Microarray analysis of differentially expressed genes in cells resistant to HIV-1

We have previously isolated two matched transformed human T cell clones: one of which is resistant to HIV-1 replication and secretes an HIV-1 resistance factor(s) (HRF) and the second which retains the susceptibility of the parental cell line to HIV-1 infection. We employed cDNA arrays to investigate the spectrum of changes in cellular gene expression that correlate with the acquisition of HIV-1 resistance and the secretion of HRF. Using a tissue based immunology/hematology array, we identified 29 transcripts that were differentially expressed by HRF(+) and HRF(-) cells. HRF(+) cells showed a selective down-regulation of 11 genes involved in transcription, several of which are implicated in either susceptibility of cells to HIV-1 or the promotion of HIV-1 transcription itself. In the group of the up-regulated genes, three were linked directly to the cellular resistance to HIV-1. One of the cDNAs placed on the array, representing the hypothetical protein KIAA0117 hybridized only with poly A+ RNA probes derived from HRF(+) cells. The specific up-regulation of two genes, the transcription repressor (CTCF) and hypothetical protein KIAA0117 was confirmed by RT-PCR and Northern blot. The role of KIAA0117 transcript in the resistance to HIV-1 replication needs to be determined.