1
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Shilts J, Wright GJ. Mapping the Human Cell Surface Interactome: A Key to Decode Cell-to-Cell Communication. Annu Rev Biomed Data Sci 2024; 7:155-177. [PMID: 38723658 DOI: 10.1146/annurev-biodatasci-102523-103821] [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: 08/25/2024]
Abstract
Proteins on the surfaces of cells serve as physical connection points to bridge one cell with another, enabling direct communication between cells and cohesive structure. As biomedical research makes the leap from characterizing individual cells toward understanding the multicellular organization of the human body, the binding interactions between molecules on the surfaces of cells are foundational both for computational models and for clinical efforts to exploit these influential receptor pathways. To achieve this grander vision, we must assemble the full interactome of ways surface proteins can link together. This review investigates how close we are to knowing the human cell surface protein interactome. We summarize the current state of databases and systematic technologies to assemble surface protein interactomes, while highlighting substantial gaps that remain. We aim for this to serve as a road map for eventually building a more robust picture of the human cell surface protein interactome.
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Affiliation(s)
- Jarrod Shilts
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, York, United Kingdom;
- School of the Biological Sciences, University of Cambridge, Cambridge, United Kingdom;
| | - Gavin J Wright
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, York, United Kingdom;
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2
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McMahon‑Cole H, Johnson A, Sadat Aghamiri S, Helikar T, Crawford LB. Modeling and Remodeling the Cell: How Digital Twins and HCMV Can Elucidate the Complex Interactions of Viral Latency, Epigenetic Regulation, and Immune Responses. CURRENT CLINICAL MICROBIOLOGY REPORTS 2023; 10:141-151. [PMID: 37901689 PMCID: PMC10601359 DOI: 10.1007/s40588-023-00201-w] [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] [Accepted: 07/12/2023] [Indexed: 10/31/2023]
Abstract
Purpose of Review Human cytomegalovirus (HCMV), while asymptomatic in most, causes significant complications during fetal development, following transplant or in immunosuppressed individuals. The host-virus interactions regulating viral latency and reactivation and viral control of the cellular environment (immune regulation, differentiation, epigenetics) are highly complex. Understanding these processes is essential to controlling infection and can be leveraged as a novel approach for understanding basic cell biology. Recent Findings Immune digital twins (IDTs) are digital simulations integrating knowledge of human immunology, physiology, and patient-specific clinical data to predict individualized immune responses and targeted treatments. Recent studies used IDTs to elucidate mechanisms of T cells, dendritic cells, and epigenetic control-all key to HCMV biology. Summary Here, we discuss how leveraging the unique biology of HCMV and IDTs will clarify immune response dynamics, host-virus interactions, and viral latency and reactivation and serve as a powerful IDT-validation platform for individualized and holistic health management.
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Affiliation(s)
- Hana McMahon‑Cole
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Alicia Johnson
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Sara Sadat Aghamiri
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Tomáš Helikar
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Lindsey B. Crawford
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
- Nebraska Center for Virology, Lincoln, NE, USA
- Nebraska Center for Integrated Biomolecular Communication, Lincoln, NE, USA
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3
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Aghamiri SS, Puniya BL, Amin R, Helikar T. A multiscale mechanistic model of human dendritic cells for in-silico investigation of immune responses and novel therapeutics discovery. Front Immunol 2023; 14:1112985. [PMID: 36993954 PMCID: PMC10040975 DOI: 10.3389/fimmu.2023.1112985] [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: 11/30/2022] [Accepted: 02/22/2023] [Indexed: 03/14/2023] Open
Abstract
Dendritic cells (DCs) are professional antigen-presenting cells (APCs) with the unique ability to mediate inflammatory responses of the immune system. Given the critical role of DCs in shaping immunity, they present an attractive avenue as a therapeutic target to program the immune system and reverse immune disease disorders. To ensure appropriate immune response, DCs utilize intricate and complex molecular and cellular interactions that converge into a seamless phenotype. Computational models open novel frontiers in research by integrating large-scale interaction to interrogate the influence of complex biological behavior across scales. The ability to model large biological networks will likely pave the way to understanding any complex system in more approachable ways. We developed a logical and predictive model of DC function that integrates the heterogeneity of DCs population, APC function, and cell-cell interaction, spanning molecular to population levels. Our logical model consists of 281 components that connect environmental stimuli with various layers of the cell compartments, including the plasma membrane, cytoplasm, and nucleus to represent the dynamic processes within and outside the DC, such as signaling pathways and cell-cell interactions. We also provided three sample use cases to apply the model in the context of studying cell dynamics and disease environments. First, we characterized the DC response to Sars-CoV-2 and influenza co-infection by in-silico experiments and analyzed the activity level of 107 molecules that play a role in this co-infection. The second example presents simulations to predict the crosstalk between DCs and T cells in a cancer microenvironment. Finally, for the third example, we used the Kyoto Encyclopedia of Genes and Genomes enrichment analysis against the model's components to identify 45 diseases and 24 molecular pathways that the DC model can address. This study presents a resource to decode the complex dynamics underlying DC-derived APC communication and provides a platform for researchers to perform in-silico experiments on human DC for vaccine design, drug discovery, and immunotherapies.
