Isoform Switching Regulates the Response to Ionizing Radiation Through SRSF1

Abstract

This study investigates how isoform switching affects the cellular response to ionizing radiation (IR), an understudied area, despite its relevance to radiotherapy in cancer treatment. We aimed to identify changes in transcript isoform expression post-IR exposure and the proteins mediating these changes, with a focus on their potential to modulate radiosensitivity. Using RNA sequencing, we analyzed the B-cell lines derived from 10 healthy individuals at three timepoints, applying the MISO algorithm to quantify alternative splicing. We examined RBP motifs within the sequences of IR-responsive isoforms and validated the Serine/Arginine-Rich Splicing Factor 1 (SRSF1) as a predominant mediator through RNA-immunoprecipitation. We further investigated the effects of SRSF1 on radiosensitivity by knocking it down in vitro and by analyzing publicly-available cancer patient data. We identified ∼1,900 radiation-responsive alternatively-spliced isoforms. Many isoforms were differentially expressed without changes in their overall gene expression. Over a third of these transcripts underwent exon skipping, while others used proximal last exons. These IR-responsive isoforms tended to be shorter transcripts missing vital domains for preventing apoptosis and promoting cell division, but retaining those necessary for DNA repair. Our combined computational, genetic and molecular analyses identified the proto-oncogene Serine/Arginine-Rich Splicing Factor 1 (SRSF1) as a mediator of these radiation-induced isoform-switching events that promote apoptosis. After exposure to DNA double-strand break-inducing agents, SRSF1 expression decreased. A reduction in SRSF1 increased radiosensitivity in vitro and among cancer patients. We establish a pivotal role for isoform switching in the cellular response to IR and propose SRSF1 as a promising biomarker for assessing radiotherapy effectiveness.