Transcriptome sequencing reveals potential mechanism of cryptic 3' splice site selection in SF3B1-mutated cancers

Area of Science:

• Molecular Biology
• Cancer Genomics
• RNA Splicing

Background:

• Mutations in the splicing factor SF3B1 are implicated in various cancers.
• These mutations are associated with aberrant RNA splicing patterns.
• Understanding SF3B1's role is crucial for cancer research.

Purpose of the Study:

• To investigate the impact of SF3B1 mutations on splice site usage.
• To identify and characterize cryptic 3' splice sites (3'SSs) in SF3B1-mutated cancers.
• To elucidate the mechanistic basis of cryptic 3'SS selection.

Main Methods:

• Analysis of transcriptome sequencing data from chronic lymphocytic leukemia, breast cancer, and uveal melanoma.
• Identification and characterization of cryptic 3'SS usage.
• Defining the sequence context required for cryptic 3'SS selection.

Main Results:

• Hundreds of cryptic 3'SSs are utilized in cancers with SF3B1 mutations.
• A specific sequence context is necessary for the observed cryptic 3'SS usage.
• SF3B1 mutations likely alter the steric hindrance around the branch point, promoting cryptic 3'SS selection.
• Ten genes showed a preference for out-of-frame cryptic 3'SSs.
• Mutations in SF3B1 HEAT 5-9 repeats specifically lead to cryptic 3'SS usage downstream of the branch point.

Conclusions:

• SF3B1 mutations drive the widespread use of cryptic 3'SSs, contributing to cancer's splicing defects.
• A mechanistic model explains how SF3B1 mutations lead to cryptic 3'SS selection.
• The identified targets and mechanistic insights will advance research into SF3B1's oncogenic functions.