Gene expression analysis of uveal melanoma tumor tissue
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE39717 | GEO | 2012/07/31
SECONDARY ACCESSION(S): PRJNA171547
REPOSITORIES: GEO
Similar Datasets
Project description:Previous studies have demonstrated two distinct classes of primary uveal melanoma tumors based on gene expression profiling. This study compares the gene expression profiles of primary uveal melanomas collected from fresh frozen samples to those collected by fine needle aspiration biopsy. Two matched metastatic samples were included to identify changes in gene expression profile with metastatic progression. Total RNA was obtained from tumor samples that were collected at the time of treatment.
2012-07-30 | E-GEOD-39717 | biostudies-arrayexpress
Project description:Uveal melanoma is the most common cancer of the eye arising from melanocytes within the choroid, ciliary bodies and iris. Almost half of uveal melanomas metastasize hematogenously to distant organs, most often the liver, where the disease becomes fatal. One of the first genetic alterations to be identified in primary uveal melanomas was monosomy 3, which was found to be strongly associated with metastasis. We used gene expression profiling to identify two phenotypically distinct classes of uveal melanomas: class 1 tumors with low-grade morphology and low metastatic risk; and class 2 tumors with aggressive morphology and high metastatic risk. Our initial studies suggested that gene expression profiling was a better predictor of metastasis than monosomy 3. For this study, BAC-array comparative genomic hybridization was used to assay genomic DNA isolated from fresh frozen primary uveal melanoma samples of known molecular class based on gene expression profiling. Independent samples were sent to the aCGH cores at the University of California, San Francisco and the Roswell Park Cancer Institute for hybridization, and log2 ratios were reported. Total genomic DNA was obtained from tumor samples that were collected at the time of treatment. Samples were analyzed by the Microarray Shared Resource at the Comprehensive Cancer Center, University of California, San Francisco or by the Microarray and Genomics Facility of the Roswell Park Cancer Institute.
2012-12-06 | E-GEOD-42739 | biostudies-arrayexpress
Project description:Uveal melanoma is the most common cancer of the eye arising from melanocytes within the choroid, ciliary bodies and iris. Almost half of uveal melanomas metastasize hematogenously to distant organs, most often the liver, where the disease becomes fatal. One of the first genetic alterations to be identified in primary uveal melanomas was monosomy 3, which was found to be strongly associated with metastasis. We used gene expression profiling to identify two phenotypically distinct classes of uveal melanomas: class 1 tumors with low-grade morphology and low metastatic risk; and class 2 tumors with aggressive morphology and high metastatic risk. Our initial studies suggested that gene expression profiling was a better predictor of metastasis than monosomy 3. For this study, BAC-array comparative genomic hybridization was used to assay genomic DNA isolated from fresh frozen primary uveal melanoma samples of known molecular class based on gene expression profiling. Independent samples were sent to the aCGH cores at the University of California, San Francisco and the Roswell Park Cancer Institute for hybridization, and log2 ratios were reported. Total genomic DNA was obtained from tumor samples that were collected at the time of treatment. Samples were analyzed by the Microarray Shared Resource at the Comprehensive Cancer Center, University of California, San Francisco or by the Microarray and Genomics Facility of the Roswell Park Cancer Institute.
2012-12-06 | E-GEOD-42738 | biostudies-arrayexpress
Project description:Primary uveal melanomas show multiple chromosomal aberrations. To identify genome variation in six human primary uveal melanomas, genome wide copy number variation (CNV) analyses were carried out in human primary uveal melanoma samples using array comparative genome hybridization.
2021-01-25 | GSE138404 | GEO
Project description:Uveal melanoma is the most common cancer of the eye arising from melanocytes within the choroid, ciliary bodies and iris. Almost half of uveal melanomas metastasize hematogenously to distant organs, most often the liver, where the disease becomes fatal. One of the first genetic alterations to be identified in primary uveal melanomas was monosomy 3, which was found to be strongly associated with metastasis. We used gene expression profiling to identify two phenotypically distinct classes of uveal melanomas: class 1 tumors with low-grade morphology and low metastatic risk; and class 2 tumors with aggressive morphology and high metastatic risk. Our initial studies suggested that gene expression profiling was a better predictor of metastasis than monosomy 3. For this study, BAC-array comparative genomic hybridization was used to assay genomic DNA isolated from fresh frozen primary uveal melanoma samples of known molecular class based on gene expression profiling. Independent samples were sent to the aCGH cores at the University of California, San Francisco and the Roswell Park Cancer Institute for hybridization, and log2 ratios were reported.
2012-12-06 | GSE42739 | GEO
Project description:Uveal melanoma is the most common cancer of the eye arising from melanocytes within the choroid, ciliary bodies and iris. Almost half of uveal melanomas metastasize hematogenously to distant organs, most often the liver, where the disease becomes fatal. One of the first genetic alterations to be identified in primary uveal melanomas was monosomy 3, which was found to be strongly associated with metastasis. We used gene expression profiling to identify two phenotypically distinct classes of uveal melanomas: class 1 tumors with low-grade morphology and low metastatic risk; and class 2 tumors with aggressive morphology and high metastatic risk. Our initial studies suggested that gene expression profiling was a better predictor of metastasis than monosomy 3. For this study, BAC-array comparative genomic hybridization was used to assay genomic DNA isolated from fresh frozen primary uveal melanoma samples of known molecular class based on gene expression profiling. Independent samples were sent to the aCGH cores at the University of California, San Francisco and the Roswell Park Cancer Institute for hybridization, and log2 ratios were reported.
