ASCO GU 2018: Evaluation of a 29 Gene Classifier for Basal/Non Basal Prediction in Muscle-Invasive Bladder Cancer FFPE Samples

San Francisco, CA ( Recent and independent muscle-invasive bladder cancer (MIBC) molecular classifications identified the basal / squamous-like (BASQ) tumors as an intrinsic and robust subtype, harboring a poor outcome and a possible chemo-sensitivity to cisplatin based regimen. The authors presented a study aimed to evaluate the diagnostic accuracy of a Nanostring classifier for tumor subtype prediction on fresh frozen plasma embeded (FFPE) specimens.


Two series of MIBC patients were used (CIT n = 51 & Stransky n = 22) for which BASQ tumors were identified previously, using Affymetrix transcriptome data obtained from frozen samples (Rebouissou, Science Trans Med 2014). 29 genes were selected to predict the basal subtype, RNA expression of matched frozen and FFPE samples was studied using Nanostring technology. To define the classifiers for Affymetrix, frozen and FFPE Nanostring expression matrix on CIT samples the centroid of each cluster was calculated using the expression of 29 genes. Internal validation used leave-one-out cross-validation to train and test the prediction accuracy of the new classifier. For external validation, the CIT samples were used as training set and the Stransky samples as validation set. Predictive accuracy expressed as percentage of correctly classified samples is provided.


Correlations between Affymetrix, frozen and FFPE Nanostring data set were checked for gene expression and samples. Using CIT samples as train and test set, the predictive accuracy for BASQ tumor identification was for Affymetrix, frozen Nanostring and FFPE Nanostring classifiers, 90.20% [78.59%; 96.74%], 88.24% [76.13%; 95.56%] and 92.16% [81.12%; 97.82%], respectively. Using training on CIT samples and test on Stransky samples, the predictive accuracy was 90.91% [70.84%; 98.88%] both for Affymetrix, frozen Nanostring and FFPE Nanostring classifiers.


The authors concluded that the 29 gene expression Nanostring codeset was able to identify reliably basal / squamous like tumors on FFPE samples from MIBC.

Presented by: Yves Allory, Department of Pathology, Paris, France

Co Authors: Nanor Sirab, Damien Drubay, David Gentien, Aurélien De Reyniès, Benoit Albaud, Aurélie Kamoun, Pascale Soyeux, Pascale Maille, Thierry Lebret, Simone Benhamou, Xavier Paoletti, Francois Radvanyi; Henri Mondor Hospital, Créteil, France; Institut Mondor de Recherches Biomédicales, Créteil, France; Gustave Roussy Institute, Villejuif, France; Curie Cancer Institute, Paris, France; Ligue Nationale Contre le Cancer, Paris, France; University Paris-Est Créteil, Créteil, France; Hôpital Foch, Suresnes, France; INSERM, Paris-Sud University, Paris, France

Written by: Hanan Goldberg, MD, Urologic Oncology Fellow (SUO), University of Toronto, Princess Margaret Cancer Centre @GoldbergHanan at the 2018 American Society of Clinical Oncology Genitourinary (ASCO GU) Cancers Symposium, February 8-10, 2018 - San Francisco, CA