Volume 69, Issue 6, Pages 1055-1061 (June 2016) Balanced Translocations Disrupting SMARCB1 Are Hallmark Recurrent Genetic Alterations in Renal Medullary Carcinomas  Julien Calderaro, Julien Masliah-Planchon, Wilfrid Richer, Laetitia Maillot, Pascale Maille, Ludovic Mansuy, Claire Bastien, Alexandre de la Taille, Hélène Boussion, Cécile Charpy, Anne Jourdain, Claire Bléchet, Gaelle Pierron, David Gentien, Laurence Choudat, Christophe Tournigand, Olivier Delattre, Yves Allory, Franck Bourdeaut  European Urology  Volume 69, Issue 6, Pages 1055-1061 (June 2016) DOI: 10.1016/j.eururo.2015.09.027 Copyright © 2015 European Association of Urology Terms and Conditions

Fig. 1 Translocations involving SMARCB1 are the only recurrent genetic features of renal medullary carcinoma (RMC). (a) General features of RMC: age in years; A, S, and C refer to the type of hemoglobin. Fusion transcripts are the number of aberrant transcripts per tumor. (b) Array comparative genomic hybridization of the five RMC samples; arrows show chromosomal break points. (c) Schematic representation of interchromosomal translocations involving SMARCB1; red blocks show exons; break points are indicated by dotted lines. (d) Fluorescence in situ hybridization using break-apart probes; green arrows indicate the RP5-930L11 probe and red arrows the RP11-164NB probe. Left panel: tumor cells (INI85) showing loss of one SMARCB1 locus and a break-apart signal corresponding to the disruption of the SMARBC1 sequence; right panel: epithelial cell of the adjacent kidney parenchyma displaying two colocalized green and red signals corresponding to two intact SMARCB1 alleles. (e) Schematic representation of the MALAT1-SMARCB1 transcript; Integrative Genomics Viewer (Broad Institute, Cambridge, MA, USA) showing the high level of expression restricted to the four last exons of SMARCB1, at a level similar to MALAT1. del=deletion; hem=hemizygous; Hom=homozygous; mut=mutation; Mut/mb=number of somatic mutations per megabase of exome (we consider the human exome to be composed of approximatively 33 Mb); RMC=renal medullary carcinoma. European Urology 2016 69, 1055-1061DOI: (10.1016/j.eururo.2015.09.027) Copyright © 2015 European Association of Urology Terms and Conditions

Fig. 2 Rhabdoid tumor of kidney (RTK) and renal medullary carcinoma (RMC) share a SMARCB1-deficiency signature. (a) Hierarchical unsupervised clustering on 3559 varying genes (Affymetrix U133Plus v.2.0); dotted line represents the absence of correlation similarity. (b) Venn diagram showing the overlap of genes sets showing up on the Welch t test (p<0.05) and fold change (|FC| ≥1.2) differential analyses between RMC and RTK and the two other cancer types. For each Venn diagram, the Fisher exact test was performed to verify the significance of the overlap of the two observed gene sets. (c) Gene Set Enrichment in SMARCA2 targets and embryonic stem cell core gene signatures in RMC and RTK compared with PRC. (d) Box plot of three genes known to be upregulated in rhabdoid cell lines and therapeutically targetable. Asterisks indicate a p value <0.05 and |FC| >1.2. ccRCC=clear cell renal cell carcinoma; FC=fold change; PRC=papillary renal cell carcinoma; RMC=renal medullary carcinoma; RTK=rhabdoid tumor of kidney. European Urology 2016 69, 1055-1061DOI: (10.1016/j.eururo.2015.09.027) Copyright © 2015 European Association of Urology Terms and Conditions

European Urology 2016 69, 1055-1061DOI: (10.1016/j.eururo.2015.09.027) Copyright © 2015 European Association of Urology Terms and Conditions

European Urology 2016 69, 1055-1061DOI: (10.1016/j.eururo.2015.09.027) Copyright © 2015 European Association of Urology Terms and Conditions

European Urology 2016 69, 1055-1061DOI: (10.1016/j.eururo.2015.09.027) Copyright © 2015 European Association of Urology Terms and Conditions

European Urology 2016 69, 1055-1061DOI: (10.1016/j.eururo.2015.09.027) Copyright © 2015 European Association of Urology Terms and Conditions