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Affiliation(s)
| | | | - Rada Amin
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Tomáš Helikar
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
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4
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Shilts J, Severin Y, Galaway F, Müller-Sienerth N, Chong ZS, Pritchard S, Teichmann S, Vento-Tormo R, Snijder B, Wright GJ. A physical wiring diagram for the human immune system. Nature 2022; 608:397-404. [PMID: 35922511 PMCID: PMC9365698 DOI: 10.1038/s41586-022-05028-x] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 06/28/2022] [Indexed: 12/14/2022]
Abstract
The human immune system is composed of a distributed network of cells circulating throughout the body, which must dynamically form physical associations and communicate using interactions between their cell-surface proteomes1. Despite their therapeutic potential2, our map of these surface interactions remains incomplete3,4. Here, using a high-throughput surface receptor screening method, we systematically mapped the direct protein interactions across a recombinant library that encompasses most of the surface proteins that are detectable on human leukocytes. We independently validated and determined the biophysical parameters of each novel interaction, resulting in a high-confidence and quantitative view of the receptor wiring that connects human immune cells. By integrating our interactome with expression data, we identified trends in the dynamics of immune interactions and constructed a reductionist mathematical model that predicts cellular connectivity from basic principles. We also developed an interactive multi-tissue single-cell atlas that infers immune interactions throughout the body, revealing potential functional contexts for new interactions and hubs in multicellular networks. Finally, we combined targeted protein stimulation of human leukocytes with multiplex high-content microscopy to link our receptor interactions to functional roles, in terms of both modulating immune responses and maintaining normal patterns of intercellular associations. Together, our work provides a systematic perspective on the intercellular wiring of the human immune system that extends from systems-level principles of immune cell connectivity down to mechanistic characterization of individual receptors, which could offer opportunities for therapeutic intervention.
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Affiliation(s)
- Jarrod Shilts
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, UK.
| | - Yannik Severin
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Francis Galaway
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, UK
| | | | - Zheng-Shan Chong
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, UK
| | - Sophie Pritchard
- Cellular Genetics Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Sarah Teichmann
- Cellular Genetics Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Roser Vento-Tormo
- Cellular Genetics Programme, Wellcome Sanger Institute, Cambridge, UK
| | - Berend Snijder
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Gavin J Wright
- Cell Surface Signalling Laboratory, Wellcome Sanger Institute, Cambridge, UK.
- Department of Biology, Hull York Medical School, York Biomedical Research Institute, University of York, York, UK.
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5
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Hoffmann C, Noel F, Grandclaudon M, Massenet-Regad L, Michea P, Sirven P, Faucheux L, Surun A, Lantz O, Bohec M, Ye J, Guo W, Rochefort J, Klijanienko J, Baulande S, Lecerf C, Kamal M, Le Tourneau C, Guillot-Delost M, Soumelis V. PD-L1 and ICOSL discriminate human Secretory and Helper dendritic cells in cancer, allergy and autoimmunity. Nat Commun 2022; 13:1983. [PMID: 35418195 PMCID: PMC9008048 DOI: 10.1038/s41467-022-29516-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 03/07/2022] [Indexed: 11/22/2022] Open
Abstract
Dendritic cells (DC) are traditionally classified according to their ontogeny and their ability to induce T cell response to antigens, however, the phenotypic and functional state of these cells in cancer does not necessarily align to the conventional categories. Here we show, by using 16 different stimuli in vitro that activated DCs in human blood are phenotypically and functionally dichotomous, and pure cultures of type 2 conventional dendritic cells acquire these states (termed Secretory and Helper) upon appropriate stimuli. PD-L1highICOSLlow Secretory DCs produce large amounts of inflammatory cytokines and chemokines but induce very low levels of T helper (Th) cytokines following co-culturing with T cells. Conversely, PD-L1lowICOSLhigh Helper DCs produce low levels of secreted factors but induce high levels and a broad range of Th cytokines. Secretory DCs bear a single-cell transcriptomic signature indicative of mature migratory LAMP3+ DCs associated with cancer and inflammation. Secretory DCs are linked to good prognosis in head and neck squamous cell carcinoma, and to response to checkpoint blockade in Melanoma. Hence, the functional dichotomy of DCs we describe has both fundamental and translational implications in inflammation and immunotherapy. Phenotypic and functional states of dendritic cells critically influence the outcome of cancer and inflammation. Authors here show by single cell transcriptomics and in vitro validation assays that dichotomous PD-L1 and ICOSL expression assign dendritic cells to secretory and helper functions, with respective predominance of inflammatory cytokine expression or T helper cytokine induction.
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Affiliation(s)
- Caroline Hoffmann
- Institut Curie, INSERM U932, Immunity and Cancer, Paris, France. .,Institut Curie, Department of Surgical Oncology, Paris & Saint-Cloud, France. .,Université Paris Sciences Lettres (PSL), Paris, France.
