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Pinilla C, Giulianotti MA, Santos RG, Houghten RA. Identification of B Cell and T Cell Epitopes Using Synthetic Peptide Combinatorial Libraries. Curr Protoc 2022; 2:e378. [PMID: 35263045 DOI: 10.1002/cpz1.378] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This article presents a combinatorial library method that consists of the synthesis and screening of mixture-based synthetic combinatorial libraries of peptide molecules to identify B and T cell epitopes. The protocols employ peptide libraries to identify peptides recognized by MAbs and T cells. The first protocol uses a positional scanning peptide library made up of hexapeptides to identify antigenic determinants recognized by MAbs. The 120 mixtures in the hexapeptide library are tested for their inhibitory activity in a competitive ELISA. The second protocol uses a decapeptide library to identify T cell peptide ligands. The 200 mixtures of the decapeptide library are tested for their ability to induce T cell activation. Support protocols cover optimization of the assay conditions for each MAb or T cell, to achieve the best level of sensitivity and reproducibility, and preparation of a hexapeptide library, along with deconvolution approaches. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Screening peptide library for antibody inhibition Basic Protocol 2: Screening a peptide library to identify CD4+ Or CD8+ T cell ligands Support Protocol 1: Optimizing antigen and antibody concentrations for screening assay Support Protocol 2: Preparing a positional scanning peptide library.
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Affiliation(s)
- Clemencia Pinilla
- Center for Translational Science, Florida International University, Port St. Lucie, Florida
| | - Marc A Giulianotti
- Center for Translational Science, Florida International University, Port St. Lucie, Florida
| | | | - Richard A Houghten
- Center for Translational Science, Florida International University, Port St. Lucie, Florida
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Tian G, Li M, Lv G. Analysis of T-Cell Receptor Repertoire in Transplantation: Fingerprint of T Cell-mediated Alloresponse. Front Immunol 2022; 12:778559. [PMID: 35095851 PMCID: PMC8790170 DOI: 10.3389/fimmu.2021.778559] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/22/2021] [Indexed: 11/13/2022] Open
Abstract
T cells play a key role in determining allograft function by mediating allogeneic immune responses to cause rejection, and recent work pointed their role in mediating tolerance in transplantation. The unique T-cell receptor (TCR) expressed on the surface of each T cell determines the antigen specificity of the cell and can be the specific fingerprint for identifying and monitoring. Next-generation sequencing (NGS) techniques provide powerful tools for deep and high-throughput TCR profiling, and facilitate to depict the entire T cell repertoire profile and trace antigen-specific T cells in circulation and local tissues. Tailing T cell transcriptomes and TCR sequences at the single cell level provides a full landscape of alloreactive T-cell clones development and biofunction in alloresponse. Here, we review the recent advances in TCR sequencing techniques and computational tools, as well as the recent discovery in overall TCR profile and antigen-specific T cells tracking in transplantation. We further discuss the challenges and potential of using TCR sequencing-based assays to profile alloreactive TCR repertoire as the fingerprint for immune monitoring and prediction of rejection and tolerance.
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Affiliation(s)
| | - Mingqian Li
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, China
| | - Guoyue Lv
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin University, Changchun, China
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Pinilla C, Appel JR, Judkowski V, Houghten RA. Identification of B cell and T cell epitopes using synthetic peptide combinatorial libraries. CURRENT PROTOCOLS IN IMMUNOLOGY 2012; Chapter 9:9.5.1-9.5.16. [PMID: 23129156 PMCID: PMC3511046 DOI: 10.1002/0471142735.im0905s99] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
This unit presents a combinatorial library method that consists of the synthesis and screening of mixture-based synthetic combinatorial libraries of peptide molecules. The protocols employ peptide libraries to identify peptides recognized by MAbs and T cells. The first protocol uses a positional scanning peptide library made up of hexapeptides to identify antigenic determinants recognized by MAbs. The 120 mixtures in the hexapeptide library are tested for their inhibitory activity in a competitive ELISA. The second protocol uses a decapeptide library to identify T cell peptide ligands. The 200 mixtures of the decapeptide library are tested for their ability to induce T cell activation. Support protocols cover optimization of the assay conditions for each MAb or T cell, to achieve the best level of sensitivity and reproducibility, and preparation of a hexapeptide library, along with deconvolution approaches.
