Brendan Frey (Deep Genomics)

Deep Ge­nomics, now flush with cash, plans to take dozens of RNA ther­a­pies to the clin­ic

It was 2002 when Bren­dan Frey no­ticed a huge gap in biotech. The hu­man genome had just been se­quenced, al­low­ing sci­en­tists to map ge­net­ic mu­ta­tions. But there weren’t enough da­ta to un­der­stand the con­se­quences of those mu­ta­tions, or re­al­ly do much about them.

Pre­dict­ing there would be an ex­plo­sion of new da­ta, Frey spent the next 13 years work­ing on a way to sift through it all. Now, thanks to ad­vances in RNA ther­a­peu­tics, med­i­cine is be­com­ing pro­gram­ma­ble, Frey said. And on Wednes­day, a slate of in­vestors bet $180 mil­lion that his com­pa­ny’s AI plat­form can make sense of it.

“What’s re­al­ly cool about RNA ther­a­peu­tics is that they’re ba­si­cal­ly a se­quence of let­ters,” Frey said. “Change the se­quence of let­ters one way, you tar­get a dif­fer­ent gene. Change it one way, you can in­crease the amount of pro­tein pro­duced by that gene. Change the se­quence of let­ters a dif­fer­ent way, you can de­crease the pro­tein.”

It’s all dig­i­tal in­for­ma­tion, Frey said. And thanks to AI and deep learn­ing tools, Deep Ge­nomics says it can do things like fig­ure out which mech­a­nisms of ac­tion will (or won’t) work against a spe­cif­ic gene, with­out per­form­ing a sin­gle ex­per­i­ment.

“We can take a gene where an­oth­er com­pa­ny would have spent two years on it and then failed and dropped it, and we can ac­tu­al­ly drug that gene, or we know to put it at the bot­tom of the list, just don’t do it now, it’s go­ing to be too hard,” he said.

In 2019, the com­pa­ny put for­ward its first pre­clin­i­cal can­di­date, a ther­a­py for Wil­son dis­ease that’s ex­pect­ed to hit the clin­ic along with three oth­er can­di­dates by 2023. Us­ing the AI sys­tem, the team says it was able to go from tar­get iden­ti­fi­ca­tion to de­clar­ing a win­ner in 18 months. Deep Ge­nomics has a to­tal of 10 can­di­dates hurtling to­ward the clin­ic, and Frey says he ex­pects to add 20 more in the near fu­ture.

The oth­er three can­di­dates ex­pect­ed to hit the clin­ic by 2023 are for fron­totem­po­ral de­men­tia, gout and Nie­mann-Pick type C dis­ease.

The AI space is teem­ing with play­ers, like Enve­da, which nabbed a $51 mil­lion Se­ries A round last month to pur­sue new ther­a­pies for Wil­son dis­ease, NASH and Parkin­son’s dis­ease. Up­on pulling in a $225 mil­lion Se­ries C round last month, In­sil­i­co CEO Alex Zha­voronkov laid out big plans to emerge as the Ama­zon or Google of the field. Around the same time, UK-based Ex­sci­en­tia splurged on the three-year-old mol­e­cule screen­ing biotech All­cyte in an at­tempt to edge out ri­vals.

What sep­a­rates Deep Ge­nomics from some of its peers — like Re­cur­sion, Ex­sci­en­tia or in­sitro — is its sole fo­cus on RNA bi­ol­o­gy, Frey said.

“We like RNA bi­ol­o­gy be­cause of that rock sol­id frame­work,” he said. “We have 100 petabytes of da­ta, so every­thing’s in place.”

Frey says the AI tech is less like a grand, all-know­ing com­put­er, and more like a work­bench, with dozens of tools that have de­fined func­tions and scopes. For ex­am­ple, one tool was built to go through data­bas­es of pa­tient mu­ta­tions and find drug tar­gets based on RNA bi­ol­o­gy — but re­searchers at the com­pa­ny re­al­ized it could al­so be used to an­a­lyze dif­fer­ent types of an­i­mal mod­els and fig­ure out which ones would re­ca­pit­u­late hu­man bi­ol­o­gy.

“That’s kind of the ad­van­tage of the work­bench metaphor is it sort of frees peo­ple up to be more cre­ative,” Frey said.

Soft­bank Vi­sion Fund 2 led the Se­ries C round, with a hand from Fi­deli­ty Man­age­ment & Re­search Com­pa­ny, Cana­di­an Pen­sion Plan In­vest­ment Board, True Ven­tures, Am­pli­tude Ven­tures, Khosla Ven­tures and Mag­net­ic Ven­tures. When asked if an IPO is in the near fu­ture, Frey said he doesn’t plan to take the com­pa­ny pub­lic at least un­til they reach the clin­ic.

“A lot of com­pa­nies have gone pub­lic pre­clin­i­cal­ly in the last year, and the prob­lem is that if they stum­ble in get­ting in­to the clin­ic, then the ex­is­tence of the com­pa­ny will be put in­to ques­tion,” he said. “We don’t want to be in that sit­u­a­tion.”

Has the mo­ment fi­nal­ly ar­rived for val­ue-based health­care?

