Deep Sequencing of Antiviral T-Cell Responses to HCMV and EBV in Humans Reveals a Stable Repertoire That Is Maintained for Many Years

Klarenbeek, Paul L.; Remmerswaal, Ester B. M.; Berge, Ineke J. M. ten; Doorenspleet, Marieke E.; Schaik, Barbera D.C. van; Esveldt, Rebecca E. E.; Koch, Sven D.; Brinke, Anja ten; Kampen, Antoine H. C. van; Bemelman, F. J.; Tak, Paul P.; Baas, Frank; Vries, Niek de; Lier, R. A. W. Van

doi:10.1371/journal.ppat.1002889

Cited by 101 publications

(99 citation statements)

References 30 publications

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“…In the most striking example, two dominant clones collectively constituted more than 35% of all CD8 + T cells in one patient (P21). Such high frequencies of EBV-reactive sequences were not observed in a recent study that used next-generation sequencing of two renal transplant recipients (14), although those patients did not receive lymphodepleting therapy. Nonetheless, changes in EBV-specific clone frequency in association with infection/activation were not uniformly observed, and EBV-specific clones were also identified in occasional patients without detectable evidence of infection (e.g., P15).…”

Section: Figurementioning

confidence: 77%

T cell repertoire following autologous stem cell transplantation for multiple sclerosis

Muraro¹,

Robins²,

Malhotra³

et al. 2014

J. Clin. Invest.

246

217

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Autologous hematopoietic stem cell transplantation (HSCT) is commonly employed for hematologic and non-hematologic malignancies. In clinical trials, HSCT has been evaluated for severe autoimmunity as a method to "reset" the immune system and produce a new, non-autoimmune repertoire. While the feasibility of eliminating the vast majority of mature T cells is well established, accurate and quantitative determination of the relationship of regenerated T cells to the baseline repertoire has been difficult to assess. Here, in a phase II study of HSCT for poor-prognosis multiple sclerosis, we used high-throughput deep TCRβ chain sequencing to assess millions of individual TCRs per patient sample. We found that HSCT has distinctive effects on CD4 + and CD8 + T cell repertoires. In CD4 + T cells, dominant TCR clones present before treatment were undetectable following reconstitution, and patients largely developed a new repertoire. In contrast, dominant CD8 + clones were not effectively removed, and the reconstituted CD8 + T cell repertoire was created by clonal expansion of cells present before treatment. Importantly, patients who failed to respond to treatment had less diversity in their T cell repertoire early during the reconstitution process. These results demonstrate that TCR characterization during immunomodulatory treatment is both feasible and informative, and may enable monitoring of pathogenic or protective T cell clones following HSCT and cellular therapies. IntroductionWhen employed for immunomodulation, the goal of autologous hematopoietic stem cell transplantation (HSCT) is to create a non-autoreactive immune compartment by altering the immune repertoire and/or function of autoreactive cells (1-3). Using T cell receptor excision circle analysis in HSCT-treated MS patients, we showed previously that even in adults, thymic output contributed to the post-treatment TCR repertoire (2, 4) and that this, plus expansion of residual cells not eliminated during conditioning, regenerated the T cell compartment (5).However, the clonal specificities of a regenerated repertoire following high-dose immunosuppressive therapy (HDIT) and autologous HSCT have not been well explored, as previous studies used CDR3 spectratyping for TCR clonal analysis, which made it impractical to sequence more than several dozen TCRs. Only a single patient receiving HSCT for autoimmune disease (ankylosing spondylitis) has had a fuller analysis of their TCR repertoire reported (6). Here, as part of a new phase II trial for poor-prognosis MS (see Methods), we have taken advantage of high-throughput deep TCRβ chain sequencing (7) to directly assess millions of TCRs per individual before and at two time points after autologous HSCT in a cohort of 24 patients.

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Section: Figurementioning

confidence: 77%

T cell repertoire following autologous stem cell transplantation for multiple sclerosis

Muraro¹,

Robins²,

Malhotra³

et al. 2014

J. Clin. Invest.

246

217

View full text Add to dashboard Cite

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“…1). This might be important for not only protecting against those infections that the immune system is already familiar with (49)(50)(51)(52)(53)77), but also for sustaining balanced regulation of the existing social network of immune cells (78,79).…”

