Repertoire Genesis, Inc.

Developed over nine years, Repertoire Immune Medicines\' Decode platform is now both “industrialized” and “scalable,” CEO Torben Straight Nissen told Fierce Biotech.\n With three Big Pharma collaborations already under its belt, Flagship Pioneering spinout Repertoire Immune Medicines has picked up another—and its biggest yet—in a further validation of the company’s immune system decoding platform.The next major drugmaker interested in what Repertoire has to offer is Eli Lilly, which has thrown down $85 million upfront and floated up to $1.84 billion more in biobucks to collaborate on potential tolerizing therapies for multiple undisclosed autoimmune disease targets, according to a Jan. 29 press release.The tolerized treatments that Repertoire and Lilly are attempting to bring to the fore will be designed to restore immune homeostasis and provide patients with durable disease remission, while at the same time eschewing the broad immune suppression that characterizes most autoimmune treatments today.Under the deal breakdown, Repertoire will spearhead work until development candidates are nominated, while Lilly will be in charge of clinical development, manufacturing and commercialization activities, should one of the partners’ tolerized therapies pass muster with regulators.Aside from the $85 million Repertoire will receive upfront, the company could tack on up to $1.84 billion more by achieving certain development and commercial milestones, as well as tiered royalties on potential sales.Lilly was no doubt enticed by the promise of Repertoire’s Decode platform. Developed over nine years, the technology is now both “industrialized” and “scalable,” Repertoire’s CEO Torben Straight Nissen, Ph.D., said in a recent interview with Fierce Biotech. At its core, the platform characterizes all components of the immune synapse—or “controlling node”—of the adaptive immune system, the CEO explained. When an antigen-presenting cell enters the body, it provides epitopes to the immune system, and Repertoire, using its platform, can “determine experimentally any epitope on any class I or class II [human leukocyte antigen] that is presented by an antigen-presenting cell,” according to Nissen.Repertoire then looks at the other side of the immune equation—T-cell receptors (TCRs)—to identify the TCRs that recognize epitopes on an antigen-presenting cell. Once those pieces come together, Repertoire’s platform can measure the effect of immune synapses on the phenotype of the T cell, “[a]nd that’s how we understand whether that interaction is relevant to disease or whether it’s just maintaining health,” Nissen explained.“Stepping back from all of that, that allows us in autoimmune disease to find the class II HLA-presented epitopes that drive autoimmune disease, and that’s really been the big missing link,” the CEO continued. Broad immunosuppression has been the go-to tactic in autoimmune disease treatment for many years, but that approach comes with considerable tradeoffs, such as high side effect burden and a lack of durable remission, Nissen said.In contrast, the CEO figures Repertoire’s approach offers a potentially “much more efficacious way and safe way” to treat autoimmune disease.The Decode platform has proven attractive to other formidable pharmas besides Lilly, with Repertoire’s other biggest collaboration coming in the form of a deal with Bristol Myers Squibb that was made back in April 2024. That team-up, which saw BMS offer $65 million upfront and pledge up to $1.8 billion in potential future payments, concerns co-development of tolerizing vaccines for up to three autoimmune diseases.Separately, Repertoire and its Decode platform have also managed to bring Roche’s Genentech unit and Pfizer into their orbit, where the partners are working on T-cell-targeted medicines for autoimmune diseases and aiming to “identify and optimize” TCR bispecifics for prostate cancer, respectively.Repertoire’s R&D calculus is slightly different in oncology, where the platform company is aiming Decode at tumor-specific epitopes, Nissen pointed out during the interview.  With a suite of Big Pharma partners now on deck, Repertoire is “not in need to raise capital,” Nissen said when asked about the company’s near-term funding strategy. The company is not currently planning an initial public offering, either. Repertoire will conduct a private round at some point in the future, potentially sometime in 2026, though the timeline is not set in stone, Nissen added.As it stands, Repertoire boasts 85 “highly productive” employees and plans to keep its hiring numbers “flat” for the time being, Nissen said. “We’ve been able to maintain that same group of employees that can execute those partnerships,” he noted, adding that some of that core group of Repertoire staffers will now be shifting over to the Lilly agreement, as well. Editor\'s note: This headline was updated on Jan. 29 at 7:24 a.m. ET to reflect the correct total potential deal value. 

