LB17. Immunosequencing of the T-Cell Receptor Repertoire Reveals Signatures Specific for Diagnosis and Characterization of Early Lyme Disease

Abstract Background Changing climate and demographic trends have led to recent increases in the incidence of tick-borne illnesses. Early diagnosis of Lyme disease (LD) is critical for initiation of antibiotics to mitigate symptoms and prevent late manifestations. In patients not presenting with a typical erythema migrans rash, 2-tiered serologic testing is recommended to support a diagnosis of LD. However, 2-tiered testing is limited by ambiguity in interpretation and low sensitivity in early disease, highlighting an unmet clinical need for alternative diagnostic approaches. We identified a clinical signal for early LD based on evaluation of the T-cell response to B. burgdorferi infection. Methods We immunosequenced T-cell receptor (TCR) repertoires in blood samples from 3 independent cohorts of patients with laboratory-confirmed or clinically diagnosed early LD and endemic/non-endemic controls to identify 251 public, LD-associated TCRs. These TCRs were used to train a classifier that identified early LD with 99% specificity. Classifier sensitivity was evaluated in 211 LD cases and 2631 endemic controls and compared to that of standard 2-tiered testing (STTT). Biologic specificity was assessed by correlating TCR assay scores with clinical measures and by mapping the antigen specificity of Lyme-associated TCRs to B. burgdorferi antigens. Figure 1. LD-associated TCRs distinguish cases (orange) from controls (blue) in training cohorts. (A) Logistic-growth curve used to define a scoring function. (B) Positive-call threshold (99th percentile in endemic controls). Results In early LD, TCR testing demonstrated a 1.9-fold increase in sensitivity compared to STTT (56% vs 30%), with a 3.1-fold increase ≤4 days from the onset of symptoms (44% vs 14%). TCR positivity predicted subsequent seroconversion in 37% of initially STTT-negative patients, suggesting the T-cell response is detectable before the humoral response. While positivity for both tests declined following treatment, greater declines in posttreatment sensitivity were observed for STTT compared to TCR testing. Higher TCR scores were associated with measures of disease severity, including abnormal liver function tests, disseminated rash, and number of symptoms. A subset of LD-associated TCRs mapped to B. burgdorferi antigens, demonstrating the high specificity of a TCR immunosequencing approach. Figure 2. Validation of the TCR classifier in the JHU cohort and other holdout endemic controls. Distribution of model scores (A) and assay sensitivity (B). Model scores (C) and ROC (D) curves by serostatus. Figure 3. Clinical correlates of TCR scoring. (A) Liver function test; (B) lymphocyte count, (C) rash presentation, (D) number of symptoms. Conclusion T-cell-based testing has potential clinical utility as a sensitive and specific diagnostic for early LD, particularly in the initial days of illness. Disclosures Sudeb C. Dalai, MD, PhD, Adaptive Biotechnologies (Employee, Shareholder) Julia Greissl, PhD, Microsoft (Employee, Shareholder) Mitch Pesesky, PhD, Adaptive Biotechnologies (Employee, Shareholder) Allison W. Rebman, MPH, Global Lyme Alliance (Research Grant or Support)Steven and Alexandra Cohen Foundation (Research Grant or Support) Mark J. Soloski, PhD, NIH grant P30 AR070254 (Grant/Research Support)Steven and Alexandra Cohen Foundation (Research Grant or Support) Elizabeth J. Horn, PhD, Adaptive Biotechnologies (Research Grant or Support)Bay Area Lyme Foundation (Research Grant or Support)Lyme Disease Biobank (Employee)Steven and Alexandra Cohen Foundation (Research Grant or Support) Jennifer N. Dines, MD, Adaptive Biotechnologies (Employee, Shareholder) Rachel M. Gittelman, PhD, Adaptive Biotechnologies (Employee, Shareholder) Thomas M. Snyder, PhD, Adaptive Biotechnologies (Employee, Shareholder) Ryan O. Emerson, PhD, Adaptive Biotechnologies (Other Financial or Material Support, Employment with Adaptive Biotechnologies during the time of this study) Edward Meeds, PhD, Microsoft (Employee, Shareholder) Thomas Manley, MD, Adaptive Biotechnologies (Other Financial or Material Support, Declares employment with Adaptive Biotechnologies during the time of this study) Ian M. Kaplan, PhD, Adaptive Biotechnologies (Employee, Shareholder) Lance Baldo, MD, Adaptive Biotechnologies (Employee, Shareholder, Leadership Interest) Jonathan M. Carlson, PhD, Microsoft (Employee, Shareholder) Harlan S. Robins, PhD, Adaptive Biotechnologies (Board Member, Employee, Shareholder) John Aucott, MD, Adaptive Biotechnologies (Advisor or Review Panel member)Bay Area Lyme Foundation (Other Financial or Material Support, Scientific Advisory Board member)Department of Health and Human Services (Other Financial or Material Support, Past Chair, 2018, HHS Tick-borne Disease Working Group, Office of HIV/AIDS and Infectious Disease Policy, Office of the Assistant Secretary of Health)Expert testimony (Other Financial or Material Support, Expert testimony)Global Lyme Alliance (Research Grant or Support)Pfizer (Consultant)Steven and Alexandra Cohen Foundation (Research Grant or Support)Tarsus Pharmaceuticals (Consultant)

