A fluorescence in situ hybridization (FISH) analysis with centromere-specific DNA probes of chromosomes 3 and 17 in pleomorphic adenomas and adenoid cystic carcinomas

The Genomic Landscape of Centromeres in Cancers

Centromere genomics remain poorly characterized in cancer, due to technologic limitations in sequencing and bioinformatics methodologies that make high-resolution delineation of centromeric loci difficult to achieve. We here leverage a highly specific and targeted rapid PCR methodology to quantitatively assess the genomic landscape of centromeres in cancer cell lines and primary tissue. PCR-based profiling of centromeres revealed widespread heterogeneity of centromeric and pericentromeric sequences in cancer cells and tissues as compared to healthy counterparts. Quantitative reductions in centromeric core and pericentromeric markers (α-satellite units and HERV-K copies) were observed in neoplastic samples as compared to healthy counterparts. Subsequent phylogenetic analysis of a pericentromeric endogenous retrovirus amplified by PCR revealed possible gene conversion events occurring at numerous pericentromeric loci in the setting of malignancy. Our findings collectively represent a more comprehensive evaluation of centromere genetics in the setting of malignancy, providing valuable insight into the evolution and reshuffling of centromeric sequences in cancer development and progression.

DNA copy number gains at loci of growth factors and their receptors in salivary gland adenoid cystic carcinoma

PURPOSE

Adenoid cystic carcinoma (ACC) is a malignant salivary gland tumor with a high mortality rate due to late, distant metastases. This study aimed at unraveling common genetic abnormalities associated with ACC. Additionally, chromosomal changes were correlated with patient characteristics and survival.

EXPERIMENTAL DESIGN

Microarray-based comparative genomic hybridization was done to a series of 18 paraffin-embedded primary ACCs using a genome-wide scanning BAC array.

RESULTS

A total of 238 aberrations were detected, representing more gains than losses (205 versus 33, respectively). Most frequent gains (>60%) were observed at 9q33.3-q34.3, 11q13.3, 11q23.3, 19p13.3-p13.11, 19q12-q13.43, 21q22.3, and 22q13.33. These loci harbor numerous growth factor [fibroblast growth factor (FGF) and platelet-derived growth factor (PDGF)] and growth factors receptor (FGFR3 and PDGFRbeta) genes. Gains at the FGF(R) regions occurred significantly more frequently in the recurred/metastasized ACCs compared with indolent ACCs. Furthermore, patients with 17 or more chromosomal aberrations had a significantly less favorable outcome than patients with fewer chromosomal aberrations (log-rank = 5.2; P = 0.02).

CONCLUSIONS

Frequent DNA copy number gains at loci of growth factors and their receptors suggest their involvement in ACC initiation and progression. Additionally, the presence of FGFR3 and PDGFRbeta in increased chromosomal regions suggests a possible role for autocrine stimulation in ACC tumorigenesis.

Genetic analysis of DNA microsatellite loci in salivary gland tumours: comparison with immunohistochemical detection of hMSH2 and p53 proteins

To investigate genetic alterations in salivary gland tumours, microsatellite instability at eight representative loci and loss of heterozygosity (LOH) on chromosome 17 were analysed by polymerase chain reaction amplification. The results were compared with immunohistochemical expression of the hMSH2 and p53 proteins. Microsatellite instability and expression loss of hMSH2 protein were not recognized in the salivary gland tumours, suggesting a low frequency of abnormalities of the mismatch repair system. LOH associated with the p53 gene was detected in approximately one-half of pleomorphic adenomas and salivary carcinomas, which often showed strong p53 immunoreactivity. These features suggest that the p53 gene plays an important role in malignant transformation of salivary gland tumours. The genetic characteristics of pleomorphic adenomas might reflect a low-grade potential for malignant progression.

Detection of numeric abnormalities of chromosome 17 and p53 deletions by fluorescence in situ hybridization in pleomorphic adenomas and carcinomas in pleomorphic adenoma. Correlation with p53 expression

BACKGROUND

A fluorescence in situ hybridization (FISH) technique using specific DNA probes allows for the detection of chromosomal aberrations and gene deletions and gains, even in interphase nuclei in human solid tumors. A high frequency of aberrations of chromosome 17 and mutation of the p53 gene have been reported in some human tumors. The correlation of p53 expression with abnormalities of chromosome 17 and p53 gene deletion in salivary gland tumors has not yet been investigated.

METHODS

The authors analyzed the numeric aberrations of chromosome 17 and p53 gene deletions in 11 paraffin embedded pleomorphic adenomas (PA) and 9 carcinomas in pleomorphic adenoma (CIPA), using FISH techniques. The centromere specific DNA probe for chromosome 17 and p53 cosmid DNA probe was used. The aberrations of chromosome 17 and p53 deletion were correlated with immunohistochemical detection of p53 protein.

RESULTS

Monosomy 17 was detected in 30.8% of CIPA cells and 29.6% of PA cells, and polysomy 17 was detected in 19.6% of CIPA cells and 9.6% of PA cells. p53 protein expression was observed in 6 of 9 CIPA specimens (66.7%) and 2 of 75 PA specimens (2.7%). Deletion of the p53 gene was frequent in p53 protein positive specimens. A statistically significant correlation existed between p53 protein expression and polysomy 17 (P = 0.0417).

CONCLUSIONS

It was observed that loss of chromosome 17 may occur in PA before its transformation to carcinoma. p53 expression was frequently associated with deletion of the p53 gene as detected by FISH. Polysomy 17 was more frequent in CIPA than PA and was associated with mutation of p53.