1
|
Bai Z, Zhang D, Gao Y, Tao B, Bao S, Enninful A, Zhang D, Su G, Tian X, Zhang N, Xiao Y, Liu Y, Gerstein M, Li M, Xing Y, Lu J, Xu ML, Fan R. Spatially Exploring RNA Biology in Archival Formalin-Fixed Paraffin-Embedded Tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579143. [PMID: 38370833 PMCID: PMC10871202 DOI: 10.1101/2024.02.06.579143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Spatial transcriptomics has emerged as a powerful tool for dissecting spatial cellular heterogeneity but as of today is largely limited to gene expression analysis. Yet, the life of RNA molecules is multifaceted and dynamic, requiring spatial profiling of different RNA species throughout the life cycle to delve into the intricate RNA biology in complex tissues. Human disease-relevant tissues are commonly preserved as formalin-fixed and paraffin-embedded (FFPE) blocks, representing an important resource for human tissue specimens. The capability to spatially explore RNA biology in FFPE tissues holds transformative potential for human biology research and clinical histopathology. Here, we present Patho-DBiT combining in situ polyadenylation and deterministic barcoding for spatial full coverage transcriptome sequencing, tailored for probing the diverse landscape of RNA species even in clinically archived FFPE samples. It permits spatial co-profiling of gene expression and RNA processing, unveiling region-specific splicing isoforms, and high-sensitivity transcriptomic mapping of clinical tumor FFPE tissues stored for five years. Furthermore, genome-wide single nucleotide RNA variants can be captured to distinguish different malignant clones from non-malignant cells in human lymphomas. Patho-DBiT also maps microRNA-mRNA regulatory networks and RNA splicing dynamics, decoding their roles in spatial tumorigenesis trajectory. High resolution Patho-DBiT at the cellular level reveals a spatial neighborhood and traces the spatiotemporal kinetics driving tumor progression. Patho-DBiT stands poised as a valuable platform to unravel rich RNA biology in FFPE tissues to study human tissue biology and aid in clinical pathology evaluation.
Collapse
Affiliation(s)
- Zhiliang Bai
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Dingyao Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yan Gao
- Center for Computational and Genomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Bo Tao
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Shuozhen Bao
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Archibald Enninful
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Daiwei Zhang
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Graham Su
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Xiaolong Tian
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Ningning Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yang Xiao
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Yang Liu
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Mark Gerstein
- Section on Biomedical Informatics and Data Science, Yale University, New Haven, CT 06520, USA
| | - Mingyao Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yi Xing
- Center for Computational and Genomic Medicine, 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
| | - Jun Lu
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Mina L. Xu
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520, USA
- Human and Translational Immunology, Yale University School of Medicine, New Haven, CT 06520, USA
| |
Collapse
|
2
|
Damelang T, Brinkhaus M, van Osch TLJ, Schuurman J, Labrijn AF, Rispens T, Vidarsson G. Impact of structural modifications of IgG antibodies on effector functions. Front Immunol 2024; 14:1304365. [PMID: 38259472 PMCID: PMC10800522 DOI: 10.3389/fimmu.2023.1304365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/11/2023] [Indexed: 01/24/2024] Open
Abstract
Immunoglobulin G (IgG) antibodies are a critical component of the adaptive immune system, binding to and neutralizing pathogens and other foreign substances. Recent advances in molecular antibody biology and structural protein engineering enabled the modification of IgG antibodies to enhance their therapeutic potential. This review summarizes recent progress in both natural and engineered structural modifications of IgG antibodies, including allotypic variation, glycosylation, Fc engineering, and Fc gamma receptor binding optimization. We discuss the functional consequences of these modifications to highlight their potential for therapeutical applications.
Collapse
Affiliation(s)
- Timon Damelang
- Sanquin Research, Department of Experimental Immunohematology and Landsteiner Laboratory, Amsterdam, Netherlands
- Sanquin Research, Department of Immunopathology, Amsterdam, Netherlands
- Department of Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
- Department of Antibody Research & Technologies’, Genmab, Utrecht, Netherlands
| | - Maximilian Brinkhaus
- Sanquin Research, Department of Experimental Immunohematology and Landsteiner Laboratory, Amsterdam, Netherlands
- Department of Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Thijs L. J. van Osch
- Sanquin Research, Department of Experimental Immunohematology and Landsteiner Laboratory, Amsterdam, Netherlands
- Department of Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Janine Schuurman
- Department of Antibody Research & Technologies’, Genmab, Utrecht, Netherlands
| | - Aran F. Labrijn
- Department of Antibody Research & Technologies’, Genmab, Utrecht, Netherlands
| | - Theo Rispens
- Sanquin Research, Department of Immunopathology, Amsterdam, Netherlands
| | - Gestur Vidarsson
- Sanquin Research, Department of Experimental Immunohematology and Landsteiner Laboratory, Amsterdam, Netherlands
- Department of Biomolecular Mass Spectrometry and Proteomics, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| |
Collapse
|
3
|
Tangherloni A, Riva SG, Myers B, Buffa FM, Cazzaniga P. MAGNETO: Cell type marker panel generator from single-cell transcriptomic data. J Biomed Inform 2023; 147:104510. [PMID: 37797704 DOI: 10.1016/j.jbi.2023.104510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 09/12/2023] [Accepted: 09/29/2023] [Indexed: 10/07/2023]
Abstract
Single-cell RNA sequencing experiments produce data useful to identify different cell types, including uncharacterized and rare ones. This enables us to study the specific functional roles of these cells in different microenvironments and contexts. After identifying a (novel) cell type of interest, it is essential to build succinct marker panels, composed of a few genes referring to cell surface proteins and clusters of differentiation molecules, able to discriminate the desired cells from the other cell populations. In this work, we propose a fully-automatic framework called MAGNETO, which can help construct optimal marker panels starting from a single-cell gene expression matrix and a cell type identity for each cell. MAGNETO builds effective marker panels solving a tailored bi-objective optimization problem, where the first objective regards the identification of the genes able to isolate a specific cell type, while the second conflicting objective concerns the minimization of the total number of genes included in the panel. Our results on three public datasets show that MAGNETO can identify marker panels that identify the cell populations of interest better than state-of-the-art approaches. Finally, by fine-tuning MAGNETO, our results demonstrate that it is possible to obtain marker panels with different specificity levels.
Collapse
Affiliation(s)
- Andrea Tangherloni
- Department of Computing Sciences, Bocconi University, Via Guglielmo Röntgen 1, Milan, 20136, Italy; Bocconi Institute for Data Science and Analytics, Bocconi University, Via Guglielmo Röntgen 1, Milan, 20136, Italy; Department of Human and Social Sciences, University of Bergamo, Piazzale S. Agostino 2, Bergamo, 24129, Italy.
| | - Simone G Riva
- Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
| | - Brynelle Myers
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, United Kingdom
| | - Francesca M Buffa
- Department of Computing Sciences, Bocconi University, Via Guglielmo Röntgen 1, Milan, 20136, Italy; Bocconi Institute for Data Science and Analytics, Bocconi University, Via Guglielmo Röntgen 1, Milan, 20136, Italy; Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, United Kingdom
| | - Paolo Cazzaniga
- Department of Human and Social Sciences, University of Bergamo, Piazzale S. Agostino 2, Bergamo, 24129, Italy; Bicocca Bioinformatics, Biostatistics, and Bioimaging Centre - B4, Via Follereau 3, Vedano al Lambro, 20854, Italy
| |
Collapse
|
4
|
Wang J, Gurupalli HV, Stafford JL. Teleost leukocyte immune-type receptors. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 147:104768. [PMID: 37414235 DOI: 10.1016/j.dci.2023.104768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 07/03/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023]
Abstract
Leukocyte immune-type receptors (LITRs) are a large family of teleost immunoregulatory receptor-types belonging to the immunoglobulin superfamily. These immune genes are phylogenetically and syntenically related to Fc receptor-like protein genes (fcrls) present in other vertebrates, including amphibians, birds, mice, and man. In vitro-based functional analyses of LITRs, using transfection approaches, have shown that LITRs have diverse immunoregulatory potentials including the activation and inhibition of several innate immune effector responses such as cell-mediated killing responses, degranulation, cytokine secretion, and phagocytosis. The purpose of this mini review is to provide an overview of fish LITR-mediated immunoregulatory potentials obtained from various teleost model systems, including channel catfish, zebrafish, and goldfish. We will also describe preliminary characterization of a new goldish LITR-specific polyclonal antibody (pAb) and discuss the significance of this tool for further investigation of the functions of fish LITRs.
Collapse
Affiliation(s)
- Jiahui Wang
- Department of Biological Sciences, University of Alberta, Alberta, Canada
| | | | - James L Stafford
- Department of Biological Sciences, University of Alberta, Alberta, Canada.
| |
Collapse
|
5
|
Mamidi MK, Huang J, Honjo K, Li R, Tabengwa EM, Neeli I, Randall NL, Ponnuchetty MV, Radic M, Leu CM, Davis RS. FCRL1 immunoregulation in B cell development and malignancy. Front Immunol 2023; 14:1251127. [PMID: 37822931 PMCID: PMC10562807 DOI: 10.3389/fimmu.2023.1251127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/01/2023] [Indexed: 10/13/2023] Open
Abstract
Immunotherapeutic targeting of surface regulatory proteins and pharmacologic inhibition of critical signaling pathways has dramatically shifted our approach to the care of individuals with B cell malignancies. This evolution in therapy reflects the central role of the B cell receptor (BCR) signaling complex and its co-receptors in the pathogenesis of B lineage leukemias and lymphomas. Members of the Fc receptor-like gene family (FCRL1-6) encode cell surface receptors with complex tyrosine-based regulation that are preferentially expressed by B cells. Among them, FCRL1 expression peaks on naïve and memory B cells and is unique in terms of its intracellular co-activation potential. Recent studies in human and mouse models indicate that FCRL1 contributes to the formation of the BCR signalosome, modulates B cell signaling, and promotes humoral responses. Progress in understanding its regulatory properties, along with evidence for its over-expression by mature B cell leukemias and lymphomas, collectively imply important yet unmet opportunities for FCRL1 in B cell development and transformation. Here we review recent advances in FCRL1 biology and highlight its emerging significance as a promising biomarker and therapeutic target in B cell lymphoproliferative disorders.
