Global mRNA expression analysis is efficient for phenotypic profiling of tumours and has been used to define molecular subtypes for almost every major tumour type. A key limitation is that most tumours are communities of both tumour and non-tumour cells. This problem is particularly pertinent when analysing advanced invasive tumours, known to induce major changes and responses in both the tumour and the surrounding tissue. To identify bladder cancer tumour-cell phenotypes and compare classification by tumour-cell phenotype with classification by global gene expression analysis, we analysed 307 advanced bladder cancers (cystectomised) both by genome gene expression analysis and by immunohistochemistry using antibodies for 28 proteins. By systematic analysis of gene and protein expression data, focusing on key molecular processes, we describe five tumour-cell phenotypes of advanced urothelial carcinoma; Urothelial-like, Genomically Unstable, Basal/SCC-like, Mesenchymal-like, and Small cell/Neuroendocrine like. We provide molecular pathological definitions for each subtype. Tumours expressing urothelial differentiation factors show inconsistent and abnormal protein expression of terminal differentiation markers, suggesting pseudo-differentiation. Cancers with different tumour-cell phenotypes may co-cluster (converge), and cases with identical tumour-cell phenotypes may cluster apart (diverge) in global mRNA analyses. This divergence/convergence suggests that broad global commonalities related to the invasive process may exist between muscle-invasive tumours regardless of specific tumour-cell phenotype. Hence, there is a systematic disagreement in subtype classification determined by global mRNA profiling and by IHC profiling at the tumour-cell level. We suggest that a combination of molecular pathology (tumour cell phenotype) and global mRNA profiling (context) is required for adequate subtype classification of muscle-invasive bladder cancer.
The Journal of pathology. 2017 Feb 13 [Epub ahead of print]
Gottfrid Sjödahl, Pontus Eriksson, Fredrik Liedberg, Mattias Höglund
Division of Urological Research, Department of Translational Medicine, Lund University, Skåne University Hospital, Malmö, Sweden., Division of Oncology and Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden.