Tangles

[SOUND: A slow, haunting ambient soundtrack. The sound of a faint, distorted heartbeat.]

Charles: Deep inside our brains, there’s a shapeless killer at work.

It passes from protein to protein, cell to cell, leaving behind a path of carnage.

[Sound of the heartbeat becoming slightly clearer, then a subtle “crackling” sound effect]

Charles: This is the world of the amyloid. This toxic ball of protein grows and accumulates for years, even decades within our cells. Slowly smothering our neurons, erasing our memories, and stealing vital bodily functions, minute by minute.

These amyloids are associated with some of our most feared neurodegenerative diseases, like Alzheimer’s and Parkinson’s disease. They’re abundant in the neurons of patients with these diseases, and oftentimes, only discovered post-mortem.¹

For decades, we’ve been hunting them down. Trying to snuff them out before they can do further damage to us.

But, things haven’t exactly been going to plan…

Time and time again, we think we’ve solved them, eliminated them from our cells once and for all, but they always find a way to come back.

They pop up in unexpected places, they change their forms, their composition, it’s like they’re mocking us.

But, maybe… we’re missing something… Maybe the amyloid has a hidden secret that we’ve been seeing, but not realizing, this entire time…

[Signals intro theme plays]

Charles: You’re listening to Signals. I’m Charles Brambell, and today, we’re taking a look at the disorderly state of amyloid theory, and how a single, unexpected protein might be the key to winning this decades’ long battle.

[Theme fades into a brief moment of silence]

Charles: So, what is an amyloid?

[Ominous ambient music kicks in]

Charles: Inside your cells, thousands of proteins float around, each with a specific job—from shuttling nutrients to providing structure. They all contribute to the well-oiled machine that is a functioning cell.

Sometimes, though, this machine malfunctions. For one reason or another, a protein can misfold and lose its structure. Think of it like a bolt coming loose from the machine.

It’s not an issue though, these things happen, and the cell has mechanisms to recycle these misfolded proteins; to patch itself up.

But a select few proteins are especially dangerous when they misfold. These proteins really like to stick together, they bundle up and form giant clumps called amyloids.

Think of it like cooking an egg. A raw egg is runny because the proteins are in their natural soluble, flowy states. But if you heat them up enough, you destroy all those carefully formed structures, and the proteins tangle up into a solid mass.

That’s kind of like what an amyloid is, a solid mass of disorderly proteins.

Charles: Now, when a bunch of proteins tangle into an amyloid, the cell can’t really untangle it. It’s kind of like how, once you cook an egg, you can’t uncook it.

Amyloids are typically too large for the cell’s recycling system to handle. So… the cell has no choice but to just live with them after they’ve formed.

Now, this is bad because amyloids disrupt cell functions; they’re toxic by nature.

They cause inflammation, block nutrient trafficking, and they can even cause other healthy proteins to misfold and join them.

The formation of an amyloid is like a dead end for a cell. The cell can’t do anything about them, so they just accumulate, growing in number, and slowly poisoning the cell from within until it dies.

This is precisely the pattern that pathologists have been seeing in the neurons of patients with Alzheimer’s and Parkinson’s disease for the past thirty years. It’s the backbone of what we call “amyloid theory”, the theory that amyloids disrupt neuron function and their presence leads to the onset of neurodegenerative disease.

[Pause]

Charles: With this information, researchers embarked on a mad dash to try to find something that could break down these amyloids and hopefully restore function to diseased and dying neurons.

In 2021, it seemed like we got just that. The FDA approved a drug called Aducanumab as a treatment for Alzheimer’s disease.

This drug is what’s known as an antibody.

[Pause]

Charles: Now, our immune system naturally produces antibodies to stick to intruders, like viruses or bacteria, and to mark them for destruction.

So, scientists cleverly engineered an antibody to seek out and tag amyloid proteins, flagging them for destruction by immune cells.

Remember how I said these tangles were too big for cells to break down? Well, our immune system is much better adapted to handling larger masses and clearing them away.

The researchers who developed this drug were basically asking the immune system for a little help in breaking down these amyloids, and they’re doing so by putting a big target on them.

And the thing is, aducanumab worked. The PET scans proved it. You could literally see the amyloids disappearing from patients’ brains. Researchers essentially made a guided missile that could pinpoint these amyloids and take them out.²

[Pause]

Charles: But, something still wasn’t right. Despite us seeing amyloids disappearing from the patients’ neurons, the clinical results were a profound disappointment because the actual cognitive benefit of this drug on patients was found to be tiny.

You see, while the drug was still awaiting approval from the FDA, there were two clinical studies done to evaluate the drug’s effectiveness. They were named EMERGE and ENGAGE.

