COVID-19 Patients Form Memory CD8+ T Cells that Recognize a Small Set of Shared Immunodominant Epitopes in SARS-CoV-2

Development of effective strategies to detect, treat, or prevent COVID-19 requires a robust understanding of the natural immune response to SARS-CoV-2, including the cellular response mediated by T cells. We used an unbiased, genome-wide screening technology, termed T-Scan, to identify specific epitopes in SARS-CoV-2 that are recognized by the memory CD8+ T cells of 25 COVID-19 convalescent patients, focusing on epitopes presented by the six most prevalent Human Leukocyte Antigen (HLA) types: A*02:01, A*01:01, A*03:01, A*11:01, A*24:02, and B*07:02. For each HLA type, the patients' T cells recognized 3-8 immunodominant epitopes that are broadly shared among patients. Remarkably, 94% of screened patients had T cells that recognized at least one of the three most dominant epitopes for a given HLA, and 53% of patients had T cells that recognized all three. Subsequent validation studies in 18 additional A*02:01 patients confirmed the presence of memory CD8+ T cells specific for the top six identified A*02:01 epitopes, and single-cell sequencing revealed that patients often have many different T cell clones targeting each epitope, but that the same T cell receptor Valpha regions are predominantly used to recognize these epitopes, even across patients. In total, we identified 29 shared epitopes across the six HLA types studied. T cells that target most of these immunodominant epitopes (27 of 29) do not cross-react with the endemic coronaviruses that cause the common cold, and the epitopes do not occur in regions with high mutational variation. Notably, only 3 of the 29 epitopes we identified reside in the spike protein, highlighting the need to design new classes of vaccines that recapitulate natural CD8+ T cell responses to SARS-CoV-2.

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ROR1 Specific T Cell Clones from Healthy Individuals Show Common T Cell Receptor Motifs

Blood ◽

10.1182/blood.v128.22.3364.3364 ◽

2016 ◽

Vol 128 (22) ◽

pp. 3364-3364

Author(s):

Falk Heidenreich ◽

Elke Ruecker-Braun ◽

Juliane S. Stickel ◽

Anne Eugster ◽

Denise Kühn ◽

...

Keyword(s):

Amino Acids ◽

T Cells ◽

T Cell ◽

Mhc Class I ◽

T Cell Receptor ◽

Cd8 T Cells ◽

Cd8 T Cell ◽

Cell Receptor ◽

T Cell Clones ◽

Cell Clones

Abstract Background Immunotherapy for CLL with new antibodies or T-cells with modified TCR relies on attractive targets. ROR1 is such a promising target since it is highly overexpressed in CLL. Chimeric antigen receptor engineered T cells and antibodies directed against the extracellular part of ROR1 have already been developed and tested in vitro or in animal models, but still there is no MHC-class I presented peptide serving as target structure for CD8+ T cells (with or without a genetically modified T cell receptor) available. Aim The aim of this study was (1) to identify an immunogenic MHC-class I presented ROR1 peptide, (2) to generate respective ROR1 peptide specific CD8+ T cell clones, and (3) to analyze the nucleotide sequence of the CDR3 region of the expressed alpha and beta T cell receptor chain. Results In mass spectrometric-based analyses of the HLA-ligandome a HLA-B*07 presented ROR1 peptide was identified in primary CLL cells of two patients. Six T cell clones specific for this particular ROR1-peptide were generated from single CD8+ T cells from 2 healthy individuals with 3 T cell clones generated from each donor. Functionality and specificity of those T cell clones were tested in cytotoxicity assays. All 6 dextramer+ CD8+ T cell clones lysed peptide loaded and HLA-B*07+ transduced K562 cells (kindly provided by Lorenz Jahn, [Jahn et al., Blood, 2015 Feb 5;125(6):949-58]). Two selected clones (XD8 and XB6) were tested for their cytotoxic potential against 2 ROR1+ HLA-B*07+ tumor cell lines (with the ROR1 peptide identified by mass spectrometry for both of them) and against 2 primary CLL cell samples. Tested clones showed a significant lysis of the respective target cells. CDR3 regions of the alpha and beta T cell receptor chain were sequenced on a single cell level. The CDR3 alpha region from each of the 3 ROR1 specific T cell clones from donor A showed some similarities to T cell clones derived from donor B (Table 1). Conclusion For the first time a MHC-class I presented ROR1 peptide antigen is reported. ROR1 positive CLL cells can be targeted by specific HLA-B*07 restricted CTLs. Respective CD8+ T cell clones with anti-leukemic activity from 2 donors share some amino acid motifs of the CDR3 alpha and beta regions. In conclusion, this information provides the possibility of generating ROR1 specific CD8+ T cells with genetically modified T cell receptors for immunotherapy and for tracking those cells after administration with next generation sequencing in peripheral blood samples of patients. Furthermore, data suggest the existence of public TCR motifs in leukemia antigen specific CTLs, which needs to be proven in follow-up experiments with larger cohorts of donors and patients. Finally, the presented strategy to identify leukemia specific peptide antigens for CD8+ T cells might be an attractive method for similar projects. Table 1 Amino acid sequences of CDR3 alpha and beta regions of the TCR of ROR1 specific CD8+ T cell clones. When comparing two clones, matching amino acids are depicted in red. The aromatic amino acids phenylalanine (F) and tyrosine (Y) are shown in blue when situated at the same position. Gaps inserted during the sequence alignment process are indicated by a hyphen '-'. Table 1. Amino acid sequences of CDR3 alpha and beta regions of the TCR of ROR1 specific CD8+ T cell clones. When comparing two clones, matching amino acids are depicted in red. The aromatic amino acids phenylalanine (F) and tyrosine (Y) are shown in blue when situated at the same position. Gaps inserted during the sequence alignment process are indicated by a hyphen '-'. Disclosures Middeke: Sanofi: Honoraria. Schetelig:Sanofi: Honoraria.

