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Flagship’s latest startup launches with bold claim: the discovery of thousands of new human proteins

The venture capital giant has committed $75 million to Cambridge biotech ProFound Therapeutics.

The new proteins that ProFound Therapeutics is working on “could provide countless new intervention points across diseases,” said Noubar Afeyan, founder and chief executive of Flagship Pioneering.Andrew Medichini/Associated Press

A Cambridge biotech company claims to have made a discovery that could rewrite biology textbooks. ProFound Therapeutics said Thursday that it had identified tens of thousands of previously unknown proteins in the human body, many of which may be involved in cancer, immunity, and metabolism.

After two years of working in stealth, ProFound has emerged with $75 million from Flagship Pioneering, the Cambridge investment firm that builds and funds its own biotech companies and is best known for its creation of the mRNA vaccine developer Moderna. ProFound will use the money to catalogue and study the new proteins, begin building a pipeline of drugs based on their findings, and potentially quadruple in size from about 25 to 100 employees by this time next year.


Flagship is unrestrained in its hopes for what its latest startup can achieve. The new proteins “could provide countless new intervention points across diseases,” Noubar Afeyan, founder and chief executive of Flagship, said in a statement. “This discovery redefines what we know about human biology and marks the beginning of a new era in biomedicine, with unlimited potential for patient impact.”

Yet such a massively overlooked aspect of human biology is the kind of discovery that would normally headline a scientific conference or appear on the cover of a prestigious academic journal. Instead, Flagship announced it in a press release.

“In due course there will be publications coming from our company and data being released,” Avak Kahvejian, ProFound’s chief executive and cofounder and a general partner at Flagship, told the Globe.

Humans only have about 20,000 genes. For many years, scientists dogmatically believed that each one encodes only a single kind of protein. They now know that cells creatively slice and dice genes to create multiple related proteins from a single gene — a process called RNA splicing. A common estimate for the number of human proteins is now around 100,000. Scientists at Flagship wondered if the true tally could be even higher.


“At Flagship we are accustomed to asking embarrassingly simple and naïve questions that put dogma into question,” said Kahvejian. One experiment led to another, and before long the company realized they were onto something “broader and bigger than we had hoped,” he added.

ProFound paired protein detection technologies with genetic tools that allow scientists to watch what parts of the human genome are being read to make proteins. In doing so, it said, researchers discovered tens of thousands of never-before-seen proteins. The new proteins are not mere products of RNA splicing, Kahvejian said. Instead, many of them came from the dark matter of the genome — the regions between genes with mysterious or unknown functions, and sometimes derisively called junk DNA.

“Every time we’ve made the mistake of assuming that things are spurious, or biological noise, or junk, we have often been wrong,” Kahvejian said.

When asked if ProFound had proved that the newly identified proteins actually have biological functions, Kahvejian said that human biology “doesn’t do useless things,” and that the company has identified proteins linked to cancer and immunology. “It is almost undeniable or inevitable that new proteins and peptides that we didn’t know of will have functions and will only help in our endeavor to improve human health,” he said.

Flagship is known for making big bets on unproven biology, which don’t always pan out. Its microbiome company Kaleido Biosciences recently shuttered. And Rubius Therapeutics, a Flagship company that aimed to make therapies out of engineered red blood cells, but has had lackluster clinical results, has seen its stock tumble 96 percent since its peak last summer.


Yet Flagship struck gold with its biggest success, Moderna, which has seemingly emboldened it to strive for even broader goals when creating new companies. Flagship’s Generate Biomedicines, for instance, raised $370 million in November to design proteins from scratch on computers. Another startup, Vesalius Therapeutics, launched with $75 million in March with the vague goal of treating common diseases.

Unlike some biotech companies, which are built around one or two drug candidates, Flagship’s firms are often centered on a novel biological idea that could be applied to developing therapies for many diseases. Kahvejian said that holds true for ProFound, which is the first and only company “exploiting and revealing this universe of undiscovered proteins,” he said. “And we think there is a cornucopia of opportunity here.”

Ryan Cross can be reached at ryan.cross@globe.com. Follow him on Twitter @RLCscienceboss.