by ecancer reporter Clare Sansom

Endometrial cancer, or cancer of the lining of the uterus, is the sixth most common cancer in women. About 5-10% of endometrial cancers are classified as uterine serous carcinoma.

This rare subtype is more common in African-American women, is not hormone sensitive, and has a poor prognosis compared to other types of endometrial cancer.

Only about 50% of women diagnosed with Stage II disease and 5-10% diagnosed with Stage IV disease survive for five years.

The genetic changes that lead to the development of serous endometrial tumours are still poorly understood. Now, however, a team of researchers led by Daphne Bell of the National Human Genome Research Institute (NHGRI), Bethesda, Maryland, USA, has investigated these genetic lesions using exome sequencing.

Bell and her co-workers used Illumina next-generation technology to sequence the exomes (protein-coding regions of genomes) of tumour and matched normal endometrial tissue from thirteen women diagnosed with uterine serous carcinoma.

A total of 1,522 somatic mutations and 22 splice junction mutations were observed in these tumours.

One “hyper-mutable” tumour had a significantly larger number of mutations than the others and was excluded from subsequent analysis, and this exclusion reduced the number of different somatic mutations observed to 516 and the number of splice junction mutations to eleven.

A total of 510 of these 527 mutations were validated using Sanger sequencing. This figure included 321 non-synonymous mutations, with the twelve remaining tumours bearing a mean of 27.5 validated non-synonymous and splice junction mutations each. About 34% of the validated non-synonymous mutations were predicted to affect protein function using bioinformatics tools.

Nine genes were found to be mutated in more than one of the serous endometrial tumours, and the researchers chose to concentrate on these in their search for driver mutations in the tumour. Only three of these – TP53, PIK3CA and PPP2R1A – had previously been implicated in the pathogenesis of this disease. All nine genes were re-sequenced in a total of 40 further serous tumours, and three further genes, CHD4, FBXW7 and SPOP, were found to be mutated at a significantly higher rate than background frequency in all serous tumours. These genes were also found to be mutated, but to a lesser extent, in the other major subtypes of endometrial cancer, clear cell and endometrioid.

The gene CHD4 encodes chromodomain helicase DNA-binding protein 4, which is a catalytic subunit of a protein complex known as NuRD that regulates the assembly of chromatin and the DNA damage response. Eighty percent of the non-synonymous CHD4 mutations found in the serous tumours were predicted to affect the protein function; half occurred in the ATPase/helicase or helicase domains, and two-thirds had been recognized in at least one rare hereditary syndrome. Taken together, these results suggest that CHD4 is likely to be a driver mutation in this cancer subtype.

The other two genes newly recognized as being extensively mutated in serous ovarian carcinoma, FBXW7 and SPOP, are both part ofubiquitin ligase complexes. These proteins catalyse the addition of a small protein, ubiquitin, to other proteins, which targets those proteins for degradation; they thus have an important role in regulating protein turnover.

The protein encoded by FBXW, F-box and WD repeat domain containing 7, is part of a complex that targets proteins involved in cellular proliferation and cell cycle progression for degradation; it therefore acts as a tumour suppressor.

The protein encoded by SPOP, speckle-type POZ protein, forms part of a ubiquitin ligase complex that has also been shown to be frequently mutated in prostate cancer. The SPOP mutations observed in this study were all localized to a domain that is involved in recognizing and binding the substrate proteins.

Taken together, these findings suggest that mutations in SPOP and FBXW7 are also driver mutations in serous ovarian tumours, and that the processes of chromatin remodeling and ubiquitination might both be targeted in the development of drugs for this aggressive cancer sub-type.

Reference

Le Gallo, M, O’Hara, A.J., Rudd, M.L. and 11 others, and the NIH Intramural Sequencing Center Comparative Sequencing Program (2012). Exome sequencing of serous endometrial tumors identifies recurrent somatic mutations in chromatin-remodeling and ubiquitin ligase complex genes. Nature, published online ahead of print 28 October 2012. doi:10.1038/ng.2455