The CRISPR gene-edited babies: a technological breakthrough or a brave new future?

  He Jiankui announcing the birth of the gene-edited twins on Youtube

He Jiankui announcing the birth of the gene-edited twins on Youtube

The announcement of the first CRISPR gene-edited babies has sparked a major polemic in the scientific community, but also in the media and the public. The research was discreetly carried by a Chinese team lead by He Jiankui at the Southern University of Science and Technology (SUST), in Shenzhen. He announced in a Youtube video: “Two beautiful little Chinese girls, Lulu and Nana, came crying into the world as healthy as any other babies a few weeks ago”. The research team have used CRISPR to deactivate the CCR5 gene in the embryos, which were then implanted into the mother. The CCR5 gene encodes for a protein that enables the HIV virus to enter in human cells. The aim was to deactivate it to reduce the risk of HIV infection, as the father was HIV-positive. This procedure has been apparently applied to eight couples. However, its success is still unclear, as no data or details were publicly released yet.

 

  Deletion/insertion in genome by CRISPR Source: Wikimedia

Deletion/insertion in genome by CRISPR Source: Wikimedia

In response to this announcement, many researchers in China and abroad condemned this experiment. Feng Zeng, the pioneer researcher in the application of CRISPR in mammalian cells, called for a global moratorium. Feng insisted that he was “deeply concerned” of the fact that the project was secretly undertaken. More than a 100 Chinese scientists have also signed a letter condemning the experiment. This announcement also coincides with the Second International Summit on Human Genome Editing in Honk Kong, where many researchers reiterated the condemnations against the experiment. It was highlighted by Qiu Renzong (Chinese Academy of Social Science) that this violates the regulation in China, which is however not penalized. In opposition, George Church (Harvard University) defended it saying that HIV was “a major and growing public health threat” and “I think this is justifiable”.

The whole story is not fully known yet, and we still need to wait a few days to have more information to find out how the experiment was conducted. However, this story puts at risk the near future of gene editing, due to the way it was carried, with the secrecy around the project and the non-respect of ethical procedures.

  Off-target effects of CRISPR Source: Wikimedia

Off-target effects of CRISPR Source: Wikimedia

At first, the issues with off targets in CRISPR gene-editing means that there are still high risks of inducing unwanted modifications in the genome. So, the babies risk irreversible damage in their genomes, potentially transmitting these to their offspring. Secondly, the way the team carried this experiment creates multiple ethical and practical issues. If the public see that scientists can decide to “engineer babies” in secret without any safety check, we risk to end up banning or restricting CRISPR even more. From an ethical point of view, using CRISPR was not a last resort solution here; other safer options exist to avoid HIV transmission from parents to their children. In practice, the cost of an IVF is not accessible to the vulnerable populations where HIV spreads. The CCR5 gene was probably an “easy” target, giving the opportunity to be the first one in the race to apply CRISPR in humans. But, the attention that this story attracts can negatively impact the public (and policy-makers’) perception of scientists and CRISPR. If the technology lacks a wide public understanding and support, it could delay the release of validated lifesaving treatments for many years.

Even if one day humanity decides to modify itself to prevent diseases, it is still too early and it is not the choice of a single person or a small group of academics. In the end, as scientists, we should do our best to bring life changing solutions, like human gene-editing, in a responsible way to make sure of the best positive impact possible.

“All conditioning aims at that: making people like their unescapable social destiny”

Aldous Huxley, Brave New World


Posted by courtesy of the PLOS Synbio Community blog, where this was originally published.

Written by: Adam Amara

Disclaimer: Views and opinions expressed in EUSynBioS Pulse articles belong solely to the writer(s). They do not reflect the opinion of the Community, the Advisory Board or the Steering Committee.

SynBioS - towards stronger international connections in synthetic biology

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Accompanying adolescence of the discipline of synthetic biology, the past five years have seen many local, national, and supranational synthetic biology groups founded around the globe. United in the aims of promoting synthetic biology research as well as professional and policy development, the associations can benefit substantially from forging and maintaining strong horizontal connections.

On October 23rd, representatives from six national and supranational synthetic biology associations - EUSynBioS (Europe), SynBio UK (United Kingdom), GASB (Germany), SynBio  Australasia (Oceania), SynBio Canada (Canada), and EBRC SPA (United States of America) came together at the 2018 EUSynBioS Symposium Toulouse to set the foundation for a new international collaborative effort, the SynBioS Consortium. The representatives introduced their history, activities, and future plans through short presentations and discussed various topics of mutual interest, such as funding, social media, and science policy.

