1
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Ma Y, Shi R, Li F, Chang H. Emerging strategies for treating autoimmune disease with genetically modified dendritic cells. Cell Commun Signal 2024; 22:262. [PMID: 38715122 PMCID: PMC11075321 DOI: 10.1186/s12964-024-01641-7] [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: 11/15/2023] [Accepted: 04/28/2024] [Indexed: 05/12/2024] Open
Abstract
Gene editing of living cells has become a crucial tool in medical research, enabling scientists to address fundamental biological questions and develop novel strategies for disease treatment. This technology has particularly revolutionized adoptive transfer cell therapy products, leading to significant advancements in tumor treatment and offering promising outcomes in managing transplant rejection, autoimmune disorders, and inflammatory diseases. While recent clinical trials have demonstrated the safety of tolerogenic dendritic cell (TolDC) immunotherapy, concerns remain regarding its effectiveness. This review aims to discuss the application of gene editing techniques to enhance the tolerance function of dendritic cells (DCs), with a particular focus on preclinical strategies that are currently being investigated to optimize the tolerogenic phenotype and function of DCs. We explore potential approaches for in vitro generation of TolDCs and provide an overview of emerging strategies for modifying DCs. Additionally, we highlight the primary challenges hindering the clinical adoption of TolDC therapeutics and propose future research directions in this field.
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Affiliation(s)
- Yunhan Ma
- School of Medicine, Jiangsu University, Zhenjiang, 212000, China
| | - Ruobing Shi
- School of Medicine, Jiangsu University, Zhenjiang, 212000, China
| | - Fujun Li
- Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, 530000, China
| | - Haocai Chang
- MOE Key Laboratory of Laser Life Science, Institute of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China.
- Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, 510631, China.
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2
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Sirvent S, Vallejo AF, Corden E, Teo Y, Davies J, Clayton K, Seaby EG, Lai C, Ennis S, Alyami R, Douilhet G, Dean LSN, Loxham M, Horswill S, Healy E, Roberts G, Hall NJ, Friedmann PS, Singh H, Bennett CL, Ardern-Jones MR, Polak ME. Impaired expression of metallothioneins contributes to allergen-induced inflammation in patients with atopic dermatitis. Nat Commun 2023; 14:2880. [PMID: 37208336 DOI: 10.1038/s41467-023-38588-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 04/29/2023] [Indexed: 05/21/2023] Open
Abstract
Regulation of cutaneous immunity is severely compromised in inflammatory skin disease. To investigate the molecular crosstalk underpinning tolerance versus inflammation in atopic dermatitis, we utilise a human in vivo allergen challenge study, exposing atopic dermatitis patients to house dust mite. Here we analyse transcriptional programmes at the population and single cell levels in parallel with immunophenotyping of cutaneous immunocytes revealed a distinct dichotomy in atopic dermatitis patient responsiveness to house dust mite challenge. Our study shows that reactivity to house dust mite was associated with high basal levels of TNF-expressing cutaneous Th17 T cells, and documents the presence of hub structures where Langerhans cells and T cells co-localised. Mechanistically, we identify expression of metallothioneins and transcriptional programmes encoding antioxidant defences across all skin cell types, that appear to protect against allergen-induced inflammation. Furthermore, single nucleotide polymorphisms in the MTIX gene are associated with patients who did not react to house dust mite, opening up possibilities for therapeutic interventions modulating metallothionein expression in atopic dermatitis.
