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1.
Cytometry A ; 85(3): 268-76, 2014 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-24464647

RESUMO

Methods to detect intracellular kinase signaling intermediates by flow cytometry have been recently developed. Termed "phospho-flow," these methods employ fluorescence-conjugated monoclonal antibodies that recognize phosphorylated epitopes of intracellular kinases, and may be combined with surface phenotypic markers to observe changes in kinase pathways by cellular subset. Effector functions, like cytokine production, are processes intrinsically linked to intracellular signaling and kinase activity within each cell. Methodologies that would simultaneously detect changes to signaling pathways as well as effector responses at the single-cell level would allow for mapping of the functional consequences induced by signaling pathway modifications. However, there are challenges to developing such a combined protocol, relating to the different kinetics of rapid signaling events and the more prolonged time required to induce and observe cytokine responses. In this report, we describe the development of an assay that accommodates differences in protocol conditions and response kinetics, merging phospho-flow cytometry, and intracellular cytokine staining methods into a single experimental protocol. We examined intracellular ERK1/2 phosphorylation and IFN-γ production by CD4+ and CD8+ T cells upon polyclonal stimulation with PMA and ionomycin, while monitoring expression of the cytolytic molecule perforin and the T cell activation marker CD38. We present a method that allows observation of kinase phosphorylation and cytokine production within the same cell after stimuli, while maintaining a stable cellular phenotype. Monitoring of signaling and effector functions in distinct immune subsets provides a platform to investigate and relate intracellular kinase signaling activity to immune cell effector function and phenotype in disease states.


Assuntos
Citocinas/biossíntese , Citometria de Fluxo , Ionomicina/farmacologia , Ativação Linfocitária/imunologia , Transdução de Sinais/efeitos dos fármacos , Subpopulações de Linfócitos T/efeitos dos fármacos , Acetato de Tetradecanoilforbol/farmacologia , Anticorpos Monoclonais/imunologia , Citocinas/imunologia , Citometria de Fluxo/métodos , Humanos , Fosforilação , Fosfotransferases/metabolismo , Transdução de Sinais/imunologia , Subpopulações de Linfócitos T/imunologia
2.
Blood ; 119(16): 3734-43, 2012 Apr 19.
Artigo em Inglês | MEDLINE | ID: mdl-22383801

RESUMO

Natural killer (NK) cells are innate lymphocytes that play an important role against viral infections and cancer. This effect is achieved through a complex mosaic of inhibitory and activating receptors expressed by NK cells that ultimately determine the magnitude of the NK-cell response. The T-cell immunoglobulin- and mucin domain-containing (Tim)-3 receptor was initially identified as a T-helper 1-specific type I membrane protein involved in regulating T-cell responses. Human NK cells transcribe the highest amounts of Tim-3 among lymphocytes. Tim-3 protein is expressed on essentially all mature CD56(dim)CD16(+) NK cells and is expressed heterogeneously in the immature CD56(bright)CD16(-) NK-cell subset in blood from healthy adults and in cord blood. Tim-3 expression was induced on CD56(bright)CD16(-) NK cells after stimulation with IL-15 or IL-12 and IL-18 in vitro, suggesting that Tim-3 is a maturation marker on NK cells. Whereas Tim-3 has been used to identify dysfunctional T cells, NK cells expressing high amounts of Tim-3 are fully responsive with respect to cytokine production and cytotoxicity. However, when Tim-3 was cross-linked with antibodies it suppressed NK cell-mediated cytotoxicity. These findings suggest that NK-cell responses may be negatively regulated when NK cells encounter target cells expressing cognate ligands of Tim-3.


Assuntos
Células Matadoras Naturais/imunologia , Subpopulações de Linfócitos/imunologia , Proteínas de Membrana/imunologia , Linfócitos T Citotóxicos/imunologia , Biomarcadores/metabolismo , Antígeno CD56/imunologia , Antígeno CD56/metabolismo , Diferenciação Celular/imunologia , Linhagem Celular , Reagentes de Ligações Cruzadas/metabolismo , Proteínas Ligadas por GPI/imunologia , Proteínas Ligadas por GPI/metabolismo , Receptor Celular 2 do Vírus da Hepatite A , Humanos , Imunofenotipagem , Células Matadoras Naturais/citologia , Ligantes , Subpopulações de Linfócitos/metabolismo , Proteínas de Membrana/metabolismo , Receptores de IgG/imunologia , Receptores de IgG/metabolismo , Linfócitos T Citotóxicos/citologia , Regulação para Cima/imunologia
3.
Cytometry A ; 83(3): 280-6, 2013 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-23426986

