Here is the current state of play on my idea that chronic fatigue syndrome might be due to an excess of senescent cells releasing inflammatory mediators. The idea is explained in a copy of the post below, which should be read before proceeding.
The best way to test the idea would be to look for p16^INK4a, a transcription elevated in senescent cells. This is relatively specific for senescence, far more so than the 74 or so inflammatory mediators which are part of the Senescence Associated Secretory Phenotype (SASP).
The best place to do this would be the Mayo clinic which is currently vigorously investigating the role of senescent cells in aging, cancer and what have you. When I was in practice, the Mayo clinic linkage system for medical records was legendary. When Elsewhere General had 10 patients in a series of disease X, Mayo would have 100. I’m sure they have seen tons of chronic fatigue patients and could easily measure p16^INK4a levels on them. I’ve corresponded with one worker there (Bennett Childs) and urged him to try the idea — e.g. measure white blood cell levels of p16^INK4a in CFS patients and compare it to controls. This is cleaner than measuring SASP, because inflammatory mediators can be released by almost any type of infection or pathologic condition. I noted today, that one researcher is working on developing senolytics, which would be the therapy of choice should my idea pan out.
I”ve written the authors of the PNAS editorial (Komaroff) and the paper (Davis) in the past week but have heard nothing back.
I’ve also contacted the Open Medicine Foundation® (OMF) which appears to be a patient organization founded by a woman whose daughter came down with it. They apparently even fund research. They said that they’d share it with their research team.
I wrote the research director of another patient organization but have heard nothing back.
The post below has been read 250 times.
I am a 79 year old retired neurologist with no academic affiliation, and no way to test the idea. Hopefully some of those I’ve been in contact with will do so. The patients are waiting.
If an idea of mine is correct, it is possible that some patients with chronic fatigue syndrome (CFS) can be treated with specific medications based on the results of a few blood tests. This is precision medicine at its finest. The data to test this idea has already been acquired, and nothing further needs to be done except to analyze it.
Athough the initial impetus for the idea happened only 3 months ago, there have been enough twists and turns that the best way explanation is by a timeline.
First some background:
As a neurologist I saw a lot of people who were chronically tired and fatigued, because neurologists deal with muscle weakness and diseases like myasthenia gravis which are associated with fatigue. Once I ruled out neuromuscular disease as a cause, I had nothing to offer then (nor did medicine). Some of these patients were undoubtedly neurotic, but there was little question in my mind that many others had something wrong that medicine just hadn’t figured out yet — not that it hasn’t been trying.
Infections of almost any sort are associated with fatigue, most probably caused by components of the inflammatory response. Anyone who’s gone through mononucleosis knows this. The long search for an infectious cause of chronic fatigue syndrome (CFS) has had its ups and downs — particularly downs — see https://luysii.wordpress.com/2011/03/25/evil-scientists-create-virus-causing-chronic-fatigue-syndrome-in-lab/
At worst many people with these symptoms are written off as crazy; at best, diagnosed as depressed and given antidepressants. The fact that many of those given antidepressants feel better is far from conclusive, since most patients with chronic illnesses are somewhat depressed.
The 1 June 2017 Cell had a long and interesting review of cellular senescence by Norman Sharpless [ vol. 169 pp. 1000 – 1011 ]. Here is some background about the entity. If you are familiar with senescent cell biology skip to the paragraph marked **** below
Cells die in a variety of ways. Some are killed (by infections, heat, toxins). This is called necrosis. Others voluntarily commit suicide (this is called apoptosis). Sometimes a cell under stress undergoes cellular senescence, a state in which it doesn’t die, but doesn’t reproduce either. Such cells have a variety of biochemical characteristics — they are resistant to apoptosis, they express molecules which prevent them from proliferating and — most importantly — they secrete a variety of proinflammatory molecules collectively called the Senescence Associated Secretory Phenotype — SASP).
At first the very existence of the senescent state was questioned, but exist it does. What is it good for? Theories abound, one being that mutation is one cause of stress, and stopping mutated cells from proliferating prevents cancer. However, senescent cells are found during fetal life; and they are almost certainly important in wound healing. They are known to accumulate the older you get and some think they cause aging.
Many stresses induce cellular senescence of which mutation is but one. The one of interest to us is chemotherapy for cancer, something obviously good as a cancer cell turned senescent has stopped proliferating. If you know anyone who has undergone chemotherapy, you know that fatigue is almost invariable.