Section: Discussionmentioning

confidence: 99%

Dynamics of Individual T Cell Repertoires: From Cord Blood to Centenarians

Britanova

Shugay

Merzlyak

et al. 2016

The Journal of Immunology

162

198

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The diversity, architecture, and dynamics of the TCR repertoire largely determine our ability to effectively withstand infections and malignancies with minimal mistargeting of immune responses. In this study, we have employed deep TCRβ repertoire sequencing with normalization based on unique molecular identifiers to explore the long-term dynamics of T cell immunity. We demonstrate remarkable stability of repertoire, where approximately half of all T cells in peripheral blood are represented by clones that persist and generally preserve their frequencies for 3 y. We further characterize the extremes of lifelong TCR repertoire evolution, analyzing samples ranging from umbilical cord blood to centenarian peripheral blood. We show that the fetal TCR repertoire, albeit structurally maintained within regulated borders due to the lower numbers of randomly added nucleotides, is not limited with respect to observed functional diversity. We reveal decreased efficiency of nonsense-mediated mRNA decay in umbilical cord blood, which may reflect specific regulatory mechanisms in development. Furthermore, we demonstrate that human TCR repertoires are functionally more similar at birth but diverge during life, and we track the lifelong behavior of CMV- and EBV-specific T cell clonotypes. Finally, we reveal gender differences in dynamics of TCR diversity constriction, which come to naught in the oldest age. Based on our data, we propose a more general explanation for the previous observations on the relationships between longevity and immunity.

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“…Quantitative PCR (qPCR) measurements to determine viral loads and serological assays to determine the presence of antiviral antibodies were done as described previously (32,33).…”

Section: Methodsmentioning

confidence: 99%

Infection History Determines the Differentiation State of Human CD8 ⁺ T Cells

Aalderen

Remmerswaal

Verstegen

et al. 2015

J Virol

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After the resolution of the acute phase of infection, otherwise quiescent antigen-experienced CD8؉ T cells confer rapid protection upon reinfection with viral pathogens or, in the case of persistent viruses, help to maintain control of the infection. Depending on the type of virus, antigen-specific CD8 ؉ T cells have distinct traits, ranging from typical memory cell properties in the case of rapidly cleared viruses to immediate effector functions for persistent viruses. We here show that both the differentiation stage, defined by the expression of cell surface markers, such as CD45RA, CCR7, CD28, and CD27, and distinct expression levels of T-bet and eomesodermin (Eomes) predict the functional profile of antigen-experienced CD8 ؉ T cells. Furthermore, virusspecific CD8؉ T cells targeting different respiratory syncytial virus-, influenza A virus-, Epstein-Barr virus (EBV)-, human cytomegalovirus (hCMV)-, and HIV-1-specific epitopes adopt distinct T-bet and Eomes expression patterns that appear to be installed early during the primary response. Importantly, the associations between surface phenotype, T-bet/Eomes expression levels, and the expression of markers that predict CD8؉ T-cell function change according to viral infection history, particularly against the background of HIV-1 and, to lesser extent, of human cytomegalovirus and/or Epstein-Barr virus infection. Thus, the functionality of human antigen-experienced CD8 ؉ T cells follows at least two dimensions, one outlined by the surface phenotype and another by the T-bet/Eomes expression levels, which are determined by previous or persistent viral challenges. IMPORTANCE Functional human CD8؉ T-cell subsets have been defined using surface markers like CD45RA, CCR7, CD28, and CD27. However, the induction of function-defining traits, like granzyme B expression, is controlled by transcription factors like T-bet and Eomes. Here, we describe how T-bet and Eomes levels distinctly relate to the expression of molecules predictive for CD8؉ T-cell function in a surface phenotype-independent manner. Importantly, we found that central memory and effector memory CD8 ؉ T-cell subsets differentially express T-bet, Eomes, and molecules predictive for function according to viral infection history, particularly so in the context of HIV-1 infection and, to lesser extent, of latent EBV-and/or hCMV-infected, otherwise healthy adults. Finally, we show that the distinct phenotypes and T-bet/Eomes levels of different virus-specific CD8 ؉ T-cell populations are imprinted early during the acute phase of primary infection in vivo. These findings broaden our understanding of CD8 ؉ Tcell differentiation. T he process of viral and host coevolvement has selected for antiviral CD8ϩ T-cell responses that are successful in ensuring survival of the host. As an apparent consequence, human circulating virus-specific CD8 ϩ T cells display distinct phenotypic and functional properties according to the virus or viral proteins they target (1-3). Acute viruses, such as respiratory syncytial vir...

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Deep Sequencing of Antiviral T-Cell Responses to HCMV and EBV in Humans Reveals a Stable Repertoire That Is Maintained for Many Years

Cited by 101 publications

References 30 publications

T cell repertoire following autologous stem cell transplantation for multiple sclerosis

T cell repertoire following autologous stem cell transplantation for multiple sclerosis

Dynamics of Individual T Cell Repertoires: From Cord Blood to Centenarians

Infection History Determines the Differentiation State of Human CD8 ⁺ T Cells

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Deep Sequencing of Antiviral T-Cell Responses to HCMV and EBV in Humans Reveals a Stable Repertoire That Is Maintained for Many Years

Cited by 101 publications

References 30 publications

T cell repertoire following autologous stem cell transplantation for multiple sclerosis

T cell repertoire following autologous stem cell transplantation for multiple sclerosis

Dynamics of Individual T Cell Repertoires: From Cord Blood to Centenarians

Infection History Determines the Differentiation State of Human CD8 + T Cells

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Product

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Infection History Determines the Differentiation State of Human CD8 ⁺ T Cells