Cancer associated fibroblasts layer on tumor microenvironment
3D rendering of cancer-associated fibroblasts CAF layer on tumor microenvironment. Credit: Marcin Klapczynski/Getty Images

Spatial biology specialists Nucleai and Propath UK have announced a partnership to develop and validate an immunofluorescence assay focused on 30 immuno-oncology protein targets that could inform the development of novel oncology biomarkers and companion diagnostics.

Dr Ken Bloom, head of Pathology at Nucleai, explained that spatial biology—the study of tissues within their multidimensional context—“is considered a new frontier and extension to molecular biology.”

In oncology, spatial biology can be used to study the tumor microenvironment and its interaction with the tumor.

“While genomic sequencing is important tool on cancer research and biomarker development for targeted therapies, it falls short when attempting to understand the immune system and the heterogeneity of tumor cells,” said Bloom. “Therefore, we believe that spatial biology will revolutionize the way we understand, investigate, and treat cancer and will become a standard tool for research institutions, pharma companies and clinicians.”

Within the partnership, Propath will use experience gained across a range of spatial proteomic and transcriptomic projects to create a novel protocol using the Lunaphore COMET automated immunofluorescence staining platform for analysis of 30 undisclosed high-value protein targets from a single tissue section.

Nucleai’s artificial intelligence ATOM platform will then be used to develop a state-of-the-art deep learning model optimized to the 30-plex assay. This will involve a number of steps that begin with experts annotating the immunofluorescence images for cell typing and phenotypic markers and end with calculation of spatial features and outcome prediction.

Furthermore, tissue samples that are accompanied by information on tumor outcomes will undergo spatial analysis by the Nucleai platform to discover novel tumor microenvironment cell patterns and signatures.

“The Nucleai deep learning model will be able to provide consistent, high accuracy, fully automated analysis for every [tissue] batch that will be stained by Propath’s 30-plex assay,” noted Bloom.

The model’s performance will be validated both quantitatively and qualitatively, which typically takes less than a month, and will then need to be clinically validated before it can be approved by the FDA and deployed to patient testing laboratories, academic centers and hospitals.

The two companies believe that the collaboration will lead to the development of novel oncology biomarkers and companion diagnostics because it is currently unknown how the spatial interaction of proteins impacts cancer treatment.

“While the 30-plex panel is pre-defined, and includes known proteins, the spatial interaction of those proteins and its effect on treatment response is yet unknown and can be leveraged as a novel drug target or a diagnostic test,” said Bloom.

“With access to data and insights as a result of spatial analysis on cohorts of patients either before and/or during treatment, the 30-plex biomarker panel can be validated to determine patients who are most likely to benefit.”

Dr Krish Soni, chief executive of Propath UK commented: “Spatial biology is transforming biopharma research by enabling deeper analysis of cell phenotypes with full spatial context in the tissue microenvironment. We are delighted to collaborate with Nucleai on this ambitious project which will empower researchers to unlock the potential of spatial biology, with relevance to programs from discovery through to translational and clinical research.”

Avi Viedman, CEO of Nucleai added: “Our strategic partnership with Propath has far-reaching implications in biomarker discovery. The collaboration allows us to develop and deploy AI-based multi-modal models to identify unique sets of previously unavailable biomarkers and drug targets. Together, we are pushing the boundaries of pathology tissue analytics.”

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