Impact on in-depth immunophenotyping of delay to peripheral blood processing

Peripheral blood mononuclear cell (PBMC) immunophenotyping is crucial in tracking activation, disease state, and response to therapy in human subjects. Many studies require shipping of blood from clinical sites to a laboratory for processing to PBMC, which can lead to delays that impact sample quality. We used an extensive cytometry by time-of-flight (CyTOF) immunophenotyping panel to analyze the impacts of delays to processing and distinct storage conditions on cell composition and quality of PBMC from seven adults across a range of ages, including two with rheumatoid arthritis. Two or more days delay to processing resulted in extensive red blood cell contamination and increased variability of cell counts. While total memory and naïve B and T cell populations were maintained, four days delay reduced frequencies of monocytes. Variation across all immune subsets increased with delays of up to seven days in processing. Unbiased clustering analysis to define more granular subsets confirmed changes in PBMC composition, including decreases of classical and non-classical monocytes, basophils, plasmacytoid dendritic cells, and follicular helper T cells, with each subset impacted at a distinct time of delay. Expression of activation markers and chemokine receptors changed by day two, with differential impacts across subsets and markers. Our data support existing recommendations to process PBMC within 36 hours of collection but provide guidance on appropriate immunophenotyping experiments with longer delays.

Infection, Rejection, and the Connection

Solid organ transplantation is a life-saving treatment for people with end-stage organ disease. Immune-mediated transplant rejection is a common complication that decreases allograft survival. Although immunosuppression is required to prevent rejection, it also increases the risk of infection. Some infections, such as cytomegalovirus and BK virus, can promote inflammatory gene expression that can further tip the balance toward rejection. BK virus and other infections can induce damage that resembles the clinical pathology of rejection, and this complicates accurate diagnosis. Moreover, T cells specific for viral infection can lead to rejection through heterologous immunity to donor antigen directly mediated by antiviral cells. Thus, viral infections and allograft rejection interact in multiple ways that are important to maintain immunologic homeostasis in solid organ transplant recipients. Better insight into this dynamic interplay will help promote long-term transplant survival.

CMV-Responsive CD4 T Cells Have a Stable Cytotoxic Phenotype Over the First Year Post-Transplant in Patients Without Evidence of CMV Viremia

Cytomegalovirus (CMV) infection is a known cause of morbidity and mortality in solid organ transplant recipients. While primary infection is controlled by a healthy immune system, CMV is never eradicated due to viral latency and periodic reactivation. Transplantation and associated therapies hinder immune surveillance of CMV. CD4 T cells are an important part of control of CMV reactivation. We therefore investigated how CMV impacts differentiation, functionality, and expansion of protective CD4 T cells from recipients of heart or kidney transplant in the first year post-transplant without evidence of CMV viremia. We analyzed longitudinal peripheral blood samples by flow cytometry and targeted single cell RNA sequencing coupled to T cell receptor (TCR) sequencing. At the time of transplant, CD4 T cells from CMV seropositive transplant recipients had a higher degree of immune aging than the seronegative recipients. The phenotype of CD4 T cells was stable over time. CMV-responsive CD4 T cells in our transplant cohort included a large proportion with cytotoxic potential. We used sequence analysis of TCRαβ to identify clonal expansion and found that clonally expanded CMV-responsive CD4 T cells were of a predominantly aged cytotoxic phenotype. Overall, our analyses suggest that the CD4 response to CMV is dominated by cytotoxicity and not impacted by transplantation in the first year. Our findings indicate that CMV-responsive CD4 T cells are homeostatically stable in the first year after transplantation and identify subpopulations relevant to study the role of this CD4 T cell population in post-transplant health.

CMV drives phenotypic changes in CD4 T cells prior to but not during the first year after solid organ transplantation

Cytomegalovirus (CMV) infection is a major complication after solid organ transplantation. The virus establishes latency after immune clearance of the primary infection. Immunosuppression impairs immune control in transplant recipients. We have previously shown that CMV drives accelerated immune aging of CD8 T cells in the first year after transplant. CMV-specific CD4 T cells also contribute to resolution of post-transplant viremia and reduce severity of disease at least in part by promoting maintenance of anti-viral CD8 T cell populations. Thus, we investigated the impact of CMV on CD4 T cell differentiation in the first year after transplant. Compared to CMV seronegative (CMV−) recipients, CMV+ recipients had an elevated frequency of aged (CD57+) CD4 T cells, with trends towards elevated PD-1+ and skewing toward memory rather than naïve phenotype. Unlike CMV-specific CD8 T cells, these phenotypes were stable over the first year after transplant, indicating these differences demonstrate a pre-established differentiation state. To correlate these findings to T cell receptor repertoire at a single cell level, we conducted single cell sequencing of TCR coupled to gene expression in CMV-responsive CD4 T cells from 6 transplant recipients from pre- to one-year post-transplant. Cell phenotypes were stable over time, and clonally expanded cells predominantly had an aged cytotoxic phenotype. Thus, CMV-responsive CD4 T cells in transplant recipients display evidence of immune aging and cytotoxicity. This is consistent with similar phenotypes in CD8 T cells, but striking in stability. Further study of this population will be important to determine whether this pre-existing phenotype is protective or pathogenic after transplant.

