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Ilangovan J, Neves JF, Santos AF. Innate lymphoid cells in immunoglobulin E-mediated food allergy. Curr Opin Allergy Clin Immunol 2024; 24:419-425. [PMID: 39132724 PMCID: PMC11356679 DOI: 10.1097/aci.0000000000001018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
PURPOSE OF REVIEW Recognition of the importance of innate lymphoid cells (ILCs) in the immune mechanisms of food allergy has grown in recent years. This review summarizes recent findings of ILCs in immunoglobulin E (IgE)-mediated food allergy. New research on ILCs in the context of the microbiome and other atopic diseases are also considered with respect to how they can inform understanding of the role of ILCs in food allergy. RECENT FINDINGS ILCs can mediate allergic and tolerogenic responses through multiple pathways. A novel subset of interleukin (IL)-10 producing ILC2s are associated with tolerance following immunotherapy to grass pollen, house dust mite allergy and lipid transfer protein allergy. ILC2s can drive food allergen-specific T cell responses in an antigen-specific manner. A memory subset of ILC2s has been identified through studies of other atopic diseases and is associated with effectiveness of response to therapy. SUMMARY The role of ILCs in food allergy and oral tolerance is relatively understudied compared to other diseases. ILCs can modulate immune responses through several mechanisms, and it is likely that these are of importance in the context of food allergy. Better understanding of theses pathways may help to answer fundamental questions regarding the development of food allergy and lead to novel therapeutic targets and treatment.
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Affiliation(s)
- Janarthanan Ilangovan
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine
- Centre for Host Microbiome Interactions
| | | | - Alexandra F. Santos
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, Faculty of Life Sciences and Medicine
- Department of Women and Children's Health (Paediatric Allergy), School of Life Course Sciences, Faculty of Life Sciences and Medicine, King's College London
- Children's Allergy Service, Guy's and St Thomas’ Hospital, London, UK
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2
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Piersma SJ. Tissue-specific features of innate lymphoid cells in antiviral defense. Cell Mol Immunol 2024; 21:1036-1050. [PMID: 38684766 PMCID: PMC11364677 DOI: 10.1038/s41423-024-01161-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 04/01/2024] [Indexed: 05/02/2024] Open
Abstract
Innate lymphocytes (ILCs) rapidly respond to and protect against invading pathogens and cancer. ILCs include natural killer (NK) cells, ILC1s, ILC2s, ILC3s, and lymphoid tissue inducer (LTi) cells and include type I, type II, and type III immune cells. While NK cells have been well recognized for their role in antiviral immunity, other ILC subtypes are emerging as players in antiviral defense. Each ILC subset has specialized functions that uniquely impact the antiviral immunity and health of the host depending on the tissue microenvironment. This review focuses on the specialized functions of each ILC subtype and their roles in antiviral immune responses across tissues. Several viruses within infection-prone tissues will be highlighted to provide an overview of the extent of the ILC immunity within tissues and emphasize common versus virus-specific responses.
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Affiliation(s)
- Sytse J Piersma
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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3
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Bennstein SB, Uhrberg M. Circulating innate lymphoid cells (cILCs): Unconventional lymphocytes with hidden talents. J Allergy Clin Immunol 2024; 154:523-536. [PMID: 39046403 DOI: 10.1016/j.jaci.2024.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/16/2024] [Accepted: 06/28/2024] [Indexed: 07/25/2024]
Abstract
Innate lymphoid cells (ILCs) are a group of lymphocytes that are devoid of antigen-specific receptors and are mainly found in tissues. The subtypes ILC1, 2, and 3 mirror T-cell functionality in terms of cytokine production and expression of key transcription factors. Although the majority of ILCs are found in tissue (tILCs), they have also been described within the circulation (cILCs). As a result of their better accessibility and putative prognostic value, human cILCs are getting more and more attention in clinical research. However, cILCs are in many aspects functionally distinct from their tILC counterparts. In fact, from the 3 ILC subsets found within the circulation, only for cILC2s could a clear functional correspondence to their tissue counterparts be established. Indeed, cILC2s are emerging as a major driver of allergic reactions with a particular role in asthma. In contrast, recent studies revealed that cILC1s and cILC3s are predominantly in an immature state and constitute progenitors for natural killer cells and ILCs, respectively. We provide an overview about the phenotype and function of the different cILC subtypes compared to tILCs in health and disease, including transcriptomic signatures, frequency dynamics, and potential clinical value. Furthermore, we will highlight the dynamics of the NKp44+ ILC3 subset, which emerges as prognostic marker in peripheral blood for inflammatory bowel disease and leukemia.
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Affiliation(s)
- Sabrina B Bennstein
- Institute for Transplantation Diagnostics and Cell Therapeutics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Institute of Immunology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany.
| | - Markus Uhrberg
- Institute for Transplantation Diagnostics and Cell Therapeutics, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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4
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Kromann EH, Jowett GM, Neves JF. Expansion and Maturation of Innate Lymphoid Cell Precursors Using Human iPSC-Derived Intestinal Organoids. Methods Mol Biol 2024. [PMID: 39214947 DOI: 10.1007/7651_2024_568] [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: 09/04/2024]
Abstract
Innate lymphoid cells (ILC) are enriched at mucosal barrier sites where they play critical roles in development and disease. Mucosal organoids offer a robust platform for the simultaneous differentiation and expansion of all subsets of mature ILC from a shared peripheral blood precursor. Critically, organoid identity drives tissue-specific imprinting of the culture-derived mature innate lymphoid cells, allowing for the study of bidirectional interactions between, e.g., intestinal organoids and intestine-specific ratios and populations of ILC. This protocol reduces the need for feeder cell lines and complex cytokine cocktails used to mature and maintain ILC, instead relying on a native niche of protein signals provided by mucosal epithelial cells. This protocol details the generation of human intestinal organoids (HIO) from human-induced pluripotent stem cells (hiPSC), and the subsequent establishment of co-cultures between HIO and ILC precursors for expansion and maturation. This approach has extensive applications for mechanistic studies of fundamental biological processes and as a potential GMP-compatible source of ILC for future cell therapies.
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Affiliation(s)
| | - Geraldine M Jowett
- Wellcome/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Joana F Neves
- Centre for Host Microbiome Interactions, King's College London, London, UK.
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5
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Huang YA, Wang X, Kim JC, Yao X, Sethi A, Strohm A, Doherty TA. PIP-seq identifies novel heterogeneous lung innate lymphocyte population activation after combustion product exposure. Sci Rep 2024; 14:20167. [PMID: 39215111 PMCID: PMC11364781 DOI: 10.1038/s41598-024-70880-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024] Open
Abstract
Innate lymphoid cells (ILCs) are a heterogeneous population that play diverse roles in airway inflammation after exposure to allergens and infections. However, how ILCs respond after exposure to environmental toxins is not well understood. Here we show a novel method for studying the heterogeneity of rare lung ILC populations by magnetic enrichment for lung ILCs followed by particle-templated instant partition sequencing (PIP-seq). Using this method, we were able to identify novel group 1 and group 2 ILC subsets that exist after exposure to both fungal allergen and burn pit-related constituents (BPC) that include dioxin, aromatic hydrocarbon, and particulate matter. Toxin exposure in combination with fungal allergen induced activation of specific ILC1/NK and ILC2 populations as well as promoted neutrophilic lung inflammation. Oxidative stress pathways and downregulation of specific ribosomal protein genes (Rpl41 and Rps19) implicated in anti-inflammatory responses were present after BPC exposure. Increased IFNγ expression and other pro-neutrophilic mediator transcripts were increased in BPC-stimulated lung innate lymphoid cells. Further, the addition of BPC induced Hspa8 (encodes HSC70) and aryl hydrocarbon transcription factor activity across multiple lung ILC subsets. Overall, using an airway disease model that develops after occupational and environmental exposures, we demonstrate an effective method to better understand heterogenous ILC subset activation.
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Affiliation(s)
- Yung-An Huang
- Divison of Allergy and Immunology, Department of Medicine, University of California San Diego, Biomedical Sciences Building, Room 5090, 9500 Gilman Drive, La Jolla, CA, 92093-0635, USA
- Veterans Affairs San Diego Health Care System, San Diego, CA, USA
| | - Xinyu Wang
- Divison of Allergy and Immunology, Department of Medicine, University of California San Diego, Biomedical Sciences Building, Room 5090, 9500 Gilman Drive, La Jolla, CA, 92093-0635, USA
- Veterans Affairs San Diego Health Care System, San Diego, CA, USA
| | - Jong-Chan Kim
- Divison of Allergy and Immunology, Department of Medicine, University of California San Diego, Biomedical Sciences Building, Room 5090, 9500 Gilman Drive, La Jolla, CA, 92093-0635, USA
- Veterans Affairs San Diego Health Care System, San Diego, CA, USA
| | - Xiang Yao
- Divison of Allergy and Immunology, Department of Medicine, University of California San Diego, Biomedical Sciences Building, Room 5090, 9500 Gilman Drive, La Jolla, CA, 92093-0635, USA
- Veterans Affairs San Diego Health Care System, San Diego, CA, USA
| | - Anshika Sethi
- Divison of Allergy and Immunology, Department of Medicine, University of California San Diego, Biomedical Sciences Building, Room 5090, 9500 Gilman Drive, La Jolla, CA, 92093-0635, USA
- Veterans Affairs San Diego Health Care System, San Diego, CA, USA
| | - Allyssa Strohm
- Divison of Allergy and Immunology, Department of Medicine, University of California San Diego, Biomedical Sciences Building, Room 5090, 9500 Gilman Drive, La Jolla, CA, 92093-0635, USA
- Veterans Affairs San Diego Health Care System, San Diego, CA, USA
| | - Taylor A Doherty
- Divison of Allergy and Immunology, Department of Medicine, University of California San Diego, Biomedical Sciences Building, Room 5090, 9500 Gilman Drive, La Jolla, CA, 92093-0635, USA.
- Veterans Affairs San Diego Health Care System, San Diego, CA, USA.
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6
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Jaeger N, Antonova AU, Kreisel D, Roan F, Lantelme E, Ziegler SF, Cella M, Colonna M. Diversity of group 1 innate lymphoid cells in human tissues. Nat Immunol 2024; 25:1460-1473. [PMID: 38956380 DOI: 10.1038/s41590-024-01885-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 05/31/2024] [Indexed: 07/04/2024]
Abstract
Group 1 innate lymphoid cells (ILC1s) are cytotoxic and interferon gamma-producing lymphocytes lacking antigen-specific receptors, which include ILC1s and natural killer (NK) cells. In mice, ILC1s differ from NK cells, as they develop independently of the NK-specifying transcription factor EOMES, while requiring the repressor ZFP683 (ZNF683 in humans) for tissue residency. Here we identify highly variable ILC1 subtypes across tissues through investigation of human ILC1 diversity by single-cell RNA sequencing and flow cytometry. The intestinal epithelium contained abundant mature EOMES- ILC1s expressing PRDM1 rather than ZNF683, alongside a few immature TCF7+PRDM1- ILC1s. Other tissues harbored NK cells expressing ZNF683 and EOMES transcripts; however, EOMES protein content was variable. These ZNF683+ NK cells are tissue-imprinted NK cells phenotypically resembling ILC1s. The tissue ILC1-NK spectrum also encompassed conventional NK cells and NK cells distinguished by PTGDS expression. These findings establish a foundation for evaluating phenotypic and functional changes within the NK-ILC1 spectrum in diseases.
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Affiliation(s)
- Natalia Jaeger
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Alina Ulezko Antonova
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel Kreisel
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Florence Roan
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA
- Division of Allergy and Infectious Diseases, University of Washington School of Medicine, Seattle, WA, USA
| | - Erica Lantelme
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Steven F Ziegler
- Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA, USA
- Department of Immunology, University of Washington School of Medicine, Seattle, WA, USA
| | - Marina Cella
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
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7
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Netskar H, Pfefferle A, Goodridge JP, Sohlberg E, Dufva O, Teichmann SA, Brownlie D, Michaëlsson J, Marquardt N, Clancy T, Horowitz A, Malmberg KJ. Pan-cancer profiling of tumor-infiltrating natural killer cells through transcriptional reference mapping. Nat Immunol 2024; 25:1445-1459. [PMID: 38956379 PMCID: PMC11291284 DOI: 10.1038/s41590-024-01884-z] [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: 10/25/2023] [Accepted: 05/30/2024] [Indexed: 07/04/2024]
Abstract
The functional diversity of natural killer (NK) cell repertoires stems from differentiation, homeostatic, receptor-ligand interactions and adaptive-like responses to viral infections. In the present study, we generated a single-cell transcriptional reference map of healthy human blood- and tissue-derived NK cells, with temporal resolution and fate-specific expression of gene-regulatory networks defining NK cell differentiation. Transfer learning facilitated incorporation of tumor-infiltrating NK cell transcriptomes (39 datasets, 7 solid tumors, 427 patients) into the reference map to analyze tumor microenvironment (TME)-induced perturbations. Of the six functionally distinct NK cell states identified, a dysfunctional stressed CD56bright state susceptible to TME-induced immunosuppression and a cytotoxic TME-resistant effector CD56dim state were commonly enriched across tumor types, the ratio of which was predictive of patient outcome in malignant melanoma and osteosarcoma. This resource may inform the design of new NK cell therapies and can be extended through transfer learning to interrogate new datasets from experimental perturbations or disease conditions.
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Affiliation(s)
- Herman Netskar
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Precision Immunotherapy Alliance, University of Oslo, Oslo, Norway
| | - Aline Pfefferle
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.
| | | | - Ebba Sohlberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Olli Dufva
- Wellcome Sanger Institute, Wellcome Genome Clymphoid cells (ILCs)ampus, Hinxton, Cambridge, UK
| | - Sarah A Teichmann
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Demi Brownlie
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Huddinge, Sweden
| | - Jakob Michaëlsson
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Nicole Marquardt
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Huddinge, Sweden
| | - Trevor Clancy
- Oslo Cancer Cluster, NEC OncoImmunity AS, Oslo, Norway
- Department of Vaccine Informatics, Institute for Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Amir Horowitz
- Department of Immunology & Immunotherapy, Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Karl-Johan Malmberg
- Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
- Precision Immunotherapy Alliance, University of Oslo, Oslo, Norway.
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.
