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Generating a detailed description of human T cell repertoire diversity is an important goal in the study of human immunology. The circulation is the source of most T cells used for studies in humans. Here we use high throughput sequencing of TCR BV19 transcripts from CD8 T cells derived from unmanipulated PBMC from an older HLA-A2 individual to provide a quantitative and qualitative description of the clonotypic CDR3 nucleotide and amino acid composition of the TCR β-chain from this subset of circulating CD8 T cells. Aggregated samples from six time points spanning ∼1.5 years were analyzed to smooth possible temporal fluctuation. BV19 encompasses the well studied RS-encoding clonotypes involved in recognition of the M1(58-66) epitope from influenza A in HLA-A2 individuals. The clonotype distribution was diverse, complex and self-similar. The amino acid composition was generally skewed in favor of glycines and there were specific amino acids observed at higher frequency at the NDN start position. The motif repertoire distribution was also diverse, complex and self-similar with respect to CDR3 length, NDN start and length.

The CD8 memory T cell repertoire to the influenza A derived M1(58-66) epitope shows a restricted V genes and CDR3 sequences usage. The repertoire is highly polyclonal and the clonotype distribution has been described as consisting of two components, one showing a power law-like distribution and the other composed of a few clonotypes with a very high relative frequency. The question is whether the complex repertoire defined by its ability to flourish in a short term recall culture corresponded to functional cells. Here we show that there is a relation between expression of the degranulation marker CD107 and cytotoxicity or IFN-γ production in CD8 T cell lines and clones. We then examine recently degranulated CD8 cells from recall cultures from four middle aged HLA-A2 subjects and show that these functional cells are polyclonal. The clonotype distributions of the CD8(+)CD107(+) repertoires are complex in the same manner as previously reported. The clonotype composition of CD8(+)CD107(+) repertoires is also very similar to CD8 only repertoires, and to CD8(+)HLA-A2-M1(58-66) pentamer positive repertoires. We postulate that multiple exposures during childhood to this conserved influenza A epitope has generated a complex functional repertoire in HLA-A2 individuals.

The repertoire complexity of CD4+ and CD8 + T cells was measured in three healthy blood donors for a number of TCR BV gene families by TCR spectra-typing. This method subdivides V family-specific PCR products based on CDR3 length. Genomic DNA was analyzed to determine the distribution of the cells bearing particular V-J rearrangements. cDNA was analyzed to measure the levels of transcripts arising from those same cells. The complexity and distribution of T cells in each lineage were equal for most BV families. Certain families showed frequent skewing in CD8 cells. Analysis of the intensity profiles of RNA versus DNA spectratypes indicated that in general, there is a constant ratio of transcript per cell for all rearranged sizes within a particular family. This ratio appeared higher in CD4 cells. Thus, steadystate levels of TCR mRNA were measured and found to be higher in CD4+ than in CD8+ cells.

The analysis of T-cell repertoires has been facilitated by the introduction of methods in which the length heterogeneity of the third complementarity region (CDR3) is used to further refine V-family-specific PCR. We call our implementation of this technique T-cell spectratyping. This method is especially important in analysis of specific expansion or retention of T cells in human immune system function. Current methodologies are cumbersome in the number of PCR reactions and gels needed for complete analysis of TCR BV repertoires. We describe here the optimized conditions for using 11 TCR BV primer pairs in multiplex PCR which allow for a more compact analysis. In addition, the two primers act as controls for each other in the PCR. The use of these primers is shown using either fluorescent or radiolabeled constant primers. The two labeling methods give comparable results. Fluorescent primers avoid the difficulties associated with use of radioactivity. Autoradiography with 32 P-labeled primers is simpler, requiring less instrumentation.