Collapse
Affiliation(s)
- Murali K. Mamidi
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Jifeng Huang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Kazuhito Honjo
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Ran Li
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Edlue M. Tabengwa
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Indira Neeli
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Nar’asha L. Randall
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Manasa V. Ponnuchetty
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Marko Radic
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, United States
| | - Chuen-Miin Leu
- Institute of Microbiology and Immunology, National Yang Ming ChiaoTung University, Taipei, Taiwan
| | - Randall S. Davis
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, United States
- Departments of Microbiology, and Biochemistry & Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
- O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States
| |
Collapse
|
6
|
Liang X, Du L, Fan Y. The potential of FCRL genes as targets for cancer treatment: insights from bioinformatics and immunology. Aging (Albany NY) 2023; 15:204766. [PMID: 37285836 PMCID: PMC10292877 DOI: 10.18632/aging.204766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 05/17/2023] [Indexed: 06/09/2023]
Abstract
Cancer is a prevalent and dangerous disease that requires a multifaceted approach to treatment. The FCRL family gene has been linked to immune function and tumor progression. Bioinformatics may help unravel their role in cancer treatment. We conducted a comprehensive analysis of the FCRL family genes in pan-cancer using publicly available databases and online tools. Specifically, we examined gene expression, prognostic significance, mutation profiles, drug resistance, as well as biological and immunomodulatory roles. Our data were sourced from The Cancer Genome Atlas, Genotype-Tissue Expression, cBioPortal, STRING, GSCALite, Cytoscape, and R software. The expression of FCRL genes varies significantly across different tumor types and normal tissues. While high expression of most FCRL genes is associated with a protective effect in many cancers, FCRLB appears to be a risk factor in several types of cancer. Alterations in FCRL family genes, particularly through amplification and mutation, are common in cancers. These genes are closely linked to classical cancer pathways such as apoptosis, epithelial-mesenchymal transition (EMT), estrogen receptor (ER) signaling, and DNA damage response. Enrichment analysis indicates that FCRL family genes are predominantly associated with immune cell activation and differentiation. Immunological assays demonstrate a strong positive correlation between FCRL family genes and tumor-infiltrating lymphocytes (TILs), immunostimulators, and immunoinhibitors. Furthermore, FCRL family genes can enhance the sensitivity of various anticancer drugs. The FCRL family genes are vital in cancer pathogenesis and progression. Targeting these genes in conjunction with immunotherapy could enhance cancer treatment efficacy. Further research is required to determine their potential as therapeutic targets.
Collapse
Affiliation(s)
- Xiao Liang
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Lei Du
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Yuchao Fan
- Department of Anesthesiology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, Sichuan Province, China
| |
Collapse
|
7
|
Yang J, Gu J, Wang H, Shi J, Lu L, She W, Wang Y. Fc receptor-like 5 gene polymorphisms and mRNA expression are associated with liver fibrosis in chronic hepatitis B. Front Microbiol 2022; 13:988464. [PMID: 36160227 PMCID: PMC9500477 DOI: 10.3389/fmicb.2022.988464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022] Open
Abstract
Objective: To investigate the associations of Fc receptor-like 5 (FCRL5) gene polymorphisms and mRNA expression with liver fibrosis in chronic hepatitis B (CHB).Methods: A total of 114 CHB patients with liver fibrosis and 120 CHB patients without liver fibrosis were selected for this study. The gender, age, body mass index (BMI), alanine transaminase (ALT) value, aspartate aminotransferase (AST) value, aspartate aminotransferase-to-platelet ratio index (APRI), and fibrosis index based on 4 factors (FIB-4) were recorded. Two polymorphisms of the FCRL5 gene (rs6427384 and rs6692977) were genotyped. The mRNA expression level of FCRL5 in peripheral blood monocytes was determined.Results: ALT, AST, APRI, and FIB-4 in patients with fibrosis were significantly higher than those in non-fibrosis patients. There was statistically significant difference between fibrosis and non-fibrosis groups in the genotype distribution (χ2 = 7.805, p = 0.020) and allele frequencies (χ2 = 13.252, p < 0.001) at FCRL5 rs6692977. When compared with CC genotype, the genotype CT or TT at rs6692977 was significantly associated with a increased risk of liver fibrosis in CHB patients (CT vs. CC: OR = 1.921, 95% CI = 1.093–3.375, p = 0.023; TT vs. CC: OR = 2.598, 95% CI = 1.067–6.324, p = 0.031). The mRNA relative expression levels of FCRL5 in patients with liver fibrosis were significantly higher than those in the non-fibrosis group (t = 13.456, p < 0.001). The fibrosis patients carried TT or CT genotype of rs6692977 had significantly higher FCRL5 mRNA expression levels than those carried CC genotype (t = 2.859, p = 0.005). The mRNA expression levels of FCRL5, APRI, and FIB-4 index showed predictive efficacy in liver fibrosis with cut-off values of 0.75 (AUC = 0.896, 95% CI = 0.856–0.935), 0.45 (AUC = 0.852, 95% CI = 0.802–0.902) and 1.84 (AUC = 0.765, 95% CI = 0.703–0.826), respectively.Conclusion: FCRL5 gene rs6692977 polymorphisms and mRNA expression levels are associated with liver fibrosis in CHB patients.
Collapse
Affiliation(s)
- Jiajia Yang
- Department of Infection Management, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Juan Gu
- Department of Clinical Laboratory, The Affiliated Yancheng Hospital, School of Medicine, Southeast University, Yancheng, China
| | - Hongmei Wang
- Department of Infection Management, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Jiayin Shi
- Department of Outpatient, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Lingyun Lu
- Department of Gastroenterology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Wanxian She
- Department of Gastroenterology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
| | - Ying Wang
- Department of Infection Management, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou, China
- *Correspondence: Ying Wang,
| |
Collapse
|
8
|
Pandey A, Malla WA, Sahu AR, Wani SA, Khan RIN, Saxena S, Ramteke PW, Praharaj MR, Kumar A, Rajak KK, Mishra B, Muthuchelvan D, Sajjanar B, Mishra BP, Singh RK, Gandham RK. Differential expression of long non-coding RNAs under Peste des petits ruminants virus (PPRV) infection in goats. Virulence 2022; 13:310-322. [PMID: 35129076 PMCID: PMC8824212 DOI: 10.1080/21505594.2022.2026564] [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] [Indexed: 12/13/2022] Open
Abstract
Peste des petits ruminants (PPR) characterized by fever, sore mouth, conjunctivitis, gastroenteritis, and pneumonia, is an acute, highly contagious viral disease of sheep and goats. The role of long non-coding RNAs (lncRNAs) in PPRV infection has not been explored to date. In this study, the transcriptome profiles of virulent Peste des petits ruminants virus (PPRV) infected goat tissues – lung and spleen were analyzed to identify the role of lncRNAs in PPRV infection. A total of 13,928 lncRNA transcripts were identified, out of which 170 were known lncRNAs. Intergenic lncRNAs (7625) formed the major chunk of the novel lncRNA transcripts. Differential expression analysis revealed that 15 lncRNAs (11 downregulated and 4 upregulated) in the PPRV infected spleen samples and 16 lncRNAs (13 downregulated and 3 upregulated) in PPRV infected lung samples were differentially expressed as compared to control. The differentially expressed lncRNAs (DElncRNAs) possibly regulate various immunological processes related to natural killer cell activation, antigen processing and presentation, and B cell activity, by regulating the expression of mRNAs through the cis- or trans-regulatory mechanism. Functional enrichment analysis of differentially expressed mRNAs (DEmRNAs) revealed enrichment of immune pathways and biological processes in concordance with the pathways in which correlated lncRNA-neighboring genes were enriched. The results suggest that a coordinated immune response is raised in both lung and spleen tissues of the goat through mRNA-lncRNA crosstalk.
Collapse
Affiliation(s)
- Aruna Pandey
- Division of Veterinary Biotechnology, ICAR-IVRI, Bareilly, India
| | | | - Amit Ranjan Sahu
- Division of Veterinary Biotechnology, ICAR-IVRI, Bareilly, India
| | - Sajad Ahmad Wani
- Division of Veterinary Biotechnology, ICAR-IVRI, Bareilly, India
| | | | - Shikha Saxena
- Division of Veterinary Biotechnology, ICAR-IVRI, Bareilly, India
| | - P W Ramteke
- Department of Biological Sciences, SHUATS, Allahabad, India
| | - Manas Ranjan Praharaj
- Genomics and Bioinformatics, National Institute of Animal Biotechnology, Hyderabad, India
| | - Amit Kumar
- Division of Animal Genetics and Breeding, ICAR-IVRI, Bareilly, India
| | | | - Bina Mishra
- Division of Biological Products, ICAR-IVRI, Bareilly, India
| | | | | | | | - Raj Kumar Singh
- Division of Veterinary Biotechnology, ICAR-IVRI, Bareilly, India
| | - Ravi Kumar Gandham
- Division of Veterinary Biotechnology, ICAR-IVRI, Bareilly, India.,Genomics and Bioinformatics, National Institute of Animal Biotechnology, Hyderabad, India
| |
Collapse
|
9
|
DeLuca JM, Murphy MK, Wang X, Wilson TJ. FCRL1 Regulates B Cell Receptor-Induced ERK Activation through GRB2. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2021; 207:2688-2698. [PMID: 34697226 PMCID: PMC8629370 DOI: 10.4049/jimmunol.2100218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 09/17/2021] [Indexed: 11/19/2022]
Abstract
Regulation of BCR signaling has important consequences for generating effective Ab responses to pathogens and preventing production of autoreactive B cells during development. Currently defined functions of Fc receptor-like (FCRL) 1 include positive regulation of BCR-induced calcium flux, proliferation, and Ab production; however, the mechanistic basis of FCRL1 signaling and its contributions to B cell development remain undefined. Molecular characterization of FCRL1 signaling shows phosphotyrosine-dependent associations with GRB2, GRAP, SHIP-1, and SOS1, all of which can profoundly influence MAPK signaling. In contrast with previous characterizations of FCRL1 as a strictly activating receptor, we discover a role for FCRL1 in suppressing ERK activation under homeostatic and BCR-stimulated conditions in a GRB2-dependent manner. Our analysis of B cells in Fcrl1 -/- mice shows that ERK suppression by FCRL1 is associated with a restriction in the number of cells surviving splenic maturation in vivo. The capacity of FCRL1 to modulate ERK activation presents a potential for FCRL1 to be a regulator of peripheral B cell tolerance, homeostasis, and activation.