****
One biochemical characteristic of the senescent cell is increased levels of a protein called p16^INK4a, which helps stop cellular proliferation. While p16^INK4a can easily be measured in tissue biopsies, tissue biopsies are inherently invasive. Fortunately, p16^INK4a can also be measured in circulating blood cells.
What caught my eye in the Cell paper was a reference to a paper about cancer [ Cancer Discov. vol. 7 pp. 165 – 176 ’17 ] by M. Demaria, in which the levels of p16^INK4a correlated with the degree of fatigue after chemotherapy. The more p16^INK4a in the blood cells the greater the fatigue.
I may have been the only reader of both papers with clinical experience wth chronic fatigue syndrome. It is extremely difficult to objectively measure a subjective complaint such as fatigue.
As an example of the difficulty in correlating subjective complaints with objective findings, consider the nearly uniform complaint of difficulty thinking in depression, with how such patients actually perform on cognitive tests — e. g. there is little if any correlation between complaints and actual performance — here’s a current reference — Scientific Reports 7, Article number: 3901(2017) — doi:10.1038/s41598-017-04353.
If the results of the Cancer paper could be replicated, p16^INK4 would be the first objective measure of a patient’s individual sense of fatigue.
So I wrote both authors, suggesting that the p16^INK4a test be run on a collection of chronic fatigue syndrome (CFS) patients. Both authors replied quickly, but thought the problem would be acquiring patients. Demaria said that Sharpless had a lab all set up to do the test.
Then fate (in the form of Donald Trump) supervened. A mere 9 days after the Cell issue appeared, Sharpless was nominated to be the head of the National Cancer Institute by President Trump. This meant Dr. Sharpless had far bigger fish to fry, and he would have to sever all connection with his lab because of conflict of interest considerations.
I also contacted a patient organization for chronic fatigue syndrome without much success. Their science advisor never responded.
There matters stood until 22 August when a paper and an editorial about it came out [ Proc. Natl. Acad. Sci. vol. 114 pp. 8914 – 8916, E7150 – E7158 ’17 ]. The paper represented a tremendous amount of data (and work). The blood levels of 51 cytokines (measures of inflammation) and adipokines (hormones released by fat) were measured in both 192 patients with CFS (which can only be defined by symptoms) and 293 healthy controls matched for age and gender.
In this paper, levels of 17 of the 51 cytokines correlated with severity of CFS. This is a striking similarity with the way the p16^INK4 levels correlated with the degree of fatigue after chemotherapy). So I looked up the individual elements of the SASP (which can be found in Annu Rev Pathol. 21010; 5: 99–118.) There are 74 of them. I wondered how many of the 51 cytokines measured in the PNAS paper were in the SASP. This is trickier than it sounds as many cytokines have far more than one name. The bottom line is that 20 SASPs are in the 51 cytokines measured in the paper.
If the fatigue of CFS is due to senescent cells and the SASPs they release, then they should be over-represented in the 17 of the 51 cytokines correlating with symptom severity. Well they are; 9 out of the 17 are SASP. However although suggestive, this increase is not statistically significant (according to my consultants on Math Stack Exchange).
After wrote I him about the new work, Dr. Sharpless noted that CFS is almost certainly a heterogeneous condition. As a clinician with decades of experience, I’ve certainly did see some of the more larcenous members of our society who used any subjective diagnosis to be compensated, as well as a variety of individuals who just wanted to withdraw from society, for whatever reason. They are undoubtedly contaminating the sample in the paper. Dr. Sharpless thought the idea, while interesting, would be very difficult to test.
But it wouldn’t at all. Not with the immense amount of data in the PNAS paper.
Here’s how. Take each of the 9 SASPs and see how their levels correlate with the other 16 (in each of the 192 CSF patients). If they correlate better with SASPs than with nonSASPs, than this would be evidence for senescent cells being the cause some cases of CFS. In particular, patients with a high level of any of the 9 SASPs should be studied for such correlations. Doing so should weed out some of the heterogeneity of the 192 patients in the sample.
This is why the idea is testable and, even better, falsifiable, making it a scientific hypothesis (a la Karl Popper). The data to refute it is in the possession of the authors of the paper.
Suppose the idea turns out to be correct and that some patients with CFS are in fact that way because, for whatever reason, they have a lot of senescent cells releasing SASPs.