RESUMO

Chemokines and their receptors play an essential role within the immune system by dictating cellular migration. In vivo, receptor-ligand interactions rarely occur in isolation as cellular recruitment and migration are complex and highly coordinated processes often involving networks of multiple chemokines and multiple receptors. Simultaneous detection of multiple chemokine receptors on the single cell level is necessary to allow immunophenotyping studies that will help understand the intricacies of these networks. Chemokine receptors undergo a basal level of ongoing internalization, intracellular trafficking, and recycling back to the cell surface, even in the absence of the ligand. In the presence of ligand, receptor-ligand interactions enhance receptor internalization, reducing the cell surface receptor concentration, making precise determination of intrinsic levels challenging. Using multicolor flow cytometry, we sought to evaluate and optimize the simultaneous detection of cell surface expression levels of CCR2, CX3CR1, and CCR5 in primary human monocytes using a single antibody panel. We observed that staining for CCR2 alone or for CX3CR1 alone showed greater expression levels than when the cells were stained with the full panel of antibodies. Fluorescent-minus-one (FMO) controls revealed that ligation of the CCR5 monoclonal antibody to the receptor interfered with detection of CX3CR1 and CCR2. Sequential addition of antibodies during the staining procedure was sufficient to restore the detection levels, suggesting close proximity and possible functional interactions between CCR2/CCR5 and CX3CR1/CCR5 in monocytes. This study highlights the importance of optimizing staining procedures and using proper controls when simultaneously evaluating expression levels of multiple chemokine receptors by flow cytometry. Concurrent assessment of multiple receptors will provide insight and greater understanding of the complex interactions involved in cellular migration.


Assuntos
Citometria de Fluxo/métodos , Monócitos/imunologia , Receptores CCR2/análise , Receptores CCR5/análise , Receptores de Quimiocinas/análise , Adulto , Anticorpos Monoclonais/imunologia , Antígenos de Superfície/análise , Antígenos de Superfície/imunologia , Receptor 1 de Quimiocina CX3C , Movimento Celular , Feminino , Humanos , Masculino , Receptores CCR2/imunologia , Receptores CCR5/imunologia , Receptores de Quimiocinas/imunologia , Coloração e Rotulagem
4.
J Virol ; 85(23): 12343-50, 2011 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-21937661

RESUMO

Mitogen-activated protein kinase (MAPK) signaling pathways are dynamic and sensitive regulators of T cell function and differentiation. Altered MAPK signaling has been associated with the inflammatory and autoimmune diseases lupus and arthritis and with some pathogenic viral infections. HIV-1 infection is characterized by chronic immune inflammation, aberrantly heightened CD8(+) T cell activation levels, and altered T cell function. The relationship between MAPK pathway function, HIV-1-induced activation (CD38 and HLA-DR), and exhaustion (Tim-3) markers in circulating CD8(+) T cells remains unknown. Phosphorylation of the MAPK effector proteins ERK and p38 was examined by "phosflow" flow cytometry in 79 recently HIV-1-infected, antiretroviral-treatment-naïve adults and 21 risk-matched HIV-1-negative controls. We identified a subset of CD8(+) T cells refractory to phorbol 12-myristate 13-acetate plus ionomycin-induced ERK1/2 phosphorylation (referred to as p-ERK1/2-refractory cells) that was greatly expanded in HIV-1-infected adults. The CD8(+) p-ERK1/2-refractory cells were highly activated (CD38(+) HLA-DR(+)) but not exhausted (Tim-3 negative), tended to have low CD8 expression, and were enriched in intermediate and late transitional memory states of differentiation (CD45RA(-) CD28(-) CD27(+/-)). Targeting MAPK pathways to restore ERK1/2 signaling may normalize immune inflammation levels and restore CD8(+) T cell function during HIV-1 infection.


Assuntos
Linfócitos T CD8-Positivos/metabolismo , Linfócitos T CD8-Positivos/virologia , Infecções por HIV/metabolismo , Infecções por HIV/virologia , HIV-1/patogenicidade , Proteínas Quinases Ativadas por Mitógeno/metabolismo , Transdução de Sinais , Adulto , Linfócitos T CD8-Positivos/patologia , Estudos de Casos e Controles , Feminino , Citometria de Fluxo , Infecções por HIV/patologia , Humanos , Ativação Linfocitária , Masculino , Proteína Quinase 1 Ativada por Mitógeno/metabolismo , Proteína Quinase 3 Ativada por Mitógeno/metabolismo , Fosforilação , Carga Viral
5.
Eur J Immunol ; 40(1): 134-41, 2010 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-19877008

RESUMO

The complexity of immunoregulation has focused attention on the CD4+ T "suppressor" regulatory cell (Treg), which helps maintain balance between immunity and tolerance. An immunoregulatory T-cell population that upon activation amplifies cellular immune responses was described in murine models more than 30 years ago; however, no study has yet identified a naturally occurring T "inducer" cell type. Here, we report that the ectoenzyme CD39/NTPDase1 (ecto-nucleoside triphosphate diphosphohydrolase 1) helps to delineate a novel population of human "inducer" CD4+ T cells (Tind) that significantly increases the proliferation and cytokine production of responder T cells in a dose-dependent manner. Furthermore, this unique Tind subset produces a distinct repertoire of cytokines in comparison to the other CD4+ T-cell subsets. We propose that this novel CD4+ T-cell population counterbalances the suppressive activity of suppressor Treg in peripheral blood and serves as a calibrator of immunoregulation.


