Tag Archives: GWAS

Ashkenazi Jews are extremely inbred

Neurologists are inherently interested in  psychosis, not least because too much dopamine in the form of L-DOPA can trigger it.  I’ve always found it remarkable that dopamine blocking agents (phenothiazines, most antipsychotics) can attack psychotic thought itself.  This is much more impressive to me than the ability of other drugs (alcohol, coffee, marihuana, cocaine) to affect mood.

So it’s always worthwhile to read another paper about the genetics of schizophrenia, a very hereditary disease.  All the risk factors we’ve found by GWAS (Genome Wide Association Studies) account for at most of 1/3 of genetic risk.  For details please see https://luysii.wordpress.com/2014/08/24/tolstoy-rides-again-schizophrenia/.

So I was interested in another crack at finding more genetic causes of schizophrenia  [ Neuron 109, 1465–1478, May 5, 2021 ].  As often happens, the most interesting thing in the paper was something totally tangential  to my original interest in it. 

Here it is —   ”  For example, the Ashkenazi Jewish (AJ) population, currently numbering >10 million individuals world- wide, effectively derives from a mere 300 founders 750 years ago ” (Carmi et al., 2014;Nat. Commun. volume 5, 4835.).  

I find this assertion incredible.  But, as explained below, there is pretty good evidence (though subtle and quite technical) that it’s correct.

Ashkenazi Jews are those found in Europe and the Americas, as opposed to Sephardic Jews, found in the mideast and Africa

This is why Ashkenazi Jews were chosen for the study. Any deleterious genes producing schizophrenia  present in the original 300 wouldn’t have been washed out by natural selection in just 30 generations in 750 years. 

The Ashkenazim make the inbreeding among French Canadians look like pikers — a population of 2 million derived from a founder population of 9000 people over the next 170 years — for details please see https://luysii.wordpress.com/2019/07/17/the-wages-of-inbreeding/.  Note that neither population tried to inbreed, it’s just that there was no one else to breed with for the French Canadians, and culturally for the Ashkenazi’s.  

At least with the French Canadians we have immigration records to tell us how large the founder population was.  How sure are we about the 300 strong founder population of present day Ashkenazi Jews?  We’re not and I’m not even though it was published in a peer reviewed reputable journal.  There is a lot of guesswork in figuring out just how large a genetic bottleneck is.  It all depends on the model used, and I don’t trust models in general.  I’ve seen too many crash and burn. For details — https://luysii.wordpress.com/2019/03/03/i-mistrust-models-2/

But the Neuron paper contains a reference to another paper providing excellent empiric evidence for a small founder population.  PLoS Genet. 14, e1007329. 2018.  Here’s a direct quote.  It’s quite a mouthful.  I’ll try to explain what the terms mean, because I think many nonscientific types are likely to be interested in the idea that Ashkenazi Jews are that inbred. 

Just skip the paragraph if it’s incomprehensible, go to *** and read the explanatory material, and then read the paragraph again. 

“We estimate that 34% of protein-coding alleles present in the Ashkenazi Jewish population at frequencies greater than 0.2% are significantly more frequent (mean 15-fold) than their maximum frequency observed in other reference populations. Arising via a well-described founder effect approximately 30 generations ago, this catalog of enriched alleles can contribute to differences in genetic risk and overall prevalence of diseases between populations.”

****

Explanatory material.

Our genetic material (DNA) is made of 4 different compounds A, T, G, C called nucleotides linked together in chromosomes.  The order is crucial, just as the order of letters in a word is crucial for meaning (consider united and untied).  So how many slots for the nucleotides are there in our genome ? — just 3,200,000,000.  

Just as combinations of dots and dashes code for letters in Morse code, combinations of  3 nucleotides code for the 20 amino acids that make up proteins. 

Proteins are big.   That for the protein  mutated in sickle cell anemia (beta-globin) contains 146 amino acids, and all it takes to produce the disease is a switch from one amino acid to another at position six.  The other 145 amino acids in the chain are unchanged. 

So sickle cell beta globin is an allele of normal beta globin (a change in the nucleotide sequence for a given gene).  Every population of people contains alleles of every protein.  Some are common (over 5% of the population showing them), but most are rare.

Tthe PLoS paper looked at  73,228 alleles of all 20,000 or so proteins that we have in our genome (yes our technology can now do those sorts of things) in the general population.  Then they looked at the alleles in the Ashkenazi population which were present at greater than 1/500 (.2%).  Then they looked at the frequency of the same allele several other nonAshkenazi population (about 5000 each of nonFinnish European, African Blacks, Latinos), and found that these alleles were 15 times less frequent (on average).   So Ashkenazi’s have some alleles that are lots more common than in other populations.  Actually it’s more than some, because about 1/3 of the alleles they studied are an average of 15 fold enriched. 

