60 results on '"Michelle A. Neller"'
Search Results
2. Complete response to PD-1 blockade following EBV-specific T-cell therapy in metastatic nasopharyngeal carcinoma
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Corey Smith, Margaret McGrath, Michelle A. Neller, Katherine K. Matthews, Pauline Crooks, Laetitia Le Texier, Benedict Panizza, Sandro Porceddu, and Rajiv Khanna
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Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Abstract Nasopharyngeal carcinoma (NPC) is an Epstein–Barr virus (EBV)-associated heterogeneous disease and is characterized by peritumoral immune infiltrate. Adoptive T-cell therapy (ACT) has emerged as a potential therapeutic strategy for NPC. However, the tumor microenvironment remains a major roadblock for the successful implementation of ACT in clinical settings. Expression of checkpoint molecules by malignant cells can inhibit the effector function of adoptively transferred EBV-specific T cells. Here we present a novel case report of a patient with metastatic NPC who was successfully treated with a combination of EBV-specific ACT and programmed cell death-1 blockade therapy. Following combination immunotherapy, the patient showed complete resolution of metastatic disease with no evidence of disease relapse for 22 months. Follow-up immunological analysis revealed dramatic restructuring of the global T-cell repertoire that was coincident with the clinical response. This case report provides an important platform for translating these findings to a larger cohort of NPC patients.
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- 2021
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3. Limited Recognition of Highly Conserved Regions of SARS-CoV-2
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Srividhya Swaminathan, Katie E. Lineburg, George R. Ambalathingal, Pauline Crooks, Emma J. Grant, Sonali V. Mohan, Jyothy Raju, Archana Panikkar, Laetitia Le Texier, Zheng Wei Marcus Tong, Keng Yih Chew, Michelle A. Neller, Kirsty R. Short, Harsha Gowda, Stephanie Gras, Rajiv Khanna, and Corey Smith
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SARS-CoV-2 ,COVID-19 ,antigen-specific CD8+ T cells ,conservation ,Microbiology ,QR1-502 - Abstract
ABSTRACT Understanding the immune response to severe acute respiratory syndrome coronavirus (SARS-CoV-2) is critical to overcome the current coronavirus disease (COVID-19) pandemic. Efforts are being made to understand the potential cross-protective immunity of memory T cells, induced by prior encounters with seasonal coronaviruses, in providing protection against severe COVID-19. In this study we assessed T-cell responses directed against highly conserved regions of SARS-CoV-2. Epitope mapping revealed 16 CD8+ T-cell epitopes across the nucleocapsid (N), spike (S), and open reading frame (ORF)3a proteins of SARS-CoV-2 and five CD8+ T-cell epitopes encoded within the highly conserved regions of the ORF1ab polyprotein of SARS-CoV-2. Comparative sequence analysis showed high conservation of SARS-CoV-2 ORF1ab T-cell epitopes in seasonal coronaviruses. Paradoxically, the immune responses directed against the conserved ORF1ab epitopes were infrequent and subdominant in both convalescent and unexposed participants. This subdominant immune response was consistent with a low abundance of ORF1ab encoded proteins in SARS-CoV-2 infected cells. Overall, these observations suggest that while cross-reactive CD8+ T cells likely exist in unexposed individuals, they are not common and therefore are unlikely to play a significant role in providing broad preexisting immunity in the community. IMPORTANCE T cells play a critical role in protection against SARS-CoV-2. Despite being highly topical, the protective role of preexisting memory CD8+ T cells, induced by prior exposure to circulating common coronavirus strains, remains less clear. In this study, we established a robust approach to specifically assess T cell responses to highly conserved regions within SARS-CoV-2. Consistent with recent observations we demonstrate that recognition of these highly conserved regions is associated with an increased likelihood of milder disease. However, extending these observations we observed that recognition of these conserved regions is rare in both exposed and unexposed volunteers, which we believe is associated with the low abundance of these proteins in SARS-CoV-2 infected cells. These observations have important implications for the likely role preexisting immunity plays in controlling severe disease, further emphasizing the importance of vaccination to generate the immunodominant T cells required for immune protection.
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- 2022
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4. Prophylactic and therapeutic strategies for Epstein–Barr virus-associated diseases: emerging strategies for clinical development
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Vijayendra Dasari, Debottam Sinha, Michelle A. Neller, Corey Smith, and Rajiv Khanna
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epstein–barr virus ,prophylactic vaccines ,therapeutic vaccines ,immunotherapies ,infectious mononucleosis ,nasopharyngeal carcinoma ,post-transplant lymphoproliferative disorder ,Internal medicine ,RC31-1245 - Abstract
Introduction: Epstein–Barr virus (EBV) infects more than 95% of the world’s population and is associated with infectious mononucleosis as well as a number of cancers in various geographical locations. Despite its significant health burden, no licenced prophylactic or therapeutic vaccines are available. Areas covered: Over the last two decades, our understanding of the role of EBV infection in the pathogenesis and immune regulation of EBV-associated diseases has provided new lines of research to conceptualize various novel prophylactic and therapeutic approaches to control EBV-associated disease. In this review, we evaluate the prophylactic and therapeutic vaccine approaches against EBV and various immunotherapeutic strategies against a number of EBV-associated malignancies. This review also describes the existing and future prospects of improved EBV-targeted therapeutic strategies. Expert opinion: It is anticipated that these emerging strategies will provide answers for the major challenges in EBV vaccine development and help improve the efficacy of novel therapeutic strategies.
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- 2019
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5. 'Off-the-shelf’ allogeneic antigen-specific adoptive T-cell therapy for the treatment of multiple EBV-associated malignancies
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Debottam Sinha, Sriganesh Srihari, Kirrliee Beckett, Laetitia Le Texier, Matthew Solomon, Archana Panikkar, George R Ambalathingal, Lea Lekieffre, Pauline Crooks, Sweera Rehan, Michelle A. Neller, Corey Smith, and Rajiv Khanna
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Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Background Epstein-Barr virus (EBV), an oncogenic human gammaherpesvirus, is associated with a wide range of human malignancies of epithelial and B-cell origin. Recent studies have demonstrated promising safety and clinical efficacy of allogeneic ‘off-the-shelf’ virus-specific T-cell therapies for post-transplant viral complications.Methods Taking a clue from these studies, we developed a highly efficient EBV-specific T-cell expansion process using a replication-deficient AdE1-LMPpoly vector that specifically targets EBV-encoded nuclear antigen 1 (EBNA1) and latent membrane proteins 1 and 2 (LMP1 and LMP2), expressed in latency II malignancies.Results These allogeneic EBV-specific T cells efficiently recognized human leukocyte antigen (HLA)-matched EBNA1-expressing and/or LMP1 and LMP2-expressing malignant cells and demonstrated therapeutic potential in a number of in vivo models, including EBV lymphomas that emerged spontaneously in humanized mice following EBV infection. Interestingly, we were able to override resistance to T-cell therapy in vivo using a ‘restriction-switching’ approach, through sequential infusion of two different allogeneic T-cell therapies restricted through different HLA alleles. Furthermore, we have shown that inhibition of the programmed cell death protein-1/programmed death-ligand 1 axis in combination with EBV-specific T-cell therapy significantly improved overall survival of tumor-bearing mice when compared with monotherapy.Conclusion These findings suggest that restriction switching by sequential infusion of allogeneic T-cell therapies that target EBV through distinct HLA alleles may improve clinical response.
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- 2021
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6. Epstein-Barr virus–specific T cell therapy for progressive multiple sclerosis
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Michael P. Pender, Peter A. Csurhes, Corey Smith, Nanette L. Douglas, Michelle A. Neller, Katherine K. Matthews, Leone Beagley, Sweera Rehan, Pauline Crooks, Tracey J. Hopkins, Stefan Blum, Kerryn A. Green, Zara A. Ioannides, Andrew Swayne, Blake T. Aftab, Kaye D. Hooper, Scott R. Burrows, Kate M. Thompson, Alan Coulthard, and Rajiv Khanna
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Medicine - Published
- 2020
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7. Pre-emptive and therapeutic adoptive immunotherapy for nasopharyngeal carcinoma: Phenotype and effector function of T cells impact on clinical response
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Corey Smith, Victor Lee, Andrea Schuessler, Leone Beagley, Sweera Rehan, Janice Tsang, Vivian Li, Randal Tiu, David Smith, Michelle A. Neller, Katherine K. Matthews, Emma Gostick, David A. Price, Jacqueline Burrows, Glen M. Boyle, Daniel Chua, Benedict Panizza, Sandro V. Porceddu, John Nicholls, Dora Kwong, and Rajiv Khanna
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adoptive immunotherapy ,epstein-barr virus ,t cells ,safety ,nasopharyngeal carcinoma ,Immunologic diseases. Allergy ,RC581-607 ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Adoptive T cell therapy has emerged as a powerful strategy to treat human cancers especially haematological malignancies. Extension of these therapies to solid cancers remains a significant challenge especially in the context of defining immunological correlates of clinical responses. Here we describe results from a clinical study investigating autologous Epstein-Barr virus (EBV)-specific T cells generated using a novel AdE1-LMPpoly vector to treat patients with nasopharyngeal carcinoma (NPC) either pre-emptively in at-risk patients with no or minimal residual disease (N/MRD) or therapeutically in patients with active recurrent/metastatic disease (ARMD). Tolerability, safety and efficacy, including progression-free survival (PFS) and overall survival (OS), were evaluated following adoptive T-cell immunotherapy. Twenty-nine patients, including 20 with ARMD and nine with N/MRD, successfully completed T-cell therapy. After a median follow-up of 18.5 months, the median PFS was 5.5 months (95% CI 2.1 to 9.0 months) and the median OS was 38.1 months (95% CI 17.2 months to not reached). Post-immunotherapy analyses revealed that disease stabilization in ARMD patients was significantly associated with the functional and phenotypic composition of in vitro-expanded T cell immunotherapy. These included a higher proportion of effector CD8+ T-cells and an increased number of EBV-specific T-cells with broader antigen specificity. These observations indicate that adoptive immunotherapy with AdE1-LMPpoly-expanded T cells stabilizes relapsed, refractory NPC without significant toxicity. Promising clinical outcomes in N/MRD patients further suggest a potential role for this approach as a consolidation treatment following first-line chemotherapy.
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- 2017
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8. Supplementary Figure 1B from Exome Sequencing to Predict Neoantigens in Melanoma
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Christopher W. Schmidt, Thomas Wölfel, Volker Lennerz, Martina Fatho, J. Alejandro Lopez, Nicholas K. Hayward, Michelle A. Neller, Julie G. Burel, and Antonia L. Pritchard
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Raw scanned data from ELISpot plate scanning reader (AID ELISpot Reader Classic); data was then processed using the AID ELISpot software to standardise and analyse the spot counts using intensity and size measurements, to provide the final data presented in Supplementary Figure 2.
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- 2023
9. Data from Exome Sequencing to Predict Neoantigens in Melanoma
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Christopher W. Schmidt, Thomas Wölfel, Volker Lennerz, Martina Fatho, J. Alejandro Lopez, Nicholas K. Hayward, Michelle A. Neller, Julie G. Burel, and Antonia L. Pritchard
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The ability to use circulating peripheral blood cells and matched tumor sequencing data as a basis for neoantigen prediction has exciting possibilities for application in the personalized treatment of cancer patients. We have used a high-throughput screening approach, combining whole-exome sequence data, mRNA microarrays, and publicly available epitope prediction algorithm output to identify mutated proteins processed and displayed by patient tumors and recognized by circulating immune cells. Matched autologous melanoma cell lines and peripheral blood mononuclear cells were used to create mixed lymphocyte tumor cell cultures, resulting in an expansion of tumor-reactive T cells to use for mutated peptide screening. Five patients were investigated, three of whom had a durable complete response (CR; 15+ years) in an autologous melanoma-pulsed dendritic cell clinical trial. We identified seven mutated antigens in total that stimulated T-effector memory cells in two of the five patients. While the procedure did not result in clinically applicable neoantigens for all patients, those identified were likely important in tumor clearance, leading to durable CR. The nature of the screening process allows results to be obtained rapidly and is easily applicable to a wide variety of different tumor types. Cancer Immunol Res; 3(9); 992–8. ©2015 AACR.
