Gene Therapy in Dogs & Random Number Generator Made from DNA
By: Niko Mccarty
Tags: Newsletter, News, Science, Tech, Biotechnology

NEWSLETTER

Gene Therapy in Dogs & Random Number Generator Made from DNA

This Week in Synthetic Biology (Issue #16)

Annie Spratt on Unsplash.

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A Gene Therapy, Tested on Dogs, Has Issues

For CRISPR-based gene therapies to work, you first need to squeeze a Cas protein and guide RNAs into a teeny tiny virus. Then, that packaged virus — bearing its gene-editing payload — has to be inserted into the body.

The most common “delivery vehicle” for gene therapies are AAVs, or adeno-associated viruses. Long considered to be extremely safe, a new study, the most in-depth of its kind, is shedding new light on their long-term efficacy.

Researchers injected nine dogs with hemophilia A, a type of bleeding disorder, with an AAV “payload”. Then, they followed the dogs over a period of ten years. The gene therapy was extremely effective. The nine treated dogs, together, only had seven bleeding episodes during the study period. Eleven untreated dogs with hemophilia, by comparison, had about twelve bleeding episodes each — every single year.

Still, the researchers found that, in the livers of six of the treated dogs, 1,741 AAV integration events had occurred. That means that viral genetic material is being inserted into genomic DNA, often near very important genes. Dr. Charles Venditti, writing on this study for Nature Biotechnology, commented that these “results increase concerns about the long-term safety of AAV gene therapy,” but also called for more long-term studies and generally praised the work. This study was published in Nature Biotechnology. Link

Random Number Generator, Made from DNA

Chemists have been synthesizing custom DNA sequences for decades. Now, with the technology reaching relative maturity — and with costs plummeting — DNA is considered a viable means to store data.

But for DNA-based storage to compete with normal hard drives, researchers need to find ways to encrypt the data stored in nucleic acids. A new study solves part of the problem, using the inherent stochasticity of DNA synthesis to create massive collections of truly random numbers. The authors argue that, by finding a means to create a large volume of random numbers, those looking to develop DNA hard drives could “guarantee security of encryption and decryption schemes for exchanging sensitive information…”

To create the random sequences, the researchers combined all four nucleotides — A,T,C,G — into a single reaction vessel and allowed the DNA strand to grow. When each strand reached a specified length, it was cleaved from the reaction chamber. Using this approach, they managed to “obtain 7 million GB of randomness from one synthesis run, which can be read out using state-of-the-art sequencing technologies at rates of [about] 300 kB/s.” This study was published in Nature Communications and is open access. Link

A Protocol for Evolution Overdrive

In 2011, a paper in Nature disclosed a method to continuously evolve biomolecules, in the laboratory, using phages (a type of virus that infects bacteria). Since that initial study, the method, called PACE — phage-assisted continuous evolution — has vastly improved. Now, instead of waiting thousands of years for a protein to evolve a new function, PACE can be used to iterate through hundreds of rounds of evolutionary selection in a few weeks.

A new paper in Nature Protocols offers an in-depth set of procedures to perform PACE (and its cousin, PANCE) experiments in the laboratory. The researchers write that their “protocol can be performed in as little as 2 weeks to complete more than 100 rounds of evolution (complete cycles of mutation, selection and replication)…” If you’re interested in adopting continuous evolution in your research group — or garage, maybe (?) — then this paper will prove useful. I suggest taking a look at David Liu’s tweet for more details. Link

CRISPR + Lipids = Cancer Gene Therapy

CRISPR-Cas9, delivered to tumors, have a pretty low genetic editing efficiency. Now, an open access study in Science Advances reports that a specific type of lipid, packaged with Cas9 mRNA and guide RNAs and injected into the brains of mice with glioblastoma, “enabled up to ~70% gene editing in vivo, which caused tumor cell apoptosis, inhibited tumor growth by 50%, and improved survival by 30%.” That’s a big improvement over some prior efforts to reduce tumor sizes with CRISPR therapies in mice. The researchers also demonstrated that the injections caused “no apparent clinical signs of toxicity,” unlike other methods for gene delivery. Link

A “Hidden” Carbon Fixation Pathway Found in E. coli

To build all the myriad molecules and structures needed for life, organisms need carbon. Plants “fix” carbon by capturing carbon dioxide in the air, and converting it into organic compounds and sugars. Animals and many bacteria, however, are heterotrophs — to survive, they need to hunt down and feed on organic compounds.

In a new study, researchers used only the genes found naturally in an E. coli bacterium to create a carbon fixation pathway.

They first identified several possible pathways for carbon fixation in E. coli and decided to experimentally implement the pathway that happened to be the shortest, which they called the GED (Gnd-Entner-Doudoroff) cycle. Then, they deleted genes to “shunt” metabolites through that specific pathway, essentially forcing the E. coli cells to use it. The team demonstrated that carbon fixation via this pathway is not only possible, but could “provide (almost) all biomass building blocks and cellular energy…” This study is open access and was published in Nature Communications. Link