2012-12-06 | GSE42738 | GEO
Project description:Primary uveal melanomas show multiple genetic alterations. To determine mutational status of six human primary uveal melanomas, we performed whole exome sequencing (WES) and called Single Nucleotide Polimorphism (SNPs) to identify somatic mutations in these human primary uveal melanomas.
2021-01-25 | GSE138664 | GEO
Project description:Lack of specific markers for invasive uveal melanoma cells prevents early diagnosis of metastasis, while no systemic treatment options are available for patients with disseminated uveal melanomas. Intra-tumor heterogeneity has been recognized in numerous cancers as the main cause of metastasis development and therapy resistance. However, in uveal melanomas the specific subpopulations and their biological function which influence tumor behavior remained unknown. Here, using scRNA-seq analysis of six different primary uveal melanomas, we uncovered previously unrecognized intratumor heterogeneity. We localized diverse tumor-associated populations and transcriptional states in primary uveal melanomas. We also unraveled a gene regulatory network underlying a poor prognosis melanoma state. Heterogeneity was demonstrated in uveal melanoma tissue using the RNAscope assay. Thus, single-cell analysis offers an unprecedented view of intratumor heterogeneity in primary uveal melanoma, identified bona fide biomarkers for metastatic cells in the primary tumor, and unravel targetable modules driving metastase formation and growth, with critical implications for prognosis and therapeutic opportunity.
2021-01-25 | GSE138433 | GEO
Project description:Uveal melanoma is an aggressive cancer that metastasizes to the liver in about half of patients, being at that time almost always fatal. Identification of patients at high risk of metastases may provide indication for a frequent follow-up for early detection of metastases and treatment. The analysis of the gene expression profiling of primary human uveal melanomas showed high expression of SDCBP (encoding for syndecan-binding protein-1 or syntenin-1), which appeared higher in patients with recurrence, whereas expression of syndecans was lower and unrelated to progression. Moreover, we found that high expression of SDCBP gene was related to metastatic progression in two additional independent dataset of uveal melanoma patients. More importantly, immunohistochemistry showed that high expression of syntenin-1 protein in primary tumours was significantly related to metastatic recurrence in our cohort of patients. Syntenin-1 expression was confirmed by RT-PCR, immunofluorescence and immunohistochemistry in cultured uveal melanoma cells or primary tumours. A pseudo-metastatic model of uveal melanoma to the liver was developed in NOD/SCID/IL2R null mice and the study of syntenin-1 expression in primary and metastatic lesions revealed higher syntenin-1 expression in metastases. The inhibition of SDCBP expression by siRNA impaired the ability of uveal melanoma cells to migrate in a woundâhealing assay. These results suggest that SDCBP is involved in uveal melanoma progression and that it represents a candidate molecular marker of metastases and a potential therapeutic target. Gene expression profiles of 29 unique samples from uveal melanoma patients were measured.
2012-04-17 | E-GEOD-27831 | biostudies-arrayexpress
Project description:Analysis of DNA from fixed tissues specimens of 58 primary uveal melanomas, with known clinical outcome, to determine gene copy number variations that were associated with survival. Abstract: Uveal melanomas can be stratified into subgroups with high or low risk of metastatic death, according to the presence of gross chromosomal abnormalities. Where a monosomy 3 uveal melanoma is detected, patient survival at three years is reduced to 50%. However, approximately 5% of patients with a disomy 3 tumour ultimately develop metastasis, and a further 5% of monosomy 3 uveal melanoma patients’ exhibit disease-free survival for more than five years. Despite extensive knowledge of the chromosomal abnormalities occurring in uveal melanoma, the genes driving metastasis are not well defined. Gene copy number variations occurring in a well-characterised cohort of 58 formalin-fixed, paraffin-embedded uveal melanoma samples were identified using the Affymetrix SNP 6.0 whole genome microarray. Four genetic sub-groups of primary uveal melanoma were represented in the patient cohort: 1) disomy 3 with long-term survival; 2) metastasizing disomy 3; 3) metastasizing monosomy 3; and 4) monosomy 3 with long-term survival. Cox regression and Kaplan-Meier survival analysis identified three genes that were associated with differences in patient survival. Patients with an amplification of CNKSR3 (6q) or RIPK1 (6p) demonstrated longer survival than those with gene deletions or no copy number change (log rank, p=0.022 and p<0.001, respectively). Conversely, those patients with an amplification of PENK (8q) showed reduced survival (log rank p<0.001). CNKSR3, RIPK1 and PENK are novel candidate metastasis regulatory genes in uveal melanoma. This is the first report of amplification of a specific gene on 6p that is associated with improved uveal melanoma patient survival and suggests that the development of uveal melanomas with a propensity to metastasise may be limited by genes on 6p. 58 samples in total. Ten disomy 3 with long-term survival. Fifteen disomy 3 with metastasising. Seventeen monosomy 3 with long-term survival. Sixteen monosomy 3 metastasising.
2013-02-01 | E-GEOD-37259 | biostudies-arrayexpress