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- 2023
10. Supplementary Figure 3 from Exome Sequencing to Predict Neoantigens in Melanoma
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Christopher W. Schmidt, Thomas Wölfel, Volker Lennerz, Martina Fatho, J. Alejandro Lopez, Nicholas K. Hayward, Michelle A. Neller, Julie G. Burel, and Antonia L. Pritchard
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Populations of IFNγ high and IFNγ low in response to tumour/peptide stimulation in MLTC at day 34 in patients (A) D05 and (B) D14
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- 2023
11. Supplementary Figure 2 from Exome Sequencing to Predict Neoantigens in Melanoma
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Christopher W. Schmidt, Thomas Wölfel, Volker Lennerz, Martina Fatho, J. Alejandro Lopez, Nicholas K. Hayward, Michelle A. Neller, Julie G. Burel, and Antonia L. Pritchard
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Raw data from the initial peptide screen across MLTC assessed by IFNγ ELISpot. The yellow line delineates 30 spots and the red line marks 40 spots. Each bar represents wells assessed in triplicate, averaged and the average background measurement subtracted. The top measurement was capped at 200 spots.
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- 2023
12. Supplementary Table 2 from Exome Sequencing to Predict Neoantigens in Melanoma
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Christopher W. Schmidt, Thomas Wölfel, Volker Lennerz, Martina Fatho, J. Alejandro Lopez, Nicholas K. Hayward, Michelle A. Neller, Julie G. Burel, and Antonia L. Pritchard
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Total raw dataset of assessment of potential neoepitope sequences through epitope prediction programs for D05, D14, D41, A02 and A06.
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- 2023
13. Supplementary Figure 5 from Exome Sequencing to Predict Neoantigens in Melanoma
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Christopher W. Schmidt, Thomas Wölfel, Volker Lennerz, Martina Fatho, J. Alejandro Lopez, Nicholas K. Hayward, Michelle A. Neller, Julie G. Burel, and Antonia L. Pritchard
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Gating strategy for CD8+ T-cell subsets. CM: Central memory; EM: Effector memory; TEMRA: Effector memory expressing CD45RA
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- 2023
14. Supplementary Table 1 from Exome Sequencing to Predict Neoantigens in Melanoma
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Christopher W. Schmidt, Thomas Wölfel, Volker Lennerz, Martina Fatho, J. Alejandro Lopez, Nicholas K. Hayward, Michelle A. Neller, Julie G. Burel, and Antonia L. Pritchard
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Cell line information and Sanger sequence confirmed mutations in each cell line.
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- 2023
15. Supplementary Figure 4 from Exome Sequencing to Predict Neoantigens in Melanoma
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Christopher W. Schmidt, Thomas Wölfel, Volker Lennerz, Martina Fatho, J. Alejandro Lopez, Nicholas K. Hayward, Michelle A. Neller, Julie G. Burel, and Antonia L. Pritchard
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Whole -exome alignment of PABPC3 compared to the PABPC1 sequence (A): PABPC3 sequencing reads alignment with PABPC1 and PABPC3 reference sequence. (B): PABPC3 dinucleotide change resulting in R -->Q amino acid change in the protein sequence.
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- 2023
16. Ablation of CD8+ T cell recognition of an immunodominant epitope in SARS-CoV-2 Omicron variants BA.1, BA.2 and BA.3
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Srividhya Swaminathan, Katie E. Lineburg, Archana Panikkar, Jyothy Raju, Lawton D. Murdolo, Christopher Szeto, Pauline Crooks, Laetitia Le Texier, Sweera Rehan, Michael J. Dewar-Oldis, Peter J. Barnard, George R. Ambalathingal, Michelle A. Neller, Kirsty R. Short, Stephanie Gras, Rajiv Khanna, and Corey Smith
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Multidisciplinary ,General Physics and Astronomy ,General Chemistry ,General Biochemistry, Genetics and Molecular Biology ,Uncategorized - Abstract
The emergence of the SARS-CoV-2 Omicron variant has raised concerns of escape from vaccine-induced immunity. A number of studies have demonstrated a reduction in antibody-mediated neutralization of the Omicron variant in vaccinated individuals. Preliminary observations have suggested that T cells are less likely to be affected by changes in Omicron. However, the complexity of human leukocyte antigen genetics and its impact upon immunodominant T cell epitope selection suggests that the maintenance of T cell immunity may not be universal. In this study, we describe the impact that changes in Omicron BA.1, BA.2 and BA.3 have on recognition by spike-specific T cells. These T cells constitute the immunodominant CD8+ T cell response in HLA-A*29:02+ COVID-19 convalescent and vaccinated individuals; however, they fail to recognize the Omicron-encoded sequence. These observations demonstrate that in addition to evasion of antibody-mediated immunity, changes in Omicron variants can also lead to evasion of recognition by immunodominant T cell responses.
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- 2023
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17. Correction: Profiling HPV-16–specific T cell responses reveals broad antigen reactivities in oropharyngeal cancer patients
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Kunal H. Bhatt, Michelle A. Neller, Sriganesh Srihari, Pauline Crooks, Lea Lekieffre, Blake T. Aftab, Howard Liu, Corey Smith, Liz Kenny, Sandro Porceddu, and Rajiv Khanna
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Immunology ,Immunology and Allergy - Published
- 2022
18. Complete response to PD-1 blockade following EBV-specific T-cell therapy in metastatic nasopharyngeal carcinoma
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Benedict Panizza, Michelle A Neller, Pauline Crooks, Sandro V. Porceddu, Laetitia Le Texier, Katherine K. Matthews, Corey Smith, Margaret McGrath, and Rajiv Khanna
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0301 basic medicine ,Cancer Research ,T cell ,Cell ,Case Report ,Cancer immunotherapy ,Disease ,Virus ,03 medical and health sciences ,0302 clinical medicine ,medicine ,Tumour virus infections ,RC254-282 ,Tumor microenvironment ,Effector ,business.industry ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,medicine.disease ,Blockade ,030104 developmental biology ,medicine.anatomical_structure ,Oncology ,Nasopharyngeal carcinoma ,030220 oncology & carcinogenesis ,Cancer research ,business - Abstract
Nasopharyngeal carcinoma (NPC) is an Epstein–Barr virus (EBV)-associated heterogeneous disease and is characterized by peritumoral immune infiltrate. Adoptive T-cell therapy (ACT) has emerged as a potential therapeutic strategy for NPC. However, the tumor microenvironment remains a major roadblock for the successful implementation of ACT in clinical settings. Expression of checkpoint molecules by malignant cells can inhibit the effector function of adoptively transferred EBV-specific T cells. Here we present a novel case report of a patient with metastatic NPC who was successfully treated with a combination of EBV-specific ACT and programmed cell death-1 blockade therapy. Following combination immunotherapy, the patient showed complete resolution of metastatic disease with no evidence of disease relapse for 22 months. Follow-up immunological analysis revealed dramatic restructuring of the global T-cell repertoire that was coincident with the clinical response. This case report provides an important platform for translating these findings to a larger cohort of NPC patients.
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- 2021
19. Pretransplant Cytomegalovirus-Specific Cellular Immunity and Risk of Viral Reactivation Following Lung Transplantation: A Prospective Cohort Study
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Katie E. Lineburg, Rajiv Khanna, Debottam Sinha, Michelle A Neller, Pauline Crooks, Katherine K. Matthews, Michelle Grant, Mohammed Altaf, George R Ambalathingal, Peter Hopkins, Corey Smith, Sweera Rehan, and Daniel C. Chambers
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Cellular immunity ,medicine.medical_treatment ,Congenital cytomegalovirus infection ,030230 surgery ,03 medical and health sciences ,0302 clinical medicine ,Immunity ,Humans ,Immunology and Allergy ,Medicine ,Lung transplantation ,Prospective Studies ,Prospective cohort study ,Immunity, Cellular ,Viral reactivation ,Lung ,business.industry ,Incidence (epidemiology) ,virus diseases ,medicine.disease ,surgical procedures, operative ,Infectious Diseases ,medicine.anatomical_structure ,Cytomegalovirus Infections ,Immunology ,Latent Infection ,030211 gastroenterology & hepatology ,business ,Lung Transplantation - Abstract
Cytomegalovirus (CMV) remains a significant burden in lung transplant recipients. Deficiencies in T-cell immunity posttransplant increase the risk of CMV-associated complications. However, it is not clear if underlying poor pretransplant immunity increases risk. To assess this, we recruited 39 prospective lung transplant patients and performed QuantiFERON-CMV on their peripheral blood. More than a third of prospective CMV-seropositive transplant recipients were CMV non-immune reactive (CMV-NIR) pretransplant. CMV-NIR status was associated with a significantly higher incidence of CMV reactivation posttransplant, demonstrating that dysfunctional CMV immunity in prospective lung transplant recipients is associated with an increased risk of viral reactivation posttransplant.
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- 2020
20. Autologous CMV-specific T cells are a safe adjuvant immunotherapy for primary glioblastoma multiforme
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Pauline Crooks, Michelle A Neller, David G. Walker, Corey Smith, Sweera Rehan, J. Paulo Martins, George R Ambalathingal, Beth Morrison, Laetitia Le Texier, Leone Beagley, Katherine K. Matthews, Sriganesh Srihari, Archana Panikkar, Rajiv Khanna, and Katie E. Lineburg
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Adult ,Male ,0301 basic medicine ,Oncology ,medicine.medical_specialty ,T-Lymphocytes ,medicine.medical_treatment ,Cytomegalovirus ,Disease-Free Survival ,Blood Transfusion, Autologous ,03 medical and health sciences ,0302 clinical medicine ,Antigen ,Cancer immunotherapy ,Internal medicine ,medicine ,Adjuvant therapy ,Humans ,Prospective Studies ,Prospective cohort study ,business.industry ,General Medicine ,Immunotherapy ,Middle Aged ,Gene signature ,Survival Rate ,Clinical trial ,030104 developmental biology ,Lymphocyte Transfusion ,030220 oncology & carcinogenesis ,Female ,Clinical Medicine ,Glioblastoma ,business ,Adjuvant ,Follow-Up Studies - Abstract
Background The recent failure of checkpoint-blockade therapies for glioblastoma multiforme (GBM) in late-phase clinical trials has directed interest towards adoptive cellular immunotherapies (ACT). In this open-label, first-in-human trial, we have assessed the safety and therapeutic potential of cytomegalovirus (CMV)-specific ACT in an adjuvant setting for patients with primary GBM, with an ultimate goal to prevent or delay recurrence and prolong overall survival. Methods Twenty-eight patients with primary GBM were recruited to this prospective study, 25 of whom were treated with in vitro-expanded autologous CMV-specific T cells. Participants were monitored for safety, progression-free survival (PFS), overall survival (OS) and immune reconstitution. Results No participants showed evidence of ACT-related toxicities. Of 25 evaluable participants, ten were alive at the completion of follow-up, while five were disease free. Reconstitution of CMV-specific T-cell immunity was evident and CMV-specific ACT may trigger bystander effect leading to additional T-cell responses to non-viral tumour-associated antigens through epitope spreading. Long-term follow-up of participants treated before recurrence showed significantly improved OS when compared to those who progressed before ACT (median 23 months, range 7-65 vs. median 14 months, range 5-19; p=0.018). Gene expression analysis of the ACT products indicated that a favourable T-cell gene signature was associated with improved long-term survival. Conclusion Data presented in this study demonstrate that CMV-specific ACT can be safely used as an adjuvant therapy for primary GBM and, if offered before recurrence, this therapy may improve overall survival of GBM patients. Trial registration anzctr.org.au: ACTRN12615000656538Funding Source:National Health & Medical Research Council (Australia)Trial registration: anzctr.org.au: ACTRN12615000656538Funding Source: Philanthropic funding &National Health & Medical Research Council (Australia).
