7

Upgrading the Biological Incinerators

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Just like our own households, cells generate garbage as an inevitable result of their normal functioning. Again like households, they are able to dispose of most of this waste—though they recycle a proportion of it that would put the most eco-friendly household to shame. But cells cannot recycle quite all the junk they create, and the portion that escapes destruction accumulates, to the cell’s eventual detriment. Several years ago I devised a new approach to this problem that exemplifies, perhaps better than any of my other contributions to this field, the value of the widely cross-disciplinary expertise that is so rare in biology today.

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Mary Shelley couldn’t ask for a more perfect scene, I thought, as I sank my trowel into the scruffy graveyard sod.

A quick scan of the horizon at Coldham’s Common would initially make you think it was a nondescript, even rather dull little field in the heart of England. But knowing its history transforms your view of the spot, opening the mind’s eye to a bleak, windswept stretch of near wilderness, dropped as if out of a Gothic horror novella into the midst of a plain bounded by football grounds and parking lots, bisected by a railway line. Though it is sometimes used for public events or cattle grazing, it spends much of the year lonely and abandoned, its sole claim to fame arising from its association with mass death.

In the late seventeenth century, the Great Plague swept its scythe across England. When its icy fingers crept into Cambridge, the plague claimed a third to a half of the residents—including sixteen of the forty professors at the University—and sent the young Isaac Newton fleeing for his life. In its wake, the survivors hastily plowed most of the plague’s victims anonymously under the unhallowed ground. Even before it became a mass grave, the area bore the taint of association with infection and death: its most enduring landmark is the remains of Cambridge’s twelfth-century Leper Hospital. As if to complete the cliché, on most days of the year Coldham’s Common is documentably several degrees colder than the cobbled streets that surround it.

The scene, then, was complete: I, the “mad scientist” (complete with long beard and pale, sunless skin), surrounded by Cambridge’s Enlightenment-era faux-Gothic castles and cathedrals, had hopped my way with an irrational furtiveness over multiple fences into the last resting place of the mortal remains of untold scores of lives, and was now digging into the soil of a mass grave, in hot pursuit of the secrets of Life and Death.

Victor Frankenstein, eat your heart out.

I must confess that the above account incorporates a small amount of poetic license: the person who performed the above task was not I but a graduate student in my University of Cambridge department, and actually she retrieved the soil sample from Midsummer Common, not the nearby Coldham’s Common. But that’s by-the-by. To understand what she was doing there, let’s take a detour out of the graveyard and into the junkyard.

The Waste of Your Life

Whether we toss things into the garbage bin without a thought, or painstakingly wash and sort our recyclables, we in the developed world generate an astounding amount of waste material every day. When we decide that we don’t need something anymore, or that it’s too damaged or rotten to be worth our efforts to salvage, we simply stuff it into a bag or bin and put it out for pickup, confident that the unsung heroes of the sanitation department will take it away and out of our concern. Thanks to an efficient waste-disposal infrastructure, a truly remarkable volume of waste material can pass through our homes, workplaces, and streets—yet these places remain clean, pleasant-smelling, and sanitary.

It wasn’t always this way, of course. For most of the history of civilization, the streets of our cities were literal cesspools, into which the citizens hurled their trash and human waste directly out of their windows without care for what—or even who!—was below them. Most of us truly cannot imagine what foul, malodorous, and dangerous places cities were until quite recently. The toll of living in such a toxic environment can be seen in the disparity of life expectancy for people living in different environments in seventeenth-century England. An Englishman would typically live to be thirty to forty years old if he lived in the countryside, but if he lived in London, he could expect just twenty-one to thirty-four years of life.

Anyone who’s lived through the kind of big-city garbage strike that nearly paralyzed London in 1976 has an idea of just how vital a functioning waste-collection system is for health and the carrying-on of the business of daily life. In shockingly short order, trash can literally be piled ten feet into the air, in precarious piles that fall apart in the wind or as new bags are added to the crude structures. And the mountains of garbage are not merely unsightly: Aside from the smell, the garbage attracts vermin, and with it, disease—particularly when the contents of the trash bags begin to spill onto the street because of attacks on the bags by animals, the elements, or the putrefaction and liquefaction of its contents. Sidewalks become increasingly impassable, and even street traffic may be impeded. People become less willing to leave the house or go into shops. A strike that lasted just nine days in 1968 came close to bringing New York City to its knees.

Well, something similar happens to your cells as they age—except that in a sense it’s worse. Rather than a temporary “interruption of service,” aging cells undergo a progressive degeneration of their waste management infrastructure that would make the worst examples of inner-city decay look like models of sanitation.

Two chapters ago, in discussing the process whereby mutant mitochondria “clonally expand” to replace all of their genetically healthy cousins in the cell, I introduced you to the lysosome—an organelle that I called the cellular “incinerator.” Actually, “recycling center” would be a more precise metaphor than incinerator, because a lysosome’s job is not to out-and-out destroy cellular wastes, but to break them down at the molecular level into more basic components that can be used as raw materials for the biosynthesis of new cellular membranes, enzymes, and other important components of the cellular machinery. The incinerator metaphor is meant to convey the extraordinary power of the lysosome’s molecular-level dismemberment of the materials that are thrown into it, as well as the chemical nature (burning is a chemical reaction, remember) of the lysosome’s methods of breaking down waste into its fundamental components.

While the cell actually has a variety of mechanisms for reprocessing damaged cellular constituents, its lysosomes deal with some of the nastiest of them, including the waste materials that are still left over after the other cell waste-disposal systems have had a go at them but failed. In addition, when those alternative waste disposal units themselves become worn-out or damaged, it falls upon the lysosomes to break them (and, often, their semi-digested contents) down. This chapter is about what goes wrong with the cell’s scrapyards of last resort and how we might avert that process.

Cleaning Up Life’s Messes

Your cells, like your household, are constantly producing and consuming goods and generating wastes of various kinds in the process. One sort of waste is akin to packaging, or disposable pens, or tacky old bric-a-brac, the possession of which has come to embarrass you. It may have served a purpose at one time, but today you have no further use for it and wish it gone. Many cellular constituents are like this: Enzymes and signalling molecules are “disposable,” produced for temporary or even one-time use in response to the immediate conditions in or around the cell, and they need to be degraded once they’ve served their purpose.

Another type of waste is more like something for which you would still have a use, except that it can no longer fulfill its purpose because it’s been broken. Just as you can turn a piece of your grandmother’s china into a jigsaw puzzle, or make your shirt unwearable at work by spilling dark red wine on it, so components of your cells—from the small (individual enzymes) to the very large (entire organelles, like a mitochondrion)—can become incapable of performing their vital cellular function after suffering molecular damage at the hands of free radicals and other products of the dirty underside of metabolism.

And a third type of waste is genuinely toxic material. Just as a useful substance (say, cottage cheese) can become a threat to your health through chemical changes (such as being taken over by mold), so normal cellular constituents sometimes become toxic to the cell through modification of their structure, or through being present in excess. As surely as, upon encountering the new ecosystem growing in your cottage cheese, you seal the container and drop it from shoulder level into the garbage, so, too, the cell needs to eliminate similar threats to its functioning.

Recycling’s Dirty Details

All of this waste (except, again, that which is destroyed by simpler machinery) is directed to the cell’s lysosomes. Functioning lysosomes ensure that it gets properly processed, removing toxic by-products of normal cellular machinery, returning usable molecular building blocks to the cell from the “slag” of the broken-down components, and making room for healthy, functioning cellular constituents.

So what exactly are these cellular incinerators? Lysosomes are membrane-bounded organelles packed full of a variety of enzymes, each of which evolved to target a “weak spot” in the chemical structure of a waste product that will accumulate in our cells and kill us if it isn’t broken down. A lysosomal enzyme first binds to a waste product that carries the kind of chemical structure that it evolved to destroy, and then twists its shape like a tiny biological crowbar, physically tearing apart the target material’s molecular joints. This is generally accomplished by a type of chemical reaction called hydrolysis, which is why such enzymes are called hydrolases (hydro being the Greek for water, as in “hydroelectric”).

