DNA Microarray Expression Profiling of Bladder Cancer Allows Identification of Noninvasive Diagnostic Markers
Purpose
There is a need in urological practice to identify new bladder cancer molecular markers to further develop noninvasive diagnostic tests. We analyzed bladder cancer gene expression profiles to determine the relevant differentially expressed genes and whether this differential expression is maintained in urine samples.
Materials and Methods
We collected 55 tissue specimens from a total of 43 patients with bladder cancer and 12 controls, and 49 urine samples from bladder washings from a total of 36 patients with bladder cancer and 13 controls between September 2003 and December 2004. DNA microarrays (GeneChip® Human Genome U133 Plus 2.0 Array) were used to identify differentially expressed genes at 3 bladder cancer stages. Selected differentially expressed genes were validated in an independent set of bladder washings by quantitative reverse transcriptase-polymerase chain reaction.
Results
Unsupervised cluster analysis of DNA microarray data showed a clear distinction in control vs tumor samples and low vs high grade tumors. Genes with at least 2-fold differential expression in controls vs tumors (2,937 probe sets or 2,295 genes) and in low vs high grade tumors (674 probe sets or 530 genes) were identified and ranked. Gene expression measurements in bladder washings of the 6 most differentially expressed genes in controls vs tumors were confirmed for the 2 over expressed genes tested by quantitative reverse transcriptase-polymerase chain reaction. All 8 selected differentially expressed genes in low vs high grade tumors were confirmed in bladder washing samples.
Conclusions
Bladder cancer analysis by DNA microarrays provides new putative mRNA markers for bladder cancer diagnosis and/or prognosis that can be extrapolated to bladder fluids.
Key Words: urinary bladder, urinary bladder neoplasms, oligonucleotide array sequence analysis, gene expression, tumor markers, biological
Abbreviations and Acronyms: BC, bladder cancer, BW, bladder washing, HG, high grade, LG, low grade, MIBC, muscle invasive BC, NMIBC, nonMIBC, PCR, polymerase chain reaction, qRT-PCR, quantitative reverse transcriptase-PCR, T2 + HG, T2-4HG
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Study received hospital ethics committee approval.
Supported by Laboratorios Fina Biotech, Spanish Urological Association Grant FIU 2007 and Fondo de Investigaciones Sanitarias Grant PI070040.
Supplementary material for this article can be obtained at http://bioinfo.ciberehd.org/mengual_et_al_2009/.
PII: S0022-5347(09)00884-2
doi:10.1016/j.juro.2009.03.084
© 2009 American Urological Association. Published by Elsevier Inc. All rights reserved.