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8
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Ran R, Trapecar M, Brubaker DK. Systematic Analysis of Human Colorectal Cancer scRNA-seq Revealed Limited Pro-tumoral IL-17 Production Potential in Gamma Delta T Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.18.604156. [PMID: 39071278 PMCID: PMC11275756 DOI: 10.1101/2024.07.18.604156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Gamma delta (γδ) T cells play a crucial role in anti-tumor immunity due to their cytotoxic properties. However, the role and extent of γδ T cells in production of pro-tumorigenic interleukin- 17 (IL-17) within the tumor microenvironment (TME) of colorectal cancer (CRC) remains controversial. In this study, we re-analyzed nine published human CRC whole-tissue single-cell RNA sequencing (scRNA-seq) datasets, identifying 18,483 γδ T cells out of 951,785 total cells, in the neoplastic or adjacent normal tissue of 165 human CRC patients. Our results confirm that tumor-infiltrating γδ T cells exhibit high cytotoxicity-related transcription in both tumor and adjacent normal tissues, but critically, none of the γδ T cell clusters showed IL-17 production potential. We also identified various γδ T cell subsets, including Teff, TRM, Tpex, and Tex, and noted an increased expression of cytotoxic molecules in tumor-infiltrating γδ T cells compared to their normal area counterparts. Our work demonstrates that γδ T cells in CRC primarily function as cytotoxic effector cells rather than IL-17 producers, mitigating the concerns about their potential pro-tumorigenic roles in CRC, highlighting the importance of accurately characterizing these cells for cancer immunotherapy research and the unneglectable cross-species discrepancy between the mouse and human immune system in the study of cancer immunology.
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Affiliation(s)
- Ran Ran
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH
| | - Martin Trapecar
- Department of Medicine, Johns Hopkins University School of Medicine, Institute for Fundamental Biomedical Research, Johns Hopkins All Children’s Hospital, St. Petersburg, FL, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Douglas K. Brubaker
- Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH
- The Blood, Heart, Lung, and Immunology Research Center, Case Western Reserve University, University Hospitals of Cleveland, Cleveland, OH
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9
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Qin M, Fang Y, Zheng Q, Peng M, Wang L, Sang X, Cao G. Tissue microenvironment induces tissue specificity of ILC2. Cell Death Discov 2024; 10:324. [PMID: 39013890 PMCID: PMC11252336 DOI: 10.1038/s41420-024-02096-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 07/04/2024] [Accepted: 07/09/2024] [Indexed: 07/18/2024] Open
Abstract
Type 2 innate lymphoid cells were found to be members of the innate immune cell family, which is involved in innate and adaptive immunity to resist the invasion of foreign antigens and induce allergic reactions caused by allergens. The advancement of ILC2 research has pointed out that ILC2s have a high degree of diversity, challenging the notion of their homogeneity as a cellular population. An increasing number of studies indicate that ILC2 is a cell population with tissue specificity which can be induced by the tissue microenvironment. In addition, crosstalk between tissues can change ILC2 functions of migration and activation. Here, we emphasize that ILC2 undergoes adaptive changes under the regulation of the tissue microenvironment and distant tissues, thereby coordinating the organization's operation. In addition, ILC2 alterations induced by the tissue microenvironment are not limited to the ILC2 cell population, and ILC2 can also transdifferentiate into another class of ILC cell population (ILC1 or ILC3). In this review, we summarized the tissue-specific effects of ILC2 by tissue microenvironment and focused on the function of ILC2 in inter-tissue crosstalk. Lastly, we discussed the transdifferentiations of ILC2 caused by the abnormal change in tissue environment.
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Affiliation(s)
- Minjing Qin
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yuanyuan Fang
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qitong Zheng
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, China
| | - Mengyun Peng
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, China
| | - Lu Wang
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xia'nan Sang
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, China.
| | - Gang Cao
- School of Pharmacy, Zhejiang Chinese Medical University, Hangzhou, China.
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García M, Carrasco García A, Weigel W, Christ W, Lira-Junior R, Wirth L, Tauriainen J, Maleki K, Vanoni G, Vaheri A, Mäkelä S, Mustonen J, Nordgren J, Smed-Sörensen A, Strandin T, Mjösberg J, Klingström J. Innate lymphoid cells are activated in HFRS, and their function can be modulated by hantavirus-induced type I interferons. PLoS Pathog 2024; 20:e1012390. [PMID: 39038044 PMCID: PMC11293681 DOI: 10.1371/journal.ppat.1012390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 08/01/2024] [Accepted: 07/03/2024] [Indexed: 07/24/2024] Open
Abstract
Hantaviruses cause the acute zoonotic diseases hemorrhagic fever with renal syndrome (HFRS) and hantavirus pulmonary syndrome (HPS). Infected patients show strong systemic inflammation and immune cell activation. NK cells are highly activated in HFRS, suggesting that also other innate lymphoid cells (ILCs) might be responding to infection. Here, we characterized peripheral ILC responses, and measured plasma levels of soluble factors and plasma viral load, in 17 Puumala virus (PUUV)-infected HFRS patients. This revealed an increased frequency of ILC2 in patients, in particular the ILC2 lineage-committed c-Kitlo ILC2 subset. Patients' ILCs showed an activated profile with increased proliferation and displayed altered expression of several homing markers. How ILCs are activated during viral infection is largely unknown. When analyzing PUUV-mediated activation of ILCs in vitro we observed that this was dependent on type I interferons, suggesting a role for type I interferons-produced in response to virus infection-in the activation of ILCs. Further, stimulation of naïve ILC2s with IFN-β affected ILC2 cytokine responses in vitro, causing decreased IL-5 and IL-13, and increased IL-10, CXCL10, and GM-CSF secretion. These results show that ILCs are activated in HFRS patients and suggest that the classical antiviral type I IFNs are involved in shaping ILC functions.
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Affiliation(s)
- Marina García
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Anna Carrasco García
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Whitney Weigel
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Wanda Christ
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Ronaldo Lira-Junior
- Section of Oral Diagnostics and Surgery, Division of Oral Diagnostics and Rehabilitation, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Lorenz Wirth
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- Mechanistic & Structural Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg, Sweden
| | - Johanna Tauriainen
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Kimia Maleki
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Giulia Vanoni
- Institut Curie, PSL University, Inserm, Immunity and Cancer, Paris, France
| | - Antti Vaheri
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Satu Mäkelä
- Department of Internal Medicine, Tampere University Hospital, Tampere, Finland
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Jukka Mustonen
- Department of Internal Medicine, Tampere University Hospital, Tampere, Finland
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Johan Nordgren
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Anna Smed-Sörensen
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Tomas Strandin
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Jenny Mjösberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Jonas Klingström
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
- Division of Molecular Medicine and Virology, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
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11
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Qin X, Lu J, Wu P, Zhang C, Shi L, Zhu P. Charting epimutation dynamics in human hematopoietic differentiation. BLOOD SCIENCE 2024; 6:e00197. [PMID: 38872911 PMCID: PMC11175913 DOI: 10.1097/bs9.0000000000000197] [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: 03/31/2024] [Accepted: 05/26/2024] [Indexed: 06/15/2024] Open
Abstract
DNA methylation plays a critical role in hematopoietic differentiation. Epimutation is a stochastic variation in DNA methylation that induces epigenetic heterogeneity. However, the effects of epimutations on normal hematopoiesis and hematopoietic diseases remain unclear. In this study, we developed a Julia package called EpiMut that enabled rapid and accurate quantification of epimutations. EpiMut was used to evaluate and provide an epimutation landscape in steady-state hematopoietic differentiation involving 13 types of blood cells ranging from hematopoietic stem/progenitor cells to mature cells. We showed that substantial genomic regions exhibited epigenetic variations rather than significant differences in DNA methylation levels between the myeloid and lymphoid lineages. Stepwise dynamics of epimutations were observed during the differentiation of each lineage. Importantly, we found that epimutation significantly enriched signals associated with lineage differentiation. Furthermore, epimutations in hematopoietic stem cells (HSCs) derived from various sources and acute myeloid leukemia were related to the function of HSCs and malignant cell disorders. Taken together, our study comprehensively documented an epimutation map and uncovered its important roles in human hematopoiesis, thereby offering insights into hematopoietic regulation.
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Affiliation(s)
- Xiaohuan Qin
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Department of Stem Cell and Regenerative Medicine, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Jiayi Lu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Department of Stem Cell and Regenerative Medicine, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Peng Wu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Department of Stem Cell and Regenerative Medicine, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Chunyong Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Department of Stem Cell and Regenerative Medicine, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Lei Shi
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Ping Zhu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Department of Stem Cell and Regenerative Medicine, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
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12
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Huang YA, Wang X, Kim JC, Yao X, Sethi A, Strohm A, Doherty TA. PIP-Seq identifies novel heterogeneous lung innate lymphocyte population activation after combustion product exposure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.24.600420. [PMID: 38979234 PMCID: PMC11230265 DOI: 10.1101/2024.06.24.600420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Innate lymphoid cells (ILCs) are a heterogeneous population that play diverse roles in airway inflammation after exposure to allergens and infections. However, how ILCs respond after exposure to environmental toxins is not well understood. Here we show a novel method for studying the heterogeneity of rare lung ILC populations by magnetic enrichment for lung ILCs followed by particle-templated instant partition sequencing (PIP-seq). Using this method, we were able to identify novel group 1 and group 2 ILC subsets that exist after exposure to both fungal allergen and burn pit-related constituents (BPC) that include dioxin, aromatic hydrocarbon, and particulate matter. Toxin exposure in combination with fungal allergen induced activation of specific ILC1/NK and ILC2 populations as well as promoted neutrophilic lung inflammation. Oxidative stress pathways and downregulation of specific ribosomal protein genes ( Rpl41 and Rps19 ) implicated in anti-inflammatory responses were present after BPC exposure. Increased IFNγ expression and other pro-neutrophilic mediator transcripts were increased in BPC-stimulated lung innate lymphoid cells. Further, the addition of BPC induced Hspa8 (encodes HSC70) and aryl hydrocarbon transcription factor activity across multiple lung ILC subsets. Overall, using an airway disease model that develops after occupational and environmental exposures, we demonstrate an effective method to better understand heterogenous ILC subset activation.
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13
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Hashemi E, McCarthy C, Rao S, Malarkannan S. Transcriptomic diversity of innate lymphoid cells in human lymph nodes compared to BM and spleen. Commun Biol 2024; 7:769. [PMID: 38918571 PMCID: PMC11199704 DOI: 10.1038/s42003-024-06450-9] [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: 10/27/2023] [Accepted: 06/12/2024] [Indexed: 06/27/2024] Open
Abstract
Innate lymphoid cells (ILCs) are largely tissue-resident, mostly described within the mucosal tissues. However, their presence and functions in the human draining lymph nodes (LNs) are unknown. Our study unravels the tissue-specific transcriptional profiles of 47,287 CD127+ ILCs within the human abdominal and thoracic LNs. LNs contain a higher frequency of CD127+ ILCs than in BM or spleen. We define independent stages of ILC development, including EILP and pILC in the BM. These progenitors exist in LNs in addition to naïve ILCs (nILCs) that can differentiate into mature ILCs. We define three ILC1 and four ILC3 sub-clusters in the LNs. ILC1 and ILC3 subsets have clusters with high heat shock protein-encoding genes. We identify previously unrecognized regulons, including the BACH2 family for ILC1 and the ATF family for ILC3. Our study is the comprehensive characterization of ILCs in LNs, providing an in-depth understanding of ILC-mediated immunity in humans.
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Affiliation(s)
- Elaheh Hashemi
- Blood Research Institute, Versiti, Milwaukee, WI, USA
- Department of Microbiology and Immunology, Medical College of Wisconsin (MCW), Milwaukee, WI, USA
| | | | - Sridhar Rao
- Blood Research Institute, Versiti, Milwaukee, WI, USA
- Division of Hematology, Oncology, and Bone Marrow Transplantation, Department of Pediatrics, MCW, Milwaukee, WI, USA
- Department of Cell Biology, Neurobiology, and Anatomy, MCW, Milwaukee, WI, USA
| | - Subramaniam Malarkannan
- Blood Research Institute, Versiti, Milwaukee, WI, USA.
- Department of Microbiology and Immunology, Medical College of Wisconsin (MCW), Milwaukee, WI, USA.
- Division of Hematology, Oncology, and Bone Marrow Transplantation, Department of Pediatrics, MCW, Milwaukee, WI, USA.
- Division of Hematology and Oncology, Department of Medicine, MCW, Milwaukee, WI, USA.
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14
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Wang L, Izadmehr S, Sfakianos JP, Tran M, Beaumont KG, Brody R, Cordon-Cardo C, Horowitz A, Sebra R, Oh WK, Bhardwaj N, Galsky MD, Zhu J. Single-cell transcriptomic-informed deconvolution of bulk data identifies immune checkpoint blockade resistance in urothelial cancer. iScience 2024; 27:109928. [PMID: 38812546 PMCID: PMC11133924 DOI: 10.1016/j.isci.2024.109928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 11/23/2023] [Accepted: 05/03/2024] [Indexed: 05/31/2024] Open
Abstract
Interactions within the tumor microenvironment (TME) significantly influence tumor progression and treatment responses. While single-cell RNA sequencing (scRNA-seq) and spatial genomics facilitate TME exploration, many clinical cohorts are assessed at the bulk tissue level. Integrating scRNA-seq and bulk tissue RNA-seq data through computational deconvolution is essential for obtaining clinically relevant insights. Our method, ProM, enables the examination of major and minor cell types. Through evaluation against existing methods using paired single-cell and bulk RNA sequencing of human urothelial cancer (UC) samples, ProM demonstrates superiority. Application to UC cohorts treated with immune checkpoint inhibitors reveals pre-treatment cellular features associated with poor outcomes, such as elevated SPP1 expression in macrophage/monocytes (MM). Our deconvolution method and paired single-cell and bulk tissue RNA-seq dataset contribute novel insights into TME heterogeneity and resistance to immune checkpoint blockade.
