Magnitude Of Cell Responses Research Articles

SARS-CoV-2 breakthrough infections enhance T cell response magnitude, breadth, and epitope repertoire

Little is known about the effect of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 or SARS2) vaccine breakthrough infections (BTIs) on the magnitude and breadth of the Tcell repertoire after exposure to different variants. We studied samples from individuals who experienced symptomatic BTIs during Delta or Omicron waves. In the pre-BTI samples, 30% of the donors exhibited substantial immune memory against non-S (spike) SARS2 antigens, consistent with previous undiagnosed asymptomatic SARS2 infections. Following symptomatic BTI, we observed (1) enhanced S-specific CD4 and CD8 Tcell responses in donors without previous asymptomatic infection, (2) expansion of CD4 and CD8 Tcell responses to non-S targets (M,N, and nsps) independent of SARS2 variant, and (3) generation of novel epitopes recognizing variant-specificmutations. These variant-specific Tcell responses accounted for 9%-15% of the total epitope repertoire. Overall, BTIs boost vaccine-induced immune responses by increasing the magnitude and by broadening the repertoire of Tcell antigens and epitopes recognized.

Magnitude of venous or capillary blood-derived SARS-CoV-2-specific T cell response determines COVID-19 immunity

T cells specific for SARS-CoV-2 are thought to protect against infection and development of COVID-19, but direct evidence for this is lacking. Here, we associated whole-blood-based measurement of SARS-CoV-2-specific interferon-γ-positive T cell responses with positive COVID-19 diagnostic (PCR and/or lateral flow) test results up to 6 months post-blood sampling. Amongst 148 participants donating venous blood samples, SARS-CoV-2-specific T cell response magnitude is significantly greater in those who remain protected versus those who become infected (P < 0.0001); relatively low magnitude T cell response results in a 43.2% risk of infection, whereas high magnitude reduces this risk to 5.4%. These findings are recapitulated in a further 299 participants testing a scalable capillary blood-based assay that could facilitate the acquisition of population-scale T cell immunity data (14.9% and 4.4%, respectively). Hence, measurement of SARS-CoV-2-specific T cells can prognosticate infection risk and should be assessed when monitoring individual and population immunity status.

Technical choices significantly alter the adaptive immune response against immunocompetent murine gliomas in a model-dependent manner.

Due to the recent rise in immunotherapy research to treat glioblastoma (GBM), immunocompetent mouse models have become increasingly crucial. However, the character and kinetics of the immune response against the most prevalent immunocompetent GBM models, GL261 and CT2A, have not been well studied, nor has the impact of commonly-used marker proteins and foreign antigens. In this study, we compared the immune response in these models using flow cytometry and immunohistochemistry as well as investigated several factors that influence the immune response, including kinetics, tumor size, and expression of commonly-used marker proteins and foreign antigens. We hypothesize that these factors influence the immune response enough to warrant consideration when studying new immunotherapeutic approaches for GBM. CT2A-Luc, but not GL261-Luc2, drastically increased the number of T cells in the brain compared with wild-type controls, and significantly altered CT2A's responsiveness to anti-PD-1 antibody therapy. Additionally, a larger cell inoculum size in the GL261 model increased the T cell response's magnitude at day 28 post-injection. CT2A and GL261 models both stimulate a peak T cell immune response at day 21 post-injection. Our results suggest that the impact of foreign proteins like luciferase on the intracranial immune response is dependent upon the model, with CT2A being more sensitive to added markers. In particular, luciferase expression in CT2A could lead to meaningful misinterpretations of results from immune checkpoint inhibitor (ICI) studies.

Proteome-Wide Zika Virus CD4 T Cell Epitope and HLA Restriction Determination.

Zika virus (ZIKV) is a mosquito-borne pathogen that caused an epidemic in 2015-2016. ZIKV-specific T cell responses are functional in animal infection models, and helper CD4 T cells promote avid Abs in the vaccine context. The small volumes of blood available from field research limit the determination of T cell epitopes for complex microbes such as ZIKV. The goal of this project was efficient determination of human ZIKV CD4 T cell epitopes at the whole proteome scale, including validation of reactivity to whole pathogen, using small blood samples from convalescent time points when T cell response magnitude may have waned. Polyclonal enrichment of candidate ZIKV-specific CD4 T cells used cell-associated virus, documenting that T cells in downstream peptide analyses also recognize whole virus after Ag processing. Sequential query of bulk ZIKV-reactive CD4 T cells with pooled/single ZIKV peptides and molecularly defined APC allowed precision epitope and HLA restriction assignments across the ZIKV proteome and enabled discovery of numerous novel ZIKV CD4 T cell epitopes. The research workflow is useful for the study of emerging infectious diseases with a very limited human blood sample availability.

