The Nobel Prize in Chemistry 2020 was awarded to Emmanuelle Charpentier and Jennifer Doudna for the discovery of the CRISPR/Cas9 genetic scissors. The technology, widely used as a genetic engineering tool, enables researchers to analyse the DNA of animals, plants and microorganisms with extremely high precision, simply and quickly. It has had a revolutionary impact on the life sciences, contributing to new cancer therapies, deeper knowledge of the Parkinson’s disease and could pave the way to curing hereditary diseases.
Here, researchers of the University who apply the Nobel Prize winning CRISPR/Cas9 method in their studies explain how they use it and why it has become indispensable.
Some of the researchers of the University of Luxembourg who apply the Nobel Prize winning CRISPR/Cas9 method: Susana Martinez, Silvia Bolognin, Carole Linster, Nadège Minoungou and Maria Pacheco
The Role of the CRISPR system in microbial communities
CRISPR/Cas9 originally stems from bacteria. It is part of the bacterial immune system and cuts DNA from viruses that infect bacteria (so-called bacteriophages) into pieces, thereby disarming the virus. As part of her doctoral thesis, Susana Martinez from the Systems Ecology Group at LCSB (Luxembourg Centre for Systems Biomedicine) analysed this defense mechanism within the microbial community (the microbiome) of the activated sludge process of a wastewater treatment plant in Luxembourg.
The goal of the project was to understand what biological factors could influence the dynamics of the microbial community during the wastewater treatment process. Wastewater, more specifically foaming sludge produced during the process relies in microbes to remove organic material from the water before being released to the environment. It is important to understand what shapes the composition of the microbial communities in this sludge, to prevent undesirable species from growing, for example.
“Besides environmental factors, biological factors such as viruses that infect bacteria can play an important role in shaping microbial communities. But it is not well understood how the CRISPR-defense system of bacteria interacts with these biological factors in microbial communities,” says Martinez.
“We observed that besides bacteriophages, so viruses that infect bacteria, another type of ‘invader’ is actually highly targeted by the CRISPR/Cas system. These so-called plasmids are circular DNA molecules often found in bacteria and are known to transfer genes between hosts. This way, they also contribute to the spread of antimicrobial resistance,” Martinez adds.
Changing the way cancer research is done
At the Department of Life Sciences and Medicine of the Faculty of Science, Technology and Medicine, researchers apply the CRISPR technology to cancer research.
For instance, the work of Nadège Minoungou is devoted to liver cancer, a leading cause of cancer-related deaths. Under the supervision of Prof. Iris Behrmann, her doctoral project focuses on inflammatory signals and how they affect long non-coding RNAs (lncRNAs), a class of RNA molecules involved in many biological processes, including cancer development. One of the methods used to investigate the functional roles of the lncRNAs is a CRISPR/Cas9-mediated modulation of candidates of interest in liver cancer cells.
Using a different approach, Dr. Maria Pacheco, a postdoctoral researcher in the team of Prof. Thomas Sauter, uses CRISPR data to build more accurate metabolic models to select drug combinations that kill specific cancer cells without affecting the healthy ones.
“The discovery of the CRISPR/Cas9 editing complex has changed the way we can do research” says Behrmann. “Besides, apart from the technology itself, the two Nobel prize winners may be role models for female students and early stage researchers. There is still some way to go towards a gender equity in science”.
Creating models of Parkinson’s disease
Postdoctoral researcher Silvia Bolognin is part of the LCSB’s Developmental and Cell Biology research group, which mainly focuses on Parkinson’s disease. Bolognin aims to understand the causes of Parkinson’s disease and how it can be stopped by using models derived directly from patients’ cells. She applies the CRISPR/Cas9 method for disease modelling. It allows to identify abnormalities in cells that are due to particular mutations in cells from Parkinson’s patients. “We can take cells from a healthy individual, introduce mutations known to cause Parkinson’s of a certain gene using CRISPR/Cas9 and then study what the mutation does to the cells. Or we look at what happens when we correct a mutation of a cell, taken from a Parkinson’s patient,” Bolognin explains.
While this bears hope for treating Parkinson’s patients with the CRISPR/Cas9 method, research will need more time: “It is difficult to say at this stage if the technology can be used to treat patients. A lot of companies are working on it, but we still have to see whether it’s completely safe to use. Our group currently focuses on using CRISPR/Cas9 as a tool to see what’s wrong in diseased cells. The majority of Parkinson’s patients have no known specific mutation which directly causes the pathology so we cannot foresee a direct application at this point.”
Studying rare diseases with the genetic scissors
Biochemist Carole Linster leads the Enzymology & Metabolism Research Group at the LCSB. She conducts research on diseases that have or could have genetic causes. She works on rare diseases like Batten Disease or Zellweger syndrome, two fatal genetically determined metabolic disorders affecting newborns and children. Zellweger disease is caused by mutations in genes called PEX, which normally encode proteins exerting important cellular functions. If these proteins are not present or do not work, metabolic perturbations with fatal consequences ensue. The aim is to investigate the functions of proteins, often enzymes, that play a role in biochemical processes in metabolism. “We use CRISPR/Cas9 to make genes disappear in certain cells or in a zebrafish animal model (which are used to study human diseases), or we use it to insert mutations. This allows us to study the role of a gene or mutation in the disease,” Linster says.