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May 26, 2019
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Mammoth Biosciences adds the final piece of the CRISPR diagnostics puzzle to its toolkit

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With the announcement today that Mammoth Biosciences has received the exclusive license from the University of California, Berkeley to the new CRISPR protein Cas14, the company now has the last piece of its diagnostics toolkit in place.

Cas14 is a newly discovered protein from the lab of Jennifer Doudna, a pioneer in gene-editing research and a member of the first research team to identify and unlock the power of CRISPR technology.

Doudna and Mammoth Biosciences co-founder Lucas Harrington were part of the team of researchers to identify the new Cas14 protein, which can identify single-stranded DNA. The journal Science published their findings in October 2018.

“With the addition of this protein that is DNA binding and target single strands, it really means we can target any nucleic acid,” says Mammoth chief executive Trevor Martin . “It’s an extension of the toolbox.”

Mammoth Biosciences lab

The licensing deal moves Mammoth one step closer toward its goal of low-cost, in-home molecular diagnostics for any illness. “The idea is we want to make this test so affordable that you can imagine going down to your CVS or Walgreens so you can bring this access to molecular level information [to questions like] if my kid has strep or flu before dropping them off to school.”

With the addition of the Cas14 protein to its portfolio, Mammoth can now run even more refined tests to assess multiple aspects of a virus or bacteria that may be present.

“When you run a single test [it’s about] how much information are you getting,” says Martin. “Are you learning that HPV is present or absent, or are you learning whether it’s a strain of HPV which has a risk of cervical cancer.”

The more granular Mammoth can be with its diagnostics, the better able the company is to determine a number of different conditions or factors that may influence treatment down the road.

Now, the company is shifting to product development and testing. The company has signed its first partnerships in the past few months with several undisclosed companies, Martin says.

Mammoth is one of the first companies to turn CRISPR’s gene editing technologies to tackle the diagnostics problem in medicine, rather than concentrate on therapies or drug development. “Even though CRISPR has taken the gene editing field by storm, we’re really at the beginning of what we’re doing.”

While applications for editing as a therapeutic tool have been tied up in patent litigation between the Berkeley lab and the Broad Institute, using CRISPR as a diagnostics tool is pretty clearly the purview of Cal. So Mammoth has fewer obstacles in its path as it works to develop its diagnostics product.

“Long term Cas14 is the most diverse protein,” says Martin, so the protein can perform more varied types of analysis. The other CRISPR proteins are limited in the types of DNA or RNA strands they can target, but the Cas14 is more flexible and can edit any sequence of proteins. 

U.S. rule changes could mean more startups would need government approval to hire immigrants

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Big changes in DC could mean that more startups will need the government’s permission before foreign nationals do work at the company.  In some cases, the foreign national will need to leave the company if the government is wary of granting that permission. 

This is tied up in the same new law that gave a once obscure government body—CFIUS—enhanced abilities to scrutinize minority, non-controlling investments by foreign entities. 

CFIUS changes have grabbed most of the headlines, but a Commerce Department process to define “emerging technologies” could have a huge effect on startups that employ foreign nationals.

Here’s what you need to know: the U.S. government has long controlled exports of sensitive technology for national security reasons.  This is done through the export controls regime, which impacts things like arms and ammunition, but also telecommunications and encryption software, among other items. 

Today, many venture-backed companies are not impacted by export controls because their technology is not on one of the control lists.  But that stands to change soon. 

Recent legislation requires the Commerce Department to evaluate controls on “emerging technologies.”  To kick off this process, in November the government identified 14 categories of technology it is looking at.  This included tech in the sweet spot of the bat for venture: AI/ML, robotics, 3D printing, and biotechnology to name a few.  It is an open question as to which of these technologies will ultimately be subject to controls and to what degree.

Image: Bryce Durbin/TechCrunch

Once something is determined to be emerging technology, the government can establish controls on the export, re-export, or transfer (in-country) of that technology.  Export controls is often thought of as the need to get a license from the government before sending a technology outside the U.S., and that is indeed a major part of what startups will need to contend with. 

