1
|
Shen Y, Voigt A, Leng X, Rodriguez AA, Nguyen CQ. A current and future perspective on T cell receptor repertoire profiling. Front Genet 2023; 14:1159109. [PMID: 37408774 PMCID: PMC10319011 DOI: 10.3389/fgene.2023.1159109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 06/12/2023] [Indexed: 07/07/2023] Open
Abstract
T cell receptors (TCR) play a vital role in the immune system's ability to recognize and respond to foreign antigens, relying on the highly polymorphic rearrangement of TCR genes. The recognition of autologous peptides by adaptive immunity may lead to the development and progression of autoimmune diseases. Understanding the specific TCR involved in this process can provide insights into the autoimmune process. RNA-seq (RNA sequencing) is a valuable tool for studying TCR repertoires by providing a comprehensive and quantitative analysis of the RNA transcripts. With the development of RNA technology, transcriptomic data must provide valuable information to model and predict TCR and antigen interaction and, more importantly, identify or predict neoantigens. This review provides an overview of the application and development of bulk RNA-seq and single-cell (SC) RNA-seq to examine the TCR repertoires. Furthermore, discussed here are bioinformatic tools that can be applied to study the structural biology of peptide/TCR/MHC (major histocompatibility complex) and predict antigenic epitopes using advanced artificial intelligence tools.
Collapse
Affiliation(s)
- Yiran Shen
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Alexandria Voigt
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Xuebing Leng
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL, United States
| | - Amy A. Rodriguez
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
| | - Cuong Q. Nguyen
- Department of Infectious Diseases and Immunology, College of Veterinary Medicine, University of Florida, Gainesville, FL, United States
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, United States
- Center of Orphaned Autoimmune Diseases, University of Florida, Gainesville, FL, United States
| |
Collapse
|
2
|
Akgul A, Maddaloni M, Jun SM, Nelson AS, Odreman VA, Hoffman C, Bhagyaraj E, Voigt A, Abbott JR, Nguyen CQ, Pascual DW. Stimulation of regulatory T cells with Lactococcus lactis expressing enterotoxigenic E. coli colonization factor antigen 1 retains salivary flow in a genetic model of Sjögren's syndrome. Arthritis Res Ther 2021; 23:99. [PMID: 33823920 PMCID: PMC8022426 DOI: 10.1186/s13075-021-02475-1] [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: 09/16/2020] [Accepted: 03/09/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Sjögren's syndrome (SjS), one of the most common autoimmune diseases, impacts millions of people annually. SjS results from autoimmune attack on exocrine (salivary and lacrimal) glands, and women are nine times more likely to be affected than men. To date, no vaccine or therapeutic exists to treat SjS, and patients must rely on lifelong therapies to alleviate symptoms. METHODS Oral treatment with the adhesin from enterotoxigenic Escherichia coli colonization factor antigen I (CFA/I) fimbriae protects against several autoimmune diseases in an antigen (Ag)-independent manner. Lactococcus lactis, which was recently adapted to express CFA/I fimbriae (LL-CFA/I), effectively suppresses inflammation by the induction of infectious tolerance via Ag-specific regulatory T cells (Tregs), that produce IL-10 and TGF-β. To test the hypothesis that CFA/I fimbriae can offset the development of inflammatory T cells via Treg induction, oral treatments with LL-CFA/I were performed on the spontaneous, genetically defined model for SjS, C57BL/6.NOD-Aec1Aec2 mice to maintain salivary flow. RESULTS Six-week (wk)-old C57BL/6.NOD-Aec1Aec2 mice were orally dosed with LL-CFA/I and treated every 3 wks; control groups were given L. lactis vector or PBS. LL-CFA/I-treated mice retained salivary flow up to 28 wks of age and showed significantly reduced incidence of inflammatory infiltration into the submandibular and lacrimal glands relative to PBS-treated mice. A significant increase in Foxp3+ and IL-10- and TGF-β-producing Tregs was observed. Moreover, LL-CFA/I significantly reduced the expression of proinflammatory cytokines, IL-6, IL-17, GM-CSF, and IFN-γ. Adoptive transfer of CD4+ T cells from LL-CFA/I-treated, not LL vector-treated mice, restored salivary flow in diseased SjS mice. CONCLUSION These data demonstrate that oral LL-CFA/I reduce or halts SjS progression, and these studies will provide the basis for future testing in SjS patients.
