Transcriptomic profiling of peripheral blood NK cells of chronic HBV, HCV and HIV patients
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA517165 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Background: NK cells during chronic viral infection have been well studied over the last decade. We performed an unbiased next-generation RNA-sequencing approach to identify commonalities or differences of the effect of HIV, HCV and HBV viremia on NK cell transcriptomes. Methods: Using cell sorting, we obtained CD3-CD56+ NK cells from blood of 6 HIV, 11 HCV, and 32 HBV infected and untreated patients. Library preparation and sequencing were done using Illumina mRNA-Seq Sample Prep Kit and the HiSeq 2000, HiSeq2500 or NextSeq 500, and further analysis by an in-house analytic pipeline. Results: In NK cells from HIV, HCV and HBV patients, transcriptome analysis identified 272, 53, and 56 differentially expressed genes, respectively (fold change >1.5, q-value 0.2). Interferon stimulated genes were induced in NK cells from HIV/HCV patients, but not during HBV infection. HIV viremia downregulated ribosome assembly genes in NK cells. In HBV, viral load and ALT variation had little effect on genes related to NK effector function. Conclusion: We compare, for the first time, NK cell transcripts of viremic HIV, HCV and HBV patients. We clearly demonstrate distinctive NK cell gene signatures in 3 different populations, suggestive for a different degree of functional alterations of the NK cell compartment as compared to healthy individuals.
2019-01-26 | GSE125686 | GEO
Project description:Hepatic complications of HCV infection, including fibrosis and cirrhosis are accelerated in HIV-infected individuals. Although liver biopsy remains the gold standard for staging HCV-associated liver disease, this test can result in serious complications and is subject to sampling error. These challenges have prompted a search for non-invasive methods for liver fibrosis staging. To this end, we compared serum proteome profiles at different stages of fibrosis in HIV/HCV co- and HCV mono-infected patients using SELDI-TOF MS.
2018-04-09 | PXD009007 | Pride
Project description:PolyA-RNA sequencing on Peripheral Blood Mononuclear Cells of HIV/HCV coinfected patients with different cirrhosis states.
2023-02-28 | E-MTAB-12251 | biostudies-arrayexpress
Project description:We conducted a prospective study in 28 HIV/HCV-coinfected patients receiving IFN-based therapy at baseline (HIV/HCV-b) and week 24 after the sustained virological response (HIV/HCV-f). Twenty-seven HIV-monoinfected patients (HIV-group) were included as a control group, which were effectively treated with cART (virological controlled and CD4+ T-cell counts over 500) for an extended period. RNA-seq analysis was performed on peripheral blood mononuclear cells (PBMCs).
2021-05-05 | E-MTAB-10232 | biostudies-arrayexpress
Project description:A total of 52 patients were analyzed: 21 of them monoinfected with HCV and 31 coinfected with HIV (HCV/HIV). HCV patients were recruited from Hospital Italiano and Hospital José María Ramos Mejía from Buenos Aires, Argentina, and HCV/HIV patients from Hospital Universitario La Paz, Hospital Infanta Leonor, Hospital Universitario La Princesa, Hospital Puerta de Hierro, from Madrid, Spain. All samples were processed at the National Center for Microbiology (Madrid). Patients were naıve of treatment for HCV. CHC infection was defined by the presence of anti-HCV antibodies in serum and detectable HCV RNA in plasma samples in at least 2 separate occasions. All HIV+ patients had HIV antibodies, CD4+ T-cells counts ≥ 500 cel/mm3 for at least one year before sample collection, and undetectable HIV viral load since they received suppressive antiretroviral treatment (ART) for at least one year. Plasma extracellular vesicles isolation and RNA purification was performed using the ExoRNeasy Serum/Plasma Midi kit (QIAGEN, Cat #77044). EVs were phenol-lysed and total RNA was purified by ethanol-based membrane binding into spin columns. Quality and integrity were evaluated by the Bioanalyzer 2100 with Agilent RNA 6000 Nano kit (Agilent). Small RNA library synthesis and sequencing were performed at Centre for Genomic Regulation (CRG) at Barcelona (Spain). Small RNA libraries were constructed with Illumina’s TruSeq Small RNA kit v.4 (Illumina) and 50nts (1x50) were sequenced in an Illumina HiSeq2500, with a single read approach.
