Omid Farokhzad (file photo)

Seer rais­es $55M as pro­teomics ap­proach­es prime time in dis­ease de­tec­tion, drug de­vel­op­ment

Omid Farokhzad was work­ing in his Har­vard nan­otech lab in 2017 when he found some­thing he knew would be­come his next com­pa­ny. Two years and, as of to­day, over $100 mil­lion in fund­ing for lat­er, he still hasn’t re­vealed what it is.

“We’ve seen them re­port­ed, but we don’t re­al­ly know what their tech­nol­o­gy is or what it does.” Stephen Williams, the CMO of So­ma­Log­ic, the most high-pro­file po­ten­tial com­peti­tor to Farokhzad’s com­pa­ny, Seer, told End­points News.

The tech­nol­o­gy was big, though, or at least Farokhzad thought so. Big enough for him to leave much of his work in Boston, where he launched two com­pa­nies, opened his own lab and spent 20 years across Har­vard and MIT, to spend most of his time build­ing Seer in Red­wood City, out­side San Fran­cis­co. What he said was this: They were try­ing to best-of-both-worlds a sci­en­tif­ic idea. They want­ed to take a study of hu­man pro­teins they said was of­ten con­duct­ed with ei­ther slip­shod speed or painstak­ing pre­ci­sion and make it both fast and metic­u­lous.

Now, ex­act­ly a year af­ter its pub­lic launch and just as So­ma­Log­ic eyes its biggest com­mer­cial ex­pan­sion, Seer is an­nounc­ing $55 mil­lion in Se­ries D fund­ing and its own piv­ot from a re­search-fo­cused com­pa­ny to one try­ing to bring the pro­teome in­to the med­ical main­stream.

“There was the mo­ment, where I said I need to do this my­self,” Farokhzad told End­points, “and if I don’t I’m go­ing to re­gret it for the rest of my life.” 

Seer, So­ma­Log­ic, and a hand­ful of oth­er com­pa­nies work on what’s be­come known as the pro­teome. For decades, it had been tossed around as a bi­o­log­i­cal what-if, as se­duc­tive as it was un­at­tain­able. Per­haps in­stead of look­ing at DNA and RNA to un­der­stand the hu­man body and its dis­or­ders, we could look at the pro­teins that ge­net­ic code makes, the ones that in most cas­es ul­ti­mate­ly do the dam­age.

The hy­po­thet­i­cals were huge. In­stead of pre­dict­ing, based on ge­net­ics, if a 50-year-old had a pre­dis­po­si­tion to heart at­tacks or di­a­betes, a doc­tor could check if there had been ac­tu­al changes in the blood that built to those ail­ments. Phar­ma com­pa­nies could bet­ter un­der­stand how their drugs worked, and re­fine ac­cord­ing­ly.

One ob­sta­cle was math­e­mat­i­cal. With pro­teins, there are sim­ply far more pos­si­bil­i­ties. DNA has four let­ters and bonds in very spe­cif­ic ways and struc­tures: A-T, G-C, the dou­ble he­lix. Pro­teins are formed from up to 20 amino acids and can bond in myr­i­ad ways, and then change af­ter their cre­ation in­to a va­ri­ety of states de­pend­ing on what bonds to them.

“You ac­tu­al­ly need a lot of com­put­ing pow­er to cal­cu­late the the­o­ret­i­cal com­plex­i­ty you can cre­ate with pro­teins,” Farokhzad said. “You’ll nev­er get there.”

The oth­er prob­lem was chem­i­cal. DNA and RNA can be repli­cat­ed and am­pli­fied in a lab. Pro­teins can­not. In­stead, re­searchers have re­lied on bi­o­log­i­cal fish­ing ex­pe­di­tions. First, they used an­ti­bod­ies, which bind to pro­teins and make them eas­i­er to spot. But each an­ti­body on­ly binds to one pro­tein. Us­ing them to iden­ti­fy every hu­man pro­tein would be, as the New York Times’ Michael Be­har put it last year, “like try­ing to cat­a­log every fish in the ocean with a net that cap­tured on­ly a sin­gle species at a time.”

