Homo sapiens
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ABSTRACT:
PROVIDER: PRJNA396898 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We analyzed the value of microRNAs (miRNAs) in plasma-derived extracellular microvesicles (EV) as biomarkers for treatment outcome in Stage IV CMM patients receiving MAPK inhibitors (MAPKis).
2017-08-03 | GSE102166 | GEO
Project description:Background: Timely diagnosis is important for successful treatment of cutaneous melanoma. Currently, Breslow tumor thickness and mitotic rate are used for malignant melanoma classification and prognosis, but these parameters can assess disease progression risk only to a certain degree. Therefore, there is a need for new melanoma protein biomarkers that would aid early and accurate diagnosis and prediction of their metastatic potential. Methodology and Findings: This retrospective case control study is based on proteomic profiling of formalin-fixed archival tissues of 31 early-stage head and neck cutaneous malignant melanoma samples using liquid chromatography / mass spectrometry. A melanoma proteomic profile was identified and protein expression levels were compared to the proteome profile of melanocytic naevi and correlated to established prognostic factors and disease-specific survival. In accordance with the American Joint Committee on Cancer guidelines, recursive partitioning multivariate analysis was used to identify potential biomarkers associated with metastatic potential of early-melanoma. Heterogeneous nuclear ribonucleoprotein M and heat shock protein 90 alpha were profiled as independent prognostic factors. Their elevated expression was clinically relevant for predicting an exceedingly high metastatic hazard ratio. These proteins were superior in estimating disease progression risk when compared to Breslow thickness and mitotic rate. Conclusions and Significance: Identification of biomarkers in early stage cutaneous head and neck melanoma is an important step towards predicting metastatic potential and prognosis of the disease. Clinical confirmation and further validation of the proteins identified in this study would provide a novel tool for identifying patients at risk for developing metastatic disease.
2019-11-27 | PXD015137 | Pride
Project description:We investigated a cohort of 34 archival cutaneous melanoma samples by Agilent 40 kb-resolution CGH array. We found a non-random distribution of precise CNAs predictive for clinical outcome. Although most of the alterations defined in this study have been already reported, we mapped novel melanoma-specific CNAs at highest accuracy. Moreover, our data revealed distinct amplifications hotspots, some of which were validated by quantitative real-time PCR, enabling the identification of novel melanoma oncogenic candidates. Keywords: Cutaneous melanoma, Copy number alterations, Biomarkers, FFPE
2013-07-01 | GSE45354 | GEO
Project description:Purpose: Utility of immunological treatment in cancer has increased; however, many patients do not respond to treatment. Identification of robust predictive biomarkers is required to correctly stratify patients. Although clinical trials based on adoptive T cell therapy (ACT) have yielded high response rates and many durable responses in melanoma, 50-60% of the patients have no clinical benefit. Herein, we searched for predictive biomarkers to ACT in melanoma. Methods: Whole exome- and transcriptome sequencing, neoantigen prediction and immune cell signature analysis were applied to pre-treatment melanoma samples from 27 patients recruited to a clinical phase I/II trial of ACT in stage IV melanoma. All patients had previously been treated with other immunotherapies. Results: We found that clinical benefit was associated with significantly higher neoantigen load (P=0.025). High mutation and neoantigen load were significantly associated with improved progression-free and overall survival (P=8x10^-4 and P=0.001, respectively). Further, gene-expression analysis of pre-treatment biopsies showed that clinical benefit was associated with strong immune activation signatures including a high MHC-I antigen processing and presentation score. Conclusions: These results improve our understanding of clinical benefit of ACT in melanoma, which can lead to clinically useful predictive biomarkers to be used for selecting patients that benefit from these highly intensive treatment regimens.
2017-12-04 | GSE100797 | GEO
Project description:Exosomes, extracellular vesicles of 30-150 nm, are released by normal and tumor cells. These nanovesicles play a major role in cell communication and can be found in biological fluids as carriers of biomarkers. Tumor exosomes can inhibit immune responses, mediate drug resistance and transform mesenchymal stem cells. In contrast to healthy donors, cancer patients’ plasma contain higher levels of exosomes. Cutaneous melanoma is a very aggressive cancer whose incidence has rapidly increased worldwide and the prognosis is generally poor, given the propensity of melanoma cells to spread to distant sites while evading immune system control.We investigated potential differences between plasma exosomes derived from healthy donors (HD) and melanoma patients at 0-I, II, and III-IV stages of disease.
