Hacking Genomes Using CRISPR

by Raed Hmadi, Alina Jeschke, Mayank Chugh & Vinodh Ilangovan

Imagine living in a world where you could change the pattern and colour of your dog’s coat simply by feeding him a special diet. Or, imagine changing your eye or hair colour to match the latest trends. A cosmos where humanity thrives for perfection by contributing offspring with desired traits and characteristics achieved via genetic manipulation. Such fantasy may not be too far!

Scientists and engineers have been able to transform yeast into ethanol, thereby producing machines which promise a renewable future by altering DNA. Researchers in China have already tried their hand at altering human embryos. Gene editing today is easier, faster, and cheaper than it ever was thanks to the sweat and determination of hundreds of scientists across the globe. CRISPR/Cas9 is the new genome editing technique that everyone is talking about and has been a subject of ruthless legal and ethical debates. Let us discover together what makes CRISPR/Cas9 such a hot affair.

Decades after the structure of DNA was unveiled and DNA sequencing was realised as an emergent milestone, a large number of researchers began searching for the origin of life by sequencing full genomes of bacteria and other primitive microbes. These microbiologists noticed iterative sequences in bacterial and microbial DNA that read the same backwards and forwards – palindromes - and labelled them as clustered regularly interspaced short palindromic repeats (CRISPR). In 2007, CRISPR sequences were demonstrated to function in adaptive immune systems in bacteria. Bacteria may also be infected with viruses, like other living creatures. Upon viral invasion, a bacterium neatly chops segments of viral DNA and incorporates them into its own genomic DNA, within these CRISPR palindromic repeats. This serves as an immunological memory for the bacteria to fight back in case it encounters the same virus again.

This discovery ignited curiosities worldwide because a unicellular organism had the power to edit genomes, and geneticists decided to explore system in depth. The combined efforts of Emmanuelle Charpentier (Max Planck Institute for Infection Biology) and Jennifer Doudna (University of California, Berkeley) revealed that CRISPR makes two strands of RNA and a corresponding protein called Cas9. The RNA strands are then activated and serve as “GPS” directions to viral DNA. Together with Cas9, these RNA strands hunt for a complementary site of 2 to 6 base pairs in the viral genome. After reaching the new “home” site, Cas9 starts gripping and snipping the viral DNA.

Inspired by this work, scientists were able to tweak the natural CRISPR potential and harness its powers to cut, copy, and replace any piece of DNA. For genome editing, the system requires two components: a guiding RNA molecule and a slicing enzyme, or Cas9. The guide RNA molecule directs the Cas9 enzyme to the target of interest in the genome, where the latter will edit and repair specific sequences with the genetic information of interest. The system can be easily administered to specific cells found within a myriad of organisms; such as, yeast, flies, mice, and plants. This system also works on cells that have been cultured in the lab. The first demonstration of the fundamentals and potential of the CRISPR system were revealed in a landmark research article published in June 2012 (http://science.sciencemag.org/content/337/6096/816). In 2013, genome editing via CRISPR in mouse and human cells by Feng Zhang (Broad Institute of MIT and Harvard) practically testified its colossal capability. From that moment onward, the rolling CRISPR snowball has gotten bigger and fiercer, as legal battles have arose between the University of California, Berkeley, Harvard University, the Massachusetts Institute of Technology (MIT), and the Broad Institute. The latest update from the U.S. Patent and Trademark Office granted a series of patents to the Broad Institute and Harvard University. On the other hand, the European Patent Office decided to grant the patents to the University of California instead.

Mechanistic principles and lawful battles apart, how is this DNA editing going to shape the world? This question has been lingering in all of our minds. Are researchers in the field cautious with their experiments and outcomes, or blindly excited? For example, there are research groups that are ‘CRISPRing’ the gene drivers in mosquitoes to suppress their populations to a level that does not support malarial transmission. This is serious work because any escapees from the lab could mate with the natural species, mutating the progenies, or wiping them out completely. However, the precautionary measures in such studies have been high and rigid. In April 2015, Chinese scientists published a study where they have tested the fidelity and efficiency of the CRISPR/Cas9 system in human embryos, aiming to target the gene that is mutated in people suffering from beta thalassemia, a potentially fatal blood disorder. The work was unsuccessful as the embryos were defective and CRISPR did not target embryonic genes with similar efficacy as it does in isolated cells. Nevertheless, the work sparked fears, grabbed attention worldwide, and led to a relaxation in the permissible codes in clinical trials by the US National Academy of Sciences. In fact, the genetic modifications for diseases such as HIV and leukemia are already underway in patient’s non-reproductive cells.

At this stage, it remains undisputed among the scientific community that the CRISPR/Cas9 technology is a powerful and versatile tool to understand several elusive biological processes in an experimentally safe situation. Its successful clinical usage is great, yet it is a slippery slope towards unethical use or germline transmissions affecting future generations. In the end, any scientific discovery has the potential to be used for good and bad. Hence we should view CRISPR/Cas9 with caution and monitor its ability to treat diseases.