Evolutionary relatedness among the highly polymorphic DRβ genes has been established based on shared nucleotide sequences and structural organization of DRβ loci. The evolution of promoter regions of the B1 ∗ 0701, B1 ∗ 0101, B1 ∗ 1501, B5 ∗ 0101 genes was analyzed by cloning and sequencing. This shows that the polymorphism and isomorphism of HLA DRβ genes extend into the 5′ flanking promoter region of the genes and that evolutionary relatedness also exists among the DRβ gene promoters. This suggests that DRβ gene promoters and coding regions coevolved. The effect of the naturally occurring nucleotide substitutions in the polymorphic and isomorphic DRβ promoters on transcriptional activity has been determined in a transient expression system. The transcriptional activity of two polymorphic DRβ promoters, B1 ∗ 1501 and B1 ∗ 0701, and two isomorphic DR2 promoters, B1 ∗ 1501 and B5 ∗ 0101, is the same for these promoters. Together these data suggest that naturally occurring substitutions do not significantly affect the transcriptional activity of these promoters. Human Immunology 41, 112–120 (1994)

Alloreactive T-cell clones were derived by limiting dilution following priming to allogeneic cells during HLA-DR1 alloantigens. Clonal specificities were determined by extensive testing on a panel of allogeneic lymphoblastoid cell lines and by blocking studies with monoclonal antibodies specific for HLA-DR, -DQ, and -DP class II molecules. Out of nine DR1-positive cell lines, three failed to stimulate a subset of the T-cell clones in conventional proliferation assays. Proliferation by all of the clones was blocked by anti-DR antibodies, not by anti-DQ or anti-DP, which was consistent with the conclusion that the HLA-DR molecule was recognized. This DR1-associated polymorphism has been identified as Dw20 by the Tenth International Histocompatibility Workshop. The molecular basis for this altered recognition of the DR1 molecule was determined by allele-specific oligonucleotide hybridization and by DNA sequencing studies. The first, second, and third hypervariable regions of all nine DR1-positive cell lines were identical. Valine and glycine were found at positions 85 and 86 of the DR 1 β 1 chain in DR1 molecules from six of the nine lymphoblastoid cell lines, whereas alanine and valine were found in the three variant (Dw20) DR1-positive cells. By analogy with class I structure, residues 85 and 86 would be located at the extreme C-terminal end of the β-chain α helix. Together or separately, these amino acid differences may define a T-cell recognition element on the DR1 molecule serving to contact allospecific T-cell receptors. Alternatively, if allorecognition involves recognition of a self peptide complexed with an allogenic MHC molecule, then it is possible that the differences T cells recognize on DR1 class II proteins arise from peptide-specific interactions with residues 85 and 86.

The immune response to allogeneic-MHC molecules can be divided into two pathways based on the nature of the antigen. In the direct pathway, T cells respond to intact allogeneic MHC molecules, while in the indirect pathway T cells respond to allo MHC-derived peptides presented by self-MHC. The T-cell repertoire used in the direct and indirect alloresponse have not been compared in the same alloantigen system. Here, HLA-DR transgenic mice are used to compare the repertoires of T cells that respond to the same alloantigen through either the direct or the indirect pathway. Separate direct and indirect DR1 anti-DR4 T-cell lines were generated and the T cell repertoire was analyzed by molecular methods. The same six Vβ families were involved in both direct and indirect cultures indicating a complete overlap in the Vβ gene usage. A partial overlap at the clonotype level was observed as two identical clonotypic TCRs were observed in both direct and indirect cultures. Interestingly, the T cells observed in both cultures were public as the same TCRs were identified in cultures developed from independent mice. These results raise the prospect that immune suppression of selected T cells during allo-transplantation can simultaneously modulate direct and indirect alloreactivities.

An interesting class of immune responses is that in which an environmental agent modifies a self-protein. Heparin induced thrombocytopenia (HIT) is associated with an antibody response in which the immunogen is a self-protein, platelet factor 4 (PF4), modified by an external agent, heparin. We tested the hypothesis that a T cell component exists in HIT, which like the humoral response, also requires the combination of heparin and PF4 to be activated. We identify here, a subset of T cells derived from a subject with severe HIT, which were expanded preferentially in 14-day in vitro cultures specifically in the presence of PF4:heparin complexes. A combination of T cell receptor spectratyping, CDR3 sequencing, and clonotype-specific probe hybridization were used to identify the responding T cells. The three BV17 T cell "clonotypes" thus identified had a CDR3 length of 10 amino acids, used BJ1.2, and displayed a conserved CDR3 sequence motif. These T cells are an example of a cellular response to environmentally altered self and are likely to be directly involved in HIT by functioning as T helper cells. The results are discussed in terms of the possible role of modification of antigen presentation by the external agent in this response.