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Affiliation(s)
- Sofia Sirvent
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Andres F Vallejo
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Emma Corden
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Ying Teo
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - James Davies
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- Department of Haematology, University College London (UCL) Cancer Institute, London, WC1E 6DD, UK
| | - Kalum Clayton
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Eleanor G Seaby
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Chester Lai
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Sarah Ennis
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Rfeef Alyami
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Gemma Douilhet
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Lareb S N Dean
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Matthew Loxham
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Sarah Horswill
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Eugene Healy
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Graham Roberts
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Nigel J Hall
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
- University Surgery Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Peter S Friedmann
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Harinder Singh
- Departments of Immunology and Computational and Systems Biology, The University of Pittsburgh, Pittsburgh, USA
| | - Clare L Bennett
- Department of Haematology, University College London (UCL) Cancer Institute, London, WC1E 6DD, UK
| | - Michael R Ardern-Jones
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- University Hospital Southampton NHS Foundation Trust, Southampton, UK
- Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Marta E Polak
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.
- Institute for Life Sciences, University of Southampton, Southampton, UK.
- Janssen R&D, 1400 McKean Road, Spring House, PA, 19477, USA.
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3
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Howell R, Davies J, Clarke MA, Appios A, Mesquita I, Jayal Y, Ringham-Terry B, Boned Del Rio I, Fisher J, Bennett CL. Localized immune surveillance of primary melanoma in the skin deciphered through executable modeling. SCIENCE ADVANCES 2023; 9:eadd1992. [PMID: 37043573 PMCID: PMC10096595 DOI: 10.1126/sciadv.add1992] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 03/10/2023] [Indexed: 06/19/2023]
Abstract
While skin is a site of active immune surveillance, primary melanomas often escape detection. Here, we have developed an in silico model to determine the local cross-talk between melanomas and Langerhans cells (LCs), the primary antigen-presenting cells at the site of melanoma development. The model predicts that melanomas fail to activate LC migration to lymph nodes until tumors reach a critical size, which is determined by a positive TNF-α feedback loop within melanomas, in line with our observations of murine tumors. In silico drug screening, supported by subsequent experimental testing, shows that treatment of primary tumors with MAPK pathway inhibitors may further prevent LC migration. In addition, our in silico model predicts treatment combinations that bypass LC dysfunction. In conclusion, our combined approach of in silico and in vivo studies suggests a molecular mechanism that explains how early melanomas develop under the radar of immune surveillance by LC.
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Affiliation(s)
| | | | - Matthew A. Clarke
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Anna Appios
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Inês Mesquita
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Yashoda Jayal
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Ben Ringham-Terry
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
| | - Isabel Boned Del Rio
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6DD, UK
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4
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Clayton K, Holbrook DJ, Vallejo A, Porter G, Sirvent S, Davies J, Pople J, Lim FL, Christodoulides M, Polak ME, Ardern-Jones MR. Skin programming of inflammatory responses to Staphylococcus aureus is compartmentalized according to epidermal keratinocyte differentiation status. Br J Dermatol 2023; 188:396-406. [PMID: 36637891 DOI: 10.1093/bjd/ljac088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 10/20/2022] [Accepted: 11/05/2022] [Indexed: 01/14/2023]
Abstract
BACKGROUND Acute cutaneous inflammation causes microbiome alterations as well as ultrastructural changes in epidermis stratification. However, the interactions between keratinocyte proliferation and differentiation status and the skin microbiome have not been fully explored. OBJECTIVES Hypothesizing that the skin microbiome contributes to regulation of keratinocyte differentiation and can modify antimicrobial responses, we examined the effect of exposure to commensal (Staphylococcus epidermidis, SE) or pathogenic (Staphylococcus aureus, SA) challenge on epidermal models. METHODS Explant biopsies were taken to investigate species-specific antimicrobial effects of host factors. Further investigations were performed in reconstituted epidermal models by bulk transcriptomic analysis alongside secreted protein profiling. Single-cell RNA sequencing analysis was performed to explore the keratinocyte populations responsible for SA inflammation. A dataset of 6391 keratinocytes from control (2044 cells), SE challenge (2028 cells) and SA challenge (2319 cells) was generated from reconstituted epidermal models. RESULTS Bacterial lawns of SA, not SE, were inhibited by human skin explant samples, and microarray analysis of three-dimensional epidermis models showed that host antimicrobial peptide expression was induced by SE but not SA. Protein analysis of bacterial cocultured models showed that SA exposure induced inflammatory mediator expression, indicating keratinocyte activation of other epidermal immune populations. Single-cell DropSeq analysis of unchallenged naive, SE-challenged and SA-challenged epidermis models was undertaken to distinguish cells from basal, spinous and granular layers, and to interrogate them in relation to model exposure. In contrast to SE, SA specifically induced a subpopulation of spinous cells that highly expressed transcripts related to epidermal inflammation and antimicrobial response. Furthermore, SA, but not SE, specifically induced a basal population that highly expressed interleukin-1 alarmins. CONCLUSIONS These findings suggest that SA-associated remodelling of the epidermis is compartmentalized to different keratinocyte populations. Elucidating the mechanisms regulating bacterial sensing-triggered inflammatory responses within tissues will enable further understanding of microbiome dysbiosis and inflammatory skin diseases, such as atopic eczema.
