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Kamel Khalili

Publications and source records attributed to Kamel Khalili.

At least 19 recordsLinked to original sources

In vivo genome editing of central nervous system SIV reservoirs in ART-suppressed rhesus macaques.

Latent human immunodeficiency virus type 1 (HIV-1) reservoirs in the central nervous system (CNS) may sustain viral persistence and neuroinflammation contributing to HIV-associated neurocognitive disorders (HAND) despite suppressive ART. AAV9-delivered CRISPR has successfully edited SIV proviral DNA in peripheral tissues with acceptable safety profiles, but the extent of in vivo genome editing in the brain remains unclear. Using SIV-infected rhesus macaques, we mapped intact proviral DNA across CNS regions and tested systemic AAV9-CRISPR-Cas9 targeting conserved sites within Ψ packaging signal and Gag region. Ten adult rhesus macaques were infected with genetically barcoded SIVmac239, suppressed with ART, then randomized to receive intravenous AAV9-SaCas9 with dual gRNAs (Ψ + Gag) or a Cas9-only control. At necropsy after viral rebound, SIV genomes were detected in multiple brain regions as well as lymphoid tissues, confirming the CNS as a persistent reservoir during ART. Barcode analysis revealed region-specific patterns consistent with compartmentalized CNS persistence. In CRISPR-treated animals, proviral editing was measurable across anatomically distinct CNS sites. These findings demonstrate that intact and potentially replication-competent virus persists in the primate brain under ART and that systemic AAV9-CRISPR can reach and edit proviral DNA in this sanctuary, supporting genome editing as a strategy toward durable remission of CNS reservoirs.

ART↗

Association of p65 and C/EBPbeta with HIV-1 LTR modulates transcription of the viral promoter.

In human immunodeficiency virus type 1 (HIV-1) latently infected cells, NF-kappaB (NF-kappaB) plays a critical role in the transcriptional induction of the HIV-1 promoter. The trans-activating ability of NF-kappaB can be modified by another nuclear factor C/EBPbeta that can physically bind to NF-kappaB and regulate its activity. Because the HIV-1 promoter also contains a C/EBPbeta site adjacent to the NF-kappaB site, the present study examined cooperative functional in vivo interaction of the p65 subunit of NF-kappaB and C/EBPbeta, and the impact of Tat in this event. We demonstrated that ectopic expression of p65 along with Tat increases p65 binding to HIV-1 LTR, and that this increase correlates with enhanced HIV-1 promoter activity. Further, co-expression of C/EBPbeta and Tat leads to a decrease in p65 binding, which allows C/EBPbeta to bind more efficiently to the LTR. Inhibition of p65 expression by siRNA significantly decreases C/EBPbeta-binding and LTR expression. Using ChIP assay, we confirmed the existence of an interchange between p65 and C/EBPbeta and their abilities to bind to the LTR in vivo. These observations demonstrate that a delicate balance of interaction between p65, C/EBPbeta, and Tat can dictate the level of HIV-1 LTR transcription.

CCAAT-Enhancer-Binding Protein-beta↗

Evidence for BAG3 modulation of HIV-1 gene transcription.

A family of co-chaperone proteins that share the Bcl-2-associated athanogene (BAG) domain are involved in a number of cellular processes, including proliferation and apoptosis. Among these proteins, BAG3 has received increased attention due to its high levels in several disease models and ability to associate with Hsp70 and a number of other molecular partners. BAG3 expression is stimulated during cell response to stressful conditions, such as exposure to high temperature, heavy metals, and certain drugs. Here, we demonstrate that BAG3 expression is elevated upon HIV-1 infection of human lymphocytes and fetal microglial cells. Furthermore, BAG3 protein was detectable in the cytoplasm of reactive astrocytes in HIV-1-associated encephalopathy biopsies, suggesting that induction of BAG3 is part of the host cell response to viral infection. To assess the impact of BAG3 upregulation on HIV-1 gene expression, we performed transcription assays and demonstrated that BAG3 can suppress transcription of the HIV-1 long terminal repeat (LTR) in microglial cells. This activity was mapped to the kappaB motif of the HIV-1 LTR. Results from in vitro and in vivo binding assays revealed that BAG3 suppresses interaction of the p65 subunit of NF-kappaB with the kappaB DNA motif of the LTR. Results from binding and transcriptional assay identified the C-terminus of BAG3 as a potential domain involved in the observed inhibitory effect of BAG3 on p65 activity. These observations reveal a previously unrecognized cell response, that is, an increase in BAG3, elicited by HIV-1 infection, and may provide a new avenue for the suppression of HIV-1 gene expression.