But perhaps far more impactful for the startup ecosystem is what’s called “deemed exports,” or the release of controlled technology to foreign persons situated in the United States, which is “deemed” to be an export to the person’s country or countries of nationality. 

“The ramifications of these changes could be tremendous if the government does not appropriately tailor what it means to be an emerging technology.”

“Release” is defined broadly to include visual inspection and oral or written exchanges regarding the technology; in other words, typical actions an engineer or scientist at a young company does.  One saving grace for some startups will be that the deemed export rule does not apply to green card holders, though does apply to employer-based visas, like the H-1B or O visa.

Let’s think about how this might play out in practice.  Imagine the government decides to control artificial intelligence as an emerging technology and that a U.S.-based AI company employs an engineer on an H-1B visa.  Under these facts, it seems the company would need an export license for the foreign national to work at the company. 

A large company might be able to set up a wall that allows the foreign national to work on non-emerging technologies, but for a startup that only does AI the ability to separate the foreign national from the emerging technology work is severely limited, if not impossible.

Obtaining these licenses would present a tremendous burden for small, high-growth startups that often build teams by attracting the best and brightest from foreign countries.

But that burden could be the least of the company’s problems if the foreign national is from a country like China. The U.S. government could be very reluctant to grant a license for someone from China to work on an emerging technology since the major motivation behind recent foreign investment scrutiny has been China. The result might be the foreign national has to leave the company entirely, exacerbating the severe talent drought in some disciplines.

IvancoVlad via Getty Images

Those working in the startup ecosystem understand the volume of foreign nationals working at high-growth companies, but also how impactful their work is to make the United States the world’s scientific and technological leader. 

In comments to the government, a consortium of life science investors backing companies in oncology, cystic fibrosis, anemia, and other areas sounded the alarm of how deemed exports could make laboratory collaboration between U.S. and foreign nationals difficult or impossible.  Certainly, this is not the result policymakers are shooting for given the public policy imperative of eradicating diseases. The ramifications of these changes could be tremendous if the government does not appropriately tailor what it means to be an emerging technology.

Comments from the National Venture Capital Association, where I work, stressed that many of the technologies the Commerce Department called out in November are not yet well-defined, which of course makes regulating them challenging. 

In addition, because many of the technologies—like AI/ML—will be widely used across many companies and industries, a broad set of controls could sweep in many unintended target companies and technologies. To alleviate these concerns, we recommended a targeted approach to classification of emerging technologies that categorizes only those technologies that have significant defense uses, and not broad commercial applications.

The U.S. government needs to tread carefully. 

The golf professional Sam Snead advised that a golf club needs to be gripped like you’re holding a live bird: firm enough so it doesn’t fly out of your hands but not so tight that you kill it. American innovation is the same in this way. 

Yes, policymakers need to consider the impact of emerging technology on national security and perhaps create some controls. But if policymakers ratchet up pressure too much, then talent, capital, and companies will flock to other countries, which means the United States loses out on the incredible benefits that high-growth startups bring to our country.  The rules of the road on emerging technologies have not been written, and each of us has an opportunity to make our voice heard during the process.

With $90 million in funding, the Ginkgo spinoff Motif joins the fight for the future of food

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Continuing its quest to become the Amazon Web Services for biomanufacturing, href=”http://ginkgobioworks.com/”>Ginkgo Bioworks has launched a new spinoff called Motif Ingredients with $90 million in funding to develop proteins that can serve as meat and dairy replacements.

It’s the second spinout for Ginkgo since late 2017 when the company partnered with Bayer to launch Joyn Bio, a startup researching and developing bacteria that could improve crop yields.

Now, with Motif, Ginkgo is tackling the wild world of protein replacements for the food and beverage industry through the spinoff of Motif Ingredients.