Assuntos
Antígenos CD/imunologia , Apirase/imunologia , Linfócitos T CD4-Positivos/imunologia , Subpopulações de Linfócitos T/imunologia , Linfócitos T CD4-Positivos/citologia , Proliferação de Células , Citocinas/biossíntese , Citocinas/imunologia , Humanos , Subpopulações de Linfócitos T/citologia
6.
PLoS Pathog ; 5(2): e1000295, 2009 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-19214220

RESUMO

Chronic immune activation and progression to AIDS are observed after SIV infection in macaques but not in natural host primate species. To better understand this dichotomy, we compared acute pathogenic SIV infection in pigtailed macaques (PTs) to non-pathogenic infection in African green monkeys (AGMs). SIVagm-infected PTs, but not SIVagm-infected AGMs, rapidly developed systemic immune activation, marked and selective depletion of IL-17-secreting (Th17) cells, and loss of the balance between Th17 and T regulatory (Treg) cells in blood, lymphoid organs, and mucosal tissue. The loss of Th17 cells was found to be predictive of systemic and sustained T cell activation. Collectively, these data indicate that loss of the Th17 to Treg balance is related to SIV disease progression.


Assuntos
Interleucina-17/imunologia , Síndrome de Imunodeficiência Adquirida dos Símios/imunologia , Subpopulações de Linfócitos T/imunologia , Linfócitos T Auxiliares-Indutores/imunologia , Linfócitos T Reguladores/imunologia , Análise de Variância , Animais , Linfócitos T CD8-Positivos/imunologia , Linfócitos T CD8-Positivos/virologia , Chlorocebus aethiops , Colo/imunologia , Colo/metabolismo , Citocinas/imunologia , Citocinas/metabolismo , Citometria de Fluxo , Fatores de Transcrição Forkhead/metabolismo , Interleucina-17/metabolismo , Linfonodos/imunologia , Linfonodos/metabolismo , Ativação Linfocitária , Macaca nemestrina , Masculino , Análise de Sequência com Séries de Oligonucleotídeos , RNA Viral/análise , RNA Viral/sangue , RNA Viral/metabolismo , Síndrome de Imunodeficiência Adquirida dos Símios/virologia , Vírus da Imunodeficiência Símia , Estatísticas não Paramétricas , Linfócitos T Auxiliares-Indutores/virologia , Linfócitos T Reguladores/virologia , Carga Viral
7.
Immunology ; 129(2): 186-96, 2010 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-19824915

RESUMO

Natural killer (NK) cells bridge the interface between innate and adaptive immunity and are implicated in the control of herpes simplex virus 2 (HSV-2) infection. In subjects infected with human immunodeficiency virus 1 (HIV-1), the critical impact of the innate immune response on disease progression has recently come into focus. Higher numbers of NK cells are associated with lower HIV-1 plasma viraemia. Individuals with the compound genotype of killer cell immunoglobulin-like receptor (KIR) 3DS1 and human leucocyte antigen (HLA)-Bw4-80I, or who have alleles of KIR3DL1 that encode proteins highly expressed on the NK cell surface, have a significant delay in disease progression. We studied the effect of HSV-2 co-infection in HIV-1-infected subjects, and show that HSV-2 co-infection results in a pan-lymphocytosis, with elevated absolute numbers of CD4(+) and CD8(+) T cells, and NK cells. The NK cells in HSV-2 co-infected subjects functioned more efficiently, with an increase in degranulation after in vitro stimulation. The number of NK cells expressing the activating receptors NKp30 and NKp46, and expressing KIR3DL1 or KIR3DS1, was inversely correlated with HIV-1 plasma viral load in subjects mono-infected with HIV-1, but not in subjects co-infected with HSV-2. This suggests that HSV-2 infection mediates changes within the NK cell population that may affect immunity in HIV-1 infection.


Assuntos
Soropositividade para HIV/imunologia , HIV-1/imunologia , Herpes Simples/imunologia , Herpesvirus Humano 2/imunologia , Células Matadoras Naturais/metabolismo , Adulto , Linfócitos T CD4-Positivos/imunologia , Linfócitos T CD4-Positivos/metabolismo , Linfócitos T CD4-Positivos/patologia , Linfócitos T CD4-Positivos/virologia , Linfócitos T CD8-Positivos/imunologia , Linfócitos T CD8-Positivos/metabolismo , Linfócitos T CD8-Positivos/patologia , Linfócitos T CD8-Positivos/virologia , Contagem de Células , Células Cultivadas , Citotoxicidade Imunológica , Progressão da Doença , Feminino , Soropositividade para HIV/complicações , Soropositividade para HIV/patologia , Soropositividade para HIV/fisiopatologia , HIV-1/patogenicidade , Antígenos HLA-B/genética , Antígenos HLA-B/metabolismo , Herpes Simples/complicações , Herpes Simples/patologia , Herpes Simples/fisiopatologia , Herpesvirus Humano 2/patogenicidade , Teste de Histocompatibilidade , Humanos , Imunidade Inata , Células Matadoras Naturais/imunologia , Células Matadoras Naturais/patologia , Células Matadoras Naturais/virologia , Linfocitose , Masculino , Pessoa de Meia-Idade , Receptores KIR3DL1/genética , Receptores KIR3DL1/metabolismo , Receptores KIR3DS1/genética , Receptores KIR3DS1/metabolismo
8.
J Clin Immunol ; 30(5): 681-92, 2010 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-20571894

