Irwin McLean's filaggrin readthrough drug could be revolutionary

Recently I predicted that nothing resembling a cure for eczema would appear for at least 25 years. I followed that up with a prediction that if a surprise cure were to emerge, it would be an anti-itch therapy.

At least one reader disagreed, and pointed me to a strategy now being developed at the University of Dundee in Scotland: drugs to stimulate or enable filaggrin expression in patients with one or two defective copies of the corresponding gene, FLG. At least one such drug is in the very earliest stages of drug development, toxicology studies in animals. If the drug succeeds in human clinical trials, we might see it in clinics in about 15 years. Potentially, such a drug could help some of the patients most severely affected by eczema.

The best review on filaggrin I’ve seen was co-written by three authors, two of whose names I am familiar with as among the biggest in the field of eczema research: Irwin McLean, who led the team that linked mutations in FLG to increased risk of developing ichthyosis vulgaris and eczema, and Donald Leung, principal investigator of the Atopic Dermatitis Research Network. (The first author is Alan Irvine, a colleague of McLean’s who works in Ireland.)

FLG is a giant, and unusual, gene, one of the last to be sequenced by the Human Genome Project. It encodes an enormous protein, profilaggrin, which contains from 10 to 12 repeats that are cleaved off into individual filaggrin units. Filaggrin itself has several important roles in the upper layers of the skin: it flattens skin cells into their characteristic final shape; it helps bind these cells together into a barrier; and it breaks down into the acidic “natural moisturizing factor.”

Many mutations have been found in FLG. Interestingly, if you take any particular ethnic group (say Japanese), there will be a characteristic profile of mutations for this group that is likely to be different than the profile for another group (say Scottish).

FLG (read from left to right; red hexagons are filaggrin units.) Common mutations in Asian and European populations. Look how early the nonsense mutation R501X appears. Figure 3A from Irvine, McLean, and Leung's NEJM review

All filaggrin variants are either “nonsense” or “frameshift” mutations in DNA that encodes protein (as opposed to so-called “junk DNA”). In a nonsense mutation, the correct DNA base has been replaced with a wrong one, and the upshot is that the protein-making machinery, known as the ribosome, runs into a code that it doesn’t recognize; it can’t add an amino acid to the growing protein, and it stops decoding profilaggrin at that point.

If the nonsense mutation occurs early enough, before the first filaggrin unit in FLG, no filaggrin gets made at all.

I believe that with a frameshift mutation (in which one or more DNA bases are missing or added) the protein is very likely to be terminated soon afterward. The end result is the same: little or no filaggrin.

In his 2006 Nature Genetics paper, McLean and his group identified two mutations, R501X (nonsense) and 2282del4 (frameshift), which have turned out to be the most common in Caucasian populations. Both R501X and 2282del4 occur early in the first filaggrin repeat. That means that if you have one such mutation, you will have one good copy of FLG and one bad copy; and if you have mutations on both your copies of FLG, you won’t have any filaggrin at all, and there is a high chance that you have eczema.

Soon after their 2006 discovery, McLean and first author Frances Smith applied for a US patent,  “Prevention/treatment of ichthyosis vulgaris, atopy and other disorders.” The patent, number 8,338,386, was granted only recently, on December 25, 2012. It makes many claims, all relating to the ability of five antibiotic drugs, or potentially tRNA molecules, to force the ribosome to read through nonsense mutations.

McLean and Smith’s patent is aimed at the nonsense mutation R501X (they say so in the patent), because it occurs so early in the gene. Such a drug would also work for nonsense mutations later in the sequence.

The drug or agent would not work on frameshift mutations such as 2282del4, as I understand it.

One cool thing about a readthrough drug would be that it would have its strongest effect on people who had nonsense mutations on both copies of FLG. A readthrough drug would theoretically make both copies functional. People with only one mutated copy of FLG would still benefit from having that number increased to two.

In the patent,“atopy” is mentioned in the title and the background information, but neither “atopy” nor “atopic dermatitis” appear in any of the 14 explicit claims. I don’t know whether this matters. I'm not an IP lawyer. It seems curious that the inventors left it out though.

Another curious fact is that only five specific drugs are mentioned: gentamicin, paromomycin, neomycin, tobramycin and negamycin. There is no discussion of the drug discovery process—any tweaking of molecules for greater effect or less toxicity—that I can see. I don’t know whether this matters either.

From what I can tell, McLean’s group has at least one of these compounds, which has most likely been altered from its original structure, in “toxicology” (which means testing in mice, rats, etc.) (see page 16). If you look at this handy graphic provided by the FDA, you will see that toxicology studies are step 2 of 12 in the drug discovery-to-market process. So it is extremely early days and you have to keep in mind that, as I keep saying, almost all drug candidates fail at some stage of clinical testing.

