03/05/2012
Paul Muhlrad

I seem to be in the confessing mood (see my first blog post), so here’s another one: Yes, Vance Taylor, I’m one of those nerds you alerted everyone about.  In fact I actually DO find genetics exhilarating!  Think about it: a four-letter alphabet — A, C, G, T — that spells a three-billion-letter instruction manual for who we are, what we do, and how we operate.  And that instruction manual is stored, read, copied, broken and repaired in virtually every one of our body’s trillions of cells — nonstop, every moment of our lives.  As a friend of mine likes to say — that’s gobsmacking!

Geneticists tend to be a clever and audacious bunch.  They get a kick out of taking a new discovery about how genes work, and quickly turning that discovery into an investigational tool that they can use to make more discoveries.  For instance, in the 1960s and 70s, scientists discovered certain enzymes that could slice through the DNA thread in certain defined positions, and other enzymes that could stitch the loose ends back together.  Those discoveries quickly ushered in the era of genetic engineering.

A while ago, one of those audacious geneticists coined a term for this style of science, where you leverage discoveries to make more discoveries.  He said it somewhat tongue-in-cheek, I think, but it stuck:  The Awesome Power of Genetics (Try to say it with some dramatic expression).  You can abbreviate it, APOG.

Neuromuscular disease researchers have taken APOG to new heights.  They’re no longer using genetic discoveries just to learn more about the diseases they study, but to develop therapies.  That’s a theme we’ll be seeing over and over at this week’s MDA Clinical Conference.  Exon-skipping, antisense oligonucleotides, premature stop codon read-through, gene therapy, RNAi — these are all therapeutic strategies that are a result of the snowballing effect of APOG.

Dr. Sanjay Bidichandani (my boss) kicked off today’s morning session with a primer:  “ABCs of Genetics.”  His task, he said, was to provide the ABCs so we’d be prepared to understand the DEFGs, etc., of all the speakers to come — a difficult task, indeed, for a 45-minute talk.  I think he did a great job covering the essential highlights, although there was a lot of material to absorb.  So his audience can be excused if they didn’t catch everything. 

First, he covered the basics of DNA structure.  The “Jeopardy” level images most of us have of DNA are either the double helix or the X-shaped chromosomes we learned about in high school.  Sanjay pointed out that, while both of those structures are accurate, DNA spends most its time partially coiled up around proteins in a form called chromatin.  Different genes can become “activated” or “silenced” depending on how tightly they are compacted in the chromatin, and this type of regulation, called “epigenetics,” is becoming increasingly recognized as important in neuromuscular disease.

He also covered important genetic terms, like locus, allele, recessive, and dominant.  Those terms can be complicated, but he explained that the most important thing is that recessive diseases are usually caused by mutations that eliminate or lower the amount of an important protein (“not enough of a good thing”).  Geneticists call this a loss-of-function mutation.  Dominant diseases, on the other hand, happen when a mutation imparts a protein (or RNA) with some new or heightened property (“too much of a good thing,” or even worse, “too much of a BAD thing”). 

This all sounds like trivia, of interest only to geneticists, but it’s actually the key to therapy development strategies.  For recessive diseases, the aim is to replace, supplement, or fix the protein that is missing or not working up to speed.  But that approach won’t work for dominant diseases.  If you release a bull in a china shop, it won’t help much to cart in more china; you have to get rid of  (or at least restrain) the bull!  I think we’ll see many examples of these two different therapeutic approaches throughout the conference.

Dr. Kevin Flanigan, from Nationwide Children’s Hospital in Columbus, Ohio, spoke next.  Dr. Flanigan is the world’s leading expert on detecting and interpreting mutations that lead to Duchenne and Becker muscular dystrophies.  Both diseases are caused by different types of mutations in the same gene, which encodes an important muscle protein called dystrophin.  As genes go, dystrophin is a monster by sheer size.   At 2.4 million base pairs, it’s the largest gene in the human genome.  It contains 79 exons (protein coding segments used as the instructions to assemble the dystrophin protein), interrupted by introns (spacer segments, which get spliced out of the final genetic instructions).  Most (about 65 percent) of the mutations in the dystrophin gene that cause DMD or BMD are large deletions — whole-scale elimination of complete segments of the gene.  And because genetic instructions come in three-letter words (Sanjay explained this earlier in his talk), it is critical whether the deletions take place between those words or within them.