RESUMO

Little is known about the manipulation of IL-17 producing CD4+ T cells (T(H)17) on a per-cell basis in humans in vivo. Previous studies on the effects of IL-2 on IL-17 secretion in non-HIV models have shown divergent results. We hypothesized that IL-2 would mediate changes in IL-17 levels among recently HIV-1-infected adults receiving anti-retroviral therapy. We measured cytokine T cell responses to CD3/CD28, HIV-1 Gag, and CMV pp65 stimulation, and changes in multiple CD4+ T cell subsets. Those who received IL-2 showed a robust expansion of naive and total CD4+ T cell counts and T-reg counts. However, after IL-2 treatment, the frequency of T(H)17 cells declined, while counts of T(H)17 cells did not change due to an expansion of the CD4+ naïve T cell population (CD27+CD45RA+). Counts of HIV-1 Gag-specific T cells declined modestly, but CMV pp65 and CD3/CD28 stimulated populations did not change. Hence, in contrast with recent studies, our results suggest IL-2 is not a potent in vivo regulator of T(H)17 cell populations in HIV-1 disease. However, IL-2-mediated T-reg expansions may selectively reduce responses to certain antigen-specific populations, such as HIV-1 Gag.


Assuntos
Linfócitos T CD4-Positivos/efeitos dos fármacos , Infecções por HIV/imunologia , Imunoterapia , Interleucina-2/administração & dosagem , Células Th17/efeitos dos fármacos , Adulto , Antirretrovirais/uso terapêutico , Anticorpos Monoclonais/imunologia , Anticorpos Monoclonais/metabolismo , Linfócitos T CD4-Positivos/imunologia , Linfócitos T CD4-Positivos/virologia , Contagem de Células , Proliferação de Células/efeitos dos fármacos , Quimioterapia Combinada , Infecções por HIV/tratamento farmacológico , HIV-1 , Humanos , Imunomodulação , Interleucina-17/biossíntese , Interleucina-17/genética , Interleucina-2/uso terapêutico , Fosfoproteínas/imunologia , Especificidade do Receptor de Antígeno de Linfócitos T , Células Th17/imunologia , Células Th17/patologia , Células Th17/virologia , Proteínas da Matriz Viral/imunologia , Produtos do Gene gag do Vírus da Imunodeficiência Humana/imunologia
9.
J Virol ; 82(10): 4785-92, 2008 May.
Artigo em Inglês | MEDLINE | ID: mdl-18305035

RESUMO

A flurry of recent reports on the role of activating and inhibitory forms of the killer cell immunoglobulin-like receptors (KIR) in natural killer (NK) cell activity against human immunodeficiency virus type 1 (HIV-1) have yielded widely divergent results. The role of the activating NK receptor encoded by the KIR3DS1 allele and its putative ligands, members of the HLA class I Bw4Ile80 cluster, in early HIV-1 disease is controversial. We selected 60 treatment-naïve adults for study from the OPTIONS cohort of individuals with early HIV-1 infection in San Francisco. We performed NK cell functional assays measuring gamma interferon (IFN-gamma) and CD107a expression by NK cells in the unstimulated state and after stimulation by the major histocompatibility complex class I-deficient 721.221 B-lymphoblastoid cell line. In addition, we measured CD38 expression (a T-cell activation marker) on T and NK cells. Persons who have at least one copy of the KIR3DS1 gene had higher IFN-gamma and CD107a expression in the unstimulated state compared to those who do not possess this gene. After stimulation, both groups experienced a large induction of IFN-gamma and CD107a, with KIR3DS1 carriers achieving a greater amount of IFN-gamma expression. Differences in effector activity correlating with KIR3DS1 were not attributable to joint carriage of HLA Bw4Ile80 and KIR3DS1. We detected a partial but not complete dependence of KIR3DS1 on the members of B*58 supertype (B*57 and B*58) leading to higher NK cell function. Possessing KIR3DS1 was associated with lower expression of CD38 on both CD8(+) T and NK cells and with a loss or weakening of the known strong associations between CD8(+) T-cell expression of CD38 mean fluorescence intensity and the HIV-1 viral load. We observed that possessing KIR3DS1 was associated with higher NK cell effector functions in early HIV-1 disease, despite the absence of HLA Bw4Ile80, a putative ligand of KIR3DS1. Carriage of KIR3DS1 was associated with diminished CD8(+) T-cell activation, as determined by expression of CD38, and a disruption of the traditional relationship between viral load and activation in HIV-1 disease, which may lead to better clinical outcomes for these individuals.


