Eco-evolutionary Guided Pathomic Analysis to Predict DCIS Upstaging

Xiao, Y.; Elmasry, M.; Bai, J.; Chen, A.; Chen, Y.; Jackson, B.; Johnson, J. O.; Gillies, R. J.; Prasanna, P.; Chen, C.; Damaghi, M.

doi:10.1101/2024.06.23.600274

bioRxiv · 10.1101/2024.06.23.600274

Eco-evolutionary Guided Pathomic Analysis to Predict DCIS Upstaging

Xiao, Y.·Elmasry, M.·Bai, J.·Chen, A.·Chen, Y.·Jackson, B.·Johnson, J. O.·Gillies, R. J.·Prasanna, P.·Chen, C.·Damaghi, M.

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Abstract

Cancers evolve in a dynamic ecosystem. Thus, characterizing cancers ecological dynamics is crucial to understanding cancer evolution and can lead to discovering novel biomarkers to predict disease progression. Ductal carcinoma in situ (DCIS) is an early-stage breast cancer characterized by abnormal epithelial cell growth confined within the milk ducts. In this study, we show that ecological analysis of hypoxia and acidosis biomarkers can significantly improve prediction of DCIS upstaging. First, we developed a novel eco-evolutionary designed approach to define habitats in the tumor intraductal microenvironment based on oxygen diffusion distance. Then, we identified cancer cells with metabolic phenotypes attributed to their habitats, including CA9 for hypoxia responding phenotype, and LAMP2b for acid adapted phenotype. Traditionally these markers have shown limited predictive capabilities for DCIS progression, if any. However, when analyzed from an ecological perspective, their power to differentiate between non-upstaged and upstaged DCIS increased significantly. Second, we discovered distinct niches with spatial patterns of these biomarkers and used the distribution of such niches to predict patient upstaging. The niches were characterized by pattern analysis of both cellular and spatial features. With a 5-fold validation on the biopsy cohort, we trained a random forest classifier to achieve the area under curve (AUC) of 0.74. Our results affirm the importance of tumor ecological features in eco-evolutionary-designed approaches for novel biomarkers discovery. SignificanceOur results affirm the importance of spatial and ecological features in eco-evolutionary-designed biomarkers discovery studies in the era of digital pathology.

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Xiao, Y., Elmasry, M., Bai, J., Chen, A., Chen, Y., Jackson, B., Johnson, J. O., Gillies, R. J., Prasanna, P., Chen, C., Damaghi, M.. 2024-06-28. Eco-evolutionary Guided Pathomic Analysis to Predict DCIS Upstaging. https://doi.org/10.1101/2024.06.23.600274

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