A relevant factor is also that currently there is no FDA-approved drug that acts by this mechanism—by causing the ribosome to ignore nonsense mutations. Ataluren, a drug to cure Duchenne muscular dystrophy and cystic fibrosis, is a readthrough drug in phase III clinical trials. The FDA is apparently especially careful when approving drugs that are “first-in-class,” or the first of their general type. So it is worth following Ataluren’s progress closely; its success could mean that we might see an eczema readthrough drug sooner.

Hat tip to Anonymous (you know who you are)

Filaggrin mutations cause distinct pattern of eczema in children

The giant protein filaggrin has several vital functions in skin. People with mutated copies of the filaggrin gene (FLG) are at risk of developing eczema that begins earlier and is more severe than usual. A new population study by Danish scientists (published in the journal PLoS ONE) now shows that children with FLG mutations develop a distinct variety of eczema, with emphasis on exposed areas such as the cheeks and the backs of the hands.

The research, led by Hans Bisgaard at the University of Copenhagen, could in the future help doctors diagnose children at risk of developing eczema and design personalized treatment for them—including therapy that could change the course of the disease.

The researchers analyzed data from the Copenhagen Study on Asthma in Childhood, which comprised 411 children born to mothers with asthma and followed them over the course of seven years, with checkups every six months (or more often, if eczema flares warranted). The scientists tested DNA from the children, checking to see if they had one of the two most common FLG mutations, known as R501X and 2282del4.

The results were not as cleancut as one might like. Roughly 15% of the 170 children who developed eczema had FLG mutations. But so did 7% of the 212 children who did not develop eczema. So clearly having mutated FLG does not guarantee eczema, and there are other factors at work to compensate for the mutation or cause disease to develop even if you have good filaggrin.

The researchers found that, in general, short- and long-term symptoms of eczema were worse in children with mutated FLG; and the disease set in earlier and flares tended to cluster in certain areas, most importantly  the cheeks and backs of the hands.

What is your child’s eczema like? Or what was yours like as a child? Does it fit this pattern? I seem to remember it concentrated on the backs of my knees and the insides of my elbows. But over the years it has moved around a lot. Maybe we will see scientists develop a catalog of eczema subtypes caused by known mutations.

Big genetics

Genetics is all pretty abstract until you find out something about yourself. I only know one thing for sure about my own genome-- I have one copy of the most common mutation for cystic fibrosis. I found this out when Hidden B and I had prenatal screening done about four years ago. The estimated chance of having this mutation is about 5%, so I was unpleasantly surprised. I'm defective! (And each of my kids has a 50% chance of being a carrier.)

On the genetics front, big big news today, although I didn't see anything appear in a major outlet. Maybe I missed it-- more likely is that the news was too complex and not attractive enough for the average reader for newspaper editors etc. to assign the story to reporters.

You'll find decent writeups at Nature News and GenomeWeb. A gigantic international research coalition, the 1000 Genomes Project (nearly as many authors as genomes) published a paper in Nature describing how they sequenced about 880 human genomes. I'll leave out the details, which, frankly, are lost on me, but the point of the work was to get a handle on how our DNA varies from one human to the next. An astonishing quote from the abstract:

"On average, each person is found to carry approximately 250 to 300 loss-of-function variants in annotated genes and 50 to 100 variants previously implicated in inherited disorders."

Hoo boy. The authors are saying, in essence: each of us is a factory reject. If we each carry 250-300 genes that ought to work but don't, imagine how much redundancy is built in. If a gene is broken, there are others to compensate for it.

This is why it's so hard to find connections between single genes and diseases. It's why scientists think it's a big deal to find that about 20% of children with eczema have loss-of-function mutations in FLG, the filaggrin gene--because 20% is a large number! (Before I studied molecular biology, I would have thought scientists would only care about mutations that were found in, say, 75% of patients with a given condition.)

And EACH of us has 50-100 variants that put us at higher than average risk for a random grab bag of inherited conditions. Tay-Sachs, anyone? Alzheimer's? If you ask me, there's no need to extend the human lifespan. I don't need to discover how many weird things I might develop if I live past 85.

A much lower-profile item: some journal called Nature Precedings (appears to be a catalog of NIH project summaries) reports an ongoing project of interest to you and me: "Skin Microbiome in Disease States: Atopic Dermatitis and Immunodeficiency." Julia Segre and Heidi Kong at the NIH are studying patients with eczema and two immunodeficient conditions to profile the populations of bacteria and other microbes that live on our eczematous and non-affected skin--and in our nostrils! (A while ago, I don't have the reference, someone discovered that nasty bacteria hide out in our nostrils. So stop picking your nose.)