mechanisms for these developmental differences in immune function remain poorly understood. We investigated the hypothesis that impaired human neonatal CD4(+) T cell immunity was due to reduced signaling by naive CD4(+) T cells following engagement of the αβ-TCR/CD3 complex and CD28. Surprisingly, calcium flux following engagement of CD3 was significantly higher in neonatal naive CD4(+) T cells from umbilical cord blood (CB) compared with naive CD4(+) T cells from adult peripheral blood. Enhanced calcium flux was also observed in adult CD4(+) recent thymic emigrants. Neonatal naive CD4(+) T cells also had higher activation-induced Erk phosphorylation. The microRNA miR-181a, which enhances activation-induced calcium flux in murine thymocytes, was expressed at significantly higher levels in CB naive CD4(+) T cells compared with adult cells. Overexpression of miR-181a in adult naive CD4(+) T cells increased activation-induced calcium flux, implying that the increased miR-181a levels of CB naive CD4(+) T cells contributed to their enhanced signaling. In contrast, AP-1-dependent transcription, which is downstream of Erk and required for full T cell activation, was decreased in CB naive CD4(+) T cells compared with adult cells. Thus, CB naive CD4(+) T cells have enhanced activation-dependent calcium flux, indicative of the retention of a thymocyte-like phenotype. Enhanced calcium signaling and Erk phosphorylation are decoupled from downstream AP-1-dependent transcription, which is reduced and likely contributes to limitations of human fetal and neonatal CD4(+) T cell immunity.
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Affiliation(s)
- Amy C Palin
- Department of Pediatrics, Program in Immunology, Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA 94305, USA
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