46 results on '"De Silva, Aruna D."'
Search Results
2. Dengue type 1 viruses circulating in humans are highly infectious and poorly neutralized by human antibodies
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Raut, Rajendra, Corbett, Kizzmekia S., Tennekoon, Rashika N., Premawansa, Sunil, Wijewickrama, Ananda, Premawansa, Gayani, Mieczkowski, Piotr, Rückert, Claudia, Ebel, Gregory D., De Silva, Aruna D., and de Silva, Aravinda M.
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- 2019
3. Nonclonal Burkholderia pseudomallei Population in Melioidosis Case Cluster, Sri Lanka
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Jayasinghearachchi, Himali S., Francis, Vaithehi R., Sathkumara, Harindra D., Krishnananthasivam, Shivankari, Masakorala, Jayanthi, Muthugama, Thilini, De Silva, Aruna D., and Corea, Enoka M.
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Burkholderia pseudomallei -- Identification and classification -- Genetic aspects ,Pseudomonas infections -- Causes of ,Health - Abstract
Melioidosis, an emerging tropical infection caused by the soil bacterium Burkholderia pseudomallei, is found most commonly in northern Australia and the tropical countries of Southeast Asia. Melioidosis is endemic in [...]
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- 2021
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4. Longitudinal Analysis of Antibody Cross-neutralization Following Zika Virus and Dengue Virus Infection in Asia and the Americas
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Montoya, Magelda, Collins, Matthew, Dejnirattisai, Wanwisa, Katzelnick, Leah C., Puerta-Guardo, Henry, Jadi, Ramesh, Schildhauer, Samuel, Supasa, Piyada, Vasanawathana, Sirijitt, Malasit, Prida, Mongkolsapaya, Juthathip, de Silva, Aruna D., Tissera, Hasitha, Balmaseda, Angel, Screaton, Gavin, de Silva, Aravinda M., and Harris, Eva
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- 2018
5. Dengue-specific [CD8.sup.+] T cell subsets display specialized transcriptomic and TCR profiles
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Tian, Yuan, Babor, Mariana, Lane, Jerome, Seumois, Gregory, Liang, Shu, Goonawardhana, N.D. Suraj, De Silva, Aruna D., Phillips, Elizabeth J., Mallal, Simon A., Antunes, Ricardo da Silva, Grifoni, Alba, Vijayanand, Pandurangan, Weiskopf, Daniela, Peters, Bjoern, and Sette, Alessandro
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Dengue virus -- Genetic aspects -- Risk factors -- Prevention ,T cells -- Research ,Transcription (Genetics) -- Research ,Viral vaccines -- Usage ,Vaccines ,Benchmarking ,Antigens ,Dengue fever ,Antigenic determinants ,Gene expression ,Genes ,Genetic research ,Health care industry - Abstract
Accumulating evidence demonstrates that [CD8.sup.+] T cells contribute to protection from severe dengue virus (DENV) disease and vaccine efficacy. Nevertheless, molecular programs associated with DENV-specific [CD8.sup.+] T cell subsets have not been defined. Here, we studied the transcriptomic profiles of human DENV-specific [CD8.sup.+] T cells isolated after stimulation with DENV epitopes from donors who had been infected with DENV multiple times and would therefore be expected to have significant levels of adaptive immunity. We found that DENV-specific [CD8.sup.+] T cells mainly consisted of effector memory subsets, namely [CD45RA.sup.-][CCR7.sup.-] effector memory (Tem) and [CD45RA.sup.+][CCR7.sup.-] effector memory re-expressing CD45RA (Temra) cells, which enacted specific gene expression profiles upon stimulation with cognate antigens. DENV-specific [CD8.sup.+] T cell subsets in general, and Temra cells in particular, were fully activated and polyfunctional, yet associated with relatively narrow transcriptional responses. Furthermore, we found that DENV-specific [CD8.sup.+] Tem and Temra cells showed some unique T cell receptor features in terms of overlap and variable (V) gene usage. This study provides a transcriptomic definition of DENV-specific activated human [CD8.sup.+] T cell subsets and defines a benchmark profile that vaccine-specific responses could aim to reproduce., Introduction Dengue virus (DENV) infection is a serious public health problem in tropical and subtropical areas, and it is estimated that approximately 390 million people are infected yearly (1). DENV [...]
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- 2019
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6. HLA-DRB1 Alleles Are Associated With Different Magnitudes of Dengue Virus-Specific CD4⁺ T-Cell Responses
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Weiskopf, Daniela, Angelo, Michael A., Grifoni, Alba, O'Rourke, Patrick H., Sidney, John, Paul, Sinu, De Silva, Aruna D., Phillips, Elizabeth, Mallal, Simon, Premawansa, Sunil, Premawansa, Gayani, Wijewickrama, Ananda, Peters, Bjoern, and Sette, Alessandro
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- 2016
7. Precursors of human CD4+ cytotoxic T lymphocytes identified by single-cell transcriptome analysis
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Patil, Veena S., Madrigal, Ariel, Schmiedel, Benjamin J., Clarke, James, O’Rourke, Patrick, de Silva, Aruna D., Harris, Eva, Peters, Bjoern, Seumois, Gregory, Weiskopf, Daniela, Sette, Alessandro, and Vijayanand, Pandurangan
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- 2018
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8. Human CD8⁺ T-Cell Responses Against the 4 Dengue Virus Serotypes Are Associated With Distinct Patterns of Protein Targets
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Weiskopf, Daniela, Cerpas, Cristhiam, Angelo, Michael A., Bangs, Derek J., Sidney, John, Paul, Sinu, Peters, Bjoern, Sanches, Françoise P., Silvera, Cassia G. T., Costa, Priscilla R., Kallas, Esper G., Gresh, Lionel, de Silva, Aruna D., Balmaseda, Angel, Harris, Eva, and Sette, Alessandro
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- 2015
9. Dengue virus infection elicits highly polarized CX3CR1⁺ cytotoxic CD4⁺ T cells associated with protective immunity
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Weiskopf, Daniela, Bangs, Derek J., Sidney, John, Kolla, Ravi V., De Silva, Aruna D., de Silva, Aravinda M., Crotty, Shane, Peters, Bjoern, and Sette, Alessandro
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- 2015
10. Comprehensive analysis of dengue virus-specific responses supports an HLA-linked protective role for CD8⁺ T cells
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Weiskopf, Daniela, Angelo, Michael A., de Azeredo, Elzinandes L., Sidney, John, Greenbaum, Jason A., Fernando, Anira N., Broadwater, Anne, Kolla, Ravi V., De Silva, Aruna D., de Silva, Aravinda M., Mattia, Kimberly A., Doranz, Benjamin J., Grey, Howard M., Shresta, Sujan, Peters, Bjoern, and Sette, Alessandro
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- 2013
11. Transcriptomics of Acute DENV-Specific CD8+ T Cells Does Not Support Qualitative Differences as Drivers of Disease Severity.
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Grifoni, Alba, Voic, Hannah, Yu, Esther Dawen, Mateus, Jose, Yan Fung, Kai Mei, Wang, Alice, Seumois, Grégory, De Silva, Aruna D., Tennekon, Rashika, Premawansa, Sunil, Premawansa, Gayani, Tippalagama, Rashmi, Wijewickrama, Ananda, Chawla, Ashu, Greenbaum, Jason, Peters, Bjoern, Pandurangan, Vijayanand, Weiskopf, Daniela, and Sette, Alessandro
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DENGUE hemorrhagic fever ,T cells ,CD8 antigen ,DENGUE ,DENGUE viruses - Abstract
While several lines of evidence suggest a protective role of T cells against disease associated with Dengue virus (DENV) infection, their potential contribution to immunopathology in the acute phase of DENV infection remains controversial, and it has been hypothesized that the more severe form of the disease (dengue hemorrhagic fever, DHF) is associated with altered T cell responses. To address this question, we determined the transcriptomic profiles of DENV-specific CD8+ T cells in a cohort of 40 hospitalized dengue patients with either a milder form of the disease (dengue fever, DF) or a more severe disease form (dengue hemorrhagic fever, DHF). We found multiple transcriptomic signatures, one associated with DENV-specific interferon-gamma responding cells and two other gene signatures, one specifically associated with the acute phase and the other with the early convalescent phase. Additionally, we found no differences in quantity and quality of DENV-specific CD8+ T cells based on disease severity. Taken together with previous findings that did not detect altered DENV-specific CD4 T cell responses, the current analysis argues against alteration in DENV-specific T cell responses as being a correlate of immunopathology. [ABSTRACT FROM AUTHOR]
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- 2022
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12. Outcomes among children and adults at risk of severe dengue in Sri Lanka: Opportunity for outpatient case management in countries with high disease burden.
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Bodinayake, Champica K., Nagahawatte, Ajith DeS, Devasiri, Vasantha, Dahanayake, Niroshana J., Wijayaratne, Gaya B., Weerasinghe, Nayani P., Premamali, Madureka, Sheng, Tianchen, Nicholson, Bradley P., Ubeysekera, Harshanie A., Kurukulasooriya, Ruvini MP, de Silva, Aruna D., Østbye, Truls, Woods, Christopher W., and Tillekeratne, L Gayani
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DENGUE hemorrhagic fever ,DENGUE ,HOSPITAL care of children ,ANTIBODY titer ,PLATELET count ,HOSPITAL admission & discharge - Abstract
Background: Healthcare systems in dengue-endemic countries are often overburdened due to the high number of patients hospitalized according to dengue management guidelines. We systematically evaluated clinical outcomes in a large cohort of patients hospitalized with acute dengue to support triaging of patients to ambulatory versus inpatient management in the future. Methods/Principal findings: From June 2017- December 2018, we conducted surveillance among children and adults with fever within the prior 7 days who were hospitalized at the largest tertiary-care (1,800 bed) hospital in the Southern Province, Sri Lanka. Patients who developed platelet count ≤100,000/μL (threshold for hospital admission in Sri Lanka) and who met at least two clinical criteria consistent with dengue were eligible for enrollment. We confirmed acute dengue by testing sera collected at enrollment for dengue NS1 antigen or IgM antibodies. We defined primary outcomes as per the 1997 and 2009 World Health Organization (WHO) classification criteria: dengue hemorrhagic fever (DHF; WHO 1997), dengue shock syndrome (DSS; WHO 1997), and severe dengue (WHO 2009). Overall, 1064 patients were confirmed as having acute dengue: 318 (17.4%) by NS1 rapid antigen testing and 746 (40.7%) by IgM antibody testing. Of these 1064 patients, 994 (93.4%) were adults ≥18 years and 704 (66.2%) were male. The majority (56, 80%) of children and more than half of adults (544, 54.7%) developed DHF during hospitalization, while 6 (8.6%) children and 22 (2.2%) adults developed DSS. Overall, 10 (14.3%) children and 113 (11.4%) adults developed severe dengue. A total of 2 (0.2%) patients died during hospitalization. Conclusions: One-half of patients hospitalized with acute dengue progressed to develop DHF and a very small number developed DSS or severe dengue. Developing an algorithm for triaging patients to ambulatory versus inpatient management should be the future goal to optimize utilization of healthcare resources in dengue-endemic countries. Author summary: In countries where dengue is prevalent, hospitals are often overwhelmed due to the high numbers of patient admissions during dengue epidemics. We studied 1064 children and adults hospitalized with acute dengue in Sri Lanka to determine the prevalence of severe disease outcomes to support the development of a system which can limit hospitalizations in the future. We found that only half of patients developed severe disease outcomes during hospitalization and only a small minority of patients developed life-threatening disease. For dengue-prevalent countries, developing systems to identify patients with acute dengue who can be managed without hospital admission should be a priority. [ABSTRACT FROM AUTHOR]
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- 2021
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13. Biogeography and genetic diversity of clinical isolates of Burkholderia pseudomallei in Sri Lanka.
