This article describes a method for the generation and propagation of human T cell clones that specifically respond to a defined alloantigen. This protocol can be adapted for cloning human T cells specific for a variety of peptide-MHC ligands.
The study of human T lymphocyte biology often involves examination of responses to activating ligands. T cells recognize and respond to processed peptide antigens presented by MHC (human ortholog HLA) molecules through the T cell receptor (TCR) in a highly sensitive and specific manner. While the primary function of T cells is to mediate protective immune responses to foreign antigens presented by self-MHC, T cells respond robustly to antigenic differences in allogeneic tissues. T cell responses to alloantigens can be described as either direct or indirect alloreactivity. In alloreactivity, the T cell responds through highly specific recognition of both the presented peptide and the MHC molecule. The robust oligoclonal response of T cells to allogeneic stimulation reflects the large number of potentially stimulatory alloantigens present in allogeneic tissues. While the breadth of alloreactive T cell responses is an important factor in initiating and mediating the pathology associated with biologically-relevant alloreactive responses such as graft versus host disease and allograft rejection, it can preclude analysis of T cell responses to allogeneic ligands. To this end, this protocol describes a method for generating alloreactive T cells from naive human peripheral blood leukocytes (PBL) that respond to known peptide-MHC (pMHC) alloantigens. The protocol applies pMHC multimer labeling, magnetic bead enrichment and flow cytometry to single cell in vitro culture methods for the generation of alloantigen-specific T cell clones. This enables studies of the biochemistry and function of T cells responding to allogeneic stimulation.
T lymphocytes are critical components of the adaptive immune system. T cells are responsible for not only directly mediating protective immune responses to pathogens through a variety of effector mechanisms, but also actively maintaining immunological self-tolerance and directing the responses of other cells in the immune system. These functions are directed through a number of integrated signals, including T cell receptor (TCR) ligation, cytokines and chemokines, and metabolites1. Of these signals, the TCR is of particular importance, as it provides the characteristic specificity that defines the T cell’s role in adaptive immunity. A TCR interacts with linear peptide antigens presented by MHC (human ortholog HLA) molecules (pMHC complexes) in a highly specific and sensitive manner to provide the signals that initiate T cell effector function. The biochemical parameters of TCR interactions with pMHC ligands provide not only the specificity for T cell activation, but also have a qualitative impact on subsequent T cell function2. Thus, studying T cell function often requires examining the responses of clonal T cells with defined antigenic specificity.
The human T cell compartment, containing approximately 1012αβ T cells, contains an estimated 107– 108 distinct αβTCRs3-4. This diverse repertoire provides opportunity for recognition of the vast array of peptides from potential pathogens that would necessitate a T cell response for protective immunity. It is estimated that the frequency of T cells responding to a given foreign antigen presented by self-MHC is on the order of 10-4– 10-7 in the absence of prior immune response to that antigen5. The naive T cell repertoire is shaped by thymic selection to ensure the ability to recognize self-MHC presenting peptide antigens and limit reactivity against self-peptide antigens, maximizing the potential utility for mediating protective immunity2. However, in violation of this designed reactivity, a relatively large frequency, 10-3– 10-4, of T cells from immunologically naive individuals respond to stimulation with allogeneic cells, recognizing both the foreign MHC molecules as well as the endogenous peptides they present6. The recognition of allogeneic pMHC ligands is structurally similar to the recognition of foreign antigens presented by self-MHC; the TCR makes critical biochemical interactions with both the allogeneic MHC molecule as well as the presented peptide7. The robust nature of the response of T cells to allogeneic stimulation results from the diversity of pMHC complexes present on the surface of allogeneic cells8. It is estimated that each MHC presents approximately 2 x 104 different endogenous peptide antigens9. This breadth of response to allogeneic stimulation is a significant aspect of the clinically-relevant pathology, such as allograft rejection or graft versus host disease (GVHD), resulting from T cell alloreactivity.