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Immunosequencing of the T-cell receptor repertoire reveals signatures specific for diagnosis and characterization of early Lyme disease

10.1101/2021.07.30.21261353 ◽

2021 ◽

Author(s):

Julia Greissl ◽

Mitch Pesesky ◽

Sudeb C. Dalai ◽

Alison W. Rebman ◽

Mark J. Soloski ◽

...

Keyword(s):

T Cell ◽

Lyme Disease ◽

T Cell Receptor ◽

Cell Response ◽

Fold Increase ◽

Cell Receptor ◽

The United States ◽

T Cell Response ◽

Severe Illness ◽

Lower Sensitivity

Lyme disease, the most common tick-borne illness in the United States, is most frequently caused by infection with Borrelia burgdorferi. Although early antibiotic treatment can prevent development of severe illness and late manifestations, diagnosis is challenging in patients who do not present with a typical erythema migrans rash. To support a diagnosis of Lyme disease in such cases, guidelines recommend 2-tiered serologic testing. However, 2-tiered testing has numerous limitations, including ambiguity in interpretation and lower sensitivity in early disease. We developed a diagnostic approach for Lyme disease based on the T-cell response to B. burgdorferi infection by immunosequencing T-cell receptor (TCR) repertoires in blood samples from 3 independent cohorts of patients with laboratory-confirmed or clinically diagnosed early Lyme disease, as well as endemic and non-endemic controls. We identified 251 public, Lyme-associated TCRs that were used to train a classifier for detection of early Lyme disease with 99% specificity. In a validation cohort of individuals with early Lyme disease, TCR testing demonstrated a 1.9-fold increase in sensitivity compared to standard 2-tiered testing (STTT; 56% versus 30%), with a 3.1-fold increase <=4 days from the onset of symptoms (44% versus 14%). TCR positivity predicted subsequent seroconversion in 37% of initially STTT-negative patients, suggesting that the T-cell response is detectable before the humoral response. While positivity for both tests declined after treatment, greater declines in posttreatment sensitivity were observed for STTT compared to TCR testing. Higher TCR scores were associated with clinical measures of disease severity, including abnormal liver function test results, disseminated rash, and number of symptoms. A subset of Lyme-associated TCRs mapped to B. burgdorferi antigens, demonstrating high specificity of a TCR immunosequencing approach. These results support the clinical utility of T-cell-based testing as a sensitive and specific diagnostic for early Lyme disease, particularly in the initial days of illness.

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Liver damage dampens anti-viral CD8 T cell response by inducing loss of surface T cell receptor expression

10.1055/s-0038-1677266 ◽

2019 ◽

Author(s):

V König ◽

K Manske ◽

S Kurz ◽

K Steiger ◽

PA Knolle ◽

...