- Published
- 2020
21. Ablation of CD8
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Srividhya, Swaminathan, Katie E, Lineburg, Archana, Panikkar, Jyothy, Raju, Lawton D, Murdolo, Christopher, Szeto, Pauline, Crooks, Laetitia, Le Texier, Sweera, Rehan, Michael J, Dewar-Oldis, Peter J, Barnard, George R, Ambalathingal, Michelle A, Neller, Kirsty R, Short, Stephanie, Gras, Rajiv, Khanna, and Corey, Smith
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Immunodominant Epitopes ,SARS-CoV-2 ,Spike Glycoprotein, Coronavirus ,Humans ,COVID-19 ,CD8-Positive T-Lymphocytes ,Antibodies, Viral ,Antibodies, Neutralizing - Abstract
The emergence of the SARS-CoV-2 Omicron variant has raised concerns of escape from vaccine-induced immunity. A number of studies have demonstrated a reduction in antibody-mediated neutralization of the Omicron variant in vaccinated individuals. Preliminary observations have suggested that T cells are less likely to be affected by changes in Omicron. However, the complexity of human leukocyte antigen genetics and its impact upon immunodominant T cell epitope selection suggests that the maintenance of T cell immunity may not be universal. In this study, we describe the impact that changes in Omicron BA.1, BA.2 and BA.3 have on recognition by spike-specific T cells. These T cells constitute the immunodominant CD8
- Published
- 2022
22. Low antigen abundance limits efficient T-cell recognition of highly conserved regions of SARS-CoV-2
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Pauline Crooks, Harsha Gowda, Archana Panikkar, Zhen Tong, Katie E. Lineburg, Rajiv Khanna, Sonali Mohan, Stephanie Gras, Kirsty R. Short, Michelle A Neller, Corey Smith, Emma J. Grant, Laetitia Le Texier, George R Ambalathingal, Keng Chew, Jyothy Raju, and Srividhya Swaminathan
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Subdominant ,viruses ,T cell ,biochemical phenomena, metabolism, and nutrition ,Biology ,medicine.disease_cause ,Virology ,Epitope ,medicine.anatomical_structure ,Immune system ,Epitope mapping ,Antigen ,medicine ,CD8 ,Coronavirus - Abstract
SummaryUnderstanding the immune response to severe acute respiratory syndrome coronavirus (SARS-CoV-2) is critical to overcome the current coronavirus disease (COVID-19) pandemic. Efforts are being made to understand the potential cross-protective immunity of memory T cells, induced by prior encounters with seasonal coronaviruses, in providing protection against severe COVID-19. In this study we assessed T-cell responses directed against highly conserved regions of SARS-CoV-2. Epitope mapping revealed 16 CD8+ T-cell epitopes across the nucleocapsid (N), spike (S) and ORF3a proteins of SARS-CoV-2 and five CD8+ T-cell epitopes encoded within the highly conserved regions of the ORF1ab polyprotein of SARS-CoV-2. Comparative sequence analysis showed high conservation of SARS-CoV-2 ORF1ab T-cell epitopes in seasonal coronaviruses. Paradoxically, the immune responses directed against the conserved ORF1ab epitopes were infrequent and subdominant in both convalescent and unexposed participants. This subdominant immune response was consistent with a low abundance of ORF1ab encoded proteins in SARS-CoV-2 infected cells. Overall, these observations suggest that while cross-reactive CD8+ T cells likely exist in unexposed individuals, they are not common and therefore are unlikely to play a significant role in providing broad pre-existing immunity in the community.
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- 2021
23. T cell repertoire remodeling following post-transplant T cell therapy coincides with clinical response
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Scott B. Campbell, Michelle A Neller, Daniel C. Chambers, Ross S Francis, Matthew Solomon, Corey Smith, Katherine K. Matthews, Laetitia Le Texier, Rajiv Khanna, Sweera Rehan, Pauline Crooks, Leone Beagley, and Dillon Corvino
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Adult ,Male ,0301 basic medicine ,Receptors, Antigen, T-Cell, alpha-beta ,T-Lymphocytes ,medicine.medical_treatment ,T cell ,Cytomegalovirus ,Context (language use) ,03 medical and health sciences ,0302 clinical medicine ,Immune system ,Immunity ,Drug Resistance, Viral ,Humans ,Medicine ,business.industry ,Repertoire ,T-cell receptor ,Organ Transplantation ,General Medicine ,Immunotherapy ,Adoptive Transfer ,Transplantation ,030104 developmental biology ,medicine.anatomical_structure ,030220 oncology & carcinogenesis ,Cytomegalovirus Infections ,Immunology ,Female ,Clinical Medicine ,business - Abstract
BACKGROUND: Impaired T cell immunity in transplant recipients is associated with infection-related morbidity and mortality. We recently reported the successful use of adoptive T cell therapy (ACT) against drug-resistant/recurrent cytomegalovirus in solid-organ transplant recipients. METHODS: In the present study, we used high-throughput T cell receptor Vβ sequencing and T cell functional profiling to delineate the impact of ACT on T cell repertoire remodeling in the context of pretherapy immunity and ACT products. RESULTS: These analyses indicated that a clinical response was coincident with significant changes in the T cell receptor Vβ landscape after therapy. This restructuring was associated with the emergence of effector memory T cells in responding patients, while nonresponders displayed dramatic pretherapy T cell expansions with minimal change following ACT. Furthermore, immune reconstitution included both adoptively transferred clonotypes and endogenous clonotypes not detected in the ACT products. CONCLUSION: These observations demonstrate that immune control following ACT requires significant repertoire remodeling, which may be impaired in nonresponders because of the preexisting immune environment. Immunological interventions that can modulate this environment may improve clinical outcomes. TRIAL REGISTRATION: Australian New Zealand Clinical Trial Registry, ACTRN12613000981729. FUNDING: This study was supported by funding from the National Health and Medical Research Council, Australia (APP1132519 and APP1062074).
- Published
- 2019
24. Adoptive T-cell therapy for pediatric cytomegalovirus-associated retinitis
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Rajiv Khanna, Rajan Patheja, Chris Fraser, Sweera Rehan, Shaheen P. Shah, Corey Smith, Shiney Seo, Pauline Crooks, and Michelle A Neller
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Male ,0301 basic medicine ,Adoptive cell transfer ,T cell ,Congenital cytomegalovirus infection ,Cytomegalovirus ,Retinitis ,chemical and pharmacologic phenomena ,Cell therapy ,03 medical and health sciences ,0302 clinical medicine ,Drug Resistance, Multiple, Viral ,immune system diseases ,hemic and lymphatic diseases ,Humans ,Medicine ,business.industry ,Hematopoietic stem cell ,Hematology ,medicine.disease ,Adoptive Transfer ,Stimulus Report ,surgical procedures, operative ,030104 developmental biology ,medicine.anatomical_structure ,Child, Preschool ,030220 oncology & carcinogenesis ,Cytomegalovirus Retinitis ,Immunology ,Bone marrow ,business ,therapeutics ,CD8 - Abstract
Primary cytomegalovirus (CMV) infection usually passes unnoticed in children or causes a nonspecific febrile illness in adults. Seropositivity is estimated at between 30% and 70% in the adult population.1 CMV becomes latent in bone marrow and reactivates when myeloid progenitor cells respond to other infections.2 Reactivation is normally controlled by virus-specific CD4+ and CD8+ T-cell responses.2,3 Impaired T-cell function increases the risk for systemic reactivation.4,5 This may be a result of a diminished primary T-cell response after allogeneic bone marrow or solid organ transplantation, or a reduction in a previously effective CMV-specific T-cell response resulting from immunosuppression.6,7 The primary ocular manifestation is a progressive necrotizing retinitis caused by a viral cytopathic effect.2 Although the majority of patients are successfully treated with antiviral agents, these agents have significant toxicities, most notably myelosuppression and nephrotoxicity. Persistent CMV infections are particularly problematic in the recipients of T-cell–depleted hematopoietic stem cell transplants (HSCTs).8 Adoptive cell therapy (ACT) with CMV-specific T cells is increasingly recognized as a treatment modality for systemic CMV, which can lead to significant reduction in viremia.1,9,10 To our knowledge, this is the first report of its successful use specifically for CMV retinitis in a pediatric setting.
- Published
- 2019
25. Rapid whole‐blood assay to detect SARS‐CoV‐2‐specific memory T‐cell immunity following a single dose of AstraZeneca ChAdOx1‐S COVID‐19 vaccine
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Lea Lekieffre, Sweera Rehan, Rajiv Khanna, George R Ambalathingal, Archana Panikkar, Sriganesh Srihari, Katie E. Lineburg, Michelle A Neller, Caitlyn Smith, Pauline Crooks, Srividhya Swaminathan, Laetitia Le Texier, Jyothy Raju, and Corey Smith
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business.industry ,Short Communication ,medicine.medical_treatment ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Immunology ,Short Communications ,T cells ,Booster dose ,RC581-607 ,SARS‐CoV‐2 ,Neutralization ,Vaccination ,medicine.anatomical_structure ,Cytokine ,COVID‐19 ,Immunity ,vaccine ,Immunology and Allergy ,Medicine ,Immunologic diseases. Allergy ,business ,Memory T cell ,General Nursing ,Whole blood - Abstract
Objectives With the ongoing emergence of SARS‐CoV‐2 variants and potential to evade vaccine‐induced neutralisation, understanding the magnitude and breadth of vaccine‐induced T‐cell immunity will be critical for the ongoing optimisation of vaccine approaches. Strategies that provide a rapid and easily translatable means of assessing virus‐specific T‐cell responses provide an opportunity to monitor the impact of vaccine rollouts in the community. In this study, we assessed whether our recently developed SARS‐CoV‐2 whole‐blood assay could be used effectively to analyse T‐cell responses following vaccination. Methods Following a median of 15 days after the first dose of the ChAdOx1‐S (AstraZeneca®) vaccine, peripheral blood was isolated from 58 participants. Blood was incubated overnight with an overlapping set of spike protein peptides and assessed for cytokine production using a cytometric bead array. Results The majority of vaccine recipients (51/58) generated a T helper 1 response (IFN‐γ and/or IL‐2) following a single dose of ChAdOx1‐S. The magnitude of the IFN‐γ and IL‐2 response strongly correlated in vaccine recipients. While the production of other cytokines was evident in individuals who did not generate IFN‐γ and IL‐2, they showed no correlation in magnitude, nor did we see a correlation between sex or age and the magnitude of the response. Conclusions The whole‐blood cytokine assay provides a rapid approach to assessing T‐cell immunity against SARS‐CoV‐2 in vaccine recipients. While the majority of participants generated a robust SARS‐CoV‐2‐specific T‐cell response following their first dose, some did not, demonstrating the likely importance of the booster dose in improving T‐cell immunity., Strategies that provide a rapid and easily translatable means of assessing SARS‐CoV‐2‐specific T‐cell responses provide an opportunity to monitor the impact of vaccine rollouts in the community. In this study, we assessed whether our recently developed SARS‐CoV‐2 whole‐blood assay could be used effectively to analyse T‐cell responses following vaccination. We demonstrated that the whole‐blood cytokine assay provides a rapid approach to assessing T‐cell immunity against SARS‐CoV‐2 in vaccine recipients.