It’s a move that’s likely going to send shockwaves through several of the alternative meat and dairy companies that were using Ginkgo as their manufacturing partner in their quest to reduce the demand for animal husbandry — a leading contributor to global warming — through the development of protein replacements.

“To help feed the world and meet consumers’ evolving food preferences, traditional and complementary nutritional sources need to co-exist. As a global dairy nutrition company, we see plant- and fermentation-produced nutrition as complementary to animal protein, and in particular cows’ milk,” said Judith Swales, the Chief Operating Officer, for the Global Consumer and Foodservice Business, of Fonterra, an investor in Ginkgo’s new spinout.

To ensure the success of its new endeavor Ginkgo has raised $90 million in financing from industry insiders like Fonterra and the global food processing and trading firm Louis Dreyfus Co., while also tapping the pool of deep-pocketed investors behind Breakthrough Energy Ventures, the climate focused investment fund financed by a global gaggle of billionaires including Marc Benioff, Jeff Bezos, Michael Bloomberg, Richard Branson, Bill Gates, Reid Hoffman, John Doerr, Vinod Khosla, Jack Ma, Neil Shen, Masayoshi Son, and Meg Whitman.

Leading Ginkgo’s latest spinout is a longtime veteran of the food and beverage industry, Jonathan McIntyre, the former head of research and development at another biotechnology startup focused on agriculture — Indigo Ag.

McIntyre, who left Indigo just two years after being named the company’s head of research and development, previously had stints at Monsanto, Nutrasweet, and PepsiCo (in both its beverage and snack divisions).

“There’s an opportunity to produce proteins,” says McIntyre. “Right now as population grows the protein supply is going to be challenged. Motif gives the ability to create proteins and make products from low cost available genetic material.”

Photo: paylessimages/iStock

Ginkgo, which will have a minority stake in the new company, will provide engineering and design work to Motif and provide some initial research and development work on roughly six to nine product lines.

That push, with the financing, and Ginkgo’s backing as the manufacturer of new proteins for Motif Ingredients should put the company in a comfortable position to achieve McIntyre’s goals of bringing his company’s first products into the market within the next two years. All Motif has to pay is cost plus slight overhead for the Ginkgo ingredients.

“We started putting Motif together around February or March of 2018,” says Ginkgo co-founder Jason Kelly of the company’s plans. “The germination of the business had its inception earlier though, from interacting with companies in the food and beverage scene. When we talked to these companies the strong sense we got was if there had been a trusted provider of outsourced protein development they would have loved to work with us.”

The demand from consumers for alternative sources of protein and dairy — that have the same flavor profiles as traditional dairy and meats — has reached an inflection point over the past few years. Certainly venture capital interest into the industry has soared along with the appetite from traditional protein purveyors like Danone, Tyson Foods, and others to take a bite out of the market.

Some industry insiders think it was Danone’s 2016 acquisition of WhiteWave in a $12.5 billion deal that was the signal which brought venture investors and food giants alike flocking to startups that were developing meat and dairy substitutes. The success of companies like Beyond Meat and Impossible Foods has only served to prove that a growing market exists for these substitutes.

At the same time, solving the problem of protein for a growing global population is critical if the world is going to reverse course on climate change. Agriculture and animal husbandry are huge contributors to the climate crisis and ones for which no solution has made it to market.

Investors think cultured proteins — fermented in tanks like brewing beer — could be an answer.

Photograph: David Parry/EPA

“Innovative or disruptive solutions are key to responding to changing consumer demand and to addressing the challenge of feeding a growing world population sustainably,” said Kristen Eshak Weldon, Head of Food Innovation & Downstream Strategy at Louis Dreyfus Company (LDC), a leading merchant and processor of agricultural goods. “In this sense, we are excited to partner with Motif, convinced that its next-generation ingredients will play a vital role.”

Breakthrough Energy Ventures certainly thinks so.

