Gene Therapy in Dogs & Random Number Generator Made from DNA (#16)

Plus: An experimental protocol for evolutionary overdrive.

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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 (in mice!)

CRISPR-Cas9, delivered to tumors, is pretty inefficient. But 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, often from other creatures.

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 experimentally implemented one of them—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

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🧫 Rapid-Fire Highlights

More research & reviews worth your time

  • Predicting a protein’s function solely from its amino acid sequence is pretty much the holy grail of molecular biology. A new study used machine learning to “infer how protein sequence maps to function.” Researchers trained a model using data from deep mutational scanning experiments, and were then able to “pinpoint key residues that dictate protein structure and function.” Cell Systems. Link

  • Bacteria have sigma factor proteins that whiz about the genome and regulate genes with a “matching” promoter sequence. Sigma factor-70, for example, controls different genes than sigma factor-32, based on slight differences in those promoter sequences. A new study reports the “predictive” design of sigma factor-70 promoters, which may enable synthetic biologists to design, and build, bacterial promoters that behave as expected. Nature Communications (Open Access). Link

  • Mangrove-dwelling protists, called thraustochytrids, can feed on a large swath of different chemical compounds. Because of this metabolic diversity, they could be useful for metabolic engineers hoping to manufacture drugs and biofuels. A new review analyzes the engineering potential of these underexplored organisms. Trends in Biotechnology. Link

  • Suckerin-12, a protein found in squid teeth, was assembled in a controllable manner outside of living cells. By adding unnatural amino acids to the suckerin-12 proteins, the researchers also found ways to covalently attach fluorophores and add other functionalities to these nano-scale building blocks. ACS Synthetic Biology. Link

  • A new study—seeking to provide a sort of physical base for nanofabrication—reported a DNA barrel, weighing 100 megadaltons and extending 250 nanometers in length, “that provides a rhombic-lattice canvas” on which to build 3D nanostructures. It’s basically a foundational structure for DNA origami. Nature Communications (Open Access). Link

  • As more people have their genomes sequenced, privacy concerns have flourished. This review takes a deeper look at the issue. Frontiers in Bioengineering and Biotechnology. Link

  • E. coli and yeast get boooooring after awhile. A new study, from Paul Freemont’s group at Imperial College, reports an improved, cell-free system from an organism called Streptomyces venezuelae. The gooey insides of these cells can be used to manufacture proteins, in vitro, with yields of 266 μg/mL. bioRxiv (Open Access). Link

  • Yes, CRISPR can cut and edit DNA. But what about epigenome engineering—changing the chemicals or proteins that bind to DNA to alter how genes are expressed? A new review highlights how catalytically inactive Cas proteins, including dCas9 and dCas12, can be used for epigenome engineering. Nucleic Acids Research (Open Access). Link

  • “Living medicines” are little microbes that can go into the human body to fight or detect disease. A new review digs deep on the topic, explaining the next frontiers in their development. ACS Synthetic Biology. Link

  • A new fluorescent protein—called mGreenLantern (lol, superhero)—is up to six times brighter than even the “enhanced” version of green fluorescent protein. In this study, researchers test out mGreenLantern in mouse, bacterial, and human cells. PNAS (Open Access). Link

📰 #SynBio in the News

  • 50 pieces of DNA were stitched together at once, assembling a complete bacteriophage genome in one go. I wrote about it. Scienceline. Link

  • A really in-depth, reported feature on genetic engineering for “improved farmed fish, oysters, and shrimp.” This article is worth your time. Science. Link

  • Remember that coral “heat-tolerance” study, from last week? Emily Mullin wrote a great, in-depth story about it. Future Human. Link

  • Scientific American published a list of the “ten emerging technologies of 2020.” Number 10 is whole-genome synthesis, and includes a nice write-up from Andrew Hessel and Sang Yup Lee. Scientific American. Link

  • Animal genes are being inserted into plants, which then grow animal cells, which are then used to…make meat? That’s discussed in Future Human’s weekly roundup of futuristic food news. Future Human. Link

  • Microsoft, Illumina, and Twist Bioscience have teamed up to store data in DNA archives. The most striking goal: the trio “estimate that 10 full-length movies could be written into DNA molecules and packed to a volume the size of a grain of salt.” That means every Tarantino movie could be stored in genetic material. Fierce Biotech. Link

  • A study in PNAS finds that CRISPR—coupled with electric currents—can be used to detect SARS-CoV-2 in 30 minutes. IEEE Spectrum. Link

  • (Not SynBio) The supply chain for wasp venom, used to treat allergic reactions, is in big trouble. (Bonus video: How to collect venom from bees.) Undark. Link

  • (Not SynBio) Synthetic soil might help farmers grow plants on Mars. Science News. Link

  • A mutation in an ‘essential gene’ could prove fatal to an organism. But a study in eLife found an entire class of fruit fly genes that are both essential, and also evolve quickly. Quanta Magazine. Link

  • Are you locked at home, tired of staring at the neon orange paint that you thought might look good in your living room, but now seems slightly garish? Take an online biotech course instead; here are twelve of them. Link

  • (Not SynBio) The big news this week: Moderna’s COVID-19 vaccine is nearly 95% effective. MIT Technology Review. Link

  • (Not SynBio) Pfizer announced that its vaccine is safe and 95% effective. They plan to file for emergency FDA approval. The New York Times. Link

  • STAT released their annual list of “Wunderkinds”, which celebrates “the unheralded heroes of science and medicine.” This year featured several CRISPR researchers. STAT. Link

  • The Lucks lab, at Northwestern, previously reported a way to quickly detect contaminants in water using some custom DNA, and a few proteins. That study was reported in the December issue of Scientific American by Susan Cosier. Check it out! Scientific American. Link

🐦 Tweets of the Week

Protein-protein interactions control everything from intracellular signals to extracellular reception. A new preprint (open access) reports an incredibly elaborate method to generate new “coiled-coil” protein pairs—small proteins that uniquely interact with a partner. Check it out! 👇

A new review (open access) at the intersection of 3D genomes and synthetic biology. If you’re interested in chromatin, and how to engineer it, check it out! 👇

Twitter avatar for @GallowayLabMITKatie Galloway @GallowayLabMIT
1/n So you love the 3D genome and want to know more about how synthetic biology will address open question in the structure and function of chromatin? This review is for you! (And it’s open access!) Think @4DNucleome meets #synbio -> @CellSystemsCP…

Nathan B. Wang 🏳️‍🌈🧬🧑🏻‍🔬 @nbwang22

After several months and lots of work, our review is finally out! In it we discuss how 🧬sequencing, 🔬 microscopy, and 🧑‍🔬 synbio approaches can be used to both understand and engineer chromatin as a dynamic system! @GallowayLabMIT @ChrisPJohnstone

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