scholarly journals Contribution of T Cell Receptor Alpha and Beta CDR3, MHC Typing, V and J Genes to Peptide Binding Prediction

2021 ◽  
Vol 12 ◽  
Author(s):  
Ido Springer ◽  
Nili Tickotsky ◽  
Yoram Louzoun

IntroductionPredicting the binding specificity of T Cell Receptors (TCR) to MHC-peptide complexes (pMHCs) is essential for the development of repertoire-based biomarkers. This affinity may be affected by different components of the TCR, the peptide, and the MHC allele. Historically, the main element used in TCR-peptide binding prediction was the Complementarity Determining Region 3 (CDR3) of the beta chain. However, recently the contribution of other components, such as the alpha chain and the other V gene CDRs has been suggested. We use a highly accurate novel deep learning-based TCR-peptide binding predictor to assess the contribution of each component to the binding.MethodsWe have previously developed ERGO-I (pEptide tcR matchinG predictiOn), a sequence-based T-cell receptor (TCR)-peptide binding predictor that employs natural language processing (NLP) -based methods. We improved it to create ERGO-II by adding the CDR3 alpha segment, the MHC typing, V and J genes, and T cell type (CD4+ or CD8+) as to the predictor. We then estimate the contribution of each component to the prediction.Results and DiscussionERGO-II provides for the first time high accuracy prediction of TCR-peptide for previously unseen peptides. For most tested peptides and all measures of binding prediction accuracy, the main contribution was from the beta chain CDR3 sequence, followed by the beta chain V and J and the alpha chain, in that order. The MHC allele was the least contributing component. ERGO-II is accessible as a webserver at http://tcr2.cs.biu.ac.il/ and as a standalone code at https://github.com/IdoSpringer/ERGO-II.

Blood ◽  
1994 ◽  
Vol 83 (3) ◽  
pp. 767-775 ◽  
Author(s):  
C Kasten-Sportes ◽  
S Zaknoen ◽  
RG Steis ◽  
WC Chan ◽  
EF Winton ◽  
...  

Abstract T-gamma lymphoproliferative disease (T-gamma LPD) is a chronic disorder of mature T cells that is associated with neutropenia and autoimmune phenomena. Although the progression of the lymphoproliferation is indolent, it is often associated with a monoclonal proliferation of T-cell-type large granular lymphocytes (LGL) that manifest multiple in vitro suppressor and cytotoxic activities. We considered the possibility that the granulocytopenia or anemia might represent an autoimmune disorder mediated by the monoclonal LGL via T-cell receptor (TCR) recognition of an antigen involved in hematopoiesis. Therefore, in an effort to characterize the usage of the TCR alpha-and beta-chain genes in patients with T-gamma LPD, we cloned and sequenced TCR alpha-and beta-chain mRNAs derived from the T-cell type LGL of five patients. The five patients studied did not use a common V alpha nor a common J alpha segment. However, an unusual finding was observed in one of the patients where the occurrence of a single variable-diversity-junctional (VDJ) rearrangement of the beta chain confirmed the monoclonal origin of the LGL proliferation. In accord with this evidence for monoclonality, many of the cells studied used a common V alpha (V alpha 19.1). In contrast to this common V alpha usage, there was a marked diversity of the J alpha segments and N-region addition that were associated with the V alpha 19.1 segment. This pattern of common V alpha usage associated with different N and J alpha segments suggests an immune-mediated selection process affecting the TCR alpha chain occurring after the transformation event that established the clone. We suggest that the T-cell-type LGL malignant clone might have developed autoreactivity conferred by the selected TCR alpha chain and that this autoreactivity might be implicated in this patient's anemia.


1994 ◽  
Vol 180 (5) ◽  
pp. 1931-1935 ◽  
Author(s):  
A M Deckhut ◽  
Y Chien ◽  
M A Blackman ◽  
D L Woodland

Several studies have suggested that there is a direct interaction between the T cell receptor (TCR) and the major histocompatibility complex (MHC) molecule during T cell recognition of superantigen. To further investigate this possibility, we have analyzed T cell recognition of a bacterial superantigen, Staphylococcal enterotoxin B (SEB), presented by a series of mutant murine I-Ek molecules in which residues of either the alpha or beta chain predicted to interact with the TCR have been substituted. Individual T cell hybridomas gave distinct patterns of responsiveness to SEB presented by the I-E beta k mutants that could not be attributed to differences in the binding of SEB to the mutants. This effect appeared to be dependent on the TCR-alpha chain because some of these hybridomas expressed identical TCR transgenic beta chains. In contrast, none of the hybridomas gave distinct patterns of responsiveness to SEB presented by the I-E alpha k mutants. Taken together, these observations support the idea that there is a functional interaction between the alpha chain of the TCR and the beta chain of the MHC class II molecule. The data also support the idea that this interaction might enhance superantigen recognition in some cases.


