Quantifiable predictive features define epitope-specific T cell receptor repertoires.

T cells are defined by a heterodimeric surface receptor, the T cell receptor (TCR), that mediates recognition of pathogen-associated epitopes through interactions with peptide and major histocompatibility complexes (pMHCs). TCRs are generated by genomic rearrangement of the germline TCR locus, a process termed V(D)J recombination, that has the potential to generate marked diversity of TCRs (estimated to range from 1015 (ref. 1) to as high as 1061 (ref. 2) possible receptors). Despite this potential diversity, TCRs from T cells that recognize the same pMHC epitope often share conserved sequence features, suggesting that it may be possible to predictively model epitope specificity. Here we report the in-depth characterization of ten epitope-specific TCR repertoires of CD8+ T cells from mice and humans, representing over 4,600 in-frame single-cell-derived TCRαß sequence pairs from 110 subjects. We developed analytical tools to characterize these epitope-specific repertoires: a distance measure on the space of TCRs that permits clustering and visualization, a robust repertoire diversity metric that accommodates the low number of paired public receptors observed when compared to single-chain analyses, and a distance-based classifier that can assign previously unobserved TCRs to characterized repertoires with robust sensitivity and specificity. Our analyses demonstrate that each epitope-specific repertoire contains a clustered group of receptors that share core sequence similarities, together with a dispersed set of diverse 'outlier' sequences. By identifying shared motifs in core sequences, we were able to highlight key conserved residues driving essential elements of TCR recognition. These analyses provide insights into the generalizable, underlying features of epitope-specific repertoires and adaptive immune recognition.

Molecular basis for universal HLA-A*0201-restricted CD8+ T-cell immunity against influenza viruses.

Memory CD8(+)T lymphocytes (CTLs) specific for antigenic peptides derived from internal viral proteins confer broad protection against distinct strains of influenza A virus (IAV). However, immune efficacy can be undermined by the emergence of escape mutants. To determine how T-cell receptor (TCR) composition relates to IAV epitope variability, we used ex vivo peptide-HLA tetramer enrichment and single-cell multiplex analysis to compare TCRs targeted to the largely conserved HLA-A*0201-M158and the hypervariable HLA-B*3501-NP418antigens. The TCRαßs for HLA-B*3501-NP418 (+)CTLs varied among individuals and across IAV strains, indicating that a range of mutated peptides will prime different NP418-specific CTL sets. Conversely, a dominant public TRAV27/TRBV19(+)TCRαß was selected in HLA-A*0201(+)donors responding to M158 This public TCR cross-recognized naturally occurring M158variants complexed with HLA-A*0201. Ternary structures showed that induced-fit molecular mimicry underpins TRAV27/TRBV19(+)TCR specificity for the WT and mutant M158peptides, suggesting the possibility of universal CTL immunity in HLA-A*0201(+)individuals. Combined with the high population frequency of HLA-A*0201, these data potentially explain the relative conservation of M158 Moreover, our results suggest that vaccination strategies aimed at generating broad protection should incorporate variant peptides to elicit cross-reactive responses against other specificities, especially those that may be relatively infrequent among IAV-primed memory CTLs.

CMV and Immunosenescence: from basics to clinics.

Alone among herpesviruses, persistent Cytomegalovirus (CMV) markedly alters the numbers and proportions of peripheral immune cells in infected-vs-uninfected people. Because the rate of CMV infection increases with age in most countries, it has been suggested that it drives or at least exacerbates "immunosenescence". This contention remains controversial and was the primary subject of the Third International Workshop on CMV & Immunosenescence which was held in Cordoba, Spain, 15-16th March, 2012. Discussions focused on several main themes including the effects of CMV on adaptive immunity and immunosenescence, characterization of CMV-specific T cells, impact of CMV infection and ageing on innate immunity, and finally, most important, the clinical implications of immunosenescence and CMV infection. Here we summarize the major findings of this workshop.

Cytomegalovirus infection and the risk of mortality and frailty in older women: a prospective observational cohort study.