AIDS Dementia Complex↗

The role of Vpr in the regulation of HIV-1 gene expression.

Expression of the viral protein R, Vpr, of HIV-1 affects many biological events in host cells including cell cycle progression, and modulates HIV-1 gene transcription. Earlier studies implicating the cellular protein p21(WAF1) (p21) in regulation of HIV-1 transcription, led us to investigate the functional and physical interaction of Vpr and p21. Our results show that Vpr modestly activated HIV-LTR in cells lacking p21 gene. Here, we describe the mechanisms by which p21 and Vpr leading to stimulation of HIV-1 transcription. Data from the protein-protein interaction experiments revealed the ability of Vpr, p21 and p300 to form a complex. Further, we show that, Vpr interacts with the N- and the C-terminal domains of p21. Furthermore, in cells expressing Vpr, p21 localizes to both the cytoplasm and the nucleus. Interestingly, expression of Vpr alleviates p21-mediated inhibition of cell departure from G1 phase. Expression of a mutant Vpr, with arginine 73 altered to serine, did not affect the ability of p21 to cause cells arrest or its sub-cellular localization. These observations reveal a new cellular partner for Vpr, and provide a new therapeutic avenue for controlling HIV-1 expression.

Binding Sites↗

Regulation of the Pur-alpha promoter by E2F-1.

Puralpha is a ubiquitously expressed multifunctional nucleic acid-binding protein that is involved in many cellular processes including transcriptional regulation, the cell cycle, oncogenic transformation, and post-natal brain development. Previously, Puralpha protein was found to bind to E2F-1, inhibit E2F-1 transcriptional activity, and reverse the effects of ectopic E2F-1 expression on cell growth. Also Puralpha binds to a GC/GA-rich sequence within its own promoter and inhibits gene expression, that is, Puralpha is autoregulated. We now report that the Puralpha promoter (pPuralpha) is induced by E2F-1 and that this activity maps to a consensus E2F-1 binding motif that is juxtaposed to the Puralpha binding site. Deletion mutants of the E2F-1 protein showed that the region between amino acid residues 88-241 is important for this activity. E2F-1-associated activation of the pPuralpha was inhibited by co-expression of Puralpha, pRb, and an RNA species with specific binding to E2F-1. Chromatin immunoprecipitation (ChIP) assay using primers that flanked the juxtaposed Puralpha and E2F-1 binding sites verified the presence of Puralpha and E2F-1 on the pPuralpha in vivo. In a Tet-inducible cell line, Puralpha delayed cell cycle progression. Thus, E2F-1 and Puralpha interplay appears to be involved in the regulation of Puralpha expression and the cell cycle.

5' Untranslated Regions↗

IRS-1-Rad51 nuclear interaction sensitizes JCV T-antigen positive medulloblastoma cells to genotoxic treatment.

The large T-antigen from human polyomavirus JC (JCV T-antigen) is suspected to play a role in malignant transformation. Previously, we reported that JCV T-antigen requires the presence of a functional insulin-like growth factor I receptor (IGF-IR) for transformation of fibroblasts and for survival of medulloblastoma cell lines; that IGF-IR is phosphorylated in medulloblastoma biopsies and that JCV T-antigen inhibits homologous recombination-directed DNA repair, causing accumulation of mutations. Here we are evaluating whether JCV T-antigen positive and negative mouse medulloblastoma cell lines, which significantly differ in their tumorigenic properties, are also different in their abilities to repair double strand breaks of DNA (DSBs). Our results show that despite much stronger tumorigenic potential, JCV T-antigen positive medulloblastoma cells are more sensitive to genotoxic agents (cisplatin and gamma-irradiation). Subsequent analysis of DNA repair of DSBs indicated that homologous recombination-directed DNA repair (HRR) was selectively attenuated in JCV T-antigen positive medulloblastoma cells. JCV T-antigen did not affect HRR directly. In the presence of JCV T-antigen, insulin receptor substrate 1 (IRS-1) translocated to the nucleus where it co-localized with Rad51, possibly attenuating HRR.