The investment firm has been busy placing bets across a number of different biologically based solutions to reduce the emissions associated with agriculture and cultivation. Pivot Bio is a startup competing with Ginkgo’s own Joyn Bio to create nitrogen fixing techniques for agriculture. And earlier this month, the firm invested as part of a $33 million round for Sustainable Bioproducts, which is using a proprietary bacteria found in a remote corner of Yellowstone National Park to make its own protein substitute.

For all of these companies, the goal is nothing less than providing a commercially viable technology to combat some of the causes of climate change in a way that’s appealing to the average consumer.

“Sustainability and accessible nutrition are among the biggest challenges facing the food industry today. Consumers are demanding mindful food options, but there’s a reigning myth that healthy and plant-based foods must come at a higher price, or cannot taste or function like the animal-based foods they aim to replicate,” said McIntyre, in a statement. “Biotechnology and fermentation is our answer, and Motif will be key to propelling the next food revolution with affordable, sustainable and accessible ingredients that meet the standards of chefs, food developers, and visionary brands.”

Up to $818 million deal between J&J and Locus Biosciences points to a new path for CRISPR therapies

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The up to $818 million deal between Locus Biosciences and Janssen Pharmaceuticals (a division of Johnson & Johnson) that was announced yesterday points toward a new path for CRISPR gene editing technologies and (potentially) the whole field of microbiome-targeted therapies.

Based in Research Triangle Park, N.C., Locus is commercializing research initially developed by scientists at North Carolina State University that focused on Cas3 proteins, which devour DNA Pac-Man-style, rather than edit it like the more well-known Cas9-based CRISPR technologies being used by companies like Caribou Biosciences, Editas Medicine, Synthego, Intellia Therapeutics, CRISPR Therapeutics and Beam Therapeutics.

While the Cas9 CRISPR technologies can edit targeted DNA — either deleting specific genetic material or replacing it with different genetic code — Cas3 simply removes DNA strains. “Its purpose is the destruction of invading DNA,” says Locus chief executive, Paul Garofolo.

The exclusive deal between Janssen Pharmaceuticals and Locus gives Janssen the exclusive license to develop, manufacture and commercialize CRISPR-Cas3-enhanced products targeting bacterial pathogens for the potential treatment of respiratory and other organ infections.

Under the terms of the deal, Locus is getting $20 million in upfront payments and could receive up to $798 million in potential future development and commercial milestone payments and any royalties on potential product sales.

A former executive at Valiant Pharmaceuticals and Paytheon, Garofolo was first introduced to the technology that would form the core of Locus as an executive in residence at North Carolina State University. It was there that he met Dr. Chase Beisel and Rodolphe Barrangou, whose research into Cas3 proteins would eventually be productized by Locus.

The company spun out of NC State in 2015 and raised its first cash from the North Carolina Biotech Center a year later.

Locus is already commercializing a version of its technology with bacteriophages designed to target e coli bacteria to treat urinary tract infections. The company is on target to begin its first clinical trials in the third quarter of the year.

The focus on bacterial infection and removing harmful bacteria while ensuring that the rest of a patient’s microbiome is intact is a huge step forward for treating diseases that scientists believe could be linked to bacterial health in a body, according to Garofolo.

“Most microbiome companies are about adding probiotics to your body,” says Garofolo, representing a thesis that introducing “good” bacteria to the body can offset any harmful pathogens that have infected it.

“Things you’re exposed to are creating the groundwork for an infection or disease, or exacerbating an existing disease,” says Garofolo. And while he believes that the microbiome is the next big field for scientific discovery, the approach of adding probiotics to a system seems less targeted and effective to him.

Already, Garofolo has managed to convince investors of his approach. In addition to the initial outside investment from the North Carolina Biotech Center, Locus has attracted $25 million in financing from investors, including Artis Ventures and the venture capital arm of the Chinese internet giant, Tencent.

Meanwhile, investors have spent millions backing alternative approaches to improving human health through the manipulation of the microbiome.

