The UBC-40 Urothelial Bladder Cancer cell line index: a genomic resource for functional studies

Abstract

Background: Urothelial bladder cancer is a highly heterogeneous disease. Cancer cell lines are useful tools for its study. This is a comprehensive genomic characterization of 40 urothelial bladder carcinoma (UBC) cell lines including information on origin, mutation status of genes implicated in bladder cancer (FGFR3, PIK3CA, TP53, and RAS), copy number alterations assessed using high density SNP arrays, uniparental disomy (UPD) events, and gene expression.

Results: Based on gene mutation patterns and genomic changes we identify lines representative of the FGFR3-driven tumor pathway and of the TP53/RB tumor suppressor-driven pathway. High-density array copy number analysis identified significant focal gains (1q32, 5p13.1-12, 7q11, and 7q33) and losses (i.e. 6p22.1) in regions altered in tumors but not previously described as affected in bladder cell lines. We also identify new evidence for frequent regions of UPD, often coinciding with regions reported to be lost in tumors. Previously undescribed chromosome X losses found in UBC lines also point to potential tumor suppressor genes. Cell lines representative of the FGFR3-driven pathway showed a lower number of UPD events.

Conclusions: Overall, there is a predominance of more aggressive tumor subtypes among the cell lines. We provide a cell line classification that establishes their relatedness to the major molecularly-defined bladder tumor subtypes. The compiled information should serve as a useful reference to the bladder cancer research community and should help to select cell lines appropriate for the functional analysis of bladder cancer genes, for example those being identified through massive parallel sequencing.

Figure 1

Genomic alterations in cell lines included in the UBC-40 panel. (A) Fraction of the genome altered (gains and losses). (B) Whole chromosome and whole chromosome arm alterations in the cell lines. (C) Fraction of the genome affected by UPDs.

Figure 2

Alterations in the most relevant oncogenes and tumor suppressors involved in UBC. (A) Comparison of mutation frequency in UBC lines and tumors. (B) Frequency of LOH or homozygous deletion of tumor supressor genes in UBC lines and tumors. (C) Association between FGFR3 mutation status and mRNA expression. (D) Association between INK4A copy status and mRNA expression. (E) Association between PTEN copy status and mRNA expression. HD = Homozygous deletion, LOH = Loss of heterozygosity, WT = Wild type.*P < 0.05 **P < 0.01.

Figure 3

Genome wide copy number calls across the genome in UBC lines. Gender and oncogene/tumor suppressor status are also annotated.

Figure 4

Genome wide assessment of regions showing UPD identified in UBC lines.

Figure 5

Genome wide copy number calls in primary bladder tumors (n = 49) with T and G annotation.

Figure 6

Clustering of UBC lines according to the expression of gene signatures used to molecularly classify primary tumors. (A) Cell lines displaying expression patterns of the “Urobasal A”, “Urobasal B”, and “SCC-like” by Sjodahl et al [12]. The “Genomically Unstable” category is poorly defined. (B) Cell lines displaying expression signatures of “Basal-like” or “Non Basal-like” tumors according to the classification of Rebouissou et al. [24].