Concluding the workshop, the representatives confirmed their interest in continuing discussions as part of the future SynBioS Consortium, which will include regular online meetings focused on exchanging advice, coordinating initiatives, and reviewing progress.

We are looking forward to advancing synthetic biology together and encourage other national synthetic biology associations to join our endeavour.

  • EUSynBioS, SynBio UK, GASB, SynBio Australasia, SynBio Canada, EBRC SP

From Asilomar to Toulouse – Bringing Researchers Together and Synthetic Biology to the Forefront

In frosty February 1975, molecular biologists gathered at Asilomar (California, USA) for a conference going down in history. Following the recombinant DNA revolution, the ethical usage of recombinant DNA in research was discussed. Many aspects of this gathering foreshadowed issues that the child of recombinant DNA technology, synthetic biology, is struggling with nowadays. Asilomar helped shape recombinant DNA technologies and bring them into the public eye by bringing together the researchers involved in this topic.

In sunny October 2018, about 100 synthetic biologists from all over the world gathered in Toulouse, from Master’s students all the way up to distinguished professors and leaders in the field of synthetic biology. In a meeting jointly organized by the European Association of Synthetic Biology Students and Post-docs (EUSynBioS) and the French Research Group on Synthetic and Systems Biology (BioSynSys) at the Institut National des Sciences Appliquées de Toulouse (INSA Toulouse), scientists had the chance to engage in fascinating presentations and discussions with their peers. This joint meeting was a first for both organisations and has shown the potential of collaboration between local and international scientific organisations to foster connection, exchange of ideas, and collaborations.

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During four days, leaders of synthetic biology such as Prof. Dr. Sven Panke from ETH Zurich, Prof. Dr. Beatrix Suess from TU Darmstadt or Prof. Dr. Jérôme Bonnet from the University of Montpellier explained their latest advances in very diverse areas of synthetic biology to the audience. Additionally, many young researchers had the chance to present their research in oral presentations and posters. Led by the idea of a circular bioeconomy powered by synthetic biology, which was illustrated by a keynote presentation by Dr. Lorie Hamelin and an open discussion with leaders in the field. This meeting in Toulouse gave to young as well as to established researchers a potential way forward in our climate change-endangered world.

Another way forward was illustrated in workshops conducted during the conference. Dr. Konstantinos Vavitsas discussed the important longstanding issue of standards in synthetic biology with the participants, Nadine Bongaerts prepared them for conversations with the public through science communication and Dr. Pablo Ivan Nikel led a career development workshop to ensure the success of the young researchers present. Accompanied by delicious French food & wines, our participants thus had plenty of exciting science around them, which would have turned the Asilomar participants green with envy!

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Yet there is an additional parallel with conferences such as Asilomar: organization, representation and the determination to bring the topic into the public eye. Next to EUSynBioS, national associations for synthetic biology such as the German Association for Synthetic Biology (GASB), Synthetic Biology Canada (SynBio Canada), Synthetic Biology Australasia (SBA), Synthetic Biology UK (SynBio UK) and the US-based Engineering Biology Research Consortium Student and Postdoc Association (EBRC SPA) also presented their organizations and plans for the future. With the aim of constructing a worldwide SynBioS Consortium to help coordinate initiatives and strengthen the ties between countries and continents, the national associations exchanged information and engaged in fruitful discussion. Analogous to Asilomar, meetings such as this symposium in Toulouse helps to shape the development of synthetic biology, both within as well as without by modulating its interaction with the general public surrounding it. This is particularly important nowadays, in a world endangered by climate-change and in which scientists and synthetic biologists need to bring forward new solutions to solve humanities’ most pressing challenges.

After four days of intense engagement on every level, the participants travelled back to their respective countries, enriched in knowledge, connections, and experiences. If our participants have even a fraction of the satisfaction we have with the event then we can consider it as a major success. See you at the next synthetic biology symposium!

Posted by courtesy of the PLOS Synbio Community blog, where this was originally published.

   Daniel Bojar    and    Adam Amara    are EUSynBioS steering committee members.    Alicia Calvo-Villamañán    is a member of the student committee at BioSynSys.

Daniel Bojar and Adam Amara are EUSynBioS steering committee members. Alicia Calvo-Villamañán is a member of the student committee at BioSynSys.

iGEM Paris Saclay 2018: MethotrExit - a HeteroGenious Cleaning Factory

Cytotoxic anticancer drugs are harmful chemicals found in hospital wastewater at high concentrations. Physical and chemical degradation methods exist but are often inefficient, unsustainable or expensive. We propose MethotrExit, a bioreactor-based approach to tackle this problem. We focused on the biotransformation of methotrexate (MTX), a widely used anticancer drug.

