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

Area of Science:

• Molecular Biology
• Genomics
• Cancer Research

Background:

• Cellular stresses can induce transcription readthrough, where RNA polymerase II extends beyond gene polyadenylation sites.
• This readthrough phenomenon has been observed in various cancer types.
• Understanding early molecular responses to targeted therapies is crucial for improving treatment outcomes.

Purpose of the Study:

• To quantify transcriptional readthrough in chronic myelogenous leukemia (CML) cells.
• To characterize the early cellular responses to imatinib, a targeted therapeutic agent.
• To investigate the role of readthrough and its associated mRNA isoforms in imatinib response and resistance.

Main Methods:

• Utilized long-read sequencing of nascent RNA to measure transcriptional readthrough.
• Analyzed changes in readthrough amount, length, and gene-specificity over time after imatinib treatment.
• Investigated mRNA isoform alterations, including readthrough chimeras, and their presence in CML and imatinib-resistant cells.

Main Results:

• Transcriptional readthrough increased in amount, length, and gene-specificity within 1 hour of imatinib exposure.
• Alterations in gene expression and alternative splicing emerged later, after initial readthrough changes.
• Imatinib-dependent mRNA isoform changes included "readthrough chimeras" linking upstream and downstream gene exons.
• Modified mRNA isoforms and chimera levels were detected at 18 hours in both sensitive and resistant CML cells, as well as patient samples.

Conclusions:

• Early, rapid increases in transcriptional readthrough occur in response to imatinib in CML cells.
• These early readthrough events appear to precede later alterations in gene expression and splicing.
• The observed changes in mRNA isoforms and readthrough chimeras suggest a cascade impacting transcription and splicing fidelity.
• These molecular changes may contribute to long-term gene expression adjustments and the development of imatinib resistance in CML.