Journal Article

MetaWise: Combined Feature Selection and Weighting Method to Link the Serum Metabolome to Treatment Response and Survival in Glioblastoma

Popa, Michael, Zhang, Longze, Krauze, Andra V., Tasci, Erdal, Garrett, Timothy J., Zhuge, Ying, Chappidi, Shreya, Camphausen, Kevin, Mackey, Megan, Sproull, Mary, Cooley Zgela, Theresa, Kates, Heather R.

2024

Overview

Glioblastoma (GBM) is a highly malignant and devastating brain cancer characterized by its ability to rapidly and aggressively grow, infiltrating brain tissue, with nearly universal recurrence after the standard of care (SOC), which comprises maximal safe resection followed by chemoirradiation (CRT). The metabolic triggers leading to the reprogramming of tumor behavior and resistance are an area increasingly studied in relation to the tumor molecular features associated with outcome. There are currently no metabolomic biomarkers for GBM. Studying the metabolomic alterations in GBM patients undergoing CRT could uncover the biochemical pathways involved in tumor response and resistance, leading to the identification of novel biomarkers and the optimization of the treatment response. The feature selection process identifies key factors to improve the model’s accuracy and interpretability. This study utilizes a combined feature selection approach, incorporating both Least Absolute Shrinkage and Selection Operator (LASSO) and Minimum Redundancy–Maximum Relevance (mRMR), alongside a rank-based weighting method (i.e., MetaWise) to link metabolomic biomarkers to CRT and the 12-month and 20-month overall survival (OS) status in patients with GBM. Our method shows promising results, reducing feature dimensionality when employed on serum-based large-scale metabolomic datasets (University of Florida) for all our analyses. The proposed method successfully identified a set of eleven serum biomarkers shared among three datasets. The computational results show that the utilized method achieves 96.711%, 92.093%, and 86.910% accuracy rates with 48, 46, and 33 selected features for the CRT, 12-month, and 20-month OS-based metabolomic datasets, respectively. This discovery has implications for developing personalized treatment plans and improving patient outcomes.

• Publisher: MDPI AG,MDPI
• Subject: Accuracy / Biomarkers / Biomarkers, Tumor - blood / Brain cancer / Brain Neoplasms - blood / Brain Neoplasms - metabolism / Brain Neoplasms - mortality / Brain Neoplasms - therapy / Business metrics / Cancer therapies / Care and treatment / Chemotherapy / Classification / Clinical outcomes / Datasets / Development and progression / Feature selection / Glioblastoma - blood / Glioblastoma - metabolism / Glioblastoma - mortality / Glioblastoma - therapy / Glioblastoma multiforme / Glioma / Health aspects / Humans / Identification and classification / Machine learning / Medical prognosis / Metabolism / Metabolome / Metabolomics / Metabolomics - methods / Methods / Patients / Performance evaluation / Physiological aspects / Statistical methods / Support vector machines / Treatment Outcome / Tumor markers