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Role of T cell receptor signaling in CD8 T cell memory

10.32469/10355/46871 ◽

2015 ◽

Author(s):

◽

Karin M. Knudson

Keyword(s):

T Cells ◽

T Cell ◽

T Cell Receptor ◽

Cd8 T Cells ◽

Immunological Memory ◽

Cell Receptor ◽

T Cell Memory ◽

Cell Memory ◽

Memory Cd8 T Cells ◽

Memory Differentiation

The generation of immunological memory is the basis for vaccination. The development of memory CD8 T cells is required for long-term protection against intracellular pathogens, such as viruses, and tumors. While the importance of memory generation has been recognized for over 30 years, the mechanism by which memory CD8 T cells arise during immune responses is still not fully understood. T cell receptor (TCR) interaction with antigen (immunogenic peptide)-bound MHC is necessary for activation and differentiation of CD8 T cells. Yet, how the resulting TCR signal regulates T cell memory is unknown. In this dissertation, we investigated the role that the TCR signal plays in memory differentiation. First, we explain how the strength of pMHC-TCR interaction affects memory generation. We also demonstrate that the signals for the development of memory are different depending on TCR ligand strength. Finally, we define a mechanism by which TCR signaling programs memory differentiation. All vaccines utilize pathogen-specific antigens to induce immunological memory. By understanding how antigenic signals program memory differentiation, it will be possible to specifically manipulate this process. We can then produce more effective and longer lasting memory cells.

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Single-cell sequencing reveals clonal expansions of pro-inflammatory synovial CD8 T cells expressing tissue-homing receptors in psoriatic arthritis

Nature Communications ◽

10.1038/s41467-020-18513-6 ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Frank Penkava ◽

Martin Del Castillo Velasco-Herrera ◽

Matthew D. Young ◽

Nicole Yager ◽

Lilian N. Nwosu ◽

...

Keyword(s):

T Cells ◽

Psoriatic Arthritis ◽

T Cell ◽

Single Cell ◽

T Cell Receptor ◽

Cd8 T Cells ◽

Cell Receptor ◽

Memory Cd8 T Cells ◽

Immune Mediated ◽

Cellular Immune

Abstract Psoriatic arthritis (PsA) is a debilitating immune-mediated inflammatory arthritis of unknown pathogenesis commonly affecting patients with skin psoriasis. Here we use complementary single-cell approaches to study leukocytes from PsA joints. Mass cytometry demonstrates a 3-fold expansion of memory CD8 T cells in the joints of PsA patients compared to peripheral blood. Meanwhile, droplet-based and plate-based single-cell RNA sequencing of paired T cell receptor alpha and beta chain sequences show pronounced CD8 T cell clonal expansions within the joints. Transcriptome analyses find these expanded synovial CD8 T cells to express cycling, activation, tissue-homing and tissue residency markers. T cell receptor sequence comparison between patients identifies clonal convergence. Finally, chemokine receptor CXCR3 is upregulated in the expanded synovial CD8 T cells, while two CXCR3 ligands, CXCL9 and CXCL10, are elevated in PsA synovial fluid. Our data thus provide a quantitative molecular insight into the cellular immune landscape of psoriatic arthritis.

