scholarly journals Identification of a unique TCR repertoire, consistent with a superantigen selection process in Children with Multi-system Inflammatory Syndrome

2020 ◽  
Author(s):  
Rebecca A Porritt ◽  
Lisa Paschold ◽  
Magali Noval Rivas ◽  
Mary Hongying Cheng ◽  
Lael M Yonker ◽  
...  

SummaryMultisystem Inflammatory Syndrome in Children (MIS-C), a hyperinflammatory syndrome associated with SARS-CoV-2 infection, shares many clinical features with toxic shock syndrome, which is triggered by bacterial superantigens. The superantigen specificity for binding different Vβ-chains results in Vβ-skewing, whereby T cells with specific Vβ-chains and diverse antigen specificity are overrepresented in the TCR repertoire. Here, we characterized the TCR repertoire of MIS-C patients and found a profound expansion of TCR Beta Variable gene (TRBV)11-2. Furthermore, TRBV11-2 skewing was remarkably correlated with MIS-C severity and serum cytokine levels. Further analysis of TRBJ gene usage and CDR3 length distribution of MIS-C expanding TRBV11-2 clones revealed extensive junctional diversity, indicating a superantigen-mediated selection process for TRBV expansion. In silico modelling indicates that polyacidic residues in TCR Vβ11-2 engage in strong interactions with the superantigen-like motif of SARS-CoV-2 spike glycoprotein. Overall, our data indicate that the immune response in MIS-C is consistent with superantigenic activation.HighlightsMultisystem Inflammatory Disease in Children (MIS-C) patients exhibit T cell receptor (TCR) repertoire skewing, with expansion of T cell Receptor Beta Variable gene (TRBV)11-2TRBV11-2 skewing correlates with MIS-C severity and cytokine stormJ gene/CDR3 diversity in MIS-C patients is compatible with a superantigen selection processIn silico modelling indicates TCR Vβ11-2 engages in CDR3-independent interactions with the polybasic insert P681RRAR in the SAg-like motif of SARS-CoV-2 spike

2021 ◽  
Vol 12 ◽  
Author(s):  
Valentina Ceglia ◽  
Erin J. Kelley ◽  
Annalee S. Boyle ◽  
Sandra Zurawski ◽  
Heather L. Mead ◽  
...  

Common approaches for monitoring T cell responses are limited in their multiplexity and sensitivity. In contrast, deep sequencing of the T Cell Receptor (TCR) repertoire provides a global view that is limited only in terms of theoretical sensitivity due to the depth of available sampling; however, the assignment of antigen specificities within TCR repertoires has become a bottleneck. This study combines antigen-driven expansion, deep TCR sequencing, and a novel analysis framework to show that homologous ‘Clusters of Expanded TCRs (CETs)’ can be confidently identified without cell isolation, and assigned to antigen against a background of non-specific clones. We show that clonotypes within each CET respond to the same epitope, and that protein antigens stimulate multiple CETs reactive to constituent peptides. Finally, we demonstrate the personalized assignment of antigen-specificity to rare clones within fully-diverse uncultured repertoires. The method presented here may be used to monitor T cell responses to vaccination and immunotherapy with high fidelity.


2018 ◽  
Vol 36 (15_suppl) ◽  
pp. e15002-e15002 ◽  
Author(s):  
Timothy Looney ◽  
Elizabeth Linch ◽  
Geoffrey Lowman ◽  
Lauren Miller ◽  
Jianping Zheng ◽  
...  

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 4954-4954
Author(s):  
Claudio Fozza ◽  
Patrizia Virdis ◽  
Salvatore Contini ◽  
Giovanna Corda ◽  
Emanuele Angelucci ◽  
...  

Abstract Abstract 4954 Introduction: Patients with myelodysplastic syndromes (MDS) and acute myeloid leukaemia (AML) with multilineage dysplasia are known to display several immunological abnormalities. Azacitidine represents a therapeutic options for these disorders and, beside the well known effects on bone marrow precursors, has been demonstrated to potentially influence T-cell polarization. The aim of this study is to monitor the kinetic of the T-cell receptor (TCR) repertoire during Azacitidine treatment in order to explore its potential ability, not only to restore the hematopoietic function, but also to reverse the immune derangement typical of these patients. Methods: Our study consists in a flow cytometric and spectratyping analysis performed on the peripheral blood of 9 patients (4 with MDS and 5 with AML with multilineage dysplasia) and 30 normal controls. Each patient is evaluated at baseline and then every 3 cycles of Azacitidine. The flow cytometry analysis is based on a panel of 24 beta variable (BV) family-specific antibodies. A BV expansion is defined as any value of BV family expression higher than the mean + 3 standard deviations calculated in controls. We then analysed the profile of the third complementarity-determining-region (CDR3) in separated helper and cytotoxic T-cells by spectratyping. After immunomagnetic CD4+/CD8+ cell separation, RNA extraction and reverse transcriptase PCR, CDR3 fragment analysis was performed through capillary electrophoresis. Spectratyping evaluation was carried out by determining the percentage of Gaussian, missing, skewed and oligoclonal beta-variable (BV) subfamilies. Results: Our patients had a median of 3 assessments during their treatment with Azacitidine. At baseline, in CD4+ cells 5 patients did not show any lymphocyte expansion while 4 of them showed a single BV expansion. One of these expansions disappeared after 3 cycles while 3 were stable during treatment. When reassessed during therapy, 2 of the patients showed each the appearance of 3 new BV expansions, some of which however disappeared at the following evaluations. Overall CD4+ expansions during the all period of study were 10 (4 at baseline and 6 emerged during treatment) and their size ranged from 7. 1% in BV 13. 6 to 23. 9% in BV 11. Within the CD8+ subset, at baseline 6 out of 9 patients showed at least one T-cell expansion. In details 2 patients showed a single expansion while 4 of them displayed 2 different BV expansions. Of these 10 baseline expansions 6 were stable during treatment, while 4 of them quickly disappeared. Noteworthy, one of these expansions which had disappeared in a patient in remission reappeared at disease relapse. Six patients showed the appearance of a single BV expansion during treatment, which once again was usually transient. Overall CD8+ expansions during the all period of evaluation were 16 (10 at baseline and 6 emerged later) and their size ranged from 2. 5% in BV 5. 3 to 50. 1% in BV 3. Preliminary data on the spectratyping analysis showed a gradual improvement in the TCR repertoire diversity, due to the progressive reduction in the frequency of non Gaussian CDR3 profiles, especially remarkable as regards the number of missing BVs. Conclusions: Our findings firstly confirmed in our patients an overall derangement of the TCR repertoire. However this pattern seems to gradually improve during Azacitidine treatment, as witnessed by the disappearance of some BV expansions observed on flow cytometry -particularly within the CD8+ subset-, as well as by the progressive restoration of the CDR3 diversity detected by spectratyping. These preliminary data seem to suggest that Azacitidine could be potentially able, not only to restore the hematopoietic function, but also to reverse the immune derangement typical of patients with MDS and AML with multilineage dysplasia. Disclosures: No relevant conflicts of interest to declare.