Cytomegalovirus (CMV), a prevalent pathogen, causes severe disease in immunocompromised humans. However, present understanding is limited regarding the long-term clinical effect of persistent CMV infection in immunocompetent adults. The authors conducted a prospective observational cohort study (1992-2002) of 635 community-dwelling women in Baltimore, Maryland, aged 70-79 years in the Women's Health and Aging Studies to examine the effect of CMV infection on the risk of frailty, a common geriatric syndrome, and mortality in older women. The effect of baseline serum CMV antibody (immunoglobulin G) concentration on the risk of 3-year incident frailty, defined by using a 5-component measure, and 5-year mortality was examined with Cox proportional hazards models. Compared with those who were CMV seronegative, women in the highest quartile of CMV antibody concentration had a greater incidence of frailty (hazard ratio = 3.46, 95% confidence interval: 1.45, 8.27) and mortality (hazard ratio = 3.81, 95% confidence interval: 1.64, 8.83). After adjustment for potential confounders, CMV antibody concentration in the highest quartile independently increased the risk of 5-year mortality (hazard ratio = 2.79, 95% confidence interval: 1.22, 6.40). Better understanding of the long-term clinical consequences of CMV infection in immunocompetent humans is needed to guide public health efforts for this widely prevalent infection.

Shifting Food Systems: Increasing Well-Being Through Plant-Based Approaches.

Growing evidence reveals food production systems and consumption practices contradict goals for environmental well-being and population health. This interdisciplinary paper reviews research for impacts from diets on non-communicable human diseases, climate change, and animal well-being. With increasing pressures to innovate and reduce economic as well as emotional costs associated with ill-health, our recommendations could positively impact policy.

Cytotoxic polyfunctionality maturation of cytomegalovirus-pp65-specific CD4 + and CD8 + T-cell responses in older adults positively correlates with response size.

Cytomegalovirus (CMV) infection is one of the most common persistent viral infections in humans worldwide and is epidemiologically associated with many adverse health consequences during aging. Previous studies yielded conflicting results regarding whether large, CMV-specific T-cell expansions maintain their function during human aging. In the current study, we examined the in vitro CMV-pp65-reactive T-cell response by comprehensively studying five effector functions (i.e., interleukin-2, tumor necrosis factor-α, interferon-γ, perforin, and CD107a expression) in 76 seropositive individuals aged 70 years or older. Two data-driven, polyfunctionality panels (IL-2-associated and cytotoxicity-associated) derived from effector function co-expression patterns were used to analyze the results. We found that, CMV-pp65-reactive CD8 + and CD4 + T cells contained similar polyfunctional subsets, and the level of polyfunctionality was related to the size of antigen-specific response. In both CD8 + and CD4 + cells, polyfunctional cells with high cytotoxic potential accounted for a larger proportion of the total response as the total response size increased. Notably, a higher serum CMV-IgG level was positively associated with a larger T-cell response size and a higher level of cytotoxic polyfunctionality. These findings indicate that CMV-pp65-specific CD4 + and CD8 + T cell undergo simultaneous cytotoxic polyfunctionality maturation during aging.

Herpesvirus Infections and Risk of Frailty and Mortality in Older Women: Women's Health and Aging Studies.

OBJECTIVES: To examine the relationship between herpesvirus infections and mortality and incident frailty risks in community-dwelling older women. DESIGN: Nested prospective cohort study. SETTING: Women's Health and Aging Studies I and II. PARTICIPANTS: Community-dwelling older women aged 70 to 79 (n = 633). MEASUREMENTS: Baseline serum antibody (immunoglobulin G) levels against four herpesviruses (herpes simplex virus types 1 (HSV-1) and 2 (HSV-2), varicella-zoster virus (VZV), 7 Epstein-Barr virus (EBV)), 3-year incident frailty rates, and 5-year mortality. RESULTS: Women seropositive for HSV-1 and HSV-2, but not VZV and EBV, had higher risk of 3-year incident frailty (HSV-1: hazard ratio (HR) = 1.90, 95% confidence interval (CI) = 0.96-3.74; HSV-2: HR = 2.10, 95% CI = 1.05-4.37) and 5-year mortality (HR = 1.73, 95% CI = 0.93-3.20; HR = 1.80, 95% CI = 0.94-3.44, respectively) than seronegative women. Incremental increases in serum HSV-1 and HSV-2 antibody levels were associated with incrementally higher risks of incident frailty and mortality. After adjustment for potential confounders, only higher serum HSV-2 antibody level was independently predictive of higher risk of mortality in older women (for each unit increase in antibody index, HR = 1.47, 95% CI = 1.05-2.07). CONCLUSION: HSV-1 and HSV-2 antibody levels are not independently associated with risk of incident frailty in older women. Only HSV-2 antibody level is independently predictive of 5-year mortality risk, with each incremental increase in the antibody level adding further risk.

