Category: News

CRISPR-Cas9 genome editing: from Cancer Treatment to Agriculture

by Jestin George

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CRISPR-Cas9 editing of the genome from NIH image gallery (Creative Commons CC2.0 from Flickr)

In 2012 the first evidence of CRISPR-Cas9 genome editing was published and since then, almost 4000 CRISPR-Cas9 articles have followed. From fundamental research to applications in biotechnology, agriculture, health care, pest control, and synthetic biology, there is no doubt that CRISPR systems will revolutionise both biological research and indeed, technology, as we know it. The astounding rate of progress over the past 5 years has not been ignored: policies are being revised and reconsidered, moratoriums and summits are being held globally, all to ensure the progression of safe and ethically driven genome-editing technology.

Recently, two jam-packed genome-editing conferences took place in Australia, both focusing on socially relevant areas of research: cancer treatment and agriculture. These meetings were aptly timed given the political landscape concerning gene-editing technology. The National Institutes of Health, USA approved CRISPR-Cas9 as a therapeutic for cancer and the Australian Office of Gene Technology Regulator (OGTR) is undergoing a technical review of its regulations. It’s Gene Technology Regulations Act (2001) is to be amended to provide clarity about how Australian law defines genetically modified organisms (GMOs). This is important because current legislation has not kept up with advancing technologies, resulting in some strange double standards. For example, two identical organisms can be defined differently (GMO and non-GMO) because of the process used to generate them. Using a simple “process-based” and not “product-based” definition of a GMO is now inappropriate and outdated. This technical review aims to implement a more evidence-based policy for assessing risk and safety. The OGTR is consulting the public on the matter until February 2018; don’t miss the opportunity to have your say here.

 

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Molecular Extravagance by Daniel Friedman (Creative Commons CC2.0 from Flickr)

The Genome Engineering for Cancer Treatment meeting (The Frank and Bobbie Fenner Conference) was held at Australian National University (ANU). One week later came the CRISPR-Cas9 in Cereal Crops workshop held by CSIRO in the beautiful seaside town of Kiama. While both meetings served as opportunities to hear about cutting-edge research in these fields, at the core these meetings showcased where the research in Australia is. Consequently both meetings provided the chance for a great deal of knowledge sharing, particularly regarding technical difficulties in applying the technique. They also both provided important non-scientific information, including: the patent and licensing landscape of CRISPR systems, bio-ethical and social considerations and strategies, and information regarding the OGTR’s technical review.

 

Australian Chief Scientist Dr Alan Finkel opened the Cancer Treatment meeting entitled “Excellence with Equity and Empathy”. In his speech, Dr Finkel offered three mantras for the success of scientific agendas: (1) speak human to humans (2) think out to the ten-year horizon and (3) regulate to facilitate, which resonated through the talks given. Dr Gaetan Burgio presented some sobering evidence for poor reproducibility in the field, attributing it to low sample sizes, lack of lab-based skills and scant reporting of methodologies. There was also a spotlight on CRISPR bioinformatic and biostatistic research. Keynote speaker Dr Veera Baladandayuthapani unpacked their work in discovering relevant targets using biostatistics. Dr Laurence Wilson discussed machine-learning approaches for improving CRISPR targeting efficiency and introduced their optimised target identification platform, GT-Scan2. This software incorporates a range of previously overlooked factors that affect editing efficiency, including chromatin structure and epigenetic markers.

 

Epigenetic editing itself was covered by Prof. Ryan Lister, who demonstrated that for heritable reconfiguration of chromatin by editing, simultaneous activity of multiple, distinct epigenetic effectors is needed. Assoc. Prof. Pilar Blancafort showed how they used epigenetic editing for reprogramming complex phenotypes in breast cancer. Dr Ben Hayley compared the various cutting-edge CRISPR activator (CRISPRa) systems available and presented the PiggyBac transposon for large cargo transgenesis, size being a limiting factor regarding viral delivery systems. But it was the extent of genome-wide editing applications being used in cancer research that was powerful to see. Such applications presented included: screening novel tumour suppressor genes, unpacking the hidden details of the critical tumor suppressor gene p53 and JAK-STAT signalling, identifying resistance mechanisms in multiple myeloma, and identifying novel drug targets for generating functional organoids in colorectal research. As Dr Finkel mentioned in his speech, Australia will be a player in the age of genome medicine.

