CAMBRIDGE, ENGLAND & SEATTLE -- The Wellcome Sanger Institute, Parse Biosciences, and the Computational Health Center at Helmholtz Munich announced a collaboration to build the foundation of a single cell atlas, focused on understanding and elucidating cancer plasticity in response to therapies. The collaboration will catalyze an ambitious future phase to develop a cancer plasticity atlas encompassing hundreds of millions of cells.

Utilizing novel organoid perturbation and Artificial Intelligence (AI) platforms, the aim is to create a comprehensive dataset to fuel foundational drug discovery models and cancer research.

Dr. Mathew Garnett, Group Leader at the Sanger Institute, and Prof. Fabian Theis, Director of the Computational Health Center at Helmholtz Munich and Associate Faculty at the Sanger Institute, will be the principal investigators in the collaboration.

Garnett’s research team has generated novel 3D organoid cultures that serve as highly scalable and functional cancer models with the ability to capture hallmarks of patient tumors. The team will use vast numbers of these tumor organoids — mini tumors in a dish — as a model to better understand cancer mechanisms of plasticity and adaptability in response to treatments.

Theis’ research team has been widely recognized for pioneering computational algorithms to solve complex biological challenges at the intersection of Artificial Intelligence and single cell genomics, in this context for in silico modeling of drug effects on cellular systems. The initiative will be run through Parse Biosciences’ GigaLab, a state-of-the-art facility purpose built for the generation of massive scale single cell RNA sequencing datasets at unprecedented speed.

The Sanger, Helmholtz Munich, and Parse teams have developed automated methods to streamline laboratory procedures in addition to the computational methods required to analyze and discover insights within datasets of this size.

The ultimate aim of the collaboration is to build a single cell reference map that will enable virtual cell modeling and potentially help predict the effect of drugs in cancer patients - where resistance might develop, from which compounds, and where to target future treatment efforts.

Garnett, Group Leader at the Wellcome Sanger Institute and collaboration co-lead, said: “We have developed a transformational platform to enable both large-scale organoid screening and the downstream data generation and analysis which has the potential to redefine our understanding of therapeutic responses in cancer. We aim to develop a community that brings the best expertise from academia and industry to progress the project. Studies of this magnitude are critical to the development of foundational models to better help us understand cancer progression and bring much needed advancement in the field.”

Theis, Director of the Computational Health Center at Helmholtz Munich and collaboration co-lead, said: “Our vision of a virtual cell perturbation model is becoming increasingly feasible with recent advances in AI — but to scale effectively, we need large, high-quality single cell perturbation datasets. This collaboration enables that scale, and I’m excited to move toward AI-driven experimental design in drug discovery.”

Dr. Charlie Roco, Chief Technology Officer at Parse Biosciences, said: “We are incredibly excited to bring the power of GigaLab to visionary partners. Leveraging Parse’s Evercode chemistry, the GigaLab can rapidly produce large single cell datasets with exceptional quality. Combining the expertise of the Wellcome Sanger Institute and Helmholtz Munich with the speed and scale achieved by the GigaLab enable the opportunity to fundamentally change our understanding of cancer.”