Flagship unveils ProFound Therapeutics with $75M to explore trove of new proteins

Fifteen years after scientists whittled down the estimated number of protein-coding genes to roughly 20,500, ProFound Therapeutics, a new company launched by Flagship Pioneering, says there are potentially tens of thousands more. 

The new company, unveiled Thursday, comes equipped with $75 million to dive headfirst into the new repository, which was uncovered by honing in on potential proteins involved in translation. The trove of new proteins effectively more than doubles the known repository and creates a new frontier to be explored for potential therapeutic targets. 

The unearthing is the result of a new approach taken by ProFound and its leaders to reconsider what exactly defines a protein-coding gene and how a protein is coded in the genome. In an interview with Fierce Biotech, CEO Avak Kahvejian Ph.D., says ProFound had to disregard some of the conventional rules for finding proteins in order to identify more. 

“It’s mostly the rules that people applied to scouring through the genome to predict what could be a protein-coding gene and what isn’t a protein-coding gene,” he said. “Those are the ones that we believe were too constraining originally and a little bit too stark.” 

The company instead focused on the translatome, a hub of RNA transcripts that’s been ignored because those transcripts weren’t thought to create proteins. But using protein detection technology, ProFound was able to corroborate those transcripts as the source of a host of new proteins that had yet to be found.

“If you look at the proteome that way, you suddenly find many more than if you simply look at the proteome by trying to find the protein parts themselves and using the technology there,” said Kahvejian. 

As a result of these findings, the company is potentially sitting on a plethora of new therapeutic options; Kahvejian calls it a “cornucopia.” Naturally, that’s opened numerous avenues for ProFound’s business development, including constructing its own pipeline of therapies based on these proteins.

Kahvenjian wouldn’t commit to what the company will do first, saying he’s agnostic to the kind of therapeutic areas and modalities the company will go after initially. But he noted that the proteins could uncover new cancer targets. Given the scope of potential therapeutic avenues, the company has also started to engage other companies outside of the Flagship network regarding potential partnerships. 

Kahvejian also wouldn’t specify how much of a runway the $75 million provides, but he said the company will prioritize investing in its platform and preclinical work that can quickly validate any potential benefit. He added he expects the size of the company to quadruple over the next year from 25 current employees to about 100. 

That preclinical work is already underway, according to Kahvejian, who says the company has already initiated rodent models to assess the biology of some of these proteins, though he wouldn’t specify which ones.