Transcriptional readthrough precedes alternative splicing programs triggered in CML cells by imatinib

TL;DR

This study shows that imatinib, a drug used for leukemia, causes early transcriptional readthrough in CML cells, which precedes changes in gene splicing and could lead to drug resistance.

Contribution

The study reveals that transcriptional readthrough occurs before splicing changes in CML cells treated with imatinib, linking it to drug resistance.

Findings

Transcriptional readthrough increases within 1 hour of imatinib treatment in CML cells.

Imatinib induces 'readthrough chimeras' by splicing exons from upstream and downstream genes.

Altered mRNA isoforms and chimeras are observed in both drug-sensitive and drug-resistant CML cells.

Abstract

Cellular stresses regulate transcriptional readthrough, whereby RNA polymerase II elongates past a gene’s polyadenylation cleavage site without RNA cleavage. Readthrough has been reported in several cancer types. Here, we use long-read sequencing of nascent RNA to quantify transcriptional readthrough in chronic myeloid leukemia (CML) cells and characterize early responses to the targeted therapeutic, imatinib. We show that the amount, length, and gene specificity of readthrough increase within 1 hour, before gene expression and alternative splicing alterations emerge. Notably, imatinib-dependent messenger RNA (mRNA) isoform changes involved “readthrough chimeras,” in which exons from an upstream gene are alternatively spliced to exons in a downstream gene. Altered mRNA isoforms and chimera levels were detected in imatinib-resistant K562 cells as well as cells of patients with CML. Thus, imatinib can provoke a cascade of early changes to transcription and splicing fidelity that may lead to longer-term adjustments in gene expression, cancer cell differentiation, and the development of therapy resistance.

Precision RNA sequencing revealed the earliest response of leukemia cells to targeted therapy: transcriptional readthrough.

Figures