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1دورية أكاديمية
المؤلفون: Cate Speake, Henry T. Bahnson, Johnna D. Wesley, Nikole Perdue, David Friedrich, Minh N. Pham, Erinn Lanxon-Cookson, William W. Kwok, Birgit Sehested Hansen, Matthias von Herrath, Carla J. Greenbaum
المصدر: Frontiers in Immunology, Vol 10 (2019)
مصطلحات موضوعية: variability, immune assays, clinical trials, type 1 diabetes, insulin secretion, Immunologic diseases. Allergy, RC581-607
الوصف: Immune analytes have been widely tested in efforts to understand the heterogeneity of disease progression, risk, and therapeutic responses in type 1 diabetes (T1D). The future clinical utility of such analytes as biomarkers depends on their technical and biological variability, as well as their correlation with clinical outcomes. To assess the variability of a panel of 91 immune analytes, we conducted a prospective study of adults with T1D (
وصف الملف: electronic resource
العلاقة: https://www.frontiersin.org/article/10.3389/fimmu.2019.02023/fullTest; https://doaj.org/toc/1664-3224Test
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2دورية أكاديمية
المؤلفون: Siriphan Manocheewa, J Victor Swain, Erinn Lanxon-Cookson, Morgane Rolland, James I Mullins
المصدر: PLoS ONE, Vol 8, Iss 6, p e66065 (2013)
الوصف: The recently available x-ray crystal structure of HIV-1 capsid hexamers has provided insight into the molecular interactions crucial for the virus's mature capsid formation. Amino acid changes at these interaction points are likely to have a strong impact on capsid functionality and, hence, viral infectivity and replication fitness. To test this hypothesis, we introduced the most frequently observed single amino acid substitution at 30 sites: 12 at the capsid hexamerization interface and 18 at non-interface sites. Mutations at the interface sites were more likely to be lethal (Fisher's exact test p = 0.027) and had greater negative impact on viral replication fitness (Wilcoxon rank sum test p = 0.040). Among the interface mutations studied, those located in the cluster of hydrophobic contacts at NTD-NTD interface and those that disrupted NTD-CTD inter-domain helix capping hydrogen bonds were the most detrimental, indicating that these interactions are particularly important for maintaining capsid structure and/or function. These functionally constrained sites provide potential targets for novel HIV drug development and vaccine immunogen design.
وصف الملف: electronic resource
العلاقة: http://europepmc.org/articles/PMC3681919?pdf=renderTest; https://doaj.org/toc/1932-6203Test
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3دورية أكاديمية
المؤلفون: Morgane Rolland, Jonathan M Carlson, Siriphan Manocheewa, J Victor Swain, Erinn Lanxon-Cookson, Wenjie Deng, Christine M Rousseau, Dana N Raugi, Gerald H Learn, Brandon S Maust, Hoosen Coovadia, Thumbi Ndung'u, Philip J R Goulder, Bruce D Walker, Christian Brander, David E Heckerman, James I Mullins
المصدر: PLoS ONE, Vol 5, Iss 9 (2010)
الوصف: Despite high potential for HIV-1 genetic variation, the emergence of some mutations is constrained by fitness costs, and may be associated with compensatory amino acid (AA) co-variation. To characterize the interplay between Cytotoxic T Lymphocyte (CTL)-mediated pressure and HIV-1 evolutionary pathways, we investigated AA co-variation in Gag sequences obtained from 449 South African individuals chronically infected with HIV-1 subtype C.Individuals with CTL responses biased toward Gag presented lower viral loads than individuals with under-represented Gag-specific CTL responses. Using methods that account for founder effects and HLA linkage disequilibrium, we identified 35 AA sites under Human Leukocyte Antigen (HLA)-restricted CTL selection pressure and 534 AA-to-AA interactions. Analysis of two-dimensional distances between co-varying residues revealed local stabilization mechanisms since 40% of associations involved neighboring residues. Key features of our co-variation analysis included sites with a high number of co-varying partners, such as HLA-associated sites, which had on average 55% more connections than other co-varying sites.Clusters of co-varying AA around HLA-associated sites (especially at typically conserved sites) suggested that cooperative interactions act to preserve the local structural stability and protein function when CTL escape mutations occur. These results expose HLA-imprinted HIV-1 polymorphisms and their interlinked mutational paths in Gag that are likely due to opposite selective pressures from host CTL-mediated responses and viral fitness constraints.
