CRISPR and Crunchier

My understanding of CRISPR/Cas9 is simple: it’s a gene-editing tool that can change the DNA in the genome of an individual cell, like genomic search-and-replace, thereby modifying the cell before it performs its function(s), such as replication (cell division in non-neurons) and protein creation (gene expression).

2017-10-25 note: CRISPR/Cas13 operates on RNA instead of DNA, which takes it out of a gene-editing role and puts it into a more traditional gene-silencing role.

What I thought were misunderstandings others had around delivery (i.e., operating on one cell or few cells vs. operating on the [trillions of] cells in a mature organism) are now coming from the scientific community. Perhaps they are riding a wave of the public’s misunderstanding toward an anticipated cusp of popularity, assuming that the knots in perception will get worked out later.

Scientists are coming forward and implying that CRISPR can change the billions of copies of one’s genome in the mature human’s brain. Whether intended or not, they make it sound like a mature organism’s genome is in a single, tweakable control center: make one tiny change in one tiny place and change a mature person’s genetic destiny (and that of their offspring) forever. Easy. Done. They gloss over that a mature person comprises trillions of copies of their genome, throughout the cells of their body. Only at the fertilization stage is there a genomic control center where changes propagate. They gloss over entirely how genetic changes might propagate within a mature organism, and to its offspring. I think the key is viral delivery, yet I’m not entirely sure.

Coming to terms

Gene delivery: e.g., viral vs. non-viral delivery.
Gene drive: the phenomenon in which the inheritance of a particular gene or set of genes is favorably biased.
Germ cell vs. somatic cell: a cell that gives rise to gametes vs. a differentiated cell in the body.
Germline: a series of germ cells each descended from earlier cells in the series, regarded as continuing through successive generations.
Meiosis: a type of cell division that reduces the chromosome number by half. In the male, this results in sperm. In the female, this results in ova.
Mosaicism: the presence of two or more populations of cells with different genotypes in one individual, who has developed from a single fertilized egg.

Why I’m scratching my head

I’m scratching my SCA3 head because of this article from 2017-06-19, titled “CRISPR/Cas9-mediated gene editing ameliorates neurotoxicity in mouse model of Huntington’s disease.”

https://www.jci.org/articles/view/92087

The abstract concludes with this:

Our studies suggest that non–allele-specific CRISPR/Cas9-mediated gene editing could be used to efficiently and permanently eliminate polyglutamine expansion–mediated neuronal toxicity in the adult brain.

A quick reading of this sounds like they are talking about eliminating a genetic defect from a mature brain. Since they are talking about eliminating toxicity only, it gets a little more nebulous:

Bilateral assumptions

In the SCA realm, I think there are various assumptions others make, which I am not ready to make, though I also make assumptions of my own. This is what I discern:

Most cells don’t matter?

Others assume that with HD, SCA, and perhaps other genetic brain diseases, only a small fraction of all cells needs to be fixed to fix the disease. In other words, most cells don’t matter.

Intuitively, I’m not ready to make that assumption. My assumption is that most cells do (or will) matter. A typical cerebellum comprises 69 billion nerve cells and 16 billion non-nerve cells. Will viral delivery fix them all? Making that assumption is a big leap.

Protein creation activity is small?

Perhaps there’s a deeper assumption that the toxic polyQ protein creation in the cerebellum is at a rate that can be matched by the cell fix rate, et voilà. Thinking of the cerebellum as a machine that churns out toxic protein at a slow rate, perhaps that machine’s churn rate can be matched by CRISPR or different technique (e.g., even gene silencing, such as ASO) .

My assumption is that a less than 100% fix rate will leave upwards of billions of ticking time bombs that are susceptible to going off later. A lot of cells might not be participating in the toxic churn now, but then they will later.

This goes along with my guess that the best that gene silencing has to offer is disease amelioration but not eradication in an individual. And by how small a percentage? How temporarily? How long until the time bombs left behind go off?

Side note: the HD article above does use ameliorates in the title (and nowhere in the body—that is telling!), which is a word I have used in a past article.

Just test it?

There seems to be a trend among some scientists: just test it and see what happens. If you get the results you’re looking for, then the nay-sayers were wrong. Results trump having an understanding, even if there’s no viable explanation.