The exact chemical details of this process aren’t terribly important for our purposes, but you should be sure to remember one key point. In order to break down a given waste product, the lysosome must have two things: the right enzyme for the job (one that targets a vulnerability in the structure of the specific waste product in question), and enough acidity in its interior for the relevant enzyme to function. This latter is required because different levels of acidity cause enzymes and other proteins to assume slightly different shapes, so that when the acidity in the lysosome is wrong, the enzyme becomes “bent out of shape” and thus no more able to do its job than is a flattened-out crowbar. Acidity is also required for the functioning of proteins that translocate some waste products into the lysosome in the first place, so that a mild neutralization of the lysosome’s acidity prevents junk from even being delivered to the recycling center to begin with.

Lysosomal enzymes, like other cellular proteins, are created out of the blueprints present in the nuclear DNA. They are then shipped into the lysosome, though by machinery very different from the mitochondrion’s TIM/TOM complex. The extra protons that create the lysosome’s acidity are actively pumped out of the main chamber of the cell and into the lysosome by an energy-(that is, ATP-) consuming pump located on its membrane (the vacuolar ATPase).

Incomplete Combustion

You won’t be surprised to learn that bad things happen if your body fails to produce a lysosomal hydrolase that is needed to break down a waste product being produced in some cell type—or if it produces a defective form of the protein that doesn’t do its job properly. In fact, this is precisely the description of a group of rare but well-established genetic disorders known as lysosomal storage diseases (LSDs).

There are about forty such diseases, but luckily only about one person in 7,500 is born with any of them. Victims of all of these diseases suffer from one or another type of failure of their lysosomal incinerators. Many of them completely lack the gene for a lysosomal enzyme, or bear a mutated copy of it, resulting in a misshapen and ineffective version of the hydrolase. In other cases, the problem is that one of the specialized transport proteins on the surface of the lysosomal membrane is missing or defective, so that the lysosome can’t bring the junk into itself to break it down.

No matter what their origin in a given patient, the result of such mutations is a deadly degenerative disease. Which organs a given mutation affects, and how severely, varies from one LSD to another, depending on exactly which missing or malfunctioning enzyme is at the root of the problem. This is because different cell types produce different wastes at different rates, and each particular waste exerts a distinct pathological impact on the cell if it isn’t degraded.

But in all cases, patients suffer pathology in major organs. In Gaucher disease, the spleen swells up and anemia develops. There are two inherited forms of Niemann-Pick disease. In the fast-acting version (Type A), the liver and spleen enlarge and the nerves degenerate starting at birth, killing its victims by age two or three. In the slower-acting variety (Type B), patients may develop fatty, yellow nodules on their eyelids, neck, or back, and an enlarged liver, spleen, and lymph nodes. And Hurler syndrome causes facial features to twist up and bone deformities to occur, along with enlargement of the spleen and liver, joint stiffness, clouding of the eye, early-onset dementia, and hearing loss.

The exact mechanistic links between the lack of effective waste disposal and particular pathologies have not all been worked out in detail, but the basic picture is clear. The undegraded waste material accumulates in the lysosome, causing it to swell up and take up too much room in the cell, impeding the traffic of other materials in the main cell body. Meanwhile, the acids and enzymes within the lysosomes are diluted, inhibiting their ability to both import and break down other wastes for which the cell does have the requisite enzymes, thereby setting up a vicious cycle.

There are also some cases in which it appears that toxic, undegraded waste accumulates in the main body of the cell. This can be either because it is not trafficked into the overburdened lysosome in the first place, or else because the failing organelle starts to leak or even bursts, spewing its toxic load—including the acids and enzymes that it carries, which are essential to lysosomal function but potentially deadly to the rest of the cell.

Lysosomal Limitations and the Deadly Dregs

In addition to the terrible, early-acting pathologies that ravage the victims of these genetic disorders, however, it’s also long been known that undegraded gunk builds up in the lysosomes of all of us as we age. Called lipofuscin (LIP-oh-few-sin¹) or popularly “age pigment,” this noxious, accumulating goo is a chemical hodge-podge of fatty and proteinaceous materials derived from membranes, reactive metals like iron and copper, and a variety of other organic molecules. It is easy to see with a microscope because it glows red when exposed to light of a particular wavelength.

Lipofuscin is actually not a single, specific compound, but a catch-all term for the mixture of stubborn waste products that refuse to be broken down after they’ve been sent to the lysosome for degradation—materials so chemically convoluted that the normal complement of lysosomal enzymes just doesn’t know how to deal with them. A combination of damage from free radicals and from glycation (the random sticking-together of different “branches” of a substance’s proteins by reaction with the sugars in your blood and cells) twists their structure back on itself like some demented child’s molecular origami, burying the vulnerable spots in their structure so that lysosomal hydrolases can’t get at them to break them down.² As a result, these materials don’t get properly degraded—and because lysosomes are in most cases unable to export them out of the cell, the material just accumulates, taking up more and more room in the lysosomes of long-lived cells like the heart and the brain.

First spotted in the nineteenth century, lipofuscin was largely ignored by biomedicine until it became a hot—and controversial—topic in biogerontology in the 1970s. At that time, it seemed just obvious to many researchers that lipofuscin must be bad for us: it slowly fills up our cells, (taking up as much as 10 percent of the total space in aged primates’ heart muscle cells, for example), and the course of its accumulation tracks the cell dysfunction seen in aging animals (including people). Indeed, the rate at which lipofuscin accumulates in a given species’ heart was found to be proportional to its rate of aging, so that adolescent, middle-aged, and old monkeys of two different species, with greatly different calendar ages but at similar stages in their life cycle, have roughly the same level of lipofuscin clogging up their cells. Many researchers outlined a mechanistic hypothesis of lipofuscin as a contributor to aging similar to what happens in the LSDs: lysosomal failure, waste accumulation, interference with cell trafficking, and the release of toxic enzymes and acidity from ruptured lysosomes.

But the point was a contentious one. Many scientists believed that lipofuscin was benign, in part precisely because it is so hard to degrade: With the reactive spots in their structure already balled up and stapled together by previous free radical and glycation damage, lipofuscin is chemically quite inert, so it doesn’t interact with essential biomolecules the way that free radicals or other toxic chemicals do. Also, speeding up the accumulation of lipofuscin in experimental animals by denying them adequate vitamin E did not shorten their lives, as one would expect of any manipulation that accelerated a real cause of aging.

But those reports were strongly disputed by other experts in the field, because it was not at all clear that the material whose accumulation was increased by vitamin E deficiency actually was lipofuscin. Much of what gets referred to by this name in the older scientific literature is actually other, related substances (often called ceroid) that share many of lipofuscin’s properties but are much easier for the cell to break down. It seemed likely that vitamin E deficiency was increasing the production of this relatively tractable material, while levels of “real” lipofuscin were unaffected.³ Moreover, while ceroid accumulation was associated with a variety of diseases (diseases in which normally degradable substances are not degraded—one could think of them as nongenetic LSDs), it was not clearly related to “normal” aging.

And so, the debate went ’round. As with many such cases in the early days of biogerontology, the data were ambiguous, the definitions were imprecise, and there was little hope of a clear resolution.

I had, myself, remained an agnostic on the subject up to and including the writing of the first draft of my doctoral thesis. But that began to change in the spring of 1998, when I met Ulf Brunk, chair of pathology at Sweden’s University of Linköping, at the Oxygen Radicals Gordon Conference in Ventura, California. After listening to his presentation of his recent results, I started taking lipofuscin more seriously as a potential nexus connecting the intricately orchestrated chaos of metabolism to the pathology of aging.

Brunk had done some first-rate work in assessing the role of lipofuscin in cultured heart cells—an important technical advance, especially because, in the body, heart cells never divide. When a cell divides, its load of cellular junk—including lipofuscin—is shared between the two daughter cells. Each now has half as much, on average, and this will continue with each new generation. If the junk is only being generated quite slowly, this dilution process will fully balance the rate of creation of new junk and an unmanageable level of junk will never accumulate. The quickly replicating skin cells that had been used in much previous work did just this—they tended to dilute out lipofuscin and other cellular junk, and so could not replicate the real effects of lysosomal buildup in critical nondividing cells like those of the heart and brain. This had long been recognised, but heart cells had been found to be notoriously hard to culture—in large part, it turns out, because of the high levels of oxygen in the atmosphere. Cultured cells are still too often grown under normal atmospheric air, despite the fact that our bodies ambiently contain only about one seventh of air’s concentration of oxygen.

