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Series GSE21589 Query DataSets for GSE21589
Status Public on Jun 01, 2010
Title The Relationship between Virus Replication and Host Gene Expression in Lymphatic Tissue during HIV-1 Infection
Organism Homo sapiens
Experiment type Expression profiling by array
Summary During HIV-1 infection, there is a massive perturbation of host gene expression, but as yet, genome-wide studies have not identified host genes affecting HIV-1 replication in lymphatic tissue, the primary site of virus-host interactions. In this study, we isolated RNA from the inguinal lymph nodes of 22 HIV-1-infected individuals and utilized a microarray approach to identify host genes critically important for viral replication in lymphatic tissue by examining gene expression associated with viral load. Strikingly, ~95% of the transcripts (558) in this data set (592 transcripts total) were negatively associated with HIV-1 replication. Genes in this subset (1) inhibit cellular activation/proliferation (ex.: TCFL5, SOCS5 and SCOS7, KLF10), (2) promote heterochromatin formation (ex.: HIC2, CREBZF, ZNF148/ZBP-89), (3) increase collagen synthesis (ex.: PLOD2, POSTN, CRTAP), and (4) reduce cellular transcription and translation. Potential anti-HIV-1 restriction factors were also identified (ex.: NR3C1, HNRNPU, PACT). Only ~5% of the transcripts (34) were positively associated with HIV-1 replication. Paradoxically, nearly all these genes function in innate and adaptive immunity, particularly highlighting a heightened interferon system. The predominance of negative correlations as well as the disconnect between host defenses and viral load point to the importance of genes that regulate target cell activation and genes that code for potentially new restriction factors as determinants of viral load rather than conventional host defenses.
 
Overall design Total RNA was isolated from the inguinal lymph nodes of 22 HIV-1-infected subjects at different clinical stages (and varying viral loads) and prepared for RNA extraction and hybridization on Affymetrix Human Genome U133 Plus 2.0 microarrays. Replicate arrays were performed for lymph node samples to minimize assay noise and host genes critically important for viral replication in lymphatic tissue were identified by examining gene expression and its association with viral load. Replicates were not performed for samples WB91 and TS35 due to limited amounts of biomaterial.
 
Contributor(s) Smith AJ, Li Q, Wietgrefe SW, Schacker TW, Reilly CS, Haase AT
Citation(s) 20935203
Submission date Apr 29, 2010
Last update date Mar 25, 2019
Contact name Anthony James Smith
E-mail(s) smit4263@umn.edu
Phone 612-624-9130
Fax 612-626-0623
Organization name University of Minnesota
Department Microbiology
Lab Ashley T. Haase
Street address 420 Delaware Street S.E.
City Minneapolis
State/province MN
ZIP/Postal code 55455
Country USA
 
Platforms (1)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Samples (42)
GSM538932 DP24a
GSM538933 DP24b
GSM538934 JS30a
Relations
BioProject PRJNA127033

Transcripts Associated with HIV-1 replication header descriptions
Probe Set I.D.
q-value
Correlation Coefficient
Gene Symbol
Gene Title
Functional Category
Functional Sub-category
Funactional Sub-sub-category
Pathway
biological process term
molecular function term
cellular component term