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Jayasinghearachchi, Himali S., Corea, Enoka M., Jayaratne, Kumari I., Fonseka, Regina A., Muthugama, Thilini A., Masakorala, Jayanthi, Ramasinghe, Ravija YC., and De Silva, Aruna D.
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GENETIC variation ,BURKHOLDERIA pseudomallei ,COMMUNITY-acquired pneumonia ,MEDICAL personnel ,KLEBSIELLA pneumoniae ,BIOGEOGRAPHY ,SOLANUM ,RICE quality - Abstract
Background: Melioidosis is a potentially fatal infectious disease caused by Burkholderia pseudomallei and the disease is endemic in SoutheastAsia and Northern Australia. It has been confirmed as endemic in Sri Lanka. Genomic epidemiology of B. pseudomallei in Sri Lanka is largely unexplored. This study aims to determine the biogeography and genetic diversity of clinical isolates of B. pseudomallei and the phylogenetic and evolutionary relationship of Sri Lankan sequence types (STs) to those found in other endemic regions of Southeast Asia and Oceania. Methods: The distribution of variably present genetic markers [Burkholderia intracellular motility A (bimA) gene variants bimA
BP /bimABM , filamentous hemagglutinin 3 (fhaB3), Yersinia-like fimbrial (YLF) and B. thailandensis-like flagellum and chemotaxis (BTFC) gene clusters and lipopolysaccharide O-antigen type A (LPS type A)] was examined among 310 strains. Multilocus sequence typing (MLST) was done for 84 clinical isolates. The phylogenetic and evolutionary relationship of Sri Lankan STs within Sri Lanka and in relation to those found in other endemic regions of Southeast t Asia and Oceania were studied using e BURST, PHYLOViZ and minimum evolutionary analysis. Results: The Sri Lankan B. pseudomallei population contained a large proportion of the rare BTFC Clade (14.5%) and bimABM allele variant (18.5%) with differential geographic distribution. Genotypes fhaB3 and LPSA were found in 80% and 86% respectively. This study reported 43 STs (including 22 novel). e-BURST analysis which include all Sri Lankan STs (71) resulted in four groups, with a large clonal group (group 1) having 46 STs, and 17 singletons. ST1137 was the commonest ST. Several STs were shared with India, Bangladesh and Cambodia. Conclusion: This study demonstrates the usefulness of high-resolution molecular typing to locate isolates within the broad geographical boundaries of B. pseudomallei at a global level and reveals that Sri Lankan isolates are intermediate between Southeast Asia and Oceania. Author summary: Burkholderia pseudomallei is an important cause of community acquired pneumonia, septicemia and abscesses in Sri Lanka. The risk of infection is increased after flooding following heavy rainfall. Risk groups include rice farmers and rural populations engaged in subsistence cultivation in home gardens. Nationwide surveillance has been carried out since 2006 and the state public health system offers free diagnostics and free antibiotic therapy. The incidence of melioidosis in Sri Lanka has increased in tandem with increased awareness among clinicians. This study reports the genetic diversity among Sri Lankan B. pseudomallei clinical isolates and shows that some variably present genes are regionally distributed. The population is intermediate between Southeast Asia and Oceania. This may reflect its past geological history. [ABSTRACT FROM AUTHOR]- Published
- 2021
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14. Characterization of Magnitude and Antigen Specificity of HLA-DP, DQ, and DRB3/4/5 Restricted DENV-Specific CD4+ T Cell Responses.
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Grifoni, Alba, Moore, Eugene, Voic, Hannah, Sidney, John, Phillips, Elizabeth, Jadi, Ramesh, Mallal, Simon, De Silva, Aruna D., De Silva, Aravinda M., Peters, Bjoern, Weiskopf, Daniela, and Sette, Alessandro
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T cells ,ANTIGENS ,DENGUE viruses ,EPITOPES ,FLOW cytometry - Abstract
Background: Dengue Virus (DENV) associated disease is a major public health problem. Assessment of HLA class II restricted DENV-specific responses is relevant for immunopathology and definition of correlates of protection. While previous studies characterized responses restricted by the HLA-DRB1 locus, the responses associated with other class II loci have not been characterized to date. Accordingly, we mapped HLA-DP, DQ, and DRB3/4/5 restricted DENV-specific CD4 T cell epitopes in PBMCs derived from the DENV endemic region Sri Lanka. Methods: We studied 12 DP, DQ, and DRB3/4/5 alleles that are commonly expressed and provide worldwide coverage >82% for each of the loci analyzed and >99% when combined. CD4+ T cells purified by negative selection were stimulated with pools of HLA-predicted binders for 2 weeks with autologous APC. Epitope reactive T cells were enumerated using IFNγ ELISPOT assay. This strategy was previously applied to identify DRB1 restricted epitopes. In parallel, membrane expression levels of HLA-DR, DP, and DQ proteins was assessed using flow cytometry. Results: Epitopes were identified for all DP, DQ, and DRB3/4/5 allelic variants albeit with magnitudes significantly lower than the ones previously observed for the DRB1 locus. This was in line with lower membrane expression of HLA-DP and DQ molecules on the PBMCs tested, as compared to HLA-DR. Significant differences between loci were observed in antigen immunodominance. Capsid responses were dominant for DRB1/3/4/5 and DP alleles but negligible for the DQ alleles. NS3 responses were dominant in the case of DRB1/3/4/5 and DQ but absent in the case of DP. NS1 responses were prominent in the case of the DP alleles, but negligible in the case of DR and DQ. In terms of epitope specificity, repertoire was largely overlapping between DRB1 and DRB3/4/5, while DP and DQ loci recognized largely distinct epitope sets. Conclusion: The HLA-DP, DQ, and DRB3/4/5 loci mediate DENV-CD4 specific immune responses of lower magnitude as compared to HLA-DRB1, consistent with their lower levels of expression. The responses are associated with distinct and characteristic patterns of immunodominance, and variable epitope overlap across loci. [ABSTRACT FROM AUTHOR]
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- 2019
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15. Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 714 adults from Colombo, Sri Lanka
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Grifoni, Alba, Weiskopf, Daniela, Lindestam Arlehamn, Cecilia S., Angelo, Michael, Leary, Shay, Sidney, John, Frazier, April, Phillips, Elizabeth, Mallal, Simon, Mack, Steven J., Tippalagama, Rashmi, Goonewardana, Suraj, Premawansa, Sunil, Premawansa, Gayani, Wijewickrama, Ananda, De Silva, Aruna D., and Sette, Alessandro
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- 2018
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16. Evaluation of the WHO 2009 classification for diagnosis of acute dengue in a large cohort of adults and children in Sri Lanka during a dengue-1 epidemic.
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Bodinayake, Champica K., Tillekeratne, L. Gayani, Nagahawatte, Ajith, Devasiri, Vasantha, Kodikara Arachchi, Wasantha, Strouse, John J., Sessions, October M., Kurukulasooriya, Ruvini, Uehara, Anna, Howe, Shiqin, Ong, Xin Mei, Tan, Sharon, Chow, Angelia, Tummalapalli, Praveen, De Silva, Aruna D., Østbye, Truls, Woods, Christopher W., Gubler, Duane J., and Reller, Megan E.
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DENGUE ,DIAGNOSIS of fever ,EPIDEMICS ,TERTIARY care ,THROMBOCYTOPENIA ,OLIGURIA ,THROAT diseases - Abstract
Background: Dengue is a leading cause of fever and mimics other acute febrile illnesses (AFI). In 2009, the World Health Organization (WHO) revised criteria for clinical diagnosis of dengue. Methodology/Principal findings: The new WHO 2009 classification of dengue divides suspected cases into three categories: dengue without warning signs, dengue with warning signs and severe dengue. We evaluated the WHO 2009 classification vs physicians’ subjective clinical diagnosis (gestalt clinical impression) in a large cohort of patients presenting to a tertiary care center in southern Sri Lanka hospitalized with acute febrile illness. We confirmed acute dengue in 388 patients (305 adults ≥ 18 years and 83 children), including 103 primary and 245 secondary cases, of 976 patients prospectively enrolled with AFI. At presentation, both adults and children with acute dengue were more likely than those with other AFI to have leukopenia and thrombocytopenia. Additionally, adults were more likely than those with other AFI to have joint pain, higher temperatures, and absence of crackles on examination whereas children with dengue were more likely than others to have sore throat, fatigue, oliguria, and elevated hematocrit and transaminases. Similarly, presence of joint pain, thrombocytopenia, and absence of cough were independently associated with secondary vs primary dengue in adults whereas no variables were different in children. The 2009 WHO dengue classification was more sensitive than physicians’ clinical diagnosis for identification of acute dengue (71.5% vs 67.1%), but was less specific. However, despite the absence of on-site diagnostic confirmation of dengue, clinical diagnosis was more sensitive on discharge (75.2%). The 2009 WHO criteria classified almost 75% as having warning signs, even though only 9 (2.3%) patients had evidence of plasma leakage and 16 (4.1%) had evidence of bleeding Conclusions/Significance: In a large cohort with AFI, we identified features predictive of dengue vs other AFI and secondary vs primary dengue in adults versus children. The 2009 WHO dengue classification criteria had high sensitivity but low specificity compared to physicians’ gestaldt diagnosis. Large cohort studies will be needed to validate the diagnostic yield of clinical impression and specific features for dengue relative to the 2009 WHO classification criteria. [ABSTRACT FROM AUTHOR]
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- 2018
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17. Precursors of human CD4+ cytotoxic T lymphocytes identified by single-cell transcriptome analysis.