| | - Floriane Noel
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U976, Hôpital Saint-Louis, 75010, Paris, France
| | - Maximilien Grandclaudon
- Institut Curie, INSERM U932, Immunity and Cancer, Paris, France.,Université Paris Sciences Lettres (PSL), Paris, France
| | - Lucile Massenet-Regad
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U976, Hôpital Saint-Louis, 75010, Paris, France.,Université Paris-Saclay, Orsay, France
| | - Paula Michea
- Institut Paoli Calmette, INSERM U1068-CNRS UMR7258-AMU UM105, Marseille, France.,Université Aix-Marseille, Marseille, France
| | - Philemon Sirven
- Institut Curie, INSERM U932, Immunity and Cancer, Paris, France.,Université Paris Sciences Lettres (PSL), Paris, France
| | - Lilith Faucheux
- Université de Paris, Institut de Recherche Saint-Louis, INSERM U976, Hôpital Saint-Louis, 75010, Paris, France.,Statistic and Epidemiologic Research Center Sorbonne Paris Cité, INSERM UMR-1153, ECSTRRA team, Paris, France
| | - Aurore Surun
- Institut Curie, SIREDO Cancer Center, Paris, France
| | - Olivier Lantz
- Institut Curie, INSERM U932, Immunity and Cancer, Paris, France.,Université Paris Sciences Lettres (PSL), Paris, France.,CIC IGR-Curie 1428, Center of Clinical Investigation, Paris, France
| | - Mylene Bohec
- Université Paris Sciences Lettres (PSL), Paris, France.,Institut Curie, NGS platform, Paris, France
| | - Jian Ye
- City of Hope Comprehensive Cancer Center, Department of Immuno-Oncology, Duarte, CA, USA
| | - Weihua Guo
- City of Hope Comprehensive Cancer Center, Department of Immuno-Oncology, Duarte, CA, USA
| | - Juliette Rochefort
- Cimi Paris, INSERM U1135, and Hospital Pitié Salpêtrière, Odontology department, Université de Paris, Paris, France
| | - Jerzy Klijanienko
- Université Paris Sciences Lettres (PSL), Paris, France.,Institut Curie, Department of pathology, Paris, France
| | - Sylvain Baulande
- Université Paris Sciences Lettres (PSL), Paris, France.,Institut Curie, NGS platform, Paris, France
| | - Charlotte Lecerf
- Université Paris Sciences Lettres (PSL), Paris, France.,Institut Curie, Department of Drug Development, and Innovation (D3i), Paris & Saint-Cloud, France
| | - Maud Kamal
- Université Paris Sciences Lettres (PSL), Paris, France.,Institut Curie, Department of Drug Development, and Innovation (D3i), Paris & Saint-Cloud, France
| | - Christophe Le Tourneau
- Université Paris-Saclay, Orsay, France.,Institut Curie, Department of Drug Development, and Innovation (D3i), Paris & Saint-Cloud, France.,Institut Curie, INSERM U900, Saint-Cloud, France
| | - Maude Guillot-Delost
- Institut Curie, INSERM U932, Immunity and Cancer, Paris, France.,Université Paris Sciences Lettres (PSL), Paris, France.,CIC IGR-Curie 1428, Center of Clinical Investigation, Paris, France
| | - Vassili Soumelis
- Institut Curie, INSERM U932, Immunity and Cancer, Paris, France. .,Université Paris Sciences Lettres (PSL), Paris, France. .,Université de Paris, Institut de Recherche Saint-Louis, INSERM U976, Hôpital Saint-Louis, 75010, Paris, France. .,Institut Curie, Clinical immunology department, Paris, France. .,Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Saint-Louis, Laboratoire d'Immunologie, F-75010, Paris, France. .,Université de Paris, Institut de Recherche Saint-Louis, INSERM U976, Hôpital Saint-Louis, 75010, Paris, France.
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6
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Wahiduzzaman M, Liu Y, Huang T, Wei W, Li Y. Cell-cell communication analysis for single-cell RNA sequencing and its applications in carcinogenesis and COVID-19. BIOSAFETY AND HEALTH 2022. [DOI: 10.1016/j.bsheal.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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7
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Moldwin RM, Nursey V, Yaskiv O, Dalvi S, Macdonald EJ, Funaro M, Zhang C, DeGouveia W, Ruzimovsky M, Rilo HR, Miller EJ, Najjar S, Tabansky I, Stern JNH. Immune cell profiles of patients with interstitial cystitis/bladder pain syndrome. J Transl Med 2022; 20:97. [PMID: 35193610 PMCID: PMC8862517 DOI: 10.1186/s12967-022-03236-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/05/2022] [Indexed: 11/10/2022] Open
Abstract
Interstitial cystitis/bladder pain syndrome (IC/BPS) is a disorder characterized by bladder pain upon filling which severely affects quality of life. Clinical presentation can vary. Local inflammatory events typify the clinical presentation of IC/BPS patients with Hunner lesions (IC/BPS-HL). It has previously been proposed that B cells are more prevalent in HL, but understanding their exact role in this environment requires a more complete immunological profile of HL. We characterized immunological dysfunction specifically in HL using immunohistochemistry. We detected significantly more plasma cells (50× increase, p < 0.0001), B cells (28× increase, p < 0.0001), T cells (3× increase, p < 0.0001), monocytes/macrophages (6× increase, p < 0.0001), granulocytes (4× increase, p < 0.0001), and natural killer cells (2× increase, p = 0.0249) in IC/BPS patients with HL than in unaffected controls (UC). Patients with IC/BPS-HL also had significantly elevated urinary levels of IL-6 (p = 0.0054), TNF-α (p = 0.0064) and IL-13 (p = 0.0304) compared to patients with IC/BPS without HL (IC/BPS-NHL). In contrast, IL-12p70 levels were significantly lower in the patients with HL than in those without these lesions (p = 0.0422). Different cytokines were elevated in the urine of IC/BPS patients with and without HL, indicating that different disease processes are active in IC/BPS patients with and without HL. Elevated levels of CD138+, CD20+, and CD3+ cells in HL are consistent B and T-cell involvement in disease processes within HL.
