Copyright ©The Author(s) 2016. Published by Baishideng Publishing Group Inc. All rights reserved.
World J Clin Infect Dis. May 25, 2016; 6(2): 6-21
Published online May 25, 2016. doi: 10.5495/wjcid.v6.i2.6
Systems biology applications to study mechanisms of human immunodeficiency virus latency and reactivation
Cory H White, Bastiaan Moesker, Angela Ciuffi, Nadejda Beliakova-Bethell
Cory H White, Graduate Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA 92093, United States
Cory H White, San Diego VA Medical Center and Veterans Medical Research Foundation, San Diego, CA 92161, United States
Bastiaan Moesker, Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, Hants SO16 6YD, United Kingdom
Angela Ciuffi, Institute of Microbiology, University Hospital of Lausanne (CHUV) and University of Lausanne, 1011 Lausanne, Switzerland
Nadejda Beliakova-Bethell, Department of Medicine, University of California San Diego, La Jolla, CA 92093, United States
Author contributions: All authors contributed equally to this paper with conception and design of the study, literature review and interpretation, manuscript preparation and approval of the final version.
Supported by The grant from the National Institutes of Health, Martin Delaney Collaboratory of AIDS Researchers for Eradication (CARE, U19 AI 096113); the Swiss National Science Foundation (grant 31003A_146579); and the University of California, San Diego Fellowships for Graduate Researchers, Frontiers of Innovation Scholars Program.
Conflict-of-interest statement: No potential conflict of interest.
Open-Access: This article is an open-access article which was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See:
Correspondence to: Nadejda Beliakova-Bethell, PhD, Department of Medicine, University of California San Diego, Stein Clinical Research Building, Rm. 303, 9500 Gilman Drive, #0679, La Jolla, CA 92093, United States.
Telephone: +1-858-5528585 Fax: +1-858-5527445
Received: September 30, 2015
Peer-review started: October 7, 2015
First decision: November 30, 2015
Revised: January 15, 2016
Accepted: March 7, 2016
Article in press: March 9, 2016
Published online: May 25, 2016
Core Tip

Core tip: Gene expression profiling and systems biology methods are reviewed with respect to their possible application in the field of human immunodeficiency virus (HIV) research. Studies profiling gene expression in latently infected and uninfected cells are summarized to illustrate application of these methods to identification of latency biomarkers and the molecular mechanisms contributing to regulation of HIV expression. Studies that measure changes in host and HIV gene expression upon treatment with latency reversing agents (LRAs) highlight uniting themes driving HIV reactivation and identify novel mechanisms of action of LRAs. The field will further benefit from increased adoption of systems biology methods in future studies.