By growing the longer-lived heart cells under more physiological levels of oxygen, Brunk was able to show how increased oxidative stress—higher levels of free radical damage, in other words—increased lipofuscin formation. He also confirmed previous suspicions about how lipofuscin accumulation could impair the ability of the cell to recycle its used-up components. And on top of that, he was also able to show that older heart cells accumulate damaged mitochondria—which they would not do if the lysosome were operating properly, since the disposal of defective cellular power plants is one of their chief responsibilities in the cellular economy.

With his collaborator Alex Terman, Brunk outlined a “garbage catastrophe” theory of aging,⁴ in which accumulating lipofuscin inside the lysosome dilutes the organelle’s acidity and supply of enzymes. In this model, lipofuscin also wastes a lot of the enzymes that the cell body produces, by sucking them up without making effective use of them, thereby diverting them away from the other, still-functional lysosomal contents against which they could be put to effective use.

As the cell’s lysosomes accumulate waste products that they aren’t equipped to handle, they become ever less able to break down materials within them. As a result, the junk in question spends more time either out in the main body of the cell, or even trapped inside the lysosome, before being “incinerated.” During that time, chemical alterations continue to occur in the structure of these wastes, mangling them further and further and making it more and more difficult for lysosomal hydrolases to reach the weak spots in their structure. As a result, even the standard cellular junk that lysosomes are, in theory, well equipped to degrade is no longer efficiently broken down, but instead accumulates—which then further dissipates the hydrolytic enzymes and acidity of the lysosome. In their culture experiments, Brunk and Terman showed that lipofuscin overload could even trigger cell death, as lysosomes become loaded with the stuff and rupture.

The data underlying this model were compelling, and I liked it at once, sneaking a short reference to it into my Cambridge biology thesis.⁵ But I wasn’t yet convinced that lysosomal failure was truly a significant contributor to aging, because if the theory were right you would expect to find evidence connecting lipofuscin to actual age-related disease, and no such evidence initially turned up when I went looking for it.

I quickly learned, however, that this seeming lack of data was more of a communication breakdown than an information vacuum. Researchers tend to get holed up in their narrowly specialized fields of study, and consequently they, too, rarely compare notes and observe the confluence of observations in different fields of science (or even subfields within those fields). I soon found that if I stopped specifically talking about “lipofuscin” and began asking researchers about the importance of lysosomal dysfunction in the diseases that they studied, I was suddenly inundated with evidence that the accumulation of junk that should be processed in the lysosome was at the heart of the matter—but that this fact was being obscured by the use of specialist jargon in referring to those wastes.

Making the Link to Pathology

Atherosclerosis

Just over a year after I was first exposed to Brunk’s suggestive data, I was attending the biennial Gordon Conference on Atherosclerosis, at which I found myself listening to a review on the complex processes that lead someone from having too much cholesterol in the blood, to having fatty plaques in the arteries (atherosclerosis), to having diagnosable coronary heart disease and eventually a heart attack. As I quickly learned, researchers had been placing lysosomal failure at the core of the molecular events that underlie the formation of atherosclerotic plaques for years before I began looking into the issue—and they did so without ever mentioning “lipofuscin.”

Most people visualise atherosclerotic arteries as being much like clogged pipes. Greasy gunk (whether it’s bacon fat or blood cholesterol) simply accumulates on the inside of the tube, coating its surface and clogging it up, and blocking the passage of fluids—be those fluids the dishwater in your sink or the blood in your arteries. In fact, however, we’ve known for some time that the process is much more complicated than this.⁶ Atherosclerosis begins with a microscopic problem in the blood vessel wall. Many things can cause or contribute to this, including friction from the passing torrent of blood flow, or the force of high blood pressure, or infection; most often, however, it’s just the accumulation of our old friend LDL, low-density lipoprotein, which has a tendency to get stuck there. The body responds to this problem just as it does to any other injury: by secreting factors that inflame the site in order to attract immune cells called macrophages. Macrophages then infiltrate the damaged tissue to help it heal by cleaning up the debris.

I didn’t tell you very much about LDL in Chapter 5; now’s the time for more detail. Despite its bad reputation, cholesterol is actually a necessary component of cell membranes. In fact, the so-called “bad” cholesterol (LDL) in the blood is actually a carrier particle, designed by your body to bring needed cholesterol to cells, and those cells in turn have specialized receptors designed to allow them to ingest it for their internal use.

In order to reach most cells, the cells that comprise the walls of our blood vessels must allow LDL to pass between them, and beyond into the surrounding tissue. But when cholesterol is chemically modified—by exposure to free radicals (oxidized LDL) or reactions with blood sugar (glycated LDL), for example—it becomes more prone to stick together and thus more immobile. Because free radicals and blood sugar are (respectively) inevitable by-products of, and necessary raw materials for, some of the most fundamental metabolic processes in the body, they are ubiquitous. Hence, LDL particles are constantly being subjected to their chemically disruptive influence. Furthermore, enzymes that are designed to call in immune cells when the vessel wall is injured also alter cholesterol in ways that make it more toxic.

That’s the main reason why having a high cholesterol level is bad for you. The more cholesterol there is in your blood, the more contact it has with these damaging agents, and the more toxic, modified cholesterol will be coursing through your body.

So, when macrophages are attracted toward an inflammatory signal, they find plenty of junk in need of removal. Initially, macrophages deal reasonably well with the gunk that they’re internalizing, and they can often successfully remove the detritus. But when an already compromised blood vessel continues to be assaulted by high blood cholesterol levels, inflammatory signals created by excess body fat, or nasties from cigarette smoke, the problem persists and macrophages hang around for longer.

As they take in more and more waste—particularly an excess of modified LDL—macrophages begin to fall behind in their work. An increasing percentage of the load of junk is not successfully processed, but instead accumulates within the macrophages’ lysosomes—or, just as bad, is puked out of the lysosomes without being properly detoxified, forming droplets of modified cholesterol in the cell body.

As this continues, macrophages eventually become the cellular counterparts to the obscenely bloated “Mr. Creosote” in the restaurant sketch in Monty Python’s The Meaning of Life. If you’ve seen this movie, you will definitely remember the scene. Mr. Creosote comes into a fine French restaurant already stuffed with food and badly nauseous, but is plied with “moules marinières, pâté de foie gras, Beluga caviar, eggs Benedictine” and sauces “rich with truffles, anchovies, Grand Marnier, bacon and cream” by the perversely codependent and outrageously “French” maître d’ (John Cleese).

Creosote becomes more and more ill as the meal progresses, but when he finally attempts to summon up the will to stop eating he is cajoled into having just one last “wafer-thin” after-dinner mint. When the spineless patron swallows the mint, a look of helpless horror fills his face; as the maître d’ runs for cover, Creosote literally explodes, his innards and lunch splattering graphically over staff and guests alike.

Imagine your blood vessels to be such a restaurant, welcoming a steady stream of customers just like Mr. Creosote in the form of macrophages that come in to dine on modified cholesterol products. Imagine that they simply refuse to leave when you’re trying to close up, but continue to stuff themselves until their “stomachs” (lysosomes) can’t take any more—and then keep going until it kills them, and your restaurant (blood vessels) becomes their final resting place.

You now know, in essence, the genesis of the “foam cells” that accumulate in your vessel walls, forming “fatty streaks” as they become numerous enough to be seen with a microscope, and eventually developing into full-blown, unstable atherosclerotic plaques—the scabbed-over messes that ultimately form at the injury site, crammed with a miasma of clotting blood, inflammatory signal molecules, and dead foam cells. Once this happens, your days are numbered. It’s only a matter of time until the pressures within and without the plaque cause it to rupture, spewing its contents into the bloodstream. This content is not a liquid but a horde of semisolid chunks, and these chunks are rapidly swept from their origin in the major arteries into progressively smaller vessels. They become stuck there, blocking off the flow of blood—sometimes into the heart (causing a heart attack), sometimes the brain (causing a stroke).

