Janice Chen is a recent PhD graduate in Molecular and Cell Biology from the University of California, Berkeley. She is the co-founder and Chief Research Officer at Mammoth Biosciences, a biotechnology company harnessing a revolutionary gene-editing tool called CRISPR – used for rapid and affordable disease detection.
CRISPR is a tool that has revolutionized the field of gene editing and is now gaining terrain outside the lab with the aim of detecting diseases through a non-invasive procedure, a revolution in its own right.
Below is the full text of her TEDx Talk titled “Could CRISPR Democratise Diagnostics?” at TEDxCERN conference.
For the past two days, you’ve been dealing with a sore throat and you just feel miserable.
Over the weekend, you develop a fever and cough and you feel too weak to even get out of bed. It’s like the worst cold you’ve ever had
You search online for a possible diagnosis and think that you might have the flu, but your symptoms also suggest a possible bacterial infection.
You decide it’s worth visiting a doctor, but because it’s the weekend, your only option is to visit the emergency services.
After an hour in the waiting room, a doctor finally examines you and sticks a swab up your nose for a flu test. She later confirms that you test positive for the flu, and sends you home with medication and instructions to rest and drink plenty of fluids.
You’re completely exhausted after the trip and hope that you didn’t spread the virus to others along the way.
What if, instead, you could directly and accurately test for the flu at home?
What if you received the prescription and treatment plan without having to step foot into a clinic? And what if the same principle could be applied to other dangerous diseases, such as Ebola or even cancer?
Today I am going to talk about a revolution in diagnostics. It involves a tool called CRISPR.
You might know CRISPR as modern genome-editing technology, but the process of CRISPR has actually existed in nature for millions of years to protect bacteria against viruses.
Bacteria, like humans, have evolved their own immune system to defend against viral infections.
Scientists eventually realized that the CRISPR immune response uses a cutting protein called Cas and an RNA molecule that guides the Cas protein to matching DNA sequence from the invading virus.
Once a Cas protein finds its target, it turns into a pair of molecular scissors small enough to fit inside a bacterium and slices apart the invader. Once it’s cut, the virus is dead and can’t harm the bacterium any longer.
In 2012, researchers from the lab of Jennifer Doudna, my former PhD adviser, were able to extract CRISPR out of bacteria and reprogram the guide RNA to target any DNA sequence. This was revolutionary.
When this kind of precision cutting is brought into a plant or animal, we can fix any faulty genes or enhance others. In short, we can rewrite the genome.
For the past six years, we’ve learned how CRISPR can help us write our genes, but today, I’m going to talk about a completely new application of CRISPR that has nothing to do with genome editing.
Last year, my colleagues and I discovered that CRISPR can also be used to help us rapidly and inexpensively read our DNA. This unexpected finding led us to reinvent CRISPR as a next-generation diagnostic.
During my time at the Doudna Lab, I wanted to understand how CRISPR proteins cut DNA. I like to imagine these tiny molecular machines made up of two macromolecules: protein and RNA.
If we zoom in further, we can break them up into their building blocks of amino acids and ribonucleotides. As a biochemist, I love being able to test this system by swapping out amino acids, tweaking ribonucleotides, and even removing entire pieces of the CRISPR protein.
It’s like solving a puzzle that nature created to help us understand how CRISPR makes a precise cut in the target DNA.
CRISPR is also like a family. There are some proteins that are closely related and others that are distant cousins.
While putting the pieces together, we unexpectedly discovered that a young member of the CRISPR family didn’t behave exactly like a pair of molecular scissors.
Whereas the older cousin, named Cas9, made a single cut in the target DNA, the younger teenager, named Cas12, misbehaved like a molecular paper shredder. Once it’s switched on, Cas12 will grab all the papers and shreds through documents regardless of their text.
Now, the cool thing about this behavior is it allows CRISPR to send a report of a target DNA in real time.
It works like this. Imagine a molecular firecracker. When Cas12 finds a match, it lights a fuse that begins to degrade until the firecracker ignites, generating a signal activated by the match. If there are any problems with the match, or if there’s no match at all, Cas12 won’t light the firecracker.
In other words, we can simply design the guide RNA to target any DNA sequence. This can be a sequence from bacteria or virus, or even a disease mutation within our own cells.
Cas12 and its programmed guide RNA will search through billions of letters to find that matching DNA target, and once it does, Cas12 starts cutting and doesn’t stop.
But we can take advantage of this activity by throwing in that molecular firecracker that gets ignited by Cas12, generating a colorful explosion indicating that the target is present.
Since its discovery in 2015, Cas12 had originally been used as a genome-editing tool, and its diagnostic ability went unnoticed for several years.
To convince ourselves and others that CRISPR diagnostics was more than just about chemical concepts, we had to first program Cas12 to detect the presence of human papillomavirus, or HPV, a common viral infection that can also cause cancer.
Getting tested every three years can also significantly reduce the risk of developing cervical cancer, but cervical cancer currently requires a Pap smear that takes place in a doctor’s office.
We imagined how a more accessible HPV test could reduce the barriers to screening. In order to move closer to that goal, we had to show that CRISPR worked in the real world.
The first test was to design Cas12 to detect specific cancer-causing HPV types in patient samples. We received blinded samples so that our results cannot be influenced.
And after comparing our results to a conventional HPV test, we were so excited to see that our CRISPR-based HPV diagnostic had almost perfect accuracy. The whole process, from start to finish, took less than an hour and only cost us pennies for a single reaction.
Since our initial discovery, we have found that Cas12 can search through fluids, such as saliva, blood or even urine, for a specific DNA match. Like a biological search engine that reads DNA quickly and accurately, CRISPR is gaining a new voice in diagnostics.
We can simply type in a query by altering the letters in the guide RNA, and the CRISPR search engine will generate a real-time report of any targets that are found.
We are only beginning to understand its potential, but are the first to take the groundbreaking steps in order to harness the power of CRISPR for DNA and RNA detection.
So, what are the possibilities of this technology?
Here are two more examples where CRISPR diagnostics can make an impact.
In 2014, West Africa experienced one of the largest and most complex Ebola outbreaks, with over 11,000 deaths in just two years. As a healthcare worker in Liberia, you are intimately aware of the precautions that need to be taken for Ebola.
One day, a patient arrives into your clinic with a fever and headache and sore throat, and everyone is instructed to wear protective equipment.