scholarly journals Simultaneously inferring T cell fate and clonality from single cell transcriptomes

2015 ◽  
Author(s):  
Michael J.T. Stubbington ◽  
Tapio Lönnberg ◽  
Valentina Proserpio ◽  
Simon Clare ◽  
Anneliese O. Speak ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Cell Fate ◽  
T Lymphocyte ◽  
Cell Receptor ◽  
Computational Method ◽  
Antigen Specificity ◽  
Synthetic Genome ◽  
Genome Library ◽  
Lineage Markers

The heterodimeric T cell receptor (TCR) comprises two protein chains that pair to determine the antigen specificity of each T lymphocyte. The enormous sequence diversity within TCR repertoires allows specific TCR sequences to be used as lineage markers for T cells that derive from a common progenitor. We have developed a computational method, called TraCeR, to reconstruct full­length, paired TCR sequences from T lymphocyte single­cell RNA­seq by combining existing assembly and alignment programs with a “synthetic genome” library comprising all possible TCR sequences. We validate this method with PCR to quantify its accuracy and sensitivity, and compare to other TCR sequencing methods. Our inferred TCR sequences reveal clonal relationships between T cells, which we put into the context of each cell’s functional state from the complete transcriptional landscape quantified from the remaining RNA­seq data. This provides a powerful tool to link T cell specificity with functional response in a variety of normal and pathological conditions. We demonstrate this by determining the distribution of members of expanded T cell clonotypes in response to Salmonella​ infection in the mouse. We show that members of the same clonotype span early activated CD4+ T cells, as well as mature effector and memory cells.

scholarly journals In Vivo Selection of T-Cell Receptor Junctional Region Sequences by HLA-A2 Human T-Cell Lymphotropic Virus Type 1 Tax11-19 Peptide Complexes

2001 ◽  
Vol 75 (2) ◽  
pp. 1065-1071 ◽  
Author(s):  
Mineki Saito ◽  
Graham P. Taylor ◽  
Akiko Saito ◽  
Yoshitaka Furukawa ◽  
Koichiro Usuku ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
T Cell Receptor ◽  
Virus Type ◽  
Cell Receptor ◽  
Antigen Specificity ◽  
Human T Cell ◽  
Cdr3 Region

ABSTRACT Using HLA-peptide tetrameric complexes, we isolated human T-cell lymphotrophic virus type 1 Tax peptide-specific CD8+ T cells ex vivo. Antigen-specific amino acid motifs were identified in the T-cell receptor Vβ CDR3 region of clonally expanded CD8+ T cells. This result directly confirms the importance of the CDR3 region in determining the antigen specificity in vivo.

scholarly journals Single-cell transcriptomics identifies multiple pathways underlying antitumor function of TCR- and CD8αβ-engineered human CD4+ T cells

2020 ◽  
Vol 6 (27) ◽  
pp. eaaz7809 ◽  
Author(s):  
Jan A. Rath ◽  
Gagan Bajwa ◽  
Benoit Carreres ◽  
Elisabeth Hoyer ◽  
Isabelle Gruber ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Single Cell ◽  
Cell Function ◽  
Xenograft Model ◽  
Cell Receptor ◽  
Target Cells ◽  
Antigen Specificity ◽  
Molecular Features ◽  
Mouse Xenograft Model

Transgenic coexpression of a class I–restricted tumor antigen–specific T cell receptor (TCR) and CD8αβ (TCR8) redirects antigen specificity of CD4+ T cells. Reinforcement of biophysical properties and early TCR signaling explain how redirected CD4+ T cells recognize target cells, but the transcriptional basis for their acquired antitumor function remains elusive. We, therefore, interrogated redirected human CD4+ and CD8+ T cells by single-cell RNA sequencing and characterized them experimentally in bulk and single-cell assays and a mouse xenograft model. TCR8 expression enhanced CD8+ T cell function and preserved less differentiated CD4+ and CD8+ T cells after tumor challenge. TCR8+CD4+ T cells were most potent by activating multiple transcriptional programs associated with enhanced antitumor function. We found sustained activation of cytotoxicity, costimulation, oxidative phosphorylation– and proliferation-related genes, and simultaneously reduced differentiation and exhaustion. Our study identifies molecular features of TCR8 expression that can guide the development of enhanced immunotherapies.

scholarly journals T cell and non-T cell compartments can independently determine resistance to Leishmania major.