So we now understand that lysosomal dysfunction is the key step in the conversion of healthy macrophages into undead foam cells—and of healthy blood vessel tissue into an atherosclerotic time bomb. This fact is widely recognized, but unfortunately, nearly all researchers are pursuing old-school, ultimately preventive treatments for the problem. Existing anti-atherosclerotic drugs try to prevent macrophages from stuffing themselves so badly, either by reducing blood cholesterol levels or by reducing LDL’s exposure to metabolically active agents (blood sugar, inflammatory enzymes, and free radicals). Drugs currently in the pipeline seek to approach the same problem from its flip side, by increasing the transport of cholesterol out of the blood, cells, or organs before it gets a chance to do its damage.

Meanwhile, basic researchers working in areas other than drug development are spending a lot of time trying to puzzle out exactly what causes macrophages’ lysosomes to fail, with the idea that, if they understood the fine details of the process, they could design drugs that would interfere in the relevant steps in the metabolic chain. Unfortunately, the evidence is consistent with many interpretations, and the data are difficult to reconcile, which has more-or-less stalled progress in developing therapies based on this model.

For instance, some researchers focus on the fact that, in test tubes, oxidized cholesterol inhibits the necessary processing (“de-esterification”) of normal (unmodified) cholesterol in the lysosomes, slowing it down enough to create a deadly backlog. Others think that modified LDL, like lipofuscin, is itself undegradable, and dilutes out the factors needed for the lysosome to degrade other materials as it accumulates. There is also evidence that something in modified LDL (or some metabolic by-product of it) is harmful to lysosomal function—such as the evidence (again in test tubes) that the oxidized cholesterol variant 7-ketocholesterol (7-KC) interferes with the activity of the membrane-bound ATPase enzyme. When this enzyme is impaired, it can’t maintain enough acidity in the cell’s lysosomes to keep their hydrolases working properly, so there are those who think that this is where we need to look for a solution. And still others think that macrophages simply take in too much LDL, so that its sheer volume overwhelms their processing capacity; if so, slowing uptake might also slow down the development of the disease.

As yet, we don’t know which school of thought is correct—and it’s unlikely that we will resolve the question definitively any time soon, because the conditions under which the relevant studies are carried out are so unlike what happens in the body. While the scientific debates continue, vascular disease caused by atherosclerosis remains the number one killer in the developed world—and other problems that arise from the same failure to process cholesterol may be related to a wide range of other age-related diseases.

Fortunately, an intervention that came to me in a flash some years ago⁷—and that has since been worked out in greater therapeutic detail in collaboration with others⁸,⁹—offers a solution that sweeps away the need for this kind of detailed molecular map of the metabolic maze. This solution does not rely on such detailed understanding of what causes lysosomal failure in atherosclerosis. Instead, it provides a way for us to clean up the lysosome itself, rather than the metabolic processes that overload it—and in a manner that will work irrespective of what leads up to its initial failure.

But before we get into that, let’s look at another fearsome disease of aging that has lysosomal dysfunction at its heart: the decay of the brain.

Neurodegenerative Disease

Except in the case of stroke—which I’ve covered above, and which is more of a one-off, traumatic injury than a degenerative process in itself—the brains of people suffering from all the major neurodegenerative diseases show evidence of inadequate lysosomal function. In most cases, the most obvious pointer is the presence of clumps of a distinctive aggregated protein material inside the brain cell: Lewy bodies in Parkinson’s disease and the boldly named “Dementia with Lewy Bodies” (DLB), aggregated huntingtin protein in Huntington’s disease, and neurofibrillary tangles (NFT), formed of aggregations of the protein tau, in Niemann-Pick and Alzheimer’s diseases.¹⁰ Yet, because these aggregates are not located within the lysosome, and are not themselves lipofuscin, the role of lysosomal dysfunction in these diseases has been obscured—so again, people specifically looking for a connection with “lipofuscin” can miss these data, obscuring the relationship.

In several cases, however, there is more direct evidence of trouble at the toxic waste dump. Some of the most remarkable such evidence has recently been found in the brains of Alzheimer’s patients, in which the breakdown of proteins through another of the main components of the cell’s recycling system (the proteasome) is badly impaired. In some victims, this may be because mutations in the gene for a protein called ubiquilin cause it to inhibit the activity of ubiquitin, a protein that “tags” proteins for breakdown in the proteasome. Both neurofibrillary tangles in Alzheimer’s and Lewy bodies in Parkinson’s disease are loaded with ubiquitin, yet the proteasome system seems incapable of picking these aggregated materials up.

The connection with the lysosomal apparatus is this: proteasomes that are not doing their job put more pressure on the lysosomal system as the defective proteasomes (and the material they have failed to destroy) are sent to the lysosome, increasing lipofuscin formation.¹¹ At least some of the waste that the proteasome fails to pick up—along with damaged proteasome units themselves—is ultimately sent to the lysosomes: this phenomenon has been definitively observed in the case of aggregates normally degraded by the proteasome in Huntington’s disease, and is probably what’s responsible for the finding of a lot of ubiquitin inside the lysosomes of the neurons of Alzheimer’s patients.

But the most dramatic hallmarks of abnormal trash disposal in Alzheimer’s disease are the signs of malfunction in the lysosomal system itself. As a bit of background: One of the main ways in which cellular rubbish gets delivered to the cellular recycling center is through a process called “macroautophagy,” in which the waste in question is swallowed whole by a membrane structure called an autophagosome or autophagic vacuole (AV), which then hooks up with the lysosome and fuses with it. (If this term rings a bell, that’s probably because I briefly mentioned it in Chapter 5 as the way in which damaged mitochondria are delivered to the lysosome.) The result, in effect, is a bigger lysosome, with a single combined membrane that surrounds both the contents of the AV and the hydrolytic enzymes (and acidity) of the original lysosome to digest that contents.

Recent studies show that this aspect of lysosomal function is in a very bad way in the brains of Alzheimer’s victims.¹² It has been known for some time that the lysosomal system in the Alzheimer’s brain is, like the proteasome, apparently both hyperactivated and inactivated: it’s as if the neuron were an unthinking driver of a car with a worn-out engine, trying unsuccessfully to compensate for its misfiring cylinders by pushing down harder on the gas pedal. The new work suggests one major reason why they fail: Their brain cells—and especially the cells located in areas of the brain that are most badly affected by the disease—are full of multilayered AV-based structures that are a lot like Russian nesting dolls, with one AV contained within another, larger one, which in turn is sequestered inside another, still larger AV.

Some of these structures seem to form when AVs fail to fuse with lysosomes, and hang around in the cell long enough to begin to take some damage, ultimately becoming so badly degraded as to be recognized as junk—at which point they are swallowed up into another autophagic vacuole. Then, the cycle repeats itself, as the new AV itself fails to fuse. In other cases, it appears that the AVs have fused with a lysosome, but that the lysosome is so weak—or perhaps so immature—that it can’t degrade the AV contents.

It’s a picture that reminds me of nothing so much as the infamous Khian Sea, a ship hired by the city of Pennsylvania in 1986 to haul its incinerator ash to an artificial island in the Bahamas for disposal. Unfortunately, the Bahamian government had not given the operators of the Khian Sea permission to dump its waste there. And so began a fourteen-year world cruise of garbage, in which the ship traveled from port to port, attempting to dispose of its load in different countries all over the world—first back up the east coast of the United States, then back down south to the Caribbean and South America, and ultimately wandering as far afield as Indonesia and the Philippines.

Ultimately, the Khian Sea—renamed and reflagged—relieved itself of its toxic burden by illegally dumping it into the Atlantic and Indian Oceans. Sooner or later, peripatetic AVs can only be expected to discharge their hazardous contents, too.

Scientists all agree about the basic facts: the major neurodegenerative diseases are characterised by the presence of aggregated proteins and lysosomal dysfunction in the brain, and it’s clear to everyone involved that there is some kind of connection between the clear failure of the cell’s waste disposal systems to deal with the aggregates and the diseases in which these disruptions occur. The question is just what that connection is. Intuitively, it makes sense that the aggregated junk sitting around in our brain cells must be bad for them. Most scientists in the field share this intuition, and indeed it’s easy to show, in relatively crude test-tube experiments, that these substances work mischief in brain cells to which they are added, including the initiation of a vicious cycle in which the accumulation of aggregates disrupts normal neuronal function, leading to further lysosomal dysfunction and protein aggregation.

