The Fifth Annual Sc2.0 and Synthetic Genomes Conference: Synthetic

Sep 16, 2016 - The Sc2.0 project is perhaps the largest synthetic biology project in the public domain, and ultimately aims to construct a new version...
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The Fifth Annual Sc2.0 and Synthetic Genomes Conference: Synthetic Genomes in High Gear Roy S. K. Walker†,‡ and Yizhi Cai*,† †

Daniel Rutherford Building G.24, School of Biological Sciences, University of Edinburgh, The King’s Buildings, Edinburgh EH9 3BF, United Kingdom ‡ Institute for Bioengineering, School of Engineering, The University of Edinburgh, Edinburgh EH9 3BF, United Kingdom ABSTRACT: The Sc2.0 project is perhaps the largest synthetic biology project in the public domain, and ultimately aims to construct a new version of the humble brewer’s yeast, Saccharomyces cerevisiae. Each year, the Sc2.0 consortium gather to discuss progress in this ambitious project and highlight new developments at the forefront of synthetic genome engineering. This viewpoint summarizes some of the key moments of the 2016 conference, including updates on the Sc2.0 project itself, mammalian synthetic biology, DNA assembly automation, HGP-Write and a panel discussion on the social and ethical perspectives of synthetic biology.

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conference began with an interesting keynote presentation from Jasper Rine (University of California), who discussed the epigenetic inheritance of gene silencing in S. cerevisiae,2 an organism that lacks DNA methylation. Rine described using a sensitive assay based on the Cre-lox system to detect heritable extremely rare loss-of-silencing events within single colonies. This assay was used to identify several novel aspects of gene repression, including the role of a recombination enhancer and links between cell metabolism and oncometabolites on gene silencing.

he Fifth Annual Sc2.0 and Synthetic Genomes conference welcomed over 150 scientists from around the world to Edinburgh, Scotland. The venue was Dynamic Earth, a visitor attraction conveniently sandwiched between Scotland’s national parliament and the dramatic cliffs of Arthur’s Seat, an extinct volcano located just outside the heart of the city. The conference was held on the 8th and 9th of July 2016, and was the highlight of a week that also saw the first Synthetic Genome Summer Course (3rd to 7th of July) and SynBioBeta Activate! Edinburgh 2016, incorporating the official opening of the Edinburgh Genome Foundry (7th of July), the UK’s first fully integrated and automated DNA production facility. Each year, members of the synthetic yeast genome (Sc2.0; www.syntheticyeast.org) consortium gather to summarize progress toward the construction of the world’s first fully synthetic eukaryotic genome. This year’s conference continued its previously expanded format, incorporating updates from Sc2.0 consortium members interspersed with presentations on mammalian synthetic biology, laboratory automation and genome engineering before culminating with a presentation from Jef Boeke (NYU Langone Medical Centre) on HGPWrite.1 An engaging panel discussion on bioethics then provided an opportunity for reflection and discussion. Overall, the conference was a resounding success. Thirty delegates and three keynote speakers presented on the current state-of-the art in genome engineering and synthetic biology, augmented by an engaging poster session, demonstrations from industry representatives and a craft beer and wine tasting on the Friday evening, with wine kindly donated from the Australian Wine Research Institute (AWRI). This was followed by a conference dinner that ended in energetic fashion with a traditional Scottish Ceilidh. Following an update of the Sc2.0 consortium by the conference chair and Sc2.0 consortium international coordinator, Patrick Yizhi Cai (University of Edinburgh), the © 2016 American Chemical Society

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SC2.0 CONSORTIUM UPDATES

Now in its fifth year, the Sc2.0 consortium has made great strides toward constructing the world’s first fully synthetic eukaryotic genome. Jef Boeke (NYU Langone Medical Centre) reported that all 16 synthetic yeast chromosomes have been assigned to laboratories located in the USA, China, the UK, Australia and Singapore, with successful integration of approximately 60% of the overall synthetic yeast genome. Highlights of this year’s conference included increasingly practical uses of the SCRaMbLE system,3 chromosome fusion, designer neochromosomes and studies into three-dimensional genome structure. Junbiao Dai (Tsinghua University) initiated proceedings by reporting on construction of synthetic chromosome XII (SynXII), and its subsequent re-engineering with even more radical design changes. Leslie Mitchell (Jef Boeke lab, New York University) discussed successfully “debugging” SynVI and Chantal Shen (Patrick Cai lab, University of Edinburgh) updated on SynII, SynVII and SynXIII. Shen’s work alone covers an impressive quarter of the entire synthetic yeast Received: August 17, 2016 Published: September 16, 2016 920

