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Genome-wide CRISPR screen identifies splicing factor SF3B4 in driving hepatocellular carcinoma
Yue Guo1, Mingjing Xu1, Hua Xue1
1Department of Surgery, Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
Abstract:
Although genome sequencings have recognized many cancer-associated genes in hepatocellular carcinoma (HCC), distinguishing their functional effect remains challenging. Leveraging on a genome-wide CRISPR knockout (KO) screening, we uncovered spliceosome factors as major survival essential genes in HCC and up-regulations of ferroptosis suppressors [particularly glutamate-cysteine ligase catalytic subunit (GCLC)] in lenvatinib resistance. Our KO screen in patient-derived HCC organoid showed splicing factor 3b subunit 4 (SF3B4) to be top-ranked, conferring prosurvival signal in HCC organoid and driving tumorigenic potentials in both hepatic progenitor organoids and hydrodynamic tail vein injection HCC murine model. The combined RNA immunoprecipitation sequencing, long-read isoform sequencing, and transcriptome revealed characteristic splicing landscape regulated by SF3B4 and identified T-box transcription factor 3 (TBX3) variant TBX3+2a as a potent downstream effector. Our findings highlighted vital roles of SF3B4 in HCC cell survival and tumor progression, and the phenomenon of ferroptosis resistance in patients unresponsive to first-line agent lenvatinib.
Insights
Spliceosome factor SF3B4 is crucial for hepatocellular carcinoma (HCC) survival and lenvatinib resistance. This study identifies SF3B4 as a key driver of HCC progression and ferroptosis resistance.
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.
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