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Biosecurity Challenges in the Genome Engineering Space – Beth Vitalis

Biosecurity Challenges in the Genome Engineering Space – Beth Vitalis

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A presentation by Beth Vitalis, Biosecurity Specialist at Inscripta, on "Biosecurity Challenges in the Genome Engineering Space."

A presentation by Beth Vitalis, Biosecurity Specialist at Inscripta, on "Biosecurity Challenges in the Genome Engineering Space."


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Biosecurity Challenges in the Genome Engineering Space – Beth Vitalis

  1. 1. Biosecurity Challenges in Genome Engineering Space Beth Vitalis, PhD Biosecurity Specialist Catalyst Biosecurity Summit Feb 22, 2019
  2. 2. 2 • Inscripta is committed to responsible, safe use of its digital genome engineering technology. • Genome engineering presents biosecurity challenges, some distinct from other areas of synthetic biology. • A call for a collaborative approach to address biosecurity challenges for genome engineering Key Points
  3. 3. 3 Inscripta’s technology and products enable digital genome engineering on an unprecedented scale
  4. 4. 4 Inscripta’s technology and products enable digital genome engineering on an unprecedented scale Effective solutions require: • Unprecedented SCALE • Superior PERFORMANCE • Greater ACCESS VarietyofEditTypes LowHigh Number of Genomic Locations 100 101 102 103 104 Number of Edits 105+ 104 103 102 101 100 Protein Engineering Site Directed Mutagenesis Pathway Engineering Expression Engineering Gene Knockout Gene Knock-in Genome-wide Base Editing Genome-wide Knockout Classical Mutagenesis Genome Engineering Genome Discovery
  5. 5. 5 Onyx™ Digital Genome Engineering Platform Inscripta Engineering Portal Generates up to 10k precisely engineered libraries of single cells at customer benchtop Design G enerate Test Learn Inscripta’s mission is to avail these tools to the public
  6. 6. 6 Inscripta is committed to safe use of its customer-empowering technology Biosecurity processes help prevent malicious or accidental production of potentially harmful organisms BIOSECURITY CONTROL WORKFLOW Genome and Edit library screening identifies potential biothreat before production Editing library kits produced in-house Up-front customer screening blocks known bad actors Customer designs edits in own lab on approved genome of choice Inherent controls prevent unauthorized use of MADzymeTM nucleases and OnyxTM platform Customer creates edits, carries out genotyping and phenotyping in own lab
  7. 7. 7 Genome engineering biosecurity considerations overlap and diverge with other synthetic biology technologies Features Shared  Customer Screening  Broad biothreat space  Reporting protocols Features Unique to Genome Engineering  Edits must be considered in the context of the genome and cell behavior o Regulatory sequence o Protein interactions  Scale issues for massively parallel genome editing o Multiple edits per cell will add complexity Collaboration is needed across Synthetic Biology AND amongst the Genome Engineering community to address Biosecurity challenges
  8. 8. 8 Genome engineering biosecurity must consider cellular context and enormous phenotypic diversity Each edit variant must be evaluated within cellular context for biothreat potential Libraries of cells with different edits expand diversity Edits can alter the function or expression of an individual protein, which in turn may have numerous cellular effects x =
  9. 9. 9 Community-based strategy to strengthen genome engineering biosecurity and minimize biorisk Define biosecurity ‘best practice’ standards for genome engineering Strategize to close resource gaps: research, DBs, test sets Instill societal confidence in genome engineering; protect the bioeconomy Recruit support from government, academia, industry Share ideas and resources Collectively address ‘challenges’ The unique challenges of biosecurity for genome engineering requires collaborative problem solving Let’s Work Together!
  10. 10. • Source here The POWER of Biology to POSITIVELY Impact the World is PROFOUND Materials Human Health Natural Products Pharmaceuticals Buildings Food EnergyClimate And Must Be Respected & Protected
  11. 11. Thank you! Elizabeth (Beth) Vitalis
  12. 12. 12 Discussion Question What concerns do YOU have about large-scale genome engineering? How might we strategize addressing these concerns?

