1
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Arriojas A, Patalano S, Macoska J, Zarringhalam K. A Bayesian noisy logic model for inference of transcription factor activity from single cell and bulk transcriptomic data. NAR Genom Bioinform 2023; 5:lqad106. [PMID: 38094309 PMCID: PMC10716740 DOI: 10.1093/nargab/lqad106] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 11/12/2023] [Accepted: 11/24/2023] [Indexed: 12/20/2023] Open
Abstract
The advent of high-throughput sequencing has made it possible to measure the expression of genes at relatively low cost. However, direct measurement of regulatory mechanisms, such as transcription factor (TF) activity is still not readily feasible in a high-throughput manner. Consequently, there is a need for computational approaches that can reliably estimate regulator activity from observable gene expression data. In this work, we present a noisy Boolean logic Bayesian model for TF activity inference from differential gene expression data and causal graphs. Our approach provides a flexible framework to incorporate biologically motivated TF-gene regulation logic models. Using simulations and controlled over-expression experiments in cell cultures, we demonstrate that our method can accurately identify TF activity. Moreover, we apply our method to bulk and single cell transcriptomics measurements to investigate transcriptional regulation of fibroblast phenotypic plasticity. Finally, to facilitate usage, we provide user-friendly software packages and a web-interface to query TF activity from user input differential gene expression data: https://umbibio.math.umb.edu/nlbayes/.
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Affiliation(s)
- Argenis Arriojas
- Department of Mathematics, University of Massachusetts Boston, Boston, MA 02125, USA
- Department of Physics, University of Massachusetts Boston, Boston, MA 02125, USA
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Susan Patalano
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Jill Macoska
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Kourosh Zarringhalam
- Department of Mathematics, University of Massachusetts Boston, Boston, MA 02125, USA
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA 02125, USA
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2
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Arriojas A, Patalano S, Macoska J, Zarringhalam K. A Bayesian Noisy Logic Model for Inference of Transcription Factor Activity from Single Cell and Bulk Transcriptomic Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539308. [PMID: 37205561 PMCID: PMC10187261 DOI: 10.1101/2023.05.03.539308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The advent of high-throughput sequencing has made it possible to measure the expression of genes at relatively low cost. However, direct measurement of regulatory mechanisms, such as Transcription Factor (TF) activity is still not readily feasible in a high-throughput manner. Consequently, there is a need for computational approaches that can reliably estimate regulator activity from observable gene expression data. In this work, we present a noisy Boolean logic Bayesian model for TF activity inference from differential gene expression data and causal graphs. Our approach provides a flexible framework to incorporate biologically motivated TF-gene regulation logic models. Using simulations and controlled over-expression experiments in cell cultures, we demonstrate that our method can accurately identify TF activity. Moreover, we apply our method to bulk and single cell transcriptomics measurements to investigate transcriptional regulation of fibroblast phenotypic plasticity. Finally, to facilitate usage, we provide user-friendly software packages and a web-interface to query TF activity from user input differential gene expression data: https://umbibio.math.umb.edu/nlbayes/.
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Affiliation(s)
- Argenis Arriojas
- Department of Mathematics, University of Massachusetts Boston, Boston, MA 02125, USA
- Department of Physics, University of Massachusetts Boston, Boston, MA 02125, USA
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Susan Patalano
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Jill Macoska
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Kourosh Zarringhalam
- Department of Mathematics, University of Massachusetts Boston, Boston, MA 02125, USA
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA 02125, USA
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3
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Zhou H, He Q, Li C, Alsharafi BLM, Deng L, Long Z, Gan Y. Focus on the tumor microenvironment: A seedbed for neuroendocrine prostate cancer. Front Cell Dev Biol 2022; 10:955669. [PMID: 35938167 PMCID: PMC9355504 DOI: 10.3389/fcell.2022.955669] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/01/2022] [Indexed: 11/13/2022] Open
Abstract
The tumor microenvironment (TME) is a microecology consisting of tumor and mesenchymal cells and extracellular matrices. The TME plays important regulatory roles in tumor proliferation, invasion, metastasis, and differentiation. Neuroendocrine differentiation (NED) is a mechanism by which castration resistance develops in advanced prostate cancer (PCa). NED is induced after androgen deprivation therapy and neuroendocrine prostate cancer (NEPC) is established finally. NEPC has poor prognosis and short overall survival and is a major cause of death in patients with PCa. Both the cellular and non-cellular components of the TME regulate and induce NEPC formation through various pathways. Insights into the roles of the TME in NEPC evolution, growth, and progression have increased over the past few years. These novel insights will help refine the NEPC formation model and lay the foundation for the discovery of new NEPC therapies targeting the TME.
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Affiliation(s)
- Hengfeng Zhou
- Andrology Center, Department of Urology, the Third Xiangya Hospital, Central South University, Changsha, China
| | - Qiangrong He
- Andrology Center, Department of Urology, the Third Xiangya Hospital, Central South University, Changsha, China
| | - Chao Li
- Andrology Center, Department of Urology, the Third Xiangya Hospital, Central South University, Changsha, China
| | | | - Liang Deng
- Andrology Center, Department of Urology, the Third Xiangya Hospital, Central South University, Changsha, China
| | - Zhi Long
- Andrology Center, Department of Urology, the Third Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Zhi Long, ; Yu Gan,
| | - Yu Gan
- Department of Urology, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Zhi Long, ; Yu Gan,
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4
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Zhao Y, Li J, Chen J, Ye M, Jin X. Functional roles of E3 ubiquitin ligases in prostate cancer. J Mol Med (Berl) 2022; 100:1125-1144. [PMID: 35816219 DOI: 10.1007/s00109-022-02229-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 12/16/2022]
Abstract
Prostate cancer (PCa) is a malignant epithelial tumor of the prostate gland with a high male cancer incidence. Numerous studies indicate that abnormal function of ubiquitin-proteasome system (UPS) is associated with the progression and metastasis of PCa. E3 ubiquitin ligases, key components of UPS, determine the specificity of substrates, and substantial advances of E3 ubiquitin ligases have been reached recently. Herein, we introduce the structures and functions of E3 ubiquitin ligases and summarize the mechanisms of E3 ubiquitin ligases-related PCa signaling pathways. In addition, some progresses in the development of inhibitors targeting E3 ubiquitin ligases are also included.