What does this mean?  It means that when a small founder population with a rare allele becomes ‘fruitful and multiplies’, the rare allele will multiply with right along with it and not be lost by outbreeding (which was certainly true of the Ashkenazis for 600 of the last 750 years).

This is the evidence that current day Ashkenazi’s come from a very small founder population.  It’s pretty good.  I hope that I’ve made this somewhat comprehensible, if not write a comment. 

Now read the paragraph again. 

To understand anything in the cell you need to understand nearly everything in the cell

Understanding how variants in one protein can either increase or decrease the risk of Parkinson’s disease requires understanding of the following: the lysosome, TMEM175, Protein kinase B, protein moonlighting, ion channel lysoK_GF, dopamine neurons among other things. So get ready for a deep dive into molecular and cellular biology.

It is now 50 years and 6 months since L-DOPA was released in the USA for Parkinson’s disease, and I was tasked as a resident by the chief with running the first L-DOPA clinic at the University of Colorado.  We are still learning about the disease as the following paper Nature vol. 591 pp. 431 – 437 ’21 will show. 

The paper describes an potassium conducting ion channel in the lysosomal membrane called LysoK_GF.  The channel is made from two proteins TMEM175 and protein kinase B (also known as AKT).

TMEM175 is an ion channel conducting potassium.  It is unlike any of the 80 or so known potassium channels.  It  contains two repeats of 6 transmembrane helices (rather than 4) and no pore loop containing the GYG potassium channel signature sequence. Lysosomes lacking it aren’t as acidic as they should be (enzymes inside the lysosome work best at acid pH).  Why loss of a potassium channel show affect lysosomal pH is a mystery (to me at least).

Genome Wide Association Studies (GWAS) have pointed to the genomic region containing TMEM175 as having risk factors for Parkinsonism.  Some variants in TMEM175 are associated with increased risk of the disease and others are associated with decreased risk — something fascinating as knowledge here should certainly tell us something about Parkinsonism.  

The other protein making up LysoK_GF is protein kinase B (also known as AKT). It is found inside the cell, sometimes associated with membranes, sometimes free in the cytoplasm. It is big containing 481 amino acids. Control of its activity is important, and Cell vol. 169 pp. 381 – 405 ’17 lists 21 separate amino acids which can be modified by such things as acetylation, phosphorylation, sumoylation, Nacetyl glucosamine, proline hydroxylation.  Well 2^21 is 2,097,152, so this should keep cell biologists busy for some time. Not only that some 100 different proteins AKT phosphorylates were known as 2017.  

TMEM175 is opened by conformational changes in AKT.  Normally the enzyme is inactive because the pleckstrin homology domain binds to the catalytic domain inhibiting enzyme activity as the substrate can’t get in.

Remarkably you can make a catalytically dead AKT, and it still works as a controller of TMEM175 activity — this is an example of a moonlighting molecule — for more please see — https://luysii.wordpress.com/2021/01/11/moonlighting-molecules/.

Normally the activity and conformation of AKT is controlled by the metabolic state of the cell (with 21 different molecular knob sites on the protein this shouldn’t be hard).  So the fact that AKT conformation controls TMEM175 conductivity which controls lysosome activity gives the metabolic state of the cell a way to control lysosomal function.  

Notice how to understand anything in the cell you must ask ‘what’s it for’, thinking that is inherently teleological. 

Now on to the two risk factors for Parkinsonism in TMEM175.  The methionine –> threonine mutation at amino acid #393 reduces the lysoK_GF current and is associated with an increased risk of parkinsonism, while the glutamine –> proline mutation at amino acid position #65 gives a channel which remains functional under conditions of nutrient starvation. 

The authors cultured dopamine neurons and found out that the full blooded channel LysoK_GF (TMEM175 + AKT) protected neurons against a variety of insults (MPTP — a known dopamine neuron toxin, hydrogen peroxide, nutrient starvation). 

TMEM175 knockout neurons accumulate more alpha-synuclein — the main constituent of the Lewy body of Parkinsonism.

So it’s all one glorious tangle, but it isn’t just molecular biological navel gazing, because it is getting close to one cause (and hopefully a treatment) of Parkinson’s disease.  