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Affiliation(s)
- Robert M Moldwin
- The Smith Institute for Urology, Northwell Health, 450 Lakeville Road New Hyde Park, Lake Success, NY, USA.,Department of Urology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, 500 Hofstra University Blvd, Hempstead, NY, USA
| | - Vishaan Nursey
- Department of Neurology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA.,Institute of Molecular Medicine, The Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | - Oksana Yaskiv
- Department of Pathology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Siddhartha Dalvi
- Department of Pathology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Eric J Macdonald
- The Smith Institute for Urology, Northwell Health, 450 Lakeville Road New Hyde Park, Lake Success, NY, USA.,Department of Urology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, 500 Hofstra University Blvd, Hempstead, NY, USA
| | - Michael Funaro
- Institute of Molecular Medicine, The Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | - Chengliang Zhang
- Institute of Molecular Medicine, The Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | - William DeGouveia
- Institute of Molecular Medicine, The Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | - Marina Ruzimovsky
- The Smith Institute for Urology, Northwell Health, 450 Lakeville Road New Hyde Park, Lake Success, NY, USA.,Department of Urology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, 500 Hofstra University Blvd, Hempstead, NY, USA
| | - Horacio R Rilo
- Department of Surgery, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | | | - Souhel Najjar
- Department of Neurology, Lenox Hill Hospital, New York, NY, USA
| | - Inna Tabansky
- Institute of Molecular Medicine, The Feinstein Institutes for Medical Research, Manhasset, NY, USA.,Department of Neurobiology and Behavior, The Rockefeller University, New York, NY, USA.,Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Joel N H Stern
- The Smith Institute for Urology, Northwell Health, 450 Lakeville Road New Hyde Park, Lake Success, NY, USA. .,Department of Urology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, 500 Hofstra University Blvd, Hempstead, NY, USA. .,Department of Neurology, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA. .,Institute of Molecular Medicine, The Feinstein Institutes for Medical Research, Manhasset, NY, USA.
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8
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Karpf L, Trichot C, Faucheux L, Legbre I, Grandclaudon M, Lahoute C, Mattoo H, Pasquier B, Soumelis V. A multivariate modeling framework to quantify immune checkpoint context-dependent stimulation on T cells. Cell Discov 2022; 8:1. [PMID: 34983927 PMCID: PMC8727669 DOI: 10.1038/s41421-021-00352-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/28/2021] [Indexed: 11/09/2022] Open
Abstract
Cells receive, and adjust to, various stimuli, which function as part of complex microenvironments forming their "context". The possibility that a given context impacts the response to a given stimulus defines "context-dependency" and it explains large parts of the functional variability of physiopathological and pharmacological stimuli. Currently, there is no framework to analyze and quantify context-dependency over multiple contexts and cellular response outputs. We established an experimental system including a stimulus of interest, applied to an immune cell type in several contexts. We studied the function of OX40 ligand (OX40L) on T helper (Th) cell differentiation, in 4 molecular (Th0, Th1, Th2, and Th17) and 11 dendritic cell (DC) contexts (monocyte-derived DC and cDC2 conditions). We measured 17 Th output cytokines in 302 observations, and developed a statistical modeling strategy to quantify OX40L context-dependency. This revealed highly variable context-dependency, depending on the output cytokine and context type itself. Among molecular contexts, Th2 was the most influential on OX40L function. Among DC contexts, the DC type rather than the activating stimuli was dominant in controlling OX40L context-dependency. This work mathematically formalizes the complex determinants of OX40L functionality, and provides a unique framework to decipher and quantify the context-dependent variability of any biomolecule or drug function.
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Affiliation(s)
- Léa Karpf
- grid.418596.70000 0004 0639 6384Institut Curie, PSL University, INSERM U932, Paris, France ,grid.508487.60000 0004 7885 7602Université de Paris, Institut de Recherche Saint-Louis, INSERM U976, Paris, France
| | - Coline Trichot
- grid.418596.70000 0004 0639 6384Institut Curie, PSL University, INSERM U932, Paris, France ,grid.508487.60000 0004 7885 7602Université de Paris, Institut de Recherche Saint-Louis, INSERM U976, Paris, France ,grid.417924.dImmunology and Inflammation Therapeutic Area, Sanofi, Vitry-sur-Seine, France
| | - Lilith Faucheux
- grid.508487.60000 0004 7885 7602Université de Paris, Institut de Recherche Saint-Louis, INSERM U976, Paris, France ,grid.508487.60000 0004 7885 7602Université de Paris, Institut de Recherche Saint-Louis, INSERM UMR-1153, ECSTRRA Team, Paris, France
| | - Iris Legbre
- grid.508487.60000 0004 7885 7602Université de Paris, Institut de Recherche Saint-Louis, INSERM U976, Paris, France
| | | | - Charlotte Lahoute
- grid.417924.dImmunology and Inflammation Therapeutic Area, Sanofi, Vitry-sur-Seine, France
| | - Hamid Mattoo
- grid.417555.70000 0000 8814 392XImmunology and Inflammation Therapeutic Area, Sanofi, Cambridge, MA USA
| | - Benoit Pasquier
- grid.417924.dImmunology and Inflammation Therapeutic Area, Sanofi, Vitry-sur-Seine, France
| | - Vassili Soumelis
- Institut Curie, PSL University, INSERM U932, Paris, France. .,Université de Paris, Institut de Recherche Saint-Louis, INSERM U976, Paris, France. .,Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Saint-Louis, Laboratoire d'Immunologie, Paris, France.
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9
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Corral-Jara KF, Rosas da Silva G, Fierro NA, Soumelis V. Modeling the Th17 and Tregs Paradigm: Implications for Cancer Immunotherapy. Front Cell Dev Biol 2021; 9:675099. [PMID: 34026764 PMCID: PMC8137995 DOI: 10.3389/fcell.2021.675099] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/12/2021] [Indexed: 12/11/2022] Open
Abstract
CD4 + T cell differentiation is governed by gene regulatory and metabolic networks, with both networks being highly interconnected and able to adapt to external stimuli. Th17 and Tregs differentiation networks play a critical role in cancer, and their balance is affected by the tumor microenvironment (TME). Factors from the TME mediate recruitment and expansion of Th17 cells, but these cells can act with pro or anti-tumor immunity. Tregs cells are also involved in tumor development and progression by inhibiting antitumor immunity and promoting immunoevasion. Due to the complexity of the underlying molecular pathways, the modeling of biological systems has emerged as a promising solution for better understanding both CD4 + T cell differentiation and cancer cell behavior. In this review, we present a context-dependent vision of CD4 + T cell transcriptomic and metabolic network adaptability. We then discuss CD4 + T cell knowledge-based models to extract the regulatory elements of Th17 and Tregs differentiation in multiple CD4 + T cell levels. We highlight the importance of complementing these models with data from omics technologies such as transcriptomics and metabolomics, in order to better delineate existing Th17 and Tregs bifurcation mechanisms. We were able to recompilate promising regulatory components and mechanisms of Th17 and Tregs differentiation under normal conditions, which we then connected with biological evidence in the context of the TME to better understand CD4 + T cell behavior in cancer. From the integration of mechanistic models with omics data, the transcriptomic and metabolomic reprograming of Th17 and Tregs cells can be predicted in new models with potential clinical applications, with special relevance to cancer immunotherapy.