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Affiliation(s)
- Yiting Zhao
- Department of Oncology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China.,Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China.,Department of Chemoradiotherapy, the Affiliated People's Hospital of Ningbo University, Ningbo, 315040, China
| | - Jinyun Li
- Department of Oncology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China.,Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China
| | - Jun Chen
- Department of Chemoradiotherapy, the Affiliated People's Hospital of Ningbo University, Ningbo, 315040, China
| | - Meng Ye
- Department of Oncology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China.,Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China
| | - Xiaofeng Jin
- Department of Oncology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China. .,Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China.
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5
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Xia L, Han Q, Duan X, Zhu Y, Pan J, Dong B, Xia W, Xue W, Sha J. m6A-induced repression of SIAH1 facilitates alternative splicing of androgen receptor variant 7 by regulating CPSF1. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 28:219-230. [PMID: 35402071 PMCID: PMC8965770 DOI: 10.1016/j.omtn.2022.03.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/12/2022] [Indexed: 01/22/2023]
Affiliation(s)
- Lei Xia
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, People’s Republic of China
| | - Qing Han
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200001, People’s Republic of China
| | - Xuehui Duan
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, People’s Republic of China
| | - Yinjie Zhu
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, People’s Republic of China
| | - Jiahua Pan
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, People’s Republic of China
| | - Baijun Dong
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, People’s Republic of China
| | - Weiliang Xia
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200001, People’s Republic of China
| | - Wei Xue
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, People’s Republic of China
- Corresponding author. Wei Xue, Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Shandong Middle road, Shanghai 200001, China.
| | - Jianjun Sha
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200001, People’s Republic of China
- Corresponding author. Jianjun Sha, Department of Urology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 145 Shandong Middle road, Shanghai 200001, China.
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6
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Zheng H, Zheng WJ, Wang ZG, Tao YP, Huang ZP, Yang L, Ouyang L, Duan ZQ, Zhang YN, Chen BN, Xiang DM, Jin G, Fang L, Zhou F, Liang B. Decreased Expression of Programmed Death Ligand-L1 by Seven in Absentia Homolog 2 in Cholangiocarcinoma Enhances T-Cell-Mediated Antitumor Activity. Front Immunol 2022; 13:845193. [PMID: 35154166 PMCID: PMC8828655 DOI: 10.3389/fimmu.2022.845193] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 01/10/2022] [Indexed: 01/03/2023] Open
Abstract
N6-methyladenosine (m6A) has been reported as an important mechanism of post-transcriptional regulation. Programmed death ligand 1 (PD-L1) is a primary immune inhibitory molecule expressed on tumor cells that promotes immune evasion. In addition, seven in absentia homolog 2 (Siah2), a RING E3 ubiquitin ligase, has been involved in tumorigenesis and cancer progression. However, the role of m6A-METTL14-Siah2-PD-L1 axis in immunotherapy remains to be elucidated. In this study, we showed that METTL14, a component of the m6A methyltransferase complex, induced Siah2 expression in cholangiocarcinoma (CCA). METTL14 was shown to enrich m6A modifications in the 3'UTR region of the Siah2 mRNA, thereby promoting its degradation in an YTHDF2-dependent manner. Furthermore, co-immunoprecipitation experiments demonstrated that Siah2 interacted with PD-L1 by promoting its K63-linked ubiquitination. We also observed that in vitro and in vivo Siah2 knockdown inhibited T cells expansion and cytotoxicity by sustaining tumor cell PD-L1 expression. The METTL14-Siah2-PD-L1-regulating axis was further confirmed in human CCA specimens. Analysis of specimens from patients receiving anti-PD1 immunotherapy suggested that tumors with low Siah2 levels were more sensitive to anti-PD1 immunotherapy. Taken together, our results evidenced a new regulatory mechanism of Siah2 by METTL14-induced mRNA epigenetic modification and the potential role of Siah2 in cancer immunotherapy.
