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1.  Heterogeneity and Breadth of Host Antibody Response to KSHV Infection Demonstrated by Systematic Analysis of the KSHV Proteome 
PLoS Pathogens  2014;10(3):e1004046.
The Kaposi sarcoma associated herpesvirus (KSHV) genome encodes more than 85 open reading frames (ORFs). Serological evaluation of KSHV infection now generally relies on reactivity to just one latent and/or one lytic protein (commonly ORF73 and K8.1). Most of the other polypeptides encoded by the virus have unknown antigenic profiles. We have systematically expressed and purified products from 72 KSHV ORFs in recombinant systems and analyzed seroreactivity in US patients with KSHV-associated malignancies, and US blood donors (low KSHV seroprevalence population). We identified several KSHV proteins (ORF38, ORF61, ORF59 and K5) that elicited significant responses in individuals with KSHV-associated diseases. In these patients, patterns of reactivity were heterogeneous; however, HIV infection appeared to be associated with breadth and intensity of serological responses. Improved antigenic characterization of additional ORFs may increase the sensitivity of serologic assays, lead to more rapid progresses in understanding immune responses to KSHV, and allow for better comprehension of the natural history of KSHV infection. To this end, we have developed a bead-based multiplex assay detecting antibodies to six KSHV antigens.
Author Summary
Kaposi sarcoma-associated herpesvirus (KSHV) is the cause of Kaposi sarcoma, primary effusion lymphoma and a form of multicentric Castleman's disease, affecting mainly persons with HIV, other immunosuppressed patients and elderly men. Such diseases are most common where KSHV prevalence is high, in sub-Saharan Africa and the Mediterranean, and amongst men who have sex with men. Various assays for the serodiagnosis of KSHV have been developed to investigate global KSHV epidemiology. ELISAs utilizing one lytic (K8.1) and one latent antigen (ORF73) are often used. However, a more complete characterization of immune responses to all KSHV antigens may have important epidemiologic and clinical applications. We systematically expressed and purified 73 of the 85 proteins encoded by KSHV and analysed serologic responses in patients with KSHV-associated malignancies compared to healthy subjects. We identified significant reactivity to ORF38, ORF61, ORF59 and K5, in addition to the known K8.1, ORF73 and ORF65. Reactivity patterns were varied; however, HIV infected individuals were reactive to more antigens, with greater intensity. Next, we developed a bead-based assay that can test a small sample simultaneously for six KSHV antigens. The new tool can improve the detection of KSHV and the characterization of asymptomatic infection and KSHV associated diseases.
doi:10.1371/journal.ppat.1004046
PMCID: PMC3968157  PMID: 24675986
3.  Intra-individual variability over time in serum cytokine levels among participants in the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial 
Cytokine  2011;56(2):145-148.
Background
Serum measurements of cytokines, mediators of various B cell and T cell activities, are important markers of inflammation and immune dysregulation. We assessed the reproducibility of serum cytokine measurements over a five-year period among participants in the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial (PLCO).
Methods
Levels of 13 cytokines [interleukin (IL) 1β, IL-2, IL-4, IL-5, IL-6, IL-7, IL-8, IL-10, IL-12p70, IL-13, interferon-gamma (IFNγ), granulocyte macrophage colony-stimulating factor (GM-CSF), and tumor necrosis factor-α (TNFα)] in stored sera from three collections (study baseline, +1 yr, and +5 yr) among 28 randomly selected PLCO participants were measured using a high-sensitivity Luminex xMap-based multiplex panel. Within- and between-subject components of variance were estimated from random effects models and were used to calculate the coefficient of variation (CV) and intraclass correlation coefficient (ICC) for analytes with <30% of samples below the limit of detection (LOD). Spearman correlation coefficients between measurements of the same analyte over time and between analytes were also calculated.
Results
Among the six cytokines with <30% of samples below the LOD, we observed excellent reproducibility for IL-6, IL-7, IL-13, and TNFα (ICC ≥ 0.73), and fair to good reproducibility for IL-8 (ICC = 0.55) and IL-10 (ICC = 0.60). Spearman correlation coefficients comparing paired measurements of each cytokine at baseline and at +5 yr were high (ρ ≥ 0.74) with the exception of IL-10 (ρ = 0.44).
Conclusions
These results suggest that measurements of most of the cytokines evaluated in this study were highly reproducible over a five-year period.
doi:10.1016/j.cyto.2011.06.012
PMCID: PMC3185107  PMID: 21764327
cytokines; inflammation; variability; serum; cancer
4.  Pre-diagnostic serum levels of cytokines and other immune markers and risk of non-Hodgkin lymphoma 
Cancer research  2011;71(14):4898-4907.
