Identification of a robust methylation classifier for cutaneous melanoma diagnosis
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ABSTRACT:
PROVIDER: PRJNA494817 | ENA |
REPOSITORIES: ENA
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Project description:Early diagnosis improves melanoma survival, yet the histopathological diagnosis of cutaneous primary melanoma can be challenging, even for expert dermatopathologists. Analysis of epigenetic alterations, such as DNA methylation, that occur in melanoma can aid in its early diagnosis. Using a genome-wide methylation screening, we assessed CpG methylation in a diverse set of 89 primary invasive melanomas, 73 nevi, and 41 melanocytic proliferations of uncertain malignant potential, classified based on interobserver review by dermatopathologists. Melanomas and nevi were split into training and validation sets. Predictive modeling in the training set using ElasticNet identified a 40-CpG classifier distinguishing 60 melanomas from 48 nevi. High diagnostic accuracy (area under the receiver operator characteristic curve = 0.996, sensitivity = 96.6%, and specificity = 100.0%) was independently confirmed in the validation set (29 melanomas, 25 nevi) and other published sample sets. The 40-CpG melanoma classifier included homeobox transcription factors and genes with roles in stem cell pluripotency or the nervous system. Application of the 40-CpG melanoma classifier to the diagnostically uncertain samples assigned melanoma or nevus status, potentially offering a diagnostic tool to assist dermatopathologists. In summary, the robust, accurate 40-CpG melanoma classifier offers a promising assay for improving primary melanoma diagnosis.
| S-EPMC6535139 | biostudies-literature
Project description:Genome wide DNA methylation profiling of 89 primary invasive FFPE melanomas and 73 nevi were evaluated using the Illumina Infinium HumanMethylation450 BeadChip array
2019-04-08 | GSE120878 | GEO
Project description:mRNA expression in RNA isolated from formalin fixed, paraffin embedded tissue from ulcerated primary cutaneous melanoma compared to non-ulcerated primary cutaneous melanoma
2022-08-13 | GSE211091 | GEO
Project description:microRNA expression in RNA isolated from formalin fixed, paraffin embedded tissue from ulcerated primary cutaneous melanoma compared to non-ulcerated primary cutaneous melanoma
2022-08-13 | GSE211090 | 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:mRNA expression in RNA isolated from formalin fixed, paraffin embedded tissue from ulcerated primary cutaneous melanoma compared to non-ulcerated primary cutaneous melanoma
2022-08-13 | GSE211093 | GEO
Project description:microRNA expression in RNA isolated from formalin fixed, paraffin embedded tissue from ulcerated primary cutaneous melanoma (n=6) compared to non-ulcerated primary cutaneous melanoma (n=6)
2022-08-13 | GSE211092 | GEO
Project description:Objectives: Small cell lung cancer (SCLC) is characterized by poor prognosis and challenging diagnosis. Screening in high-risk smokers results in a reduction in lung cancer mortality, however, screening efforts are primarily focused on non-small cell lung cancer (NSCLC). SCLC diagnosis and surveillance remain significant challenges. The aberrant expression of circulating microRNAs (miRNAs/miRs) is reported in many tumors and can provide insights into the pathogenesis of tumor development and progression. Here, we conducted a comprehensive assessment of circulating miRNAs in SCLC with a goal of developing a miRNA-based biomarker classifier to assist in SCLC diagnoses. Materials and Methods: We profiled deregulated circulating cell-free miRNA in the plasma of SCLC patients. We tested selected miRs on a training cohort and created a classifier by integrating miRNA expression and patient clinical data. Finally, we applied the classifier on a validation dataset. Results: We determined that miR-375-3p can discriminate between SCLC and NSCLC patients, and between SCLC and Squamous Cell Carcinoma patients. Moreover, we found that a model comprising miR-375-3p, miR-320b, and miR-144-3p can be integrated with race and age to distinguish metastatic SCLC from a control group. Conclusion: This study proposes a miRNA-based biomarker classifier for SCLC that considers clinical demographics with specific cut offs to inform SCLC diagnosis.
2023-10-31 | GSE240758 | GEO
Project description:Objectives: Small cell lung cancer (SCLC) is characterized by poor prognosis and challenging diagnosis. Screening in high-risk smokers results in a reduction in lung cancer mortality, however, screening efforts are primarily focused on non-small cell lung cancer (NSCLC). SCLC diagnosis and surveillance remain significant challenges. The aberrant expression of circulating microRNAs (miRNAs/miRs) is reported in many tumors and can provide insights into the pathogenesis of tumor development and progression. Here, we conducted a comprehensive assessment of circulating miRNAs in SCLC with a goal of developing a miRNA-based biomarker classifier to assist in SCLC diagnoses. Materials and Methods: We profiled deregulated circulating cell-free miRNA in the plasma of SCLC patients. We tested selected miRs on a training cohort and created a classifier by integrating miRNA expression and patient clinical data. Finally, we applied the classifier on a validation dataset. Results: We determined that miR-375-3p can discriminate between SCLC and NSCLC patients, and between SCLC and Squamous Cell Carcinoma patients. Moreover, we found that a model comprising miR-375-3p, miR-320b, and miR-144-3p can be integrated with race and age to distinguish metastatic SCLC from a control group. Conclusion: This study proposes a miRNA-based biomarker classifier for SCLC that considers clinical demographics with specific cut offs to inform SCLC diagnosis.
2023-10-31 | GSE240757 | GEO
Project description:In this experiment, FFPE samples of 41 primary cutaneous melanoma, 2 metastatic melanoma and 6 normal skin were used for DNA extraction and genotyping by Affymetrix OncoScan FFPE Assay, in order to define chromosomal alterations in copy number and loss of heterozygosity. Genomic damage was then correlated with clinical features of melanoma.
2015-11-01 | E-MTAB-3481 | biostudies-arrayexpress