Basically, these two studies measured cognitive function on an 18-point clinical scale. They both studied groups of patients with amyloid-induced Alzheimer’s disease and they would measure how much their cognitive decline slowed with different doses of the drug.

In one study, they found that a high dose of the drug slowed cognitive decline in these patients by an average just 0.39 points over 18 months. While that difference was statistically significant in one of the two major trials, the result was still iffy at best.

That’s because the other, nearly identical trial showed the drug had no measurable benefit over placebo at all.³

To further complicate matters, some argued that a change of 0.39 points on the 18 point scale was clinically imperceptible—it wouldn’t be noticeable to a patient, their family, or their doctors, and it wouldn’t improve their well being.

The fact that this small change couldn’t even be reproduced by a twin study was a major red flag for the FDA.

The controversy ended up being so profound that the FDA’s own independent expert panel voted 10 to 0 (with one abstention) against recommending approval, arguing that evidence of the drug benefit was unconvincing.⁴

Yet, in a highly controversial move, the FDA overruled its own advisors and approved aducanumab for clinical use. They based this not on clear proof it helped patients, but on its proven ability to clear amyloid plaques—banking on the hope that it might eventually lead to a benefit.⁵

This decision split the medical community and laid bare the crisis: we had a drug that successfully attacked the presumed cause of dementia but failed to reliably change the course of the disease. The link between amyloids and the dementia was breaking down.

[Pause]

Charles: This forced researchers to confront a question they had been quietly asking for years. What if there wasn’t a direct link between amyloids and disease? What if it was more complicated than we thought?

The core principles of the amyloid hypothesis were coming into question.

But, the thing is, challenging the amyloid hypothesis was incredibly difficult. It wasn’t just a theory at this point; it was the narrative. It was elegant, intuitive, and it gave the field a single target to focus on.

I mean, I really need to emphasize this: amyloid theory had organized decades worth of research and attracted billions of dollars in funding, it essentially defined the entire field of neurodegenerative disease research. To oppose amyloid theory would be to oppose nearly thirty years of combined research effort.

But the failure of Aducanumab couldn’t be ignored. It showed that there was undeniably something happening between amyloid formation and disease onset that we’ve been overlooking this whole time, and it was just a matter of time before the cracks in the theory started to show themselves.

[Pause]

Charles: One of the most powerful clues came from a study that began back in the 1980s. It’s now known as the Nun Survivor Study. So, in this study Epidemiologist Dr. David Snowdon had an idea. To truly understand brain aging, he needed to study a stable population whose lives were well-documented. He and he found just that:

[Faint churchbells ring out]

The School Sisters of Notre Dame is a population of over 670 nuns from several convents that all agreed to participate in Dr. Snowdon’s study.

These women agreed to take annual cognitive tests—including memory quizzes, problem-solving tasks, and story recalls—and, crucially, they all pledged to donate their brains to research after they passed away. This combination of mental snapshots throughout their lives as well as a physical examination of their brains postmortem was a dataset we’ve never really been able to analyze before.

And the results of the decades-long project were unsettling, to say the least. Looking over the data, researchers found that many of the participants had brains that were absolutely riddled with classic signs of advanced neurodegenerative disease, including dense amyloid plaques and other protein tangles.

And yet, their yearly cognitive tests showed many of them displayed no significant signs of dementia or cognitive dysfunction while they were alive.

The presence of amyloids in their brains didn’t seem to affect them at all.⁶

[Pause]

Charles: But, looking back, now we have two completely different stories.

On one hand, you have Aducanumab: where amyloids are eliminated, but disease still remains.

On the other hand, you have the Nun Study: where amyloids are abundant, but for some reason the disease is nowhere to be found.

The link between amyloids and neurodegenerative disease was starting to seem less obvious, the very foundation of decades worth of research was not just a straight line anymore. It was full of exceptions and contradictions. It seemed like the smoking gun we had been chasing for thirty years was looking more and more like a red herring.

[Music fades out]

[Sigh]

Charles: So, where does that leave us? If amyloids weren’t directly causing brain disease, then what was? At this point, the field was stuck….

Well, a new lead would emerge not from researching dementia, but from the study of a different disease: ALS. In this sector, scientists had been looking at their own mysterious protein. It was called TDP-43, and it would turn the entire field on its head.

[Advertisement music]

Charles: This is where I would put an advertisement, if I had one. If you would like to advertise your biological products or services here, shoot me an email via my website signalsbio.net. That’s spelled “signals” “B” “I” “O” (dot) net. Thanks, and let’s continue on with the story of TDP-43.

[Advertisement music fades out]

Charles: The story of TDP-43 begins back in 1995. Researchers at the University of Texas discovered a new protein in human cells infected with HIV, of all things. They named it TDP-43.⁷ Its job seemed pretty niche: they found that it helped HIV activate some of its genes. A notable find, sure, but it seemed like TDP would just remain kind of a footnote in the grand scheme of things.

Charles: And it was, for over a decade following its discovery.

That would change in 2006, though, when a team at UPenn was studying amyloids found in the neurons of ALS patients.

You see, different diseases have their own specific proteins that can identify or characterize them, their molecular fingerprints, per se.

So, researchers wanted to see what sort of fingerprint the amyloids in ALS were leaving behind.

And, the surprising answer turned out to be TDP-43. And it wasn’t in its normal state either; instead, it had been chemically altered and chopped into fragments, forcing it to clump into amyloid-like fibrils.⁸

Now, this was big news. Here was TDP-43, a DNA binder that usually lives in the nucleus… suddenly starting to malfunction and pop up in places where it shouldn’t, and it seems to be killing cells.

[PAUSE]

Charles: So now researchers were hooked, they wanted to find out everything they could about this mysterious protein, and why it was undergoing such a drastic change in behavior. They wanted to see if it had functions besides just activating HIV genes.

[inquisitive music]

Charles: The easiest way to figure out what a gene does is to see what happens when an organism doesn’t have it. To see what kinds of functions or structures go missing when a protein goes missing. So, in 2009, a lab removed the TDP-43 gene from mice to see what happens to them.

The result was… catastrophic. It turns out, mouse embryos born without TDP aren’t viable; for some reason, they die before they reach adulthood.⁹

So, researchers tried removing TDP from adult mice, but they found that all of the mice quickly developed severe muscle wasting. Their muscles withered away as if the mice suddenly turned 80 years old overnight. And all of them subsequently died.¹⁰

This told them something crucial: TDP-43 wasn’t just involved in disease; it was essential both for early development and for maintaining healthy muscle.

And, this wasn’t just seen in mice either. The same lethal effect was seen when other labs removed TDP from fruit flies and from zebrafish. This means that whatever this protein does, it’s so fundamental to life that its function has been preserved across species for hundreds of millions of years. It is, in all likelihood, just as essential in humans.¹¹

[Pause]

Charles: But, that leaves us with a problem. We’re stuck, once again. Because if you keep TDP in your cells, it forms deadly aggregates. But if you get rid of it, your muscles waste away and you die. It’s a lose-lose situation.

But at least, we know two things now: 1) That this protein is essential for muscle cell survival, and 2) it forms toxic amyloids in neurons.

So in 2018, researchers at CU Boulder tried connecting the dots by asking: Does TDP form amyloids in muscle cells? To answer this, they started scanning for the protein in mouse models of ALS.

Charles: And, they found what they were looking for. In these diseased muscle cells, amyloids containing TDP were popping up all over the cell. They named these structures “myo-granules” to distinguish them from amyloids, but for my purpose, I’m going to use them interchangeably.¹²

To the researchers, their discovery of amyloids in muscle cells was notable, but it still didn’t answer the core question: What is TDP-43’s actual job in muscle?

To find its normal function, they needed to see it in action. And they reasoned that if this protein is so essential for muscle to develop and function, it should be most active when muscle is growing. So, they gave healthy, undiseased mice a minor muscle injury—kind of like the cellular equivalent of a hard workout and then they watched as the muscles regrew to try and see TDP working in its intended state.

But, what they saw next was shocking.

[Pause]

Charles: Within hours of the injury, the healthy muscle cells flooded with myo-granules containing TDP. It lit up like a Christmas tree with TDP markers, and they were all tangled up just like the deadly amyloids we saw in neurons.¹²

[Another pause]

Charles: What? Let’s be clear about how shocking this was. This wasn’t in a diseased animal. This was in a normal mouse, responding to a normal, everyday injury. The same structures that were suspected of causing deadly, incurable disease were now appearing in normal, healthy cells.

Which doesn’t make sense at all. I mean, I don’t get debilitating disease every time I lift weights or strain a muscle. So, what were these deadly myo-granules doing here?

Well the team continued to watch and wait… and they found a pattern: the myo-granules would peak in number a few days after the injury, but after about 30 days, they were all but gone, completely disappeared.¹²

As it turns out, the timescale of myo-granule formation and dissolution closely matched the timescale for muscle repair itself.

These were huge findings, because they pointed to two things: One: The body has a built in way to both assemble and, importantly, disassemble these myo-granules, which we thought was impossible before. And two: the close correlation between myo-granule presence and muscle repair pointed to myo-granules possibly having some sort of function in muscle repair.¹²

[PAUSE]

Charles: So, what was that function? Well, the researchers further analyzed the composition of these myo-granules, and they found a clue. Inside these dense clumps of protein, TDP-43 was tightly binding to messenger RNA.

