Recognition of Higher Order Patterns in Proteins: Immunologic Kernels

Bremel, Robert D.; Homan, E. Jane

doi:10.1371/journal.pone.0070115

Cited by 20 publications

(31 citation statements)

References 53 publications

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“…yielding a decamer peptide. This is consistent with prior observations that indicate that a decamer may be more likely to be initially excised than a nonamer (23). This selection process yielded a ranking of peptides for further study, where four were selected for testing.…”

Section: Resultssupporting

confidence: 93%

“…The amino acid substitutions in the exposed positions included P4: I>L, P5: N>Q, P6: F>I, A, L or Y, P7: E>D, P8: K>R. The B. melitensis proteome and the proteomes of an array of other pathogenic and microbiome bacteria were then searched to determine the occurrence of each of the alternate TCEM pentamer motifs P4-P8. Where a near neighbor was identified in B. melitensis , the flanking amino acids were noted, and the predicted binding to murine MHC I alleles was determined in the context of the native Brucella protein using previously described methods (21), and the probability of cathepsin cleavage at the C terminus of that peptide determined (22, 23).…”

Section: Methodsmentioning

confidence: 99%

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BrucellaPeptide Cross-Reactive MHC I Presentation Activates SIINFEKL-Specific TCR Expressing T Cells

Harms

Khan

Hall³

et al. 2018

Preprint

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Running Title: Brucella peptides are cross-reactive with SIINFEKL 7 8 ABSTRACT 25Brucella spp are intracellular pathogenic bacteria remarkable in their ability to escape 26 immune surveillance and therefore inflict a state of chronic disease within the host. To 27 enable further immune response studies, Brucella were engineered to express the well 28 characterized chicken ovalbumin (OVA). Surprisingly, we found that CD8 T cells bearing 29 T cell receptors (TCR) nominally specific for the OVA peptide SIINFEKL (OT-1) reacted 30 to parental Brucella-infected targets as well as OVA-expressing Brucella variants in 31 cytotoxicity assays. Furthermore, splenocytes from Brucella immunized mice produced 32 IFN- and exhibited cytotoxicity in response to SIINFEKL-pulsed target cells. To 33 determine if the SIINFEKL-reactive OT-1 TCR could be cross-reacting to Brucella 34 peptides, we searched the Brucella proteome using an algorithm to generate a list of 35 near-neighbor nonamer peptides that would bind to H2K b . Selecting five Brucella 36 peptide candidates, along with controls, we verified that several of these peptides 37 mimicked SIINFEKL resulting in T cell activation through the "SIINFEKL-specific" TCR. 38 3 Activation was dependent on peptide concentration as well as sequence. Our results 39 underscore the complexity and ubiquity of cross-reactivity in T cell recognition. This 40 cross-reactivity may enable microbes such as Brucella to escape immune surveillance 41 by presenting peptides similar to the host, and may also lead to the activation of 42 autoreactive T cells. 43 44 45 the Institutional Animal Care and Use Committee (IACUC) with strict adherence. 100 101 Cells and Cell culture. Brucella melitensis 16M strains and all Escherichia coli strains 102 used in this project were cultured in Brain Heart Infusion (BHI) broth or agar at 37C. 103 6 Mouse dendritic cell line DC 2.4 (H2K b ), and mouse monocyte cell line LADMAC were 104 cultured in RPMI supplemented with 10% FCS, and 1mM sodium pyruvate (R10) in a 105 humidified 37C incubator with 5% CO 2 . The B3Z CD8 + T cell hybridoma cell line, 106 specific for the SIINFEKL (OVA 257-264 /K b ) peptide of OVA, was a kind gift from Dr. J.D. 107 Sauer (University of Wisconsin-Madison). B3Z cells were cultured in R10 + 500 g/ml 108 G418 (Geneticin). Bone marrow derived macrophages (BMDM) were prepared by the 109 culturing of bone marrow cells from the tibia/fibula of mice in R10 conditioned with 20% 110 LADMAC supernatant. 111 112 Plasmid and transposon engineering. We used the EZ-Tn5™ (Lucigen) transposon 113 mutagenesis system for random insertion into the Brucella genome following the 114 manufacturer's recommended protocol. The insert was cloned into the transposon 115 construction vector pMOD™-3 so that rescue cloning could be 116 performed to determine the insertion site within the transformed Brucella. The partial 117 OVA sequence was amplified from the vector pPL2erm-ActA100-B8R-OVA (kind gift 118 from Dr. J.D. Sauer). Primers incorporated a B...

