title: Genome-wide search for the genes accountable for the induced resistance to HIV-1 infection in activated CD4+ T cells: apparent transcriptional signatures, co-expression networks and possible cellular processes.
abstract: BACKGROUND
  Upon co-stimulation with CD3/CD28 antibodies, activated CD4 + T cells were found to lose their susceptibility to HIV-1 infection, exhibiting an induced resistant phenotype. This rather unexpected phenomenon has been repeatedly confirmed but the underlying cell and molecular mechanisms are still unknown.
  
  
  METHODS
  We first replicated the reported system using the specified Dynal beads with PHA/IL-2-stimulated and un-stimulated cells as controls. Genome-wide expression and analysis were then performed by using Agilent whole genome microarrays and established bioinformatics tools.
  
  
  RESULTS
  We showed that following CD3/CD28 co-stimulation, a homogeneous population emerged with uniform expression of activation markers CD25 and CD69 as well as a memory marker CD45RO at high levels. These cells differentially expressed 7,824 genes when compared with the controls on microarrays. Series-Cluster analysis identified 6 distinct expression profiles containing 1,345 genes as the representative signatures in the permissive and resistant cells. Of them, 245 (101 potentially permissive and 144 potentially resistant) were significant in gene ontology categories related to immune response, cell adhesion and metabolism. Co-expression networks analysis identified 137 "key regulatory" genes (84 potentially permissive and 53 potentially resistant), holding hub positions in the gene interactions. By mapping these genes on KEGG pathways, the predominance of actin cytoskeleton functions, proteasomes, and cell cycle arrest in induced resistance emerged. We also revealed an entire set of previously unreported novel genes for further mining and functional validation.
  
  
  CONCLUSIONS
  This initial microarray study will stimulate renewed interest in exploring this system and open new avenues for research into HIV-1 susceptibility and its reversal in target cells, serving as a foundation for the development of novel therapeutic and clinical treatments.
authors: Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Jiaochang East Road 32, Kunming, Yunnan Province, 650223 China.
authors: Wen-Wen
authors: WW
authors: Xu
authors: Miao-Jun
authors: MJ
authors: Han
authors: Dai
authors: D
authors: Chen
authors: Ling
authors: L
authors: Chen
authors: Yan
authors: Y
authors: Guo
authors: Andrew
authors: A
authors: Willden
authors: Di-Qiu
authors: DQ
authors: Liu
authors: Hua-Tang
authors: HT
authors: Zhang
mesh_terms: D000906:Antibodies / Q000494:pharmacology; D018106:CD28 Antigens / Q000276:immunology / Q000378:metabolism; D017252:CD3 Complex / Q000276:immunology / Q000378:metabolism; D015496:CD4-Positive T-Lymphocytes / Q000187:drug effects / Q000276:immunology / Q000378:metabolism*; D016000:Cluster Analysis; D004198:Disease Susceptibility; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D015894:Genome, Human; D015658:HIV Infections / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D015497:HIV-1 / Q000378:metabolism; D006801:Humans; D008213:Lymphocyte Activation; D020411:Oligonucleotide Array Sequence Analysis; D054399:Receptors, CCR6 / Q000378:metabolism; D019718:Receptors, CXCR4 / Q000378:metabolism; D014764:Viral Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D000906:Antibodies; C106311:CCR6 protein, human; D018106:CD28 Antigens; D017252:CD3 Complex; C527276:CXCR4 protein, human; D054399:Receptors, CCR6; D019718:Receptors, CXCR4; D014764:Viral Proteins
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