My Contribution to the ALS Ice Bucket Challenge — with Science!

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Transcript of video:

I’ve been waiting for this for two weeks So thank you to Syros Pharmaceuticals for challenging me and my lab to take the ALS ice bucket challenge. ALS is short for Amyotrophic Lateral Sclerosis. It’s a neurodegenerative disease that messes with a body’s muscle control not by screwing with the muscles themselves but by screwing with the nerves that control them by sending signals. It’s also called “Lou Gehrig’s Disease” but maybe the most commonly known case right now is Professor Stephen Hawking.

So when I was challenged I wanted to make mine a little different from the millions of other videos out there. And I got to thinking. You know, they never tell you what kind of ice you have to use…

This is dry ice. Now water ice is just frozen water. Frozen H2O. This is dry ice, which is frozen carbon dioxide in these pellets like this. Now carbon dioxide is one of the major waste products when we breath out, when we exhale. And that’s why it’s so important that I have proper ventilation in here, and one reason you shouldn’t try this at home, without proper supervision. Um, this stuff can build up in a room, and can make it really difficult for your body to get rid of the CO2 in your bloodstream. You can see this gas being added to the air in this sublimation reaction, where the solid carbon dioxide pellets are going to the gas carbon dioxide without being liquid in between.

So why am I doing this with dry ice? Well, this is sort of an homage to the researchers out there that are taking a look at ALS from a biological research perspective. Um, this stuff, this dry ice is commonly seen in every biology lab. We use it for the same reason you put your food in a freezer or food in a refrigerator: to keep stuff from breaking down when we need it– to keep cells from breaking down and the cell products inside from breaking down. And it’s really helpful to be able to freeze your cells, thaw them, and come back and do the experiment you couldn’t do right now. Now I cannot over-stress how bad of an idea this is– what I’m about to do. No one should ever do it. Don’t do it at home, don’t do it at work, don’t do it under proper supervision. No one should do this. Um, in addition to the suffocation hazard that I’ve hopefully taken care of, this stuff is really really cold. Water ice forms at about, uh, zero degrees Celsius, 32 degrees Fahrenheit. This dry ice forms when carbon dioxide gets down to, oh, a balmy 56 below zero Celsius, and 70 degrees below zero Fahrenheit? So this stuff’s really cold. And what I’m about to do is not a good idea.

But I’m gonna do it anyway. Because it’s important to support research into many diseases, not the least of which is ALS. Now everyone’s saying donate to ALS, and I have. I’ve donated to ALSA, the ALS association at ALSA.org. But pick a disease, pick a disease that’s close to your heart. Somebody that you know, somebody that you’ve met, somebody you went to school with. There are a lot of these foundations out there that need your help. What they do is they take your money and they redistribute it to labs who are doing work to try and diagnose, try to treat, try to cure a lot of these really nasty diseases that are still out there causing a lot of pain for a lot of people. So I encourage you to pick a disease close to your heart, pick a disease that you care about, and get out there and help fund it. It’s getting harder and harder to fund scientific research, so I do this– Cheers, to the researchers that make all this stuff possible For science!

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How We Drugged a Leukemia’s Favorite Transcription Network

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If we “cure cancer” in the woods and no one is there to read about it, will patients reap the rewards? I did computational analyses for a recent paper in Nature that describes a new chemical that kills leukemia cells and how we think it does so. Somehow this has escaped mention by nearly all science press. </sour grapes> Surprisingly, this chemical messes with a process all cells need to do– healthy and cancer, yet it doesn’t kill all kinds of cells. So, not only did we invent a chemical that kills cancer cells, but we also identified a new way to specifically target cancers with drugs.

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Our head model for how THZ1 works: CDK7 (red) normally puts phosphate molecules (blue) onto the tail of RNA Pol II, which is part of its “transcribe now” signal. Left unchecked in a leukemia, cells multiply. But THZ1 binds to and prevents addition of the phosphate, preventing RNA Pol II from transcribing and killing the cells.

Our collaborators at the Dana-Farber Cancer Institute (Harvard Med’s cancer wing) created a chemical compound called THZ1, named after its most direct inventor, Tinghu Zhang. This drug binds to and de-activates a protein called CDK7, short for cyclin-dependent kinase 7. Kinases are proteins that stick phosphate molecules onto other proteins, cyclin-dependent ones involve the cell cycle, and CDK7 was the 7th one discovered. THZ1, the drug, binds to CDK7 and prevents it from adding phosphate molecules to its target proteins.

By testing THZ1 across a bunch of cell types, we saw that our chemical does a number on leukemias. It kills leukemia cells in a dish, and it kills them in mice. We’re pretty happy with this, but my job was to figure out what it’s doing to cells that makes them die. In doing so, we saw that THZ1 is a great tool for figuring out how biology works in addition to being a potential drug.