So­ma­Log­ic built it­self on the dis­cov­ery that nu­cle­ic acids called ap­tamers could be used to iden­ti­fy far more pro­teins at once. They built a data­base of 5,000 hu­man pro­teins, and then use ma­chine learn­ing to see how changes in those pro­teins’ struc­tures and quan­ti­ty cor­re­late with cer­tain health fac­tors. Af­ter decades of de­vel­op­ment and years of clin­i­cal tests, they launched their So­maSig­nal for med­ical prac­tices in Sep­tem­ber and bur­nished it with a De­cem­ber study in Na­ture that scanned 17,000 par­tic­i­pants for those 5,000 pro­teins and pre­dict­ed for di­a­betes and heart at­tack, among oth­er health is­sues.

Those who test­ed as high-risk could then be re­ferred to pre­ven­ta­tive mea­sures they may not oth­er­wise have re­ceived.

Stephen Williams came to So­ma­Log­ic in 2009 af­ter near­ly 20 years in ex­per­i­men­tal and clin­i­cal de­vel­op­ment at Pfiz­er

Click on the im­age to see the full-sized ver­sion

“We tried to de­vel­op 13 mod­els for 13 health is­sues, and we suc­ceed­ed with 11,” Williams said, adding they failed on­ly on weight pre­dic­tions and cur­rent di­et. “We re­al­ly an­swered the ques­tion: Can pro­teins be­come a sole in­for­ma­tion source?”

Farokhzad’s cri­tique is that this is a ‘bi­ased’ ap­proach: So­ma­Log­ic can on­ly look for the pro­teins it has ap­tamers for and it al­so can’t look deeply in­to spe­cif­ic changes. He said his Seer will be ‘un­bi­ased,’ rapid­ly iden­ti­fy­ing every pro­tein – at least 20,000 – and all the changes that can oc­cur with­in them and then use their own ma­chine learn­ing to find pat­terns. “Fast and broad,” he likes to call it.

“To re­al­ly un­der­stand pro­teomics, you have to do it in an un­bi­ased ap­proach,” he said.  “New bi­ol­o­gy is al­ways dri­ven by what we don’t know yet.”

Out in Red­wood City, Farokhzad has set up a Seer head­quar­ters with 40 em­ploy­ees and plans to ex­pand to 80 with the new fund­ing. He said they’ve spent the last year with their heads down try­ing to per­fect the sci­ence. Afraid biobanks might con­t­a­m­i­nate sam­ples with poor pro­ce­dures, they’ve set up 70 clin­i­cal sites na­tion­wide to build their data­base.

Oth­er folks have used an un­bi­ased ap­proach – help­ing build data­bas­es like the Hu­man Pro­teome Pro­ject, which now counts 19,823 pro­teins – but comb­ing through all those amino acids takes for­ev­er. Farokhzad has promised to make it fast enough to work with drug com­pa­nies (they al­ready have part­ners) and un­veil scans like those of­fered by So­ma­Log­ic.

If the tech holds up, it would have big im­pli­ca­tions for ear­ly de­tec­tion, un­veil­ing pre­vi­ous­ly hid­den changes in the body that presage dis­ease. Farokhzard claims it could help clin­i­cal tri­als, nam­ing Alzheimer’s and the hy­poth­e­sis that some of the drugs that failed might work if they treat a pa­tient ear­ly – at a stage we can’t yet de­tect. Like many in pro­teomics, he talks about it like a new fron­tier.

“We’re ba­si­cal­ly open­ing the flood­gate of ac­cess to pro­teom­ic in­for­ma­tion,” he said.

In So­ma­Log­ic’s view, though, that grand vi­sion isn’t nec­es­sary. All ap­proach­es are bi­ased, Williams said. The ques­tion is whether you can make pre­dic­tions that can be put to med­ical use.

“The ques­tion is whether you can mea­sure some­thing that is use­ful or ac­tion­able, not whether there’s some in­her­ent truth,” he said. “For our busi­ness, we don’t need to un­der­stand what the bi­ol­o­gy is. We let the ma­chine learn­ing pick out the best com­bi­na­tion of mea­sure­ments.”