2023-02-27 | E-MTAB-11811 | biostudies-arrayexpress
Project description:A total of 117 HIV-1 infected patients were analyzed. These individuals were categorized in three different groups according to their infectious status for HCV: A) HIV+/HCV+ group, (n=45) patients with HIV infection and active HCV-chronic infection naïve to any HCV treatment (positive PCR and positive HCV antibodies); B) HIV+/HCV- group, (n=36) patients who had been exposed to HCV but experienced spontaneous viral clearance during the first 6 months after HCV infection (negative PCR and positive HCV antibodies); C) HIV+ group, (n=36) HIV+ mono-infected patients that had never been infected with HCV (negative PCR, negative HCV antibody and no previous HCV treatment). Briefely, peripheral venous blood samples were collected in EDTA tubes, and PBMCs were isolated within the first 4 hours after extraction.Total RNA including miRNAs were isolated from PBMCs with the miRNeasy Mini kit (Qiagen). Quality and integrity were evaluated by the Bioanalyzer 2100 with Agilent RNA 6000 Nano kit (Agilent). Only those samples with RIN > 7.5 were sequenced. Small RNA library synthesis and sequencing were performed at Centre for Genomic Regulation (CRG) at Barcelona (Spain). Small RNA libraries were constructed with Illumina’s TruSeq Small RNA kit v.4 (Illumina) and 50nts (1x50) were sequenced in an Illumina HiSeq2500, with a single read approach.
2021-11-23 | E-MTAB-8274 | biostudies-arrayexpress
Project description:The aim of this study was to identify differential gene and protein expression associated with GBV-C that may be of importance in reduction of HCV-related liver disease. GB virus C (GBV-C) infection leads to improved outcomes in human immunodeficiency virus (HIV) infection. Furthermore, GBV-C has been shown to reduce hepatitis C virus (HCV)-related liver disease in HCV/HIV co-infection.
2011-05-10 | GSE16593 | GEO
Project description:The aim of this study was to identify differential gene and protein expression associated with GBV-C that may be of importance in reduction of HCV-related liver disease. GB virus C (GBV-C) infection leads to improved outcomes in human immunodeficiency virus (HIV) infection. Furthermore, GBV-C has been shown to reduce hepatitis C virus (HCV)-related liver disease in HCV/HIV co-infection. We aimed to identify differential gene expression associated with GBV-C in HCV/HIV co-infection by comparing RNA expression from liver biopsies of HCV/HIV co-infected patients with and without GBV-C infection. Liver biopsies were obtained from 10 Patients with HCV/HIV co-infection; 4 of these patients were positive for GBV-C infection and 6 were negative for GBV-C infection. The tissue was stored in RNAlater and RNA was extracted for hybridisation to Affymetrix Human Genome U133 plus 2.0 microarrays at the University of Texas Medical Branch Molecular Genomics Core Laboratory. The data was analysed for genes differentially expressed between GBV-C positive and negative patients using Partek Genomics suite and applying a custom CDF file (Hs133P_Hs_UG_8), available from Molecular and Behavioural Neuroscience Institute, University of Michigan.
2011-05-10 | E-GEOD-16593 | biostudies-arrayexpress
Project description:PolyA-RNA sequencing on Peripheral Blood Mononuclear Cells in patients infected with HIV and healthy donnors. Patients were effectively treated with cART (virological controlled and CD4+ T-cell counts over 500) for an extended period. HIV infected patients were not coinfected with HCV or HBV.
2020-05-31 | E-MTAB-8249 | biostudies-arrayexpress
Project description:We conducted a prospective study in 33 HIV/HCV-coinfected patients receiving IFN-based therapy at baseline (HIV+/HCV+) and week 36 after the sustained virological response (HIV+/HCV-). Twenty-six HIV-monoinfected patients (HIV+) and 9 patients that achieved the sustained virological response 36 weeks before (HCV-) were included as a control group. The HIV+ patients were effectively treated with cART (virological controlled and CD4+ T-cell counts over 500) for an extended period. RNA-seq analysis was performed on peripheral blood mononuclear cells (PBMCs).
2022-01-04 | E-MTAB-10703 | biostudies-arrayexpress