Alithea Bio is collaborating with HLA-Compass to develop an AI-driven platform designed to enhance the development of immunotherapies by making them safer and more targeted. Can you provide a brief overview of Alithea Bio and how the concept for establishing the company came into being? Alithea Bio …
Alithea Bio is collaborating with HLA-Compass to develop an AI-driven platform designed to enhance the development of immunotherapies by making them safer and more targeted. Can you provide a brief overview of Alithea Bio and how the concept for establishing the company came into being? Alithea Bio is a biotech startup based in Freiburg, founded in 2019. We are working with HLA-Compass to create an AI-powered platform that combines immunopeptidomics, mass spectrometry, and proprietary HLA-peptide data to make immunotherapies, cancer vaccines, and personalized medicine safer and more targeted. The idea for founding the company was not a single epiphany but rather a realization on my part. My co-founder, Prof. Dr. Tim Fugmann, is the driving force behind Alithea Bio's scientific endeavors. As someone with international business development experience but no prior lab leadership, I bring a unique perspective to the company. This blend of expertise is key to our success: many outstanding research findings fail to translate into practical applications because research teams often lack the skills to turn them into viable businesses. When I took over management in 2022, my primary objective was to establish a scalable market presence grounded in scientific substance. My goal is to bridge the gap between research and the market's willingness to pay for innovative solutions. What is your vision for Alithea Bio, and how do you envision long-term changes in cancer immunotherapy development? Our vision is a world where cancer is curable, which may seem ambitious but is rooted in a specific problem: approximately 1.7 million people in Germany live with a cancer diagnosis, and nearly 230,000 die from it each year. Many promising therapies falter not due to scientific shortcomings but because they are unclear about whether they will also target healthy tissue. Estimates suggest that between 16,000 and 58,000 people in Germany die annually from side effects and medication interactions, a risk particularly significant in cancer treatments. With Alithea Bio, we aim to address this gap by providing accurate measurements rather than estimates. We utilize our HLA-Compass to identify the target structures a therapy is likely to hit before the first clinical trial begins. In the long term, this should shift the development of immunotherapies away from trial and error on patients towards decisions based on real data. Our objective is for the HLA-Compass to become the standard for immunoncology within the next few years, applicable to research, hospitals, pharmaceuticals, and biotech companies alike. Which patient populations does Alithea Bio primarily focus on, and what challenges do your technologies address? We primarily work with pharmaceutical and biotech companies developing new immunotherapies, TCR-based drugs, TCR mimetics, or cancer vaccines, as well as academic and clinical partners such as CHOP – Children's Hospital Philadelphia. The challenge that all these partners share is the same: they need to determine early on whether a target peptide is truly tumor-specific or if it also occurs in healthy tissue, posing a safety risk. That's where we come in.
Our portfolio boasts over 200 completed customer projects in partnership with companies such as DeckBio in the USA and DAAN in South Korea, demonstrating that this question can be addressed prior to the commencement of clinical studies using highly sensitive mass spectrometry and one of the largest reference databases of its kind. For our partners, this translates into reduced capital expenditure on candidates that ultimately fail due to toxicity, coupled with increased confidence in therapies that successfully navigate the approval process. Alithea Bio combines immunopeptidomics, mass spectrometry, and artificial intelligence. From your perspective, what sets this combination apart? Data collection is now feasible for almost every biotech startup. What makes immunopeptidomics particularly noteworthy is the challenge of generating data. We measure extremely rare peptides present on the surface of tumor cells. To produce qualitative and sensitive data, the entire process must function seamlessly. This allows us to lose many peptides during sample preparation for ultra-sensitive measurements in the lab. Furthermore, the method of mass spectrometry must be tailored to the tissue being examined and adjusted accordingly depending on the question at hand. The successful synergy behind this is the result of years of research and optimization of the processes. This enables us to generate up to 80 percent more data than our competitors. The true art lies in extracting insights from raw laboratory data that can be utilized by a pharmaceutical company for its decision-making processes. To achieve this, we have developed our own bioinformatics and AI models to extract valuable information from raw laboratory data that is essential for the development of the next generation of therapeutics. Many databases remain well-intentioned archives from which no concrete answer can be derived. Our combination of immunopeptidomics, mass spectrometry, and AI is therefore not an academic tool, but a decision-making instrument. Specifically, using highly sensitive mass spectrometry, we measure which peptides are actually presented on tumor and healthy tissue, currently exceeding 23 million immunopeptidomic data points. AI models assist us in identifying patterns within this vast amount of data, for instance, as we recently demonstrated in the so-called
Our partners reap significant benefits from time savings and enhanced security. The probability of drugs successfully completing clinical trials increases by more than 38 percent. Our clients can now identify earlier whether a target peptide is exclusively tumor-specific or also present in healthy tissue, thereby potentially excluding high-risk candidates before embarking on costly clinical trials. This not only saves resources but also boosts the likelihood that a therapy will reach patients. Unfortunately, we currently have too few approved immunotherapies, and patients are often limited to what we offer. However, tomorrow's scenario promises to be vastly different, with many more approved therapies available, thereby significantly increasing patients' chances of recovery. The development of new cancer treatments is inherently associated with high risks. How can Alithea Bio assist in identifying suitable target structures earlier and predicting potential side effects more accurately? We have developed a process that demonstrates, even before the first clinical trial, whether a novel cell or immune therapy may attack healthy cells. This is achieved through the integration of highly sensitive mass spectrometry and our extensive reference database comprising tumor and healthy tissue samples. A notable example of this is our recent study on the so-called 'dark genome': ancient viruses, known as HERVs, account for almost 8 percent of our genome and have long been considered a reliable indicator of tumor presence. When we screened thousands of healthy and tumor samples overnight using HLA-Compass, we identified more than 34,000 unique HERV-derived peptides, and found that many of these signals do not occur exclusively in tumor tissue. Such insights prevent promising drug candidates from failing in clinical trials due to toxicity, thereby avoiding unnecessary waste. What role do large biological datasets and Artificial Intelligence play in the development of personalized cancer immunotherapies? They are the fundamental building blocks for personalized medicine to become a reality. Over the years, we have established our own infrastructure at Alithea Bio: currently comprising more than 1.4 million measured peptides from over 4,580 samples, combined with AI models for safety prediction and immunogenicity. Our mission is to create the most diverse database, encompassing all genders, ethnic backgrounds, and cancer types, thereby ensuring that therapies of tomorrow are safe and effective for everyone. These data provide valuable insights into what a single body truly requires, enabling therapies to be tailored precisely to its needs. Instead of a one-size-fits-all approach, this creates the opportunity to treat each patient individually. And that is also the reason why we consistently invest in our own database, since 2024 with our own laboratory and mass spectrometer in Berlin: Only with a truly large, well-curated database can AI models be trained to reliably distinguish between healthy and sick, safe and risky. As a TechBio company at the intersection of biotechnology, data science, and artificial intelligence, we face numerous challenges.
