How could you study epigenetics? Thought experiment from a dreamer

This blog is part autobiography part roadmap. 

I am often asked “Do you miss it-being a scientist”

The short answer is “I didn’t dream of being an IT consultant.”

Longer answer is, as with all things that are part of being an adult, more complicated.

• I miss discovery- the joy designing a method to answer a question and then actually knowing- for a brief moment in time- something that no one else knows.
• I miss immersing myself in a problem and building a solution.
• I don’t miss, university politics; having to know who’s ass to kiss and watching my back for potential theft of ideas.
• I don’t miss the bullshit publication process that sometimes is used for competitive reasons.
• I don’t miss trying to write a grant that appears to be both novel and safe at the same time.
• I don’t miss the bureaucracy of universities policies that protect senior faculty but burden junior faculty.

I have been “out of the game” for half a decade now but I still pay attention to science and design experiments in my head and sometimes write them down.

I was an Assistant Professor running a small lab for about 4 years, my lab was centered on a set of enzymes that control the expression of genes in response to cell signals and environmental stimuli. These enzymes are commonly known as epigenetic regulators. The work we did was pretty good given the lack of funding, the fact that the enzymes had been described literally a year before I started my lab and I was trying to combine a novel class of genes with a novel set of methods (I was part of one of the groups that published the early papers describing the histone demethylase enzymes).[Synopsis of my lab]

My real interest, however has always been in learning the answer to the fundamental question “How do you make a brain?”  

I think now, I would ask a slightly different question; which has “how do we fix the brain when it isn’t made right.” One thing that age and distance has given me is perspective or perhaps empathy I don’t honestly know the difference. I have two small children both of whom are pretty awesome- unfortunately both have inherited some of my flaws. So I am often struck by how does the brain manifest these “flaws” even if there are no major changes or developmental issues.

How would one go after such questions?

Five years ago the answer was Stem Cells with maybe some mouse genetics thrown in for good measure. Now? I would go another direction. I think the single biggest issue in epigenetic research as well as neuroscience is the lack correlation data between phenotype (what it looks like in the whole organism), genotype (what genes play a role) and biochemical output (how well does the “engine” function”). Much like astrophysics and quantum physics have mathematic models which provide probability maps for specific core particles and/or forces, Epigenetics needs probability maps for phenotype and genotype- a Heisenberg probability if you will.

As I have mentioned in other posts, epigenetics is essentially grammar for the genome. It is a big, unwieldy mess of a field that is likely at least three separate full fields that we do not have names for as of yet. Sticking with the analogy the “field” of epigenetics is at the point where Western civilization was in the late 1700s/early 1800s where we knew some words and potentially some word relationships in the Egyptian cuneiform but we were largely blind to what was actually being said in hieroglyphs until the Rosetta stone was found. To me the rosetta stone for epigenetics will be cross species mapping of real world consequences.

For example; we know that there is a link between obesity in dogs and their owners. That is a real world cross species phenotype- why don’t we look at what genes expression and epigenetic patterns are changed as both lose weight? There is still validity to the idea mammalian biology is conserved at the physiological level.

What I would do if I was starting now would be to focus on dogs as a main model; they live with us, they often eat like us, they have behaviours which at their core are similar enough to ours but distinct across breeds. Furthermore access to their health records would have less risk and potentially greater detail as most veterinarians have a depth of knowledge on their patients over a whole lifetime – and for some clients multiple dog lifetimes.

For me, I would focus on brain cancer- as a scientist it is a fascinating process to take a cell that is programmed to not multiply and make it multiply and it is a cancer type that has repercussions to ones body, dignity and family.

The lab would have five facets;

1.     Define a set of neurologic symptoms that could be tested for by a veterinarian in clinic.

a.     Use standard indications from observation.

b.     A set of typical blood markers that are used for “unhealthy’ as part of the analysis.

c.     X-rays to define rough location, size and prognosis

2.     Test brain tumour samples across gene expression, “Epigenetic profile”, potentially genome mutations

3.     Use samples to grow models tumours, testing their gene expression profile and epigenetics profile for changes in culture.

a.     Where possible have normal age specific controls across breeds (or at least a general “mutt” control)

4.     Longitudinal studies of dogs with tumors after various therapies.

5.     Map epigenetic changes in tumour versus normal as well as fresh tumour versus in culture.

I was “classically” trained as a mouse geneticist where we had the clean clear; I deleted a gene what happened to my cell type? I learned [the very hard way-  hello consulting ;{ ] that there are no one-to-one relationships in any cell type when we deal with epigenetics- it is the system that protects the cell from single points of failure.