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Affiliation(s)
- Kalum Clayton
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Daniel J Holbrook
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Andres Vallejo
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Gemma Porter
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Sofia Sirvent
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, UK
| | - James Davies
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Jenny Pople
- Unilever, Colworth Science Park, Sharnbrook, Bedford, UK
| | - Fei Ling Lim
- Unilever, Colworth Science Park, Sharnbrook, Bedford, UK
| | - Myron Christodoulides
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Marta E Polak
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, UK.,Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Michael R Ardern-Jones
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, UK.,Department of Dermatology, University Hospitals Southampton NHS Foundation Trust, Southampton, UK
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5
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Chopra A, Gupta A. Skin as an immune organ and the site of biomimetic, non-invasive vaccination. MEDICINE IN NOVEL TECHNOLOGY AND DEVICES 2022. [DOI: 10.1016/j.medntd.2022.100196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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6
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Davies J, Sirvent S, Vallejo AF, Clayton K, Douilhet G, Keeler PS, West J, Ardern-Jones M, MacArthur BD, Singh H, Polak ME. Transcriptional programming of immunoregulatory responses in human Langerhans cells. Front Immunol 2022; 13:892254. [PMID: 36203560 PMCID: PMC9530347 DOI: 10.3389/fimmu.2022.892254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 08/25/2022] [Indexed: 11/27/2022] Open
Abstract
Human epidermal Langerhans cells (LCs) maintain immune homeostasis in the skin. To examine transcriptional programming of human primary LCs during homeostasis, we performed scRNA-seq analysis of LCs before and after migration from the epidermis, coupled with functional assessment of their regulatory T cell priming capabilities. The analysis revealed that steady-state LCs exist in a continuum of maturation states and upregulate antigen presentation genes along with an immunoregulatory module including the genes IDO1, LGALS1, LAMTOR1, IL4I, upon their migration. The migration-induced transition in genomic state is accompanied by the ability of LCs to more efficiently prime regulatory T cell responses in co-culture assays. Computational analyses of the scRNAseq datasets using SCENIC and Partial Information Decomposition in Context identified a set of migration-induced transcription factors including IRF4, KLF6 and RelB as key nodes within a immunoregulatory gene regulatory network. These findings support a model in which efficient priming of immunoregulatory responses by LCs is dependent on coordinated upregulation of a migration-coupled maturation program with a immunoregulation-promoting genomic module.