Assuntos
Infecções por HIV/imunologia , Infecções por HIV/virologia , HIV-1/imunologia , Células Matadoras Naturais/imunologia , Receptores KIR3DS1/imunologia , ADP-Ribosil Ciclase 1/biossíntese , Adulto , Linfócitos T CD8-Positivos/imunologia , Feminino , Citometria de Fluxo , Genótipo , Infecções por HIV/genética , Antígenos HLA-B/genética , Humanos , Interferon gama/biossíntese , Proteína 1 de Membrana Associada ao Lisossomo/biossíntese , Masculino , Receptores KIR3DS1/genética , São Francisco , Linfócitos T/imunologia
10.
Retrovirology ; 5: 26, 2008 Mar 13.
Artigo em Inglês | MEDLINE | ID: mdl-18339206

RESUMO

APOBEC3G and APOBEC3F are human cytidine deaminases that serve as innate antiviral defense mechanisms primarily by introducing C-to-U changes in the minus strand DNA of retroviruses during replication (resulting in G-to-A mutations in the genomic sense strand sequence). The HIV-1 Vif protein counteracts this defense by promoting the proteolytic degradation of APOBEC3G and APOBEC3F in the host cell. In the absence of Vif expression, APOBEC3 is incorporated into HIV-1 virions and the viral genome undergoes extensive G-to-A mutation, or "hypermutation", typically rendering it non-viable within a single replicative cycle. Consequently, Vif is emerging as an attractive target for pharmacological intervention and therapeutic vaccination. Although a highly effective Vif inhibitor may result in mutational meltdown of the viral quasispecies, a partially effective Vif inhibitor may accelerate the evolution of drug resistance and immune escape due to the codon structure and recombinogenic nature of HIV-1. This hypothesis rests on two principal assumptions which are supported by experimental evidence: a) there is a dose response between intracellular APOBEC concentration and degree of viral hypermutation, and, b) HIV-1 can tolerate an elevated mutation rate, and a true error or extinction threshold is as yet undetermined. Rigorous testing of this hypothesis will have timely and critical implications for the therapeutic management of HIV/AIDS, and delve into the complexities underlying the induction of lethal mutagenesis in a viral pathogen.


Assuntos
Citidina Desaminase/metabolismo , Citosina Desaminase/metabolismo , HIV-1/genética , Mutação , Produtos do Gene vif do Vírus da Imunodeficiência Humana/metabolismo , Desaminase APOBEC-3G , Sequência de Aminoácidos , Sequência de Bases , Protease de HIV/genética , Transcriptase Reversa do HIV/genética , Humanos , Dados de Sequência Molecular , Mutação/efeitos dos fármacos , Produtos do Gene vif do Vírus da Imunodeficiência Humana/antagonistas & inibidores
11.
AIDS ; 20(16): 2123-5, 2006 Oct 24.
Artigo em Inglês | MEDLINE | ID: mdl-17053362

RESUMO

We sought to determine whether pretreatment low pol replication capacity (polRC) is associated with CD4 T-cell count gains during antiretroviral therapy (ART). Patients were recruited at north American and Australian sites. Viral polRC was measured before starting ART in all subjects. We examined 243 individuals for a median 260 days after initiating ART. Low baseline polRC was associated with greater CD4 T-cell gains independent of virological responses.


Assuntos
Fármacos Anti-HIV/uso terapêutico , Genes pol/fisiologia , Infecções por HIV/tratamento farmacológico , HIV-1/fisiologia , Terapia Antirretroviral de Alta Atividade , Contagem de Linfócito CD4 , Seguimentos , Infecções por HIV/imunologia , Infecções por HIV/virologia , HIV-1/genética , HIV-1/isolamento & purificação , Humanos , Prognóstico , RNA Viral/sangue , Replicação Viral/genética
12.
AIDS Res Hum Retroviruses ; 22(1): 52-6, 2006 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-16438646

RESUMO

Human endogenous retrovirus K (HERV-K) is distinctive among the retroviruses that comprise about 8% of the human genome in that multiple HERV-K proviruses encode full-length viral proteins, and many HERV-K proviruses formed during recent human evolution. HERV-K gag proteins are found in the cytoplasm of primary tumor cells of patients with seminoma. We identified HERV-K-specific T cells in patients with a past history of seminoma using the interferon-gamma ELISPOT assay and an MHC-HERV-K peptide-specific tetramer. A minority of apparently healthy subjects without evident germ cell tumors also made HERV-K-specific T cell responses. In summary, we detected T cell reactivity to HERV-K peptides in both past seminoma patients and a minority of apparently healthy controls.


Assuntos
Anticorpos Antivirais/análise , Retrovirus Endógenos/imunologia , Seminoma/imunologia , Linfócitos T/imunologia , Anticorpos Antivirais/sangue , Retrovirus Endógenos/genética , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Seminoma/metabolismo , Seminoma/virologia , Linfócitos T/metabolismo , Integração Viral
13.
Stat Appl Genet Mol Biol ; 3: Article2; discussion article 7, article 9, 2004.
Artigo em Inglês | MEDLINE | ID: mdl-16646798

RESUMO

The problem of relating genotype (as represented by amino acid sequence) to phenotypes is distinguished from standard regression problems by the nature of sequence data. Here we investigate an instance of such a problem where the phenotype of interest is HIV-1 replication capacity and contiguous segments of protease and reverse transcriptase sequence constitutes genotype. A variety of data analytic methods have been proposed in this context. Shortcomings of select techniques are contrasted with the advantages afforded by tree-structured methods. However, tree-structured methods, in turn, have been criticized on grounds of only enjoying modest predictive performance. A number of ensemble approaches (bagging, boosting, random forests) have recently emerged, devised to overcome this deficiency. We evaluate random forests as applied in this setting, and detail why prediction gains obtained in other situations are not realized. Other approaches including logic regression, support vector machines and neural networks are also applied. We interpret results in terms of HIV-1 reverse transcriptase structure and function.

