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The Gene Editing Tsunami and the 10 SynBio Highlights of 2015

When we decided to crowdsource a review of the year from the synthetic biology community we weren’t sure what the response would be – but it has been fantastic! So good in fact, that we have decided to split the result into several parts. In this installment we have picked out 10 scientific highlights, and this will be followed by pieces on business, ethics and the future. We hope you enjoy reading, so much happened this year there are some things you might have missed!

The Gene Editing Tsunami

“I put my head together with some of Oxford’s top synthetic biology PhD students and we all agreed that this was the year of CRISPR – gene drives, embryonic editing, immuno-safe pig organs and more.”
Max Jamilly, PhD student in synthetic biology, Oxford

2015 was definitely the year of CRISPR. Hard to not note its importance now and for the future.
Dr. Charles Ebikeme, scientist and writer

“The maturation of the CRISPR-Cas system based technologies excites me, because they have huge potential to fundamentally enhance our targeted genome editing toolbox.”
Dr. Gerd Moe-Behrens, Leukippos institute

Can you hear that deafening roar approaching? CRISPR,CRISPR,CRISPR! In 2015 there was no escaping the exponential rise of the genome editing technique known as CRISPR-Cas9, which allows precise editing of DNA, is quick, cheap and easy to use, and works in almost every species it has been tried in. You could barely open a webpage without seeing some click bait linking to the latest bright use of the technology, ranging from CRISPR mediated epigenome editing to optogenetics. The propaganda appeared to work, and by far the greatest number of replies to our survey nominated CRISPR developments – you are obviously still excited… and so are we!!! There is a reason for this; the best quote I heard explaining it came during the GARNet/OpenPlant CRISPR workshop in September, when Prof. Holger Putcha aptly described the technology as a tsunami, up there with PCR in terms of its impact upon molecular biology. When major news outlets began to pick up the story, and you see tabloids in the UK talking about “crispr”, you know this technology is going to be important for everyone – not just scientists. We will return to specific examples of how gene editing has been making waves, but first we should calm down a little and reflect that other exciting science has being going on too.

1. Humanizing Yeast

2015 saw growing excitement in applying synthetic biology to tackle medical questions. Prof. Eriko Takano, director at the University of Manchester’s SYNBIOCHEM institute, nominated the “Systematic humanization of yeast genes published in Scienceas it shows we are “beginning to test the limits of cross species SynBio.” In this work Karchoo and colleagues at the University of Texas replaced 414 yeast genes with their human orthologs, and found nearly half of these could be humanized. Prof. Edward Marcotte who is lead author on the study explains “it’s often hard to study human genes directly, especially in the context of a living cell or person, but by putting those genes into yeast, we can take advantage of [its] relatively simplicity. Yeast complementation assays make it feasible to study millions of variants of a human gene, letting us directly measure which mutations break its function… it’s fairly easy to perform high-throughput screens for genetic interactions, suppressor mutants, and even drug-gene interactions, so the humanized yeast should give us a powerful platform for studying at least a subset of human genes.”

 2. Manufacturing Meds

path5701Poppy seeds are the main source of opiates used for the production of painkillers. Work that introduced the opiate biosynthesis pathway into yeast paves the way for design and synthesis of novel medicinal compounds. An impressive feat of metabolic engineering, the challenge involved protein engineering, strain optimization, and the expression of 23 enzymes from plants, mammals, bacteria and yeast in order to create the painkiller hydrocodone (and 21 for thebaine). This and complementary work (also this) published in 2015 has led to fears about ‘home brew heroin’. However, you won’t need to worry anytime soon – at current titres, a single tablet of hydrocodone (5 mg) would require a thousand of litres of yeast!

3. Genomic Blueprint

René Davis chose “the mapping of the human epigenome” as the scientific achievement of the year. A massive project which involved “integrative analysis of 111 reference human epigenomes … profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression” means we now have a blueprint of mammalian regulatory networks which could help guide design of genetic circuits. René commented “it’s an incredible effort that sets an example for large-scale, open, scientific collaboration and provides a foundation for the study and engineering of mammalian biology.”

4. Shaping The Microbiome

For Dr. Tom Ellis the “most exciting paper of 2015 took synbio tools into the gut. It was a great example of synbio moving on from lab E. coli and into microbes with real-world importance.” In this paper Mimee and colleagues developed a system for engineering the human commensal bacterium, Bacteroides thetaiotaomicron, which could help facilitate efforts to engineer the microbiome and improve therapeutic delivery.

5. Fighting Infectious Disease

The development of the CRISPR gene drive technology in yeast as well as in other organisms such as drosophila or malaria anopheles mosquitoes. While there is still a long way to go, this technology has seen incredible progress throughout the year, and offers a lot of excitement as well as challenges and fears. There are great promises and massive potential and hopes for the control of deadly infectious diseases in the near future.”
Dr. Gaétan Burgio, ANU

mosThe deployment of gene editing tools to unleash ‘gene drives’ was probably one of the most revolutionary developments of the year, but also one of the most controversial. An idea with a long history (see references within), the ‘mutagenic-chain reaction’ was published in March – a method that used CRISPR-Cas9 to convert heterozygous to homozygous mutations in drosophila. This was followed by two reports of groups engineering species of mosquito to make them infertile with a view to tackling malaria. This technology has the potential to spread a desired mutation through a population, which could help combat infectious disease (see Gaétan’s piece for more details), but has also raised concerns about unanticipated ecological change. The potential dangers have again lead to calls for caution and better regulation, which resulted in researchers coming together to provide a set of recommendations that were published in Science. Further attempts to calm these fears are being pursued, and DiCarlo and colleagues published a paper in November which demonstrated the reversibility of gene drives in Saccharomyces cerevisiae.

