USP20 as a super-enhancer-regulated gene drives T-ALL progression via HIF1A deubiquitination

Ling Xu; Zimu Zhang; Juanjuan Yu; Tongting Ji; Jia Cheng; Xiaodong Fei; Xinran Chu; Yanfang Tao; Yan Xu; Pengju Yang; Wenyuan Liu; Gen Li; Yongping Zhang; Yan Li; Fenli Zhang; Ying Yang; Bi Zhou; Yumeng Wu; Zhongling Wei; Yanling Chen; Jianwei Wang; Di Wu; Xiaolu Li; Yang Yang; Guanghui Qian; Hongli Yin; Shuiyan Wu; Shuqi Zhang; Dan Liu; Jun-Jie Fan; Lei Shi; Xiaodong Wang; Shaoyan Hu; Jun Lu; Jian Pan

doi:10.1016/j.apsb.2025.07.003

USP20 as a super-enhancer-regulated gene drives T-ALL progression via HIF1A deubiquitination

Acta Pharm Sin B. 2025 Sep;15(9):4751-4771. doi: 10.1016/j.apsb.2025.07.003. Epub 2025 Jul 5.

Authors

Ling Xu^{1

2}, Zimu Zhang³, Juanjuan Yu¹, Tongting Ji¹, Jia Cheng¹, Xiaodong Fei⁴, Xinran Chu⁵, Yanfang Tao⁶, Yan Xu², Pengju Yang¹, Wenyuan Liu⁷, Gen Li³, Yongping Zhang⁵, Yan Li², Fenli Zhang⁸, Ying Yang⁸, Bi Zhou^{1

9}, Yumeng Wu^{1

10}, Zhongling Wei⁵, Yanling Chen¹, Jianwei Wang³, Di Wu³, Xiaolu Li³, Yang Yang³, Guanghui Qian³, Hongli Yin³, Shuiyan Wu⁵, Shuqi Zhang¹¹, Dan Liu¹², Jun-Jie Fan⁵, Lei Shi¹³, Xiaodong Wang¹⁴, Shaoyan Hu⁵, Jun Lu⁵, Jian Pan³

Affiliations

¹ Children's Hospital of Soochow University, Suzhou 215003, China.
² Department of Pediatrics, the Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000 China.
³ Institute of Pediatric Research, Children's Hospital of Soochow University, Suzhou 215003, China.
⁴ Department of Radiology, Children's Hospital of Soochow University, Suzhou 215003, China.
⁵ Department of Hematology, Children's Hospital of Soochow University, Suzhou 215003, China.
⁶ Department of Traditional Chinese Medicine, Children's Hospital of Soochow University, Suzhou 215003, China.
⁷ Department of Pediatrics, the Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China.
⁸ Clinical Medicine, Guizhou Medical University, Guiyang 550000, China.
⁹ Department of Pediatric, Suzhou Hospital of AnHui Medical University, Suzhou 234000, China.
¹⁰ Department of Pediatric, the First Affiliated Hospital of Bengbu Medical College, Bengbu 233004, China.
¹¹ Department of Pediatrics, the First Affiliated Hospital of Wannan Medical College, Wuhu 241002, China.
¹² Department of Blood Transfusion, Children's Hospital of Soochow University, Suzhou 215003, China.
¹³ Department of Medicinal Chemistry, Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.
¹⁴ Department of Orthopaedics, Children's Hospital of Soochow University, Suzhou 215003, China.

Abstract

T-cell acute lymphoblastic leukemia (T-ALL) is a highly aggressive hematologic malignancy with a poor prognosis, despite advancements in treatment. Many patients struggle with relapse or refractory disease. Investigating the role of the super-enhancer (SE) regulated gene ubiquitin-specific protease 20 (USP20) in T-ALL could enhance targeted therapies and improve clinical outcomes. Analysis of histone H3 lysine 27 acetylation (H3K27ac) chromatin immunoprecipitation sequencing (ChIP-seq) data from six T-ALL cell lines and seven pediatric samples identified USP20 as an SE-regulated driver gene. Utilizing the Cancer Cell Line Encyclopedia (CCLE) and BloodSpot databases, it was found that USP20 is specifically highly expressed in T-ALL. Knocking down USP20 with short hairpin RNA (shRNA) increased apoptosis and inhibited proliferation in T-ALL cells. In vivo studies showed that USP20 knockdown reduced tumor growth and improved survival. The USP20 inhibitor GSK2643943A demonstrated similar anti-tumor effects. Mass spectrometry, RNA-Seq, and immunoprecipitation revealed that USP20 interacted with hypoxia-inducible factor 1 subunit alpha (HIF1A) and stabilized it by deubiquitination. Cleavage under targets and tagmentation (CUT&Tag) results indicated that USP20 co-localized with HIF1A, jointly modulating target genes in T-ALL. This study identifies USP20 as a therapeutic target in T-ALL and suggests GSK2643943A as a potential treatment strategy.

Keywords: GSK2643943A; H3K27ac ChIP-seq; HIF1A; Potential target; Super enhancer; T-ALL; Transcription regulation; USP20.