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Patil, Veena S., Madrigal, Ariel, Schmiedel, Benjamin J., Clarke, James, O’Rourke, Patrick, de Silva, Aruna D., Harris, Eva, Peters, Bjoern, Seumois, Gregory, Weiskopf, Daniela, Sette, Alessandro, and Vijayanand, Pandurangan
- Abstract
CD4
+ cytotoxic T lymphocytes (CD4-CTLs) have been reported to play a protective role in several viral infections. However, little is known in humans about the biology of CD4-CTL generation, their functional properties, and heterogeneity, especially in relation to other well-described CD4+ memory T cell subsets. We performed single-cell RNA sequencing in more than 9000 cells to unravel CD4-CTL heterogeneity, transcriptional profile, and clonality in humans. Single-cell differential gene expression analysis revealed a spectrum of known transcripts, including several linked to cytotoxic and costimulatory function that are expressed at higher levels in the TEMRA (effector memory T cells expressing CD45RA) subset, which is highly enriched for CD4-CTLs, compared with CD4+ T cells in the central memory (TCM ) and effector memory (TEM ) subsets. Simultaneous T cell antigen receptor (TCR) analysis in single cells and bulk subsets revealed that CD4-TEMRA cells show marked clonal expansion compared with TCM and TEM cells and that most of CD4-TEMRA were dengue virus (DENV)–specific in donors with previous DENV infection. The profile of CD4-TEMRA was highly heterogeneous across donors, with four distinct clusters identified by the single-cell analysis. We identified distinct clusters of CD4-CTL effector and precursor cells in the TEMRA subset; the precursor cells shared TCR clonotypes with CD4-CTL effectors and were distinguished by high expression of the interleukin-7 receptor. Our identification of a CD4-CTL precursor population may allow further investigation of how CD4-CTLs arise in humans and, thus, could provide insights into the mechanisms that may be used to generate durable and effective CD4-CTL immunity. [ABSTRACT FROM AUTHOR]- Published
- 2018
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18. Unique phenotypes and clonal expansions of human CD4 effector memory T cells re-expressing CD45RA.
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Yuan Tian, Babor, Mariana, Lane, Jerome, Schulten, Veronique, Patil, Veena S., Seumois, Grégory, Rosales, Sandy L., Burel, Julie, Zapardiel-Gonzalo, Jose, Vijayanand, Pandurangan, Weiskopf, Daniela, Sette, Alessandro, Peters, Bjoern, Tennekoon, Rashika N., De Silva, Aruna D., Zheng Fu, Greenbaum, Jason A., Picarda, Gaelle, Premawansa, Sunil, and Premawansa, Gayani
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PHENOTYPES ,T cells ,CLONE cells ,CD4 antigen ,DENGUE viruses - Abstract
The expression of CD45RA is generally associated with naive T cells. However, a subset of effector memory T cells re-expresses CD45RA (termed TEMRA) after antigenic stimulation with unknown molecular characteristics and functions. CD4 TEMRA cells have been implicated in protective immunity against pathogens such as dengue virus (DENV). Here we show that not only the frequency but also the phenotype of CD4 TEMRA cells are heterogeneous between individuals. These cells can be subdivided into two major subsets based on the expression of the adhesion G protein-coupled receptor GPR56, and GPR56
+ TEMRA cells display a transcriptional and proteomic program with cytotoxic features that is distinct from effector memory T cells. Moreover, GPR56+ TEMRA cells have higher levels of clonal expansion and contain the majority of virus-specific TEMRA cells. Overall, this study reveals the heterogeneity of CD4 TEMRA cells and provides insights into T-cell responses against DENV and other viral pathogens. [ABSTRACT FROM AUTHOR]- Published
- 2017
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19. Global Assessment of Dengue Virus-Specific CD4+ T Cell Responses in Dengue-Endemic Areas.
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Grifoni, Alba, Angelo, Michael A., Lopez, Benjamin, O'Rourke, Patrick H., Sidney, John, Cerpas, Cristhiam, Balmaseda, Angel, Silveira, Cassia G. T., Maestri, Alvino, Costa, Priscilla R., Durbin, Anna P., Diehl, Sean A., Phillips, Elizabeth, Mallal, Simon, De Silva, Aruna D., Nchinda, Godwin, Nkenfou, Celine, Collins, Matthew H., de Silva, Aravinda M., and Mei Qiu Lim
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DENGUE ,CD4 antigen ,T cells - Abstract
Background: Dengue is a major public health problem worldwide. Assessment of adaptive immunity is important to understanding immunopathology and to define correlates of protection against dengue virus (DENV). To enable global assessment of CD4
+ T cell responses, we mapped HLA-DRB1-restricted DENV-specific CD4+ T cell epitopes in individuals previously exposed to DENV in the general population of the dengue-endemic region of Managua, Nicaragua. Methods: HLA class II epitopes in the population of Managua were identified by an in vitro IFNγ ELISPOT assay. CD4+ T cells purified by magnetic bead negative selection were stimulated with HLA-matched epitope pools in the presence of autologous antigen-presenting cells, followed by pool deconvolution to identify specific epitopes. The epitopes identified in this study were combined with those previously identified in the DENV endemic region of Sri Lanka, to generate a "megapool" (MP) consisting of 180 peptides specifically designed to achieve balanced HLA and DENV serotype coverage. The DENV CD4MP180 was validated by intracellular cytokine staining assays. Results: We detected responses directed against a total of 431 epitopes, representing all 4 DENV serotypes, restricted by 15 different HLA-DRB1 alleles. The responses were associated with a similar pattern of protein immunodominance, overall higher magnitude of responses, as compared to what was observed previously in the Sri Lanka region. Based on these epitope mapping studies, we designed a DENV CD4 MP180 with higher and more consistent coverage, which allowed the detection of CD4+ T cell DENV responses ex vivo in various cohorts of DENV exposed donors worldwide, including donors from Nicaragua, Brazil, Singapore, Sri Lanka, and U.S. domestic flavivirus-naïve subjects immunized with Tetravalent Dengue Live-Attenuated Vaccine (TV005). This broad reactivity reflects that the 21 HLA-DRB1 alleles analyzed in this and previous studies account for more than 80% of alleles present with a phenotypic frequency ≥5% worldwide, corresponding to 92% phenotypic coverage of the general population (i.e., 92% of individuals express at least one of these alleles). Conclusion: The DENV CD4 MP180 can be utilized to measure ex vivo responses to DENV irrespective of geographical location. [ABSTRACT FROM AUTHOR]- Published
- 2017
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20. Emergence of Epidemic Dengue-1 Virus in the Southern Province of Sri Lanka.
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Bodinayake, Champica K., Tillekeratne, L. Gayani, Nagahawatte, Ajith, Devasiri, Vasantha, Kodikara Arachichi, Wasantha, Strouse, John J., Sessions, October M., Kurukulasooriya, Ruvini, Uehara, Anna, Howe, Shiqin, Ong, Xin Mei, Tan, Sharon, Chow, Angelia, Tummalapalli, Praveen, De Silva, Aruna D., Østbye, Truls, Woods, Christopher W., Gubler, Duane J., and Reller, Megan E.
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DENGUE viruses ,EPIDEMIOLOGY ,DENGUE ,PREVENTIVE medicine ,ETIOLOGY of diseases ,SEROTYPES ,DISEASE prevalence - Abstract
Background: Dengue is a frequent cause of acute febrile illness with an expanding global distribution. Since the 1960s, dengue in Sri Lanka has been documented primarily along the heavily urbanized western coast with periodic shifting of serotypes. Outbreaks from 2005–2008 were attributed to a new clade of DENV-3 and more recently to a newly introduced genotype of DENV-1. In 2007, we conducted etiologic surveillance of acute febrile illness in the Southern Province and confirmed dengue in only 6.3% of febrile patients, with no cases of DENV-1 identified. To re-evaluate the importance of dengue as an etiology of acute febrile illness in this region, we renewed fever surveillance in the Southern Province to newly identify and characterize dengue. Methodology/Principal Findings: A cross-sectional surveillance study was conducted at the largest tertiary care hospital in the Southern Province from 2012–2013. A total of 976 patients hospitalized with acute undifferentiated fever were enrolled, with 64.3% male and 31.4% children. Convalescent blood samples were collected from 877 (89.6%). Dengue virus isolation, dengue RT-PCR, and paired IgG ELISA were performed. Acute dengue was confirmed as the etiology for 388 (39.8%) of 976 hospitalizations, with most cases (291, 75.0%) confirmed virologically and by multiple methods. Among 351 cases of virologically confirmed dengue, 320 (91.2%) were due to DENV-1. Acute dengue was associated with self-reported rural residence, travel, and months having greatest rainfall. Sequencing of selected dengue viruses revealed that sequences were most closely related to those described from China and Southeast Asia, not nearby India. Conclusions/Significance: We describe the first epidemic of DENV-1 in the Southern Province of Sri Lanka in a population known to be susceptible to this serotype because of prior study. Dengue accounted for 40% of acute febrile illnesses in the current study. The emergence of DENV-1 as the foremost serotype in this densely populated but agrarian population highlights the changing epidemiology of dengue and the need for continued surveillance and prevention. [ABSTRACT FROM AUTHOR]
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- 2016
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21. Dengue virus infection elicits highly polarized CX3CR1+ cytotoxic CD4+ T cells associated with protective immunity.
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Weiskopf, Daniela, Bangs, Derek J., Sidney, John, Kolla, Ravi V., De Silva, Aruna D., de Silva, Aravinda M., Crotty, Shane, Peters, Bjoern, and Sette, Alessandro
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DENGUE viruses ,CD4 antigen ,CYTOTOXIC T cells ,FLOW cytometry ,HLA histocompatibility antigens - Abstract
Dengue virus (DENV) is a rapidly spreading pathogen with unusual pathogenesis, and correlates of protection from severe dengue disease and vaccine efficacy have not yet been established. Although DENV-specific CD8
+ T-cell responses have been extensively studied, the breadth and specificity of CD4+ T-cell responses remains to be defined. Here we define HLA-restricted CD4+ T-cell epitopes resulting from natural infection with dengue virus in a hyperepidemic setting. Ex vivo flow-cytometric analysis of DENVspecific CD4+ T cells revealed that the virus-specific cells were highly polarized, with a strong bias toward a CX3CR1+ Eomesodermin+ perforin+ granzyme B+ CD45RA+ CD4 CTL phenotype. Importantly, these cells correlated with a protective HLA DR allele, and we demonstrate that these cells have direct ex vivo DENV-specific cytolytic activity. We speculate that cytotoxic dengue-specific CD4+ T cells may play a role in the control of dengue infection in vivo, and this immune correlate may be a key target for dengue virus vaccine development. [ABSTRACT FROM AUTHOR]- Published
- 2015
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22. Correction: Outcomes among children and adults at risk of severe dengue in Sri Lanka: Opportunity for outpatient case management in countries with high disease burden.
