Nick Plugis, Avak Kahvejian, Cristina Rondinone, Milind Kamkolkar and Chad Nusbaum. (Cellarity)

Cel­lar­i­ty, Flag­ship's $50M bet on net­work bi­ol­o­gy, mar­ries ma­chine learn­ing and sin­gle-cell tech for drug dis­cov­ery

Cel­lar­i­ty start­ed with a sim­ple — but far from easy — idea that Avak Kahve­jian and his team were float­ing around at Flag­ship Pi­o­neer­ing: to dig­i­tal­ly en­code a cell.

As he and his se­nior as­so­ciate Nick Plugis dug deep­er in­to the con­cept, they found that most of the mod­els oth­ers have de­vel­oped take a bot­tom-up ap­proach, where they as­sem­ble the mol­e­cules in­side cells and the con­nec­tions be­tween them from scratch. What if they opt for a top-down ap­proach, aid­ed by sin­gle-cell tran­scrip­tomics and ma­chine learn­ing, to gauge the be­hav­ior of the en­tire cel­lu­lar net­work?

“If you look at cell be­hav­ior from the per­spec­tive of a mol­e­c­u­lar net­work un­der­ly­ing it, then you free your­self from the tra­di­tion­al ap­proach of one-di­men­sion­al, two-di­men­sion­al, three-di­men­sion­al tar­get-based or phe­no­typ­ic-based drug dis­cov­ery ap­proach­es,” Kahve­jian, who took on the CEO role, told End­points News. “What it al­lows you to do is to use the net­work changes as your read­out.”

Flag­ship ded­i­cat­ed $50 mil­lion to get the biotech start­ed, which is how Cel­lar­i­ty has been fund­ing the build­out of its plat­form and an­i­mal ex­per­i­ments to ver­i­fy their ini­tial hy­pothe­ses in the past two years.

By in­ter­twin­ing wet labs and a dig­i­tal twin dubbed the Cel­lar­i­um, Kahve­jian be­lieves his biotech hasn’t just “re-ar­chi­tect­ed” ther­a­peu­tic dis­cov­ery, but al­so the or­ga­ni­za­tion of an AI up­start. Chad Nus­baum, founder of the Broad Tech­nol­o­gy Labs, leads the tech­ni­cal unit churn­ing out da­ta; while Milind Kamkolkar has joined as chief dig­i­tal & da­ta of­fi­cer af­ter pi­o­neer­ing the role at Sanofi.

“I want­ed to build stuff. I didn’t want to just keep sourc­ing stuff,” Kamkolkar said of his de­ci­sion to leave the phar­ma gi­ant, where ex­ter­nal part­ner­ship was the pro­to­col for gain­ing dig­i­tal com­pe­ten­cy.

It’s the com­plete op­po­site at Cel­lar­i­ty, as they are build­ing a new en­gine that can be bro­ken down in­to three lay­ers. He calls the first “da­ta in­ges­tion” — chan­nel­ing all the in­for­ma­tion gen­er­at­ed by Nus­baum’s team with mul­ti­ple method­olo­gies and species in­to a data­base where sci­en­tists can plot and cu­rate knowl­edge. Then they en­ter the ex­plo­ration lay­er, in­ter­ro­gat­ing the cell be­hav­iors while an­a­lyz­ing how well ex­ist­ing and new com­pounds can per­turb the cells. On the last lay­er, they vi­su­al­ize the find­ings by cre­at­ing a satel­lite im­age of sorts.

Right now Cel­lar­i­ty has about 250 of these dig­i­tal guides on dif­fer­ent dis­eases, which they call Cel­lar­i­ty Maps. And they can en­com­pass every step of the tra­di­tion­al drug dis­cov­ery process.

“The ma­chines are in­cred­i­bly ca­pa­ble of par­al­leliz­ing and col­laps­ing what typ­i­cal­ly used to be a lin­ear process to try to un­der­stand whether the im­pact of that drug ac­tu­al­ly does have tox­i­c­i­ty or side ef­fects,” Kamkolkar added.

With 40 staffers on board, Cel­lar­i­ty has gone broad with its tech plat­form, prob­ing any­thing from ep­ithe­lial bar­ri­er dis­or­ders and on­col­o­gy to hema­to­log­i­cal dis­or­ders and neu­rol­o­gy. The plat­form can ac­com­mo­date mul­ti­ple ther­a­peu­tic modal­i­ties, Kahve­jian said, and they’ve test­ed both small and large mol­e­cules. He isn’t dis­clos­ing a time­line for when they might steer their lead can­di­dates in­to the clin­ic, but he’s not shy about the am­bi­tion to tack­le “dozens of pro­grams” at a time, and part­ner­ing as he sees fit.

As of Sep­tem­ber, Cristi­na Rondi­none, the for­mer head of car­dio­vas­cu­lar, re­nal and meta­bol­ic dis­eases at As­traZeneca, has al­so joined as pres­i­dent to help grow the com­pa­ny and push it to the next stage, en­abling down­stream clin­i­cal de­vel­op­ment of leads.

The new hires will find them­selves in a hor­i­zon­tal or­ga­ni­za­tion where no one do­main su­per­sedes the oth­er, Kahve­jian said, and where bi­ol­o­gists, tech­nol­o­gists, and the com­pu­ta­tion­al folks work to­geth­er in an in­te­grat­ed and mul­ti­lin­gual en­vi­ron­ment where in­sights are gen­er­at­ed more quick­ly and are “ac­tion­able the minute they are gen­er­at­ed.”

Kamkolkar re­called the sur­prise of a ma­chine learn­ing sci­en­tist when he found out that he was to spend time in labs and see how the da­ta are gen­er­at­ed.

