I support Movember

You go, guys, but…what can I do to support a charity fundraiser for men’s health issues when the gimmick is to grow a moustache? It’s not as if I can grow a second one. I guess all I can do is urge all of you poor barefaced men to join Movember, and let your face do its manly thing.

But then, there’s the dilemma — I have to tell you to not shave it off in December, so you won’t be able to do it again. What’s with all these guys with naked lips, anyway? Don’t you get cold? How do you filter plankton?

Another cancer story…tomorrow

You people have been marvelous, and our cancer fundraiser has reached over $8300 — and I said I’d tell you about oncomirs, micro RNAs involved in cancer, when we reached $7500. But it’s been a very long week, I’m going to go pass out, so it’ll have to wait until tomorrow.

If you throw more money at the Leukemia & Lymphoma Society while I’m sleeping, you’ll make me feel even more guilty about not getting the article to you promptly. Go ahead, make me suffer.

$6672? MORE!

We’re still idling along, raising money for Light the Night and our battle against cancer. I promised another post on mechanisms of cancer when we hit $7500 — you don’t want me lying about, doin’ nothin’, growing fat(ter) on the government teat, do you? Make me work, reach our next goal.

The current sum doesn’t yet include the contents of the envelope that came in the mail today: 500 Hong Kong Dollars! Which I will exchange next time I’m near an airport.


We’re getting up there

The FtB cancer fundraiser has picked your pockets for $6352 so far. Did you all have a payday on the first of the month? Feel like kicking in a little more?

If the Republicans got you furloughed from your job, I’m sorry, we can wait for them to get their butts kicked by the court of public opinion so you can get back to work.

P.S. The Skepchicks are gaining on us. Maybe I need to start trolling MRA sites to get them to give money to a Man, ‘stead of those chicks.

Cancer reminder!

I don’t want you to forget just because it has scrolled off the first page, but Freethoughtblogs is fundraising for the Leukemia & Lymphoma Society. We’ve raised $5887 so far, but we’re aiming for $10,000…and I’ve also promised another cancer biology post if we reach $7500. So cough up if you can!

Another important fact: the Todd Stiefel Foundation is offering matching funds, so it’s like your money will be magically doubled.

What are tumor suppressor genes?

I’m trying to raise money for the The Leukemia & Lymphoma Society, and I promised to do a few things if we reached certain goals. I said I’d write a post explaining what tumor suppressor genes are, while wearing a pirate hat and nothing else, if we raised $5000. Shiver me timbers, I did! And it’s cold!


If you want more, go to my Light the Night fundraising page and throw money at it. I’ll write about microRNAs and cancer when we hit $7500. Note that we’re also getting matching funds from the Todd Stiefel Foundation, so join in, it’s a good deal.

There’s a basic principle in biological homeostasis (and it’s also true in cybernetics) that for every process that turns something on, you have an anti-process that turns it off. When you look at what’s going on inside the cell, you’ll often get the impression that it’s spinning its wheels — every protein, for instance, is being degraded at about the same rate that it’s being synthesized. The whole cell is in a state of dynamic equilibrium, in which it might look like the concentration of some protein is constant overall, but when you look closely, individual protein molecules are being constantly made, instantly targeted for destruction, and dismantled…only to be nearly instantly replaced by a duplicate. Everything is in a state of flux, and it looks terribly wasteful, but it means that everything is fluid and flexible and the cell is incredibly responsive to subtle cues.

Last time I wrote about oncogenes, genes that are activators of crucial cellular processes like cell division, and I told you that these play a role in cancer by sending faulty signals that switch on uncontrolled cell division. Given the above principle, you might expect that if there are gene products that turn on cell division, there ought to also be gene products that turn off cell division, a kind of anti-oncogene. And there are! They’re called tumor suppressor genes.

While acting in opposition to oncogenes, tumor suppressor genes typically exhibit another difference in behavior that sets them apart. Cancer causing mutations in oncogenes are usually dominant: that is, the mutation doesn’t just knock out the gene, it has to make a hyperactive gene, and just one mutant copy gone rogue is enough to start switching on cellular activity. Tumor suppressor gene mutations tend to be recessive.

You’ve usually got two copies of every gene. A tumor suppressor works to shut down renegade activity, and a cancer-causing mutation in one is most often simply going to be a mutation that destroys the gene — but since you’ve got two copies, it has a backup. Cancer needs to kill both copies of the tumor suppressor to escape from its anti-tumor actions.

