Overview of transcriptomics and epigenomics approaches in the diagnosis, prognosis, and therapeutics of primary brain cancers.

Abstract

Genome-wide approaches have unveiled multiple aspects of primary brain and spinal cord cancers regarding oncogenic processes, the tumor microenvironment, and mechanisms of resistance and sensitivity to therapy (among many others). In this review, we provide a brief overview of the possibilities that the current and highly diverse omics techniques offer for genomic landscape characterization, and how they can enhance our understanding of gliomas and glioneuronal tumors. More specifically, we discuss available methodologies for transcriptomics profiling (gene expression, alternative splicing, RNA modifications) and epitranscriptomics profiling (DNA methylation and hydroxymethylation, histone covalent modifications, chromatin accessible regions) at the level of bulk tissue, sorted and single cells, and biofluids. Multiomics integration of cancer-associated molecular alterations, including mapping of long-distant DNA interactions, enables a better understanding of tumor biology, providing clues concerning patient stratification, biomarker discovery, identification of key oncologic players with clinical utility, and potential novel therapeutic interventions. Furthermore, these multiomics have generated diverse and extensive databases that are available to the scientific community. Finally, we discuss that widespread implementation of omics into the clinic is still challenging but holds good prospects for effectiveness in the near future.