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Affiliation(s)
- Hao Zheng
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China,Department of Reproductive Heredity Center, Changhai Hospital, Second Military Medical University, Shanghai, China,Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China,Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai, China,Shanghai Key Laboratory of Hepatobiliary Tumor Biology (EHBH), Shanghai, China
| | - Wen-juan Zheng
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhen-guang Wang
- Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China,Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai, China,Shanghai Key Laboratory of Hepatobiliary Tumor Biology (EHBH), Shanghai, China
| | - Yuan-ping Tao
- National Liver Tissue Bank, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Zhi-ping Huang
- Department of Hepatobiliary Surgery, General Hospital of Southern Theatre Command, Guangzhou, China
| | - Le Yang
- National Liver Tissue Bank, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Liu Ouyang
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital of Second Military Medical University, Shanghai, China
| | - Zhi-qing Duan
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yi-nuo Zhang
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Bo-ning Chen
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Dai-min Xiang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Gang Jin
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital of Second Military Medical University, Shanghai, China
| | - Lu Fang
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China,*Correspondence: Lu Fang, ; Fan Zhou, ; Bo Liang,
| | - Fan Zhou
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China,*Correspondence: Lu Fang, ; Fan Zhou, ; Bo Liang,
| | - Bo Liang
- Department of General Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China,*Correspondence: Lu Fang, ; Fan Zhou, ; Bo Liang,
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7
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Ballar Kirmizibayrak P, Erbaykent-Tepedelen B, Gozen O, Erzurumlu Y. Divergent Modulation of Proteostasis in Prostate Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1233:117-151. [PMID: 32274755 DOI: 10.1007/978-3-030-38266-7_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Proteostasis regulates key cellular processes such as cell proliferation, differentiation, transcription, and apoptosis. The mechanisms by which proteostasis is regulated are crucial and the deterioration of cellular proteostasis has been significantly associated with tumorigenesis since it specifically targets key oncoproteins and tumor suppressors. Prostate cancer (PCa) is the second most common cause of cancer death in men worldwide. Androgens mediate one of the most central signaling pathways in all stages of PCa via the androgen receptor (AR). In addition to their regulation by hormones, PCa cells are also known to be highly secretory and are particularly prone to ER stress as proper ER function is essential. Alterations in various complex signaling pathways and cellular processes including cell cycle control, transcription, DNA repair, apoptosis, cell adhesion, epithelial-mesenchymal transition (EMT), and angiogenesis are critical factors influencing PCa development through key molecular changes mainly by posttranslational modifications in PCa-related proteins, including AR, NKX3.1, PTEN, p53, cyclin D1, and p27. Several ubiquitin ligases like MDM2, Siah2, RNF6, CHIP, and substrate-binding adaptor SPOP; deubiquitinases such as USP7, USP10, USP26, and USP12 are just some of the modifiers involved in the regulation of these key proteins via ubiquitin-proteasome system (UPS). Some ubiquitin-like modifiers, especially SUMOs, have been also closely associated with PCa. On the other hand, the proteotoxicity resulting from misfolded proteins and failure of ER adaptive capacity induce unfolded protein response (UPR) that is an indispensable signaling mechanism for PCa development. Lastly, ER-associated degradation (ERAD) also plays a crucial role in prostate tumorigenesis. In this section, the relationship between prostate cancer and proteostasis will be discussed in terms of UPS, UPR, SUMOylation, ERAD, and autophagy.
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Affiliation(s)
| | | | - Oguz Gozen
- Faculty of Medicine, Department of Physiology, Ege University, Izmir, Turkey
| | - Yalcin Erzurumlu
- Faculty of Pharmacy, Department of Biochemistry, Suleyman Demirel University, Isparta, Turkey
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8
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Identification and characterization of small molecule inhibitors of the ubiquitin ligases Siah1/2 in melanoma and prostate cancer cells. Cancer Lett 2019; 449:145-162. [PMID: 30771432 DOI: 10.1016/j.canlet.2019.02.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 12/10/2018] [Accepted: 02/10/2019] [Indexed: 12/12/2022]
Abstract
Inhibition of ubiquitin ligases with small molecule remains a very challenging task, given the lack of catalytic activity of the target and the requirement of disruption of its interactions with other proteins. Siah1/2, which are E3 ubiquitin ligases, are implicated in melanoma and prostate cancer and represent high-value drug targets. We utilized three independent screening approaches in our efforts to identify small-molecule Siah1/2 inhibitors: Affinity Selection-Mass Spectrometry, a protein thermal shift-based assay and an in silico based screen. Inhibitors were assessed for their effect on viability of melanoma and prostate cancer cultures, colony formation, prolyl-hydroxylase-HIF1α signaling, expression of selected Siah2-related transcripts, and Siah2 ubiquitin ligase activity. Several analogs were further characterized, demonstrating improved efficacy. Combination of the top hits identified in the different assays demonstrated an additive effect, pointing to complementing mechanisms that underlie each of these Siah1/2 inhibitors.
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9
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Angeles AK, Bauer S, Ratz L, Klauck SM, Sültmann H. Genome-Based Classification and Therapy of Prostate Cancer. Diagnostics (Basel) 2018; 8:E62. [PMID: 30200539 PMCID: PMC6164491 DOI: 10.3390/diagnostics8030062] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 08/28/2018] [Accepted: 08/29/2018] [Indexed: 12/19/2022] Open
Abstract
In the past decade, multi-national and multi-center efforts were launched to sequence prostate cancer genomes, transcriptomes, and epigenomes with the aim of discovering the molecular underpinnings of tumorigenesis, cancer progression, and therapy resistance. Multiple biological markers and pathways have been discovered to be tumor drivers, and a molecular classification of prostate cancer is emerging. Here, we highlight crucial findings of these genome-sequencing projects in localized and advanced disease. We recapitulate the utility and limitations of current clinical practices to diagnosis, prognosis, and therapy, and we provide examples of insights generated by the molecular profiling of tumors. Novel treatment concepts based on these molecular alterations are currently being addressed in clinical trials and will lead to an enhanced implementation of precision medicine strategies.
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Affiliation(s)
- Arlou Kristina Angeles
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, Heidelberg D-69120, Germany.
| | - Simone Bauer
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, Heidelberg D-69120, Germany.
| | - Leonie Ratz
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, Heidelberg D-69120, Germany.
| | - Sabine M Klauck
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, Heidelberg D-69120, Germany.
| | - Holger Sültmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), and National Center for Tumor Diseases (NCT), Im Neuenheimer Feld 460, Heidelberg D-69120, Germany.
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10
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ARF1 promotes prostate tumorigenesis via targeting oncogenic MAPK signaling. Oncotarget 2018; 7:39834-39845. [PMID: 27213581 PMCID: PMC5129974 DOI: 10.18632/oncotarget.9405] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 03/11/2016] [Indexed: 11/25/2022] Open
Abstract
ADP-ribosylation factor 1 (ARF1) is a crucial regulator in vesicle-mediated membrane trafficking and involved in the activation of signaling molecules. However, virtually nothing is known about its function in prostate cancer. Here we have demonstrated that ARF1 expression is significantly elevated in prostate cancer cells and human tissues and that the expression levels of ARF1 correlate with the activation of mitogen-activated protein kinases (MAPK) ERK1/2. Furthermore, we have shown that overexpression and knockdown of ARF1 produce opposing effects on prostate cancer cell proliferation, anchorage-independent growth and tumor growth in mouse xenograft models and that ARF1-mediated cell proliferation can be abolished by the Raf1 inhibitor GW5074 and the MEK inhibitors U0126 and PD98059. Moreover, inhibition of ARF1 activation achieved by mutating Thr48 abolishes ARF1's abilities to activate the ERK1/2 and to promote cell proliferation. These data demonstrate that the aberrant MAPK signaling in prostate cancer is, at least in part, under the control of ARF1 and that, similar to Ras, ARF1 is a critical regulator in prostate cancer progression. These data also suggest that ARF1 may represent a key molecular target for prostate cancer therapeutics and diagnosis.