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Affiliation(s)
- Li Wang
- Department of Precision Medicine, Aitia, Somerville, MA 02143, USA
- Department of Medicine, Division of Hematology Oncology, Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, New York, NY 10029, USA
| | - Sudeh Izadmehr
- Department of Medicine, Division of Hematology Oncology, Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, New York, NY 10029, USA
| | - John P. Sfakianos
- Department of Urology; Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michelle Tran
- Department of Medicine, Division of Hematology Oncology, Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, New York, NY 10029, USA
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Kristin G. Beaumont
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rachel Brody
- Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carlos Cordon-Cardo
- Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Amir Horowitz
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - William K. Oh
- Department of Medicine, Division of Hematology Oncology, Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, New York, NY 10029, USA
| | - Nina Bhardwaj
- Department of Medicine, Division of Hematology Oncology, Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, New York, NY 10029, USA
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Matthew D. Galsky
- Department of Medicine, Division of Hematology Oncology, Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, New York, NY 10029, USA
| | - Jun Zhu
- Department of Medicine, Division of Hematology Oncology, Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, New York, NY 10029, USA
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15
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Horn V, Sonnenberg GF. Group 3 innate lymphoid cells in intestinal health and disease. Nat Rev Gastroenterol Hepatol 2024; 21:428-443. [PMID: 38467885 PMCID: PMC11144103 DOI: 10.1038/s41575-024-00906-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/05/2024] [Indexed: 03/13/2024]
Abstract
The gastrointestinal tract is an immunologically rich organ, containing complex cell networks and dense lymphoid structures that safeguard this large absorptive barrier from pathogens, contribute to tissue physiology and support mucosal healing. Simultaneously, the immune system must remain tolerant to innocuous dietary antigens and trillions of normally beneficial microorganisms colonizing the intestine. Indeed, a dysfunctional immune response in the intestine underlies the pathogenesis of numerous local and systemic diseases, including inflammatory bowel disease, food allergy, chronic enteric infections or cancers. Here, we discuss group 3 innate lymphoid cells (ILC3s), which have emerged as orchestrators of tissue physiology, immunity, inflammation, tolerance and malignancy in the gastrointestinal tract. ILC3s are abundant in the developing and healthy intestine but their numbers or function are altered during chronic disease and cancer. The latest studies provide new insights into the mechanisms by which ILC3s fundamentally shape intestinal homeostasis or disease pathophysiology, and often this functional dichotomy depends on context and complex interactions with other cell types or microorganisms. Finally, we consider how this knowledge could be harnessed to improve current treatments or provoke new opportunities for therapeutic intervention to promote gut health.
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Affiliation(s)
- Veronika Horn
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Joan and Sanford I. Weill Department of Medicine, Division of Gastroenterology & Hepatology, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Department of Microbiology & Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Gregory F Sonnenberg
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA.
- Joan and Sanford I. Weill Department of Medicine, Division of Gastroenterology & Hepatology, Weill Cornell Medicine, Cornell University, New York, NY, USA.
- Department of Microbiology & Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA.
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16
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Lahire S, Fichel C, Rubaszewski O, Lerévérend C, Audonnet S, Visneux V, Perotin JM, Deslée G, Le Jan S, Potteaux S, Le Naour R, Pommier A. Elastin-derived peptides favor type 2 innate lymphoid cells in chronic obstructive pulmonary disease. Am J Physiol Lung Cell Mol Physiol 2024; 326:L812-L820. [PMID: 38712445 DOI: 10.1152/ajplung.00306.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 03/22/2024] [Accepted: 04/22/2024] [Indexed: 05/08/2024] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a condition characterized by chronic airway inflammation and obstruction, primarily caused by tobacco smoking. Although the involvement of immune cells in COPD pathogenesis is well established, the contribution of innate lymphoid cells (ILCs) remains poorly understood. ILCs are a type of innate immune cells that participate in tissue remodeling processes, but their specific role in COPD has not been fully elucidated. During COPD, the breakdown of pulmonary elastin generates elastin peptides that elicit biological activities on immune cells. This study aimed to investigate the presence of ILC in patients with COPD and examine the impact of elastin peptides on their functionality. Our findings revealed an elevated proportion of ILC2 in the peripheral blood of patients with COPD, and a general activation of ILC as indicated by an increase in their cytokine secretion capacity. Notably, our study demonstrated that serum from patients with COPD promotes ILC2 phenotype, likely due to the elevated concentration of IL-5, a cytokine known to favor ILC2 activation. Furthermore, we uncovered that this increase in IL-5 secretion is partially attributed to its secretion by macrophages upon stimulation by elastin peptides, suggesting an indirect role of elastin peptides on ILC in COPD. These findings shed light on the involvement of ILC in COPD and provide insights into the potential interplay between elastin breakdown, immune cells, and disease progression. Further understanding of the mechanisms underlying ILC activation and their interaction with elastin peptides could contribute to the development of novel therapeutic strategies for COPD management.NEW & NOTEWORTHY Elastin-derived peptides, generated following alveolar degradation during emphysema in patients with COPD, are able to influence the response of type 2 innate lymphoid cells. We show that the orientation of innate lymphoid cells in patients with COPD is shifted toward a type 2 profile and that elastin peptides are indirectly participating in that shift through their influence of macrophages, which in turn impact innate lymphoid cells.
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Affiliation(s)
- Sarah Lahire
- Université de Reims Champagne Ardenne, Immuno-Régulation dans les Maladies Auto-Immunes, Inflammatoires et le Cancer (IRMAIC), Reims, France
| | - Caroline Fichel
- Université de Reims Champagne Ardenne, Immuno-Régulation dans les Maladies Auto-Immunes, Inflammatoires et le Cancer (IRMAIC), Reims, France
| | - Océane Rubaszewski
- Université de Reims Champagne Ardenne, Immuno-Régulation dans les Maladies Auto-Immunes, Inflammatoires et le Cancer (IRMAIC), Reims, France
| | - Cédric Lerévérend
- Université de Reims Champagne Ardenne, Immuno-Régulation dans les Maladies Auto-Immunes, Inflammatoires et le Cancer (IRMAIC), Reims, France
- Institut Godinot, Unicancer, Reims, France
| | - Sandra Audonnet
- Université de Reims Champagne Ardenne, Plateforme de cytométrie en flux, URCACyt, Reims, France
| | - Vincent Visneux
- CHU de Reims, Service des maladies respiratoires, Reims, France
| | - Jeanne-Marie Perotin
- CHU de Reims, Service des maladies respiratoires, Reims, France
- Université de Reims Champagne Ardenne, Inserm UMR-S 1250 Pathologies Pulmonaires et Plasticité Cellulaire (P3Cell), Reims, France
| | - Gaëtan Deslée
- CHU de Reims, Service des maladies respiratoires, Reims, France
- Université de Reims Champagne Ardenne, Inserm UMR-S 1250 Pathologies Pulmonaires et Plasticité Cellulaire (P3Cell), Reims, France
| | - Sébastien Le Jan
- Université de Reims Champagne Ardenne, Immuno-Régulation dans les Maladies Auto-Immunes, Inflammatoires et le Cancer (IRMAIC), Reims, France
| | - Stéphane Potteaux
- Université de Reims Champagne Ardenne, Immuno-Régulation dans les Maladies Auto-Immunes, Inflammatoires et le Cancer (IRMAIC), Reims, France
- Institut Godinot, Unicancer, Reims, France
- Délégation régionale Inserm Paris Ile-de France Centre Nord, Paris, France
| | - Richard Le Naour
- Université de Reims Champagne Ardenne, Immuno-Régulation dans les Maladies Auto-Immunes, Inflammatoires et le Cancer (IRMAIC), Reims, France
| | - Arnaud Pommier
- Université de Reims Champagne Ardenne, Immuno-Régulation dans les Maladies Auto-Immunes, Inflammatoires et le Cancer (IRMAIC), Reims, France
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17
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Castro Dopico X, Guryleva M, Mandolesi M, Corcoran M, Coquet JM, Murrell B, Karlsson Hedestam GB. Maintenance of caecal homeostasis by diverse adaptive immune cells in the rhesus macaque. Clin Transl Immunology 2024; 13:e1508. [PMID: 38707998 PMCID: PMC11063928 DOI: 10.1002/cti2.1508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 03/04/2024] [Accepted: 04/15/2024] [Indexed: 05/07/2024] Open
Abstract
Objectives The caecum bridges the small and large intestine and plays a front-line role in discriminating gastrointestinal antigens. Although dysregulated in acute and chronic conditions, the tissue is often overlooked immunologically. Methods To address this issue, we applied single-cell transcriptomic-V(D)J sequencing to FACS-isolated CD45+ caecal patch/lamina propria leukocytes from a healthy (5-year-old) female rhesus macaque ex vivo and coupled these data to VDJ deep sequencing reads from haematopoietic tissues. Results We found caecal NK cells and ILC3s to co-exist with a spectrum of effector T cells partially derived from SOX4 + recent thymic emigrants. Tolerogenic Vγ8Vδ1-T cells, plastic CD4+ T helper cells and GZMK + EOMES + and TMIGD2 + tissue-resident memory CD8+ T cells were present and differed metabolically. An IL13 + GATA3 + Th2 subset expressing eicosanoid pathway enzymes was accompanied by IL1RL1 + GATA3 + regulatory T cells and a minor proportion of IgE+ plasma cells (PCs), illustrating tightly regulated type 2 immunity devoid of ILC2s. In terms of B lymphocyte lineages, caecal patch antigen-presenting memory B cells sat alongside germinal centre cells undergoing somatic hypermutation and differentiation into IGF1 + PCs. Prototypic gene expression signatures decreased across PC clusters, and notably, expanded IgA clonotypes could be traced in VDJ deep sequencing reads from additional compartments, including the bone marrow, supporting that these cells contribute a steady stream of systemic antibodies. Conclusions The data advance our understanding of caecal immunological function, revealing processes involved in barrier maintenance and molecular networks relevant to disease.
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Affiliation(s)
- Xaquin Castro Dopico
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden
| | - Mariia Guryleva
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden
| | - Marco Mandolesi
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden
| | - Martin Corcoran
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden
| | - Jonathan M Coquet
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden
- Department of Immunology and MicrobiologyUniversity of CopenhagenCopenhagenDKDenmark
| | - Ben Murrell
- Department of Microbiology, Tumor and Cell BiologyKarolinska InstitutetStockholmSweden
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18
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Rückert T, Romagnani C. Extrinsic and intrinsic drivers of natural killer cell clonality. Immunol Rev 2024; 323:80-106. [PMID: 38506411 DOI: 10.1111/imr.13324] [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] [Indexed: 03/21/2024]
Abstract
Clonal expansion of antigen-specific lymphocytes is the fundamental mechanism enabling potent adaptive immune responses and the generation of immune memory. Accompanied by pronounced epigenetic remodeling, the massive proliferation of individual cells generates a critical mass of effectors for the control of acute infections, as well as a pool of memory cells protecting against future pathogen encounters. Classically associated with the adaptive immune system, recent work has demonstrated that innate immune memory to human cytomegalovirus (CMV) infection is stably maintained as large clonal expansions of natural killer (NK) cells, raising questions on the mechanisms for clonal selection and expansion in the absence of re-arranged antigen receptors. Here, we discuss clonal NK cell memory in the context of the mechanisms underlying clonal competition of adaptive lymphocytes and propose alternative selection mechanisms that might decide on the clonal success of their innate counterparts. We propose that the integration of external cues with cell-intrinsic sources of heterogeneity, such as variegated receptor expression, transcriptional states, and somatic variants, compose a bottleneck for clonal selection, contributing to the large size of memory NK cell clones.
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Affiliation(s)
- Timo Rückert
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Immunology, Berlin, Germany
| | - Chiara Romagnani
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Immunology, Berlin, Germany
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19
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Lu HF, Zhou YC, Luo DD, Yang DH, Wang XJ, Cheng BH, Zeng XH. ILC2s: Unraveling the innate immune orchestrators in allergic inflammation. Int Immunopharmacol 2024; 131:111899. [PMID: 38513576 DOI: 10.1016/j.intimp.2024.111899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 03/05/2024] [Accepted: 03/17/2024] [Indexed: 03/23/2024]
Abstract
The prevalence rate of allergic diseases including asthma, atopic rhinitis (AR) and atopic dermatitis (AD) has been significantly increasing in recent decades due to environmental changes and social developments. With the study of innate lymphoid cells, the crucial role played by type 2 innate lymphoid cells (ILC2s) have been progressively unveiled in allergic diseases. ILC2s, which are a subset of innate lymphocytes initiate allergic responses. They respond swiftly during the onset of allergic reactions and produce type 2 cytokines, working in conjunction with T helper type 2 (Th2) cells to induce and sustain type 2 immune responses. The role of ILC2s represents an intriguing frontier in immunology; however, the intricate immune mechanisms of ILC2s in allergic responses remain relatively poorly understood. To gain a comphrehensive understanding of the research progress of ILC2, we summarize recent advances in ILC2s biology in pathologic allergic inflammation to inspire novel approaches for managing allergic diseases.
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Affiliation(s)
- Hui-Fei Lu
- Department of Graduate and Scientific Research, Zhuhai Campus of Zunyi Medical University, Zhuhai 519041, China; Department of Otolaryngology, Shenzhen Key Laboratory of Otolaryngology, Shenzhen Institute of Otolaryngology, Shenzhen Longgang Otolaryngology Hospital, Shenzhen, 518172, China
| | - Yi-Chi Zhou
- Department of Gastroenterology, Beijing University of Chinese Medicine Shenzhen Hospital (Longgang), Shenzhen 518172, China
| | - Dan-Dan Luo
- Department of Graduate and Scientific Research, Zhuhai Campus of Zunyi Medical University, Zhuhai 519041, China
| | - Dun-Hui Yang
- Department of Otolaryngology, Shenzhen Key Laboratory of Otolaryngology, Shenzhen Institute of Otolaryngology, Shenzhen Longgang Otolaryngology Hospital, Shenzhen, 518172, China
| | - Xi-Jia Wang
- Department of Graduate and Scientific Research, Zhuhai Campus of Zunyi Medical University, Zhuhai 519041, China
| | - Bao-Hui Cheng
- Department of Otolaryngology, Shenzhen Key Laboratory of Otolaryngology, Shenzhen Institute of Otolaryngology, Shenzhen Longgang Otolaryngology Hospital, Shenzhen, 518172, China.
| | - Xian-Hai Zeng
- Department of Graduate and Scientific Research, Zhuhai Campus of Zunyi Medical University, Zhuhai 519041, China; Department of Otolaryngology, Shenzhen Key Laboratory of Otolaryngology, Shenzhen Institute of Otolaryngology, Shenzhen Longgang Otolaryngology Hospital, Shenzhen, 518172, China.
