Full-length transcript alterations in human bronchial epithelial cells with U2AF1 S34F mutations

Area of Science:

• Molecular Biology
• Genomics
• Cancer Research

Background:

• The U2AF1 gene is frequently mutated in lung adenocarcinoma.
• These mutations cause widespread changes in pre-mRNA splicing.
• Full-length mRNA isoforms affected by U2AF1 mutations are not well understood.

Purpose of the Study:

• To investigate the impact of the U2AF1 S34F mutation on full-length mRNA isoform expression and function.
• To identify novel transcript isoforms generated due to U2AF1 mutations.
• To provide a comprehensive resource of U2AF1-associated isoforms in lung cells.

Main Methods:

• High-throughput long-read cDNA sequencing was performed on isogenic human bronchial epithelial cells.
• Cells with and without the U2AF1 S34F mutation were analyzed.
• Transcriptome-wide isoform identification and expression analysis were conducted.

Main Results:

• 49,366 multi-exon transcript isoforms were identified, with over half not matching existing databases.
• 198 transcript isoforms showed significant expression and usage changes; 32% were missed by short-read assembly.
• Down-regulation of immune gene isoforms and isoforms targeted by nonsense-mediated decay was observed in mutant cells.

Conclusions:

• The U2AF1 S34F mutation significantly alters the landscape of full-length mRNA isoforms in lung cells.
• Many novel transcript isoforms are generated, impacting gene expression and potentially translational output.
• This study provides a valuable resource for understanding U2AF1-driven splicing alterations in lung adenocarcinoma.