Collapse
Affiliation(s)
- Jenna M DeLuca
- Department of Microbiology, Miami University, Oxford, OH
| | | | - Xin Wang
- Department of Microbiology, Miami University, Oxford, OH
| | | |
Collapse
|
10
|
Marion MC, Ramos PS, Bachali P, Labonte AC, Zimmerman KD, Ainsworth HC, Heuer SE, Robl RD, Catalina MD, Kelly JA, Howard TD, Lipsky PE, Grammer AC, Langefeld CD. Nucleic Acid-Sensing and Interferon-Inducible Pathways Show Differential Methylation in MZ Twins Discordant for Lupus and Overexpression in Independent Lupus Samples: Implications for Pathogenic Mechanism and Drug Targeting. Genes (Basel) 2021; 12:genes12121898. [PMID: 34946847 PMCID: PMC8701117 DOI: 10.3390/genes12121898] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 12/27/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a chronic, multisystem, autoimmune inflammatory disease with genomic and non-genomic contributions to risk. We hypothesize that epigenetic factors are a significant contributor to SLE risk and may be informative for identifying pathogenic mechanisms and therapeutic targets. To test this hypothesis while controlling for genetic background, we performed an epigenome-wide analysis of DNA methylation in genomic DNA from whole blood in three pairs of female monozygotic (MZ) twins of European ancestry, discordant for SLE. Results were replicated on the same array in four cell types from a set of four Danish female MZ twin pairs discordant for SLE. Genes implicated by the epigenetic analyses were then evaluated in 10 independent SLE gene expression datasets from the Gene Expression Omnibus (GEO). There were 59 differentially methylated loci between unaffected and affected MZ twins in whole blood, including 11 novel loci. All but two of these loci were hypomethylated in the SLE twins relative to the unaffected twins. The genes harboring these hypomethylated loci exhibited increased expression in multiple independent datasets of SLE patients. This pattern was largely consistent regardless of disease activity, cell type, or renal tissue type. The genes proximal to CpGs exhibiting differential methylation (DM) in the SLE-discordant MZ twins and exhibiting differential expression (DE) in independent SLE GEO cohorts (DM-DE genes) clustered into two pathways: the nucleic acid-sensing pathway and the type I interferon pathway. The DM-DE genes were also informatically queried for potential gene–drug interactions, yielding a list of 41 drugs including a known SLE therapy. The DM-DE genes delineate two important biologic pathways that are not only reflective of the heterogeneity of SLE but may also correlate with distinct IFN responses that depend on the source, type, and location of nucleic acid molecules and the activated receptors in individual patients. Cell- and tissue-specific analyses will be critical to the understanding of genetic factors dysregulating the nucleic acid-sensing and IFN pathways and whether these factors could be appropriate targets for therapeutic intervention.
Collapse
Affiliation(s)
- Miranda C. Marion
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; (M.C.M.); (H.C.A.)
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA;
| | - Paula S. Ramos
- Division of Rheumatology and Immunology, Department of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA;
| | - Prathyusha Bachali
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Adam C. Labonte
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Kip D. Zimmerman
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA;
| | - Hannah C. Ainsworth
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; (M.C.M.); (H.C.A.)
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA;
| | - Sarah E. Heuer
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
- The Jackson Laboratory, Tufts Graduate School of Biomedical Sciences, Bar Harbor, ME 04609, USA
| | - Robert D. Robl
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Michelle D. Catalina
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Jennifer A. Kelly
- Arthritis and Clinical Immunology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA;
| | - Timothy D. Howard
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA;
| | - Peter E. Lipsky
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Amrie C. Grammer
- AMPEL BioSolutions, LLC and RILITE Research Institute, Charlottesville, VA 22902, USA; (P.B.); (A.C.L.); (S.E.H.); (R.D.R.); (M.D.C.); (P.E.L.); (A.C.G.)
| | - Carl D. Langefeld
- Department of Biostatistics and Data Science, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA; (M.C.M.); (H.C.A.)
- Center for Precision Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA;
- Correspondence:
| |
Collapse
|
11
|
Carr DJJ, Berube AN, Filiberti A, Gmyrek GB. Lack of neonatal Fc receptor does not diminish the efficacy of the HSV-1 0ΔNLS vaccine against ocular HSV-1 challenge. Vaccine 2021; 39:2526-2536. [PMID: 33814229 DOI: 10.1016/j.vaccine.2021.03.075] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/08/2021] [Accepted: 03/20/2021] [Indexed: 02/07/2023]
Abstract
The neonatal Fc receptor (FcRn) is constitutively expressed in the cornea and is up-regulated in response to herpes simplex virus type 1 (HSV-1). Previously, we found targeting cornea FcRn expression by small interfering RNA-mediated knockdown reduced the local efficacy of HSV-1 0ΔNLS vaccinated C57BL/6 mice against ocular challenge with HSV-1. The current study was undertaken to evaluate the HSV-1 0ΔNLS vaccine efficacy in FcRn deficient (FcRn KO) mice challenged with HSV-1. Whereas there was little neutralizing antibody detected in the serum of HSV-1 0ΔNLS vaccinated FcRn KO mice, these mice exhibited the same degree of protection against ocular challenge with HSV-1 as wild type (WT) C57BL/6 mice as measured by cumulative survival, infectious virus shed or retained in tissue, and corneal pathology including opacity and neovascularization. Mock-vaccinated FcRn KO mice were found to be more sensitive to ocular HSV-1 infection compared to mock-vaccinated (WT) mice in terms of cumulative survival and virus shedding. In addition, the FcRn KO mice generated significantly fewer effector (CD3+CD44+CD62L-) and central (CD3+CD44+CD62L+) memory CD8+ T cells compared to the WT mice 7 days post infection. Collectively, mock-vaccinated FcRn KO mice are susceptible to ocular HSV-1 infection but HSV-1 0ΔNLS vaccinated FcRn KO mice are resistant suggesting that in addition to the FcRn, other pathways are involved in mediating the protective effect of the HSV-1 0ΔNLS vaccine against subsequent HSV-1 challenge.
Collapse
Affiliation(s)
- Daniel J J Carr
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
| | - Amanda N Berube
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Adrian Filiberti
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Grzegorz B Gmyrek
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| |
Collapse
|
12
|
Identification of distinct LRC- and Fc receptor complex-like chromosomal regions in fish supports that teleost leukocyte immune-type receptors are distant relatives of mammalian Fc receptor-like molecules. Immunogenetics 2021; 73:93-109. [PMID: 33410929 DOI: 10.1007/s00251-020-01193-3] [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: 09/21/2020] [Accepted: 11/17/2020] [Indexed: 01/17/2023]
Abstract
Leukocyte immune-type receptors (LITRs) are a large family of immunoregulatory receptor-types originally identified in the channel catfish (Ictalurus punctatus (Ip)LITRs). Phylogenetic analyses of LITRs show that they share distant evolutionary relationships with important mammalian immunoregulatory receptors belonging to the Fc receptors family and the leukocyte receptor complex (LRC), but their syntenic relationships with these immunoglobulin superfamily members have not been investigated. To further examine the possible evolutionary connections between teleost LITRs and various mammalian immunoregulatory receptor-types, we surveyed the genomic databases of representative vertebrate taxa and our results show that teleost LITRs generally exist in large genomic clusters, which are linked to vangl2, arhgef11, and slam family genes, features that are also shared by amphibian and mammalian Fc receptor-like molecules (FCRLs). Moreover, detailed phylogenetic comparisons between the individual Ig-like domains of LITRs and mammalian FCRLs shows that these receptors share related Ig-like domains indicative of their common ancestry. However, contrary to our previous reports, no supportive evidence for phylogenetic relationships between the Ig-like domains of LITRs with the Ig-like domains of LRC-encoded mammalian immunoregulatory receptors was found. We also identified an LRC-like region in the zebrafish genome, but no expanded litr-related genes were located in this region. Similarly, no lilr-related genes were found in spotted gar, a representative basal ray-finned fish. Finally, two distantly related fcrls and an LRC-like gene were identified in the elephant shark genome, suggesting that the loss of an immunoregulatory receptor-containing LRC region may be unique to ray-finned fish.
Collapse
|
13
|
Raj P, Song R, Zhu H, Riediger L, Jun DJ, Liang C, Arana C, Zhang B, Gao Y, Wakeland BE, Dozmorov I, Zhou J, Kelly JA, Lauwerys BR, Guthridge JM, Olsen NJ, Nath SK, Pasare C, van Oers N, Gilkeson G, Tsao BP, Gaffney PM, Gregersen PK, James JA, Zuo X, Karp DR, Li QZ, Wakeland EK. Deep sequencing reveals a DAP1 regulatory haplotype that potentiates autoimmunity in systemic lupus erythematosus. Genome Biol 2020; 21:281. [PMID: 33213505 PMCID: PMC7677828 DOI: 10.1186/s13059-020-02184-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 10/19/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Systemic lupus erythematosus (SLE) is a clinically heterogeneous autoimmune disease characterized by the development of anti-nuclear antibodies. Susceptibility to SLE is multifactorial, with a combination of genetic and environmental risk factors contributing to disease development. Like other polygenic diseases, a significant proportion of estimated SLE heritability is not accounted for by common disease alleles analyzed by SNP array-based GWASs. Death-associated protein 1 (DAP1) was implicated as a candidate gene in a previous familial linkage study of SLE and rheumatoid arthritis, but the association has not been explored further. RESULTS We perform deep sequencing across the DAP1 genomic segment in 2032 SLE patients, and healthy controls, and discover a low-frequency functional haplotype strongly associated with SLE risk in multiple ethnicities. We find multiple cis-eQTLs embedded in a risk haplotype that progressively downregulates DAP1 transcription in immune cells. Decreased DAP1 transcription results in reduced DAP1 protein in peripheral blood mononuclear cells, monocytes, and lymphoblastoid cell lines, leading to enhanced autophagic flux in immune cells expressing the DAP1 risk haplotype. Patients with DAP1 risk allele exhibit significantly higher autoantibody titers and altered expression of the immune system, autophagy, and apoptosis pathway transcripts, indicating that the DAP1 risk allele mediates enhanced autophagy, leading to the survival of autoreactive lymphocytes and increased autoantibody. CONCLUSIONS We demonstrate how targeted sequencing captures low-frequency functional risk alleles that are missed by SNP array-based studies. SLE patients with the DAP1 genotype have distinct autoantibody and transcription profiles, supporting the dissection of SLE heterogeneity by genetic analysis.