Animals↗

MH2 domain of Smad3 reduces HIV-1 Tat-induction of cytokine secretion.

HIV-1 infection of the central nervous system (CNS) is associated with dysregulation of several important cytokines and chemokines, which are involved in inflammatory process. Earlier studies ascribed a critical role for Tat, a potent viral transcription activator, in this process by enhancing the expression of several immunomodulators including TGFbeta and MCP-1. Investigation of signaling pathways which are controlled by these cytokines led to identification of MH2 domain of Smad3, the downstream activator of TGFbeta pathway, as a modulator of MCP-1 promoter activity. The level of MCP-1 is increased in AIDS patients with neurologic problems, through recruitment of inflammatory cells, which can contribute to neuropathogenesis of AIDS. Therefore, we attempted to investigate the effect of MH2 on expression of MCP-1 and other immunolmodulators in CNS cells. By employing an adenovirus expression vector, we demonstrated that MH2 can decrease the levels of Tat-induced activation of MCP-1 and several other cytokines and chemokines in astrocytic cells. In addition, we showed that MH2 significantly reduced the activity of cytokines produced by cultures of adenovirus-MH2 transduced cells as measured by the transmigration of human PBMC cells. Thus, MH2 domain of Smad3 is a potential agent that may be developed as an inhibitor for the cytokine-mediated inflammatory responses in the brain and may have the potential to prevent transmigration of HIV-1-infected monocytes across the blood brain barrier in AIDS patients.

AIDS Dementia Complex↗

Reciprocal transactivation between HIV-1 and other human viruses.

A variety of rare clinical syndromes are seen with strikingly increased prevalence in HIV-1-infected individuals, many with underlying viral etiologies. The emergence of these diseases in AIDS reflects a reduction in the ability of the immune system to mount an adequate defense against viruses in general due to the damage inflicted to the immune system by HIV-1 infection. However, in many cases, it has been found that HIV-1 can enhance the level of expression and hence the life cycle of other viruses independently of immunosuppression through specific interactions with the viruses. This can occur either directly by HIV-1 proteins such as Tat enhancing the activity of heterologous viral promoters, and/or indirectly by HIV-1 inducing the expression of cytokines and activation of their downstream signaling that eventually promotes the multiplication of the other virus. In a reciprocal manner, the effects of other viruses can enhance the pathogenicity of HIV-1 infection in individuals with AIDS through stimulation of the HIV-1 promoter activity and genome expression. The purpose of this review is to examine the cross-interactions between these viruses and HIV-1.

Gene Expression Regulation, Viral↗

HIV-1 associated dementia: symptoms and causes.

Despite the use of highly active antiretroviral therapy (HAART), neuronal cell death remains a problem that is frequently found in the brains of HIV-1-infected patients. HAART has successfully prevented many of the former end-stage complications of AIDS, however, with increased survival times, the prevalence of minor HIV-1 associated cognitive impairment appears to be rising among AIDS patients. Further, HIV-1 associated dementia (HAD) is still prevalent in treated patients as well as attenuated forms of HAD and CNS opportunistic disorders. HIV-associated cognitive impairment correlates with the increased presence in the CNS of activated, though not necessarily HIV-1-infected, microglia and CNS macrophages. This suggests that indirect mechanisms of neuronal injury and loss/death occur in HIV/AIDS as a basis for dementia since neurons are not themselves productively infected by HIV-1. In this review, we discussed the symptoms and causes leading to HAD. Outcome from this review will provide new information regarding mechanisms of neuronal loss in AIDS patients.

AIDS Dementia Complex↗

Role of Pur alpha in targeting mRNA to sites of translation in hippocampal neuronal dendrites.

