INTEGRATIVE PREDICTIVE MODELING OF METASTASIS IN MELANOMA CANCER

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2022-2-08

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KUTLAY, AYŞEGÜL

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This study focused on identifying the regulatory impact of genetic biomarkers for monitoring metastatic molecular signatures of melanoma by investigating the consolidated effect of miRNA, mRNA, and DNA methylation. We developed multiple machine learning models to distinguish the metastasis by integrating miRNA, mRNA, and DNA methylation markers. We used the TCGA melanoma dataset to differentiate metastatic melanoma samples by assessing a set of predictive models. An iterative combination of differentially expressed miRNA, mRNA, and methylation signatures is used as candidate markers to reveal each new biomarker category's impact. In each iteration, the performances of the combined models are calculated. The choice of feature selection method and under and oversampling approaches are analyzed during all comparisons. Selected biomarkers of the highest performing models are further analyzed for the biological interpretation of functional enrichment. MiRNA biomarkers can identify metastatic melanoma with an 81% F-score in the initial model. The addition of mRNA markers upon miRNA increased F-score to 92 %. In the final integrated model, the inclusion of the methylation data resulted in a similar F-score of 92% but produced a stable model with low variance across multiple trials. Our results support the role of miRNA regulation in metastatic melanoma as miRNA markers models metastasis outcomes with high accuracy. Moreover, the integrated evaluation of miRNA with mRNA and Methylation biomarkers increases the model's accuracy. It populates selected biomarkers on the metastasis-associated pathways of melanoma, such as "Osteoclast," "Rap1 Signaling" "and "Chemokine Signaling" Pathways.

Subject Keywords

Machine Learning, Metastatic Molecular Signatures, miRNA, mRNA, DNA Methylation

URI

https://hdl.handle.net/11511/96330

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Graduate School of Informatics, Thesis

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Citation Formats

A. KUTLAY, “INTEGRATIVE PREDICTIVE MODELING OF METASTASIS IN MELANOMA CANCER,” Ph.D. - Doctoral Program, Middle East Technical University, 2022.