Abstract P4-09-08: AI-based quantitation of cancer cell and fibroblast nuclear morphology reflects transcriptomic heterogeneity and predicts survival in breast cancer
Authors: Abel John , Kirkup Christian , Kos Filip , Gerardin Ylaine , Srinivasan Sandhya , Brosnan-Cashman Jacqueline , Leidal Ken , Vasudevan Sanjana , Rajan Deepta , Jain Suyog , Prakash Aaditya , Padigela Harshith , Conway Jake , Patel Neel , Trotter Benjamin , Yu Limin , Taylor-Weiner Amaro , Krause Emma L. , Bronnimann Matthew , Chambre Laura , Glass Ben , Parmar Chintan , Hennek Stephanie , Khosla Archit , Resnick Murray , Beck Andrew H. , Montalto Michael , Najdawi Fedaa , Drage Michael G. , Wapinski Ilan 
Published: March 2023

Background: Morphological features of cancer cell nuclei are routinely used to assess disease severity and prognosis, and cancer nuclear morphology has been linked to genomic alterations. Quantitative analyses of the nuclear features of cancer cells and other tumor-resident cell types, such as cancer-associated fibroblasts (CAFs), may reveal novel biomarkers for prognosis and treatment response. Here, we applied a pan-cancer nucleus detection and segmentation algorithm and a cell classification model to hematoxylin and eosin (H&E)-stained whole slide images (WSIs) of breast cancer specimens, enabling the measurement of morphological features of nuclei of multiple cell types within a tumor. Methods: Convolutional Neural Network models for 1) nucleus detection and segmentation and 2) cell classification were deployed on H&E-stained WSIs from The Cancer Genome Atlas (TCGA) breast cancer dataset (primary surgical resections; N=890). Separate models were trained to segment regions of stromal subtypes, such as inflamed and fibroblastic stroma. Nuclear features (area, axis length, eccentricity, color, and texture) were computed and aggregated across each slide to summarize slide-level nuclear morphology for each cell type. Next-generation sequencing-based metrics of genomic instability (N=774) and gene expression (N=868) were acquired and paired with TCGA WSIs. Gene set enrichment analysis was performed using the Molecular Signatures Database. Spearman correlation compared nuclear features to genomic instability metrics. Linear regression was used to assess the relationship between nuclear features and bulk gene expression. Multivariable Cox regression with age and ordinal tumor stage as covariates was used to find association between overall survival (OS) and nuclear features. All reported results were significant (p&lt; 0.05) when adjusted for false discovery rate via the Benjamini-Hochberg procedure. Results: Variation in cancer cell nuclear area, a quantitative metric related to pathologist-assessed nuclear pleomorphism, was calculated by the standard deviation of the nuclear area of cancer cells across a WSI. This feature was associated with genomic instability, as measured by aneuploidy score (r=0.448) and homologous recombination deficiency score (r=0.382), and reduced OS. In contrast, the variability in fibroblast and lymphocyte nuclear areas did not correlate with either metric of genomic instability (all r&lt; 0.1, p&gt;0.05). Furthermore, an association between variation in cancer cell nuclear area with the expression of cell cycle and proliferation pathway genes was observed, suggesting that increased nuclear size heterogeneity may indicate a more aggressive cancer phenotype. Features quantifying CAF nuclear morphology were also assessed, revealing that CAF nucleus shape (larger minor axis length) was associated with lower OS, as well as the expression of gene sets involved in extracellular matrix remodeling and degradation. Conclusions: The nuclear morphologies of breast cancer cells and CAFs reflect underlying genomic and transcriptomic properties of the tumor and correlates with patient outcome. The application of digital pathology analysis of breast cancer histopathology slides enables the integrative study of genomics, transcriptomics, tumor morphology, and overall survival to support research into disease biology research and biomarker discovery.

Citation Format: John Abel, Christian Kirkup, Filip Kos, Ylaine Gerardin, Sandhya Srinivasan, Jacqueline Brosnan-Cashman, Ken Leidal, Sanjana Vasudevan, Deepta Rajan, Suyog Jain, Aaditya Prakash, Harshith Padigela, Jake Conway, Neel Patel, Benjamin Trotter, Limin Yu, Amaro Taylor-Weiner, Emma L. Krause, Matthew Bronnimann, Laura Chambre, Ben Glass, Chintan Parmar, Stephanie Hennek, Archit Khosla, Murray Resnick, Andrew H. Beck, Michael Montalto, Fedaa Najdawi, Michael G. Drage, Ilan Wapinski. AI-based quantitation of cancer cell and fibroblast nuclear morphology reflects transcriptomic heterogeneity and predicts survival in breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P4-09-08.