While severe immune dysregulation is an established risk factor for non-Hodgkin lymphoma (NHL), it is unclear whether subclinical immune system function influences lymphomagenesis. To address this question, we conducted a nested case-control study within the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial to investigate whether circulating levels of cytokines and other immune markers are associated with future risk of NHL. Selected cytokines [interleukin (IL)-4, IL-6, IL-10, tumor necrosis factor (TNF)-α] and other immune markers [soluble TNF receptor 1 (sTNF-R1), sTNF-R2, C-reactive protein (CRP), sCD27] were measured in prediagnostic serum specimens from 297 incident NHL cases and 297 individually matched controls. Odds ratios (OR) and 95% confidence intervals (CI) relating quartiles of analyte concentration to NHL risk were calculated using conditional logistic regression. Statistically significant associations with increased NHL risk were observed for elevated serum levels of sTNF-R1 (quartile 4 vs. quartile 1: OR 1.7, 95% CI 1.1–2.8; Ptrend=0.02) and sCD27 (OR 5.3, 95% CI 2.9–9.4; Ptrend<0.0001). These associations remained in analyses of cases diagnosed 6+ years following blood collection (sTNF-R1: OR 2.1, 95% CI 1.0–4.0, Ptrend=0.01; sCD27: OR 4.1, 95% CI 1.9–8.5, Ptrend=0.0001). Elevated levels of IL-10, TNF-α and sTNF-R2 were also significantly associated with increased risk of NHL overall; however, these associations weakened with increasing time from blood collection to case diagnosis, and were null for cases diagnosed 6+ years post-collection. Our findings for sTNF-R1 and sCD27, possible markers for inflammatory and B-cell stimulatory states respectively, support a role for subclinical inflammation and chronic B-cell stimulation in lymphomagenesis.
doi:10.1158/0008-5472.CAN-11-0165
PMCID: PMC3138883  PMID: 21632552
non-Hodgkin lymphoma; cohort studies; serum; cytokines; soluble markers; immune system
6.  KSHV MicroRNA Sequence Analysis and KS Risk in an European AIDS-KS Case Control Study 
The Journal of infectious diseases  2010;202(7):1126-1135.
Background
We recently identified polymorphisms in KSHV encoded microRNA (miRNA) sequences from clinical subjects. Here, we examine whether any of these may contribute to KS risk in a European AIDS-KS case control study.
Methods
KSHV viral load in peripheral blood was determined by real-time quantitative PCR. Samples that had detectable viral loads were used to amplify the 2.8 kbp microRNA encoding region plus a 646 bp fragment of the K12/T0.7 gene. Additionally, we characterized an 840 bp fragment of the K1 gene to determine KSHV subtypes.
Results
KSHV viral DNA was detected in PBMC of 49.6% cases and 6.8% controls and viral loads tended to be higher in cases. Sequences from the miRNA encoding regions were conserved overall but distinct polymorphisms were detected some of which occurred in pri-miRNAs, pre-miRNAs or mature miRNAs.
Conclusions
Patients with Kaposi’s sarcoma were more likely to have detectable viral loads than controls without disease. Despite high conservation in KSHV miRNA encoded sequences, polymorphisms were observed including some that have been previously reported. Some polymorphisms could affect mature miRNA processing and appear to be associated with KS risk.
doi:10.1086/656045
PMCID: PMC2932837  PMID: 20715927
7.  Lack of Detection of Xenotropic Murine Leukemia Virus-Related Virus in HIV-1 Lymphoma Patients 
Advances in Virology  2011;2011:797820.
Xenotropic murine leukemia virus-related virus (XMRV) is a gammaretrovirus reported to be associated with human prostate cancer and chronic fatigue syndrome. Since retroviruses cause various cancers, and XMRV replication might be facilitated by HIV-1 co-infection, we asked whether certain patients with HIV-associated lymphomas are infected with XMRV. Analysis of PMBCs and plasma from 26 patients failed to detect XMRV by PCR, ELISA, or Western blot, suggesting a lack of association between XMRV and AIDS-associated lymphomas.
doi:10.1155/2011/797820
PMCID: PMC3265315  PMID: 22312354
8.  Serum cytokine analysis in a positive chemoprevention trial: Selenium, Interleukin-2 and an association with squamous preneoplastic disease 
This study represents a multiplex cytokine analysis of serum from a 10-month randomized, controlled trial of 238 subjects that investigated the effects of selenomethionine and/or celecoxib in subjects with mild or moderate esophageal squamous dysplasia. The original chemoprevention study found that among those with mild dysplasia, selenomethionine treatment favorably altered dysplasia grade. The current analysis found that selenomethionine down-regulated IL-2 by 9% (p=0.04), while celecoxib down-regulated IL-7 by 11% (p=0.006) and up-regulated IL-13 by 17% (p=0.008). In addition, an increase in IL-7 tertile from baseline to t10 was significantly associated with an increase in dysplasia grade, both overall (OR=1.47, p=0.03) and among those with mild dysplasia at t0 (OR=2.53 p=0.001). An increase in IL-2 tertile from baseline to t10 was also non-significantly associated with worsening dysplasia for all participants (OR=1.32 p=0.098), and significantly associated with worsening dysplasia among those with mild dysplasia at baseline (OR=2.0 p=0.01). The association of increased IL-2 with worsening dysplasia remained significant in those on selenomethionine treatment who began the trial with mild dysplasia (OR=2.52 p=0.03). The current study shows that selenomethionine supplementation decreased serum IL-2 levels, while celecoxib treatment decreased IL-7 levels and increased IL-13 levels during a 10 month randomized chemoprevention trial. An increase in IL-2 or IL-7 was associated with increased severity of dysplasia over the course of the trial, especially in those who began the trial with mild dysplasia. The favorable effect of selenomethionine on esophageal dysplasia in the original trial may have been mediated in part by its effect on reducing levels of IL-2.