But others have a different take on these phenomena. Surprisingly, some scientists think that protein aggregates may in some sense be protective. The idea is that while the aggregates themselves may in the long term interfere with cell function by blocking cellular traffic with their sheer size, the soluble, highly reactive units that make up the aggregate are a much more immediate threat to the health of the cell. By handcuffing these units together into a single cellular chain gang, the cell can keep them from attacking other cellular apparatus in their environment, preventing a deadly short-term threat to cellular health.

And then there are those who view the aggregates as being more of an epiphenomenon: a sign that something is wrong with the cell, but not an actual contributor to pathology. In this model, undegraded protein deposits are more like gunsmoke than actual guns or the bullets they fire: in themselves they are more-or-less harmless, but their presence is an unmistakeable signal that you’re in a crime scene. Perhaps, for instance, some other contaminant is building up in the lysosome, preventing it from properly incinerating cellular garbage, so that the aggregates build up—but the aggregates themselves aren’t the source of the problem or a major contributor to cellular pathology. This is still a bad thing to have happening, of course, because cells rely on a functional lysosome—both to break down benign cellular constituents that are past their useful life in order to make use of their building blocks for future cellular construction projects, and to destroy genuinely toxic wastes. But the source of the problem is to be found elsewhere than the obvious piles of trash cluttering about the main body of the cell.

For example, Alzheimer’s patients may have more defective mitochondria in need of recycling than healthy people do, putting demands on the lysosome that it just can’t satisfy; once the lysosome fails, other components may form the observed aggregates, but it’s still the dysfunctional mitochondria that started the ball rolling downhill. But again, it’s pretty hard to escape the conclusion that the resulting protein clumps constitute cellular “speed bumps” that must eventually cause the cell some serious problems of their own.

Unfortunately, there is substantial evidence—both in neurodegenerative disease and in aging—to support each of these positions. “Unfortunately,” I say, because I feel it is paralysing researchers in their quest for cures. Researchers spent much of the 1990s in entrenched holy wars between the “BAPtists” (named for “Beta-Amyloid Protein”) and the “Tauists” (named for the tau-based neurofibrillary tangles or NFTs), each of which expended considerable effort in trying to prove their favored candidate to be the primary problem in Alzheimer’s disease. (“What’s beta-amyloid?” I hear you cry. You’ll learn plenty about that in Chapter 8.) Today, there is a similar feud simmering over the different interpretations of the role of protein aggregates generally in neurodegenerative disease. And in old-school thinking—in which the goal is to find drugs that will shut down the metabolic processes that lead to a disease outcome, or at least perturb that aspect of the pathway that causes the most harm—issues of this kind must be definitively resolved in detail before we can even begin to design treatments for humans, since interfering with metabolic pathways is a risky business that can only lead to harm if the process that you’re blocking turns out to be an innocent bystander.

Even more so than with atherosclerosis, then, traditional medical approaches to neurodegenerative disease are, with respect to protein aggregates, at a standstill because of inadequate understanding of the link between the junk in question and the disease itself.¹³ Again, however, I have a solution in mind that sweeps aside the need to resolve these ambiguities.

Macular Degeneration

While I don’t wish to tease you, I do want to go over the critical role of undegraded aggregates in a third important aspect of aging before finally revealing my proposed therapy for all diseases involving lysosomal failure—including aging itself. This third age-related problem is age-related macular degeneration (AMD).

There is some relief from suspense in this section, inasmuch as there is no controversy about the involvement of aggregates in AMD. This is a classic case of how biochemical cycles with which we absolutely cannot dispense lead to the destruction of the systems in which they are embedded. Vision, like all of life’s processes, is ultimately mediated by a carefully controlled, complex chemical chain reaction, and our conscious perceptions correspond in a one-to-one fashion with the particular electrochemical phenomena that this cascade triggers in our brains. In order to perceive an object, the energy from the light that reflects off it and into the lens of our eyes must be translated into the chemical signalling language that corresponds to our subjective “sight” of the object.

For our purposes, the important step in this translation process—important because fatal to the cells that suffer it, and hence to our eyesight—is the (nearly) perpetual cycle of a derivative of vitamin A between two forms.¹⁴ The rods and cones of your eyes contain the “storage” form of this compound (11-cis-retinal), which is chemically transformed into an “activated” derivative (all-trans-retinal) when it absorbs energy from incoming light. This activated form is used as a signal to turn on the electrochemical firing of the optic nerve, which carries the signal to your brain; then, normally, an enzyme converts it back into its “storage” form, readying it for the next burst of incoming light.

But any system that relies on chemically unstable components always runs the risk that their reactive chemistry will spill over the tight controls of the system they’re meant to serve. In this case, all-trans-retinal can react with some of the fatlike molecules that make up the cell membrane, leading through a complex series of steps to the formation of a stubborn end product called A2E. This compound is completely resistant to digestion within the lysosome, so it’s a major source of undegraded junk in the lysosomes of these cells. Over time, so much A2E is produced and absorbed into the lysosome without being degraded that it can take up as much as one fifth of the total cell volume in the cells that accumulate it. These unfortunate cells make up the retinal pigmented epithelium (RPE) of the eye—a part responsible for maintaining the function of the light-sensing areas of the retina.

But again, because of the specialist terminology in use (A2E, rather than “lipofuscin”), the role of lysosomal inadequacy has been—and you will pardon the unfortunate pun!—obscured.

Toxic Waste Problem—Toxic Waste Solution

By the morning that I was throwing some clothes into a duffel bag for the 1999 Society for Free Radical Research meeting in Dresden, I had come to see lysosomal inadequacy—and the resulting accumulation of cellular waste products—as perhaps the key step linking the mitochondrial mutation-driven rise in oxidative stress with age with the actual pathology of aging. Remember from Chapter 5 that, by then, I had a scheme for how mitochondrial mutations in a few cells could propagate toxins to mitochondrially healthy cells elsewhere. What I didn’t explain in Chapter 5, not least because when I developed the Reductive Hotspot Hypothesis I didn’t know it, was just how these “toxins” are toxic—what harm they might do to the cells that ingest them.

But now, a year later, this mystery was beginning to resolve. It was clear, once one got over one’s attachment to the term “lipofuscin,” that the failure to dispose of specific waste products was at the root of the most terrible diseases that accompany biological aging: atherosclerosis, age-related macular degeneration, and neurodegenerative diseases like Alzheimer’s. It was just that the kind of waste that was linked to a given disease was specific to the cell type and the particular diagnosis.

As it happened, Ulf Brunk was again presenting his data in Dresden. As I listened to his talk and contemplated his slides—the telltale red glow of lipofuscin choking cells, his computer-generated diagrams illustrating his and Terman’s “garbage catastrophe” theory—I saw that it was a waste of time to argue about whether lipofuscin contributes to “aging” in the narrow sense. Clearly, we needed a way to solve this problem if we were to protect our bodies from age-related pathology. But I also became convinced that it would not be enough to try to prevent the accumulation of this junk “upstream” by obviating mitochondrial mutations. We were also going to have to deal with the junk directly.

But how? With the recalcitrant materials in question being so multifarious, and with the metabolic pathways, chemical identities, and even specific role in pathology of these materials being still largely unknown, it seemed that no classic “magic bullet” approach—one small molecule to match one therapeutic target—would work. And simply putting the lysosome into overdrive wouldn’t really solve the problem: While, as later animal studies would show,¹⁵,¹⁶ simply souping up lysosomal activity or topping up their existing enzyme supply could slow down the progression of lysosomal storage diseases, such approaches could not ultimately stop those diseases. It is the very nature of the problem that the body simply does not have the enzymes to degrade the really ugly junk—and thus, that it will choke up your cells, steal your mind, blind you, and clog your arteries later, if not sooner.

Ulf’s talk ended, and with a hundred other scientists I got up and streamed into the outer hall for the coffee break. The red glow of lipofuscin on the slides had gotten me to thinking of the stuff as the toxic waste that it is, and of the aging cell as a tiny contaminated environmental site equipped with a woefully inadequate waste management system. So the job of restoring the cell to health was really a kind of environmental cleanup job, and what was needed was a biomedical superfund project to develop new remediation technologies capable of dealing with materials that had so far evaded the lysosome’s capacities.

Superfund!