Keyword(s):

T Cell ◽

T Cell Receptor ◽

Liver Damage ◽

Cell Response ◽

Cd8 T Cell ◽

Cell Receptor ◽

T Cell Response ◽

Receptor Expression

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Diacylglycerol Kinase alpha in X Linked Lymphoproliferative Disease Type 1

International Journal of Molecular Sciences ◽

10.3390/ijms22115816 ◽

2021 ◽

Vol 22 (11) ◽

pp. 5816

Author(s):

Suresh Velnati ◽

Sara Centonze ◽

Federico Girivetto ◽

Gianluca Baldanzi

Keyword(s):

T Cell ◽

T Cell Receptor ◽

Adaptor Protein ◽

Diacylglycerol Kinase ◽

Cell Receptor ◽

Lymphoproliferative Disease ◽

Disease Type ◽

T Cell Response ◽

Receptor Signalling

Diacylglycerol kinases are intracellular enzymes that control the balance between the secondary messengers diacylglycerol and phosphatidic acid. DGKα and DGKζ are the prominent isoforms that restrain the intensity of T cell receptor signalling by metabolizing PLCγ generated diacylglycerol. Thus, their activity must be tightly controlled to grant cellular homeostasis and refine immune responses. DGKα is specifically inhibited by strong T cell activating signals to allow for full diacylglycerol signalling which mediates T cell response. In X-linked lymphoproliferative disease 1, deficiency of the adaptor protein SAP results in altered T cell receptor signalling, due in part to persistent DGKα activity. This activity constrains diacylglycerol levels, attenuating downstream pathways such as PKCθ and Ras/MAPK and decreasing T cell restimulation induced cell death. This is a form of apoptosis triggered by prolonged T cell activation that is indeed defective in CD8+ cells of X-linked lymphoproliferative disease type 1 patients. Accordingly, inhibition or downregulation of DGKα activity restores in vitro a correct diacylglycerol dependent signal transduction, cytokines production and restimulation induced apoptosis. In animal disease models, DGKα inhibitors limit CD8+ expansion and immune-mediated tissue damage, suggesting the possibility of using inhibitors of diacylglycerol kinase as a new therapeutic approach.

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CD4+ T cells specific for glycoprotein B from cytomegalovirus exhibit extreme conservation of T-cell receptor usage between different individuals

Blood ◽

10.1182/blood-2007-04-079863 ◽

2008 ◽

Vol 111 (4) ◽

pp. 2053-2061 ◽

Cited By ~ 25

Author(s):

Laura Crompton ◽

Naeem Khan ◽

Rajiv Khanna ◽

Laxman Nayak ◽

Paul A. H. Moss

Keyword(s):

T Cells ◽

T Cell ◽

T Cell Receptor ◽

Cell Response ◽

Cd4 T Cells ◽

Clonal Selection ◽

Cell Receptor ◽

T Cell Response ◽

Cd4 T Cell ◽

Extreme Conservation

Antigen-specific CD8+ cytotoxic T cells often demonstrate extreme conservation of T-cell receptor (TCR) usage between different individuals, but similar characteristics have not been documented for CD4+ T cells. CD4+ T cells predominantly have a helper immune role, but a cytotoxic CD4+ T-cell subset has been characterized, and we have studied the cytotoxic CD4+ T-cell response to a peptide from human cytomegalovirus glycoprotein B presented through HLA-DRB*0701. We show that this peptide elicits a cytotoxic CD4+ T-cell response that averages 3.6% of the total CD4+ T-cell repertoire of cytomegalovirus-seropositive donors. Moreover, CD4+ cytotoxic T-cell clones isolated from different individuals exhibit extensive conservation of TCR usage, which indicates strong T-cell clonal selection for peptide recognition. Remarkably, this TCR sequence was recently reported in more than 50% of cases of CD4+ T-cell large granular lymphocytosis. Immunodominance of cytotoxic CD4+ T cells thus parallels that of CD8+ subsets and suggests that cytotoxic effector function is critical to the development of T-cell clonal selection, possibly from immune competition secondary to lysis of antigen-presenting cells. In addition, these TCR sequences are highly homologous to those observed in HLA-DR7+ patients with CD4+ T-cell large granular lymphocytosis and implicate cytomegalovirus as a likely antigenic stimulus for this disorder.

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The lew rat T cell response repertoire to an autoantigen and its regulation by anti-T cell receptor antibody

Journal of Neuroimmunology ◽

10.1016/0165-5728(87)90243-8 ◽

1987 ◽

Vol 16 (1) ◽

pp. 75

Author(s):

Ellen Heber-Katz ◽

Makoto Owhashi ◽

Mary Pat Happ

Keyword(s):

T Cell ◽

T Cell Receptor ◽

Cell Response ◽

Cell Receptor ◽

T Cell Response ◽

Receptor Antibody

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Generation of diversity in T cell receptor repertoire specific for pigeon cytochrome c.

