Genetics of clear cell renal carcinoma: new tumor suppressor genes and aberrant chromatin regulation

PhD ceremony: Mr. G. Duns, 14.30 uur, Aula Academiegebouw, Broerstraat 5, Groningen

Dissertation: Genetics of clear cell renal carcinoma: new tumor suppressor genes and aberrant chromatin regulation

Promotor(s): prof. R.M.W. Hofstra

Faculty: Medical Sciences

Clear cell renal cell carcinoma (ccRCC) is genomically characterized by the frequent loss of the short arm of chromosome 3 (3p), suggesting the presence of tumor suppressor genes (TSGs) in this genomic region. This thesis presents the search for these TSGs. Using a method called GINI, we identified inactivating mutations in histone methyltransferase gene SETD2, located at 3p21, in several ccRCC samples. SETD2 trimethylates histone 3 at position K36, a modification which has been suggested to be involved in alternative splicing. SETD2 knockdown in renal cells indeed resulted in an apparent change in alternative splicing for a set of genes, several of which are interesting with respect to tumorigenic development. Targeted exome sequencing of ten primary ccRCC tumors revealed inactivating mutations in the known ccRCC tumor suppressor gene VHL, but also in PBRM1, and BAP1 in six, seven, and one of these tumors, respectively. PBRM1 and BAP1 are both located at 3p21 and code for the chromatin targeting subunit of the SWI/SNF chromatin-remodeling complex and an enzyme involved in histone deubiquitination, respectively. Sequencing of PBRM1 in ccRCC-derived cell lines confirmed its frequent inactivation in ccRCC, suggesting that this is a major TSG for ccRCC. Thus, 3p harbors several genes that do contribute to ccRCC development. Several of these genes encode proteins that modify histone tails or remodel chromatin, suggesting that aberrant chromatin regulation is a core driver event in the development of ccRCC.