Genomic and real-time PCR transcriptional analysis of the KIR repertoire. (A) The size of the NK-cell compartment was analyzed by flow cytometry (% CD3⁻CD56⁺CD16⁺ cells) in exposed HIV-infected IDU (HIV, ▴) exposed HIV-uninfected IDU (EU, •), and unexposed control blood donors (C, □). (B) Real-time PCR analysis of altered KIR transcript patterns in HIV and EUs. KIR2DL4, KIR3DL2, KIR2DL3, and KIR3DL1 mRNA transcript levels are represented as relative copy numbers per 10⁶GAPDH transcripts. KIR2DL3 transcript levels where examined according to the alternative KIR2DL3⁺KIR2DS2⁻KIR2DL2⁻ or KIR2DL3⁺KIR2DS2⁺KIR2DL2⁺ genomic gene combinations (middle left) and also plotted according to the size of the phenotypically defined GL183⁺ NK-cell subset (middle right). A high percentage of GL183⁺ NK cells (> 50% of GL183⁺ NK cells within CD3⁻CD56⁺ NK cells) identified a specific subgroup of KIR2DL3⁺KIR2DS2⁻KIR2DL2⁻ EU individuals who exhibit higher KIR2DL3 transcript levels in the absence of KIR2DS2/KIR2DL2 transcription (boxed area). Activating KIR3DS1/inhibitory KIR3DL1 transcript ratio is represented (bottom right). EUs with higher KIR3DS1/KIR3DL1 ratios as compared with C and HIV⁺ are boxed. Horizontal bars represent the median and the 25th and 75th percentiles.