It suddenly occurred to me that this was more than a metaphor. (If you’ve never heard of Superfund, be patient—I’ll explain shortly.) There were actual land sites all over the planet that should be very badly contaminated by lipofuscin, because their soil has been seeded with the stuff for generations. I speak, of course, of graveyards. Think about it: hundreds of bodies put into the ground—sometimes en masse, as happened throughout Europe during the horrors of the Plague, and more recently following acts of genocide in Rwanda and elsewhere. These soils should be chockablock with aggregates from their inhabitants’ decaying bodies.

Yet, to my knowledge, there was no accumulation of lipofuscin in cemeteries—and if there were, we certainly ought to be aware of it, because lipofuscin is fluorescent. Months later, when I was discussing the issue with fellow Cambridge scientist John Archer, he would put the disconnect succinctly: “Why don’t graveyards glow in the dark?”

Soil microorganisms struck me as the most likely explanation. Bacteria, fungi, and other microbes normally play a role in turning our remains into compost, of course, but it was not so immediately obvious that they would be able to digest something so resistant to enzymatic action as lipofuscin. And yet, I recalled, we’d known for decades that soil microbes display an astonishing diversity in their choice of food.

Scientists became interested in this phenomenon in the 1950s, when it was noted that the levels of many hard-to-degrade pollutants at contaminated sites were present at much lower levels than would have been expected. A big part of the explanation turned out to be the rapid evolution of quickly reproducing organisms like bacteria. Any highly energy-rich substance represents a potential feast—and thus, an ecological niche—for any organism possessing the enzymes needed to digest that material and liberate its stored energy. The presence of high levels of such a material therefore creates a powerful evolutionary “pull,” driving the evolution of the necessary enzymes in microorganisms that come into contact with it. And this is especially so if the substance is not easy to break down, because then the chances are good that most of the other organisms in the vicinity will not have enzymes capable of this degradation.

It was proposed in 1952 that these forces might well be so strong as to guarantee that, given enough time, evolution would find a way to create microbes with the capacity to digest anything we throw at them that is both carbon-based and rich enough in energy to be a worthwhile fuel source. This was given the immensely memorable name “the microbial infallibility hypothesis.” While it has turned out to be a bit of an overstatement—no one has yet discovered the microorganism that can eat Teflon, for instance—studies over the next few decades tended to confirm the general principle. U.S. Geological Survey scientists collected case studies showing that microorganisms were breaking down significant amounts of a variety of organic chemical pollutants in wastewater. Oil spills, chlorinated solvents, pesticides—you name it: soil bacteria learned how to digest almost anything that was thrown at them, leaving only harmless residues like carbon dioxide and water.

Scientists’ first attempts to harness this power failed, because they were trying to invent organisms to order, imitating what nature was already doing very well. But eventually, researchers realized that they just weren’t as smart (nor, more accurately, as fast) as the forces of nature. Out of these observations developed bioremediation: the exploitation of evolution’s ability to generate novel digestive capacities in microorganisms for the intentional cleanup of contaminated environments. “Superfund” was the name of a U.S. government initiative to stimulate and commercialize bioremediation research.

Sipping my coffee in Dresden, my mind brought this train of thought full circle, feeding back into my original musing on the lysosome as an inadequate toxic waste disposal system. The lysosome already deals with the cell’s waste products using enzymes to break them down into their constituents. But it is not equipped with the capacity to deal with every possible waste material. This is just what you’d expect from evolutionary theory. Remember, again, as we discussed in Chapter 3, that evolution only designs your body to last as long as your environmental niche will allow it to last. In the Paleolithic environment in which we evolved, that meant about three decades—far less time than it takes lipofuscin or atherosclerotic cholesterol aggregates to build up to life-threatening levels.

For this reason, evolution has never bothered to equip the lysosome with enzymes designed to deal with these wastes, because it has never had a good reason to do so. But, as we’ve seen, it seems very likely that evolutionary forces have pushed soil microorganisms to develop these capacities in order to exploit a new fuel source—an issue, for them, of day-to-day survival. Not only do evolutionary theory and the “microbial infallibility hypothesis” predict this, but it also seems to be confirmed by the absence of large accumulations of lipofuscin in mass grave sites: were it not so, all such locations would have an eerie glow about them, instead of such a phenomenon being confined to cheesy horror flicks.

Suddenly it came together. The imaginative spark of metaphor had fallen upon the very concrete fuel of data in the oxygen-rich environment of evolutionary theory, and a fire began to burn in my brain. These two observations implied that we could perform a sort of medical bioremediation, in which we would identify the soil bacteria that already clean up our undegraded junk after we have died, determine the enzymes that allow them to do it—and then deliver these enzymes into the lysosomes of people who were still alive to benefit from it. Figure 1 gives a graphical depiction of this cycle.

These enzymes would give new powers to our cellular recycling centers, allowing them to process materials that presently go undegraded within us—not just preventing, but reversing their pathological accumulation. Our brains would be cleared of neurofibrillary tangles; the dying macrophages in our arteries would gain new life, letting them clear out the oxidized LDL toxins and allowing the necrotic vessel tissue to finally heal; the blind would see. And aging cells all over our bodies, choking on their own filth, would become clean and new again.

Figure 1. Medical bioremediation, exploiting the microbial enzymes that turn dead people into decomposed people, may retard many of the processes that turn young people into old and eventually dead people in the first place.

Normally, when new ideas come to me, I give myself a few days to try to punch holes in them before bouncing them off anyone else. But this time I felt supremely confident. Taking my nose out of my coffee, I scanned the hall for Dr. Brunk. I spotted him across the room: chubby, graying, earnest but with a mien of compassion that made you think of him as an aging social crusader. In a few purposeful strides I was confronting him.

“Listen, Ulf,” I said quickly, “I’ve just had the most fabulous idea…”

A Quick-and-Dirty Test

I was a little disappointed by Brunk’s reaction, though I was not sure how much of what I was seeing was a reflection of his assessment of the feasibility of the entire scheme versus its inherent audacity or my jumbled, hot-off-the-fire delivery. Perhaps it was just Nordic caution. Whatever it was, it was clear that, while not dismissive of the proposal, Brunk was clearly not experiencing spontaneous combustion from the white heat of my brain-wave.

Still, I pressed him for his thoughts on possible ways to perform preliminary tests of the idea. The first thing, we agreed, would be to test the sturdiness of the very foundation of the castle that I had just constructed in the air: the idea that soil microorganisms are, indeed, routinely digesting lipofuscin in corpses. Fortunately, there was a reasonably straightforward way to execute such a test: collect some soil microorganisms from a site likely to be “enriched” in human remains, and then see if they could break down lipofuscin in a test tube.

It turned out that what you might think to be the easy part—getting the lipofuscin needed to test the abilities of graveyard bacteria—was actually almost impossible to pull off in the real world. There are only small amounts of lipofuscin in most of our cells, and the tissues in which there’s more (such as the heart) are not so readily available, so to get a useful quantity of the stuff would be a challenge. But Brunk said that he could whip me up a batch of an excellent substitute: the synthetic lipofuscin used by people working in his field, which is created by merely exposing mitochondria to enough ultraviolet radiation to induce cross-linking of their membrane proteins. The resulting recalcitrant gunk has the same fluorescence spectrum as the real thing, and seems to also have the same physical and chemical properties—which is as you’d expect, since most experts think lipofuscin largely is the remains of unsuccessfully degraded mitochondria, damaged by the effects of free radicals and left festering in the lysosome.

The next thing would be to gather microorganisms from soil that had been exposed to a large supply of lipofuscin, to look for the ones that, in my hypothesis, had been responsible for breaking the stuff down. My mind had already leapt ahead to the fact that John Archer—the man who would later make the “glowing graveyard” quip—was working on bioremediation at Cambridge. As such, he was well-versed in the techniques used by scientists in the industry to isolate and culture bacterial strains capable of digesting classical toxic waste materials, and to identify and clone the genes involved in producing the enzymes responsible for that capacity. If I could enlist his help, we could do the same thing for lipofuscin-digesting hydrolases.

Tomb Raider

Fortunately, John was immediately fascinated by the whole idea, and agreed to give it a go. So it was that his graduate student would find herself, like a good mad scientist, at Midsummer Common in the twilight of a late summer day, digging into the soil of an ancient mass grave with a trowel, seeking not bodies but tiny, mysterious creatures imbued with the power to turn the most stubborn, aggregated junk in our bodies into compost.

