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1.
Nature ; 623(7987): 608-615, 2023 Nov.
Article in English | MEDLINE | ID: mdl-37938768

ABSTRACT

Cell therapies have yielded durable clinical benefits for patients with cancer, but the risks associated with the development of therapies from manipulated human cells are understudied. For example, we lack a comprehensive understanding of the mechanisms of toxicities observed in patients receiving T cell therapies, including recent reports of encephalitis caused by reactivation of human herpesvirus 6 (HHV-6)1. Here, through petabase-scale viral genomics mining, we examine the landscape of human latent viral reactivation and demonstrate that HHV-6B can become reactivated in cultures of human CD4+ T cells. Using single-cell sequencing, we identify a rare population of HHV-6 'super-expressors' (about 1 in 300-10,000 cells) that possess high viral transcriptional activity, among research-grade allogeneic chimeric antigen receptor (CAR) T cells. By analysing single-cell sequencing data from patients receiving cell therapy products that are approved by the US Food and Drug Administration2 or are in clinical studies3-5, we identify the presence of HHV-6-super-expressor CAR T cells in patients in vivo. Together, the findings of our study demonstrate the utility of comprehensive genomics analyses in implicating cell therapy products as a potential source contributing to the lytic HHV-6 infection that has been reported in clinical trials1,6-8 and may influence the design and production of autologous and allogeneic cell therapies.


Subject(s)
CD4-Positive T-Lymphocytes , Herpesvirus 6, Human , Immunotherapy, Adoptive , Receptors, Chimeric Antigen , Virus Activation , Virus Latency , Humans , CD4-Positive T-Lymphocytes/immunology , CD4-Positive T-Lymphocytes/virology , Clinical Trials as Topic , Gene Expression Regulation, Viral , Genomics , Herpesvirus 6, Human/genetics , Herpesvirus 6, Human/isolation & purification , Herpesvirus 6, Human/physiology , Immunotherapy, Adoptive/adverse effects , Immunotherapy, Adoptive/methods , Infectious Encephalitis/complications , Infectious Encephalitis/virology , Receptors, Chimeric Antigen/immunology , Roseolovirus Infections/complications , Roseolovirus Infections/virology , Single-Cell Gene Expression Analysis , Viral Load
2.
Nat Immunol ; 17(9): 1067-74, 2016 09.
Article in English | MEDLINE | ID: mdl-27455421

ABSTRACT

The activating natural killer (NK)-cell receptor KIR3DS1 has been linked to the outcome of various human diseases, including delayed progression of disease caused by human immunodeficiency virus type 1 (HIV-1), yet a ligand that would account for its biological effects has remained unknown. We screened 100 HLA class I proteins and found that KIR3DS1 bound to HLA-F, a result we confirmed biochemically and functionally. Primary human KIR3DS1(+) NK cells degranulated and produced antiviral cytokines after encountering HLA-F and inhibited HIV-1 replication in vitro. Activation of CD4(+) T cells triggered the transcription and surface expression of HLA-F mRNA and HLA-F protein, respectively, and induced binding of KIR3DS1. HIV-1 infection further increased the transcription of HLA-F mRNA but decreased the binding of KIR3DS1, indicative of a mechanism for evading recognition by KIR3DS1(+) NK cells. Thus, we have established HLA-F as a ligand of KIR3DS1 and have demonstrated cell-context-dependent expression of HLA-F that might explain the widespread influence of KIR3DS1 in human disease.


Subject(s)
CD4-Positive T-Lymphocytes/immunology , HIV Infections/immunology , HIV-1/physiology , Histocompatibility Antigens Class I/metabolism , Killer Cells, Natural/immunology , Receptors, KIR3DS1/metabolism , Cytokines/metabolism , Cytotoxicity, Immunologic , Disease Progression , Histocompatibility Antigens Class I/genetics , Humans , Immune Evasion , Jurkat Cells , Ligands , Lymphocyte Activation , Primary Cell Culture , Receptors, KIR3DS1/agonists , Receptors, KIR3DS1/genetics , Virus Latency , Virus Replication
4.
Mol Ther ; 31(3): 676-685, 2023 03 01.
Article in English | MEDLINE | ID: mdl-36518079

ABSTRACT

A chromosome 14 inversion was found in a patient who developed bone marrow aplasia following treatment with allogeneic chimeric antigen receptor (CAR) Tcells containing gene edits made with transcription activator-like effector nucleases (TALEN). TALEN editing sites were not involved at either breakpoint. Recombination signal sequences (RSSs) were found suggesting recombination-activating gene (RAG)-mediated activity. The inversion represented a dominant clone detected in the context of decreasing absolute CAR Tcell and overall lymphocyte counts. The inversion was not associated with clinical consequences and wasnot detected in the drug product administered to this patient or in any drug product used in this or other trials using the same manufacturing processes. Neither was the inversion detected in this patient at earlier time points or in any other patient enrolled in this or other trials treated with this or other product lots. This case illustrates that spontaneous, possibly RAG-mediated, recombination events unrelated to gene editing can occur in adoptive cell therapy studies, emphasizes the need for ruling out off-target gene editing sites, and illustrates that other processes, such as spontaneous V(D)J recombination, can lead to chromosomal alterations in infused cells independent of gene editing.


