High-Resolution Subtyping of Pediatric Low-Grade Glioma Using an Integrated Meta-Clustering Framework

Abstract

Pediatric low-grade glioma (pLGG) is the most common type of brain tumor in children, accounting for approximately 30% of all central nervous system tumors in children. pLGG has multiple molecular subtypes that differ in disease progression, recurrence patterns, and treatment responses. Conventional wet lab approaches including molecular profiling and histopathological studies for pLGG characterization are time consuming, costly, and laborious. Recently, methods based on artificial intelligence (AI) or machine learning (ML) have been widely used for pLGG molecular categorization, but most of them can only identify two or three pLGG subtypes. To more comprehensively characterize the molecular subtypes of pLGG and their potential biological and therapeutic significance, we develop an integrated meta-clustering approach, namely Meta-pLGG, that can explore high resolution molecular subtypes and their transcriptional heterogeneity for pLGG. Specifically, we first performed multiple rounds of random projection (RP) to generate dimension-reduced feature vectors from pLGG transcriptomics data, each of which was subsequently clustered by different clustering algorithms including hierarchical clustering, K-means, Self-Organizing Maps (SOM), Non-negative Matrix Factorization (NMF), Gaussian Mixture Model (GMM), and Spectral Clustering, as base clustering methods. Then, to yield robust clustering performance, we integrated the clustering results of these RP based individual clustering algorithms by adopting a weighted meta-clustering (wMetaC) approach. Results based on 532 pLGG patients suggested that our proposed approach demonstrated superior stability and discriminative powers for higher resolution pLGG subtyping compared to conventional approaches. Based on consensus matrix analysis, we identified two major pLGG mega-subtypes, with one further subdivided into three subgroups and the other into two. Then, we performed cluster specific differential gene expression analysis, molecular pathway analysis, and gene-drug-disease association analysis. The results showed that the identified five subgroups exhibited significant subtype-specific transcriptomic heterogeneity. In summary, our meta-clustering approach demonstrated much higher performance and robustness in identifying higher resolution molecular subtypes of pLGG, revealing the molecular heterogeneity within pLGG and potentially providing new insights for more precise molecular subtyping and precision therapy.