Biased TCR gene usage in alloreactive T cells specific for a structurally dissimilar MHC alloantigen

TCR Sequencing in Mouse Models of Allorecognition Unveils the Features of Directly and Indirectly Activated Clonotypes

Allorecognition is known to involve a large number of lymphocytes carrying diverse T-cell receptor repertoire. Thus, one way to understand allorecognition and rejection mechanisms is via high-throughput sequencing of T-cell receptors. In this study, in order to explore and systematize the properties of the alloreactive T-cell receptor repertoire, we modeled direct and indirect allorecognition pathways using material from inbred mice in vitro and in vivo. Decoding of the obtained T-cell receptor genes using high-throughput sequencing revealed some features of the alloreactive repertoires. Thus, alloreactive T-cell receptor repertoires were characterized by specific V-gene usage patterns, changes in CDR3 loop length, and some amino acid occurrence probabilities in the CDR3 loop. Particularly pronounced changes were observed for directly alloreactive clonotypes. We also revealed a clustering of directly and indirectly alloreactive clonotypes by their ability to bind a single antigen; amino acid patterns of the CDR3 loop of alloreactive clonotypes; and the presence in alloreactive repertoires of clonotypes also associated with infectious, autoimmune, and tumor diseases. The obtained results were determined by the modeling of the simplified allorecognition reaction in inbred mice in which stimulation was performed with a single MHCII molecule. We suppose that the decomposition of the diverse alloreactive TCR repertoire observed in humans with transplants into such simple reactions will help to find alloreactive repertoire features; e.g., a dominant clonotype or V-gene usage pattern, which may be targeted to correct the entire rejection reaction in patients. In this work, we propose several technical ways for such decomposition analysis, including separate modeling of the indirect alloreaction pathway and clustering of alloreactive clonotypes according to their ability to bind a single antigen, among others.

Clonotype analysis of human alloreactive T cells: a novel approach to studying peripheral tolerance in a transplant recipient

The recognition of allo-MHC and associated peptides on the surface of graft-derived APC by host T cells (direct pathway allorecognition) plays an important role in acute rejection after organ transplantation. However, the status of the direct pathway T cells in stable long term transplants remains unclear. To detect alloreactive T cell clones in PBL and the allograft during the transplant tolerance, we utilized RT-PCR instead of functional assays, which tend to underestimate their in vivo frequencies. We established alloreactive CD4+ and CD8+ T cell clones from peripheral blood sampled during the stable tolerance phase of a patient whose graft maintained good function for 9 years, 7 without immunosuppression. We analyzed the sequence of TCR Vbeta and Valpha genes and made clonotype-specific probes that allowed us to detect each clone in peripheral blood or biopsy specimens obtained during a 1-year period before and after the rapid onset of chronic rejection. We found an unexpectedly high level of donor HLA-specific T cell clonotype mRNA in peripheral blood during the late tolerance phase. Strong signals for two CD4+ clonotypes were detected in association with focal T cell infiltrates in the biopsy. Chronic rejection was associated with a reduction in direct pathway T cell clonotype mRNA in peripheral blood and the graft. Our data are inconsistent with the hypothesis that direct pathway T cells are involved only in early acute rejection events and suggest the possibility that some such T cells may contribute to the maintenance of peripheral tolerance to an allograft.

Analysis of the T-cell receptors utilized for allogeneic HLA-DR recognition: comparison of different responder-cell donors possessing an identical HLA-DR allele

We examined whether individuals with an identical HLA-DR type utilized the same T-cell receptors (TCRs) to recognize a given allogeneic HLA-DR molecule. CD4+ T cells from three responder-cell donors possessing the DRB*0901 allele were stimulated with HLA-DRB1*0406 molecules, subjected to the primary mixed lymphocyte reaction (MLR) and the TCRs of the activated CD4+ T cells were analysed using single strand conformation polymorphism (SSCP) and random cDNA clone sequencing. The responder cells of each donor yielded many dominant SSCP bands in several TCRAV and TCRBV segments, but none of these dominant SSCP bands derived from two or three responders. Random cDNA sequence analysis demonstrated that the alloreactive TCRs were diverse, but each of the three responder-cell donors showed some dominant cDNA clones. However, no amino acid sequence identities or similarities among the dominant cDNAs of these donors were detected. These results indicate that certain T-cell clones from each individual's TCR repertoire pool expand preferentially as a result of allogeneic HLA-DR recognition but these clones are not necessarily common to different individuals, even when their responder cells possess identical DR alleles and are stimulated with the same alloantigen.

In the absence of the invariant chain, HLA-DR molecules display a distinct array of peptides which is influenced by the presence or absence of HLA-DM

The independent influences of invariant chain (Ii) and HLA-DM molecules on the array of naturally processed peptides displayed by HLA-DR molecules were studied using transfected cell lines. The absence of Ii led to an altered set of HLA-DR-bound peptides as judged by the discriminating responses of alloreactive T cell clones. While most T cell clones raised against DR+Ii+DM+ peripheral blood mononuclear cells (PBMC) failed to respond to DR+Ii-DM- cells, T cell clones raised against DR+Ii-DM- transfectants were not stimulated by DR+Ii+DM+ cells. Furthermore, coexpression of HLA-DM with HLA-DR1 in the absence of Ii augmented responses of anti-PBMC T cell clones but inhibited allorecognition by T cell clones raised against DR+Ii-DM- transfectants. The conformational integrity of the class II molecules, as judged by serology, suggests that the patterns of reactivity of the T cell clones reflect specificity for different alloantigen-bound peptides. Hence, discordant regulation of expression of major histocompatibility complex class II, Ii, and HLA-DM molecules in vivo may lead to the display of novel self-peptides and possible interruption of self-tolerance.

T cells receptor beta-chain repertoires are nonrandomly selected in responses to HLA-DR1

T cell receptor (TCR) beta-chain usage by HLA-DR1 alloreactive T cell lines was examined to determine whether common TCR gene segments were used preferentially. We have demonstrated previously that a DR1-specific, human renal allograft-derived T cell line and replicate, anti-DR1 mixed lymphocyte reactions (MLR), established from an unrelated responder/stimulator pair, were selected for T cells expressing V beta 8. In this report V beta 8+ beta-chains from these T cell lines were sequenced to assess clonality and determine the contribution made by the beta-chain junctional regions. All 11 V beta 8+ cDNA clones sequenced from the allograft-derived T cell lines used J beta 2.7 and C beta 2 and had identical junctions, indicating the presence of a predominant V beta 8+ clone. All seven V beta 8+ sequences from the first anti-DR1 MLR and eight of the nine fron the second also used J beta 2.7 and C beta 2 were identical to one another, indicating that a common V beta 8+ clone was selected in these replicate cultures. The sequences of the predominant V beta 8+ beta-chains from the allograft-derived T-cell line and the MLR differed by only 10 nucleotides and four amino acids at the VDJ beta junction. To determine the reproducibility of TCR V beta selection in responses to DR1, additional MLR were established by pairing three different DR1+ stimulators with the same responder. The TCR repertoires of the resulting DR1-specific cell lines were examined. A preference was seen for utilization for certain homologous TCR V beta segments. The data suggest that particular TCR V beta or V beta/J beta combinations may be selected in alloresponses as evidenced either utilization of highly similar beta-chains or homologous V beta segments.