Now, messenger RNA, or mRNA, are kind of like the instructions that tell your cells how to build proteins. The specific instructions found inside the myo-granules encode for proteins that build sarcomeres, which are the contractile units inside your muscle cells.¹²

Seeing this, the researchers proposed a theory: When a muscle is injured, it needs to repair itself fast. It doesn’t have time to pick and choose from complex genetic instructions.

So in response, it calls up TDP-43.

In the nucleus, TDP-43 proteins clump up into a big ball, packing all the necessary RNA instructions inside to make sort of a “repair kit” for the cell. This ball of protein and RNA is what we see as a myo-granule. The myo-granule scrambles out of the nucleus and into the cytoplasm, where it starts directing the cell’s manufacturing plants to make a bunch of proteins to repair all of the muscle damage.¹²

Once the cell is finished repairing, it’s able to somehow get rid of these myo-granules all on its own, and the cell returns to normal.

Essentially, the research team proposed that myo-granules aren’t just toxic waste sitting in our cells. Instead, they’re a tool that the cell uses for a very important function.¹²

[Sigh]

Charles: This changes how we view amyloids as a whole. I mean, we now have evidence of a type of amyloid being purposefully created by a cell and then using its disordered structure to accomplish a task for that cell. I mean, what’s stopping this from being true for other amyloids too? What if all of the protein tangles we’ve been seeing this whole time, you know the ones we’ve labeled as the enemy, actually have hidden functions we just haven’t uncovered yet.

This really changes everything…

[Insightful music plays]

Charles: So, where does that leave us?

Well, the story of TDP-43 forces a fundamental rethink in the field as a whole. For decades, we’ve been fighting neurodegenerative disease with a scorched-earth sort of strategy: we find amyloids and we destroy them because they’re bad. But this story reveals that this whole time, amyloids might have been framed by other cellular malfunctions.

Maybe in these diseases, there are other underlying or harder to detect issues with our cells’ machinery that can cause amyloids to build up, or not clear themselves away when they’re supposed to. Maybe there are certain cases where amyloids might be toxic, or they might be harmful, but we can’t be sure of that yet. One thing is clear, though, that at least some of them are created to help us.

And I’m not just talking about TDP-43. We’re now discovering other functional amyloids in biology—from large tangles of nucleic acids that help form our skin’s pigment to clumps of proteins involved in creating long-term memories.¹⁹

So now, the goal is no longer just to destroy amyloids. The goal is figuring out what the amyloid is trying to tell us about the cell.

If these structures are functional, then their accumulation is a sign that the cell’s control systems have broken down. The future of treatment isn’t about eliminating the amyloid itself, but it’s about repairing the underlying failure that caused the amyloids to appear.

Like, what if one day we could read the composition of an amyloid and tell which specific cellular mechanism has failed in that patient’s neurons? Could we then design therapies that don’t attack the amyloid, but restore the cell’s control of that mechanism?

The story of TDP teaches us that the difference between a tool and a weapon is context. The most promising path forward may be to listen to what these structures are telling us about the health of the cell, and to help the cell regain whatever function has been lost.

Charles: This new perspective comes with its own complexities and mysteries, but it’s the first perspective we’ve had that truly fits into our biology. We’re learning why we’ve evolved to keep these amyloids in our bodies over millions of years, why they show up so frequently across different cell types and systems and even species.

So, at the end of the day the future of treating these diseases lies not in declaring war on our body’s own proteins, but in better understanding what’s actually going wrong inside of a diseased cell. Once we find a definitive cause for the presence of all these different amyloids in all these different diseases, we can start to attack the problem at its source. And maybe one day, we’ll finally solve all of these problems.

[Outro theme plays]

Charles: Whew, that was a lot, right? Started out with a problem, went on a trip through drugs, nuns, muscles, and now we’re left with basically another problem. But at least we’re a little closer to the truth, I think. That’s how science works, right?

Anyways, this is Signals, I’m Charles Brambell and thank you so much for tuning into my show. This is the first episode and I’m still figuring things out but I’m gonna make it a biweekly show. If you have any interesting topics in biology that you want to hear about or have feedback, comments, literally whatever, feel free to leave a comment on YouTube or my website signalsbio.com. The website might not be up yet if you’re a really early listener, but it will be eventually. And on there, you’ll be able to find a transcript for this episode and also all of my sources if you want to do any further reading on your own.

I should be on Youtube, Soundcloud, and Spotify (but I’m still trying to figure out apple music right now). A huge thank you goes out to Blaizun Diamond, the always honest Damian Sonsino, Noura Sarsam, Zachary Cook, Timmy Turner, Luca, Drale, and everyone else who’s helped me along the way. Love you all, and I’ll be back in two weeks with another episode. See ya.