What the Hell? - Epigenetics
So you should all know the basics of genetics now! If you don’t read my blog post “What the Hell? - Genetics”.
To re-cap, your genetic code is held in a library. Each book is a gene. When the gene is “read” this creates RNA and the RNA can be translated into a protein. Genes/books can be coding genes or non-coding DNA. Your genes are made up of four letters in different sequences (A, T, G, C). You also have different sections in your library depending on the function of your cells e.g. brain, liver, skin.
As I’ve mentioned before, key players in your genetic code being translated into a protein are the readers or “transcription factors”. But like any library you need some way of controlling all the pesky people running around. If transcription factors could pick up any book they want as many times as they wanted you get complete chaos. This happens in cancer where transcription factors get a hold of books they shouldn’t (called oncogenes) leading to cancer cells growing uncontrollably. The “people” that control this are your librarians also known as your “epigenome”. They control what books you can access, when you can take them out and how long you can take them out for.
What is epigenetics?
Epigenetics by definition is any act that alters gene expression without altering the genetic code. There’s a lot more to epigenetics than just controlling gene expression but for now we’ll just discuss this area.
I’m going to talk about two main branches or epigenetics – Histone post-translational modifications and DNA methylation.
You have 22 pairs of normal chromosomes and 1 pair of sex chromosomes (XX or XY). The chromosomes are numbered by their size, where the largest pair is number 1 and the smallest pair is number 22 (see picture).
So we have our DNA in our nucleus as chromosomes but if all of your DNA is packaged so tight how do the readers get access? Little markers are placed on the histones, which tell the DNA to be open or closed. If the marks say “open” then the DNA unwinds from the histones allowing the readers to have access to the gene(s). An example of this (see picture) is called "Acetylation". An acetyl mark is added to histones. This tells the DNA to unwind, giving access to transcription factors. When the acetyl mark is removed the DNA closes up again, repressing gene expression.
DNA methylation can also control gene expression. As I've told you before your genetic code is made up of four letters: A (Adenosine), T (Thymine), G (Guanine), C (Cytosine). DNA methylation happens at a C which has to be beside a G (i.e. CG). This is called a CpG site (the "p" means beside or 5' to). A methyl group is added onto the C (or cytosine). This prevents transcription factors or readers getting access to DNA, preventing gene expression (see pictures). For those that are interested a methyl group is a carbon with three hydrogens (CH3). The methyl group is put on by a DNA methyltransferase (this is an ezyme).
For those less interested, imagine you are trying to get access to a fridge. If the door is unlocked you can get in and eat but if the door is locked you can't get in. No food for you mister!
But why is this important?
Beside the fact my entire PhD is based on epigenetics......
Back to the library. We've talked before about wanting our cells to stay the way they are. No one wants a liver cell in their eye. Epiegenetics controls this. The librarians tell the readers what books they can access. They create the sections of books for different cell types and the barriers to prevent skin cells from acting like stomach cells (you'd excrete a lot of acid and mucus from your arms...gross). They also control how many times you can access the book - if you want a book to only be read once or all the time (house keeping genes) and how many copies of the book you take out. This is important for many diseases especially for cancer. In each cell you have two copies of a gene. Usually you only need one copy to be functional to live. But if your cells decide to express both copies this could lead to massive changes in the growth of the cell. For example, there is a gene called IGF2 which is important in growth and development. But we only want ONE copy of this gene. Two copies would be like super sizing all your meals. You are going to get very fat very quickly. IGF2 is one of these "oncogenes" I mentioned earlier. Loss of epigenetic marks around the second copy of this gene can lead to massive increases in tumour cell growth.
Cancer is a very clever reader and can trick librarians. It can cause librarians to be distracted, allowing the cancer cell access to genes it shouldn't be allowed near (this can be loss of DNA methylation or hypomethylation) OR it can make the librarians super strict and shut down access to genes a normal cell would have access to (this can be gain of methylation or hypermethylation). Hypomethylation tends to happen to genes that will help cancer cells while hypermethylation tends to happen to genes that will hinder cancer cells.
There are other areas of epigenetics I haven't covered, like microRNAs and also the other roles of epigenetic modifications besides gene expression control. For now this is just a brief introduction to get you familiar with the basic ideas of epigenetics. If you have any questions or want more detail please don't hesitate to contact me!!
World Cancer Day 4th Feb 2017
Today is World Cancer Day. It's a day to remember those who have lost their lives to cancer but also to celebrate their lives and the lives of those who have survived. Cancer sadly affects us all, either directly or indirectly, and we have all lost someone we know. But we do know people who have beaten cancer and come out survivors in the end. I started my career in cancer research back in my undergraduate at the same time when someone very close to me was diagnosed with breast cancer. She is like a second mother to me and hearing of her illness was devastating. But she fought tooth and nail and came out a survivor. Her perseverance and bravery have always been an inspiration to me. I think of her when I find my own work weighing me down. I remember what I do is for her and the thousands of women and men suffering with breast cancer. Remembering her bravery keeps me brave.