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20
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Ding J, Garber JJ, Uchida A, Lefkovith A, Carter GT, Vimalathas P, Canha L, Dougan M, Staller K, Yarze J, Delorey TM, Rozenblatt-Rosen O, Ashenberg O, Graham DB, Deguine J, Regev A, Xavier RJ. An esophagus cell atlas reveals dynamic rewiring during active eosinophilic esophagitis and remission. Nat Commun 2024; 15:3344. [PMID: 38637492 PMCID: PMC11026436 DOI: 10.1038/s41467-024-47647-0] [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: 09/08/2023] [Accepted: 04/09/2024] [Indexed: 04/20/2024] Open
Abstract
Coordinated cell interactions within the esophagus maintain homeostasis, and disruption can lead to eosinophilic esophagitis (EoE), a chronic inflammatory disease with poorly understood pathogenesis. We profile 421,312 individual cells from the esophageal mucosa of 7 healthy and 15 EoE participants, revealing 60 cell subsets and functional alterations in cell states, compositions, and interactions that highlight previously unclear features of EoE. Active disease displays enrichment of ALOX15+ macrophages, PRDM16+ dendritic cells expressing the EoE risk gene ATP10A, and cycling mast cells, with concomitant reduction of TH17 cells. Ligand-receptor expression uncovers eosinophil recruitment programs, increased fibroblast interactions in disease, and IL-9+IL-4+IL-13+ TH2 and endothelial cells as potential mast cell interactors. Resolution of inflammation-associated signatures includes mast and CD4+ TRM cell contraction and cell type-specific downregulation of eosinophil chemoattractant, growth, and survival factors. These cellular alterations in EoE and remission advance our understanding of eosinophilic inflammation and opportunities for therapeutic intervention.
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Affiliation(s)
- Jiarui Ding
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Computer Science, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - John J Garber
- Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.
- Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.
| | - Amiko Uchida
- Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Ariel Lefkovith
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Grace T Carter
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Praveen Vimalathas
- Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
- Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Lauren Canha
- Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Michael Dougan
- Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Kyle Staller
- Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Joseph Yarze
- Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Toni M Delorey
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Orit Rozenblatt-Rosen
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Genentech, South San Francisco, CA, 94080, USA
| | - Orr Ashenberg
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Daniel B Graham
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Jacques Deguine
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA.
- Genentech, South San Francisco, CA, 94080, USA.
| | - Ramnik J Xavier
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.
- Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA.
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21
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Stamper CT, Marchalot A, Tibbitt CA, Weigel W, Jangard M, Theorell J, Mjösberg J. Single-cell RNA sequencing of cells from fresh or frozen tissue reveals a signature of freezing marked by heightened stress and activation. Eur J Immunol 2024; 54:e2350660. [PMID: 38304946 DOI: 10.1002/eji.202350660] [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: 07/10/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 02/03/2024]
Abstract
Thawing of viably frozen human tissue T cells, ILCs, and NK cells and subsequent single-cell RNA sequencing reveals that recovery of cellular subclusters is variably impacted. While freeze-thawing does not alter the transcriptional profiles of cells, it upregulates genes and gene pathways associated with stress and activation.
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Affiliation(s)
- Christopher T Stamper
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Anne Marchalot
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Christopher A Tibbitt
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
- Clinical Lung and Allergy Research Unit, Medical Unit for Lung and Allergy Diseases, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Whitney Weigel
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Mattias Jangard
- ENT Unit, Sophiahemmet University Research Laboratory and Sophiahemmet Hospital, Stockholm, Sweden
| | - Jakob Theorell
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, Stockholm, Sweden
| | - Jenny Mjösberg
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
- Clinical Lung and Allergy Research Unit, Medical Unit for Lung and Allergy Diseases, Karolinska University Hospital Huddinge, Stockholm, Sweden
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22
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Padilla CM, Valenzi E, Tabib T, Nazari B, Sembrat J, Rojas M, Fuschiotti P, Lafyatis R. Increased CD8+ tissue resident memory T cells, regulatory T cells and activated natural killer cells in systemic sclerosis lungs. Rheumatology (Oxford) 2024; 63:837-845. [PMID: 37310903 PMCID: PMC10907815 DOI: 10.1093/rheumatology/kead273] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 06/15/2023] Open
Abstract
OBJECTIVE Multiple observations indicate a role for lymphocytes in driving autoimmunity in SSc. While T and NK cells have been studied in SSc whole blood and bronchoalveolar lavage fluid, their role remains unclear, partly because no studies have analysed these cell types in SSc-interstitial lung disease (ILD) lung tissue. This research aimed to identify and analyse the lymphoid subpopulations in SSc-ILD lung explants. METHODS Lymphoid populations from 13 SSc-ILD and 6 healthy control (HC) lung explants were analysed using Seurat following single-cell RNA sequencing. Lymphoid clusters were identified by their differential gene expression. Absolute cell numbers and cell proportions in each cluster were compared between cohorts. Additional analyses were performed using pathway analysis, pseudotime and cell ligand-receptor interactions. RESULTS Activated CD16+ NK cells, CD8+ tissue resident memory T cells and Treg cells were proportionately higher in SSc-ILD compared with HC lungs. Activated CD16+ NK cells in SSc-ILD showed upregulated granzyme B, IFN-γ and CD226. Amphiregulin, highly upregulated by NK cells, was predicted to interact with epidermal growth factor receptor on several bronchial epithelial cell populations. Shifts in CD8+ T cell populations indicated a transition from resting to effector to tissue resident phenotypes in SSc-ILD. CONCLUSIONS SSc-ILD lungs show activated lymphoid populations. Activated cytotoxic NK cells suggest they may kill alveolar epithelial cells, while their expression of amphiregulin suggests they may also induce bronchial epithelial cell hyperplasia. CD8+ T cells in SSc-ILD appear to transition from resting to the tissue resident memory phenotype.
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Affiliation(s)
- Cristina M Padilla
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Eleanor Valenzi
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Banafsheh Nazari
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - John Sembrat
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Mauricio Rojas
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Ohio State University College of Medicine, Columbus, OH, USA
| | - Patrizia Fuschiotti
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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23
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Teunissen MBM, Pilgaard Møller LB, Løvendorf MB, Skov L, Bonefeld CM, Bekkenk MW, Clark RA, Mann M, Dyring-Andersen B. In-Depth Proteomic Map of Innate Lymphoid Cells from Healthy Human Skin and Blood. J Invest Dermatol 2024; 144:316-330.e3. [PMID: 37544588 DOI: 10.1016/j.jid.2023.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/23/2023] [Accepted: 07/14/2023] [Indexed: 08/08/2023]
Abstract
Innate lymphoid cells (ILCs) are essential players in the skin-associated immune system, nevertheless little is known about their proteomes and proteomic diversity. In this study, we describe about 6,600 proteins constitutively expressed by ILC2s and ILC3s from healthy human skin and blood using state-of-the-art proteomics. Although the vast majority of proteins was expressed by both ILC subsets and in both compartments, the skin ILC2s and ILC3s were more distinct than their counterparts in blood. Only skin ILC3s expressed uniquely detected proteins. Our in-depth proteomic dataset allowed us to define the cluster of differentiation marker profiles of the ILC subsets, explore distribution and abundance of proteins known to have immunological functions, as well as identify subset-specific proteins that have not previously been implicated in ILC biology. Taken together, our analyses substantially expand understanding of the protein expression signatures of ILC subsets. Going forward, these proteomic datasets will serve as valuable resources for future studies of ILC biology.
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Affiliation(s)
- Marcel B M Teunissen
- Department of Dermatology and Amsterdam institute for Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, The Netherlands.
| | - Line B Pilgaard Møller
- Novo Nordisk Foundation (NNF) Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marianne B Løvendorf
- Department of Dermatology and Allergy, Copenhagen University Hospital - Herlev and Gentofte Hospital, Hellerup, Denmark; The Leo Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lone Skov
- Department of Dermatology and Allergy, Copenhagen University Hospital - Herlev and Gentofte Hospital, Hellerup, Denmark
| | - Charlotte M Bonefeld
- The Leo Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marcel W Bekkenk
- Department of Dermatology and Amsterdam institute for Infection and Immunity, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Rachael A Clark
- Department of Dermatology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Matthias Mann
- Novo Nordisk Foundation (NNF) Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Beatrice Dyring-Andersen
- Novo Nordisk Foundation (NNF) Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Dermatology and Allergy, Copenhagen University Hospital - Herlev and Gentofte Hospital, Hellerup, Denmark; The Leo Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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24
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Li Z, Ma R, Tang H, Guo J, Shah Z, Zhang J, Liu N, Cao S, Marcucci G, Artis D, Caligiuri MA, Yu J. Therapeutic application of human type 2 innate lymphoid cells via induction of granzyme B-mediated tumor cell death. Cell 2024; 187:624-641.e23. [PMID: 38211590 DOI: 10.1016/j.cell.2023.12.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 09/18/2023] [Accepted: 12/07/2023] [Indexed: 01/13/2024]
Abstract
The therapeutic potential for human type 2 innate lymphoid cells (ILC2s) has been underexplored. Although not observed in mouse ILC2s, we found that human ILC2s secrete granzyme B (GZMB) and directly lyse tumor cells by inducing pyroptosis and/or apoptosis, which is governed by a DNAM-1-CD112/CD155 interaction that inactivates the negative regulator FOXO1. Over time, the high surface density expression of CD155 in acute myeloid leukemia cells impairs the expression of DNAM-1 and GZMB, thus allowing for immune evasion. We describe a reliable platform capable of up to 2,000-fold expansion of human ILC2s within 4 weeks, whose molecular and cellular ILC2 profiles were validated by single-cell RNA sequencing. In both leukemia and solid tumor models, exogenously administered expanded human ILC2s show significant antitumor effects in vivo. Collectively, we demonstrate previously unreported properties of human ILC2s and identify this innate immune cell subset as a member of the cytolytic immune effector cell family.
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Affiliation(s)
- Zhenlong Li
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA 91010, USA; Hematologic Malignancies Research Institute, City of Hope National Medical Center, Los Angeles, CA 91010, USA
| | - Rui Ma
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA 91010, USA; Hematologic Malignancies Research Institute, City of Hope National Medical Center, Los Angeles, CA 91010, USA
| | - Hejun Tang
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA 91010, USA; Hematologic Malignancies Research Institute, City of Hope National Medical Center, Los Angeles, CA 91010, USA
| | - Jiamin Guo
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA 91010, USA; Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute, City of Hope, Los Angeles, CA 91010, USA
| | - Zahir Shah
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA 91010, USA; Hematologic Malignancies Research Institute, City of Hope National Medical Center, Los Angeles, CA 91010, USA
| | - Jianying Zhang
- Department of Computational and Quantitative Medicine, City of Hope National Medical Center, Los Angeles, CA 91010, USA
| | - Ningyuan Liu
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA 91010, USA; Hematologic Malignancies Research Institute, City of Hope National Medical Center, Los Angeles, CA 91010, USA
| | - Shuai Cao
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA 91010, USA; Hematologic Malignancies Research Institute, City of Hope National Medical Center, Los Angeles, CA 91010, USA
| | - Guido Marcucci
- Gehr Family Center for Leukemia Research, Hematologic Malignancies Research Institute, Department of Hematologic Malignancies Translational Science, City of Hope National Medical Center, Los Angeles, CA 91010, USA
| | - David Artis
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY 10021, USA
| | - Michael A Caligiuri
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA 91010, USA; Hematologic Malignancies Research Institute, City of Hope National Medical Center, Los Angeles, CA 91010, USA; City of Hope Comprehensive Cancer Center, Los Angeles, CA 91010, USA.
| | - Jianhua Yu
- Department of Hematology & Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, CA 91010, USA; Hematologic Malignancies Research Institute, City of Hope National Medical Center, Los Angeles, CA 91010, USA; City of Hope Comprehensive Cancer Center, Los Angeles, CA 91010, USA; Department of Immuno-Oncology, City of Hope, Los Angeles, CA 91010, USA.
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25
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Kral M, van der Vorst EP, Surnov A, Weber C, Döring Y. ILC2-mediated immune crosstalk in chronic (vascular) inflammation. Front Immunol 2023; 14:1326440. [PMID: 38179045 PMCID: PMC10765502 DOI: 10.3389/fimmu.2023.1326440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/05/2023] [Indexed: 01/06/2024] Open
Abstract
Crosstalk between innate and adaptive immunity is pivotal for an efficient immune response and to maintain immune homeostasis under steady state conditions. As part of the innate immune system, type 2 innate lymphoid cells (ILC2s) have emerged as new important regulators of tissue homeostasis and repair by fine-tuning innate-adaptive immune cell crosstalk. ILC2s mediate either pro- or anti-inflammatory immune responses in a context dependent manner. Inflammation has proven to be a key driver of atherosclerosis, resembling the key underlying pathophysiology of cardiovascular disease (CVD). Notably, numerous studies point towards an atheroprotective role of ILC2s e.g., by mediating secretion of type-II cytokines (IL-5, IL-13, IL-9). Boosting these protective responses may be suitable for promising future therapy, although these protective cues are currently incompletely understood. Additionally, little is known about the mechanisms by which chemokine/chemokine receptor signaling shapes ILC2 functions in vascular inflammation and atherosclerosis. Hence, this review will focus on the latest findings regarding the protective and chemokine/chemokine receptor guided interplay between ILC2s and other immune cells like T and B cells, dendritic cells and macrophages in atherosclerosis. Further, we will elaborate on potential therapeutic implications which result or could be distilled from the dialogue of ILC2s with cells of the immune system in cardiovascular diseases.