Collapse
Affiliation(s)
- Ali Akgul
- Department of Infectious Diseases & Immunology, College of Veterinary Medicine, University of Florida, P.O. Box 110880, Gainesville, FL, 32611, United States
| | - Massimo Maddaloni
- Department of Infectious Diseases & Immunology, College of Veterinary Medicine, University of Florida, P.O. Box 110880, Gainesville, FL, 32611, United States
| | - Sang Mu Jun
- Department of Infectious Diseases & Immunology, College of Veterinary Medicine, University of Florida, P.O. Box 110880, Gainesville, FL, 32611, United States
| | - Andrew S Nelson
- Department of Infectious Diseases & Immunology, College of Veterinary Medicine, University of Florida, P.O. Box 110880, Gainesville, FL, 32611, United States
| | - Vanessa Aguilera Odreman
- Department of Infectious Diseases & Immunology, College of Veterinary Medicine, University of Florida, P.O. Box 110880, Gainesville, FL, 32611, United States
| | - Carol Hoffman
- Department of Infectious Diseases & Immunology, College of Veterinary Medicine, University of Florida, P.O. Box 110880, Gainesville, FL, 32611, United States
| | - Ella Bhagyaraj
- Department of Infectious Diseases & Immunology, College of Veterinary Medicine, University of Florida, P.O. Box 110880, Gainesville, FL, 32611, United States
| | - Alexandria Voigt
- Department of Infectious Diseases & Immunology, College of Veterinary Medicine, University of Florida, P.O. Box 110880, Gainesville, FL, 32611, United States
| | - Jeffrey R Abbott
- Department of Veterinary Microbiology & Pathology, Washington State University, P.O. Box 647040, Pullman, WA, 99164, United States
| | - Cuong Q Nguyen
- Department of Infectious Diseases & Immunology, College of Veterinary Medicine, University of Florida, P.O. Box 110880, Gainesville, FL, 32611, United States
| | - David W Pascual
- Department of Infectious Diseases & Immunology, College of Veterinary Medicine, University of Florida, P.O. Box 110880, Gainesville, FL, 32611, United States.
| |
Collapse
|
3
|
Peck AB, Nguyen CQ. What can Sjögren's syndrome-like disease in mice contribute to human Sjögren's syndrome? Clin Immunol 2017; 182:14-23. [PMID: 28478104 DOI: 10.1016/j.clim.2017.05.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 05/01/2017] [Accepted: 05/01/2017] [Indexed: 12/12/2022]
Abstract
For decades, Sjögren's syndrome (SS) and Sjögren's syndrome-like (SS-like) disease in patients and mouse models, respectively, have been intensely investigated in attempts to identify the underlying etiologies, the pathophysiological changes defining disease phenotypes, the nature of the autoimmune responses, and the propensity for developing B cell lymphomas. An emerging question is whether the generation of a multitude of mouse models and the data obtained from their studies is actually important to the understanding of the human disease and potential interventional therapies. In this brief report, we comment on how and why mouse models can stimulate interest in specific lines of research that apparently parallel aspects of human SS. Focusing on two mouse models, NOD and B6·Il14α, we present the possible relevance of mouse models to human SS, highlighting a few selected disease-associated biological processes that have baffled both SS and SS-like investigations for decades.
Collapse
Affiliation(s)
- Ammon B Peck
- Department of Pathology and Infectious Diseases, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA; Center for Orphan Autoimmune Disorders, College of Dentistry, University of Florida, Gainesville, FL 32608, USA.
| | - Cuong Q Nguyen
- Department of Pathology and Infectious Diseases, College of Veterinary Medicine, University of Florida, Gainesville, FL 32608, USA; Center for Orphan Autoimmune Disorders, College of Dentistry, University of Florida, Gainesville, FL 32608, USA; Department of Oral Biology, College of Dentistry, University of Florida, FL 32608, USA
| |
Collapse
|