Journal of Experimental Medicine ◽

10.1084/jem.165.2.279 ◽

1987 ◽

Vol 165 (2) ◽

pp. 279-301 ◽

Cited By ~ 63

Author(s):

S B Sorger ◽

S M Hedrick ◽

P J Fink ◽

M A Bookman ◽

L A Matis

Keyword(s):

T Cell ◽

Cytochrome C ◽

T Cell Receptor ◽

Cell Lines ◽

Dna Sequences ◽

Cell Receptor ◽

T Cell Response ◽

Beta Chain ◽

Antigen Specificity ◽

T Cell Lines

17 T cell clones and 3 T cell lines, specific for pigeon cytochrome c, were analyzed for fine specificity and rearranged T cell receptor (TCR) gene elements. Clones of similar fine specificities were grouped into one of four phenotypes, and correlations between phenotype differences and gene usage could be made. All the lines and clones rearranged a member of the V alpha 2B4 gene family to a limited number of J alpha regions. The beta chain was made up of one of three non-cross-hybridizing V beta regions, each rearranging to only one or two J beta s. The use of alternate V beta regions could be correlated with phenotype differences, which were manifested either as MHC- or MHC and antigen-specificity changes. In addition, the presence of alloreactivity, which defined a phenotype difference, could be correlated solely with the use of an alternate J alpha region. These observations were substantiated by prospective analyses of pigeon cytochrome c-specific T cell lines that were selected for alternate MHC specificity or alloreactivity and were found to express the correlated alpha and beta chain rearrangements. Previously, the TCR DNA sequences from two clones, each representing a variant of one phenotype, showed sequence differences only in the N regions of their TCR genes. Since only these two variants, using identical V alpha-J alpha and V beta-J beta gene elements, were repeatedly observed in this study, we would predict that the junctional diversity differences are selectable. In this T cell response, all the gene elements involved in the generation of diversity appear to be selected, and may therefore be important in the determination of TCR specificity. This high degree of receptor gene selection represents a fundamental difference from the diversity seen in several extensively analyzed antibody responses.

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Cross-recognition of HLA DR4 alloantigen by virus-specific CD8+ T cells: a new paradigm for self-/nonself-recognition

Blood ◽

10.1182/blood-2009-05-222596 ◽

2009 ◽

Vol 114 (11) ◽

pp. 2244-2253 ◽

Cited By ~ 48

Author(s):

Michael Rist ◽

Corey Smith ◽

Melissa J. Bell ◽

Scott R. Burrows ◽

Rajiv Khanna

Keyword(s):

T Cells ◽

T Cell ◽

T Cell Receptor ◽

Cd8 T Cells ◽

Allograft Rejection ◽

Functional Characterization ◽

Cell Receptor ◽

T Cell Response ◽

Cell Repertoire ◽

Diverse Range

Abstract The ability of CD8+ T cells to engage a diverse range of peptide–major histocompatibility complex (MHC) complexes can also lead to cross-recognition of self and nonself peptide-MHC complexes and thus directly contribute toward allograft rejection or autoimmunity. Here we present a novel form of cross-recognition by herpes virus–specific CD8+ cytotoxic T cells that challenges the current paradigm of self/non-self recognition. Functional characterization of a human leukocyte antigen (HLA) Cw*0602-restricted cytomegalovirus-specific CD8+ T-cell response revealed an unusual dual specificity toward a pp65 epitope and the alloantigen HLA DR4. This cross-recognition of HLA DR4 alloantigen was critically dependent on the coexpression of HLA DM and was preferentially directed toward the B-cell lineage. Furthermore, allostimulation of peripheral blood lymphocytes with HLA DRB*0401-expressing cells rapidly expanded CD8+ T cells, which recognized the pp65 epitope in the context of HLA Cw*0602. T-cell repertoire analysis revealed 2 dominant populations expressing T-cell receptor beta variable (TRBV)4-3 or TRBV13, with cross-reactivity exclusively mediated by the TRBV13+ clonotypes. More importantly, cross-reactive TRBV13+ clonotypes displayed markedly lower T-cell receptor binding affinity and a distinct pattern of peptide recognition, presumably mimicking a structure presented on the HLA DR4 allotype. These results illustrate a novel mechanism whereby virus-specific CD8+ T cells can cross-recognize HLA class II molecules and may contribute toward allograft rejection and/or autoimmunity.

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