How do Anesthetics Work?

Ask a simple question, and get an answer that gets weirder the deeper you dig.

Anesthesia is wonderful. Quite simply, it makes bearable, even unnoticeable, what would be impossible or excruciating. It is also one of the most mysterious phenomena short of consciousness itself. All animals can be anesthetized, from bacteria on up. All sorts of chemicals can be used, from xenon to simple ethers, to complex fluoride-substituted forever chemicals, all with similar effects. Yet there are also complex sub-branches of anesthesia, like pain relief, muscular immobilization, shutdown of consciousness, and amnesia against remembering what happened, that chemicals affect differentially. It resembles sleep, and shares some circuitry with that process, but is of course is induced quite differently.

The first red herring was the Meyer–Overton rule, established back in 1899, that showed that anesthetic potency correlates closely with the lipophilicity of the chemical, from nitrogen (not very good) to xenon (pretty good) to chloroform (very good). All the forever (heavily fluorinated) chemicals used as modern anesthetics, like isoflurane and sevoflurane, have extremely high lipophilicity. This suggested that the mechanism of action was simply mixing into membranes somehow, altering their structure, and thus neuronal action.. something along that line. 

Structures of several general anesthetics. 8 is isoflurane.

But when researchers looked more closely there were some chemical differences that did not track with this hypothesis. Chiral enantiomers behaved differently in some cases, indicating that these chemicals do bind to something (that is, a protein) specifically. Also, variant genes started cropping up that conferred resistance to anesthesia or were found to bind particular anesthetics at working concentrations. Also, more complex, injectable anesthetics like fentanyl and propofol have slightly more defined targets and modes of action. So while anesthetics clearly partition to membranes, and the binding sites are often at protein-membrane interfaces, the modern theory of how they work is that they bind to ion channels and neurotransmitter receptors and affect their functions. Proteins generally have hydrophobic interiors, so the lipophilicity of these chemicals may track with binding / disrupting protein interiors as much as membrane interiors. And other proteins such as microtubules have been drawn into the discussion as well (leading indirectly to some very unfortunate theories about consciousness). 

But which key protein do they bind? Here again, mysteries abound, as they do not bind just one, but many. And not just that, they turn some of their targets on, others off. One target is the GABA receptor, which characterizes the major inhibitory neurons of the central nervous system. These are turned on. At high concentrations, anesthetics can even turn these receptors on without any GABA neurotransmitter present. Another is the NMDA receptor, which is the target of opioids, and of ketamine. These receptors are turned off. So, for some reason, still somewhat obscure, the net result of many specific bindings to an array of channels by an array of chemicals results in ... anesthesia.

A recent paper raised my interest in this area, as its authors demonstrated yet another target for inhaled anesthetics like isoflurane, and dove with exquisite detail into its mechanism. They were working on the ryanodine receptor, which isn't even a cell surface protein, but sits in the endoplasmic reticulum (or sarcoplasmic reticulum in muscles) and conducts calcium out of these organelles. This receptor is huge- the largest known- coding over five thousand amino acids (RYR1 of humans), due to numerous built-in regulatory structures. For example, it is sensitive to caffeine, but in a different location than where it is sensitive to isoflurane. Calcium is a very important signal within cells, key to muscle activity, and also to neuronal activation. The endoplasmic reticulum serves as a storehouse of calcium, from which signals can be sparked as needed by outside signals, including a spike in calcium itself (thus creating a positive feedback loop). These receptors (a family of three in human) are named for an obscure chemical (indeed a poison) that activates these channels, and all three are expressed in the brain. 

The authors were led to this receptor because mutations were known to cause malignant hyperthermia, a side effect of a few of the common anesthesia drugs where body temperature rises uncontrollably, driven from muscle tissue, where ryanodine receptors in the sarcoplasmic reticulum are particularly common and heavily used to regulate muscle activity and metabolism. That suggested that anesthetics such as isoflurane might bind to this receptor directly, turning it on. That was indeed the case. They started with cultured cells expressing each receptor family member in turn, and tested each receptor's response to isoflurane. Internal (cytoplasmic) calcium rose especially with the family member RYR1. That led to various control experiments and a hunt (by mutating and doctoring the RYR1 protein) for the particular region being bound by the anesthetic. After a lengthy search, they found residue 4000 was a critical one, as a mutation from methionine to phenylalanine reduced the isoflurane response about ten-fold. This is part of a binding pocket as shown below.

Structure of isoflurane, (B), bound to the RYR1 protein pocket. This is a pocket that happens to also bind another activator of this channel, 4-CMC. A layout of the whole active binding pocket is given on the right. At bottom are calcium channel responses of the wild-type and point mutant forms of RYR1, showing the dramatic effect these single site mutations have on isoflurane response.

Fine, but what about anesthesia? The next step was to test this mutation in whole mice, where, lo and behold, isoflurane anesthesia of otherwise normal mice was made slightly more difficult by this mutant form of RYR1. Additionally, these mice had no other observable problems- not in behavior, not in sleep. That is remarkable as a finding about anesthesia, but the effect was quite small- about 10% or so shift in the needed concentration of isoflurane. They go on to mention that this is similar in scale to knockouts or mutations in other known targets of anesthetic drugs:

• 10% shift in the curve from the M4000F mutation of RYR1
• 14% shift in the isoflurane curve from a mutation in GABA receptor, GABAAR.
• 5% shift in the isoflurane curve (though a 20% or more shift for halothane) for mutations in KCNK9, a potassium channel.

What this is telling us is that there are many targets for anesthetic drugs. They are spread over many neurotransmitter and physiological systems. They each contribute modestly (and variably, depending on the drug) to the net effect of any one drug. The various affected channels and membrane receptors curiously combine to achieve anesthesia across all animals and even microorganisms, which naturally also rely on channels and transmembrane receptors for their various sensing and motion activation needs. We are left with a blended hypothesis where yes, there are specific protein targets for each anesthetic that mediate their action. On the other hand, these targets are far from unique, spread across many proteins, yet are also highly conserved, looking almost like they are implicit in the nature of transmembrane proteins in general. 

One gets the distinct impression that there should be endogenous equivalents, as there are for opioids and cannabinoids- some internal molecule that provides sedation when needed, such as for deep illness or end-of-life crisis. That molecule has not yet been found, but the natural world abounds in sedatives, (alcohol is certainly one), so the logic of anesthesia becomes one of biological and evolutionary logic, as much as one of chemical mechanism.

• Jack Smith
• What is vice signaling?
• A do-nothing Friedman Fed, or a Trumpy Fed? It is hard to know which is worse. Or which we will get.

Links Only

Due to the press of other activities, only links this week.

• Wingnut medicine.
• Video of a fault slipping during an earthquake... look in the background.
• The original unitary executive.
• How about some free mid-day electricity?
• More Supreme injustice.
• Jay Bhattacharya is a stooge.

Dopamine: Get up and Go, or Lie Down and Die

The chemistry of motivation.

