Recoding Human Cells to Make them Virus Proof

On May 1, around 200 scientists from the Genome Project-write (GP-write) met in Boston and announced the first target of their project: the creation of cells that cannot be infected by viruses.

What is the Genome Project-write?

GP-write includes sub-projects like the Human Genome Project-write (HGP-write), which was formally announced on June 2, 2016, and is an extension of the Genome Projects, which were launched in 1984. These projects were created to develop ways to read DNA in microbes, plants and multiple animal species, including humans.

GP-write was initially met by some level of panic and alarm, as some of the media misrepresented the project and people’s imaginations ran amok. Suggestions of “secret meetings” and stories of scientists creating designer babies and superhumans were doing the rounds, regardless of the actual scientific reality of the project. However, stories of mutants, superhumans, and manbearpigs are greatly exaggerated.

The newly created GP-write project will be managed by the Center of Excellence for Engineering Biology, a new nonprofit organization. With a firm commitment to cost reduction, safety, and ethical conduct, there could be considerable scientific advances as a result of this project.

The Genome Project-write (GP-write) is an open, international research project led by a multidisciplinary group of scientific leaders who will oversee a reduction in the costs of engineering and testing large genomes in cell lines more than 1,000-fold within ten years.

GP-write will include whole genome engineering of human cell lines and other organisms of agricultural and public health significance. Thus, the Human Genome Project-write (HGP-write) will be a critical core activity within GP-write focused on synthesizing human genomes in whole or in part. It will also be explicitly limited to work in cells, and organoids derived from them only. Because of the special challenges surrounding human genomes, this activity will include an expanded examination of the ethical, legal and social implications of the project.

Engineering virus-resistant cells

Jef Boeke, one of the four leaders of GP-write, said, “There is very strong reason to believe that we can produce cells that would be completely resistant to all known viruses.” He continued further: “It should also be possible to engineer other traits, including resistance to prions and cancer.”

The project takes the original Human Genome Project and builds upon it. The GP-write project could see rapid progress, given the sheer number of collaborating labs comparing data, verifying the results, and conducting safety analysis. This could be a game changer for stem cell therapies, as these robust, virus-proof cells could be used to treat a variety of diseases.

The team plans to engineer resistance to viruses using a technique known as recoding; this depends on the fact that much of the genetic code is redundant. Each three-letter sequence of DNA letters is known as a codon, and these codes are specific to the production of a particular amino acid. The chart below shows the codons for each amino acid.

Hundreds or even thousands of amino acids are linked together to create proteins; these signal our cells to perform certain functions, and they include insulin, collagen, myosin, and many thousands of others.

Despite this deeper complexity, there are just 20 amino acids and a “stop” signal, and there are 64 combinations of the four DNA nucleotides. However, life can continue with only one codon for each amino acid. For example, during recoding, you might choose the GTT in, say, valine, and whenever the three redundant ones (GTC, GTA, and GTG) appear in the genome, they are replaced by GTT. This essentially means that every time one codon is replaced by another, you are removing one codon from the genetic codebook and reducing the complexity.

But why would we bother doing this?

Here is where the viral resistance comes in. Because the genes of a virus contain these redundant codons, the virus can enter the cell and take control of the cell’s genetic machinery. In the case of a recoded cell, the virus would not be able to take over the control system and use it to create more viruses; the cell would lack the ability to create the viral proteins it needs to proliferate, and so the cell would be immune to viral infection.

George Church, one of the GP-write project leaders, has already tested the approach in E.coli. His team replaced all 321 instances of one redundant codon in its genome, which rendered the bacteria resistant to the bacteriophage T7 virus. Church took this a step further in 2016 and replaced seven redundant codons in around half of the same bacteria’s genome [1]. This required the replacement of 62,214 redundant codons with synonymous alternatives across all protein-coding genes.

The project aims to make virus-proof human cells within 10 years, but to do that, the number of codon replacements would be around 400,000 in order to affect around 20,000 protein-coding genes. This is a monumental task, and it is why the GP-write leaders suggest that writing genomes from scratch, not editing them with CRISPR, is a better approach.

Jef Boeke said, “We have nothing against CRISPR. We love it and use it all the time. But we’re talking about changes that are just massive. It’s like if you’re editing a short story: if you’re changing so much of it, you might as well just rewrite the whole damn thing.”

In order to build a genome from scratch, it would mean synthesizing DNA one nucleotide at a time and joining thousands of these together. While it is possible to do this with today’s technology, it is a laborious and slow process. To give you an idea, it costs around a dollar to synthesize 10 DNA letters, meaning that it would cost $300 million to do the human genome.

The GP-write project team aims to drive down synthesis costs by a factor of 1,000, thus making the idea a much more practical proposition. Church has already indicated that he wants to synthesize all human genes through joining 200-letter-long strands, which we can do now with currently expensive technology. Those familiar with Church will almost certainly know that he has been instrumental in driving down the costs of gene editing in the past, and the members of this project are confident that they can do so again here.

Conclusion

There is huge potential here for not only reducing costs and contamination but also for creating in vivo therapies that potentially introduce replacement cells that are impervious to viruses, such as HIV, resistant to other diseases, such as cancer, and even resistant to damage from aging and radiation. A look at the goals of the project published last year makes it quite clear that the ultimate goal is to develop this for in vivo therapies, such as stem cell transplants.

There is an unmet need for an “Ultrasafe human cell line” designed to serve as a platform for many biomedical applications, from production of biologics, to modeling cell and tissue behaviors, to actual ex vivo and ultimately in vivo therapeutic applications.

As we improve our ability to edit and create genomes from scratch, a world of options opens up for combating diseases, and we look forward to seeing more progress from the GP-write team.

Literature

[1] Ostrov, N., Landon, M., Guell, M., Kuznetsov, G., Teramoto, J., Cervantes, N., … & Shrock, E. (2016). Design, synthesis, and testing toward a 57-codon genome. Science, 353(6301), 819-822.