14.
AIDS ; 16(2): 201-7, 2002 Jan 25.
Artigo em Inglês | MEDLINE | ID: mdl-11807304

RESUMO

BACKGROUND: Sustained elevations in CD4 cell counts commonly occur despite incomplete viral suppression with protease inhibitor-based antiretroviral therapy. OBJECTIVES: To determine the incidence and risk factors associated with return of CD4 cell count to pre-therapy levels in patients experiencing virologic failure of protease inhibitor therapy. DESIGN: This is a clinic-based cohort study of HIV-infected adults who failed to maintain durable viral suppression on a protease inhibitor-based regimen. MAIN OUTCOME MEASURES: Virologic failure was defined as persistent plasma HIV RNA level > 500 copies/ml. Immunologic failure was defined as return of CD4 cell count to pre-therapy levels. RESULTS: A total of 291 patients experienced virologic failure on a protease inhibitor-based regimen and had a treatment-mediated CD4 cell increase above pre-therapy levels at the time of virologic failure. If patient data were censored at the time a successful salvage regimen was initiated, then the median time to immunologic failure after the onset of virologic failure was 3 years. If patient data were also censored at the time therapy was discontinued, then 36.8% of the cohort experienced immunologic failure after 3 years of continuous virologic failure. The change in viral load from a pre-treatment baseline, and not the absolute level of viremia achieved, was a strong and independent predictor of immunologic failure. Discontinuing therapy was associated with immunologic failure independent of viral load changes. CONCLUSION: Reduction in T CD4+ cell numbers may eventually occur during prolonged virologic failure of a protease inhibitor-based regimen and is predicted by the degree of virologic suppression below a pre-therapy 'set-point'.


Assuntos
Linfócitos T CD4-Positivos/efeitos dos fármacos , Infecções por HIV/tratamento farmacológico , Inibidores da Protease de HIV/uso terapêutico , HIV-1/efeitos dos fármacos , Viremia/tratamento farmacológico , Adulto , Terapia Antirretroviral de Alta Atividade , Contagem de Linfócito CD4 , Linfócitos T CD4-Positivos/citologia , Progressão da Doença , Infecções por HIV/sangue , Infecções por HIV/imunologia , Infecções por HIV/virologia , HIV-1/genética , Humanos , Indinavir/uso terapêutico , Nelfinavir/uso terapêutico , RNA Viral/sangue , Ritonavir/uso terapêutico , Saquinavir/uso terapêutico , Fatores de Tempo , Falha de Tratamento , Viremia/sangue , Viremia/imunologia , Viremia/virologia
15.
AIDS ; 18(12): 1683-9, 2004 Aug 20.
Artigo em Inglês | MEDLINE | ID: mdl-15280779

RESUMO

OBJECTIVES: Primary, or transmitted, drug resistance is common among treatment naive patients recently infected with HIV-1, and impairs response to anti-retroviral therapy. We previously observed that patients with secondary resistance (developed in response to anti-retroviral treatment) who chose to stop an anti-retroviral regimen experience rapid overgrowth of drug resistant viruses by wild-type virus of higher pol replication capacity. We sought to determine if primary drug resistance would be lost at a rapid rate, and viral pol replication capacity would increase, in the absence of treatment. METHODS: We tracked drug resistance phenotype, genotype, viral pol replication capacity (single cycle recombinant assay incorporating a segment of the patient pol gene [pol RC]), plasma HIV-1 RNA, and CD4 T cell counts in the absence of treatment among patients in early HIV-1 infection. RESULTS: Six of 22 patients had evidence of primary drug resistance to at least one class of drug; three resistant to protease inhibitors, three resistant to non-nucleoside reverse transcriptase inhibitors, and four resistant to nucleoside reverse transcriptase inhibitors. All six patients maintained evidence of drug resistance for the period of observation. Among patients with baseline primary drug resistance pol RC did not increase over time. CONCLUSION: The selection environment of early infection is determined by immune pressure, and stochastic events, not viral pol replication capacity. In contrast to secondary resistant infections that are rapidly overgrown when therapy is stopped, primary drug resistance persists over time. Surveillance and clinical detection of primary resistance is feasible in the first year of infection.