1995 ◽  
Vol 181 (3) ◽  
pp. 845-855 ◽  
Author(s):  
A H Shankar ◽  
R G Titus
Keyword(s):  
T Cells ◽  
T Cell ◽  
T Cell Receptor ◽  
Leishmania Major ◽  
Cell Receptor ◽  
Disease Outcome ◽  
Chimeric Mice ◽  
Antigen Specificity ◽  
Ifn Gamma ◽  
Cell Compartments

In experimental murine cutaneous leishmaniasis caused by Leishmania major (Lm), the cellular determinants governing development of protective or exacerbative T cells are not well understood. We, therefore, attempted to determine the influence of T cell and non-T cell compartments on disease outcome. To this end, T cell chimeric mice were constructed using adult thymectomized lethally irradiated, bone marrow-reconstituted (ATXBM) animals of genetically resistant, C57BL/6, or susceptible, BALB/c, backgrounds. These hosts were engrafted with naive T cell populations from H-2-congenic susceptible, BALB.B6-H-2b, or resistant, C57BL/6.C-H-2d, animals, respectively. Chimeric mice were then infected with Lm, and disease outcome was monitored. BALB/c T cell chimeric mice, BALB/c ATXBM hosts given naive C57BL/6.C-H-2d T cells, resolved their infections as indicated by reductions in both lesion size and parasite numbers. Furthermore, the mice developed typical Th1 (interferon[IFN]-gamma hiinterleukin[IL]-4lo) cytokine patterns. In contrast, both sham chimeric, BALB/c ATXBM hosts given naive BALB/c T cells, and control irradiated euthymic mice succumbed to infection, producing Th2 profiles (IFN-gamma loIL-4hiIL-10hi). C57BL/6 T cell chimeras, C57BL/6 ATXBM hosts given naive BALB.B6-H-2b T cells, resolved their infections as did C57BL/6 sham chimeras and euthymic controls. Interestingly, whereas C57BL/6 control animals produced Th1 cytokines, chimeric animals progressed from Th0 (IFN-gamma hiIL-4hiIL-10hi) to Th2 (IFN-gamma loIL-4hiIL-10hi) cytokine profiles as cure ensued. Both reconstitution and chimeric status of all mice were confirmed by flow cytometry. In addition, T cell receptor V beta usage of Lm-specific blasts was determined. In all cases, V beta use was multiclonal, involving primarily V beta 2, 4, 6, 8.1, 8.2, 8.3, 10, and 14, with relative V beta frequencies differing between H-2b and H-2d animals. Most importantly, however, these differences did not segregate between cure and noncure outcomes. These findings indicate that: (a) genetic traits determining cure in Lm infection can direct disease outcome from both T cell and non-T cell compartments; (b) the presence of the curing genotype in only one compartment is sufficient to confer cure; (c) curing genotype T cells autonomously assume a Th1 cytokine profile-mediating cure; (d) noncuring genotype T cells can mediate cure in a curing environment, despite the onset of Th2 cytokine production; and lastly, (e) antigen specificity of responding T cells, as assessed by V beta T cell receptor diversity, is not a critical determinant of disease outcome.

scholarly journals Priming of T cells to Fas-mediated proliferative signals by interleukin-7

Blood ◽  
2008 ◽  
Vol 112 (4) ◽  
pp. 1195-1204 ◽  
Author(s):  
Bence Rethi ◽  
Nancy Vivar ◽  
Stefano Sammicheli ◽  
Caroline Fluur ◽  
Nicolas Ruffin ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
T Lymphocyte ◽  
Cell Receptor ◽  
Cell Depletion ◽  
Activated T Cells ◽  
T Cell Depletion ◽  
Interleukin 7 ◽  
Costimulatory Signals ◽  
Opposing Effects

Abstract T-cell depletion associated with HIV infection or cytoreductive therapies triggers potential T-cell regenerative mechanisms such as peripheral T-lymphocyte expansion to weak antigenic stimuli and the increased availability of interleukin-7 (IL-7), a cytokine with potent antiapoptotic and proliferative activities. Deleterious mechanisms also associated with lymphopenia, such as increased Fas expression and apoptosis of T cell, however, may result in opposing effects. In this study, we show that Fas molecules, primarily associated with T-cell depletion in lymphopenic settings, may also contribute to compensatory T-cell expansion through transmitting costimulatory signals to suboptimally activated T cells. Proliferation of T lymphocytes in response to concomitant Fas and T-cell receptor (TCR) triggering was shown to be increased in HIV-infected individuals compared with noninfected controls. As IL-7 levels are often elevated in lymphopenic individuals in association with increased Fas expression, we analyzed whether IL-7 would influence Fas-mediated proliferative signals in T cells. We show that IL-7 is able to increase the efficacy of Fas to induce proliferation of suboptimally activated T cells. Thus, high IL-7 levels associated with lymphopenic conditions may simultaneously induce sensitivity to Fas-mediated apoptosis in nonactivated T cells and increase Fas-induced costimulatory signals in T cells recognizing low-affinity antigens.

