Recycling Cellular Waste


On April 26, 2003, engineer, adventurer and Aspen local Aaron Ralston was making his way down remote Blue John Canyon just south of Canyonlands National Park. Canyoneering is a strange activity, requiring some hiking, some climbing and maybe some swimming. Blue John was no exception.

recyling1At a place where the floor fell away, Ralston found himself “chimneying” downward, using his hands and feet to press against the tight, opposing walls the way a child might climb the inside of a door frame. A boulder blocked his descent. And as Ralston scrambled down and around the boulder, it moved, crushing his right arm and pinning it against the canyon wall. You know the rest of the story: Five days later, the delirious and severely dehydrated Ralston used the 2-inch blade on his multi-tool to cut off his arm so he could live.

Every cell in your body has a similar ability. In times of stress, your cells sacrifice parts of themselves to save the whole. The process is called autophagy (literally, in Greek, “to eat oneself”) and here’s how it works: In your cells are many tiny things that float around doing stuff (to use the scientific terminology). One of these things is called a lysosome. Think of lysosomes as little sacks of acid into which your cells throw proteins, pathogens, and even other cellular things that are either malfunctioning or extra. Whatever the material, like ripping apart a Lego kit, lysosomes break it down and recycle it into energy or building blocks for other, more important things.

But lysosomes can’t just float around the cell looking for things to recycle. Instead, they depend on other things called authophagosomes that act as dump trucks, bringing recyclable material to the lysosome. These autophagosomes are constantly assembling themselves and unlike most “things,” autophagosomes have two cell walls—an inner and an outer—so they can encapsulate dangerous recyclable material inside their inner wall. The autophagosome encases material and brings it to the lysosome; then the two organelles fuse together and the material passes from dump truck to recycling facility.

Autophagy is a wonderful thing. It helped you survive in that testy period just after birth when you lost the umbilical connection to your mother; it now helps you survive between meals; and it engulfs and degrades junk you would rather not float around your cells, including but not limited to damaged or mutated proteins that could other¬wise cause cancer. So the headline is this: Autophagy helps your cells survive stress and protects you against cancer.

But, unfortunately, the same protection that autophagy offers to your healthy cells, it also offers to any cancer cells that grow despite your body’s best attempts at suppressing them.

There’s a paradox: The body uses autophagy to keep itself safe from cancer and cancer cells use autophagy to keep themselves safe from all the doctors and researchers at the University of Colorado Cancer Center who would very much like to make them go away. So we’re left with a dilemma. To combat cancer, should we boost or lower autophagy?


recycling2“A common lab technique is to treat cells with what’s called the IC50 of a drug—the drug concentration at which half of the cells should die and half should survive,” says Andrew Thorburn, PhD, deputy director at CU Cancer Center, and one of the world’s leading experts on this paradox of autophagy.

“Now, cancer scientists have traditionally thought of this stochastically—that is, at this concentration, it’s chance that 50 percent of cells live while 50 percent of cells die. What our work is showing is that this cell death and survival might not be chance at all. Which cells live and which cells die when faced with an anti-cancer drug may be determined in part, or even in large part, by autophagy,” Thorburn says.

But, again, it’s not as simple as squelching autophagy to nix cancer cells’ protection.

Take this recent finding from CU postdoc Jacob Gump, working in the Thorburn Lab: Imagine you have dishes of cells, some with high autophagy and some with low autophagy, and then you hit these cells with two drugs known to activate the machinery that leads to cell death. Gump found that with one drug (abbreviated TRAIL), cancer cells were protected by autophagy, but with the other drug (called Fas ligand), autoph¬agy sensitized cells to the drug.

But what if we were able to manipulate autophagy and patients on one drug would benefit while patients on the other drug would not?

“If this finding applies in human contexts, decreasing autophagy could make a cancer cell you’re trying to kill more or less resistant to whatever you’re using to try to kill it,” Thorburn says.

So which cells are which? What cancers are hurt, helped or indifferent to autophagy?

Working in Thorburn’s lab, Paola Maycotte, PhD, postdoctoral researcher, has one important answer.


“Sometimes with cells, the answer comes from trying new techniques on many cell lines, noticing what works, and then working to discover why the technique worked,” Maycotte says. In this case, Maycotte and colleagues gathered a panel of breast cancer cell lines, turned off autophagy in these cells, and watched closely.

“One wonderful thing about working in the system of an academic medical and research center is that we have access to these important cells for our experiments,” Maycotte says, crediting CU Cancer Center’s Tissue Culture Shared Resource for providing the cell panel.

After knocking down autophagy in these many kinds of breast cancer cells, Maycotte found a striking result: Nixing autophagy made chemotherapy drugs more effective in all cell lines tested, but even more striking was the result specifically in triple-negative breast cancers—the most dangerous form of the disease that is still without a targeted treatment.

“Most of our studies imagine making existing drugs more effective by raising or lowering autophagy, but in the case of triple-negative breast cancer cells, many were so addicted to autophagy that when we limited it, these cells died without even the addi¬tion of another drug,” Maycotte says.

