It has been five years since the introduction of CRISPR technology, a fast and highly accurate method of editing DNA in living organisms. CRISPR has revolutionized medical research, drug development, and agriculture, but the process still requires considerable time to identify and build a library of “guide RNA” used to locate the specific genes to be cut or modified.
In this context, Yole Développement’s (Yole) analyst, Asma Siari, Technology and Market Analyst in Biotechnologies & Molecular Innovations and co-author of the report CRISPR Technology & Market Overview: from Lab to Industry 2018, had the opportunity to interview Kevin Holden, Head of Science at Synthego – a key player in the genome engineering field. Synthego has developed an innovative scientific instrumentation, industrial automation, and software-driven “smart factory” for producing optimized guide RNA that targets DNA in organisms ranging from bacteria to humans. Through intensive automation, Synthego has cut the cost of synthetic guide RNA by nearly 80% and drastically accelerated production.
The following is a summary of their discussion.
(Source: CRISPR Technology & Market Overview: from Lab to Industry 2018 – Yole Développement)
Asma Siari (AS): Could you briefly introduce Synthego and its primary work focus in the genome editing field?
Kevin Holden (KH): Synthego is a genome engineering company based in Silicon Valley, California, and founded by two former SpaceX engineers with the goal to bring automation and standardization into the genome engineering field. We are a group of engineers, chemists, synthetic biologists, and computational biologists that collaborates to build software-driven, automated platforms enabling standardization. Our achievements include a novel chemical synthesis architecture that can generate, at scale, the reagents used for CRISPR genome engineering. We have also developed an automated system to utilize these reagents as part of a platform that performs CRISPR-based engineering of cell lines, also at scale.
AS: Synthego’s hardware platform facilitates the synthesis of guide RNA, a key ingredient for guiding CRISPR technology to a specific place on the genome. What is the science behind the platform? How does it work, and what are its advantages over existing technologies?
KH: Our software-driven “smart factory” allows for efficient, highly reproducible chemical synthesis of guide RNA: the key reagent used in CRISPR genome engineering. A key advantage of our new synthesis architecture is that it allows us to synthesize research-use-only (RUO) 100 nucleotide, full-length single-guide RNA (sgRNA) – which, as both Jennifer Doudna’s and George Church’s labs showed several years ago, is the optimal RNA format for programming the Cas9 nuclease in CRISPR genome engineering. Because they are synthesized chemically, the sgRNAs we generate can also be protected using nucleotide modifications that provide stability in exonuclease environments within cells, and also prevent innate intracellular immune responses.
We’ve made some patent-protected, proprietary innovations to RNA synthesis chemistry that include the use of software to enact process control over the synthesis. This allows us to very accurately track what we synthesize at single-nucleotide resolution. This is very important as we build out cGMP capabilities for the sgRNA in the coming year that will allow us to provide high-quality, inexpensive material for preclinical and ultimately regulated clinical trials for gene therapies.
We also employ a 28-metric quality-control evaluation of every compound we generate, since quality is very important for ensuring accuracy and reproducibility. The factory we developed is built in such a way that we can run multiple syntheses in parallel, and easily expand the factory footprint or “print” the factory elsewhere in the world. It’s very flexible. Our platform also allows us to produce sgRNA material in volumes varying from micrograms to grams, in tubes or in plates, while also significantly reducing the time and waste associated with older synthesis technologies.
AS: NGS is the gold standard for genome editing analysis. However, NGS’ cost and turnaround time create significant bottlenecks in the CRISPR workflow. Do you think that ICE has the potential to become a standard for CRISPR analysis?
KH: It can certainly become a standard, and I think we are already seeing evidence of this. The feedback from the research community has been overwhelmingly positive with respect to the Inference of CRISPR Editing (ICE) tool. It’s free, allows batch analysis of up to 700 samples at a time, and can handle complex editing scenarios – for example, three sgRNAs multiplexed in a local fashion in order to produce an exon dropout, which is what we use for our gene knockout strategy – and now, there is a knock-in analysis tool in beta. The outputs are saved as unique URLs which are easy to share amongst colleagues, or the entire software package can be downloaded from GitHub and used locally.
While NGS will always remain “the truth” for genome analysis, being able to use Sanger sequencing data (which can be obtained next-day in most of the world’s major biotechnology hubs) makes available a much cheaper alternative that can yield very valuable, accurate information. In the BioRxiv submission we made for ICE, we show that there is a strong correlation between its ability to deconvolute mixed Sanger traces in an edited cell population and what we observe using NGS. Many places do not have the access or budget to utilize NGS, so this is a very good alternative. And for Synthego, it fits very nicely into the workflow we have for our automated CRISPR-based cell engineering platform.
AS: What are the key applications addressed by Synthego today? Why has the company made the choice to address these areas? Also, is Synthego involved in CAR T-cell therapy?
KH: Today, the products and services we provide address several genome engineering areas. For starters, there are the bioinformatic tools, i.e. the gene-knockout guide designer and the ICE tool we just discussed. We developed these tools to support our own work, and we are happy that we can help other scientists in their work too. We’ll release more software tools in the future, and continue to make these free and useful for scientists.
On the reagent side, we’re providing access to the most efficient way to utilize CRISPR: using chemically modified, synthetic sgRNAs. These have enabled a large group of researchers (working on immortalized cell lines and human primary cells) to develop new disease models and work on potential gene therapies. Indeed, we have customers that utilize our reagents to develop CAR-T cell therapies, and some of them will eventually require a switch from RUO to GMP material for these therapies. When that time comes, we’ll be ready to support them. That said, at the moment we are not directly involved in developing any such therapies ourselves.