Subject(s)
Hematopoietic Stem Cell Transplantation , Receptors, Chimeric Antigen , Humans , Gene Editing , Transcription Activator-Like Effector Nucleases/genetics , T-Lymphocytes , Receptors, Chimeric Antigen/genetics , Immunotherapy, Adoptive/adverse effects
5.
Immunity ; 41(6): 1001-12, 2014 Dec 18.
Article in English | MEDLINE | ID: mdl-25526311

ABSTRACT

Decreased HIV-specific CD8(+) T cell proliferation is a hallmark of chronic infection, but the mechanisms of decline are unclear. We analyzed gene expression profiles from antigen-stimulated HIV-specific CD8(+) T cells from patients with controlled and uncontrolled infection and identified caspase-8 as a correlate of dysfunctional CD8(+) T cell proliferation. Caspase-8 activity was upregulated in HIV-specific CD8(+) T cells from progressors and correlated positively with disease progression and programmed cell death-1 (PD-1) expression, but negatively with proliferation. In addition, progressor cells displayed a decreased ability to upregulate membrane-associated caspase-8 activity and increased necrotic cell death following antigenic stimulation, implicating the programmed cell death pathway necroptosis. In vitro necroptosis blockade rescued HIV-specific CD8(+) T cell proliferation in progressors, as did silencing of necroptosis mediator RIPK3. Thus, chronic stimulation leading to upregulated caspase-8 activity contributes to dysfunctional HIV-specific CD8(+) T cell proliferation through activation of necroptosis and increased cell death.


Subject(s)
CD8-Positive T-Lymphocytes/immunology , Caspase 8/metabolism , HIV Infections/immunology , HIV/physiology , Programmed Cell Death 1 Receptor/metabolism , CD8-Positive T-Lymphocytes/virology , Cell Proliferation/genetics , Cells, Cultured , Disease Progression , Enzyme Activation , Gene Expression Regulation , HIV Core Protein p24/immunology , Humans , Necrosis , Peptide Fragments/immunology , Programmed Cell Death 1 Receptor/genetics , RNA, Small Interfering/genetics , Receptor-Interacting Protein Serine-Threonine Kinases/genetics , Receptor-Interacting Protein Serine-Threonine Kinases/metabolism , Transcriptome , Viral Load
6.
Nature ; 517(7534): 386-90, 2015 01 15.
Article in English | MEDLINE | ID: mdl-25363763

ABSTRACT

T-cell immunoglobulin domain and mucin domain-3 (TIM-3, also known as HAVCR2) is an activation-induced inhibitory molecule involved in tolerance and shown to induce T-cell exhaustion in chronic viral infection and cancers. Under some conditions, TIM-3 expression has also been shown to be stimulatory. Considering that TIM-3, like cytotoxic T lymphocyte antigen 4 (CTLA-4) and programmed death 1 (PD-1), is being targeted for cancer immunotherapy, it is important to identify the circumstances under which TIM-3 can inhibit and activate T-cell responses. Here we show that TIM-3 is co-expressed and forms a heterodimer with carcinoembryonic antigen cell adhesion molecule 1 (CEACAM1), another well-known molecule expressed on activated T cells and involved in T-cell inhibition. Biochemical, biophysical and X-ray crystallography studies show that the membrane-distal immunoglobulin-variable (IgV)-like amino-terminal domain of each is crucial to these interactions. The presence of CEACAM1 endows TIM-3 with inhibitory function. CEACAM1 facilitates the maturation and cell surface expression of TIM-3 by forming a heterodimeric interaction in cis through the highly related membrane-distal N-terminal domains of each molecule. CEACAM1 and TIM-3 also bind in trans through their N-terminal domains. Both cis and trans interactions between CEACAM1 and TIM-3 determine the tolerance-inducing function of TIM-3. In a mouse adoptive transfer colitis model, CEACAM1-deficient T cells are hyper-inflammatory with reduced cell surface expression of TIM-3 and regulatory cytokines, and this is restored by T-cell-specific CEACAM1 expression. During chronic viral infection and in a tumour environment, CEACAM1 and TIM-3 mark exhausted T cells. Co-blockade of CEACAM1 and TIM-3 leads to enhancement of anti-tumour immune responses with improved elimination of tumours in mouse colorectal cancer models. Thus, CEACAM1 serves as a heterophilic ligand for TIM-3 that is required for its ability to mediate T-cell inhibition, and this interaction has a crucial role in regulating autoimmunity and anti-tumour immunity.


Subject(s)
Antigens, CD/metabolism , Cell Adhesion Molecules/metabolism , Immune Tolerance/immunology , Membrane Proteins/metabolism , Receptors, Virus/metabolism , T-Lymphocytes/immunology , T-Lymphocytes/metabolism , Animals , Antigens, CD/chemistry , Antigens, CD/immunology , Autoimmunity/immunology , Cell Adhesion Molecules/chemistry , Cell Adhesion Molecules/immunology , Cell Line , Colorectal Neoplasms/immunology , Disease Models, Animal , Female , Hepatitis A Virus Cellular Receptor 2 , Humans , Inflammation/immunology , Inflammation/pathology , Ligands , Male , Membrane Proteins/chemistry , Membrane Proteins/immunology , Mice , Mice, Inbred BALB C , Mice, Inbred C57BL , Models, Molecular , Mucous Membrane/immunology , Mucous Membrane/pathology , Protein Conformation , Protein Multimerization , Receptors, Virus/chemistry , Receptors, Virus/immunology
7.
Mol Ther ; 27(6): 1126-1138, 2019 06 05.
Article in English | MEDLINE | ID: mdl-31005597