Tumor infiltrating lymphocytes (TIL) therapy in metastatic melanoma: boosting of neoantigen-specific T cell reactivity and long-term follow-up

Treatment of metastatic melanoma with autologous tumor infiltrating lymphocytes (TILs) is currently applied in several centers. Robust and remarkably consistent overall response rates, of around 50% of treated patients, have...

Polyfunctional endogenous EBV-specific T cell response in nasopharyngeal carcinoma

Abstract Nasopharyngeal carcinoma (NPC) is associated with Epstein-Barr virus (EBV) infection and can be treated by adoptive transfer of EBV-specific T cells. Although EBV-specific T cell immune response has been identified in NPC, the phenotype and functionality of EBV-specific, tissue-resident memory T cells has not been explored. Tumor-infiltrating lymphocytes (TILs) were isolated from newly-diagnosed NPC and two types of EBV-unrelated malignancies; oral squamous cell carcinoma (OSCC) and renal cell carcinoma (RCC) tissue samples. We found that endogenous EBV-specific T cell response can be detected in the all the tissue types, including NPC, OSCC and RCC, but were rare in peripheral blood. In all tissues, EBV-specific T cells in tumor tissues exhibit resident memory phenotype characterized by high CD69 and CD103 expression and also an exhaustion phenotype characterized by high CD39 and PD-1 expression. Unexpectedly, EBV-specific T cell frequency as well as response magnitude were not enhanced in NPC when compared to other tissue types. The lack of an enhanced EBV-specific T cell response magnitude in NPC tissue confirms the concept that enhancement of EBV-specific immunity by adoptive T cell therapy may improve the outcome of NPC.

Roles of PD-1/PD-L1 Pathway: Signaling, Cancer, and Beyond.

Immunotherapies that target PD-1/PD-L1 axis have shown unprecedented success in a wide variety of human cancers. PD-1 is one of the key coinhibitory receptors expressed on T cells upon T cell activation. After engagement with its ligands, mainly PD-L1, PD-1 is activated and recruits the phosphatase SHP-2 in proximity to T cell receptor (TCR) and CD28 signaling. This event results in dephosphorylation and attenuation of key molecules in TCR and CD28 pathway, leading to inhibition of T cell proliferation, activation, cytokine production, altered metabolism and cytotoxic T lymphocytes (CTLs) killer functions, and eventual death of activated T cells. Bodies evolve coinhibitory pathways controlling T cell response magnitude and duration to limit tissue damage and maintain self-tolerance. However, tumor cells hijack these inhibitory pathways to escape host immune surveillance by overexpression of PD-L1. This provides the scientific rationale for clinical application of immune checkpoint inhibitors in oncology. The aberrantly high expression of PD-L1 in tumor microenvironment (TME) can be attributable to the "primary" activation of multiple oncogenic signaling and the "secondary" induction by inflammatory factors such as IFN-γ. Clinically, antibodies targeting PD-1/PD-L1 reinvigorate the "exhausted" T cells in TME and show remarkable objective response and durable remission with acceptable toxicity profile in large numbers of tumors such as melanoma, lymphoma, and mismatch-repair deficient tumors. Nevertheless, most patients are still refractory to anti-PD-1/PD-L1 therapy. Identifying the predictive biomarkers and design rational PD-1-based combination therapy become the priorities in cancer immunotherapy. PD-L1 expression, cytotoxic T lymphocytes infiltration, and tumor mutation burden (TMB) are generally considered as the most important factors affecting the effectiveness of PD-1/PD-L1 blockade. The revolution in cancer immunotherapy achieved by PD-1/PD-L1 blockade offers the paradigm for scientific translation from bench to bedside. The next decades will without doubt witness the renaissance of immunotherapy.

Extrinsically derived TNF is primarily responsible for limiting antiviral CD8+ T cell response magnitude.

