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Series GSE33933 Query DataSets for GSE33933
Status Public on Apr 27, 2012
Title Gene expression in the blood of SIV infected Rhesus macaques following in vivo PD-1 blockade
Organism Macaca mulatta
Experiment type Expression profiling by array
Summary Hyperimmune activation is one of the strong predictors of disease progression during pathogenic immunodeficiency virus infections and is mediated in part by sustained type I interferon (IFN) signaling. Combination antiretroviral therapy suppresses hyperimmune activation only partially in HIV-infected individuals. Here, we show that blockade of Programmed Death-1 (PD-1) during chonic SIV infection significantly reduces the expression of transcripts associated with type I IFN signaling in the blood and colorectal tissue of rhesus macaques (RM). The effect of PD-1 blockade on type I IFN signaling was durable and persisted under high viremia, a condition that is seen in nonprogressive SIV infection in their natural hosts. The reduced type I IFN signaling was associated with enhanced expression of some of the junction-associated genes in the colorectal tissue and a profound decrease in LPS levels in plasma suggesting a possible repair of gut associated junctions and decreased microbial translocation. The reduced type I IFN signaling was also associated with enhanced immunity against gut resident pathogenic bacteria, control of gut associated opportunistic infections and survival of SIV-infected RMs. These results reveal novel mechanisms by which PD-1 blockade enhances survival of SIV-infected RMs and have implications for development of novel therapeutic approaches to control HIV/AIDS.
 
Overall design SIV negative controls (n=4); SIV infected and control antibody (SYNAGIS) treated (n=3); and SIV infected Programmed Death 1 antibody (PD-1 Ab) treated (n=3) groups of Rhesus macaques PBMCs were isolated by Ficoll-paque plus medium (Amersham) and were lysed in to RNA later reagent (Qiagen) and samples were homogenized with Qiagen Shredder (Qiagen). RNA was extracted with Rneasy mini kit (Qiagen) and was used for microarray experiments. Rhesus GeneChip assays were performed in the Yerkes Microarray Core Facility (www.microarray.emory.edu), one of the Affymetrix Microarray Core Labs.The 0.5µg of total RNA sample was analyzed on Rhesus Macaque Genome GeneChip that consists of over 52,000 probe sets (Affymetrix, Santa Clara, CA). Target RNA labeling, hybridization and post-hybridization processing were performed following the Affymetrix GeneChip Expression Analysis standard protocols. In brief, RNA sample was first reverse-transcribed using T7-Oligo(dT) Promoter Primer and SuperScript II in the first-strand cDNAs synthesis reaction. Following RNase H-mediated second-stranded cDNA synthesis, the double-stranded cDNAs were purified by use of a GeneChip sample clean-up module and served as templates in the generation of biotinylated complementary RNAs (cRNAs) in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix by in vitro transcription (IVT) reaction. The biotinylated cRNAs were cleaned up, fragmented, and hybridized to the rhesus macaque expression arrays at 45°C for 16 h with constant rotation at 60 rpm. The gene chips were then washed and stained with Affymetrix fluidics stations 450 and scanned on Affymetrix scanner 3000. The images are processed to collect raw data with GeneChip Operating Software (GCOS) 1.4.
 
Contributor(s) Shetty RD, Amara RR
Citation(s) 22523065
Submission date Nov 23, 2011
Last update date Jul 18, 2012
Contact name RAVI DYAVAR SHETTY
E-mail(s) rdyavar@emory.edu
Phone 404-727-9233
Organization name emory university
Department Microbiology and Immunology
Lab Rama Amara
Street address 954 Gatewood RD NE
City Atlanta
State/province Georgia
ZIP/Postal code 30329
Country USA
 
Platforms (1)
GPL3535 [Rhesus] Affymetrix Rhesus Macaque Genome Array
Samples (10)
GSM838989 RBm11_SIVnegative_PBMCs
GSM838990 RIg11_SIVnegative_PBMCs
GSM838991 RGj11_SIVnegative_PBMCs
Relations
BioProject PRJNA148215

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE33933_RAW.tar 46.2 Mb (http)(custom) TAR (of CEL)
GSE33933_fold_change.txt.gz 2.6 Mb (ftp)(http) TXT
Raw data provided as supplementary file
Processed data included within Sample table
Processed data are available on Series record

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