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GEN News Highlights : Sep 21, 2011

Scientists Identify Fusion Gene in 15% of Serous Ovarian Cancers

Investigators say resulting transcript combines 5’ exons from ESRRA and 3’ exons from C11orf20.

Scientists have identified a gene fusion in some 15% of serous ovarian tumor samples studied, which they say could represent the basis of a biomarker for early detection of this form of cancer. The fusion occurs between the two neighboring genes ESRRA and C11orf20. ESRRA encodes a ligand-independent member of the nuclear-hormone receptor superfamily that is related to the estrogen receptor, and C11orf20 is a conserved but so far uncharacterized gene located immediately upstream of ESRRA.

The researchers, led by Patrick O. Brown, M.D., and Julia Salzman, M.D., at Stanford University School of Medicine, identified the fusion transcript by carrying out deep paired-end sequencing of mRNA from serous ovarian cancers. Deep sequencing of the corresponding genomic region confirmed that it resulted from a chromosomal rearrangement.

The scientists claim the fusion transcript may play a role in the pathogenesis of significant portion of serous ovarian cancers. “This kind of genetic lesion can escape detection by any of the methods traditionally used to detect chromosome rearrangements in cancer,” Dr. Brown remarks. “But I think these local rearrangements that have previously flown under our radar might actually turn out to be among the most frequent genetic lesions in cancer.” The team reports its findings in PLoS Biology in a paper titled “ESRRA-C11orf20 Is a Recurrent Gene Fusion in Serous Ovarian Carcinoma.”

Although recurrent gene fusions are among the most tumor-specific molecular markers known, few have been identified in commonly occurring cancers that often have multiple, complex chromosomal rearrangements that are hard to analyze using traditional cytogenetic approaches,” the authors note. Serous ovarian cancer is the common form of ovarian cancer, and is especially lethal because it is usually only detected at a late stage in its progression.

To look for gene fusions that might represent early molecular markers of (and potential targets for) serous cancer, the team analyzed a pool of mRNA isolated from 12 primary serous ovarian cancers by combining deep, paired-end sequencing of tumor RNA with statistical bioinformatics. This approach led to identification of ESRRA-C11orf20 fusion transcripts that combined 5’ exons from ESRRA and 3’ exons from C11orf20.

Using RT-PCR followed by Sanger sequencing, the researchers subsequently found the transcript in 10 out of another 67 cases of serous cancer, suggesting a prevalence rate of 15%. “Nearly all positive cases expressed one or both of the two ESRRA-C11orf20 fusion isoforms previously observed in our tumor pool," they report, although a single patient exclusively expressed a third isoform.

The ESRRA protein consists of an N-terminal regulatory domain (NTD), a DNA binding domain (DBD) comprising two zinc-fingers, and a putative ligand-binding domain (LBD). While the fusion transcripts identified in serous cancer all encode the NTD and the first zinc-finger of the DBD, they lack both the second zinc-finger and the LBD. While a functional role for the ESSRA-C11orf20 fusion remains to be established, two of the three fusion isoforms observed were predicted to encode fusion proteins containing the N-terminal portion of the ESRRA protein and the C-terminal portion of the predicted C11orf20 protein.

Significantly, all of the fusion-positive tumors identified expressed at least one of the in-frame isoforms, and the resulting transcripts retain important functional features of ESRRA including the first zinc-finger domain that is critical for the DNA sequence specificity of ESRRA, as well as a phosphorylation site and a phosphorylation-dependent sumoylation site that have been shown to regulate transcriptional activation by ESRRA, the authors state.

“We were able to detect the ESRRA-C11orf20 fusion, based on UHTS analysis of either RNA or genomic DNA, only by conducting a deliberate focused search for evidence of structural rearrangements,” the authors stress. “We suggest that chromosomal rearrangements involving nearby or adjacent genes may comprise a substantial fraction of oncogenic mutations that have heretofore escaped detection...The ESSRA-C11orf20 fusion is, to our knowledge, the first recurrent gene fusion to be identified in serous ovarian cancer. This fusion gene and its components are now high-priority targets for further investigation of their potential roles in pathogenesis and as potential diagnostic or therapeutic targets.”