TNF is a pro-inflammatory cytokine produced by both lymphoid and non-lymphoid cells. As a consequence of the widespread expression of its receptors (TNFR1 and 2), TNF plays a role in many important biological processes. In the context of influenza A virus (IAV) infection, TNF has variably been implicated in mediating immunopathology as well as suppression of the immune response. Although a number of cell types are able to produce TNF, the ability of CD8+ T cells to produce TNF following viral infection is a hallmark of their effector function. As such, the regulation and role of CD8+ T cell-derived TNF following viral infection is of great interest. Here, we show that the biphasic production of TNF by CD8+ T cells following in vitro stimulation corresponds to distinct patterns of epigenetic modifications. Further, we show that a global loss of TNF during IAV infection results in an augmentation of the peripheral virus-specific CD8+ T cell response. Subsequent adoptive transfer experiments demonstrated that this attenuation of the CD8+ T cell response was largely, but not exclusively, conferred by extrinsic TNF, with intrinsically-derived TNF making only modest contributions. In conclusion, TNF exerts an immunoregulatory role on CD8+ T cell responses following IAV infection, an effect that is largely mediated by extrinsically-derived TNF.

Abstract A80: Functionally significant heterogeneity in apparently homogenous naive CD8 T cell populations

Abstract Functional heterogeneity in apparently homogenous T cell populations has been well reported. However, what factors lead to such variations within a T cell population is still unclear. Depending upon the time of egress from the thymus and duration of residence in the periphery, individual cells would be of relatively different ages, however, consequences of such cellular aging have not been addressed. We observed that naive CD8 T cells from aged mice have lower coreceptor levels than naive CD8 T cells of young mice. Further, when naive T cells from young mice are separated into coreceptor-hi and coreceptor-lo subsets, we find that coreceptor-lo cells are smaller, respond poorly and are more susceptible to death. Similar coreceptor-lo associated defects were observed even in TCR-transgenic monoclonal CD8 T cell population. However, this phenotype is an outcome of peripheral residence, as coreceptor-lo and coreceptor-hi subsets of single-positive (SP) thymocytes do not show these differences. We show that coreceptor levels reduce over time, as a result of MHC-I mediated tonic signals and lower CD8 levels can be used as a surrogate marker to identify relatively aged cells in a naive CD8 T cell population. Thus, our data show that apparently unimodally distributed coreceptor heterogeneity among naive T cells, simplistically expected to be due to intrinsic noise, is not only correlated with major functional variation but is modulated by extrinsic microenvironmental cues in vivo. These findings indicate that ensemble averages may not represent individual cell function, even for a unimodal normal distribution of single cell measurements, highlighting the importance of distinguishing between population versus individual T cell responses to antigen encounter. At the population level, CD8 T cell response magnitude increases with ligand dose as well as with ligand affinity. However, whether ligand density and affinity only modulate the frequency of responding T cells and/or alters responses at the single cell level is unclear. We observed that the early activation response of individual naive CD8 T cell is binary such that the frequency of CD69 expressing cells increases with increment in ligand density or affinity, but the levels of CD69 expression in individual responding cells remain constant and variations in baseline cellular metabolic status between individual T cells may contribute to the differences in their activation thresholds. We show that ligand density and affinity determine the extent of TCR internalization in responding CD8 T cells, which in turn regulates the time to cell cycle entry. TCR internalization, which is commonly thought of as a mechanism to attenuate TCR-mediated signaling, was found to be associated with sustained TCR signaling via PI3K, leading to rapid metabolic reprogramming and when the degradation of internalized TCR complex is prevented, the duration of signaling is extended possibly from endosomal compartments, leading to better T cell response. Collectively, our findings reveal that heterogeneity among T cells for signal receptivity as well as microenvironmental influences experienced during their life history shape individual T cell responses and understanding the basis of heterogeneity within putatively homogenous T cell populations is significant for understanding of immune T cell responses. Citation Format: Renu Balyan, Rupali Gund, Chitra Ebenezer, Thyagarajan Krishnamurthy, Amanpreet Singh Chawla, Jeannine Durdik, Anna George, Vineeta Bal, Satyajit Rath. Functionally significant heterogeneity in apparently homogenous naive CD8 T cell populations. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2016 Oct 20-23; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2017;5(3 Suppl):Abstract nr A80.

HLA targeting efficiency correlates with human T cell response magnitude and with mortality from influenza A infection (P6082)

Abstract Experimental and computational evidence suggests that human leukocyte antigens (HLAs) preferentially bind conserved regions of viral proteins, a concept we term “targeting efficiency,” and that this preference can provide improved clearance of infection in several viral systems. One potential advantage of targeting conserved regions of a virus is the higher likelihood of cross-reactive protection from other viral strains, including those newly introduced, such as pH1N1. We hypothesized that individuals that targeted less conserved regions of influenza- A viruses would have weaker T-cell responses following infection with pH1N1. To test this hypothesis, T cell responses to A/H1N1 (2009) were measured from PBMCs obtained from a household cohort study performed during the 2009-2010 influenza season. We found that HLA targeting efficiency scores significantly correlated with IFNγ ELISpot responses (p=0.042, multiple regression). A further population-based analysis found that the carriage frequencies of the alleles with the lowest targeting efficiencies, A*24, were associated with pH1N1 mortality (r=0.37, p=0.031). Interestingly, these are common in certain indigenous populations in which increased pH1N1 morbidity has been reported. The computational tools utilized in this study may be useful predictors of potential morbidity and identify immunologic differences of new variant influenza strains more accurately than evolutionary sequence comparisons.