The sense of being immersed in a Gothic horror novella lasted only a moment. Having scooped up the soil and brought it back to the lab, John and his student isolated the microbes and put them in petri dishes with the synthetic lipofuscin as their only potential food supply. Then, we waited to see if the force of natural selection would reveal the existence of strains that were capable of surviving on a diet of pure lipofuscin.

Almost immediately, the microbes that we had isolated began to give off the characteristic red glow of lipofuscin under the fluorescing light of the specialized microscopes. This was not yet a success, because all it meant was that the microbes were engulfing the material; they weren’t necessarily digesting it. But it was not long before clear differences began to emerge among different strains. Most of the colonies of microbes were in a state of growth arrest, failing to thrive for lack of nourishment. But a few of them were clearly enjoying a ghoulish feast: their numbers were expanding rapidly as their hydrolytic enzymes slowly broke the stubborn goo down into usable components, tearing apart its complex organic chemical bonds to release the stored energy. Within short order, we had a sample of microorganisms equipped with enzymes that could digest lipofuscin in the same way that the enzymes in your stomach digest a steak.

The hypothesis had been confirmed. The next challenge would be to move those enzymes into our own lysosomes. No one has done this yet, and indeed there is a sense in which the task sits just where it was when I finished my work with John Archer. Fortunately, however, we do not have to create an entirely new field of medicine in order to get going with this idea (which I will from here on call “LysoSENS”). That’s because the fundamental biotechnology required to pull it off is already in clinical use. Pioneering physicians have been introducing “foreign” lysosomal enzymes into patients for several years—not in aging, but in the lysosomal storage diseases.

Cleaning Out the Drain

Lysosomal storage diseases, the syndromes that we now know to be the result of mutations in genes that code for our normal complement of lysosomal enzymes, had been known for decades before researchers figured out what was causing them. Once their origins became clear, however, a way to treat most LSDs became apparent: enzyme replacement therapy (ERT—don’t confuse the abbreviation with estrogen replacement therapy). In individuals lacking an enzyme for some common metabolic waste, undegraded cellular waste products build up within the lysosome (and also outside it in the main body of the cell), and cellular dysfunction inevitably results. Therefore, it was reasoned, if the right enzyme could be delivered to the lysosome, the cellular recycling center would return to normal function, the piled-up garbage would be broken down, cells would return to health, and victims would be able to lead normal lives.

After a few decades of work, victims of three of the most common LSDs are now being successfully treated with such therapies. There are, for instance, about four thousand people now living normal lives despite having Gaucher’s disease, thanks to regular injections of the lysosomal enzyme that their cells are unable to produce for themselves. The drug development process has been reasonably clear, although technically challenging. In one disease after another, scientists have identified the enzyme whose absence causes the disorder; modified it in various ways to allow it to be injected, taken up by cells, and delivered to the patient’s lysosome, where they function exactly like the same enzyme does in the rest of us when it is produced by our own cells; and watched as symptoms have disappeared, lives have been extended, and victims have been enabled to live the life that the rest of us take for granted.

Of course, the same fundamental problem faces all of us in the case of diseases of long-term lysosomal failure: we will all ultimately suffer from age-related “lysosomal storage diseases” (such as age-related neurodegenerative disease, macular degeneration, and atherosclerosis), even though only a tiny proportion of the population is stricken with the currently recognized congenital ones (Gaucher’s disease and the like). While the exact origins of the two kinds of LSDs are different (rare genetic mutations in genes for lysosomal hydrolases that are otherwise part of the species’ standard evolutionary legacy in the congenital LSDs, versus never having evolved the enzymes needed to break down neurofibrillary tangles, A2E, etc., in the age-related diseases), the molecular natures of both congenital and age-related LSDs are essentially the same—and as anti-aging bioengineers, that is quite sufficient to let us do our job, which is to clean out the accumulating molecular damage. To arrive at that destination, we will need to address a series of specific challenges. Fortunately, in all cases we have options available with which we already have experience, or for which the solutions are clearly in sight and under development by researchers in other fields of biomedicine.

First Challenge: Identifying Suitable Enzymes

Our “grave robber” raid on Midsummer Common proved that the enzymes exist to degrade the highly cross-linked remains of mitochondria—believed to be the single largest contributor to lipofuscin. However, we still don’t know exactly what enzyme or series of enzymes is doing the job. Moreover, enzymes that degrade this synthetic lipofuscin will not be enough: we also need to identify other enzymes that will deal with wastes clogging up lysosomes in a variety of tissues and associated with various disease states.

This doesn’t necessarily mean enzymes that will degrade any known aggregate, such as neurofibrillary tangles. As we discussed above, the messes that we see are not necessarily the ones causing the problems: they may be the gunsmoke rather than the gun itself. For instance, it’s possible that some other junk is actually responsible for backing up the system, and thus that the aggregates that pile up like so much trash in the street are simply what results when the lysosome can’t keep up with its normal load. In fact, the problem might not even be the presence of undegradable materials: in several diseases, some researchers have presented evidence to suggest that the problem is a substance (for instance, A2E in macular degeneration) that directly inhibits the activity of the pump responsible for keeping lysosomes acidic enough for their enzymes to work.

Fortunately, we again don’t need to trouble ourselves with this. Once again, our job is not to tease apart the minutiae of metabolism, but to clean up age-related damage. To do that, we can follow the example of the bioremediation experts: throw enzymes at the problem until the problem is solved (normal lysosomal function is restored), and then identify the enzyme that did it. That’s a simple task in principle—but when the bioremediation field first got going thirty years ago, it was a long slog to actually narrow down which of hundreds of enzymes in a strain of microorganisms were responsible for breaking down the wastes of interest.

One of my reasons for optimism, therefore, is the fact that so much progress was made in those days—and today, we have much more sophisticated molecular tools available to do the job. One is a method called molecular fingerprinting, but that term is a little bit misleading. It suggests a process of finding a clear, unique identifier of an individual—like a fingerprint—and then finding the individual that bears that same identifier. Instead, molecular fingerprinting is based on the fact that the members of a closely knit family of organisms tend to carry genes with broadly similar sequences, and that (similarly) genes for a range of enzymes with broadly similar functions within such a community also tend to have a similar stretches of code.

This allows us to winnow our way down to the genes (and, therefore, enzymes) of interest from either of two angles. One option is to focus on a class of enzymes for whose encoding genes we are searching (in this case, hydrolase enzymes), and then to look for genes that match the overall pattern and are expressed in large amounts when the parent organism is feasting on the contents of the dysfunctional lysosomes. The other option is to identify, within a community of organisms, which specific ones are thriving best when only given those contents as nourishment—and which therefore carry the genes encoding those enzymes most effectively tearing their contents down.

Another powerful tool at our disposal is DNA microarrays, or gene chips. These are tools that identify, in real time, which genes in an organism are being actively expressed at a given moment. So, if we can isolate strains that are doing well on a diet of lysosomal detritus, we can sequence their genetic libraries, and then test which of those genes are being used intensively when they are feasting on the stuff.

We can also use techniques that allow us to “knock out” (simply remove) specific genes in such strains, and then retest them. When we knock out a given gene in a strain of microbe and see that the mutants starve on a diet that was previously their version of a gourmand’s wet dream, we can infer that the gene in question encodes a protein that is critical to the sequence of processes involved in digesting such materials. We can then identify these genes, and see whether the enzymes they encode are the crucial ones that will fill in the weak spot in our human hydrolytic arsenal.

Second Challenge: Getting Them to the Cells

Once we have enzymes in hand that will do the job, we’ll have to find ways of getting them into the cells that need them. Not every cell type will be confronted with the same kinds of waste: as we’ve seen above, particular disease states are characterized by specific aggregated waste products, and (as is especially likely in the case of A2E in macular degeneration) this is the result of the particular metabolic pathways that produces them. How much we have to do to address this challenge will depend on exactly how we’re going to get them into the body at all—for which there are again multiple options.