Long term would be to identify a set of parameters that can be linked to cancer and then go back and start testing the enzymes that are directly linked to the epigenetic modifications that are related to the phenotype. 

Whatever happend to cancer and bad luck? The story of known unknowns

Back in 2015, Bert Vogelstein et al, wrote a really interesting theorectical paper regarding essentially "What we don't know about cancer." 

We sort of already knew what caused bad luck but we can't really articulate what it is.

 (The "Bad Luck" article itself is behind the paywall but this editorial is a really good primer on what was ACTUALLY said by the authors)

I believe, like many in my field (when I still had one) that bad luck is simply physiology that we do not understand (Yes a direct rip off of Arthur C Clarke)

Vogelstien et al caused a media explosion to start off 2015 with the bad luck line- Forbes, Huffington Post have run with it.

A year later we haven’t heard much about the stochastic models (a fancy word for random) While hesitate to wade back into this morass of jargon, layman interpretation and poor analogies- I will. I think it is important to recognize that the authors were in no way suggesting we (society) should just stop trying to prevent cancer or that individuals have no way to decrease their risk.

I also think it is important to note that this was not about media attention. Bert Vogelstein is one of the fathers of cancer research- He doesn't need media attention to get funding. The point the scientists are trying to make is that some types of tissues make more copies and that is why certain tissues have higher rate of cancer. They also acknowledge that there are areas where we have limited research and therefore may be the source of "bad luck."

One of the biological control mechanisms that is part of the randomness of cancer is an area of study call Epigenetics. This new area of study controls mutations, rate of cell divisions, amongst other "things", in a cell specific manner.

What is Epigenetics?

In a practical sense epigenetics is an in-depth look at how genes regulate each other. Genes are, at their strictest definition, the precursors to the proteins (or certain RNAs) that perform (most of) the jobs that make life possible. While genes are the stars of the show, in terms of regulation of biological processes, they are the least interesting part of the genome. The interesting part is the so-called junk DNA or more accurately non-coding DNA-as in it does not code for a protein. If genes are the stars, then non-coding DNA are the role players and the scenery that move the show forward.

The dance of how these proteins and their modifications is choregraphed is WHAT epigenetics does for the cell.

Non-coding DNA essentially act as the context for why a gene should expressed; for example certain cell specific genes will be epigenetically regulated so as to NOT be expressed in the wrong tissue. This occurs through a series biochemical and physical changes to a gene that as a group are as a group considered epigenetic regulators.

Epigenetic processes are the key to providing organisms the flexibility to respond to the environment. So what about these processes make them so important? As with any regulatory process-it depends.

The best analogy is the "genome as the book of life". If genes are the words by which an organism is "made" then epigenetics is everything else in the book. (see here for a presentation on this topic)

[I prefer the script and scenery analogy above but the book analogy fits better with the general "Book of Life" analogy for DNA]

 At the lowest level it is the sentence structure that allows the words to have meaning. At the highest level it is the chapter order that gives the story a linear order. Unlike a real book each tissue in the body can shuffle each of these elements on the fly....a choose your own adventure book based on cell type.

Keeping with this analogy the various tools that each cell uses to keep track of their progress though the choose your own adventure would be the epigenetic machinery. This machinery provides, the grammar, syntax and paragraph structure that allows the cell to respond to each potentially different path.

As anyone who has every read a choose your own adventure, part of the fun is tracing back and making a different decision. In a cell this ability to track back is vital as it allows certain cell types to re-populate after injury or during normal growth. To bring it back to cancer, the flexibility that is inherent in a choose your own adventure book leaves cells vulnerable to errors.

Imagine that each cell has their own copy of the “Book” and everytime they divide they have to make a copy of the book for their kids. The only problem is that they have to do it by had one letter at a time. Obviously, there are going to be errors but for the most part they do not change the word or change sentence meaning. On occasion though the errors do change sentence structure or alter a word. In a nutshell this is any disease; an alteration of the “Book.” Cancer is in someways a step further, just like there are verbs, nouns, adjectives, etc in language there are categories of genes. When the growth category of words are altered you get cancer or when you alter the grammar (epigenetics) that provides rules for “cancer words” then you get cancer.

What we still don’t understand is how many words need to be altered or how much can you bastardize the grammar of the genome before you get cancer. That is part of why cancer appears to be bad luck, we simply do not understand the language or the grammar rules sufficiently to judge the quality of words that we find in cells.

To put in plainer; we don’t understand genetics or epigenetics well enough yet to make predictions.

