The Futile Cycle

Yet another article from Nature today on RNA therapeutics, this time on using RNAi to stop angiogenesis in the eye to prevent blindness. Some people have seen that the VEGFR receptor can be targeting for knockdown by RNA interference using short 21-nucleotide siRNAs. Apparently, no one bothered to do the control here.

The authors of this paper did the control, in which one uses a “scrambled” or off-target siRNA to show that the effect of the silencing is sequence-specific. Except, in this case, the effect wasn’t sequence-specific. In fact, any old RNA would work, as long as it was longer than 21 nucleotides.

This might ring some bells about innate immunity. One of the early problems with RNAi in humans was that long double-stranded RNAs, which can be chopped up in cells to form the siRNAs, cause human cells to become inflamed. Specifically, the RNAs activated some Toll-like receptors, leading to a mounting of the innate immune response. This immune response was originally evolved to combat RNA viruses, which often have double-stranded RNA genomes or go through a double-stranded RNA intermediate during infection. This problem was later solved by using pre-made short RNAs, which don’t really induce the immune system response.

In this paper, it seems the authors have found this effect at play again. Many of the RNAs they tried activate the immune response, which in turn causes the cell to suppress angiogenesis!

Yesterday in Nature was a really exciting paper on miRNA-targeting therapeutics: Locked-Nucleic Acid-based knockdown of miRNAs in vivo!

microRNAs (miRNAs) are really tiny regulatory RNAs (about 22 nucleotides long); efficient, specific hybridization would normally require something much longer. Recently, though, the use of “locked nucleic acids” has become more popular. These are RNA analogues that have an extra bridge in the ribose sugar, making oligos of them rigid. Entropically, this greatly enhances binding of the LNAs to the RNAs, which means that one can use them for things like in situ hybridization much more easily and specifically! Not only that, but the use of LNAs instead of normal RNAs means that the half-lives of the oligos become much longer, similar to what one would see with morpholinos.

The authors injected LNAs into monkeys in order to target miR-122, which regulates cholesterol metabolism (among other things). They managed to effectively silence the miR-122 and they showed a drop in cholesterol levels!

Very exciting stuff!

To coincide with that amusing pseudoscience advertisement, I just came across a new paper in Cell explaining how cyclosporine A can lead to excessive hair growth in patients. Apparently, by modulating calcium signaling in hair follicle stem cells, cyclosporine A can tip stem cells out of their quiescent state earlier than normal, leading to more cell division and thus more hair. Elaine Fuchs has been studying hair follicle stem cells as a model system for differentiation and development, and this is a really neat paper that ties those topics together with cell-cycle regulation via an interesting signaling system.

One amusing assay that they conduct on mice is to shave them or dye their hair to look at the rates of hair growth. It seems to be a pretty common assay in the hair-growth and baldness fields of research, but I haven’t seen it before, and the pictures are funny to look at (my apologies to those who are touchy about mouse humiliation):

Abel Pharmboy has a link to a really neat article concerning primate geophagy (dirt eating). The authors of the article noticed that chimps tend to eat dirt right before they eat leaves of Trichilia rubescens, a plant that contains anti-malarial substances. The really cool part is that they found that something in the dirt might enhance the anti-malarial activity of the plant substance! Chimps may have evolved (culturally or biologically) to do some pharmacy! Now that’s cool!

Boston’s Mayor Thomas Menino apparently thinks that in-store health clinics (such as MinuteClinic) are unethical because they (gasp) make money off of sick people!

Wait, so what about pharmaceutical companies, medical device manufacturers, health insurance companies, doctors, nurses, ambulance workers, hospital staffers, and scientists who do research on clinical diseases (among others)? Maybe they shouldn’t be making money either! That would really encourage them to succeed in helping others!

And farmers shouldn’t be driven by profits, because they’re making money off of hungry people! And homebuilders shouldn’t be driven by profits, because they’re making money off of people looking for shelter!

To think that Boston would have a mayor so economically and morally illiterate.

Via Eurekalert, apparently having ultra-low cholesterol can be bad for you. Is this that surprising?

See, what I thought was really surprising was that other studies had, up until now, shown that having extremely low amounts of cholesterol (via high doses of statins) didn’t cause health problems. Cholesterol is an essential molecule in the body, and lowering cholesterol to less than natural levels seems like it would do harm…and now, apparently it does.

A great post from Marginal Revolution, where Tyler Cowen talks about how soldiers in the military seem to be eating quite well, on average. Of course, that’s not what he’s really talking about, but check out the post for a great analogy on why military systems aren’t necessarily generalizable to the public.