Repertoire Immune Medicines has added a fourth pharmaceutical partner by teaming up with Eli Lilly. The Indianapolis pharma joins Bristol Myers Squibb and Genentech in allying with Repertoire on so-called tolerizing vaccines for autoimmune diseases. Lilly will fork over $85 million to kick off its alliance, the companies said Thursday morning. The biobucks package carries as much as $1.84 billion in potential payouts if certain development and commercial benchmarks are met. Repertoire CEO Torben Straight Nissen told Endpoints News the companies have been in discussions for about 15 months. The new partners didn’t disclose which specific autoimmune conditions they’ll consider for the medicines that are yet to be created under the pact. The Flagship Pioneering-founded startup’s experimental therapies aim to bring the immune system back to a healthy, balanced state without requiring generalized immune suppression. They won’t be one-time treatments, but Nissen said he expects the medicines to require “infrequent administration.” Clinical testing will shed light on how infrequent that is. Nissen said the tolerizing therapies are “akin” to the regulatory T cell field, which has been building interest following a 2025 Nobel Prize for work in the field. Multiple startups are angling into the so-called Tregs, with varying approaches at TRexBio, Sonoma Biotherapeutics, GentiBio, Quell Therapeutics and elsewhere. “There’s really a lot of momentum being generated in the space of Tregs and the impact that they can have in autoimmune disease,” Nissen said. Repertoire is working on expanding “multiple populations of Tregs against multiple disease-driving epitopes,” the CEO said. With that approach, the startup’s medicines should be a “very efficacious product compared to other therapies that are maybe more specific to one or two populations of Tregs.” While the bulk of attention has focused on obesity and diabetes drugs, Lilly has been building out a long lineup of autoimmune drugs as well. It has multiple Phase 3 prospects, a handful of mid-stage candidates, and at least 13 assets in Phase 1, according to Lilly’s website. Outside of the autoimmune space, Repertoire and its incubator Flagship are working with Pfizer to create T cell receptor bispecific drugs for metastatic prostate cancer. Terms weren’t disclosed in that December deal . Repertoire had been in the clinic with a cell-therapy-based approach, but ended that small Phase 1 test in 2022 and then reduced its headcount . The company has remained at about 80 employees over the past year, Nissen said. The Zurich and Cambridge, MA startup hopes to make a return to human trials with TCR bispecifics for a litany of cancers, cancer vaccines for lung squamous carcinoma and melanoma, and a tolerizing therapy for type 1 diabetes. All of those programs are advancing, “but with the greatest emphasis right now on the partnered programs,” Nissen said. There’s room for additional pharma collaborations, he said. Nissen told Endpoints last April that the startup aimed to get back into the clinic with a TCR bispecific by the end of 2025. The company will reveal more details in the coming months about its internal pipeline plans, Nissen said this week. The biotech was founded in 2019 after merging Flagship startups Cogen Immune Medicines and Torque Therapeutics. Repertoire last disclosed a $189 million Series B in April 2021. Its backers include Flagship, SoftBank Vision Fund2, Alaska Permanent Fund, Invus and others.

Eli Lilly is paying $85 million upfront to partner with Repertoire Immune Medicines on the development of tolerising therapies for multiple autoimmune diseases, marking another major pharma partnership for the Flagship Pioneering-backed biotech. The agreement carries up to $1.84 billion in development and commercial milestones, plus tiered royalties, as Lilly pushes deeper into immunology approaches designed to correct rather than suppress the immune system. Repertoire will lead collaboration activities up until candidates are nominated, after which Lilly will take over clinical development, manufacturing, regulatory affairs and commercialisation. The deal centres on Repertoire's DECODE platform, which maps the entire immune synapse — the complex junction between a T-cell and a cell that presents an intracellular antigen on its surface — to identify the T-cell receptors and specific antigen fragments known as epitopes that drive disease. The goal is to create therapies that restore immune homeostasis and provide lasting remission without broadly weakening the body's defences like current treatments often do. The collaboration "affords us the opportunity to translate the unique discoveries produced by our DECODE platform into potentially paradigm-shifting new medicines for autoimmune patients by addressing the root cause of the immune dysregulation and resetting their immune system to a healthier state," said Torben Straight Nissen, chief executive at Repertoire, in a release Thursday.The Lilly deal follows a series of large autoimmune partnerships for Repertoire over the last two years. In 2025, the company signed a collaboration with Roche's Genentech unit worth up to $765 million and earlier struck a deal with Bristol Myers Squibb worth nearly $1.9 billion in total to develop tolerising vaccines.