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Affiliation(s)
- Maria Kral
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians University Munich, Munich, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
| | - Emiel P.C. van der Vorst
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians University Munich, Munich, Germany
- Aachen-Maastricht Institute for CardioRenal Disease (AMICARE), Interdisciplinary Center for Clinical Research (IZKF), Institute for Molecular Cardiovascular Research (IMCAR), RWTH Aachen University, Aachen, Germany
| | - Alexey Surnov
- Type 1 Diabetes Immunology (TDI), Helmholtz Diabetes Center (HDC), Helmholtz Center Munich, Munich, Germany
| | - Christian Weber
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians University Munich, Munich, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University Medical Centre, Maastricht, Netherlands
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Yvonne Döring
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians University Munich, Munich, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
- Department of Angiology, Swiss Cardiovascular Center, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research (DBMR) Bern University Hospital, University of Bern, Bern, Switzerland
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26
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Peng J, Tang W, Rawson J, Miao L, Gonzalez N, Yin R, Chen J, Ji M, Li Z, Gao A, Wu AZ, Shively JE, Kandeel F, Li J. One-Step Automatic Radiosynthesis and Evaluation of [ 18F]TM-30089 as GPR44 Radiotracer. Pharmaceuticals (Basel) 2023; 16:1480. [PMID: 37895951 PMCID: PMC10610095 DOI: 10.3390/ph16101480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Recently, a G-protein coupled receptor 44 (GPR44) was discovered to play a significant role in the process of inflammation-related diseases, including cancer and diabetes. However, the precise role of GPR44 has yet to be fully elucidated. Currently, there is a strong and urgent need for the development of GPR44 radiotracers as a non-invasive methodology to explore the exact mechanism of GPR44 on inflammation-related diseases and monitor the progress of therapy. TM-30089 is a potent GPR44 antagonist that exhibits a high specificity and selectivity for GPR44. Its structure contains a fluorine nuclide, which could potentially be replaced with 18F. In the present study, we successfully took a highly effective synthesis strategy that pretreated the unprotected carboxylic acid group of the precursor and developed a feasible one-step automatic radiosynthesis strategy for [18F]TM-30089 with a high radiochemical purity and a good radiochemical yield. We further evaluated this radiotracer using mice models implanted with 1.1 B4 cell lines (GPR44-enriched cell lines) and human islets (high GPR44 expression), respectively. The results revealed the persistent and specific uptake of [18F]TM-30089 in GPR44 region, indicating that [18F]TM-30089 is a promising candidate for targeting GPR44. Further evaluation is ongoing.
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Affiliation(s)
- Jiangling Peng
- Department of Translational Research & Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Wei Tang
- Department of Translational Research & Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Jeffrey Rawson
- Department of Translational Research & Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Lynn Miao
- Department of Translational Research & Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Nelson Gonzalez
- Department of Translational Research & Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Runkai Yin
- Department of Translational Research & Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Jiaqi Chen
- Department of Translational Research & Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Melinda Ji
- Department of Translational Research & Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Zhixuan Li
- Department of Translational Research & Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Anna Gao
- Department of Translational Research & Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Andy Z. Wu
- Department of Translational Research & Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - John E. Shively
- Department of Immunology & Theranostics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Fouad Kandeel
- Department of Translational Research & Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Junfeng Li
- Department of Translational Research & Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
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27
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Koprivica I, Stanisavljević S, Mićanović D, Jevtić B, Stojanović I, Miljković Đ. ILC3: a case of conflicted identity. Front Immunol 2023; 14:1271699. [PMID: 37915588 PMCID: PMC10616800 DOI: 10.3389/fimmu.2023.1271699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/02/2023] [Indexed: 11/03/2023] Open
Abstract
Innate lymphoid cells type 3 (ILC3s) are the first line sentinels at the mucous tissues, where they contribute to the homeostatic immune response in a major way. Also, they have been increasingly appreciated as important modulators of chronic inflammatory and autoimmune responses, both locally and systemically. The proper identification of ILC3 is of utmost importance for meaningful studies on their role in immunity. Flow cytometry is the method of choice for the detection and characterization of ILC3. However, the analysis of ILC3-related papers shows inconsistency in ILC3 phenotypic definition, as different inclusion and exclusion markers are used for their identification. Here, we present these discrepancies in the phenotypic characterization of human and mouse ILC3s. We discuss the pros and cons of using various markers for ILC3 identification. Furthermore, we consider the possibilities for the efficient isolation and propagation of ILC3 from different organs and tissues for in-vitro and in-vivo studies. This paper calls upon uniformity in ILC3 definition, isolation, and propagation for the increased possibility of confluent interpretation of ILC3's role in immunity.
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Affiliation(s)
| | | | | | | | | | - Đorđe Miljković
- Department of Immunology, Institute for Biological Research “Siniša Stanković” - National Institute of Republic of Serbia, University of Belgrade, Belgrade, Serbia
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28
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Bahhar I, Eş Z, Köse O, Turna A, Günlüoğlu MZ, Çakır A, Duralı D, Magnusson FC. The IL-25/ILC2 axis promotes lung cancer with a concomitant accumulation of immune-suppressive cells in tumors in humans and mice. Front Immunol 2023; 14:1244437. [PMID: 37781372 PMCID: PMC10540623 DOI: 10.3389/fimmu.2023.1244437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/21/2023] [Indexed: 10/03/2023] Open
Abstract
Background Group 2 innate lymphoid cells (ILC2) can be activated by interleukin (IL)-33 or IL-25. IL-25-activated ILC2 cells help protect the host against helminth infection while exacerbating allergic-like inflammation and tissue damage in the lung. In the context of cancer, IL-33-activated ILC2 cells were found to bear anti-tumoral functions in lung cancer while IL-25-activated ILC2 cells promoted tumorigenesis in colorectal cancer. The role of IL-25-activated ILC2 cells in lung cancer remains to be addressed. Methods We examined the overall survival of human non-small cell lung cancer (NSCLC) patients according to IL25 expression as well as the distribution of ILC2 cells and regulatory T cells (Tregs) in various NSCLC patient tissues and peripheral blood (PB) of healthy donors (HDs). We analyzed the effect of adoptive transfer of IL-25-activated ILC2 cells on tumor growth, metastasis and survival in a heterotopic murine model of lung cancer. Results We report that human NSCLC patients with high IL-25 expression have reduced overall survival. Moreover, NSCLC patients bear increased frequencies of ILC2s compared to HDs. Frequencies of Tregs were also increased in NSCLC patients, concomitantly with ILC2s. In mice bearing heterotopic lung cancer, adoptive transfer of IL-25-activated ILC2s led to increased tumor growth, increased metastasis and reduced survival. The frequencies of monocytic myeloid-derived suppressor cells (M-MDSCs) were found to be increased in the tumors of mice that received ILC2s as compared to controls. Conclusion Overall, our results indicate that the IL-25/ILC2 axis promotes lung cancer potentially by recruiting immune-suppressive cells to the tumors both in humans and in mice, and that it may therefore represent a suitable novel target for NSCLC immunotherapeutic development.
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Affiliation(s)
- Ilham Bahhar
- Cancer Research Center, Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Türkiye
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Türkiye
| | - Zeynep Eş
- Cancer Research Center, Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Türkiye
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Türkiye
| | - Oğuzhan Köse
- Cancer Research Center, Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Türkiye
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Türkiye
| | - Akif Turna
- Department of Thoracic Surgery, Cerrahpasa Medical School, Istanbul University-Cerrahpasa, Fatih, Istanbul, Türkiye
| | - Mehmet Zeki Günlüoğlu
- Department of Thoracic Surgery, Faculty of Medicine, Istanbul Medipol University, Istanbul, Türkiye
| | - Aslı Çakır
- Department of Pathology, Faculty of Medicine, Istanbul Medipol University, Istanbul, Türkiye
| | - Deniz Duralı
- Cancer Research Center, Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Türkiye
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Türkiye
- Department of Medical Microbiology, International School of Medicine, Istanbul Medipol University, Istanbul, Türkiye
| | - Fay C. Magnusson
- Cancer Research Center, Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Türkiye
- Regenerative and Restorative Medicine Research Center (REMER), Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Türkiye
- Department of Medical Microbiology, International School of Medicine, Istanbul Medipol University, Istanbul, Türkiye
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29
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Falquet M, Su Z, Wyss T, Ercolano G, Trabanelli S, Jandus C. Dynamic single-cell regulomes characterize human peripheral blood innate lymphoid cell subpopulations. iScience 2023; 26:107728. [PMID: 37694139 PMCID: PMC10483052 DOI: 10.1016/j.isci.2023.107728] [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: 03/13/2023] [Revised: 07/25/2023] [Accepted: 08/21/2023] [Indexed: 09/12/2023] Open
Abstract
Innate lymphoid cells (ILCs) are plastic immune cells divided into 3 main subsets, characterized by distinct phenotypic and functional profiles. Using single cell approaches, heightened heterogeneity of mouse ILCs has been appreciated, imprinted by tissue signals that shape their transcriptome and epigenome. Intra-subset diversity has also been observed in human ILCs. However, combined transcriptomic and epigenetic analyses of single ILCs in humans are lacking. Here, we show high transcriptional and epigenetic heterogeneity among human circulating ILCs in healthy individuals. We describe phenotypically distinct subclusters and diverse chromatin accessibility within main ILC populations, compatible with differentially poised states. We validate the use of this healthy donor-based analysis as resource dataset to help inferring ILC changes occurring in disease conditions. Overall, our work provides insights in the complex human ILC biology. We anticipate it to facilitate hypothesis-driven studies in patients, without the need to perform single cell OMICs using precious patients' material.
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Affiliation(s)
- Maryline Falquet
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland
- Geneva Center for Inflammation Research, Geneva, Switzerland
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Ziyang Su
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland
- Geneva Center for Inflammation Research, Geneva, Switzerland
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Tania Wyss
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland
- Geneva Center for Inflammation Research, Geneva, Switzerland
- Translational Data Science Facility, AGORA Cancer Research Center, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Giuseppe Ercolano
- Department of Experimental Pharmacology, University of Naples Federico II, Naples, Italy
| | - Sara Trabanelli
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland
- Geneva Center for Inflammation Research, Geneva, Switzerland
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Camilla Jandus
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- Ludwig Institute for Cancer Research, Lausanne Branch, Lausanne, Switzerland
- Geneva Center for Inflammation Research, Geneva, Switzerland
- Translational Research Center for Oncohematology, Department of Medicine, Faculty of Medicine, University of Geneva, Geneva, Switzerland
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Ryu S, Lim M, Kim J, Kim HY. Versatile roles of innate lymphoid cells at the mucosal barrier: from homeostasis to pathological inflammation. Exp Mol Med 2023; 55:1845-1857. [PMID: 37696896 PMCID: PMC10545731 DOI: 10.1038/s12276-023-01022-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 09/13/2023] Open
Abstract
Innate lymphoid cells (ILCs) are innate lymphocytes that do not express antigen-specific receptors and largely reside and self-renew in mucosal tissues. ILCs can be categorized into three groups (ILC1-3) based on the transcription factors that direct their functions and the cytokines they produce. Their signature transcription factors and cytokines closely mirror those of their Th1, Th2, and Th17 cell counterparts. Accumulating studies show that ILCs are involved in not only the pathogenesis of mucosal tissue diseases, especially respiratory diseases, and colitis, but also the resolution of such diseases. Here, we discuss recent advances regarding our understanding of the biology of ILCs in mucosal tissue health and disease. In addition, we describe the current research on the immune checkpoints by which other cells regulate ILC activities: for example, checkpoint molecules are potential new targets for therapies that aim to control ILCs in mucosal diseases. In addition, we review approved and clinically- trialed drugs and drugs in clinical trials that can target ILCs and therefore have therapeutic potential in ILC-mediated diseases. Finally, since ILCs also play important roles in mucosal tissue homeostasis, we explore the hitherto sparse research on cell therapy with regulatory ILCs. This review highlights various therapeutic approaches that could be used to treat ILC-mediated mucosal diseases and areas of research that could benefit from further investigation.
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Affiliation(s)
- Seungwon Ryu
- Department of Microbiology, Gachon University College of Medicine, Incheon, 21999, South Korea
| | - MinYeong Lim
- Laboratory of Mucosal Immunology, Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, South Korea
- Institute of Allergy and Clinical Immunology, Seoul National University Medical Research Center, Seoul, South Korea
- CIRNO, Sungkyunkwan University, Suwon, South Korea
| | - Jinwoo Kim
- Laboratory of Mucosal Immunology, Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, South Korea
- Institute of Allergy and Clinical Immunology, Seoul National University Medical Research Center, Seoul, South Korea
- CIRNO, Sungkyunkwan University, Suwon, South Korea
| | - Hye Young Kim
- Laboratory of Mucosal Immunology, Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, 03080, South Korea.
- Institute of Allergy and Clinical Immunology, Seoul National University Medical Research Center, Seoul, South Korea.
- CIRNO, Sungkyunkwan University, Suwon, South Korea.
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Raabe J, Kaiser KM, ToVinh M, Finnemann C, Lutz P, Hoffmeister C, Bischoff J, Goeser F, Kaczmarek DJ, Glowka TR, Manekeller S, Charpentier A, Langhans B, Nischalke HD, Toma M, Strassburg CP, Spengler U, Abdallah AT, Krämer B, Nattermann J. Identification and characterization of a hepatic IL-13-producing ILC3-like population potentially involved in liver fibrosis. Hepatology 2023; 78:787-802. [PMID: 37029085 DOI: 10.1097/hep.0000000000000350] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 12/12/2022] [Indexed: 04/09/2023]
Abstract
BACKGROUND AND AIMS Human innate lymphoid cells (ILCs) are critically involved in the modulation of homeostatic and inflammatory processes in various tissues. However, only little is known about the composition of the intrahepatic ILC pool and its potential role in chronic liver disease. Here, we performed a detailed characterization of intrahepatic ILCs in both healthy and fibrotic livers. APPROACH AND RESULTS A total of 50 livers (nonfibrotic = 22, and fibrotic = 29) were analyzed and compared with colon and tonsil tissue (each N = 14) and peripheral blood (N = 32). Human intrahepatic ILCs were characterized ex vivo and on stimulation using flow cytometry and single-cell RNA sequencing. ILC differentiation and plasticity were analyzed by both bulk and clonal expansion experiments. Finally, the effects of ILC-derived cytokines on primary human HSteCs were studied. Unexpectedly, we found that an "unconventional" ILC3-like cell represented the major IL-13-producing liver ILC subset. IL-13 + ILC3-like cells were specifically enriched in the human liver, and increased frequencies of this cell type were found in fibrotic livers. ILC3-derived IL-13 production induced upregulation of proinflammatory genes in HSteCs, indicating a potential role in the regulation of hepatic fibrogenesis. Finally, we identified KLRG1-expressing ILC precursors as the potential progenitor of hepatic IL-13 + ILC3-like cells. CONCLUSIONS We identified a formerly undescribed subset of IL-13-producing ILC3-like cells that is enriched in the human liver and may be involved in the modulation of chronic liver disease.
