A team of scientists has developed new nanomapping technology that could transform the way disease-causing genetic mutations are diagnosed and discovered.
Described in a study that included NYU Professor Bud Mishra and published in the journal Nature Communications, this novel approach uses high-speed atomic force microscopy (AFM) combined with a CRISPR-based chemical barcoding technique to map DNA, complementing DNA sequencing while processing large sections of the genome at a much faster rate.
The work was led by Virginia Commonwealth University physicist Jason Reed.
The human genome is made up of billions of DNA base pairs. Unraveled, it stretches to a length of nearly six feet long. When cells divide, they must make a copy of their DNA for the new cell. However, sometimes various sections of the DNA are copied incorrectly or pasted together at the wrong location, leading to genetic mutations that cause diseases such as cancer.
DNA sequencing is so precise that it can analyze individual base pairs of DNA. But in order to analyze large sections of the genome to find genetic mutations, technicians must determine millions of tiny sequences and then piece them together with computer software. In contrast, biomedical imaging techniques such as fluorescence in situ hybridization (FISH) can only analyze DNA at a resolution of several hundred thousand base pairs.
Reed’s new high-speed AFM method can map DNA to a resolution of tens of base pairs while creating images up to a million base pairs in size. And it does it using a fraction of the amount of specimen required for DNA sequencing.
“DNA sequencing is a powerful tool, but it is still quite expensive and has several technological and functional limitations that make it difficult to map large areas of the genome efficiently and accurately,” says Reed. “Our approach bridges the gap between DNA sequencing and other physical mapping techniques that lack resolution. It can be used as a stand-alone method or it can complement DNA sequencing by reducing complexity and error when piecing together the small bits of genome analyzed during the sequencing process.”
“The new technology makes it feasible to combine it with next generation sequencing technology to correct the human draft genomes and, more broadly, enhance the efficiency while lowering the cost of this process,” explains Mishra, a professor at NYU’s Courant Institute of Mathematical Sciences.
A co-inventor of optical mapping, a genomic technique for large-scale projects, Mishra adds that “nano-mapping seems to be at a Goldilocks tipping point: not too slow, not too short, not too buggy, not too expensive, and not too computationally intensive. We plan to work further with Reed and others to exploit these features of nano-mapping to make it widely applicable.”
In order to actually identify genetic mutations in DNA, the researchers had to develop a way to place markers or labels on the surface of the DNA molecules so they could recognize patterns and irregularities. A chemical barcoding solution was developed using a form of CRISPR technology.
CRISPR has made a lot of headlines recently in regard to gene editing. CRISPR is an enzyme that scientists have been able to “program” using targeting RNA in order to cut DNA at precise locations that the cell then repairs on its own. Reed’s team altered the chemical reaction conditions of the CRISPR enzyme so that it only sticks to the DNA and does not actually cut it.
“Because the CRISPR enzyme is a protein that’s physically bigger than the DNA molecule, it’s perfect for this barcoding application,” says Reed. “We were amazed to discover this method is nearly 90 percent efficient at bonding to the DNA molecules. And because it’s easy to see the CRISPR proteins, you can spot genetic mutations among the patterns in DNA.”
To demonstrate the technique’s effectiveness, the researchers mapped genetic translocations present in lymph node biopsies of lymphoma patients. Translocations occur when one section of the DNA gets copied and pasted to the wrong place in the genome. They are especially prevalent in blood cancers such as lymphoma but occur in other cancers as well.
While there are many potential uses for this technology, Reed and his team are focusing on medical applications. They are currently developing software based on existing algorithms that can analyze patterns in sections of DNA up to and over a million base pairs in size. Once completed, it would not be hard to imagine this shoe-box-sized instrument in pathology labs assisting in the diagnosis and treatment of diseases linked to genetic mutations.
This study was supported by National Institutes of Health grants R01GM094388 and R01CA185189, the National Cancer Institute (5U54CA193313-03), and, in part, by VCU Massey Cancer Center’s National Cancer Institute Support Grant P30CA016059.