Prevention of Viral Hepatitis and HIV in Drug Users - A Hepatitis B Model for HIV & An HB Vaccine Model for HIV Vaccine Trials in Drug Users (DASH)
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PROVIDER: PRJNA693897 | ENA |
REPOSITORIES: ENA
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Project description:Prevention of Viral Hepatitis and HIV in Drug Users - A Hepatitis B Model for HIV & An HB Vaccine Model for HIV Vaccine Trials in Drug Users (DASH)
| PRJNA693898 | ENA
Project description:HIV and Methamphetamine study - Translational Methamphetamine AIDS Research Center - Dopamine-regulated inflammatory biomarkers A digital transcript panel was custom-made based on Hs_NeuroPath_v1 (Nanostring) to accommodate dopamine-regulated inflammatory genes that were previously identified in vitro, and hypothesized to cluster HIV+ Methamphetamine users.
2024-07-31 | GSE273630 | GEO
Project description:<p>The overarching goal of this project is to identify and characterize genetic determinants of HIV 1 susceptibility and resistance in samples of African American (AA) and European American (EA) injection drug users (IDUs) by conducting (1) a case/control genome-wide association (GWA) study of HIV 1 infection (positive/negative); (2) a case-only GWA study of viral load among HIV+ IDUs. The study uses existing samples and data from Urban Health Study (UHS) (PI: Alex Kral), which was the longest-running study of street-recruited IDUs in North America, from 1986-2005. UHS was a serial, cross-sectional sero-epidemiological study. Data were collected every 6 months in communities with a high prevalence of injection drug use in the San Francisco Bay Area. It used targeted sampling in neighborhoods at easily accessible community field sites, such as churches, single room occupancy hotels, and community centers. Eligibility criteria for initial entry to the study were (1) injection drug use in past 30 days; (2) ability to provide informed consent; and (3) age 18 or older. The UHS cohort includes over 9,000 African American and European American IDUs whose serum samples have been stored and data are available on HIV antibody status, HIV risk behaviors, drug abuse and demographics.</p> <p>The current study includes 984 HIV+ cases and 2,243 HIV- controls. Approximately two HIV- controls per case were frequency matched on: (1) self-reported ancestry; (2) sex; (3) age; (4) year of ascertainment; and (5) HIV risk class. This GWAS (DA026141) was funded by the National Institute on Drug Abuse (NIDA; PI: Eric O. Johnson). Funding support for genotyping, which was performed at the Johns Hopkins University Center for Inherited Disease Research (CIDR), was provided by NIDA and the NIH contract "High throughput genotyping for studying the genetic contributions to human disease"(HHSN268200782096C). </p>
| phs000454.v1.p1 | EGA
Project description:<p>The overarching goal of this project is to identify and characterize genetic determinants of HIV 1 susceptibility and resistance in samples of African American (AA) and European American (EA) injection drug users (IDUs) by conducting (1) a case/control genome-wide association (GWA) study of HIV 1 infection (positive/negative); (2) a case-only GWA study of viral load among HIV+ IDUs. The study uses existing samples and data from Urban Health Study (UHS) (PI: Alex Kral), which was the longest-running study of street-recruited IDUs in North America, from 1986-2005. UHS was a serial, cross-sectional sero-epidemiological study. Data were collected every 6 months in communities with a high prevalence of injection drug use in the San Francisco Bay Area. It used targeted sampling in neighborhoods at easily accessible community field sites, such as churches, single room occupancy hotels, and community centers. Eligibility criteria for initial entry to the study were (1) injection drug use in past 30 days; (2) ability to provide informed consent; and (3) age 18 or older. The UHS cohort includes over 9,000 African American and European American IDUs whose serum samples have been stored and data are available on HIV antibody status, HIV risk behaviors, drug abuse and demographics.</p> <p>The current study includes 984 HIV+ cases and 2,243 HIV- controls. Approximately two HIV- controls per case were frequency matched on: (1) self-reported ancestry; (2) sex; (3) age; (4) year of ascertainment; and (5) HIV risk class. This GWAS (DA026141) was funded by the National Institute on Drug Abuse (NIDA; PI: Eric O. Johnson). Funding support for genotyping, which was performed at the Johns Hopkins University Center for Inherited Disease Research (CIDR), was provided by NIDA and the NIH contract "High throughput genotyping for studying the genetic contributions to human disease"(HHSN268200782096C). </p>