ABSTRACT

Clinical success of autologous CD19-directed chimeric antigen receptor T cells (CAR Ts) in acute lymphoblastic leukemia and non-Hodgkin lymphoma suggests that CAR Ts may be a promising therapy for hematological malignancies, including multiple myeloma. However, autologous CAR T therapies have limitations that may impact clinical use, including lengthy vein-to-vein time and manufacturing constraints. Allogeneic CAR T (AlloCAR T) therapies may overcome these innate limitations of autologous CAR T therapies. Unlike autologous cell therapies, AlloCAR T therapies employ healthy donor T cells that are isolated in a manufacturing facility, engineered to express CARs with specificity for a tumor-associated antigen, and modified using gene-editing technology to limit T cell receptor (TCR)-mediated immune responses. Here, transcription activator-like effector nuclease (TALEN) gene editing of B cell maturation antigen (BCMA) CAR Ts was used to confer lymphodepletion resistance and reduced graft-versus-host disease (GvHD) potential. The safety profile of allogeneic BCMA CAR Ts was further enhanced by incorporating a CD20 mimotope-based intra-CAR off switch enabling effective CAR T elimination in the presence of rituximab. Allogeneic BCMA CAR Ts induced sustained antitumor responses in mice supplemented with human cytokines, and, most importantly, maintained their phenotype and potency after scale-up manufacturing. This novel off-the-shelf allogeneic BCMA CAR T product is a promising candidate for clinical evaluation.


Subject(s)
B-Cell Maturation Antigen/immunology , Cell Transplantation/methods , Immunotherapy, Adoptive/methods , Multiple Myeloma/therapy , Receptors, Chimeric Antigen/immunology , T-Lymphocytes/immunology , T-Lymphocytes/transplantation , Animals , Antineoplastic Agents, Immunological/therapeutic use , B-Cell Maturation Antigen/genetics , Blood Donors , Cell Line, Tumor , Cell Transplantation/adverse effects , Cytotoxicity, Immunologic/genetics , Gene Editing , Genetic Vectors , Graft vs Host Disease/therapy , Humans , Immunotherapy, Adoptive/adverse effects , Mice , Mice, Inbred NOD , Mice, SCID , Multiple Myeloma/pathology , Progression-Free Survival , Receptors, Chimeric Antigen/genetics , Receptors, Chimeric Antigen/metabolism , Rituximab/therapeutic use , T-Lymphocytes/metabolism , Transcription Activator-Like Effector Nucleases/genetics , Transduction, Genetic , Transplantation, Homologous/methods
8.
Nature ; 484(7395): 519-23, 2012 Mar 25.
Article in English | MEDLINE | ID: mdl-22446628

ABSTRACT

The 2009 H1N1 influenza pandemic showed the speed with which a novel respiratory virus can spread and the ability of a generally mild infection to induce severe morbidity and mortality in a subset of the population. Recent in vitro studies show that the interferon-inducible transmembrane (IFITM) protein family members potently restrict the replication of multiple pathogenic viruses. Both the magnitude and breadth of the IFITM proteins' in vitro effects suggest that they are critical for intrinsic resistance to such viruses, including influenza viruses. Using a knockout mouse model, we now test this hypothesis directly and find that IFITM3 is essential for defending the host against influenza A virus in vivo. Mice lacking Ifitm3 display fulminant viral pneumonia when challenged with a normally low-pathogenicity influenza virus, mirroring the destruction inflicted by the highly pathogenic 1918 'Spanish' influenza. Similar increased viral replication is seen in vitro, with protection rescued by the re-introduction of Ifitm3. To test the role of IFITM3 in human influenza virus infection, we assessed the IFITM3 alleles of individuals hospitalized with seasonal or pandemic influenza H1N1/09 viruses. We find that a statistically significant number of hospitalized subjects show enrichment for a minor IFITM3 allele (SNP rs12252-C) that alters a splice acceptor site, and functional assays show the minor CC genotype IFITM3 has reduced influenza virus restriction in vitro. Together these data reveal that the action of a single intrinsic immune effector, IFITM3, profoundly alters the course of influenza virus infection in mouse and humans.


Subject(s)
Influenza A virus/pathogenicity , Membrane Proteins/metabolism , Orthomyxoviridae Infections/mortality , RNA-Binding Proteins/metabolism , Alleles , Amino Acid Sequence , Animals , Cytokines/immunology , England/epidemiology , Gene Deletion , Humans , Influenza A Virus, H1N1 Subtype/classification , Influenza A Virus, H1N1 Subtype/growth & development , Influenza A Virus, H1N1 Subtype/pathogenicity , Influenza A Virus, H3N2 Subtype/classification , Influenza A Virus, H3N2 Subtype/growth & development , Influenza A Virus, H3N2 Subtype/pathogenicity , Influenza A virus/classification , Influenza A virus/growth & development , Influenza B virus/classification , Influenza B virus/growth & development , Influenza B virus/pathogenicity , Influenza, Human/complications , Influenza, Human/epidemiology , Influenza, Human/mortality , Influenza, Human/virology , Leukocytes/immunology , Lung/pathology , Lung/virology , Membrane Proteins/chemistry , Membrane Proteins/deficiency , Membrane Proteins/genetics , Mice , Mice, Inbred C57BL , Mice, Knockout , Molecular Sequence Data , Orthomyxoviridae Infections/complications , Orthomyxoviridae Infections/pathology , Pneumonia, Viral/etiology , Pneumonia, Viral/pathology , Pneumonia, Viral/prevention & control , Polymorphism, Single Nucleotide/genetics , RNA-Binding Proteins/chemistry , RNA-Binding Proteins/genetics , Scotland/epidemiology , Virus Replication
9.
PLoS Pathog ; 11(7): e1005050, 2015 Jul.
Article in English | MEDLINE | ID: mdl-26181333