Analysis of influence of HLA-B broad specific Bw4 motif on HCV specific T cell response

Objective To study the influence of Bw4 broad specific motif on hepatitis C virus (HCV) specific T cell response.Methods The 86 patients with HCV infection were enrolled in this study,who had history of non-standard paid blood donation.The sequence specific primer SSP-PCR and specific primer Amplification Refractory Mutation system was used to analyze HLA type.The T cell response,using PBMCs stimulated by HCV nonstructural protein NS3,NS4 and NS5 was tested by ELISPOT assay.Results There were 29 (33.7％) cases with homozygosity Bw4/4,38 cases (44.2％) with heterozygosity Bw4/6 and 19(22.1％) cases with homozygosity Bw6/6 in 86 patients with HCV infection.HCV viral loads in Bw4/4group,Bw4/6 group and Bw6/6 group were (3.98±0.32) Log (copy/ml),(5.22± 0.29) Log (copy/ml),(5.04±0.38) Log(copy/ml),respectively and there was a significant difference in HCV load among three groups(P=0.0153).The 24 cases with HCV infection were test HCV specific T cell response divided homozygosity Bw4/4 group and non-homozygosity Bw4/4 group.The HCV specific T cell response frequency in homozygosity Bw4/4 group and non-homozygosity Bw4/4 group was 50％ (5/10) and 14.28％ (2/14,respectively.The HCV specific T cell response magnitude in homozygosity Bw4/4 group and non-homozygosity Bw4/4 group was 70 SFU/106 PBMC (0-2020 SFU/106 PBMC)and 0 SFU/106 PBMC (0-200 SFU/106 PBMC).The response magnitude and frequency in homozygosity Bw4/4 group was significantly higher than that of non-homozygosity Bw4/4 group,P value was 0.0450 and 0.069,respectively.In homozygosity Bw4/4 group NS5 induced T cell response was dominant.The NS5 specific T cell response frequency in Bw4/4 group and non-Bw4/4 group was 50％ and 7.14％,respectively,and the difference was nearly significant(P=0.050).Conclusion The HCV-infected blood donors with homozygosity for HLA-Bw4 alleles is associated with a significant lower HCV virus load and stronger HCV specific T cell response,compared with non-homozygosity Bw4/4 group. Key words: Hepatitis virus C; HLA; ELISPOT; T cell response

Human CD8+and CD4+T Cell Memory to Lymphocytic Choriomeningitis Virus Infection

Although cellular immunity to acute lymphocytic choriomeningitis virus (LCMV) infection has been well characterized in experimental studies in mice, the T cell response to this virus in humans is incompletely understood. Thus, we analyzed the breadths, magnitudes, and differentiation phenotypes of memory LCMV-specific CD8(+) and CD4(+) T cells in three human donors displaying a variety of disease outcomes after accidental needle stick injury or exposure to LCMV. Although only a small cohort of donors was analyzed at a single time point postinfection, several interesting observations were made. First, we were able to detect LCMV-specific CD8(+) and CD4(+) T cell responses directly ex vivo at 4 to 8 years after exposure, demonstrating the longevity of T cell memory in humans. Second, unlike in murine models of LCMV infection, we found that the breadths of memory CD8(+) and CD4(+) T cell responses were not significantly different from one another. Third, it seemed that the overall CD8(+) T cell response was augmented with increasing severity of disease, while the LCMV-specific CD4(+) T cell response magnitude was highly variable between the three different donors. Next, we found that LCMV-specific CD8(+) T cells in the three donors analyzed seemed to undergo an effector memory differentiation program distinct from that of CD4(+) T cells. Finally, the levels of expression of memory, costimulatory, and inhibitory receptors on CD8(+) and CD4(+) T cell subsets, in some instances, correlated with disease outcome. These data demonstrate for the first time LCMV-specific CD8(+) and CD4(+) T cells in infected humans and begin to provide new insights into memory T cell responses following an acute virus infection.

