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Derivation and characterization of ubiquitin-specific protease 18 inhibitors
Blessing O. Ogunlade, Kevin N. Dalby, Samuel C. Okpechi, Eun Jeong Cho, Liliya Tyutyunyk-Massey, Zibo Chen, Xiuxia Liu, Joseph Ivanic, Brian Luke, Shyamal D. Desai, Yair Alfaro, Ashwini K. Devkota, Rae M. Sammons, Gilbert G. Privé, Xi Liu, Ethan Dmitrovsky
Blessing O. Ogunlade, Kevin N. Dalby, Samuel C. Okpechi, Eun Jeong Cho, Liliya Tyutyunyk-Massey, Zibo Chen, Xiuxia Liu, Joseph Ivanic, Brian Luke, Shyamal D. Desai, Yair Alfaro, Ashwini K. Devkota, Rae M. Sammons, Gilbert G. Privé, Xi Liu, Ethan Dmitrovsky
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Research Article Cell biology Oncology

Derivation and characterization of ubiquitin-specific protease 18 inhibitors

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Abstract

Ubiquitin-Specific Protease 18 (USP18) is a deISGylation enzyme and antineoplastic target. To develop USP18 inhibitors, an enzymatically active human recombinant USP18 protein was engineered suitable for high-throughput screening of ~80,000 chemical compounds. Three of them substantially inhibited USP18 enzymatic activity, with β-lapachone having prominent antineoplastic activity. Independent β-lapachone treatments of murine and human lung cancer cell lines statistically significantly reduced proliferation and increased apoptosis. Gain of USP18 expression antagonized these effects. β-Lapachone treatments statistically significantly repressed lung cancer xenograft growth. β-Lapachone increased reactive oxygen species (ROS), but antineoplastic effects occurred at dosages with negligible ROS production. ROS scavenger treatments did not rescue β-lapachone effects at these concentrations, consistent with an ROS-independent mechanism. IFN-Stimulated Response Element (ISRE) reporter assays following β-lapachone treatment activated this reporter. USP18 cotransfection antagonized this activity. β-Lapachone treatments increased global ISGylation. RNA-seq of lung cancer cells engineered with or without enhanced USP18 expression showed specific pathways affected by β-lapachone treatment. Proteomic analysis of these treated cells revealed known and new ISGylated proteins. In silico modeling identified a unique USP18 pocket where these USP18 inhibitors bind. Engineered mutation of this pocket disrupted β-lapachone activity. Taken together, β-lapachone is an antineoplastic tool compound useful for USP18 inhibitor development.

Authors

Blessing O. Ogunlade, Kevin N. Dalby, Samuel C. Okpechi, Eun Jeong Cho, Liliya Tyutyunyk-Massey, Zibo Chen, Xiuxia Liu, Joseph Ivanic, Brian Luke, Shyamal D. Desai, Yair Alfaro, Ashwini K. Devkota, Rae M. Sammons, Gilbert G. Privé, Xi Liu, Ethan Dmitrovsky

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Figure 7

Proteomic analyses reveal β-lapachone treatment affected ISG15-related proteins.

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Proteomic analyses reveal β-lapachone treatment affected ISG15-related p...
(A) ISG15 immunoprecipitation followed by mass spectrometry proteomics analysis was performed in A549 lung cancer cells that expressed an empty vector or a USP18 expression construct, and these transfectants were treated with β-lapachone (2.5 μM) or vehicle treatments. Comparative proteomic analyses identified potential ISG15-conjugated proteins whose levels were increased by β-lapachone and rescued by engineered USP18 overexpression. Among the ISG15-conjugated targets detected, 86 were previously reported ISG15 substrates and 70 were found as new ISG15-conjugated proteins. (B) Functional categorization of the β-lapachone treatment arm that regulated ISG15 conjugates revealed broad distribution across multiple cellular processes. (C) Immunoblot validation of the representative ISG15-conjugated protein, DYNLL1, confirmed that its expression was regulated by β-lapachone–treatment relative to vehicle controls (quantification is shown). Data are shown as mean ± SD. *P < 0.05, **P < 0.01, and ***P < 0.001. (D) TCGA lung adenocarcinoma cohort analyses demonstrated that several β-lapachone upregulated ISG15-conjugated proteins, including DYNLL1, HAUS6, LAMB3, BANF1, EIF5A, and ANXA2P2, were statistically significantly associated with lung cancer survival outcomes. (E) Four previously unrecognized ISG15-conjugated proteins, PCBP2, NME1, TUBA1C, and TUBA4A, were confirmed as β-lapachone regulated ISG15 targets whose elevated expression predicted an unfavorable survival in TCGA lung adenocarcinoma cases. Survival analysis for D and E highlighted species was performed using the Kaplan-Meier method, using the log-rank test. A P value below 0.05 was deemed statistically significant.

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