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Bodinayake, Champica K., Nagahawatte, Ajith DeS, Devasiri, Vasantha, Dahanayake, Niroshana J., Wijayaratne, Gaya B., Weerasinghe, Nayani P., Premamali, Madureka, Sheng, Tianchen, Nicholson, Bradley P., Ubeysekera, Harshanie A., Kurukulasooriya, Ruvini MP, de Silva, Aruna D., Østbye, Truls, Woods, Christopher W., and Tillekeratne, L. Gayani
- Subjects
DENGUE hemorrhagic fever ,DENGUE ,COUNTRIES - Abstract
The correct name is: Bradley P. Nicholson. Reference 1 Bodinayake CK, Nagahawatte AD, Devasiri V, Dahanayake NJ, Wijayaratne GB, Weerasinghe NP, et al. (2021) Outcomes among children and adults at risk of severe dengue in Sri Lanka: Opportunity for outpatient case management in countries with high disease burden. [Extracted from the article]
- Published
- 2022
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23. Properties of MHC Class I Presented Peptides That Enhance Immunogenicity.
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Calis, Jorg J. A., Maybeno, Matt, Greenbaum, Jason A., Weiskopf, Daniela, De Silva, Aruna D., Sette, Alessandro, Keşmir, Can, and Peters, Bjoern
- Subjects
MAJOR histocompatibility complex ,T cells ,EPITOPES ,AMINO acids ,PEPTIDES ,CELLULAR immunity - Abstract
T-cells have to recognize peptides presented on MHC molecules to be activated and elicit their effector functions. Several studies demonstrate that some peptides are more immunogenic than others and therefore more likely to be T-cell epitopes. We set out to determine which properties cause such differences in immunogenicity. To this end, we collected and analyzed a large set of data describing the immunogenicity of peptides presented on various MHC-I molecules. Two main conclusions could be drawn from this analysis: First, in line with previous observations, we showed that positions P4–6 of a presented peptide are more important for immunogenicity. Second, some amino acids, especially those with large and aromatic side chains, are associated with immunogenicity. This information was combined into a simple model that was used to demonstrate that immunogenicity is, to a certain extent, predictable. This model (made available at http://tools.iedb.org/immunogenicity/) was validated with data from two independent epitope discovery studies. Interestingly, with this model we could show that T-cells are equipped to better recognize viral than human (self) peptides. After the past successful elucidation of different steps in the MHC-I presentation pathway, the identification of variables that influence immunogenicity will be an important next step in the investigation of T-cell epitopes and our understanding of cellular immune responses. [ABSTRACT FROM AUTHOR]
- Published
- 2013
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24. Molecular Signatures of Dengue Virus-Specific IL-10/IFN-γ Co-producing CD4 T Cells and Their Association with Dengue Disease.
- Author
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Tian, Yuan, Seumois, Grégory, De-Oliveira-Pinto, Luzia M., Mateus, Jose, Herrera-de la Mata, Sara, Kim, Cheryl, Hinz, Denise, Goonawardhana, N.D. Suraj, de Silva, Aruna D., Premawansa, Sunil, Premawansa, Gayani, Wijewickrama, Ananda, Balmaseda, Angel, Grifoni, Alba, Vijayanand, Pandurangan, Harris, Eva, Peters, Bjoern, Sette, Alessandro, and Weiskopf, Daniela
- Abstract
Dengue virus (DENV) can cause diseases ranging from dengue fever (DF) to more severe dengue hemorrhagic fever/dengue shock syndrome (DHF/DSS). Whether antiviral T cells contribute to the protection against or pathogenesis of severe disease is not well defined. Here, we identified antigen-specific IL-10
+ IFN-γ+ double-positive (DP) CD4 T cells during acute DENV infection. While the transcriptomic signatures of DP cells partially overlapped with those of cytotoxic and type 1 regulatory CD4 T cells, the majority of them were non-cytotoxic/Tr1 and included IL21 , IL22 , CD109 , and CCR1. Although we observed a higher frequency of DP cells in DHF, the transcriptomic profile of DP cells was similar in DF and DHF, suggesting that DHF is not associated with the altered phenotypic or functional attributes of DP cells. Overall, this study revealed a DENV-specific DP cell subset in patients with acute dengue disease and argues against altered DP cells as a determinant of DHF. • DENV-specific IL-10+ IFN-γ+ DP CD4 T cells are prominent during acute disease • Most DP cell DE genes are non-cytotoxic/Tr1 and include IL21 , IL22 , CD109 , and CCR1 • DP cells have similar gene expression in DF and DHF, despite higher frequency in DHF • Disease severity is not associated with altered DP cell phenotype or functionality Tian et al. identify and characterize antigen-specific IL-10+ IFN-γ+ double-positive (DP) CD4 T cells in acute dengue patients. DP cells display similar transcriptomic profiles in mild DF and severe DHF, despite their increased frequency in DHF, suggesting that DHF is not associated with the altered phenotype or functionality of DP cells. [ABSTRACT FROM AUTHOR]- Published
- 2019
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25. Prior Dengue Virus Exposure Shapes T Cell Immunity to Zika Virus in Humans
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Diehl, Sean A., de-Oliveira-Pinto, Luzia Maria, Harris, Eva, Magnani, Diogo M., Grifoni, Alba, Coloma, Josefina, Cox, Josephine, O'Rourke, Patrick H., Paul, Sinu, Solomon, Tom, Turtle, Lance, Norris, Phillip J., Watkins, David I., Sette, Alessandro, Cerpas, Cristhiam, de Silva, Aruna D., Graham, Barney S., Pham, John, Crowe, James E., Maestri, Alvino, Damasco, Paulo Vieira, Sidney, John, Vivanco-Cid, Hector, Silveira, Cassia G.T., Kuan, Guillermina, Busch, Michael, Balmaseda, Angel, Durbin, Anna, Stone, Mars, Mallal, Simon, Phillips, Elizabeth, Ricciardi, Michael J., Ledgerwood, Julie E., de Silva, Aravinda M., Kallas, Esper G., Martini, Sheridan R., Costa, Priscilla R., Weiskopf, Daniela, de Azeredo, Elzinandes Leal, Peters, Bjoern, and Collins, Matthew
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viruses ,virus diseases ,biochemical phenomena, metabolism, and nutrition ,3. Good health - Abstract
While progress has been made in characterizing humoral immunity to Zika virus (ZIKV) in humans, little is known regarding the corresponding T cell responses to ZIKV. Here, we investigate the kinetics and viral epitopes targeted by T cells responding to ZIKV and address the critical question of whether preexisting dengue virus (DENV) T cell immunity modulates these responses. We find that memory T cell responses elicited by prior infection with DENV or vaccination with tetravalent dengue attenuated vaccines (TDLAV) recognize ZIKV-derived peptides. This cross-reactivity is explained by the sequence similarity of the two viruses, as the ZIKV peptides recognized by DENV-elicited memory T cells are identical or highly conserved in DENV and ZIKV. DENV exposure prior to ZIKV infection also influences the timing and magnitude of the T cell response. ZIKV-reactive T cells in the acute phase of infection are detected earlier and in greater magnitude in DENV-immune patients. Conversely, the frequency of ZIKV-reactive T cells continues to rise in the convalescent phase in DENV-naive donors but declines in DENV-preexposed donors, compatible with more efficient control of ZIKV replication and/or clearance of ZIKV antigen. The quality of responses is also influenced by previous DENV exposure, and ZIKV-specific CD8 T cells from DENV-preexposed donors selectively upregulated granzyme B and PD1, unlike DENV-naive donors. Finally, we discovered that ZIKV structural proteins (E, prM, and C) are major targets of both the CD4 and CD8 T cell responses, whereas DENV T cell epitopes are found primarily in nonstructural proteins. IMPORTANCE The issue of potential ZIKV and DENV cross-reactivity and how preexisting DENV T cell immunity modulates Zika T cell responses is of great relevance, as the two viruses often cocirculate and Zika virus has been spreading in geographical regions where DENV is endemic or hyperendemic. Our data show that memory T cell responses elicited by prior infection with DENV recognize ZIKV-derived peptides and that DENV exposure prior to ZIKV infection influences the timing, magnitude, and quality of the T cell response. Additionally, we show that ZIKV-specific responses target different proteins than DENV-specific responses, pointing toward important implications for vaccine design against this global threat.
26. Global Assessment of Dengue Virus-Specific CD4+ T Cell Responses in Dengue-Endemic Areas
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Sidney, John, Diehl, Sean A., Satchidanandam, Vijaya, Grifoni, Alba, Costa, Priscilla R., Sette, Alessandro, Macary, Paul A., Nchinda, Godwin, de Silva, Aravinda M., Desai, Anita, Turtle, Lance, Cerpas, Cristhiam, Rivino, Laura, Harris, Eva, Ravi, Vasanthapram, Peters, Bjoern, Phillips, Elizabeth, Solomon, Tom, de Silva, Aruna D., Tatullo, Filippo, Nkenfou, Celine, Durbin, Anna P., Coloma, Josefina, Lim, Mei Qiu, O'Rourke, Patrick H., Weiskopf, Daniela, Collins, Matthew H., Kallas, Esper G., Lopez, Benjamin, Angelo, Michael A., Maestri, Alvino, Balmaseda, Angel, Silveira, Cassia G.T., and Mallal, Simon
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viruses ,virus diseases ,biochemical phenomena, metabolism, and nutrition ,3. Good health - Abstract
Dengue is a major public health problem worldwide. Assessment of adaptive immunity is important to understanding immunopathology and to define correlates of protection against dengue virus (DENV). To enable global assessment of CD4+ T cell responses, we mapped HLA-DRB1-restricted DENV-specific CD4+ T cell epitopes in individuals previously exposed to DENV in the general population of the dengue-endemic region of Managua, Nicaragua.
27. Pre-existing T Cell Memory against Zika Virus.
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Schouest, Blake, Grifoni, Alba, Pham, John, Mateus, Jose, Sydney, John, Brien, James D., De Silva, Aruna D., Balmaseda, Angel, Harris, Eva, Sette, Alessandro, and Weiskopf, Daniela
- Subjects
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ZIKA virus , *ZIKA virus infections , *DENGUE viruses , *CELLULAR immunity , *T cells , *ARBOVIRUS diseases , *EPITOPES - Abstract
The mosquito-borne Zika virus (ZIKV) has spread rapidly into regions where dengue virus (DENV) is endemic, and flavivirus cross-reactive T cell responses have been observed repeatedly in animal models and in humans. Preexisting cellular immunity to DENV is thought to contribute to protection in subsequent ZIKV infection, but the epitope targets of cross-reactive T cell responses have not been comprehensively identified. Using human blood samples from the regions of Nicaragua and Sri Lanka where DENV is endemic that were collected before the global spread of ZIKV in 2016, we employed an in vitro expansion strategy to map ZIKV T cell epitopes in ZIKV-unexposed, DENV-seropositive donors. We identified 93 epitopes across the ZIKV proteome, and we observed patterns of immunodominance that were dependent on antigen size and sequence identity to DENV. We confirmed the immunogenicity of these epitopes through a computational HLA binding analysis, and we showed that cross-reactive T cells specifically recognize ZIKV peptides homologous to DENV sequences. We also found that these CD4 responses were derived from the memory T cell compartment. These data have implications for understanding the dynamics of flavivirus-specific T cell immunity in areas of endemicity. [ABSTRACT FROM AUTHOR]
- Published
- 2021
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28. T Cell Responses Induced by Attenuated Flavivirus Vaccination Are Specific and Show Limited Cross-Reactivity with Other Flavivirus Species.