- Published
- 2021
26. Pre-Existing Cellular Immunity to SARS-CoV-2 Through an Immunodominant Epitope
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Athena Nguyen, Keng Yih Chew, Emma J. Grant, Sweera Rehan, Dhilshan Jayasinghe, Alan Riboldi-Tunnicliffe, Lea Lekieffre, Stephanie Gras, Katie E. Lineburg, Jyothy Raju, Rajiv Khanna, Pauline Crooks, Christian A. Lobos, Demetra S.M. Chatzileontiadou, Hannah Sloane, Michelle A Neller, Weisan Chen, Tong Zwm, Srividhya Swaminathan, H. Halim, Corey Smith, Jacqueline M. Burrows, Lloyd D'Orsogna, Archana Panikkar, Kirsty R. Short, and C. Szeto
- Subjects
Protective immunity ,Cellular immunity ,Immune system ,Political science ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Immunology ,education ,Pandemic ,Conflict of interest ,Immunology and Allergy ,Medical research ,Virology ,Epitope - Abstract
Significant efforts are being made worldwide to understand the immune response to SARS-CoV-2, responsible for the COVID-19 pandemic, including the role of pre-existing T cell immunity. Understanding the mechanisms that promote cross-recognition by T cells induced by seasonal coronaviruses will be critical for future predictions on the role of pre-existing immunity in protection against severe disease. We demonstrate that the SARS-CoV-2 nucleocapsid (N) protein induces an immunodominant response in HLA-B7+ COVID-19-recovered individuals that is also readily detectable in unexposed donors. This immunodominant response is driven by a single N-encoded epitope that displays a high degree of conservation with the homologous region in circulating coronaviruses. We show that T cell-mediated cross-reactivity can be detected towards the circulating OC43/HKU-1 coronaviruses, but not the 229E or NL63 coronaviruses, due to different peptide conformations. This cross-reactivity is driven by private T cell receptor repertoires with a bias for TRBV27 and a long CDR3b loop in unexposed and COVID-19-recovered individuals. Together, our findings demonstrate the basis of pre-existing immunity to a conserved and highly immunogenic SARS-CoV-2 epitope driven by cross-reactive memory T cells, suggesting long-lived protective immunity. Funding: This work was supported by generous donations from the QIMR Berghofer COVID 19 appeal, and financial contributions from Monash University, Australian Nuclear Science and Technology Organisation (ANSTO, AISNE ECR grants), Australian Research Council (ARC), National Health and Medical Research Council (NHMRC), and the Medical Research Future Fund (MRFF). H.S. is supported by an Australian Government Research Training Program Scholarship, E.J.G. was supported by an NHMRC CJ Martin Fellowship (#1110429) and is supported by an Australian Research Council DECRA (DE210101479), K.R.S.is supported by an Australian Research Council DECRA (DE180100512), S.G. is supported by and NHMRC SRF (#1159272). Conflict of Interest: The authors declare no competing interests. Ethical Approval: This study was performed according to the principles of the Declaration of Helsinki.Ethics approval to undertake the research was obtained from the QIMR Berghofer Medical Research Institute Human Research Ethics Committee and Monash University Human Research Ethics Committee.
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- 2021
27. Rapid detection of SARS‐CoV‐2‐specific memory T‐cell immunity in recovered COVID‐19 cases
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José Paulo Martins, Archana Panikkar, Sriganesh Srihari, Srividhya Swaminathan, Katherine K. Matthews, George R Ambalathingal, Mohammed Altaf, Corey Smith, Jyothy Raju, Michelle A Neller, Katie E. Lineburg, Rajiv Khanna, and Pauline Crooks
- Subjects
lcsh:Immunologic diseases. Allergy ,0301 basic medicine ,Cellular immunity ,Coronavirus disease 2019 (COVID-19) ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,viruses ,Immunology ,Biology ,SARS‐CoV‐2 ,03 medical and health sciences ,0302 clinical medicine ,Immunity ,COVID‐19 ,medicine ,Immunology and Allergy ,General Nursing ,Whole blood ,T‐cell response ,Original Articles ,biochemical phenomena, metabolism, and nutrition ,In vitro ,030104 developmental biology ,medicine.anatomical_structure ,antigen‐specific ,Original Article ,lcsh:RC581-607 ,Memory T cell ,CD8 ,030215 immunology - Abstract
Objectives There is emerging evidence that SARS‐CoV‐2‐specific memory T‐cell responses are likely to provide critical long‐term protection against COVID‐19. Strategies to rapidly assess T‐cell responses are therefore likely to be important for assessing immunity in the global population. Methods Here, we have developed a rapid immune‐monitoring strategy to assess virus‐specific memory T‐cell responses in the peripheral blood of COVID‐19 convalescent individuals. We validated SARS‐CoV‐2‐specific memory T‐cell responses detected in whole blood using in vitro expansion with SARS‐CoV‐2 proteins. Results T‐cell immunity characterised by the production of IFN‐γ and IL‐2 could be consistently detected in the whole blood of recovered participants. T cells predominantly recognised structural SARS‐CoV‐2 proteins. In vitro expansion demonstrated that while CD8+ T cells recognised nucleocapsid protein, spike protein and ORF3a, CD4+ T cells more broadly targeted multiple SARS‐CoV‐2 proteins. Conclusion These observations provide a timely monitoring approach for identifying SARS‐CoV‐2 cellular immunity and may serve as a diagnostic for the stratification of risk in immunocompromised and other at‐risk individuals., T‐cell immunity is likely critical for the control of COVID‐19. We have developed a rapid assay to detect T‐cell immunity in whole blood, and demonstrate the effectiveness of this assay in individuals who have recovered from COVID‐19.
- Published
- 2020
28. SARS-CoV-2-specific T cells generated for adoptive immunotherapy are capable of recognizing multiple SARS-CoV-2 variants
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Archana Panikkar, Katie E. Lineburg, Jyothy Raju, Keng Yih Chew, George R. Ambalathingal, Sweera Rehan, Srividhya Swaminathan, Pauline Crooks, Laetitia Le Texier, Leone Beagley, Shannon Best, Matthew Solomon, Katherine K. Matthews, Sriganesh Srihari, Michelle A. Neller, Kirsty R. Short, Rajiv Khanna, and Corey Smith
- Subjects
Adult ,Male ,SARS-CoV-2 ,T-Lymphocytes ,Immunology ,Epitopes, T-Lymphocyte ,Middle Aged ,Immunotherapy, Adoptive ,Microbiology ,Immunophenotyping ,Young Adult ,HEK293 Cells ,HLA Antigens ,Virology ,Genetics ,Humans ,Female ,Parasitology ,Molecular Biology - Abstract
Adoptive T-cell immunotherapy has provided promising results in the treatment of viral complications in humans, particularly in the context of immunocompromised patients who have exhausted all other clinical options. The capacity to expand T cells from healthy immune individuals is providing a new approach to anti-viral immunotherapy, offering rapid off-the-shelf treatment with tailor-made human leukocyte antigen (HLA)-matched T cells. While most of this research has focused on the treatment of latent viral infections, emerging evidence that SARS-CoV-2-specific T cells play an important role in protection against COVID-19 suggests that the transfer of HLA-matched allogeneic off-the-shelf virus-specific T cells could provide a treatment option for patients with active COVID-19 or at risk of developing COVID-19. We initially screened 60 convalescent individuals and based on HLA typing and T-cell response profile, 12 individuals were selected for the development of a SARS-CoV-2-specific T-cell bank. We demonstrate that these T cells are specific for up to four SARS-CoV-2 antigens presented by a broad range of both HLA class I and class II alleles. These T cells show consistent functional and phenotypic properties, display cytotoxic potential against HLA-matched targets and can recognize HLA-matched cells infected with different SARS-CoV-2 variants. These observations demonstrate a robust approach for the production of SARS-CoV-2-specific T cells and provide the impetus for the development of a T-cell repository for clinical assessment.
- Published
- 2022
29. Profiling HPV-16–specific T cell responses reveals broad antigen reactivities in oropharyngeal cancer patients
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Corey Smith, Sriganesh Srihari, Kunal H. Bhatt, Howard Liu, Sandro V. Porceddu, Liz Kenny, Michelle A Neller, Lea Lekieffre, Pauline Crooks, Rajiv Khanna, and Blake T. Aftab
- Subjects
CD4-Positive T-Lymphocytes ,Male ,Tumor Immunology ,Oncology ,medicine.medical_specialty ,Multivariate analysis ,T-Lymphocytes ,T cell ,Immunology ,CD8-Positive T-Lymphocytes ,T cell response ,Article ,Antigen ,Antigens, Neoplasm ,Internal medicine ,medicine ,T cell immunity ,Humans ,Immunology and Allergy ,Human papillomavirus 16 ,business.industry ,Papillomavirus Infections ,Case-control study ,virus diseases ,Middle Aged ,Oropharyngeal Neoplasms ,stomatognathic diseases ,medicine.anatomical_structure ,Case-Control Studies ,Cohort ,Female ,business ,CD8 - Abstract
Proteome-wide profiling of HPV-specific T cell immunity in oropharyngeal cancer (OPC) patients reveals broad and multiple antigen-specific reactivities directed to HPV-encoded proteins E1, E2, E4, E5 E6, E7, and L1. These observations provide novel insights for future development of cellular immunotherapies for HPV-associated OPC patients., Cellular immunotherapeutics targeting the human papillomavirus (HPV)–16 E6 and E7 proteins have achieved limited success in HPV-positive oropharyngeal cancer (OPC). Here we have conducted proteome-wide profiling of HPV-16–specific T cell responses in a cohort of 66 patients with HPV-associated OPC and 22 healthy individuals. Unexpectedly, HPV-specific T cell responses from OPC patients were not constrained to the E6 and E7 antigens; they also recognized E1, E2, E4, E5, and L1 proteins as dominant targets for virus-specific CD8+ and CD4+ T cells. Multivariate analysis incorporating tumor staging, treatment status, and smoking history revealed that treatment status had the most significant impact on HPV-specific CD8+ and CD4+ T cell immunity. Specifically, the breadth and overall strength of HPV-specific T cell responses were significantly higher before the commencement of curative therapy than after therapy. These data provide the first glimpse of the overall human T cell response to HPV in a clinical setting and offer groundbreaking insight into future development of cellular immunotherapies for HPV-associated OPC patients., Graphical Abstract
- Published
- 2020
30. T-cell adoptive immunotherapy for BK nephropathy in renal transplantation
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Corey Smith, George R Ambalathingal, George John, Leo Francis, Sadia Jahan, Sweera Rehan, Carla Scuderi, Michelle A Neller, Pauline Crooks, and Rajiv Khanna
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medicine.medical_specialty ,medicine.medical_treatment ,T-Lymphocytes ,Short Communication ,Urology ,030230 surgery ,medicine.disease_cause ,Immunotherapy, Adoptive ,Nephropathy ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,BK virus ,Biopsy ,medicine ,Humans ,T‐cell adoptive immunotherapy ,Transplantation ,Polyomavirus Infections ,Everolimus ,medicine.diagnostic_test ,business.industry ,BKPyV nephropathy ,Australia ,Middle Aged ,medicine.disease ,Kidney Transplantation ,Tacrolimus ,Tumor Virus Infections ,Infectious Diseases ,chemistry ,Leukocytes, Mononuclear ,030211 gastroenterology & hepatology ,Female ,Hemodialysis ,business ,medicine.drug ,Cidofovir - Abstract
Introduction BK virus (BKPyV) nephropathy occurs in 1%‐10% of kidney transplant recipients, with suboptimal therapeutic options. Case A 54‐year‐old woman received a transplant in March 2017. BKPyV was detected at 1.5 × 102 copies/mL within a month, necessitating halving of mycophenolate and addition of leflunomide. Allograft histology in December showed polyomavirus nephropathy treated with intravenous immunoglobulin and cessation of mycophenolate. In February 2018, cidofovir and ciprofloxacin were commenced. In April, tacrolimus was reduced while introducing everolimus. A second graft biopsy in August showed increasing polyoma virus infection and a subsequent biopsy in September for worsening renal function showed 30% of tubular reactivity for simian virus 40 (SV40). Allogeneic BKPyV‐reactive T cells were generated from the patient's daughter and infused over 10 sessions starting late September. The fourth allograft biopsy in November 2018 demonstrated involvement of BKPyV in 50% of tubules. Allograft function continued to decline, requiring hemodialysis from December 2018. Allograft nephrectomy after 6 months showed
- Published
- 2020
31. Pre-clinical development of T-cell immunotherapy for covid-19
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Corey Smith, Srividhya Swaminathan, K. Matthews, Katie E. Lineburg, Archana Panikkar, Pauline Crooks, Sweera Rehan, Rajiv Khanna, G. Ambalathingal Thomas, Michelle A Neller, and Jyothy Raju
- Subjects
Cancer Research ,Transplantation ,2019-20 coronavirus outbreak ,Coronavirus disease 2019 (COVID-19) ,business.industry ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Immunology ,Cell Biology ,Virology ,Article ,Oncology ,Immunology and Allergy ,Medicine ,business ,T cell immunotherapy ,Genetics (clinical) - Published
- 2021
32. CD8+ T cells specific for an immunodominant SARS-CoV-2 nucleocapsid epitope cross-react with selective seasonal coronaviruses
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Lea Lekieffre, Zhen Wei Marcus Tong, Michelle A Neller, Jacqueline M. Burrows, Keng Yih Chew, Alan Riboldi-Tunnicliffe, Dhilshan Jayasinghe, Archana Panikkar, Kirsty R. Short, Jyothy Raju, Christopher Szeto, Andrea T. Nguyen, Emma J. Grant, Demetra S.M. Chatzileontiadou, Hanim Halim, Stephanie Gras, Sweera Rehan, Weisan Chen, Lloyd D'Orsogna, Corey Smith, Rajiv Khanna, Hannah Sloane, Srividhya Swaminathan, Katie E. Lineburg, Pauline Crooks, and Christian A. Lobos
- Subjects
Models, Molecular ,0301 basic medicine ,cross-reactivity ,viruses ,Immunology ,Receptors, Antigen, T-Cell ,Epitopes, T-Lymphocyte ,CD8-Positive T-Lymphocytes ,Cross Reactions ,Biology ,medicine.disease_cause ,Cross-reactivity ,Article ,immune response ,Epitope ,Virus ,HLA-B7 Antigen ,03 medical and health sciences ,0302 clinical medicine ,Immune system ,seasonal coronaviruses ,medicine ,Coronavirus Nucleocapsid Proteins ,Humans ,Immunology and Allergy ,Cytotoxic T cell ,Amino Acid Sequence ,Peptide sequence ,Coronavirus ,Immunodominant Epitopes ,SARS-CoV-2 ,T-cell receptor ,COVID-19 ,virus diseases ,Virology ,HLA ,030104 developmental biology ,Infectious Diseases ,030220 oncology & carcinogenesis ,immunodominant epitope ,Peptides ,CD8+ T cell ,Immunologic Memory - Abstract
Efforts are being made worldwide to understand the immune response to SARS-CoV-2, the virus responsible for the COVID-19 pandemic, including the impact of T cell immunity and cross-recognition with seasonal coronaviruses. Screening SARS-CoV-2 peptide pools revealed that the nucleocapsid (N) protein induced an immunodominant response in HLA-B7+ COVID-19-recovered individuals that was also detectable in unexposed donors. A single N-encoded epitope that was highly conserved across circulating coronaviruses drove this immunodominant response. In vitro peptide stimulation and crystal structure analyses revealed T cell-mediated cross-reactivity towards circulating OC43 and HKU-1 beta coronaviruses, but not 229E or NL63 alpha coronaviruses, due to different peptide conformations. TCR sequencing indicated cross-reactivity was driven by private T cell receptor repertoires with a bias for TRBV27 and a long CDR3β loop. Together, our findings demonstrate the basis of selective T cell cross-reactivity towards an immunodominant SARS-CoV-2 epitope and its homologues from seasonal coronaviruses, suggesting long-lived protective immunity., Graphical Abstract, The impact of seasonal coronaviruses on immune responses to SARS-CoV-2 is an active area of research. Here, Lineburg et al identify CD8+ T cells specific for a conserved and immunodominant SARS-CoV-2 epitope in HLA-B7+ individuals. Furthermore, SARS-CoV-2 epitope-specific CD8+ T cells display cross-reactivity to beta but not alpha coronaviruses due to distinct peptide–HLA conformations.