This work was supported by funding from the NIH to LEH (NIDDK 5K01DK123196) and AAA (Stanford PreRenal Initiative, NIDDK KUH 1R25DK122957) and the Department of Veterans Affairs to JSM (CSR&D 1I01CX001971).

Functional Consequences of Memory Inflation after Solid Organ Transplantation

CMV is a major infectious complication following solid organ transplantation. Reactivation of CMV leads to memory inflation, a process in which CD8 T cells expand over time. Memory inflation is associated with specific changes in T cell function, including increased oligoclonality, decreased cytokine production, and terminal differentiation. To address whether memory inflation during the first year after transplantation in human subjects alters T cell differentiation and function, we employed single-cell-matched TCRαβ and targeted gene expression sequencing. Expanded T cell clones exhibited a terminally differentiated, immunosenescent, and polyfunctional phenotype whereas rare clones were less differentiated. Clonal expansion occurring between pre- and 3 mo posttransplant was accompanied by enhancement of polyfunctionality. In contrast, polyfunctionality and differentiation state were largely maintained between 3 and 12 mo posttransplant. Highly expanded clones had a higher degree of polyfunctionality than rare clones. Thus, CMV-responsive CD8 T cells differentiated during the pre- to posttransplant period then maintained their differentiation state and functional capacity despite posttransplant clonal expansion.

Evolution of Cytomegalovirus-Responsive T Cell Clonality following Solid Organ Transplantation

CMV infection is a significant complication after solid organ transplantation. We used single cell TCR αβ sequencing to determine how memory inflation impacts clonality and diversity of the CMV-responsive CD8 and CD4 T cell repertoire in the first year after transplantation in human subjects. We observed CD8 T cell inflation but no changes in clonal diversity, indicating homeostatic stability in clones. In contrast, the CD4 repertoire was diverse and stable over time, with no evidence of CMV-responsive CD4 T cell expansion. We identified shared CDR3 TCR motifs among patients but no public CMV-specific TCRs. Temporal changes in clonality in response to transplantation and in the absence of detectable viral reactivation suggest changes in the repertoire immediately after transplantation followed by an expansion with stable clonal competition that may mediate protection.

Association of Premature Immune Aging and Cytomegalovirus After Solid Organ Transplant

Immune function is altered with increasing age. Infection with cytomegalovirus (CMV) accelerates age-related immunological changes resulting in expanded oligoclonal memory CD8 T cell populations with impaired proliferation, signaling, and cytokine production. As a consequence, elderly CMV seropositive (CMV⁺) individuals have increased mortality and impaired responses to other infections in comparison to seronegative (CMV^–) individuals of the same age. CMV is also a significant complication after organ transplantation, and recent studies have shown that CMV-associated expansion of memory T cells is accelerated after transplantation. Thus, we investigated whether immune aging is accelerated post-transplant, using a combination of telomere length, flow cytometry phenotyping, and single cell RNA sequencing. Telomere length decreased slightly in the first year after transplantation in a subset of both CMV⁺ and CMV^– recipients with a strong concordance between CD57⁺ cells and short telomeres. Phenotypically aged cells increased post-transplant specifically in CMV⁺ recipients, and clonally expanded T cells were enriched for terminally differentiated cells post-transplant. Overall, these findings demonstrate a pattern of accelerated aging of the CD8 T cell compartment in CMV⁺ transplant recipients.

Transplantation and CMV promote premature aging of CD8 T cells

Cytomegalovirus (CMV) infection is a significant contributor to both immune aging and complications after solid organ transplantation. A major mediator of both effects is viral reactivation, in which latent CMV in the host undergoes new replication requiring immune control. Immunocompetent CMV seropositive individuals display hallmarks of CD8 T cell aging earlier than CMV seronegative individuals, including shortened telomeres, defects in proliferation and signaling, and altered cytokine production. In the context of transplantation, immunosuppression impairs immune control, leading to negative impacts including late-term graft loss. We hypothesized that T cell aging is accelerated after transplant in CMV+ individuals, regardless of detectable viral reactivation. To address this hypothesis, we measured telomere length and conducted phenotyping through flow cytometry and targeted single cell RNA sequencing. We found a statistical increase in CD57 expression which correlated with a trend towards decreased telomere length in the first year after transplantation. We found that CD57+ CD8 T cells expanded in the first year after transplantation specifically in CMV+ recipients. We also found that clonal expansion was associated with a terminally differentiated phenotype, defined as CD45RA+ CD27− CCR7−. Overall, our data demonstrate an enhanced aging phenotype in the first year post-transplant in CMV seropositive individuals, based on CD57+ expression and terminal differentiation. These findings suggest that CD8 T cell aging may be an important factor to understanding immunity in transplant recipients.

