Journal Club, Next Meeting November 30

I have pushed back the journal club for November 30 instead of November 23 for two reasons: (1) may decide to let you off the hook for class the week of Thanksgiving and (2) we can talk about an article while enjoying scrumptious desserts for the lab party.

In previous journal clubs, we have focused on therapeutics and seen how our nemesis, the antibody, has captured most of the therapeutics world. We discussed why this is, how antibodies have the advantage in some respects, but how aptamers show great promise with their many benefits. Over the summer, we talked about aptamers involved in drug delivery. If you are interested, those articles were:

• Lupold et al. Identification and characterization of nuclease-stabilized RNA molecules that bind human prostate cancer cells via the prostate-specific membrane antigen. Cancer Res (2002) vol. 62 (14) pp. 4029-33
• Chu et al. Aptamer:toxin conjugates that specifically target prostate tumor cells. Cancer Res (2006) vol. 66 (12) pp. 5989-92

For this month's journal club, I would like to focus on aptamers used for diagnostics.

• Davis et al. Staining of cell surface human CD4 with 2'-F-pyrimidine-containing RNA aptamers for flow cytometry. Nucleic Acids Research (1998) vol. 26 (17) pp. 3915-24

I chose an older paper for a number of reasons:

1. The authors developed the technique in a previous paper circa 1996
2. I would like to familiarize you with the procedures of flow cytometry
3. They selected against a conserved extracellular glycoprotein receptor
4. They showed potential binding sites using known antibodies
5. CD4 is a target of HIV
6. They used modified RNA for selection
7. The company was NeXstar Pharmaceuticals which later became SomaLogic with whom I've previously mentioned.
8. Jayasena, the directing author, published many aptamer related papers in the 1990's.

Questions I would like you to address:

1. Find original paper where aptamers were used in flow cytometry diagnostics (ref in paper). How does flow cytometry work?
2. How many papers has Jayasena published? Can you recreate his career based on publications?
3. What other methods had been developed at the time of writing for diagnostic aptamers? What has been developed since then? (Hint - check out a recent review for a summary)
4. What was novel about this paper?
5. Explain how CD4 is involved T cell recognition in addition to HIV infection (HINT: this will also require outside reading of a review article)
6. The authors utilized 2'-Fluoro modified nucleotides. What other modifications could they have used had they done the selection today? (HINT: look up current selections with modifications and modifications in general such as that discussed in another post on this blog).
7. Which region of the membrane do these aptamers bind to? What evidence shows this?

As always, please read the article and post questions in the comments section. This is especially true for the mentors.

Cheers! - Brad