Today is also a day to raise awareness. Prevention is key in reducing cancer cases. There are many preventative steps we can all take to ensure we don't get cancer or help diagnose cancer earlier. Health and lifestyle factors (known as risk factors) influence the chances of developing cancer a lot. And we can reduce this influence by changing small habits. The most common campaigns ask us to reduce our alcohol intake and stop smoking (all very important steps which I encourage). It is also important to keep an eye on what we eat and exercise more, a balanced, healthy diet and 3 hours exercise over at least three days (i.e. 30 minutes 6 days a week). We also want to keep an eye on our bodies, get to know what's normal for us so we can spot when something isn't normal. For women regular smear tests, mammograms and breast checks (and men). For men, regularly checking for testicular lumps and prostate exams. And for everyone keeping an eye on your organs and bodily functions (such as your bowel movements, indigestion, coughing and moles/skin abnormalities - http://www.cancerresearchuk.org/about-cancer/cancer-symptoms).
By being more aware of ourselves and the steps we can take to detect cancer early we can together reduce cancer diagnosis and beat cancer before it begins.
The Unity Band is a symbol of our united front against cancer and a pledge to help beat cancer sooner. I helped sell some Unity Bands yesterday (3rd Feb) in Shepherd's Bush Underground Station. I was there as a scientist to do a "taste test" demo with the public to show how important personalised medicine is to cancer diagnosis and treatment. The demo was devised by research engagement officers and scientists working with CRUK. While we are all the same species we don't all look the same and there are subtle differences between us. Tumours are the same. While they all might be located in one area, for example the breast, they are not all the same tumour and don't act the same way. This can make treatment challenging. Personalised medicine focuses on these small differences and tries to tailor treatment for the individual rather than the masses.
For me, I spent my World Cancer Day in work doing what I do best. I hope that my small contribution to cancer research may help someone beat cancer sooner.
Experiments 101 - Cell Culture
Cell Culture, also known as tissue culture or TC, is where the majority of experiments start. A lot of cancer research depends on what we call “models”. The drugs, therapies, interventions etc. we test can be very harmful to humans. It’s also very difficult to watch cancer progression in someone already suffering. You use models such as “cell models” and “animal models” to mimic the human body. It’s not always perfect, but it’s better than giving a highly toxic drug to someone on a hunch it might work. The first stage of model testing is "cell modelling". If the results are promising, you move on to "animal models" or if there is good indication of the safety it may move straight to humans.
What are “Cell Models”?
Cell models are cells from tumours which are grown indefinitely outside of the body and are experimented on. “Cell line” is the name given to these cells. Cell lines come from actual people. The most famous is the HeLa cell line, which came from an African-America woman, Henrietta Lacks, with cervical cancer in the 1950’s and 1960’s (for more information you can read the book “The Immortal Lives of Henrietta Lacks” by Rebecca Skloot, which is very good - not sponsored just enjoyed the book). Cancer has a very unique characteristic which makes it hell to get rid of. Cancer cells are immortal. Like a vampire (though not as sensitive to sunlight) cancer cells cannot die. They will continue to grow and multiply as long as there is a steady blood supply (very like vampires so). Why blood? Blood carries food and oxygen all around your body and removes all the bad stuff from your organs such as toxins and carbon dioxide.
But back to cell lines. When a tumour is taken from the body you can isolate individual cells. You grow them and if they keep growing they’re known as a cell line. The vast majority of cells from tumours from a person cannot make a cell line. It’s like a lottery to which will survive.
Cell lines are named after the person they come from (like Henrietta Lacks) or from the institution they were isolated in. The most common breast cancer cell line is MCF7. MCF stands for the institute where it was “made” – The Michigan Cancer Foundation. 7 stands for the 7th attempt (the successful attempt) to “make” the cell line. The cells were from the mammary tumour of 69-yr old Frances Mallon, a nun in the convent of the Immaculate Heart of Mary in Michigan. This cell line is a model for oestrogen receptor (ER) positive breast cancer. ER+ is one of the most common mutations in certain breast cancers.
What are 2D and 3D “Cell Models”?
As you can see in the pictures, cells typically grow in 2 dimensions, i.e. they sit flat on the plastic and grow side by side. But you are not flat! You are in 3 dimensions. 2D culture is very easy, it’s cheap and it’s (relatively) fast. But if cancer has taught us anything it’s that they constantly mutate. When cells grow constantly in 2D they start to lose the ability to do certain things they would normally do in your body, for example the way they attach to each other. This is where 3 dimensional culture comes in. 3D culture allows the cells to attach to each other, typically in a ball or sphere (see pictures). These “spheroids” more closely resemble the body, giving researchers a better idea of what’s happening. The only problem is 3D culture takes A LOT of time, skill and patience. It is in fact very difficult and is not done in standard experiments yet.
One final thing about cell culture, which anyone who has ever done it will attest to. Cell culture is back breaking. Because these cells are so important but also because they themselves can contaminate other cells very easily, you entire work is kept sterile. You are in a hood (see pictures) with a constant stream of filtered air. You can’t put lids etc. down so your arms are constantly in the air (not really able to rest on the hood) and you can only open the window a small amount, meaning a lot of awkward stretching. You could be in cell culture for hours and hours slogging through 3 to 4 different cell lines and making up lots of different experiments. And usually this is almost every day. But you cannot leave it, even for a day. These annoying little cells are the fulcrum around which your experiments are based.
It’s odd to think about wanting to keep such deadly cells “healthy” and “happy” when all you want to do in the body is destroy them. But to destroy something like cancer you have to understand it, so I’ll keep the little feckers happy if it means keeping a human healthy.
My name is Caitriona and I am a PhD student at Imperial College London, UK.