Genomic analyses of early responses to radiation in glioblastoma reveal new alterations at transcription, splicing, and translation levels

Saket Choudhary,Wenzheng Li,Andrew D Smith,Suzanne C Burns,Hoda Mirsafian,Luiz O Penalva,Xiufen Lei,Dat T Vo,Mei Qiao

doi:10.1038/s41598-020-65638-1

Abstract

High-dose radiation is the main component of glioblastoma therapy. Unfortunately, radio-resistance is a common problem and a major contributor to tumor relapse. Understanding the molecular mechanisms driving response to radiation is critical for identifying regulatory routes that could be targeted to improve treatment response. We conducted an integrated analysis in the U251 and U343 glioblastoma cell lines to map early alterations in the expression of genes at three levels: transcription, splicing, and translation in response to ionizing radiation. Changes at the transcriptional level were the most prevalent response. Downregulated genes are strongly associated with cell cycle and DNA replication and linked to a coordinated module of expression. Alterations in this group are likely driven by decreased expression of the transcription factor FOXM1 and members of the E2F family. Genes involved in RNA regulatory mechanisms were affected at the mRNA, splicing, and translation levels, highlighting their importance in radiation-response. We identified a number of oncogenic factors, with an increased expression upon radiation exposure, including BCL6, RRM2B, IDO1, FTH1, APIP, and LRIG2 and lncRNAs NEAT1 and FTX. Several of these targets have been previously implicated in radio-resistance. Therefore, antagonizing their effects post-radiation could increase therapeutic efficacy. Our integrated analysis provides a comprehensive view of early response to radiation in glioblastoma. We identify new biological processes involved in altered expression of various oncogenic factors and suggest new target options to increase radiation sensitivity and prevent relapse.

Highlights

High-dose radiation is the main component of glioblastoma therapy
A Principal Component Analysis (PCA) performed on RNA-Seq and Ribo-Seq read counts revealed that most variation can be explained by the cell type along the first principal component, while radiation time-related changes were captured along the second principal component (Supplementary Fig. S1B)
Downregulated genes are mainly involved in transcription regulation and include 18 zinc finger transcription factors displaying high expression correlation in glioblastoma samples from The Cancer Genome Atlas (TCGA) (Supplementary Table S1)

Summary

Introduction

High-dose radiation is the main component of glioblastoma therapy. radio-resistance is a common problem and a major contributor to tumor relapse. We conducted an integrated analysis in the U251 and U343 glioblastoma cell lines to map early alterations in the expression of genes at three levels: transcription, splicing, and translation in response to ionizing radiation. Genes involved in RNA regulatory mechanisms were affected at the mRNA, splicing, and translation levels, highlighting their importance in radiation-response. We identified a number of oncogenic factors, with an increased expression upon radiation exposure, including BCL6, RRM2B, IDO1, FTH1, APIP, and LRIG2 and lncRNAs NEAT1 and FTX Several of these targets have been previously implicated in radioresistance. To elucidate expression responses to radiation, we conducted an integrated study in U251 and U343 glioblastoma cell lines covering transcription (mRNAs and lncRNAs), splicing, and translation. We identified several oncogenic factors and genes associated with poor survival in glioblastoma that displayed increased expression upon radiation exposure. Many have been implicated in radio-resistance, and their inhibition in combination with radiation could increase therapy efficacy

Methods

Results

Conclusion