Human immunodeficiency virus type I-specific CD8+T cell subset abnormalities in chronic infection persist through effective antiretroviral therapy

BackgroundEffective highly active antiretroviral therapy (HAART) reduces human immunodeficiency virus (HIV) replication, restores CD4+ T lymphocyte counts and greatly reduces the incidence of opportunistic infections. While this demonstrates improved generalized immune function, rapid rebound to pre-treatment viral replication levels following treatment interruption indicates little improvement in immune control of HIV replication. The extent to which HAART can normalize HIV-specific CD8+ T cell function over time in individuals with chronic infection remains an important unresolved issue. In this study, we evaluated the magnitude, general specificity and character of HIV specific CD8+ T cell responses at four time points across 2-9 years in 2 groups of chronically infected individuals separated on the basis of either effective antiretroviral suppression or ongoing replication of HIV.MethodsPeripheral blood mononuclear cells (PBMC) were stimulated with overlapping 15mer peptides spanning HIV Gag, Pol, Env and Nef proteins. Cells producing interferon-γ (IFN-γ) or interleukin-2 (IL-2) were enumerated by ELISPOT and phenotyped by flow cytometry.Results and ConclusionsThe magnitude of the HIV-specific CD8+ T cell response ranged from < .01 to approximately 1.0% of PBMC and was significantly greater in the group with detectable viral replication. Stronger responses reflected higher numbers of CD8+CD45RA- effector memory cells producing IFN-γ, but not IL-2. Magnitude, general specificity and character of the HIV-specific CD8+ T cell response changed little over the study period. While antiretroviral suppression of HIV in chronic infection reduces HIV-specific CD8+ T cell response magnitude in the short term, it had no significant effect on response character over periods up to 9 years.

Differential Gene Expression in Primary Human Skin Keratinocytes and Fibroblasts in Response to Ionizing Radiation

Although skin is usually exposed during human exposures to ionizing radiation, there have been no thorough examinations of the transcriptional response of skin fibroblasts and keratinocytes to radiation. The transcriptional response of quiescent primary fibroblasts and keratinocytes exposed to from 10 cGy to 5 Gy and collected 4 h after treatment was examined. RNA was isolated and examined by microarray analysis for changes in the levels of gene expression. Exposure to ionizing radiation altered the expression of 279 genes across both cell types. Changes in RNA expression could be arranged into three main categories: (1) changes in keratinocytes but not in fibroblasts, (2) changes in fibroblasts but not in keratinocytes, and (3) changes in both. All of these changes were primarily of p53 target genes. Similar radiation-induced changes were induced in immortalized fibroblasts or keratinocytes. In separate experiments, protein was collected and analyzed by Western blotting for expression of proteins observed in microarray experiments to be overexpressed at the mRNA level. Both Q-PCR and Western blot analysis experiments validated these transcription changes. Our results are consistent with changes in the expression of p53 target genes as indicating the magnitude of cell responses to ionizing radiation.

Interleukin-31 and Oncostatin-M Mediate Distinct Signaling Reactions and Response Patterns in Lung Epithelial Cells

Lung epithelial cells are primary targets of oncostatin M (OSM) and, to a lower degree, of interleukin (IL)-6 and IL-31, all members of the IL-6 cytokine family. The OSM receptor (OSMR) signals through activation of STAT and mitogen-activated protein kinase pathways to induce genes encoding differentiated cell functions, reduce cell-cell interaction, and suppress cell proliferation. IL-31 functions through the heteromeric IL-31 receptor, which shares with OSMR the OSMRbeta subunit, but does not engage gp130, the common subunit of all other IL-6 cytokine receptors. Because the response of epithelial cells to IL-31 is unknown, the action of IL-31 was characterized in the human alveolar epithelial cell line A549 in which the expression of the ligand-binding IL-31Ralpha subunit was increased. IL-31 initiated signaling that differed from other IL-6 cytokines by the particularly strong recruitment of the STAT3, ERK, JNK, and Akt pathways. IL-31 was highly effective in suppressing proliferation by altering expression of cell cycle proteins, including up-regulation of p27(Kip1) and down-regulation of cyclin B1, CDC2, CDK6, MCM4, and retinoblastoma. A single STAT3 recruitment site (Tyr-721) in the cytoplasmic domain of IL-31Ralpha exerts a dominant function in the entire receptor complex and is critical for gene induction, morphological changes, and growth inhibition. The data suggest that inflammatory and immune reactions involving activated T-cells regulate functions of epithelial cells by IL-6 cytokines through receptor-defined signaling reactions.