Data table
Probe Set I.D. q-value Correlation Coefficient Gene Symbol Gene Title Functional Category Functional Sub-category Funactional Sub-sub-category Pathway biological process term molecular function term cellular component term
214012_at 0.067593155 -0.213559904 ERAP1 endoplasmic reticulum aminopeptidase 1 Immune Activation Moderators of Activation and Inflammation Antigen Presentation & Immune Response --- angiogenesis /// proteolysis /// membrane protein ectodomain proteolysis /// immune response /// regulation of blood pressure /// regulation of blood pressure /// response to bacterium /// antigen processing and presentation of endogenous peptide antigen via MHC class I /// antigen processing and presentation of endogenous peptide antigen via MHC class I /// regulation of innate immune response /// fat cell differentiation /// positive regulation of angiogenesis "aminopeptidase activity /// aminopeptidase activity /// receptor activity /// interleukin-6 receptor binding /// interleukin-1, Type II receptor binding /// protein binding /// peptidase activity /// metalloexopeptidase activity /// metallopeptidase activity /// zinc ion binding /// zinc ion binding /// hydrolase activity /// metal ion binding" extracellular region /// cytoplasm /// endoplasmic reticulum /// endoplasmic reticulum /// endoplasmic reticulum lumen /// endoplasmic reticulum membrane /// cytosol /// membrane /// integral to membrane /// integral to membrane
211734_s_at 0.035079499 -0.170429975 FCER1A "Fc fragment of IgE, high affinity I, receptor for; alpha polypeptide" Immune Defenses C' & FcRs --- activation of MAPK activity /// positive regulation of type I hypersensitivity /// serotonin secretion /// signal transduction /// cell surface receptor linked signal transduction /// activation of JNK activity /// leukotriene biosynthetic process /// positive regulation of mast cell degranulation /// positive regulation of interleukin-3 biosynthetic process /// positive regulation of granulocyte macrophage colony-stimulating factor biosynthetic process /// positive regulation of peptidyl-tyrosine phosphorylation /// positive regulation of calcium-mediated signaling receptor activity /// IgE receptor activity /// IgE binding plasma membrane /// plasma membrane /// integral to plasma membrane /// integral to plasma membrane /// external side of plasma membrane /// membrane /// integral to membrane
203305_at 0.06982994 -0.155978445 F13A1 "coagulation factor XIII, A1 polypeptide" "Tissue Repair, Remodeling" "Extracellular Matrix Structural Components, Cells, & Tissues" blood vessel related --- blood coagulation /// blood coagulation /// peptide cross-linking protein-glutamine gamma-glutamyltransferase activity /// protein-glutamine gamma-glutamyltransferase activity /// calcium ion binding /// acyltransferase activity /// transferase activity /// metal ion binding extracellular region /// extracellular region /// extracellular region /// cytoplasm
215784_at 0.067593155 -0.149014292 CD1E CD1e molecule Immune Activation Moderators of Activation and Inflammation Antigen Presentation & Immune Response --- immune response /// immune response /// antigen processing and presentation --- Golgi membrane /// lysosome /// endosome /// Golgi apparatus /// integral to plasma membrane /// membrane /// integral to membrane /// endosome lumen /// lysosomal lumen
1554636_at 0.062243524 -0.148199655 --- --- ??? ??? --- --- --- ---
238919_at 0.067593155 -0.133823477 --- --- ??? ??? --- --- --- ---
229963_at 0.067593155 -0.120938643 BEX5 "brain expressed, X-linked 5" "Tissue Repair, Remodeling" "Nerve-related Growth Factors, Receptors, & Guidnace Molecules " --- --- --- cytoplasm
238458_at 0.067593155 -0.118107165 EFHA2 "EF-hand domain family, member A2" Immune Activation Signal Transduction --- --- calcium ion binding membrane /// integral to membrane
226189_at 0.067593155 -0.116809392 ITGB8 "integrin, beta 8" Immune Activation Moderators of Activation and Inflammation "Inhibitors of T, B Cell Activation & Proliferation" Activator of TGF-? signaling pathway ganglioside metabolic process /// cell adhesion /// cell adhesion /// cell-matrix adhesion /// integrin-mediated signaling pathway receptor activity /// binding /// protein binding integrin complex /// integrin complex /// membrane /// integral to membrane
242358_at 0.067593155 -0.112711382 --- --- ??? ??? --- --- --- ---
232088_x_at 0.067593155 -0.110538181 --- --- ??? ??? --- --- --- ---
222161_at 0.06982994 -0.110466413 NAALAD2 N-acetylated alpha-linked acidic dipeptidase 2 "Tissue Repair, Remodeling" "Nerve Related Growth Factors, Receptors" --- proteolysis /// proteolysis /// neurotransmitter catabolic process catalytic activity /// carboxypeptidase activity /// carboxypeptidase activity /// peptidase activity /// serine-type peptidase activity /// metallopeptidase activity /// dipeptidyl-peptidase activity /// zinc ion binding /// hydrolase activity /// dipeptidase activity /// dipeptidase activity /// metal ion binding membrane /// integral to membrane /// integral to membrane
226018_at 0.067593155 -0.109389863 C7orf41 chromosome 7 open reading frame 41 ??? ??? --- --- --- ---
205802_at 0.067593155 -0.109065561 TRPC1 "transient receptor potential cation channel, subfamily C, member 1" Immune Activation Signal Transduction --- transport /// ion transport /// calcium ion transport /// calcium ion transport receptor activity /// ion channel activity /// calcium channel activity /// calcium channel activity /// calcium ion binding /// protein binding /// store-operated calcium channel activity plasma membrane /// integral to plasma membrane /// membrane /// integral to membrane
1557132_at 0.067593155 -0.109052738 WDR17 WD repeat domain 17 Immune Activation Signal Transduction --- --- --- ---
228084_at 0.067593155 -0.108829335 PLA2G12A "phospholipase A2, group XIIA" Metabolism Lipids & Sugars --- phospholipid metabolic process /// lipid catabolic process phospholipase A2 activity /// calcium ion binding /// hydrolase activity /// metal ion binding /// calcium-dependent phospholipase A2 activity extracellular region /// extracellular region /// cytoplasm
227202_at 0.06982994 -0.108784979 CNTN1 Contactin 2 precursor (CNTN1) "Tissue Repair, Remodeling" "Nerve Related Growth Factors, Receptors" --- cell adhesion /// cell adhesion /// Notch signaling pathway protein binding membrane fraction /// plasma membrane /// membrane /// anchored to membrane
242107_x_at 0.067593155 -0.108501715 --- --- ??? ??? --- --- --- ---
244387_at 0.067593155 -0.107925359 --- --- ??? ??? --- --- --- ---
223764_x_at 0.058654821 -0.107717871 NIPSNAP3B nipsnap homolog 3B (C. elegans) Immune Activation Moderators of Activation and Inflammation Antigen Presentation & Immune Response --- --- --- ---

Total number of rows: 753

Table truncated, full table size 163 Kbytes.




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Supplementary file Size Download File type/resource
GSE21589_RAW.tar 360.7 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table

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