In a landmark collaboration, DeepLife and Centre Léon Bérard (CLB)—led by oncologist Pierre Saintigny—have unveiled the Oral Mucosa Cell Atlas (OMC-Atlas), a revolutionary tool mapping cellular evolution from healthy tissue to oral squamous cell carcinoma (OSCC). This cell atlas promises to transform early detection, biomarker discovery, and precision therapies for a disease that claims over 350,000 lives annually¹.

How the OMC-Atlas will change our understanding of oral cancer

Around 90-95% of oral cancer cases are oral squamous cell carcinoma (OSCC), yet over 60% of cases are diagnosed at late stages, leading to a 50% survival rate. OSCC can be classified into three grades ranging from well-differentiated (Grade I) to poorly differentiated (Grade III). Treatment involves curative resection and despite recent advancements, OSCC’s aggressive nature leads to relapse or refractory in approximately 30% of cases, significantly impacting patient survival rates.

The OMC-Atlas project combines transcriptomic data available in the DeepLife OmicStore catalog with unpublished single cell RNA sequencing patient data from the CLB into a unique, state-of-the-art cell atlas. This tool enhances the understanding of phenotypic changes during tumorigenesis - showing how healthy mouth cells slowly change into cancer cells over time. This will help researchers spot early warning signs of oral cancer, identify new biomarkers and potential therapies, giving patients a better chance at beating the disease. 

The OMC-Atlas deciphers:

• Cellular trajectories of epithelial, immune, and stromal cells across tumorigenesis.
• Critical transition points where oral potentially malignant disorders (OPMDs) progress to OSCC (which occurs in 20-30% of cases).
• Vulnerabilities for therapeutic targeting and prognostic biomarkers.
• Molecular shifts from dysplasia to metastasis

“This atlas is a game-changer for understanding head and neck cancer aggressive nature and recurrence risks. It is a powerful resource for understanding cellular changes during tumorigenesis from normal mucosa, preneoplasia and cancer. By using AI to reveal cellular drivers of OSCC, we can identify potential targets for therapies and biomarkers for monitoring. Our work with DeepLife is just beginning, our goal is to foster innovative approaches for early detection and improved patient management.” - Prof. Pierre Saintigny, Centre Léon Bérard

Cell atlases drive future innovation in oral cancer research 

By utilizing the OMC-Atlas, Pierre Saintigny’s team at CLB aims to identify various cell types in the oral mucosa, assess their phenotypic diversity and observe their changes during different stages of oral tumorigenesis. 

Future directions include: 

• AI-driven drug discovery: Leveraging the atlas to prioritize repurposed compounds.
• Clinical validation: Partnering with hospitals to test biomarkers in prospective trials.
• Global dissemination: DeepLife and CLB look forward to publishing the results of this research later in 2025.

"The OMC-Atlas isn't just data - it's a roadmap to earlier diagnoses and personalized treatments in oral cancer. By helping us decode the cellular mechanisms driving tumorigenesis, it brings us closer to truly precision oncology. We're proud to partner with CLB in this leap toward precision oncology." - Jonathan Baptista, Co-founder & CEO, DeepLife

Together, we’re rewriting the future of oral cancer care—one cell at a time. DeepLife and Pierre Saintigny’s team are also members of the ongoing COST (European Cooperation in Science and Technology) funded INTERCEPT (INTercEption of oRal CancEr develoPmenT) Action working group on oral cancer, which addresses the challenge of unmet oral potentially malignant disorders (OPMD). INTERCEPT will develop future strategies of personalized OPMD preventative and care approaches, powered by new technology to improve early detection and patient monitoring.  

Researchers and clinicians are invited to join our efforts in AI-guided precision oncology - reach out to our scientific collaboration team to explore potential opportunities. The OMC-Atlas is available upon request, with access granted following the establishment of a collaborative agreement.

About Centre Léon Bérard (CLB)

Centre Léon Bérard (CLB) is a member of the Unicancer network, which brings together 18 French Cancer Centres and one affiliated organization. It is recognized as an international center of reference in oncology. Based in Lyon - France’s second-largest city - CLB performs a triple mission of care, research and education, with the constant objective to increase the quality and accessibility of care for cancer patients. For more information, visit their website.

About the team of Pierre Saintigny

Pierre Saintigny is a Medical Oncologist, Professor of Medicine at University Claude Bernard Lyon 1, Coordinator of the Department of Translational Medicine and team leader at the Cancer Research Center of Lyon. His team - Integrated Analysis of the Dynamic of Cancer - focuses on the global biological changes occurring during oral tumorigenesis. The team integrates clinical, pathological, cellular and molecular profiles both in human samples and preclinical models to unravel the dynamic changes during early stages of tumorigenesis and under the selective pressure of therapy, to reveal vulnerabilities that may in turn translate into new treatment and prevention strategies.