To understand how THZ1 works, we compared the same kind of cells treated with it to those treated with a control chemical. All cells transcribe DNA genes into messenger RNAs (mRNAs). This is largely done by a group of proteins that form a molecular machine called RNA Polymerase II (RNA PolII). PolII is like a molecular photocopier, and phosphate molecules on its long, protein tail are important to its function. CDK7 is responsible for adding some of the phosphate molecules PolII needs to function onto a longish protein tail of PolII.

Like most of my more pride-inducing findings, our first results came under the pressure of and just ahead of a deadline, in this case, the Thursday night before a Friday morning presentation of our work. We had just gotten data from T cell leukemia cells treated with THZ1. Specifically, we got the levels of mRNA transcripts per gene for all genes by performing an expression microarray experiment. This experiment measures how many molecules of mRNA per gene that existed in a pool of cells, so we compared the counts of mRNAs in untreated cells vs. cells treated with THZ1.

We treated cells with THZ1 and measured the levels of all transcripts. Each transcript is a row. The color represents how different this transcript’s level is compared to control. The greener it is, the less mRNA for that gene in the THZ1-treated cells.

After some biologically-informed data normalization, we saw that virtually all genes had lower mRNA levels in the THZ1-treated sample than in the untreated sample. This made a degree of sense– if most genes get transcribed into mRNA by the action of PolII, and, if you mess with CDK7’s ability to add phosphate groups to PolII’s tail, it can’t transcribe. But this also didn’t make complete sense– all cell types need PolII to transcribe, and not all cells died at the same rate when treated with THZ1. Nearing midnight, our collective brains alternated between bursts of insight and longings for bed.

We treated different kinds of cells with THZ1 and counted how many cells lived compared to an untreated control. Each cell type is a line; the first four are leukemias. Each point is the percent (1.0 = 100%) of the cells that survived at that level of drug treatment.

So how could a chemical that inhibits the function of a machine necessary for all cells to stay alive have specific effects on specific cell types? Well, we thought, not all cell types transcribe the same genes, since not all genes are important for all cell types. Only a specific subset (~1/2 to 2/3) are transcribed in a given cell type, and only a small number (~3-10) seem responsible for making/keeping that cell type’s identity. So we followed a hunch that there was something about the T cell acute lymphoblastic leukemia cell identity genes that made these genes and cells susceptible to futzing with a part of general transcription.

Thanks to the work of many leukemia and transcription researchers, we have a pretty good sense of the important genes in this particular kind of leukemia, including the genes responsible for keeping this cancer cancerous: RUNX1, TAL1, and GATA3. These genes encode transcription factor proteins that help control each other’s transcription, i.e. GATA3 protein from the GATA3 gene helps control the transcription of the TAL1 gene, etc. Our microarray experiments showed that the RUNX1 gene encodes a RUNX1 mRNA whose levels go down a lot when you treat cells with THZ1. In fact, it doesn’t take a lot of THZ1 to make the RUNX1 mRNA levels go down 10 times as much, since it is equally sensitive to low dose (1x) and high dose (10x) treatment.

We knew two things that led us to a hypothesis:
1) Not all genes react in the same way to messing with CDK7, but all genes do react.
2) Not all genes are equally important for a given cell to have a certain identity and live.
What if the transcription of all genes going down was related to a regulator gene going down first?

So we did another experiment. We suppressed the level of RUNX1 transcription and used another microarray experiment to ask how all genes responded. We saw that the same genes whose transcription went down the most in response to THZ1 also went down a lot when RUNX1 was suppressed. This makes us think that genes controlled by RUNX1 are sensitive to THZ1 chemical treatment. This also might explain why not all cell types are equally sensitive to THZ1 in the same way– maybe there are genes that are important for some cell type or identity that dictate if that cell type is sensitive to CDK7 inhibition by THZ1 or not.

Yeah, we’re pretty excited about this one. Some of our other collaborators are taking the compound through more tests, hoping it becomes a drug that patients actually get. Because, after all: http://xkcd.com/1217/. As for me, this was my second big project in the lab, and I moved abruptly from transcription mechanics into drugging cancer– not bad for a computer geek. Oh, and that Friday meeting? Knocked it out of the park.

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What is a stem cell?

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Tree1You started out as one cell– wicked, right? Now look at you! Brain, skin, blood, all of these can be traced back to that first cell that was you. Since you’re bigger that one cell, this cell had to make more of itself. Since you’re more complicated than a blob of identical cells, they had to specialize to become brain, skin, and blood. These cells that 1) make more of themselves for a long time and 2) can specialize to become other cell types are called stem cells. “Stem cells” is a category more than one specific cell type. Members vary widely, and they differ in the kinds and number of cells they can become.