DOI: 10.1021/acssynbio.6b00227 ACS Synth. Biol. 2016, 5, 920−922

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MAMMALIAN SYNTHETIC BIOLOGY October 2015 saw the launch of the UK Centre for Mammalian Synthetic Biology at Edinburgh University. Mammalian systems present unique opportunities for synthetic biology, with implications in healthcare and improved understanding of complex biological systems. Four talks highlighted the great potential in this rapidly developing subject area. Jamie Davies (University of Edinburgh) reviewed how simple rules can lead to complex pattern formation, with examples of spontaneous self-organization of kidney tissue from stem cells.5 Karen Polizzi (Imperial College London) then emphasized that orthogonality can occasionally be over-rated, not least when developing mammalian cell biosensors to further understand the metabolism of cells during therapeutic glycoprotein production. Yvonne Chen (University of California) discussed engineering T-Cells to express bispecific chimeric antigen receptors (CARs), containing a true OR-gate signal computation, to target either the CD19 or CD20 antigens of malignant B-cells. This is a promising approach that aims to reduce the risk of “antigen escape”, where antigen-free cancerous cells proliferate, in T-cell therapy for B-cell malignancies.6 Finally, Joshua Leonard (Northwestern University) discussed designbased engineering of cells7 that may be tailored to release tumor-killing factors in vivo.

genome. Tom Ellis (Imperial College) then reported on the construction of SynXI and applying SCRaMbLE to generate strains with improved thermotolerance and more efficient xylose utilization. Jingchuan Luo (Jef Boeke lab, NYU Langone Medical Centre) gave an excellent talk on the construction of SynVIII and SynI and described an efficient system to fuse wild type chromosomes together, which will be used to probe the extent to which chromosome number can be manipulated. Matthew Chang (National University of Singapore) and Sakkie Pretorius (Macquarie University), relative newcomers to the Sc2.0 consortium, are making excellent progress synthesizing SynXV (NUS), SynXIV (Macquarie and AWRI) and SynXVI (Macquarie). Pretorius also discussed constructing a neochromosome containing all of the nonessential, strain-specific genes responsible for the differentiating properties of distinct, industrially relevant yeast strains. The second day began with a keynote presentation from Maitreya Dunham (University of Washington), who discussed the evolution and engineering of cell aggregation (flocculation) in yeast. During long continuous culturing, the common laboratory strain, S288C, can spontaneously evolve the ability to aggregate on surfaces despite containing a nonsense mutation in FLO8. Understanding this mechanism led the Dunham lab to engineer cells with greatly reduced flocculation. Consortium talks continued with Joel Bader (John Hopkins University) who described statistical models to determine the bias of position-dependent gene codon usage, important due to synthetic biology’s extensive reliance on synonymous recoding. Roy Walker (Patrick Cai lab, University of Edinburgh) reported on the construction of a tRNA neochromosome, a designer neochromosome that houses the 275 tRNA genes to be deleted in the final synthetic yeast strain. Romain Koszul (Institut Pasteur Paris) then presented work on engineering synthetic chromosomes to improve resolution in Hi-C analysis from his work on 3D genome structure. Further exemplifying the thematic diversity of this year’s conference, Lars Steinmetz (Stanford University) delivered an excellent talk on transcriptomic heterogeneity and the role of pervasive transcription in gene regulation. Steinmetz explained how bidirectional transcription can contribute to an available pool of up to 1.8 million individual transcript isoforms per cell,4 with extensive cell-to-cell heterogeneity. Future work will explore the effects of SCRaMbLE on pervasive transcription. Last but certainly not least, Zexiong Xie and Yi Wu (Yingjin Yuan lab, Tianjin University) gave an update on SynV and SynX before Michael Shen (Jef Boeke lab, NYU School of Medicine) and Yi Wu (Yingjin Yuan lab, Tianjin University) discussed tachytelic (accelerated) evolution and the benefits of SCRaMbLE in heterozygous diploids. This year’s conference also featured a series of excellent flash talks from Sc2.0 Fellowship members, and included the following: S. cerevisiae adaptive evolution in response to loss of genes previously considered essential (Gaowen Liu, A*STAR Singapore); gPCR-based biosensors (William Shaw, Imperial College London); human artificial chromosome/yeast shuttle vectors (Alina Chan, Harvard Medical School); alterations to genome structure in synthetic strains (Heloise Muller, Institut Pasteur Paris); a selector method to improve SCRaMbLE (Zhouqing Luo, Tsinghua University); and benefits of long-read sequencing technology for genomic characterization of SCRaMbLE’d genomes (Aaron Brooks, EMBL).