Cells expressing HLA DR7 contain two functional DRβ genes, DRB1 and DRB4, whose mRNA is present at different levels. We examined whether the mRNA levels are due to differential transcriptional regulation or post-transcriptional regulation. As part of this analysis, a novel series of upstream elements was identified. Analysis of the proximal promoter activity, using a transient expression system, showed that the isomorphic promoter activities of B1 and B4 are about equal. RNase protection analysis of steady-state pre-mRNA and mRNA levels shows that the DR7 B1 pre-mRNA levels are 3 to 4 fold higher than B4 pre-mRNA levels. However, the B1 mRNA levels are increased seven fold relative to the B4 mRNA levels. The disproportionate increase of the mRNA levels relative to the corresponding pre-mRNA levels indicates that regulation also occurs at the posttranscriptional level. Human Immunology 50, 111–120 (1996)

The mRNA levels of LMP7, HLA-DMA, and HLA-DMB genes, all located within the HLA-D region, were analyzed in the “bare lymphocyte” line SJO, which had been shown to be characterized by a transcription defect of class II genes (DP, DQ, and DR). This was done using semiquantitative PCR amplification of cDNA generated from total RNA. The results show that the transcription of the LMP7 gene in SJO cells is equivalent to that in the control B-cell line Raji. In contrast, the HLA-DM gene transcripts were not present in the SJO cell line. This observation indicates that the promoter similarity between the classic class II genes and HLA-DM is sufficient for the SJO defect to extend to the DM loci.

T-cell receptor α-chain cDNA were generated from unstimulated peripheral blood mononuclear cells of a DR2,3,52a individual using a modified anchor PCR method. Fifty-six cDNA clones were identified representing 47 distinct T-cell receptor clonotypes and 26 VA loci. This analysis identified a new VA gene family VA30, and aew member of the VA6 gene family.

Fourteen alleles have been identified by analysis of the nucleotide sequences encoding the HLA-DQB1 chain. This study describes the detection of these 14 alleles by selective gene amplification and sequence-specific hybridization with nonradioactive oligonucleotide probes. These techniques were employed to create an oligotyping system with two levels of resolution that provide versatility and the capacity for comprehensive detection of all polymorphic sequences. An initial low-resolution assay was employed to detect four major groups of alleles that are associated with the DQw1-w4 serological specificities. A further high-resolution assay was then employed to differentiate 14 individual DQB1 alleles. Appropriate control measures were also included to detect carry-over and to confirm hybridization specificity. This system was used to analyze the allele frequencies of DQB1-0301, -0302, and -0303 in 115 DQB1-03 ∗∗ Caucasian blood donors. Allele frequencies of oligotypes DQB1-05 ∗∗ and DQB1-06 ∗∗ were analyzed in 112 DQB1-01 ∗∗ Caucasian blood donors. This system was also utilized to identify oligotypes designated DQB1-0501 through DQB1-0503 and DQB1-0601 through DQB1-0605 in 35 Tenth International Histocompatibility Workshop DQw1 cell lines to examine the correlation with serological and cellular specificities. In one of these cell lines, an unexpected linkage was discovered between the DRB1 and DQB1 loci, suggesting a recombination event. Oligotyping is a precise and accurate method for directly defining polymorphic sequences and it promises to have a major impact on the future direction of HLA typing.

LB-Q1 and LB-Q4 are two subtypes of DRw52, defined by proliferative T-cell clones. These subtypes represent a polymorphism of the DRβIII gene. Similar subtypes of DRw52 can be defined by oligonucleotide typing, serology and RFLP analysis. In the present study we compared these typing techniques on a panel of 22 HLA-D homozygous, DRw52-positive typing cells. All typing techniques correlated very well. Three subtypes of DRw52 could be identified. Our results show that typing for cellularly defined structures can be done with a variety of noncellular techniques. This observation has important implications for matching in unrelated bone marrow transplantation and for disease association studies.