ABSTRACT

HIV-2 and SIVMAC are AIDS-causing, zoonotic lentiviruses that jumped to humans and rhesus macaques, respectively, from SIVSM-bearing sooty mangabey monkeys. Cross-species transmission events such as these sometimes necessitate virus adaptation to species-specific, host restriction factors such as TRIM5. Here, a new human restriction activity is described that blocks viruses of the SIVSM/SIVMAC/HIV-2 lineage. Human T, B, and myeloid cell lines, peripheral blood mononuclear cells and dendritic cells were 4 to >100-fold less transducible by VSV G-pseudotyped SIVMAC, HIV-2, or SIVSM than by HIV-1. In contrast, transduction of six epithelial cell lines was equivalent to that by HIV-1. Substitution of HIV-1 CA with the SIVMAC or HIV-2 CA was sufficient to reduce HIV-1 transduction to the level of the respective vectors. Among such CA chimeras there was a general trend such that CAs from epidemic HIV-2 Group A and B isolates were the most infectious on human T cells, CA from a 1° sooty mangabey isolate was the least infectious, and non-epidemic HIV-2 Group D, E, F, and G CAs were in the middle. The CA-specific decrease in infectivity was observed with either HIV-1, HIV-2, ecotropic MLV, or ALV Env pseudotypes, indicating that it was independent of the virus entry pathway. As2O3, a drug that suppresses TRIM5-mediated restriction, increased human blood cell transduction by SIVMAC but not by HIV-1. Nonetheless, elimination of TRIM5 restriction activity did not rescue SIVMAC transduction. Also, in contrast to TRIM5-mediated restriction, the SIVMAC CA-specific block occurred after completion of reverse transcription and the formation of 2-LTR circles, but before establishment of the provirus. Transduction efficiency in heterokaryons generated by fusing epithelial cells with T cells resembled that in the T cells, indicative of a dominant-acting SIVMAC restriction activity in the latter. These results suggest that the nucleus of human blood cells possesses a restriction factor specific for the CA of HIV-2/SIVMAC/SIVSM and that cross-species transmission of SIVSM to human T cells necessitated adaptation of HIV-2 to this putative restriction factor.


Subject(s)
Antiviral Agents/pharmacology , Capsid/microbiology , HIV-2/drug effects , Leukocytes, Mononuclear/virology , Simian Immunodeficiency Virus/drug effects , Virus Integration/drug effects , Animals , Cell Line , Dendritic Cells/drug effects , Dendritic Cells/virology , HIV-2/genetics , HIV-2/immunology , Humans , Leukocytes, Mononuclear/immunology , Simian Immunodeficiency Virus/genetics , T-Lymphocytes/drug effects , T-Lymphocytes/virology
10.
Nature ; 472(7343): 361-5, 2011 Apr 21.
Article in English | MEDLINE | ID: mdl-21512573

ABSTRACT

TRIM5 is a RING domain-E3 ubiquitin ligase that restricts infection by human immunodeficiency virus (HIV)-1 and other retroviruses immediately following virus invasion of the target cell cytoplasm. Antiviral potency correlates with TRIM5 avidity for the retrovirion capsid lattice and several reports indicate that TRIM5 has a role in signal transduction, but the precise mechanism of restriction is unknown. Here we demonstrate that TRIM5 promotes innate immune signalling and that this activity is amplified by retroviral infection and interaction with the capsid lattice. Acting with the heterodimeric, ubiquitin-conjugating enzyme UBC13-UEV1A (also known as UBE2N-UBE2V1), TRIM5 catalyses the synthesis of unattached K63-linked ubiquitin chains that activate the TAK1 (also known as MAP3K7) kinase complex and stimulate AP-1 and NFκB signalling. Interaction with the HIV-1 capsid lattice greatly enhances the UBC13-UEV1A-dependent E3 activity of TRIM5 and challenge with retroviruses induces the transcription of AP-1 and NF-κB-dependent factors with a magnitude that tracks with TRIM5 avidity for the invading capsid. Finally, TAK1 and UBC13-UEV1A contribute to capsid-specific restriction by TRIM5. Thus, the retroviral restriction factor TRIM5 has two additional activities that are linked to restriction: it constitutively promotes innate immune signalling and it acts as a pattern recognition receptor specific for the retrovirus capsid lattice.