Gotterdamerung — The Twilight of the GWAS

Life may be like a well, but cellular biochemistry and gene function is like a mattress.  Push on it anywhere and everything changes, because it’s all hooked together.  That’s the only conclusion possible if a review of genome wide association studies (GWAS) is correct [ Cell vol. 169 pp. 1177 – 1186 ’17 ].

 It’s been a scandal for years that GWAS studies as they grow larger and larger are still missing large amounts of the heritability of known very heritable conditions (e.g. schizophrenia, height).  It’s been called the dark matter of the genome (e.g. we know it’s there, but we don’t know what it is).

If you’re a little shaky about how GWAS works have a look at https://luysii.wordpress.com/2014/08/24/tolstoy-rides-again-schizophrenia/ — it will come up again later in this post.

We do know that less than 10% of the SNPs found by GWAS lie in protein coding genes — this means either that they are randomly distributed, or that they are in regions controlling gene expression.  Arguing for randomness — the review states that the heritability contributed by each chromosome tends to be closely proportional to chromosome length.  Schizophrenia is known to be quite heritable, and monozygotic twins have a concordance rate of 40%.  Yet an amazing study (which is quoted but which I have not read) estimates that nearly 100% of all 1 megabase windows in the human genome contribute to schizophrenia heritability (Nature Genet. vol. 47 pp. 1385 – 1392 ’15). Given the 3.2 gigaBase size of our genome that’s 3,200 loci.

Another example is the GIANT study about the heritability of height.  The study was based on 250,000 people and some 697 gene wide significant loci were found.  In aggregate they explain a mere SIXTEEN PERCENT.

So what is going on?

It gets back to the link posted earlier. The title —  “Tolstoy rides again”  isn’t a joke.  It refers to the opening sentence of Anna Karenina — “Happy families are all alike; every unhappy family is unhappy in its own way”.  So there are many routes to schizophrenia (and they are spread all over the genome).

The authors of the review think that larger and larger GWAS studies (some are planned with over a million participants) are not going to help and are probably a waste of money.  Whether the review is Gotterdamerung for GWAS isn’t clear, but the review is provocative.The review is new and it will be interesting to see the response by the GWAS people.

So what do they think is going on?  Namely that everything in organismal and cellular biochemistry, genetics and physiology is related to everything else.  Push on it in one place and like a box spring mattress, everything changes.  The SNPs found outside the DNA coding for proteins are probably changing the control of protein synthesis of all the genes.

The dark matter of the genome is ‘the plan’ which makes the difference between animate and inanimate matter.   For more on this please see — https://luysii.wordpress.com/2015/12/15/it-aint-the-bricks-its-the-plan-take-ii/

Fascinating and enjoyable to be alive at such a time in genetics, biochemistry and molecular biology.

Play the (genetic) hand you’ve been dealt but don’t spindle, fold or mutilate your cards

Back in the day, computers were programmed by inserting multiple punch cards https://en.wikipedia.org/wiki/Punched_card, each containing a machine instruction. At the bottom of the card it said “do not fold, spindle, or mutilate”. My wife used them back then when she expected to be a widow if and when I got sent to Vietnam.

So it is with you and the genetic hand of coronary artery disease risk you’ve been dealt. [ Cell vol. 167 p. 1431 ’16 ] refers to a recent New England Journal of Medicine article –2016;DOI:http://dx.doi.org/10.1056/NEJMoa1605086.

It’s a very good study, with large numbers of participants in three prospective cohorts — 7814 participants in the Atherosclerosis Risk in Communities (ARIC) study, 21,222 in the Women’s Genome Health Study (WGHS), and 22,389 in the Malmö Diet and Cancer Study (MDCS) — plus 4260 participants in the cross-sectional BioImage Study for whom genotype and covariate data were available. Adherence to a healthy lifestyle among the participants was also determined using a scoring system consisting of four factors: no current smoking, no obesity, regular physical activity, and a healthy diet (hardly complicated).

As you probably know, Genome Wide Association Studies have identified over 50 places in our genomes in which slight variations (the technical term is single nucleotide polymorphisms — SNPs ) are associated with increased risk of coronary artery disease. Since vascular disease is a generalized problem, these SNPs also increase the risk of other vascular problems, notably stroke. None of them increases the risk very much, and even together they don’t explain much of the genetic risk of vascular disease (which we know is there). However, they were all determined (at least in the 4260) and a genetic risk score was calculated. So there were people with high, low and medium degrees of risk.

In all risk groups, high, low, whatever, a simple healthy lifestyle (no smoking, not fat, some exercise, healthy diet) decreased the coronary event rate (heart attack, death) by nearly half. So how bad was high risk? Bad indeed, the event rate in the high risk group was nearly twice that of the low risk group.