My thoughts: this is very dangerous territory. This might be where we are in 2017, but it’s very unsettling. Certainly, this is the impetus behind many thousands of drug repurposing investigations, including trigriluzole.

Final thoughts

It remains my understanding that polyQ genetic defects and their diseases, such as HD and SCA, aren’t eradicable from an individual if born (conceived) with one. I came to that realization a while ago. Still, there might be some future disease-modifying treatments that reduce symptoms by attacking the disease rather than the symptoms, but with no expectation of eradicating the disease from an individual, just ameliorating it—fractionally and temporarily. That’s the middle ground that’s opening up. And since life itself is temporary, temporary might be good enough.

Addendum—what is CRISPR good for?

If you’re born with SCA(3), there is no way to completely rid your brain of it. On the other hand, CRISPR with viral delivery could eventually be used to fix a large fraction of the troublesome brain cells, if fixed before they die. The fewer and younger the cells are, the better. That is, the fertilization stage offers a fix opportunity, but the newborn stage is the next best time.

The assumption I’m apparently supposed to make is that eventually delivery and efficacy (or is it effectiveness?) of drugs will improve to the point that SCA3 in an adult is stretched out to beyond one’s lifetime: the disease is not cured or eradicated from an individual, but perhaps the individual could avoid having to deal with the disease, except when having children, since germ cells can still pass on the defect.

That is so many decades past my lifetime, if ever, it barely registers with me.

What is non-viral CRISPR potentially good for?

CRISPR’s first trial applications (in 2017) are towards some cancers. What is cancer, in basic terms? Cancer is abnormal cell growth, often involving tumors, though leukemia is different (i.e., abnormally-formed white blood cells). Since cancer involves cells and the mutations of genes contained therein, it’s considered genetic, though not in the same sense as SCA, which involves a single hereditary defect in a single DNA location, replicated trillions of times; tumorous cancer is more local, random, and can be triggered externally—for example, by radiation, by cigarette smoke, etc.

Being explored now is using CRISPR to destroy cancerous cells as an alternative to chemotherapy or surgery, where (relatively few) damaged cells are essentially piggybacking on (relatively many) healthy cells, which is very different from the idea of modifying billions of neurons in the SCA brain.

My understanding of diabetes and some other diseases is that when the brain is not the attack target of the disease, there is more potential to treat the destruction caused by the disease. This goes for some kidney diseases and other non-brain organ diseases.

Even with muscular dystrophy, the disease attack target is the muscles, not the brain, which opens some therapeutic possibilities involving both CRISPR and stem cells. I don’t mean to sound like I’m predicting panaceas for everything I don’t understand, as others are willing to do for SCA and HD. Quite simply, ameliorative therapy applied to damaged muscles simply sounds more beneficial than ameliorative therapy applied to a damaged brain.

Neuronal destruction in (most of) the brain cannot be fixed—or fully prevented post-zygote stage—and parts of the brain are not replaceable. For the foreseeable decades, I think the best case for genetic brain diseases such as SCA and HD (in adults) will be super-expensive ameliorative treatments that prolong a miserable life. As such, they will be largely undesirable, and undesirability will hinder the unspoken implication of ameliorative treatments magically evolving into cures, despite pharmaceutical companies being on a profit-driven, 20-year patent cycle.

More fundamentally, I don’t see why pharmaceutical companies would accommodate those unwilling to use decades-old IVF+PGD (USD 20,000 or so) or worst case, unwilling to use genetic testing of any kind and bank on an option for USD 1,000,000+ risky (i.e., spinal cord injections) and imperfect therapy on an asymptomatic newborn, or child.

My earlier thoughts on CRISPR.

Humor.

2018-04-20 (release). Movie ridiculousness: “Rampage“. Genetically modifying a gentle ape transforms him into a raging monster.

2018-06-11: “Edited cells might cause cancer

2018-06-12: “How Cells Fend Off Gene Editing

One Reply to “CRISPR and Crunchier”

  1. Thanks Jens.A time machine in genetically reverse gear sounds like the ticket. Read your bit on crispr and your analysis helps to keep my expectations real.For me that is important as I deal with the ‘disorder’.

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