Thursday, April 23, 2015

The Next Revolution in Genetics

Scientific research often moves incrementally. An observation made, a paper published, results repeated and/or expanded upon, a new discovery made. Wash...Rinse....Repeat. In fact, a majority of scientific research occurs this way. Laboratories across the world contribute snippets to a particular story of which only years later everyone can look back at and see the multiple-layers and colors and contributions that now make up a rich tapestry. Research in cancer, aging, development, neuroscience, physics, chemistry, etc. is done in this way.

But sometimes the ground literally shakes.

Sir Isaac Newton's Theory of Gravity revolutionized not only mathematics but how we think and interact with the world. Then Albert Einstein decided to be all genius-like and published his papers on relativity. He single-handily destroyed the accepted concepts of physics that Newton built and to this day physicists are still confirming and visualizing Einstein's theories and ideas. This is remarkable in several ways. First, Einstein postulated his theories without the aid of calculators or computers. He used very complex mathematics and science to predict astronomical phenomena that scientists are still confirming with the aid of super computers, particle colliders, and the most powerful telescopes in the world. Not only will Einstein's name live on indefinitely, but his work is truly a shining example of the scientific method at its most basic level. He predicted and now his work is still being confirmed.

The discovery of penicillin revolutionized medicine and contributed to the global increase in human lifespan. When the structure of DNA was elucidated the world of genetic research took off and molecular biology was born.

These are all examples of events that shook the scientific world; much like the atomic bomb changed the course of human history, or when the Berlin Wall fell, or how the events of September 11th have ushered in a new era of American fear, surveillance, and Islamophobia. All of us were alive during the events of 9/11. I remember exactly where I was when I first heard the news that one of the towers in NYC had been hit by a plane. I watched live when another passenger jet struck the second tower. I couldn't help but wonder what the world would be like the next day. Sometimes discoveries in science can alter the world in far-reaching ways as well, for both good and bad.

One of those seismic events in the scientific world occurred in the 1980's; a ground-breaking discovery that in the span of a few years has literally shaped and changed how every laboratory in the world performs molecular biology. And when I say literally  I'm not being hyperbolic. This technique is so widely used that it is often over-looked by scientists because it is so routine. But to this day I can't think of another technique (other than the one I'm going to introduce below) that has so revolutionized the way biomedical research is conducted it has changed the world. 

So what am I talking about? What was discovered in the 1980's and is so important? Now for a quick history lesson in science. The technique discovered in the 1980's is called Polymerase Chain Reaction (PCR). It was invented by Dr. Kerry Mullis, for which he won the Nobel Prize. PCR is a technique used by biologists to study any gene in any organism. Mullis used bacterial proteins and designed PCR to generate copies of DNA. You can think of PCR technology as a molecular photocopier. Any DNA region of interest can be copied thousands of times over, such that even with small starting amounts of DNA a specific gene can be targeted and amplified to high abundance so there is enough starting material to work with and study. This method changed molecular biology and medicine as we know it. And in case you are thinking to yourself: a molecular photocopier? Who gives a shit?! Well you should give two shits, plus another next Tuesday. Because whether or not you know it PCR has affected your life in someway. 

Have you ever been on trial for murder? Probably not, but PCR is used to amplify DNA found in blood from a crime scene.

Ever needed a paternity test? PCR would have been used.


Ever been genetically tested for cancer gene mutations? Or for genealogy purposes? PCR was used.

Ever eaten a GMO food? PCR was used to create it. 

Ever taken an antibiotic, insulin , or a host of other medications? PCR contributed in the creation of a majority of them. 

The creation of new cancer therapies, vaccines, studies of human evolution and population epidemiology, smoking behavior studies, neurological tests....all examples of fields of study and research that have made use of PCR technology. 

So needless to say, PCR changed A LOT and in a small amount of time. But there are limits to PCR technology. For example PCR is generally conducted in a test tube and the amplified DNA can only be studied or manipulated for a particular downstream application. For example, PCR is used to study the function of a gene and is used to help mass produce insulin for diabetics.  For many scientists and doctors the next step is using this tool (and others like it) in molecular biology to make the next jump: to truly being able to cure someone of a disease or to prevent one from developing. This idea is packaged together and known as Personalized Medicine. Ideally, a doctor would be able to analyze your unique genome (and everyone is truly unique in this regard) and use that to predict what would be the best possible medication for you to use for any type of disease. Or to predict if you will develop a disease. Or perhaps to predict if you will pass that gene down to your kids.

We are still far from that point in several aspects. But in some ways we are closer than ever before. 

The new technology I want to talk about today, that is currently undergoing a unique revolution, is called CRISPR. CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats  (we don't have to worry about that name any more for this discussion). CRISPR sequences occur in bacterial genomes and are actual sequences of DNA. You can think of them as road markers or exit signs on a highway telling someone where they are on a highway.  Cas9, a protein also found in bacteria, is short for CRISPR-associated protein 9. It can bind to DNA and is guided to specific locations in the genome. Cas9 recognizes the CRISPR sequences in the bacterial genome and binds to them preferentially, as if Cas9 read the road map and knows where on the highway to drive to. This entire system was first discovered in bacteria and it is a defense mechanism that bacteria employ to protect themselves from viral infection (yes, bacteria are also susceptible to viruses). It's part of the bacterial immune system and was first discovered in 1987. Over the last two decades incremental discoveries have propelled CRISPR into the thoughts and experiments of many scientists around the world. This year however the field has exploded.

