dh003i's Journal: RNAi or asRNA as a medical treatment

idea in progress...facts and research to come

Well, I guess I haven't told anyone here what I do for a living -- I research molecular genetic on S. cerevisiae, a yeast. Anyways, because I'm a biologist, I take great interest in various biological developments. Most prominent among them is RNAi/asRNA.

RNAi is anti-sense mRNA: an RNA transcript of the non-coding strand of DNA. Because of its complementarity with mRNA, it hybridizes to mRNA, forming double-stranded RNA. This effectively prevents that gene's mRNA product from being translated into a protein. Thus, RNAi can be used to prevent the translation of mRNA -> protein for specific proteins.

With this in mind, it occured to me that RNAi could have a use in treating HIV, for example. HIV, as all of you know, is human immuno defeciency virus: It's a retrovirus, its genome encoded by RNA, not DNA. Once it enters the cell, its genome is reverse-transcribed by by its reverse transcriptase -- a polymerase which uses RNA as a template to make DNA. The HIV DNA is then incorporated into the genome by an Integrase, and then goes through a dormant phase, before it eventually activates and spreads. If you're interested in the HIV life-cycle, here's my summary (summarized from HIV1: 15 Proteins and an RNA) [this requires some knowledge of biology to understand].

1. Viral transcripts expressed the promoter with Tat (a protein) greatly enhancing the rate of transcription.
2. Regulated by Rev, spliced and genomic-length RNAs transported from nucleus to cytoplasm, where may be translated or packaged.
3. Viral mRNAs translated in cytoplasm; Gag and Gag-Pol polyproteins become localize to cell membrane. Env mRNA translated at ER.
4. Core particle assembled from Gag and Gag-Pol polyproteins, Vif, Vpr, Nef, and genomic RNA; immature virion starts budding from cell surface. To provide SU and TM proteins for outer membrane coat during budding, Env polyprotein released from complexes with CD4 (cell surface HIV-1 receptor), coexpressed with Env in the ER
5. Vpu assists by promoting CD4 degradation.
6. Env transported to cell surface, where its prevented from binding ti CD4.
7. Nef promotes endocytosis and degradation of surface CD4.
8. Particle buds and releases from SU- and TM-coated cell surface.
9. Virion matures.
10. TM undergoes conformational change, promoting virus-cell membrane fusion, allowing entry of core into cell.
11. Virion core then uncoated, exposing viral nucleoprotein complex, containing MA, RT, IN, Vpr, and RNA.
12. Complex transported to nucleus.
13. Genomic RNA reverse transcribed by RT into partially duplex linear DNA.
14. IN catalyzes integration of viral DNA into host chromosome and DNA repaired. Virus life-cycle now complete.

Note that HIV has only nine genes, encoding 15 proteins. To my knowledge, the 15 proteins encoded by the HIV genome have little homology to any proteins in the host, H. sapiens. Thus, using RNAi -- which blocks the translation of its complementary strand to protein -- one could block the synthesis of all HIV proteins, effectively preventing HIV from carrying out its life-cycle beyond integration with the human genome.

The problem with this is that HIV, like everything else, evolves. One solution to this might be to use RNAi to all of the HIV-proteins, making evolutionary adaptations more difficult. Another problem is there are many different strains of HIV, thus you would need to PCR amplify and sequence the HIV DNA from any infected person. Another problem is how to administer the RNAi, and the possible cost implications. I believe RNAi is expensive -- but then again, so are any other "treatments" for AIDS. This is a treatment, not a cure.

Just in case you're wondering, this is not just a bunch of hand-waiving I'm doing here. This is a real prospect, which others have written on and thought of before me. Take a look at my refs. I plan on writing more on this topic.

RNA interference--a new weapon against HIV and beyond. N Engl J Med 2002 Oct 24;347(17):1364-7.

Frankel AD, Young JA. HIV-1: fifteen proteins and an RNA. Annu Rev Biochem 1998;67:1-25.

Shahabuddin M, Khan AS. Inhibition of human immunodeficiency virus type 1 by packageable, multigenic antisense RNA. Antisense Nucleic Acid Drug Dev 2000 Jun;10(3):141-51