A recent paper got me interested in the dopamine neurotransmitter system. There are a limited number of neurotransmitters, (roughly a hundred), which are used for all communication at synapses between neurons. The more common transmitters are used by many cells and anatomical regions, making it hazardous in the extreme to say that a particular transmitter is "for" something or other. But there are themes, and some transmitters are more "niche" than others. Serotonin and dopamine are specially known for their motivational valence and involvement in depression, schizophrenia, addiction, and bipolar disorder, among many other maladies.

This paper described the reason why cancer patients waste away- a syndrome called cachexia. This can happen in other settings, like extreme old age, and in other illnesses. The authors ascribe cachexia (using mice implanted with tumors) to the immune system's production of IL6, one of scores of cytokines, or signaling proteins that manage the vast distributed organ that is our immune system. IL6 is pro-inflammatory, promoting inflammation, fever, and production of antibody-producing B cells, among many other things. These authors find that it binds to the area postrema in the brain stem, where many other blood-borne signals are sensed by the brain- signals that are generally blocked by the blood-brain barrier system.

The binding of IL6 at this location then activates a series of neuronal connections that these authors document, ending up inhibiting dopamine signaling out of the ventral tegmental area (VTA) in the lower midbrain, ultimately reducing dopamine action in the nucleus accumbens, where it is traditionally associated with reward, addiction, and schizophrenia. These authors use optically driven engineered neurons at an intermediate location, the parabrachial nucleus, (PBN), to reproduce how neuron activation there drives inhibition downstream, as the natural IL6 signal also does.  

Schematic of the experimental setup and anatomical locations. The graph shows how dopamine is strongly reduced under cachexia, consequent to the IL6 circuitry the authors reveal.

What is the rationale of all this? When we are sick, our body enters a quite different state- lethargic, barely motivated, apathetic, and resting. All this is fine if our immune system has things under control, uses our energy for its own needs, and returns us to health forthwith, but it is highly problematic if the illness goes on longer. This work shows in a striking and extreme way what had already been known- that prominent dopamine-driven circuits are core micro-motivational regulators in our brains. For an effective review of this area, one can watch a video by Robert Lustig, outlining at a very high level the relationship of the dopamine and serotonin systems.

Treatment of tumor-laden mice with an antibody to IL6 that reduces its activity relieves them of cachexia symptoms and significantly extends their lifespans.

It is something that the Buddhists understood thousands of years ago, and which the Rolling Stones and the advertising industry have taken up more recently. While meditation may not grant access to the molecular and neurological details, it seems to have convinced the Buddha that we are on a treadmill of desire, always unsatisfied, always reaching out for the next thing that might bring us pleasure, but which ultimately just feeds the cycle. Controlling that desire is the surest way to avoid suffering. Nowhere is that clearer than in addiction- real, clinical addictions that are all driven by the dopamine system. No matter what your drug of choice- gambling, sugar, alcohol, cocaine, heroin- the pleasure that they give is fleeting and alerts the dopamine system to motivate the user to seek more of the same. There are a variety of dopamine pathways, including those affecting Parkinson's and reproductive functions, but the ones at issue here are the mesolimbic and mesocortical circuits, that originate in the midbrain VTA and extend respectively to the nucleus accumbens in the lower forebrain, and to the cerebral cortex. These are integrated with the rest of our cognition, enabling motivation to find the root causes of a pleasurable experience, and raise the priority of actions that repeat those root causes. 

So, if you gain pleasure from playing a musical instrument, then the dopamine system will motivate you to practice more. But if you gain pleasure from cocaine, the dopamine system will motivate you to seek out a dealer, and spend your last dollar for the next fix. And then steal some more dollars. This system shows specifically the dampening behavior that is so tragic in addictions. Excess activation of dopamine-driven neurons can be lethal to those cells. So they adjust to keep activation in an acceptable range. That is, they keep you unsatisfied, in order to allow new stimuli to motivate you to adjust to new realities. No matter how much pleasure you give yourself, and especially the more intense that pleasure, it is never enough because this system always adjusts the baseline to match. One might think of dopamine as the micro-manager, always pushing for the next increment of action, no matter how much you have accomplished before, no matter how rosy or bleak the outlook. It gets us out of bed and moving through our day, from one task to the next.

In contrast, the serotonin system is the macro-manager, conveying feelings of general contentment, after a life well-lived and a series of true accomplishments. Short-circuiting this system with SSRIs like prozac carries its own set of hazards, like lack of general motivation and emotional blunting, but it does not have the risk of addiction, because serotonin, as Lustig portrays it, is an inhibitory neurotransmitter, with no risk of over-excitement. The brain does not re-set the baseline of serotonin the same way that it continually resets the baseline of dopamine.

How does all this play out in other syndromes? Depression is, like cachexia, at least in part syndrome of insufficient dopamine. Conversely, bipolar disorder in its manic phase appears to involve excess dopamine, causing hyperactivity and wildly excessive motivation, flitting from one task to the next. But what have dopamine antagonists like haloperidol and clozapine been used for most traditionally? As anti-psychotics in the treatment of schizophrenia. And that is a somewhat weird story. 

Everyone knows that the medication of schizophrenia is a haphazard affair, with serious side effects and limited efficacy. A tradeoff between therapeutic effects and others that make the recipient worse off. A paper from a decade ago outlined why this may be the case- the causal issues of schizophrenia do not lie in the dopamine system at all, but in circuits far upstream. These authors suggest that ultimately schizophrenia may derive from chronic stress in early life, as do so many other mental health maladies. It is a trail of events that raise the stress hormone cortisol, which diminishes cortical inhibition of hippocampal stress responses, and specifically diminishes the GABA (another neurotransmitter) inhibitory interneurons in the hippocampus. 

It is the ventral hippocampus that has a controlling influence over the VTA that in turn originates the relevant dopamine circuitry. The theory is that the ventral hippocampus sets the contextual (emotional) tone for the dopamine system, on top of which episodic stimulation takes place from other, more cognitive and perception-based sources. Over-activity of this hippocampal regulation raises the gain of the other signals, raising dopamine far more than appropriate, and also lowering it at other times. Thus treating schizophrenia with dopamine antagonists counteracts the extreme highs of the dopamine system, which in the nucleus accumbens can lead to hallucinations, delusions, paranoia, and manic activity, but it is a blunt instrument, also impairing general motivation, and further reducing cognitive, affect, parkinsonism, and other problems caused by low dopamine that occurs during schizophrenia in other systems such as the meso-cortical and the nigrostriatal dopamine pathways.

Manipulation of neurotransmitters is always going to be a rough job, since they serve diverse cells and pathways in our brains. Wikipedia routinely shows tables of binding constants for drugs (clozapine, for instance) to dozens of different neurotransmitter receptors. Each drug has its own profile, hitting some receptors more and others less, sometimes in curious, idiosyncratic patterns, and (surprisingly) across different neurotransmitter types. While some of these may occasionally hit a sweet spot, the biology and its evolutionary background has little relation to our current needs for clinical therapies, particularly when we have not yet truly plumbed the root causes of the syndromes we are trying to treat. Nor is precision medicine in the form of gene therapies or single-molecule tailored drugs necessarily the answer, since the transmitter receptors noted above are not conveniently confined to single clinical syndromes either. We may in the end need specific, implantable and computer-driven solutions or surgeries that respect the anatomical complexity of the brain.