Of all these breast cancers, triple-negative tumors were by far the most dependent on autophagy. The reason why depends on something called STAT3, which in breast and many other cancers makes tumors harder to kill and makes cells more likely to grow and spread. In other words, having too much STAT3 makes most tumors aggres¬sive. However, in triple-negative breast cancer, STAT3 may also be the cancer’s Achilles heel. Not only does the breast cancer use STAT3 to drive its aggressive growth, it also depends heavily on the STAT3-type growth for its survival. If you take away a cell’s ability to use STAT3 it withers and dies.

Drugs that inhibit autophagy do just that: They block the ability of STAT3-addicted, triple-negative breast cancer cells to use the survival and growth signals they need in order to stay alive.


Meanwhile, at the University of Colorado Boulder, about 30 miles northwest of Thorburn’s lab, Joaquin Espinosa, PhD, a molecular biologist, has been exploring autophagy from another angle.

“Andrew [Thorburn] was up here on campus giving a talk about his findings and I realized that what he was saying could explain some of the things we had been seeing in our lab,” Espinosa says.

Espinosa, like Thorburn, has a specific, world-renowned expertise. Espinosa’s expertise is with a gene called p53, which is also known as the tumor-suppressor gene. When it notices DNA damage, p53 calls in repair machinery. And (like autophagy), when DNA damage is beyond repair, p53 puts machinery in motion that kills the cell before it can do harm.

Now the next part gets a little tricky, so stick with it.

The p53 protein kills cells by bursting little creatures called mitochondria that live in your cells. They are literally “creatures” because mitochondria aren’t built from your DNA and instead have their own. In fact, because you inherit mitochondrial DNA from your mother, science can see the existence of what it calls (in shorthand and with no intentional biblical reference) a “mitochondrial Eve.” We are all the descendants of one early human female that lived about 140,000
years ago.

For the purpose of this article, that’s just cool trivia. More relevant is the fact that in addition to being the body’s energy factories, mitochondria also hold poisonous, cell-death chemicals. Woe be unto the cell that pops its mitochondria.
But just as autophagy keeps us cancer free by recycling dangerous proteins, the p53 gene keeps us cancer free by exploding mitochondria, thus killing cells with damaged DNA.

“And we realized that autophagy was encapsulating and safely degrading these distressed mitochondria before they could release their cell-death chemicals,” Espinosa says. In other words, autophagy was protecting cancer cells from the release of mito¬chondrial poisons that should have resulted in the death of the cancerous cell.

It was as if by eating themselves, these zombie cancer cells could be brought back from the dead. Literally, in a video that accompanies the group’s paper describing this finding (Cell Reports, March 2014), you can see mitochondria release their death-signaling poisons, at which point the cells are technically “dead.” But then you can see rescue by autophagy and these cells go on to recover and divide. They are back from the beyond.

“You take down autophagy and cell death goes up,” Espinosa says.

Importantly, the cells that are killed in this way are only the cells that p53 has recognized as holding damaged DNA. Healthy tissue is unharmed while cancer cells are killed.


All this deep-science talk of p53, STAT3 and IC50 is enough to make your brain pop right along with those poison-containing mitochondria. Add the strange soup of autophagy, in which it’s sometimes helpful and sometimes hurtful in cancer care, and it can quickly seem like we’re years or decades away from its use. Except if you type in “chloroquine AND cancer” at the website, you’ll quickly see otherwise. Inhibiting autophagy is being tried right now in cancers ranging from lung to pancre¬atic and breast to brain.

Surprisingly, it’s being done with a malaria drug.

The drug chloroquine was developed in 1934, but only after World War II was it put into use for the prevention of malaria. Chloroquine does a couple of things: In malaria it keeps the parasite from “digesting” a toxic molecule until the malaria parasite eventually drowns in its own metabolic waste. In autophagy, chloroquine keeps the autophagosome from being able to fuse with the lysosome so it can’t deliver recyclable material.

Most of the trials of chloroquine are in their early stages. For example, a Phase I trial of chloroquine with erlotinib in lung cancer found the drug combination was “well tolerated.” For results, you’ll have to wait. A trial at the National Institute of Neurology and Neurosurgery in Mexico City offered promising “midterm survival” results. That’s about it in terms of human results right now.

Yet, it’s the kind of interest that starts as a groundswell.

You can see the study of autophagy gaining traction at the base of CU Cancer Center’s research pyramid—the labs of molecular biologists, pharmacologists and geneticists. You can see the excitement building toward the level of translational researchers who turn deep science into possible clinical techniques. And the possibility of manipulating autophagy to control cancer is just now starting to reach a human population here at CU Cancer Center and other cutting-edge research institutions. Might this odd, complicated and largely overlooked mechanism, as Thorburn suggests, create the difference between which cancer cells live and which die in the presence of chemotherapy?

“Many people think we know the effects of autophagy, but I think we’re just touching the tip of the iceberg of its relevance to patients,” says Maycotte.



About the author: Garth Sundem

In addition to writing for the University of Colorado Cancer Center, Garth is the author of the books The Geeks' Guide to World Domination, Brain Candy, and Geek Logik. Contact him at garth.sundem [at]

Comments are closed.