After choosing an appropriate chassis strains, we designed synthetic cassettes encoding a new biotransformation pathway using a heterologous carboxypeptidase in Escherichia coli. In only 5 hours, MethotrExit drastically removes MTX from the media. However, the degradation of anticancer drugs and the biotransformation pathway itself can be toxic. To overcome these issues, Biobricks bringing heterogeneity in enzyme expression were built to ensure the survival of a subpopulation. Modeling of this system highlights the interest of a division of labor between ‘cleaning’ and ‘stem’ bacterial cells.

 From left to right, in the back: Yueying Zhu, Ousman Bao, Guillaume Garnier, Kenn Papadopoulo, Arthur Radoux, Julie Miesch, William Briand, Britany Marta, Clémence Maupu. In the front: Raphaël Guegan, Julie Rojahn, Mahnaz Sabeti Azad (advisor), Céline Aubry (advisor), Stéphanie Bury-Moné (instructor). Advisors not present on the picture: Phillipe Bouloc, Sylvie Lautru, Olivier Namy, Arnaud Ferre

From left to right, in the back: Yueying Zhu, Ousman Bao, Guillaume Garnier, Kenn Papadopoulo, Arthur Radoux, Julie Miesch, William Briand, Britany Marta, Clémence Maupu. In the front: Raphaël Guegan, Julie Rojahn, Mahnaz Sabeti Azad (advisor), Céline Aubry (advisor), Stéphanie Bury-Moné (instructor). Advisors not present on the picture: Phillipe Bouloc, Sylvie Lautru, Olivier Namy, Arnaud Ferre

Choice of an appropriate chassis for the ‘Cleaning Factory’

Escherichia coli is a good chassis since it naturally expresses the AbgT permease which imports folate analogs such as MTX (Green J. 2002). After analysing the MTX-sensitivity of several E. coli K12 WT and efflux pump mutants, we decided to choose both the WT and ΔtolC strains as chassis. Indeed the former presents a strong MTX-resistance (up to 1264 µM MTX) while the latter is MTX-sensitive but devoid of MTX efflux pump. This may limit MTX efflux and favor MTX biotransformation within the cell.

Design of the MTX biotransformation pathway

We focused our attention on two enzymes, Pseudomonas carboxypeptidase G2 (CPG2 or ‘glucarpidase’) and a folylpoly-γ-glutamate synthetase (FolC) (Figure 1.A). CPG2 is the key enzyme that rapidly converts MTX into less toxic metabolites glutamate and DAMPA (2,4-diamino-N10-methylpteroic acid-d3), (Widemann, Sung et al. 2000), (Larimer, Slavnic et al. 2014). We also tested the interest of co-expressing FolC that may enhance MTX catabolism by coupling MTX to polyglutamate (Chabner, Allegra et al. 1985) (Kwon, Lu et al. 2008).

The biotransformation of MTX was monitored by HPLC analysis and bioassays using the E. coli K12 acrA1 mutant as an indicative strain. In only 5 h of incubation with our ‘Cleaning Factories’, MTX was nearly completely removed from LB medium (Figure 1.B).

  Figure 1 :  A) The MTX-biotransformation pathway and division of labor strategy.  B) HPLC analysis of MTX medium incubated with a ‘MTX-Cleaning Factory’. LB medium containing MTX (512 µM) was incubated during 5 h at 37°C with control bacteria (E. coli K12 pSB1C3-tet (BBa_R0040)) or with one of our ‘MTX Cleaning Factory’ (E. coli WT pSB1C3-folC-cpg2 (BBa_K2688009)). The supernatants were filtrated and analysed by HPLC with a reverse phase C18 column. Detection was made using UV spectrophotometry at 303 nm.  C) The ‘HeteroGenious’ device. Interplay between Ler and H-NS for the modulation of LEE5 promoter activity; Fluorescent microscopy of E. coli K12 harboring pSB1C3-LEE5_GFP_native (BBa_K2688012) cultured in LB at 37°C during 24 h.

Figure 1:

A) The MTX-biotransformation pathway and division of labor strategy.