• Thoughts about corruption.
• The Fed is extraordinarily powerful.
• But our Stable Genius is going downhill.
• The real deal with autism.

An Uneasy Relationship With the Air

Review of Airborne, by Carl Zimmer. 

The pandemic was tough on everyone. But it had especially damaging effects on the political system, and on its relationship to the scientific community. Now the wingnuts are in charge, blowing up the health and research system, which obviously is not going to end well, whatever its defects and whatever their motivations.

While the scientific community had some astounding wins in this pandemic, in virus testing and vaccine production, there were also appalling misses. The US's first attempt at creating a test failed, at the most critical time. We were asleep at the wheel of public health, again at the earliest time, in controlling travel and quarantining travelers. But worst of all was the groupthink that resisted, tooth and nail, the aerosol nature of viral transmission of Covid. That is, at the core, what Zimmer's book is about, and it is a harrowing story.

He spends most of the book strolling through the long history of "aerobiology", which is to say, the study of microbes in the air. There are the fungal spores, the plant pests, the pollen, the vast amount of oceanic debris. But of most interest to us are the diseases, like tuberculosis, and anthrax. The field took a detour into biowarfare in the mid-20th century, from which it never really recovered, since so much of that science was secret, and in its shadow, the sporadic earlier public studies that looked carefully into disease transmission by aerosols were, sadly, forgotten. 

So it became a commonplace at the CDC and other public health entities, among all the so-called infectious disease specialists, that respiratory viruses like influenza, colds, and coronaviruses spread not by aerosols, but by contact, surfaces, and large droplets. This made infection control easy, (at least in principle), in that keeping a few feet away from sick people would be sufficient for safety, perhaps plus surgical masks in extreme situations. There was a curious disinterest in the older studies that had refuted this concept, and little interest in doing new ones, because "everyone knows" what the virus behavior is.

It is hard to explain all this in purely scientific terms. I think everyone knew at some level that the true nature of respiratory virus transmission was not well-understood, because we clearly had not managed to control it, either in residential or in hospital settings. It is hard to grapple with invisible things, and easy to settle into conventional, even mythical, trains of thought. First there were miasmas, then there were Koch's postulates and contact by fluids. It was hard to come full circle and realize that, yes, miasmas were sort of a thing after all, in the form of aerosols of infectious particles. It was also all too easy to say that little evidence supported aerosol spread, since the work that had been done had been forgotten, and the area was unfashionable for new work, given the conventional wisdom.

Even more significantly, the implications of aerosol spread of viruses are highly unpleasant, even frightening. The air we need every minute of our lives is suspect. It is a bit like the relationship we have with food- deeply conflicted and fraught, with fears, excesses, and rituals. One has to eat, but our food is full of psychological valences, possible poisons, cultural baggage, judgement, libraries full of advice. No one really wanted to go there for air as well. So I think scientists, even those calling themselves infectious disease specialists, (of all things), settled into a comfortable conventional wisdom, that droplets were the only game in town.

But what did this say about the larger research enterprise? What did it mean that, even while medical/bio research community was sequencing genomes and penetrating into obscure and complex regions of molecular biology, we had not done, or at least not appreciated and implemented, the most basic research of public health- how infectious diseases really spread, and how to protect people from them? It constituted gross negligence by the medical research community- no two ways about it. And that appears to have caused the public at large to question what on earth they were funding. A glorious enterprise of discovery, perhaps, but one that was not very focused on actual human health.

A timeline of research/policy

• Sprawling work on airborne infection in 1955. 

• Earliest glimmer in latest pandemic, May 2020. 

• Deeper followup, October 2020.

• Even deeper followup, August 2021. Later, 2023.

• Critics still can not believe aerosol spread, November, 2022.

• Hospital HVAC requirements currently go to MERV 8, not enough.

• Current CDC guidance mentions aerosols only from "procedures", not from people, though masks are recommended.

Aerosol spread of disease requires two things- that aerosols are produced, and that the infectious microbes remain infectious while in those aerosols. The former is clear enough. We sneeze, after all. Even normal breathing creates fine aerosols. The latter is where scientific doubt has been more common, since many viruses are not armored, but have loose coats and membranes derived from our own, delicate cells. Viruses like HIV don't survive in aerosols, and don't spread that way. But it turns out that Covid viruses have a half life of about two hours in aerosols. 

The implications of that are quite stunning. It means that viruses can hang around in the air for many hours. Indoor spaces with poor ventilation- which means practically all indoor spaces- can fill up with infectious particles from one or a few infected people, and be an invisible epidemic cloud. No wonder everyone eventually got Covid. 

What to do about it? Well, the earliest aerobiology experiments on infectious disease went directly to UV light disinfection, which is highly effective, and remains so today. But UV light is dangerous to us as well as microbes, so needs to be well-shielded. As part of an air handling system, though, UV light is an excellent solution. Additional research has found that far-UV, at 222 nm, is both effective against airborne microbes and safe for human eyes and skin, creating an outstanding way to clear the air. Another approach is HEPA filtration of air, either as part of an air handling / exchange system, or as stand-alone appliances. Another is better ventilation overall, bringing in more outside air, though that has high energy costs. Lastly, there are masks, which are only partially effective, and the place no one really wants to go. But given a lack of responsibility by those in charge of our built environment, masks are the lowest common denominator- the one thing we can all do to protect ourselves and others. And not just any mask, but the N95 high-quality filtration mask or respirator.

The pandemic threw some sharp light into our public institutions. We sequenced these viruses in a hurry, but couldn't figure out how they spread. We created vaccines in record time, but wasted untold effort and expense on cleaning surfaces, erecting plexiglass shields, and demanding masking, rather than taking responsibility for guarding and cleaning public air spaces in a more holistic way. It is a disconcerting record, and there remains quite a bit yet to do.

• Poor (and personalized) policy means poor science and poor vaccines.
• Department of injustice and thought crime.
• Who needs new music?
• Putin and money.
• Another argument for public schools.
• Another biological thing that didn't exist, until it did- lymph drainage in the brain.
• No wonder no one wants to become a primary care physician.
• The Japanese ice age.

Covid Builds a Fortress Within

 Viral proteins build peculiar vesicles to hide the viral replication apparatus.

SARS-CoV is still with us, a brutal addition to the already extensive army of respiratory viruses infecting humanity. While most people clear it, we have a hard time doing so, a testament to a tough evolutionary arms race. A fair portion of our extremely complicated immune system is devoted to viruses, including basics like recognizing double-stranded RNA and viral replication structures. A trick that coronaviruses and allied species possess has gradually come to light, which is the formation of vesicular structures that appear to host their replication apparatus. 