The best known tumor suppressor gene is BRCA1, and it exhibits this behavior. BRCA1 is a good gene — it’s working to protect you from breast cancer. For most of us, every cell in our body has two functional copies of BRCA1. It’s like having two cops patrolling the beat, prepared to fight off any cancer threat, and for cancer to succeed, it has to kill off both. Even one left functional can suppress any effort by the cell to go hyperactive and proliferate. A mutation that knocks out one copy is rare, but two mutations that knock out both are even more rare — it follows two-hit kinetics, which means you multiply the probability of the two events together.

You will occasionally hear about someone being at high risk of cancer because they carry a bad allele of BRCA1 — Angeline Jolie was in the news about this recently. What has happened here is that the person was born inheriting one broken copy of the BRCA1 gene — their cells only have one cop on the beat. They aren’t born with cancer — that one copy of BRCA1 is sufficient to keep them safe — but now they are at much higher risk of an accidental mutation taking out their sole protector than if they had two.

Another well known tumor suppressor gene is Rb, the gene that when mutant can lead to retinoblastoma, or cancers of the eye. It also exhibits two hit kinetics, in that familial retinoblastoma is caused by inheritance of one mutant Rb allele, so that all it takes is one mutation later in life to lead to cancer. Sporadic retinoblastoma, that is retinoblastoma without previous examples in the family, is much rarer, because it requires a first somatic mutation and a second mutation later to take out the second copy.


Having an enabling mutation in one copy at birth so greatly increases the chance of retinoblastoma that afflicted individuals are likely to have bilateral cancers affecting both eyes, while it’s so rare in sporadic cases that it is almost always unilateral, affecting only one eye.

OK, you understand the principle. Last time, I wrote about the oncogene Ras, which, to make it simple switches on the mitotic machinery and promotes cell division. Does it have an anti-gene product that opposes Ras and switches off cell division?

Of course there is. Several actually. One example: recall that I told you that Ras is activated by binding GTP, and deactivated by converting GTP to GDP, and that Ras itself has GTPase activity and therefore works to switch itself off. There are also tumor suppressor proteins that are called GAPs, or GTPase activating proteins, that enhance Ras’s GTPase activity. One of them, called NF1 or Neurofibromin, binds to Ras and elevates its potency as a GTPase approximately 1000-fold — it basically makes Ras ultra-good at shutting down and doing nothing.


Oncogenes and tumor suppressors are the yin and yang of cellular regulation. Cancer cells often contain hyperactive oncogenes, and have shut down tumor suppressors…which suggests that one strategy for treating cancer is to develop inhibitors of oncogenes, and to repair, replace, or elevate expression of tumor suppressors. And that’s a rather pat explanation of some viable general strategies that of course encounter all kinds of additional complexities.

Donovan S, Shannon KM, Bollag G (2002) GTPase activating proteins: critical regulators of intracellular signaling.. Biochim Biophys Acta 1602(1):23-45.

Hanahan D, Weinberg RA (2011) Hallmarks of cancer: the next generation. Cell 144(5):646-74.

Weinberg, RA (2014) Biology of Cancer. Garland Science, New York.

No one “lets” the #FtBullies win!

In a post at Skepchick announcing new incentives for their cancer fundraiser, Melanie Mallon says, “We can’t let the #FTBullies win!” Don’t worry, we’re sitting here on top of over $5000 raised for the Light the Night foundation, and no one has to let us win. We shall seize victory in our iron grip and raise it high against the pathetic resistance of our feeble competitors. Because that is what we do.

And yes, I noticed that we topped the second of my fundraising goals. Once I finish this pile of grading — this gigantic, overwhelming pile of grading — I’ll get writing on that. Your job is to get cracking and bring us over $7500 so I have to write another post on microRNAs and cancer, and then get us to $10K for a hangout discussion.

You’re going to make me work again, aren’t you?

Donations to the Light the Night Fundraiser are getting awfully close to the next landmark of $5000; we’re at $4748. Get there and I’m going to have to write a post about tumor suppressors, and I know you’re all just panting away with lust for that.

Then there’s a long stretch to $10K, so maybe I should add something at $7500. A post on micro RNAs and cancer, I think?

By the way, we’re getting matching funds from Todd Stiefel, who has now promised to get a red buzz-mohawk if we hit $20K. That’s a really long stretch, but if we make that, I’ll have to think of something even better. What is it with everyone doing exotic things to their hair? We’re supposed to be public intellectuals, shouldn’t we be doing weird things with our brains?

What are oncogenes?