B) HPLC analysis of MTX medium incubated with a ‘MTX-Cleaning Factory’. LB medium containing MTX (512 µM) was incubated during 5 h at 37°C with control bacteria (E. coli K12 pSB1C3-tet (BBa_R0040)) or with one of our ‘MTX Cleaning Factory’ (E. coli WT pSB1C3-folC-cpg2 (BBa_K2688009)). The supernatants were filtrated and analysed by HPLC with a reverse phase C18 column. Detection was made using UV spectrophotometry at 303 nm.

C) The ‘HeteroGenious’ device. Interplay between Ler and H-NS for the modulation of LEE5 promoter activity; Fluorescent microscopy of E. coli K12 harboring pSB1C3-LEE5_GFP_native (BBa_K2688012) cultured in LB at 37°C during 24 h.

Ensuring the maintenance of the bacterial population – towards the ‘HeteroGenious Cleaning Factory’

We observed that the chassis strains harboring both cpg2 and folC expression cassettes present a slight growth delay. Indeed, drug degradation pathways may be associated with a fitness cost. Therefore, we wanted our bioreactor to harbor a heterogeneous synthetic transgene expression. Only two parts are required to implement this ‘HeteroGenious’ system in E. coli: Ler (‘LEE encoded regulator’) and its target LEE5 promoter (Figure 1.C) (Leh, Khodr et al. 2017). The competition between Ler and H-NS (naturally present in E. coli) for LEE5 binding can generate a heterogeneous transgene expression. Modeling a heterogeneous expression of the synthetic pathway within the ‘cleaning factory’ population highlights the interest of a division of labor between ‘cleaning’ and ‘stem-like’ bacterial cells.

Conclusion

We obtained E. coli strains that efficiently remove MTX from culture medium, and a two-part device that can generate heterogeneity of transgene expression within a bacterial population. This study opens new insight concerning the design of ‘Cleaning Factories’. Moreover, E. coli strains able to degrade MTX could be of potential interest as probiotics to treat MTX intoxication.




References

Baba T. et al. (2006) Mol Syst Biol 2: 2006 0008

Chabner B. A. et al. (1985) J Clin Invest 76(3): 907-912

Green J. N. B. et al. (2002) Proceedings of the 12th International Symposium on Pteridines and Folates, National Institutes of Health, Bethesda, Maryland, June 17–22, 2001

Kwon Y. K. et al. (2008) Nat Chem Biol 4(10): 602-608

Larimer C. M. et al. (2014) Adv Enzyme Res 2(1): 39-48 

Leh H. et al. (2017) MBio 8(4)

Widemann B. C. et al. (2000) J Pharmacol Exp Ther 294(3): 894-901.



3 Questions for Prof. Barbara Di Ventura

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In our most recent iteration of the ‘3 Questions For’ interview format, we speak with Prof. Barbara Di Ventura at the BIOSS Centre for Biological Signalling Studies at the University of Freiburg, Germany. Her group is pushing the boundaries of optogenetics and uses light-regulated methods to study cell division and chromosome segregation in bacteria. Herein, and in general, the Di Ventura lab has a strong focus on protein dynamics.

When and why did you move into the field of synthetic biology?

I would say 2002 is the year that marks my entry into the field of synthetic biology. After I graduated in Computer Engineering at the University of Rome “La Sapienza” I moved to Heidelberg to start my PhD at the EMBL in the group of Luis Serrano. At the beginning, the idea was for me to do only mathematical modeling of biological processes. After some months, however, Luis told me I should rather learn to do experiments on my own not to have to wait for others to give me data to model. That’s when I came into the field of synthetic biology, as the project I selected dealt with the transplantation of the p53-Mdm2 module into yeast to study its properties as an oscillator. I think that for someone like me who trained as an engineer, synthetic biology is the most natural way of entering into molecular biology. Eventually we are engineering cells instead of cars or buildings! And we do use computers a lot.


What is the single most important piece of advice that you would give to a current PhD student or a post-doc?

To those working in the field of synthetic biology I would say: take the chance to make the world a better place! To those not working in the field of synthetic biology I would say: what are you waiting for? Join synbio!!


In which areas do you see the main challenges and opportunities for synthetic biology?

The first area that comes into my mind is medicine. There is so much that synthetic biology can do here. The most intriguing to me is the transformation of the concept of treatment from “taking a drug” into “having a synthetic circuit monitor your state of health and react in case anything goes wrong”. Of course, the challenges are many since we need to break down the natural – and understandable – barrier of fear and skepticism that surrounds the idea of introducing something man-made (yet living!!) into our bodies. Moreover, we surely need to go down a long way to make sure that this method is safe and effective. Beyond medicine, synthetic biology can bring a revolution in so many other fields – energy, food production, environment, just to name a few.