The deeper dive:

While the book analogy is interesting and useful, the beauty of the system in my opinion is that all of this is managed through biochemistry: small differences in enzyme kinetics and subtle changes in protein binding. This biochemistry leads to a wide variety of markers that can be used to denote parts of the genome.

The cell uses different types of biochemical markers for each of the particular categories; grammar, pages, chapters. Each of the different markers has a different eased of use – sort of like an e-book where how you can jump as a reader is very dependent on how the author thought you would move through the book. The ease of use is a function of the biochemical processes by which the cell adds or remove the markers. If this all seems like overkill just to express a gene...it sort of is.

All of the added layers and differing ease of use allows the cell to add very tight regulatory control. This allows the cell to mix and match different markers to make bookmarks or highlight favorite passages, often used paragraph, etc. In general the chapter markers are direct methylation of the DNA. As the name suggests it is the addition (or subtraction) of methyl groups to DNA. This alters the affinity of DNA to a subset of proteins that occlude the DNA-basically hiding the genes. Removing the methyl groups abolishes this occlusion.

Sentence structure this is more complicated but in general there are 2 types of post translation modifications that are most commonly seen as having a definitive role in this process. This usually involves the structural proteins that surround DNA. These proteins are the histones and they allow 2 linear metres of DNA to be packed a volume of 0.00001 metres. An amazing feat in and of itself! Histones can be modified in a wide variety of ways too numerous to mention here. (see here for a review)

Full disclosure; my laboratory studied the role of histones in epigenetics so I am biased when in comes to how interesting these proteins are in the scheme of life

The combinatorial placement of these proteins and modifications on DNA allows for a very precise grammar to be used. So precise that cells can communicate exactly which protein should be expressed to their neighbor. Given that there may be as many as 31 thousand that is quite impressive. What are histones? that is another story for another post. The bottom line here is that these proteins control access to the DNA- as well as generally protecting cells from misusing cancer genes and/or accidently erasing instructions.

As always I love feedback and this is one of my works in progress.

Lets focus on the the actual science not media fluff

Enough already all of the articles and blogs about how "epigenetics" is the cause of aggression or socio-economic disparity. 

Epigenetic modifications to the genome are not more important than genes, they are not separate from genes. They are how we regulate genes, genes are not binary- they are not on or off. They are used at certain levels for certain tasks ("grow an arm" will use the same genes as "grow a heart" but in much different dosages).

Epigenetics are akin to a thermostat. You wouldn't blame the thermostat for causing winter? No you use the thermostat to respond to winter.

Epigenetics is the same! It is the control mechanism that the body uses to respond to the environment. In this case the environment being EVERYTHING outside the nucleus of a single cell. Yes everything, cell signals, hormones, hunger, emotions, temperature, toxins- everything. 

Understanding epigenetics is like particle physics, we can be statistically certain but we can NOT be definitive about the role of any single epigenetic modification's role in a disease state or trait inheritance. 

It is mind-boggling how complex the potential role of epigenetics is in any disease. We do not even understand how it works at the single cell level, and we have people suggesting that "epigenetics" explains complex traits just because nothing else has explained that trait?!.....its frustrating. Epigenetics is not magic, it is at least 20 different types of gene regulation. That is all it is...its boring fundamental science. 

I get it; its hard to explain epigenetics but we are reaching Fox news area of truthiness with some of the blogs and "news" about Epigenetics. We, as the educated science community, need to hold ourselves to a higher standard. Epigenetics is part of everyday life; differences in twins, calico cats, Zebra spots. Lets appropriately educate the public using everyday examples and then go deeper. I have found people are more excited by the basics and a honest approach than being oversold. We get that enough nowadays with the 24 hour news cycle and 365 political campaigning. 

Lets not be part of the solution by "misspeaking" the wonderful nature of epigenetics. We should be exciting the public to the potential rather than selling snake oil.

What is epigenetics?

It's a question that I am often asked. The answer is complicated. Since, in my opinion, the viewpoint of the field shifts based on where the next sexy science that can generate money is coming from. 


So lets start with the word epigenetics and its semantic meaning. If we start by breaking down the word, we can see what the word and field has come to mean in the last twenty years. The first part epi is from Greek meaning above. Genetics....well realistically it is a galaxy of smaller fields dedicated to studying what genes are, how they are involved in disease and development, and how genes regulate each other. 

So epigenetics is the study of processes above genetics.........which is where the etiology fails to be useful. Hence the confusion amongst scientists and the public at large.


In a practical sense epigenetics is a in-depth look at how genes regulate each other. Genes are, at their strictest definition, the precursors to the proteins that perform (most of) the jobs that make life possible. 