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Regulatory CD8 T cells that recognize Qa-1 expressed by CD4 T-helper cells inhibit rejection of heart allografts

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1918950117 ◽

2020 ◽

Vol 117 (11) ◽

pp. 6042-6046 ◽

Cited By ~ 1

Author(s):

John Y. Choi ◽

Siawosh K. Eskandari ◽

Songjie Cai ◽

Ina Sulkaj ◽

Jean Pierre Assaker ◽

...

Keyword(s):

T Cells ◽

T Cell ◽

Cd8 T Cells ◽

Cytotoxic T Lymphocyte ◽

Human Leukocyte ◽

Cell Receptor ◽

Antibody Responses ◽

Heart Graft ◽

Transplanted Organs ◽

Class Ib

Induction of longstanding immunologic tolerance is essential for survival of transplanted organs and tissues. Despite recent advances in immunosuppression protocols, allograft damage inflicted by antibody specific for donor organs continues to represent a major obstacle to graft survival. Here we report that activation of regulatory CD8 T cells (CD8 Treg) that recognize the Qa-1 class Ib major histocompatibility complex (MHC), a mouse homolog of human leukocyte antigen-E (HLA-E), inhibits antibody-mediated immune rejection of heart allografts. We analyzed this response using a mouse model that harbors a point mutation in the class Ib MHC molecule Qa-1, which disrupts Qa-1 binding to the T cell receptor (TCR)–CD8 complex and impairs the CD8 Treg response. Despite administration of cytotoxic T lymphocyte antigen 4 (CTLA-4) immunoglobulin (Ig), Qa-1 mutant mice developed robust donor-specific antibody responses and accelerated heart graft rejection. We show that these allo-antibody responses reflect diminished Qa-1–restricted CD8 Treg-mediated suppression of host follicular helper T cell-dependent antibody production. These findings underscore the critical contribution of this Qa-1/HLA-E-dependent regulatory pathway to maintenance of transplanted organs and suggest therapeutic approaches to ameliorate allograft rejection.

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T Cell–Independent Interleukin 15rα Signals Are Required for Bystander Proliferation

Journal of Experimental Medicine ◽

10.1084/jem.194.8.1187 ◽

2001 ◽

Vol 194 (8) ◽

pp. 1187-1194 ◽

Cited By ~ 131

Author(s):

James P. Lodolce ◽

Patrick R. Burkett ◽

David L. Boone ◽

Marcia Chien ◽

Averil Ma

Keyword(s):

T Cells ◽

T Cell ◽

Cd8 T Cells ◽

Bone Marrow Cells ◽

Cd8 T Cell ◽

Cell Receptor ◽

Poly I:C ◽

T Cell Homeostasis ◽

Memory Cd8 T Cells

Cytokine driven or “bystander” proliferation of T cells occurs in vivo independently of major histocompatibility complex–T cell receptor interactions. This process may be important for supporting T cell homeostasis and facilitating T cell responses to microbial antigens, and may involve the cytokine interleukin (IL)-15. In this study, we find that IL-15Rα–deficient (IL-15Rα−/−) mice fail to undergo poly I:C or IL-15 driven bystander proliferation of CD8+ T cells. Surprisingly, IL-15Rα−/− CD8+ T cells proliferate in response to poly I:C when adoptively transferred into normal mice, and normal CD8+ T cells fail to proliferate in IL-15Rα−/− mice. Normal mice reconstituted with IL-15Rα−/− bone marrow cells also fail to exhibit bystander responses. Thus, CD8+ T cell independent IL-15Rα signals from radiation sensitive hematopoietic cells are likely required for bystander responses. Moreover, normal CD8+ T cells proliferate in IL-15Rα−/− mice after treatment with IL-15. Therefore, IL-15Rα signals may mediate a positive feedback loop involving the further physiological production of IL-15. These findings provide new insights into how IL-15Rα supports memory phenotype CD8+ T cell proliferation, and suggest novel mechanisms by which memory CD8+ T cells are maintained in vivo.