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- 2021
33. Prophylactic and therapeutic strategies for Epstein-Barr virus-associated diseases: emerging strategies for clinical development
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Rajiv Khanna, Vijayendra Dasari, Corey Smith, Michelle A Neller, and Debottam Sinha
- Subjects
0301 basic medicine ,Epstein-Barr Virus Infections ,Herpesvirus 4, Human ,Mononucleosis ,Immunology ,Population ,medicine.disease_cause ,Post-transplant lymphoproliferative disorder ,Virus ,03 medical and health sciences ,0302 clinical medicine ,hemic and lymphatic diseases ,Drug Discovery ,medicine ,030212 general & internal medicine ,education ,Pharmacology ,education.field_of_study ,Nasopharyngeal Carcinoma ,business.industry ,Nasopharyngeal Neoplasms ,Viral Vaccines ,medicine.disease ,Virology ,Epstein–Barr virus ,Lymphoproliferative Disorders ,030104 developmental biology ,Nasopharyngeal carcinoma ,Molecular Medicine ,Immunotherapy ,business - Abstract
Epstein-Barr virus (EBV) infects more than 95% of the world's population and is associated with infectious mononucleosis as well as a number of cancers in various geographical locations. Despite its significant health burden, no licenced prophylactic or therapeutic vaccines are available. Areas covered: Over the last two decades, our understanding of the role of EBV infection in the pathogenesis and immune regulation of EBV-associated diseases has provided new lines of research to conceptualize various novel prophylactic and therapeutic approaches to control EBV-associated disease. In this review, we evaluate the prophylactic and therapeutic vaccine approaches against EBV and various immunotherapeutic strategies against a number of EBV-associated malignancies. This review also describes the existing and future prospects of improved EBV-targeted therapeutic strategies. Expert opinion: It is anticipated that these emerging strategies will provide answers for the major challenges in EBV vaccine development and help improve the efficacy of novel therapeutic strategies.
- Published
- 2019
34. Impact of pre‐therapy glioblastoma multiforme microenvironment on clinical response to autologous CMV‐specific T‐cell therapy
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John M. Nicholls, Katherine K. Matthews, Reshma Shakya, Michelle A Neller, Rajiv Khanna, Corey Smith, Beth Morrison, and David G. Walker
- Subjects
lcsh:Immunologic diseases. Allergy ,0301 basic medicine ,CD3 ,T cell ,medicine.medical_treatment ,Immunology ,glioblastoma multiforme ,03 medical and health sciences ,0302 clinical medicine ,medicine ,tumor microenvironment ,Immunology and Allergy ,General Nursing ,Tumor microenvironment ,Gene knockdown ,biology ,Pre-Therapy ,business.industry ,Immunosuppression ,3. Good health ,030104 developmental biology ,medicine.anatomical_structure ,cytomegalovirus (CMV) ,030220 oncology & carcinogenesis ,biology.protein ,Cancer research ,Immunohistochemistry ,Original Article ,Antibody ,lcsh:RC581-607 ,business ,adoptive immunotherapy - Abstract
Objectives Clinical response to antibody‐based immunotherapies targeting checkpoint inhibitors is critically dependent on the tumor immune microenvironment (TIME). However, the precise impact of the TIME on adoptive cellular immunotherapy remains unexplored. Here we have conducted a long‐term follow‐up analysis of patients with recurrent glioblastoma multiforme (GBM) who were treated with autologous CMV‐specific T‐cell therapy to delineate the potential impact of the TIME on their clinical response. Methods Multiplexed immunohistochemical analysis of CD3, PD‐L1 and Sox‐2 in GBM tissue biopsies obtained before autologous T‐cell therapy was carried out and correlated with long‐term survival of GBM patients adoptively treated with T‐cell therapy. Results Tumor microenvironment analyses revealed that the pre‐treatment cellular composition of the tumor tissue may influence the subsequent response to adoptive T‐cell therapy. GBM patients who showed prolonged overall survival following T‐cell therapy had a significantly lower number of tumor‐infiltrating CD3+ T cells in recurrent tumors than that in patients with short‐term survival. Furthermore, long‐term surviving patients showed low or undetectable PD‐L1 expression in tumor cells in recurrent GBM biopsies. Conclusion We hypothesise that lack of PD‐L1‐mediated immunosuppression in the TIME may allow efficient immune control following adoptive T‐cell therapy. Future studies combining anti‐PD‐L1 or genetically modified T cells with PD‐1 receptor knockdown could be considered to improve clinical responses in patients who have high PD‐L1 expression in their tumors., The precise role of tumor immune microenvironment (TIME) on clinical response to adoptive cellular immunotherapies remains largely unexplored. In this paper, we have analysed the impact of TIME on the clinical response of glioblastoma patients who showed either long‐term or short‐term overall survival following adoptive T‐cell therapy.
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- 2019
35. Epstein-Barr virus–specific T cell therapy for progressive multiple sclerosis
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Nanette L. Douglas, Rajiv Khanna, Leone Beagley, Pauline Crooks, Zara A. Ioannides, Corey Smith, Michelle A Neller, Kate Thompson, Stefan Blum, Blake T. Aftab, Andrew Swayne, Alan Coulthard, Michael P. Pender, Sweera Rehan, Scott R. Burrows, Kaye D. Hooper, Kerryn A. Green, Tracey Hopkins, Katherine K. Matthews, and Peter A. Csurhes
- Subjects
Adult ,Male ,0301 basic medicine ,Oncology ,Herpesvirus 4, Human ,medicine.medical_specialty ,Multiple Sclerosis ,T-Lymphocytes ,T cell ,medicine.disease_cause ,Immunotherapy, Adoptive ,Viral Matrix Proteins ,03 medical and health sciences ,0302 clinical medicine ,Antigen ,Internal medicine ,hemic and lymphatic diseases ,medicine ,Humans ,Cytotoxic T cell ,Adverse effect ,Aged ,business.industry ,Multiple sclerosis ,General Medicine ,Middle Aged ,medicine.disease ,Magnetic Resonance Imaging ,Epstein–Barr virus ,Clinical trial ,Treatment Outcome ,030104 developmental biology ,medicine.anatomical_structure ,Epstein-Barr Virus Nuclear Antigens ,Medicine ,Female ,Corrigendum ,business ,030217 neurology & neurosurgery ,CD8 ,Research Article - Abstract
BACKGROUND. Increasing evidence indicates a role for EBV in the pathogenesis of multiple sclerosis (MS). EBV-infected autoreactive B cells might accumulate in the CNS because of defective cytotoxic CD8+ T cell immunity. We sought to determine the feasibility and safety of treating progressive MS patients with autologous EBV-specific T cell therapy. METHODS. An open-label phase I trial was designed to treat 5 patients with secondary progressive MS and 5 patients with primary progressive MS with 4 escalating doses of in vitro–expanded autologous EBV-specific T cells targeting EBV nuclear antigen 1, latent membrane protein 1 (LMP1), and LMP2A. Following adoptive immunotherapy, we monitored the patients for safety and clinical responses. RESULTS. Of the 13 recruited participants, 10 received the full course of T cell therapy. There were no serious adverse events. Seven patients showed improvement, with 6 experiencing both symptomatic and objective neurological improvement, together with a reduction in fatigue, improved quality of life, and, in 3 patients, reduced intrathecal IgG production. All 6 patients receiving T cells with strong EBV reactivity showed clinical improvement, whereas only 1 of the 4 patients receiving T cells with weak EBV reactivity showed improvement (P = 0.033, Fisher’s exact test). CONCLUSION. EBV-specific adoptive T cell therapy was well tolerated. Clinical improvement following treatment was associated with the potency of EBV-specific reactivity of the administered T cells. Further clinical trials are warranted to determine the efficacy of EBV-specific T cell therapy in MS. TRIAL REGISTRATION. Australian New Zealand Clinical Trials Registry, ACTRN12615000422527. FUNDING. MS Queensland, MS Research Australia, Perpetual Trustee Company Ltd., and donations from private individuals who wish to remain anonymous.
