Nanopore sequencing: how bacterial proteins led to user-friendly DNA analysis devices
Nanopore sequencing: how bacterial proteins led to user-friendly DNA analysis devices
What if your general practitioner could analyze your DNA to instantly identify your illness and the most appropriate treatment? Soon, this will no longer be science fiction, thanks to VIB-VUB professor Han Remaut's contributions to groundbreaking DNA sequencing technology. By describing the structure of a bacterial protein with highly useful structural features, Remaut and his lab helped bring nanopore sequencing technology to a new level.
"About fifteen years ago, during my post-doctoral years at Birkbeck College in the UK, I became intrigued by the mysterious behaviour of protein transport across bacterial cell surfaces," explains Remaut. "When I joined VIB in 2009, we didn't yet have specific applications in mind, but the pervasive scientific enigma of curli - extracellular bacterial fibres with unique structural characteristics - was clear. Today, the nanopore sequencing technology based on our groundwork contributes to the battle against COVID-19 and has a bright future, not only in medicine but also in domains like ecology and forensic science.
"This story is a beautiful example of what can be achieved with what we call 'blue skies research' – basic research at the front of scientific knowledge without immediately apparent applications. When investigating natural phenomena that defy our current knowledge, you're bound to uncover new breakthroughs with applications in biotechnology and beyond."
The innovator
The human genome exposed
Nanopore sequencing technology leads DNA strands through proteins peppered with tiny holes called nanopores. The nucleotides (DNA components) of the strands cause minor variations in the electric currents that pass through the nanopore. By measuring these variations, the genetic sequence of the DNA strands can be determined, offering a wealth of information about the human genome, on the spot and in real time. VIB's Remaut lab made an important breakthrough in the development of nanopore sequencing technology by resolving the structure of CsgG, a bacterial pore protein with unique characteristics.
Remaut: "The structural composition of CsgG – a protein channel with a well-defined constriction – allows stable currents that can generate superior quality data compared to other nanopore sensors. Not long after publishing our findings in Nature magazine in 2014, we teamed up with British biotech company Oxford Nanopore Technologies (ONT). They finetuned the structure of the CsgG nanopore to integrate it into cutting-edge electronic sensing devices that can simply be inserted into computers through a USB port. The discovery went from publication to commercial rollout in less than two years, which is extremely fast."
Meanwhile, Remaut and ONT have been investigating an advanced nanopore to enhance the accuracy of these sensing devices. Remaut: "We engineered a natural binding partner of CsgG to introduce a dual constriction in the nanopore. Having two constrictions capable of identifying DNA components simultaneously enables us to interpret DNA strands in regions where a single reader still made occasional errors."
Mobile water clinics, humpback whale slime and COVID-19
DNA sequencing has led to many breakthroughs in the 21st century, from the fast development of cancer treatments adapted to each patient's genetic profile, to the identification of thousands of new hereditary diseases and a growing awareness that our intestinal flora plays a crucial role in diseases such as obesity and Alzheimer’s. Nanopore sequencers have accelerated this process and are now being used all over the world, offering advantages in a wide range of research domains.
One exciting project is the launch of 'mobile water clinics' in Africa. Using ONT devices, the water quality in remote water wells can be tested on a regular basis to see if the water contains the DNA of pathogens such as Ebola, diphtheria, salmonella, or cholera. The ability to do that on site using small hand-held devices puts an end to the need to transport research samples hundreds of kilometers to the nearest lab.
Other striking applications are the search for DNA-containing life on Mars, or the analysis of humpback whale slime collected by a drone flying over the animal's blowhole, enabling scientists to monitor the whale population's health and measure the impact of climate change.
The nanopore technology has also proved very useful in the fight against COVID-19. A few months after the outbreak of the coronavirus, ONT launched a new, low-cost test called LamPORE destined for the British market. The detection assay incorporates VIB's nanopore technology and is designed for rapid, on-site testing – results are available in less than two hours (read the origin story about COVID-19).
Accurate diagnosis and personalized treatment
According to Remaut, nanopore sequencers will soon be everywhere: "I'm convinced that a DNA sequencing device will be found in every doctor’s office within five to ten years. When a patient comes by with a respiratory infection, the doctor will immediately be able to detect which bacterium or virus is causing the illness by testing a saliva sample with the device plugged into their computer. It will even be possible to verify which antibiotics bacteria are resistant to, and which ones can help the patient recover."
Proof of the technology's success can also be found in ONT's imminent entry into the London Stock Exchange. The company has already raised over half a billion pounds and its value has recently been estimated at 2.5 billion pounds. The recent breakthroughs are only the beginning of this high-impact story.
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