Sestrins teach old T cells new tricks

Sestrin proteins dampen TCR signaling and induce antigen-independent natural killer-like cytotoxicity in highly differentiated CD8 T cells.

To debug or not to debug, a question worth asking

Recipient antibiotic pre-treatment protects both mice and humans from ischemia-reperfusion injury after liver transplantation.

Abstract 449: Transplantation Alters Function and Clonality of Cytomegalovirus-Responsive T Cells

Background: Cytomegalovirus (CMV) infection is a major complication of organ transplantation. CMV establishes lifelong latency in infected individuals. Healthy people are protected from CMV reactivation by immune memory, but immunosuppression limits protection in transplant recipients. Despite antiviral prophylaxis strategies, long-term survival is impaired. CMV-responsive memory CD8 T cells expand during the first year after transplantation in the absence of detectable viremia. The observed expansion correlates with protection against CMV. The objective of this study was to determine whether these cells are protective, utilizing innovative single cell sequencing analyses to probe their functional characteristics.

Methods: Mononuclear cells from peripheral blood of heart and kidney transplant recipients pre- and three months and one year post-transplant were stimulated with immunodominant CMV peptides. Single IFN gamma+ CMV-responsive T cells were index sorted into 96 well plates, and nested PCR, barcoding, and sequencing performed to analyze T cell receptor (TCR) and a panel of functional genes.

Results: Expanded CMV-responsive T cells tend to express a limited number of dominant CMV-responsive TCR clones. Clonally expanded CMV-responsive T cells express multiple antiviral proteins. The TCR repertoire may change from pre- to post-transplant. Once established at three months, clonal dominance is maintained until at least one year. The number of antiviral proteins expressed per clonally expanded T cell increases between these time points.

Conclusions: Protection from CMV post-transplant correlates with maintenance of TCR clonality and increased number of functions per cell. The stability of clonality post-transplant contrasts with the expansion of the total T cell population, and suggests that clonal expansion in the absence of disease recapitulates the pre-existing repertoire. The increased number of functions suggests that the expanded population may become more protective. The potential impact on clinical practice would be to provide further information on the relationship between the T cell response to CMV and long-term outcomes after transplantation.

Single cell immune profiling in transplantation research

Recently developed single-cell profiling technologies hold promise to provide new insights including analysis of population heterogeneity and linkage of antigen receptors with gene expression. These technologies produce complex data sets that require knowledge of bioinformatics for appropriate analysis. In this minireview, we discuss several single-cell immune profiling technologies for gene and protein expression, including cytometry by time-of-flight, RNA sequencing, and antigen receptor sequencing, as well as key considerations for analysis that apply to each. Because of the critical importance of data analysis for high parameter single cell analysis, we discuss essential factors in analysis of these data, including quality control, quantification, examples of methods for high dimensional analysis, immune repertoire analysis, and preparation of analysis pipelines. We provide examples of, and suggestions for, application of these innovative methods to transplantation research.

Cytomegalovirus-Responsive CD8+ T Cells Expand After Solid Organ Transplantation in the Absence of CMV Disease

Cytomegalovirus (CMV) is a major cause of morbidity and mortality in solid organ transplant recipients. Approximately 60% of adults are CMV seropositive, indicating previous exposure. Following resolution of the primary infection, CMV remains in a latent state. Reactivation is controlled by memory T cells in healthy individuals; transplant recipients have reduced memory T cell function due to chronic immunosuppressive therapies. In this study, CD8⁺ T cell responses to CMV polypeptides immediate-early-1 and pp65 were analyzed in 16 CMV-seropositive kidney and heart transplant recipients longitudinally pretransplantation and posttransplantation. All patients received standard of care maintenance immunosuppression, antiviral prophylaxis, and CMV viral load monitoring, with approximately half receiving T cell-depleting induction therapy. The frequency of CMV-responsive CD8⁺ T cells, defined by the production of effector molecules in response to CMV peptides, increased during the course of 1 year posttransplantation. The increase commenced after the completion of antiviral prophylaxis, and these T cells tended to be terminally differentiated effector cells. Based on this small cohort, these data suggest that even in the absence of disease, antigenic exposure may continually shape the CMV-responsive T cell population posttransplantation.

