Pathologic T-cell response in ischaemic failing hearts elucidated by T-cell receptor sequencing and phenotypic characterization

2019 ◽  
Vol 40 (48) ◽  
pp. 3924-3933 ◽  
Author(s):  
Ting-Ting Tang ◽  
Yi-Cheng Zhu ◽  
Nian-Guo Dong ◽  
Si Zhang ◽  
Jie Cai ◽  
...  

Abstract Aims A persistent cardiac T-cell response initiated by myocardial infarction is linked to subsequent adverse ventricular remodelling and progression of heart failure. No data exist on T-cell receptor (TCR) repertoire changes in combination with phenotypic characterization of T cells in ischaemic failing human hearts. Methods and results Analysis of TCR repertoire with high-throughput sequencing revealed that compared with T cells in control hearts, those in ischaemic failing hearts showed a clonally expanded TCR repertoire but similar usage patterns of TRBV-J rearrangements and V gene segments; compared with T cells in peripheral blood, those in ischaemic failing hearts exhibited a restricted and clonally expanded TCR repertoire and different usage patterns of TRBV-J rearrangements and V gene segments, suggesting the occurrence of tissue-specific T-cell expansion in ischaemic failing hearts. Consistently, TCR clonotype sharing was prominent in ischaemic failing hearts, especially in hearts of patients who shared human leucocyte antigen (HLA) alleles. Furthermore, ischaemia heart failure (IHF) heart-associated clonotypes were more frequent in peripheral blood of IHF patients than in that of controls. Heart-infiltrating T cells displayed memory- and effector-like characteristics. Th1 cells were the predominant phenotype among CD4+ T cells; CD8+ T cells were equally as abundant as CD4+ T cells and produced high levels of interferon-γ, granzyme B, and perforin. Conclusion We provide novel evidence for a tissue-specific T-cell response predominated by Th1 cells and cytotoxic CD8+ T cells in ischaemic failing human hearts that may contribute to the progression of heart failure.

2021 ◽  
Author(s):  
Kevin Mohammed ◽  
Austin Meadows ◽  
Sandra Hatem ◽  
Viviana Simon ◽  
Anitha D Jayaprakash ◽  
...  

Early, high-resolution metrics are needed to ascertain the immune response to vaccinations. The T cell receptor (TCR), a heterodimer of one α and one β chain, is a promising target, with the complete TCR repertoire reflecting the T cells present in an individual. To this end, we developed Tseek, an unbiased and accurate method for profiling the TCR repertoire by sequencing the TCR α and β chains and developing a suite of tools for repertoire analysis. An added advantage is the ability to non-invasively analyze T cells in peripheral blood mononuclear cells (PBMCs). Tseek and the analytical suite were used to explore the T cell response to both the COVID-19 mRNA vaccine (n=9) and the seasonal inactivated Influenza vaccine (n=5) at several time points. Neutralizing antibody titers were also measured in the covid vaccine samples. The COVID-19 vaccine elicited a broad T cell response involving multiple expanded clones, whereas the Influenza vaccine elicited a narrower response involving fewer clones. Many distinct T cell clones responded at each time point, over a month, providing temporal details lacking in the antibody measurements, especially before the antibodies are detectable. In individuals recovered from a SARS-CoV-2 infection, the first vaccine dose elicited a robust T cell response, while the second dose elicited a comparatively weaker response, indicating a saturation of the response. The physical symptoms experienced by the recipients immediately following the vaccinations were not indicative of the TCR/antibody responses, while a weak TCR response seemed to presage a weak antibody response. We also found that the TCR repertoire acts as an individual fingerprint: donors of blood samples taken years apart could be identified solely based upon their TCR repertoire, hinting at other surprising uses the TCR repertoire may have. These results demonstrate the promise of TCR repertoire sequencing as an early and sensitive measure of the adaptive immune response to vaccination, which can help improve immunogen selection and optimize vaccine dosage and spacing between doses.


Blood ◽  
2008 ◽  
Vol 111 (4) ◽  
pp. 2053-2061 ◽  
Author(s):  
Laura Crompton ◽  
Naeem Khan ◽  
Rajiv Khanna ◽  
Laxman Nayak ◽  
Paul A. H. Moss

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.


2016 ◽  
Author(s):  
Shaked Afik ◽  
Kathleen B. Yates ◽  
Kevin Bi ◽  
Samuel Darko ◽  
Jernej Godec ◽  
...  