A key hurdle lies in converting outstanding scientific achievements into a viable business model. Many research breakthroughs fail to reach practical application, not due to the quality of the science, but because researchers often lack the expertise to turn their findings into a commercial proposition. I bring an international business development perspective to Alithea Bio, which has been instrumental in our approach. This challenge is also a broader issue for Europe as a whole, where we invest approximately seven times less per capita on cancer research than the US. This disparity stems from both resource constraints and a trust deficit: investors and funding agencies tend to be hesitant to support initiatives that do not take science and business models equally seriously. As a woman in an industry where female founders of deep-tech startups often face significant capital shortfalls compared to their male counterparts, I am acutely aware of this challenge. The development of innovative cancer therapies necessitates close collaboration between research institutions and industry leaders. The success of Alithea Bio is heavily reliant on partnerships, as our vision of eradicating cancer cannot be achieved alone. We will initiate partnerships with academic institutions, which provide us with access to tissue samples from donors, enabling us to measure them and share the resulting data with our partners for their own research purposes. Furthermore, many university hospitals and universities have their own research on topics such as cancer vaccines and are eager to collaborate with us. These partnerships are not supplementary to our business model; they are its core component. Through collaboration with customers like the Children's Hospital of Philadelphia, Deck Bio, and several large pharmaceutical companies, our platform will become a valuable tool that informs real investment decisions. Cross-border collaborations also play a pivotal role for us, as evidenced by the German-British funding program from ZiM, which has facilitated the development of our model. Such partnerships between research, industry, and public funding demonstrate the potential for Europe to bring together science, capital, and industry in a more cohesive manner, rather than operating in separate silos. Alithea Bio is currently focusing on several key technological developments and growth objectives. We are continuously expanding our database by analyzing the 'dark genome,' specifically viral peptide signals that have been under-recorded in the past. At the same time, we are working to further establish HLA-Compass as a tool for our partners to ensure safety and inform decision-making. The next milestone is to make HLA-Compass compatible with agents, as research will increasingly be supported by agents in the future. Our technological progress is driven by the continuous generation of data. On the growth side, we are currently completing our next funding round to expand our team and laboratory capacity.
Our ambition is to increase our global presence, building on the success we achieved at the VivaTech Awards 2026 in Paris, where we won two prestigious awards. We aim to forge new partnerships with pharmaceutical and biotech companies across Europe, ultimately becoming the go-to authority for immunoncology. To achieve this, we need to be able to provide accurate answers to the most critical questions from both the scientific community and industry, thereby establishing trust in our data. What do you envision as the future of personalized cancer treatment, and what role should Alithea Bio play in it over the long term? I firmly believe that the future of cancer medicine lies in shifting away from a one-size-fits-all approach to treatments tailored to each individual's unique biological profile. This necessitates our ability to identify safe and effective target structures at an earlier stage with greater certainty. In the long run, I envision Alithea Bio and HLA-Compass as the platform where clinics can access information before and during patient treatment to offer each patient the most suitable therapy that is both effective and safe. This vision is not just a promise but a commitment to the next generation, to a world where cancer is curable. If you're a founder looking to establish a company in biotechnology or TechBio, I would advise you to: Clearly define the problem at hand. In the deep-tech sector, the technology may be mature, but the impact needs to be demonstrated. A steadfast conviction can only be effective if it's grounded in the potential impact and the team, not just the product or technology. Learn to distinguish between 'no' and 'not yet'. Initially, you'll encounter numerous rejections from customers, investors, and sometimes even potential employees. The key lies in identifying which 'no' is a 'not yet' and persisting with the few individuals who can genuinely support you. Treat scientific research and business models with equal importance from the outset. Many outstanding research findings fail to translate into practice not because the science isn't robust enough, but because there's a lack of individuals who can provide clarity on when invested capital will yield returns. Instead of seeking the most accomplished researchers, focus on assembling teams that can effectively bridge the gap between science and practice. Be bold, market-driven, and agile. This requires a founding team that's willing to make decisions, even if it means deviating from the original plan, and that focuses on developing solutions that meet market needs, not just those that are scientifically intriguing. This includes consulting with experienced founders and remaining committed to your objectives. Image: Prof. Dr. Tim Fugmann and Fanny Giannou, photo credits: Alithea Biotechnology GmbH We would like to extend our gratitude to Fanny Giannou for the interview.