Coronavirus-infected cells display a variety of vesicular structures, including "zippered" endoplasmic reticulum, convoluted membranes (CV), dense membrane spherules (DMS) and double-membrane vesicles (DMV). The endoplasmic reticulum (ER) is the cellular organelle where membrane proteins and secreted proteins are first made, before they are sorted out to various other membrane systems and the outside (and where the bulk of membrane lipid production happens, among much else). Coronaviruses appear to commandeer the ER and divert its membranes to the new structures. It is the DMV that turns out to have an important function- hosting viral replication. How do we know this? Researchers recently turned to a classic technique- radioactive labeling of new RNA production in infected cells, followed by electron microscopy combined with auto-radiography. The image below shows in stunning detail various organelles within an infected cell, and the black dots are film grains turned by the radioactive RNA to mark synthesis sites. They are quite closely aligned with the DMV structures.

Exquisite auto-radiograph and electron micrograph of a SARS-CoV-infected cell. The mitochondria (m) are most apparent, followed by the viral replication organelles (RO, aka DMV), followed by the endoplasmic reticulum (ER), lipid droplets (LD), nucleus (N), and virion-containing region (VCR). The black dots from photo-sensitive film exposed by radioactive RNA is clustered around the DMV structures.

This finding leads to several questions. How do these structures form? And, given the need for replication to both get inputs such as nucleotides and to export outputs like the virus's genomic RNAs, why use membranes that are impermeable to such molecules? Why use two membranes, when one suffices for most cellular organelles like the ER, lysosomes, peroxisomes, etc? This had puzzled the field for some time. Now, it turns out (in another recent paper) a couple of powerful viral proteins solve both questions at once. Coronavirus products nsp3 and nsp4 have long been known as important for viral success, but recent work puts them at the heart of DMV formation, into what is now called a replication organelle (RO), as well as a DMV. They are expressed in the ER and seem to play the leading role (along with several host proteins and lipids) in curving its membranes into the DMV shape. They also form dimeric pairs (nsp3 on one membrane, and nsp4 on a facing membrane) that seal two membranes together, as seen in the DMV structure. And thirdly, they, once fully assembled and mated, form a pore which keeps out pretty much everything big, but lets through single stranded RNA and small molecules.

Structure determination of the multimeric nsp3/4 pore structure from purified DMV vesicles, several views. Note the tight pore going through the center, and differential sizes of the inner and outer membrane rings. It is a protein complex that both bends the membrane and keeps only the most essential traffic going through it.

This structure is beautiful in a way. The central pore, at about 1.5 nm, is lined with positive charges like lysine and asparagine, the better to conduct negatively charged RNA. The inner membrane structure is tighter than that of the outer membrane, the better to curve those membranes into the observed spherical size. While it is a little hard to believe that such DMV vesicles, even studded with such a bespoke pore, can conduct the kind of traffic, both in and out, needed to sustain high rates of viral replication, that is quite evidently how it works. These researchers make a few mutations in the newly revealed key positively charged central pore amino acids to show that, if those charges are lost, replication of the virus was "abolished". This creates an obvious drug target as well- some chemical that plugs this pore or otherwise blocks the assembly of this ornate structure.

Additionally, the assembly of all this out of flat ER was also studied. The nsp3/4 proteins are originally connected end-to-end and do a delicate dance of pulling on each other (after cleavage) to dramatically curve the membrane between them, forming a tight loop from the (future) outside DMV membrane to the (future) inside one. On the other hand, another way they can assemble (right side in diagram below) is from separated (ER) membranes, leading to the "zippered" ER conformation that is also seen in infected cells. Whether the latter can be transformed into the former remains a question. 

Models for assembly of the linked nsp3-nsp4 proteins into the curved membranes of the DMV pore, with super-curvature at the pore junction between outside and inside membranes. TM stands for transmembrane domain, NTD for N-terminal domain (front), CTD for C-terminal domain (rear), and Ecto for the ecto-domains of each protein that are not within the membrane.

It is naturally implicit in this work that, if the pores of nsp3/4 allow through the absolute essentials of viral replication, they also block the various cellular sensors of viral presence, such as the RIG and TLR proteins, thus delaying the host response. Perhaps the RNAs allowed out are modified prior to exit to make them look more host-like. All those assumptions have yet to be nailed down explicitly. At any rate, viral assembly takes place elsewhere, so it is not entirely clear yet what exactly is being hidden here.

There were some technical innovations along the way to these results. These researchers tagged the nsp proteins in a way that allowed them to easily purify DMV vesicles out of whole cells, speeding their cry-electron microscopy work of getting these structures. Did they just use the Alpha fold program and do all this the easy way? Not at all. They did use Alpha fold to refine some of the structures, to extract more atomic detail. But they notably did not trust the AI to cook this kind of finding up from scratch. Some things still need to be done empirically, if you really want the truth.

• How much good do social programs do?
• Fire sale in Ukraine.
• Leave that soil be!

The Genome Remains Murky

A brilliant case study identifying the molecular cause of certain neuro-developmental disorders shows how difficult genome-based diagnoses remain.

Molecular medicine is increasingly effective in assessing both hereditary syndromes and cancers. The sequencing approach generally comes in two flavors- whole genome sequencing, or exome sequencing, where only the most important (protein-coding) parts are sampled. In each case, the hunt is for mutations (more blandly called variants) that cause the syndrome being investigated, from among the large number of variants we all carry. This approach is becoming standard-of-care in oncology, due to tremendous influence and clinical significance of cancer-driving mutations, many of which now match directly to tailored treatments that address them (thus the "precision" in precision medicine).

But another arm of precision medicine is the hunt for causes of congenital problems. There are innumerable genetic disorders whose causal analysis can lead not only to an informative diagnosis, and sometimes to useful treatments, but also to fundamental understanding of human biology. Sufferers of these syndromes may spend a lifetime searching for a diagnosis, being shuffled from one doctor or center to another and subject to various forms of hypothetical medicine, before some deep sequencing pinpoints the cause of their disease and founds a new diagnostic category that provides, if not relief, at least understanding and a medical home. 

A recent paper from Britain provided a classic of this form, investigating the causes of neurodevelopmental (NDD) disorders, which encompass a huge range of problems from mild to severe. They comment that even after the most modern analysis and intensive sequencing, 60% of NDD cases still can not be assigned causes. A large part of the problem is that, despite knowing the full sequence of the human genome, its function is less well-understood. The protein-coding genes (20,000 of those, roughly) are delineated and studied pretty closely. But that only accounts for 1 to 2% of the genome. The rest ranges from genes for a blizzard of non-coding RNAs, some of which are critical, to large regulatory regions with smatterings of important sites, to junk of various kinds- pseudogenes, relic retroviruses, repetitive elements, etc. The importance of any of these elements (and individual DNA base positions within them) varies tremendously. This means specifically that exome sequencing is not going to cut it. Exome sequencing focuses on a very small part of the genome, which is fine if your syndrome (such as a common cancer) is well characterized and known to arise from the usual suspects. But for orphan syndromes, it does not cast a wide enough net. Secondly, even with full genome sequencing, so little is known about the remoter regions of the genome that assigning a function to variations found there is difficult to impossible. It takes statistical analysis of incidence of the variation vs the incidence of the syndrome.

