Although non-coding RNAs comprise a majority of the human transcriptome, there remain critical gaps in our knowledge of the role of these molecules in most human pathologies, including HIV/AIDS. Here, we propose to decipher the mechanisms of non-coding RNAs, and their associated ribonucleoprotein complexes, in regulating HIV-1 infection of primary macrophages, particularly after exposure to Methamphetamine (METH). These studies will build on a powerful set of preliminary data that implicate several short and long non-coding RNAs in the regulation of HIV and response to METH. We propose to integrate several state-of-the-art post-genome technologies and newly developed experimental methodologies, including next generation sequencing and nanoparticle delivery systems, to provide important insights into the activity of these molecules in both promoting and restricting HIV replication. These analyses are designed to comprehensively identify non-coding RNAs that regulate these processes in primary human macrophages, and experimentally delineate their cellular or viral targets. Taken together, these studies will provide significant knowledge towards the molecular and cellular mechanisms underlying RNA-based host-pathogen interactions and antiviral functions.

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PROJECT NARRATIVE A significant proportion of the genes contained in the human genome do not encode proteins, and thus are termed 'non-coding RNAs'. Their role in a number of human physiological processes, including in infectious disease, are beginning to be appreciated. In this application, we are proposing to elucidate the role of non-coding RNAs in HIV infection, particularly in the context of Methamphetamine abuse. These studies will enable a more comprehensive understanding of the molecular basis for viral pathogenesis, and provide novel therapeutic opportunities for the treatment of HIV/AIDS.

National Institute of Health (NIH)
National Institute on Drug Abuse (NIDA)
Research Project (R01)
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Special Emphasis Panel (ZDA1-SXC-E (14))
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Caulder, Mark
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Sanford-Burnham Medical Research Institute
La Jolla
United States
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Xiong, Xiao-Peng; Kurthkoti, Krishna; Chang, Kung-Yen et al. (2016) miR-34 Modulates Innate Immunity and Ecdysone Signaling in Drosophila. PLoS Pathog 12:e1006034
Gong, Danyang; Kim, Yong Hoon; Xiao, Yuchen et al. (2016) A Herpesvirus Protein Selectively Inhibits Cellular mRNA Nuclear Export. Cell Host Microbe 20:642-653
Han, Jingfen; Cai, Jia; Borjihan, Wuyinga et al. (2015) Preparation of novel curdlan nanoparticles for intracellular siRNA delivery. Carbohydr Polym 117:324-30
Sakurai, Kumi; Talukdar, Indrani; Patil, Veena S et al. (2014) Kinome-wide functional analysis highlights the role of cytoskeletal remodeling in somatic cell reprogramming. Cell Stem Cell 14:523-34
Yang, Chao-Shun; Chang, Kung-Yen; Rana, Tariq M (2014) Genome-wide functional analysis reveals factors needed at the transition steps of induced reprogramming. Cell Rep 8:327-37
Lin, Nianwei; Chang, Kung-Yen; Li, Zhonghan et al. (2014) An evolutionarily conserved long noncoding RNA TUNA controls pluripotency and neural lineage commitment. Mol Cell 53:1005-19
Li, Zhonghan; Chao, Ti-Chun; Chang, Kung-Yen et al. (2014) The long noncoding RNA THRIL regulates TNF? expression through its interaction with hnRNPL. Proc Natl Acad Sci U S A 111:1002-7
Patil, Veena S; Zhou, Rui; Rana, Tariq M (2014) Gene regulation by non-coding RNAs. Crit Rev Biochem Mol Biol 49:16-32
Yang, Chao-Shun; Rana, Tariq M (2013) Learning the molecular mechanisms of the reprogramming factors: let's start from microRNAs. Mol Biosyst 9:10-7
Shen, Yang; Altman, Michael D; Ali, Akbar et al. (2013) Testing the substrate-envelope hypothesis with designed pairs of compounds. ACS Chem Biol 8:2433-41

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