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Schäfer PSL, Dimitrov D, Villablanca EJ, Saez-Rodriguez J. Integrating single-cell multi-omics and prior biological knowledge for a functional characterization of the immune system. Nat Immunol 2024; 25:405-417. [PMID: 38413722 DOI: 10.1038/s41590-024-01768-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 01/16/2024] [Indexed: 02/29/2024]
Abstract
The immune system comprises diverse specialized cell types that cooperate to defend the host against a wide range of pathogenic threats. Recent advancements in single-cell and spatial multi-omics technologies provide rich information about the molecular state of immune cells. Here, we review how the integration of single-cell and spatial multi-omics data with prior knowledge-gathered from decades of detailed biochemical studies-allows us to obtain functional insights, focusing on gene regulatory processes and cell-cell interactions. We present diverse applications in immunology and critically assess underlying assumptions and limitations. Finally, we offer a perspective on the ongoing technological and algorithmic developments that promise to get us closer to a systemic mechanistic understanding of the immune system.
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Affiliation(s)
- Philipp Sven Lars Schäfer
- Institute for Computational Bioscience, Faculty of Medicine and Heidelberg University Hospital, Heidelberg University, Heidelberg, Germany
| | - Daniel Dimitrov
- Institute for Computational Bioscience, Faculty of Medicine and Heidelberg University Hospital, Heidelberg University, Heidelberg, Germany
| | - Eduardo J Villablanca
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institute and Karolinska University Hospital, Stockholm, Sweden
- Center of Molecular Medicine, Stockholm, Sweden
| | - Julio Saez-Rodriguez
- Institute for Computational Bioscience, Faculty of Medicine and Heidelberg University Hospital, Heidelberg University, Heidelberg, Germany.
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2
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Ganguly D. Multi-omics studies in interpreting the evolving standard model for immune functions. Brief Funct Genomics 2024; 23:75-81. [PMID: 36905355 DOI: 10.1093/bfgp/elad003] [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: 08/27/2022] [Revised: 01/11/2023] [Accepted: 01/23/2023] [Indexed: 03/12/2023] Open
Abstract
A standard model that is able to generalize data on myriad involvement of the immune system in organismal physio-pathology and to provide a unified evolutionary teleology for immune functions in multicellular organisms remains elusive. A number of such 'general theories of immunity' have been proposed based on contemporaneously available data, starting with the usual description of self-nonself discrimination, followed by the 'danger model' and the more recent 'discontinuity theory.' More recent data deluge on involvement of immune mechanisms in a wide variety of clinical contexts, a number of which fail to get readily accommodated into the available teleologic standard models, makes deriving a standard model of immunity more challenging. But technological advances enabling multi-omics investigations into an ongoing immune response, covering genome, epigenome, coding and regulatory transcriptome, proteome, metabolome and tissue-resident microbiome, bring newer opportunities for developing a more integrative insight into immunocellular mechanisms within different clinical contexts. The new ability to map the heterogeneity of composition, trajectory and endpoints of immune responses, in both health and disease, also necessitates incorporation into the potential standard model of immune functions, which again can only be achieved through multi-omics probing of immune responses and integrated analyses of the multi-dimensional data.
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Affiliation(s)
- Dipyaman Ganguly
- IICB-Translational Research Unit of Excellence, CSIR-Indian Institute of Chemical Biology, Kolkata, India
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3
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Jin L, Chen Y, Muzaffar S, Li C, Mier-Aguilar CA, Khan J, Kashyap MP, Liu S, Srivastava R, Deshane JS, Townes TM, Elewski BE, Elmets CA, Crossman DK, Raman C, Athar M. Epigenetic switch reshapes epithelial progenitor cell signatures and drives inflammatory pathogenesis in hidradenitis suppurativa. Proc Natl Acad Sci U S A 2023; 120:e2315096120. [PMID: 38011564 PMCID: PMC10710069 DOI: 10.1073/pnas.2315096120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/25/2023] [Indexed: 11/29/2023] Open
Abstract
Hidradenitis suppurativa (HS) is a complex inflammatory skin disease with undefined mechanistic underpinnings. Here, we investigated HS epithelial cells and demonstrated that HS basal progenitors modulate their lineage restriction and give rise to pathogenic keratinocyte clones, resulting in epidermal hyperproliferation and dysregulated inflammation in HS. When comparing to healthy epithelial stem/progenitor cells, in HS, we identified changes in gene signatures that revolve around the mitotic cell cycle, DNA damage response and repair, as well as cell-cell adhesion and chromatin remodeling. By reconstructing cell differentiation trajectory and CellChat modeling, we identified a keratinocyte population specific to HS. This population is marked by S100A7/8/9 and KRT6 family members, triggering IL1, IL10, and complement inflammatory cascades. These signals, along with HS-specific proinflammatory cytokines and chemokines, contribute to the recruitment of certain immune cells during the disease progression. Furthermore, we revealed a previously uncharacterized role of S100A8 in regulating the local chromatin environment of target loci in HS keratinocytes. Through the integration of genomic and epigenomic datasets, we identified genome-wide chromatin rewiring alongside the switch of transcription factors (TFs), which mediated HS transcriptional profiles. Importantly, we identified numerous clinically relevant inflammatory enhancers and their coordinated TFs in HS basal CD49fhigh cells. The disruption of the S100A enhancer using the CRISPR/Cas9-mediated approach or the pharmacological inhibition of the interferon regulatory transcription factor 3 (IRF3) efficiently reduced the production of HS-associated inflammatory regulators. Our study not only uncovers the plasticity of epidermal progenitor cells in HS but also elucidates the epigenetic mechanisms underlying HS pathogenesis.
