USP39 phase separates into the nucleolus and drives lung adenocarcinoma progression by promoting GLI1 expression - Research Open Access

Sep 23, 2026

USP39 undergoes liquid-liquid phase separation (LLPS) to form nucleolus-localized condensates, linking membraneless organelle biology to lung cancer progression. The nucleolus is a major LLPS-derived organelle, while deubiquitylating enzymes (DUBs) are emerging therapeutic targets; however, how nucleolar DUB phase separation contributes to lung cancer development remained unclear. Methods use GFP-USP39 fusion protein imaging, FRAP, and in vitro LLPS assays, combined with transcriptomics, Western blot, RT-PCR, luciferase reporters, and functional tumor models. Results show USP39 phase separation depends on an N-terminal disordered region (1-103), suppressing lung cancer growth and migration when knocked down, reducing GLI1 oncogenic transcription, and restricting xenograft formation. Downregulation of USP39 therefore offers a potential therapeutic strategy for lung adenocarcinoma.

LanguageEnglish

CategoryHealthcare

FormatPDF

Pages18

Reading Time45 min

AccessFree to download

Background

LLPS and membraneless organelles

DUBs as cancer targets and study gap

Methods

USP39 LLPS characterization

USP39 target identification and functional assays

In vitro and in vivo tumor experiments

Results

USP39 nucleolar phase separation and required region

USP39 knockdown effects on growth and migration

Regulation of GLI1 and xenograft suppression

Conclusions

USP39 as a therapeutic target via GLI1 regulation

Cheng et al. Cell Communication and Signaling (2025) 23:56 [https://doi.org/10.1186/s12964-025-02059-5](https://doi.org/10.1186/s12964-025-02059-5) Cell Communication and Signaling RESEARCH Open Access USP39 phase separates into the nucleolus and drives lung adenocarcinoma progression by promoting GLI1 expression Shaoxuan Cheng 1†, Zhiyuan Qiu 1†, Ziyi Zhang 1, Yuxuan Li 1, Yue Zhu 1, Yuxin Zhou 1, Yinghui Yang 1, Yaowen Zhang 1, DianYang 1, Yingqiu Zhang 1, Han Liu 1, Zhaoxia Dai2*, Shu-Lan Sun3* and Shuyan Liu 1* Abstract Background Intracellular membraneless organelles formed by liquid-liquid phase separation (LLPS) function in diverse physiological processes and have been linked to tumor-promoting properties. The nucleolus is one of the largest membraneless organelle formed through LLPS. Deubiquitylating enzymes (DUBs) emerge as novel therapeutic targets against human cancers. However, the nucleolar phase separation of DUBs and association with lung cancer development have remained incompletely investigated till now. Methods GFP-USP39 fusion proteins were analyzed for LLPS properties using immunofluorescence, fluorescence recovery after photobleaching (FRAP) and in vitro LLPS assays. Intrinsically-disordered regions of USP39 were analyzed by PhaSepDB database. Transcriptomic profiling, Western blot, RT-PCR and luciferase reporter assays were conducted to identify targets regulated by USP39 . The effects of USP39 depletion on tumor progression were tested using doxycycline-inducible USP39 knockdown and rescue lung adenocarcinoma cells both in vitro and in vivo by performing MTT, colony formation, EdU staining, transwell and tumor xenograft model experiments. Results USP39 phase separates into nucleoli depending upon its N-terminal disordered region with amino acid residues 1-103. Lung cancer cell growth and migration were dramatically inhibited by USP39 knockdown, which was rescued by exogenous USP39 complementation. Moreover, knockdown of USP39 reduced oncogenic transcription effector GLI1 levels. Finally, USP39 downregulation restricted the formation of lung cancer xenografts in nude mice. Conclusions USP39 undergoes LLPS in the nucleolus and promotes tumor progression by regulating GLI1 expression. Downregulation of USP39 effectively suppressed lung cancer growth, and therefore targeting USP39 provides novel therapeutic strategy to treat lung cancer. Keywords LLPS, Nucleolus, USP39, GLI1, Lung adenocarcinoma †Shaoxuan Cheng and Zhiyuan Qiu contributed equally to this work. *Correspondence: Zhaoxia Dai [daizhaoxia@dmu.edu.cn](daizhaoxia@dmu.edu.cn)[ ](daizhaoxia@dmu.edu.cn)Shu-Lan Sun [sunshulan@dl ut.edu.cn](sunshulan@dl ut.edu.cn)[ ](sunshulan@dl ut.edu.cn)Shuyan Liu [liusy@dmu.edu.cn](liusy@dmu.edu.cn) 1Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning Province, China 2The Second Department of Thoracic Medical Oncology, Second Hospital of Dalian Medical University, Dalian, Liaoning Province, China 3Central Laboratory, Cancer Hospital, Cancer Hospital of China Medical University, Dalian University of Technology, Liaoning Cancer Hospital & Institute, Shenyang, China © The Author(s) 2025. Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use

FAQs

What is the main finding about USP39 in this study?

USP39 undergoes LLPS in the nucleolus. This nucleolar phase separation promotes lung adenocarcinoma progression by regulating GLI1 expression.

Which region of USP39 is required for nucleolar phase separation?

USP39 phase separation into nucleoli depends on its N-terminal disordered region, specifically amino acid residues 1-103.

How does USP39 affect lung cancer cells when it is depleted?

USP39 knockdown dramatically inhibits lung cancer cell growth and migration, reduces GLI1 levels, and restricts the formation of lung cancer xenografts in nude mice.

Sep 23, 2026

Uploaded by Emma Wilson