| phs000454 | dbGaP
Project description:Methcathinone (ephedrone) is relatively easily accessible for abuse. Its users develop an extrapyramidal syndrome and it is not known if this is caused by methcathinone itself, by side-ingredients (manganese), or both. In the present study we aimed to clarify molecular mechanisms underlying this condition. We used microarrays to analyze whole genome gene expression patterns of peripheral blood from 20 methcathinone users and 20 matched controls. Gene expression profile data were analyzed by Bayesian modelling and functional annotation. Of 28,869 genes on the microarrays, 326 showed statistically significant differential expression with FDR adjusted p-values below 0.05. Quantitative RT-PCR confirmed differential expression for the most of the genes selected for validation. Functional annotation and network analysis indicated activation of a gene network that included immunological disease, cellular movement and cardiovascular disease functions (enrichment score 42). As HIV and HCV infections were confounding factors, we performed additional stratification of patients. A similar functional activation of the “immunological disease” category was evident when we compared patients according to injection status (past versus current users, balanced for HIV and HCV infection). However, this difference was not large therefore the major effect was related to the HIV status of the patients. Mn-methcathinone abusers have blood RNA expression patterns that mostly reflect their HIV and HCV infections. However, despite the strong confounding effect from infection, some modest drug abuse effects on gene expression were detected. 40 samples, 20 healthy volunteers and 20 illicit methcathinone users
2011-04-19 | E-GEOD-28686 | biostudies-arrayexpress
Project description:Successful development of HIV-vaccination strategies will also depend on the ability to use novel approaches to analyse and integrate immunogenicity data generated in vaccine trials. The ANRS VAC 18 trial evaluated the immunogenicity of HIV-LIPO-5 vaccine (5 HIV peptides coupled to a palmytoil tail) administered at W0, 4, 12 and 24 in healthy volunteers. 62-69% of vaccinees developed HIV-specific ELISpot responses by W26. Here we present extensive immunogenicity assessments in a subset of vaccinees using ELISpot, lymphoproliferation, intracellular cytokine staining (ICS), cytokine multiplex and transcriptomic analyses. Peripheral blood mononuclear cells from volunteers collected before and following vaccinations were stimulated with HIV LIPO 5 vaccine, Gag peptides contained or not in the vaccine as controls. Different time points and stimulation conditions were compared, using false discovery rate to control for test multiplicity. 74% and 30% of vaccinees had cultured ELISpot and lymphoproliferation responses at W14, respectively. Ex-vivo ICS showed mainly single IL-2 producing cells. Secretion of IFN-γ, TNF-α, IL-5, and IL-13 increased significantly in response to Gag stimulation after culture at W14 compared to W0. An induction of metallothionein genes was consistently detected after HIV-LIPO-5 stimulation at W0 and W14 related to the adjuvant effect of the lipid tail. After vaccination (W14), significant probes increased substantially (>1200 probes) including IFN-γ, CXCL9, IL2RA, TNFAIP6, CCL3L1 and IL-6 W14 (fold change > 100%). In conclusion, HIV LIPO-5 vaccination elicited memory precursor responses with a Th1 and Th2 profile. The signature profile before vaccination provides information about the adjuvant effect of the lipid tail. Consistently with cytokine responses, vaccination is associated with a modulation in gene expression. This combined approach allowed to identify new signatures of HIV vaccine response and indicates that HIV-LIPO-5 could be further developed as a prime component of heterologous prime boost strategies. PBMC mRNA of 12 healthy volunteers, stimulate in four different conditions (HIV-LIPO-5, Gag+, Gag-, NS) during 6 and 24 hours before and after vaccination (week 0 and week 14)
2013-07-30 | E-GEOD-39506 | biostudies-arrayexpress