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Human CD8+ T cells store CXCR1 in a distinct intracellular compartment and up-regulate it rapidly to the cell surface upon activation

Blood ◽

10.1182/blood-2005-04-1366 ◽

2005 ◽

Vol 106 (12) ◽

pp. 3718-3724 ◽

Cited By ~ 16

Author(s):

Olivier Gasser ◽

Anna Missiou ◽

Ceylan Eken ◽

Christoph Hess

Keyword(s):

T Cells ◽

T Cell ◽

Cell Surface ◽

Cd8 T Cells ◽

Chemokine Receptors ◽

Secretory Pathway ◽

Cell Receptor ◽

Intracellular Compartment ◽

Memory Cd8 T Cells ◽

Activated Neutrophils

Activation and subsequent differentiation of naive CD8+ T cells lead to the development of memory subsets with distinct homing and effector capacities. On nonlymphoid homing subsets, expression of “inflammatory” chemokine receptors (such as CXCR3, CCR5, CX3CR1, and CXCR1) is believed to promote migration into sites of infection/inflammation. Here we show that CXCR1 can be up-regulated to the cell surface within minutes of activating human CD8+ T cells. No concurrent up-regulation of other inflammatory chemokine receptors was observed. Up-regulation of CXCR1 preferentially occurred on central memory CD8+ T cells—that is, cells with a lymph node homing phenotype—and was functionally relevant. Immunofluorescence microscopy showed CXCR1 to be present in intracellular vesicles that do not significantly colocalize with perforin, RANTES (regulated upon activation normal T cell expressed and secreted), or the lysosomal marker CD63. By contrast, partial colocalization with the Golgi marker GM130, the constitutive secretory pathway marker β2-microglobulin, and the early endosome marker EEA1 was observed. Up-regulation of CXCR1 did not occur after T-cell receptor cross-linking. By contrast, supernatants from activated neutrophils, but not from monocytes or dendritic cells, induced its up-regulation. These results suggest that CD8+ T cells can rapidly adapt their homing properties by mobilizing CXCR1 from a distinct intracellular compartment.

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CD8+ T cell signature in acute SARS-CoV-2 infection identifies memory precursors

10.1101/2021.07.22.453029 ◽

2021 ◽

Author(s):

Sarah Adamo ◽

Jan Michler ◽

Yves Zurbuchen ◽

Carlo Cervia ◽

Patrick Taeschler ◽

...

Keyword(s):

T Cells ◽

T Cell ◽

Cd8 T Cells ◽

Acute Infection ◽

Mammalian Target Of Rapamycin ◽

Cell Receptor ◽

Effector Memory ◽

Memory Cd8 T Cells ◽

Transcriptional Signature ◽

One Year

Immunological memory is a hallmark of adaptive immunity and facilitates an accelerated and enhanced immune response upon re-infection with the same pathogen. Since the outbreak of the ongoing coronavirus disease 19 (COVID-19) pandemic, a key question has focused on whether severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific T cells stimulated during acute infection give rise to long-lived memory T cells. Using spectral flow cytometry combined with cellular indexing of transcriptomes and T cell receptor (TCR) sequencing we longitudinally characterize individual SARS-CoV-2-specific CD8+ T cells of COVID-19 patients from acute infection to one year into recovery and find a distinct signature identifying long-lived memory CD8+ T cells. SARS-CoV-2-specific memory CD8+ T cells persisting one year after acute infection re-express CD45RA and interleukin-7 receptor alpha (CD127), upregulate T cell factor-1 (TCF1), and maintain low CCR7, thus resembling CD45RA+ effector-memory T (TEMRA) cells. Tracking individual clones of SARS-CoV-2-specific CD8+ T cells, we reveal that an interferon signature marks clones giving rise to long-lived cells, whereas prolonged proliferation and mammalian target of rapamycin (mTOR) signaling are associated with clone contraction and disappearance. Collectively, we identify a transcriptional signature differentiating short- from long-lived memory CD8+ T cells following an acute virus infection in humans.

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Single-cell sequencing reveals a clonal expansion of pro-inflammatory synovial CD8 T cells expressing tissue homing receptors in psoriatic arthritis

10.1101/704494 ◽

2019 ◽

Author(s):

Frank Penkava ◽

Martin Del Castillo Velasco-Herrera ◽

Matthew D Young ◽

Nicole Yager ◽

Alicia Lledo Lara ◽

...

Keyword(s):

T Cells ◽

Psoriatic Arthritis ◽

T Cell ◽

Single Cell ◽

Cd8 T Cells ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Developmental State ◽

Cell Receptor ◽

Memory Cd8 T Cells

AbstractPsoriatic arthritis (PsA) is a debilitating immune-mediated inflammatory arthritis of unknown pathogenesis commonly affecting patients with skin psoriasis. We used three complementary single cell approaches to study leukocytes from PsA joints. Mass cytometry (CyTOF) demonstrated marked (>3 fold) expansion of memory CD8 T cells in the joints compared to matched blood. Further exploration of the memory CD8 compartment using both droplet and plate based single cell RNA sequencing of paired alpha and beta chain T cell receptor sequences identified pronounced CD8 T cell clonal expansions within the joints, strongly suggesting antigen driven expansion. These clonotypes exhibited distinct gene expression profiles including cycling, activation, tissue homing and tissue residency markers. Pseudotime analysis of these clonal CD8 populations identified trajectories in which tissue residency can represent an intermediate developmental state giving rise to activated, cycling and exhausted CD8 populations. Comparing T-cell clonality across patients further revealed specificity convergence of clones against a putative common antigen. We identify chemokine receptor CXCR3 as upregulated in expanded synovial clones, and elevation of two CXCR3 ligands, CXCL9 and CXCL10, in PsA synovial fluid.

