Biological Analyses-Derived Translational Findings in the T Cell Receptor Alpha Chain Knockout Mouse as an Experimental Model for Ulcerative Colitis

Inflammatory bowel disease (IBD) is a group of chronic inflammatory disorders that affects many individuals throughout their lives. Ulcerative colitis (UC) and Crohn’s disease (CD) are two major forms of IBD. Until the early 1990s, a murine model of spontaneous chronic colitis was unavailable. As a major breakthrough in the basic research field of IBD, three genetically manipulated murine chronic colitis models, including interleukin (IL)-2 knockout (KO), IL-10 KO, and T cell receptor alpha chain (TCRα) KO models, were established in 1993. Since then, complicated immunobiological mechanisms during the development of UC have been gradually discovered by utilizing a wide variety of murine models of IBD, including the TCRα KO mouse model. In particular, it has been recognized that four major factors, including enteric, environmental, and immunological factors as well as enteric microbiota are highly and mutually involved in the pathogenesis of UC. As a pioneer of the TCRα KO murine model of UC, our group has identified that the interactions between the unique TCRα-β+ T cell population and antigen-presenting cells, including dendritic cells and B cells, play a key role for the development and regulation of UC-like chronic colitis, respectively. Here we have summarized clinically proven pathogenic and regulatory factors which have been identified by this novel TCRα KO murine model of UC in the past nearly three decades.

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

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.

Nine residues in HLA-DQ molecules determine with susceptibility and resistance to type 1 diabetes among young children in Sweden

HLA-DQ molecules account over 50% genetic risk of type 1 diabetes (T1D), but little is known about associated residues. Through next generation targeted sequencing technology and deep learning of DQ residue sequences, the aim was to uncover critical residues and their motifs associated with T1D. Our analysis uncovered (αa1, α44, α157, α196) and (β9, β30, β57, β70, β135) on the HLA-DQ molecule. Their motifs captured all known susceptibility and resistant T1D associations. Three motifs, “DCAA-YSARD” (OR = 2.10, p = 1.96*10−20), “DQAA-YYARD” (OR = 3.34, 2.69*10−72) and “DQDA-YYARD” (OR = 3.71, 1.53*10−6) corresponding to DQ2.5 and DQ8.1 (the latter two motifs) associated with susceptibility. Ten motifs were significantly associated with resistance to T1D. Collectively, homozygous DQ risk motifs accounted for 43% of DQ-T1D risk, while homozygous DQ resistant motifs accounted for 25% protection to DQ-T1D risk. Of the identified nine residues five were within or near anchoring pockets of the antigenic peptide (α44, β9, β30, β57 and β70), one was the N-terminal of the alpha chain (αa1), one in the CD4-binding region (β135), one in the putative cognate TCR-induced αβ homodimerization process (α157), and one in the intra-membrane domain of the alpha chain (α196). Finding these critical residues should allow investigations of fundamental properties of host immunity that underlie tolerance to self and organ-specific autoimmunity.