Companies like Second Genome, Viome and Ubiome are all using approaches that identify bacteria in the human body and try to regulate the production of that bacteria through diet and probiotic pills. It’s an approach that allows these companies to skirt the more stringent requirements the Food and Drug Administration has put in place for drugs.

That doesn’t mean that extensive amounts of research haven’t gone into the development of these probiotics. Seed, a Los Angeles-based startup that launched last year, has recruited as its chief scientist George Reid, the leading scientist on microbial health and the microbiome.

Founded by Raja Dhir, a graduate from the University of Southern California and a leading researcher on microbiotics in his own right, and Ara Katz, the former chief marketing officer of BeachMint and an MIT Media Lab fellow, Seed focuses on developing probiotic treatments using well-established research.

“Foundational to our approach is that it’s not which microbes are present in your gut… It’s based on looking at what specific microbes can do to a healthy individual to improve that status of health independent of what is already present,” Dhir said in an interview around the company’s launch last June. “It’s a little bit less exciting from a tech perspective, but it’s hardcore grounded in basic science… The question is, does this have changes and effects in validated bio-makers in a controlled and placebo setting?”

Dhir said that a basic understanding of how different bacteria can influence health is necessary before getting into the benefits of personalization.

These things can dance between drugs and nutrition,” Dhir said. “Probacteria are an additional lever that people should pull… like diet and exercise and cessation of smoking… In every correspondence we always have been and need to be clear that this should never be seen as a replacement of therapies.”

By contrast, the tools that Locus is developing are very much therapies with potentially far-reaching implications for illnesses, from irritable bowel syndrome to gastrointestinal cancers and even neurological disorders.

“The science [around the microbiome] is early, but it is very well-known that a potentially deadly pathogen should be removed from your body,” Garofolo said.

Sophia Genetics bags $77M Series E, with 850+ hospitals signed up to its “data-driven medicine”

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Another sizeable cash injection for big data biotech: Sophia Genetics has announced a $77M Series E funding round, bringing its total raised to $140M since the business was founded back in 2011.

The company, which applies AI to DNA sequencing to enable what it dubs “data-driven medicine”, last closed a $30M Series D in fall 2017.

The Series E was led by Generation Investment Management . Also investing: European private equity firm, Idinvest Partners. Existing investors, including Balderton Capital and Alychlo, also participated in the round.

When we last spoke to Sophia Genetics it had around 350 hospitals linked via its SaaS platform, and was then adding around 10 new hospitals per month.

Now it says its Sophia AI platform is being used by more than 850 hospitals across 77 countries, and it claims to have supported the diagnosis of more than 300,000 patients.

The basic idea is to improve diagnoses by enabling closer collaboration and knowledge sharing between hospitals via the Sophia AI platform, with an initial focus on oncology, hereditary cancer, metabolic disorders, pediatrics and cardiology. 

Expert (human) insights across the network of hospital users are used to collectively enhance genomic diagnostics, and push towards predictive analysis, by feeding and training AI algorithms intended to enhance the reading and analysis of DNA sequencing data.

Sophia Genetics describes its approach as the “democratization” of DNA sequencing expertise.

Commenting on the Series E in a statement, Lilly Wollman, co-head of Generation’s growth equity team said: “We believe that leveraging genetic sequencing and advanced digital analysis will enable a more sustainable healthcare system. Sophia Genetics is a leader in the preventive and personalized medicine revolution, enabling the development of targeted therapeutics, thereby vastly improving health outcomes. We admire Sophia Genetics not just for its differentiated analytics capability across genomic and radiomic data, but also for its exceptional team and culture”.

The new funding will be put towards further expanding the number of hospitals using Sophia Genetics’ technology, and also on growing its headcount with a plan to ramp up hiring in the US especially.

The Swiss-founded firm is now co-based in Lausanne and Boston, US.

In another recent development the company added radiomics capabilities to its platform last year, allowing for what it describes as “a prediction of the evolution of a tumour”, which it suggests can help inform a physician’s choice of treatment for the patient.

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