Subject(s)
Capsid/chemistry , Capsid/immunology , Carrier Proteins/immunology , Carrier Proteins/metabolism , Immunity, Innate/immunology , Retroviridae/immunology , Antiviral Restriction Factors , Carrier Proteins/genetics , Cell Line , Enzyme Activation , HEK293 Cells , HIV-1/chemistry , HIV-1/immunology , Humans , Lipopolysaccharides/immunology , Lipopolysaccharides/pharmacology , MAP Kinase Kinase Kinases/metabolism , NF-kappa B/metabolism , Protein Binding , Receptors, Pattern Recognition/immunology , Receptors, Pattern Recognition/metabolism , Retroviridae/chemistry , Signal Transduction/drug effects , Signal Transduction/immunology , Transcription Factor AP-1/metabolism , Transcription Factors/metabolism , Tripartite Motif Proteins , Ubiquitin/metabolism , Ubiquitin-Conjugating Enzymes/metabolism , Ubiquitin-Protein Ligases/genetics , Ubiquitin-Protein Ligases/immunology , Ubiquitin-Protein Ligases/metabolism
12.
Ann Neurol ; 78(1): 115-27, 2015 Jul.
Article in English | MEDLINE | ID: mdl-25914168

ABSTRACT

OBJECTIVE: A proportion of multiple sclerosis (MS) patients experience disease activity despite treatment. The early identification of the most effective drug is critical to impact long-term outcome and to move toward a personalized approach. The aim of the present study is to identify biomarkers for further clinical development and to yield insights into the pathophysiology of disease activity. METHODS: We performed a genome-wide association study in interferon-ß (IFNß)-treated MS patients followed by validation in 3 independent cohorts. The role of the validated variant was examined in several RNA data sets, and the function of the presumed target gene was explored using an RNA interference approach in primary T cells in vitro. RESULTS: We found an association between rs9828519(G) and nonresponse to IFNß (pdiscovery = 4.43 × 10(-8)) and confirmed it in a meta-analysis across 3 replication data sets (preplication = 7.78 × 10(-4)). Only 1 gene is found in the linkage disequilibrium block containing rs9828519: SLC9A9. Exploring the function of this gene, we see that SLC9A9 mRNA expression is diminished in MS subjects who are more likely to have relapses. Moreover, SLC9A9 knockdown in T cells in vitro leads an increase in expression of IFNγ, which is a proinflammatory molecule. INTERPRETATION: This study identifies and validates the role of rs9828519, an intronic variant in SLC9A9, in IFNß-treated subjects, demonstrating a successful pharmacogenetic screen in MS. Functional characterization suggests that SLC9A9, an Na(+) -H(+) exchanger found in endosomes, appears to influence the differentiation of T cells to a proinflammatory fate and may have a broader role in MS disease activity, outside of IFNß treatment.


Subject(s)
Adjuvants, Immunologic/therapeutic use , Cytokines/immunology , Interferon-beta/therapeutic use , Multiple Sclerosis, Relapsing-Remitting/genetics , Sodium-Hydrogen Exchangers/genetics , T-Lymphocytes/immunology , Adolescent , Adult , Cell Differentiation/genetics , Cells, Cultured , Cohort Studies , Cytokines/genetics , Cytokines/metabolism , Female , Gene Expression Profiling , Gene Knockdown Techniques , Humans , In Vitro Techniques , Interferon beta-1a , Interferon beta-1b , Leukocytes, Mononuclear/metabolism , Male , Middle Aged , Multiple Sclerosis, Relapsing-Remitting/drug therapy , Multiple Sclerosis, Relapsing-Remitting/immunology , RNA, Small Interfering , T-Lymphocytes/metabolism , Young Adult
13.
PLoS Med ; 12(11): e1001900; discussion e1001900, 2015 Nov.
Article in English | MEDLINE | ID: mdl-26575988

ABSTRACT

BACKGROUND: Viruses can evade immune surveillance, but the underlying mechanisms are insufficiently understood. Here, we sought to understand the mechanisms by which natural killer (NK) cells recognize HIV-1-infected cells and how this virus can evade NK-cell-mediated immune pressure. METHODS AND FINDINGS: Two sequence mutations in p24 Gag associated with the presence of specific KIR/HLA combined genotypes were identified in HIV-1 clade C viruses from a large cohort of infected, untreated individuals in South Africa (n = 392), suggesting viral escape from KIR+ NK cells through sequence variations within HLA class I-presented epitopes. One sequence polymorphism at position 303 of p24 Gag (TGag303V), selected for in infected individuals with both KIR2DL3 and HLA-C*03:04, enabled significantly better binding of the inhibitory KIR2DL3 receptor to HLA-C*03:04-expressing cells presenting this variant epitope compared to the wild-type epitope (wild-type mean 18.01 ± 10.45 standard deviation [SD] and variant mean 44.67 ± 14.42 SD, p = 0.002). Furthermore, activation of primary KIR2DL3+ NK cells from healthy donors in response to HLA-C*03:04+ target cells presenting the variant epitope was significantly reduced in comparison to cells presenting the wild-type sequence (wild-type mean 0.78 ± 0.07 standard error of the mean [SEM] and variant mean 0.63 ± 0.07 SEM, p = 0.012). Structural modeling and surface plasmon resonance of KIR/peptide/HLA interactions in the context of the different viral sequence variants studied supported these results. Future studies will be needed to assess processing and antigen presentation of the investigated HIV-1 epitope in natural infection, and the consequences for viral control. CONCLUSIONS: These data provide novel insights into how viruses can evade NK cell immunity through the selection of mutations in HLA-presented epitopes that enhance binding to inhibitory NK cell receptors. Better understanding of the mechanisms by which HIV-1 evades NK-cell-mediated immune pressure and the functional validation of a structural modeling approach will facilitate the development of novel targeted immune interventions to harness the antiviral activities of NK cells.