 

The CRISPR-Cas9 in Cereal Crops meeting opened with an impressive overview of metabolic engineering by CSIRO’s Agriculture and Food innovation leader Dr Allan Green. It was inspiring and motivating as a biotechnologist to hear about the success of Australian companies GoResources and NuSeed -which use engineered organisms to provide clean energy and improved crop productivity- as well as NxtOil technology. Prof. Caixia Gao showed their impressive work on wheat editing, and is soon to publish a novel protocol for biolistic delivery of Cas9 ribonucleoprotein (RNP). Prof. Gao also demonstrated an in vivo screen for assessing optimal CRISPR guide RNAs (gRNA) using protoplasts instead of in vitro DNA digests. Given the research presented by Dr Wilson regarding the effect of chromatin structure and epigenetic markers on Cas9 targeting efficiency, this in vivo validation technique is an important tool for plant editing. Yao-Guang Liu presented their work on DSDecodeM, an online tool for automating chromatogram analysis. During screening, chromatogram analysis usually requires manual analysis of sometimes-vast numbers of sequencing reads which can be very time-costly.

 

Prof. Jimmy Botella gave a hilarious but impressive overview of their CRISPR-mediated ultrafast breeding for adding one or two traits to an otherwise elite line in just two generations. Dr Mike Jones demonstrated how they used gene editing to create low gluten index (GI) potatoes. He also spoke to the importance of genome editing techniques for modifying properties of existing cultivars without introducing external DNA, given the lengthy time frame of breeding and market acceptance. Dr Mick Ayliffe commented on the benefits of gene stacking for durable, longer-lived pathogen resistance by delivering numerous genes on one locus. He also showed their unsuccessful efforts to bring a “pseudogene back from the dead,” an attempt to restore resistance traits. It served as a reminder that destroying gene function is much easier than creating it, even with gene editing tools like CRISPR.

 

Dr Heather Bray, Dr Lucy Carter, Dr Aditi Mankad and Craig Cormick all gave fantastic insights into dealing with social acceptance and considering the broader implications and ethics. They reminded scientists to also think like human beings, echoing Dr Finkel’s opening speech. Food is not only about sustenance; it is about ceremony, ritual. Values, not information, determine views. People need to know who is benefiting from what technologies, both directly and financially, more than they need to understand the science. While the societal and ethical elements to CRISPR are tricky to navigate, one thing that is clear is that the deficit model –the idea that the public would be more on board if only they knew as much as us scientists– does not work.

 

While evidence of the widespread success and application of CRISPR technology is clear, the CRISPR revolution is only just beginning. We are excited that Australia, as Dr Finkel commented in his speech, is going to be a key player.

jestin george

 

Jestin George is a PhD student at the University of Technology Sydney, working on genetically engineering the microalga, Chlamydomonas reinhardtii, for applications in biotechnology. She is member of the executive board and assistant communications officer of Synthetic Biology Australasia.

iGEM results, great representation by Australasian teams

A highlight in the Synthetic biology calendar is the iGEM giant jamboree. igemlogo_officiallogo-copyThis November, nearly 5,400 participants from 310 teams representing 44 countries across the globe gathered in Boston to present their synthetic biology projects and interact with each other.

Our corner of the world was well-represented by two Australian and one New Zealand team.

Team Macquarie won “Best Energy Project” and obtained a gold medal with their project H2ydroGEM.  They designed the Hydrogen Gas Producing Gene Custer aimed for a clean and sustainable fuel resource. According to the team “(we) sought to imitate the most efficient natural mechanism for the transduction of energy – photosynthesis. By engineering it into E. coli, ‘green’ hydrogen fuel can be produced simply from sunlight and water. With successful gas production, our team then moved on to tackle the next big issue of hydrogen energy-it’s safe storage.” With impressive yields of Hydrogen gas produced this is not the last we hear of this project.

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Picture by Team Macquarie

Team Sydney Australia with their project DISCO (Designing Insulin that is Single-Chain and Open source) also won a gold medal. As they write in their website, “(our team) aims to produce stable insulin using an efficient, cost-effective and simple method. We produced a proinsulin identical in sequence to human proinsulin, and we also designed and produced our own single-chain insulin that we have named ‘Winsulin’.”

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Picture from team Sydney_Australia

 

 

Last but not least, team SECA_NZ decided to tackle an important issue of New Zealand kiwi producers face, cold temperatures that threaten production. According to their website, “(our vision is to) have crop plants that do not require costly interventions in order to be protected from winter temperatures. We hope that in time farmers will not fear the oncoming of winter, or have their livelihood threatened by a sudden frost. Genetic engineering provides an avenue for this.”  The team was nominated for Enterpreneurship prize.

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Meet the team SECA_NZ

Our warm congratulations to all three teams, and we hope to see more great projects from the next generation of our future synthetic biologists!

 

 

 

 

2016 iGEM Local Teams Meet-Up

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The four Australian iGEM teams and their supervisors came together on Friday evening (14/10/16) for the inaugural local teams meet-up, supported by SBA.  The venue was a somewhat shabby 1970’s era tutorial room in the Biochemistry building at the University of Sydney. Luckily, the science presented by these young synthetic biologists was far from shabby.