ABSTRACTThe T cell compartment must contain diversity in both TCR repertoire and cell state to provide effective immunity against pathogens1,2. However, it remains unclear how differences in the TCR contribute to heterogeneity in T cell state at the single cell level because most analysis of the TCR repertoire has, to date, aggregated information from populations of cells. Single cell RNA-sequencing (scRNA-seq) can allow simultaneous measurement of TCR sequence and global transcriptional profile from single cells. However, current protocols to directly sequence the TCR require the use of long sequencing reads, increasing the cost and decreasing the number of cells that can be feasibly analyzed. Here we present a tool that can efficiently extract TCR sequence information from standard, short-read scRNA-seq libraries of T cells: TCR Reconstruction Algorithm for Paired-End Single cell (TRAPeS). We apply it to investigate heterogeneity in the CD8+T cell response in humans and mice, and show that it is accurate and more sensitive than previous approaches3,4. We applied TRAPeS to single cell RNA-seq of CD8+T cells specific for a single epitope from Yellow Fever Virus5. We show that the recently-described "naive-like" memory population of YFV-specific CD8+T cells have significantly longer CDR3 regions and greater divergence from germline sequence than do effector-memory phenotype CD8+T cells specific for YFV. This suggests that TCR usage contributes to heterogeneity in the differentiation state of the CD8+T cell response to YFV. TRAPeS is publicly available, and can be readily used to investigate the relationship between the TCR repertoire and cellular phenotype.


2018 ◽  
Author(s):  
Alina Huth ◽  
Xiaoling Liang ◽  
Stefan Krebs ◽  
Helmut Blum ◽  
Andreas Moosmann

AbstractCytomegalovirus (CMV) is a prevalent human pathogen. The virus cannot be eliminated from the body, but is kept in check by CMV-specific T cells. Patients with an insufficient T-cell response, such as transplant recipients, are at high risk of developing CMV disease. However, the CMV-specific T-cell repertoire is complex, and is not yet clear which T cells protect best against virus reactivation and disease. Here we present a highly resolved characterization of CMV-specific CD8+ T cells based on enrichment by specific peptide stimulation and mRNA sequencing of their T-cell receptor β chains (TCRβ). Our analysis included recently identified T-cell epitopes restricted through HLA-C, whose presentation is resistant to viral immunomodulation, and well-studied HLA-B-restricted epitopes. In 8 healthy virus carriers, we identified a total of 1052 CMV-specific TCRβ chains. HLA-C-restricted, CMV-specific TCRβ clonotypes theex vivoT-cell response, and contributed the highest-frequency clonotype of the entire repertoire in 2 of 8 donors. We analyzed sharing and similarity of CMV-specific TCRβ sequences and identified 63 public or related sequences belonging to 17 public TCRβ families. In our cohort and in an independent cohort of 352 donors, the cumulative frequency of these public TCRβ family members was a highly discriminatory indicator of carrying both CMV infection and the relevant HLA type. Based on these findings, we propose CMV-specific TCRβ signatures as a biomarker for an antiviral T-cell response to identify patients in need of treatment and to guide future development of immunotherapy.


Pathogens ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 650
Author(s):  
Kilian Schober ◽  
Pim Fuchs ◽  
Jonas Mir ◽  
Monika Hammel ◽  
Lorenzo Fanchi ◽  
...  

Evolutionary processes govern the selection of T cell clonotypes that are optimally suited to mediate efficient antigen-specific immune responses against pathogens and tumors. While the theoretical diversity of T cell receptor (TCR) sequences is vast, the antigen-specific TCR repertoire is restricted by its peptide epitope and the presenting major histocompatibility complex (pMHC). It remains unclear how many TCR sequences are recruited into an antigen-specific T cell response, both within and across different organisms, and which factors shape both of these distributions. Infection of mice with ovalbumin-expressing cytomegalovirus (IE2-OVA-mCMV) represents a well-studied model system to investigate T cell responses given their size and longevity. Here we investigated > 180,000 H2kb/SIINFEKL-recognizing TCR CDR3α or CDR3β sequences from 25 individual mice spanning seven different time points during acute infection and memory inflation. In-depth repertoire analysis revealed that from a pool of highly diverse, but overall limited sequences, T cell responses were dominated by public clonotypes, partly with unexpectedly extreme degrees of sharedness between individual mice (“supra-public clonotypes”). Public clonotypes were found exclusively in a fraction of TCRs with a high generation probability. Generation probability and degree of sharedness select for highly functional TCRs, possibly mediated through elevating intraindividual precursor frequencies of clonotypes.


