Temporal transcriptional response to latency reversing agents identifies specific factors regulating HIV-1 viral transcriptional switch. Issue 1 (December 2015)

• Record Type: Journal Article
• Authors: Venkatachari, Narasimhan; Zerbato, Jennifer; Jain, Siddhartha; Mancini, Allison; Chattopadhyay, Ansuman; Sluis-Cremer, Nicolas; Bar-Joseph, Ziv; Ayyavoo, Velpandi
• Is Part Of: Retrovirology. Volume 12:Issue 1(2015)
• Page Start: 1
• Page End: 22
• Publication Date: 2015-12
• Subjects: HIV-1 -- Latency -- Transcripts -- SDREM -- Gene expression -- Transcription factors; Retroviruses -- Periodicals; 579.2569
• DOI: 10.1186/s12977-015-0211-3
• Languages: English
• ISSNs: 1742-4690

Abstract

Abstract Background Latent HIV-1 reservoirs are identified as one of the major challenges to achieve HIV-1 cure. Currently available strategies are associated with wide variability in outcomes both in patients and CD4+ T cell models. This underlines the critical need to develop innovative strategies to predict and recognize ways that could result in better reactivation and eventual elimination of latent HIV-1 reservoirs. Results and discussion In this study, we combined genome wide transcriptome datasets post activation with Systems Biology approach (Signaling and Dynamic Regulatory Events Miner, SDREM analyses) to reconstruct a dynamic signaling and regulatory network involved in reactivation mediated by specific activators using a latent cell line. This approach identified several critical regulators for each treatment, which were confirmed in follow-up validation studies using small molecule inhibitors. Results indicate that signaling pathways involving JNK and related factors as predicted by SDREM are essential for virus reactivation by suberoylanilide hydroxamic acid. ERK1/2 and NF-κB pathways have the foremost role in reactivation with prostratin and TNF-α, respectively. JAK-STAT pathway has a central role in HIV-1 transcription. Additional evaluation, using other latent J-Lat cell clones and primary T cell model, also confirmed that many of the cellular factors associated with latency reversing agents are similar, though minor differences are identified. JAK-STAT and NF-κB related pathways are critical for reversal of HIV-1 latency in primary resting T cells. Conclusion These results validate our combinatorial approach to predict the regulatory cellular factors and pathways responsible for HIV-1 reactivation in latent HIV-1 harboring cell line models. JAK-STAT have a role in reversal of latency in all the HIV-1 latency models tested, including primary CD4+ T cells, with additional cellular pathways such as NF-κB, JNK and ERK 1/2 that may have complementary role in reversal of HIV-1 latency.