Collapse
Affiliation(s)
- Prithvi Raj
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Ran Song
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Honglin Zhu
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Linley Riediger
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Dong-Jae Jun
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Chaoying Liang
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Carlos Arana
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Bo Zhang
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Yajing Gao
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Benjamin E Wakeland
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Igor Dozmorov
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jinchun Zhou
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jennifer A Kelly
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Bernard R Lauwerys
- Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, 1200, Bruxelles, Belgium
| | - Joel M Guthridge
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Nancy J Olsen
- Division of Rheumatology, Department of Medicine, Penn State Medical School, State College, PA, USA
| | - Swapan K Nath
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Chandrashekhar Pasare
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Nicolai van Oers
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Gary Gilkeson
- Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC, USA
| | - Betty P Tsao
- Division of Rheumatology and Immunology, Medical University of South Carolina, Charleston, SC, USA
| | - Patrick M Gaffney
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | | | - Judith A James
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, 73104, USA
| | - Xiaoxia Zuo
- Department of Rheumatology and Immunology, Xiangya Hospital, Central South University, Changsha, 410008, China.
| | - David R Karp
- Rheumatic Diseases Division, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Quan-Zhen Li
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Edward K Wakeland
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| |
Collapse
|
14
|
Phalke S, Aviszus K, Rubtsova K, Rubtsov A, Barkes B, Powers L, Warner B, Crooks JL, Kappler JW, Fernández-Pérez ER, Maier LA, Hamzeh N, Marrack P. Age-associated B Cells Appear in Patients with Granulomatous Lung Diseases. Am J Respir Crit Care Med 2020; 202:1013-1023. [PMID: 32501729 DOI: 10.1164/rccm.201911-2151oc] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Rationale: A subpopulation of B cells (age-associated B cells [ABCs]) is increased in mice and humans with infections or autoimmune diseases. Because depletion of these cells might be valuable in patients with certain lung diseases, the goal was to find out if ABC-like cells were at elevated levels in such patients.Objectives: To measure ABC-like cell percentages in patients with lung granulomatous diseases.Methods: Peripheral blood and BAL cells from patients with sarcoidosis, beryllium sensitivity, or hypersensitivity pneumonitis and healthy subjects were analyzed for the percentage of B cells that were ABC-like, defined by expression of CD11c, low levels of CD21, FcRL 1-5 (Fc receptor-like protein 1-5) expression, and, in some cases, T-bet.Measurements and Main Results: ABC-like cells in blood were at low percentages in healthy subjects and higher percentages in patients with sarcoidosis as well as at high percentages among BAL cells of patients with sarcoidosis, beryllium disease, and hypersensitivity pneumonitis. Treatment of patients with sarcoidosis led to reduced percentages of ABC-like cells in blood.Conclusions: Increased levels of ABC-like cells in patients with sarcoidosis may be useful in diagnosis. The increase in percentage of ABC-like cells in patients with lung granulomatous diseases and decrease in treated patients suggests that depletion of these cells may be valuable.
Collapse
Affiliation(s)
| | | | | | | | | | - Linda Powers
- Department of Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Brenda Warner
- Department of Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - James L Crooks
- Department of Biomedical Research.,Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, Colorado.,Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado; and
| | - John W Kappler
- Department of Biomedical Research.,Department of Immunology and Microbiology, University Colorado Anschutz Medical Campus, Aurora, Colorado
| | | | | | - Nabeel Hamzeh
- Department of Medicine, and.,Department of Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Philippa Marrack
- Department of Biomedical Research.,Department of Immunology and Microbiology, University Colorado Anschutz Medical Campus, Aurora, Colorado
| |
Collapse
|
15
|
Abstract
To investigate the role of the altered activation of the immune system in the prognosis of patients affected by laryngeal squamous cell carcinoma (LSCC). We analyzed 56 patients with advanced LSCC divided into two groups according to their prognosis: the first group relapsed within 24 months after treatment, the second group had no evidence of disease at 2 years. The presence of stromal tumor infiltrating lymphocytes (TILs) at the tumor-host border was investigated. In 43 patients we evaluated the expression of 395 genes related to immune system activation through a next generation sequencing panel. Priority-LASSO models and clustering analyses were integrated with multivariate Cox proportional hazard modeling to identify independent genes associated with relapse and estimate hazard ratios in relation to gene expression and TILs. TILs and the expression of genes related with immune system activation (FCGR1A, IFNA17, FCRLA, NCR3, KREMEN1, CD14, CD3G, CD19, CD20 and CD79A) were significantly associated with prognostic factors or disease specific survival. In patients with lymph node metastases and advanced T stage (pT4), the expression of other genes was altered. Low TILs count was highly associated with relapse within 2 years (p < 0.001). Low TILs and altered expression of specific genes associated with tumor-immune systems interactions emerged as independent risk factors, associated to poor prognosis and relapse within 2 years in advanced LSCC. Evaluation of patients' immune profile could be useful for prognosis and future therapeutic approaches towards personalized therapy.
Collapse
|
16
|
Davis RS. Roles for the FCRL6 Immunoreceptor in Tumor Immunology. Front Immunol 2020; 11:575175. [PMID: 33162991 PMCID: PMC7591390 DOI: 10.3389/fimmu.2020.575175] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/01/2020] [Indexed: 01/12/2023] Open
Abstract
Members of the Fc receptor-like (FCRL1-6) gene family encode transmembrane glycoproteins that are preferentially expressed by B cells and generally repress responses via cytoplasmic tyrosine-based regulation. Given their distribution and function, there is a growing appreciation for their roles in lymphoproliferative disorders and as immunotherapeutic targets. In contrast to FCRL1-5, FCRL6 is distinctly expressed outside the B lineage by cytotoxic T and NK lymphocytes. Its restricted expression by these orchestrators of cell-mediated immunity, along with its inhibitory properties and extracellular interactions with MHCII/HLA-DR, represent a newly appreciated axis with relevance in tolerance and cancer defense. The significance of FCRL6 in this arena has been recently demonstrated by its upregulation in HLA-DR+ tumor samples from melanoma, breast, and lung cancer patients who relapsed following PD-1 blockade. These findings imply a potential mechanistic role for FCRL6 in adaptive evasion to immune checkpoint therapy. Here we review these new developments in the FCRL field and identify new evidence for the prognostic significance of FCRL6 in malignancies that collectively indicate its potential as a biomarker and therapeutic target.
Collapse
Affiliation(s)
- Randall S Davis
- Departments of Medicine, Microbiology, and Biochemistry & Molecular Genetics, The Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States
| |
Collapse
|
17
|
Polverino F, Curtis JL. The ABCs of Granulomatous Lung Diseases: Age-associated B Cells. Am J Respir Crit Care Med 2020; 202:922-924. [PMID: 32603192 PMCID: PMC7528779 DOI: 10.1164/rccm.202006-2261ed] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Francesca Polverino
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, Arizona
| | - Jeffrey L Curtis
- Medical Service, VA Ann Arbor Healthcare System, Ann Arbor, Michigan
- Graduate Program in Immunology and
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| |
Collapse
|
18
|
Palli R, Seaton KE, Piepenbrink MS, Hural J, Goepfert PA, Laher F, Buchbinder SP, Churchyard G, Gray GE, Robinson HL, Huang Y, Janes H, Kobie JJ, Keefer MC, Tomaras GD, Thakar J. Impact of vaccine type on HIV-1 vaccine elicited antibody durability and B cell gene signature. Sci Rep 2020; 10:13031. [PMID: 32747654 PMCID: PMC7398916 DOI: 10.1038/s41598-020-69007-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 06/16/2020] [Indexed: 12/11/2022] Open
Abstract
Efficacious HIV-1 vaccination requires elicitation of long-lived antibody responses. However, our understanding of how different vaccine types elicit durable antibody responses is lacking. To assess the impact of vaccine type on antibody responses, we measured IgG isotypes against four consensus HIV antigens from 2 weeks to 10 years post HIV-1 vaccination and used mixed effects models to estimate half-life of responses in four human clinical trials. Compared to protein-boosted regimens, half-lives of gp120-specific antibodies were longer but peak magnitudes were lower in Modified Vaccinia Ankara (MVA)-boosted regimens. Furthermore, gp120-specific B cell transcriptomics from MVA-boosted and protein-boosted vaccines revealed a distinct signature at a peak (2 weeks after last vaccination) including CD19, CD40, and FCRL2-5 activation along with increased B cell receptor signaling. Additional analysis revealed contributions of RIG-I-like receptor pathway and genes such as SMAD5 and IL-32 to antibody durability. Thus, this study provides novel insights into vaccine induced antibody durability and B-cell receptor signaling.
Collapse
Affiliation(s)
- Rohith Palli
- Medical Scientist Training Program, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
- Biophysics, Structural, and Computational Biology Program, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Kelly E Seaton
- Duke Human Vaccine Institute and Departments of Surgery, Immunology, and Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Michael S Piepenbrink
- Infectious Diseases Division, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - John Hural
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Paul A Goepfert
- Infectious Diseases Division, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Fatima Laher
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Susan P Buchbinder
- Bridge HIV, San Francisco Department of Public Health and Departments of Medicine, Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | | | - Glenda E Gray
- Perinatal HIV Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- South African Medical Research Council, Cape Town, South Africa
| | | | - Yunda Huang
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Holly Janes
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, USA
| | - James J Kobie
- Infectious Diseases Division, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Michael C Keefer
- Department of Medicine, Infectious Diseases Division, University of Rochester School of Medicine and Dentistry, Rochester, NY, USA
| | - Georgia D Tomaras
- Duke Human Vaccine Institute and Departments of Surgery, Immunology, and Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Juilee Thakar
- Department of Microbiology and Immunology, University of Rochester, Rochester, NY, 14620, USA.