The hosts (USyd team) kicked off proceedings with a presentation on their project entitled FRESH (Fruit Ripeness Ethylene Sensor (Hopefully)) The idea was that the regulatory elements used by bacteria which grow on ethylene could be hijacked, and linked to a colorimetric output, such as the amilCP chromoprotein. The team succeeded in making some new chromoprotein variants via error prone PCR, but at the time of writing, are still pursuing the goal of proving that the regulatory genes and promoters function as expected. The ‘human practices’ elements of the USyd project included outreach to students at schools, at the university Open Day, and at the Australian museum during Science Week; they also interacted with the fresh fruit industry to get ideas about the marketability of their biosensor.

The UNSW team followed on with a presentation on their project “BLEB”, which aimed to make E.coli strains that create outer membrane vesicles (OMVs) for use in all manner of biotechnology applications. These OMVs are very attractive potential SynBio tools; for example, they allow the different enzymes from a single metabolic pathway to be brought together in a defined space, which contains a ‘friendly’ biochemical environment. OMVs are also attractive since they are not themselves GMOs, and thus would available for applications in which whole cells would not be legal. The UNSW team human practices included surveying various local experts in both environmental and medical biotechnology, to determine whether there was a market for their OMVs, and also engaging with school students at functions hosted by outreach organisations B.Inspired and Aspire.

After a break for pizza and drinks, the science resumed with the Macquarie Uni team showcasing the latest instalment of their grand plan to create a photosynthetic E.coli. As always, the team impressed with the amount of progress, submitting many new parts to the Registry, and edging even-closer to this ambitious goal. The team also unveiled a new twist on the project, which was a plan for a portable hydrogen generator, to take advantage of this potentially very useful by-product from the photosynthetic apparatus. We were also entertained by a short movie the Maq. team had produced, interviewing rural folks about how they could use the hydrogen source, and getting feedback on the design, as part of their human practices work.

Finally, the University of Melbourne iGEM team presented their work on engineering star peptides. Special thanks must go to Rob Naturani for making the trip solo to represent his team, a heroic effort on behalf of his comrades south of the border. The star scaffold system is an intriguing and versatile platform technology which allows cross-linking of different proteins, for example as a way of enhancing reaction kinetics via enzyme colocalisation. The Melbourne 2016 project improved the design of the 2014 team by adding split inteins to the star scaffold, with the idea that these would enable joining to other target proteins, with the intein simultaneously self-splicing out of the picture. A very cool concept.

Will bellies full of pizza and heads full of science, the teams and their supervisors headed home. It was a great night, with both honest constructive criticism and hearty pats on the back shared between teams. There was a genuine feeling of community, which is really what iGEM is all about.

Dr. Nick Coleman | Senior Lecturer in Microbiology
School of Life and Environmental Sciences | Faculty of Science
THE UNIVERSITY OF SYDNEY

Upcoming Synthetic Biology meetings/conferences

  1. Unlocking the potential of synthetic biology to enhance human health”: a web-based conference on synthetic biology, 27th-29th September 2016 regonline.co.uk/virtualsynbiol06
  2. There is a synthetic biology session at the upcoming ComBio2016 conference in Brisbane, https://www.asbmb.org.au/combio2016/, 3 – 7 October 2016
  3. SynBioBeta SF 2016” October 4th-6th, 2016, South San Francisco Conference Center, San Francisco, CA http://synbiobeta.com/conferences/synbiobeta-sf-2016/
  4. Synthetic Biology for Natural Products” in Cancun, Mexico, 5th-8th March 2017 https://www.fusion-conferences.com/conference58.php syntheticbiology_banner
  5. Cambridge Healthtech Institute’s Inaugural Plant-Based Expression and Synthetic Biology Conference: Enabling the Power of Plants. January 10-11, 2017, San Diego, CA, USA http://www.chi-peptalk.com/plant-based-expression-conference/
  6. BioBricks Foundation SB7.0: the Seventh International Meeting on Synthetic Biology” will take place 13-16 June 2017 at the National University of Singapore (https://biobricks.org/ conference web site not yet available)
  7. SBA’s second conference will be held on 21-22nd September 2017 in Sydney; check the ‘Meetings’ tab for updates

Australia is on track to producing a new generation of Synthetic Biologists

With excellent results at the 2015 Genetically Engineered Machine competition (iGEM). All four Australian teams received medals in the 230 team strong international competition.

Team UNSW led by Marc Wilkins was awarded a gold medal for igemlogo_officiallogo-copytheir Endosymbio project.

Team Macquarie led by Louise Brown and Rob Willows were awarded a gold medal for their Solar Synthesisers project and were runners up for Best Energy Project, Best Model and Best New Basic Part.

Team Sydney led by Nicholas Coleman were awarded gold for their MycoMimic Project and were runners up for Best Integrated Human Practices, Best Model and Best Education and Public Engagement.

Team ANU led by Colin Jackson were awarded a bronze for the Phytogeneic Project.

Congratulations to everyone involved.