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Affiliation(s)
- Karla F. Corral-Jara
- Computational Systems Biology Team, Institut de Biologie de l’Ecole Normale Supérieure, CNRS UMR 8197, INSERM U1024, Ecole Normale Supérieure, PSL Research University, Paris, France
| | | | - Nora A. Fierro
- Department of Immunology, Biomedical Research Institute, National Autonomous University of Mexico, Mexico City, Mexico
| | - Vassili Soumelis
- Université de Paris, INSERM U976, France and AP-HP, Hôpital Saint-Louis, Immunology-Histocompatibility Department, Paris, France
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10
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Saichi M, Ladjemi MZ, Korniotis S, Rousseau C, Ait Hamou Z, Massenet-Regad L, Amblard E, Noel F, Marie Y, Bouteiller D, Medvedovic J, Pène F, Soumelis V. Single-cell RNA sequencing of blood antigen-presenting cells in severe COVID-19 reveals multi-process defects in antiviral immunity. Nat Cell Biol 2021; 23:538-551. [PMID: 33972731 DOI: 10.1038/s41556-021-00681-2] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 04/06/2021] [Indexed: 02/03/2023]
Abstract
COVID-19 can lead to life-threatening respiratory failure, with increased inflammatory mediators and viral load. Here, we perform single-cell RNA-sequencing to establish a high-resolution map of blood antigen-presenting cells (APCs) in 15 patients with moderate or severe COVID-19 pneumonia, at day 1 and day 4 post admission to intensive care unit or pulmonology department, as well as in 4 healthy donors. We generated a unique dataset of 81,643 APCs, including monocytes and rare dendritic cell (DC) subsets. We uncovered multi-process defects in antiviral immune defence in specific APCs from patients with severe disease: (1) increased pro-apoptotic pathways in plasmacytoid DCs (pDCs, key effectors of antiviral immunity), (2) a decrease of the innate sensors TLR9 and DHX36 in pDCs and CLEC9a+ DCs, respectively, (3) downregulation of antiviral interferon-stimulated genes in monocyte subsets and (4) a decrease of major histocompatibility complex (MHC) class II-related genes and MHC class II transactivator activity in cDC1c+ DCs, suggesting viral inhibition of antigen presentation. These novel mechanisms may explain patient aggravation and suggest strategies to restore the defective immune defence.
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Affiliation(s)
| | - Maha Zohra Ladjemi
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris, Paris, France.,Service de Médecine Intensive & Réanimation, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris. Centre & Université de Paris, Paris, France
| | | | - Christophe Rousseau
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris, Paris, France
| | - Zakaria Ait Hamou
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris, Paris, France.,Service de Médecine Intensive & Réanimation, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris. Centre & Université de Paris, Paris, France
| | - Lucile Massenet-Regad
- Université de Paris, INSERM U976, Paris, France.,Université Paris-Saclay, Saint-Aubin, France
| | - Elise Amblard
- Université de Paris, INSERM U976, Paris, France.,Université de Paris, Centre de Recherches Interdisciplinaires, Paris, France
| | | | - Yannick Marie
- Institut du Cerveau (ICM), Plateforme de Génotypage Séquençage, Paris, France.,Sorbonne Universités, Université Pierre et Marie Curie, Paris, France
| | - Delphine Bouteiller
- Institut du Cerveau (ICM), Plateforme de Génotypage Séquençage, Paris, France
| | | | - Frédéric Pène
- Institut Cochin, INSERM U1016, CNRS UMR8104, Université de Paris, Paris, France.,Service de Médecine Intensive & Réanimation, Hôpital Cochin, Assistance Publique-Hôpitaux de Paris. Centre & Université de Paris, Paris, France
| | - Vassili Soumelis
- Université de Paris, INSERM U976, Paris, France. .,AP-HP, Hôpital Saint-Louis, Laboratoire d'Immunologie-Histocompatibilité, Paris, France.
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11
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Hatscher L, Lehmann CHK, Purbojo A, Onderka C, Liang C, Hartmann A, Cesnjevar R, Bruns H, Gross O, Nimmerjahn F, Ivanović-Burmazović I, Kunz M, Heger L, Dudziak D. Select hyperactivating NLRP3 ligands enhance the T H1- and T H17-inducing potential of human type 2 conventional dendritic cells. Sci Signal 2021; 14:14/680/eabe1757. [PMID: 33906973 DOI: 10.1126/scisignal.abe1757] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The detection of microorganisms and danger signals by pattern recognition receptors on dendritic cells (DCs) and the consequent formation of inflammasomes are pivotal for initiating protective immune responses. Although the activation of inflammasomes leading to secretion of the cytokine IL-1β is typically accompanied by pyroptosis (an inflammatory form of lytic programmed cell death), some cells can survive and exist in a state of hyperactivation. Here, we found that the conventional type 2 DC (cDC2) subset is the major human DC subset that is transcriptionally and functionally poised for inflammasome formation and response without pyroptosis. When cDC2 were stimulated with ligands that relatively weakly activated the inflammasome, the cells did not enter pyroptosis but instead secreted IL-12 family cytokines and IL-1β. These cytokines induced prominent T helper type 1 (TH1) and TH17 responses that were superior to those seen in response to Toll-like receptor (TLR) stimulation alone or to stronger, classical inflammasome ligands. These findings not only define the human cDC2 subpopulation as a prime target for the treatment of inflammasome-dependent inflammatory diseases but may also inform new approaches for adjuvant and vaccine development.