- Department of Biostatistics and Computational Biology, University of Rochester, Rochester, NY, 14620, USA.
| |
Collapse
|
19
|
Kim CC, Baccarella AM, Bayat A, Pepper M, Fontana MF. FCRL5 + Memory B Cells Exhibit Robust Recall Responses. Cell Rep 2020; 27:1446-1460.e4. [PMID: 31042472 PMCID: PMC6530801 DOI: 10.1016/j.celrep.2019.04.019] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/02/2019] [Accepted: 04/02/2019] [Indexed: 12/12/2022] Open
Abstract
FCRL5+ atypical memory B cells (atMBCs) expand in many chronic human infections, including recurrent malaria, but studies have drawn opposing conclusions about their function. Here, in mice infected with Plasmodium chabaudi, we demonstrate expansion of an antigen-specific FCRL5+ population that is distinct from previously described FCRL5+ innate-like murine subsets. Comparative analyses reveal overlapping phenotypic and transcriptomic signatures between FCRL5+ B cells from Plasmodium-infected mice and atMBCs from Plasmodium-exposed humans. In infected mice, FCRL5 is expressed on the majority of antigen-specific germinal-center-derived memory B cells (MBCs). Upon challenge, FCRL5+ MBCs rapidly give rise to antibody-producing cells expressing additional atypical markers, demonstrating functionality in vivo. Moreover, atypical markers are expressed on antigen-specific MBCs generated by immunization in both mice and humans, indicating that the atypical phenotype is not restricted to chronic settings. This study resolves conflicting interpretations of atMBC function and suggests FCRL5+ B cells as an attractive target for vaccine strategies.
Collapse
Affiliation(s)
- Charles C Kim
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alyssa M Baccarella
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Aqieda Bayat
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Marion Pepper
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Mary F Fontana
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Immunology, University of Washington School of Medicine, Seattle, WA 98109, USA.
| |
Collapse
|
20
|
Liu Y, Goroshko S, Leung LYT, Dong S, Khan S, Campisi P, Propst EJ, Wolter NE, Grunebaum E, Ehrhardt GRA. FCRL4 Is an Fc Receptor for Systemic IgA, but Not Mucosal Secretory IgA. THE JOURNAL OF IMMUNOLOGY 2020; 205:533-538. [DOI: 10.4049/jimmunol.2000293] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/15/2020] [Indexed: 12/25/2022]
|
21
|
McGrath-Morrow SA, Ndeh R, Helmin KA, Khuder B, Rothblum-Oviatt C, Collaco JM, Wright J, Reyfman PA, Lederman HM, Singer BD. DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype. Sci Rep 2020; 10:7479. [PMID: 32366930 PMCID: PMC7198504 DOI: 10.1038/s41598-020-64514-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/13/2020] [Indexed: 12/19/2022] Open
Abstract
People with ataxia-telangiectasia (A-T) display phenotypic variability with regard to progression of immunodeficiency, sino-pulmonary disease, and neurologic decline. To determine the association between differential gene expression, epigenetic state, and phenotypic variation among people with A-T, we performed transcriptional and genome-wide DNA methylation profiling in patients with mild and classic A-T progression as well as healthy controls. RNA and genomic DNA were isolated from peripheral blood mononuclear cells for transcriptional and DNA methylation profiling with RNA-sequencing and modified reduced representation bisulfite sequencing, respectively. We identified 555 genes that were differentially expressed among the control, mild A-T, and classic A-T groups. Genome-wide DNA methylation profiling revealed differential promoter methylation in cis with 146 of these differentially expressed genes. Functional enrichment analysis identified significant enrichment in immune, growth, and apoptotic pathways among the methylation-regulated genes. Regardless of clinical phenotype, all A-T participants exhibited downregulation of critical genes involved in B cell function (PAX5, CD79A, CD22, and FCRL1) and upregulation of several genes associated with senescence and malignancy, including SERPINE1. These findings indicate that gene expression differences may be associated with phenotypic variability and suggest that DNA methylation regulates expression of critical immune response genes in people with A-T.
Collapse
Affiliation(s)
- Sharon A McGrath-Morrow
- Eudowood Division of Pediatric Respiratory Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA.
| | - Roland Ndeh
- Eudowood Division of Pediatric Respiratory Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Kathryn A Helmin
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Basil Khuder
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | | | - Joseph M Collaco
- Eudowood Division of Pediatric Respiratory Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jennifer Wright
- Eudowood Division of Pediatric, Allergy and Immunology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Paul A Reyfman
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Howard M Lederman
- Eudowood Division of Pediatric, Allergy and Immunology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Benjamin D Singer
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| |
Collapse
|
22
|
Yousefi Z, Eskandari N. Prognostic significance of Fc receptor-like 1 in patients with chronic lymphocytic leukemia, hairy cell leukemia, and various B-cell non-Hodgkin's lymphoma. Leuk Res Rep 2019; 12:100181. [PMID: 31467839 PMCID: PMC6710560 DOI: 10.1016/j.lrr.2019.100181] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 06/06/2019] [Accepted: 08/09/2019] [Indexed: 11/20/2022] Open
Abstract
Fc receptor-like 1 (FCRL1) positively regulates B-cell responses and may involve in the pathogenesis of B-cell malignancies. This study examined the expression pattern of FCRL1 in B-cell non-Hodgkin's lymphoma patients using real-time PCR and flow cytometry. The results revealed higher levels of FCRL1 expression in diffuse large B-cell lymphoma, hairy cell leukemia, and Burkitt lymphoma patients compared with control groups. There was a significant reduction in the levels of FCRL1 expression in chronic lymphocytic leukemia and mantle cell lymphoma patients compared with healthy individuals. These findings suggest FCRL1 as an excellent marker for the prognosis or immunotherapy of B-cell malignancies.
Collapse
Affiliation(s)
- Zahra Yousefi
- Department of Immunology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Nahid Eskandari
- Department of Immunology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
- Applied Physiology Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| |
Collapse
|
23
|
de Taeye SW, Rispens T, Vidarsson G. The Ligands for Human IgG and Their Effector Functions. Antibodies (Basel) 2019; 8:E30. [PMID: 31544836 PMCID: PMC6640714 DOI: 10.3390/antib8020030] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/16/2019] [Accepted: 04/18/2019] [Indexed: 01/17/2023] Open
Abstract
Activation of the humoral immune system is initiated when antibodies recognize an antigen and trigger effector functions through the interaction with Fc engaging molecules. The most abundant immunoglobulin isotype in serum is Immunoglobulin G (IgG), which is involved in many humoral immune responses, strongly interacting with effector molecules. The IgG subclass, allotype, and glycosylation pattern, among other factors, determine the interaction strength of the IgG-Fc domain with these Fc engaging molecules, and thereby the potential strength of their effector potential. The molecules responsible for the effector phase include the classical IgG-Fc receptors (FcγR), the neonatal Fc-receptor (FcRn), the Tripartite motif-containing protein 21 (TRIM21), the first component of the classical complement cascade (C1), and possibly, the Fc-receptor-like receptors (FcRL4/5). Here we provide an overview of the interactions of IgG with effector molecules and discuss how natural variation on the antibody and effector molecule side shapes the biological activities of antibodies. The increasing knowledge on the Fc-mediated effector functions of antibodies drives the development of better therapeutic antibodies for cancer immunotherapy or treatment of autoimmune diseases.
Collapse
Affiliation(s)
- Steven W de Taeye
- Sanquin Research, Dept Immunopathology and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, 1066 CX Amsterdam, The Netherlands.
- Sanquin Research, Dept Experimental Immunohematology and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, 1066 CX Amsterdam, The Netherlands.
| | - Theo Rispens
- Sanquin Research, Dept Immunopathology and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, 1066 CX Amsterdam, The Netherlands.
| | - Gestur Vidarsson
- Sanquin Research, Dept Experimental Immunohematology and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, 1066 CX Amsterdam, The Netherlands.
| |
Collapse
|
24
|
Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression. Cell 2018; 175:1701-1715.e16. [PMID: 30449622 DOI: 10.1016/j.cell.2018.10.022] [Citation(s) in RCA: 475] [Impact Index Per Article: 79.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 08/16/2018] [Accepted: 10/05/2018] [Indexed: 01/19/2023]
Abstract
While many genetic variants have been associated with risk for human diseases, how these variants affect gene expression in various cell types remains largely unknown. To address this gap, the DICE (database of immune cell expression, expression quantitative trait loci [eQTLs], and epigenomics) project was established. Considering all human immune cell types and conditions studied, we identified cis-eQTLs for a total of 12,254 unique genes, which represent 61% of all protein-coding genes expressed in these cell types. Strikingly, a large fraction (41%) of these genes showed a strong cis-association with genotype only in a single cell type. We also found that biological sex is associated with major differences in immune cell gene expression in a highly cell-specific manner. These datasets will help reveal the effects of disease risk-associated genetic polymorphisms on specific immune cell types, providing mechanistic insights into how they might influence pathogenesis (https://dice-database.org).