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11
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Maina PK, Shao P, Liu Q, Fazli L, Tyler S, Nasir M, Dong X, Qi HH. c-MYC drives histone demethylase PHF8 during neuroendocrine differentiation and in castration-resistant prostate cancer. Oncotarget 2016; 7:75585-75602. [PMID: 27689328 PMCID: PMC5342763 DOI: 10.18632/oncotarget.12310] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 09/20/2016] [Indexed: 02/06/2023] Open
Abstract
Epigenetic factors play critical roles in prostate cancer (PCa) development. However, how they contribute to neuroendocrine differentiation (NED) and castration-resistant PCa (CRPC) is not fully understood. Using bioinformatics and biochemical approaches to analyze cell-based models of NED and CRPC, we found a cluster of epigenetic factors whose expression is downregulated during NED and upregulated in CRPC (i.e. follow a Down-Up pattern). Two histone demethylases within this cluster, PHF8 and KDM3A, are post-transcriptionally regulated by c-MYC through miR-22, which targets both PHF8 and KDM3A. We also found that the c-MYC/miR-22/PHF8 axis is downstream of androgen receptor (AR) signaling in CRPC cells. The co-expression of PHF8 with AR in clinical CRPC samples, normal mouse prostate, and adenocarcinomas of the prostate during PCa progression in a transgenic (TRAMP) mouse model supports the connection between PHF8 and AR. Knockdown of PHF8 impedes cell cycle progression in CRPC cells and has more profound effects on their growth than on the parental LNCaP cell line. Furthermore, PHF8 knockdown sensitizes LNCaP-Abl cells to the AR antagonist enzalutamide. Our data reveal novel mechanisms that underlie the regulation of PHF8 and KDM3A during NED and in CRPC, and support the candidacy of PHF8 as a therapeutic target in CRPC.
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MESH Headings
- 3' Untranslated Regions
- Animals
- Cell Cycle/drug effects
- Cell Cycle/genetics
- Cell Cycle Checkpoints/genetics
- Cell Line, Tumor
- Cell Proliferation/genetics
- Cell Survival/genetics
- Epigenesis, Genetic
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic/drug effects
- Genes, myc
- Histone Demethylases/genetics
- Humans
- Interleukin-6/metabolism
- Interleukin-6/pharmacology
- Jumonji Domain-Containing Histone Demethylases/genetics
- Jumonji Domain-Containing Histone Demethylases/metabolism
- Male
- Mice
- MicroRNAs/genetics
- Models, Biological
- Neoplasm Grading
- Neuroendocrine Tumors/genetics
- Neuroendocrine Tumors/metabolism
- Neuroendocrine Tumors/pathology
- Prostatic Neoplasms, Castration-Resistant/genetics
- Prostatic Neoplasms, Castration-Resistant/metabolism
- Prostatic Neoplasms, Castration-Resistant/pathology
- RNA Interference
- Receptors, Androgen/genetics
- Receptors, Androgen/metabolism
- Transcription Factors/genetics
- Transcriptome
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Affiliation(s)
- Peterson Kariuki Maina
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52246, USA
| | - Peng Shao
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52246, USA
| | - Qi Liu
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52246, USA
| | - Ladan Fazli
- Vancouver Prostate Center, Department of Urology Sciences, University of British Columbia, Vancouver, BC V6H 3Z6, Canada
| | - Scott Tyler
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52246, USA
| | - Moman Nasir
- Department of Health and Human Physiology, College of Liberal Arts and Sciences, University of Iowa, Iowa City, IA 52242, USA
| | - Xuesen Dong
- Vancouver Prostate Center, Department of Urology Sciences, University of British Columbia, Vancouver, BC V6H 3Z6, Canada
| | - Hank Heng Qi
- Department of Anatomy and Cell Biology, Carver College of Medicine, University of Iowa, Iowa City, IA 52246, USA
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12
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Zhang Q, Wang Z, Hou F, Harding R, Huang X, Dong A, Walker JR, Tong Y. The substrate binding domains of human SIAH E3 ubiquitin ligases are now crystal clear. Biochim Biophys Acta Gen Subj 2016; 1861:3095-3105. [PMID: 27776223 DOI: 10.1016/j.bbagen.2016.10.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 10/03/2016] [Accepted: 10/19/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND Seven in absentia homologs (SIAHs) comprise a family of highly conserved E3 ubiquitin ligases that play an important role in regulating signalling pathways in tumorigenesis, including the DNA damage repair and hypoxia response pathways. SIAH1 and SIAH2 have been found to function as a tumour repressor and a proto-oncogene, respectively, despite the high sequence identity of their substrate binding domains (SBDs). Ubiquitin-specific protease USP19 is a deubiquitinase that forms a complex with SIAHs and counteracts the ligase function. Much effort has been made to find selective inhibitors of the SIAHs E3 ligases. Menadione was reported to inhibit SIAH2 specifically. METHODS We used X-ray crystallography, peptide array, bioinformatic analysis, and biophysical techniques to characterize the structure and interaction of SIAHs with deubiquitinases and literature reported compounds. RESULTS We solved the crystal structures of SIAH1 in complex with a USP19 peptide and of the apo form SIAH2. Phylogenetic analysis revealed the SIAH/USP19 complex is conserved in evolution. We demonstrated that menadione destabilizes both SIAH1 and SIAH2 non-specifically through covalent modification. CONCLUSIONS The SBDs of SIAH E3 ligases are structurally similar with a subtle stability difference. USP19 is the only deubiquitinase that directly binds to SIAHs through the substrate binding pocket. Menadione is not a specific inhibitor for SIAH2. GENERAL SIGNIFICANCE The crystallographic models provide structural insights into the substrate binding of the SIAH family E3 ubiquitin ligases that are critically involved in regulating cancer-related pathways. Our results suggest caution should be taken when using menadione as a specific SIAH2 inhibitor.