وصف الملف: electronic resource
العلاقة: http://europepmc.org/articles/PMC2931691?pdf=renderTest; https://doaj.org/toc/1932-6203Test
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المؤلفون: Johnna D. Wesley, Carla J. Greenbaum, William W. Kwok, Matthias von Herrath, David Friedrich, Erinn Lanxon-Cookson, Birgit Sehested Hansen, Cate Speake, M. N. Pham, Henry T. Bahnson, Nikole Perdue
المصدر: Frontiers in Immunology, Vol 10 (2019)
Frontiers in Immunologyمصطلحات موضوعية: 0301 basic medicine, Oncology, Male, Longitudinal study, insulin secretion, Intraclass correlation, type 1 diabetes, T-Lymphocytes, CD8-Positive T-Lymphocytes, Correlation, 0302 clinical medicine, Immunology and Allergy, Myeloid Cells, Longitudinal Studies, Prospective Studies, Prospective cohort study, Original Research, C-Peptide, Middle Aged, 3. Good health, Killer Cells, Natural, Female, Adult, lcsh:Immunologic diseases. Allergy, medicine.medical_specialty, Adolescent, Immunology, immune assays, Context (language use), 03 medical and health sciences, Young Adult, Internal medicine, medicine, Humans, Autoantibodies, Type 1 diabetes, clinical trials, business.industry, variability, Autoantibody, medicine.disease, Clinical trial, 030104 developmental biology, Diabetes Mellitus, Type 1, Diabetes Mellitus, Type 2, business, lcsh:RC581-607, Immunologic Memory, Biomarkers, 030215 immunology
الوصف: Immune analytes have been widely tested in efforts to understand the heterogeneity of disease progression, risk, and therapeutic responses in type 1 diabetes (T1D). The future clinical utility of such analytes as biomarkers depends on their technical and biological variability, as well as their correlation with clinical outcomes. To assess the variability of a panel of 91 immune analytes, we conducted a prospective study of adults with T1D (
الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::023b985053f9164c712078a7c458d18bTest
https://www.frontiersin.org/article/10.3389/fimmu.2019.02023/fullTest -
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المؤلفون: Cate Speake, Henry T. Bahnson, Johnna D. Wesley, Nikole Perdue, David Friedrich, Minh N. Pham, Erinn Lanxon-Cookson, William W. Kwok, Birgit Sehested Hansen, Matthias von Herrath, Carla J. Greenbaum
مصطلحات موضوعية: Immunology, Applied Immunology (incl. Antibody Engineering, Xenotransplantation and T-cell Therapies), Autoimmunity, Cellular Immunology, Humoural Immunology and Immunochemistry, Immunogenetics (incl. Genetic Immunology), Innate Immunity, Transplantation Immunology, Tumour Immunology, Immunology not elsewhere classified, Genetic Immunology, Animal Immunology, Veterinary Immunology, variability, immune assays, clinical trials, type 1 diabetes, insulin secretion
الوصف: Immune analytes have been widely tested in efforts to understand the heterogeneity of disease progression, risk, and therapeutic responses in type 1 diabetes (T1D). The future clinical utility of such analytes as biomarkers depends on their technical and biological variability, as well as their correlation with clinical outcomes. To assess the variability of a panel of 91 immune analytes, we conducted a prospective study of adults with T1D (<3 years from diagnosis), at 9–10 visits over 1 year. Autoantibodies and frequencies of T-cell, natural killer cell, and myeloid subsets were evaluated; autoreactive T-cell frequencies and function were also measured. We calculated an intraclass correlation coefficient (ICC) for each marker, which is a relative measure of between- and within-subject variability. Of the 91 analytes tested, we identified 35 with high between- and low within-subject variability, indicating their potential ability to be used to stratify subjects. We also provide extensive data regarding technical variability for 64 of the 91 analytes. To pilot the concept that ICC can be used to identify analytes that reflect biological outcomes, the association between each immune analyte and C-peptide was also evaluated using partial least squares modeling. CD8 effector memory T-cell (CD8 EM) frequency exhibited a high ICC and a positive correlation with C-peptide, which was also seen in an independent dataset of recent-onset T1D subjects. More work is needed to better understand the mechanisms underlying this relationship. Here we find that there are a limited number of technically reproducible immune analytes that also have a high ICC. We propose the use of ICC to define within- and between-subject variability and measurement of technical variability for future biomarker identification studies. Employing such a method is critical for selection of analytes to be tested in the context of future clinical trials aiming to understand heterogeneity in disease progression and response to therapy.