Collapse
|
25
|
Lu X, Zhang Q, Wang Y, Zhang L, Zhao H, Chen C, Wang Y, Liu S, Lu T, Wang F, Yan F. Molecular classification and subtype-specific characterization of skin cutaneous melanoma by aggregating multiple genomic platform data. J Cancer Res Clin Oncol 2018; 144:1635-1647. [PMID: 29948145 DOI: 10.1007/s00432-018-2684-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 06/05/2018] [Indexed: 01/07/2023]
Abstract
PURPOSE Traditional classification of melanoma is widely utilized with little apparent results making the development of robust classifiers that can guide therapies an urgency. Successful seminal research on classification has provided a wider understanding of cancer from multiple molecular profiles, respectively. However, it may ignore the complementary nature of the information provided by different types of data, which motivated us to subtype melanoma by aggregating multiple genomic platform data. METHODS Aggregating three omics data of 328 melanoma samples, melanoma subtyping was performed by three clustering methods. Differences across subtypes were extracted by functional enrichment, epigenetically silencing, gene mutations and clinical features. Subtypes were further distinguished by putative biomarkers. RESULTS Functional enrichment of the subtype-specific differential expression genes endowed subtypes new designation: immune, melanin and ion, in which the first subtype was enriched for immune system, the second was characterized by melanin and pigmentation, and the third was enriched for ion-involved transmission process. Subtypes also differed in age, Breslow thickness, tumor site, mutation frequency of BRAF, PTGS2, CDKN2A, CDKN2B and incidence of epigenetically silencing for IL15RA, EPSTI1, LXN, CDKN1B genes. CONCLUSIONS Skin cutaneous melanoma can be robustly divided into three subtypes by SNFCC+. Compared with the TCGA classification derived from gene expression, the subtypes we presented share concordance, but new traits are excavated. Such a genomic classification offers insights to further personalize therapeutic decision-making and melanoma management.
Collapse
Affiliation(s)
- Xiaofan Lu
- Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, 210009, People's Republic of China
| | - Qianyuan Zhang
- Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, 210009, People's Republic of China
| | - Yue Wang
- Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, 210009, People's Republic of China
| | - Liya Zhang
- Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, 210009, People's Republic of China
| | - Huiling Zhao
- Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, 210009, People's Republic of China
| | - Chen Chen
- Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, 210009, People's Republic of China
| | - Yaoyan Wang
- Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, 210009, People's Republic of China
| | - Shengjie Liu
- Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, 210009, People's Republic of China
| | - Tao Lu
- State Key Laboratory of Natural Medicine, China Pharmaceutical University, Nanjing, 210009, People's Republic of China.
| | - Fei Wang
- Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, 210009, People's Republic of China.
| | - Fangrong Yan
- Research Center of Biostatistics and Computational Pharmacy, China Pharmaceutical University, Nanjing, 210009, People's Republic of China.
| |
Collapse
|
26
|
Simon-Lorière E, Duong V, Tawfik A, Ung S, Ly S, Casadémont I, Prot M, Courtejoie N, Bleakley K, Buchy P, Tarantola A, Dussart P, Cantaert T, Sakuntabhai A. Increased adaptive immune responses and proper feedback regulation protect against clinical dengue. Sci Transl Med 2018; 9:9/405/eaal5088. [PMID: 28855396 DOI: 10.1126/scitranslmed.aal5088] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 04/03/2017] [Accepted: 06/28/2017] [Indexed: 12/28/2022]
Abstract
Clinical symptoms of dengue virus (DENV) infection, the most prevalent arthropod-borne viral disease, range from classical mild dengue fever to severe, life-threatening dengue shock syndrome. However, most DENV infections cause few or no symptoms. Asymptomatic DENV-infected patients provide a unique opportunity to decipher the host immune responses leading to virus elimination without negative impact on an individual's health. We used an integrated approach of transcriptional profiling and immunological analysis to compare a Cambodian population of strictly asymptomatic viremic individuals with clinical dengue patients. Whereas inflammatory pathways and innate immune response pathways were similar between asymptomatic individuals and clinical dengue patients, expression of proteins related to antigen presentation and subsequent T cell and B cell activation pathways was differentially regulated, independent of viral load and previous DENV infection history. Feedback mechanisms controlled the immune response in asymptomatic viremic individuals, as demonstrated by increased activation of T cell apoptosis-related pathways and FcγRIIB (Fcγ receptor IIB) signaling associated with decreased anti-DENV-specific antibody concentrations. Together, our data illustrate that symptom-free DENV infection in children is associated with increased activation of the adaptive immune compartment and proper control mechanisms, leading to elimination of viral infection without excessive immune activation, with implications for novel vaccine development strategies.
Collapse
Affiliation(s)
- Etienne Simon-Lorière
- Functional Genetics of Infectious Diseases Unit, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France.,CNRS, Unité de Recherche Associée 3012, 75015 Paris, France
| | - Veasna Duong
- Virology Unit, Institut Pasteur du Cambodge, International Network of Pasteur Institutes, 12201 Phnom Penh, Cambodia
| | - Ahmed Tawfik
- Functional Genetics of Infectious Diseases Unit, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France.,CNRS, Unité de Recherche Associée 3012, 75015 Paris, France
| | - Sivlin Ung
- Immunology Group, Institut Pasteur du Cambodge, International Network of Pasteur Institutes, 12201 Phnom Penh, Cambodia
| | - Sowath Ly
- Epidemiology and Public Health Unit, Institut Pasteur du Cambodge, International Network of Pasteur Institutes, 12201 Phnom Penh, Cambodia
| | - Isabelle Casadémont
- Functional Genetics of Infectious Diseases Unit, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France.,CNRS, Unité de Recherche Associée 3012, 75015 Paris, France
| | - Matthieu Prot
- Functional Genetics of Infectious Diseases Unit, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France.,CNRS, Unité de Recherche Associée 3012, 75015 Paris, France
| | - Noémie Courtejoie
- Functional Genetics of Infectious Diseases Unit, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France.,CNRS, Unité de Recherche Associée 3012, 75015 Paris, France
| | - Kevin Bleakley
- INRIA Saclay, 91120 Palaiseau, France.,Département de Mathématiques d'Orsay, 91400 Orsay, France
| | - Philippe Buchy
- Virology Unit, Institut Pasteur du Cambodge, International Network of Pasteur Institutes, 12201 Phnom Penh, Cambodia.,GlaxoSmithKline (GSK) Vaccines, 637421 Singapore, Singapore
| | - Arnaud Tarantola
- Epidemiology and Public Health Unit, Institut Pasteur du Cambodge, International Network of Pasteur Institutes, 12201 Phnom Penh, Cambodia.,GlaxoSmithKline (GSK) Vaccines, 637421 Singapore, Singapore
| | - Philippe Dussart
- Virology Unit, Institut Pasteur du Cambodge, International Network of Pasteur Institutes, 12201 Phnom Penh, Cambodia
| | - Tineke Cantaert
- Immunology Group, Institut Pasteur du Cambodge, International Network of Pasteur Institutes, 12201 Phnom Penh, Cambodia.
| | - Anavaj Sakuntabhai
- Functional Genetics of Infectious Diseases Unit, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France. .,CNRS, Unité de Recherche Associée 3012, 75015 Paris, France
| |
Collapse
|
27
|
Cheng HD, Stöckmann H, Adamczyk B, McManus CA, Ercan A, Holm IA, Rudd PM, Ackerman ME, Nigrovic PA. High-throughput characterization of the functional impact of IgG Fc glycan aberrancy in juvenile idiopathic arthritis. Glycobiology 2017; 27:1099-1108. [PMID: 28973482 PMCID: PMC5881781 DOI: 10.1093/glycob/cwx082] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/30/2017] [Accepted: 09/09/2017] [Indexed: 12/19/2022] Open
Abstract
Juvenile idiopathic arthritis (JIA) encompasses all forms of chronic idiopathic arthritis that arise before age 16. Previous studies have found JIA to be associated with lower Fc galactosylation of circulating IgG, but the overall spectrum of glycan changes and the net impact on IgG function are unknown. Using ultra performance liquid chromatography (UPLC), we compared IgG glycosylation in 54 subjects with recent-onset untreated JIA with 98 healthy pediatric controls, paired to biophysical profiling of affinity for 20 IgG receptors using a high-throughput multiplexed microsphere assay. Patients with JIA exhibited an increase in hypogalactosylated and hyposialylated IgG glycans, but no change in fucosylation or bisection, together with alteration in the spectrum of IgG ligand binding. Supervised machine learning demonstrated a robust capacity to discriminate JIA subjects from controls using either glycosylation or binding data. The binding signature was driven predominantly by enhanced affinity for Fc receptor like protein 5 (FcRL5), a noncanonical Fc receptor expressed on B cells. Affinity for FcRL5 correlated inversely with galactosylation and sialylation, a relationship confirmed through enzymatic manipulation. These results demonstrate the capacity of combined structural and biophysical IgG phenotyping to define the overall functional impact of IgG glycan changes and implicate FcRL5 as a potential cellular sensor of IgG glycosylation.
Collapse
Affiliation(s)
- Hao D Cheng
- Molecular and Cellular Biology Program, Dartmouth College, Hanover, 03755 NH, USA
| | - Henning Stöckmann
- NIBRT-The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co. Dublin A94 X099, Ireland
| | - Barbara Adamczyk
- NIBRT-The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co. Dublin A94 X099, Ireland
| | - Ciara A McManus
- NIBRT-The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co. Dublin A94 X099, Ireland
| | - Altan Ercan
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Boston, MA, USA
| | - Ingrid A Holm
- Division of Endocrinology, Boston Children’s Hospital, Boston, MA, USA
| | - Pauline M Rudd
- NIBRT-The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co. Dublin A94 X099, Ireland
| | - Margaret E Ackerman
- Molecular and Cellular Biology Program, Dartmouth College, Hanover, 03755 NH, USA
- Thayer School of Engineering, Dartmouth College, Hanover, 03755 NH, USA
| | - Peter A Nigrovic
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Immunology, Boston Children’s Hospital, Boston, MA, USA
| |
Collapse
|
28
|
Lee CH, Romain G, Yan W, Watanabe M, Charab W, Todorova B, Lee J, Triplett K, Donkor M, Lungu OI, Lux A, Marshall N, Lindorfer MA, Goff ORL, Balbino B, Kang TH, Tanno H, Delidakis G, Alford C, Taylor RP, Nimmerjahn F, Varadarajan N, Bruhns P, Zhang YJ, Georgiou G. IgG Fc domains that bind C1q but not effector Fcγ receptors delineate the importance of complement-mediated effector functions. Nat Immunol 2017; 18:889-898. [PMID: 28604720 DOI: 10.1038/ni.3770] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 05/16/2017] [Indexed: 12/17/2022]
Abstract
Engineered crystallizable fragment (Fc) regions of antibody domains, which assume a unique and unprecedented asymmetric structure within the homodimeric Fc polypeptide, enable completely selective binding to the complement component C1q and activation of complement via the classical pathway without any concomitant engagement of the Fcγ receptor (FcγR). We used the engineered Fc domains to demonstrate in vitro and in mouse models that for therapeutic antibodies, complement-dependent cell-mediated cytotoxicity (CDCC) and complement-dependent cell-mediated phagocytosis (CDCP) by immunological effector molecules mediated the clearance of target cells with kinetics and efficacy comparable to those of the FcγR-dependent effector functions that are much better studied, while they circumvented certain adverse reactions associated with FcγR engagement. Collectively, our data highlight the importance of CDCC and CDCP in monoclonal-antibody function and provide an experimental approach for delineating the effect of complement-dependent effector-cell engagement in various therapeutic settings.