These authors used a trove of data- the Genomics England 100,000 genomes project, focusing on the ~9,000 genomes in this collection from people with NDD syndromes. (Plus additional genomes collected elsewhere.) (We can note in passing that Britain's nationalized health system remains at the forefront of innovative research and care.) What they found was an unusually high incidence of a particular mutation in a non-protein-coding gene called RNU4-2. The product of this gene is an RNA called U4, which is an important part of the spliceosome, where it pairs RNA-to-RNA with another RNA, U6, in a key step of selecting the first (5-prime) side of an intron that is to be spliced out of mRNA messages. This gene would never have come up in exome analysis, being non-protein-coding. Yet it is critically important, as splicing happens to the vast majority of human genes. Additionally, differential splicing- the selection of alternative exons and splice sites in a regulated way- happens frequently in developmental programs and neurological cell types. There is a class of syndromes called spliceosomopathies that are caused by defects in mRNA splicing, and tend to appear as syndromes in these processes.

As shown in the images (all based on a large corpus of other work on spliceosomes), RNU4-2/U4 pairs intimately with the U6 spliceosomal RNA, and the mutation found by the current group (which is a single nucleotide insertion) causes a bulge in this pairing, as marked. Meanwhile, the U6 RNA pairs at the same time with the exon-intron junction of the target mRNA (bottom image), at a site that is very close to the U4 pairing region (top image). The upshot is that this single base insertion into U4 causes some portion of the target mRNAs to be mis-spliced, using non-natural 5 prime splice sites and thus altering their encoded proteins. This may cause minor problems in the protein, but more often will cause a shift in translation frame, a premature stop codon, and total loss of the functional protein. So this tiny mutation can have severe effects and is indeed genetically dominant- that is, one copy overrides a second wild-type copy to generate the NDD diseases that were studied.

The U4 RNA (teal) paired with the U6 RNA (gray), within an early spliceosome complex. The mutation studied here is pointed out in black (n.64_65insT - i.e. insertion of a T). Note how it would cause a bulge in the pairing. Importantly, the location in the U6 RNA that pairs with the mRNA (see below) is right next door, at the ACAGAGA (light gray). The authors use this structural work from others to suggest how the mutation they found can alter selected splicing sites and thus lead to disease. Other single nucleotide insertions that cause similar syndromes are marked with black arrows, while single nucleotide substitutions that cause less severe syndromes are marked with orange RNA segments.

The U6 RNA (pink) paired with its mRNA target to be spliced. It binds right at the intron (gray) exon (black) boundary, where the cut will eventually be made the remove the intron. The bump from the mis-paired mutant U4 RNA (see above) distorts this binding, sending U6 to select wrong locations for spicing.

The researchers went on to survey this and other spliceosomal RNA genes for similar mutations, and found few to none outside the region marked in the diagram above. For example, there is a highly similar gene called RNU4-1. But this gene is expressed about 100-fold less in brain and other tissues, making RNU4-2 the principal source of U4 RNA, and much more significant as a causal factor for NDD. It appears that other locations in RNU4-2 (and other spliceosomal RNA genes) are even more important than the one mutated location found here, thus are never found, being lethal and heavily selected against, in this highly conserved gene. 

They also noted that, while this RNU4-2 mutation is severe, and thus must happen spontaneously (i.e. not inherited from parents), it only occurrs on the maternal alleles, not paternal alleles in the affected children. They speculate that this may be due to effects this gene may have in male gametogenesis, killing affected sperm preferentially, but not affected oocytes. Lastly, this set of mutations (in the small region shown in the first figure above) appears to account for, in their estimation, about 0.4 % of all NDD seen in Britain. This is a remarkably high rate for such a particular mutation that is not heritable. They speculate that some mutation hotspot kind of process may be causing these events, above the general mutation rate. What this all says about so-called "intelligent design", one may be reluctant to explore too deeply. On the other hand, this still leaves plenty of room to hunt for additional variations that cause these syndromes.

In this research, we see that clinically critical variations can pop up in many places, not just among the "usual suspects", genetically and genomically speaking. While much of the human genome is junk, most of it is also expressed (as RNA) and all of it is fair game for clinically important (if tragic) effects. The NDD syndromes caused by the mutation studied here are very severe- for more so than the ADD or mild autism diagnoses that make up most of the NDD spectrum. Understanding the causal nexus between the genome and human biology and its pathologies, remains an ongoing and complicated scientific adventure.

• Playing the heel. Being the heel. 
• It sure is great to be the victim.
• Oh, right.. now we really know what is going on.
• More spiritual warfare.
• Another grift.

What Causes Cancer? What is Cancer?

There is some frustration in the literature.

Fifty years into the war on cancer, what have we learned and gained? We do not have a general cure, though we have a few cures and a lot of treatments. We have a lot of understanding, but no comprehensive theory or guide to practice. While some treatments are pin-point specific to certain proteins and even certain mutated forms of those proteins, most treatments remain empirical, even crude, and few provide more than a temporary respite. Cancer remains an enormous challenge, clinically and intellectually.

Recently, a prominent journal ran a provocative commentary about the origins of cancer, trashing the reigning model of "Somatic Mutation Theory", or SMT. Which is the proposition that cancer is caused by mutations that "drive" cell proliferation, and thus tumor growth. I was surprised at the cavalier insinuations being thrown around by these authors, their level of trash talk, and the lack of either compelling evidence or coherent alternative model. Some of their critiques have a fair basis, as discussed below, but to say, as the title does, that this is "The End of the Genetic Paradigm of Cancer" is simply wrong.

"It is said that the wise only believe in what they can see, and the fools only see what they can believe in. The latter attitude cements paradigms, and paradigms are amplified by any new-looking glass that puts one’s way of seeing the world on steroids. In cancer research, such a self-fulfilling prophecy has been fueled by next-generation DNA sequencing."

"However, in the quest for predictive biomarkers and molecular targets, the cancer research community has abandoned deep thinking for deep sequencing, interpreting data through the lens of clinical translation detached from fundamental biology."

Whew!

The main critique, once the gratuitous insults and obligatory references to Kuhn and Feynman are cleared away, is that cancer does not resemble other truly clonal disease / population processes, like viral or bacterial infections. In such processes, (which have become widely familiar after the COVID and HIV pandemics), a founder genotype can be identified, and its descendants clearly derive from that founder, while accumulating additional mutations that may respond to the Darwinian pressures, such as the immune system and other host defenses. While many cancers are clearly driven by some founding mutation, when treatments against that particular "driver" protein are given, resistance emerges, indicating that the cancer is a more diverse population with a very active mutation and adaptation process. 

Additionally, tumors are not just clones fo the driving cell, but have complex structure and genetic variety. Part of this is due to the mutator phenotypes that arise during carcinogenesis, that blow up the genome and cause large numbers of additional mutations- many deleterious, but some carrying advantages. More significantly, tumors arise from and continue to exist in the context of organs and tissues. They can not just grow wildly as though they were on a petri plate, but must generate, for example, vascular structures and a "microenvironment" including other cells that facilitate their life. Similarly, metastasis is highly context-dependent and selective- only very few of the cells released by a tumor land in a place they find conducive to new growth. This indicates, again, that the organ setting of cancer cells is critically important, and accounts in large part for this overall difference between cancers and more straightforward clonal processes. 