Still, Williams said that when their long­time part­ner No­var­tis – which us­es So­ma­Log­ic’s tech to un­der­stand the mech­a­nisms of their drugs, among oth­er things – needs a high­er res­o­lu­tion look at what So­ma­Log­ic tech­nol­o­gy turns up, they di­rect them to a dif­fer­ent plat­form. Seer is de­vel­op­ing a com­mer­cial scan like So­ma­Log­ic’s and, like So­ma­Log­ic, even­tu­al­ly hopes to put out a (some­what con­tro­ver­sial) chip any­one can use, but their eas­i­est niche may be in drug de­vel­op­ment.

The in­dus­try will know soon enough. So­maSig­nal is on­ly avail­able in Col­orado for now, but a big­ger roll­out is pend­ing and they just hired a new com­mer­cial of­fi­cer. Af­ter two years in rel­a­tive ob­scu­ri­ty, Farokhzad said Seer will soon be open­ing up, and a prod­uct launch is sched­uled for 2021.

“Our tech­nol­o­gy risk is now large­ly put to rest and what lays ahead of us is ba­si­cal­ly prod­uct de­vel­op­ment and com­mer­cial­iza­tion,” he said.  “Now we’ve got to ex­e­cute.”

Inside FDA HQ (File photo)

The FDA just ap­proved the third Duchenne MD drug. And reg­u­la­tors still don’t know if any of them work

Last year Sarepta hit center stage with the FDA’s controversial reversal of its CRL for the company’s second Duchenne muscular dystrophy drug — after the biotech was ambushed by agency insiders ready to reject a second pitch based on the same disease biomarker used for the first approval for eteplirsen, without actual data on the efficacy of the drug.

On Wednesday the FDA approved the third Duchenne MD drug, based on the same biomarker. And regulators were ready to act yet again despite the lack of efficacy data.

Endpoints News

Keep reading Endpoints with a free subscription

Unlock this story instantly and join 87,700+ biopharma pros reading Endpoints daily — and it's free.

Cell and Gene Con­tract Man­u­fac­tur­ers Must Em­brace Dig­i­ti­za­tion

The Cell and Gene Industry is growing at a staggering 30% CAGR and is estimated to reach $14B by 20251. A number of cell, gene and stem cell therapy sponsors currently have novel drug substances and products and many rely on Contract Development Manufacturing Organizations (CDMO) to produce them with adherence to stringent regulatory cGMP conditions. Cell and gene manufacturing for both autologous (one to one) and allogenic (one to many) treatments face difficult issues such as: a complex supply chain, variability on patient and cellular level, cell expansion count and a tight scheduling of lot disposition process. This complexity affects quality, compliance and accountability in the entire vein-to-vein process for critically ill patients.

Franz-Werner Haas, CureVac CEO

UP­DAT­ED: On the heels of a snap $1B raise, Cure­Vac out­lines plans to seek emer­gency OK for their Covid-19 vac­cine in a mat­ter of months

CureVac is going from being one of the quietest players in the race to develop a new vaccine to fight the worst public health crisis in a century to a challenger for the multibillion-dollar market that awaits the first vaccines to make it over the finish line. Typically low-key at a time of brash comments and incredibly ambitious development timelines from the leaders, CureVac now is jumping straight into the spotlight.

Endpoints News

Keep reading Endpoints with a free subscription

Unlock this story instantly and join 87,700+ biopharma pros reading Endpoints daily — and it's free.

US gov­ern­ment re­port­ed­ly be­gins prepar­ing for Covid-19 chal­lenge tri­als. Are they eth­i­cal?

Controversial human challenge trials for potential Covid-19 vaccines reportedly have a new booster — the US government.

Scientists working for the government have begun manufacturing a strain of the novel coronavirus that could be used in such studies, Reuters reported Friday morning. The trials would enroll healthy volunteers to be vaccinated and then intentionally infected with a weakened coronavirus.

Endpoints News

Keep reading Endpoints with a free subscription

Unlock this story instantly and join 87,700+ biopharma pros reading Endpoints daily — and it's free.