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Affiliation(s)
- Lukas Hatscher
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Christian H K Lehmann
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Ariawan Purbojo
- Department of Pediatric Cardiac Surgery, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Constantin Onderka
- Department of Chemistry and Pharmacy, Friedrich-Alexander University Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Chunguang Liang
- Chair of Medical Informatics, Friedrich-Alexander University Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Arndt Hartmann
- Department of Pathology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Robert Cesnjevar
- Department of Pediatric Cardiac Surgery, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Heiko Bruns
- Department of Internal Medicine 5-Hematology/Oncology, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Olaf Gross
- Institute of Neuropathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany.,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104 Freiburg, Germany.,Center for Basics in NeuroModulation (NeuroModulBasics), Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Falk Nimmerjahn
- Institute of Genetics, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | - Ivana Ivanović-Burmazović
- Department of Chemistry and Pharmacy, Friedrich-Alexander University Erlangen-Nürnberg, 91058 Erlangen, Germany.,Department Chemistry, Ludwigs Maximilians University, 81377 Munich, Germany
| | - Meik Kunz
- Chair of Medical Informatics, Friedrich-Alexander University Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Lukas Heger
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Diana Dudziak
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, 91052 Erlangen, Germany. .,Institute of Genetics, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany.,Deutsches Zentrum Immuntherapie, 91054 Erlangen, Germany.,Comprehensive Cancer Center Erlangen-European Metropolitan Area of Nuremberg, 91054 Erlangen, Germany.,Medical Immunology Campus Erlangen, 91054 Erlangen, Germany
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12
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Hatscher L, Amon L, Heger L, Dudziak D. Inflammasomes in dendritic cells: Friend or foe? Immunol Lett 2021; 234:16-32. [PMID: 33848562 DOI: 10.1016/j.imlet.2021.04.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/31/2021] [Accepted: 04/03/2021] [Indexed: 12/14/2022]
Abstract
Inflammasomes are cytosolic multiprotein complexes that crucially contribute to host defense against pathogens but are also involved in the pathogenesis of autoinflammatory diseases. Inflammasome formation leads to activation of effector caspases (caspase-1, 4, 5, or 11), the proteolytic maturation of IL-1β and IL-18 as well as cleavage of the pore-forming protein Gasdermin D. Dendritic cells are major regulators of immune responses as they bridge innate and adaptive immunity. We here summarize the current knowledge on inflammasome expression and formation in murine bone marrow-, human monocyte-derived as well as murine and human primary dendritic cells. Further, we discuss both, the beneficial and detrimental, involvement of inflammasome activation in dendritic cells in cancer, infections, and autoimmune diseases. As inflammasome activation is typically accompanied by Gasdermin d-mediated pyroptosis, which is an inflammatory form of programmed cell death, inflammasome formation in dendritic cells seems ill-advised. Therefore, we propose that hyperactivation, which is inflammasome activation without the induction of pyroptosis, may be a general model of inflammasome activation in dendritic cells to enhance Th1, Th17 as well as cytotoxic T cell responses.
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Affiliation(s)
- Lukas Hatscher
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, 91052, Erlangen, Germany
| | - Lukas Amon
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, 91052, Erlangen, Germany
| | - Lukas Heger
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, 91052, Erlangen, Germany.
| | - Diana Dudziak
- Laboratory of Dendritic Cell Biology, Department of Dermatology, University Hospital Erlangen, Friedrich-Alexander University of Erlangen-Nürnberg, 91052, Erlangen, Germany; Medical Immunology Campus Erlangen, Germany; Deutsches Zentrum Immuntherapie (DZI), Germany; Comprehensive Cancer Center Erlangen-European Metropolitan Area of Nuremberg (CCC ER-EMN), Germany.
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13
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Corral-Jara KF, Chauvin C, Abou-Jaoudé W, Grandclaudon M, Naldi A, Soumelis V, Thieffry D. Interplay between SMAD2 and STAT5A is a critical determinant of IL-17A/IL-17F differential expression. MOLECULAR BIOMEDICINE 2021; 2:9. [PMID: 35006414 PMCID: PMC8607379 DOI: 10.1186/s43556-021-00034-3] [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: 03/04/2021] [Indexed: 02/08/2023] Open
Abstract
Interleukins (IL)-17A and F are critical cytokines in anti-microbial immunity but also contribute to auto-immune pathologies. Recent evidence suggests that they may be differentially produced by T-helper (Th) cells, but the underlying mechanisms remain unknown. To address this question, we built a regulatory graph integrating all reported upstream regulators of IL-17A and F, completed by ChIP-seq data analyses. The resulting regulatory graph encompasses 82 components and 136 regulatory links. The graph was then supplemented by logical rules calibrated with original flow cytometry data using naive CD4+ T cells, in conditions inducing IL-17A or IL-17F. The model displays specific stable states corresponding to virtual phenotypes explaining IL-17A and IL-17F differential regulation across eight cytokine stimulatory conditions. Our model analysis points to the transcription factors NFAT2A, STAT5A and SMAD2 as key regulators of the differential expression of IL-17A and IL-17F, with STAT5A controlling IL-17F expression, and an interplay of NFAT2A, STAT5A and SMAD2 controlling IL-17A expression. We experimentally observed that the production of IL-17A was correlated with an increase of SMAD2 transcription, and the expression of IL-17F correlated with an increase of BLIMP-1 transcription, together with an increase of STAT5A expression (mRNA), as predicted by our model. Interestingly, RORγt presumably plays a more determinant role in IL-17A expression as compared to IL-17F expression. In conclusion, we propose the first mechanistic model accounting for the differential expression of IL-17A and F in Th cells, providing a basis to design novel therapeutic interventions in auto-immune and inflammatory diseases.