Schematic of cancer development, from a much more conventional and thorough review of the field.

Cancer cells need to work with the developmental paradigms of the organism. For instance, the notorious "EMT", or epithelial-mesenchymal transition is a hallmark of de-differentiation of many cancer cells. They frequently regress in developmental terms to recover some of the proliferative and self-repair potential of stem cells. What developmental program is available or allowed in a particular tissue will vary tremendously. Thus cancer is not caused by each and every oncogenic mutation, and each organ has particular and distinct mutations that tend to cause cancers within it. Indeed, some organs hardly foster any cancers at all, while other organs with more active (and perhaps evolutionarily recent) patterns of proliferation (such as breast tissue, or prostate tissue) show high rates of cancer. Given the organ setting, cancer "driver" mutations need not only unleash the cell's own proliferation, but re-engineer its relations with other cells to remove their inhibition of its over-growth, and pursuade them to provide the environment it needs- nutritionally, by direct contact, by growth factors, vascular formation, immune interactions, etc., in a sort of para-organ formation process. It is a complicated job, and one mutation is, empirically, rarely enough.

"Instead, cancer can be broadly understood as “development gone awry”. Within this perspective, the tissue organization field theory is based on two principles that unite phylogenesis and ontogenesis."

"The organicist perspective is based on the interdependency of the organism and its organs. It recognizes a circular causal regimen by closure of constraints that makes parts interdependent, wherein these constraints are not only molecules, but also biophysical force."

As an argument or alternative theory, this leaves quite a bit to be desired, and does not obviate the role of  initiating mutations in the process.

It remains, however, that oncogenic mutations cause cancer, and treatments that address those root causes have time and again shown themselves to be effective cancer treatments, if tragically incomplete. The rise of shockingly effective immunotherapies for cancer have shown, however, that the immune system takes a more holistic approach to attacking disease than such "precision" single-target therapies, and can make up for the vagaries of the tissue environment and the inflammatory, developmental, and mutational derangements that happen later in cancer development. 

In one egregious citation, the authors hail an observation that certain cancers need both a mutation and a chemical treatment to get started, and that the order of these events is not set in stone. Traditionally, the mutation is induced first, and then the chemical treatment, which causes inflammation, comes second. They state: 

"The qualitative dichotomy between a mutagenic initiator that creates ’cancer cells’ and the non-genetic, tissue-perturbing promoter that expands them may not be as clear-cut. Indeed, the reverse experiment (first treatment with the promoter followed by the initiator) equally produces tumors. This result refutes the classical model that requires that the mutagenic (alleged) initiator must act first."

The citation is to a paper entitled "The reverse experiment in two-stage skin carcinogenesis. It cannot be genuinely performed, but when approximated, it is not innocuous". This paper dates from 1993, long before sequencing was capable of evaluating the mutation profiles of cancer cells. Additionally, the authors of this paper themselves point out (in the quote below) a significant assymetry in the treatments. Their results are not "equal":

"The two substances showed a reciprocal enhancing effect, which was sometimes weak, sometimes additive, and sometimes even synergistic, and was statistically most significant when the results were assessed from the time of DMBA application. Although the reverse experiment was not in any way innocuous it always resulted in a lower tumor crop than the classical sequence of DMBA followed by a course of TPA treatment. 

However, the lower tumor crop in the reverse experiment cannot be used to prove a qualitative difference between initiators and promoters."

(DMBA is the mutagen, while TPA is the inflammatory accelerant.)

So chemical treatment can prepare the ground for subsequent mutant generation in forming cancers in this system, while being much less efficient than the traditional order of events. This is not a surprise, given that this chemical (TPA) treatment causes relatively long-term inflammation and cell proliferation on its own.

"An epistemic shift towards a biological theory of cancer may still be an uphill battle in the current climate of thought created by the ease of data collection and a culture of research that discourages ’disruptive science’. Here, we have made an argument for dropping the SMT and its epicycles. We presented new and old but sidelined theoretical alternatives to the SMT that embrace theory and organismal biology and can guide experiments and data interpretation. We expect that the diminishing returns from the ceaselessly growing databases of somatic mutations, the equivalent to Darwin’s gravel pit, may soon reach a pivot point."

One rarely reads such grandiloquent summaries (or mixed metaphors) in scientific papers! But here they are truly beating up on straw men. In the end, it is true that cancer is quite unlike clonal infectious diseases, and for this, as for many other reasons, has had scientists scratching their heads for decades, if not centuries. But rest assured that this chest-thumping condescension is quite unnecessary, since those in the field are quite aware of these difficulties. The various nebulous alternatives these authors offer, whether the "epigenetic landscape", the "tissue organization field theory", or the "biological theory of cancer" all have kernels of logic, but the SMT remains the foundation-stone of cancer study and treatment, while being, for all the reasons enumerated above and by these authors, only part of the edifice, not the whole truth.

• Some more thoughts about crypto.
• Resistance is up to congress, ultimately.
• China takes purges quite a bit more seriously than we do.
• But we are getting there.

Sugar is the Enemy

Diabetes, cardiovascular health, and blood glucose monitoring.

Christmas brought a book titled "Outlive: The Science and Art of Longevity". Great, I thought- something light and quick, in the mode Gweneth Paltrow or Deepak Chopra. I have never been into self-help or health fad and diet books. Much to my surprise, however, it turned out to be a rather rigorous program of preventative medicine, with a side of critical commentary on our current medical system. A system that puts various thresholds, such as blood sugar and blood pressure, at levels that represent serious disease, and cares little about what led up to them. Among the many recommendations and areas of focus, blood glucose levels stand out, both for their pervasive impact on health and aging, and also because there are new technologies and science that can bring its dangers out of the shadows.

Reading: 

• Outlive
• The many facets and forms of damage by high blood sugar, at the level of molecular biology.
• Recent analyses of blood sugar variability, from researchers at Stanford
• ... with tool for anyone with a CGM to upload their own data

Where do cardiovascular problems, the biggest source of mortality, come from? Largely from metabolic problems in the control of blood sugar. Diabetics know that uncontrolled blood sugar is lethal, on both the acute and long-terms. But the rest of us need to realize that the damage done by swings in blood sugar are more insidious and pervasive than commonly appreciated. Both microvascular (what is commonly associated with diabetes, in the form of problems with the small vessels of the kidney, legs, and eyes) and macrovascular (atherosclerosis) are due to high and variable blood sugar. The molecular biology of this was impressively unified in 2005 in the paper above, which argues that excess glucose clogs the mitochondrial respiration mechanisms. Their membrane voltage maxes out, reactive forms of oxygen accumulate, and glucose intermediates pile up in the cell. This leads to at least four different and very damaging consequences for the cell, including glucose modification (glycation) of miscellaneous proteins, a reduction of redox damage repair capacity, inflammation, and increased fatty acid export from adipocytes to endothelial (blood vessel) cells. Not good!