- Author
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Grifoni, Alba, Voic, Hannah, Dhanda, Sandeep Kumar, Kidd, Conner K., Brien, James D., Buus, Søren, Stryhn, Anette, Durbin, Anna P., Whitehead, Stephen, Diehl, Sean A., De Silva, Aruna D., Balmaseda, Angel, Harris, Eva, Weiskopf, Daniela, and Sette, Alessandro
- Subjects
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T cells , *JAPANESE B encephalitis , *YELLOW fever , *BLOOD cells , *VACCINATION - Abstract
Members of the flavivirus genus share a high level of sequence similarity and often circulate in the same geographical regions. However, whether T cells induced by one viral species cross-react with other related flaviviruses has not been globally addressed. In this study, we tested pools of epitopes derived from dengue (DENV), Zika (ZIKV), Japanese encephalitis (JEV), West Nile (WNV), and yellow fever (YFV) viruses by intracellular cytokine staining (ICS) using peripheral blood mononuclear cells (PBMCs) of individuals naturally exposed to DENV or immunized with DENV (TV005) or YF17D vaccine. CD8 T cell responses recognized epitopes from multiple flaviviruses; however, the magnitude of cross-reactive responses was consistently severalfold lower than those to the autologous epitope pools and was associated with lower expression of activation markers such as CD40L, CD69, and CD137. Next, we characterized the antigen sensitivity of short-term T cell lines (TCL) representing 29 different individual epitope/donor combinations. TCL derived from DENV monovalent vaccinees induced CD8 and CD4 T cells that cross-reacted within the DENV serocomplex but were consistently associated with 100-fold-lower antigen sensitivity for most other flaviviruses, with no cross-recognition of YFV-derived peptides. CD8 and CD4 TCL from YF17D vaccinees were associated with very limited cross-reactivity with any other flaviviruses and in five out of eight cases 1,000-foldlower antigen sensitivity. Overall, our data suggest limited cross-reactivity for both CD4 and CD8 T cell responses between flaviviruses and have implications for understanding immunity elicited by natural infection and strategies to develop live attenuated vaccines against flaviviral species. [ABSTRACT FROM AUTHOR]
- Published
- 2020
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- View/download PDF
29. Dengue-specific CD8+ T cell subsets display specialized transcriptomic and TCR profiles.
- Author
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Yuan Tian, Babor, Mariana, Lane, Jerome, Seumois, Grégory, Shu Liang, Suraj Goonawardhana, N. D., De Silva, Aruna D., Phillips, Elizabeth J., Mallal, Simon A., da Silva Antunes, Ricardo, Grifoni, Alba, Vijayanand, Pandurangan, Weiskopf, Daniela, Peters, Bjoern, Sette, Alessandro, Tian, Yuan, Liang, Shu, and Goonawardhana, N D Suraj
- Subjects
- *
T cells , *T cell receptors , *TRANSVERSE electromagnetic cells , *GENE expression profiling , *VACCINE effectiveness - Abstract
Accumulating evidence demonstrates that CD8+ T cells contribute to protection from severe dengue virus (DENV) disease and vaccine efficacy. Nevertheless, molecular programs associated with DENV-specific CD8+ T cell subsets have not been defined. Here, we studied the transcriptomic profiles of human DENV-specific CD8+ T cells isolated after stimulation with DENV epitopes from donors who had been infected with DENV multiple times and would therefore be expected to have significant levels of adaptive immunity. We found that DENV-specific CD8+ T cells mainly consisted of effector memory subsets, namely CD45RA-CCR7- effector memory (Tem) and CD45RA+CCR7- effector memory re-expressing CD45RA (Temra) cells, which enacted specific gene expression profiles upon stimulation with cognate antigens. DENV-specific CD8+ T cell subsets in general, and Temra cells in particular, were fully activated and polyfunctional, yet associated with relatively narrow transcriptional responses. Furthermore, we found that DENV-specific CD8+ Tem and Temra cells showed some unique T cell receptor features in terms of overlap and variable (V) gene usage. This study provides a transcriptomic definition of DENV-specific activated human CD8+ T cell subsets and defines a benchmark profile that vaccine-specific responses could aim to reproduce. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
30. Cutting Edge: Transcriptional Profiling Reveals Multifunctional and Cytotoxic Antiviral Responses of Zika Virus-Specific CD8+ T Cells.
- Author
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Grifoni, Alba, Pham, John, Yuan Tian, Rosales, Sandy L., Seumois, Grégory, Sidney, John, Vijayanand, Pandurangan, Weiskopf, Daniela, Peters, Bjoern, Sette, Alessandro, de Silva, Aruna D., Ricciardi, Michael J., Ledgerwood, Julie E., Harris, Eva, Costa-Ramos, Priscilla, Kallas, Esper, Premkumar, Lakshmanane, de Silva, Aravinda M., Collins, Matthew H., and Stone, Mars
- Abstract
Zika virus (ZIKV) constitutes an increasing public health problem. Previous studies have shown that CD8+ T cells play an important role in ZIKV-specific protective immunity. We have previously defined antigenic targets of the ZIKV-specific CD8+ T cell response in humans. In this study, we characterized the quality and phenotypes of these responses by a combined use of flow cytometry and transcriptomic methods, using PBMCs from donors deriving from different geographical locations collected in the convalescent phase of infection. We show that ZIKVspecific CD8+ T cells are characterized by a polyfunctional IFN-γ signature with upregulation of TNF-α, TNF receptors, and related activation markers, such as CD69, as well as a cytotoxic signature characterized by strong upregulation of GZMB and CRTAM. The signature is stable and not influenced by previous dengue virus exposure, geographical location, or time of sample collection postinfection. To our knowledge, this work elucidates the first in-depth characterization of human CD8+ T cells responding to ZIKV infection. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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- View/download PDF
31. Prior Dengue Virus Exposure Shapes T Cell Immunity to Zika Virus in Humans.
- Author
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Grifoni, Alba, Pham, John, Sidney, John, O'Rourke, Patrick H., Paul, Sinu, Peters, Bjoern, Martini, Sheridan R., de Silva, Aruna D., Ricciardi, Michael J., Magnani, Diogo M., Silveira, Cassia G. T., Maestri, Alvino, Costa, Priscilla R., de-Oliveira-Pinto, Luzia Maria, de Azeredo, Elzinandes Leal, Vieira Damasco, Paulo, Phillips, Elizabeth, Simon Mallal, de Silva, Aravinda M., and Collins, Matthew
- Subjects
- *
ZIKA virus infections , *DENGUE , *T cells , *CROSS reactions (Immunology) , *CD8 antigen , *VIRAL proteins , *EPITOPES , *IMMUNOLOGY - Abstract
While progress has been made in characterizing humoral immunity to Zika virus (ZIKV) in humans, little is known regarding the corresponding T cell responses to ZIKV. Here, we investigate the kinetics and viral epitopes targeted by T cells responding to ZIKV and address the critical question of whether preexisting dengue virus (DENV) T cell immunity modulates these responses. We find that memory T cell responses elicited by prior infection with DENV or vaccination with tetravalent dengue attenuated vaccines (TDLAV) recognize ZIKV-derived peptides. This cross-reactivity is explained by the sequence similarity of the two viruses, as the ZIKV peptides recognized by DENV-elicited memory T cells are identical or highly conserved in DENV and ZIKV. DENV exposure prior to ZIKV infection also influences the timing and magnitude of the T cell response. ZIKV-reactive T cells in the acute phase of infection are detected earlier and in greater magnitude in DENV-immune patients. Conversely, the frequency of ZIKV-reactive T cells continues to rise in the convalescent phase in DENV-naive donors but declines in DENV-preexposed donors, compatible with more efficient control of ZIKV replication and/or clearance of ZIKV antigen. The quality of responses is also influenced by previous DENV exposure, and ZIKV-specific CD8 T cells from DENV-preexposed donors selectively upregulated granzyme B and PD1, unlike DENV-naive donors. Finally, we discovered that ZIKV structural proteins (E, prM, and C) are major targets of both the CD4 and CD8 T cell responses, whereas DENV T cell epitopes are found primarily in nonstructural proteins. IMPORTANCE The issue of potential ZIKV and DENV cross-reactivity and how preexisting DENV T cell immunity modulates Zika T cell responses is of great relevance, as the two viruses often cocirculate and Zika virus has been spreading in geographical regions where DENV is endemic or hyperendemic. Our data show that memory T cell responses elicited by prior infection with DENV recognize ZIKV-derived peptides and that DENV exposure prior to ZIKV infection influences the timing, magnitude, and quality of the T cell response. Additionally, we show that ZIKV-specific responses target different proteins than DENV-specific responses, pointing toward important implications for vaccine design against this global threat. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
32. Patterns of Cellular Immunity Associated with Experimental Infection with rDEN2Δ30 (Tonga/74) Support Its Suitability as a Human Dengue Virus Challenge Strain.
- Author
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Grifoni, Alba, Angelo, Michael, Sidney, John, Paul, Sinu, Peters, Bjoern, de Silva, Aruna D., Phillips, Elizabeth, Mallal, Simon, Diehl, Sean A., Botten, Jason, Boyson, Jonathan, Kirkpatrick, Beth D., Whitehead, Stephen S., Durbin, Anna P., Sette, Alessandro, and Weiskopf, Daniela
- Subjects
- *
DENGUE , *THERAPEUTICS , *CELLULAR immunity , *DELETION mutation , *SEROTYPES , *DENGUE viruses - Abstract
A deletion variant of the dengue virus (DENV) serotype 2 (DENV2) Tonga/74 strain lacking 30 nucleotides from its 3= untranslated region (rDEN2Δ30) has previously been established for use in a controlled human DENV challenge model. To evaluate if this model is appropriate for the derivation of correlates of protection for DENV vaccines on the basis of cellular immunity, we wanted to compare the cellular immune response to this challenge strain to the response induced by natural infection. To achieve this, we predicted HLA class I- and class II-restricted peptides from rDEN2Δ30 and used them in a gamma interferon enzyme-linked immunosorbent spot assay to interrogate CD8+ and CD4+ T cell responses in healthy volunteers infected with rDEN2Δ30. At the level of CD8 responses, vigorous ex vivo responses were detected in approximately 80% of donors. These responses were similar in terms of the magnitude and the numbers of epitopes recognized to the responses previously observed in peripheral blood mononuclear cells from donors from regions where DENV is hyperendemic. The similarity extended to the immunodominance hierarchy of the DENV nonstructural proteins, with NS3, NS5, and NS1 being dominant in both donor cohorts. At the CD4 level, the responses to rDEN2Δ30 vaccination were less vigorous than those to natural DENV infection and were more focused on nonstructural proteins. The epitopes recognized following rDEN2Δ30 infection and natural infection were largely overlapping for both the CD8 (100%) and CD4 (85%) responses. Finally, rDEN2Δ30 induced stronger CD8 responses than other, more attenuated DENV isolates. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
33. Human CD4+ T Cell Responses to an Attenuated Tetravalent Dengue Vaccine Parallel Those Induced by Natural Infection in Magnitude, HLA Restriction, and Antigen Specificity.
