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Studies Reveal New Prostate Cancer Mutation Profiles, Subtypes

NEW YORK (GenomeWeb News) – A pair of studies published online yesterday are providing new details about the mutational profiles and pathways that can contribute to prostate cancer.

In Nature, a University of Michigan-led team used exome sequencing, array comparative genome hybridization-based copy number analyses, and gene expression profiling to characterize mutation patterns in 50 tumor samples collected at autopsy from men who died with metastatic, castration-resistant prostate cancer, along with 11 non-treated tumors from individuals with high-grade but localized forms of the disease.

"Our integrated, exome-based profiling of the mutational landscape of [castration-resistant prostate cancer] is notable for representing a large cohort of heavily pre-treated patients with lethal metastatic disease, which are not commonly studied," University of Michigan pathology researcher Scott Tomlins, the study's senior author, and colleagues explained, "and provides insights into the resistance mechanisms that evolve in refractory tumors."

Through integrated analyses of these and other samples, the researchers uncovered new genes and mutation patterns in metastatic, castration resistant forms of the disease — defining a prostate cancer subtype marked by CHD1 gene mutations in the process.

Previous research has already identified some of the recurrent genetic alterations contributing to prostate cancer, the researchers explained, including fusions between the TMPRSS2 and ERG genes or other members of the ETS transcription factor family, which are found in a substantial fraction of prostate cancers.

In an effort to get a more complete picture of the mutations involved in metastatic, treatment-resistant forms of the disease, Tomlins and his co-workers sequenced and compared the exomes of 50 extensively treated castration-resistant prostate tumors from individuals with lethal forms of the disease and 11 non-treated, localized high-grade tumors.

They also did aCGH and gene expression analyses on both castration-resistant and localized tumors, as well as matched benign tumor tissue, using Compendia Biosciences' Oncomine tool to process and analyze their data.

Though the overall mutation rate was relatively low in the tumors, including those exposed to extensive treatment, researchers did find nine genes with recurrent somatic mutations. Six of the genes had been implicated in the disease before, while three — MLL2, OR5L1, and CDK12 — were new.

Consistent with past results, their analysis suggested that PTEN and WNT signaling pathways are often altered in prostate cancer. Potential driver mutations also turned up in known tumor suppressor genes and oncogenes, as well as genes from pathways involved in cell checkpoints, DNA damage repair, and androgen receptor signaling.

The exomes also contained mutations to genes from histone or chromatin modification-related pathways, the team noted. For instance, one of the newly discovered genes, MLL2, codes for a histone methyltransferase enzyme belonging to a protein complex that interacts with the androgen receptor.

Mutations to other androgen receptor-related genes such as FOXA1, ASXL1, and UTX turned up when the researchers brought together both mutation and copy number information to look at the mutational landscape in each of the tumors.

That analysis also helped in uncovering a prostate cancer subtype characterized by mutations to the chromatin-modifying enzyme gene CHD1, while the researchers' subsequent experiments indicated that most tumors containing CHD1 alterations do not harbor ETS gene family fusions.

Through a series of follow-up experiments, the team explored the biological basis for some of the mutations detected, looking, for instance, at physical interactions between the androgen receptor and the gene products of mutated genes, including FOXA1.

Meanwhile, a group led by investigators at Weill Cornell Medical College, Broad Institute, and Dana-Farber Cancer Institute demonstrated that recurrent mutations in the ubiquitin ligase-coding gene called SPOP define a non-ETS gene fusion containing prostate cancer subtype. That study, which hinged on exome sequencing of more than 100 treatment-naïve prostate tumors, appeared online yesterday in Nature Genetics.

After using the Agilent SureSelect system to capture coding sequences from tumor and normal samples from 112 US and Australian patients who had undergone prostatectomy surgery, the team sequenced the exomes to an average depth of 118 times over around 89 percent of the targeted sequence with the Illumina HiSeq 2000.

They also used RNA sequencing to assess transcription in a subset of the exome-sequenced tumors and in another 41 tumors.

Most of the exomes contained between 10 and 105 mutations apiece, they found, though one was much more highly mutated, harboring almost 1,000 mutations. The study authors noted that the extensive mutation found in that tumor, which was excluded from subsequent analyses, appeared to be a consequence of a frameshift mutation to the mismatch repair gene MSH6.

After sifting through the list of mutations in the remaining tumors to look for those that were predicted to be non-synonymous, the team found a dozen mutation-enriched genes.

These included well-known cancer genes such as TP53, PTEN, and PIK3CA, along with other recurrently mutated genes such as FOXA1, MED12, and SPOP. The latter, an E3 ubiquitin ligase-coding gene, was mutated in 6 percent to 15 percent of tumors from the discovery group or additional cohorts, which included hundreds more primary prostate tumors and metastases tested by targeted gene and RNA-sequencing.

None of the exome sequences that contained SPOP mutations had TMPRSS2-ERG or alternative ERG fusions, researchers explained, though alterations to the gene were sometimes accompanied by deletions to regions of chromosomes 5 and 6.

Given the SPOP gene product's role in helping to mark proteins for destruction through ubiquitin-mediated pathways, researchers speculated that mutations to the gene might contribute to cancer development or progression through deregulation of yet unidentified cellular processes.

"[T]here might be an accumulation of proteins in the cell that aren't cleaned out and this might lead to cancer growth, or the mutations could be removing proteins that help prevent unchecked cell growth," co-corresponding author Mark Rubin, an experimental pathology and urology researcher at Weill Cornell Medical College, said in a statement.

Those involved in the study noted that additional studies will be needed to explore the genetic, epigenetic, and transcriptional interplay within this and other prostate cancer subtypes and to determine whether the presence of SPOP alterations correspond to any discernible prognostic or treatment outcome patterns.

"While there is still a need for increased discovery, it does appear that the overall genetic landscape of prostate cancer is taking shape," Broad and Dana-Farber researcher Levi Garraway, co-corresponding author on the study, said in a statement.

He added that a "better understanding of the biology and possible therapeutic avenues linked to these alterations has become a very high priority."

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