Stephen Hawking R. I. P.

Stephen Hawking, brilliant mathematician and physicist has died.  Forget all that. He did something for my patients with motor neuron disease that I, as a neurologist, could not do.  He gave them hope.

What has chemistry done for them?  Quite a bit, but there’s so much left.

Chemistry, when successful, just becomes part of the wallpaper and ignored. All genome sequencing depends on what some chemist did.

For one spectacular example of what, without chemistry, would be impossible is Infantile Spinal Muscular Atrophy (Werdnig Hoffmann disease).  For the actual molecular biology behind it — please see — https://luysii.wordpress.com/2016/12/25/tidings-of-great-joy/.   Knowing the cause has led to not one but two specific therapies — an antisense oligonucleotide and a virus which infects neurons and actually changes the gene.

So knowing what the cause of a disease is should lead to a treatment, shouldn’t it?  Hold that thought.  Sometimes one form of motor neuron disease (amyotrophic lateral sclerosis or ALS) can be hereditary.  Find out what is being inherited to find how ALS is caused.

Well, the first protein in which a mutation is associated with familial ALS (FALS) was found exactly 25 years ago.  It is called superoxide dismutase (SOD1).  Over 150 mutations have been found in the protein associated with FALS, and yet despite literally thousands of papers on the subject we don’t know if the mutations cause a loss of function, a gain of function (and if so what that function is), an increased tendency to fold incorrectly, and on and on and on.  It’s a fascinating puzzle for the protein chemist and over the years my notes on the papers I’ve read about SOD1 have ballooned to some 25,000 words.

If you’re tired of working on SOD1, try a few of the other proteins in which mutations have been associated with FALS — Alsin, TAF15, Ubiquilin, Optineurin, TBK1 etc. etc.  The list is long.

Now it’s biology’s turn.  Motor neurons go from the spinal cord (mostly) and brain to produce muscle contraction.  Why should only this tiny (but crucial) minority of cells be affected.  The nerve fibers leave the spinal cord and travel to muscle in nerves which contain sensory nerve fibers making the same long trip, yet somehow these nerves are spared.

More than that, why should these mutations affect only these neurons, and that often after decades.  Also why should great athletes (Lou Gehrig, Ezzard Charles, etc. etc. ) get the disease.

One closing point.  Hawking shows why, in any disease median survival (when 50% of those afflicted die) is much a more meaningful statistic than average duration of survival.  Although he gave my patients great hope, they all died within a few years even as he mightily extended average survival.

 

Tidings of great joy

One of the hardest things I had to do as a doc was watch an infant girl waste away and die of infantile spinal muscular atrophy (Werdnig Hoffmann disease) over the course of a year. Something I never thought would happen (a useful treatment) may be at hand. The actual papers are not available yet, but two placebo controlled trials with a significant number of patients (84, 121) in each were stopped early because trial monitors (not in any way involved with the patients) found the treated group was doing much, much better than the placebo. A news report of the trials is available [ Science vol. 354 pp. 1359 – 1360 ’16 (16 December) ].

The drug, a modified RNA molecule, (details not given) binds to another RNA which codes for the missing protein. In what follows a heavy dose of molecular biology will be administered to the reader. Hang in there, this is incredibly rational therapy based on serious molecular biological knowledge. Although daunting, other therapies of this sort for other neurologic diseases (Huntington’s Chorea, FrontoTemporal Dementia) are currently under study.

If you want to start at ground zero, I’ve written a series https://luysii.wordpress.com/category/molecular-biology-survival-guide/ which should tell you enough to get started. Start here — https://luysii.wordpress.com/2010/07/07/molecular-biology-survival-guide-for-chemists-i-dna-and-protein-coding-gene-structure/
and follow the links to the next two.

Here we go if you don’t want to plow through all three

Our genes occur in pieces. Dystrophin is the protein mutated in the commonest form of muscular dystrophy. The gene for it is 2,220,233 nucleotides long but the dystrophin contains ‘only’ 3685 amino acids, not the 770,000+ amino acids the gene could specify. What happens? The whole gene is transcribed into an RNA of this enormous length, then 78 distinct segments of RNA (called introns) are removed by a gigantic multimegadalton machine called the spliceosome, and the 79 segments actually coding for amino acids (these are the exons) are linked together and the RNA sent on its way.

All this was unknown in the 70s and early 80s when I was running a muscular dystrophy clininc and taking care of these kids. Looking back, it’s miraculous that more of us don’t have muscular dystrophy; there is so much that can go wrong with a gene this size, let along transcribing and correctly splicing it to produce a functional protein.

One final complication — alternate splicing. The spliceosome removes introns and splices the exons together. But sometimes exons are skipped or one of several exons is used at a particular point in a protein. So one gene can make more than one protein. The record holder is something called the Dscam gene in the fruitfly which can make over 38,000 different proteins by alternate splicing.

There is nothing worse than watching an infant waste away and die. That’s what Werdnig Hoffmann disease is like, and I saw one or two cases during my years at the clinic. It is also called infantile spinal muscular atrophy. We all have two genes for the same crucial protein (called unimaginatively SMN). Kids who have the disease have mutations in one of the two genes (called SMN1) Why isn’t the other gene protective? It codes for the same sequence of amino acids (but using different synonymous codons). What goes wrong?

[ Proc. Natl. Acad. Sci. vol. 97 pp. 9618 – 9623 ’00 ] Why is SMN2 (the centromeric copy (e.g. the copy closest to the middle of the chromosome) which is normal in most patients) not protective? It has a single translationally silent nucleotide difference from SMN1 in exon 7 (e.g. the difference doesn’t change amino acid coded for). This disrupts an exonic splicing enhancer and causes exon 7 skipping leading to abundant production of a shorter isoform (SMN2delta7). Thus even though both genes code for the same protein, only SMN1 actually makes the full protein.

More background. The molecular machine which removes the introns is called the spliceosome. It’s huge, containing 5 RNAs (called small nuclear RNAs, aka snRNAs), along with 50 or so proteins with a total molecular mass again of around 2,500,000 kiloDaltons. Think about it chemists. Design 50 proteins and 5 RNAs with probably 200,000+ atoms so they all come together forming a machine to operate on other monster molecules — such as the mRNA for Dystrophin alluded to earlier. Hard for me to believe this arose by chance, but current opinion has it that way.

Splicing out introns is a tricky process which is still being worked on. Mistakes are easy to make, and different tissues will splice the same pre-mRNA in different ways. All this happens in the nucleus before the mRNA is shipped outside where the ribosome can get at it.

The papers [ Science vol. 345 pp. 624 – 625, 688 – 693 ’14 ].describe a small molecule which acts on the spliceosome to increase the inclusion of SMN2 exon 7. It does appear to work in patient cells and mouse models of the disease, even reversing weakness.

I was extremely skeptical when I read the papers two years ago. Why? Because just about every protein we make is spliced (except histones), and any molecule altering the splicing machinery seems almost certain to produce effects on many genes, not just SMN2. If it really works, these guys should get a Nobel.

Well, I shouldn’t have been so skeptical. I can’t say much more about the chemistry of the drug (nusinersen) until the papers come out.

Fortunately, the couple (a cop and a nurse) took the 25% risk of another child with the same thing and produced a healthy infant a few years later.