While genes are the stars of the show, in terms of regulation of biological processes, they are the least interesting part of the genome. The interesting part is the so-called junk DNA or more accurately non-coding DNA. If genes are the stars, then non-coding DNA are the role players and the scenery that move the show forward. 


The dance of how these proteins and modifications is choregraphed is epigenetics. 


Non-coding DNA regions control which genes are expressed and when they are expressed. This occurs through RNA molecules, binding of proteins and enzymatic modification of these proteins. Its more complex that what I am highlighting but the core message here is that Epigenetics is about controlling access to the genome by RNA and proteins through the non-coding regions of genomic DNA. 


Epigenetic processes are the key to providing organisms the flexibility to respond to the environment. So what about these processes make them so important?  As with any regulatory process-it depends. 


The best analogy is the "genome as the book of life". If genes are the words by which an organism is "made" then epigenetics is everything else in the book. At the lowest level it is the sentence structure that allows the words to have meaning. At the highest level it is the chapter order that gives the story a linear order. Unlike a real book each tissue in the body can shuffle each of these elements on the fly....a choose your own adventure book based on cell type. Further flexibility arises from how each individual cell interprets the story that it is given.

While the book analogy is interesting and useful, the beauty of the system in my opinion is that all of this is managed through biochemistry: small differences in enzyme kinetics and subtle changes in protein binding. This biochemistry leads to a wide variety of markers that can be used to denote parts of the genome.


The cell uses different types of markers for each of the particular categories; grammar, pages, chapters. Each of the different markers that the cell can use for these categories has varying ease of use. The ease of use is a function of the biochemical processes by which the cell adds or remove the markers. If this all seems like overkill just to express a gene...it sort of is. Adding layers and differing ease of use allows the cell to add very tight regulatory control. This allows the cell to mix and match different markers to make bookmarks or highlight favorite passages, often used paragraph, etc.  

In general the chapter markers are direct methylation of the DNA. As the name suggests it is the addition (or subtraction) of methyl groups to DNA. This alters the affinity of DNA to a subset of proteins that occlude the DNA-basically hiding the genes. Removing the methyl groups abolishes this occlusion.

Sentence structure this is more complicated but in general there are 2 types of post translation modifications that are most commonly seen as having a definitive role in this process. This usually involves the structural proteins that surrond DNA. These proteins are the histones and they allow 2 linear metres of DNA to be packed a volume of 0.00001 metres. An amazing feat in and of itself!

Histones can be modified in a wide variety of ways too numerous to mention here. The combinatorial placement of these proteins and modifications on DNA allows for a very precise grammar to be used. So precise that cells can communicate exactly which protein should be expressed to their neighbor. Given that there may be as many as 31 thousand that is quite impressive. What are histones? that is another story for another post. The bottom line here is that these proteins control access to the DNA. The modifications on these proteins act to either loosen the structure and increase access or glue the proteins together blocking access.

So what you say? Well the answer is variation: variety in cells (brain VS muscle), variations between twins, variation in cell response, variety in drug response, variation in disease. Epigenetics is the root cause of variation at every level: species, organism, tissue, cells.

So until we understand how this biochemical signature is modified we can't really understand how cancers vary from person to person or in a bigger picture how we retain biodiversity. 

Rare diseases and open access.

Ive found myself completely mesmerized by the open access/open science debate. As a recovering bench scientist, it has made me think about a variety of things but one that is really interesting is the implications for Rare disease research and speed of turning great benchwork into viable drug targets. Ill deal with the larger debate on open access separately but I wanted to put forward something today(Feb 28th 2015 Rare disease day). 

2016 update: In my opinion not much has change in Rare diseases in the last year. There have been some moves forward but like anything in the drug and/or therapeutic research- it is time consuming. I hope that the silence is because we are getting to the point where folks have rolled up there sleeves and are working not talking. 

I am really excited about the prospects for increasing the speed that potential drug targets can go from bench to bedside. The new technologies (gene sequencing, clinical data) can provide faster turn around time through efficient data sharing and new genomics technology. The real potential pay off is through new clinical data that will be available once EMR is implemented widely. The value of that much data combined with the new genome sequencing technologies can really provide some much needed guidance about the genotype phenotype relationships that may link certain rare diseases. I say may since it will really come down to data quality and wide dissemination of that data. Getting clinical data into the hands of molecular biologists and biochemist who can do the bench research is vital to drug design. 

