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Genetic Alterations in the Molecular Subtypes of Bladder Cancer : Illustration in the Cancer Genome Atlas Dataset

Choi, Woonyoung; Ochoa, Andrea; McConkey, David J.; Aine, Mattias LU ; Höglund, Mattias LU ; Kim, William Y.; Real, Francisco X; Kiltie, Anne E.; Milsom, Ian and Dyrskjøt, Lars, et al. (2017) In European Urology 72(3). p.354-365
Abstract

Context: Recent whole genome mRNA expression profiling studies revealed that bladder cancers can be grouped into molecular subtypes, some of which share clinical properties and gene expression patterns with the intrinsic subtypes of breast cancer and the molecular subtypes found in other solid tumors. The molecular subtypes in other solid tumors are enriched with specific mutations and copy number aberrations that are thought to underlie their distinct progression patterns, and biological and clinical properties. Objective: The availability of comprehensive genomic data from The Cancer Genome Atlas (TCGA) and other large projects made it possible to correlate the presence of DNA alterations with tumor molecular subtype membership. Our... (More)

Context: Recent whole genome mRNA expression profiling studies revealed that bladder cancers can be grouped into molecular subtypes, some of which share clinical properties and gene expression patterns with the intrinsic subtypes of breast cancer and the molecular subtypes found in other solid tumors. The molecular subtypes in other solid tumors are enriched with specific mutations and copy number aberrations that are thought to underlie their distinct progression patterns, and biological and clinical properties. Objective: The availability of comprehensive genomic data from The Cancer Genome Atlas (TCGA) and other large projects made it possible to correlate the presence of DNA alterations with tumor molecular subtype membership. Our overall goal was to determine whether specific DNA mutations and/or copy number variations are enriched in specific molecular subtypes. Evidence: We used the complete TCGA RNA-seq dataset and three different published classifiers developed by our groups to assign TCGA's bladder cancers to molecular subtypes, and examined the prevalence of the most common DNA alterations within them. We interpreted the results against the background of what was known from the published literature about the prevalence of these alterations in nonmuscle-invasive and muscle-invasive bladder cancers. Evidence synthesis: The results confirmed that alterations involving RB1 and NFE2L2 were enriched in basal cancers, whereas alterations involving FGFR3 and KDM6A were enriched in luminal tumors. Conclusions: The results further reinforce the conclusion that the molecular subtypes of bladder cancer are distinct disease entities with specific genetic alterations. Patient summary: Our observation showed that some of subtype-enriched mutations and copy number aberrations are clinically actionable, which has direct implications for the clinical management of patients with bladder cancer. We analyzed the prevalence of the most common genomic alterations in the bladder cancer molecular subtypes. The results have important implications for our understanding of bladder cancer etiology and the development of molecular subtype-specific therapies.

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publication status
published
subject
keywords
DNA alterations, Molecular subtypes, Muscle-invasive bladder cancer
in
European Urology
volume
72
issue
3
pages
354 - 365
publisher
Elsevier
external identifiers
  • scopus:85016487785
  • wos:000407960100020
ISSN
0302-2838
DOI
10.1016/j.eururo.2017.03.010
language
English
LU publication?
yes
id
1d5d583f-16a8-40a4-b455-8e0cf24bb54d
date added to LUP
2017-04-19 11:22:20
date last changed
2017-09-18 13:32:37
@article{1d5d583f-16a8-40a4-b455-8e0cf24bb54d,
  abstract     = {<p>Context: Recent whole genome mRNA expression profiling studies revealed that bladder cancers can be grouped into molecular subtypes, some of which share clinical properties and gene expression patterns with the intrinsic subtypes of breast cancer and the molecular subtypes found in other solid tumors. The molecular subtypes in other solid tumors are enriched with specific mutations and copy number aberrations that are thought to underlie their distinct progression patterns, and biological and clinical properties. Objective: The availability of comprehensive genomic data from The Cancer Genome Atlas (TCGA) and other large projects made it possible to correlate the presence of DNA alterations with tumor molecular subtype membership. Our overall goal was to determine whether specific DNA mutations and/or copy number variations are enriched in specific molecular subtypes. Evidence: We used the complete TCGA RNA-seq dataset and three different published classifiers developed by our groups to assign TCGA's bladder cancers to molecular subtypes, and examined the prevalence of the most common DNA alterations within them. We interpreted the results against the background of what was known from the published literature about the prevalence of these alterations in nonmuscle-invasive and muscle-invasive bladder cancers. Evidence synthesis: The results confirmed that alterations involving RB1 and NFE2L2 were enriched in basal cancers, whereas alterations involving FGFR3 and KDM6A were enriched in luminal tumors. Conclusions: The results further reinforce the conclusion that the molecular subtypes of bladder cancer are distinct disease entities with specific genetic alterations. Patient summary: Our observation showed that some of subtype-enriched mutations and copy number aberrations are clinically actionable, which has direct implications for the clinical management of patients with bladder cancer. We analyzed the prevalence of the most common genomic alterations in the bladder cancer molecular subtypes. The results have important implications for our understanding of bladder cancer etiology and the development of molecular subtype-specific therapies.</p>},
  author       = {Choi, Woonyoung and Ochoa, Andrea and McConkey, David J. and Aine, Mattias and Höglund, Mattias and Kim, William Y. and Real, Francisco X and Kiltie, Anne E. and Milsom, Ian and Dyrskjøt, Lars and Lerner, Seth P.},
  issn         = {0302-2838},
  keyword      = {DNA alterations,Molecular subtypes,Muscle-invasive bladder cancer},
  language     = {eng},
  number       = {3},
  pages        = {354--365},
  publisher    = {Elsevier},
  series       = {European Urology},
  title        = {Genetic Alterations in the Molecular Subtypes of Bladder Cancer : Illustration in the Cancer Genome Atlas Dataset},
  url          = {http://dx.doi.org/10.1016/j.eururo.2017.03.010},
  volume       = {72},
  year         = {2017},
}