Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi, India.
Mol Biol Rep. 2024 Oct 30;51(1):1102. doi: 10.1007/s11033-024-10037-2.
The presence of latent HIV reservoirs continues to be the biggest obstacle to achieving an HIV cure. Thus, long non-coding RNAs (lncRNAs) may serve as the preferred targets for HIV latency reversal. The goal of the study was to identify prospective lncRNAs for subsequent in vitro molecular and functional characterization.
RNA-sequencing was performed in latently HIV-infected monocytic cell line (U1) under stimulated and unstimulated condition using Illumina-HiSeqX platform, followed by its validation using qRT-PCR assay. Gene ontology (GO), KEGG pathway, and co-expression analyses were performed to identify the enriched biological processes and pathways in U1 cells post-stimulation with the latency reversal agent SAHA. A total of 3,576 and 1,467 significantly altered lncRNAs and protein-coding genes respectively, were identified in SAHA-stimulated U1 cells compared to unstimulated ones. The GO and KEGG pathway analyses of the differentially expressed protein-coding genes showed the enrichment of diverse biological processes and pathways respectively, in SAHA-stimulated U1 cells. Co-expression analysis between lncRNAs and protein-coding gene pairs, helped predict potential pathways with which these lncRNAs are associated. Further in vitro validation in HIV-infected monocytes showed that the expression of the top two candidate lncRNAs, LINC01231 and LINC00560, are specific to HIV infection.
Transcriptome analysis revealed changes in the expression of numerous lncRNAs and protein-coding genes following stimulation with SAHA. Co-expression analysis identified candidate lncRNAs and their associated biological pathways. However, additional in vitro experimental exploration using gene knockdown strategies is needed to ascertain the specific role of LINC01231 and LINC00560 lncRNAs in latently infected monocytes.
潜伏的 HIV 储库的存在仍然是实现 HIV 治愈的最大障碍。因此，长非编码 RNA（lncRNA）可能成为逆转 HIV 潜伏期的首选靶标。本研究的目的是鉴定潜在的 lncRNA，以便随后进行体外分子和功能特征分析。
使用 Illumina-HiSeqX 平台对潜伏感染的单核细胞系（U1）在刺激和非刺激条件下进行 RNA 测序，然后使用 qRT-PCR 测定进行验证。进行基因本体论（GO）、KEGG 通路和共表达分析，以鉴定在潜伏逆转剂 SAHA 刺激后 U1 细胞中富集的生物学过程和通路。与未刺激的 U1 细胞相比，SAHA 刺激的 U1 细胞中分别有 3576 个和 1467 个显著改变的 lncRNA 和蛋白编码基因。差异表达蛋白编码基因的 GO 和 KEGG 通路分析显示，SAHA 刺激的 U1 细胞中分别富集了不同的生物学过程和通路。lncRNA 和蛋白编码基因对之间的共表达分析有助于预测这些 lncRNA 相关的潜在通路。在 HIV 感染的单核细胞中的进一步体外验证表明，前两个候选 lncRNA（LINC01231 和 LINC00560）的表达是 HIV 感染特有的。
转录组分析显示，在 SAHA 刺激后，大量 lncRNA 和蛋白编码基因的表达发生变化。共表达分析鉴定了候选 lncRNA 及其相关的生物学通路。然而，需要使用基因敲低策略进行更多的体外实验探索，以确定 LINC01231 和 LINC00560 lncRNA 在潜伏感染的单核细胞中的具体作用。