Derek Lowe has an excellent blog post on the scam of touting “natural” remedies as somehow better than “artificial” ones. Shame on the New York Times for not doing its groundwork; then again, what do you expect of the mainstream media, facts?

As everyone probably already knows, the 2007 Nobel Prize in Medicine or Physiology went to Mario Capecchi, Martin J. Evans, and Oliver Smithies for developing a way to create transgenic mice by targeting genes. Smithies and Capecchi developed the methodology for creating cells which had specific genes knocked out, while Evans developed a lot of the methodology for using these techniques in stem cells to create live mice that would carry these induced mutations. The knock-out mouse is now one of the most versatile models we have for testing questions about genes and diseases. A good explanation of the process that they developed is explained here.

I know a lot of people just skim the press release, but there are some really interesting nuggets in the “Advanced Information” section of the announcement. For example, Evans first tried to use cancer cells to make mice, but (as you would expect), the cells were just too sick to actually make a good organism. So he actually went through and found the cells the we now use as “Embryonic Stem Cells,” which he used to create mice that were a mosaic of cells of two different mice.

Another thing was that Capecchi and Evans both wrote grants proposing this research (on gene targeting) to the NIH and the UK Medical Research Council (respectively), but both were rejected, because the reviewers thought it would be too hard and unlikely to succeed!

Finally, though this isn’t mentioned on the Nobel website, Capecchi had a really hard life as a child. His mother was arrested and put away in a concentration camp during World War II (for being an anti-Fascist bohemian), and he was left alone for four years as a street urchin. Fortunately, he was later found (very sick and malnutritioned) by his mother (who survived). He moved to the US, went to school, then college, worked under Jim Watson at Harvard, and then went on to have a massively successful career (though, as I mentioned above, not without a few hiccups along that path as well). It’s an amazing life story, and the Nobel Prize surely can’t go to a better person.

Clifford J. Rosen has written a perspective in the New England Journal of Medicine summarizing his views on the FDA Advisory meeting on rosiglitazone (a.k.a. Avandia), which he was chair of.

I agree with his main conclusion, that rosiglitazone is probably not as good as some alternatives, but I have to say, his article’s stance on observational studies and meta-analyses was rather poorly presented. The main data he cites for showing that pioglitazone is better than rosiglitazone for cardiovascular risk is Gerrits et al., basically an observational meta-analysis. On the other hand, he essentially seems to dismiss the observaitional studies by Wellpoint, a health care insurer, which was much larger. I’m giving him the benefit of the doubt that he’s being self-consistent, but the way the article is written wrongly portrays his references. Consider that he says,

Moreover, we are facing a troubling paradox: preliminary data that were presented at the meeting and published by Gerrits et al. suggest that among the thiazolidinediones — a class of drugs that has been shown to improve metabolic control — rosiglitazone may increase cardiovascular risk whereas pioglitazone may reduce it.

Later on, when he mentions the Wellpoint study, he concludes,

The contrasts among the levels of evidence and the results regarding the safety of rosiglitazone raised new questions about relative and absolute risks but also highlighted the weaknesses of observational studies examining events that are common and whose rates are likely to be increased only slightly by a given drug, even in a large cohort (such as that used by WellPoint, which comprised 160,000 patient records).

Note that he never mentions that the Gerrits study is essentially an observational study, too, comprised of data pulled from a large health care insurer. So, the way he wrote the article casts a falsely bad impression on the studies showing little increase in cardiovascular risk for rosiglitazone compared to the alternatives, while not casting the same sort of critical eye at the studies that seem to support his conclusions.

A better (and I find, more convincing) argument would have been that pioglitazone has been demonstrated, in a clinical trial, to have fewer cardiovascular events than placebo, whereas rosiglitazone has not been shown conclusively to have less or more. So, if faced with a choice, it’s easy to recommend pioglitazone over rosiglitazone.

That argument would be much clearer than what he did, which was to simply cite a whole slough of meta-analyses and observational studies (the only non-meta-analysis data he cites at all are two clinical trials, both basically mum on cardiovascular risk), cast doubt on some of them, and then leave the reader to weigh one against the other while making the (unwarrented) conclusion that “a new ‘wonder drug,’ approved prematurely and for the wrong reasons by a weakened and underfunded government agency subjected to pressure from industry, had caused undue harm to patients.” Weighing meta-analyses that conflict with each other is for Ph.D. level statisticians, and I (nor, do I think, most of the readers of the NEJM) am not up to it. I’m still not terribly convinced that rosiglitazone has absolutely hurt patients; I think it’s premature to say so (otherwise, why not pull it from the market?), but certainly there are much more effective alternatives. Clifford Rosen just didn’t make a good case for it.