DNA Methylation Profiling in Rare Sellar Esthesioneuroblastoma
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE211634 | GEO | 2022/10/04
REPOSITORIES: GEO
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Project description:We profiled DNA methylation in fresh-frozen oncocytoma and chRCC tumors and tumor-adjacent adjacent normal tissue to identify a signature of differentially methylated CpG sites that robustly distinguish oncocytoma from chRCC. DNA methylation profiles were generated for renal oncocytomas (n=12), primary kidney chromophobes (chRCC) (n=8) and primary kidney clear cell carcinomas (ccRCC) (n=2). Also profiled were three oncocytic neoplasms of unclear pathological diagnosis, including two masses described as hybrid oncocytic/chromophobe type (n=2), and one mass described as hybrid oncocytic renal neoplasm. Also profiled were histologically normal adjacent kidney parenchyma tissue (NKP) from a subset of these patients, including NKP from oncocytoma (n=7), chRCC (n=5), ccRCC (n=1), hybrid oncocytic/chromophobe type (n=1), and hybrid oncocytic renal neoplasm (n=1) bearing kidneys (combined n=15 NKP).
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Project description:DNA Methylation Profiling in Rare Sellar Esthesioneuroblastoma
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Project description:Myoepithelioma, mixed tumor and parachordoma are rare soft tissue tumors thought to represent different morphologic variants of the same family of tumors, hereafter referred to as MMP tumors. The genetic basis of these neoplasms is poorly investigated. However, they morphologically resemble mixed tumor of the salivary glands (a.k.a. pleomorphic adenoma). This is the first study characterizing whole genome DNA copy number changes in MMP tumors and the genomic imbalances detected in four MMP tumors and one pleomorphic adenoma were diverse. The only recurrent aberration of known importance for tumor development was homo- and heterozygous deletions of the region in 9p21-22 which harbors the CDKN2A and CDKN2B genes. Defined by the deletion in case 3, the region 1.27-4.82 Mb on chromosome 19 was heterozygously lost in all cases, including the pleomorphic adenoma. A complex pattern of aberrations was seen in the primary tumor of case 2 with amplifications, interrupted by normal copy numbers and losses, of regions on chromosomes 6, 9, and 13. Keywords: comparative genomic hybridization, soft tissue myoepithelioma, mixed tumor, parachordoma, pleomorphic adenoma Cases 1-3 and 5-6 were analyzed using 32k array CGH and male genomic DNA (Promega) was used as reference.
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Project description:Colorectal laterally spreading tumors (LSTs) are rare comparing to adenomas but are becoming more prevalent. Unlike many neoplasms in colons, LST grows to extremely large size, usually greater than 10mm in diameter while rarely invades deeply. Also, there is a low tendency for LSTs to become cancerous. The epigenetic landscape of LST has not been defined. In this study, we used a genome-wide methylation profiling technology, i.e. the Illumina Human Methylation 450K array, to query the main epigenetic difference between LST and para-cancerous samples. Our results suggest that LST displays significant decrease in DNA methylation, especially in some intergenic regions (IGR). By integration of public data for adenomas and colorectal cancers, we defined the commonality and specific epigenetic signatures for these three types of neoplasms in colon, in particular LST and adenomas which represent precancerous conditions. These three diseases shared little specific DNA methylation abnormalities. However, our pathway-level analysis revealed that certain pathways were common targets of epimutation. More interestingly, different diseases seem to employ distinct epigenetic insult to disturb these pathways. Between LST and adenoma, we found eight pathways were commonly targeted but the epi-mutation patterns were opposite between the two diseases. Comparison between precancerous conditions and invasive states revealed the key pathways governing the progression to malignancy, including CAMs and PI3K-Akt pathways.
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Project description:Myoepithelioma, mixed tumor and parachordoma are rare soft tissue tumors thought to represent different morphologic variants of the same family of tumors, hereafter referred to as MMP tumors. The genetic basis of these neoplasms is poorly investigated. However, they morphologically resemble mixed tumor of the salivary glands (a.k.a. pleomorphic adenoma). This is the first study characterizing whole genome DNA copy number changes in MMP tumors and the genomic imbalances detected in four MMP tumors and one pleomorphic adenoma were diverse. The only recurrent aberration of known importance for tumor development was homo- and heterozygous deletions of the region in 9p21-22 which harbors the CDKN2A and CDKN2B genes. Defined by the deletion in case 3, the region 1.27-4.82 Mb on chromosome 19 was heterozygously lost in all cases, including the pleomorphic adenoma. A complex pattern of aberrations was seen in the primary tumor of case 2 with amplifications, interrupted by normal copy numbers and losses, of regions on chromosomes 6, 9, and 13. Keywords: comparative genomic hybridization, soft tissue myoepithelioma, mixed tumor, parachordoma, pleomorphic adenoma
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