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Affiliation(s)
- James Davies
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Sofia Sirvent
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Andres F. Vallejo
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Kalum Clayton
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Gemma Douilhet
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Patrick S. Keeler
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Jonathan West
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Michael Ardern-Jones
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Ben D. MacArthur
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Harinder Singh
- Center for Systems Immunology, Departments of Immunology and Computational and Systems Biology, The University of Pittsburgh, Pittsburgh, PA, United States
- *Correspondence: Marta E. Polak, ; Harinder Singh,
| | - Marta E. Polak
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
- Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
- *Correspondence: Marta E. Polak, ; Harinder Singh,
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7
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The Roles of Skin Langerhans Cells in Immune Tolerance and Cancer Immunity. Vaccines (Basel) 2022; 10:vaccines10091380. [PMID: 36146458 PMCID: PMC9503294 DOI: 10.3390/vaccines10091380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/14/2022] [Accepted: 08/19/2022] [Indexed: 12/19/2022] Open
Abstract
Langerhans cells (LC) are a unique population of tissue-resident macrophages with dendritic cell (DC) functionality that form a network of cells across the epidermis of the skin. Their location at the skin barrier suggests an important role for LC as immune sentinels at the skin surface. The classification of LC as DC over the past few decades has driven the scientific community to extensively study how LC function as DC-like cells that prime T cell immunity. However, LC are a unique type of tissue-resident macrophages, and recent evidence also supports an immunoregulatory role of LC at steady state and during specific inflammatory conditions, highlighting the impact of cutaneous environment in shaping LC functionality. In this mini review, we discuss the recent literature on the immune tolerance function of LC in homeostasis and disease conditions, including malignant transformation and progression; as well as LC functional plasticity for adaption to microenvironmental cues and the potential connection between LC population heterogeneity and functional diversity. Future investigation into the molecular mechanisms that LC use to integrate different microenvironment cues and adapt immunological responses for controlling LC functional plasticity is needed for future breakthroughs in tumor immunology, vaccine development, and treatments for inflammatory skin diseases.
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8
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MUM1/IRF4 is Highly Expressed in Dermatopathic Lymphadenopathy: Potential Utility in Diagnosis and Differential Diagnosis. Am J Surg Pathol 2022; 46:1514-1523. [PMID: 35877199 DOI: 10.1097/pas.0000000000001935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Dermatopathic lymphadenopathy (DL) is a distinctive type of lymph node hyperplasia that typically occurs in the setting of chronic dermatologic diseases. DL generally self-resolves following disappearance of the underlying skin stimulus and does not require any specific therapy. We recently observed multiple myeloma oncogene 1/interferon regulatory factor 4 (MUM1/IRF4) expression in a case of DL using immunohistochemical methods. The goal of this study was to systematically assess DL cases for MUM1/IRF4 expression and to survey other histiocytic and Langerhans cell lesions. We particularly focused on Langerhans cell histiocytosis (LCH) because the differential diagnosis of DL versus LCH in lymph nodes can be challenging. We identified high expression of MUM1/IRF4 in all 22 cases of DL tested. Specifically, MUM1/IRF4+ dendritic cells comprised 50% to 90% (median, 80%) of all dendritic cells in the paracortex of dermatopathic lymph nodes, always showing moderate or strong intensity. Among 10 DL cases stained for MUM1/IRF4 and langerin/CD207 using dual immunohistochemistry, MUM1/IRF4+ and langerin+ Langerhans cells represented 5% to 60% (median, 30%) of paracortical dendritic cells. MUM1/IRF4 was also positive in reactive Langerhans cells in skin biopsy specimens of all cases of spongiotic dermatitis (n=10) and normal skin (n=15), and was negative in all cases of LCH (n=24), Rosai-Dorfman disease (n=10), follicular dendritic cell sarcoma (n=5) and histiocytic sarcoma (n=4). In aggregate, our findings support the utility of MUM1/IRF4 to highlight the dendritic cells of DL and to distinguish DL from other histiocytic and Langerhans cells lesions.