This would mean that it would be time to start trials of senolyic drugs which destroy senescent cells on the group with elevated SASPs. Fortunately, a few senolytics are currently inc linical use. This would be precision medicine at its finest.
Being able to alleviate the symptoms of CFS would be worthwhile in itself, but SASP levels could also be run on all sorts of conditions associated with fatigue, most notably infection. This might lead to symptomatic treatment at least. Having gone through mono in med school, I would have loved to have been able to take something to keep me from falling asleep all the time.
This post is mostly something I posted on the Skeptical Chymist 2 years ago. Along with the previous post “Why should a protein have just one shape (or any shape for that matter)” both will be referred to in the next one –“Gentlemen start your motors”, concerning the improbability of the chemistry underlying our existence and whether it is reasonable to believe that it arose by chance.
In the early days of quantum mechanics Einstein and Bohr threw thought experiments (gedanken experiments) at each other like teenagers tossing cherry bombs. None of the gedanken experiments were regarded as remotely possible back then, although thanks to Bell and Aspect, quantum nonlocality and entanglement now have a solid experimental basis. To read more about this you can’t do much better than “The Age of Entanglement” by Louisa Gilder.
Frankly, I doubt that most strings of amino acids have a dominant shape (e.g., biological meaning), and even if they did, they couldn’t find it quickly enough (theLevinthal paradox). For details see the previous post.
How would you prove me wrong? The same way you’d prove a pair of dice was loaded. Just make (using solid-phase protein synthesis a la Merrifield) a bunch of random strings of amino acids (each 41 amino acids long) and see how many have a dominant shape. Any sequence forming a crystal does have a dominant shape, if the sequence doesn’t crystallize, use NMR to look at it in solution. You can’t make all of them, because the earth doesn’t have enough mass to do so (see “https://luysii.wordpress.com/2009/12/20/how-many-proteins-can-be-made-using-the-entire-earth-mass-to-do-so/). That’s why this is a gedanken experiment — it can’t possibly be performed in toto.
Even so, the experiment is over (and I’m wrong) if even 1% of the proteins you make turn out to have a dominant shape.
However, choosing a random string of amino acids is far from trivial. Some amino acids appear more frequently than others depending on the protein. Proteins are definitely not a random collection of amino acids. Consider collagen. In its various forms (there are over 20, coded for by at least 30 distinct genes) collagen accounts for 25% of body protein. Statistically, each of the 20 amino acids should account for 5% of the protein, yet one amino acid (glycine) accounts for 30% and proline another 15%. Even knowing this, the statistical chances of producing 300 copies in a row of glycine–any amino acid–any amino acid by a random distribution of the glycines are less than zilch. But one type of bovine collagen protein has over 300 such copies in its 1042 amino acids.
One further example of the nonrandomness of proteins. If you were picking out a series of letters randomly hoping to form a word, you would not expect a series of 10 ‘a’s to show up. But we normally contain many such proteins, and for some reason too many copies of the repeated amino acid produce some of the neurological diseases I (ineffectually) battled as a physician. Normal people have 11 to 34 glutamines in a row in a huge (molecular mass 384 kiloDaltons — that’s over 3000 amino acids) protein known as huntingtin. In those unfortunate individuals withHuntington’s chorea, the number of repeats expands to over 40. One of Max Perutz’s last papers [Proc. Natl. Acad. Sci. USA 99, 5591–5595 (2002)] tried to figure out why this was so harmful.
On to the actual experiment. Suppose you had made 1,000,000 distinct random sequence proteins containing 41 amino acids and none of them had a dominant shape. This proves/disproves nothing. 10^6 is fewer than the possibilities inherent in a string of 5 amino acids, and you’ve only explored 10^6/(20^41) of the possibilities.
Would Karl Popper, philosopher of science, even allow the question of how commonly proteins have a dominant shape to be called scientific? Much of what I know about Popper comes from a fascinating book “Wittgenstein’s Poker” and it isn’t pleasant. Questions not resolvable by experiment fall outside Popper’s canon of questions scientific. The gedanken experiment described can resolve the question one way, but not the other. In this respect it’s like the halting problem in computer science (there is no general rule to tell if a program will terminate).