Study of human T cell alloreactive responses has traditionally relied upon examining polyclonal responses of naive T cells following stimulation with allogeneic cells. Repeated stimulation with the same allogeneic cell line combined with limiting dilution analyses is capable of generating clonal T cells with defined recognition of allogeneic HLA10. However, this approach is problematic for examining responses to individual allogeneic pMHC ligands, as the large and diverse repertoire of endogenous pMHC complexes present for a given allogeneic HLA stimulates a broad repertoire of T cells. This bulk population stimulation and limiting dilution approach would require screening of large numbers of clones to isolate T cells with the desired reactivity against a single pMHC ligand. Additionally, the frequency of T cells responding to an individual allogeneic pMHC ligand is relatively low among naive T cell populations, which presents a barrier to efficient generation of human T cell clones responsive to a given antigen.
Identification and isolation of antigen-specific T cells from polyclonal populations have been enabled by the development of fluorophore-labeled pMHC multimers11. This approach utilizes specific peptide antigens loaded into recombinant soluble biotinylated MHC molecules, which are labeled by binding to a streptavidin-labeled fluorophore. Multimerization of pMHC increases the avidity, compensating for the intrinsically low (µM) affinity of TCR for soluble pMHC ligands. Labeled cells can be identified and isolated by flow cytometry. However, this approach is still limited by the low frequency of antigen-specific T cells among naive T cell populations, which are typically orders of magnitude less than the limit of accurate identification and quantification on most flow cytometers. To address this limitation, a method of pMHC tetramer labeling and subsequent magnetic bead enrichment for tetramer-labeled cells has been developed12. This method has demonstrated reliable detection, enumeration, and isolation of low-frequency antigen-specific T cells.
This protocol describes an effective protocol for the generation of human T cell clones that specifically respond to individual allogeneic pMHC ligands. The protocol applies pMHC (HLA) multimer labeling and enrichment for the isolation of alloantigen-specific human T cells with flow cytometry cell sorting and a robust method for in vitro culture of human T cells to enable production of T cell clones from single sorted cells (overview in Figure 1).
NOTE: This protocol requires use of peripheral blood samples from human volunteers. All research with human subjects should be reviewed and approved by a Human Studies Institutional Review Board to ensure compliance with the Declaration of Helsinki (2013) and the Health Insurance Portability and Accountability Act of 1996.
1. Isolation of T cells from Whole Blood
2. Magnetic Enrichment of Alloantigen-specific T cells
3. Preparation of T cells for Single-cell Flow Cytometry Cell Sorting
4. Isolation of Tetramer-labeled T cells by Single-cell Flow Cytometry Sorting
5. Culture and Expansion of Alloantigen-specific T cell Clones
6. Long-term Re-stimulation and Culture of T cell Clones
This protocol describes the generation of clonal human T cell cultures with defined alloantigen specificity via a magnetic bead enrichment and single-cell flow cytometry sorting strategy. Figure 1 provides an outline of the process.
Figure 1: Protocol overview. The protocol described here provides a reliable method for generation of alloantigen-specific human T cell clones from peripheral blood. The process of single T cell isolation and setting up the cell culture is expected to take approximately 4.5 hr. Expansion of the T cell clones requires multiple rounds of non-specific T cell stimulation and culture, each taking 14 days. Clonal cultures can be tested for alloantigen specificity 28 days after isolation, and cultures can be further expanded for additional testing by repeated rounds of stimulation.
The expected yield of alloantigen-specific T cells will depend on the donor, the alloantigen used, and the corresponding frequency of reactive T cells in the donor. An average healthy donor will have 4.5 – 10.0 x 106 leukocytes/ml of blood, with approximately 20% T lymphocytes. Figure 2 illustrates the results of measuring the binding of T cells from a HLA-DR4 (HLA-DRB1*04:01)-negative donor to a specific alloantigen, amino acid residues 30-48 of the HLA-A2 protein (DTQFVRFDSDAASQRMEPR, A230-48) presented by the class II molecule HLA-DR413.
Figure 2: Flow cytometry sorting of alloantigen tetramer-labeled cells for generating single cell cultures. A. Flow cytometric identification and isolation of A230-48/HLA-DR4 tetramer-labeled T cells from a HLA-DR4-negative donor. T cells enriched for tetramer-labeled cells by magnetic bead selection were sorted by flow cytometry, gating on singlet CD5+CD14–CD19–tetramer+ lymphocytes as illustrated. Tetramer-unlabeled cells were used as a fluorescence-minus one control to establish gating for tetramer+ cells. B. Tetramer+ T cells were sorted into a 96-well round-bottom tissue culture plate containing 100 µl human T cell culture medium. The plate set-up included positive and negative control wells as indicated.