Blood ◽  
1987 ◽  
Vol 69 (3) ◽  
pp. 908-912 ◽  
Author(s):  
J Jr Mirro ◽  
G Kitchingman ◽  
FG Behm ◽  
SB Murphy ◽  
RM Goorha

Abstract T cell differentiation was investigated by determining the relationship of T cell receptor (Ti) gene rearrangement and transcription to the expression of surface and cytoplasmic T3 antigen using blast cells from five children with acute lymphoblastic leukemia of thymic origin. Patterns of monoclonal antibody (MoAb) reactivity indicated that these cases were representative of the three recognized stages (I, II, III) of human thymocyte development. The T3 antigen, which becomes linked to the Ti to form a functional T cell receptor complex on mature thymocytes, was expressed on the cell surface in two cases (stage III). However, in the remaining three cases that were surface T3 negative (stages I and II), large amounts of T3 were identified in the cytoplasm by immunoperoxidase staining and flow cytometry. Leukemic blasts from all five patients showed rearranged genes encoding the beta-chain portion of the Ti heterodimer. RNA transcripts of Ti beta-chain genes were also evident in lymphoblasts from all five cases, but transcripts coding for the alpha-chain portion of Ti were found only in cases that expressed T3 on the cell surface. Thus the absence of surface T3 (and presumably Ti) coincides with the absence of Ti alpha-chain RNA, suggesting that transcription of alpha-chain genes is a critical regulatory event in the surface expression of the Ti-T3 complex. Leukemic T cells that rearrange and express Ti beta-chain genes but lack Ti alpha-chain messenger RNA (mRNA) may represent a stage of differentiation analogous to pre-B cells, where heavy-chain immunoglobulin (Ig) genes are rearranged and expressed but light-chain Ig genes are not expressed.


Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 823-823
Author(s):  
Marleen M Van Loenen ◽  
Renate de Boer ◽  
Gerdien L Volbeda ◽  
Avital L Amir ◽  
Renate S. Hagedoorn ◽  
...  

Abstract T cell receptor transfer to engineer tumor specific T cells is being explored as a strategy for adoptive immunotherapy. By retroviral introduction of T cell receptors (TCRs), large numbers of T cells with defined antigen specificity can be obtained. The in vivo efficacy of adoptively transferred TCR engineered T cells has been demonstrated in mouse studies and recently the first clinical trial with TCR engineered T cells was performed in melanoma patients. However, a potential drawback of TCR gene transfer is the formation of mixed TCR dimers. Chains of the introduced TCR can pair with the endogenous TCR chains, resulting in unknown specificities, and potentially in harmful reactivity against patient HLA molecules. We investigated whether TCR gene transfer leads to the generation of new detrimental reactivities by creating T cells that expressed mixed TCR dimers. To be able to discriminate between the antigen specificity of the mixed TCR dimers and the introduced as well as the endogenous TCR, we transduced mono-specific T cells with seven different antigen specific TCRs. As mono-specific T cells we used CMV-pp50 specific HLA-A1 restricted T cells. The transduced T cells were analyzed for newly acquired specificities against a large HLA-typed EBV-LCL panel covering almost all HLA class I and II molecules. We transduced several polyclonal virus specific T cell populations with the seven different antigen specific TCRs, and showed that in all T cell populations at least one of the seven TCR-transduced populations acquired new alloreactivities. Furthermore, by randomly combining TCR alpha and beta chains derived from different T cell clones we created 60 mixed TCR dimers of which 17 acquired alloreactivity. These results indicate that recombination of the introduced TCR chains with the endogenous TCR chains frequently gives rise to new allospecificities. To ascertain that the newly acquired alloreactivities were exerted by mixed TCR dimers, we introduced only TCR alpha or beta chains into CMV-pp50 specific monoclonal T cells, and demonstrated for example, that the introduction of a CMV pp65 specific TCR alpha chain led to a newly acquired reactivity that was HLA B58 restricted. The introduction of only the beta chain of a minor histocompatibility antigen (mHag) HA-1 specific TCR led to a newly acquired HLA B52 specific reactivity. Furthermore, we analyzed whether mixed TCR dimers consisting of conserved TCRs with the same specificity could acquire new harmful reactivity. We recombined mHag HA-2 specific TCR alpha and beta chains from 4 different T cell clones. Of the 12 mixed TCR dimers, a combination of the mHag HA-2 specific TCR alpha chain derived from the HA2.6 T cell clone with the mHag HA-2 specific beta chain of clone HA2.19 resulted in alloreactivity that was HLA DQ3 restricted. These results indicate that each recombination of TCR chains after TCR gene transfer can potentially result in a harmful new reactivity. In conclusion, mixed TCR dimers due to pairing of endogenous TCR chains with introduced TCR chains acquire potentially dangerous reactivities, both class I and class II restricted. To limit the chance of generating self- or alloreactive T cells, TCRs may be constructed allowing selective pairing of the TCR alpha chain with the corresponding TCR beta chain. Alternatively, we propose to use virus specific T cells as host cells for TCR gene transfer. Since they consist of a restricted TCR repertoire, the number of different chimeric TCRs formed will be limited. By introducing into these T cells as controls only the alpha or beta chain of the TCR of interest, the reactivity of these T cells and harmful reactivities of the mixed TCR dimers can be tested against different patient derived cell types.