Different cDNA clones have been isolated that encode each of the three chains of HLA-DR antigens: alpha, intermediate and beta, as well as another beta chain, most likely DC. Whereas the DR alpha and intermediate chains seem encoded by single genes, the DR and DC beta chains are most likely encoded by multiple genes; furthermore, their polymorphism can be readily detected by restriction analysis of cellular DNA. Several genomic DNA clones were isolated for the DR and DC beta chain genes and for the intermediate chain gene. The sum of all distinct cDNA clones and genomic DNA clones for HLA-DR beta chains, isolated from a heterozygous cell line, represent five genes. This implies the existence of at least three nonallelic DR beta chain genes in addition to the DC beta chain genes. The complete sequence of one of the DR beta chains is presented. A genomic DNA clone for a DR beta chain was transferred into mouse L cells and found to be expressed into RNA of the same size as DR beta mRNA. The finding, among the genes for class II antigens, of multiple genes for the beta chain of HLA-DR, distinct from those of other known subregions such as DC, emphasizes the importance of gene transfer experiments, where individual genes can be expressed and tested for their functional role in the immune response.

In this study we have examined the results of probing with synthetic oligomers at the DRβIII locus, together with restriction fragment length polymorphisms defined by BglII digestion and a cDNA DRα probe, and Taq 1 digestion and a genomic DQα probe. We have demonstrated heterogeneity of the human leukocyte antigen DR3 and close association of the DRα, DRβIII, and DXα genes. Two DR3-related preferential allelic associations have been identified, which may prove useful in family analysis as well as for investigations of DR3-related diseases.

The polymorphism of HLA class II molecules in man is particularly evident when comparisons between population groups are made. This study describes a DR3 haplotype commonly present in the American black population. Unlike the Northern European population, in which almost all DR3 individuals are DQw2, approximately 50% of DR3-positive American blacks express a DQw4 allelic product. This study characterizes the DR subregion of that haplotype. cDNA sequence analysis has revealed a DR beta gene which differs at several positions from previously described DR3 beta 1 genes. It is postulated that a gene-conversion-like event with a DRw52 beta gene as donor has generated some of these differences. The haplotype carries a DRw52a allele as defined by oligonucleotide hybridization studies. DNA restriction fragment analysis using a family and several unrelated individuals has allowed us to identify DR alpha and beta fragments associated with the DR3(w18),DQw4 haplotype. The most striking observation is that the DR3(w18),DQw4 haplotype differs from DR3(w17),DQw2 haplotypes at multiple class II loci. Several genetic mechanisms including reciprocal recombination, gene conversion, and point mutation were involved in generating the differences between these haplotypes. Once established, the DR3(w18),DQw4 haplotype appears to be relatively stable in the population.

Among MHC class II antigens, the DRw6/Dw6 complex represents a special situation where typing on a routine basis is often troublesome, mainly because monospecific alloantisera are rare and individual subtypes numerous. We demonstrate here that the use of oligonucleotide DNA typing permits an analysis of the polymorphism within DRw6 haplotypes and provides a molecular basis for correlations with functional data. Synthetic oligonucleotide probes, most of them locus- and allele-specific, were derived from the DNA sequences of three alleles of locus DRB1 and three alleles of locus DRB3. These probes allow the positive identification of distinct DRw6 subtypes. As analyzed on a panel of 26 well-defined DRw6 cell lines, oligotyping allows a direct and absolute correlation with the DRw13 serologic specificity and with the cellularly defined Dw9,Dw16,Dw18, and Dw19 specificities. Correlations of the polymorphism at the DRB1 locus with the polymorphism at the DRB3 locus (DRw52 alleles) allow us to identify preferential allelic associations such as DRw13-Dw18-DRw52a/52b, DRw13-Dw19-DRw52c, and DRw13/Dw19 haplotype, the Dw19 cellular reactivity might involve, at least DRw14-Dw9-DRw52b. In view of the absolute segregation of the DRw52c allele with the DRw13/Dw19 haplotype, the Dw19 cellular reactivity might involve, at least in part, epitopes on the DRw52c allele. The identification of DRw6 subtypes, as well as of other HLA class II subspecificities, by oligotyping can now complement and possibly replace serologic and cellular typing. It represents a particularly useful contribution to the optimization of class II matching in the case of bone marrow transplantation with unrelated donors.

To investigate the DRw14 specificity using well-defined cells, the first domain sequences of the B1 locus from a DRw14; Dw9 cell line, TEM and from a DRw14; Dw16 cell line, AMALA were determined. Both sequences reveal a cluster of polymorphisms in the third hyperpolymorphic region indicative of gene conversion-like mechanisms