THE FATE OF DONOR T-CELL RECEPTOR TRANSGENIC T CELLS WITH KNOWN HOST ANTIGEN SPECIFICITY IN A GRAFT-VERSUS-HOST DISEASE MODEL1

1999 ◽  
Vol 68 (1) ◽  
pp. 141-149 ◽  
Author(s):  
Bimalangshu Dey ◽  
Yong-Guang Yang ◽  
Frederic Preffer ◽  
Akira Shimizu ◽  
Kirsten Swenson ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
T Cell Receptor ◽  
Graft Versus Host Disease ◽  
Cell Receptor ◽  
Antigen Specificity ◽  
Host Disease ◽  
Graft Versus Host

scholarly journals Ligation of Cytotoxic T Lymphocyte Antigen-4 to T Cell Receptor Inhibits T Cell Activation and Directs Differentiation into Foxp3+Regulatory T Cells

2012 ◽  
Vol 287 (14) ◽  
pp. 11098-11107 ◽  
Author(s):  
Jozsef Karman ◽  
Ji-Lei Jiang ◽  
Nathan Gumlaw ◽  
Hongmei Zhao ◽  
Juanita Campos-Rivera ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Regulatory T Cells ◽  
T Cell Receptor ◽  
T Cell Activation ◽  
T Lymphocyte ◽  
Cell Activation ◽  
Cytotoxic T Lymphocyte ◽  
Cell Receptor ◽  
Lymphocyte Antigen

scholarly journals Repertoire Development and the Control of Cytotoxic/Effector Function in HumanγδT Cells

2010 ◽  
Vol 2010 ◽  
pp. 1-11 ◽  
Author(s):  
Elizabeth M. Urban ◽  
Andrei I. Chapoval ◽  
C. David Pauza
Keyword(s):  
T Cells ◽  
T Cell ◽  
Human Peripheral Blood ◽  
Cell Subset ◽  
Cell Receptor ◽  
Effector Function ◽  
Repertoire Selection ◽  
Cd56 Expression ◽  
Lineage Markers ◽  
Cytotoxic Effector

T cells develop into two major populations distinguished by their T cell receptor (TCR) chains. Cells with theαβTCR generally express CD4 or CD8 lineage markers and mostly fall into helper or cytotoxic/effector subsets. Cells expressing the alternateγδTCR in humans generally do not express lineage markers, do not require MHC for antigen presentation, and recognize nonpeptidic antigens. We are interested in the dominant Vγ2Vδ2+ T cell subset in human peripheral blood and the control of effector function in this population. We review the literature onγδT cell generation and repertoire selection, along with recent work on CD56 expression and defining a cytotoxic/effector lineage within the phosphoantigen-reactive Vγ2Vδ2 cells. A unique mechanism for MHC-independent repertoire selection is linked to the control of effector function that is vital to the role forγδT cells in tumor surveillance. Better understanding of these mechanisms will improve our ability to exploit this population for tumor immunotherapy.

scholarly journals PD-1 preferentially inhibits the activation of low-affinity T cells

2021 ◽  
Vol 118 (35) ◽  
pp. e2107141118
Author(s):  
Kenji Shimizu ◽  
Daisuke Sugiura ◽  
Il-mi Okazaki ◽  
Takumi Maruhashi ◽  
Tatsuya Takemoto ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Signal Strength ◽  
Cell Receptor ◽  
Antigen Specificity ◽  
Inhibitory Effects ◽  
Response Characteristics ◽  
Cell Responses ◽  
Inducible Genes ◽  
Deficient Mice

Anti–PD-1 therapies can activate tumor-specific T cells to destroy tumors. However, whether and how T cells with different antigen specificity and affinity are differentially regulated by PD-1 remain vaguely understood. Upon antigen stimulation, a variety of genes is induced in T cells. Recently, we found that T cell receptor (TCR) signal strength required for the induction of genes varies across different genes and PD-1 preferentially inhibits the induction of genes that require stronger TCR signal. As each T cell has its own response characteristics, inducibility of genes likely differs across different T cells. Accordingly, the inhibitory effects of PD-1 are also expected to differ across different T cells. In the current study, we investigated whether and how factors that modulate T cell responsiveness to antigenic stimuli influence PD-1 function. By analyzing TCRs with different affinities to peptide–MHC complexes (pMHC) and pMHCs with different affinities to TCR, we demonstrated that PD-1 inhibits the expression of TCR-inducible genes efficiently when TCR:pMHC affinity is low. In contrast, affinities of peptides to MHC and MHC expression levels did not affect PD-1 sensitivity of TCR-inducible genes although they markedly altered the dose responsiveness of T cells by changing the efficiency of pMHC formation, suggesting that the strength of individual TCR signal is the key determinant of PD-1 sensitivity. Accordingly, we observed a preferential expansion of T cells with low-affinity to tumor-antigen in PD-1–deficient mice upon inoculation of tumor cells. These results demonstrate that PD-1 imposes qualitative control of T cell responses by preferentially suppressing low-affinity T cells.