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Affiliation(s)
- Qi Zhang
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Zhongduo Wang
- Fisheries College, Guangdong Ocean University, Zhanjiang, Guangdong 524025, China
| | - Feng Hou
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Rachel Harding
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Xinyi Huang
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Aiping Dong
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - John R Walker
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Yufeng Tong
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada; Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5G 1L7, Canada.
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13
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Chen H, Wang N, Yang G, Guo Y, Shen Y, Wang X, Zhang P, Xu Y. The expression and function of E3 ligase SIAH2 in acute T lymphoblastic leukemia. Leuk Res 2016; 42:28-36. [PMID: 26859780 DOI: 10.1016/j.leukres.2016.01.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 01/10/2016] [Accepted: 01/24/2016] [Indexed: 11/17/2022]
Abstract
INTRODUCTION The seven in absentia homolog 2 (SIAH2) protein plays a significant role in human cancer by regulating hypoxia-inducible factor-a (HIF-1α); however, its role in T-cell acute lymphoblastic leukemia (T-ALL) is less clear. METHODS Immunofluorescence evaluation of SIAH2 protein expression and location were conducted in Jurkat cell (a T-ALL cell line) as well as in bone marrow mononuclear cells (BMMNCs) from T-ALL and idiopathic thrombocytopenic purpura (ITP) patients. The expression of SIAH2 mRNA was also examined by quantitative real-time PCR (qRT-PCR) in these cells. Lentivirus-packed shRNA targeting on SIAH2 (Lv-shSIAH2) was used to knock down SIAH2 expression in Jurkat cells. Cell proliferation, apoptosis, invasion and protein levels were then determined by CCK-8 assay, annexin V-PI assay, transwell and Western blotting, respectively. RESULTS The mRNA expression of SIAH2 in BMMNCs from primary T-ALL patients was significantly higher than cells from ITP patients (P=0.0312); There were significant positive associations between SIAH2 expression and the extramedullary infiltration (EMI) (P=0.0003), especially with the mediastinal lymph node metastasis (P=0.0168) and the pleural effusion (P=0.014). However, SIAH2 expression in T-ALL BMMNCs was not correlated with age, gender, white cell count or the clinical risk classification. SIAH2 knockdown by shRNA led to increased apoptosis and decreased proliferation, migration and invasion of Jurkat cells. Moreover, Prolyl Hydroxylase (PHD), P27 and Caspase3 were upregulated and HIF-1α, VEGF, VEGF Receptor 2, MMP-13, CyclinE1, C-myc and BCL2 were downregulated in SIAH2 knockdown Jurkat cells. CONCLUSIONS Our results suggest that SIAH2 regulates multi processes in T-ALL and may be an attractive therapeutic target.
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Affiliation(s)
- Hongxia Chen
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400014, PR China; Key Laboratory of Pediatrics in Chongqing, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400014, PR China; China International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400014, PR China
| | - Ning Wang
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400014, PR China; Key Laboratory of Pediatrics in Chongqing, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400014, PR China; China International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400014, PR China
| | - Guicun Yang
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400014, PR China; Department of Hematology and Oncology, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400014, PR China; Key Laboratory of Pediatrics in Chongqing, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400014, PR China; China International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400014, PR China
| | - Yuxia Guo
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400014, PR China; Department of Hematology and Oncology, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400014, PR China; Key Laboratory of Pediatrics in Chongqing, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400014, PR China; China International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400014, PR China
| | - Yali Shen
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400014, PR China; Department of Hematology and Oncology, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400014, PR China; Key Laboratory of Pediatrics in Chongqing, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400014, PR China; China International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400014, PR China
| | - Xiaojing Wang
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400014, PR China; Key Laboratory of Pediatrics in Chongqing, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400014, PR China; China International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400014, PR China
| | - Ping Zhang
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400014, PR China; Key Laboratory of Pediatrics in Chongqing, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400014, PR China; China International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400014, PR China
| | - Youhua Xu
- Ministry of Education Key Laboratory of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400014, PR China; Department of Hematology and Oncology, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400014, PR China; Key Laboratory of Pediatrics in Chongqing, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400014, PR China; China International Science and Technology Cooperation Center for Child Development and Disorders, Children's Hospital of Chongqing Medical University, Yuzhong, Chongqing 400014, PR China.
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Knauer SK, Mahendrarajah N, Roos WP, Krämer OH. The inducible E3 ubiquitin ligases SIAH1 and SIAH2 perform critical roles in breast and prostate cancers. Cytokine Growth Factor Rev 2015; 26:405-13. [DOI: 10.1016/j.cytogfr.2015.04.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Accepted: 04/27/2015] [Indexed: 12/15/2022]
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15
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Qi J, Kim H, Scortegagna M, Ronai ZA. Regulators and effectors of Siah ubiquitin ligases. Cell Biochem Biophys 2014; 67:15-24. [PMID: 23700162 DOI: 10.1007/s12013-013-9636-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The Siah ubiquitin ligases are members of the RING finger E3 ligases. The Siah E3s are conserved from fly to mammals. Primarily implicated in cellular stress responses, Siah ligases play a key role in hypoxia, through the regulation of HIF-1α transcription stability and activity. Concomitantly, physiological conditions associated with varying oxygen tension often highlight the importance of Siah, as seen in cancer and neurodegenerative disorders. Notably, recent studies also point to the role of these ligases in fundamental processes including DNA damage response, cellular organization and polarity. This review summarizes the current understanding of upstream regulators and downstream effectors of Siah.
