Identification of novel lncRNAs associated with sensitivity of HIV antiretroviral therapy: a two-stage matched case-control study

To identify long non-coding RNAs (lncRNAs) that may function as potential biomarkers of sensitivity to antiretroviral therapy (ART) against human immunodeficiency virus (HIV) infection. A two-stage case-control study was conducted. In the screening stage, peripheral blood lymphocytes of six subjects receiving lamivudine-based ART (3 ART-resistant and 3 ART-sensitive subjects) were subjected to comprehensive microarray expression profiling to seek lncRNAs associated with ART sensitivity. Secondly, during the validation stage, promising lncRNAs were evaluated via a 1:4 matched case-control study using 50 subjects (10 ART-resistant and 40 ART-sensitive subjects with matching durations of ART). As the result, seven lncRNAs were screened out (<i>P</i> &lt; 1.06 × 10^-3) in the first stage. Among these, two lncRNAs (n341598 and n407911) survived validation conducted at the second-stage (n341598: <i>P</i> &lt; 0.001; n407911: <i>P</i> = 0.007), while another lncRNA n406445 showed marginally significant (<i>P</i> = 0.049). All three showed higher expression in ART-resistant subjects compared to that in ART-sensitive subjects. The area under the ROC curve (AUC) for n341598 was 0.867 (95% CI: 0.796–0.966; <i>P</i> &lt; 0.001), which was better than that for n406445 (0.702) and n407911 (0.780). Meanwhile, the AUC for n341598 was better than that of any combination of the three lncRNAs. Taken together, our study identified three highly expressed lncRNAs in patients with HIV ART-resistant, among which the lncRNA n341598 may be an optimal biomarker to distinguish ART-resistant and ART-sensitive patients. Further studies to reveal the molecular mechanisms underlying the regulation of ART sensitivity by n341598 are warranted to complement our findings.