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Affiliation(s)
- Karla Fabiola Corral-Jara
- Computational Systems Biology Team, Institut de Biologie de l'École Normale Supérieure, CNRS UMR8197, INSERM U1024, École Normale Supérieure, PSL Université, 75005, Paris, France
| | - Camille Chauvin
- Integrative Biology of Human Dendritic Cells and T Cells Team, Institut de Recherche St-Louis, U976, Hôpital Saint Louis, 75010, Paris, France
| | - Wassim Abou-Jaoudé
- Computational Systems Biology Team, Institut de Biologie de l'École Normale Supérieure, CNRS UMR8197, INSERM U1024, École Normale Supérieure, PSL Université, 75005, Paris, France
| | - Maximilien Grandclaudon
- Institut Curie, Centre de Recherche, PSL Research University, 75005 Paris, France; INSERM U932, Immunity and Cancer, 75005, Paris, France
| | - Aurélien Naldi
- Computational Systems Biology Team, Institut de Biologie de l'École Normale Supérieure, CNRS UMR8197, INSERM U1024, École Normale Supérieure, PSL Université, 75005, Paris, France
| | - Vassili Soumelis
- Integrative Biology of Human Dendritic Cells and T Cells Team, Institut de Recherche St-Louis, U976, Hôpital Saint Louis, 75010, Paris, France.
| | - Denis Thieffry
- Computational Systems Biology Team, Institut de Biologie de l'École Normale Supérieure, CNRS UMR8197, INSERM U1024, École Normale Supérieure, PSL Université, 75005, Paris, France.
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14
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Armingol E, Officer A, Harismendy O, Lewis NE. Deciphering cell-cell interactions and communication from gene expression. Nat Rev Genet 2021; 22:71-88. [PMID: 33168968 PMCID: PMC7649713 DOI: 10.1038/s41576-020-00292-x] [Citation(s) in RCA: 501] [Impact Index Per Article: 167.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2020] [Indexed: 12/13/2022]
Abstract
Cell-cell interactions orchestrate organismal development, homeostasis and single-cell functions. When cells do not properly interact or improperly decode molecular messages, disease ensues. Thus, the identification and quantification of intercellular signalling pathways has become a common analysis performed across diverse disciplines. The expansion of protein-protein interaction databases and recent advances in RNA sequencing technologies have enabled routine analyses of intercellular signalling from gene expression measurements of bulk and single-cell data sets. In particular, ligand-receptor pairs can be used to infer intercellular communication from the coordinated expression of their cognate genes. In this Review, we highlight discoveries enabled by analyses of cell-cell interactions from transcriptomic data and review the methods and tools used in this context.
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Affiliation(s)
- Erick Armingol
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, La Jolla, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Adam Officer
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA, USA
| | - Olivier Harismendy
- Division of Biomedical Informatics, University of California, San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
- Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
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15
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Van Den Eeckhout B, Tavernier J, Gerlo S. Interleukin-1 as Innate Mediator of T Cell Immunity. Front Immunol 2021; 11:621931. [PMID: 33584721 PMCID: PMC7873566 DOI: 10.3389/fimmu.2020.621931] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/08/2020] [Indexed: 12/19/2022] Open
Abstract
The three-signal paradigm tries to capture how the innate immune system instructs adaptive immune responses in three well-defined actions: (1) presentation of antigenic peptides in the context of MHC molecules, which allows for a specific T cell response; (2) T cell co-stimulation, which breaks T cell tolerance; and (3) secretion of polarizing cytokines in the priming environment, thereby specializing T cell immunity. The three-signal model provides an empirical framework for innate instruction of adaptive immunity, but mainly discusses STAT-dependent cytokines in T cell activation and differentiation, while the multi-faceted roles of type I IFNs and IL-1 cytokine superfamily members are often neglected. IL-1α and IL-1β are pro-inflammatory cytokines, produced following damage to the host (release of DAMPs) or upon innate recognition of PAMPs. IL-1 activity on both DCs and T cells can further shape the adaptive immune response with variable outcomes. IL-1 signaling in DCs promotes their ability to induce T cell activation, but also direct action of IL-1 on both CD4+ and CD8+ T cells, either alone or in synergy with prototypical polarizing cytokines, influences T cell differentiation under different conditions. The activities of IL-1 form a direct bridge between innate and adaptive immunity and could therefore be clinically translatable in the context of prophylactic and therapeutic strategies to empower the formation of T cell immunity. Understanding the modalities of IL-1 activity during T cell activation thus could hold major implications for rational development of the next generation of vaccine adjuvants.