scholarly journals CD4+ T cell subsets present stable relationships in their T cell receptor repertoires

2020 ◽  
Author(s):  
Shiyu Wang ◽  
Longlong Wang ◽  
Ya Liu
Keyword(s):  
T Cells ◽  
Cell Differentiation ◽  
T Cell ◽  
T Cell Receptor ◽  
Cd4 T Cells ◽  
Cell Receptor ◽  
T Cell Subsets ◽  
Cd4 T Cell ◽  
Antigen Specificity ◽  
Sequence Composition

AbstractCD4+ T cells are key components of adaptive immunity. The cell differentiation equips CD4+ T cells with new functions. However, the effect of cell differentiation on T cell receptor (TCR) repertoire is not investigated. Here, we examined the features of TCR beta (TCRB) repertoire of the top clones within naïve, memory and regular T cell (Treg) subsets: repertoire structure, gene usage, length distribution and sequence composition. First, we found that memory subsets and Treg would be discriminated from naïve by the features of TCRB repertoire. Second, we found that the correlations between the features of memory subsets and naïve were positively related to differentiation levels of memory subsets. Third, we found that public clones presented a reduced proportion and a skewed sequence composition in differentiated subsets. Furthermore, we found that public clones led naïve to recognize a broader spectrum of antigens than other subsets. Our findings suggest that TCRB repertoire of CD4+ T cell subsets is skewed in a differentiation-depended manner. Our findings show that the variations of public clones contribute to these changes. Our findings indicate that the reduce of public clones in differentiation trim the antigen specificity of CD4+ T cells. The study unveils the physiological effect of memory formation and facilitates the selection of proper CD4+ subset for cellular therapy.

scholarly journals Quantitative Analysis of T-Cell Receptor β Variable-Gene Usage in Cutaneous Late-Phase Reactions: Implications for T-Lymphocyte Recruitment in Cutaneous Inflammation

1999 ◽  
Vol 6 (1) ◽  
pp. 85-88 ◽  
Author(s):  
Stuart R. Lessin ◽  
Bernice M. Benoit ◽  
Guoqing Li ◽  
Ann Moskovitz ◽  
Burton Zweiman
Keyword(s):  
T Cells ◽  
T Cell ◽  
T Cell Receptor ◽  
T Lymphocyte ◽  
Memory T Cells ◽  
Immunoglobulin E ◽  
Late Phase ◽  
Cell Receptor ◽  
T Cell Subsets ◽  
Variable Gene

ABSTRACT To determine if functionally distinct T-lymphocyte (T cell) subsets accumulate in late-phase immunoglobulin E-mediated reactions (LPR), we quantitatively analyzed the immunophenotype and the T-cell receptor β variable-gene (Vβ) repertoire of T cells in cutaneous LPR. Peripheral blood and skin biopsies were obtained 6 or 24 h after sensitive subjects were challenged with intradermal injections of grass pollen allergen (Ag) and control (C) solution. The frequency of cells expressing CD3, CD4, CD8, CD45RO, and CD25/mm2 was determined by immunohistochemistry in nine subjects. Vβ usage was assessed by reverse transcription-PCR in five of nine subjects. A significantly greater frequency of CD3+ and CD45RO+ (memory) T cells was detected in Ag sites than in C sites at 24 h after challenge but not at 6 h. The frequency of activated (CD25+) and helper (CD4+) T cells appeared to be increased in Ag sites as well, though not significantly. Vβ6 was the most commonly expressed Vβ detected in Ag sites, but it was also detected in accompanying C sites. Vβ2 was the most commonly expressed Vβ detected in C sites. Sequence analysis in one case revealed Vβ expression in a 6-h Ag site to be essentially polyclonal. Our findings suggest that memory T cells with Vβ expression similar to that in normal skin accumulate in developing cutaneous LPR. The limited usage of Vβ suggests a preferential recruitment or retention of reactive T cells from an endogenous subset of skin-homing T cells with its own skewed Vβ repertoire.

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