Single-Cell Analysis of T-Cell Receptor αß Repertoire.

The unbiased, paired analysis of T-cell receptor (TCR) α- and ß-chain usage at the single-cell level provides a valuable window of understanding into the TCR repertoire and the nature of the immune response. Earlier technologies for TCR repertoire analysis were often limited to examining TCR complementarity-determining region 3 (CDR3) ß expression or required in vitro cloning procedures that can artificially skew the TCR repertoire from its in vivo state. We describe here a direct ex vivo, single-cell-based strategy for the clonotypic analysis of TCRαß repertoires that utilizes multiplexed panels of TCRα and TCRß-specific primers in a nested PCR to amplify expressed transcripts from individual, epitope-specific T cells. This strategy yields the paired TCRαß sequences of any given population of αß T cells of interest.

Immunologic changes in frail older adults.

UNLABELLED: Several studies have shown a heightened inflammatory state in frail older adults, marked by high serum levels of interleukin-6 and C-reactive protein and an increased number of circulating leukocytes. Activation of monocytes and macrophages, marked by increased levels of neopterin, may contribute to chronic inflammation in the frail older adult. However, the reduced mononuclear cell response to lipopolysaccharide in vitro suggests the existence of defective activation pathways within the innate immune system possibly due to desensitization. Conversely, the expansion of CD8(+) T cells, and specifically those expressing the CCR5 chemokine receptor, above and beyond the levels observed in senescence, points to the involvement of adaptive immune pathways. In line with these observations, frail older adults exhibit a reduced antibody response to pneumococcal and influenza vaccines. Collectively, these observations support the existence of a dysregulated immune system in frail older adults and highlight the need for strategies to improve its function. ABBREVIATIONS: AIDS, acquired immunodeficiency syndrome; CCL, CC-chemokine receptor ligand; CCR, CC-chemokine receptor; CHS, Cardiovascular Health Study; CMV, cytomegalovirus; GTP, guanosine trisphosphate; HAART, highly active anti-retroviral therapy; HIV, human immunodeficiency virus; IDO, indoleamine-pyrrole 2,3-dioxygenase; IL, interleukin; IFN, interferon; MACS, Multicenter AIDS Cohort Study; NH2PPP, dihydro-neopterin trisphosphate; Tc, T cytotoxic; TCR, T-cell receptor; TEMRA, T effector memory cells re-expressing CD45RA; Th, T helper; TNF, tumor necrosis factor; WHAS, Women's Health and Aging Study.

T cell receptor αß diversity inversely correlates with pathogen-specific antibody levels in human cytomegalovirus infection.

A diverse T cell receptor (TCR) repertoire capable of recognizing a broad range of antigenic peptides is thought to be central to effective pathogen-specific immunity by counteracting escape mutations, selecting high-avidity T cells, and providing T cell specificities with comprehensive functional characteristics. However, evidence that TCR diversity is important for the successful control of human infections is limited. A single-cell strategy for the clonotypic analysis of human CD8⁺ TCRαß repertoires was used to probe the diversity and magnitude of individual human cytomegalovirus (CMV)-specific CD8⁺ T cells recovered directly ex vivo. We found that CD8⁺ TCRαß repertoire diversity, but not the size of the CD8⁺ T cell response, was inversely related to circulating CMV-specific antibody levels, a measure that has been correlated epidemiologically with differential mortality risks and found here to be higher in persons with detectable (versus undetectable) CMV viral loads. Overall, our findings indicate that CD8⁺ T cell diversity may be more important than T cell abundance in limiting the negative consequences of CMV persistence, demonstrate high prevalence of both TCRα and TCRß public motif usage, and suggest that a highly diverse TCRαß repertoire may be an important benchmark and target in the success of immunotherapeutic strategies.

