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Cao N, Wan Z, Chen D, Tang L. Deciphering peri-implantitis: Unraveling signature genes and immune cell associations through bioinformatics and machine learning. Medicine (Baltimore) 2024; 103:e37862. [PMID: 38640305 PMCID: PMC11030017 DOI: 10.1097/md.0000000000037862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/16/2024] [Accepted: 03/20/2024] [Indexed: 04/21/2024] Open
Abstract
Early diagnosis of peri-implantitis (PI) is crucial to understand its pathological progression and prevention. This study is committed to investigating the signature genes, relevant signaling pathways and their associations with immune cells in PI. We analyzed differentially expressed genes (DEGs) from a PI dataset in the gene expression omnibus database. Functional enrichment analysis was conducted for these DEGs. Weighted Gene Co-expression Network Analysis was used to identify specific modules. Least absolute shrinkage and selection operator and support vector machine recursive feature elimination were ultimately applied to identify the signature genes. These genes were subsequently validated in an external dataset. And the immune cells infiltration was classified using CIBERSORT. A total of 180 DEGs were screened from GSE33774. Weighted Gene Co-expression Network Analysis revealed a significant association between the MEturquoise module and PI (cor = 0.6, P < .0001). Least absolute shrinkage and selection operator and support vector machine recursive feature elimination algorithms were applied to select the signature genes, containing myeloid-epithelial-reproductive tyrosine kinase, microfibrillar-associated protein 5, membrane-spanning 4A 4A, tribbles homolog 1. In the validation on the external dataset GSE106090, all these genes achieved area under curve values exceeding 0.95. GSEA analysis showed that these genes were correlated with the NOD-like receptor signaling pathway, metabolism of xenobiotics by cytochrome P450, and arachidonic acid metabolism. CIBERSORT revealed elevated levels of macrophage M2 and activated mast cells in PI. This study provides novel insights into understanding the molecular mechanisms of PI and contributes to advancements in its early diagnosis and prevention.
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Affiliation(s)
- Ning Cao
- Department of Implant Dentistry, College & Hospital of Stomatology, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Key Laboratory of the Rehabilitation and Reconstruction of Oral and Maxillofacial Research, Nanning, China
- Key Laboratory of Research and Application of Stomatological Equipment (College of Stomatology, Hospital of Stomatology, Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
- Guangxi Clinical Research Center for Craniofacial Deformity, Nanning, China
| | - Ziwei Wan
- Guangxi Key Laboratory of the Rehabilitation and Reconstruction of Oral and Maxillofacial Research, Nanning, China
- Key Laboratory of Research and Application of Stomatological Equipment (College of Stomatology, Hospital of Stomatology, Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
- Guangxi Clinical Research Center for Craniofacial Deformity, Nanning, China
| | - Donghui Chen
- Department of Implant Dentistry, College & Hospital of Stomatology, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Key Laboratory of the Rehabilitation and Reconstruction of Oral and Maxillofacial Research, Nanning, China
- Key Laboratory of Research and Application of Stomatological Equipment (College of Stomatology, Hospital of Stomatology, Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
- Guangxi Clinical Research Center for Craniofacial Deformity, Nanning, China
| | - Li Tang
- Department of Implant Dentistry, College & Hospital of Stomatology, Guangxi Medical University, Nanning, Guangxi, China
- Guangxi Key Laboratory of the Rehabilitation and Reconstruction of Oral and Maxillofacial Research, Nanning, China
- Key Laboratory of Research and Application of Stomatological Equipment (College of Stomatology, Hospital of Stomatology, Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
- Guangxi Clinical Research Center for Craniofacial Deformity, Nanning, China
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McClory SE, Bardhan O, Rome KS, Giles JR, Baxter AE, Xu L, Gimotty PA, Faryabi RB, Wherry EJ, Pear WS, Jordan MS. The pseudokinase Trib1 regulates the transition of exhausted T cells to a KLR + CD8 + effector state, and its deletion improves checkpoint blockade. Cell Rep 2023; 42:112905. [PMID: 37527035 PMCID: PMC10540077 DOI: 10.1016/j.celrep.2023.112905] [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: 12/02/2022] [Revised: 06/22/2023] [Accepted: 07/14/2023] [Indexed: 08/03/2023] Open
Abstract
CD8+ T cell exhaustion (TEX) impairs the ability of T cells to clear chronic infection or cancer. While TEX are hypofunctional, some TEX retain effector gene signatures, a feature associated with killer lectin-like receptor (KLR) expression. Although KLR+ TEX (TKLR) may improve control of chronic antigen, the signaling molecules regulating this population are poorly understood. Using single-cell RNA sequencing (scRNA-seq), flow cytometry, RNA velocity, and single-cell T cell receptor sequencing (scTCR-seq), we demonstrate that deleting the pseudokinase Trib1 shifts TEX toward CX3CR1+ intermediates with robust enrichment of TKLR via clonal T cell expansion. Adoptive transfer studies demonstrate this shift toward CD8+ TKLR in Trib1-deficient cells is CD8 intrinsic, while CD4-depletion studies demonstrate CD4+ T cells are required for improved viral control in Trib1 conditional knockout mice. Further, Trib1 loss augments anti-programmed death-ligand 1 (PD-L1) blockade to improve viral clearance. These data identify Trib1 as an important regulator of CD8+ TEX whose targeting enhances the TKLR effector state and improves checkpoint inhibitor therapy.