Using genetic inactivation in the mouse, PURA, encoding Pur alpha, is demonstrated to be essential for developmentally-timed dendrite formation in the cerebellum and hippocampus. Comparison of RNA species bound by Pur alpha prompts the hypothesis that Pur alpha functions with non-coding RNA in transport of certain mRNA molecules to sites of translation in dendrites. Pur alpha binds to human BC200 RNA, implicated in dendritic targeting, and this has homologies to 7SL RNA, implicated in compartmentalized translation. Results using hippocampal rat neurons in situ show that Pur alpha binds to BC1 RNA, implicated in dendritic targeting as a mouse counterpart of BC200, and to mRNA molecules translated in dendrites; Pur alpha is specifically located in dendrites, where it is colocalized with Map2, but not in axons, where it fails to colocalize with Ankyrin G. Pur alpha and Staufen are colocalized at dendritic sites of mRNA translation. Microtubule disruptors inhibit Pur alpha dendritic targeting and allow its mislocalization to axons. Using mouse brain, double-RNA immunoprecipitation places Pur alpha together with Staufen or FMRP on BC1 RNA and specific mRNA species in vivo. These results help define a mechanism by which Pur alpha targets specific mRNA molecules to sites of dendritic translation.

Animals↗

Tubulin-mediated binding of human immunodeficiency virus-1 Tat to the cytoskeleton causes proteasomal-dependent degradation of microtubule-associated protein 2 and neuronal damage.

One of the hallmarks of human immunodeficiency virus (HIV)-1 associated pathology in the CNS is deterioration of neuronal processes. Although there is mounting evidence of neuronal toxicity and cell death induced by the HIV-1 transactivating factor Tat, the molecular events linked directly to its detrimental effect on neuronal cells remain unclear. In this study, we used rat embryonic cortical neurons and demonstrated that Tat causes rapid degradation of microtubule-associated protein 2 (MAP2) and the collapse of cytoskeletal filaments. The mechanism of Tat action on MAP2 stability involved Tat-mediated translocation of the proteasome to the site of microtubule filaments. Immunohistochemical analysis of clinical samples from patients with HIV encephalopathy further revealed a significant decrease in MAP2 with predominant cytoplasmic 20S in cortical neurons near microglial nodules. These findings indicate a novel mechanism for the action of Tat on neuronal cells. It involves proteasome-mediated MAP2 degradation and may account for the loss of MAP2 and neuronal damage observed in the brain of AIDS patients with neurological dysfunctions.

Animals↗

Glioblastoma multiforme with small cell neuronal-like component: association with human neurotropic JC virus.

The human polyomavirus JCV, the etiological agent of progressive multifocal leukoencephalopathy, has been associated with primitive neuroectodermal tumors and various glial-derived tumors, including glioblastoma multiforme (GBM). Here we describe the unique clinical case of a 54-year-old man who presented with headaches, hemiparesis and drowsiness. T1 and T2 magnetic resonance images revealed a large solid tumor with a cystic component located in the right temporal lobe, with extension into the parietal lobe. Histologically, the tumor was composed of two areas, a main area of large neoplastic cells with pleomorphic atypical nuclei and abundant cytoplasm, which by immunohistochemistry was reactive for glial fibrillary acidic protein, mixed with several foci of poorly differentiated tumoral cells with elongated nuclei and scant cytoplasm, negative for GFAP, but robustly immunoreactive for synaptophysin and phosphoneurofilaments. Results from PCR in laser capture microdissected cells from both areas of the tumor revealed the presence of DNA sequences corresponding to the early, late and control regions (CR) of the JCV genome and expression of JCV proteins T-antigen and Agnoprotein in both phenotypes. No evidence for capsid protein was observed, excluding productive viral infection. Sequencing demonstrated the presence of the JCV Mad-1 strain with distinct point mutations in the CR of isolates from both, GBM and small cell architectural areas. The presence of JCV DNA sequences and expression of viral proteins further reinforces the role of the widely spread human neurotropic virus in early transformation and in the development of brain tumors.

Brain Neoplasms↗

Human polyomavirus JCV late leader peptide region contains important regulatory elements.