Would Ludwig Wittgenstein, uberphilosopher, think the question philosophical? Probably not. His major work “Tractatus Logico-Philosophicus” concludes with “What we cannot speak of we must pass over in silence”. While he’s the uberphilosopher he’s also the antiscientist. It’s exactly what we don’t know which leads to the juiciest speculation and most creative experiments in any field of science. That’s what I loved about organic chemistry years ago (and now). It is nearly always possible to design a molecule from scratch to test an idea. There was no reason to make [7]paracyclophane, other than to get up close and personal with the ring current.
If the probability or improbability of our existence, to which the gedanken experiment speaks, isn’t a philosophical question, what is?
Back then, this post produced the following excellent comment.
I’m not sure your assessment of what Popper would regard as science is accurate. Popper advocated “falsifiability”, i.e. that a statement cannot be proved true, only false. Non-scientific statements are those for which evidence that they are false cannot be found. You are in fact giving a perfect example of a situation where falsifiability is useful. If you tested, as you suggested, a million random proteins and many of them formed structures reliably, this would in fact disprove the hypothesis fairly conclusively (if only probabilistically). The fact that the test was passed by the first million proteins would be evidence that the theory was true (though obviously not concrete).
Also, it is relatively easy to choose what random proteins to make. Just use a random number generator (a pseudorandom generator would do too, probably). It doesn’t matter that they would be unlikely to produce a specific sequence generated in nature, as we are looking at specifically wanting to look at random sequences. The idea that 300 glycines is particularly unusual if protein generation is random is probably one which should be treated with a degree of caution. As the sequence was not specified as an unusual sequence beforehand, there are a large number of possible sequences that you could have seized on, and so care is needed.
This is only the most obvious experiment that could be carried out to test this idea, and I’m sure with advances, there is the distinct chance that more ingenious ways could be devised.
Additionally the the mass restriction is not in fact terribly useful except as an illustration that there is a massively large number of proteins, as once you have made and tested a protein, you can in fact reuse its atoms to make another protein.
Finally, I haven’t read Wittgenstein, but that final quote does not really support your statement that he is “anti-science” or would be against the production of novel cyclophanes. Organic chemistry clearly lies in the realm of “what we can speak”, as we are in fact speaking about it.
Posted by: MCliffe
My response —
MCliffe — thank you for your very thoughtful comments on the post. It’s great to know that someone out there is reading them.
Popper and the logical positivists solved many philosophical problems by declaring them meaningless (which Popper later took to mean not falsifiable). Things got to such a point in the 50s that Bertrand Russell was moved to came up with the meaningful (to most) but non-falsifiable statement — In the event of a nuclear war we shall all be dead.
You are quite right that it is easy to make a random sequence of amino acids using a computer. It’s been shown again and again that our intuitive notion of randomness is usually incorrect. I chose collagen because it is the most common protein in our body, and because it is highly nonrandom. Huntingtin was used because I dealt with its effects as a Neurologist (and because there are 8 more diseases with too many identical amino acids in a row — all of which for some unfathomable reason produce neurologic disease — they are called triplet diseases because it takes 3 nucleotides of DNA to code for a single amino acid).
Even accepting 300 glycines in 1000 or so amino acids (collagen) and putting that frequency into the random generator and turning it on, we would not expect those 300 glycines to appear at position n, position n+4, n+7, . . . , n + 898 randomly.
The idea of using the atoms over and over to escape the mass restriction is clever. Unfortunately it runs up against a time restriction. Let us suppose there is a super-industrious post-doc who can make a new protein every nanosecond (reusing the atoms). There are 60 * 60 * 24 * 365 = 31,536,000 ~ 10^7 seconds in a year and 10^10 years (more or less) since the big bang. This is 10^9 * 10^7 * 10 ^10 = 10^26 different proteins he could make since the dawn of time. But there are 20^41 = 2^41 * 10^41 proteins of length 41 amino acids. 2^41 = 2,199,023,255,552 = 10^12. So he has only tested 10^26 of 10^53 possible 41 amino acid proteins in all this time.
This is what I was getting at by saying the the gedanken experiment was not a priori falsifiable — we lack the time, space and mass to run it to completion. As you note, it could well end quite early if I’m wrong. Suppose 10^9/10^53 of the proteins DO have a dominant shape — the postdoc will be very unlikely to find any of them.
I think your final point is well taken. My reading of “Wittgenstein’s Poker” is that what he was saying in his last sentence really was “What we cannot speak (with certainty) of we must pass over in silence”. We cannot speak of the outcome of this Gedanken experiment with any degree of certainty.
Once again Thanks