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9
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Distinct human Langerhans cell subsets orchestrate reciprocal functions and require different developmental regulation. Immunity 2021; 54:2305-2320.e11. [PMID: 34508661 DOI: 10.1016/j.immuni.2021.08.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 05/19/2021] [Accepted: 08/11/2021] [Indexed: 12/22/2022]
Abstract
Langerhans cells (LCs) play a pivotal role in skin homeostasis, and the heterogeneity of LCs has long been considered. In this study, we have identified two steady-state (LC1 and LC2) and two activated LC subsets in the epidermis of human skin and in LCs derived from CD34+ hemopoietic stem cells (HSC-LCs) by utilizing single-cell RNA sequencing and mass cytometry. Analysis of HSC-LCs at multiple time-points during differentiation revealed that EGR1 and Notch signaling were among the top pathways regulating the bifurcation of LC1 and LC2. LC1 were characterized as classical LCs, mainly related to innate immunity and antigen processing. LC2 were similar to monocytes or myeloid dendritic cells, involving in immune responses and leukocyte activation. LC1 remained stable under inflammatory microenvironment, whereas LC2 were prone to being activated and demonstrated elevated expression of immuno-suppressive molecules. We revealed distinct human LC subsets that require different developmental regulation and orchestrate reciprocal functions.
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10
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Baglaenko Y, Macfarlane D, Marson A, Nigrovic PA, Raychaudhuri S. Genome editing to define the function of risk loci and variants in rheumatic disease. Nat Rev Rheumatol 2021; 17:462-474. [PMID: 34188205 PMCID: PMC10782829 DOI: 10.1038/s41584-021-00637-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2021] [Indexed: 02/06/2023]
Abstract
Discoveries in human genetic studies have revolutionized our understanding of complex rheumatic and autoimmune diseases, including the identification of hundreds of genetic loci and single nucleotide polymorphisms that potentially predispose individuals to disease. However, in most cases, the exact disease-causing variants and their mechanisms of action remain unresolved. Functional follow-up of these findings is most challenging for genomic variants that are in non-coding genomic regions, where the large majority of common disease-associated variants are located, and/or that probably affect disease progression via cell type-specific gene regulation. To deliver on the therapeutic promise of human genetic studies, defining the mechanisms of action of these alleles is essential. Genome editing technology, such as CRISPR-Cas, has created a vast toolbox for targeted genetic and epigenetic modifications that presents unprecedented opportunities to decipher disease-causing loci, genes and variants in autoimmunity. In this Review, we discuss the past 5-10 years of progress in resolving the mechanisms underlying rheumatic disease-associated alleles, with an emphasis on how genomic editing techniques can enable targeted dissection and mechanistic studies of causal autoimmune risk variants.
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Affiliation(s)
- Yuriy Baglaenko
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Dana Macfarlane
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Alexander Marson
- Gladstone Institutes, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
- Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, University of California, San Francisco, San Francisco, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Peter A Nigrovic
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Immunology, Boston Children's Hospital, Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK.
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11
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Davies J, Vallejo AF, Sirvent S, Porter G, Clayton K, Qumbelo Y, Stumpf P, West J, Gray CM, Chigorimbo-Murefu NTL, MacArthur B, Polak ME. An IRF1-IRF4 Toggle-Switch Controls Tolerogenic and Immunogenic Transcriptional Programming in Human Langerhans Cells. Front Immunol 2021; 12:665312. [PMID: 34211464 PMCID: PMC8239435 DOI: 10.3389/fimmu.2021.665312] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/25/2021] [Indexed: 12/27/2022] Open
Abstract
Langerhans cells (LCs) reside in the epidermis as a dense network of immune system sentinels, coordinating both immunogenic and tolerogenic immune responses. To determine molecular switches directing induction of LC immune activation, we performed mathematical modelling of gene regulatory networks identified by single cell RNA sequencing of LCs exposed to TNF-alpha, a key pro-inflammatory signal produced by the skin. Our approach delineated three programmes of LC phenotypic activation (immunogenic, tolerogenic or ambivalent), and confirmed that TNF-alpha enhanced LC immunogenic programming. Through regulon analysis followed by mutual information modelling, we identified IRF1 as the key transcription factor for the regulation of immunogenicity in LCs. Application of a mathematical toggle switch model, coupling IRF1 with tolerance-inducing transcription factors, determined the key set of transcription factors regulating the switch between tolerance and immunogenicity, and correctly predicted LC behaviour in LCs derived from different body sites. Our findings provide a mechanistic explanation of how combinatorial interactions between different transcription factors can coordinate specific transcriptional programmes in human LCs, interpreting the microenvironmental context of the local tissue microenvironments.