RBC Capital Markets’ Healthcare Technology Analyst, Sean Dodge, spotlights a new breed of tech-enabled providers who are rapidly transforming the way clinicians deliver healthcare, and explores the key question: can this accelerating revolution overturn the US healthcare system?

Key points

Tech-enabled healthcare providers are poised to help the US transition to value, not volume, as the basis for reward.
The move to value-based care has policy momentum, but is risky and complex for clinicians.
Outsourced tech specialists are emerging to provide the required expertise, while healthcare and tech are also converging through M&A.
Value-based care remains in its early stages, but the transition is accelerating and represents a huge addressable market.

Lat­est on ul­tra-rare dis­ease ap­proval; Pos­i­tive, if mixed, signs for Bio­gen's ALS drug; Clay Sie­gall finds a new job; and more

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FDA spells out how can­cer drug de­vel­op­ers can use one tri­al for both ac­cel­er­at­ed and full ap­provals

The FDA’s Oncology Center of Excellence has been a bright spot within the agency in terms of speeding new treatments to patients. That flexibility was on full display this morning as FDA released new draft guidance spelling out exactly how oncology drug developers can fulfill both the accelerated and full approval’s requirements with just a single randomized controlled trial.

While Congress recently passed legislation that will allow FDA to require confirmatory trials to be recruiting and ongoing prior to granting an accelerated approval, the agency is now making clear that the initial trial used to win the AA, if designed appropriately, can also serve as the trial for converting the accelerated approval into a full approval.

Clay Siegall, Morphimmune CEO

Up­dat­ed: Ex-Seagen chief Clay Sie­gall emerges as CEO of pri­vate biotech

Clay Siegall will be back in the CEO seat, taking the helm of a private startup working on targeted cancer therapies.

It’s been almost a year since Siegall resigned from Seagen, the biotech he co-founded and led for more than 20 years, in the wake of domestic violence allegations by his then-wife. His eventual successor, David Epstein, sold the company to Pfizer in a $43 billion deal unveiled last week.

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FDA ad­vi­sors unan­i­mous­ly rec­om­mend ac­cel­er­at­ed ap­proval for Bio­gen's ALS drug

A panel of outside advisors to the FDA unanimously recommended that the agency grant accelerated approval to Biogen’s ALS drug tofersen despite the drug failing the primary goal of its Phase III study, an endorsement that could pave a path forward for the treatment.

By a 9-0 vote, members of the Peripheral and Central Nervous System Drugs Advisory Committee said there was sufficient evidence that tofersen’s effect on a certain protein associated with ALS is reasonably likely to predict a benefit for patients. But panelists stopped short of advocating for a full approval, voting 3-5 against (with one abstention) and largely citing the failed pivotal study.

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No­vo Nordisk oral semaglu­tide tri­al shows re­duc­tion in blood sug­ar, plus weight loss

Novo Nordisk is testing higher levels of its oral version of its GLP-1, semaglutide, and its type 2 diabetes trial results released today show reductions in blood sugar as well as weight loss.

In the Phase IIIb trial, Novo compared its oral semaglutide in 25 mg and 50 mg doses with the 14 mg version that’s currently the maximum approved dose. The trial looked at how the doses compared when added to a stable dose of one to three oral antidiabetic medicines in people with type 2 diabetes who were in need of an intensified treatment.

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Sijmen de Vries, Pharming CEO

FDA ap­proves Pharm­ing drug for ul­tra-rare im­mun­od­e­fi­cien­cy dis­ease

US regulators cleared an ultra-rare drug from Pharming Group, by way of Novartis, on Friday afternoon.

The Dutch biotech said the FDA greenlit leniolisib for an immunodeficiency disease known as activated phosphoinositide 3-kinase delta (PI3Kδ) syndrome, or APDS. People 12 years and older can receive the oral drug, to be marketed as Joenja, beginning early next month, Pharming said, five days ahead of the decision deadline set by the FDA as part of a priority review.

Eu­ro­pean doc­tors di­al up dig­i­tal com­mu­ni­ca­tion with phar­mas, but still lean to­ward in-per­son med meet­ings, study finds

As in-person sales rep access declines in the big five European countries, a corresponding uptick in virtual rep access is happening. It’s not surprising, but it does run counter to pharma companies’ assessment – along with long-held sales rep sway in Europe – that in-person access hadn’t changed.

CMI Media Group and Medscape’s recent study reports that 75% of physicians in the EU5 countries of Spain, Germany, Italy, France and the UK already limit engagements with pharma sales reps, and 25% of those surveyed plan to decrease time with reps.

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Judge al­lows ex­pert tes­ti­mo­ny in GSK tri­al al­leg­ing Zan­tac link to can­cer

A California judge will allow a plaintiff in a state court case to introduce expert testimony connecting a potential carcinogen in former blockbuster medicine Zantac to cancer.

The order was handed down on Thursday from state judge Evelio Grillo, who is now allowing both parties to introduce expert testimony in an upcoming trial after what’s known as a Sargon hearing, where a judge determines the admissibility of expert witnesses and expert opinions.