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Affiliation(s)
- Jan Raabe
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
| | - Kim M Kaiser
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
| | - Michael ToVinh
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
| | - Claudia Finnemann
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
| | - Philipp Lutz
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
| | | | - Jenny Bischoff
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
| | - Felix Goeser
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
| | | | - Tim R Glowka
- Department of Surgery, University Hospital Bonn, Bonn, Germany
| | | | - Arthur Charpentier
- Department of Otorhinolaryngology, University Hospital Bonn, Bonn, Germany
| | - Bettina Langhans
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
| | | | - Marieta Toma
- Department of Pathology, University Hospital Bonn, Bonn, Germany
| | | | - Ulrich Spengler
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
| | - Ali T Abdallah
- Interdisciplinary Center for Clinical Research, RWTH Aachen University, Aachen, Germany
- The German Center for Infection Research (DZIF)
| | - Benjamin Krämer
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
- The German Center for Infection Research (DZIF)
| | - Jacob Nattermann
- Department of Internal Medicine I, University Hospital Bonn, Bonn, Germany
- The German Center for Infection Research (DZIF)
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Wang X, Kong Y, Zheng B, Zhao X, Zhao M, Wang B, Liu C, Yan P. Tissue-resident innate lymphoid cells in asthma. J Physiol 2023; 601:3995-4012. [PMID: 37488944 DOI: 10.1113/jp284686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/10/2023] [Indexed: 07/26/2023] Open
Abstract
Asthma is a chronic airway inflammatory disease whose global incidence increases annually. The role of innate lymphoid cells (ILCs) is a crucial aspect of asthma research with respect to different endotypes of asthma. Based on its pathological and inflammatory features, asthma is divided into type 2 high and type 2 low endotypes. Type-2 high asthma is distinguished by the activation of type 2 immune cells, including T helper 2 (Th2) cells and ILC2s; the production of cytokines interleukin (IL)-4, IL-5 and IL-13; eosinophilic aggregation; and bronchial hyper-responsiveness. Type-2 low asthma represents a variety of endotypes other than type 2 high endotype such as the IL-1β/ILC3/neutrophil endotype and a paucigranulocytic asthma, which may be insensitive to corticosteroid treatment and/or associated with obesity. The complexity of asthma is due to the involvement of multiple cell types, including tissue-resident ILCs and other innate immune cells including bronchial epithelial cells, dendritic cells, macrophages and eosinophils, which provide immediate defence against viruses, pathogens and allergens. On this basis, innate immune cells and adaptive immune cells combine to induce the pathological condition of asthma. In addition, the plasticity of ILCs increases the heterogeneity of asthma. This review focuses on the phenotypes of tissue-resident ILCs and their roles in the different endotypes of asthma, as well as the mechanisms of tissue-resident ILCs and other immune cells. Based on the phenotypes, roles and mechanisms of immune cells, the therapeutic strategies for asthma are reviewed.
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Affiliation(s)
- Xiaoxu Wang
- The Second Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yue Kong
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Bingqing Zheng
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xiaomin Zhao
- Department of traditional Chinese medicine, Shandong Traditional Chinese Medicine College, YanTai, China
| | - Mingzhe Zhao
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Bin Wang
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Chang Liu
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Peizheng Yan
- Shandong University of Traditional Chinese Medicine, Jinan, China
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Hu L, Han M, Deng Y, Gong J, Hou Z, Zeng Y, Zhang Y, He J, Zhong C. Genetic distinction between functional tissue-resident and conventional natural killer cells. iScience 2023; 26:107187. [PMID: 37404378 PMCID: PMC10316664 DOI: 10.1016/j.isci.2023.107187] [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: 04/20/2023] [Revised: 06/01/2023] [Accepted: 06/16/2023] [Indexed: 07/06/2023] Open
Abstract
Tissue-residential natural killer (trNK) cells act as pioneering responders during infectious challenges. However, their discrimination with conventional NK (cNK) cells is still an issue. Through an integrative transcriptome comparison of the two NK subgroups from different tissues, we have defined two genesets capable of efficiently distinguishing them. Based on the two genesets, a fundamental difference between the activation of trNK and cNK is identified and further confirmed. Mechanistically, we have discovered a particular role of chromatin landscape in regulating the trNK activation. In addition, IL-21R and IL-18R are respectively highly expressed by trNK and cNK, indicating a role of cytokine milieu in determining their differential activation. Indeed, IL-21 is particularly critical in accessorily promoting trNK activation using a bunch of bifunctional transcription factors. Together, this study sheds light on the bona fide difference between trNK and cNK, which will further expand our knowledge about their distinct functionalities during immune responses.
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Affiliation(s)
- Luni Hu
- Institute of Systems Biomedicine, Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Mengwei Han
- Institute of Systems Biomedicine, Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yichen Deng
- Institute of Systems Biomedicine, Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jingjing Gong
- Institute of Systems Biomedicine, Peking University Health Science Center, Beijing 100191, China
| | - Zhiyuan Hou
- Institute of Systems Biomedicine, Peking University Health Science Center, Beijing 100191, China
| | - Yanyu Zeng
- Institute of Systems Biomedicine, Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yime Zhang
- Institute of Systems Biomedicine, Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jing He
- Department of Rheumatology and Immunology, Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis, Peking University People’s Hospital, Beijing, China
| | - Chao Zhong
- Institute of Systems Biomedicine, Department of Immunology, NHC Key Laboratory of Medical Immunology (Peking University), Beijing Key Laboratory of Tumor Systems Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
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Alisjahbana A, Mohammad I, Gao Y, Evren E, Willinger T. Single-cell RNA sequencing of human lung innate lymphoid cells in the vascular and tissue niche reveals molecular features of tissue adaptation. DISCOVERY IMMUNOLOGY 2023; 2:kyad007. [PMID: 38650756 PMCID: PMC11034571 DOI: 10.1093/discim/kyad007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/06/2023] [Accepted: 06/23/2023] [Indexed: 04/25/2024]
Abstract
Innate lymphoid cells (ILCs) are sentinels of healthy organ function, yet it is unknown how ILCs adapt to distinct anatomical niches within tissues. Here, we used a unique humanized mouse model, MISTRG mice transplanted with human hematopoietic stem and progenitor cells (HSPCs), to define the gene signatures of human ILCs in the vascular versus the tissue (extravascular) compartment of the lung. Single-cell RNA sequencing in combination with intravascular cell labeling demonstrated that heterogeneous populations of human ILCs and natural killer (NK) cells occupied the vascular and tissue niches in the lung of HSPC-engrafted MISTRG mice. Moreover, we discovered that niche-specific cues shape the molecular programs of human ILCs in the distinct sub-anatomical compartments of the lung. Specifically, extravasation of ILCs into the lung tissue was associated with the upregulation of genes involved in the acquisition of tissue residency, cell positioning within the lung, sensing of tissue-derived signals, cellular stress responses, nutrient uptake, and interaction with other tissue-resident immune cells. We also defined a core tissue signature shared between human ILCs and NK cells in the extravascular space of the lung, consistent with imprinting by signals from the local microenvironment. The molecular characterization of human ILCs and NK cells in the vascular and tissue niches of the lung provides new knowledge on the mechanisms of ILC tissue adaptation and represents a resource for further studies.
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Affiliation(s)
- Arlisa Alisjahbana
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Imran Mohammad
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Department of Otolaryngology-Head and Neck Surgery, Stanford Cancer Institute, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Yu Gao
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Elza Evren
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
- Comprehensive Pneumology Center (CPC) with the CPC-M bioArchive/Institute of Lung Health and Immunity (LHI), Helmholtz Zentrum München; Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Tim Willinger
- Department of Medicine Huddinge, Center for Infectious Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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35
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Kim Y, Greenleaf WJ, Bendall SC. Systems biology approaches to unravel lymphocyte subsets and function. Curr Opin Immunol 2023; 82:102323. [PMID: 37028221 PMCID: PMC10330158 DOI: 10.1016/j.coi.2023.102323] [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: 02/02/2023] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 04/09/2023]
Abstract
Single-cell technologies have revealed the extensive heterogeneity and complexity of the immune system. Systems biology approaches in immunology have taken advantage of the high-parameter, high-throughput data and analyzed immune cell types in a 'bottom-up' data-driven method. This approach has discovered previously unrecognized cell types and functions. Especially for human immunology, in which experimental manipulations are challenging, systems approach has become a successful means to investigate physiologically relevant contexts. This review focuses on the recent findings in lymphocyte biology, from their development, differentiation into subsets, and heterogeneity in their functions, enabled by these systems approaches. Furthermore, we review examples of the application of findings from systems approach studies and discuss how now to leave the rich dataset in the curse of high dimensionality.
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Affiliation(s)
- YeEun Kim
- Immunology Graduate Program, Stanford University, Stanford, CA, USA; Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Sean C Bendall
- Department of Pathology, Stanford University, Stanford, CA, USA.
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36
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Jiang S, Zheng Y, Lv B, He S, Yang W, Wang B, Zhou J, Liu S, Li D, Lin J. Single-cell landscape dissecting the transcription and heterogeneity of innate lymphoid cells in ischemic heart. Front Immunol 2023; 14:1129007. [PMID: 37228603 PMCID: PMC10203554 DOI: 10.3389/fimmu.2023.1129007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 04/24/2023] [Indexed: 05/27/2023] Open
Abstract
Background Until now, few articles have revealed the potential roles of innate lymphoid cells (ILCs) in cardiovascular diseases. However, the infiltration of ILC subsets in ischemic myocardium, the roles of ILC subsets in myocardial infarction (MI) and myocardial ischemia-reperfusion injury (MIRI) and the related cellular and molecular mechanisms have not been described with a sufficient level of detail. Method In the current study, 8-week-old male C57BL/6J mice were divided into three groups: MI, MIRI and sham group. Single-cell sequencing technology was used to perform dimensionality reduction clustering of ILC to analyze the ILC subset landscape at a single-cell resolution, and finally flow cytometry was used to confirm the existence of the new ILC subsets in different disease groups. Results Five ILC subsets were found, including ILC1, ILC2a, ILC2b, ILCdc and ILCt. It is worth noting that ILCdc, ILC2b and ILCt were identified as new ILC subclusters in the heart. The cellular landscapes of ILCs were revealed and signal pathways were predicted. Furthermore, pseudotime trajectory analysis exhibited different ILC statuses and traced related gene expression in normal and ischemic conditions. In addition, we established a ligand-receptor-transcription factor-target gene regulatory network to disclose cell communications among ILC clusters. Moreover, we further revealed the transcriptional features of the ILCdc and ILC2a subsets. Finally, the existence of ILCdc was confirmed by flow cytometry. Conclusion Collectively, by characterizing the spectrums of ILC subclusters, our results provide a new blueprint for understanding ILC subclusters' roles in myocardial ischemia diseases and further potential treatment targets.
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Affiliation(s)
- Shijiu Jiang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Cardiology, The First Affiliated Hospital, Shihezi University, Shihezi, Xinjiang, China
| | - Yuqi Zheng
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bingjie Lv
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shaolin He
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenling Yang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Boyuan Wang
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jin Zhou
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shangwei Liu
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dazhu Li
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jibin Lin
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Key Laboratory of Biological Targeted Therapy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Hubei Provincial Engineering Research Center of Immunological Diagnosis and Therapy for Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Kokkinou E, Soini T, Pandey RV, van Acker A, Theorell J, Czarnewski P, Kvedaraite E, Vandamme N, Lourda M, Sorini C, Weigel W, Carrasco A, Tibbitt CA, Schlums H, Lindforss U, Nordenvall C, Ljunggren M, Ideström M, Svensson M, Henter JI, Villablanca EJ, Bryceson YT, Rolandsdotter H, Mjösberg J. The single-cell transcriptional landscape of innate and adaptive lymphocytes in pediatric-onset colitis. Cell Rep Med 2023; 4:101038. [PMID: 37160121 DOI: 10.1016/j.xcrm.2023.101038] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 12/15/2022] [Accepted: 04/14/2023] [Indexed: 05/11/2023]
Abstract
Innate lymphoid cells (ILCs) are considered innate counterparts of adaptive T cells; however, their common and unique transcriptional signatures in pediatric inflammatory bowel disease (pIBD) are largely unknown. Here, we report a dysregulated colonic ILC composition in pIBD colitis that correlates with inflammatory activity, including accumulation of naive-like CD45RA+CD62L- ILCs. Weighted gene co-expression network analysis (WGCNA) reveals modules of genes that are shared or unique across innate and adaptive lymphocytes. Shared modules include genes associated with activation/tissue residency, naivety/quiescence, and antigen presentation. Lastly, nearest-neighbor-based analysis facilitates the identification of "most inflamed" and "least inflamed" lymphocytes in pIBD colon with unique transcriptional signatures. Our study reveals shared and unique transcriptional signatures of colonic ILCs and T cells in pIBD. We also provide insight into the transcriptional regulation of colonic inflammation, deepening our understanding of the potential mechanisms involved in pIBD.
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Affiliation(s)
- Efthymia Kokkinou
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Tea Soini
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Ram Vinay Pandey
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Aline van Acker
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Jakob Theorell
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden; Psychiatry Southwest, Health Care Services Stockholm County, Huddinge, Sweden
| | - Paulo Czarnewski
- Science for Life Laboratory, Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Stockholm University, Solna, Sweden
| | - Egle Kvedaraite
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden; Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Department of Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Niels Vandamme
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, Ghent, Belgium; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Magda Lourda
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden; Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Chiara Sorini
- Immunology and Allergy Unit, Department of Medicine, Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Whitney Weigel
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Anna Carrasco
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Christopher Andrew Tibbitt
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Heinrich Schlums
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Ulrik Lindforss
- Department of Molecular Medicine and Surgery, Karolinska Institutet and Center for Digestive Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Caroline Nordenvall
- Department of Molecular Medicine and Surgery, Karolinska Institutet and Center for Digestive Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Malin Ljunggren
- Department of Molecular Medicine and Surgery, Karolinska Institutet and Center for Digestive Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Maja Ideström
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Pediatric Gastroenterology, Hepatology and Nutrition Unit, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Mattias Svensson
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Jan-Inge Henter
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden; Theme of Children's Health, Karolinska University Hospital, Stockholm, Sweden
| | - Eduardo J Villablanca
- Immunology and Allergy Unit, Department of Medicine, Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Yenan T Bryceson
- Center for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Helena Rolandsdotter
- Department of Gastroenterology, Sachs' Children and Youth Hospital, Stockholm, Sweden; Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Jenny Mjösberg
- Center for Infectious Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden.