Subject(s)
Genetic Variation , HIV Core Protein p24/genetics , HIV-1/genetics , HLA-C Antigens/genetics , Immune Evasion , Killer Cells, Natural/immunology , gag Gene Products, Human Immunodeficiency Virus/genetics , Cohort Studies , Epitopes , Female , Genotype , HIV Infections/immunology , HIV-1/immunology , HLA-C Antigens/immunology , Humans , Male , RNA, Viral/genetics , Receptors, KIR2DL3/immunology , Reverse Transcriptase Polymerase Chain Reaction , Sequence Analysis, RNA , South Africa
14.
J Neuroinflammation ; 12: 245, 2015 Dec 30.
Article in English | MEDLINE | ID: mdl-26714756

ABSTRACT

BACKGROUND: Fingolimod (FTY720), the first oral treatment for multiple sclerosis (MS), blocks immune cell trafficking and prevents disease relapses by downregulation of sphingosine-1-phosphate receptor. We determined the effect of FTY720 on human T cell activation and effector function. METHODS: T cells from MS patients and healthy controls were isolated to measure gene expression profiles in the presence or absence of FTY720 using nanostring and quantitative real-time polymerase chain reaction (qPCR). Cytokine protein expression was measured using luminex assay and flow cytometry analysis. Lentivirus vector carrying short hairpin RNA (shRNA) was used to knock down the expression of specific genes in CD4+ T cells. Chromatin immunoprecipitation was performed to assess T cell factor 1 (TCF-1) binding to promoter regions. Luciferase assays were performed to test the direct regulation of interferon gamma (IFN-γ) and granzyme B (GZMB) by TCF-1. Western blot analysis was used to assess the phosphorylation status of Akt and GSK3ß. RESULTS: We showed that FTY720 treatment not only affects T cell trafficking but also T cell activation. Patients treated with FTY720 showed a significant reduction in circulating CD4 T cells. Activation of T cells in presence of FTY720 showed a less inflammatory phenotype with reduced production of IFN-γ and GZMB. This decreased effector phenotype of FTY720-treated T cells was dependent on the upregulation of TCF-1. FTY720-induced TCF-1 downregulated the pathogenic cytokines IFN-γ and GZMB by binding to their promoter/enhancer regions and mediating epigenetic modifications. Furthermore, we observed that TCF-1 expression was lower in T cells from multiple sclerosis patients than in those from healthy individuals, and FTY720 treatment increased TCF-1 expression in multiple sclerosis patients. CONCLUSIONS: These results reveal a previously unknown mechanism of the effect of FTY720 on human CD4+ T cell modulation in multiple sclerosis and demonstrate the role of TCF-1 in human T cell activation and effector function.


Subject(s)
CD4-Positive T-Lymphocytes/metabolism , Fingolimod Hydrochloride/pharmacology , Immunosuppressive Agents/pharmacology , Multiple Sclerosis/metabolism , T Cell Transcription Factor 1/biosynthesis , Up-Regulation/physiology , CD4-Positive T-Lymphocytes/drug effects , Female , Fingolimod Hydrochloride/therapeutic use , Humans , Immunosuppressive Agents/therapeutic use , Male , Multiple Sclerosis/drug therapy , Up-Regulation/drug effects
15.
J Virol ; 87(1): 257-72, 2013 Jan.
Article in English | MEDLINE | ID: mdl-23077300

ABSTRACT

Members of the tripartite interaction motif (TRIM) family of E3 ligases are emerging as critical regulators of innate immunity. To identify new regulators, we carried out a screen of 43 human TRIM proteins for the ability to activate NF-κB, AP-1, and interferon, hallmarks of many innate immune signaling pathways. We identified 16 TRIM proteins that induced NF-κB and/or AP-1. We found that one of these, TRIM62, functions in the TRIF branch of the TLR4 signaling pathway. Knockdown of TRIM62 in primary macrophages led to a defect in TRIF-mediated late NF-κB, AP-1, and interferon production after lipopolysaccharide challenge. We also discovered a role for TRIM15 in the RIG-I-mediated interferon pathway upstream of MAVS. Knockdown of TRIM15 limited virus/RIG-I ligand-induced interferon production and enhanced vesicular stomatitis virus replication. In addition, most TRIM proteins previously identified to inhibit murine leukemia virus (MLV) demonstrated an ability to induce NF-κB/AP-1. Interfering with the NF-κB and AP-1 signaling induced by the antiretroviral TRIM1 and TRIM62 proteins rescued MLV release. In contrast, human immunodeficiency virus type 1 (HIV-1) gene expression was increased by TRIM proteins that induce NF-κB. HIV-1 resistance to inflammatory TRIM proteins mapped to the NF-κB sites in the HIV-1 long terminal repeat (LTR) U3 and could be transferred to MLV. Thus, our work identifies new TRIM proteins involved in innate immune signaling and reinforces the striking ability of HIV-1 to exploit innate immune signaling for the purpose of viral replication.


Subject(s)
Adaptor Proteins, Signal Transducing/metabolism , HIV-1/immunology , Immunity, Innate , Leukemia Virus, Murine/immunology , Membrane Proteins/metabolism , Signal Transduction , Vesiculovirus/immunology , Adaptor Proteins, Signal Transducing/genetics , Gene Knockdown Techniques , Humans , Interferons/metabolism , Membrane Proteins/genetics , NF-kappa B/metabolism , Transcription Factor AP-1/metabolism
16.
J Virol ; 87(14): 7837-52, 2013 Jul.
Article in English | MEDLINE | ID: mdl-23658454