Assuntos
Antirretrovirais/uso terapêutico , Farmacorresistência Viral/imunologia , Infecções por HIV/tratamento farmacológico , HIV-1 , Replicação Viral/imunologia , Adulto , Antirretrovirais/imunologia , Contagem de Linfócito CD4 , Farmacorresistência Viral/genética , Genes pol/genética , Genes pol/imunologia , Genótipo , Infecções por HIV/genética , Infecções por HIV/imunologia , Inibidores da Protease de HIV/imunologia , Inibidores da Protease de HIV/uso terapêutico , HIV-1/efeitos dos fármacos , HIV-1/imunologia , Humanos , Fenótipo , RNA Viral/sangue , Inibidores da Transcriptase Reversa/imunologia , Inibidores da Transcriptase Reversa/uso terapêutico , Replicação Viral/genética
16.
AIDS ; 16(8): 1103-11, 2002 May 24.
Artigo em Inglês | MEDLINE | ID: mdl-12004268

RESUMO

OBJECTIVE: To determine whether treatment with growth hormone (GH) enhances thymopoiesis in individuals infected with HIV-1. METHODS: Five HIV-1-infected adults were treated with GH for 6-12 months in a prospective open-label study. Immunological analyses were performed before GH treatment and repeated at 3 month intervals after GH initiation. Thymic mass was analysed using computed tomography with quantitative density and volume analysis. Analysis of circulating lymphocytes, including naive and memory T cell subsets, was performed using multiparameter flow cytometry. RESULTS: GH treatment was associated with a marked increase in thymic mass in all GH recipients. Circulating naive CD4 T cells also increased significantly in all patients during GH therapy, suggesting an enhancement of thymopoiesis. CONCLUSION: GH has significant effects on the human immune system, including the reversal of thymic atrophy in HIV-1-infected adults. De-novo T cell production may thus be inducible in immunodeficient adults.


Assuntos
Fármacos Anti-HIV/uso terapêutico , Linfócitos T CD4-Positivos/efeitos dos fármacos , Infecções por HIV/tratamento farmacológico , Hormônio do Crescimento Humano/uso terapêutico , Timo/efeitos dos fármacos , Adulto , Infecções por HIV/imunologia , Infecções por HIV/patologia , Hormônio do Crescimento Humano/efeitos adversos , Humanos , Leucopoese/efeitos dos fármacos , Masculino , Pessoa de Meia-Idade , Timo/patologia
18.
AIDS Res Hum Retroviruses ; 30(2): 142-6, 2014 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-23984974

RESUMO

Coronary artery calcium (CAC) is a validated subclinical measure of atherosclerosis. Studies in the general population have linked blood inflammatory biomarkers including monocyte chemoattractant protein-1 (MCP-1) and tumor necrosis factor (TNF)-α with the burden of CAC, but this relationship is often lost following correction for traditional cardiovascular risk factors. We assessed the relationship of various biomarkers to CAC, specifically in HIV-infected individuals on potent antiretroviral therapy (ART). Analyses utilized entry data from participants in the Hawaii Aging with HIV-Cardiovascular (HAHC-CVD) study. Computerized tomography examinations for CAC were obtained locally and analyzed by a central reading center in blinded fashion. Plasma biomarkers were assessed by multiplexing using Milliplex Human Cardiovascular Disease panels. Among a cohort of 130 subjects [88% male, median (IQR) age of 51 (46-57) years, CD4 count of 492 (341-635) cells/mm(3), 86.9% with HIV RNA ≤50 copies/ml], CAC was present in 46.9% of subjects. In univariate analyses higher levels of log-transformed MCP-1 and TNF-α were associated with the presence of CAC (p<0.05). In multivariate logistic regression models, MCP-1 and TNF-α remained significant after adjustment for traditional cardiovascular (CVD) risk factors. Similar results were found when analyses were assessed by Framingham risk score categories or when restricted to subjects with plasma HIV RNA ≤50 copies/ml. In contrast to findings in the general population, higher MCP-1 and TNF-α predict the presence of CAC independent of traditional CVD risk factors in HIV-infected subjects fully suppressed on ART, suggesting that HIV-mediated immune activation may play a role in CVD risk.


Assuntos
Aterosclerose/diagnóstico , Cálcio/análise , Quimiocina CCL2/sangue , Doença da Artéria Coronariana/diagnóstico , Infecções por HIV/complicações , Plasma/química , Fator de Necrose Tumoral alfa/sangue , Aterosclerose/diagnóstico por imagem , Biomarcadores/sangue , Estudos de Coortes , Doença da Artéria Coronariana/diagnóstico por imagem , Doença da Artéria Coronariana/patologia , Feminino , Havaí , Humanos , Estudos Longitudinais , Masculino , Pessoa de Meia-Idade , Tomografia Computadorizada por Raios X
19.
AIDS Res Hum Retroviruses ; 30(7): 654-64, 2014 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-24786365