Dr. Flanigan used this analogy:

THE BIG RED DOG RAN AND SAT

This sentence makes sense, even if it is a little silly.  Now let’s delete a letter (the G) from within one of the words:

THE BIR EDD OGR ANA NDS AT

Now the sentence is utter nonsense.  A gene containing the same type of deletion is similarly unintelligible.

Instead, let’s delete an entire word “BIG”:

THE RED DOG RAN AND SAT
 
Now the sentence makes sense again, even if it may not contain quite as much information.  Dr. Flanigan explained that this is what accounts, almost all the time, for the difference between Duchenne and Becker muscular dystrophy.  Duchenne mutations are “out-of-frame.”  They break up genes within the words and turn the genetic instructions into gobbledygook.  Becker deletions are clean slices between words.  They result in instructions that, while less thorough than the unscathed gene, still contain enough information to make a partially functional dystrophin protein.

Much of the remainder of Dr. Flanigan’s talk described several modern mutation-detection tests that his lab has developed for dystrophin.  Together, these tests can detect around 95 percent of dystrophin mutations.  To learn more about genetic testing, you can visit www.genetests.org.

Dr. Michael Shy, a neurologist from the University of Iowa, and a member of MDA’s Medical Advisory Committee (and co-chair of this conference), spoke next.  Dr. Shy presented an inspiring talk on the implications of genetics for therapy development.  Using just a few of the many examples (Duchenne/Becker muscular dystrophy, spinal muscular atrophy, myotonic dystrophy, Friedreich’s ataxia, and Charcot-Marie-Tooth disease), Dr. Shy showed how the identification of the disease-causing gene has been critical for guiding rational approaches to therapy, many of which are currently in clinical trials (or, in the case of Pompe disease, extending lives).

He next discussed the value of animal models for understanding disease mechanisms and for screening possible therapeutic agents.  Small animal models, in particular, such as fruitflies, worms and zebrafish, are indispensable for large-scale drug screening.  He showed a video of a gee-whiz robotic workstation carrying out a high-throughput screen that can test more than a half-a-million compounds in less than two weeks!

With all the discussion on genetics and genetic testing, the next pair of speakers provided a key component to the conversation:  genetic counseling.  Carly Siskind and Shawna Feely are genetic counselors from Stanford University and the University of Iowa, respectively.  As they titled their talk, they covered many of the practical, legal and ethical issues in genetic testing “From Soup to Nuts.”   I had no idea what a desperate shortage of genetic counselors exists in the United States; Shawna is one of only eight genetic counselors in the state of Iowa!  Here are some informative Web links that Carly and Shawna provided for learning about genetic testing for neuromuscular diseases:

• evs.gs.washington.edu/EVS/
• dmd.nl/
• molgen.ua.ac.be/cmtmutations/Mutations/
• hihg.med.miami.edu/gvd-nmd

The final talk of the morning session came from Dr. Jerry Mendell, the other co-chair (with Dr. Shy) of the MDA Clinical Conference.  Dr. Mendell presented an exciting pilot study, which he led and recently published, for a newborn screening plan for Duchenne/Becker muscular dystrophy.  We saw in the previous talks how important it is not only to identify infants with dystrophin mutations, but to know exactly what type of mutation (e.g., in-frame or out-of-frame deletions or insertions) they have.  This will become even more important as therapies emerge, since several of these therapies (e.g., exon-skipping and premature stop codon read-through) will depend on knowing the nature of the mutation. 

Dr. Mendell proposes a two-tier testing plan.  The first step tests for levels of CK (a muscle enzyme that typically leaks from damaged muscles into the bloodstream) in dried blood spots collected from newborns (many states routinely collect blood spots for testing other genetic conditions).  If a blood spot shows abnormally elevated CK levels, the same dried blood sample is then subjected to DNA testing.  After four phases of pilot tests, Dr. Mendell’s group developed a test that was highly effective at identifying dystrophin mutations, and had a false-positive rate of only about 1 in 200.  Because most of the screen involves CK testing (which costs only one dollar per test) rather than DNA testing (which currently costs $150 per test), the Mendell method represents a huge cost savings over plans that use DNA testing from the start. 

This was an exciting talk, and sparked a robust discussion from the audience.  Dr. Mendell also made a bit of news by letting slip a little secret:  MDA will be hosting a symposium this fall, co-chaired by Dr. Mendell, focused on newborn screening for DMD/BMD!  You can read more about Dr. Mendell’s newborn screening plan in the Quest News Online article Efficient System Developed for DMD Newborn Screening.

Tomorrow:  Immunology!  See you all tonight at the bowling lanes …