Even better, healthy lifestyle decreased risk the most just where you’d want it — in the highest risk group. You can reduce your risk of being eaten by a bear by not going to Yellowstone by 99% or more but so what.

This work is to be believed, because the number of events is high enough –1230 coronary events were observed in the ARIC cohort (median follow-up, 18.8 years), 971 coronary events in the WGHS cohort (median follow-up, 20.5 years), and 2902 coronary events in the MDCS cohort (median follow-up, 19.4 years).

So as my late father said (who lived to 100) when asked what his secret was “I chose my parents very carefully”. Well, we can’t do that, but don’t spindle the cards.

Have Tibetans illuminated a path to the dark matter (of the genome)?

I speak not of the Dalai Lama’s path to enlightenment (despite the title).  Tall people tend to have tall kids. Eye color and hair color is also hereditary to some extent.  Pitched battles have been fought over just how much of intelligence (assuming one can measure it) is heritable.  Now that genome sequencing is approaching a price of $1,000/genome, people have started to look at variants in the genome to help them find the genetic contribution to various diseases, in the hopes of understanding andtreating them better.

Frankly, it’s been pretty much of a bust.  Height is something which is 80% heritable, yet the 20 leading candidate variants picked up by genome wide association studies (GWAS) account for 3% of the variance [ Nature vol. 461 pp. 458 – 459 ’09 ].  This has happened again and again particularly with diseases.  A candidate gene (or region of the genome), say for schizophrenia, or autism,  is described in one study, only to be shot down by the next.   This is likely due to the fact that many different genetic defects can be associated with schizophrenia — there are a lot of ways the brain cannot work well.  For details — see https://luysii.wordpress.com/2010/04/25/tolstoy-was-right-about-hereditary-diseases-imagine-that/. or see https://luysii.wordpress.com/2010/07/29/tolstoy-rides-again-autism-spectrum-disorder/.

Typically, even when an  association of a disease with a genetic variant is found, the variant only increases the risk of the disorder by 2% or less.  The bad thing is that when you lump them all of the variants you’ve discovered together (for something like height) and add up the risk, you never account for over 50% of the heredity.  It isn’t for want of looking as by 2010 some 600 human GWAS studies had been published  [ Neuron vol. 68 p. 182 ’10 ].  Yet lots of the studies have shown various disease to have a degree of heritability (particularly schizophrenia).  The fact that we’ve been unable to find the DNA variants causing the heritability was totally unexpected.  Like the dark matter in galaxies, which we know is there by the way the stars spin around the galactic center, this missing heritability has been called the  dark matter of the genome.

Which brings us to Proc. Natl. Acad. Sci. vol. 109 pp. 7391 – 7396 ’12.  It concerns an awful disease causing blindness in kids called Leber’s hereditary optic neuropathy.  The ’cause’ has been found. It is a change of 1 base from thymine to cytosine in the gene for a protein (NADH dehydrogenase subunit 1) causing a change at amino acid #30 from tyrosine to histidine.  The mutation is found in mitochondrial DNA not nuclear DNA, making it easier to find (it occurs at position 3394 of the 16,569 nucleotide mitochondrial DNA).

Mitochondria in animal cells, and chloroplasts in plant cells, are remnants of bacteria which moved inside cells as we know them today (rest in peace Lynn Margulis).

Some 25% of Tibetans have the 3394 T–>C mutations, but they see just fine.  It appears to be an adaptation to altitude, because the same mutation is found in nonTibetans on the Indian subcontinent living about 1500 meters (about as high as Denver).  However, if you have the same genetic change living below this altitude you get Lebers.

This is a spectacular demonstration of the influence of environment on heredity.  Granted that the altitude you live at is a fairly impressive environmental change, but it’s at least possible that more subtle changes (temperature, humidity, air conditions etc. etc.) might also influence disease susceptibility to the same genetic variant.  This certainly is one possible explanation for the failure of GWAS to turn up much.  The authors make no mention of this in their paper, so these ideas may actually be (drumroll please) original.

If such environmental influences on the phenotypic expression of genetic changes are common, it might be yet another explanation for why drug discovery is so hard.  Consider CETP (Cholesterol Ester Transfer Protein) and the very expensive failure of drugs inhibiting it. Torcetrapib was associated with increased deaths in a trial of 15,000 people for 18 – 20 months.  Perhaps those dying somehow lived in a different environment.  Perhaps others were actually helped by the drug