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Affiliation(s)
| | - Jon R Appel
- Torrey Pines Institute for Molecular Studies, San Diego, California
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Judkowski V, Bunying A, Ge F, Appel JR, Law K, Sharma A, Raja- Gabaglia C, Norori P, Santos RG, Giulianotti MA, Slifka MK, Douek DC, Graham BS, Pinilla C. GM-CSF production allows the identification of immunoprevalent antigens recognized by human CD4+ T cells following smallpox vaccination. PLoS One 2011; 6:e24091. [PMID: 21931646 PMCID: PMC3170313 DOI: 10.1371/journal.pone.0024091] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Accepted: 07/29/2011] [Indexed: 12/25/2022] Open
Abstract
The threat of bioterrorism with smallpox and the broad use of vaccinia vectors for other vaccines have led to the resurgence in the study of vaccinia immunological memory. The importance of the role of CD4+ T cells in the control of vaccinia infection is well known. However, more CD8+ than CD4+ T cell epitopes recognized by human subjects immunized with vaccinia virus have been reported. This could be, in part, due to the fact that most of the studies that have identified human CD4+ specific protein-derived fragments or peptides have used IFN-γ production to evaluate vaccinia specific T cell responses. Based on these findings, we reasoned that analyzing a large panel of cytokines would permit us to generate a more complete analysis of the CD4 T cell responses. The results presented provide clear evidence that TNF-α is an excellent readout of vaccinia specificity and that other cytokines such as GM-CSF can be used to evaluate the reactivity of CD4+ T cells in response to vaccinia antigens. Furthermore, using these cytokines as readout of vaccinia specificity, we present the identification of novel peptides from immunoprevalent vaccinia proteins recognized by CD4+ T cells derived from smallpox vaccinated human subjects. In conclusion, we describe a “T cell–driven” methodology that can be implemented to determine the specificity of the T cell response upon vaccination or infection. Together, the single pathogen in vitro stimulation, the selection of CD4+ T cells specific to the pathogen by limiting dilution, the evaluation of pathogen specificity by detecting multiple cytokines, and the screening of the clones with synthetic combinatorial libraries, constitutes a novel and valuable approach for the elucidation of human CD4+ T cell specificity in response to large pathogens.
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Affiliation(s)
- Valeria Judkowski
- Torrey Pines Institute for Molecular Studies, San Diego, California, United States of America
| | - Alcinette Bunying
- Torrey Pines Institute for Molecular Studies, San Diego, California, United States of America
| | - Feng Ge
- Torrey Pines Institute for Molecular Studies, San Diego, California, United States of America
| | - Jon R. Appel
- Torrey Pines Institute for Molecular Studies, San Diego, California, United States of America
| | - Kingyee Law
- Torrey Pines Institute for Molecular Studies, San Diego, California, United States of America
| | - Atima Sharma
- Torrey Pines Institute for Molecular Studies, San Diego, California, United States of America
| | - Claudia Raja- Gabaglia
- Torrey Pines Institute for Molecular Studies, San Diego, California, United States of America
| | - Patricia Norori
- Torrey Pines Institute for Molecular Studies, San Diego, California, United States of America
| | - Radleigh G. Santos
- Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida, United States of America
| | - Marc A. Giulianotti
- Torrey Pines Institute for Molecular Studies, Port St. Lucie, Florida, United States of America
| | - Mark K. Slifka
- Vaccine and Gene Therapy Institute, Oregon Health and Science University, Beaverton, Oregon, United States of America
| | - Daniel C. Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Barney S. Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Clemencia Pinilla
- Torrey Pines Institute for Molecular Studies, San Diego, California, United States of America
- * E-mail:
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Abdul-Alim CS, Li Y, Yee C. Conditional superagonist CTL ligands for the promotion of tumor-specific CTL responses. THE JOURNAL OF IMMUNOLOGY 2010; 184:6514-21. [PMID: 20483791 DOI: 10.4049/jimmunol.0900448] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Although it has been demonstrated that CTLs can be raised against tumor-associated self-antigens, achieving consistent and effective clinical responses has proven challenging. Superagonist altered peptide ligands (APLs) can often elicit potent antitumor CTL responses where the native tumor-associated epitope fails. Current methods have identified a limited number of superagonist APLs, including the prototypic 27L mutant of MART-1. However, more comprehensive screening strategies would be desirable. In this study, we use a novel genetic screen, involving recombinant technology and class I Ag cross-presentation, to search for supraoptimal superagonists of the 27L MART-1 mutant by surveying the effectiveness of virtually every single amino acid substitution mutant of 27L to activate human Ag-specific CTL clones recognizing the wild-type MART-1(26-35) epitope. We identify three novel mutant epitopes with superagonist properties that are functionally superior to 27L; however, the ability of a given analogue to act as superagonist varies among patients and suggests that a given superagonist APL may be ideally suited to different patients. These findings endorse the use of comprehensive methods to establish panels of potential superagonist APLs to individualize tumor peptide vaccines among patients.
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Affiliation(s)
- C Siddiq Abdul-Alim
- Program in Immunology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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Houghten RA, Pinilla C, Giulianotti MA, Appel JR, Dooley CT, Nefzi A, Ostresh JM, Yu Y, Maggiora GM, Medina-Franco JL, Brunner D, Schneider J. Strategies for the use of mixture-based synthetic combinatorial libraries: scaffold ranking, direct testing in vivo, and enhanced deconvolution by computational methods. ACTA ACUST UNITED AC 2007; 10:3-19. [PMID: 18067268 DOI: 10.1021/cc7001205] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Richard A Houghten
- Torrey Pines Institute for Molecular Studies, 3550 General Atomics Court, San Diego, California 92121, USA.
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