Blood ◽  
2002 ◽  
Vol 100 (6) ◽  
pp. 2153-2158 ◽  
Author(s):  
Emmanuel Hermann ◽  
Carine Truyens ◽  
Cristina Alonso-Vega ◽  
Jos Even ◽  
Patricia Rodriguez ◽  
...  

Abstract Fetal/neonatal immune responses generally are considered to be immature and weaker than that of adults. We have studied the cord-blood T cells of newborns congenitally infected with Trypanosoma cruzi, the protozoan agent of Chagas disease. Our data demonstrate a predominant activation of CD8 T cells expressing activation markers and armed to mediate effector functions. The analysis of the T-cell receptor beta chain variable repertoire shows the oligoclonal expansion of these T lymphocytes, indicating that activation was driven by parasite antigens. Indeed, we have detected parasite-specific CD8 T cells secreting interferon-γ after coincubation with live T cruzi. This response is enhanced in the presence of recombinant interleukin-15, which limits the T-cell spontaneous apoptosis. These findings point out that the fetal immune system is more competent than previously appreciated, since fetuses exposed to live pathogens are able to develop an adultlike immune CD8 T-cell response.


Blood ◽  
2002 ◽  
Vol 100 (6) ◽  
pp. 2153-2158
Author(s):  
Emmanuel Hermann ◽  
Carine Truyens ◽  
Cristina Alonso-Vega ◽  
Jos Even ◽  
Patricia Rodriguez ◽  
...  

Fetal/neonatal immune responses generally are considered to be immature and weaker than that of adults. We have studied the cord-blood T cells of newborns congenitally infected with Trypanosoma cruzi, the protozoan agent of Chagas disease. Our data demonstrate a predominant activation of CD8 T cells expressing activation markers and armed to mediate effector functions. The analysis of the T-cell receptor beta chain variable repertoire shows the oligoclonal expansion of these T lymphocytes, indicating that activation was driven by parasite antigens. Indeed, we have detected parasite-specific CD8 T cells secreting interferon-γ after coincubation with live T cruzi. This response is enhanced in the presence of recombinant interleukin-15, which limits the T-cell spontaneous apoptosis. These findings point out that the fetal immune system is more competent than previously appreciated, since fetuses exposed to live pathogens are able to develop an adultlike immune CD8 T-cell response.


2021 ◽  
Author(s):  
Mark A Pilkinton ◽  
Wyatt J McDonnell ◽  
Louise Barnett ◽  
Abha Chopra ◽  
Rama Gangula ◽  
...  

Cellular immune responses to Gag correlate with improved HIV viral control. The full extent of cellular immune responses comprise both the number of epitopes recognized by CD4+ and CD8+ T cells, as well as the diversity of the T cell receptor (TCR) repertoire directed against each epitope. The optimal diversity of the responsive TCR repertoire is unclear. Therefore, we evaluated the TCR diversity of CD4+ and CD8+ T cells responding to HIV-1 Gag to determine if TCR diversity correlates with clinical or virologic metrics. Previous studies of TCR repertoires have been limited primarily to CD8+ T cell responses directed against a small number of well-characterized T cell epitopes restricted by specific human leucocyte antigens. We stimulated peripheral blood mononuclear cells from 21chronic HIV-infected individuals overnight with a pool of HIV-1 Gag peptides, followed by sorting of activated CD4+ and CD8+ T cells and TCR deep sequencing. We found Gag-reactive CD8+ T cells to be more oligoclonal, with a few dominant TCRs comprising the bulk of the repertoire, compared to the highly diverse TCR repertoires of Gag-reactive CD4+ T cells. HIV viral sequencing of the same donors revealed that high CD4+ T cell TCR diversity was strongly associated with lower HIV Gag genetic diversity. We conclude that the TCR repertoire of Gag-reactive CD4+ T helper cells display substantial diversity without a clearly dominant circulating TCR clonotype, in contrast to a hierarchy of dominant TCR clonotypes in the Gag-reactive CD8+ T cells, and may serve to limit HIV diversity during chronic infection. IMPORTANCE Human T cells recognize portions of viral proteins bound to host molecules (human leucocyte antigens) on the surface of infected cells. T cells recognize these foreign proteins through their T cell receptors (TCRs), which are formed by the assortment of several available V, D and J genes to create millions of combinations of unique TCRs. We measured the diversity of T cells responding to the HIV Gag protein. We found the CD8+ T cell response is primarily made up of a few dominant unique TCRs whereas the CD4+ T cell subset has a much more diverse repertoire of TCRs. We also found there was less change in the virus sequences in subjects with more diverse TCR repertoires. HIV has a high mutation rate, which allows it to evade the immune response. Our findings describe the characteristics of a virus-specific T cell response that may allow it to limit viral evolution.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 1737-1737 ◽  
Author(s):  
Kayo Kondo ◽  
Jan A. Burger ◽  
Keating Micheal ◽  
Jamie Tran ◽  
Muharrem Muftuoglu ◽  
...  