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Affiliation(s)
- Susan E McClory
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Oishi Bardhan
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kelly S Rome
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Josephine R Giles
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Amy E Baxter
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lanwei Xu
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Phyllis A Gimotty
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Robert B Faryabi
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - E John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Warren S Pear
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Martha S Jordan
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Institute for Immunology and Immune Health, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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McClory SE, Bardhan O, Rome KS, Giles JR, Baxter AE, Xu L, Gimotty PA, Faryabi RB, Wherry EJ, Pear WS, Jordan MS. The pseudokinase Trib1 regulates the transition of exhausted T cells to a KLR + CD8 + effector state and its deletion improves checkpoint blockade. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.16.528833. [PMID: 36824931 PMCID: PMC9948998 DOI: 10.1101/2023.02.16.528833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
T cell exhaustion (T EX ) impairs the ability of T cells to clear chronic infection or cancer. While exhausted T cells are hypofunctional, some exhausted T cells retain effector gene signatures, a feature that is associated with expression of KLRs (killer lectin-like receptors). Although KLR + T cells may improve control of chronic antigen, the signaling molecules regulating this population are poorly understood. Using scRNA-seq, flow cytometry, RNA velocity, and scTCR-seq, we demonstrate that deleting the pseudokinase Trib1 shifts T EX towards CX3CR1 + intermediates (T INT ) with robust enrichment of KLR + CD8 + T cells (T KLR ) via clonal T cell expansion. These changes are associated with globally increased KLR gene expression throughout the exhaustion program. Further, Trib1 loss augments anti-PD-L1 blockade to improve viral clearance by expanding the T KLR population. Together, these data identify Trib1 as an important regulator of T cell exhaustion whose targeting enhances the KLR + effector state and improves the response to checkpoint inhibitor therapy.
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Affiliation(s)
- Susan E. McClory
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Oishi Bardhan
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kelly S. Rome
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Josephine R. Giles
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Amy E. Baxter
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lanwei Xu
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Phyllis A. Gimotty
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert B. Faryabi
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - E. John Wherry
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Warren S. Pear
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Martha S. Jordan
- Department of Pathology and Laboratory Medicine, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Rubin SA, Baron CS, Pessoa Rodrigues C, Duran M, Corbin AF, Yang SP, Trapnell C, Zon LI. Single-cell analyses reveal early thymic progenitors and pre-B cells in zebrafish. J Exp Med 2022; 219:e20220038. [PMID: 35938989 PMCID: PMC9365674 DOI: 10.1084/jem.20220038] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 06/11/2022] [Accepted: 07/06/2022] [Indexed: 02/06/2023] Open
Abstract
The zebrafish has proven to be a valuable model organism for studying hematopoiesis, but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single-cell RNA sequencing on ∼70,000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus, elucidated B- and T-cell developmental trajectories, and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic-like cell populations and provided evidence in support of the existence of a pre-B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies.
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Affiliation(s)
- Sara A. Rubin
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA
| | - Chloé S. Baron
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA
| | - Cecilia Pessoa Rodrigues
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA
| | - Madeleine Duran
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Alexandra F. Corbin
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA
| | - Song P. Yang
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Leonard I. Zon
- Stem Cell Program and Division of Hematology/Oncology, Boston Children’s Hospital and Dana-Farber Cancer Institute, Boston, MA
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA
- Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, MA
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