Merck partners with Flagship startup Quotient to search for genetic clues to IBD
Merck is not making a single inflammatory bowel disease bet. It is buying the discovery stack.
The company’s new partnership with Flagship-backed Quotient Therapeutics makes the most sense when read next to Merck’s roughly $10.8 billion acquisition of Prometheus Biosciences in 2023. Prometheus brought Merck a lead IBD mechanism in TL1A and a patient-data engine around it. Quotient brings something earlier and messier: a way to search diseased tissue itself for the next mechanism before the current one has even finished proving itself. That is not a one-off deal. It is platform layering.
Per Quotient’s announcement, Merck will pay $20 million upfront, with Quotient eligible for up to $2.2 billion in development, regulatory, and commercial milestones, to discover novel IBD targets using Quotient’s somatic genomics platform. No target is named. No candidate is disclosed. No human efficacy data exists. That is exactly why the deal is revealing. Merck is spending real money not on a molecule, but on the machinery for finding molecules.
Rachel’s question is the right one: is this a strategic read on where IBD drug discovery is going, or just another expensive fishing expedition in a lab coat? The best evidence for the former is timing. Merck is still waiting for the big clinical test of the Prometheus thesis, but it already has Phase 3 trials underway for tulisokibart, formerly known as MK-7240, in ulcerative colitis and Crohn’s disease, according to its own TL1A program page. In other words, Merck is seeding the sequel engine before the first marquee chapter has reached its verdict.
That matters because the competitive field is already crowded with companies that do not intend to let Merck own the next era of IBD. Roche paid more than $7 billion to acquire Telavant and its TL1A-directed antibody rights. AbbVie spent 2024 expanding Skyrizi into ulcerative colitis. Johnson & Johnson did the same with Tremfya in ulcerative colitis. If everyone serious already has molecules, the next moat is not just one more molecule. It is a better way to decide what to build after the current wave peaks.
Quotient’s pitch is that diseased tissue contains that map. At launch, Flagship said the company combines tissue phenotyping, single-cell genotyping, and computation to read naturally occurring somatic mutations in patient samples. This is not a standard genome-wide association study looking at inherited risk across populations, and it is not a classic CRISPR perturbation engine in tidy lab models. The bet is that chronic inflammation leaves scars in the gut, those scars follow their own evolutionary logic, and those patterns may point toward targets competitors miss when they start from cleaner systems.
The scientific why-now is more grounded than the marketing copy. A 2020 Cell paper, indexed by PubMed, sequenced 446 colonic crypts from 46 patients with IBD and found a 2.4-fold increase in mutation burden in affected tissue compared with healthy colon. The study also found widespread clonal expansions and positive selection in genes including ARID1A, FBXW7, PIGR, and ZC3H12A, along with pathways involving interleukin-17 and Toll-like receptor signaling. The cleanest way to say it is also the most useful: inflamed gut tissue is not just damaged. It evolves.
A Wellcome Sanger Institute summary of that work makes the human stakes easier to see. Repeated inflammation appears to reshape the same patches of colon over time, helping explain why disease can recur in stubborn local patterns and why longstanding IBD can raise colorectal cancer risk. That does not magically turn somatic genomics into a drug. Biotech has financed plenty of elegant maps that never became medicines. But it does explain why this target class only recently became legible at platform scale. In 2020, this was an intriguing biology story. Now Merck is writing checks as if it could be a discovery system.
Merck’s own framing still deserves a skeptical eyebrow. On its IBD page, the company argues there are no disease-modifying treatments for Crohn’s disease or ulcerative colitis. That is stronger language than the field has earned; existing therapies can reduce inflammation and induce remission for some patients, even if they fall short of a durable reset. But the overreach is also clarifying. Merck is signaling that it does not want to compete only on having another anti-inflammatory asset. It wants a pipeline that can keep generating follow-on targets if TL1A works, and rescue the strategy with adjacent biology if TL1A disappoints.
Quotient’s partners page suggests Merck is not alone in seeing the company as a target-discovery shop rather than a one-program startup. Pfizer signed on in 2024 for cardiovascular and renal disease work. GSK followed in 2025 across COPD, idiopathic pulmonary fibrosis, and MASH. Serious pharma companies do not all write blank checks for the same scientific romance by accident. They buy engines when they think the bottleneck is no longer making drugs against known targets, but finding better targets before everyone else does.
So no, this does not look like a random fishing expedition, though biotech is always happy to wear a lab coat while casting a very wide net. It looks like a strategic bet that in IBD, the discovery layer is becoming the competitive advantage. Merck bought Prometheus for a lead mechanism. It is now buying Quotient for a way to read the tissue damage underneath the disease and keep generating the next mechanism before rivals catch up. For readers deciding what to build or fund, that is the real signal: in one of biotech’s hottest inflammation markets, the money is moving below the drug and into the engine that finds the drug.