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Method Article
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Qa-1 (HLA-E in human) belongs to a group of non-classical major histocompatibility complex 1b molecules. Immunization with Qa-1-binding epitopes has been shown to augment tissue-specific immune regulation and ameliorate several autoimmune diseases. Herein we describe an overlapping peptide library strategy for the identification of Qa-1 epitopes in a protein.
Qa-1 (HLA-E in human) belongs to a group of non-classical major histocompatibility complex 1b (MHC-Ib) molecules. Recent data suggest that Qa-1 molecules play important roles in surveying cells for structural and functional integrity, inducing immune regulation, and limiting immune responses to viral infections. Additionally, functional augmentation of Qa-1-restricted CD8+ T cells through epitope immunization has shown therapeutic effects in several autoimmune disease animal models, e.g. experimental allergic encephalomyelitis, collagen-induced arthritis, and non-obese diabetes. Therefore, there is an urgent need for a method that can efficiently and quickly identify functional Qa-1 epitopes in a protein. Here, we describe a protocol that utilizes Qa-1-restricted CD8+ T cell lines specific for an overlapping peptide (OLP) library for determining Qa-1 epitopes in a protein. This OLP library contains 15-mer overlapping peptides that cover the whole length of a protein, and adjacent peptides overlap by 11 amino acids. Using this protocol, we recently identified a 9-mer Qa-1 epitope in myelin oligodendrocyte glycoprotein (MOG). This newly mapped MOG Qa-1 epitope was shown to induce epitope-specific, Qa-1-restricted CD8+ T cells that enhanced myelin-specific immune regulation. Therefore, this protocol is useful for future investigation of novel targets and functions of Qa-1-restricted CD8+ T cells.
Qa-1 belongs to a group of non-classical major histocompatibility complex 1b (MHC-Ib) molecules in mice. Its human homolog is HLA-E. Previous evidence has demonstrated that Qa-1 molecules have important biological functions. Firstly, Qa-1 molecules play an important role in surveying cells for structural and functional integrity. In this regard, Qa-1 molecules have evolved several strategies to monitor the normal function of a cell. One such strategy enables Qa-1 molecules to form complexes with a processed leader peptide (epitope), i.e. the Qa-1 determinant modifier (Qdm) that is processed from classical MHC-Ia molecules in the endoplasmic reticulum1. These Qa-1/Qdm complexes later display on the surface of a cell and bind to inhibitory NKG2A receptors on NK cells to inhibit NK killing activity2. If the expression of MHC-Ia molecules is lost, a cell (e.g. a malignant cell) becomes sensitive to NK killing2. The other strategy enables Qa-1 molecules to form new Qa-1/epitope complexes on the surface of a cell that is deficient in TAP (transporter associated with antigen processing)3 and/or ERAAP (endoplasmic reticulum aminopeptidase associated with antigen processing)4 (both deficiencies often occur in malignant cells). The cell that expresses these new Qa-1/epitope complexes can then be recognized and eliminated by the epitope-specific Qa-1-restricted CD8+ T cells. Secondly, Qa-1 molecules induce immune regulation5. In this regard, Qa-1/epitope complexes have been shown to stimulate CD8+ regulatory T (Treg) cells that are important for the prevention of immune-mediated damage of self-tissues6,7,8,9,10. Thirdly, Qa-1-restricted CD8+ Treg cells have been shown to limit immune responses against viral infection11.
Therefore, specific augmentation of epitope-specific Qa-1-restrictred CD8+ T cells is a potentially promising strategy for the elimination of abnormal cells, for the enhancement of immune regulation, and for the control of the magnitude of virus-induced immune responses. While it has not been determined whether augmentation of epitope-specific Qa-1-restricted CD8+ T cells can enhance immune surveillance and limit virus-induced immune responses, our laboratories and others have clearly demonstrated that immunization with Qa-1 epitopes can augment the function of Qa-1-restricted CD8+ Treg cells specific for pathogenic autoimmune CD4+ T cells, leading to efficient control of CD4+ T cell-mediated autoimmune diseases in a variety of animal models such as experimental allergic encephalomyelitis (an animal model of human multiple sclerosis)6,10, collagen-induced arthritis (an animal model of human rheumatoid arthritis)7, and non-obese diabetes (an animal model of human type 1 diabetes)8. Additionally, we have discovered that immunization with a tissue-specific Qa-1 epitope leads to specific control of immune-mediated inflammation in that tissue through augmentation of CD8+ Treg cells12. The above successes of preclinical studies indicate a need for a full evaluation of Qa-1 epitope immunization for the treatment of tissue-specific immune-mediated diseases and potentially for the therapy of other diseases associated with deficiencies in TAP and ERAAP.
Accordingly, there is a demand for a technology that can reliably and quickly analyze Qa-1 epitopes in a protein. In this regard, a limited number of biologically important Qa-1 epitopes has been described. Most of these Qa-1 epitopes were identified serendipitously during the study of CD8+ T cell responses to bacteria13, cells deficient in TAP3, cells deficient in ERAAP4, and cells that cause EAE6,9. Therefore, a high throughput technique is desirable for the identification of biologically important Qa-1 epitopes in a defined protein. In the following, we describe an overlapping peptide (OLP) library strategy that maps functional Qa-1 epitopes in a protein using Qa-1-resrticted CD8+ T cell lines specific for the OLP pool (OLP_pool) of a protein.
All experiments were done in compliance with an Institutional Animal Care and Use Protocol approved by Animal Care and Use Committee at the University of Texas at El Paso and Loma Linda University.