 6. Immunosafe Organs

CRISPR-CAS9 to transform pigs into organ factories
Dr. Filippo Menolascina, SynSys, Edinburgh

Nominated twice, October saw reports that the Church lab at MIT have used gene-editing to create pigs which could serve as suitable donors of organs for human transplantation. This was achieved by smashing gene editing records with the removal of 62 porcine endogenous retroviruses, which could cause disease, and by altering >20 genes including those that have been shown to trigger immune responses and blood clotting.

7. Synthetic Immunobiology

Dr. Filippo Menolascina also highlighted advances in “[synthetic Chimeric Antigen Receptor] CAR Therapy” where T cells are engineered to express receptors to specific antigens. Gene editing has reinvigorated this field as a result of the potential to disable immunoregulatory genes and facilitate the incorporation of novel receptors. A good example was published by Sather and colleagues in September, where they utilized the knowledge that people carrying a naturally occurring non-functional allele of the T cell receptor gene CCR5 are HIV resistant. Using megaTAL nucleases, the authors deleted the CCR5 T cell receptor and replaced it with a HIV-specific CAR. The engineered cells were rendered resistant to HIV infection and were effective at killing HIV infected cells in vitro. In the future, synbio could also play in developing CAR therapy through the design of ON/OFF switches to prevent run away T cell activation.

8. Gene Edited Products – Coming To a Home Near You?

I couldn’t let a review of the year go without mentioning the Beijing Genome Institute’s (BGI) decision to start selling micro-pigs (created by gene editing) at the cost of $1600. In a Nature commentary piece it is stated “in future, customers will be offered pigs with different coat colours and patterns”... 2015 saw an increase in the application gene-editing to livestock (and talk of a ‘cloning factory’ opening in China) which could help raise productivity to feed the growing global population. 

micropigIn this regard, perhaps the most important development was the landmark ruling which made AquAdvantage Salmon the first genetically modified animal approved for human consumption by the US Food and Drug Administration (FDA). The salmon are engineered to overexpress a growth hormone causing them to reach harvest size in half the time (16-18 months compared to 3 years) which could be a big boost to producers. However, these developments have reignited the debate about genetically modified species and raised a range of ethical and regulatory questions which were recently covered in an excellent article in the NYT. Existing regulations have failed to keep up with technological developments, which has resulted in cases where the US Department of Agriculture found it was unable to rule on the use of genetically modified grasses. Resultantly 2016 will see the FDA undertake a year long review process to update regulations established in 1992 which could have a big impact upon future directions in this field.

9. New Kids On The Block

“No doubt, [it was] the evolution of CRISPR-Cas9 system.”
Dr. Prash Suravajhala, PostDoc, Department of Molecular Biology and Genetics, Aarhus University

The commonly used CRISPR-Cas9 system from Streptococcus pyogenes (SpCas9) has immense potential, but there are limitations which need to be addressed. Due to the size of SpCas9 (~4.2 kb), packaging and delivery into mammalian cells via adeno-associated virus vectors (AVV) is problematic. 2015 saw adoption of smaller Cas9 genes from Staphylococcus aureus which could help solve this problem. Additionally although CRISPR-Cas9 can target specific sequences, guide RNAs must also recognize a short sequence known as protospacer adjacent motif (PAM). Researchers created a modified Cas9 with relaxed PAM specificity, which increases the number of potential target sequences by two to four fold without affecting the number of off targets.

However, perhaps the most important limitation of the standard CRISPR-Cas9 system is the potential to cause off target mutations by unspecific binding to genomic DNA. Although the rates are low – they are unacceptably high when researchers start considering the possibility of editing the human genome. 2015 saw CRISPR fused to DNA binding domains which increased specificity, and in December the lab of Dr Feng Zhang at MIT published a major breakthrough when they reported the creation of an engineered Cas9 that has significantly reduced off-target mutations.

Additionally, Dr Zhang’s lab announced the discovery of Cpf1 this year, which has comparable, if not better potential than Cas9 as a gene editing tool (see here for a good review). This finding could spur on researchers to search for similar editing tools, which if successful could have profound effects on the commercial landscape.

 10. The BIG Quesion

“Nothing compares to the decision to start developing disease treatments using in-human gene editing. 2016 will be a very exciting year!”
Max Jamilly, PhD student in synthetic biology, University of Oxford

“Although the technology is now available to edit human genomes, it raises serious ethical concerns about the responsible use of the technology. It also brings public awareness to the field of synthetic biology and challenges us proactively engage the public to shape, rather than stifle, scientific progress.”
Khalid K. Alam, PhD student, University of Missouri

May saw the first published attempt to edit genes in human embryos, and scientists such as those at the Crick Institute applied for permission to carry out similar research. CRISPR has great potential to treat genetic disorders, but due to the risks of heritable off-target mutations and re-emergence of concerns about designer babies, many scientists called for a moratorium on research. This started a dialogue that ended with the recent International Summit on Human Gene Editing held at The National Academy of Sciences from the 1st to the 3rd of December, and for more information check out a summary by Rhiannon Morris and Chris Wallis on our blog.

Summary: Cutting Through The Hype

Finally, former PLOS Synbio Community editor David Shifrin provided a thought with which to finish:

The meteoric rise of CRISPR has opened up the conversation about synbio, getting people interested in the science, not just the rhetoric.

With great potential benefits, but also dangers, 2015 saw the continuing maturation of tools for synthetic biology –  now society must decide how to use them.

 

We wanted to offer a big thanks to all those people who contributed, and to apologise to those of you we bugged. Comments are welcome, what was your favourite development of 2015? do you think we have missed something?

Discussion

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