2023-05-09 | PXD024434 | Pride
Project description:Recent development of new therapies with immune checkpoint inhibitors (ICIs) and MAPK-inhibitors (MAPKis) have significantly improved the outcome in metastatic cutaneous melanoma (CM). However, therapy response is limited to subgroups of patients and clinically useful predictive biomarkers for treatment outcome are lacking. To discover treatment-related systemic changes in plasma and potential biomarkers associated with treatment outcomes, we analysed 45 plasma samples from 24 patients with metastatic (stage IV) CM, using HiRIEF LC-MS/MS, collected before (pre-trm) and during treatment (trm). Of these, 27 samples were taken from 15 metastatic CM patients treated with ICIs (13 pre-trm and 14 trm samples; 12 matched) and 9 patients treated with MAPKis (9 matched). Matched samples were trm and pre-trm samples taken from the same individual before treatment and after the first cycle of treatment (before the second cycle). We have analysed the change in the plasma protein levels during treatment by comparing the plasma levels in the trm samples to the pre-trm samples, to detect treatment-induced alterations in the plasma proteome. We have analysed the patients treated with ICIs separately from the patients treated with MAPKis, to detect treatment-specific changes for both.
2020-07-13 | PXD017201 | Pride
Project description:We investigated a cohort of 34 archival cutaneous melanoma samples by Agilent 40 kb-resolution CGH array. We found a non-random distribution of precise CNAs predictive for clinical outcome. Although most of the alterations defined in this study have been already reported, we mapped novel melanoma-specific CNAs at highest accuracy. Moreover, our data revealed distinct amplifications hotspots, some of which were validated by quantitative real-time PCR, enabling the identification of novel melanoma oncogenic candidates. Keywords: Cutaneous melanoma, Copy number alterations, Biomarkers, FFPE We examined 34 primary melanoma formalin-fixed and paraffin-embedded (FFPE) samples by using array comparative genomic hybridization (aCGH) for DNA copy number alterations (CNAs). Genomic DNA was extracted, referred to a sex-matched diploid commercial control DNA (Promega Corporation, Madison, WI, cat. G1417 and G1521), and hybridized on the Agilent SurePrint G3 Human CGH Microarray 8x60k, cat. G4827A.
2013-07-01 | E-GEOD-45354 | biostudies-arrayexpress
Project description:We performed microRNA sequencing of primary human FFPE Acral Melanoma (AM), Cutaneous Melanoma (CM), Acral Nevi (AN), and Cutaneous Nevi (CN). We found that previously identified ratios of microRNAs, particularly miR-21-5p and miR-211-5p, were able to accurately classify benign and malignant melanocytic neoplasia, both in non-acral cutaneous melanomas and nevi (CM vs CN), as well as matched acral melanoma and nevi (AM vs AN). Receiver operating characteristic area under the curve (AUC) of Ensemble models trained using these microRNA ratios demonstrated AUCs of 0.88-0.90 across these melanoma subtypes, suggesting the potential utility of these ratios as a biomarker of malignancy in melanocytic neoplasia.
2024-08-14 | GSE266413 | GEO
Project description:Purpose: The incidence of malignant melanoma is increasing worldwide in fair-skinned populations. Melanomas respond poorly to systemic therapy, and metastatic melanomas inevitably become fatal. Although spontaneous regression, likely due to immune defense activation, rarely occurs, we lack a biological rationale and predictive markers in selecting patients for immune therapy. Experimental Design: We performed unsupervised hierarchical clustering of global gene expression data from stage IV melanomas in 57 patients. For further characterization, we used immunohistochemistry of selected markers, genome-wide DNA copy number analysis, genetic and epigenetic analysis of the Q3 CDKN2A locus, and NRAS/BRAF mutation screening. Results: The analysis revealed four distinct subtypes with gene signatures characterized by expression of immune response, pigmentation differentiation, proliferation, or stromal composition genes. Although all subtypes harbored NRAS and BRAF mutations, there was a significant difference between subtypes (P < 0.01), with no BRAF/NRAS wild-type samples in the proliferative subtype. Additionally, the proliferative subtype was characterized by a high frequency of CDKN2A homozygous deletions (P < 0.01). We observed a different prognosis between the subtypes (P = 0.01), with a particularly poor survival for patients harboring tumors of the proliferative subtype compared with the others (P = 0.003). Importantly, the clinical relevance of the subtypes was validated in an independent cohort of 44 stage III and IV melanomas. Moreover, low expression of an a priori defined gene set associated with immune response signaling was significantly associated with poor outcome (P = 0.001). Conclusions: Our data reveal a biologically based taxonomy of malignant melanomas with prognostic effect and support an influence of the antitumoral immune response on outcome. Expression profiles of 57 lymphnode and subcutaneous melanoma metastases
2010-06-16 | E-GEOD-22153 | biostudies-arrayexpress
Project description:Transcriptomic identification of miR-205 target genes potentially involved in metastasis and survival of cutaneous malignant melanoma. We evaluated whole-genome mRNA expression profiling associated with different miR-205 expression levels in melanoma cells. Differential expression analysis, target prediction using TargetScan algorithm and functional analysis were performed to find those miR-205 associated genes involved in progression of melanoma.
2020-03-19 | E-MTAB-8202 | biostudies-arrayexpress