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Lim JX, Lai CY, Mallett GE, McDonald D, Hulme G, Laba S, Shapanis A, Payne M, Patterson W, Alexander M, Coxhead J, Filby A, Plummer R, Lovat PE, Sciume G, Healy E, Amarnath S. Programmed cell death-1 receptor-mediated regulation of Tbet +NK1.1 - innate lymphoid cells within the tumor microenvironment. Proc Natl Acad Sci U S A 2023; 120:e2216587120. [PMID: 37098069 PMCID: PMC10161089 DOI: 10.1073/pnas.2216587120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 03/07/2023] [Indexed: 04/26/2023] Open
Abstract
Innate lymphoid cells (ILCs) play a key role in tissue-mediated immunity and can be controlled by coreceptor signaling. Here, we define a subset of ILCs that are Tbet+NK1.1- and are present within the tumor microenvironment (TME). We show programmed death-1 receptor (PD-1) expression on ILCs within TME is found in Tbet+NK1.1- ILCs. PD-1 significantly controlled the proliferation and function of Tbet+NK1.1- ILCs in multiple murine and human tumors. We found tumor-derived lactate enhanced PD-1 expression on Tbet+NK1.1- ILCs within the TME, which resulted in dampened the mammalian target of rapamycin (mTOR) signaling along with increased fatty acid uptake. In line with these metabolic changes, PD-1-deficient Tbet+NK1.1- ILCs expressed significantly increased IFNγ and granzyme B and K. Furthermore, PD-1-deficient Tbet+NK1.1- ILCs contributed toward diminished tumor growth in an experimental murine model of melanoma. These data demonstrate that PD-1 can regulate antitumor responses of Tbet+NK1.1- ILCs within the TME.
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Affiliation(s)
- Jing Xuan Lim
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
- Newcastle University Centre for Cancer, Medical School, Newcastle University,Newcastle upon TyneNE2 4HH, United Kingdom
| | - Chester Y. Lai
- Dermatopharmacology, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, SouthamptonSO16 6YD, United Kingdom
- Dermatology, University Hospital Southampton NHS Foundation Trust, SouthamptonSO16 6YD, United Kingdom
| | - Grace E. Mallett
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
- Newcastle University Centre for Cancer, Medical School, Newcastle University,Newcastle upon TyneNE2 4HH, United Kingdom
| | - David McDonald
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
| | - Gillian Hulme
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
| | - Stephanie Laba
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
| | - Andrew Shapanis
- Dermatopharmacology, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, SouthamptonSO16 6YD, United Kingdom
| | - Megan Payne
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
| | - Warren Patterson
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
| | - Michael Alexander
- Newcastle University Centre for Cancer, Medical School, Newcastle University,Newcastle upon TyneNE2 4HH, United Kingdom
| | - Jonathan Coxhead
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
| | - Andrew Filby
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
| | - Ruth Plummer
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
- Newcastle University Translational and Clinical Research Institute, Medical School, Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
| | - Penny E. Lovat
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
- Newcastle University Translational and Clinical Research Institute, Medical School, Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
| | - Giuseppe Sciume
- Department of Molecular Medicine, Sapienza University of Rome Laboratory affiliation to Institute Pasteur Italia-Fondazione Cenci Bolognetti, Rome00161, Italy
| | - Eugene Healy
- Dermatopharmacology, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, SouthamptonSO16 6YD, United Kingdom
- Dermatology, University Hospital Southampton NHS Foundation Trust, SouthamptonSO16 6YD, United Kingdom
| | - Shoba Amarnath
- Newcastle University Biosciences Institute, Medical School, Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
- Newcastle University Centre for Cancer, Medical School, Newcastle University,Newcastle upon TyneNE2 4HH, United Kingdom
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Tamadaho RSE, Osei-Mensah J, Arndts K, Debrah LB, Debrah AY, Layland LE, Hoerauf A, Pfarr K, Ritter M. Reduced Type 2 Innate Lymphocyte Cell Frequencies in Patent Wuchereria bancrofti-Infected Individuals. Pathogens 2023; 12:pathogens12050665. [PMID: 37242335 DOI: 10.3390/pathogens12050665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/06/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Approximately 51 million individuals suffer from lymphatic filariasis (LF) caused mainly by the filarial worm Wuchereria bancrofti. Mass drug administration (MDA) programs led to a significant reduction in the number of infected individuals, but the consequences of the treatment and clearance of infection in regard to host immunity remain uncertain. Thus, this study investigates the composition of myeloid-derived suppressor cells (MDSCs), macrophage subsets and innate lymphoid cells (ILCs), in patent (circulating filarial antigen (CFA)+ microfilariae (MF)+) and latent (CFA+MF-) W. bancrofti-infected individuals, previously W. bancrofti-infected (PI) individuals cured of the infection due to MDA, uninfected controls (endemic normal (EN)) and individuals who suffer from lymphoedema (LE) from the Western Region of Ghana. Frequencies of ILC2 were significantly reduced in W. bancrofti-infected individuals, while the frequencies of MDSCs, M2 macrophages, ILC1 and ILC3 were comparable between the cohorts. Importantly, clearance of infection due to MDA restored the ILC2 frequencies, suggesting that ILC2 subsets might migrate to the site of infection within the lymphatic tissue. In general, the immune cell composition in individuals who cured the infection were comparable to the uninfected individuals, showing that filarial-driven changes of the immune responses require an active infection and are not maintained upon the clearance of the infection.
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Affiliation(s)
- Ruth S E Tamadaho
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn (UKB), 53127 Bonn, Germany
| | - Jubin Osei-Mensah
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), UPO, PMB, Kumasi 00233, Ghana
- Department of Pathobiology, School of Veterinary Medicine, Kwame Nkrumah University of Science and Technology, UPO, PMB, Kumasi 00233, Ghana
| | - Kathrin Arndts
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn (UKB), 53127 Bonn, Germany
| | - Linda Batsa Debrah
- Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), UPO, PMB, Kumasi 00233, Ghana
- Department of Clinical Microbiology, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, UPO, PMB, Kumasi 00233, Ghana
| | - Alexander Y Debrah
- Faculty of Allied Health Sciences, Kwame Nkrumah University of Science and Technology, UPO, PMB, Kumasi 00233, Ghana
| | - Laura E Layland
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn (UKB), 53127 Bonn, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 53127 Bonn, Germany
| | - Achim Hoerauf
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn (UKB), 53127 Bonn, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 53127 Bonn, Germany
- German-West African Centre for Global Health and Pandemic Prevention (G-WAC), Partner Site Bonn, 53127 Bonn, Germany
| | - Kenneth Pfarr
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn (UKB), 53127 Bonn, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 53127 Bonn, Germany
| | - Manuel Ritter
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn (UKB), 53127 Bonn, Germany
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Ruf B, Greten TF, Korangy F. Innate lymphoid cells and innate-like T cells in cancer - at the crossroads of innate and adaptive immunity. Nat Rev Cancer 2023; 23:351-371. [PMID: 37081117 DOI: 10.1038/s41568-023-00562-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/13/2023] [Indexed: 04/22/2023]
Abstract
Immunotherapies targeting conventional T cells have revolutionized systemic treatment for many cancers, yet only a subset of patients benefit from these approaches. A better understanding of the complex immune microenvironment of tumours is needed to design the next generation of immunotherapeutics. Innate lymphoid cells (ILCs) and innate-like T cells (ILTCs) are abundant, tissue-resident lymphocytes that have recently been shown to have critical roles in many types of cancers. ILCs and ILTCs rapidly respond to changes in their surrounding environment and act as the first responders to bridge innate and adaptive immunity. This places ILCs and ILTCs as pivotal orchestrators of the final antitumour immune response. In this Review, we outline hallmarks of ILCs and ILTCs and discuss their emerging role in antitumour immunity, as well as the pathophysiological adaptations leading to their pro-tumorigenic function. We explore the pleiotropic, in parts redundant and sometimes opposing, mechanisms that underlie the delicate interplay between the different subsets of ILCs and ILTCs. Finally, we highlight their role in amplifying and complementing conventional T cell functions and summarize immunotherapeutic strategies for targeting ILCs and ILTCs in cancer.
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Affiliation(s)
- Benjamin Ruf
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Centre for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tim F Greten
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Centre for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- NCI CCR Liver Cancer Program, National Institutes of Health, Bethesda, MD, USA
| | - Firouzeh Korangy
- Gastrointestinal Malignancy Section, Thoracic and Gastrointestinal Malignancies Branch, Centre for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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Li S, Wang CS, Montel-Hagen A, Chen HC, Lopez S, Zhou O, Dai K, Tsai S, Satyadi W, Botero C, Wong C, Casero D, Crooks GM, Seet CS. Strength of CAR signaling determines T cell versus ILC differentiation from pluripotent stem cells. Cell Rep 2023; 42:112241. [PMID: 36906850 PMCID: PMC10315155 DOI: 10.1016/j.celrep.2023.112241] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 01/04/2023] [Accepted: 02/23/2023] [Indexed: 03/13/2023] Open
Abstract
Generation of chimeric antigen receptor (CAR) T cells from pluripotent stem cells (PSCs) will enable advances in cancer immunotherapy. Understanding how CARs affect T cell differentiation from PSCs is important for this effort. The recently described artificial thymic organoid (ATO) system supports in vitro differentiation of PSCs to T cells. Unexpectedly, PSCs transduced with a CD19-targeted CAR resulted in diversion of T cell differentiation to the innate lymphoid cell 2 (ILC2) lineage in ATOs. T cells and ILC2s are closely related lymphoid lineages with shared developmental and transcriptional programs. Mechanistically, we show that antigen-independent CAR signaling during lymphoid development enriched for ILC2-primed precursors at the expense of T cell precursors. We applied this understanding to modulate CAR signaling strength through expression level, structure, and presentation of cognate antigen to demonstrate that the T cell-versus-ILC lineage decision can be rationally controlled in either direction, providing a framework for achieving CAR-T cell development from PSCs.
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Affiliation(s)
- Suwen Li
- Department of Medicine, Division of Hematology-Oncology, David Geffen School of Medicine (DGSOM), University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Chloe S Wang
- Department of Medicine, Division of Hematology-Oncology, David Geffen School of Medicine (DGSOM), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Amélie Montel-Hagen
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ho-Chung Chen
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Shawn Lopez
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Olivia Zhou
- Department of Medicine, Division of Hematology-Oncology, David Geffen School of Medicine (DGSOM), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Kristy Dai
- Department of Medicine, Division of Hematology-Oncology, David Geffen School of Medicine (DGSOM), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Steven Tsai
- Department of Medicine, Division of Hematology-Oncology, David Geffen School of Medicine (DGSOM), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - William Satyadi
- Department of Medicine, Division of Hematology-Oncology, David Geffen School of Medicine (DGSOM), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Carlos Botero
- Department of Medicine, Division of Hematology-Oncology, David Geffen School of Medicine (DGSOM), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Claudia Wong
- Department of Medicine, Division of Hematology-Oncology, David Geffen School of Medicine (DGSOM), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - David Casero
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Gay M Crooks
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Broad Stem Cell Research Center (BSCRC), David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center (JCCC), David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Christopher S Seet
- Department of Medicine, Division of Hematology-Oncology, David Geffen School of Medicine (DGSOM), University of California, Los Angeles, Los Angeles, CA 90095, USA; Broad Stem Cell Research Center (BSCRC), David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Jonsson Comprehensive Cancer Center (JCCC), David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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42
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Ma Z, Wang J, Hu L, Wang S. Function of Innate Lymphoid Cells in Periodontal Tissue Homeostasis: A Narrative Review. Int J Mol Sci 2023; 24:ijms24076099. [PMID: 37047071 PMCID: PMC10093809 DOI: 10.3390/ijms24076099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/16/2023] [Accepted: 03/18/2023] [Indexed: 04/14/2023] Open
Abstract
Periodontitis is an irreversible inflammatory response that occurs in periodontal tissues. Given the size and diversity of natural flora in the oral mucosa, host immunity must strike a balance between pathogen identification and a complicated system of tolerance. The innate immune system, which includes innate lymphoid cells (ILCs), certainly plays a crucial role in regulating this homeostasis because pathogens are quickly recognized and responded to. ILCs are a recently discovered category of tissue-resident lymphocytes that lack adaptive antigen receptors. ILCs are found in both lymphoid and non-lymphoid organs and are particularly prevalent at mucosal barrier surfaces, where they control inflammatory response and homeostasis. Recent studies have shown that ILCs are important players in periodontitis; however, the mechanisms that govern the innate immune response in periodontitis still require further investigation. This review focuses on the intricate crosstalk between ILCs and the microenvironment in periodontal tissue homeostasis, with the purpose of regulating or improving immune responses in periodontitis prevention and therapy.
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Affiliation(s)
- Zhiyu Ma
- Beijing Laboratory of Oral Health, School of Basic Medicine, School of Stomatology, Capital Medical University, Beijing 100050, China
| | - Jinsong Wang
- Beijing Laboratory of Oral Health, School of Basic Medicine, School of Stomatology, Capital Medical University, Beijing 100050, China
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Capital Medical University Beijing 100070, China
| | - Lei Hu
- Beijing Laboratory of Oral Health, School of Basic Medicine, School of Stomatology, Capital Medical University, Beijing 100050, China
- Department of Prosthodontics, School of Stomatology, Capital Medical University, Beijing 100050, China
- Immunology Research Center for Oral and Systemic Health, Beijing Friendship Hospital, Capital Medical University, Beijing 100070, China
| | - Songlin Wang
- Beijing Laboratory of Oral Health, School of Basic Medicine, School of Stomatology, Capital Medical University, Beijing 100050, China
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Capital Medical University Beijing 100070, China
- Immunology Research Center for Oral and Systemic Health, Beijing Friendship Hospital, Capital Medical University, Beijing 100070, China
- Laboratory for Oral and General Health Integration and Translation, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- Research Unit of Tooth Development and Regeneration, Chinese Academy of Medical Sciences, Beijing 100700, China
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43
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Laufer Britva R, Keren A, Bertolini M, Ullmann Y, Paus R, Gilhar A. Involvement of ILC1-like innate lymphocytes in human autoimmunity, lessons from alopecia areata. eLife 2023; 12:80768. [PMID: 36930216 PMCID: PMC10023162 DOI: 10.7554/elife.80768] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 02/22/2023] [Indexed: 03/11/2023] Open
Abstract
Here, we have explored the involvement of innate lymphoid cells-type 1 (ILC1) in the pathogenesis of alopecia areata (AA), because we found them to be significantly increased around lesional and non-lesional HFs of AA patients. To further explore these unexpected findings, we first co-cultured autologous circulating ILC1-like cells (ILC1lc) with healthy, but stressed, organ-cultured human scalp hair follicles (HFs). ILClc induced all hallmarks of AA ex vivo: they significantly promoted premature, apoptosis-driven HF regression (catagen), HF cytotoxicity/dystrophy, and most important for AA pathogenesis, the collapse of the HFs physiological immune privilege. NKG2D-blocking or IFNγ-neutralizing antibodies antagonized this. In vivo, intradermal injection of autologous activated, NKG2D+/IFNγ-secreting ILC1lc into healthy human scalp skin xenotransplanted onto SCID/beige mice sufficed to rapidly induce characteristic AA lesions. This provides the first evidence that ILC1lc, which are positive for the ILC1 phenotype and negative for the classical NK markers, suffice to induce AA in previously healthy human HFs ex vivo and in vivo, and further questions the conventional wisdom that AA is always an autoantigen-dependent, CD8 +T cell-driven autoimmune disease.
