AI start-up Profluent nabs Lilly as first big pharma partner

California, US AI start-up Profluent has signed a major alliance with pharma group Eli Lilly, worth up to $2.25 billion, that will focus on gene-editing therapies.

Profluent has attracted attention since its launch in 2022 for its technology platform, which has the potential in some cases to allow entire genes to be inserted into DNA, in contrast to the more localised editing that can be achieved using current approaches like CRISPR/Cas9 or base editing.

The goal of the partnership with Lilly is to use Profluent's AI models to design recombinase editors capable of inserting long, kilobase-scale stretches of DNA at precise locations in the genome, according to a LinkedIn post from the company.

Details of the collaboration are still thin on the ground, with no indication of the target diseases or even the number of programmes covered by the deal, or any breakdown of how it is structured financially. Lilly will receive an exclusive license to advance selected recombinases through in vivo research, preclinical development, clinical studies, and commercialisation.

"Many genetic diseases involve hundreds of different mutations across patients – no single edit can address them all. Inserting a complete functional gene with a recombinase editor opens the potential to address diseases with high mutational heterogeneity using a single therapeutic, rather than developing a separate editor for every variant," says the biotech in the post.

"This has been a long-sought goal in the gene editing field, but current tools can't reliably make insertions at that scale," it continues. "Naturally occurring recombinases could, but are limited in where they can act and traditional metagenomic discovery and protein engineering approaches can't precisely control their targeting."

Profluent believes that its genome editors and large language models (LLMs) – which combine to create what it calls "programmable biology" – can solve that problem, and said its collaboration with Lilly will "turn that capability into medicines."

Last November, Profluent raised $106 million from a raft of backers, including Bezos Expeditions, the investment vehicle for Amazon founder Jeff Bezos, to support the development of the platform.

Lilly, meanwhile, has been building its capabilities in gene-editing technologies of late, including signing a recombinase-based partnership with Germany's Seamless Therapeutics in January, worth over $1.2 billion, that is focusing on therapeutic candidates for hearing loss.

The company also opened the $700 million Boston-based Lilly Institute for Genetic Medicine in 2024, which employs around 500 scientists and researchers working on candidates in diseases like diabetes, obesity, and neurodegeneration.