Project description:Successful development of HIV-vaccination strategies will also depend on the ability to use novel approaches to analyse and integrate immunogenicity data generated in vaccine trials. The ANRS VAC 18 trial evaluated the immunogenicity of HIV-LIPO-5 vaccine (5 HIV peptides coupled to a palmytoil tail) administered at W0, 4, 12 and 24 in healthy volunteers. 62-69% of vaccinees developed HIV-specific ELISpot responses by W26. Here we present extensive immunogenicity assessments in a subset of vaccinees using ELISpot, lymphoproliferation, intracellular cytokine staining (ICS), cytokine multiplex and transcriptomic analyses. Peripheral blood mononuclear cells from volunteers collected before and following vaccinations were stimulated with HIV LIPO 5 vaccine, Gag peptides contained or not in the vaccine as controls. Different time points and stimulation conditions were compared, using false discovery rate to control for test multiplicity. 74% and 30% of vaccinees had cultured ELISpot and lymphoproliferation responses at W14, respectively. Ex-vivo ICS showed mainly single IL-2 producing cells. Secretion of IFN-γ, TNF-α, IL-5, and IL-13 increased significantly in response to Gag stimulation after culture at W14 compared to W0. An induction of metallothionein genes was consistently detected after HIV-LIPO-5 stimulation at W0 and W14 related to the adjuvant effect of the lipid tail. After vaccination (W14), significant probes increased substantially (>1200 probes) including IFN-γ, CXCL9, IL2RA, TNFAIP6, CCL3L1 and IL-6 W14 (fold change > 100%). In conclusion, HIV LIPO-5 vaccination elicited memory precursor responses with a Th1 and Th2 profile. The signature profile before vaccination provides information about the adjuvant effect of the lipid tail. Consistently with cytokine responses, vaccination is associated with a modulation in gene expression. This combined approach allowed to identify new signatures of HIV vaccine response and indicates that HIV-LIPO-5 could be further developed as a prime component of heterologous prime boost strategies.
2013-07-30 | GSE39506 | GEO
Project description:The time course of whole blood gene expression was measured after the fourth immunisation at month 6 in participants who had been randomised into vaccine or placebo group 1 of the clinical protocol HVTN087 - A phase 1 trial to evaluate the safety, tolerability, and immunogenicity of an IL-12 pDNA enhanced HIV-1 multi-antigen pDNA vaccine delivered intramuscularly with electroporation, with an HIV-1 rVSV vaccine boost, in healthy HIV-uninfected adult participants (NCT01578889).
2022-01-12 | GSE125019 | GEO
Project description:A safe and effective vaccine for the prevention of human immunodeficiency virus type 1 (HIV-1) infection is a global priority. Tthe efficacy of a DNA prime–recombinant adenovirus type 5 boost (DNA/rAd5) vaccine regimen was testd in persons at increased risk for HIV-1 infection in the United States. The DNA/rAd5 vaccine regimen did not reduce either the rate of HIV-1 acquisition or the viral-load set point in the population studied. System biology analysis, including RNA-sequencing, was used to identify markers of risk of HIV-1 acquisition.
2021-09-23 | GSE181859 | GEO
Project description:Methcathinone (ephedrone) is relatively easily accessible for abuse. Its users develop an extrapyramidal syndrome and it is not known if this is caused by methcathinone itself, by side-ingredients (manganese), or both. In the present study we aimed to clarify molecular mechanisms underlying this condition. We used microarrays to analyze whole genome gene expression patterns of peripheral blood from 20 methcathinone users and 20 matched controls. Gene expression profile data were analyzed by Bayesian modelling and functional annotation. Of 28,869 genes on the microarrays, 326 showed statistically significant differential expression with FDR adjusted p-values below 0.05. Quantitative RT-PCR confirmed differential expression for the most of the genes selected for validation. Functional annotation and network analysis indicated activation of a gene network that included immunological disease, cellular movement and cardiovascular disease functions (enrichment score 42). As HIV and HCV infections were confounding factors, we performed additional stratification of patients. A similar functional activation of the “immunological disease” category was evident when we compared patients according to injection status (past versus current users, balanced for HIV and HCV infection). However, this difference was not large therefore the major effect was related to the HIV status of the patients. Mn-methcathinone abusers have blood RNA expression patterns that mostly reflect their HIV and HCV infections. However, despite the strong confounding effect from infection, some modest drug abuse effects on gene expression were detected.
2011-04-19 | GSE28686 | GEO