Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Immune profile and mitotic index of metastatic melanoma lesions enhance clinical staging in predicting patient survival.

ABSTRACT: Although remission rates for metastatic melanoma are generally very poor, some patients can survive for prolonged periods following metastasis. We used gene expression profiling, mitotic index (MI), and quantification of tumor infiltrating leukocytes (TILs) and CD3+ cells in metastatic lesions to search for a molecular basis for this observation and to develop improved methods for predicting patient survival. We identified a group of 266 genes associated with postrecurrence survival. Genes positively associated with survival were predominantly immune response related (e.g., ICOS, CD3d, ZAP70, TRAT1, TARP, GZMK, LCK, CD2, CXCL13, CCL19, CCR7, VCAM1) while genes negatively associated with survival were cell proliferation related (e.g., PDE4D, CDK2, GREF1, NUSAP1, SPC24). Identification of genes associated with survival of metastatic melanoma Survival Analysis was performed using Statistical Analysis of Microarrays B D denotes same patient with multiple reccurences

ORGANISM(S): Homo sapiens

SUBMITTER: Dusan Bogunovic

PROVIDER: E-GEOD-19234 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Immune profile and mitotic index of metastatic melanoma lesions enhance clinical staging in predicting patient survival.

Bogunovic Dusan D O'Neill David W DW Belitskaya-Levy Ilana I Vacic Vladimir V Yu Yi-Lo YL Adams Sylvia S Darvishian Farbod F Berman Russell R Shapiro Richard R Pavlick Anna C AC Lonardi Stefano S Zavadil Jiri J Osman Iman I Bhardwaj Nina N

Proceedings of the National Academy of Sciences of the United States of America 20091113 48

Although remission rates for metastatic melanoma are generally very poor, some patients can survive for prolonged periods following metastasis. We used gene expression profiling, mitotic index (MI), and quantification of tumor infiltrating leukocytes (TILs) and CD3+ cells in metastatic lesions to search for a molecular basis for this observation and to develop improved methods for predicting patient survival. We identified a group of 266 genes associated with postrecurrence survival. Genes posit ...[more]

PMID: 19915147

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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.

Dataset Information

Immune profile and mitotic index of metastatic melanoma lesions enhance clinical staging in predicting patient survival.

Publications

Immune profile and mitotic index of metastatic melanoma lesions enhance clinical staging in predicting patient survival.

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