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GEN News Highlights : Aug 5, 2011

Scientists Identify Mutations in Two Tumor Suppressor Genes in Oligodendrogliomas

CIC and F UBP1 alterations at 19q and 1p found in two third of tumor samples sequenced.

Scientists have identified mutations in two tumor suppressor genes that are associated with oligodendrogliomas, the second most common form of brain tumor in adults. The team carried out exomic sequencing of an initial seven oligodendrogliomas and identified somatic mutations in the CIC gene at chromosome 19q in six cases as well as mutations in FUBP1 at chromosome 1p in two of the tumors.

The researchers then sequenced another 27 oligodendrogliomas and identified CIC mutations in 12 tumors and FUBP1 mutations in three tumors. Fifty-eight percent of the mutations were predicted to result in truncations of the encoded proteins.

The team, led by Duke University Medical Center’s Hai Yan, M.D., and Johns Hopkins’ Bert Vogelstein, M.D., Nickolas Papadopoulos, M.D., and Kenneth W. Kinzler, M.D., report their research in Science Express. The paper is titled “Mutations in CIC and FUBP1 Contribute to Human Oligodendroglioma.”

The co-deletion of chromosomal arms 1p  and 19q is a characteristic event in oligodendroglial tumors that results from a recurring unbalanced translocation. Up to 70% of oligodendroglioma patients have these DNA fusions, and most of them respond better to chemotherapy and radiation than those who lack the deletions in the chromosomes, the authors report.

Scientists have, however struggled to find mutations in the second copies of 1p and 19q that allow oligodendrogliomas to develop, even though assessment for loss of heterozygosity events at 1p and 19q is now commonly carried out in oligodendroglioma patients because of the therapeutic implications.

To try and identify the genes at 1p and 19q involved in LOH, the Duke and Johns Hopkins team sequenced the coding exons of 20,687 genes in DNA from seven anaplastic oligodendrogliomas. Using their previously described methods for accurately identifying somatic mutations, they picked out a total of 225 nonsynonymous mutations affecting some 200 genes among the seven tumors.

On chromosome 1p they identified eight somatically mutated genes, but only two with mutations in more than one tumor: FUBP1 (far upstream element [FUSE] binding protein 1) and NOTCH2. On chromosome 19q, there were three genetically altered genes identified, two of which were only mutated in a single tumor each.

The third, CIC (homolog of the Drosophila capicua gene), was mutated in six of the seven tumors. In each of these six cases, the fraction of mutant alleles was high, consistent with loss of the nonmutated allele, the authors note.

To validate these results and determine the spectrum of FUBP1, NOTCH2, and CIC mutations in oligodendrogliomas, the researchers then examined tumor DNA from an additional 27 cancers and  matched normal cells. While no  additional mutations in NOTCH2 were found, mutations in FUBP1 were identified in three tumors, and CIC mutations were found in 12 cases.

Of the 16 mutations, 14 appeared to be homozygous. At this high frequency, “the probability that these mutations were passengers rather than drivers was <10-8 for both genes,” the team adds. Moreover, of the 27 cases (out of the 34 evalauted in total) with 19q loss, 18 cases (67%) contained intragenic mutations of CIC, while none of the 8 ODs without 19q loss contained CIC mutations.

Significantly, all of the FUBP1 mutations and more than 25% of the CIC mutations identified in the oligodendroglioma samples were predicted to inactivate their encoded proteins as they altered splice sites, produced stop codons, or generated out-of-frame insertions or deletions. This type of mutation is commonly observed in tumor suppressor genes but has never been observed in bona fide oncogenes.
In contrast, when the team evaluated the presence of CIC and FUBP1 mutations in 92 tumors of the nervous system and 206 non-nervous system tumors, they found only three missense mutaitons in CIC, and no truncating alterations.

In Drosophila the protein encoded by CIC has been shown to be a downstream component of receptor tyrosine kinase (RTK) pathways, and the most highly conserved functional domain of the cic protein is the HMG (high mobility group) box through which it binds to DNA.

“Importantly, 8 of the 11 missense mutations we observed in  oligodendrogliomas were located in this domain,” the researchers state. The protein encoded by FUBP1, meanwhile, binds to single-stranded DNA and in particular the far-upstream element (FUSE) of the MYC oncogene. “Our data, showing that FUBP1 is inactivated by mutations, are consistent with the idea that FUBP1 mutations lead to MYC activation in these tumors.

“The identification of inactivating mutations of CIC or FUBP1 in a substantial fraction of oligodendrogliomas is expected to provide important insights into the pathogenesis of these tumors as well as help refine methods currently used for their diagnosis, prognosis, and treatment,” the authors conclude. The findings could also help in the design of new therapeutic approaches, Dr. Yan adds.

“Tumor suppressor genes like the ones we found, CIC or FUBP1, won’t be targeted directly by small molecules because the mutated gene products result in loss of function, but the pathways that these genes are involved in could be targeted. Another very important feature is that the genes could be used as biomarkers to distinguish this type of cancer from other types of cancers.”

Their next step will be to test whether patients with CIC and FUBP1 mutations have the same favorable prognosis as those who have the chromosome 1 and 19 fusion, says co-author Chetan Bettegowda, M.D., Ph.D., chief resident in the department of neurosurgery at Johns Hopkins. "We can focus now on when these mutations develop during tumor formation, whether they can guide prognosis, and how they might form targets for therapy."