2021 ◽  
Author(s):  
Valentina Ceglia ◽  
Erin J Kelley ◽  
Annalee S Boyle ◽  
Yves Levy ◽  
Gerard Zurawski ◽  
...  

Common approaches for monitoring T cell responses are limited in their multiplexity and sensitivity. In contrast, deep sequencing of the T Cell Receptor (TCR) repertoire offers a global view whose theoretical sensitivity is limited only by the depth of available sampling. However, assignment of antigen specificities within TCR repertoires has become a bottleneck. Here, we combine antigen-driven expansion, deep TCR sequencing and a novel analysis framework to show that homologous "Clusters of Expanded TCRs (CETs)" can be confidently identified without cell isolation, and assigned to antigen against a background of non-specific clones. We show that clonotypes within each CET respond to the same epitope, and that protein antigens stimulate multiple CETs reactive to constituent peptides. Finally, we demonstrate the personalized assignment of antigen-specificity to rare clones within fully-diverse unexpanded repertoires. The method presented here may be used to monitor T cell responses to vaccination and immunotherapy with high fidelity.


2021 ◽  
Author(s):  
Magdalena L Russell ◽  
Aisha Souquette ◽  
David M Levine ◽  
E Kaitlynn Allen ◽  
Guillermina Kuan ◽  
...  

Every T cell receptor (TCR) repertoire is shaped by a complex probabilistic tangle of genetically determined biases and immune exposures. T cells combine a random V(D)J recombination process with a selection process to generate highly diverse and functional TCRs. The extent to which an individual's genetic background is associated with their resulting TCR repertoire diversity has yet to be fully explored. Using a previously published repertoire sequencing dataset paired with high-resolution genome-wide genotyping from a large human cohort, we infer specific genetic loci associated with V(D)J recombination probabilities using genome-wide association inference. We show that V(D)J gene usage profiles are associated with variation in the TCRB locus and, specifically for the functional TCR repertoire, variation in the major histocompatibility complex locus. Further, we identify specific variations in the genes encoding the Artemis protein and the TdT protein to be associated with biasing junctional nucleotide deletion and N-insertion, respectively. These results refine our understanding of genetically-determined TCR repertoire biases by confirming and extending previous studies on the genetic determinants of V(D)J gene usage and providing the first examples of trans genetic variants which are associated with modifying junctional diversity. Together, these insights lay the groundwork for further explorations into how immune responses vary between individuals.


2012 ◽  
Vol 295 (6) ◽  
pp. 922-927 ◽  
Author(s):  
Jixi Wang ◽  
Aibing Wang ◽  
Heqing Zeng ◽  
Lantao Liu ◽  
Wenhao Jiang ◽  
...  

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Hongyi Zhang ◽  
Xiaowei Zhan ◽  
Bo Li

AbstractSimilarity in T-cell receptor (TCR) sequences implies shared antigen specificity between receptors, and could be used to discover novel therapeutic targets. However, existing methods that cluster T-cell receptor sequences by similarity are computationally inefficient, making them impractical to use on the ever-expanding datasets of the immune repertoire. Here, we developed GIANA (Geometric Isometry-based TCR AligNment Algorithm) a computationally efficient tool for this task that provides the same level of clustering specificity as TCRdist at 600 times its speed, and without sacrificing accuracy. GIANA also allows the rapid query of large reference cohorts within minutes. Using GIANA to cluster large-scale TCR datasets provides candidate disease-specific receptors, and provides a new solution to repertoire classification. Querying unseen TCR-seq samples against an existing reference differentiates samples from patients across various cohorts associated with cancer, infectious and autoimmune disease. Our results demonstrate how GIANA could be used as the basis for a TCR-based non-invasive multi-disease diagnostic platform.


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