1993 ◽  
Vol 90 (23) ◽  
pp. 11401-11405 ◽  
Author(s):  
C N Levelt ◽  
P Mombaerts ◽  
A Iglesias ◽  
S Tonegawa ◽  
K Eichmann

Thymic repertoire selection requires the expression of the alpha beta CD3 T-cell receptor (TCR) together with the coreceptors CD4 and CD8. The appearance of CD4 and CD8 on thymocytes is the hallmark of a complex maturation step, accompanied by downregulation of the interleukin 2 receptor (IL-2R) alpha chain, arrest of rearrangement (i.e., allelic exclusion) of the TCR beta-chain locus, a burst of cell divisions, and reduction in cell size. This maturation step is inhibited in TCR beta-chain-deficient mouse strains and may depend on surface expression of an immature TCR complex containing CD3 and TCR beta chains but no TCR alpha chain. Here we show that the CD4+8+ double-positive (DP) stage can be induced by treatment of fetal thymic organ cultures with anti-CD3 epsilon monoclonal antibodies in several TCR beta-chain-deficient mouse strains: severe combined immunodeficient (scid) mice, mice carrying a mutation in the recombination activating gene 1 (Rag-1), or mice carrying a deletion in the TCR beta-chain locus itself. These findings suggest that CD3 epsilon is expressed on the thymocyte surface independent of and prior to the TCR beta chain. The data are consistent with the notion that in wild-type mice the DP stage is induced by transmembrane signaling through an immature CD3-TCR beta-chain complex, which can be bypassed by crosslinking of CD3 epsilon alone.


Blood ◽  
1987 ◽  
Vol 69 (3) ◽  
pp. 908-912
Author(s):  
J Jr Mirro ◽  
G Kitchingman ◽  
FG Behm ◽  
SB Murphy ◽  
RM Goorha

T cell differentiation was investigated by determining the relationship of T cell receptor (Ti) gene rearrangement and transcription to the expression of surface and cytoplasmic T3 antigen using blast cells from five children with acute lymphoblastic leukemia of thymic origin. Patterns of monoclonal antibody (MoAb) reactivity indicated that these cases were representative of the three recognized stages (I, II, III) of human thymocyte development. The T3 antigen, which becomes linked to the Ti to form a functional T cell receptor complex on mature thymocytes, was expressed on the cell surface in two cases (stage III). However, in the remaining three cases that were surface T3 negative (stages I and II), large amounts of T3 were identified in the cytoplasm by immunoperoxidase staining and flow cytometry. Leukemic blasts from all five patients showed rearranged genes encoding the beta-chain portion of the Ti heterodimer. RNA transcripts of Ti beta-chain genes were also evident in lymphoblasts from all five cases, but transcripts coding for the alpha-chain portion of Ti were found only in cases that expressed T3 on the cell surface. Thus the absence of surface T3 (and presumably Ti) coincides with the absence of Ti alpha-chain RNA, suggesting that transcription of alpha-chain genes is a critical regulatory event in the surface expression of the Ti-T3 complex. Leukemic T cells that rearrange and express Ti beta-chain genes but lack Ti alpha-chain messenger RNA (mRNA) may represent a stage of differentiation analogous to pre-B cells, where heavy-chain immunoglobulin (Ig) genes are rearranged and expressed but light-chain Ig genes are not expressed.