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Affiliation(s)
- James Davies
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Andres F Vallejo
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Sofia Sirvent
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Gemma Porter
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Kalum Clayton
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Yamkela Qumbelo
- Division of Immunology, Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Patrick Stumpf
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Jonathan West
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Clive M Gray
- Division of Immunology, Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Nyaradzo T L Chigorimbo-Murefu
- Division of Immunology, Institute of Infectious Disease and Molecular Medicine, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Ben MacArthur
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Marta E Polak
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.,Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
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12
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Bennett CL. Switching between tolerance and immunity: Do counter-acting gene networks dictate Langerhans cell function in the skin? Bioessays 2021; 43:e2100072. [PMID: 33782997 DOI: 10.1002/bies.202100072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 03/09/2021] [Indexed: 01/14/2023]
Affiliation(s)
- Clare L Bennett
- Department of Haematology, University College London (UCL) Cancer Institute, London, UK
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Iwabuchi R, Ide K, Terahara K, Wagatsuma R, Iwaki R, Matsunaga H, Tsunetsugu-Yokota Y, Takeyama H, Takahashi Y. Development of an Inflammatory CD14 + Dendritic Cell Subset in Humanized Mice. Front Immunol 2021; 12:643040. [PMID: 33790912 PMCID: PMC8005643 DOI: 10.3389/fimmu.2021.643040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/16/2021] [Indexed: 12/12/2022] Open
Abstract
Humanized mouse models are attractive experimental models for analyzing the development and functions of human dendritic cells (DCs) in vivo. Although various types of DC subsets, including DC type 3 (DC3s), have been identified in humans, it remains unclear whether humanized mice can reproduce heterogeneous DC subsets. CD14, classically known as a monocyte/macrophage marker, is reported as an indicator of DC3s. We previously observed that some CD14+ myeloid cells expressed CD1c, a pan marker for bona fide conventional DC2 (cDC2s), in humanized mouse models in which human FLT3L and GM-CSF genes were transiently expressed using in vivo transfection (IVT). Here, we aimed to elucidate the identity of CD14+CD1c+ DC-like cells in humanized mouse models. We found that CD14+CD1c+ cells were phenotypically different from cDC2s; CD14+CD1c+ cells expressed CD163 but not CD5, whereas cDC2s expressed CD5 but not CD163. Furthermore, CD14+CD1c+ cells primed and polarized naïve CD4+ T cells toward IFN-γ+ Th1 cells more profoundly than cDC2s. Transcriptional analysis revealed that CD14+CD1c+ cells expressed several DC3-specific transcripts, such as CD163, S100A8, and S100A9, and were clearly segregated from cDC2s and monocytes. When lipopolysaccharide was administered to the humanized mice, the frequency of CD14+CD1c+ cells producing IL-6 and TNF-α was elevated, indicating a pro-inflammatory signature. Thus, humanized mice are able to sustain development of functional CD14+CD1c+ DCs, which are equivalent to DC3 subset observed in humans, and they could be useful for analyzing the development and function of DC3s in vivo.
