Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1068520 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27709900_1.fastq.gz | Fastqsanger.gz | |||
| SRR27709900_2.fastq.gz | Fastqsanger.gz | |||
| SRR27709901_1.fastq.gz | Fastqsanger.gz | |||
| SRR27709901_2.fastq.gz | Fastqsanger.gz | |||
| SRR27709902_1.fastq.gz | Fastqsanger.gz |
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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
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.
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Project description:Karyotyping by SNP array of primary uveal melanoma samples, uveal melanoma cell lines and normal controls
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Project description:G protein alpha q and 11 are mutated in 80% of uveal melanoma. We observed that treatment with the BRD4 inhibitor JQ1 resulted in different phenotypic responses in G-protein mutant uveal melanoma cell lines and wild type uveal melanoma cell lines. We used microarrarys to profile the gene expression changes occuring in wild type and mutant cell lines in response to treament with JQ1 Uveal melanoma cells were profiled in triplicate on Affymetrix Human Genome U133A 2.0 Array arrays per manufacturer's instructions
2015-02-19 | E-GEOD-66048 | biostudies-arrayexpress
Project description:Expression Data from Uveal Melanoma patient-derived xenograft and tumor of origin
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Project description:Uveal melanoma is a highly aggressive cancer with a strong propensity for metastasis, yet little is known about the biological mechanisms underlying this metastatic potential. We recently showed that most metastasizing uveal melanomas, which exhibit a class 2 gene expression profile, contain inactivating mutations in the tumor suppressor BAP1. The aim of this study was to investigate the role of BAP1 in uveal melanoma progression. To that end, uveal melanoma cells were studied following stable shRNA-mediated depletion of BAP1. RNA was isolated from three independent uveal melanoma cell lines each stably depleted using shRNA for either BAP1 or the control gene GFP. Two biological replicates were performed for each cell line.
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Project description:Uveal melanoma is the most common primary intraocular neoplasm, arising from melanocytes of the choroid plexus, ciliary body, and iris of the eye. The mechanism of tumorigenesis in uveal melanoma still remains unclear, resulting in poor outcomes of systemic therapies available for the treatment of uveal melanoma. Currently, ADP-ribosylation factor-like 4C (ARL4C), an ARF-Like small GTP-binding protein, has been confirmed to be closely involved in the occurrence of various tumors, including colorectal, lung, liver, gastric and ovarian cancers as well as glioblastoma. Here, we found that ARL4C was strongly expressed in uveal melanoma cells and widely distributed in the cytosol and nucleus. The proliferation and metastasis capabilities of OCM-1 and 92-1 uveal melanoma cells were significantly decreased after ARL4C knockdown both in vitro and in vivo. Furthermore, over-expression of ARL4C in ARL4C-depleted cells can significantly rescue the abilities of proliferation and metastasis in above both cells. In addition, direct injection of ARL4C small interfering RNA (siRNA) into OCM-1 cell-derived tumors inhibited tumor growth in immunodeficient mice. Therefore, ARL4C tightly participates in tumorigenesis and might represent a novel therapeutic target to uveal melanoma. We believe that small molecule drugs targeting ARL4C could be explored and further applied to clinical therapy of uveal melanoma in years or decades to come.
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