Transcription is a complex process that relies on the cooperative interaction between sequence-specific factors and the basal transcription machinery. The strength of a promoter depends on upstream or downstream cis-acting DNA elements, which bind transcription factors. In this study, we investigated whether DNA elements located downstream of the JCV late promoter, encompassing the late leader peptide region, which encodes agnoprotein, play regulatory roles in the JCV lytic cycle. For this purpose, the entire coding region of the leader peptide was deleted and the functional consequences of this deletion were analyzed. We found that viral gene expression and replication were drastically reduced. Gene expression also decreased from a leader peptide point mutant but to a lesser extent. This suggested that the leader peptide region of JCV might contain critical cis-acting DNA elements to which transcription factors bind and regulate viral gene expression and replication. We analyzed the entire coding region of the late leader peptide by a footprinting assay and identified three major regions (region I, II and III) that were protected by nuclear proteins. Further investigation of the first two protected regions by band shift assays revealed a new band that appeared in new infection cycles, suggesting that viral infection induces new factors that interact with the late leader peptide region of JCV. Analysis of the effect of the leader peptide region on the promoter activity of JCV by transfection assays demonstrated that this region has a positive and negative effect on the large T antigen (LT-Ag)-mediated activation of the viral early and late promoters, respectively. Furthermore, a partial deletion analysis of the leader peptide region encompassing the protected regions I and II demonstrated a significant down-regulation of viral gene expression and replication. More importantly, these results were similar to that obtained from a complete deletion of the late leader peptide region, indicating the critical importance of these two protected regions in JCV regulation. Altogether, these findings suggest that the late leader peptide region contains important regulatory elements to which transcription factors bind and contribute to the JCV gene regulation and replication.

Blotting, Northern↗

T-antigen of the human polyomavirus JC attenuates faithful DNA repair by forcing nuclear interaction between IRS-1 and Rad51.

JC polyomavirus (JCV), which infects 90% of the human population, is detectable in human tumors. Its early protein, JCV T-antigen, transforms cells in vitro and is tumorigenic in experimental animals. Although T-antigen-mediated transformation involves genetic alterations of the affected cells, the mechanism underlying this genomic instability is not known. We show that JCV T-antigen inhibits homologous recombination DNA repair (HRR), which results in an accumulation of mutations. T-antigen does not operate directly but utilizes a cytosolic molecule, insulin receptor substrate 1 (IRS-1). Following T-antigen-mediated nuclear translocation, IRS-1 binds Rad51 at the site of damaged DNA. This T-antigen-mediated inhibition of HRR does not function in cells lacking IRS-1, and can be reproduced in the absence of T-antigen by IRS-1 with artificial nuclear localization signal. Our observations define a new mechanism by which viral protein utilizes cytosolic molecule to inhibit faithful DNA repair, and suggest how polyomaviruses could compromise stability of the genome. (c) 2005 Wiley-Liss, Inc.

Animals↗

JC virus large T-antigen and IGF-I signaling system merge to affect DNA repair and genomic integrity.

The progression of cancer is often associated with genomic instability, which may develop as a result of compromised defense mechanisms responsible for the maintenance of chromosomal integrity. These include defects in telomere preservation, chromosomal segregation, and DNA repair. In this review, we discuss molecular interactions between viral and cellular signaling components, which interfere with DNA repair mechanisms, and possibly contribute to the development of a mutagenic phenotype. Our studies indicate that large T-antigen from the human polyomavirus JC (JCV T-antigen) inhibits homologous recombination directed DNA repair (HRR)-causing accumulation of mutations in the affected cells (JCP 2005, in press). Surprisingly, T-antigen does not operate directly, but utilizes insulin receptor substrate 1 (IRS-1), which is the major signaling molecule for insulin-like growth factor I receptor (IGF-IR). Following T-antigen-mediated nuclear translocation, IRS-1 binds Rad51 at the site of damaged DNA. This T-antigen-mediated inhibition of HRR does not function in cells lacking IRS-1, and can be reproduced in the absence of T-antigen by IRS-1 with an artificial nuclear localization signal. The interplay described between the IGF-IR signaling system and JCV T-antigen in the process of DNA repair could be relevant, since nearly 90% of the human population is seropositive for JC virus, JCV T-antigen transforms cells in vitro, is tumorigenic in experimental animals, and the presence of JC virus has been shown in an increasing number of biopsies of human cancer.

Animals↗

Cooperativity between Rad51 and C/EBP family transcription factors modulates basal and Tat-induced activation of the HIV-1 LTR in astrocytes.