Right now, for instance, doctors treat LSD patients by intravenously injecting modified forms of their missing lysosomal enzyme. Of course, the enzyme does the patient no good when it’s just floating around in the bloodstream, and it might even do some harm if it were active (since it might start attacking functional proteins), so the enzymes are tweaked in ways to ensure that they go where they’re needed. First, they are targeted to the right cells. In Gaucher’s disease, for instance, macrophages are especially vulnerable to the lack of the enzyme that causes the disease. Therefore, the enzyme is hitched to targeting molecules that are already recognised by macrophages as passports to entry. The same trick might, therefore, be used to target enzymes needed to clear away the substances that cause macrophage lysosomes to fail in atherosclerosis.

This method has the advantage of being relatively simple to implement in the short term, and indeed of already being in use for a recognized disease (so that we have a large body of practical, clinical experience with the basic technique on which to draw). It does, however, face a variety of limitations. Most notably, there’s a big difficulty in using it to move enzymes past the protective blood-brain barrier, which is a highly effective shield designed to guard your brain against exposure to the many potentially toxic substances floating around in your blood. Obviously, injecting enzymes that cannot reach the brain will seriously limit their benefits—and represents an almost complete barrier against their use for age-related neurodegenerative disease. Even today, some Gaucher’s patients develop neurological complications as a result of their enzyme deficiency, and injected hydrolases are of little help to such patients.

Fortunately, scientists are making progress in coming up with ways to move proteins across the blood-brain barrier—and in the future, we can expect to have much more powerful delivery systems. In the relatively short term, we should be able to develop a form of cell therapy, involving seeding the patient with cells that produce the needed enzyme and secrete it into the bloodstream or into the fluid bathing surrounding cells.¹⁷ This would therefore act like a biological version of the nicotine patch, providing a continuous dose of the enzyme. This might be extremely useful: right now, LSD victims rely on regular injections of heroic amounts of their needed enzyme, and it’s possible that the sheer quantity of (several) enzymes required to combat all types of lysosomal failure due to aging or age-associated disease might make injection impractical. One reason why so much enzyme is needed is that some of these enzymes are proteases—that’s to say, they break down proteins—but enzymes are proteins, so proteases in the lysosome actually destroy themselves and each other.

And, of course, the ideal would be to modify our own cells using somatic gene therapy, introducing DNA to instruct the relevant cells to produce the very enzymes that they need to stay healthy. This, and the cell therapy option too, are still a long way away from the anti-aging clinic—but again, fortunately, the major hurdles will be tackled first for a variety of better-recognized diseases, from sickle cell anemia to the severe combined immunodeficiency disease that creates “bubble babies.” Thus, we can expect to ride on their coattails to a certain extent. Indeed, once somatic gene therapy is available for use in treating relatively common genetic disorders, it will doubtless be seized upon by LSD researchers as a way to replace genes for the lysosomal hydrolases missing in their patients. Again, the specific use of gene therapy to provide better solutions for LSD victims will be a useful source of information and collaboration to develop a gene therapy version of the LysoSENS project.

Third Challenge: Getting Them to the Lysosome

This is similar to the second challenge, above: lysosomal enzymes do us no good—and might conceivably even cause us some problems—if they wind up (or, in the case of gene therapy, are synthesized) inside the cells where they’re needed but are not then localized in the lysosome where the junk accumulates and where the acidity is available to let them do their work. Again, one potential solution is already in use in the LSDs: the use of molecules of the sugar mannose 6-phosphate, which is recognized and taken up—along with its cargo—by the lysosome.

But again, we are also in the process of learning to hide a few other cards in our sleeves. We might be able to use a backdoor solution, by turning a targeting system that is currently used to ensure wastes get delivered to the lysosome into a method of sending enzymes into the heart of the same system. (This system is called chaperone-mediated autophagy.) Lysosomes would take the enzyme up just as if it were any of numerous classes of cellular detritus, but would instead incorporate a hydrolase capable of preserving and restoring its normal functioning.

We might also be able to take advantage of targeting systems already in use in the organism from which we originally isolated the enzymes in question. Bioremediation typically uses bacteria as the microorganism of choice because they digest their food quickly. Fungi, by contrast, are usually viewed as too slow-acting and slow-growing to provide viable solutions for oil slicks or contaminated chemical spill sites. But in a slowly accumulating, low-volume toxic waste problem like age-related lysosomal failure, these issues would be less of a problem. The advantage of using fungi is that they—like us, and unlike bacteria—have a lysosome-like structure of their own, called the vacuole, which shares many of the key characteristics of the human equivalent (including, for instance, the need for an acidic internal milieu to work properly). Enzymes taken from such sources, then, might come already equipped with a range of features that would be useful for the LysoSENS project in humans.

Fourth Challenge: Potential Side Effects

Even once we have ways to deliver useful enzymes to the lysosomes of affected cells, we will still face the key challenge of preventing the intervention itself from causing us harm. One potential issue is that the enzymes in question might, as suggested earlier, also be active elsewhere than in the lysosome. One reason to expect that this won’t pose a major challenge is the fact that, as already mentioned a few times, lysosomal enzymes typically require a very acidic environment to function properly, so they will probably be nearly inactive in the main body of the cell.

We might also, however, further modify the enzyme so that it only becomes active after it has been taken up by the lysosome. One possible such modification would be to attach an extended sequence of amino acids that would prevent the enzyme from being active, but that would be cleaved off by enzymes present and active in the lysosome, liberating the active form for duty at its destination. This concept sounds really tricky, but it is already used by the cell for the safe delivery of some members of the standard human lysosomal enzyme complement, so the technique should be adaptable without overmuch heroics.

Another potential worry is that the enzyme might cause an immune reaction, just as any “foreign” protein might. But experience with the LSDs suggests that this will not be as big a problem as one might at first expect. Remember that, for a person who was born unable to produce the hydrolytic enzymes that the rest of us take for granted, these proteins are every bit as “foreign” as the microbial hydrolases will be to all of us. Normally, we learn to be tolerant of the proteins of our own bodies because our immune system is exposed to them early on in our prenatal and childhood development, allowing it to recognize them as “self.” Having never been exposed to such proteins in early life (because without the gene, the protein can’t be constructed), LSD victims lack immune tolerance to them. And in such patients, immune reactions do occur. But, reassuringly, they are always mild, and they taper off with time. This seems to be because enzyme replacement therapy delivers enzymes to the lysosome in a way that does not allow the cell to hack them up and to display them on its cell surface, alerting a suspicious immune system to their presence.

Moreover, even if the experience with the newly introduced enzymes is not the same (for instance, if we find reasons to use gene therapy and chaperone-mediated autophagy rather than ERT), we aren’t necessarily stuck. Dampening down an excessive immune response is a necessary part of many medical procedures, from organ transplants to over-the-counter allergy medications, and we are getting better at it all the time. We might also eventually be able to produce the protein within the bone marrow, as has already been done with some lysosomal enzymes; this might also help to induce tolerance, because of the role of bone marrow cells in immunity.

Inside, Outside

As you can see, there are quite a few hurdles to be overcome before we will be able to use novel hydrolytic enzymes to clear out the junk in our cells, preventing or reversing many of the most debilitating health problems of old age. But, as I’ve shown, perfectly plausible solutions to all of these problems seem to exist that are either already in use in treating the recognized (congenital) LSDs, or else have clear routes to implementation that are the subject of intense study by researchers the world over. Identify the enzymes we need, and a first-generation therapy might look much like ERT for lysosomal storage diseases today: expensive, inconvenient, and limited in its scope, but lifesaving. And as we go on, we will progressively improve the therapy, making it more comprehensive and advancing its safety and efficiency in lockstep with the advance of gene therapy and other enabling technologies that will also be exploitable in LSD treatment.

As in previous cases, the pursuit of this solution will depend on an interdisciplinary synthesis of research performed in areas that have, ostensibly, little to do with aging, and original work done by scientists dedicated to the goal of adapting existing technologies to the novel problems associated with the aging process. What is clearly needed is to get private and public capital devoted to the latter half of the equation, which suffers from a serious lack of investment of dollars and brainpower, and without which the greatest killer of all in the modern world will continue to cripple, torture, and kill our fellow human beings in enormous new cohorts every day.

Let me now turn from the junk within our cells to some of the aggregated junk coating our cells, exploring how it is harmful, what can be done about it, and how its threats to your health—and its therapeutic solutions—are intimately tied up with the lysosomal failure problem that we’ve been exploring here.