ABSTRACT

The interferon-induced transmembrane protein 3 (IFITM3) gene is an interferon-stimulated gene that inhibits the replication of multiple pathogenic viruses in vitro and in vivo. IFITM3 is a member of a large protein superfamily, whose members share a functionally undefined area of high amino acid conservation, the CD225 domain. We performed mutational analyses of IFITM3 and identified multiple residues within the CD225 domain, consisting of the first intramembrane domain (intramembrane domain 1 [IM1]) and a conserved intracellular loop (CIL), that are required for restriction of both influenza A virus (IAV) and dengue virus (DENV) infection in vitro. Two phenylalanines within IM1 (F75 and F78) also mediate a physical association between IFITM proteins, and the loss of this interaction decreases IFITM3-mediated restriction. By extension, similar IM1-mediated associations may contribute to the functions of additional members of the CD225 domain family. IFITM3's distal N-terminal domain is also needed for full antiviral activity, including a tyrosine (Y20), whose alteration results in mislocalization of a portion of IFITM3 to the cell periphery and surface. Comparative analyses demonstrate that similar molecular determinants are needed for IFITM3's restriction of both IAV and DENV. However, a portion of the CIL including Y99 and R87 is preferentially needed for inhibition of the orthomyxovirus. Several IFITM3 proteins engineered with rare single-nucleotide polymorphisms demonstrated reduced expression or mislocalization, and these events were associated with enhanced viral replication in vitro, suggesting that possessing such alleles may impact an individual's risk for viral infection. On the basis of this and other data, we propose a model for IFITM3-mediated restriction.


Subject(s)
Dengue Virus/physiology , Influenza A virus/physiology , Membrane Proteins/genetics , Membrane Proteins/metabolism , RNA-Binding Proteins/genetics , RNA-Binding Proteins/metabolism , Virus Replication/physiology , Amino Acid Sequence , Animals , Cell Culture Techniques , Cloning, Molecular , Conserved Sequence/genetics , DNA Mutational Analysis , DNA, Complementary/genetics , Dogs , HEK293 Cells , HeLa Cells , Humans , Immunoblotting , Immunoprecipitation , Madin Darby Canine Kidney Cells , Mass Spectrometry , Microscopy, Confocal , Models, Biological , Molecular Sequence Data , Polymorphism, Single Nucleotide/genetics , Protein Structure, Tertiary/genetics , Virus Replication/genetics
17.
PLoS Pathog ; 7(10): e1002337, 2011 Oct.
Article in English | MEDLINE | ID: mdl-22046135

ABSTRACT

To replicate, viruses must gain access to the host cell's resources. Interferon (IFN) regulates the actions of a large complement of interferon effector genes (IEGs) that prevent viral replication. The interferon inducible transmembrane protein family members, IFITM1, 2 and 3, are IEGs required for inhibition of influenza A virus, dengue virus, and West Nile virus replication in vitro. Here we report that IFN prevents emergence of viral genomes from the endosomal pathway, and that IFITM3 is both necessary and sufficient for this function. Notably, viral pseudoparticles were inhibited from transferring their contents into the host cell cytosol by IFN, and IFITM3 was required and sufficient for this action. We further demonstrate that IFN expands Rab7 and LAMP1-containing structures, and that IFITM3 overexpression is sufficient for this phenotype. Moreover, IFITM3 partially resides in late endosomal and lysosomal structures, placing it in the path of invading viruses. Collectively our data are consistent with the prediction that viruses that fuse in the late endosomes or lysosomes are vulnerable to IFITM3's actions, while viruses that enter at the cell surface or in the early endosomes may avoid inhibition. Multiple viruses enter host cells through the late endocytic pathway, and many of these invaders are attenuated by IFN. Therefore these findings are likely to have significance for the intrinsic immune system's neutralization of a diverse array of threats.


Subject(s)
Cytosol/virology , Influenza A virus/drug effects , Influenza, Human/immunology , Interferon-gamma/pharmacology , Membrane Proteins/metabolism , RNA-Binding Proteins/metabolism , Virus Internalization/drug effects , Animals , Chickens , Cytosol/drug effects , Cytosol/metabolism , HeLa Cells , Host-Pathogen Interactions , Humans , Influenza A virus/growth & development , Influenza A virus/pathogenicity , Influenza, Human/virology , Interferon-gamma/immunology , Membrane Proteins/immunology , RNA-Binding Proteins/immunology , Virus Replication
18.
J Virol ; 85(10): 5183-96, 2011 May.
Article in English | MEDLINE | ID: mdl-21345949

ABSTRACT

Previous studies identified clones of the U937 promonocytic cell line that were either permissive or nonpermissive for human immunodeficiency virus type 1 (HIV-1) replication. These clones were investigated further in the search for host restriction factors that could explain their differential capacity to support HIV-1 replication. Among known HIV-1 restriction factors screened, tripartite motif-containing protein 22 (TRIM22) was the only factor constitutively expressed in nonpermissive and absent in permissive U937 cells. Stable TRIM22 knockdown (KD) rescued HIV-1 long-terminal-repeat (LTR)-driven transcription in KD-nonpermissive cells to the levels observed in permissive cells. Conversely, transduction-mediated expression of TRIM22 in permissive cells reduced LTR-driven luciferase expression by ∼7-fold, supporting a negative role of TRIM22 in HIV-1 transcription. This finding was further confirmed in the human T cell line A3.01 expressing TRIM22. Moreover, overexpression of TRIM22 in 293T cells significantly impaired basal and phorbol myristate acetate-ionomycin-induced HIV-1 LTR-driven gene expression, whereas inhibition of tumor necrosis factor alpha-induced viral transcription was a consequence of lower basal expression. In agreement, TRIM22 equally inhibited an LTR construct lacking the tandem NF-κB binding sites. In addition, TRIM22 did not affect Tat-mediated LTR transactivation. Finally, these effects were independent of TRIM22 E3 ubiquitin-ligase activity. In the context of replication-competent virus, significantly higher levels of HIV-1 production were observed in KD-nonpermissive versus control nonpermissive U937 cells after infection. In contrast, lower peak levels of HIV-1 replication characterized U937 and A3.01 cells expressing TRIM22 versus their control transduced counterpart. Thus, nuclear TRIM22 significantly impairs HIV-1 replication, likely by interfering with Tat- and NF-κB-independent LTR-driven transcription.