While people may be familiar with the most controversial kind of stem cells, embryonic stem cells (ESCs), you may not know that you have stem cells in you right now. For just one, you have blood stem cells in your bone marrow. These hematopoietic (blood-forming) stem cells can become every kind of blood cells, red or white. In fact, one true hematopoietic stem cell can remake all of the blood: if you irradiate a mouse such that all the blood cells die (akin to radiation treatment for leukemia), and then you put in one hematopoietic stem cell, this stem cell can remake all of the different kinds of blood cells, and the mouse lives.

If stem cells can go from less specialized to more specialized and remake whole systems, can we go the other way? Can we take a very specialized kind of cell and make it go back to a less specialized stem cell? Yes! Since every cell keeps the same DNA instructions but only uses different subsets, we just have to tell the cell to use a “be a stem cell” subset of DNA instructions. Yeah… just.

It’s hard to do, but you can tell a specialized blood cell to become a any-cell-making stem cell– to make them a “pluripotent” stem cell. This process is a switching-on or “induction” of a subset of DNA instructions that say “be a pluripotent stem cell.” It results in a really powerful bunch of cells that might just hold the ability to repair whole systems– brain, skin, or blood. These are induced pluripotent stem cells. These are iPS cells.

I’m writing this at a stem cell conference. It sounds like the problem has (for now) changed from “how do we make stem cells from specialized cells” to “how do we make specialized cells from stem cells.” It turns out we don’t have a great sense of how you go from that one first cell to all of the different cell types. For example, there are several stages in between fertilized egg and blood that we’re still identifying. But we’re working on it.

Our goal: take a bit of your skin or blood (big pools of cells with easy access), induce the right genes to make them iPS cells, then turn these iPS cells into the kind of cell you need replaced. Maybe we fight Parkinson’s with neurons for your brain, baldness with hair follicle cells for your skin, or HIV with helper T cells for your blood, and each of them from iPS cells.

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What the Ghostbusters Taught Me About Communicating

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I was rewatching Ghostbusters II, and Winston Zeddemore taught me something about how to communicate a complex subject effectively.

It was a throwaway scene that looked uncomfortably familiar. There was a problem, and the team needed the help of someone in power. They turned to the mayor, trying to convince him that there was a river of evil, thought-responsive pink slime under the city. Ray (Dan Aykroyd) tried first.

Ray’s plan:
1) Kiss butt.
2) Describe in sciency words (like “psychomagnotheric”) the problem.
3) Expect the mayor to do something.

What was the result? The mayor didn’t get it, and Ray was nearly responsible for the destruction of NYC.

Now the Ghostbusters are four people: two egghead academics (Ray and Egon), one wildcard (Pete), and one regular guy (Winston). Winston saved the day and taught us all an important lesson about communicating a complicated, technical, yet important scientific point.

Winston’s plan:
1) Know his audience is an unfamiliar with this field and might be antagonistic.
2) Explain the essential takeaway of the problem without relying on jargon.
3) Make his audience care by connecting with something they care about.

The mayor is visibly more inclined to think about this version of the story.

So what can we learn from Winston’s technique?

The only hard-fast rule of communication as far as I can tell is KNOW THY AUDIENCE. Ray and Egon use big words that an uninitiated listener wouldn’t know. Would you stop and listen to anyone (even in a lab coat) talking about psychomagnotheric anything? No, because you don’t care. The words important to us as scientists usually mean little to those outside our immediate fields. I know it’s a big deal with someone successfully performs crystallography for an important protein, but try telling that to the mayor of New York City.

Why not say what you would say after “basically…?” When I write something complicated, and can feel myself wording it into knots, I reboot and start the sentence again with “basically.” For some reason, this is especially useful for writing first sentence of paragraphs of science manuscripts. My goal is to write these so that the paper is understandable by reading only these first sentences. Start with the big point.

In the end, both Ray and Winston failed. This was at least partly because they didn’t know exactly what it is they wanted from mayor. This may have doomed them to fail the first round, but because of Winston’s tactics, the mayor knew to call the Ghostbusters when it all went south.

Thank you for saving the world, Winston Zeddemore, with your superior communication skills.

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Enhancers Are Not Switches – Why We Should Kill a Bad Metaphor

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“All models are wrong, but some models are useful.” So said George E.P. Box. Models are mental shortcuts that simplify complex thoughts/events/etc. There’s nothing really wrong with explaining a complex idea using a model– in fact the quality of your model can show how well you understand the full concept. But “enhancers are genomic switches” is an outdated model that is causing us issues in explaining new findings. I’m not going to just bury this metaphor but also suggest a replacement– “Enhancers are genomic boardrooms.”

