Emad A Rakha1, Mansour Alsaleem1, Khloud A ElSharawy1, Michael S Toss1, Sara Raafat1, Raluca Mihai1, Fayyaz A Minhas2, Andrew R Green1, Nasir M Rajpoot2, Leslie W Dalton3, Nigel P Mongan4,5. 1. School of Medicine, University of Nottingham, Nottingham City Hospital, Nottingham, UK. 2. Department of Computer Science, University of Warwick, Coventry, UK. 3. Department of Histopathology, South Austin Hospital, Austin, TX, USA. 4. Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA. 5. Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, University of Nottingham Biodiscovery Institute, Nottingham, UK.
Abstract
AIMS: Tumour genotype and phenotype are related and can predict outcome. In this study, we hypothesised that the visual assessment of breast cancer (BC) morphological features can provide valuable insight into underlying molecular profiles. METHODS AND RESULTS: The Cancer Genome Atlas (TCGA) BC cohort was used (n = 743) and morphological features, including Nottingham grade and its components and nucleolar prominence, were assessed utilising whole-slide images (WSIs). Two independent scores were assigned, and discordant cases were utilised to represent cases with intermediate morphological features. Differentially expressed genes (DEGs) were identified for each feature, compared among concordant/discordant cases and tested for specific pathways. Concordant grading was observed in 467 of 743 (63%) of cases. Among concordant case groups, eight common DEGs (UGT8, DDC, RGR, RLBP1, SPRR1B, CXorf49B, PSAPL1 and SPRR2G) were associated with overall tumour grade and its components. These genes are related mainly to cellular proliferation, differentiation and metabolism. The number of DEGs in cases with discordant grading was larger than those identified in concordant cases. The largest number of DEGs was observed in discordant grade 1:3 cases (n = 1185). DEGs were identified for each discordant component. Some DEGs were uniquely associated with well-defined specific morphological features, whereas expression/co-expression of other genes was identified across multiple features and underlined intermediate morphological features. CONCLUSION: Morphological features are probably related to distinct underlying molecular profiles that drive both morphology and behaviour. This study provides further evidence to support the use of image-based analysis of WSIs, including artificial intelligence algorithms, to predict tumour molecular profiles and outcome.
AIMS: Tumour genotype and phenotype are related and can predict outcome. In this study, we hypothesised that the visual assessment of breast cancer (BC) morphological features can provide valuable insight into underlying molecular profiles. METHODS AND RESULTS: The Cancer Genome Atlas (TCGA) BC cohort was used (n = 743) and morphological features, including Nottingham grade and its components and nucleolar prominence, were assessed utilising whole-slide images (WSIs). Two independent scores were assigned, and discordant cases were utilised to represent cases with intermediate morphological features. Differentially expressed genes (DEGs) were identified for each feature, compared among concordant/discordant cases and tested for specific pathways. Concordant grading was observed in 467 of 743 (63%) of cases. Among concordant case groups, eight common DEGs (UGT8, DDC, RGR, RLBP1, SPRR1B, CXorf49B, PSAPL1 and SPRR2G) were associated with overall tumour grade and its components. These genes are related mainly to cellular proliferation, differentiation and metabolism. The number of DEGs in cases with discordant grading was larger than those identified in concordant cases. The largest number of DEGs was observed in discordant grade 1:3 cases (n = 1185). DEGs were identified for each discordant component. Some DEGs were uniquely associated with well-defined specific morphological features, whereas expression/co-expression of other genes was identified across multiple features and underlined intermediate morphological features. CONCLUSION: Morphological features are probably related to distinct underlying molecular profiles that drive both morphology and behaviour. This study provides further evidence to support the use of image-based analysis of WSIs, including artificial intelligence algorithms, to predict tumour molecular profiles and outcome.
Authors: Paul Gamble; Ronnachai Jaroensri; Hongwu Wang; Fraser Tan; Melissa Moran; Trissia Brown; Isabelle Flament-Auvigne; Emad A Rakha; Michael Toss; David J Dabbs; Peter Regitnig; Niels Olson; James H Wren; Carrie Robinson; Greg S Corrado; Lily H Peng; Yun Liu; Craig H Mermel; David F Steiner; Po-Hsuan Cameron Chen Journal: Commun Med (Lond) Date: 2021-07-14