Abstract INTRODUCTION: The Bruton's tyrosine kinase (BTK) inhibitor ibrutinib is a covalent inhibitor of BTK, a member of the B-cell receptor (BCR) signaling pathway and induces objective clinical responses in the majority of CLL patients (Byrd et al., NEJM 2013). Interestingly this drug also inhibits L2-inducible T cell kinase (ITK), an essential enzyme for the development and effector function of Th2 and Th17 cells, and has been shown to shift the balance towards a Th1 response. The purpose of the study was to determine how ibrutinib influences the Th1/Th17/T regulatory cell response, expression of immune checkpoint blockade molecules on T cells and the functional pathogen-specific T cell recovery. METHODS: Here we present data from a clinical trial of ibrutinib versus ibrutinib + rituximab in previously treated patients (NCT02007044). Peripheral blood and serum were collected at baseline, 3 months and 6 months during therapy. Multicolor flow cytometry was used to characterize B cell subsets, T-cell subsets, expression of PD-1, PD-L1 and CTLA-4 and T-cell effector function. For statistical analysis of pre-treatment to on-treatment measurements the paired Student t-test was used. RESULTS: Here we report on the phenotypic and functional recovery of immune subsets in 41 CLL patients treated with ibrutinib (n=17) or ibrutinib + rituximab (n=25). Both PD-1 and PD-L1 were expressed at high levels on CLL cells. Interestingly, by 3 and 6 months, there was a significant decrease in PD-1 expression from a pre-treatment median of 15% to 4% (at 3 months) and 3% (at 6 months; P<0.0001). Similarly, PD-L1 levels decreased from 5% to 3% and 2% respectively (P=0.004) (Fig. 1). We next sought to determine the functional impact of ibrutinib therapy on T cell subsets and function. After an initial reduction from a pretreatment level of4800/µL to 3000/µL at 3 months (P=0.003), CD3+ T cells increased to 4000 (µL) by 6 months; P=0.03. This was associated with a significant down-regulation of PD-1 expression on T cells from 28% pre-treatment to 24% and 21% at 3 and 6 months respectively (Fig.2 ) (P<0.0001). A significant reduction in the frequencies of regulatory T cells (Teg) (8% vs. 7% vs 6% respectively; P=0.004) was also documented. Ibrutinib has been reported to skew the T cell response toward a Th1 profile. We stimulated PBMC with PMA/Inomycin and performed intracellular staining for IFN-γ, IL-2, TNF-α and IL-17. Following ibrutinib therapy, there was a significant improvement in the CD8+ IFN-γ (P=0.04) and TNF-α response (P=0.01), and a reduction in the CD4+IL-17 response. To understand the functional relevance of these results, we are currently analyzing the CD8+ T cell response to stimulation with CEF (epitopes derived from CMV, EBV and Influenza) as a surrogate for pathogen-specific T cell recovery. CONCLUSION: Based on these data we propose that ibrutinib therapy can modulate the T cell response through multiple mechanisms which include (i) direct inhibition of ITK and skewing of the T cell response toward a Th1 profile; (ii) reduction in PD1/PDL1 expression on B and T cells and (iii). suppression of Tregs. It is unclear how ibrutinib influences the PD1/PDL1 interaction and whether this is a direct effect of the drug on essential components of B and T cell-receptor signaling or whether it is an indirect effect related to a reduction in the leukemia burden. Mechanistic studies to understand how ibrutinib modulates the PD1/PL1 axis are currently underway. Figure 1. Ibrutinib therapy is associated with a reduction in PDL1 expression on the surface of CD19+ B cells. Figure 1. Ibrutinib therapy is associated with a reduction in PDL1 expression on the surface of CD19+ B cells. Figure 2. Ibrutinib therapy is associated with a reduction in PD1 expression on the surface of CD3+ T cells. Figure 2. Ibrutinib therapy is associated with a reduction in PD1 expression on the surface of CD3+ T cells. Disclosures Burger: Pharmacyclics LLC, an AbbVie Company: Research Funding. Wierda:Glaxo-Smith-Kline Inc.: Research Funding; Celgene Corp.: Consultancy. Rezvani:Pharmacyclics: Research Funding.


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