So why is CRISPR important? Because CRISPR is now in the  midst of a major revolution....one that could usher in the next gigantic advancements in genetic engineering, molecular biology, and personalized medicine. Seemingly every week a dozen new research articles are coming out in top journals describing the uses of the technology to study disease, normal development, and other important questions in medicine. Oftentimes this is very controversial, as I'll discuss in a few paragraphs.

CRISPR is a different technology than PCR. It doesn't amplify or copy DNA. Instead, CRISPR/Cas9 systems are used to make very specific changes in very specific regions of the genome. For those who don't spend their lives working on the bench, think of this system as a highly specialized DNA editing machine. CRISPR technology allows scientists to target genes, down to a single nucleotide, and change them. Just like an eraser or white-out marker used on a mispeled wrod or wrds. CRISPR/Cas9 will edit the DNA and correct the mutation (or make a mutation). This has enormous implications in biomedical research not only because this is now an unprecedented level of control in genetics, it may also allow scientists to actually correct DNA mutations in humans that cause disease.  

But herein lies the real issue with CRISPR technology and why everyone, including those outside of science, needs to at least understand why this is important. What scientists truly have in their hands right now is a game-changing tool. It is theoretically possible to make precise corrections in mutated human genes in order to have viable, healthy offspring. There is hope now for parents with genetic diseases who want to have children but don't in fear that they are passing along familial mutations that their kids will inherit. This is a step beyond what Britain legalized earlier this year in which in vitro fertilization can be used to surpass genetic mutations in the mitochondrial genome in mothers with mitochondrial diseases. CRISPR allows for the editing and correction of those genes in the cell's nucleus, where most (99%) of our genetic information is found. Several reports have already come out within the last month detailing how CRISPR has been used to make mutational changes in fruit fly egg and sperm cells and that these mutational changes are inherited in future generations of flies. This is the first proof of concept that specific changes in an animal's germ-line (i.e. sex cells) can be heritable. Additionally, just yesterday a laboratory in China published research in which they used non-viable human embryos to show that CRISPR can be used to change genetic information in human germ-line cells. (These embryos are not capable of developing into a baby.) This is the first ever published report on the use of CRISPR technology in human germ cells. A good news summary can be found here, with links to the article, and new reports indicate that several other labs in China are pursuing similar research.

The ethical issues with this technology are very important and are the main reason why I'm writing this article. While this game-changing tool will almost certainly be used to understand and combat human disease; this tool could also be used for less noble purposes. Similar to PCR, CRISPR technology is easy to use, cheap to set up, and currently unregulated in the United States by the FDA - let alone in China or Russia or many other countries. The EU does have stringent laws in place about human germ-line editing and hopefully the FDA follows this example as a starting point. There is no doubt this technology will be widely used in many, many laboratories in the next few years (like PCR) and the conversation needs to kick into high gear about the Orwellian implications that this technology could be used for. The experiments j from China have met with some technical difficulties however. Much needs to be worked out before this would ever be remotely considered for medical use in viable embryos. But to also point out, both Nature and Science would not publish this work due to the ethical considerations.  

Thankfully some of the major players in CRISPR research, including Dr. Jennifer Doudna, Dr. David Baltimore, and others, have met with scientific, legal, social, and ethical experts to discuss the implications of CRISPR research. A month ago they issued a joint statement in Science calling for a complete moratorium on CRISPR-related research in human germ line cells. Scientists do understand the implications and this technology is so new, and moving so fast, regulations need to be in place to prevent nefarious use of it.  It really is a revolution.

So what's my take on all of this? I've asked myself that question repeatedly for the last two months. At work we've held journal club discussions about these papers and I even saw Dr. Doudna present a history of CRISPR technology and its future implications at a conference at the NIH last month. (She's wickedly smart and I bet she wins a Noble Prize for her work in the field.) As a geneticist I must always be aware of what the implications of my research are going to be and that's why I'm writing this out today. *I don't use CRISPR in my research in case you are wondering* Personally, I am in complete agreement with Dr. Duodna and her collaborative warning to other scientists. CRISPR-related work in human germ line cells must stop until the broader implications have been thoroughly considered. Unfortunately, other countries may not listen to this warning, and the FDA moves so glacially slow I'm sure there are labs in the states pursuing similar types of experiments (admittedly this is just a hunch I have no actual proof of that).

But I'm also making sure I keep my eye on the bigger picture. Yes, this technology can be misused, but the idea that Mendelian and other complex diseases could be corrected and eliminated is an amazing opportunity and which needs to be explored, albeit in a controlled and safe manner. Remember, with creation of the atomic bomb we also now enjoy nuclear energy that is cheap and clean, fuel for rockets to go to Mars, and maybe someday even cold fusion!

Okay, so perhaps comparing CRISPR to the atomic bomb is a little overboard (comparing it to a laser-guided cruise missile is probably more apt). The challenge today is for scientists and non-scientists to keep this all in perspective, move forward in a safe and purposeful way, and start a conversation that puts the appropriate rules in place quickly so that we can continue to pursue novel research that benefits others. Hopefully these few paragraphs on the subject get you thinking about all of the implications as well.