Editor's Notes

  • Thank you to Catalyst, I feel honored to participate in this landmark event and proud to represent Inscripta here.
  • Today will talk a bit about inscripta’s commitment to biosecurity for responsible, safe use of its digital genome engineering technology.
    Then I will describe how the power of Genome engineering to accelerate biological discovery presents biosecurity challenges, some distinct from other areas of synthetic biology.
    Will end with a call for a community-based strategy to address and solve our problems, establish Biosecurity ‘Best Practices’ and promote societal trust in this rising technology
  • Inscripta enables Genome engineering on unprecedented scale
    How does this work?
  • leading strategy for scientists to make biological discoveries Is to study the effects of genomic perturbations
    Historically, these genomic changes have occurred through natural evolution or deliberately through various methods of mutation and engineering. Some approaches have strengths in targeting numerous loci across the genome with huge numbers of edits, however, limited by edit type. Other approaches, here on the Y axis have advantage of allowing a variety of edit types, single base pair or codon changes, insertions/deletions, promoter swaps, focused edits on area of interest such as protein engine,.. Yet remain limited to discrete regions of the genome. Trade off. Inscripta’s innovative chemistry pulls us into this outer quadrant to dramatically increase the genotypic assortment and thus phenotypic diversity that can result from a single experiment. Hence the scale like we’ve never seen…chemistry and protocols provide superior performance. Access is important to Inscripta
  • And our mission is to make these tools widely available to any one who seeks this unbound biological exploration. Onyx platform gives this awesome power to customers. Suite of instrument, software and reagents in the customers own lab which is where they carry out the iterative design, generate, test ,and learn cycle, each round zoning in on key breakthroughs in their own research or product development. Customer empowerment facilitates high impact discoveries, yet must be addressed in Biosecurity system.
  • With Biosecurity a priority, Inscripta proactively implement screening processes with a goal to identify and help prevent deliberate or accidental production of a biorisk
    Here we underlie biosec controls unto the customer ‘journey’ to discovery
    Since customer directs their own edits, we follow standard protocols to screen out known bad actors upfront, unlikely, yet non-zero
    Edit library kits are produced at Inscripta, and likewise we have inhouse screening processes designed to rapidly identify potential biothreat invoking sequence before reagent production.
    The kits are shipped to customers to carry out the genome engineering in their own lab. Biosecurity is upheld though through various inherent controls. For example the use of ‘barcodes’ on reagents to prevent unauthorized and unscreened use.
    Inscripta Enables and inspire others to be first to make break through discoveries.  We are committed to ensuring SAFE use of this customer-centric technology
  • However, as we have developed our biosec system, we have encountered challenges that are unique to GE, as well as addressed biosec features shared across synbio
    As we are discussing here today Biosecurity in synBiology requires inclusive, ongoing dialogue across the industry.
    Shared Bioscurity needs include upfront customer screening, identif of biothreat across a broad space, and proactive reporting protocols to avoid ad hoc, poorly planned reactive responses
    Let’s look at biosec considerations thst GE brings to us::
    The advantage of high-throughput genome wide engineering to capture enormous phenotypic diversity has a flip side The potential functional impacts of edits on cell behavior are complex and we must consider regulatory effects and protein interactions. Scale issues result from the huge numbers, esp when multiple edits/cell. Wow! This is getting complicated. These phenomena are conceptualized on the next slide so we can take a closer look.
    Continued communication across synbio is important, yet we also need collaboration within the GE community to address these novel challenges
  • This cartoon represents how key strength of genome engineering, the enormous scale of phenotypic diversity that may be probed, also underlies its major biosecurity dilemmas. The functional effect of a given edit in say, an Ecoli genome, may alter multiple cell processes. Even if a cell has only one edit, whether it be to a regulatory region that affects expression of one or more proteins, or a coding region that changes the shape of a single protein, the protein interactions and pathways that could be altered may be complex, and difficult to predict.
    Multiply this times libraries with up 1000s cells, the range of functional effects and emergent properties resulting from a typical experiment could be huge. Rigorous Biosecurity ought to evaluate each variant in genomic context
    Furthermore as technology advances, multiple edits/cell, or combination editing, will result in an exponential increase in number of variants. Yikes! A clever systems biology approach will be needed to evaluate the enormity of edit variant combinations within cellular context
    Clearly, predicting biothreat of genome wide engineering is daunting!
  • Yet there is hope, as we are gathered for this event, we appreciate that with a community based strategy, we can begin to tackle these biosecurity challenges through open minded dialogue and collaborative problem solving
    Inscripta is rising to this challenge yet want this to be a community-driven.
    How can a community, with a common interest in GE, work together to prioritize and strengthen its biosecurity. Sharing ideas
    important to define Best Practices, set norms and standards. In order to do so, we will need to meet resource gaps. Research to help develop curated DBs, and complex sequence sets needed to test screening algorithms. Compilation of phenotypic results to help predict emergent properties
    we need to address biosecurity challenges, as a group, pursue support from other stakeholders, help influence legislation and acquire needed resources
    We recognize the vast benefits of GE across numerous sectors, thus major contributor to Bioeconomy, it will be critical to Communicate the truth about the benefits and risks of GE to the public, to instill societ trust and protect Bioeconomy
  • Genome Engineering technology must thrive since The POWER of Biology is PROFOUND. As scientists are equipped to explore biological systems at an unprecedented scale, we are better positioned to solve some of society’s most pressing problems.
    Yet as access and scale of this technology expands, we must continue to work together to respect and protect the power of Biology.
  • Discussion Qs: (need one for small groups in audience to discuss)

    What do you foresee as the most daunting GE specific Biosecurity challenge, and how might we strategize addressing it? (last half might be too much for this situation)

    What biosecurity related topics are most critical for the Genome Engineering community to address

    What concerns do you have about the kinds of large-scale genomic engineering that the Onyx represents