Genome-wide CRISPR screen identifies splicing factor SF3B4 in driving hepatocellular carcinoma

Area of Science:

• Oncology
• Molecular Biology
• Genetics

Background:

• Genome sequencing has identified cancer-associated genes in hepatocellular carcinoma (HCC), but their functional roles are often unclear.
• Understanding gene function is critical for developing targeted therapies for HCC.

Purpose of the Study:

• To identify essential survival genes in HCC using genome-wide CRISPR knockout screening.
• To investigate the role of spliceosome factors and ferroptosis regulators in HCC and lenvatinib resistance.

Main Methods:

• Genome-wide CRISPR knockout screening in HCC organoids.
• Analysis of spliceosome factors and ferroptosis suppressors, including glutamate-cysteine ligase catalytic subunit (GCLC).
• RNA immunoprecipitation sequencing, long-read isoform sequencing, and transcriptome analysis to identify SF3B4 targets.

Main Results:

• Spliceosome factors are essential for HCC cell survival.
• SF3B4 was identified as a top-ranked gene, promoting HCC organoid survival and tumorigenesis in vivo.
• SF3B4 regulates a specific splicing landscape, with T-box transcription factor 3 (TBX3) variant TBX3+2a identified as a downstream effector.
• Upregulation of ferroptosis suppressors like GCLC was observed in lenvatinib-resistant HCC.

Conclusions:

• SF3B4 plays a vital role in HCC cell survival and tumor progression.
• SF3B4 is implicated in ferroptosis resistance in patients unresponsive to lenvatinib.
• Targeting SF3B4 may offer a therapeutic strategy for lenvatinib-resistant HCC.