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Affiliation(s)
- Bram Van Den Eeckhout
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Jan Tavernier
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Orionis Biosciences BV, Ghent, Belgium
| | - Sarah Gerlo
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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16
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Modelling of Immune Checkpoint Network Explains Synergistic Effects of Combined Immune Checkpoint Inhibitor Therapy and the Impact of Cytokines in Patient Response. Cancers (Basel) 2020; 12:cancers12123600. [PMID: 33276543 PMCID: PMC7761568 DOI: 10.3390/cancers12123600] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/23/2020] [Accepted: 11/30/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary The future of cancer immunotherapy relies on a combination of individually targeted therapies. However, a lot of experiments are needed to define the most effective combinations of drugs. A computational and modelling approach could help reduce the number of experiments and suggest optimal treatments to test. This article presents a logical model of T cell activation influenced by immune checkpoints, and explores the effect of these checkpoints, suggests mechanisms that would explain why some treatments might be better suited than others. The model includes not only programmed cell death protein 1 (PD1) and cytotoxic T-lymphocyte-associated protein 4 (CTL4) downstream pathways but also those of other immune checkpoints such as T cell immunoglobulin and ITIM (immunoreceptor tyrosine-based inhibition motif) domain (TIGIT), lymphocyte activation gene 3 (LAG3), T cell immunoglobulin and mucin domain-containing protein 3 (TIM3), cluster of differentiation 226 (CD226), inducible T-cell costimulator (ICOS), and tumour necrosis factor receptors (TNFRs). Abstract After the success of the new generation of immune therapies, immune checkpoint receptors have become one important center of attention of molecular oncologists. The initial success and hopes of anti-programmed cell death protein 1 (anti-PD1) and anti-cytotoxic T-lymphocyte-associated protein 4 (anti-CTLA4) therapies have shown some limitations since a majority of patients have continued to show resistance. Other immune checkpoints have raised some interest and are under investigation, such as T cell immunoglobulin and ITIM (immunoreceptor tyrosine-based inhibition motif) domain (TIGIT), inducible T-cell costimulator (ICOS), and T cell immunoglobulin and mucin domain-containing protein 3 (TIM3), which appear as promising targets for immunotherapy. To explore their role and study possible synergetic effects of these different checkpoints, we have built a model of T cell receptor (TCR) regulation including not only PD1 and CTLA4, but also other well studied checkpoints (TIGIT, TIM3, lymphocyte activation gene 3 (LAG3), cluster of differentiation 226 (CD226), ICOS, and tumour necrosis factor receptors (TNFRs)) and simulated different aspects of T cell biology. Our model shows good correspondence with observations from available experimental studies of anti-PD1 and anti-CTLA4 therapies and suggest efficient combinations of immune checkpoint inhibitors (ICI). Among the possible candidates, TIGIT appears to be the most promising drug target in our model. The model predicts that signal transducer and activator of transcription 1 (STAT1)/STAT4-dependent pathways, activated by cytokines such as interleukin 12 (IL12) and interferon gamma (IFNG), could improve the effect of ICI therapy via upregulation of Tbet, suggesting that the effect of the cytokines related to STAT3/STAT1 activity is dependent on the balance between STAT1 and STAT3 downstream signalling.
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17
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Hao Shi, Yan KK, Ding L, Qian C, Chi H, Yu J. Network Approaches for Dissecting the Immune System. iScience 2020; 23:101354. [PMID: 32717640 PMCID: PMC7390880 DOI: 10.1016/j.isci.2020.101354] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/21/2020] [Accepted: 07/08/2020] [Indexed: 02/06/2023] Open
Abstract
The immune system is a complex biological network composed of hierarchically organized genes, proteins, and cellular components that combat external pathogens and monitor the onset of internal disease. To meet and ultimately defeat these challenges, the immune system orchestrates an exquisitely complex interplay of numerous cells, often with highly specialized functions, in a tissue-specific manner. One of the major methodologies of systems immunology is to measure quantitatively the components and interaction levels in the immunologic networks to construct a computational network and predict the response of the components to perturbations. The recent advances in high-throughput sequencing techniques have provided us with a powerful approach to dissecting the complexity of the immune system. Here we summarize the latest progress in integrating omics data and network approaches to construct networks and to infer the underlying signaling and transcriptional landscape, as well as cell-cell communication, in the immune system, with a focus on hematopoiesis, adaptive immunity, and tumor immunology. Understanding the network regulation of immune cells has provided new insights into immune homeostasis and disease, with important therapeutic implications for inflammation, cancer, and other immune-mediated disorders.
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Affiliation(s)
- Hao Shi
- Departments of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Koon-Kiu Yan
- Departments of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Liang Ding
- Departments of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Chenxi Qian
- Departments of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hongbo Chi
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jiyang Yu
- Departments of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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18
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Lapuente-Santana Ó, Eduati F. Toward Systems Biomarkers of Response to Immune Checkpoint Blockers. Front Oncol 2020; 10:1027. [PMID: 32670886 PMCID: PMC7326813 DOI: 10.3389/fonc.2020.01027] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/22/2020] [Indexed: 12/13/2022] Open
Abstract
Immunotherapy with checkpoint blockers (ICBs), aimed at unleashing the immune response toward tumor cells, has shown a great improvement in overall patient survival compared to standard therapy, but only in a subset of patients. While a number of recent studies have significantly improved our understanding of mechanisms playing an important role in the tumor microenvironment (TME), we still have an incomplete view of how the TME works as a whole. This hampers our ability to effectively predict the large heterogeneity of patients' response to ICBs. Systems approaches could overcome this limitation by adopting a holistic perspective to analyze the complexity of tumors. In this Mini Review, we focus on how an integrative view of the increasingly available multi-omics experimental data and computational approaches enables the definition of new systems-based predictive biomarkers. In particular, we will focus on three facets of the TME toward the definition of new systems biomarkers. First, we will review how different types of immune cells influence the efficacy of ICBs, not only in terms of their quantification, but also considering their localization and functional state. Second, we will focus on how different cells in the TME interact, analyzing how inter- and intra-cellular networks play an important role in shaping the immune response and are responsible for resistance to immunotherapy. Finally, we will describe the potential of looking at these networks as dynamic systems and how mathematical models can be used to study the rewiring of the complex interactions taking place in the TME.
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Affiliation(s)
- Óscar Lapuente-Santana
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Federica Eduati
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
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