2014 Update: With the roll-out of ACA starting to happen and the FDA crackdown on 23andMe. The landscape for studying and curing Rare Diseases just got a little better. For more information on the 23andMe nonsense there is plenty of information on the imbroglio but this one from the Huffington Post is the least sensationalist. My opinion is that the FDA made a decision based on the specific businesses lack of response it is not an indictment of consumer genetics or any paternalistic over-reach. Mathew Herper has a really great analysis of the stupidity and or hubris that 23andMe showed.  The Global Genes Project has a nice blog on the relationship between Rare diseases and ACA. 

The bad news is that the sequester has set research back years if not decades and may have very well rob a whole generation of scientists of their careers (this author included). Tom Ulrich of Boston Children Hospital has a nice blog on the subject.

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2015 Update: The new interesting initiative is precision medicine in US. I really am proud of the way Global Genes Project is coming along. I was briefly involved when Nicole Boice started the initiative. I look forward seeing how it continues to grow in 2015. I think it does a great job of keeping the conversation on awareness and providing a site to aggregate "best practices" for the Rare disease community. 

I really hope that the continued access to healthcare that we started to see in 2014 continues. The key will be what do we do with the basic information that clinics gather about their rare diseases patients? How do we make that shareable across clinics. This in my opinion will be the key to consistent diagnosis and clear symptons, which will then better inform scientists of which genes contribute to the phenotype. This is the basis of drug discovery and treatments. 

Right now is a real nexus of information due to the convergence of new technologies with "new" fields of studies. Epigenetics is the study of how and why genes get turned, the best analogy is: if the whole genome is the book of life, genes are the words and epigenetics is the sentence, paragraph and chapter structure that gives the words meaning. The other area is off-shoot of stem cell research; induced pluripotent stem cells (iPSCs). iPSCs as the name implies are induced to become stem cells from a variety of other cell types, the most clinically relevant being skin and blood. While the debate rages iPSCs and their value for replacing non-working cells with new ones [regenerative medicine] one thing that is not in doubt is the power of these cells for modeling disease. iPSCs can be made from patient samples and then shared with other researchers. This may seem trivial but the more people looking at the same model the quicker the core problem can be found. If done right the sharing of the iPSCs to researchers who use different techniques (biochemists, molecular biologists, cancer, etc) will provide a 360 degree view of the disease. 

Update 2014: Unfortunately it seems that iPSC research is becoming marred with scandal. The new "most promising" discovering may be "less real" than one would hope.....Paul Knoepler has a blog on the subject. BTW if you have any interest in stem cells you should follow Knoepler's blog he is an excellent writer and a top notch scientist.

Update 2015: I think we are past the really bad period, unfortunately it has also diminished the enthusiasm for iPSCS as models. Although I am not surprised, it has recently been shown that iPSCs form different sub-types of cells based on their tissue of origin (see here for neural and here for heart). This seriously limits the usefulness of iPSCs for drug discovery and would just exacerbate the reproducibility issues that are plaguing science in general but particularly stem cell research. 

Once this happens it's likely that links will be found that can make drug discovery and testing palatable for biotech and big pharma. Drug discovery is expensive but if the community can gather enough information about the molecular and biochemical characteristics of rare diseases then the existing "orphan drugs" can be tested against the characteristics rather than any single disease. 

Update 2015: The orphan drug area is one where we are starting to see movement. The recent announcement by the CF foundation recieving $3.3B for the patent rights to Kalydeco. It is an interesting approach that should be considered by any rare diseases group looking to expand support and the potential therapies for their disease. 

As always the caution is who should get the money, how do you ensure that the cost of the drug to sufferers is appropriate? If the foundation funds the study (in part) do they have an obligation to ensure that the cost of teh therapy be reasonable to the average person?

The elephant in the room is of course paying for all of this. Scientists need to be able to publish to get grants to pay for post docs and reagents. While there is some money available from disease foundations but it doesn't cover all the costs that a lab needs to run. That is the job of the NIH. However their mandate really requires that grants are given out based on WIDE applicability of the research and the grantee's history of research in that area. Unfortunately this model does not serve the rare community very well nor does it foster the wide range of scientific endeavor. There hundreds of examples where a rare disease has lead to unique insight into a biological pathway that was key to some cancer or other disease. 

Update 2014: Rare disease research will survive but we need to start to fast track new funding models that focus on highly innovative projects. We know what hasn't worked we need some research that is different.

Update 2015: Unfortunately I can't say there has been too much movement on this. Frankly scientific funding is horrible right now. I think for rare disease foundations there is an opportunity to foster young scientists to be advocates and invested in their disease but this requires a new way of thinking about how to fund rather then WHAT to fund.