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Affiliation(s)
- Rimma Laufer Britva
- Skin Research Laboratory, Rappaport Faculty of Medicine, Technion – Israel Institute of TechnologyHaifaIsrael
- Department of Dermatology, Rambam Health Care CampusHaifaIsrael
| | - Aviad Keren
- Skin Research Laboratory, Rappaport Faculty of Medicine, Technion – Israel Institute of TechnologyHaifaIsrael
| | | | - Yehuda Ullmann
- Department of Plastic Surgery, Rambam Medical CenterHaifaIsrael
| | - Ralf Paus
- Monasterium LaboratoryMünsterGermany
- Dr. Phillip Frost Department of Dermatology & Cutaneous Surgery, Miller School of Medicine, University of MiamiMiamiUnited States
- CUTANEONHamburgGermany
| | - Amos Gilhar
- Skin Research Laboratory, Rappaport Faculty of Medicine, Technion – Israel Institute of TechnologyHaifaIsrael
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Smith KJ, Sciumè G, Amarnath S. Twenty-One Flavors of Type 1 Innate Lymphoid Cells with PD-1 (Programmed Cell Death-1 Receptor) Sprinkles. DISCOVERY IMMUNOLOGY 2023; 2:kyad003. [PMID: 38567059 PMCID: PMC10917210 DOI: 10.1093/discim/kyad003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/16/2023] [Accepted: 02/06/2023] [Indexed: 04/04/2024]
Abstract
Innate lymphoid cells (ILCs) are tissue-resident immune cells that have been recently implicated in initiating and driving anti-tumor responses. ILCs are classified into three main groups, namely type 1 ILCs (ILC1), type 2 ILCs, and type 3 ILCs. All three groups have been implicated in either eliciting pro or anti-tumor immune responses in different cancer subtypes with the consensus that ILCs cannot be overlooked within the field of anti-tumor immune responses. In this review, we will specifically expand on the knowledge on ILC1, their characterization, function, and plasticity in anti-cancer immune responses. Within this premise, we will discuss caveats of ILC1 characterization, and expand on the expression and function of immune checkpoint receptors within ILC1 subsets, specifically focusing on the role of programmed cell death-1 receptor in controlling specific ILC1 responses. We summarize that ILC1s are a vital component in initiating anti-tumor responses and can be boosted by checkpoint receptors.
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Affiliation(s)
- Katie J Smith
- The Biosciences Institute, Newcastle University Biosciences Institute, Newcastle upon Tyne, UK
- The Centre for Cancer, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
- Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Giuseppe Sciumè
- Department of Molecular Medicine, Laboratory affiliated to Istituto Pasteur Italia – Fondazione Cenci Bolognetti, Sapienza University of Rome, Rome, Italy
| | - Shoba Amarnath
- The Biosciences Institute, Newcastle University Biosciences Institute, Newcastle upon Tyne, UK
- The Centre for Cancer, Newcastle University Centre for Cancer, Newcastle upon Tyne, UK
- Medical School, Newcastle University, Newcastle upon Tyne, UK
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45
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McDaniel MM, Lara HI, von Moltke J. Initiation of type 2 immunity at barrier surfaces. Mucosal Immunol 2023; 16:86-97. [PMID: 36642383 DOI: 10.1016/j.mucimm.2022.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 01/15/2023]
Abstract
Although seemingly unrelated, parasitic worms, venoms, and allergens all induce a type 2 immune response. The effector functions and clinical features of type 2 immunity are well-defined, but fundamental questions about the initiation of type 2 immunity remain unresolved. How are these enormously diverse type 2 stimuli first detected? How are type 2 helper T cells primed and regulated? And how do mechanisms of type 2 initiation vary across tissues? Here, we review the common themes governing type 2 immune sensing and explore aspects of T cell priming and effector reactivation that make type 2 helper T cells a unique T helper lineage. Throughout the review, we emphasize the importance of non-hematopoietic cells and highlight how the unique anatomy and physiology of each barrier tissue shape mechanisms of type 2 immune initiation.
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Affiliation(s)
- Margaret M McDaniel
- Department of Immunology, University of Washington School of Medicine, Seattle, USA.
| | - Heber I Lara
- Department of Immunology, University of Washington School of Medicine, Seattle, USA
| | - Jakob von Moltke
- Department of Immunology, University of Washington School of Medicine, Seattle, USA
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Song P, Cao K, Mao Y, Ai S, Sun F, Hu Q, Liu S, Wang M, Lu X, Guan W, Shen X. Tissue specific imprinting on innate lymphoid cells during homeostasis and disease process revealed by integrative inference of single-cell transcriptomics. Front Immunol 2023; 14:1127413. [PMID: 36960063 PMCID: PMC10028295 DOI: 10.3389/fimmu.2023.1127413] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/20/2023] [Indexed: 03/09/2023] Open
Abstract
Introduction Innate lymphoid cells (ILCs) are key components of the immune system, yet the similarity and distinction of the properties across tissues under homeostasis, inflammation and tumor process remain elusive. Methods Here we performed integrative inference of ILCs to reveal their transcriptional profiles and heterogeneity from single-cell genomics. We collected a large number of ILCs from human six different tissues which can represent unique immune niches (circulation, lymphoid tissue, normal and inflamed mucosa, tumor microenvironment), to systematically address the transcriptional imprinting. Results ILCs are profoundly imprinted by their organ of residence, and tissue-specific distinctions are apparent under pathological conditions. In the hepatocellular carcinoma microenvironment, we identified intermediate c-kit+ ILC2 population, and lin-CD127- NK-like cells that expressed markers of cytotoxicity including CCL5 and IFNG. Additionally, CD127+CD94+ ILC1s were preferentially enriched in inflamed ileum from patients with Crohn's disease. Discussion These analyses depicted a comprehensive characterization of ILC anatomical distribution and subset heterogeneity, and provided a base line for future temporal or spatial studies focused on tissue-specific ILC-mediated immunity.
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Affiliation(s)
- Peng Song
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Ke Cao
- Department of Critical Care Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Yonghuan Mao
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, China
| | - Shichao Ai
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Feng Sun
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Qiongyuan Hu
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Song Liu
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Meng Wang
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Xiaofeng Lu
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
- *Correspondence: Xiaofei Shen, ; Wenxian Guan, ; Xiaofeng Lu,
| | - Wenxian Guan
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
- *Correspondence: Xiaofei Shen, ; Wenxian Guan, ; Xiaofeng Lu,
| | - Xiaofei Shen
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
- Department of Gastrointestinal Surgery, Nanjing Drum Tower Hospital, Drum Tower Clinical Medical College of Nanjing Medical University, Nanjing, China
- *Correspondence: Xiaofei Shen, ; Wenxian Guan, ; Xiaofeng Lu,
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Identification of two migratory colon ILC2 populations differentially expressing IL-17A and IL-5/IL-13. SCIENCE CHINA. LIFE SCIENCES 2023; 66:67-80. [PMID: 35881219 DOI: 10.1007/s11427-022-2127-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/12/2022] [Indexed: 02/04/2023]
Abstract
Group 2 innate lymphoid cells (ILC2s) play important tissue resident roles in anti-parasite immunity, allergic immune response, tissue homeostasis, and tumor immunity. ILC2s are considered tissue resident cells with little proliferation at steady state. Recent studies have shown that a subset of small intestinal ILC2s could leave their residing tissues, circulate and migrate to different organs, including lung, liver, mesenteric LN and spleen, upon activation. However, it remains unknown whether other ILC populations with migratory behavior exist. In this study, we find two major colon ILC2 populations with potential to migrate to the lung in response to IL-25 stimulation. One subset expresses IL-17A and resembles inflammatory ILC2s (iILC2s) but lacks CD27 expression, whereas the other expresses CD27 but not IL-17A. In addition, the IL-17A+ ILC2s express lower levels of CD127, CD25, and ST2 than CD27+ ILC2s, which express higher levels of IL-5 and IL-13. Surprisingly, we found that both colon ILC2 populations still maintained their colonic features of preferential expression of IL-17A and CD27, IL-5/IL-13, respectively. Together, our study identifies two migratory colon ILC2 subsets with unique surface markers and cytokine profiles which are critical in regulating lung and colon immunity and homeostasis.
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Colpitts SJ, Budd MA, Monajemi M, Reid KT, Murphy JM, Ivison S, Verchere CB, Levings MK, Crome SQ. Strategies for optimizing CITE-seq for human islets and other tissues. Front Immunol 2023; 14:1107582. [PMID: 36936943 PMCID: PMC10014726 DOI: 10.3389/fimmu.2023.1107582] [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: 11/25/2022] [Accepted: 01/30/2023] [Indexed: 03/05/2023] Open
Abstract
Defining the immunological landscape of human tissue is an important area of research, but challenges include the impact of tissue disaggregation on cell phenotypes and the low abundance of immune cells in many tissues. Here, we describe methods to troubleshoot and standardize Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq) for studies involving enzymatic digestion of human tissue. We tested epitope susceptibility of 92 antibodies commonly used to differentiate immune lineages and cell states on human peripheral blood mononuclear cells following treatment with an enzymatic digestion cocktail used to isolate islets. We observed CD4, CD8a, CD25, CD27, CD120b, CCR4, CCR6, and PD1 display significant sensitivity to enzymatic treatment, effects that often could not be overcome with alternate antibodies. Comparison of flow cytometry-based CITE-seq antibody titrations and sequencing data supports that for the majority of antibodies, flow cytometry accurately predicts optimal antibody concentrations for CITE-seq. Comparison by CITE-seq of immune cells in enzymatically digested islet tissue and donor-matched spleen not treated with enzymes revealed little digestion-induced epitope cleavage, suggesting increased sensitivity of CITE-seq and/or that the islet structure may protect resident immune cells from enzymes. Within islets, CITE-seq identified immune cells difficult to identify by transcriptional signatures alone, such as distinct tissue-resident T cell subsets, mast cells, and innate lymphoid cells (ILCs). Collectively this study identifies strategies for the rational design and testing of CITE-seq antibodies for single-cell studies of immune cells within islets and other tissues.
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Affiliation(s)
- Sarah J. Colpitts
- Department of Immunology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Toronto General Hospital Research Institute, Ajmera Transplant Centre, University Health Network, Toronto, ON, Canada
| | - Matthew A. Budd
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Mahdis Monajemi
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Kyle T. Reid
- Department of Immunology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Toronto General Hospital Research Institute, Ajmera Transplant Centre, University Health Network, Toronto, ON, Canada
| | - Julia M. Murphy
- Department of Immunology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Toronto General Hospital Research Institute, Ajmera Transplant Centre, University Health Network, Toronto, ON, Canada
| | - Sabine Ivison
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - C. Bruce Verchere
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, Canada and Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Megan K. Levings, ; Sarah Q. Crome, ; C. Bruce Verchere,
| | - Megan K. Levings
- Department of Surgery, University of British Columbia, Vancouver, BC, Canada
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, Canada
- *Correspondence: Megan K. Levings, ; Sarah Q. Crome, ; C. Bruce Verchere,
| | - Sarah Q. Crome
- Department of Immunology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Toronto General Hospital Research Institute, Ajmera Transplant Centre, University Health Network, Toronto, ON, Canada
- *Correspondence: Megan K. Levings, ; Sarah Q. Crome, ; C. Bruce Verchere,
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Li M, Wang Z, Jiang W, Lu Y, Zhang J. The role of group 3 innate lymphoid cell in intestinal disease. Front Immunol 2023; 14:1171826. [PMID: 37122757 PMCID: PMC10140532 DOI: 10.3389/fimmu.2023.1171826] [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: 02/22/2023] [Accepted: 04/03/2023] [Indexed: 05/02/2023] Open
Abstract
Group 3 innate lymphoid cells (ILC3s), a novel subpopulation of lymphocytes enriched in the intestinal mucosa, are currently considered as key sentinels in maintaining intestinal immune homeostasis. ILC3s can secrete a series of cytokines such as IL-22 to eliminate intestinal luminal antigens, promote epithelial tissue repair and mucosal barrier integrity, and regulate intestinal immunity by integrating multiple signals from the environment and the host. However, ILC3 dysfunction may be associated with the development and progression of various diseases in the gut. Therefore, in this review, we will discuss the role of ILC3 in intestinal diseases such as enteric infectious diseases, intestinal inflammation, and tumors, with a focus on recent research advances and discoveries to explore potential therapeutic targets.
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Group 2 innate lymphoid cells in human asthma. Allergol Int 2022; 72:194-200. [PMID: 36585333 DOI: 10.1016/j.alit.2022.12.001] [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: 11/24/2022] [Accepted: 11/30/2022] [Indexed: 12/30/2022] Open
Abstract
Asthma is characterized by increased airway hyperresponsiveness, reversible airflow limitation, and remodeling due to allergic airway inflammation. Asthma has been proposed to be classified into various phenotypes by cluster analyses integrating clinical information and laboratory data. Recently, asthma has been classified into two major endotypes, Type 2-high and Type 2-low asthma, and various subtypes based on the underlying molecular mechanisms. In Type 2-high asthma, Th2 cells, together with group 2 innate lymphoid cells (ILC2s), produce type 2 cytokines such as IL-4, IL-5, IL-9, and IL-13, which play crucial roles in causing airway inflammation. The roles of ILC2s in asthma pathogenesis have been analyzed primarily in murine models, demonstrating their importance not only in IL-33- or papain-induced innate asthma models but also in house dust mite (HDM)- or ovalbumin (OVA)-induced acquired asthma models evoked in an antigen-specific manner. Recently, evidence regarding the roles of ILC2s in human asthma is also accumulating. This minireview summarizes the roles of ILC2s in asthma, emphasizing human studies.
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