I’m trying to raise money for the The Leukemia &amp Lymphoma Society, and I promised to do a few things if we reached certain goals. I said I’d write a post explaining what oncogenes are, while wearing a pirate hat, if we raised $2500. So here you go, arrr.


If you want more, go to my Light the Night fundraising page and throw money at it. I’ll write the next part when we hit $5000. Note that we’re also getting matching funds from the Todd Stiefel Foundation, so join in, it’s a good deal.

Cancer is not a creative, original disease; it has not been honed by ages of evolution to craft novel lines of attack on your body. Instead, it’s an opportunistic thief. Cancer misuses and perverts existing processes in your cells to send them out of control. Everything cancer does is simply the same thing your cells normally do, only amplified and unconstrained, driven by damage to the genes that would normally regulate their behavior.

Here’s a metaphor, a car with a dangerous defect. It has acquired a glitch in the accelerator so that every time you start it up, it immediately roars up to full speed, as if you’d floored the pedal. The problem hasn’t created anything new in the car, it’s just taken something you normally need to do, that is, regulate the speed of the machine, and stripped you of all ability to control it. That’s what an oncogene does; it is a gene that is normally involved in controlling the rate of cell proliferation, for instance, and a mutation has broken it in such a way that it now tells the cell to divide as rapidly as possible.

Now if you were driving down the freeway and suddenly your accelerator were stuck and you couldn’t slow it down, you’d have alternative strategies to stop (and so does the cell). You could hit the brakes or shift gears or turn off the ignition key. Cancers acquire another set of mutations that destroy the ability to shut off cell processes, analogous to breaking the brake pedal or snapping off the gear shift handle. These genes that can block the effects of out-of-control cell regulators are called tumor suppressors, and I’ll write about those at another time. Today I focus on oncogenes, regulators of the cell that must be damaged by mutation to produce an excessive response.

The first concern that comes to everyone’s mind is that you don’t want to have your cells running amuck — no one wants cancer. Just as you can do your best to maintain your car, you can also live sensibly — eat in moderation, avoid carcinogens or other behaviors that expose you to radiation, and get regular checkups — to reduce the likelihood of deleterious mutations. But they can happen anyway, through no fault of your own. Every time your cells divide, there is a very small chance of an error in replication that inserts a mutation into an oncogene. Just existing, even while doing everything exactly right to maximize your health, brings with it a base chance for a mutation. Given normal rates of cell division, every single one of you reading this is going to acquire about 20,000 DNA lesions today and every day. Almost every one of them will be patched up by DNA repair mechanisms (you have no idea how important DNA repair is to your continued health), but even so, one will occasionally slip through — over your lifetime, your cells will acquire an estimated 10,000 mutations. Live long enough, playing these odds, and cancer is essentially inevitable.

So cancer is fundamentally a chance process. There is no reason people get cancer, no purpose behind it, and everyone is susceptible. Some behaviors can increase the odds — smoking, failing to use sunblock — and you can also inherit genetic predispositions that increase the likelihood of acquiring a full set of mutations that lead to cancer, but ultimately, no one is at fault for cancer.

So what can go wrong? The diagram below is a simplified illustration of the various signaling networks in the cell. These are some of the pathways by which cells are told to regulate their behavior.


I’m going to focus on just the greenish box in the middle, the one labeled “Proliferation Circuits”, just to keep it simple. Think of that as the accelerator peddle for your cells. Sometimes your cells need to be encouraged to proliferate. For example, during childhood there are general signals to encourage stable patterns of growth, and during adolescence there may be novel hormonal signals to encourage new growth of selected populations of cells. If you’re injured, local growth factors are secreted to encourage cells to divide and repair the damage. So that’s what you’re seeing on the far left: growth factors and hormones can send a signal to the cell to give it permission to grow.

In order for a signal to be received, the cell has receptors on its surface that can bind to the growth factors and hormones. When a receptor binds to a signal, it changes to send a signal to other proteins (all those green circles) inside the cell. Think of it as like a doorbell; growth factor comes calling, presses the doorbell/receptor, the bell rings/sends a chemical signal into the interior, all the proteins get busy.

You can probably imagine how this system could get broken already. What if the receptor were damaged in such a way that it constantly sent a signal inwards, even if no growth factor were present (this is called becoming constitutively active)? What if one of the internal proteins were damaged in such a way to become constitutively active, so that it acted as if it were seeing the receptor as bound to a growth factor, even if it wasn’t? Now the cell is being constantly lied to by its sensory apparatus, and behaves as if it were being constantly told by the body to divide and divide and divide — it is on the road to being cancerous.