RESUMO

Galectin-9 (Gal-9) is a ß-galactosidase-binding lectin that promotes apoptosis, tissue inflammation, and T cell immune exhaustion, and alters HIV infection in part through engagement with the T cell immunoglobulin mucin domain-3 (Tim-3) receptor and protein disulfide isomerases (PDI). Gal-9 was initially thought to be an eosinophil attractant, but is now known to mediate multiple complex signaling events that affect T cells in both an immunosuppressive and inflammatory manner. To understand the kinetics of circulating Gal-9 levels during HIV infection we measured Gal-9 in plasma during HIV acquisition, in subjects with chronic HIV infection with differing virus control, and in uninfected individuals. During acute HIV infection, circulating Gal-9 was detected as early as 5 days after quantifiable HIV RNA and tracked plasma levels of interleukin (IL)-10, tumor necrosis factor (TNF)-α, and IL-1ß. In chronic HIV infection, Gal-9 levels positively correlated with plasma HIV RNA levels (r=0.29; p=0.023), and remained significantly elevated during suppressive antiretroviral therapy (median: 225.3 pg/ml) and in elite controllers (263.3 pg/ml) compared to age-matched HIV-uninfected controls (54 pg/ml). Our findings identify Gal-9 as a novel component of the first wave of the cytokine storm in acute HIV infection that is sustained at elevated levels in virally suppressed subjects and suggest that Gal-9:Tim-3 crosstalk remains active in elite controllers and antiretroviral (ARV)-suppressed subjects, potentially contributing to ongoing inflammation and persistent T cell dysfunction.


Assuntos
Galectinas/imunologia , Infecções por HIV/imunologia , Proteínas de Membrana/metabolismo , RNA Viral/sangue , Antirretrovirais/uso terapêutico , Terapia Antirretroviral de Alta Atividade , Galectinas/sangue , Infecções por HIV/tratamento farmacológico , HIV-1/genética , Receptor Celular 2 do Vírus da Hepatite A , Humanos , Tolerância Imunológica/imunologia , Interleucina-10/sangue , Interleucina-1beta/sangue , Isomerases de Dissulfetos de Proteínas/metabolismo , Linfócitos T/imunologia , Fator de Necrose Tumoral alfa/sangue
20.
PLoS One ; 9(2): e90330, 2014.
Artigo em Inglês | MEDLINE | ID: mdl-24587328

RESUMO

BACKGROUND: Rates of insulin resistance are increased in HIV-infected patients on stable antiretroviral therapy (ART). Such increase may partially be due to HIV-induced immune dysregulation involving monocytes (MO) and its subsets. MATERIALS AND METHODS: Cross-sectional analysis of 141 HIV-infected subjects age ≥ 40 years on stable ART. Homeostatic model assessment-insulin resistance (HOMA-IR) and rates of metabolic syndrome were calculated. Subjects were classified by fasting glucose and oral glucose tolerance test (OGTT) into clinical diabetes categories. Multi-parametric flow cytometry was used to determine MO subset percentages: [classical (CD14(++)CD16(-)), intermediate (CD14(++)CD16(+)), non-classical (CD14(low/+)CD16(++)), and a recently identified fourth (CD14(low/+)CD16(-)) 'transitional' MO subset] and percentage of activated (CD38(+)HLA-DR(+)) CD8 T cells. Absolute levels of cells were calculated using clinical CBC and T cell subset data. Multiple plasma soluble biomarkers were assessed by Luminex technology. RESULTS: Median age 50 years, CD4 count (percent) 505 cells/µL (29%), and 89% male. Total MO (r=-0.23, p=0.006) and classical and non-classical MO subsets correlated negatively with CD4 percent. No correlations were seen with CD4 count as absolute values. Log-total MO and log-classical MO predicted HOMA-IR independently of HIV immuno-virologic and diabetes risk factors (ß=0.42, p=0.02 and ß=0.35, p=0.02, respectively) and were increased in subjects with metabolic syndrome (p=0.03 and p=0.05 respectively). Total and/or subset MO levels correlated with multiple soluble plasma biomarkers including CRP, IL-6, MMP-9, MPO, SAA, SAP and tPAI-1, with tPAI-1 independently predicting HOMA-IR (ß=0.74, p<0.001). CONCLUSIONS: MO levels increase with worsening HIV immune dysregulation as assessed by CD4 percent. CD4 percent may provide additional information about MO and metabolic risk in this population beyond absolute values. MO, and specifically classical MO, may contribute to insulin resistance and metabolic syndrome during chronic HIV infection. Multiple soluble plasma biomarkers including tPAI-1 increase with increase in MO. Levels of tPAI-1 independently predict the development of insulin resistance.


Assuntos
Infecções por HIV/imunologia , Infecções por HIV/metabolismo , Resistência à Insulina/imunologia , Monócitos/imunologia , Fatores Etários , Biomarcadores/sangue , Biomarcadores/metabolismo , Glicemia , Estudos Transversais , Diabetes Mellitus/diagnóstico , Diabetes Mellitus/imunologia , Diabetes Mellitus/metabolismo , Feminino , Humanos , Imunofenotipagem , Contagem de Linfócitos , Masculino , Síndrome Metabólica/imunologia , Síndrome Metabólica/metabolismo , Pessoa de Meia-Idade , Monócitos/metabolismo , Fatores de Risco , Subpopulações de Linfócitos T/imunologia , Subpopulações de Linfócitos T/metabolismo
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