Trevor Martin (Mammoth)

Eye­ing in-vi­vo edit­ing, Mam­moth li­cens­es Jen­nifer Doud­na’s new CRISPR en­zyme

Last month, Jennifer Doudna revealed in Science a new, “hyper-compact” CRISPR enzyme that was half the size of traditional CRISPR enzymes and could, she suspected, offer a new, more versatile tool for gene editing.

Now, the University of California-Berkeley has licensed that enzyme, known as Casφ, exclusively to a biotech startup she and two former students set up three years ago: Mammoth Biosciences. It’s the second new CRISPR protein Mammoth has licensed from Doudna’s lab, after they licensed Cas14 in 2019.

Sanofi vet Kather­ine Bowdish named CEO of PIC Ther­a­peu­tics; As the world Terns: Liv­er dis­ease biotech makes ex­ec­u­tive changes

PIC Therapeutics hasn’t raised much money, yet. But the fledgling biotech has attracted a high-profile player to the helm.

The Boston-based biotech has handed the reins to Katherine Bowdish as its president and CEO. Bowdish will also join the board of directors of PIC. Bowdish joins from Sanofi where she served as VP and head of R&D strategy, as well as helping launch and lead Sanofi Sunrise, a venture investment and partnering vehicle at Sanofi. Before that, Bowdish held several exec roles at Permeon Biologics, Anaphore, Alexion Pharmaceuticals and Prolifaron (acquired by Alexion).

Clockwise from left: Canaccord Genuity principal Michelle Gilson, Canaccord Genuity CSO Brian Mueller and BioMarin CSO Hank Fuchs (Canaccord Genuity webcast)

Bio­Marin CSO diss­es ri­vals for the he­mo­phil­ia A gene ther­a­py crown: Way be­hind, fac­ing big re­cruit­ment chal­lenges and at best a .6 on the gen-one scale

The leader in the race to a hemophilia A gene therapy does not like to be compared unfavorably to the competition. And when their top execs do the comparing, don’t look for any modesty — BioMarin, they say, owns the lead.

As Factor VIII expression wanes over time, quite a few analysts have raised questions about the kind of future BioMarin’s gene therapy — a supposed once-and-done treatment — faces if it stops working. But just 7 days away from their PDUFA date, with high odds of success, the top execs clearly feel that they are way out front, while promising their rivals will discover there’s a tough slog ahead trying to pursue trials where large numbers of patients are ineligible for new therapies.

Endpoints Premium

Premium subscription required

Unlock this article along with other benefits by subscribing to one of our paid plans.

Cal­lid­i­tas bets up to $102M on a biotech buy­out, snag­ging a once-failed PBC drug

After spending years developing its oral formulation of the corticosteroid budesonide, Sweden’s Calliditas now has its sights set on the primary biliary cholangitis field.

The company will buy out France-based Genkyotex, and it’s willing to bet up to €87 million ($102 million) that Genkyotex’s failed Phase II drug, GKT831, will do better in late-stage trials.

Under the current agreement, Calliditas $CALT will initially pay €20.3 million in cash for 62.7% of Genkyotex (or €2.80 a piece for 7,236,515 shares) in early October, then circle back for the rest of Genkyotex’s shares under the same terms. If nothing changes, the whole buyout will cost Calliditas €32.3 million, plus up to  €55 million in contingent rights.

James Wilson, WuXi Global Forum at JPM20

FDA puts up a red light for Pas­sage Bio’s first gene ther­a­py pro­gram, de­lay­ing a pro­gram from James Wilson's group at Penn

Gene therapy pioneer James Wilson spearheaded animal studies demonstrating the potential of new treatments injected directly into the brain, looking to jumpstart a once-and-done fix for an extraordinarily rare disease called GM1 gangliosidosis in infants. His team at the University of Pennsylvania published their work on monkeys and handed it over to Passage Bio, a Wilson-inspired startup building a pipeline of gene therapies — with an IND for PBGM01 to lead the way.

Endpoints News

Keep reading Endpoints with a free subscription

Unlock this story instantly and join 87,700+ biopharma pros reading Endpoints daily — and it's free.