Collapse
Affiliation(s)
- Chang-Han Lee
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - Gabrielle Romain
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, USA
| | - Wupeng Yan
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Makiko Watanabe
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - Wissam Charab
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - Biliana Todorova
- Institut Pasteur, Department of Immunology, Unit of Antibodies in Therapy and Pathology, Paris, France.,INSERM, U760, Paris, France
| | - Jiwon Lee
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - Kendra Triplett
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA
| | - Moses Donkor
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - Oana I Lungu
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - Anja Lux
- Institute of Genetics, Department of Biology, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Nicholas Marshall
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - Margaret A Lindorfer
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Odile Richard-Le Goff
- Institut Pasteur, Department of Immunology, Unit of Antibodies in Therapy and Pathology, Paris, France.,INSERM, U760, Paris, France
| | - Bianca Balbino
- Institut Pasteur, Department of Immunology, Unit of Antibodies in Therapy and Pathology, Paris, France.,INSERM, U760, Paris, France.,Université Pierre et Marie Curie, Paris, France
| | - Tae Hyun Kang
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - Hidetaka Tanno
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - George Delidakis
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - Corrine Alford
- Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA
| | - Ronald P Taylor
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Falk Nimmerjahn
- Institute of Genetics, Department of Biology, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Navin Varadarajan
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas, USA
| | - Pierre Bruhns
- Institut Pasteur, Department of Immunology, Unit of Antibodies in Therapy and Pathology, Paris, France.,INSERM, U760, Paris, France
| | - Yan Jessie Zhang
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA.,Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, Texas, USA
| | - George Georgiou
- Department of Chemical Engineering, University of Texas at Austin, Austin, Texas, USA.,Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, USA.,Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA.,Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, Texas, USA.,Center for Systems and Synthetic Biology University of Texas at Austin, Austin, Texas, USA
| |
Collapse
|
29
|
Fontana MF, Baccarella A, Craft JF, Boyle MJ, McIntyre TI, Wood MD, Thorn KS, Anidi C, Bayat A, Chung MR, Hamburger R, Kim CY, Pearman E, Pham J, Tang JJ, Boon L, Kamya MR, Dorsey G, Feeney ME, Kim CC. A Novel Model of Asymptomatic Plasmodium Parasitemia That Recapitulates Elements of the Human Immune Response to Chronic Infection. PLoS One 2016; 11:e0162132. [PMID: 27583554 PMCID: PMC5008831 DOI: 10.1371/journal.pone.0162132] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 08/17/2016] [Indexed: 11/18/2022] Open
Abstract
In humans, immunity to Plasmodium sp. generally takes the form of protection from symptomatic malaria (i.e., 'clinical immunity') rather than infection ('sterilizing immunity'). In contrast, mice infected with Plasmodium develop sterilizing immunity, hindering progress in understanding the mechanistic basis of clinical immunity. Here we present a novel model in which mice persistently infected with P. chabaudi exhibit limited clinical symptoms despite sustaining patent parasite burdens for many months. Characterization of immune responses in persistently infected mice revealed development of CD4+ T cell exhaustion, increased production of IL-10, and expansion of B cells with an atypical surface phenotype. Additionally, persistently infected mice displayed a dramatic increase in circulating nonclassical monocytes, a phenomenon that we also observed in humans with both chronic Plasmodium exposure and asymptomatic infection. Following pharmacological clearance of infection, previously persistently infected mice could not control a secondary challenge, indicating that persistent infection disrupts the sterilizing immunity that typically develops in mouse models of acute infection. This study establishes an animal model of asymptomatic, persistent Plasmodium infection that recapitulates several central aspects of the immune response in chronically exposed humans. As such, it provides a novel tool for dissection of immune responses that may prevent development of sterilizing immunity and limit pathology during infection.
Collapse
Affiliation(s)
- Mary F. Fontana
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, 94143, United States of America
| | - Alyssa Baccarella
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, 94143, United States of America
| | - Joshua F. Craft
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, 94143, United States of America
| | - Michelle J. Boyle
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, 94143, United States of America
- The Burnet Institute, Center for Biomedical Research, Melbourne, Australia
| | - Tara I. McIntyre
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, 94143, United States of America
| | - Matthew D. Wood
- Department of Pathology, Division of Neuropathology, University of California San Francisco, San Francisco, California, 94143, United States of America
| | - Kurt S. Thorn
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, 94158, United States of America
| | - Chioma Anidi
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, 94143, United States of America
| | - Aqieda Bayat
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, 94143, United States of America
| | - Me Ree Chung
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, 94143, United States of America
| | - Rebecca Hamburger
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, 94143, United States of America
| | - Chris Y. Kim
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, 94143, United States of America
| | - Emily Pearman
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, 94143, United States of America
| | - Jennifer Pham
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, 94143, United States of America
| | - Jia J. Tang
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, 94143, United States of America
| | - Louis Boon
- EPIRUS Biopharmaceuticals, Utrecht, Netherlands BV
| | - Moses R. Kamya
- School of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Grant Dorsey
- Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, California, 94143, United States of America
| | - Margaret E. Feeney
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, 94143, United States of America
- Division of Pediatric Infectious Diseases and Global Health, Department of Pediatrics, University of California San Francisco, San Francisco, California, 94143, United States of America
| | - Charles C. Kim
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, 94143, United States of America
- * E-mail:
| |
Collapse
|
30
|
Getahun A, Cambier JC. Of ITIMs, ITAMs, and ITAMis: revisiting immunoglobulin Fc receptor signaling. Immunol Rev 2016; 268:66-73. [PMID: 26497513 DOI: 10.1111/imr.12336] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Receptors for immunoglobulin Fc regions play multiple critical roles in the immune system, mediating functions as diverse as phagocytosis, triggering degranulation of basophils and mast cells, promoting immunoglobulin class switching, and preventing excessive activation. Transmembrane signaling associated with these functions is mediated primarily by two amino acid sequence motifs, ITAMs (immunoreceptor tyrosine-based activation motifs) and ITIMs (immunoreceptor tyrosine-based inhibition motifs) that act as the receptors' interface with activating and inhibitory signaling pathways, respectively. While ITAMs mobilize activating tyrosine kinases and their consorts, ITIMs mobilize opposing tyrosine and inositol-lipid phosphatases. In this review, we will discuss our current understanding of signaling by these receptors/motifs and their sometimes blurred lines of function.
Collapse
Affiliation(s)
- Andrew Getahun
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - John C Cambier
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| |
Collapse
|
31
|
Abstract
Members of the family of Fc receptor-like (FcRL) proteins, homologous to FcγRI, have been identified by multiple research groups. Consequently, they have been described using multiple nomenclatures including Fc receptor homologs (FcRH), immunoglobulin superfamily receptor translocation-associated genes (IRTA), immunoglobulin-Fc-gp42-related genes (IFGP), Src homology 2 domain-containing phosphatase anchor proteins (SPAP), and B cell cross-linked by anti-immunoglobulin M-activating sequences (BXMAS). They are now referred to under a unified nomenclature as FCRL. Eight different human FCRL genes have been identified, all of which appear to be related to the genes of the immunoglobulin superfamily (IgSF) of cellular adhesion molecules. These type 1 transmembrane glycoproteins are composed of different combinations of 5 types of immunoglobulin-like domains, with each protein consisting of 3 to 9 domains, and no individual domain type conserved throughout all of the FCRL proteins. Ligands for the majority of the FCRLs remain unknown. In general, FCRL expression is restricted to lymphocytes and is primarily expressed in B-lymphocytes, supporting FCRL’s involvement in a variety of immune disorders. Most FCRLs functionally repress B-cell activation; however, they might have dual roles in lymphocyte functions as these proteins often possess immunoreceptor tyrosine activation (ITAM) and inhibitory (ITIM) motif elements. The biological functions of these newly recognized FCRL proteins are just beginning to emerge, and might provide the insight necessary for understanding pathophysiology of lymphocyte disorders and treating different immune diseases.
