Tag Archives: Dscam

Maybe chemistry just isn’t that important in wiring the brain

Even the strongest chemical ego may not survive a current paper which states that the details of ligand receptor binding just aren’t that important in wiring the fetal brain.

The paper starts noting that there isn’t enough information in our 3.2 gigaBase genome to specify each and every synapse. Each cubic milliMeter of cerebral cortex is stated to contain a billion of them [ Cell vol. 163 pp. 277 – 280 ’15 ].

If you have enough receptors and ligands and use them combinatorially, you actually can specify quite a few synapses. We have 70 different protocadherin gene products found on the neuronal surface. They can bind to each other and themselves. The fruitfly has the dscam genes which guide axons to their proper position. Because of alternative splicing some 38,016 dscam isoforms are possible.

It’s not too hard to think of these different proteins on the neuronal surface as barcodes, specifying which neuron will bind to which.

Not so, says [ Cell vol. 163 pp. 285 – 291 ’15 ]. What is important is that there are lot of them, and that a neuron expressing one of them is unlikely to bump into another neuron carrying the same one. Neurons ‘like’ to form synapses, and will even form synapses with themselves (one process synapsing on another) if nothing else is around. These self synapses are called autapses. How likely is this? Well under each square millimeter of cortex in man there are some 100,000 neurons, and each neuron has multiple dendrites and axons. Self synapse formation is a real problem.

The paper says that the structure of all these protocadherins, dscams and similar surface molecules is irrelevant to what program they are carrying out — not synapsing on yourself. If a process bumps into another in the packed cortex with the same surface molecule, the ‘homophilic’ binding prevents self-synapse formation. So the chemical diversity is just the instantiation of the ‘don’t synapse with yourself’ rule — what’s important is that there is a lot of diversity. Just what this diversity is chemically is less important than there is a lot of it.

This is another example of “It’s not the bricks, it’s the plan” in another guise — https://luysii.wordpress.com/2015/09/27/it-aint-the-bricks-its-the-plan/


I sincerely hope it works, but I’m very doubtful

A fascinating series of papers offers hope (in the form of a small molecule) for the truly horrible Werdnig Hoffman disease which basically kills infants by destroying neurons in their spinal cord. For why this is especially poignant for me, see the end of the post.

First some background:

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.

Intellectually fascinating but ghastly to watch.

This brings us to the current papers [ Science vol. 345 pp. 624 – 625, 688 – 693 ’14 ].

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 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.

Why am I skeptical? 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.

Why does the paper grip me so. I watched the beautiful infant daughter of a cop and a nurse die of it 30 – 40 years ago. Even with all the degrees, all the training I was no better for the baby than my immigrant grandmother dispensing emotional chicken soup from her dry goods store (she only had a 4th grade education). Fortunately, the couple took the 25% risk of another child with WH and produced a healthy infant a few years later.

A second reason — a beautiful baby grandaughter came into our world 24 hours ago.

Poets and religious types may intuit how miraculous our existence is, but the study of molecular biology proves it (to me at least).