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Affiliation(s)
- Ryutaro Iwabuchi
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, Japan.,Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan.,Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Keigo Ide
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan.,Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Kazutaka Terahara
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ryota Wagatsuma
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Rieko Iwaki
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hiroko Matsunaga
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
| | - Yasuko Tsunetsugu-Yokota
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, Japan.,Department of Medical Technology, School of Human Sciences, Tokyo University of Technology, Tokyo, Japan
| | - Haruko Takeyama
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan.,Computational Bio Big-Data Open Innovation Laboratory, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.,Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan.,Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
| | - Yoshimasa Takahashi
- Department of Immunology, National Institute of Infectious Diseases, Tokyo, Japan
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Polak ME, Singh H. Tolerogenic and immunogenic states of Langerhans cells are orchestrated by epidermal signals acting on a core maturation gene module. Bioessays 2021; 43:e2000182. [PMID: 33645739 DOI: 10.1002/bies.202000182] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 12/11/2022]
Abstract
Langerhans cells (LCs), residing in the epidermis, are able to induce potent immunogenic responses and also to mediate immune tolerance. We propose that tolerogenic and immunogenic responses of LCs are directed by signaling from the epidermis and involve counter-acting gene circuits that are coupled to a core maturation gene module. We base our analysis on recent genetic and genomic findings facilitating the understanding of the molecular mechanisms controlling these divergent immune functions. Comparing gene regulatory network (GRN) analyses of various types of dendritic cells (DCs) including LCs we integrate signaling-dependent (TGFβ, EpCAM, β-Catenin) and transcription factor (IRF4, IRF1, NFκB) regulated gene circuits that appear to orchestrate the distinctive LC functional states. Our model proposes, that while epidermal signaling in the steady-state promotes LC tolerogenic function, the disruption of cell-cell contacts coupled with inflammatory signaling induces LC immunogenic programing. The conceptual framework emphasizes the sensing of discrete epidermal and inflammatory cues by resident LCs in dictating their genomic programing and cell state dynamics.
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Affiliation(s)
- Marta E Polak
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, UK.,Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Harinder Singh
- Center for Systems Immunology, Departments of Immunology and Computational and Systems Biology, The University of Pittsburgh, Pittsburgh, Pennsylvania, USA
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Oulee A, Ma F, Teles RMB, de Andrade Silva BJ, Pellegrini M, Klechevsky E, Harman AN, Rhodes JW, Modlin RL. Identification of Genes Encoding Antimicrobial Proteins in Langerhans Cells. Front Immunol 2021; 12:695373. [PMID: 34512625 PMCID: PMC8426439 DOI: 10.3389/fimmu.2021.695373] [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: 04/14/2021] [Accepted: 08/06/2021] [Indexed: 12/03/2022] Open
Abstract
Langerhans cells (LCs) reside in the epidermis where they are poised to mount an antimicrobial response against microbial pathogens invading from the outside environment. To elucidate potential pathways by which LCs contribute to host defense, we mined published LC transcriptomes deposited in GEO and the scientific literature for genes that participate in antimicrobial responses. Overall, we identified 31 genes in LCs that encode proteins that contribute to antimicrobial activity, ten of which were cross-validated in at least two separate experiments. Seven of these ten antimicrobial genes encode chemokines, CCL1, CCL17, CCL19, CCL2, CCL22, CXCL14 and CXCL2, which mediate both antimicrobial and inflammatory responses. Of these, CCL22 was detected in seven of nine transcriptomes and by PCR in cultured LCs. Overall, the antimicrobial genes identified in LCs encode proteins with broad antibacterial activity, including against Staphylococcus aureus, which is the leading cause of skin infections. Thus, this study illustrates that LCs, consistent with their anatomical location, are programmed to mount an antimicrobial response against invading pathogens in skin.
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Affiliation(s)
- Aislyn Oulee
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Feiyang Ma
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Rosane M B Teles
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Bruno J de Andrade Silva
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Eynav Klechevsky
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United States
| | - Andrew N Harman
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,School of Medical Sciences, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia
| | - Jake W Rhodes
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, NSW, Australia.,School of Medical Sciences, Faculty of Medicine and Health Sydney, The University of Sydney, Westmead, NSW, Australia
| | - Robert L Modlin
- Division of Dermatology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
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