A multiple regional epigenetic silencing phenotype of bladder tumor
characterized by the silencing of several chromosomal regions has been
identified, according to study findings.
Researchers from several institutions in France analyzed RNA from 57
bladder tumors and compared those results with those from normal urothelium.
The researchers used Affymetrix microarrays and real-time quantitative
polymerase chain reaction to search for chromosomal regions affected by
epigenetic silencing in cancer.
Verification of epigenetic silencing was achieved using gene
re-expression after the treatment of bladder cell lines with
5-aza-deoxycytidine and trichostatin A. The researchers used bisulfite
sequencing and histone methylation to study DNA methylation; they used
chromatin immunoprecipitation to study acetylation.
Tumors with multiple regional epigenetic silencing were distinguished
from those without by clustering software. The association of the multiple
regional epigenetic silencing phenotype with histopathologic and molecular
types of bladder cancer also was explored by clustering.
A second panel of 40 tumor samples was used to confirm the results of
the initial analysis. The secondary results were extended in vitro with seven
bladder cancer cell lines.
An epigenetic mechanism silenced seven chromosomal regions of contiguous
genes, according to the results. No associations between epigenetic silencing
and DNA methylation were observed. However, the researchers observed
associations between epigenetic silencing and histone H3K9 and H3K27
methylation and histone H3K9 hypoacetylation.
A subgroup of 26 tumors was also examined. In this group, all seven
chromosomal regions were concordantly silenced, which the researchers said
defined a multiple regional epigenetic silencing phenotype. They noted that
these tumors exhibited a carcinoma in situ-associated gene expression signature
in 25 of these 26 tumors; by comparison, zero of 31 tumors that were not
multiple regional epigenetic silencing phenotype did not exhibit this gene
These same tumors also carried FGFR3 mutations at a rate of one
of 26, compared with 22 of 31 nonmultiple regional epigenetic silencing
phenotype tumors, (P<10–6), and contained 76% of the
muscle-invasive tumors, according to the results.
“Cell lines derived from aggressive bladder tumors presented
epigenetic silencing of the same regions,” the researchers wrote.
This type of work is indicative of where the field of solid tumor translational research is going. That is, it looks for specific genetic events, in this case gene silencing via methylation, that may influence tumor biology. Although this report is preliminary in a small number of pts, eventually we would like to use such an analysis to profile individual tumors to chose specific therapies, or to better prognosticate outcome with information that adds value to standard clinical and pathologic variables.
– Brian I. Rini, MD
Department of Solid Tumor Oncology,
Cleveland Clinic Taussig Cancer Institute
Disclosures: Dr. Rini reports consulting and research support from Pfizer, GSK.