OHSU researchers use breakthrough “barcode” method to improve gene therapy

Gene therapy holds the promise of curing many diseases—but this promise has been thwarted by the steep technical challenge of delivering new genes into cells. One potential solution to this challenge is to use adeno-associated virus (AAV), which is an ideal vector because it does not cause disease in humans. Despite AAV’s many advantages, however, currently available AAV vectors can be used only in limited cases because engineering the viral capsid, or shell, has been painstaking and burdensome.

That process may be about to change. In a paper published Friday, January 17 in Nature Communications, OHSU researchers in the lab of Hiroyuki Nakai, M.D., Ph.D., associate professor of Molecular and Medical Genetics, describe a new technique with the potential to significantly broaden the spectrum of diseases that can be treated with gene therapy. The new method takes advantage of next-generation DNA sequencing technology and is similar to the idea behind the barcode technology used in retail stores.

The researchers incorporated a unique DNA barcode into each mutant virus, mixed all of the mutant viruses into a library, and analyzed them at the same time by reading their barcodes. Because of high-throughput DNA-sequencing technology, the researchers were able to collect biological information from hundreds of mutant viruses in multiple samples at a time. By applying this new method to large sets of engineered mutant AAVs, they showed the new method has potential to reveal clues on how to create a vector that is more desirable for human gene therapy applications.

“The initial whole-human genome sequencing of one person took more than 10 years and cost hundreds of millions of dollars, but now we are able to do the same thing in a week using next-generation sequencing, “ said Dr. Nakai, “The same applies to our method. A study that would take many years if we used the previously available methods can be done in a much shorter period of time at much cheaper cost using our method.”

Kei Adachi, Ph.D., a postdoctoral fellow in Dr. Nakai’s Lab, is first author on the study. Other collaborators include Tatsuji Enoki and Yasuhiro Kawano from Takara Bio Inc., and Michael Veraz, a graduate student at OHSU.

This research was funded by a Public Health Service grant (R01 DK078388) and a Sponsored Research Fund from Takara Bio Inc., and in part by the National Institutes of Health through resources provided by the National Resource for Biomedical Supercomputing (P41 RR06009), which is part of the Pittsburgh Supercomputing Center.

Image caption: An Illustration of barcoded adeno-associated virus (AAV) mutant library. Each mutant viral shell is labeled by a DNA barcode, a unique short DNA sequence incorporated into the viral genome within the shell. Biological information of each viral shell in a large mixture of viruses can be collected by reading millions of barcodes using the next generation DNA sequencing technology.

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Comments

  1. Will this technology be able to be applied to supposed “healthy” cells that may be prone to cancer? It seems like this might be an excellent way to track and study cause and progression of certain cancer cells.

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