Genome-wide CRISPR screen reveals an uncharacterized spliceosome regulator as new candidate immunotherapy target

Tong Shao , Chuanyang Liu , Jingyu Kuang , Sisi Xie , Ying Qu , Yingying Li , Lulu Zhang , Fangzhou Liu , Yanhua Qi , Tao Hou , Ming Li , Sujuan Zhang , Yu Liu , Zhixiang Yuan , Jiali Liu , Yanming Hu , Jingyang Wang , Chenghu Song , Shaowei Zhang , Lingyun Zhu , Jianzhong Shao , Aifu Lin , Wenjun Mao , Guangchuan Wang , Lvyun Zhu

iMeta ›› 2025, Vol. 4 ›› Issue (6) : e70096

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iMeta ›› 2025, Vol. 4 ›› Issue (6) :e70096 DOI: 10.1002/imt2.70096
RESEARCH ARTICLE
Genome-wide CRISPR screen reveals an uncharacterized spliceosome regulator as new candidate immunotherapy target
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Abstract

Cancer immune evasion is orchestrated by tumor-intrinsic molecular constraints that remain incompletely defined. Here, we performed an in vivo genome-wide clustered regularly interspaced short palindromic repeats (CRISPR) loss-of-function screen to catalogue gene regulatory determinants of immune evasion in cancer cells. We identify C9ORF50 as a novel splicing regulator whose inhibition profoundly sensitizes cancer to immune surveillance. Integrated multi-omics profiling reveals this intrinsically disordered protein exhibits liquid–liquid phase separation properties and forms nuclear condensates that colocalize with spliceosome components. Genetic ablation correlates with intron retention in multiple spliceosome components and cytoplasmic accumulation of double-stranded RNA, which is associated with type I interferon activation and enhances chemokine-mediated T cell recruitment. As a result, C9ORF50 inhibition amplifies tumor cell immunogenicity, enhancing T cell infiltration in poorly infiltrated tumors. Clinically, elevated C9ORF50 expression correlates with poor survival and diminished lymphoid infiltration across malignancies. Therapeutic targeting of C9ORF50 using RNA interference enhances T cell infiltration and suppresses tumor growth. Our work identifies C9ORF50 as a candidate therapeutic target that modulates RNA splicing and tumor immunity, suggesting splicing regulation as a potential strategy to enhance immunotherapy responses.

Keywords

antitumor immunity / C9ORF50 / CRISPR screen / intrinsically disordered protein / liquid–liquid phase separation / RNA splicing / therapeutic targets

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Tong Shao, Chuanyang Liu, Jingyu Kuang, Sisi Xie, Ying Qu, Yingying Li, Lulu Zhang, Fangzhou Liu, Yanhua Qi, Tao Hou, Ming Li, Sujuan Zhang, Yu Liu, Zhixiang Yuan, Jiali Liu, Yanming Hu, Jingyang Wang, Chenghu Song, Shaowei Zhang, Lingyun Zhu, Jianzhong Shao, Aifu Lin, Wenjun Mao, Guangchuan Wang, Lvyun Zhu. Genome-wide CRISPR screen reveals an uncharacterized spliceosome regulator as new candidate immunotherapy target. iMeta, 2025, 4(6): e70096 DOI:10.1002/imt2.70096

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