Subject(s)
HIV-1/growth & development , HIV-1/immunology , Repressor Proteins/metabolism , Transcription, Genetic , Virus Replication , Cell Line , Humans , Minor Histocompatibility Antigens , Monocytes/immunology , Monocytes/virology , T-Lymphocytes/immunology , T-Lymphocytes/virology , Tripartite Motif Proteins
19.
Proc Natl Acad Sci U S A ; 106(40): 17019-24, 2009 Oct 06.
Article in English | MEDLINE | ID: mdl-19805154

ABSTRACT

Plasma cells daily secrete their own mass in antibodies, which fold and assemble in the endoplasmic reticulum (ER). To reach these levels, cells require pERp1, a novel lymphocyte-specific small ER-resident protein, which attains expression levels as high as BiP when B cells differentiate into plasma cells. Although pERp1 has no homology with known ER proteins, it does contain a CXXC motif typical for oxidoreductases. In steady state, the CXXC cysteines are locked by two parallel disulfide bonds with a downstream C(X)(6)C motif, and pERp1 displays only modest oxidoreductase activity. pERp1 emerged as a dedicated folding factor for IgM, associating with both heavy and light chains and promoting assembly and secretion of mature IgM.


Subject(s)
Endoplasmic Reticulum/metabolism , Immunoglobulin M/metabolism , Molecular Chaperones/metabolism , Plasma Cells/metabolism , Amino Acid Sequence , Animals , B-Lymphocytes/metabolism , B-Lymphocytes/ultrastructure , Cell Differentiation , Cell Line, Tumor , Electrophoresis, Gel, Two-Dimensional , Endoplasmic Reticulum Chaperone BiP , HeLa Cells , Heat-Shock Proteins/genetics , Heat-Shock Proteins/metabolism , Humans , Immunoblotting , Mass Spectrometry , Mice , Microscopy, Fluorescence , Microscopy, Immunoelectron , Molecular Chaperones/genetics , Oxidoreductases/metabolism , Plasma Cells/cytology , RNA Interference , Sulfhydryl Compounds/metabolism
20.
Retrovirology ; 8: 49, 2011 Jun 22.
Article in English | MEDLINE | ID: mdl-21696578

ABSTRACT

BACKGROUND: Vpx is a virion-associated protein encoded by SIVSM, a lentivirus endemic to the West African sooty mangabey (Cercocebus atys). HIV-2 and SIVMAC, zoonoses resulting from SIVSM transmission to humans or Asian rhesus macaques (Macaca mulatta), also encode Vpx. In myeloid cells, Vpx promotes reverse transcription and transduction by these viruses. This activity correlates with Vpx binding to DCAF1 (VPRBP) and association with the DDB1/RBX1/CUL4A E3 ubiquitin ligase complex. When delivered experimentally to myeloid cells using VSV G-pseudotyped virus-like particles (VLPs), Vpx promotes reverse transcription of retroviruses that do not normally encode Vpx. RESULTS: Here we show that Vpx has the extraordinary ability to completely rescue HIV-1 transduction of human monocyte-derived dendritic cells (MDDCs) from the potent antiviral state established by prior treatment with exogenous type 1 interferon (IFN). The magnitude of rescue was up to 1,000-fold, depending on the blood donor, and was also observed after induction of endogenous IFN and IFN-stimulated genes (ISGs) by LPS, poly(I:C), or poly(dA:dT). The effect was relatively specific in that Vpx-associated suppression of soluble IFN-ß production, of mRNA levels for ISGs, or of cell surface markers for MDDC differentiation, was not detected. Vpx did not rescue HIV-2 or SIVMAC transduction from the antiviral state, even in the presence of SIVMAC or HIV-2 VLPs bearing additional Vpx, or in the presence of HIV-1 VLPs bearing all accessory genes. In contrast to the effect of Vpx on transduction of untreated MDDCs, HIV-1 rescue from the antiviral state was not dependent upon Vpx interaction with DCAF1 or on the presence of DCAF1 within the MDDC target cells. Additionally, although Vpx increased the level of HIV-1 reverse transcripts in MDDCs to the same extent whether or not MDDCs were treated with IFN or LPS, Vpx rescued a block specific to the antiviral state that occurred after HIV-1 cDNA penetrated the nucleus. CONCLUSION: Vpx provides a tool for the characterization of a potent, new HIV-1 restriction activity, which acts in the nucleus of type 1 IFN-treated dendritic cells.


Subject(s)
Dendritic Cells/immunology , Dendritic Cells/virology , HIV-1/growth & development , Interferon Type I/immunology , Viral Regulatory and Accessory Proteins/metabolism , Cells, Cultured , Humans , Transduction, Genetic , Viral Regulatory and Accessory Proteins/immunology
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