First, what is the full definition of an “enhancer?” This is trickier than one would guess for a thing that was discovered decades ago. Protein-coding DNA genes get transcribed (photocopied) into mRNA transcripts. Enhancers are also pieces of DNA that “enhance” the transcription of these protein-coding genes. So if you just have the piece of protein-coding DNA in your experiment, it gets transcribed at level X. If you have the protein-coding gene and the enhancer on a piece of DNA, the protein-coding gene gets transcribed more. This is how we used to think of enhancers.

As genomes evolved from simple, circular bacterial DNA to the linear chromosome structure seen in humans, bits of DNA changed or got re-purposed. We can find substantial similarity between the parts of our genomes that code for proteins and the protein-coding genes from our distant ancestors. This is less true of enhancers– they tend to be less “conserved” across evolution. We know many parts of the human genome have certain characteristics of enhancers, but the DNA letters in their spans are tough to find in mice and bacteria. This may mean that, when and where genes are used/transcribed/expressed is the big difference between us and other animals. Gene use/transcription/expression is controlled by enhancers.

Bacteria have one cell type; humans have hundreds. Enhancers in humans control when and where genes are turned on. This is why many researchers and press releases have said that “enhancers are switches.” They can have the effect of some gene or genes being turned on when the enhancer is active. What an “active enhancer” really means is what leads to the breakdown of the metaphor of “enhancers are switches.”

Enhancers are regions of DNA. They don’t have letters in the right order to code for protein though, and enhancers are often hundreds or thousands of letters away from the pieces of DNA that do. So how do enhancers have anything to do with transcription if they can be so far away? Well, DNA is kind of like an old school phone cord. Sure, it twists in the familiar helix shape, but it also loops like string. This way, enhancers can loop toward the genes whose transcription they control in 3D space. What it does when it gets there is only recently starting to be appreciated.

drawing5

Actually, enhancers are like boardrooms. When a meeting is held in a boardroom, decision-makers congregate, and they have some knowledge of the whole system that’s needed to make a decision. The decision-makers of the cell are proteins that bind to DNA to conclude whether or not a gene should be transcribed.

Some protein-coding genes have the right recipe to make proteins that act as signals. (To get technical for a moment, they’re called “transcription factors.”) These signals can mean something about the state of the cell– I’m attacking virus– or the environment the cell is in– it’s hot out– or even something about the type of cell it is– I’m a nerve cell. Production of a certain protein can be the end result of a signal-processing pathway and usually means that some gene needs to be transcribed. So these signalling proteins, whose very existence means something about the cell, bind to enhancers that are responsible for controlling transcription of certain genes. These enhancers get bound by a bunch of other proteins and loop in 3D space to the start of the protein-coding target gene. In this way, enhancers aggregate signals from several information sources to decide whether or not to transcribe given genes.

1) Information-carrying protein binds enhancer
2) Enhancer loops to some target gene
3) Protein-coding gene is transcribed
4) Protein made from transcribed
[Optional] 5) GOTO 1

Why does the “switch” metaphor suck? Calling enhancers “switches” limits the amount of things we can say about the latest findings, the majority of which have to do with what’s going on at/with enhancers. Sure, the end result can be expression of a certain gene, but the switches familiar to a lay audience usually involve only one input and are geographically close to the thing they’re controlling. Enhancers can be really far away in the genome and accumulate decisions made from several bits of information.

The proteins binding to DNA are the managers of different departments that have come to the enhancer boardroom. They have made the decision about if transcription of some gene is right for their purview. If all the department managers bind to DNA, signifying their intent, then transcription happens. They don’t flip switches– they make decision by combining information from many sources.

Some boardrooms are more important than others and decisions made within them can have broad or focused impact. For instance, the enhancers controlling genes whose proteins specify cell type have huge reach and can influence nearly every other gene in the genome. Or, perhaps the decision is more focused on whether or not a certain protein pump needs to be on to get more of chemical X into a cell. Calling enhancers switches makes them too egalitarian.

If you’ve made it this far and hate me for my proposal, fine. But you should also know that enhancers don’t really “enhance” transcription, and the thought-leaders in this field are considering burying the term itself. More on that maybe some other time.

While they live though, enhancers thus are not switches, but they are boardrooms. QED. RIP, bad metaphor.

Tl;dr: Enhancers are DNA segments that bind protein signals and control whether or not a gene is transcribed. Calling enhancers “switches” totally undersells the important part. Protein signals are section managers that meet in the enhancer boardroom to decide to transcribe.

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