A TLR9-dependent checkpoint governs B cell responses to DNA-containing antigens

Mature B cell pools retain a substantial proportion of polyreactive and self-reactive clonotypes, suggesting that activation checkpoints exist to reduce the initiation of autoreactive B cell responses. Here, we have described a relationship among the B cell receptor (BCR), TLR9, and cytokine signals that regulate B cell responses to DNA-containing antigens. In both mouse and human B cells, BCR ligands that deliver a TLR9 agonist induce an initial proliferative burst that is followed by apoptotic death. The latter mechanism involves p38-dependent G1 cell-cycle arrest and subsequent intrinsic mitochondrial apoptosis and is shared by all preimmune murine B cell subsets and CD27- human B cells. Survival or costimulatory signals rescue B cells from this fate, but the outcome varies depending on the signals involved. B lymphocyte stimulator (BLyS) engenders survival and antibody secretion, whereas CD40 costimulation with IL-21 or IFN-γ promotes a T-bet+ B cell phenotype. Finally, in vivo immunization studies revealed that when protein antigens are conjugated with DNA, the humoral immune response is blunted and acquires features associated with T-bet+ B cell differentiation. We propose that this mechanism integrating BCR, TLR9, and cytokine signals provides a peripheral checkpoint for DNA-containing antigens that, if circumvented by survival and differentiative cues, yields B cells with the autoimmune-associated T-bet+ phenotype.

The effect of lymphodepletion on specificity and function of cytomegalovirus-responsive CD8 T cells in transplant recipients

Polyfunctional CD8 T cells produce multiple cytokines and effector molecules in order to control chronic viral infections, such as cytomegalovirus (CMV), a cause of allograft damage in transplant patients. Healthy individuals resolve primary CMV infection rapidly and control viral reactivation with memory T cells. IFNγ production by CD8 T cells protects from CMV, but the role of polyfunctional T cells in immunosuppressed transplant patients is not fully understood. We measured responses to CMV polypeptides IE-1 and pp65 to characterize the effects of T cell depletion on T cell specificity and polyfunctionality. In this study we identified polyfunctionality as co-expression of IFNγ, TNFα, and/or the degranulation marker CD107a. We analyzed T cell responses in pre- to a year post-transplant PBMC samples from cardiac and renal transplant patients. Treatment included anti-viral prophylaxis and 3 drug immunosuppression, with T cell depleting induction therapy in some patients. The 3 normal donors and 12 pre-transplant samples analyzed fall into 3 groups on the basis of IE-1 and pp65 specificity: equal response to both or dominant for either IE-1 or pp65. Almost all cells with exactly two functions were TNFα+. In some patients, lymphodepletion led to an early loss of polyfunctional T cells. However, polyfunctional CD8 T cells returned to pre-transplant levels by day 180. In addition, 3 patients displayed shifts from their pre-transplant IE-1 vs pp65 specificity post-transplant, while specificity was consistent over a year post-transplant in the other 8. In conclusion, pre-transplant TNFα expression is predictive of polyfunctionality, and further study is needed to determine the effect of T cell depletion on fine antigen specificity.

Caught Off Center: Rethinking the Requirements for Antibody Affinity Maturation

Antibody affinity maturation involves selective survival of high affinity B cells and is thought to require the germinal center (GC) microenvironment. In this issue of Immunity, Di Niro et al. (2015) challenge this view, showing that low affinity B cells initiate Salmonella responses and affinity mature outside of GCs.

ICOS and Bcl6-dependent pathways maintain a CD4 T cell population with memory-like properties during tuberculosis

Protective CD4 T cells specific for M. tuberculosis (Mtb) are maintained in the lungs during active Mtb infection. Similar to memory CD4 T cells, persistence of these Mtb-specific cells requires intrinsic expression of Bcl6 and ICOS.

Immune control of persistent infection with Mycobacterium tuberculosis (Mtb) requires a sustained pathogen-specific CD4 T cell response; however, the molecular pathways governing the generation and maintenance of Mtb protective CD4 T cells are poorly understood. Using MHCII tetramers, we show that Mtb-specific CD4 T cells are subject to ongoing antigenic stimulation. Despite this chronic stimulation, a subset of PD-1⁺ cells is maintained within the lung parenchyma during tuberculosis (TB). When transferred into uninfected animals, these cells persist, mount a robust recall response, and provide superior protection to Mtb rechallenge when compared to terminally differentiated Th1 cells that reside preferentially in the lung-associated vasculature. The PD-1⁺ cells share features with memory CD4 T cells in that their generation and maintenance requires intrinsic Bcl6 and intrinsic ICOS expression. Thus, the molecular pathways required to maintain Mtb-specific CD4 T cells during ongoing infection are similar to those that maintain memory CD4 T cells in scenarios of antigen deprivation. These results suggest that vaccination strategies targeting the ICOS and Bcl6 pathways in CD4 T cells may provide new avenues to prevent TB.