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Affiliation(s)
- Jianfei Qi
- Signal Transduction Program, Cancer Center, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA
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16
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Abstract
Prostate cancer treatment is dominated by strategies to control androgen receptor (AR) activity. AR has an impact on prostate cancer development through the regulation of not only transcription networks but also genomic stability and DNA repair, as manifest in the emergence of gene fusions. Whole-genome maps of AR binding sites and transcript profiling have shown changes in the recruitment and regulatory effect of AR on transcription as prostate cancer progresses. Defining other factors that are involved in this reprogramming of AR function gives various opportunities for cancer detection and therapeutic intervention.
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Affiliation(s)
- Ian G Mills
- Prostate Cancer Research Group, Centre for Molecular Medicine Norway (NCMM), University of Oslo and Oslo University Hospitals, N-0318 Oslo, Norway;Departments of Cancer Prevention and Urology, Institute of Cancer Research and Oslo University Hospitals, N-0424 Oslo, Norway;Uro-Oncology Research Group, Cambridge Research Institute, University of Cambridge, Robinson Way, Cambridge CB2 0RE, UK
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17
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Rimsa V, Eadsforth TC, Hunter WN. Two high-resolution structures of the human E3 ubiquitin ligase Siah1. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1339-43. [PMID: 24316825 PMCID: PMC3855715 DOI: 10.1107/s1744309113031448] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 11/18/2013] [Indexed: 01/07/2023]
Abstract
Siah1 is an E3 ubiquitin ligase that contributes to proteasome-mediated degradation of multiple targets in key cellular processes and which shows promise as a therapeutic target in oncology. Structures of a truncated Siah1 bound to peptide-based inhibitors have been reported. Here, new crystallization conditions have allowed the determination of a construct encompassing dual zinc-finger subdomains and substrate-binding domains at significantly higher resolution. Although the crystals appear isomorphous, two structures present distinct states in which the spatial orientation of one zinc-finger subdomain differs with respect to the rest of the dimeric protein. Such a difference, which is indicative of conformational freedom, infers potential biological relevance related to recognition of binding partners. The crystallization conditions and improved models of Siah1 may aid future studies investigating Siah1-ligand complexes.
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Affiliation(s)
- Vadim Rimsa
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Thomas C. Eadsforth
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - William N. Hunter
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
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18
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Stebbins JL, Santelli E, Feng Y, De SK, Purves A, Motamedchaboki K, Wu B, Ronai ZA, Liddington RC, Pellecchia M. Structure-based design of covalent Siah inhibitors. ACTA ACUST UNITED AC 2013; 20:973-82. [PMID: 23891150 DOI: 10.1016/j.chembiol.2013.06.008] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 06/13/2013] [Accepted: 06/17/2013] [Indexed: 11/30/2022]
Abstract
The E3 ubiquitin ligase Siah regulates key cellular events that are central to cancer development and progression. A promising route to Siah inhibition is disrupting its interactions with adaptor proteins. However, typical of protein-protein interactions, traditional unbiased approaches to ligand discovery did not produce viable hits against this target, despite considerable effort and a multitude of approaches. Ultimately, a rational structure-based design strategy was successful for the identification of Siah inhibitors in which peptide binding drives specific covalent bond formation with the target. X-ray crystallography, mass spectrometry, and functional data demonstrate that these peptide mimetics are efficient covalent inhibitors of Siah and antagonize Siah-dependent regulation of Erk and Hif signaling in the cell. The proposed strategy may result useful as a general approach to the design of peptide-based inhibitors of other protein-protein interactions.
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Affiliation(s)
- John L Stebbins
- Signal Transduction Program and Cell Death Program, Cancer Center, Sanford-Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA
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19
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Rick FG, Schally AV, Block NL, Abi-Chaker A, Krishan A, Szalontay L. Mechanisms of synergism between antagonists of growth hormone-releasing hormone and antagonists of luteinizing hormone-releasing hormone in shrinking experimental benign prostatic hyperplasia. Prostate 2013; 73:873-83. [PMID: 23280565 DOI: 10.1002/pros.22633] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 12/03/2012] [Indexed: 12/30/2022]
Abstract
BACKGROUND Benign prostatic hyperplasia (BPH) affects aging men. Combined therapy with antagonists of growth hormone-releasing hormone (GHRH) and of luteinizing hormone-releasing hormone (LHRH or GnRH) induces prostate shrinkage in rat models. We investigated the mechanisms of action of this combination on cell cycle traverse and expression of prostatic genes. METHODS Effects of GHRH antagonist, JMR-132 (40 µg/day), the LHRH antagonist, cetrorelix (0.625 mg/kg), and their combination were evaluated on testosterone-induced benign prostatic hyperplasia in male Wistar rats. Influence of JMR-132, cetrorelix, and their combinations on cell viability was assessed by MTS assay in BPH-1 human prostate epithelial cells and WPMY-1 normal prostate stromal cells. Cell cycle was analyzed by laser flow cytometry. Real-time PCR arrays were performed. RESULTS The combination of antagonists caused marked shrinkage of rat prostate (29.5%). In vitro, JMR-132 plus cetrorelix (both 5µM) produced synergistic (57.4%) inhibition of growth of BPH-1 cells, but a lesser inhibition (46%) of WPMY-1 cells. Co-treatment of with JMR-132 plus cetrorelix induced a significant increase of BPH-1 cells blocked in S-phase plus cells with lower G0 /G1 and G2 /M DNA content. Significant changes in expression of >40 gene transcripts related to growth factors, inflammatory cytokines, and signal transduction were identified. CONCLUSIONS GHRH antagonist and LHRH antagonist combination potentiates rat prostate weight reduction and synergistically inhibits of growth of BPH-1 leading to cell cycle arrest in S-phase. These effects were lesser in normal stromal prostate cell line, WPMY-1. Our findings suggest that GHRH antagonists could be useful for BPH therapy, possibly in combination with LHRH antagonists.