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Affiliation(s)
- Lin Jin
- Center for Epigenomics and Translational Research in Inflammatory Skin Diseases, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL35294
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
- Research Center of Excellence in Arsenicals, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL35294
| | - Yunjia Chen
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL35294
| | - Suhail Muzaffar
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
- Research Center of Excellence in Arsenicals, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL35294
| | - Chao Li
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL35294
| | - Carlos A. Mier-Aguilar
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
| | - Jasim Khan
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
- Research Center of Excellence in Arsenicals, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL35294
| | - Mahendra P. Kashyap
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
- Research Center of Excellence in Arsenicals, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL35294
| | - Shanrun Liu
- Institutional Research Core Program, Flow Cytometry and Singe Cell Core, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
| | - Ritesh Srivastava
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
- Research Center of Excellence in Arsenicals, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL35294
| | - Jessy S. Deshane
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL35294
| | - Tim M. Townes
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL35294
| | - Boni E. Elewski
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
| | - Craig A. Elmets
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
| | - David K. Crossman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL35294
| | - Chander Raman
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
| | - Mohammad Athar
- Center for Epigenomics and Translational Research in Inflammatory Skin Diseases, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL35294
- Department of Dermatology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL35294
- Research Center of Excellence in Arsenicals, Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL35294
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Saadey AA, Yousif A, Osborne N, Shahinfar R, Chen YL, Laster B, Rajeev M, Bauman P, Webb A, Ghoneim HE. Rebalancing TGFβ1/BMP signals in exhausted T cells unlocks responsiveness to immune checkpoint blockade therapy. Nat Immunol 2023; 24:280-294. [PMID: 36543960 DOI: 10.1038/s41590-022-01384-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/03/2022] [Indexed: 12/24/2022]
Abstract
T cell dysfunctionality prevents the clearance of chronic infections and cancer. Furthermore, epigenetic programming in dysfunctional CD8+ T cells limits their response to immunotherapies, including immune checkpoint blockade (ICB). However, it is unclear which upstream signals drive acquisition of dysfunctional epigenetic programs, and whether therapeutically targeting these signals can remodel terminally dysfunctional T cells to an ICB-responsive state. Here we innovate an in vitro model system of stable human T cell dysfunction and show that chronic TGFβ1 signaling in posteffector CD8+ T cells accelerates their terminal dysfunction through stable epigenetic changes. Conversely, boosting bone morphogenetic protein (BMP) signaling while blocking TGFβ1 preserved effector and memory programs in chronically stimulated human CD8+ T cells, inducing superior responses to tumors and synergizing the ICB responses during chronic viral infection. Thus, rebalancing TGFβ1/BMP signals provides an exciting new approach to unleash dysfunctional CD8+ T cells and enhance T cell immunotherapies.
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Affiliation(s)
- Abbey A Saadey
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH, USA
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Amir Yousif
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH, USA
- Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, Columbus, OH, USA
| | - Nicole Osborne
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Roya Shahinfar
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Yu-Lin Chen
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Brooke Laster
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Meera Rajeev
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Parker Bauman
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Amy Webb
- Biomedical Informatics Shared Resources, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Hazem E Ghoneim
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH, USA.
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH, USA.
- Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, Columbus, OH, USA.
- The Pelotonia Institute for Immuno-Oncology, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
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Single-Cell Gene Expression Analysis Revealed Immune Cell Signatures of Delta COVID-19. Cells 2022; 11:cells11192950. [PMID: 36230912 PMCID: PMC9563974 DOI: 10.3390/cells11192950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/04/2022] [Accepted: 09/15/2022] [Indexed: 11/17/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) is accompanied by a cytokine storm with the release of many proinflammatory factors and development of respiratory syndrome. Several SARS-CoV-2 lineages have been identified, and the Delta variant (B.1.617), linked with high mortality risk, has become dominant in many countries. Understanding the immune responses associated with COVID-19 lineages may therefore aid the development of therapeutic and diagnostic strategies. Multiple single-cell gene expression studies revealed innate and adaptive immunological factors and pathways correlated with COVID-19 severity. Additional investigations covering host–pathogen response characteristics for infection caused by different lineages are required. Here, we performed single-cell transcriptome profiling of blood mononuclear cells from the individuals with different severity of the COVID-19 and virus lineages to uncover variant specific molecular factors associated with immunity. We identified significant changes in lymphoid and myeloid cells. Our study highlights that an abundant population of monocytes with specific gene expression signatures accompanies Delta lineage of SARS-CoV-2 and contributes to COVID-19 pathogenesis inferring immune components for targeted therapy.
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