- Published
- 2018
36. 'Off-the-shelf’ allogeneic antigen-specific adoptive T-cell therapy for the treatment of multiple EBV-associated malignancies
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Lea Lekieffre, Pauline Crooks, George R Ambalathingal, Debottam Sinha, Rajiv Khanna, Sweera Rehan, Sriganesh Srihari, Matthew Solomon, Michelle A Neller, Laetitia Le Texier, Corey Smith, Kirrliee Beckett, and Archana Panikkar
- Subjects
lymphocytes ,0301 basic medicine ,Epstein-Barr Virus Infections ,Herpesvirus 4, Human ,Cancer Research ,Lymphoma ,T-Lymphocytes ,medicine.medical_treatment ,Mice ,0302 clinical medicine ,HLA Antigens ,hemic and lymphatic diseases ,Immunology and Allergy ,Vector (molecular biology) ,Immune Checkpoint Inhibitors ,RC254-282 ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,medicine.anatomical_structure ,Oncology ,030220 oncology & carcinogenesis ,Molecular Medicine ,Female ,immunotherapy ,Programmed cell death ,Cell Survival ,T cell ,Immunology ,Human leukocyte antigen ,adoptive ,Virus ,Viral Matrix Proteins ,03 medical and health sciences ,Antigen ,In vivo ,Cell Line, Tumor ,medicine ,Animals ,Humans ,Transplantation, Homologous ,Cell Proliferation ,Pharmacology ,Immune Cell Therapies and Immune Cell Engineering ,business.industry ,Immunotherapy ,tumor-infiltrating ,immunity ,Xenograft Model Antitumor Assays ,030104 developmental biology ,Epstein-Barr Virus Nuclear Antigens ,Cancer research ,business ,cellular - Abstract
BackgroundEpstein-Barr virus (EBV), an oncogenic human gammaherpesvirus, is associated with a wide range of human malignancies of epithelial and B-cell origin. Recent studies have demonstrated promising safety and clinical efficacy of allogeneic ‘off-the-shelf’ virus-specific T-cell therapies for post-transplant viral complications.MethodsTaking a clue from these studies, we developed a highly efficient EBV-specific T-cell expansion process using a replication-deficient AdE1-LMPpoly vector that specifically targets EBV-encoded nuclear antigen 1 (EBNA1) and latent membrane proteins 1 and 2 (LMP1 and LMP2), expressed in latency II malignancies.ResultsThese allogeneic EBV-specific T cells efficiently recognized human leukocyte antigen (HLA)-matched EBNA1-expressing and/or LMP1 and LMP2-expressing malignant cells and demonstrated therapeutic potential in a number of in vivo models, including EBV lymphomas that emerged spontaneously in humanized mice following EBV infection. Interestingly, we were able to override resistance to T-cell therapy in vivo using a ‘restriction-switching’ approach, through sequential infusion of two different allogeneic T-cell therapies restricted through different HLA alleles. Furthermore, we have shown that inhibition of the programmed cell death protein-1/programmed death-ligand 1 axis in combination with EBV-specific T-cell therapy significantly improved overall survival of tumor-bearing mice when compared with monotherapy.ConclusionThese findings suggest that restriction switching by sequential infusion of allogeneic T-cell therapies that target EBV through distinct HLA alleles may improve clinical response.
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- 2021
37. Autologous Adoptive T-cell Therapy for Recurrent or Drug-resistant Cytomegalovirus Complications in Solid Organ Transplant Recipients: A Single-arm Open-label Phase I Clinical Trial
- Author
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Leone Beagley, Ross S Francis, Chien-Li Holmes-Liew, Matthew Solomon, Peter Hopkins, Scott B. Campbell, Pauline Crooks, Corey Smith, Rajiv Khanna, Scott C. McKenzie, Sweera Rehan, Daniel C. Chambers, Mark Holmes, and Michelle A Neller
- Subjects
0301 basic medicine ,Microbiology (medical) ,Adult ,Male ,medicine.medical_specialty ,T cell ,T-Lymphocytes ,030106 microbiology ,Congenital cytomegalovirus infection ,Phases of clinical research ,Cytomegalovirus ,Drug resistance ,Transplantation, Autologous ,03 medical and health sciences ,Young Adult ,0302 clinical medicine ,Immune system ,Recurrence ,Internal medicine ,medicine ,Humans ,030212 general & internal medicine ,Prospective Studies ,Adverse effect ,business.industry ,Middle Aged ,medicine.disease ,Adoptive Transfer ,Transplantation ,Clinical trial ,Infectious Diseases ,medicine.anatomical_structure ,Treatment Outcome ,Cytomegalovirus Infections ,Female ,business - Abstract
BACKGROUND: Opportunistic infections including cytomegalovirus (CMV) are a major cause of morbidity and mortality in solid organ transplant (SOT) recipients. The recurrent and protracted use of anti-viral drugs with eventual emergence of drug resistance represents a significant constraint to therapy. While adoptive T-cell therapy has been successfully used in haematopoietic stem cell transplant recipients, its extension to the SOT setting poses a considerable challenge because of the inhibitory effects of immunosuppressive drugs on the virus-specific T-cell response in vivo, and the perceived risk of graft rejection. METHODS: In this prospective study, 22 SOT recipients (13 renal, 8 lung and 1 heart) with recurrent or ganciclovir-resistant CMV infection were recruited and of these, 13 patients were treated with in vitro-expanded autologous CMV-specific T cells. These patients were monitored for safety, clinical symptoms and immune reconstitution. RESULTS: Autologous CMV-specific T-cell manufacture was attempted for 21 patients, and was successful in 20 cases. The use of this adoptive immunotherapy was associated with no therapy-related serious adverse events. Eleven (84%) of the thirteen treated patients showed improvement in symptoms, including complete resolution or reduction in DNAemia, CMV-associated end organ disease and/or the cessation or reduced use of anti-viral drugs. Furthermore, many of these patients showed co-incident increased frequency of CMV-specific T cells in peripheral blood following completion of T-cell therapy. CONCLUSIONS: The data presented here demonstrate for the first time the clinical safety of CMV-specific adoptive T-cell therapy and its potential therapeutic benefit for SOT patients with recurrent and/or drug-resistant CMV infection or disease.
- Published
- 2018
38. Pre-emptive and therapeutic adoptive immunotherapy for nasopharyngeal carcinoma: Phenotype and effector function of T cells impact on clinical response
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Vivian S. W. Li, Andrea Schuessler, Leone Beagley, David D. Smith, Dora Lai Wan Kwong, Sandro V. Porceddu, David Price, Randal Tiu, Katherine K. Matthews, Glen M. Boyle, Janice Tsang, Emma Gostick, Daniel Chua, Sweera Rehan, John M. Nicholls, Jacqueline M. Burrows, Victor C. S. Lee, Michelle A Neller, Rajiv Khanna, Benedict Panizza, and Corey Smith
- Subjects
0301 basic medicine ,Oncology ,safety ,lcsh:Immunologic diseases. Allergy ,medicine.medical_specialty ,medicine.medical_treatment ,T cell ,Immunology ,Context (language use) ,lcsh:RC254-282 ,03 medical and health sciences ,0302 clinical medicine ,Internal medicine ,medicine ,Immunology and Allergy ,t cells ,Original Research ,Chemotherapy ,epstein-barr virus ,business.industry ,nasopharyngeal carcinoma ,Immunotherapy ,medicine.disease ,lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,Minimal residual disease ,3. Good health ,030104 developmental biology ,medicine.anatomical_structure ,Tolerability ,Nasopharyngeal carcinoma ,030220 oncology & carcinogenesis ,QR180 ,RC0321 ,business ,lcsh:RC581-607 ,adoptive immunotherapy ,CD8 - Abstract
Adoptive T cell therapy has emerged as a powerful strategy to treat human cancers especially haematological malignancies. Extension of these therapies to solid cancers remains a significant challenge especially in the context of defining immunological correlates of clinical responses. Here we describe results from a clinical study investigating autologous Epstein-Barr virus (EBV)-specific T cells generated using a novel AdE1-LMPpoly vector to treat patients with nasopharyngeal carcinoma (NPC) either pre-emptively in at-risk patients with no or minimal residual disease (N/MRD) or therapeutically in patients with active recurrent/metastatic disease (ARMD). Tolerability, safety and efficacy, including progression-free survival (PFS) and overall survival (OS), were evaluated following adoptive T-cell immunotherapy. Twenty-nine patients, including 20 with ARMD and nine with N/MRD, successfully completed T-cell therapy. After a median follow-up of 18.5 months, the median PFS was 5.5 months (95% CI 2.1 to 9.0 months) and the median OS was 38.1 months (95% CI 17.2 months to not reached). Post-immunotherapy analyses revealed that disease stabilization in ARMD patients was significantly associated with the functional and phenotypic composition of in vitro-expanded T cell immunotherapy. These included a higher proportion of effector CD8+ T-cells and an increased number of EBV-specific T-cells with broader antigen specificity. These observations indicate that adoptive immunotherapy with AdE1-LMPpoly-expanded T cells stabilizes relapsed, refractory NPC without significant toxicity. Promising clinical outcomes in N/MRD patients further suggest a potential role for this approach as a consolidation treatment following first-line chemotherapy.
- Published
- 2017
39. A Molecular Basis for the Interplay between T Cells, Viral Mutants, and Human Leukocyte Antigen Micropolymorphism
- Author
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Yu Chih Liu, James McCluskey, John J. Miles, Scott R. Burrows, Michelle A Neller, Stephanie Gras, Anthony W. Purcell, Jamie Rossjohn, and Zhenjun Chen
- Subjects
Herpesvirus 4, Human ,Protein Conformation ,animal diseases ,T-Lymphocytes ,T cell ,Immunology ,Molecular Sequence Data ,Receptors, Antigen, T-Cell ,chemical and pharmacologic phenomena ,Human leukocyte antigen ,Polymorphism, Single Nucleotide ,Biochemistry ,Epitope ,Virus ,Epitopes ,Immune system ,Antigen ,hemic and lymphatic diseases ,MHC class I ,medicine ,Humans ,Amino Acid Sequence ,Molecular Biology ,Alleles ,Genetics ,biology ,T-cell receptor ,Cell Biology ,biochemical phenomena, metabolism, and nutrition ,Virology ,Molecular Docking Simulation ,medicine.anatomical_structure ,biology.protein ,bacteria ,HLA-B35 Antigen - Abstract
Mutations within T cell epitopes represent a common mechanism of viral escape from the host protective immune response. The diverse T cell repertoire and the extensive human leukocyte antigen (HLA) polymorphism across populations is the evolutionary response to viral mutation. However, the molecular basis underpinning the interplay between HLA polymorphism, the T cell repertoire, and viral escape is unclear. Here we investigate the T cell response to a HLA-B*35:01- and HLA-B*35:08-restricted (407)HPVGEADYFEY(417) epitope from Epstein-Barr virus and naturally occurring variants at positions 4 and 5 thereof. Each viral variant differently impacted on the epitope's flexibility and conformation when bound to HLA-B*35:08 or HLA-B*35:01. We provide a molecular basis for understanding how the single residue polymorphism that discriminates between HLA-B*35:01/08 profoundly impacts on T cell receptor recognition. Surprisingly, one viral variant (P5-Glu to P5-Asp) effectively changed restriction preference from HLA-B*35:01 to HLA-B*35:08. Collectively, our study portrays the interplay between the T cell response, viral escape, and HLA polymorphism, whereby HLA polymorphism enables altered presentation of epitopes from different strains of Epstein-Barr virus.
- Published
- 2014
40. Missense single nucleotide polymorphisms in the human T cell receptor loci control variable gene usage in the T cell repertoire
- Author
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John J. Miles, Jamie Rossjohn, Stephanie Gras, Scott R. Burrows, Thomas Elliott, Michelle A Neller, Rebekah M Brennan, and Jacqueline M. Burrows
- Subjects
Adult ,CD4-Positive T-Lymphocytes ,Genetics ,Receptors, Antigen, T-Cell, alpha-beta ,T cell ,T-cell receptor ,Immunoglobulin Variable Region ,Mutation, Missense ,chemical and pharmacologic phenomena ,Single-nucleotide polymorphism ,Hematology ,Human leukocyte antigen ,CD8-Positive T-Lymphocytes ,Biology ,Polymorphism, Single Nucleotide ,Molecular biology ,Immune system ,medicine.anatomical_structure ,medicine ,Humans ,5-HT5A receptor ,Gene ,CD8 - Abstract
[Extract] T cells play a central role in immunity as both regulators and effectors of immune function, following recognition of antigenic peptides presented by human leucocyte antigens (HLA) via the αβ T cell receptor (TCR). As such, the genes that encode the TCR have long been considered candidates for disease association. The human TCR is assembled from a total of 174 gene segments on chromosomes 7 and 14. Each α-chain is encoded by a variable (TRAV), a joining and a constant gene, while each β-chain is encoded by a variable (TRBV), a diversity, a joining and a constant gene (Davis & Bjorkman, 1988).