“Yeah, you’re gonna have to go in labs,” Kamkolkar ba­si­cal­ly said. “It’s quite unique.”

Op­ti­miz­ing Cell and Gene Ther­a­py De­vel­op­ment and Pro­duc­tion: How Tech­nol­o­gy Providers Like Corn­ing Life Sci­ences are Spurring In­no­va­tion

Remarkable advances in cell and gene therapy over the last decade offer unprecedented therapeutic promise and bring new hope for many patients facing diseases once thought incurable. However, for cell and gene therapies to reach their full potential, researchers, manufacturers, life science companies, and academics will need to work together to solve the significant challenges facing the industry.

Pfiz­er, Sarep­ta and two oth­ers sug­gest Duchenne drug safe­ty is­sues tied to "class ef­fect"

Since the first experimental Duchenne gene therapy programs came about, the space has proven rife with safety issues and patient deaths in clinical trials. Pfizer and three biotechs now think they’ve found a reason why.

The four companies suggested there may be a “class effect” causing the adverse events in Duchenne gene therapies, they wrote in a new study. They specifically highlighted how side effects in five patients across three trials, who all showed muscle weakness with cardiac involvement, were “strikingly similar.”

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Pre­sent­ing a live End­points News event: Man­ag­ing a biotech in tur­bu­lent times

Biotech is one of the smartest, best educated industries on the planet. PhDs abound. We’ve had a long enough track record to see a new generation of savvy, experienced execs coming together to run startups.

And in these times, they are being tested as never before.

Biotech is going through quite a rough patch right now. For 2 years, practically anyone with a decent resume and some half-baked ideas on biotech could start a company and get it funded. The pandemic made it easy in many ways to pull off an IPO, with traditional road shows shut down in exchange for a series of quick Zoom meetings. Generalist investors flocked as the numbers raised soared into the stratosphere.

Martin Shkreli (Dennis Van Tine/MediaPunch/IPX)

In­fa­mous biotech ex­ec Mar­tin Shkre­li gets out of prison, hits the street

Martin Shkreli, the infamous biotech CEO who made headlines for his jeering assault on a legion of critics in and out of Congress, is back on the streets after 4 years inside a federal penitentiary.

Shkreli’s attorney put out a statement Wednesday afternoon saying that the “pharma bro” had been transferred to a halfway house in New York with a few more months to go under federal custody, slated to end September 14. Attorney Benjamin Brafman acknowledged the release and vowed that he and Shkreli are keeping quiet.

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De­spite fed­er­al ef­forts to di­ver­si­fy clin­i­cal tri­als, progress re­mains 'stag­nan­t' — re­port

While calls to diversify clinical trials have grown louder in recent years — gaining support from federal agencies such as the FDA and NIH — progress has largely stalled, according to a new report from the National Academies of Sciences, Engineering and Medicine.

Swaths of patients in racial and ethnic minority groups, as well as LGBTQIA+, pregnant and older adult populations continue to be left out of clinical trials. While some advances have been made in the last 30 years — women now account for roughly half of clinical trial participants — growth in other areas remains stagnant, according to the report, which was mandated by Congress and sponsored by the NIH.

Paul Chaplin, Bavarian Nordic president and CEO

Bavar­i­an Nordic se­cures BAR­DA con­tract for small­pox vac­cine

It seems that smallpox vaccination production is weighing on the mind of the US government. And manufacturer Bavarian Nordic is the latest company to benefit.

Just a few days after Emergent, a company that has made government contracts its lifeblood, acquired the exclusive rights to Tembexa from Chimerix, with a $225 million cash payment and an expected BARDA contract, the agency has offered a contract for smallpox vaccine production.

Frank Pallone (D-NJ), House Energy and Commerce Committee chair (Kevin Dietsch/Pool via AP Images)

House com­mit­tee unan­i­mous­ly ad­vances FDA user fee leg­is­la­tion with ac­cel­er­at­ed ap­proval tweaks

The House Energy and Commerce Committee on Wednesday offered a rare show of bipartisan support for a bill that would provide the FDA with user fees for the next five years.

The committee voted 55-0 to advance the quinquennial user fee bill to the full House floor, which if approved, will allow the FDA to use biopharma funds to hire new reviewers, and hit new marks as outlined in the user fee deals that the FDA and biopharma companies forged over the past several years.

Lina Khan, FTC chair (Saul Loeb/Pool via AP)

New FTC com­mis­sion­er could turn the tide for an in­ves­ti­ga­tion in­to PBMs

The Senate last week voted along party lines, 51-50, with Vice President Kamala Harris casting the tie-breaker, to make President Biden appointee Alvaro Bedoya the deciding vote on a split 2-2 Federal Trade Commission.

The addition of Bedoya to the FTC could not only spell more trouble for biopharma M&A activity, as he may align with his Democrat partners to break the FTC ties, but it may also mean that FTC Chair Lina Khan has what she needs to move forward on a study around the pharma middlemen known as pharmacy benefit managers.

Henrietta Lacks

UP­DAT­ED: Fed­er­al judge weighs mo­tion to dis­miss HeLa law­suit against Ther­mo Fish­er

The story of Henrietta Lacks’ immortal cell line and her family’s fight for justice caught the attention of national media outlets and Hollywood years ago. Now, the case faces an uncertain fate as a Baltimore federal judge considers tossing the case.

After a hearing on Tuesday, Judge Deborah Boardman is weighing Thermo Fisher’s motion to dismiss the claims against it on the grounds that the statute of limitations has passed, and the continuing harm doctrine does not apply. Boardman is grappling with the “extraordinarily unique facts” of the case, according to Maryland Matters, which first reported the news.