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Section: Resultssupporting

confidence: 93%

Section: Methodsmentioning

confidence: 99%

BrucellaPeptide Cross-Reactive MHC I Presentation Activates SIINFEKL-Specific TCR Expressing T Cells

Harms

Khan

Hall³

et al. 2018

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Adding more realism, there will be cooperative influences at different positions, leading to positional correlations in amino acid preferences and reducing the number of compatible peptides (69). But although the example is shown for 9-mers, longer peptides are processed, presented, and recognized, which will increase the number of compatible peptides (70).…”

Section: Rationalizing the Specificity/cross-reactivity Duality Of Tcrsmentioning

confidence: 99%

Emerging Concepts in TCR Specificity: Rationalizing and (Maybe) Predicting Outcomes

Singh

Riley

Baker

et al. 2017

The Journal of Immunology

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T cell specificity emerges from a myriad of processes, ranging from the biological pathways that control T cell signaling to the structural and physical mechanisms that influence how TCRs bind antigen/MHC. Of these processes, the binding specificity of the TCR is a key component. However, TCR specificity is enigmatic: TCRs are at once specific but also cross-reactive. Although long-appreciated, this duality continues to puzzle immunologists and has implications for the development of TCR-based therapeutics. Here we review TCR specificity, emphasizing results that have emerged from structural and physical studies of TCR binding. We show how the TCR specificity/cross-reactivity duality can be rationalized from structural and biophysical principles. There is excellent agreement between predictions from these principles and classic predictions about the scope of TCR cross-reactivity. We demonstrate how these same principles can also explain amino acid preferences in immunogenic epitopes and highlight opportunities for structural considerations in predictive immunology.

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“…In silico models based on these assumptions suggest that nearly half of CSF BCR variable regions from MS patients harbor potential antigenic idiotopes (9). These models included prediction of HLA-DR affinities (25,26), likelihood of endosomal processing by cysteine cathepsins (27,28) and modeling of tolerance likelihood based on T cell exposed motifs (TCEM) (9,29). It has previously been suggested that frequently occurring TCEM in variable regions (i.e., germline framework motifs) could be tolerogenic, while rare motifs [i.e., complementarity determining region (CDR) 3 or motifs resulting from mutations] potentially could be stimulatory to T cells (10,29).…”

Section: Introductionmentioning

confidence: 99%

“…The prediction models used to predict cathepsin cleavage, HLA affinity and TCEM of IGHV have been validated in silico (25)(26)(27)29), and for cathepsin cleavage also in vitro using monoclonal antibodies (28). It has however not been verified whether this or any other in silico model actually predicts a repertoire of idiotopes that actually have a corresponding T cell repertoire.…”

Section: Introductionmentioning

confidence: 99%

CD4+ T Cells in the Blood of MS Patients Respond to Predicted Epitopes From B cell Receptors Found in Spinal Fluid

et al. 2020

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B cells are important pathogenic players in multiple sclerosis (MS), but their exact role is not known. We have previously demonstrated that B cells from cerebrospinal fluid (CSF) of MS patients can activate T cells that specifically recognize antigenic determinants (idiotopes) from their B cell receptors (BCRs). The aim of this study was to evaluate whether in silico prediction models could identify antigenic idiotopes of immunoglobulin heavy-chain variable (IGHV) transcriptomes in MS patients. We utilized a previously assembled dataset of CSF IGHV repertoires from MS patients. To guide selection of potential antigenic idiotopes, we used in silico predicted HLA-DR affinity, endosomal processing, as well as transcript frequency from nine MS patients. Idiotopes with predicted low affinity and low likelihood of cathepsins cleavage were inert controls. Peripheral blood mononuclear cells from these patients were stimulated with the selected idiotope peptides in presence of anti-CD40 for 12 h. T cells were then labeled for activation status with anti-CD154 antibodies and CD3 + CD4 + T cells phenotyped as memory (CD45RO +) or naïve (CD45RO −), with potential for brain migration (CXCR3 and/or CCR6 expression). Anti-CD14 and-CD8 were utilized to exclude monocytes and CD8 + T cells. Unstimulated cells or insulin peptides were negative controls, and EBNA-1 peptides or CD3/CD28 beads were positive controls. The mean proportion of responding memory CD4 + T cells from all nine MS patients was significantly higher for idiotope peptides with predicted high HLA-DR affinity and high likelihood of cathepsin cleavage, than toward predicted inert peptides. Responses were mainly observed toward peptides affiliated with the CDR3 region. Activated memory CD4 + T cells expressed the chemokine receptor CCR6, affiliated with a Th17 phenotype and allowing passage into the central nervous system (CNS). This in vitro study suggests that that antigenic properties of BCR idiotopes can be identified in silico using HLA affinity and endosomal processing predictions. It further indicates that MS patients have a memory T cell repertoire capable of recognizing frequent BCR idiotopes found in endogenous CSF, and that these T cells express chemokine receptors allowing them to reach the CSF B cells expressing these idiotopes.

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Recognition of Higher Order Patterns in Proteins: Immunologic Kernels

Cited by 20 publications

References 53 publications

BrucellaPeptide Cross-Reactive MHC I Presentation Activates SIINFEKL-Specific TCR Expressing T Cells

BrucellaPeptide Cross-Reactive MHC I Presentation Activates SIINFEKL-Specific TCR Expressing T Cells

Emerging Concepts in TCR Specificity: Rationalizing and (Maybe) Predicting Outcomes

CD4+ T Cells in the Blood of MS Patients Respond to Predicted Epitopes From B cell Receptors Found in Spinal Fluid

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