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NETWORK OF FOUNDRIES The UK Synthetic Biology Roadmap aims to develop a worldleading synthetic biology community in the UK,8 one of the “Eight Great Technologies” in which the UK can be a world leader. The UK Biotechnology and Biological Sciences Research Council (BBSRC) has consequently funded five centers for DNA synthesis across the UK through the “Synthetic Biology for Growth” program. A Labcyte-sponsored session featured four of these foundries, including the recently opened Edinburgh Genome Foundry (EGF) managed by Hille Tekotte. Tekotte described the EGF’s unique capacities in fully automated, large-scale DNA construction. James Johnson described the synthetic biology foundry located at the Centre for Genomic Research at the University of Liverpool, before Nicola J. Patron, fresh into her role at the Earlham Institute (previously TGAC) in Norwich, described her work on synthetic biology in plants. Finally, Paul Freemont presented an overview of the DNA synthesis and construction foundry at Imperial College, London. Freemont observes that, while each foundry shares a common foundation based on automation, repositories of parts, small-scale liquid handling and phenotyping/sequencing facilities, a heterogeneous approach toward DNA assembly is their major strength.

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HGP-WRITE Human Genome Project-Write1 proposes the construction of a synthetic human genome, potentially a major leap in synthetic genome engineering. Jef Boeke (NYU Langone Medical Centre) framed this project as an enabler of new technologies that will improve the incorporation of large DNA molecules into mammalian cells and massively reduce the overall cost of assembling such large-scale DNA, potentially by a factor of 1000 in 10 years. Perhaps recognizing the ongoing debate and controversy surrounding this project, Boeke emphasized responsible innovation: the project will be performed in cells that will be “engineered for safety”, and contain a germline firewall such that synthetic cells will never become a living 921

DOI: 10.1021/acssynbio.6b00227 ACS Synth. Biol. 2016, 5, 920−922

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human. Advantages of the overall project could include new knowledge about genome fundamentals, as well as spinoff technologies that may include engineered universal T-cells and next-generation gene therapy. While the Sc2.0 consortium could serve as a model for HGP-Write moving forward, overall, the use of Saccharomyces cerevisiae as a host for construction will be essential.

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AUTHOR INFORMATION

Corresponding Author

*E-mail: [email protected]. Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS We acknowledge generous support from conference sponsors, in particular BBSRC (BB/M005690/1 to YC), Labcyte, Twist Bioscience, Molecular Devices, ThermoFisher Scientific, Gen9, Autodesk and SULSA. We are grateful to Liz Fletcher, Julie Fyffe, Anais Moisy and Emily Scher for their help in organizing the meeting. We also thank Anais Moisy who designed the artwork used for conference communication and for this publication.

