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Comprehensive Target Screening and Cellular Profiling of the Cancer-Active Compound b-AP15 Indicate Abrogation of Protein Homeostasis and Organelle Dysfunction as the Primary Mechanism of Action
Linköping University, Department of Biomedical and Clinical Sciences, Division of Clinical Chemistry and Pharmacology. Linköping University, Faculty of Medicine and Health Sciences.ORCID iD: 0000-0002-5645-3346
Linköping University, Department of Biomedical and Clinical Sciences, Division of Clinical Chemistry and Pharmacology. Linköping University, Faculty of Medicine and Health Sciences.
Linköping University, Department of Biomedical and Clinical Sciences, Division of Clinical Chemistry and Pharmacology. Linköping University, Faculty of Medicine and Health Sciences.
Linköping University, Department of Biomedical and Clinical Sciences. Linköping University, Faculty of Medicine and Health Sciences. Department of Pharmacy, Central University of South Bihar, Gaya, India.
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2022 (English)In: Frontiers in Oncology, E-ISSN 2234-943X, Vol. 12, article id 852980Article in journal (Refereed) Published
Abstract [en]

Dienone compounds have been demonstrated to display tumor-selective anti-cancer activity independently of the mutational status of TP53. Previous studies have shown that cell death elicited by this class of compounds is associated with inhibition of the ubiquitin-proteasome system (UPS). Here we extend previous findings by showing that the dienone compound b-AP15 inhibits proteasomal degradation of long-lived proteins. We show that exposure to b-AP15 results in increased association of the chaperones VCP/p97/Cdc48 and BAG6 with proteasomes. Comparisons between the gene expression profile generated by b-AP15 to those elicited by siRNA showed that knock-down of the proteasome-associated deubiquitinase (DUB) USP14 is the closest related to drug response. USP14 is a validated target for b-AP15 and we show that b-AP15 binds covalently to two cysteines, Cys203 and Cys257, in the ubiquitin-binding pocket of the enzyme. Consistent with this, deletion of USP14 resulted in decreased sensitivity to b-AP15. Targeting of USP14 was, however, found to not fully account for the observed proteasome inhibition. In search for additional targets, we utilized genome-wide CRISPR/Cas9 library screening and Proteome Integral Solubility Alteration (PISA) to identify mechanistically essential genes and b-AP15 interacting proteins respectively. Deletion of genes encoding mitochondrial proteins decreased the sensitivity to b-AP15, suggesting that mitochondrial dysfunction is coupled to cell death induced by b-AP15. Enzymes known to be involved in Phase II detoxification such as aldo-ketoreductases and glutathione-S-transferases were identified as b-AP15-targets using PISA. The finding that different exploratory approaches yielded different results may be explained in terms of a “target” not necessarily connected to the “mechanism of action” thus highlighting the importance of a holistic approach in the identification of drug targets. We conclude that b-AP15, and likely also other dienone compounds of the same class, affect protein degradation and proteasome function at more than one level.

Place, publisher, year, edition, pages
Frontiers Media SA , 2022. Vol. 12, article id 852980
Keywords [en]
b-AP15, proteasome inhibitor, mitochondrial dysfunction, dienone, Michael acceptor, target screening
National Category
Cancer and Oncology
Identifiers
URN: urn:nbn:se:liu:diva-184797DOI: 10.3389/fonc.2022.852980ISI: 000876131200001PubMedID: 35530310OAI: oai:DiVA.org:liu-184797DiVA, id: diva2:1656431
Note

Funding: This research was funded by Cancerfonden, Vetenskapsrådet (grant 2018-02570) and Radiumhemmets forskningsfonder. CFG acknowledges support from the National Genomics Infrastructure, SNIC (project 2017-7-265), and the Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX). RZ acknowledges the Knut and Alice Wallenberg Foundation (grant KAW 2015.0063).

Available from: 2022-05-05 Created: 2022-05-05 Last updated: 2024-04-15Bibliographically approved
In thesis
1. Identifying Essential Deubiquitinase Interactions and Targeting Protein Ubiquitination in Cancer
Open this publication in new window or tab >>Identifying Essential Deubiquitinase Interactions and Targeting Protein Ubiquitination in Cancer
2024 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Cancer is the second leading cause of death globally and is one of the most pressing health issues today. While significant advances have been made in cancer treatment, drug resistance and toxicity remain formidable obstacles to successful therapy. Thus, there is a need to find novel targets that pave the way for new cancer therapeutics. Ubiquitination, the process of tagging substrate proteins with ubiquitin molecules, regulates many of the pathways that underlie cancer progression. This thesis aims to explore innovative strategies for combating cancer by focusing on crucial elements within the ubiquitination machinery, specifically the Ubiquitin-Proteasome System (UPS) and deubiquitinases (DUBs). In Paper I, we employed the Connectivity Map to discern UPS inhibitors by analyzing the gene expression patterns of various compounds in comparison to those induced by proteasome perturbation. In Paper II, we employed orthogonal methods to identify the primary mechanism for the cytotoxicity of b-AP15. Here, we showed that pharmacologic doses of b-AP15 resulted in strong proteasome inhibition and that cytotoxicity is mediated through the mitochondria and influenced by the proteasome-associated DUB, USP14. In Paper III, we explored the role of USP14 in colorectal cancer cells and evaluated its potential as a cancer target. We found that the genetic deletion of USP14 confers a quiescent phenotype to cancer cells. In Paper IV, we used CRISPR-based screens to search for new deubiquitinase targets. We identified deubiquitinase interactions essential for cancer and explored the possibility of combinatorial deubiquitinase targeting. We pinpointed highly-networked deubiquitinases (PSMD14, USP9X, USP39, and USP7) and deubiquitinase pairs represent promising drug targets. This thesis underscores the importance of the ubiquitination process in the search for novel cancer therapeutics and provides new avenues to explore in developing therapies based on the inhibition of deubiquitinases.

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2024. p. 79
Series
Linköping University Medical Dissertations, ISSN 0345-0082 ; 1905
Keywords
Cancer, Deubiquitinase, b-AP15, Ubiquitin-proteasome system
National Category
Cancer and Oncology
Identifiers
urn:nbn:se:liu:diva-202461 (URN)10.3384/9789180755610 (DOI)9789180755603 (ISBN)9789180755610 (ISBN)
Public defence
2024-05-16, Online through Zoom (contact padraig.darcy@liu.se) Papaver, Building 511, Campus US, Linköping, 09:00 (English)
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Available from: 2024-04-15 Created: 2024-04-15 Last updated: 2024-04-15Bibliographically approved

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Gubat, JohannesSelvaraju, KarthikSjöstrand, LindaTurkina, Maria VLinder, StigD´arcy, Pádraig

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Gubat, JohannesSelvaraju, KarthikSjöstrand, LindaKumar Singh, DhananjayTurkina, Maria VLinder, StigD´arcy, Pádraig
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