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Affiliation(s)
- Ferenc G Rick
- Veterans Affairs Medical Center and South Florida Veterans Affairs Foundation for Research and Education, Miami, Florida 33125, USA.
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20
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Hebron ML, Lonskaya I, Sharpe K, Weerasinghe PPK, Algarzae NK, Shekoyan AR, Moussa CEH. Parkin ubiquitinates Tar-DNA binding protein-43 (TDP-43) and promotes its cytosolic accumulation via interaction with histone deacetylase 6 (HDAC6). J Biol Chem 2013; 288:4103-15. [PMID: 23258539 PMCID: PMC3567661 DOI: 10.1074/jbc.m112.419945] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The importance of E3 ubiquitin ligases, involved in the degradation of misfolded proteins or promotion of protein-protein interaction, is increasingly recognized in neurodegeneration. TDP-43 is a predominantly nuclear protein, which regulates the transcription of thousands of genes and binds to mRNA of the E3 ubiquitin ligase Parkin to regulate its expression. Wild type and mutated TDP-43 are detected in ubiquitinated forms within the cytosol in several neurodegenerative diseases. We elucidated the mechanisms of TDP-43 interaction with Parkin using transgenic A315T mutant TDP-43 (TDP43-Tg) mice, lentiviral wild type TDP-43, and Parkin gene transfer rat models. TDP-43 expression increased Parkin mRNA and protein levels. Lentiviral TDP-43 increased the levels of nuclear and cytosolic protein, whereas Parkin co-expression mediated Lys-48 and Lys-63-linked ubiquitin to TDP-43 and led to cytosolic co-localization of Parkin with ubiquitinated TDP-43. Parkin and TDP-43 formed a multiprotein complex with HDAC6, perhaps to mediate TDP-43 translocation. In conclusion, Parkin ubiquitinates TDP-43 and facilitates its cytosolic accumulation through a multiprotein complex with HDAC6.
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Affiliation(s)
- Michaeline L. Hebron
- From the Department of Neuroscience, Georgetown University Medical Center, Washington, D. C. 20007
| | - Irina Lonskaya
- From the Department of Neuroscience, Georgetown University Medical Center, Washington, D. C. 20007
| | - Kaydee Sharpe
- From the Department of Neuroscience, Georgetown University Medical Center, Washington, D. C. 20007
| | | | - Norah K. Algarzae
- From the Department of Neuroscience, Georgetown University Medical Center, Washington, D. C. 20007
| | - Ashot R. Shekoyan
- From the Department of Neuroscience, Georgetown University Medical Center, Washington, D. C. 20007
| | - Charbel E.-H. Moussa
- From the Department of Neuroscience, Georgetown University Medical Center, Washington, D. C. 20007, To whom correspondence should be addressed: Laboratory for Dementia and Parkinsonism, Dept. of Neuroscience, Georgetown University School of Medicine, 3970 Reservoir Rd., NW, TRB, Rm. WP09B, Washington, D. C. 20057. Tel.: 202-687-7328; Fax: 202-687-0617; E-mail:
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Abstract
Hypoxia-inducible factors (HIFs) control cellular adaptation to oxygen deprivation. Cancer cells engage HIFs to sustain their growth in adverse conditions, thus promoting a cellular reprograming that includes metabolism, proliferation, survival and mobility. HIFs overexpression in human cancer biopsies correlates with high metastasis and mortality. A recent report has elucidated a novel mechanism for HIFs regulation in triple-negative breast cancer. Specifically, the basic helix-loop-helix (bHLH), Sharp-1, serves HIF1α to the proteasome and promotes its O2-indendpendet degradation, counteracting HIF-mediated metastasis. These findings shed light on how HIFs are manipulated during cancer pathogenesis.
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Affiliation(s)
- Ivano Amelio
- Medical Research Council, Toxicology Unit, Leicester University, Leicester, UK
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22
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Krämer OH, Stauber RH, Bug G, Hartkamp J, Knauer SK. SIAH proteins: critical roles in leukemogenesis. Leukemia 2012; 27:792-802. [PMID: 23038274 DOI: 10.1038/leu.2012.284] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The delicate balance between the synthesis and the degradation of proteins ensures cellular homeostasis. Proteases act in an irreversible manner and therefore have to be strictly regulated. The ubiquitin-proteasome system (UPS) is a major pathway for the proteolytic degradation of cellular proteins. As dysregulation of the UPS is observed in most cancers including leukemia, the UPS is a valid target for therapeutic intervention strategies. Ubiquitin-ligases selectively bind substrates to target them for poly-ubiquitinylation and proteasomal degradation. Therefore, pharmacological modulation of these proteins could allow a specific level of control. Increasing evidence accumulates that ubiquitin-ligases termed mammalian seven in absentia homologs (SIAHs) are not only critical for the pathogenesis of solid tumors but also for leukemogenesis. However, the relevance and therapeutic potential of SIAH-dependent processes has not been fully elucidated. Here, we summarize functions of SIAH ubiquitin-ligases in leukemias, how they select leukemia-relevant substrates for proteasomal degradation, and how the expression and activity of SIAH1 and SIAH2 can be modulated in vivo. We also discuss that epigenetic drugs belonging to the group of histone deacetylase inhibitors induce SIAH-dependent proteasomal degradation to accelerate the turnover of leukemogenic proteins. In addition, our review highlights potential areas for future research on SIAH proteins.
