Expression Data from Uveal Melanoma patient-derived xenograft and tumor of origin
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ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE78033 | GEO | 2016/02/18
SECONDARY ACCESSION(S): PRJNA312390
REPOSITORIES: GEO
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Project description:A high percentage of uveal melanoma patients develop metastatic tumors that predominately occur in the liver. To identify genes associated with metastasis in this pathology, we studied 63 molecular profiles derived from gene expression microarrays performed from enuceated primary tumors. Metastasis free survival analysis was performed to obtain clinical and genomic variables associated to metastasis occurrence. We also compared within the 57 tumors with at least 36 months follow-up, 28 uveal melanoma from patients who developed liver metastases (meta1 group) with 29 tumors arising from patients without metastases (or later metastases, i.e. after 36 months) (meta0 group). The transcriptome of 63 uveal melanoma from enucleation of untreated patients were analyzed using Affymetrix U133plus2 Arrays.
2010-12-14 | E-GEOD-22138 | biostudies-arrayexpress
Project description:Development of liver metastasis remains the most common cause of mortality in uveal melanoma (UM). Although advances in genomics allowed the direct evaluation of clinical samples of this eye cancer, there is still a need for reliable preclinical models to progress from correlative studies to mechanistic investigations. A few UM cell lines have been characterized, but so far the translation of basic knowledge to the clinic for the treatment of metastatic disease has been incremental at best. The aim of this study was to determine whether the properties of UM cell lines at various passages were similar to their corresponding primary tumors. Two primary uveal melanoma tumors and their derivative cell lines at three different passages are analyzed by gene profiling
2014-09-09 | E-GEOD-61228 | biostudies-arrayexpress
Project description:Despite advances in surgery and radiotherapy of uveal melanoma (UM), many patients develop distant metastases that poorly respond to therapy. Improved therapies for the metastatic disease are therefore urgently needed. Expression of the epidermal growth factor receptor (EGFR), a target of kinase inhibitors and humanized antibodies in use for several cancers, had been reported. 48 human UMs were analyzed by expression profiling. Evidence for signaling in tumors was obtained through the application of a UM-specific EGF signature. The EGFR specific kinase inhibitor, Gefitinib, and the humanized monoclonal antibody, Cetuximab, were tested for their effect on EGFR signaling. Natural killer cell mediated antibody-dependent cellular cytotoxicity (ADCC) and TNF-alpha release was analyzed for Cetuximab. EGFR appears suited as a novel molecular drug target for therapy of uveal melanoma. Gene expression profiles of 19 unique samples from uveal melanoma patients were measured.
2013-11-18 | E-GEOD-51880 | 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: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:A high percentage of uveal melanoma patients develop metastatic tumors that predominately occur in the liver. To identify genes associated with metastasis in this pathology, we studied 63 molecular profiles derived from gene expression microarrays performed from enuceated primary tumors. Metastasis free survival analysis was performed to obtain clinical and genomic variables associated to metastasis occurrence. We also compared within the 57 tumors with at least 36 months follow-up, 28 uveal melanoma from patients who developed liver metastases (meta1 group) with 29 tumors arising from patients without metastases (or later metastases, i.e. after 36 months) (meta0 group).
2010-12-14 | GSE22138 | 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: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.
2012-07-31 | GSE39717 | GEO