- Author
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Angelo, Michael A., Grifoni, Alba, O'Rourke, Patrick H., Sidney, John, Paul, Sinu, Peters, Bjoern, de Silva, Aruna D., Phillips, Elizabeth, Mallal, Simon, Diehl, Sean A., Kirkpatrick, Beth D., Whitehead, Stephen S., Durbin, Anna P., Sette, Alessandro, and Weiskopf, Daniela
- Subjects
- *
DENGUE viruses , *T cells , *MONONUCLEAR leukocytes , *MAJOR histocompatibility complex , *CYTOKINES , *ANTIGENS , *NATURAL immunity - Abstract
Dengue virus (DENV) is responsible for growing numbers of infections worldwide and has proven to be a significant challenge for vaccine development. We previously demonstrated that CD8+ T cell responses elicited by a dengue live attenuated virus (DLAV) vaccine resemble those observed after natural infection. In this study, we screened peripheral blood mononuclear cells (PBMCs) from donors vaccinated with a tetravalent DLAV vaccine (TV005) with pools of dengue virusderived predicted major histocompatibility complex (MHC) class II binding peptides. The definition of CD4+ T cell responses after live vaccination is important because CD4+ T cells are known contributors to host immunity, including cytokine production, help for CD8+ T and B cells, and direct cytotoxicity against infected cells. While responses to all antigens were observed, DENV-specific CD4+ T cells were focused predominantly on the capsid and nonstructural NS3 and NS5 antigens. Importantly, CD4+ T cell responses in vaccinees were similar in magnitude and breadth to those after natural infection, recognized the same antigen hierarchy, and had similar profiles of HLA restriction. We conclude that TV005 vaccination has the capacity to elicit CD4+ cell responses closely mirroring those observed in a population associated with natural immunity. IMPORTANCE The development of effective vaccination strategies against dengue virus infection is of high global public health interest. Here we study the CD4 T cell responses elicited by a tetravalent live attenuated dengue vaccine and show that they resemble responses seen in humans naturally exposed to dengue virus. This is an important issue, since it is likely that optimal immunity induced by a vaccine requires induction of CD4+ responses against the same antigens as those recognized as dominant in natural infection. Detailed knowledge of the T cell response may further contribute to the identification of robust correlates of protection against dengue virus. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
34. An Integrated Workflow To Assess Technical and Biological Variability of Cell Population Frequencies in Human Peripheral Blood by Flow Cytometry.
- Author
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Burel, Julie G., Yu Qian, Lindestam Arlehamn, Cecilia, Weiskopf, Daniela, Zapardiel-Gonzalo, Jose, Taplitz, Randy, Gilman, Robert H., Mayuko Saito, De Silva, Aruna D., Vijayanand, Pandurangan, Scheuermann, Richard H., Sette, Alessandro, and Peters, Bjoern
- Subjects
- *
CELL populations , *T cells , *FLOW cytometry , *CRYOPRESERVATION of organs, tissues, etc. , *ETHNICITY , *PHYSIOLOGY - Abstract
In the context of large-scale human system immunology studies, controlling for technical and biological variability is crucial to ensure that experimental data support research conclusions. In this study, we report on a universal workflow to evaluate both technical and biological variation in multiparameter flow cytometry, applied to the development of a 10-color panel to identify all major cell populations and T cell subsets in cryopreserved PBMC. Replicate runs from a control donation and comparison of different gating strategies assessed the technical variability associated with each cell population and permitted the calculation of a quality control score. Applying our panel to a large collection of PBMC samples, we found that most cell populations showed low intraindividual variability over time. In contrast, certain subpopulations such as CD56 T cells and Temra CD4 T cells were associated with high interindividual variability. Age but not gender had a significant effect on the frequency of several populations, with a drastic decrease in naive T cells observed in older donors. Ethnicity also influenced a significant proportion of immune cell population frequencies, emphasizing the need to account for these covariates in immune profiling studies. We also exemplify the usefulness of our workflow by identifying a novel cell-subset signature of latent tuberculosis infection. Thus, our study provides a universal workflow to establish and evaluate any flow cytometry panel in systems immunology studies. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
35. Immunodominant Dengue Virus-Specific CD8+ T Cell Responses Are Associated with a Memory PD-1+ Phenotype.
- Author
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de Alwis, Ruklanthi, Bangs, Derek J., Angelo, Michael A., Cerpas, Cristhiam, Fernando, Anira, Sidney, John, Peters, Bjoern, Gresh, Lionel, Balmaseda, Angel, de Silva, Aruna D., Harris, Eva, Sette, Alessandro, and Weiskopf, Daniela
- Subjects
- *
DENGUE viruses , *CD8 antigen , *T cells , *VIRAL proteins , *PHENOTYPES , *GENE expression - Abstract
Dengue disease is a large public health problem that mainly afflicts tropical and subtropical regions. Understanding of the correlates of protection against dengue virus (DENV) is poor and hinders the development of a successful human vaccine. The present study aims to define DENV-specific CD8+ T cell responses in general and those of HLA alleles associated with dominant responses in particular. In human blood donors in Nicaragua, we observed a striking dominance of HLA B-restricted responses in general and of the allele B*35:01 in particular. Comparing these patterns to those in the general population of Sri Lanka, we found a strong correlation between restriction of the HLA allele and the breadth and magnitude of CD8+ T cell responses, suggesting that HLA genes profoundly influence the nature of responses. The majority of gamma interferon (IFN-+) responses were associated with effector memory phenotypes, which were also detected in non-B*35:01-expressing T cells. However, only the B*35:01 DENV-specific T cells were associated with marked expression of the programmed death 1 protein (PD-1). These cells did not coexpress other inhibitory receptors and were able to proliferate in response to DENV-specific stimulation. Thus, the expression of particular HLA class I alleles is a defining characteristic influencing the magnitude and breadth of CD8 responses, and a distinct, highly differentiated phenotype is specifically associated with dominant CD8+ T cells. These results are of relevance for both vaccine design and the identification of robust correlates of protection in natural immunity. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
36. Insights into HLA-Restricted T Cell Responses in a Novel Mouse Model of Dengue Virus Infection Point toward New Implications for Vaccine Design.
- Author
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Weiskopf, Daniela, Yauch, Lauren E., Angelo, Michael A., John, Daisy V., Greenbaum, Jason A., Sidney, John, Kolla, Ravi V., De Silva, Aruna D., de Silva, Aravinda M., Grey, Howard, Peters, Bjoern, Shresta, Sujan, and Sette, Alessandro
- Subjects
- *
T cells , *LYMPHOCYTES , *DENGUE viruses , *VACCINATION , *TRANSGENIC mice , *THERAPEUTICS - Abstract
The frequency of dengue virus (DENV) infection has increased dramatically in the last few decades, and the lack of a vaccine has led to significant morbidity and mortality worldwide. To date, a convenient murine system to study human T cell responses to DENV has not been available. Mice transgenic for HLA are widely used to model human immune responses, and it has been shown that mouse-passaged DENV is able to replicate to significant levels in IFN-α/βR-/- mice. To cover a wide range of HLA phenotypes, we backcrossed IFN-α/βR-/- mice with HLA A*0201, A*0101, A*1101, B*0702, and DRB1*0101-transgenic mice. A DENV proteome-wide screen identified a total of 42 epitopes across all HLA-transgenic IFN-α/βR-/- strains tested. In contrast, only eight of these elicited responses in the corresponding IFN-α/βR+/+ mice. We were able to identify T cell epitopes from 9 out of the 10 DENV proteins. However, the majority of responses were derived from the highly conserved nonstructural proteins NS3 and NS5. The relevance of this model is further demonstrated by the fact that most of the epitopes identified in our murine system are also recognized by PBMC from DENV-exposed human donors, and a dominance of HLA B*0702-restricted responses has been detected in both systems. Our results provide new insights into HLA-restricted T cell responses against DENV, and we describe in this study a novel murine model that allows the investigation of T cell-mediated immune mechanisms relevant to vaccine design. [ABSTRACT FROM AUTHOR]
- Published
- 2011
- Full Text
- View/download PDF
37. A novel method for characterizing cell-cell interactions at single-cell resolution reveals unique signatures in blood T cell-monocyte complexes during infection.
- Author
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Kang N, Chawla A, Hillman H, Tippalagama R, Kim C, Mikulski Z, Seumois G, Vijayanand P, Scriba TJ, De Silva AD, Balmaseda A, Harris E, Weiskopf D, Sette A, Arlehamn CL, Peters B, and Burel JG
- Abstract
Communication between immune cells through direct contact is a critical feature of immune responses. Here, we developed a novel high-throughput method to study the transcriptome and adaptive immune receptor repertoire of single cells forming complexes without needing bioinformatic deconvolution. We found that T cells and monocytes forming complexes in blood during active tuberculosis (TB) and dengue hold unique transcriptomic signatures indicative of TCR/MCH-II immune synapses. Additionally, T cells in complexes showed enrichment for effector phenotypes, imaging and transcriptomic features of active TCR signaling, and increased immune activity at diagnosis compared to after anti-TB therapy. We also found evidence for bidirectional RNA exchange between T cells and monocytes, since complexes were markedly enriched for "dual-expressing" cells (i.e., co-expressing T cell and monocyte genes). Thus, studying immune cell complexes at a single-cell resolution offers novel perspectives on immune synaptic interactions occurring in blood during infection., Competing Interests: Conflict of interest DW is a consultant for Moderna.
- Published
- 2024
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38. Burkholderia pseudomallei in soil and natural water bodies in rural Sri Lanka: A hidden threat to public health.
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Jayasinghearachchi HS, Muthugama TA, Masakorala J, Kulasekara US, Jayaratne K, Jayatunga DADN, De Silva AD, and Corea EM
- Abstract
Burkholderia pseudomallei is the causative agent of the potentially fatal infection, melioidosis. This study provides the first evidence for the presence of B. pseudomallei in soil and water in Sri Lanka. Targeted sampling of soil and natural water sources was done between November 2019 and October 2020 over eight field visits encompassing the neighborhood of 28 culture and/or antibody-positive melioidosis patients in northwestern, western and southern Sri Lanka. A total of eight environmental isolates of B. pseudomallei (BPs-env1 to BPs-env8) were cultured from 116 soil and 117 natural water samples collected from 72 locations. The presence of B. pseudomallei in soil and natural water in these areas poses a risk of melioidosis for populations cultivating crops in such soils and using untreated water from these sources for drinking, bathing, and other domestic purposes. Identifying sites positive for B. pseudomallei may help to mitigate risk by raising public awareness of contaminated environmental sources and allowing soil and water remediation., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Jayasinghearachchi, Muthugama, Masakorala, Kulasekara, Jayaratne, Jayatunga, De Silva and Corea.)