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Affiliation(s)
- O H Krämer
- Center for Molecular Biomedicine (CMB), Department of Biochemistry, University of Jena, Jena, Germany.
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23
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Vainio P, Lehtinen L, Mirtti T, Hilvo M, Seppänen-Laakso T, Virtanen J, Sankila A, Nordling S, Lundin J, Rannikko A, Orešič M, Kallioniemi O, Iljin K. Phospholipase PLA2G7, associated with aggressive prostate cancer, promotes prostate cancer cell migration and invasion and is inhibited by statins. Oncotarget 2012; 2:1176-90. [PMID: 22202492 PMCID: PMC3282076 DOI: 10.18632/oncotarget.397] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Prostate cancer is the second leading cause of cancer mortality in men in developed countries. Due to the heterogeneous nature of the disease, design of novel personalized treatments is required to achieve efficient therapeutic responses. We have recently identified phospholipase 2 group VII (PLA2G7) as a potential drug target especially in ERG oncogene positive prostate cancers. Here, the expression profile of PLA2G7 was studied in 1137 prostate cancer and 409 adjacent non-malignant prostate tissues using immunohistochemistry to validate its biomarker potential and putative association with disease progression. In order to reveal the molecular alterations induced by PLA2G7 impairment, lipidomic and gene expression profiling was performed in response to PLA2G7 silencing in cultured prostate cancer cells. Moreover, the antineoplastic effect of statins combined with PLA2G7 impairment was studied in prostate cancer cells to evaluate the potential of repositioning of in vivo compatible drugs developed for other indications towards anti-cancer purposes. The results indicated that PLA2G7 is a cancer-selective biomarker in 50% of prostate cancers and associates with aggressive disease. The alterations induced by PLA2G7 silencing highlighted the potential of PLA2G7 inhibition as an anti-proliferative, pro-apoptotic and anti-migratorial therapeutic approach in prostate cancer. Moreover, the anti-proliferative effect of PLA2G7 silencing was potentiated by lipid-lowering statins in prostate cancer cells. Taken together, our results support the potential of PLA2G7 as a biomarker and a drug target in prostate cancer and present a rationale for combining PLA2G7 inhibition with the use of statins in prostate cancer management.
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Affiliation(s)
- Paula Vainio
- Medical Biotechnology, VTT Technical Research Centre of Finland, and Turku Centre for Biotechnology, University of Turku, Finland
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Abstract
In recent years, numerous new targets have been identified and new experimental therapeutics have been developed. Importantly, existing non-cancer drugs found novel use in cancer therapy. And even more importantly, new original therapeutic strategies to increase potency, selectivity and decrease detrimental side effects have been evaluated. Here we review some recent advances in targeting cancer.
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Affiliation(s)
- Zoya N Demidenko
- Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA.
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25
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Chantry A. WWP2 ubiquitin ligase and its isoforms: new biological insight and promising disease targets. Cell Cycle 2011; 10:2437-9. [PMID: 21750408 DOI: 10.4161/cc.10.15.16874] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
A number of recent papers on the WWP2 E3 ubiquitin ligase and two novel WWP2 isoforms have revealed important biological insight and disease-specific functions, and also impacted on our understanding of ubiquitin ligases in cell cycle regulation, apoptosis and differentiation. Gene knockout studies suggest a developmental role for WWP2 in chondrogenesis via mechanisms involving cartilage-specific transcription factors. Furthermore, WWP2 isoforms have been shown to selectively target oncogenic signaling pathways linked to both the pTEN tumour suppressor and the TGFβ/Smad signaling pathway. Here, it is suggested that WWP2 isoforms have now emerged as central physiological regulators as well as promising new disease targets, and that the challenge ahead is to now develop highly selective WWP2 inhibitors with utility in cartilage disease such as osteoarthritis and as new anticancer strategies.
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Affiliation(s)
- Andrew Chantry
- School of Biological Sciences, University of East Anglia, Norwich, UK.
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Animal models relevant to human prostate carcinogenesis underlining the critical implication of prostatic stem/progenitor cells. Biochim Biophys Acta Rev Cancer 2011; 1816:25-37. [PMID: 21396984 DOI: 10.1016/j.bbcan.2011.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2011] [Revised: 02/27/2011] [Accepted: 03/01/2011] [Indexed: 12/17/2022]
Abstract
Recent development of animal models relevant to human prostate cancer (PC) etiopathogenesis has provided important information on the specific functions provided by key gene products altered during disease initiation and progression to locally invasive, metastatic and hormone-refractory stages. Especially, the characterization of transgenic mouse models has indicated that the inactivation of distinct tumor suppressor proteins such as phosphatase tensin homolog deleted on chromosome 10 (PTEN), Nkx3.1, p27(KIP1), p53 and retinoblastoma (pRb) may cooperate for the malignant transformation of prostatic stem/progenitor cells into PC stem/progenitor cells and tumor development and metastases. Moreover, the sustained activation of diverse oncogenic signaling elements, including epidermal growth factor receptor (EGFR), sonic hedgehog, Wnt/β-catenin, c-Myc, Akt and nuclear factor-kappaB (NF-κB) also may contribute to the acquisition of more aggressive and hormone-refractory phenotypes by PC stem/progenitor cells and their progenies during disease progression. Importantly, it has also been shown that an enrichment of PC stem/progenitor cells expressing stem cell-like markers may occur after androgen deprivation therapy and docetaxel treatment in the transgenic mouse models of PC suggesting the critical implication of these immature PC cells in treatment resistance, tumor re-growth and disease recurrence. Of clinical interest, the molecular targeting of distinct gene products altered in PC cells by using different dietary compounds has also been shown to counteract PC initiation and progression in animal models supporting their potential use as chemopreventive or chemotherapeutic agents for eradicating the total tumor cell mass, improving current anti-hormonal and chemotherapies and preventing disease relapse.
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