From a starting number of 2.0 x 107 leukocytes we found a frequency of alloantigen-specific cells of 1/4776 T cells:
1.1×106 tetramer-enriched cells x 0.992 (singlets) x 0.744 (lymphocytes) x 0.477 (CD5+CD14–CD19–) x 0.0034 (tetramer+ T cells) / 2.0 x 107 peripheral blood leukocytes x 0.314 (pre-enrichment CD3+)
From the starting 2.0×107 leukocytes we were able to isolate 88 individual tetramer-labeled T cells for culture. After 2 rounds of anti-CD3/CD28 microbead stimulation and culture as described we identified 2 growth-positive cultures by microscopic examination (representative example of growth 10 days after single cell isolation and culture shown in Figure 3.A). Clonal cultures were expanded to 1 ml as described, and alloantigen specificity was assessed by examining binding of the A230-48/HLA-DR4 tetramer (Figure 3.B).
Figure 3. Evaluation of T cell cultures. A. Microscopic examination of 96-well plate T cell cultures. Representative example of T cell culture 10 days after isolation of individual T cells by flow cytometry sorting. Cells were stimulated with 0.5 µl anti-CD3/CD28 microbeads/well (examples indicated by arrowhead) in a volume of 200 µl human T cell culture medium. B. T cell alloantigen specificity of clonal T cell cultures evaluated by flow cytometry analysis of pMHC tetramer labeling. Clonal T cell cultures of flow cytometry isolated CD5+CD14–CD19– A230-48/HLA-DR4 tetramer+ lymphocytes were examined for A230-48/HLA-DR4 tetramer binding after 4 weeks of in vitro culture. Tetramer-unlabeled cells were used as a fluorescence-minus one control to establish gating for tetramer+ cells.
T cell alloreactivity is a long-studied and clinically-relevant phenomenon. The robust proliferative and effector responses of T cells to allogeneic stimulation has enabled extensive analyses of human T cell responses in vitro through relatively straightforward mixed lymphocyte reactions of peripheral blood T cells against inactivated allogeneic cells. However, these primary alloreactive T cell responses are oligoclonal, comprised of a large number of individual T cells responding to specific alloantigens. This diversity in the T cell response impairs the ability to examine the biochemistry of pMHC ligand recognition driving alloreactive T cell responses. The standard solution to this challenge has been to generate clonal T cell lines through repeated stimulation with a given allogeneic cell line and limiting dilution analysis. While this approach is capable of generating clonal T cell lines with a single specificity, it may not reflect the original composition of the oligoclonal response of naive T cells. Additionally, this approach does not directly identify the specific pMHC alloantigen recognized (even narrowing the response to a single HLA molecule still presents the challenge of finding the stimulatory peptide from among the estimated 2×104 endogenous peptides presented under steady-state conditions), complicating biochemical characterization of T cell ligand recognition in alloreactivity.
The protocol presented here utilizes fluorescently-labeled pMHC multimers, magnetic bead enrichment, and flow cytometry cell sorting to identify and isolate human T cells specific for individual allogeneic pMHC ligands. This technique has become a powerful tool for examining antigen-specific T cell responses12. Our increasing understanding of the highly peptide-specific nature of T cell recognition of allogeneic pMHC complexes7,8 has enabled us to adapt this approach to the study of alloreactive T cells in both mice14 and humans15. This approach uniquely enables examination of the composition of the naive T cell populations that comprise the initial oligoclonal alloreactive response. Furthermore, combination of the pMHC multimer labeling approach with in vitro tissue culture facilitates generation of clonal T cell cultures that can be used to dissect the biochemistry of allogeneic pMHC ligand recognition, a question that cannot adequately be addressed via studying polyclonal T cell responses and is significantly impaired by traditional T cell cloning methods.