Transcription of the HIV-1 genome is a complex event that requires functional and physical communication of cellular proteins that recognize the LTR sequence with viral proteins, most notably, Tat. Moreover, studies have revealed the ability of Tat to induce transcription of a variety of cellular genes whose products can affect the status of cells, thus contributing to the pathogenesis of AIDS. Recently, we demonstrated that expression of Tat in astrocytes and other neural cells leads to upregulation of Rad51, a major component of DNA repair via homologous recombination. The unscheduled upregulation of Rad51, in turn, has an impact upon the extent of chromosomal abnormalities that are seen in Tat-producing cells. Here, we asked whether an elevation in Rad51 levels influences the extent of viral gene transcription in astrocytic cells. Our results demonstrate that ectopic expression of Rad51 enhances the basal- and the Tat-induced transcription of the LTR promoter. This event requires cooperativity from the C/EBP family of transcription factors including C/EBPbeta and C/EBPbeta homologous protein (CHOP). Similar to Tat, we showed that Rad51 interacts with C/EBPbeta and augments its interaction with the DNA motif spanning nucleotides -120 to -94 of the LTR. Interestingly, Tat exhibited the capacity to augment the synergism between Rad51 and C/EBPbeta. Our results also demonstrate that the level of activation of the LTR by CHOP and Tat, either alone or together, is elevated in the presence of the SW1/SNF1 chromatin remodeling complex. These observations unravel a new pathway for Tat activation of the LTR that includes the positive feedback loop involving Rad51 and C/EBPbeta family proteins.

Astrocytes↗

Dysregulation of NGF-signaling and Egr-1 expression by Tat in neuronal cell culture.

Examination of signal transduction pathways that modulate neuronal cell differentiation and protection against apoptosis has revealed a central role for the MAPK/Erk cascade. The activation of MAPK/Erk through the TrkA NGF signaling pathway is critical for growth and survival of neuronal cells. Here, we investigate the impact of HIV-1 Tat on the NGF-signaling pathway in SK-N-MC neuroblastoma cells. Expression of Tat decreased cell growth and induced apoptosis. Our results revealed dysregulation of various steps involved in the NGF pathway including suppression of MAPK, and inhibition of the promoter activity of Egr-1, a key pleiotropic mediator of the expression of genes involved in cell growth upon expression of Tat in SK-N-MC cells. Similarly, exposure of SK-N-MC to conditioned media derived from cells expressing Tat decreased phosphorylation of MAPK and reduced the level of Egr-1 protein expression in SK-N-MC cells. Furthermore, MAPK was able to phosphorylate Puralpha, a cellular protein that plays an important role in neuronal cell function and differentiation, and this was inhibited by Tat. The ability of Puralpha to interact with a GA/GC-rich sequence positioned upstream from the transcription start site of the Egr-1 promoter provided a rationale to examine Egr-1 expression. Expression of Tat decreased NGF-induced Egr-1 levels in SK-N-MC cells and reduced binding of Puralpha to the Egr-1 promoter. All of these observations support a model where the interplay between Tat and Puralpha dysregulates the NGF pathway including the MAPK/Erk network, resulting in reduced expression and activity of Egr-1 in neuronal cells.

Cell Cycle↗

Cdk9 phosphorylates p53 on serine 392 independently of CKII.

The tumor suppressor p53 is an important cellular protein, which controls cell cycle progression. Phosphorylation is one of the mechanisms by which p53 is regulated. Here we report the interaction of p53 with another key regulator, cdk9, which together with cyclin T1 forms the positive transcription elongation complex, p-TEFb. This complex cooperates with the HIV-1 Tat protein to cause the phosphorylation of the carboxyl terminal domain (CTD) of RNA polymerase II and this facilitates the elongation of HIV-1 transcription. We demonstrate that cdk9 phosphorylates p53 on serine 392 through their direct physical interaction. Results from protein-protein interaction assays revealed that cdk9 interacts with the C-terminal domain (aa 361-393) of p53, while p53 interacts with the N-terminal domain of cdk9. Transfection and protein binding assays (EMSA and ChIP) demonstrated the ability of p53 to bind and activate the cdk9 promoter. Interestingly, cdk9 phosphorylates serine 392 of p53, which could be also phosphorylated by casein kinase II. Kinase assays demonstrated that cdk9 phosphorylates p53 independently of CKII. These studies demonstrate the existence of a feedback-loop between p53 and cdk9, pinpointing a novel mechanism by which p53 regulates the basal transcriptional machinery.

Brain Neoplasms↗