- Published
- 2014
41. HLA Peptide Length Preferences Control CD8+ T Cell Responses
- Author
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Nathan P. Croft, James McCluskey, John J. Miles, Scott R. Burrows, Rajiv Khanna, Stephanie Gras, Jamie Rossjohn, Andrew David Welland, Rebekah M Brennan, Lucy C. Sullivan, Jacqueline M. Burrows, Anthony W. Purcell, Andrew G. Brooks, Melissa J Rist, Alexander Theodossis, Michelle A Neller, and Zhenjun Chen
- Subjects
HLA-B18 Antigen ,Immunology ,Epitopes, T-Lymphocyte ,Peptide ,Human leukocyte antigen ,CD8-Positive T-Lymphocytes ,Biology ,Polymorphism, Single Nucleotide ,HLA-B44 Antigen ,Immune system ,Humans ,Immunology and Allergy ,Cytotoxic T cell ,Histone octamer ,Cells, Cultured ,chemistry.chemical_classification ,Genetics ,Molecular biology ,Peptide Fragments ,Protein Structure, Tertiary ,BZLF1 ,Dodecameric protein ,chemistry ,Leukocytes, Mononuclear ,Trans-Activators ,Binding Sites, Antibody ,CD8 - Abstract
Class I HLAs generally present peptides of 8–10 aa in length, although it is unclear whether peptide length preferences are affected by HLA polymorphism. In this study, we investigated the CD8+ T cell response to the BZLF1 Ag of EBV, which includes overlapping sequences of different size that nevertheless conform to the binding motif of the large and abundant HLA-B*44 supertype. Whereas HLA-B*18:01+ individuals responded strongly and exclusively to the octamer peptide 173SELEIKRY180, HLA-B*44:03+ individuals responded to the atypically large dodecamer peptide 169EECDSELEIKRY180, which encompasses the octamer peptide. Moreover, the octamer peptide bound more stably to HLA-B*18:01 than did the dodecamer peptide, whereas, conversely, HLA-B*44:03 bound only the longer peptide. Furthermore, crystal structures of these viral peptide–HLA complexes showed that the Ag-binding cleft of HLA-B*18:01 was more ideally suited to bind shorter peptides, whereas HLA-B*44:03 exhibited characteristics that favored the presentation of longer peptides. Mass spectrometric identification of > 1000 naturally presented ligands revealed that HLA-B*18:01 was more biased toward presenting shorter peptides than was HLA-B*44:03. Collectively, these data highlight a mechanism through which polymorphism within an HLA class I supertype can diversify determinant selection and immune responses by varying peptide length preferences.
- Published
- 2013
42. High Frequency of Herpesvirus-Specific Clonotypes in the Human T Cell Repertoire Can Remain Stable over Decades with Minimal Turnover
- Author
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Scott R. Burrows, Melissa J Rist, Michelle A Neller, John J. Miles, and Jacqueline M. Burrows
- Subjects
Adult ,Male ,Time Factors ,T-Lymphocytes ,T cell ,Molecular Sequence Data ,Immunology ,Receptors, Antigen, T-Cell ,Blood Donors ,Biology ,medicine.disease_cause ,Microbiology ,Viral infection ,Virus ,Virology ,medicine ,Humans ,Amino Acid Sequence ,Aged ,T cell repertoire ,T-cell receptor ,Genetic Variation ,Cytomegalovirus ,Sequence Analysis, DNA ,Middle Aged ,medicine.anatomical_structure ,Epstein barr ,Insect Science ,Healthy individuals ,Receptors, Virus ,Pathogenesis and Immunity - Abstract
High-throughput T cell receptor sequencing on sequentially banked blood samples from healthy individuals has shown that high-frequency clonotypes can remain relatively stable for up to 18 years, with minimal inflation, deflation, or turnover. These populations included T cell expansions specific for Epstein-Barr virus. Thus, in spite of exposure to a barrage of microorganisms over the course of life, the dominant clonotypes in the mature peripheral T cell repertoire can alter surprisingly little.
- Published
- 2013
43. Tracking the repertoire of human adult and neonatal T cells duringex vivoamplification
- Author
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John J. Miles, Andrew K. Sewell, Michelle A Neller, and Scott R. Burrows
- Subjects
Adult ,T-Lymphocytes ,CD3 ,T cell ,Infant, Newborn ,Receptors, Antigen, T-Cell ,CD28 ,Hematology ,Biology ,Fetal Blood ,Lymphocyte Activation ,Peripheral blood mononuclear cell ,Molecular biology ,Haematopoiesis ,medicine.anatomical_structure ,Antigens, CD ,Immunology ,Leukocytes, Mononuclear ,biology.protein ,medicine ,Humans ,Cytotoxic T cell ,Stem cell ,Ex vivo - Abstract
[Extract] In times of limited material, expansion of T cells in vitro has become a standard practice across many clinical and basic immunological procedures; such as haematopoietic stem cell transplantation, the study of biopsy specimens, immunomonitoring of clinical trial patients and the study of samples from neonates and children. Classically, mitogenic lectins, such as phytohaemagglutinin (PHA-P) or the phorbol esterphorbol 12-myristate 13-acetate, have been used for initiating T cell expansion. However, a more physiologically relevant method of T cell stimulation mimics the interaction with antigen-presenting cells through the use of anti-CD3 and anti-CD28 monoclonal antibodies (mAb) (Martin et al, 1986). This procedure has been improved in recent years, by fusing anti-CD3 and anti-CD28 mAb to microbead structures (Pene et al, 2003). Here, the initial signal is provided by CD3 molecule activation and the co-stimulatory signal is provided by CD28 molecule activation. In this study, we assessed whether human T-activator CD3/CD28 Dynabeads or PHA-P could amplify T cells from human umbilical cord blood (UCB) or adult peripheral blood mononuclear cells (PBMC) without distorting the baseline ex vivo T cell repertoire.
- Published
- 2012
44. Allelic polymorphism in the T cell receptor and its impact on immune responses
- Author
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Scott R. Burrows, Yu Chih Liu, Stephanie Gras, James McCluskey, Jacqueline M. Burrows, Melissa J. Bell, Zhenjun Chen, Anthony W. Purcell, Jamie Rossjohn, Andrew G. Brooks, Michelle A Neller, Rebekah M Brennan, Lucy C. Sullivan, Lars Kjer-Nielsen, John J. Miles, and Rajiv Khanna
- Subjects
Models, Molecular ,Linkage disequilibrium ,T cell ,Molecular Sequence Data ,Immunology ,Receptors, Antigen, T-Cell ,chemical and pharmacologic phenomena ,Human leukocyte antigen ,Major histocompatibility complex ,Polymorphism, Single Nucleotide ,Protein Structure, Secondary ,Article ,Epitope ,Epitopes ,Antigen ,Cell Line, Tumor ,medicine ,HLA-B Antigens ,Humans ,Immunology and Allergy ,Amino Acid Sequence ,Alleles ,Genetics ,biology ,T-cell receptor ,Immunity ,Surface Plasmon Resonance ,Molecular biology ,medicine.anatomical_structure ,Mutation ,biology.protein ,HLA-B35 Antigen ,Peptides - Abstract
In comparison to human leukocyte antigen (HLA) polymorphism, the impact of allelic sequence variation within T cell receptor (TCR) loci is much less understood. Particular TCR loci have been associated with autoimmunity, but the molecular basis for this phenomenon is undefined. We examined the T cell response to an HLA-B*3501–restricted epitope (HPVGEADYFEY) from Epstein-Barr virus (EBV), which is frequently dominated by a TRBV9*01+ public TCR (TK3). However, the common allelic variant TRBV9*02, which differs by a single amino acid near the CDR2β loop (Gln55→His55), was never used in this response. The structure of the TK3 TCR, its allelic variant, and a nonnaturally occurring mutant (Gln55→Ala55) in complex with HLA-B*3501HPVGEADYFEY revealed that the Gln55→His55 polymorphism affected the charge complementarity at the TCR–peptide-MHC interface, resulting in reduced functional recognition of the cognate and naturally occurring variants of this EBV peptide. Thus, polymorphism in the TCR loci may contribute toward variability in immune responses and the outcome of infection.
- Published
- 2010
45. T Cell Epitope Clustering in the Highly Immunogenic BZLF1 Antigen of Epstein-Barr Virus
- Author
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Melissa J Rist, Scott R. Burrows, Michelle A Neller, and Jacqueline M. Burrows
- Subjects
Herpesvirus 4, Human ,T cell ,viruses ,Immunology ,Cellular Response to Infection ,Epitopes, T-Lymphocyte ,Immunodominance ,Human leukocyte antigen ,Biology ,CD8-Positive T-Lymphocytes ,Microbiology ,Epitope ,Antigen ,Virology ,medicine ,Antigenic variation ,Humans ,biochemical phenomena, metabolism, and nutrition ,medicine.anatomical_structure ,Epitope mapping ,Polyclonal B cell response ,Insect Science ,Trans-Activators ,Epitope Mapping - Abstract
Polymorphism in the human leukocyte antigen (HLA) loci ensures that the CD8 + T cell response to viruses is directed against a diverse range of antigenic epitopes, thereby minimizing the impact of virus escape mutation across the population. The BZLF1 antigen of Epstein-Barr virus is an immunodominant target for CD8 + T cells, but the response has been characterized only in the context of a limited number of HLA molecules due to incomplete epitope mapping. We have now greatly expanded the number of defined CD8 + T cell epitopes from BZLF1, allowing the response to be evaluated in a much larger proportion of the population. Some regions of the antigen fail to be recognized by CD8 + T cells, while others include clusters of overlapping epitopes presented by different HLA molecules. These highly immunogenic regions of BZLF1 include polymorphic sequences, such that up to four overlapping epitopes are impacted by a single amino acid variation common in different regions of the world. This focusing of the immune response to limited regions of the viral protein could be due to sequence similarity to human proteins creating “immune blind spots” through self-tolerance. This study significantly enhances the understanding of the immune response to BZLF1, and the precisely mapped T cell epitopes may be directly exploited in vaccine development and adoptive immunotherapy. IMPORTANCE Epstein-Barr virus (EBV) is an important human pathogen, associated with several malignancies, including nasopharyngeal carcinoma and Hodgkin lymphoma. T lymphocytes are critical for virus control, and clinical trials aimed at manipulating this arm of the immune system have demonstrated efficacy in treating these EBV-associated diseases. These trials have utilized information on the precise location of viral epitopes for T cell recognition, for either measuring or enhancing responses. In this study, we have characterized the T cell response to the highly immunogenic BZLF1 antigen of EBV by greatly expanding the number of defined T cell epitopes. An unusual clustering of epitopes was identified, highlighting a small region of BZLF1 that is targeted by the immune response of a high proportion of the world's population. This focusing of the immune response could be utilized in developing vaccines/therapies with wide coverage, or it could potentially be exploited by the virus to escape the immune response.
