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.”

At the In­flec­tion Point for the Next Gen­er­a­tion of Can­cer Im­munother­a­py

While oncology researchers have long pursued the potential of cellular immunotherapies for the treatment of cancer, it was unclear whether these therapies would ever reach patients due to the complexity of manufacturing and costs of development. Fortunately, the recent successful development and regulatory approval of chimeric antigen receptor-engineered T (CAR-T) cells have demonstrated the significant benefit of these therapies to patients.

Tillman Gerngross (Adagio)

Till­man Gern­gross on Omi­cron: 'It is a grim sit­u­a­tion...we’re go­ing to see a sig­nif­i­cant drop in vac­cine ef­fi­ca­cy'

Tillman Gerngross, the rarely shy Dartmouth professor, biotech entrepreneur and antibody expert, has been warning for over a year that the virus behind Covid-19 would likely continue to mutate, potentially in ways that avoid immunity from infection and the best defenses scientists developed. He spun out a company, Adagio, to build a universal antibody, one that could snuff out any potential mutation.

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In­cor­po­rat­ing Ex­ter­nal Da­ta in­to Clin­i­cal Tri­als: Com­par­ing Dig­i­tal Twins to Ex­ter­nal Con­trol Arms

Most drug development professionals are familiar with the nerve-racking wait for the read-out of a large trial. If it’s negative, is the investigational therapy ineffective? Or could the failure result from an unforeseen flaw in the design or execution of the protocol, rather than a lack of efficacy? The team could spend weeks analyzing data, but a definitive answer may be elusive due to insufficient power for such analyses in the already completed trial. These problems are only made worse if the trial had lower enrollment, or higher dropout than expected due to an unanticipated event like COVID-19. And if a trial is negative, the next one is likely to be larger and more costly — if it happens at all.

More man­u­fac­tur­ing is­sues: Fen­nec preps for sec­ond CRL for po­ten­tial hear­ing loss drug

Shares of Fennec Pharmaceuticals stock were cut almost in half early Monday as the company said manufacturing issues caused another FDA rejection of its reformulated version of sodium thiosulfate, which is intended to help kids who lose hearing due to chemo treatment.

The biotech had resubmitted an NDA for the drug to treat platinum-based, chemo-related ototoxicity in young children earlier this year. The first NDA was denied by the FDA last year, with the agency citing manufacturing issues with the biotech’s supplier.

Róbert Wessman, Alvogen CEO

Biotech bil­lion­aire Róbert Wess­man en­gi­neers $450M deal for Alvo­gen sub­sidiaries

Alvogen is handing off two of its subsidiaries to CEO Róbert Wessman and his healthcare investment firm Aztiq — who has now tied the two together in a massive biobucks deal.

In an alliance with Thailand’s PTT Group subsidiary Innobic, the two companies signed an agreement last week to buy a 100% stake in Alvogen Emerging Market Holdings Limited (AEMH) for $475 million from Alvogen, buying out shareholders such as CVC Capital Partners and Singapore’s Temasek. And now, the group is the majority shareholder of Alvogen’s former Asian subsidiary Lotus Pharmaceuticals and the only shareholder of Alvogen Malta, the owner of B2B pharma Adalvo.

Like the flu vac­cine every year, the FDA could move quick­ly on a vari­ant-tar­get­ed Covid vac­cine

In the same way that the FDA signs off on flu vaccines every year without requiring large clinical trials to measure their efficacy, the FDA may employ a similar strategy in authorizing variant-focused versions of the mRNA vaccines.

As the world braces for more data on the latest variant Omicron, which may reduce vaccine efficacy, top vaccine developers like Moderna and Pfizer-BioNTech have promised they can pull together a new vaccine targeted against a specific Covid variant in about 100 days. Since Omicron emerged last week, Pfizer-BioNTech, Moderna and J&J have all said they’ve begun work on Omicron-specific vaccines, if needed.

Thanks­giv­ing edi­tion: Top 15 End­points sto­ries of 2021; Can you name that vac­cine?; Mer­ck­'s Covid an­tivi­ral dis­ap­points; FDA nom­i­nee's in­dus­try ties; and more

Welcome back to Endpoints Weekly, your review of the week’s top biopharma headlines. Want this in your inbox every Saturday morning? Current Endpoints readers can visit their reader profile to add Endpoints Weekly. New to Endpoints? Sign up here.

Happy Thanksgiving to all those who are celebrating it — although, if we are being honest, this week’s abbreviated edition is really for those who are not. Wherever you’re tuning in from, we appreciate your support, hope you find this recap helpful and we wish you a wonderful weekend.

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Troy Wilson, Kura CEO

UP­DAT­ED: FDA hits the red light on an ear­ly-stage AML study af­ter a pa­tient dies

The FDA has slapped a clinical hold on the early-stage program for one of Kura Oncology’s cancer drugs following a patient’s death in a clinical trial.

The biotech $KURA reported early Wednesday that the Phase Ib study of KO-539 for acute myeloid leukemia would be halted, suspending enrollment, while researchers and the FDA probed the death. Patients already on the drug can continue taking it.

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What were End­points read­ers tun­ing in­to this year? Here’s a look at our 15 most pop­u­lar re­ports of the year (so far)

At the beginning of this year, I laid out a basic objective for Endpoints News as we headed to our 5th anniversary. We’ve long been doing a fine job covering the breaking news in R&D — if I do say so myself — but we needed to expand our horizons on industry coverage, increase the staff and go much, much deeper when the stories demanded it.

In a phrase: broader and deeper.

It’s safe to say, based on our daily web traffic, that you all seemed to like this idea. We’ve doubled the staff — thanks to a growing group of paid subscribers — ramped up the daily report and now publish a regular slate of in-depth articles. And traffic — those clicks you always read about — have gone up in volume too. Monthly sessions are up 43%, to close to 1.5 million. Unique readers are up 63%, to 874,480 in October, after setting a record of close to a million the month before. Page views are running at 3 million-plus a month. And the overall number of subscribers has surged to 124,000.

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