Collapse
Affiliation(s)
- Mollie Capone
- Department of Microbiology and Immunology, and Hollings Cancer Center, Medical University of South Carolina, 173 Ashley Avenue, BSB-201, Charleston, SC 29425, USA
| | - John Matthew Bryant
- Department of Microbiology and Immunology, and Hollings Cancer Center, Medical University of South Carolina, 173 Ashley Avenue, BSB-201, Charleston, SC 29425, USA
| | - Natalie Sutkowski
- Department of Microbiology and Immunology, and Hollings Cancer Center, Medical University of South Carolina, 173 Ashley Avenue, BSB-201, Charleston, SC 29425, USA
| | - Azizul Haque
- Department of Microbiology and Immunology, and Hollings Cancer Center, Medical University of South Carolina, 173 Ashley Avenue, BSB-201, Charleston, SC 29425, USA
| |
Collapse
|
32
|
Hempel RJ, Bannantine JP, Stabel JR. Transcriptional Profiling of Ileocecal Valve of Holstein Dairy Cows Infected with Mycobacterium avium subsp. Paratuberculosis. PLoS One 2016; 11:e0153932. [PMID: 27093613 PMCID: PMC4836751 DOI: 10.1371/journal.pone.0153932] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 04/06/2016] [Indexed: 12/22/2022] Open
Abstract
Johne’s disease is a chronic infection of the small intestine caused by Mycobacterium avium subspecies paratuberculosis (MAP), an intracellular bacterium. The events of pathogen survival within the host cell(s), chronic inflammation and the progression from asymptomatic subclinical stage to an advanced clinical stage of infection, are poorly understood. This study examines gene expression in the ileocecal valve (ICV) of Holstein dairy cows at different stages of MAP infection. The ICV is known to be a primary site of MAP colonization and provides an ideal location to identify genes that are relevant to the progression of this disease. RNA was prepared from ICV tissues and RNA-Seq was used to compare gene transcription between clinical, subclinical, and uninfected control animals. Interpretation of the gene expression data was performed using pathway analysis and gene ontology categories containing multiple differentially expressed genes. Results demonstrated that many of the pathways that had strong differential gene expression between uninfected control and clinical cows were related to the immune system, such as the T- and B-cell receptor signaling, apoptosis, NOD-like receptor signaling, and leukocyte transendothelial migration pathways. In contrast, the comparison of gene transcription between control and subclinical cows identified pathways that were primarily involved in metabolism. The results from the comparison between clinical and subclinical animals indicate recruitment of neutrophils, up regulation of lysosomal peptidases, increase in immune cell transendothelial migration, and modifications of the extracelluar matrix. This study provides important insight into how cattle respond to a natural MAP infection at the gene transcription level within a key target tissue for infection.
Collapse
Affiliation(s)
- Randy J. Hempel
- USDA-Agricultural Research Service (ARS), National Animal Disease Center, Ames, Iowa, United States of America
| | - John P. Bannantine
- USDA-Agricultural Research Service (ARS), National Animal Disease Center, Ames, Iowa, United States of America
| | - Judith R. Stabel
- USDA-Agricultural Research Service (ARS), National Animal Disease Center, Ames, Iowa, United States of America
- * E-mail:
| |
Collapse
|
33
|
Taylor EB, Moulana M, Stuge TB, Quiniou SMA, Bengten E, Wilson M. A Leukocyte Immune-Type Receptor Subset Is a Marker of Antiviral Cytotoxic Cells in Channel Catfish, Ictalurus punctatus. THE JOURNAL OF IMMUNOLOGY 2016; 196:2677-89. [PMID: 26856701 DOI: 10.4049/jimmunol.1502166] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 01/03/2016] [Indexed: 11/19/2022]
Abstract
Channel catfish, Ictalurus punctatus, leukocyte immune type receptors (LITRs) represent a multigene family that encodes Ig superfamily proteins that mediate activating or inhibitory signaling. In this study, we demonstrate the use of mAb CC41 to monitor viral cytotoxic responses in catfish and determine that CC41 binds to a subset of LITRs on the surface of catfish clonal CTLs. Homozygous gynogenetic catfish were immunized with channel catfish virus (CCV)-infected MHC-matched clonal T cells (G14D-CCV), and PBL were collected at various times after immunization for flow cytometric analyses. The percentage of CC41(+) cells was significantly increased 5 d after primary immunization with G14D-CCV and at 3 d after a booster immunization as compared with control fish only injected with G14D. Moreover, CC41(+) cells magnetically isolated from the PBL specifically killed CCV-infected targets as measured by (51)Cr release assays and expressed messages for CD3γδ, perforin, and at least one of the CD4-like receptors as analyzed by RNA flow cytometry. When MLC effector cells derived from a G14D-CCV-immunized fish were preincubated with CC41 mAb, killing of G14D-CCV targets was reduced by ∼40%, suggesting that at least some LITRs have a role in target cell recognition and/or cytotoxicity. The availability of a LITR-specific mAb has allowed, to our knowledge for the first time, functional characterization of LITRs in an autologous system. In addition, the identification of an LITR subset as a cytotoxic cell marker will allow for more effective monitoring of catfish immune responses to pathogens.
Collapse
Affiliation(s)
- Erin B Taylor
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS 39216
| | - Mohadetheh Moulana
- Warmwater Aquaculture Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Stoneville, MS 38776; and
| | - Tor B Stuge
- Immunology Research Group, Department of Medical Biology, Faculty of Health Sciences, University of Tromso-Arctic University of Norway, N-9037 Tromso, Norway
| | - Sylvie M A Quiniou
- Warmwater Aquaculture Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Stoneville, MS 38776; and
| | - Eva Bengten
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS 39216
| | - Melanie Wilson
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS 39216;
| |
Collapse
|
34
|
Abstract
Coelomic cavity–derived B-1 and splenic marginal zone (MZ) B lymphocytes play principal roles in frontline host protection at homeostasis and during primary humoral immune responses. Although they share many features that enable rapid and broad-based defense against pathogens, these innate-like subsets have disparate B cell receptor (BCR) signaling features. Members of the Fc receptor–like (FCRL) family are preferentially expressed by B cells and possess tyrosine-based immunoregulatory function. An unusual characteristic of many of these cell surface proteins is the presence of both inhibitory (ITIM) and activating (ITAM-like) motifs in their cytoplasmic tails. In mice, FCRL5 is a discrete marker of splenic MZ and peritoneal B-1 B cells and has both ITIM and ITAM-like sequences. Recent work explored its signaling properties and identified that FCRL5 differentially influences innate-like BCR function. Closer scrutiny of these differences disclosed the ability of FCRL5 to counter-regulate BCR activation by recruiting SHP-1 and Lyn to its cytoplasmic motifs. Furthermore, the disparity in FCRL5 regulation between MZ and B-1 B cells correlated with relative intracellular concentrations of SHP-1. These findings validate and extend our understanding of the unique signaling features in innate-like B cells and provide new insight into the complexity of FCRL modulation.
Collapse
Affiliation(s)
- Randall S Davis
- Departments of Medicine, Microbiology, and Biochemistry and Molecular Genetics, and the Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama
| |
Collapse
|
35
|
Portugal S, Tipton CM, Sohn H, Kone Y, Wang J, Li S, Skinner J, Virtaneva K, Sturdevant DE, Porcella SF, Doumbo OK, Doumbo S, Kayentao K, Ongoiba A, Traore B, Sanz I, Pierce SK, Crompton PD. Malaria-associated atypical memory B cells exhibit markedly reduced B cell receptor signaling and effector function. eLife 2015; 4. [PMID: 25955968 PMCID: PMC4444601 DOI: 10.7554/elife.07218] [Citation(s) in RCA: 211] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 05/06/2015] [Indexed: 01/06/2023] Open
Abstract
Protective antibodies in Plasmodium falciparum malaria are only acquired after years of repeated infections. Chronic malaria exposure is associated with a large increase in atypical memory B cells (MBCs) that resemble B cells expanded in a variety of persistent viral infections. Understanding the function of atypical MBCs and their relationship to classical MBCs will be critical to developing effective vaccines for malaria and other chronic infections. We show that VH gene repertoires and somatic hypermutation rates of atypical and classical MBCs are indistinguishable indicating a common developmental history. Atypical MBCs express an array of inhibitory receptors and B cell receptor (BCR) signaling is stunted in atypical MBCs resulting in impaired B cell responses including proliferation, cytokine production and antibody secretion. Thus, in response to chronic malaria exposure, atypical MBCs appear to differentiate from classical MBCs becoming refractory to BCR-mediated activation and potentially interfering with the acquisition of malaria immunity. DOI:http://dx.doi.org/10.7554/eLife.07218.001 The human immune system works to protect individuals from harmful microbes, such as the parasites that cause malaria. One line of defense is to produce a large array of proteins called antibodies that specifically bind to microbes to mark them for destruction by the immune system. The immune system also produces long-lived memory B cells that are able to mount a quicker and more effective antibody response if the microbe enters the body again. This means that most people only become ill with a particular disease the first time they encounter the microbe that causes it. However, malaria is unusual in that it can take many years of exposure to the parasite that causes it before an individual produces enough antibodies and memory B cells to be protected from the disease. There is also no vaccine that provides effective and long-lasting protection against malaria. Vaccinations rely on stimulating the body's natural defenses, and so understanding more about antibodies and memory B cells in relation to malaria may aid future efforts to develop a vaccine. Researchers have discovered that many of the memory B cells that accumulate in people who have been exposed to the malaria parasite over long-periods of time are different from the normal memory B cells. But it was not clear what role these ‘atypical’ cells play in immunity to malaria. To address this question, Portugal et al. studied the genetics and activity of B cells collected from children and adults living in Mali who—by living in a region where malaria is common—had been repeatedly exposed to the parasite. The experiments indicate that atypical and normal memory B cells both develop from the same precursor cells. However, the genes that are active in each cell type are different, resulting in the atypical cells being less able to respond to the parasite than the normal memory B cells. Portugal et al.'s findings suggest that the atypical cells develop from normal memory B cells during long-term exposure to malaria, which may delay the development of immunity to this disease. Future challenges include understanding what drives the formation of the atypical memory B cells in malaria, and finding out why they are less active than the normal cells. This could aid the development of vaccines and/or therapies that restore their activity in patients. DOI:http://dx.doi.org/10.7554/eLife.07218.002
Collapse
Affiliation(s)
- Silvia Portugal
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, United States
| | - Christopher M Tipton
- Departments of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, United States
| | - Haewon Sohn
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, United States
| | - Younoussou Kone
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Jing Wang
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, United States
| | - Shanping Li
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, United States
| | - Jeff Skinner
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, United States
| | - Kimmo Virtaneva
- Rocky Mountain Laboratory Research Technologies Section, Genomics Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, United States
| | - Daniel E Sturdevant
- Rocky Mountain Laboratory Research Technologies Section, Genomics Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, United States
| | - Stephen F Porcella
- Rocky Mountain Laboratory Research Technologies Section, Genomics Unit, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, United States
| | - Ogobara K Doumbo
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Safiatou Doumbo
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Kassoum Kayentao
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Aissata Ongoiba
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Boubacar Traore
- Malaria Research and Training Centre, Department of Epidemiology of Parasitic Diseases, International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, Bamako, Mali
| | - Inaki Sanz
- Departments of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, United States
| | - Susan K Pierce
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, United States
| | - Peter D Crompton
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, United States
| |
Collapse
|