Further on the product side, we now deliver engineered cell lines for gene knockouts and custom knock-ins in over 700 immortalized cell lines. We can deliver these at very low prices and quick turnaround times thanks to the automated platform we’ve developed for CRISPR-based cell engineering. These cell lines target numerous applications, including the generation of in vitro models of disease, drug-target identification and validation, antibody validation, gene-tagging, safety assessment, and basic biological research. CRISPR is a powerful molecular biology tool, and by generating cell lines we hope to bring not only access to scientists who want to utilize CRISPR’s many applications in their own research, but also to enable standardization for research at the cellular level. This helps all of us develop more reproducible methods and more reliable data, which will translate into stronger therapies, models, cures, etc. We can help scientists to engineer the genomic modifications they want in their cell lines so that they can focus on their research and not spend months optimizing the genome engineering.
AS: Synthego raised $110 million in a series C financing round. How will you use this money?
KH: Synthego will use this capital to invest and expand its RNA and cell engineering factories, in order to increase capacity and meet customer demand. This includes enabling synthesis of clinical-grade RNA for therapeutics. We’ll also use the money to develop more powerful informatics tools and bring new products to market that we feel will benefit the research community. A portion of the funds will be used to increase employee headcount and allow us to focus on new R&D efforts. This includes exploring, from an engineering perspective, how we can work to decrease gene therapy cost in the future.
AS: Several gene therapies are already on the market, but these cost hundreds of thousands of dollars for patients. CRISPR has the potential to provide gene therapy at affordable costs. Do you believe that CRIPSR will reduce overall gene therapy cost for the patient?
KH: It’s possible that, after the initial trials are successful, subsequent treatment programs could become less expensive. However, these treatments will only be available to a select few people. In their current state, gene therapies are likely to remain very expensive, so the real question is, “Who will have access to these technologies?” Our vision as a company is to utilize novel engineering approaches to try and provide access to these therapies to the millions of people who could benefit from them. Ultimately it will be a scientific and an engineering challenge to try and reduce the cost of these therapies, but we believe it’s an area we can positively impact.
AS: As an early-stage company, what is Synthego’s business model for generating revenue from CRISPR?
KH: We currently generate revenue from the sale of CRISPR reagents and the sale of CRISPR-engineered cell lines. The software-driven automated approaches we’ve taken to build-out both of these factories allow us to generate economies of scale for these markets. As an early-stage company, it’s important for us to not only develop useful scientific approaches and data to help our customers, but also to generate revenue and new products that can ultimately provide great benefit to the research community, as well as provide materials to clinicians who want to treat patients suffering from genetic diseases. As Synthego’s growth continues, we will expand into other markets where we can also generate revenue through innovation and disruptive approaches.
AS: To conclude this interview, how much potential does CRISPR have for cell/gene therapy? What are the remaining barriers, and how will Synthego help overcome them?
KH: There is huge potential for genome editing technologies like CRISPR to have an impact on cell and gene therapies. It may be the current version of CRISPR that is the most effective, or it may be that newer techniques like base-editing become the favored approach. I think the discovery of the CRISPR nucleases will continue driving forward the discovery of other programmable nucleases which could serve as appropriate platforms for cell and gene therapies. Overall, given the ease and effectiveness with which CRISPR can be utilized for genome engineering compared to older methods, it is likely to become a very effective method for these therapies in the future.
I think we’ll see the gene therapies first, and then later the development of cell therapies, but there are significant barriers to overcome, such as the ability to effectively deliver CRISPR components into diseased cells or tissues with high levels of specificity. Synthego has a role to play in the development of clinical-grade sgRNA for ex vivo and in vivo therapy applications, as well as providing research-grade materials to evaluate therapies in primary human cells; and also in engineering cells for scientists in order to build in vitro models of diseases for the genetic conditions they study. Furthermore, our R&D efforts for developing gene-therapy automation technologies could help to drive down some of the associated costs. With our full-stack engineering approach to CRISPR genome engineering, we’re confident we can help researchers working at all levels of the discovery and research process.
Kevin Holden, PhD, is Head of Science at Synthego in Redwood City, California. He is part of a team responsible for integrating synthetic biology workflows (such as CRISPR genome engineering), into novel automation platforms for cell engineering. He also oversees collaborations with key opinion leaders in the CRISPR research community, and supports commercial activities by coordinating technical field-application support for Synthego’s portfolio of genome engineering solutions. Kevin frequently represents Synthego at academic and industry conferences, presenting the company’s latest research and development efforts.
Kevin has over 10 years of biotechnology experience in synthetic biology and genome engineering, and earned his PhD in Microbiology with a Designated Emphasis in Biotechnology from The University of California, Davis. He is originally from the United Kingdom and immigrated to the United States in his youth.
As a Technology & Market Analyst, Biotechnologies & Molecular Innovations, Medical Technologies in the Life Sciences & Healthcare division at Yole Développement (Yole), Asma Siari is involved in the development of technology & market reports as well as the production of custom consulting projects.
After a Master’s degree in Biotechnologies, Diagnostic Therapeutics & Management, Asma served as Research Assistant at the Moores Cancer Center (San Diego, CA).
She is a coauthor in two scientific publications published in the Molecular Cancer Research Journal.
Asma Siari graduated with an Advanced Master’s degree in International Strategy & Marketing BtoB from EM Lyon Business School (France).
CRISPR-based products in biotech, agritech and diagnostics markets will reach $5B in 2023 before extra growth comes from therapeutic applications. – Get more here
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