Continuous glucose monitored concentrations from three representative subjects, over one day. These exemplify the low, moderate, and severe variability classes, as defined by the Stanford group. Line segments are individually classed as to whether they fall into those same categories. There were 57 subject in the study, of all ages, none with an existing diagnosis of diabetes. Yet five of them had diabetes by traditional criteria, and fourteen had pre-diabetes by those criteria. By this scheme, 25 had severe variability as their "glucotype", 25 had moderate variability, and only 7 had low variability. As these were otherwise random subjects selected to not have diabetes, this is not great news about our general public health, or the health system.

Additionally, a revolution has occurred in blood glucose monitoring, where anyone can now buy a relatively simple device (called a CGM) that gives continuous blood glucose monitoring to a cell phone, and associated analytical software. This means that the fasting blood glucose level that is the traditional test is obsolete. The recent paper from Stanford (and the literature it cites) suggests, indeed, that it is variability in blood glucose that is damaging to our tissues, more so than sustained high levels.

One might ask why, if blood glucose is such a damaging and important mechanism of aging, hasn't evolution developed tighter control over it. Other ions and metabolites are kept under much tighter ranges. Sodium ranges between 135 to 145 mM, and calcium from 8.8 to 10.7 mM. Well, glucose is our food, and our need for glucose internally is highly variable. Our livers are tiny brains that try very hard to predict what we need, based on our circadian rhythms, our stress levels, our activity both current and expected. It is a difficult job, especially now that stress rarely means physical activity, and nor does travel, in our automobiles. But mainly, this is a problem of old age, so evolution cares little about it. Getting a bigger spurt of energy for a stressful event when we, in our youth, are in crisis may, in the larger scheme of things, outweigh the slow decay of the cardiovascular system in old age. Not to mention that traditional diets were not very generous at all, certainly not in sugar and refined carbohydrates.

• First, Twitter was turned into a dumpster fire, next the US.
• US government to be rebranded as X.
• Truth must die.
• "Not strictly constitutional"
• Let's go there.

A Hunt for Causes of Atherosclerosis

Using the most advanced tools of molecular biology to sift through the sands of the genome for a little gold.

Blood vessels have a hard life. Every time you put on shoes, the vessels in your feet get smashed and smooshed, for hours on end. And do they complain? Generally, not much. They bounce back and make do with the room you give them. All through the body, vessels are subject to the pumping of the heart, and variations in blood volume brought on by our salt balance. They have to move when we do, and deal with it whenever we sit or lie on them. Curiously, it is the veins in our legs and calves, that are least likely to be crushed in daily life, that accumulate valve problems and go varicose. Atherosclerosis is another, much more serious problem in larger vessels, also brought on by age and injury, where injury and inflammation of the lining endothelial cells can lead to thickening, lipid/cholesterol accumulation, necrosis, calcification, and then flow restriction and fragmentation risk. 

Cross-section of a sclerotic blood vessel. LP stands for lipid pool, while the box shows necrotic and calcified bits of tissue.

The best-known risk factors for atherosclerosis are lipid-related, such as lack of liver re-capture of blood lipids, or lack of uptake around the body, keeping cholesterol and other lipid levels high in the blood. But genetic studies have found hundreds of areas of the genome with risk-conferring (or risk-reducing) variants, most of which are not related to lipid management. These genome-wide association studies (or GWAS) look for correlations between genetic markers and disease in large populations. So they pick up a lot of low-impact genetic variations that are difficult to study, due to their large number and low impact, which can often imply peripheral / indirect function. High-impact variations (mutations) tend to not survive in the population very long, but when found tend to be far more directly involved and informative.

A recent paper harnessed a variety of modern tools and methods to extract more from the poor information provided by GWAS. They come up with a fascinating tradeoff / link between atherosclerosis and cerebral cavernous malformation (CCM), which is distinct blood vessel syndrome that can also lead to rupture and death. The authors set up a program of analysis that was prodigious, and only possible with the latest tools. 

The first step was to select a cell line that could model the endothelial cells at issue. Then they loaded these cells with custom expression-reducing RNA regulators against each one of the ~1600 genes found in the neighborhood of the mutations uncovered by the GWAS analyses above, plus 600 control genes. Then they sequenced all the RNA messages from these single cells, each of which had received one of these "knock-down" RNA regulators. This involved a couple hundred thousand cells and billions of sequencing reads- no simple task! The point was to gather comprehensive data on what other genes were being affected by the genetic lesion found in the GWAS population, and then to (algorithmically) assemble them into coherent functional groups and pathways which could both identify which genes were actually being affected by the original mutations, and also connect them to the problems resulting in atherosclerosis.

Not to be outdone, they went on to harness the AlphaFold program to hunt for interactions among the proteins participating in some of the pathways they resolved through this vast pipeline, to confirm that the connections they found make sense.

They came up with about fifty different regulated molecular programs (or pathways), of which thirteen were endothelial cell specific. Things like angiogenesis, wound healing, flow response, cell migration, and osmoregulation came up, and are naturally of great relevance. Five of these latter programs were particularly strongly connected to coronary artery disease risk, and mostly concerned endothelial-specific programs of cell adhesion. Which makes sense, as the lack of strong adhesion contributes to injury and invasion by macrophages and other detritus from the blood, and adhesion among the endothelial cells plays a central role in their ability / desire to recover from injury, adjust to outside circumstances, reshape the vessel they are in, etc.

Genes near GWAS variations and found as regulators of other endothelial-related genes are mapped into a known pathway (a) of molecular signaling. The color code of changed expression refers to the effect that the marked gene had on other genes within the five most heavily disease-linked programs/pathways. The numbers refer to those programs, (8=angiogenesis and osmoregulation, 48=cell adhesion, 35=focal adhesion, related to cell adhesion, 39=basement membrane, related to cell polarity and adhesion, 47=angiogenesis, or growth of blood vessels). At bottom (c) is a layout of 41 regulated genes within the five disease-related programs, and how they are regulated by knockdown of the indicated genes on the X axis. Lastly, in d, some of these target genes have known effects on atherosclerosis or vascular barrier syndromes when mutated. And this appears to generally correlate with the regulatory effects of the highlighted pathway genes.

"Two regulators of this (CCM) pathway, CCM2 and TLNRD1, are each linked to a CAD (coronary artery disease) risk variant, regulate other CAD risk genes and affect atheroprotective processes in endothelial cells. ... Specifically, we show that knockdown of TLNRD1 or CCM2 mimics the effects of atheroprotective laminar blood flow, and that the poorly characterized gene TLNRD1 is a newly identified regulator in the CCM pathway."

On the other hand, excessive adhesiveness and angiogenesis can be a problem as well, as revealed by the reverse correlation they found with CCM syndrome. The interesting thing was that the gene CCM2 came up as one of strongest regulators of the five core programs associated with atherosclerosis risk mutations. As can be guessed from its name, it can harbor mutations that lead to CCM. CCM is a relatively rare syndrome (at least compared with coronary artery disease) of localized patches of malformed vessels in the brain, which are prone to rupture, which can be lethal. CCM2 is part of a protein complex, with KRIT1 and PDCD10, and part of a known pathway from fluid flow sensing receptors to transcription regulators (TFs) that turn on genes relevant to the endothelial cells. As shown in the diagram above, this pathway is full of genes that came up in this pathway analysis, from the atherosclerosis GWAS mutations. Note that there is a repression effect in the diagram above (a) between the CCM complex and the MAP kinase cascade that sends signals downstream, accounting for the color reversal at this stage of the diagram.

