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.”

ZS Per­spec­tive: 3 Pre­dic­tions on the Fu­ture of Cell & Gene Ther­a­pies

The field of cell and gene therapies (C&GTs) has seen a renaissance, with first generation commercial therapies such as Kymriah, Yescarta, and Luxturna laying the groundwork for an incoming wave of potentially transformative C&GTs that aim to address diverse disease areas. With this renaissance comes several potential opportunities, of which we discuss three predictions below.

Allogenic Natural Killer (NK) Cells have the potential to displace current Cell Therapies in oncology if proven durable.

Despite being early in development, Allogenic NKs are proving to be an attractive new treatment paradigm in oncology. The question of durability of response with allogenic therapies is still an unknown. Fate Therapeutics’ recent phase 1 data for FT516 showed relatively quicker relapses vs already approved autologous CAR-Ts. However, other manufacturers, like Allogene for their allogenic CAR-T therapy ALLO-501A, are exploring novel lymphodepletion approaches to improve persistence of allogenic cells. Nevertheless, allogenic NKs demonstrate a strong value proposition relative to their T cell counterparts due to comparable response rates (so far) combined with the added advantage of a significantly safer AE profile. Specifically, little to no risk of graft versus host disease (GvHD), cytotoxic release syndrome (CRS), and neurotoxicity (NT) have been seen so far with allogenic NK cells (Fig. 1). In addition, being able to harness an allogenic cell source gives way to operational advantages as “off-the-shelf” products provide improved turnaround time (TAT), scalability, and potentially reduced cost. NKs are currently in development for a variety of overlapping hematological indications with chimeric antigen receptor T cells (CAR-Ts) today, and the question remains to what extent they will disrupt the current cell therapy landscape. Click for more details.

Graphic: Kathy Wong for Endpoints News

What kind of biotech start­up wins a $3B syn­di­cate, woos a gallery of mar­quee sci­en­tists and re­cruits GSK's Hal Bar­ron as CEO in a stun­ner? Let Rick Klaus­ner ex­plain

It started with a question about a lifetime’s dream on a walk with tech investor Yuri Milner.

At the beginning of the great pandemic, former NCI chief and inveterate biotech entrepreneur Rick Klausner and the Facebook billionaire would traipse Los Altos Hills in Silicon Valley Saturday mornings and talk about ideas.

Milner’s question on one of those mornings on foot: “What do you want to do?”

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Chamath Palihapitiya and Pablo Legorreta

Bil­lion­aires Chamath Pal­i­hapi­tiya and Pablo Legor­re­ta hatch an $825M SPAC for cell ther­a­py biotech

Three years after Royalty Pharma chief Pablo Legorreta led a group of investors to buy up a pair of biotechs and create a new startup called ProKidney, the biotech is jumping straight into an $825 million public shell created by SPAC king and tech billionaire Chamath Palihapitiya.

ProKidney was founded 6 years ago but really got going at the beginning of 2019 with the $62 million acquisition of inRegen, which was working on an autologous — from the patient — cell therapy for kidney disease. After extracting kidney cells from patients, researchers expand the cells in the lab and then inject them back into patients, aiming to restore the kidneys of patients suffering from CKD.

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FDA+ roundup: FDA's neu­ro­science deputy de­parts amid on­go­ing Aduhelm in­ves­ti­ga­tions; Califf on the ropes?

Amid increased scrutiny into the close ties between FDA and Biogen prior to the controversial accelerated approval of Aduhelm, the deputy director of the FDA’s office of neuroscience has called it quits after more than two decades at the agency.

Eric Bastings will now take over as VP of development strategy at Ionis Pharmaceuticals, the company said Wednesday, where he will provide senior clinical and regulatory leadership in support of Ionis’ pipeline.

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Sec­ondary patents prove to be key in biosim­i­lar block­ing strate­gies, re­searchers find

While the US biosimilars industry has generally been a disappointment since its inception, with FDA approving 33 biosimilars since 2015, just a fraction of those have immediately followed their approvals with launches. And more than a handful of biosimilars for two of the biggest blockbusters of all time — AbbVie’s Humira and Amgen’s Enbrel — remain approved by FDA but still have not launched because of legal settlements.

Hal Barron (GSK via YouTube)

GSK R&D chief Hal Bar­ron jumps ship to run a $3B biotech start­up, Tony Wood tapped to re­place him

In a stunning switch, GlaxoSmithKline put out word early Wednesday that R&D chief Hal Barron is exiting the company after 4 years — a relatively brief run for the man chosen by CEO Emma Walmsley in late 2017 to turn around the slow-footed pharma giant.

Barron is being replaced by Tony Wood, a close associate of Barron’s who’s taking one of the top jobs in Big Pharma R&D. He’ll be closer to home, though, for GSK. Barron has been running a UK and Philadelphia-based research organization from his perch in San Francisco.

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CBO: Medicare ne­go­ti­a­tions will ham­per drug de­vel­op­ment more than pre­vi­ous­ly thought

As President Biden’s Build Back Better Act — and, with it, potentially the Democrats’ last shot at major drug pricing reforms in the foreseeable future — remains on life support, the Congressional Budget Office isn’t helping their case.

The CBO last week released a new slide deck, outlining an update to its model on how Medicare negotiations might take a bite out of new drugs making it to market. The new model estimates a 10% long-term reduction in the number of new drugs, whereas a previous CBO report from August estimated that 8% fewer new drugs will enter the market over 30 years.

Joshua Brumm, Dyne Therapeutics CEO

FDA or­ders DMD tri­al halt, rais­ing ques­tions about a whole class of promis­ing drugs

Dyne Therapeutics’ stock took a nasty hit this morning after the biotech put out word that the FDA had slapped a clinical hold on their top program for Duchenne muscular dystrophy. And now speculation is bouncing around Biotwitter that there could be a class effect at work here that would implicate other drug developers in the freeze.

Dyne execs didn’t have a whole lot to say about why the FDA sidelined their IND for DYNE-251 in DMD while “requesting additional clinical and non-clinical information for” the drug.

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CEO Lex Rovner (64x Bio)

A George Church spin­out fight­ing the vi­ral vec­tor bot­tle­neck in cell and gene ther­a­py lands $55M

A synthetic biology company spun out of George Church’s lab is set to tackle the gene therapy manufacturing bottleneck, and it just landed $55 million in a Series A financing round to do so.

64x Bio comes out of the Harvard Department of Genetics. CEO Lex Rovner and her team — which right now, sits around 10 people — are looking to tackle a key hurdle for major companies: manufacturing cell and gene therapies.