- Published
- 2023
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39. Cutting Edge: Transcriptional Profiling Reveals Multifunctional and Cytotoxic Antiviral Responses of Zika Virus-Specific CD8 + T Cells.
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Grifoni A, Costa-Ramos P, Pham J, Tian Y, Rosales SL, Seumois G, Sidney J, de Silva AD, Premkumar L, Collins MH, Stone M, Norris PJ, Romero CME, Durbin A, Ricciardi MJ, Ledgerwood JE, de Silva AM, Busch M, Peters B, Vijayanand P, Harris E, Falconar AK, Kallas E, Weiskopf D, and Sette A
- Subjects
- Antigens, Viral immunology, Cells, Cultured, Cytotoxicity, Immunologic, Epitopes, T-Lymphocyte immunology, Gene Expression Profiling, Granzymes genetics, Humans, Immunoglobulins genetics, Immunophenotyping, Interferon-gamma genetics, Receptors, Tumor Necrosis Factor genetics, Tumor Necrosis Factor-alpha genetics, CD8-Positive T-Lymphocytes physiology, Zika Virus physiology, Zika Virus Infection immunology
- Abstract
Zika virus (ZIKV) constitutes an increasing public health problem. Previous studies have shown that CD8
+ T cells play an important role in ZIKV-specific protective immunity. We have previously defined antigenic targets of the ZIKV-specific CD8+ T cell response in humans. In this study, we characterized the quality and phenotypes of these responses by a combined use of flow cytometry and transcriptomic methods, using PBMCs from donors deriving from different geographical locations collected in the convalescent phase of infection. We show that ZIKV-specific CD8+ T cells are characterized by a polyfunctional IFN-γ signature with upregulation of TNF-α, TNF receptors, and related activation markers, such as CD69, as well as a cytotoxic signature characterized by strong upregulation of GZMB and CRTAM. The signature is stable and not influenced by previous dengue virus exposure, geographical location, or time of sample collection postinfection. To our knowledge, this work elucidates the first in-depth characterization of human CD8+ T cells responding to ZIKV infection., (Copyright © 2018 by The American Association of Immunologists, Inc.)- Published
- 2018
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40. Development of Envelope Protein Antigens To Serologically Differentiate Zika Virus Infection from Dengue Virus Infection.
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Premkumar L, Collins M, Graham S, Liou GA, Lopez CA, Jadi R, Balmaseda A, Brackbill JA, Dietze R, Camacho E, De Silva AD, Giuberti C, Dos Reis HL, Singh T, Heimsath H, Weiskopf D, Sette A, Osorio JE, Permar SR, Miley MJ, Lazear HM, Harris E, and de Silva AM
- Subjects
- Antibodies, Neutralizing blood, Antibodies, Viral blood, Cross Reactions, Dengue blood, Dengue virology, Dengue Virus isolation & purification, Enzyme-Linked Immunosorbent Assay, Epitopes genetics, Epitopes immunology, Humans, Immunoglobulin G blood, Longitudinal Studies, Population Surveillance, Recombinant Proteins genetics, Recombinant Proteins immunology, Time Factors, Viral Envelope Proteins chemistry, Viral Envelope Proteins genetics, Zika Virus isolation & purification, Zika Virus Infection blood, Zika Virus Infection virology, Antigens, Viral metabolism, Dengue diagnosis, Dengue Virus immunology, Serologic Tests methods, Viral Envelope Proteins immunology, Zika Virus immunology, Zika Virus Infection diagnosis
- Abstract
Zika virus (ZIKV) is an emerging flavivirus that can cause birth defects and neurologic complications. Molecular tests are effective for diagnosing acute ZIKV infection, although the majority of infections produce no symptoms at all or present after the narrow window in which molecular diagnostics are dependable. Serology is a reliable method for detecting infections after the viremic period; however, most serological assays have limited specificity due to cross-reactive antibodies elicited by flavivirus infections. Since ZIKV and dengue virus (DENV) widely cocirculate, distinguishing ZIKV infection from DENV infection is particularly important for diagnosing individual cases or for surveillance to coordinate public health responses. Flaviviruses also elicit type-specific antibodies directed to non-cross-reactive epitopes of the infecting virus; such epitopes are attractive targets for the design of antigens for development of serological tests with greater specificity. Guided by comparative epitope modeling of the ZIKV envelope protein, we designed two recombinant antigens displaying unique antigenic regions on domain I (Z-EDI) and domain III (Z-EDIII) of the ZIKV envelope protein. Both the Z-EDI and Z-EDIII antigens consistently detected ZIKV-specific IgG in ZIKV-immune sera but not cross-reactive IgG in DENV-immune sera in late convalescence (>12 weeks postinfection). In contrast, during early convalescence (2 to 12 weeks postinfection), secondary DENV-immune sera and some primary DENV-immune sera cross-reacted with the Z-EDI and Z-EDIII antigens. Analysis of sequential samples from DENV-immune individuals demonstrated that Z-EDIII cross-reactivity peaked in early convalescence and declined steeply over time. The Z-EDIII antigen has much potential as a diagnostic antigen for population-level surveillance and for detecting past infections in patients., (Copyright © 2018 American Society for Microbiology.)
- Published
- 2018
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41. Precursors of human CD4 + cytotoxic T lymphocytes identified by single-cell transcriptome analysis.
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Patil VS, Madrigal A, Schmiedel BJ, Clarke J, O'Rourke P, de Silva AD, Harris E, Peters B, Seumois G, Weiskopf D, Sette A, and Vijayanand P
- Subjects
- Gene Expression Profiling methods, Humans, Immunologic Memory immunology, Leukocytes, Mononuclear immunology, Lymphocyte Activation immunology, Receptors, Antigen, T-Cell immunology, Single-Cell Analysis methods, CD4-Positive T-Lymphocytes immunology, T-Lymphocytes, Cytotoxic immunology, Transcriptome immunology
- Abstract
CD4
+ cytotoxic T lymphocytes (CD4-CTLs) have been reported to play a protective role in several viral infections. However, little is known in humans about the biology of CD4-CTL generation, their functional properties, and heterogeneity, especially in relation to other well-described CD4+ memory T cell subsets. We performed single-cell RNA sequencing in more than 9000 cells to unravel CD4-CTL heterogeneity, transcriptional profile, and clonality in humans. Single-cell differential gene expression analysis revealed a spectrum of known transcripts, including several linked to cytotoxic and costimulatory function that are expressed at higher levels in the TEMRA (effector memory T cells expressing CD45RA) subset, which is highly enriched for CD4-CTLs, compared with CD4+ T cells in the central memory (TCM ) and effector memory (TEM ) subsets. Simultaneous T cell antigen receptor (TCR) analysis in single cells and bulk subsets revealed that CD4-TEMRA cells show marked clonal expansion compared with TCM and TEM cells and that most of CD4-TEMRA were dengue virus (DENV)-specific in donors with previous DENV infection. The profile of CD4-TEMRA was highly heterogeneous across donors, with four distinct clusters identified by the single-cell analysis. We identified distinct clusters of CD4-CTL effector and precursor cells in the TEMRA subset; the precursor cells shared TCR clonotypes with CD4-CTL effectors and were distinguished by high expression of the interleukin-7 receptor. Our identification of a CD4-CTL precursor population may allow further investigation of how CD4-CTLs arise in humans and, thus, could provide insights into the mechanisms that may be used to generate durable and effective CD4-CTL immunity., (Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)- Published
- 2018
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42. Unique phenotypes and clonal expansions of human CD4 effector memory T cells re-expressing CD45RA.
- Author
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Tian Y, Babor M, Lane J, Schulten V, Patil VS, Seumois G, Rosales SL, Fu Z, Picarda G, Burel J, Zapardiel-Gonzalo J, Tennekoon RN, De Silva AD, Premawansa S, Premawansa G, Wijewickrama A, Greenbaum JA, Vijayanand P, Weiskopf D, Sette A, and Peters B
- Subjects
- Adolescent, Adult, Aged, CD4-Positive T-Lymphocytes classification, CD8-Positive T-Lymphocytes classification, CD8-Positive T-Lymphocytes immunology, Cells, Cultured, Core Binding Factor Alpha 3 Subunit biosynthesis, Gene Expression Profiling, Granzymes biosynthesis, Heterogeneous-Nuclear Ribonucleoproteins biosynthesis, Humans, Immunologic Memory immunology, Male, Middle Aged, Perforin biosynthesis, Receptors, CCR7 metabolism, Signaling Lymphocytic Activation Molecule Family biosynthesis, T-Box Domain Proteins biosynthesis, Young Adult, CD4-Positive T-Lymphocytes immunology, Cytomegalovirus immunology, Dengue Virus immunology, Herpesvirus 4, Human immunology, Leukocyte Common Antigens metabolism, Receptors, G-Protein-Coupled metabolism
- Abstract
The expression of CD45RA is generally associated with naive T cells. However, a subset of effector memory T cells re-expresses CD45RA (termed TEMRA) after antigenic stimulation with unknown molecular characteristics and functions. CD4 TEMRA cells have been implicated in protective immunity against pathogens such as dengue virus (DENV). Here we show that not only the frequency but also the phenotype of CD4 TEMRA cells are heterogeneous between individuals. These cells can be subdivided into two major subsets based on the expression of the adhesion G protein-coupled receptor GPR56, and GPR56
+ TEMRA cells display a transcriptional and proteomic program with cytotoxic features that is distinct from effector memory T cells. Moreover, GPR56+ TEMRA cells have higher levels of clonal expansion and contain the majority of virus-specific TEMRA cells. Overall, this study reveals the heterogeneity of CD4 TEMRA cells and provides insights into T-cell responses against DENV and other viral pathogens.- Published
- 2017
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43. Global Assessment of Dengue Virus-Specific CD4 + T Cell Responses in Dengue-Endemic Areas.