PANEL DISCUSSION: SC2.0 IN CONTEXT: POSTCARDS FROM A DIFFERENT SPECIES

Following the overview of HGP-Write was an excellent panel discussion on the social and ethical perspectives of synthetic biology by Jane Calvert (University of Edinburgh), Emma Frow (Arizona State University), Debra Mathews (John Hopkins University) and Erika Szymanski (University of Edinburgh). The Sc2.0 consortium encourages free and critical debate, with the conference and panel discussion presenting an open forum for engaging discussion. Debra Mathews began by discussing HGP-Write and stating her opposition to the project in its current form. Matthews suggested that stronger scientific justification is necessary for a project with so many ethical implications, and that compromise is not a negative concept. Jane Calvert then reflected that, compared with sequencing, synthesis involves more choices; therefore, we need to pay greater attention to values. Calvert asked what the relationship is between engineering and evolution, and whether we should rethink the concept of a species. Calvert stated that diverse and unusual groups, which include not just biologists, but also artists, designers and social scientists, can open up the field of synthetic biology. Finally, Erika Szymanski asked who are the collaborators in the Sc2.0 consortium: are they tools, colleagues or yeast? Szymanski noted that the consortium is breaking boundaries between disciplines, and that we need new ways of thinking to work and collaborate with people based on trust and mutual understanding. In the final keynote presentation, Pamela Silver (Harvard University), described introducing programmed Escherichia coli into the mammalian gut to act as a diagnostic tool.9 These programmed bacteria stably colonise the gut, and become biological sensors with memory, with applications including the ability to detect exposure to salmonella bacteria

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REFERENCES

(1) Boeke, J. D., Church, G., Hessel, A., Kelley, N. J., Arkin, A., Cai, Y., et al. (2016) The Genome Project-Write. Science 353 (6295), 126− 7. (2) Dodson, A. E., and Rine, J. (2015) Heritable capture of heterochromatin dynamics in Saccharomyces cerevisiae. eLife, DOI: 10.7554/eLife.05007. (3) Shen, Y., Stracquadanio, G., Wang, Y., Yang, K., Mitchell, L. A., Xue, Y. X., et al. (2016) SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes. Genome Res. 26 (1), 36−49. (4) Pelechano, V., Wei, W., and Steinmetz, L. M. (2013) Extensive transcriptional heterogeneity revealed by isoform profiling. Nature 497 (7447), 127−31. (5) Davies, J. A., and Chang, C. H. (2014) Engineering kidneys from simple cell suspensions: an exercise in self-organization. Pediatr. Nephrol. 29 (4), 519−24. (6) Zah, E., Lin, M. Y., Silva-Benedict, A., Jensen, M. C., and Chen, Y. Y. (2016) T Cells Expressing CD19/CD20 Bispecific Chimeric Antigen Receptors Prevent Antigen Escape by Malignant B Cells. Cancer Immunol. Res. 4 (7), 639−41. (7) Daringer, N. M., Dudek, R. M., Schwarz, K. A., and Leonard, J. N. (2014) Modular extracellular sensor architecture for engineering mammalian cell-based devices. ACS Synth. Biol. 3 (12), 892−902. (8) Group UKSBRc, Clarke, L., Adams, J., Sutton, P., Bainbridge, J., and Birney, E., et al. (2012) A Synthetic Biology Roadmap for the U.K., TSB Technology Strategy Board. (9) Kotula, J. W., Kerns, S. J., Shaket, L. A., Siraj, L., Collins, J. J., Way, J. C., et al. (2014) Programmable bacteria detect and record an environmental signal in the mammalian gut. Proc. Natl. Acad. Sci. U. S. A. 111 (13), 4838−43.

SUMMARY AND CONCLUSION

The Fifth Annual Sc2.0 and Synthetic Genomes Conference is the latest in a series of annual consortia events that are growing in quality and delegate count as the Sc2.0 consortium expands. The multidisciplinary and varied set of speakers helped contribute to debate and open discussion, with talks on mammalian synthetic biology and reflections on HGP-Write generating new perspectives in this rapidly growing subject area. Of particular note in the Edinburgh meeting were conference demographics: presentations from younger scientists represent the next generation of scientific talent, with a 50:50 gender ratio of conference speakers providing a fantastic benchmark for future events. In 2017, the Sixth Annual Sc2.0 and Synthetic Genomes Conference will take place in Singapore, together with the SB7.0 conference. 922

DOI: 10.1021/acssynbio.6b00227 ACS Synth. Biol. 2016, 5, 920−922