Let’s look a little bit closer at that pathway and give some of those green balls a name. This is the Ras-Raf signaling pathway.


It’s a bit Rube-Goldbergian, but hey, that’s biology. In the top left corner you see something called EGFR, short for epidermal growth factor receptor. That’s our doorbell; the asterisk after the name in this diagram means that you see it mutated fairly frequently in human cancers. The box explains that it is seen to be damaged in 10-20% of certain kinds of cancers; when it’s mutated, it acts as if its signal, TGFα (Transforming Growth Factor Alpha) is always present. EGFR may also be perfectly normal, except that it is overexpressed, that is, present in a far greater number of copies on the cell surface, which makes the cell particularly sensitive to tiny quantities of growth factor. This happens even more frequently in many cancers.

The next steps in the pathway involve switching on Sos/Grb2, which activates Ras (look at the box; Ras is very commonly mutated in a great many cancers), which activates Raf, which activates MEK, which activates ERK, which promotes DNA replication. This is called a signaling cascade, and these kinds of sequences are all over the place in the cell. The advantages of this pattern is that many steps can be amplification steps, where one activated protein switches on many copies of the next protein in the sequence, and also each step is an opportunity for regulation.

Now be strong: I’m going to look even more closely at a key oncogene, Ras. Ras is important; it’s a central regulator of proliferative processes in the cell, and it is commonly one of the proteins made constitutively active in cancers.


How is Ras switched on and off? In order to be active, Ras needs to be bound to a small molecule called GTP, guanine triphosphate, a base with three phosphate groups attached to it. It must be three; anything less, it isn’t active, so if it is bound to GDP, guanine diphosphate, it is inert. When it is bound to GTP, Ras changes shape to open up a binding site that can dock with the next protein in the chain, Raf, and activate it in turn.

Ras is switched on by the previous protein in the chain, SOS. SOS is a guanine exchange factor, and from the name, you can guess what it does: it swaps out the stultifying GDP molecule from Ras and replaces it with the energizing GTP molecule. Which allows it to bind with Raf, which then activates MEK, etc.

What switches Ras off? Ras is also an enzyme, specifically a GTPase — it cleaves its own GTP into a GDP. It turns itself off! What this means is that it acts as a kind of momentary switch. When a growth factor molecule arrives at the cell, Ras will respond by briefly initiating the cell division machinery, and then shutting itself down. It needs a sustained signal to keep cell division humming — a little triggering flicker of a random molecule bumping into the cell is not enough. This makes a lot of sense for cell cycle control. Ras is a reluctant activator, always hesitating and drawing back, and it needs constant prodding from external signals to keep doing its job.

Except when it’s mutated.

The most common cancer-inducing mutation in Ras is a single amino acid change in the 12th codon of its gene that greatly reduces the effectiveness of its GTPase activity. It binds GTP, becomes active, and then does not cleave the GTP — it clings to it instead. It switches from being a reluctant activator of cell division to instead being an avid, hyperactive activator — any transient signal, even a bit of noise, becomes an excuse to tell the cell to start dividing madly.

And that’s the beginning of a cancer, a rogue protein, made by an oncogene, that’s telling the normal, healthy cellular machinery to do its thing when it shouldn’t.

There’s much more to cancer than that, of course — cancer is more than just excessive cell division, and also the cell has many fail-safes, the tumor suppressor genes, that are supposed to put the brakes on when renegade proteins are going wild. But — oh, and this is cruel of me — to hear that part of the story, you’ll have to donate to my Light the Night fundraising page. When we get to $5000, I’ll tell you all about tumor suppressors.

Croce CM (2008) Oncogenes and cancer. N Engl J Med. 358(5):502-11.

Hanahan D, Weinberg RA (2011) Hallmarks of cancer: the next generation. Cell 144(5):646-74.

Hesketh R (2013) Introduction to Cancer Biology. Cambridge University Press.

Skepchick joins the race

When I announced our participation in the Light the Night fundraising drive, I mentioned that another network would be joining in, too, and that we might have to set up another challenge award for beating them. Well, here they are: Skepchick has formed a team, and since our goal is to raise $10,000, they’ve set their goal to $10,001. Ooooh, it’s on.

So what should I do if Freethoughtblogs outdoes Skepchick? Given that we’ve raised $4000 so far, and they’ve raised less than $100, I think it should be a very very small forfeit, don’t you? Just to be fair?