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Grifoni A, Angelo MA, Lopez B, O'Rourke PH, Sidney J, Cerpas C, Balmaseda A, Silveira CGT, Maestri A, Costa PR, Durbin AP, Diehl SA, Phillips E, Mallal S, De Silva AD, Nchinda G, Nkenfou C, Collins MH, de Silva AM, Lim MQ, Macary PA, Tatullo F, Solomon T, Satchidanandam V, Desai A, Ravi V, Coloma J, Turtle L, Rivino L, Kallas EG, Peters B, Harris E, Sette A, and Weiskopf D
- Abstract
Background: Dengue is a major public health problem worldwide. Assessment of adaptive immunity is important to understanding immunopathology and to define correlates of protection against dengue virus (DENV). To enable global assessment of CD4
+ T cell responses, we mapped HLA-DRB1-restricted DENV-specific CD4+ T cell epitopes in individuals previously exposed to DENV in the general population of the dengue-endemic region of Managua, Nicaragua., Methods: HLA class II epitopes in the population of Managua were identified by an in vitro IFNγ ELISPOT assay. CD4+ T cells purified by magnetic bead negative selection were stimulated with HLA-matched epitope pools in the presence of autologous antigen-presenting cells, followed by pool deconvolution to identify specific epitopes. The epitopes identified in this study were combined with those previously identified in the DENV endemic region of Sri Lanka, to generate a "megapool" (MP) consisting of 180 peptides specifically designed to achieve balanced HLA and DENV serotype coverage. The DENV CD4MP180 was validated by intracellular cytokine staining assays., Results: We detected responses directed against a total of 431 epitopes, representing all 4 DENV serotypes, restricted by 15 different HLA-DRB1 alleles. The responses were associated with a similar pattern of protein immunodominance, overall higher magnitude of responses, as compared to what was observed previously in the Sri Lanka region. Based on these epitope mapping studies, we designed a DENV CD4 MP180 with higher and more consistent coverage, which allowed the detection of CD4+ T cell DENV responses ex vivo in various cohorts of DENV exposed donors worldwide, including donors from Nicaragua, Brazil, Singapore, Sri Lanka, and U.S. domestic flavivirus-naïve subjects immunized with Tetravalent Dengue Live-Attenuated Vaccine (TV005). This broad reactivity reflects that the 21 HLA-DRB1 alleles analyzed in this and previous studies account for more than 80% of alleles present with a phenotypic frequency ≥5% worldwide, corresponding to 92% phenotypic coverage of the general population (i.e., 92% of individuals express at least one of these alleles)., Conclusion: The DENV CD4 MP180 can be utilized to measure ex vivo responses to DENV irrespective of geographical location.- Published
- 2017
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44. Human CD4 + T Cell Responses to an Attenuated Tetravalent Dengue Vaccine Parallel Those Induced by Natural Infection in Magnitude, HLA Restriction, and Antigen Specificity.
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Angelo MA, Grifoni A, O'Rourke PH, Sidney J, Paul S, Peters B, de Silva AD, Phillips E, Mallal S, Diehl SA, Kirkpatrick BD, Whitehead SS, Durbin AP, Sette A, and Weiskopf D
- Subjects
- Adolescent, Adult, Antibodies, Viral immunology, Antibody Specificity, CD4-Positive T-Lymphocytes virology, Cells, Cultured, Dengue immunology, Dengue virology, Female, Humans, Male, Middle Aged, Vaccines, Attenuated immunology, Viral Proteins immunology, Young Adult, CD4-Positive T-Lymphocytes immunology, Dengue prevention & control, Dengue Vaccines immunology, Dengue Virus immunology, HLA Antigens genetics, Vaccination
- Abstract
Dengue virus (DENV) is responsible for growing numbers of infections worldwide and has proven to be a significant challenge for vaccine development. We previously demonstrated that CD8
+ T cell responses elicited by a dengue live attenuated virus (DLAV) vaccine resemble those observed after natural infection. In this study, we screened peripheral blood mononuclear cells (PBMCs) from donors vaccinated with a tetravalent DLAV vaccine (TV005) with pools of dengue virus-derived predicted major histocompatibility complex (MHC) class II binding peptides. The definition of CD4+ T cell responses after live vaccination is important because CD4+ T cells are known contributors to host immunity, including cytokine production, help for CD8+ T and B cells, and direct cytotoxicity against infected cells. While responses to all antigens were observed, DENV-specific CD4+ T cells were focused predominantly on the capsid and nonstructural NS3 and NS5 antigens. Importantly, CD4+ T cell responses in vaccinees were similar in magnitude and breadth to those after natural infection, recognized the same antigen hierarchy, and had similar profiles of HLA restriction. We conclude that TV005 vaccination has the capacity to elicit CD4+ cell responses closely mirroring those observed in a population associated with natural immunity. IMPORTANCE The development of effective vaccination strategies against dengue virus infection is of high global public health interest. Here we study the CD4 T cell responses elicited by a tetravalent live attenuated dengue vaccine and show that they resemble responses seen in humans naturally exposed to dengue virus. This is an important issue, since it is likely that optimal immunity induced by a vaccine requires induction of CD4+ responses against the same antigens as those recognized as dominant in natural infection. Detailed knowledge of the T cell response may further contribute to the identification of robust correlates of protection against dengue virus., (Copyright © 2017 American Society for Microbiology.)- Published
- 2017
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45. Immunodominant Dengue Virus-Specific CD8+ T Cell Responses Are Associated with a Memory PD-1+ Phenotype.
- Author
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de Alwis R, Bangs DJ, Angelo MA, Cerpas C, Fernando A, Sidney J, Peters B, Gresh L, Balmaseda A, de Silva AD, Harris E, Sette A, and Weiskopf D
- Subjects
- Alleles, Cytotoxicity, Immunologic, Dengue genetics, Dengue virology, Epitopes, T-Lymphocyte immunology, Gene Expression, HLA Antigens genetics, HLA Antigens immunology, HLA-A24 Antigen genetics, HLA-A24 Antigen immunology, HLA-B35 Antigen genetics, HLA-B35 Antigen immunology, Humans, Immunophenotyping, Interferon-gamma metabolism, Lymphocyte Activation immunology, Nicaragua, Phenotype, Programmed Cell Death 1 Receptor genetics, T-Cell Antigen Receptor Specificity immunology, T-Lymphocyte Subsets immunology, T-Lymphocyte Subsets metabolism, CD8-Positive T-Lymphocytes immunology, CD8-Positive T-Lymphocytes metabolism, Dengue immunology, Dengue metabolism, Dengue Virus immunology, Immunologic Memory, Programmed Cell Death 1 Receptor metabolism
- Abstract
Unlabelled: Dengue disease is a large public health problem that mainly afflicts tropical and subtropical regions. Understanding of the correlates of protection against dengue virus (DENV) is poor and hinders the development of a successful human vaccine. The present study aims to define DENV-specific CD8(+)T cell responses in general and those of HLA alleles associated with dominant responses in particular. In human blood donors in Nicaragua, we observed a striking dominance of HLA B-restricted responses in general and of the allele B*35:01 in particular. Comparing these patterns to those in the general population of Sri Lanka, we found a strong correlation between restriction of the HLA allele and the breadth and magnitude of CD8(+)T cell responses, suggesting that HLA genes profoundly influence the nature of responses. The majority of gamma interferon (IFN-γ) responses were associated with effector memory phenotypes, which were also detected in non-B*35:01-expressing T cells. However, only the B*35:01 DENV-specific T cells were associated with marked expression of the programmed death 1 protein (PD-1). These cells did not coexpress other inhibitory receptors and were able to proliferate in response to DENV-specific stimulation. Thus, the expression of particular HLA class I alleles is a defining characteristic influencing the magnitude and breadth of CD8 responses, and a distinct, highly differentiated phenotype is specifically associated with dominant CD8(+)T cells. These results are of relevance for both vaccine design and the identification of robust correlates of protection in natural immunity., Importance: Dengue is an increasingly significant public health problem as its mosquito vectors spread over greater areas; no vaccines against the virus have yet been approved. An important step toward vaccine development is defining protective immune responses; toward that end, we here characterize the phenotype of the immunodominant T cell responses. These DENV-reactive T cells express high levels of the receptor programmed death 1 protein (PD-1), while those from disease-susceptible alleles do not. Not only does this represent a possible correlate of immunodominance, but it raises the hypothesis that PD-1 might be a regulator that prevents excessive damage while preserving antiviral function. Further, as this study employs distinct populations (Nicaraguan and Sri Lankan donors), we also confirmed that this pattern holds despite geographic and ethnic differences. This finding indicates that HLA type is the major determinant in shaping T cell responses., (Copyright © 2016, American Society for Microbiology. All Rights Reserved.)
- Published
- 2016
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46. The human CD8+ T cell responses induced by a live attenuated tetravalent dengue vaccine are directed against highly conserved epitopes.
- Author
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Weiskopf D, Angelo MA, Bangs DJ, Sidney J, Paul S, Peters B, de Silva AD, Lindow JC, Diehl SA, Whitehead S, Durbin A, Kirkpatrick B, and Sette A
- Subjects
- Adolescent, Adult, Dengue Vaccines administration & dosage, Enzyme-Linked Immunospot Assay, Female, Humans, Interferon-gamma metabolism, Male, Middle Aged, National Institutes of Health (U.S.), United States, Vaccines, Attenuated administration & dosage, Vaccines, Attenuated immunology, Young Adult, Antigens, Viral immunology, CD8-Positive T-Lymphocytes immunology, Dengue Vaccines immunology, Dengue Virus immunology, Epitopes immunology
- Abstract
Unlabelled: The incidence of infection with any of the four dengue virus serotypes (DENV1 to -4) has increased dramatically in the last few decades, and the lack of a treatment or vaccine has contributed to significant morbidity and mortality worldwide. A recent comprehensive analysis of the human T cell response against wild-type DENV suggested an human lymphocyte antigen (HLA)-linked protective role for CD8(+) T cells. We have collected one-unit blood donations from study participants receiving the monovalent or tetravalent live attenuated DENV vaccine (DLAV), developed by the U.S. National Institutes of Health. Peripheral blood mononuclear cells from these donors were screened in gamma interferon enzyme-linked immunosorbent spot assays with pools of predicted, HLA-matched, class I binding peptides covering the entire DENV proteome. Here, we characterize for the first time CD8(+) T cell responses after live attenuated dengue vaccination and show that CD8(+) T cell responses in vaccinees were readily detectable and comparable to natural dengue infection. Interestingly, whereas broad responses to structural and nonstructural (NS) proteins were observed after monovalent vaccination, T cell responses following tetravalent vaccination were, dramatically, focused toward the highly conserved NS proteins. Epitopes were highly conserved in a vast variety of field isolates and able to elicit multifunctional T cell responses. Detailed knowledge of the T cell response will contribute to the identification of robust correlates of protection in natural immunity and following vaccination against DENV., Importance: The development of effective vaccination strategies against dengue virus (DENV) infection and clinically significant disease is a task of high global public health value and significance, while also being a challenge of significant complexity. A recent efficacy trial of the most advanced dengue vaccine candidate, demonstrated only partial protection against all four DENV serotypes, despite three subsequent immunizations and detection of measurable neutralizing antibodies to each serotype in most subjects. These results challenge the hypothesis that seroconversion is the only reliable correlate of protection. Here, we show that CD8(+) T cell responses in vaccinees were readily detectable and comparable to natural dengue virus infection. Detailed knowledge of the T cell response may further contribute to the identification of robust correlates of protection in natural immunity and vaccination against DENV., (Copyright © 2015, American Society for Microbiology. All Rights Reserved.)
- Published
- 2015
- Full Text
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