doi:10.1158/1940-6207.CAPR-09-0269
PMCID: PMC2900463  PMID: 20587703
chemoprevention; interleukin-2; preneoplasia; gastrointestinal tract; selenium
9.  Reactivation of Kaposi’s sarcoma-associated herpesvirus by natural products from Kaposi’s sarcoma endemic regions 
Kaposi’s sarcoma (KS) and its causative agent, Kaposi’s sarcoma associated herpesvirus (KSHV/HHV-8), a gamma2 herpesvirus, have distinctive geographical distributions that are largely unexplained. We propose the “oncoweed” hypothesis to explain these differences, namely that environmental cofactors present in KS endemic regions cause frequent reactivation of KSHV in infected subjects, leading to increased viral shedding and transmission leading to increased prevalence of KSHV infection as well as high viral load levels and antibody titers. Reactivation also plays a role in the pathogenesis of KSHV-associated malignancies. To test this hypothesis, we employed an in vitro KSHV reactivation assay that measured increases in KSHV viral load in KSHV infected primary effusion lymphoma (PEL) cells and screened aqueous natural product extracts from KS endemic regions. Of 4,842 extracts from 38 countries, 184 (5%) caused KSHV reactivation. Extracts that caused reactivation came from a wide variety of plant families, and extracts from Africa, where KSHV is highly prevalent, caused the greatest level of reactivation. Time course experiments were performed using 28 extracts that caused the highest levels of reactivation. The specificity of the effects on viral replication was examined using transcriptional profiling of all viral mRNAs. The array data indicated that the natural extracts caused an ordered cascade of lytic replication similar to that seen after induction with synthetic activators. These in vitro data provide support for the “oncoweed” hypothesis by demonstrating basic biological plausibility.
doi:10.1002/ijc.22205
PMCID: PMC2857915  PMID: 17066452
Kaposi’s sarcoma associated herpesvirus; natural products; reactivation
10.  Hepatitis C Virus Genotype 4 in Ugandan Children and Their Mothers 
Emerging Infectious Diseases  2006;12(9):1440-1443.
In Kampala, Uganda, in 2001, hepatitis C virus antibodies were found in 27 (4%) of 603 children and in 62 (12%) of 525 of their mothers. However, only ≈10% of positive results were confirmed by reverse transcription–PCR, which suggests frequent false-positive results or viral clearance. All sequenced types were genotype 4.
doi:10.3201/eid1209.040168
PMCID: PMC3294722  PMID: 17073099
hepatitis C virus; genotype 4; Africa; epidemiology; phylogeny; sequencing; sickle cell anemia; transmission
11.  Infection of Lymphoid Cells by Integration-Defective Human Immunodeficiency Virus Type 1 Increases De Novo Methylation 
Journal of Virology  2001;75(20):9753-9761.
DNA methylation, by regulating the transcription of genes, is a major modifier of the eukaryotic genome. DNA methyltransferases (DNMTs) are responsible for both maintenance and de novo methylation. We have reported that human immunodeficiency virus type 1 (HIV-1) infection increases DNMT1 expression and de novo methylation of genes such as the gamma interferon gene in CD4+ cells. Here, we examined the mechanism(s) by which HIV-1 infection increases the cellular capacity to methylate genes. While the RNAs and proteins of all three DNMTs (1, 3a, and 3b) were detected in Hut 78 lymphoid cells, only the expression of DNMT1 was significantly increased 3 to 5 days postinfection. This increase was observed with either wild-type HIV-1 or an integrase (IN) mutant, which renders HIV replication defective, due to the inability of the provirus to integrate into the host genome. Unintegrated viral DNA is a common feature of many retroviral infections and is thought to play a role in pathogenesis. These results indicate another mechanism by which unintegrated viral DNA affects the host. In addition to the increase in overall genomic methylation, hypermethylation and reduced expression of the p16INK4A gene, one of the most commonly altered genes in human cancer, were seen in cells infected with both wild-type and IN-defective HIV-1. Thus, infection of lymphoid cells with integration-defective HIV-1 can increase the methylation of CpG islands in the promoters of genes such as the p16INK4A gene, silencing their expression.
doi:10.1128/JVI.75.20.9753-9761.2001
PMCID: PMC114547  PMID: 11559808

Results 1-11 (11)