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TCGA Bladder Cancer Study Reveals Recurrent Mutations, Possible Treatment Targets

NEW YORK (GenomeWeb News) – Genes involved in chromatin regulation are amongst those most prone to recurrent mutation in urothelial bladder cancer, according to a new Nature study from members of the Cancer Genome Atlas. Results from their large, integrated analysis hint that that pathway — and others — might serve as treatment targets for the disease in the future.

Changes to chromatin regulation appear to be an emerging theme across many cancer types, John Weinstein, bioinformatics and computational biology chair at the University of Texas MD Anderson Cancer Center, told GenomeWeb Daily News. Still, he noted that the burden of mutations and alterations affecting chromatin-modifying genes was more pronounced in bladder cancer than has been reported in other cancers studied so far.

For their new study, he and other members of the TCGA team used a combination of exome-, transcriptome-, and/or whole-genome sequencing to assess tumor and normal samples from 131 individuals with high-grade, muscle-invasive urothelial carcinoma of the bladder.

With these and other data, the researchers found dozens of recurrently mutated genes, tracked down potential treatment targets in more than two-thirds of the tumors, and used expression data to define four main sub-types of the disease.

Roughly 150,000 individuals around the world die from urothelial bladder cancer annually, the researchers noted. A handful of recurrent fusions, copy number changes, and mutations had previously been detected in the tumors, including alterations affecting genes in chromatin remodeling pathways, though the complete suite of genetic glitches contributing to the condition had not been defined.

As in past TCGA studies, Weinstein noted, the new analysis of bladder cancer brought together DNA, RNA, protein, and epigenomic profiles in an effort to characterize and come up with theoretical treatment targets for muscle-invasive urothelial bladder carcinoma tumors.

The researchers used Illumina's HiSeq 2000 do exome sequencing on tumor-normal pairs from 130 individuals with urothelial bladder cancer, generating 100-fold average coverage of each. With the same platform, they also did RNA sequencing on the complete tumor set of 131 tumors and low-pass whole-genome sequencing on 114 tumors.

Copy number profiling with Affymetrix SNP 6.0 arrays provided data to complement copy number patterns detected by whole-genome sequencing. And the team turned to Illumina Infinium arrays to assess DNA methylation patterns in the tumors and reverse-phase protein arrays to profile their protein and phosphoprotein expression.

When they sorted through the protein-coding sequences, investigators identified 32 genes that were mutated in a significant proportion of the bladder cancer tumors, including new and known bladder cancer contributors. Among the recurrently mutated genes were members of well-known kinase signaling pathways and pathways involved in controlling cell cycle progression and regulating chromatin.

Together, the DNA and RNA sequence data also made it possible to find shifts in microRNA profiles in the tumors, as well as fusions involving the FGFR3 gene and, in a small fraction of the tumors, evidence of viral interlopers.

Five of the bladder cancers tested contained transcripts stemming from a cytomegalovirus, human papillomavirus 16, or human herpesvirus. Two more tumors housed DNA from HPV16 or human herpesvirus but no apparent viral transcripts.

Because such viral sequences were found in just a handful of the bladder tumors tested so far, Weinstein said, it's tricky to determine their clinical significance, if any. He noted that the team is planning to assess around 200 more bladder cancer tumors in the next year, which may clarify these potential relationships while refining and validating other findings from the current analysis.

Epidemiological data indicated that some 72 percent of the bladder cancer tumors came from individuals with a history of smoking.

The investigators did not detect any obvious tobacco-associated mutation signatures in tumors from patients with a self-reported history of smoking. Nevertheless, the bladder tumors tended to contain a large number of DNA changes — coming in just behind lung cancer and melanoma in their average number of genetic glitches per tumor.

"That was, at the time, one of the surprises: that [the high mutation rate] didn't seem to be related to smoking history," Weinstein said. "Whether it relates to exposures of the bladder of other kinds is a live question."

In urothelial bladder cancer patients who had never smoked, researchers did detect a slight uptick in cytosine to guanine mutations, while roughly a third of tumors from those who smoked showed signs of DNA hypermethylation.

Features from the expression-based urothelial bladder cancer sub-types, meanwhile, suggested that some forms of the disease share genetic features with breast, lung, or head and neck sub-types characterized in the past.

For example, a subset of the bladder cancer tumors were marked by mutations, amplifications, or expression shifts involving HER2, hinting that some forms of the disease might respond to treatments developed for HER2-altered breast cancers.

Other possible treatment targets turned up as well, including the alterations to signaling and chromatin-related pathways. All told, the team found potentially targetable genetic glitches in 69 percent of the tumors. While promising, though, Weinstein cautioned that such gene- or pathway-focused therapeutic options still need to be tested through appropriate clinical trials.