Using this approach, it can be expected that T cells specific for a given alloantigen pMHC should be identifiable for isolation and culture. However, the efficacy of this approach is dependent on multiple variables. First, the frequency of T cells from an immunologically naive donor that recognize a single alloantigen pMHC is relatively low (on the order of 1/103– 1/106) and varies between individuals. The ability to isolate pMHC-specific T cells depends on their abundance, as not all isolated cells will successfully expand to generate clonal cultures. The efficiency of the protocol can be influenced by several factors including the nature of the peptide used and the viability of the cells during preparation and isolation. The success of this technique also requires identification of allogeneic pMHC ligands capable of being re-folded into fluorescently-labeled multimers from recombinantly expressed HLA molecules and synthesized peptides. While there are multiple descriptions in the literature of identified peptides presented by specific HLA alleles, not all peptide re-fold in solution equally well. The efficacy of pMHC re-folding depends on several factors, including peptide length, solubility, and affinity for the MHC peptide binding pocket16. The ability of pMHC multimers to label antigen-specific T cells is also dependent on the peptide used. The affinity of the peptide for the MHC as well as the affinity of the TCR for the pMHC complex influences the binding of the fluorophore-labeled pMHC multimer. Weak binding can result in low shifts in fluorescence intensity, which can lead to difficulty in identifying antigen-specific cells by flow cytometry. These are significant technical hurdles that can impair the efficient isolation of alloantigen-specific T cells. In addition to these technical limitations, a significant biological caveat to this approach should be noted. T cell binding of pMHC tetramers is limited to TCRs with relatively high ligand affinity. This feature results in excluding T cells with low affinity for a ligand from identification and analysis. This is significant, as these low-affinity T cells are capable of substantial contribution to primary T cell responses17. However, even with these limitations, the approach described here is an efficient tool for the generation of clonal human T cells with defined antigen specificity. While the focus presented here is identification and isolation of human T cells specific for allogeneic pMHC ligands, the T cell identification, isolation, and culture techniques can be easily adapted to other pMHC specificities.
The authors have nothing to disclose.
The author would like to thank the NIH Tetramer Core Facility for tetramer production. The author would also like to thank E.D. O’Connor and K.E. Marquez at the UCSD Human Embryonic Stem Cell Core Facility flow cytometry laboratory for assistance in cell sorting. This work was funded by National Institutes of Health grant K08AI085039 (G.P.M.).
Name of Reagent/ Equipment | Company | Catalog Number | Comments/Description |
Sodium heparin venous blood collection tube 16 x 100 mm | Becton, Dickenson and Company | 366480 | |
Lymphoprep | Stemcell Technologies | 7801 | |
Rosette Sep Human T Cell Enrichment Kit | Stemcell Technologies | 15061 | |
Dulbecco's PBS, 1x without Ca or Mg | Corning | 21-031-CV | |
Bovine serum albumin | Sigma-Aldrich | A7906 | |
EDTA | Sigma-Aldrich | E6635 | |
Fluorophore-labeled pMHC tetramer | NIH Tetramer Facility | NA | |
EasySep Biotin Selection Kit | Stemcell Technologies | 18553 | |
EasySep Selection magnet | Stemcell Technologies | 18000 | |
TruStain FcX Human Fc blocking solution | Biolegend | 422301 | |
Anti-CD5 PE-Cy7 (clone UCHT2) | Biolegend | 300621 | |
Anti-CD14 FITC (clone HCD14) | Biolegend | 325603 | |
Anti-CD19 FITC (clone HIB19) | Biolegend | 302205 | |
Iscove's DMEM, without b-ME or L-glutamine | Corning | 15-016-CV | |
HEPES | Corning | 25-060-CI | |
b-Mercaptoethanol | Life Technologies | 21985-023 | |
Glutamax | Life Technologies | 35050061 | |
Gentamicin sulfate (50 mg/ml) | Omega Scientific | GT-50 | |
Human AB serum, male donor | Omega Scientific | HS-30 | |
Recombinant human IL-2 | Peprotech | AF 200-02 | |
Dynabeads Human T-Activator CD3/CD28 | Life Technologies | 11131D | |
Media | |||
Cell sorting buffer | |||
PBS, pH 7.4 | 1 L | ||
BSA | 10g | ||
EDTA (0.5 M) | 2 ml | ||
Human T Cell Culture Medium | |||
Iscove's DMEM | 351.6 ml | ||
Heat-inactivated human AB serum | 40 ml | ||
HEPES (1 M) | 4 ml | ||
Glutamax (100 x) | 4 ml | ||
Gentamicin (50 mg/ml) | 0.4 ml | ||
b-mercaptoethanol (14.3 M) | 1.4 ml | ||
Recombinant human IL-2 (1 mg/ml) | 1 ml |