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T cell receptor and IL-2 signaling strength control memory CD8+ T cell functional fitness via chromatin remodeling

10.1101/2021.10.19.464978 ◽

2021 ◽

Author(s):

Shu Shien Chin ◽

Erik Guillen ◽

Laurent Chorro ◽

Sooraj Achar ◽

Susanne Oberle ◽

...

Keyword(s):

Cell Cycle ◽

T Cells ◽

T Cell ◽

T Cell Receptor ◽

Cd8 T Cells ◽

Cd8 T Cell ◽

Cell Receptor ◽

Chromatin Accessibility ◽

Functional Fitness ◽

Memory Cd8 T Cells

Cognate antigen signal controls CD8+ T cell priming, expansion size and effector versus memory cell fates, but it is not known if and how it modulates the functional features of memory CD8+ T cells. Here we show that the strength of T cell receptor (TCR) signaling determines the requirement for interleukin-2 (IL-2) signals to form a pool of memory CD8+ T cells that competitively re-expand upon secondary antigen encounter. Combining strong TCR and intact IL-2 signaling synergistically induces genome-wide chromatin accessibility in regions targeting a wide breadth of biological processes, consistent with their greater functional fitness. Chromatin accessibility in promoters of genes encoding for stem cell, cell cycle and calcium-related proteins correlated with faster intracellular calcium accumulation, initiation of cell cycle and more robust expansion. High-dimensional flow-cytometry analysis also highlights higher subset diversity and phenotypes. These results formally establish that epitope selection in vaccine design strongly impacts memory CD8+ T cell epigenetic programming and functions.

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Clonal cytotoxic T cells are expanded in myeloma and reside in the CD8+CD57+CD28− compartment

Blood ◽

10.1182/blood.v98.9.2817 ◽

2001 ◽

Vol 98 (9) ◽

pp. 2817-2827 ◽

Cited By ~ 96

Author(s):

Daniel M.-Y. Sze ◽

Gillian Giesajtis ◽

Ross D. Brown ◽

Maria Raitakari ◽

John Gibson ◽

...

Keyword(s):

T Cells ◽

T Cell ◽

Cd8 T Cells ◽

Cytotoxic T Cells ◽

Variable Region ◽

Cell Receptor ◽

Cell Clones ◽

Apoptotic Marker ◽

Cd8 Cell ◽

Length Analysis

Abstract The occurrence of clonal T cells in multiple myeloma (MM), as defined by the presence of rearrangements in the T-cell receptor (TCR)–β chains detected on Southern blotting, is associated with an improved prognosis. Recently, with the use of specific anti–TCR-variable-β (anti–TCRVβ) antibodies, the presence in MM patients of expanded populations of T cells expressing particular Vβ regions was reported. The majority of these T-cell expansions have the phenotype of cytotoxic T cells (CD8+CD57+ and perforin positive). Since Vβ expansions can result from either a true clonal population or a polyclonal response, the clonality of CD8+TCRVβ+ T cells was tested by TCRVβ complementarity-determining region 3 length analysis and DNA sequencing of the variable region of the TCR. In this report, the CD57+ and CD57− subpopulations within expanded TCRVβ+CD8+ cell populations are compared, and it is demonstrated that the CD57+ subpopulations are generally monoclonal or biclonal, whereas the corresponding CD57− cells are frequently polyclonal. The oligoclonality of CD57+ expanded CD8+ T cells but not their CD57− counterparts was also observed in age-matched controls, in which the T-cell expansions were mainly CD8−. The CD8+CD57+ clonal T cells had a low rate of turnover and expressed relatively lower levels of the apoptotic marker CD95 than their CD57− counterparts. Taken together, these findings demonstrate that MM is associated with CD57+CD8+ T-cell clones, raising the possibility that the expansion and accumulation of activated clonal CD8+ T cells in MM may be the result of persistent stimulation by tumor-associated antigens, combined with a reduced cellular death rate secondary to reduced expression of the apoptosis-related molecule CD95.

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