Not only did they find that this known set of three CCM gene are implicated in the atherosclerosis mutation results, but one of the genes they dug up through their pipeline, TLNRD1, turned out to be a fourth, hitherto unknown, member of the CCM complex, shown via the AlphaFold program to dock very neatly with the others. It is loss of function mutations of genes encoding this complex, which inhibits the expression of endothelial cell pro-cell adhesion and pro-angiogenesis sets of genes, that cause CCM, unleashing these angiogenesis genes to do too much. 

The logic of this pathway overall is that proper fluid flow at the cell surface, as expected in well-formed blood vessels, activates the pathway to the CCM complex, which then represses programs of new or corrective angiogenesis and cell adhesion- the tissue is OK as it is. Conversely, when turbulent flow is sensed, the CCM complex is turned down, and its target genes are turned up, activating repair, revision, and angiogenesis pathways that can presumably adjust the vessel shape to reduce turbulence, or simply strengthen it.

Under this model, malformations may occur during brain development when/where turbulent flow occurs, reducing CCM activation, which is abetted by mutations that help the CCM complex to fall apart, resulting (rarely) in run-away angiogenesis. The common variants dealt with in this paper, that decrease risk of cardiovascular disease / atherosclerosis, appear to have similar, but much weaker effects, promoting angiogenesis, including recovery from injury and adhesion between endothelial cells. In this way, they keep the endothelium tighter and more resistant to injury, invasion by macrophages, and all the downstream sequelae that result in atherosclerosis. Thus strong reduction of CCM gene function is dangerous in CCM syndrome, but more modest reductions are protective in atherosclerosis, setting up a sensitive evolutionary tradeoff that we are clearly still on the knife's edge of. I won't get into the nature of the causal mutations themselves, but they are likely to be diffuse and regulatory in the latter case.

Image of the CCM complex, which regulates response to blood flow, and whose mutations are relevant both to CCM and to atherosclerosis. The structures of TLNRD1 and the docking complex are provided by AlphaFold. 

This method is particularly powerful by being unbiased in its downstream gene and pattern finding, because it samples every expressed gene in the cell and automatically creates related pathways from this expression data, given the perturbations (knockdown of expression) of single target genes. It does not depend on using existing curated pathways and literature that would make it difficult to find new components of pathways. (Though in this case the "programs" it found align pretty closely with known pathways.) On the other hand, while these authors claim that this method is widely applicable, it is extremely arduous and costly, as evidenced by the contribution of 27 authors at top-flight institutions, an unusually large number in this field. So, for diseases and GWAS data sets that are highly significant, with plenty of funding, this may be a viable method of deeper analysis. Otherwise, it is beyond the means of a regular lab.

• A backgrounder on sedition, treason, and insurrection.
• And why it matters.
• Jan 6 was an attempted putsch.
• Trumpies for Putin.
• Solar is a no-brainer.
• NDAs are blatantly illegal and immoral. One would think we would value truth over lies.

Dangerous Memories

Some memory formation involves extracellular structures, DNA damage, and immune component activation / inflammation.

The physical nature of memories in the brain is under intensive scrutiny. The leading general theory is that of positive reinforcement, where neurons that are co-activated strengthen their connections, enhancing their ability to co-fire and thus to express the same pattern again in the future. The nature of these connections has been somewhat nebulous, assumed to just be the size and stability of their synaptic touch-points. But it turns out that there is a great deal more going on.

A recent paper started with a fishing expedition, looking at changes in gene expression in neurons at various time points after the mice were subjected to a fear learning regimen. They took this out to much longer time points (up to a month) than had been contemplated previously. At short times, a bunch of well-known signals and growth-oriented gene expression happened. At the longest time points, organization of a structure called the perineural net (PNN) was read out of the gene expression signals. This is a extracellular matrix sheath that appears to stabilize neuronal connections and play a role in long-term memory and learning. 

But the real shocker came at the intermediate time point of about four days. Here, there was overexpression of TLR9, which is an immune system detector of broken / bacterial DNA, and inducer in turn of inflammatory responses. This led the authors down a long rabbit hole of investigating what kind of DNA fragmentation is activating this signal, how common this is, how influential it is for learning, and what the downstream pathways are. Apparently, neuronal excitation, particularly over-excitation that might be experienced under intense fear conditions, isn't just stressful in a semiotic sense, but is highly stressful to the participating neurons. There are signs of mitochondrial over-activity and oxidative stress, which lead to DNA breakage in the nucleus, and even nuclear perforation. It is a shocking situation for cells that need to survive for the lifetime of the animal. Granted, these are not germ cells that prioritize genomic stability above all else, but getting your DNA broken just for the purpose of signaling a stress response that feeds into memory formation? That is weird.

Some neuronal cell bodies after fear learning. The red dye is against a marker of DNA repair proteins, which form tight dots around broken DNA. The blue is a general DNA stain, and the green is against a component of the nuclear envelope, showing here that nuclear envelopes have broken in many of these cells.

The researchers found that there are classic signs of DNA breakage, which are what is turning on the TLR9 protein, such as seeing concentrated double-strand DNA repair complexes. All this stress also turned on proteases called caspases, though not the cell suicide program that these caspases typically initiate. Many of the DNA break and repair complexes were, thanks to nuclear perforation, located diffusely at the centrosome, not in the nucleus. TLR9 turns on an inflammatory response via NFKB / RELA. This is clearly a huge event for these cells, not sending them into suicide, but all the alarms short of that are going off.

The interesting part was when the researchers asked whether, by deleting the TLR9 or related genes in the pathway, they could affect learning. Yes, indeed- the fear memory was dependent on the expression of this gene in neurons, and on this cell stress pathway, which appears to be the precondition of setting up the perineural net structures and overall stabilization. Additionally, the DNA damage still happened, but was not properly recognized and repaired in the absence of TLR9, creating an even more dangerous situation for the affected neurons- of genomic instability amidst unrepaired DNA.

When TRL9 is knocked out, DNA repair is cancelled. At bottom are wild-type cells, and at top are mouse neurons after fear learning that have had the gene TLR9 deleted. The red dye is against DNA repair proteins, as is the blue dye in the right-most frames. The top row is devoid of these repair activities.

This paper and its antecedent literature are making the case that memory formation (at least under these somewhat traumatic conditions- whether this is true for all kinds of memory formation remains to be seen) has commandeered ancient, diverse, and quite dangerous forms of cell stress response. It is no picnic in the park with madeleines. It is an all-hands-on-deck disaster scene that puts the cell into a permanently altered trajectory, and carries a variety of long-term risks, such as cancer formation from all the DNA breakage and end-joining repair, which is not very accurate. They mention in passing that some drugs have been recently developed against TLR9, which are being used to dampen inflammatory activities in the brain. But this new work indicates that such drugs are likely double-edged swords, that could impair both learning and the long-term health of treated neurons and brains.

• Cutting the line to the American Dream.