الإتاحة: https://doi.org/10.3389/fimmu.2019.02023.s002Test
https://figshare.com/articles/dataset/Data_Sheet_2_Systematic_Assessment_of_Immune_Marker_Variation_in_Type_1_Diabetes_A_Prospective_Longitudinal_Study_pdf/9822800Test -
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المؤلفون: Nicole Frahm, Janine Maenza, Moon S. Kim, Ellie Casey, James I. Mullins, Brendan B. Larsen, Suvankar Ghorai, Dylan H. Westfall, J. Sunshine, Wenje Deng, Ann C. Collier, Erinn Lanxon-Cookson, Morgane Rolland, Hong Zhao, Lennie Chen, Brandon S. Maust
المصدر: Journal of Virology. 89:10303-10318
مصطلحات موضوعية: Entropy, Molecular Sequence Data, Primary Cell Culture, Immunology, Mutant, Population, Epitopes, T-Lymphocyte, Cellular Response to Infection, Biology, gag Gene Products, Human Immunodeficiency Virus, Microbiology, Epitope, Deep sequencing, Virus, Interferon-gamma, Immune system, Virology, HIV Seropositivity, Humans, Amino Acid Sequence, Selection, Genetic, education, Immune Evasion, Genetics, education.field_of_study, Base Sequence, High-Throughput Nucleotide Sequencing, Viral Load, Founder Effect, CTL, Insect Science, Viral evolution, Mutation, HIV-1, Interleukin-2, Genetic Fitness, T-Lymphocytes, Cytotoxic
الوصف: To understand the interplay between host cytotoxic T-lymphocyte (CTL) responses and the mechanisms by which HIV-1 evades them, we studied viral evolutionary patterns associated with host CTL responses in six linked transmission pairs. HIV-1 sequences corresponding to full-length p17 and p24 gag were generated by 454 pyrosequencing for all pairs near the time of transmission, and seroconverting partners were followed for a median of 847 days postinfection. T-cell responses were screened by gamma interferon/interleukin-2 (IFN-γ/IL-2) FluoroSpot using autologous peptide sets reflecting any Gag variant present in at least 5% of sequence reads in the individual's viral population. While we found little evidence for the occurrence of CTL reversions, CTL escape processes were found to be highly dynamic, with multiple epitope variants emerging simultaneously. We found a correlation between epitope entropy and the number of epitope variants per response ( r = 0.43; P = 0.05). In cases in which multiple escape mutations developed within a targeted epitope, a variant with no fitness cost became fixed in the viral population. When multiple mutations within an epitope achieved fitness-balanced escape, these escape mutants were each maintained in the viral population. Additional mutations found to confer escape but undetected in viral populations incurred high fitness costs, suggesting that functional constraints limit the available sites tolerable to escape mutations. These results further our understanding of the impact of CTL escape and reversion from the founder virus in HIV infection and contribute to the identification of immunogenic Gag regions most vulnerable to a targeted T-cell attack. IMPORTANCE Rapid diversification of the viral population is a hallmark of HIV-1 infection, and understanding the selective forces driving the emergence of viral variants can provide critical insight into the interplay between host immune responses and viral evolution. We used deep sequencing to comprehensively follow viral evolution over time in six linked HIV transmission pairs. We then mapped T-cell responses to explore if mutations arose due to adaption to the host and found that escape processes were often highly dynamic, with multiple mutations arising within targeted epitopes. When we explored the impact of these mutations on replicative capacity, we found that dynamic escape processes only resolve with the selection of mutations that conferred escape with no fitness cost to the virus. These results provide further understanding of the complicated viral-host interactions that occur during early HIV-1 infection and may help inform the design of future vaccine immunogens.
الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9af9938b0de73a4994faf6394672499fTest
https://doi.org/10.1128/jvi.01876-15Test -
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المؤلفون: J. Victor Swain, Brandon S. Maust, J. Sunshine, Jan McClure, Siriphan Manocheewa, Yi Liu, Moon S. Kim, Erinn Lanxon-Cookson, Morgane Rolland, Ushnal Rao, Wenjie Deng, James I. Mullins
المصدر: Journal of Visualized Experiments : JoVE
مصطلحات موضوعية: DNA Replication, Issue 99, media_common.quotation_subject, General Chemical Engineering, Immunology, HIV Core Protein p24, Human immunodeficiency virus (HIV), Clone (cell biology), Biology, Virus Replication, medicine.disease_cause, Competition (biology), General Biochemistry, Genetics and Molecular Biology, Multiplicity of infection, Replication (statistics), medicine, Humans, media_common, Protocol (science), Genetics, Recombinant, General Immunology and Microbiology, General Neuroscience, 3. Good health, Viral replication fitness, HEK293 Cells, Viral replication, Mutagenesis, DNA, Viral, Mutation, HIV-1, Fitness calculation, Growth competition, Pairwise comparison
الوصف: In vitro fitness assays are essential tools for determining viral replication fitness for viruses such as HIV-1. Various measurements have been used to extrapolate viral replication fitness, ranging from the number of viral particles per infectious unit, growth rate in cell culture, and relative fitness derived from multiple-cycle growth competition assays. Growth competition assays provide a particularly sensitive measurement of fitness since the viruses are competing for cellular targets under identical growth conditions. There are several experimental factors to consider when conducting growth competition assays, including the multiplicity of infection (MOI), sampling times, and viral detection and fitness calculation methods. Each factor can affect the end result and hence must be considered carefully during the experimental design. The protocol presented here includes steps from constructing a new recombinant HIV-1 clone to performing growth competition assays and analyzing the experimental results. This protocol utilizes experimental parameter values previously shown to yield consistent and robust results. Alternatives are discussed, as some parameters need to be adjusted according to the cell type and viruses being studied. The protocol contains two alternative viral detection methods to provide flexibility as the availability of instruments, reagents and expertise varies between laboratories.
الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::501d5eab4ed0059cd91d2953439797ebTest
https://doi.org/10.3791/52610-vTest -
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المؤلفون: Siriphan Manocheewa, Dylan H. Westfall, Moon S. Kim, Erinn Lanxon-Cookson, J. V. Swain, Morgane Rolland, Peter B. Gilbert, James I. Mullins, Brendan B. Larsen
المصدر: Journal of virology. 87(10)
مصطلحات موضوعية: media_common.quotation_subject, Immunology, Human immunodeficiency virus (HIV), Biology, medicine.disease_cause, Virus Replication, Microbiology, Competition (biology), Conserved sequence, Evolution, Molecular, Virology, medicine, Humans, Selection, Genetic, Conserved Sequence, media_common, Sequence (medicine), Immune Evasion, Genetics, Replicative capacity, AIDS Vaccines, Mutation, Genetic Diversity and Evolution, Insect Science, Proteome, HIV-1
الوصف: To overcome the problem of HIV-1 variability, candidate vaccine antigens have been designed to be composed of conserved elements of the HIV-1 proteome. Such candidate vaccines could be improved with a better understanding of both HIV-1 evolutionary constraints and the fitness cost of specific mutations. We evaluated the in vitro fitness cost of 23 mutations engineered in the HIV-1 subtype B Gag-p24 Center-of-Tree (COT) protein through fitness competition assays. While some mutations at conserved sites exacted a high fitness cost, as expected under the assumption that the most conserved residue confers the highest fitness, there was no overall strong relationship between sequence conservation and replicative capacity. By comparing sites that have evolved since the beginning of the epidemic to those that have remain unchanged, we found that sites that have evolved over time were more likely to correspond to HLA-associated sites and that their mutation had limited fitness costs. Our data showed no transcendent link between high conservation and high fitness cost, indicating that merely focusing on conserved segments of HIV-1 would not be sufficient for a successful vaccine strategy. Nonetheless, a subset of sites exacted a high fitness cost upon mutation—these sites have been under selective pressure to change since the beginning of the epidemic but have proved virtually nonmutable and could constitute preferred targets for vaccine design.
الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::66574f0287d8109f16de8e08835259bfTest
https://pubmed.ncbi.nlm.nih.gov/23468488Test -
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المؤلفون: Dylan H. Westfall, James I. Mullins, Robert A. Smith, Moon S. Kim, J. Victor Swain, Siriphan Manocheewa, Brandon S. Maust, Erinn Lanxon-Cookson, Morgane Rolland
المصدر: Journal of virological methods. 194(1-2)
مصطلحات موضوعية: Genetics, Mutation, Virus Cultivation, media_common.quotation_subject, viruses, Mutant, Drug resistance, Biology, medicine.disease_cause, Virus Replication, Competition (biology), Article, Multiplicity of infection, Viral replication, Cell culture, Virology, Drug Resistance, Viral, medicine, HIV-1, Leukocytes, Mononuclear, Humans, Pairwise comparison, Cells, Cultured, media_common
الوصف: Cell culture growth competition assays of human immunodeficiency virus type 1 (HIV-1) are used to estimate viral fitness and quantify the impact of mutations conferring drug resistance and immunological escape. A comprehensive study of growth competition assays was conducted and identified experimental parameters that can impact measurements of relative fitness including multiplicity of infection, viral input ratio, number, timing and interval of time points used to evaluate selective outgrowth, and the algorithm for calculating fitness values. An optimized protocol is developed here that is a multi-point growth competition assay that resolves reproducibly small differences in viral fitness. The optimized protocol uses an MOI of 0.005, a consistent ratio of mutant: parental viruses (70:30), and a multipoint [1 + s 4,7] algorithm that uses data points within the logarithmic phase of viral growth for assessing fitness differences
الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a7c4f2aa6ca1e34cf4701b5365eb8130Test
https://pubmed.ncbi.nlm.nih.gov/23933395Test -
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المؤلفون: J. Victor Swain, Erinn Lanxon-Cookson, Sarah Holte, Yi Liu, Lennie Chen, James I. Mullins, Moon S. Kim, Ushnal Rao, Philip Konopa, Jan McClure
المصدر: Journal of virological methods. 189(1)
مصطلحات موضوعية: Genetics, viruses, Mutant, HIV Core Protein p24, env Gene Products, Human Immunodeficiency Virus, Biology, Real-Time Polymerase Chain Reaction, Virus Replication, Virology, gag Gene Products, Human Immunodeficiency Virus, Virus, Article, Cell Line, Chimera (genetics), Real-time polymerase chain reaction, Viral replication, Amino Acid Substitution, Cell culture, Mutation, TaqMan, HIV-1, vif Gene Products, Human Immunodeficiency Virus, Humans, Gene
الوصف: Fixation of mutations in human immunodeficiency virus type 1 (HIV-1), such as those conferring drug resistance and immune escape, can result in a change in replication fitness. To assess these changes, a real-time TaqMan PCR detection assay and statistical methods for data analysis were developed to estimate sensitively relative viral fitness in competitive viral replication experiments in cell culture. Chimeric viruses with the gene of interest in an HIV-1NL4-3 backbone were constructed in two forms, vifA (native vif gene in NL4-3) and vifB (vif gene with six synonymous nucleotide differences from vifA). Subsequently, mutations of interest were introduced into the chimeric viruses in NL4-3VifA backbones, and the mutants were competed against the chimera with the isogenic viral sequence in the NL4-3VifB backbone in cell culture. In order to assess subtle fitness differences, culture supernatants were sampled longitudinally, and the viruses differentially quantified using vifA- and vifB-specific primers in real-time PCR assays. Based on an exponential net growth model, the growth rate of each virus was determined and the fitness cost of the mutation(s) distinguishing the two viruses represented as the net growth rate difference between the mutant and the native variants. Using this assay, the fitness impact of eight amino acid substitutions was quantitated at highly conserved sites in HIV-1 Gag and Env.
الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::530bf8abba1db979491199d11b78b9c5Test
https://pubmed.ncbi.nlm.nih.gov/23201292Test
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