1993 ◽  
Vol 177 (2) ◽  
pp. 541-546 ◽  
Author(s):  
J H Park ◽  
R Mitnacht ◽  
N Torres-Nagel ◽  
T Hünig

The role of interleukin (IL)2 in intrathymic T cell development is highly controversial, and nothing is known about IL-2R expression on thymocytes of the T cell receptor (TCR) alpha/beta lineage undergoing TCR-driven differentiation events. We analyze here IL-2R alpha and beta mRNA expression in an in vitro system where newly generated rat CD4,8 double positive (DP) thymocytes respond to TCR ligation plus IL-2 (but not to either stimulus alone) with rapid differentiation to functional CD8 single positive T cells (Hünig, T., and R. Mitnacht. 1991. J. Exp. Med. 173:561). TCR ligation induced expression of IL-2R beta (but not alpha) chain mRNA in DP thymocytes. Addition of IL-2 then lead to functional maturation and expression of the IL-2R alpha chain. To investigate if the CD8 T cells generated via this IL-2R beta-driven pathway in vitro correspond to the bulk of CD8 T cells seeding peripheral lymphoid organs in vivo, we compared their phenotype to that of lymph node CD8 T cells. Surprisingly, analysis of CD8 cell surface expression using a novel anti-CD8 monoclonal antibody specific for the alpha/beta heterodimeric isoform, and of CD8 alpha and beta chain mRNA revealed that T cells generated by TCR ligation plus IL-2 resemble thymus-independent rather than thymus-derived CD8 cells in that they express CD8 alpha without beta chains. These findings demonstrate that TCR crosslinking induces functional IL-2R on immature DP rat thymocytes. In addition, they show that at least in vitro, CD8 alpha/alpha T cells are generated from TCR-stimulated DP thymocytes (which express the CD8 alpha/beta in the heterodimeric isoform) along an IL-2-driven pathway of T cell differentiation.


Blood ◽  
1994 ◽  
Vol 83 (3) ◽  
pp. 767-775 ◽  
Author(s):  
C Kasten-Sportes ◽  
S Zaknoen ◽  
RG Steis ◽  
WC Chan ◽  
EF Winton ◽  
...  

T-gamma lymphoproliferative disease (T-gamma LPD) is a chronic disorder of mature T cells that is associated with neutropenia and autoimmune phenomena. Although the progression of the lymphoproliferation is indolent, it is often associated with a monoclonal proliferation of T-cell-type large granular lymphocytes (LGL) that manifest multiple in vitro suppressor and cytotoxic activities. We considered the possibility that the granulocytopenia or anemia might represent an autoimmune disorder mediated by the monoclonal LGL via T-cell receptor (TCR) recognition of an antigen involved in hematopoiesis. Therefore, in an effort to characterize the usage of the TCR alpha-and beta-chain genes in patients with T-gamma LPD, we cloned and sequenced TCR alpha-and beta-chain mRNAs derived from the T-cell type LGL of five patients. The five patients studied did not use a common V alpha nor a common J alpha segment. However, an unusual finding was observed in one of the patients where the occurrence of a single variable-diversity-junctional (VDJ) rearrangement of the beta chain confirmed the monoclonal origin of the LGL proliferation. In accord with this evidence for monoclonality, many of the cells studied used a common V alpha (V alpha 19.1). In contrast to this common V alpha usage, there was a marked diversity of the J alpha segments and N-region addition that were associated with the V alpha 19.1 segment. This pattern of common V alpha usage associated with different N and J alpha segments suggests an immune-mediated selection process affecting the TCR alpha chain occurring after the transformation event that established the clone. We suggest that the T-cell-type LGL malignant clone might have developed autoreactivity conferred by the selected TCR alpha chain and that this autoreactivity might be implicated in this patient's anemia.


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