Thyroid autoantibodies are associated with a reduced prevalence of frailty in community-dwelling older women.

CONTEXT: The contribution of autoimmunity to the multisystem dysregulation that characterizes the frailty syndrome in older adults is unknown. OBJECTIVE: The aim of the study was to investigate the relationship between thyroid antibodies and frailty in older women. DESIGN, SETTING, AND PARTICIPANTS: We conducted a cross-sectional study nested within the Women's Health and Aging Studies I and II. Thyroglobulin antibodies (TgAbs), thyroid peroxidase antibodies (TPOAbs), and antinuclear antibodies were measured in the baseline sera of 641 community-dwelling older women. MAIN OUTCOME MEASURE: Frailty was defined using a validated five-component measure. RESULTS: The prevalence of prefrailty and frailty was lower in TgAb-positive than negative older women (37.1 vs. 47.8% and 6.7 vs.11.9%, respectively; P = 0.01 and 0.03). The prevalence of prefrailty, but not frailty, was lower in TPOAb-positive than negative women (38.9 vs. 48.0% and 10.1 vs. 11.3%; P = 0.04 and 0.34). After adjustment for covariates including serum thyroid stimulation hormone concentration and thyroid medication usage in multinomial regression models, TgAb-positive older women had lower odds of prefrailty and frailty compared with TgAb-negative women (odds ratio 0.57 and 0.30; 95% confidence interval 0.34-0.98 and 0.10-0.85, respectively). Similarly, TPOAb-positive older women had lower odds of frailty compared with TPOAb-negative women (odds ratio 0.44; 95% confidence interval 0.20-0.96). These trends were not observed with antinuclear antibodies. CONCLUSION: Independent of thyroid function status, community-dwelling older women who are seropositive for TgAbs and TPOAbs are less likely to be frail than seronegative women.

T-lymphocytes expressing CC chemokine receptor-5 are increased in frail older adults.

OBJECTIVES: To evaluate the frequencies of T-lymphocytes expressing CC chemokine receptor-5 (CCR5(+) T-cells) and their relationship with frailty in older adults. DESIGN: Case-control study with an age-, race-, and sex-matched design. SETTING: General Clinical Research Center. PARTICIPANTS: Community-dwelling adults aged 72 and older from Baltimore, Maryland. METHODS: Frailty was determined using five validated criteria: weakness, slow walking speed, fatigue, low physical activity, and weight loss. Those meeting three or more of these five criteria were defined as frail and those with none as nonfrail. Complete blood counts were performed to obtain peripheral lymphocyte counts using an automated (Coulter) counter. Peripheral blood was collected for surface immunofluorescent staining of CCR5 and other T-cell markers. RESULTS: Twenty-six frail and matched nonfrail participants (mean age+/-standard deviation 83.8+/-5.3, range 72-94) completed the study. Frail participants had higher CCR5(+), CCR5(+)CD8(+), and CCR5(+)CD45RO(-) T-cell counts than matched nonfrail controls (349+/-160/mm(3) vs 194+/-168/mm(3), P=.02; 208+/-98/mm(3) vs 105+/-62/mm(3), P=.02; and 189+/-149/mm(3) vs 52+/-36/mm(3), P=.01; respectively). Furthermore, there was a trend toward graded increase in these T-cell counts across the frailty scores in frail participants (e.g., CCR5(+)CD8(+) counts of 123+/-52/mm(3), 248+/-115/mm(3), and 360+/-215/mm(3) for those with frailty scores of 3, 4, and 5, respectively). CONCLUSION: These initial results suggest an expansion of the CCR5(+) T-cell subpopulation in frailty. They provide a basis for further characterization of CCR5(+) T-cells and their role in frailty, with potential therapeutic implications.