Please note that we have stopped the regular imports of Gene Expression Omnibus (GEO) data into ArrayExpress. This may not be the latest version of this experiment.

E-GEOD-28128 - Comparative analysis of genomic features of human HIV-1 infection and primate models of SIV infection

Status
Released on 3 June 2011, last updated on 27 March 2012
Organism
Homo sapiens
Samples (79)
Array (1)
Protocols (7)
Description
High levels of HIV-1 replication during the chronic phase of infection are usually associated with rapid disease progression (RP). However, a minority of HIV-infected individuals remain asymptomatic and show persistently high CD4+ T cell counts despite high viremia for many years (viremic non progressors, VNP). The latter profile is reminiscent of the non-pathogenic model of SIV infection in natural hosts such as the sooty mangabey. We used various genomic approaches to examine 66 RP and 6 VNP defined according to strict criteria. RP were characterized by depletion of protective HLA alleles, enrichment of HLA alleles associated with disease progression, and a characteristic transcriptome profile of CD4+ and CD8+ T cells similar to that observed in pathogenic SIV infection of rhesus macaque. In contrast, VNPs presented lower expression of interferon stimulated genes than RP, and shared with SIV-infected sooty mangabeys a common profile of regulation of a set of genes that includes CASP1, CD38, LAG3, TNFSF13B, SOCS1 and EEF1D. The estimated 8% of RP and 0.1% of VNP in human cohorts represent two subsets of HIV-infected individuals whose analysis may inform our understanding of HIV pathogenesis. Selection criteria rapid progressors (RP): HIV seroconversion window <1 year WITH documented negative and positive serology or biological proof of primary infection. AND One of A) or B) A) >2 CD4+ T cell counts below 350 cells/µl within 3 years of seroconversion AND no subsequent rise of CD4+ T cells above 350 cells/µl in the absence of ART. B) ART initiated within 3 years of seroconversion AND CD4+ T cell count within 1 month of ART-start <350 cells/µl. Selection criteria viremic non progressors (VNP): > 3 years of follow-up AND median HIV viremia from >3 measurements >100'000 viral RNA copies/ml AND HIV viremia consistently above 10’000 copies/ml AND CD4+ T cell count above 350 cells/µl AND no ART during follow-up. Selection criteria elite/viremic controllers (EC): see Casado et al. 2010. Host and viral genetic correlates of clinical definitions of HIV-1 disease progression. PLoS ONE 5:e11079. Total RNA from 41 samples obtained from CD4 T cells from HIV infected individuals to identify associations between gene expression and different distinct patterns of disease progression Total RNA from 38 samples obtained from CD8 T cells from HIV infected individuals to identify associations between gene expression and different distinct
Experiment type
transcription profiling by array 
Contacts
Amalio Telenti, Andri Rauch, Annelys Roque, Bernard Hirschel, Daniel Douek, Eduard Palou, Enos Bernasconi, Guido Silvestri, Huldrych F Günthard, Itziar Erkizia, Jacques Fellay, Javier Martinez-Picado, Jose M Miró, Judith Dalmau, Julia Liebner, Julià Blanco, Manuel Battegay, Margalida Rotger, Marta Massanella, Matthew Woods, Matthias Hoffmann, Netanya G Sandler, Patrick Descombes, Paul de Bakker, Paul McLaren, Raquel Martinez, Steve Bosinger
Citation
Comparative transcriptomics of extreme phenotypes of human HIV-1 infection and SIV infection in sooty mangabey and rhesus macaque. Rotger M, Dalmau J, Rauch A, McLaren P, Bosinger SE, Martinez R, Sandler NG, Roque A, Liebner J, Battegay M, Bernasconi E, Descombes P, Erkizia I, Fellay J, Hirschel B, Miró JM, Palou E, Hoffmann M, Massanella M, Blanco J, Woods M, Günthard HF, de Bakker P, Douek DC, Silvestri G, Martinez-Picado J, Telenti A. , PMID:21555857
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-28128.idf.txt
Sample and data relationshipE-GEOD-28128.sdrf.txt
Processed data (1)E-GEOD-28128.processed.1.zip
Array designA-MEXP-1173.adf.txt
Links