1. Generation of an OLP Library Covering the Whole Length of a Protein
2. Priming of Kb-/- Db-/- CD8+ T Cells with the OLP_pool-pulsed Kb-/- Db-/- Dendritic cells (DCs).
NOTE: There are two major Qa-1 alleles: one is Qa-1a, and the other is Qa-1b. Since the animals commonly used for academic research, e.g. C57BL/6 and Balb/c mice, carry Qa-1b, this protocol describes the procedure for mapping Qa-1b epitopes in a protein. CD8+ T cells used in this protocol are purified from Kb-/-Db-/- mice (C57BL/6 background) in which CD8+ T cells are restricted mostly by non-classical MHC-Ib molecules including Qa-1.
3. Restimulation of the Primed CD8+ T Cells with Macrophages Pulsed with the OLP_pool
4. Determination of OLP_pool-specific, Qa-1-restricted Response in an OLP_pool-restimulated CD8+ T Cell Line
NOTE: OLP_pool-specific, Qa-1-restricted response in an OLP_pool-restimulated CD8+ T cell line is determined by IFNγ secretion following stimulation by the OLP_pool in the presence of C1R or C1R.Qa-1b cells using an IFNγ ELISPOT assay. C1R cells can be obtained commercially. C1R.Qa-1b cells can be generated by transducing the C1R cells with the Qa-1 lentiviral vector.
5. Determination of Individual Peptides in the OLP_pool which Stimulate to the Qa-1 Restricted IFN-γ Secretion in an OLP_pool-specific CD8+ T Cell Line
6. Identification of the Optimal Qa-1 Epitope in a 15-mer OLP which Stimulates the Epitope-specific, Qa-1-restricted Response in an OLP_pool-specific CD8+ T Cell Line
Design of an OLP library covering the whole length of a protein
Beginning at the N-terminus of a protein, each peptide is 15 amino acids (15-mer). Hence, the first peptide spans position 1 to position 15. The N-terminus of the second peptide overlaps with the C-terminus of the first peptide by 11 amino acid. Hence, the second peptide spans the position 5 to position 19. Design the rest of the peptides to the end of C-terminus of th...
Here, we have described a protocol for analyzing Qa-1 epitopes in a protein. In relation to this protocol, several other strategies were also reported previously. First, allogeneic CD8+ T cell lines and clones were used for the identification of the Qdm1. Second, a putative Qa-1-binding motif from the analysis of Qdm was used for the identification of the HSP60p216-224 and a TCRBV8.1 epitope9,18. Third, individual overlapping pe...
Authors declare no conflict of interest.
We thank Penelope Garcia for her technical assistance and preparation of this manuscript. This work was supported by a Research Innovation Grant (RIG) from the Department of Medicine at Loma Linda University (681205-2967) and a pilot grant from National Multiple Sclerosis Society (PP1685) to XT.
Name | Company | Catalog Number | Comments |
The protein to be analyzed | N/A | N/A | Sequence of the protein can be obtained from NCBI |
Dimethyl sulfoxide (DMSO) | Sigma-Aldrich | Cat#: D2650 SIGMA | DMSO should be sterile and cell culture tested. |
Kb-/-Db-/- mice | The Lackson Laboratory | Stock#: 019995 | We used Taconic H2-KbH2-Db doube knockout mice (Cat#: 4215-F and 4215-M) which however are not available anymore. |
AIM V Serum Free Medium | ThermoFisher Scientific | Cat#: 12055091 | |
2-mercaptoethanol | ThermoFisher Scientific | Cat#: 21985023 | |
Sodium pyruvate | ThermoFisher Scientific | Cat#: 11360070 | |
Nonessential Amino Acids | ThermoFisher Scientific | Cat#: 11140076 | |
Dynabeads CD8 Positive Isolation Kit | ThermoFisher Scientific | Cat#: 11333D | |
Bio-Gel P-100 | Bio-Rad | Cat#: 150-4171 | |
Phoshate Balanced Solution (PBS) | ThermoFisher Scientific | Cat#: 20012027 | |
Trasfer pipette | Globe Scientific | Mfg#: 137238 | |
Murine M-CSF | PeproTech | Cat#: 315-02 | |
48-well tissue culture plates | USA Scientific | Cat#: CC7682-7548 | |
Corning Costar TC-treated Multiple well Plates, 96-well, V-shaped bottom | Sigma-Aldrich | Cat#: Z372129 Sigma | |
1ml deep 06-well PP plate, sterile | USA Scientific | Item#: 1896-1110 | |
Recombinant murine IL-2 | PeproTech | Cat#: 212-12 | |
Recombinant murine IL-7 | PeproTech | Cat#L: 217-17 | |
Capture anti-IFN-γ antibody | BD Biosciences | Cat#: 551881 | |
ELISPOT plate | Sigma-Aldrich | Cat#: S2EM004M99 | |
C1R | ATCC | Cat#: ATCC CRL-1993 | |
C1R.Qa-1b | Custom made (GenBank access#: NM_010398.3) | ||
Qa-1 lentiviral vector | GeneCopoeia | Product#: Mm02955 | |
Detection anti-IFN-γ antibody | BD Biosciences | Cat#: 551881 | |
Tween20 | Sigma-Aldrich | Cat#: P9416 | |
Streptavidin-HRP | BD Biosciences | Cat#: BD557630 | |
AEC substrate | BD Biosciences | Cat#: 551951 | |
ImmunoSpot Analyzer | ImmunoSpot | Any immunoSpot analyer should work for this purpose. |
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