- Published
- 2014
46. High Efficiency Ex Vivo Cloning of Antigen-Specific Human Effector T Cells
- Author
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Catherine M. Lanagan, Linda E. O′Connor, Antonia L. Pritchard, Michelle A Neller, Michael H.-L. Lai, Nathan R. Martinez, and Christopher W. Schmidt
- Subjects
CD4-Positive T-Lymphocytes ,Herpesvirus 4, Human ,Cytomegalovirus ,CD8-Positive T-Lymphocytes ,Memory T cells ,Spectrum Analysis Techniques ,Cellular types ,Medicine and Health Sciences ,Cytotoxic T cell ,Immune Response ,Antigens, Viral ,Cells, Cultured ,Multidisciplinary ,Effector ,Infectious Disease Immunology ,Flow Cytometry ,Vaccination and Immunization ,Spectrophotometry ,Medicine ,White blood cells ,Cytophotometry ,Clone (B-cell biology) ,Research Article ,Tumor Immunology ,Cell biology ,Blood cells ,Science ,Immune Cells ,Immunology ,Molecular Sequence Data ,T cells ,Enzyme-Linked Immunosorbent Assay ,Streptamer ,Molecular cloning ,Biology ,Research and Analysis Methods ,Interferon-gamma ,Antigen ,Antigens, Neoplasm ,Humans ,Amino Acid Sequence ,Cell Proliferation ,Cloning ,Biology and life sciences ,Molecular biology ,Animal cells ,Leukocytes, Mononuclear ,Clinical Immunology ,Ex vivo ,T-Lymphocytes, Cytotoxic - Abstract
While cloned T cells are valuable tools for the exploration of immune responses against viruses and tumours, current cloning methods do not allow inferences to be made about the function and phenotype of a clone's in vivo precursor, nor can precise cloning efficiencies be calculated. Additionally, there is currently no general method for cloning antigen-specific effector T cells directly from peripheral blood mononuclear cells, without the need for prior expansion in vitro. Here we describe an efficient method for cloning effector T cells ex vivo. Functional T cells are detected using optimised interferon gamma capture following stimulation with viral or tumour cell-derived antigen. In combination with multiple phenotypic markers, single effector T cells are sorted using a flow cytometer directly into multi-well plates, and cloned using standard, non antigen-specific expansion methods. We provide examples of this novel technology to generate antigen-reactive clones from healthy donors using Epstein-Barr virus and cytomegalovirus as representative viral antigen sources, and from two melanoma patients using autologous melanoma cells. Cloning efficiency, clonality, and retention/loss of function are described. Ex vivo effector cell cloning provides a rapid and effective method of deriving antigen-specific T cells clones with traceable in vivo precursor function and phenotype.
- Published
- 2014
47. Exploration of peptides bound to MHC class I molecules in melanoma
- Author
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Nicholas K. Hayward, Jeffrey J. Gorman, Antonia L. Pritchard, Christopher W. Schmidt, Michelle A Neller, and Marcus L. Hastie
- Subjects
Molecular Sequence Data ,Peptide ,Dermatology ,Human leukocyte antigen ,Biology ,Mass spectrometry ,General Biochemistry, Genetics and Molecular Biology ,Epitope ,Antibodies ,Mass Spectrometry ,Epitopes ,Immune system ,Antigen ,Antigens, Neoplasm ,Cell Line, Tumor ,MHC class I ,Humans ,Amino Acid Sequence ,RNA, Messenger ,Melanoma ,chemistry.chemical_classification ,Histocompatibility Antigens Class I ,Immunity ,Reproducibility of Results ,Molecular biology ,Gene Expression Regulation, Neoplastic ,Oncology ,chemistry ,Proteome ,biology.protein ,Peptides ,Protein Processing, Post-Translational ,Algorithms ,Protein Binding ,Subcellular Fractions - Abstract
Advancements in high-resolution HPLC and mass spectrometry have reinvigorated the application of this technology to identify peptides eluted from immunopurified MHC class I molecules. Three melanoma cell lines were assessed using w6/32 isolation, peptide elution and HPLC purification; peptides were identified by mass spectrometry. A total of 13,829 peptides were identified; 83-87% of these were 8-11 mers. Only approximately 15% have been described before. Subcellular locations of the source proteins showed even sampling; mRNA expression and total protein length were predictive of the number of peptides detected from a single protein. HLA-type binding prediction for 10,078 9/10 mer peptides assigned 88-95% to a patient-specific HLA subtype, revealing a disparity in strength of predicted binding. HLA-B*27-specific isolation successfully identified some peptides not found using w6/32. Sixty peptides were selected for immune screening, based on source protein and predicted HLA binding; no new peptides recognized by antimelanoma T cells were discovered. Additionally, mass spectrometry was unable to identify several epitopes targeted ex vivo by one patient's T cells.
- Published
- 2014
48. CD8+ T cells from a novel T cell receptor transgenic mouse induce liver-stage immunity that can be boosted by blood-stage infection in rodent malaria
- Author
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Diana S. Hansen, Lei Shong Lau, William R. Heath, Julia L. Gregory, Francis R. Carbone, Scott R. Burrows, Tania F. de Koning-Ward, Kenneth M. Murphy, Christian R. Engwerda, Gayle M. Davey, Catherine Q Nie, Ashraful Haque, Yi-Hsuan Lin, Anthony T. Papenfuss, Anton Cozijnsen, Vanessa Mollard, Claerwen M. Jones, Michelle A Neller, Angelika Sturm, John J. Miles, Geoffrey I. McFadden, Daniel Fernandez-Ruiz, and Brendan S. Crabb
- Subjects
Male ,Plasmodium berghei ,Priming (immunology) ,CD8-Positive T-Lymphocytes ,Interleukin 21 ,Mice ,Cytotoxic T cell ,Biology (General) ,Immune Response ,Cells, Cultured ,Adoptive Transfer ,3. Good health ,medicine.anatomical_structure ,Blood ,Liver ,Plasmodium chabaudi ,Sporozoites ,Research Article ,QH301-705.5 ,T cell ,Immunology ,Immunization, Secondary ,Receptors, Antigen, T-Cell ,Mice, Transgenic ,Immunopathology ,Biology ,Major histocompatibility complex ,Microbiology ,Antigen ,Virology ,Anopheles ,parasitic diseases ,Genetics ,medicine ,Animals ,Molecular Biology ,Immunity to Infections ,Life Cycle Stages ,Immunity ,Biology and Life Sciences ,Plasmodium yoelii ,RC581-607 ,biology.organism_classification ,R1 ,Acquired Immune System ,Malaria ,Mice, Inbred C57BL ,Immune System ,biology.protein ,Parasitology ,Clinical Immunology ,Immunologic diseases. Allergy ,CD8 - Abstract
To follow the fate of CD8+ T cells responsive to Plasmodium berghei ANKA (PbA) infection, we generated an MHC I-restricted TCR transgenic mouse line against this pathogen. T cells from this line, termed PbT-I T cells, were able to respond to blood-stage infection by PbA and two other rodent malaria species, P. yoelii XNL and P. chabaudi AS. These PbT-I T cells were also able to respond to sporozoites and to protect mice from liver-stage infection. Examination of the requirements for priming after intravenous administration of irradiated sporozoites, an effective vaccination approach, showed that the spleen rather than the liver was the main site of priming and that responses depended on CD8α+ dendritic cells. Importantly, sequential exposure to irradiated sporozoites followed two days later by blood-stage infection led to augmented PbT-I T cell expansion. These findings indicate that PbT-I T cells are a highly versatile tool for studying multiple stages and species of rodent malaria and suggest that cross-stage reactive CD8+ T cells may be utilized in liver-stage vaccine design to enable boosting by blood-stage infections., Author Summary Malaria is a disease caused by Plasmodium species, which have a highly complex life cycle involving both liver and blood stages of mammalian infection. To prevent disease, one strategy has been to induce CD8+ T cells against liver-stage parasites, usually by immunization with stage-specific antigens. Here we describe a T cell receptor specificity that recognizes an antigen expressed in both the liver and blood stages of several rodent Plasmodium species. We generated a T cell receptor transgenic mouse with this specificity and showed that T cells from this line could protect against liver-stage infection. We used this novel tool to identify the site and cell-type involved in priming to a recently developed intravenous attenuated sporozoite vaccine shown to have efficacy in humans. We showed that CD8+ T cells with this specificity could protect against liver-stage infection while causing pathology to the blood stage. Finally, we provided evidence that T cells with cross-stage specificity can be primed and boosted on alternative stages, raising the possibility that antigens expressed in multiple stages might be ideal vaccine candidates for generating strong immunity to liver-stage parasites.
- Published
- 2014
49. Multivariate Analysis Using High Definition Flow Cytometry Reveals Distinct T Cell Repertoires between the Fetal–Maternal Interface and the Peripheral Blood
- Author
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Brigitte Santner-Nanan, Ralph Nanan, Peter Hsu, Steven Joung, Rebekah M Brennan, Michelle A Neller, Scott R. Burrows, and John J. Miles
- Subjects
lcsh:Immunologic diseases. Allergy ,pre-eclampsia ,T cell ,Placenta ,Immunology ,Biology ,CD8+ T cells ,Flow cytometry ,Pathogenesis ,medicine ,Immunology and Allergy ,Cytotoxic T cell ,Compartment (development) ,T cell receptor (TCR) ,Original Research ,Fetus ,decidual mononuclear cells ,medicine.diagnostic_test ,Repertoire ,Decidua ,Peripheral Blood ,R1 ,CD4+ T cells ,medicine.anatomical_structure ,pregnancy ,lcsh:RC581-607 ,T cell repertoire ,Treg cells - Abstract
The human T cell compartment is a complex system and while some information is known on repertoire composition and dynamics in the peripheral blood, little is known about repertoire composition at different anatomical sites. Here, we determine the T cell receptor beta variable (TRBV) repertoire at the decidua and compare it with the peripheral blood during normal pregnancy and pre-eclampsia. We found total T cell subset disparity of up to 58% between sites, including large signature TRBV expansions unique to the fetal–maternal interface. Defining the functional nature and specificity of compartment-specific T cells will be necessary if we are to understand localized immunity, tolerance, and pathogenesis.
- Published
- 2014
- Full Text
- View/download PDF
50. Highly divergent T-cell receptor binding modes underlie specific recognition of a bulged viral peptide bound to a human leukocyte antigen class I molecule
- Author
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David Price, Emma Gostick, Jamie Rossjohn, James McCluskey, Anthony W. Purcell, Scott R. Burrows, Stephanie Gras, John J. Miles, Yu Chih Liu, and Michelle A Neller
- Subjects
Herpesvirus 4, Human ,Immunology ,Receptors, Antigen, T-Cell ,chemical and pharmacologic phenomena ,Complementarity determining region ,Human leukocyte antigen ,Biology ,CD8-Positive T-Lymphocytes ,Major histocompatibility complex ,Biochemistry ,Epitope ,Protein Structure, Secondary ,T cell receptor binding ,03 medical and health sciences ,Viral Proteins ,0302 clinical medicine ,X-ray Crystallography ,Structural Biology ,RZ ,Viral Immunology ,Molecular Biology ,030304 developmental biology ,Genetics ,0303 health sciences ,T-cell Receptor ,T-cell receptor ,hemic and immune systems ,Cell Biology ,MHC restriction ,Complementarity Determining Regions ,R1 ,Protein Structure, Tertiary ,Structural biology ,biology.protein ,HLA-B35 Antigen ,Peptides ,Major Histocompatibility Complex (MHC) ,030215 immunology - Abstract
Background: The mechanisms by which T cell receptors (TCRs) engage lengthy peptides bound to human leukocyte antigens (HLA) is unclear. Results: We have determined the structures of two TCRs binding to a 13-residue bulged peptide presented by HLA-B*35:08. Conclusion: TCRs can adopt markedly differing docking strategies upon engaging lengthy bulged peptides. Significance: The human T-cell repertoire is sufficiently robust to deal with viral determinants of atypical length., Human leukocyte antigen (HLA)-I molecules can present long peptides, yet the mechanisms by which T-cell receptors (TCRs) recognize featured pHLA-I landscapes are unclear. We compared the binding modes of three distinct human TCRs, CA5, SB27, and SB47, complexed with a “super-bulged” viral peptide (LPEPLPQGQLTAY) restricted by HLA-B*35:08. The CA5 and SB27 TCRs engaged HLA-B*35:08LPEP similarly, straddling the central region of the peptide but making limited contacts with HLA-B*35:08. Remarkably, the CA5 TCR did not contact the α1-helix of HLA-B*35:08. Differences in the CDR3β loop between the CA5 and SB27 TCRs caused altered fine specificities. Surprisingly, the SB47 TCR engaged HLA-B*35:08LPEP using a completely distinct binding mechanism, namely “bypassing” the bulged peptide and making extensive contacts with the extreme N-terminal end of HLA-B*35:08. This docking footprint included HLA-I residues not observed previously as TCR contact sites. The three TCRs exhibited differing patterns of alloreactivity toward closely related or distinct HLA-I allotypes. Thus, the human T-cell repertoire comprises a range of TCRs that can interact with “bulged” pHLA-I epitopes using unpredictable strategies, including the adoption of atypical footprints on the MHC-I.
- Published
- 2013
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